BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 017048
(378 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3OLC|X Chain X, Crystal Structure Of The N-Terminal Region Of Topbp1
Length = 298
Score = 66.2 bits (160), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 37/87 (42%), Positives = 50/87 (57%), Gaps = 5/87 (5%)
Query: 58 FSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHP-QCTHLVVQSFGGRKFEHALKHGS 116
F G +ICVTGL RK+V + T + GGQY L +CTHL+VQ G+K+E A
Sbjct: 200 FLGCIICVTGLCGLDRKEVQQLTVKHGGQYXGQLKXNECTHLIVQEPKGQKYECA----K 255
Query: 117 RNGLYIVTLGWFVDSVRRNVRLSESLY 143
R ++ VT WF DS+ + ES+Y
Sbjct: 256 RWNVHCVTTQWFFDSIEKGFCQDESIY 282
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 28/54 (51%)
Query: 55 NAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKF 108
N S + I T L KE R++V + + GG+ DL+ THL+ G +K+
Sbjct: 103 NXVXSDVTISCTSLEKEKREEVHKYVQXXGGRVYRDLNVSVTHLIAGEVGSKKY 156
>pdb|2XNH|A Chain A, Structure And Function Of The Rad9-Binding Region Of The
Dna Damage Checkpoint Adaptor Topbp1
Length = 287
Score = 66.2 bits (160), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 37/87 (42%), Positives = 50/87 (57%), Gaps = 5/87 (5%)
Query: 58 FSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHP-QCTHLVVQSFGGRKFEHALKHGS 116
F G +ICVTGL RK+V + T + GGQY L +CTHL+VQ G+K+E A
Sbjct: 200 FLGCIICVTGLCGLDRKEVQQLTVKHGGQYXGQLKXNECTHLIVQEPKGQKYECA----K 255
Query: 117 RNGLYIVTLGWFVDSVRRNVRLSESLY 143
R ++ VT WF DS+ + ES+Y
Sbjct: 256 RWNVHCVTTQWFFDSIEKGFCQDESIY 282
Score = 34.7 bits (78), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 28/54 (51%)
Query: 55 NAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKF 108
N S + I T L KE R++V + + GG+ DL+ THL+ G +K+
Sbjct: 103 NXVXSDVTISCTSLEKEKREEVHKYVQXXGGRVYRDLNVSVTHLIAGEVGSKKY 156
>pdb|2XNK|A Chain A, Structure And Function Of The Rad9-Binding Region Of The
Dna Damage Checkpoint Adaptor Topbp1
pdb|2XNK|B Chain B, Structure And Function Of The Rad9-Binding Region Of The
Dna Damage Checkpoint Adaptor Topbp1
pdb|2XNK|C Chain C, Structure And Function Of The Rad9-Binding Region Of The
Dna Damage Checkpoint Adaptor Topbp1
pdb|2XNK|D Chain D, Structure And Function Of The Rad9-Binding Region Of The
Dna Damage Checkpoint Adaptor Topbp1
Length = 292
Score = 66.2 bits (160), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 38/94 (40%), Positives = 52/94 (55%), Gaps = 5/94 (5%)
Query: 58 FSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHP-QCTHLVVQSFGGRKFEHALKHGS 116
F G +ICVTGL RK+V + T + GGQY L +CTHL+VQ G+K+E A
Sbjct: 202 FLGCIICVTGLCGLDRKEVQQLTVKHGGQYXGQLKXNECTHLIVQEPKGQKYECA----K 257
Query: 117 RNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDE 150
R ++ VT WF DS+ + ES+Y + E
Sbjct: 258 RWNVHCVTTQWFFDSIEKGFCQDESIYKTEPRPE 291
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 28/54 (51%)
Query: 55 NAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKF 108
N S + I T L KE R++V + + GG+ DL+ THL+ G +K+
Sbjct: 105 NXVXSDVTISCTSLEKEKREEVHKYVQXXGGRVYRDLNVSVTHLIAGEVGSKKY 158
>pdb|3L46|A Chain A, Crystal Structure Of The Second Brct Domain Of Epithelial
Cell Transforming 2 (Ect2)
pdb|3L46|B Chain B, Crystal Structure Of The Second Brct Domain Of Epithelial
Cell Transforming 2 (Ect2)
Length = 112
Score = 51.6 bits (122), Expect = 7e-07, Method: Composition-based stats.
Identities = 30/89 (33%), Positives = 44/89 (49%), Gaps = 8/89 (8%)
Query: 57 PFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQS--FGGRKFEHALKH 114
PF ++ G S E + + E TE GG+Y P +CTHLVV+ FE + K
Sbjct: 21 PFQDCILSFLGFSDEEKTNMEEMTEMQGGKYLPLGDERCTHLVVEENIVKDLPFEPSKK- 79
Query: 115 GSRNGLYIVTLGWFVDSVRRNVRLSESLY 143
LY+V WF S++ + R E++Y
Sbjct: 80 -----LYVVKQEWFWGSIQMDARAGETMY 103
>pdb|2COU|A Chain A, Solution Structure Of The Second Brct Domain Of Epithelial
Cell Transforming 2
Length = 109
Score = 49.7 bits (117), Expect = 3e-06, Method: Composition-based stats.
Identities = 28/89 (31%), Positives = 44/89 (49%), Gaps = 8/89 (8%)
Query: 57 PFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQ--SFGGRKFEHALKH 114
PF ++ G S E + + E TE GG Y P +CTHL+V+ + FE + K
Sbjct: 12 PFQDCILSFLGFSDEEKHSMEEMTEMQGGSYLPVGDERCTHLIVEENTVKDLPFEPSKK- 70
Query: 115 GSRNGLYIVTLGWFVDSVRRNVRLSESLY 143
L++V WF S++ + R E++Y
Sbjct: 71 -----LFVVKQEWFWGSIQMDARAGETMY 94
>pdb|2D8M|A Chain A, Solution Structure Of The First Brct Domain Of Dna-Repair
Protein Xrcc1
Length = 129
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 35/86 (40%), Gaps = 4/86 (4%)
Query: 58 FSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSR 117
G+V+ ++G R ++ + LG +Y PD THL+ K+ L G R
Sbjct: 23 LQGVVVVLSGFQNPFRSELRDKALELGAKYRPDWTRDSTHLICAFANTPKYSQVLGLGGR 82
Query: 118 NGLYIVTLGWFVDSVRRNVRLSESLY 143
IV W +D R RL Y
Sbjct: 83 ----IVRKEWVLDCHRMRRRLPSQRY 104
>pdb|3PD7|A Chain A, Crystal Structure Of The Sixth Brct Domain Of Human Topbp1
pdb|3PD7|B Chain B, Crystal Structure Of The Sixth Brct Domain Of Human Topbp1
Length = 107
Score = 35.4 bits (80), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 40/92 (43%), Gaps = 5/92 (5%)
Query: 54 ANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALK 113
A P +V+CV+ + + ++ LG Y TH + Q GR + +
Sbjct: 12 APKPLHKVVVCVSKKLSKKQSELNGIAASLGADYRRSFDETVTHFIYQ---GRPNDTNRE 68
Query: 114 HGS--RNGLYIVTLGWFVDSVRRNVRLSESLY 143
+ S G++IV+ W +D + L ESLY
Sbjct: 69 YKSVKERGVHIVSEHWLLDCAQECKHLPESLY 100
>pdb|3JVE|A Chain A, Crystal Structure Of The Sixth Brct Domain Of Topbp1
Length = 109
Score = 34.7 bits (78), Expect = 0.089, Method: Composition-based stats.
Identities = 24/92 (26%), Positives = 40/92 (43%), Gaps = 5/92 (5%)
Query: 54 ANAPFSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALK 113
A P +V+CV+ + + ++ LG Y TH + Q GR + +
Sbjct: 14 APKPLHKVVVCVSKKLSKKQSELNGIAASLGADYRWSFDETVTHFIYQ---GRPNDTNRE 70
Query: 114 HGS--RNGLYIVTLGWFVDSVRRNVRLSESLY 143
+ S G++IV+ W +D + L ESLY
Sbjct: 71 YKSVKERGVHIVSEHWLLDCAQECKHLPESLY 102
>pdb|3FA2|A Chain A, Crystal Structure Of The Brca1 Associated Ring Domain
(Bard1) Tandem Brct Domains
pdb|3FA2|B Chain B, Crystal Structure Of The Brca1 Associated Ring Domain
(Bard1) Tandem Brct Domains
Length = 218
Score = 34.7 bits (78), Expect = 0.096, Method: Compositional matrix adjust.
Identities = 47/192 (24%), Positives = 72/192 (37%), Gaps = 28/192 (14%)
Query: 57 PFS---GLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALK 113
PF+ LV+ +GLS E +K + E L + + TH+VV G + LK
Sbjct: 4 PFTRDGPLVLIGSGLSSEQQKMLSELAVILKAKKYTEFDSTVTHVVVP---GDAVQSTLK 60
Query: 114 --HGSRNGLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSC 171
G NG +I+ W +RR V E Y + G +LNR
Sbjct: 61 CMLGILNGCWILKFEWVKACLRRKVCEQEEKYEIP----EGPRRSRLNR--------EQL 108
Query: 172 LPAGIYEAKQFNATG--KHERDSNRSMNSTLSGCSMY-----VDSDVSEELRNKVFEAAT 224
LP +++ F G KH N T G + DSDV++ + + A
Sbjct: 109 LPK-LFDGCYFYLWGTFKHHPKDNLIKLVTAGGGQILSRKPKPDSDVTQTINTVAYHARP 167
Query: 225 NEGATLVNQWFV 236
+ Q+ +
Sbjct: 168 DSDQRFCTQYII 179
>pdb|2NTE|A Chain A, Crystal Structure Of The Bard1 Brct Domains
pdb|2NTE|B Chain B, Crystal Structure Of The Bard1 Brct Domains
Length = 210
Score = 33.9 bits (76), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 45/185 (24%), Positives = 69/185 (37%), Gaps = 25/185 (13%)
Query: 61 LVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALK--HGSRN 118
LV+ +GLS E +K + E L + + TH+VV G + LK G N
Sbjct: 3 LVLIGSGLSSEQQKMLSELAVILKAKKYTEFDSTVTHVVVP---GDAVQSTLKCMLGILN 59
Query: 119 GLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYE 178
G +I+ W +RR V E Y + G +LNR LP +++
Sbjct: 60 GCWILKFEWVKACLRRKVCEQEEKYEIP----EGPRRSRLNR--------EQLLPK-LFD 106
Query: 179 AKQFNATG--KHERDSNRSMNSTLSGCSMY-----VDSDVSEELRNKVFEAATNEGATLV 231
F G KH N T G + DSDV++ + + A +
Sbjct: 107 GCYFYLWGTFKHHPKDNLIKLVTAGGGQILSRKPKPDSDVTQTINTVAYHARPDSDQRFC 166
Query: 232 NQWFV 236
Q+ +
Sbjct: 167 TQYII 171
>pdb|2R1Z|A Chain A, Crystal Structure Of The Bard1 Brct Repeat
pdb|2R1Z|B Chain B, Crystal Structure Of The Bard1 Brct Repeat
Length = 209
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 45/185 (24%), Positives = 69/185 (37%), Gaps = 25/185 (13%)
Query: 61 LVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALK--HGSRN 118
LV+ +GLS E +K + E L + + TH+VV G + LK G N
Sbjct: 2 LVLIGSGLSSEQQKMLSELAVILKAKKYTEFDSTVTHVVVP---GDAVQSTLKCMLGILN 58
Query: 119 GLYIVTLGWFVDSVRRNVRLSESLYTVKSIDEHGMHLDKLNRLVGFAGTENSCLPAGIYE 178
G +I+ W +RR V E Y + G +LNR LP +++
Sbjct: 59 GCWILKFEWVKACLRRKVCEQEEKYEIP----EGPRRSRLNR--------EQLLPK-LFD 105
Query: 179 AKQFNATG--KHERDSNRSMNSTLSGCSMY-----VDSDVSEELRNKVFEAATNEGATLV 231
F G KH N T G + DSDV++ + + A +
Sbjct: 106 GCYFYLWGTFKHHPKDNLIKLVTAGGGQILSRKPKPDSDVTQTINTVAYHARPDSDQRFC 165
Query: 232 NQWFV 236
Q+ +
Sbjct: 166 TQYII 170
>pdb|1DGS|A Chain A, Crystal Structure Of Nad+-Dependent Dna Ligase From T.
Filiformis
pdb|1DGS|B Chain B, Crystal Structure Of Nad+-Dependent Dna Ligase From T.
Filiformis
Length = 667
Score = 28.5 bits (62), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 26/54 (48%)
Query: 58 FSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHA 111
SGL +TG R++V RLG + + + + ++LVV G K E A
Sbjct: 588 LSGLTFVLTGELSRPREEVKALLGRLGAKVTDSVSRKTSYLVVGENPGSKLEKA 641
>pdb|1L7B|A Chain A, Solution Nmr Structure Of Brct Domain Of T. Thermophilus:
Northeast Structural Genomics Consortium Target Wr64tt
Length = 92
Score = 28.5 bits (62), Expect = 7.3, Method: Composition-based stats.
Identities = 16/54 (29%), Positives = 25/54 (46%)
Query: 58 FSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHA 111
GL +TG R++V RLG + + + + ++LVV G K E A
Sbjct: 8 LKGLTFVITGELSRPREEVKALLRRLGAKVTDSVSRKTSYLVVGENPGSKLEKA 61
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.319 0.133 0.390
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,716,859
Number of Sequences: 62578
Number of extensions: 356573
Number of successful extensions: 894
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 871
Number of HSP's gapped (non-prelim): 16
length of query: 378
length of database: 14,973,337
effective HSP length: 100
effective length of query: 278
effective length of database: 8,715,537
effective search space: 2422919286
effective search space used: 2422919286
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)