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)