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= 013656
         (438 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 = 30.4 bits (67), Expect = 2.3,   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 = 30.0 bits (66), Expect = 2.4,   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|1F0C|A Chain A, Structure Of The Viral Serpin Crma
          Length = 305

 Score = 29.6 bits (65), Expect = 3.9,   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|1C8O|A Chain A, 2.9 A Structure Of Cleaved Viral Serpin Crma
          Length = 300

 Score = 29.3 bits (64), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 17/40 (42%), Positives = 26/40 (65%), Gaps = 2/40 (5%)

Query: 81  LSGILLQIFYGFLGSWTAYLISVLYVEYRSRKEKENVSFK 120
           +S +L  ++YG  GS TA  +S  YVE  + K K+++SFK
Sbjct: 23  ISSVLTILYYGANGS-TAEQLS-KYVEKEADKNKDDISFK 60


>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 = 28.9 bits (63), Expect = 5.6,   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


  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
   0.330    0.140    0.460 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,207,041
Number of Sequences: 62578
Number of extensions: 480992
Number of successful extensions: 1136
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1135
Number of HSP's gapped (non-prelim): 5
length of query: 438
length of database: 14,973,337
effective HSP length: 102
effective length of query: 336
effective length of database: 8,590,381
effective search space: 2886368016
effective search space used: 2886368016
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 53 (25.0 bits)