Query gi|254781143|ref|YP_003065556.1| hypothetical protein CLIBASIA_05235 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 35 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Mon May 30 05:08:03 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781143.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 TIGR02196 GlrX_YruB Glutaredox 40.8 12 0.0003 18.8 0.9 20 10-29 28-47 (79) 2 pfam04568 IATP Mitochondrial A 15.3 1.2E+02 0.0029 14.2 2.6 30 4-33 50-79 (90) 3 pfam11873 DUF3393 Domain of un 7.9 1.8E+02 0.0045 13.4 1.0 15 19-33 162-176 (200) 4 COG2877 KdsA 3-deoxy-D-manno-o 7.5 99 0.0025 14.5 -0.4 27 5-31 127-157 (279) 5 KOG2668 consensus 7.4 2.2E+02 0.0057 12.9 1.3 24 2-25 217-240 (428) 6 TIGR01362 KDO8P_synth 3-deoxy- 4.8 1.7E+02 0.0042 13.5 -0.5 26 6-31 114-143 (279) 7 COG5559 Uncharacterized conser 4.7 3.4E+02 0.0088 12.0 1.2 14 20-33 22-35 (65) 8 TIGR02403 trehalose_treC alpha 3.7 3.8E+02 0.0098 11.8 0.6 18 3-20 435-452 (555) 9 pfam02048 Enterotoxin_ST Heat- 3.6 3.7E+02 0.0095 11.9 0.5 11 6-16 14-24 (54) 10 TIGR00462 genX lysyl-tRNA synt 3.6 3.6E+02 0.0091 12.0 0.4 10 3-12 22-31 (330) No 1 >TIGR02196 GlrX_YruB Glutaredoxin-like protein, YruB-family; InterPro: IPR011911 Glutaredoxins , , , also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system . Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond . It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro. This glutaredoxin-like protein family contains the conserved CxxC motif and includes the Clostridium pasteurianum protein YruB which has been cloned from a rubredoxin operon . Somewhat related to NrdH, it is unknown whether this protein actually interacts with glutathione/glutathione reducatase, or, like NrdH, some other reductant system.. Probab=40.78 E-value=12 Score=18.81 Aligned_cols=20 Identities=45% Similarity=0.479 Sum_probs=17.1 Q ss_pred HHHHHHHHHHHHHHHHHHHH Q ss_conf 33103454310899999976 Q gi|254781143|r 10 AEINIKKQQADAEYLLKKKL 29 (35) Q Consensus 10 aeinikkqqadaeyllkkkl 29 (35) .|+||.+..+++|+|+|+-= T Consensus 28 ~~~dV~~d~~A~~~~~k~~g 47 (79) T TIGR02196 28 EEIDVEKDSAAREELLKKLG 47 (79) T ss_pred EEECCCCCHHHHHHHHHHHC T ss_conf 76343369788999999838 No 2 >pfam04568 IATP Mitochondrial ATPase inhibitor, IATP. ATP synthase inhibitor prevents the enzyme from switching to ATP hydrolysis during collapse of the electrochemical gradient, for example during oxygen deprivation ATP synthase inhibitor forms a one to one complex with the F1 ATPase, possibly by binding at the alpha-beta interface. It is thought to inhibit ATP synthesis by preventing the release of ATP. The minimum inhibitory region for bovine inhibitor is from residues 39 to 72. The inhibitor has two oligomeric states, dimer (the active state) and tetramer. At low pH, the inhibitor forms a dimer via antiparallel coiled coil interactions between the C terminal regions of two monomers. At high pH, the inhibitor forms tetramers and higher oligomers by coiled coil interactions involving the N terminus and inhibitory region, thus preventing the inhibitory activity. Probab=15.34 E-value=1.2e+02 Score=14.23 Aligned_cols=30 Identities=27% Similarity=0.372 Sum_probs=19.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 132112331034543108999999765531 Q gi|254781143|r 4 KRAKIQAEINIKKQQADAEYLLKKKLQSQQ 33 (35) Q Consensus 4 krakiqaeinikkqqadaeyllkkklqsqq 33 (35) ||-+-+-+.-|++++..----||++|+.|+ T Consensus 50 krE~A~E~~y~rq~ekEqL~~Lk~~l~~q~ 79 (90) T pfam04568 50 KREAAQEEEYFRQKEKEQLAALKEKLEEHK 79 (90) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 888872889999999999999999999999 No 3 >pfam11873 DUF3393 Domain of unknown function (DUF3393). This domain is functionally uncharacterized. This domain is found in bacteria. This presumed domain is typically between 188 to 206 amino acids in length. This domain is found associated with pfam01464. Probab=7.88 E-value=1.8e+02 Score=13.36 Aligned_cols=15 Identities=40% Similarity=0.744 Sum_probs=11.3 Q ss_pred HHHHHHHHHHHHHHH Q ss_conf 108999999765531 Q gi|254781143|r 19 ADAEYLLKKKLQSQQ 33 (35) Q Consensus 19 adaeyllkkklqsqq 33 (35) --|.||++.+||+.. T Consensus 162 rfAdYLi~~~Lk~~~ 176 (200) T pfam11873 162 RYADYLIKNKLKTRK 176 (200) T ss_pred HHHHHHHHHHHHEEE T ss_conf 899999984662044 No 4 >COG2877 KdsA 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane] Probab=7.49 E-value=99 Score=14.54 Aligned_cols=27 Identities=37% Similarity=0.450 Sum_probs=18.0 Q ss_pred HHHHHHHHHHHHHHH----HHHHHHHHHHHH Q ss_conf 321123310345431----089999997655 Q gi|254781143|r 5 RAKIQAEINIKKQQA----DAEYLLKKKLQS 31 (35) Q Consensus 5 rakiqaeinikkqqa----daeyllkkklqs 31 (35) -||..+-|||||-|- |-.+.+.|.+.+ T Consensus 127 ~AkTg~~vNvKKgQFLaPwdMkniv~K~~~~ 157 (279) T COG2877 127 AAKTGAVVNVKKGQFLAPWDMKNIVEKFLET 157 (279) T ss_pred HHHHCCEEEECCCCCCCHHHHHHHHHHHHHC T ss_conf 9975884761265515866755599999853 No 5 >KOG2668 consensus Probab=7.36 E-value=2.2e+02 Score=12.91 Aligned_cols=24 Identities=42% Similarity=0.569 Sum_probs=16.8 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 511321123310345431089999 Q gi|254781143|r 2 ELKRAKIQAEINIKKQQADAEYLL 25 (35) Q Consensus 2 elkrakiqaeinikkqqadaeyll 25 (35) ||+.++..-|+|.++-+||--|-| T Consensus 217 el~Ka~~dveV~~~~aEA~lAyel 240 (428) T KOG2668 217 ELIKAATDVEVNTNKAEADLAYEL 240 (428) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 988753246666527878999998 No 6 >TIGR01362 KDO8P_synth 3-deoxy-8-phosphooctulonate synthase; InterPro: IPR006269 These sequences describe 2-dehydro-3-deoxyphosphooctonate aldolase. Alternate names include 3-deoxy-d-manno-octulosonic acid 8-phosphate and KDO-8 phosphate synthetase. It catalyzes the aldol condensation of phosphoenolpyruvate with D-arabinose 5-phosphate. phosphoenolpyruvate + D-arabinose 5-phosphate + H_2O = 2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate In Gram-negative bacteria, this is the first step in the biosynthesis of 3-deoxy-D-manno-octulosonate, part of the oligosaccharide core of lipopolysaccharide. ; GO: 0008676 3-deoxy-8-phosphooctulonate synthase activity, 0008152 metabolic process, 0005737 cytoplasm. Probab=4.77 E-value=1.7e+02 Score=13.50 Aligned_cols=26 Identities=35% Similarity=0.434 Sum_probs=17.0 Q ss_pred HHHHHHHHHHHHHH----HHHHHHHHHHHH Q ss_conf 21123310345431----089999997655 Q gi|254781143|r 6 AKIQAEINIKKQQA----DAEYLLKKKLQS 31 (35) Q Consensus 6 akiqaeinikkqqa----daeyllkkklqs 31 (35) |+.-+-|||||-|= |-++...|.+.+ T Consensus 114 A~TG~ivNvKKGQFLsP~dM~nv~~K~~~~ 143 (279) T TIGR01362 114 AKTGKIVNVKKGQFLSPWDMKNVVEKVLKT 143 (279) T ss_pred HHCCCEEEECCCCCCCHHHHHHHHHHHHHC T ss_conf 823986860588638712115899999872 No 7 >COG5559 Uncharacterized conserved small protein [Function unknown] Probab=4.68 E-value=3.4e+02 Score=12.04 Aligned_cols=14 Identities=43% Similarity=0.603 Sum_probs=10.0 Q ss_pred HHHHHHHHHHHHHH Q ss_conf 08999999765531 Q gi|254781143|r 20 DAEYLLKKKLQSQQ 33 (35) Q Consensus 20 daeyllkkklqsqq 33 (35) -+|||+.|++...| T Consensus 22 Y~EfLlek~~k~~~ 35 (65) T COG5559 22 YIEFLLEKKAKKKQ 35 (65) T ss_pred HHHHHHHHHHCCCC T ss_conf 99999998851757 No 8 >TIGR02403 trehalose_treC alpha,alpha-phosphotrehalase; InterPro: IPR012769 Trehalose is a glucose disaccharide that serves in many biological systems as a compatible solute for protection against hyperosmotic and thermal stress. This family describes trehalose-6-phosphate hydrolase, product of the treC (or treA) gene, which is often found together with a trehalose uptake transporter and a trehalose operon repressor.; GO: 0008788 alphaalpha-phosphotrehalase activity, 0005993 trehalose catabolic process, 0005737 cytoplasm. Probab=3.69 E-value=3.8e+02 Score=11.83 Aligned_cols=18 Identities=44% Similarity=0.422 Sum_probs=0.0 Q ss_pred CHHHHHHHHHHHHHHHHH Q ss_conf 113211233103454310 Q gi|254781143|r 3 LKRAKIQAEINIKKQQAD 20 (35) Q Consensus 3 lkrakiqaeinikkqqad 20 (35) |.-|+=+.+||..++.+| T Consensus 435 l~va~Ny~~INve~~~~D 452 (555) T TIGR02403 435 LGVATNYKEINVEKALAD 452 (555) T ss_pred CCCCCCHHHHHHHHHHCC T ss_conf 888778778889997417 No 9 >pfam02048 Enterotoxin_ST Heat-stable enterotoxin ST. This family consists of the heat stable enterotoxin ST from Escherichia coli. ST is a small peptide of 18 or 19 amino acid residues produced by enterotoxigenic E. coli and is one of the causes of acute diarrhoea in infants and travellers in developing countries. ST triggers a biological response by binding to a membrane-associated guanylyl cyclase C which is located on intestinal epithelial cell membranes. Probab=3.64 E-value=3.7e+02 Score=11.88 Aligned_cols=11 Identities=45% Similarity=0.516 Sum_probs=0.0 Q ss_pred HHHHHHHHHHH Q ss_conf 21123310345 Q gi|254781143|r 6 AKIQAEINIKK 16 (35) Q Consensus 6 akiqaeinikk 16 (35) ++|.+|+|-|+ T Consensus 14 ~~It~Ev~kk~ 24 (54) T pfam02048 14 EPITAEVNKKA 24 (54) T ss_pred CHHHHHHHHHH T ss_conf 34689998873 No 10 >TIGR00462 genX lysyl-tRNA synthetase homolog GenX; InterPro: IPR004525 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . This entry represents lysyl-tRNA synthetases from bacteria, as well as other related proteins. Escherichia coli, Haemophilus influenzae, and Aquifex aeolicus each have a protein closely homologous to the C-terminal region of lysyl-tRNA synthetase (LysS). Multiple sequence alignment of these proteins with the homologous regions of collected LysS proteins shows that these proteins form a distinct set rather than just similar truncations of LysS, so they appear to be orthologous. The protein is termed PoxA or GenX after its designation in E. coli. Its function is unknown.; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm. Probab=3.59 E-value=3.6e+02 Score=11.97 Aligned_cols=10 Identities=90% Similarity=0.986 Sum_probs=0.0 Q ss_pred CHHHHHHHHH Q ss_conf 1132112331 Q gi|254781143|r 3 LKRAKIQAEI 12 (35) Q Consensus 3 lkrakiqaei 12 (35) ||||+|-++| T Consensus 22 LkRa~~i~~i 31 (330) T TIGR00462 22 LKRAKIIAEI 31 (330) T ss_pred HHHHHHHHHH T ss_conf 8899999999 Done!