RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780329|ref|YP_003064742.1| 30S ribosomal protein S6 [Candidatus Liberibacter asiaticus str. psy62] (135 letters) >1cqm_A Ribosomal protein S6; alzheimer disease, oligomerization; 1.65A {Thermus thermophilus} SCOP: d.58.14.1 PDB: 1cqn_A 1qjh_A 1ris_A 1fka_F 1gix_I* 1hnw_F* 1hnx_F* 1hnz_F* 1hr0_F 1i94_F* 1i95_F* 1i96_F* 1i97_F* 1ibk_F* 1ibl_F* 1ibm_F 1j5e_F 1jgo_I* 1jgp_I* 1jgq_I* ... Length = 101 Score = 110 bits (276), Expect = 1e-25 Identities = 24/100 (24%), Positives = 49/100 (49%) Query: 1 MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYY 60 M+ YE +L ++ Q+ Q ++ G V V LG+R +AY I K+ + Y+ Sbjct: 1 MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVAILGLRRLAYPIAKDPQGYF 60 Query: 61 VFMNIASPPAAIHEMKRKMRIDENVLRSLTLLVDSHEQSP 100 ++ + P ++++ R++RI +NV R + + + Sbjct: 61 LWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLAN 100 >3ofo_F 30S ribosomal protein S6; protein biosynthesis, ribosomes, RNA, tRNA, transfer, eryThr ketolide, macrolide, antibiotic, EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 3fih_F* 3iy8_F 2wwl_F 3ofp_F 2gy9_F 2gyb_F Length = 100 Score = 107 bits (269), Expect = 8e-25 Identities = 31/100 (31%), Positives = 53/100 (53%), Gaps = 1/100 (1%) Query: 1 MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYY 60 M+ YE VF++ D S +Q+ I +Y + I G++ + + G R +AY I K KA+Y Sbjct: 1 MRHYEIVFMVHPDQS-EQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHY 59 Query: 61 VFMNIASPPAAIHEMKRKMRIDENVLRSLTLLVDSHEQSP 100 V MN+ +P I E++ R ++ V+RS+ + Sbjct: 60 VLMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEA 99 >3i1m_F 30S ribosomal protein S6; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1p6g_F 1p87_F* 1vs7_F* 2avy_F 2aw7_F 1vs5_F 2i2u_F 2i2p_F* 2qan_F* 2qb9_F* 2qbb_F* 2qbd_F 2qbf_F 2qbh_F* 2qbj_F* 2qou_F* 2qow_F* 2qoy_F* 2qp0_F* 2vho_F ... Length = 135 Score = 99.6 bits (248), Expect = 2e-22 Identities = 33/126 (26%), Positives = 59/126 (46%), Gaps = 1/126 (0%) Query: 1 MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYY 60 M+ YE VF++ D S Q + I +Y + I G++ + + G R +AY I K KA+Y Sbjct: 1 MRHYEIVFMVHPDQSEQ-VPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHY 59 Query: 61 VFMNIASPPAAIHEMKRKMRIDENVLRSLTLLVDSHEQSPTLTIQRHDRDDRNDRFPRDR 120 V MN+ +P I E++ R ++ V+RS+ + + ++ D + Sbjct: 60 VLMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANE 119 Query: 121 NVDRKQ 126 D + Sbjct: 120 TADDAE 125 >3bbn_F Ribosomal protein S6; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Length = 168 Score = 98.5 bits (245), Expect = 4e-22 Identities = 22/106 (20%), Positives = 48/106 (45%), Gaps = 9/106 (8%) Query: 1 MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKA-- 58 ++ YE + +LR D++ + +Y+ L+ G V G+ +AY I++ KA Sbjct: 62 LRQYETMAVLRPDMTEDERLTLTQKYEELLVAGGAMYVEVFNRGVIPLAYSIKRKNKAGE 121 Query: 59 -------YYVFMNIASPPAAIHEMKRKMRIDENVLRSLTLLVDSHE 97 Y+ + P +I ++ + D++V+RS + + + Sbjct: 122 TNNYLDGIYLLFTYFTKPESISPLEAALVTDDDVIRSSSFKIRKRK 167 >1vmb_A 30S ribosomal protein S6; TM0603, structural genomics, JCSG, protein structure initiative, PSI, joint center for structural genomics; 1.70A {Thermotoga maritima} SCOP: d.58.14.1 Length = 140 Score = 94.6 bits (235), Expect = 7e-21 Identities = 20/116 (17%), Positives = 52/116 (44%), Gaps = 1/116 (0%) Query: 1 MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQEN-GGEVRLVNELGMRTIAYRIRKNRKAY 59 ++YE +F++ ++ ++ ++ + + + +I+E G++ V +GMR AY I+K + Sbjct: 18 ERIYESMFIIAPNVPEEERENLVERVKKIIEERVKGKIDKVERMGMRKFAYEIKKFNEGD 77 Query: 60 YVFMNIASPPAAIHEMKRKMRIDENVLRSLTLLVDSHEQSPTLTIQRHDRDDRNDR 115 Y + + E++ R+ ++R T E+ + + + Sbjct: 78 YTVIYFRCDGQNLQELENFYRVTPEIIRWQTFRRFDLEKKERKAQREKAAAEATES 133 >2j5a_A 30S ribosomal protein S6; ribonucleoprotein, RNA-binding, rRNA-binding, protein folding; 2.3A {Aquifex aeolicus} SCOP: d.58.14.1 Length = 110 Score = 91.5 bits (227), Expect = 6e-20 Identities = 29/101 (28%), Positives = 54/101 (53%), Gaps = 1/101 (0%) Query: 1 MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYY 60 ++ YE VF ++ +S +++K Q + I++ GGE+ + GMR +AY I+K A Y Sbjct: 7 LRYYETVFAVKPTLSEEEMKKKFEQVKEFIKQKGGEILYEEDWGMRQLAYPIQKFNNARY 66 Query: 61 VFMNI-ASPPAAIHEMKRKMRIDENVLRSLTLLVDSHEQSP 100 + P +E+ +++IDE+V+R L + + E Sbjct: 67 FLVQFKTENPQLPNELDFQLKIDEDVIRWLNIQIKESEVKK 107 >2kjw_A TS9, 30S ribosomal protein S6; S6 permutant, solution structure, backbone dynamics, folding, ribonucleoprotein, RNA-binding, rRNA-binding; NMR {Thermus thermophilus} Length = 96 Score = 57.5 bits (139), Expect = 9e-10 Identities = 16/54 (29%), Positives = 24/54 (44%) Query: 1 MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRK 54 YE +L ++ Q+ Q ++ G V V ELG+R +AY I K Sbjct: 43 PGRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAK 96 >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 = 0.003 Identities = 13/75 (17%), Positives = 28/75 (37%), Gaps = 21/75 (28%) Query: 82 DENVLRSLTLL----VDSHEQSPTLTIQ---RHDRDDRNDRFP----RDRNVDRKQ---- 126 +V +++T+L V +E P ++ D + N+ P N+ ++Q Sbjct: 293 FVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDY 352 Query: 127 ------HVSEEKPLS 135 H+ K + Sbjct: 353 VNKTNSHLPAGKQVE 367 Score = 30.7 bits (69), Expect = 0.13 Identities = 14/69 (20%), Positives = 30/69 (43%), Gaps = 18/69 (26%) Query: 13 DISSQQIKDTIGQY-QSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAA 71 +++ +Q++D + + L E+ LVN G KN V ++ PP + Sbjct: 343 NLTQEQVQDYVNKTNSHLPAGKQVEISLVN--G--------AKN----LV---VSGPPQS 385 Query: 72 IHEMKRKMR 80 ++ + +R Sbjct: 386 LYGLNLTLR 394 >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 = 31.9 bits (71), Expect = 0.049 Identities = 8/28 (28%), Positives = 14/28 (50%), Gaps = 6/28 (21%) Query: 82 DENVLR----SLTLLVDSHEQSPTLTIQ 105 ++ L+ SL L D + +P L I+ Sbjct: 18 EKQALKKLQASLKLYAD--DSAPALAIK 43 >2bkk_A Aminoglycoside 3'-phosphotransferase; transferase/peptide, transferase/designed protein complex, CO-crystallization, inhibitor design; HET: ADP; 2.15A {Enterococcus faecalis} PDB: 1j7l_A* 1j7i_A* 1j7u_A* 3h8p_A* 1l8t_A* 2b0q_A* Length = 264 Score = 25.4 bits (54), Expect = 4.1 Identities = 11/66 (16%), Positives = 27/66 (40%), Gaps = 9/66 (13%) Query: 16 SQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEM 75 S ++K I +Y+S+ G V Y++ + Y+ M + +++ Sbjct: 7 SPELKKLIEKYRSVKDTEGMSPAKV---------YKLVGENENLYLKMTDSRYKGTTYDV 57 Query: 76 KRKMRI 81 +R+ + Sbjct: 58 EREKDM 63 >2h84_A Steely1; thiolase-fold, type III polyketide synthase, PKS, chalcone- stilbene synthase superfamily, type I PKS; HET: P6G; 2.90A {Dictyostelium discoideum AX4} Length = 374 Score = 24.5 bits (52), Expect = 8.6 Identities = 2/21 (9%), Positives = 7/21 (33%) Query: 66 ASPPAAIHEMKRKMRIDENVL 86 AS + ++ + + Sbjct: 335 ASVIFVMDHARKSKSLPTYSI 355 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 0.320 0.135 0.375 Gapped Lambda K H 0.267 0.0690 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 1,080,340 Number of extensions: 45278 Number of successful extensions: 121 Number of sequences better than 10.0: 1 Number of HSP's gapped: 116 Number of HSP's successfully gapped: 14 Length of query: 135 Length of database: 5,693,230 Length adjustment: 82 Effective length of query: 53 Effective length of database: 3,705,222 Effective search space: 196376766 Effective search space used: 196376766 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 (21.8 bits) S2: 51 (23.5 bits)