Query gi|254780147|ref|YP_003064560.1| 50S ribosomal protein L11 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 142 No_of_seqs 113 out of 1395 Neff 5.5 Searched_HMMs 23785 Date Sun May 22 14:59:32 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780147.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 3bbo_K Ribosomal protein L11; 100.0 0 0 365.6 10.1 140 1-141 72-211 (224) 2 1mms_A Protein (ribosomal prot 100.0 0 0 358.9 15.4 140 2-142 1-140 (140) 3 2ftc_G L11MT, MRP-L11, 39S rib 100.0 0 0 350.1 16.1 141 2-142 1-145 (145) 4 3egv_B 50S ribosomal protein L 100.0 0 0 352.3 9.8 138 3-141 1-138 (146) 5 1vq8_I 50S ribosomal protein L 100.0 0 0 351.7 7.5 137 5-142 1-137 (162) 6 3ofq_I 50S ribosomal protein L 100.0 0 0 365.5 -15.0 141 2-142 1-141 (141) 7 2zkr_i 60S ribosomal protein L 100.0 0 0 330.2 5.3 139 1-142 1-145 (165) 8 3cjs_B 50S ribosomal protein L 100.0 2.9E-29 1.2E-33 192.3 10.2 71 3-74 2-72 (72) 9 1wib_A 60S ribosomal protein L 100.0 2E-29 8.3E-34 193.3 3.4 78 5-85 15-92 (92) 10 1hc8_A Ribosomal protein L11; 99.9 3.2E-28 1.3E-32 186.2 5.7 76 67-142 1-76 (76) 11 1qa6_A Ribosomal protein L11; 99.9 3.9E-24 1.6E-28 162.0 5.3 67 72-138 1-67 (67) 12 1no4_A Late, head morphogenesi 29.2 14 0.00058 17.2 0.9 25 26-50 26-50 (97) 13 2vqe_M 30S ribosomal protein S 27.6 32 0.0014 15.0 3.2 52 73-130 26-78 (126) 14 2k53_A A3DK08 protein; NESG, C 25.3 36 0.0015 14.8 4.2 37 13-49 30-66 (76) 15 1hh2_P NUSA, N utilization sub 21.0 44 0.0018 14.3 5.2 69 9-78 233-316 (344) No 1 >3bbo_K Ribosomal protein L11; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1 Probab=100.00 E-value=0 Score=365.61 Aligned_cols=140 Identities=46% Similarity=0.795 Sum_probs=138.0 Q ss_pred CCCCEEEEEEEEEECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCEEEEEECCCCHHHHH Q ss_conf 98423689999994455668970446866429998999999999977543797513899983895299998597489999 Q gi|254780147|r 1 MAKVVSRIVKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVTCYKDKSFTFTMSQPPVSFFL 80 (142) Q Consensus 1 M~k~v~~~ikl~v~aG~A~p~PplGp~LG~~Gini~~f~k~fN~~T~~~~~g~~v~V~i~v~~dksf~~~i~~P~~s~li 80 (142) |+|+++++|||+|+||+|+|+|||||+|||+|||+|+||+|||++|++|+ |++|||+|++|+||+|+|++++||+|||| T Consensus 72 ~aKkvv~~IKL~V~AGkA~PaPPlGPaLGp~GINi~~Fck~fN~~Tk~~k-G~~VpV~ItV~~Dksf~f~iktPptS~Li 150 (224) T 3bbo_K 72 KAKKVIGVIKLALEAGKATPAPPVGPALGSKGVNIMAFCKDYNARTADKP-GFVIPVEITVFDDKSFTFILKTPPASVLL 150 (224) T ss_dssp CCCCCSSEEEECCBTTBCCCSTTTTTTTTTTSSCTTSSHHHHHHHGGGSC-SSBCCEEEEECSSSCEEEEECCCCTTHHH T ss_pred CCCEEEEEEEEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCC-CCCCCEEEEEECCCCEEEEECCCCHHHHH T ss_conf 87347899999985474168998751013469899999999999973458-97443699997686279998699678998 Q ss_pred HHHCCCCCCCCCCCCCEEEEECHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHEEECCEEEE Q ss_conf 9633766678899963010125999999999988540678789999997743021452893 Q gi|254780147|r 81 KKEVGIKSGSKLPGKESCGSITRENIRKIAQLKMQDMGAIDIEGAMRMVEGSACSMGISVV 141 (142) Q Consensus 81 kk~~g~~kgs~~p~~~~~g~it~~~i~eIAk~K~~d~~~~~l~~~vk~VlGTa~SmGi~V~ 141 (142) ++++|+++||++|+++++|+||++|+||||+.|++|+++.+|+++||+|+|||+||||+|| T Consensus 151 kkaagi~kGS~~p~~~~vG~ITl~qv~eIAk~K~~dlna~~L~aavK~VlGTArSMGI~Vd 211 (224) T 3bbo_K 151 LKASGAEKGSKDPQMEKVGKITIDQLRGIATEKLPDLNCTTIESAMRIIAGTAANMGIDID 211 (224) T ss_dssp HHHHTCSSCCSSTTTSCCEEECHHHHHHHHHHTCTTSCCSSHHHHHHHHHHHHTTTTEEEC T ss_pred HHHCCCCCCCCCCCCCEEEEEEHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHEECEEEEE T ss_conf 8643776678899861645763999999999987763652599999996822625868997 No 2 >1mms_A Protein (ribosomal protein L11); RNA-protein complex, RNA, ribosome, translocation, thiostrepton; 2.57A {Thermotoga maritima} SCOP: a.4.7.1 d.47.1.1 PDB: 1mvr_L 1oln_A* 1giy_L 1mj1_L* 1ml5_l* 1yl3_L 2b66_K 2b9n_K 2b9p_K 2jq7_A* 2k3f_A 1eg0_K 1jqm_A 1jqs_A 1jqt_A 1r2w_A 1r2x_A 487d_L 1pn8_L 1pn7_L Probab=100.00 E-value=0 Score=358.91 Aligned_cols=140 Identities=51% Similarity=0.884 Sum_probs=137.8 Q ss_pred CCCEEEEEEEEEECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCEEEEEECCCCHHHHHH Q ss_conf 84236899999944556689704468664299989999999999775437975138999838952999985974899999 Q gi|254780147|r 2 AKVVSRIVKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVTCYKDKSFTFTMSQPPVSFFLK 81 (142) Q Consensus 2 ~k~v~~~ikl~v~aG~A~p~PplGp~LG~~Gini~~f~k~fN~~T~~~~~g~~v~V~i~v~~dksf~~~i~~P~~s~lik 81 (142) ||++++.|+|+++||+|+|+|||||+|||+|||+|+||+|||++|++|+ |++|||+|++|+||+|+|++++||+||||+ T Consensus 1 aK~v~~~ikl~v~aG~A~p~Pplgp~LG~~Gin~~~f~k~fN~~T~~~~-g~~v~V~i~v~~dksf~~~v~~P~~s~li~ 79 (140) T 1mms_A 1 AKKVAAQIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKA-GMILPVVITVYEDKSFTFIIKTPPASFLLK 79 (140) T ss_dssp ------CEEEEEETTCCCCTTTTTHHHHTTTCCHHHHHHHHHHHTTTSC-SSEEEEEEEECTTSCEEEEECCCCHHHHHH T ss_pred CCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCC-CCCEEEEEEEECCCCEEEEECCCCHHHHHH T ss_conf 9716899999976575079998641013579898999999999986216-982138999957972799986997799998 Q ss_pred HHCCCCCCCCCCCCCEEEEECHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHEEECCEEEEC Q ss_conf 6337666788999630101259999999999885406787899999977430214528939 Q gi|254780147|r 82 KEVGIKSGSKLPGKESCGSITRENIRKIAQLKMQDMGAIDIEGAMRMVEGSACSMGISVVD 142 (142) Q Consensus 82 k~~g~~kgs~~p~~~~~g~it~~~i~eIAk~K~~d~~~~~l~~~vk~VlGTa~SmGi~V~~ 142 (142) +++|+++||++|+++++|+||++|+||||+.|++|+++++|+++||+|+||||||||+||| T Consensus 80 k~~g~~kgs~~p~~~~vG~it~~~v~eIAk~K~~~~~~~~l~~~vk~VlGTa~SmGi~V~~ 140 (140) T 1mms_A 80 KAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSLEAAMKIIEGTAKSMGIEVVD 140 (140) T ss_dssp HHHTCSSCCSSTTTSCCEEECHHHHHHHHHHHGGGCCCSSHHHHHHHHHHHHTTTTEEEC- T ss_pred HHCCCCCCCCCCCCCCCCEEEHHHHHHHHHHHHHHCCCCCHHHHHHHHHEEHEECEEEEEC T ss_conf 7026667767999841518709999999999887607788999999534113457489989 No 3 >2ftc_G L11MT, MRP-L11, 39S ribosomal protein L11, mitochondrial; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} PDB: 3iy9_G Probab=100.00 E-value=0 Score=350.07 Aligned_cols=141 Identities=38% Similarity=0.746 Sum_probs=137.4 Q ss_pred CCCEEEEEEEEEECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCEEEEEECCCCHHHHHH Q ss_conf 84236899999944556689704468664299989999999999775437975138999838952999985974899999 Q gi|254780147|r 2 AKVVSRIVKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVTCYKDKSFTFTMSQPPVSFFLK 81 (142) Q Consensus 2 ~k~v~~~ikl~v~aG~A~p~PplGp~LG~~Gini~~f~k~fN~~T~~~~~g~~v~V~i~v~~dksf~~~i~~P~~s~lik 81 (142) .|++.++|||+|+||+|+|+|||||+|||+|||+++||++||++|++|++|+++||+|++|+||+|+|++++||+||||+ T Consensus 1 k~~i~~vikl~v~aG~A~p~PplGp~LG~~Gin~~~f~k~fN~~Tk~~~~g~~v~v~i~v~~dksf~~~v~~P~~s~ll~ 80 (145) T 2ftc_G 1 KPEVGGVIRAIVRAGLAMPGPPLGPVLGQRGVSINQFCKEFNERTKDIKEGIPLPTKILVKPDRTFEIKIGQPTVSYFLK 80 (145) T ss_pred CCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEEEECCCEEEEEECCCCHHHHHH T ss_conf 97504999999856752789987521245698989999999998776439970679999947970999987998799999 Q ss_pred HHCCCCCCCCCCCCCEEEEECHHHHHHHHHHHHHH----CCCCCHHHHHHHHHHHEEECCEEEEC Q ss_conf 63376667889996301012599999999998854----06787899999977430214528939 Q gi|254780147|r 82 KEVGIKSGSKLPGKESCGSITRENIRKIAQLKMQD----MGAIDIEGAMRMVEGSACSMGISVVD 142 (142) Q Consensus 82 k~~g~~kgs~~p~~~~~g~it~~~i~eIAk~K~~d----~~~~~l~~~vk~VlGTa~SmGi~V~~ 142 (142) +++|+++||++|+++++|+||++|+||||+.|++| |++.+|+++||+|+||||||||+|+. T Consensus 81 k~~g~~kgs~~p~~~~vG~it~~~v~eIAk~K~~d~~~~l~~~~l~~~vk~VlGTa~SmGi~V~k 145 (145) T 2ftc_G 81 AAAGIEKGARQTGKEVAGLVTLKHVYEIARIKAQDEAFALQDVPLSSVVRSIIGSARSLGIRVVK 145 (145) T ss_pred HHCCCCCCCCCCCCEEEEEECHHHHHHHHHHHCCCCHHHCCCCCHHHHHHHHHHHHEECEEEEEC T ss_conf 86288877555687676136399999999987706332335878999999988004347589979 No 4 >3egv_B 50S ribosomal protein L11, ribosomal protein L11 methyltransferase; post-translational modification, multiple methyltransferase, cytoplasm; HET: SAH 4MM; 1.75A {Thermus thermophilus} SCOP: d.47.1.1 PDB: 2e34_A 2e35_A 2e36_A 2h8w_A 2hgj_L 2hgq_L 2hgu_L 2j01_K 2j03_K 2jl6_K 2jl8_K 2klm_A 2nxn_B 2wh2_K 2wh4_K 2wrj_K 2wrl_K 2x9s_K 2x9u_K 3cjt_B* ... Probab=100.00 E-value=0 Score=352.29 Aligned_cols=138 Identities=49% Similarity=0.842 Sum_probs=135.8 Q ss_pred CCEEEEEEEEEECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCEEEEEECCCCHHHHHHH Q ss_conf 42368999999445566897044686642999899999999997754379751389998389529999859748999996 Q gi|254780147|r 3 KVVSRIVKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVTCYKDKSFTFTMSQPPVSFFLKK 82 (142) Q Consensus 3 k~v~~~ikl~v~aG~A~p~PplGp~LG~~Gini~~f~k~fN~~T~~~~~g~~v~V~i~v~~dksf~~~i~~P~~s~likk 82 (142) |+++++|||+++||+|+|+|||||+|||+|||+|+||++||++|++|+ |.++||+|++|+||+|+|++++||+||||++ T Consensus 1 K~v~~~ikl~v~aG~A~p~PplGP~LG~~Gini~~f~k~fN~~T~~~~-g~~vpV~i~v~~dksf~~~i~~P~~s~ll~k 79 (146) T 3egv_B 1 KKVVAVVKLQLPAGAATPAPPVGPALGQHGANIMEFVKAFNAATANMG-DAIVPVEITIYADRSFTFVTKTPPASYLIRK 79 (146) T ss_dssp CCEEEEEEEEEETTCCCSSTTHHHHHHTTTCCHHHHHHHHHHHTTTST-TCEEEEEEEEETTSCEEEEECCCCHHHHC-- T ss_pred CCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCC-CCCCEEEEEECCCCCEEEEECCCCHHHHHHH T ss_conf 937899999977574379998630003579898999999999975216-9954069997289628999869966999997 Q ss_pred HCCCCCCCCCCCCCEEEEECHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHEEECCEEEE Q ss_conf 33766678899963010125999999999988540678789999997743021452893 Q gi|254780147|r 83 EVGIKSGSKLPGKESCGSITRENIRKIAQLKMQDMGAIDIEGAMRMVEGSACSMGISVV 141 (142) Q Consensus 83 ~~g~~kgs~~p~~~~~g~it~~~i~eIAk~K~~d~~~~~l~~~vk~VlGTa~SmGi~V~ 141 (142) ++|+++||++|+++++|+||++|+||||+.|++||++.+|+++||+|+||||||||+|+ T Consensus 80 ~~g~~kgs~~~~~~~~g~it~~~v~eIAk~K~~dl~~~~l~~~vk~VlGTa~SmGi~V~ 138 (146) T 3egv_B 80 AAGLEKGAHKPGREKVGRITWEQVLEIAKQKMPDLNTTDLEAAARMIAGSARSMGVEVV 138 (146) T ss_dssp ----------------------------------------------------------- T ss_pred HHCCCCCCCCCCCEEEEEEEHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHEECEEEEE T ss_conf 43214566789972512788999999999987765552499999985600435768999 No 5 >1vq8_I 50S ribosomal protein L11P; 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: a.4.7.1 PDB: 1vq4_I* 1vq5_I* 1vq6_I* 1vq7_I* 1s72_I* 1vq9_I* 1vqk_I* 1vql_I* 1vqm_I* 1vqn_I* 1vqo_I* 1vqp_I* 1yhq_I* 1yi2_I* 1yij_I* 1yit_I* 1yj9_I* 1yjn_I* 1yjw_I* 2otl_I* ... Probab=100.00 E-value=0 Score=351.69 Aligned_cols=137 Identities=26% Similarity=0.561 Sum_probs=133.7 Q ss_pred EEEEEEEEEECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCEEEEEECCCCHHHHHHHHC Q ss_conf 36899999944556689704468664299989999999999775437975138999838952999985974899999633 Q gi|254780147|r 5 VSRIVKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVTCYKDKSFTFTMSQPPVSFFLKKEV 84 (142) Q Consensus 5 v~~~ikl~v~aG~A~p~PplGp~LG~~Gini~~f~k~fN~~T~~~~~g~~v~V~i~v~~dksf~~~i~~P~~s~likk~~ 84 (142) +.++|||+|+||+|+|+|||||+|||+|||+|+||++||++|++|+ |++|||+|++|+||+|+|++++||+||||++++ T Consensus 1 ~~~~ikl~v~aG~A~p~Pplgp~LG~~Gini~~f~k~fN~~T~~~~-g~~v~V~i~v~~dksf~~~v~~Pp~s~llkkaa 79 (162) T 1vq8_I 1 MAGTIEVLVPGGEANPGPPLGPELGPTPVDVQAVVQEINDQTAAFD-GTEVPVTVKYDDDGSFEIEVGVPPTAELIKDEA 79 (162) T ss_dssp -------------------------------------------------------------------CCCCHHHHHHHTT T ss_pred CCEEEEEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCC-CCEEEEEEEEECCCCEEEEECCCCHHHHHHHHH T ss_conf 9469999987686179998640003579898999999999987538-976669999974885689985898799999972 Q ss_pred CCCCCCCCCCCCEEEEECHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHEEECCEEEEC Q ss_conf 7666788999630101259999999999885406787899999977430214528939 Q gi|254780147|r 85 GIKSGSKLPGKESCGSITRENIRKIAQLKMQDMGAIDIEGAMRMVEGSACSMGISVVD 142 (142) Q Consensus 85 g~~kgs~~p~~~~~g~it~~~i~eIAk~K~~d~~~~~l~~~vk~VlGTa~SmGi~V~~ 142 (142) |+++||++|+++++|+||++|+||||+.|++|+++.+|+++||+|+||||||||+|+. T Consensus 80 gi~kgs~~p~~~~vG~It~~qv~eIAk~K~~d~~~~~l~~~vk~VlGTa~SmGi~V~g 137 (162) T 1vq8_I 80 GFETGSGEPQEDFVADLSVDQVKQIAEQKHPDLLSYDLTNAAKEVVGTCTSLGVTIEG 137 (162) T ss_dssp SCCSCCSSTTTSCCEEECHHHHHHHHHHTTTTCCCSSHHHHHHHHHHHTTTTTEEEC- T ss_pred CCCCCCCCCCCCCCCEECHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCEEEEEC T ss_conf 6677789999754660649999999999714015589999999999826325599977 No 6 >3ofq_I 50S ribosomal protein L11; protein biosynthesis, ribosomes, RNA, tRNA, transfer, antibi EXIT, peptidyl, ribosomal subunit, large; 3.10A {Escherichia coli} PDB: 1p85_G 1p86_G 2awb_I 2aw4_I 2i2v_I 2j28_I 2i2t_I* 2qao_I* 2qba_I* 2qbc_I* 2qbe_I 2qbg_I 2qbi_I* 2qbk_I* 2qov_I 2qox_I 2qoz_I* 2qp1_I* 2rdo_I 2vhm_I ... Probab=100.00 E-value=0 Score=365.46 Aligned_cols=141 Identities=55% Similarity=0.901 Sum_probs=139.3 Q ss_pred CCCEEEEEEEEEECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCEEEEEECCCCHHHHHH Q ss_conf 84236899999944556689704468664299989999999999775437975138999838952999985974899999 Q gi|254780147|r 2 AKVVSRIVKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVTCYKDKSFTFTMSQPPVSFFLK 81 (142) Q Consensus 2 ~k~v~~~ikl~v~aG~A~p~PplGp~LG~~Gini~~f~k~fN~~T~~~~~g~~v~V~i~v~~dksf~~~i~~P~~s~lik 81 (142) ||++.++|||+++||+|+|+|||||+|||+|||+|+||++||++|++|+.|+++||+|++|+||+|+|++++||+||||+ T Consensus 1 aK~v~~~ikl~v~aG~A~p~PplGP~LG~~Gini~~f~k~fN~~T~~~k~g~~vpV~Itv~~dksf~~~i~~Pp~s~li~ 80 (141) T 3ofq_I 1 AKKVQAYVKLQVAAGMANPSPPVGPALGQQGVNIMEFCKAFNAKTDSIEKGLPIPVVITVYADRSFTFVTKTPPAAVLLK 80 (141) T ss_dssp CCCCCCCCCCCCCTTCCSSSSSSSTTTCSSSCCSSTTTSTTSSTTTTTCSSSCCCCCCCCCSSSCCCCCCCCCCSTTTGG T ss_pred CCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEEEEEECCCEEEEEECCCCHHHHHH T ss_conf 97247999999755852799987511135698989999999998763107964778999957952999977997599998 Q ss_pred HHCCCCCCCCCCCCCEEEEECHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHEEECCEEEEC Q ss_conf 6337666788999630101259999999999885406787899999977430214528939 Q gi|254780147|r 82 KEVGIKSGSKLPGKESCGSITRENIRKIAQLKMQDMGAIDIEGAMRMVEGSACSMGISVVD 142 (142) Q Consensus 82 k~~g~~kgs~~p~~~~~g~it~~~i~eIAk~K~~d~~~~~l~~~vk~VlGTa~SmGi~V~~ 142 (142) +++|+++||++|+++++|+||++|+||||+.|++||++.+|+++||+|+||||||||+|+| T Consensus 81 k~~g~~kgs~~p~~~~vG~it~~~v~eIAk~K~~dl~~~~l~~~vk~V~GTa~SmGi~V~~ 141 (141) T 3ofq_I 81 KAAGIKSGSGKPNKDKVGKISRAQLQEIAQTKAADMTGADIEAMTRSIEGTARSMGLVVED 141 (141) T ss_dssp GSSSCSSCCSSSSSSCCCCCCTTSTTTSSSSSSSSSSCCSTTSSSHHHHTTTTTTSCCCCC T ss_pred HHCCCCCCCCCCCCCCCCEEEHHHHHHHHHHHHHHHCCCCHHHHHHHHHEEEEECEEEEEC T ss_conf 7427764468998642564719999999999888766788999999845312447589879 No 7 >2zkr_i 60S ribosomal protein L12; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 3jyw_K 1s1i_K Probab=100.00 E-value=0 Score=330.22 Aligned_cols=139 Identities=22% Similarity=0.300 Sum_probs=126.3 Q ss_pred CCCCE----EEEEEEEEECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCEEEEEECCCCH Q ss_conf 98423----68999999445566897044686642999899999999997754379751389998389529999859748 Q gi|254780147|r 1 MAKVV----SRIVKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVTCYKDKSFTFTMSQPPV 76 (142) Q Consensus 1 M~k~v----~~~ikl~v~aG~A~p~PplGp~LG~~Gini~~f~k~fN~~T~~~~~g~~v~V~i~v~~dksf~~~i~~P~~ 76 (142) |.+++ +++|+|+|+||+|+|+|||||+|||+|||+|+||++||++|++|+ |++|||+|++|+|++|.+.+ ||+ T Consensus 1 m~~k~~~~~v~~ikl~v~~G~A~P~PplGpaLG~~GiNi~~f~k~fN~~T~~~~-G~~VpV~Itv~~d~~~~~~~--p~~ 77 (165) T 2zkr_i 1 MPPKFDPNEIKVVYLRCTGGEVGATSALAPKIGPLGLSPKKVGDDIAKATGDWK-GLRITVKLTIQNRQAQIEVV--PSA 77 (165) T ss_dssp -----------------------------------------------------------------------CCCC--CCH T ss_pred CCCCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCC-CCEEEEEEEEECCEEEEEEC--CCC T ss_conf 969988880699999972575489997652114568789999999999875337-94565899994564799973--880 Q ss_pred HHHHHHHC--CCCCCCCCCCCCEEEEECHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHEEECCEEEEC Q ss_conf 99999633--7666788999630101259999999999885406787899999977430214528939 Q gi|254780147|r 77 SFFLKKEV--GIKSGSKLPGKESCGSITRENIRKIAQLKMQDMGAIDIEGAMRMVEGSACSMGISVVD 142 (142) Q Consensus 77 s~likk~~--g~~kgs~~p~~~~~g~it~~~i~eIAk~K~~d~~~~~l~~~vk~VlGTa~SmGi~V~~ 142 (142) |+++++++ +..+|+..++++++|+||++|+||||+.|++||++++|+++||+|+||||||||+||. T Consensus 78 s~~~lk~~~~~~~~gs~~~~~e~vG~It~~qv~eIAk~K~~dl~~~~l~~a~k~V~GTArSMGI~VeG 145 (165) T 2zkr_i 78 SALIIKALKEPPRDRKKQKNIKHSGNITFDEIVNIARQMRHRSLARELSGTIKEILGTAQSVGCNVDG 145 (165) T ss_dssp HHHHHHHHTCSSCCSSTTTCSSCSEEECHHHHHHHHHHHTTTCCCSSHHHHHHHHHHHHHHHTEEEC- T ss_pred HHHHHHHHCCCCCCCCCCCCCEEEEEECHHHHHHHHHHHHHHHCCCCHHHHHHHHHEEHEEEEEEEEC T ss_conf 69999986677556788875405513539999999995441014799999999855566034689857 No 8 >3cjs_B 50S ribosomal protein L11, ribosomal protein L11 methyltransferase; S-adenosyl-L-methionine dependent methyltransferase; 1.37A {Thermus thermophilus} SCOP: d.47.1.1 PDB: 3cju_B* 2bcw_A Probab=99.96 E-value=2.9e-29 Score=192.29 Aligned_cols=71 Identities=54% Similarity=0.881 Sum_probs=67.9 Q ss_pred CCEEEEEEEEEECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCEEEEEECCC Q ss_conf 423689999994455668970446866429998999999999977543797513899983895299998597 Q gi|254780147|r 3 KVVSRIVKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVTCYKDKSFTFTMSQP 74 (142) Q Consensus 3 k~v~~~ikl~v~aG~A~p~PplGp~LG~~Gini~~f~k~fN~~T~~~~~g~~v~V~i~v~~dksf~~~i~~P 74 (142) |++.++|||+++||+|+|+|||||+|||+|||+|+||++||++|++++ |..+||+|++|+||||+|++++| T Consensus 2 Kkv~~~ikl~i~aG~A~P~PPvGpaLGq~GiNi~~Fck~fN~~T~~~~-g~~vpv~I~v~~Dksf~f~ik~P 72 (72) T 3cjs_B 2 KKVVAVVKLQLPAGKATPAPPVGPALGQHGANIMEFVKAFNAATANMG-DAIVPVEITIYADRSFTFVTKTP 72 (72) T ss_dssp CCEEEEEEEEEETTCCCSSTTHHHHHHTTTCCHHHHHHHHHHHHGGGC-SCEEEEEEEEETTSCEEEEECCC T ss_pred CCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCC-CCCEEEEEEEECCCCEEEEECCC T ss_conf 643589999986677788999775101258788999999999876435-99367999997798389996088 No 9 >1wib_A 60S ribosomal protein L12; N-terminal domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, ribosome; NMR {Mus musculus} SCOP: d.47.1.1 Probab=99.95 E-value=2e-29 Score=193.28 Aligned_cols=78 Identities=19% Similarity=0.333 Sum_probs=74.9 Q ss_pred EEEEEEEEEECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCEEEEEECCCCHHHHHHHHC Q ss_conf 36899999944556689704468664299989999999999775437975138999838952999985974899999633 Q gi|254780147|r 5 VSRIVKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVTCYKDKSFTFTMSQPPVSFFLKKEV 84 (142) Q Consensus 5 v~~~ikl~v~aG~A~p~PplGp~LG~~Gini~~f~k~fN~~T~~~~~g~~v~V~i~v~~dksf~~~i~~P~~s~likk~~ 84 (142) .+++|+|+|+||+|+|+|||||+|||+|||+|+||++||++|++|+ |++|||+|+| +||+|+|++ +||+|+||++++ T Consensus 15 ~v~~Ikl~v~gG~A~p~PplgPaLG~~Gini~~f~k~fN~~T~~~k-G~~VpV~ItV-~dR~f~~~v-~Pp~S~L~~~aa 91 (92) T 1wib_A 15 EVKVVYLRCTGGEVGATSALAPKIGPLGLSPKKVGDDIAKATGDWK-GLRITVKLTI-QNRQAQIEV-VPSASALSGPSS 91 (92) T ss_dssp SCEEEEEEEETTCCCCSSCSHHHHTTTCSCHHHHHHHHHHHTTTTT-TSEEEEEEEE-ETTEEECCB-CSCCCCCCCCSC T ss_pred CEEEEEEEEECCCCCCCCCCCCHHCCCCCCHHHHHHHHHHHHHHCC-CCEEEEEEEE-ECCEEEEEE-ECCHHHHHHHHC T ss_conf 0799999984575378997650003568779999999999863316-9875699999-486589999-388999988741 Q ss_pred C Q ss_conf 7 Q gi|254780147|r 85 G 85 (142) Q Consensus 85 g 85 (142) | T Consensus 92 G 92 (92) T 1wib_A 92 G 92 (92) T ss_dssp C T ss_pred C T ss_conf 9 No 10 >1hc8_A Ribosomal protein L11; ribosome, ribosomal RNA, tertiary structure, RNA-protein; HET: GTP; 2.8A {Bacillus stearothermophilus} SCOP: a.4.7.1 PDB: 1y39_A* 1aci_A 1fow_A 1fox_A 1foy_A 2fow_A Probab=99.94 E-value=3.2e-28 Score=186.17 Aligned_cols=76 Identities=50% Similarity=0.817 Sum_probs=75.1 Q ss_pred EEEEECCCCHHHHHHHHCCCCCCCCCCCCCEEEEECHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHEEECCEEEEC Q ss_conf 9999859748999996337666788999630101259999999999885406787899999977430214528939 Q gi|254780147|r 67 FTFTMSQPPVSFFLKKEVGIKSGSKLPGKESCGSITRENIRKIAQLKMQDMGAIDIEGAMRMVEGSACSMGISVVD 142 (142) Q Consensus 67 f~~~i~~P~~s~likk~~g~~kgs~~p~~~~~g~it~~~i~eIAk~K~~d~~~~~l~~~vk~VlGTa~SmGi~V~~ 142 (142) |+|++++||+||||++++|+++||++|+++.+|+||++|+||||+.|++||++.+|+++||+|+||||||||+||| T Consensus 1 F~f~~ktPP~s~llkkaagi~kGs~~p~~~~vG~it~~qv~eIAk~K~~dl~~~~l~~a~k~V~GTarSmGI~Ved 76 (76) T 1hc8_A 1 FTFITKTPPAAVLLKKAAGIESGSGEPNRNKVATIKRDKVREIAELKMPDLNAASIEAAMRMIEGTARSMGIVVEN 76 (76) T ss_dssp -CCCCCCCCHHHHHHHHHTCSCCCSSTTTCCCEEECHHHHHHHHHHSGGGCCCSSHHHHHHHHHHHHHHHTEEEC- T ss_pred CEEEECCCCHHHHHHHHHCCCCCCCCCCCEEEEEECHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHEECEEEEEC T ss_conf 9489758988999999978887789988715565669999999998750238989999999978105016689769 No 11 >1qa6_A Ribosomal protein L11; ribosomal RNA, tertiary structur,E RNA-protein interaction, minor groove binding, antibiotic binding; 2.80A {Geobacillus stearothermophilus} SCOP: a.4.7.1 PDB: 1c04_C Probab=99.89 E-value=3.9e-24 Score=162.03 Aligned_cols=67 Identities=51% Similarity=0.837 Sum_probs=66.1 Q ss_pred CCCCHHHHHHHHCCCCCCCCCCCCCEEEEECHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHEEECCE Q ss_conf 5974899999633766678899963010125999999999988540678789999997743021452 Q gi|254780147|r 72 SQPPVSFFLKKEVGIKSGSKLPGKESCGSITRENIRKIAQLKMQDMGAIDIEGAMRMVEGSACSMGI 138 (142) Q Consensus 72 ~~P~~s~likk~~g~~kgs~~p~~~~~g~it~~~i~eIAk~K~~d~~~~~l~~~vk~VlGTa~SmGi 138 (142) ++||+||||++++|+++||++|+++++|+||++|+||||+.|++|||+.+++++||+|+|||||||| T Consensus 1 KtPP~s~llkkaagi~kGs~~p~~~~vG~it~~qv~eIAk~K~~dl~~~~l~~a~k~v~GtArSMGI 67 (67) T 1qa6_A 1 KTPPAAVLLKKAAGIESGSGEPNRNKVATIKRDKVREIAELKMPDLNAASIEAAMRMIEGTARSMGI 67 (67) T ss_dssp CCSCHHHHHHHHHTCSCCCCTTSSCCCCCCTTTHHHHHHHHHGGGCCCSSHHHHHHHHHHHHHHHTC T ss_pred CCCCHHHHHHHHHCCCCCCCCCCCCCHHHCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCC T ss_conf 9898899999997889788999983220126999999999875103899999999999988983489 No 12 >1no4_A Late, head morphogenesis protein; coiled-coil, viral protein; 2.20A {Bacillus phage PHI29} SCOP: h.1.24.1 PDB: 1noh_A Probab=29.22 E-value=14 Score=17.21 Aligned_cols=25 Identities=24% Similarity=0.324 Sum_probs=21.5 Q ss_pred HHHHHCCCCHHHHHHHHHHHHHHHH Q ss_conf 6866429998999999999977543 Q gi|254780147|r 26 PAIGQAGIPIMAFCKAFNAATEGME 50 (142) Q Consensus 26 p~LG~~Gini~~f~k~fN~~T~~~~ 50 (142) -+|.|+.+|-..|.-+||+.|+... T Consensus 26 e~lqqlr~~ygs~vse~~dlt~~~e 50 (97) T 1no4_A 26 EALQQLRVNYGSFVSEYNDLTKSHE 50 (97) T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999999887679999888878899 No 13 >2vqe_M 30S ribosomal protein S13, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: a.156.1.1 PDB: 1gix_P* 1hnw_M* 1hnx_M* 1hnz_M* 1hr0_M 1ibk_M* 1ibl_M* 1ibm_M 1j5e_M 1jgo_P* 1jgp_P* 1jgq_P* 1mj1_P* 1ml5_P* 1n32_M* 1n33_M* 1n34_M 1n36_M 1xmo_M* 1xmq_M* ... Probab=27.63 E-value=32 Score=15.04 Aligned_cols=52 Identities=6% Similarity=0.022 Sum_probs=36.7 Q ss_pred CCCHHHHHHHHCCCCCCCCCCCCCEEEEECHHHHHHHHHHHHHH-CCCCCHHHHHHHHH Q ss_conf 97489999963376667889996301012599999999998854-06787899999977 Q gi|254780147|r 73 QPPVSFFLKKEVGIKSGSKLPGKESCGSITRENIRKIAQLKMQD-MGAIDIEGAMRMVE 130 (142) Q Consensus 73 ~P~~s~likk~~g~~kgs~~p~~~~~g~it~~~i~eIAk~K~~d-~~~~~l~~~vk~Vl 130 (142) .+..|..|.+.+|++. ...+|++|-+|+.+|......+ +...+|+..+++=+ T Consensus 26 G~~~A~~Ic~~lGId~------~~kvg~Lt~~qi~~l~~~i~~~~~i~~~L~~~~~~~i 78 (126) T 2vqe_M 26 GKARAKEALEKTGINP------ATRVKDLTEAEVVRLREYVENTWKLEGELRAEVAANI 78 (126) T ss_dssp CSHHHHHHTTTTTCCT------TSBGGGCCHHHHHHHHHHHHTTSCCHHHHHHHHHHHH T ss_pred CHHHHHHHHHHCCCCC------CCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHH T ss_conf 8999999999859796------6301639999999999998314511478999999989 No 14 >2k53_A A3DK08 protein; NESG, CMR9, structural genomics, PSI-2, protein structure initiative; NMR {Clostridium thermocellum atcc 27405} Probab=25.32 E-value=36 Score=14.79 Aligned_cols=37 Identities=16% Similarity=0.079 Sum_probs=30.1 Q ss_pred EECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHH Q ss_conf 9445566897044686642999899999999997754 Q gi|254780147|r 13 IESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGM 49 (142) Q Consensus 13 v~aG~A~p~PplGp~LG~~Gini~~f~k~fN~~T~~~ 49 (142) ..++..++.-+|..+.--+|+|+-.|.++.|+..++- T Consensus 30 C~gc~~a~~~tL~eaa~~~gid~~~ll~eLn~~i~~~ 66 (76) T 2k53_A 30 CLGCPSSMGESIEDACAVHGIDADKLVKELNEYFEKK 66 (76) T ss_dssp CCSSCCCCCSBHHHHHHHHTCCHHHHHHHHHHHHHHH T ss_pred CCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 8578776667099999994979999999999999977 No 15 >1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A Probab=20.97 E-value=44 Score=14.27 Aligned_cols=69 Identities=19% Similarity=0.337 Sum_probs=44.6 Q ss_pred EEEEEECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHH---------------HHHHCCCCCEEEEEEECCCEEEEEECC Q ss_conf 99999445566897044686642999899999999997---------------754379751389998389529999859 Q gi|254780147|r 9 VKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAAT---------------EGMEKGIPIPTTVTCYKDKSFTFTMSQ 73 (142) Q Consensus 9 ikl~v~aG~A~p~PplGp~LG~~Gini~~f~k~fN~~T---------------~~~~~g~~v~V~i~v~~dksf~~~i~~ 73 (142) -|+-|.+-..+- -|+|-..|+.|.++..+.++.|..- ..+.+-..+.|.+.-..++++...+.. T Consensus 233 tKvAV~s~d~~i-DpvGa~vG~~G~ri~~i~~el~ge~idii~~s~d~~~fi~nal~Pa~v~~v~~~~~~~~~~~v~v~~ 311 (344) T 1hh2_P 233 TKVAVASNDPNV-DPIGACIGEGGSRIAAILKELKGEKLDVLKWSDDPKQLIANALAPATVIEVEILDKENKAARVLVPP 311 (344) T ss_dssp EEEEEEESSTTS-CHHHHHHCTTSTTHHHHHHHTTTCEEEEEECCSSHHHHHHHHTCSSCCSEEEEEETTTTEEEEEECT T ss_pred EEEEEEECCCCC-CCCEEEECCCCCHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCEEEEEEECCCCCEEEEEECH T ss_conf 469999348875-5101456589717999999857993589966899999999844956301899973888779999880 Q ss_pred CCHHH Q ss_conf 74899 Q gi|254780147|r 74 PPVSF 78 (142) Q Consensus 74 P~~s~ 78 (142) -.-|. T Consensus 312 ~~~~~ 316 (344) T 1hh2_P 312 TQLSL 316 (344) T ss_dssp TSHHH T ss_pred HHHHH T ss_conf 24026 Done!