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= psy4238
         (67 letters)

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

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



>pdb|3IZ6|C Chain C, Localization Of The Small Subunit Ribosomal Proteins Into
           A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
           Ribosome
          Length = 195

 Score = 72.0 bits (175), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 33/45 (73%), Positives = 40/45 (88%)

Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRK 53
           RV +Q+VNIPSF+VR++S+KHIDFSL SPFGGG  GRVKRKN +K
Sbjct: 137 RVGRQIVNIPSFMVRVESEKHIDFSLTSPFGGGPPGRVKRKNQKK 181


>pdb|3IZB|C Chain C, Localization Of The Small Subunit Ribosomal Proteins Into
           A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
           Translating 80s Ribosome
 pdb|3O2Z|E Chain E, Yeast 80s Ribosome. This Entry Consists Of The 40s Subunit
           Of The First 80s In The Asymmetric Unit.
 pdb|3O30|E Chain E, Yeast 80s Ribosome. This Entry Consists Of The 40s Subunit
           Of The Second 80s In The Asymmetric Unit.
 pdb|3U5C|J Chain J, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 40s
           Subunit, Ribosome A
 pdb|3U5G|J Chain J, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 40s
           Subunit, Ribosome B
          Length = 197

 Score = 65.1 bits (157), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 28/39 (71%), Positives = 33/39 (84%)

Query: 12  KQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKN 50
           KQ+VNIPSF+VRLDS+KHIDF+  SPFGG   GRV R+N
Sbjct: 138 KQIVNIPSFMVRLDSEKHIDFAPTSPFGGARPGRVARRN 176


>pdb|1S1H|D Chain D, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex From
           Yeast Obtained By Docking Atomic Models For Rna And
           Protein Components Into A 11.7 A Cryo-Em Map. This File,
           1s1h, Contains 40s Subunit. The 60s Ribosomal Subunit Is
           In File 1s1i
          Length = 179

 Score = 64.7 bits (156), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 28/39 (71%), Positives = 33/39 (84%)

Query: 12  KQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKN 50
           KQ+VNIPSF+VRLDS+KHIDF+  SPFGG   GRV R+N
Sbjct: 120 KQIVNIPSFMVRLDSEKHIDFAPTSPFGGARPGRVARRN 158


>pdb|2XZM|D Chain D, 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|D Chain D, 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 = 181

 Score = 58.9 bits (141), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 27/45 (60%), Positives = 34/45 (75%)

Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRK 53
           +V K +VN+PSF+VR DS+K IDF+  SP GGG  GR KRKN +K
Sbjct: 135 KVGKNLVNVPSFMVRTDSEKSIDFASTSPLGGGREGRTKRKNAKK 179


>pdb|3ZEY|6 Chain 6, High-resolution Cryo-electron Microscopy Structure Of The
           Trypanosoma Brucei Ribosome
          Length = 190

 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 24/39 (61%), Positives = 29/39 (74%)

Query: 10  VRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKR 48
           V KQ+V IPSF+VR+ S+ HI F+  SPFG G  GRVKR
Sbjct: 135 VAKQIVTIPSFIVRVSSEHHIAFADASPFGNGRPGRVKR 173


>pdb|3JYV|D Chain D, Structure Of The 40s Rrna And Proteins And PE TRNA FOR
           EUKARYOTIC Ribosome Based On Cryo-Em Map Of Thermomyces
           Lanuginosus Ribosome At 8.9a Resolution
          Length = 158

 Score = 48.9 bits (115), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 20/26 (76%), Positives = 24/26 (92%)

Query: 12  KQVVNIPSFVVRLDSQKHIDFSLNSP 37
           KQ+VNIPSF+VRLDS+KHIDF+  SP
Sbjct: 133 KQIVNIPSFMVRLDSEKHIDFAPTSP 158


  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    0.144    0.432 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,688,589
Number of Sequences: 62578
Number of extensions: 50296
Number of successful extensions: 94
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 88
Number of HSP's gapped (non-prelim): 6
length of query: 67
length of database: 14,973,337
effective HSP length: 38
effective length of query: 29
effective length of database: 12,595,373
effective search space: 365265817
effective search space used: 365265817
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)