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= 003220
         (838 letters)

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

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



>pdb|1RQ8|A Chain A, Solution Structure Of The Hypothetical Protein Sav1595
           From Staphylococcus Aureus, A Putative Rna Binding
           Protein
          Length = 104

 Score = 31.6 bits (70), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 18/84 (21%), Positives = 41/84 (48%)

Query: 376 LTLEEATEMRKKGRKLIPICKLGKNGVYCDLAKNVREAFEVCELVRINCQGMNGSDYRKI 435
           LT ++   +R     + PI ++GK G+  ++ K + +  E  EL++++    N  D +++
Sbjct: 2   LTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKEL 61

Query: 436 GAKLRDLVPCVLISFEREHILMWR 459
              L +     L+      I+++R
Sbjct: 62  AETLSEATRSELVQVIGSMIVIYR 85


>pdb|1PN3|A Chain A, Crystal Structure Of Tdp-Epi-Vancosaminyltransferase Gtfa
           In Complexes With Tdp And The Acceptor Substrate Dvv.
 pdb|1PN3|B Chain B, Crystal Structure Of Tdp-Epi-Vancosaminyltransferase Gtfa
           In Complexes With Tdp And The Acceptor Substrate Dvv.
 pdb|1PNV|A Chain A, Crystal Structure Of Tdp-Epi-Vancosaminyltransferase Gtfa
           In Complexes With Tdp And Vancomycin
 pdb|1PNV|B Chain B, Crystal Structure Of Tdp-Epi-Vancosaminyltransferase Gtfa
           In Complexes With Tdp And Vancomycin
          Length = 404

 Score = 30.0 bits (66), Expect = 5.1,   Method: Compositional matrix adjust.
 Identities = 26/114 (22%), Positives = 43/114 (37%), Gaps = 24/114 (21%)

Query: 168 FKYSYTEAPKAKPLKLREAAFSPFGPTTMGRPWTGRAPLPPSKKKLKEFDSFQLXXXXXX 227
           + Y YT+    +P    +   SP  PT +G   TG   LP  +    E ++F        
Sbjct: 169 YDYGYTD----QPWLAADPVLSPLRPTDLGTVQTGAWILPDERPLSAELEAFLAA----- 219

Query: 228 XXXXXXXXXXYLPGTGPRYVSTREEILGEPLTADEVRELVESAKRSSRQLNMGR 281
                        G+ P YV         P TAD  +  +++ + S R++ + R
Sbjct: 220 -------------GSTPVYVGFGSS--SRPATADAAKMAIKAVRASGRRIVLSR 258


>pdb|2EJA|A Chain A, Crystal Structure Of Uroporphyrinogen Decarboxylase From
           Aquifex Aeolicus
 pdb|2EJA|B Chain B, Crystal Structure Of Uroporphyrinogen Decarboxylase From
           Aquifex Aeolicus
          Length = 338

 Score = 29.6 bits (65), Expect = 8.1,   Method: Compositional matrix adjust.
 Identities = 46/168 (27%), Positives = 72/168 (42%), Gaps = 26/168 (15%)

Query: 384 MRKKGRKLIPICKLGKNGV--YCDLAKNVREAFEVCELVRINCQGMNGSDYRKIGAKLRD 441
           MR+ GR + P  +  +N V  + +L KNV  A E+  L       + G D   I + +  
Sbjct: 24  MRQAGRYM-PEYRKIRNRVKNFLELCKNVDLATEISLL----PLKILGVDAIIIFSDI-- 76

Query: 442 LVPCVLISFEREHI------LMWRGQEWKSSILKPGNDSEDAKESKVDGSISVAP---PT 492
           LVP   +  + E +      L W G   K S LK  + S++A   ++   +  A    P 
Sbjct: 77  LVPLEPLGVKVEFVEGEGPKLSWSG---KVSDLKKYDPSQNAYVYEIIKRVKEAQDEVPV 133

Query: 493 AGNGSAPSLTQMLLVEGGSLNTFNSSI-----SPKGYEEVQSALRENL 535
            G   AP      L+EGG+   F S+      +PK Y+ +   L E +
Sbjct: 134 IGFAGAPFTLLSYLIEGGASKDFKSTKLFMWENPKEYKRLMDILTETV 181


  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
   0.312    0.129    0.370 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,390,190
Number of Sequences: 62578
Number of extensions: 886063
Number of successful extensions: 1584
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1583
Number of HSP's gapped (non-prelim): 10
length of query: 838
length of database: 14,973,337
effective HSP length: 107
effective length of query: 731
effective length of database: 8,277,491
effective search space: 6050845921
effective search space used: 6050845921
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 56 (26.2 bits)