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= 041425
         (366 letters)

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

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



>pdb|1TUE|A Chain A, The X-Ray Structure Of The Papillomavirus Helicase In
           Complex With Its Molecular Matchmaker E2
 pdb|1TUE|D Chain D, The X-Ray Structure Of The Papillomavirus Helicase In
           Complex With Its Molecular Matchmaker E2
 pdb|1TUE|F Chain F, The X-Ray Structure Of The Papillomavirus Helicase In
           Complex With Its Molecular Matchmaker E2
 pdb|1TUE|H Chain H, The X-Ray Structure Of The Papillomavirus Helicase In
           Complex With Its Molecular Matchmaker E2
 pdb|1TUE|K Chain K, The X-Ray Structure Of The Papillomavirus Helicase In
           Complex With Its Molecular Matchmaker E2
 pdb|1TUE|M Chain M, The X-Ray Structure Of The Papillomavirus Helicase In
           Complex With Its Molecular Matchmaker E2
          Length = 212

 Score = 33.1 bits (74), Expect = 0.25,   Method: Compositional matrix adjust.
 Identities = 29/108 (26%), Positives = 45/108 (41%), Gaps = 21/108 (19%)

Query: 216 QYSSTTIISFFGAIQSAILSLIIERNLPGWVLKGKLETIGVIYCGMVGSGLCYVGMSWCV 275
           +Y     I+F GA++S               LKG  +   +++CG   +G  Y GMS+  
Sbjct: 35  RYQQIEFITFLGALKS--------------FLKGTPKKNCLVFCGPANTGKSYFGMSFIH 80

Query: 276 KKRGPVF-----TSAF--SPLTQIVVAIFDFSVLRERIYLGSALGSIL 316
             +G V      TS F   PLT   VA+ D +      Y  + + + L
Sbjct: 81  FIQGAVISFVNSTSHFWLEPLTDTKVAMLDDATTTCWTYFDTYMRNAL 128


>pdb|2ZXC|A Chain A, Seramidase Complexed With C2
 pdb|2ZXC|B Chain B, Seramidase Complexed With C2
 pdb|2ZWS|A Chain A, Crystal Structure Analysis Of Neutral Ceramidase From
           Pseudomonas Aeruginosa
          Length = 646

 Score = 30.0 bits (66), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 15/49 (30%), Positives = 26/49 (53%)

Query: 268 YVGMSWCVKKRGPVFTSAFSPLTQIVVAIFDFSVLRERIYLGSALGSIL 316
           +V M+  +++R PV TSA +P        F   V+ +  Y+G + G +L
Sbjct: 479 FVDMAVALRERLPVETSAIAPDLSCCQMNFQTGVVADDPYIGKSFGDVL 527


  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
   0.327    0.140    0.432 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,904,975
Number of Sequences: 62578
Number of extensions: 376411
Number of successful extensions: 805
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 804
Number of HSP's gapped (non-prelim): 2
length of query: 366
length of database: 14,973,337
effective HSP length: 100
effective length of query: 266
effective length of database: 8,715,537
effective search space: 2318332842
effective search space used: 2318332842
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 52 (24.6 bits)