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Conserved domains on  [gi|1841994279|ref|YP_009782175|]
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recombinase [Staphylococcus phage IME-SA1]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RecA super family cl33895
RecA/RadA recombinase [Replication, recombination and repair];
29-71 1.56e-05

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


The actual alignment was detected with superfamily member COG0468:

Pssm-ID: 440236 [Multi-domain]  Cd Length: 351  Bit Score: 40.54  E-value: 1.56e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1841994279  29 LSDTNRADIKnVIPTMVPQYDYILG-GGIPLGRLTEVYGLTGSG 71
Cdd:COG0468    33 LGDKARQDVE-VISTGSLALDIALGvGGLPRGRIVEIYGPESSG 75
 
Name Accession Description Interval E-value
RecA COG0468
RecA/RadA recombinase [Replication, recombination and repair];
29-71 1.56e-05

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


Pssm-ID: 440236 [Multi-domain]  Cd Length: 351  Bit Score: 40.54  E-value: 1.56e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1841994279  29 LSDTNRADIKnVIPTMVPQYDYILG-GGIPLGRLTEVYGLTGSG 71
Cdd:COG0468    33 LGDKARQDVE-VISTGSLALDIALGvGGLPRGRIVEIYGPESSG 75
RecA cd00983
recombinase A; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 40-71 3.33e-05

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: 39.46  E-value: 3.33e-05
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1841994279  40 VIPTMVPQYDYILG-GGIPLGRLTEVYGLTGSG 71
Cdd:cd00983     4 VIPTGSLSLDIALGiGGLPRGRIIEIYGPESSG 36
PRK09302 PRK09302
circadian clock protein KaiC; Reviewed
 41-71 4.32e-05

circadian clock protein KaiC; Reviewed


Pssm-ID: 236461 [Multi-domain]  Cd Length: 509  Bit Score: 39.48  E-value: 4.32e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1841994279  41 IPTMVPQYDYILGGGIPLGRLTEVYGLTGSG 71
Cdd:PRK09302   13 LPTGIEGFDDITHGGLPKGRPTLVSGTAGTG 43
ATPase pfam06745
KaiC; This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and ...
 41-71 9.90e-05

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: 38.00  E-value: 9.90e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1841994279  41 IPTMVPQYDYILGGGIPLGRLTEVYGLTGSG 71
Cdd:pfam06745   1 VKTGIPGLDEILKGGFPEGRVVLITGGPGTG 31
circ_KaiC TIGR02655
circadian clock protein KaiC; Members of this family are the circadian clock protein KaiC, ...
 41-71 2.38e-04

circadian clock protein KaiC; Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. [Cellular processes, Other]


Pssm-ID: 131703 [Multi-domain]  Cd Length: 484  Bit Score: 37.24  E-value: 2.38e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1841994279  41 IPTMVPQYDYILGGGIPLGRLTEVYGLTGSG 71
Cdd:TIGR02655   3 IRTMIEGFDDISHGGLPIGRSTLVSGTSGTG 33
 
Name Accession Description Interval E-value
RecA COG0468
RecA/RadA recombinase [Replication, recombination and repair];
29-71 1.56e-05

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


Pssm-ID: 440236 [Multi-domain]  Cd Length: 351  Bit Score: 40.54  E-value: 1.56e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1841994279  29 LSDTNRADIKnVIPTMVPQYDYILG-GGIPLGRLTEVYGLTGSG 71
Cdd:COG0468    33 LGDKARQDVE-VISTGSLALDIALGvGGLPRGRIVEIYGPESSG 75
RecA cd00983
recombinase A; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 40-71 3.33e-05

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: 39.46  E-value: 3.33e-05
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1841994279  40 VIPTMVPQYDYILG-GGIPLGRLTEVYGLTGSG 71
Cdd:cd00983     4 VIPTGSLSLDIALGiGGLPRGRIIEIYGPESSG 36
PRK09302 PRK09302
circadian clock protein KaiC; Reviewed
 41-71 4.32e-05

circadian clock protein KaiC; Reviewed


Pssm-ID: 236461 [Multi-domain]  Cd Length: 509  Bit Score: 39.48  E-value: 4.32e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1841994279  41 IPTMVPQYDYILGGGIPLGRLTEVYGLTGSG 71
Cdd:PRK09302   13 LPTGIEGFDDITHGGLPKGRPTLVSGTAGTG 43
radA PRK04301
DNA repair and recombination protein RadA; Validated
 34-71 5.19e-05

DNA repair and recombination protein RadA; Validated


Pssm-ID: 235273 [Multi-domain]  Cd Length: 317  Bit Score: 39.09  E-value: 5.19e-05
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1841994279  34 RADIKNvIPTMVPQYDYILGGGIPLGRLTEVYGLTGSG 71
Cdd:PRK04301   78 RKNVGK-ITTGSKELDELLGGGIETQSITEFYGEFGSG 114
KaiC-like cd01124
Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most studied in cyanobacteria. ...
 41-71 8.37e-05

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: 38.40  E-value: 8.37e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1841994279  41 IPTMVPQYDYILGGGIPLGRLTEVYGLTGSG 71
Cdd:cd01124     1 VKTGIPGLDELLGGGIPKGSVTLLTGGPGTG 31
Rad51B cd19493
RAD51B recombinase; RAD51B recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 49-71 8.81e-05

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: 38.45  E-value: 8.81e-05
                          10        20
                  ....*....|....*....|...
gi 1841994279  49 DYILGGGIPLGRLTEVYGLTGSG 71
Cdd:cd19493     1 DTALAGGLPLGAITEITGASGSG 23
ATPase pfam06745
KaiC; This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and ...
 41-71 9.90e-05

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: 38.00  E-value: 9.90e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1841994279  41 IPTMVPQYDYILGGGIPLGRLTEVYGLTGSG 71
Cdd:pfam06745   1 VKTGIPGLDEILKGGFPEGRVVLITGGPGTG 31
circ_KaiC TIGR02655
circadian clock protein KaiC; Members of this family are the circadian clock protein KaiC, ...
 41-71 2.38e-04

circadian clock protein KaiC; Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. [Cellular processes, Other]


Pssm-ID: 131703 [Multi-domain]  Cd Length: 484  Bit Score: 37.24  E-value: 2.38e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1841994279  41 IPTMVPQYDYILGGGIPLGRLTEVYGLTGSG 71
Cdd:TIGR02655   3 IRTMIEGFDDISHGGLPIGRSTLVSGTSGTG 33
KaiC-N cd19485
N-terminal domain of Circadian Clock Protein Kaic; KaiC is a circadian clock protein, most ...
 41-71 4.95e-04

N-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: 410893 [Multi-domain]  Cd Length: 226  Bit Score: 36.19  E-value: 4.95e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1841994279  41 IPTMVPQYDYILGGGIPLGRLTEVYGLTGSG 71
Cdd:cd19485     1 LPTGIEGFDDITHGGLPKGRPTLICGTAGTG 31
XRCC3 cd19491
XRCC3 recombinase; XRCC3 (X-ray repair complementing defective repair in Chinese hamster cells ...
 49-71 9.56e-04

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: 35.35  E-value: 9.56e-04
                          10        20
                  ....*....|....*....|...
gi 1841994279  49 DYILGGGIPLGRLTEVYGLTGSG 71
Cdd:cd19491     2 DELLGGGIPVGGITEIAGESGAG 24
Rad51 pfam08423
Rad51; Rad51 is a DNA repair and recombination protein and is a homolog of the bacterial ...
 47-71 1.10e-03

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: 35.36  E-value: 1.10e-03
                          10        20
                  ....*....|....*....|....*
gi 1841994279  47 QYDYILGGGIPLGRLTEVYGLTGSG 71
Cdd:pfam08423  25 ELDKLLGGGIETGSITEIFGEFRTG 49
recomb_radA TIGR02236
DNA repair and recombination protein RadA; This family consists exclusively of archaeal RadA ...
 19-71 1.34e-03

DNA repair and recombination protein RadA; This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 131290 [Multi-domain]  Cd Length: 310  Bit Score: 35.10  E-value: 1.34e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1841994279  19 DLGK-ELGLTLLSdtNRADIKNvIPTMVPQYDYILGGGIPLGRLTEVYGLTGSG 71
Cdd:TIGR02236  57 DLGGfETADDVLE--RRKTIGK-ITTGSKELDELLGGGIETQAITEVFGEFGSG 107
archRadA cd19515
archaeal recombinase Rad51/RadA; This group includes the archaeal protein RadA which is a ...
 41-71 1.76e-03

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: 34.65  E-value: 1.76e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1841994279  41 IPTMVPQYDYILGGGIPLGRLTEVYGLTGSG 71
Cdd:cd19515     1 ISTGSKELDKLLGGGIETQAITEVFGEFGSG 31
RecA pfam00154
recA bacterial DNA recombination protein; RecA is a DNA-dependent ATPase and functions in DNA ...
 19-71 2.19e-03

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: 34.30  E-value: 2.19e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1841994279  19 DLGKElGLTLLSDTNRADIKnVIPTMVPQYDYILG-GGIPLGRLTEVYGLTGSG 71
Cdd:pfam00154  13 QFGKG-SIMKLGDEKKLDVE-TISTGSLALDIALGiGGYPKGRIIEIYGPESSG 64
radB PRK09361
DNA repair and recombination protein RadB; Provisional
 37-71 3.71e-03

DNA repair and recombination protein RadB; Provisional


Pssm-ID: 236482 [Multi-domain]  Cd Length: 225  Bit Score: 33.68  E-value: 3.71e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1841994279  37 IKNVIPTMVPQYDYILGGGIPLGRLTEVYGLTGSG 71
Cdd:PRK09361    1 MDERLPTGCKMLDELLGGGFERGTITQIYGPPGSG 35
recA PRK09519
intein-containing recombinase RecA;
29-71 4.73e-03

intein-containing recombinase RecA;


Pssm-ID: 77219 [Multi-domain]  Cd Length: 790  Bit Score: 33.53  E-value: 4.73e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1841994279  29 LSDTNRADIkNVIPTMVPQYDYILG-GGIPLGRLTEVYGLTGSG 71
Cdd:PRK09519   30 LGDEARQPI-SVIPTGSIALDVALGiGGLPRGRVIEIYGPESSG 72
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
41-71 6.70e-03

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


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 32.97  E-value: 6.70e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1841994279  41 IPTMVPQYDYILGGGIPLGRLTEVYGLTGSG 71
Cdd:COG0467     2 VPTGIPGLDELLGGGLPRGSSTLLSGPPGTG 32
 
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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