RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780330|ref|YP_003064743.1| 30S ribosomal protein S18 [Candidatus Liberibacter asiaticus str. psy62] (83 letters) >3i1m_R 30S ribosomal protein S18; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_R* 1vs5_R 3i1o_R 3i1q_R 3i1s_R 3i1z_R 3i21_R 2qal_R* 1p6g_R 1p87_R 2aw7_R 2avy_R 2i2u_R 2i2p_R* 2qan_R* 2qb9_R* 2qbb_R* 2qbd_R 2qbf_R 2qbh_R* ... Length = 75 Score = 88.9 bits (221), Expect = 2e-19 Identities = 35/66 (53%), Positives = 46/66 (69%) Query: 17 RRKSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLG 76 RRK C + +G IDYKDI L ++++ GKIVPSRI+ K QR+LA+AIKRARYL Sbjct: 7 RRKFCRFTAEGVQEIDYKDIATLKNYITESGKIVPSRITGTRAKYQRQLARAIKRARYLS 66 Query: 77 LIAYVN 82 L+ Y + Sbjct: 67 LLPYTD 72 >3ofo_R 30S ribosomal protein S18; protein biosynthesis, ribosomes, RNA, tRNA, transfer, eryThr ketolide, macrolide, antibiotic, EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 3fih_R* 3iy8_R 2wwl_R 3ofp_R Length = 55 Score = 81.1 bits (201), Expect = 5e-17 Identities = 30/52 (57%), Positives = 39/52 (75%) Query: 31 IDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLGLIAYVN 82 IDYKDI L ++++ GKIVPSRI+ K QR+LA+AIKRARYL L+ Y + Sbjct: 2 IDYKDIATLKNYITESGKIVPSRITGTRAKYQRQLARAIKRARYLSLLPYTD 53 >3bbn_R Ribosomal protein S18; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1 Length = 103 Score = 80.2 bits (198), Expect = 1e-16 Identities = 28/75 (37%), Positives = 52/75 (69%), Gaps = 2/75 (2%) Query: 8 PLLRRNVSHRRKSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAK 67 P ++ S RR+ P+ + RIDY+++ L++RF+S++GKI+ R++ ++ K+QR + Sbjct: 7 PFIKSKRSFRRRLPPI--QSGDRIDYRNMSLISRFISEQGKILSRRVNRLTLKQQRLITS 64 Query: 68 AIKRARYLGLIAYVN 82 AIK+AR L L+ ++N Sbjct: 65 AIKQARILSLLPFLN 79 >2vqe_R 30S ribosomal protein S18; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: a.4.8.1 PDB: 1fka_R 1fjg_R 1gix_U* 1hnw_R* 1hnx_R* 1hnz_R* 1hr0_R 1ibk_R* 1ibl_R* 1ibm_R 1j5e_R 1jgo_U* 1jgp_U* 1jgq_U* 1ml5_U* 1n32_R* 1n33_R* 1n34_R 1n36_R 1xmo_R* ... Length = 88 Score = 75.2 bits (185), Expect = 4e-15 Identities = 28/66 (42%), Positives = 41/66 (62%) Query: 17 RRKSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLG 76 R+ + DY+++ +L RFLS+ GKI+P R + +S K+QR LAK IKRAR LG Sbjct: 18 RKAKVKATLGEFDLRDYRNVEVLKRFLSETGKILPRRRTGLSGKEQRILAKTIKRARILG 77 Query: 77 LIAYVN 82 L+ + Sbjct: 78 LLPFTE 83 >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 = 28.4 bits (63), Expect = 0.41 Identities = 21/119 (17%), Positives = 30/119 (25%), Gaps = 62/119 (52%) Query: 3 EVAPTPLL----------------------------------RRN-------------VS 15 E P+P+L +N Sbjct: 332 EGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNL 391 Query: 16 HRRK-SCPLSGKGAPRIDYKD--IRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKR 71 RK P SG RI + + ++ NRFL P ++S H L A Sbjct: 392 TLRKAKAP-SGLDQSRIPFSERKLKFSNRFL-------P--VASPFHSHL--LVPASDL 438 Score = 27.6 bits (61), Expect = 0.63 Identities = 7/48 (14%), Positives = 16/48 (33%), Gaps = 15/48 (31%) Query: 37 RLLNRFLSQ-----RGKIVPSRISSVSHKKQRELAKAIKRARYLGLIA 79 +L +F G ++ + EL ++LG ++ Sbjct: 32 QLQEQFNKILPEPTEGFAADDEPTTPA-----ELV-----GKFLGYVS 69 Score = 25.3 bits (55), Expect = 3.7 Identities = 10/42 (23%), Positives = 20/42 (47%), Gaps = 6/42 (14%) Query: 47 GKIVPSRISSVSHKKQRELAKAIKRA-RYLGL-----IAYVN 82 + VPS + S+S+ Q ++ + + +L I+ VN Sbjct: 331 NEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVN 372 >1l6j_A Matrix metalloproteinase-9; twisted beta sheet flanked by helices, hydrolase; 2.50A {Homo sapiens} SCOP: a.20.1.2 d.92.1.11 g.14.1.2 g.14.1.2 g.14.1.2 Length = 425 Score = 26.9 bits (59), Expect = 1.3 Identities = 13/63 (20%), Positives = 24/63 (38%), Gaps = 5/63 (7%) Query: 16 HRRKSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKR-ARY 74 +R+S + G R + D +L +L + G + + S L A+ + Sbjct: 3 RQRQSTLVLFPGDLRTNLTDRQLAEEYLYRYGYTRVAEMRGESK----SLGPALLLLQKQ 58 Query: 75 LGL 77 L L Sbjct: 59 LSL 61 >1su3_A Interstitial collagenase; prodomain, hemopexin domain, exocite, structural proteomics in europe, spine, structural genomics, hydrolase; HET: EPE; 2.20A {Homo sapiens} SCOP: a.20.1.2 b.66.1.1 d.92.1.11 PDB: 2clt_A 1fbl_A* Length = 450 Score = 25.5 bits (55), Expect = 3.2 Identities = 6/52 (11%), Positives = 19/52 (36%), Gaps = 1/52 (1%) Query: 27 GAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKR-ARYLGL 77 +D+ L+ ++L + + + + + +K+ + GL Sbjct: 3 ATLETQEQDVDLVQKYLEKYYNLKNDGRQVEKRRNSGPVVEKLKQMQEFFGL 54 >3g64_A Putative enoyl-COA hydratase; alpha-beta structure, structural genomics, PSI-2, protein structure initiative; 2.05A {Streptomyces coelicolor A3} Length = 279 Score = 25.3 bits (54), Expect = 3.7 Identities = 9/62 (14%), Positives = 24/62 (38%), Gaps = 19/62 (30%) Query: 22 PLSGKGAPRIDYKDIRL----------LNRFLSQRGKIVPSRISSVSHKKQRELAKAIKR 71 P +G AP +++ +R+ L R P ++++++ + +L + Sbjct: 5 PFTGSAAPTPEWRHLRVEITDGVATVTLAR---------PDKLNALTFEAYADLRDLLAE 55 Query: 72 AR 73 Sbjct: 56 LS 57 >3meb_A Aspartate aminotransferase; pyridoxal phosphate, structural genomics, seattle structural genomics center for infectious disease; HET: PLP; 1.90A {Giardia lamblia atcc 50803} Length = 448 Score = 24.7 bits (53), Expect = 5.3 Identities = 7/28 (25%), Positives = 14/28 (50%), Gaps = 4/28 (14%) Query: 49 IVPS--RIS--SVSHKKQRELAKAIKRA 72 +V + R+S ++ +A+AI A Sbjct: 413 LVKAGGRMSMCGLTESNCDYVAEAIHDA 440 >2ji4_A Phosphoribosyl pyrophosphate synthetase-associated protein 2; phosphorylation, nucleotide biosynthesis, transferase; 2.55A {Homo sapiens} PDB: 2c4k_A* Length = 379 Score = 23.9 bits (51), Expect = 9.0 Identities = 9/24 (37%), Positives = 13/24 (54%), Gaps = 2/24 (8%) Query: 54 ISSVSHKKQRELAKAIKRARYLGL 77 S+ S+ EL+K I A LG+ Sbjct: 33 FSANSNSSCMELSKKI--AERLGV 54 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 0.323 0.136 0.386 Gapped Lambda K H 0.267 0.0804 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 703,911 Number of extensions: 27481 Number of successful extensions: 79 Number of sequences better than 10.0: 1 Number of HSP's gapped: 78 Number of HSP's successfully gapped: 15 Length of query: 83 Length of database: 5,693,230 Length adjustment: 51 Effective length of query: 32 Effective length of database: 4,456,786 Effective search space: 142617152 Effective search space used: 142617152 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 (22.0 bits) S2: 50 (22.9 bits)