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= 002248
         (947 letters)

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

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



>pdb|1VJI|A Chain A, Gene Product Of At1g76680 From Arabidopsis Thaliana
 pdb|2Q3R|A Chain A, Ensemble Refinement Of The Protein Crystal Structure Of
           At1g76680 From Arabidopsis Thaliana
          Length = 372

 Score = 39.3 bits (90), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 29/113 (25%), Positives = 51/113 (45%), Gaps = 7/113 (6%)

Query: 627 KDQNGVKLQELSDQLEQKDKQIQKMYLELDHSSSQ--LIDEHKSEAQKHEALSTEIHMLR 684
            D+ G++L   +D +E  D     + L +  S ++  ++  H  EA+       E+H   
Sbjct: 229 PDRVGIRLSPFADYMESGDTNPGALGLYMAESLNKYGILYCHVIEARMKTM--GEVHACP 286

Query: 685 TEIEKLRK--EQYNLSEHGKRRDDNKPKVSTGETDML-IQKWNRERDDLEKKF 734
             +  +RK  +   +S  G  R+D    VS G TD++   +W     DL K+F
Sbjct: 287 HTLMPMRKAFKGTFISAGGFTREDGNEAVSKGRTDLVAYGRWFLANPDLPKRF 339


>pdb|2LEM|A Chain A, Monomeric Mouse Apoai(1-216)
          Length = 216

 Score = 30.0 bits (66), Expect = 6.0,   Method: Compositional matrix adjust.
 Identities = 37/136 (27%), Positives = 72/136 (52%), Gaps = 11/136 (8%)

Query: 407 KERNKDKEVDMLKQKIRDQGDEIQFFKKHAEDLEIYIKQLTEDCQVLE----QENQCLTS 462
           +E NKD  ++ +KQK++   DE Q  KK  ED+E+Y ++ +     L+    Q+ Q L  
Sbjct: 83  QEMNKD--LEEVKQKVQPYLDEFQ--KKWKEDVELYRQKASPQGAELQESARQKLQELQG 138

Query: 463 KLEKIQQQESMKSRECIESLATIKELESQSERLEDKIKQQSEEYSESLISINELECQVKE 522
           +L  + ++   + R  ++SL T  +L   SE++ + + Q+  E  +S  ++NE     K 
Sbjct: 139 RLSPVAEEFRDRMRTHVDSLRT--QLAPHSEQMRESLAQRLAEL-KSNPTLNEYHSSAKS 195

Query: 523 LKRELDKQAQEFEDDI 538
             + L ++A+   +D+
Sbjct: 196 HLKSLGEKARPALEDL 211


  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
   0.309    0.126    0.334 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23,873,871
Number of Sequences: 62578
Number of extensions: 921540
Number of successful extensions: 2846
Number of sequences better than 100.0: 101
Number of HSP's better than 100.0 without gapping: 34
Number of HSP's successfully gapped in prelim test: 67
Number of HSP's that attempted gapping in prelim test: 2641
Number of HSP's gapped (non-prelim): 232
length of query: 947
length of database: 14,973,337
effective HSP length: 108
effective length of query: 839
effective length of database: 8,214,913
effective search space: 6892312007
effective search space used: 6892312007
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: 56 (26.2 bits)