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= 039475
         (286 letters)

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

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



>pdb|3E6J|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor (Vlr)
           Rbc36 In Complex With H-Trisaccharide
          Length = 229

 Score = 48.5 bits (114), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 54/185 (29%), Positives = 82/185 (44%), Gaps = 39/185 (21%)

Query: 32  TNSCQEKLRHLTLMLGLPT-------------KFPVSIFDAKKLRSLSLFYDSKGQSAAS 78
           T  C+ K RH ++  G+PT             K    +FD+  L +L   Y    Q  A 
Sbjct: 23  TVDCRSK-RHASVPAGIPTNAQILYLHDNQITKLEPGVFDS--LINLKELYLGSNQLGAL 79

Query: 79  PVLQGLFDQLTCLRALKIEELWYGDQTIEIPKGL-ENLIHLRYLKLSAVEELSETCYCPS 137
           PV  G+FD LT L  L +      +Q   +P  + + L+HL+ L +           C  
Sbjct: 80  PV--GVFDSLTQLTVLDLGT----NQLTVLPSAVFDRLVHLKELFMC----------CNK 123

Query: 138 LKRLPQGRGKLINLRHLIFDKDYLAYMANG-FERLTSLRTLSGFTVARVGGKYSSEACNL 196
           L  LP+G  +L +L HL  D++ L  + +G F+RL+SL     F     G  +  E  ++
Sbjct: 124 LTELPRGIERLTHLTHLALDQNQLKSIPHGAFDRLSSLTHAYLF-----GNPWDCECRDI 178

Query: 197 EGLRN 201
             LRN
Sbjct: 179 MYLRN 183


>pdb|2O6Q|A Chain A, Structural Diversity Of The Hagfish Variable Lymphocyte
           Receptors A29
          Length = 270

 Score = 36.2 bits (82), Expect = 0.024,   Method: Compositional matrix adjust.
 Identities = 30/95 (31%), Positives = 48/95 (50%), Gaps = 21/95 (22%)

Query: 52  FPVSIFDA-KKLRSLSLFYDSKGQSAASPVLQGLFDQLTCLRALKIEELWYGDQTIEIPK 110
            P  +FD+  KL  LSL Y+         + +G+FD+LT L+ L++    Y +Q   +P+
Sbjct: 124 LPPRVFDSLTKLTYLSLGYNE-----LQSLPKGVFDKLTSLKELRL----YNNQLKRVPE 174

Query: 111 G-LENLIHLRYLKLSAVEELSETCYCPSLKRLPQG 144
           G  + L  L+ LKL   +          LKR+P+G
Sbjct: 175 GAFDKLTELKTLKLDNNQ----------LKRVPEG 199


>pdb|3H09|A Chain A, The Structure Of Haemophilus Influenzae Iga1 Protease
 pdb|3H09|B Chain B, The Structure Of Haemophilus Influenzae Iga1 Protease
          Length = 989

 Score = 30.0 bits (66), Expect = 1.4,   Method: Composition-based stats.
 Identities = 27/84 (32%), Positives = 36/84 (42%), Gaps = 10/84 (11%)

Query: 159 DYLAYMANGFERLTSLRTLSGFTVARVGGKYSSEACNLEGLRN--LNHLRQFLRICGLGN 216
           DY  Y+    ++L+  + L+ F    V G       NL G  N  L     F  I G GN
Sbjct: 771 DYTGYVTCTTDKLSD-KALNSFNATNVSGN-----VNLSGNANFVLGKANLFGTISGTGN 824

Query: 217 LQMRLKINA--HLEKKKNLVHLTL 238
            Q+RL  N+  HL    N+  L L
Sbjct: 825 SQVRLTENSHWHLTGDSNVNQLNL 848


>pdb|3M19|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor
           Vlra.R5.1
 pdb|3M19|B Chain B, Crystal Structure Of Variable Lymphocyte Receptor
           Vlra.R5.1
          Length = 251

 Score = 29.6 bits (65), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 40/135 (29%), Positives = 61/135 (45%), Gaps = 22/135 (16%)

Query: 47  GLPTKFPVSIFDAKKLRSLSLFYDSKGQSAASPVLQGLFDQLTCLRALKIEELWYGDQTI 106
           GL T    +     KL  L+L Y+     +A     G+FD LT L  L +      +Q  
Sbjct: 46  GLATLSDATFRGLTKLTWLNLDYNQLQTLSA-----GVFDDLTELGTLGLAN----NQLA 96

Query: 107 EIPKGL-ENLIHLRYLKLSAVEELSETCYCPSLKRLPQGR-GKLINLRHLIFDKDYLAYM 164
            +P G+ ++L  L  L L   +          LK LP G   +L  L+ L  + + L  +
Sbjct: 97  SLPLGVFDHLTQLDKLYLGGNQ----------LKSLPSGVFDRLTKLKELRLNTNQLQSI 146

Query: 165 -ANGFERLTSLRTLS 178
            A  F++LT+L+TLS
Sbjct: 147 PAGAFDKLTNLQTLS 161


>pdb|3M18|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor
           Vlra.R2.1 In Complex With Hen Egg Lysozyme
          Length = 251

 Score = 29.6 bits (65), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 40/135 (29%), Positives = 61/135 (45%), Gaps = 22/135 (16%)

Query: 47  GLPTKFPVSIFDAKKLRSLSLFYDSKGQSAASPVLQGLFDQLTCLRALKIEELWYGDQTI 106
           GL T    +     KL  L+L Y+     +A     G+FD LT L  L +      +Q  
Sbjct: 46  GLATLSDATFRGLTKLTWLNLDYNQLQTLSA-----GVFDDLTELGTLGLAN----NQLA 96

Query: 107 EIPKGL-ENLIHLRYLKLSAVEELSETCYCPSLKRLPQGR-GKLINLRHLIFDKDYLAYM 164
            +P G+ ++L  L  L L   +          LK LP G   +L  L+ L  + + L  +
Sbjct: 97  SLPLGVFDHLTQLDKLYLGGNQ----------LKSLPSGVFDRLTKLKELRLNTNQLQSI 146

Query: 165 -ANGFERLTSLRTLS 178
            A  F++LT+L+TLS
Sbjct: 147 PAGAFDKLTNLQTLS 161


  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
   0.322    0.138    0.403 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,665,562
Number of Sequences: 62578
Number of extensions: 283205
Number of successful extensions: 498
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 495
Number of HSP's gapped (non-prelim): 7
length of query: 286
length of database: 14,973,337
effective HSP length: 98
effective length of query: 188
effective length of database: 8,840,693
effective search space: 1662050284
effective search space used: 1662050284
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)