RPS-BLAST 2.2.22 [Sep-27-2009]

Database: pdb70 
           24,244 sequences; 5,693,230 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* ...
          Length = 75

 Score = 88.9 bits (221), Expect = 2e-19
 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


>3ofo_R 30S ribosomal protein S18; protein biosynthesis, ribosomes, RNA,
          tRNA, transfer, eryThr ketolide, macrolide, antibiotic,
          EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 3fih_R*
          3iy8_R 2wwl_R 3ofp_R
          Length = 55

 Score = 81.1 bits (201), Expect = 5e-17
 Identities = 30/52 (57%), Positives = 39/52 (75%)

Query: 31 IDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLGLIAYVN 82
          IDYKDI  L  ++++ GKIVPSRI+    K QR+LA+AIKRARYL L+ Y +
Sbjct: 2  IDYKDIATLKNYITESGKIVPSRITGTRAKYQRQLARAIKRARYLSLLPYTD 53


>3bbn_R Ribosomal protein S18; small ribosomal subunit, spinach
          chloroplast ribosome, ribonucleoprotein particle,
          macromolecular complex; 9.40A {Spinacea oleracea} SCOP:
          i.1.1.1
          Length = 103

 Score = 80.2 bits (198), Expect = 1e-16
 Identities = 28/75 (37%), Positives = 52/75 (69%), Gaps = 2/75 (2%)

Query: 8  PLLRRNVSHRRKSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAK 67
          P ++   S RR+  P+  +   RIDY+++ L++RF+S++GKI+  R++ ++ K+QR +  
Sbjct: 7  PFIKSKRSFRRRLPPI--QSGDRIDYRNMSLISRFISEQGKILSRRVNRLTLKQQRLITS 64

Query: 68 AIKRARYLGLIAYVN 82
          AIK+AR L L+ ++N
Sbjct: 65 AIKQARILSLLPFLN 79


>2vqe_R 30S ribosomal protein S18; tRNA-binding, rRNA-binding,
          metal-binding, zinc-finger, translation; HET: TM2 PAR;
          2.5A {Thermus thermophilus} SCOP: a.4.8.1 PDB: 1fka_R
          1fjg_R 1gix_U* 1hnw_R* 1hnx_R* 1hnz_R* 1hr0_R 1ibk_R*
          1ibl_R* 1ibm_R 1j5e_R 1jgo_U* 1jgp_U* 1jgq_U* 1ml5_U*
          1n32_R* 1n33_R* 1n34_R 1n36_R 1xmo_R* ...
          Length = 88

 Score = 75.2 bits (185), Expect = 4e-15
 Identities = 28/66 (42%), Positives = 41/66 (62%)

Query: 17 RRKSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLG 76
          R+     +       DY+++ +L RFLS+ GKI+P R + +S K+QR LAK IKRAR LG
Sbjct: 18 RKAKVKATLGEFDLRDYRNVEVLKRFLSETGKILPRRRTGLSGKEQRILAKTIKRARILG 77

Query: 77 LIAYVN 82
          L+ +  
Sbjct: 78 LLPFTE 83


>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 = 28.4 bits (63), Expect = 0.41
 Identities = 21/119 (17%), Positives = 30/119 (25%), Gaps = 62/119 (52%)

Query: 3   EVAPTPLL----------------------------------RRN-------------VS 15
           E  P+P+L                                   +N               
Sbjct: 332 EGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNL 391

Query: 16  HRRK-SCPLSGKGAPRIDYKD--IRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKR 71
             RK   P SG    RI + +  ++  NRFL       P  ++S  H     L  A   
Sbjct: 392 TLRKAKAP-SGLDQSRIPFSERKLKFSNRFL-------P--VASPFHSHL--LVPASDL 438



 Score = 27.6 bits (61), Expect = 0.63
 Identities = 7/48 (14%), Positives = 16/48 (33%), Gaps = 15/48 (31%)

Query: 37 RLLNRFLSQ-----RGKIVPSRISSVSHKKQRELAKAIKRARYLGLIA 79
          +L  +F         G       ++ +     EL       ++LG ++
Sbjct: 32 QLQEQFNKILPEPTEGFAADDEPTTPA-----ELV-----GKFLGYVS 69



 Score = 25.3 bits (55), Expect = 3.7
 Identities = 10/42 (23%), Positives = 20/42 (47%), Gaps = 6/42 (14%)

Query: 47  GKIVPSRISSVSHKKQRELAKAIKRA-RYLGL-----IAYVN 82
            + VPS + S+S+  Q ++   + +   +L       I+ VN
Sbjct: 331 NEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVN 372


>1l6j_A Matrix metalloproteinase-9; twisted beta sheet flanked by
          helices, hydrolase; 2.50A {Homo sapiens} SCOP: a.20.1.2
          d.92.1.11 g.14.1.2 g.14.1.2 g.14.1.2
          Length = 425

 Score = 26.9 bits (59), Expect = 1.3
 Identities = 13/63 (20%), Positives = 24/63 (38%), Gaps = 5/63 (7%)

Query: 16 HRRKSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKR-ARY 74
           +R+S  +   G  R +  D +L   +L + G    + +   S      L  A+    + 
Sbjct: 3  RQRQSTLVLFPGDLRTNLTDRQLAEEYLYRYGYTRVAEMRGESK----SLGPALLLLQKQ 58

Query: 75 LGL 77
          L L
Sbjct: 59 LSL 61


>1su3_A Interstitial collagenase; prodomain, hemopexin domain, exocite,
          structural proteomics in europe, spine, structural
          genomics, hydrolase; HET: EPE; 2.20A {Homo sapiens}
          SCOP: a.20.1.2 b.66.1.1 d.92.1.11 PDB: 2clt_A 1fbl_A*
          Length = 450

 Score = 25.5 bits (55), Expect = 3.2
 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


>3g64_A Putative enoyl-COA hydratase; alpha-beta structure, structural
          genomics, PSI-2, protein structure initiative; 2.05A
          {Streptomyces coelicolor A3}
          Length = 279

 Score = 25.3 bits (54), Expect = 3.7
 Identities = 9/62 (14%), Positives = 24/62 (38%), Gaps = 19/62 (30%)

Query: 22 PLSGKGAPRIDYKDIRL----------LNRFLSQRGKIVPSRISSVSHKKQRELAKAIKR 71
          P +G  AP  +++ +R+          L R         P ++++++ +   +L   +  
Sbjct: 5  PFTGSAAPTPEWRHLRVEITDGVATVTLAR---------PDKLNALTFEAYADLRDLLAE 55

Query: 72 AR 73
            
Sbjct: 56 LS 57


>3meb_A Aspartate aminotransferase; pyridoxal phosphate, structural
           genomics, seattle structural genomics center for
           infectious disease; HET: PLP; 1.90A {Giardia lamblia
           atcc 50803}
          Length = 448

 Score = 24.7 bits (53), Expect = 5.3
 Identities = 7/28 (25%), Positives = 14/28 (50%), Gaps = 4/28 (14%)

Query: 49  IVPS--RIS--SVSHKKQRELAKAIKRA 72
           +V +  R+S   ++      +A+AI  A
Sbjct: 413 LVKAGGRMSMCGLTESNCDYVAEAIHDA 440


>2ji4_A Phosphoribosyl pyrophosphate synthetase-associated protein 2;
          phosphorylation, nucleotide biosynthesis, transferase;
          2.55A {Homo sapiens} PDB: 2c4k_A*
          Length = 379

 Score = 23.9 bits (51), Expect = 9.0
 Identities = 9/24 (37%), Positives = 13/24 (54%), Gaps = 2/24 (8%)

Query: 54 ISSVSHKKQRELAKAIKRARYLGL 77
           S+ S+    EL+K I  A  LG+
Sbjct: 33 FSANSNSSCMELSKKI--AERLGV 54


  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
   0.323    0.136    0.386 

Gapped
Lambda     K      H
   0.267   0.0804    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 703,911
Number of extensions: 27481
Number of successful extensions: 79
Number of sequences better than 10.0: 1
Number of HSP's gapped: 78
Number of HSP's successfully gapped: 15
Length of query: 83
Length of database: 5,693,230
Length adjustment: 51
Effective length of query: 32
Effective length of database: 4,456,786
Effective search space: 142617152
Effective search space used: 142617152
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 (22.9 bits)