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= 032308
         (143 letters)

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

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



>pdb|3B9T|A Chain A, Crystal Structure Of Predicted AcetamidaseFORMAMIDASE
           (YP_546212.1) From Methylobacillus Flagellatus Kt At
           1.58 A Resolution
 pdb|3B9T|B Chain B, Crystal Structure Of Predicted AcetamidaseFORMAMIDASE
           (YP_546212.1) From Methylobacillus Flagellatus Kt At
           1.58 A Resolution
 pdb|3B9T|C Chain C, Crystal Structure Of Predicted AcetamidaseFORMAMIDASE
           (YP_546212.1) From Methylobacillus Flagellatus Kt At
           1.58 A Resolution
 pdb|3B9T|D Chain D, Crystal Structure Of Predicted AcetamidaseFORMAMIDASE
           (YP_546212.1) From Methylobacillus Flagellatus Kt At
           1.58 A Resolution
          Length = 484

 Score = 28.1 bits (61), Expect = 1.8,   Method: Composition-based stats.
 Identities = 11/27 (40%), Positives = 16/27 (59%)

Query: 91  EPEQTIQIRIVDYALQLESTPSVSGTT 117
           EP   +++RIVD AL+  + P   G T
Sbjct: 173 EPGDVLEVRIVDVALRPSANPEFKGKT 199


>pdb|3DMK|A Chain A, Crystal Structure Of Down Syndrome Cell Adhesion Molecule
           (Dscam) Isoform 1.30.30, N-Terminal Eight Ig Domains
 pdb|3DMK|B Chain B, Crystal Structure Of Down Syndrome Cell Adhesion Molecule
           (Dscam) Isoform 1.30.30, N-Terminal Eight Ig Domains
 pdb|3DMK|C Chain C, Crystal Structure Of Down Syndrome Cell Adhesion Molecule
           (Dscam) Isoform 1.30.30, N-Terminal Eight Ig Domains
          Length = 816

 Score = 27.7 bits (60), Expect = 2.5,   Method: Composition-based stats.
 Identities = 12/44 (27%), Positives = 24/44 (54%)

Query: 78  LVRCISASEPGTCEPEQTIQIRIVDYALQLESTPSVSGTTIVLS 121
           L +CI+ S+ G  E    + +  + Y  Q+E    V+G T++++
Sbjct: 504 LYKCIAKSKVGVAEHSAKLNVYGLPYIRQMEKKAIVAGETLIVT 547


>pdb|3IZR|FF Chain f, Localization Of The Large Subunit Ribosomal Proteins Into
           A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
           Ribosome
          Length = 112

 Score = 26.2 bits (56), Expect = 6.5,   Method: Compositional matrix adjust.
 Identities = 10/21 (47%), Positives = 14/21 (66%)

Query: 68  DNGASCGRQYLVRCISASEPG 88
           D G +CG+ Y V C+S  +PG
Sbjct: 80  DLGTACGKYYRVCCLSILDPG 100


>pdb|1YSH|C Chain C, Localization And Dynamic Behavior Of Ribosomal Protein
          L30e
          Length = 104

 Score = 26.2 bits (56), Expect = 6.6,   Method: Compositional matrix adjust.
 Identities = 10/21 (47%), Positives = 14/21 (66%)

Query: 68 DNGASCGRQYLVRCISASEPG 88
          D G +CG+ Y V C+S  +PG
Sbjct: 75 DLGTACGKYYRVCCLSILDPG 95


  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    0.133    0.404 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,054,891
Number of Sequences: 62578
Number of extensions: 150031
Number of successful extensions: 259
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 254
Number of HSP's gapped (non-prelim): 8
length of query: 143
length of database: 14,973,337
effective HSP length: 89
effective length of query: 54
effective length of database: 9,403,895
effective search space: 507810330
effective search space used: 507810330
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: 46 (22.3 bits)