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= 048313
         (252 letters)

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

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



>pdb|2A25|A Chain A, Crystal Structure Of Siah1 Sbd Bound To The Peptide
           Ekpaavvapittg From Sip
          Length = 193

 Score = 38.5 bits (88), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 25/94 (26%), Positives = 43/94 (45%), Gaps = 14/94 (14%)

Query: 71  VLESIQVTCENEDHGCKEKMSYSKKYDHGKACHHA--RCSCPLAACNFVGSFNQIYQHFR 128
           V  S+   C+    GC+  + +++K DH + C      C CP A+C + GS + +  H  
Sbjct: 1   VANSVLFPCKYASSGCEITLPHTEKADHEELCEFRPYSCPCPGASCKWQGSLDAVMPHL- 59

Query: 129 GVHKHAAEEFVYDKVLRITLSVHHDLIFLQEEKN 162
            +H+H +          IT     D++FL  + N
Sbjct: 60  -MHQHKS----------ITTLQGEDIVFLATDIN 82


>pdb|1K2F|A Chain A, Siah, Seven In Absentia Homolog
 pdb|1K2F|B Chain B, Siah, Seven In Absentia Homolog
          Length = 190

 Score = 35.8 bits (81), Expect = 0.022,   Method: Compositional matrix adjust.
 Identities = 23/91 (25%), Positives = 42/91 (46%), Gaps = 14/91 (15%)

Query: 74  SIQVTCENEDHGCKEKMSYSKKYDHGKACHHA--RCSCPLAACNFVGSFNQIYQHFRGVH 131
           S+   C+    GC+  + +++K +H + C      C CP A+C + GS + +  H   +H
Sbjct: 1   SVLFPCKYASSGCEITLPHTEKAEHEELCEFRPYSCPCPGASCKWQGSLDAVMPHL--MH 58

Query: 132 KHAAEEFVYDKVLRITLSVHHDLIFLQEEKN 162
           +H +          IT     D++FL  + N
Sbjct: 59  QHKS----------ITTLQGEDIVFLATDIN 79


>pdb|2AN6|A Chain A, Protein-Peptide Complex
 pdb|2AN6|B Chain B, Protein-Peptide Complex
 pdb|2AN6|C Chain C, Protein-Peptide Complex
 pdb|2AN6|D Chain D, Protein-Peptide Complex
          Length = 191

 Score = 35.8 bits (81), Expect = 0.023,   Method: Compositional matrix adjust.
 Identities = 23/91 (25%), Positives = 42/91 (46%), Gaps = 14/91 (15%)

Query: 74  SIQVTCENEDHGCKEKMSYSKKYDHGKACHHA--RCSCPLAACNFVGSFNQIYQHFRGVH 131
           S+   C+    GC+  + +++K +H + C      C CP A+C + GS + +  H   +H
Sbjct: 2   SVLFPCKYASSGCEITLPHTEKAEHEELCEFRPYSCPCPGASCKWQGSLDAVMPHL--MH 59

Query: 132 KHAAEEFVYDKVLRITLSVHHDLIFLQEEKN 162
           +H +          IT     D++FL  + N
Sbjct: 60  QHKS----------ITTLQGEDIVFLATDIN 80


>pdb|1RMD|A Chain A, Rag1 Dimerization Domain
          Length = 116

 Score = 28.1 bits (61), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 25/79 (31%), Positives = 38/79 (48%), Gaps = 11/79 (13%)

Query: 33  AECGNGHIVCNRC---CIELMNK-CPSCRLPIG----HSRSIAMEKVLESIQVTCENEDH 84
            E    H+ C  C   C+++M   CPSCR P       S   +   +L S+ V C  +D 
Sbjct: 37  VETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLESPVKSFLNILNSLMVKCPAQD- 95

Query: 85  GCKEKMSYSKKYDHGKACH 103
            C E++S  +KY+H  + H
Sbjct: 96  -CNEEVSL-EKYNHHVSSH 112


>pdb|3SQD|A Chain A, Crystal Structure Of Human Ptip Brct56-Gamma H2ax Complex
 pdb|3SQD|B Chain B, Crystal Structure Of Human Ptip Brct56-Gamma H2ax Complex
          Length = 219

 Score = 28.1 bits (61), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 15/57 (26%), Positives = 30/57 (52%), Gaps = 12/57 (21%)

Query: 32  VAECGNGHIVCNRCCIELMNKCPSCRLPIGHSRSIAMEKVLESIQVTCENEDHGCKE 88
           + EC  G +         ++K PS R  + H ++ ++ ++   I ++CEN+ H C+E
Sbjct: 144 IVECAGGKV---------LSKQPSFRKLMEHKQNSSLSEI---ILISCENDLHLCRE 188


  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
   0.324    0.137    0.451 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,588,614
Number of Sequences: 62578
Number of extensions: 289044
Number of successful extensions: 853
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 836
Number of HSP's gapped (non-prelim): 17
length of query: 252
length of database: 14,973,337
effective HSP length: 97
effective length of query: 155
effective length of database: 8,903,271
effective search space: 1380007005
effective search space used: 1380007005
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 50 (23.9 bits)