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= 022151
         (302 letters)

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

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



>pdb|2AJ3|A Chain A, Crystal Structure Of A Cross-Reactive Hiv-1 Neutralizing
          Cd4-Binding Site Antibody Fab M18
 pdb|2AJ3|C Chain C, Crystal Structure Of A Cross-Reactive Hiv-1 Neutralizing
          Cd4-Binding Site Antibody Fab M18
 pdb|2AJ3|E Chain E, Crystal Structure Of A Cross-Reactive Hiv-1 Neutralizing
          Cd4-Binding Site Antibody Fab M18
          Length = 213

 Score = 32.7 bits (73), Expect = 0.27,   Method: Compositional matrix adjust.
 Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 11/64 (17%)

Query: 31 VLYSSTAEESGEPVDLADSMRENSLTMCSSRRGTIAGLEPVNFITLATPHLGVRGKKQLP 90
          ++YS++  +SG P   + S      T+      TI+GL+P +F T    HL     K+ P
Sbjct: 46 LMYSASTLQSGVPSRFSGSGSGTEFTL------TISGLQPEDFATYYCQHL-----KRYP 94

Query: 91 FLFG 94
          + FG
Sbjct: 95 YTFG 98


>pdb|3CFX|A Chain A, Crystal Structure Of M. Acetivorans Periplasmic Binding
           Protein Moda/wtpa With Bound Tungstate
 pdb|3CFX|B Chain B, Crystal Structure Of M. Acetivorans Periplasmic Binding
           Protein Moda/wtpa With Bound Tungstate
          Length = 296

 Score = 30.8 bits (68), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 13/40 (32%), Positives = 24/40 (60%), Gaps = 5/40 (12%)

Query: 90  PFLFGVSFLE-----KLALPLAPILVGQTGSQLFLMDGRP 124
           P ++GV+        +LA     +L+G+TG Q+F+ +G+P
Sbjct: 255 PIVYGVTIPNNAENSELATEFVALLLGETGQQIFIENGQP 294


>pdb|3K6U|A Chain A, M. Acetivorans Molybdate-binding Protein (moda) In
           Unliganded Open Form
 pdb|3K6V|A Chain A, M. Acetivorans Molybdate-Binding Protein (Moda) In
           Citrate-Bound Open Form
 pdb|3K6W|A Chain A, Apo And Ligand Bound Structures Of Moda From The Archaeon
           Methanosarcina Acetivorans
 pdb|3K6X|A Chain A, M. Acetivorans Molybdate-Binding Protein (Moda) In
           Molybdate-Bound Close Form With 2 Molecules In
           Asymmetric Unit Forming Beta Barrel
 pdb|3K6X|B Chain B, M. Acetivorans Molybdate-Binding Protein (Moda) In
           Molybdate-Bound Close Form With 2 Molecules In
           Asymmetric Unit Forming Beta Barrel
          Length = 354

 Score = 30.4 bits (67), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 13/40 (32%), Positives = 24/40 (60%), Gaps = 5/40 (12%)

Query: 90  PFLFGVSFLE-----KLALPLAPILVGQTGSQLFLMDGRP 124
           P ++GV+        +LA     +L+G+TG Q+F+ +G+P
Sbjct: 293 PIVYGVTIPNNAENSELATEFVALLLGETGQQIFIENGQP 332


>pdb|1YBY|A Chain A, Conserved Hypothetical Protein Cth-95 From Clostridium
           Thermocellum
 pdb|1YBY|B Chain B, Conserved Hypothetical Protein Cth-95 From Clostridium
           Thermocellum
          Length = 215

 Score = 28.9 bits (63), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 10/27 (37%), Positives = 17/27 (62%)

Query: 50  MRENSLTMCSSRRGTIAGLEPVNFITL 76
           ++EN +    S +G + G+EP NF+ L
Sbjct: 135 VKENEIVKVLSHKGNVFGIEPPNFVEL 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
   0.319    0.134    0.399 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,618,628
Number of Sequences: 62578
Number of extensions: 343142
Number of successful extensions: 714
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 711
Number of HSP's gapped (non-prelim): 4
length of query: 302
length of database: 14,973,337
effective HSP length: 98
effective length of query: 204
effective length of database: 8,840,693
effective search space: 1803501372
effective search space used: 1803501372
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)