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)