RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780245|ref|YP_003064658.1| 50S ribosomal protein L18
[Candidatus Liberibacter asiaticus str. psy62]
         (120 letters)



>3ofq_O 50S ribosomal protein L18; protein biosynthesis, ribosomes, RNA,
           tRNA, transfer, antibi EXIT, peptidyl, ribosomal
           subunit, large; 3.10A {Escherichia coli} PDB: 3fik_O
           2wwq_O 3ofr_O* 3i1n_O 1p85_M 1p86_M 1vs8_O 1vs6_O 2aw4_O
           2awb_O 1vt2_O 2i2v_O 2j28_O 2i2t_O* 2qao_O* 2qba_O*
           2qbc_O* 2qbe_O 2qbg_O 2qbi_O* ...
          Length = 116

 Score =  109 bits (274), Expect = 2e-25
 Identities = 50/117 (42%), Positives = 69/117 (58%), Gaps = 2/117 (1%)

Query: 4   KKKVLARRISRIRRHLKSVSRGRLRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRS 63
           KK    RR +R RR L+ +  G  RL V R+ +HIY Q+I  +    LV+AS++ + +  
Sbjct: 2   KKSARIRRATRARRKLQEL--GATRLVVHRTPRHIYAQVIAPNGSEVLVAASTVEKAIAE 59

Query: 64  SLKTGANIVAATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGVSF 120
            LK   N  AA AVG  + ERA++ G+K V FDR    Y GR+ ALADA R+ G+ F
Sbjct: 60  QLKYTGNKDAAAAVGKAVAERALEKGIKDVSFDRSGFQYHGRVQALADAAREAGLQF 116


>3bbo_Q Ribosomal protein L18; large ribosomal subunit, spinach chloroplast
           ribosome, ribonucleoprotein particle, macromolecular
           complex; 9.40A {Vitis vinifera}
          Length = 161

 Score =  101 bits (254), Expect = 3e-23
 Identities = 47/120 (39%), Positives = 70/120 (58%), Gaps = 3/120 (2%)

Query: 3   TKKKVLARRISRIRRHLKSVSRGRLRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLR 62
           T+++    R  RIR+ ++     R RL V RS+KH+Y Q+IDDS  HTL SAS++ + + 
Sbjct: 43  TRREDRTARHVRIRKKVEGTP-ERPRLCVFRSNKHLYVQVIDDSKMHTLASASTMQKSIS 101

Query: 63  SSL--KTGANIVAATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGVSF 120
             L   +   I  A  VG ++    ++ G+  V FDRG + Y GR+ ALADA R+ G+ F
Sbjct: 102 EELDYSSSPTIEVAKKVGEVIASACLEKGITKVAFDRGGYPYHGRVKALADAAREKGLQF 161


>3i1n_O 50S ribosomal protein L18; ribosome structure, protein-RNA complex,
           acetylation, ribonucleoprotein, ribosomal protein,
           RNA-binding, rRNA- binding, methylation; 3.19A
           {Escherichia coli k-12} PDB: 1p85_M 1p86_M 1vs8_O 2aw4_O
           2awb_O 1vs6_O 2i2v_O 2j28_O 2i2t_O* 2qao_O* 2qba_O*
           2qbc_O* 2qbe_O 2qbg_O 2qbi_O* 2qbk_O* 2qov_O 2qox_O
           2qoz_O* 2qp1_O* ...
          Length = 117

 Score =  101 bits (252), Expect = 5e-23
 Identities = 50/117 (42%), Positives = 69/117 (58%), Gaps = 2/117 (1%)

Query: 4   KKKVLARRISRIRRHLKSVSRGRLRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRS 63
           KK    RR +R RR L+ +  G  RL V R+ +HIY Q+I  +    LV+AS++ + +  
Sbjct: 3   KKSARIRRATRARRKLQEL--GATRLVVHRTPRHIYAQVIAPNGSEVLVAASTVEKAIAE 60

Query: 64  SLKTGANIVAATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGVSF 120
            LK   N  AA AVG  + ERA++ G+K V FDR    Y GR+ ALADA R+ G+ F
Sbjct: 61  QLKYTGNKDAAAAVGKAVAERALEKGIKDVSFDRSGFQYHGRVQALADAAREAGLQF 117


>1ovy_A 50S ribosomal protein L18; ribosome; NMR {Geobacillus
           stearothermophilus} SCOP: c.55.4.1
          Length = 120

 Score =  100 bits (251), Expect = 7e-23
 Identities = 55/118 (46%), Positives = 77/118 (65%), Gaps = 3/118 (2%)

Query: 3   TKKKVLARRISRIRRHLKSVSRGRLRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLR 62
            +  V  +R +RIR+ +   +  R RLSV RS+KHIY QIIDD+   T+VSAS+L++   
Sbjct: 6   DRNAVRKKRHARIRKKIFGTT-ERPRLSVFRSNKHIYAQIIDDTKSATIVSASTLDKEFG 64

Query: 63  SSLKTGANIVAATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGVSF 120
               +  NI AA  VG L+ +RA++ G+K V FDRG +LY GR+ ALADA R+ G+ F
Sbjct: 65  L--DSTNNIEAAKKVGELVAKRALEKGIKQVVFDRGGYLYHGRVKALADAAREAGLEF 120


>2j01_S 50S ribosomal protein L18; ribosome, tRNA, paromomycin, mRNA,
           translation; 2.8A {Thermus thermophilus} SCOP: c.55.4.1
           PDB: 1vsp_M 2hgj_R 2hgq_R 2hgu_R 1vsa_M 2j03_S 2jl6_S
           2jl8_S 2v47_S 2v49_S 2wdi_S 2wdj_S 2wdl_S 2wdn_S 2wh2_S
           2wh4_S 3d5b_S 3d5d_S 3f1f_S 3f1h_S ...
          Length = 112

 Score = 98.7 bits (246), Expect = 3e-22
 Identities = 57/118 (48%), Positives = 70/118 (59%), Gaps = 7/118 (5%)

Query: 3   TKKKVLARRISRIRRHLKSVSRGRLRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLR 62
            +     RR  R+R  +K    GRLRLSV RS KHIY QIIDD  G TLVSASSL   L+
Sbjct: 2   ARLTAYERRKFRVRNRIKRT--GRLRLSVFRSLKHIYAQIIDDEKGVTLVSASSLALKLK 59

Query: 63  SSLKTGANIVAATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGVSF 120
                G     A  VG  L E+A+ +G+K V FDRG + Y GR+ ALA+  R+GG+ F
Sbjct: 60  -----GNKTEVARQVGRALAEKALALGIKQVAFDRGPYKYHGRVKALAEGAREGGLEF 112


>2zjr_L 50S ribosomal protein L18; ribosome, large ribosomal subunit,
           ribonucleoprotein, RNA-binding, rRNA-binding,
           tRNA-binding, methylation; 2.91A {Deinococcus
           radiodurans} SCOP: c.55.4.1 PDB: 1sm1_M* 2zjp_L* 2zjq_L
           1nkw_M 3cf5_L* 3dll_L* 1nwy_M* 1nwx_M* 1xbp_M* 1pnu_M
           1pny_M 1vor_P 1vou_P 1vow_P 1voy_P 1vp0_P
          Length = 114

 Score = 89.9 bits (223), Expect = 1e-19
 Identities = 60/122 (49%), Positives = 75/122 (61%), Gaps = 10/122 (8%)

Query: 1   MATKKKVLARRISRIRRHLKSVSR--GRLRLSVCRSSKHIYGQIIDDSIGHTLVSASSLN 58
           MAT   +  RR  R RR +++ +   GRLRLSV RSSKHIY QIIDDS G TL +AS   
Sbjct: 1   MATATTI--RRKLRTRRKVRTTTAASGRLRLSVYRSSKHIYAQIIDDSRGQTLAAAS--- 55

Query: 59  EPLRSSLKTGANIVAATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGV 118
               ++LK+G     A AVG  L     + G+K V FDRG + Y GR+ ALADA R+GG+
Sbjct: 56  ---SAALKSGNKTDTAAAVGKALXXXXXEKGIKQVVFDRGSYKYHGRVKALADAAREGGL 112

Query: 119 SF 120
            F
Sbjct: 113 DF 114


>1vq8_N 50S ribosomal protein L18P; 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.55.4.1 PDB:
           1vq4_N* 1vq5_N* 1vq6_N* 1vq7_N* 1s72_N* 1vq9_N* 1vqk_N*
           1vql_N* 1vqm_N* 1vqn_N* 1vqo_N* 1vqp_N* 1yhq_N* 1yi2_N*
           1yij_N* 1yit_N* 1yj9_N* 1yjn_N* 1yjw_N* 2otj_N* ...
          Length = 187

 Score = 81.1 bits (200), Expect = 5e-17
 Identities = 33/129 (25%), Positives = 55/129 (42%), Gaps = 10/129 (7%)

Query: 1   MAT----KKKVLARRISRIRRH--LKSVSRGRLRLSVCRSSKHIYGQII--DDSIGHTLV 52
           MAT    K  +  RR +R   H  L+ +  G+ RL   +S+KH+  Q++    +   TL 
Sbjct: 1   MATGPRYKVPMRRRREARTDYHQRLRLLKSGKPRLVARKSNKHVRAQLVTLGPNGDDTLA 60

Query: 53  SASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKVGVKSVYFDRGKH--LYCGRIAALA 110
           SA S +           N+ +A   G L   RA + GV+    D G +      ++ A+ 
Sbjct: 61  SAHSSDLAEYGWEAPTGNMPSAYLTGLLAGLRAQEAGVEEAVLDIGLNSPTPGSKVFAIQ 120

Query: 111 DAVRKGGVS 119
           +     G+ 
Sbjct: 121 EGAIDAGLD 129


>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 = 46.5 bits (110), Expect = 1e-06
 Identities = 32/169 (18%), Positives = 54/169 (31%), Gaps = 66/169 (39%)

Query: 3   TKKKVLARRISRIRRHLKSVSRGRLRLSVCRSSKHIYGQIID------------DS---- 46
           T   ++   I      L  + R          ++ ++ Q ++            D     
Sbjct: 179 TYHVLVGDLIKFSAETLSELIRTT------LDAEKVFTQGLNILEWLENPSNTPDKDYLL 232

Query: 47  --------IG-----HTLVSASSLN-EP--LRSSLK--TGAN--IVAATAVG-------- 78
                   IG     H +V+A  L   P  LRS LK  TG +  +V A A+         
Sbjct: 233 SIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESF 292

Query: 79  NLLVERAVKV----GVKSVYFDRGKHLYCGRI----AALADAVRKG-GV 118
            + V +A+ V    GV+        +          + L D++    GV
Sbjct: 293 FVSVRKAITVLFFIGVRC-------YEAYPNTSLPPSILEDSLENNEGV 334



 Score = 27.6 bits (61), Expect = 0.70
 Identities = 12/79 (15%), Positives = 23/79 (29%), Gaps = 26/79 (32%)

Query: 49  HTLVSASSLNEPLRSSLKTGANIV----AATAVGN---------LLVERA----VKV--- 88
           H L  A+ L +   ++L     ++     A  +            L         ++   
Sbjct: 102 HAL--AAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAI 159

Query: 89  ----GVKSVYFDRGKHLYC 103
               G    YF+  + LY 
Sbjct: 160 FGGQGNTDDYFEELRDLYQ 178


>3jyw_E 60S ribosomal protein L5; eukaryotic ribosome, RACK1 protein,
           flexible fitting; 8.90A {Thermomyces lanuginosus} PDB:
           1s1i_E
          Length = 237

 Score = 37.5 bits (87), Expect = 8e-04
 Identities = 24/88 (27%), Positives = 38/88 (43%), Gaps = 3/88 (3%)

Query: 10  RRISRIRRHLKSVSRGRLRLSVCRSSKHIYGQIIDDSIG--HTLVSASSLNEPLRSSLKT 67
           +R   + +H    +  + RL V  ++K I  QII  +I     L +A S   P       
Sbjct: 22  QRKRLVTQHKAKYNTPKYRLVVRFTNKDIICQIISSTITGDVVLAAAYSHELPRYGITHG 81

Query: 68  GANIVAATAVGNLLVERAV-KVGVKSVY 94
             N  AA A G L+  R + ++G+   Y
Sbjct: 82  LTNWAAAYATGLLIARRTLQRLGLDETY 109


>2zkr_n 60S ribosomal protein L5; protein-RNA complex, 60S ribosomal
           subunit, ribosomal protein/RNA complex; 8.70A {Canis
           familiaris}
          Length = 297

 Score = 35.9 bits (83), Expect = 0.002
 Identities = 19/89 (21%), Positives = 37/89 (41%), Gaps = 5/89 (5%)

Query: 10  RRISRIRRHLKSVSRGRLRLSVCRSSKHIYGQIIDDSIG--HTLVSASSLNEPLRSSLKT 67
            R   + +     +  + R+ V  +++ I  QI    I     + +  + +E  +  +K 
Sbjct: 32  ARKRLVIQDKNKYNTPKYRMIVRVTNRDIICQIAYARIEGDMIVCARYA-HELPKYGVKV 90

Query: 68  GA-NIVAATAVGNLLVERAV-KVGVKSVY 94
           G  N  AA   G LL  R + + G+  +Y
Sbjct: 91  GLTNYAAAYCTGLLLARRLLNRFGMDKIY 119


>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 = 28.0 bits (61), Expect = 0.47
 Identities = 10/32 (31%), Positives = 18/32 (56%), Gaps = 9/32 (28%)

Query: 56 SLNEPLRSSLKTGANIVAATAVGNLLVERAVK 87
          +L + L++SLK  A+  +A A+       A+K
Sbjct: 21 ALKK-LQASLKLYADD-SAPAL-------AIK 43


>2go7_A Hydrolase, haloacid dehalogenase-like family; NP_346487.1,
           structural genomics, PSI, protein structure initiative;
           2.10A {Streptococcus pneumoniae TIGR4} SCOP: c.108.1.6
          Length = 207

 Score = 27.1 bits (58), Expect = 0.93
 Identities = 13/33 (39%), Positives = 17/33 (51%)

Query: 82  VERAVKVGVKSVYFDRGKHLYCGRIAALADAVR 114
           VE A   G++S+ F    +    RI ALAD  R
Sbjct: 170 VEFAQNSGIQSINFLESTYEGNHRIQALADISR 202


>2vbf_A Branched-chain alpha-ketoacid decarboxylase; KDCA, flavoprotein,
           THDP-dependent enzymes, thiamine pyrophosphate, lyase;
           HET: TPP; 1.60A {Lactococcus lactis} PDB: 2vbg_A*
          Length = 570

 Score = 27.3 bits (59), Expect = 0.94
 Identities = 12/65 (18%), Positives = 27/65 (41%), Gaps = 9/65 (13%)

Query: 54  ASSLNEPLRSS--LKTGANIVAATAVGNLLVERAVKVGVKSVYFDRGKHLYCG-RIAALA 110
            SS      SS  +  G+++ +   VG+ L++R  ++G++ ++         G       
Sbjct: 2   GSSXXXXXXSSGLVPRGSHMASMYTVGDYLLDRLHELGIEEIF------GVPGDYNLQFL 55

Query: 111 DAVRK 115
           D +  
Sbjct: 56  DQIIS 60


>2vbi_A Pyruvate decarboxylase; thiamine pyrophosphate, lyase,
           flavoprotein, THDP-dependent enzyme; HET: TPP; 2.75A
           {Acetobacter pasteurianus}
          Length = 566

 Score = 27.4 bits (59), Expect = 0.94
 Identities = 11/40 (27%), Positives = 16/40 (40%), Gaps = 7/40 (17%)

Query: 77  VGNLLVERAVKVGVKSVYFDRGKHLYCG-RIAALADAVRK 115
           VG  L ER V++G+K  +         G     L D +  
Sbjct: 5   VGMYLAERLVQIGLKHHF------AVAGDYNLVLLDQLLL 38


>2wvg_A PDC, pyruvate decarboxylase; thiamine diphosphate, lyase,
           flavoprotein, metal-binding, alcohol fermentation; HET:
           TPU; 1.75A {Zymomonas mobilis} PDB: 2wva_A* 2wvh_A
           1zpd_A*
          Length = 568

 Score = 25.7 bits (55), Expect = 3.1
 Identities = 11/40 (27%), Positives = 16/40 (40%), Gaps = 7/40 (17%)

Query: 77  VGNLLVERAVKVGVKSVYFDRGKHLYCG-RIAALADAVRK 115
           VG  L ER V++G+K  +         G     L D +  
Sbjct: 5   VGTYLAERLVQIGLKHHF------AVAGDYNLVLLDNLLL 38


>1y03_A RSS3, antifreeze peptide SS-3; type I antifreeze protein,
          sculpin, spectroscopy, solution structure, A-helix; NMR
          {Myoxocephalus scorpius} PDB: 1y04_A
          Length = 35

 Score = 25.5 bits (54), Expect = 3.3
 Identities = 9/19 (47%), Positives = 14/19 (73%)

Query: 56 SLNEPLRSSLKTGANIVAA 74
          S+N P R++ KT A+ +AA
Sbjct: 2  SMNAPARAAAKTAADALAA 20


>3m6y_A 4-hydroxy-2-oxoglutarate aldolase; structural genomics, MCSG,
           lyase, PSI-2, protein structure initiative; HET: MSE;
           1.45A {Bacillus cereus} PDB: 3n73_A 3mux_A
          Length = 275

 Score = 24.6 bits (53), Expect = 5.6
 Identities = 7/14 (50%), Positives = 9/14 (64%)

Query: 37  HIYGQIIDDSIGHT 50
           H+Y  IID   G+T
Sbjct: 242 HVYSSIIDKETGNT 255


>1gqi_A Alpha-glucuronidase; (alpha-beta)8 barrel, glycoside hydrolase;
           1.48A {Pseudomonas cellulosa} SCOP: c.1.8.10 d.92.2.2
           PDB: 1gqj_A* 1gqk_A* 1gql_A* 1h41_A*
          Length = 708

 Score = 24.6 bits (53), Expect = 5.8
 Identities = 9/20 (45%), Positives = 12/20 (60%)

Query: 99  KHLYCGRIAALADAVRKGGV 118
              +  +IAALADA R  G+
Sbjct: 214 SDQFLQKIAALADAFRPYGI 233


>2kdp_A Histone deacetylase complex subunit SAP30; SIN3, zinc finger
          motif, nucleic acid interaction, nucleus, repressor,
          transcription; NMR {Homo sapiens}
          Length = 71

 Score = 24.1 bits (52), Expect = 7.4
 Identities = 7/24 (29%), Positives = 19/24 (79%)

Query: 16 RRHLKSVSRGRLRLSVCRSSKHIY 39
          +R  KS+S+ ++++ + +S++H+Y
Sbjct: 27 KRIQKSISQKKVKIELDKSARHLY 50


>3m0z_A Putative aldolase; MCSG, PSI-2, structural genomics, protein
           structure initiative, midwest center for structural
           genomics, lyase; HET: MSE; 1.20A {Klebsiella pneumoniae
           subsp} PDB: 3nzr_A 3lm7_A
          Length = 249

 Score = 24.1 bits (52), Expect = 8.2
 Identities = 8/14 (57%), Positives = 10/14 (71%)

Query: 37  HIYGQIIDDSIGHT 50
           HIY  IID + G+T
Sbjct: 219 HIYSSIIDKASGNT 232


>3lm7_A Putative 4-hydroxy-2-oxoglutarate aldolase / 2-
           dehydro-3-deoxyphosphogluconate aldolase...; structural
           genomics, PSI-2; 1.90A {Yersinia enterocolitica}
          Length = 249

 Score = 24.0 bits (52), Expect = 9.7
 Identities = 8/14 (57%), Positives = 9/14 (64%)

Query: 37  HIYGQIIDDSIGHT 50
           HIY  IID   G+T
Sbjct: 219 HIYSSIIDSKTGNT 232


  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
   0.322    0.134    0.371 

Gapped
Lambda     K      H
   0.267   0.0608    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 944,207
Number of extensions: 36488
Number of successful extensions: 150
Number of sequences better than 10.0: 1
Number of HSP's gapped: 136
Number of HSP's successfully gapped: 35
Length of query: 120
Length of database: 5,693,230
Length adjustment: 81
Effective length of query: 39
Effective length of database: 3,729,466
Effective search space: 145449174
Effective search space used: 145449174
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 (23.3 bits)