Query gi|254780331|ref|YP_003064744.1| 50S ribosomal protein L9 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 179 No_of_seqs 119 out of 1863 Neff 6.4 Searched_HMMs 23785 Date Mon May 30 08:30:23 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780331.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 1div_A Ribosomal protein L9; r 100.0 0 0 320.3 13.4 148 14-161 1-149 (149) 2 3bbo_J Ribosomal protein L9; l 100.0 0 0 322.5 2.6 159 1-160 37-197 (197) 3 1nkw_F 50S ribosomal protein L 100.0 2.8E-45 0 304.9 14.4 145 14-160 1-145 (146) 4 2j01_I 50S ribosomal protein L 100.0 2.8E-45 0 305.4 6.2 147 14-161 1-148 (148) 5 3ofq_H 50S ribosomal protein L 100.0 0 0 316.0 -8.2 147 14-160 1-149 (149) 6 2hba_A BL17, 50S ribosomal pro 99.8 2.1E-20 9E-25 147.8 2.7 51 14-64 1-51 (52) 7 3fbi_A Mediator of RNA polymer 37.5 20 0.00083 15.7 2.8 22 48-69 20-41 (84) 8 3fio_A A cystathionine beta-sy 32.2 12 0.0005 17.1 0.9 25 98-122 30-54 (70) 9 3k2v_A Putative D-arabinose 5- 31.1 25 0.0011 15.0 3.3 55 78-132 49-105 (149) 10 2yzi_A Hypothetical protein PH 28.2 29 0.0012 14.7 2.8 25 96-120 44-68 (138) 11 2yvy_A MGTE, Mg2+ transporter 26.7 30 0.0012 14.6 2.2 16 97-112 178-193 (278) 12 3gby_A Uncharacterized protein 26.7 25 0.001 15.1 1.8 21 97-117 106-126 (128) 13 3kpb_A Uncharacterized protein 26.5 31 0.0013 14.5 3.0 24 96-119 38-61 (122) 14 1yav_A Hypothetical protein BS 23.7 35 0.0015 14.1 2.7 22 96-117 121-142 (159) 15 1m2d_A [2Fe-2S] ferredoxin; th 23.5 29 0.0012 14.6 1.7 30 96-125 67-99 (110) 16 2auv_A Potential NAD-reducing 22.9 25 0.0011 15.0 1.3 20 98-117 65-84 (85) 17 2oux_A Magnesium transporter; 22.0 37 0.0016 13.9 3.2 40 78-117 220-259 (286) 18 2ef7_A Hypothetical protein ST 21.7 38 0.0016 13.9 3.2 21 97-117 105-125 (133) 19 2nyc_A Nuclear protein SNF4; b 21.4 38 0.0016 13.9 3.0 21 97-117 49-69 (144) 20 2ahq_A Sigma-54, RNA polymeras 21.3 38 0.0016 13.8 2.4 23 105-127 37-59 (76) 21 3kxr_A Magnesium transporter, 20.8 40 0.0017 13.8 3.0 39 79-117 136-174 (205) 22 2uv4_A 5'-AMP-activated protei 20.5 40 0.0017 13.7 3.0 22 97-118 59-80 (152) No 1 >1div_A Ribosomal protein L9; rRNA-binding; 2.60A {Geobacillus stearothermophilus} SCOP: d.99.1.1 d.100.1.1 PDB: 1giy_K 1yl3_K 2b66_I 2b9n_I 2b9p_I 487d_K Probab=100.00 E-value=0 Score=320.26 Aligned_cols=148 Identities=30% Similarity=0.537 Sum_probs=144.3 Q ss_pred EEEEEEEECCCCCCCCCEEEECCCCEEEEECCCCCEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 33465201117587783888277632110143787301220146888778999998422346789999887654321000 Q gi|254780331|r 14 MEVILLQNVTNLGPMGEVVKVKNGYARNYLLPKKKALRANKENKILFESQRSVLEAANLEKKAKYEGISKDLAKKNFSLI 93 (179) Q Consensus 14 mkVIL~~dv~~lG~~Gdiv~Vk~GyaRN~LiP~~~A~~aT~~n~~~~~~~~~~~~~~~~~~~~~a~~~~~~L~~~~l~i~ 93 (179) |||||++||++||+.||+|+|+||||||||||+|+|++||++|+++++.+++..+++..+..+.|+.++++|++..++|. T Consensus 1 MkVIL~~dv~~lG~~GdvV~Vk~GyaRNyLiP~g~A~~aT~~n~~~~~~~~~~~~~~~~~~~~~a~~l~~~l~~~~i~i~ 80 (149) T 1div_A 1 MKVIFLKDVKGKGKKGEIKNVADGYANNFLFKQGLAIEATPANLKALEAQKQKEQRQAAEELANAKKLKEQLEKLTVTIP 80 (149) T ss_dssp CEEEECSBSSSBGGGTEEEECCTTHHHHTTTTTTSEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEEEE T ss_pred CEEEEECCCCCCCCCCCEEEECCCCHHHHHCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEE T ss_conf 97999044114798899999877014566155682455588889999999999999888887778889999730557999 Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHH-CCCCCCHHHHCCCCCCCCEEEEEEEEEECCCEEEEEEEEEEECH Q ss_conf 255654310034107899999986-08876866630265643205499999963972999999997251 Q gi|254780331|r 94 RAAGDTGYLYGSVSSRDIADLLIE-EGFDVNRGQINLKSPIKSVGIHNIMISLHADVSTTITLNVARST 161 (179) Q Consensus 94 ~k~~e~gkLfGsVt~~dI~~~L~~-~gi~I~k~~I~l~~pIk~~G~y~V~I~L~~~V~a~i~V~V~~~~ 161 (179) +++|++|+||||||+.||+++|.+ .|++|++++|.|++|||++|+|+|+|+||++|+++|+|+|++++ T Consensus 81 ~k~~~~gklfGsVt~~~I~~~l~~~~gi~i~k~~i~l~~~Ik~~G~y~v~i~l~~~v~~~i~v~V~~ek 149 (149) T 1div_A 81 AKAGEGGRLFGSITSKQIAESLQAQHGLKLDKRKIELADAIRALGYTNVPVKLHPEVTATLKVHVTEQK 149 (149) T ss_dssp ECBCGGGEEEEEECHHHHHHHHHHHHCCCCCGGGBCCCSCEEESEEEEEEEEEETTEEEEEEEEEEECC T ss_pred EEECCCCCCCCCCCHHHHHHHHHHHCCCCCCHHHHCCCCCCCCCEEEEEEEEECCCEEEEEEEEEEECC T ss_conf 974699975022489999999998519821743422445752546689999953997999999999578 No 2 >3bbo_J Ribosomal protein L9; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Arabidopsis thaliana} SCOP: i.1.1.1 Probab=100.00 E-value=0 Score=322.50 Aligned_cols=159 Identities=27% Similarity=0.450 Sum_probs=152.3 Q ss_pred CCEEECCCCCCCCEEEEEEEECCCCCCCCCEEEECCCCEEEEECCCCCEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 93132121024303346520111758778388827763211014378730122014688877899999842234678999 Q gi|254780331|r 1 MYDTQKNKKGKKIMEVILLQNVTNLGPMGEVVKVKNGYARNYLLPKKKALRANKENKILFESQRSVLEAANLEKKAKYEG 80 (179) Q Consensus 1 ~~~~~~~kk~~~~mkVIL~~dv~~lG~~Gdiv~Vk~GyaRN~LiP~~~A~~aT~~n~~~~~~~~~~~~~~~~~~~~~a~~ 80 (179) .|.++++||.+++|||||++||++||++||+|+|++|||||||||+|+|++||++|+++++.+++.+++...+..++++. T Consensus 37 ~~~~~a~kk~kk~~kVIL~~dV~~lGk~GdvV~Vk~GyaRNfLiP~g~A~~aT~~nl~~~~~~~~~~~~~~~~~~~~a~~ 116 (197) T 3bbo_J 37 NFEVVSQKKAKKLRKVILKEDVTDLGKQGQLLDVKAGFFRNFLLPTGKAQLMTPLLLKELKMEDERIEAEKQRVKEEAQQ 116 (197) T ss_dssp -------------CCCCCCSCSSSSCSSCCCSCCCSSSCCCCCTTTTCCCCCCHHHHHHHHTTTHHHHGGGTTTTHHHHT T ss_pred EEEEEEECCCCCEEEEEEECCCCCCCCCCCEEEECCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 17999861457405899905412489999999987733440143677265624999999999999999888887767999 Q ss_pred HHHHHHHH-HHHHCCCCCCCCCCCCCCCHHHHHHHHHHC-CCCCCHHHHCCCCCCCCEEEEEEEEEECCCEEEEEEEEEE Q ss_conf 98876543-210002556543100341078999999860-8876866630265643205499999963972999999997 Q gi|254780331|r 81 ISKDLAKK-NFSLIRAAGDTGYLYGSVSSRDIADLLIEE-GFDVNRGQINLKSPIKSVGIHNIMISLHADVSTTITLNVA 158 (179) Q Consensus 81 ~~~~L~~~-~l~i~~k~~e~gkLfGsVt~~dI~~~L~~~-gi~I~k~~I~l~~pIk~~G~y~V~I~L~~~V~a~i~V~V~ 158 (179) ++.+|+++ .+.+.++++++|+||||||+.||+++|.++ |++|++++|.|+ ||+++|+|+|+|+||+||+++|+|+|+ T Consensus 117 l~~~l~~~~~~~i~~~~~~~g~LfGSVT~~dI~~~L~~q~g~~V~k~~I~l~-~IK~lG~y~V~V~Lh~eV~a~ikV~Vv 195 (197) T 3bbo_J 117 LAMVFQTVGAFKVKRKGGKGKLIFGSVTAQDLVDIIKSQLQKDIDKRLVSLP-EIRETGEYIAELKLHPDVTARVKINVF 195 (197) T ss_dssp HHHHSSSCCCCBCCCCBCTTSSBSSCCSSHHHHGGGTSSSSCCCCSTTCCSC-CCSSSSCEEECCCCBTTBCCCEEEBCC T ss_pred HHHHHHCCCEEEEEEECCCCCCCCCCCCHHHHHHHHHHHCCCCCCHHEECCC-CCCCCEEEEEEEEECCCEEEEEEEEEE T ss_conf 9998730002443431254544555769999999998733982265026363-453458689999944996999999999 Q ss_pred EC Q ss_conf 25 Q gi|254780331|r 159 RS 160 (179) Q Consensus 159 ~~ 160 (179) ++ T Consensus 196 A~ 197 (197) T 3bbo_J 196 AN 197 (197) T ss_dssp CC T ss_pred EC T ss_conf 69 No 3 >1nkw_F 50S ribosomal protein L9; ribosome, large subunit, X- RAY structure, peptidyl-transferase, peptide bond formation; 3.10A {Deinococcus radiodurans} SCOP: i.1.1.2 PDB: 1nwx_F* 1nwy_F* 1sm1_F* 1xbp_F* 1pnu_F 1pny_F 1vor_I 1vou_I 1vow_I 1voy_I 1vp0_I Probab=100.00 E-value=2.8e-45 Score=304.88 Aligned_cols=145 Identities=37% Similarity=0.586 Sum_probs=141.4 Q ss_pred EEEEEEEECCCCCCCCCEEEECCCCEEEEECCCCCEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 33465201117587783888277632110143787301220146888778999998422346789999887654321000 Q gi|254780331|r 14 MEVILLQNVTNLGPMGEVVKVKNGYARNYLLPKKKALRANKENKILFESQRSVLEAANLEKKAKYEGISKDLAKKNFSLI 93 (179) Q Consensus 14 mkVIL~~dv~~lG~~Gdiv~Vk~GyaRN~LiP~~~A~~aT~~n~~~~~~~~~~~~~~~~~~~~~a~~~~~~L~~~~l~i~ 93 (179) |+|||++|+ +||+.||+|+|++|||||||||+|+|+|||++|+++++.++...+++..+..+.|+.++++|++..+++. T Consensus 1 MkvIL~~~~-~lG~~GdiV~Vk~GyaRN~LiP~~~A~~at~~nl~~~~~~~~~~~~~~~~~~~~a~~~~~~l~~~~l~~~ 79 (146) T 1nkw_F 1 MQVILLEPS-RLGKTGEVVSVKDGYARNWLIPQGLAVSATRTNMKTLEAQLRSIEKRQAQEKAVAEDLASRLNGVAVELS 79 (146) T ss_pred CEEEEEECC-CCCCCCCEEEECCHHHHHHHCCCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 979998447-7898899899876103244066670666789999999999999999999989999999998640455554 Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHCCCCCCHHHHCCCCCCCCEEEEEEEEEECCCEEEEEEEEEEEC Q ss_conf 2556543100341078999999860887686663026564320549999996397299999999725 Q gi|254780331|r 94 RAAGDTGYLYGSVSSRDIADLLIEEGFDVNRGQINLKSPIKSVGIHNIMISLHADVSTTITLNVARS 160 (179) Q Consensus 94 ~k~~e~gkLfGsVt~~dI~~~L~~~gi~I~k~~I~l~~pIk~~G~y~V~I~L~~~V~a~i~V~V~~~ 160 (179) +++++ |+||||||+.||+++|.+.|++|++++|.||+||+++|+|+|+|+||++|+++++|+|+++ T Consensus 80 ~~~~~-g~LfGsVt~~dI~~~l~~~g~~I~k~~I~l~~~Ik~~G~y~V~v~l~~~V~~~l~v~V~a~ 145 (146) T 1nkw_F 80 VRAGE-GKIYGAVTHQDVANSLDQLGFDVDRRKIDMPKTVKEVGEYDIAYRAHPEVTIPMKLVVHAA 145 (146) T ss_pred HCCCC-CCCCCCCCHHHHHHHHHHCCCEECHHHCCCCCCCCCCEEEEEEEEECCCEEEEEEEEEEEC T ss_conf 21345-4465546899999999984980169993599721364899999993498799999999978 No 4 >2j01_I 50S ribosomal protein L9; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} SCOP: d.99.1.1 d.100.1.1 PDB: 2j03_I 2jl6_I 2jl8_I 2v47_I 2v49_I 2wdi_I 2wdj_I 2wdl_I 2wdn_I 2wh2_I 2x9s_I 2x9u_I 2xg0_I 2xg2_I 3hux_I 3huz_I 3i8f_K 3i8i_K 3i9c_K 3i9e_K ... Probab=100.00 E-value=2.8e-45 Score=305.43 Aligned_cols=147 Identities=34% Similarity=0.537 Sum_probs=141.7 Q ss_pred EEEEEEEECCCCCCCCCEEEECCCCEEEEECCCCCEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 33465201117587783888277632110143787301220146888778999998422346789999887654321000 Q gi|254780331|r 14 MEVILLQNVTNLGPMGEVVKVKNGYARNYLLPKKKALRANKENKILFESQRSVLEAANLEKKAKYEGISKDLAKKNFSLI 93 (179) Q Consensus 14 mkVIL~~dv~~lG~~Gdiv~Vk~GyaRN~LiP~~~A~~aT~~n~~~~~~~~~~~~~~~~~~~~~a~~~~~~L~~~~l~i~ 93 (179) |||||++||++||+.||+|+|+||||||||||+|+|+|||++|+++++.+++..+.+..+..+.+..++..+++..+.+. T Consensus 1 MkVIL~~dv~~lG~~Gdvv~Vk~GyarN~LiP~~~A~~at~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~ 80 (148) T 2j01_I 1 MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATESNLKALEARIRAQAKRLAERKAEAERLKEILENLTLTIP 80 (148) T ss_dssp CEEEECSCCSSSCSTTCEEECCHHHHHHTTTTTTSEEECCHHHHHHHHHHHHHHHHHSSSTTTTTHHHHHHHTTCBCCCC T ss_pred CEEEEECCCCCCCCCCCEEEECCCCHHHHHCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEE T ss_conf 97999144103798899999877222355165571555799999999999999876656678999999987532204778 Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHC-CCCCCHHHHCCCCCCCCEEEEEEEEEECCCEEEEEEEEEEECH Q ss_conf 2556543100341078999999860-8876866630265643205499999963972999999997251 Q gi|254780331|r 94 RAAGDTGYLYGSVSSRDIADLLIEE-GFDVNRGQINLKSPIKSVGIHNIMISLHADVSTTITLNVARST 161 (179) Q Consensus 94 ~k~~e~gkLfGsVt~~dI~~~L~~~-gi~I~k~~I~l~~pIk~~G~y~V~I~L~~~V~a~i~V~V~~~~ 161 (179) ++++ +|+||||||+.+|+++|.++ |++|++++|.|++||+++|+|+|+|+||++|+++|+|+|++++ T Consensus 81 ~k~~-~g~LfGsVt~~~I~~~l~~~~~i~I~~~~I~l~~pIk~~G~y~V~v~l~~~v~~~i~v~Vv~~e 148 (148) T 2j01_I 81 VRAG-ETKIYGSVTAKDIAEALSRQHGVTIDPKRLALEKPIKELGEYVLTYKPHPEVPIQLKVSVVAQE 148 (148) T ss_dssp CCBC-SSSBSSCCCHHHHHHHHHTTTCCCCCTTTTCCSSCCCSCEEEECCCSSSSCCCCEEEECCC--- T ss_pred EECC-CCCCCCCCCHHHHHHHHHHHCCCEECHHHEECCCCHHCCEEEEEEEEECCCEEEEEEEEEEECC T ss_conf 6046-6423156489999999998549765499951788210138889999954988999999999688 No 5 >3ofq_H 50S ribosomal protein L9; protein biosynthesis, ribosomes, RNA, tRNA, transfer, antibi EXIT, peptidyl, ribosomal subunit, large; 3.10A {Escherichia coli} PDB: 1p85_F 1p86_F 1vs8_H 1vs6_H 2aw4_H 2awb_H 2gya_F 2gyc_F 1vt2_H 2i2v_H 2j28_H 2i2t_H* 2qao_H* 2qba_H* 2qbc_H* 2qbe_H 2qbg_H 2qbi_H* 2qbk_H* 2qov_H ... Probab=100.00 E-value=0 Score=316.05 Aligned_cols=147 Identities=37% Similarity=0.632 Sum_probs=142.6 Q ss_pred EEEEEEEECCCCCCCCCEEEECCCCEEEEECCCCCEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHH Q ss_conf 334652011175877838882776321101437873012201468887789999984223467899998876543-2100 Q gi|254780331|r 14 MEVILLQNVTNLGPMGEVVKVKNGYARNYLLPKKKALRANKENKILFESQRSVLEAANLEKKAKYEGISKDLAKK-NFSL 92 (179) Q Consensus 14 mkVIL~~dv~~lG~~Gdiv~Vk~GyaRN~LiP~~~A~~aT~~n~~~~~~~~~~~~~~~~~~~~~a~~~~~~L~~~-~l~i 92 (179) |||||++||++||+.||+|+|++|||||||||+|+|++||++|+++++.+++..+++..+....|+.++++|+++ .++| T Consensus 1 MkVIL~~dV~~lG~~GdiV~Vk~GyARN~LiP~~~Av~at~~n~~~~~~~~~~~~~~~~~~~~~a~~~~~~l~~l~~~~i 80 (149) T 3ofq_H 1 MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRAELEAKLAEVLAAANARAEKINALETVTI 80 (149) T ss_dssp CCCEESSCCSSSCCSSCCCCCCTTTTTTTTTTTTSEECCCSHHHHHHHHHHHHHHHHHHTTTTTCCCCCSTTSSCCCCCS T ss_pred CEEEECCCCCCCCCCCCEEEECCHHHHHHHCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEE T ss_conf 97999144115798999999873434776165684444458889999999999987767887789999986402217987 Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCHHHHCCC-CCCCCEEEEEEEEEECCCEEEEEEEEEEEC Q ss_conf 02556543100341078999999860887686663026-564320549999996397299999999725 Q gi|254780331|r 93 IRAAGDTGYLYGSVSSRDIADLLIEEGFDVNRGQINLK-SPIKSVGIHNIMISLHADVSTTITLNVARS 160 (179) Q Consensus 93 ~~k~~e~gkLfGsVt~~dI~~~L~~~gi~I~k~~I~l~-~pIk~~G~y~V~I~L~~~V~a~i~V~V~~~ 160 (179) .+++|++|+||||||+.||+++|+++|++|++++|.+| +|||++|+|+|+|+||++|+++++|+|+++ T Consensus 81 ~~k~~e~gkLfGsVt~~~I~~~l~~~g~~i~k~~i~l~~~pIK~~G~~~V~v~L~~~V~a~i~v~V~~e 149 (149) T 3ofq_H 81 ASKAGDEGKLFGSIGTRDIADAVTAAGVEVAKSEVRLPNGVLRTTGEHEVSFQVHSEVFAKVIVNVVAE 149 (149) T ss_dssp CCCCCTTSSCCSCCCSCCSCCSSSCSSSCCCSCCSCCSSSSCCCSSCCCCCCCSSSSCCCCCCCCCCCC T ss_pred EEEECCCCCCCCCCCHHHHHHHHHHCCCCCCHHHEECCCCCCCCCEEEEEEEEECCCEEEEEEEEEEEC T ss_conf 764189984457426999999999859911589811788552063778999996599199999999979 No 6 >2hba_A BL17, 50S ribosomal protein L9; NTL9, K12M, RNA binding protein; 1.25A {Geobacillus stearothermophilus} SCOP: d.100.1.1 PDB: 1cqu_A 2hbb_A 2hvf_A Probab=99.79 E-value=2.1e-20 Score=147.83 Aligned_cols=51 Identities=37% Similarity=0.651 Sum_probs=49.4 Q ss_pred EEEEEEEECCCCCCCCCEEEECCCCEEEEECCCCCEECCCCHHHHHHHHHH Q ss_conf 334652011175877838882776321101437873012201468887789 Q gi|254780331|r 14 MEVILLQNVTNLGPMGEVVKVKNGYARNYLLPKKKALRANKENKILFESQR 64 (179) Q Consensus 14 mkVIL~~dv~~lG~~Gdiv~Vk~GyaRN~LiP~~~A~~aT~~n~~~~~~~~ 64 (179) |||||++||++||+.||+|+|+||||||||||+|+|++||++|+++++.++ T Consensus 1 MkVIL~~dV~~lG~~Gdiv~Vk~GyaRN~Lip~~~A~~at~~~~~~~~~~k 51 (52) T 2hba_A 1 MKVIFLKDVKGMGKKGEIKNVADGYANNFLFKQGLAIEATPANLKALEAQK 51 (52) T ss_dssp CEEEESSCBTTTBCTTCEEECCHHHHHHTTTTTTSEEECCHHHHHHHHHHH T ss_pred CEEEEECCCCCCCCCCCEEEECCHHHHHHHCCCCCCHHCCHHHHHHHHHHH T ss_conf 979990532157878989998540056660667851337999999999860 No 7 >3fbi_A Mediator of RNA polymerase II transcription subunit 7; proline-rich stretches, right-handed four-helix bundle, protein-protein complex; 2.80A {Saccharomyces cerevisiae} PDB: 3fbn_A Probab=37.53 E-value=20 Score=15.68 Aligned_cols=22 Identities=9% Similarity=-0.135 Sum_probs=15.7 Q ss_pred CEECCCCHHHHHHHHHHHHHHH Q ss_conf 7301220146888778999998 Q gi|254780331|r 48 KALRANKENKILFESQRSVLEA 69 (179) Q Consensus 48 ~A~~aT~~n~~~~~~~~~~~~~ 69 (179) +=..-|++|++.++..++.... T Consensus 20 f~K~FT~ENl~kL~e~k~~~~~ 41 (84) T 3fbi_A 20 YVKFFTQSNLEKLPKYKEKKAA 41 (84) T ss_dssp GGGGCCHHHHHHHHHHHHHHHC T ss_pred HHHHCCHHHHHHHHHHHHHHHH T ss_conf 8885699999999999987643 No 8 >3fio_A A cystathionine beta-synthase domain protein fused to A Zn-ribbon-like domain; PF1953,APC40009,cystathionine beta-synthase domain protein; 1.81A {Pyrococcus furiosus} PDB: 3ghd_A Probab=32.23 E-value=12 Score=17.06 Aligned_cols=25 Identities=28% Similarity=0.496 Sum_probs=19.9 Q ss_pred CCCCCCCCCCHHHHHHHHHHCCCCC Q ss_conf 5431003410789999998608876 Q gi|254780331|r 98 DTGYLYGSVSSRDIADLLIEEGFDV 122 (179) Q Consensus 98 e~gkLfGsVt~~dI~~~L~~~gi~I 122 (179) ++|+++|-+|..||...+...+... T Consensus 30 d~~~lvGIvT~~Di~~~~~~~~~~~ 54 (70) T 3fio_A 30 EGDEILGVVTERDILDKVVAKGKNP 54 (70) T ss_dssp ETTEEEEEEEHHHHHHHTTTTTCCG T ss_pred ECCEEEEEEEHHHHHHHHHHCCCCC T ss_conf 8998627986999999998569981 No 9 >3k2v_A Putative D-arabinose 5-phosphate isomerase; KPSF-like protein, CBS domain, , structural genomics, PSI-2; HET: MSE CMK; 1.95A {Klebsiella pneumoniae subsp} PDB: 3fna_A* Probab=31.13 E-value=25 Score=14.98 Aligned_cols=55 Identities=11% Similarity=0.171 Sum_probs=32.3 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCC--CCCCHHHHCCCCC Q ss_conf 999988765432100025565431003410789999998608--8768666302656 Q gi|254780331|r 78 YEGISKDLAKKNFSLIRAAGDTGYLYGSVSSRDIADLLIEEG--FDVNRGQINLKSP 132 (179) Q Consensus 78 a~~~~~~L~~~~l~i~~k~~e~gkLfGsVt~~dI~~~L~~~g--i~I~k~~I~l~~p 132 (179) ..+....+....+..-.=++++|+|.|-||..||...+.... ....-+.|--..| T Consensus 49 l~~a~~~m~~~~~~~~~Vvd~~~~l~GiiT~~Di~r~~~~~~~~~~~~V~~imt~~p 105 (149) T 3k2v_A 49 LRDALLEITRKNLGMTAICDDDMNIIGIFTDGDLRRVFDTGVDMRDASIADVMTRGG 105 (149) T ss_dssp HHHHHHHHHHHTSSEEEEECTTCBEEEEEEHHHHHHHHCSSSCCTTCBHHHHSEESC T ss_pred HHHHHHHHHHHCCCEEEEEECCCCEEEEEECHHHHHHHHHCCCCCCCEEEECCCCCE T ss_conf 999999855746988999958993999997005654333122344305640454450 No 10 >2yzi_A Hypothetical protein PH0107; sheet/helix/sheet/sheet/helix, structural genomics, unknown function, NPPSFA; 2.25A {Pyrococcus horikoshii} SCOP: d.37.1.1 Probab=28.16 E-value=29 Score=14.66 Aligned_cols=25 Identities=28% Similarity=0.440 Sum_probs=16.5 Q ss_pred CCCCCCCCCCCCHHHHHHHHHHCCC Q ss_conf 5654310034107899999986088 Q gi|254780331|r 96 AGDTGYLYGSVSSRDIADLLIEEGF 120 (179) Q Consensus 96 ~~e~gkLfGsVt~~dI~~~L~~~gi 120 (179) ++++|+++|-||..||...+...+. T Consensus 44 vd~~~~~~Giit~~Di~~~~~~~~~ 68 (138) T 2yzi_A 44 INDDGNVVGFFTKSDIIRRVIVPGL 68 (138) T ss_dssp ECTTSCEEEEEEHHHHHHHTTTTCC T ss_pred EECCCEEEEEEEHHHHHHHHHHCCC T ss_conf 9389839999877898887764044 No 11 >2yvy_A MGTE, Mg2+ transporter MGTE; membrane protein, transport protein; 2.30A {Thermus thermophilus HB8} PDB: 2yvz_A Probab=26.71 E-value=30 Score=14.57 Aligned_cols=16 Identities=38% Similarity=0.594 Sum_probs=7.8 Q ss_pred CCCCCCCCCCCHHHHH Q ss_conf 6543100341078999 Q gi|254780331|r 97 GDTGYLYGSVSSRDIA 112 (179) Q Consensus 97 ~e~gkLfGsVt~~dI~ 112 (179) .++|+|-|.|+..++. T Consensus 178 d~~~~l~G~v~~~dLl 193 (278) T 2yvy_A 178 DEKGRLKGVLSLRDLI 193 (278) T ss_dssp CTTCBEEEEEEHHHHH T ss_pred CCCCCEECCCCHHHHH T ss_conf 7655641013199998 No 12 >3gby_A Uncharacterized protein CT1051; CBS domain, structural genomics, PSI-2, protein structure initiative; HET: EPE; 1.66A {Chlorobium tepidum tls} Probab=26.66 E-value=25 Score=15.07 Aligned_cols=21 Identities=33% Similarity=0.477 Sum_probs=11.4 Q ss_pred CCCCCCCCCCCHHHHHHHHHH Q ss_conf 654310034107899999986 Q gi|254780331|r 97 GDTGYLYGSVSSRDIADLLIE 117 (179) Q Consensus 97 ~e~gkLfGsVt~~dI~~~L~~ 117 (179) +++|++.|=||..||...|.+ T Consensus 106 d~~g~~~Giit~~dil~~l~~ 126 (128) T 3gby_A 106 DEDGRYEGVVSRKRILGFLAE 126 (128) T ss_dssp CTTCBEEEEEEHHHHHHHHHT T ss_pred CCCCEEEEEEEHHHHHHHHHH T ss_conf 689969999999999999982 No 13 >3kpb_A Uncharacterized protein MJ0100; CBS domain, S-adenosylmethionine, conformational change, unknown function; HET: SAM; 1.60A {Methanocaldococcus jannaschii} PDB: 3kpd_A* 3kpc_A* Probab=26.47 E-value=31 Score=14.47 Aligned_cols=24 Identities=33% Similarity=0.489 Sum_probs=15.6 Q ss_pred CCCCCCCCCCCCHHHHHHHHHHCC Q ss_conf 565431003410789999998608 Q gi|254780331|r 96 AGDTGYLYGSVSSRDIADLLIEEG 119 (179) Q Consensus 96 ~~e~gkLfGsVt~~dI~~~L~~~g 119 (179) ++++|++.|-||..|+...+.... T Consensus 38 vd~~~~~~G~it~~dl~~~~~~~~ 61 (122) T 3kpb_A 38 VDEHGKLVGIITSWDIAKALAQNK 61 (122) T ss_dssp ECTTSBEEEEECHHHHHHHHHTTC T ss_pred EECCCCEEEEEEHHHHHHHHCCCC T ss_conf 908992999988999987650389 No 14 >1yav_A Hypothetical protein BSU14130; cystathionine beta synthase (CBS) domain, structural genomics, protein structure initiative, PSI; 2.10A {Bacillus subtilis} SCOP: d.37.1.1 Probab=23.69 E-value=35 Score=14.14 Aligned_cols=22 Identities=18% Similarity=0.187 Sum_probs=11.1 Q ss_pred CCCCCCCCCCCCHHHHHHHHHH Q ss_conf 5654310034107899999986 Q gi|254780331|r 96 AGDTGYLYGSVSSRDIADLLIE 117 (179) Q Consensus 96 ~~e~gkLfGsVt~~dI~~~L~~ 117 (179) ++++|++-|=||..||.+++.. T Consensus 121 Vde~g~~~GIIT~~Dil~~l~~ 142 (159) T 1yav_A 121 ENDEQVFEGIFTRRVVLKELNK 142 (159) T ss_dssp ECTTCBEEEEEEHHHHHHHHHH T ss_pred EECCCEEEEEEEHHHHHHHHHH T ss_conf 9449979999889999999999 No 15 >1m2d_A [2Fe-2S] ferredoxin; thioredoxin-like fold, [2Fe-2S] cluster, Cys59Ser variant, electron transport; 1.05A {Aquifex aeolicus} SCOP: c.47.1.11 PDB: 1m2a_A 1f37_A 1m2b_A Probab=23.52 E-value=29 Score=14.57 Aligned_cols=30 Identities=27% Similarity=0.439 Sum_probs=23.3 Q ss_pred CCCCCCCCCCCCHHHHHHHHHHC---CCCCCHH Q ss_conf 56543100341078999999860---8876866 Q gi|254780331|r 96 AGDTGYLYGSVSSRDIADLLIEE---GFDVNRG 125 (179) Q Consensus 96 ~~e~gkLfGsVt~~dI~~~L~~~---gi~I~k~ 125 (179) +.++|..|+-||+.+|.+.+.++ |-.+++- T Consensus 67 I~P~g~~Y~~v~p~~v~~Iv~~hl~~g~pv~~l 99 (110) T 1m2d_A 67 VYPDGVWYGQVKPEDVDEIVEKHLKGGEPVERL 99 (110) T ss_dssp EETTTEEECSCCGGGHHHHHHHTTTTSCCCGGG T ss_pred EECCCCEEECCCHHHHHHHHHHHHHCCCEEEEE T ss_conf 907977781599999999999999799470356 No 16 >2auv_A Potential NAD-reducing hydrogenase subunit; thioredoxin, thiordoxin-like, oxidoreductase; NMR {Desulfovibrio fructosovorans} Probab=22.89 E-value=25 Score=14.99 Aligned_cols=20 Identities=25% Similarity=0.471 Sum_probs=16.4 Q ss_pred CCCCCCCCCCHHHHHHHHHH Q ss_conf 54310034107899999986 Q gi|254780331|r 98 DTGYLYGSVSSRDIADLLIE 117 (179) Q Consensus 98 e~gkLfGsVt~~dI~~~L~~ 117 (179) =||++|+.+|+.++.+.|.+ T Consensus 65 id~~~y~~vt~e~v~~il~~ 84 (85) T 2auv_A 65 VGEKVYGNVTPGQVKKILAE 84 (85) T ss_dssp EGGGCCCCSSSSHHHHHHHH T ss_pred ECCEEECCCCHHHHHHHHHH T ss_conf 99998778899999999971 No 17 >2oux_A Magnesium transporter; 10001B, structural genomics, PSI-2, protein structure initiative, nysgxrc; 2.16A {Enterococcus faecalis V583} SCOP: a.118.26.1 d.37.1.1 Probab=22.00 E-value=37 Score=13.93 Aligned_cols=40 Identities=20% Similarity=0.341 Sum_probs=23.2 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHH Q ss_conf 9999887654321000255654310034107899999986 Q gi|254780331|r 78 YEGISKDLAKKNFSLIRAAGDTGYLYGSVSSRDIADLLIE 117 (179) Q Consensus 78 a~~~~~~L~~~~l~i~~k~~e~gkLfGsVt~~dI~~~L~~ 117 (179) .+..++.+....+..--=+.++|+|-|-||..||.+.+.+ T Consensus 220 ~eeaa~~~~~~~l~~lPVVD~~g~LvGiIT~~Dii~~i~e 259 (286) T 2oux_A 220 QEDVAQTIRDYDFLAVPVTDYDDHLLGIVTVDDIIDVIDD 259 (286) T ss_dssp HHHHHHHHHHHTCSEEEEECTTCBEEEEEEHHHHHHHHHH T ss_pred HHHHHHHHHHCCCCEEEEECCCCEEEEEEEHHHHHHHHHH T ss_conf 9999999997399766188579969999789999999999 No 18 >2ef7_A Hypothetical protein ST2348; CBS-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.10A {Sulfolobus tokodaii} SCOP: d.37.1.1 Probab=21.70 E-value=38 Score=13.89 Aligned_cols=21 Identities=38% Similarity=0.548 Sum_probs=11.4 Q ss_pred CCCCCCCCCCCHHHHHHHHHH Q ss_conf 654310034107899999986 Q gi|254780331|r 97 GDTGYLYGSVSSRDIADLLIE 117 (179) Q Consensus 97 ~e~gkLfGsVt~~dI~~~L~~ 117 (179) +++|++.|=||..||..++.+ T Consensus 105 d~~~~~~Giit~~Di~~~l~~ 125 (133) T 2ef7_A 105 DDKGNLKGIISIRDITRAIDD 125 (133) T ss_dssp CTTSCEEEEEEHHHHHHHHHH T ss_pred ECCCEEEEEEEHHHHHHHHHH T ss_conf 489969999999999999978 No 19 >2nyc_A Nuclear protein SNF4; bateman2 domain, AMP kinase, protein binding; 1.90A {Saccharomyces cerevisiae} SCOP: d.37.1.1 PDB: 2nye_A Probab=21.39 E-value=38 Score=13.85 Aligned_cols=21 Identities=24% Similarity=0.468 Sum_probs=12.2 Q ss_pred CCCCCCCCCCCHHHHHHHHHH Q ss_conf 654310034107899999986 Q gi|254780331|r 97 GDTGYLYGSVSSRDIADLLIE 117 (179) Q Consensus 97 ~e~gkLfGsVt~~dI~~~L~~ 117 (179) .++|++.|-||..||...+.. T Consensus 49 d~~~~~iGiis~~Di~~~l~~ 69 (144) T 2nyc_A 49 DENGYLINVYEAYDVLGLIKG 69 (144) T ss_dssp CTTCBEEEEEEHHHHHHHHHT T ss_pred ECCCEEEEEEEECHHHHHHHC T ss_conf 279929999986020134322 No 20 >2ahq_A Sigma-54, RNA polymerase sigma factor RPON; sigma-54,sigma factors, solution structure, transcription; NMR {Aquifex aeolicus} PDB: 2o8k_A 2o9l_A Probab=21.34 E-value=38 Score=13.85 Aligned_cols=23 Identities=39% Similarity=0.700 Sum_probs=19.9 Q ss_pred CCCHHHHHHHHHHCCCCCCHHHH Q ss_conf 41078999999860887686663 Q gi|254780331|r 105 SVSSRDIADLLIEEGFDVNRGQI 127 (179) Q Consensus 105 sVt~~dI~~~L~~~gi~I~k~~I 127 (179) +.+-..|++.|.+.|+.|.++-| T Consensus 37 PlSD~~i~~~L~~~Gi~IaRRTV 59 (76) T 2ahq_A 37 PYSDQEIANILKEKGFKVARRTV 59 (76) T ss_dssp CCCHHHHHHHHTTTSSCCCHHHH T ss_pred CCCHHHHHHHHHHCCCCEEHHHH T ss_conf 97699999999986995531619 No 21 >3kxr_A Magnesium transporter, putative; cystathionine beta-synthase, Mg2+ transporter, structural genomics, PSI-2; 2.41A {Shewanella oneidensis mr-1} Probab=20.76 E-value=40 Score=13.77 Aligned_cols=39 Identities=21% Similarity=0.239 Sum_probs=21.8 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHH Q ss_conf 999887654321000255654310034107899999986 Q gi|254780331|r 79 EGISKDLAKKNFSLIRAAGDTGYLYGSVSSRDIADLLIE 117 (179) Q Consensus 79 ~~~~~~L~~~~l~i~~k~~e~gkLfGsVt~~dI~~~L~~ 117 (179) ...+..+....+..--=++++|+|-|-||..||.+.+.+ T Consensus 136 ~ea~~~~~~~~~~~lPVVD~~g~lvGiIt~~Dil~~i~e 174 (205) T 3kxr_A 136 LDAAEAIEHSREIELPVIDDAGELIGRVTLRAATALVRE 174 (205) T ss_dssp HHHHHHHHTSSCSEEEEECTTSBEEEEEEHHHHHHHHHH T ss_pred HHHHHHHHHCCCCEEEEECCCCEEEEEEEHHHHHHHHHH T ss_conf 999999997697365388759989999889999999999 No 22 >2uv4_A 5'-AMP-activated protein kinase subunit gamma-1; transferase, CBS domain, lipid synthesis, fatty acid biosynthesis; HET: AMP; 1.33A {Homo sapiens} PDB: 2uv5_A* 2uv6_A* 2uv7_A* Probab=20.49 E-value=40 Score=13.74 Aligned_cols=22 Identities=23% Similarity=0.315 Sum_probs=15.0 Q ss_pred CCCCCCCCCCCHHHHHHHHHHC Q ss_conf 6543100341078999999860 Q gi|254780331|r 97 GDTGYLYGSVSSRDIADLLIEE 118 (179) Q Consensus 97 ~e~gkLfGsVt~~dI~~~L~~~ 118 (179) +++|++.|-||..||...+... T Consensus 59 d~~~~lvGiit~~di~~~~~~~ 80 (152) T 2uv4_A 59 DEKGRVVDIYSKFDVINLAAEK 80 (152) T ss_dssp CTTSBEEEEEEHHHHHHHHHCS T ss_pred CCCCCEEEEEEHHHHHHHHHCC T ss_conf 0898199999623226676505 Done!