RPS-BLAST 2.2.26 [Sep-21-2011]

Database: pdb70 
           27,921 sequences; 6,701,793 total letters

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

Query= psy14373
         (65 letters)



>3lkd_A Type I restriction-modification system methyltransferase subunit;
           Q5M500_STRT2, STU0711, NESG, SUR80, structural genomics,
           PSI-2; 2.25A {Streptococcus thermophilus}
          Length = 542

 Score = 27.3 bits (61), Expect = 0.27
 Identities = 7/23 (30%), Positives = 13/23 (56%), Gaps = 2/23 (8%)

Query: 27  AKLN--LHDFKFDDIHMEDDDTL 47
           A++N  LH    ++  + + DTL
Sbjct: 264 ARMNMILHGVPIENQFLHNADTL 286


>2ed6_A 25KDA structural protein VP25; beta barrel, N-terminal helix
          protruding region, viral protein; 2.00A {Shrimp white
          spot syndrome virus} SCOP: b.170.1.1
          Length = 170

 Score = 27.0 bits (59), Expect = 0.37
 Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 5  ILTHTQSLIQCQRVQSLRVPSAAKLNLHDFKFDDIHMEDDDTLKVRSNCG 54
          I THT + I+    ++LR+P  A++    FK  D+  + D   K++   G
Sbjct: 6  IETHTDN-IETNMDENLRIPVTAEVGSGYFKMTDVSFDSDTLGKIKIRNG 54


>3mwb_A Prephenate dehydratase; L-Phe, PSI, MCSG, structural genomics,
           midwest center for ST genomics, protein structure
           initiative, lyase; HET: MSE PHE; 2.00A {Arthrobacter
           aurescens}
          Length = 313

 Score = 25.3 bits (56), Expect = 1.2
 Identities = 6/16 (37%), Positives = 9/16 (56%)

Query: 2   VFRILTHTQSLIQCQR 17
           + RI TH  +  QC+ 
Sbjct: 105 IKRISTHGHAWAQCRL 120


>3luy_A Probable chorismate mutase; structural genomics, APC38059,
           3-phenylp PSI-2, protein structure initiative; HET: PPY;
           2.00A {Bifidobacterium adolescentis}
          Length = 329

 Score = 25.0 bits (55), Expect = 1.8
 Identities = 5/16 (31%), Positives = 6/16 (37%)

Query: 2   VFRILTHTQSLIQCQR 17
                 H   L QC+R
Sbjct: 110 ARIATAHPHGLAQCKR 125


>2v8p_A 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase;
          nucleotide-binding, isoprene biosynthesis, transferase,
          ATP-binding, non-mevalonate; HET: CDP ADP; 2.1A
          {Aquifex aeolicus} PDB: 2v2v_A* 2v2q_A* 2v34_A* 2v2z_A*
          2vf3_A*
          Length = 271

 Score = 24.8 bits (55), Expect = 2.2
 Identities = 13/57 (22%), Positives = 25/57 (43%), Gaps = 21/57 (36%)

Query: 19 QSLRVPSAAKLNL------------HDFK--------FDDIHMEDDDTLKVRSNCGL 55
            ++V S AK+NL            H+          +D+I++  +  L+V +N G+
Sbjct: 3  HMIKVLSPAKINLGLWVLGRLPSGYHEILTLYQEIPFYDEIYIR-EGVLRVETNIGI 58


>2qmw_A PDT, prephenate dehydratase; APC85812, prephenate dehydratase
           (PDT), staphylococcus aureu aureus MU50, structural
           genomics, PSI-2; 2.30A {Staphylococcus aureus subsp}
           SCOP: c.94.1.1 d.58.18.3
          Length = 267

 Score = 24.4 bits (54), Expect = 2.7
 Identities = 1/16 (6%), Positives = 7/16 (43%)

Query: 2   VFRILTHTQSLIQCQR 17
           + ++ +   ++ Q   
Sbjct: 101 IKKVYSIAPAISQTTN 116


>2qmx_A Prephenate dehydratase; APC86053, L-Phe inhibition, PDT, CHL
           tepidum TLS, structural genomics, PSI-2, protein
           structure initiative; HET: PHE; 2.30A {Chlorobium
           tepidum tls}
          Length = 283

 Score = 24.0 bits (53), Expect = 4.2
 Identities = 5/14 (35%), Positives = 10/14 (71%)

Query: 4   RILTHTQSLIQCQR 17
           + ++H Q+L+QC  
Sbjct: 101 KAMSHPQALVQCHN 114


>3kgb_A Thymidylate synthase 1/2; ssgcid, NIH, niaid, SBRI, UW, decode,
           methyltransferase, nucleotide biosynt transferase,
           structural genomics; 2.20A {Encephalitozoon cuniculi}
          Length = 294

 Score = 23.4 bits (51), Expect = 6.5
 Identities = 3/20 (15%), Positives = 8/20 (40%)

Query: 24  PSAAKLNLHDFKFDDIHMED 43
           P   +     F+++D  +  
Sbjct: 262 PKGPRTEPEHFQYEDFELVG 281


>3d8d_A Amyloid beta A4 precursor protein-binding family 1; alpha-beta
           structure, phosphotyrosine binding domain; 2.20A {Homo
           sapiens} PDB: 3d8e_A 3d8f_A
          Length = 148

 Score = 23.2 bits (49), Expect = 6.9
 Identities = 10/48 (20%), Positives = 22/48 (45%), Gaps = 1/48 (2%)

Query: 9   TQSLIQCQRVQSLRVPSAAKLNLHDFKFDDIHMEDDDTLKVRSNCGLC 56
           +Q+L+  Q + S+RV    + +  +  F  +   D  T  ++ +   C
Sbjct: 73  SQALLHAQPIISIRVWGVGRDSGRERDFAYV-ARDKLTQMLKCHVFRC 119


>1bkp_A Thymidylate synthase A; methyltransferase, DTMP synthase; 1.70A
           {Bacillus subtilis} SCOP: d.117.1.1 PDB: 1bko_A 1bsf_A
           1bsp_A 1b02_A*
          Length = 278

 Score = 23.4 bits (51), Expect = 7.9
 Identities = 4/14 (28%), Positives = 8/14 (57%)

Query: 30  NLHDFKFDDIHMED 43
           + +DF  DD  + +
Sbjct: 252 DFYDFTIDDFKLIN 265


  Database: pdb70
    Posted date:  Sep 4, 2012  3:40 AM
  Number of letters in database: 6,701,793
  Number of sequences in database:  27,921
  
Lambda     K      H
   0.326    0.134    0.397 

Gapped
Lambda     K      H
   0.267   0.0769    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 892,469
Number of extensions: 36976
Number of successful extensions: 106
Number of sequences better than 10.0: 1
Number of HSP's gapped: 106
Number of HSP's successfully gapped: 11
Length of query: 65
Length of database: 6,701,793
Length adjustment: 36
Effective length of query: 29
Effective length of database: 5,696,637
Effective search space: 165202473
Effective search space used: 165202473
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (23.3 bits)