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= 010207
         (515 letters)

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

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



>pdb|3TJ1|A Chain A, Crystal Structure Of Rna Polymerase I Transcription
           Initiation Factor Rrn3
 pdb|3TJ1|B Chain B, Crystal Structure Of Rna Polymerase I Transcription
           Initiation Factor Rrn3
          Length = 649

 Score = 53.5 bits (127), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 62/271 (22%), Positives = 102/271 (37%), Gaps = 59/271 (21%)

Query: 291 LDSLMVL---------TFEHLESCEGTG-------------------RLIEFVMFYACAL 322
           LDS++ L         T E LES EG G                   R I+++MF+    
Sbjct: 354 LDSILTLVSTHVEEQVTPESLESGEGVGVFNTLTTLFKTHVLPTYYTRSIQYIMFHVSQQ 413

Query: 323 DPENCGLRFATMLADVFVSGLYPPLTRMSAVSYLASFLSRARFLSPCFIVSLLKRLVDWC 382
             E     F   L D+  +       ++ ++ YL S+++RA+ LS   I+ +   L  W 
Sbjct: 414 QLELMD-SFLVTLIDISFAVNEAAEKKIKSLQYLGSYIARAKKLSRTQIIFVASYLTSWL 472

Query: 383 LEYCNILGGDINPKA----HRVFYSGCQAIMYVLCFRMRSIMDIPRLKSQLLLMPLETVL 438
             Y      +++ +      + FY+  QA+ Y+ CFR     D        L    + ++
Sbjct: 473 NRYVIEREEEVDQRGGMERFKHFYAAFQALCYIFCFRHNIFRDTDGNWECELDKFFQRMV 532

Query: 439 KHDLNPLKVCLPSVV---SEFLQQSKAARLFTVSETFVFNDLLESELSRAFGGLER---- 491
               NPLK C  +V+   +   QQ   A  F++ E    N+ L   + +A    +     
Sbjct: 533 ISKFNPLKFCNENVMLMFARIAQQESVAYCFSIIEN-NNNERLRGIIGKADSDKKENSAQ 591

Query: 492 ------------------LDMFFPFDPCLLK 504
                             L  +FP+DP  LK
Sbjct: 592 ANTTSSSWSLATRQQFIDLQSYFPYDPLFLK 622


>pdb|2OI2|A Chain A, Streptococcus Pneumoniae Mevalonate Kinase In Complex With
           Diphosphomevalonate
          Length = 292

 Score = 30.8 bits (68), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 33/131 (25%), Positives = 54/131 (41%), Gaps = 10/131 (7%)

Query: 20  ISDLELVYHVREALTSVQSGDNDNYNQLVAVMHLSGRLDPDNRALLETSLKALSGAVSYI 79
           I+D  +  H REA+  VQ+   D     +  +H  G L    +A +  S K   G    +
Sbjct: 166 IADTGVYGHTREAIQVVQNKGKDA----LPFLHALGELT--QQAEIAISQKDAEGLGQIL 219

Query: 80  DISHHESLLVSIFGMSMWNYDPDVMDALKGLIISLAASNGKYVDSCLTMLVSNFTPPSYF 139
             +H   L +   G+S    D  V  AL    +    S G  +  C+  LV+N T     
Sbjct: 220 SQAH---LHLKEIGVSSLEADSLVETALSHGALGAKMSGGG-LGGCIIALVTNLTHAQEL 275

Query: 140 LDKLKEPHGLE 150
            ++L+E   ++
Sbjct: 276 AERLEEKGAVQ 286


>pdb|3D45|A Chain A, Crystal Structure Of Mouse Parn In Complex With M7gpppg
 pdb|3D45|B Chain B, Crystal Structure Of Mouse Parn In Complex With M7gpppg
          Length = 507

 Score = 30.8 bits (68), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 14/74 (18%)

Query: 337 DVFVSGLYPPLTRMSAVSYLASFLS--------RARFLSPCFIVSLLKRLVDWCLEYCNI 388
           D +++GL      +S  +YL S LS        R++ + P F    L R++D  + Y N+
Sbjct: 377 DAYITGL----CFISMANYLGSLLSPPKMCVSARSKLIEPFFNKLFLMRVMD--IPYLNL 430

Query: 389 LGGDINPKAHRVFY 402
            G D+ PK   V +
Sbjct: 431 EGPDLQPKRDHVLH 444


  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
   0.324    0.139    0.409 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,388,030
Number of Sequences: 62578
Number of extensions: 488678
Number of successful extensions: 1357
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1354
Number of HSP's gapped (non-prelim): 7
length of query: 515
length of database: 14,973,337
effective HSP length: 103
effective length of query: 412
effective length of database: 8,527,803
effective search space: 3513454836
effective search space used: 3513454836
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (25.4 bits)