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= 028492
         (208 letters)

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

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



>pdb|2KMF|A Chain A, Solution Structure Of Psb27 From Cyanobacterial
           Photosystem Ii
          Length = 115

 Score = 54.7 bits (130), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 31/104 (29%), Positives = 58/104 (55%), Gaps = 2/104 (1%)

Query: 103 SGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAG 162
           SG  L   Y +    ++ TLRE++ + P+D  N +   D+A+  I DY+S +R +    G
Sbjct: 8   SGTGLTGNYSQDTLTVIATLREAI-DLPQDAPNRQEVQDTARGQINDYISRYRRKGDAGG 66

Query: 163 EESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAEK 206
            +S+  ++ A+ SLA +Y+  G + P+P ++K  +  +   AE+
Sbjct: 67  LKSFTTMQTALNSLAGYYTSYG-ARPIPEKLKKRLQLEFTQAER 109


>pdb|2KND|A Chain A, Psb27 Structure From Synechocystis
          Length = 110

 Score = 54.7 bits (130), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 31/104 (29%), Positives = 58/104 (55%), Gaps = 2/104 (1%)

Query: 103 SGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAG 162
           SG  L   Y +    ++ TLRE++ + P+D  N +   D+A+  I DY+S +R +    G
Sbjct: 3   SGTGLTGNYSQDTLTVIATLREAI-DLPQDAPNRQEVQDTARGQINDYISRYRRKGDAGG 61

Query: 163 EESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAEK 206
            +S+  ++ A+ SLA +Y+  G + P+P ++K  +  +   AE+
Sbjct: 62  LKSFTTMQTALNSLAGYYTSYG-ARPIPEKLKKRLQLEFTQAER 104


>pdb|2Y6X|A Chain A, Structure Of Psb27 From Thermosynechococcus Elongatus
          Length = 113

 Score = 36.2 bits (82), Expect = 0.014,   Method: Compositional matrix adjust.
 Identities = 22/88 (25%), Positives = 49/88 (55%), Gaps = 2/88 (2%)

Query: 118 LVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLA 177
           L+ +LRE++   P++  N +     A++ + D+ + +R   ++    S++ ++ A+ SLA
Sbjct: 19  LISSLREAIAL-PENDPNKKAAQAEARKKLNDFFALYRRDDSLRSLSSFMTMQTALNSLA 77

Query: 178 SFYSKAGPSAPLPGEVKSEILNDLDTAE 205
             YS + P+ PLP ++K+ +  +    E
Sbjct: 78  GHYS-SYPNRPLPEKLKARLEQEFKQVE 104


>pdb|2UXT|A Chain A, Sufi Protein From Escherichia Coli
 pdb|2UXT|B Chain B, Sufi Protein From Escherichia Coli
 pdb|2UXV|A Chain A, Sufi Protein From Escherichia Coli
 pdb|2UXV|B Chain B, Sufi Protein From Escherichia Coli
          Length = 451

 Score = 26.9 bits (58), Expect = 8.2,   Method: Compositional matrix adjust.
 Identities = 24/97 (24%), Positives = 42/97 (43%), Gaps = 19/97 (19%)

Query: 30  SRTHVVLPPVEAASSRRHVISCSSTALVAILTFNCGLAPLPVQAE--------------D 75
           SR  V L  + A++SRR+ +  +    + +++ + G  P PV  +              D
Sbjct: 198 SRGWVRLRLLNASNSRRYQLQMNDGRPLHVISGDQGFLPAPVSVKQLSLAPGERREILVD 257

Query: 76  MSNGQD-----EKEEGVVGAIKSLFDPNEKTKSGKVL 107
           MSNG +      +   +V  I+  F+P+    S  VL
Sbjct: 258 MSNGDEVSITCGEAASIVDRIRGFFEPSSILVSTLVL 294


  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
   0.310    0.126    0.347 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,642,747
Number of Sequences: 62578
Number of extensions: 209112
Number of successful extensions: 531
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 523
Number of HSP's gapped (non-prelim): 20
length of query: 208
length of database: 14,973,337
effective HSP length: 94
effective length of query: 114
effective length of database: 9,091,005
effective search space: 1036374570
effective search space used: 1036374570
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 49 (23.5 bits)