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= 029020
         (200 letters)

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

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



>pdb|1XIZ|A Chain A, Structural Genomics, The Crystal Structure Of Domain Iia
           Of Putative Phosphotransferase System Specific For
           MannitolFRUCTOSE FROM SALMONELLA TYPHIMURIUM
 pdb|1XIZ|B Chain B, Structural Genomics, The Crystal Structure Of Domain Iia
           Of Putative Phosphotransferase System Specific For
           MannitolFRUCTOSE FROM SALMONELLA TYPHIMURIUM
          Length = 159

 Score = 29.3 bits (64), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 15/41 (36%), Positives = 20/41 (48%)

Query: 143 NVQTWVSAALTDDDTCLDGLAALDGEVKDSIRTRVSNVAEV 183
           NV  W+   + D+D     L   D E+  SI TR+S   EV
Sbjct: 119 NVLGWIMDVIQDEDFMQQLLVMNDDEIYQSIYTRISERGEV 159


>pdb|3LF6|A Chain A, Crystal Structure Of Hiv Epitope-Scaffold
           4e10_1xiza_s0_001_n
 pdb|3LF6|B Chain B, Crystal Structure Of Hiv Epitope-Scaffold
           4e10_1xiza_s0_001_n
          Length = 161

 Score = 28.5 bits (62), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 14/38 (36%), Positives = 20/38 (52%)

Query: 141 ISNVQTWVSAALTDDDTCLDGLAALDGEVKDSIRTRVS 178
           I+NV  W+   + D+D     L   D E+  SI TR+S
Sbjct: 123 ITNVLWWIMDVIQDEDFMQQLLVMNDDEIYQSIYTRIS 160


>pdb|1ZUN|B Chain B, Crystal Structure Of A Gtp-Regulated Atp Sulfurylase
           Heterodimer From Pseudomonas Syringae
          Length = 434

 Score = 28.5 bits (62), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 27/98 (27%), Positives = 41/98 (41%), Gaps = 12/98 (12%)

Query: 12  PVLCIMGMAKAGTITELPSHNGDSIFIETSCKSTRYRTVCVQSLLPYAYKIQRSPLQMAL 71
           P L   G A  GT+     H GD I +  S KS+R     V+S++ +        L+ A 
Sbjct: 254 PNLNFRGFA--GTLASGIVHKGDEIVVLPSGKSSR-----VKSIVTF-----EGELEQAG 301

Query: 72  EALSVSLSRTKSADSFVSNLVKHKDLKPREQQPIDDCL 109
              +V+L+     D    +L+ H D  P+     D  L
Sbjct: 302 PGQAVTLTXEDEIDISRGDLLVHADNVPQVSDAFDAXL 339


>pdb|3T43|A Chain A, Crystal Structure Of Hiv Epitope-Scaffold
           4e10_1xiza_s0_006_c
 pdb|3T43|B Chain B, Crystal Structure Of Hiv Epitope-Scaffold
           4e10_1xiza_s0_006_c
          Length = 162

 Score = 27.7 bits (60), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 15/41 (36%), Positives = 20/41 (48%)

Query: 141 ISNVQTWVSAALTDDDTCLDGLAALDGEVKDSIRTRVSNVA 181
           I+NV  W+   + D D     L   D E+  SI TR+S  A
Sbjct: 98  ITNVLWWIMDVIQDADFMQQLLVMNDDEIYQSIYTRISEAA 138


>pdb|4DWE|A Chain A, Crystal Structure Of A Hypothetical Protein (Bacova_03992)
           From Bacteroides Ovatus Atcc 8483 At 2.01 A Resolution
          Length = 480

 Score = 26.6 bits (57), Expect = 8.7,   Method: Compositional matrix adjust.
 Identities = 13/42 (30%), Positives = 20/42 (47%)

Query: 24  TITELPSHNGDSIFIETSCKSTRYRTVCVQSLLPYAYKIQRS 65
           T   L   NGD  +I+ + +  + RT+C QS     Y  Q +
Sbjct: 227 TCKXLAEPNGDKNYIKAALRYDKIRTLCAQSGATKLYPFQEN 268


  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    0.130    0.369 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,933,702
Number of Sequences: 62578
Number of extensions: 166731
Number of successful extensions: 540
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 526
Number of HSP's gapped (non-prelim): 22
length of query: 200
length of database: 14,973,337
effective HSP length: 94
effective length of query: 106
effective length of database: 9,091,005
effective search space: 963646530
effective search space used: 963646530
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: 49 (23.5 bits)