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= psy2702
(87 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1ZXO|A Chain A, X-Ray Crystal Structure Of Protein Q8a1p1 From Bacteroides
Thetaiotaomicron. Northeast Structural Genomics
Consortium Target Btr25.
pdb|1ZXO|F Chain F, X-Ray Crystal Structure Of Protein Q8a1p1 From Bacteroides
Thetaiotaomicron. Northeast Structural Genomics
Consortium Target Btr25.
pdb|1ZXO|B Chain B, X-Ray Crystal Structure Of Protein Q8a1p1 From Bacteroides
Thetaiotaomicron. Northeast Structural Genomics
Consortium Target Btr25.
pdb|1ZXO|D Chain D, X-Ray Crystal Structure Of Protein Q8a1p1 From Bacteroides
Thetaiotaomicron. Northeast Structural Genomics
Consortium Target Btr25.
pdb|1ZXO|C Chain C, X-Ray Crystal Structure Of Protein Q8a1p1 From Bacteroides
Thetaiotaomicron. Northeast Structural Genomics
Consortium Target Btr25.
pdb|1ZXO|E Chain E, X-Ray Crystal Structure Of Protein Q8a1p1 From Bacteroides
Thetaiotaomicron. Northeast Structural Genomics
Consortium Target Btr25
Length = 291
Score = 27.3 bits (59), Expect = 2.1, Method: Composition-based stats.
Identities = 13/38 (34%), Positives = 26/38 (68%), Gaps = 5/38 (13%)
Query: 19 DLMKDELPALMKEEKPDLMKDAKYDLMKNELLDLMQKE 56
D++K++LPA +KEE +K ++DL E++D + ++
Sbjct: 155 DILKNQLPATLKEE---FLK--QFDLTPPEIIDRVYRQ 187
>pdb|1EHY|A Chain A, X-Ray Structure Of The Epoxide Hydrolase From
Agrobacterium Radiobacter Ad1
pdb|1EHY|B Chain B, X-Ray Structure Of The Epoxide Hydrolase From
Agrobacterium Radiobacter Ad1
pdb|1EHY|C Chain C, X-Ray Structure Of The Epoxide Hydrolase From
Agrobacterium Radiobacter Ad1
pdb|1EHY|D Chain D, X-Ray Structure Of The Epoxide Hydrolase From
Agrobacterium Radiobacter Ad1
Length = 294
Score = 26.2 bits (56), Expect = 4.4, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 5/59 (8%)
Query: 19 DLMKDELPALMKEEKPDLMKDAKYDLMK-----NELLDLMQKEKPDLVQEEMSDLMKHK 72
D++ +L EKPDL +KY L K LLD + EK +V + + ++ HK
Sbjct: 57 DVIVPDLRGFGDSEKPDLNDLSKYSLDKAADDQAALLDALGIEKAYVVGHDFAAIVLHK 115
>pdb|3IZR|M Chain M, Localization Of The Large Subunit Ribosomal Proteins
Into A 5.5 A Cryo-Em Map Of Triticum Aestivum
Translating 80s Ribosome
Length = 140
Score = 26.2 bits (56), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 21/31 (67%), Gaps = 1/31 (3%)
Query: 13 MQEGKPDLMKDELPA-LMKEEKPDLMKDAKY 42
+++GKPDL K +PA ++++ KP KD +
Sbjct: 65 VKKGKPDLRKKVMPAVIVRQRKPWRRKDGVF 95
>pdb|1VT4|I Chain I, Structure Of The Drosophila Apoptosome
pdb|1VT4|J Chain J, Structure Of The Drosophila Apoptosome
pdb|1VT4|K Chain K, Structure Of The Drosophila Apoptosome
pdb|1VT4|L Chain L, Structure Of The Drosophila Apoptosome
pdb|1VT4|M Chain M, Structure Of The Drosophila Apoptosome
pdb|1VT4|N Chain N, Structure Of The Drosophila Apoptosome
pdb|1VT4|O Chain O, Structure Of The Drosophila Apoptosome
pdb|1VT4|P Chain P, Structure Of The Drosophila Apoptosome
pdb|3IZ8|A Chain A, Structure Of The Drosophila Apoptosome
pdb|3IZ8|B Chain B, Structure Of The Drosophila Apoptosome
pdb|3IZ8|C Chain C, Structure Of The Drosophila Apoptosome
pdb|3IZ8|D Chain D, Structure Of The Drosophila Apoptosome
pdb|3IZ8|E Chain E, Structure Of The Drosophila Apoptosome
pdb|3IZ8|F Chain F, Structure Of The Drosophila Apoptosome
pdb|3IZ8|G Chain G, Structure Of The Drosophila Apoptosome
pdb|3IZ8|H Chain H, Structure Of The Drosophila Apoptosome
Length = 1221
Score = 25.4 bits (54), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 26/43 (60%), Gaps = 1/43 (2%)
Query: 29 MKEEKPDLM-KDAKYDLMKNELLDLMQKEKPDLVQEEMSDLMK 70
+K KP + D KY+ + N +LD + K + +L+ + +DL++
Sbjct: 527 LKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLR 569
>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae
Length = 93
Score = 25.4 bits (54), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 11/42 (26%), Positives = 20/42 (47%)
Query: 40 AKYDLMKNELLDLMQKEKPDLVQEEMSDLMKHKMSVLMKDEK 81
+ Y NE D+++ E PD+ ++ + K L +EK
Sbjct: 26 SAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEK 67
>pdb|1J5N|A Chain A, Solution Structure Of The Non-Sequence-Specific Hmgb
Protein Nhp6a In Complex With Sry Dna
pdb|1LWM|A Chain A, Solution Structure Of The Sequence-Non-Specific Hmgb
Protein Nhp6a
Length = 93
Score = 25.4 bits (54), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 11/42 (26%), Positives = 20/42 (47%)
Query: 40 AKYDLMKNELLDLMQKEKPDLVQEEMSDLMKHKMSVLMKDEK 81
+ Y NE D+++ E PD+ ++ + K L +EK
Sbjct: 26 SAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEK 67
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 0.130 0.347
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,573,588
Number of Sequences: 62578
Number of extensions: 90815
Number of successful extensions: 269
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 261
Number of HSP's gapped (non-prelim): 25
length of query: 87
length of database: 14,973,337
effective HSP length: 55
effective length of query: 32
effective length of database: 11,531,547
effective search space: 369009504
effective search space used: 369009504
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: 45 (21.9 bits)