RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780329|ref|YP_003064742.1| 30S ribosomal protein S6
[Candidatus Liberibacter asiaticus str. psy62]
         (135 letters)



>1cqm_A Ribosomal protein S6; alzheimer disease, oligomerization; 1.65A
           {Thermus thermophilus} SCOP: d.58.14.1 PDB: 1cqn_A
           1qjh_A 1ris_A 1fka_F 1gix_I* 1hnw_F* 1hnx_F* 1hnz_F*
           1hr0_F 1i94_F* 1i95_F* 1i96_F* 1i97_F* 1ibk_F* 1ibl_F*
           1ibm_F 1j5e_F 1jgo_I* 1jgp_I* 1jgq_I* ...
          Length = 101

 Score =  110 bits (276), Expect = 1e-25
 Identities = 24/100 (24%), Positives = 49/100 (49%)

Query: 1   MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYY 60
           M+ YE   +L  ++   Q+       Q  ++  G  V  V  LG+R +AY I K+ + Y+
Sbjct: 1   MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVAILGLRRLAYPIAKDPQGYF 60

Query: 61  VFMNIASPPAAIHEMKRKMRIDENVLRSLTLLVDSHEQSP 100
           ++  +  P   ++++ R++RI +NV R + +       + 
Sbjct: 61  LWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLAN 100


>3ofo_F 30S ribosomal protein S6; protein biosynthesis, ribosomes, RNA,
           tRNA, transfer, eryThr ketolide, macrolide, antibiotic,
           EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 3fih_F*
           3iy8_F 2wwl_F 3ofp_F 2gy9_F 2gyb_F
          Length = 100

 Score =  107 bits (269), Expect = 8e-25
 Identities = 31/100 (31%), Positives = 53/100 (53%), Gaps = 1/100 (1%)

Query: 1   MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYY 60
           M+ YE VF++  D S +Q+   I +Y + I    G++  + + G R +AY I K  KA+Y
Sbjct: 1   MRHYEIVFMVHPDQS-EQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHY 59

Query: 61  VFMNIASPPAAIHEMKRKMRIDENVLRSLTLLVDSHEQSP 100
           V MN+ +P   I E++   R ++ V+RS+ +         
Sbjct: 60  VLMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEA 99


>3i1m_F 30S ribosomal protein S6; ribosome structure, protein-RNA complex,
           ribonucleoprotein, ribosomal protein, RNA-binding,
           rRNA-binding, antibiotic resistance; 3.19A {Escherichia
           coli k-12} PDB: 1p6g_F 1p87_F* 1vs7_F* 2avy_F 2aw7_F
           1vs5_F 2i2u_F 2i2p_F* 2qan_F* 2qb9_F* 2qbb_F* 2qbd_F
           2qbf_F 2qbh_F* 2qbj_F* 2qou_F* 2qow_F* 2qoy_F* 2qp0_F*
           2vho_F ...
          Length = 135

 Score = 99.6 bits (248), Expect = 2e-22
 Identities = 33/126 (26%), Positives = 59/126 (46%), Gaps = 1/126 (0%)

Query: 1   MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYY 60
           M+ YE VF++  D S Q +   I +Y + I    G++  + + G R +AY I K  KA+Y
Sbjct: 1   MRHYEIVFMVHPDQSEQ-VPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHY 59

Query: 61  VFMNIASPPAAIHEMKRKMRIDENVLRSLTLLVDSHEQSPTLTIQRHDRDDRNDRFPRDR 120
           V MN+ +P   I E++   R ++ V+RS+ +         +  ++  D          + 
Sbjct: 60  VLMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANE 119

Query: 121 NVDRKQ 126
             D  +
Sbjct: 120 TADDAE 125


>3bbn_F Ribosomal protein S6; small ribosomal subunit, spinach chloroplast
           ribosome, ribonucleoprotein particle, macromolecular
           complex; 9.40A {Spinacea oleracea}
          Length = 168

 Score = 98.5 bits (245), Expect = 4e-22
 Identities = 22/106 (20%), Positives = 48/106 (45%), Gaps = 9/106 (8%)

Query: 1   MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKA-- 58
           ++ YE + +LR D++  +      +Y+ L+   G     V   G+  +AY I++  KA  
Sbjct: 62  LRQYETMAVLRPDMTEDERLTLTQKYEELLVAGGAMYVEVFNRGVIPLAYSIKRKNKAGE 121

Query: 59  -------YYVFMNIASPPAAIHEMKRKMRIDENVLRSLTLLVDSHE 97
                   Y+     + P +I  ++  +  D++V+RS +  +   +
Sbjct: 122 TNNYLDGIYLLFTYFTKPESISPLEAALVTDDDVIRSSSFKIRKRK 167


>1vmb_A 30S ribosomal protein S6; TM0603, structural genomics, JCSG,
           protein structure initiative, PSI, joint center for
           structural genomics; 1.70A {Thermotoga maritima} SCOP:
           d.58.14.1
          Length = 140

 Score = 94.6 bits (235), Expect = 7e-21
 Identities = 20/116 (17%), Positives = 52/116 (44%), Gaps = 1/116 (0%)

Query: 1   MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQEN-GGEVRLVNELGMRTIAYRIRKNRKAY 59
            ++YE +F++  ++  ++ ++ + + + +I+E   G++  V  +GMR  AY I+K  +  
Sbjct: 18  ERIYESMFIIAPNVPEEERENLVERVKKIIEERVKGKIDKVERMGMRKFAYEIKKFNEGD 77

Query: 60  YVFMNIASPPAAIHEMKRKMRIDENVLRSLTLLVDSHEQSPTLTIQRHDRDDRNDR 115
           Y  +        + E++   R+   ++R  T      E+      +     +  + 
Sbjct: 78  YTVIYFRCDGQNLQELENFYRVTPEIIRWQTFRRFDLEKKERKAQREKAAAEATES 133


>2j5a_A 30S ribosomal protein S6; ribonucleoprotein, RNA-binding,
           rRNA-binding, protein folding; 2.3A {Aquifex aeolicus}
           SCOP: d.58.14.1
          Length = 110

 Score = 91.5 bits (227), Expect = 6e-20
 Identities = 29/101 (28%), Positives = 54/101 (53%), Gaps = 1/101 (0%)

Query: 1   MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYY 60
           ++ YE VF ++  +S +++K    Q +  I++ GGE+    + GMR +AY I+K   A Y
Sbjct: 7   LRYYETVFAVKPTLSEEEMKKKFEQVKEFIKQKGGEILYEEDWGMRQLAYPIQKFNNARY 66

Query: 61  VFMNI-ASPPAAIHEMKRKMRIDENVLRSLTLLVDSHEQSP 100
             +      P   +E+  +++IDE+V+R L + +   E   
Sbjct: 67  FLVQFKTENPQLPNELDFQLKIDEDVIRWLNIQIKESEVKK 107


>2kjw_A TS9, 30S ribosomal protein S6; S6 permutant, solution structure,
          backbone dynamics, folding, ribonucleoprotein,
          RNA-binding, rRNA-binding; NMR {Thermus thermophilus}
          Length = 96

 Score = 57.5 bits (139), Expect = 9e-10
 Identities = 16/54 (29%), Positives = 24/54 (44%)

Query: 1  MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRK 54
             YE   +L  ++   Q+       Q  ++  G  V  V ELG+R +AY I K
Sbjct: 43 PGRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAK 96


>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
           acyl-carrier-protein, beta-ketoacyl reductase,
           beta-ketoacyl synthase, dehydratase; 4.00A
           {Saccharomyces cerevisiae}
          Length = 2006

 Score = 35.7 bits (82), Expect = 0.003
 Identities = 13/75 (17%), Positives = 28/75 (37%), Gaps = 21/75 (28%)

Query: 82  DENVLRSLTLL----VDSHEQSPTLTIQ---RHDRDDRNDRFP----RDRNVDRKQ---- 126
             +V +++T+L    V  +E  P  ++      D  + N+  P       N+ ++Q    
Sbjct: 293 FVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDY 352

Query: 127 ------HVSEEKPLS 135
                 H+   K + 
Sbjct: 353 VNKTNSHLPAGKQVE 367



 Score = 30.7 bits (69), Expect = 0.13
 Identities = 14/69 (20%), Positives = 30/69 (43%), Gaps = 18/69 (26%)

Query: 13  DISSQQIKDTIGQY-QSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAA 71
           +++ +Q++D + +    L      E+ LVN  G         KN     V   ++ PP +
Sbjct: 343 NLTQEQVQDYVNKTNSHLPAGKQVEISLVN--G--------AKN----LV---VSGPPQS 385

Query: 72  IHEMKRKMR 80
           ++ +   +R
Sbjct: 386 LYGLNLTLR 394


>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
           photosynthetic reaction center, peripheral antenna; HET:
           CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
          Length = 154

 Score = 31.9 bits (71), Expect = 0.049
 Identities = 8/28 (28%), Positives = 14/28 (50%), Gaps = 6/28 (21%)

Query: 82  DENVLR----SLTLLVDSHEQSPTLTIQ 105
           ++  L+    SL L  D  + +P L I+
Sbjct: 18  EKQALKKLQASLKLYAD--DSAPALAIK 43


>2bkk_A Aminoglycoside 3'-phosphotransferase; transferase/peptide,
          transferase/designed protein complex,
          CO-crystallization, inhibitor design; HET: ADP; 2.15A
          {Enterococcus faecalis} PDB: 1j7l_A* 1j7i_A* 1j7u_A*
          3h8p_A* 1l8t_A* 2b0q_A*
          Length = 264

 Score = 25.4 bits (54), Expect = 4.1
 Identities = 11/66 (16%), Positives = 27/66 (40%), Gaps = 9/66 (13%)

Query: 16 SQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEM 75
          S ++K  I +Y+S+    G     V         Y++    +  Y+ M  +      +++
Sbjct: 7  SPELKKLIEKYRSVKDTEGMSPAKV---------YKLVGENENLYLKMTDSRYKGTTYDV 57

Query: 76 KRKMRI 81
          +R+  +
Sbjct: 58 EREKDM 63


>2h84_A Steely1; thiolase-fold, type III polyketide synthase, PKS,
           chalcone- stilbene synthase superfamily, type I PKS;
           HET: P6G; 2.90A {Dictyostelium discoideum AX4}
          Length = 374

 Score = 24.5 bits (52), Expect = 8.6
 Identities = 2/21 (9%), Positives = 7/21 (33%)

Query: 66  ASPPAAIHEMKRKMRIDENVL 86
           AS    +   ++   +    +
Sbjct: 335 ASVIFVMDHARKSKSLPTYSI 355


  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
   0.320    0.135    0.375 

Gapped
Lambda     K      H
   0.267   0.0690    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,080,340
Number of extensions: 45278
Number of successful extensions: 121
Number of sequences better than 10.0: 1
Number of HSP's gapped: 116
Number of HSP's successfully gapped: 14
Length of query: 135
Length of database: 5,693,230
Length adjustment: 82
Effective length of query: 53
Effective length of database: 3,705,222
Effective search space: 196376766
Effective search space used: 196376766
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: 51 (23.5 bits)