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= 028962
         (201 letters)

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

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



>pdb|2KVO|A Chain A, Solution Nmr Structure Of Photosystem Ii Reaction Center
           Psb28 Protein From Synechocystis Sp.(Strain Pcc 6803),
           Northeast Structural Genomics Consortium Target Sgr171
          Length = 120

 Score =  108 bits (270), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 51/97 (52%), Positives = 69/97 (71%), Gaps = 1/97 (1%)

Query: 75  IQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQ 134
           IQF +G  E  VP+V+L+KS++G +GMA F F EP++  +     DITG Y+ID+EG + 
Sbjct: 4   IQFSKGVAETVVPEVRLSKSKNGQSGMAKFYFLEPTIL-AKESTDDITGMYLIDDEGEII 62

Query: 135 SVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMER 171
           + +V  KF+NGRP+ IEA  I+ S  EWDRFMRFMER
Sbjct: 63  TREVKGKFINGRPTAIEATVILNSQPEWDRFMRFMER 99


>pdb|3LVT|A Chain A, The Crystal Structure Of A Protein In The Glycosyl
           Hydrolase Family 38 From Enterococcus Faecalis To 2.55a
          Length = 899

 Score = 29.6 bits (65), Expect = 1.1,   Method: Composition-based stats.
 Identities = 14/53 (26%), Positives = 31/53 (58%)

Query: 105 SFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMR 157
           +FS+   F+ +G+IG+   F+   E+  + + +V+A+  N   S ++A Y ++
Sbjct: 555 TFSKLLTFEDTGDIGNEYIFFKPTEDQGITTENVTAEITNKENSPVKASYQIK 607


>pdb|2GH9|A Chain A, Thermus Thermophilus Maltotriose Binding Protein Bound
           With Maltotriose
          Length = 386

 Score = 28.5 bits (62), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 33/129 (25%), Positives = 50/129 (38%), Gaps = 23/129 (17%)

Query: 76  QFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQS 135
           +FI G  +    D+ +T   D    MA     +  V +  G+   +T  Y+ D    LQ 
Sbjct: 45  KFILGAPQGQAADLVVTVPHDWVGEMA-----QAGVLEPVGKY--VTQAYLAD----LQG 93

Query: 136 VDVSAKFVNGR----PSRIEA-------KYIMRSPREWDRFMRFMERQMVKALLDSHLSL 184
           V V A    GR    P+  E+       KY+   PR W+ F+   ++    A     L  
Sbjct: 94  VAVEAFTFGGRLMGLPAFAESVALIYNKKYVKEPPRTWEEFLALAQKLTTGATF-GFLYN 152

Query: 185 MQKPYALFS 193
           +  PY  F 
Sbjct: 153 IGDPYFNFG 161


>pdb|3ZTH|A Chain A, Crystal Structure Of Stu0660 Of Streptococcus Thermophilus
 pdb|3ZTH|B Chain B, Crystal Structure Of Stu0660 Of Streptococcus Thermophilus
          Length = 350

 Score = 28.1 bits (61), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 10/32 (31%), Positives = 19/32 (59%)

Query: 97  GSNGMAIFSFSEPSVFDSSGEIGDITGFYMID 128
            S  ++IF + EP++ D + EI   + ++ ID
Sbjct: 48  SSEDLSIFDYEEPTILDEAREIVKRSSYHYID 79


  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    0.132    0.401 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,515,252
Number of Sequences: 62578
Number of extensions: 210474
Number of successful extensions: 450
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 444
Number of HSP's gapped (non-prelim): 7
length of query: 201
length of database: 14,973,337
effective HSP length: 94
effective length of query: 107
effective length of database: 9,091,005
effective search space: 972737535
effective search space used: 972737535
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: 49 (23.5 bits)