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= psy672
         (314 letters)

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

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



>pdb|1YUZ|A Chain A, Partially Reduced State Of Nigerythrin
 pdb|1YUZ|B Chain B, Partially Reduced State Of Nigerythrin
          Length = 202

 Score = 33.1 bits (74), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 21/107 (19%), Positives = 43/107 (40%), Gaps = 7/107 (6%)

Query: 86  AHVNYVKFPEQLAPTKVAFQGIGNFPGVVGCVDCTHVPIQLPSVENGENFRNRK-----G 140
           AH  Y  F +  A  +  ++ I          +  H+ ++   V   E    +       
Sbjct: 43  AHAKYTAFAK--AAREQGYEQIARLFEATAAAELIHIGLEYALVAEMEPGYEKPTVAAPS 100

Query: 141 TFSLNVQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSRVCHRFERGEV 187
            +S ++ +I G N EI++    +P  +  ++   NS+  H F R ++
Sbjct: 101 AYSCDLNLISGANGEIYETSDMYPAFIRKAQEEGNSKAVHVFTRAKL 147


>pdb|1YUX|A Chain A, Mixed Valant State Of Nigerythrin
 pdb|1YUX|B Chain B, Mixed Valant State Of Nigerythrin
 pdb|1YV1|A Chain A, Fully Reduced State Of Nigerythrin (All Ferrous)
 pdb|1YV1|B Chain B, Fully Reduced State Of Nigerythrin (All Ferrous)
          Length = 202

 Score = 33.1 bits (74), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 21/107 (19%), Positives = 43/107 (40%), Gaps = 7/107 (6%)

Query: 86  AHVNYVKFPEQLAPTKVAFQGIGNFPGVVGCVDCTHVPIQLPSVENGENFRNRK-----G 140
           AH  Y  F +  A  +  ++ I          +  H+ ++   V   E    +       
Sbjct: 43  AHAKYTAFAK--AAREQGYEQIARLFEATAAAELIHIGLEYALVAEMEPGYEKPTVAAPS 100

Query: 141 TFSLNVQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSRVCHRFERGEV 187
            +S ++ +I G N EI++    +P  +  ++   NS+  H F R ++
Sbjct: 101 AYSCDLNLISGANGEIYETSDMYPAFIRKAQEEGNSKAVHVFTRAKL 147


>pdb|4GZI|A Chain A, Active-site Mutant Of Potato Endo-1,3-beta-glucanase In
           Complex With Laminaratriose
 pdb|4GZJ|A Chain A, Active-site Mutant Of Potato Endo-1,3-beta-glucanase In
           Complex With Laminaratriose And Laminaratetrose
          Length = 323

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

Query: 146 VQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSRVCH 180
            + +GG N+EI    SGWP   H +    N+R  +
Sbjct: 222 TEKLGGQNIEIIVSASGWPSEGHPAATLKNARTYY 256


>pdb|3UR7|A Chain A, Higher-density Crystal Structure Of Potato
           Endo-1,3-beta-glucanase
 pdb|3UR7|B Chain B, Higher-density Crystal Structure Of Potato
           Endo-1,3-beta-glucanase
 pdb|3UR8|A Chain A, Lower-density Crystal Structure Of Potato
           Endo-1,3-beta-glucanase
 pdb|3UR8|B Chain B, Lower-density Crystal Structure Of Potato
           Endo-1,3-beta-glucanase
          Length = 323

 Score = 29.3 bits (64), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 12/35 (34%), Positives = 18/35 (51%)

Query: 146 VQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSRVCH 180
            + +GG N+EI    SGWP   H +    N+R  +
Sbjct: 222 TEKLGGQNIEIIVSESGWPSEGHPAATLKNARTYY 256


>pdb|1N8Y|C Chain C, Crystal Structure Of The Extracellular Region Of Rat Her2
          Length = 608

 Score = 28.9 bits (63), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 8/39 (20%)

Query: 160 VSGWPGSVHDSRIFTNSRVCHRFERGEVRGILLGDSGYA 198
           +S WP S+ D  +F N R+        +RG +L D  Y+
Sbjct: 391 ISAWPDSLRDLSVFQNLRI--------IRGRILHDGAYS 421


  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
   0.323    0.137    0.427 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,687,923
Number of Sequences: 62578
Number of extensions: 352590
Number of successful extensions: 636
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 633
Number of HSP's gapped (non-prelim): 6
length of query: 314
length of database: 14,973,337
effective HSP length: 99
effective length of query: 215
effective length of database: 8,778,115
effective search space: 1887294725
effective search space used: 1887294725
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (24.3 bits)