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= psy15072
         (97 letters)

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

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



>pdb|3U5C|FF Chain f, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 40s
           Subunit, Ribosome A
          Length = 152

 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 21/37 (56%), Positives = 26/37 (70%)

Query: 9   NVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGN 45
            VD  GK+ +LRREC++  CGAGVF+A   DR YCG 
Sbjct: 107 KVDAEGKVTKLRRECSNPTCGAGVFLANHKDRLYCGK 143


>pdb|3U5G|FF Chain f, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 40s
           Subunit, Ribosome B
          Length = 152

 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 21/37 (56%), Positives = 26/37 (70%)

Query: 9   NVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGN 45
            VD  GK+ +LRREC++  CGAGVF+A   DR YCG 
Sbjct: 107 KVDAEGKVTKLRRECSNPTCGAGVFLANHKDRLYCGK 143


>pdb|3ZEY|9 Chain 9, High-resolution Cryo-electron Microscopy Structure Of The
           Trypanosoma Brucei Ribosome
          Length = 153

 Score = 42.7 bits (99), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 19/37 (51%), Positives = 22/37 (59%)

Query: 9   NVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGN 45
           N D + K+ R R EC +  CGAGVFMA    R YCG 
Sbjct: 109 NDDGSFKVERTRDECPNPNCGAGVFMAQHKGRKYCGK 145


>pdb|2XZM|9 Chain 9, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit
           In Complex With Initiation Factor 1. This File Contains
           The 40s Subunit And Initiation Factor For Molecule 1
 pdb|2XZN|9 Chain 9, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit
           In Complex With Initiation Factor 1. This File Contains
           The 40s Subunit And Initiation Factor For Molecule 2
          Length = 189

 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 17/44 (38%), Positives = 27/44 (61%), Gaps = 2/44 (4%)

Query: 10  VDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVE 53
           ++ NGK+   ++ C   +CG G+FMA   DRHYCG    +L ++
Sbjct: 103 LENNGKVSLQQKGC--PKCGPGIFMAKHYDRHYCGKCHLTLKID 144


>pdb|3J20|Y Chain Y, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
          Revealed By Cryo-em: Implications For Evolution Of
          Eukaryotic Ribosomes (30s Ribosomal Subunit)
          Length = 50

 Score = 32.7 bits (73), Expect = 0.055,   Method: Compositional matrix adjust.
 Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 3/45 (6%)

Query: 1  MSNEWQVCNVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGN 45
          M  +W++  + ++GK+ R  + C   +CG GVFMA   DR  CG 
Sbjct: 1  MGQKWKLYEI-KDGKVIRKNKFCP--RCGPGVFMADHGDRWACGK 42


>pdb|2K4X|A Chain A, Solution Structure Of 30s Ribosomal Protein S27a From
          Thermoplasma Acidophilum
          Length = 55

 Score = 30.8 bits (68), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 15/33 (45%), Positives = 21/33 (63%), Gaps = 2/33 (6%)

Query: 13 NGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGN 45
          +GK+ R  R C   +CG GVF+A  +DR+ CG 
Sbjct: 11 DGKLVRKHRFCP--RCGPGVFLAEHADRYSCGR 41


  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
   0.326    0.137    0.422 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,762,997
Number of Sequences: 62578
Number of extensions: 83834
Number of successful extensions: 176
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 169
Number of HSP's gapped (non-prelim): 7
length of query: 97
length of database: 14,973,337
effective HSP length: 63
effective length of query: 34
effective length of database: 11,030,923
effective search space: 375051382
effective search space used: 375051382
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 45 (21.9 bits)