Query gi|254781036|ref|YP_003065449.1| hypothetical protein CLIBASIA_04690 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 65 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Mon May 30 04:13:30 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781036.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK12358 putative 6-phosphoglu 38.0 9 0.00023 20.5 -0.0 45 20-64 60-111 (239) 2 pfam02794 HlyC RTX toxin acylt 25.8 39 0.001 17.2 1.6 21 2-24 86-106 (134) 3 COG2994 HlyC ACP:hemolysin acy 23.7 23 0.0006 18.4 0.1 12 2-13 104-115 (148) 4 TIGR00095 TIGR00095 putative m 23.3 28 0.00071 18.0 0.4 20 4-23 64-83 (210) 5 pfam08068 DKCLD DKCLD (NUC011) 19.6 44 0.0011 17.0 0.8 15 13-27 35-49 (59) 6 TIGR00977 LeuA_rel 2-isopropyl 15.7 62 0.0016 16.2 0.8 25 10-46 127-151 (543) 7 COG4171 SapC ABC-type antimicr 14.5 1E+02 0.0026 15.1 1.6 40 9-48 83-143 (296) 8 TIGR01176 fum_red_Fp fumarate 13.6 74 0.0019 15.8 0.7 31 33-63 58-93 (585) 9 pfam00859 CTF_NFI CTF/NF-I fam 11.5 58 0.0015 16.4 -0.3 13 17-29 4-16 (295) 10 pfam08497 Radical_SAM_N Radica 11.2 1.7E+02 0.0043 14.0 2.0 39 7-45 31-100 (298) No 1 >PRK12358 putative 6-phosphogluconolactonase; Provisional Probab=37.97 E-value=9 Score=20.55 Aligned_cols=45 Identities=20% Similarity=0.261 Sum_probs=33.5 Q ss_pred HCCCCHHHHHHHH-------HHHHHHHHHHHCCCCHHHHHHHEECCHHHHHC Q ss_conf 1201544413232-------02476531111045546512330057277630 Q gi|254781036|r 20 SGVFNLDSLLVDF-------SVSLKEHFFDTYSIPWHSIFYFVSENSKEYCK 64 (65) Q Consensus 20 sgvfnldsllvdf-------svslkehffdtysipwhsifyfvsenskeyck 64 (65) --+||+|-...+- .-.++++||+.-.||--.|+.+-.|+.++|.+ T Consensus 60 v~~f~lDE~~~~~~~~~~~~~~~l~~~l~~~~~i~~~~i~~~~~e~~~~ye~ 111 (239) T PRK12358 60 CHYYNFDEIPFRGKEGEGVTITNLRNLFFTPAGIKEENIHKLTIDNYREHDQ 111 (239) T ss_pred EEEEEEEEECCCCCCCHHHHHHHHHHHCCCCCCCCHHHCCCCCHHHHHHHHH T ss_conf 7999610555898555356999999965775799978869997677999999 No 2 >pfam02794 HlyC RTX toxin acyltransferase family. Members of this family are enzymes EC:2.3.1.-. involved in fatty acylation of the protoxins (HlyA) at lysine residues, thereby converting them to the active toxin. Acyl-acyl carrier protein (ACP) is the essential acyl donor. This family show a number of conserved residues that are possible candidates for participation in acyl transfer. Site-directed mutagenesis of the single conserved histidine residue in Hemolysin C from Escherichia coli resulted in complete inactivation of the enzyme. Probab=25.76 E-value=39 Score=17.24 Aligned_cols=21 Identities=38% Similarity=0.896 Sum_probs=13.8 Q ss_pred CCCCHHHHHHHHHHHHHHHCCCC Q ss_conf 11521255699999998612015 Q gi|254781036|r 2 WIAPFGSLGVAVLSRYVKSGVFN 24 (65) Q Consensus 2 wiapfgslgvavlsryvksgvfn 24 (65) ||||||. ...+.|.+...+|- T Consensus 86 ~iAPfGh--~~~i~r~lr~~~f~ 106 (134) T pfam02794 86 WIAPFGH--ARAIYRDLRRRIFP 106 (134) T ss_pred EECCCCC--HHHHHHHHHHCCCC T ss_conf 9568997--69999999854499 No 3 >COG2994 HlyC ACP:hemolysin acyltransferase (hemolysin-activating protein) [Posttranslational modification, protein turnover, chaperones] Probab=23.67 E-value=23 Score=18.40 Aligned_cols=12 Identities=58% Similarity=1.102 Sum_probs=7.7 Q ss_pred CCCCHHHHHHHH Q ss_conf 115212556999 Q gi|254781036|r 2 WIAPFGSLGVAV 13 (65) Q Consensus 2 wiapfgslgvav 13 (65) ||||||.---.+ T Consensus 104 ~iAPfGh~r~~~ 115 (148) T COG2994 104 WIAPFGHSRQMV 115 (148) T ss_pred EECCCCCHHHHH T ss_conf 972578418899 No 4 >TIGR00095 TIGR00095 putative methyltransferase; InterPro: IPR004398 This is a family of conserved hypothetical proteins, which includes a putative methylase.. Probab=23.27 E-value=28 Score=18.03 Aligned_cols=20 Identities=60% Similarity=0.710 Sum_probs=17.3 Q ss_pred CCHHHHHHHHHHHHHHHCCC Q ss_conf 52125569999999861201 Q gi|254781036|r 4 APFGSLGVAVLSRYVKSGVF 23 (65) Q Consensus 4 apfgslgvavlsryvksgvf 23 (65) |-=|+||+--|||+-++-+| T Consensus 64 AGsG~LG~EALSRgA~~~~f 83 (210) T TIGR00095 64 AGSGSLGLEALSRGAKSAVF 83 (210) T ss_pred CCCHHHHHHHHHHCCCEEEE T ss_conf 06446537664014162378 No 5 >pfam08068 DKCLD DKCLD (NUC011) domain. This is a TruB_N/PUA domain associated N-terminal domain of Dyskerin-like proteins. Probab=19.62 E-value=44 Score=17.01 Aligned_cols=15 Identities=47% Similarity=0.831 Sum_probs=12.0 Q ss_pred HHHHHHHHCCCCHHH Q ss_conf 999998612015444 Q gi|254781036|r 13 VLSRYVKSGVFNLDS 27 (65) Q Consensus 13 vlsryvksgvfnlds 27 (65) -+..|+++|+.|||. T Consensus 35 ~i~~~i~~GvInlDK 49 (59) T pfam08068 35 PIEEYIKYGVINLDK 49 (59) T ss_pred CHHHHHHCCEEEECC T ss_conf 899998579677037 No 6 >TIGR00977 LeuA_rel 2-isopropylmalate synthase/homocitrate synthase family protein; InterPro: IPR005675 This model represents largely uncharacterised proteins related to 2-isopropylmalate synthases and homocitrate synthases but phylogenetically distinct. ; GO: 0046912 transferase activity transferring acyl groups acyl groups converted into alkyl on transfer, 0019752 carboxylic acid metabolic process. Probab=15.66 E-value=62 Score=16.23 Aligned_cols=25 Identities=44% Similarity=0.826 Sum_probs=15.3 Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 6999999986120154441323202476531111045 Q gi|254781036|r 10 GVAVLSRYVKSGVFNLDSLLVDFSVSLKEHFFDTYSI 46 (65) Q Consensus 10 gvavlsryvksgvfnldsllvdfsvslkehffdtysi 46 (65) .|+-|.||+..-+|. -|||||-|.- T Consensus 127 Tv~YLk~~~~~VIyD------------AEHfFDGYka 151 (543) T TIGR00977 127 TVAYLKRYADEVIYD------------AEHFFDGYKA 151 (543) T ss_pred HHHHHHHHCCEEEEE------------CCCCCCCCCC T ss_conf 999998721225630------------2002463457 No 7 >COG4171 SapC ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms] Probab=14.49 E-value=1e+02 Score=15.12 Aligned_cols=40 Identities=38% Similarity=0.564 Sum_probs=27.2 Q ss_pred HHHHHHHHHHHHCCCCHHH-HHHHHHHH-------------------HHHHHHHHC-CCCH Q ss_conf 5699999998612015444-13232024-------------------765311110-4554 Q gi|254781036|r 9 LGVAVLSRYVKSGVFNLDS-LLVDFSVS-------------------LKEHFFDTY-SIPW 48 (65) Q Consensus 9 lgvavlsryvksgvfnlds-llvdfsvs-------------------lkehffdty-sipw 48 (65) ||-.||||......+.+.+ ++|.+++. .-.|++||. |||- T Consensus 83 lGRDvlSRli~Gt~~t~G~allvt~~a~l~g~~lGi~AG~t~gl~s~~lnHilDt~lSiPs 143 (296) T COG4171 83 LGRDVLSRLISGTAPTVGGALLVTLAATICGGVLGIFAGATHGLRSAVLNHILDTLLSIPS 143 (296) T ss_pred CHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 0088999997067523413999999999999999999977777899999999999973589 No 8 >TIGR01176 fum_red_Fp fumarate reductase, flavoprotein subunit; InterPro: IPR005884 In bacteria two distinct, membrane-bound, enzyme complexes are responsible for the interconversion of fumarate and succinate (1.3.99.1 from EC): fumaratereductase (Frd) is used in anaerobic growth, and succinate dehydrogenase (Sdh) is used in aerobic growth. Both complexes consist of two main components: a membrane-extrinsic component composed of a FAD-binding flavoprotein and an iron-sulphur protein; and an hydrophobic component composed of a membrane anchor protein and/or a cytochrome B. In eukaryotes mitochondrial succinate dehydrogenase (ubiquinone) (1.3.5.1 from EC) is an enzyme composed of two subunits: a FAD flavoprotein and and iron-sulphur protein. The flavoprotein subunit is a protein of about 60 to 70 Kd to which FAD is covalently bound to a histidine residue which is located in the N-terminal section of the protein . The sequence around that histidine is well conserved in Frd and Sdh from various bacterial and eukaryotic species . The terms succinate dehydrogenase and fumarate reductase may be used interchangeably in certain systems. However, a number of species have distinct complexes, with the fumarate reductase active under anaerobic conditions. This model represents the fumarate reductase flavoprotein subunit from several such species in which a distinct succinate dehydrogenase is also found. ; GO: 0016491 oxidoreductase activity, 0006118 electron transport, 0009061 anaerobic respiration. Probab=13.56 E-value=74 Score=15.82 Aligned_cols=31 Identities=48% Similarity=0.715 Sum_probs=22.9 Q ss_pred HHHHHHHHHHHCCC-CH----HHHHHHEECCHHHHH Q ss_conf 02476531111045-54----651233005727763 Q gi|254781036|r 33 SVSLKEHFFDTYSI-PW----HSIFYFVSENSKEYC 63 (65) Q Consensus 33 svslkehffdtysi-pw----hsifyfvsenskeyc 63 (65) .-||.+||-||-+= -| ..+=|||.+..+|.. T Consensus 58 ~DSld~H~~DTV~GGDWLC~QD~Ve~FV~~ap~E~~ 93 (585) T TIGR01176 58 DDSLDEHFHDTVSGGDWLCEQDVVEYFVAEAPKELV 93 (585) T ss_pred CCCHHHHCCCCCCCCCCCCCHHHHHHHHHHCCHHHH T ss_conf 412454144534566432202189998741334566 No 9 >pfam00859 CTF_NFI CTF/NF-I family transcription modulation region. Probab=11.45 E-value=58 Score=16.37 Aligned_cols=13 Identities=46% Similarity=0.935 Sum_probs=10.0 Q ss_pred HHHHCCCCHHHHH Q ss_conf 9861201544413 Q gi|254781036|r 17 YVKSGVFNLDSLL 29 (65) Q Consensus 17 yvksgvfnldsll 29 (65) +|+|||||...|. T Consensus 4 FVTSGVfsVtELv 16 (295) T pfam00859 4 FVTSGVFSVTELV 16 (295) T ss_pred CEECCCCCHHHEE T ss_conf 1202423014314 No 10 >pfam08497 Radical_SAM_N Radical SAM N-terminal. This domain tends to occur to the N-terminus of the pfam04055 domain in hypothetical bacterial proteins. Probab=11.25 E-value=1.7e+02 Score=13.97 Aligned_cols=39 Identities=28% Similarity=0.510 Sum_probs=27.6 Q ss_pred HHHHHHHHHHHHHHCCC-------------------------------CHHHHHHHHHHHHHHHHHHHCC Q ss_conf 25569999999861201-------------------------------5444132320247653111104 Q gi|254781036|r 7 GSLGVAVLSRYVKSGVF-------------------------------NLDSLLVDFSVSLKEHFFDTYS 45 (65) Q Consensus 7 gslgvavlsryvksgvf-------------------------------nldsllvdfsvslkehffdtys 45 (65) -|.|+|+++|...+--| |+||++-.+..+.|-.--|.|| T Consensus 31 PsFG~AiIgR~Le~~GyrVgIIaQPdw~~~~df~~lG~PrLffgVsaGn~DSMVn~YTa~kK~R~~DaYt 100 (298) T pfam08497 31 PSFGMAIIGRVLEAQGFRVGIIAQPDWRSDEDFKRLGRPRLFFGVTAGNMDSMVNHYTADKKLRSDDAYT 100 (298) T ss_pred CCHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCCCCCCC T ss_conf 5306899999999869659897189989847899729984798863664888887614444434546869 Done!