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= 038355
         (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 =  107 bits (267), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 54/89 (60%), Positives = 64/89 (71%)

Query: 1   HIVTNKELLPRPVDPKGKTSKRIHFERNVIREVAGFAPYEKRIDALLKVGKDXXXXXXXX 60
           H+VT +EL PRP D KGK +KR+HF RN+IREVAGFAPYEKRI  LLKVGKD        
Sbjct: 18  HVVTKRELPPRPSDRKGKGTKRVHFVRNLIREVAGFAPYEKRITELLKVGKDKRALKVAK 77

Query: 61  XXXCTYERAKMKHGEMSNVLCRMRATGGG 89
               T++RAK K  EMS+VL +MR+ GGG
Sbjct: 78  RKLGTHKRAKKKREEMSSVLRKMRSAGGG 106


>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 = 50.4 bits (119), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 31/64 (48%), Positives = 35/64 (54%), Gaps = 3/64 (4%)

Query: 12 PVDPKGKTSKRIHFERNVIREVAGFAPYEKRIDALLKVG--KDXXXXXXXXXXXC-TYER 68
           V  KGK  KR+   R VIREV GFAPYEKRI  L+K G  KD             T+ R
Sbjct: 27 AVQRKGKLGKRVALVRQVIREVTGFAPYEKRIIELIKAGSAKDSKKATKIARKRLGTHRR 86

Query: 69 AKMK 72
          AK+K
Sbjct: 87 AKVK 90


>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 = 49.7 bits (117), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 26/82 (31%), Positives = 43/82 (52%)

Query: 3  VTNKELLPRPVDPKGKTSKRIHFERNVIREVAGFAPYEKRIDALLKVGKDXXXXXXXXXX 62
          VT+    P+    KG  S R  F R+++RE+AG +PYE+R+  L++   +          
Sbjct: 17 VTSMTPAPKISYKKGAASNRTKFVRSLVREIAGLSPYERRLIDLIRNSGEKRARKVAKKR 76

Query: 63 XCTYERAKMKHGEMSNVLCRMR 84
            ++ RAK K  EM+N++   R
Sbjct: 77 LGSFTRAKAKVEEMNNIIAASR 98


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

 Score = 34.3 bits (77), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 13/32 (40%), Positives = 23/32 (71%)

Query: 21 KRIHFERNVIREVAGFAPYEKRIDALLKVGKD 52
          K++   + +I ++ GF+P E+R+  LL+VGKD
Sbjct: 43 KKLRAVKAIISDLVGFSPMERRVQELLRVGKD 74


>pdb|2IVF|C Chain C, Ethylbenzene Dehydrogenase From Aromatoleum Aromaticum
          Length = 214

 Score = 25.4 bits (54), Expect = 8.9,   Method: Compositional matrix adjust.
 Identities = 11/24 (45%), Positives = 16/24 (66%)

Query: 69  AKMKHGEMSNVLCRMRATGGGKKK 92
           A+ ++GE + +LCR  ATG G  K
Sbjct: 153 AQHRNGEWNVILCRSMATGDGLAK 176


  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
   0.319    0.136    0.401 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,439,128
Number of Sequences: 62578
Number of extensions: 66526
Number of successful extensions: 128
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 121
Number of HSP's gapped (non-prelim): 6
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 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)