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= 032901
         (130 letters)

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

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



>pdb|3U5C|AA Chain a, The Structure Of The Eukaryotic Ribosome At 3.0 A
          Resolution. This Entry Contains Proteins Of The 40s
          Subunit, Ribosome A
 pdb|3U5G|AA Chain a, The Structure Of The Eukaryotic Ribosome At 3.0 A
          Resolution. This Entry Contains Proteins Of The 40s
          Subunit, Ribosome B
          Length = 119

 Score = 82.8 bits (203), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 41/64 (64%), Positives = 46/64 (71%), Gaps = 2/64 (3%)

Query: 18 VKFIRCSNCGKCCPK--AIKRFLVRNIVEQAAVRDVQEACVYDGYTLPKLYAKMQYCVSC 75
          VK +RC NC K  PK  AIKR  +RNIVE AAVRD+ EA VY  Y LPK Y K+ YCVSC
Sbjct: 18 VKPVRCVNCSKSIPKDKAIKRMAIRNIVEAAAVRDLSEASVYPEYALPKTYNKLHYCVSC 77

Query: 76 AIHS 79
          AIH+
Sbjct: 78 AIHA 81


>pdb|3ZEY|V Chain V, High-resolution Cryo-electron Microscopy Structure Of
          The Trypanosoma Brucei Ribosome
          Length = 111

 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 30/67 (44%), Positives = 46/67 (68%), Gaps = 4/67 (5%)

Query: 18 VKFIRCSNCGKCCPK--AIKRFLVRNIVEQAAVRDVQEACVY--DGYTLPKLYAKMQYCV 73
          V+ + C NC +  PK  ++ RF+VR +++QA+ RDV EA +    G+ +PKLY K +YC+
Sbjct: 20 VRPVHCFNCSRLVPKDKSVGRFVVRRMLDQASARDVAEASLIYGSGFPMPKLYMKQRYCI 79

Query: 74 SCAIHSH 80
          +CAIHS 
Sbjct: 80 ACAIHSR 86


>pdb|2XZM|5 Chain 5, 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|5 Chain 5, 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 = 119

 Score = 62.4 bits (150), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 28/67 (41%), Positives = 46/67 (68%), Gaps = 4/67 (5%)

Query: 18 VKFIRCSNCGK--CCPKAIKRFLVRNIVEQAAVRDVQEACVYDG--YTLPKLYAKMQYCV 73
           + + C+NCG+     KA+KR+ VR++V+ ++ RD+Q+   ++     +PKLY K+QYC+
Sbjct: 18 TRTVPCTNCGRQVAKDKAVKRYTVRDMVDPSSKRDIQQKLAFENEKQGIPKLYVKLQYCI 77

Query: 74 SCAIHSH 80
          SCAIHS 
Sbjct: 78 SCAIHSR 84


>pdb|3AWI|A Chain A, Bifunctional Trna Modification Enzyme Mnmc From
           Escherichia Coli
 pdb|3AWI|B Chain B, Bifunctional Trna Modification Enzyme Mnmc From
           Escherichia Coli
 pdb|3AWI|C Chain C, Bifunctional Trna Modification Enzyme Mnmc From
           Escherichia Coli
 pdb|3AWI|D Chain D, Bifunctional Trna Modification Enzyme Mnmc From
           Escherichia Coli
 pdb|3AWI|E Chain E, Bifunctional Trna Modification Enzyme Mnmc From
           Escherichia Coli
 pdb|3AWI|F Chain F, Bifunctional Trna Modification Enzyme Mnmc From
           Escherichia Coli
          Length = 688

 Score = 26.6 bits (57), Expect = 4.0,   Method: Composition-based stats.
 Identities = 10/40 (25%), Positives = 20/40 (50%)

Query: 39  VRNIVEQAAVRDVQEACVYDGYTLPKLYAKMQYCVSCAIH 78
           V +I     + ++++   YDGY  P+  A   +C+  + H
Sbjct: 503 VSHIPTTPELAELKQVLCYDGYLTPQNPANQHHCIGASYH 542


>pdb|3PS9|A Chain A, Crystal Structure Of Mnmc From E. Coli
          Length = 676

 Score = 26.6 bits (57), Expect = 4.0,   Method: Composition-based stats.
 Identities = 10/40 (25%), Positives = 20/40 (50%)

Query: 39  VRNIVEQAAVRDVQEACVYDGYTLPKLYAKMQYCVSCAIH 78
           V +I     + ++++   YDGY  P+  A   +C+  + H
Sbjct: 491 VSHIPTTPELAELKQVLCYDGYLTPQNPANQHHCIGASYH 530


  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
   0.330    0.139    0.461 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,008,089
Number of Sequences: 62578
Number of extensions: 51115
Number of successful extensions: 135
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: 126
Number of HSP's gapped (non-prelim): 6
length of query: 130
length of database: 14,973,337
effective HSP length: 88
effective length of query: 42
effective length of database: 9,466,473
effective search space: 397591866
effective search space used: 397591866
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 45 (21.9 bits)