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= 007452
(603 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 = 48.1 bits (113), Expect = 1e-05, Method: Composition-based stats.
Identities = 24/53 (45%), Positives = 34/53 (64%), Gaps = 2/53 (3%)
Query: 202 KKRKPWTAEEDLELISAVQKCGEGNWANILRGDFKW-DRTASQLSQRWNILRK 253
+KR+ W EED L S V+K GEGNW+ IL +K+ +RT+ L RW ++K
Sbjct: 1 RKRQAWLWEEDKNLRSGVRKYGEGNWSKILL-HYKFNNRTSVMLKDRWRTMKK 52
>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 = 47.0 bits (110), Expect = 3e-05, Method: Composition-based stats.
Identities = 23/51 (45%), Positives = 30/51 (58%)
Query: 203 KRKPWTAEEDLELISAVQKCGEGNWANILRGDFKWDRTASQLSQRWNILRK 253
KR+ W EED L S V+K GEGNW+ IL +RT+ L RW ++K
Sbjct: 1 KRQAWLWEEDKNLRSGVRKYGEGNWSKILLHYKFNNRTSVMLKDRWRTMKK 51
>pdb|1IV6|A Chain A, Solution Structure Of The Dna Complex Of Human Trf1
Length = 70
Score = 46.6 bits (109), Expect = 4e-05, Method: Composition-based stats.
Identities = 23/52 (44%), Positives = 31/52 (59%)
Query: 202 KKRKPWTAEEDLELISAVQKCGEGNWANILRGDFKWDRTASQLSQRWNILRK 253
+KR+ W EED L S V+K GEGNW+ IL +RT+ L RW ++K
Sbjct: 9 RKRQAWLWEEDKNLRSGVRKYGEGNWSKILLHYKFNNRTSVMLKDRWRTMKK 60
>pdb|1ITY|A Chain A, Solution Structure Of The Dna Binding Domain Of Human Trf1
Length = 69
Score = 46.6 bits (109), Expect = 4e-05, Method: Composition-based stats.
Identities = 23/52 (44%), Positives = 31/52 (59%)
Query: 202 KKRKPWTAEEDLELISAVQKCGEGNWANILRGDFKWDRTASQLSQRWNILRK 253
+KR+ W EED L S V+K GEGNW+ IL +RT+ L RW ++K
Sbjct: 8 RKRQAWLWEEDKNLRSGVRKYGEGNWSKILLHYKFNNRTSVMLKDRWRTMKK 59
>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 = 42.7 bits (99), Expect = 5e-04, Method: Composition-based stats.
Identities = 20/51 (39%), Positives = 30/51 (58%)
Query: 203 KRKPWTAEEDLELISAVQKCGEGNWANILRGDFKWDRTASQLSQRWNILRK 253
K++ WT EE + + VQK GEGNWA I + +RTA + RW +++
Sbjct: 10 KKQKWTVEESEWVKAGVQKYGEGNWAAISKNYPFVNRTAVMIKDRWRTMKR 60
>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 = 42.7 bits (99), Expect = 6e-04, Method: Composition-based stats.
Identities = 20/51 (39%), Positives = 30/51 (58%)
Query: 203 KRKPWTAEEDLELISAVQKCGEGNWANILRGDFKWDRTASQLSQRWNILRK 253
K++ WT EE + + VQK GEGNWA I + +RTA + RW +++
Sbjct: 1 KKQKWTVEESEWVKAGVQKYGEGNWAAISKNYPFVNRTAVMIKDRWRTMKR 51
>pdb|1XG1|A Chain A, Solution Structure Of Myb-Domain Of Human Trf2
Length = 67
Score = 42.4 bits (98), Expect = 7e-04, Method: Composition-based stats.
Identities = 20/51 (39%), Positives = 30/51 (58%)
Query: 203 KRKPWTAEEDLELISAVQKCGEGNWANILRGDFKWDRTASQLSQRWNILRK 253
K++ WT EE + + VQK GEGNWA I + +RTA + RW +++
Sbjct: 13 KKQKWTVEESEWVKAGVQKYGEGNWAAISKNYPFVNRTAVMIKDRWRTMKR 63
>pdb|1VF9|A Chain A, Solution Structure Of Human Trf2
Length = 64
Score = 42.4 bits (98), Expect = 8e-04, Method: Composition-based stats.
Identities = 20/51 (39%), Positives = 30/51 (58%)
Query: 203 KRKPWTAEEDLELISAVQKCGEGNWANILRGDFKWDRTASQLSQRWNILRK 253
K++ WT EE + + VQK GEGNWA I + +RTA + RW +++
Sbjct: 10 KKQKWTVEESEWVKAGVQKYGEGNWAAISKNYPFVNRTAVMIKDRWRTMKR 60
>pdb|1VFC|A Chain A, Solution Structure Of The Dna Complex Of Human Trf2
Length = 63
Score = 42.4 bits (98), Expect = 8e-04, Method: Composition-based stats.
Identities = 20/51 (39%), Positives = 30/51 (58%)
Query: 203 KRKPWTAEEDLELISAVQKCGEGNWANILRGDFKWDRTASQLSQRWNILRK 253
K++ WT EE + + VQK GEGNWA I + +RTA + RW +++
Sbjct: 9 KKQKWTVEESEWVKAGVQKYGEGNWAAISKNYPFVNRTAVMIKDRWRTMKR 59
>pdb|1H8A|C Chain C, Crystal Structure Of Ternary Protein-Dna Complex3
Length = 128
Score = 37.0 bits (84), Expect = 0.030, Method: Composition-based stats.
Identities = 20/53 (37%), Positives = 27/53 (50%), Gaps = 8/53 (15%)
Query: 200 PRKKRKPWTAEEDLELISAVQKCGEGNWANI---LRGDFKWDRTASQLSQRWN 249
P + PWT EED +I VQK G W++I L+G R Q +RW+
Sbjct: 23 PELNKGPWTKEEDQRVIEHVQKYGPKRWSDIAKHLKG-----RIGKQCRERWH 70
>pdb|1GVD|A Chain A, Crystal Structure Of C-Myb R2 V103l Mutant
Length = 52
Score = 35.8 bits (81), Expect = 0.072, Method: Composition-based stats.
Identities = 20/49 (40%), Positives = 25/49 (51%), Gaps = 8/49 (16%)
Query: 204 RKPWTAEEDLELISAVQKCGEGNWANI---LRGDFKWDRTASQLSQRWN 249
+ PWT EED LI VQK G W+ I L+G R Q +RW+
Sbjct: 3 KGPWTKEEDQRLIKLVQKYGPKRWSVIAKHLKG-----RIGKQCRERWH 46
>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 = 35.0 bits (79), Expect = 0.14, Method: Composition-based stats.
Identities = 20/53 (37%), Positives = 26/53 (49%), Gaps = 8/53 (15%)
Query: 200 PRKKRKPWTAEEDLELISAVQKCGEGNWANI---LRGDFKWDRTASQLSQRWN 249
P + PWT EED +I VQK G W+ I L+G R Q +RW+
Sbjct: 54 PELIKGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLKG-----RIGKQCRERWH 101
>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 = 35.0 bits (79), Expect = 0.14, Method: Composition-based stats.
Identities = 12/24 (50%), Positives = 18/24 (75%)
Query: 207 WTAEEDLELISAVQKCGEGNWANI 230
WTA+E++ L+ AV CG GNW ++
Sbjct: 11 WTAQEEMALLEAVMDCGFGNWQDV 34
>pdb|1MBG|A Chain A, Mouse C-Myb Dna-Binding Domain Repeat 2
pdb|1MBH|A Chain A, Mouse C-Myb Dna-Binding Domain Repeat 2
Length = 53
Score = 34.7 bits (78), Expect = 0.17, Method: Composition-based stats.
Identities = 19/49 (38%), Positives = 25/49 (51%), Gaps = 8/49 (16%)
Query: 204 RKPWTAEEDLELISAVQKCGEGNWANI---LRGDFKWDRTASQLSQRWN 249
+ PWT EED +I VQK G W+ I L+G R Q +RW+
Sbjct: 3 KGPWTKEEDQRVIELVQKYGPKRWSVIAKHLKG-----RIGKQCRERWH 46
>pdb|1GV5|A Chain A, Crystal Structure Of C-Myb R2
Length = 52
Score = 34.7 bits (78), Expect = 0.18, Method: Composition-based stats.
Identities = 19/49 (38%), Positives = 25/49 (51%), Gaps = 8/49 (16%)
Query: 204 RKPWTAEEDLELISAVQKCGEGNWANI---LRGDFKWDRTASQLSQRWN 249
+ PWT EED +I VQK G W+ I L+G R Q +RW+
Sbjct: 3 KGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLKG-----RIGKQCRERWH 46
>pdb|1MSE|C Chain C, Solution Structure Of A Specific Dna Complex Of The Myb
Dna- Binding Domain With Cooperative Recognition Helices
pdb|1MSF|C Chain C, Solution Structure Of A Specific Dna Complex Of The Myb
Dna- Binding Domain With Cooperative Recognition Helices
Length = 105
Score = 34.3 bits (77), Expect = 0.21, Method: Composition-based stats.
Identities = 19/49 (38%), Positives = 25/49 (51%), Gaps = 8/49 (16%)
Query: 204 RKPWTAEEDLELISAVQKCGEGNWANI---LRGDFKWDRTASQLSQRWN 249
+ PWT EED +I VQK G W+ I L+G R Q +RW+
Sbjct: 4 KGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLKG-----RIGKQCRERWH 47
>pdb|1GV2|A Chain A, Crystal Structure Of C-Myb R2r3
Length = 105
Score = 33.9 bits (76), Expect = 0.25, Method: Composition-based stats.
Identities = 19/49 (38%), Positives = 25/49 (51%), Gaps = 8/49 (16%)
Query: 204 RKPWTAEEDLELISAVQKCGEGNWANI---LRGDFKWDRTASQLSQRWN 249
+ PWT EED +I VQK G W+ I L+G R Q +RW+
Sbjct: 4 KGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLKG-----RIGKQCRERWH 47
>pdb|2AJE|A Chain A, Solution Structure Of The Arabidopsis Thaliana Telomeric
Repeat-Binding Protein Dna Binding Domain
Length = 105
Score = 33.9 bits (76), Expect = 0.29, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 2/55 (3%)
Query: 199 PPRKKRKPWTAEEDLELISAVQKCGEGNWANILRGDFK--WDRTASQLSQRWNIL 251
P R+ R+P++ E L+ AV+K G G W ++ F+ RT L +W L
Sbjct: 8 PQRRIRRPFSVAEVEALVQAVEKLGTGRWRDVKLCAFEDADHRTYVDLKDKWKTL 62
>pdb|1A5J|A Chain A, Chicken B-Myb Dna Binding Domain, Repeat 2 And Repeat3,
Nmr, 32 Structures
Length = 110
Score = 32.3 bits (72), Expect = 0.73, Method: Composition-based stats.
Identities = 19/53 (35%), Positives = 26/53 (49%), Gaps = 8/53 (15%)
Query: 200 PRKKRKPWTAEEDLELISAVQKCGEGNWANI---LRGDFKWDRTASQLSQRWN 249
P + PWT EED ++I V+K G W I L+G R Q +RW+
Sbjct: 3 PDLVKGPWTKEEDQKVIELVKKYGTKQWTLIAKHLKG-----RLGKQCRERWH 50
>pdb|2ELK|A Chain A, Solution Structure Of The Sant Domain Of Fission Yeast
Spcc24b10.08c Protein
Length = 58
Score = 32.3 bits (72), Expect = 0.76, Method: Composition-based stats.
Identities = 13/24 (54%), Positives = 17/24 (70%)
Query: 207 WTAEEDLELISAVQKCGEGNWANI 230
W A+E+L LI A + G GNWA+I
Sbjct: 12 WGADEELLLIDACETLGLGNWADI 35
>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 = 31.2 bits (69), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 206 PWTAEEDLELISAVQKCGEGNWANILRGDFKWDRTASQLSQRWNILRKKHG 256
PWTAEED L+ +Q+ G WA I F RT + RW + K G
Sbjct: 64 PWTAEEDALLVQKIQEYGR-QWAII--AKFFPGRTDIHIKNRWVTISNKLG 111
>pdb|3TED|A Chain A, Crystal Structure Of The Chd1 Dna-Binding Domain In
Complex With A Dna Duplex
Length = 271
Score = 30.8 bits (68), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 15/24 (62%)
Query: 207 WTAEEDLELISAVQKCGEGNWANI 230
WT EED +L+ V K G G+W I
Sbjct: 172 WTKEEDEKLLIGVFKYGYGSWTQI 195
>pdb|2XB0|X Chain X, Dna-Binding Domain From Saccharomyces Cerevisiae
Chromatin- Remodelling Protein Chd1
Length = 270
Score = 30.8 bits (68), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 15/24 (62%)
Query: 207 WTAEEDLELISAVQKCGEGNWANI 230
WT EED +L+ V K G G+W I
Sbjct: 171 WTKEEDEKLLIGVFKYGYGSWTQI 194
>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 = 30.0 bits (66), Expect = 4.0, Method: Composition-based stats.
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 201 RKKRKPWTAEEDLELISAVQKCGEGNWANI-LRG-DFKWDRTASQLSQRWNIL 251
R+ R+P++ E L+ AV+ G G W ++ +R D RT L +W L
Sbjct: 1 RRIRRPFSVAEVEALVEAVEHLGTGRWRDVKMRAFDNADHRTYVDLKDKWKTL 53
>pdb|2ROH|A Chain A, The Dna Binding Domain Of Rtbp1
Length = 122
Score = 29.6 bits (65), Expect = 4.6, Method: Composition-based stats.
Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 201 RKKRKPWTAEEDLELISAVQKCGEGNWANILRGDFK--WDRTASQLSQRWNIL 251
R+ R+P+T E L+ AV+ G G W ++ F+ RT L +W L
Sbjct: 28 RRIRRPFTVAEVELLVEAVEHLGTGRWRDVKFRAFENVHHRTYVDLKDKWKTL 80
>pdb|2JUH|A Chain A, Solution Structure Of Dna Binding Domain Of Ngtrf1
Length = 121
Score = 28.9 bits (63), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 201 RKKRKPWTAEEDLELISAVQKCGEGNWANI-LRG-DFKWDRTASQLSQRWNIL 251
R+ R+P++ E L+ AV+ G G W ++ +R D RT L +W L
Sbjct: 14 RRIRRPFSVAEVEALVEAVEHLGTGRWRDVKMRAFDNADHRTYVDLKDKWKTL 66
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
0.308 0.124 0.344
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,293,711
Number of Sequences: 62578
Number of extensions: 438448
Number of successful extensions: 818
Number of sequences better than 100.0: 30
Number of HSP's better than 100.0 without gapping: 23
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 789
Number of HSP's gapped (non-prelim): 36
length of query: 603
length of database: 14,973,337
effective HSP length: 104
effective length of query: 499
effective length of database: 8,465,225
effective search space: 4224147275
effective search space used: 4224147275
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 54 (25.4 bits)