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= 035712
         (563 letters)

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

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



>pdb|2LLK|A Chain A, Solution Nmr Structure Of The N-Terminal Myb-Like 1 Domain
           Of The Human Cyclin-D-Binding Transcription Factor 1
           (Hdmp1), Northeast Structural Genomics Consortium (Nesg)
           Target Id Hr8011a
          Length = 73

 Score = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/57 (38%), Positives = 35/57 (61%), Gaps = 2/57 (3%)

Query: 436 RAHIIFQRDENR--KWTPEELELVRKFHEKHGSNWKMLANALGKHRFHVKDAWRRVR 490
           R ++ FQ D N   K+TPEE+E +++   KHG++W  +  ALG+    VKD  R ++
Sbjct: 11  RENLYFQGDRNHVGKYTPEEIEKLKELRIKHGNDWATIGAALGRSASSVKDRCRLMK 67


>pdb|1H88|C Chain C, Crystal Structure Of Ternary Protein-Dna Complex1
 pdb|1H89|C Chain C, Crystal Structure Of Ternary Protein-Dna Complex2
          Length = 159

 Score = 42.7 bits (99), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 34/114 (29%), Positives = 56/114 (49%), Gaps = 19/114 (16%)

Query: 448 KWTPEELELVRKFHEKHGSN-WKMLANAL-GKHRFHVKDAWRRVRLPNQKKGQWSQEEYQ 505
           +WT EE E ++K  E++G++ WK++AN L  +     +  W++V  P   KG W++EE Q
Sbjct: 8   RWTREEDEKLKKLVEQNGTDDWKVIANYLPNRTDVQCQHRWQKVLNPELIKGPWTKEEDQ 67

Query: 506 KLFDLVNMDLRMRALEEKKTKHGMLRDNISWEAISDKLATRSNAICCMKWYDQL 559
           ++  LV              K+G  R    W  I+  L  R    C  +W++ L
Sbjct: 68  RVIKLVQ-------------KYGPKR----WSVIAKHLKGRIGKQCRERWHNHL 104


>pdb|3OSF|A Chain A, The Structure Of Protozoan Parasite Trichomonas Vaginalis
           Myb2 In Complex With Mre-2f-13 Dna
 pdb|3OSF|D Chain D, The Structure Of Protozoan Parasite Trichomonas Vaginalis
           Myb2 In Complex With Mre-2f-13 Dna
 pdb|3OSG|A Chain A, The Structure Of Protozoan Parasite Trichomonas Vaginalis
           Myb2 In Complex With Mre-1-12 Dna
 pdb|3OSG|D Chain D, The Structure Of Protozoan Parasite Trichomonas Vaginalis
           Myb2 In Complex With Mre-1-12 Dna
          Length = 126

 Score = 42.4 bits (98), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 19/60 (31%), Positives = 35/60 (58%), Gaps = 1/60 (1%)

Query: 445 ENRKWTPEELELVRKFHEKHGSNWKMLANAL-GKHRFHVKDAWRRVRLPNQKKGQWSQEE 503
           + +K+TPEE E++++   +HGS+WKM+A     ++    +D W+    P+     W+ EE
Sbjct: 10  KKQKFTPEEDEMLKRAVAQHGSDWKMIAATFPNRNARQCRDRWKNYLAPSISHTPWTAEE 69



 Score = 35.0 bits (79), Expect = 0.098,   Method: Composition-based stats.
 Identities = 30/116 (25%), Positives = 51/116 (43%), Gaps = 23/116 (19%)

Query: 372 RGKRFSKEEDEMIKRAVMNYIETHGLGEEGLNMVLHCRSHPEVKHCWKEIGSALPWRPYD 431
           + ++F+ EEDEM+KRAV      HG   + +      R+  + +  WK            
Sbjct: 10  KKQKFTPEEDEMLKRAVAQ----HGSDWKMIAATFPNRNARQCRDRWKN----------- 54

Query: 432 SIYYRAHIIFQRDENRKWTPEELELVRKFHEKHGSNWKMLANAL-GKHRFHVKDAW 486
              Y A  I     +  WT EE  L+ +  +++G  W ++A    G+   H+K+ W
Sbjct: 55  ---YLAPSI----SHTPWTAEEDALLVQKIQEYGRQWAIIAKFFPGRTDIHIKNRW 103


  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
   0.311    0.130    0.377 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,778,010
Number of Sequences: 62578
Number of extensions: 711694
Number of successful extensions: 1517
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 1502
Number of HSP's gapped (non-prelim): 34
length of query: 563
length of database: 14,973,337
effective HSP length: 104
effective length of query: 459
effective length of database: 8,465,225
effective search space: 3885538275
effective search space used: 3885538275
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: 54 (25.4 bits)