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= psy2364
         (119 letters)

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

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



>pdb|2F8X|M Chain M, Crystal Structure Of Activated Notch, Csl And Maml On
          Hes-1 Promoter Dna Sequence
 pdb|3NBN|C Chain C, Crystal Structure Of A Dimer Of Notch Transcription
          Complex Trimers On Hes1 Dna
 pdb|3NBN|F Chain F, Crystal Structure Of A Dimer Of Notch Transcription
          Complex Trimers On Hes1 Dna
 pdb|3V79|M Chain M, Structure Of Human Notch1 Transcription Complex
          Including Csl, Ram, Ank, And Maml-1 On Hes-1 Promoter
          Dna Sequence
          Length = 63

 Score = 48.9 bits (115), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 26/58 (44%), Positives = 37/58 (63%)

Query: 7  PKRQAVVDRLRRRIENYRRHQSDCVPRYDHSFNGLVERDIQETLLLKQKYLESKAKRS 64
          P+  AV++RLRRRIE  RRH S C  RY+      +E + Q T  L Q+ +++KAKR+
Sbjct: 3  PRHSAVMERLRRRIELCRRHHSTCEARYEAVSPERLELERQHTFALHQRCIQAKAKRA 60


>pdb|4DUF|A Chain A, Cytochrome P450 Bm3h-2g9 Mri Sensor Bound To Serotonin
 pdb|4DUF|B Chain B, Cytochrome P450 Bm3h-2g9 Mri Sensor Bound To Serotonin
 pdb|4DUF|C Chain C, Cytochrome P450 Bm3h-2g9 Mri Sensor Bound To Serotonin
 pdb|4DUF|D Chain D, Cytochrome P450 Bm3h-2g9 Mri Sensor Bound To Serotonin
          Length = 471

 Score = 26.2 bits (56), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 17/32 (53%), Positives = 20/32 (62%), Gaps = 1/32 (3%)

Query: 43  ERDIQETLLLKQKYLESKAKRSKNKPEKKLPS 74
           E DI+ETLLLK +    KAK SK  P   +PS
Sbjct: 430 ELDIKETLLLKPEGFVVKAK-SKKIPLGGIPS 460


>pdb|4DUC|A Chain A, Cytochrome P450 Bm3h-2g9 Mri Sensor, No Ligand
 pdb|4DUC|B Chain B, Cytochrome P450 Bm3h-2g9 Mri Sensor, No Ligand
          Length = 472

 Score = 26.2 bits (56), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 17/32 (53%), Positives = 20/32 (62%), Gaps = 1/32 (3%)

Query: 43  ERDIQETLLLKQKYLESKAKRSKNKPEKKLPS 74
           E DI+ETLLLK +    KAK SK  P   +PS
Sbjct: 431 ELDIKETLLLKPEGFVVKAK-SKKIPLGGIPS 461


>pdb|2PVP|A Chain A, Crystal Structure Of D-Alanine-D-Alanine Ligase From
           Helicobacter Pylori
 pdb|2PVP|B Chain B, Crystal Structure Of D-Alanine-D-Alanine Ligase From
           Helicobacter Pylori
          Length = 367

 Score = 26.2 bits (56), Expect = 5.1,   Method: Composition-based stats.
 Identities = 18/48 (37%), Positives = 24/48 (50%), Gaps = 1/48 (2%)

Query: 30  CVPRYDHSFNGLVERDIQETLLLKQKYLE-SKAKRSKNKPEKKLPSQL 76
           C  + D  F+ + E + QE L  KQKYL+ S+ K  K      L  QL
Sbjct: 241 CKIKKDFCFSYIEEPNKQEFLDFKQKYLDFSRNKAPKASLSNALEEQL 288


>pdb|3QI8|B Chain B, Evolved Variant Of Cytochrome P450 (Bm3, Cyp102a1)
 pdb|3QI8|A Chain A, Evolved Variant Of Cytochrome P450 (Bm3, Cyp102a1)
          Length = 472

 Score = 25.8 bits (55), Expect = 7.0,   Method: Compositional matrix adjust.
 Identities = 17/32 (53%), Positives = 19/32 (59%), Gaps = 1/32 (3%)

Query: 43  ERDIQETLLLKQKYLESKAKRSKNKPEKKLPS 74
           E DI+ETL LK K    KAK SK  P   +PS
Sbjct: 431 ELDIEETLTLKPKGFVIKAK-SKKIPLGGIPS 461


  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
   0.319    0.133    0.390 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,281,464
Number of Sequences: 62578
Number of extensions: 116287
Number of successful extensions: 276
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 274
Number of HSP's gapped (non-prelim): 7
length of query: 119
length of database: 14,973,337
effective HSP length: 81
effective length of query: 38
effective length of database: 9,904,519
effective search space: 376371722
effective search space used: 376371722
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)