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= psy444
         (495 letters)

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

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



>pdb|4FLA|A Chain A, Crystal Structure Of Human Rprd1b, Carboxy-Terminal Domain
 pdb|4FLA|B Chain B, Crystal Structure Of Human Rprd1b, Carboxy-Terminal Domain
 pdb|4FLA|C Chain C, Crystal Structure Of Human Rprd1b, Carboxy-Terminal Domain
 pdb|4FLA|D Chain D, Crystal Structure Of Human Rprd1b, Carboxy-Terminal Domain
          Length = 152

 Score = 32.0 bits (71), Expect = 0.84,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 24/42 (57%)

Query: 344 KRKDEEIKRLKEEIGKYKMLVQERDQLANMLEEYKQNAKDVV 385
           K  DE    L E  G+    +++R QLA ML EY QN KDV+
Sbjct: 75  KTVDEACLLLAEYNGRLAAELEDRRQLARMLVEYTQNQKDVL 116


>pdb|1KGG|A Chain A, Structure Of Beta-Lactamase Glu166gln:asn170asp Mutant
          Length = 258

 Score = 28.5 bits (62), Expect = 7.8,   Method: Compositional matrix adjust.
 Identities = 31/107 (28%), Positives = 52/107 (48%), Gaps = 21/107 (19%)

Query: 84  QHLEKIKKEFKELQEKYQRDLNQKTETIRSLTNKNLELKVQYEEEIDNRDTRIKELTSDT 143
             ++K+K+  KEL +K              +TN      V+Y+ E+D    + K+ TS  
Sbjct: 111 GGIKKVKQRLKELGDK--------------VTNP-----VRYQIELDYYSPKSKKDTSTP 151

Query: 144 SEIDKIVSRKDAEIEKLSKENEKLSMDLVFKENQEVTELMKEVDKKD 190
           +   K +++  A   KLSKEN+K  +DL+   N+    L+K+   KD
Sbjct: 152 AAFGKTLNKLIAN-GKLSKENKKFLLDLML-NNKSGDTLIKDGVPKD 196


>pdb|2QJ0|A Chain A, Structure Of The Yeast U-Box-Containing Ubiquitin Ligase
           Ufd2p
          Length = 982

 Score = 28.5 bits (62), Expect = 7.8,   Method: Compositional matrix adjust.
 Identities = 15/38 (39%), Positives = 20/38 (52%)

Query: 337 AGLLTKEKRKDEEIKRLKEEIGKYKMLVQERDQLANML 374
            G L+ E++   EIK LKEEI K K +    D  A  +
Sbjct: 419 GGTLSFEEKXGSEIKALKEEIEKVKKIAANHDVFARFI 456


  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
   0.309    0.128    0.325 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,218,053
Number of Sequences: 62578
Number of extensions: 480152
Number of successful extensions: 2822
Number of sequences better than 100.0: 287
Number of HSP's better than 100.0 without gapping: 78
Number of HSP's successfully gapped in prelim test: 209
Number of HSP's that attempted gapping in prelim test: 2441
Number of HSP's gapped (non-prelim): 517
length of query: 495
length of database: 14,973,337
effective HSP length: 103
effective length of query: 392
effective length of database: 8,527,803
effective search space: 3342898776
effective search space used: 3342898776
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 53 (25.0 bits)