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= psy3897
         (240 letters)

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

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



>pdb|1WLJ|A Chain A, Human Isg20
          Length = 189

 Score = 73.9 bits (180), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 58/161 (36%), Positives = 89/161 (55%), Gaps = 19/161 (11%)

Query: 80  VYALDTEMV----YTVHGLEVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDF 135
           V A+D EMV    +   GL  AR ++VNV G ++Y+  ++P+ EI DY T+ SG++ +  
Sbjct: 7   VVAMDCEMVGLGPHRESGL--ARCSLVNVHGAVLYDKFIRPEGEITDYRTRVSGVTPQHM 64

Query: 136 I-RNPYKTLKDVQNDLMGFVSKDSIIVGHGLENDLRALKLIHS--NIIDTSV--LFPHSF 190
           +   P+   +     L+    K  ++VGH L++D +ALK   S   I DTS   L     
Sbjct: 65  VGATPFAVARLEILQLL----KGKLVVGHDLKHDFQALKEDMSGYTIYDTSTDRLLWREA 120

Query: 191 GLPY--RRSLKSIVSQLLHQSIQSGT--HDSFEDARACIDL 227
            L +  R SL+ +  +LLH+SIQ+    H S EDARA ++L
Sbjct: 121 KLDHCRRVSLRVLSERLLHKSIQNSLLGHSSVEDARATMEL 161


>pdb|2P1J|A Chain A, Crystal Structure Of A Polc-Type Dna Polymerase Iii
           Exonuclease Domain From Thermotoga Maritima
 pdb|2P1J|B Chain B, Crystal Structure Of A Polc-Type Dna Polymerase Iii
           Exonuclease Domain From Thermotoga Maritima
          Length = 186

 Score = 41.2 bits (95), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 27/83 (32%), Positives = 50/83 (60%), Gaps = 6/83 (7%)

Query: 95  EVARVTVVNVDGRLI---YNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLM 151
           E+  +  V + G  I   Y+TL+KP  EI   +++ +GI+ ++ + N  +++++V  + +
Sbjct: 30  EIIEIGAVKIQGGQIVDEYHTLIKPSREISRKSSEITGIT-QEMLENK-RSIEEVLPEFL 87

Query: 152 GFVSKDSIIVGHGLENDLRALKL 174
           GF+ +DSIIV H    D R L+L
Sbjct: 88  GFL-EDSIIVAHNANFDYRFLRL 109


>pdb|1X1O|A Chain A, Crystal Structure Of Project Id Tt0268 From Thermus
          Thermophilus Hb8
 pdb|1X1O|B Chain B, Crystal Structure Of Project Id Tt0268 From Thermus
          Thermophilus Hb8
 pdb|1X1O|C Chain C, Crystal Structure Of Project Id Tt0268 From Thermus
          Thermophilus Hb8
          Length = 286

 Score = 34.3 bits (77), Expect = 0.056,   Method: Compositional matrix adjust.
 Identities = 14/43 (32%), Positives = 21/43 (48%)

Query: 21 SVWERKSLFRKLPPRTGFNPVCTSGLRISALDHVGGINGPLEG 63
           +W  + +F    PRT F P+   G R++    V  + GPL G
Sbjct: 57 GLWVAERVFALADPRTAFTPLVAEGARVAEGTEVARVRGPLRG 99


>pdb|1WRU|A Chain A, Structure Of Central Hub Elucidated By X-Ray Analysis Of
           Gene Product 44; Baseplate Component Of Bacteriophage Mu
          Length = 379

 Score = 30.0 bits (66), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 17/44 (38%), Positives = 22/44 (50%), Gaps = 1/44 (2%)

Query: 32  LPPRTGF-NPVCTSGLRISALDHVGGINGPLEGYVKTKPRKSPP 74
           L PR GF  PV +        D  GGI+  +E Y +  P K+PP
Sbjct: 333 LAPREGFLVPVESDRKNRKGGDSNGGIDALVEDYYRRHPEKTPP 376


>pdb|2VDJ|A Chain A, Crystal Structure Of Homoserine O-acetyltransferase (meta)
           From Bacillus Cereus With Homoserine
          Length = 301

 Score = 28.1 bits (61), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 13/43 (30%), Positives = 26/43 (60%)

Query: 107 RLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQND 149
           RLI NT ++ D  ++   +  S   A++ + + YKT +D++N+
Sbjct: 56  RLIGNTPLQLDVHLLHMESHLSRNVAQEHLTSFYKTFRDIENE 98


>pdb|2GHR|A Chain A, Crystal Structure Of Homoserine O-Succinyltransferase
           (Np_981826.1) From Bacillus Cereus Atcc 10987 At 2.40 A
           Resolution
          Length = 302

 Score = 28.1 bits (61), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 13/43 (30%), Positives = 26/43 (60%)

Query: 107 RLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQND 149
           RLI NT ++ D  ++   +  S   A++ + + YKT +D++N+
Sbjct: 57  RLIGNTPLQLDVHLLHXESHLSRNVAQEHLTSFYKTFRDIENE 99


  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
   0.320    0.138    0.411 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,242,208
Number of Sequences: 62578
Number of extensions: 290529
Number of successful extensions: 587
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 572
Number of HSP's gapped (non-prelim): 26
length of query: 240
length of database: 14,973,337
effective HSP length: 96
effective length of query: 144
effective length of database: 8,965,849
effective search space: 1291082256
effective search space used: 1291082256
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)