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= 021549
         (311 letters)

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

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



>pdb|3SYY|A Chain A, Crystal Structure Of An Alkaline Exonuclease (Lhk-Exo)
           From Laribacter Hongkongensis
 pdb|3SZ4|A Chain A, Crystal Structure Of Lhk-Exo In Complex With Damp
 pdb|3SZ5|A Chain A, Crystal Structure Of Lhk-Exo In Complex With
           5-Phosphorylated Oligothymidine (Dt)4
          Length = 216

 Score = 61.6 bits (148), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 54/164 (32%), Positives = 77/164 (46%), Gaps = 16/164 (9%)

Query: 67  MLQRSDEWFALRRDKLTTSTFS-----TALGFWKGKRR--SELWHEKVFSLETQVIENSK 119
           M QR++EWFA R  K+T S  +     T  G+   ++   +EL  +++    TQ I  S 
Sbjct: 1   MEQRTEEWFAARLGKVTASRVADVMTKTKSGYAASRQNYMAELICQRLTG--TQEIRFSN 58

Query: 120 RCAMEWGVLNEAAAIDRYKSITGHDVSSLGFAVHAEEQLDWLGASPDGLLGCFPGGGILE 179
             AM+ G   E  A  RY   TG  V+ +G   H    +   GASPDGL+G     G++E
Sbjct: 59  -AAMQRGTELEPHARARYIIETGEIVTEVGLIDHP--TIAGFGASPDGLVG---DTGLIE 112

Query: 180 VKCPYNKGKPEIALPWSTVPFYYMPQVQGQMEILDREWVDLYCW 223
           +KCP      E        P  Y+ Q+Q QM    R+W D   +
Sbjct: 113 IKCPNTWTHIETIKTGKPKP-EYIKQMQTQMACTGRQWCDFVSY 155


>pdb|3CYG|A Chain A, Crystal Structure Of An Uncharacterized Protein From
           Fervidobacterium Nodosum Rt17-B1
 pdb|3CYG|B Chain B, Crystal Structure Of An Uncharacterized Protein From
           Fervidobacterium Nodosum Rt17-B1
          Length = 222

 Score = 30.0 bits (66), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 12/35 (34%), Positives = 18/35 (51%), Gaps = 4/35 (11%)

Query: 164 SPDGLLGCFPGGGILEVKCPYNKGKPEIALPWSTV 198
           S DGL+  +P   +     PY  G PE  +PW+ +
Sbjct: 171 SKDGLIIXYPHYDL----APYASGXPEFVIPWNVI 201


  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    0.135    0.436 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,331,624
Number of Sequences: 62578
Number of extensions: 385889
Number of successful extensions: 644
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: 642
Number of HSP's gapped (non-prelim): 3
length of query: 311
length of database: 14,973,337
effective HSP length: 99
effective length of query: 212
effective length of database: 8,778,115
effective search space: 1860960380
effective search space used: 1860960380
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: 51 (24.3 bits)