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= psy13005
         (130 letters)

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

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



>pdb|1QLE|C Chain C, Cryo-structure Of The Paracoccus Denitrificans
           Four-subunit Cytochrome C Oxidase In The Completely
           Oxidized State Complexed With An Antibody Fv Fragment
          Length = 273

 Score = 29.3 bits (64), Expect = 0.64,   Method: Compositional matrix adjust.
 Identities = 11/25 (44%), Positives = 18/25 (72%)

Query: 16  GFVLYLASTIMFVVYLIWAFIPDSI 40
           GF+L++ S +MF V   WAFI +++
Sbjct: 89  GFILFIMSEVMFFVAWFWAFIKNAL 113


>pdb|4IQX|A Chain A, Mutant P44s P169s M296i Of Foot-and-mouth Disease Virus
           Rna-dependent Rna Polymerase
          Length = 481

 Score = 25.4 bits (54), Expect = 9.2,   Method: Composition-based stats.
 Identities = 12/29 (41%), Positives = 18/29 (62%), Gaps = 2/29 (6%)

Query: 99  DKKETVPGGIPSACDIP--ISTVCEMLYL 125
           +K+ TV GGIPS C     I+T+   +Y+
Sbjct: 287 NKRITVEGGIPSGCSATSIINTILNNIYV 315


>pdb|3NL0|A Chain A, Mutant P44s M296i Of Foot-And-Mouth Disease Virus
           Rna-Dependent Rna Polymerase
          Length = 475

 Score = 25.4 bits (54), Expect = 9.2,   Method: Composition-based stats.
 Identities = 12/29 (41%), Positives = 18/29 (62%), Gaps = 2/29 (6%)

Query: 99  DKKETVPGGIPSACDIP--ISTVCEMLYL 125
           +K+ TV GGIPS C     I+T+   +Y+
Sbjct: 287 NKRITVEGGIPSGCSATSIINTILNNIYV 315


>pdb|3KNA|A Chain A, M296i Mutant Of Foot-And-Mouth Disease Virus
           Rna-Polymerase In Complex With A Template- Primer Rna
 pdb|3KOA|A Chain A, M296i Mutant Of Foot-And-Mouth Disease Virus
           Rna-Polymerase In Complex With A Template- Primer Rna
           And Gtp
          Length = 476

 Score = 25.4 bits (54), Expect = 9.2,   Method: Composition-based stats.
 Identities = 12/29 (41%), Positives = 18/29 (62%), Gaps = 2/29 (6%)

Query: 99  DKKETVPGGIPSACDIP--ISTVCEMLYL 125
           +K+ TV GGIPS C     I+T+   +Y+
Sbjct: 287 NKRITVEGGIPSGCSATSIINTILNNIYV 315


>pdb|3KLV|A Chain A, M296i G62s Mutant Of Foot-And-Mouth Disease Virus
           Rna-Polymerase In Complex With A Template- Primer Rna
          Length = 476

 Score = 25.4 bits (54), Expect = 9.2,   Method: Composition-based stats.
 Identities = 12/29 (41%), Positives = 18/29 (62%), Gaps = 2/29 (6%)

Query: 99  DKKETVPGGIPSACDIP--ISTVCEMLYL 125
           +K+ TV GGIPS C     I+T+   +Y+
Sbjct: 287 NKRITVEGGIPSGCSATSIINTILNNIYV 315


  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
   0.323    0.139    0.438 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,552,529
Number of Sequences: 62578
Number of extensions: 114888
Number of successful extensions: 135
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 131
Number of HSP's gapped (non-prelim): 8
length of query: 130
length of database: 14,973,337
effective HSP length: 88
effective length of query: 42
effective length of database: 9,466,473
effective search space: 397591866
effective search space used: 397591866
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)