RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780626|ref|YP_003065039.1| 30S ribosomal protein S20 [Candidatus Liberibacter asiaticus str. psy62] (90 letters) >2vqe_T 30S ribosomal protein S20; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: a.7.6.1 PDB: 1gix_W* 1hnw_T* 1hnx_T* 1hnz_T* 1hr0_T 1j5e_T 1jgo_W* 1jgp_W* 1jgq_W* 1ml5_W* 1yl4_W 2b64_T* 2b9m_T* 2b9o_T* 2f4v_T* 2ow8_u* 2qnh_u* 2uxb_T* 1fjg_T* 2uxd_T* ... Length = 106 Score = 73.2 bits (180), Expect = 1e-14 Identities = 33/90 (36%), Positives = 54/90 (60%) Query: 1 MANKDSAKKMIRKIARRTLINKSRRSSVRSFMRHANEAITFGKIEEATEACRKAESVIQK 60 SA K R+ +R L NK+++S++++ + A + GK EEA + RKAES+I K Sbjct: 6 PKRNLSALKRHRQSLKRRLRNKAKKSAIKTLSKKAVQLAQEGKAEEALKIMRKAESLIDK 65 Query: 61 AKSKGIFHGNAASRKVSRLSKRLKGILTSA 90 A H NAA+R+ SRL ++++ +L +A Sbjct: 66 AAKGSTLHKNAAARRKSRLMRKVRQLLEAA 95 >3ofo_T 30S ribosomal protein S20; protein biosynthesis, ribosomes, RNA, tRNA, transfer, eryThr ketolide, macrolide, antibiotic, EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 3fih_T* 2wwl_T 3ofp_T 2qal_T* 1p6g_T 1p87_T 2aw7_T 2avy_T 2i2u_T 2i2p_T* 2qan_T* 2qb9_T* 2qbb_T* 2qbd_T 2qbf_T 2qbh_T* 2qbj_T* 2qou_T* 2qow_T* 2qoy_T* ... Length = 85 Score = 71.6 bits (176), Expect = 4e-14 Identities = 24/84 (28%), Positives = 44/84 (52%) Query: 3 NKDSAKKMIRKIARRTLINKSRRSSVRSFMRHANEAITFGKIEEATEACRKAESVIQKAK 62 N SAKK + + N SRRS +R+F++ AI G A +A + + ++ + Sbjct: 1 NIKSAKKRAIQSEKARKHNASRRSMMRTFIKKVYAAIEAGDKAAAQKAFNEMQPIVDRQA 60 Query: 63 SKGIFHGNAASRKVSRLSKRLKGI 86 +KG+ H N A+R + L+ ++ + Sbjct: 61 AKGLIHKNKAARHKANLTAQINKL 84 >3bbn_T Ribosomal protein S20; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Arabidopsis thaliana} Length = 202 Score = 71.6 bits (175), Expect = 4e-14 Identities = 29/99 (29%), Positives = 44/99 (44%), Gaps = 9/99 (9%) Query: 1 MANKDSAKKMIRKIARRTLINKSRRSSVRSFMRHANEAITFGK---------IEEATEAC 51 DSA K R+ +R + NKS++S R+ M+ EA+ K I + Sbjct: 84 TKKADSAAKRARQAEKRRVYNKSKKSEARTRMKKVLEALEGLKKKTDAQADEIVTVEKLI 143 Query: 52 RKAESVIQKAKSKGIFHGNAASRKVSRLSKRLKGILTSA 90 +A S I KA H N +R+ SRL++R K + Sbjct: 144 GEAYSAIDKAVKVKALHKNTGARRKSRLARRKKAVEIHH 182 >3i1m_T 30S ribosomal protein S20; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_T* 3e1a_N 3e1c_N 1vs5_T 3i1o_T 3i1q_T 3i1s_T 3i1z_T 3i21_T 2qal_T* 1p6g_T 1p87_T 2aw7_T 2avy_T 2i2u_T 2i2p_T* 2qan_T* 2qb9_T* 2qbb_T* 2qbd_T ... Length = 87 Score = 68.1 bits (167), Expect = 4e-13 Identities = 26/86 (30%), Positives = 46/86 (53%) Query: 1 MANKDSAKKMIRKIARRTLINKSRRSSVRSFMRHANEAITFGKIEEATEACRKAESVIQK 60 MAN SAKK + + N SRRS +R+F++ AI G A +A + + ++ + Sbjct: 1 MANIKSAKKRAIQSEKARKHNASRRSMMRTFIKKVYAAIEAGDKAAAQKAFNEMQPIVDR 60 Query: 61 AKSKGIFHGNAASRKVSRLSKRLKGI 86 +KG+ H N A+R + L+ ++ + Sbjct: 61 QAAKGLIHKNKAARHKANLTAQINKL 86 >1uc2_A PH1602, hypothetical protein PH1602; structural genomics, unknown function; HET: SUC; 2.15A {Pyrococcus horikoshii} SCOP: d.261.1.1 Length = 481 Score = 27.3 bits (60), Expect = 0.85 Identities = 15/71 (21%), Positives = 28/71 (39%), Gaps = 6/71 (8%) Query: 9 KMIRKIARRTLINKSRRSSVRSFMRHANEAITFGKIEEATEACRKAESVIQKAKSKGIFH 68 + RK A R R + + + A EEA A + ++V++ GI Sbjct: 409 VLSRKAATRQYRGDRIRQELLNRGIYVRAASMRVVAEEAPGAYKNVDNVVKVVSEAGI-- 466 Query: 69 GNAASRKVSRL 79 ++ V+R+ Sbjct: 467 ----AKLVARM 473 >3ip4_A Glutamyl-tRNA(Gln) amidotransferase subunit A; multi protein complex, ligase, ATP-binding, nucleotide- binding; 1.90A {Staphylococcus aureus subsp} PDB: 2df4_A 2dqn_A* 2g5h_A 2g5i_A* 2f2a_A Length = 485 Score = 26.7 bits (58), Expect = 1.2 Identities = 9/70 (12%), Positives = 22/70 (31%), Gaps = 9/70 (12%) Query: 6 SAKKMIRKIARRTLINKSRRSSVRSFMRHANE------AITFGKIEEATEACRKAESVIQ 59 S + ++ I + + V+ E + E A + ++ + + Sbjct: 7 SVENLLTLIKDKKI---KPSDVVKDIYDAIEETDPTIKSFLALDKENAIKKAQELDELQA 63 Query: 60 KAKSKGIFHG 69 K + G G Sbjct: 64 KDQMDGKLFG 73 >2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio} Length = 307 Score = 25.7 bits (55), Expect = 2.7 Identities = 11/27 (40%), Positives = 14/27 (51%) Query: 38 AITFGKIEEATEACRKAESVIQKAKSK 64 AI KI EA E KAE ++ + K Sbjct: 1 AIAAQKISEAHEHIAKAEKYLKTSFMK 27 >1zbp_A Hypothetical protein VPA1032; alpha-beta protein, structural genomics, PSI, protein structure initiative; 2.40A {Vibrio parahaemolyticus rimd 2210633} SCOP: e.61.1.1 Length = 273 Score = 25.1 bits (54), Expect = 3.8 Identities = 6/23 (26%), Positives = 13/23 (56%) Query: 32 MRHANEAITFGKIEEATEACRKA 54 M A++ G++++A E +A Sbjct: 1 MTQWKNALSEGQLQQALELLIEA 23 >2epg_A Hypothetical protein TTHA1785; alpha-beta fold, structural genomics, NPPSFA; 2.10A {Thermus thermophilus HB8} Length = 487 Score = 25.0 bits (54), Expect = 4.2 Identities = 16/75 (21%), Positives = 28/75 (37%), Gaps = 14/75 (18%) Query: 9 KMIRKIARRTLINKSRRSSVRSFMRHANEAITFGK----IEEATEACRKAESVIQKAKSK 64 KM R A++ R ++ + + EE EA + V++ + Sbjct: 415 KMSRHQAKKVA----RERNLVKELAERGILVRAATRATVDEEMPEAYKDVSLVVEAVEGA 470 Query: 65 GIFHGNAASRKVSRL 79 GI +KV+RL Sbjct: 471 GI------GKKVARL 479 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 0.316 0.124 0.319 Gapped Lambda K H 0.267 0.0739 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 626,028 Number of extensions: 22744 Number of successful extensions: 116 Number of sequences better than 10.0: 1 Number of HSP's gapped: 113 Number of HSP's successfully gapped: 17 Length of query: 90 Length of database: 5,693,230 Length adjustment: 57 Effective length of query: 33 Effective length of database: 4,311,322 Effective search space: 142273626 Effective search space used: 142273626 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: 50 (23.0 bits)