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= 003570
         (810 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 = 0.008,   Method: Compositional matrix adjust.
 Identities = 29/113 (25%), Positives = 51/113 (45%), Gaps = 7/113 (6%)

Query: 490 KDQNGVKLQELSDQLEQKDKQIQKMYLELDHSSSQ--LIDEHKSEAQKHEALSTEIHMLR 547
            D+ G++L   +D +E  D     + L +  S ++  ++  H  EA+       E+H   
Sbjct: 229 PDRVGIRLSPFADYMESGDTNPGALGLYMAESLNKYGILYCHVIEARMKTM--GEVHACP 286

Query: 548 TEIEKLRK--EQYNLSEHGKRRDDNKPKVSTGETDML-IQKWNRERDDLEKKF 597
             +  +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 = 4.9,   Method: Compositional matrix adjust.
 Identities = 34/131 (25%), Positives = 70/131 (53%), Gaps = 9/131 (6%)

Query: 275 DKEVDMLKQKIRDQGDEIQFFKKHAEDLEIYIKQLTEDCQVLE----QENQCLTSKLEKI 330
           +K+++ +KQK++   DE Q  KK  ED+E+Y ++ +     L+    Q+ Q L  +L  +
Sbjct: 86  NKDLEEVKQKVQPYLDEFQ--KKWKEDVELYRQKASPQGAELQESARQKLQELQGRLSPV 143

Query: 331 QQQESMKSRECIESLATIKELESQSERLEDKIKQQSEEYSESLISINELECQVKELKREL 390
            ++   + R  ++SL T  +L   SE++ + + Q+  E  +S  ++NE     K   + L
Sbjct: 144 AEEFRDRMRTHVDSLRT--QLAPHSEQMRESLAQRLAEL-KSNPTLNEYHSSAKSHLKSL 200

Query: 391 DKQAQEFEDDI 401
            ++A+   +D+
Sbjct: 201 GEKARPALEDL 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
   0.307    0.124    0.323 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,744,700
Number of Sequences: 62578
Number of extensions: 737280
Number of successful extensions: 2624
Number of sequences better than 100.0: 116
Number of HSP's better than 100.0 without gapping: 38
Number of HSP's successfully gapped in prelim test: 78
Number of HSP's that attempted gapping in prelim test: 2412
Number of HSP's gapped (non-prelim): 256
length of query: 810
length of database: 14,973,337
effective HSP length: 107
effective length of query: 703
effective length of database: 8,277,491
effective search space: 5819076173
effective search space used: 5819076173
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 56 (26.2 bits)