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= 030417
         (177 letters)

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

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



>pdb|2WSC|N Chain N, Improved Model Of Plant Photosystem I
 pdb|2WSE|N Chain N, Improved Model Of Plant Photosystem I
 pdb|2WSF|N Chain N, Improved Model Of Plant Photosystem I
          Length = 170

 Score =  123 bits (308), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 67/130 (51%), Positives = 85/130 (65%), Gaps = 7/130 (5%)

Query: 1   MAAMNSSVLACNYAISGSAGSSELNAKIVS---VSTPAVHGHKMPVIRAQQVDVSKESRG 57
           M+AMNS+VLACNYA SG    S+LNAK+ S   V++P +   K+P+I+A Q  V+ ES+ 
Sbjct: 1   MSAMNSTVLACNYARSGC---SDLNAKLTSMPSVASPQLSALKLPLIKAHQAKVT-ESKS 56

Query: 58  TDGRRXXXXXXXXXXXXXXXXXXXXXXXXGVIDEYLERSKANKELNDQKRLATSGANFAR 117
             GRR                        GVI+EYLE+SK NKELND+KRLAT+GANFAR
Sbjct: 57  DQGRRSALVYLAATLFTAAAAASNSSANAGVIEEYLEKSKTNKELNDKKRLATTGANFAR 116

Query: 118 AYTVQFGTCK 127
           AYTV+FG+CK
Sbjct: 117 AYTVEFGSCK 126


>pdb|2O01|N Chain N, The Structure Of A Plant Photosystem I Supercomplex At 3.4
           Angstrom Resolution
 pdb|3LW5|N Chain N, Improved Model Of Plant Photosystem I
          Length = 85

 Score = 77.0 bits (188), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 34/41 (82%), Positives = 40/41 (97%)

Query: 87  GVIDEYLERSKANKELNDQKRLATSGANFARAYTVQFGTCK 127
           GVI+EYLE+SK NKELND+KRLAT+GANFARAYTV+FG+CK
Sbjct: 1   GVIEEYLEKSKTNKELNDKKRLATTGANFARAYTVEFGSCK 41


  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
   0.316    0.128    0.376 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,300,725
Number of Sequences: 62578
Number of extensions: 135065
Number of successful extensions: 215
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 212
Number of HSP's gapped (non-prelim): 3
length of query: 177
length of database: 14,973,337
effective HSP length: 92
effective length of query: 85
effective length of database: 9,216,161
effective search space: 783373685
effective search space used: 783373685
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: 48 (23.1 bits)