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= psy17953
         (234 letters)

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

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



>pdb|3U5C|G Chain G, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 40s
           Subunit, Ribosome A
 pdb|3U5G|G Chain G, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 40s
           Subunit, Ribosome B
 pdb|3J16|C Chain C, Models Of Ribosome-Bound Dom34p And Rli1p And Their
           Ribosomal Binding Partners
          Length = 236

 Score =  149 bits (377), Expect = 9e-37,   Method: Compositional matrix adjust.
 Identities = 78/119 (65%), Positives = 93/119 (78%), Gaps = 10/119 (8%)

Query: 15  RVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDSNLSVLALVVVRKGEQEIPGLTDTTIPR 74
           R++LLL+K  SCYRPRR GERKRKSVRG IV  +L+VLALV+V+KGEQE+ GLTDTT+P+
Sbjct: 72  RIKLLLTKNVSCYRPRRDGERKRKSVRGAIVGPDLAVLALVIVKKGEQELEGLTDTTVPK 131

Query: 75  RLGPKRASKIRKLFNLSKEDDVRQYVIKRTLPPKPAKEGKKKVRKLY-KAPKIQRLITP 132
           RLGPKRA+ IRK F LSKEDDVR +VI+R +          K  K Y KAPKIQRL+TP
Sbjct: 132 RLGPKRANNIRKFFGLSKEDDVRDFVIRREVT---------KGEKTYTKAPKIQRLVTP 181


>pdb|2XZM|Y Chain Y, 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|Y Chain Y, 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 = 293

 Score =  129 bits (324), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 74/121 (61%), Positives = 90/121 (74%), Gaps = 10/121 (8%)

Query: 15  RVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDSNLSVLALVVVRKGEQEIPGLTDTTIPR 74
           RVRLLLS+GHSC+  RR+G RKRKSVRGCIV  ++ VLAL +V+KG  EI GLT  T+PR
Sbjct: 72  RVRLLLSEGHSCFTSRRSGFRKRKSVRGCIVGPDMRVLALQIVKKGVAEIDGLTTVTLPR 131

Query: 75  RLGPKRASKIRKLFNLSKEDD---VRQYVIKRTLPPKPAKEGKKKVRKLYKAPKIQRLIT 131
           +LGPKRA+ I+KLF L KEDD   +++ VI+RT   K AK GK +     K PKIQRLIT
Sbjct: 132 KLGPKRANNIKKLFGLKKEDDPILIKKSVIRRTF--KTAK-GKDRT----KCPKIQRLIT 184

Query: 132 P 132
           P
Sbjct: 185 P 185


>pdb|3ZEY|3 Chain 3, High-resolution Cryo-electron Microscopy Structure Of The
           Trypanosoma Brucei Ribosome
          Length = 250

 Score =  122 bits (305), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 68/120 (56%), Positives = 87/120 (72%), Gaps = 9/120 (7%)

Query: 15  RVRLLLSKGHSCYRPRR--TGERKRKSVRGCIVDSNLSVLALVVVRKGEQEIPGLTDTTI 72
           RV LL+ +G   +   R   GER+RKS+RGCI+ S+++VL + V + GEQ I G+TD ++
Sbjct: 73  RVSLLVKRGAVGFNTFRGYQGERRRKSLRGCILGSDIAVLNVTVEKVGEQPIEGVTDVSV 132

Query: 73  PRRLGPKRASKIRKLFNLSKEDDVRQYVIKRTLPPKPAKEGKKKVRKLYKAPKIQRLITP 132
           PRRLGPKRA+KIRKLFNL + DDVR+YVI+R    K  KEGKK     +KAPKIQRLIT 
Sbjct: 133 PRRLGPKRANKIRKLFNLGRTDDVRKYVIRR----KVTKEGKK---DRFKAPKIQRLITS 185


>pdb|3J20|G Chain G, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
           Revealed By Cryo-em: Implications For Evolution Of
           Eukaryotic Ribosomes (30s Ribosomal Subunit)
          Length = 125

 Score = 37.0 bits (84), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 18/32 (56%), Positives = 25/32 (78%), Gaps = 1/32 (3%)

Query: 14  RRVRLLLSKGHSCYRPRRTGERKRKSVRGCIV 45
           RRVR+LLSKG   +RP+  GER++K+VRG  +
Sbjct: 82  RRVRVLLSKG-PGFRPKEKGERRKKTVRGNTI 112


  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    0.137    0.407 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,777,947
Number of Sequences: 62578
Number of extensions: 125555
Number of successful extensions: 339
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 332
Number of HSP's gapped (non-prelim): 4
length of query: 234
length of database: 14,973,337
effective HSP length: 96
effective length of query: 138
effective length of database: 8,965,849
effective search space: 1237287162
effective search space used: 1237287162
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: 50 (23.9 bits)