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= 016074
         (396 letters)

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

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



>pdb|2NTY|A Chain A, Rop4-Gdp-Prone8
 pdb|2NTY|B Chain B, Rop4-Gdp-Prone8
 pdb|2WBL|A Chain A, Three-Dimensional Structure Of A Binary Rop-Prone Complex
 pdb|2WBL|B Chain B, Three-Dimensional Structure Of A Binary Rop-Prone Complex
          Length = 365

 Score =  254 bits (650), Expect = 4e-68,   Method: Compositional matrix adjust.
 Identities = 124/261 (47%), Positives = 182/261 (69%), Gaps = 1/261 (0%)

Query: 120 DVETMKERFSKLLLGEDITGGRLGVTTALALSNAITNLAASVFGELWKLEPLLEERKSRW 179
           D+E MK+RF+KLLLGED++GG  GV++ALALSNAITNLAAS+FGE  KL+P+ ++R++RW
Sbjct: 10  DMEMMKDRFAKLLLGEDMSGGGKGVSSALALSNAITNLAASIFGEQTKLQPMPQDRQARW 69

Query: 180 QREMDWLLSPTNFMVELVPARQNAANGQTLEIMTPKARADIHMNLPALQKLDSMLIETLD 239
           ++E+DWLLS T+ +VE VP++Q + +G   EIM  + R D+ MN+PAL+KLD+MLI+TLD
Sbjct: 70  KKEIDWLLSVTDHIVEFVPSQQTSKDGVCTEIMVTRQRGDLLMNIPALRKLDAMLIDTLD 129

Query: 240 SMV-NTEFWYAEVGSRAEGRNKSTRESKRWWLPLAQVPASGLSDSGRKKMLSQCRVVYQV 298
           +   + EFWY    S    + ++ R + +WWLP  +VP  GLS+  R+ +  Q   V QV
Sbjct: 130 NFRGHNEFWYVSRDSEEGQQARNDRTNDKWWLPPVKVPPGGLSEPSRRMLYFQKDSVTQV 189

Query: 299 FKAAKSINENVLLEMPVPTIIKDVLPKSGKTSLGEELYKVLTAESISSGEMINFLNLKSE 358
            KAA +IN  VL EM +P    D LPK+G+ SLG+ +YK +T E     + +  L++ +E
Sbjct: 190 QKAAMAINAQVLSEMEIPESYIDSLPKNGRASLGDSIYKSITEEWFDPEQFLAMLDMSTE 249

Query: 359 HSALEAINKLEAAVFTWKERI 379
           H  L+  N++EA+V  WK ++
Sbjct: 250 HKVLDLKNRIEASVVIWKRKL 270


>pdb|2NTX|A Chain A, Prone8
 pdb|2NTX|B Chain B, Prone8
          Length = 365

 Score =  226 bits (577), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 119/261 (45%), Positives = 173/261 (66%), Gaps = 1/261 (0%)

Query: 120 DVETMKERFSKLLLGEDITGGRLGVTTALALSNAITNLAASVFGELWKLEPLLEERKSRW 179
           D E  K+RF+KLLLGED +GG  GV++ALALSNAITNLAAS+FGE  KL+P  ++R++RW
Sbjct: 10  DXEXXKDRFAKLLLGEDXSGGGKGVSSALALSNAITNLAASIFGEQTKLQPXPQDRQARW 69

Query: 180 QREMDWLLSPTNFMVELVPARQNAANGQTLEIMTPKARADIHMNLPALQKLDSMLIETLD 239
           ++E+DWLLS T+ +VE VP++Q + +G   EI   + R D+  N+PAL+KLD+ LI+TLD
Sbjct: 70  KKEIDWLLSVTDHIVEFVPSQQTSKDGVCTEIXVTRQRGDLLXNIPALRKLDAXLIDTLD 129

Query: 240 SMV-NTEFWYAEVGSRAEGRNKSTRESKRWWLPLAQVPASGLSDSGRKKMLSQCRVVYQV 298
           +   + EFWY    S    + ++ R + +WWLP  +VP  GLS+  R+ +  Q   V QV
Sbjct: 130 NFRGHNEFWYVSRDSEEGQQARNDRTNDKWWLPPVKVPPGGLSEPSRRXLYFQKDSVTQV 189

Query: 299 FKAAKSINENVLLEMPVPTIIKDVLPKSGKTSLGEELYKVLTAESISSGEMINFLNLKSE 358
            KAA +IN  VL E  +P    D LPK+G+ SLG+ +YK +T E     + +  L+  +E
Sbjct: 190 QKAAXAINAQVLSEXEIPESYIDSLPKNGRASLGDSIYKSITEEWFDPEQFLAXLDXSTE 249

Query: 359 HSALEAINKLEAAVFTWKERI 379
           H  L+  N++EA+V  WK ++
Sbjct: 250 HKVLDLKNRIEASVVIWKRKL 270


>pdb|3AH5|A Chain A, Crystal Structure Of Flavin Dependent Thymidylate Synthase
           Thyx From Helicobacter Pylori Complexed With Fad And
           Dump
 pdb|3AH5|B Chain B, Crystal Structure Of Flavin Dependent Thymidylate Synthase
           Thyx From Helicobacter Pylori Complexed With Fad And
           Dump
 pdb|3AH5|C Chain C, Crystal Structure Of Flavin Dependent Thymidylate Synthase
           Thyx From Helicobacter Pylori Complexed With Fad And
           Dump
 pdb|3AH5|D Chain D, Crystal Structure Of Flavin Dependent Thymidylate Synthase
           Thyx From Helicobacter Pylori Complexed With Fad And
           Dump
 pdb|3AH5|E Chain E, Crystal Structure Of Flavin Dependent Thymidylate Synthase
           Thyx From Helicobacter Pylori Complexed With Fad And
           Dump
 pdb|3AH5|F Chain F, Crystal Structure Of Flavin Dependent Thymidylate Synthase
           Thyx From Helicobacter Pylori Complexed With Fad And
           Dump
          Length = 216

 Score = 28.9 bits (63), Expect = 5.0,   Method: Compositional matrix adjust.
 Identities = 16/40 (40%), Positives = 24/40 (60%)

Query: 334 ELYKVLTAESISSGEMINFLNLKSEHSALEAINKLEAAVF 373
           E YK   A SI++  + NFL L+S + AL+ +  L  A+F
Sbjct: 152 ESYKTHLAYSINARSLQNFLTLRSSNKALKEMQDLAKALF 191


  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
   0.316    0.130    0.382 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,296,733
Number of Sequences: 62578
Number of extensions: 371898
Number of successful extensions: 1007
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1001
Number of HSP's gapped (non-prelim): 5
length of query: 396
length of database: 14,973,337
effective HSP length: 101
effective length of query: 295
effective length of database: 8,652,959
effective search space: 2552622905
effective search space used: 2552622905
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)