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= psy3587
         (195 letters)

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

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



>pdb|3CNL|A Chain A, Crystal Structure Of Gnp-Bound Ylqf From T. Maritima
 pdb|3CNN|A Chain A, Gtp-Bound Structure Of Tm Ylqf
 pdb|3CNO|A Chain A, Gdp-Bound Structue Of Tm Ylqf
          Length = 262

 Score = 34.7 bits (78), Expect = 0.036,   Method: Compositional matrix adjust.
 Identities = 16/56 (28%), Positives = 31/56 (55%), Gaps = 3/56 (5%)

Query: 45  SVSRTPGHTKHFQTIFLTDNIRLCDCPGLVFPSKVPKPLQ---VLMGSFPIAQLRE 97
           SV   PG TK  Q   L + +++ D PG+++ +   + L    +L+GS P+ ++ +
Sbjct: 126 SVGAQPGITKGIQWFSLENGVKILDTPGILYKNIFSEDLAAKLLLVGSLPVERIED 181



 Score = 29.3 bits (64), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 11/33 (33%), Positives = 19/33 (57%)

Query: 3   SVSRTPGHTKHFQTIFLTDNIRLCDCPGLVFPS 35
           SV   PG TK  Q   L + +++ D PG+++ +
Sbjct: 126 SVGAQPGITKGIQWFSLENGVKILDTPGILYKN 158


>pdb|1PUI|A Chain A, Structure Of Engb Gtpase
 pdb|1PUI|B Chain B, Structure Of Engb Gtpase
          Length = 210

 Score = 32.3 bits (72), Expect = 0.16,   Method: Compositional matrix adjust.
 Identities = 23/83 (27%), Positives = 36/83 (43%), Gaps = 20/83 (24%)

Query: 47  SRTPGHTKHFQTIFLTDNIRLCDCPGLVF---PSKVPKPLQVLMGSFPIAQLREPYSTVQ 103
           S+TPG T+      + D  RL D PG  +   P ++ +  Q  +G              +
Sbjct: 56  SKTPGRTQLINLFEVADGKRLVDLPGYGYAEVPEEMKRKWQRALG--------------E 101

Query: 104 YLAERMD---LIKLLHIKHPDDD 123
           YL +R     L+ L+ I+HP  D
Sbjct: 102 YLEKRQSLQGLVVLMDIRHPLKD 124


>pdb|3BWW|A Chain A, Crystal Structure Of A Duf692 Family Protein (Hs_1138)
           From Haemophilus Somnus 129pt At 2.20 A Resolution
          Length = 307

 Score = 27.7 bits (60), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 13/54 (24%), Positives = 24/54 (44%), Gaps = 1/54 (1%)

Query: 4   VSRTPGHTKHFQTIFLTDNIRLCDCPGLVFPSKVPKPLQVVSVSRTPGHTKHFQ 57
           +S      K + T F +D++  C+C G ++   +P P    +V  T    +  Q
Sbjct: 77  LSSIKAXIKQYNTPFFSDHLSFCECDGHLY-DLLPXPFTDEAVKHTAARIREVQ 129



 Score = 27.7 bits (60), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 17/68 (25%), Positives = 28/68 (41%), Gaps = 1/68 (1%)

Query: 30  GLVFPSKVPKPLQVVSVSRTPGHTKHFQTIFLTDNIRLCDCPGLVFPSKVPKPLQVLMGS 89
           GL        PL    +S      K + T F +D++  C+C G ++   +P P       
Sbjct: 61  GLSLSLGGQAPLDKELLSSIKAXIKQYNTPFFSDHLSFCECDGHLY-DLLPXPFTDEAVK 119

Query: 90  FPIAQLRE 97
              A++RE
Sbjct: 120 HTAARIRE 127


  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
   0.324    0.138    0.439 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,815,134
Number of Sequences: 62578
Number of extensions: 215970
Number of successful extensions: 567
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 564
Number of HSP's gapped (non-prelim): 6
length of query: 195
length of database: 14,973,337
effective HSP length: 94
effective length of query: 101
effective length of database: 9,091,005
effective search space: 918191505
effective search space used: 918191505
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 bits)