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= psy318
         (438 letters)

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

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



>pdb|2QGZ|A Chain A, Crystal Structure Of A Putative Primosome Component From
           Streptococcus Pyogenes Serotype M3. Northeast Structural
           Genomics Target Dr58
          Length = 308

 Score = 32.0 bits (71), Expect = 0.61,   Method: Compositional matrix adjust.
 Identities = 23/60 (38%), Positives = 32/60 (53%), Gaps = 8/60 (13%)

Query: 55  FSFFQDKVKQ-----PKGLYIYGAVGGGKT-MLMDIFYESCETK--QKQRVHFNKFMLDV 106
           FS   D V+Q      KGLY+YG +G GK+ +L  + +E  E K      +HF  F +DV
Sbjct: 137 FSAILDFVEQYPSAEQKGLYLYGDMGIGKSYLLAAMAHELSEKKGVSTTLLHFPSFAIDV 196


>pdb|4B4T|I Chain I, Near-Atomic Resolution Structural Model Of The Yeast 26s
           Proteasome
          Length = 437

 Score = 31.6 bits (70), Expect = 0.93,   Method: Compositional matrix adjust.
 Identities = 12/20 (60%), Positives = 16/20 (80%)

Query: 62  VKQPKGLYIYGAVGGGKTML 81
           +K PKG+ +YGA G GKT+L
Sbjct: 213 IKPPKGVILYGAPGTGKTLL 232


>pdb|4B4T|J Chain J, Near-Atomic Resolution Structural Model Of The Yeast 26s
           Proteasome
          Length = 405

 Score = 30.4 bits (67), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 11/20 (55%), Positives = 15/20 (75%)

Query: 62  VKQPKGLYIYGAVGGGKTML 81
           + QPKG+ +YG  G GKT+L
Sbjct: 179 IAQPKGVILYGPPGTGKTLL 198


>pdb|4B4T|L Chain L, Near-Atomic Resolution Structural Model Of The Yeast 26s
           Proteasome
          Length = 437

 Score = 30.0 bits (66), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 11/20 (55%), Positives = 15/20 (75%)

Query: 62  VKQPKGLYIYGAVGGGKTML 81
           +K PKG+ +YG  G GKT+L
Sbjct: 212 IKPPKGVLLYGPPGTGKTLL 231


>pdb|2VTY|A Chain A, Vaccinia Virus Anti-Apoptotic F1l Is A Novel Bcl-2-Like
           Domain Swapped Dimer
          Length = 182

 Score = 28.9 bits (63), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 25/83 (30%), Positives = 41/83 (49%), Gaps = 6/83 (7%)

Query: 199 ILKRLFTELFQLGVVV-VATSNRAPDDLYKNGLQRSNFLPFIDVLKTYCDVASLNSNIDY 257
           IL  L TE   + + V    S +  DDLY+    ++    +ID++  YCD  S + N   
Sbjct: 47  ILDYLSTERDHVMMAVRYYMSKQRLDDLYRQLPTKTR--SYIDIINIYCDKVSNDYN--- 101

Query: 258 RSLKANAEESSTKTYFVKNFANE 280
           R +    + +STK++ V +  NE
Sbjct: 102 RDMNIMYDMASTKSFTVYDINNE 124


>pdb|2QZ4|A Chain A, Human Paraplegin, Aaa Domain In Complex With Adp
          Length = 262

 Score = 28.9 bits (63), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 15/48 (31%), Positives = 22/48 (45%)

Query: 34 VKQLDNVYVSIKNYAPQSKSMFSFFQDKVKQPKGLYIYGAVGGGKTML 81
          V  +    + ++ +    KS   F Q   K PKG  + G  G GKT+L
Sbjct: 8  VAGMHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLL 55


  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    0.135    0.389 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,650,776
Number of Sequences: 62578
Number of extensions: 439589
Number of successful extensions: 969
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 963
Number of HSP's gapped (non-prelim): 10
length of query: 438
length of database: 14,973,337
effective HSP length: 102
effective length of query: 336
effective length of database: 8,590,381
effective search space: 2886368016
effective search space used: 2886368016
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: 53 (25.0 bits)