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= psy2383
         (391 letters)

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

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



>pdb|1OLT|A Chain A, Coproporphyrinogen Iii Oxidase (Hemn) From Escherichia
           Coli Is A Radical Sam Enzyme
          Length = 457

 Score =  104 bits (260), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 93/398 (23%), Positives = 171/398 (42%), Gaps = 34/398 (8%)

Query: 16  PLSLYIHFPWCIKKCPYCDFHSYEIKKNISEKKYLEALLIDVELSLPIILNRKIHTIFIG 75
           PLSLY+H P+C K C +C  +    ++     +YL+AL  ++    P+   R +  +  G
Sbjct: 52  PLSLYVHIPFCHKLCYFCGCNKIVTRQQHKADQYLDALEQEIVHRAPLFAGRHVSQLHWG 111

Query: 76  GGTPSLISDTGLDYXXXXXXXXXXXXXXXSITLEANPSTFEIEKFHSYSIIGINRLSIGI 135
           GGTP+ ++   +                  I++E +P   E++        G NRLS+G+
Sbjct: 112 GGTPTYLNKAQISRLMKLLRENFQFNADAEISIEVDPREIELDVLDHLRAEGFNRLSMGV 171

Query: 136 QSFNNKYLNILGRTHDSK----QAKYAIEIAKQYFNNFNLDLIYALPNQTLSELMLDLNY 191
           Q FN +   ++ R  D +       +A EI    F + N+DLIY LP QT       L  
Sbjct: 172 QDFNKEVQRLVNREQDEEFIFALLNHAREIG---FTSTNIDLIYGLPKQTPESFAFTLKR 228

Query: 192 AIQYSPPHLSLYSLTIEPNTYFF--KYPPLSMPSNDEN-AVMQDKITSLLKNNYY----- 243
             + +P  LS+++    P  +    K     +PS  +   ++Q+ I  L ++ Y      
Sbjct: 229 VAELNPDRLSVFNYAHLPTIFAAQRKIKDADLPSPQQKLDILQETIAFLTQSGYQFIGMD 288

Query: 244 ----KNYEISAYSKTGYESQHNLNYWKFG--DYLGIGAGSHSKLSFPNYIIRQIR----Y 293
                + E++   + G   ++   Y   G  D LG+G  + S +    Y   Q      Y
Sbjct: 289 HFARPDDELAVAQREGVLHRNFQGYTTQGDTDLLGMGVSAISMIG-DCYAQNQKELKQYY 347

Query: 294 KNPNIYLKNIFSGNSIAKSKKIEK---KCLIFEFMLNALRLKDGFSPNLFFERTGINIKI 350
           +  +     ++ G ++ +   I +   K LI  F L+   ++  +   LF +    ++K+
Sbjct: 348 QQVDEQGNALWRGIALTRDDCIRRDVIKSLICNFRLDYSPIEQQWDL-LFADYFAEDLKL 406

Query: 351 IESKLKNAEKLGLLKRNNKNIKPTSFGRYFLNDLQQIF 388
           +    K+    GL+  + K I+ T+ GR  + ++   F
Sbjct: 407 LAPLAKD----GLVDVDEKGIQVTAKGRLLIRNICMCF 440


  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    0.139    0.409 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,446,405
Number of Sequences: 62578
Number of extensions: 473226
Number of successful extensions: 1201
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1198
Number of HSP's gapped (non-prelim): 2
length of query: 391
length of database: 14,973,337
effective HSP length: 101
effective length of query: 290
effective length of database: 8,652,959
effective search space: 2509358110
effective search space used: 2509358110
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: 52 (24.6 bits)