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Conserved domains on  [gi|19924125|ref|NP_598332|]
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DNA repair protein RAD51 homolog 4 isoform 4 [Homo sapiens]

Protein Classification

P-loop NTPase family protein( domain architecture ID 1562424)

P-loop NTPase (nucleoside triphosphate hydrolase) family protein contains two conserved sequence signatures, the Walker A motif (the P-loop proper) and Walker B motif which bind, respectively, the beta and gamma phosphate moieties of the bound nucleotide (typically ATP or GTP), and a Mg(2+) cation

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 36-186 4.76e-43

P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families.


The actual alignment was detected with superfamily member cd19489:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 209  Bit Score: 143.93  E-value: 4.76e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19924125  36 LEEVAQKCGLSY--KAEALRRIQVVHAFDIFQMLDVLQELRGTVAQQVTGSSGTVKVVVVDSVTAVVSPLLGGQQR-EGL 112
Cdd:cd19489  53 LAQILKSRAQDAeeIDKALQRIRVVRVFDPYELLDLLEELRNTLSQQQENLYSRLKLVIIDSLSALISPLLGGSKHsEGH 132

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19924125 113 ALMMQLARELKTLARDLGMAVVVTNHITRDRDSG---RLKPALGRSWSFVPSTRILLDTIEGAGASGGRRMACLAKS 186
Cdd:cd19489 133 ALLASLARLLKKLAAEYQIAVLVTNLTVRGGDGGqqgSTKPALGEYWESVPSTRLLLSRDENDPEESGVCTATLLKS 209
 
Name Accession Description Interval E-value
Rad51D cd19489
RAD51D recombinase; RAD51D recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 36-186 4.76e-43

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: 143.93  E-value: 4.76e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19924125  36 LEEVAQKCGLSY--KAEALRRIQVVHAFDIFQMLDVLQELRGTVAQQVTGSSGTVKVVVVDSVTAVVSPLLGGQQR-EGL 112
Cdd:cd19489  53 LAQILKSRAQDAeeIDKALQRIRVVRVFDPYELLDLLEELRNTLSQQQENLYSRLKLVIIDSLSALISPLLGGSKHsEGH 132

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19924125 113 ALMMQLARELKTLARDLGMAVVVTNHITRDRDSG---RLKPALGRSWSFVPSTRILLDTIEGAGASGGRRMACLAKS 186
Cdd:cd19489 133 ALLASLARLLKKLAAEYQIAVLVTNLTVRGGDGGqqgSTKPALGEYWESVPSTRLLLSRDENDPEESGVCTATLLKS 209
radB PRK09361
DNA repair and recombination protein RadB; Provisional
 110-157 1.01e-04

DNA repair and recombination protein RadB; Provisional


Pssm-ID: 236482 [Multi-domain]  Cd Length: 225  Bit Score: 41.77  E-value: 1.01e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 19924125  110 EGLALMMQLARELKTL---ARDLGMAVVVTNHITRDRDSGRLKPALGRS---WS 157
Cdd:PRK09361 129 DNSKLNRELGRQLTHLlklARKHDLAVVITNQVYSDIDSDGLRPLGGHTlehWS 182
Rad51 pfam08423
Rad51; Rad51 is a DNA repair and recombination protein and is a homolog of the bacterial ...
 117-166 5.87e-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: 36.90  E-value: 5.87e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 19924125   117 QLARELKTLARDLGMAVVVTNHITRDRDSGRL-------KPALGRSWSFVPSTRILL 166
Cdd:pfam08423 164 KFLRTLQRLADEFGVAVVITNQVVAQVDGAAGmfsgdpkKPIGGHIMAHASTTRLSL 220
 
Name Accession Description Interval E-value
Rad51D cd19489
RAD51D recombinase; RAD51D recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 36-186 4.76e-43

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: 143.93  E-value: 4.76e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19924125  36 LEEVAQKCGLSY--KAEALRRIQVVHAFDIFQMLDVLQELRGTVAQQVTGSSGTVKVVVVDSVTAVVSPLLGGQQR-EGL 112
Cdd:cd19489  53 LAQILKSRAQDAeeIDKALQRIRVVRVFDPYELLDLLEELRNTLSQQQENLYSRLKLVIIDSLSALISPLLGGSKHsEGH 132

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19924125 113 ALMMQLARELKTLARDLGMAVVVTNHITRDRDSG---RLKPALGRSWSFVPSTRILLDTIEGAGASGGRRMACLAKS 186
Cdd:cd19489 133 ALLASLARLLKKLAAEYQIAVLVTNLTVRGGDGGqqgSTKPALGEYWESVPSTRLLLSRDENDPEESGVCTATLLKS 209
RecA-like cd01393
RecA family; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 48-168 7.82e-16

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: 72.39  E-value: 7.82e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19924125  48 KAEALRRIQVVHAFDifqmlDVLQELRGTVAQQVTGSSGTVKVVVVDSVTAVVSPLLGGQ------QREGLALMMQLARE 121
Cdd:cd01393  60 LAEALSRLLYFRPPD-----TLAHLLALDSLPESLFPPPNTSLVVVDSVSALFRKAFPRGgdgdssSSLRARLLSQLARA 134

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
gi 19924125 122 LKTLARDLGMAVVVTNHITRDRDSG----RLKPALGRSWSFVPSTRILLDT 168
Cdd:cd01393 135 LQKLAAQFNLAVVVTNQVTTKIRGGsgasLVPPALGNTWEHSVSTRLLLYR 185
Rad51C cd19492
RAD51C recombinase; RAD51C recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 114-187 4.71e-12

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: 61.86  E-value: 4.71e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19924125 114 LMMQLARELKTLARDLGMAVVVTNHIT---RDRDSGRLKPALGRSWSFVPSTRILLdtiegaGASGGRRMACLAKSS 187
Cdd:cd19492 102 LLNGLAQLLHSLARQHNLAVVLTNQVTtkiSEDGQSQLVPALGESWSHACTTRLFL------TWDEKQRFAHLYKSP 172
Rad51B cd19493
RAD51B recombinase; RAD51B recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 50-187 9.30e-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: 41.92  E-value: 9.30e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19924125  50 EALRRIQVVHAFDIFQMLDVLQELRGTVAQQVTGssgtvkVVVVDSVTAVVSPLLGGQQREGLALMMQLARE---LKTLA 126
Cdd:cd19493  86 EMLKRVAVVRVTTLAQLLERLPNLEEHILSSGVR------LVVIDSIAALVRREFGGSDGEVTERHNALAREassLKRLA 159

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19924125 127 RDLGMAVVVTNHITR-----DRDSGRLKPALGRSWSFVPSTRILLDtiegAGASGGRRMACLAKSS 187
Cdd:cd19493 160 EEFRIAVLVTNQATThfgdaGDGSSGVTAALGDAWAHAVNTRLRLE----RCLLQLRRVLEIVKSP 221
radB PRK09361
DNA repair and recombination protein RadB; Provisional
 110-157 1.01e-04

DNA repair and recombination protein RadB; Provisional


Pssm-ID: 236482 [Multi-domain]  Cd Length: 225  Bit Score: 41.77  E-value: 1.01e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 19924125  110 EGLALMMQLARELKTL---ARDLGMAVVVTNHITRDRDSGRLKPALGRS---WS 157
Cdd:PRK09361 129 DNSKLNRELGRQLTHLlklARKHDLAVVITNQVYSDIDSDGLRPLGGHTlehWS 182
XRCC3 cd19491
XRCC3 recombinase; XRCC3 (X-ray repair complementing defective repair in Chinese hamster cells ...
 114-166 1.73e-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: 41.51  E-value: 1.73e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19924125 114 LMMQLARELKTLARDLGMAVVVTNHIT-------------------------RDRDSGRLKPALGRSWSFVPSTRILL 166
Cdd:cd19491 143 YLRRLADHLKRLADKYNLAVVVVNQVTdrfdsssdasglgvldylsqfssfsGGVSGNRKVPALGLTWANLVNTRLML 220
Rad51 pfam08423
Rad51; Rad51 is a DNA repair and recombination protein and is a homolog of the bacterial ...
 117-166 5.87e-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: 36.90  E-value: 5.87e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 19924125   117 QLARELKTLARDLGMAVVVTNHITRDRDSGRL-------KPALGRSWSFVPSTRILL 166
Cdd:pfam08423 164 KFLRTLQRLADEFGVAVVITNQVVAQVDGAAGmfsgdpkKPIGGHIMAHASTTRLSL 220
 
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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