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= psy10214
         (415 letters)

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

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



>pdb|3U5C|B Chain B, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 40s
           Subunit, Ribosome A
 pdb|3U5G|B Chain B, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 40s
           Subunit, Ribosome B
          Length = 255

 Score = 29.3 bits (64), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 17/37 (45%), Positives = 24/37 (64%)

Query: 103 LLSALKPELIVKEVNMVTKDIVDLRHDLARKEELIKR 139
           L S L PE+I KE+   TKDI  L++   RK +L+K+
Sbjct: 184 LTSKLIPEVINKEIENATKDIFPLQNIHVRKVKLLKQ 220


>pdb|3HUM|A Chain A, Crystal Structure Of Penicillin Binding Protein 4 From
           Staphylococcus Aureus Col In Complex With Cefotaxime
 pdb|3HUM|B Chain B, Crystal Structure Of Penicillin Binding Protein 4 From
           Staphylococcus Aureus Col In Complex With Cefotaxime
 pdb|3HUN|A Chain A, Crystal Structure Of Penicillin Binding Protein 4 From
           Staphylococcus Aureus Col In Complex With Ampicillin
 pdb|3HUN|B Chain B, Crystal Structure Of Penicillin Binding Protein 4 From
           Staphylococcus Aureus Col In Complex With Ampicillin
          Length = 453

 Score = 28.9 bits (63), Expect = 5.9,   Method: Compositional matrix adjust.
 Identities = 23/86 (26%), Positives = 42/86 (48%), Gaps = 4/86 (4%)

Query: 111 LIVKEVNMVTKDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQSCLQVLTKEDEVSTT 170
           ++ K+V+  T D VDL ++ A+   +   H+      +N  S L+S      K+ E + T
Sbjct: 168 ILAKKVSKNTSDFVDLMNNKAKAIGMKNTHFVNPTGAEN--SRLRSFAPTKYKDQERTVT 225

Query: 171 LEKDE--IKLEIDQATLKFLDLARQM 194
             +D   + L + + T K LD  +Q+
Sbjct: 226 TARDYAILDLHVIKETPKILDFTKQL 251


>pdb|1TVF|A Chain A, Crystal Structure Of Penicillin-Binding Protein 4 (Pbp4)
           From Staphylococcus Aureus
 pdb|1TVF|B Chain B, Crystal Structure Of Penicillin-Binding Protein 4 (Pbp4)
           From Staphylococcus Aureus
          Length = 369

 Score = 28.5 bits (62), Expect = 7.0,   Method: Compositional matrix adjust.
 Identities = 23/86 (26%), Positives = 42/86 (48%), Gaps = 4/86 (4%)

Query: 111 LIVKEVNMVTKDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQSCLQVLTKEDEVSTT 170
           ++ K+V+  T D VDL ++ A+   +   H+      +N  S L+S      K+ E + T
Sbjct: 132 ILAKKVSKNTSDFVDLMNNKAKAIGMKNTHFVNPTGAEN--SRLRSFAPTKYKDQERTVT 189

Query: 171 LEKDE--IKLEIDQATLKFLDLARQM 194
             +D   + L + + T K LD  +Q+
Sbjct: 190 TARDYAILDLHVIKETPKILDFTKQL 215


  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
   0.320    0.136    0.379 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,492,621
Number of Sequences: 62578
Number of extensions: 215280
Number of successful extensions: 680
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 678
Number of HSP's gapped (non-prelim): 7
length of query: 415
length of database: 14,973,337
effective HSP length: 101
effective length of query: 314
effective length of database: 8,652,959
effective search space: 2717029126
effective search space used: 2717029126
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)