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= 041684
         (100 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 =  119 bits (299), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 58/95 (61%), Positives = 69/95 (72%)

Query: 2  IAPKLPNTDLFVGLNKGHVVTKKELLPRPANRKGKTSKRVHFERNVIREVAGFTPYEKTI 61
          +AP  P + LFVG+NKGHVVTK+EL PRP++RKGK +KRVHF RN+IREVAGF PYEK I
Sbjct: 1  MAPSQPKSGLFVGINKGHVVTKRELPPRPSDRKGKGTKRVHFVRNLIREVAGFAPYEKRI 60

Query: 62 TELLKVDEDXXXXXXXXXXXSTHEGTKTKCEEMSN 96
          TELLKV +D            TH+  K K EEMS+
Sbjct: 61 TELLKVGKDKRALKVAKRKLGTHKRAKKKREEMSS 95


>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 = 59.3 bits (142), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 30/91 (32%), Positives = 48/91 (52%)

Query: 9  TDLFVGLNKGHVVTKKELLPRPANRKGKTSKRVHFERNVIREVAGFTPYEKTITELLKVD 68
          T + +GLNKG  VT     P+ + +KG  S R  F R+++RE+AG +PYE+ + +L++  
Sbjct: 5  TGIAIGLNKGKKVTSMTPAPKISYKKGAASNRTKFVRSLVREIAGLSPYERRLIDLIRNS 64

Query: 69 EDXXXXXXXXXXXSTHEGTKTKCEEMSNASA 99
           +            +    K K EEM+N  A
Sbjct: 65 GEKRARKVAKKRLGSFTRAKAKVEEMNNIIA 95


>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 = 57.4 bits (137), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 32/57 (56%), Positives = 37/57 (64%), Gaps = 3/57 (5%)

Query: 13 VGLNKGHVVTK--KELLPRPA-NRKGKTSKRVHFERNVIREVAGFTPYEKTITELLK 66
          VG+NKG + T+  K+L    A  RKGK  KRV   R VIREV GF PYEK I EL+K
Sbjct: 7  VGINKGFITTQLEKKLQKHSAVQRKGKLGKRVALVRQVIREVTGFAPYEKRIIELIK 63


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

 Score = 46.2 bits (108), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 20/65 (30%), Positives = 37/65 (56%)

Query: 6  LPNTDLFVGLNKGHVVTKKELLPRPANRKGKTSKRVHFERNVIREVAGFTPYEKTITELL 65
          +P T +  G NKG+  T++   P   +R     K++   + +I ++ GF+P E+ + ELL
Sbjct: 10 VPRTGIIAGFNKGYKTTRRARRPSSNDRYALPHKKLRAVKAIISDLVGFSPMERRVQELL 69

Query: 66 KVDED 70
          +V +D
Sbjct: 70 RVGKD 74


>pdb|1AOR|A Chain A, Structure Of A Hyperthermophilic Tungstopterin Enzyme,
           Aldehyde Ferredoxin Oxidoreductase
 pdb|1AOR|B Chain B, Structure Of A Hyperthermophilic Tungstopterin Enzyme,
           Aldehyde Ferredoxin Oxidoreductase
          Length = 605

 Score = 27.3 bits (59), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 13/24 (54%), Positives = 15/24 (62%)

Query: 14  GLNKGHVVTKKELLPRPANRKGKT 37
           G NKGH V  KE+LPR    +G T
Sbjct: 563 GPNKGHTVRLKEMLPRYYKLRGWT 586


  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    0.362 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,540,703
Number of Sequences: 62578
Number of extensions: 80495
Number of successful extensions: 111
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 106
Number of HSP's gapped (non-prelim): 5
length of query: 100
length of database: 14,973,337
effective HSP length: 66
effective length of query: 34
effective length of database: 10,843,189
effective search space: 368668426
effective search space used: 368668426
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 45 (21.9 bits)