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= 014417
         (425 letters)

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

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



>pdb|3SE9|L Chain L, Crystal Structure Of Broadly And Potently Neutralizing
           Antibody Vrc- Pg04 In Complex With Hiv-1 Gp120
 pdb|4I3R|L Chain L, Crystal Structure Of The Outer Domain Of Hiv-1 Gp120 In
           Complex With Vrc-pg04 Space Group P3221
 pdb|4I3S|L Chain L, Crystal Structure Of The Outer Domain Of Hiv-1 Gp120 In
           Complex With Vrc-pg04 Space Group P21
          Length = 208

 Score = 29.3 bits (64), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 26/104 (25%), Positives = 40/104 (38%), Gaps = 4/104 (3%)

Query: 122 NPVQFLEIVRGKSLAFVGDSVGRNQMESLLCLLASEANPEDISHKYTSETDYFKRWYYTE 181
            P + L     K  + + D    +Q      L  +   PED +  Y  + ++F +    E
Sbjct: 40  QPPKLLIFATSKRASGIPDRFSGSQFGKQYTLTITRMEPEDFARYYCQQLEFFGQGTRLE 99

Query: 182 YKFTVATLWSPFLVKSSDADPNGHSANN---LMNLYLDEADESW 222
            + TVA   S F+   SD      +A+    L N Y  EA   W
Sbjct: 100 IRRTVAAP-SVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQW 142


>pdb|2UUD|H Chain H, Crystal Structure Of The Tepc15-Vk45.1 Anti-2-Phenyl-5-
           Oxazolone Nq10-1.12 Scfv In Complex With The Hapten
 pdb|2UUD|J Chain J, Crystal Structure Of The Tepc15-Vk45.1 Anti-2-Phenyl-5-
           Oxazolone Nq10-1.12 Scfv In Complex With The Hapten
          Length = 121

 Score = 28.1 bits (61), Expect = 8.8,   Method: Composition-based stats.
 Identities = 15/69 (21%), Positives = 31/69 (44%), Gaps = 9/69 (13%)

Query: 119 PLFNPVQFLEIVRGKSLAFVGD---------SVGRNQMESLLCLLASEANPEDISHKYTS 169
           P    +++L  +R K+  +  D         ++ R+  +S+L L  +    ED +  Y +
Sbjct: 40  PPGKALEWLAFIRNKANGYTTDYSASVKGRFTISRDNSQSILYLQMNTLRAEDSATYYCA 99

Query: 170 ETDYFKRWY 178
             DY+  W+
Sbjct: 100 RGDYYGAWF 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
   0.321    0.136    0.434 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,222,581
Number of Sequences: 62578
Number of extensions: 553305
Number of successful extensions: 1054
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1054
Number of HSP's gapped (non-prelim): 2
length of query: 425
length of database: 14,973,337
effective HSP length: 102
effective length of query: 323
effective length of database: 8,590,381
effective search space: 2774693063
effective search space used: 2774693063
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: 53 (25.0 bits)