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= 043780
         (386 letters)

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

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



>pdb|4B4T|O Chain O, Near-Atomic Resolution Structural Model Of The Yeast 26s
           Proteasome
          Length = 393

 Score =  174 bits (442), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 115/377 (30%), Positives = 191/377 (50%), Gaps = 23/377 (6%)

Query: 15  PELGEWYNALADLYQKKLWHQLTLKLEQFVAHAVFQAGDALIQLYHNFITDFETKINLLK 74
           P L   +      Y++KLW QL+  L +F   A  ++    ++LY NF++ F  KIN L 
Sbjct: 20  PSLHPLFEQFEKFYEEKLWFQLSESLTKFFDDA--KSTPLRLRLYDNFVSKFYDKINQLS 77

Query: 75  LAHFAVIVSRQYPEKQAAISYLEGV--------IEKLRATNEQRKEEPILYIKMQIAMFK 126
           +  + +   +   +   ++ YL+ +         +K R    +   + IL I  +IA   
Sbjct: 78  VVKYLLASLKDSKDFDESLKYLDDLKAQFQELDSKKQRNNGSKDHGDGILLIDSEIARTY 137

Query: 127 LEQGDRKECKKLLEDGKSTLDSMTDIDPSVYANYYWVSSQYHKFHQEFAEFYKCALLYLA 186
           L + D  + + LL+D + TLD    I   +  ++Y  +SQY KF  +F  FY  +LLYL+
Sbjct: 138 LLKNDLVKARDLLDDLEKTLDKKDSIPLRITNSFYSTNSQYFKFKNDFNSFYYTSLLYLS 197

Query: 187 Y----TSVEXXXXXXXXXXXXXXXXXXXXGDNIYNFGELLAHPIINSLTG-TKVEWLYYI 241
                TS+                     GD IYNFGELL HPI+ ++   +  +WL+ +
Sbjct: 198 TLEPSTSI---TLAERQQLAYDLSISALLGDKIYNFGELLHHPIMETIVNDSNYDWLFQL 254

Query: 242 LQAFNSGDLVRYQELCRVHNAALRAQPALVENEKKLLEKINILCLMEIIFSRPSEDRTIP 301
           L A   GD  ++  L +V  + +   P L ++E  L +KI ++ L+E +F +    R + 
Sbjct: 255 LNALTVGDFDKFDSLIKVQISKI---PILAQHESFLRQKICLMTLIETVFVKNI--RMLS 309

Query: 302 LSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVSWVQPRVLGIPQIKSLRDR 361
              I++ T L  ++VEHL+M+++S+ L++G IDQV   V +SWVQPR++   QI  ++DR
Sbjct: 310 FEDISKATHLPKDNVEHLVMRAISLGLLKGSIDQVNELVTISWVQPRIISGDQITKMKDR 369

Query: 362 LDSWLGKVHTALLSIEA 378
           L  W  +V      +EA
Sbjct: 370 LVEWNDQVEKLGKKMEA 386


  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    0.397 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,723,184
Number of Sequences: 62578
Number of extensions: 405298
Number of successful extensions: 946
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 940
Number of HSP's gapped (non-prelim): 3
length of query: 386
length of database: 14,973,337
effective HSP length: 101
effective length of query: 285
effective length of database: 8,652,959
effective search space: 2466093315
effective search space used: 2466093315
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)