RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780712|ref|YP_003065125.1| 30S ribosomal protein S16 [Candidatus Liberibacter asiaticus str. psy62] (116 letters) >3bn0_A 30S ribosomal protein S16; ribonucleoprotein, ribosome; 2.00A {Aquifex aeolicus} SCOP: d.27.1.1 Length = 112 Score = 119 bits (300), Expect = 1e-28 Identities = 37/115 (32%), Positives = 59/115 (51%), Gaps = 5/115 (4%) Query: 1 MTLKIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQ 60 M ++IRLA G K YRIVV +++SPR+GK+I+ LGT++P + E+++ Sbjct: 1 MAVRIRLAKFGRKHHPIYRIVVMDAKSPREGKYIDILGTYDPKRKV----LINVYPEKVK 56 Query: 61 HWMSKGAQPTDRILFFLDKAGLIKR-SPQNNPKKSQPKKKALERLASKKNADEHA 114 W+ KG + + R L G++K P+ K E+ SKK+ A Sbjct: 57 EWVLKGVELSHRAKAILWNHGILKEVVPEGYEMKRVGDYYVFEKRESKKSKGGEA 111 >3ofo_P 30S ribosomal protein S16; protein biosynthesis, ribosomes, RNA, tRNA, transfer, eryThr ketolide, macrolide, antibiotic, EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 1p6g_P 1p87_P* 1vs7_P* 2avy_P 2aw7_P 1vs5_P 2i2u_P 2i2p_P* 2qan_P* 2qb9_P* 2qbb_P* 2qbd_P 2qbf_P 2qbh_P* 2qbj_P* 2qou_P* 2qow_P* 2qoy_P* 2qp0_P* 2vho_P ... Length = 82 Score = 111 bits (279), Expect = 4e-26 Identities = 30/78 (38%), Positives = 51/78 (65%), Gaps = 1/78 (1%) Query: 3 LKIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHW 62 + IRLA G+K R Y++VVA+SR+ R+G+FIE++G +NP + E ++ +RI HW Sbjct: 2 VTIRLARHGAKKRPFYQVVVADSRNARNGRFIERVGFFNP-IASEKEEGTRLDLDRIAHW 60 Query: 63 MSKGAQPTDRILFFLDKA 80 + +GA +DR+ + + Sbjct: 61 VGQGATISDRVAALIKEV 78 >3mr8_P 30S ribosomal protein S16; ribosome, termination, RF1, amber, STOP UAG; 3.62A {Thermus thermophilus} PDB: 1pnx_P 1voq_P 1vos_P 1vov_P 1vox_P 1voz_P 1pns_P 3ms0_P 3fic_P* 1emw_A 1fjg_P* 1hnw_P* 1hnx_P* 1hnz_P* 1hr0_P 1i94_P* 1i95_P* 1i96_P* 1i97_P* 1ibk_P* ... Length = 83 Score = 106 bits (266), Expect = 2e-24 Identities = 38/83 (45%), Positives = 56/83 (67%), Gaps = 2/83 (2%) Query: 3 LKIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHW 62 +KIRLA GSK HYRIVV ++R RDGK+IEK+G ++P + L+ ++ ER ++W Sbjct: 2 VKIRLARFGSKHNPHYRIVVTDARRKRDGKYIEKIGYYDPRKTTPDWLK--VDVERARYW 59 Query: 63 MSKGAQPTDRILFFLDKAGLIKR 85 +S GAQPTD L +AG+ ++ Sbjct: 60 LSVGAQPTDTARRLLRQAGVFRQ 82 >1jgq_S 30S ribosomal protein S16; ribosome assembly, protein synthesis, LIFE; HET: 2MG H2U M2G OMC OMG YG PSU 5MC 7MG 5MU 1MA 4SU; 5.00A {Thermus thermophilus} SCOP: i.1.1.1 PDB: 1jgo_S* 1jgp_S* 1gix_S* 1ml5_S* 1emw_A 1fjg_P* 1hnw_P* 1hnx_P* 1hnz_P* 1hr0_P 1i94_P* 1i95_P* 1i96_P* 1i97_P* 1ibk_P* 1ibl_P* 1ibm_P 1j5e_P 1n32_P* 1n33_P* ... Length = 91 Score = 105 bits (265), Expect = 2e-24 Identities = 39/90 (43%), Positives = 56/90 (62%), Gaps = 5/90 (5%) Query: 3 LKIRLACGGSKSRH---HYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERI 59 +KIRLA GSK HYRIVV ++R RDGK+IEK+G ++P K P ++ ER Sbjct: 2 VKIRLARFGSKHNPHYPHYRIVVTDARRKRDGKYIEKIGYYDP--RKTTPDWLKVDVERA 59 Query: 60 QHWMSKGAQPTDRILFFLDKAGLIKRSPQN 89 ++W+S GAQPTD L +AG+ ++ + Sbjct: 60 RYWLSVGAQPTDTARRLLRQAGVFRQEARE 89 >3i1m_P 30S ribosomal protein S16; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1p6g_P 1p87_P* 1vs7_P* 2avy_P 2aw7_P 1vs5_P 2i2u_P 2i2p_P* 2qan_P* 2qb9_P* 2qbb_P* 2qbd_P 2qbf_P 2qbh_P* 2qbj_P* 2qou_P* 2qow_P* 2qoy_P* 2qp0_P* 2vho_P ... Length = 82 Score = 100 bits (251), Expect = 7e-23 Identities = 30/78 (38%), Positives = 51/78 (65%), Gaps = 1/78 (1%) Query: 3 LKIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHW 62 + IRLA G+K R Y++VVA+SR+ R+G+FIE++G +NP + E ++ +RI HW Sbjct: 2 VTIRLARHGAKKRPFYQVVVADSRNARNGRFIERVGFFNP-IASEKEEGTRLDLDRIAHW 60 Query: 63 MSKGAQPTDRILFFLDKA 80 + +GA +DR+ + + Sbjct: 61 VGQGATISDRVAALIKEV 78 >3bbn_P Ribosomal protein S16; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Length = 88 Score = 98.3 bits (245), Expect = 4e-22 Identities = 30/92 (32%), Positives = 49/92 (53%), Gaps = 5/92 (5%) Query: 3 LKIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHW 62 +K+RL G K R YRIV + RS R+G+ ++K+G ++P + +N I + Sbjct: 2 VKLRLKRCGRKQRAVYRIVAIDVRSRREGRDLQKVGFYDPIKSQT-----YLNVPAILDF 56 Query: 63 MSKGAQPTDRILFFLDKAGLIKRSPQNNPKKS 94 + KGAQPT+ + L +A + K N K + Sbjct: 57 LEKGAQPTETVYDILKRAEVFKEFRLNQTKFN 88 >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 = 33.4 bits (75), Expect = 0.013 Identities = 10/20 (50%), Positives = 15/20 (75%), Gaps = 2/20 (10%) Query: 97 KKKALERL-AS-KKNADEHA 114 +K+AL++L AS K AD+ A Sbjct: 18 EKQALKKLQASLKLYADDSA 37 >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 = 29.9 bits (67), Expect = 0.15 Identities = 20/83 (24%), Positives = 32/83 (38%), Gaps = 23/83 (27%) Query: 48 NPLRFTMNF-----ERIQHWMS--------KGAQPTDRIL----------FFLDKAGLIK 84 NP+ T++F +RI+ S G T++I F + GL+ Sbjct: 1668 NPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLS 1727 Query: 85 RSPQNNPKKSQPKKKALERLASK 107 + P + +K A E L SK Sbjct: 1728 ATQFTQPALTLMEKAAFEDLKSK 1750 >2ae0_X Membrane-bound lytic murein transglycosylase A; double-PSI beta-barrel, small mixed parallel/antiparallel six stranded beta barrel; 2.00A {Escherichia coli} SCOP: b.52.1.4 PDB: 2pjj_A 2pic_A 2pi8_A* 2gae_A Length = 345 Score = 25.2 bits (55), Expect = 4.2 Identities = 5/28 (17%), Positives = 11/28 (39%) Query: 51 RFTMNFERIQHWMSKGAQPTDRILFFLD 78 + + +Q W+ G + F +D Sbjct: 56 NQSNVYNAVQEWLRAGGDTRNMRQFGID 83 >2pbe_A AAD6, aminoglycoside 6-adenylyltransferase; NYSGXRC, aminoglycoside 6-adenyltransferase, PSI-2, structural genomics; 2.65A {Bacillus subtilis} SCOP: a.160.1.5 d.218.1.13 Length = 294 Score = 24.8 bits (54), Expect = 5.0 Identities = 7/55 (12%), Positives = 18/55 (32%), Gaps = 6/55 (10%) Query: 47 ENPLRFTMNF---ERIQHWMSKGAQPTDRILFFLDKAGLIKRSPQNNPKKSQPKK 98 E+ + + + + + ++L DK I N ++ K+ Sbjct: 97 EDGNKLDLTLIPIREAEDYFANNDGLV-KVLL--DKDSFINYKVTPNDRQYWIKR 148 >1kqn_A Nmnat, nicotinamide mononucleotide adenylyl transferase; nucleotidyltransferase superfamily; HET: NAD; 2.20A {Homo sapiens} SCOP: c.26.1.3 PDB: 1kqo_A* 1kr2_A* 1kku_A 1gzu_A* Length = 279 Score = 24.4 bits (52), Expect = 6.9 Identities = 6/28 (21%), Positives = 12/28 (42%) Query: 86 SPQNNPKKSQPKKKALERLASKKNADEH 113 SP + K + A R+ + A ++ Sbjct: 49 SPVGDAYKKKGLIPAYHRVIMAELATKN 76 >1gqp_A DOC1/APC10; cell cycle, APC10/DOC1, APC/cyclosome, ubiquitination, E3 ubiquitin ligase, beta sandwich, jelly roll; 2.2A {Saccharomyces cerevisiae} SCOP: b.18.1.9 Length = 221 Score = 23.9 bits (51), Expect = 8.7 Identities = 12/37 (32%), Positives = 17/37 (45%), Gaps = 1/37 (2%) Query: 34 IEKLGTWNPTLPKE-NPLRFTMNFERIQHWMSKGAQP 69 + L W P+ K NP+ F ++ W S G QP Sbjct: 55 VTHLALWKPSSFKLGNPVDFALDDNYDTFWQSDGGQP 91 >1u09_A Polyprotein; protein-DNA complex, RNA-dependent RNA polymerase, transferase; 1.91A {Foot-and-mouth disease virus c-s8c1} SCOP: e.8.1.4 PDB: 1wne_A 2e9r_X* 2e9t_A* 2e9z_A* 2ec0_A 2f8e_X* 2d7s_A* Length = 476 Score = 23.8 bits (51), Expect = 9.3 Identities = 5/46 (10%), Positives = 15/46 (32%), Gaps = 8/46 (17%) Query: 29 RDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSKGAQPTDRIL 74 R G + P + + E I + ++ ++++ Sbjct: 388 RHFHMDYGTGFYKPVMASK-------TLEAILSF-ARRGTIQEKLI 425 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 0.131 0.396 Gapped Lambda K H 0.267 0.0757 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 1,042,711 Number of extensions: 45193 Number of successful extensions: 130 Number of sequences better than 10.0: 1 Number of HSP's gapped: 123 Number of HSP's successfully gapped: 19 Length of query: 116 Length of database: 5,693,230 Length adjustment: 79 Effective length of query: 37 Effective length of database: 3,777,954 Effective search space: 139784298 Effective search space used: 139784298 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)