Query gi|254781220|ref|YP_003065633.1| hypothetical protein CLIBASIA_05635 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 130 No_of_seqs 2 out of 4 Neff 1.5 Searched_HMMs 23785 Date Wed Jun 1 01:49:51 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781220.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 1efn_B HIV-1 NEF protein; comp 8.4 62 0.0026 13.0 0.0 24 101-124 98-121 (152) 2 1sva_1 Simian virus 40; virus 8.2 89 0.0038 12.0 0.7 10 22-32 51-60 (361) 3 2qwu_A Intracellular growth lo 6.2 1.1E+02 0.0044 11.5 0.3 17 76-92 108-124 (211) 4 3hyn_A Putative signal transdu 6.1 69 0.0029 12.7 -0.7 42 15-56 46-87 (189) 5 2au5_A Conserved domain protei 6.0 1.2E+02 0.0052 11.1 2.3 56 29-85 44-102 (139) 6 1sr8_A Cobalamin biosynthesis 5.4 1.3E+02 0.0056 10.8 0.5 14 21-34 170-183 (298) 7 3b42_A GSU0935, methyl-accepti 5.4 1.3E+02 0.0057 10.8 1.3 50 42-91 4-53 (135) 8 1ata_A Ascaris trypsin inhibit 5.0 96 0.004 11.8 -0.5 11 94-111 9-19 (62) 9 1eai_C Protein (chymotrypsin/e 4.8 1E+02 0.0043 11.6 -0.5 11 94-111 8-18 (61) 10 2hj3_A Sulfhydryl oxidase ERV1 4.8 92 0.0038 11.9 -0.7 19 16-35 82-100 (125) No 1 >1efn_B HIV-1 NEF protein; complex (SH3 domain/viral enhancer), proto-oncogene, transferase, tyrosine-protein kinase, phosphorylation; 2.50A {Human immunodeficiency virus 1} SCOP: d.102.1.1 PDB: 1avv_A 1avz_A 2nef_A Probab=8.45 E-value=62 Score=13.01 Aligned_cols=24 Identities=29% Similarity=0.349 Sum_probs=17.0 Q ss_pred HHHHHCCCCHHHHHHCCCHHHHHH Q ss_conf 444312777035673867567665 Q gi|254781220|r 101 DEAREDCEGCENCSEHPDQEHKED 124 (130) Q Consensus 101 dE~~~D~E~~E~~~EHPDQEHkED 124 (130) ++..++.+|..||--||-|.|.-| T Consensus 98 ~~~ee~~~~e~~~LLHP~~~~g~d 121 (152) T 1efn_B 98 DKVEEANKGENTSLLHPVSLHGMD 121 (152) T ss_dssp ------------------------ T ss_pred CCCCCCCCCCCCCCCCCHHHCCCC T ss_conf 556666777445167841015677 No 2 >1sva_1 Simian virus 40; virus coat protein, icosahedral virus; 3.10A {Simian virus 40} SCOP: b.121.6.1 Probab=8.16 E-value=89 Score=11.98 Aligned_cols=10 Identities=50% Similarity=1.232 Sum_probs=6.3 Q ss_pred CCCCCCCCCCC Q ss_conf 88324688865 Q gi|254781220|r 22 VNPRMGIEPES 32 (130) Q Consensus 22 ~N~rmgiePe~ 32 (130) .||||| +|+. T Consensus 51 LnPrmG-~~~~ 60 (361) T 1sva_1 51 LNPQMG-NPDE 60 (361) T ss_dssp ECCBSC-CSSS T ss_pred ECCCCC-CCCH T ss_conf 447669-9853 No 3 >2qwu_A Intracellular growth locus, subunit C; structure, IGLC, cell invasion; 1.65A {Francisella tularensis subsp} Probab=6.23 E-value=1.1e+02 Score=11.52 Aligned_cols=17 Identities=12% Similarity=0.200 Sum_probs=11.1 Q ss_pred HHHHHHHHHHHHHHHHC Q ss_conf 99999878778888741 Q gi|254781220|r 76 IVLAKAHKRRLELKIFE 92 (130) Q Consensus 76 I~L~kA~~r~L~~~ife 92 (130) -+.+||.+...+.|+-. T Consensus 108 s~ilqa~atdmkiklgn 124 (211) T 2qwu_A 108 SSILQASATDMKIKLGN 124 (211) T ss_dssp HHHHHHHGGGCCEEECC T ss_pred HHHHHCCCCCEEEEECC T ss_conf 99986366412787267 No 4 >3hyn_A Putative signal transduction protein; YP_002936568.1, structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.20A {Eubacterium rectale atcc 33656} Probab=6.15 E-value=69 Score=12.69 Aligned_cols=42 Identities=24% Similarity=0.403 Sum_probs=29.1 Q ss_pred HHHHHHCCCCCCCCCCCCCEEHHHHHHHHHHHHHHHHHHHHH Q ss_conf 136663788324688865011157887999999748899998 Q gi|254781220|r 15 NYEFLSAVNPRMGIEPESNYEVEVIEKLERALKTSKKLIHFR 56 (130) Q Consensus 15 N~~F~S~~N~rmgiePe~~~E~ev~E~Le~~l~~~~~~i~~~ 56 (130) +|.|..+-..---+.-+|+-|-.+-++|.+-|+.|+.+|-+- T Consensus 46 dF~f~d~Hd~~~~vrd~S~~e~tiK~rLreRI~~sk~vIvLi 87 (189) T 3hyn_A 46 SFPFNDAHDKTYNVRDGSDWEKTLKPRLHTRLDNSKNIILFL 87 (189) T ss_dssp TSSCCBTTTTCCCTTSCCCTTTTHHHHHHHHHHTEEEEEEEC T ss_pred CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCEEEEEE T ss_conf 886654001334556777548999999999984488499998 No 5 >2au5_A Conserved domain protein; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; 2.10A {Enterococcus faecalis V583} SCOP: a.244.1.1 Probab=6.05 E-value=1.2e+02 Score=11.10 Aligned_cols=56 Identities=25% Similarity=0.142 Sum_probs=32.9 Q ss_pred CCCCCEEHHHHHH-HHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHH Q ss_conf 8865011157887-9999997488999986446788--8799999999999999987877 Q gi|254781220|r 29 EPESNYEVEVIEK-LERALKTSKKLIHFRDRTIRTH--ILEDLIEEVNRIIVLAKAHKRR 85 (130) Q Consensus 29 ePe~~~E~ev~E~-Le~~l~~~~~~i~~~~Rt~~T~--i~~D~~ee~~~~I~L~kA~~r~ 85 (130) +|+.--+|+---+ |+++..-|..||---- -++.- -.+.+|+++++.|-|--|-+++ T Consensus 44 ~P~VL~~ME~~P~WL~Es~~~~Q~~iV~SL-~~~~N~~~~~~L~~E~~~Li~LY~~~~~~ 102 (139) T 2au5_A 44 SPIVLAEMEKDPNWLEEAAGGMQGVIVQSL-LEDENFSSVEQLKGELARLIRLYFALAKD 102 (139) T ss_dssp CHHHHHHHHHCTTHHHHHHHHHHHHHHHHH-TTCTTCSSHHHHHHHHHHHHHHHHHHHTT T ss_pred CHHHHHHHHHCCHHHHHHHHHHHHHHHHHH-HCCCCCCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 999999885183089999867677889877-52578574999999999999999999876 No 6 >1sr8_A Cobalamin biosynthesis protein (CBID); structural genomics, PSI, protein structure initiative; 1.90A {Archaeoglobus fulgidus dsm 4304} SCOP: e.54.1.1 Probab=5.39 E-value=1.3e+02 Score=10.85 Aligned_cols=14 Identities=21% Similarity=0.304 Sum_probs=10.6 Q ss_pred CCCCCCCCCCCCCE Q ss_conf 78832468886501 Q gi|254781220|r 21 AVNPRMGIEPESNY 34 (130) Q Consensus 21 ~~N~rmgiePe~~~ 34 (130) .-|||+||.--+|| T Consensus 170 T~NprLGI~GGISI 183 (298) T 1sr8_A 170 TGNEKVGIKGGISI 183 (298) T ss_dssp TCGGGGTCBSEECB T ss_pred CCCHHCCCCCCEEE T ss_conf 15601086568765 No 7 >3b42_A GSU0935, methyl-accepting chemotaxis protein, putative; PAS domain, C-type heme containing sensor, unknown function, signaling protein; HET: HEM; 1.90A {Geobacter sulfurreducens} Probab=5.36 E-value=1.3e+02 Score=10.83 Aligned_cols=50 Identities=24% Similarity=0.371 Sum_probs=0.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999974889999864467888799999999999999987877888874 Q gi|254781220|r 42 LERALKTSKKLIHFRDRTIRTHILEDLIEEVNRIIVLAKAHKRRLELKIF 91 (130) Q Consensus 42 Le~~l~~~~~~i~~~~Rt~~T~i~~D~~ee~~~~I~L~kA~~r~L~~~if 91 (130) ++.+...+..+-..-..+.+....++.++++..+|.-+++....+...|| T Consensus 4 ~~~~~~~a~~la~~v~~~l~~~M~~G~~~~~~~~i~~i~~~~~i~~i~I~ 53 (135) T 3b42_A 4 LDLQLKNARNLAGLIIHDIDGYMMKGDSSEVDRFISAVKSKNFIMDLRVF 53 (135) T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHSTTTTCEEEEE T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCEEEEEE T ss_conf 89999999999999999999999869999999999999702685089998 No 8 >1ata_A Ascaris trypsin inhibitor; proteinase inhibitor(trypsin); NMR {Ascaris suum} SCOP: g.22.1.1 PDB: 1atb_A 1atd_A 1ate_A Probab=5.00 E-value=96 Score=11.78 Aligned_cols=11 Identities=64% Similarity=1.600 Sum_probs=0.0 Q ss_pred HHHHHHHHHHHHCCCCHH Q ss_conf 146654344431277703 Q gi|254781220|r 94 NEVWRLLDEAREDCEGCE 111 (130) Q Consensus 94 ~E~WrlldE~~~D~E~~E 111 (130) ||+| .+|-||| T Consensus 9 NE~W-------~~CggCE 19 (62) T 1ata_A 9 NEQW-------TKCGGCE 19 (62) T ss_dssp SCEE-------ESSCSCC T ss_pred CCEE-------EECCCCH T ss_conf 6600-------4636730 No 9 >1eai_C Protein (chymotrypsin/elastase isoinhibitor 1); serine proteinase, ascaris SUMM, protein inhibitor; 2.40A {Ascaris suum} SCOP: g.22.1.1 Probab=4.80 E-value=1e+02 Score=11.63 Aligned_cols=11 Identities=73% Similarity=1.836 Sum_probs=0.0 Q ss_pred HHHHHHHHHHHHCCCCHH Q ss_conf 146654344431277703 Q gi|254781220|r 94 NEVWRLLDEAREDCEGCE 111 (130) Q Consensus 94 ~E~WrlldE~~~D~E~~E 111 (130) ||+| .+|-+|| T Consensus 8 NE~W-------~eC~~CE 18 (61) T 1eai_C 8 NEVW-------TECTGCE 18 (61) T ss_dssp TCEE-------ESSBCCC T ss_pred CCEE-------EECCCHH T ss_conf 6511-------3664663 No 10 >2hj3_A Sulfhydryl oxidase ERV1P; four-helix bundle, flavin adenine dinucleotide, oxidoreductase; HET: FAD; 2.50A {Arabidopsis thaliana} Probab=4.80 E-value=92 Score=11.92 Aligned_cols=19 Identities=21% Similarity=0.146 Sum_probs=0.0 Q ss_pred HHHHHCCCCCCCCCCCCCEE Q ss_conf 36663788324688865011 Q gi|254781220|r 16 YEFLSAVNPRMGIEPESNYE 35 (130) Q Consensus 16 ~~F~S~~N~rmgiePe~~~E 35 (130) +.||..||-|.|- |..+++ T Consensus 82 ~~~HN~VN~rLgK-p~~~~~ 100 (125) T 2hj3_A 82 CHVHNTVNRSLGK-LVFPCE 100 (125) T ss_dssp HHHHHHHHHHTTC-CCCCTT T ss_pred HHHHHHHHHHCCC-CCCCHH T ss_conf 9999999998599-987889 Done!