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= 029217
         (197 letters)

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

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



>pdb|3U5C|G Chain G, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 40s
           Subunit, Ribosome A
 pdb|3U5G|G Chain G, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 40s
           Subunit, Ribosome B
 pdb|3J16|C Chain C, Models Of Ribosome-Bound Dom34p And Rli1p And Their
           Ribosomal Binding Partners
          Length = 236

 Score =  142 bits (358), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 89/188 (47%), Positives = 106/188 (56%), Gaps = 5/188 (2%)

Query: 2   GGCDKQGFPMKQGVLTPGRVRLLLHRGTPCFXXXXXXXXXXXXXXXXXCIVSPDLSVLNL 61
           GG DKQGFPMKQGVL P R++LLL +   C+                  IV PDL+VL L
Sbjct: 54  GGNDKQGFPMKQGVLLPTRIKLLLTKNVSCYRPRRDGERKRKSVRG--AIVGPDLAVLAL 111

Query: 62  VIVKKGEHDLPGLTDTEKPRMRGPKRASKIRKLFNLSKEDDVRKYVNTYRRTFTTKSGKK 121
           VIVKKGE +L GLTDT  P+  GPKRA+ IRK F LSKEDDVR +V   RR   TK  K 
Sbjct: 112 VIVKKGEQELEGLTDTTVPKRLGPKRANNIRKFFGLSKEDDVRDFV--IRRE-VTKGEKT 168

Query: 122 VSKAPKIQRLVTPLTLXXXXXXXXXXXXXXXXXXXXXXEYQKLLATRLKEQRERRSESLA 181
            +KAPKIQRLVTP  L                      EY +LLA RL E++  ++E   
Sbjct: 169 YTKAPKIQRLVTPQRLQRKRHQRALKVRNAQAQREAAAEYAQLLAKRLSERKAEKAEIRK 228

Query: 182 KKRSRLSA 189
           ++ S L A
Sbjct: 229 RRASSLKA 236


>pdb|2XZM|Y Chain Y, 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|Y Chain Y, 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 = 293

 Score =  125 bits (315), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 79/175 (45%), Positives = 93/175 (53%), Gaps = 8/175 (4%)

Query: 2   GGCDKQGFPMKQGVLTPGRVRLLLHRGTPCFXXXXXXXXXXXXXXXXXCIVSPDLSVLNL 61
           GG DK GFPMKQGV+  GRVRLLL  G  CF                 CIV PD+ VL L
Sbjct: 54  GGNDKDGFPMKQGVMVRGRVRLLLSEGHSCFTSRRSGFRKRKSVRG--CIVGPDMRVLAL 111

Query: 62  VIVKKGEHDLPGLTDTEKPRMRGPKRASKIRKLFNLSKEDD---VRKYVNTYRRTFTTKS 118
            IVKKG  ++ GLT    PR  GPKRA+ I+KLF L KEDD   ++K V   RRTF T  
Sbjct: 112 QIVKKGVAEIDGLTTVTLPRKLGPKRANNIKKLFGLKKEDDPILIKKSV--IRRTFKTAK 169

Query: 119 GKKVSKAPKIQRLVTPLTLXXXXXXXXXXXXXXXXXXXXXXEYQKLLATRLKEQR 173
           GK  +K PKIQRL+TP  +                      EY+K L +  K+QR
Sbjct: 170 GKDRTKCPKIQRLITPERILRKKVYKAEKTQRYVKTNAAKEEYEKFL-SEWKKQR 223


>pdb|3ZEY|3 Chain 3, High-resolution Cryo-electron Microscopy Structure Of The
           Trypanosoma Brucei Ribosome
          Length = 250

 Score =  124 bits (312), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 66/132 (50%), Positives = 80/132 (60%), Gaps = 2/132 (1%)

Query: 2   GGCDKQGFPMKQGVLTPGRVRLLLHRGTPCFXXXXXXXXXXXXXXXXXCIVSPDLSVLNL 61
           GG DK+GFPM QGV+ P RV LL+ RG   F                 CI+  D++VLN+
Sbjct: 55  GGSDKEGFPMVQGVMAPSRVSLLVKRGAVGFNTFRGYQGERRRKSLRGCILGSDIAVLNV 114

Query: 62  VIVKKGEHDLPGLTDTEKPRMRGPKRASKIRKLFNLSKEDDVRKYVNTYRRTFTTKSGKK 121
            + K GE  + G+TD   PR  GPKRA+KIRKLFNL + DDVRKYV   RR  T +  K 
Sbjct: 115 TVEKVGEQPIEGVTDVSVPRRLGPKRANKIRKLFNLGRTDDVRKYV--IRRKVTKEGKKD 172

Query: 122 VSKAPKIQRLVT 133
             KAPKIQRL+T
Sbjct: 173 RFKAPKIQRLIT 184


>pdb|3J20|G Chain G, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
          Revealed By Cryo-em: Implications For Evolution Of
          Eukaryotic Ribosomes (30s Ribosomal Subunit)
          Length = 125

 Score = 36.2 bits (82), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 17/31 (54%), Positives = 21/31 (67%), Gaps = 1/31 (3%)

Query: 2  GGCDKQGFPMKQGVLTPGRVRLLLHRGTPCF 32
          GG DK GFPM+  +  P RVR+LL +G P F
Sbjct: 65 GGTDKDGFPMRPDIHGPRRVRVLLSKG-PGF 94


  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
   0.318    0.134    0.380 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,189,291
Number of Sequences: 62578
Number of extensions: 118478
Number of successful extensions: 206
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 195
Number of HSP's gapped (non-prelim): 4
length of query: 197
length of database: 14,973,337
effective HSP length: 94
effective length of query: 103
effective length of database: 9,091,005
effective search space: 936373515
effective search space used: 936373515
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)