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= 016164
         (394 letters)

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

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



>pdb|4B4T|W Chain W, Near-Atomic Resolution Structural Model Of The Yeast 26s
           Proteasome
          Length = 268

 Score =  220 bits (560), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 116/237 (48%), Positives = 157/237 (66%), Gaps = 3/237 (1%)

Query: 1   MVLEATLICIDNSEWMRNGDYAPSRFQAQTEAANLICGAKTQLNPENTVGVMTMAGKGVR 60
           MVLEAT++ IDNSE+ RNGD+  +RF+AQ ++   I  AK   NPENTVG+++ AG   R
Sbjct: 1   MVLEATVLVIDNSEYSRNGDFPRTRFEAQIDSVEFIFQAKRNSNPENTVGLISGAGANPR 60

Query: 61  VLVTPTSDLGKILACMHGLEIGGELNLAAGIQVAQLALKHRQNKKQQQRIIVFVGSPIKH 120
           VL T T++ GKILA +H  +I G+L++A  +Q+AQL LKHRQNK Q QRI+ FV SPI  
Sbjct: 61  VLSTFTAEFGKILAGLHDTQIEGKLHMATALQIAQLTLKHRQNKVQHQRIVAFVCSPISD 120

Query: 121 EKKVLEMIGRKLKKNSVALDIVNFGEDDEGNTEKLEALLAAVNN--NDSSHLVHVPPGPN 178
            +  L  + + LKKN+VA+DI+NFGE  E NTE L+  +AAVNN   ++SHL+ V PGP 
Sbjct: 121 SRDELIRLAKTLKKNNVAVDIINFGE-IEQNTELLDEFIAAVNNPQEETSHLLTVTPGPR 179

Query: 179 ALSDVLLSTPIFTGDGEXXXXXXXXXXXXXXXXXXXYEFGVDPNLDPELALALRVSM 235
            L + + S+PI   +G                     +FGVDP++DPELA+ALR+SM
Sbjct: 180 LLYENIASSPIILEEGSSGMGAFGGSGGDSDANGTFMDFGVDPSMDPELAMALRLSM 236


>pdb|2X5N|A Chain A, Crystal Structure Of The Sprpn10 Vwa Domain
          Length = 192

 Score =  191 bits (486), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 95/191 (49%), Positives = 128/191 (67%), Gaps = 2/191 (1%)

Query: 2   VLEATLICIDNSEWMRNGDYAPSRFQAQTEAANLICGAKTQLNPENTVGVMTMAGKGVRV 61
           VLEAT+I IDNSEWM NGDY P+RF+AQ +  ++I   K   NPEN  G+MT+     +V
Sbjct: 1   VLEATMILIDNSEWMINGDYIPTRFEAQKDTVHMIFNQKINDNPENMCGLMTIGDNSPQV 60

Query: 62  LVTPTSDLGKILACMHGLEIGGELNLAAGIQVAQLALKHRQNKKQQQRIIVFVGSPIKHE 121
           L T T D GK L+ MH L + G      GIQ+AQLALKHR+NK Q+QRI+ FVGSPI  +
Sbjct: 61  LSTLTRDYGKFLSAMHDLPVRGNAKFGDGIQIAQLALKHRENKIQRQRIVAFVGSPIVED 120

Query: 122 KKVLEMIGRKLKKNSVALDIVNFGEDDEGNTEKLEALLAAVNNNDSSHLVHVPPGPNALS 181
           +K L  + +++KKN+VA+DI++ GE    N   L+  + A N++DS HLV +PP P  LS
Sbjct: 121 EKNLIRLAKRMKKNNVAIDIIHIGELQ--NESALQHFIDAANSSDSCHLVSIPPSPQLLS 178

Query: 182 DVLLSTPIFTG 192
           D++  +PI  G
Sbjct: 179 DLVNQSPIGQG 189


>pdb|2KDE|A Chain A, Nmr Structure Of Major S5a (196-306):k48 Linked
           Diubiquitin Species
 pdb|2KDF|A Chain A, Nmr Structure Of Minor S5a (196-306):k48 Linked
           Diubiquitin Species
          Length = 111

 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 18/21 (85%), Positives = 20/21 (95%)

Query: 215 YEFGVDPNLDPELALALRVSM 235
           +EFGVDP+ DPELALALRVSM
Sbjct: 9   FEFGVDPSADPELALALRVSM 29


>pdb|1YX4|A Chain A, Structure Of S5a Bound To Monoubiquitin Provides A Model
           For Polyubiquitin Recognition
 pdb|1YX5|A Chain A, Solution Structure Of S5a Uim-1UBIQUITIN COMPLEX
 pdb|1YX6|A Chain A, Solution Structure Of S5a Uim-2UBIQUITIN COMPLEX
          Length = 132

 Score = 43.1 bits (100), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 18/21 (85%), Positives = 20/21 (95%)

Query: 215 YEFGVDPNLDPELALALRVSM 235
           +EFGVDP+ DPELALALRVSM
Sbjct: 30  FEFGVDPSADPELALALRVSM 50


>pdb|1OYZ|A Chain A, X-Ray Structure Of Yiba_ecoli Northeast Structural
           Genomics Consortium Target Et31
          Length = 280

 Score = 32.3 bits (72), Expect = 0.45,   Method: Compositional matrix adjust.
 Identities = 15/41 (36%), Positives = 27/41 (65%)

Query: 102 QNKKQQQRIIVFVGSPIKHEKKVLEMIGRKLKKNSVALDIV 142
           Q+K ++ RI   +G   + +K+VL ++  +LKKN+V  DI+
Sbjct: 202 QDKNEEVRIEAIIGLSYRKDKRVLSVLCDELKKNTVYDDII 242


>pdb|2WPV|A Chain A, Crystal Structure Of S. Cerevisiae Get4-Get5 Complex
 pdb|2WPV|C Chain C, Crystal Structure Of S. Cerevisiae Get4-Get5 Complex
 pdb|2WPV|E Chain E, Crystal Structure Of S. Cerevisiae Get4-Get5 Complex
 pdb|2WPV|G Chain G, Crystal Structure Of S. Cerevisiae Get4-Get5 Complex
          Length = 312

 Score = 31.6 bits (70), Expect = 0.72,   Method: Compositional matrix adjust.
 Identities = 13/40 (32%), Positives = 26/40 (65%)

Query: 346 DMSQLLADQAFVSSILASLPGVDPEDPSVKDVLTSMQNQS 385
           D++++  D   V+ ++  +  +DP +P++KDV+T M N S
Sbjct: 84  DLAEVKVDDISVARLVRLIAELDPSEPNLKDVITGMNNWS 123


>pdb|3LKU|A Chain A, Crystal Structure Of S. Cerevisiae Get4 In Complex With An
           N-Terminal Fragment Of Get5
 pdb|3LKU|C Chain C, Crystal Structure Of S. Cerevisiae Get4 In Complex With An
           N-Terminal Fragment Of Get5
 pdb|3LKU|E Chain E, Crystal Structure Of S. Cerevisiae Get4 In Complex With An
           N-Terminal Fragment Of Get5
          Length = 292

 Score = 29.3 bits (64), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 12/40 (30%), Positives = 25/40 (62%)

Query: 346 DMSQLLADQAFVSSILASLPGVDPEDPSVKDVLTSMQNQS 385
           D++++  D   V+ ++  +  +DP +P++KDV+T   N S
Sbjct: 76  DLAEVKVDDISVARLVRLIAELDPSEPNLKDVITGXNNWS 115


>pdb|3IYG|E Chain E, Ca Model Of Bovine TricCCT DERIVED FROM A 4.0 ANGSTROM
           Cryo-Em Map
          Length = 515

 Score = 28.1 bits (61), Expect = 7.8,   Method: Compositional matrix adjust.
 Identities = 16/45 (35%), Positives = 25/45 (55%)

Query: 119 KHEKKVLEMIGRKLKKNSVALDIVNFGEDDEGNTEKLEALLAAVN 163
           K+EK+  E + R++K+    L +  +G DDE N   L+  L AV 
Sbjct: 257 KYEKEKFEEMIRQIKETGANLAVCQWGFDDEANHLLLQNDLPAVR 301


  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
   0.311    0.128    0.352 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,697,881
Number of Sequences: 62578
Number of extensions: 346717
Number of successful extensions: 715
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 700
Number of HSP's gapped (non-prelim): 15
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 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 52 (24.6 bits)