Query         gi|254780651|ref|YP_003065064.1| hypothetical protein CLIBASIA_02690 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 30
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Sun May 29 20:41:58 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780651.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK04115 hypothetical protein;  38.6      15 0.00038   19.5   1.2   24    7-30     17-40  (130)
  2 pfam01886 DUF61 Protein of unk  35.9      17 0.00045   19.2   1.2   24    7-30     21-44  (132)
  3 pfam06488 L_lac_phage_MSP Lact  27.5      44  0.0011   17.3   2.1   20    4-23    190-209 (301)
  4 pfam07765 KIP1 KIP1-like prote  19.4      62  0.0016   16.6   1.5   13    2-14     38-50  (74)
  5 pfam08140 Cuticle_1 Crustacean  14.2      80   0.002   16.1   1.0   16   15-30     25-40  (40)
  6 TIGR02562 cas3_yersinia CRISPR  14.1      73  0.0019   16.3   0.8   20    5-24    594-613 (1153)
  7 pfam10830 DUF2553 Protein of u  10.5   1E+02  0.0025   15.6   0.6   16   15-30     40-55  (76)
  8 COG1849 Uncharacterized protei  10.4 1.7E+02  0.0044   14.5   1.8   20    1-20      2-21  (90)
  9 TIGR01933 hflK HflK protein; I   8.8 1.1E+02  0.0028   15.4   0.3   14   16-29      7-20  (285)
 10 COG2952 Uncharacterized protei   8.1 2.4E+02  0.0061   13.8   1.8   12    7-18    131-142 (183)

No 1  
>PRK04115 hypothetical protein; Provisional
Probab=38.63  E-value=15  Score=19.50  Aligned_cols=24  Identities=29%  Similarity=0.275  Sum_probs=16.4

Q ss_pred             HHHHHHHHHHHHCCEEECCCEECC
Q ss_conf             899999999850413346822049
Q gi|254780651|r    7 KRIKGYLKIMESGLVLRNGSFYRF   30 (30)
Q Consensus         7 krikgylkimesglvlrngsfyrf   30 (30)
                      |...--|+--...+++||||+|+|
T Consensus        17 ktL~ELL~ed~P~v~~rdGs~h~~   40 (130)
T PRK04115         17 KTLCELLKEDKPYVILRDGSRHYI   40 (130)
T ss_pred             HHHHHHHHCCCCEEEECCCCEEEE
T ss_conf             469999727698599318956866


No 2  
>pfam01886 DUF61 Protein of unknown function DUF61. Protein found in Archaebacteria. These proteins have no known function.
Probab=35.89  E-value=17  Score=19.20  Aligned_cols=24  Identities=38%  Similarity=0.455  Sum_probs=15.9

Q ss_pred             HHHHHHHHHHHHCCEEECCCEECC
Q ss_conf             899999999850413346822049
Q gi|254780651|r    7 KRIKGYLKIMESGLVLRNGSFYRF   30 (30)
Q Consensus         7 krikgylkimesglvlrngsfyrf   30 (30)
                      |..+--|+--....++||||.|+|
T Consensus        21 ktL~eLL~e~~P~i~lrdGs~h~~   44 (132)
T pfam01886        21 KTLKELLKEDKPYIILRDGSRHYF   44 (132)
T ss_pred             HHHHHHHHCCCCEEEECCCCEEEE
T ss_conf             679999828798599318954755


No 3  
>pfam06488 L_lac_phage_MSP Lactococcus lactis bacteriophage major structural protein. This family consists of several Lactococcus lactis bacteriophage major structural proteins.
Probab=27.55  E-value=44  Score=17.30  Aligned_cols=20  Identities=40%  Similarity=0.664  Sum_probs=16.9

Q ss_pred             HHHHHHHHHHHHHHHCCEEE
Q ss_conf             47889999999985041334
Q gi|254780651|r    4 SFGKRIKGYLKIMESGLVLR   23 (30)
Q Consensus         4 sfgkrikgylkimesglvlr   23 (30)
                      -+|...|.+.|-|||||.+-
T Consensus       190 iwgeqakdfakkmesglfi~  209 (301)
T pfam06488       190 IWGEQAKDFAKKMESGLFII  209 (301)
T ss_pred             HHHHHHHHHHHHHHCCEEEE
T ss_conf             24577789998754562796


No 4  
>pfam07765 KIP1 KIP1-like protein. This is a family of sequences found exclusively in plants. They are similar to kinase interacting protein 1 (KIP1), which has been found to interact with the kinase domain of PRK1, a receptor-like kinase. This particular region contains two coiled-coils, which are described as motifs involved in protein-protein interactions. It has also been suggested that the protein's coiled- coils allow it to dimerize in vivo.
Probab=19.39  E-value=62  Score=16.60  Aligned_cols=13  Identities=62%  Similarity=0.835  Sum_probs=10.1

Q ss_pred             CHHHHHHHHHHHH
Q ss_conf             5047889999999
Q gi|254780651|r    2 ADSFGKRIKGYLK   14 (30)
Q Consensus         2 adsfgkrikgylk   14 (30)
                      +|||.||-..|.+
T Consensus        38 gdSfakrAemyy~   50 (74)
T pfam07765        38 ADSFAKRAEMYYK   50 (74)
T ss_pred             CCCHHHHHHHHHH
T ss_conf             5418999999983


No 5  
>pfam08140 Cuticle_1 Crustacean cuticle protein repeat. This family consists of the cuticle proteins from the Cancer pagurus and the Homarus americanus. These proteins are isolated from the calcified regions of the crustacean and they contain two copies of an 18 residue sequence motif, which thus far has been found only in crustacean calcified exoskeletons.
Probab=14.17  E-value=80  Score=16.06  Aligned_cols=16  Identities=44%  Similarity=0.584  Sum_probs=12.1

Q ss_pred             HHHHCCEEECCCEECC
Q ss_conf             9850413346822049
Q gi|254780651|r   15 IMESGLVLRNGSFYRF   30 (30)
Q Consensus        15 imesglvlrngsfyrf   30 (30)
                      +-+||.|+.||..-.|
T Consensus        25 ~GpSG~V~sdG~nvQf   40 (40)
T pfam08140        25 IGPSGAVLSDGKNVQF   40 (40)
T ss_pred             ECCCEEEEECCCEECC
T ss_conf             7684259768838029


No 6  
>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3, Yersinia-type; InterPro: IPR013395    The helicase encoded in many CRISPR-associated (cas) gene clusters is designated Cas3. The Yersinia-type helicase Cas3 proteins differ from the more common Cas3 proteins by being considerably larger, though they still share a number of motifs, and replace Cas3 in some CRISPR/cas loci in a number of Proteobacteria, including Yersinia pestis, Chromobacterium violaceum, Erwinia carotovora subsp. atroseptica SCRI1043, Photorhabdus luminescens subsp. laumondii TTO1, Legionella pneumophila, etc..
Probab=14.07  E-value=73  Score=16.26  Aligned_cols=20  Identities=30%  Similarity=0.516  Sum_probs=17.5

Q ss_pred             HHHHHHHHHHHHHHCCEEEC
Q ss_conf             78899999999850413346
Q gi|254780651|r    5 FGKRIKGYLKIMESGLVLRN   24 (30)
Q Consensus         5 fgkrikgylkimesglvlrn   24 (30)
                      =|+.|+--|.||-|-|||-.
T Consensus       594 gG~~i~p~LRllsSDLiLDE  613 (1153)
T TIGR02562       594 GGHHIAPMLRLLSSDLILDE  613 (1153)
T ss_pred             CCEEHHHHHHHHHHHHEECC
T ss_conf             56107889987532320048


No 7  
>pfam10830 DUF2553 Protein of unknown function (DUF2553). This family of bacterial proteins has no known function.
Probab=10.46  E-value=1e+02  Score=15.61  Aligned_cols=16  Identities=31%  Similarity=0.744  Sum_probs=13.3

Q ss_pred             HHHHCCEEECCCEECC
Q ss_conf             9850413346822049
Q gi|254780651|r   15 IMESGLVLRNGSFYRF   30 (30)
Q Consensus        15 imesglvlrngsfyrf   30 (30)
                      .|++|.+..++.|||.
T Consensus        40 ~L~~GY~~e~~K~yr~   55 (76)
T pfam10830        40 ELKSGYSFEDGKFYKT   55 (76)
T ss_pred             EECCCCEEECCEEEEE
T ss_conf             8638855508889998


No 8  
>COG1849 Uncharacterized protein conserved in archaea [Function unknown]
Probab=10.44  E-value=1.7e+02  Score=14.48  Aligned_cols=20  Identities=30%  Similarity=0.763  Sum_probs=16.1

Q ss_pred             CCHHHHHHHHHHHHHHHHCC
Q ss_conf             95047889999999985041
Q gi|254780651|r    1 MADSFGKRIKGYLKIMESGL   20 (30)
Q Consensus         1 madsfgkrikgylkimesgl   20 (30)
                      |++-...||.-|++++|..|
T Consensus         2 ~~~~l~ekiekYi~~leeaL   21 (90)
T COG1849           2 MAEELAEKIEKYIELLEEAL   21 (90)
T ss_pred             CHHHHHHHHHHHHHHHHHHH
T ss_conf             27899999999999899999


No 9  
>TIGR01933 hflK HflK protein; InterPro: IPR010201   The accumulation of abnormal membrane proteins is something which must be avoided in order to maintain cell viability. In Escherichia coli, the membrane-bound, ATP-dependent protease FtsH plays a central role in the degradation of these abnormal proteins . Known substrates of this protease include several lambda bacteriophage proteins, the heat-shock transcription factor sigma-32, and the unassembled form of the membrane protein SecY. While FtsH is active as a protease on its own, in vivo it forms a complex with a membrane-bound HflKC heterodimer. HflKC has a generally inhibitory effect on the protease activity of FtsH, though the mechanism of this inhibition is not known. The HflK and HflC polypeptides are paralogous, and often encoded by tandem genes within bacterial genomes.   This entry represents the HflK subunit of the HflKC heterodimer.; GO: 0005515 protein binding, 0016021 integral to membrane.
Probab=8.78  E-value=1.1e+02  Score=15.41  Aligned_cols=14  Identities=50%  Similarity=0.819  Sum_probs=9.3

Q ss_pred             HHHCCEEECCCEEC
Q ss_conf             85041334682204
Q gi|254780651|r   16 MESGLVLRNGSFYR   29 (30)
Q Consensus        16 mesglvlrngsfyr   29 (30)
                      -|.|.|||=|.|.|
T Consensus         7 ~e~gVVlRfGk~~~   20 (285)
T TIGR01933         7 AERGVVLRFGKYHR   20 (285)
T ss_pred             CCCCEEECCCCHHH
T ss_conf             33604510331022


No 10 
>COG2952 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=8.13  E-value=2.4e+02  Score=13.82  Aligned_cols=12  Identities=67%  Similarity=0.861  Sum_probs=9.2

Q ss_pred             HHHHHHHHHHHH
Q ss_conf             899999999850
Q gi|254780651|r    7 KRIKGYLKIMES   18 (30)
Q Consensus         7 krikgylkimes   18 (30)
                      +-|-|||||-|+
T Consensus       131 ~si~~yLKIyE~  142 (183)
T COG2952         131 KSIDTYLKIYES  142 (183)
T ss_pred             HHHHHHHHHHHH
T ss_conf             999999999999


Done!