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= 038963
         (117 letters)

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

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



>pdb|2OLS|A Chain A, The Crystal Structure Of The Phosphoenolpyruvate Synthase
           From Neisseria Meningitidis
          Length = 794

 Score = 29.6 bits (65), Expect = 0.46,   Method: Composition-based stats.
 Identities = 15/35 (42%), Positives = 19/35 (54%), Gaps = 3/35 (8%)

Query: 44  TVSPVSGDEGFVQLGRPMLMAVSLADSIFDKLPKA 78
           TVS   GD GF+  G   L+ V + D   D +PKA
Sbjct: 452 TVSCAEGDTGFIYAG---LLDVQITDVALDNMPKA 483


>pdb|1M9L|A Chain A, Relaxation-Based Refined Structure Of Chlamydomonas Outer
           Arm Dynein Light Chain 1
          Length = 199

 Score = 26.2 bits (56), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 2/49 (4%)

Query: 40  DNSGTVSPVSGDEGF--VQLGRPMLMAVSLADSIFDKLPKAWFIYLFIG 86
           +N   +S +SG E    + LGR ++  +   D++ D L + W  Y  I 
Sbjct: 59  NNIEKISSLSGMENLRILSLGRNLIKKIENLDAVADTLEELWISYNQIA 107


>pdb|1DS9|A Chain A, Solution Structure Of Chlamydomonas Outer Arm Dynein Light
           Chain 1
          Length = 198

 Score = 26.2 bits (56), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 2/49 (4%)

Query: 40  DNSGTVSPVSGDEGF--VQLGRPMLMAVSLADSIFDKLPKAWFIYLFIG 86
           +N   +S +SG E    + LGR ++  +   D++ D L + W  Y  I 
Sbjct: 58  NNIEKISSLSGMENLRILSLGRNLIKKIENLDAVADTLEELWISYNQIA 106


  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
   0.331    0.146    0.471 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,969,902
Number of Sequences: 62578
Number of extensions: 103068
Number of successful extensions: 210
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 210
Number of HSP's gapped (non-prelim): 3
length of query: 117
length of database: 14,973,337
effective HSP length: 80
effective length of query: 37
effective length of database: 9,967,097
effective search space: 368782589
effective search space used: 368782589
T: 11
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 45 (21.9 bits)