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= 025248
         (255 letters)

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

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



>pdb|1X3S|A Chain A, Crystal Structure Of Human Rab18 In Complex With Gppnhp
          Length = 195

 Score = 28.9 bits (63), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 13/32 (40%), Positives = 18/32 (56%)

Query: 28  GDSGVIFVHDLSQRRTKTSLQKWAVEIATSGT 59
           G  GVI V+D+++R T   L  W  E+ T  T
Sbjct: 87  GAQGVILVYDVTRRDTFVKLDNWLNELETYCT 118


>pdb|1G16|A Chain A, Crystal Structure Of Sec4-Gdp
 pdb|1G16|B Chain B, Crystal Structure Of Sec4-Gdp
 pdb|1G16|C Chain C, Crystal Structure Of Sec4-Gdp
 pdb|1G16|D Chain D, Crystal Structure Of Sec4-Gdp
          Length = 170

 Score = 28.1 bits (61), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 9/23 (39%), Positives = 17/23 (73%)

Query: 28 GDSGVIFVHDLSQRRTKTSLQKW 50
          G  G+I V+D++  RT T++++W
Sbjct: 75 GAXGIILVYDITDERTFTNIKQW 97


>pdb|4B4T|N Chain N, Near-Atomic Resolution Structural Model Of The Yeast 26s
           Proteasome
          Length = 945

 Score = 28.1 bits (61), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 3/33 (9%)

Query: 179 LDENSSDDDKFYSSGYSSDPY---NMLPPLPAQ 208
           + E   +D++FY + YSS PY   NM   LP Q
Sbjct: 846 IKETKENDEEFYKNKYSSKPYKVDNMTRILPQQ 878


>pdb|1G17|A Chain A, Crystal Structure Of Sec4-Guanosine-5'-(Beta,Gamma)-
          Imidotriphosphate
 pdb|1G17|B Chain B, Crystal Structure Of Sec4-Guanosine-5'-(Beta,Gamma)-
          Imidotriphosphate
          Length = 170

 Score = 28.1 bits (61), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 9/23 (39%), Positives = 17/23 (73%)

Query: 28 GDSGVIFVHDLSQRRTKTSLQKW 50
          G  G+I V+D++  RT T++++W
Sbjct: 75 GAMGIILVYDITDERTFTNIKQW 97


>pdb|1CJL|A Chain A, Crystal Structure Of A Cysteine Protease Proform
          Length = 312

 Score = 28.1 bits (61), Expect = 5.0,   Method: Compositional matrix adjust.
 Identities = 12/30 (40%), Positives = 17/30 (56%)

Query: 81  NKADVAAKEGTRGSSGNLVDAARQWVEKQG 110
           N  D +  EG  G +G L+D A Q+V+  G
Sbjct: 144 NLVDCSGPEGNEGCNGGLMDYAFQYVQDNG 173


  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
   0.313    0.130    0.380 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,284,793
Number of Sequences: 62578
Number of extensions: 207427
Number of successful extensions: 401
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 397
Number of HSP's gapped (non-prelim): 6
length of query: 255
length of database: 14,973,337
effective HSP length: 97
effective length of query: 158
effective length of database: 8,903,271
effective search space: 1406716818
effective search space used: 1406716818
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 bits)