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= 041207
         (126 letters)

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

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



>pdb|3ZF7|N Chain N, High-resolution Cryo-electron Microscopy Structure Of The
           Trypanosoma Brucei Ribosome
          Length = 218

 Score = 74.3 bits (181), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 38/72 (52%), Positives = 50/72 (69%)

Query: 1   AAGIPKKLAPTIGVSVDHRRKNRSLEGLQSNVQRLKTYKAKLVVFPRRARKFKAGDSAPE 60
           AAG+  + A TIG+ VD RRKN+S EG+  NVQRLKTY +KLV+FP   +K + GD+  E
Sbjct: 87  AAGVKPRYARTIGIRVDRRRKNKSEEGMNINVQRLKTYMSKLVLFPLNRKKPQKGDATEE 146

Query: 61  ELATATQVQGPY 72
           E+  ATQ +  Y
Sbjct: 147 EVKAATQDRSRY 158


>pdb|4A18|U Chain U, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 26s Rrna And
           Proteins Of Molecule 1
 pdb|4A1B|U Chain U, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 26s Rrna And
           Proteins Of Molecule 3.
 pdb|4A1D|U Chain U, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 26s Rrna And
           Proteins Of Molecule 4.
 pdb|4A19|U Chain U, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 26s Rrna And
           Proteins Of Molecule 2
          Length = 206

 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 42/114 (36%), Positives = 60/114 (52%), Gaps = 4/114 (3%)

Query: 1   AAGIPKKLAPTIGVSVDHRRKNRSLEGLQSNVQRLKTYKAKLVVFPRRARKFKAG---DS 57
           AAGI    A +IG+ VDHRRKNR  E L+ N +RL  Y +KLV+FPR   K K G   D+
Sbjct: 80  AAGISAAFAQSIGIKVDHRRKNRCQESLELNKKRLLAYVSKLVLFPRHQGKAKKGLVNDT 139

Query: 58  APEELATATQVQGPYMPIAPERPTVELVKVTQDMKSFKAYDKLRIERVNERHFG 111
           A    A    +Q   +P+       + V    +++  K Y  +R E+ N++  G
Sbjct: 140 ADTSSAAQNALQTS-VPLPSVSKREKAVSNIAELRKKKVYRIIRQEKTNQKWDG 192


>pdb|3U5E|L Chain L, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 60s
           Subunit, Ribosome A
 pdb|3U5I|L Chain L, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 60s
           Subunit, Ribosome B
 pdb|4B6A|L Chain L, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
           With Arx1 And Rei1
          Length = 199

 Score = 63.9 bits (154), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 43/111 (38%), Positives = 60/111 (54%), Gaps = 11/111 (9%)

Query: 1   AAGIPKKLAPTIGVSVDHRRKNRSLEGLQSNVQRLKTYKAKLVVFPRRARKFKAGDSAPE 60
           AAG+    A TIG++VDHRR+NR+ E   +NVQRLK Y++K++VFPR  +       APE
Sbjct: 82  AAGLTAAYARTIGIAVDHRRQNRNQEIFDANVQRLKEYQSKIIVFPRNGK-------APE 134

Query: 61  ELATATQVQGPYMPIAPERPTVELVKVTQDMKSFKAYDKLRIERVNERHFG 111
             A          PIA     VE   V  + +S  A+  LR+ R  ++  G
Sbjct: 135 --AEQVLSAAATFPIAQPATDVEARAVQDNGES--AFRTLRLARSEKKFRG 181


>pdb|2CDU|A Chain A, The Crystal Structure Of Water-Forming Nad(P)h Oxidase
           From Lactobacillus Sanfranciscensis
 pdb|2CDU|B Chain B, The Crystal Structure Of Water-Forming Nad(P)h Oxidase
           From Lactobacillus Sanfranciscensis
          Length = 452

 Score = 25.8 bits (55), Expect = 5.8,   Method: Composition-based stats.
 Identities = 14/47 (29%), Positives = 26/47 (55%), Gaps = 3/47 (6%)

Query: 57  SAPEELATA---TQVQGPYMPIAPERPTVELVKVTQDMKSFKAYDKL 100
           S+PEEL+      Q++     + PE  T+++  +  + +  +AYDKL
Sbjct: 63  SSPEELSNLGANVQMRHQVTNVDPETKTIKVKDLITNEEKTEAYDKL 109


>pdb|2QNK|A Chain A, Crystal Structure Of Human 3-hydroxyanthranilate
           3,4-dioxygenase
          Length = 286

 Score = 25.4 bits (54), Expect = 7.4,   Method: Compositional matrix adjust.
 Identities = 11/28 (39%), Positives = 18/28 (64%)

Query: 5   PKKLAPTIGVSVDHRRKNRSLEGLQSNV 32
           P++ A T+G+ V+ RR    L+GL+  V
Sbjct: 93  PQRFANTVGLVVERRRLETELDGLRYYV 120


  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
   0.318    0.132    0.369 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,071,919
Number of Sequences: 62578
Number of extensions: 100409
Number of successful extensions: 231
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 226
Number of HSP's gapped (non-prelim): 7
length of query: 126
length of database: 14,973,337
effective HSP length: 87
effective length of query: 39
effective length of database: 9,529,051
effective search space: 371632989
effective search space used: 371632989
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)