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= psy6664
         (624 letters)

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

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



>pdb|2B3P|A Chain A, Crystal Structure Of A Superfolder Green Fluorescent
           Protein
          Length = 244

 Score = 32.3 bits (72), Expect = 0.74,   Method: Compositional matrix adjust.
 Identities = 35/146 (23%), Positives = 61/146 (41%), Gaps = 24/146 (16%)

Query: 134 RSVSWLRRTEYISTEQTRFQPQ-VMDKVEAK----------VGFSIKKNFKEDNLYMDRD 182
           R++S+     Y +  + +F+   +++++E K          +G  ++ NF   N+Y+  D
Sbjct: 94  RTISFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHNVYITAD 153

Query: 183 SQVKAIEKTFA------DSKLPIEKHYSKPNVTPVEIMPV-YPDFKYWKYPCAQVIFDSD 235
            Q   I+  F       D  + +  HY +   TP+   PV  PD  Y      Q +   D
Sbjct: 154 KQKNGIKANFKIRHNVEDGSVQLADHYQQN--TPIGDGPVLLPDNHYL---STQSVLSKD 208

Query: 236 PAPVGRPIPAQIEEMSQAMIRGVMDE 261
           P    R     +E ++ A I   MDE
Sbjct: 209 PNEK-RDHMVLLEFVTAAGITHGMDE 233


>pdb|1KYP|A Chain A, Crystal Structure Of An Apo Green Fluorescent Protein Zn
           Biosensor
 pdb|1KYR|A Chain A, Crystal Structure Of A Cu-Bound Green Fluorescent Protein
           Zn Biosensor
 pdb|1KYS|A Chain A, Crystal Structure Of A Zn-Bound Green Fluorescent Protein
           Biosensor
          Length = 237

 Score = 30.8 bits (68), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 35/146 (23%), Positives = 60/146 (41%), Gaps = 24/146 (16%)

Query: 134 RSVSWLRRTEYISTEQTRFQPQ-VMDKVEAK----------VGFSIKKNFKEDNLYMDRD 182
           R++S+     Y +  + +F+   +++++E K          +G  ++ NF   N+Y+  D
Sbjct: 95  RTISFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSGNVYITAD 154

Query: 183 SQVKAIEKTFA------DSKLPIEKHYSKPNVTPVEIMPV-YPDFKYWKYPCAQVIFDSD 235
            Q   I+  F       D  + +  HY +   TP+   PV  PD  Y      Q     D
Sbjct: 155 KQKNGIKANFKIRHNIEDGSVQLADHYQQN--TPIGDGPVLLPDNHYL---STQSALSKD 209

Query: 236 PAPVGRPIPAQIEEMSQAMIRGVMDE 261
           P    R     +E ++ A I   MDE
Sbjct: 210 PNEK-RDHMVLLEFVTAAGITHGMDE 234


>pdb|3BQU|D Chain D, Crystal Structure Of The 2f5 Fab'-3h6 Fab Complex
          Length = 241

 Score = 30.8 bits (68), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 21/80 (26%), Positives = 32/80 (40%), Gaps = 1/80 (1%)

Query: 253 AMIRGVMDESGEQFVAYFLPTAETLDKRKLDQLSNLE-YTDEQEYEYKMAREYNWNVKSK 311
           A ++     SG  F  YF+   +    + LD +  +  YT    Y  K   +  + V + 
Sbjct: 35  ASVKMSCKASGYSFTDYFMHWVKQSHGKSLDWIGYINCYTGATNYSQKFKGKATFTVDTS 94

Query: 312 SCKGYEENYFLIVRDDAVYY 331
           S   Y +   L   D AVYY
Sbjct: 95  SNTAYMQFNSLTSEDSAVYY 114


  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
   0.315    0.131    0.378 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,881,317
Number of Sequences: 62578
Number of extensions: 486087
Number of successful extensions: 1374
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1374
Number of HSP's gapped (non-prelim): 4
length of query: 624
length of database: 14,973,337
effective HSP length: 105
effective length of query: 519
effective length of database: 8,402,647
effective search space: 4360973793
effective search space used: 4360973793
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (25.4 bits)