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= 041804
         (403 letters)

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

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



>pdb|4G24|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
           A. Thaliana With Mn
 pdb|4G26|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
           A. Thaliana With Ca
          Length = 501

 Score = 32.0 bits (71), Expect = 0.65,   Method: Compositional matrix adjust.
 Identities = 21/111 (18%), Positives = 48/111 (43%), Gaps = 9/111 (8%)

Query: 184 MDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSE---------GVDFAMRV 234
           +D+  K G   +A++LY E ++ G+++    YN ++    ++E         G+     +
Sbjct: 33  LDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDI 92

Query: 235 YREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITY 285
           +++M      P+  T     +L         A+ ++ +M   G  P + +Y
Sbjct: 93  FKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSY 143


>pdb|3ODH|A Chain A, Structure Of OkraiDNA COMPLEX
 pdb|3ODH|B Chain B, Structure Of OkraiDNA COMPLEX
 pdb|3ODH|E Chain E, Structure Of OkraiDNA COMPLEX
 pdb|3ODH|F Chain F, Structure Of OkraiDNA COMPLEX
          Length = 194

 Score = 30.0 bits (66), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 2/44 (4%)

Query: 298 ILGLFDRMIESG--IRPKMDTYVMLLRKFGRWGFLRPVFVVWKK 339
           ++G+ +R+I  G  I P  D Y  L  + G +  L P F VW++
Sbjct: 116 VMGMLERVIIGGVLILPSRDMYNYLTDRVGNFRELEPYFSVWRQ 159


>pdb|4G23|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
           A. Thaliana With Mn
 pdb|4G25|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
           A. Thaliana, Semet Substituted Form With Sr
          Length = 501

 Score = 28.5 bits (62), Expect = 6.2,   Method: Compositional matrix adjust.
 Identities = 11/45 (24%), Positives = 24/45 (53%)

Query: 184 MDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGV 228
           +D   K G   +A++LY E ++ G+++    YN ++    ++E  
Sbjct: 33  LDXCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAA 77


>pdb|1W3B|A Chain A, The Superhelical Tpr Domain Of O-Linked Glcnac Transferase
           Reveals Structural Similarities To Importin Alpha.
 pdb|1W3B|B Chain B, The Superhelical Tpr Domain Of O-Linked Glcnac Transferase
           Reveals Structural Similarities To Importin Alpha
          Length = 388

 Score = 28.5 bits (62), Expect = 6.9,   Method: Compositional matrix adjust.
 Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 2/63 (3%)

Query: 65  PNHATFRIMFK-RYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQEL 123
           PNHA         Y    L++ A+ T+ +  E       +YCNL +AL E   V EA++ 
Sbjct: 234 PNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQPHFPDAYCNLANALKEKGSVAEAED- 292

Query: 124 CFG 126
           C+ 
Sbjct: 293 CYN 295


  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    0.443 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,666,244
Number of Sequences: 62578
Number of extensions: 546206
Number of successful extensions: 1656
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1647
Number of HSP's gapped (non-prelim): 12
length of query: 403
length of database: 14,973,337
effective HSP length: 101
effective length of query: 302
effective length of database: 8,652,959
effective search space: 2613193618
effective search space used: 2613193618
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 53 (25.0 bits)