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= 035914
         (93 letters)

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

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



>pdb|3IZR|KK Chain k, Localization Of The Large Subunit Ribosomal Proteins Into
           A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
           Ribosome
          Length = 112

 Score =  109 bits (272), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 61/105 (58%), Positives = 71/105 (67%), Gaps = 17/105 (16%)

Query: 1   MVPKQSNTGLFVGLSKG-----------------KTSKGVDFERNVIREVAGFASYKKGI 43
           M P Q  +GLFVG++KG                 K +K V F RN+IREVAGFA Y+K I
Sbjct: 1   MAPSQPKSGLFVGINKGHVVTKRELPPRPSDRKGKGTKRVHFVRNLIREVAGFAPYEKRI 60

Query: 44  NKLLKVGKDKRTLKVAKKKLGAHKRAKMKREEMSNVLRWTRATGG 88
            +LLKVGKDKR LKVAK+KLG HKRAK KREEMS+VLR  R+ GG
Sbjct: 61  TELLKVGKDKRALKVAKRKLGTHKRAKKKREEMSSVLRKMRSAGG 105


>pdb|3IZS|KK Chain k, Localization Of The Large Subunit Ribosomal Proteins
          Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
          Translating 80s Ribosome
 pdb|3U5E|II Chain i, The Structure Of The Eukaryotic Ribosome At 3.0 A
          Resolution. This Entry Contains Proteins Of The 60s
          Subunit, Ribosome A
 pdb|3U5I|II Chain i, The Structure Of The Eukaryotic Ribosome At 3.0 A
          Resolution. This Entry Contains Proteins Of The 60s
          Subunit, Ribosome B
 pdb|4B6A|II Chain i, Cryo-Em Structure Of The 60s Ribosomal Subunit In
          Complex With Arx1 And Rei1
          Length = 100

 Score = 58.2 bits (139), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 34/94 (36%), Positives = 54/94 (57%), Gaps = 17/94 (18%)

Query: 8  TGLFVGLSKGK-----------------TSKGVDFERNVIREVAGFASYKKGINKLLKVG 50
          TG+ +GL+KGK                  S    F R+++RE+AG + Y++ +  L++  
Sbjct: 5  TGIAIGLNKGKKVTSMTPAPKISYKKGAASNRTKFVRSLVREIAGLSPYERRLIDLIRNS 64

Query: 51 KDKRTLKVAKKKLGAHKRAKMKREEMSNVLRWTR 84
           +KR  KVAKK+LG+  RAK K EEM+N++  +R
Sbjct: 65 GEKRARKVAKKRLGSFTRAKAKVEEMNNIIAASR 98


>pdb|4A18|Q Chain Q, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 26s Rrna And
           Proteins Of Molecule 1
 pdb|4A1B|Q Chain Q, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 26s Rrna And
           Proteins Of Molecule 3.
 pdb|4A1D|Q Chain Q, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 26s Rrna And
           Proteins Of Molecule 4.
 pdb|4A19|Q Chain Q, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 26s Rrna And
           Proteins Of Molecule 2
          Length = 104

 Score = 57.8 bits (138), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 35/72 (48%), Positives = 47/72 (65%), Gaps = 3/72 (4%)

Query: 16  KGKTSKGVDFERNVIREVAGFASYKKGINKLLKVG--KD-KRTLKVAKKKLGAHKRAKMK 72
           KGK  K V   R VIREV GFA Y+K I +L+K G  KD K+  K+A+K+LG H+RAK+K
Sbjct: 31  KGKLGKRVALVRQVIREVTGFAPYEKRIIELIKAGSAKDSKKATKIARKRLGTHRRAKVK 90

Query: 73  REEMSNVLRWTR 84
           +  +   +R  R
Sbjct: 91  KALLEEAVRAQR 102


>pdb|3ZF7|MM Chain m, High-resolution Cryo-electron Microscopy Structure Of The
           Trypanosoma Brucei Ribosome
          Length = 109

 Score = 47.8 bits (112), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/53 (43%), Positives = 37/53 (69%)

Query: 29  VIREVAGFASYKKGINKLLKVGKDKRTLKVAKKKLGAHKRAKMKREEMSNVLR 81
           +I ++ GF+  ++ + +LL+VGKDKR LK  KK+LG+ K AK +R ++   LR
Sbjct: 51  IISDLVGFSPMERRVQELLRVGKDKRALKFCKKRLGSIKAAKKRRAKVEEALR 103


>pdb|3OAA|D Chain D, Structure Of The E.Coli F1-Atp Synthase Inhibited By
           Subunit Epsilon
 pdb|3OAA|E Chain E, Structure Of The E.Coli F1-Atp Synthase Inhibited By
           Subunit Epsilon
 pdb|3OAA|F Chain F, Structure Of The E.Coli F1-Atp Synthase Inhibited By
           Subunit Epsilon
 pdb|3OAA|L Chain L, Structure Of The E.Coli F1-Atp Synthase Inhibited By
           Subunit Epsilon
 pdb|3OAA|M Chain M, Structure Of The E.Coli F1-Atp Synthase Inhibited By
           Subunit Epsilon
 pdb|3OAA|N Chain N, Structure Of The E.Coli F1-Atp Synthase Inhibited By
           Subunit Epsilon
 pdb|3OAA|T Chain T, Structure Of The E.Coli F1-Atp Synthase Inhibited By
           Subunit Epsilon
 pdb|3OAA|U Chain U, Structure Of The E.Coli F1-Atp Synthase Inhibited By
           Subunit Epsilon
 pdb|3OAA|V Chain V, Structure Of The E.Coli F1-Atp Synthase Inhibited By
           Subunit Epsilon
 pdb|3OAA|BB Chain b, Structure Of The E.Coli F1-Atp Synthase Inhibited By
           Subunit Epsilon
 pdb|3OAA|CC Chain c, Structure Of The E.Coli F1-Atp Synthase Inhibited By
           Subunit Epsilon
 pdb|3OAA|DD Chain d, Structure Of The E.Coli F1-Atp Synthase Inhibited By
           Subunit Epsilon
          Length = 459

 Score = 25.8 bits (55), Expect = 6.0,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 4   KQSNTGLFVGLSKGKTSKGVDFERNVIREVAGFASYKKGINKLLKVGKD 52
           K    GLF G   GKT   ++  RN+  E +G++ +  G+ +  + G D
Sbjct: 141 KGGKVGLFGGAGVGKTVNMMELIRNIAIEHSGYSVF-AGVGERTREGND 188


>pdb|2B1X|A Chain A, Crystal Structure Of Naphthalene 1,2-dioxygenase From
           Rhodococcus Sp.
 pdb|2B1X|C Chain C, Crystal Structure Of Naphthalene 1,2-dioxygenase From
           Rhodococcus Sp.
 pdb|2B1X|E Chain E, Crystal Structure Of Naphthalene 1,2-dioxygenase From
           Rhodococcus Sp.
 pdb|2B24|A Chain A, Crystal Structure Of Naphthalene 1,2-Dioxygenase From
           Rhodococcus Sp. Bound To Indole
 pdb|2B24|C Chain C, Crystal Structure Of Naphthalene 1,2-Dioxygenase From
           Rhodococcus Sp. Bound To Indole
 pdb|2B24|E Chain E, Crystal Structure Of Naphthalene 1,2-Dioxygenase From
           Rhodococcus Sp. Bound To Indole
          Length = 470

 Score = 25.8 bits (55), Expect = 6.0,   Method: Composition-based stats.
 Identities = 14/37 (37%), Positives = 21/37 (56%), Gaps = 2/37 (5%)

Query: 6   SNTGLFVGLSKGKTSKGVDFERN--VIREVAGFASYK 40
           SNTG  VG+  GK + G   +++   +R +   ASYK
Sbjct: 116 SNTGSLVGVPAGKDAYGNQLKKSDWNLRPMPNLASYK 152


  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
   0.312    0.129    0.354 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,554,183
Number of Sequences: 62578
Number of extensions: 83479
Number of successful extensions: 202
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 193
Number of HSP's gapped (non-prelim): 8
length of query: 93
length of database: 14,973,337
effective HSP length: 60
effective length of query: 33
effective length of database: 11,218,657
effective search space: 370215681
effective search space used: 370215681
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 45 (21.9 bits)