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Conserved domains on  [gi|1958668994|ref|XP_038945470|]
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breast cancer type 2 susceptibility protein homolog isoform X4 [Rattus norvegicus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
BRCA2DBD_OB2 cd04494
BRCA2DBD_OB2: A subfamily of OB folds corresponding to the second OB fold (OB2) of the ...
 2734-3012 5.57e-122

BRCA2DBD_OB2: A subfamily of OB folds corresponding to the second OB fold (OB2) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD. BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. It also facilitates filament formation. Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility. BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA).


:

Pssm-ID: 239940  Cd Length: 251  Bit Score: 385.65  E-value: 5.57e-122
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668994 2734 PLSSLFSDGGNVGCVDVIVQRVYPLQWVEKTVSGSYIFRNEREEEKEALRFAEAQQKKLEALFTKVHTELKEHEEDIAQR 2813
Cdd:cd04494      1 PLSSLYDSGGLVGCVDVIILRVYPLQWVEKTSEGGSVFRSERAEEREARLHAQRQQKKLEALFSKIQEEFEKEEEDNNQR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668994 2814 RVLSRALTRQQVHALQDGAELYAAVQDASDPEHLEvysaltggrparvgrtaaasavsqcvkcpqTCFSEEQLRALNNYR 2893
Cdd:cd04494     81 RPRSRTRTRQNVTDLQDGAELYEALEAAADPSFLE------------------------------AELSEEQLEALSNYQ 130

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668994 2894 QMLSDKKQARIQSEFRKALEAAEKEEGL-SRDVSTVWKLRVTSYK-KREKSALLSIWRPSSDLPSLLTEGQRYRIYHLSV 2971
Cdd:cd04494    131 QLQNEKKQARLQEEFRKAVEEALKEEGLsKRDVTPVWKLRVTDYRsKPEKSGLLSIWRPTEDLRSLLTEGKRYRIYGLAT 210

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|.
gi 1958668994 2972 SKSKNKFEWPSIQLTATKRTQYQQLPVSSETLLQLYQPREL 3012
Cdd:cd04494    211 SNSKKRSGNEEVQLTATKKTRYQPLPVSQRELFQPFQPRKA 251
BRCA-2_helical pfam09169
BRCA2, helical; Members of this family adopt a helical structure, consisting of a four-helix ...
 2411-2597 5.59e-103

BRCA2, helical; Members of this family adopt a helical structure, consisting of a four-helix cluster core (alpha 1, alpha 8, alpha 9, alpha 10) and two successive beta-hairpins (beta 1 to beta 4). An approx. 50-amino acid segment that contains four short helices (alpha 2 to alpha 4), meanders around the surface of the core structure. In BRCA2, the alpha 9 and alpha 10 helices pack with BRCA-2_OB1 (pfam09103) through van der Waals contacts involving hydrophobic and aromatic residues, and also through side-chain and backbone hydrogen bonds. The domain binds the 70-amino acid DSS1 (deleted in split-hand/split foot syndrome) protein, which was originally identified as one of three genes that map to a 1.5-Mb locus deleted in an inherited developmental malformation syndrome.


:

Pssm-ID: 462700  Cd Length: 187  Bit Score: 328.15  E-value: 5.59e-103
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668994 2411 MSSLQNARDLQDIRIKNKERHHLCPQPGSLYLTKSSTLPRISLQAAVGDSVPSACSPKQLYMYGVSKACISVNSKNAEYF 2490
Cdd:pfam09169    1 QSNLLLARDLQDMRIKKKSRQIIRPQPGSLYLKKSSVVRRISLKAAVGGCPPSHYSEKQLYYGGVCKVSLIIASENAESF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668994 2491 QFAIEDHFGKEALCAGKGFRLADGGWLIPSDDGKAGKEEFYRALCDTPGVDPKLISSVWVSNHYRWIVWKLAAMEFAFPK 2570
Cdd:pfam09169   81 QFFDDDFFGKEFLLNGGGIQLADGGLLIPNDGGVAGKEEFYRALCDTPGVDPKLISAWWVYNHYRWIVWKLAAMERFFPK 160

                          170       180
                   ....*....|....*....|....*..
gi 1958668994 2571 EFANRCLNPERVLLQLKYRYDVEIDNS 2597
Cdd:pfam09169  161 EFGRRCLTPERVLLQLKYRYDVEIDKS 187
BRCA-2_OB1 pfam09103
BRCA2, oligonucleotide/oligosaccharide-binding, domain 1; Members of this family assume an OB ...
 2600-2726 5.68e-64

BRCA2, oligonucleotide/oligosaccharide-binding, domain 1; Members of this family assume an OB fold, which consists of a highly curved five-stranded beta-sheet that closes on itself to form a beta-barrel. OB1 has a shallow groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for weak single strand DNA binding. The domain also binds the 70-amino acid DSS1 (deleted in split-hand/split foot syndrome) protein, which was originally identified as one of three genes that map to a 1.5-Mb locus deleted in an inherited developmental malformation syndrome.


:

Pssm-ID: 462678  Cd Length: 123  Bit Score: 213.58  E-value: 5.68e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668994 2600 SALKKILERDDTAAKTLVLCVSDIISLSTNVSETSgskaSSEDSNKVDTIELTDGWYAVKAQLDPPLLALVKSGRLTVGQ 2679
Cdd:pfam09103    1 SALRKILERDDSASKPMVLCVSAIISSESNSEETG----SGTVDNTKAILELTDGWYSIKAVLDAPLTRLVRRGKIRVGQ 76

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1958668994 2680 KIITQGAELVGSPDACAPLEAPDSLRLKISANSTRPARWHSKLGFFH 2726
Cdd:pfam09103   77 KLAICGAELVGSKEPCSPLEAPDSVRLKISANSTRRARWDAKLGFQR 123
BRCA2 pfam00634
BRCA2 repeat; The alignment covers only the most conserved region of the repeat.
 1200-1228 5.63e-08

BRCA2 repeat; The alignment covers only the most conserved region of the repeat.


:

Pssm-ID: 459881  Cd Length: 29  Bit Score: 50.91  E-value: 5.63e-08
                           10        20
                   ....*....|....*....|....*....
gi 1958668994 1200 EFGGFCSALGTKLSVSNEALRKAMKLFSD 1228
Cdd:pfam00634    1 SFLGFQTASGKKISVSEESLQKAKKLFRD 29
BRCA2 pfam00634
BRCA2 repeat; The alignment covers only the most conserved region of the repeat.
 1408-1436 1.80e-07

BRCA2 repeat; The alignment covers only the most conserved region of the repeat.


:

Pssm-ID: 459881  Cd Length: 29  Bit Score: 49.37  E-value: 1.80e-07
                           10        20
                   ....*....|....*....|....*....
gi 1958668994 1408 FNISFQTASGKNIRVSKESLNKSVNILDQ 1436
Cdd:pfam00634    1 SFLGFQTASGKKISVSEESLQKAKKLFRD 29
BRCA2 pfam00634
BRCA2 repeat; The alignment covers only the most conserved region of the repeat.
 1942-1970 3.12e-07

BRCA2 repeat; The alignment covers only the most conserved region of the repeat.


:

Pssm-ID: 459881  Cd Length: 29  Bit Score: 48.60  E-value: 3.12e-07
                           10        20
                   ....*....|....*....|....*....
gi 1958668994 1942 TYGIFSTASGKAVQVSDASLEKARQVFSE 1970
Cdd:pfam00634    1 SFLGFQTASGKKISVSEESLQKAKKLFRD 29
BRCA2 pfam00634
BRCA2 repeat; The alignment covers only the most conserved region of the repeat.
 1641-1669 1.22e-05

BRCA2 repeat; The alignment covers only the most conserved region of the repeat.


:

Pssm-ID: 459881  Cd Length: 29  Bit Score: 43.98  E-value: 1.22e-05
                           10        20
                   ....*....|....*....|....*....
gi 1958668994 1641 SALACYTGDSRKTCVGESSLSKGKKWLRE 1669
Cdd:pfam00634    1 SFLGFQTASGKKISVSEESLQKAKKLFRD 29
BRCA2 pfam00634
BRCA2 repeat; The alignment covers only the most conserved region of the repeat.
 987-1015 4.75e-05

BRCA2 repeat; The alignment covers only the most conserved region of the repeat.


:

Pssm-ID: 459881  Cd Length: 29  Bit Score: 42.43  E-value: 4.75e-05
                           10        20
                   ....*....|....*....|....*....
gi 1958668994  987 FGGSFRTASNKEIKLSEDNVKKSKMFFKD 1015
Cdd:pfam00634    1 SFLGFQTASGKKISVSEESLQKAKKLFRD 29
BRCA2 pfam00634
BRCA2 repeat; The alignment covers only the most conserved region of the repeat.
 1508-1534 5.09e-05

BRCA2 repeat; The alignment covers only the most conserved region of the repeat.


:

Pssm-ID: 459881  Cd Length: 29  Bit Score: 42.43  E-value: 5.09e-05
                           10        20
                   ....*....|....*....|....*..
gi 1958668994 1508 LSFHTASGKKVKIMQESLDKVKNLFDE 1534
Cdd:pfam00634    3 LGFQTASGKKISVSEESLQKAKKLFRD 29
BRCA-2_OB3 super family cl48040
BRCA2, oligonucleotide/oligosaccharide-binding, domain 3; Members of this family assume an OB ...
 3010-3029 4.36e-03

BRCA2, oligonucleotide/oligosaccharide-binding, domain 3; Members of this family assume an OB fold, which consists of a highly curved five-stranded beta-sheet that closes on itself to form a beta-barrel. OB3 has a pronounced groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for strong ssDNA binding.


The actual alignment was detected with superfamily member pfam09104:

Pssm-ID: 462679  Cd Length: 139  Bit Score: 39.95  E-value: 4.36e-03
                           10        20
                   ....*....|....*....|
gi 1958668994 3010 RELLPFSKLSDPAFQPPCSE 3029
Cdd:pfam09104    1 REVTPFSDLLNPSFQPPCGE 20
 
Name Accession Description Interval E-value
BRCA2DBD_OB2 cd04494
BRCA2DBD_OB2: A subfamily of OB folds corresponding to the second OB fold (OB2) of the ...
 2734-3012 5.57e-122

BRCA2DBD_OB2: A subfamily of OB folds corresponding to the second OB fold (OB2) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD. BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. It also facilitates filament formation. Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility. BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA).


Pssm-ID: 239940  Cd Length: 251  Bit Score: 385.65  E-value: 5.57e-122
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668994 2734 PLSSLFSDGGNVGCVDVIVQRVYPLQWVEKTVSGSYIFRNEREEEKEALRFAEAQQKKLEALFTKVHTELKEHEEDIAQR 2813
Cdd:cd04494      1 PLSSLYDSGGLVGCVDVIILRVYPLQWVEKTSEGGSVFRSERAEEREARLHAQRQQKKLEALFSKIQEEFEKEEEDNNQR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668994 2814 RVLSRALTRQQVHALQDGAELYAAVQDASDPEHLEvysaltggrparvgrtaaasavsqcvkcpqTCFSEEQLRALNNYR 2893
Cdd:cd04494     81 RPRSRTRTRQNVTDLQDGAELYEALEAAADPSFLE------------------------------AELSEEQLEALSNYQ 130

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668994 2894 QMLSDKKQARIQSEFRKALEAAEKEEGL-SRDVSTVWKLRVTSYK-KREKSALLSIWRPSSDLPSLLTEGQRYRIYHLSV 2971
Cdd:cd04494    131 QLQNEKKQARLQEEFRKAVEEALKEEGLsKRDVTPVWKLRVTDYRsKPEKSGLLSIWRPTEDLRSLLTEGKRYRIYGLAT 210

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|.
gi 1958668994 2972 SKSKNKFEWPSIQLTATKRTQYQQLPVSSETLLQLYQPREL 3012
Cdd:cd04494    211 SNSKKRSGNEEVQLTATKKTRYQPLPVSQRELFQPFQPRKA 251
BRCA-2_helical pfam09169
BRCA2, helical; Members of this family adopt a helical structure, consisting of a four-helix ...
 2411-2597 5.59e-103

BRCA2, helical; Members of this family adopt a helical structure, consisting of a four-helix cluster core (alpha 1, alpha 8, alpha 9, alpha 10) and two successive beta-hairpins (beta 1 to beta 4). An approx. 50-amino acid segment that contains four short helices (alpha 2 to alpha 4), meanders around the surface of the core structure. In BRCA2, the alpha 9 and alpha 10 helices pack with BRCA-2_OB1 (pfam09103) through van der Waals contacts involving hydrophobic and aromatic residues, and also through side-chain and backbone hydrogen bonds. The domain binds the 70-amino acid DSS1 (deleted in split-hand/split foot syndrome) protein, which was originally identified as one of three genes that map to a 1.5-Mb locus deleted in an inherited developmental malformation syndrome.


Pssm-ID: 462700  Cd Length: 187  Bit Score: 328.15  E-value: 5.59e-103
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668994 2411 MSSLQNARDLQDIRIKNKERHHLCPQPGSLYLTKSSTLPRISLQAAVGDSVPSACSPKQLYMYGVSKACISVNSKNAEYF 2490
Cdd:pfam09169    1 QSNLLLARDLQDMRIKKKSRQIIRPQPGSLYLKKSSVVRRISLKAAVGGCPPSHYSEKQLYYGGVCKVSLIIASENAESF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668994 2491 QFAIEDHFGKEALCAGKGFRLADGGWLIPSDDGKAGKEEFYRALCDTPGVDPKLISSVWVSNHYRWIVWKLAAMEFAFPK 2570
Cdd:pfam09169   81 QFFDDDFFGKEFLLNGGGIQLADGGLLIPNDGGVAGKEEFYRALCDTPGVDPKLISAWWVYNHYRWIVWKLAAMERFFPK 160

                          170       180
                   ....*....|....*....|....*..
gi 1958668994 2571 EFANRCLNPERVLLQLKYRYDVEIDNS 2597
Cdd:pfam09169  161 EFGRRCLTPERVLLQLKYRYDVEIDKS 187
BRCA-2_OB1 pfam09103
BRCA2, oligonucleotide/oligosaccharide-binding, domain 1; Members of this family assume an OB ...
 2600-2726 5.68e-64

BRCA2, oligonucleotide/oligosaccharide-binding, domain 1; Members of this family assume an OB fold, which consists of a highly curved five-stranded beta-sheet that closes on itself to form a beta-barrel. OB1 has a shallow groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for weak single strand DNA binding. The domain also binds the 70-amino acid DSS1 (deleted in split-hand/split foot syndrome) protein, which was originally identified as one of three genes that map to a 1.5-Mb locus deleted in an inherited developmental malformation syndrome.


Pssm-ID: 462678  Cd Length: 123  Bit Score: 213.58  E-value: 5.68e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668994 2600 SALKKILERDDTAAKTLVLCVSDIISLSTNVSETSgskaSSEDSNKVDTIELTDGWYAVKAQLDPPLLALVKSGRLTVGQ 2679
Cdd:pfam09103    1 SALRKILERDDSASKPMVLCVSAIISSESNSEETG----SGTVDNTKAILELTDGWYSIKAVLDAPLTRLVRRGKIRVGQ 76

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1958668994 2680 KIITQGAELVGSPDACAPLEAPDSLRLKISANSTRPARWHSKLGFFH 2726
Cdd:pfam09103   77 KLAICGAELVGSKEPCSPLEAPDSVRLKISANSTRRARWDAKLGFQR 123
BRCA2DBD_OB1 cd04493
BRCA2DBD_OB1: A subfamily of OB folds corresponding to the first OB fold (OB1) of the ...
 2612-2724 3.49e-47

BRCA2DBD_OB1: A subfamily of OB folds corresponding to the first OB fold (OB1) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD. BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. It also facilitates filament formation. Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility. BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA). BRCA2DBD OB1 binds DNA weakly.


Pssm-ID: 239939  Cd Length: 100  Bit Score: 164.71  E-value: 3.49e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668994 2612 AAKTLVLCVSDIISLSTnvsetsgskasseDSNKVDTIELTDGWYAVKAQLDPPLLALVKSGRLTVGQKIITQGAELVGS 2691
Cdd:cd04493      1 ASRLMVLCVSGINSEER-------------LSPHMPIIELTDGWYSIRAQLDPPLTNLVRKGKLRVGQKLRICGAELLGS 67

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1958668994 2692 PDACAPLEAPDSLRLKISANSTRPARWHSKLGF 2724
Cdd:cd04493     68 ANPCSPLEAPDSVRLKINANSTRRARWDARLGF 100
Tower pfam09121
Tower; Members of this family adopt a secondary structure consisting of a pair of long, ...
 2761-2802 3.86e-16

Tower; Members of this family adopt a secondary structure consisting of a pair of long, antiparallel alpha-helices (the stem) that support a three-helix bundle (3HB) at their end. The 3HB contains a helix-turn-helix motif and is similar to the DNA binding domains of the bacterial site-specific recombinases, and of eukaryotic Myb and homeodomain transcription factors. The Tower domain has an important role in the tumour suppressor function of BRCA2, and is essential for appropriate binding of BRCA2 to DNA.


Pssm-ID: 462684  Cd Length: 42  Bit Score: 74.32  E-value: 3.86e-16
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1958668994 2761 VEKTVSGSYIFRNEREEEKEALRFAEAQQKKLEALFTKVHTE 2802
Cdd:pfam09121    1 MEKKPDGGFVFRNERAEEKEARRYAEAQQKALEALFAKIQAE 42
BRCA2 pfam00634
BRCA2 repeat; The alignment covers only the most conserved region of the repeat.
 1200-1228 5.63e-08

BRCA2 repeat; The alignment covers only the most conserved region of the repeat.


Pssm-ID: 459881  Cd Length: 29  Bit Score: 50.91  E-value: 5.63e-08
                           10        20
                   ....*....|....*....|....*....
gi 1958668994 1200 EFGGFCSALGTKLSVSNEALRKAMKLFSD 1228
Cdd:pfam00634    1 SFLGFQTASGKKISVSEESLQKAKKLFRD 29
BRCA2 pfam00634
BRCA2 repeat; The alignment covers only the most conserved region of the repeat.
 1408-1436 1.80e-07

BRCA2 repeat; The alignment covers only the most conserved region of the repeat.


Pssm-ID: 459881  Cd Length: 29  Bit Score: 49.37  E-value: 1.80e-07
                           10        20
                   ....*....|....*....|....*....
gi 1958668994 1408 FNISFQTASGKNIRVSKESLNKSVNILDQ 1436
Cdd:pfam00634    1 SFLGFQTASGKKISVSEESLQKAKKLFRD 29
BRCA2 pfam00634
BRCA2 repeat; The alignment covers only the most conserved region of the repeat.
 1942-1970 3.12e-07

BRCA2 repeat; The alignment covers only the most conserved region of the repeat.


Pssm-ID: 459881  Cd Length: 29  Bit Score: 48.60  E-value: 3.12e-07
                           10        20
                   ....*....|....*....|....*....
gi 1958668994 1942 TYGIFSTASGKAVQVSDASLEKARQVFSE 1970
Cdd:pfam00634    1 SFLGFQTASGKKISVSEESLQKAKKLFRD 29
BRCA2 pfam00634
BRCA2 repeat; The alignment covers only the most conserved region of the repeat.
 1641-1669 1.22e-05

BRCA2 repeat; The alignment covers only the most conserved region of the repeat.


Pssm-ID: 459881  Cd Length: 29  Bit Score: 43.98  E-value: 1.22e-05
                           10        20
                   ....*....|....*....|....*....
gi 1958668994 1641 SALACYTGDSRKTCVGESSLSKGKKWLRE 1669
Cdd:pfam00634    1 SFLGFQTASGKKISVSEESLQKAKKLFRD 29
BRCA2 pfam00634
BRCA2 repeat; The alignment covers only the most conserved region of the repeat.
 987-1015 4.75e-05

BRCA2 repeat; The alignment covers only the most conserved region of the repeat.


Pssm-ID: 459881  Cd Length: 29  Bit Score: 42.43  E-value: 4.75e-05
                           10        20
                   ....*....|....*....|....*....
gi 1958668994  987 FGGSFRTASNKEIKLSEDNVKKSKMFFKD 1015
Cdd:pfam00634    1 SFLGFQTASGKKISVSEESLQKAKKLFRD 29
BRCA2 pfam00634
BRCA2 repeat; The alignment covers only the most conserved region of the repeat.
 1508-1534 5.09e-05

BRCA2 repeat; The alignment covers only the most conserved region of the repeat.


Pssm-ID: 459881  Cd Length: 29  Bit Score: 42.43  E-value: 5.09e-05
                           10        20
                   ....*....|....*....|....*..
gi 1958668994 1508 LSFHTASGKKVKIMQESLDKVKNLFDE 1534
Cdd:pfam00634    3 LGFQTASGKKISVSEESLQKAKKLFRD 29
BRCA-2_OB3 pfam09104
BRCA2, oligonucleotide/oligosaccharide-binding, domain 3; Members of this family assume an OB ...
 3010-3029 4.36e-03

BRCA2, oligonucleotide/oligosaccharide-binding, domain 3; Members of this family assume an OB fold, which consists of a highly curved five-stranded beta-sheet that closes on itself to form a beta-barrel. OB3 has a pronounced groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for strong ssDNA binding.


Pssm-ID: 462679  Cd Length: 139  Bit Score: 39.95  E-value: 4.36e-03
                           10        20
                   ....*....|....*....|
gi 1958668994 3010 RELLPFSKLSDPAFQPPCSE 3029
Cdd:pfam09104    1 REVTPFSDLLNPSFQPPCGE 20
 
Name Accession Description Interval E-value
BRCA2DBD_OB2 cd04494
BRCA2DBD_OB2: A subfamily of OB folds corresponding to the second OB fold (OB2) of the ...
 2734-3012 5.57e-122

BRCA2DBD_OB2: A subfamily of OB folds corresponding to the second OB fold (OB2) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD. BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. It also facilitates filament formation. Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility. BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA).


Pssm-ID: 239940  Cd Length: 251  Bit Score: 385.65  E-value: 5.57e-122
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668994 2734 PLSSLFSDGGNVGCVDVIVQRVYPLQWVEKTVSGSYIFRNEREEEKEALRFAEAQQKKLEALFTKVHTELKEHEEDIAQR 2813
Cdd:cd04494      1 PLSSLYDSGGLVGCVDVIILRVYPLQWVEKTSEGGSVFRSERAEEREARLHAQRQQKKLEALFSKIQEEFEKEEEDNNQR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668994 2814 RVLSRALTRQQVHALQDGAELYAAVQDASDPEHLEvysaltggrparvgrtaaasavsqcvkcpqTCFSEEQLRALNNYR 2893
Cdd:cd04494     81 RPRSRTRTRQNVTDLQDGAELYEALEAAADPSFLE------------------------------AELSEEQLEALSNYQ 130

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668994 2894 QMLSDKKQARIQSEFRKALEAAEKEEGL-SRDVSTVWKLRVTSYK-KREKSALLSIWRPSSDLPSLLTEGQRYRIYHLSV 2971
Cdd:cd04494    131 QLQNEKKQARLQEEFRKAVEEALKEEGLsKRDVTPVWKLRVTDYRsKPEKSGLLSIWRPTEDLRSLLTEGKRYRIYGLAT 210

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|.
gi 1958668994 2972 SKSKNKFEWPSIQLTATKRTQYQQLPVSSETLLQLYQPREL 3012
Cdd:cd04494    211 SNSKKRSGNEEVQLTATKKTRYQPLPVSQRELFQPFQPRKA 251
BRCA-2_helical pfam09169
BRCA2, helical; Members of this family adopt a helical structure, consisting of a four-helix ...
 2411-2597 5.59e-103

BRCA2, helical; Members of this family adopt a helical structure, consisting of a four-helix cluster core (alpha 1, alpha 8, alpha 9, alpha 10) and two successive beta-hairpins (beta 1 to beta 4). An approx. 50-amino acid segment that contains four short helices (alpha 2 to alpha 4), meanders around the surface of the core structure. In BRCA2, the alpha 9 and alpha 10 helices pack with BRCA-2_OB1 (pfam09103) through van der Waals contacts involving hydrophobic and aromatic residues, and also through side-chain and backbone hydrogen bonds. The domain binds the 70-amino acid DSS1 (deleted in split-hand/split foot syndrome) protein, which was originally identified as one of three genes that map to a 1.5-Mb locus deleted in an inherited developmental malformation syndrome.


Pssm-ID: 462700  Cd Length: 187  Bit Score: 328.15  E-value: 5.59e-103
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668994 2411 MSSLQNARDLQDIRIKNKERHHLCPQPGSLYLTKSSTLPRISLQAAVGDSVPSACSPKQLYMYGVSKACISVNSKNAEYF 2490
Cdd:pfam09169    1 QSNLLLARDLQDMRIKKKSRQIIRPQPGSLYLKKSSVVRRISLKAAVGGCPPSHYSEKQLYYGGVCKVSLIIASENAESF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668994 2491 QFAIEDHFGKEALCAGKGFRLADGGWLIPSDDGKAGKEEFYRALCDTPGVDPKLISSVWVSNHYRWIVWKLAAMEFAFPK 2570
Cdd:pfam09169   81 QFFDDDFFGKEFLLNGGGIQLADGGLLIPNDGGVAGKEEFYRALCDTPGVDPKLISAWWVYNHYRWIVWKLAAMERFFPK 160

                          170       180
                   ....*....|....*....|....*..
gi 1958668994 2571 EFANRCLNPERVLLQLKYRYDVEIDNS 2597
Cdd:pfam09169  161 EFGRRCLTPERVLLQLKYRYDVEIDKS 187
BRCA-2_OB1 pfam09103
BRCA2, oligonucleotide/oligosaccharide-binding, domain 1; Members of this family assume an OB ...
 2600-2726 5.68e-64

BRCA2, oligonucleotide/oligosaccharide-binding, domain 1; Members of this family assume an OB fold, which consists of a highly curved five-stranded beta-sheet that closes on itself to form a beta-barrel. OB1 has a shallow groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for weak single strand DNA binding. The domain also binds the 70-amino acid DSS1 (deleted in split-hand/split foot syndrome) protein, which was originally identified as one of three genes that map to a 1.5-Mb locus deleted in an inherited developmental malformation syndrome.


Pssm-ID: 462678  Cd Length: 123  Bit Score: 213.58  E-value: 5.68e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668994 2600 SALKKILERDDTAAKTLVLCVSDIISLSTNVSETSgskaSSEDSNKVDTIELTDGWYAVKAQLDPPLLALVKSGRLTVGQ 2679
Cdd:pfam09103    1 SALRKILERDDSASKPMVLCVSAIISSESNSEETG----SGTVDNTKAILELTDGWYSIKAVLDAPLTRLVRRGKIRVGQ 76

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1958668994 2680 KIITQGAELVGSPDACAPLEAPDSLRLKISANSTRPARWHSKLGFFH 2726
Cdd:pfam09103   77 KLAICGAELVGSKEPCSPLEAPDSVRLKISANSTRRARWDAKLGFQR 123
BRCA2DBD_OB1 cd04493
BRCA2DBD_OB1: A subfamily of OB folds corresponding to the first OB fold (OB1) of the ...
 2612-2724 3.49e-47

BRCA2DBD_OB1: A subfamily of OB folds corresponding to the first OB fold (OB1) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD. BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. It also facilitates filament formation. Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility. BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA). BRCA2DBD OB1 binds DNA weakly.


Pssm-ID: 239939  Cd Length: 100  Bit Score: 164.71  E-value: 3.49e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668994 2612 AAKTLVLCVSDIISLSTnvsetsgskasseDSNKVDTIELTDGWYAVKAQLDPPLLALVKSGRLTVGQKIITQGAELVGS 2691
Cdd:cd04493      1 ASRLMVLCVSGINSEER-------------LSPHMPIIELTDGWYSIRAQLDPPLTNLVRKGKLRVGQKLRICGAELLGS 67

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1958668994 2692 PDACAPLEAPDSLRLKISANSTRPARWHSKLGF 2724
Cdd:cd04493     68 ANPCSPLEAPDSVRLKINANSTRRARWDARLGF 100
Tower pfam09121
Tower; Members of this family adopt a secondary structure consisting of a pair of long, ...
 2761-2802 3.86e-16

Tower; Members of this family adopt a secondary structure consisting of a pair of long, antiparallel alpha-helices (the stem) that support a three-helix bundle (3HB) at their end. The 3HB contains a helix-turn-helix motif and is similar to the DNA binding domains of the bacterial site-specific recombinases, and of eukaryotic Myb and homeodomain transcription factors. The Tower domain has an important role in the tumour suppressor function of BRCA2, and is essential for appropriate binding of BRCA2 to DNA.


Pssm-ID: 462684  Cd Length: 42  Bit Score: 74.32  E-value: 3.86e-16
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1958668994 2761 VEKTVSGSYIFRNEREEEKEALRFAEAQQKKLEALFTKVHTE 2802
Cdd:pfam09121    1 MEKKPDGGFVFRNERAEEKEARRYAEAQQKALEALFAKIQAE 42
BRCA2 pfam00634
BRCA2 repeat; The alignment covers only the most conserved region of the repeat.
 1200-1228 5.63e-08

BRCA2 repeat; The alignment covers only the most conserved region of the repeat.


Pssm-ID: 459881  Cd Length: 29  Bit Score: 50.91  E-value: 5.63e-08
                           10        20
                   ....*....|....*....|....*....
gi 1958668994 1200 EFGGFCSALGTKLSVSNEALRKAMKLFSD 1228
Cdd:pfam00634    1 SFLGFQTASGKKISVSEESLQKAKKLFRD 29
BRCA2 pfam00634
BRCA2 repeat; The alignment covers only the most conserved region of the repeat.
 1408-1436 1.80e-07

BRCA2 repeat; The alignment covers only the most conserved region of the repeat.


Pssm-ID: 459881  Cd Length: 29  Bit Score: 49.37  E-value: 1.80e-07
                           10        20
                   ....*....|....*....|....*....
gi 1958668994 1408 FNISFQTASGKNIRVSKESLNKSVNILDQ 1436
Cdd:pfam00634    1 SFLGFQTASGKKISVSEESLQKAKKLFRD 29
BRCA2 pfam00634
BRCA2 repeat; The alignment covers only the most conserved region of the repeat.
 1942-1970 3.12e-07

BRCA2 repeat; The alignment covers only the most conserved region of the repeat.


Pssm-ID: 459881  Cd Length: 29  Bit Score: 48.60  E-value: 3.12e-07
                           10        20
                   ....*....|....*....|....*....
gi 1958668994 1942 TYGIFSTASGKAVQVSDASLEKARQVFSE 1970
Cdd:pfam00634    1 SFLGFQTASGKKISVSEESLQKAKKLFRD 29
BRCA2 pfam00634
BRCA2 repeat; The alignment covers only the most conserved region of the repeat.
 1641-1669 1.22e-05

BRCA2 repeat; The alignment covers only the most conserved region of the repeat.


Pssm-ID: 459881  Cd Length: 29  Bit Score: 43.98  E-value: 1.22e-05
                           10        20
                   ....*....|....*....|....*....
gi 1958668994 1641 SALACYTGDSRKTCVGESSLSKGKKWLRE 1669
Cdd:pfam00634    1 SFLGFQTASGKKISVSEESLQKAKKLFRD 29
BRCA2 pfam00634
BRCA2 repeat; The alignment covers only the most conserved region of the repeat.
 987-1015 4.75e-05

BRCA2 repeat; The alignment covers only the most conserved region of the repeat.


Pssm-ID: 459881  Cd Length: 29  Bit Score: 42.43  E-value: 4.75e-05
                           10        20
                   ....*....|....*....|....*....
gi 1958668994  987 FGGSFRTASNKEIKLSEDNVKKSKMFFKD 1015
Cdd:pfam00634    1 SFLGFQTASGKKISVSEESLQKAKKLFRD 29
BRCA2 pfam00634
BRCA2 repeat; The alignment covers only the most conserved region of the repeat.
 1508-1534 5.09e-05

BRCA2 repeat; The alignment covers only the most conserved region of the repeat.


Pssm-ID: 459881  Cd Length: 29  Bit Score: 42.43  E-value: 5.09e-05
                           10        20
                   ....*....|....*....|....*..
gi 1958668994 1508 LSFHTASGKKVKIMQESLDKVKNLFDE 1534
Cdd:pfam00634    3 LGFQTASGKKISVSEESLQKAKKLFRD 29
BRCA-2_OB3 pfam09104
BRCA2, oligonucleotide/oligosaccharide-binding, domain 3; Members of this family assume an OB ...
 3010-3029 4.36e-03

BRCA2, oligonucleotide/oligosaccharide-binding, domain 3; Members of this family assume an OB fold, which consists of a highly curved five-stranded beta-sheet that closes on itself to form a beta-barrel. OB3 has a pronounced groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for strong ssDNA binding.


Pssm-ID: 462679  Cd Length: 139  Bit Score: 39.95  E-value: 4.36e-03
                           10        20
                   ....*....|....*....|
gi 1958668994 3010 RELLPFSKLSDPAFQPPCSE 3029
Cdd:pfam09104    1 REVTPFSDLLNPSFQPPCGE 20
 
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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