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= psy5060
         (145 letters)

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

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



>pdb|2D8R|A Chain A, Solution Structure Of The Thap Domain Of The Human Thap
          Domain-Containing Protein 2
          Length = 99

 Score = 55.1 bits (131), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 27/67 (40%), Positives = 38/67 (56%), Gaps = 2/67 (2%)

Query: 17 FGRFPEDKLRRKQWCIAMKRDKWKPSKHSKICSAHFTEDSFETNAWSERKKLSDTAVPSI 76
          F RFP D  RRK+W   ++R  + P KH+ +CS HF    F+    + R K+   AVP+I
Sbjct: 29 FHRFPLDPKRRKEWVRLVRRKNFVPGKHTFLCSKHFEASCFDLTGQTRRLKMD--AVPTI 86

Query: 77 FTFPDHL 83
          F F  H+
Sbjct: 87 FDFCTHI 93


>pdb|2KO0|A Chain A, Solution Structure Of The Thap Zinc Finger Of Thap1 In
          Complex With Its Dna Target
 pdb|2L1G|A Chain A, Rdc Refined Solution Structure Of The Thap Zinc Finger
          Of Thap1 In Complex With Its 16bp Rrm1 Dna Target
          Length = 87

 Score = 49.3 bits (116), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 25/50 (50%), Positives = 34/50 (68%), Gaps = 2/50 (4%)

Query: 28 KQWCIAMKRDKWKPSKHSKICSAHFTEDSFETNAWSERKKLSDTAVPSIF 77
          K+W  A++R  +KP+K+S ICS HFT DSF+    S  K L + AVP+IF
Sbjct: 34 KEWEAAVRRKNFKPTKYSSICSEHFTPDSFKRE--SNNKLLKENAVPTIF 81


>pdb|2JTG|A Chain A, Solution Structure Of The Thap-Zinc Finger Of Thap1
          Length = 87

 Score = 45.8 bits (107), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 23/50 (46%), Positives = 32/50 (64%), Gaps = 2/50 (4%)

Query: 28 KQWCIAMKRDKWKPSKHSKICSAHFTEDSFETNAWSERKKLSDTAVPSIF 77
          K+W  A++R  +KP+K+S ICS HFT D F+       K L + AVP+IF
Sbjct: 34 KEWEAAVRRKNFKPTKYSSICSEHFTPDCFKREC--NNKLLKENAVPTIF 81


>pdb|4AN2|A Chain A, Crystal Structures Of Human Mek1 With Carboxamide-Based
           Allosteric Inhibitor Xl518 (Gdc-0973), Or Related
           Analogs.
 pdb|4AN3|A Chain A, Crystal Structures Of Human Mek1 With Carboxamide-Based
           Allosteric Inhibitor Xl518 (Gdc-0973), Or Related
           Analogs.
 pdb|4AN9|A Chain A, Crystal Structures Of Human Mek1 With Carboxamide-Based
           Allosteric Inhibitor Xl518 (Gdc-0973), Or Related
           Analogs.
 pdb|4ANB|A Chain A, Crystal Structures Of Human Mek1 With Carboxamide-Based
           Allosteric Inhibitor Xl518 (Gdc-0973), Or Related
           Analogs
          Length = 301

 Score = 28.1 bits (61), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 7/62 (11%)

Query: 53  TEDSFETNAWSERKKLSDTAVP-------SIFTFPDHLMKTPCPRKQPAVRSLSAQEYMF 105
           T  S +++ WS    L + AV        +IF   D+++  P P+   AV SL  Q+++ 
Sbjct: 181 THYSVQSDIWSMGLSLVEMAVGRYPRPPMAIFELLDYIVNEPPPKLPSAVFSLEFQDFVN 240

Query: 106 VC 107
            C
Sbjct: 241 KC 242


  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
   0.322    0.131    0.443 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,799,335
Number of Sequences: 62578
Number of extensions: 177916
Number of successful extensions: 244
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 240
Number of HSP's gapped (non-prelim): 4
length of query: 145
length of database: 14,973,337
effective HSP length: 89
effective length of query: 56
effective length of database: 9,403,895
effective search space: 526618120
effective search space used: 526618120
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 47 (22.7 bits)