RPS-BLAST 2.2.22 [Sep-27-2009]

Database: pdb70 
           24,244 sequences; 5,693,230 total letters

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

Query= gi|254780194|ref|YP_003064607.1| 50S ribosomal protein L31
[Candidatus Liberibacter asiaticus str. psy62]
         (74 letters)



>1vs6_Z 50S ribosomal protein L31; ribosome, kasugamycin; 3.46A
          {Escherichia coli} SCOP: d.325.1.2 PDB: 1vs8_Z 2aw4_Z
          2awb_Z 2j28_Z 2rdo_Z 2vhm_Z 2vhn_Z 3bbx_Z 3e1b_S 3e1d_S
          Length = 70

 Score = 86.3 bits (214), Expect = 1e-18
 Identities = 25/72 (34%), Positives = 35/72 (48%), Gaps = 4/72 (5%)

Query: 1  MKKNIHPETHLITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQ 60
          MKK+IHP+   IT   + G   + RST   +   + LD+    H  + G  Q+    GG+
Sbjct: 1  MKKDIHPKYEEITASCSCGNVMKIRSTVGHD---LNLDVCSKCHPFFTGK-QRDVATGGR 56

Query: 61 VSRFKKRFAGLS 72
          V RF KRF    
Sbjct: 57 VDRFNKRFNIPG 68


>1nkw_Y 50S ribosomal protein L31; ribosome, large subunit, X- RAY
          structure, peptidyl-transferase, peptide bond
          formation; 3.10A {Deinococcus radiodurans} SCOP:
          i.1.1.2 PDB: 1nwx_Y* 1nwy_Y* 1pnu_Y 1pny_Y 1sm1_Y*
          1vor_1 1vou_1 1vow_1 1voy_1 1vp0_1 1xbp_Y* 1yl3_4
          2b66_4 2b9n_4 2b9p_4
          Length = 73

 Score = 84.8 bits (210), Expect = 4e-18
 Identities = 19/72 (26%), Positives = 33/72 (45%), Gaps = 5/72 (6%)

Query: 1  MKKNIHPETHLITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQ 60
          M+K++HP+     ++       +T ST  E    + +D+    H  W  G ++  D  G+
Sbjct: 1  MQKDLHPKAVPCKIIYQGQVVMETMSTRPE----IHVDVWSGVHPFWT-GEERFLDTEGR 55

Query: 61 VSRFKKRFAGLS 72
          V +F KRF    
Sbjct: 56 VDKFNKRFGDSY 67


>3bbo_1 Ribosomal protein L31; large ribosomal subunit, spinach chloroplast
           ribosome, ribonucleoprotein particle, macromolecular
           complex; 9.40A {Arabidopsis thaliana}
          Length = 144

 Score = 83.1 bits (205), Expect = 1e-17
 Identities = 25/73 (34%), Positives = 35/73 (47%), Gaps = 5/73 (6%)

Query: 1   MKKNIHPETHLITVVMTD-GTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGG 59
            KK +HPE H    V  +      T  T KE      +D+   +H  ++G R  +     
Sbjct: 49  RKKELHPEFHEDAKVYCNGELVMTTGGTKKE----YVVDVWSGNHPFYLGNRSALMVDAD 104

Query: 60  QVSRFKKRFAGLS 72
           QV +F+KRFAGLS
Sbjct: 105 QVEKFRKRFAGLS 117


>3f1f_4 50S ribosomal protein L31; RF2, ribosome, termination, tRNA;
          3.00A {Thermus thermophilus} PDB: 3d5d_4 3d5b_4 3f1h_4
          Length = 97

 Score = 78.4 bits (193), Expect = 4e-16
 Identities = 18/69 (26%), Positives = 35/69 (50%), Gaps = 5/69 (7%)

Query: 1  MKKNIHPETHLITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQ 60
          +K+ IHP+     ++   G   +T ST  E    + +++    H  +  G+Q+  D  G+
Sbjct: 27 VKEGIHPKLVPARIICGCGNVIETYSTKPE----IYVEVCSKCHPFYT-GQQRFVDTEGR 81

Query: 61 VSRFKKRFA 69
          V RF++R+ 
Sbjct: 82 VERFQRRYG 90


>2j01_4 50S ribosomal protein L31; ribosome, tRNA, paromomycin, mRNA,
          translation; 2.8A {Thermus thermophilus} SCOP:
          d.325.1.2 PDB: 2hgq_3 2hgj_3 2hgu_3 2j03_4 2v47_4
          2v49_4 2wdi_4 2wdj_4 2wdl_4 2wdn_4 2wh2_4 3hux_4 3huz_4
          3fin_4 2wh4_4
          Length = 71

 Score = 76.3 bits (188), Expect = 2e-15
 Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 5/72 (6%)

Query: 1  MKKNIHPETHLITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQ 60
          MK+ IHP+     ++   G   +T ST  E    + +++    H  +  G+Q+  D  G+
Sbjct: 1  MKEGIHPKLVPARIICGCGNVIETYSTKPE----IYVEVCSKCHPFYT-GQQRFVDTEGR 55

Query: 61 VSRFKKRFAGLS 72
          V RF++R+    
Sbjct: 56 VERFQRRYGDSY 67


>1nsc_A Neuraminidase; hydrolase(O-glycosyl); HET: NAG SIA; 1.70A
           {Influenza b virus} SCOP: b.68.1.1 PDB: 1a4g_A* 1nsb_A*
           1a4q_A* 1nsd_A* 1b9v_A* 1b9s_A* 1b9t_A* 1inv_A* 1ivb_A*
           1inf_A* 1vcj_A*
          Length = 390

 Score = 25.9 bits (57), Expect = 2.3
 Identities = 7/27 (25%), Positives = 14/27 (51%), Gaps = 3/27 (11%)

Query: 13  TVVMTDGT---QYQTRSTWKEEGAVMK 36
            +++TDG+     + R     EG ++K
Sbjct: 161 YLMITDGSASGISKCRFLKIREGRIIK 187


>1v0z_A Neuraminidase; glycosidase, hydrolase; HET: NAG MAN BMA; 1.84A
           {Influenza a virus} PDB: 1w1x_A* 1w20_A* 1w21_A* 2cml_A*
          Length = 389

 Score = 25.5 bits (56), Expect = 3.1
 Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 5/34 (14%)

Query: 13  TVVMTDGT---QYQTRSTWKEEGAVMKLDIDPLS 43
            VVMTDG    +  T+  + +EG + K  I+ L+
Sbjct: 158 PVVMTDGPANNRAATKIIYFKEGKIQK--IEELA 189


  Database: pdb70
    Posted date:  Jan 26, 2011 11:21 AM
  Number of letters in database: 5,693,230
  Number of sequences in database:  24,244
  
Lambda     K      H
   0.319    0.134    0.407 

Gapped
Lambda     K      H
   0.267   0.0618    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 658,340
Number of extensions: 24157
Number of successful extensions: 47
Number of sequences better than 10.0: 1
Number of HSP's gapped: 37
Number of HSP's successfully gapped: 7
Length of query: 74
Length of database: 5,693,230
Length adjustment: 43
Effective length of query: 31
Effective length of database: 4,650,738
Effective search space: 144172878
Effective search space used: 144172878
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.3 bits)