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= 012112
         (471 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 =  109 bits (273), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 78/312 (25%), Positives = 141/312 (45%), Gaps = 28/312 (8%)

Query: 53  PTSAYIHLPFCRKRCHYCDFPIVALGSSPTQTNDDDPRVSNYIQLLCREIIATKP---GH 109
           P S Y+H+PFC K C++C       G +   T     +   Y+  L +EI+   P   G 
Sbjct: 52  PLSLYVHIPFCHKLCYFC-------GCNKIVTRQQH-KADQYLDALEQEIVHRAPLFAGR 103

Query: 110 KTSPPLETVFFGGGTPSLVPPRFVSSILDTLTDKFGLSLDAEISMEMDPGTFDARKMEEL 169
             S     + +GGGTP+ +    +S ++  L + F  + DAEIS+E+DP   +   ++ L
Sbjct: 104 HVS----QLHWGGGTPTYLNKAQISRLMKLLRENFQFNADAEISIEVDPREIELDVLDHL 159

Query: 170 MDLGVNRVSLGVQAFQDELLKSCGRAHGLKEVYEAIEIVKLCGVENWSLDLISSLPHQTP 229
              G NR+S+GVQ F  E+ +   R    + ++  +   +  G  + ++DLI  LP QTP
Sbjct: 160 RAEGFNRLSMGVQDFNKEVQRLVNREQDEEFIFALLNHAREIGFTSTNIDLIYGLPKQTP 219

Query: 230 QMWEESLRRTVGAQPKHVSVYDLQVEQGTKFGILYTPGEFPLPTETQSANFYRMASSMLS 289
           + +  +L+R     P  +SV++      T F       +  LP+  Q  +  +   + L+
Sbjct: 220 ESFAFTLKRVAELNPDRLSVFNY-AHLPTIFAAQRKIKDADLPSPQQKLDILQETIAFLT 278

Query: 290 SAGYR-----HY-----EISSYGEDG--YECKHNLTYWKNKPFYGFGLGSASYLGGLRFS 337
            +GY+     H+     E++    +G  +      T   +    G G+ + S +G     
Sbjct: 279 QSGYQFIGMDHFARPDDELAVAQREGVLHRNFQGYTTQGDTDLLGMGVSAISMIGDCYAQ 338

Query: 338 RPRRMKEFVDYV 349
             + +K++   V
Sbjct: 339 NQKELKQYYQQV 350


>pdb|2Z1K|A Chain A, Crystal Structure Of Ttha1563 From Thermus Thermophilus
           Hb8
 pdb|2Z1K|B Chain B, Crystal Structure Of Ttha1563 From Thermus Thermophilus
           Hb8
 pdb|2Z1K|C Chain C, Crystal Structure Of Ttha1563 From Thermus Thermophilus
           Hb8
 pdb|2Z1K|D Chain D, Crystal Structure Of Ttha1563 From Thermus Thermophilus
           Hb8
          Length = 475

 Score = 30.4 bits (67), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 7/54 (12%)

Query: 212 GVENWSLDLISSLPHQTPQMWEESLRRTVGAQPKHVSVYDLQVE-----QGTKF 260
           GV+ W LD+ + +P   P  W E  +R  GA P+   V ++  E     QG  F
Sbjct: 195 GVDGWRLDVPNEIP--DPTFWREFRQRVKGANPEAYIVGEIWEEADFWLQGDXF 246


>pdb|2Q1F|A Chain A, Crystal Structure Of Chondroitin Sulfate Lyase Abc From
           Bacteroides Thetaiotaomicron Wal2926
 pdb|2Q1F|B Chain B, Crystal Structure Of Chondroitin Sulfate Lyase Abc From
           Bacteroides Thetaiotaomicron Wal2926
          Length = 1022

 Score = 29.3 bits (64), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 16/42 (38%), Positives = 19/42 (45%)

Query: 63  CRKRCHYCDFPIVALGSSPTQTNDDDPRVSNYIQLLCREIIA 104
            RK  H+ D  IV LGS    TN D P  +   QL   +  A
Sbjct: 738 ARKSFHFIDGXIVCLGSDIENTNXDYPTETTIFQLAVTDKAA 779


  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    0.136    0.413 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,499,324
Number of Sequences: 62578
Number of extensions: 613334
Number of successful extensions: 1398
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1393
Number of HSP's gapped (non-prelim): 4
length of query: 471
length of database: 14,973,337
effective HSP length: 102
effective length of query: 369
effective length of database: 8,590,381
effective search space: 3169850589
effective search space used: 3169850589
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: 53 (25.0 bits)