RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780247|ref|YP_003064660.1| 30S ribosomal protein S8 [Candidatus Liberibacter asiaticus str. psy62] (129 letters) >1i6u_A 30S ribosomal protein S8P; protein-RNA interactions, ribosome, RNA, X-RAY crystallography; 2.60A {Methanocaldococcus jannaschii} SCOP: d.140.1.1 Length = 130 Score = 138 bits (349), Expect = 4e-34 Identities = 40/127 (31%), Positives = 61/127 (48%), Gaps = 4/127 (3%) Query: 4 LGDMLTRIRNANLRYKPSVVI-PFSRLHARVLDVLKTEGYIGEYCEIDAGKGRIQLKVDL 62 L + L I N K V I P S+L RVL V++ GYIGE+ I+ G+ I + Sbjct: 7 LANALNHISNCERVGKKVVYIKPASKLIGRVLKVMQDNGYIGEFEFIEDGRAGIFKVELI 66 Query: 63 KYHNGASVIRKIDCVSKPGRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQARECKVGG 122 N I+ V K G + GI+IV+T++GVM+ +A++ +GG Sbjct: 67 GKINKCGAIKPRFPVKKFGYEKFEKRYLPA---RDFGILIVSTTQGVMSHEEAKKRGLGG 123 Query: 123 EVLCSVF 129 +L V+ Sbjct: 124 RLLAYVY 130 >2vqe_H 30S ribosomal protein S8, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: d.140.1.1 PDB: 1eg0_E* 1fka_H 1gix_K* 1hnw_H* 1hnx_H* 1hnz_H* 1hr0_H 1ibk_H* 1ibl_H* 1ibm_H 1j5e_H 1jgo_K* 1jgp_K* 1jgq_K* 1ml5_K* 1n32_H* 1n33_H* 1n34_H 1n36_H 1pns_H ... Length = 138 Score = 136 bits (344), Expect = 1e-33 Identities = 54/133 (40%), Positives = 74/133 (55%), Gaps = 7/133 (5%) Query: 4 LGDMLTRIRNANLRYKPSVVIPFSRLHARVLDVLKTEGYIGEYCEIDAGK-------GRI 56 + DMLTRIRNA YK S +P SR +L +L EG+I Y +D + Sbjct: 6 IADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLRVYLKY 65 Query: 57 QLKVDLKYHNGASVIRKIDCVSKPGRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQAR 116 + VI I +SKPGRR+Y K+IP+V GLGI I++TSKGV+ +AR Sbjct: 66 GPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLTDREAR 125 Query: 117 ECKVGGEVLCSVF 129 + VGGE++C V+ Sbjct: 126 KLGVGGELICEVW 138 >1s03_H 30S ribosomal protein S8; protein-RNA complex, SPC operon, transcription/RNA complex; 2.70A {Escherichia coli} SCOP: d.140.1.1 PDB: 1p6g_H 1p87_H 2avy_H 2aw7_H 2i2p_H 2i2u_H 2qal_H* 2qan_H* 2qb9_H* 2qbb_H* 2qbd_H 2qbf_H 2qbh_H* 2qbj_H* 2qou_H* 2qow_H* 2qoy_H* 2qp0_H* 2vho_H 2vhp_H ... Length = 129 Score = 134 bits (338), Expect = 7e-33 Identities = 52/125 (41%), Positives = 77/125 (61%), Gaps = 2/125 (1%) Query: 4 LGDMLTRIRNANLRYKPSVVIPFSRLHARVLDVLKTEGYIGEYCEIDAGKGRIQLKVDLK 63 + DMLTRIRN K +V +P S+L + +VLK EG+I ++ K + ++ LK Sbjct: 6 IADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPEL--ELTLK 63 Query: 64 YHNGASVIRKIDCVSKPGRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQARECKVGGE 123 Y G +V+ I VS+PG R+Y ++P+V GLGI +V+TSKGVM AR+ +GGE Sbjct: 64 YFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAGLGGE 123 Query: 124 VLCSV 128 ++C V Sbjct: 124 IICYV 128 >3bbn_H Ribosomal protein S8; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Length = 134 Score = 131 bits (331), Expect = 5e-32 Identities = 39/129 (30%), Positives = 75/129 (58%), Gaps = 3/129 (2%) Query: 4 LGDMLTRIRNANLRYKPSVVIPFSRLHARVLDVLKTEGYIGEYCEIDAG-KGRIQLKVDL 62 + D++T IRNA++ K +V I + + ++ +L EG+I + K + L + Sbjct: 6 IADIITCIRNADMNRKGTVRIVSTNITENIVKILLREGFIENARKHQERNKYFLVLTLRH 65 Query: 63 KYHNGASVIR--KIDCVSKPGRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQARECKV 120 + + + + VS+PG R+YS+++ IP++ G+GI I++TS+G+M +AR + Sbjct: 66 RRNKKGPYLNTFHLKRVSRPGLRIYSNYQRIPRILGGMGIAILSTSRGIMTDREARLEGI 125 Query: 121 GGEVLCSVF 129 GGE+LC ++ Sbjct: 126 GGEILCYIW 134 >1sei_A Ribosomal protein S8; prokaryotic, rRNA-binding; 1.90A {Geobacillus stearothermophilus} SCOP: d.140.1.1 Length = 130 Score = 129 bits (326), Expect = 2e-31 Identities = 50/125 (40%), Positives = 78/125 (62%), Gaps = 1/125 (0%) Query: 4 LGDMLTRIRNANLRYKPSVVIPFSRLHARVLDVLKTEGYIGEYCEIDAGKGRIQLKVDLK 63 + DMLT IRNAN+ + +P S++ + ++LK EG+I +Y I+ K I L++ LK Sbjct: 6 IADMLTAIRNANMVRHEKLEVPASKIKREIAEILKREGFIRDYEYIEDNKQGI-LRIFLK 64 Query: 64 YHNGASVIRKIDCVSKPGRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQARECKVGGE 123 Y VI + +SKPG R+Y ++P+V NGLGI I++TS+GV+ +AR+ GGE Sbjct: 65 YGPNERVITGLKRISKPGLRVYVKAHEVPRVLNGLGIAILSTSQGVLTDKEARQKGTGGE 124 Query: 124 VLCSV 128 ++ V Sbjct: 125 IIAYV 129 >2zkq_h 40S ribosomal protein S15AE; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_H Length = 130 Score = 108 bits (270), Expect = 5e-25 Identities = 39/130 (30%), Positives = 57/130 (43%), Gaps = 4/130 (3%) Query: 1 MSCLGDMLTRIRNANLRYKPSVVI-PFSRLHARVLDVLKTEGYIGEYCEIDAGKGRIQLK 59 M+ L D L I NA R K V+I P S++ R L V+ GYIGE+ ID + + Sbjct: 4 MNVLADALKSINNAEKRGKRQVLIRPCSKVIVRFLTVMMKHGYIGEFEIIDDHRAGKIVV 63 Query: 60 VDLKYHNGASVIRKIDCVSKPGRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQARECK 119 N VI V + + + G +++TTS G+M +AR Sbjct: 64 NLTGRLNKCGVISPRFDVQLKDLEKWQNNLLPSR---QFGFIVLTTSAGIMDHEEARRKH 120 Query: 120 VGGEVLCSVF 129 GG++L F Sbjct: 121 TGGKILGFFF 130 >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 = 33.4 bits (76), Expect = 0.016 Identities = 27/159 (16%), Positives = 46/159 (28%), Gaps = 76/159 (47%) Query: 13 NANLR--YKPSVV----IPFS----RLHARVL---------------DVLKTEGYIGEYC 47 N LR PS + IPFS + R L D++ + + Sbjct: 390 NLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLIN-KDLVKNNV 448 Query: 48 EIDAGKGRIQLKV---------DLKYHNGASVIRK-IDCV-SKPGRRLYSSFKDIPQVCN 96 +A +++ DL+ S+ + +DC+ P Sbjct: 449 SFNAK----DIQIPVYDTFDGSDLR-VLSGSISERIVDCIIRLP--------VKWETTTQ 495 Query: 97 ---------------GLGIMIVTTSK-----GV---MAG 112 GLG++ T + GV +AG Sbjct: 496 FKATHILDFGPGGASGLGVL---THRNKDGTGVRVIVAG 531 Score = 25.3 bits (55), Expect = 3.8 Identities = 11/45 (24%), Positives = 18/45 (40%), Gaps = 13/45 (28%) Query: 1 MSCLGDMLTRIRNAN-LRYKPSVVIPFSRLHARVLDV-LKTE-GY 42 S LG + R ++ +R VI A LD+ + G+ Sbjct: 509 ASGLGVLTHRNKDGTGVR-----VI-----VAGTLDINPDDDYGF 543 >2g40_A Conserved hypothetical protein; 6459694, structural genomics, PSI, protein structure initiative, joint center for structural genomics; 1.70A {Deinococcus radiodurans} SCOP: c.124.1.7 Length = 224 Score = 24.9 bits (54), Expect = 5.4 Identities = 11/52 (21%), Positives = 18/52 (34%), Gaps = 6/52 (11%) Query: 6 DMLTRIRNANLRYKPSVVIPFSRLHAR----VLDVLKT--EGYIGEYCEIDA 51 +MLT I A +P + P+ +L + Y Y + A Sbjct: 25 EMLTTINRAIAGSRPEALPPYPVPAPLSRAEILHQFEDRILDYGAAYTHVSA 76 >1m1h_A Transcription antitermination protein NUSG; transcription termination, RNP motif, immunoglobulin fold, nucleic acid interaction; 1.95A {Aquifex aeolicus} SCOP: b.114.1.1 d.58.42.1 PDB: 1m1g_A 1npp_A 1npr_A Length = 248 Score = 24.3 bits (52), Expect = 8.1 Identities = 3/23 (13%), Positives = 10/23 (43%) Query: 40 EGYIGEYCEIDAGKGRIQLKVDL 62 + G E+ K ++ + + + Sbjct: 209 MNFTGTVEEVHPEKRKLTVMISI 231 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 0.324 0.141 0.426 Gapped Lambda K H 0.267 0.0573 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 1,107,446 Number of extensions: 47392 Number of successful extensions: 157 Number of sequences better than 10.0: 1 Number of HSP's gapped: 148 Number of HSP's successfully gapped: 14 Length of query: 129 Length of database: 5,693,230 Length adjustment: 82 Effective length of query: 47 Effective length of database: 3,705,222 Effective search space: 174145434 Effective search space used: 174145434 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 51 (23.8 bits)