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= 047228
         (280 letters)

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

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



>pdb|2P65|A Chain A, Crystal Structure Of The First Nucleotide Binding Domain
           Of Chaperone Clpb1, Putative, (Pv089580) From Plasmodium
           Vivax
          Length = 187

 Score = 29.3 bits (64), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 29/79 (36%), Positives = 37/79 (46%), Gaps = 9/79 (11%)

Query: 149 MQIGAERTKNVLILMSDTGGGHRASAEAIRDAFKIEFGD-----EYRIFVK-DVCKEYAG 202
           +QI + RTKN  IL+ D G G  A  E +  A KI  GD     + R  V  D+    AG
Sbjct: 35  IQILSRRTKNNPILLGDPGVGKTAIVEGL--AIKIVQGDVPDSLKGRKLVSLDLSSLIAG 92

Query: 203 WP-LNDMERSYKFMVKHVQ 220
                D E   K ++K VQ
Sbjct: 93  AKYRGDFEERLKSILKEVQ 111


>pdb|1S1H|I Chain I, 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,
           1s1h, Contains 40s Subunit. The 60s Ribosomal Subunit Is
           In File 1s1i
          Length = 142

 Score = 27.3 bits (59), Expect = 8.7,   Method: Compositional matrix adjust.
 Identities = 13/33 (39%), Positives = 20/33 (60%)

Query: 148 LMQIGAERTKNVLILMSDTGGGHRASAEAIRDA 180
           L+ +G ++  N+ I +  TGGGH +   AIR A
Sbjct: 51  LLLVGLDKFSNIDIRVRVTGGGHVSQVYAIRQA 83


>pdb|3IZB|I Chain I, Localization Of The Small Subunit Ribosomal Proteins Into
           A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
           Translating 80s Ribosome
 pdb|3O2Z|J Chain J, Yeast 80s Ribosome. This Entry Consists Of The 40s Subunit
           Of The First 80s In The Asymmetric Unit.
 pdb|3O30|J Chain J, Yeast 80s Ribosome. This Entry Consists Of The 40s Subunit
           Of The Second 80s In The Asymmetric Unit.
 pdb|3U5C|Q Chain Q, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 40s
           Subunit, Ribosome A
 pdb|3U5G|Q Chain Q, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 40s
           Subunit, Ribosome B
          Length = 143

 Score = 27.3 bits (59), Expect = 8.7,   Method: Compositional matrix adjust.
 Identities = 13/33 (39%), Positives = 20/33 (60%)

Query: 148 LMQIGAERTKNVLILMSDTGGGHRASAEAIRDA 180
           L+ +G ++  N+ I +  TGGGH +   AIR A
Sbjct: 52  LLLVGLDKFSNIDIRVRVTGGGHVSQVYAIRQA 84


>pdb|3JYV|I Chain I, Structure Of The 40s Rrna And Proteins And PE TRNA FOR
           EUKARYOTIC Ribosome Based On Cryo-Em Map Of Thermomyces
           Lanuginosus Ribosome At 8.9a Resolution
          Length = 138

 Score = 27.3 bits (59), Expect = 9.0,   Method: Compositional matrix adjust.
 Identities = 13/33 (39%), Positives = 20/33 (60%)

Query: 148 LMQIGAERTKNVLILMSDTGGGHRASAEAIRDA 180
           L+ +G ++  N+ I +  TGGGH +   AIR A
Sbjct: 47  LLLVGLDKFSNIDIRVRVTGGGHVSQVYAIRQA 79


  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
   0.325    0.137    0.435 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,614,565
Number of Sequences: 62578
Number of extensions: 271851
Number of successful extensions: 636
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: 633
Number of HSP's gapped (non-prelim): 4
length of query: 280
length of database: 14,973,337
effective HSP length: 98
effective length of query: 182
effective length of database: 8,840,693
effective search space: 1609006126
effective search space used: 1609006126
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.3 bits)