RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

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



>2zjr_G 50S ribosomal protein L13; ribosome, large ribosomal
           subunit, ribonucleoprotein, RNA-binding, rRNA-binding,
           tRNA-binding, methylation; 2.91A {Deinococcus
           radiodurans} (G:)
          Length = 174

 Score =  170 bits (433), Expect = 6e-44
 Identities = 63/147 (42%), Positives = 91/147 (61%), Gaps = 1/147 (0%)

Query: 4   TFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKV 63
                    E+ W++VDA G+ +GRLA+ IA R+RGK++P +TP+   GD VV+INA++V
Sbjct: 29  VKTYIPKNDEQNWVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVINAAQV 88

Query: 64  AFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKN 123
           A +GKK D K Y R+TGY GG+K  TA+E L+   P  +++ A+  MLP+G   R     
Sbjct: 89  ALTGKKLDDKVYTRYTGYQGGLKTETAREALSKH-PERVIEHAVFGMLPKGRQGRAMHTR 147

Query: 124 LHIYAEDHHPHEAQKPVFMDIAKMNPK 150
           L +YA + HPH AQKP  +    +  K
Sbjct: 148 LKVYAGETHPHSAQKPQVLKTQPLEVK 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* ... (J:)
          Length = 142

 Score =  168 bits (426), Expect = 4e-43
 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  AVTGNKRTDKVYYHHTGHIGGIKQATFEEMIARR-PERVIEIAVKGMLPKGPLGRAMFRK 121

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


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

 Score =  166 bits (422), Expect = 1e-42
 Identities = 65/156 (41%), Positives = 97/156 (62%), Gaps = 4/156 (2%)

Query: 1   MIPTFFQKSSE---VEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVI 57
              T++ KS++    +KKW +VDA  LI+GR+AS IA+ +RGKN  +YTPS D G  V++
Sbjct: 96  WNTTWYPKSADHVPTDKKWYVVDATDLILGRMASTIAIHIRGKNLASYTPSVDMGAFVIV 155

Query: 58  INASKVAFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLA 117
           +NA KVA SGKK  QK Y RH+G PGG+K+ T  ++     P  I++ A+  MLP+G L 
Sbjct: 156 VNADKVAVSGKKRTQKLYRRHSGRPGGLKEETFDQLQK-RIPERIIEHAVRGMLPKGRLG 214

Query: 118 RKQMKNLHIYAEDHHPHEAQKPVFMDIAKMNPKNSR 153
           R    +L +Y    HPH+AQ+P+ + +     +  +
Sbjct: 215 RYLFNHLKVYKGAEHPHQAQQPIDLPLRDKRIRVEK 250


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

 Score =  165 bits (419), Expect = 3e-42
 Identities = 65/144 (45%), Positives = 102/144 (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   +++LA   P  +L+ A+  MLP+GPL R+ 
Sbjct: 81  DKIRVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATH-PERVLEHAVKGMLPKGPLGRRL 139

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


>2ftc_H L13MT, MRP-L13, 39S ribosomal protein L13, mitochondrial;
           mitochondrial ribosome, large ribosomal subunit,
           ribosomal RNA; 12.10A {Bos taurus} (H:17-148)
          Length = 132

 Score =  163 bits (413), Expect = 1e-41
 Identities = 52/131 (39%), Positives = 81/131 (61%), Gaps = 1/131 (0%)

Query: 16  WILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTY 75
           W L+D K    G+LA+  ++RL+G +KP Y   +D GDHVVI+N   +AFSG K++QK Y
Sbjct: 2   WYLLDGKMQPPGKLAAMASIRLQGLHKPVYHALSDCGDHVVIMNTRHIAFSGNKWEQKVY 61

Query: 76  YRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHE 135
             HTGYPGG ++ TA ++     P  I+K AI  MLP+    R  M+ LH++ +++ P +
Sbjct: 62  SSHTGYPGGFRQVTAAQLHLRD-PVAIVKLAIYGMLPKNLHRRTMMERLHLFPDEYIPED 120

Query: 136 AQKPVFMDIAK 146
             K +  ++ +
Sbjct: 121 ILKNLVEELPQ 131


>3jyw_M 60S ribosomal protein L16(A); eukaryotic ribosome, RACK1
           protein, flexible fitting; 8.90A {Thermomyces
           lanuginosus} PDB: 1s1i_M (M:1-141)
          Length = 141

 Score =  132 bits (333), Expect = 3e-32
 Identities = 30/139 (21%), Positives = 56/139 (40%), Gaps = 14/139 (10%)

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

Query: 77  RHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPR-GPLARKQMKNLHIYAEDHHPHE 135
                       T       A P+ I  KA+  M+       +  ++ L ++     P++
Sbjct: 49  HDFLRKATAFNKTRGPFHFRA-PSRIFYKALRGMVSHKTARGKAALERLKVFEGIPPPYD 107

Query: 136 AQKPVFMDIAKMNPKNSRR 154
            +K V +  A    +    
Sbjct: 108 KKKRVVVPQALRVLRLKPG 126


>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} (J:)
          Length = 145

 Score =  127 bits (320), Expect = 7e-31
 Identities = 29/147 (19%), Positives = 56/147 (38%), Gaps = 18/147 (12%)

Query: 9   SSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGK 68
           S       ++VDA+  I+GR+ASQ+A              A DG+ V ++NA +   +G+
Sbjct: 2   SVAEFDADVIVDARDCIMGRVASQVA------------EQALDGETVAVVNAERAVITGR 49

Query: 69  KYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPR-GPLARKQMKNLHIY 127
           +      Y      G               P  I K+ I  MLP      R+  +++ +Y
Sbjct: 50  EEQIVEKYEKRVDIGN-----DNGYFYPKRPDGIFKRTIRGMLPHKKQRGREAFESVRVY 104

Query: 128 AEDHHPHEAQKPVFMDIAKMNPKNSRR 154
             + +  + +      + +++      
Sbjct: 105 LGNPYDEDGEVLDGTSLDRLSNIKFVT 131


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

 Score =  122 bits (308), Expect = 2e-29
 Identities = 30/138 (21%), Positives = 56/138 (40%), Gaps = 14/138 (10%)

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

Query: 78  HTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPR-GPLARKQMKNLHIYAEDHHPHEA 136
                  +                I+++ I  MLP      RK  + L +Y       + 
Sbjct: 51  QRTGLRTLTNPRRGPFYPKR-SDEIVRRTIRGMLPWKTDRGRKAFRRLKVYVGIPKEFQD 109

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


>2j01_N 50S ribosomal protein L13; ribosome, tRNA, paromomycin,
           mRNA, translation; 2.8A {Thermus thermophilus}
           (N:1-63,N:93-140)
          Length = 111

 Score =  118 bits (298), Expect = 4e-28
 Identities = 49/141 (34%), Positives = 77/141 (54%), Gaps = 32/141 (22%)

Query: 4   TFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKV 63
           T+  K  +VE +W+L+DA+G  +GRLA++IA  LRGK++P +TP+   GD VV++NA K+
Sbjct: 3   TYVPK--QVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKI 60

Query: 64  AFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKN 123
             +                                P  +L+ A+  MLP+GPL R+  K 
Sbjct: 61  RVTT------------------------------HPERVLEHAVKGMLPKGPLGRRLFKR 90

Query: 124 LHIYAEDHHPHEAQKPVFMDI 144
           L +YA   HPH+AQ+P  +++
Sbjct: 91  LKVYAGPDHPHQAQRPEKLEV 111


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

 Score =  115 bits (290), Expect = 2e-27
 Identities = 25/143 (17%), Positives = 54/143 (37%), Gaps = 14/143 (9%)

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

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

Query: 132 HPHEAQKPVFMDIAKMNPKNSRR 154
            P++ +K + +  A    +    
Sbjct: 110 PPYDKKKRMVVPAALKVVRLKPT 132


>2j01_N 50S ribosomal protein L13; ribosome, tRNA, paromomycin,
          mRNA, translation; 2.8A {Thermus thermophilus}
          (N:64-92)
          Length = 29

 Score = 35.1 bits (80), Expect = 0.004
 Identities = 16/29 (55%), Positives = 23/29 (79%)

Query: 67 GKKYDQKTYYRHTGYPGGIKKTTAKEILA 95
          GKK +QK Y R++GYPGG+KK   +++LA
Sbjct: 1  GKKLEQKIYTRYSGYPGGLKKIPLEKMLA 29


>3c85_A Putative glutathione-regulated potassium-efflux system
          protein KEFB; TRKA domain; HET: AMP; 1.90A {Vibrio
          parahaemolyticus rimd 2210633} (A:)
          Length = 183

 Score = 26.2 bits (57), Expect = 2.4
 Identities = 4/42 (9%), Positives = 9/42 (21%)

Query: 25 IVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFS 66
          I       +      K              V+I+   ++   
Sbjct: 12 IYQHSGKWLQETAAEKLNQRDQLINPGHAQVLILGXGRIGTG 53


>1h2w_A Prolyl endopeptidase; hydrolase, prolyl oligopeptidase,
          amnesia, alpha/ beta- hydrolase, beta-propeller, serine
          protease; 1.39A {Sus scrofa} (A:378-428)
          Length = 51

 Score = 25.4 bits (56), Expect = 3.4
 Identities = 11/27 (40%), Positives = 17/27 (62%), Gaps = 2/27 (7%)

Query: 61 SKVAFSGKKYDQKTYYRHTGY--PGGI 85
          S V +SG+K D + +Y+ T +  PG I
Sbjct: 4  SVVGYSGQKKDTEIFYQFTSFLSPGII 30


>2h1q_A Hypothetical protein; ZP_00559375.1, structural genomics,
           PSI-2, protein structure initiative; 2.01A
           {Desulfitobacterium hafniense dcb-2} (A:)
          Length = 270

 Score = 25.2 bits (55), Expect = 4.4
 Identities = 3/32 (9%), Positives = 8/32 (25%)

Query: 77  RHTGYPGGIKKTTAKEILAGASPTNILKKAIA 108
           R       +     +         N ++ +I 
Sbjct: 66  RXPXLTQNLLGLPLRVAAGCVKSWNYVEASIG 97


>3h9e_A Glyceraldehyde-3-phosphate dehydrogenase, testis- specific;
           oxidoreductase, structural genomics, structural genomics
           consortium, SGC, cytoplasm; HET: NAD; 1.72A {Homo
           sapiens} PDB: 2vyn_D* 2vyv_D* (A:1-155,A:321-346)
          Length = 181

 Score = 25.1 bits (54), Expect = 5.0
 Identities = 10/37 (27%), Positives = 16/37 (43%), Gaps = 4/37 (10%)

Query: 39  GKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTY 75
           G N+  Y P        ++ NAS+  +S +  D   Y
Sbjct: 137 GVNENDYNPG----SMNIVSNASEYGYSHRVVDLLRY 169


>2hur_A NDK, nucleoside diphosphate kinase, NDP kinase; type II
           tetramer, signaling protein,transferase; 1.62A
           {Escherichia coli} (A:)
          Length = 142

 Score = 24.6 bits (53), Expect = 6.8
 Identities = 11/50 (22%), Positives = 17/50 (34%), Gaps = 4/50 (8%)

Query: 101 NILKKAIARMLPRGPLARKQMKNLHIY---AEDHHPHEAQKPVFMDIAKM 147
           N++    AR    G       K LH+    A   +     KP F  + + 
Sbjct: 17  NVIGNIFARFEAAG-FKIVGTKMLHLTVEQARGFYAEHDGKPFFDGLVEF 65


>2zb4_A Prostaglandin reductase 2; rossmann fold, alternative
          splicing, cytoplasm, NADP, oxidoreductase; HET: NAP
          5OP; 1.63A {Homo sapiens} PDB: 2zb7_A* 2zb8_A* 2w98_A*
          2vna_A* 2w4q_A* 1vj1_A 2zb3_A* (A:133-318)
          Length = 186

 Score = 24.1 bits (51), Expect = 7.9
 Identities = 12/71 (16%), Positives = 21/71 (29%)

Query: 13 EKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQ 72
            K ++V       G +A QI   L          + +    +        A + KK + 
Sbjct: 28 SNKTMVVSGAAGACGSVAGQIGHFLGCSRVVGICGTHEKCILLTSELGFDAAINYKKDNV 87

Query: 73 KTYYRHTGYPG 83
              R +   G
Sbjct: 88 AEQLRESCPAG 98


>1vbk_A Hypothetical protein PH1313; structural genomics, riken
           structural genomics/proteomics initiative, RSGI, NPPSFA;
           1.90A {Pyrococcus horikoshii OT3} (A:173-291)
          Length = 119

 Score = 24.4 bits (53), Expect = 8.2
 Identities = 6/47 (12%), Positives = 14/47 (29%)

Query: 1   MIPTFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTP 47
                 +   +   K ++   +   +    S+I    +    P Y P
Sbjct: 71  SFDRVLKLIRDFGVKGVIKGLRPNDLNSEVSEITEDFKMFPVPVYYP 117


>2np9_A DPGC; protein inhibitor complex, oxidoreductase; HET: YE1;
           2.45A {Streptomyces toyocaensis} PDB: 2pg8_A*
           (A:148-237,A:286-402)
          Length = 207

 Score = 24.3 bits (52), Expect = 8.3
 Identities = 6/22 (27%), Positives = 14/22 (63%)

Query: 103 LKKAIARMLPRGPLARKQMKNL 124
           +++++ R+     LA ++M NL
Sbjct: 183 IERSLTRLDGDAVLANRRMLNL 204


>3c8u_A Fructokinase; YP_612366.1, putative fructose transport
          system kinase, structural genomics, joint center for
          structural genomics, JCSG; 1.95A {Silicibacter SP}
          (A:1-61,A:124-208)
          Length = 146

 Score = 23.9 bits (52), Expect = 8.9
 Identities = 8/30 (26%), Positives = 12/30 (40%)

Query: 29 LASQIALRLRGKNKPTYTPSADDGDHVVII 58
          L++ +A  L  +  P      D    V II
Sbjct: 38 LSNPLAAALSAQGLPAEVVPXDGFCRVAII 67


  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
   0.317    0.133    0.386 

Gapped
Lambda     K      H
   0.267   0.0641    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 1,214,118
Number of extensions: 52109
Number of successful extensions: 140
Number of sequences better than 10.0: 1
Number of HSP's gapped: 122
Number of HSP's successfully gapped: 22
Length of query: 155
Length of database: 4,956,049
Length adjustment: 81
Effective length of query: 74
Effective length of database: 2,217,844
Effective search space: 164120456
Effective search space used: 164120456
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: 51 (23.6 bits)