BLASTP 2.2.18 [Mar-02-2008]


Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, 
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. Schäffer, and Yi-Kuo Yu (2005) "Protein database
searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.

Query= SODEF17
         (71 letters)

Database: pdb_seqres.txt 
           148,210 sequences; 34,549,591 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

1gps_A mol:protein length:47  GAMMA-1-P THIONIN                        37   0.009
1gpt_A mol:protein length:47  GAMMA-1-H THIONIN                        35   0.016
1mr4_A mol:protein length:47  Nicotiana alata plant defensin 1 (...    35   0.021

>1gps_A mol:protein length:47  GAMMA-1-P THIONIN
          Length = 47

 Score = 36.6 bits (83), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 19/50 (38%), Positives = 30/50 (60%), Gaps = 4/50 (8%)

Query: 8  ICKSRSHEYKGRCIQDMDCNAACVKESESYTGGFCNGRPPFKQCFCTKPC 57
          IC+ RS  +KG C+ + +C   C  + E + GG C+G  PF++C C + C
Sbjct: 2  ICRRRSAGFKGPCMSNKNCAQVC--QQEGWGGGNCDG--PFRRCKCIRQC 47



>1gpt_A mol:protein length:47  GAMMA-1-H THIONIN
          Length = 47

 Score = 35.4 bits (80), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 18/50 (36%), Positives = 30/50 (60%), Gaps = 4/50 (8%)

Query: 8  ICKSRSHEYKGRCIQDMDCNAACVKESESYTGGFCNGRPPFKQCFCTKPC 57
          IC+ RS  +KG C+ + +C   C++  E + GG C+G  P ++C C + C
Sbjct: 2  ICRRRSAGFKGPCVSNKNCAQVCMQ--EGWGGGNCDG--PLRRCKCMRRC 47



>1mr4_A mol:protein length:47  Nicotiana alata plant defensin 1
          (NaD1)
          Length = 47

 Score = 35.0 bits (79), Expect = 0.021,   Method: Compositional matrix adjust.
 Identities = 20/49 (40%), Positives = 28/49 (57%), Gaps = 4/49 (8%)

Query: 9  CKSRSHEYKGRCIQDMDCNAACVKESESYTGGFCNGRPPFKQCFCTKPC 57
          CK+ S+ + G CI    C  AC+  SE +T G C+     ++C CTKPC
Sbjct: 3  CKTESNTFPGICITKPPCRKACI--SEKFTDGHCSK--ILRRCLCTKPC 47



  Database: pdb_seqres.txt
    Posted date:  Feb 4, 2010  7:32 PM
  Number of letters in database: 34,549,591
  Number of sequences in database:  148,210
  
Lambda     K      H
   0.323    0.136    0.486 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 148210
Number of Hits to DB: 5,965,613
Number of extensions: 245324
Number of successful extensions: 178
Number of sequences better than 1.0e-01: 3
Number of HSP's gapped: 178
Number of HSP's successfully gapped: 3
Length of query: 71
Length of database: 34,549,591
Length adjustment: 41
Effective length of query: 30
Effective length of database: 28,472,981
Effective search space: 854189430
Effective search space used: 854189430
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 74 (33.1 bits)