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= 028231
         (211 letters)

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

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



>pdb|3LMD|A Chain A, Crystal Structure Of Geranylgeranyl Pyrophosphate Synthase
           From Corynebacterium Glutamicum Atcc 13032
 pdb|3Q2Q|A Chain A, Crystal Structure Of Geranylgeranyl Pyrophosphate Synthase
           From Corynebacterium Glutamicum Complexed With Calcium
           And Isoprenyl Diphosphate
          Length = 360

 Score = 29.3 bits (64), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 17/52 (32%), Positives = 25/52 (48%)

Query: 25  YDSSIPEHREALRALWNAAFPDEELRDLISEQWKEMGWQGKDPSTDFRGGGF 76
           +  + PEH +AL+    A     ++ D I + + E    GK P TD R G F
Sbjct: 214 HAGAAPEHIDALKNFGAAVGMIFQIVDDIIDIFSETHESGKTPGTDLREGVF 265


>pdb|2CYB|A Chain A, Crystal Structure Of Tyrosyl-Trna Synthetase Complexed
          With L-Tyrosine From Archaeoglobus Fulgidus
 pdb|2CYB|B Chain B, Crystal Structure Of Tyrosyl-Trna Synthetase Complexed
          With L-Tyrosine From Archaeoglobus Fulgidus
          Length = 323

 Score = 28.5 bits (62), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 3/55 (5%)

Query: 34 EALRALWNAA---FPDEELRDLISEQWKEMGWQGKDPSTDFRGGGFISLENLLYL 85
          E LR +   A     +EELR LI  + K   + G +PS +   G  ++++ L+ L
Sbjct: 5  EKLRLITRNAEEVVTEEELRQLIETKEKPRAYVGYEPSGEIHLGHMMTVQKLMDL 59


>pdb|2LF2|A Chain A, Solution Nmr Structure Of The Ahsa1-Like Protein
          Chu_1110 From Cytophaga Hutchinsonii, Northeast
          Structural Genomics Consortium Target Chr152
          Length = 175

 Score = 27.3 bits (59), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 20/66 (30%), Positives = 31/66 (46%), Gaps = 12/66 (18%)

Query: 19 LRIDVAYDSSIPEHRE---------ALRALWNAAFPDEELRDLISEQWKEMGWQGKDPST 69
          +R D+A D S+ +  +         A+RA+   AF   E+ D   + W    W+ K  S 
Sbjct: 1  MRTDLALDFSVNKENKTITIKREFAAVRAIVWEAFTRAEILD---QWWAPKPWKAKTKSM 57

Query: 70 DFRGGG 75
          DF+ GG
Sbjct: 58 DFKEGG 63


  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
   0.325    0.138    0.433 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,881,867
Number of Sequences: 62578
Number of extensions: 222921
Number of successful extensions: 800
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 788
Number of HSP's gapped (non-prelim): 13
length of query: 211
length of database: 14,973,337
effective HSP length: 95
effective length of query: 116
effective length of database: 9,028,427
effective search space: 1047297532
effective search space used: 1047297532
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 bits)