RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780626|ref|YP_003065039.1| 30S ribosomal protein S20
[Candidatus Liberibacter asiaticus str. psy62]
         (90 letters)



>2vqe_T 30S ribosomal protein S20; tRNA-binding, rRNA-binding,
          metal-binding, zinc-finger, translation; HET: TM2 PAR;
          2.5A {Thermus thermophilus} SCOP: a.7.6.1 PDB: 1gix_W*
          1hnw_T* 1hnx_T* 1hnz_T* 1hr0_T 1j5e_T 1jgo_W* 1jgp_W*
          1jgq_W* 1ml5_W* 1yl4_W 2b64_T* 2b9m_T* 2b9o_T* 2f4v_T*
          2ow8_u* 2qnh_u* 2uxb_T* 1fjg_T* 2uxd_T* ...
          Length = 106

 Score = 73.2 bits (180), Expect = 1e-14
 Identities = 33/90 (36%), Positives = 54/90 (60%)

Query: 1  MANKDSAKKMIRKIARRTLINKSRRSSVRSFMRHANEAITFGKIEEATEACRKAESVIQK 60
               SA K  R+  +R L NK+++S++++  + A +    GK EEA +  RKAES+I K
Sbjct: 6  PKRNLSALKRHRQSLKRRLRNKAKKSAIKTLSKKAVQLAQEGKAEEALKIMRKAESLIDK 65

Query: 61 AKSKGIFHGNAASRKVSRLSKRLKGILTSA 90
          A      H NAA+R+ SRL ++++ +L +A
Sbjct: 66 AAKGSTLHKNAAARRKSRLMRKVRQLLEAA 95


>3ofo_T 30S ribosomal protein S20; protein biosynthesis, ribosomes, RNA,
          tRNA, transfer, eryThr ketolide, macrolide, antibiotic,
          EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 3fih_T*
          2wwl_T 3ofp_T 2qal_T* 1p6g_T 1p87_T 2aw7_T 2avy_T
          2i2u_T 2i2p_T* 2qan_T* 2qb9_T* 2qbb_T* 2qbd_T 2qbf_T
          2qbh_T* 2qbj_T* 2qou_T* 2qow_T* 2qoy_T* ...
          Length = 85

 Score = 71.6 bits (176), Expect = 4e-14
 Identities = 24/84 (28%), Positives = 44/84 (52%)

Query: 3  NKDSAKKMIRKIARRTLINKSRRSSVRSFMRHANEAITFGKIEEATEACRKAESVIQKAK 62
          N  SAKK   +  +    N SRRS +R+F++    AI  G    A +A  + + ++ +  
Sbjct: 1  NIKSAKKRAIQSEKARKHNASRRSMMRTFIKKVYAAIEAGDKAAAQKAFNEMQPIVDRQA 60

Query: 63 SKGIFHGNAASRKVSRLSKRLKGI 86
          +KG+ H N A+R  + L+ ++  +
Sbjct: 61 AKGLIHKNKAARHKANLTAQINKL 84


>3bbn_T Ribosomal protein S20; small ribosomal subunit, spinach chloroplast
           ribosome, ribonucleoprotein particle, macromolecular
           complex; 9.40A {Arabidopsis thaliana}
          Length = 202

 Score = 71.6 bits (175), Expect = 4e-14
 Identities = 29/99 (29%), Positives = 44/99 (44%), Gaps = 9/99 (9%)

Query: 1   MANKDSAKKMIRKIARRTLINKSRRSSVRSFMRHANEAITFGK---------IEEATEAC 51
               DSA K  R+  +R + NKS++S  R+ M+   EA+   K         I    +  
Sbjct: 84  TKKADSAAKRARQAEKRRVYNKSKKSEARTRMKKVLEALEGLKKKTDAQADEIVTVEKLI 143

Query: 52  RKAESVIQKAKSKGIFHGNAASRKVSRLSKRLKGILTSA 90
            +A S I KA      H N  +R+ SRL++R K +    
Sbjct: 144 GEAYSAIDKAVKVKALHKNTGARRKSRLARRKKAVEIHH 182


>3i1m_T 30S ribosomal protein S20; ribosome structure, protein-RNA
          complex, ribonucleoprotein, ribosomal protein,
          RNA-binding, rRNA-binding, antibiotic resistance; 3.19A
          {Escherichia coli k-12} PDB: 1vs7_T* 3e1a_N 3e1c_N
          1vs5_T 3i1o_T 3i1q_T 3i1s_T 3i1z_T 3i21_T 2qal_T*
          1p6g_T 1p87_T 2aw7_T 2avy_T 2i2u_T 2i2p_T* 2qan_T*
          2qb9_T* 2qbb_T* 2qbd_T ...
          Length = 87

 Score = 68.1 bits (167), Expect = 4e-13
 Identities = 26/86 (30%), Positives = 46/86 (53%)

Query: 1  MANKDSAKKMIRKIARRTLINKSRRSSVRSFMRHANEAITFGKIEEATEACRKAESVIQK 60
          MAN  SAKK   +  +    N SRRS +R+F++    AI  G    A +A  + + ++ +
Sbjct: 1  MANIKSAKKRAIQSEKARKHNASRRSMMRTFIKKVYAAIEAGDKAAAQKAFNEMQPIVDR 60

Query: 61 AKSKGIFHGNAASRKVSRLSKRLKGI 86
            +KG+ H N A+R  + L+ ++  +
Sbjct: 61 QAAKGLIHKNKAARHKANLTAQINKL 86


>1uc2_A PH1602, hypothetical protein PH1602; structural genomics, unknown
           function; HET: SUC; 2.15A {Pyrococcus horikoshii} SCOP:
           d.261.1.1
          Length = 481

 Score = 27.3 bits (60), Expect = 0.85
 Identities = 15/71 (21%), Positives = 28/71 (39%), Gaps = 6/71 (8%)

Query: 9   KMIRKIARRTLINKSRRSSVRSFMRHANEAITFGKIEEATEACRKAESVIQKAKSKGIFH 68
            + RK A R       R  + +   +   A      EEA  A +  ++V++     GI  
Sbjct: 409 VLSRKAATRQYRGDRIRQELLNRGIYVRAASMRVVAEEAPGAYKNVDNVVKVVSEAGI-- 466

Query: 69  GNAASRKVSRL 79
               ++ V+R+
Sbjct: 467 ----AKLVARM 473


>3ip4_A Glutamyl-tRNA(Gln) amidotransferase subunit A; multi protein
          complex, ligase, ATP-binding, nucleotide- binding;
          1.90A {Staphylococcus aureus subsp} PDB: 2df4_A 2dqn_A*
          2g5h_A 2g5i_A* 2f2a_A
          Length = 485

 Score = 26.7 bits (58), Expect = 1.2
 Identities = 9/70 (12%), Positives = 22/70 (31%), Gaps = 9/70 (12%)

Query: 6  SAKKMIRKIARRTLINKSRRSSVRSFMRHANE------AITFGKIEEATEACRKAESVIQ 59
          S + ++  I  + +        V+       E      +      E A +  ++ + +  
Sbjct: 7  SVENLLTLIKDKKI---KPSDVVKDIYDAIEETDPTIKSFLALDKENAIKKAQELDELQA 63

Query: 60 KAKSKGIFHG 69
          K +  G   G
Sbjct: 64 KDQMDGKLFG 73


>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein
          structure initiative, PSI, center for eukaryotic
          structural genomics, CESG; HET: MSE; 2.60A {Danio
          rerio}
          Length = 307

 Score = 25.7 bits (55), Expect = 2.7
 Identities = 11/27 (40%), Positives = 14/27 (51%)

Query: 38 AITFGKIEEATEACRKAESVIQKAKSK 64
          AI   KI EA E   KAE  ++ +  K
Sbjct: 1  AIAAQKISEAHEHIAKAEKYLKTSFMK 27


>1zbp_A Hypothetical protein VPA1032; alpha-beta protein, structural
          genomics, PSI, protein structure initiative; 2.40A
          {Vibrio parahaemolyticus rimd 2210633} SCOP: e.61.1.1
          Length = 273

 Score = 25.1 bits (54), Expect = 3.8
 Identities = 6/23 (26%), Positives = 13/23 (56%)

Query: 32 MRHANEAITFGKIEEATEACRKA 54
          M     A++ G++++A E   +A
Sbjct: 1  MTQWKNALSEGQLQQALELLIEA 23


>2epg_A Hypothetical protein TTHA1785; alpha-beta fold, structural
           genomics, NPPSFA; 2.10A {Thermus thermophilus HB8}
          Length = 487

 Score = 25.0 bits (54), Expect = 4.2
 Identities = 16/75 (21%), Positives = 28/75 (37%), Gaps = 14/75 (18%)

Query: 9   KMIRKIARRTLINKSRRSSVRSFMRHANEAITFGK----IEEATEACRKAESVIQKAKSK 64
           KM R  A++      R  ++   +      +         EE  EA +    V++  +  
Sbjct: 415 KMSRHQAKKVA----RERNLVKELAERGILVRAATRATVDEEMPEAYKDVSLVVEAVEGA 470

Query: 65  GIFHGNAASRKVSRL 79
           GI       +KV+RL
Sbjct: 471 GI------GKKVARL 479


  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
   0.316    0.124    0.319 

Gapped
Lambda     K      H
   0.267   0.0739    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 626,028
Number of extensions: 22744
Number of successful extensions: 116
Number of sequences better than 10.0: 1
Number of HSP's gapped: 113
Number of HSP's successfully gapped: 17
Length of query: 90
Length of database: 5,693,230
Length adjustment: 57
Effective length of query: 33
Effective length of database: 4,311,322
Effective search space: 142273626
Effective search space used: 142273626
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.0 bits)