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= 008766
(554 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ROH|A Chain A, The Dna Binding Domain Of Rtbp1
Length = 122
Score = 63.9 bits (154), Expect = 2e-10, Method: Composition-based stats.
Identities = 36/87 (41%), Positives = 49/87 (56%), Gaps = 9/87 (10%)
Query: 433 RRKHHRAWTLSEVMKLVEGVSKYGAGRWSEIKRLAFASYSYRTSVDLKDKWRNLLKASLA 492
+R+ R +T++EV LVE V G GRW ++K AF + +RT VDLKDKW+ L+ A
Sbjct: 27 QRRIRRPFTVAEVELLVEAVEHLGTGRWRDVKFRAFENVHHRTYVDLKDKWKTLVHT--A 84
Query: 493 QTPPDSRMGARKHASSVPIPMPVLLRV 519
P R GA P+P +L RV
Sbjct: 85 SIAPQQRRGA-------PVPQELLDRV 104
>pdb|2AJE|A Chain A, Solution Structure Of The Arabidopsis Thaliana Telomeric
Repeat-Binding Protein Dna Binding Domain
Length = 105
Score = 62.8 bits (151), Expect = 5e-10, Method: Composition-based stats.
Identities = 34/87 (39%), Positives = 49/87 (56%), Gaps = 9/87 (10%)
Query: 433 RRKHHRAWTLSEVMKLVEGVSKYGAGRWSEIKRLAFASYSYRTSVDLKDKWRNLLKASLA 492
+R+ R ++++EV LV+ V K G GRW ++K AF +RT VDLKDKW+ L+ A
Sbjct: 9 QRRIRRPFSVAEVEALVQAVEKLGTGRWRDVKLCAFEDADHRTYVDLKDKWKTLVHT--A 66
Query: 493 QTPPDSRMGARKHASSVPIPMPVLLRV 519
+ P R G P+P +L RV
Sbjct: 67 KISPQQRRGE-------PVPQELLNRV 86
>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 = 60.8 bits (146), Expect = 2e-09, Method: Composition-based stats.
Identities = 34/86 (39%), Positives = 47/86 (54%), Gaps = 9/86 (10%)
Query: 434 RKHHRAWTLSEVMKLVEGVSKYGAGRWSEIKRLAFASYSYRTSVDLKDKWRNLLKASLAQ 493
R+ R ++++EV LVE V G GRW ++K AF + +RT VDLKDKW+ L+ A
Sbjct: 1 RRIRRPFSVAEVEALVEAVEHLGTGRWRDVKMRAFDNADHRTYVDLKDKWKTLVHT--AS 58
Query: 494 TPPDSRMGARKHASSVPIPMPVLLRV 519
P R G P+P +L RV
Sbjct: 59 IAPQQRRGE-------PVPQDLLDRV 77
>pdb|2JUH|A Chain A, Solution Structure Of Dna Binding Domain Of Ngtrf1
Length = 121
Score = 60.8 bits (146), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 36/88 (40%), Positives = 51/88 (57%), Gaps = 11/88 (12%)
Query: 433 RRKHHRAWTLSEVMKLVEGVSKYGAGRWSEIKRLAFASYSYRTSVDLKDKWRNLLK-ASL 491
+R+ R ++++EV LVE V G GRW ++K AF + +RT VDLKDKW+ L+ AS+
Sbjct: 13 QRRIRRPFSVAEVEALVEAVEHLGTGRWRDVKMRAFDNADHRTYVDLKDKWKTLVHTASI 72
Query: 492 AQTPPDSRMGARKHASSVPIPMPVLLRV 519
A P R G P+P +L RV
Sbjct: 73 A---PQQRRGE-------PVPQDLLDRV 90
>pdb|2CKX|A Chain A, Crystal Structure Of Ngtrf1, Double-Stranded Telomeric
Repeat Binding Factor From Nicotiana Tabacum
Length = 83
Score = 59.7 bits (143), Expect = 4e-09, Method: Composition-based stats.
Identities = 33/82 (40%), Positives = 45/82 (54%), Gaps = 9/82 (10%)
Query: 438 RAWTLSEVMKLVEGVSKYGAGRWSEIKRLAFASYSYRTSVDLKDKWRNLLKASLAQTPPD 497
R ++++EV LVE V G GRW ++K AF + +RT VDLKDKW+ L+ A P
Sbjct: 1 RPFSVAEVEALVEAVEHLGTGRWRDVKMRAFDNADHRTYVDLKDKWKTLVHT--ASIAPQ 58
Query: 498 SRMGARKHASSVPIPMPVLLRV 519
R G P+P +L RV
Sbjct: 59 QRRGE-------PVPQDLLDRV 73
>pdb|1IV6|A Chain A, Solution Structure Of The Dna Complex Of Human Trf1
Length = 70
Score = 45.4 bits (106), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 26/59 (44%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 433 RRKHHRAWTLSEVMKLVEGVSKYGAGRWSEIKRLAFASYSYRTSVDLKDKWRNLLKASL 491
R + +AW E L GV KYG G WS+I L ++ RTSV LKD+WR + K L
Sbjct: 7 RARKRQAWLWEEDKNLRSGVRKYGEGNWSKI--LLHYKFNNRTSVMLKDRWRTMKKLKL 63
>pdb|1ITY|A Chain A, Solution Structure Of The Dna Binding Domain Of Human Trf1
Length = 69
Score = 45.4 bits (106), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 26/59 (44%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 433 RRKHHRAWTLSEVMKLVEGVSKYGAGRWSEIKRLAFASYSYRTSVDLKDKWRNLLKASL 491
R + +AW E L GV KYG G WS+I L ++ RTSV LKD+WR + K L
Sbjct: 6 RARKRQAWLWEEDKNLRSGVRKYGEGNWSKI--LLHYKFNNRTSVMLKDRWRTMKKLKL 62
>pdb|1BA5|A Chain A, Dna-Binding Domain Of Human Telomeric Protein, Htrf1, Nmr,
18 Structures
Length = 53
Score = 42.4 bits (98), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 24/50 (48%), Positives = 29/50 (58%), Gaps = 2/50 (4%)
Query: 439 AWTLSEVMKLVEGVSKYGAGRWSEIKRLAFASYSYRTSVDLKDKWRNLLK 488
AW E L GV KYG G WS+I L ++ RTSV LKD+WR + K
Sbjct: 5 AWLWEEDKNLRSGVRKYGEGNWSKI--LLHYKFNNRTSVMLKDRWRTMKK 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 = 42.4 bits (98), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 24/50 (48%), Positives = 29/50 (58%), Gaps = 2/50 (4%)
Query: 439 AWTLSEVMKLVEGVSKYGAGRWSEIKRLAFASYSYRTSVDLKDKWRNLLK 488
AW E L GV KYG G WS+I L ++ RTSV LKD+WR + K
Sbjct: 4 AWLWEEDKNLRSGVRKYGEGNWSKI--LLHYKFNNRTSVMLKDRWRTMKK 51
>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 = 38.1 bits (87), Expect = 0.013, Method: Composition-based stats.
Identities = 19/51 (37%), Positives = 30/51 (58%), Gaps = 6/51 (11%)
Query: 438 RAWTLSEVMKLVEGVSKYGAGRWSEIKRLAFASYSY--RTSVDLKDKWRNL 486
+ WT+ E + GV KYG G W+ I + +Y + RT+V +KD+WR +
Sbjct: 3 QKWTVEESEWVKAGVQKYGEGNWAAISK----NYPFVNRTAVMIKDRWRTM 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 = 38.1 bits (87), Expect = 0.014, Method: Composition-based stats.
Identities = 19/51 (37%), Positives = 30/51 (58%), Gaps = 6/51 (11%)
Query: 438 RAWTLSEVMKLVEGVSKYGAGRWSEIKRLAFASYSY--RTSVDLKDKWRNL 486
+ WT+ E + GV KYG G W+ I + +Y + RT+V +KD+WR +
Sbjct: 12 QKWTVEESEWVKAGVQKYGEGNWAAISK----NYPFVNRTAVMIKDRWRTM 58
>pdb|1VF9|A Chain A, Solution Structure Of Human Trf2
Length = 64
Score = 37.7 bits (86), Expect = 0.018, Method: Composition-based stats.
Identities = 19/51 (37%), Positives = 30/51 (58%), Gaps = 6/51 (11%)
Query: 438 RAWTLSEVMKLVEGVSKYGAGRWSEIKRLAFASYSY--RTSVDLKDKWRNL 486
+ WT+ E + GV KYG G W+ I + +Y + RT+V +KD+WR +
Sbjct: 12 QKWTVEESEWVKAGVQKYGEGNWAAISK----NYPFVNRTAVMIKDRWRTM 58
>pdb|1XG1|A Chain A, Solution Structure Of Myb-Domain Of Human Trf2
Length = 67
Score = 37.7 bits (86), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 28/48 (58%), Gaps = 4/48 (8%)
Query: 440 WTLSEVMKLVEGVSKYGAGRWSEI-KRLAFASYSYRTSVDLKDKWRNL 486
WT+ E + GV KYG G W+ I K F + RT+V +KD+WR +
Sbjct: 17 WTVEESEWVKAGVQKYGEGNWAAISKNYPFVN---RTAVMIKDRWRTM 61
>pdb|1VFC|A Chain A, Solution Structure Of The Dna Complex Of Human Trf2
Length = 63
Score = 37.4 bits (85), Expect = 0.019, Method: Composition-based stats.
Identities = 19/51 (37%), Positives = 30/51 (58%), Gaps = 6/51 (11%)
Query: 438 RAWTLSEVMKLVEGVSKYGAGRWSEIKRLAFASYSY--RTSVDLKDKWRNL 486
+ WT+ E + GV KYG G W+ I + +Y + RT+V +KD+WR +
Sbjct: 11 QKWTVEESEWVKAGVQKYGEGNWAAISK----NYPFVNRTAVMIKDRWRTM 57
>pdb|1H8A|C Chain C, Crystal Structure Of Ternary Protein-Dna Complex3
Length = 128
Score = 32.7 bits (73), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 4/55 (7%)
Query: 440 WTLSEVMKLVEGVSKYGAGRWSEIKRLAFASYSYRTSVDLKDKWRNLLKASLAQT 494
WT E +++E V KYG RWS+I + R +++W N L + +T
Sbjct: 30 WTKEEDQRVIEHVQKYGPKRWSDIAK----HLKGRIGKQCRERWHNHLNPEVKKT 80
>pdb|3TED|A Chain A, Crystal Structure Of The Chd1 Dna-Binding Domain In
Complex With A Dna Duplex
Length = 271
Score = 32.7 bits (73), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 18/29 (62%)
Query: 440 WTLSEVMKLVEGVSKYGAGRWSEIKRLAF 468
WT E KL+ GV KYG G W++I+ F
Sbjct: 172 WTKEEDEKLLIGVFKYGYGSWTQIRDDPF 200
>pdb|2XB0|X Chain X, Dna-Binding Domain From Saccharomyces Cerevisiae
Chromatin- Remodelling Protein Chd1
Length = 270
Score = 32.3 bits (72), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 18/29 (62%)
Query: 440 WTLSEVMKLVEGVSKYGAGRWSEIKRLAF 468
WT E KL+ GV KYG G W++I+ F
Sbjct: 171 WTKEEDEKLLIGVFKYGYGSWTQIRDDPF 199
>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 = 30.4 bits (67), Expect = 3.0, Method: Composition-based stats.
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 4/48 (8%)
Query: 440 WTLSEVMKLVEGVSKYGAGRWSEIKRLAFASYSYRTSVDLKDKWRNLL 487
WT E +++E V KYG RWS I + R +++W N L
Sbjct: 6 WTKEEDQRVIELVQKYGPKRWSVIAK----HLKGRIGKQCRERWHNHL 49
>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 = 3.2, Method: Composition-based stats.
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 440 WTLSEVMKLVEGVSKYGAGRWSEIKRLAFASYSYRTSVDLKDKWRNLLKASLAQT 494
WT E ++++ V KYG RWS I + R +++W N L + +T
Sbjct: 61 WTKEEDQRVIKLVQKYGPKRWSVIAK----HLKGRIGKQCRERWHNHLNPEVKKT 111
>pdb|1GVD|A Chain A, Crystal Structure Of C-Myb R2 V103l Mutant
Length = 52
Score = 29.6 bits (65), Expect = 4.0, Method: Composition-based stats.
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 4/48 (8%)
Query: 440 WTLSEVMKLVEGVSKYGAGRWSEIKRLAFASYSYRTSVDLKDKWRNLL 487
WT E +L++ V KYG RWS I + R +++W N L
Sbjct: 6 WTKEEDQRLIKLVQKYGPKRWSVIAK----HLKGRIGKQCRERWHNHL 49
>pdb|1A5J|A Chain A, Chicken B-Myb Dna Binding Domain, Repeat 2 And Repeat3,
Nmr, 32 Structures
Length = 110
Score = 28.9 bits (63), Expect = 8.1, Method: Composition-based stats.
Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 440 WTLSEVMKLVEGVSKYGAGRWSEIKRLAFASYSYRTSVDLKDKWRNLLKASLAQT 494
WT E K++E V KYG +W+ I + R +++W N L + ++
Sbjct: 10 WTKEEDQKVIELVKKYGTKQWTLIAK----HLKGRLGKQCRERWHNHLNPEVKKS 60
>pdb|1GV5|A Chain A, Crystal Structure Of C-Myb R2
Length = 52
Score = 28.5 bits (62), Expect = 9.4, Method: Composition-based stats.
Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 4/48 (8%)
Query: 440 WTLSEVMKLVEGVSKYGAGRWSEIKRLAFASYSYRTSVDLKDKWRNLL 487
WT E ++++ V KYG RWS I + R +++W N L
Sbjct: 6 WTKEEDQRVIKLVQKYGPKRWSVIAK----HLKGRIGKQCRERWHNHL 49
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 0.127 0.354
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,899,045
Number of Sequences: 62578
Number of extensions: 562414
Number of successful extensions: 1093
Number of sequences better than 100.0: 27
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 1064
Number of HSP's gapped (non-prelim): 29
length of query: 554
length of database: 14,973,337
effective HSP length: 104
effective length of query: 450
effective length of database: 8,465,225
effective search space: 3809351250
effective search space used: 3809351250
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: 54 (25.4 bits)