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= 021452
         (312 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 = 3e-40,   Method: Compositional matrix adjust.
 Identities = 79/201 (39%), Positives = 134/201 (66%), Gaps = 7/201 (3%)

Query: 107 EEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQSEANIRMILKYLIPVKLS 166
           +++    +VTY YY GR  +F+ +F  A++ LS+A  +C+  S+ N RMIL YL+PVK+ 
Sbjct: 6   DDYSTAQRVTYKYYVGRKAMFDSDFKQAEEYLSFAFEHCHRSSQKNKRMILIYLLPVKML 65

Query: 167 IGILPKDWLLEKYNLVEYSNIVQALRRGDXXXXXXXXXXXXDQFLRSGVYLVLEKLELQV 226
           +G +P   LL+KY+L++++ + +A+  G+              F+R G++L+LEKL++  
Sbjct: 66  LGHMPTVELLKKYHLMQFAEVTRAVSEGNLLLLHEALAKHEAFFIRCGIFLILEKLKIIT 125

Query: 227 YQRLFKKIYIIQKQKDPSKAHQMKLDVIVKALKWLEM-DMDVDEVECIVAILIHKNLVKG 285
           Y+ LFKK+Y++       K HQ+ LD  + ALK++++ D+D+DEV+CI+A LI+   VKG
Sbjct: 126 YRNLFKKVYLL------LKTHQLSLDAFLVALKFMQVEDVDIDEVQCILANLIYMGHVKG 179

Query: 286 YFAHKSKVVVLSKQDPFPKLN 306
           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 = 45.1 bits (105), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 55/237 (23%), Positives = 100/237 (42%), Gaps = 26/237 (10%)

Query: 21  SELGIRLGFGSIADRELASNGKSPEKLKAAGSFLMKVFGVLAGK----------GSKRVG 70
           +E  I L  G +    L  + +S + L    S L ++F  +             G +R+ 
Sbjct: 117 TEFIINLA-GKLDSFHLQLHTRSHQFLSHISSILSRLFNSIKPPRGNASSTNIPGKQRI- 174

Query: 71  ALYLTCQLFKIYFKLGTVHLCRSVIRSIETARIF-DFEEFPKRDKVTYMYYTGRLEVFNE 129
            LYL  +L  IYF++ +  LC ++ ++ +   +   F E+    ++ Y Y  GR  + N 
Sbjct: 175 LLYLVNKLNNIYFRIESPQLCSNIFKNFQPKSMLAHFNEYQLDQQIEYRYLLGRYYLLNS 234

Query: 130 NFPAADQKLSYA---LINCNPQSEANIR---MILKYLIPVKLSIGILPKDW-----LLEK 178
               A  + + A   L+N    ++A  R    IL Y+IP  L +G + K W      L +
Sbjct: 235 QVHNAFVQFNEAFQSLLNLPLTNQAITRNGTRILNYMIPTGLILGKMVK-WGPLRPFLSQ 293

Query: 179 YNLVEYSNIVQALRRGDXXXXXXXXXXXXDQFL-RSGVYLVLEKLELQVYQRLFKKI 234
             +  +S + + +R G+                 R  + ++LEKL +  Y+ L K +
Sbjct: 294 ETIDNWSVLYKHVRYGNIQGVSLWLRQNERHLCARQLLIVLLEKLPMVTYRNLIKTV 350


>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 = 4.9,   Method: Compositional matrix adjust.
 Identities = 13/25 (52%), Positives = 16/25 (64%)

Query: 235 YIIQKQKDPSKAHQMKLDVIVKALK 259
           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
   0.323    0.140    0.410 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,584,912
Number of Sequences: 62578
Number of extensions: 325623
Number of successful extensions: 517
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 511
Number of HSP's gapped (non-prelim): 7
length of query: 312
length of database: 14,973,337
effective HSP length: 99
effective length of query: 213
effective length of database: 8,778,115
effective search space: 1869738495
effective search space used: 1869738495
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (24.3 bits)