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= 044251
         (686 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 = 33.9 bits (76), Expect = 0.31,   Method: Compositional matrix adjust.
 Identities = 31/111 (27%), Positives = 49/111 (44%), Gaps = 9/111 (8%)

Query: 524 LDGFAKQGQYLEARDVVSEFGKIGLQPTLMTYNMLMNAYG---RGGQTSKLPQL------ 574
           LD  +K+G  LEA  +  E  + G+Q +   YN+L+          ++S  P L      
Sbjct: 33  LDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDI 92

Query: 575 LKEMATLNIKPDSVTYSTMIYAFVRVRDFKRAFFYHKQMVKSGQVPDVKSY 625
            K+M    + P+  T++      V   D + AF   KQM   G  P ++SY
Sbjct: 93  FKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSY 143



 Score = 30.8 bits (68), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 46/227 (20%), Positives = 90/227 (39%), Gaps = 15/227 (6%)

Query: 295 EKMNRKGVKLS-QEVVGALMKSFCD----EGLKNEALIIQMEMEKKGIPSNAIVYNTLIN 349
           E ++RK  K + Q+   AL+K   D    +G   EAL +  E  + G+  +   YN L+ 
Sbjct: 10  ENLSRKAKKKAIQQSPEALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLY 69

Query: 350 AYCKSNQLEEAE---------GLFQEMKTKGLKPTSATFNILMDAYSRRMQPEIVEKLLL 400
               +    E+           +F++M    + P  ATF         +  PE+   ++ 
Sbjct: 70  VCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVK 129

Query: 401 ELQDMGLEPNAKSYTCLISAYGRPRKMSDMAADAFLRMKRVGIKPTSHSYTALIHAYSVG 460
           +++  G++P  +SY   +  + R +  +D A +    M    + P      AL+      
Sbjct: 130 QMKAFGIQPRLRSYGPALFGFCR-KGDADKAYEVDAHMVESEVVPEEPELAALLKVSMDT 188

Query: 461 GWHEKAYAAFENMLREEIKPSIETYTALLDAFRRSGDTGMMMKIWKL 507
              +K Y   + +     + S  T+  + + F+    T   +K W +
Sbjct: 189 KNADKVYKTLQRLRDLVRQVSKSTFDMIEEWFKSEVATKTGVKKWDV 235


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

 Score = 32.7 bits (73), Expect = 0.71,   Method: Compositional matrix adjust.
 Identities = 18/76 (23%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 520 FNILLDGFAKQGQYLEARDVVSEFGKIGLQPTLMTYNMLMNAYGRGGQTS-KLPQLLKEM 578
           +N ++ G+A+QG + E   V+      GL P L++Y   +   GR  Q +  + + L++M
Sbjct: 168 YNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQM 227

Query: 579 ATLNIKPDSVTYSTMI 594
           +   +K  ++  + ++
Sbjct: 228 SQEGLKLQALFTAVLL 243


>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 = 30.4 bits (67), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 29/111 (26%), Positives = 47/111 (42%), Gaps = 9/111 (8%)

Query: 524 LDGFAKQGQYLEARDVVSEFGKIGLQPTLMTYNMLMNAYG---RGGQTSKLPQL------ 574
           LD  +K+G  LEA  +  E  + G+Q +   YN+L+          ++S  P L      
Sbjct: 33  LDXCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDI 92

Query: 575 LKEMATLNIKPDSVTYSTMIYAFVRVRDFKRAFFYHKQMVKSGQVPDVKSY 625
            K+     + P+  T++      V   D + AF   KQ    G  P ++SY
Sbjct: 93  FKQXIVDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSY 143


  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
   0.320    0.133    0.391 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,711,731
Number of Sequences: 62578
Number of extensions: 741589
Number of successful extensions: 1430
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 1414
Number of HSP's gapped (non-prelim): 13
length of query: 686
length of database: 14,973,337
effective HSP length: 105
effective length of query: 581
effective length of database: 8,402,647
effective search space: 4881937907
effective search space used: 4881937907
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)