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= psy4875
         (100 letters)

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

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



>pdb|6PAX|A Chain A, Crystal Structure Of The Human Pax-6 Paired Domain-Dna
           Complex Reveals A General Model For Pax Protein-Dna
           Interactions
          Length = 133

 Score =  116 bits (291), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 54/64 (84%), Positives = 59/64 (92%)

Query: 10  LVHRYYETGSIRPRAIGGSKPRVATAEVVSKISHYKRECPSIFAWEIRDRLLQEGVCSND 69
           ++ RYY TGSIRPRAIGGSKPRVAT EVVSKI+ YK+ECPSIFAWEIRDRLL EGVC+ND
Sbjct: 53  ILGRYYATGSIRPRAIGGSKPRVATPEVVSKIAQYKQECPSIFAWEIRDRLLSEGVCTND 112

Query: 70  NIPS 73
           NIPS
Sbjct: 113 NIPS 116


>pdb|2K27|A Chain A, Solution Structure Of Human Pax8 Paired Box Domain
          Length = 159

 Score =  100 bits (248), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 45/64 (70%), Positives = 53/64 (82%)

Query: 10  LVHRYYETGSIRPRAIGGSKPRVATAEVVSKISHYKRECPSIFAWEIRDRLLQEGVCSND 69
           ++ RYYETGSIRP  IGGSKP+VAT +VV KI  YKR+ P++FAWEIRDRLL EGVC ND
Sbjct: 61  ILGRYYETGSIRPGVIGGSKPKVATPKVVEKIGDYKRQNPTMFAWEIRDRLLAEGVCDND 120

Query: 70  NIPS 73
            +PS
Sbjct: 121 TVPS 124


>pdb|1K78|A Chain A, Pax5(1-149)+ets-1(331-440)+dna
 pdb|1K78|E Chain E, Pax5(1-149)+ets-1(331-440)+dna
 pdb|1K78|I Chain I, Pax5(1-149)+ets-1(331-440)+dna
 pdb|1MDM|A Chain A, Inhibited Fragment Of Ets-1 And Paired Domain Of Pax5
           Bound To Dna
          Length = 149

 Score = 96.3 bits (238), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 43/64 (67%), Positives = 53/64 (82%)

Query: 10  LVHRYYETGSIRPRAIGGSKPRVATAEVVSKISHYKRECPSIFAWEIRDRLLQEGVCSND 69
           ++ RYYETGSI+P  IGGSKP+VAT +VV KI+ YKR+ P++FAWEIRDRLL E VC ND
Sbjct: 68  ILGRYYETGSIKPGVIGGSKPKVATPKVVEKIAEYKRQNPTMFAWEIRDRLLAERVCDND 127

Query: 70  NIPS 73
            +PS
Sbjct: 128 TVPS 131


>pdb|1PDN|C Chain C, Crystal Structure Of A Paired Domain-Dna Complex At 2.5
           Angstroms Resolution Reveals Structural Basis For Pax
           Developmental Mutations
          Length = 128

 Score = 84.0 bits (206), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 36/64 (56%), Positives = 49/64 (76%)

Query: 10  LVHRYYETGSIRPRAIGGSKPRVATAEVVSKISHYKRECPSIFAWEIRDRLLQEGVCSND 69
           +++RY ETGSIRP  IGGSKPR+AT E+ ++I  YKR  P +F+WEIR++L++EGVC   
Sbjct: 53  ILNRYQETGSIRPGVIGGSKPRIATPEIENRIEEYKRSSPGMFSWEIREKLIREGVCDRS 112

Query: 70  NIPS 73
             PS
Sbjct: 113 TAPS 116


>pdb|3ZXS|A Chain A, Cryptochrome B From Rhodobacter Sphaeroides
 pdb|3ZXS|B Chain B, Cryptochrome B From Rhodobacter Sphaeroides
 pdb|3ZXS|C Chain C, Cryptochrome B From Rhodobacter Sphaeroides
          Length = 522

 Score = 26.6 bits (57), Expect = 3.8,   Method: Composition-based stats.
 Identities = 12/33 (36%), Positives = 20/33 (60%), Gaps = 4/33 (12%)

Query: 27  GSKPRVATAEVVSKISHYKRECPSIFAWEIRDR 59
           GSKP V++   + ++S Y R C    A+ ++DR
Sbjct: 430 GSKPYVSSGAYIDRMSDYCRGC----AYAVKDR 458


>pdb|4ILK|A Chain A, Crystal Structure Of Short Chain Alcohol Dehydrogenase
          (rspb) From E. Coli Cft073 (efi Target Efi-506413)
          Complexed With Cofactor Nadh
 pdb|4ILK|B Chain B, Crystal Structure Of Short Chain Alcohol Dehydrogenase
          (rspb) From E. Coli Cft073 (efi Target Efi-506413)
          Complexed With Cofactor Nadh
          Length = 359

 Score = 25.8 bits (55), Expect = 5.6,   Method: Composition-based stats.
 Identities = 13/44 (29%), Positives = 25/44 (56%)

Query: 27 GSKPRVATAEVVSKISHYKRECPSIFAWEIRDRLLQEGVCSNDN 70
          GS  +    E  +++S  +RE P+  A E+R ++   G+C +D+
Sbjct: 18 GSHMKSILIEKPNQLSIIEREIPTPSAGEVRVKVKLAGICGSDS 61


  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
   0.323    0.139    0.444 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,016,055
Number of Sequences: 62578
Number of extensions: 102968
Number of successful extensions: 170
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 160
Number of HSP's gapped (non-prelim): 12
length of query: 100
length of database: 14,973,337
effective HSP length: 66
effective length of query: 34
effective length of database: 10,843,189
effective search space: 368668426
effective search space used: 368668426
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)