RPS-BLAST 2.2.22 [Sep-27-2009] Database: mmdb70 33,805 sequences; 4,956,049 total letters Searching..................................................done Query= gi|254780250|ref|YP_003064663.1| 50S ribosomal protein L24 [Candidatus Liberibacter asiaticus str. psy62] (102 letters) >2j01_Y 50S ribosomal protein L24; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} (Y:1-78) Length = 78 Score = 76.6 bits (189), Expect = 1e-15 Identities = 30/71 (42%), Positives = 42/71 (59%), Gaps = 1/71 (1%) Query: 3 KIRTGDRVLVLAGKDKGKAGQVMGVVRKSGRAFVQGVNIVKRHQRQTP-NKEAGIISKEA 61 ++ GD VLV +GK KG+ G+V V+ K V+GVNIVK+ R +P + G I KEA Sbjct: 6 HVKKGDTVLVASGKYKGRVGKVKEVLPKKYAVIVEGVNIVKKAVRVSPKYPQGGFIEKEA 65 Query: 62 SIHLSNLSLID 72 +H S + I Sbjct: 66 PLHASKVRPIC 76 >2zjr_R 50S ribosomal protein L24; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} (R:1-87) Length = 87 Score = 76.3 bits (188), Expect = 1e-15 Identities = 22/73 (30%), Positives = 46/73 (63%), Gaps = 1/73 (1%) Query: 3 KIRTGDRVLVLAGKDKGKAGQVMGVVRKSGRAFVQGVNIVKRHQRQTP-NKEAGIISKEA 61 + GD V+VL+GK KG+ G+V+ + + + V+GVN++ ++ + + N + G +E Sbjct: 15 HFKKGDTVIVLSGKHKGQTGKVLLALPRDQKVVVEGVNVITKNVKPSMTNPQGGQEQREL 74 Query: 62 SIHLSNLSLIDKD 74 ++H S ++L+D + Sbjct: 75 ALHASKVALVDPE 87 >3bbo_W Ribosomal protein L24; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} (W:1-140) Length = 140 Score = 71.1 bits (174), Expect = 5e-14 Identities = 22/73 (30%), Positives = 42/73 (57%), Gaps = 1/73 (1%) Query: 3 KIRTGDRVLVLAGKDKGKAGQVMGVVRKSGRAFVQGVNIVKRHQRQTP-NKEAGIISKEA 61 ++ GD V V++G +KGK G++ + + + ++ +N +H + ++ II EA Sbjct: 68 HVKVGDTVKVISGGEKGKIGEISKIHKHNSTVIIKDLNFKTKHVKSKEEGEQGQIIKIEA 127 Query: 62 SIHLSNLSLIDKD 74 +IH SN+ LI K+ Sbjct: 128 AIHSSNVMLILKE 140 >1vq8_T 50S ribosomal protein L24P; 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} (T:20-120) Length = 101 Score = 69.0 bits (169), Expect = 2e-13 Identities = 17/87 (19%), Positives = 30/87 (34%), Gaps = 11/87 (12%) Query: 3 KIRTGDRVLVLAGKDKGKAGQVMGVVRKSGRAFVQGVNIVKRHQRQTPNKEAGIISKEAS 62 ++ GD V VL G G+ G+V+ V V+ V + K + Sbjct: 23 RVNAGDTVEVLRGDFAGEEGEVINVDLDKAVIHVEDVTLEKTDGEE----------VPRP 72 Query: 63 IHLSNLSLID-KDGKQVRVGFSFVDGK 88 + SN+ + D + R + Sbjct: 73 LDTSNVRVTDLDLEDEKREARLESEDD 99 >3i1n_U 50S ribosomal protein L24; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1vs8_U 1vs6_U 3i1p_U 3i1r_U 3i1t_U 3i20_U 3i22_U 3e1b_O 3e1d_O 2qam_U* 1p85_S 1p86_S 2awb_U 2aw4_U 2i2v_U 2i2t_U* 2qao_U* 2qba_U* 2qbc_U* 2qbe_U ... (U:1-25,U:67-104) Length = 63 Score = 51.9 bits (125), Expect = 3e-08 Identities = 32/101 (31%), Positives = 41/101 (40%), Gaps = 41/101 (40%) Query: 1 MEKIRTGDRVLVLAGKDKGKAGQVMGVVRKSGRAFVQGVNIVKRHQRQTPNKEAGIISKE 60 KIR D V+VL GKDKGK G+V Sbjct: 2 AAKIRRDDEVIVLTGKDKGKRGKV------------------------------------ 25 Query: 61 ASIHLSNLSLID-KDGKQVRVGFSFVDGKKIRIAKRSGEPI 100 +SN+++ + GK RVGF F DGKK+R K + E I Sbjct: 26 ----VSNVAIFNAATGKADRVGFRFEDGKKVRFFKSNSETI 62 >3i1n_U 50S ribosomal protein L24; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1vs8_U 1vs6_U 3i1p_U 3i1r_U 3i1t_U 3i20_U 3i22_U 3e1b_O 3e1d_O 2qam_U* 1p85_S 1p86_S 2awb_U 2aw4_U 2i2v_U 2i2t_U* 2qao_U* 2qba_U* 2qbc_U* 2qbe_U ... (U:26-66) Length = 41 Score = 48.4 bits (116), Expect = 3e-07 Identities = 18/40 (45%), Positives = 27/40 (67%), Gaps = 2/40 (5%) Query: 27 VVRKSGRAFVQGVNIVKRHQRQTP--NKEAGIISKEASIH 64 V SG+ V+G+N+VK+HQ+ P N+ GI+ KEA+I Sbjct: 2 NVLSSGKVIVEGINLVKKHQKPVPALNQPGGIVEKEAAIQ 41 >1kwg_A Beta-galactosidase; TIM barrel, glycoside hydrolase family 42, trimer; 1.60A {Thermus thermophilus} (A:1-394) Length = 394 Score = 32.7 bits (72), Expect = 0.018 Identities = 3/29 (10%), Positives = 7/29 (24%) Query: 70 LIDKDGKQVRVGFSFVDGKKIRIAKRSGE 98 +Q+ G D + + Sbjct: 354 QAPFAQEQMHAGLHRPDSAPDQGFFEAKR 382 >2ftc_N Mitochondrial ribosomal protein L24; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} PDB: 3iy9_N (N:1-31) Length = 31 Score = 29.8 bits (67), Expect = 0.14 Identities = 13/23 (56%), Positives = 17/23 (73%) Query: 7 GDRVLVLAGKDKGKAGQVMGVVR 29 GD V +L GKD GK G+V+ V+R Sbjct: 1 GDTVEILEGKDAGKQGKVVQVIR 23 >1qd6_C Protein (outer membrane phospholipase (ompla)); anti-parallel beta barrel dimer, membrane protein; HET: HDS; 2.10A {Escherichia coli} (C:) Length = 240 Score = 25.8 bits (57), Expect = 2.1 Identities = 9/20 (45%), Positives = 10/20 (50%), Gaps = 2/20 (10%) Query: 69 SLIDKDGKQ--VRVGFSFVD 86 SLID + Q V VG D Sbjct: 219 SLIDYNFNQTRVGVGVMLND 238 >1qd5_A Outer membrane phospholipase A; anti-parallel beta barrel, membrane protein; HET: BOG; 2.17A {Escherichia coli} (A:) Length = 275 Score = 25.5 bits (56), Expect = 2.4 Identities = 9/20 (45%), Positives = 10/20 (50%), Gaps = 2/20 (10%) Query: 69 SLIDKDGKQ--VRVGFSFVD 86 SLID + Q V VG D Sbjct: 254 SLIDYNFNQTRVGVGVMLND 273 >3gqh_A Preneck appendage protein; beta barrel, viral protein; 1.80A {Bacillus phage PHI29} PDB: 3gqk_A* (A:1-109) Length = 109 Score = 25.5 bits (56), Expect = 2.7 Identities = 7/28 (25%), Positives = 14/28 (50%), Gaps = 1/28 (3%) Query: 74 DGKQVRVG-FSFVDGKKIRIAKRSGEPI 100 G+ + G ++ KIR A++ + I Sbjct: 10 GGQVIETGYLVTLEKGKIRKAEKGEKII 37 >3gqn_A Preneck appendage protein; coiled coil, beta helix, beta barrel, ATP binding, viral protein; HET: ATP; 2.15A {Bacillus phage PHI29} (A:605-772) Length = 168 Score = 25.2 bits (55), Expect = 3.1 Identities = 7/28 (25%), Positives = 14/28 (50%), Gaps = 1/28 (3%) Query: 74 DGKQVRVG-FSFVDGKKIRIAKRSGEPI 100 G+ + G ++ KIR A++ + I Sbjct: 15 GGQVIETGYLVTLEKGKIRKAEKGEKII 42 >2wwb_L 60S ribosomal protein L26-A; ribosome, protein EXIT tunnel, cotranslational protein translocation, protein conducting channel; 6.48A {Triticum aestivum} PDB: 2wwa_L 2ww9_L 1s1i_U (L:26-70,L:100-112) Length = 58 Score = 24.7 bits (54), Expect = 5.0 Identities = 10/21 (47%), Positives = 14/21 (66%) Query: 4 IRTGDRVLVLAGKDKGKAGQV 24 IR D VLV+ G KG+ G++ Sbjct: 25 IRRDDEVLVVRGSKKGQEGKI 45 >1xdn_A RNA editing ligase MP52; HET: MSE ATP; 1.20A {Trypanosoma brucei} (A:43-194) Length = 152 Score = 24.5 bits (53), Expect = 5.1 Identities = 8/21 (38%), Positives = 10/21 (47%), Gaps = 5/21 (23%) Query: 82 FSFV-----DGKKIRIAKRSG 97 F D + +R AKRSG Sbjct: 4 FGIYLINQGDHEVVRFAKRSG 24 >1ygy_A PGDH, D-3-phosphoglycerate dehydrogenase; oxidoreductase, serine biosynthesis, structural genomics, PSI, protein structure initiative; HET: TAR; 2.30A {Mycobacterium tuberculosis} (A:323-452) Length = 130 Score = 23.9 bits (52), Expect = 7.3 Identities = 13/69 (18%), Positives = 24/69 (34%), Gaps = 11/69 (15%) Query: 34 AFVQGVNIVKRHQRQTPNKEAGIISKEASIHLSNLSLIDKDGKQVRV-GFSFVDGKKIRI 92 A +GV ++PN + + + + DG V V G + +I Sbjct: 69 AAERGVTAEICKASESPNHRSVVD----------VRAVGADGSVVTVSGTLYGPQLSQKI 118 Query: 93 AKRSGEPID 101 + +G D Sbjct: 119 VQINGRHFD 127 >1lkf_A LUKF, HLGB, leukocidin F subunit; leukotoxin, hemolysin, pore-forming toxin; 1.90A {Staphylococcus aureus} (A:) Length = 299 Score = 23.7 bits (51), Expect = 8.5 Identities = 5/55 (9%), Positives = 17/55 (30%), Gaps = 8/55 (14%) Query: 48 QTPNKEAGIISKEASIHLSNLSLIDKDG--------KQVRVGFSFVDGKKIRIAK 94 ++ +K+ ++ +I+ + D + V S + + Sbjct: 44 KSYDKDTLVLKATGNINSGFVKPNPNDYDFSKLYWGAKYNVSISSQSNDSVNVVD 98 >1lpl_A Hypothetical 25.4 kDa protein F53F4.3 in chromosome V; structural genomics, CAP-Gly domain, cytoskeleton, tubulin, PSI; 1.77A {Caenorhabditis elegans} (A:) Length = 95 Score = 23.6 bits (51), Expect = 9.0 Identities = 8/27 (29%), Positives = 12/27 (44%) Query: 1 MEKIRTGDRVLVLAGKDKGKAGQVMGV 27 + I G+R V G + G+V V Sbjct: 9 AKNIMVGNRCEVTVGAQMARRGEVAYV 35 Database: mmdb70 Posted date: Jun 20, 2010 3:12 AM Number of letters in database: 4,956,049 Number of sequences in database: 33,805 Lambda K H 0.317 0.137 0.373 Gapped Lambda K H 0.267 0.0623 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 33805 Number of Hits to DB: 739,785 Number of extensions: 29773 Number of successful extensions: 175 Number of sequences better than 10.0: 1 Number of HSP's gapped: 169 Number of HSP's successfully gapped: 36 Length of query: 102 Length of database: 4,956,049 Length adjustment: 60 Effective length of query: 42 Effective length of database: 2,927,749 Effective search space: 122965458 Effective search space used: 122965458 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: 50 (23.3 bits)