Query gi|254780242|ref|YP_003064655.1| 50S ribosomal protein L15 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 151 No_of_seqs 152 out of 2062 Neff 6.3 Searched_HMMs 23785 Date Tue May 24 01:04:27 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780242.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_N Ribosomal protein L15; 100.0 0 0 368.8 1.8 147 1-151 65-220 (257) 2 2j01_P 50S ribosomal protein L 100.0 0 0 337.6 8.1 141 1-151 1-148 (150) 3 2zjr_I 50S ribosomal protein L 100.0 0 0 337.2 6.3 142 1-151 1-143 (156) 4 3ofq_L 50S ribosomal protein L 100.0 0 0 336.1 3.1 141 2-149 1-142 (143) 5 1vq8_L 50S ribosomal protein L 100.0 8.7E-43 0 242.3 9.7 136 11-151 2-144 (165) 6 2zkr_l 60S ribosomal protein L 100.0 1.5E-34 6.2E-39 199.4 9.3 137 12-151 6-147 (148) 7 3jyw_V 60S ribosomal protein L 100.0 7.8E-34 3.3E-38 195.7 5.8 130 16-151 2-142 (142) 8 1vq8_O 50S ribosomal protein L 99.2 2.7E-11 1.1E-15 78.2 6.1 75 55-150 25-99 (116) 9 2zkr_o 60S ribosomal protein L 98.6 4.2E-08 1.8E-12 61.6 4.7 80 55-151 42-123 (188) 10 2zkr_l 60S ribosomal protein L 98.5 2.1E-08 8.8E-13 63.2 1.2 67 12-84 3-78 (148) 11 3jyw_O 60S ribosomal protein L 98.3 1.3E-08 5.4E-13 64.3 -3.1 79 55-150 23-103 (121) 12 3jyw_V 60S ribosomal protein L 98.2 5.3E-07 2.2E-11 55.8 3.3 53 12-64 1-54 (142) 13 1vq8_L 50S ribosomal protein L 91.4 0.12 4.9E-06 28.0 3.1 62 10-83 14-75 (165) 14 3ofq_E 50S ribosomal protein L 61.8 6.4 0.00027 18.9 3.5 121 20-143 48-198 (201) 15 2ftc_D Mitochondrial ribosomal 42.8 8.7 0.00036 18.3 1.6 35 109-143 139-175 (175) 16 3bbn_P Ribosomal protein S16; 42.4 12 0.0005 17.5 2.3 44 63-109 36-79 (88) 17 3mr8_P 30S ribosomal protein S 39.0 20 0.00084 16.4 3.0 45 63-109 36-82 (83) 18 2j01_F 50S ribosomal protein L 37.2 15 0.00061 17.1 2.0 39 109-147 168-209 (210) 19 1vq8_C 50S ribosomal protein L 27.3 9.5 0.0004 18.1 -0.2 35 109-143 205-245 (246) 20 3bn0_A 30S ribosomal protein S 21.1 29 0.0012 15.5 1.2 45 63-109 37-81 (112) No 1 >3bbo_N Ribosomal protein L15; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Pisum sativum} Probab=100.00 E-value=0 Score=368.81 Aligned_cols=147 Identities=39% Similarity=0.649 Sum_probs=135.4 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCEEEECCC-CCCCCCC---CCCEEE Q ss_conf 97666888999876761020315789898578776676423689866-444316853011676-3554656---552147 Q gi|254780242|r 1 MKLNEISYDKGSCKVKKRVARGIGSGTGKTAGRGVKGQKSRSGVSVR-GFEGGQMPLYRRLPK-RGFVNIA---GSDFVT 75 (151) Q Consensus 1 m~L~~l~~~~g~~~~~kR~GRG~gsg~Gkt~GrG~kGqk~Rsg~~~~-gfEGGQ~Pl~rrlPK-rGF~~~~---~~~~~~ 75 (151) |+||||+|++||+++++|||||+|||+|||||||||||+||||+.++ ||||||||||||||| |||++.+ ..+|.+ T Consensus 65 mkLn~Lkp~~gs~k~kkRvGRG~gSG~GKTsGRG~KGQkaRsG~~~~~gFEGGQmPL~RRlPK~RGF~n~~~~~~~~~~~ 144 (257) T 3bbo_N 65 FRLDNLGPQPGSRKRPKRKGRGIAAGQGASCGFGMRGQKSRSGPGIMRGFEGGQMPLYRRLPKLRGIAGGMHAGLPKYVN 144 (257) T ss_dssp CCCSSSCCCCCCCSCCCCCSSCCCCSCSSSCSSSCCCCGGGTSSCSSTTCCSSCSSTTSCCCCCSSCCCCCSSCCSSSSC T ss_pred EECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCCEEEEE T ss_conf 67477889999866774532688899886688988778888899999971789976465048767767866676206899 Q ss_pred EEHHHHHHHHCCCCCCCCCCCCHHHHHHCCCCC----CCCCCEEEECCCCCCCCEEEEEEEECHHHHHHHHHCCCEEEEC Q ss_conf 751120454302455533223355554308625----4433204630443144148999982699999999749889989 Q gi|254780242|r 76 ISLGLLQAYIDKDRLDCSSEIDASVLVASGLVR----RSQRGIRILSDGDLKAKVVLRVSGASASAVEKVEKLGGQVIVI 151 (151) Q Consensus 76 iNL~~L~~~i~~~~~~~~~~Id~~~L~~~gli~----~~~~~vKiLg~Gel~~ki~I~v~~~S~sA~ekIE~aGG~v~ii 151 (151) |||+.|+. ..+++.++||+++|++.++|. +..++|||||+|||+.||+|+|++||++|+|+||+|||+|++| T Consensus 145 vNL~~L~~----~~~~~~~~It~e~L~~~glI~~~~kk~k~~VKILG~Gel~~kI~Ikv~~~SksAkekIEkAGGsV~ii 220 (257) T 3bbo_N 145 VNLTDIEN----AGFQDGEEVSLETLKAKRVINPSGRERKLPLKILADGELSKKLTIKAGAFSTSAKEKLEYAGCSLIVL 220 (257) T ss_dssp SCSSCCSC----SSTTTTTTTCCSSCCSSSCSSSSCCCCSCCCCCCCSSCCCSSCCCCSSCCTGGGTTSSTTTTCCEECC T ss_pred EEECHHHH----HCCCCCCCCCHHHHHHCCCCCCHHHHCCCCEEEECCCCCCCCEEEEEEEECHHHHHHHHHCCCEEEEE T ss_conf 86101133----10253233689999876763200010565769952881753669999998999999999849979997 No 2 >2j01_P 50S ribosomal protein L15; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} SCOP: c.12.1.1 PDB: 1vsp_J 2hgj_O 2hgq_O 2hgu_O 1vsa_J 2j03_P 2jl6_P 2jl8_P 2v47_P 2v49_P 2wdi_P 2wdj_P 2wdl_P 2wdn_P 2wh2_P 2wh4_P 2wrj_P 2wrl_P 2wro_P 2wrr_P ... Probab=100.00 E-value=0 Score=337.62 Aligned_cols=141 Identities=39% Similarity=0.626 Sum_probs=127.1 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CC-CCCCCCCCEEEECCCCCCCCCC-----CCCE Q ss_conf 976668889998767610203157898985787766764236898-66-4443168530116763554656-----5521 Q gi|254780242|r 1 MKLNEISYDKGSCKVKKRVARGIGSGTGKTAGRGVKGQKSRSGVS-VR-GFEGGQMPLYRRLPKRGFVNIA-----GSDF 73 (151) Q Consensus 1 m~L~~l~~~~g~~~~~kR~GRG~gsg~Gkt~GrG~kGqk~Rsg~~-~~-gfEGGQ~Pl~rrlPKrGF~~~~-----~~~~ 73 (151) |+||||+|++||+++++|+|||+|||+|||||||||||+||||+. .+ +|||||||||||||||||++++ ..+| T Consensus 1 m~L~~l~~~~g~~k~~kR~GRG~gsg~Gkt~GrG~kGqk~RsG~~~~~~~fEGGq~Pl~rrlPKrGF~~~~~~~~~~~~~ 80 (150) T 2j01_P 1 MKLSDLRPNPGANKRRKRVGRGPGSGHGKTATRGHKGQKSRSGGLKDPRRFEGGRSTTLMRLPKRGMQGQVPGEIKRPRY 80 (150) T ss_dssp ----CCSSSCCCSSCCCCCCCCSCSSSSSCTTCSSCCSSSCSSCCCCSSSCCSSSCTTCCSCCCCCSCCCSSCSCCCCCE T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCEEEECCCCCCCEEEEEE T ss_conf 95244889989864773665778889896689989988767788868762147876777227633120355442122342 Q ss_pred EEEEHHHHHHHHCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCCCCCCEEEEEEEECHHHHHHHHHCCCEEEEC Q ss_conf 477511204543024555332233555543086254433204630443144148999982699999999749889989 Q gi|254780242|r 74 VTISLGLLQAYIDKDRLDCSSEIDASVLVASGLVRRSQRGIRILSDGDLKAKVVLRVSGASASAVEKVEKLGGQVIVI 151 (151) Q Consensus 74 ~~iNL~~L~~~i~~~~~~~~~~Id~~~L~~~gli~~~~~~vKiLg~Gel~~ki~I~v~~~S~sA~ekIE~aGG~v~ii 151 (151) .+|||++|+.+ +.++++++|++++++++. ++|||||+||++ ||+|+|++||++|+|+||+|||+|++| T Consensus 81 ~~inl~~l~~~--------~~~~~~~~L~~~glik~~-~~vKiLG~Ge~k-~l~I~v~~~S~sA~ekIE~aGG~v~ii 148 (150) T 2j01_P 81 QGVNLKDLARF--------EGEVTPELLVRAGLLKKG-YRLKILGEGEAK-PLKVVAHAFSKSALEKLKAAGGEPVLL 148 (150) T ss_dssp EEEETTTTTTS--------CSCCCTTTTTTSSSCSSC-CEEEEECSSCCC-SSCCCCSBCCHHHHHHHHTSCCCCCCC T ss_pred EHHHHHHHHCC--------CCCCCHHHHHHCCCCCCC-CCEEEEECCCEE-EEEEEEEEECHHHHHHHHHCCCEEEEE T ss_conf 02335454113--------322569999873755578-678998079478-789998986899999999869989996 No 3 >2zjr_I 50S ribosomal protein L15; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: c.12.1.1 PDB: 1nwx_J* 1nwy_J* 1sm1_J* 1xbp_J* 2zjp_I* 2zjq_I 1nkw_J 3cf5_I* 3dll_I* 1pnu_J 1pny_J 1vor_M 1vou_M 1vow_M 1voy_M 1vp0_M Probab=100.00 E-value=0 Score=337.24 Aligned_cols=142 Identities=47% Similarity=0.722 Sum_probs=134.1 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCEEEECCCCCCCCCCCCCEEEEEHH Q ss_conf 97666888999876761020315789898578776676423689866-44431685301167635546565521477511 Q gi|254780242|r 1 MKLNEISYDKGSCKVKKRVARGIGSGTGKTAGRGVKGQKSRSGVSVR-GFEGGQMPLYRRLPKRGFVNIAGSDFVTISLG 79 (151) Q Consensus 1 m~L~~l~~~~g~~~~~kR~GRG~gsg~Gkt~GrG~kGqk~Rsg~~~~-gfEGGQ~Pl~rrlPKrGF~~~~~~~~~~iNL~ 79 (151) |+||||+|+|||+++++|+|||+| |+|||||||||||+||||+..+ +|||||||||||+|||||+|+ ..+|.+|||+ T Consensus 1 m~l~~l~~~~g~~k~rkr~grG~g-g~Gkt~GrG~KGqk~RsG~~~~~~feGGq~Pl~rr~PKrGF~~~-~~~~~~vnl~ 78 (156) T 2zjr_I 1 MKLHDLKPTPGSRKDRKRVGRGPG-GTDKTAGRGHKGQKSRSGAGKGAFFEGGRSRLIARLPKRGFNNV-GTTYEVVKLS 78 (156) T ss_dssp ---CCCCCCSSTTTCCCCSSSCCC-CCCSCSSSCCCCSSSSSCCSCCCSCSCCSSSSTTTSCCCCCCCC-CCCCCEECHH T ss_pred CCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCC-CCEEEEEEHH T ss_conf 952548889898337743668899-89977898888756577989888524686561330674588876-6416788878 Q ss_pred HHHHHHCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCCCCCCEEEEEEEECHHHHHHHHHCCCEEEEC Q ss_conf 204543024555332233555543086254433204630443144148999982699999999749889989 Q gi|254780242|r 80 LLQAYIDKDRLDCSSEIDASVLVASGLVRRSQRGIRILSDGDLKAKVVLRVSGASASAVEKVEKLGGQVIVI 151 (151) Q Consensus 80 ~L~~~i~~~~~~~~~~Id~~~L~~~gli~~~~~~vKiLg~Gel~~ki~I~v~~~S~sA~ekIE~aGG~v~ii 151 (151) .|+.+++ .+||++.|.+++||+...++||||++|+|+.+++|+|++||++|+++||+|||+|+|+ T Consensus 79 ~L~~~~~-------~~i~~~~L~~~~li~~~~~~VKiLg~Gel~~ki~I~~~~~S~sA~~~IE~aGG~V~l~ 143 (156) T 2zjr_I 79 QLQDLED-------TTFDRDTLEAYRLVRRKNRPVKLLASGEISRAVTVHVDAASAAAIKAVEAAGGRVVLP 143 (156) T ss_dssp HHTTSCC-------CCCCTTTTHHHHHCCCCSSCCEECCCCCCCCCCCCCCSEECHHHHHHHGGGSCCCCCC T ss_pred HHHCCCC-------CCHHHHHHHHHCEEECCCCCEEEECCCCCCCCEEEEEEEECHHHHHHHHHCCCEEEEE T ss_conf 8320233-------3311566655161203676446750783557678999980999999999869989996 No 4 >3ofq_L 50S ribosomal protein L15; protein biosynthesis, ribosomes, RNA, tRNA, transfer, antibi EXIT, peptidyl, ribosomal subunit, large; 3.10A {Escherichia coli} PDB: 3fik_L 2wwq_L 3ofr_L* 3i1n_L 1p85_J 1p86_J 1vs8_L 1vs6_L 2aw4_L 2awb_L 1vt2_L 2i2v_L 2j28_L 2i2t_L* 2qao_L* 2qba_L* 2qbc_L* 2qbe_L 2qbg_L 2qbi_L* ... Probab=100.00 E-value=0 Score=336.09 Aligned_cols=141 Identities=43% Similarity=0.628 Sum_probs=134.4 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCEEEECCCCCCCCCCCCCEEEEEHHH Q ss_conf 7666888999876761020315789898578776676423689866-444316853011676355465655214775112 Q gi|254780242|r 2 KLNEISYDKGSCKVKKRVARGIGSGTGKTAGRGVKGQKSRSGVSVR-GFEGGQMPLYRRLPKRGFVNIAGSDFVTISLGL 80 (151) Q Consensus 2 ~L~~l~~~~g~~~~~kR~GRG~gsg~Gkt~GrG~kGqk~Rsg~~~~-gfEGGQ~Pl~rrlPKrGF~~~~~~~~~~iNL~~ 80 (151) +||||+|+|||+++++|+|||+|||+|+|||||||||+||||+.++ +|||||||||||+|||||++.+...|.++||++ T Consensus 1 kl~~l~~~~g~~k~~kR~gRG~gsg~Gkt~GrG~kGq~~Rsg~~~r~gfEGGq~Pl~rr~PK~Gf~~~~~~~~~~~~l~~ 80 (143) T 3ofq_L 1 RLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFEGGQMPLYRRLPKFGFTSRKAAITAEIRLSD 80 (143) T ss_dssp CCSSCCCSTTCCCCCCCCSSCTTTTCTTTTSCCSSSTTTSSSCCCCTTCCSSSCCHHHHSCCCCCCCSSSSSEEECCTTS T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCEEEEEEEEEE T ss_conf 96557789999557615667788998966888788887677989798636885624756652155543330368898600 Q ss_pred HHHHHCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCCCCCCEEEEEEEECHHHHHHHHHCCCEEE Q ss_conf 045430245553322335555430862544332046304431441489999826999999997498899 Q gi|254780242|r 81 LQAYIDKDRLDCSSEIDASVLVASGLVRRSQRGIRILSDGDLKAKVVLRVSGASASAVEKVEKLGGQVI 149 (151) Q Consensus 81 L~~~i~~~~~~~~~~Id~~~L~~~gli~~~~~~vKiLg~Gel~~ki~I~v~~~S~sA~ekIE~aGG~v~ 149 (151) |+.+ +.++||+++|++.+|+......||||+.|||+.||+|+|++||++|+++||+|||+|+ T Consensus 81 l~~~-------~~~~i~~~~L~~~gli~~~~~~vKvLg~Gel~~kl~I~v~~~S~sA~~~Ie~aGG~V~ 142 (143) T 3ofq_L 81 LAKV-------EGGVVDLNTLKAANIIGIQIEFAKVILAGEVTTPVTVRGLRVTKGARAAIEAAGGKIE 142 (143) T ss_dssp TTCS-------SSSCBCTTTTTTSSSSCTTCCEEECCCCSCCCSCCEECSSCCCSSSSTTTSTTTCEEC T ss_pred HHHC-------CCCCCCHHHHHHCCCCCCCCCCEEEEECCCCCCCEEEEEEEECHHHHHHHHHHCCEEE T ss_conf 2221-------1442038888750620244311278626834466699999819999999998298563 No 5 >1vq8_L 50S ribosomal protein L15P; 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: c.12.1.1 PDB: 1vq4_L* 1vq5_L* 1vq6_L* 1vq7_L* 1s72_L* 1vq9_L* 1vqk_L* 1vql_L* 1vqm_L* 1vqn_L* 1vqo_L* 1vqp_L* 1yhq_L* 1yi2_L* 1yij_L* 1yit_L* 1yj9_L* 1yjn_L* 1yjw_L* 2otj_L* ... Probab=100.00 E-value=8.7e-43 Score=242.31 Aligned_cols=136 Identities=22% Similarity=0.244 Sum_probs=115.0 Q ss_pred CCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCC--CCCEEEEEHHHHHHHHCC Q ss_conf 98767610203157898985-787766764236898664443168530116763554656--552147751120454302 Q gi|254780242|r 11 GSCKVKKRVARGIGSGTGKT-AGRGVKGQKSRSGVSVRGFEGGQMPLYRRLPKRGFVNIA--GSDFVTISLGLLQAYIDK 87 (151) Q Consensus 11 g~~~~~kR~GRG~gsg~Gkt-~GrG~kGqk~Rsg~~~~gfEGGQ~Pl~rrlPKrGF~~~~--~~~~~~iNL~~L~~~i~~ 87 (151) .|+++++|+|||+|||+|+| ||||||||++|+|+..+ |+|+|+++|||||++++ +.+|.+|||..|+.+++. T Consensus 2 ~sk~~k~R~gRg~G~G~~k~~~GrG~KGqk~RsG~~~~-----~~~~~~~~pkrGf~~~~~~~~~~~~inl~~L~~~~~~ 76 (165) T 1vq8_L 2 TSKKKRQRGSRTHGGGSHKNRRGAGHRGGRGDAGRDKH-----EFHNHEPLGKSGFKRPQKVQEEAATIDVREIDENVTL 76 (165) T ss_dssp CCHHHHCTTCSSTTCSSTTSSCSGGGGTSSTTTTTTTT-----TCTTSCCSCCCCCCCCGGGCCCEEEEEHHHHHHTTGG T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-----CCCCCCCCCCCCCCCCCCCCEEEEEECHHHHHHHHHH T ss_conf 88746666786746799988898979998857798778-----8866766972488887665225754136778887754 Q ss_pred CCCC----CCCCCCHHHHHHCCCCCCCCCCEEEECCCCCCCCEEEEEEEECHHHHHHHHHCCCEEEEC Q ss_conf 4555----332233555543086254433204630443144148999982699999999749889989 Q gi|254780242|r 88 DRLD----CSSEIDASVLVASGLVRRSQRGIRILSDGDLKAKVVLRVSGASASAVEKVEKLGGQVIVI 151 (151) Q Consensus 88 ~~~~----~~~~Id~~~L~~~gli~~~~~~vKiLg~Gel~~ki~I~v~~~S~sA~ekIE~aGG~v~ii 151 (151) ...+ ....++...|.+..++.....+|||||+|+|+.||+|+|++||++|+++||+|||+|+|+ T Consensus 77 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~vKILG~Gel~~kl~I~a~~~S~sA~ekIE~aGG~v~l~ 144 (165) T 1vq8_L 77 LAADDVAEVEDGGFRVDVRDVVEEADDADYVKVLGAGQVRHELTLIADDFSEGAREKVEGAGGSVELT 144 (165) T ss_dssp GTTSCCCC-----CEEEGGGTCTTCTTSSEEEEECCSCCCSCCEEEESEECHHHHHHHHHTTCEEEEC T ss_pred HCCCCCCCCCCCCHHHHHHHHHCCCCCCCCEEEECCCCCCCCEEEEEEECCHHHHHHHHHCCCEEEEE T ss_conf 01122111123401676886401124565279963782077779998861999999999849989995 No 6 >2zkr_l 60S ribosomal protein L27A; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Probab=100.00 E-value=1.5e-34 Score=199.41 Aligned_cols=137 Identities=18% Similarity=0.164 Sum_probs=104.1 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC--C-CCCCCCCCEEEECCCCCCCC-CCCCCEEEEEHHHHHHHHCC Q ss_conf 87676102031578989857877667642368986--6-44431685301167635546-56552147751120454302 Q gi|254780242|r 12 SCKVKKRVARGIGSGTGKTAGRGVKGQKSRSGVSV--R-GFEGGQMPLYRRLPKRGFVN-IAGSDFVTISLGLLQAYIDK 87 (151) Q Consensus 12 ~~~~~kR~GRG~gsg~Gkt~GrG~kGqk~Rsg~~~--~-gfEGGQ~Pl~rrlPKrGF~~-~~~~~~~~iNL~~L~~~i~~ 87 (151) .++++.|.+|+.|+|+.+ .+|||+||++|+|... + +||++|||+|+++|+++|++ .++.+|.+|||++|+.+++. T Consensus 6 kK~rk~Rg~r~~G~G~~g-~~rg~~g~~g~~gg~~~~~~~~~~~~~~~~~k~g~~~~~~~~~~~~~~~inL~~L~~~~~~ 84 (148) T 2zkr_l 6 RKTRKLRGHVSHGHGRIG-KHRKHPGGRGNAGGMHHHRINFDKYHPGYFGKVGMKHYHLKRNQSFCPTVNLDKPWTLVSE 84 (148) T ss_dssp CHHHHTTTTSCSSCCSCS-CC--CCSCSSSTTTTTTTCSSCTTTC------------------CCCCEEETHHHHHHTTT T ss_pred CCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECHHHHHHHHHH T ss_conf 764757789783899998-9898899998889875887665687876326589768886776417214539999876440 Q ss_pred CCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCCCCC-CEEEEEEEECHHHHHHHHHCCCEEEEC Q ss_conf 4555332233555543086254433204630443144-148999982699999999749889989 Q gi|254780242|r 88 DRLDCSSEIDASVLVASGLVRRSQRGIRILSDGDLKA-KVVLRVSGASASAVEKVEKLGGQVIVI 151 (151) Q Consensus 88 ~~~~~~~~Id~~~L~~~gli~~~~~~vKiLg~Gel~~-ki~I~v~~~S~sA~ekIE~aGG~v~ii 151 (151) ...+.....+. +....+.......+|||++||++. +|+|+|++||++|+|+||+|||+|+|| T Consensus 85 ~~~~~~~~~~~--~~~~~~~~~~~g~~KlLg~G~~~kk~i~I~~~~~S~sA~ekIE~aGG~V~lv 147 (148) T 2zkr_l 85 QTRVNAAKNKT--GVAPIIDVVRSGYYKVLGKGKLPKQPVIVKAKFFSRRAEEKIKSVGGACVLV 147 (148) T ss_dssp TTSSCTTTTEE--EHHHHSTTCSSSCCEEECCSCCCSSCCEEEESEECHHHHHHHHHTTCEEEEC T ss_pred CCEEHHHHHHC--CCCCEEEEECCCCEEEECCCCCCCCCEEEEEEECCHHHHHHHHHCCCEEEEE T ss_conf 43102233213--5521001112422687158850462189998713989999999869889995 No 7 >3jyw_V 60S ribosomal protein L28; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} PDB: 1s1i_V Probab=100.00 E-value=7.8e-34 Score=195.67 Aligned_cols=130 Identities=23% Similarity=0.187 Sum_probs=100.7 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCEEEECC-----CCCCCC----CCCCCEEEEEHHHHHHHH Q ss_conf 6102031578989857877667642368986-644431685301167-----635546----565521477511204543 Q gi|254780242|r 16 KKRVARGIGSGTGKTAGRGVKGQKSRSGVSV-RGFEGGQMPLYRRLP-----KRGFVN----IAGSDFVTISLGLLQAYI 85 (151) Q Consensus 16 ~kR~GRG~gsg~Gkt~GrG~kGqk~Rsg~~~-~gfEGGQ~Pl~rrlP-----KrGF~~----~~~~~~~~iNL~~L~~~i 85 (151) ++|++|| ++|||+||+||++|+|... +|||++|+|+|++.| ++||.+ .++.+|.+|||++|+.++ T Consensus 2 K~rk~RG-----~~t~G~G~~gq~~~~gg~g~~g~~~~~~~~~~~~~~~~~~~~gfr~~~~~~~~~~~~~inl~~L~~~~ 76 (142) T 3jyw_V 2 KTRKHRG-----HVSAGKGRIGKHRKHPGGGMAGGEHHHRINMDKYHPGYFGKVGMRYFHKQQAHFWKPVLNLDKLWTLI 76 (142) T ss_dssp CHHHHHT-----TCCTTTCSTTCSTTTTTSSCCCSSCCSSSSCSSCSSSSSCCCSCCCSSSSTTCCCCCCCCHHHHHTTT T ss_pred CCCCCCC-----CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEHHHHHHHC T ss_conf 7565538-----96847998989898976899987789887652688775477998788746533064258899998653 Q ss_pred CCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCCCCC-CEEEEEEEECHHHHHHHHHCCCEEEEC Q ss_conf 024555332233555543086254433204630443144-148999982699999999749889989 Q gi|254780242|r 86 DKDRLDCSSEIDASVLVASGLVRRSQRGIRILSDGDLKA-KVVLRVSGASASAVEKVEKLGGQVIVI 151 (151) Q Consensus 86 ~~~~~~~~~~Id~~~L~~~gli~~~~~~vKiLg~Gel~~-ki~I~v~~~S~sA~ekIE~aGG~v~ii 151 (151) +...++....++...+.. .+.......+|||++||++. ||+|+|++||++|+|+||+|||+|++| T Consensus 77 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~KlLg~Ge~~k~~i~I~a~~~S~sA~ekIE~aGG~v~~i 142 (142) T 3jyw_V 77 PEDKRDQYLKSASKETAP-VIDTLAAGYGKILGKGRIPNVPVIVKARFVSKLAEEKIRAAGGVVELI 142 (142) T ss_dssp TTCCSSBTTTTBCCSTTT-CCSTTTSSCCCCCCCSCCCSCCCCEECSSCCHHHHHHHHHHTCCEECC T ss_pred CCCCCCHHHHHHHCCCCC-CCCCCCCCEEEEECCCCCCCCCEEEEEEECCHHHHHHHHHCCCEEEEC T ss_conf 035431346553045542-100112434798337744667589998853989999999839989969 No 8 >1vq8_O 50S ribosomal protein L18E; 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: c.12.1.1 PDB: 1vq4_O* 1vq5_O* 1vq6_O* 1vq7_O* 1s72_O* 1vq9_O* 1vqk_O* 1vql_O* 1vqm_O* 1vqn_O* 1vqo_O* 1vqp_O* 1yhq_O* 1yi2_O* 1yij_O* 1yit_O* 1yj9_O* 1yjn_O* 1yjw_O* 2otj_O* ... Probab=99.18 E-value=2.7e-11 Score=78.22 Aligned_cols=75 Identities=17% Similarity=0.341 Sum_probs=57.6 Q ss_pred CEEEECCCCCCCCCCCCCEEEEEHHHHHHHHCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCCCCCCEEEEEEEEC Q ss_conf 53011676355465655214775112045430245553322335555430862544332046304431441489999826 Q gi|254780242|r 55 PLYRRLPKRGFVNIAGSDFVTISLGLLQAYIDKDRLDCSSEIDASVLVASGLVRRSQRGIRILSDGDLKAKVVLRVSGAS 134 (151) Q Consensus 55 Pl~rrlPKrGF~~~~~~~~~~iNL~~L~~~i~~~~~~~~~~Id~~~L~~~gli~~~~~~vKiLg~Gel~~ki~I~v~~~S 134 (151) |+++.+-+|= ..++..+.+|||++|+.+... ++++ + -+.||||+|+++.+++|.|+.|| T Consensus 25 ~~wk~va~rL--~~srr~r~~VnLski~~~~k~-----~~~v---------v-----vpgKVLg~G~l~~k~~V~A~~fS 83 (116) T 1vq8_O 25 AVWGDVAERL--EKPRRTHAEVNLGRIERYAQE-----DETV---------V-----VPGKVLGSGVLQKDVTVAAVDFS 83 (116) T ss_dssp HHHHHHHHHH--TSCTTTSEEEEHHHHHHHCCT-----TSEE---------E-----EEEEEECCSCCCSCCEEEEEEEC T ss_pred HHHHHHHHHH--HCCCCCCCCCCHHHHHHHCCC-----CCEE---------E-----EEEEEECCCEECCCEEEEEECCC T ss_conf 7999999998--345446887559999975768-----9989---------9-----97589678747678899971417 Q ss_pred HHHHHHHHHCCCEEEE Q ss_conf 9999999974988998 Q gi|254780242|r 135 ASAVEKVEKLGGQVIV 150 (151) Q Consensus 135 ~sA~ekIE~aGG~v~i 150 (151) ++|+++||+|||.+++ T Consensus 84 ~sA~~kIe~aGg~iti 99 (116) T 1vq8_O 84 GTAETKIDQVGEAVSL 99 (116) T ss_dssp HHHHHHHHHHSEEEEH T ss_pred HHHHHHHHHCCCEEEH T ss_conf 8999999981988988 No 9 >2zkr_o 60S ribosomal protein L18; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Probab=98.58 E-value=4.2e-08 Score=61.60 Aligned_cols=80 Identities=16% Similarity=0.180 Sum_probs=55.1 Q ss_pred CEEEECCCCCCCCCCCCCEEEEEHHHHHHHHCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCCCCC--CEEEEEEE Q ss_conf 5301167635546565521477511204543024555332233555543086254433204630443144--14899998 Q gi|254780242|r 55 PLYRRLPKRGFVNIAGSDFVTISLGLLQAYIDKDRLDCSSEIDASVLVASGLVRRSQRGIRILSDGDLKA--KVVLRVSG 132 (151) Q Consensus 55 Pl~rrlPKrGF~~~~~~~~~~iNL~~L~~~i~~~~~~~~~~Id~~~L~~~gli~~~~~~vKiLg~Gel~~--ki~I~v~~ 132 (151) |+++.+-+|=| ..+.++.+|||+.|+.+.....- +++++ +| .=|||++|.|.. +++|-+.. T Consensus 42 ~f~k~VakRL~--~srrnr~~vnLSrI~r~~k~~~~-e~~~v---------VV-----vGkVl~dgrl~~vPKltV~AL~ 104 (188) T 2zkr_o 42 TFNQVVLKRLF--MSRTNRPPLSLSRMIRKMKLPGR-ENKTA---------VV-----VGTVTDDVRILEVPKLKVCALR 104 (188) T ss_dssp HHHHHHHHHHH--SCTTTSCEEEHHHHHSCSSSCCS-TTSEE---------EE-----EEEEECSSCCCCCSSCCEEEEE T ss_pred HHHHHHHHHHH--CCCCCCCCCCHHHHHHHHHCCCC-CCCEE---------EE-----ECCCCCCCEEECCCCEEEEEEE T ss_conf 88999999973--54336897549999998304576-68748---------88-----6126487102036754899997 Q ss_pred ECHHHHHHHHHCCCEEEEC Q ss_conf 2699999999749889989 Q gi|254780242|r 133 ASASAVEKVEKLGGQVIVI 151 (151) Q Consensus 133 ~S~sA~ekIE~aGG~v~ii 151 (151) ||++|+++|++|||+|..+ T Consensus 105 fS~~Ar~kI~~aGGk~lT~ 123 (188) T 2zkr_o 105 VSSRARSRILKAGGKILTF 123 (188) T ss_dssp ECHHHHHHHHHHSSCEEEH T ss_pred ECHHHHHHHHHCCCEEEEH T ss_conf 1378999999759879769 No 10 >2zkr_l 60S ribosomal protein L27A; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Probab=98.49 E-value=2.1e-08 Score=63.17 Aligned_cols=67 Identities=22% Similarity=0.132 Sum_probs=46.1 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEE--------ECCCCCCCCCCCCCE-EEEEHHHHH Q ss_conf 87676102031578989857877667642368986644431685301--------167635546565521-477511204 Q gi|254780242|r 12 SCKVKKRVARGIGSGTGKTAGRGVKGQKSRSGVSVRGFEGGQMPLYR--------RLPKRGFVNIAGSDF-VTISLGLLQ 82 (151) Q Consensus 12 ~~~~~kR~GRG~gsg~Gkt~GrG~kGqk~Rsg~~~~gfEGGQ~Pl~r--------rlPKrGF~~~~~~~~-~~iNL~~L~ 82 (151) |+.+++|++|| |.|||+|++||.++.+.. .+++|||.|.+. .++++||.+++.... ..+++-.|+ T Consensus 3 sr~kK~rk~Rg-----~r~~G~G~~g~~rg~~g~-~g~~gg~~~~~~~~~~~~~~~~~k~g~~~~~~~~~~~~~~~inL~ 76 (148) T 2zkr_l 3 SRLRKTRKLRG-----HVSHGHGRIGKHRKHPGG-RGNAGGMHHHRINFDKYHPGYFGKVGMKHYHLKRNQSFCPTVNLD 76 (148) T ss_dssp ---CHHHHTTT-----TSCSSCCSCSCC--CCSC-SSSTTTTTTTCSSCTTTC------------------CCCCEEETH T ss_pred CCCCCCCCCCC-----CCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECHH T ss_conf 88776475778-----978389999898988999-988898758876656878763265897688867764172145399 Q ss_pred HH Q ss_conf 54 Q gi|254780242|r 83 AY 84 (151) Q Consensus 83 ~~ 84 (151) .+ T Consensus 77 ~L 78 (148) T 2zkr_l 77 KP 78 (148) T ss_dssp HH T ss_pred HH T ss_conf 99 No 11 >3jyw_O 60S ribosomal protein L18(A); eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} PDB: 1s1i_O Probab=98.33 E-value=1.3e-08 Score=64.27 Aligned_cols=79 Identities=18% Similarity=0.254 Sum_probs=57.1 Q ss_pred CEEEECCCCCCCCCCCCCEEEEEHHHHHHHHCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCCCCC--CEEEEEEE Q ss_conf 5301167635546565521477511204543024555332233555543086254433204630443144--14899998 Q gi|254780242|r 55 PLYRRLPKRGFVNIAGSDFVTISLGLLQAYIDKDRLDCSSEIDASVLVASGLVRRSQRGIRILSDGDLKA--KVVLRVSG 132 (151) Q Consensus 55 Pl~rrlPKrGF~~~~~~~~~~iNL~~L~~~i~~~~~~~~~~Id~~~L~~~gli~~~~~~vKiLg~Gel~~--ki~I~v~~ 132 (151) |+++.+-||=|. .+.+..+|||+.|+.+.+..- .+++++ +| .=|||++|.+.. +++|-|-. T Consensus 23 ~f~k~VakrL~~--sr~~r~~vnLski~r~~~~~~-~e~~~v---------VV-----~GkVl~dg~l~~vpkl~V~Al~ 85 (121) T 3jyw_O 23 PFNKVVLKALFL--SKINRPPVSVSRIARALKQEG-AANKTV---------VV-----VGTVTDDARIFEFPKTTVAALR 85 (121) T ss_dssp HHHHHHHHTTTS--CSTTSCCBCHHHHHHHTTTTS-CSSSEE---------EE-----SSCBCCCSCCCSSSCCCEECSS T ss_pred HHHHHHHHHHHC--CCCCCCCCCHHHHHHHHHCCC-CCCCEE---------EE-----EEEECCCCEEECCCCEEEEEEE T ss_conf 889999999837--544799714999999845447-779879---------99-----7237388214116762799986 Q ss_pred ECHHHHHHHHHCCCEEEE Q ss_conf 269999999974988998 Q gi|254780242|r 133 ASASAVEKVEKLGGQVIV 150 (151) Q Consensus 133 ~S~sA~ekIE~aGG~v~i 150 (151) ||++|+++|++|||+|.. T Consensus 86 fS~~Ar~kI~~aGG~~lt 103 (121) T 3jyw_O 86 FTAGARAKIVKAGGECIT 103 (121) T ss_dssp BCTTTTTHHHHHTCCBCC T ss_pred CCHHHHHHHHHCCCEEEE T ss_conf 257999999974997977 No 12 >3jyw_V 60S ribosomal protein L28; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} PDB: 1s1i_V Probab=98.22 E-value=5.3e-07 Score=55.83 Aligned_cols=53 Identities=15% Similarity=0.092 Sum_probs=43.2 Q ss_pred CCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCC Q ss_conf 8767610203157898-9857877667642368986644431685301167635 Q gi|254780242|r 12 SCKVKKRVARGIGSGT-GKTAGRGVKGQKSRSGVSVRGFEGGQMPLYRRLPKRG 64 (151) Q Consensus 12 ~~~~~kR~GRG~gsg~-Gkt~GrG~kGqk~Rsg~~~~gfEGGQ~Pl~rrlPKrG 64 (151) +++++.|-+|+.|.|+ |+++++|+.|+....+...++|+++|+|+++++|+++ T Consensus 1 tK~rk~RG~~t~G~G~~gq~~~~gg~g~~g~~~~~~~~~~~~~~~~~~~~gfr~ 54 (142) T 3jyw_V 1 TKTRKHRGHVSAGKGRIGKHRKHPGGGMAGGEHHHRINMDKYHPGYFGKVGMRY 54 (142) T ss_dssp CCHHHHHTTCCTTTCSTTCSTTTTTSSCCCSSCCSSSSCSSCSSSSSCCCSCCC T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC T ss_conf 975655389684799898989897689998778988765268877547799878 No 13 >1vq8_L 50S ribosomal protein L15P; 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: c.12.1.1 PDB: 1vq4_L* 1vq5_L* 1vq6_L* 1vq7_L* 1s72_L* 1vq9_L* 1vqk_L* 1vql_L* 1vqm_L* 1vqn_L* 1vqo_L* 1vqp_L* 1yhq_L* 1yi2_L* 1yij_L* 1yit_L* 1yj9_L* 1yjn_L* 1yjw_L* 2otj_L* ... Probab=91.40 E-value=0.12 Score=28.00 Aligned_cols=62 Identities=18% Similarity=0.118 Sum_probs=31.6 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCEEEEEHHHHHH Q ss_conf 99876761020315789898578776676423689866444316853011676355465655214775112045 Q gi|254780242|r 10 KGSCKVKKRVARGIGSGTGKTAGRGVKGQKSRSGVSVRGFEGGQMPLYRRLPKRGFVNIAGSDFVTISLGLLQA 83 (151) Q Consensus 10 ~g~~~~~kR~GRG~gsg~Gkt~GrG~kGqk~Rsg~~~~gfEGGQ~Pl~rrlPKrGF~~~~~~~~~~iNL~~L~~ 83 (151) .|+=+..+.-|||.-.+++. +|. +++ ++. ++|+|.+|.+|+..+.+..-..+...+|+.+.. T Consensus 14 ~G~G~~k~~~GrG~KGqk~R-sG~-~~~-----~~~-----~~~~~pkrGf~~~~~~~~~~~~inl~~L~~~~~ 75 (165) T 1vq8_L 14 HGGGSHKNRRGAGHRGGRGD-AGR-DKH-----EFH-----NHEPLGKSGFKRPQKVQEEAATIDVREIDENVT 75 (165) T ss_dssp TTCSSTTSSCSGGGGTSSTT-TTT-TTT-----TCT-----TSCCSCCCCCCCCGGGCCCEEEEEHHHHHHTTG T ss_pred CCCCCCCCCCCCCCCCCCCC-CCC-CCC-----CCC-----CCCCCCCCCCCCCCCCCEEEEEECHHHHHHHHH T ss_conf 46799988898979998857-798-778-----886-----676697248888766522575413677888775 No 14 >3ofq_E 50S ribosomal protein L4; protein biosynthesis, ribosomes, RNA, tRNA, transfer, antibi EXIT, peptidyl, ribosomal subunit, large; 3.10A {Escherichia coli} PDB: 1p85_C 1p86_C 1vs8_E 1vs6_E 2aw4_E 2awb_E 1vt2_E 2i2v_E 2j28_E 2i2t_E* 2qao_E* 2qba_E* 2qbc_E* 2qbe_E 2qbg_E 2qbi_E* 2qbk_E* 2qov_E 2qox_E 2qoz_E* ... Probab=61.80 E-value=6.4 Score=18.93 Aligned_cols=121 Identities=21% Similarity=0.282 Sum_probs=53.7 Q ss_pred CCCCCCCCCCCCCCCCCCC-CCCCCCCC-CCCCCCCCCEEEECCCCCCCCCCCCCEEEEEH-HHHHHHHCCCCCCCC--- Q ss_conf 0315789898578776676-42368986-64443168530116763554656552147751-120454302455533--- Q gi|254780242|r 20 ARGIGSGTGKTAGRGVKGQ-KSRSGVSV-RGFEGGQMPLYRRLPKRGFVNIAGSDFVTISL-GLLQAYIDKDRLDCS--- 93 (151) Q Consensus 20 GRG~gsg~Gkt~GrG~kGq-k~Rsg~~~-~gfEGGQ~Pl~rrlPKrGF~~~~~~~~~~iNL-~~L~~~i~~~~~~~~--- 93 (151) .|+.-+|-|+---+ +||. .||.|... |-|-||-..+=-+ |+.=+...+++.+. +-| ..|...+..+.+-.- T Consensus 48 ~R~eV~gsgkKp~~-QKGtGrAR~Gs~rsP~~rgGG~a~gp~-pr~~~~klnkK~~~-lal~~aLs~k~~~~~l~vvd~~ 124 (201) T 3ofq_E 48 TRAEVTGSGKKPWR-QKGTGRARSGSIKSPIWRSGGVTFAAR-PQDHSQKVNKKMYR-GALKSILSELVRQDRLIVVEKF 124 (201) T ss_dssp CTTTCCSCCCCCCC-TTTSSSCCCCCTTCTTSSSCCCTTCCC-SCCCCCCCCTTTTH-HHHHHHHHHHHHTTCBCCCSSC T ss_pred CHHHCCCCCCEECC-CCCCCCCCCCCCCCCEECCCEEECCCC-CCCCHHHHHHHHHH-HHHHHHHHHHHHHCCCEEECCC T ss_conf 11110377754236-587867875578656566980688998-55423777779999-9999999999984486761001 Q ss_pred -----CCCCH-HHHHHC--------------CCC--CCCCCCEEEECCCCCCCC--EEEEEEEECHHHHHHHHH Q ss_conf -----22335-555430--------------862--544332046304431441--489999826999999997 Q gi|254780242|r 94 -----SEIDA-SVLVAS--------------GLV--RRSQRGIRILSDGDLKAK--VVLRVSGASASAVEKVEK 143 (151) Q Consensus 94 -----~~Id~-~~L~~~--------------gli--~~~~~~vKiLg~Gel~~k--i~I~v~~~S~sA~ekIE~ 143 (151) .+=++ ..|... .+. ..+...|+++-..+++.- +.-..-.+|++|.+.||+ T Consensus 125 ~~~~~kTK~~~~~l~~l~~~~~LiV~~~~~enl~~S~RNi~~v~v~~~~~lNvyDlLk~~~lVit~~Al~~Lee 198 (201) T 3ofq_E 125 SVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSLIAFDKVVMTADAVKQVEE 198 (201) T ss_dssp CCCSSCTTTTTTTTTTTTCCSBCCBCSSCCTTTTTSSSSCSSCCCBCSTTCCHHHHTTSSBBCCCTTHHHHHHH T ss_pred CCCCCCHHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHCCCCCEEEECCCCCHHHHHCCCCEEEEHHHHHHHHH T ss_conf 24689749999998760656157763764277999983879965864488569999668949987899999999 No 15 >2ftc_D Mitochondrial ribosomal protein L4 isoform A, mitochondrial 39S ribosomal protein L3; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} PDB: 3iy9_D Probab=42.84 E-value=8.7 Score=18.25 Aligned_cols=35 Identities=9% Similarity=0.091 Sum_probs=23.7 Q ss_pred CCCCCEEEECCCCCCCC--EEEEEEEECHHHHHHHHH Q ss_conf 44332046304431441--489999826999999997 Q gi|254780242|r 109 RSQRGIRILSDGDLKAK--VVLRVSGASASAVEKVEK 143 (151) Q Consensus 109 ~~~~~vKiLg~Gel~~k--i~I~v~~~S~sA~ekIE~ 143 (151) .+...|+++...+++.- +.-+.--+|++|++.||. T Consensus 139 rNi~~v~v~~~~~lNv~dlL~~~~lvit~~Al~~leE 175 (175) T 2ftc_D 139 SRLKTFNLIPAVGLNVHSMLKHQTLVLTLPTVAFLED 175 (175) T ss_pred HCCCCCEEEECCCCCHHHHHCCCEEEEEHHHHHHHHC T ss_conf 3658833643587339999669929986899888439 No 16 >3bbn_P Ribosomal protein S16; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Probab=42.43 E-value=12 Score=17.55 Aligned_cols=44 Identities=11% Similarity=0.265 Sum_probs=28.6 Q ss_pred CCCCCCCCCCEEEEEHHHHHHHHCCCCCCCCCCCCHHHHHHCCCCCC Q ss_conf 35546565521477511204543024555332233555543086254 Q gi|254780242|r 63 RGFVNIAGSDFVTISLGLLQAYIDKDRLDCSSEIDASVLVASGLVRR 109 (151) Q Consensus 63 rGF~~~~~~~~~~iNL~~L~~~i~~~~~~~~~~Id~~~L~~~gli~~ 109 (151) -||.++...+ ..+|++.+..|+..+-- +++++ ...|..+|+..+ T Consensus 36 lG~ynP~~~~-~~l~~eri~~Wl~~GAq-pS~~V-~~LL~~~g~~~~ 79 (88) T 3bbn_P 36 VGFYDPIKSQ-TYLNVPAILDFLEKGAQ-PTETV-YDILKRAEVFKE 79 (88) T ss_dssp CCCBCTTSSC-BCCCTTTSSSSTTSSCE-ECTTT-SSSSTTTTSSSC T ss_pred EEEECCCCCC-CCCCHHHHHHHHHCCCC-CCHHH-HHHHHHCCCHHH T ss_conf 5006699985-41478999999996995-58999-999998083366 No 17 >3mr8_P 30S ribosomal protein S16; ribosome, termination, RF1, amber, STOP UAG; 3.62A {Thermus thermophilus} PDB: 1pnx_P 1voq_P 1vos_P 1vov_P 1vox_P 1voz_P 1pns_P 3ms0_P 3fic_P* 1emw_A 1fjg_P* 1hnw_P* 1hnx_P* 1hnz_P* 1hr0_P 1i94_P* 1i95_P* 1i96_P* 1i97_P* 1ibk_P* ... Probab=39.03 E-value=20 Score=16.36 Aligned_cols=45 Identities=11% Similarity=0.296 Sum_probs=28.9 Q ss_pred CCCCCCCC--CCEEEEEHHHHHHHHCCCCCCCCCCCCHHHHHHCCCCCC Q ss_conf 35546565--521477511204543024555332233555543086254 Q gi|254780242|r 63 RGFVNIAG--SDFVTISLGLLQAYIDKDRLDCSSEIDASVLVASGLVRR 109 (151) Q Consensus 63 rGF~~~~~--~~~~~iNL~~L~~~i~~~~~~~~~~Id~~~L~~~gli~~ 109 (151) -||.|+.. .+...+|++.+..|+..+--- ++++ ...|..+|+... T Consensus 36 lG~YnP~~~~~~~i~i~~eRi~~WL~~GAqp-S~~V-~~Ll~~~gi~~~ 82 (83) T 3mr8_P 36 IGYYDPRKTTPDWLKVDVERARYWLSVGAQP-TDTA-RRLLRQAGVFRQ 82 (83) T ss_dssp CEEECTTCCSTTSEEECHHHHHHHHHTCCCC-CHHH-HHHHHHHTSSCC T ss_pred EEEECCCCCCCCEEEECHHHHHHHHHCCCCC-CHHH-HHHHHHCCCCCC T ss_conf 8888999888501564699999999878906-7899-999998388567 No 18 >2j01_F 50S ribosomal protein L4; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} SCOP: c.22.1.1 PDB: 2hgq_F 2hgj_F 2hgu_F 2j03_F 2jl6_F 2jl8_F 2v47_F 2v49_F 2wdi_F 2wdj_F 2wdl_F 2wdn_F 2wh2_F 2wh4_F 2wrj_F 2wrl_F 2wro_F 2wrr_F 2x9s_F 2x9u_F ... Probab=37.16 E-value=15 Score=17.09 Aligned_cols=39 Identities=21% Similarity=0.176 Sum_probs=23.7 Q ss_pred CCCCCEEEECCCCCCC--CEEEEEEEECHHHHHHHHH-CCCE Q ss_conf 4433204630443144--1489999826999999997-4988 Q gi|254780242|r 109 RSQRGIRILSDGDLKA--KVVLRVSGASASAVEKVEK-LGGQ 147 (151) Q Consensus 109 ~~~~~vKiLg~Gel~~--ki~I~v~~~S~sA~ekIE~-aGG~ 147 (151) .+...|.++...+++. =+.-+.--+|++|.+.||+ .||+ T Consensus 168 rNi~~v~v~~~~~lnv~dlL~~~~lvit~~Al~~l~e~l~g~ 209 (210) T 2j01_F 168 RNLPWVVTLAPEGLNVYDIVRTERLVMDLDAWEVFQNRIGGE 209 (210) T ss_dssp TTCTTEEEECGGGCCHHHHHHSSEEEEEHHHHHHHHHTCC-- T ss_pred HCCCCCEEEECCCCCHHHHHCCCCEEEEHHHHHHHHHHHCCC T ss_conf 477997786338822999856996998789999999996678 No 19 >1vq8_C 50S ribosomal protein L4E; 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: c.22.1.1 PDB: 1k73_E* 1k8a_E* 1k9m_E* 1kc8_E* 1kd1_E* 1kqs_C* 1m1k_E* 1m90_E* 1n8r_E* 1nji_E* 1q7y_E* 1q81_E* 1q82_E* 1q86_E* 1qvf_C 1qvg_C 1s72_C* 1vq4_C* 1vq5_C* 1vq6_C* ... Probab=27.33 E-value=9.5 Score=18.05 Aligned_cols=35 Identities=17% Similarity=0.288 Sum_probs=19.6 Q ss_pred CCCCCEEEECCCCCCCCEE------EEEEEECHHHHHHHHH Q ss_conf 4433204630443144148------9999826999999997 Q gi|254780242|r 109 RSQRGIRILSDGDLKAKVV------LRVSGASASAVEKVEK 143 (151) Q Consensus 109 ~~~~~vKiLg~Gel~~ki~------I~v~~~S~sA~ekIE~ 143 (151) .+...|+++...+|+.-=- -..--+|++|+++||+ T Consensus 205 rNip~v~v~~~~~lNvydLl~~~~~~r~vV~T~~Al~~l~e 245 (246) T 1vq8_C 205 RNLAGADVATASEVNTEDLAPGGAPGRLTVFTESALAEVAE 245 (246) T ss_dssp TTSTTCEEEETTTCCHHHHSGGGCCCCCEEEEHHHHHHGGG T ss_pred CCCCCCEEEECCCCCHHHHCCCCCCCCEEEEEHHHHHHHHC T ss_conf 18999669756884099902668668609983999999854 No 20 >3bn0_A 30S ribosomal protein S16; ribonucleoprotein, ribosome; 2.00A {Aquifex aeolicus} SCOP: d.27.1.1 Probab=21.12 E-value=29 Score=15.54 Aligned_cols=45 Identities=11% Similarity=0.166 Sum_probs=31.5 Q ss_pred CCCCCCCCCCEEEEEHHHHHHHHCCCCCCCCCCCCHHHHHHCCCCCC Q ss_conf 35546565521477511204543024555332233555543086254 Q gi|254780242|r 63 RGFVNIAGSDFVTISLGLLQAYIDKDRLDCSSEIDASVLVASGLVRR 109 (151) Q Consensus 63 rGF~~~~~~~~~~iNL~~L~~~i~~~~~~~~~~Id~~~L~~~gli~~ 109 (151) -||.|+...+...+|.+.|..|+..+-- +++++ ...|...|++.. T Consensus 37 lG~YnP~~~~~i~l~~eri~~Wl~~GAq-ps~~V-~~lL~~~Gll~~ 81 (112) T 3bn0_A 37 LGTYDPKRKVLINVYPEKVKEWVLKGVE-LSHRA-KAILWNHGILKE 81 (112) T ss_dssp EEEEETTTTEEEEECHHHHHHHHHTTCE-EEHHH-HHHHHHTTHHHH T ss_pred EEEECCCCCCCCCCCHHHHHHHHHCCCC-CCHHH-HHHHHHCCCCCC T ss_conf 2377587642124689999999987897-47999-999998598644 Done!