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= 019472
         (340 letters)

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

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



>pdb|4B4T|R Chain R, Near-Atomic Resolution Structural Model Of The Yeast 26s
           Proteasome
          Length = 429

 Score =  245 bits (626), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 120/284 (42%), Positives = 185/284 (65%), Gaps = 4/284 (1%)

Query: 61  FYIQIGDKEKALEQLKVTESKTVAVGQKMDLVFYTLQLGFFYMDFDLISKSIDKAKSLFE 120
           +Y QIGDK+ A + L  + SK ++ G K+D++    +LGFFY D   + + ++   S+ E
Sbjct: 140 YYAQIGDKDNAEKTLGKSLSKAISTGAKIDVMLTIARLGFFYNDQLYVKEKLEAVNSMIE 199

Query: 121 EGGDWERKNRLKVYEGLYCMSTRNFKKAASLFLDSISTFTTYELFPYDTFIFYTVLTSII 180
           +GGDWER+NR K Y G++C++ RNFK+AA L +DS++TFT+ EL  Y++   Y  +T + 
Sbjct: 200 KGGDWERRNRYKTYYGIHCLAVRNFKEAAKLLVDSLATFTSIELTSYESIATYASVTGLF 259

Query: 181 SLDRVSLKQKVVDAPEILTVIGKIPYL---SEFLNSLYDCQYKSFFSAFAGLTEQIKLD- 236
           +L+R  LK KV+D+PE+L++I     L   S    SLY   Y S+F         + +  
Sbjct: 260 TLERTDLKSKVIDSPELLSLISTTAALQSISSLTISLYASDYASYFPYLLETYANVLIPC 319

Query: 237 RYLYPHFRYYMREVRTVVYSQFLESYKSVTIEAMAKAFGVTVEFIDVELSRFIAAGKLHC 296
           +YL  H  +++RE+R  VY+Q LESYK++++++MA AFGV+V F+D +L +FI   +L+C
Sbjct: 320 KYLNRHADFFVREMRRKVYAQLLESYKTLSLKSMASAFGVSVAFLDNDLGKFIPNKQLNC 379

Query: 297 KIDKVAGVLETNRPDAKNALYQATIKQGDFLLNRIQKLSRVIDL 340
            ID+V G++ETNRPD KNA Y   +KQGD LL ++QK    + L
Sbjct: 380 VIDRVNGIVETNRPDNKNAQYHLLVKQGDGLLTKLQKYGAAVRL 423


  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
   0.324    0.139    0.398 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,039,609
Number of Sequences: 62578
Number of extensions: 344030
Number of successful extensions: 1048
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 1045
Number of HSP's gapped (non-prelim): 2
length of query: 340
length of database: 14,973,337
effective HSP length: 99
effective length of query: 241
effective length of database: 8,778,115
effective search space: 2115525715
effective search space used: 2115525715
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 52 (24.6 bits)