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= psy7514
         (347 letters)

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

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



>pdb|2LS4|A Chain A, 1h Chemical Shift Assignments For The Third Transmembrane
           Domain From The Human Copper Transport 1
          Length = 24

 Score = 40.8 bits (94), Expect = 0.001,   Method: Composition-based stats.
 Identities = 18/24 (75%), Positives = 18/24 (75%)

Query: 313 YNVALCIAVVAGAACGYFLFGWKK 336
           YN  LCIAV AGA  GYFLF WKK
Sbjct: 1   YNGYLCIAVAAGAGTGYFLFSWKK 24


>pdb|2LS3|A Chain A, 1h Chemical Shift Assignments For The Secondary
           Transmembrane Domain From Human Copper Transport 1
          Length = 29

 Score = 40.0 bits (92), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 15/27 (55%), Positives = 23/27 (85%)

Query: 288 PHFIQTLLHVLQITMSFLLMLVFMTYN 314
            H +QT+LH++Q+ +S+ LML+FMTYN
Sbjct: 1   KHLLQTVLHIIQVVISYFLMLIFMTYN 27


>pdb|2E6K|A Chain A, X-Ray Structure Of Thermus Thermopilus Hb8 Tt0505
 pdb|2E6K|B Chain B, X-Ray Structure Of Thermus Thermopilus Hb8 Tt0505
 pdb|2E6K|C Chain C, X-Ray Structure Of Thermus Thermopilus Hb8 Tt0505
 pdb|2E6K|D Chain D, X-Ray Structure Of Thermus Thermopilus Hb8 Tt0505
          Length = 651

 Score = 30.4 bits (67), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 15/43 (34%), Positives = 23/43 (53%), Gaps = 3/43 (6%)

Query: 38  CHDMDSHEGMDHMGMSMAFHWGYNEVILF---NQWKISTPSGL 77
             D D  EG+     S+A HWG +++I+F   N+  I  P+ L
Sbjct: 157 ASDGDLXEGVSGEAASLAGHWGLSKLIVFWDDNRISIDGPTDL 199



 Score = 30.4 bits (67), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 15/43 (34%), Positives = 23/43 (53%), Gaps = 3/43 (6%)

Query: 174 CHDMDSHEGMDHMGMSMAFHWGYNEVILF---NQWKISTPSGL 213
             D D  EG+     S+A HWG +++I+F   N+  I  P+ L
Sbjct: 157 ASDGDLXEGVSGEAASLAGHWGLSKLIVFWDDNRISIDGPTDL 199


>pdb|4GA0|A Chain A, Structure Of The N-Terminal Domain Of Nup358
          Length = 150

 Score = 28.1 bits (61), Expect = 8.0,   Method: Compositional matrix adjust.
 Identities = 20/62 (32%), Positives = 28/62 (45%), Gaps = 3/62 (4%)

Query: 72  STPSGLIASMVGIFFLAALYEGVKYYREYLFWKTYNDLHYRSIPAQQRIS---SVEENKD 128
           STPS    SM G +F    YE  +Y     +  TY ++  R   A + +     +EEN D
Sbjct: 23  STPSPRQKSMKGFYFAKLYYEAKEYDLAKKYICTYINVQERDPKAHRFLGLLYELEENTD 82

Query: 129 TA 130
            A
Sbjct: 83  KA 84



 Score = 28.1 bits (61), Expect = 8.0,   Method: Compositional matrix adjust.
 Identities = 20/62 (32%), Positives = 28/62 (45%), Gaps = 3/62 (4%)

Query: 208 STPSGLIASMVGIFFLAALYEGVKYYREYLFWKTYNDLHYRSIPAQQRIS---SVEENKD 264
           STPS    SM G +F    YE  +Y     +  TY ++  R   A + +     +EEN D
Sbjct: 23  STPSPRQKSMKGFYFAKLYYEAKEYDLAKKYICTYINVQERDPKAHRFLGLLYELEENTD 82

Query: 265 TA 266
            A
Sbjct: 83  KA 84


  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
   0.325    0.137    0.443 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,510,096
Number of Sequences: 62578
Number of extensions: 305801
Number of successful extensions: 644
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 640
Number of HSP's gapped (non-prelim): 7
length of query: 347
length of database: 14,973,337
effective HSP length: 100
effective length of query: 247
effective length of database: 8,715,537
effective search space: 2152737639
effective search space used: 2152737639
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 bits)