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Conserved domains on  [gi|1139715601|gb|APZ84608|]
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RAD51 recombinase, partial [Zea mays subsp. mays]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN03186 super family cl31979
DNA repair protein RAD51 homolog; Provisional
 1-77 3.14e-53

DNA repair protein RAD51 homolog; Provisional


The actual alignment was detected with superfamily member PLN03186:

Pssm-ID: 178728 [Multi-domain]  Cd Length: 342  Bit Score: 167.99  E-value: 3.14e-53
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1139715601   1 VVITNQVVAQVDGAAMFAGPQIKPIGGNIMAHASTTRLFLRKGRGEERICKVISSPCLAEAEARFQISSEGVTDVKD 77
Cdd:PLN03186  266 VVITNQVVAQVDGSAFFAGPQLKPIGGNIMAHASTTRLALRKGRGENRICKVISSPCLPEAEARFSISSEGVTDVKD 342
 
Name Accession Description Interval E-value
PLN03186 PLN03186
DNA repair protein RAD51 homolog; Provisional
 1-77 3.14e-53

DNA repair protein RAD51 homolog; Provisional


Pssm-ID: 178728 [Multi-domain]  Cd Length: 342  Bit Score: 167.99  E-value: 3.14e-53
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1139715601   1 VVITNQVVAQVDGAAMFAGPQIKPIGGNIMAHASTTRLFLRKGRGEERICKVISSPCLAEAEARFQISSEGVTDVKD 77
Cdd:PLN03186  266 VVITNQVVAQVDGSAFFAGPQLKPIGGNIMAHASTTRLALRKGRGENRICKVISSPCLPEAEARFSISSEGVTDVKD 342
Rad51 cd19513
RAD51D recombinase; RAD51 recombinase plays an essential role in DNA repair by homologous ...
 1-74 5.72e-51

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: 159.02  E-value: 5.72e-51
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1139715601   1 VVITNQVVAQVDGAAMFAGPQIKPIGGNIMAHASTTRLFLRKGRGEERICKVISSPCLAEAEARFQISSEGVTD 74
Cdd:cd19513   162 VVITNQVVAQVDGAAMFAGDPKKPIGGNIMAHASTTRLYLRKGRGETRICKIYDSPCLPEAEAVFAITEDGIGD 235
recomb_RAD51 TIGR02239
DNA repair protein RAD51; This eukaryotic sequence family consists of RAD51, a protein ...
 1-77 3.73e-46

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: 149.10  E-value: 3.73e-46
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1139715601   1 VVITNQVVAQVDGAA-MFAGPQIKPIGGNIMAHASTTRLFLRKGRGEERICKVISSPCLAEAEARFQISSEGVTDVKD 77
Cdd:TIGR02239 239 VVITNQVVAQVDGAGsMFAGDPKKPIGGNIMAHASTTRLSLRKGRGEQRICKIYDSPCLPESEAMFAIYEDGIGDPKE 316
Rad51 pfam08423
Rad51; Rad51 is a DNA repair and recombination protein and is a homolog of the bacterial ...
 1-75 5.20e-45

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: 144.37  E-value: 5.20e-45
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1139715601   1 VVITNQVVAQVDGAA-MFAGPQIKPIGGNIMAHASTTRLFLRKGRGEERICKVISSPCLAEAEARFQISSEGVTDV 75
Cdd:pfam08423 180 VVITNQVVAQVDGAAgMFSGDPKKPIGGHIMAHASTTRLSLRKGRGEQRICKIYDSPCLPESEAVFAIGSGGIIDP 255
 
Name Accession Description Interval E-value
PLN03186 PLN03186
DNA repair protein RAD51 homolog; Provisional
 1-77 3.14e-53

DNA repair protein RAD51 homolog; Provisional


Pssm-ID: 178728 [Multi-domain]  Cd Length: 342  Bit Score: 167.99  E-value: 3.14e-53
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1139715601   1 VVITNQVVAQVDGAAMFAGPQIKPIGGNIMAHASTTRLFLRKGRGEERICKVISSPCLAEAEARFQISSEGVTDVKD 77
Cdd:PLN03186  266 VVITNQVVAQVDGSAFFAGPQLKPIGGNIMAHASTTRLALRKGRGENRICKVISSPCLPEAEARFSISSEGVTDVKD 342
Rad51 cd19513
RAD51D recombinase; RAD51 recombinase plays an essential role in DNA repair by homologous ...
 1-74 5.72e-51

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: 159.02  E-value: 5.72e-51
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1139715601   1 VVITNQVVAQVDGAAMFAGPQIKPIGGNIMAHASTTRLFLRKGRGEERICKVISSPCLAEAEARFQISSEGVTD 74
Cdd:cd19513   162 VVITNQVVAQVDGAAMFAGDPKKPIGGNIMAHASTTRLYLRKGRGETRICKIYDSPCLPEAEAVFAITEDGIGD 235
recomb_RAD51 TIGR02239
DNA repair protein RAD51; This eukaryotic sequence family consists of RAD51, a protein ...
 1-77 3.73e-46

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: 149.10  E-value: 3.73e-46
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1139715601   1 VVITNQVVAQVDGAA-MFAGPQIKPIGGNIMAHASTTRLFLRKGRGEERICKVISSPCLAEAEARFQISSEGVTDVKD 77
Cdd:TIGR02239 239 VVITNQVVAQVDGAGsMFAGDPKKPIGGNIMAHASTTRLSLRKGRGEQRICKIYDSPCLPESEAMFAIYEDGIGDPKE 316
Rad51 pfam08423
Rad51; Rad51 is a DNA repair and recombination protein and is a homolog of the bacterial ...
 1-75 5.20e-45

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: 144.37  E-value: 5.20e-45
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1139715601   1 VVITNQVVAQVDGAA-MFAGPQIKPIGGNIMAHASTTRLFLRKGRGEERICKVISSPCLAEAEARFQISSEGVTDV 75
Cdd:pfam08423 180 VVITNQVVAQVDGAAgMFSGDPKKPIGGHIMAHASTTRLSLRKGRGEQRICKIYDSPCLPESEAVFAIGSGGIIDP 255
PTZ00035 PTZ00035
Rad51 protein; Provisional
 1-77 9.11e-44

Rad51 protein; Provisional


Pssm-ID: 185407 [Multi-domain]  Cd Length: 337  Bit Score: 143.60  E-value: 9.11e-44
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1139715601   1 VVITNQVVAQVDGAAMFAGPQIKPIGGNIMAHASTTRLFLRKGRGEERICKVISSPCLAEAEARFQISSEGVTDVKD 77
Cdd:PTZ00035  261 VVITNQVMADVDGASMFVADPKKPIGGHIIAHASTTRLSLRKGRGEQRICKIYDSPNLPESEAVFAISEGGIIDAKD 337
Rad51_DMC1_archRadA cd01123
recombinase Rad51, DMC1, and archaeal RadA; This group of recombinases includes the eukaryotic ...
 1-72 1.61e-35

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: 119.56  E-value: 1.61e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1139715601   1 VVITNQVVAQVDGAAMFAGPQIKPIGGNIMAHASTTRLFLRKGRGEERICKVISSPCLAEAEARFQISSEGV 72
Cdd:cd01123   162 VVVTNQVVAQVDGAMMFAADPKKPIGGNILAHASTTRLYLRKGRGETRICKIYDSPCLPEAEAVFAITADGV 233
DMC1 cd19514
homologous-pairing protein DMC1; DMC1 has a central role in homologous recombination in ...
 1-74 7.97e-35

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: 117.84  E-value: 7.97e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1139715601   1 VVITNQVVAQVDGAAMFAGPQIKPIGGNIMAHASTTRLFLRKGRGEERICKVISSPCLAEAEARFQISSEGVTD 74
Cdd:cd19514   163 VFITNQVTADPGAAMTFQADPKKPIGGHILAHASTTRISLRKGRGEERIAKIYDSPDLPENEATFAITAGGIAD 236
PLN03187 PLN03187
meiotic recombination protein DMC1 homolog; Provisional
 1-77 1.02e-29

meiotic recombination protein DMC1 homolog; Provisional


Pssm-ID: 215620 [Multi-domain]  Cd Length: 344  Bit Score: 107.17  E-value: 1.02e-29
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1139715601   1 VVITNQVVAQVDGAAMFAGPQiKPIGGNIMAHASTTRLFLRKGRGEERICKVISSPCLAEAEARFQISSEGVTDVKD 77
Cdd:PLN03187  269 VYMTNQVIADPGGGMFISDPK-KPAGGHVLAHAATIRLMLRKGKGEQRVCKVFDAPNLPEAEAEFQITSGGIMDAKD 344
recomb_DMC1 TIGR02238
meiotic recombinase Dmc1; This model describes DMC1, a subfamily of a larger family of DNA ...
 1-75 1.75e-28

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: 103.32  E-value: 1.75e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1139715601   1 VVITNQVVAQVDGAAMFAGPQIKPIGGNIMAHASTTRLFLRKGRGEERICKVISSPCLAEAEARFQISSEGVTDV 75
Cdd:TIGR02238 239 VFVTNQVQADPGATMTFIADPKKPIGGHVLAHASTTRILLRKGRGEERVAKLYDSPDMPEAEASFQITEGGIADA 313
radA PRK04301
DNA repair and recombination protein RadA; Validated
 1-75 1.47e-26

DNA repair and recombination protein RadA; Validated


Pssm-ID: 235273 [Multi-domain]  Cd Length: 317  Bit Score: 98.03  E-value: 1.47e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1139715601   1 VVITNQVVAQVDgaaMFAGPQIKPIGGNIMAHASTTRLFLRKGRGEERICKVISSPCLAEAEARFQISSEGVTDV 75
Cdd:PRK04301  246 VVVTNQVMARPD---AFFGDPTQPIGGHILGHTATFRIYLRKSKGNKRIARLVDSPHLPEGEAVFRITEEGIRDA 317
archRadA cd19515
archaeal recombinase Rad51/RadA; This group includes the archaeal protein RadA which is a ...
 1-74 1.02e-24

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: 91.66  E-value: 1.02e-24
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1139715601   1 VVITNQVVAQVDgaaMFAGPQIKPIGGNIMAHASTTRLFLRKGRGEERICKVISSPCLAEAEARFQISSEGVTD 74
Cdd:cd19515   163 VLVTNQVMAKPD---AFFGDPTQAIGGHILGHAATFRVYLRKGKGGKRIARLVDSPHLPEGEAVFRITEKGIED 233
radB PRK09361
DNA repair and recombination protein RadB; Provisional
 1-76 1.98e-07

DNA repair and recombination protein RadB; Provisional


Pssm-ID: 236482 [Multi-domain]  Cd Length: 225  Bit Score: 45.62  E-value: 1.98e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1139715601   1 VVITNQVVAQVDGAAmfagpqIKPIGGNIMAHASTTRLFLRKGRGEERICKVISSPCLAEAE-ARFQISSEGVTDVK 76
Cdd:PRK09361  155 VVITNQVYSDIDSDG------LRPLGGHTLEHWSKTILRLEKFRNGKRRATLEKHRSRPEGEsAEFRITDRGIEIID 225
RecA-like cd01393
RecA family; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 1-42 5.20e-06

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: 41.57  E-value: 5.20e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1139715601   1 VVITNQVVAQVDGaaMFAGPQIKPIGGNIMAHASTTRLFLRK 42
Cdd:cd01393   146 VVVTNQVTTKIRG--GSGASLVPPALGNTWEHSVSTRLLLYR 185
Rad51C cd19492
RAD51C recombinase; RAD51C recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 1-56 5.90e-06

RAD51C recombinase; RAD51C 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. RAD51C, together with the other RAD51 paralogs, RAD51B, RAD51D, XRCC3, and XRCC2, helps recruit RAD51 to the break site. Additionally, RAD51C acts as a mediator in the early steps of DNA damage signaling.


Pssm-ID: 410900 [Multi-domain]  Cd Length: 172  Bit Score: 41.44  E-value: 5.90e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1139715601   1 VVITNQVVAQVDGAAmfaGPQIKPIGGNIMAHASTTRLFLRKGRGeERICKVISSP 56
Cdd:cd19492   121 VVLTNQVTTKISEDG---QSQLVPALGESWSHACTTRLFLTWDEK-QRFAHLYKSP 172
Rad51B cd19493
RAD51B recombinase; RAD51B recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 1-56 2.77e-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: 40.00  E-value: 2.77e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1139715601   1 VVITNQVVAQVDGAAMFAGpQIKPIGGNIMAHASTTRLFLRKGRGEE-RICKVISSP 56
Cdd:cd19493   166 VLVTNQATTHFGDAGDGSS-GVTAALGDAWAHAVNTRLRLERCLLQLrRVLEIVKSP 221
archRadB cd01394
archaeal RadB; The archaeal protein RadB shares similarity RadA, the archaeal functional ...
 1-72 8.78e-05

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: 38.45  E-value: 8.78e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1139715601   1 VVITNQVVAQVDGAamfagpQIKPIGGNIMAHASTTRLFLRKGRGEERICKVISSPCLAEAE-ARFQISSEGV 72
Cdd:cd01394   149 VVITNQVYSDIDDD------RLKPVGGTLLEHWSKAIIRLEKSPPGLRRATLEKHRSRPEGQsAGFRITDRGI 215
 
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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