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= 048403
         (300 letters)

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

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



>pdb|2HMA|A Chain A, The Crystal Structure Of Trna
           (5-Methylaminomethyl-2-Thiouridylate)- Methyltransferase
           Trmu From Streptococcus Pneumoniae
          Length = 376

 Score = 57.0 bits (136), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 72/258 (27%), Positives = 105/258 (40%), Gaps = 53/258 (20%)

Query: 1   MDAISSMEFDYVASGHYANVVHSSADH----KDKPSVKDQTYFLSHLSQAQLRRLIFHL- 55
           +D   ++  DYVA+GHYA V           +   + KDQTYFLS LSQ QL++  F L 
Sbjct: 116 LDYAITLGADYVATGHYARVARDEDGTVHXLRGVDNGKDQTYFLSQLSQEQLQKTXFPLG 175

Query: 56  -VLYPRLTIPME-------------GI--ILEAETGDFLE-------------------K 80
            +  P +    E             GI  I E    +FL                    +
Sbjct: 176 HLEKPEVRRLAEEAGLSTAKKKDSTGICFIGEKNFKNFLSNYLPAQPGRXXTVDGRDXGE 235

Query: 81  HRGFWFYTIGQHQELGLLYIVYR-----YVVEKDIENNIVFVSRNYYSFDKKRHLFHAGS 135
           H G  +YTIGQ   LG+           +VV KD+  NI++V + +Y          A  
Sbjct: 236 HAGLXYYTIGQRGGLGIGGQHGGDNAPWFVVGKDLSKNILYVGQGFYHDSLXSTSLEASQ 295

Query: 136 LKLLSGLPPEKISQLHSVFY----NCSLTIEHCEDGGEDIAVVQLSEDDQGLAAGQFAAF 191
           +      P E   +  + F     +  +T+ H +  GE   V+  +E  + +  GQ   F
Sbjct: 296 VHFTREXPEEFTLECTAKFRYRQPDSKVTV-HVK--GEKTEVI-FAEPQRAITPGQAVVF 351

Query: 192 YQGRRCLGSGVILEAWDD 209
           Y G  CLG G+I  A+ D
Sbjct: 352 YDGEECLGGGLIDNAYRD 369


>pdb|2DER|A Chain A, Cocrystal Structure Of An Rna Sulfuration Enzyme Mnma And
           Trna-Glu In The Initial Trna Binding State
 pdb|2DER|B Chain B, Cocrystal Structure Of An Rna Sulfuration Enzyme Mnma And
           Trna-Glu In The Initial Trna Binding State
 pdb|2DET|A Chain A, Cocrystal Structure Of An Rna Sulfuration Enzyme Mnma And
           Trna-Glu In The Pre-Reaction State
 pdb|2DEU|A Chain A, Cocrystal Structure Of An Rna Sulfuration Enzyme Mnma And
           Trna-Glu In The Adenylated Intermediate State
 pdb|2DEU|B Chain B, Cocrystal Structure Of An Rna Sulfuration Enzyme Mnma And
           Trna-Glu In The Adenylated Intermediate State
          Length = 380

 Score = 55.1 bits (131), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 64/250 (25%), Positives = 98/250 (39%), Gaps = 53/250 (21%)

Query: 3   AISSMEFDYVASGHY---ANVVHSSADHKDKPSVKDQTYFLSHLS--------------- 44
           A   +  DY+A+GHY   A+V   S   +   S KDQ+YFL  LS               
Sbjct: 127 AAEDLGADYIATGHYVRRADVDGKSRLLRGLDSNKDQSYFLYTLSHEQIAQSLFPVGELE 186

Query: 45  QAQLRRLIFHLVLYPRLTIPMEGIILEAE---------------------TGDFLEKHRG 83
           + Q+R++   L L         GI    E                      GD + +H+G
Sbjct: 187 KPQVRKIAEDLGLVTAKKKDSTGICFIGERKFREFLGRYLPAQPGKIITVDGDEIGEHQG 246

Query: 84  FWFYTIGQHQELGLLYIVYR-----YVVEKDIENNIVFVSRNY-----YSFDKKRHLFHA 133
             ++T+GQ + LG+           YVV+KD+ENNI+ V++ +      S        H 
Sbjct: 247 LMYHTLGQRKGLGIGGTKEGTEEPWYVVDKDVENNILVVAQGHEHPRLMSVGLIAQQLHW 306

Query: 134 GSLKLLSGLPPEKISQLHSVFYNCSLTIEHCEDGGEDIAVVQLSEDDQGLAAGQFAAFYQ 193
              +  +G     +   +    +   T++  +D   D   V   E    +  GQ A FY 
Sbjct: 307 VDREPFTGTMRCTVKTRYRQ-TDIPCTVKALDD---DRIEVIFDEPVAAVTPGQSAVFYN 362

Query: 194 GRRCLGSGVI 203
           G  CLG G+I
Sbjct: 363 GEVCLGGGII 372


>pdb|2IOY|A Chain A, Crystal Structure Of Thermoanaerobacter Tengcongensis
           Ribose Binding Protein
 pdb|2IOY|B Chain B, Crystal Structure Of Thermoanaerobacter Tengcongensis
           Ribose Binding Protein
          Length = 283

 Score = 30.8 bits (68), Expect = 0.95,   Method: Compositional matrix adjust.
 Identities = 25/104 (24%), Positives = 50/104 (48%), Gaps = 8/104 (7%)

Query: 159 LTIEHCEDGGEDIAVVQLSEDDQGLAAGQFAAFYQGRRCLGSGVILEAWDDQGFPVCKKA 218
           +TI+   +GG+   V  ++ D+  +  G+ AA +  +   G G ++E    +G P    A
Sbjct: 86  ITIDRSANGGD--VVCHIASDN--VKGGEMAAEFIAKALKGKGNVVEL---EGIPGASAA 138

Query: 219 LEIARMEDKSKLGKPVKIKVKLQTPMEFDNNKGIESSRNLFNGQ 262
            +  +  D++ + K   IK+  +   +FD +KG+    N+   Q
Sbjct: 139 RDRGKGFDEA-IAKYPDIKIVAKQAADFDRSKGLSVMENILQAQ 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
   0.320    0.137    0.412 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,248,177
Number of Sequences: 62578
Number of extensions: 388703
Number of successful extensions: 926
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 916
Number of HSP's gapped (non-prelim): 8
length of query: 300
length of database: 14,973,337
effective HSP length: 98
effective length of query: 202
effective length of database: 8,840,693
effective search space: 1785819986
effective search space used: 1785819986
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: 51 (24.3 bits)