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= 028765
         (204 letters)

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

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



>pdb|2VU4|A Chain A, Structure Of Psbp Protein From Spinacia Oleracea At 1.98 A
           Resolution
          Length = 190

 Score =  191 bits (485), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 103/187 (55%), Positives = 114/187 (60%), Gaps = 60/187 (32%)

Query: 77  AYGESANVFGKPKTNTDFLPYNGDGFKLSIPSKWNPSKEREFPGQVLRYEDNFDSNTNIL 136
           AYGE+ANVFGKPK NT+F+PYNGDGFKL +PSKWNPSKE+EFPGQVLRYEDNFD+ +N L
Sbjct: 5   AYGEAANVFGKPKKNTEFMPYNGDGFKLLVPSKWNPSKEKEFPGQVLRYEDNFDATSN-L 63

Query: 137 EASVRP-----------PYYFLS------------------------------------- 148
              V+P           P  FLS                                     
Sbjct: 64  SVLVQPTDKKSITDFGSPEDFLSQVDYLLGKQAYFGKTDSEGGFDSGVVASANVLESSTP 123

Query: 149 -----------VLTRTADGDEGGKHQLITATVKGGKLYICKAQAGDKRWFKGTRKYVEST 197
                      VLTRTADGDEGGKHQ+I ATVK GKLYICKAQAGDKRWFKG +K+VES 
Sbjct: 124 VVDGKQYYSITVLTRTADGDEGGKHQVIAATVKDGKLYICKAQAGDKRWFKGAKKFVESA 183

Query: 198 ASSFSVA 204
            SSFSVA
Sbjct: 184 TSSFSVA 190


>pdb|1V2B|A Chain A, Crystal Structure Of Psbp Protein In The Oxygen-Evolving
           Complex Of Photosystem Ii From Higher Plants
 pdb|1V2B|B Chain B, Crystal Structure Of Psbp Protein In The Oxygen-Evolving
           Complex Of Photosystem Ii From Higher Plants
          Length = 177

 Score =  168 bits (426), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 90/177 (50%), Positives = 106/177 (59%), Gaps = 58/177 (32%)

Query: 86  GKPKTNTDFLPYNGDGFKLSIPSKWNPSKEREFPGQVLRYEDN----------------- 128
           GKPKT+TDF  YNGDGFKL IPSKWNP+KE E+PGQVLR+EDN                 
Sbjct: 1   GKPKTDTDFQTYNGDGFKLQIPSKWNPNKEVEYPGQVLRFEDNFDATSNVIVAITPTDKK 60

Query: 129 ---------------------------------FDSNT----NILEASVRP----PYYFL 147
                                            F+S+     N+LE S        YY+L
Sbjct: 61  SITDFGSPEQFLSQVDYLLGRQAYSGKTDSEGGFESDAVAIANVLETSTAEVGGKQYYYL 120

Query: 148 SVLTRTADGDEGGKHQLITATVKGGKLYICKAQAGDKRWFKGTRKYVESTASSFSVA 204
           S+LTRTADG+EGGKHQL+TATV  GKLYICKAQAGDKRWFKG +K+VE+TA+SFS+A
Sbjct: 121 SILTRTADGNEGGKHQLVTATVNDGKLYICKAQAGDKRWFKGAKKFVENTATSFSLA 177


>pdb|2XB3|A Chain A, The Structure Of Cyanobacterial Psbp
          Length = 165

 Score = 30.4 bits (67), Expect = 0.71,   Method: Compositional matrix adjust.
 Identities = 20/62 (32%), Positives = 32/62 (51%), Gaps = 3/62 (4%)

Query: 144 YYFLS-VLTRTADGDEGG-KHQLITATVKGGKLYICKAQAGDKRWFKGTRKYVESTASSF 201
           YY L   +T   DG+    +H L +  V  GK+Y     A ++RW K   ++ ++  SSF
Sbjct: 104 YYILEYAVTLPGDGNTAQQRHNLSSIAVSRGKVYTLSVSAPEERWPKVEDQF-KTIVSSF 162

Query: 202 SV 203
           +V
Sbjct: 163 TV 164


>pdb|2LNJ|A Chain A, Solution Structure Of Cyanobacterial Psbp (Cyanop) From
           Synechocystis Sp. Pcc 6803
          Length = 170

 Score = 27.7 bits (60), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 19/60 (31%), Positives = 25/60 (41%), Gaps = 3/60 (5%)

Query: 144 YYFLSVLTRTADGDEGGKHQLITATVKGGKLYICKAQAGDKRWFKGTRKYVESTASSFSV 203
           YY L    R   GD   +H L + T   GKL        + RW    +   ++ ASSF V
Sbjct: 113 YYTLEY--RVLVGDNVERHDLASVTTNRGKLITFDLSTAEDRW-DTVKSLFDTVASSFHV 169


  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
   0.314    0.129    0.376 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,263,405
Number of Sequences: 62578
Number of extensions: 254672
Number of successful extensions: 484
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 480
Number of HSP's gapped (non-prelim): 9
length of query: 204
length of database: 14,973,337
effective HSP length: 94
effective length of query: 110
effective length of database: 9,091,005
effective search space: 1000010550
effective search space used: 1000010550
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)