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= 020653
(323 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1BA5|A Chain A, Dna-Binding Domain Of Human Telomeric Protein, Htrf1,
Nmr, 18 Structures
Length = 53
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 34/53 (64%), Gaps = 4/53 (7%)
Query: 4 PKQKWTAEEEAALKAGVRKHGTGKWRTILSDPEFSAILHSRSNVDLKDKWRNI 56
+Q W EE+ L++GVRK+G G W IL +F+ +R++V LKD+WR +
Sbjct: 2 KRQAWLWEEDKNLRSGVRKYGEGNWSKILLHYKFN----NRTSVMLKDRWRTM 50
>pdb|1W0T|A Chain A, Htrf1 Dna-Binding Domain In Complex With Telomeric Dna.
pdb|1W0T|B Chain B, Htrf1 Dna-Binding Domain In Complex With Telomeric Dna
Length = 53
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 34/53 (64%), Gaps = 4/53 (7%)
Query: 4 PKQKWTAEEEAALKAGVRKHGTGKWRTILSDPEFSAILHSRSNVDLKDKWRNI 56
+Q W EE+ L++GVRK+G G W IL +F+ +R++V LKD+WR +
Sbjct: 1 KRQAWLWEEDKNLRSGVRKYGEGNWSKILLHYKFN----NRTSVMLKDRWRTM 49
>pdb|3SJM|A Chain A, Crystal Structure Analysis Of Trf2-Dbd-Dna Complex
pdb|3SJM|B Chain B, Crystal Structure Analysis Of Trf2-Dbd-Dna Complex
Length = 64
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/52 (44%), Positives = 32/52 (61%), Gaps = 4/52 (7%)
Query: 5 KQKWTAEEEAALKAGVRKHGTGKWRTILSDPEFSAILHSRSNVDLKDKWRNI 56
KQKWT EE +KAGV+K+G G W I + F +R+ V +KD+WR +
Sbjct: 11 KQKWTVEESEWVKAGVQKYGEGNWAAISKNYPFV----NRTAVMIKDRWRTM 58
>pdb|1IV6|A Chain A, Solution Structure Of The Dna Complex Of Human Trf1
Length = 70
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/52 (42%), Positives = 34/52 (65%), Gaps = 4/52 (7%)
Query: 5 KQKWTAEEEAALKAGVRKHGTGKWRTILSDPEFSAILHSRSNVDLKDKWRNI 56
+Q W EE+ L++GVRK+G G W IL +F+ +R++V LKD+WR +
Sbjct: 11 RQAWLWEEDKNLRSGVRKYGEGNWSKILLHYKFN----NRTSVMLKDRWRTM 58
>pdb|1VF9|A Chain A, Solution Structure Of Human Trf2
Length = 64
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/52 (44%), Positives = 32/52 (61%), Gaps = 4/52 (7%)
Query: 5 KQKWTAEEEAALKAGVRKHGTGKWRTILSDPEFSAILHSRSNVDLKDKWRNI 56
KQKWT EE +KAGV+K+G G W I + F +R+ V +KD+WR +
Sbjct: 11 KQKWTVEESEWVKAGVQKYGEGNWAAISKNYPFV----NRTAVMIKDRWRTM 58
>pdb|1ITY|A Chain A, Solution Structure Of The Dna Binding Domain Of Human
Trf1
Length = 69
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/52 (42%), Positives = 34/52 (65%), Gaps = 4/52 (7%)
Query: 5 KQKWTAEEEAALKAGVRKHGTGKWRTILSDPEFSAILHSRSNVDLKDKWRNI 56
+Q W EE+ L++GVRK+G G W IL +F+ +R++V LKD+WR +
Sbjct: 10 RQAWLWEEDKNLRSGVRKYGEGNWSKILLHYKFN----NRTSVMLKDRWRTM 57
>pdb|1XG1|A Chain A, Solution Structure Of Myb-Domain Of Human Trf2
Length = 67
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/52 (44%), Positives = 32/52 (61%), Gaps = 4/52 (7%)
Query: 5 KQKWTAEEEAALKAGVRKHGTGKWRTILSDPEFSAILHSRSNVDLKDKWRNI 56
KQKWT EE +KAGV+K+G G W I + F +R+ V +KD+WR +
Sbjct: 14 KQKWTVEESEWVKAGVQKYGEGNWAAISKNYPFV----NRTAVMIKDRWRTM 61
>pdb|1VFC|A Chain A, Solution Structure Of The Dna Complex Of Human Trf2
Length = 63
Score = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/52 (44%), Positives = 32/52 (61%), Gaps = 4/52 (7%)
Query: 5 KQKWTAEEEAALKAGVRKHGTGKWRTILSDPEFSAILHSRSNVDLKDKWRNI 56
KQKWT EE +KAGV+K+G G W I + F +R+ V +KD+WR +
Sbjct: 10 KQKWTVEESEWVKAGVQKYGEGNWAAISKNYPFV----NRTAVMIKDRWRTM 57
>pdb|1W0U|A Chain A, Htrf2 Dna-Binding Domain In Complex With Telomeric Dna.
pdb|1W0U|B Chain B, Htrf2 Dna-Binding Domain In Complex With Telomeric Dna
Length = 55
Score = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/52 (44%), Positives = 32/52 (61%), Gaps = 4/52 (7%)
Query: 5 KQKWTAEEEAALKAGVRKHGTGKWRTILSDPEFSAILHSRSNVDLKDKWRNI 56
KQKWT EE +KAGV+K+G G W I + F +R+ V +KD+WR +
Sbjct: 2 KQKWTVEESEWVKAGVQKYGEGNWAAISKNYPFV----NRTAVMIKDRWRTM 49
>pdb|2ROH|A Chain A, The Dna Binding Domain Of Rtbp1
Length = 122
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 32/58 (55%), Gaps = 6/58 (10%)
Query: 5 KQKWTAEEEAALKAGVRKHGTGKWRTILSDPEFSAI--LHSRSNVDLKDKWRNINVTA 60
++ +T E L V GTG+WR D +F A +H R+ VDLKDKW+ + TA
Sbjct: 31 RRPFTVAEVELLVEAVEHLGTGRWR----DVKFRAFENVHHRTYVDLKDKWKTLVHTA 84
>pdb|2AJE|A Chain A, Solution Structure Of The Arabidopsis Thaliana Telomeric
Repeat-Binding Protein Dna Binding Domain
Length = 105
Score = 34.7 bits (78), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 24/52 (46%), Positives = 31/52 (59%), Gaps = 3/52 (5%)
Query: 9 TAEEEAALKAGVRKHGTGKWRTILSDPEFSAILHSRSNVDLKDKWRNINVTA 60
AE EA ++A V K GTG+WR + F H R+ VDLKDKW+ + TA
Sbjct: 18 VAEVEALVQA-VEKLGTGRWRDV-KLCAFEDADH-RTYVDLKDKWKTLVHTA 66
>pdb|3TED|A Chain A, Crystal Structure Of The Chd1 Dna-Binding Domain In
Complex With A Dna Duplex
Length = 271
Score = 33.5 bits (75), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 16/28 (57%)
Query: 8 WTAEEEAALKAGVRKHGTGKWRTILSDP 35
WT EE+ L GV K+G G W I DP
Sbjct: 172 WTKEEDEKLLIGVFKYGYGSWTQIRDDP 199
>pdb|2XB0|X Chain X, Dna-Binding Domain From Saccharomyces Cerevisiae
Chromatin- Remodelling Protein Chd1
Length = 270
Score = 33.5 bits (75), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 16/28 (57%)
Query: 8 WTAEEEAALKAGVRKHGTGKWRTILSDP 35
WT EE+ L GV K+G G W I DP
Sbjct: 171 WTKEEDEKLLIGVFKYGYGSWTQIRDDP 198
>pdb|2JUH|A Chain A, Solution Structure Of Dna Binding Domain Of Ngtrf1
Length = 121
Score = 33.1 bits (74), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 28/53 (52%), Gaps = 2/53 (3%)
Query: 8 WTAEEEAALKAGVRKHGTGKWRTILSDPEFSAILHSRSNVDLKDKWRNINVTA 60
++ E AL V GTG+WR + F H R+ VDLKDKW+ + TA
Sbjct: 20 FSVAEVEALVEAVEHLGTGRWRDVKMRA-FDNADH-RTYVDLKDKWKTLVHTA 70
>pdb|2CKX|A Chain A, Crystal Structure Of Ngtrf1, Double-Stranded Telomeric
Repeat Binding Factor From Nicotiana Tabacum
Length = 83
Score = 32.7 bits (73), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 23/52 (44%), Positives = 30/52 (57%), Gaps = 3/52 (5%)
Query: 9 TAEEEAALKAGVRKHGTGKWRTILSDPEFSAILHSRSNVDLKDKWRNINVTA 60
AE EA ++A V GTG+WR + F H R+ VDLKDKW+ + TA
Sbjct: 5 VAEVEALVEA-VEHLGTGRWRDVKMRA-FDNADH-RTYVDLKDKWKTLVHTA 53
>pdb|2QHB|A Chain A, Crystal Structure Of Ngtrf Complexed With Telomeric Dna
pdb|2QHB|B Chain B, Crystal Structure Of Ngtrf Complexed With Telomeric Dna
Length = 86
Score = 32.7 bits (73), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 23/52 (44%), Positives = 30/52 (57%), Gaps = 3/52 (5%)
Query: 9 TAEEEAALKAGVRKHGTGKWRTILSDPEFSAILHSRSNVDLKDKWRNINVTA 60
AE EA ++A V GTG+WR + F H R+ VDLKDKW+ + TA
Sbjct: 9 VAEVEALVEA-VEHLGTGRWRDVKMRA-FDNADH-RTYVDLKDKWKTLVHTA 57
>pdb|3OSF|A Chain A, The Structure Of Protozoan Parasite Trichomonas
Vaginalis Myb2 In Complex With Mre-2f-13 Dna
pdb|3OSF|D Chain D, The Structure Of Protozoan Parasite Trichomonas
Vaginalis Myb2 In Complex With Mre-2f-13 Dna
pdb|3OSG|A Chain A, The Structure Of Protozoan Parasite Trichomonas
Vaginalis Myb2 In Complex With Mre-1-12 Dna
pdb|3OSG|D Chain D, The Structure Of Protozoan Parasite Trichomonas
Vaginalis Myb2 In Complex With Mre-1-12 Dna
Length = 126
Score = 32.3 bits (72), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 30/54 (55%), Gaps = 7/54 (12%)
Query: 2 GAPKQKWTAEEEAALKAGVRKHGTGKWRTILSDPEFSAILHSRSNVDLKDKWRN 55
A KQK+T EE+ LK V +HG+ W+ I +A +R+ +D+W+N
Sbjct: 8 AAKKQKFTPEEDEMLKRAVAQHGSD-WKMI------AATFPNRNARQCRDRWKN 54
>pdb|1MBE|A Chain A, Mouse C-Myb Dna-Binding Domain Repeat 1
pdb|1MBF|A Chain A, Mouse C-Myb Dna-Binding Domain Repeat 1
Length = 53
Score = 31.6 bits (70), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 29/52 (55%), Gaps = 6/52 (11%)
Query: 5 KQKWTAEEEAALKAGVRKHGTGKWRTILSDPEFSAILHSRSNVDLKDKWRNI 56
K +WT EE+ LK V ++GT W+ I + L +R++V + +W+ +
Sbjct: 3 KTRWTREEDEKLKKLVEQNGTDDWKVI------ANYLPNRTDVQCQHRWQKV 48
>pdb|1GUU|A Chain A, Crystal Structure Of C-Myb R1
Length = 52
Score = 31.6 bits (70), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 29/52 (55%), Gaps = 6/52 (11%)
Query: 5 KQKWTAEEEAALKAGVRKHGTGKWRTILSDPEFSAILHSRSNVDLKDKWRNI 56
K +WT EE+ LK V ++GT W+ I + L +R++V + +W+ +
Sbjct: 3 KTRWTREEDEKLKKLVEQNGTDDWKVI------ANYLPNRTDVQCQHRWQKV 48
>pdb|4B4C|A Chain A, Crystal Structure Of The Dna-Binding Domain Of Human Chd1
Length = 211
Score = 30.8 bits (68), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 8 WTAEEEAALKAGVRKHGTGKWRTILSDPEFS 38
W E+++ L G+ ++G G W I DP+ S
Sbjct: 137 WGKEDDSNLLIGIYEYGYGSWEMIKMDPDLS 167
>pdb|1H88|C Chain C, Crystal Structure Of Ternary Protein-Dna Complex1
pdb|1H89|C Chain C, Crystal Structure Of Ternary Protein-Dna Complex2
Length = 159
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 29/52 (55%), Gaps = 6/52 (11%)
Query: 5 KQKWTAEEEAALKAGVRKHGTGKWRTILSDPEFSAILHSRSNVDLKDKWRNI 56
K +WT EE+ LK V ++GT W+ I + L +R++V + +W+ +
Sbjct: 6 KTRWTREEDEKLKKLVEQNGTDDWKVI------ANYLPNRTDVQCQHRWQKV 51
>pdb|2D9A|A Chain A, Solution Structure Of Rsgi Ruh-050, A Myb Dna-Binding
Domain In Mouse Cdna
Length = 60
Score = 28.9 bits (63), Expect = 4.5, Method: Composition-based stats.
Identities = 13/29 (44%), Positives = 18/29 (62%)
Query: 5 KQKWTAEEEAALKAGVRKHGTGKWRTILS 33
K KWT EE+ L+A VR+ G W+ + S
Sbjct: 8 KVKWTHEEDEQLRALVRQFGQQDWKFLAS 36
>pdb|4DVG|B Chain B, Crystal Structure Of E. Histolytica Formin1 Bound To
Ehrho1-Gtpgammas
Length = 353
Score = 28.5 bits (62), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 12/45 (26%), Positives = 27/45 (60%), Gaps = 1/45 (2%)
Query: 6 QKWTAEEEAALKAGVRKHGTGKWRTILSDPEFSA-ILHSRSNVDL 49
Q++ +++ ++ + TG WR ++DP++ A +L +R + DL
Sbjct: 39 QEYEKKQKKDIRIQLNAQKTGNWRNAITDPKYLADLLKTRDDXDL 83
>pdb|2LXF|A Chain A, Solution Nmr Structure Of A Potential Acylphosphatase From
Giardia Lamblia, Seattle Structural Genomics Center For
Infectious Disease Target Gilaa.01396.A
Length = 121
Score = 28.1 bits (61), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 23/43 (53%)
Query: 220 VSVPKRSPKLLLEGRQKGSPKAQKKEINILTKSLVDADLSRMR 262
V PK ++ KGSPK+ K+++I S VDAD +R
Sbjct: 78 VQGPKEQVDAFVKYLHKGSPKSVVKKVSIHASSRVDADGFEIR 120
>pdb|1YQA|A Chain A, Engineering The Structural Stability And Functional
Properties Of The Gi Domain Into The Intrinsically
Unfolded Gii Domain Of The Yeast Linker Histone Hho1p
Length = 87
Score = 27.7 bits (60), Expect = 8.0, Method: Composition-based stats.
Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 154 KLILEAISNLKEPNGSDRASIASYIEDQY---WAPANLRKLLATKLKFLSANGTLIKAK 209
++IL+++ L + GS R + Y++D Y + +N L + +K NG L++ K
Sbjct: 12 EMILKSMPQLNDGKGSSRIVLKKYVKDTYPIVGSASNFDYLFNSAIKKCVENGELVQPK 70
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
0.313 0.128 0.376
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,923,490
Number of Sequences: 62578
Number of extensions: 298857
Number of successful extensions: 541
Number of sequences better than 100.0: 30
Number of HSP's better than 100.0 without gapping: 21
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 509
Number of HSP's gapped (non-prelim): 33
length of query: 323
length of database: 14,973,337
effective HSP length: 99
effective length of query: 224
effective length of database: 8,778,115
effective search space: 1966297760
effective search space used: 1966297760
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (24.3 bits)