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= 030302
         (179 letters)

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

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



>pdb|3U5C|K Chain K, The Structure Of The Eukaryotic Ribosome At 3.0 A
          Resolution. This Entry Contains Proteins Of The 40s
          Subunit, Ribosome A
 pdb|3U5G|K Chain K, The Structure Of The Eukaryotic Ribosome At 3.0 A
          Resolution. This Entry Contains Proteins Of The 40s
          Subunit, Ribosome B
          Length = 105

 Score =  115 bits (287), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 52/98 (53%), Positives = 70/98 (71%)

Query: 1  MIIPEKNRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFA 60
          M++P+++R +I +YLFQEGV  AKKD+N AKH EID  NL VIK +QS  S+ YV+  F+
Sbjct: 1  MLMPKEDRNKIHQYLFQEGVVVAKKDFNQAKHEEIDTKNLYVIKALQSLTSKGYVKTQFS 60

Query: 61 WMHYYWYLTNDGIEFLRTYLNLPSEIVPATLKKSAKPA 98
          W +YY+ LT +G+E+LR YLNLP  IVP T  +   P 
Sbjct: 61 WQYYYYTLTEEGVEYLREYLNLPEHIVPGTYIQERNPT 98


>pdb|3ZEY|D Chain D, High-resolution Cryo-electron Microscopy Structure Of
          The Trypanosoma Brucei Ribosome
          Length = 172

 Score = 81.3 bits (199), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 37/95 (38%), Positives = 57/95 (60%), Gaps = 5/95 (5%)

Query: 3  IPEKNRKEICKYLFQEGVCYAKKD-----YNLAKHPEIDVPNLQVIKLMQSFKSREYVRE 57
          +P+ +R ++ ++ F EGV   KKD               +P LQV++LM+S KSR  ++E
Sbjct: 5  VPKSSRDDVYRFFFTEGVVSCKKDPLGTWKGTLGGKTFKLPTLQVMQLMRSLKSRGLIKE 64

Query: 58 TFAWMHYYWYLTNDGIEFLRTYLNLPSEIVPATLK 92
           FAW H+YW L ++GI ++R YL L ++ VP T K
Sbjct: 65 QFAWRHFYWTLNDEGINYMRKYLYLGADAVPNTHK 99


>pdb|2XZM|7 Chain 7, 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|7 Chain 7, 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 = 162

 Score = 65.5 bits (158), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 34/85 (40%), Positives = 49/85 (57%), Gaps = 2/85 (2%)

Query: 11 ICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTN 70
          I K L Q+GV   KKD+    H E  VPNL    L++S K R ++ E F W   Y+YL  
Sbjct: 12 IYKQLLQDGVFVLKKDFE-GHHEETGVPNLHCYILVRSLKDRGFLEEIFNWGFTYYYLNK 70

Query: 71 DGIEFLRTYLNLPSE-IVPATLKKS 94
          +G E+L+T L + ++ ++P T K S
Sbjct: 71 EGCEYLKTKLGISADNVIPKTFKAS 95


>pdb|1UAA|A Chain A, E. Coli Rep HelicaseDNA COMPLEX
 pdb|1UAA|B Chain B, E. Coli Rep HelicaseDNA COMPLEX
          Length = 673

 Score = 26.9 bits (58), Expect = 5.4,   Method: Composition-based stats.
 Identities = 20/48 (41%), Positives = 25/48 (52%), Gaps = 5/48 (10%)

Query: 48  SFKSREYVRETFAWMHYYWYLTN--DGIEFLRTYLNLPSEIVPATLKK 93
           SF SR  +++  A++     LTN  D   FLR       EI PATLKK
Sbjct: 376 SFFSRPEIKDLLAYLRV---LTNPDDDSAFLRIVNTPKREIGPATLKK 420


  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
   0.321    0.136    0.423 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,334,069
Number of Sequences: 62578
Number of extensions: 118473
Number of successful extensions: 258
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: 253
Number of HSP's gapped (non-prelim): 5
length of query: 179
length of database: 14,973,337
effective HSP length: 93
effective length of query: 86
effective length of database: 9,153,583
effective search space: 787208138
effective search space used: 787208138
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)