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Conserved domains on  [gi|2397023167|gb|WAK88860|]
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recombinase A, partial [Rhizobium rhizogenes]

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
 1-116 2.76e-93

recombinase A; Provisional


The actual alignment was detected with superfamily member PRK09354:

Pssm-ID: 236476 [Multi-domain]  Cd Length: 349  Bit Score: 272.05  E-value: 2.76e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   1 TISTGSLSLDIALGIGGLPKGRIVEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLLISQ 80
Cdd:PRK09354   40 VISTGSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKLGVDIDNLLVSQ 119

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2397023167  81 PDTGEQALEITDTLVRSGAVDILVVDSVAALTPRAE 116
Cdd:PRK09354  120 PDTGEQALEIADTLVRSGAVDLIVVDSVAALVPKAE 155
 
Name Accession Description Interval E-value
recA PRK09354
recombinase A; Provisional
 1-116 2.76e-93

recombinase A; Provisional


Pssm-ID: 236476 [Multi-domain]  Cd Length: 349  Bit Score: 272.05  E-value: 2.76e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   1 TISTGSLSLDIALGIGGLPKGRIVEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLLISQ 80
Cdd:PRK09354   40 VISTGSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKLGVDIDNLLVSQ 119

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2397023167  81 PDTGEQALEITDTLVRSGAVDILVVDSVAALTPRAE 116
Cdd:PRK09354  120 PDTGEQALEIADTLVRSGAVDLIVVDSVAALVPKAE 155
RecA COG0468
RecA/RadA recombinase [Replication, recombination and repair];
1-116 1.18e-90

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


Pssm-ID: 440236 [Multi-domain]  Cd Length: 351  Bit Score: 265.50  E-value: 1.18e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   1 TISTGSLSLDIALGIGGLPKGRIVEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLLISQ 80
Cdd:COG0468    43 VISTGSLALDIALGVGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGIAAFIDAEHALDPEYAKKLGVDIDNLLVSQ 122

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2397023167  81 PDTGEQALEITDTLVRSGAVDILVVDSVAALTPRAE 116
Cdd:COG0468   123 PDTGEQALEIAETLVRSGAVDLIVVDSVAALVPKAE 158
RecA cd00983
recombinase A; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 1-116 1.59e-83

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: 243.23  E-value: 1.59e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   1 TISTGSLSLDIALGIGGLPKGRIVEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLLISQ 80
Cdd:cd00983     4 VIPTGSLSLDIALGIGGLPRGRIIEIYGPESSGKTTLALHAIAEAQKLGGTAAFIDAEHALDPEYAKKLGVDIDNLLVSQ 83

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2397023167  81 PDTGEQALEITDTLVRSGAVDILVVDSVAALTPRAE 116
Cdd:cd00983    84 PDTGEQALEIADTLIRSGAVDLIVVDSVAALVPKAE 119
RecA pfam00154
recA bacterial DNA recombination protein; RecA is a DNA-dependent ATPase and functions in DNA ...
 1-116 4.10e-83

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: 243.46  E-value: 4.10e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   1 TISTGSLSLDIALGIGGLPKGRIVEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLLISQ 80
Cdd:pfam00154  32 TISTGSLALDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKLGVDIDNLLVSQ 111

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2397023167  81 PDTGEQALEITDTLVRSGAVDILVVDSVAALTPRAE 116
Cdd:pfam00154 112 PDTGEQALEIADMLVRSGAIDLIVVDSVAALVPKAE 147
tigrfam_recA TIGR02012
protein RecA; This model describes orthologs of the recA protein. RecA promotes hybridization ...
 1-116 1.76e-82

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: 243.82  E-value: 1.76e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   1 TISTGSLSLDIALGIGGLPKGRIVEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLLISQ 80
Cdd:TIGR02012  35 TISTGSLALDLALGVGGLPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYARKLGVDIDNLLVSQ 114

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2397023167  81 PDTGEQALEITDTLVRSGAVDILVVDSVAALTPRAE 116
Cdd:TIGR02012 115 PDTGEQALEIAETLVRSGAVDIIVVDSVAALVPKAE 150
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 20-115 3.67e-09

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


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 51.22  E-value: 3.67e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   20 KGRIVEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLLISqpDTGEQALEITDTLVRSGA 99
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS--GSGELRLRLALALARKLK 78

                           90
                   ....*....|....*.
gi 2397023167  100 VDILVVDSVAALTPRA 115
Cdd:smart00382  79 PDVLILDEITSLLDAE 94
 
Name Accession Description Interval E-value
recA PRK09354
recombinase A; Provisional
 1-116 2.76e-93

recombinase A; Provisional


Pssm-ID: 236476 [Multi-domain]  Cd Length: 349  Bit Score: 272.05  E-value: 2.76e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   1 TISTGSLSLDIALGIGGLPKGRIVEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLLISQ 80
Cdd:PRK09354   40 VISTGSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKLGVDIDNLLVSQ 119

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2397023167  81 PDTGEQALEITDTLVRSGAVDILVVDSVAALTPRAE 116
Cdd:PRK09354  120 PDTGEQALEIADTLVRSGAVDLIVVDSVAALVPKAE 155
RecA COG0468
RecA/RadA recombinase [Replication, recombination and repair];
1-116 1.18e-90

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


Pssm-ID: 440236 [Multi-domain]  Cd Length: 351  Bit Score: 265.50  E-value: 1.18e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   1 TISTGSLSLDIALGIGGLPKGRIVEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLLISQ 80
Cdd:COG0468    43 VISTGSLALDIALGVGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGIAAFIDAEHALDPEYAKKLGVDIDNLLVSQ 122

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2397023167  81 PDTGEQALEITDTLVRSGAVDILVVDSVAALTPRAE 116
Cdd:COG0468   123 PDTGEQALEIAETLVRSGAVDLIVVDSVAALVPKAE 158
RecA cd00983
recombinase A; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 1-116 1.59e-83

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: 243.23  E-value: 1.59e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   1 TISTGSLSLDIALGIGGLPKGRIVEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLLISQ 80
Cdd:cd00983     4 VIPTGSLSLDIALGIGGLPRGRIIEIYGPESSGKTTLALHAIAEAQKLGGTAAFIDAEHALDPEYAKKLGVDIDNLLVSQ 83

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2397023167  81 PDTGEQALEITDTLVRSGAVDILVVDSVAALTPRAE 116
Cdd:cd00983    84 PDTGEQALEIADTLIRSGAVDLIVVDSVAALVPKAE 119
RecA pfam00154
recA bacterial DNA recombination protein; RecA is a DNA-dependent ATPase and functions in DNA ...
 1-116 4.10e-83

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: 243.46  E-value: 4.10e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   1 TISTGSLSLDIALGIGGLPKGRIVEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLLISQ 80
Cdd:pfam00154  32 TISTGSLALDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKLGVDIDNLLVSQ 111

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2397023167  81 PDTGEQALEITDTLVRSGAVDILVVDSVAALTPRAE 116
Cdd:pfam00154 112 PDTGEQALEIADMLVRSGAIDLIVVDSVAALVPKAE 147
tigrfam_recA TIGR02012
protein RecA; This model describes orthologs of the recA protein. RecA promotes hybridization ...
 1-116 1.76e-82

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: 243.82  E-value: 1.76e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   1 TISTGSLSLDIALGIGGLPKGRIVEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLLISQ 80
Cdd:TIGR02012  35 TISTGSLALDLALGVGGLPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYARKLGVDIDNLLVSQ 114

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2397023167  81 PDTGEQALEITDTLVRSGAVDILVVDSVAALTPRAE 116
Cdd:TIGR02012 115 PDTGEQALEIAETLVRSGAVDIIVVDSVAALVPKAE 150
recA PRK09519
intein-containing recombinase RecA;
2-116 5.35e-57

intein-containing recombinase RecA;


Pssm-ID: 77219 [Multi-domain]  Cd Length: 790  Bit Score: 187.99  E-value: 5.35e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   2 ISTGSLSLDIALGIGGLPKGRIVEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLLISQP 81
Cdd:PRK09519   41 IPTGSIALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHALDPDYAKKLGVDTDSLLVSQP 120

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2397023167  82 DTGEQALEITDTLVRSGAVDILVVDSVAALTPRAE 116
Cdd:PRK09519  121 DTGEQALEIADMLIRSGALDIVVIDSVAALVPRAE 155
RecA-like cd01393
RecA family; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 21-116 3.56e-28

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: 101.28  E-value: 3.56e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167  21 GRIVEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYAR-----------KLGVDLQNLLISQPDTGEQALE 89
Cdd:cd01393     1 GKITEIYGPPGSGKTQLALQLAANALLLGGGVVWIDTEGAFPPSRLVqileaspsselELAEALSRLLYFRPPDTLAHLL 80

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2397023167  90 ITDTLVRSGA----VDILVVDSVAALTPRAE 116
Cdd:cd01393    81 ALDSLPESLFpppnTSLVVVDSVSALFRKAF 111
archRadB cd01394
archaeal RadB; The archaeal protein RadB shares similarity RadA, the archaeal functional ...
 2-111 1.29e-18

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


Pssm-ID: 410882 [Multi-domain]  Cd Length: 216  Bit Score: 76.97  E-value: 1.29e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   2 ISTGSLSLDIALGiGGLPKGRIVEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEhALDP-----VYARKLGVDLQNL 76
Cdd:cd01394     1 LSTGSKSLDSLLG-GGVERGTITQIYGPPGSGKTNICLQLAVEAAKQGKKVVYIDTE-GLSPerfqqIAGERFESIASNI 78

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2397023167  77 LISQP-DTGEQALEITDT--LVRSGAVDILVVDSVAAL 111
Cdd:cd01394    79 IVFEPySFDEQGVAIQEAekLLKSDKVDLVVVDSATAL 116
radB PRK09361
DNA repair and recombination protein RadB; Provisional
 2-111 1.88e-13

DNA repair and recombination protein RadB; Provisional


Pssm-ID: 236482 [Multi-domain]  Cd Length: 225  Bit Score: 63.73  E-value: 1.88e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   2 ISTGSLSLDIALGiGGLPKGRIVEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEhALDPVYARKLGVD-----LQNL 76
Cdd:PRK09361    5 LPTGCKMLDELLG-GGFERGTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYIDTE-GLSPERFKQIAGEdfeelLSNI 82

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2397023167  77 LISQP-DTGEQALEITDT--LVRSGaVDILVVDSVAAL 111
Cdd:PRK09361   83 IIFEPsSFEEQSEAIRKAekLAKEN-VGLIVLDSATSL 119
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
2-111 2.02e-13

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


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 63.40  E-value: 2.02e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   2 ISTGSLSLDIALGiGGLPKGRIVEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPV--YARKLGVDLQ----- 74
Cdd:COG0467     2 VPTGIPGLDELLG-GGLPRGSSTLLSGPPGTGKTTLALQFLAEGLRRGEKGLYVSFEESPEQLlrRAESLGLDLEeyies 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2397023167  75 -NLLISQPDTGEQALEITDTL------VRSGAVDILVVDSVAAL 111
Cdd:COG0467    81 gLLRIIDLSPEELGLDLEELLarlreaVEEFGAKRVVIDSLSGL 124
COG4544 COG4544
Uncharacterized conserved protein [Function unknown];
1-115 6.82e-13

Uncharacterized conserved protein [Function unknown];


Pssm-ID: 443609 [Multi-domain]  Cd Length: 230  Bit Score: 62.25  E-value: 6.82e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   1 TISTGSLSLDIALGIGGLPKGRIVEIYGPE-SSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLLIS 79
Cdd:COG4544    28 VLPTGFAALDAALPGGGLPRGALHEILGPApGIGELGLLLPLLARLAQAGGPVLWIAPPYDLYAPGLAAAGLDPERLLLV 107

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2397023167  80 QPDTGEQALEITDTLVRSGAVDILVVDsVAALTPRA 115
Cdd:COG4544   108 RARRPADALWAAEEALRSGACGAVVAW-LERLDLTA 142
recomb_radB TIGR02237
DNA repair and recombination protein RadB; This family consists exclusively of archaeal RadB ...
 9-111 2.55e-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: 60.51  E-value: 2.55e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   9 LDIALGiGGLPKGRIVEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEhALDPVYARKLGVD-----LQNLLISQP-- 81
Cdd:TIGR02237   1 IDELLG-GGVERGTITQIYGPPGSGKTNICMILAVNAARQGKKVVYIDTE-GLSPERFKQIAEDrperaLSNFIVFEVfd 78

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2397023167  82 -DTGEQALEITDTLVRSGAVDILVVDSVAAL 111
Cdd:TIGR02237  79 fDEQGVAIQKTSKFIDRDSASLVVVDSFTAL 109
KaiC-like cd01124
Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most studied in cyanobacteria. ...
 2-111 1.90e-10

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: 55.35  E-value: 1.90e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   2 ISTGSLSLDIALGiGGLPKGRIVEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVY--ARKLGVDL-----Q 74
Cdd:cd01124     1 VKTGIPGLDELLG-GGIPKGSVTLLTGGPGTGKTLFGLQFLYAGAKNGEPGLFFTFEESPERLLrnAKSFGWDFdemedE 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2397023167  75 NLLI--SQPDTGEQALEITDTL------VRSGAVDILVVDSVAAL 111
Cdd:cd01124    80 GKLIivDAPPTEAGRFSLDELLsrilsiIKSFKAKRVVIDSLSGL 124
DMC1 cd19514
homologous-pairing protein DMC1; DMC1 has a central role in homologous recombination in ...
 2-111 2.33e-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: 52.74  E-value: 2.33e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   2 ISTGSLSLDIALGiGGLPKGRIVEIYGPESSGKTTLALQTIAEAQ------KKGGICAFVDAEHALDP----VYARKLGV 71
Cdd:cd19514     1 ISTGSTELDKLLG-GGIESMSITEVFGEFRTGKTQLSHTLCVTAQlpgsmgGGGGKVAYIDTEGTFRPdrirPIAERFGV 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2397023167  72 D----LQNLLISQPDTGEQALEITDTL----VRSGAVDILVVDSVAAL 111
Cdd:cd19514    80 DhdavLDNILYARAYTSEHQMELLDYVaakfHEEAVFRLLIIDSIMAL 127
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 20-115 3.67e-09

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


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 51.22  E-value: 3.67e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   20 KGRIVEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLLISqpDTGEQALEITDTLVRSGA 99
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS--GSGELRLRLALALARKLK 78

                           90
                   ....*....|....*.
gi 2397023167  100 VDILVVDSVAALTPRA 115
Cdd:smart00382  79 PDVLILDEITSLLDAE 94
Rad51 pfam08423
Rad51; Rad51 is a DNA repair and recombination protein and is a homolog of the bacterial ...
 2-111 3.92e-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: 52.30  E-value: 3.92e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   2 ISTGSLSLDIALGiGGLPKGRIVEIYGPESSGKTTLALQTIAEAQ---KKGGI---CAFVDAEHALDPV----YARKLGV 71
Cdd:pfam08423  19 ITTGSKELDKLLG-GGIETGSITEIFGEFRTGKTQLCHTLCVTCQlplEMGGGegkALYIDTEGTFRPErlvaIAERYGL 97

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2397023167  72 DLQNLLISQP-------DTGEQALEITDTLVRSGAVDILVVDSVAAL 111
Cdd:pfam08423  98 DPEDVLDNVAyaraynsEHQMQLLQQAAAMMSESRFALLIVDSATAL 144
Rad51B cd19493
RAD51B recombinase; RAD51B recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 10-111 8.72e-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: 51.17  E-value: 8.72e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167  10 DIALGiGGLPKGRIVEIYGPESSGKTTLALQTIAEA---QKKGG---ICAFVDAEHAL------------DPVYARK--- 68
Cdd:cd19493     1 DTALA-GGLPLGAITEITGASGSGKTQFALTLASSAampARKGGldgGVLYIDTESKFsaerlaeiaearFPEAFSGfme 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 2397023167  69 ----LGVDLQNLLISQPDTGEQALEITDTL---VRSGAVDILVVDSVAAL 111
Cdd:cd19493    80 enerAEEMLKRVAVVRVTTLAQLLERLPNLeehILSSGVRLVVIDSIAAL 129
Rad51_DMC1_archRadA cd01123
recombinase Rad51, DMC1, and archaeal RadA; This group of recombinases includes the eukaryotic ...
 2-111 1.90e-08

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: 50.22  E-value: 1.90e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   2 ISTGSLSLDIALGiGGLPKGRIVEIYGPESSGKT----TLAL--QTIAEAQKKGGICAFVDAEHALDPV----YARKLGV 71
Cdd:cd01123     1 ITTGSKELDKLLG-GGIETGSITEMFGEFRTGKTqlchTLAVtcQLPIDRGGGEGKAIYIDTEGTFRPErlraIAQRFGL 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2397023167  72 D----LQNLLISQPDTGEQALEITD---TLVRSGAVDILVVDSVAAL 111
Cdd:cd01123    80 DpddvLDNVAYARAFNSDHQTQLLDqaaAMMVESRFKLLIVDSATAL 126
radA PRK04301
DNA repair and recombination protein RadA; Validated
 2-116 7.78e-08

DNA repair and recombination protein RadA; Validated


Pssm-ID: 235273 [Multi-domain]  Cd Length: 317  Bit Score: 48.72  E-value: 7.78e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   2 ISTGSLSLDIALGiGGLPKGRIVEIYGPESSGKTTLALQTIAEAQ---KKGGI---CAFVDAE--------------HAL 61
Cdd:PRK04301   84 ITTGSKELDELLG-GGIETQSITEFYGEFGSGKTQICHQLAVNVQlpeEKGGLegkAVYIDTEgtfrperieqmaeaLGL 162

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2397023167  62 DP-------VYARKLGVDLQNLLIsqpdtgEQALEitdtLVRSG-AVDILVVDSVAALTpRAE 116
Cdd:PRK04301  163 DPdevldniHVARAYNSDHQMLLA------EKAEE----LIKEGeNIKLVIVDSLTAHF-RAE 214
ATPase pfam06745
KaiC; This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and ...
 2-112 9.43e-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: 48.40  E-value: 9.43e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   2 ISTGSLSLDiALGIGGLPKGRIVEIYGPESSGKTTLALQ-TIAEAQKKGGICAFVDA-EHALDPVY-ARKLGVDLQNLL- 77
Cdd:pfam06745   1 VKTGIPGLD-EILKGGFPEGRVVLITGGPGTGKTIFGLQfLYNGALKYGEPGVFVTLeEPPEDLREnARSFGWDLEKLEe 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2397023167  78 --------ISQPDTGEQALEITDTL----------VRSGAVDILVVDSVAALT 112
Cdd:pfam06745  80 egklaiidASTSGIGIAEVEDRFDLeelierlreaIREIGAKRVVIDSITTLF 132
recomb_DMC1 TIGR02238
meiotic recombinase Dmc1; This model describes DMC1, a subfamily of a larger family of DNA ...
 2-111 1.41e-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: 48.24  E-value: 1.41e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   2 ISTGSLSLDIALGiGGLPKGRIVEIYGPESSGKTTLALQTIAEAQ------KKGGICAFVDAEHALDP----VYARKLGV 71
Cdd:TIGR02238  78 ITTGSQALDGILG-GGIESMSITEVFGEFRCGKTQLSHTLCVTAQlpremgGGNGKVAYIDTEGTFRPdrirAIAERFGV 156

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2397023167  72 D----LQNLLISQPDTGEQALEITDTLVRSGAVD---ILVVDSVAAL 111
Cdd:TIGR02238 157 DpdavLDNILYARAYTSEHQMELLDYLAAKFSEEpfrLLIVDSIMAL 203
archRadA cd19515
archaeal recombinase Rad51/RadA; This group includes the archaeal protein RadA which is a ...
 2-116 1.66e-07

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: 47.74  E-value: 1.66e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   2 ISTGSLSLDIALGiGGLPKGRIVEIYGPESSGKTTLALQTIAEAQK---KGGI---CAFVDAEHALDP----VYARKLGV 71
Cdd:cd19515     1 ISTGSKELDKLLG-GGIETQAITEVFGEFGSGKTQLCHQLAVNVQLppeEGGLngkAVYIDTENTFRPerimQMAKALGL 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2397023167  72 D----LQNLLISQP-DTGEQAL---EITDTLVRSGAVDILVVDSVAALTpRAE 116
Cdd:cd19515    80 DpdevLDNIYVARAyNSNHQMLlveKAEDLIKEGNNIKLLIVDSLTSHF-RAE 131
PLN03187 PLN03187
meiotic recombination protein DMC1 homolog; Provisional
 2-111 2.25e-07

meiotic recombination protein DMC1 homolog; Provisional


Pssm-ID: 215620 [Multi-domain]  Cd Length: 344  Bit Score: 47.46  E-value: 2.25e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   2 ISTGSLSLDIALGiGGLPKGRIVEIYGPESSGKT----TLALQTIAEAQKKGGI--CAFVDAEHALDP----VYARKLGV 71
Cdd:PLN03187  108 ITTGSQALDELLG-GGIETRCITEAFGEFRSGKTqlahTLCVTTQLPTEMGGGNgkVAYIDTEGTFRPdrivPIAERFGM 186

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 2397023167  72 D----LQNLLISQPDTGEQaleITDTLVRSGA------VDILVVDSVAAL 111
Cdd:PLN03187  187 DadavLDNIIYARAYTYEH---QYNLLLGLAAkmaeepFRLLIVDSVIAL 233
KaiC-like_N cd19488
N-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock ...
 2-113 3.88e-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: 46.57  E-value: 3.88e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   2 ISTGSLSLDIALGiGGLPKGRIVEIYGPESSGKTTLALQTIAEAQKKGGICAFV---DAEHALDPVyARKLGVDLQNLLI 78
Cdd:cd19488     1 ISTGIPGLDDILR-GGLPPRRLYLVEGAPGTGKTTLALQFLLEGAANGETGLYItlsETEQELRAV-ALSHGWSLDGIHI 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2397023167  79 ---SQPDTGEQALEITDTL----VRSGAVDILVVDSVAALTP 113
Cdd:cd19488    79 felSPSESALDAAQQYTILhpseLELSETTRLIFERVERLKP 120
RadA_SMS_N cd01121
bacterial RadA DNA repair protein; Sms or bacterial RadA is a DNA repair protein that plays a ...
 2-108 7.16e-07

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


Pssm-ID: 410866 [Multi-domain]  Cd Length: 268  Bit Score: 45.99  E-value: 7.16e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   2 ISTGSLSLDIALGiGGLPKGRIVEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPV--YARKLGVDLQNLLIs 79
Cdd:cd01121    64 ISTGIGELDRVLG-GGLVPGSVVLIGGDPGIGKSTLLLQVAARLAQRGGKVLYVSGEESLSQIklRAERLGLGSDNLYL- 141

                          90       100
                  ....*....|....*....|....*....
gi 2397023167  80 qpdTGEQALEITDTLVRSGAVDILVVDSV 108
Cdd:cd01121   142 ---LAETNLEAILAEIEELKPSLVVIDSI 167
PTZ00035 PTZ00035
Rad51 protein; Provisional
 2-111 1.36e-06

Rad51 protein; Provisional


Pssm-ID: 185407 [Multi-domain]  Cd Length: 337  Bit Score: 45.37  E-value: 1.36e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   2 ISTGSLSLDIALGiGGLPKGRIVEIYGPESSGKT----TLAL--QTIAEAQKKGGICAFVDAEHALDP----VYARKLGV 71
Cdd:PTZ00035  100 ITTGSTQLDKLLG-GGIETGSITELFGEFRTGKTqlchTLCVtcQLPIEQGGGEGKVLYIDTEGTFRPerivQIAERFGL 178

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 2397023167  72 D----LQNLLISQPDTGEQALEItdtLVRSGA------VDILVVDSVAAL 111
Cdd:PTZ00035  179 DpedvLDNIAYARAYNHEHQMQL---LSQAAAkmaeerFALLIVDSATAL 225
KaiC-like_C cd19487
C-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock ...
 2-109 8.75e-06

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: 8.75e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   2 ISTGSLSLDIALGiGGLPKGRIVEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYAR--KLGVDLQ----- 74
Cdd:cd19487     1 VSSGVPELDELLG-GGLERGTSTLLIGPAGVGKSTLALQFAKAAAARGERSVLFSFDESIGTLFERseALGIDLRamvek 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2397023167  75 -NLLISQPDT-----GEQALEITDTLVRSGAvDILVVDSVA 109
Cdd:cd19487    80 gLLSIEQIDPaelspGEFAQRVRTSVEQEDA-RVVVIDSLN 119
XRCC3 cd19491
XRCC3 recombinase; XRCC3 (X-ray repair complementing defective repair in Chinese hamster cells ...
 9-111 1.29e-05

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: 42.28  E-value: 1.29e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   9 LDIALGiGGLPKGRIVEIYGPESSGKTTLALQTIAEAQ------KKGGICAFVDAEHAL-------------DPVYARKL 69
Cdd:cd19491     1 LDELLG-GGIPVGGITEIAGESGAGKTQLCLQLALTVQlprelgGLGGGAVYICTESSFpskrlqqlasslpKRYHLEKA 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2397023167  70 GVDLQNLLISQPDTGEQALEITDT----LVRSGAVDILVVDSVAAL 111
Cdd:cd19491    80 KNFLDNIFVEHVADLETLEHCLNYqlpaLLERGPIRLVVIDSIAAL 125
Rad51 cd19513
RAD51D recombinase; RAD51 recombinase plays an essential role in DNA repair by homologous ...
 2-111 1.72e-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: 41.92  E-value: 1.72e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   2 ISTGSLSLDIALGiGGLPKGRIVEIYGPESSGKT----TLAL--QTIAEAQKKGGICAFVDAE----------------- 58
Cdd:cd19513     1 ITTGSKELDKLLG-GGIETGSITELFGEFRTGKTqlchTLAVtcQLPIDQGGGEGKALYIDTEgtfrperllaiaerygl 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2397023167  59 ---HALDPV-YARKLGVDLQNLLISQpdtgeqaleiTDTLVRSGAVDILVVDSVAAL 111
Cdd:cd19513    80 ngeDVLDNVaYARAYNTDHQMQLLIQ----------ASAMMAESRYALLIVDSATAL 126
recomb_RAD51 TIGR02239
DNA repair protein RAD51; This eukaryotic sequence family consists of RAD51, a protein ...
 1-111 2.27e-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: 41.63  E-value: 2.27e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   1 TISTGSLSLDIALGiGGLPKGRIVEIYGPESSGKT----TLALQTIAEAQKKG--GICAFVDAE---------------- 58
Cdd:TIGR02239  77 QLTTGSKELDKLLG-GGIETGSITEIFGEFRTGKTqlchTLAVTCQLPIDQGGgeGKALYIDTEgtfrperllaiaeryg 155

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2397023167  59 ----HALDPV-YARKLGVDLQNLLISQpdtgeqaleiTDTLVRSGAVDILVVDSVAAL 111
Cdd:TIGR02239 156 lnpeDVLDNVaYARAYNTDHQLQLLQQ----------AAAMMSESRFALLIVDSATAL 203
FlaH COG2874
Archaellum biogenesis ATPase ArlH/FlaH [Cell motility];
1-40 5.16e-05

Archaellum biogenesis ATPase ArlH/FlaH [Cell motility];


Pssm-ID: 442121  Cd Length: 230  Bit Score: 40.59  E-value: 5.16e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2397023167   1 TISTGSLSLDIALGiGGLPKGRIVEIYGPESSGKTTLALQ 40
Cdd:COG2874     2 IISTGNDELDKRLG-GGIPLGSLVLIEGENGTGKSVLSQQ 40
KaiC_C cd19484
C-terminal domain of Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most ...
 2-112 8.35e-05

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


Pssm-ID: 410892 [Multi-domain]  Cd Length: 218  Bit Score: 40.00  E-value: 8.35e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   2 ISTGSLSLDIALGIGGLPKGRIVEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVY--ARKLGVDLQNLLIS 79
Cdd:cd19484     1 ISTGIPRLDAMLGGGGFFRGSSILVSGATGTGKTLLAASFADAACRRGERCLYFAFEESPAQLIrnAKSIGIDLEQMERK 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2397023167  80 Q---------PDTG-EQALEITDTLVRSGAVDILVVDSVAALT 112
Cdd:cd19484    81 GllkiicarpELYGlEDHLIIIKSEINEFKPSRVIVDPLSALA 123
PLN03186 PLN03186
DNA repair protein RAD51 homolog; Provisional
 1-111 1.11e-04

DNA repair protein RAD51 homolog; Provisional


Pssm-ID: 178728 [Multi-domain]  Cd Length: 342  Bit Score: 39.72  E-value: 1.11e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   1 TISTGSLSLDIALGiGGLPKGRIVEIYGPESSGKT----TLALQTIAEAQKKG--GICAFVDAEHALDP----VYARKLG 70
Cdd:PLN03186  104 QITTGSRELDKILE-GGIETGSITEIYGEFRTGKTqlchTLCVTCQLPLDQGGgeGKAMYIDTEGTFRPqrliQIAERFG 182

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2397023167  71 VD----LQNLLISQPDTGEQALEItdtLVRSGA------VDILVVDSVAAL 111
Cdd:PLN03186  183 LNgadvLENVAYARAYNTDHQSEL---LLEAASmmaetrFALMIVDSATAL 230
Rad51D cd19489
RAD51D recombinase; RAD51D recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 16-45 1.51e-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: 39.16  E-value: 1.51e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 2397023167  16 GGLPKGRIVEIYGPESSGKTTLALQTIAEA 45
Cdd:cd19489     2 GGLRTGEITELVGESSSGKTQLCLTAAANV 31
PRK10851 PRK10851
sulfate/thiosulfate ABC transporter ATP-binding protein CysA;
10-75 1.90e-04

sulfate/thiosulfate ABC transporter ATP-binding protein CysA;


Pssm-ID: 182778 [Multi-domain]  Cd Length: 353  Bit Score: 39.30  E-value: 1.90e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2397023167  10 DIALGIgglPKGRIVEIYGPESSGKTTLaLQTIA--EAQKKGGICaF----VDAEHALDpvyaRKLGVDLQN 75
Cdd:PRK10851   20 DISLDI---PSGQMVALLGPSGSGKTTL-LRIIAglEHQTSGHIR-FhgtdVSRLHARD----RKVGFVFQH 82
ATPase_2 pfam01637
ATPase domain predominantly from Archaea; This family contain a conserved P-loop motif that is ...
 23-57 3.80e-04

ATPase domain predominantly from Archaea; This family contain a conserved P-loop motif that is involved in binding ATP. There are eukaryote members as well as archaeal members in this family.


Pssm-ID: 376582 [Multi-domain]  Cd Length: 222  Bit Score: 38.07  E-value: 3.80e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 2397023167  23 IVEIYGPESSGKTTLALQTIAEAQKKGGICAFVDA 57
Cdd:pfam01637  22 IYVIYGPEGCGKTALLRESIENLLDLGYYVIYYDP 56
PRK09302 PRK09302
circadian clock protein KaiC; Reviewed
 2-112 3.86e-04

circadian clock protein KaiC; Reviewed


Pssm-ID: 236461 [Multi-domain]  Cd Length: 509  Bit Score: 38.32  E-value: 3.86e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   2 ISTGSLSLDIALGiGGLPKGRIVEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVY--ARKLGVDLQN---- 75
Cdd:PRK09302  255 ISSGVPDLDEMLG-GGFFRGSIILVSGATGTGKTLLASKFAEAACRRGERCLLFAFEESRAQLIrnARSWGIDLEKmeek 333

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2397023167  76 --LLI--SQPD-TG-EQALEITDTLVRSGAVDILVVDSVAALT 112
Cdd:PRK09302  334 glLKIicARPEsYGlEDHLIIIKREIEEFKPSRVAIDPLSALA 376
XRCC2 cd19490
XRCC2 recombinase; XRCC2 (X-ray repair complementing defective repair in Chinese hamster cells ...
 21-43 3.96e-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: 38.10  E-value: 3.96e-04
                          10        20
                  ....*....|....*....|...
gi 2397023167  21 GRIVEIYGPESSGKTTLALQTIA 43
Cdd:cd19490     1 GDVIEITGPSGSGKTELLYHLAA 23
AAA_24 pfam13479
AAA domain; This AAA domain is found in a wide variety of presumed phage proteins.
 20-108 6.03e-04

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


Pssm-ID: 433243  Cd Length: 199  Bit Score: 37.31  E-value: 6.03e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167  20 KGRIVEIYGPESSGKTTLAlqtiAEAQKKggicAFVDAEHALDPVYARKLgvDLQNLLISQPDTGEQALEITDTLVRSga 99
Cdd:pfam13479   1 KKLKILIYGPSGIGKTTFA----KTLPKP----LFLDTEKGSKALDGDRF--PDIVIRDSWQDFLDAIDELTAAELAD-- 68


                  ....*....
gi 2397023167 100 VDILVVDSV 108
Cdd:pfam13479  69 YKTIVIDTV 77
NadR3 COG3172
Nicotinamide riboside kinase [Coenzyme transport and metabolism]; Nicotinamide riboside kinase ...
 22-40 1.66e-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: 35.95  E-value: 1.66e-03
                          10
                  ....*....|....*....
gi 2397023167  22 RIVeIYGPESSGKTTLALQ 40
Cdd:COG3172    10 KIV-LLGAESTGKTTLARA 27
ABC_UvrA_I cd03270
ATP-binding cassette domain I of the excision repair protein UvrA; Nucleotide excision repair ...
 18-48 2.53e-03

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


Pssm-ID: 213237 [Multi-domain]  Cd Length: 226  Bit Score: 35.70  E-value: 2.53e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2397023167  18 LPKGRIVEIYGPESSGKTTLALQTI-AEAQKK 48
Cdd:cd03270    18 IPRNKLVVITGVSGSGKSSLAFDTIyAEGQRR 49
uvra TIGR00630
excinuclease ABC, A subunit; This family is a member of the ABC transporter superfamily of ...
 18-48 3.17e-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: 3.17e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2397023167  18 LPKGRIVEIYGPESSGKTTLALQTI-AEAQKK 48
Cdd:TIGR00630  19 IPRDKLVVITGLSGSGKSSLAFDTIyAEGQRR 50
PRK06067 PRK06067
flagellar accessory protein FlaH; Validated
 2-116 3.19e-03

flagellar accessory protein FlaH; Validated


Pssm-ID: 180381  Cd Length: 234  Bit Score: 35.33  E-value: 3.19e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167   2 ISTGSLSLDIALGiGGLPKGRIVEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAE--------------HALDPVYAR 67
Cdd:PRK06067    7 ISTGNEELDRKLG-GGIPFPSLILIEGDHGTGKSVLSQQFVYGALKQGKKVYVITTEntsksylkqmesvkIDISDFFLW 85

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2397023167  68 -KLGVDLQNLLISQ--PDTGEQALEITDTLVRSGAVDILVVDSVAALTPRAE 116
Cdd:PRK06067   86 gYLRIFPLNTEGFEwnSTLANKLLELIIEFIKSKREDVIIIDSLTIFATYAE 137
COG1373 COG1373
Predicted ATPase, AAA+ superfamily [General function prediction only];
18-77 3.78e-03

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


Pssm-ID: 440984 [Multi-domain]  Cd Length: 405  Bit Score: 35.30  E-value: 3.78e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167  18 LPKGRIVEIYGPESSGKTTLALQTIAEAQKkggiCAFVDAEhalDPVYARKLGVDLQNLL 77
Cdd:COG1373    17 LDNRKAVVITGPRQVGKTTLLKQLAKELEN----ILYINLD---DPRLRALAEEDPDDLL 69
PRK09302 PRK09302
circadian clock protein KaiC; Reviewed
 16-54 5.04e-03

circadian clock protein KaiC; Reviewed


Pssm-ID: 236461 [Multi-domain]  Cd Length: 509  Bit Score: 35.24  E-value: 5.04e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 2397023167  16 GGLPKGRIVEIYGPESSGKTTLALQTIAEaqkkgGICAF 54
Cdd:PRK09302   26 GGLPKGRPTLVSGTAGTGKTLFALQFLVN-----GIKRF 59
PAXNEB pfam05625
PAXNEB protein; PAXNEB or PAX6 neighbour is found in several eukaryotic organizms. PAXNED is ...
 1-38 5.07e-03

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


Pssm-ID: 461696  Cd Length: 359  Bit Score: 34.88  E-value: 5.07e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 2397023167   1 TISTGSLSLDIALGiGGLPKGRIVEIygpESSGKTTLA 38
Cdd:pfam05625  18 TTSTGTPSLDKLLG-GGLPLGSSLLI---EEDGTTDFA 51
RepA COG3598
RecA-family ATPase [Replication, recombination and repair];
18-116 5.47e-03

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


Pssm-ID: 442817 [Multi-domain]  Cd Length: 313  Bit Score: 34.88  E-value: 5.47e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167  18 LPKGRIVEIYGPESSGKTTLALQ---TIAEAQK------KGGICAFVDAE----------HALDPVYARKLGVDLQNLLI 78
Cdd:COG3598    10 LPEGGVTLLAGPPGTGKSFLALQlaaAVAAGGPwlgrrvPPGKVLYLAAEddrgelrrrlKALGADLGLPFADLDGRLRL 89

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2397023167  79 SQPDTGEQALEITDTL---VRSGAVDILVVDSVAALTPRAE 116
Cdd:COG3598    90 LSLAGDLDDTDDLEALeraIEEEGPDLVVIDPLARVFGGDE 130
AAA_22 pfam13401
AAA domain;
22-115 9.42e-03

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 33.47  E-value: 9.42e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023167  22 RIVEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPV-YARKLGVDLQNLLISQPDTGEQALEITDTLVRSGAV 100
Cdd:pfam13401   6 GILVLTGESGTGKTTLLRRLLEQLPEVRDSVVFVDLPSGTSPKdLLRALLRALGLPLSGRLSKEELLAALQQLLLALAVA 85

                          90
                  ....*....|....*
gi 2397023167 101 DILVVDSVAALTPRA 115
Cdd:pfam13401  86 VVLIIDEAQHLSLEA 100
 
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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