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= 032481
         (140 letters)

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

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



>pdb|2QQK|L Chain L, Neuropilin-2 A1a2b1b2 Domains In Complex With A
          Semaphorin-Blocking Fab
 pdb|2QQL|L Chain L, Neuropilin-2 A1a2b1b2 Domains In Complex With A
          Semaphorin-Blocking Fab
          Length = 214

 Score = 27.7 bits (60), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 2/49 (4%)

Query: 5  ICFAIFFVLNALIWGEKSSGAVPFATMFALVFLWFGISIPLVFVGSYIG 53
           C A   V  A+ W ++  G  P   +++  FL+ G  +P  F GS  G
Sbjct: 22 TCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSG--VPSRFSGSGSG 68


>pdb|2ZT9|B Chain B, Crystal Structure Of The Cytochrome B6f Complex From
          Nostoc Sp. Pcc 7120
 pdb|4H44|B Chain B, 2.70 A Cytochrome B6f Complex Structure From Nostoc Pcc
          7120
          Length = 160

 Score = 25.8 bits (55), Expect = 7.9,   Method: Compositional matrix adjust.
 Identities = 17/49 (34%), Positives = 26/49 (53%), Gaps = 7/49 (14%)

Query: 44 PLVFVGSYIGFKKPAIEDPVKTNK------IPRQILEQPWYMNPIFSIL 86
          P+V +GS+      A+ DP  T +       P +IL + WY+ P+F IL
Sbjct: 41 PIVIMGSFACIVALAVLDPAMTGEPANPFATPLEILPE-WYLYPVFQIL 88


  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
   0.335    0.151    0.509 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,485,790
Number of Sequences: 62578
Number of extensions: 119178
Number of successful extensions: 253
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 252
Number of HSP's gapped (non-prelim): 4
length of query: 140
length of database: 14,973,337
effective HSP length: 89
effective length of query: 51
effective length of database: 9,403,895
effective search space: 479598645
effective search space used: 479598645
T: 11
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.6 bits)
S2: 46 (22.3 bits)