Query gi|254780319|ref|YP_003064732.1| 50S ribosomal protein L35 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 67 No_of_seqs 108 out of 707 Neff 5.0 Searched_HMMs 23785 Date Mon May 30 08:46:35 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780319.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 2zjr_3 50S ribosomal protein L 100.0 3.1E-29 1.3E-33 162.0 6.3 65 1-66 1-65 (66) 2 2j01_8 50S ribosomal protein L 99.9 1.2E-28 4.9E-33 159.2 3.0 64 1-65 1-64 (65) 3 3ofq_3 50S ribosomal protein L 99.9 9.8E-27 4.1E-31 149.8 3.9 64 2-66 1-64 (64) 4 3bbo_5 Ribosomal protein L35; 99.9 8.9E-25 3.7E-29 140.2 0.3 63 3-66 91-153 (159) 5 3c8l_A FTSZ-like protein of un 7.7 1E+02 0.0043 12.7 0.9 14 52-66 67-80 (122) 6 3jyw_M 60S ribosomal protein L 7.1 50 0.0021 14.2 -1.0 13 54-66 73-85 (178) 7 2jra_A Protein RPA2121; domain 3.9 2.1E+02 0.009 11.2 1.7 18 7-24 48-65 (67) 8 1vq8_J 50S ribosomal protein L 3.3 2.5E+02 0.01 10.8 1.2 11 55-65 79-89 (145) 9 3heq_A Major prion protein; ce 2.5 2.6E+02 0.011 10.8 -0.3 41 25-67 1-41 (142) 10 2v1y_A Phosphatidylinositol-4, 2.3 3.3E+02 0.014 10.2 0.4 6 62-67 25-30 (108) No 1 >2zjr_3 50S ribosomal protein L35; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: d.301.1.1 PDB: 2zjp_3* 1sm1_3 2zjq_3 3cf5_3* 3dll_3* 1nwy_3* 1nwx_3* 1xbp_3* 1nkw_3 1yl3_8 2b66_8 2b9n_8 2b9p_8 1pnu_3 1pny_3 1vor_5 1vou_5 1vow_5 1voy_5 1vp0_5 Probab=99.95 E-value=3.1e-29 Score=162.02 Aligned_cols=65 Identities=45% Similarity=0.581 Sum_probs=63.6 Q ss_pred CCCCCCCCHHHEEEEECCCCEEEECCCCCCCCCCCCCCHHHHHCCCCEEECHHHHHHHHHHHCCCC Q ss_conf 987323301212257759980970324885254158804654146986837778999999858688 Q gi|254780319|r 1 MPKMKTNSSSKKRFSITATGKVRAQAAGKRHGMIKRSNKFIRNARGTMVLASADAKKVIRNYLPNG 66 (67) Q Consensus 1 MPKmKT~k~akKRFk~T~sGKvkr~~agk~H~l~~Ks~krkR~lr~~~~v~~~~~~~i~r~llPYg 66 (67) |||||||+||+|||++||||+|++++||++|+++++|++++|+|+++.+|+++|.++|.+ ||||| T Consensus 1 MPKmKT~k~akKRfkvT~sGKv~r~~a~k~H~l~~Ks~k~kR~lr~~~~v~~~~~k~ik~-lLPyg 65 (66) T 2zjr_3 1 MPKMKTHKMAKRRIKITGTGKVMAFKSGKRHQNTGKSGDEIRGKGKGFVLAKAEWARMKL-MLPRG 65 (66) T ss_pred CCCCCCCHHHHHEEEECCCCCEEECCCCCCCCCCCCCHHHHHHCCCCEEECHHHHHHHHH-HCCCC T ss_conf 997543122352057768987865537776665558888998657985478999999999-67899 No 2 >2j01_8 50S ribosomal protein L35; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} SCOP: d.301.1.1 PDB: 1vsp_a 2hgj_7 2hgq_7 2hgu_7 1vsa_a 2j03_8 2jl6_8 2jl8_8 2v47_8 2v49_8 2wdi_8 2wdj_8 2wdl_8 2wdn_8 2wh2_8 2wh4_8 2wrj_8 2wrl_8 2wro_8 2wrr_8 ... Probab=99.94 E-value=1.2e-28 Score=159.23 Aligned_cols=64 Identities=47% Similarity=0.612 Sum_probs=62.6 Q ss_pred CCCCCCCCHHHEEEEECCCCEEEECCCCCCCCCCCCCCHHHHHCCCCEEECHHHHHHHHHHHCCC Q ss_conf 98732330121225775998097032488525415880465414698683777899999985868 Q gi|254780319|r 1 MPKMKTNSSSKKRFSITATGKVRAQAAGKRHGMIKRSNKFIRNARGTMVLASADAKKVIRNYLPN 65 (67) Q Consensus 1 MPKmKT~k~akKRFk~T~sGKvkr~~agk~H~l~~Ks~krkR~lr~~~~v~~~~~~~i~r~llPY 65 (67) |||||||+||+|||++||||||++++||++|+++++|.+++|+|+++.+|+++|.++|.+ |||| T Consensus 1 MPKmKT~k~a~KRfkvT~sGKi~r~~ag~~H~l~~Ks~k~kR~lr~~~~v~~~~~k~ik~-lLPY 64 (65) T 2j01_8 1 MPKMKTHKGAKKRVKITASGKVVAMKTGKRHLNWQKSGKEIRQKGRKFVLAKPEAERIKL-LLPY 64 (65) T ss_dssp -CCCCCCHHHHHHCEECSSSCEEECCTTTTTCSSCSCCSTTTSCSCEECCSSHHHHHHTT-TTTC T ss_pred CCCCCCCHHHHHEEEECCCCCEEECCCCCCCCCCCCCHHHHHHCCCCEEECHHHHHHHHH-HCCC T ss_conf 997643211351157768987874416777765448888898657985587999999998-3899 No 3 >3ofq_3 50S ribosomal protein L35; protein biosynthesis, ribosomes, RNA, tRNA, transfer, antibi EXIT, peptidyl, ribosomal subunit, large; 3.10A {Escherichia coli} PDB: 2awb_3 2aw4_3 2i2v_3 2j28_3 2i2t_3* 2qao_3* 2qba_3* 2qbc_3* 2qbe_3 2qbg_3 2qbi_3* 2qbk_3* 2qov_3 2qox_3 2qoz_3* 2qp1_3* 2rdo_3 2vhm_3 2vhn_3 2wwq_7* ... Probab=99.93 E-value=9.8e-27 Score=149.82 Aligned_cols=64 Identities=33% Similarity=0.449 Sum_probs=62.3 Q ss_pred CCCCCCCHHHEEEEECCCCEEEECCCCCCCCCCCCCCHHHHHCCCCEEECHHHHHHHHHHHCCCC Q ss_conf 87323301212257759980970324885254158804654146986837778999999858688 Q gi|254780319|r 2 PKMKTNSSSKKRFSITATGKVRAQAAGKRHGMIKRSNKFIRNARGTMVLASADAKKVIRNYLPNG 66 (67) Q Consensus 2 PKmKT~k~akKRFk~T~sGKvkr~~agk~H~l~~Ks~krkR~lr~~~~v~~~~~~~i~r~llPYg 66 (67) ||||||+||+|||++||||+|++++||++|++++||.+++|+|+++++|+++|.++|.+ ||||. T Consensus 1 PKmKT~k~akKRfk~T~sGKikr~~a~~~H~l~~Ks~k~kR~lr~~~~v~~~~~k~vkk-lLPYa 64 (64) T 3ofq_3 1 PKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIA-CLPYA 64 (64) T ss_dssp CCCCCCTTGGGSCCCCSSSCCCCCCSSCSSCCSSSCHHHHHHHSSCCCCCHHHHHHHHH-HCSCC T ss_pred CCCCCCHHHHHCEEECCCCCEEECCCCCCCCCCCCCHHHHHHCCCCEEECHHHHHHHHH-HCCCC T ss_conf 98764123463046778997864417777665458988998767982478999999998-68899 No 4 >3bbo_5 Ribosomal protein L35; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Probab=99.89 E-value=8.9e-25 Score=140.24 Aligned_cols=63 Identities=35% Similarity=0.456 Sum_probs=60.9 Q ss_pred CCCCCCHHHEEEEECCCCEEEECCCCCCCCCCCCCCHHHHHCCCCEEECHHHHHHHHHHHCCCC Q ss_conf 7323301212257759980970324885254158804654146986837778999999858688 Q gi|254780319|r 3 KMKTNSSSKKRFSITATGKVRAQAAGKRHGMIKRSNKFIRNARGTMVLASADAKKVIRNYLPNG 66 (67) Q Consensus 3 KmKT~k~akKRFk~T~sGKvkr~~agk~H~l~~Ks~krkR~lr~~~~v~~~~~~~i~r~llPYg 66 (67) |||||+||+|||++||+|||+|++||++|++++||.+++|+|+++.+|+++|.++|.+ ||||- T Consensus 91 KMKThKgAkKRFKvTgsGKvkR~rAgkrHll~kKS~krKRrLRk~~~Vs~sd~K~Ikk-lLPY~ 153 (159) T 3bbo_5 91 KMKTHKASAKRFRVTGKGKIVRRRAGKQHLLAKKNTKRKNRLSKLIQVDRSDYDNVIG-ALPYL 153 (159) T ss_dssp CCCCCHHHHTTCCBCSSSCBEEECSSCTTCCSSCCSSCTTSCSEEECCSTHHHHTTTT-TTTC- T ss_pred CCCCCHHHHCEEEECCCCCEEECCCCCCCCCCCCCHHHHHHCCCCEEECHHHHHHHHH-HCCCC T ss_conf 6455331241158757975866527777665458998998657985477999999998-57983 No 5 >3c8l_A FTSZ-like protein of unknown function; ZP_00109722.1, conserved hypothetical protein (LIN0512_FAM), structural genomics; HET: MSE; 1.22A {Nostoc punctiforme pcc 73102} Probab=7.67 E-value=1e+02 Score=12.69 Aligned_cols=14 Identities=29% Similarity=0.413 Sum_probs=9.3 Q ss_pred HHHHHHHHHHHCCCC Q ss_conf 778999999858688 Q gi|254780319|r 52 SADAKKVIRNYLPNG 66 (67) Q Consensus 52 ~~~~~~i~r~llPYg 66 (67) .-|...+ +..|||| T Consensus 67 ~VD~~~v-~~~lPyG 80 (122) T 3c8l_A 67 QVREEEV-LAVLPFG 80 (122) T ss_dssp GCCHHHH-HTTSCSS T ss_pred HHCHHHH-HHHCCCC T ss_conf 2048889-9768877 No 6 >3jyw_M 60S ribosomal protein L16(A); eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} PDB: 1s1i_M Probab=7.14 E-value=50 Score=14.23 Aligned_cols=13 Identities=15% Similarity=0.133 Sum_probs=8.7 Q ss_pred HHHHHHHHHCCCC Q ss_conf 8999999858688 Q gi|254780319|r 54 DAKKVIRNYLPNG 66 (67) Q Consensus 54 ~~~~i~r~llPYg 66 (67) -.++.++.||||. T Consensus 73 Il~rAVrGMLP~K 85 (178) T 3jyw_M 73 IFYKALRGMVSHK 85 (178) T ss_dssp HHHHHTTSSSCSS T ss_pred HHHHHHHCCCCCC T ss_conf 9999984568999 No 7 >2jra_A Protein RPA2121; domain-swapped dimer, structural genomics, PSI, protein structure initiative; NMR {Rhodopseudomonas palustris CGA009} Probab=3.92 E-value=2.1e+02 Score=11.15 Aligned_cols=18 Identities=17% Similarity=0.333 Sum_probs=12.9 Q ss_pred CCHHHEEEEECCCCEEEE Q ss_conf 301212257759980970 Q gi|254780319|r 7 NSSSKKRFSITATGKVRA 24 (67) Q Consensus 7 ~k~akKRFk~T~sGKvkr 24 (67) |-|.-=|.++|..||++- T Consensus 48 H~g~~Y~LR~Tr~gKLIL 65 (67) T 2jra_A 48 HGDDRYRLRLTSQNKLIL 65 (67) T ss_dssp ETTEEEEEEECTTSCEEE T ss_pred ECCCEEEEEECCCCCEEE T ss_conf 799089978835896786 No 8 >1vq8_J 50S ribosomal protein L13P; 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.21.1.1 PDB: 1giy_M 1jj2_I 1k73_K* 1k8a_K* 1k9m_K* 1kc8_K* 1kd1_K* 1kqs_I* 1m1k_K* 1m90_K* 1ml5_m* 1n8r_K* 1nji_K* 1q7y_K* 1q81_K* 1q82_K* 1q86_K* 1qvf_I 1qvg_I 1s72_J* ... Probab=3.25 E-value=2.5e+02 Score=10.82 Aligned_cols=11 Identities=45% Similarity=0.766 Sum_probs=7.8 Q ss_pred HHHHHHHHCCC Q ss_conf 99999985868 Q gi|254780319|r 55 AKKVIRNYLPN 65 (67) Q Consensus 55 ~~~i~r~llPY 65 (67) ..+.++.|||| T Consensus 79 l~raVrGMLP~ 89 (145) T 1vq8_J 79 FKRTIRGMLPH 89 (145) T ss_dssp HHHHHHTTTTT T ss_pred HHHHHHCCCCC T ss_conf 99998415899 No 9 >3heq_A Major prion protein; cell membrane, disease mutation, disulfide bond, glycoprotein, golgi apparatus, GPI-anchor, lipoprotein, membrane, polymorphism; 1.80A {Homo sapiens} PDB: 2k1d_A 1fkc_A 1fo7_A 3haf_A 3hj5_A 1qm0_A 1qm1_A 3hes_A 3her_A 1b10_A 2joh_A 2fj3_A 2jom_A 2kfo_A 2k5o_A 2kfm_A 2kfl_A Probab=2.47 E-value=2.6e+02 Score=10.77 Aligned_cols=41 Identities=20% Similarity=0.123 Sum_probs=0.0 Q ss_pred CCCCCCCCCCCCCCHHHHHCCCCEEECHHHHHHHHHHHCCCCC Q ss_conf 3248852541588046541469868377789999998586889 Q gi|254780319|r 25 QAAGKRHGMIKRSNKFIRNARGTMVLASADAKKVIRNYLPNGI 67 (67) Q Consensus 25 ~~agk~H~l~~Ks~krkR~lr~~~~v~~~~~~~i~r~llPYg~ 67 (67) .+.|..|....|.+|.+-.+......+.+-+ |.-.+.-|+| T Consensus 1 ~~gg~~~~q~~kppK~ktn~K~va~aAaaGA--v~G~~~GY~l 41 (142) T 3heq_A 1 GQGGGTHSQWNKPSKPKTNMKHMAGAAAAGA--VVGGLGGYML 41 (142) T ss_dssp --------------------------------------CCCEE T ss_pred CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH--HHHCCHHHHH T ss_conf 9988777777899998321999998876533--5413201311 No 10 >2v1y_A Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha isoform; cancer, SH2 domain, SH3 domain, transferase, oncogenic mutations, HOST-virus interaction; 2.4A {Bos taurus} Probab=2.32 E-value=3.3e+02 Score=10.24 Aligned_cols=6 Identities=67% Similarity=1.359 Sum_probs=0.0 Q ss_pred HCCCCC Q ss_conf 586889 Q gi|254780319|r 62 YLPNGI 67 (67) Q Consensus 62 llPYg~ 67 (67) |||+|+ T Consensus 25 LLPnGi 30 (108) T 2v1y_A 25 LLPNGM 30 (108) T ss_dssp ECTTSC T ss_pred ECCCEE T ss_conf 868605 Done!