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= psy9603
         (150 letters)

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

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



>pdb|1BB1|A Chain A, Crystal Structure Of A Designed, Thermostable
          Heterotrimeric Coiled Coil
          Length = 36

 Score = 31.6 bits (70), Expect = 0.20,   Method: Composition-based stats.
 Identities = 13/33 (39%), Positives = 26/33 (78%)

Query: 26 DMASIKVDMGSIKEDMGSIKDDMGSIKEDMASI 58
          ++A+I+ +  +IKE++ +IKD + +IKE +A+I
Sbjct: 3  EIAAIEYEQAAIKEEIAAIKDKIAAIKEYIAAI 35



 Score = 27.7 bits (60), Expect = 2.6,   Method: Composition-based stats.
 Identities = 12/29 (41%), Positives = 23/29 (79%)

Query: 2  IKEDMGSIKEDMASIKEDMVSIKEDMASI 30
          I+ +  +IKE++A+IK+ + +IKE +A+I
Sbjct: 7  IEYEQAAIKEEIAAIKDKIAAIKEYIAAI 35



 Score = 27.3 bits (59), Expect = 3.1,   Method: Composition-based stats.
 Identities = 12/33 (36%), Positives = 25/33 (75%)

Query: 12 DMASIKEDMVSIKEDMASIKVDMGSIKEDMGSI 44
          ++A+I+ +  +IKE++A+IK  + +IKE + +I
Sbjct: 3  EIAAIEYEQAAIKEEIAAIKDKIAAIKEYIAAI 35



 Score = 26.2 bits (56), Expect = 6.6,   Method: Composition-based stats.
 Identities = 11/33 (33%), Positives = 25/33 (75%)

Query: 5  DMGSIKEDMASIKEDMVSIKEDMASIKVDMGSI 37
          ++ +I+ + A+IKE++ +IK+ +A+IK  + +I
Sbjct: 3  EIAAIEYEQAAIKEEIAAIKDKIAAIKEYIAAI 35


>pdb|3R4A|A Chain A, Crystal Structure Of The 4-Helix Coiled Coil Cc-Tet
 pdb|3R4A|B Chain B, Crystal Structure Of The 4-Helix Coiled Coil Cc-Tet
 pdb|3R4A|C Chain C, Crystal Structure Of The 4-Helix Coiled Coil Cc-Tet
 pdb|3R4A|D Chain D, Crystal Structure Of The 4-Helix Coiled Coil Cc-Tet
          Length = 34

 Score = 30.4 bits (67), Expect = 0.41,   Method: Composition-based stats.
 Identities = 11/31 (35%), Positives = 26/31 (83%)

Query: 12 DMASIKEDMVSIKEDMASIKVDMGSIKEDMG 42
          ++A+IK+++ +IK+++A+IK ++ +IK+  G
Sbjct: 3  ELAAIKQELAAIKKELAAIKWELAAIKQGAG 33



 Score = 28.1 bits (61), Expect = 1.7,   Method: Composition-based stats.
 Identities = 10/31 (32%), Positives = 24/31 (77%)

Query: 33 DMGSIKEDMGSIKDDMGSIKEDMASIKEDIG 63
          ++ +IK+++ +IK ++ +IK ++A+IK+  G
Sbjct: 3  ELAAIKQELAAIKKELAAIKWELAAIKQGAG 33


>pdb|3R4H|A Chain A, Crystal Structure Of The 4-Helix Coiled Coil
          Cc-Tet-Phi22
 pdb|3R4H|B Chain B, Crystal Structure Of The 4-Helix Coiled Coil
          Cc-Tet-Phi22
 pdb|3R4H|C Chain C, Crystal Structure Of The 4-Helix Coiled Coil
          Cc-Tet-Phi22
 pdb|3R4H|D Chain D, Crystal Structure Of The 4-Helix Coiled Coil
          Cc-Tet-Phi22
 pdb|3R4H|E Chain E, Crystal Structure Of The 4-Helix Coiled Coil
          Cc-Tet-Phi22
 pdb|3R4H|F Chain F, Crystal Structure Of The 4-Helix Coiled Coil
          Cc-Tet-Phi22
          Length = 34

 Score = 30.0 bits (66), Expect = 0.50,   Method: Composition-based stats.
 Identities = 11/31 (35%), Positives = 26/31 (83%)

Query: 12 DMASIKEDMVSIKEDMASIKVDMGSIKEDMG 42
          ++A+IK+++ +IK+++A+IK ++ +IK+  G
Sbjct: 3  ELAAIKQELAAIKKELAAIKXELAAIKQGAG 33



 Score = 28.1 bits (61), Expect = 1.8,   Method: Composition-based stats.
 Identities = 10/31 (32%), Positives = 24/31 (77%)

Query: 33 DMGSIKEDMGSIKDDMGSIKEDMASIKEDIG 63
          ++ +IK+++ +IK ++ +IK ++A+IK+  G
Sbjct: 3  ELAAIKQELAAIKKELAAIKXELAAIKQGAG 33


>pdb|4DZK|A Chain A, A De Novo Designed Coiled Coil Cc-Tri-N13
          Length = 32

 Score = 27.3 bits (59), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 9/28 (32%), Positives = 24/28 (85%)

Query: 12 DMASIKEDMVSIKEDMASIKVDMGSIKE 39
          ++A+IK+++ + K+++A+IK ++ +IK+
Sbjct: 2  EIAAIKQEIAANKKEIAAIKWEIAAIKQ 29


  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
   0.313    0.140    0.395 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,283,276
Number of Sequences: 62578
Number of extensions: 265874
Number of successful extensions: 621
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 568
Number of HSP's gapped (non-prelim): 65
length of query: 150
length of database: 14,973,337
effective HSP length: 90
effective length of query: 60
effective length of database: 9,341,317
effective search space: 560479020
effective search space used: 560479020
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 47 (22.7 bits)