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= 011966
         (474 letters)

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

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



>pdb|3AFC|A Chain A, Mouse Semaphorin 6a Extracellular Domain
 pdb|3AFC|B Chain B, Mouse Semaphorin 6a Extracellular Domain
 pdb|3AL8|A Chain A, Plexin A2  SEMAPHORIN 6A COMPLEX
          Length = 556

 Score = 31.6 bits (70), Expect = 0.91,   Method: Compositional matrix adjust.
 Identities = 16/48 (33%), Positives = 22/48 (45%), Gaps = 7/48 (14%)

Query: 179 CATTVFIPSFHNYRLWS-------FLGLGMTTYTAWYLTIAAFVHGQV 219
           C T  F PS  NYR+ +       F G+    Y A +  IA F  G++
Sbjct: 121 CGTNAFNPSCRNYRVDTLETFGDEFSGMARCPYDAKHANIALFADGKL 168


>pdb|3OKW|A Chain A, Mouse Semaphorin 6a, Extracellular Domains 1-2
 pdb|3OKW|B Chain B, Mouse Semaphorin 6a, Extracellular Domains 1-2
 pdb|3OKY|B Chain B, Plexin A2 In Complex With Semaphorin 6a
          Length = 565

 Score = 31.6 bits (70), Expect = 0.92,   Method: Compositional matrix adjust.
 Identities = 16/48 (33%), Positives = 22/48 (45%), Gaps = 7/48 (14%)

Query: 179 CATTVFIPSFHNYRLWS-------FLGLGMTTYTAWYLTIAAFVHGQV 219
           C T  F PS  NYR+ +       F G+    Y A +  IA F  G++
Sbjct: 120 CGTNAFNPSCRNYRVDTLETFGDEFSGMARCPYDAKHANIALFADGKL 167


>pdb|1C8O|A Chain A, 2.9 A Structure Of Cleaved Viral Serpin Crma
          Length = 300

 Score = 28.9 bits (63), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 16/40 (40%), Positives = 26/40 (65%), Gaps = 2/40 (5%)

Query: 75  LSGIILQIFYGIMGSWTAYLISVLYVEYRSRKEKENVSFK 114
           +S ++  ++YG  GS TA  +S  YVE  + K K+++SFK
Sbjct: 23  ISSVLTILYYGANGS-TAEQLS-KYVEKEADKNKDDISFK 60


>pdb|1F0C|A Chain A, Structure Of The Viral Serpin Crma
          Length = 305

 Score = 28.9 bits (63), Expect = 6.5,   Method: Compositional matrix adjust.
 Identities = 14/40 (35%), Positives = 23/40 (57%), Gaps = 2/40 (5%)

Query: 75  LSGIILQIFYGIMGSWTAYLISVLYVEYRSRKEKENVSFK 114
           +S ++  ++YG  GS    L    YVE  + K K+++SFK
Sbjct: 23  ISSVLTILYYGANGSTAEQLSK--YVEKEADKNKDDISFK 60


  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
   0.328    0.139    0.452 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,877,050
Number of Sequences: 62578
Number of extensions: 494587
Number of successful extensions: 863
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: 863
Number of HSP's gapped (non-prelim): 4
length of query: 474
length of database: 14,973,337
effective HSP length: 102
effective length of query: 372
effective length of database: 8,590,381
effective search space: 3195621732
effective search space used: 3195621732
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 53 (25.0 bits)