Query gi|254781132|ref|YP_003065545.1| hypothetical protein CLIBASIA_05170 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 31 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Mon May 30 04:55:48 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781132.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 pfam06884 DUF1264 Protein of u 19.6 26 0.00067 17.9 -0.3 14 2-15 73-86 (171) 2 pfam08958 DUF1871 Domain of un 19.1 65 0.0016 16.2 1.6 22 3-24 11-33 (79) 3 KOG4389 consensus 11.1 1.8E+02 0.0046 14.2 2.1 23 3-25 478-500 (601) 4 pfam09809 MRP-L27 Mitochondria 10.6 1.5E+02 0.0038 14.5 1.5 18 14-31 73-90 (113) 5 pfam08469 NPHI_C Nucleoside tr 9.9 85 0.0022 15.6 0.1 10 3-12 97-106 (148) 6 pfam10183 ESSS ESSS subunit of 9.1 1.4E+02 0.0037 14.6 1.0 18 2-19 66-83 (151) 7 COG3664 XynB Beta-xylosidase [ 8.5 1.9E+02 0.0048 14.1 1.4 25 4-28 34-58 (428) 8 pfam11757 RSS_P20 Suppressor o 8.1 1.8E+02 0.0047 14.1 1.2 25 4-28 96-120 (137) 9 KOG1024 consensus 7.7 1E+02 0.0026 15.3 -0.3 12 20-31 440-451 (563) 10 KOG0738 consensus 5.5 3.4E+02 0.0087 12.9 2.3 26 2-30 181-206 (491) No 1 >pfam06884 DUF1264 Protein of unknown function (DUF1264). This family contains a number of bacterial and eukaryotic proteins of unknown function that are approximately 200 residues long. Some family members are annotated as putative lipoproteins. Probab=19.56 E-value=26 Score=17.95 Aligned_cols=14 Identities=50% Similarity=0.987 Sum_probs=10.5 Q ss_pred CCCCCCCCCCCHHH Q ss_conf 88841321113468 Q gi|254781132|r 2 ENPLWYSHEYDDEA 15 (31) Q Consensus 2 enplwysheyddea 15 (31) |.+||-||+|.-.. T Consensus 73 EkklWHsH~~EVkS 86 (171) T pfam06884 73 EKKLWHSHEYEVKS 86 (171) T ss_pred HHHCCCCCCCEEEC T ss_conf 88614642011003 No 2 >pfam08958 DUF1871 Domain of unknown function (DUF1871). This set of hypothetical proteins is produced by prokaryotes pertaining to the Bacillus genus. Probab=19.09 E-value=65 Score=16.18 Aligned_cols=22 Identities=41% Similarity=0.661 Sum_probs=15.8 Q ss_pred CCCCCCC-CCCHHHHHHHHHHHH Q ss_conf 8841321-113468999999766 Q gi|254781132|r 3 NPLWYSH-EYDDEAKDLVSAVSR 24 (31) Q Consensus 3 nplwysh-eyddeakdlvsavsr 24 (31) +|.-|.. -||.||-|.|.||+. T Consensus 11 DPF~~G~d~YetEa~dvv~Av~~ 33 (79) T pfam08958 11 DPFQYGEDFYETEAADVVQAVYD 33 (79) T ss_pred CCCCCCCCCCHHHHHHHHHHHHH T ss_conf 96456854112379999999980 No 3 >KOG4389 consensus Probab=11.07 E-value=1.8e+02 Score=14.15 Aligned_cols=23 Identities=39% Similarity=0.491 Sum_probs=18.4 Q ss_pred CCCCCCCCCCHHHHHHHHHHHHH Q ss_conf 88413211134689999997667 Q gi|254781132|r 3 NPLWYSHEYDDEAKDLVSAVSRD 25 (31) Q Consensus 3 nplwysheyddeakdlvsavsrd 25 (31) -|||||..|.+|.|+|-+.+-|- T Consensus 478 ~PL~~s~nYt~~E~~ls~rim~~ 500 (601) T KOG4389 478 IPLNYSRNYTKEEKILSRRIMRY 500 (601) T ss_pred CCCCCCCCCCHHHHHHHHHHHHH T ss_conf 63563446468999999999999 No 4 >pfam09809 MRP-L27 Mitochondrial ribosomal protein L27. Members of this family of proteins are components of the mitochondrial ribosome large subunit. They are also involved in apoptosis and cell cycle regulation. Probab=10.64 E-value=1.5e+02 Score=14.55 Aligned_cols=18 Identities=50% Similarity=0.565 Sum_probs=15.6 Q ss_pred HHHHHHHHHHHHHHHCCC Q ss_conf 689999997667653169 Q gi|254781132|r 14 EAKDLVSAVSRDLITKDY 31 (31) Q Consensus 14 eakdlvsavsrdlitkdy 31 (31) .|+||.+++-..-|.+|| T Consensus 73 ta~~lf~~~~a~~i~~df 90 (113) T pfam09809 73 TAKDLFNAVYAPKIFKDF 90 (113) T ss_pred CHHHHHHHHHHHHHHHHH T ss_conf 789999988879999886 No 5 >pfam08469 NPHI_C Nucleoside triphosphatase I C-terminal. This viral domain is found to the C-terminus of Poxvirus nucleoside triphosphatase phosphohydrolase I (NPH I) together with the helicase conserved C-terminal domain (pfam00271). Probab=9.91 E-value=85 Score=15.63 Aligned_cols=10 Identities=40% Similarity=1.169 Sum_probs=7.9 Q ss_pred CCCCCCCCCC Q ss_conf 8841321113 Q gi|254781132|r 3 NPLWYSHEYD 12 (31) Q Consensus 3 nplwysheyd 12 (31) .|.|||+.++ T Consensus 97 ~nIwYs~s~~ 106 (148) T pfam08469 97 QNIWYSKSYR 106 (148) T ss_pred CEEEEECCCH T ss_conf 7058984411 No 6 >pfam10183 ESSS ESSS subunit of NADH:ubiquinone oxidoreductase (complex I). This subunit is part of the mitochondrial NADH:ubiquinone oxidoreductase (complex I). It carries mitochondrial import sequences. Probab=9.07 E-value=1.4e+02 Score=14.59 Aligned_cols=18 Identities=22% Similarity=0.087 Sum_probs=12.3 Q ss_pred CCCCCCCCCCCHHHHHHH Q ss_conf 888413211134689999 Q gi|254781132|r 2 ENPLWYSHEYDDEAKDLV 19 (31) Q Consensus 2 enplwysheyddeakdlv 19 (31) .|+.||.-.|+|+..|.- T Consensus 66 Knw~s~Gf~~~D~~~D~~ 83 (151) T pfam10183 66 KNWDSHGYDYKDPKEDRW 83 (151) T ss_pred CCCCCCCCCCCCHHHHHH T ss_conf 186102778888266677 No 7 >COG3664 XynB Beta-xylosidase [Carbohydrate transport and metabolism] Probab=8.45 E-value=1.9e+02 Score=14.08 Aligned_cols=25 Identities=36% Similarity=0.531 Sum_probs=20.4 Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHH Q ss_conf 8413211134689999997667653 Q gi|254781132|r 4 PLWYSHEYDDEAKDLVSAVSRDLIT 28 (31) Q Consensus 4 plwysheyddeakdlvsavsrdlit 28 (31) -+||+-+|+||--|..+...+|+|- T Consensus 34 ~~~~~~t~~d~i~d~~~~~~~~~ie 58 (428) T COG3664 34 KLFYPFTYIDEIIDTLLDLGLDLIE 58 (428) T ss_pred CCCCCHHHHHHHHHHHHHHCCHHHH T ss_conf 0458747777887878772557999 No 8 >pfam11757 RSS_P20 Suppressor of RNA silencing P21-like. This is a large family of putative suppressors of RNA silencing proteins, P20-P25, from ssRNA positive-strand viruses such as Closterovirus, Potyvirus and Cucumovirus families. RNA silencing is one of the major mechanisms of defence against viruses, and, in response, some viruses have evolved or acquired functions for suppression of RNA silencing. These counter-defencive viral proteins with RNA silencing suppressor (RSS) activity were originally discovered in the members of plant virus genera Potyvirus and Cucumovirus. Each of the conserved blocks of amino acids found in P21-like proteins corresponds to a computer-predicted alpha-helix, with the most C-terminal element being 42 residues long. This suggests conservation of the predominantly alpha-helical secondary structure in the P21-like proteins. Probab=8.07 E-value=1.8e+02 Score=14.13 Aligned_cols=25 Identities=28% Similarity=0.215 Sum_probs=20.2 Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHH Q ss_conf 8413211134689999997667653 Q gi|254781132|r 4 PLWYSHEYDDEAKDLVSAVSRDLIT 28 (31) Q Consensus 4 plwysheyddeakdlvsavsrdlit 28 (31) +.=||+-+.+.-|-.++||-+||+. T Consensus 96 ~~~~s~i~~~kvk~~~~aVl~dlS~ 120 (137) T pfam11757 96 HVPFSEVMRTKLKLVVKAVISDLSR 120 (137) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9987999987117889999999889 No 9 >KOG1024 consensus Probab=7.67 E-value=1e+02 Score=15.26 Aligned_cols=12 Identities=67% Similarity=0.958 Sum_probs=0.0 Q ss_pred HHHHHHHHHCCC Q ss_conf 997667653169 Q gi|254781132|r 20 SAVSRDLITKDY 31 (31) Q Consensus 20 savsrdlitkdy 31 (31) ||.||||...|| T Consensus 440 saLSRDLFP~DY 451 (563) T KOG1024 440 SALSRDLFPGDY 451 (563) T ss_pred CHHCCCCCCCCC T ss_conf 311114376653 No 10 >KOG0738 consensus Probab=5.51 E-value=3.4e+02 Score=12.90 Aligned_cols=26 Identities=38% Similarity=0.668 Sum_probs=0.0 Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHHCC Q ss_conf 88841321113468999999766765316 Q gi|254781132|r 2 ENPLWYSHEYDDEAKDLVSAVSRDLITKD 30 (31) Q Consensus 2 enplwysheyddeakdlvsavsrdlitkd 30 (31) +.+.+-+-+|| ++||.++.||.+..+ T Consensus 181 ~~~~f~~~~~d---~~Lve~lerdIl~~n 206 (491) T KOG0738 181 EDKKFDSLGYD---ADLVEALERDILQRN 206 (491) T ss_pred CCCCCCCCCCH---HHHHHHHHHHHHCCC T ss_conf 66778753104---899999988886059 Done!