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= 005345
         (701 letters)

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

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



>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p
          Length = 400

 Score = 30.8 bits (68), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 17/45 (37%), Positives = 24/45 (53%)

Query: 508 NFNFLHDAMSFDSIWDEIIRCGSTDPSIYIISWNDHFFVLKIEQE 552
           NF+F   A ++        R G    +I +I+WND F + KIEQE
Sbjct: 332 NFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIEQE 376


>pdb|1LIL|A Chain A, Bence Jones Protein Cle, A Lambda Iii Immunoglobulin
           Light- Chain Dimer
 pdb|1LIL|B Chain B, Bence Jones Protein Cle, A Lambda Iii Immunoglobulin
           Light- Chain Dimer
          Length = 212

 Score = 29.6 bits (65), Expect = 6.5,   Method: Composition-based stats.
 Identities = 38/145 (26%), Positives = 61/145 (42%), Gaps = 9/145 (6%)

Query: 65  LTEEGDEVGDGVVQWNNQDFHYSGHVFPWELHF------TIFNGLNQGQRQKVTAMGTAT 118
           +T  G+++GD  V W  Q    S  V  ++ +         F+G + G    +T  GT T
Sbjct: 19  ITCSGEKLGDAYVCWYQQRPGQSPVVVIYQDNRRPSGIPERFSGSSSGNTATLTISGTQT 78

Query: 119 LNLAKYANSDKEKELQIKVPLTVSGDTIEGDPYLCLSFRLIESRFAQESLQAGQRSIVPL 178
           L+ A Y     +    + V    +  T+ G P    S  L     + E LQA + ++V L
Sbjct: 79  LDEADYYCQVWDSNASV-VFGGGTKLTVLGQPKAAPSVTLFPP--SSEELQANKATLVCL 135

Query: 179 TTSPTSGEAVPMGKDELSAVKAGLQ 203
            +    G      K + S VKAG++
Sbjct: 136 ISDFYPGAVTVAWKADSSPVKAGVE 160


>pdb|3UJI|L Chain L, Crystal Structure Of Anti-Hiv-1 V3 Fab 2558 In Complex
           With Mn Peptide
          Length = 209

 Score = 29.6 bits (65), Expect = 6.7,   Method: Composition-based stats.
 Identities = 38/146 (26%), Positives = 59/146 (40%), Gaps = 9/146 (6%)

Query: 64  NLTEEGDEVGDGVVQWNNQDFHYSGHVFPWELHFTI------FNGLNQGQRQKVTAMGTA 117
           ++T  GD +GD  V W  Q    S  +  +E           F+G   G    +T  GT 
Sbjct: 19  SITCSGDILGDKYVSWYQQKSGQSPLLVIYEDTKRPSGIPDRFSGSKSGNTATLTISGTQ 78

Query: 118 TLNLAKYANSDKEKELQIKVPLTVSGDTIEGDPYLCLSFRLIESRFAQESLQAGQRSIVP 177
            ++ A Y     +  L + V    +  T+ G P    S  L     + E LQA + ++V 
Sbjct: 79  AMDEADYYCQAWDSTLGV-VFGGGTKVTVLGQPKAAPSVTLFPP--SSEELQANKATLVC 135

Query: 178 LTTSPTSGEAVPMGKDELSAVKAGLQ 203
           L +    G      K + S VKAG++
Sbjct: 136 LISDFYPGAVTVAWKADSSPVKAGVE 161


>pdb|4DAG|L Chain L, Structure Of The Human Metapneumovirus Fusion Protein With
           Neutralizing Antibody Identifies A Pneumovirus Antigenic
           Site
          Length = 213

 Score = 28.9 bits (63), Expect = 9.7,   Method: Composition-based stats.
 Identities = 36/146 (24%), Positives = 58/146 (39%), Gaps = 10/146 (6%)

Query: 64  NLTEEGDEVGDGVVQWNNQDFHYSGHVFPWELHF------TIFNGLNQGQRQKVTAMGTA 117
           ++T  GD++GD    W  Q    S  +  ++           F+G N G    +T  GT 
Sbjct: 19  SITCSGDKLGDKYASWYQQKPGQSPVLVIYQDSERPSGIPERFSGSNSGNTATLTISGTQ 78

Query: 118 TLNLAKYANSDKEKELQIKVPLTVSGDTIEGDPYLCLSFRLIESRFAQESLQAGQRSIVP 177
            ++ A Y     +    +    T    T+ G P    S  L     + E LQA + ++V 
Sbjct: 79  AMDEADYYCQAWDSSTAVFGGGTTL--TVLGQPKAAPSVTLFPP--SSEELQANKATLVC 134

Query: 178 LTTSPTSGEAVPMGKDELSAVKAGLQ 203
           L +    G      K + S VKAG++
Sbjct: 135 LISDFYPGAVTVAWKADSSPVKAGVE 160


  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
   0.318    0.134    0.402 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,528,308
Number of Sequences: 62578
Number of extensions: 848789
Number of successful extensions: 2229
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: 2220
Number of HSP's gapped (non-prelim): 12
length of query: 701
length of database: 14,973,337
effective HSP length: 106
effective length of query: 595
effective length of database: 8,340,069
effective search space: 4962341055
effective search space used: 4962341055
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)