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= 008855
         (551 letters)

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

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



>pdb|1RGO|A Chain A, Structural Basis For Recognition Of The Mrna Class Ii Au-
           Rich Element By The Tandem Zinc Finger Domain Of Tis11d
          Length = 70

 Score = 36.6 bits (83), Expect = 0.033,   Method: Composition-based stats.
 Identities = 20/61 (32%), Positives = 26/61 (42%), Gaps = 6/61 (9%)

Query: 261 KMCFKFIYSGSCPRGEKCNFRHDTDAREQCLRG------VCLDFIIKGKCEKGPECSYKH 314
           ++C  F  SG+C  GEKC F H         R       +C  F   G C  GP C + H
Sbjct: 7   ELCRPFEESGTCKYGEKCQFAHGFHELRSLTRHPKYKTELCRTFHTIGFCPYGPRCHFIH 66

Query: 315 S 315
           +
Sbjct: 67  N 67


>pdb|1M9O|A Chain A, Nmr Structure Of The First Zinc Binding Domain Of
           Nup475TTPTIS11
          Length = 77

 Score = 32.0 bits (71), Expect = 0.81,   Method: Compositional matrix adjust.
 Identities = 19/65 (29%), Positives = 28/65 (43%), Gaps = 6/65 (9%)

Query: 261 KMCFKFIYSGSCPRGEKCNFRHDTDAREQCLRG------VCLDFIIKGKCEKGPECSYKH 314
           ++C  +  SG C  G KC F H      Q  R       +C  F ++G+C  G  C + H
Sbjct: 13  ELCRTYSESGRCRYGAKCQFAHGLGELRQANRHPKYKTELCHKFKLQGRCPYGSRCHFIH 72

Query: 315 SLQND 319
           +   D
Sbjct: 73  NPTED 77


>pdb|3RSB|A Chain A, Structure Of The Archaeal Gtp:adocbi-P Guanylyltransferase
           (Coby) From Methanocaldococcus Jannaschii
 pdb|3RSB|B Chain B, Structure Of The Archaeal Gtp:adocbi-P Guanylyltransferase
           (Coby) From Methanocaldococcus Jannaschii
 pdb|3RSB|C Chain C, Structure Of The Archaeal Gtp:adocbi-P Guanylyltransferase
           (Coby) From Methanocaldococcus Jannaschii
 pdb|3RSB|D Chain D, Structure Of The Archaeal Gtp:adocbi-P Guanylyltransferase
           (Coby) From Methanocaldococcus Jannaschii
          Length = 196

 Score = 32.0 bits (71), Expect = 0.81,   Method: Compositional matrix adjust.
 Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 3/75 (4%)

Query: 312 YKHSLQNDDSQRTHRSE-NASANRSKECWFCLSSP--SVESHLIVSVGEYYYCALPKGPL 368
           YK+ +  D S + +  + N       E +  +SS   +++S +I S+ +Y+YC   K P 
Sbjct: 67  YKNIVVIDTSGKGYIEDLNECIGYFSEPFLVVSSDLINLKSKIINSIVDYFYCIKAKTPD 126

Query: 369 VEDHVLVIPVEHVPN 383
           VE   + IP E  PN
Sbjct: 127 VEALAVXIPKEKYPN 141


>pdb|2KBT|A Chain A, Attachment Of An Nmr-Invisible Solubility Enhancement Tag
           (Inset) Using A Sortase-Mediated Protein Ligation Method
          Length = 142

 Score = 30.0 bits (66), Expect = 3.8,   Method: Composition-based stats.
 Identities = 18/64 (28%), Positives = 27/64 (42%)

Query: 240 SQYWRYDVSQKRQKHGGGDGDKMCFKFIYSGSCPRGEKCNFRHDTDAREQCLRGVCLDFI 299
           S Y   D S+   + GGG G  M +K I +G   +GE      D    E+  +    D  
Sbjct: 55  SNYVEEDYSEYLPETGGGSGSSMTYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNG 114

Query: 300 IKGK 303
           + G+
Sbjct: 115 VDGE 118


  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
   0.316    0.132    0.395 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,521,681
Number of Sequences: 62578
Number of extensions: 691337
Number of successful extensions: 1515
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1499
Number of HSP's gapped (non-prelim): 15
length of query: 551
length of database: 14,973,337
effective HSP length: 104
effective length of query: 447
effective length of database: 8,465,225
effective search space: 3783955575
effective search space used: 3783955575
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (25.4 bits)