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!