RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780145|ref|YP_003064558.1| 50S ribosomal protein L10 [Candidatus Liberibacter asiaticus str. psy62] (172 letters) >2j01_J 50S ribosomal protein L10; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} PDB: 2j03_J 3d5b_J 3d5d_J Length = 173 Score = 119 bits (300), Expect = 3e-28 Identities = 42/173 (24%), Positives = 90/173 (52%), Gaps = 4/173 (2%) Query: 1 MNRQGKSVEISELSKIFS-SSGSIVVAHYKGISVAQIKDLRKKMREAGGGVKVAKNRLVK 59 M + ++ L + + GS + +Y+G+ + LR+ +++ G + VAKN L++ Sbjct: 1 MPNKRNVELLATLKENLERAQGSFFLVNYQGLPAKETHALRQALKQNGARLFVAKNTLIR 60 Query: 60 IAIRDTSIRGISDLFVGQSLIVYSDSPVIAPKISVSFSNDNNEFR--VLGGVVEKGVLNQ 117 +A+++ + + D G S +V+ + PV A K V F+ N + V G+++ +L Sbjct: 61 LALKELGLPEL-DGLQGPSAVVFYEDPVAAAKTLVQFAKSNPKGIPQVKSGLLQGQILTA 119 Query: 118 DSIKQIASLPDLEGIRAGIISAIQSNATRLVRLLGTPQTQVVRAISAFVDKNQ 170 ++ +A LP ++ +RA ++ +Q+ LV +LG ++V + A+ +K Sbjct: 120 KDVEALAELPTMDELRAELVGVLQAPMAELVGVLGGVARELVGILEAYAEKKA 172 >1zav_A 50S ribosomal protein L10; ribosome structure and function, L10-L12 complex structure, L10E structure, L7/12 ribosomal stalk; 1.90A {Thermotoga maritima} SCOP: d.58.62.1 PDB: 1zaw_A 1zax_A Length = 180 Score = 119 bits (299), Expect = 4e-28 Identities = 49/178 (27%), Positives = 90/178 (50%), Gaps = 7/178 (3%) Query: 1 MNRQGKSVEISELSKIFSSSGSIVVAHYKGISVAQIKDLRKKMREA---GGGVKVAKNRL 57 + RQ K + + E+S+IF + I+ A + G +VA + +LR ++RE G +V KN L Sbjct: 3 LTRQQKELIVKEMSEIFKKTSLILFADFLGFTVADLTELRSRLREKYGDGARFRVVKNTL 62 Query: 58 VKIAIRDTSIRGISDLFVGQSLIVYSDS--PVIAPKISVSFSND--NNEFRVLGGVVEKG 113 + +A+++ G + G + ++Y PV A KI +F D + R+ GG +E Sbjct: 63 LNLALKNAEYEGYEEFLKGPTAVLYVTEGDPVEAVKIIYNFYKDKKADLSRLKGGFLEGK 122 Query: 114 VLNQDSIKQIASLPDLEGIRAGIISAIQSNATRLVRLLGTPQTQVVRAISAFVDKNQQ 171 + ++ IA LP E + A ++ +++ T LV L +V ++A +K + Sbjct: 123 KFTAEEVENIAKLPSKEELYAMLVGRVKAPITGLVFALSGILRNLVYVLNAIKEKKSE 180 >1vq8_G Acidic ribosomal protein P0 homolog; 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: j.84.1.1 PDB: 1k73_I* 1k8a_I* 1k9m_I* 1kc8_I* 1kd1_I* 1kqs_G* 1m1k_I* 1m90_I* 1n8r_I* 1nji_I* 1q7y_I* 1q81_I* 1q82_I* 1q86_I* 1qvf_G 1qvg_G 1s72_G* 1vq4_G* 1vq5_G* 1vq6_G* ... Length = 348 Score = 74.9 bits (184), Expect = 8e-15 Identities = 19/98 (19%), Positives = 46/98 (46%), Gaps = 4/98 (4%) Query: 3 RQGKSVEISELSKIFSSSGSIVVAHYKGISVAQIKDLRKKMREAGGGVKVAKNRLVKIAI 62 + K E+ + ++ S S+ V + GI Q++D+R+ + ++V++N L++ A+ Sbjct: 13 PEWKQEEVDAIVEMIESYESVGVVNIAGIPSRQLQDMRRDLHG-TAELRVSRNTLLERAL 71 Query: 63 R--DTSIRGISDLFVGQSLIVY-SDSPVIAPKISVSFS 97 D + ++ GQ ++ D+P + + Sbjct: 72 DDVDDGLEDLNGYITGQVGLIGTDDNPFSLFQELEASK 109 >3a1y_G Acidic ribosomal protein P0; stalk, ribosomal protein,helix SPIN, ribonucleoprotein; 2.13A {Pyrococcus horikoshii} Length = 284 Score = 71.8 bits (176), Expect = 7e-14 Identities = 20/100 (20%), Positives = 46/100 (46%), Gaps = 8/100 (8%) Query: 1 MNRQGKSVEISELSKIFSSSGSIVVAHYKGISVAQIKDLRKKMREAGGGVKVAKNRLVKI 60 + K E+ EL+K+ S I + + + +R+ +RE GG ++V++N L+++ Sbjct: 3 HVAEWKKKEVEELAKLIKSYPVIALVDVSSMPAYPLSQMRRLIRENGGLLRVSRNTLIEL 62 Query: 61 AIRDTS-------IRGISDLFVGQSLIVY-SDSPVIAPKI 92 AI+ + + + + + I+ + +P K Sbjct: 63 AIKKAAKELGKPELEKLVEYIDRGAGILVTNMNPFKLYKF 102 >3jsy_A Acidic ribosomal protein P0 homolog; ribonucleoprotein; 1.60A {Methanocaldococcus jannaschii} Length = 213 Score = 63.1 bits (153), Expect = 4e-11 Identities = 13/93 (13%), Positives = 40/93 (43%), Gaps = 8/93 (8%) Query: 6 KSVEISELSKIFSSSGSIVVAHYKGISVAQIKDLRKKMREAGGGVKVAKNRLVKIAIRDT 65 K E+ L + S + + + Q++++R K+R+ +++++N L+ A+++ Sbjct: 5 KIEEVKTLKGLIKSKPVVAIVDMMDVPAPQLQEIRDKIRD-KVKLRMSRNTLIIRALKEA 63 Query: 66 -------SIRGISDLFVGQSLIVYSDSPVIAPK 91 + +++ + I+ +D Sbjct: 64 AEELNNPKLAELANYVERGAAILVTDMNPFKLY 96 >3jyw_8 60S ribosomal protein LP0; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} Length = 118 Score = 62.6 bits (152), Expect = 4e-11 Identities = 21/94 (22%), Positives = 41/94 (43%), Gaps = 6/94 (6%) Query: 3 RQGKSVEISELSKIFSSSGSIVVAHYKGISVAQIKDLRKKMREAGGGVKVAKNRLVKIAI 62 R+ K+ ++L + S+ V +S Q+ ++RK++R V + KN +V+ AI Sbjct: 3 REKKAEYFAKLREYLEEYKSLFVVGVDNVSSQQMHEVRKELRG-RAVVLMGKNTMVRRAI 61 Query: 63 RDTS-----IRGISDLFVGQSLIVYSDSPVIAPK 91 R + G V+++ P+ K Sbjct: 62 RGFLSDLPDFEKLLPFVKGYVGFVFTNEPLTEIK 95 >2zkr_g 60S acidic ribosomal protein P0; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Length = 317 Score = 57.6 bits (139), Expect = 2e-09 Identities = 13/86 (15%), Positives = 31/86 (36%), Gaps = 6/86 (6%) Query: 6 KSVEISELSKIFSSSGSIVVAHYKGISVAQIKDLRKKMREAGGGVKVAKNRLVKIAIRDT 65 KS ++ ++ + + Q++ +R +R V + KN +++ AIR Sbjct: 10 KSNYFLKIIQLLDDYPKCFIVGADNVGSKQMQQIRMSLRG-KAVVLMGKNTMMRKAIRGH 68 Query: 66 S-----IRGISDLFVGQSLIVYSDSP 86 + + G V++ Sbjct: 69 LENNPALEKLLPHIRGNVGFVFTKED 94 >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 = 0.029 Identities = 8/21 (38%), Positives = 14/21 (66%), Gaps = 3/21 (14%) Query: 77 Q-SLIVYSD--SPVIAPKISV 94 Q SL +Y+D +P +A K ++ Sbjct: 26 QASLKLYADDSAPALAIKATM 46 >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 = 29.5 bits (66), Expect = 0.42 Identities = 17/127 (13%), Positives = 32/127 (25%), Gaps = 25/127 (19%) Query: 63 RDT---SIRGISDLFVGQSLIVYSDSPVIAPKISVSF---------SNDNNEFR-VLGGV 109 ++ + ++ F D P ++ F + +F VL Sbjct: 34 QEQFNKILPEPTEGFAAD------DEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLC 87 Query: 110 V---EKGVLNQDSIKQ-IASLPDLEGIRAGIISAIQSNATRLVRLLGTPQTQVVRAISAF 165 + E L + I A L + N + P + SA Sbjct: 88 LTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSN--SAL 145 Query: 166 VDKNQQG 172 +G Sbjct: 146 FRAVGEG 152 Score = 28.8 bits (64), Expect = 0.64 Identities = 31/167 (18%), Positives = 49/167 (29%), Gaps = 83/167 (49%) Query: 7 SVEISELSKIFSSSGSIVVAHYK------GISVAQIKDLRKKMREAGG---GVKVAKNRL 57 S+ IS I G I +AHY G + + LR ++ A G G+ A Sbjct: 233 SIPIS-CPLI----GVIQLAHYVVTAKLLGFTPGE---LRSYLKGATGHSQGLVTA---- 280 Query: 58 VKIAIRDT---------------------------------------------------S 66 V IA D+ S Sbjct: 281 VAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLS 340 Query: 67 IRGISDLFVGQSLIVYSDSPVIAP---KISVSFSN--DNNEFRVLGG 108 I ++ V Q + ++S + P ++ +S N N V+ G Sbjct: 341 ISNLTQEQV-QDYVNKTNSHL--PAGKQVEISLVNGAKN--L-VVSG 381 Score = 27.2 bits (60), Expect = 2.2 Identities = 15/88 (17%), Positives = 28/88 (31%), Gaps = 24/88 (27%) Query: 80 IVYSDSPVIAPKISVS--FSN-DNNEFR---VLGGVVEKGVLNQDSIKQIASL-----PD 128 + + P K S S F + + GG +G D +++ L Sbjct: 130 RIMAKRPF--DKKSNSALFRAVGEGNAQLVAIFGG---QGN-TDDYFEELRDLYQTYHVL 183 Query: 129 LEGIRAGIISAIQSNATRLVRLLGTPQT 156 + + I+ +A L L+ T Sbjct: 184 VGDL-------IKFSAETLSELIRTTLD 204 >1bgx_T TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhibition, helix-coil dynamics, inhibitor design, complex (polymerase/inhibitor); 2.30A {Thermus aquaticus} SCOP: a.60.7.1 c.120.1.2 c.55.3.5 e.8.1.1 PDB: 1cmw_A 1tau_A* 1taq_A* 1ktq_A* 5ktq_A* 3ktq_A* 1jxe_A* 4ktq_A* 1qtm_A* 2ktq_A* 1qss_A* 1qsy_A* Length = 832 Score = 28.0 bits (61), Expect = 1.1 Identities = 3/42 (7%), Positives = 15/42 (35%) Query: 30 GISVAQIKDLRKKMREAGGGVKVAKNRLVKIAIRDTSIRGIS 71 I + + ++ ++ V+ + ++ R + + Sbjct: 683 AIPYEEAQAFIERYFQSFPKVRAWIEKTLEEGRRRGYVETLF 724 >3cf4_A Acetyl-COA decarbonylase/synthase alpha subunit; methanomicrobia, iron-nikel-sulfur, 4Fe-NI-4S, oxidoreductase; 2.00A {Methanosarcina barkeri} Length = 807 Score = 26.1 bits (57), Expect = 4.1 Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 1/53 (1%) Query: 24 VVAHYKGISVAQIKDLRKKMREAGGGVKVAKNRLVKIAIRDTSIRGISDLFVG 76 ++ + I+ QI + + MR G V A+ R + + + GI +G Sbjct: 471 ILNVIEKIAQKQIAEEKGLMRAGRGQVSDAEIRAEGLNLVMGTTPGII-AIIG 522 >2egz_A 3-dehydroquinate dehydratase; aquifex aeolicus VF5, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: TLA; 1.75A {Aquifex aeolicus} PDB: 2ysw_A Length = 219 Score = 26.1 bits (57), Expect = 4.8 Identities = 11/85 (12%), Positives = 25/85 (29%), Gaps = 15/85 (17%) Query: 9 EISELSKIFSSSGSIVVAHY----KGISVAQIKDLRKKMREAGGGVKVAKNRLVKIAIRD 64 + +L I +G ++ Y I+++ ++ GG K+A Sbjct: 96 LLVKLYNITKEAGKKLIISYHNFELTPPNWIIREVLREGYRYGGIPKIA----------- 144 Query: 65 TSIRGISDLFVGQSLIVYSDSPVIA 89 D+ + + I Sbjct: 145 VKANSYEDVARLLCISRQVEGEKIL 169 >2tpt_A Thymidine phosphorylase; transferase, salvage pathway; 2.60A {Escherichia coli K12} SCOP: a.46.2.1 c.27.1.1 d.41.3.1 PDB: 1azy_A 1tpt_A 1otp_A Length = 440 Score = 25.5 bits (55), Expect = 5.8 Identities = 5/43 (11%), Positives = 17/43 (39%), Gaps = 1/43 (2%) Query: 21 GSIVVAHY-KGISVAQIKDLRKKMREAGGGVKVAKNRLVKIAI 62 ++ + + +++ + L MR++G + L + Sbjct: 40 AALAMTIFFHDMTMPERVSLTMAMRDSGTVLDWKSLHLNGPIV 82 >3f7c_A Protein of unknown function (DUF416); YP_958225.1, structural genomics, joint center for structural genomics, JCSG; HET: CIT; 2.00A {Marinobacter aquaeolei VT8} Length = 200 Score = 25.5 bits (56), Expect = 7.1 Identities = 5/23 (21%), Positives = 10/23 (43%) Query: 25 VAHYKGISVAQIKDLRKKMREAG 47 + +Y+ A + +LR G Sbjct: 168 LYYYRTPKEAFLAELRAGAANDG 190 >1vqu_A Anthranilate phosphoribosyltransferase 2; 17130499, structural genomics, joint center for structural genomics, JCSG, protein structure initiative; 1.85A {Nostoc SP} Length = 374 Score = 25.3 bits (54), Expect = 7.2 Identities = 9/48 (18%), Positives = 19/48 (39%), Gaps = 1/48 (2%) Query: 21 GSIVVAHY-KGISVAQIKDLRKKMREAGGGVKVAKNRLVKIAIRDTSI 67 G+I+ A KG+S ++ + + ++ + I SI Sbjct: 63 GAILTALNFKGVSADELTGMAEVLQSQSKMGTGENYSQLPITNSPFSI 110 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 0.133 0.349 Gapped Lambda K H 0.267 0.0614 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 1,308,905 Number of extensions: 57892 Number of successful extensions: 212 Number of sequences better than 10.0: 1 Number of HSP's gapped: 206 Number of HSP's successfully gapped: 23 Length of query: 172 Length of database: 5,693,230 Length adjustment: 86 Effective length of query: 86 Effective length of database: 3,608,246 Effective search space: 310309156 Effective search space used: 310309156 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 (21.6 bits) S2: 53 (24.4 bits)