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Conserved domains on  [gi|391883664|gb|AFM46183|]
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recombination protein A, partial [Bradyrhizobium sp. 5S4]

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
 4-154 5.39e-121

recombinase A; Provisional


The actual alignment was detected with superfamily member PRK09354:

Pssm-ID: 236476 [Multi-domain]  Cd Length: 349  Bit Score: 344.08  E-value: 5.39e-121
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664   4 DRSMDVETVSSGSLGLDIALGVGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHALDPVYARKLGVNI 83
Cdd:PRK09354  33 DAAMDVEVISTGSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKLGVDI 112

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 391883664  84 DELLISQPDTGEQALEICDTLVRSGAVDVLVVDSVAALVPKAELEGEMGDALPGLQARLMSQALRKLTASI 154
Cdd:PRK09354 113 DNLLVSQPDTGEQALEIADTLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGNI 183
 
Name Accession Description Interval E-value
recA PRK09354
recombinase A; Provisional
 4-154 5.39e-121

recombinase A; Provisional


Pssm-ID: 236476 [Multi-domain]  Cd Length: 349  Bit Score: 344.08  E-value: 5.39e-121
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664   4 DRSMDVETVSSGSLGLDIALGVGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHALDPVYARKLGVNI 83
Cdd:PRK09354  33 DAAMDVEVISTGSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKLGVDI 112

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 391883664  84 DELLISQPDTGEQALEICDTLVRSGAVDVLVVDSVAALVPKAELEGEMGDALPGLQARLMSQALRKLTASI 154
Cdd:PRK09354 113 DNLLVSQPDTGEQALEIADTLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGNI 183
RecA COG0468
RecA/RadA recombinase [Replication, recombination and repair];
4-154 4.47e-116

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


Pssm-ID: 440236 [Multi-domain]  Cd Length: 351  Bit Score: 331.75  E-value: 4.47e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664   4 DRSMDVETVSSGSLGLDIALGVGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHALDPVYARKLGVNI 83
Cdd:COG0468   36 KARQDVEVISTGSLALDIALGVGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGIAAFIDAEHALDPEYAKKLGVDI 115

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 391883664  84 DELLISQPDTGEQALEICDTLVRSGAVDVLVVDSVAALVPKAELEGEMGDALPGLQARLMSQALRKLTASI 154
Cdd:COG0468  116 DNLLVSQPDTGEQALEIAETLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGAI 186
RecA pfam00154
recA bacterial DNA recombination protein; RecA is a DNA-dependent ATPase and functions in DNA ...
 8-154 9.48e-108

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: 307.40  E-value: 9.48e-108
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664    8 DVETVSSGSLGLDIALGVGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHALDPVYARKLGVNIDELL 87
Cdd:pfam00154  29 DVETISTGSLALDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKLGVDIDNLL 108

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 391883664   88 ISQPDTGEQALEICDTLVRSGAVDVLVVDSVAALVPKAELEGEMGDALPGLQARLMSQALRKLTASI 154
Cdd:pfam00154 109 VSQPDTGEQALEIADMLVRSGAIDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGSI 175
tigrfam_recA TIGR02012
protein RecA; This model describes orthologs of the recA protein. RecA promotes hybridization ...
 4-154 1.31e-107

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: 309.30  E-value: 1.31e-107
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664    4 DRSMDVETVSSGSLGLDIALGVGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHALDPVYARKLGVNI 83
Cdd:TIGR02012  28 KTVMDVETISTGSLALDLALGVGGLPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYARKLGVDI 107

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 391883664   84 DELLISQPDTGEQALEICDTLVRSGAVDVLVVDSVAALVPKAELEGEMGDALPGLQARLMSQALRKLTASI 154
Cdd:TIGR02012 108 DNLLVSQPDTGEQALEIAETLVRSGAVDIIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGAL 178
RecA cd00983
recombinase A; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 8-154 5.03e-107

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: 304.48  E-value: 5.03e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664   8 DVETVSSGSLGLDIALGVGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHALDPVYARKLGVNIDELL 87
Cdd:cd00983    1 DVEVIPTGSLSLDIALGIGGLPRGRIIEIYGPESSGKTTLALHAIAEAQKLGGTAAFIDAEHALDPEYAKKLGVDIDNLL 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 391883664  88 ISQPDTGEQALEICDTLVRSGAVDVLVVDSVAALVPKAELEGEMGDALPGLQARLMSQALRKLTASI 154
Cdd:cd00983   81 VSQPDTGEQALEIADTLIRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGSL 147
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 30-150 8.38e-08

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


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 48.52  E-value: 8.38e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664    30 KGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHALDPVYARKLGVNIDELLISqpDTGEQALEICDTLVRSGA 109
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS--GSGELRLRLALALARKLK 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 391883664   110 VDVLVVDSVAALVPKAELEGEMGDALPGLQARLMSQALRKL 150
Cdd:smart00382  79 PDVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKNLTV 119
 
Name Accession Description Interval E-value
recA PRK09354
recombinase A; Provisional
 4-154 5.39e-121

recombinase A; Provisional


Pssm-ID: 236476 [Multi-domain]  Cd Length: 349  Bit Score: 344.08  E-value: 5.39e-121
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664   4 DRSMDVETVSSGSLGLDIALGVGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHALDPVYARKLGVNI 83
Cdd:PRK09354  33 DAAMDVEVISTGSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKLGVDI 112

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 391883664  84 DELLISQPDTGEQALEICDTLVRSGAVDVLVVDSVAALVPKAELEGEMGDALPGLQARLMSQALRKLTASI 154
Cdd:PRK09354 113 DNLLVSQPDTGEQALEIADTLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGNI 183
RecA COG0468
RecA/RadA recombinase [Replication, recombination and repair];
4-154 4.47e-116

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


Pssm-ID: 440236 [Multi-domain]  Cd Length: 351  Bit Score: 331.75  E-value: 4.47e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664   4 DRSMDVETVSSGSLGLDIALGVGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHALDPVYARKLGVNI 83
Cdd:COG0468   36 KARQDVEVISTGSLALDIALGVGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGIAAFIDAEHALDPEYAKKLGVDI 115

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 391883664  84 DELLISQPDTGEQALEICDTLVRSGAVDVLVVDSVAALVPKAELEGEMGDALPGLQARLMSQALRKLTASI 154
Cdd:COG0468  116 DNLLVSQPDTGEQALEIAETLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGAI 186
RecA pfam00154
recA bacterial DNA recombination protein; RecA is a DNA-dependent ATPase and functions in DNA ...
 8-154 9.48e-108

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: 307.40  E-value: 9.48e-108
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664    8 DVETVSSGSLGLDIALGVGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHALDPVYARKLGVNIDELL 87
Cdd:pfam00154  29 DVETISTGSLALDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKLGVDIDNLL 108

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 391883664   88 ISQPDTGEQALEICDTLVRSGAVDVLVVDSVAALVPKAELEGEMGDALPGLQARLMSQALRKLTASI 154
Cdd:pfam00154 109 VSQPDTGEQALEIADMLVRSGAIDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGSI 175
tigrfam_recA TIGR02012
protein RecA; This model describes orthologs of the recA protein. RecA promotes hybridization ...
 4-154 1.31e-107

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: 309.30  E-value: 1.31e-107
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664    4 DRSMDVETVSSGSLGLDIALGVGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHALDPVYARKLGVNI 83
Cdd:TIGR02012  28 KTVMDVETISTGSLALDLALGVGGLPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYARKLGVDI 107

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 391883664   84 DELLISQPDTGEQALEICDTLVRSGAVDVLVVDSVAALVPKAELEGEMGDALPGLQARLMSQALRKLTASI 154
Cdd:TIGR02012 108 DNLLVSQPDTGEQALEIAETLVRSGAVDIIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGAL 178
RecA cd00983
recombinase A; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 8-154 5.03e-107

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: 304.48  E-value: 5.03e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664   8 DVETVSSGSLGLDIALGVGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHALDPVYARKLGVNIDELL 87
Cdd:cd00983    1 DVEVIPTGSLSLDIALGIGGLPRGRIIEIYGPESSGKTTLALHAIAEAQKLGGTAAFIDAEHALDPEYAKKLGVDIDNLL 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 391883664  88 ISQPDTGEQALEICDTLVRSGAVDVLVVDSVAALVPKAELEGEMGDALPGLQARLMSQALRKLTASI 154
Cdd:cd00983   81 VSQPDTGEQALEIADTLIRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGSL 147
recA PRK09519
intein-containing recombinase RecA;
9-154 1.62e-72

intein-containing recombinase RecA;


Pssm-ID: 77219 [Multi-domain]  Cd Length: 790  Bit Score: 231.52  E-value: 1.62e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664   9 VETVSSGSLGLDIALGVGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHALDPVYARKLGVNIDELLI 88
Cdd:PRK09519  38 ISVIPTGSIALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHALDPDYAKKLGVDTDSLLV 117

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 391883664  89 SQPDTGEQALEICDTLVRSGAVDVLVVDSVAALVPKAELEGEMGDALPGLQARLMSQALRKLTASI 154
Cdd:PRK09519 118 SQPDTGEQALEIADMLIRSGALDIVVIDSVAALVPRAELEGEMGDSHVGLQARLMSQALRKMTGAL 183
RecA-like cd01393
RecA family; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 31-151 4.49e-35

RecA family; RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response. RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs RadA and RadB.


Pssm-ID: 410881 [Multi-domain]  Cd Length: 185  Bit Score: 120.15  E-value: 4.49e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664  31 GRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHALDPVYAR-----------KLGVNIDELLISQPDTGEQALE 99
Cdd:cd01393    1 GKITEIYGPPGSGKTQLALQLAANALLLGGGVVWIDTEGAFPPSRLVqileaspsselELAEALSRLLYFRPPDTLAHLL 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 391883664 100 ICDTLVRSGA----VDVLVVDSVAALVPKAELEGEMGDALPGLQARLMSQALRKLT 151
Cdd:cd01393   81 ALDSLPESLFpppnTSLVVVDSVSALFRKAFPRGGDGDSSSSLRARLLSQLARALQ 136
archRadB cd01394
archaeal RadB; The archaeal protein RadB shares similarity RadA, the archaeal functional ...
 12-121 2.18e-14

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: 67.34  E-value: 2.18e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664  12 VSSGSLGLDIALGvGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEhALDP-----VYARKLGVNIDEL 86
Cdd:cd01394    1 LSTGSKSLDSLLG-GGVERGTITQIYGPPGSGKTNICLQLAVEAAKQGKKVVYIDTE-GLSPerfqqIAGERFESIASNI 78

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 391883664  87 LISQP-DTGEQALEICDT--LVRSGAVDVLVVDSVAAL 121
Cdd:cd01394   79 IVFEPySFDEQGVAIQEAekLLKSDKVDLVVVDSATAL 116
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
12-121 5.31e-13

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


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 63.78  E-value: 5.31e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664  12 VSSGSLGLDIALGvGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHALDPV--YARKLGVNIDELL-- 87
Cdd:COG0467    2 VPTGIPGLDELLG-GGLPRGSSTLLSGPPGTGKTTLALQFLAEGLRRGEKGLYVSFEESPEQLlrRAESLGLDLEEYIes 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 391883664  88 ----ISQPDTGEQALEICDTL------VRSGAVDVLVVDSVAAL 121
Cdd:COG0467   81 gllrIIDLSPEELGLDLEELLarlreaVEEFGAKRVVIDSLSGL 124
KaiC-like cd01124
Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most studied in cyanobacteria. ...
 12-121 1.73e-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: 59.58  E-value: 1.73e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664  12 VSSGSLGLDIALGvGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHALDPVY--ARKLGVNIDE---- 85
Cdd:cd01124    1 VKTGIPGLDELLG-GGIPKGSVTLLTGGPGTGKTLFGLQFLYAGAKNGEPGLFFTFEESPERLLrnAKSFGWDFDEmede 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 391883664  86 --LLISQPDTGEQALEICDTL-------VRSGAVDVLVVDSVAAL 121
Cdd:cd01124   80 gkLIIVDAPPTEAGRFSLDELlsrilsiIKSFKAKRVVIDSLSGL 124
recomb_radB TIGR02237
DNA repair and recombination protein RadB; This family consists exclusively of archaeal RadB ...
 19-149 4.46e-11

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: 58.20  E-value: 4.46e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664   19 LDIALGvGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEhALDPVYARKLGVNIDELLISQ------PD 92
Cdd:TIGR02237   1 IDELLG-GGVERGTITQIYGPPGSGKTNICMILAVNAARQGKKVVYIDTE-GLSPERFKQIAEDRPERALSNfivfevFD 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 391883664   93 TGEQALEICDT--LVRSGAVDVLVVDSVAALVpKAELEGEMGDALPGL--QARLMSQALRK 149
Cdd:TIGR02237  79 FDEQGVAIQKTskFIDRDSASLVVVDSFTALY-RLELSDDRISRNRELarQLTLLLSLARK 138
COG4544 COG4544
Uncharacterized conserved protein [Function unknown];
9-116 1.07e-10

Uncharacterized conserved protein [Function unknown];


Pssm-ID: 443609 [Multi-domain]  Cd Length: 230  Bit Score: 57.63  E-value: 1.07e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664   9 VETVSSGSLGLDIALGVGGLPKGRVVEIYGPE-SSGKTTLALHTVAEGQKKGGICAFIDAEHALDPVYARKLGVNIDELL 87
Cdd:COG4544   26 RAVLPTGFAALDAALPGGGLPRGALHEILGPApGIGELGLLLPLLARLAQAGGPVLWIAPPYDLYAPGLAAAGLDPERLL 105

                         90       100
                 ....*....|....*....|....*....
gi 391883664  88 ISQPDTGEQALEICDTLVRSGAVDVLVVD 116
Cdd:COG4544  106 LVRARRPADALWAAEEALRSGACGAVVAW 134
Rad51B cd19493
RAD51B recombinase; RAD51B recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 20-135 1.06e-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: 54.63  E-value: 1.06e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664  20 DIALGvGGLPKGRVVEIYGPESSGKTTLALHTVAE-------GQKKGGiCAFIDAEHALDP-------------VYARKL 79
Cdd:cd19493    1 DTALA-GGLPLGAITEITGASGSGKTQFALTLASSaamparkGGLDGG-VLYIDTESKFSAerlaeiaearfpeAFSGFM 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 391883664  80 GVNIDELLISQ------PDTGEQALEICDTL---VRSGAVDVLVVDSVAALVPKaELEGEMGDAL 135
Cdd:cd19493   79 EENERAEEMLKrvavvrVTTLAQLLERLPNLeehILSSGVRLVVIDSIAALVRR-EFGGSDGEVT 142
radB PRK09361
DNA repair and recombination protein RadB; Provisional
 10-130 1.09e-09

DNA repair and recombination protein RadB; Provisional


Pssm-ID: 236482 [Multi-domain]  Cd Length: 225  Bit Score: 54.87  E-value: 1.09e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664  10 ETVSSGSLGLDIALGvGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEhALDPVYARKL-GVNIDELL- 87
Cdd:PRK09361   3 ERLPTGCKMLDELLG-GGFERGTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYIDTE-GLSPERFKQIaGEDFEELLs 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 391883664  88 ---ISQP-DTGEQALEICDT--LVRSGaVDVLVVDSVAALVpKAELEGE 130
Cdd:PRK09361  81 niiIFEPsSFEEQSEAIRKAekLAKEN-VGLIVLDSATSLY-RLELEDE 127
KaiC-like_N cd19488
N-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock ...
 12-65 8.12e-08

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: 49.65  E-value: 8.12e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 391883664  12 VSSGSLGLDIALGvGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFI 65
Cdd:cd19488    1 ISTGIPGLDDILR-GGLPPRRLYLVEGAPGTGKTTLALQFLLEGAANGETGLYI 53
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 30-150 8.38e-08

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


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 48.52  E-value: 8.38e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664    30 KGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHALDPVYARKLGVNIDELLISqpDTGEQALEICDTLVRSGA 109
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS--GSGELRLRLALALARKLK 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 391883664   110 VDVLVVDSVAALVPKAELEGEMGDALPGLQARLMSQALRKL 150
Cdd:smart00382  79 PDVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKNLTV 119
Rad51 pfam08423
Rad51; Rad51 is a DNA repair and recombination protein and is a homolog of the bacterial ...
 12-121 1.38e-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: 49.22  E-value: 1.38e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664   12 VSSGSLGLDIALGvGGLPKGRVVEIYGPESSGKTTLAlHTVA-------EGQKKGGICAFIDAEHALDPV----YARKLG 80
Cdd:pfam08423  19 ITTGSKELDKLLG-GGIETGSITEIFGEFRTGKTQLC-HTLCvtcqlplEMGGGEGKALYIDTEGTFRPErlvaIAERYG 96

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 391883664   81 VNIDELLISQP-------DTGEQALEICDTLVRSGAVDVLVVDSVAAL 121
Cdd:pfam08423  97 LDPEDVLDNVAyaraynsEHQMQLLQQAAAMMSESRFALLIVDSATAL 144
ATPase pfam06745
KaiC; This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and ...
 12-122 4.30e-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: 47.63  E-value: 4.30e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664   12 VSSGSLGLDIALGvGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGI-CAFIDA-EHALDPVY-ARKLGVNIDELL- 87
Cdd:pfam06745   1 VKTGIPGLDEILK-GGFPEGRVVLITGGPGTGKTIFGLQFLYNGALKYGEpGVFVTLeEPPEDLREnARSFGWDLEKLEe 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 391883664   88 --------ISQPDTGEQALEICDTL----------VRSGAVDVLVVDSVAALV 122
Cdd:pfam06745  80 egklaiidASTSGIGIAEVEDRFDLeelierlreaIREIGAKRVVIDSITTLF 132
Rad51_DMC1_archRadA cd01123
recombinase Rad51, DMC1, and archaeal RadA; This group of recombinases includes the eukaryotic ...
 12-121 8.92e-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: 46.75  E-value: 8.92e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664  12 VSSGSLGLDIALGvGGLPKGRVVEIYGPESSGKTTLAlHTVA-------EGQKKGGICAFIDAEHALDPV----YARKLG 80
Cdd:cd01123    1 ITTGSKELDKLLG-GGIETGSITEMFGEFRTGKTQLC-HTLAvtcqlpiDRGGGEGKAIYIDTEGTFRPErlraIAQRFG 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 391883664  81 VNIDELL----ISQPDTGEQALEICD---TLVRSGAVDVLVVDSVAAL 121
Cdd:cd01123   79 LDPDDVLdnvaYARAFNSDHQTQLLDqaaAMMVESRFKLLIVDSATAL 126
XRCC3 cd19491
XRCC3 recombinase; XRCC3 (X-ray repair complementing defective repair in Chinese hamster cells ...
 19-150 1.65e-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: 46.13  E-value: 1.65e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664  19 LDIALGvGGLPKGRVVEIYGPESSGKTTLALH-------TVAEGQKKGGiCAFIDAEHAL----------------DPVY 75
Cdd:cd19491    1 LDELLG-GGIPVGGITEIAGESGAGKTQLCLQlaltvqlPRELGGLGGG-AVYICTESSFpskrlqqlasslpkryHLEK 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664  76 ARKLGVNIdeLLISQPDTgeQALEICDT-----LVRSGAVDVLVVDSVAALVpKAELEGEMGDALpgLQARLMSQALRKL 150
Cdd:cd19491   79 AKNFLDNI--FVEHVADL--ETLEHCLNyqlpaLLERGPIRLVVIDSIAALF-RSEFDTSRSDLV--ERAKYLRRLADHL 151
XRCC2 cd19490
XRCC2 recombinase; XRCC2 (X-ray repair complementing defective repair in Chinese hamster cells ...
 31-153 8.16e-06

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: 43.88  E-value: 8.16e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664  31 GRVVEIYGPESSGKTTLALHTVA--------EGQKKGG--ICA-FIDAEHALDPVyarKLgVNIDELLISQ--------- 90
Cdd:cd19490    1 GDVIEITGPSGSGKTELLYHLAArcilpsswGGVPLGGleAAVvFIDTDGRFDIL---RL-RSILEARIRAaiqaanssd 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664  91 -PDTGEQALEIC--------------------------DTLVRSGAVDVLVVDSVAALVPKAELEGEMGDALPGLQARLM 143
Cdd:cd19490   77 dEEDVEEIAREClqrlhifrchsslqllatllslenylLSLSANPELGLLLIDSISAFYWQDRFSAELARAAPLLQEAAL 156

                        170
                 ....*....|...
gi 391883664 144 ---SQALRKLTAS 153
Cdd:cd19490  157 raiLRELRRLRRR 169
recomb_DMC1 TIGR02238
meiotic recombinase Dmc1; This model describes DMC1, a subfamily of a larger family of DNA ...
 9-121 3.36e-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: 42.46  E-value: 3.36e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664    9 VETVSSGSLGLDIALGvGGLPKGRVVEIYGPESSGKTTLAlHTVA-------EGQKKGGICAFIDAEHALDP----VYAR 77
Cdd:TIGR02238  75 VLKITTGSQALDGILG-GGIESMSITEVFGEFRCGKTQLS-HTLCvtaqlprEMGGGNGKVAYIDTEGTFRPdrirAIAE 152

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 391883664   78 KLGVN----IDELLISQPDTGEQALE---ICDTLVRSGAVDVLVVDSVAAL 121
Cdd:TIGR02238 153 RFGVDpdavLDNILYARAYTSEHQMElldYLAAKFSEEPFRLLIVDSIMAL 203
AAA_24 pfam13479
AAA domain; This AAA domain is found in a wide variety of presumed phage proteins.
 30-118 5.72e-05

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


Pssm-ID: 433243  Cd Length: 199  Bit Score: 41.16  E-value: 5.72e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664   30 KGRVVEIYGPESSGKTTLALHTvaegqkkgGICAFIDAEHALDPVYARKLGVnidellISQPDTGEQALEICDTLVRSGA 109
Cdd:pfam13479   1 KKLKILIYGPSGIGKTTFAKTL--------PKPLFLDTEKGSKALDGDRFPD------IVIRDSWQDFLDAIDELTAAEL 66

                          90
                  ....*....|.
gi 391883664  110 V--DVLVVDSV 118
Cdd:pfam13479  67 AdyKTIVIDTV 77
KaiC-like_C cd19487
C-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock ...
 12-84 7.46e-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: 41.13  E-value: 7.46e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 391883664  12 VSSGSLGLDIALGvGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHALDPVYARKLGVNID 84
Cdd:cd19487    1 VSSGVPELDELLG-GGLERGTSTLLIGPAGVGKSTLALQFAKAAAARGERSVLFSFDESIGTLFERSEALGID 72
PLN03187 PLN03187
meiotic recombination protein DMC1 homolog; Provisional
 5-121 8.65e-05

meiotic recombination protein DMC1 homolog; Provisional


Pssm-ID: 215620 [Multi-domain]  Cd Length: 344  Bit Score: 41.30  E-value: 8.65e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664   5 RSMDVETVSSGSLGLDIALGvGGLPKGRVVEIYGPESSGKTTLAlHTVAEG----QKKGGIC---AFIDAEHALDP---- 73
Cdd:PLN03187 101 KRKSVVRITTGSQALDELLG-GGIETRCITEAFGEFRSGKTQLA-HTLCVTtqlpTEMGGGNgkvAYIDTEGTFRPdriv 178

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 391883664  74 VYARKLGVN----IDELLISQPDTGEQ---ALEICDTLVRSGAVDVLVVDSVAAL 121
Cdd:PLN03187 179 PIAERFGMDadavLDNIIYARAYTYEHqynLLLGLAAKMAEEPFRLLIVDSVIAL 233
archRadA cd19515
archaeal recombinase Rad51/RadA; This group includes the archaeal protein RadA which is a ...
 12-121 8.70e-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: 40.81  E-value: 8.70e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664  12 VSSGSLGLDIALGvGGLPKGRVVEIYGPESSGKTTLAlHTVAEG----QKKGGI---CAFIDAEHALDP----VYARKLG 80
Cdd:cd19515    1 ISTGSKELDKLLG-GGIETQAITEVFGEFGSGKTQLC-HQLAVNvqlpPEEGGLngkAVYIDTENTFRPerimQMAKALG 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 391883664  81 VNIDELL-----ISQPDTGEQAL---EICDTLVRSGAVDVLVVDSVAAL 121
Cdd:cd19515   79 LDPDEVLdniyvARAYNSNHQMLlveKAEDLIKEGNNIKLLIVDSLTSH 127
recomb_RAD51 TIGR02239
DNA repair protein RAD51; This eukaryotic sequence family consists of RAD51, a protein ...
 5-121 9.68e-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: 41.25  E-value: 9.68e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664    5 RSMDVETVSSGSLGLDIALGvGGLPKGRVVEIYGPESSGKTTLAlHTVA------EGQKKG-GICAFIDAEHALDPV--- 74
Cdd:TIGR02239  71 RRQEVIQLTTGSKELDKLLG-GGIETGSITEIFGEFRTGKTQLC-HTLAvtcqlpIDQGGGeGKALYIDTEGTFRPErll 148

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 391883664   75 -YARKLGVNIDELLIS-------QPDTGEQALEICDTLVRSGAVDVLVVDSVAAL 121
Cdd:TIGR02239 149 aIAERYGLNPEDVLDNvayarayNTDHQLQLLQQAAAMMSESRFALLIVDSATAL 203
PLN03186 PLN03186
DNA repair protein RAD51 homolog; Provisional
 8-151 9.89e-05

DNA repair protein RAD51 homolog; Provisional


Pssm-ID: 178728 [Multi-domain]  Cd Length: 342  Bit Score: 41.26  E-value: 9.89e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664   8 DVETVSSGSLGLDIALGvGGLPKGRVVEIYGPESSGKTTLAlHTVA----------EGQKKggiCAFIDAEHALDP---- 73
Cdd:PLN03186 101 EIIQITTGSRELDKILE-GGIETGSITEIYGEFRTGKTQLC-HTLCvtcqlpldqgGGEGK---AMYIDTEGTFRPqrli 175

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664  74 VYARKLGVNIDELL----ISQPDTGEQALEIcdtLVRSGA------VDVLVVDSVAALVpKAELEGEmGDalpgLQAR-- 141
Cdd:PLN03186 176 QIAERFGLNGADVLenvaYARAYNTDHQSEL---LLEAASmmaetrFALMIVDSATALY-RTEFSGR-GE----LSARqm 246

                        170
                 ....*....|
gi 391883664 142 LMSQALRKLT 151
Cdd:PLN03186 247 HLGKFLRSLQ 256
radA PRK04301
DNA repair and recombination protein RadA; Validated
 5-87 1.11e-04

DNA repair and recombination protein RadA; Validated


Pssm-ID: 235273 [Multi-domain]  Cd Length: 317  Bit Score: 41.02  E-value: 1.11e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664   5 RSMDVETVSSGSLGLDIALGvGGLPKGRVVEIYGPESSGKTTLAlHTVAEG----QKKGGI---CAFIDAEHALDP---- 73
Cdd:PRK04301  77 RRKNVGKITTGSKELDELLG-GGIETQSITEFYGEFGSGKTQIC-HQLAVNvqlpEEKGGLegkAVYIDTEGTFRPerie 154

                         90
                 ....*....|....
gi 391883664  74 VYARKLGVNIDELL 87
Cdd:PRK04301 155 QMAEALGLDPDEVL 168
RepA COG3598
RecA-family ATPase [Replication, recombination and repair];
28-126 1.83e-04

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


Pssm-ID: 442817 [Multi-domain]  Cd Length: 313  Bit Score: 40.27  E-value: 1.83e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664  28 LPKGRVVEIYGPESSGKTTLALH---TVAEGQK------KGGICAFIDAE----------HALDPVYARKLGVNIDELLI 88
Cdd:COG3598   10 LPEGGVTLLAGPPGTGKSFLALQlaaAVAAGGPwlgrrvPPGKVLYLAAEddrgelrrrlKALGADLGLPFADLDGRLRL 89

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 391883664  89 SQPDTGEQALEICDTL---VRSGAVDVLVVDSVAALVPKAE 126
Cdd:COG3598   90 LSLAGDLDDTDDLEALeraIEEEGPDLVVIDPLARVFGGDE 130
Rad51 cd19513
RAD51D recombinase; RAD51 recombinase plays an essential role in DNA repair by homologous ...
 12-121 2.01e-04

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


Pssm-ID: 410921 [Multi-domain]  Cd Length: 235  Bit Score: 39.99  E-value: 2.01e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664  12 VSSGSLGLDIALGvGGLPKGRVVEIYGPESSGKTTLAlHTVA-------EGQKKGGICAFIDAEHALDPV----YARKLG 80
Cdd:cd19513    1 ITTGSKELDKLLG-GGIETGSITELFGEFRTGKTQLC-HTLAvtcqlpiDQGGGEGKALYIDTEGTFRPErllaIAERYG 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 391883664  81 VNIDELLIS-------QPDTGEQALEICDTLVRSGAVDVLVVDSVAAL 121
Cdd:cd19513   79 LNGEDVLDNvayarayNTDHQMQLLIQASAMMAESRYALLIVDSATAL 126
Rad51D cd19489
RAD51D recombinase; RAD51D recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 26-56 4.16e-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: 4.16e-04
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 391883664  26 GGLPKGRVVEIYGPESSGKT----TLALHTVAEGQ 56
Cdd:cd19489    2 GGLRTGEITELVGESSSGKTqlclTAAANVASRSG 36
KaiC_C cd19484
C-terminal domain of Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most ...
 12-121 6.49e-04

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


Pssm-ID: 410892 [Multi-domain]  Cd Length: 218  Bit Score: 38.46  E-value: 6.49e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664  12 VSSGSLGLDIALGVGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHALDPVY--ARKLGVNIDELLIS 89
Cdd:cd19484    1 ISTGIPRLDAMLGGGGFFRGSSILVSGATGTGKTLLAASFADAACRRGERCLYFAFEESPAQLIrnAKSIGIDLEQMERK 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 391883664  90 Q---------PDTG-EQALEICDTLVRSGAVDVLVVDSVAAL 121
Cdd:cd19484   81 GllkiicarpELYGlEDHLIIIKSEINEFKPSRVIVDPLSAL 122
PTZ00035 PTZ00035
Rad51 protein; Provisional
 12-121 1.13e-03

Rad51 protein; Provisional


Pssm-ID: 185407 [Multi-domain]  Cd Length: 337  Bit Score: 38.06  E-value: 1.13e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664  12 VSSGSLGLDIALGvGGLPKGRVVEIYGPESSGKTTLAlHTVA-------EGQKKGGICAFIDAEHALDP----VYARKLG 80
Cdd:PTZ00035 100 ITTGSTQLDKLLG-GGIETGSITELFGEFRTGKTQLC-HTLCvtcqlpiEQGGGEGKVLYIDTEGTFRPerivQIAERFG 177

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 391883664  81 VNIDELL----ISQPDTGEQALEIcdtLVRSGAVDV------LVVDSVAAL 121
Cdd:PTZ00035 178 LDPEDVLdniaYARAYNHEHQMQL---LSQAAAKMAeerfalLIVDSATAL 225
PRK09302 PRK09302
circadian clock protein KaiC; Reviewed
 10-121 1.77e-03

circadian clock protein KaiC; Reviewed


Pssm-ID: 236461 [Multi-domain]  Cd Length: 509  Bit Score: 37.55  E-value: 1.77e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 391883664  10 ETVSSGSLGLDIALGvGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHALDPVY--ARKLGVNIDE-- 85
Cdd:PRK09302 253 ERISSGVPDLDEMLG-GGFFRGSIILVSGATGTGKTLLASKFAEAACRRGERCLLFAFEESRAQLIrnARSWGIDLEKme 331

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 391883664  86 ----LLI--SQPD-TG-EQALEICDTLVRSGAVDVLVVDSVAAL 121
Cdd:PRK09302 332 ekglLKIicARPEsYGlEDHLIIIKREIEEFKPSRVAIDPLSAL 375
NadR3 COG3172
Nicotinamide riboside kinase [Coenzyme transport and metabolism]; Nicotinamide riboside kinase ...
 32-48 2.91e-03

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


Pssm-ID: 442405 [Multi-domain]  Cd Length: 178  Bit Score: 36.34  E-value: 2.91e-03
                         10
                 ....*....|....*..
gi 391883664  32 RVVeIYGPESSGKTTLA 48
Cdd:COG3172   10 KIV-LLGAESTGKTTLA 25
PRK09302 PRK09302
circadian clock protein KaiC; Reviewed
 5-55 3.56e-03

circadian clock protein KaiC; Reviewed


Pssm-ID: 236461 [Multi-domain]  Cd Length: 509  Bit Score: 36.78  E-value: 3.56e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 391883664   5 RSMDVETVSSGSLGLDIALGvGGLPKGRVVEIYGPESSGKTTLALHTVAEG 55
Cdd:PRK09302   6 ASPGIEKLPTGIEGFDDITH-GGLPKGRPTLVSGTAGTGKTLFALQFLVNG 55
uvra TIGR00630
excinuclease ABC, A subunit; This family is a member of the ABC transporter superfamily of ...
 28-58 7.90e-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: 35.76  E-value: 7.90e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 391883664   28 LPKGRVVEIYGPESSGKTTLALHTV-AEGQKK 58
Cdd:TIGR00630  19 IPRDKLVVITGLSGSGKSSLAFDTIyAEGQRR 50
ATPase_2 pfam01637
ATPase domain predominantly from Archaea; This family contain a conserved P-loop motif that is ...
 36-67 9.74e-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: 34.99  E-value: 9.74e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 391883664   36 IYGPESSGKTTLALHTVAEGQKKGGICAFIDA 67
Cdd:pfam01637  25 IYGPEGCGKTALLRESIENLLDLGYYVIYYDP 56
 
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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