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= 032245
         (144 letters)

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

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



>pdb|2WSC|H Chain H, Improved Model Of Plant Photosystem I
 pdb|2WSE|H Chain H, Improved Model Of Plant Photosystem I
 pdb|2WSF|H Chain H, Improved Model Of Plant Photosystem I
          Length = 144

 Score =  177 bits (450), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 87/125 (69%), Positives = 99/125 (79%)

Query: 1   MASLATIAAVQPATIKGLGGSSLAGTKLTVKPTRQSFRPKSFKAGAVVAKYGDKSVYFDL 60
           MASLAT+AAVQP T+KGL GSS+AGTKL +KP RQSF+  + ++GA+VAKYGDKSVYFDL
Sbjct: 1   MASLATLAAVQPTTLKGLAGSSIAGTKLHIKPARQSFKLNNVRSGAIVAKYGDKSVYFDL 60

Query: 61  EDLGNTTGQWDLYGSDAPSPYNSLQSKFFETFAAPFTKRXXXXXXXXXXXXSTLAYFSAT 120
           ED+ NTTGQWD+YGSDAPSPYNSLQSKFFETFAAPFTKR            S L Y SA 
Sbjct: 61  EDIANTTGQWDVYGSDAPSPYNSLQSKFFETFAAPFTKRGLLLKFLILGGGSLLTYVSAN 120

Query: 121 ASGDI 125
           A  D+
Sbjct: 121 APQDV 125


>pdb|3LW5|H Chain H, Improved Model Of Plant Photosystem I
          Length = 69

 Score =  100 bits (250), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 51/67 (76%), Positives = 51/67 (76%)

Query: 59  DLEDLGNTTGQWDLYGSDAPSPYNSLQSKFFETFAAPFTKRXXXXXXXXXXXXSTLAYFS 118
           DLEDLGNTTGQWD YGSDAPSPYN LQSK FETFAAPFTKR            STLAY S
Sbjct: 1   DLEDLGNTTGQWDSYGSDAPSPYNPLQSKLFETFAAPFTKRGLLLKFLILGGGSTLAYLS 60

Query: 119 ATASGDI 125
           ATASGDI
Sbjct: 61  ATASGDI 67


>pdb|2O01|H Chain H, The Structure Of A Plant Photosystem I Supercomplex At 3.4
           Angstrom Resolution
          Length = 75

 Score = 72.8 bits (177), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 36/56 (64%), Positives = 38/56 (67%)

Query: 70  WDLYGSDAPSPYNSLQSKFFETFAAPFTKRXXXXXXXXXXXXSTLAYFSATASGDI 125
           WD+YGSDAPSPYNSLQSKFFETFAAPFTKR            S L Y SA A  D+
Sbjct: 1   WDVYGSDAPSPYNSLQSKFFETFAAPFTKRGLLLKFLILGGGSLLTYVSANAPQDV 56


>pdb|1APA|A Chain A, X-Ray Structure Of A Pokeweed Antiviral Protein, Coded By
           A New Genomic Clone, At 0.23 Nm Resolution. A Model
           Structure Provides A Suitable Electrostatic Field For
           Substrate Binding
          Length = 266

 Score = 26.9 bits (58), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 21/79 (26%), Positives = 32/79 (40%), Gaps = 12/79 (15%)

Query: 14  TIKGLGGSSLAGTKLTVKPTRQSFRPKSFKAGAVVAK------------YGDKSVYFDLE 61
           T+K  G   L  T LT K    + +  S K   ++ K            Y  K  Y   +
Sbjct: 36  TLKCYGIPMLPNTNLTPKYLLVTLQDSSLKTITLMLKRNNLYVMGYADTYNGKCRYHIFK 95

Query: 62  DLGNTTGQWDLYGSDAPSP 80
           D+ NTT + D+  +  P+P
Sbjct: 96  DISNTTERNDVMTTLCPNP 114


  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
   0.315    0.129    0.369 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,185,371
Number of Sequences: 62578
Number of extensions: 117562
Number of successful extensions: 241
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 238
Number of HSP's gapped (non-prelim): 5
length of query: 144
length of database: 14,973,337
effective HSP length: 89
effective length of query: 55
effective length of database: 9,403,895
effective search space: 517214225
effective search space used: 517214225
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: 46 (22.3 bits)