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= 005023
         (718 letters)

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

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



>pdb|3IRA|A Chain A, The Crystal Structure Of One Domain Of The Conserved
           Protein From Methanosarcina Mazei Go1
          Length = 173

 Score =  129 bits (325), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 57/130 (43%), Positives = 83/130 (63%), Gaps = 3/130 (2%)

Query: 2   GRRSFCGGTKTRRTHFL---INTCHWCHVMEVESFEDEGVAKLLNDWFVSIKVDREERPD 58
           G  +F    K  +  FL    +TCHWCH+M  ESFEDE VA L+N+ FVSIKVDREERPD
Sbjct: 28  GEEAFEKARKENKPVFLSIGYSTCHWCHMMAHESFEDEEVAGLMNEAFVSIKVDREERPD 87

Query: 59  VDKVYMTYVQALYGGGGWPLSVFLSPDLKPLMGGTYFPPEDKYGRPGFKTILRKVKDAWD 118
           +D +YMT  Q + G GGWPL++ ++P  KP   GTY P   ++ + G   ++ ++K+ W+
Sbjct: 88  IDNIYMTVCQIILGRGGWPLNIIMTPGKKPFFAGTYIPKNTRFNQIGMLELVPRIKEIWE 147

Query: 119 KKRDMLAQSG 128
           ++ + +  S 
Sbjct: 148 QQHEEVLDSA 157


>pdb|2LST|A Chain A, Solution Structure Of A Thioredoxin From Thermus
          Thermophilus
          Length = 130

 Score = 30.8 bits (68), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 22/73 (30%), Positives = 30/73 (41%), Gaps = 10/73 (13%)

Query: 15 THFLINTCHWCHVMEVESFEDEGVAKLLNDWFV--SIKVDREERPDVDKVYMTYVQALYG 72
           +F    C +C  M      D GV++LL   FV  S+ VD  E  ++ + Y         
Sbjct: 24 VYFHSEHCPYCQQMNTFVLSDPGVSRLLEARFVVASVSVDTPEGQELARRYRV------- 76

Query: 73 GGGWPLSVFLSPD 85
            G P  VFL P 
Sbjct: 77 -PGTPTFVFLVPK 88


>pdb|1D02|A Chain A, Crystal Structure Of Muni Restriction Endonuclease In
           Complex With Cognate Dna
 pdb|1D02|B Chain B, Crystal Structure Of Muni Restriction Endonuclease In
           Complex With Cognate Dna
          Length = 202

 Score = 30.0 bits (66), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 14/35 (40%), Positives = 19/35 (54%)

Query: 653 IHIDPADTEEMDFWEEHNSNNASMARNNFSADKVV 687
           I  DP    E+ FW +H  +N  M R N S +K+V
Sbjct: 156 ITRDPKRVREITFWYDHYQDNYFMWRPNESGEKLV 190


  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
   0.319    0.135    0.408 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,420,473
Number of Sequences: 62578
Number of extensions: 992937
Number of successful extensions: 1952
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1948
Number of HSP's gapped (non-prelim): 8
length of query: 718
length of database: 14,973,337
effective HSP length: 106
effective length of query: 612
effective length of database: 8,340,069
effective search space: 5104122228
effective search space used: 5104122228
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)