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= psy5654
         (224 letters)

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

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



>pdb|2WP1|A Chain A, Structure Of Brdt Bromodomain 2 Bound To An Acetylated
           Histone H3 Peptide
 pdb|2WP1|B Chain B, Structure Of Brdt Bromodomain 2 Bound To An Acetylated
           Histone H3 Peptide
          Length = 126

 Score = 30.8 bits (68), Expect = 0.58,   Method: Compositional matrix adjust.
 Identities = 19/69 (27%), Positives = 35/69 (50%), Gaps = 9/69 (13%)

Query: 111 KVLQNTKVITNIKECSSVVEELMRNELVTFDCEGINPGIKGQITLFSLGLLSGQVYIFDL 170
           KVL+  KV   +K CS +++E++  + + +     NP     +   +LGL +     +D+
Sbjct: 5   KVLKTVKVTEQLKHCSEILKEMLAKKHLPYAWPFYNP-----VDADALGLHN----YYDV 55

Query: 171 VTCPEVVGT 179
           V  P  +GT
Sbjct: 56  VKNPMDLGT 64


>pdb|2FBT|A Chain A, Wrn Exonuclease
 pdb|2FBV|A Chain A, Wrn Exonuclease, Mn Complex
 pdb|2FBX|A Chain A, Wrn Exonuclease, Mg Complex
 pdb|2FBY|A Chain A, Wrn Exonuclease, Eu Complex
 pdb|2FC0|A Chain A, Wrn Exonuclease, Mn Dgmp Complex
          Length = 205

 Score = 30.0 bits (66), Expect = 0.97,   Method: Compositional matrix adjust.
 Identities = 29/99 (29%), Positives = 44/99 (44%), Gaps = 9/99 (9%)

Query: 124 ECSSVVEE----LMRNELVTFDCEG---INPGIKGQITLFSLGLLSGQVYIFDLVTCPEV 176
           +CS + E+    L   ++V FD E     N G  G++ L  L +   + Y+F + +    
Sbjct: 30  DCSFLSEDISMSLSDGDVVGFDMEWPPLYNRGKLGKVALIQLCVSESKCYLFHVSSMS-- 87

Query: 177 VGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLRN 215
           V   GL  LLE++ V K       D   L   F I L+N
Sbjct: 88  VFPQGLKMLLENKAVKKAGVGIEGDQWKLLRDFDIKLKN 126


>pdb|2H3G|X Chain X, Structure Of The Type Iii Pantothenate Kinase (Coax) From
           Bacillus Anthracis
          Length = 268

 Score = 27.3 bits (59), Expect = 6.8,   Method: Compositional matrix adjust.
 Identities = 13/23 (56%), Positives = 18/23 (78%), Gaps = 1/23 (4%)

Query: 174 PEVVGTGGLSKLL-ESENVIKVI 195
           P+V+ TGGL+KL+ E  NVI V+
Sbjct: 215 PKVIATGGLAKLISEESNVIDVV 237


>pdb|3SAF|A Chain A, Crystal Structure Of The Human Rrp6 Catalytic Domain With
           D313n Mutation In The Active Site
 pdb|3SAF|B Chain B, Crystal Structure Of The Human Rrp6 Catalytic Domain With
           D313n Mutation In The Active Site
 pdb|3SAG|A Chain A, Crystal Structure Of The Human Rrp6 Catalytic Domain With
           D313n Mutation In The Active Site
 pdb|3SAG|B Chain B, Crystal Structure Of The Human Rrp6 Catalytic Domain With
           D313n Mutation In The Active Site
          Length = 428

 Score = 26.9 bits (58), Expect = 8.3,   Method: Compositional matrix adjust.
 Identities = 13/39 (33%), Positives = 22/39 (56%)

Query: 182 LSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQ 220
           L++ L    ++KV H   +D   L + FG+ + N+FDT 
Sbjct: 174 LNESLTDPAIVKVFHGADSDIEWLQKDFGLYVVNMFDTH 212


>pdb|3SAH|A Chain A, Crystal Structure Of The Human Rrp6 Catalytic Domain With
           Y436a Mutation In The Catalytic Site
 pdb|3SAH|B Chain B, Crystal Structure Of The Human Rrp6 Catalytic Domain With
           Y436a Mutation In The Catalytic Site
          Length = 428

 Score = 26.9 bits (58), Expect = 8.5,   Method: Compositional matrix adjust.
 Identities = 13/39 (33%), Positives = 22/39 (56%)

Query: 182 LSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQ 220
           L++ L    ++KV H   +D   L + FG+ + N+FDT 
Sbjct: 174 LNESLTDPAIVKVFHGADSDIEWLQKDFGLYVVNMFDTH 212


  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
   0.314    0.131    0.365 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,168,770
Number of Sequences: 62578
Number of extensions: 233792
Number of successful extensions: 375
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 369
Number of HSP's gapped (non-prelim): 10
length of query: 224
length of database: 14,973,337
effective HSP length: 95
effective length of query: 129
effective length of database: 9,028,427
effective search space: 1164667083
effective search space used: 1164667083
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 49 (23.5 bits)