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= 003965
         (783 letters)

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

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



>pdb|3FUT|A Chain A, Apo-Form Of T. Thermophilus 16s Rrna A1518 And A1519
           Methyltransferase (Ksga) In Space Group P21212
 pdb|3FUT|B Chain B, Apo-Form Of T. Thermophilus 16s Rrna A1518 And A1519
           Methyltransferase (Ksga) In Space Group P21212
          Length = 271

 Score = 34.7 bits (78), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 33/111 (29%), Positives = 53/111 (47%), Gaps = 21/111 (18%)

Query: 193 FYKEDVGQELVVSVHHFPMIL---CPLSPRVF-VLPSEGSVAEACL-------SVEHEDS 241
           F  +  GQ  +VS  H   I+    P +  VF V P  G++  A L       ++E +  
Sbjct: 20  FADKRFGQNFLVSEAHLRRIVEAARPFTGPVFEVGPGLGALTRALLEAGAEVTAIEKDLR 79

Query: 242 LSPVLPPIGTGL-----FSDG-----DDVPPGAILTAHLIYHLASKMDLKM 282
           L PVL    +GL     F D      ++VP G++L A+L YH+A+ +  ++
Sbjct: 80  LRPVLEETLSGLPVRLVFQDALLYPWEEVPQGSLLVANLPYHIATPLVTRL 130


>pdb|3FUU|A Chain A, T. Thermophilus 16s Rrna A1518 And A1519 Methyltransferase
           (Ksga) In Complex With Adenosine In Space Group P212121
 pdb|3FUV|A Chain A, Apo-Form Of T. Thermophilus 16s Rrna A1518 And A1519
           Methyltransferase (Ksga) In Space Group P43212
 pdb|3FUV|B Chain B, Apo-Form Of T. Thermophilus 16s Rrna A1518 And A1519
           Methyltransferase (Ksga) In Space Group P43212
 pdb|3FUV|C Chain C, Apo-Form Of T. Thermophilus 16s Rrna A1518 And A1519
           Methyltransferase (Ksga) In Space Group P43212
 pdb|3FUW|A Chain A, T. Thermophilus 16s Rrna A1518 And A1519 Methyltransferase
           (Ksga) In Complex With 5'-Methylthioadenosine In Space
           Group P212121
 pdb|3FUX|A Chain A, T. Thermophilus 16s Rrna A1518 And A1519 Methyltransferase
           (Ksga) In Complex With 5'-Methylthioadenosine In Space
           Group P212121
 pdb|3FUX|B Chain B, T. Thermophilus 16s Rrna A1518 And A1519 Methyltransferase
           (Ksga) In Complex With 5'-Methylthioadenosine In Space
           Group P212121
 pdb|3FUX|C Chain C, T. Thermophilus 16s Rrna A1518 And A1519 Methyltransferase
           (Ksga) In Complex With 5'-Methylthioadenosine In Space
           Group P212121
          Length = 271

 Score = 34.7 bits (78), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 33/111 (29%), Positives = 53/111 (47%), Gaps = 21/111 (18%)

Query: 193 FYKEDVGQELVVSVHHFPMIL---CPLSPRVF-VLPSEGSVAEACL-------SVEHEDS 241
           F  +  GQ  +VS  H   I+    P +  VF V P  G++  A L       ++E +  
Sbjct: 20  FADKRFGQNFLVSEAHLRRIVEAARPFTGPVFEVGPGLGALTRALLEAGAEVTAIEKDLR 79

Query: 242 LSPVLPPIGTGL-----FSDG-----DDVPPGAILTAHLIYHLASKMDLKM 282
           L PVL    +GL     F D      ++VP G++L A+L YH+A+ +  ++
Sbjct: 80  LRPVLEETLSGLPVRLVFQDALLYPWEEVPQGSLLVANLPYHIATPLVTRL 130


>pdb|2XTL|A Chain A, Structure Of The Major Pilus Backbone Protein From
           Streptococcus Agalactiae
 pdb|2XTL|B Chain B, Structure Of The Major Pilus Backbone Protein From
           Streptococcus Agalactiae
          Length = 452

 Score = 32.7 bits (73), Expect = 0.88,   Method: Compositional matrix adjust.
 Identities = 24/84 (28%), Positives = 38/84 (45%), Gaps = 4/84 (4%)

Query: 450 RRMKDGTVLIKKWLQEALRQENLTVNVRSRPGSATKSELQAMIKALAKNQSSLVRNRGII 509
            R+   T L+KK  +   R+  +  +       +TKS L A +KA     + L + +   
Sbjct: 281 ERLAGATFLVKKDGKYLARKSGVATDAEKAAVDSTKSALDAAVKAY----NDLTKEKQEG 336

Query: 510 QFATAALAALDESHSARWDAFISA 533
           Q   +ALA + E   A  DAF+ A
Sbjct: 337 QDGKSALATVSEKQKAYNDAFVKA 360


  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
   0.318    0.134    0.384 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,300,740
Number of Sequences: 62578
Number of extensions: 839138
Number of successful extensions: 2483
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 2482
Number of HSP's gapped (non-prelim): 4
length of query: 783
length of database: 14,973,337
effective HSP length: 106
effective length of query: 677
effective length of database: 8,340,069
effective search space: 5646226713
effective search space used: 5646226713
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)