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= 005659
         (685 letters)

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

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



>pdb|4A0K|A Chain A, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic
           Site Containing Dna-Duplex
          Length = 742

 Score = 32.0 bits (71), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 31/133 (23%), Positives = 53/133 (39%), Gaps = 12/133 (9%)

Query: 542 RKVDILGMIVGIIGSKDQLVNEYRVMLADKLLNKSDYEIDSEIRTLELLKIHFGESSMQR 601
           R +D + ++   I  KD     Y+  LA +LL      +D+E   L  LK   G +   +
Sbjct: 414 RTLDKIMILFRFIHGKDVFEAFYKKDLAKRLLVGKSASVDAEKSMLSKLKHECGAAFTSK 473

Query: 602 CEIMLNDLIDSKRTNANIKATIEKQXXXXXXXXXXXXXXXXXDATIISSNFWP---PMQV 658
            E M  D+  SK    + K  ++ Q                    I++  +WP   PM+V
Sbjct: 474 LEGMFKDMELSKDIMVHFKQHMQNQSDSGPIDLT---------VNILTMGYWPTYTPMEV 524

Query: 659 WSTLFLIMISIIY 671
             T  +I +  ++
Sbjct: 525 HLTPEMIKLQEVF 537


>pdb|2HYE|C Chain C, Crystal Structure Of The Ddb1-cul4a-rbx1-sv5v Complex
          Length = 759

 Score = 31.6 bits (70), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 31/133 (23%), Positives = 53/133 (39%), Gaps = 12/133 (9%)

Query: 542 RKVDILGMIVGIIGSKDQLVNEYRVMLADKLLNKSDYEIDSEIRTLELLKIHFGESSMQR 601
           R +D + ++   I  KD     Y+  LA +LL      +D+E   L  LK   G +   +
Sbjct: 431 RTLDKIMILFRFIHGKDVFEAFYKKDLAKRLLVGKSASVDAEKSMLSKLKHECGAAFTSK 490

Query: 602 CEIMLNDLIDSKRTNANIKATIEKQXXXXXXXXXXXXXXXXXDATIISSNFWP---PMQV 658
            E M  D+  SK    + K  ++ Q                    I++  +WP   PM+V
Sbjct: 491 LEGMFKDMELSKDIMVHFKQHMQNQSDSGPIDLT---------VNILTMGYWPTYTPMEV 541

Query: 659 WSTLFLIMISIIY 671
             T  +I +  ++
Sbjct: 542 HLTPEMIKLQEVF 554


>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 = 2.3,   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 = 8.5,   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


  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    0.397 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,046,234
Number of Sequences: 62578
Number of extensions: 854290
Number of successful extensions: 1919
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1914
Number of HSP's gapped (non-prelim): 9
length of query: 685
length of database: 14,973,337
effective HSP length: 105
effective length of query: 580
effective length of database: 8,402,647
effective search space: 4873535260
effective search space used: 4873535260
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: 55 (25.8 bits)