RPS-BLAST 2.2.22 [Sep-27-2009]

Database: mmdb70 
           33,805 sequences; 4,956,049 total letters

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

Query= gi|254780330|ref|YP_003064743.1| 30S ribosomal protein S18
[Candidatus Liberibacter asiaticus str. psy62]
         (83 letters)



>3i1m_R 30S ribosomal protein S18; ribosome structure, protein-RNA
          complex, ribonucleoprotein, ribosomal protein,
          RNA-binding, rRNA-binding, antibiotic resistance; 3.19A
          {Escherichia coli k-12} PDB: 1vs7_R* 1vs5_R 3i1o_R
          3i1q_R 3i1s_R 3i1z_R 3i21_R 2qal_R* 1p6g_R 1p87_R
          2aw7_R 2avy_R 2i2u_R 2i2p_R* 2qan_R* 2qb9_R* 2qbb_R*
          2qbd_R 2qbf_R 2qbh_R* ... (R:)
          Length = 75

 Score = 78.9 bits (195), Expect = 2e-16
 Identities = 35/66 (53%), Positives = 46/66 (69%)

Query: 17 RRKSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLG 76
          RRK C  + +G   IDYKDI  L  ++++ GKIVPSRI+    K QR+LA+AIKRARYL 
Sbjct: 7  RRKFCRFTAEGVQEIDYKDIATLKNYITESGKIVPSRITGTRAKYQRQLARAIKRARYLS 66

Query: 77 LIAYVN 82
          L+ Y +
Sbjct: 67 LLPYTD 72


>2vqe_R 30S ribosomal protein S18; tRNA-binding, rRNA-binding,
          metal-binding, zinc-finger, translation; HET: TM2 PAR;
          2.5A {Thermus thermophilus} (R:)
          Length = 88

 Score = 75.2 bits (185), Expect = 3e-15
 Identities = 29/78 (37%), Positives = 43/78 (55%)

Query: 5  APTPLLRRNVSHRRKSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRE 64
          A      +    R+     +       DY+++ +L RFLS+ GKI+P R + +S K+QR 
Sbjct: 6  AKPKKEAQRRPSRKAKVKATLGEFDLRDYRNVEVLKRFLSETGKILPRRRTGLSGKEQRI 65

Query: 65 LAKAIKRARYLGLIAYVN 82
          LAK IKRAR LGL+ +  
Sbjct: 66 LAKTIKRARILGLLPFTE 83


>3bbn_R Ribosomal protein S18; small ribosomal subunit, spinach
          chloroplast ribosome, ribonucleoprotein particle,
          macromolecular complex; 9.40A {Spinacea oleracea} (R:)
          Length = 103

 Score = 70.9 bits (174), Expect = 6e-14
 Identities = 23/66 (34%), Positives = 44/66 (66%)

Query: 17 RRKSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLG 76
            +      +   RIDY+++ L++RF+S++GKI+  R++ ++ K+QR +  AIK+AR L 
Sbjct: 14 SFRRRLPPIQSGDRIDYRNMSLISRFISEQGKILSRRVNRLTLKQQRLITSAIKQARILS 73

Query: 77 LIAYVN 82
          L+ ++N
Sbjct: 74 LLPFLN 79


>1slm_A Stromelysin-1; hydrolase, metalloprotease, fibroblast,
          collagen degradation; 1.90A {Homo sapiens} (A:1-83)
          Length = 83

 Score = 26.0 bits (57), Expect = 2.0
 Identities = 12/52 (23%), Positives = 22/52 (42%), Gaps = 1/52 (1%)

Query: 27 GAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKR-ARYLGL 77
          GA R +   + L+ ++L     +       V  K    + K I+   ++LGL
Sbjct: 5  GAARGEDTSMNLVQKYLENYYDLKKDVKQFVRRKDSGPVVKKIREMQKFLGL 56


>1su3_A Interstitial collagenase; prodomain, hemopexin domain,
          exocite, structural proteomics in europe, spine,
          structural genomics, hydrolase; HET: EPE; 2.20A {Homo
          sapiens} (A:1-81)
          Length = 81

 Score = 25.7 bits (56), Expect = 2.1
 Identities = 6/52 (11%), Positives = 19/52 (36%), Gaps = 1/52 (1%)

Query: 27 GAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKR-ARYLGL 77
                 +D+ L+ ++L +   +          +    + + +K+   + GL
Sbjct: 3  ATLETQEQDVDLVQKYLEKYYNLKNDGRQVEKRRNSGPVVEKLKQMQEFFGL 54


>3gh1_A Predicted nucleotide-binding protein; structural genomics,
           protein structure initiative; 1.90A {Vibrio cholerae o1
           biovar el tor str} PDB: 2pmb_A (A:83-462)
          Length = 380

 Score = 24.9 bits (54), Expect = 3.5
 Identities = 11/33 (33%), Positives = 16/33 (48%), Gaps = 1/33 (3%)

Query: 22  PLSGKGAPRIDYKDIRLLNRFLSQ-RGKIVPSR 53
           P    G P +  K  +LLN F++Q R K+    
Sbjct: 330 PFEXHGDPVLXKKXDQLLNDFVAQNRXKLPGGS 362


>2waq_C DNA-directed RNA polymerase RPO1C subunit; multi-subunit,
           transcription; 3.35A {Sulfolobus shibatae} PDB: 2wb1_C
           3hkz_C 2pmz_C (C:64-116,C:277-330)
          Length = 107

 Score = 23.6 bits (51), Expect = 9.0
 Identities = 4/22 (18%), Positives = 11/22 (50%)

Query: 31  IDYKDIRLLNRFLSQRGKIVPS 52
           +D + I L+   +++ G +   
Sbjct: 85  VDMRHILLVADVMTRTGVVRQI 106


  Database: mmdb70
    Posted date:  Jun 20, 2010  3:12 AM
  Number of letters in database: 4,956,049
  Number of sequences in database:  33,805
  
Lambda     K      H
   0.323    0.136    0.386 

Gapped
Lambda     K      H
   0.267   0.0710    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 613,738
Number of extensions: 22796
Number of successful extensions: 62
Number of sequences better than 10.0: 1
Number of HSP's gapped: 62
Number of HSP's successfully gapped: 9
Length of query: 83
Length of database: 4,956,049
Length adjustment: 47
Effective length of query: 36
Effective length of database: 3,367,214
Effective search space: 121219704
Effective search space used: 121219704
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 (22.0 bits)
S2: 50 (23.1 bits)