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= psy9768
         (406 letters)

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

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



>pdb|3T5X|A Chain A, Pcid2:dss1 Structure
          Length = 203

 Score =  238 bits (606), Expect = 5e-63,   Method: Compositional matrix adjust.
 Identities = 114/202 (56%), Positives = 151/202 (74%)

Query: 201 SSQYKDKSSLSQQITYKYYVGRKAMFDSDYKTANEYLTFAFQRCHKSSKKNKRLILIYLV 260
            S  KD  S +Q++TYKYYVGRKAMFDSD+K A EYL+FAF+ CH+SS+KNKR+ILIYL+
Sbjct: 1   GSHMKDDYSTAQRVTYKYYVGRKAMFDSDFKQAEEYLSFAFEHCHRSSQKNKRMILIYLL 60

Query: 261 PVKMLLGFMPTRELLDKYDLLQLWDVTVAVKGGQINQLSDAMTKHQTFFIKCGIYLILEK 320
           PVKMLLG MPT ELL KY L+Q  +VT AV  G +  L +A+ KH+ FFI+CGI+LILEK
Sbjct: 61  PVKMLLGHMPTVELLKKYHLMQFAEVTRAVSEGNLLLLHEALAKHEAFFIRCGIFLILEK 120

Query: 321 LKMITYRNFYNIHKDINKNSVVELQQFLQALHYVEGKHIDLEDTHCLLCNLIHDGQLKGY 380
           LK+ITYRN +     + K   + L  FL AL +++ + +D+++  C+L NLI+ G +KGY
Sbjct: 121 LKIITYRNLFKKVYLLLKTHQLSLDAFLVALKFMQVEDVDIDEVQCILANLIYMGHVKGY 180

Query: 381 ISLAHQKVVLSKTDPFPKLSAI 402
           IS  HQK+V+SK +PFP LS +
Sbjct: 181 ISHQHQKLVVSKQNPFPPLSTV 202


>pdb|3T5V|B Chain B, Sac3:thp1:sem1 Complex
 pdb|3T5V|E Chain E, Sac3:thp1:sem1 Complex
          Length = 455

 Score = 58.5 bits (140), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 53/188 (28%), Positives = 89/188 (47%), Gaps = 21/188 (11%)

Query: 160 NRTSEN-DSKKWGMLPFVNQLFKVYFRISKLHLMKPLIRAIESSQ---YKDKSSLSQQIT 215
           N +S N   K+  +L  VN+L  +YFRI    L   + +  +      + ++  L QQI 
Sbjct: 162 NASSTNIPGKQRILLYLVNKLNNIYFRIESPQLCSNIFKNFQPKSMLAHFNEYQLDQQIE 221

Query: 216 YKYYVGRKAMFDSDYKTANEYLTFAFQR------CHKSSKKNKRLILIYLVPVKMLLGFM 269
           Y+Y +GR  + +S    A      AFQ        +++  +N   IL Y++P  ++LG M
Sbjct: 222 YRYLLGRYYLLNSQVHNAFVQFNEAFQSLLNLPLTNQAITRNGTRILNYMIPTGLILGKM 281

Query: 270 ----PTRELLDKYDLLQLWDVTVA-VKGGQINQLSDAMTKHQTFFIKCG---IYLILEKL 321
               P R  L + + +  W V    V+ G I  +S  + +++     C    + ++LEKL
Sbjct: 282 VKWGPLRPFLSQ-ETIDNWSVLYKHVRYGNIQGVSLWLRQNERHL--CARQLLIVLLEKL 338

Query: 322 KMITYRNF 329
            M+TYRN 
Sbjct: 339 PMVTYRNL 346


>pdb|4B4T|S Chain S, Near-Atomic Resolution Structural Model Of The Yeast 26s
           Proteasome
          Length = 523

 Score = 38.5 bits (88), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 38/168 (22%), Positives = 75/168 (44%), Gaps = 20/168 (11%)

Query: 166 DSKKWGMLPFVNQLFKVYFRISKLHLMKPLIRAIESSQYKDKSSLSQQITYKYYVGRKAM 225
           D++   ML  +N + + +    ++      I  +E       SSL  +  Y +Y+ +   
Sbjct: 226 DNETKAML--INLILRDFLNNGEVDSASDFISKLEYPHTDVSSSLEAR--YFFYLSKINA 281

Query: 226 FDSDYKTANEYLTFAFQRCHKSSKKNKRLILIYL-------VPVKMLLGFMPTRELLDKY 278
              DY TANEY+  A ++   +SK      L +L         +++L+G +P      + 
Sbjct: 282 IQLDYSTANEYIIAAIRKAPHNSKS-----LGFLQQSNKLHCCIQLLMGDIPELSFFHQS 336

Query: 279 D----LLQLWDVTVAVKGGQINQLSDAMTKHQTFFIKCGIYLILEKLK 322
           +    LL  + +T AVK G + + +  +TK++   +K   Y +  +L+
Sbjct: 337 NMQKSLLPYYHLTKAVKLGDLKKFTSTITKYKQLLLKDDTYQLCVRLR 384


>pdb|1XG7|A Chain A, Conserved Hypothetical Protein Pfu-877259-001 From
           Pyrococcus Furiosus
 pdb|1XG7|B Chain B, Conserved Hypothetical Protein Pfu-877259-001 From
           Pyrococcus Furiosus
          Length = 250

 Score = 28.9 bits (63), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 14/82 (17%)

Query: 217 KYYVGRKAMFDSDYKTANEYLTFAFQRCHKSSKKNKRLILIYLVPVKMLLGFMPTREL-- 274
           +Y+ GR+   DS +K   E+L          SK N+RLI   L  ++ + GF+ T  L  
Sbjct: 77  RYFSGREV--DSIWKAYGEFLP--------KSKNNRRLIEAKLNRIRKVEGFLSTLTLKD 126

Query: 275 LDKY--DLLQLWDVTVAVKGGQ 294
           L+ Y  ++  LW   + + G +
Sbjct: 127 LEGYYKNMKMLWKALIKIMGSR 148


  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    0.397 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,252,832
Number of Sequences: 62578
Number of extensions: 434897
Number of successful extensions: 998
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 991
Number of HSP's gapped (non-prelim): 7
length of query: 406
length of database: 14,973,337
effective HSP length: 101
effective length of query: 305
effective length of database: 8,652,959
effective search space: 2639152495
effective search space used: 2639152495
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: 53 (25.0 bits)