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= 012081
(471 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 = 67.0 bits (162), 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 = 35.0 bits (79), Expect = 0.088, 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 = 67.0 bits (162), 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: 202 FLGCIICVTGLCGLDRKEVQQLTVKHGGQYXGQLKXNECTHLIVQEPKGQKYECA----K 257
Query: 117 RNGLYIVTLGWFVDSVRRNVRLSESLY 143
R ++ VT WF DS+ + ES+Y
Sbjct: 258 RWNVHCVTTQWFFDSIEKGFCQDESIY 284
Score = 35.0 bits (79), 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: 105 NXVXSDVTISCTSLEKEKREEVHKYVQXXGGRVYRDLNVSVTHLIAGEVGSKKY 158
>pdb|2XNH|A Chain A, Structure And Function Of The Rad9-Binding Region Of The
Dna Damage Checkpoint Adaptor Topbp1
Length = 287
Score = 67.0 bits (162), 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 = 35.0 bits (79), Expect = 0.090, 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|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 = 50.8 bits (120), Expect = 2e-06, 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 = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
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 = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 36/88 (40%), Gaps = 4/88 (4%)
Query: 58 FSGLVICVTGLSKEARKQVMEATERLGGQYSPDLHPQCTHLVVQSFGGRKFEHALKHGSR 117
G+V+ ++G R ++ + LG +Y PD THL+ K+ L G R
Sbjct: 23 LQGVVVVLSGFQNPFRSELRDKALELGAKYRPDWTRDSTHLICAFANTPKYSQVLGLGGR 82
Query: 118 NGLYIVTLGWFVDSVRRNVRLSESLYTV 145
IV W +D R RL Y +
Sbjct: 83 ----IVRKEWVLDCHRMRRRLPSQRYLM 106
>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 = 35.8 bits (81), Expect = 0.060, 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 CMLGILNGCWILKFEWVKACLRRKVCEQEEKYEI----PEGPRRSRLNR--------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|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 = 0.064, 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 = 35.0 bits (79), Expect = 0.082, 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: 14 APKPLHKVVVCVSKKLSKKQSELNGIAASLGADYRWSFDETVTHFIYQ---GRPNDTNRE 70
Query: 114 HGS--RNGLYIVTLGWFVDSVRRNVRLSESLY 143
+ S G++IV+ W +D + L ESLY
Sbjct: 71 YKSVKERGVHIVSEHWLLDCAQECKHLPESLY 102
>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 = 35.0 bits (79), Expect = 0.090, 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 GCWILKFEWVKACLRRKVCEQEEKYEI----PEGPRRSRLNR--------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 = 35.0 bits (79), Expect = 0.092, 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 GCWILKFEWVKACLRRKVCEQEEKYEI----PEGPRRSRLNR--------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|2PMZ|B Chain B, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|R Chain R, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|3HKZ|B Chain B, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|J Chain J, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 1124
Score = 32.0 bits (71), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 33/79 (41%)
Query: 311 PEDAQSCKNKISQEKRQQTVNLAKNGVRSRRSRRMQTCQTPIRPLTPSSLLDSICWSISE 370
PE QS +N +Q + L + R R P RPL + LD I ++
Sbjct: 658 PEHNQSPRNTYQSAMAKQALGLYAANYQLRTDTRAHLLHYPQRPLVQTRALDIIGYTNRP 717
Query: 371 PTSTASIYTDSFSGEDVNE 389
+ A + SF+G ++ +
Sbjct: 718 AGNNAILAVMSFTGYNMED 736
>pdb|2WAQ|B Chain B, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|B Chain B, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|R Chain R, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2Y0S|B Chain B, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|R Chain R, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|B Chain B, Rnap At 3.2ang
pdb|4B1O|B Chain B, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|R Chain R, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 1131
Score = 32.0 bits (71), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 33/79 (41%)
Query: 311 PEDAQSCKNKISQEKRQQTVNLAKNGVRSRRSRRMQTCQTPIRPLTPSSLLDSICWSISE 370
PE QS +N +Q + L + R R P RPL + LD I ++
Sbjct: 661 PEHNQSPRNTYQSAMAKQALGLYAANYQLRTDTRAHLLHYPQRPLVQTRALDIIGYTNRP 720
Query: 371 PTSTASIYTDSFSGEDVNE 389
+ A + SF+G ++ +
Sbjct: 721 AGNNAILAVISFTGYNMED 739
>pdb|1J4B|A Chain A, Recombinant Mouse-muscle Adenylosuccinate Synthetase
pdb|1IWE|A Chain A, Imp Complex Of The Recombinant Mouse-Muscle
Adenylosuccinate Synthetase
pdb|1IWE|B Chain B, Imp Complex Of The Recombinant Mouse-Muscle
Adenylosuccinate Synthetase
pdb|1LNY|A Chain A, Crystal Structure Of The Recombinant Mouse-Muscle
Adenylosuccinate Synthetase Complexed With 6-Phosphoryl-
Imp, Gdp And Mg
pdb|1LNY|B Chain B, Crystal Structure Of The Recombinant Mouse-Muscle
Adenylosuccinate Synthetase Complexed With 6-Phosphoryl-
Imp, Gdp And Mg
pdb|1LON|A Chain A, Crystal Structure Of The Recombinant Mouse-Muscle
Adenylosuccinate Synthetase Complexed With
6-Phosphoryl-Imp, Gdp And Hadacidin
pdb|1LOO|A Chain A, Crystal Structure Of The Mouse-Muscle Adenylosuccinate
Synthetase Ligated With Gtp
pdb|1MEZ|A Chain A, Structure Of The Recombinant Mouse-Muscle Adenylosuccinate
Synthetase Complexed With Samp, Gdp, So4(2-), And Mg(2+)
pdb|1MF0|A Chain A, Structure Of The Recombinant Mouse-Muscle Adenylosuccinate
Synthetase Complexed With Amp, Gdp, Hpo4(2-), And Mg(2+)
pdb|1MF1|A Chain A, Structure Of The Recombinant Mouse-Muscle Adenylosuccinate
Synthetase Complexed With Amp
pdb|2DGN|A Chain A, Mouse Muscle Adenylosuccinate Synthetase Partially Ligated
Complex With Gtp, 2'-Deoxy-Imp
Length = 457
Score = 30.8 bits (68), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 28/107 (26%), Positives = 47/107 (43%), Gaps = 12/107 (11%)
Query: 371 PTSTASIYTDSFSGEDVNEHHPSVFFDAEADGKDSEASFANLTRMLTESEKSELIFKNH- 429
P+ + SF G V H P +F +AE K+ + + + L S+++ L+F H
Sbjct: 86 PSGIINTKAVSFIGNGVVIHLPGLFEEAE---KNEKKGLKDWEKRLIISDRAHLVFDFHQ 142
Query: 430 FLTILFPVDRFAEMGPS--------SRTYFSDNGFTCLQVLDYIYEF 468
+ L V R A+ G + TY S T L++ D + +F
Sbjct: 143 AVDGLQEVQRQAQEGKNIGTTKKGIGPTYSSKAARTGLRICDLLSDF 189
>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 = 28.9 bits (63), 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 = 28.9 bits (63), Expect = 7.1, 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
0.317 0.132 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,148,917
Number of Sequences: 62578
Number of extensions: 507782
Number of successful extensions: 1277
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1251
Number of HSP's gapped (non-prelim): 21
length of query: 471
length of database: 14,973,337
effective HSP length: 102
effective length of query: 369
effective length of database: 8,590,381
effective search space: 3169850589
effective search space used: 3169850589
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)