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= 016147
         (394 letters)

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

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



>pdb|4B4T|P Chain P, Near-Atomic Resolution Structural Model Of The Yeast 26s
           Proteasome
          Length = 445

 Score =  242 bits (618), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 140/353 (39%), Positives = 216/353 (61%), Gaps = 23/353 (6%)

Query: 36  DLDTRIELIKTLNSVSAGKIYVEIERARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGA 95
           DL+TRI +I+T+  V+  KI+VE+ERAR+ K L +IK+E+G I EAAD++ E+ VET+G+
Sbjct: 111 DLNTRISVIETIRVVTENKIFVEVERARVTKDLVEIKKEEGKIDEAADILCELQVETYGS 170

Query: 96  MAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKEKKKPKEGDNVVEEAP 155
           M  +EKI FILEQ+ L + + DY +A +LSRKI  + F        K PK          
Sbjct: 171 MEMSEKIQFILEQMELSILKGDYSQATVLSRKILKKTF--------KNPKYES------- 215

Query: 156 ADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYEIPYIKEDPAQWMPVLRKICWY 215
                   LK  YY L+++   H  +YLE+ +  + IY+   IK D A+W PVL  I ++
Sbjct: 216 --------LKLEYYNLLVKISLHKREYLEVAQYLQEIYQTDAIKSDEAKWKPVLSHIVYF 267

Query: 216 LVLAPHDPMQSSLLNSTLEDKNLSEIPNFRLLLKQLVTMEVIQWTSLWNTYKDEFENETN 275
           LVL+P+  +Q+ L++    D NL ++ +   L+K   T E+++W  +  TY+     +  
Sbjct: 268 LVLSPYGNLQNDLIHKIQNDNNLKKLESQESLVKLFTTNELMRWPIVQKTYEPVLNEDDL 327

Query: 276 MLGGSLGAKAAEDLRQRIIEHNILVVSKYYSRITLKRLAELLCLSIQEAEKHLSDMVVSK 335
             GG       EDL++R+IEHN+ V+S+YYSRITL RL ELL L+  + E ++SD+V   
Sbjct: 328 AFGGEANKHHWEDLQKRVIEHNLRVISEYYSRITLLRLNELLDLTESQTETYISDLVNQG 387

Query: 336 ALVAKIDRPQGIVCFQVAKDSNDILNSWAMNLEKLLDLVEKSCHQIHKETMVH 388
            + AK++RP  IV F+  K+S+ +LN W+ N+++LL+ +E   H I KE ++H
Sbjct: 388 IIYAKVNRPAKIVNFEKPKNSSQLLNEWSHNVDELLEHIETIGHLITKEEIMH 440


>pdb|1UFM|A Chain A, Solution Structure Of The Pci Domain
          Length = 84

 Score = 46.2 bits (108), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 26/68 (38%), Positives = 38/68 (55%)

Query: 289 LRQRIIEHNILVVSKYYSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIV 348
           L + +IEHN+L  SK Y+ IT + L  LL +   +AEK  S M+    +   ID+  GIV
Sbjct: 12  LDRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDGIV 71

Query: 349 CFQVAKDS 356
            F+  + S
Sbjct: 72  HFETREAS 79


>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 = 35.4 bits (80), Expect = 0.049,   Method: Compositional matrix adjust.
 Identities = 16/56 (28%), Positives = 34/56 (60%)

Query: 293 IIEHNILVVSKYYSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIV 348
           ++E N+  + + YSR+ +  +AE + L + + EK LS M++ K     +D+ +G++
Sbjct: 302 MLEQNLCRIIEPYSRVQVAHVAESIQLPMPQVEKKLSQMILDKKFSGILDQGEGVL 357


  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
   0.321    0.136    0.389 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,459,120
Number of Sequences: 62578
Number of extensions: 411222
Number of successful extensions: 1055
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 1051
Number of HSP's gapped (non-prelim): 18
length of query: 394
length of database: 14,973,337
effective HSP length: 101
effective length of query: 293
effective length of database: 8,652,959
effective search space: 2535316987
effective search space used: 2535316987
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: 52 (24.6 bits)