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= 025427
         (253 letters)

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

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



>pdb|3TXM|A Chain A, Crystal Structure Of Rpn6 From Drosophila Melanogaster,
           Gd(3+) Complex
 pdb|3TXN|A Chain A, Crystal Structure Of Rpn6 From Drosophila Melanogaster,
           Native Data
          Length = 394

 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 54/219 (24%), Positives = 100/219 (45%), Gaps = 28/219 (12%)

Query: 15  QTVKLYYRLGKYKEMMDAYREMLTYIKSAVTRNYSEKCINNIMD-FVSGSASQNFSLLRE 73
           Q  +LY + GK KE+ D  +    ++ S++++  + K + +++D F+   A     +   
Sbjct: 24  QQGELYKQEGKAKELADLIKVTRPFL-SSISKAKAAKLVRSLVDMFLDMDAGTGIEV--- 79

Query: 74  FYQTTLKALEEAKNE-RLWFKTNL--KLCKIWFDMGEYGRM----SKILKELHKSCQRED 126
             Q     +E AK E R + + +L  +L  ++FD   Y       +++L+EL K      
Sbjct: 80  --QLCKDCIEWAKQEKRTFLRQSLEARLIALYFDTALYTEALALGAQLLRELKK------ 131

Query: 127 GTDDQKKGSQLLEVYAIEIQMYTETXXXXXXXXXXXXXXXXXSAI--PHPRIMGIIRECG 184
             DD+   + L+EV  +E + Y                    +AI  P P++ G +    
Sbjct: 132 -LDDK---NLLVEVQLLESKTYHALSNLPKARAALTSARTTANAIYCP-PKVQGALDLQS 186

Query: 185 GKMHMA-ERQWADAATDFFEAFKNYDEAGNQRRIQCLKY 222
           G +H A ER +  A + F+EAF+ +D   + + +  LKY
Sbjct: 187 GILHAADERDFKTAFSYFYEAFEGFDSVDSVKALTSLKY 225


>pdb|3TTL|A Chain A, Crystal Structure Of Apo-Spue
 pdb|3TTL|B Chain B, Crystal Structure Of Apo-Spue
          Length = 340

 Score = 27.7 bits (60), Expect = 7.1,   Method: Compositional matrix adjust.
 Identities = 17/71 (23%), Positives = 33/71 (46%), Gaps = 3/71 (4%)

Query: 35  EMLTYIKSAVTRNYSEKCINNIMDFVSGSASQNFSLLREFYQTTLKALEEAKNERLWFKT 94
           E+LT ++  V+  +S K I+   D  +G+    F    + +Q   +A E  K   + +  
Sbjct: 185 EVLTKVRPYVSYFHSSKYIS---DLANGNICVAFGYSGDVFQAAARAEEAGKGIDIQYVI 241

Query: 95  NLKLCKIWFDM 105
             +   +WFD+
Sbjct: 242 PKEGANLWFDL 252


>pdb|3TTN|A Chain A, Crystal Structures Of Polyamine Receptors Spud And Spue
           From Pseudomonas Aeruginosa
 pdb|3TTN|B Chain B, Crystal Structures Of Polyamine Receptors Spud And Spue
           From Pseudomonas Aeruginosa
          Length = 340

 Score = 27.3 bits (59), Expect = 7.5,   Method: Compositional matrix adjust.
 Identities = 17/71 (23%), Positives = 33/71 (46%), Gaps = 3/71 (4%)

Query: 35  EMLTYIKSAVTRNYSEKCINNIMDFVSGSASQNFSLLREFYQTTLKALEEAKNERLWFKT 94
           E+LT ++  V+  +S K I+   D  +G+    F    + +Q   +A E  K   + +  
Sbjct: 185 EVLTKVRPYVSYFHSSKYIS---DLANGNICVAFGYSGDVFQAAARAEEAGKGIDIQYVI 241

Query: 95  NLKLCKIWFDM 105
             +   +WFD+
Sbjct: 242 PKEGANLWFDL 252


>pdb|3RKV|A Chain A, C-Terminal Domain Of Protein C56c10.10, A Putative
          Peptidylprolyl Isomerase, From Caenorhabditis Elegans
          Length = 162

 Score = 27.3 bits (59), Expect = 8.7,   Method: Compositional matrix adjust.
 Identities = 13/38 (34%), Positives = 21/38 (55%)

Query: 9  GFKALKQTVKLYYRLGKYKEMMDAYREMLTYIKSAVTR 46
            +AL+Q     +    YKE +DAYR+ LT + + + R
Sbjct: 10 SVEALRQKGNELFVQKDYKEAIDAYRDALTRLDTLILR 47


  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
   0.322    0.135    0.411 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,352,930
Number of Sequences: 62578
Number of extensions: 218152
Number of successful extensions: 583
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 582
Number of HSP's gapped (non-prelim): 5
length of query: 253
length of database: 14,973,337
effective HSP length: 97
effective length of query: 156
effective length of database: 8,903,271
effective search space: 1388910276
effective search space used: 1388910276
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)