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Conserved domains on  [gi|2397023175|gb|WAK88864|]
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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 1.18e-91

recombinase A; Provisional


The actual alignment was detected with superfamily member PRK09354:

Pssm-ID: 236476 [Multi-domain]  Cd Length: 349  Bit Score: 267.81  E-value: 1.18e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   1 TVSTGSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQGLLISQ 80
Cdd:PRK09354   40 VISTGSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKLGVDIDNLLVSQ 119

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2397023175  81 PDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAE 116
Cdd:PRK09354  120 PDTGEQALEIADTLVRSGAVDLIVVDSVAALVPKAE 155
 
Name Accession Description Interval E-value
recA PRK09354
recombinase A; Provisional
 1-116 1.18e-91

recombinase A; Provisional


Pssm-ID: 236476 [Multi-domain]  Cd Length: 349  Bit Score: 267.81  E-value: 1.18e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   1 TVSTGSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQGLLISQ 80
Cdd:PRK09354   40 VISTGSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKLGVDIDNLLVSQ 119

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2397023175  81 PDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAE 116
Cdd:PRK09354  120 PDTGEQALEIADTLVRSGAVDLIVVDSVAALVPKAE 155
RecA COG0468
RecA/RadA recombinase [Replication, recombination and repair];
1-116 6.88e-89

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


Pssm-ID: 440236 [Multi-domain]  Cd Length: 351  Bit Score: 260.87  E-value: 6.88e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   1 TVSTGSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQGLLISQ 80
Cdd:COG0468    43 VISTGSLALDIALGVGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGIAAFIDAEHALDPEYAKKLGVDIDNLLVSQ 122

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2397023175  81 PDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAE 116
Cdd:COG0468   123 PDTGEQALEIAETLVRSGAVDLIVVDSVAALVPKAE 158
RecA cd00983
recombinase A; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 1-116 5.16e-82

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: 239.38  E-value: 5.16e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   1 TVSTGSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQGLLISQ 80
Cdd:cd00983     4 VIPTGSLSLDIALGIGGLPRGRIIEIYGPESSGKTTLALHAIAEAQKLGGTAAFIDAEHALDPEYAKKLGVDIDNLLVSQ 83

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2397023175  81 PDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAE 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 5.18e-82

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: 240.38  E-value: 5.18e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   1 TVSTGSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQGLLISQ 80
Cdd:pfam00154  32 TISTGSLALDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKLGVDIDNLLVSQ 111

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2397023175  81 PDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAE 116
Cdd:pfam00154 112 PDTGEQALEIADMLVRSGAIDLIVVDSVAALVPKAE 147
tigrfam_recA TIGR02012
protein RecA; This model describes orthologs of the recA protein. RecA promotes hybridization ...
 1-116 8.65e-81

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: 239.58  E-value: 8.65e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   1 TVSTGSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQGLLISQ 80
Cdd:TIGR02012  35 TISTGSLALDLALGVGGLPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYARKLGVDIDNLLVSQ 114

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2397023175  81 PDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAE 116
Cdd:TIGR02012 115 PDTGEQALEIAETLVRSGAVDIIVVDSVAALVPKAE 150
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 20-115 1.43e-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: 52.38  E-value: 1.43e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   20 KGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQGLLISqpDTGEQALEITDTLVRSGA 99
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS--GSGELRLRLALALARKLK 78

                           90
                   ....*....|....*.
gi 2397023175  100 VDVLVVDSVAALTPRA 115
Cdd:smart00382  79 PDVLILDEITSLLDAE 94
 
Name Accession Description Interval E-value
recA PRK09354
recombinase A; Provisional
 1-116 1.18e-91

recombinase A; Provisional


Pssm-ID: 236476 [Multi-domain]  Cd Length: 349  Bit Score: 267.81  E-value: 1.18e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   1 TVSTGSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQGLLISQ 80
Cdd:PRK09354   40 VISTGSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKLGVDIDNLLVSQ 119

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2397023175  81 PDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAE 116
Cdd:PRK09354  120 PDTGEQALEIADTLVRSGAVDLIVVDSVAALVPKAE 155
RecA COG0468
RecA/RadA recombinase [Replication, recombination and repair];
1-116 6.88e-89

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


Pssm-ID: 440236 [Multi-domain]  Cd Length: 351  Bit Score: 260.87  E-value: 6.88e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   1 TVSTGSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQGLLISQ 80
Cdd:COG0468    43 VISTGSLALDIALGVGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGIAAFIDAEHALDPEYAKKLGVDIDNLLVSQ 122

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2397023175  81 PDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAE 116
Cdd:COG0468   123 PDTGEQALEIAETLVRSGAVDLIVVDSVAALVPKAE 158
RecA cd00983
recombinase A; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 1-116 5.16e-82

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: 239.38  E-value: 5.16e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   1 TVSTGSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQGLLISQ 80
Cdd:cd00983     4 VIPTGSLSLDIALGIGGLPRGRIIEIYGPESSGKTTLALHAIAEAQKLGGTAAFIDAEHALDPEYAKKLGVDIDNLLVSQ 83

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2397023175  81 PDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAE 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 5.18e-82

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: 240.38  E-value: 5.18e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   1 TVSTGSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQGLLISQ 80
Cdd:pfam00154  32 TISTGSLALDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKLGVDIDNLLVSQ 111

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2397023175  81 PDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAE 116
Cdd:pfam00154 112 PDTGEQALEIADMLVRSGAIDLIVVDSVAALVPKAE 147
tigrfam_recA TIGR02012
protein RecA; This model describes orthologs of the recA protein. RecA promotes hybridization ...
 1-116 8.65e-81

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: 239.58  E-value: 8.65e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   1 TVSTGSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQGLLISQ 80
Cdd:TIGR02012  35 TISTGSLALDLALGVGGLPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYARKLGVDIDNLLVSQ 114

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2397023175  81 PDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAE 116
Cdd:TIGR02012 115 PDTGEQALEIAETLVRSGAVDIIVVDSVAALVPKAE 150
recA PRK09519
intein-containing recombinase RecA;
2-116 1.22e-56

intein-containing recombinase RecA;


Pssm-ID: 77219 [Multi-domain]  Cd Length: 790  Bit Score: 187.22  E-value: 1.22e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   2 VSTGSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQGLLISQP 81
Cdd:PRK09519   41 IPTGSIALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHALDPDYAKKLGVDTDSLLVSQP 120

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2397023175  82 DTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAE 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 1.97e-27

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: 99.35  E-value: 1.97e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175  21 GRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYAR-----------KLGVDLQGLLISQPDTGEQALE 89
Cdd:cd01393     1 GKITEIYGPPGSGKTQLALQLAANALLLGGGVVWIDTEGAFPPSRLVqileaspsselELAEALSRLLYFRPPDTLAHLL 80

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2397023175  90 ITDTLVRSGA----VDVLVVDSVAALTPRAE 116
Cdd:cd01393    81 ALDSLPESLFpppnTSLVVVDSVSALFRKAF 111
archRadB cd01394
archaeal RadB; The archaeal protein RadB shares similarity RadA, the archaeal functional ...
 2-111 3.27e-17

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


Pssm-ID: 410882 [Multi-domain]  Cd Length: 216  Bit Score: 73.50  E-value: 3.27e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   2 VSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEhALDP-----VYARKLGVDLQGL 76
Cdd:cd01394     1 LSTGSKSLDSLLG-GGVERGTITQIYGPPGSGKTNICLQLAVEAAKQGKKVVYIDTE-GLSPerfqqIAGERFESIASNI 78

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2397023175  77 LISQP-DTGEQALEITDT--LVRSGAVDVLVVDSVAAL 111
Cdd:cd01394    79 IVFEPySFDEQGVAIQEAekLLKSDKVDLVVVDSATAL 116
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
2-111 2.81e-13

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


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 63.01  E-value: 2.81e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   2 VSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPV--YARKLGVDL-----Q 74
Cdd:COG0467     2 VPTGIPGLDELLG-GGLPRGSSTLLSGPPGTGKTTLALQFLAEGLRRGEKGLYVSFEESPEQLlrRAESLGLDLeeyieS 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2397023175  75 GLLI--------SQPDTGEQALEITDtLVRSGAVDVLVVDSVAAL 111
Cdd:COG0467    81 GLLRiidlspeeLGLDLEELLARLRE-AVEEFGAKRVVIDSLSGL 124
COG4544 COG4544
Uncharacterized conserved protein [Function unknown];
1-115 1.39e-12

Uncharacterized conserved protein [Function unknown];


Pssm-ID: 443609 [Multi-domain]  Cd Length: 230  Bit Score: 61.48  E-value: 1.39e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   1 TVSTGSLSLDIALGIGGLPKGRIIEIYGPE-SSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQGLLIS 79
Cdd:COG4544    28 VLPTGFAALDAALPGGGLPRGALHEILGPApGIGELGLLLPLLARLAQAGGPVLWIAPPYDLYAPGLAAAGLDPERLLLV 107

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2397023175  80 QPDTGEQALEITDTLVRSGAVDVLVVDsVAALTPRA 115
Cdd:COG4544   108 RARRPADALWAAEEALRSGACGAVVAW-LERLDLTA 142
radB PRK09361
DNA repair and recombination protein RadB; Provisional
 2-111 1.10e-11

DNA repair and recombination protein RadB; Provisional


Pssm-ID: 236482 [Multi-domain]  Cd Length: 225  Bit Score: 58.72  E-value: 1.10e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   2 VSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEhALDPVYARKLGVD-----LQGL 76
Cdd:PRK09361    5 LPTGCKMLDELLG-GGFERGTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYIDTE-GLSPERFKQIAGEdfeelLSNI 82

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2397023175  77 LISQP-DTGEQALEITDT--LVRSGaVDVLVVDSVAAL 111
Cdd:PRK09361   83 IIFEPsSFEEQSEAIRKAekLAKEN-VGLIVLDSATSL 119
recomb_radB TIGR02237
DNA repair and recombination protein RadB; This family consists exclusively of archaeal RadB ...
 9-111 4.14e-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: 57.04  E-value: 4.14e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   9 LDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEhALDPVYARKLGVD-----LQGLLISQP-- 81
Cdd:TIGR02237   1 IDELLG-GGVERGTITQIYGPPGSGKTNICMILAVNAARQGKKVVYIDTE-GLSPERFKQIAEDrperaLSNFIVFEVfd 78

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2397023175  82 -DTGEQALEITDTLVRSGAVDVLVVDSVAAL 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 1.01e-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: 56.12  E-value: 1.01e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   2 VSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVY--ARKLGVDL-----Q 74
Cdd:cd01124     1 VKTGIPGLDELLG-GGIPKGSVTLLTGGPGTGKTLFGLQFLYAGAKNGEPGLFFTFEESPERLLrnAKSFGWDFdemedE 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2397023175  75 GLLI--SQPDTGEQALEITDTL------VRSGAVDVLVVDSVAAL 111
Cdd:cd01124    80 GKLIivDAPPTEAGRFSLDELLsrilsiIKSFKAKRVVIDSLSGL 124
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 20-115 1.43e-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: 52.38  E-value: 1.43e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   20 KGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQGLLISqpDTGEQALEITDTLVRSGA 99
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS--GSGELRLRLALALARKLK 78

                           90
                   ....*....|....*.
gi 2397023175  100 VDVLVVDSVAALTPRA 115
Cdd:smart00382  79 PDVLILDEITSLLDAE 94
ATPase pfam06745
KaiC; This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and ...
 2-112 1.05e-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: 50.71  E-value: 1.05e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   2 VSTGSLSLDiALGIGGLPKGRIIEIYGPESSGKTTLALQ-TIAEAQKKGGICAFVDA-EHALDPVY-ARKLGVDLQ---- 74
Cdd:pfam06745   1 VKTGIPGLD-EILKGGFPEGRVVLITGGPGTGKTIFGLQfLYNGALKYGEPGVFVTLeEPPEDLREnARSFGWDLEklee 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2397023175  75 -GLL----ISQPDTGEQALEITDTL----------VRSGAVDVLVVDSVAALT 112
Cdd:pfam06745  80 eGKLaiidASTSGIGIAEVEDRFDLeelierlreaIREIGAKRVVIDSITTLF 132
Rad51 pfam08423
Rad51; Rad51 is a DNA repair and recombination protein and is a homolog of the bacterial ...
 2-111 3.05e-08

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


Pssm-ID: 462471 [Multi-domain]  Cd Length: 255  Bit Score: 49.61  E-value: 3.05e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   2 VSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQ---KKGGI---CAFVDAEHALDPV----YARKLGV 71
Cdd:pfam08423  19 ITTGSKELDKLLG-GGIETGSITEIFGEFRTGKTQLCHTLCVTCQlplEMGGGegkALYIDTEGTFRPErlvaIAERYGL 97

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2397023175  72 DLQGLLISQP-------DTGEQALEITDTLVRSGAVDVLVVDSVAAL 111
Cdd:pfam08423  98 DPEDVLDNVAyaraynsEHQMQLLQQAAAMMSESRFALLIVDSATAL 144
Rad51B cd19493
RAD51B recombinase; RAD51B recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 10-111 4.51e-08

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


Pssm-ID: 410901 [Multi-domain]  Cd Length: 222  Bit Score: 49.24  E-value: 4.51e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175  10 DIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEA---QKKGG---ICAFVDAEHAL------------DPVYARK--- 68
Cdd:cd19493     1 DTALA-GGLPLGAITEITGASGSGKTQFALTLASSAampARKGGldgGVLYIDTESKFsaerlaeiaearFPEAFSGfme 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 2397023175  69 ----LGVDLQGLLISQPDTGEQALEITDTL---VRSGAVDVLVVDSVAAL 111
Cdd:cd19493    80 enerAEEMLKRVAVVRVTTLAQLLERLPNLeehILSSGVRLVVIDSIAAL 129
DMC1 cd19514
homologous-pairing protein DMC1; DMC1 has a central role in homologous recombination in ...
 2-111 3.02e-07

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: 46.97  E-value: 3.02e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   2 VSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQ------KKGGICAFVDAEHALDP----VYARKLGV 71
Cdd:cd19514     1 ISTGSTELDKLLG-GGIESMSITEVFGEFRTGKTQLSHTLCVTAQlpgsmgGGGGKVAYIDTEGTFRPdrirPIAERFGV 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2397023175  72 D----LQGLLISQPDTGEQALEITDTL----VRSGAVDVLVVDSVAAL 111
Cdd:cd19514    80 DhdavLDNILYARAYTSEHQMELLDYVaakfHEEAVFRLLIIDSIMAL 127
KaiC-like_N cd19488
N-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock ...
 2-113 4.50e-07

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


Pssm-ID: 410896 [Multi-domain]  Cd Length: 225  Bit Score: 46.19  E-value: 4.50e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   2 VSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFV---DAEHALDPVyARKLGVDLQGLLI 78
Cdd:cd19488     1 ISTGIPGLDDILR-GGLPPRRLYLVEGAPGTGKTTLALQFLLEGAANGETGLYItlsETEQELRAV-ALSHGWSLDGIHI 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2397023175  79 ---SQPDTGEQALEITDTL----VRSGAVDVLVVDSVAALTP 113
Cdd:cd19488    79 felSPSESALDAAQQYTILhpseLELSETTRLIFERVERLKP 120
radA PRK04301
DNA repair and recombination protein RadA; Validated
 2-116 1.11e-06

DNA repair and recombination protein RadA; Validated


Pssm-ID: 235273 [Multi-domain]  Cd Length: 317  Bit Score: 45.64  E-value: 1.11e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   2 VSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQ---KKGGI---CAFVDAE--------------HAL 61
Cdd:PRK04301   84 ITTGSKELDELLG-GGIETQSITEFYGEFGSGKTQICHQLAVNVQlpeEKGGLegkAVYIDTEgtfrperieqmaeaLGL 162

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2397023175  62 DP-------VYARKLGVDLQGLLIsqpdtgEQALEitdtLVRSG-AVDVLVVDSVAALTpRAE 116
Cdd:PRK04301  163 DPdevldniHVARAYNSDHQMLLA------EKAEE----LIKEGeNIKLVIVDSLTAHF-RAE 214
Rad51_DMC1_archRadA cd01123
recombinase Rad51, DMC1, and archaeal RadA; This group of recombinases includes the eukaryotic ...
 2-111 1.30e-06

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


Pssm-ID: 410868 [Multi-domain]  Cd Length: 234  Bit Score: 45.21  E-value: 1.30e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   2 VSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKT----TLAL--QTIAEAQKKGGICAFVDAEHALDPV----YARKLGV 71
Cdd:cd01123     1 ITTGSKELDKLLG-GGIETGSITEMFGEFRTGKTqlchTLAVtcQLPIDRGGGEGKAIYIDTEGTFRPErlraIAQRFGL 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2397023175  72 D----LQGLLISQPDTGEQALEITD---TLVRSGAVDVLVVDSVAAL 111
Cdd:cd01123    80 DpddvLDNVAYARAFNSDHQTQLLDqaaAMMVESRFKLLIVDSATAL 126
archRadA cd19515
archaeal recombinase Rad51/RadA; This group includes the archaeal protein RadA which is a ...
 2-116 3.78e-06

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


Pssm-ID: 410923 [Multi-domain]  Cd Length: 233  Bit Score: 43.89  E-value: 3.78e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   2 VSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQK---KGGI---CAFVDAE--------------HAL 61
Cdd:cd19515     1 ISTGSKELDKLLG-GGIETQAITEVFGEFGSGKTQLCHQLAVNVQLppeEGGLngkAVYIDTEntfrperimqmakaLGL 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2397023175  62 DP-------VYARKLGVDLQGLLISQpdtgeqaleITDTLVRSGAVDVLVVDSVAALTpRAE 116
Cdd:cd19515    80 DPdevldniYVARAYNSNHQMLLVEK---------AEDLIKEGNNIKLLIVDSLTSHF-RAE 131
PRK09302 PRK09302
circadian clock protein KaiC; Reviewed
 2-112 9.58e-06

circadian clock protein KaiC; Reviewed


Pssm-ID: 236461 [Multi-domain]  Cd Length: 509  Bit Score: 42.95  E-value: 9.58e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   2 VSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVY--ARKLGVDLQ----- 74
Cdd:PRK09302  255 ISSGVPDLDEMLG-GGFFRGSIILVSGATGTGKTLLASKFAEAACRRGERCLLFAFEESRAQLIrnARSWGIDLEkmeek 333

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2397023175  75 GLL---ISQPD-TG-EQALEITDTLVRSGAVDVLVVDSVAALT 112
Cdd:PRK09302  334 GLLkiiCARPEsYGlEDHLIIIKREIEEFKPSRVAIDPLSALA 376
KaiC-like_C cd19487
C-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock ...
 2-109 1.37e-05

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


Pssm-ID: 410895 [Multi-domain]  Cd Length: 219  Bit Score: 42.29  E-value: 1.37e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   2 VSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYAR--KLGVDL-----Q 74
Cdd:cd19487     1 VSSGVPELDELLG-GGLERGTSTLLIGPAGVGKSTLALQFAKAAAARGERSVLFSFDESIGTLFERseALGIDLramveK 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2397023175  75 GLLI------SQPDTGEQALEITDTLVRSGAvDVLVVDSVA 109
Cdd:cd19487    80 GLLSieqidpAELSPGEFAQRVRTSVEQEDA-RVVVIDSLN 119
recomb_DMC1 TIGR02238
meiotic recombinase Dmc1; This model describes DMC1, a subfamily of a larger family of DNA ...
 2-111 1.38e-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: 1.38e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   2 VSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQ------KKGGICAFVDAEHALDP----VYARKLGV 71
Cdd:TIGR02238  78 ITTGSQALDGILG-GGIESMSITEVFGEFRCGKTQLSHTLCVTAQlpremgGGNGKVAYIDTEGTFRPdrirAIAERFGV 156

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2397023175  72 D----LQGLLISQPDTGEQALEITDTLVRSGAVD---VLVVDSVAAL 111
Cdd:TIGR02238 157 DpdavLDNILYARAYTSEHQMELLDYLAAKFSEEpfrLLIVDSIMAL 203
RadA_SMS_N cd01121
bacterial RadA DNA repair protein; Sms or bacterial RadA is a DNA repair protein that plays a ...
 2-108 1.61e-05

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: 42.13  E-value: 1.61e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   2 VSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPV--YARKLGVDLQGLLIs 79
Cdd:cd01121    64 ISTGIGELDRVLG-GGLVPGSVVLIGGDPGIGKSTLLLQVAARLAQRGGKVLYVSGEESLSQIklRAERLGLGSDNLYL- 141

                          90       100
                  ....*....|....*....|....*....
gi 2397023175  80 qpdTGEQALEITDTLVRSGAVDVLVVDSV 108
Cdd:cd01121   142 ---LAETNLEAILAEIEELKPSLVVIDSI 167
KaiC_C cd19484
C-terminal domain of Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most ...
 2-112 2.72e-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: 41.16  E-value: 2.72e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   2 VSTGSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVY--ARKLGVDLQGLLIS 79
Cdd:cd19484     1 ISTGIPRLDAMLGGGGFFRGSSILVSGATGTGKTLLAASFADAACRRGERCLYFAFEESPAQLIrnAKSIGIDLEQMERK 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2397023175  80 Q---------PDTG-EQALEITDTLVRSGAVDVLVVDSVAALT 112
Cdd:cd19484    81 GllkiicarpELYGlEDHLIIIKSEINEFKPSRVIVDPLSALA 123
PLN03187 PLN03187
meiotic recombination protein DMC1 homolog; Provisional
 2-111 3.45e-05

meiotic recombination protein DMC1 homolog; Provisional


Pssm-ID: 215620 [Multi-domain]  Cd Length: 344  Bit Score: 41.30  E-value: 3.45e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   2 VSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKT----TLALQTIAEAQKKGGI--CAFVDAEHALDP----VYARKLGV 71
Cdd:PLN03187  108 ITTGSQALDELLG-GGIETRCITEAFGEFRSGKTqlahTLCVTTQLPTEMGGGNgkVAYIDTEGTFRPdrivPIAERFGM 186

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 2397023175  72 D----LQGLLISQPDTGEQaleITDTLVRSGA------VDVLVVDSVAAL 111
Cdd:PLN03187  187 DadavLDNIIYARAYTYEH---QYNLLLGLAAkmaeepFRLLIVDSVIAL 233
XRCC3 cd19491
XRCC3 recombinase; XRCC3 (X-ray repair complementing defective repair in Chinese hamster cells ...
 9-40 3.71e-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: 41.12  E-value: 3.71e-05
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2397023175   9 LDIALGiGGLPKGRIIEIYGPESSGKTTLALQ 40
Cdd:cd19491     1 LDELLG-GGIPVGGITEIAGESGAGKTQLCLQ 31
Rad51 cd19513
RAD51D recombinase; RAD51 recombinase plays an essential role in DNA repair by homologous ...
 2-111 1.30e-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: 39.61  E-value: 1.30e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   2 VSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKT----TLAL--QTIAEAQKKGGICAFVDAE----------------- 58
Cdd:cd19513     1 ITTGSKELDKLLG-GGIETGSITELFGEFRTGKTqlchTLAVtcQLPIDQGGGEGKALYIDTEgtfrperllaiaerygl 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2397023175  59 ---HALDPV-YARKLGVDLQGLLISQpdtgeqaleiTDTLVRSGAVDVLVVDSVAAL 111
Cdd:cd19513    80 ngeDVLDNVaYARAYNTDHQMQLLIQ----------ASAMMAESRYALLIVDSATAL 126
AAA_24 pfam13479
AAA domain; This AAA domain is found in a wide variety of presumed phage proteins.
 20-108 1.35e-04

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


Pssm-ID: 433243  Cd Length: 199  Bit Score: 39.23  E-value: 1.35e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175  20 KGRIIEIYGPESSGKTTLAlqtiAEAQKKggicAFVDAEHALDPVYARKLGVDLQGLliSQPDTGEQALEITDTLVRSga 99
Cdd:pfam13479   1 KKLKILIYGPSGIGKTTFA----KTLPKP----LFLDTEKGSKALDGDRFPDIVIRD--SWQDFLDAIDELTAAELAD-- 68


                  ....*....
gi 2397023175 100 VDVLVVDSV 108
Cdd:pfam13479  69 YKTIVIDTV 77
PTZ00035 PTZ00035
Rad51 protein; Provisional
 2-111 1.35e-04

Rad51 protein; Provisional


Pssm-ID: 185407 [Multi-domain]  Cd Length: 337  Bit Score: 39.60  E-value: 1.35e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   2 VSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKT----TLAL--QTIAEAQKKGGICAFVDAEHALDP----VYARKLGV 71
Cdd:PTZ00035  100 ITTGSTQLDKLLG-GGIETGSITELFGEFRTGKTqlchTLCVtcQLPIEQGGGEGKVLYIDTEGTFRPerivQIAERFGL 178

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 2397023175  72 D----LQGLLISQPDTGEQALEItdtLVRSGAVDV------LVVDSVAAL 111
Cdd:PTZ00035  179 DpedvLDNIAYARAYNHEHQMQL---LSQAAAKMAeerfalLIVDSATAL 225
recomb_RAD51 TIGR02239
DNA repair protein RAD51; This eukaryotic sequence family consists of RAD51, a protein ...
 1-111 1.60e-04

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: 39.32  E-value: 1.60e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   1 TVSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKT----TLALQTIAEAQKKG--GICAFVDAE---------------- 58
Cdd:TIGR02239  77 QLTTGSKELDKLLG-GGIETGSITEIFGEFRTGKTqlchTLAVTCQLPIDQGGgeGKALYIDTEgtfrperllaiaeryg 155

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2397023175  59 ----HALDPV-YARKLGVDLQGLLISQpdtgeqaleiTDTLVRSGAVDVLVVDSVAAL 111
Cdd:TIGR02239 156 lnpeDVLDNVaYARAYNTDHQLQLLQQ----------AAAMMSESRFALLIVDSATAL 203
FlaH COG2874
Archaellum biogenesis ATPase ArlH/FlaH [Cell motility];
1-40 1.72e-04

Archaellum biogenesis ATPase ArlH/FlaH [Cell motility];


Pssm-ID: 442121  Cd Length: 230  Bit Score: 39.05  E-value: 1.72e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2397023175   1 TVSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQ 40
Cdd:COG2874     2 IISTGNDELDKRLG-GGIPLGSLVLIEGENGTGKSVLSQQ 40
ATPase_2 pfam01637
ATPase domain predominantly from Archaea; This family contain a conserved P-loop motif that is ...
 23-57 2.22e-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: 38.84  E-value: 2.22e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 2397023175  23 IIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDA 57
Cdd:pfam01637  22 IYVIYGPEGCGKTALLRESIENLLDLGYYVIYYDP 56
XRCC2 cd19490
XRCC2 recombinase; XRCC2 (X-ray repair complementing defective repair in Chinese hamster cells ...
 21-43 2.40e-04

XRCC2 recombinase; XRCC2 (X-ray repair complementing defective repair in Chinese hamster cells 2) recombinase, a RAD51 paralog, plays an important role in DNA repair by homologous recombination (HR). HR is an important error-free repair mechanism for chromosomal double-strand break (DSB) which otherwise leads to cell cycle arrest and death. XRCC2, together with the other RAD51 paralogs, RAD51B, RAD51C, RAD51D, and XRCC3, helps recruit RAD51 to the break site.


Pssm-ID: 410898 [Multi-domain]  Cd Length: 226  Bit Score: 38.48  E-value: 2.40e-04
                          10        20
                  ....*....|....*....|...
gi 2397023175  21 GRIIEIYGPESSGKTTLALQTIA 43
Cdd:cd19490     1 GDVIEITGPSGSGKTELLYHLAA 23
Rad51D cd19489
RAD51D recombinase; RAD51D recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 16-45 2.49e-04

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


Pssm-ID: 410897 [Multi-domain]  Cd Length: 209  Bit Score: 38.39  E-value: 2.49e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 2397023175  16 GGLPKGRIIEIYGPESSGKTTLALQTIAEA 45
Cdd:cd19489     2 GGLRTGEITELVGESSSGKTQLCLTAAANV 31
PRK10851 PRK10851
sulfate/thiosulfate ABC transporter ATP-binding protein CysA;
10-74 7.86e-04

sulfate/thiosulfate ABC transporter ATP-binding protein CysA;


Pssm-ID: 182778 [Multi-domain]  Cd Length: 353  Bit Score: 37.37  E-value: 7.86e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2397023175  10 DIALGIgglPKGRIIEIYGPESSGKTTLaLQTIA--EAQKKGGICaF----VDAEHALDpvyaRKLGVDLQ 74
Cdd:PRK10851   20 DISLDI---PSGQMVALLGPSGSGKTTL-LRIIAglEHQTSGHIR-FhgtdVSRLHARD----RKVGFVFQ 81
AAA_22 pfam13401
AAA domain;
22-115 9.27e-04

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 36.17  E-value: 9.27e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175  22 RIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPV-YARKLGVDLQGLLISQPDTGEQALEITDTLVRSGAV 100
Cdd:pfam13401   6 GILVLTGESGTGKTTLLRRLLEQLPEVRDSVVFVDLPSGTSPKdLLRALLRALGLPLSGRLSKEELLAALQQLLLALAVA 85

                          90
                  ....*....|....*
gi 2397023175 101 DVLVVDSVAALTPRA 115
Cdd:pfam13401  86 VVLIIDEAQHLSLEA 100
PLN03186 PLN03186
DNA repair protein RAD51 homolog; Provisional
 1-111 1.65e-03

DNA repair protein RAD51 homolog; Provisional


Pssm-ID: 178728 [Multi-domain]  Cd Length: 342  Bit Score: 36.25  E-value: 1.65e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   1 TVSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKT----TLALQTIAEAQKKG--GICAFVDAEHALDP----------- 63
Cdd:PLN03186  104 QITTGSRELDKILE-GGIETGSITEIYGEFRTGKTqlchTLCVTCQLPLDQGGgeGKAMYIDTEGTFRPqrliqiaerfg 182

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2397023175  64 ----------VYARKLGVDLQGLLIsqpdtgeqaLEITDTLVRSgAVDVLVVDSVAAL 111
Cdd:PLN03186  183 lngadvlenvAYARAYNTDHQSELL---------LEAASMMAET-RFALMIVDSATAL 230
PAXNEB pfam05625
PAXNEB protein; PAXNEB or PAX6 neighbour is found in several eukaryotic organizms. PAXNED is ...
 1-38 2.19e-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: 36.04  E-value: 2.19e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 2397023175   1 TVSTGSLSLDIALGiGGLPKGRIIEIygpESSGKTTLA 38
Cdd:pfam05625  18 TTSTGTPSLDKLLG-GGLPLGSSLLI---EEDGTTDFA 51
COG1373 COG1373
Predicted ATPase, AAA+ superfamily [General function prediction only];
18-77 2.24e-03

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


Pssm-ID: 440984 [Multi-domain]  Cd Length: 405  Bit Score: 36.08  E-value: 2.24e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175  18 LPKGRIIEIYGPESSGKTTLALQTIAEAQKkggiCAFVDAEhalDPVYARKLGVDLQGLL 77
Cdd:COG1373    17 LDNRKAVVITGPRQVGKTTLLKQLAKELEN----ILYINLD---DPRLRALAEEDPDDLL 69
ABC_UvrA_I cd03270
ATP-binding cassette domain I of the excision repair protein UvrA; Nucleotide excision repair ...
 18-48 3.07e-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: 35.31  E-value: 3.07e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2397023175  18 LPKGRIIEIYGPESSGKTTLALQTI-AEAQKK 48
Cdd:cd03270    18 IPRNKLVVITGVSGSGKSSLAFDTIyAEGQRR 49
PRK09302 PRK09302
circadian clock protein KaiC; Reviewed
 16-54 3.96e-03

circadian clock protein KaiC; Reviewed


Pssm-ID: 236461 [Multi-domain]  Cd Length: 509  Bit Score: 35.24  E-value: 3.96e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 2397023175  16 GGLPKGRIIEIYGPESSGKTTLALQTIAEaqkkgGICAF 54
Cdd:PRK09302   26 GGLPKGRPTLVSGTAGTGKTLFALQFLVN-----GIKRF 59
uvra TIGR00630
excinuclease ABC, A subunit; This family is a member of the ABC transporter superfamily of ...
 18-48 5.66e-03

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


Pssm-ID: 273184 [Multi-domain]  Cd Length: 925  Bit Score: 34.99  E-value: 5.66e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2397023175  18 LPKGRIIEIYGPESSGKTTLALQTI-AEAQKK 48
Cdd:TIGR00630  19 IPRDKLVVITGLSGSGKSSLAFDTIyAEGQRR 50
NadR3 COG3172
Nicotinamide riboside kinase [Coenzyme transport and metabolism]; Nicotinamide riboside kinase ...
 22-40 6.93e-03

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


Pssm-ID: 442405 [Multi-domain]  Cd Length: 178  Bit Score: 34.41  E-value: 6.93e-03
                          10
                  ....*....|....*....
gi 2397023175  22 RIIEIYGPESSGKTTLALQ 40
Cdd:COG3172     9 KKIVLLGAESTGKTTLARA 27
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 18-116 7.83e-03

The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.


Pssm-ID: 99707 [Multi-domain]  Cd Length: 151  Bit Score: 34.04  E-value: 7.83e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175  18 LPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGicafvdaehaldPVYARKLGVDLQGLLISqPDTGEQALEITDTLVRS 97
Cdd:cd00009    16 LPPPKNLLLYGPPGTGKTTLARAIANELFRPGA------------PFLYLNASDLLEGLVVA-ELFGHFLVRLLFELAEK 82

                          90
                  ....*....|....*....
gi 2397023175  98 GAVDVLVVDSVAALTPRAE 116
Cdd:cd00009    83 AKPGVLFIDEIDSLSRGAQ 101
PRK06067 PRK06067
flagellar accessory protein FlaH; Validated
 2-116 8.98e-03

flagellar accessory protein FlaH; Validated


Pssm-ID: 180381  Cd Length: 234  Bit Score: 34.18  E-value: 8.98e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175   2 VSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAE--------------HALDPVYAR 67
Cdd:PRK06067    7 ISTGNEELDRKLG-GGIPFPSLILIEGDHGTGKSVLSQQFVYGALKQGKKVYVITTEntsksylkqmesvkIDISDFFLW 85

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2397023175  68 -KLGV---DLQGLLISqPDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAE 116
Cdd:PRK06067   86 gYLRIfplNTEGFEWN-STLANKLLELIIEFIKSKREDVIIIDSLTIFATYAE 137
Tdk COG1435
Thymidine kinase [Nucleotide transport and metabolism]; Thymidine kinase is part of the ...
 21-106 9.56e-03

Thymidine kinase [Nucleotide transport and metabolism]; Thymidine kinase is part of the Pathway/BioSystem: Pyrimidine salvage


Pssm-ID: 441044  Cd Length: 192  Bit Score: 33.92  E-value: 9.56e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2397023175  21 GRIIEIYGPESSGKTTLALQTI--AEAQKKGGIC--AFVDAEHALDPVYARkLGVDLQGLLISQPDtgeqalEITDTLVR 96
Cdd:COG1435     4 GKLEFIYGPMFSGKSEELLRRAhnYEEAGQKVLLfkPAIDDRYGEGKIVSR-IGLSREAIPVDDDT------DILELVRE 76

                          90
                  ....*....|
gi 2397023175  97 SGAVDVLVVD 106
Cdd:COG1435    77 GPDVDVVLID 86
 
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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