RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780246|ref|YP_003064659.1| 50S ribosomal protein L6
[Candidatus Liberibacter asiaticus str. psy62]
         (177 letters)



>3ofq_G 50S ribosomal protein L6; protein biosynthesis, ribosomes, RNA,
           tRNA, transfer, antibi EXIT, peptidyl, ribosomal
           subunit, large; 3.10A {Escherichia coli} PDB: 1p85_E
           1p86_E 2awb_G 2aw4_G 2i2v_G 2j28_G 2i2t_G* 2qao_G*
           2qba_G* 2qbc_G* 2qbe_G 2qbg_G 2qbi_G* 2qbk_G* 2qov_G
           2qox_G 2qoz_G* 2qp1_G* 2rdo_G 2vhm_G ...
          Length = 176

 Score =  197 bits (501), Expect = 2e-51
 Identities = 73/176 (41%), Positives = 109/176 (61%)

Query: 2   SRIGKKAIQVPLGVDVAVEDHEIKVKGPKGQLSFMMSDGISVTLQEGMLSVATINGSKKA 61
           SR+ K  + VP GVDV +    I +KG  G+L+  ++D + V   +  L+    +G    
Sbjct: 1   SRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYADG 60

Query: 62  RAAWGMSRTMINNLFHGVTKGYERKLEISGVGCRAFMDGRNLKMSLGFSHDVLYTPLEGI 121
            A  G +R ++N++  GVT+G+ +KL++ GVG RA + G  + +SLGFSH V +    GI
Sbjct: 61  WAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAGI 120

Query: 122 SIFVSKPTEIIVSGIDKQKVGHVAAEIRSYRSAEPYKGKGIRYSGEVIIRKEGKKK 177
           +      TEI++ G DKQ +G VAA++R+YR  EPYKGKG+RY+ EV+  KE KKK
Sbjct: 121 TAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAKKK 176


>1nkw_E 50S ribosomal protein L6; ribosome, large subunit, X- RAY
           structure, peptidyl-transferase, peptide bond formation;
           3.10A {Deinococcus radiodurans} SCOP: i.1.1.2 PDB:
           1sm1_E*
          Length = 212

 Score =  187 bits (476), Expect = 1e-48
 Identities = 80/176 (45%), Positives = 110/176 (62%)

Query: 1   MSRIGKKAIQVPLGVDVAVEDHEIKVKGPKGQLSFMMSDGISVTLQEGMLSVATINGSKK 60
           MSRIGK+ I VP GV V  +D   KVKGPKG+L+   +  ++V      L V   + ++K
Sbjct: 28  MSRIGKQPIAVPSGVTVNAQDGVFKVKGPKGELTVPYNTELTVRQDGDQLLVERPSDAQK 87

Query: 61  ARAAWGMSRTMINNLFHGVTKGYERKLEISGVGCRAFMDGRNLKMSLGFSHDVLYTPLEG 120
            RA  G++RT++ N   GV+ GY   LE+ GVG RA + G+ L+M++G+SH V+  P  G
Sbjct: 88  HRALHGLTRTLVANAVKGVSDGYTINLELRGVGFRAKLTGKALEMNIGYSHPVIIEPPAG 147

Query: 121 ISIFVSKPTEIIVSGIDKQKVGHVAAEIRSYRSAEPYKGKGIRYSGEVIIRKEGKK 176
           ++  V +PT I VSGIDKQ VG VAA +R  R  + Y GKG+R+ GE I  K GK 
Sbjct: 148 VTFAVPEPTRIDVSGIDKQLVGQVAANVRKVRKPDAYHGKGVRFVGEQIALKAGKA 203


>1rl6_A Protein (ribosomal protein L6); RNA-binding protein, gentamicin
           resistance, alpha/beta protein; 2.00A {Geobacillus
           stearothermophilus} SCOP: d.141.1.1 d.141.1.1 PDB:
           1giy_H 1ml5_h* 1c04_B 1yl3_H 2b66_H 2b9n_H 2b9p_H 1eg0_J
           487d_J
          Length = 177

 Score =  167 bits (423), Expect = 2e-42
 Identities = 82/175 (46%), Positives = 117/175 (66%)

Query: 2   SRIGKKAIQVPLGVDVAVEDHEIKVKGPKGQLSFMMSDGISVTLQEGMLSVATINGSKKA 61
           SR+GKK I++P GV V V  + + VKGPKG+L+      +++T++  +++V   +  K  
Sbjct: 1   SRVGKKPIEIPAGVTVTVNGNTVTVKGPKGELTRTFHPDMTITVEGNVITVTRPSDEKHH 60

Query: 62  RAAWGMSRTMINNLFHGVTKGYERKLEISGVGCRAFMDGRNLKMSLGFSHDVLYTPLEGI 121
           RA  G +R+++ N+  GV+KGYE+ LE+ GVG RA   G+ L +S+G+SH V   P EG+
Sbjct: 61  RALHGTTRSLLANMVEGVSKGYEKALELVGVGYRASKQGKKLVLSVGYSHPVEIEPEEGL 120

Query: 122 SIFVSKPTEIIVSGIDKQKVGHVAAEIRSYRSAEPYKGKGIRYSGEVIIRKEGKK 176
            I V   T+IIV G DKQ+VG +AA IR+ R  EPYKGKGIRY GE++  KEGK 
Sbjct: 121 EIEVPSQTKIIVKGADKQRVGELAANIRAVRPPEPYKGKGIRYEGELVRLKEGKT 175


>3i1n_G 50S ribosomal protein L6; ribosome structure, protein-RNA complex,
           acetylation, ribonucleoprotein, ribosomal protein,
           RNA-binding, rRNA- binding, methylation; 3.19A
           {Escherichia coli k-12} PDB: 1vs8_G 3e1b_3 3e1d_3 1vs6_G
           3i1p_G 3i1r_G 3i1t_G 3i20_G 3i22_G 2qam_G* 1p85_E 1p86_E
           2awb_G 2aw4_G 2i2v_G 2j28_G 2i2t_G* 2qao_G* 2qba_G*
           2qbc_G* ...
          Length = 177

 Score =  163 bits (413), Expect = 2e-41
 Identities = 74/177 (41%), Positives = 110/177 (62%)

Query: 1   MSRIGKKAIQVPLGVDVAVEDHEIKVKGPKGQLSFMMSDGISVTLQEGMLSVATINGSKK 60
           MSR+ K  + VP GVDV +    I +KG  G+L+  ++D + V   +  L+    +G   
Sbjct: 1   MSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYAD 60

Query: 61  ARAAWGMSRTMINNLFHGVTKGYERKLEISGVGCRAFMDGRNLKMSLGFSHDVLYTPLEG 120
             A  G +R ++N++  GVT+G+ +KL++ GVG RA + G  + +SLGFSH V +    G
Sbjct: 61  GWAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAG 120

Query: 121 ISIFVSKPTEIIVSGIDKQKVGHVAAEIRSYRSAEPYKGKGIRYSGEVIIRKEGKKK 177
           I+      TEI++ G DKQ +G VAA++R+YR  EPYKGKG+RY+ EV+  KE KKK
Sbjct: 121 ITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAKKK 177


>3bbo_I Ribosomal protein L6; large ribosomal subunit, spinach chloroplast
           ribosome, ribonucleoprotein particle, macromolecular
           complex; 9.40A {Arabidopsis thaliana}
          Length = 223

 Score =  162 bits (412), Expect = 3e-41
 Identities = 76/177 (42%), Positives = 113/177 (63%), Gaps = 1/177 (0%)

Query: 1   MSRIGKKAIQVPLGVDVAVEDHEIKVKGPKGQLSFMMSDGISVT-LQEGMLSVATINGSK 59
            SRIGK+ I VP  V +A+E  ++KVKGP G+L+      + +T  + G L V     ++
Sbjct: 43  ESRIGKQPIAVPSNVTIALEGQDLKVKGPLGELALTYPREVELTKEESGFLRVKKTVETR 102

Query: 60  KARAAWGMSRTMINNLFHGVTKGYERKLEISGVGCRAFMDGRNLKMSLGFSHDVLYTPLE 119
           +A    G+ RT+ +N+  GV+KG+E+KL + GVG RA +DG+ L ++LGFSH V     +
Sbjct: 103 RANQMHGLFRTLTDNMVVGVSKGFEKKLILVGVGYRATVDGKELVLNLGFSHPVKMQIPD 162

Query: 120 GISIFVSKPTEIIVSGIDKQKVGHVAAEIRSYRSAEPYKGKGIRYSGEVIIRKEGKK 176
            + + V + T I VSG DK ++G  AA +R +R  EPYKGKG++YS E++ RKEGK 
Sbjct: 163 SLKVKVEENTRITVSGYDKSEIGQFAATVRKWRPPEPYKGKGVKYSDEIVRRKEGKA 219


>2j01_H 50S ribosomal protein L6; ribosome, tRNA, paromomycin, mRNA,
           translation; 2.8A {Thermus thermophilus} SCOP: d.141.1.1
           d.141.1.1 PDB: 1vsp_F 2hgj_H 2hgq_H 2hgu_H 1vsa_F 2j03_H
           2jl6_H 2jl8_H 2v47_H 2v49_H 2wdi_H 2wdj_H 2wdl_H 2wdn_H
           2wh2_H 2wh4_H 3d5b_H 3d5d_H 3f1f_H 3f1h_H ...
          Length = 180

 Score =  161 bits (409), Expect = 6e-41
 Identities = 81/176 (46%), Positives = 115/176 (65%)

Query: 1   MSRIGKKAIQVPLGVDVAVEDHEIKVKGPKGQLSFMMSDGISVTLQEGMLSVATINGSKK 60
           MSRIG+  I VP GV V V    +KVKGPKG+L   +S  + V ++EG++ V   +  ++
Sbjct: 1   MSRIGRLPIPVPKGVSVEVAPGRVKVKGPKGELEVPVSPEMRVVVEEGVVRVERPSDERR 60

Query: 61  ARAAWGMSRTMINNLFHGVTKGYERKLEISGVGCRAFMDGRNLKMSLGFSHDVLYTPLEG 120
            ++  G++RT+I N   GV++GY ++L I G+G RA + GR L++++GFSH V+  P EG
Sbjct: 61  HKSLHGLTRTLIANAVKGVSEGYSKELLIKGIGYRARLVGRALELTVGFSHPVVVEPPEG 120

Query: 121 ISIFVSKPTEIIVSGIDKQKVGHVAAEIRSYRSAEPYKGKGIRYSGEVIIRKEGKK 176
           I+  V +PT + VSGIDKQKVG VAA IR+ R    Y  KGI Y+GE +  K GK 
Sbjct: 121 ITFEVPEPTRVRVSGIDKQKVGQVAANIRAIRKPSAYHEKGIYYAGEPVRLKPGKA 176


>2zjr_E 50S ribosomal protein L6; ribosome, large ribosomal subunit,
           ribonucleoprotein, RNA-binding, rRNA-binding,
           tRNA-binding, methylation; 2.91A {Deinococcus
           radiodurans} SCOP: d.141.1.1 d.141.1.1 PDB: 1nwx_E*
           1xbp_E* 2zjp_E* 2zjq_E 1nwy_E 3cf5_E* 3dll_E* 1pnu_E
           1pny_E 1vor_H 1vou_H 1vow_H 1voy_H 1vp0_H
          Length = 185

 Score =  161 bits (407), Expect = 1e-40
 Identities = 80/176 (45%), Positives = 110/176 (62%)

Query: 1   MSRIGKKAIQVPLGVDVAVEDHEIKVKGPKGQLSFMMSDGISVTLQEGMLSVATINGSKK 60
           MSRIGK+ I VP GV V  +D   KVKGPKG+L+   +  ++V      L V   + ++K
Sbjct: 1   MSRIGKQPIAVPSGVTVNAQDGVFKVKGPKGELTVPYNTELTVRQDGDQLLVERPSDAQK 60

Query: 61  ARAAWGMSRTMINNLFHGVTKGYERKLEISGVGCRAFMDGRNLKMSLGFSHDVLYTPLEG 120
            RA  G++RT++ N   GV+ GY   LE+ GVG RA + G+ L+M++G+SH V+  P  G
Sbjct: 61  HRALHGLTRTLVANAVKGVSDGYTINLELRGVGFRAKLTGKALEMNIGYSHPVIIEPPAG 120

Query: 121 ISIFVSKPTEIIVSGIDKQKVGHVAAEIRSYRSAEPYKGKGIRYSGEVIIRKEGKK 176
           ++  V +PT I VSGIDKQ VG VAA +R  R  + Y GKG+R+ GE I  K GK 
Sbjct: 121 VTFAVPEPTRIDVSGIDKQLVGQVAANVRKVRKPDAYHGKGVRFVGEQIALKAGKA 176


>3jyw_H 60S ribosomal protein L9(A); eukaryotic ribosome, RACK1 protein,
           flexible fitting; 8.90A {Thermomyces lanuginosus} PDB:
           1s1i_H
          Length = 179

 Score =  143 bits (362), Expect = 2e-35
 Identities = 45/181 (24%), Positives = 80/181 (44%), Gaps = 17/181 (9%)

Query: 6   KKAIQVPLGVDVAVEDHEIKVKGPKGQLS--FMMSDGISVTLQEGMLSVATINGSKKARA 63
           ++ I+VP GV V+++   +KV GP+G L+      D     +   ++ VA  NG +K  A
Sbjct: 2   EQQIEVPEGVTVSIKSRIVKVVGPRGTLTKNLKHIDVTFTKVNNQLIKVAVHNGGRKHVA 61

Query: 64  AWGMSRTMINNLFHGVTKGYERKLEISGVGCRAFM--------DGRNLKMSLGFSHDVLY 115
           A    +++++N+  GVTKGY+ K+          +            ++  LG       
Sbjct: 62  ALRTVKSLVDNMITGVTKGYKYKMRYVYAHFPINVNIVEKDGAKFIEVRNFLGDKKIRNV 121

Query: 116 TPLEGISIFVS--KPTEIIVSGIDKQKVGHVAAEIRSYRSAEPYKGKGIR--YSGEVIIR 171
              +G++I  S     EI++SG   + V   AA++   +     + K IR    G  +  
Sbjct: 122 PVRDGVTIEFSTNVKDEIVLSGNSVEDVSQNAADL---QQICRVRNKDIRKFLDGIYVSH 178

Query: 172 K 172
           K
Sbjct: 179 K 179


>2zkr_e 60S ribosomal protein L9; protein-RNA complex, 60S ribosomal
           subunit, ribosomal protein/RNA complex; 8.70A {Canis
           familiaris}
          Length = 192

 Score =  134 bits (337), Expect = 1e-32
 Identities = 38/187 (20%), Positives = 73/187 (39%), Gaps = 17/187 (9%)

Query: 1   MSRIGKKAIQVPLGVDVAVEDHEIKVKGPKGQLSFMMS----DGISVTLQEGMLSVATIN 56
            + +  + + +P  VD+ ++   + VKGP+G L    +    +   +  ++  L V    
Sbjct: 2   KTILSNQTVDIPENVDITLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKWW 61

Query: 57  GSKKARAAWGMSRTMINNLFHGVTKGYERKLEISGVGCRAFMDGR--------NLKMSLG 108
           G++K  A      + + N+  GVT G+  K+          +  +           +   
Sbjct: 62  GNRKELATVRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGEK 121

Query: 109 FSHDVLYTPLEGISIFVSKPTEIIVSGIDKQKVGHVAAEIRSYRSAEPYKGKGIR--YSG 166
           +   V   P    S+  ++  E+I+ G D + V + AA I   + A   K K IR    G
Sbjct: 122 YIRRVRMRPGVACSVSQAQKDELILEGNDIELVSNSAALI---QQATTVKNKDIRKFLDG 178

Query: 167 EVIIRKE 173
             +  K 
Sbjct: 179 IYVSEKG 185


>1vq8_E 50S ribosomal protein L6P; 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: d.141.1.1 d.141.1.1
           PDB: 1vq4_E* 1vq5_E* 1vq6_E* 1vq7_E* 1s72_E* 1vq9_E*
           1vqk_E* 1vql_E* 1vqm_E* 1vqn_E* 1vqo_E* 1vqp_E* 1yhq_E*
           1yi2_E* 1yij_E* 1yit_E* 1yj9_E* 1yjn_E* 1yjw_E* 2otj_E*
           ...
          Length = 178

 Score =  122 bits (308), Expect = 4e-29
 Identities = 42/182 (23%), Positives = 78/182 (42%), Gaps = 12/182 (6%)

Query: 1   MSRIGKKAIQVPLGVDVAVEDHEIKVKGPKGQLSFMMSD-GISVTLQEGMLSVATINGSK 59
           M R+    +++P  VD   +  +I V+G  G ++  +    I V++    + + +   + 
Sbjct: 1   MPRV---ELEIPEDVDAEQDHLDITVEGDNGSVTRRLWYPDIDVSVDGDTVVIESDEDNA 57

Query: 60  KARAAWGMSRTMINNLFHGVTKGYERKLEISGVGC--RAFMDGRNLKMSLGFSHDVLY-T 116
           K  +  G  ++ I N+FHGVT+G+E  +E+       +  ++G  + +           T
Sbjct: 58  KTMSTIGTFQSHIENMFHGVTEGWEYGMEVFYSHFPMQVNVEGDEVVIENFLGEKAPRRT 117

Query: 117 PLEGISIFVSKPTEIIVSGIDKQKVGHVAAEIRSYRSAEPYKGKGIR--YSGEVIIRKEG 174
            + G +       E+ VSG D + VG  AA+I           K +R    G  I RK  
Sbjct: 118 TIHGDTDVEIDGEELTVSGPDIEAVGQTAADIEQLT---RINDKDVRVFQDGVYITRKPN 174

Query: 175 KK 176
           + 
Sbjct: 175 RG 176


>2cql_A OK/SW-CL.103, 60S ribosomal protein L9; N-terminal domain, alpha
          and beta (A+B), structural genomics, NPPSFA; NMR {Homo
          sapiens} SCOP: d.141.1.1
          Length = 100

 Score = 74.2 bits (182), Expect = 1e-14
 Identities = 21/90 (23%), Positives = 39/90 (43%), Gaps = 5/90 (5%)

Query: 1  MSRI-GKKAIQVPLGVDVAVEDHEIKVKGPKGQLSFMMS----DGISVTLQEGMLSVATI 55
          M  I   + + +P  VD+ ++   + VKGP+G L    +    +   +  ++  L V   
Sbjct: 8  MKTILSNQTVDIPENVDITLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKW 67

Query: 56 NGSKKARAAWGMSRTMINNLFHGVTKGYER 85
           G++K  A      + + N+  GVT G   
Sbjct: 68 WGNRKELATVRTICSHVQNMIKGVTLGSGP 97


>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 = 35.7 bits (82), Expect = 0.006
 Identities = 34/211 (16%), Positives = 70/211 (33%), Gaps = 84/211 (39%)

Query: 4   IGKKAIQV-------PLGVDVAVEDHEIKVKGPKGQLSFMMS-DGIS-VTLQEGM----- 49
           IG +  +        P  ++ ++E++E       G  S M+S   ++   +Q+ +     
Sbjct: 306 IGVRCYEAYPNTSLPPSILEDSLENNE-------GVPSPMLSISNLTQEQVQDYVNKTNS 358

Query: 50  -------LSVATING-----------S--------KKARAAWGMSRTMINNLFHGVTKGY 83
                  + ++ +NG           S        +KA+A  G+ ++ I   F       
Sbjct: 359 HLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRI--PFS------ 410

Query: 84  ERKLEISGVGCRAFMDGRNLKMSLGFSHDVLYTPLEGISIFVSKPTEIIVSGIDKQKVGH 143
           ERKL+ S          R L ++  F H    + L      +   +++I      + +  
Sbjct: 411 ERKLKFS---------NRFLPVASPF-H----SHL------LVPASDLI-----NKDLVK 445

Query: 144 VAAEIRSYRSAEP----YKGKGIRYSGEVII 170
                 +     P    + G  +R     I 
Sbjct: 446 NNVSFNAKDIQIPVYDTFDGSDLRVLSGSIS 476


>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 = 27.3 bits (59), Expect = 1.9
 Identities = 9/33 (27%), Positives = 16/33 (48%), Gaps = 5/33 (15%)

Query: 137 DKQKVGHVAAEIRSYR--SAEPYKGKGIRYSGE 167
           +KQ +  + A ++ Y   SA P     I+ + E
Sbjct: 18  EKQALKKLQASLKLYADDSA-P--ALAIKATME 47


>2jug_A TUBC protein; docking domain, dimer, nonribosomal peptide
          synthetase, tubulysin, ligase, phosphopantetheine,
          biosynthetic protein; NMR {Angiococcus disciformis}
          Length = 78

 Score = 25.9 bits (57), Expect = 4.9
 Identities = 7/22 (31%), Positives = 13/22 (59%)

Query: 13 LGVDVAVEDHEIKVKGPKGQLS 34
          LGV + VE   ++ + P G ++
Sbjct: 17 LGVRLWVEGERLRFQAPPGVMT 38


>3eq2_A Probable two-component response regulator; adaptor sigmas,
           signaling protein; 3.40A {Pseudomonas aeruginosa}
          Length = 394

 Score = 25.4 bits (55), Expect = 8.0
 Identities = 7/30 (23%), Positives = 13/30 (43%)

Query: 12  PLGVDVAVEDHEIKVKGPKGQLSFMMSDGI 41
           P+G+       +  ++ P      + SDGI
Sbjct: 309 PVGLFDDATYDDRVMELPPSFSLSLFSDGI 338


  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    0.135    0.381 

Gapped
Lambda     K      H
   0.267   0.0595    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,497,137
Number of extensions: 65934
Number of successful extensions: 128
Number of sequences better than 10.0: 1
Number of HSP's gapped: 116
Number of HSP's successfully gapped: 17
Length of query: 177
Length of database: 5,693,230
Length adjustment: 86
Effective length of query: 91
Effective length of database: 3,608,246
Effective search space: 328350386
Effective search space used: 328350386
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 (21.6 bits)
S2: 53 (24.5 bits)