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)