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= 009487
         (533 letters)

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

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



>pdb|3SF5|B Chain B, Crystal Structure Of Helicobacter Pylori Urease Accessory
           Protein UrefH COMPLEX
 pdb|3SF5|D Chain D, Crystal Structure Of Helicobacter Pylori Urease Accessory
           Protein UrefH COMPLEX
          Length = 265

 Score = 30.8 bits (68), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 23/101 (22%), Positives = 47/101 (46%), Gaps = 4/101 (3%)

Query: 82  RTFVSKFWRHFDVYSKVAVLEKNKPLIYDDEVHEVLCKALEEICMEIQYQEKCLFMLVHA 141
           R   ++ ++   +++K+++L+  KP+ YD+ + +     L  +CM   Y      +LV+ 
Sbjct: 146 RVARNELFKFNRLHTKISILQDEKPIYYDNTILDPKTTDLNNMCMFDGYTHYLNLVLVNC 205

Query: 142 ---IESPRDCSLEGKPILDSEVHLFAKYQLMVSSVLMASLP 179
              +   R+C  E + + D  V   A   L V ++   S P
Sbjct: 206 PIELSGVRECIEESEGV-DGAVSETASSHLCVKALAKGSEP 245


>pdb|1YJ8|A Chain A, Initial Structural Analysis Of Plasmodium Falciparum
           Glycerol-3- Phosphate Dehydrogenase
 pdb|1YJ8|B Chain B, Initial Structural Analysis Of Plasmodium Falciparum
           Glycerol-3- Phosphate Dehydrogenase
 pdb|1YJ8|C Chain C, Initial Structural Analysis Of Plasmodium Falciparum
           Glycerol-3- Phosphate Dehydrogenase
          Length = 375

 Score = 29.3 bits (64), Expect = 6.1,   Method: Compositional matrix adjust.
 Identities = 15/40 (37%), Positives = 22/40 (55%)

Query: 284 HNLAGEDYRSSVLEPIKAWIQAVPLQFLNALLAYLGESES 323
           HN+      +SV+      I  VP Q+L ++LA + ESES
Sbjct: 89  HNIVAHSDLASVINDADLLIFIVPCQYLESVLASIKESES 128


>pdb|1A26|A Chain A, The Catalytic Fragment Of Poly(Adp-Ribose) Polymerase
           Complexed With Carba-Nad
 pdb|1PAX|A Chain A, The Catalytic Fragment Of Poly(Adp-Ribose) Polymerase
           Complexed With 3,4-Dihydro-5-Methyl-Isoquinolinone
 pdb|2PAW|A Chain A, The Catalytic Fragment Of Poly(Adp-Ribose) Polymerase
 pdb|2PAX|A Chain A, The Catalytic Fragment Of Poly(Adp-Ribose) Polymerase
           Complexed With 4-Amino-1,8-Naphthalimide
 pdb|3PAX|A Chain A, The Catalytic Fragment Of Poly(Adp-Ribose) Polymerase
           Complexed With 3-Methoxybenzamide
 pdb|4PAX|A Chain A, The Catalytic Fragment Of Poly(Adp-Ribose) Polymerase
           Complexed With
           8-Hydroxy-2-Methyl-3-Hydro-Quinazolin-4-One
          Length = 361

 Score = 28.9 bits (63), Expect = 7.0,   Method: Compositional matrix adjust.
 Identities = 26/97 (26%), Positives = 46/97 (47%), Gaps = 20/97 (20%)

Query: 189 YFKGRLEELSTIMDGE-----LEDGNDSQDKDDMDLDEKGKQRTGEMDIDQSNNHGKFSE 243
           Y + +++ L  ++D E     L  GN+  DKD +D++ + K RT    +D      K SE
Sbjct: 104 YIQAKVQMLDNLLDIEVAYSLLRGGNEDGDKDPIDINYE-KLRTDIKVVD------KDSE 156

Query: 244 KSKLVKHIGKVVHDLRTLGFTSMTENAYASAIFSLLK 280
           ++K++K   K  H        + T NAY   +  + +
Sbjct: 157 EAKIIKQYVKNTH--------AATHNAYDLKVVEIFR 185


>pdb|1EFY|A Chain A, Crystal Structure Of The Catalytic Fragment Of Poly (Adp-
           Ribose) Polymerase Complexed With A Benzimidazole
           Inhibitor
          Length = 350

 Score = 28.9 bits (63), Expect = 8.1,   Method: Compositional matrix adjust.
 Identities = 26/97 (26%), Positives = 46/97 (47%), Gaps = 20/97 (20%)

Query: 189 YFKGRLEELSTIMDGE-----LEDGNDSQDKDDMDLDEKGKQRTGEMDIDQSNNHGKFSE 243
           Y + +++ L  ++D E     L  GN+  DKD +D++ + K RT    +D      K SE
Sbjct: 96  YIQAKVQMLDNLLDIEVAYSLLRGGNEDGDKDPIDINYE-KLRTDIKVVD------KDSE 148

Query: 244 KSKLVKHIGKVVHDLRTLGFTSMTENAYASAIFSLLK 280
           ++K++K   K  H        + T NAY   +  + +
Sbjct: 149 EAKIIKQYVKNTH--------AATHNAYDLKVVEIFR 177


  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
   0.318    0.136    0.401 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,424,122
Number of Sequences: 62578
Number of extensions: 710452
Number of successful extensions: 1661
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1658
Number of HSP's gapped (non-prelim): 5
length of query: 533
length of database: 14,973,337
effective HSP length: 103
effective length of query: 430
effective length of database: 8,527,803
effective search space: 3666955290
effective search space used: 3666955290
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: 54 (25.4 bits)