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= 030809
         (171 letters)

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

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



>pdb|3BBO|Z Chain Z, Homology Model For The Spinach Chloroplast 50s Subunit
           Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome
          Length = 173

 Score =  159 bits (403), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 94/159 (59%), Positives = 110/159 (69%), Gaps = 4/159 (2%)

Query: 3   MSLSIAS--TTTITFPTEPFSKIPKSTFNGVQIRQSWPIRTPLRFATXXXXXXXXXAVVM 60
           +SLSIA+  T  I       +    S+F+GV+I+     R P   A          +VVM
Sbjct: 2   LSLSIATPGTAAIFRRGTASATSTSSSFHGVRIQHQVSARVPA--AATISSSSPKPSVVM 59

Query: 61  MAKREEEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFXXXXXXXXXXLT 120
           M+KRE E+KEIR+KTTE++ EEVVDLKGELFMLRLQKS RNEFKSS+F          LT
Sbjct: 60  MSKREAELKEIRSKTTEQLQEEVVDLKGELFMLRLQKSARNEFKSSDFRRMKKQVARMLT 119

Query: 121 VKRERELEEGINKRLSRKLDRQWKKSIVVRPPPSLKKLQ 159
           VKRERE++EGI KRLSRKLDRQWKKSIV RPPPSLKKLQ
Sbjct: 120 VKREREIKEGIKKRLSRKLDRQWKKSIVPRPPPSLKKLQ 158


>pdb|1S1I|X Chain X, 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, 1s1i, Contains 60s Subunit. The 40s Ribosomal
          Subunit Is In File 1s1h.
 pdb|2WW9|N Chain N, Cryo-Em Structure Of The Active Yeast Ssh1 Complex Bound
          To The Yeast 80s Ribosome
 pdb|2WWA|N Chain N, Cryo-Em Structure Of Idle Yeast Ssh1 Complex Bound To
          The Yeast 80s Ribosome
 pdb|2WWB|N Chain N, Cryo-Em Structure Of The Mammalian Sec61 Complex Bound
          To The Actively Translating Wheat Germ 80s Ribosome
 pdb|3IZS|CC Chain c, Localization Of The Large Subunit Ribosomal Proteins
          Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
          Translating 80s Ribosome
 pdb|3O58|CC Chain c, Yeast 80s Ribosome. This Entry Consists Of The 60s
          Subunit Of The First 80s In The Asymmetric Unit.
 pdb|3O5H|CC Chain c, Yeast 80s Ribosome. This Entry Consists Of The 60s
          Subunit Of The Second 80s In The Asymmetric Unit.
 pdb|3U5E|HH Chain h, The Structure Of The Eukaryotic Ribosome At 3.0 A
          Resolution. This Entry Contains Proteins Of The 60s
          Subunit, Ribosome A
 pdb|3U5I|HH Chain h, The Structure Of The Eukaryotic Ribosome At 3.0 A
          Resolution. This Entry Contains Proteins Of The 60s
          Subunit, Ribosome B
 pdb|4B6A|HH Chain h, Cryo-Em Structure Of The 60s Ribosomal Subunit In
          Complex With Arx1 And Rei1
          Length = 120

 Score = 29.3 bits (64), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 13/28 (46%), Positives = 21/28 (75%)

Query: 70 EIRAKTTEEINEEVVDLKGELFMLRLQK 97
          E+R K+ E++  ++VDLK EL  L++QK
Sbjct: 8  ELRTKSKEQLASQLVDLKKELAELKVQK 35


>pdb|3JYW|X Chain X, Structure Of The 60s Proteins For Eukaryotic Ribosome
          Based On Cryo-Em Map Of Thermomyces Lanuginosus
          Ribosome At 8.9a Resolution
          Length = 86

 Score = 28.9 bits (63), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 13/28 (46%), Positives = 21/28 (75%)

Query: 70 EIRAKTTEEINEEVVDLKGELFMLRLQK 97
          E+R K+ E++  ++VDLK EL  L++QK
Sbjct: 7  ELRTKSKEQLASQLVDLKKELAELKVQK 34


  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
   0.315    0.128    0.348 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,374,073
Number of Sequences: 62578
Number of extensions: 88754
Number of successful extensions: 317
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 310
Number of HSP's gapped (non-prelim): 9
length of query: 171
length of database: 14,973,337
effective HSP length: 92
effective length of query: 79
effective length of database: 9,216,161
effective search space: 728076719
effective search space used: 728076719
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 bits)