Query gi|254780471|ref|YP_003064884.1| cytochrome o ubiquinol oxidase subunit IV [Candidatus Liberibacter asiaticus str. psy62] Match_columns 119 No_of_seqs 101 out of 264 Neff 4.7 Searched_HMMs 23785 Date Mon May 30 11:32:24 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780471.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 2bg9_B Acetylcholine receptor 24.8 29 0.0012 13.7 9.1 25 85-109 339-363 (370) 2 3aag_A General glycosylation p 23.8 30 0.0013 13.6 2.1 19 9-27 52-70 (291) 3 1lgh_A LH II, B800/850, light 17.4 42 0.0018 12.8 3.8 30 35-68 9-38 (56) 4 1ydl_A TFIIH, general transcri 15.0 12 0.00049 15.9 -1.9 15 7-21 3-17 (79) 5 1m56_D Cytochrome C oxidase; m 14.8 38 0.0016 13.0 0.6 15 4-18 3-17 (51) 6 2zjs_Y Preprotein translocase 13.8 52 0.0022 12.3 5.6 53 51-103 117-170 (434) 7 2onk_C Molybdate/tungstate ABC 11.2 64 0.0027 11.8 3.2 15 1-15 1-15 (284) 8 3eam_A GLR4197 protein; pentam 10.6 66 0.0028 11.7 9.0 23 22-44 225-247 (317) 9 2f2f_C CDT C, cytolethal diste 10.5 46 0.0019 12.6 0.0 23 17-39 1-23 (186) 10 3f4m_A Tumor necrosis factor, 9.9 71 0.003 11.5 2.7 55 25-84 71-126 (161) No 1 >2bg9_B Acetylcholine receptor protein, beta chain; ION channel/receptor, ION channel, electron microscopy, ION transport, postsynaptic membrane; 4.00A {Torpedo marmorata} Probab=24.78 E-value=29 Score=13.69 Aligned_cols=25 Identities=20% Similarity=0.656 Sum_probs=10.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 9999999999999999998511304 Q gi|254780471|r 85 IFTIIMVAICFVGSMWVMYHLNNNM 109 (119) Q Consensus 85 ~Ft~~ii~iiv~GSiWIM~~l~~nM 109 (119) +|-.+.+++.+.|++.|..+-.+|- T Consensus 339 ~~~~~~~~~~~i~t~~i~~~~~~~~ 363 (370) T 2bg9_B 339 LFLYIFITMCSIGTFSIFLDASHNV 363 (370) T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHS T ss_pred HHHHHHHHHHHHHHHHEEEECCCCC T ss_conf 9999999999998885074077789 No 2 >3aag_A General glycosylation pathway protein; multidomain, transferase; HET: MLY; 2.80A {Campylobacter jejuni RM1221} Probab=23.82 E-value=30 Score=13.58 Aligned_cols=19 Identities=16% Similarity=0.083 Sum_probs=15.9 Q ss_pred CCCCCCCCHHHHHHHHHHH Q ss_conf 8777888525689999999 Q gi|254780471|r 9 MNMHSYGTKKQCLVGFILS 27 (119) Q Consensus 9 ~~~~~hgs~k~yliGFiLs 27 (119) +|+..|.+.+.|.++++|+ T Consensus 52 ~DGg~h~g~~~y~va~~ls 70 (291) T 3aag_A 52 VDGGXHLGXDNFFPSFALS 70 (291) T ss_dssp CBTTBCCHHHHHHHHHHHH T ss_pred CCCCCCCCHHHHHHHHHHC T ss_conf 2586333227788888747 No 3 >1lgh_A LH II, B800/850, light harvesting complex II; bacteriochlorophyll, dexter energy transfer, foerster exciton transfer mechanism; HET: BCL LYC DET HTO; 2.40A {Phaeospirillum molischianum} SCOP: f.3.1.1 Probab=17.38 E-value=42 Score=12.79 Aligned_cols=30 Identities=13% Similarity=0.294 Sum_probs=21.4 Q ss_pred HHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999806578846999999999999999999999 Q gi|254780471|r 35 FGIVMKGFFLDKNIMCLTIVLCAIAQIIVHLVFF 68 (119) Q Consensus 35 F~lV~~~~~~~~~~~~~~I~~~Av~Qi~VqL~~F 68 (119) ||+|.. |.+.+.++.+..+++-+.||.+-| T Consensus 9 iWlVvN----PaTWL~pi~~av~v~ai~VH~~vl 38 (56) T 1lgh_A 9 IWLVIN----PSTWLPVIWIVATVVAIAVHAAVL 38 (56) T ss_dssp HHHHSC----HHHHHHHHHHHHHHHHHHHHHHHH T ss_pred EEEEEC----CHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999977----415489999999999999999987 No 4 >1ydl_A TFIIH, general transcription factor IIH, polypeptide 5; alpha-beta protein, structural genomics, PSI, protein structure initiative; 2.30A {Homo sapiens} SCOP: d.295.1.1 PDB: 2jnj_A Probab=15.04 E-value=12 Score=15.87 Aligned_cols=15 Identities=47% Similarity=0.642 Sum_probs=9.5 Q ss_pred CCCCCCCCCCHHHHH Q ss_conf 898777888525689 Q gi|254780471|r 7 HNMNMHSYGTKKQCL 21 (119) Q Consensus 7 h~~~~~~hgs~k~yl 21 (119) |.+..+||||.|+.+ T Consensus 3 ~~~~~~~~~~~KGvL 17 (79) T 1ydl_A 3 HHHHHHSHGTRKGML 17 (79) T ss_dssp ------CCCCCCCEE T ss_pred CCCCCCCCCCCCEEE T ss_conf 543432358866489 No 5 >1m56_D Cytochrome C oxidase; membrane protein, oxidoreductase; HET: HEA PEH; 2.30A {Rhodobacter sphaeroides} SCOP: f.23.8.1 PDB: 1m57_D* Probab=14.80 E-value=38 Score=13.04 Aligned_cols=15 Identities=27% Similarity=0.361 Sum_probs=10.4 Q ss_pred CCCCCCCCCCCCCHH Q ss_conf 888898777888525 Q gi|254780471|r 4 DNIHNMNMHSYGTKK 18 (119) Q Consensus 4 ~~~h~~~~~~hgs~k 18 (119) |+.|...+|.||++- T Consensus 3 ~HkH~~~~H~hGeMD 17 (51) T 1m56_D 3 DHSHPAHGHVAGSMD 17 (51) T ss_dssp -------CCCTTCSC T ss_pred CCCCCCCCCCCCCCC T ss_conf 665665567788532 No 6 >2zjs_Y Preprotein translocase SECY subunit; translocon, SEC, protein-conducting-channel, membrane, protein transport, translocation, transmembrane, transport; 3.20A {Thermus thermophilus} PDB: 2zqp_Y Probab=13.78 E-value=52 Score=12.25 Aligned_cols=53 Identities=11% Similarity=-0.036 Sum_probs=27.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999999999999704778765025-99999999999999999999998 Q gi|254780471|r 51 LTIVLCAIAQIIVHLVFFLHMSTKVEDGWS-IMAMIFTIIMVAICFVGSMWVMY 103 (119) Q Consensus 51 ~~I~~~Av~Qi~VqL~~FLHl~~~~~~~~n-~~a~~Ft~~ii~iiv~GSiWIM~ 103 (119) .+.+.+|++|..+....+...+.+.-.... .....|...++..++.||.-+|+ T Consensus 117 ~ltl~~a~iqa~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~L~~Gs~~l~w 170 (434) T 2zjs_Y 117 IGGIALGAFQGFFLATAFLGAEGGRFLLPGWSPGPFFWFVVVVTQVAGIALLLW 170 (434) T ss_dssp HHHHHHHHHHHHHHHHHTTSSSSSTTBCTTCCSSHHHHHHHHHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 999999999999999998535787435214680378999999999999999999 No 7 >2onk_C Molybdate/tungstate ABC transporter, permease protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: f.58.1.1 Probab=11.16 E-value=64 Score=11.79 Aligned_cols=15 Identities=33% Similarity=0.425 Sum_probs=6.2 Q ss_pred CCCCCCCCCCCCCCC Q ss_conf 987888898777888 Q gi|254780471|r 1 MKYDNIHNMNMHSYG 15 (119) Q Consensus 1 m~~~~~h~~~~~~hg 15 (119) |.|.+.|.++.|+-| T Consensus 1 ~~~~~~~~~~~~~~g 15 (284) T 2onk_C 1 MGHHHHHHHHHHSSG 15 (284) T ss_dssp --------------- T ss_pred CCCCCCCCCCCCCCC T ss_conf 975322210235678 No 8 >3eam_A GLR4197 protein; pentameric ligand-gated ION-channel, membrane protein, transport protein; HET: LMT PC1; 2.90A {Gloeobacter violaceus} PDB: 3ehz_A 3lsv_A 3ei0_A Probab=10.62 E-value=66 Score=11.68 Aligned_cols=23 Identities=22% Similarity=0.434 Sum_probs=13.2 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCC Q ss_conf 99999999999999999806578 Q gi|254780471|r 22 VGFILSLILTIIPFGIVMKGFFL 44 (119) Q Consensus 22 iGFiLsiiLT~iaF~lV~~~~~~ 44 (119) +++....+||.++|-.+..+.+| T Consensus 225 ~~l~it~lL~~~~~~~~~~~~lP 247 (317) T 3eam_A 225 VTLVVSTLIAHIAFNILVETNLP 247 (317) T ss_dssp HHHHHHHHHHHHHHHHHHHHHSC T ss_pred EEEEEHHHHHHHHHHHHHHHHCC T ss_conf 79996599999999998874489 No 9 >2f2f_C CDT C, cytolethal distending toxin C; actinobacillus actinomycetemcomitans, oligomerization, stability and toxic activity; 2.40A {Aggregatibacter actinomycetemcomitans} SCOP: b.42.2.1 Probab=10.51 E-value=46 Score=12.56 Aligned_cols=23 Identities=35% Similarity=0.514 Sum_probs=18.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 25689999999999999999998 Q gi|254780471|r 17 KKQCLVGFILSLILTIIPFGIVM 39 (119) Q Consensus 17 ~k~yliGFiLsiiLT~iaF~lV~ 39 (119) +|+|++-|.++++++.....-.. T Consensus 1 mkK~~i~f~~~l~~~~~s~~~~~ 23 (186) T 2f2f_C 1 MKKYLLSFLLSMILTLTSHAESN 23 (186) T ss_dssp ----------------------- T ss_pred CCHHHHHHHHHHHHHCCCCCCCC T ss_conf 93248999999997511455468 No 10 >3f4m_A Tumor necrosis factor, alpha-induced protein 8- like protein 2; TIPE2, immune homeostasis, tnfaip8, immune system; 1.70A {Homo sapiens} Probab=9.88 E-value=71 Score=11.53 Aligned_cols=55 Identities=18% Similarity=0.332 Sum_probs=36.3 Q ss_pred HHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHH-HHHH Q ss_conf 99999999999999806578846999999999999999999999704778765025-9999 Q gi|254780471|r 25 ILSLILTIIPFGIVMKGFFLDKNIMCLTIVLCAIAQIIVHLVFFLHMSTKVEDGWS-IMAM 84 (119) Q Consensus 25 iLsiiLT~iaF~lV~~~~~~~~~~~~~~I~~~Av~Qi~VqL~~FLHl~~~~~~~~n-~~a~ 84 (119) .-.+.+|+++|+=|-+. + +++.+...+--| -+.+-|++ ==|++.+|.+|.| ++.+ T Consensus 71 ~~~~amt~iSFyevdfT-f-D~~~L~~~L~ec--r~~L~~lV-~~HLT~KS~~RI~~VF~~ 126 (161) T 3f4m_A 71 LRQGAMTALSFGEVDFT-F-EAAVLAGLLTEC--RDVLLELV-EHHLTPKSHGRIRHVFDH 126 (161) T ss_dssp HHHHHHHHHHHTSTTSC-C-CHHHHHHHHHHH--HHHHHHHH-TTTSCHHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHCCCEE-E-CHHHHHHHHHHH--HHHHHHHH-HHHCCHHHHHHHHHHHHC T ss_conf 99888998522011134-2-699999999999--99999999-876876357679999860 Done!