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= 036566
         (420 letters)

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

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



>pdb|2BBR|A Chain A, Crystal Structure Of Mc159 Reveals Molecular Mechanism Of
           Disc Assembly And Vflip Inhibition
          Length = 195

 Score = 31.2 bits (69), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 17/65 (26%), Positives = 36/65 (55%), Gaps = 1/65 (1%)

Query: 28  LRSFSLWSMKKVPELESALSRNRRWI-VNNQIKNIILRLPSQVATVKYLQKKFKTLDLQG 86
           LR+  L++    P L +ALS + R++ +   ++N+ L  PS V+ +  + +  + LDL  
Sbjct: 112 LRALRLFACNLNPSLSTALSESSRFVELVLALENVGLVSPSSVSVLADMLRTLRRLDLCQ 171

Query: 87  KAINW 91
           + + +
Sbjct: 172 QLVEY 176


>pdb|2QJ0|A Chain A, Structure Of The Yeast U-Box-Containing Ubiquitin Ligase
           Ufd2p
          Length = 982

 Score = 30.8 bits (68), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 15/56 (26%), Positives = 26/56 (46%)

Query: 348 LMQEGLHEYNQRHRLMNLEKKKKRGMMPVRSEKSEDVRTEISQQDVIGDKLGGLFD 403
           L+ EGL    + H + N    + RG  P R E+ ++++T ++          GL D
Sbjct: 708 LLDEGLSNLAEVHNIQNELDNRARGAPPTREEEDKELQTRLASASRQAKSSCGLAD 763


>pdb|3M62|A Chain A, Crystal Structure Of Ufd2 In Complex With The
           Ubiquitin-Like (Ubl) Domain Of Rad23
 pdb|3M63|A Chain A, Crystal Structure Of Ufd2 In Complex With The
           Ubiquitin-Like (Ubl) Domain Of Dsk2
          Length = 968

 Score = 30.4 bits (67), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 15/56 (26%), Positives = 26/56 (46%)

Query: 348 LMQEGLHEYNQRHRLMNLEKKKKRGMMPVRSEKSEDVRTEISQQDVIGDKLGGLFD 403
           L+ EGL    + H + N    + RG  P R E+ ++++T ++          GL D
Sbjct: 694 LLDEGLSNLAEVHNIQNELDNRARGAPPTREEEDKELQTRLASASRQAKSSCGLAD 749


>pdb|2QIZ|A Chain A, Structure Of The Yeast U-Box-Containing Ubiquitin Ligase
           Ufd2p
          Length = 982

 Score = 30.0 bits (66), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 15/56 (26%), Positives = 26/56 (46%)

Query: 348 LMQEGLHEYNQRHRLMNLEKKKKRGMMPVRSEKSEDVRTEISQQDVIGDKLGGLFD 403
           L+ EGL    + H + N    + RG  P R E+ ++++T ++          GL D
Sbjct: 708 LLDEGLSNLAEVHNIQNELDNRARGAPPTREEEDKELQTRLASASRQAKSSCGLAD 763


>pdb|3DXW|A Chain A, The Crystal Structure Of Alpha-Amino-Epsilon-Caprolactam
           Racemase From Achromobacter Obae Complexed With Epsilon
           Caprolactam
 pdb|3DXW|B Chain B, The Crystal Structure Of Alpha-Amino-Epsilon-Caprolactam
           Racemase From Achromobacter Obae Complexed With Epsilon
           Caprolactam
          Length = 452

 Score = 30.0 bits (66), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 14/43 (32%), Positives = 26/43 (60%), Gaps = 2/43 (4%)

Query: 331 ELIEKDPLVVVKDKFGELMQEGLHEYNQRHRLMNLEKKKKRGM 373
           E I++D L  + ++ G L+++GL E  +RH L+     + RG+
Sbjct: 327 ETIDRDDLPAMAERKGRLLRDGLSELAKRHPLIG--DIRGRGL 367


>pdb|2ZUK|A Chain A, The Crystal Structure Of Alpha-Amino-Epsilon-Caprolactam
           Racemase From Achromobacter Obae Complexed With Epsilon
           Caprolactam (Different Binding Mode)
 pdb|2ZUK|B Chain B, The Crystal Structure Of Alpha-Amino-Epsilon-Caprolactam
           Racemase From Achromobacter Obae Complexed With Epsilon
           Caprolactam (Different Binding Mode)
 pdb|3DXV|A Chain A, The Crystal Structure Of Alpha-Amino-Epsilon-Caprolactam
           Racemase From Achromobacter Obae
 pdb|3DXV|B Chain B, The Crystal Structure Of Alpha-Amino-Epsilon-Caprolactam
           Racemase From Achromobacter Obae
          Length = 439

 Score = 30.0 bits (66), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 14/43 (32%), Positives = 26/43 (60%), Gaps = 2/43 (4%)

Query: 331 ELIEKDPLVVVKDKFGELMQEGLHEYNQRHRLMNLEKKKKRGM 373
           E I++D L  + ++ G L+++GL E  +RH L+     + RG+
Sbjct: 314 ETIDRDDLPAMAERKGRLLRDGLSELAKRHPLIG--DIRGRGL 354


  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    0.136    0.408 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,165,685
Number of Sequences: 62578
Number of extensions: 484223
Number of successful extensions: 964
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 958
Number of HSP's gapped (non-prelim): 7
length of query: 420
length of database: 14,973,337
effective HSP length: 101
effective length of query: 319
effective length of database: 8,652,959
effective search space: 2760293921
effective search space used: 2760293921
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)