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= 047104
         (80 letters)

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

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



>pdb|3U04|A Chain A, Crystal Structure Of Peptide Deformylase From Ehrlichia
          Chaffeensis In Complex With Actinonin
          Length = 190

 Score = 30.8 bits (68), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 14/52 (26%), Positives = 22/52 (42%)

Query: 15 ALAYAFDQIIAEKKIFGGTTPKTVSDKEWWEETDKKFQAWPRVAGPPVVMNP 66
           L  A  Q+   K+I     P+   D E  E  + K + +    GP  ++NP
Sbjct: 46 GLGLAAVQVGVHKRILVMNVPEEFEDSEDIENVEDKIEGYELYGGPYCIINP 97


>pdb|3OCA|A Chain A, Crystal Structure Of Peptide Deformylase From Ehrlichia
           Chaffeensis
 pdb|3OCA|B Chain B, Crystal Structure Of Peptide Deformylase From Ehrlichia
           Chaffeensis
          Length = 209

 Score = 30.8 bits (68), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 14/52 (26%), Positives = 22/52 (42%)

Query: 15  ALAYAFDQIIAEKKIFGGTTPKTVSDKEWWEETDKKFQAWPRVAGPPVVMNP 66
            L  A  Q+   K+I     P+   D E  E  + K + +    GP  ++NP
Sbjct: 65  GLGLAAVQVGVHKRILVMNVPEEFEDSEDIENVEDKIEGYELYGGPYCIINP 116


>pdb|1KPS|B Chain B, Structural Basis For E2-Mediated Sumo Conjugation Revealed
           By A Complex Between Ubiquitin Conjugating Enzyme Ubc9
           And Rangap1
 pdb|1KPS|D Chain D, Structural Basis For E2-Mediated Sumo Conjugation Revealed
           By A Complex Between Ubiquitin Conjugating Enzyme Ubc9
           And Rangap1
          Length = 171

 Score = 27.3 bits (59), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 10/31 (32%), Positives = 21/31 (67%)

Query: 46  ETDKKFQAWPRVAGPPVVMNPISRQNFIVKS 76
           +++ K +A P + GP +V+N + RQ++  K+
Sbjct: 108 KSEDKIKAIPSLHGPLMVLNHVVRQDYFPKA 138


>pdb|4FE7|A Chain A, Structure Of Xylose-binding Transcription Activator Xylr
          Length = 412

 Score = 26.6 bits (57), Expect = 4.0,   Method: Composition-based stats.
 Identities = 12/43 (27%), Positives = 19/43 (44%)

Query: 18  YAFDQIIAEKKIFGGTTPKTVSDKEWWEETDKKFQAWPRVAGP 60
           YAF Q++AE+K  G       +  E W+    +   W +   P
Sbjct: 161 YAFRQLVAEEKYRGVVYQGLETAPENWQHAQNRLADWLQTLPP 203


>pdb|4FE4|A Chain A, Crystal Structure Of Apo E. Coli Xylr
 pdb|4FE4|B Chain B, Crystal Structure Of Apo E. Coli Xylr
 pdb|4FE4|C Chain C, Crystal Structure Of Apo E. Coli Xylr
          Length = 392

 Score = 26.6 bits (57), Expect = 4.1,   Method: Composition-based stats.
 Identities = 12/43 (27%), Positives = 19/43 (44%)

Query: 18  YAFDQIIAEKKIFGGTTPKTVSDKEWWEETDKKFQAWPRVAGP 60
           YAF Q++AE+K  G       +  E W+    +   W +   P
Sbjct: 141 YAFRQLVAEEKYRGVVYQGLETAPENWQHAQNRLADWLQTLPP 183


  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
   0.317    0.131    0.404 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,456,419
Number of Sequences: 62578
Number of extensions: 87542
Number of successful extensions: 175
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 170
Number of HSP's gapped (non-prelim): 5
length of query: 80
length of database: 14,973,337
effective HSP length: 49
effective length of query: 31
effective length of database: 11,907,015
effective search space: 369117465
effective search space used: 369117465
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)