RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

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



>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 ... (K:)
          Length = 129

 Score =  149 bits (378), Expect = 1e-37
 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


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

 Score =  143 bits (363), Expect = 6e-36
 Identities = 51/128 (39%), Positives = 74/128 (57%)

Query: 2   PKSPSRIRNRERKNIVSGRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPF 61
               S  ++   + I  G  HV ++FNNT +T+TD  G  ++W+S    GF G+++ +PF
Sbjct: 13  NGRISSRKSASARKIPKGVIHVQASFNNTIVTVTDVRGRVVSWASAGTCGFRGTKRGTPF 72

Query: 62  AAQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAHNGC 121
           AAQ A  +        GM   EV + G G GRD+ALRA+R  G  +  + DVT + HNGC
Sbjct: 73  AAQTAAGNAIRTVVEQGMQRAEVMIKGPGLGRDAALRAIRRSGILLSFVRDVTPMPHNGC 132

Query: 122 RPRKRRRI 129
           RP K+RR+
Sbjct: 133 RPPKKRRV 140


>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}
           (K:)
          Length = 129

 Score =  143 bits (362), Expect = 8e-36
 Identities = 60/125 (48%), Positives = 88/125 (70%)

Query: 4   SPSRIRNRERKNIVSGRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAA 63
           +    + + ++ + SGRA++ +++NNT +TITDP GN I WSS  V+G+ GSRK +P+AA
Sbjct: 2   AKKPSKKKVKRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYAA 61

Query: 64  QVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAHNGCRP 123
           Q+A  D + KA  +GM S++V V G GAGR+ A+RAL+A G  + SI D T + HNGCRP
Sbjct: 62  QLAALDAAKKAMAYGMQSVDVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCRP 121

Query: 124 RKRRR 128
           +K+ R
Sbjct: 122 KKKFR 126


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

 Score =  130 bits (327), Expect = 9e-32
 Identities = 40/132 (30%), Positives = 66/132 (50%), Gaps = 9/132 (6%)

Query: 6   SRIRNRERKNIVSGRAHVVSTFNNTRITITDPHGN-TIAWSSPKVVGFSGSRKNSPFAAQ 64
           S +      + V G A + ++FN+T + +TD  G  TIA  +  +   +   ++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} (k:)
          Length = 151

 Score =  124 bits (312), Expect = 5e-30
 Identities = 38/135 (28%), Positives = 58/135 (42%), Gaps = 9/135 (6%)

Query: 3   KSPSRIRNRERKNIVSGRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSRKN-SPF 61
           +  S          V G  H+ ++FN+T + +TD  G          +     R   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


>2imh_A Hypothetical protein UNP Q5LQD5_silpo; structural genomics,
           unknown function, PSI-2, protein structure initiative;
           HET: MSE; 1.57A {Silicibacter pomeroyi} (A:1-210)
          Length = 210

 Score = 25.8 bits (57), Expect = 2.1
 Identities = 7/33 (21%), Positives = 12/33 (36%)

Query: 32  ITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQ 64
           +   D  GN  A++  +     GS   +   A 
Sbjct: 86  LAAXDLLGNAAAFTGSENQDIKGSVTFASGIAS 118


>1hwx_A GDH, glutamate dehydrogenase; allostery, abortive complex,
           oxidoreductase; HET: GLU GTP NAI; 2.50A {Bos taurus}
           (A:242-372)
          Length = 131

 Score = 25.3 bits (55), Expect = 2.7
 Identities = 8/38 (21%), Positives = 13/38 (34%)

Query: 84  VKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAHNGC 121
             V G G     ++R L   G   V++ +      N  
Sbjct: 6   FAVQGFGNVGLHSMRYLHRFGAKCVAVGESDGSIWNPD 43


>3cwf_A Alkaline phosphatase synthesis sensor protein PHOR; PAS
          domain, structural genomics, PSI-2, protein structure
          initiative; HET: EPE; 2.20A {Bacillus subtilis subsp}
          (A:)
          Length = 122

 Score = 25.2 bits (55), Expect = 3.4
 Identities = 2/20 (10%), Positives = 6/20 (30%)

Query: 24 VSTFNNTRITITDPHGNTIA 43
               +   ++ D  G  + 
Sbjct: 43 AGGALDVSASVIDTDGKVLY 62


>2vqe_N 30S ribosomal protein S14 type Z; tRNA-binding,
          rRNA-binding, metal-binding, zinc-finger, translation;
          HET: TM2 PAR; 2.5A {Thermus thermophilus} (N:)
          Length = 61

 Score = 25.0 bits (55), Expect = 3.5
 Identities = 11/33 (33%), Positives = 12/33 (36%), Gaps = 4/33 (12%)

Query: 1  MPKSPSRIRNRERKNIVSGRAH-VVSTFNNTRI 32
           PK   R   R    +  GRA  V   F   RI
Sbjct: 13 TPKFKVRAYTR---CVRCGRARSVYRFFGLCRI 42


>3e7d_A COBH, precorrin-8X methylmutase; ssgcid, decode,
           braba00006A, structural genomics, seattle structural
           genomics center for infectious disease; 1.80A {Brucella
           abortus} (A:)
          Length = 212

 Score = 24.7 bits (54), Expect = 5.1
 Identities = 9/25 (36%), Positives = 12/25 (48%), Gaps = 3/25 (12%)

Query: 94  DSALRALRAIGFTIVSICDVTMIAH 118
            +   AL A G  I+  CD  M+A 
Sbjct: 64  KAGRNALLA-GAPIL--CDARMVAE 85


>3di4_A Uncharacterized protein DUF1989; YP_165628.1, protein of
          unknown function (DUF1989), structural genomics; 1.60A
          {Silicibacter pomeroyi dss-3} (A:28-286)
          Length = 259

 Score = 24.4 bits (53), Expect = 5.2
 Identities = 6/51 (11%), Positives = 11/51 (21%), Gaps = 6/51 (11%)

Query: 2  PKSPSRIRNRERKNIVSGRAHVVSTFNNTRITITDPHGN----TIAWSSPK 48
           ++ +R           GR   V         I+   G         +   
Sbjct: 14 ARASARKTGEVLVPPREGRCFEVKA--GQFFRISSVEGPQVGDLNLHNLHD 62


>2odr_A Phosphoseryl-tRNA synthetase; phosphoserine tRNA
          synthetase class II, ligase; 3.23A {Methanococcus
          maripaludis S2} (A:550-614)
          Length = 65

 Score = 24.3 bits (52), Expect = 5.8
 Identities = 3/6 (50%), Positives = 6/6 (100%)

Query: 81 SLEVKV 86
          ++EVK+
Sbjct: 1  NVEVKI 6


>1jdp_A NPR-C, atrial natriuretic peptide clearance receptor;
           hormone/receptor complex, natriuretic peptide receptor,
           allosteric activation, signaling protein; HET: NDG NAG;
           2.00A {Homo sapiens} (A:137-284,A:358-441)
          Length = 232

 Score = 24.3 bits (52), Expect = 6.5
 Identities = 3/49 (6%), Positives = 10/49 (20%), Gaps = 6/49 (12%)

Query: 13  RKNIVSGRAHVVSTFNNTRITITDPHGNTIAWSS---PK---VVGFSGS 55
             ++ +G   V+  +                W           +    +
Sbjct: 169 MTDVEAGTQEVIGDYFGKEGRFEMRPNVKYPWGPLKLRIDENRIVEHTN 217


>2axq_A Saccharopine dehydrogenase; rossmann fold variant,
           saccharopine reductase fold (domain II), alpha/beta
           protein; 1.70A {Saccharomyces cerevisiae}
           (A:1-145,A:408-458)
          Length = 196

 Score = 23.9 bits (51), Expect = 7.1
 Identities = 8/54 (14%), Positives = 14/54 (25%)

Query: 71  SAKAQNHGMSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAHNGCRPR 124
           S+           V + G G      +  L A     V++   T+         
Sbjct: 13  SSGHIEGRHMGKNVLLLGSGFVAQPVIDTLAANDDINVTVACRTLANAQALAKP 66


>1f2v_A COBH, precorrin-8X methylmutase; alpha-beta WIND, doubly
           wound sheet, isomerase; 2.10A {Pseudomonas
           denitrificans} (A:)
          Length = 219

 Score = 23.9 bits (52), Expect = 7.2
 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


>2a9f_A Putative malic enzyme ((S)-malate:NAD+ oxidoreductase
           (decarboxylating)); hypothetical protein, structural
           genomics, PSI; 2.50A {Streptococcus pyogenes}
           (A:187-318)
          Length = 132

 Score = 23.8 bits (51), Expect = 7.5
 Identities = 12/37 (32%), Positives = 18/37 (48%)

Query: 84  VKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAHNG 120
           + V+G G+   S  R L A G T V++ D   I +  
Sbjct: 5   IVVNGGGSAGLSITRKLLAAGATKVTVVDKFGIINEQ 41


>2f6r_A COA synthase, bifunctional coenzyme A synthase; 18044849,
           bifunctional coenzyme A synthase (COA synthase),
           structural genomics; HET: ACO UNL; 1.70A {Mus musculus}
           (A:1-105,A:181-281)
          Length = 206

 Score = 23.7 bits (51), Expect = 8.9
 Identities = 6/21 (28%), Positives = 12/21 (57%)

Query: 88  GLGAGRDSALRALRAIGFTIV 108
             G+G+ S  + L+ +G  I+
Sbjct: 83  ISGSGKSSVAQRLKNLGAYII 103


  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
   0.319    0.130    0.385 

Gapped
Lambda     K      H
   0.267   0.0594    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 963,214
Number of extensions: 36974
Number of successful extensions: 147
Number of sequences better than 10.0: 1
Number of HSP's gapped: 143
Number of HSP's successfully gapped: 23
Length of query: 129
Length of database: 4,956,049
Length adjustment: 77
Effective length of query: 52
Effective length of database: 2,353,064
Effective search space: 122359328
Effective search space used: 122359328
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: 50 (23.3 bits)