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= 025096
         (258 letters)

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

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



>pdb|3T5X|A Chain A, Pcid2:dss1 Structure
          Length = 203

 Score =  162 bits (409), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 79/201 (39%), Positives = 134/201 (66%), Gaps = 7/201 (3%)

Query: 53  EEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQSEANIRMILKYLIPVKLS 112
           +++    +VTY YY GR  +F+ +F  A++ LS+A  +C+  S+ N RMIL YL+PVK+ 
Sbjct: 6   DDYSTAQRVTYKYYVGRKAMFDSDFKQAEEYLSFAFEHCHRSSQKNKRMILIYLLPVKML 65

Query: 113 IGILPKDWLLEKYNLVEYSNIVQALRRGDXXXXXXXXXXXXDQFLRSGVYLVLEKLELQV 172
           +G +P   LL+KY+L++++ + +A+  G+              F+R G++L+LEKL++  
Sbjct: 66  LGHMPTVELLKKYHLMQFAEVTRAVSEGNLLLLHEALAKHEAFFIRCGIFLILEKLKIIT 125

Query: 173 YQRLFKKIYIIQKQKDPSKAHQMKLDVIVKALKWLEM-DMDVDEVECIVAILIHKNLVKG 231
           Y+ LFKK+Y++       K HQ+ LD  + ALK++++ D+D+DEV+CI+A LI+   VKG
Sbjct: 126 YRNLFKKVYLL------LKTHQLSLDAFLVALKFMQVEDVDIDEVQCILANLIYMGHVKG 179

Query: 232 YFAHKSKVVVLSKQDPFPKLN 252
           Y +H+ + +V+SKQ+PFP L+
Sbjct: 180 YISHQHQKLVVSKQNPFPPLS 200


>pdb|3T5V|B Chain B, Sac3:thp1:sem1 Complex
 pdb|3T5V|E Chain E, Sac3:thp1:sem1 Complex
          Length = 455

 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 45/183 (24%), Positives = 82/183 (44%), Gaps = 15/183 (8%)

Query: 11  GSKRVGALYLTCQLFKIYFKLGTVHLCRSVIRSIETARIF-DFEEFPKRDKVTYMYYTGR 69
           G +R+  LYL  +L  IYF++ +  LC ++ ++ +   +   F E+    ++ Y Y  GR
Sbjct: 170 GKQRI-LLYLVNKLNNIYFRIESPQLCSNIFKNFQPKSMLAHFNEYQLDQQIEYRYLLGR 228

Query: 70  LEVFNENFPAADQKLSYA---LINCNPQSEA---NIRMILKYLIPVKLSIGILPKDW--- 120
             + N     A  + + A   L+N    ++A   N   IL Y+IP  L +G + K W   
Sbjct: 229 YYLLNSQVHNAFVQFNEAFQSLLNLPLTNQAITRNGTRILNYMIPTGLILGKMVK-WGPL 287

Query: 121 --LLEKYNLVEYSNIVQALRRGDXXXXXXXXXXXXDQFL-RSGVYLVLEKLELQVYQRLF 177
              L +  +  +S + + +R G+                 R  + ++LEKL +  Y+ L 
Sbjct: 288 RPFLSQETIDNWSVLYKHVRYGNIQGVSLWLRQNERHLCARQLLIVLLEKLPMVTYRNLI 347

Query: 178 KKI 180
           K +
Sbjct: 348 KTV 350


>pdb|3R0H|A Chain A, Structure Of Inad Pdz45 In Complex With Ng2 Peptide
 pdb|3R0H|B Chain B, Structure Of Inad Pdz45 In Complex With Ng2 Peptide
 pdb|3R0H|C Chain C, Structure Of Inad Pdz45 In Complex With Ng2 Peptide
 pdb|3R0H|D Chain D, Structure Of Inad Pdz45 In Complex With Ng2 Peptide
 pdb|3R0H|E Chain E, Structure Of Inad Pdz45 In Complex With Ng2 Peptide
 pdb|3R0H|F Chain F, Structure Of Inad Pdz45 In Complex With Ng2 Peptide
 pdb|3R0H|G Chain G, Structure Of Inad Pdz45 In Complex With Ng2 Peptide
 pdb|3R0H|H Chain H, Structure Of Inad Pdz45 In Complex With Ng2 Peptide
          Length = 206

 Score = 28.5 bits (62), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 14/56 (25%), Positives = 31/56 (55%), Gaps = 1/56 (1%)

Query: 171 QVYQRLFKK-IYIIQKQKDPSKAHQMKLDVIVKALKWLEMDMDVDEVECIVAILIH 225
           Q++   ++K + +   + DP +  +  +D++ KA K L + +  +E+ C +A LI 
Sbjct: 90  QLFHTTYEKAVTLTVFRADPPELEKFNVDLMKKAGKELGLSLSPNEIGCTIADLIQ 145


>pdb|1DKR|A Chain A, Crystal Structures Of Bacillus Subtilis
           Phosphoribosylpyrophosphate Synthetase: Molecular Basis
           Of Allosteric Inhibition And Activation.
 pdb|1DKR|B Chain B, Crystal Structures Of Bacillus Subtilis
           Phosphoribosylpyrophosphate Synthetase: Molecular Basis
           Of Allosteric Inhibition And Activation.
 pdb|1DKU|A Chain A, Crystal Structures Of Bacillus Subtilis
           Phosphoribosylpyrophosphate Synthetase: Molecular Basis
           Of Allosteric Inhibition And Activation.
 pdb|1DKU|B Chain B, Crystal Structures Of Bacillus Subtilis
           Phosphoribosylpyrophosphate Synthetase: Molecular Basis
           Of Allosteric Inhibition And Activation.
 pdb|1IBS|A Chain A, Phosphoribosyldiphosphate Synthetase In Complex With
           Cadmium Ions
 pdb|1IBS|B Chain B, Phosphoribosyldiphosphate Synthetase In Complex With
           Cadmium Ions
          Length = 317

 Score = 28.5 bits (62), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 13/25 (52%), Positives = 16/25 (64%)

Query: 181 YIIQKQKDPSKAHQMKLDVIVKALK 205
           YIIQ   DP   H M+L ++V ALK
Sbjct: 60  YIIQSTSDPVNEHIMELLIMVDALK 84


  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
   0.324    0.141    0.411 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,028,256
Number of Sequences: 62578
Number of extensions: 256863
Number of successful extensions: 591
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 584
Number of HSP's gapped (non-prelim): 8
length of query: 258
length of database: 14,973,337
effective HSP length: 97
effective length of query: 161
effective length of database: 8,903,271
effective search space: 1433426631
effective search space used: 1433426631
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 50 (23.9 bits)