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= 004532
         (746 letters)

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

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



>pdb|1WID|A Chain A, Solution Structure Of The B3 Dna-Binding Domain Of Rav1
          Length = 130

 Score = 63.2 bits (152), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 36/103 (34%), Positives = 54/103 (52%), Gaps = 2/103 (1%)

Query: 160 MFCKTLTASDTSTHGGFSVPRRAAEDCFPPLDYSQQRPSQELVAKDLHGLEWRFRHIYRG 219
           +F K +T SD        +P+  AE  FP    +       L  +D++G  WRFR+ Y  
Sbjct: 13  LFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYWN 72

Query: 220 QPRRHLLTTGWSAFVNKKKLVSGDAVLFLR--GEDGELRLGIR 260
             + ++LT GWS FV +K L +GD V F R  G+D +L +G +
Sbjct: 73  SSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSNGQDQQLYIGWK 115


>pdb|1XR4|A Chain A, X-ray Crystal Structure Of Putative Citrate Lyase Alpha
           Chain/citrate- Acp Transferase [salmonella Typhimurium]
 pdb|1XR4|B Chain B, X-ray Crystal Structure Of Putative Citrate Lyase Alpha
           Chain/citrate- Acp Transferase [salmonella Typhimurium]
          Length = 509

 Score = 31.6 bits (70), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 16/48 (33%), Positives = 24/48 (50%)

Query: 593 NPPYSLNDQEKEQRVNCQSFFHNSEIYGGKHASSSFLDHSFRGGDQEV 640
           N P+  ++ EK +R  C S        G K+  +    H+FRGGD+ V
Sbjct: 30  NSPWLASETEKRRRKICDSLEEAIRRSGLKNGXTISFHHAFRGGDKVV 77


>pdb|2Y2Z|A Chain A, Ligand-Free Form Of Tetr-Like Repressor Simr
 pdb|2Y30|A Chain A, Simocyclinone D8 Bound Form Of Tetr-Like Repressor Simr
 pdb|2Y30|B Chain B, Simocyclinone D8 Bound Form Of Tetr-Like Repressor Simr
 pdb|2Y31|A Chain A, Simocyclinone C4 Bound Form Of Tetr-Like Repressor Simr
 pdb|2Y31|B Chain B, Simocyclinone C4 Bound Form Of Tetr-Like Repressor Simr
 pdb|3ZQL|A Chain A, Dna-Bound Form Of Tetr-Like Repressor Simr
 pdb|3ZQL|B Chain B, Dna-Bound Form Of Tetr-Like Repressor Simr
 pdb|3ZQL|C Chain C, Dna-Bound Form Of Tetr-Like Repressor Simr
 pdb|3ZQL|D Chain D, Dna-Bound Form Of Tetr-Like Repressor Simr
          Length = 267

 Score = 30.4 bits (67), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 12/25 (48%), Positives = 17/25 (68%)

Query: 630 DHSFRGGDQEVMDSIGQSNEHISPP 654
           D  FR G + ++DSIG S + +SPP
Sbjct: 223 DQRFRSGLERLLDSIGASLDRLSPP 247


  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
   0.317    0.136    0.414 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,073,813
Number of Sequences: 62578
Number of extensions: 934844
Number of successful extensions: 1630
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1627
Number of HSP's gapped (non-prelim): 8
length of query: 746
length of database: 14,973,337
effective HSP length: 106
effective length of query: 640
effective length of database: 8,340,069
effective search space: 5337644160
effective search space used: 5337644160
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)