Query gi|254780988|ref|YP_003065401.1| hypothetical protein CLIBASIA_04445 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 151 No_of_seqs 2 out of 4 Neff 1.3 Searched_HMMs 33803 Date Wed Jun 1 19:56:20 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780988.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 >1v54_C Cytochrome C oxidase p 36.1 24 0.00072 16.7 2.3 45 66-110 147-191 (192) 2 >1m56_C Cytochrome C oxidase; 31.6 34 0.001 15.8 2.4 27 84-110 169-195 (196) 3 >3bz1_T PSII-T, PSII-TC, photo 22.8 43 0.0013 15.3 1.6 13 130-142 8-20 (32) 4 >3e6c_C CPRK, cyclic nucleotid 20.5 48 0.0014 15.0 1.5 33 106-138 10-42 (103) 5 >1zvz_B Talin 1, metavinculin; 17.8 43 0.0013 15.2 0.8 17 62-78 3-19 (26) 6 >1ft9_A Carbon monoxide oxidat 16.6 48 0.0014 15.0 0.8 30 109-138 14-43 (90) 7 >3iwz_A CAP-like, catabolite a 15.9 48 0.0014 15.0 0.6 20 119-138 22-41 (72) 8 >3b9w_A Ammonium transporter f 10.9 1.2E+02 0.0034 12.8 5.1 44 94-137 71-123 (242) 9 >3d0s_A Transcriptional regula 10.5 1.2E+02 0.0036 12.7 1.4 30 109-138 13-42 (80) 10 >1xkm_A Distinctin chain A; po 10.1 1.2E+02 0.0037 12.6 1.4 9 86-94 8-16 (26) No 1 >>1v54_C Cytochrome C oxidase polypeptide III; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} (C:70-261) Probab=36.13 E-value=24 Score=16.70 Aligned_cols=45 Identities=20% Similarity=0.395 Sum_probs=23.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 444421117777521238887888997899999999999999877 Q gi|254780988|r 66 ARLQNQANEDQFERESKAMIFFNALIRPFTTLFWIILYPLLIWWG 110 (151) Q Consensus 66 ar~~~qaned~~~~~~k~~~~f~alirp~tt~fwii~yplliww~ 110 (151) +..-.+.-..+..++.....-..++---|...-|+.+|+++-+|| T Consensus 147 ~~~~~~~~~~~~~~~~~~~~~~~~~YWHFvd~vWi~lf~~~Yl~g 191 (192) T 1v54_C 147 IVCFFRQLKFHFTSNHHFGFEAAAWYWHFVDVVWLFLYVSIYWWG 191 (192) T ss_dssp HHHHHHHHTTCCCSSCCHHHHHHHHHHHHHHHHHHHHHHHTTTTT T ss_pred HHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 999999980689844006899999997578876898888888428 No 2 >>1m56_C Cytochrome C oxidase; membrane protein, oxidoreductase; HET: HEA PEH; 2.30A {Rhodobacter sphaeroides} (C:71-266) Probab=31.57 E-value=34 Score=15.83 Aligned_cols=27 Identities=19% Similarity=0.512 Sum_probs=14.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 887888997899999999999999877 Q gi|254780988|r 84 MIFFNALIRPFTTLFWIILYPLLIWWG 110 (151) Q Consensus 84 ~~~f~alirp~tt~fwii~yplliww~ 110 (151) ..-..++---|...-||.+|+++-+|| T Consensus 169 ~~~~~~~YWHFVD~vWi~lf~~~Ylwg 195 (196) T 1m56_C 169 GFEAAIWYWHFVDVVWLFLFASIYIWG 195 (196) T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHTTTC T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCC T ss_conf 999999999889988998888886227 No 3 >>3bz1_T PSII-T, PSII-TC, photosystem II reaction center protein T; electron transport photosystem, membrane complex, transmembrane alpha-helix; HET: CLA PHO HEM PL9 BCR DGD LHG SQD LMG LMT; 2.90A {Thermosynechococcus elongatus} PDB: 1s5l_T* 2axt_T* 3bz2_T* 3a0b_T* 3a0h_T* (T:) Probab=22.76 E-value=43 Score=15.27 Aligned_cols=13 Identities=38% Similarity=0.815 Sum_probs=9.2 Q ss_pred HHHHHHHHHHHHH Q ss_conf 8999999887657 Q gi|254780988|r 130 DIIACILGFWFTD 142 (151) Q Consensus 130 ~iiacilgfw~td 142 (151) -|.|||.|..|-. T Consensus 8 ~i~acii~lfffa 20 (32) T 3bz1_T 8 FIFACIIALFFFA 20 (32) T ss_dssp HHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHH T ss_conf 9999999999999 No 4 >>3e6c_C CPRK, cyclic nucleotide-binding protein; CPRK, halorespiration; HET: DNA 3C4; 1.80A {Desulfitobacterium hafniense} (C:148-250) Probab=20.50 E-value=48 Score=14.95 Aligned_cols=33 Identities=21% Similarity=0.255 Sum_probs=15.9 Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 998774304326474455333478899999988 Q gi|254780988|r 106 LIWWGVEKGYLTKDPLTLLAPFTQDIIACILGF 138 (151) Q Consensus 106 liww~v~~g~~~~dpltll~pftq~iiacilgf 138 (151) |++..-+-|..+.+.-.+--|+||+-||+.+|- T Consensus 10 Ll~l~~~~g~~~~~~~~i~~~lt~~~LA~~lG~ 42 (103) T 3e6c_C 10 FYELCSSQGKRVGDTYEITMPLSQKSIGEITGV 42 (103) T ss_dssp HHHHHHHHCEEETTEEEEECCCCHHHHHHHHTC T ss_pred HHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHCC T ss_conf 987999818765655356788689999989799 No 5 >>1zvz_B Talin 1, metavinculin; complex, protein binding; 1.80A {Gallus gallus} (B:) Probab=17.83 E-value=43 Score=15.23 Aligned_cols=17 Identities=41% Similarity=0.432 Sum_probs=13.5 Q ss_pred CEEHHHHHHHHHHHHHH Q ss_conf 60034444211177775 Q gi|254780988|r 62 PVRLARLQNQANEDQFE 78 (151) Q Consensus 62 pvrlar~~~qaned~~~ 78 (151) -+|-|||-+||..|-+. T Consensus 3 mvrqarilaqatsdlvn 19 (26) T 1zvz_B 3 MVRQARILAQATSDLVN 19 (26) T ss_dssp CHHHHHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHHHHHH T ss_conf 89999999998899999 No 6 >>1ft9_A Carbon monoxide oxidation system transcription regulator; heme sensor, catabolite gene activator protein; HET: HEM; 2.60A {Rhodospirillum rubrum} (A:133-222) Probab=16.62 E-value=48 Score=14.99 Aligned_cols=30 Identities=23% Similarity=0.285 Sum_probs=19.1 Q ss_pred HHHHHCCCCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 774304326474455333478899999988 Q gi|254780988|r 109 WGVEKGYLTKDPLTLLAPFTQDIIACILGF 138 (151) Q Consensus 109 w~v~~g~~~~dpltll~pftq~iiacilgf 138 (151) -+-.-|.-+.++..+--|+||+-||.++|- T Consensus 14 l~~~~g~~~~~~~~i~~~lt~~~lA~~lg~ 43 (90) T 1ft9_A 14 HANTTGRQTQGGVIVSVDFTVEEIANLIGS 43 (90) T ss_dssp TCBCCCSCC--CCCCEECCCHHHHHHHHCS T ss_pred HHHHHCCCCCCCEEEECHHHHHHHHHHHCC T ss_conf 999838665684278542889999998499 No 7 >>3iwz_A CAP-like, catabolite activation-like protein; XCC, pathogenicity, CRP, CLP, C-DI-GMP receptor, quorum sensing, DNA-binding; 2.30A {Xanthomonas campestris PV} (A:159-230) Probab=15.87 E-value=48 Score=14.95 Aligned_cols=20 Identities=15% Similarity=0.252 Sum_probs=12.5 Q ss_pred CCHHHHHHHHHHHHHHHHHH Q ss_conf 74455333478899999988 Q gi|254780988|r 119 DPLTLLAPFTQDIIACILGF 138 (151) Q Consensus 119 dpltll~pftq~iiacilgf 138 (151) ++-..--|+||+-||+++|- T Consensus 22 ~~~~~~~~~t~~~lA~~lG~ 41 (72) T 3iwz_A 22 HPQGTQLRVSRQELARLVGC 41 (72) T ss_dssp ETTEEEEECCHHHHHHHHTC T ss_pred CCCCEEECCCHHHHHHHHCC T ss_conf 88713517799999989798 No 8 >>3b9w_A Ammonium transporter family; membrane protein, ammonia transport, rhesus protein, transport protein; HET: BOG; 1.30A {Nitrosomonas europaea} PDB: 3bhs_A 3b9y_A* 3b9z_A* (A:39-167,A:295-407) Probab=10.92 E-value=1.2e+02 Score=12.76 Aligned_cols=44 Identities=14% Similarity=0.186 Sum_probs=30.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCC---------CCCHHHHHHHHHHHHHHHHH Q ss_conf 999999999999998774304326---------47445533347889999998 Q gi|254780988|r 94 FTTLFWIILYPLLIWWGVEKGYLT---------KDPLTLLAPFTQDIIACILG 137 (151) Q Consensus 94 ~tt~fwii~yplliww~v~~g~~~---------~dpltll~pftq~iiacilg 137 (151) +-+++.+++||+..||.-..|.+. +-+.-+.+.+.-=..+++|| T Consensus 71 i~al~~v~vY~~~~~~vw~~Gwl~~lG~~DfaGs~vVH~fGgyfGLava~vLg 123 (242) T 3b9w_A 71 LLALFIVPVYLLNEWLVLDNASGLTEGFQDSAGSIAIHAFGAYFGLGVSIALT 123 (242) T ss_dssp HHHHHHHHHHHHHHHHHTTCTTSSCTTCCCTTCTTTTHHHHHHHHHHHHHHHC T ss_pred HHHHHHHHHHHHHHEEECCCCCCCCCCCCCCCCCEEEEHHHHHHHHHHHHHEE T ss_conf 99999998755222131479852113641036745541643799999987335 No 9 >>3d0s_A Transcriptional regulatory protein; CAMP receptor protein (CRP), dimer, inactive(APO, unliganded) form, allostery, DNA binding; 2.00A {Mycobacterium tuberculosis} PDB: 3i54_A* 3i59_A* (A:148-227) Probab=10.46 E-value=1.2e+02 Score=12.66 Aligned_cols=30 Identities=23% Similarity=0.231 Sum_probs=16.0 Q ss_pred HHHHHCCCCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 774304326474455333478899999988 Q gi|254780988|r 109 WGVEKGYLTKDPLTLLAPFTQDIIACILGF 138 (151) Q Consensus 109 w~v~~g~~~~dpltll~pftq~iiacilgf 138 (151) .+-.-|....+.-.+--|+||+-||.++|- T Consensus 13 l~~~~~~~~~~~~~i~~~~t~~~la~~lg~ 42 (80) T 3d0s_A 13 LAQRFGTQEGGALRVTHDLTQEEIAQLVGA 42 (80) T ss_dssp HHHHHEEEETTEEEEECCCCHHHHHHHHTS T ss_pred HHHHCCCCCCCCEEEEECCCHHHHHHHHCC T ss_conf 787607877886135547899999999799 No 10 >>1xkm_A Distinctin chain A; pore-forming peptide, heterodimer, structure, homodimer, disulfide, four-helix bundle, antibiotic; NMR {Synthetic} (A:) Probab=10.12 E-value=1.2e+02 Score=12.59 Aligned_cols=9 Identities=44% Similarity=0.648 Sum_probs=0.0 Q ss_pred HHHHHHHHH Q ss_conf 788899789 Q gi|254780988|r 86 FFNALIRPF 94 (151) Q Consensus 86 ~f~alirp~ 94 (151) ||+|||..+ T Consensus 8 gftaliktl 16 (26) T 1xkm_A 8 GFTALIKTL 16 (26) T ss_dssp HHHHHHHHH T ss_pred CHHHHHHHH T ss_conf 689999998 Done!