Query         gi|254781139|ref|YP_003065552.1| hypothetical protein CLIBASIA_05205 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 65
No_of_seqs    3 out of 5
Neff          1.5 
Searched_HMMs 39220
Date          Mon May 30 06:01:24 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781139.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 KOG2544 consensus               31.3      21 0.00052   18.5   0.9   33   12-44    665-697 (711)
  2 TIGR00469 pheS_mito phenylalan  18.9      34 0.00088   17.4   0.1   26   31-56    106-132 (460)
  3 PRK10202 ebgC cryptic beta-D-g  13.4      42  0.0011   16.9  -0.5   33    7-44     13-45  (149)
  4 cd03591 CLECT_collectin_like C  12.8 1.1E+02  0.0028   14.7   1.5   30   29-58     22-51  (114)
  5 pfam06869 DUF1258 Protein of u  10.4 1.5E+02  0.0037   14.1   1.4   31   32-62     74-104 (258)
  6 pfam06212 GRIM-19 GRIM-19 prot  10.3      58  0.0015   16.2  -0.7   31   15-55     62-92  (130)
  7 TIGR00505 ribA GTP cyclohydrol   9.8 1.2E+02  0.0031   14.5   0.9   19   27-45     50-71  (227)
  8 PRK03600 nrdI ribonucleotide r   9.6 1.1E+02  0.0029   14.7   0.6   15   44-58     60-74  (136)
  9 PRK02551 hypothetical protein;   9.4   1E+02  0.0026   14.9   0.3   16   43-58     80-95  (154)
 10 COG5269 ZUO1 Ribosome-associat   9.2      99  0.0025   15.0   0.2   18   43-63    164-181 (379)

No 1  
>KOG2544 consensus
Probab=31.31  E-value=21  Score=18.54  Aligned_cols=33  Identities=21%  Similarity=0.403  Sum_probs=28.1

Q ss_pred             HHHHCCEEEEHHCCHHHHCCCCEEEEECCCCHH
Q ss_conf             643154100010004222056812011254078
Q gi|254781139|r   12 RKKNRDWQRIASIPVSILKDSHLLQAHTEGDDV   44 (65)
Q Consensus        12 r~~~~dW~rvASiPlnvah~~~LvqAHsEGDD~   44 (65)
                      -++.|||..+|++.-.|+.+++.|+.|.--+-.
T Consensus       665 ~akdRd~aT~A~Vta~Il~Ga~ivRVHdvk~~s  697 (711)
T KOG2544         665 EAKDRDAATVACVTAGILFGANIVRVHDVKNNS  697 (711)
T ss_pred             CHHHHCCHHHHHHHHHHCCCCCEEEEEECHHHH
T ss_conf             833301045665656650575259984012346


No 2  
>TIGR00469 pheS_mito phenylalanyl-tRNA synthetase; InterPro: IPR004530   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 .   Phenylalanyl-tRNA synthetase (6.1.1.20 from EC) is an alpha2/beta2 tetramer composed of 2 subunits that belongs to class IIc. In eubacteria, a small subunit (pheS gene) can be designated as beta (E. coli) or alpha subunit (nomenclature adopted in InterPro). Reciprocally the large subunit (pheT gene) can be designated as alpha (E. coli) or beta (see IPR004531 from INTERPRO and IPR004532 from INTERPRO). In all other kingdoms the two subunits have equivalent length in eukaryota, and can be identified by specific signatures. The enzyme from Thermus thermophilus has an alpha 2 beta 2 type quaternary structure and is one of the most complicated members of the synthetase family. Identification of phenylalanyl-tRNA synthetase as a member of class II aaRSs was based only on sequence alignment of the small alpha-subunit with other synthetases .   This family describes the mitochondrial phenylalanyl-tRNA synthetases. Unlike all other known phenylalanyl-tRNA synthetases, the mitochondrial form demonstrated from yeast is monomeric. It is similar to but longer than the alpha subunit (PheS) of the alpha 2 beta 2 form found in bacteria, Archaea, and eukaryotes, and shares the characteristic motifs of class II aminoacyl-tRNA ligases.; GO: 0000166 nucleotide binding, 0004826 phenylalanine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006432 phenylalanyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=18.94  E-value=34  Score=17.37  Aligned_cols=26  Identities=38%  Similarity=0.728  Sum_probs=20.0

Q ss_pred             CCCEEEEECCCCHH-HHHHHHCCCCCC
Q ss_conf             56812011254078-999970266641
Q gi|254781139|r   31 DSHLLQAHTEGDDV-WVNKWLNNRDNA   56 (65)
Q Consensus        31 ~~~LvqAHsEGDD~-~VkrwLNn~DNr   56 (65)
                      ..||+||||-.-.+ ...+-+||+||-
T Consensus       106 ~~HLLR~HT~AH~~E~~~~~~~~sdni  132 (460)
T TIGR00469       106 ETHLLRAHTSAHELELISKILDDSDNI  132 (460)
T ss_pred             CCHHHHHCCCHHHHHHHHCCCCCCCCC
T ss_conf             300333302134545442223532111


No 3  
>PRK10202 ebgC cryptic beta-D-galactosidase subunit beta; Reviewed
Probab=13.43  E-value=42  Score=16.90  Aligned_cols=33  Identities=27%  Similarity=0.299  Sum_probs=21.9

Q ss_pred             HHHHHHHHHCCEEEEHHCCHHHHCCCCEEEEECCCCHH
Q ss_conf             66666643154100010004222056812011254078
Q gi|254781139|r    7 CAMATRKKNRDWQRIASIPVSILKDSHLLQAHTEGDDV   44 (65)
Q Consensus         7 cama~r~~~~dW~rvASiPlnvah~~~LvqAHsEGDD~   44 (65)
                      |--.-|||+|--..|++|+ |+..+    -+||-||+-
T Consensus        13 ~yr~grkW~R~~EaI~~i~-~~~~g----v~ysIGDsl   45 (149)
T PRK10202         13 IYASGKKWQRCVEAIENID-NIQPG----VAHSIGDSL   45 (149)
T ss_pred             ECCCCHHHHHHHHHHHHHC-CCCCC----CEEECCCEE
T ss_conf             0267378999999986121-36877----468727747


No 4  
>cd03591 CLECT_collectin_like C-type lectin-like domain (CTLD) of the type found in human collectins including lung surfactant proteins A and D, mannose- or mannan binding lectin (MBL), and CL-L1 (collectin liver 1). CLECT_collectin_like: C-type lectin-like domain (CTLD) of the type found in human collectins including lung surfactant proteins A and D, mannose- or mannan binding lectin (MBL), and CL-L1 (collectin liver 1).  CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. The CTLDs of these collectins bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, or apoptotic cells) and mediate functions associated with killing and phagocytosis.  MBPs recognize high mannose oligosaccharides in a calcium dependent manner, bind to a broad range of pathogens, and trigger cell killing by activating the complement pathway.  MBP also acts directly as an opsonin.  SP-A and SP-D in addition to functioning as host defense components, a
Probab=12.84  E-value=1.1e+02  Score=14.74  Aligned_cols=30  Identities=3%  Similarity=0.188  Sum_probs=23.9

Q ss_pred             HCCCCEEEEECCCCHHHHHHHHCCCCCCEE
Q ss_conf             205681201125407899997026664100
Q gi|254781139|r   29 LKDSHLLQAHTEGDDVWVNKWLNNRDNASW   58 (65)
Q Consensus        29 ah~~~LvqAHsEGDD~~VkrwLNn~DNraW   58 (65)
                      ..+.+|+.-+|+....++..++.......|
T Consensus        22 ~~gg~La~i~s~~e~~~l~~~~~~~~~~~w   51 (114)
T cd03591          22 EAGGTLAMPRNAAENAAIASYVKKGNTYAF   51 (114)
T ss_pred             HCCCEECCCCCHHHHHHHHHHHHCCCCCEE
T ss_conf             769999363999999999998616797489


No 5  
>pfam06869 DUF1258 Protein of unknown function (DUF1258). This family represents a conserved region approximately 260 residues long within a number of hypothetical proteins of unknown function that seem to be specific to C. elegans. Note that this family contains a number of conserved cysteine and histidine residues.
Probab=10.41  E-value=1.5e+02  Score=14.12  Aligned_cols=31  Identities=23%  Similarity=0.474  Sum_probs=24.6

Q ss_pred             CCEEEEECCCCHHHHHHHHCCCCCCEEHHCC
Q ss_conf             6812011254078999970266641000023
Q gi|254781139|r   32 SHLLQAHTEGDDVWVNKWLNNRDNASWRTSE   62 (65)
Q Consensus        32 ~~LvqAHsEGDD~~VkrwLNn~DNraWRt~E   62 (65)
                      ++.-..|.-+..-|-++|++..||.-|-+++
T Consensus        74 eg~n~~h~l~spffsk~~~~Es~n~l~ls~~  104 (258)
T pfam06869        74 EGRNSSHNLNSPFFSKKWLSESDNHLWLSTV  104 (258)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHCCCEEEEEEE
T ss_conf             4787667656467766665407660578889


No 6  
>pfam06212 GRIM-19 GRIM-19 protein. This family consists of several eukaryotic gene associated with retinoic-interferon-induced mortality 19 (GRIM-19) proteins. GRIM-19, was reported to encode a small protein primarily distributed in the nucleus and was able to promote cell death induced by IFN-# and RA. A bovine homologue of GRIM-19 was co-purified with mitochondrial NADH:ubiquinone oxidoreductase (complex I) in bovine heart. Therefore, its exact cellular localisation and function are unclear. It has now been discovered that GRIM-19 is a specific interacting protein which negatively regulates Stat3 activity.
Probab=10.31  E-value=58  Score=16.18  Aligned_cols=31  Identities=26%  Similarity=0.352  Sum_probs=23.7

Q ss_pred             HCCEEEEHHCCHHHHCCCCEEEEECCCCHHHHHHHHCCCCC
Q ss_conf             15410001000422205681201125407899997026664
Q gi|254781139|r   15 NRDWQRIASIPVSILKDSHLLQAHTEGDDVWVNKWLNNRDN   55 (65)
Q Consensus        15 ~~dW~rvASiPlnvah~~~LvqAHsEGDD~~VkrwLNn~DN   55 (65)
                      ..-|.|+|-+|+-.        |  |.|-+|++++.-|.+.
T Consensus        62 E~~~aR~al~PlLq--------A--E~DR~~lr~~~~~~~~   92 (130)
T pfam06212        62 EDRSARNAILPLLQ--------A--ERDRRYLKQLRRNREE   92 (130)
T ss_pred             HHHHHHHHHHHHHH--------H--HHHHHHHHHHHHHHHH
T ss_conf             99998999999998--------7--9999999999993999


No 7  
>TIGR00505 ribA GTP cyclohydrolase II; InterPro: IPR000926   GTP cyclohydrolase II catalyses the first committed step in the biosynthesis of riboflavin. The enzyme converts GTP and water to formate, 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)- pyrimidine and pyrophosphate, and requires magnesium as a cofactor. It is sometimes found as a bifunctional enzyme with 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP_synthase) IPR000422 from INTERPRO. ; GO: 0003935 GTP cyclohydrolase II activity, 0009231 riboflavin biosynthetic process.
Probab=9.81  E-value=1.2e+02  Score=14.50  Aligned_cols=19  Identities=32%  Similarity=0.494  Sum_probs=13.9

Q ss_pred             HHHCCCCEEEEECC---CCHHH
Q ss_conf             22205681201125---40789
Q gi|254781139|r   27 SILKDSHLLQAHTE---GDDVW   45 (65)
Q Consensus        27 nvah~~~LvqAHsE---GDD~~   45 (65)
                      +-+|..-|||-|||   ||--|
T Consensus        50 ~~a~~~~LvRiHSECLTGd~l~   71 (227)
T TIGR00505        50 SDAHNDVLVRIHSECLTGDALH   71 (227)
T ss_pred             CCCCCCEEEEEECCHHHHHHHH
T ss_conf             3566880378831100222211


No 8  
>PRK03600 nrdI ribonucleotide reductase stimulatory protein; Reviewed
Probab=9.65  E-value=1.1e+02  Score=14.71  Aligned_cols=15  Identities=27%  Similarity=0.355  Sum_probs=12.7

Q ss_pred             HHHHHHHCCCCCCEE
Q ss_conf             899997026664100
Q gi|254781139|r   44 VWVNKWLNNRDNASW   58 (65)
Q Consensus        44 ~~VkrwLNn~DNraW   58 (65)
                      .-|.+|||+.+|+.+
T Consensus        60 ~~v~~FL~~~~N~~~   74 (136)
T PRK03600         60 KQVIRFLNDEHNRKL   74 (136)
T ss_pred             HHHHHHHHCCCCHHH
T ss_conf             899998837303546


No 9  
>PRK02551 hypothetical protein; Provisional
Probab=9.38  E-value=1e+02  Score=14.89  Aligned_cols=16  Identities=13%  Similarity=0.225  Sum_probs=12.6

Q ss_pred             HHHHHHHHCCCCCCEE
Q ss_conf             7899997026664100
Q gi|254781139|r   43 DVWVNKWLNNRDNASW   58 (65)
Q Consensus        43 D~~VkrwLNn~DNraW   58 (65)
                      ..-|.+|||+.+||+.
T Consensus        80 ~~~v~~FLn~~~Nr~~   95 (154)
T PRK02551         80 TTPLGEFIAYHNNAQR   95 (154)
T ss_pred             CHHHHHHHCCHHHHHH
T ss_conf             3679988455554754


No 10 
>COG5269 ZUO1 Ribosome-associated chaperone zuotin [Translation, ribosomal structure and biogenesis / Posttranslational modification, protein turnover, chaperones]
Probab=9.21  E-value=99  Score=14.99  Aligned_cols=18  Identities=39%  Similarity=0.671  Sum_probs=11.4

Q ss_pred             HHHHHHHHCCCCCCEEHHCCC
Q ss_conf             789999702666410000237
Q gi|254781139|r   43 DVWVNKWLNNRDNASWRTSEG   63 (65)
Q Consensus        43 D~~VkrwLNn~DNraWRt~EG   63 (65)
                      +-|-.-|-|   -+||||||-
T Consensus       164 e~FY~FW~n---FdSWRtFE~  181 (379)
T COG5269         164 EEFYEFWSN---FDSWRTFEP  181 (379)
T ss_pred             HHHHHHHHH---CCCCCCCCC
T ss_conf             999999970---342103540


Done!