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= 044476
         (376 letters)

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

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



>pdb|1K87|A Chain A, Crystal Structure Of E.coli Puta (residues 1-669)
          Length = 669

 Score = 31.6 bits (70), Expect = 0.73,   Method: Compositional matrix adjust.
 Identities = 25/83 (30%), Positives = 36/83 (43%), Gaps = 1/83 (1%)

Query: 166 IDTEEVRVLSFDLAGFFKQVDEFVKAGGGGGVLDMPAWAAKEPRTIEFWTDVAERGRRVL 225
           ID EE   L   L    K   E   AG  G    + A+  + P  I++  D+A R RR L
Sbjct: 369 IDAEEADRLEISLDLLEKLCFEPELAGWNGIGFVIQAYQKRCPLVIDYLIDLATRSRRRL 428

Query: 226 ARCGSRGRWWRAGCENTHV-GLE 247
                +G +W +  +   + GLE
Sbjct: 429 MIRLVKGAYWDSEIKRAQMDGLE 451


>pdb|2PLA|A Chain A, Crystal Structure Of Human Glycerol-3-Phosphate
           Dehydrogenase 1-Like Protein
 pdb|2PLA|B Chain B, Crystal Structure Of Human Glycerol-3-Phosphate
           Dehydrogenase 1-Like Protein
          Length = 349

 Score = 30.0 bits (66), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 2/33 (6%)

Query: 121 QRPQNNNDALSLIKK--LLDKAPLLVPIYRNCY 151
           Q PQ + +   ++K+  LLDK PL   +Y+ CY
Sbjct: 300 QGPQTSAEVYRILKQKGLLDKFPLFTAVYQICY 332


>pdb|3MZ4|A Chain A, Crystal Structure Of D101l Mn2+ Hdac8 Complexed With M344
 pdb|3MZ4|B Chain B, Crystal Structure Of D101l Mn2+ Hdac8 Complexed With M344
 pdb|3MZ6|A Chain A, Crystal Structure Of D101l Fe2+ Hdac8 Complexed With M344
 pdb|3MZ7|A Chain A, Crystal Structure Of D101l Co2+ Hdac8 Complexed With M344
          Length = 389

 Score = 29.3 bits (64), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 13/25 (52%), Positives = 17/25 (68%)

Query: 343 QHPRKCSKEGDDDHQKSSVKQLGHV 367
           QH +K S+EGDDDH  S    LG++
Sbjct: 77  QHLQKVSQEGDDDHPDSIEYGLGYL 101


>pdb|3EW8|A Chain A, Crystal Structure Analysis Of Human Hdac8 D101l Variant
          Length = 388

 Score = 29.3 bits (64), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 13/25 (52%), Positives = 17/25 (68%)

Query: 343 QHPRKCSKEGDDDHQKSSVKQLGHV 367
           QH +K S+EGDDDH  S    LG++
Sbjct: 77  QHLQKVSQEGDDDHPDSIEYGLGYL 101


>pdb|3EWF|A Chain A, Crystal Structure Analysis Of Human Hdac8 H143a Variant
           Complexed With Substrate.
 pdb|3EWF|B Chain B, Crystal Structure Analysis Of Human Hdac8 H143a Variant
           Complexed With Substrate.
 pdb|3EWF|C Chain C, Crystal Structure Analysis Of Human Hdac8 H143a Variant
           Complexed With Substrate.
 pdb|3EWF|D Chain D, Crystal Structure Analysis Of Human Hdac8 H143a Variant
           Complexed With Substrate
          Length = 388

 Score = 28.9 bits (63), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 13/24 (54%), Positives = 16/24 (66%)

Query: 343 QHPRKCSKEGDDDHQKSSVKQLGH 366
           QH +K S+EGDDDH  S    LG+
Sbjct: 77  QHLQKVSQEGDDDHPDSIEYGLGY 100


>pdb|3F06|A Chain A, Crystal Structure Analysis Of Human Hdac8 D101a Variant.
 pdb|3F06|B Chain B, Crystal Structure Analysis Of Human Hdac8 D101a Variant
          Length = 388

 Score = 28.9 bits (63), Expect = 5.1,   Method: Compositional matrix adjust.
 Identities = 13/24 (54%), Positives = 16/24 (66%)

Query: 343 QHPRKCSKEGDDDHQKSSVKQLGH 366
           QH +K S+EGDDDH  S    LG+
Sbjct: 77  QHLQKVSQEGDDDHPDSIEYGLGY 100


>pdb|3MZ3|A Chain A, Crystal Structure Of Co2+ Hdac8 Complexed With M344
 pdb|3MZ3|B Chain B, Crystal Structure Of Co2+ Hdac8 Complexed With M344
 pdb|3RQD|A Chain A, Ideal Thiolate-Zinc Coordination Geometry In Depsipeptide
           Binding To Histone Deacetylase 8
 pdb|3RQD|B Chain B, Ideal Thiolate-Zinc Coordination Geometry In Depsipeptide
           Binding To Histone Deacetylase 8
          Length = 389

 Score = 28.9 bits (63), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 13/24 (54%), Positives = 16/24 (66%)

Query: 343 QHPRKCSKEGDDDHQKSSVKQLGH 366
           QH +K S+EGDDDH  S    LG+
Sbjct: 77  QHLQKVSQEGDDDHPDSIEYGLGY 100


>pdb|3F07|A Chain A, Crystal Structure Analysis Of Human Hdac8 Complexed With
           Apha In A New Monoclinic Crystal Form
 pdb|3F07|B Chain B, Crystal Structure Analysis Of Human Hdac8 Complexed With
           Apha In A New Monoclinic Crystal Form
 pdb|3F07|C Chain C, Crystal Structure Analysis Of Human Hdac8 Complexed With
           Apha In A New Monoclinic Crystal Form
 pdb|3F0R|A Chain A, Crystal Structure Analysis Of Human Hdac8 Complexed With
           Trichostatin A In A New Monoclinic Crystal Form
 pdb|3F0R|B Chain B, Crystal Structure Analysis Of Human Hdac8 Complexed With
           Trichostatin A In A New Monoclinic Crystal Form
 pdb|3F0R|C Chain C, Crystal Structure Analysis Of Human Hdac8 Complexed With
           Trichostatin A In A New Monoclinic Crystal Form
          Length = 388

 Score = 28.9 bits (63), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 13/24 (54%), Positives = 16/24 (66%)

Query: 343 QHPRKCSKEGDDDHQKSSVKQLGH 366
           QH +K S+EGDDDH  S    LG+
Sbjct: 77  QHLQKVSQEGDDDHPDSIEYGLGY 100


>pdb|3EZT|A Chain A, Crystal Structure Analysis Of Human Hdac8 D101e Variant
 pdb|3EZT|B Chain B, Crystal Structure Analysis Of Human Hdac8 D101e Variant
          Length = 388

 Score = 28.9 bits (63), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 13/24 (54%), Positives = 16/24 (66%)

Query: 343 QHPRKCSKEGDDDHQKSSVKQLGH 366
           QH +K S+EGDDDH  S    LG+
Sbjct: 77  QHLQKVSQEGDDDHPDSIEYGLGY 100


>pdb|2V5W|A Chain A, Crystal Structure Of Hdac8-Substrate Complex
 pdb|2V5W|B Chain B, Crystal Structure Of Hdac8-Substrate Complex
          Length = 388

 Score = 28.9 bits (63), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 13/24 (54%), Positives = 16/24 (66%)

Query: 343 QHPRKCSKEGDDDHQKSSVKQLGH 366
           QH +K S+EGDDDH  S    LG+
Sbjct: 77  QHLQKVSQEGDDDHPDSIEYGLGY 100


>pdb|1T64|A Chain A, Crystal Structure Of Human Hdac8 Complexed With
           Trichostatin A
 pdb|1T64|B Chain B, Crystal Structure Of Human Hdac8 Complexed With
           Trichostatin A
 pdb|1T67|A Chain A, Crystal Structure Of Human Hdac8 Complexed With Ms-344
 pdb|1T69|A Chain A, Crystal Structure Of Human Hdac8 Complexed With Saha
 pdb|1VKG|A Chain A, Crystal Structure Of Human Hdac8 Complexed With Cra-19156
 pdb|1VKG|B Chain B, Crystal Structure Of Human Hdac8 Complexed With Cra-19156
 pdb|1W22|A Chain A, Crystal Structure Of Inhibited Human Hdac8
 pdb|1W22|B Chain B, Crystal Structure Of Inhibited Human Hdac8
          Length = 377

 Score = 28.9 bits (63), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 13/24 (54%), Positives = 16/24 (66%)

Query: 343 QHPRKCSKEGDDDHQKSSVKQLGH 366
           QH +K S+EGDDDH  S    LG+
Sbjct: 77  QHLQKVSQEGDDDHPDSIEYGLGY 100


>pdb|3SFF|A Chain A, Crystal Structure Of Human Hdac8 Inhibitor Complex, An
           Amino Acid Derived Inhibitor
 pdb|3SFH|A Chain A, Crystal Structure Of Human Hdac8 Inhibitor Complex, An
           Amino Acid Derived Inhibitor
          Length = 378

 Score = 28.9 bits (63), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 13/24 (54%), Positives = 16/24 (66%)

Query: 343 QHPRKCSKEGDDDHQKSSVKQLGH 366
           QH +K S+EGDDDH  S    LG+
Sbjct: 78  QHLQKVSQEGDDDHPDSIEYGLGY 101


>pdb|3EZP|A Chain A, Crystal Structure Analysis Of Human Hdac8 D101n Variant
 pdb|3EZP|B Chain B, Crystal Structure Analysis Of Human Hdac8 D101n Variant
          Length = 388

 Score = 28.9 bits (63), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 13/24 (54%), Positives = 16/24 (66%)

Query: 343 QHPRKCSKEGDDDHQKSSVKQLGH 366
           QH +K S+EGDDDH  S    LG+
Sbjct: 77  QHLQKVSQEGDDDHPDSIEYGLGY 100


>pdb|2V5X|A Chain A, Crystal Structure Of Hdac8-Inhibitor Complex
 pdb|2V5X|B Chain B, Crystal Structure Of Hdac8-Inhibitor Complex
          Length = 388

 Score = 28.9 bits (63), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 13/24 (54%), Positives = 16/24 (66%)

Query: 343 QHPRKCSKEGDDDHQKSSVKQLGH 366
           QH +K S+EGDDDH  S    LG+
Sbjct: 77  QHLQKVSQEGDDDHPDSIEYGLGY 100


>pdb|3GQJ|A Chain A, Crystal Structure Of Cell Inhibiting Factor (Cif) From
           Photorhabdus Luminescens
          Length = 261

 Score = 28.1 bits (61), Expect = 7.3,   Method: Compositional matrix adjust.
 Identities = 12/35 (34%), Positives = 22/35 (62%)

Query: 160 GNPVFYIDTEEVRVLSFDLAGFFKQVDEFVKAGGG 194
           GN + + D  + ++++ DLA  F+++DE V   GG
Sbjct: 22  GNKLLWNDNWQDKIINRDLANIFEKIDESVSELGG 56


>pdb|4FBJ|A Chain A, Structure Of The Cif:nedd8 Complex - Photorhabdus
           Luminescens Cycle Inhibiting Factor In Complex With
           Human Nedd8
          Length = 261

 Score = 28.1 bits (61), Expect = 7.5,   Method: Compositional matrix adjust.
 Identities = 12/35 (34%), Positives = 22/35 (62%)

Query: 160 GNPVFYIDTEEVRVLSFDLAGFFKQVDEFVKAGGG 194
           GN + + D  + ++++ DLA  F+++DE V   GG
Sbjct: 22  GNKLLWNDNWQDKIINRDLANIFEKIDESVSELGG 56


  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
   0.319    0.135    0.429 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,170,715
Number of Sequences: 62578
Number of extensions: 461643
Number of successful extensions: 853
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 827
Number of HSP's gapped (non-prelim): 28
length of query: 376
length of database: 14,973,337
effective HSP length: 100
effective length of query: 276
effective length of database: 8,715,537
effective search space: 2405488212
effective search space used: 2405488212
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)