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 33803 Date Tue May 24 02:47:12 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780242.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 >3i1n_L 50S ribosomal protein 100.0 0 0 311.8 9.5 142 1-149 1-143 (144) 2 >3bbo_N Ribosomal protein L15; 100.0 0 0 318.3 2.0 147 1-151 65-220 (257) 3 >2j01_P 50S ribosomal protein 100.0 0 0 311.0 6.4 146 1-151 1-148 (150) 4 >2zjr_I 50S ribosomal protein 100.0 0 0 311.2 6.1 142 1-151 1-143 (156) 5 >1vq8_L 50S ribosomal protein 100.0 0 0 260.3 8.9 136 11-151 2-144 (165) 6 >2zkr_l 60S ribosomal protein 100.0 2.4E-42 0 240.8 8.4 135 12-151 3-147 (148) 7 >3jyw_O 60S ribosomal protein 99.9 9.5E-30 2.8E-34 175.2 -3.2 88 47-151 15-104 (121) 8 >3jyw_V 60S ribosomal protein 99.9 8.3E-25 2.5E-29 149.4 3.6 92 59-151 1-94 (94) 9 >1vq8_O 50S ribosomal protein 99.5 6.8E-15 2E-19 97.8 4.8 62 71-151 1-62 (78) 10 >2zkr_o 60S ribosomal protein 98.4 3.1E-07 9.3E-12 57.8 4.4 64 72-150 2-67 (133) 11 >2j01_F 50S ribosomal protein 33.6 16 0.00048 17.6 1.0 36 109-144 168-205 (210) 12 >3i1m_P 30S ribosomal protein 24.3 55 0.0016 14.9 3.4 58 40-106 7-80 (82) 13 >3cuq_A Vacuolar-sorting prote 23.1 34 0.001 16.0 1.1 40 75-120 34-73 (91) 14 >3bn0_A 30S ribosomal protein 21.8 34 0.001 15.9 1.0 45 63-109 37-81 (112) 15 >2ftc_E Mitochondrial ribosoma 21.6 63 0.0019 14.6 2.6 16 135-150 56-71 (72) 16 >1m0s_A Ribose-5-phosphate iso 20.7 66 0.0019 14.5 3.3 28 123-150 4-32 (77) 17 >1dd3_A 50S ribosomal protein 20.2 68 0.002 14.4 2.8 16 135-150 55-70 (71) No 1 >>3i1n_L 50S ribosomal protein L15; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1p85_J 1p86_J 1vs8_L 2aw4_L 2awb_L 1vs6_L 2i2v_L 2j28_L 2i2t_L* 2qao_L* 2qba_L* 2qbc_L* 2qbe_L 2qbg_L 2qbi_L* 2qbk_L* 2qov_L 2qox_L 2qoz_L* 2qp1_L* ... (L:) Probab=100.00 E-value=0 Score=311.82 Aligned_cols=142 Identities=43% Similarity=0.634 Sum_probs=138.1 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 ~~L~~l~~~~g~~~~k~R~gRg~gsG~gkt~grg~kg~~~r~g~~~~~gfeggq~p~~~~~pK~Gf~~~~~~~~~~inl~ 80 (144) T 3i1n_L 1 MRLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFEGGQMPLYRRLPKFGFTSRKAAITAEIRLS 80 (144) T ss_dssp -CTTSCCCCTTTSCCCCCCSSCSTTSSCSTTSSCSSSTTSSSSCCCCTTCCTTSCCHHHHSCCCCCCCSTGGGEEECCST T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCEEECCCCCCEEEEEEEEH T ss_conf 96365878988841640467878899997888888998776798868664567555521165340121231058776600 Q ss_pred HHHHHHCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCCCCCCEEEEEEEECHHHHHHHHHCCCEEE Q ss_conf 2045430245553322335555430862544332046304431441489999826999999997498899 Q gi|254780242|r 80 LLQAYIDKDRLDCSSEIDASVLVASGLVRRSQRGIRILSDGDLKAKVVLRVSGASASAVEKVEKLGGQVI 149 (151) Q Consensus 80 ~L~~~i~~~~~~~~~~Id~~~L~~~gli~~~~~~vKiLg~Gel~~ki~I~v~~~S~sA~ekIE~aGG~v~ 149 (151) +|+.+++ ++||.+.|.+.+++......+|||++|+|+.||+|+|++||++|+|+||+|||+|+ T Consensus 81 ~l~~~~~-------~~i~~~~l~~~~i~~~~~~~~KlLg~G~l~~~l~Ikv~~~S~~A~ekIe~aGG~v~ 143 (144) T 3i1n_L 81 DLAKVEG-------GVVDLNTLKAANIIGIQIEFAKVILAGEVTTPVTVRGLRVTKGARAAIEAAGGKIE 143 (144) T ss_dssp TTTTSSS-------SEECTTTTTTTTSSCTTCCEEECCCCCCCCSCCEEESSBCCHHHHHHHHHTTCEEE T ss_pred HHHHHHC-------CCCHHHHHHHCCEEECCCEEEEEECCCCCCCCEEEEEEEECHHHHHHHHHHCCEEE T ss_conf 1223230-------34103454432656401000178606831677799999858999999998198552 No 2 >>3bbo_N Ribosomal protein L15; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Pisum sativum} (N:) Probab=100.00 E-value=0 Score=318.26 Aligned_cols=147 Identities=38% Similarity=0.620 Sum_probs=134.6 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCEEEECCC----CCCCCCCCCCEEE Q ss_conf 97666888999876761020315789898578776676423689866-444316853011676----3554656552147 Q gi|254780242|r 1 MKLNEISYDKGSCKVKKRVARGIGSGTGKTAGRGVKGQKSRSGVSVR-GFEGGQMPLYRRLPK----RGFVNIAGSDFVT 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 ~~L~nL~~~~garkkkkR~gRG~gsG~Gkt~GrG~KGQk~R~G~~~~~gFeGGqtpl~rr~PK~~~~~gf~~~~~~~~~~ 144 (257) T 3bbo_N 65 FRLDNLGPQPGSRKRPKRKGRGIAAGQGASCGFGMRGQKSRSGPGIMRGFEGGQMPLYRRLPKLRGIAGGMHAGLPKYVN 144 (257) T ss_dssp CCCSSSCCCCCCCSCCCCCSSCCCCSCSSSCSSSCCCCGGGTSSCSSTTCCSSCSSTTSCCCCCSSCCCCCSSCCSSSSC T ss_pred EECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCEEEEEE T ss_conf 67477889999855763101677889984278888888888899988662578850178226536634755442368885 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 iNL~~L~~~i~~~~~~----i~~~~l~~~~~~~~~~~~~~~~vKlLg~G~~~~~i~I~v~~aS~sAi~kIE~aGG~v~~~ 220 (257) T 3bbo_N 145 VNLTDIENAGFQDGEE----VSLETLKAKRVINPSGRERKLPLKILADGELSKKLTIKAGAFSTSAKEKLEYAGCSLIVL 220 (257) T ss_dssp SCSSCCSCSSTTTTTT----TCCSSCCSSSCSSSSCCCCSCCCCCCCSSCCCSSCCCCSSCCTGGGTTSSTTTTCCEECC T ss_pred ECCHHHHHHCCCCCCH----HHHHHHHHCCCCCCCCCCCCCCEEEECCCEECCCEEEEEEEECHHHHHHHHHCCCEEEEE T ss_conf 1110133321353110----105568766763010002443248851770644679999985899999999849979995 No 3 >>2j01_P 50S ribosomal protein L15; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} (P:) Probab=100.00 E-value=0 Score=310.98 Aligned_cols=146 Identities=36% Similarity=0.515 Sum_probs=134.9 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CC-CCCCCCCCEEEECCCCCCCCCCCCCEEEEEH Q ss_conf 976668889998767610203157898985787766764236898-66-4443168530116763554656552147751 Q gi|254780242|r 1 MKLNEISYDKGSCKVKKRVARGIGSGTGKTAGRGVKGQKSRSGVS-VR-GFEGGQMPLYRRLPKRGFVNIAGSDFVTISL 78 (151) Q Consensus 1 m~L~~l~~~~g~~~~~kR~GRG~gsg~Gkt~GrG~kGqk~Rsg~~-~~-gfEGGQ~Pl~rrlPKrGF~~~~~~~~~~iNL 78 (151) |+||||+|+||++++++|+|||+|||+|||||||||||++|+|.. .+ +|||||||||||+||+||+++++..|.++|| T Consensus 1 m~l~~L~~~~g~k~~kkR~gRg~gsG~Gkt~grG~kGq~~r~g~~~~~~~feggq~Pl~rr~pK~Gf~~~~~~~~~~~~l 80 (150) T 2j01_P 1 MKLSDLRPNPGANKRRKRVGRGPGSGHGKTATRGHKGQKSRSGGLKDPRRFEGGRSTTLMRLPKRGMQGQVPGEIKRPRY 80 (150) T ss_dssp ----CCSSSCCCSSCCCCCCCCSCSSSSSCTTCSSCCSSSCSSCCCCSSSCCSSSCTTCCSCCCCCSCCCSSCSCCCCCE T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCEEHHCCCCCCEEEEEE T ss_conf 96355888989863763666788899896699999898888888767741137887654147600010345542111343 Q ss_pred HHHHHHHCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCCCCCCEEEEEEEECHHHHHHHHHCCCEEEEC Q ss_conf 1204543024555332233555543086254433204630443144148999982699999999749889989 Q gi|254780242|r 79 GLLQAYIDKDRLDCSSEIDASVLVASGLVRRSQRGIRILSDGDLKAKVVLRVSGASASAVEKVEKLGGQVIVI 151 (151) Q Consensus 79 ~~L~~~i~~~~~~~~~~Id~~~L~~~gli~~~~~~vKiLg~Gel~~ki~I~v~~~S~sA~ekIE~aGG~v~ii 151 (151) ..|+.+++.+.+ ++||++.|+++++++... .+|||++|++ .||+|+|++||++|+|+||+|||+|++| T Consensus 81 ~~l~~~~~~~~~---~~i~~~~l~~~~~v~~~~-~vKlLg~G~~-~ki~i~v~~~S~~A~~kIe~aGG~v~~v 148 (150) T 2j01_P 81 QGVNLKDLARFE---GEVTPELLVRAGLLKKGY-RLKILGEGEA-KPLKVVAHAFSKSALEKLKAAGGEPVLL 148 (150) T ss_dssp EEEETTTTTTSC---SCCCTTTTTTSSSCSSCC-EEEEECSSCC-CSSCCCCSBCCHHHHHHHHTSCCCCCCC T ss_pred EHHHHHHHHCCC---CCCCHHHHHHCCCCCCCC-CEEEECCCCE-EEEEEEEEECCHHHHHHHHHCCCEEEEE T ss_conf 044566653344---335699999708655587-1788648857-6579998861899999999869989996 No 4 >>2zjr_I 50S ribosomal protein L15; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} (I:) Probab=100.00 E-value=0 Score=311.23 Aligned_cols=142 Identities=46% Similarity=0.700 Sum_probs=135.7 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~R~gRG~~s-~Gkt~grg~kGqk~R~G~~~~~gfeggq~pl~r~~PK~Gf~~-~~~~~~~inl~ 78 (156) T 2zjr_I 1 MKLHDLKPTPGSRKDRKRVGRGPGG-TDKTAGRGHKGQKSRSGAGKGAFFEGGRSRLIARLPKRGFNN-VGTTYEVVKLS 78 (156) T ss_dssp ---CCCCCCSSTTTCCCCSSSCCCC-CCSCSSSCCCCSSSSSCCSCCCSCSCCSSSSTTTSCCCCCCC-CCCCCCEECHH T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCCC-CCCEEEHHHHH T ss_conf 9625488898985577425788999-998889988887778898988761468677201145357676-54243302087 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~~~~l~~~~~~~~Kllg~G~l~~~i~I~~~~~S~~A~~~Ie~aGG~v~~~ 143 (156) T 2zjr_I 79 QLQDLED-------TTFDRDTLEAYRLVRRKNRPVKLLASGEISRAVTVHVDAASAAAIKAVEAAGGRVVLP 143 (156) T ss_dssp HHTTSCC-------CCCCTTTTHHHHHCCCCSSCCEECCCCCCCCCCCCCCSEECHHHHHHHGGGSCCCCCC T ss_pred HHHHHHC-------CCCHHHHHHHHCEECCCCCCEEEECCCCCCCCEEEEEEEECHHHHHHHHHCCCEEEEE T ss_conf 6542110-------1201445555150101466457752884557678999980999999999869989996 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} (L:) Probab=100.00 E-value=0 Score=260.32 Aligned_cols=136 Identities=21% Similarity=0.219 Sum_probs=125.0 Q ss_pred CCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCEEEEEHHHHHHHHCCCC Q ss_conf 987676102031578989857-8776676423689866444316853011676355465655214775112045430245 Q gi|254780242|r 11 GSCKVKKRVARGIGSGTGKTA-GRGVKGQKSRSGVSVRGFEGGQMPLYRRLPKRGFVNIAGSDFVTISLGLLQAYIDKDR 89 (151) Q Consensus 11 g~~~~~kR~GRG~gsg~Gkt~-GrG~kGqk~Rsg~~~~gfEGGQ~Pl~rrlPKrGF~~~~~~~~~~iNL~~L~~~i~~~~ 89 (151) .++++++|+|||+|||+|+|+ ||||+||++|+ ||||||||||+|+||+||.+++...|.++||+.|+.|++.+. T Consensus 2 ~s~~~k~R~gRg~gsG~gk~~~g~G~kG~~~r~-----Gfeggq~p~~~r~pK~Gf~~~~~~~~~~v~l~~l~~~~~~~~ 76 (165) T 1vq8_L 2 TSKKKRQRGSRTHGGGSHKNRRGAGHRGGRGDA-----GRDKHEFHNHEPLGKSGFKRPQKVQEEAATIDVREIDENVTL 76 (165) T ss_dssp CCHHHHCTTCSSTTCSSTTSSCSGGGGTSSTTT-----TTTTTTCTTSCCSCCCCCCCCGGGCCCEEEEEHHHHHHTTGG T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-----CCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEHHHHHHHHHH T ss_conf 886366366757367999888989798888776-----988788714557422367677866534666315458888876 Q ss_pred C------CCCCCCCHHHHHHCCCCCCCCCCEEEECCCCCCCCEEEEEEEECHHHHHHHHHCCCEEEEC Q ss_conf 5------5332233555543086254433204630443144148999982699999999749889989 Q gi|254780242|r 90 L------DCSSEIDASVLVASGLVRRSQRGIRILSDGDLKAKVVLRVSGASASAVEKVEKLGGQVIVI 151 (151) Q Consensus 90 ~------~~~~~Id~~~L~~~gli~~~~~~vKiLg~Gel~~ki~I~v~~~S~sA~ekIE~aGG~v~ii 151 (151) + +...+++.+.|...+++.....++||||+|+|+.||+|+|++||++|+++||+|||+|+++ T Consensus 77 ~~~~~~~~~~~~i~~~~l~~~~~~~~~~~~~KvLg~G~l~~~i~I~~~~~S~~A~~kIE~aGG~v~~~ 144 (165) T 1vq8_L 77 LAADDVAEVEDGGFRVDVRDVVEEADDADYVKVLGAGQVRHELTLIADDFSEGAREKVEGAGGSVELT 144 (165) T ss_dssp GTTSCCCC-----CEEEGGGTCTTCTTSSEEEEECCSCCCSCCEEEESEECHHHHHHHHHTTCEEEEC T ss_pred HCCCCCCCCCCCHHHHHHHHHCCCCCCCCCEEEECCCCCCCCEEEEEEECCHHHHHHHHHCCCEEEEE T ss_conf 30123101123301677887411334565279947883287879999972989999999859989994 No 6 >>2zkr_l 60S ribosomal protein L27A; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} (l:) Probab=100.00 E-value=2.4e-42 Score=240.78 Aligned_cols=135 Identities=21% Similarity=0.196 Sum_probs=113.5 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCEEEECC----CCCCCCC----CCCCEEEEEHHHHH Q ss_conf 876761020315789898578776676423689866-44431685301167----6355465----65521477511204 Q gi|254780242|r 12 SCKVKKRVARGIGSGTGKTAGRGVKGQKSRSGVSVR-GFEGGQMPLYRRLP----KRGFVNI----AGSDFVTISLGLLQ 82 (151) Q Consensus 12 ~~~~~kR~GRG~gsg~Gkt~GrG~kGqk~Rsg~~~~-gfEGGQ~Pl~rrlP----KrGF~~~----~~~~~~~iNL~~L~ 82 (151) ++++++|+|||++||.|+ +|||||++|+|...+ +|||||||||||+| |+||+++ ++.+|.+|||++|+ T Consensus 3 s~k~k~R~gRG~~sg~gg---~g~kgqk~r~g~~~~~gfeggq~p~~rr~Pk~~gk~Gf~~~~~~~~~~~~~~inl~~l~ 79 (148) T 2zkr_l 3 SRLRKTRKLRGHVSHGHG---RIGKHRKHPGGRGNAGGMHHHRINFDKYHPGYFGKVGMKHYHLKRNQSFCPTVNLDKPW 79 (148) T ss_dssp ---CHHHHTTTTSCSSCC---SCSCC--CCSCSSSTTTTTTTCSSCTTTC------------------CCCCEEETHHHH T ss_pred CCCCCCCCCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEHHHHH T ss_conf 887654657888786889---89898988989888786557643344668663256897788557765060057799998 Q ss_pred HHHCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCCCC-CCEEEEEEEECHHHHHHHHHCCCEEEEC Q ss_conf 54302455533223355554308625443320463044314-4148999982699999999749889989 Q gi|254780242|r 83 AYIDKDRLDCSSEIDASVLVASGLVRRSQRGIRILSDGDLK-AKVVLRVSGASASAVEKVEKLGGQVIVI 151 (151) Q Consensus 83 ~~i~~~~~~~~~~Id~~~L~~~gli~~~~~~vKiLg~Gel~-~ki~I~v~~~S~sA~ekIE~aGG~v~ii 151 (151) +|+|.+++|+...++...+ ..+.......+|||++|++. .||+|+|++||++|+++||+|||+|++| T Consensus 80 ~l~~~~~~~~~~~~~~~~~--~~~~~~~~~~~Kvlg~G~~~k~~i~I~v~~~S~~A~~~IE~aGG~v~~v 147 (148) T 2zkr_l 80 TLVSEQTRVNAAKNKTGVA--PIIDVVRSGYYKVLGKGKLPKQPVIVKAKFFSRRAEEKIKSVGGACVLV 147 (148) T ss_dssp HHTTTTTSSCTTTTEEEHH--HHSTTCSSSCCEEECCSCCCSSCCEEEESEECHHHHHHHHHTTCEEEEC T ss_pred HHCCCCCEEHHHHHHCCCC--CCCCCCCCCEEEECCCCCCCCCCEEEEEEEECHHHHHHHHHCCCEEEEE T ss_conf 6421341203344320542--1110000121576147740574689998861999999999869989995 No 7 >>3jyw_O 60S ribosomal protein L18(A); eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} PDB: 1s1i_O (O:) Probab=99.94 E-value=9.5e-30 Score=175.17 Aligned_cols=88 Identities=16% Similarity=0.181 Sum_probs=76.6 Q ss_pred CCCCCCCCCEEEECCCCCCCCCCCCCEEEEEHHHHHHHHCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCCCCC-- Q ss_conf 644431685301167635546565521477511204543024555332233555543086254433204630443144-- Q gi|254780242|r 47 RGFEGGQMPLYRRLPKRGFVNIAGSDFVTISLGLLQAYIDKDRLDCSSEIDASVLVASGLVRRSQRGIRILSDGDLKA-- 124 (151) Q Consensus 47 ~gfEGGQ~Pl~rrlPKrGF~~~~~~~~~~iNL~~L~~~i~~~~~~~~~~Id~~~L~~~gli~~~~~~vKiLg~Gel~~-- 124 (151) .||||||||||||||||||+| +++|.+|||+.|+.+++.+.+ |.+.+... +|||++|+++. T Consensus 15 ~gfEggQ~Pl~rrlpKrgf~~--~~~~~~vnl~~i~~~~~~~~v------~~~~lv~~---------gKVL~~G~l~~~~ 77 (121) T 3jyw_O 15 FLARRTDAPFNKVVLKALFLS--KINRPPVSVSRIARALKQEGA------ANKTVVVV---------GTVTDDARIFEFP 77 (121) T ss_dssp HHHTTSCCHHHHHHHHTTTSC--STTSCCBCHHHHHHHTTTTSC------SSSEEEES---------SCBCCCSCCCSSS T ss_pred HHHHHHCCHHHHHHHHHHHCC--CCCCCCCCHHHHHHHHHCCCC------CCCEEEEE---------EEECCCCEEECCC T ss_conf 998864768899999997144--446897359999998644578------89889997---------3471883141278 Q ss_pred CEEEEEEEECHHHHHHHHHCCCEEEEC Q ss_conf 148999982699999999749889989 Q gi|254780242|r 125 KVVLRVSGASASAVEKVEKLGGQVIVI 151 (151) Q Consensus 125 ki~I~v~~~S~sA~ekIE~aGG~v~ii 151 (151) |++|++++||++|+++||+|||+|+.+ T Consensus 78 ki~I~a~~~S~sA~~kIe~AGG~v~~~ 104 (121) T 3jyw_O 78 KTTVAALRFTAGARAKIVKAGGECITL 104 (121) T ss_dssp CCCEECSSBCTTTTTHHHHHTCCBCCS T ss_pred CEEEEEEECCHHHHHHHHHCCCEEEEH T ss_conf 717999971478999999759979889 No 8 >>3jyw_V 60S ribosomal protein L28; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} PDB: 1s1i_V (V:49-142) Probab=99.90 E-value=8.3e-25 Score=149.41 Aligned_cols=92 Identities=22% Similarity=0.150 Sum_probs=74.8 Q ss_pred ECCCCCCCC-CCCCCEEEEEHHHHHHHHCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCCC-CCCEEEEEEEECHH Q ss_conf 167635546-5655214775112045430245553322335555430862544332046304431-44148999982699 Q gi|254780242|r 59 RLPKRGFVN-IAGSDFVTISLGLLQAYIDKDRLDCSSEIDASVLVASGLVRRSQRGIRILSDGDL-KAKVVLRVSGASAS 136 (151) Q Consensus 59 rlPKrGF~~-~~~~~~~~iNL~~L~~~i~~~~~~~~~~Id~~~L~~~gli~~~~~~vKiLg~Gel-~~ki~I~v~~~S~s 136 (151) |||||||++ +++.+|.+|||++|+.|++.+++++.+.++.+.+...... ....++||||+|++ +.|++|+|++||++ T Consensus 1 RlPKrGF~~~~~~~~~~~inl~~L~~~~~~~~~~~~~~l~~~~~~~~~~~-~~~~~vKvLg~G~~~k~~i~I~a~~~S~~ 79 (94) T 3jyw_V 1 KVGMRYFHKQQAHFWKPVLNLDKLWTLIPEDKRDQYLKSASKETAPVIDT-LAAGYGKILGKGRIPNVPVIVKARFVSKL 79 (94) T ss_dssp CCSCCCSSSSTTCCCCCCCCHHHHHTTTTTCCSSBTTTTBCCSTTTCCST-TTSSCCCCCCCSCCCSCCCCEECSSCCHH T ss_pred CCCCCCCCCCCCCCEEEEEEHHHHHHHHHCCCCCHHHHHHHCCCCCCCCC-CCCCCEEECCCCCCCCCCEEEEEEECCHH T ss_conf 58988887576530532587899997644034203343321033321221-10020588558413666389998843989 Q ss_pred HHHHHHHCCCEEEEC Q ss_conf 999999749889989 Q gi|254780242|r 137 AVEKVEKLGGQVIVI 151 (151) Q Consensus 137 A~ekIE~aGG~v~ii 151 (151) |+++||+|||+|+++ T Consensus 80 A~~~Ie~aGG~v~~v 94 (94) T 3jyw_V 80 AEEKIRAAGGVVELI 94 (94) T ss_dssp HHHHHHHHTCCEECC T ss_pred HHHHHHHCCCEEEEC T ss_conf 999999849989969 No 9 >>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} (O:39-116) Probab=99.53 E-value=6.8e-15 Score=97.78 Aligned_cols=62 Identities=21% Similarity=0.330 Sum_probs=53.6 Q ss_pred CCEEEEEHHHHHHHHCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCCCCCCEEEEEEEECHHHHHHHHHCCCEEEE Q ss_conf 52147751120454302455533223355554308625443320463044314414899998269999999974988998 Q gi|254780242|r 71 SDFVTISLGLLQAYIDKDRLDCSSEIDASVLVASGLVRRSQRGIRILSDGDLKAKVVLRVSGASASAVEKVEKLGGQVIV 150 (151) Q Consensus 71 ~~~~~iNL~~L~~~i~~~~~~~~~~Id~~~L~~~gli~~~~~~vKiLg~Gel~~ki~I~v~~~S~sA~ekIE~aGG~v~i 150 (151) ++|.+|||++|+.+.+.+.+. ..++||||+|+++.+++|.+++||++|+|+||+|||+|++ T Consensus 1 K~~~~VNL~~L~~~~~~~~~~-------------------~~~~KvLg~G~l~~~l~V~A~~fS~sA~ekIe~aGG~v~~ 61 (78) T 1vq8_O 1 RTHAEVNLGRIERYAQEDETV-------------------VVPGKVLGSGVLQKDVTVAAVDFSGTAETKIDQVGEAVSL 61 (78) T ss_dssp TTSEEEEHHHHHHHCCTTSEE-------------------EEEEEEECCSCCCSCCEEEEEEECHHHHHHHHHHSEEEEH T ss_pred CCCCCCCHHHHHHHCCCCCEE-------------------EEEEEEECCCEECCCEEEEEEECCHHHHHHHHHCCCEEEH T ss_conf 468762099999646699989-------------------9966796678676887999863278899999980987988 Q ss_pred C Q ss_conf 9 Q gi|254780242|r 151 I 151 (151) Q Consensus 151 i 151 (151) + T Consensus 62 ~ 62 (78) T 1vq8_O 62 E 62 (78) T ss_dssp H T ss_pred H T ss_conf 9 No 10 >>2zkr_o 60S ribosomal protein L18; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} (o:56-188) Probab=98.39 E-value=3.1e-07 Score=57.82 Aligned_cols=64 Identities=16% Similarity=0.145 Sum_probs=48.1 Q ss_pred CEEEEEHHHHHHHHCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCCCCC--CEEEEEEEECHHHHHHHHHCCCEEE Q ss_conf 21477511204543024555332233555543086254433204630443144--1489999826999999997498899 Q gi|254780242|r 72 DFVTISLGLLQAYIDKDRLDCSSEIDASVLVASGLVRRSQRGIRILSDGDLKA--KVVLRVSGASASAVEKVEKLGGQVI 149 (151) Q Consensus 72 ~~~~iNL~~L~~~i~~~~~~~~~~Id~~~L~~~gli~~~~~~vKiLg~Gel~~--ki~I~v~~~S~sA~ekIE~aGG~v~ 149 (151) ++.+|||+.|+.+.....- +++++ +| .=+||+++.|.. +++|-+..||++|+++|++|||+|. T Consensus 2 nr~~vslskI~r~~k~~~~-e~~~v---------VV-----vGkVldd~rl~~vPkltV~AL~fS~~Ar~kI~~aGG~~l 66 (133) T 2zkr_o 2 NRPPLSLSRMIRKMKLPGR-ENKTA---------VV-----VGTVTDDVRILEVPKLKVCALRVSSRARSRILKAGGKIL 66 (133) T ss_dssp TSCEEEHHHHHSCSSSCCS-TTSEE---------EE-----EEEEECSSCCCCCSSCCEEEEEECHHHHHHHHHHSSCEE T ss_pred CCCCCCHHHHHHHHHCCCC-CCCEE---------EE-----EEEECCCCEEECCCCEEEEEEEECHHHHHHHHHCCCEEE T ss_conf 5766439999998314466-79858---------99-----755648703521575599999732789999997599796 Q ss_pred E Q ss_conf 8 Q gi|254780242|r 150 V 150 (151) Q Consensus 150 i 150 (151) . T Consensus 67 t 67 (133) T 2zkr_o 67 T 67 (133) T ss_dssp E T ss_pred E T ss_conf 4 No 11 >>2j01_F 50S ribosomal protein L4; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} (F:) Probab=33.63 E-value=16 Score=17.65 Aligned_cols=36 Identities=17% Similarity=0.006 Sum_probs=24.4 Q ss_pred CCCCCEEEECCCCCCC--CEEEEEEEECHHHHHHHHHC Q ss_conf 4433204630443144--14899998269999999974 Q gi|254780242|r 109 RSQRGIRILSDGDLKA--KVVLRVSGASASAVEKVEKL 144 (151) Q Consensus 109 ~~~~~vKiLg~Gel~~--ki~I~v~~~S~sA~ekIE~a 144 (151) .+...|.++..-+|+. =+.-..--+|++|.+.||.. T Consensus 168 rNi~~v~v~~~~~lnv~dll~~~~ivit~~Al~~l~e~ 205 (210) T 2j01_F 168 RNLPWVVTLAPEGLNVYDIVRTERLVMDLDAWEVFQNR 205 (210) T ss_dssp TTCTTEEEECGGGCCHHHHHHSSEEEEEHHHHHHHHHT T ss_pred HCCCCCEEEECCCCCHHHHHCCCCEEEEHHHHHHHHHH T ss_conf 47689678633881299986689499878999999999 No 12 >>3i1m_P 30S ribosomal protein S16; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1p6g_P 1p87_P* 1vs7_P* 2avy_P 2aw7_P 1vs5_P 2i2u_P 2i2p_P* 2qan_P* 2qb9_P* 2qbb_P* 2qbd_P 2qbf_P 2qbh_P* 2qbj_P* 2qou_P* 2qow_P* 2qoy_P* 2qp0_P* 2vho_P ... (P:) Probab=24.27 E-value=55 Score=14.86 Aligned_cols=58 Identities=21% Similarity=0.399 Sum_probs=33.7 Q ss_pred CCCCCCCCCCCCCCCCEEE------ECCC-------CCCCCCCC---CCEEEEEHHHHHHHHCCCCCCCCCCCCHHHHHH Q ss_conf 2368986644431685301------1676-------35546565---521477511204543024555332233555543 Q gi|254780242|r 40 SRSGVSVRGFEGGQMPLYR------RLPK-------RGFVNIAG---SDFVTISLGLLQAYIDKDRLDCSSEIDASVLVA 103 (151) Q Consensus 40 ~Rsg~~~~gfEGGQ~Pl~r------rlPK-------rGF~~~~~---~~~~~iNL~~L~~~i~~~~~~~~~~Id~~~L~~ 103 (151) +|.|...+ |+|| |-|. -||.++.. .+...+|.+.+..|+..+--- .+++ ...|.. T Consensus 7 ~r~G~k~~-------P~YrIVv~d~r~~RdGk~iE~lG~Y~P~~~~~~~~i~l~~eri~~Wl~~GAqp-t~~V-~~ll~~ 77 (82) T 3i1m_P 7 ARHGAKKR-------PFYQVVVADSRNARNGRFIERVGFFNPIASEKEEGTRLDLDRIAHWVGQGATI-SDRV-AALIKE 77 (82) T ss_dssp EECSCTTS-------CCEEEEEEETTSCTTSCCSEECEEECSCCCSSSCCEEECHHHHHHHHHTCCEE-CTTH-HHHHTT T ss_pred CCCCCCCC-------CEEEEEEEECCCCCCCCCEEEEEEECCCCCCCCCCEEECHHHHHHHHHCCCCC-CHHH-HHHHHH T ss_conf 13899899-------85899996678888985711253788877898434566799999999975977-8999-999999 Q ss_pred CCC Q ss_conf 086 Q gi|254780242|r 104 SGL 106 (151) Q Consensus 104 ~gl 106 (151) +|+ T Consensus 78 ~gi 80 (82) T 3i1m_P 78 VNK 80 (82) T ss_dssp SCS T ss_pred HHH T ss_conf 863 No 13 >>3cuq_A Vacuolar-sorting protein SNF8; ESCRT, MBV, VPS, alternative splicing, coiled coil, cytoplasm, nucleus, protein transport; 2.61A {Homo sapiens} PDB: 2zme_A (A:61-151) Probab=23.07 E-value=34 Score=15.97 Aligned_cols=40 Identities=20% Similarity=0.321 Sum_probs=28.4 Q ss_pred EEEHHHHHHHHCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCC Q ss_conf 7751120454302455533223355554308625443320463044 Q gi|254780242|r 75 TISLGLLQAYIDKDRLDCSSEIDASVLVASGLVRRSQRGIRILSDG 120 (151) Q Consensus 75 ~iNL~~L~~~i~~~~~~~~~~Id~~~L~~~gli~~~~~~vKiLg~G 120 (151) .|.|++|...+.+.+-....+|+.+++..+ ...+|+||+| T Consensus 34 li~l~el~~~l~k~r~~~~~~Is~dDi~rA------i~~L~~LG~G 73 (91) T 3cuq_A 34 LITLEELHQQVLKGRGKFAQDVSQDDLIRA------IKKLKALGTG 73 (91) T ss_dssp EEEHHHHHHHHHHTTTTCCSSCCHHHHHHH------HHHHGGGBTT T ss_pred EEEHHHHHHHHHHHCCCCCCCCCHHHHHHH------HHHHHHCCCC T ss_conf 658999999999855776676699999999------9999984998 No 14 >>3bn0_A 30S ribosomal protein S16; ribonucleoprotein, ribosome; 2.00A {Aquifex aeolicus} (A:) Probab=21.84 E-value=34 Score=15.93 Aligned_cols=45 Identities=11% Similarity=0.166 Sum_probs=33.1 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 iG~YdP~~~k~~~l~~~ri~~Wl~~GAq-pt~~V-~~ll~~~gi~~~ 81 (112) T 3bn0_A 37 LGTYDPKRKVLINVYPEKVKEWVLKGVE-LSHRA-KAILWNHGILKE 81 (112) T ss_dssp EEEEETTTTEEEEECHHHHHHHHHTTCE-EEHHH-HHHHHHTTHHHH T ss_pred EEEECCCCCCCEEECHHHHHHHHHCCCC-CCHHH-HHHHHHCCCCCC T ss_conf 5562799975423689999999997498-47999-999997697400 No 15 >>2ftc_E Mitochondrial ribosomal protein L7/12, mitochondrial 39S ribosomal protein L3; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} (E:66-137) Probab=21.60 E-value=63 Score=14.56 Aligned_cols=16 Identities=25% Similarity=0.532 Sum_probs=13.2 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 56 E~ik~~Le~aGA~Vel 71 (72) T 2ftc_E 56 EKIKAALEAVGGTVVL 71 (72) T ss_pred HHHHHHHHHCCCEEEE T ss_conf 9999999985997973 No 16 >>1m0s_A Ribose-5-phosphate isomerase A; D-ribose 5-phosphate isomerase, northeast structural genomics consortium, IR21, structural genomics, PSI; HET: CIT; 1.90A {Haemophilus influenzae} (A:126-202) Probab=20.70 E-value=66 Score=14.46 Aligned_cols=28 Identities=18% Similarity=0.157 Sum_probs=15.5 Q ss_pred CCCEEEEEEEECH-HHHHHHHHCCCEEEE Q ss_conf 4414899998269-999999974988998 Q gi|254780242|r 123 KAKVVLRVSGASA-SAVEKVEKLGGQVIV 150 (151) Q Consensus 123 ~~ki~I~v~~~S~-sA~ekIE~aGG~v~i 150 (151) +.|+-|||.-++- ...+.+++.|++.++ T Consensus 4 ~~piPvEV~P~a~~~v~~~l~~lG~~~~l 32 (77) T 1m0s_A 4 TFPLPVEVIPMARSQVGRKLAALGGSPEY 32 (77) T ss_dssp SSCEEEEECGGGHHHHHHHHHHTTCEEEE T ss_pred CCCEEEEEEHHHHHHHHHHHHHCCCCCCC T ss_conf 99778998167889999999982899523 No 17 >>1dd3_A 50S ribosomal protein L7/L12; dimer formation, flexibility, hinge region, four-helix- bundle, five-helix- bundle, alpha-beta structure; 2.00A {Thermotoga maritima} (A:58-128) Probab=20.17 E-value=68 Score=14.40 Aligned_cols=16 Identities=25% Similarity=0.393 Sum_probs=13.3 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 55 E~iK~~Le~aGA~Vei 70 (71) T 1dd3_A 55 EEIKKKLEEAGAEVEL 70 (71) T ss_dssp HHHHHHHHHTTCEEEE T ss_pred HHHHHHHHHCCCEEEE T ss_conf 9999999985997973 Done!