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= 019025
         (347 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 = 30.8 bits (68), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 7/54 (12%)

Query: 185 CATTVFIPSFHNYRIWS-------FLGLGMTTYTAWYLTIAAVVHGQVEGASHT 231
           C T  F PS  NYR+ +       F G+    Y A +  IA    G++  A+ T
Sbjct: 121 CGTNAFNPSCRNYRVDTLETFGDEFSGMARCPYDAKHANIALFADGKLYSATVT 174


>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 = 30.4 bits (67), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 7/54 (12%)

Query: 185 CATTVFIPSFHNYRIWS-------FLGLGMTTYTAWYLTIAAVVHGQVEGASHT 231
           C T  F PS  NYR+ +       F G+    Y A +  IA    G++  A+ T
Sbjct: 120 CGTNAFNPSCRNYRVDTLETFGDEFSGMARCPYDAKHANIALFADGKLYSATVT 173


>pdb|3GE5|A Chain A, Crystal Structure Of A Putative Nad(P)h:fmn Oxidoreductase
           (Pg0310) From Porphyromonas Gingivalis W83 At 1.70 A
           Resolution
 pdb|3GE5|B Chain B, Crystal Structure Of A Putative Nad(P)h:fmn Oxidoreductase
           (Pg0310) From Porphyromonas Gingivalis W83 At 1.70 A
           Resolution
          Length = 198

 Score = 29.3 bits (64), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 19/62 (30%), Positives = 23/62 (37%), Gaps = 17/62 (27%)

Query: 192 PSFHNYRIWSFLGLGMTTYTAWYLTIAAVVHGQVEGASHTAPTKLVLYFTGATNILYTFG 251
           PS HNY+ W FL                 V  + EG    AP     +F GA   + T G
Sbjct: 64  PSAHNYQPWHFL-----------------VVREEEGRKRLAPCSQQPWFPGAPIYIITLG 106

Query: 252 GH 253
            H
Sbjct: 107 DH 108


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

 Score = 29.3 bits (64), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 15/40 (37%), Positives = 23/40 (57%), Gaps = 2/40 (5%)

Query: 81  LSGILLQIFYGFLGSWTAYLISVLYVEYRSRKEKENVSFK 120
           +S +L  ++YG  GS    L    YVE  + K K+++SFK
Sbjct: 23  ISSVLTILYYGANGSTAEQLSK--YVEKEADKNKDDISFK 60


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

 Score = 29.3 bits (64), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 15/40 (37%), Positives = 23/40 (57%), Gaps = 2/40 (5%)

Query: 81  LSGILLQIFYGFLGSWTAYLISVLYVEYRSRKEKENVSFK 120
           +S +L  ++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    0.138    0.452 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,718,833
Number of Sequences: 62578
Number of extensions: 380903
Number of successful extensions: 1085
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 1084
Number of HSP's gapped (non-prelim): 8
length of query: 347
length of database: 14,973,337
effective HSP length: 100
effective length of query: 247
effective length of database: 8,715,537
effective search space: 2152737639
effective search space used: 2152737639
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: 52 (24.6 bits)