Query         gi|254780931|ref|YP_003065344.1| hypothetical protein CLIBASIA_04150 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 56
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Mon May 30 00:59:18 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780931.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 pfam09556 RE_HaeIII HaeIII res  95.3   0.022 5.6E-07   34.5   3.9   52    2-53    132-183 (300)
  2 pfam05061 Pox_A11 Poxvirus A11  42.9     6.4 0.00016   21.0  -0.2   12    1-12     21-32  (309)
  3 COG4383 Mu-like prophage prote  24.0      28 0.00071   17.5   0.5   20   19-38     51-70  (517)
  4 pfam10957 DUF2758 Protein of u  22.0      24 0.00061   17.8  -0.1   16   24-39     17-32  (60)
  5 pfam01736 Polyoma_agno Polyoma  17.1      98  0.0025   14.5   2.1   19   22-49     22-40  (62)
  6 TIGR00803 nst UDP-galactose tr  15.4      61  0.0015   15.6   0.7   23   24-46    102-125 (235)
  7 PHA02105 hypothetical protein   14.8      99  0.0025   14.4   1.7   18    2-19     21-38  (68)
  8 TIGR00004 TIGR00004 endoribonu  13.5      40   0.001   16.6  -0.7   17   19-35     68-84  (129)
  9 COG5248 TAF19 Transcription in  13.1      66  0.0017   15.4   0.4   13   23-35      5-17  (126)
 10 pfam11387 DUF2795 Protein of u  12.1      95  0.0024   14.5   0.9   11    1-11      4-14  (44)

No 1  
>pfam09556 RE_HaeIII HaeIII restriction endonuclease. This family includes the HaeIII (recognizes and cleaves GG^CC) restriction endonuclease.
Probab=95.33  E-value=0.022  Score=34.52  Aligned_cols=52  Identities=25%  Similarity=0.590  Sum_probs=47.9

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             8765499999999999754202334245532053228999999999999998
Q gi|254780931|r    2 DYPCNKEYFKTISTVFGKLGDMRAQNIFLKDIKDKDIIFYLHILIAFEKVID   53 (56)
Q Consensus         2 dypcnkeyfktistvfgklgdmraqniflkdikdkdiifylhiliafekvid   53 (56)
                      .-||.+.||..|..+|..|...++++....+|.+|+--.|.-+|-||-.-|.
T Consensus       132 gipcSq~Ywd~I~PiF~~Le~~k~~g~~w~~i~~KEe~vYvPLL~AFi~El~  183 (300)
T pfam09556       132 GIPSSQNYFDEINPLFEELEELKKEGELWRNISNKEERIYVPLLKAFIREIE  183 (300)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCEEHHHHHHHHHHHHH
T ss_conf             8975076787777899999999862860111766320151999999999999


No 2  
>pfam05061 Pox_A11 Poxvirus A11 Protein. Family of conserved Chordopoxvirinae A11 family proteins. Conserved region spans entire protein in the majority of family members.
Probab=42.91  E-value=6.4  Score=21.00  Aligned_cols=12  Identities=50%  Similarity=0.689  Sum_probs=9.5

Q ss_pred             CCCCCCHHHHHH
Q ss_conf             987654999999
Q gi|254780931|r    1 MDYPCNKEYFKT   12 (56)
Q Consensus         1 mdypcnkeyfkt   12 (56)
                      ++|||||.|--|
T Consensus        21 d~YP~NKnYEIT   32 (309)
T pfam05061        21 DGYPSNKNYEIT   32 (309)
T ss_pred             CCCCCCCCCEEE
T ss_conf             788877772321


No 3  
>COG4383 Mu-like prophage protein gp29 [Function unknown]
Probab=24.00  E-value=28  Score=17.49  Aligned_cols=20  Identities=45%  Similarity=0.743  Sum_probs=17.7

Q ss_pred             HHHHHHHHHHHHHHCCCCHH
Q ss_conf             54202334245532053228
Q gi|254780931|r   19 KLGDMRAQNIFLKDIKDKDI   38 (56)
Q Consensus        19 klgdmraqniflkdikdkdi   38 (56)
                      .-|||+||.-...||..||-
T Consensus        51 ErGDl~AQseL~aDiEEkDt   70 (517)
T COG4383          51 ERGDLRAQSELFADIEEKDT   70 (517)
T ss_pred             HCCCHHHHHHHHHHHHHHHH
T ss_conf             52355667888755665201


No 4  
>pfam10957 DUF2758 Protein of unknown function (DUF2758). This family of proteins has no known function.
Probab=22.03  E-value=24  Score=17.85  Aligned_cols=16  Identities=44%  Similarity=0.775  Sum_probs=13.2

Q ss_pred             HHHHHHHHHCCCCHHH
Q ss_conf             3342455320532289
Q gi|254780931|r   24 RAQNIFLKDIKDKDII   39 (56)
Q Consensus        24 raqniflkdikdkdii   39 (56)
                      ++-|.|||.|.++++|
T Consensus        17 ~~vN~FLk~i~e~~li   32 (60)
T pfam10957        17 DEVNVFLKKIDDDQLI   32 (60)
T ss_pred             HHHHHHHHHCCCCCEE
T ss_conf             9999999727804479


No 5  
>pfam01736 Polyoma_agno Polyomavirus agnoprotein. This family consist of the DNA binding protein or agnoprotein from various polyomaviruses. This protein is highly basic and can bind single stranded and double stranded DNA. Mutations in the agnoprotein produce smaller viral plaques, hence its function is not essential for growth in tissue culture cells but something has slowed in the normal replication cycle. There is also evidence suggesting that the agnogene and agnoprotein act as regulators of structural protein synthesis.
Probab=17.05  E-value=98  Score=14.46  Aligned_cols=19  Identities=53%  Similarity=0.840  Sum_probs=14.4

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHHHHHH
Q ss_conf             0233424553205322899999999999
Q gi|254780931|r   22 DMRAQNIFLKDIKDKDIIFYLHILIAFE   49 (56)
Q Consensus        22 dmraqniflkdikdkdiifylhiliafe   49 (56)
                      .-|||.||         ||.|..|..|-
T Consensus        22 kkraqrif---------if~lelll~fc   40 (62)
T pfam01736        22 KKRAQRIF---------IFVLELLLQFC   40 (62)
T ss_pred             HHHHHHHH---------HHHHHHHHHHH
T ss_conf             57778899---------99999999983


No 6  
>TIGR00803 nst UDP-galactose transporter; InterPro: IPR004689   Nucleotide-sugar transporters (NSTs) are found in the Golgi apparatus and the endoplasmic reticulum of eukaryotic cells. Members of the family have been sequenced from yeast, protozoans and animals. Animals such as Caenorhabditis elegans possess many of these transporters. Humans have at least two closely related isoforms of the UDP-galactose:UMP exchange transporter.   NSTs generally appear to function by antiport mechanisms, exchanging a nucleotide-sugar for a nucleotide. Thus, CMP-sialic acid is exchanged for CMP; GDP-mannose is preferentially exchanged for GMP, and UDP-galactose and UDP-N-acetylglucosamine are exchanged for UMP (or possibly UDP). Other nucleotide sugars (e.g., GDP-fucose, UDP-xylose, UDP-glucose, UDP-N-acetylgalactosamine, etc.) may also be transported in exchange for various nucleotides, but their transporters have not been molecularly characterised. Each compound appears to be translocated by its own transport protein. Transport allows the compound, synthesized in the cytoplasm, to be exported to the lumen of the Golgi apparatus or the endoplasmic reticulum where it is used for the synthesis of glycoproteins and glycolipids. ; GO: 0005338 nucleotide-sugar transmembrane transporter activity, 0015780 nucleotide-sugar transport, 0016021 integral to membrane.
Probab=15.43  E-value=61  Score=15.61  Aligned_cols=23  Identities=39%  Similarity=0.405  Sum_probs=18.8

Q ss_pred             HHHHHHHHHCCCCHHH-HHHHHHH
Q ss_conf             3342455320532289-9999999
Q gi|254780931|r   24 RAQNIFLKDIKDKDII-FYLHILI   46 (56)
Q Consensus        24 raqniflkdikdkdii-fylhili   46 (56)
                      -+.-+|.|-.||+|.. ||.|++-
T Consensus       102 ~~~~Yf~~~lk~~~~~Pfw~~~l~  125 (235)
T TIGR00803       102 FAGVYFEKILKDKDTSPFWVRNLQ  125 (235)
T ss_pred             HHHHHHHHCCCCCCCCCHHHHHHH
T ss_conf             631024331677778614357889


No 7  
>PHA02105 hypothetical protein
Probab=14.84  E-value=99  Score=14.45  Aligned_cols=18  Identities=39%  Similarity=0.779  Sum_probs=15.8

Q ss_pred             CCCCCHHHHHHHHHHHHH
Q ss_conf             876549999999999975
Q gi|254780931|r    2 DYPCNKEYFKTISTVFGK   19 (56)
Q Consensus         2 dypcnkeyfktistvfgk   19 (56)
                      .||.|.|-|....+||.-
T Consensus        21 eyp~~~e~~~ql~svfsi   38 (68)
T PHA02105         21 EYPVELELFDQLKTVFSI   38 (68)
T ss_pred             CCCCCHHHHHHHHHHCCC
T ss_conf             465207889988876135


No 8  
>TIGR00004 TIGR00004 endoribonuclease L-PSP, putative; InterPro: IPR006056   This family includes proteins encoded by the yabJ gene from Bacillus subtilis that is required for adenine-mediated repression of purine biosynthetic genes in vivo and codes for an acid-soluble, 14-kDa protein. The structure of this protein has been solved  and the protein is found to form a homotrimer. The trimer has a deep cleft that is a probably ligand binding site and possibly forms an enzymatic active site. However the ligand and reaction are unknown..
Probab=13.50  E-value=40  Score=16.63  Aligned_cols=17  Identities=35%  Similarity=0.702  Sum_probs=11.9

Q ss_pred             HHHHHHHHHHHHHHCCC
Q ss_conf             54202334245532053
Q gi|254780931|r   19 KLGDMRAQNIFLKDIKD   35 (56)
Q Consensus        19 klgdmraqniflkdikd   35 (56)
                      .++|.=--++||+||.|
T Consensus        68 ~~~~vVK~TvfL~D~~d   84 (129)
T TIGR00004        68 SLDDVVKTTVFLTDLND   84 (129)
T ss_pred             CCCCEEEEEEEECCHHH
T ss_conf             84666888663026566


No 9  
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=13.12  E-value=66  Score=15.41  Aligned_cols=13  Identities=54%  Similarity=0.869  Sum_probs=9.2

Q ss_pred             HHHHHHHHHHCCC
Q ss_conf             2334245532053
Q gi|254780931|r   23 MRAQNIFLKDIKD   35 (56)
Q Consensus        23 mraqniflkdikd   35 (56)
                      .|.||.|.||||.
T Consensus         5 ~rr~nLF~KDiks   17 (126)
T COG5248           5 ARRVNLFMKDIKS   17 (126)
T ss_pred             HHHHHHHHHHHHH
T ss_conf             6788778889999


No 10 
>pfam11387 DUF2795 Protein of unknown function (DUF2795). This family of proteins has no known function.
Probab=12.11  E-value=95  Score=14.54  Aligned_cols=11  Identities=36%  Similarity=0.782  Sum_probs=8.3

Q ss_pred             CCCCCCHHHHH
Q ss_conf             98765499999
Q gi|254780931|r    1 MDYPCNKEYFK   11 (56)
Q Consensus         1 mdypcnkeyfk   11 (56)
                      +|||.+|+-.-
T Consensus         4 ~~yPa~K~~Lv   14 (44)
T pfam11387         4 VDYPATKDELI   14 (44)
T ss_pred             CCCCCCHHHHH
T ss_conf             99987899999


Done!