RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780584|ref|YP_003064997.1| 50S ribosomal protein L28 [Candidatus Liberibacter asiaticus str. psy62] (97 letters) >3bbo_Y Ribosomal protein L28; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Nicotiana tabacum} Length = 151 Score = 80.3 bits (198), Expect = 9e-17 Identities = 24/80 (30%), Positives = 42/80 (52%), Gaps = 2/80 (2%) Query: 1 MSRVCELTKKTVMSGNKVSHANNKTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVE 60 R+C T K NKVSH+N+KT++ NL + + ++ +LR+S A++++E Sbjct: 74 ARRICPFTGKKSNRANKVSHSNHKTKKLQFVNLQYKRIWWEAGKRYVKLRLSTKAIKTIE 133 Query: 61 RQGGLDRFLSNSKKENLSAR 80 + GLD +LS + Sbjct: 134 K-NGLDAVA-KKAGIDLSKK 151 >3ofq_X 50S ribosomal protein L28; protein biosynthesis, ribosomes, RNA, tRNA, transfer, antibi EXIT, peptidyl, ribosomal subunit, large; 3.10A {Escherichia coli} PDB: 2i2v_X 2wwq_0* 3fik_X 2i2t_X 3ofr_X* 3i1n_X 1vt2_X* 2qao_Z* 2qba_Z* 2qbc_Z* 2qbe_Z 2qbg_Z 2qbi_Z* 2qbk_Z* 2qov_Z 2qox_Z 2qoz_Z* 2qp1_Z* 2z4l_Z* 2z4n_Z* ... Length = 77 Score = 77.3 bits (191), Expect = 7e-16 Identities = 27/72 (37%), Positives = 43/72 (59%), Gaps = 1/72 (1%) Query: 2 SRVCELTKKTVMSGNKVSHANNKTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVER 61 SRVC++T K ++GN SHA N T+RRFLPNL + ++ LR+S +R +++ Sbjct: 1 SRVCQVTGKRPVTGNNRSHALNATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVIDK 60 Query: 62 QGGLDRFLSNSK 73 G+D L+ + Sbjct: 61 -KGIDTVLAELR 71 >3i1n_X 50S ribosomal protein L28; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 2qao_Z* 2qba_Z* 2qbc_Z* 2qbe_Z 2qbg_Z 2qbi_Z* 2qbk_Z* 2qov_Z 2qox_Z 2qoz_Z* 2qp1_Z* 2z4l_Z* 2z4n_Z* 3df2_Z 3df4_Z 2qam_Z 3i1p_X 3i1r_X 3i1t_X 3i20_X ... Length = 78 Score = 77.0 bits (190), Expect = 8e-16 Identities = 28/76 (36%), Positives = 44/76 (57%), Gaps = 1/76 (1%) Query: 1 MSRVCELTKKTVMSGNKVSHANNKTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVE 60 MSRVC++T K ++GN SHA N T+RRFLPNL + ++ LR+S +R ++ Sbjct: 1 MSRVCQVTGKRPVTGNNRSHALNATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVID 60 Query: 61 RQGGLDRFLSNSKKEN 76 + G+D L+ + Sbjct: 61 K-KGIDTVLAELRARG 75 >2jz6_A 50S ribosomal protein L28; structure, NESG, ribonucleoprotein, structural genomics, PSI-2, protein structure initiative; NMR {Thermotoga maritima MSB8} SCOP: d.325.1.1 Length = 77 Score = 70.4 bits (173), Expect = 8e-14 Identities = 20/74 (27%), Positives = 39/74 (52%), Gaps = 5/74 (6%) Query: 1 MSRVCELTKKTVMSGNKVSHANNKTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVE 60 M++ CE+ K SGN VSH++ K+ R F PNL ++ ++ ++R+ L+S Sbjct: 6 MAKRCEVCGKAPRSGNTVSHSDKKSERWFRPNLQKVRVVLPD-GTIKRMRVCTSCLKS-- 62 Query: 61 RQGGLDRFLSNSKK 74 G + +++ + Sbjct: 63 --GKVKKYVGQVSE 74 >2jl6_1 50S ribosomal protein L28, 50S ribosomal protein L25; methylation, translation, paromomycin, tRNA-binding, tRNA, zinc, mRNA, ribosome, repressor, RNA-binding; 3.45A {Thermus thermophilus} PDB: 2jl8_1 Length = 89 Score = 59.5 bits (144), Expect = 2e-10 Identities = 15/74 (20%), Positives = 29/74 (39%), Gaps = 15/74 (20%) Query: 1 MSRVCELTKKTVMSGNKVSH-------------ANNKTRRRFLPNLCRITLISDIMEQKY 47 MS+VCE++ K + N + ++RR PNL ++ + Q+ Sbjct: 1 MSKVCEISGKRPIVANSIQRRGKAKREGGVGKKTTGISKRRQYPNLQKVRVRVA--GQEI 58 Query: 48 QLRISKCALRSVER 61 R++ + V Sbjct: 59 TFRVAASHIPKVYE 72 >2j01_1 50S ribosomal protein L28; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} SCOP: d.325.1.1 PDB: 2j03_1 2v47_1 2v49_1 2wdi_1 2wdj_1 2wdl_1 2wdn_1 2wh2_1 2wh4_1 3hux_1 3huz_1 3f1f_1 1vsp_V 1vsa_V 3d5d_1 3d5b_1 3f1h_1 3fin_1 Length = 98 Score = 57.5 bits (139), Expect = 6e-10 Identities = 19/104 (18%), Positives = 40/104 (38%), Gaps = 22/104 (21%) Query: 1 MSRVCELTKKTVMSGNKVSH-------------ANNKTRRRFLPNLCRITLISDIMEQKY 47 MS+VCE++ K + N + ++RR PNL ++ + Q+ Sbjct: 1 MSKVCEISGKRPIVANSIQRRGKAKREGGVGKKTTGISKRRQYPNLQKVRVRVA--GQEI 58 Query: 48 QLRISKCALRSVERQGGLDRFLSNSKKENLSA-RMRTLRSQILK 90 R++ + V + +K L + ++ ++LK Sbjct: 59 TFRVAASHIPKV------YELVERAKGLKLEGLSPKEIKKELLK 96 >2zjr_U 50S ribosomal protein L28; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: d.325.1.1 PDB: 2zjp_U 2zjq_U 3cf5_U* 3dll_U* Length = 81 Score = 54.8 bits (132), Expect = 4e-09 Identities = 18/76 (23%), Positives = 28/76 (36%), Gaps = 15/76 (19%) Query: 1 MSRVCELTKKTVMSGNKV-------------SHANNKTRRRFLPNLCRITLISDIMEQKY 47 MSR C LT K + N V T+R NL + + + Q Sbjct: 1 MSRECYLTGKKNLVVNSVIRRGKARADGGVGRKTTGITKRVQRANLHKKAIREN--GQVK 58 Query: 48 QLRISKCALRSVERQG 63 + +S ALR++ + Sbjct: 59 TVWLSANALRTLSKGP 74 >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 = 27.6 bits (61), Expect = 0.80 Identities = 19/101 (18%), Positives = 35/101 (34%), Gaps = 29/101 (28%) Query: 7 LTKKTVMSG---NKVSHANNKTR--RRFLPNLCRIT------LISD----IMEQ--KYQL 49 L K SG +++ + K + RFLP + L+ I + K + Sbjct: 393 LRKAKAPSGLDQSRIPFSERKLKFSNRFLP----VASPFHSHLLVPASDLINKDLVKNNV 448 Query: 50 RISKCALR-SV-ERQGGLDRFLSNSKKENLSARMRTLRSQI 88 + ++ V + G D L ++S R + I Sbjct: 449 SFNAKDIQIPVYDTFDGSD--LRVL-SGSISER---IVDCI 483 >1u04_A Argonaute, hypothetical protein PF0537; RNAI, silencing, PIWI, PAZ, RISC, slicer, RNAse H, hydrolase/gene regulation complex; 2.25A {Pyrococcus furiosus dsm 3638} SCOP: b.34.14.1 c.55.3.10 PDB: 1z25_A 1z26_A Length = 771 Score = 26.2 bits (57), Expect = 1.8 Identities = 13/75 (17%), Positives = 29/75 (38%), Gaps = 2/75 (2%) Query: 12 VMSGNKVSHANNKTRRRFL-PNLCRITLISDIMEQKYQLRISKCA-LRSVERQGGLDRFL 69 +++ NK + +L P L T ++ +E I + L ER+ L+ L Sbjct: 246 ILAKFASKIKKNKNYKIYLLPQLVVPTYNAEQLESDVAKEILEYTKLMPEERKELLENIL 305 Query: 70 SNSKKENLSARMRTL 84 + + + + + Sbjct: 306 AEVDSDIIDKSLSEI 320 >1vh4_A SUFD protein; structural genomics, protein binding protein; 1.75A {Escherichia coli} SCOP: b.80.6.1 PDB: 2zu0_A* Length = 435 Score = 24.6 bits (52), Expect = 5.2 Identities = 8/30 (26%), Positives = 16/30 (53%) Query: 40 SDIMEQKYQLRISKCALRSVERQGGLDRFL 69 S+ ++Q + L ++ RS + Q L + L Sbjct: 10 SNALQQWHHLFEAEGTKRSPQAQQHLQQLL 39 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 0.319 0.128 0.342 Gapped Lambda K H 0.267 0.0730 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 699,669 Number of extensions: 26007 Number of successful extensions: 78 Number of sequences better than 10.0: 1 Number of HSP's gapped: 71 Number of HSP's successfully gapped: 13 Length of query: 97 Length of database: 5,693,230 Length adjustment: 63 Effective length of query: 34 Effective length of database: 4,165,858 Effective search space: 141639172 Effective search space used: 141639172 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 (21.8 bits) S2: 50 (23.0 bits)