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 33803 Date Wed Jun 1 11:58:41 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780319.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 >2zjr_3 50S ribosomal protein 100.0 1E-28 3E-33 160.3 6.1 65 1-66 1-65 (66) 2 >3i1n_3 50S ribosomal protein 99.9 5.5E-29 1.6E-33 161.6 3.6 65 1-66 1-65 (65) 3 >2j01_8 50S ribosomal protein 99.9 2.1E-28 6.3E-33 158.7 3.0 65 1-66 1-65 (65) 4 >3bbo_5 Ribosomal protein L35; 99.9 2.8E-25 8.4E-30 143.4 0.3 65 1-66 89-153 (159) 5 >3c8l_A FTSZ-like protein of u 6.5 1.8E+02 0.0054 12.2 0.9 13 53-66 68-80 (122) 6 >3gqw_A Fatty acid AMP ligase; 6.1 1.1E+02 0.0033 13.3 -0.5 14 13-26 62-75 (95) 7 >3c5e_A Acyl-coenzyme A synthe 5.1 1.3E+02 0.0038 13.0 -0.6 13 14-26 88-100 (115) 8 >3ipl_A 2-succinylbenzoate--CO 4.5 2E+02 0.0058 12.1 0.0 13 14-26 80-92 (103) 9 >2jra_A Protein RPA2121; domai 4.5 2.7E+02 0.008 11.4 1.7 17 7-23 48-64 (67) 10 >3hrz_C Cobra venom factor; se 4.4 1.7E+02 0.0049 12.4 -0.4 8 14-21 48-55 (67) No 1 >>2zjr_3 50S ribosomal protein L35; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} (3:) Probab=99.95 E-value=1e-28 Score=160.28 Aligned_cols=65 Identities=45% Similarity=0.581 Sum_probs=63.4 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~akKRFk~T~sGKvkr~~agk~H~l~~Ks~k~kR~Lr~~~~v~~~~~k~ik~-~Lpy~ 65 (66) T 2zjr_3 1 MPKMKTHKMAKRRIKITGTGKVMAFKSGKRHQNTGKSGDEIRGKGKGFVLAKAEWARMKL-MLPRG 65 (66) T ss_pred CCCCCCCHHHHHHEEECCCCCEEECCCCCCCCCCCCCHHHHHHCCCCEEECHHHHHHHHH-HCCCC T ss_conf 997643221353136778987860627776455337988998667985577999999999-67899 No 2 >>3i1n_3 50S ribosomal protein L35; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1vs8_3 1vs6_3 3i1p_3 3i1r_3 3i1t_3 3i20_3 3i22_3 2qam_3* 2awb_3 2aw4_3 2i2v_3 2j28_3 2i2t_3* 2qao_3* 2qba_3* 2qbc_3* 2qbe_3 2qbg_3 2qbi_3* 2qbk_3* ... (3:) Probab=99.95 E-value=5.5e-29 Score=161.57 Aligned_cols=65 Identities=34% Similarity=0.464 Sum_probs=63.5 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~sGKi~r~~agk~H~~~~Ks~k~kR~L~~~~~v~~~~~k~ik~-~LPy~ 65 (65) T 3i1n_3 1 MPKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIA-CLPYA 65 (65) T ss_dssp -CCCCCCTTGGGTCCCCTTSCCCEECSSCSSCCTTSCHHHHHHHSSEECCCHHHHHHHHH-TCTTC T ss_pred CCCCCCCHHHHHHEEECCCCCEEECCCCCCCCCCCCCHHHHHHCCCCEEECHHHHHHHHH-HCCCC T ss_conf 997642043564125778998862538876144247988898578984468999999998-68899 No 3 >>2j01_8 50S ribosomal protein L35; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} (8:) Probab=99.94 E-value=2.1e-28 Score=158.71 Aligned_cols=65 Identities=46% Similarity=0.599 Sum_probs=63.2 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~a~KRFk~T~sGKikr~~a~k~H~l~~Ks~krkR~Lr~~~~v~~~~~k~ikk-~LPy~ 65 (65) T 2j01_8 1 MPKMKTHKGAKKRVKITASGKVVAMKTGKRHLNWQKSGKEIRQKGRKFVLAKPEAERIKL-LLPYE 65 (65) T ss_dssp -CCCCCCHHHHHHCEECSSSCEEECCTTTTTCSSCSCCSTTTSCSCEECCSSHHHHHHTT-TTTC- T ss_pred CCCCCCCHHHHHHEEECCCCCEEECCCCCCCCCCCCCHHHHHHCCCCEEECHHHHHHHHH-HCCCC T ss_conf 997643212353046778987864306787765548888898647983367999999998-28999 No 4 >>3bbo_5 Ribosomal protein L35; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} (5:) Probab=99.90 E-value=2.8e-25 Score=143.41 Aligned_cols=65 Identities=34% Similarity=0.408 Sum_probs=62.8 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 89 ~~KmKT~k~a~KRFk~t~~Gk~~r~~agk~H~~~kKs~~~krrLr~~~~v~~~~~~~i~k-~lpy~ 153 (159) T 3bbo_5 89 GYKMKTHKASAKRFRVTGKGKIVRRRAGKQHLLAKKNTKRKNRLSKLIQVDRSDYDNVIG-ALPYL 153 (159) T ss_dssp --CCCCCHHHHTTCCBCSSSCBEEECSSCTTCCSSCCSSCTTSCSEEECCSTHHHHTTTT-TTTC- T ss_pred CCCCCCCHHHHHEEEECCCCCEEECCCCCCCCCCCCCHHHHHHCCCCEEECHHHHHHHHH-HCCCH T ss_conf 766564341240047767975855417776564448998998657985467989999999-57971 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} (A:) Probab=6.49 E-value=1.8e+02 Score=12.23 Aligned_cols=13 Identities=31% Similarity=0.440 Sum_probs=8.7 Q ss_pred HHHHHHHHHHCCCC Q ss_conf 78999999858688 Q gi|254780319|r 53 ADAKKVIRNYLPNG 66 (67) Q Consensus 53 ~~~~~i~r~llPYg 66 (67) -|...+ +..|||| T Consensus 68 vD~~~v-~~~lPyG 80 (122) T 3c8l_A 68 VREEEV-LAVLPFG 80 (122) T ss_dssp CCHHHH-HTTSCSS T ss_pred CCHHHH-HHHCCCC T ss_conf 259999-9768877 No 6 >>3gqw_A Fatty acid AMP ligase; FAAL, E. coli, ATP-dependent AMP-binding enzyme family,, structural genomics, PSI-2, protein structure initiative; HET: ZZ9; 3.00A {Escherichia coli O6} (A:482-576) Probab=6.07 E-value=1.1e+02 Score=13.31 Aligned_cols=14 Identities=21% Similarity=0.252 Sum_probs=9.0 Q ss_pred EEEECCCCEEEECC Q ss_conf 25775998097032 Q gi|254780319|r 13 RFSITATGKVRAQA 26 (67) Q Consensus 13 RFk~T~sGKvkr~~ 26 (67) .|=.|+||||.|.. T Consensus 62 ~lP~T~sGKi~R~~ 75 (95) T 3gqw_A 62 SIPRTSSGKPARAE 75 (95) T ss_dssp CSCBCTTSSBCHHH T ss_pred CCCCCCCCCHHHHH T ss_conf 43669986663999 No 7 >>3c5e_A Acyl-coenzyme A synthetase ACSM2A, mitochondrial precursor; middle-chain acyl-COA synthetase, xenobiotic/medium-chain fatty acid-COA ligase; HET: ATP; 1.60A {Homo sapiens} PDB: 2vze_A 3b7w_A* 3day_A* 3eq6_A* 3eyn_A* 3gpc_A* 2wd9_A* (A:456-570) Probab=5.08 E-value=1.3e+02 Score=12.99 Aligned_cols=13 Identities=31% Similarity=0.478 Sum_probs=8.4 Q ss_pred EEECCCCEEEECC Q ss_conf 5775998097032 Q gi|254780319|r 14 FSITATGKVRAQA 26 (67) Q Consensus 14 Fk~T~sGKvkr~~ 26 (67) |=.|+||||-|.. T Consensus 88 lP~T~sGKidR~~ 100 (115) T 3c5e_A 88 LPKTVTGKIQRAK 100 (115) T ss_dssp CCBCTTCCBCHHH T ss_pred CCCCCCCCCCHHH T ss_conf 7879887754898 No 8 >>3ipl_A 2-succinylbenzoate--COA ligase; structural genomics, acyl-protein synthetase, PSI-2, protein structure initiative; 2.30A {Staphylococcus aureus subsp} (A:399-501) Probab=4.54 E-value=2e+02 Score=12.09 Aligned_cols=13 Identities=31% Similarity=0.529 Sum_probs=8.7 Q ss_pred EEECCCCEEEECC Q ss_conf 5775998097032 Q gi|254780319|r 14 FSITATGKVRAQA 26 (67) Q Consensus 14 Fk~T~sGKvkr~~ 26 (67) |=.|+|||+.|.. T Consensus 80 lP~t~sGKi~r~~ 92 (103) T 3ipl_A 80 LPYTSTGKLQRNK 92 (103) T ss_dssp CC----------- T ss_pred CCCCCCCCCCHHH T ss_conf 7869886826899 No 9 >>2jra_A Protein RPA2121; domain-swapped dimer, structural genomics, PSI, protein structure initiative; NMR {Rhodopseudomonas palustris CGA009} (A:) Probab=4.52 E-value=2.7e+02 Score=11.41 Aligned_cols=17 Identities=18% Similarity=0.376 Sum_probs=0.0 Q ss_pred CCHHHEEEEECCCCEEE Q ss_conf 30121225775998097 Q gi|254780319|r 7 NSSSKKRFSITATGKVR 23 (67) Q Consensus 7 ~k~akKRFk~T~sGKvk 23 (67) |-|.-=|.++|..||++ T Consensus 48 H~G~~Y~LR~Tr~GKLI 64 (67) T 2jra_A 48 HGDDRYRLRLTSQNKLI 64 (67) T ss_dssp ETTEEEEEEECTTSCEE T ss_pred ECCEEEEEEECCCCCEE T ss_conf 79918997882479577 No 10 >>3hrz_C Cobra venom factor; serine protease, glycosilated, multi-domain, complement system, convertase, complement alternate pathway, complement pathway; HET: NAG P6G; 2.20A {Naja kaouthia} PDB: 3frp_B* 3hs0_C* (C:1-67) Probab=4.42 E-value=1.7e+02 Score=12.45 Aligned_cols=8 Identities=38% Similarity=0.796 Sum_probs=0.0 Q ss_pred EEECCCCE Q ss_conf 57759980 Q gi|254780319|r 14 FSITATGK 21 (67) Q Consensus 14 Fk~T~sGK 21 (67) |.|||+|+ T Consensus 48 f~VtA~G~ 55 (67) T 3hrz_C 48 ITVTASGD 55 (67) T ss_dssp EEEEEEES T ss_pred EEEEEEEE T ss_conf 99999988 Done!