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= psy5120
         (138 letters)

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

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



>pdb|3G7S|A Chain A, Crystal Structure Of A Long-Chain-Fatty-Acid-Coa Ligase
           (Fadd1) From Archaeoglobus Fulgidus
 pdb|3G7S|B Chain B, Crystal Structure Of A Long-Chain-Fatty-Acid-Coa Ligase
           (Fadd1) From Archaeoglobus Fulgidus
          Length = 549

 Score = 28.1 bits (61), Expect = 1.7,   Method: Composition-based stats.
 Identities = 16/41 (39%), Positives = 20/41 (48%), Gaps = 2/41 (4%)

Query: 52  GEFKWAGPVHGPRNVLVNTLRATLLQLESSIIPAFMHVNWP 92
           G F WA P     NVLVNTL ++    + S +  F    WP
Sbjct: 269 GTFSWAVP--PALNVLVNTLESSNKTYDWSYLKVFATGAWP 307


>pdb|1QVR|A Chain A, Crystal Structure Analysis Of Clpb
 pdb|1QVR|B Chain B, Crystal Structure Analysis Of Clpb
 pdb|1QVR|C Chain C, Crystal Structure Analysis Of Clpb
          Length = 854

 Score = 26.9 bits (58), Expect = 3.8,   Method: Composition-based stats.
 Identities = 13/34 (38%), Positives = 17/34 (50%)

Query: 50  PTGEFKWAGPVHGPRNVLVNTLRATLLQLESSII 83
           P G F + GP    +  L  TL ATL   E ++I
Sbjct: 587 PIGSFLFLGPTGVGKTELAKTLAATLFDTEEAMI 620


>pdb|4FCT|A Chain A, Crystal Structure Of The C-Terminal Domain Of Clpb
 pdb|4FD2|A Chain A, Crystal Structure Of The C-Terminal Domain Of Clpb
 pdb|4FD2|B Chain B, Crystal Structure Of The C-Terminal Domain Of Clpb
 pdb|4FD2|D Chain D, Crystal Structure Of The C-Terminal Domain Of Clpb
          Length = 308

 Score = 26.6 bits (57), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 13/34 (38%), Positives = 17/34 (50%)

Query: 50 PTGEFKWAGPVHGPRNVLVNTLRATLLQLESSII 83
          P G F + GP    +  L  TL ATL   E ++I
Sbjct: 43 PIGSFLFLGPTGVGKTELAKTLAATLFDTEEAMI 76


>pdb|4FCV|A Chain A, Crystal Structure Of The C-Terminal Domain Of Clpb
 pdb|4FCV|B Chain B, Crystal Structure Of The C-Terminal Domain Of Clpb
 pdb|4FCV|C Chain C, Crystal Structure Of The C-Terminal Domain Of Clpb
 pdb|4FCW|A Chain A, Crystal Structure Of The C-Terminal Domain Of Clpb
 pdb|4FCW|C Chain C, Crystal Structure Of The C-Terminal Domain Of Clpb
 pdb|4FCW|F Chain F, Crystal Structure Of The C-Terminal Domain Of Clpb
          Length = 311

 Score = 25.8 bits (55), Expect = 8.0,   Method: Compositional matrix adjust.
 Identities = 13/34 (38%), Positives = 16/34 (47%)

Query: 50 PTGEFKWAGPVHGPRNVLVNTLRATLLQLESSII 83
          P G F + GP    +  L  TL ATL   E + I
Sbjct: 46 PIGSFLFLGPTGVGKTELAKTLAATLFDTEEAXI 79


>pdb|1MEC|3 Chain 3, Conformational Variability Of A Picornavirus Capsid: Ph-
           Dependent Structural Changes Of Mengo Virus Related To
           Its Host Receptor Attachment Site And Disassembly
          Length = 231

 Score = 25.8 bits (55), Expect = 8.8,   Method: Compositional matrix adjust.
 Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 10/70 (14%)

Query: 59  PVHG-----PRNVLVNTLRATLLQLESSIIPAFMHVNWPSLRKPWISAVNTSVKARDFAR 113
           P++G     P N +V   +  L   E + IP F+    P+   P+I A NT+VK +  A 
Sbjct: 24  PIYGKTPVAPANYMVGEYKDFL---EIAQIPTFIGNKMPN-AVPYIEASNTAVKTQPLAV 79

Query: 114 AMIVLQ-ACI 122
             + L  +C+
Sbjct: 80  YQVTLSCSCL 89


  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
   0.322    0.130    0.403 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,724,568
Number of Sequences: 62578
Number of extensions: 125833
Number of successful extensions: 351
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 347
Number of HSP's gapped (non-prelim): 6
length of query: 138
length of database: 14,973,337
effective HSP length: 89
effective length of query: 49
effective length of database: 9,403,895
effective search space: 460790855
effective search space used: 460790855
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 46 (22.3 bits)