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= psy398
         (162 letters)

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

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



>pdb|4B4T|R Chain R, Near-Atomic Resolution Structural Model Of The Yeast 26s
           Proteasome
          Length = 429

 Score = 79.7 bits (195), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 58/181 (32%), Positives = 90/181 (49%), Gaps = 26/181 (14%)

Query: 1   MAPYYKEVCEEF-------------------GW-KMDEKFYTEMKDANEKRLKELDLEHE 40
           MAPYYK +CEE+                    W K D++ Y E+   NE ++KEL+ + +
Sbjct: 59  MAPYYKYLCEEYLVNNGQSDLEHDEKSDSLNEWIKFDQELYNELCKKNESKIKELNEKIQ 118

Query: 41  KNMMDEEDQV--SGIWQAKLDYLCSIGDRAEAFKLADSKFADKTNPKSHRIDAVFTLFRI 98
           K   D+E ++  +  W    +Y   IGD+  A K    K   K      +ID + T+ R+
Sbjct: 119 KLEEDDEGELEQAQAWINLGEYYAQIGDKDNAEKTL-GKSLSKAISTGAKIDVMLTIARL 177

Query: 99  AYFHGCDIQAMTAAIEKATELIEGISGGDWSARNKLKAYEGVYCLAIRQYCRAAELFVDV 158
            +F+  D   +   +E    +IE   GGDW  RN+ K Y G++CLA+R +  AA+L VD 
Sbjct: 178 GFFYN-DQLYVKEKLEAVNSMIE--KGGDWERRNRYKTYYGIHCLAVRNFKEAAKLLVDS 234

Query: 159 I 159
           +
Sbjct: 235 L 235


>pdb|4B4T|T Chain T, Near-Atomic Resolution Structural Model Of The Yeast 26s
           Proteasome
          Length = 274

 Score = 26.6 bits (57), Expect = 6.6,   Method: Compositional matrix adjust.
 Identities = 12/27 (44%), Positives = 17/27 (62%)

Query: 38  EHEKNMMDEEDQVSGIWQAKLDYLCSI 64
           ++E  MM EEDQ + I +  +DY  SI
Sbjct: 244 DYEDEMMHEEDQKTNIIEKAMDYAISI 270


>pdb|1UHW|A Chain A, Solution Structure Of The Dep Domain Of Mouse Pleckstrin
          Length = 109

 Score = 26.2 bits (56), Expect = 8.4,   Method: Compositional matrix adjust.
 Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 8/64 (12%)

Query: 20 FYTEMKDANEKRLKELDLEHEKNMMDEEDQVSGIWQAKLDYLCS---IGDRAEAFKLADS 76
           Y  MKD  EK +KEL+LE +K + +     SG+    +D+L S   + +R E   ++ S
Sbjct: 11 LYLSMKDP-EKGIKELNLEKDKKVFNHCLTGSGV----IDWLVSNKLVRNRQEGLMISAS 65

Query: 77 KFAD 80
            ++
Sbjct: 66 LLSE 69


  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
   0.321    0.135    0.407 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,821,273
Number of Sequences: 62578
Number of extensions: 178627
Number of successful extensions: 424
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 419
Number of HSP's gapped (non-prelim): 5
length of query: 162
length of database: 14,973,337
effective HSP length: 91
effective length of query: 71
effective length of database: 9,278,739
effective search space: 658790469
effective search space used: 658790469
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 bits)