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= 042287
         (97 letters)

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

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



>pdb|3IZ6|Z Chain Z, Localization Of The Small Subunit Ribosomal Proteins
          Into A 5.5 A Cryo-Em Map Of Triticum Aestivum
          Translating 80s Ribosome
          Length = 62

 Score =  102 bits (253), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 52/62 (83%), Positives = 52/62 (83%)

Query: 36 MGKVHGSLARAGKVRGQTPXXXXXXXXXXPRGRAHKRMQYNRRFVTAVVGFGKKRGPNSS 95
          MGKVHGSLARAGKVRGQTP          PRGRAHKRMQYNRRFVTAVVGFGKKRGPNSS
Sbjct: 1  MGKVHGSLARAGKVRGQTPKVAKQDKKKKPRGRAHKRMQYNRRFVTAVVGFGKKRGPNSS 60

Query: 96 EK 97
          EK
Sbjct: 61 EK 62


>pdb|3ZEY|Y Chain Y, High-resolution Cryo-electron Microscopy Structure Of
          The Trypanosoma Brucei Ribosome
          Length = 66

 Score = 59.3 bits (142), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 28/54 (51%), Positives = 36/54 (66%)

Query: 36 MGKVHGSLARAGKVRGQTPXXXXXXXXXXPRGRAHKRMQYNRRFVTAVVGFGKK 89
          MGKVHGSLARAGKV+ QTP          PRGRA KR++Y +R++   +  G+K
Sbjct: 1  MGKVHGSLARAGKVKNQTPKVSKQEKKKQPRGRAFKRLKYTQRYLAKTLKAGEK 54


>pdb|3IZB|Z Chain Z, Localization Of The Small Subunit Ribosomal Proteins
          Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
          Translating 80s Ribosome
 pdb|3U5C|EE Chain e, The Structure Of The Eukaryotic Ribosome At 3.0 A
          Resolution. This Entry Contains Proteins Of The 40s
          Subunit, Ribosome A
 pdb|3U5G|EE Chain e, The Structure Of The Eukaryotic Ribosome At 3.0 A
          Resolution. This Entry Contains Proteins Of The 40s
          Subunit, Ribosome B
 pdb|3J16|E Chain E, Models Of Ribosome-Bound Dom34p And Rli1p And Their
          Ribosomal Binding Partners
          Length = 63

 Score = 55.5 bits (132), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 30/55 (54%), Positives = 36/55 (65%)

Query: 36 MGKVHGSLARAGKVRGQTPXXXXXXXXXXPRGRAHKRMQYNRRFVTAVVGFGKKR 90
          M KVHGSLARAGKV+ QTP          P+GRA+KR+ Y RRFV   +  GK+R
Sbjct: 1  MAKVHGSLARAGKVKSQTPKVEKTEKPKKPKGRAYKRLLYTRRFVNVTLVNGKRR 55


>pdb|2XZM|X Chain X, 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|X Chain X, 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 = 80

 Score = 51.2 bits (121), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 26/61 (42%), Positives = 39/61 (63%), Gaps = 3/61 (4%)

Query: 36 MGKVHGSLARAGKVRGQTPXXXXXXX-XXXPRGRAHKRMQYNRRFVTAVVGFG--KKRGP 92
          MG++HG+LA+AGKVR QTP           P+GR++KR+ YNRR+   ++     K++ P
Sbjct: 1  MGRMHGTLAKAGKVRKQTPKVEKKDKPRKTPKGRSYKRILYNRRYAPHILATDPKKRKSP 60

Query: 93 N 93
          N
Sbjct: 61 N 61


>pdb|3J0L|X Chain X, Core Of Mammalian 80s Pre-Ribosome In Complex With Trnas
          Fitted To A 9.8a Cryo-Em Map: Classic Pre State 1
 pdb|3J0O|X Chain X, Core Of Mammalian 80s Pre-Ribosome In Complex With Trnas
          Fitted To A 9a Cryo-Em Map: Classic Pre State 2
 pdb|3J0P|X Chain X, Core Of Mammalian 80s Pre-Ribosome In Complex With Trnas
          Fitted To A 10.6a Cryo-Em Map: Rotated Pre State 1
 pdb|3J0Q|X Chain X, Core Of Mammalian 80s Pre-Ribosome In Complex With Trnas
          Fitted To A 10.6a Cryo-Em Map: Rotated Pre State 2
          Length = 68

 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/55 (40%), Positives = 33/55 (60%), Gaps = 3/55 (5%)

Query: 42 SLARAGKVRGQTPXXXXXXX-XXXPRGRAHKRMQYNRRFVTAVVGFG--KKRGPN 93
          +LA+AGKVR QTP           P+GR++KR+ YNRR+   ++     K++ PN
Sbjct: 1  TLAKAGKVRKQTPKVEKKDKPRKTPKGRSYKRILYNRRYAPHILATDPKKRKSPN 55


  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
   0.321    0.135    0.405 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,164,140
Number of Sequences: 62578
Number of extensions: 53522
Number of successful extensions: 64
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 57
Number of HSP's gapped (non-prelim): 5
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: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)