RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780292|ref|YP_003064705.1| 50S ribosomal protein L13
[Candidatus Liberibacter asiaticus str. psy62]
         (155 letters)



>3ofq_J 50S ribosomal protein L13; protein biosynthesis, ribosomes, RNA,
           tRNA, transfer, antibi EXIT, peptidyl, ribosomal
           subunit, large; 3.10A {Escherichia coli} PDB: 1p85_H
           1p86_H 1vs8_J 1vs6_J 2aw4_J 2awb_J 2gya_H 2gyc_H 1vt2_J
           2i2v_J 2i2t_J* 2qao_J* 2qba_J* 2qbc_J* 2qbe_J 2qbg_J
           2qbi_J* 2qbk_J* 2qov_J 2qox_J ...
          Length = 142

 Score =  179 bits (456), Expect = 2e-46
 Identities = 65/141 (46%), Positives = 94/141 (66%), Gaps = 1/141 (0%)

Query: 4   TFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKV 63
           TF  K   V++ W +VDA G  +GRLA+++A RLRGK+K  YTP  D GD+++++NA KV
Sbjct: 3   TFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNADKV 62

Query: 64  AFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKN 123
           A +G K   K YY HTG+ GGIK+ T +E++A   P  +++ A+  MLP+GPL R   + 
Sbjct: 63  AVTGNKRTDKVYYHHTGHIGGIKQATFEEMIA-RRPERVIEIAVKGMLPKGPLGRAMFRK 121

Query: 124 LHIYAEDHHPHEAQKPVFMDI 144
           L +YA + H H AQ+P  +DI
Sbjct: 122 LKVYAGNEHNHAAQQPQVLDI 142


>3f1f_N 50S ribosomal protein L13; RF2, ribosome, termination, tRNA; 3.00A
           {Thermus thermophilus} PDB: 1vsa_H 3d5d_N 3d5b_N 3f1h_N
          Length = 163

 Score =  176 bits (448), Expect = 2e-45
 Identities = 64/144 (44%), Positives = 101/144 (70%), Gaps = 3/144 (2%)

Query: 1   MIPTFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINA 60
           ++ T+  K  +VE +W+L+DA+G  +GRLA++IA  LRGK++P +TP+   GD VV++NA
Sbjct: 23  LVKTYVPK--QVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNA 80

Query: 61  SKVAFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQ 120
            K+  +GKK +QK Y R++GYPGG+KK   +++L    P  +L+ A+  MLP+GPL R+ 
Sbjct: 81  DKIRVTGKKLEQKIYTRYSGYPGGLKKIPLEKML-ATHPERVLEHAVKGMLPKGPLGRRL 139

Query: 121 MKNLHIYAEDHHPHEAQKPVFMDI 144
            K L +YA   HPH+AQ+P  +++
Sbjct: 140 FKRLKVYAGPDHPHQAQRPEKLEV 163


>3bbo_L Ribosomal protein L13; large ribosomal subunit, spinach chloroplast
           ribosome, ribonucleoprotein particle, macromolecular
           complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1
          Length = 250

 Score =  168 bits (426), Expect = 6e-43
 Identities = 65/153 (42%), Positives = 97/153 (63%), Gaps = 4/153 (2%)

Query: 4   TFFQKSSE---VEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINA 60
           T++ KS++    +KKW +VDA  LI+GR+AS IA+ +RGKN  +YTPS D G  V+++NA
Sbjct: 99  TWYPKSADHVPTDKKWYVVDATDLILGRMASTIAIHIRGKNLASYTPSVDMGAFVIVVNA 158

Query: 61  SKVAFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQ 120
            KVA SGKK  QK Y RH+G PGG+K+ T  ++     P  I++ A+  MLP+G L R  
Sbjct: 159 DKVAVSGKKRTQKLYRRHSGRPGGLKEETFDQL-QKRIPERIIEHAVRGMLPKGRLGRYL 217

Query: 121 MKNLHIYAEDHHPHEAQKPVFMDIAKMNPKNSR 153
             +L +Y    HPH+AQ+P+ + +     +  +
Sbjct: 218 FNHLKVYKGAEHPHQAQQPIDLPLRDKRIRVEK 250


>2zjr_G 50S ribosomal protein L13; ribosome, large ribosomal subunit,
           ribonucleoprotein, RNA-binding, rRNA-binding,
           tRNA-binding, methylation; 2.91A {Deinococcus
           radiodurans} SCOP: c.21.1.1 PDB: 1nwx_H* 1nwy_H* 1sm1_H*
           1xbp_H* 2zjp_G* 2zjq_G 1nkw_H 3cf5_G* 3dll_G* 1pnu_H
           1pny_H 1vor_K 1vou_K 1vow_K 1voy_K 1vp0_K
          Length = 174

 Score =  152 bits (384), Expect = 4e-38
 Identities = 63/141 (44%), Positives = 91/141 (64%), Gaps = 1/141 (0%)

Query: 10  SEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKK 69
              E+ W++VDA G+ +GRLA+ IA R+RGK++P +TP+   GD VV+INA++VA +GKK
Sbjct: 35  KNDEQNWVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVINAAQVALTGKK 94

Query: 70  YDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAE 129
            D K Y R+TGY GG+K  TA+E L+   P  +++ A+  MLP+G   R     L +YA 
Sbjct: 95  LDDKVYTRYTGYQGGLKTETAREALSK-HPERVIEHAVFGMLPKGRQGRAMHTRLKVYAG 153

Query: 130 DHHPHEAQKPVFMDIAKMNPK 150
           + HPH AQKP  +    +  K
Sbjct: 154 ETHPHSAQKPQVLKTQPLEVK 174


>3i1n_J 50S ribosomal protein L13; ribosome structure, protein-RNA complex,
           acetylation, ribonucleoprotein, ribosomal protein,
           RNA-binding, rRNA- binding, methylation; 3.19A
           {Escherichia coli k-12} PDB: 1p85_H 1p86_H 1vs8_J 2aw4_J
           2awb_J 2gya_H 2gyc_H 1vs6_J 2i2v_J 2i2t_J* 2qao_J*
           2qba_J* 2qbc_J* 2qbe_J 2qbg_J 2qbi_J* 2qbk_J* 2qov_J
           2qox_J 2qoz_J* ...
          Length = 142

 Score =  145 bits (366), Expect = 5e-36
 Identities = 65/141 (46%), Positives = 94/141 (66%), Gaps = 1/141 (0%)

Query: 4   TFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKV 63
           TF  K   V++ W +VDA G  +GRLA+++A RLRGK+K  YTP  D GD+++++NA KV
Sbjct: 3   TFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNADKV 62

Query: 64  AFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKN 123
           A +G K   K YY HTG+ GGIK+ T +E++A   P  +++ A+  MLP+GPL R   + 
Sbjct: 63  AVTGNKRTDKVYYHHTGHIGGIKQATFEEMIA-RRPERVIEIAVKGMLPKGPLGRAMFRK 121

Query: 124 LHIYAEDHHPHEAQKPVFMDI 144
           L +YA + H H AQ+P  +DI
Sbjct: 122 LKVYAGNEHNHAAQQPQVLDI 142


>3jyw_M 60S ribosomal protein L16(A); eukaryotic ribosome, RACK1 protein,
           flexible fitting; 8.90A {Thermomyces lanuginosus} PDB:
           1s1i_M
          Length = 178

 Score =  144 bits (364), Expect = 9e-36
 Identities = 29/140 (20%), Positives = 59/140 (42%), Gaps = 18/140 (12%)

Query: 17  ILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYY 76
           +++D KG +VGRLAS +A +L              G  +V++ A ++  SG+ +  K  Y
Sbjct: 1   VVIDGKGHLVGRLASVVAKQLLN------------GQKIVVVRAEELNISGEFFRNKLKY 48

Query: 77  RHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLP-RGPLARKQMKNLHIYAEDHHPHE 135
                       T        +P+ I  KA+  M+  +    +  ++ L ++     P++
Sbjct: 49  HDFLRKATAFNKTRGPFHF-RAPSRIFYKALRGMVSHKTARGKAALERLKVFEGIPPPYD 107

Query: 136 AQKPV----FMDIAKMNPKN 151
            +K V     + + ++ P  
Sbjct: 108 KKKRVVVPQALRVLRLKPGR 127


>2j01_N 50S ribosomal protein L13; ribosome, tRNA, paromomycin, mRNA,
           translation; 2.8A {Thermus thermophilus} SCOP: c.21.1.1
           PDB: 2hgq_M 2hgj_M 2hgu_M 2j03_N 2jl6_N 2jl8_N 2v47_N
           2v49_N 2wdi_N 2wdj_N 2wdl_N 2wdn_N 2wh2_N 2wh4_N 3hux_N
           3huz_N 3fin_N 1vsp_H
          Length = 140

 Score =  143 bits (361), Expect = 2e-35
 Identities = 62/135 (45%), Positives = 96/135 (71%), Gaps = 1/135 (0%)

Query: 10  SEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKK 69
            +VE +W+L+DA+G  +GRLA++IA  LRGK++P +TP+   GD VV++NA K+  +GKK
Sbjct: 7   KQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKK 66

Query: 70  YDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAE 129
            +QK Y R++GYPGG+KK   +++L    P  +L+ A+  MLP+GPL R+  K L +YA 
Sbjct: 67  LEQKIYTRYSGYPGGLKKIPLEKML-ATHPERVLEHAVKGMLPKGPLGRRLFKRLKVYAG 125

Query: 130 DHHPHEAQKPVFMDI 144
             HPH+AQ+P  +++
Sbjct: 126 PDHPHQAQRPEKLEV 140


>2ftc_H L13MT, MRP-L13, 39S ribosomal protein L13, mitochondrial;
           mitochondrial ribosome, large ribosomal subunit,
           ribosomal RNA; 12.10A {Bos taurus}
          Length = 148

 Score =  137 bits (347), Expect = 7e-34
 Identities = 53/138 (38%), Positives = 84/138 (60%), Gaps = 1/138 (0%)

Query: 7   QKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFS 66
           Q+ +   + W L+D K    G+LA+  ++RL+G +KP Y   +D GDHVVI+N   +AFS
Sbjct: 9   QQWATFARIWYLLDGKMQPPGKLAAMASIRLQGLHKPVYHALSDCGDHVVIMNTRHIAFS 68

Query: 67  GKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHI 126
           G K++QK Y  HTGYPGG ++ TA ++     P  I+K AI  MLP+    R  M+ LH+
Sbjct: 69  GNKWEQKVYSSHTGYPGGFRQVTAAQL-HLRDPVAIVKLAIYGMLPKNLHRRTMMERLHL 127

Query: 127 YAEDHHPHEAQKPVFMDI 144
           + +++ P +  K +  ++
Sbjct: 128 FPDEYIPEDILKNLVEEL 145


>1j3a_A 50S ribosomal protein L13P; rRNA binding, ribosomal assembly,
           ribosome; 1.60A {Pyrococcus horikoshii} SCOP: c.21.1.1
          Length = 142

 Score =  119 bits (300), Expect = 2e-28
 Identities = 30/138 (21%), Positives = 58/138 (42%), Gaps = 14/138 (10%)

Query: 18  LVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYR 77
           +++A GLI+GRLAS++A  L             +G+ VVI+NA K   +G +    + Y+
Sbjct: 3   IINADGLILGRLASRVAKML------------LEGEEVVIVNAEKAVITGNREVIFSKYK 50

Query: 78  HTGYPGGIKKTTAKEILAGASPTNILKKAIARMLP-RGPLARKQMKNLHIYAEDHHPHEA 136
                  +                I+++ I  MLP +    RK  + L +Y       + 
Sbjct: 51  QRTGLRTLTNPRRGPFYPK-RSDEIVRRTIRGMLPWKTDRGRKAFRRLKVYVGIPKEFQD 109

Query: 137 QKPVFMDIAKMNPKNSRR 154
           ++   +  A ++  +  +
Sbjct: 110 KQLETIVEAHVSRLSRPK 127


>2zkr_j 60S ribosomal protein L13A; protein-RNA complex, 60S ribosomal
           subunit, ribosomal protein/RNA complex; 8.70A {Canis
           familiaris}
          Length = 203

 Score =  118 bits (296), Expect = 8e-28
 Identities = 27/145 (18%), Positives = 59/145 (40%), Gaps = 16/145 (11%)

Query: 13  EKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQ 72
           E + +++D +G ++GRLA+ +A ++              G  VV++    +  SG  Y  
Sbjct: 3   EVQVLVLDGRGHLLGRLAAIVAKQV------------LLGRKVVVVRCEGINISGNFYRN 50

Query: 73  KTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLP-RGPLARKQMKNLHIYAEDH 131
           K  Y            +        +P+ I  + +  MLP +    +  +  L ++    
Sbjct: 51  KLNYLAFLRKRMNTNPSRGPYDF-RAPSRIFWRTVRGMLPHKTKRGQAALDRLKVFDGIP 109

Query: 132 HPHEAQKPVFMDIA--KMNPKNSRR 154
            P++ +K + +  A   +  K +R+
Sbjct: 110 PPYDKKKRMVVPAALKVVRLKPTRK 134


>1vq8_J 50S ribosomal protein L13P; ribosome 50S, protein-protein complex,
           RNA-RNA complex, protein-RNA complex, peptidyl
           transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS;
           2.20A {Haloarcula marismortui} SCOP: c.21.1.1 PDB:
           1giy_M 1jj2_I 1k73_K* 1k8a_K* 1k9m_K* 1kc8_K* 1kd1_K*
           1kqs_I* 1m1k_K* 1m90_K* 1ml5_m* 1n8r_K* 1nji_K* 1q7y_K*
           1q81_K* 1q82_K* 1q86_K* 1qvf_I 1qvg_I 1s72_J* ...
          Length = 145

 Score =  110 bits (277), Expect = 1e-25
 Identities = 27/139 (19%), Positives = 57/139 (41%), Gaps = 18/139 (12%)

Query: 14  KKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQK 73
              ++VDA+  I+GR+ASQ+A +              DG+ V ++NA +   +G++    
Sbjct: 7   DADVIVDARDCIMGRVASQVAEQA------------LDGETVAVVNAERAVITGREEQIV 54

Query: 74  TYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLP-RGPLARKQMKNLHIYAEDHH 132
             Y      G        +      P  I K+ I  MLP +    R+  +++ +Y  + +
Sbjct: 55  EKYEKRVDIGNDNGYFYPK-----RPDGIFKRTIRGMLPHKKQRGREAFESVRVYLGNPY 109

Query: 133 PHEAQKPVFMDIAKMNPKN 151
             + +      + +++   
Sbjct: 110 DEDGEVLDGTSLDRLSNIK 128


>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
           photosynthetic reaction center, peripheral antenna; HET:
           CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
          Length = 154

 Score = 35.4 bits (80), Expect = 0.006
 Identities = 11/32 (34%), Positives = 17/32 (53%), Gaps = 7/32 (21%)

Query: 117 ARKQMK-NLHIYAEDHHPHEAQKPVFMDIAKM 147
           A K+++ +L +YA+D  P  A K      A M
Sbjct: 21  ALKKLQASLKLYADDSAPALAIK------ATM 46



 Score = 29.2 bits (64), Expect = 0.37
 Identities = 13/49 (26%), Positives = 19/49 (38%), Gaps = 21/49 (42%)

Query: 13 EKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINAS 61
          EK+ +    K L       Q +L+L       Y   ADD    + I A+
Sbjct: 18 EKQAL----KKL-------QASLKL-------Y---ADDSAPALAIKAT 45


>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 = 31.1 bits (70), Expect = 0.11
 Identities = 24/117 (20%), Positives = 38/117 (32%), Gaps = 53/117 (45%)

Query: 33  IALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYR--------HTGYPGG 84
           + L LR K K      A  G     ++ S++ FS +K   K   R        H+     
Sbjct: 389 LNLTLR-KAK------APSG-----LDQSRIPFSERK--LKFSNRFLPVASPFHSHL--- 431

Query: 85  IKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHEAQKPVF 141
                    L  AS   ++ K + +             N+   A+D      Q PV+
Sbjct: 432 ---------LVPASD--LINKDLVK------------NNVSFNAKD-----IQIPVY 460


>3khk_A Type I restriction-modification system methylation subunit;
           structural genomics, PSI-2, protein structure
           initiative; 2.55A {Methanosarcina mazei}
          Length = 544

 Score = 25.6 bits (55), Expect = 5.1
 Identities = 7/30 (23%), Positives = 13/30 (43%)

Query: 40  KNKPTYTPSADDGDHVVIINASKVAFSGKK 69
           K+K       D    V+ I+A K+ +   +
Sbjct: 445 KDKNAKNGKRDRRGQVLFIDARKLGYMKDR 474


  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
   0.317    0.133    0.386 

Gapped
Lambda     K      H
   0.267   0.0622    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,373,441
Number of extensions: 62423
Number of successful extensions: 176
Number of sequences better than 10.0: 1
Number of HSP's gapped: 159
Number of HSP's successfully gapped: 19
Length of query: 155
Length of database: 5,693,230
Length adjustment: 84
Effective length of query: 71
Effective length of database: 3,656,734
Effective search space: 259628114
Effective search space used: 259628114
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: 52 (24.0 bits)