Query gi|254781186|ref|YP_003065599.1| hypothetical protein CLIBASIA_05465 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 45 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 23785 Date Wed Jun 1 01:36:14 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781186.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 3kz5_E Protein SOPB; partition 20.3 29 0.0012 16.9 1.1 15 2-16 7-21 (52) 2 1ci4_A Protein (barrier-TO-aut 13.3 66 0.0028 15.1 1.5 27 14-40 23-49 (89) 3 1b22_A DNA repair protein RAD5 8.7 59 0.0025 15.4 -0.0 25 14-38 30-54 (114) 4 2inp_L Phenol hydroxylase comp 7.7 67 0.0028 15.1 -0.1 40 4-43 24-63 (89) 5 2mob_A Protein (methane monoox 7.4 47 0.002 15.9 -1.0 40 4-43 62-101 (138) 6 1ckv_A Protein (protein B); hy 6.9 1.1E+02 0.0046 14.0 0.7 40 5-44 64-103 (141) 7 2qkw_A Avirulence protein; thr 5.4 1E+02 0.0042 14.2 -0.2 28 1-28 11-39 (164) 8 1mzu_A PPR; photoactive yellow 5.3 2E+02 0.0086 12.6 1.6 34 6-40 31-66 (129) 9 1u8x_X Maltose-6'-phosphate gl 3.1 3E+02 0.012 11.8 0.7 22 4-25 160-182 (472) 10 2k7m_A GAP junction alpha-5 pr 3.0 3.2E+02 0.014 11.6 0.8 11 1-11 38-48 (109) No 1 >3kz5_E Protein SOPB; partition, segregation, F plasmid, DNA-binding protein, DNA- DNA binding protein; 1.58A {Escherichia coli} Probab=20.29 E-value=29 Score=16.89 Aligned_cols=15 Identities=47% Similarity=0.837 Sum_probs=12.6 Q ss_pred CCCCCCCEEEEEECC Q ss_conf 844368779998346 Q gi|254781186|r 2 AHQYNPDAIVLYANG 16 (45) Q Consensus 2 ahqynpdaivlyang 16 (45) .||+-|.|.+||... T Consensus 7 rhqFaPGAtalYKGd 21 (52) T 3kz5_E 7 RHQFAPGATVLYKGD 21 (52) T ss_dssp EEEEETTEEEEEETT T ss_pred CCCCCCCCEEEEECC T ss_conf 232068723566177 No 2 >1ci4_A Protein (barrier-TO-autointegration factor (BAF) ); DNA binding protein, retroviral integration, preintegration complex; 1.90A {Homo sapiens} SCOP: a.60.5.1 PDB: 1qck_A 2bzf_A 2ezx_A 2ezy_A 2ezz_A 2odg_A Probab=13.33 E-value=66 Score=15.13 Aligned_cols=27 Identities=33% Similarity=0.454 Sum_probs=24.1 Q ss_pred ECCCHHHHHHHHHCCCCCHHHHHHCCH Q ss_conf 346012237676408824799983002 Q gi|254781186|r 14 ANGIGAVTANYLENLNYSPIEKILGQR 40 (45) Q Consensus 14 angigavtanylenlnyspiekilgqr 40 (45) -.|||.+-+.-|++-.|.---..|||- T Consensus 23 l~GIG~~lg~~L~~kGfdKAy~vLGqf 49 (89) T 1ci4_A 23 LAGIGEVLGKKLEERGFDKAYVVLGQF 49 (89) T ss_dssp STTCCHHHHHHHHHTTCCSHHHHHHHH T ss_pred CCCCCHHHHHHHHHCCCCHHHHHHHHH T ss_conf 478648999999985853999999999 No 3 >1b22_A DNA repair protein RAD51; DNA binding, riken structural genomics/proteomics initiative, RSGI, structural genomics, DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: a.60.4.1 Probab=8.75 E-value=59 Score=15.38 Aligned_cols=25 Identities=24% Similarity=0.333 Sum_probs=20.4 Q ss_pred ECCCHHHHHHHHHCCCCCHHHHHHC Q ss_conf 3460122376764088247999830 Q gi|254781186|r 14 ANGIGAVTANYLENLNYSPIEKILG 38 (45) Q Consensus 14 angigavtanylenlnyspiekilg 38 (45) ..|||+.++.-|.+-.|..|++|+- T Consensus 30 ~~Gvg~~~i~KL~~aG~~Tv~~Ia~ 54 (114) T 1b22_A 30 QCGINANDVKKLEEAGFHTVEAVAY 54 (114) T ss_dssp HTTCSHHHHHHHHTTCCSSGGGBTS T ss_pred HCCCCHHHHHHHHHCCCCHHHHHHH T ss_conf 6899999999999969744999984 No 4 >2inp_L Phenol hydroxylase component PHM; DIIRON, four-helix bundle, regulatory protein, oxidoreductase; 2.30A {Pseudomonas stutzeri} PDB: 2inn_L 1hqi_A Probab=7.75 E-value=67 Score=15.09 Aligned_cols=40 Identities=25% Similarity=0.244 Sum_probs=28.5 Q ss_pred CCCCCEEEEEECCCHHHHHHHHHCCCCCHHHHHHCCHHHC Q ss_conf 4368779998346012237676408824799983002321 Q gi|254781186|r 4 QYNPDAIVLYANGIGAVTANYLENLNYSPIEKILGQRSSV 43 (45) Q Consensus 4 qynpdaivlyangigavtanylenlnyspiekilgqrssv 43 (45) +-||++.|.+-.+.=-+.+.----++...||..||+.-.+ T Consensus 24 ~dNP~~~V~d~~a~vrI~a~g~l~i~r~tieE~lGr~~~~ 63 (89) T 2inp_L 24 EDNPDAEMQHQPAMIRIQAEKRLVINRETMEEKLGRDWDV 63 (89) T ss_dssp SSCTTCEEEEETTEEEEECBSEEEECHHHHHHHHTSCCCG T ss_pred HHCCCCEEEECCCEEEEECCCEEEEEHHHHHHHHCCCCCH T ss_conf 5897979982587899903984999878979985898617 No 5 >2mob_A Protein (methane monooxygenase regulatory protein B); oxidoreductase, methane oxidation; NMR {Methylosinus trichosporium} SCOP: d.137.1.1 Probab=7.41 E-value=47 Score=15.88 Aligned_cols=40 Identities=23% Similarity=0.248 Sum_probs=28.0 Q ss_pred CCCCCEEEEEECCCHHHHHHHHHCCCCCHHHHHHCCHHHC Q ss_conf 4368779998346012237676408824799983002321 Q gi|254781186|r 4 QYNPDAIVLYANGIGAVTANYLENLNYSPIEKILGQRSSV 43 (45) Q Consensus 4 qynpdaivlyangigavtanylenlnyspiekilgqrssv 43 (45) .-||++.|-+..+.=-+.+.----++..-||..||+.-.+ T Consensus 62 ~DNP~~~V~drpa~vRIda~g~L~i~retIeE~LGR~~d~ 101 (138) T 2mob_A 62 AKNPSIVVEDKAGFWWIKADGAIEIDAAEAGELLGKPFSV 101 (138) T ss_dssp HTSSCCEEEECSSCEEEEESSEEEEECHHHHHHTCSTHHH T ss_pred CCCCCEEEEECCCEEEEECCCEEEEEHHHHHHHHCCCCCH T ss_conf 4599869970587799904982998788989985898738 No 6 >1ckv_A Protein (protein B); hydroxylase regulatory protein; NMR {Escherichia coli} SCOP: d.137.1.1 Probab=6.94 E-value=1.1e+02 Score=14.02 Aligned_cols=40 Identities=25% Similarity=0.243 Sum_probs=28.6 Q ss_pred CCCCEEEEEECCCHHHHHHHHHCCCCCHHHHHHCCHHHCC Q ss_conf 3687799983460122376764088247999830023217 Q gi|254781186|r 5 YNPDAIVLYANGIGAVTANYLENLNYSPIEKILGQRSSVA 44 (45) Q Consensus 5 ynpdaivlyangigavtanylenlnyspiekilgqrssva 44 (45) -||++.|.+..+.=-+.+.----++..-||..||+.-.+. T Consensus 64 ~nP~~~V~dr~ayvRI~a~g~L~i~retIeE~LGR~~d~~ 103 (141) T 1ckv_A 64 VNPTVNVEDRAGYWWIKANGKIEVDCDEISELLGRQFNVY 103 (141) T ss_dssp TCSCCEEEECSSSEEEEESSEEEECSSHHHHHTTTTCCST T ss_pred CCCCEEEEECCCEEEEECCCEEEEEHHHHHHHHCCCCCHH T ss_conf 8995699835877999139839987889899858977389 No 7 >2qkw_A Avirulence protein; three-helix bundle motif, AVRPTO-PTO duplex, layered beta- sheets, transferas; HET: SEP TPO; 3.20A {Pseudomonas syringae} SCOP: a.8.8.1 PDB: 1r5e_A Probab=5.43 E-value=1e+02 Score=14.20 Aligned_cols=28 Identities=36% Similarity=0.433 Sum_probs=14.2 Q ss_pred CCCCCC-CCEEEEEECCCHHHHHHHHHCC Q ss_conf 984436-8779998346012237676408 Q gi|254781186|r 1 MAHQYN-PDAIVLYANGIGAVTANYLENL 28 (45) Q Consensus 1 mahqyn-pdaivlyangigavtanylenl 28 (45) ||||-| ||-.---++.-.-||..-|-|+ T Consensus 11 MAHQVNSPDRvsNnsgd~n~vt~~qllnv 39 (164) T 2qkw_A 11 MAHQVNSPDRVSNNSGDEDNVTSSQLLSV 39 (164) T ss_dssp ------------------CCCCHHHHHHH T ss_pred HHHHCCCCCCCCCCCCCCCCCCHHHHHHH T ss_conf 65533884314567898665468999999 No 8 >1mzu_A PPR; photoactive yellow protein, PAS, PYP, signaling protein; HET: HC4; 2.00A {Rhodospirillum centenum} SCOP: d.110.3.1 Probab=5.31 E-value=2e+02 Score=12.64 Aligned_cols=34 Identities=18% Similarity=0.255 Sum_probs=19.1 Q ss_pred CCCEEEEEE-CC-CHHHHHHHHHCCCCCHHHHHHCCH Q ss_conf 687799983-46-012237676408824799983002 Q gi|254781186|r 6 NPDAIVLYA-NG-IGAVTANYLENLNYSPIEKILGQR 40 (45) Q Consensus 6 npdaivlya-ng-igavtanylenlnyspiekilgqr 40 (45) -|++|++.- .| |-.+.....+-+.|+| |.++|+. T Consensus 31 ~p~Gv~~~D~dg~I~~~N~aa~~ilG~s~-eeliGr~ 66 (129) T 1mzu_A 31 LPVGAIQVDGSGVIHRYNRTESRLSGRIP-ERVIGRN 66 (129) T ss_dssp CSSEEEEEETTCBEEEECHHHHHHHCCCH-HHHTTSB T ss_pred CCCEEEEECCCCCEEEECHHHHHHHCCCH-HHHCCCC T ss_conf 99069999899979999489999978497-9986994 No 9 >1u8x_X Maltose-6'-phosphate glucosidase; structural genomics, PSI, protein structure initiative, MCSG, NAD-dependent; HET: G6P NAD; 2.05A {Bacillus subtilis} SCOP: c.2.1.5 d.162.1.2 Probab=3.10 E-value=3e+02 Score=11.82 Aligned_cols=22 Identities=36% Similarity=0.581 Sum_probs=15.6 Q ss_pred CCCCCEEEE-EECCCHHHHHHHH Q ss_conf 436877999-8346012237676 Q gi|254781186|r 4 QYNPDAIVL-YANGIGAVTANYL 25 (45) Q Consensus 4 qynpdaivl-yangigavtanyl 25 (45) +|.|||+++ |+|-.+.+|---. T Consensus 160 e~~PdAwllNyTNP~~ivt~al~ 182 (472) T 1u8x_X 160 KYSPDAWMLNYSNPAAIVAEATR 182 (472) T ss_dssp HHCTTCEEEECCSCHHHHHHHHH T ss_pred HHCCCEEEEEECCHHHHHHHHHH T ss_conf 66998499981786899999999 No 10 >2k7m_A GAP junction alpha-5 protein; cell junction, cell membrane, membrane, transmembrane, membrane protein; NMR {Rattus norvegicus} Probab=3.05 E-value=3.2e+02 Score=11.63 Aligned_cols=11 Identities=36% Similarity=0.706 Sum_probs=7.7 Q ss_pred CCCCCCCCEEE Q ss_conf 98443687799 Q gi|254781186|r 1 MAHQYNPDAIV 11 (45) Q Consensus 1 mahqynpdaiv 11 (45) ||||-|+|..+ T Consensus 38 masqqN~dnla 48 (109) T 2k7m_A 38 MGSRKNPDPLA 48 (109) T ss_dssp TSSCSCCCSSS T ss_pred HHHCCCCCCHH T ss_conf 55103742012 Done!