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)