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= 028054
(214 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1PA6|B Chain B, Crystal Structure Of The Oxytricha Nova Telomere
End-Binding Protein Complexed With Noncognate Ssdna
Ggggttttgagg
pdb|1PH2|B Chain B, Crystal Structure Of The Oxytricha Nova Telomere End-
Binding Protein Complexed With Noncognate Ssdna
Ggggttttg
pdb|1PH3|B Chain B, Crystal Structure Of The Oxytricha Nova Telomere
End-Binding Protein Complexed With Noncognate Ssdna
Ggggttttggtg
pdb|1PH4|B Chain B, Crystal Structure Of The Oxytricha Nova Telomere
End-Binding Protein Complexed With Noncognate Ssdna
Ggggttttggcg
pdb|1PH5|B Chain B, Crystal Structure Of The Oxytricha Nova Telomere End-
Binding Protein Complexed With Noncognate Ssdna
Ggggttttg(3dr)gg
pdb|1PH7|B Chain B, Crystal Structure Of The Oxytricha Nova Telomere
End-Binding Protein Complexed With Noncognate Ssdna
Ggggttttgigg
pdb|1PH8|B Chain B, Crystal Structure Of The Oxytricha Nova Telomere End-
Binding Protein Complexed With Noncognate Ssdna
Ggggttttgcgg
pdb|1PH9|B Chain B, Crystal Structure Of The Oxytricha Nova Telomere
End-Binding Protein Complexed With Noncognate Ssdna
Ggggttttgagg
pdb|1PHJ|B Chain B, Crystal Structure Of The Oxytricha Nova Telomere End-
Binding Protein Complexed With Noncognate Ssdna Gg(3dr)
Gttttgggg
Length = 216
Score = 28.5 bits (62), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 24/41 (58%), Gaps = 5/41 (12%)
Query: 49 NFLVTEGYVDAAEKFRMESGTE-----PDIDLATITDRMAV 84
+FLVT+GY A F E+ E P++++ +TD++ V
Sbjct: 41 HFLVTDGYFFVAPYFTKEAVNEFHAKFPNVNIVDLTDKVIV 81
>pdb|1PH1|B Chain B, Crystal Structure Of The Oxytricha Nova Telomere End-
Binding Protein Complexed With Noncognate Ssdna
Ggggttttggggt
pdb|1PH6|B Chain B, Crystal Structure Of The Oxytricha Nova Telomere End-
Binding Protein Complexed With Noncognate Ssdna
Ggggttttgtgg
Length = 217
Score = 28.5 bits (62), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 24/41 (58%), Gaps = 5/41 (12%)
Query: 49 NFLVTEGYVDAAEKFRMESGTE-----PDIDLATITDRMAV 84
+FLVT+GY A F E+ E P++++ +TD++ V
Sbjct: 42 HFLVTDGYFFVAPYFTKEAVNEFHAKFPNVNIVDLTDKVIV 82
>pdb|1OTC|B Chain B, The O. Nova Telomere End Binding Protein Complexed With
Single Strand Dna
pdb|1JB7|B Chain B, Dna G-Quartets In A 1.86 A Resolution Structure Of An
Oxytricha Nova Telomeric Protein-Dna Complex
Length = 260
Score = 28.1 bits (61), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 24/41 (58%), Gaps = 5/41 (12%)
Query: 49 NFLVTEGYVDAAEKFRMESGTE-----PDIDLATITDRMAV 84
+FLVT+GY A F E+ E P++++ +TD++ V
Sbjct: 49 HFLVTDGYFFVAPYFTKEAVNEFHAKFPNVNIVDLTDKVIV 89
>pdb|3LPZ|A Chain A, Crystal Structure Of C. Therm. Get4
Length = 336
Score = 28.1 bits (61), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 18/35 (51%)
Query: 28 EWEKKLNDVKIRKEDMNKLVMNFLVTEGYVDAAEK 62
+W KK D +++ +V V EG +AAEK
Sbjct: 123 DWSKKFGDYPAGDPELHHVVGTLYVEEGEFEAAEK 157
>pdb|2I0Q|B Chain B, Crystal Structure Of A Telomere Single-Strand
Dna-Protein Complex From O. Nova With Full-Length Alpha
And Beta Telomere Proteins
Length = 385
Score = 27.3 bits (59), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 24/41 (58%), Gaps = 5/41 (12%)
Query: 49 NFLVTEGYVDAAEKFRMESGTE-----PDIDLATITDRMAV 84
+FLVT+GY A F E+ E P++++ +TD++ V
Sbjct: 49 HFLVTDGYFFVAPYFTKEAVNEFHAKFPNVNIVDLTDKVIV 89
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
0.317 0.132 0.361
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,245,032
Number of Sequences: 62578
Number of extensions: 179298
Number of successful extensions: 516
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 514
Number of HSP's gapped (non-prelim): 7
length of query: 214
length of database: 14,973,337
effective HSP length: 95
effective length of query: 119
effective length of database: 9,028,427
effective search space: 1074382813
effective search space used: 1074382813
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)