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= 032763
         (134 letters)

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

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



>pdb|3U5C|K Chain K, The Structure Of The Eukaryotic Ribosome At 3.0 A
          Resolution. This Entry Contains Proteins Of The 40s
          Subunit, Ribosome A
 pdb|3U5G|K Chain K, The Structure Of The Eukaryotic Ribosome At 3.0 A
          Resolution. This Entry Contains Proteins Of The 40s
          Subunit, Ribosome B
          Length = 105

 Score = 60.5 bits (145), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 25/53 (47%), Positives = 35/53 (66%)

Query: 1  MQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYLNLPSEIVPATLKKSAKPA 53
          +QS  S+ YV+  F+W +YY+ LT +G+E+LR YLNLP  IVP T  +   P 
Sbjct: 46 LQSLTSKGYVKTQFSWQYYYYTLTEEGVEYLREYLNLPEHIVPGTYIQERNPT 98


>pdb|3ZEY|D Chain D, High-resolution Cryo-electron Microscopy Structure Of The
           Trypanosoma Brucei Ribosome
          Length = 172

 Score = 56.6 bits (135), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 24/51 (47%), Positives = 34/51 (66%)

Query: 1   MQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYLNLPSEIVPATLKKSAK 51
           M+S KSR  ++E FAW H+YW L ++GI ++R YL L ++ VP T K   K
Sbjct: 53  MRSLKSRGLIKEQFAWRHFYWTLNDEGINYMRKYLYLGADAVPNTHKVDHK 103


>pdb|2XZM|7 Chain 7, 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|7 Chain 7, 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 = 162

 Score = 42.7 bits (99), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 18/50 (36%), Positives = 31/50 (62%), Gaps = 1/50 (2%)

Query: 1  MQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYLNLPSE-IVPATLKKS 49
          ++S K R ++ E F W   Y+YL  +G E+L+T L + ++ ++P T K S
Sbjct: 46 VRSLKDRGFLEEIFNWGFTYYYLNKEGCEYLKTKLGISADNVIPKTFKAS 95


>pdb|1UAA|A Chain A, E. Coli Rep HelicaseDNA COMPLEX
 pdb|1UAA|B Chain B, E. Coli Rep HelicaseDNA COMPLEX
          Length = 673

 Score = 26.9 bits (58), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 24/48 (50%), Gaps = 5/48 (10%)

Query: 3   SFKSREYVRETFAWMHYYWYLTN--DGIEFLRTYLNLPSEIVPATLKK 48
           SF SR  +++  A   Y   LTN  D   FLR       EI PATLKK
Sbjct: 376 SFFSRPEIKDLLA---YLRVLTNPDDDSAFLRIVNTPKREIGPATLKK 420


  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    0.133    0.421 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,875,112
Number of Sequences: 62578
Number of extensions: 49316
Number of successful extensions: 127
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: 124
Number of HSP's gapped (non-prelim): 4
length of query: 134
length of database: 14,973,337
effective HSP length: 88
effective length of query: 46
effective length of database: 9,466,473
effective search space: 435457758
effective search space used: 435457758
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: 46 (22.3 bits)