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= psy12638
         (334 letters)

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

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



>pdb|3S1S|A Chain A, Characterization And Crystal Structure Of The Type Iig
           Restriction Endonuclease Bpusi
          Length = 878

 Score = 28.9 bits (63), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 24/103 (23%), Positives = 48/103 (46%), Gaps = 21/103 (20%)

Query: 181 LNSRNAELMLKNRQLELLMIQAFTQKNILLLKVIRNMSIHSNVKHYFVDYIGDIANCVQK 240
           + S  A+ ++KN+Q         T+K +L+++V R  S  S+ ++               
Sbjct: 54  VGSIEADFVIKNKQ---------TKKYLLIVEVKRTKSQVSSTRYRL--------QAQSY 96

Query: 241 EKDENIKLE----CLGTLEVINFIGTAASDPISAEHFCKNSTV 279
            ++ NIK+E    CL  LE+I+F     + P+ ++   + S +
Sbjct: 97  VREANIKVEQHYYCLTNLEIIDFFKHDPNKPVVSQQIIEPSPI 139


>pdb|1V71|A Chain A, Crystal Structure Of S.pombe Serine Racemase
 pdb|1WTC|A Chain A, Crystal Structure Of S.ponbe Serine Racemase Complex With
           Amppcp
 pdb|2ZPU|A Chain A, Crystal Structure Of Modified Serine Racemase From
           S.Pombe.
 pdb|2ZR8|A Chain A, Crystal Structure Of Modified Serine Racemase Complexed
           With Serine
          Length = 323

 Score = 28.9 bits (63), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 11/29 (37%), Positives = 19/29 (65%), Gaps = 1/29 (3%)

Query: 35  NCNCYGLIVPKSKREGRQDSRKLSVYHVN 63
           NC  YG + P++  +G+Q  RK S+ H++
Sbjct: 201 NCEVYG-VEPEAGNDGQQSFRKGSIVHID 228


>pdb|1XM9|A Chain A, Structure Of The Armadillo Repeat Domain Of Plakophilin 1
          Length = 457

 Score = 28.5 bits (62), Expect = 5.8,   Method: Compositional matrix adjust.
 Identities = 36/122 (29%), Positives = 57/122 (46%), Gaps = 18/122 (14%)

Query: 40  GLIVPKSKRE-GRQDSR--KLSVYHVN---------KEQMANLNLIEKLPRILMIEDSNL 87
           GL +PK+ +    QD +   +  Y++          K+Q+  L  I KL  +L   + N+
Sbjct: 1   GLTIPKAVQYLSSQDEKYQAIGAYYIQHTCFQDESAKQQVYQLGGICKLVDLLRSPNQNV 60

Query: 88  QSSTLKLLFNLSF--DTNLREKIIKIGFLPKLVSLLEEGKH---QKIILQLLYHLSIEDR 142
           Q +    L NL F   TN  E   + G + + VSLL    +   QK +  LL++LS  D 
Sbjct: 61  QQAAAGALRNLVFRSTTNKLETRRQNG-IREAVSLLRRTGNAEIQKQLTGLLWNLSSTDE 119

Query: 143 VK 144
           +K
Sbjct: 120 LK 121


>pdb|2NSA|A Chain A, Structures Of And Interactions Between Domains Of Trigger
           Factor From Themotoga Maritim
          Length = 170

 Score = 27.7 bits (60), Expect = 8.7,   Method: Compositional matrix adjust.
 Identities = 20/60 (33%), Positives = 33/60 (55%), Gaps = 9/60 (15%)

Query: 47  KREGRQDSRKLSVYHVNKEQMANLNLIEKLPRILMIEDSNLQSSTLKLLFNLSFDTNLRE 106
           K+EG++      +Y V  ++     L+EKLP I+ IE S+    TL++L N + +   RE
Sbjct: 14  KKEGKE------IYDVEXKESXREQLLEKLPEIVEIEISD---RTLEILVNEAINRLKRE 64


  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
   0.322    0.137    0.391 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,743,207
Number of Sequences: 62578
Number of extensions: 321920
Number of successful extensions: 746
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 745
Number of HSP's gapped (non-prelim): 16
length of query: 334
length of database: 14,973,337
effective HSP length: 99
effective length of query: 235
effective length of database: 8,778,115
effective search space: 2062857025
effective search space used: 2062857025
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: 52 (24.6 bits)