RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780238|ref|YP_003064651.1| 30S ribosomal protein S11
[Candidatus Liberibacter asiaticus str. psy62]
         (129 letters)



>3ofo_K 30S ribosomal protein S11; protein biosynthesis, ribosomes, RNA,
           tRNA, transfer, eryThr ketolide, macrolide, antibiotic,
           EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 3fih_K*
           3iy8_K 2wwl_K 3ofp_K 3i1m_K 1vs7_K* 3e1a_C 3e1c_C 1vs5_K
           3i1o_K 3i1q_K 3i1s_K 3i1z_K 3i21_K 3kc4_K 3or9_K 3ora_K
           2qal_K* 1p6g_K 1p87_K ...
          Length = 117

 Score =  154 bits (392), Expect = 4e-39
 Identities = 61/117 (52%), Positives = 82/117 (70%)

Query: 13  RKNIVSGRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSA 72
           RK +  G AH+ ++FNNT +TITD  GN + W++    GF GSRK++PFAAQVA + C+ 
Sbjct: 1   RKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTPFAAQVAAERCAD 60

Query: 73  KAQNHGMSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAHNGCRPRKRRRI 129
             + +G+ +LEV V G G GR+S +RAL A GF I +I DVT I HNGCRP K+RR+
Sbjct: 61  AVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHNGCRPPKKRRV 117


>3i1m_K 30S ribosomal protein S11; ribosome structure, protein-RNA complex,
           ribonucleoprotein, ribosomal protein, RNA-binding,
           rRNA-binding, antibiotic resistance; 3.19A {Escherichia
           coli k-12} PDB: 1vs7_K* 3e1a_C 3e1c_C 1vs5_K 3i1o_K
           3i1q_K 3i1s_K 3i1z_K 3i21_K 2qal_K* 1p6g_K 1p87_K 2aw7_K
           2avy_K 2i2u_K 2i2p_K* 2qan_K* 2qb9_K* 2qbb_K* 2qbd_K ...
          Length = 129

 Score =  146 bits (369), Expect = 1e-36
 Identities = 67/129 (51%), Positives = 89/129 (68%)

Query: 1   MPKSPSRIRNRERKNIVSGRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSRKNSP 60
           M K+P R R R RK +  G AH+ ++FNNT +TITD  GN + W++    GF GSRK++P
Sbjct: 1   MAKAPIRARKRVRKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTP 60

Query: 61  FAAQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAHNG 120
           FAAQVA + C+   + +G+ +LEV V G G GR+S +RAL A GF I +I DVT I HNG
Sbjct: 61  FAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHNG 120

Query: 121 CRPRKRRRI 129
           CRP K+RR+
Sbjct: 121 CRPPKKRRV 129


>2vqe_K 30S ribosomal protein S11, 30S ribosomal protein S6; tRNA-binding,
           rRNA-binding, metal-binding, zinc-finger, translation;
           HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: c.55.4.1
           PDB: 1gix_N* 1hnw_K* 1hnx_K* 1hnz_K* 1hr0_K 1ibk_K*
           1ibl_K* 1ibm_K 1j5e_K 1jgo_N* 1jgp_N* 1jgq_N* 1ml5_N*
           1n32_K* 1n33_K* 1n34_K 1n36_K 1xmo_K* 1xmq_K* 1xnq_K*
           ...
          Length = 129

 Score =  142 bits (360), Expect = 2e-35
 Identities = 64/128 (50%), Positives = 91/128 (71%), Gaps = 2/128 (1%)

Query: 1   MPKSPSRIRNRERKNIVSGRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSRKNSP 60
           M K PS+   + ++ + SGRA++ +++NNT +TITDP GN I WSS  V+G+ GSRK +P
Sbjct: 1   MAKKPSK--KKVKRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTP 58

Query: 61  FAAQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAHNG 120
           +AAQ+A  D + KA  +GM S++V V G GAGR+ A+RAL+A G  + SI D T + HNG
Sbjct: 59  YAAQLAALDAAKKAMAYGMQSVDVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNG 118

Query: 121 CRPRKRRR 128
           CRP+K+ R
Sbjct: 119 CRPKKKFR 126


>3bbn_K Ribosomal protein S11; small ribosomal subunit, spinach chloroplast
           ribosome, ribonucleoprotein particle, macromolecular
           complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1
          Length = 140

 Score =  136 bits (344), Expect = 1e-33
 Identities = 51/124 (41%), Positives = 74/124 (59%)

Query: 6   SRIRNRERKNIVSGRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQV 65
           S  ++   + I  G  HV ++FNNT +T+TD  G  ++W+S    GF G+++ +PFAAQ 
Sbjct: 17  SSRKSASARKIPKGVIHVQASFNNTIVTVTDVRGRVVSWASAGTCGFRGTKRGTPFAAQT 76

Query: 66  ATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAHNGCRPRK 125
           A  +        GM   EV + G G GRD+ALRA+R  G  +  + DVT + HNGCRP K
Sbjct: 77  AAGNAIRTVVEQGMQRAEVMIKGPGLGRDAALRAIRRSGILLSFVRDVTPMPHNGCRPPK 136

Query: 126 RRRI 129
           +RR+
Sbjct: 137 KRRV 140


>1s1h_K RP59A, 40S ribosomal protein S14-A; 80S ribosome, 40S ribosomal
           subunit, EEF2, tRNA translocation, sordarin, cryo-EM;
           11.70A {Saccharomyces cerevisiae} SCOP: i.1.1.1
          Length = 136

 Score =  118 bits (298), Expect = 3e-28
 Identities = 38/132 (28%), Positives = 62/132 (46%), Gaps = 9/132 (6%)

Query: 6   SRIRNRERKNIVSGRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSR-KNSPFAAQ 64
           S +      + V G A + ++FN+T + +TD  G          +     R ++SP+AA 
Sbjct: 1   SNVVQARDNSQVFGVARIYASFNDTFVHVTDLSGKETIARVTGGMKVKADRDESSPYAAM 60

Query: 65  VATDDCSAKAQNHGMSSLEVKVSGL--------GAGRDSALRALRAIGFTIVSICDVTMI 116
           +A  D +AK +  G++++ VK+           G G  +ALRAL   G  I  I DVT +
Sbjct: 61  LAAQDVAAKCREVGITAVHVKIRATGGTRTKTPGPGGQAALRALARSGLRIGRIEDVTPV 120

Query: 117 AHNGCRPRKRRR 128
             +  R +  RR
Sbjct: 121 PSDSTRKKGGRR 132


>2zkq_k 40S ribosomal protein S14E; protein-RNA complex, 40S ribosomal
           subunit, ribosomal protein/RNA complex; 8.70A {Canis
           familiaris}
          Length = 151

 Score =  118 bits (297), Expect = 4e-28
 Identities = 37/135 (27%), Positives = 60/135 (44%), Gaps = 9/135 (6%)

Query: 3   KSPSRIRNRERKNIVSGRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGF-SGSRKNSPF 61
           +  S          V G  H+ ++FN+T + +TD  G          +   +   ++SP+
Sbjct: 13  QVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGKETICRVTGGMKVKADRDESSPY 72

Query: 62  AAQVATDDCSAKAQNHGMSSLEVKVSG--------LGAGRDSALRALRAIGFTIVSICDV 113
           AA +A  D + + +  G+++L +K+           G G  SALRAL   G  I  I DV
Sbjct: 73  AAMLAAQDVAQRCKELGITALHIKLRATGGNRTKTPGPGAQSALRALARSGMKIGRIEDV 132

Query: 114 TMIAHNGCRPRKRRR 128
           T I  +  R +  RR
Sbjct: 133 TPIPSDSTRRKGGRR 147


>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 = 36.5 bits (84), Expect = 0.002
 Identities = 25/126 (19%), Positives = 36/126 (28%), Gaps = 47/126 (37%)

Query: 3   KSP-----SRIRNRERKNIVSGRAHVVSTFNNTRITITDP-HGNTIAWSSPKVVGFSGSR 56
           K+P     SRI   ERK   S R      F    + +  P H                  
Sbjct: 397 KAPSGLDQSRIPFSERKLKFSNR------F----LPVASPFH------------------ 428

Query: 57  KNSPF---AAQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALRALRAIGFTIV-SICD 112
             S     A+ +   D      +     +++ V     G D     LR +  +I   I D
Sbjct: 429 --SHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSD-----LRVLSGSISERIVD 481

Query: 113 VTMIAH 118
              I  
Sbjct: 482 --CIIR 485


>3g4n_A Aerolysin; toxin, cytolytic toxin, pore-forming toxin, membrane,
           secreted; 2.10A {Aeromonas hydrophila} PDB: 3g4o_A
           1pre_A 1z52_A 3c0n_A 3c0m_A 3c0o_A*
          Length = 470

 Score = 25.6 bits (56), Expect = 3.8
 Identities = 10/49 (20%), Positives = 15/49 (30%)

Query: 7   RIRNRERKNIVSGRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGS 55
              +R+    V G A   S    +   +T  +     WS     G S  
Sbjct: 190 TQSDRQLVKTVVGWAVNDSDTPQSGYDVTLRYDTATNWSKTNTYGLSEK 238


>1f2v_A COBH, precorrin-8X methylmutase; alpha-beta WIND, doubly wound
           sheet, isomerase; 2.10A {Pseudomonas denitrificans}
           SCOP: c.23.17.1 PDB: 1i1h_A*
          Length = 219

 Score = 25.1 bits (55), Expect = 5.4
 Identities = 12/25 (48%), Positives = 15/25 (60%), Gaps = 3/25 (12%)

Query: 94  DSALRALRAIGFTIVSICDVTMIAH 118
            SA  AL+A G  I+  CD  M+AH
Sbjct: 71  SSARAALKA-GAPIL--CDAEMVAH 92


>3oa2_A WBPB; oxidoreductase, sugar biosynthesis, dehydrogenase; HET: NAD;
           1.50A {Pseudomonas aeruginosa}
          Length = 318

 Score = 24.3 bits (52), Expect = 8.4
 Identities = 6/17 (35%), Positives = 11/17 (64%)

Query: 97  LRALRAIGFTIVSICDV 113
           +RA++  G  +VS  D+
Sbjct: 20  MRAIKDTGNCLVSAYDI 36


>3i0p_A Malate dehydrogenase; araerobic parasitic protozoan, amoebic
           dysentery, ssgcid, niaid, infectious disease, structural
           genomics; HET: NAD; 2.60A {Entamoeba histolytica}
          Length = 365

 Score = 24.3 bits (52), Expect = 9.1
 Identities = 13/83 (15%), Positives = 25/83 (30%), Gaps = 1/83 (1%)

Query: 41  TIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSG-LGAGRDSALRA 99
           +I   +       G+         +       KA+ +GM  + V+ S   G     +L A
Sbjct: 75  SIIRETSTTCVLDGNNGFGHVNGTIGMKMAIEKAKKYGMGMVVVRNSTHFGIAGYYSLLA 134

Query: 100 LRAIGFTIVSICDVTMIAHNGCR 122
            +     I      + +A     
Sbjct: 135 AQEGCIGICGTNARSSVAATFGD 157


>2vqe_N 30S ribosomal protein S14 type Z; tRNA-binding, rRNA-binding,
          metal-binding, zinc-finger, translation; HET: TM2 PAR;
          2.5A {Thermus thermophilus} SCOP: g.39.1.7 PDB: 1gix_Q*
          1hnw_N* 1hnx_N* 1hnz_N* 1hr0_N 1ibk_N* 1ibl_N* 1ibm_N
          1jgo_Q* 1jgp_Q* 1jgq_Q* 1ml5_Q* 1xmo_N* 1xmq_N* 1xnq_N*
          1xnr_N* 1yl4_Q 2b64_N* 2b9m_N* 2b9o_N* ...
          Length = 61

 Score = 24.2 bits (53), Expect = 9.4
 Identities = 11/34 (32%), Positives = 13/34 (38%), Gaps = 4/34 (11%)

Query: 2  PKSPSRIRNRERKNIVSGRAH-VVSTFNNTRITI 34
          PK   R   R    +  GRA  V   F   RI +
Sbjct: 14 PKFKVRAYTR---CVRCGRARSVYRFFGLCRICL 44


  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    0.130    0.385 

Gapped
Lambda     K      H
   0.267   0.0668    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,086,164
Number of extensions: 43591
Number of successful extensions: 148
Number of sequences better than 10.0: 1
Number of HSP's gapped: 144
Number of HSP's successfully gapped: 18
Length of query: 129
Length of database: 5,693,230
Length adjustment: 82
Effective length of query: 47
Effective length of database: 3,705,222
Effective search space: 174145434
Effective search space used: 174145434
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)