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= psy4290
         (135 letters)

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

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



>pdb|2RGW|A Chain A, Catalytic Subunit Of M. Jannaschii Aspartate
           Transcarbamoylase
 pdb|2RGW|B Chain B, Catalytic Subunit Of M. Jannaschii Aspartate
           Transcarbamoylase
 pdb|2RGW|C Chain C, Catalytic Subunit Of M. Jannaschii Aspartate
           Transcarbamoylase
 pdb|2RGW|D Chain D, Catalytic Subunit Of M. Jannaschii Aspartate
           Transcarbamoylase
 pdb|2RGW|E Chain E, Catalytic Subunit Of M. Jannaschii Aspartate
           Transcarbamoylase
 pdb|2RGW|F Chain F, Catalytic Subunit Of M. Jannaschii Aspartate
           Transcarbamoylase
 pdb|3E2P|A Chain A, Catalytic Subunit Of M. Jannaschii Aspartate
           Transcarbamoylase In An Orthorhombic Crystal Form
 pdb|3E2P|B Chain B, Catalytic Subunit Of M. Jannaschii Aspartate
           Transcarbamoylase In An Orthorhombic Crystal Form
 pdb|3E2P|C Chain C, Catalytic Subunit Of M. Jannaschii Aspartate
           Transcarbamoylase In An Orthorhombic Crystal Form
 pdb|3E2P|D Chain D, Catalytic Subunit Of M. Jannaschii Aspartate
           Transcarbamoylase In An Orthorhombic Crystal Form
 pdb|3E2P|E Chain E, Catalytic Subunit Of M. Jannaschii Aspartate
           Transcarbamoylase In An Orthorhombic Crystal Form
 pdb|3E2P|F Chain F, Catalytic Subunit Of M. Jannaschii Aspartate
           Transcarbamoylase In An Orthorhombic Crystal Form
 pdb|3E2P|I Chain I, Catalytic Subunit Of M. Jannaschii Aspartate
           Transcarbamoylase In An Orthorhombic Crystal Form
 pdb|3E2P|J Chain J, Catalytic Subunit Of M. Jannaschii Aspartate
           Transcarbamoylase In An Orthorhombic Crystal Form
 pdb|3E2P|K Chain K, Catalytic Subunit Of M. Jannaschii Aspartate
           Transcarbamoylase In An Orthorhombic Crystal Form
 pdb|3E2P|L Chain L, Catalytic Subunit Of M. Jannaschii Aspartate
           Transcarbamoylase In An Orthorhombic Crystal Form
 pdb|3E2P|M Chain M, Catalytic Subunit Of M. Jannaschii Aspartate
           Transcarbamoylase In An Orthorhombic Crystal Form
 pdb|3E2P|N Chain N, Catalytic Subunit Of M. Jannaschii Aspartate
           Transcarbamoylase In An Orthorhombic Crystal Form
 pdb|4EKN|B Chain B, Structure Of The Catalytic Chain Of Methanococcus
           Jannaschii Aspartate Transcarbamoylase In A Hexagonal
           Crystal Form
          Length = 306

 Score = 26.2 bits (56), Expect = 6.4,   Method: Compositional matrix adjust.
 Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 5/54 (9%)

Query: 65  VPWTSLGSSSV---EVVIDTIGYLSGIFECMAAIHALNGRYATALQYAILLVPI 115
           +  T L SSSV   E +IDTI  +SG  + +   H   G    A +Y+   VPI
Sbjct: 70  ITMTDLKSSSVAKGESLIDTIRVISGYADIIVLRHPSEGAARLASEYS--QVPI 121


>pdb|2W27|A Chain A, Crystal Structure Of The Bacillus Subtilis Ykui Protein,
           With An Eal Domain, In Complex With Substrate C-Di-Gmp
           And Calcium
 pdb|2W27|B Chain B, Crystal Structure Of The Bacillus Subtilis Ykui Protein,
           With An Eal Domain, In Complex With Substrate C-Di-Gmp
           And Calcium
          Length = 431

 Score = 25.8 bits (55), Expect = 7.3,   Method: Composition-based stats.
 Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 8/71 (11%)

Query: 16  LQEFFRSTLQLHLWEGQACFHNLELDLEALESLVPFHFVSGHINELRIKVPWTSLGSSSV 75
           L+E+    ++LH +  +   HN E D+E L  ++ ++   G      IK+   ++G  S 
Sbjct: 130 LKEYEAKGIELHRFVLEITEHNFEGDIEQLYHMLAYYRTYG------IKIAVDNIGKESS 183

Query: 76  EVVIDTIGYLS 86
              +D I  LS
Sbjct: 184 N--LDRIALLS 192


  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    0.135    0.425 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,734,757
Number of Sequences: 62578
Number of extensions: 129600
Number of successful extensions: 201
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 201
Number of HSP's gapped (non-prelim): 3
length of query: 135
length of database: 14,973,337
effective HSP length: 88
effective length of query: 47
effective length of database: 9,466,473
effective search space: 444924231
effective search space used: 444924231
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: 46 (22.3 bits)