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= psy6913
         (380 letters)

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

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



>pdb|3E5Y|A Chain A, Crystal Structure Of Trmh Family Rna Methyltransferase
           From Burkholderia Pseudomallei
 pdb|3E5Y|B Chain B, Crystal Structure Of Trmh Family Rna Methyltransferase
           From Burkholderia Pseudomallei
          Length = 160

 Score = 30.8 bits (68), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 13/34 (38%), Positives = 17/34 (50%)

Query: 341 RAFSIGDWFVFNQVCKNVEPLIFREFVHDLAKRL 374
           RAF  GDWFVF    + + P +   F  +   RL
Sbjct: 95  RAFEPGDWFVFGAETRGLAPALVDRFAPEQRVRL 128


>pdb|3UIE|A Chain A, Crystal Structure Of Adenosine 5'-Phosphosulfate Kinase
           From Arabidopsis Thaliana In Complex With Amppnp And Aps
 pdb|3UIE|B Chain B, Crystal Structure Of Adenosine 5'-Phosphosulfate Kinase
           From Arabidopsis Thaliana In Complex With Amppnp And Aps
 pdb|3UIE|C Chain C, Crystal Structure Of Adenosine 5'-Phosphosulfate Kinase
           From Arabidopsis Thaliana In Complex With Amppnp And Aps
 pdb|4FXP|A Chain A, Crystal Structure Of Adenosine 5'-Phosphosulfate Kinase
           From Arabidopsis Thaliana In Complex With Sulfate And
           Aps
 pdb|4FXP|B Chain B, Crystal Structure Of Adenosine 5'-Phosphosulfate Kinase
           From Arabidopsis Thaliana In Complex With Sulfate And
           Aps
 pdb|4FXP|C Chain C, Crystal Structure Of Adenosine 5'-Phosphosulfate Kinase
           From Arabidopsis Thaliana In Complex With Sulfate And
           Aps
          Length = 200

 Score = 30.8 bits (68), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 19/60 (31%), Positives = 29/60 (48%), Gaps = 8/60 (13%)

Query: 125 PRYLWKIWEGGRIRMIVQ-------ELNCPIIVGGKQGTKEMEEKRKMIVDYFHNNLHLQ 177
           P+ L+K+   G+I+            LNC I +G + GT  +E   K +V Y  N  +LQ
Sbjct: 141 PKGLYKLARAGKIKGFTGIDDPYEPPLNCEISLGREGGTSPIEMAEK-VVGYLDNKGYLQ 199


>pdb|3F7F|A Chain A, Structure Of Nup120
 pdb|3F7F|B Chain B, Structure Of Nup120
 pdb|3F7F|C Chain C, Structure Of Nup120
 pdb|3F7F|D Chain D, Structure Of Nup120
          Length = 729

 Score = 27.7 bits (60), Expect = 9.6,   Method: Compositional matrix adjust.
 Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 6/53 (11%)

Query: 5   FSSLRSLLKLDQIAIDNTVFRLHYKVTVVILVTFSLIVTSRQYIGDPIDCIVD 57
           F+S+ SL  L Q+        +HY++T+ +L+TF L     +  G  I  ++D
Sbjct: 610 FTSIISLESLHQL------LSIHYRITLQVLLTFVLFDLDTEIFGQHISTLLD 656


>pdb|3H7N|A Chain A, Structure Of Nup120
 pdb|3H7N|B Chain B, Structure Of Nup120
 pdb|3H7N|C Chain C, Structure Of Nup120
 pdb|3H7N|D Chain D, Structure Of Nup120
          Length = 729

 Score = 27.7 bits (60), Expect = 9.9,   Method: Compositional matrix adjust.
 Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 6/53 (11%)

Query: 5   FSSLRSLLKLDQIAIDNTVFRLHYKVTVVILVTFSLIVTSRQYIGDPIDCIVD 57
           F+S+ SL  L Q+        +HY++T+ +L+TF L     +  G  I  ++D
Sbjct: 610 FTSIISLESLHQL------LSIHYRITLQVLLTFVLFDLDTEIFGQHISTLLD 656


  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
   0.329    0.143    0.458 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,313,982
Number of Sequences: 62578
Number of extensions: 466817
Number of successful extensions: 866
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 865
Number of HSP's gapped (non-prelim): 11
length of query: 380
length of database: 14,973,337
effective HSP length: 101
effective length of query: 279
effective length of database: 8,652,959
effective search space: 2414175561
effective search space used: 2414175561
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 52 (24.6 bits)