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= 038522
         (590 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 = 38.9 bits (89), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 40/166 (24%), Positives = 73/166 (43%), Gaps = 23/166 (13%)

Query: 348 ASLNLGRQIHAFAFKYQSSYDAAVGNALIDMYAKSGEIADANRAFDEMGDK--------- 398
            S NL R+    A   Q S +A +   L DM +K G++ +A R +DE             
Sbjct: 8   PSENLSRKAKKKAI--QQSPEALLKQKL-DMCSKKGDVLEALRLYDEARRNGVQLSQYHY 64

Query: 399 NVISWTSLIAGYAKHGYGHEAI----ELYKKMKHEGMVPNDVTFLSLLFACSHTGLTCEG 454
           NV+ +   +A  A     +  +    +++K+M  + +VPN+ TF +     +   +  + 
Sbjct: 65  NVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPNEATFTN----GARLAVAKDD 120

Query: 455 WELFTDMINKYR---ILPRAEHFSCVVDLFARRGQLESAYNMIRQM 497
            E+  DM+ + +   I PR   +   +  F R+G  + AY +   M
Sbjct: 121 PEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHM 166


>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 = 30.0 bits (66), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 36/162 (22%), Positives = 68/162 (41%), Gaps = 23/162 (14%)

Query: 348 ASLNLGRQIHAFAFKYQSSYDAAVGNALIDMYAKSGEIADANRAFDEMGDK--------- 398
            S NL R+    A   Q S +A +   L D  +K G++ +A R +DE             
Sbjct: 8   PSENLSRKAKKKAI--QQSPEALLKQKL-DXCSKKGDVLEALRLYDEARRNGVQLSQYHY 64

Query: 399 NVISWTSLIAGYAKHGYGHEAI----ELYKKMKHEGMVPNDVTFLSLLFACSHTGLTCEG 454
           NV+ +   +A  A     +  +    +++K+   + +VPN+ TF +     +   +  + 
Sbjct: 65  NVLLYVCSLAEAATESSPNPGLSRGFDIFKQXIVDKVVPNEATFTN----GARLAVAKDD 120

Query: 455 WELFTDMINKYR---ILPRAEHFSCVVDLFARRGQLESAYNM 493
            E   D + + +   I PR   +   +  F R+G  + AY +
Sbjct: 121 PEXAFDXVKQXKAFGIQPRLRSYGPALFGFCRKGDADKAYEV 162


>pdb|2F3O|A Chain A, Crystal Structure Of A Glycyl Radical Enzyme From
           Archaeoglobus Fulgidus
 pdb|2F3O|B Chain B, Crystal Structure Of A Glycyl Radical Enzyme From
           Archaeoglobus Fulgidus
          Length = 776

 Score = 29.3 bits (64), Expect = 6.9,   Method: Compositional matrix adjust.
 Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 1/70 (1%)

Query: 455 WELFTDMINKYRILPRAEHFSCVVDLFARRGQLESAYNMIRQMNIKPTASLWSAILGACS 514
           +  F   I + RI  R   F  + +L+ +  ++  A++ + +      A+  +  +G C 
Sbjct: 283 YPFFKKDIGEGRI-NRELAFDILANLWIKTNEIVPAFDSLLEQYFSGQATNQAVTIGGCD 341

Query: 515 IYGNTSLGEL 524
           IYGN +  EL
Sbjct: 342 IYGNDATNEL 351


  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
   0.323    0.136    0.406 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,771,692
Number of Sequences: 62578
Number of extensions: 667078
Number of successful extensions: 1340
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: 1332
Number of HSP's gapped (non-prelim): 12
length of query: 590
length of database: 14,973,337
effective HSP length: 104
effective length of query: 486
effective length of database: 8,465,225
effective search space: 4114099350
effective search space used: 4114099350
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)