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= 028754
         (204 letters)

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

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



>pdb|2YXL|A Chain A, Crystal Structure Of Ph0851
          Length = 450

 Score = 31.2 bits (69), Expect = 0.37,   Method: Compositional matrix adjust.
 Identities = 18/51 (35%), Positives = 30/51 (58%), Gaps = 4/51 (7%)

Query: 73  LSECVHDLLDLAGRMLVMGGRLVYFY-PVLREDSTRNP---FPEHPCFKLV 119
           +S+   +LL+ A R++  GGRL+Y    + +E++ +N       HP FKLV
Sbjct: 364 MSQLQRELLESAARLVKPGGRLLYTTCSIFKEENEKNIRWFLNVHPEFKLV 414


>pdb|3M6W|A Chain A, Multi-Site-Specific 16s Rrna Methyltransferase Rsmf From
           Thermus Thermophilus In Space Group P21212 In Complex
           With S-Adenosyl-L- Methionine
          Length = 464

 Score = 30.0 bits (66), Expect = 0.92,   Method: Compositional matrix adjust.
 Identities = 22/65 (33%), Positives = 29/65 (44%), Gaps = 4/65 (6%)

Query: 58  DDKRVGHIPSTAPYCLSECVHDLLDLAGRMLVMGGRLVY----FYPVLREDSTRNPFPEH 113
           D +   H   +AP  ++E    LL  A R+L  GG LVY    F P   E    +    H
Sbjct: 189 DREAARHWGPSAPKRMAEVQKALLAQASRLLGPGGVLVYSTCTFAPEENEGVVAHFLKAH 248

Query: 114 PCFKL 118
           P F+L
Sbjct: 249 PEFRL 253


>pdb|3M6U|A Chain A, Multi-Site-Specific 16s Rrna Methyltransferase Rsmf From
           Thermus Thermophilus In Space Group 43
 pdb|3M6U|B Chain B, Multi-Site-Specific 16s Rrna Methyltransferase Rsmf From
           Thermus Thermophilus In Space Group 43
 pdb|3M6V|A Chain A, Multi-Site-Specific 16s Rrna Methyltransferase Rsmf From
           Thermus Thermophilus In Space Group P2 In Complex With
           S-Adenosyl-L- Methionine
 pdb|3M6V|B Chain B, Multi-Site-Specific 16s Rrna Methyltransferase Rsmf From
           Thermus Thermophilus In Space Group P2 In Complex With
           S-Adenosyl-L- Methionine
          Length = 464

 Score = 30.0 bits (66), Expect = 0.97,   Method: Compositional matrix adjust.
 Identities = 22/65 (33%), Positives = 29/65 (44%), Gaps = 4/65 (6%)

Query: 58  DDKRVGHIPSTAPYCLSECVHDLLDLAGRMLVMGGRLVY----FYPVLREDSTRNPFPEH 113
           D +   H   +AP  ++E    LL  A R+L  GG LVY    F P   E    +    H
Sbjct: 189 DREAARHWGPSAPKRMAEVQKALLAQASRLLGPGGVLVYSTCTFAPEENEGVVAHFLKAH 248

Query: 114 PCFKL 118
           P F+L
Sbjct: 249 PEFRL 253


>pdb|3M6X|A Chain A, Multi-Site-Specific 16s Rrna Methyltransferase Rsmf From
           Thermus Thermophilus In Space Group P21212
          Length = 464

 Score = 28.9 bits (63), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 22/65 (33%), Positives = 28/65 (43%), Gaps = 4/65 (6%)

Query: 58  DDKRVGHIPSTAPYCLSECVHDLLDLAGRMLVMGGRLVY----FYPVLREDSTRNPFPEH 113
           D +   H   +AP   +E    LL  A R+L  GG LVY    F P   E    +    H
Sbjct: 189 DREAARHWGPSAPKRXAEVQKALLAQASRLLGPGGVLVYSTCTFAPEENEGVVAHFLKAH 248

Query: 114 PCFKL 118
           P F+L
Sbjct: 249 PEFRL 253


  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    0.437 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,000,079
Number of Sequences: 62578
Number of extensions: 208528
Number of successful extensions: 383
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 377
Number of HSP's gapped (non-prelim): 10
length of query: 204
length of database: 14,973,337
effective HSP length: 94
effective length of query: 110
effective length of database: 9,091,005
effective search space: 1000010550
effective search space used: 1000010550
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: 49 (23.5 bits)