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= 045379
         (352 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 = 35.4 bits (80), Expect = 0.044,   Method: Compositional matrix adjust.
 Identities = 30/123 (24%), Positives = 56/123 (45%), Gaps = 9/123 (7%)

Query: 168 GLLEKAEAVFREMRKYGLPPSAVVYNS--YIDGLLKGG-----NP--QKAVEIFQRMKRD 218
           G + +A  ++ E R+ G+  S   YN   Y+  L +       NP   +  +IF++M  D
Sbjct: 40  GDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVD 99

Query: 219 CCQPSTETYTLMINLYGKASKSFMALKLFNEMRSHKCKPNICTYTALVNAFAREGLCEEA 278
              P+  T+T    L        MA  +  +M++   +P + +Y   +  F R+G  ++A
Sbjct: 100 KVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKA 159

Query: 279 EEI 281
            E+
Sbjct: 160 YEV 162


>pdb|3SPA|A Chain A, Crystal Structure Of Human Mitochondrial Rna Polymerase
          Length = 1134

 Score = 28.5 bits (62), Expect = 6.0,   Method: Compositional matrix adjust.
 Identities = 12/41 (29%), Positives = 25/41 (60%)

Query: 262 YTALVNAFAREGLCEEAEEIFEQLQGAGIEPDVYAYNALME 302
           Y A++  +AR+G  +E   +   ++ AG+ PD+ +Y A ++
Sbjct: 168 YNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQ 208


  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
   0.321    0.136    0.414 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,432,945
Number of Sequences: 62578
Number of extensions: 417470
Number of successful extensions: 852
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 843
Number of HSP's gapped (non-prelim): 9
length of query: 352
length of database: 14,973,337
effective HSP length: 100
effective length of query: 252
effective length of database: 8,715,537
effective search space: 2196315324
effective search space used: 2196315324
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)