Query         gi|254780962|ref|YP_003065375.1| hypothetical protein CLIBASIA_04315 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 49
No_of_seqs    2 out of 4
Neff          1.1 
Searched_HMMs 39220
Date          Mon May 30 02:36:42 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780962.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR01848 PHA_reg_PhaR polyhyd  54.3     6.9 0.00018   21.1   1.5   15    5-19     30-44  (109)
  2 cd06414 GH25_LytC-like The Lyt  34.8      21 0.00055   18.6   1.5   34    2-36     17-50  (191)
  3 cd06416 GH25_Lys1-like Lys-1 i  30.9      30 0.00077   17.8   1.7   31    2-36     17-47  (196)
  4 cd06525 GH25_Lyc-like Lyc mura  17.2      79   0.002   15.7   1.7   32    2-37     16-47  (184)
  5 cd06419 GH25_muramidase_2 Unch  17.2      87  0.0022   15.5   1.9   31    2-36     24-54  (190)
  6 COG3099 Uncharacterized protei  16.4      59  0.0015   16.4   0.8   41    5-47     44-96  (108)
  7 smart00641 Glyco_25 Glycosyl h  15.5 1.3E+02  0.0032   14.7   2.7   30    2-35     17-46  (109)
  8 cd06412 GH25_CH-type CH-type (  15.2      88  0.0023   15.4   1.5   31    2-36     17-47  (199)
  9 pfam07279 DUF1442 Protein of u  14.0      94  0.0024   15.3   1.4   16    5-20    113-128 (218)
 10 cd06413 GH25_muramidase_1 Unch  13.7 1.2E+02  0.0032   14.7   1.9   32    2-37     19-50  (191)

No 1  
>TIGR01848 PHA_reg_PhaR polyhydroxyalkanoate synthesis repressor PhaR; InterPro: IPR010134   This entry identifies the polyhydroxyalkanoate synthesis repressor, PhaR and related proteins. The gene for PhaR regulatory protein is found in general near other genes encoding proteins associated with polyhydroxyalkanoate (PHA) granule biosynthesis and utilization. It is found to be a DNA-binding homotetramer that is also capable of binding short chain hydroxyalkanoic acids and PHA granules. PhaR may regulate the expression of itself, of the phasins that coat granules, and of enzymes that direct carbon flux into polymers stored in granules. The C-terminal region is poorly conserved in this family of proteins..
Probab=54.33  E-value=6.9  Score=21.11  Aligned_cols=15  Identities=47%  Similarity=0.678  Sum_probs=13.1

Q ss_pred             CCCCEEEEEECCCCC
Q ss_conf             678509999514441
Q gi|254780962|r    5 NSGAEFVLIDAKSDG   19 (49)
Q Consensus         5 nsgaefvlidak~d~   19 (49)
                      -+|.||..+|||++-
T Consensus        30 ~~G~ef~V~D~Ksg~   44 (109)
T TIGR01848        30 VEGREFKVVDAKSGD   44 (109)
T ss_pred             HCCCCEEEEECCCCC
T ss_conf             279870687547898


No 2  
>cd06414 GH25_LytC-like The LytC lysozyme of Streptococcus pneumoniae is a bacterial cell wall hydrolase that cleaves the beta1-4-glycosydic bond located between the N-acetylmuramoyl-N-glucosaminyl residues of the cell wall polysaccharide chains.   LytC is composed of a C-terminal glycosyl hydrolase family 25 (GH25) domain and an N-terminal choline-binding module (CBM) consisting of eleven homologous repeats that specifically recognizes the choline residues of pneumococcal lipoteichoic and teichoic acids. This domain arrangement is the reverse of the major pneumococcal autolysin, LytA, and the CPL-1-like lytic enzymes of the pneumococcal bacteriophages, in which the CBM (consisting of six repeats) is at the C-terminus. This model represents the C-terminal catalytic domain of the LytC-like enzymes.
Probab=34.79  E-value=21  Score=18.58  Aligned_cols=34  Identities=29%  Similarity=0.346  Sum_probs=24.1

Q ss_pred             CCCCCCCEEEEEECCCCCHHHCCCCCCHHHHHHHH
Q ss_conf             60367850999951444122225447401245588
Q gi|254780962|r    2 AIKNSGAEFVLIDAKSDGYKHLGFKKPIFKNNIME   36 (49)
Q Consensus         2 aiknsgaefvlidak~d~~khlgfkkpifknnime   36 (49)
                      ++|++|.+||.|-| +.+.....+..|-|.+|+-+
T Consensus        17 ~vk~~gv~fviiKa-s~gteg~~~~D~~~~~n~~~   50 (191)
T cd06414          17 KVKASGVDFAIIRA-GYGGYGELQEDKYFEENIKG   50 (191)
T ss_pred             HHHHCCCCEEEEEE-CCCCCCCCEECHHHHHHHHH
T ss_conf             99877994999996-13667872148789999999


No 3  
>cd06416 GH25_Lys1-like Lys-1 is a lysozyme encoded by the Caenorhabditis elegans lys-1 gene. This gene is one of a several lysozyme genes upregulated upon infection by the Gram-negative bacterial pathogen Serratia marcescens.  Lys-1 contains a glycosyl hydrolase family 25 (GH25) catalytic domain.  This family also includes Lys-5 from Caenorhabditis elegans.
Probab=30.93  E-value=30  Score=17.83  Aligned_cols=31  Identities=32%  Similarity=0.389  Sum_probs=23.4

Q ss_pred             CCCCCCCEEEEEECCCCCHHHCCCCCCHHHHHHHH
Q ss_conf             60367850999951444122225447401245588
Q gi|254780962|r    2 AIKNSGAEFVLIDAKSDGYKHLGFKKPIFKNNIME   36 (49)
Q Consensus         2 aiknsgaefvlidak~d~~khlgfkkpifknnime   36 (49)
                      ++|++|.+|+.|.|...    .|+.-|-|+.|+-.
T Consensus        17 ~vk~~G~~faiIra~eg----~~~~D~~~~~n~~~   47 (196)
T cd06416          17 CLKNNGYSFAIIRAYRS----NGSFDPNSVTNIKN   47 (196)
T ss_pred             HHHHCCCEEEEEEEECC----CCCCCHHHHHHHHH
T ss_conf             99987983999999756----99578448999999


No 4  
>cd06525 GH25_Lyc-like Lyc muramidase is an autolytic lysozyme (autolysin) from Clostridium acetobutylicum encoded by the lyc gene.  Lyc has a glycosyl hydrolase family 25 (GH25) catalytic domain.  Endo-N-acetylmuramidases are lysozymes (also referred to as peptidoglycan hydrolases) that degrade bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues.
Probab=17.23  E-value=79  Score=15.69  Aligned_cols=32  Identities=38%  Similarity=0.546  Sum_probs=24.1

Q ss_pred             CCCCCCCEEEEEECCCCCHHHCCCCCCHHHHHHHHH
Q ss_conf             603678509999514441222254474012455887
Q gi|254780962|r    2 AIKNSGAEFVLIDAKSDGYKHLGFKKPIFKNNIMEN   37 (49)
Q Consensus         2 aiknsgaefvlidak~d~~khlgfkkpifknnimen   37 (49)
                      ++|.+|.+||.|-+-. |   -.+..|-|++|+-+-
T Consensus        16 ~~k~~Gv~fviiKate-G---~~~~D~~~~~n~~~a   47 (184)
T cd06525          16 AVKDSGVEVVYIKATE-G---TTFVDSYFNENYNGA   47 (184)
T ss_pred             HHHHCCCCEEEEEEEC-C---CCCCCHHHHHHHHHH
T ss_conf             9997799599999973-9---986385789999999


No 5  
>cd06419 GH25_muramidase_2 Uncharacterized bacterial muramidase containing a glycosyl hydrolase family 25 (GH25) catalytic domain.  Endo-N-acetylmuramidases are lysozymes (also referred to as peptidoglycan hydrolases) that degrade bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues.
Probab=17.21  E-value=87  Score=15.48  Aligned_cols=31  Identities=19%  Similarity=0.394  Sum_probs=23.4

Q ss_pred             CCCCCCCEEEEEECCCCCHHHCCCCCCHHHHHHHH
Q ss_conf             60367850999951444122225447401245588
Q gi|254780962|r    2 AIKNSGAEFVLIDAKSDGYKHLGFKKPIFKNNIME   36 (49)
Q Consensus         2 aiknsgaefvlidak~d~~khlgfkkpifknnime   36 (49)
                      ++|++|.+||.|-|..-    ..|.-|-|..|.-.
T Consensus        24 ~vk~~gi~Fv~iKATEG----~~~~D~~f~~n~~~   54 (190)
T cd06419          24 SLQSNGISFVYLRATQG----ASYFDDNFLSNFSR   54 (190)
T ss_pred             HHHHCCCEEEEEEEECC----CCCCCHHHHHHHHH
T ss_conf             99868982999995079----87578679999999


No 6  
>COG3099 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=16.41  E-value=59  Score=16.36  Aligned_cols=41  Identities=32%  Similarity=0.699  Sum_probs=26.1

Q ss_pred             CCCCEEEEEECCCCCHHHCCCCC-C-HH----------HHHHHHHHHHHHHHHHC
Q ss_conf             67850999951444122225447-4-01----------24558877543343340
Q gi|254780962|r    5 NSGAEFVLIDAKSDGYKHLGFKK-P-IF----------KNNIMENMIGRMSLRRE   47 (49)
Q Consensus         5 nsgaefvlidak~d~~khlgfkk-p-if----------knnimenmig~mslrre   47 (49)
                      ..|||||  |...||..|.||.- | +|          .|..|.....||-+.|+
T Consensus        44 RGgaElv--d~adDW~e~vgf~idpe~yAEV~iGLvnee~de~dDVFAr~Lisr~   96 (108)
T COG3099          44 RGGAELV--DPADDWQEHVGFDIDPEFYAEVVIGLVNEEDDEIDDVFARFLISRE   96 (108)
T ss_pred             CCCEEEE--CCCHHHHHHCCCCCCHHHHHHEEEEEECCCCCHHHHHHHHHHHCCC
T ss_conf             5881642--5311178740951387673103676303655528899999986238


No 7  
>smart00641 Glyco_25 Glycosyl hydrolases family 25.
Probab=15.50  E-value=1.3e+02  Score=14.67  Aligned_cols=30  Identities=23%  Similarity=0.635  Sum_probs=22.8

Q ss_pred             CCCCCCCEEEEEECCCCCHHHCCCCCCHHHHHHH
Q ss_conf             6036785099995144412222544740124558
Q gi|254780962|r    2 AIKNSGAEFVLIDAKSDGYKHLGFKKPIFKNNIM   35 (49)
Q Consensus         2 aiknsgaefvlidak~d~~khlgfkkpifknnim   35 (49)
                      +.+|+|+.|+.|+|-..    -+++-|.|.-|..
T Consensus        17 ~v~~~g~~fa~iKateG----~~y~d~~f~~~~~   46 (109)
T smart00641       17 KVRNTGASFAFMKATEG----AGYTPPYYSYQYF   46 (109)
T ss_pred             HHHCCCCEEEEEEEECC----CCCCCCCHHHHHH
T ss_conf             53058975998771215----9965911788899


No 8  
>cd06412 GH25_CH-type CH-type (Chalaropsis-type) lysozymes represent one of four functionally-defined classes of peptidoglycan hydrolases (also referred to as endo-N-acetylmuramidases) that cleave bacterial cell wall peptidoglycans.  CH-type lysozymes exhibit both lysozyme (acetylmuramidase) and diacetylmuramidase activity. The first member of this family to be described was a muramidase from the fungus Chalaropsis.  However, a majority of the CH-type lysozymes are found in bacteriophages and Gram-positive bacteria such as Streptomyces and Clostridium.  CH-type lysozymes have a single glycosyl hydrolase family 25 (GH25) domain with an unusual beta/alpha-barrel fold in which the last strand of the barrel is antiparallel to strands beta7 and beta1.  Most CH-type lysozymes appear to lack the cell wall-binding domain found in other GH25 muramidases.
Probab=15.19  E-value=88  Score=15.45  Aligned_cols=31  Identities=23%  Similarity=0.507  Sum_probs=23.2

Q ss_pred             CCCCCCCEEEEEECCCCCHHHCCCCCCHHHHHHHH
Q ss_conf             60367850999951444122225447401245588
Q gi|254780962|r    2 AIKNSGAEFVLIDAKSDGYKHLGFKKPIFKNNIME   36 (49)
Q Consensus         2 aiknsgaefvlidak~d~~khlgfkkpifknnime   36 (49)
                      ++|++|..||.|-|. +|   .++..|-|..|+-+
T Consensus        17 ~vk~~gv~FaiiKat-eG---~~~~D~~~~~n~~~   47 (199)
T cd06412          17 GAAANGARFAYVKAT-EG---TSYTNPRFSSQYNG   47 (199)
T ss_pred             HHHHCCCCEEEEEEE-CC---CCCCCHHHHHHHHH
T ss_conf             998689949999985-69---87538679999999


No 9  
>pfam07279 DUF1442 Protein of unknown function (DUF1442). This family consists of several hypothetical Arabidopsis thaliana proteins of around 225 residues in length. The function of this family is unknown.
Probab=14.02  E-value=94  Score=15.32  Aligned_cols=16  Identities=25%  Similarity=0.609  Sum_probs=12.8

Q ss_pred             CCCCEEEEEECCCCCH
Q ss_conf             6785099995144412
Q gi|254780962|r    5 NSGAEFVLIDAKSDGY   20 (49)
Q Consensus         5 nsgaefvlidak~d~~   20 (49)
                      -+|+.|++||.|..-+
T Consensus       113 ~~~vDF~vVDck~~e~  128 (218)
T pfam07279       113 LQGVDFLVVDWKRKEF  128 (218)
T ss_pred             CCCCCEEEEECCCHHH
T ss_conf             5578789984422678


No 10 
>cd06413 GH25_muramidase_1 Uncharacterized bacterial muramidase containing a glycosyl hydrolase family 25 (GH25) catalytic domain.  Endo-N-acetylmuramidases are lysozymes (also referred to as peptidoglycan hydrolases) that degrade bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues.
Probab=13.70  E-value=1.2e+02  Score=14.70  Aligned_cols=32  Identities=22%  Similarity=0.354  Sum_probs=23.7

Q ss_pred             CCCCCCCEEEEEECCCCCHHHCCCCCCHHHHHHHHH
Q ss_conf             603678509999514441222254474012455887
Q gi|254780962|r    2 AIKNSGAEFVLIDAKSDGYKHLGFKKPIFKNNIMEN   37 (49)
Q Consensus         2 aiknsgaefvlidak~d~~khlgfkkpifknnimen   37 (49)
                      ++|++|..||.|-|. +|.   ++..|-|..|+.+-
T Consensus        19 ~vk~~gi~fviiKat-eG~---~~~D~~~~~n~~~a   50 (191)
T cd06413          19 RVRAQGVSFAYIKAT-EGG---DHVDKRFAENWRGA   50 (191)
T ss_pred             HHHHCCCCEEEEEEE-ECC---CCCCHHHHHHHHHH
T ss_conf             999779989999997-088---87486899999999


Done!