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= psy17485
         (237 letters)

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

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



>pdb|3SE7|A Chain A, Ancient Vana
 pdb|3SE7|B Chain B, Ancient Vana
 pdb|3SE7|C Chain C, Ancient Vana
 pdb|3SE7|D Chain D, Ancient Vana
 pdb|3SE7|E Chain E, Ancient Vana
 pdb|3SE7|F Chain F, Ancient Vana
          Length = 346

 Score = 30.4 bits (67), Expect = 0.89,   Method: Compositional matrix adjust.
 Identities = 28/86 (32%), Positives = 44/86 (51%), Gaps = 10/86 (11%)

Query: 4   YLVSQPDGLSTDRFWNVTLDLDSIPVNFALLQLVGVKVSKREGDS---SLMQLKEEFRTY 60
           YLV++  G++T  FW VT D + IP +  L   V VK   R G S   S +  +E+ +  
Sbjct: 137 YLVARSAGIATPNFWTVTAD-EKIPTD-QLTYPVFVK-PARSGSSFGVSKVAREEDLQGA 193

Query: 61  ESLRREHDAQIV----EIATEAGLRI 82
               RE+D++++     I TE G  +
Sbjct: 194 VEAAREYDSKVLIEEAVIGTEIGCAV 219


>pdb|4I4T|E Chain E, Crystal Structure Of Tubulin-rb3-ttl-zampanolide Complex
 pdb|4I50|E Chain E, Crystal Structure Of Tubulin-stathmin-ttl-epothilone A
           Complex
 pdb|4I55|E Chain E, Crystal Structure Of Tubulin-stathmin-ttl Complex
 pdb|4IIJ|E Chain E, Crystal Structure Of Tubulin-stathmin-ttl-apo Complex
 pdb|4IHJ|E Chain E, Crystal Structure Of Tubulin-stathmin-ttl-adp Complex
          Length = 143

 Score = 29.3 bits (64), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 12/63 (19%), Positives = 39/63 (61%), Gaps = 4/63 (6%)

Query: 64  RREHDAQIVEIATEAG---LRIAPDQWSSLLYGDA-SRKSHMQSIIDKLQNPQSFAQSVQ 119
           +REH+ ++++ A E     +++A ++ +  +  +  +R++H+ +++++LQ     A+ V+
Sbjct: 73  KREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLERLQEKDKHAEEVR 132

Query: 120 VSR 122
            ++
Sbjct: 133 KNK 135


>pdb|1SA0|E Chain E, Tubulin-Colchicine: Stathmin-Like Domain Complex
 pdb|1Z2B|E Chain E, Tubulin-Colchicine-Vinblastine: Stathmin-Like Domain
           Complex
 pdb|3DU7|E Chain E, Tubulin-Colchicine-Phomopsin A: Stathmin-Like Domain
           Complex
 pdb|3E22|E Chain E, Tubulin-Colchicine-Soblidotin: Stathmin-Like Domain
           Complex
 pdb|3HKB|E Chain E, Tubulin: Rb3 Stathmin-Like Domain Complex
 pdb|3HKC|E Chain E, Tubulin-Abt751: Rb3 Stathmin-Like Domain Complex
 pdb|3HKD|E Chain E, Tubulin-Tn16 : Rb3 Stathmin-Like Domain Complex
 pdb|3HKE|E Chain E, Tubulin-T138067: Rb3 Stathmin-Like Domain Complex
 pdb|3N2G|E Chain E, Tubulin-Nsc 613863: Rb3 Stathmin-Like Domain Complex
 pdb|3N2K|E Chain E, Tubulin-Nsc 613862: Rb3 Stathmin-Like Domain Complex
 pdb|1SA1|E Chain E, Tubulin-Podophyllotoxin: Stathmin-Like Domain Complex
          Length = 142

 Score = 29.3 bits (64), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 12/63 (19%), Positives = 39/63 (61%), Gaps = 4/63 (6%)

Query: 64  RREHDAQIVEIATEAG---LRIAPDQWSSLLYGDA-SRKSHMQSIIDKLQNPQSFAQSVQ 119
           +REH+ ++++ A E     +++A ++ +  +  +  +R++H+ +++++LQ     A+ V+
Sbjct: 72  KREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLERLQEKDKHAEEVR 131

Query: 120 VSR 122
            ++
Sbjct: 132 KNK 134


>pdb|3UT5|E Chain E, Tubulin-colchicine-ustiloxin: Stathmin-like Domain Complex
 pdb|4EB6|E Chain E, Tubulin-vinblastine: Stathmin-like Complex
          Length = 142

 Score = 28.5 bits (62), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 12/63 (19%), Positives = 39/63 (61%), Gaps = 4/63 (6%)

Query: 64  RREHDAQIVEIATEAG---LRIAPDQWSSLLYGDA-SRKSHMQSIIDKLQNPQSFAQSVQ 119
           +REH+ ++++ A E     +++A ++ +  +  +  +R++H+ +++++LQ     A+ V+
Sbjct: 72  KREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLERLQEKDKHAEEVR 131

Query: 120 VSR 122
            ++
Sbjct: 132 KNK 134


>pdb|3RYC|E Chain E, Tubulin: Rb3 Stathmin-Like Domain Complex
 pdb|3RYF|E Chain E, Gtp-Tubulin: Rb3 Stathmin-Like Domain Complex
 pdb|3RYH|E Chain E, Gmpcpp-Tubulin: Rb3 Stathmin-Like Domain Complex
 pdb|3RYI|E Chain E, Gdp-Tubulin: Rb3 Stathmin-Like Domain Complex
          Length = 143

 Score = 28.5 bits (62), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 12/63 (19%), Positives = 39/63 (61%), Gaps = 4/63 (6%)

Query: 64  RREHDAQIVEIATEAG---LRIAPDQWSSLLYGDA-SRKSHMQSIIDKLQNPQSFAQSVQ 119
           +REH+ ++++ A E     +++A ++ +  +  +  +R++H+ +++++LQ     A+ V+
Sbjct: 73  KREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLERLQEKDKHAEEVR 132

Query: 120 VSR 122
            ++
Sbjct: 133 KNK 135


>pdb|4DCM|A Chain A, Crystal Structure Of Methyltransferase Rlmg Modifying
           G1835 Of 23s Rrna In Escherichia Coli
          Length = 375

 Score = 28.1 bits (61), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 31/115 (26%), Positives = 50/115 (43%), Gaps = 15/115 (13%)

Query: 68  DAQIVEIATEAGLRIAPDQWSSLLYGDASRKSHMQSIIDKLQNPQSFA---------QSV 118
           D+ I E+AT   LR+     SS+ + D++     Q  +  ++ P++ A         + V
Sbjct: 66  DSYISELATRENLRLNGIDESSVKFLDSTADYPQQPGVVLIKVPKTLALLEQQLRALRKV 125

Query: 119 QVSRTRSPSPSLYRSVEPAVLRPVCTVQGSNPTSCTLSRPMQRKLIGLINCQILE 173
             S TR  + +  R +  + L     V G  PT+ TL+    R    LINC   E
Sbjct: 126 VTSDTRIIAGAKARDIHTSTLELFEKVLG--PTTTTLAWKKAR----LINCTFNE 174


>pdb|2F1T|A Chain A, Outer Membrane Protein Ompw
 pdb|2F1T|B Chain B, Outer Membrane Protein Ompw
 pdb|2F1T|C Chain C, Outer Membrane Protein Ompw
 pdb|2F1V|A Chain A, Outer Membrane Protein Ompw
 pdb|2F1V|B Chain B, Outer Membrane Protein Ompw
 pdb|2F1V|C Chain C, Outer Membrane Protein Ompw
 pdb|2F1V|D Chain D, Outer Membrane Protein Ompw
 pdb|2F1V|E Chain E, Outer Membrane Protein Ompw
 pdb|2F1V|F Chain F, Outer Membrane Protein Ompw
          Length = 197

 Score = 27.7 bits (60), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 15/39 (38%), Positives = 19/39 (48%)

Query: 183 AARSIGPQSKARTPHRTSIGERAVTELNLQHQNPQQLSA 221
           A  +IG +  A TP R  IG RA  ++   H  P  L A
Sbjct: 47  ATDNIGVELLAATPFRHKIGTRATGDIATVHHLPPTLMA 85


  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
   0.317    0.130    0.378 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,319,894
Number of Sequences: 62578
Number of extensions: 216743
Number of successful extensions: 391
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 387
Number of HSP's gapped (non-prelim): 9
length of query: 237
length of database: 14,973,337
effective HSP length: 96
effective length of query: 141
effective length of database: 8,965,849
effective search space: 1264184709
effective search space used: 1264184709
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)