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= 006718
         (634 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 =  393 bits (1010), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 189/367 (51%), Positives = 263/367 (71%), Gaps = 20/367 (5%)

Query: 129 DVEMMKERFAKLLLGEDMSGCGNGVSTALAISNAITNLCATLFGQLWRLEPLPLEKKAMW 188
           D+EMMK+RFAKLLLGEDMSG G GVS+ALA+SNAITNL A++FG+  +L+P+P +++A W
Sbjct: 10  DMEMMKDRFAKLLLGEDMSGGGKGVSSALALSNAITNLAASIFGEQTKLQPMPQDRQARW 69

Query: 189 RREMEWFLCVSDHIVELTPSWQTFPDGSKLEVMTCRPRSDLYINLPALRKLDNMLLEILD 248
           ++E++W L V+DHIVE  PS QT  DG   E+M  R R DL +N+PALRKLD ML++ LD
Sbjct: 70  KKEIDWLLSVTDHIVEFVPSQQTSKDGVCTEIMVTRQRGDLLMNIPALRKLDAMLIDTLD 129

Query: 249 SFE-NTEFWYVDQGILASEADGSTSFRRALQRQEEKWWLPVPRVPLGGLHENTRKQLQHK 307
           +F  + EFWYV +       D     +    R  +KWWLP  +VP GGL E +R+ L  +
Sbjct: 130 NFRGHNEFWYVSR-------DSEEGQQARNDRTNDKWWLPPVKVPPGGLSEPSRRMLYFQ 182

Query: 308 RDCTNQILKAAMAINSITLADMEVPESYFESLPKNGRVSLGDLIYRYISSDQFSPEYLLE 367
           +D   Q+ KAAMAIN+  L++ME+PESY +SLPKNGR SLGD IY+ I+ + F PE  L 
Sbjct: 183 KDSVTQVQKAAMAINAQVLSEMEIPESYIDSLPKNGRASLGDSIYKSITEEWFDPEQFLA 242

Query: 368 CLDLSSEHQATEIANRVEAAMYVWRKRTNSKPANXXXXXXXXXXWGLVKEFVVDTEKREL 427
            LD+S+EH+  ++ NR+EA++ +W+++ ++K             WG      V  EKREL
Sbjct: 243 MLDMSTEHKVLDLKNRIEASVVIWKRKLHTKDTK--------SSWG----SAVSLEKREL 290

Query: 428 LADRAESLLLCLKQWFPGLPQTTLDMSKIQYNKDVGKSILESYSRVLESLAFNIVARIDD 487
             +RAE++L+ LKQ FPGLPQ++LD+SKIQ+NKDVG+++LESYSR+LESLA+ +++RI+D
Sbjct: 291 FEERAETILVLLKQKFPGLPQSSLDISKIQFNKDVGQAVLESYSRILESLAYTVMSRIED 350

Query: 488 LLYVDDL 494
           +LY D L
Sbjct: 351 VLYTDTL 357


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

 Score =  354 bits (908), Expect = 1e-97,   Method: Compositional matrix adjust.
 Identities = 182/367 (49%), Positives = 251/367 (68%), Gaps = 20/367 (5%)

Query: 129 DVEMMKERFAKLLLGEDMSGCGNGVSTALAISNAITNLCATLFGQLWRLEPLPLEKKAMW 188
           D E  K+RFAKLLLGED SG G GVS+ALA+SNAITNL A++FG+  +L+P P +++A W
Sbjct: 10  DXEXXKDRFAKLLLGEDXSGGGKGVSSALALSNAITNLAASIFGEQTKLQPXPQDRQARW 69

Query: 189 RREMEWFLCVSDHIVELTPSWQTFPDGSKLEVMTCRPRSDLYINLPALRKLDNMLLEILD 248
           ++E++W L V+DHIVE  PS QT  DG   E+   R R DL  N+PALRKLD  L++ LD
Sbjct: 70  KKEIDWLLSVTDHIVEFVPSQQTSKDGVCTEIXVTRQRGDLLXNIPALRKLDAXLIDTLD 129

Query: 249 SFE-NTEFWYVDQGILASEADGSTSFRRALQRQEEKWWLPVPRVPLGGLHENTRKQLQHK 307
           +F  + EFWYV +       D     +    R  +KWWLP  +VP GGL E +R+ L  +
Sbjct: 130 NFRGHNEFWYVSR-------DSEEGQQARNDRTNDKWWLPPVKVPPGGLSEPSRRXLYFQ 182

Query: 308 RDCTNQILKAAMAINSITLADMEVPESYFESLPKNGRVSLGDLIYRYISSDQFSPEYLLE 367
           +D   Q+ KAA AIN+  L++ E+PESY +SLPKNGR SLGD IY+ I+ + F PE  L 
Sbjct: 183 KDSVTQVQKAAXAINAQVLSEXEIPESYIDSLPKNGRASLGDSIYKSITEEWFDPEQFLA 242

Query: 368 CLDLSSEHQATEIANRVEAAMYVWRKRTNSKPANXXXXXXXXXXWGLVKEFVVDTEKREL 427
            LD S+EH+  ++ NR+EA++ +W+++ ++K             WG      V  EKREL
Sbjct: 243 XLDXSTEHKVLDLKNRIEASVVIWKRKLHTKDTK--------SSWG----SAVSLEKREL 290

Query: 428 LADRAESLLLCLKQWFPGLPQTTLDMSKIQYNKDVGKSILESYSRVLESLAFNIVARIDD 487
             +RAE++L+ LKQ FPGLPQ++LD+SKIQ+NKDVG+++LESYSR+LESLA+ + +RI+D
Sbjct: 291 FEERAETILVLLKQKFPGLPQSSLDISKIQFNKDVGQAVLESYSRILESLAYTVXSRIED 350

Query: 488 LLYVDDL 494
           +LY D L
Sbjct: 351 VLYTDTL 357


>pdb|2Z1Q|A Chain A, Crystal Structure Of Acyl Coa Dehydrogenase
 pdb|2Z1Q|B Chain B, Crystal Structure Of Acyl Coa Dehydrogenase
          Length = 577

 Score = 31.2 bits (69), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 22/104 (21%), Positives = 47/104 (45%), Gaps = 13/104 (12%)

Query: 183 EKKAMWRREMEWFLCVSDHIV----------ELTPSWQTFPDGSKLEVMTCRPRSDLYIN 232
           E+K +W++   W L V + +           E+  + +TF +   L ++      +L +N
Sbjct: 3   EEKKLWQKGGGWLLEVPERVYTPEDFDESVKEIARTTRTFVEREVLPLLERMEHGELELN 62

Query: 233 LPALRK---LDNMLLEILDSFENTEFWYVDQGILASEADGSTSF 273
           +P +RK   L  + +++ + +   +   V   ++A E  GS  F
Sbjct: 63  VPLMRKAGELGLLAIDVPEEYGGLDLPKVISTVVAEELSGSGGF 106


  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
   0.315    0.131    0.381 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,230,354
Number of Sequences: 62578
Number of extensions: 675328
Number of successful extensions: 1447
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1436
Number of HSP's gapped (non-prelim): 9
length of query: 634
length of database: 14,973,337
effective HSP length: 105
effective length of query: 529
effective length of database: 8,402,647
effective search space: 4445000263
effective search space used: 4445000263
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 54 (25.4 bits)