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= 038235
         (514 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|3PRY|A Chain A, Crystal Structure Of The Middle Domain Of Human Hsp90-Beta
           Refined At 2.3 A Resolution
 pdb|3PRY|B Chain B, Crystal Structure Of The Middle Domain Of Human Hsp90-Beta
           Refined At 2.3 A Resolution
 pdb|3PRY|C Chain C, Crystal Structure Of The Middle Domain Of Human Hsp90-Beta
           Refined At 2.3 A Resolution
          Length = 268

 Score = 30.0 bits (66), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 8/70 (11%)

Query: 155 GVCRDGTDEVDVSMRLDEFLRKHTSEDNDSFSKILEKVNR-KRKERYQFLLEGEKRD--- 210
           G+  D T+      RL E LR HTS+  D  + + E V+R K  ++  + + GE ++   
Sbjct: 158 GIHEDSTN----RRRLSELLRYHTSQSGDEMTSLSEYVSRMKETQKSIYYITGESKEQVA 213

Query: 211 NNNLIEDVKK 220
           N+  +E V+K
Sbjct: 214 NSAFVERVRK 223


>pdb|1A3Q|A Chain A, Human Nf-Kappa-B P52 Bound To Dna
 pdb|1A3Q|B Chain B, Human Nf-Kappa-B P52 Bound To Dna
          Length = 285

 Score = 28.5 bits (62), Expect = 8.5,   Method: Compositional matrix adjust.
 Identities = 19/75 (25%), Positives = 38/75 (50%), Gaps = 2/75 (2%)

Query: 147 VGVELSGEGVCRDGTDEVDVSMRLDEFLRKHTSEDNDSFSKILEKVNRKR-KERYQFLLE 205
           VG + S  G+C       D++ + +     H ++ N     +++K+ R+R + R Q L E
Sbjct: 74  VGKQCSELGICAVSVGPKDMTAQFNNLGVLHVTKKN-MMGTMIQKLQRQRLRSRPQGLTE 132

Query: 206 GEKRDNNNLIEDVKK 220
            E+R+     +++KK
Sbjct: 133 AEQRELEQEAKELKK 147


>pdb|3TZE|A Chain A, Crystal Structure Of A Tryptophanyl-Trna Synthetase From
           Encephalitozoon Cuniculi Bound To Tryptophan
 pdb|3TZE|B Chain B, Crystal Structure Of A Tryptophanyl-Trna Synthetase From
           Encephalitozoon Cuniculi Bound To Tryptophan
          Length = 406

 Score = 28.5 bits (62), Expect = 9.2,   Method: Compositional matrix adjust.
 Identities = 30/112 (26%), Positives = 50/112 (44%), Gaps = 25/112 (22%)

Query: 115 GKIRTQTETPGSTFARNFTPFDEFDVNITTPKVGVELSGEGVCRDGTDEVDVSMRLDEFL 174
           G +  QT+ PGS   +  TP+D            VE+         TDEV V++  D+ +
Sbjct: 10  GTLEAQTQGPGSMAEQRITPWD------------VEVV-------STDEVPVAIDYDKII 50

Query: 175 RKHTSED-NDSFSKILEKVNRKRKERYQFLLEG---EKRDNNNLIEDVKKDR 222
            +   E  N + +  LEK++   K  + F   G     RD N L++++  +R
Sbjct: 51  NQFGCEKFNQALADRLEKLS--GKPAHYFFRRGIVFAHRDFNLLLDEIANNR 100


>pdb|3DO7|B Chain B, X-Ray Structure Of A Nf-Kb P52RELBDNA COMPLEX
          Length = 293

 Score = 28.5 bits (62), Expect = 9.3,   Method: Compositional matrix adjust.
 Identities = 19/75 (25%), Positives = 38/75 (50%), Gaps = 2/75 (2%)

Query: 147 VGVELSGEGVCRDGTDEVDVSMRLDEFLRKHTSEDNDSFSKILEKVNRKR-KERYQFLLE 205
           VG + S  G+C       D++ + +     H ++ N     +++K+ R+R + R Q L E
Sbjct: 74  VGKQCSELGICAVSVGPKDMTAQFNNLGVLHVTKKN-MMGTMIQKLQRQRLRSRPQGLTE 132

Query: 206 GEKRDNNNLIEDVKK 220
            E+R+     +++KK
Sbjct: 133 AEQRELEQEAKELKK 147


  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
   0.311    0.131    0.379 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,188,461
Number of Sequences: 62578
Number of extensions: 734626
Number of successful extensions: 1444
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1441
Number of HSP's gapped (non-prelim): 7
length of query: 514
length of database: 14,973,337
effective HSP length: 103
effective length of query: 411
effective length of database: 8,527,803
effective search space: 3504927033
effective search space used: 3504927033
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)