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= psy5480
         (446 letters)

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

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



>pdb|2VXT|H Chain H, Crystal Structure Of Human Il-18 Complexed To Murine
           Reference Antibody 125-2h Fab
 pdb|2VXU|H Chain H, Crystal Structure Of Murine Reference Antibody 125-2h Fab
           Fragment
 pdb|2VXU|I Chain I, Crystal Structure Of Murine Reference Antibody 125-2h Fab
           Fragment
          Length = 216

 Score = 31.2 bits (69), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 22/70 (31%), Positives = 41/70 (58%), Gaps = 8/70 (11%)

Query: 171 IDKTLISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKST-----LLALSN 225
           +D++  ++F+  ++NS+ TSE  AV  C + L+F  +   V +S +K+T      LA  +
Sbjct: 72  VDQSSTTAFM--HLNSL-TSEDSAVYFCARGLRFWGQGTLVTVSAAKTTPPSVYPLAPGS 128

Query: 226 PSNTNPIVSL 235
            + TN +V+L
Sbjct: 129 AAQTNSMVTL 138


>pdb|2QK9|A Chain A, Human Rnase H Catalytic Domain Mutant D210n In Complex
           With 18-Mer RnaDNA HYBRID
 pdb|2QKK|A Chain A, Human Rnase H Catalytic Domain Mutant D210n In Complex
           With 14-Mer RnaDNA HYBRID
 pdb|2QKK|B Chain B, Human Rnase H Catalytic Domain Mutant D210n In Complex
           With 14-Mer RnaDNA HYBRID
 pdb|2QKK|E Chain E, Human Rnase H Catalytic Domain Mutant D210n In Complex
           With 14-Mer RnaDNA HYBRID
 pdb|2QKK|F Chain F, Human Rnase H Catalytic Domain Mutant D210n In Complex
           With 14-Mer RnaDNA HYBRID
 pdb|2QKK|I Chain I, Human Rnase H Catalytic Domain Mutant D210n In Complex
           With 14-Mer RnaDNA HYBRID
 pdb|2QKK|J Chain J, Human Rnase H Catalytic Domain Mutant D210n In Complex
           With 14-Mer RnaDNA HYBRID
 pdb|2QKK|M Chain M, Human Rnase H Catalytic Domain Mutant D210n In Complex
           With 14-Mer RnaDNA HYBRID
 pdb|2QKK|N Chain N, Human Rnase H Catalytic Domain Mutant D210n In Complex
           With 14-Mer RnaDNA HYBRID
 pdb|2QKK|R Chain R, Human Rnase H Catalytic Domain Mutant D210n In Complex
           With 14-Mer RnaDNA HYBRID
 pdb|2QKK|S Chain S, Human Rnase H Catalytic Domain Mutant D210n In Complex
           With 14-Mer RnaDNA HYBRID
 pdb|2QKK|W Chain W, Human Rnase H Catalytic Domain Mutant D210n In Complex
           With 14-Mer RnaDNA HYBRID
          Length = 154

 Score = 29.3 bits (64), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 12/34 (35%), Positives = 18/34 (52%)

Query: 242 DLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNPS 275
           + L  G  + ++  P H+G  GNE  DR AR  +
Sbjct: 116 ERLTQGMDIQWMHVPGHSGFIGNEEADRLAREGA 149


>pdb|3APO|A Chain A, Crystal Structure Of Full-Length Erdj5
          Length = 780

 Score = 28.5 bits (62), Expect = 7.2,   Method: Compositional matrix adjust.
 Identities = 17/63 (26%), Positives = 29/63 (46%), Gaps = 2/63 (3%)

Query: 332 SPEDFKPFIMIGRTGSIKPVIGPWPSSDRQSRYEEVVICRMRIGHTRATHGHLFKRAPPS 391
           +P+ F   ++ G+T  +     PW    +    E  ++ RM  G  RA  G +  +A P 
Sbjct: 663 TPQTFNEKVLQGKTHWVVDFYAPWSGPSQNFAPEFELLARMIKGKVRA--GKVDCQAYPQ 720

Query: 392 TCR 394
           TC+
Sbjct: 721 TCQ 723


  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    0.420 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,812,601
Number of Sequences: 62578
Number of extensions: 505818
Number of successful extensions: 1001
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1000
Number of HSP's gapped (non-prelim): 3
length of query: 446
length of database: 14,973,337
effective HSP length: 102
effective length of query: 344
effective length of database: 8,590,381
effective search space: 2955091064
effective search space used: 2955091064
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: 53 (25.0 bits)