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= 024128
(272 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 50.8 bits (120), Expect = 8e-07, Method: Composition-based stats.
Identities = 24/52 (46%), Positives = 35/52 (67%), Gaps = 4/52 (7%)
Query: 5 KQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNM 56
KQKWT EE E ++AGV K+G G W I ++ PF+ +R+ + +KD+WR M
Sbjct: 11 KQKWTVEESEWVKAGVQKYGEGNWAAISKN---YPFV-NRTAVMIKDRWRTM 58
>pdb|1XG1|A Chain A, Solution Structure Of Myb-Domain Of Human Trf2
Length = 67
Score = 50.1 bits (118), Expect = 1e-06, Method: Composition-based stats.
Identities = 24/52 (46%), Positives = 35/52 (67%), Gaps = 4/52 (7%)
Query: 5 KQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNM 56
KQKWT EE E ++AGV K+G G W I ++ PF+ +R+ + +KD+WR M
Sbjct: 14 KQKWTVEESEWVKAGVQKYGEGNWAAISKN---YPFV-NRTAVMIKDRWRTM 61
>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 = 49.7 bits (117), Expect = 2e-06, Method: Composition-based stats.
Identities = 24/52 (46%), Positives = 35/52 (67%), Gaps = 4/52 (7%)
Query: 5 KQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNM 56
KQKWT EE E ++AGV K+G G W I ++ PF+ +R+ + +KD+WR M
Sbjct: 2 KQKWTVEESEWVKAGVQKYGEGNWAAISKN---YPFV-NRTAVMIKDRWRTM 49
>pdb|1VF9|A Chain A, Solution Structure Of Human Trf2
Length = 64
Score = 49.3 bits (116), Expect = 2e-06, Method: Composition-based stats.
Identities = 23/52 (44%), Positives = 33/52 (63%), Gaps = 4/52 (7%)
Query: 5 KQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNM 56
KQKWT EE E ++AGV K+G G W I ++ F +R+ + +KD+WR M
Sbjct: 11 KQKWTVEESEWVKAGVQKYGEGNWAAISKNYPF----VNRTAVMIKDRWRTM 58
>pdb|1VFC|A Chain A, Solution Structure Of The Dna Complex Of Human Trf2
Length = 63
Score = 48.9 bits (115), Expect = 3e-06, Method: Composition-based stats.
Identities = 23/52 (44%), Positives = 33/52 (63%), Gaps = 4/52 (7%)
Query: 5 KQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNM 56
KQKWT EE E ++AGV K+G G W I ++ F +R+ + +KD+WR M
Sbjct: 10 KQKWTVEESEWVKAGVQKYGEGNWAAISKNYPF----VNRTAVMIKDRWRTM 57
>pdb|1BA5|A Chain A, Dna-Binding Domain Of Human Telomeric Protein, Htrf1,
Nmr, 18 Structures
Length = 53
Score = 48.1 bits (113), Expect = 5e-06, Method: Composition-based stats.
Identities = 22/52 (42%), Positives = 33/52 (63%), Gaps = 4/52 (7%)
Query: 5 KQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNM 56
+Q W EE++ LR+GV K+G G W I +FN +R+++ LKD+WR M
Sbjct: 3 RQAWLWEEDKNLRSGVRKYGEGNWSKILLHYKFN----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 = 47.8 bits (112), Expect = 6e-06, Method: Composition-based stats.
Identities = 22/52 (42%), Positives = 33/52 (63%), Gaps = 4/52 (7%)
Query: 5 KQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNM 56
+Q W EE++ LR+GV K+G G W I +FN +R+++ LKD+WR M
Sbjct: 2 RQAWLWEEDKNLRSGVRKYGEGNWSKILLHYKFN----NRTSVMLKDRWRTM 49
>pdb|1ITY|A Chain A, Solution Structure Of The Dna Binding Domain Of Human
Trf1
Length = 69
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 22/52 (42%), Positives = 33/52 (63%), Gaps = 4/52 (7%)
Query: 5 KQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNM 56
+Q W EE++ LR+GV K+G G W I +FN +R+++ LKD+WR M
Sbjct: 10 RQAWLWEEDKNLRSGVRKYGEGNWSKILLHYKFN----NRTSVMLKDRWRTM 57
>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: Composition-based stats.
Identities = 22/52 (42%), Positives = 33/52 (63%), Gaps = 4/52 (7%)
Query: 5 KQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNM 56
+Q W EE++ LR+GV K+G G W I +FN +R+++ LKD+WR M
Sbjct: 11 RQAWLWEEDKNLRSGVRKYGEGNWSKILLHYKFN----NRTSVMLKDRWRTM 58
>pdb|2ROH|A Chain A, The Dna Binding Domain Of Rtbp1
Length = 122
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 29/101 (28%), Positives = 47/101 (46%), Gaps = 12/101 (11%)
Query: 5 KQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPF--LFSRSNIDLKDKWRNMSVSAPR 62
++ +T E E L V GTG+W RD +F F + R+ +DLKDKW+ + +A
Sbjct: 31 RRPFTVAEVELLVEAVEHLGTGRW----RDVKFRAFENVHHRTYVDLKDKWKTLVHTA-- 84
Query: 63 EKSRTLKPKAGSDAPAVPLSTPQTSALPAAVPIDASADPIT 103
++ P+ AP + A A +D+S +T
Sbjct: 85 ----SIAPQQRRGAPVPQELLDRVLAAQAYWSVDSSGRIVT 121
>pdb|3TED|A Chain A, Crystal Structure Of The Chd1 Dna-Binding Domain In
Complex With A Dna Duplex
Length = 271
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 15/28 (53%), Positives = 18/28 (64%)
Query: 8 WTAEEEEALRAGVAKHGTGKWKNIQRDP 35
WT EE+E 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 = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 15/28 (53%), Positives = 18/28 (64%)
Query: 8 WTAEEEEALRAGVAKHGTGKWKNIQRDP 35
WT EE+E L GV K+G G W I+ DP
Sbjct: 171 WTKEEDEKLLIGVFKYGYGSWTQIRDDP 198
>pdb|2AJE|A Chain A, Solution Structure Of The Arabidopsis Thaliana Telomeric
Repeat-Binding Protein Dna Binding Domain
Length = 105
Score = 35.0 bits (79), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 28/51 (54%), Gaps = 6/51 (11%)
Query: 12 EEEALRAGVAKHGTGKWKNIQRDPEFNPF--LFSRSNIDLKDKWRNMSVSA 60
E EAL V K GTG+W RD + F R+ +DLKDKW+ + +A
Sbjct: 20 EVEALVQAVEKLGTGRW----RDVKLCAFEDADHRTYVDLKDKWKTLVHTA 66
>pdb|2JUH|A Chain A, Solution Structure Of Dna Binding Domain Of Ngtrf1
Length = 121
Score = 34.3 bits (77), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 28/49 (57%), Gaps = 2/49 (4%)
Query: 12 EEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSVSA 60
E EAL V GTG+W++++ N R+ +DLKDKW+ + +A
Sbjct: 24 EVEALVEAVEHLGTGRWRDVKMRAFDNA--DHRTYVDLKDKWKTLVHTA 70
>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 = 33.5 bits (75), Expect = 0.15, Method: Composition-based stats.
Identities = 18/56 (32%), Positives = 32/56 (57%), Gaps = 2/56 (3%)
Query: 5 KQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSVSA 60
++ ++ E EAL V GTG+W++++ N R+ +DLKDKW+ + +A
Sbjct: 4 RRPFSVAEVEALVEAVEHLGTGRWRDVKMRAFDNA--DHRTYVDLKDKWKTLVHTA 57
>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 = 32.7 bits (73), Expect = 0.20, Method: Composition-based stats.
Identities = 16/52 (30%), Positives = 30/52 (57%), Gaps = 6/52 (11%)
Query: 5 KQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNM 56
K +WT EE+E L+ V ++GT WK I +L +R+++ + +W+ +
Sbjct: 3 KTRWTREEDEKLKKLVEQNGTDDWKVIAN------YLPNRTDVQCQHRWQKV 48
>pdb|1GUU|A Chain A, Crystal Structure Of C-Myb R1
Length = 52
Score = 32.7 bits (73), Expect = 0.20, Method: Composition-based stats.
Identities = 16/52 (30%), Positives = 30/52 (57%), Gaps = 6/52 (11%)
Query: 5 KQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNM 56
K +WT EE+E L+ V ++GT WK I +L +R+++ + +W+ +
Sbjct: 3 KTRWTREEDEKLKKLVEQNGTDDWKVIAN------YLPNRTDVQCQHRWQKV 48
>pdb|2CKX|A Chain A, Crystal Structure Of Ngtrf1, Double-Stranded Telomeric
Repeat Binding Factor From Nicotiana Tabacum
Length = 83
Score = 32.3 bits (72), Expect = 0.27, Method: Composition-based stats.
Identities = 18/53 (33%), Positives = 30/53 (56%), Gaps = 2/53 (3%)
Query: 8 WTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSVSA 60
++ E EAL V GTG+W++++ N R+ +DLKDKW+ + +A
Sbjct: 3 FSVAEVEALVEAVEHLGTGRWRDVKMRAFDNA--DHRTYVDLKDKWKTLVHTA 53
>pdb|1XUV|A Chain A, X-Ray Crystal Structure Of Protein Mm0500 From
Methanosarcina Mazei. Northeast Structural Genomics
Consortium Target Mar10.
pdb|1XUV|B Chain B, X-Ray Crystal Structure Of Protein Mm0500 From
Methanosarcina Mazei. Northeast Structural Genomics
Consortium Target Mar10.
pdb|1XUV|C Chain C, X-Ray Crystal Structure Of Protein Mm0500 From
Methanosarcina Mazei. Northeast Structural Genomics
Consortium Target Mar10
Length = 178
Score = 31.2 bits (69), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 34/77 (44%), Gaps = 10/77 (12%)
Query: 15 ALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSVSAPREKSRTLKPKAGS 74
AL+ K+G G W+ IQ+DPE N + F N D V+ P T + +
Sbjct: 59 ALKIFEPKNG-GSWQYIQKDPEGNEYAFHGVNHD---------VTEPERIISTFEFEGLP 108
Query: 75 DAPAVPLSTPQTSALPA 91
+ V L T + ALP
Sbjct: 109 EKGHVILDTARFEALPG 125
>pdb|4B4C|A Chain A, Crystal Structure Of The Dna-Binding Domain Of Human Chd1
Length = 211
Score = 31.2 bits (69), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 10/31 (32%), Positives = 19/31 (61%)
Query: 8 WTAEEEEALRAGVAKHGTGKWKNIQRDPEFN 38
W E++ L G+ ++G G W+ I+ DP+ +
Sbjct: 137 WGKEDDSNLLIGIYEYGYGSWEMIKMDPDLS 167
>pdb|2D9A|A Chain A, Solution Structure Of Rsgi Ruh-050, A Myb Dna-Binding
Domain In Mouse Cdna
Length = 60
Score = 30.4 bits (67), Expect = 1.1, Method: Composition-based stats.
Identities = 14/25 (56%), Positives = 16/25 (64%)
Query: 5 KQKWTAEEEEALRAGVAKHGTGKWK 29
K KWT EE+E LRA V + G WK
Sbjct: 8 KVKWTHEEDEQLRALVRQFGQQDWK 32
>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 = 1.3, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 33/57 (57%), Gaps = 7/57 (12%)
Query: 1 MGN-PKQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNM 56
MG+ K +WT EE+E L+ V ++GT WK I +L +R+++ + +W+ +
Sbjct: 1 MGHLGKTRWTREEDEKLKKLVEQNGTDDWKVIA------NYLPNRTDVQCQHRWQKV 51
>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 = 29.6 bits (65), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 29/51 (56%), Gaps = 7/51 (13%)
Query: 5 KQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRN 55
KQK+T EE+E L+ VA+HG+ WK I +R+ +D+W+N
Sbjct: 11 KQKFTPEEDEMLKRAVAQHGSD-WKMIAAT------FPNRNARQCRDRWKN 54
>pdb|2HX1|A Chain A, Crystal Structure Of Possible Sugar Phosphatase, Had
Superfamily (Zp_00311070.1) From Cytophaga Hutchinsonii
Atcc 33406 At 2.10 A Resolution
pdb|2HX1|B Chain B, Crystal Structure Of Possible Sugar Phosphatase, Had
Superfamily (Zp_00311070.1) From Cytophaga Hutchinsonii
Atcc 33406 At 2.10 A Resolution
pdb|2HX1|C Chain C, Crystal Structure Of Possible Sugar Phosphatase, Had
Superfamily (Zp_00311070.1) From Cytophaga Hutchinsonii
Atcc 33406 At 2.10 A Resolution
pdb|2HX1|D Chain D, Crystal Structure Of Possible Sugar Phosphatase, Had
Superfamily (Zp_00311070.1) From Cytophaga Hutchinsonii
Atcc 33406 At 2.10 A Resolution
Length = 284
Score = 29.3 bits (64), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 105 ESARSSAPKYNALIFEAISALKEPNG 130
ES +S PKY + F+A LK NG
Sbjct: 5 ESFKSLLPKYKCIFFDAFGVLKTYNG 30
>pdb|4FXG|A Chain A, Complement C4 In Complex With Masp-2
pdb|4FXG|D Chain D, Complement C4 In Complex With Masp-2
pdb|4FXK|A Chain A, Human Complement C4
Length = 656
Score = 28.9 bits (63), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 40/87 (45%), Gaps = 3/87 (3%)
Query: 40 FLFSRSNIDLKDKWRNMSVSAPREKSRTLKPKAGSDAPAVPLSTPQTSALPAAVPIDASA 99
F+ S ++DL R++ AP ++ +GS A +P+ T + P +VP
Sbjct: 343 FVSSPFSLDLSKTKRHLVPGAPFLLQALVREMSGSPASGIPVKVSATVSSPGSVPEVQDI 402
Query: 100 DPITDESARSSAPKYNALIFEAISALK 126
TD S + S P +I + IS L+
Sbjct: 403 QQNTDGSGQVSIP---IIIPQTISELQ 426
>pdb|2RQP|A Chain A, The Solution Structure Of Heterochromatin Protein
1-Binding Protein 74 Histone H1 Like Domain
Length = 88
Score = 27.7 bits (60), Expect = 6.6, Method: Composition-based stats.
Identities = 15/34 (44%), Positives = 21/34 (61%)
Query: 107 ARSSAPKYNALIFEAISALKEPNGSDVSAILSYI 140
A S PK +A++ EAI A + +G+ V AI YI
Sbjct: 5 ASSPRPKMDAILTEAIKACFQKSGASVVAIRKYI 38
>pdb|3LEC|A Chain A, The Crystal Structure Of A Protein In The Nadb-Rossmann
Superfamily From Streptococcus Agalactiae To 1.8a
Length = 230
Score = 27.7 bits (60), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 20 VAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRN 55
V KHG ++ F PFL S + K+KW+N
Sbjct: 160 VVKHGHXNLT--AKELRFGPFLLSNNTTVFKEKWQN 193
>pdb|1X41|A Chain A, Solution Structure Of The Myb-Like Dna Binding Domain Of
Human Transcriptional Adaptor 2-Like, Isoform B
Length = 60
Score = 27.3 bits (59), Expect = 9.1, Method: Composition-based stats.
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 8 WTAEEEEALRAGVAKHGTGKWKNI 31
WTA+EE AL V G G W+++
Sbjct: 11 WTAQEEMALLEAVMDCGFGNWQDV 34
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
0.310 0.126 0.358
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,743,738
Number of Sequences: 62578
Number of extensions: 227657
Number of successful extensions: 488
Number of sequences better than 100.0: 38
Number of HSP's better than 100.0 without gapping: 27
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 447
Number of HSP's gapped (non-prelim): 42
length of query: 272
length of database: 14,973,337
effective HSP length: 97
effective length of query: 175
effective length of database: 8,903,271
effective search space: 1558072425
effective search space used: 1558072425
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 51 (24.3 bits)