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= 025243
         (255 letters)

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

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



>pdb|1IMV|A Chain A, 2.85 A Crystal Structure Of Pedf
          Length = 398

 Score = 29.3 bits (64), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 22/82 (26%), Positives = 38/82 (46%), Gaps = 9/82 (10%)

Query: 47  VLIYKLTTKNTCSGLSLKTQELTAMFLALRLVCSIIMEADIH----TVLDFAT-----LA 97
           VL+  L+     S LSL   E T   +   L   +I   DIH     +LD  T     L 
Sbjct: 58  VLLSPLSVATALSALSLGADERTESIIHRALYYDLISSPDIHGTYKELLDTVTAPQKNLK 117

Query: 98  STAWVIYMIRFKLKSTYIKELD 119
           S + +++  + ++KS+++  L+
Sbjct: 118 SASRIVFEKKLRIKSSFVAPLE 139


>pdb|1GQQ|A Chain A, Murc - Crystal Structure Of The Apo-Enzyme From
           Haemophilus Influenzae
 pdb|1GQQ|B Chain B, Murc - Crystal Structure Of The Apo-Enzyme From
           Haemophilus Influenzae
 pdb|1GQY|A Chain A, Murc- Crystal Structure Of The Enzyme From Haemophilus
           Influenzae Complexed With Amppcp
 pdb|1GQY|B Chain B, Murc- Crystal Structure Of The Enzyme From Haemophilus
           Influenzae Complexed With Amppcp
          Length = 475

 Score = 26.9 bits (58), Expect = 9.8,   Method: Compositional matrix adjust.
 Identities = 27/85 (31%), Positives = 36/85 (42%), Gaps = 20/85 (23%)

Query: 51  KLTTKNTCSGLS----LKTQELTAMFLALRLVCSII--MEADIHTVLDFATLASTAWVIY 104
           K   KN   G S     +  E  A FL L+ + S++  ME D                 Y
Sbjct: 156 KSAGKNAHLGASRYLIAEADESDASFLHLQPMVSVVTNMEPD-------------HMDTY 202

Query: 105 MIRF-KLKSTYIKELDNFPIYYIAV 128
              F K+K+TY+K L N P Y +AV
Sbjct: 203 EGDFEKMKATYVKFLHNLPFYGLAV 227


  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
   0.333    0.141    0.435 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,438,198
Number of Sequences: 62578
Number of extensions: 223039
Number of successful extensions: 472
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 470
Number of HSP's gapped (non-prelim): 3
length of query: 255
length of database: 14,973,337
effective HSP length: 97
effective length of query: 158
effective length of database: 8,903,271
effective search space: 1406716818
effective search space used: 1406716818
T: 11
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.5 bits)
S2: 50 (23.9 bits)