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= 014097
(430 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 60.5 bits (145), Expect = 2e-09, Method: Composition-based stats.
Identities = 25/64 (39%), Positives = 43/64 (67%), Gaps = 1/64 (1%)
Query: 356 QRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRDKWRNLLR-ASYAHQK 414
+R ++++EV L++ + G G+W D+K F ++ HRT +DL+DKW+ L+ AS A Q+
Sbjct: 4 RRPFSVAEVEALVEAVEHLGTGRWRDVKMRAFDNADHRTYVDLKDKWKTLVHTASIAPQQ 63
Query: 415 NKGE 418
+GE
Sbjct: 64 RRGE 67
>pdb|2CKX|A Chain A, Crystal Structure Of Ngtrf1, Double-Stranded Telomeric
Repeat Binding Factor From Nicotiana Tabacum
Length = 83
Score = 60.1 bits (144), Expect = 2e-09, Method: Composition-based stats.
Identities = 25/63 (39%), Positives = 42/63 (66%), Gaps = 1/63 (1%)
Query: 357 RMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRDKWRNLLR-ASYAHQKN 415
R ++++EV L++ + G G+W D+K F ++ HRT +DL+DKW+ L+ AS A Q+
Sbjct: 1 RPFSVAEVEALVEAVEHLGTGRWRDVKMRAFDNADHRTYVDLKDKWKTLVHTASIAPQQR 60
Query: 416 KGE 418
+GE
Sbjct: 61 RGE 63
>pdb|2JUH|A Chain A, Solution Structure Of Dna Binding Domain Of Ngtrf1
Length = 121
Score = 59.3 bits (142), Expect = 4e-09, Method: Composition-based stats.
Identities = 25/64 (39%), Positives = 43/64 (67%), Gaps = 1/64 (1%)
Query: 356 QRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRDKWRNLLR-ASYAHQK 414
+R ++++EV L++ + G G+W D+K F ++ HRT +DL+DKW+ L+ AS A Q+
Sbjct: 17 RRPFSVAEVEALVEAVEHLGTGRWRDVKMRAFDNADHRTYVDLKDKWKTLVHTASIAPQQ 76
Query: 415 NKGE 418
+GE
Sbjct: 77 RRGE 80
>pdb|2ROH|A Chain A, The Dna Binding Domain Of Rtbp1
Length = 122
Score = 57.0 bits (136), Expect = 2e-08, Method: Composition-based stats.
Identities = 25/63 (39%), Positives = 41/63 (65%), Gaps = 1/63 (1%)
Query: 356 QRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRDKWRNLLR-ASYAHQK 414
+R +T++EV L++ + G G+W D+K F + HRT +DL+DKW+ L+ AS A Q+
Sbjct: 31 RRPFTVAEVELLVEAVEHLGTGRWRDVKFRAFENVHHRTYVDLKDKWKTLVHTASIAPQQ 90
Query: 415 NKG 417
+G
Sbjct: 91 RRG 93
>pdb|2AJE|A Chain A, Solution Structure Of The Arabidopsis Thaliana Telomeric
Repeat-Binding Protein Dna Binding Domain
Length = 105
Score = 56.6 bits (135), Expect = 2e-08, Method: Composition-based stats.
Identities = 23/64 (35%), Positives = 41/64 (64%), Gaps = 1/64 (1%)
Query: 356 QRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRDKWRNLLR-ASYAHQK 414
+R ++++EV L+ + + G G+W D+K F + HRT +DL+DKW+ L+ A + Q+
Sbjct: 13 RRPFSVAEVEALVQAVEKLGTGRWRDVKLCAFEDADHRTYVDLKDKWKTLVHTAKISPQQ 72
Query: 415 NKGE 418
+GE
Sbjct: 73 RRGE 76
>pdb|1ITY|A Chain A, Solution Structure Of The Dna Binding Domain Of Human Trf1
Length = 69
Score = 34.3 bits (77), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 356 QRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRDKWRNL 405
++ W E L G+ ++G G W+ I LL ++RT + L+D+WR +
Sbjct: 10 RQAWLWEEDKNLRSGVRKYGEGNWSKI--LLHYKFNNRTSVMLKDRWRTM 57
>pdb|1IV6|A Chain A, Solution Structure Of The Dna Complex Of Human Trf1
Length = 70
Score = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 2/47 (4%)
Query: 359 WTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRDKWRNL 405
W E L G+ ++G G W+ I LL ++RT + L+D+WR +
Sbjct: 14 WLWEEDKNLRSGVRKYGEGNWSKI--LLHYKFNNRTSVMLKDRWRTM 58
>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 = 33.5 bits (75), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 2/47 (4%)
Query: 359 WTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRDKWRNL 405
W E L G+ ++G G W+ I LL ++RT + L+D+WR +
Sbjct: 5 WLWEEDKNLRSGVRKYGEGNWSKI--LLHYKFNNRTSVMLKDRWRTM 49
>pdb|1BA5|A Chain A, Dna-Binding Domain Of Human Telomeric Protein, Htrf1, Nmr,
18 Structures
Length = 53
Score = 33.5 bits (75), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 2/47 (4%)
Query: 359 WTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRDKWRNL 405
W E L G+ ++G G W+ I LL ++RT + L+D+WR +
Sbjct: 6 WLWEEDKNLRSGVRKYGEGNWSKI--LLHYKFNNRTSVMLKDRWRTM 50
>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 = 32.0 bits (71), Expect = 0.66, Method: Composition-based stats.
Identities = 14/52 (26%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 356 QRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRDKWRNLLR 407
++ WT+ E + G+ ++G G W I + +RT + ++D+WR + R
Sbjct: 11 KQKWTVEESEWVKAGVQKYGEGNWAAISKNY--PFVNRTAVMIKDRWRTMKR 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 = 32.0 bits (71), Expect = 0.71, Method: Composition-based stats.
Identities = 14/52 (26%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 356 QRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRDKWRNLLR 407
++ WT+ E + G+ ++G G W I + +RT + ++D+WR + R
Sbjct: 2 KQKWTVEESEWVKAGVQKYGEGNWAAISKNY--PFVNRTAVMIKDRWRTMKR 51
>pdb|1VF9|A Chain A, Solution Structure Of Human Trf2
Length = 64
Score = 31.6 bits (70), Expect = 0.91, Method: Composition-based stats.
Identities = 14/52 (26%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 356 QRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRDKWRNLLR 407
++ WT+ E + G+ ++G G W I + +RT + ++D+WR + R
Sbjct: 11 KQKWTVEESEWVKAGVQKYGEGNWAAISKNY--PFVNRTAVMIKDRWRTMKR 60
>pdb|1XG1|A Chain A, Solution Structure Of Myb-Domain Of Human Trf2
Length = 67
Score = 31.6 bits (70), Expect = 0.96, Method: Composition-based stats.
Identities = 14/52 (26%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 356 QRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRDKWRNLLR 407
++ WT+ E + G+ ++G G W I + +RT + ++D+WR + R
Sbjct: 14 KQKWTVEESEWVKAGVQKYGEGNWAAISKNY--PFVNRTAVMIKDRWRTMKR 63
>pdb|1VFC|A Chain A, Solution Structure Of The Dna Complex Of Human Trf2
Length = 63
Score = 31.6 bits (70), Expect = 0.96, Method: Composition-based stats.
Identities = 14/52 (26%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 356 QRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRDKWRNLLR 407
++ WT+ E + G+ ++G G W I + +RT + ++D+WR + R
Sbjct: 10 KQKWTVEESEWVKAGVQKYGEGNWAAISKNY--PFVNRTAVMIKDRWRTMKR 59
>pdb|1H8A|C Chain C, Crystal Structure Of Ternary Protein-Dna Complex3
Length = 128
Score = 30.8 bits (68), Expect = 1.4, Method: Composition-based stats.
Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 4/52 (7%)
Query: 355 NQRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRDKWRNLL 406
N+ WT E ++I+ + ++G +W+DI + L R R++W N L
Sbjct: 26 NKGPWTKEEDQRVIEHVQKYGPKRWSDIAKHL----KGRIGKQCRERWHNHL 73
>pdb|3TED|A Chain A, Crystal Structure Of The Chd1 Dna-Binding Domain In
Complex With A Dna Duplex
Length = 271
Score = 30.0 bits (66), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 359 WTLSEVMKLIDGISQFGVGKWTDIK 383
WT E KL+ G+ ++G G WT I+
Sbjct: 172 WTKEEDEKLLIGVFKYGYGSWTQIR 196
>pdb|2XB0|X Chain X, Dna-Binding Domain From Saccharomyces Cerevisiae
Chromatin- Remodelling Protein Chd1
Length = 270
Score = 30.0 bits (66), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 359 WTLSEVMKLIDGISQFGVGKWTDIK 383
WT E KL+ G+ ++G G WT I+
Sbjct: 171 WTKEEDEKLLIGVFKYGYGSWTQIR 195
>pdb|2K9N|A Chain A, Solution Nmr Structure Of The R2r3 Dna Binding Domain Of
Myb1 Protein From Protozoan Parasite Trichomonas
Vaginalis
pdb|2KDZ|A Chain A, Structure Of The R2r3 Dna Binding Domain Of Myb1 Protein
From Protozoan Parasite Trichomonas Vaginalis In Complex
With Mre-1MRE-2r Dna
Length = 107
Score = 28.1 bits (61), Expect = 8.8, Method: Composition-based stats.
Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 5/57 (8%)
Query: 359 WTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRDKWRNLLRASYAHQKN 415
W+ E M L +++G KW I + L +R+ ++R++W + R HQK+
Sbjct: 56 WSPEEDMLLDQKYAEYG-PKWNKISKFL----KNRSDNNIRNRWMMIARHRAKHQKS 107
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
0.316 0.132 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,553,906
Number of Sequences: 62578
Number of extensions: 365500
Number of successful extensions: 719
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 702
Number of HSP's gapped (non-prelim): 20
length of query: 430
length of database: 14,973,337
effective HSP length: 102
effective length of query: 328
effective length of database: 8,590,381
effective search space: 2817644968
effective search space used: 2817644968
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)