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= 036120
         (779 letters)

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

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



>pdb|2R17|C Chain C, Functional Architecture Of The Retromer Cargo-Recognition
           Complex
 pdb|2R17|D Chain D, Functional Architecture Of The Retromer Cargo-Recognition
           Complex
          Length = 298

 Score =  214 bits (546), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 129/301 (42%), Positives = 180/301 (59%), Gaps = 20/301 (6%)

Query: 466 DFKEEQNSVARLIHMLYNDDSEEMLKIICTVRKHIMTGGPKRLPFTVPPLVFSALRLV-R 524
           DF +EQ+ V R IH+L ++D ++   I+ T RKH   GG +R+ FT+PPLVF+A +L  R
Sbjct: 1   DFADEQSLVGRFIHLLRSEDPDQQYLILNTARKHFGAGGNQRIRFTLPPLVFAAYQLAFR 60

Query: 525 QLQNQDGDVAGEEEPATPKKIFQLLNQTIETLLYVPSPEMALRLYLQCAEAANDCDLE-- 582
             +N   D   E++    +KIF   +QTI  L+     E+ LRL+LQ A AA +   E  
Sbjct: 61  YKENSKVDDKWEKKC---QKIFSFAHQTISALIKAELAELPLRLFLQGALAAGEIGFENH 117

Query: 583 -PVAYEFFTQAFMLYEEEIADSKAQVTAIHLIIGTLQRISVFGIENRDTLTHKATGYSAR 641
             VAYEF +QAF LYE+EI+DSKAQ+ AI LIIGT +R   F  EN + L  +    +++
Sbjct: 118 ETVAYEFXSQAFSLYEDEISDSKAQLAAITLIIGTFERXKCFSEENHEPLRTQCALAASK 177

Query: 642 LLKKPDQCRAVYACSHLFWVD---DQDG--IKDGERVLLCLKRALRIANAAQQMANVARG 696
           LLKKPDQ RAV  C+HLFW     D++G  +  G+RV  CLK+AL+IAN           
Sbjct: 178 LLKKPDQGRAVSTCAHLFWSGRNTDKNGEELHGGKRVXECLKKALKIANQCXD------- 230

Query: 697 SSGPVVLFVEILNKYLYFFEKGNTQITASAIQSLIELITSEMQS-ESTTLDPADNAFFAS 755
            S  V LF+EILN+Y+YF+EK N  +T   +  LI+ I  ++ + ES+      N  F +
Sbjct: 231 PSLQVQLFIEILNRYIYFYEKENDAVTIQVLNQLIQKIREDLPNLESSEETEQINKHFHN 290

Query: 756 T 756
           T
Sbjct: 291 T 291


>pdb|2QV2|A Chain A, A Role Of The Lowe Syndrome Protein Ocrl In Early Steps Of
           The Endocytic Pathway
          Length = 342

 Score = 30.0 bits (66), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 25/96 (26%), Positives = 50/96 (52%), Gaps = 7/96 (7%)

Query: 385 DSRATKQVVALLSAPLDKYNDILMDHLDDGTNKVMAMVIIQSIMKNSTCISTAEKVEVLF 444
           D   +K  V +L++  DK  DIL+ HLD G +  + +    S     +C  T+  +E L 
Sbjct: 76  DVYVSKDSVTILNSGEDKIEDILVLHLDRGKDYFLTI----SGNYLPSCFGTS--LEALC 129

Query: 445 ELIKGLIKDLDGAAQDELDEEDFKEEQNSVARLIHM 480
            + K  I+++      +L+E+ F E++ S+ +++ +
Sbjct: 130 RM-KRPIREVPVTKLIDLEEDSFLEKEKSLLQMVPL 164


>pdb|3QIS|A Chain A, Recognition Of The F&h Motif By The Lowe Syndrome Protein
           Ocrl
          Length = 366

 Score = 30.0 bits (66), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 25/96 (26%), Positives = 50/96 (52%), Gaps = 7/96 (7%)

Query: 385 DSRATKQVVALLSAPLDKYNDILMDHLDDGTNKVMAMVIIQSIMKNSTCISTAEKVEVLF 444
           D   +K  V +L++  DK  DIL+ HLD G +  + +    S     +C  T+  +E L 
Sbjct: 100 DVYVSKDSVTILNSGEDKIEDILVLHLDRGKDYFLTI----SGNYLPSCFGTS--LEALC 153

Query: 445 ELIKGLIKDLDGAAQDELDEEDFKEEQNSVARLIHM 480
            + K  I+++      +L+E+ F E++ S+ +++ +
Sbjct: 154 RM-KRPIREVPVTKLIDLEEDSFLEKEKSLLQMVPL 188


  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
   0.320    0.136    0.385 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,349,700
Number of Sequences: 62578
Number of extensions: 843680
Number of successful extensions: 1899
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1891
Number of HSP's gapped (non-prelim): 5
length of query: 779
length of database: 14,973,337
effective HSP length: 106
effective length of query: 673
effective length of database: 8,340,069
effective search space: 5612866437
effective search space used: 5612866437
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)