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= 042752
         (415 letters)

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

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



>pdb|3ULQ|A Chain A, Crystal Structure Of The Anti-Activator Rapf Complexed
           With The Response Regulator Coma Dna Binding Domain
          Length = 383

 Score = 30.4 bits (67), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 13/38 (34%), Positives = 24/38 (63%), Gaps = 3/38 (7%)

Query: 121 RSLHHIG---HGQNPYEQAISIIGKTLSAFDEDNLIPC 155
           R+L++IG   + Q+ YE AI    + ++ F+E N++P 
Sbjct: 225 RTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPS 262


>pdb|2JPS|A Chain A, Nab2 N-Terminal Domain
 pdb|3LCN|A Chain A, Nab2:gfd1 Complex
 pdb|3LCN|B Chain B, Nab2:gfd1 Complex
          Length = 105

 Score = 29.3 bits (64), Expect = 4.5,   Method: Composition-based stats.
 Identities = 24/87 (27%), Positives = 39/87 (44%), Gaps = 8/87 (9%)

Query: 182 EEVLTQYREIVPSLRLAGPTSFAPIIEMATTIVEKSGGQYHVLLIIADGQVTRSVDTQHG 241
           +E  T+  +++ + +LAG  +F   I        K   +Y VLLI+  G V   VD    
Sbjct: 3   QEQYTENLKVIVAEKLAGIPNFNEDI--------KYVAEYIVLLIVNGGTVESVVDELAS 54

Query: 242 QLSSQEQKTIDAIVQASEFPLSIILVG 268
              S  + T+  +VQ + F L  +  G
Sbjct: 55  LFDSVSRDTLANVVQTAFFALEALQQG 81


>pdb|2V75|A Chain A, N-Terminal Domain Of Nab2
          Length = 104

 Score = 29.3 bits (64), Expect = 4.5,   Method: Composition-based stats.
 Identities = 24/87 (27%), Positives = 39/87 (44%), Gaps = 8/87 (9%)

Query: 182 EEVLTQYREIVPSLRLAGPTSFAPIIEMATTIVEKSGGQYHVLLIIADGQVTRSVDTQHG 241
           +E  T+  +++ + +LAG  +F   I        K   +Y VLLI+  G V   VD    
Sbjct: 3   QEQYTENLKVIVAEKLAGIPNFNEDI--------KYVAEYIVLLIVNGGTVESVVDELAS 54

Query: 242 QLSSQEQKTIDAIVQASEFPLSIILVG 268
              S  + T+  +VQ + F L  +  G
Sbjct: 55  LFDSVSRDTLANVVQTAFFALEALQQG 81


>pdb|3PG5|A Chain A, Crystal Structure Of Protein Dip2308 From Corynebacterium
           Diphtheriae, Northeast Structural Genomics Consortium
           Target Cdr78
 pdb|3PG5|B Chain B, Crystal Structure Of Protein Dip2308 From Corynebacterium
           Diphtheriae, Northeast Structural Genomics Consortium
           Target Cdr78
 pdb|3PG5|C Chain C, Crystal Structure Of Protein Dip2308 From Corynebacterium
           Diphtheriae, Northeast Structural Genomics Consortium
           Target Cdr78
 pdb|3PG5|D Chain D, Crystal Structure Of Protein Dip2308 From Corynebacterium
           Diphtheriae, Northeast Structural Genomics Consortium
           Target Cdr78
          Length = 361

 Score = 28.1 bits (61), Expect = 9.1,   Method: Compositional matrix adjust.
 Identities = 19/69 (27%), Positives = 30/69 (43%), Gaps = 2/69 (2%)

Query: 123 LHHIGHGQNPYEQAISIIGKTLSAFDEDNLIPCFGFGDASTHDQDVFSFYPDDICCNGFE 182
           L H     + Y+     +G +L  F+   L+ C  F   +    D+FSF+        F+
Sbjct: 144 LAHAXERDDRYDVIFFDVGPSLGPFNRTVLLGCDAF--VTPTATDLFSFHAFGNLARWFD 201

Query: 183 EVLTQYREI 191
             +TQY EI
Sbjct: 202 AWVTQYAEI 210


>pdb|3A3J|A Chain A, Crystal Structures Of Penicillin Binding Protein 5 From
           Haemophilus Influenzae
          Length = 344

 Score = 28.1 bits (61), Expect = 9.6,   Method: Compositional matrix adjust.
 Identities = 19/83 (22%), Positives = 35/83 (42%), Gaps = 11/83 (13%)

Query: 255 VQASEFPLSIILVGVGDGPWDMMKEFDDNIPARAFDNFQFVNFTEIMSKNMD-LSRKETE 313
           V  ++    +I+V   D    + +    N+P          NF E M+K +     K T 
Sbjct: 86  VSVADLNRGVIVVSGNDATVALAEHISGNVP----------NFVETMNKYVQQFGLKNTN 135

Query: 314 FALAALMEIPSQYKATLELGILG 336
           F     ++ P+QY +  ++ I+G
Sbjct: 136 FTTPHGLDDPNQYSSARDMAIIG 158


  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
   0.320    0.135    0.407 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,204,691
Number of Sequences: 62578
Number of extensions: 453049
Number of successful extensions: 937
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 936
Number of HSP's gapped (non-prelim): 7
length of query: 415
length of database: 14,973,337
effective HSP length: 101
effective length of query: 314
effective length of database: 8,652,959
effective search space: 2717029126
effective search space used: 2717029126
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)