Query         gi|255764504|ref|YP_003064930.2| DNA-methyltransferase MKpn2kI [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 101
No_of_seqs    120 out of 974
Neff          6.3 
Searched_HMMs 39220
Date          Mon May 30 00:37:44 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 255764504.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK10458 DNA cytosine methylas 100.0 2.7E-31   7E-36  199.1   7.9  100    1-101   271-379 (470)
  2 TIGR00675 dcm DNA-cytosine met  99.8 1.9E-20 4.8E-25  137.4   5.8   98    1-98    165-311 (425)
  3 pfam00145 DNA_methylase C-5 cy  99.3 1.3E-11 3.4E-16   87.1   6.8   76    1-76    141-224 (319)
  4 cd00315 Cyt_C5_DNA_methylase C  99.1 1.3E-10 3.3E-15   81.4   5.9   44    1-44    143-189 (275)
  5 COG0270 Dcm Site-specific DNA   99.0   2E-10 5.2E-15   80.3   4.2   30    1-30    147-176 (328)
  6 KOG0919 consensus               83.1    0.33 8.4E-06   27.9   0.1   55    1-57    149-219 (338)
  7 smart00151 SWIB SWI complex, B  62.6     3.2 8.2E-05   22.2   0.9   43   29-71      1-43  (77)
  8 LOAD_swib consensus             51.9     6.2 0.00016   20.6   0.9   44   28-71      8-51  (85)
  9 pfam02201 SWIB SWIB/MDM2 domai  38.8      13 0.00033   18.8   0.9   44   29-72      1-44  (76)
 10 COG4386 Mu-like prophage tail   33.9      27  0.0007   16.9   1.9   17    6-22     28-44  (487)
 11 TIGR01289 LPOR light-dependent  27.4      24 0.00061   17.3   0.7   35    8-42    131-166 (321)
 12 pfam00863 Peptidase_C4 Peptida  23.0      68  0.0017   14.7   2.4   18    4-21     98-115 (233)
 13 COG0400 Predicted esterase [Ge  22.2      45  0.0012   15.7   1.3   20    2-23     90-109 (207)

No 1  
>PRK10458 DNA cytosine methylase; Provisional
Probab=99.97  E-value=2.7e-31  Score=199.13  Aligned_cols=100  Identities=36%  Similarity=0.705  Sum_probs=87.4

Q ss_pred             CCHHHCCCCCCCCEEEEEEEECCC---CCCCCCCC----CCCCCCHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             983435797376279999984788---87558887----77777844531256774323468899889978765553201
Q gi|255764504|r    1 MKACDFGVPQRRERLYIIDFLNPS---VEFKFPTP----LGIKPRLGDILEEHIDDKSTISNKLWEGHQKRKENNKIAGK   73 (101)
Q Consensus         1 Lna~dfGvPQ~ReRvfiVg~~~~~---~~f~~P~~----~~~~~~l~diL~~~vd~k~~ls~~~~~~l~~~~~~~k~~g~   73 (101)
                      |||+|| |||||||||||||+++.   ..|+++..    +...+.+.|+|++.|+++|++|+++|+++.+++.+|+.+|+
T Consensus       271 LNskdF-VPQnRERIfIVGFrkdl~~~~~F~l~d~~~~fP~k~~~l~diLe~~vd~KY~lS~kl~~~l~~~~~kh~~kgn  349 (470)
T PRK10458        271 IDGKHF-LPQHRERIVLVGFRRDLNLKADFTLRDISRCYPAQRPTLAELLDPVVDAKYILTPVLWKYLYRYAKKHQARGN  349 (470)
T ss_pred             ECCCCC-CCCCCCEEEEEEEECCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCEEECHHHHHHHHHHHHHHHHCCC
T ss_conf             315667-8888767999998056554457663431211898888520124366787434676788999999999874257


Q ss_pred             CCCCEEECCC--CCCCCCEEECCCCCCCCC
Q ss_conf             3552043488--775033010403587639
Q gi|255764504|r   74 GFGYGLFFEN--SATTNTLSARYYKDGSEI  101 (101)
Q Consensus        74 GFg~~~~~~~--~~~~~Ti~arY~Kdg~e~  101 (101)
                      |||++++++.  +.+|+||+|||||||+||
T Consensus       350 GfGyg~v~~~n~~~v~rTLsARy~kdGseI  379 (470)
T PRK10458        350 GFGYGLVYPNNPESVTRTLSARYYKDGAEI  379 (470)
T ss_pred             CCCCCEECCCCCCCCCCEEECCCCCCCCEE
T ss_conf             766413656766665520112446898603


No 2  
>TIGR00675 dcm DNA-cytosine methyltransferase; InterPro: IPR001525 C-5 cytosine-specific DNA methylases (2.1.1.73 from EC) (C5 Mtase) are enzymes that specifically methylate the C-5 carbon of cytosines in DNA to produce C5-methylcytosine , , . In mammalian cells, cytosine-specific methyltransferases methylate certain CpG sequences, which are believed to modulate gene expression and cell differentiation. In bacteria, these enzymes are a component of restriction-modification systems and serve as valuable tools for the manipulation of DNA , . The structure of HhaI methyltransferase (M.HhaI) has been resolved to 2.5 A : the molecule folds into 2 domains - a larger catalytic domain containing catalytic and cofactor binding sites, and a smaller DNA recognition domain.; GO: 0003677 DNA binding, 0006306 DNA methylation.
Probab=99.81  E-value=1.9e-20  Score=137.45  Aligned_cols=98  Identities=39%  Similarity=0.701  Sum_probs=80.7

Q ss_pred             CCHHHCC-CCCCCCEEEEEEEE----------CC--CCCCCCCCC------CCCCCCHHHHHCCCC--CCCCCCCHHHHH
Q ss_conf             9834357-97376279999984----------78--887558887------777778445312567--743234688998
Q gi|255764504|r    1 MKACDFG-VPQRRERLYIIDFL----------NP--SVEFKFPTP------LGIKPRLGDILEEHI--DDKSTISNKLWE   59 (101)
Q Consensus         1 Lna~dfG-vPQ~ReRvfiVg~~----------~~--~~~f~~P~~------~~~~~~l~diL~~~v--d~k~~ls~~~~~   59 (101)
                      |||+||| |||+||||||||||          +.  ...|+||.|      ......++|+|+..+  |.+|++|+..|+
T Consensus       165 LNa~dFGNvPQ~ReRiyIvG~r~~~~~~~~~~~~~~~~~F~fP~p~~~~~~~~~~~~~~d~~~~~~~~~~k~~~~~~~~~  244 (425)
T TIGR00675       165 LNAKDFGNVPQNRERIYIVGFRKDLPKLKESTDFDDKLNFEFPKPIELKGKVAKKKRIGDLLDKSVDLEEKYYLSEEKKN  244 (425)
T ss_pred             HHHHHCCCCCCCEEEEEEEEEECCCCHHHHHHHHHCCCCCCCCCCHHHCCCCCCCCEECCCCCCCCCCCCCCCCCHHHHH
T ss_conf             61665178766505899998514520122221011032457887333304432120113221345665655442489987


Q ss_pred             HHHHHHHHHHHH---------------HCCCCCE-------EECCC--CCCCCCEEE----CCCCCC
Q ss_conf             899787655532---------------0135520-------43488--775033010----403587
Q gi|255764504|r   60 GHQKRKENNKIA---------------GKGFGYG-------LFFEN--SATTNTLSA----RYYKDG   98 (101)
Q Consensus        60 ~l~~~~~~~k~~---------------g~GFg~~-------~~~~~--~~~~~Ti~a----rY~Kdg   98 (101)
                      ++....+.+...               +.++++.       +....  +..+.||++    |||+++
T Consensus       245 ~~~~~~~~~~~~~~~~~~~~~W~Dg~~~~~~~~~~~n~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  311 (425)
T TIGR00675       245 GLLLLLENMRKKEGSLAKILIWMDGRVGTGEQLGSENVDDGFYNRESKSSILRTLSADKIKKYYLEG  311 (425)
T ss_pred             HHHHHHHCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCC
T ss_conf             6765442044112641330000034103322234332235421688801005653164312111235


No 3  
>pfam00145 DNA_methylase C-5 cytosine-specific DNA methylase.
Probab=99.26  E-value=1.3e-11  Score=87.06  Aligned_cols=76  Identities=39%  Similarity=0.738  Sum_probs=53.4

Q ss_pred             CCHHHCCCCCCCCEEEEEEEECCCC------CCCCCCCCCCCCCHHHHHCCC--CCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             9834357973762799999847888------755888777777844531256--77432346889988997876555320
Q gi|255764504|r    1 MKACDFGVPQRRERLYIIDFLNPSV------EFKFPTPLGIKPRLGDILEEH--IDDKSTISNKLWEGHQKRKENNKIAG   72 (101)
Q Consensus         1 Lna~dfGvPQ~ReRvfiVg~~~~~~------~f~~P~~~~~~~~l~diL~~~--vd~k~~ls~~~~~~l~~~~~~~k~~g   72 (101)
                      |||+||||||+|+|+||||++++..      .+.+|.+......+.|+++..  .+.++.++...+.........+...+
T Consensus       141 lna~dyGvPQ~R~R~fiig~r~~~~~~~~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  220 (319)
T pfam00145       141 LNASDYGVPQNRERVFIVGIRNDLILNFPVPEFDFPKPSTATDTIRDLLEEPSLDENKYNLSDKFVENHERRKPTTKAPG  220 (319)
T ss_pred             CCHHHCCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCC
T ss_conf             77888089876418999998167555568885558888640021656303567765454244545444666310367777


Q ss_pred             CCCC
Q ss_conf             1355
Q gi|255764504|r   73 KGFG   76 (101)
Q Consensus        73 ~GFg   76 (101)
                      .+++
T Consensus       221 ~~~~  224 (319)
T pfam00145       221 GGYP  224 (319)
T ss_pred             CCCC
T ss_conf             7743


No 4  
>cd00315 Cyt_C5_DNA_methylase Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the mammalian genome. These effects include transcriptional repression via inhibition of transcription factor binding or the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability.
Probab=99.11  E-value=1.3e-10  Score=81.41  Aligned_cols=44  Identities=43%  Similarity=0.689  Sum_probs=32.0

Q ss_pred             CCHHHCCCCCCCCEEEEEEEECCCCCCC---CCCCCCCCCCHHHHHC
Q ss_conf             9834357973762799999847888755---8887777778445312
Q gi|255764504|r    1 MKACDFGVPQRRERLYIIDFLNPSVEFK---FPTPLGIKPRLGDILE   44 (101)
Q Consensus         1 Lna~dfGvPQ~ReRvfiVg~~~~~~~f~---~P~~~~~~~~l~diL~   44 (101)
                      |||+||||||+|+|+||||++++.....   +|.+.....+++|+|.
T Consensus       143 l~a~~~GvPQ~R~R~fiva~~~~~~~~~~~~~~~~~~~~~~~~d~~~  189 (275)
T cd00315         143 LNASDYGVPQNRERVFIIGIRKDLILNFFSPFPKPSEKKKTLKDILR  189 (275)
T ss_pred             ECHHHCCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHHHC
T ss_conf             67999799977618999988688775556778888566575999860


No 5  
>COG0270 Dcm Site-specific DNA methylase [DNA replication, recombination, and repair]
Probab=99.03  E-value=2e-10  Score=80.31  Aligned_cols=30  Identities=37%  Similarity=0.804  Sum_probs=25.2

Q ss_pred             CCHHHCCCCCCCCEEEEEEEECCCCCCCCC
Q ss_conf             983435797376279999984788875588
Q gi|255764504|r    1 MKACDFGVPQRRERLYIIDFLNPSVEFKFP   30 (101)
Q Consensus         1 Lna~dfGvPQ~ReRvfiVg~~~~~~~f~~P   30 (101)
                      |||+||||||+||||||||++++...+.+.
T Consensus       147 lna~dyGvPQ~ReRvfiig~~~~~~~~~~~  176 (328)
T COG0270         147 LNAADYGVPQSRERVFIVGFRRDNIDLDPN  176 (328)
T ss_pred             ECHHHCCCCCCCCEEEEEEECCCCCCCCCC
T ss_conf             039885999865379999743665444533


No 6  
>KOG0919 consensus
Probab=83.10  E-value=0.33  Score=27.85  Aligned_cols=55  Identities=29%  Similarity=0.599  Sum_probs=36.6

Q ss_pred             CCHHHCCCCCCCCEEEEEEEECCCCCCCCCC---------------CCCCCCCHHHHHCCCCCCCCCCC-HHH
Q ss_conf             9834357973762799999847888755888---------------77777784453125677432346-889
Q gi|255764504|r    1 MKACDFGVPQRRERLYIIDFLNPSVEFKFPT---------------PLGIKPRLGDILEEHIDDKSTIS-NKL   57 (101)
Q Consensus         1 Lna~dfGvPQ~ReRvfiVg~~~~~~~f~~P~---------------~~~~~~~l~diL~~~vd~k~~ls-~~~   57 (101)
                      |...-||||-.|-|.|.++-+.  .+|.||-               .....+.+.|+||.++|...|+- +..
T Consensus       149 LsPtqfniPNsR~Ryy~iArl~--~~F~~~G~~s~d~~~qFseiaqk~g~Vk~i~d~lE~~~d~s~ylvp~~v  219 (338)
T KOG0919         149 LSPTQFNIPNSRYRYYCIARLG--ADFPFAGGKSWDEMPQFSEIAQKQGLVKQIADILEENVDPSDYLVPDDV  219 (338)
T ss_pred             CCCCCCCCCCCCHHEEEHHHHC--CCCCCCCCCCCCCCCCHHHHHHHCCHHHHHHHHHHHCCCHHHCCCCHHH
T ss_conf             3611258987300012034407--9887889864024510589987503699999998723899881087889


No 7  
>smart00151 SWIB SWI complex, BAF60b domains.
Probab=62.57  E-value=3.2  Score=22.24  Aligned_cols=43  Identities=16%  Similarity=0.339  Sum_probs=34.6

Q ss_pred             CCCCCCCCCCHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             8887777778445312567743234688998899787655532
Q gi|255764504|r   29 FPTPLGIKPRLGDILEEHIDDKSTISNKLWEGHQKRKENNKIA   71 (101)
Q Consensus        29 ~P~~~~~~~~l~diL~~~vd~k~~ls~~~~~~l~~~~~~~k~~   71 (101)
                      ||+|......|..+|.......--+..++|+|++.+...+...
T Consensus         1 ~~kp~~lS~~La~~lG~~~~sR~~v~k~lw~YIK~n~Lqdp~n   43 (77)
T smart00151        1 ITKKVTLSPELAKVLGAPEMTRTEIIKRLWEYIKEHNLQDPQN   43 (77)
T ss_pred             CCCCCCCCHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             9988668999999878886669999999999999817988766


No 8  
>LOAD_swib consensus
Probab=51.88  E-value=6.2  Score=20.59  Aligned_cols=44  Identities=18%  Similarity=0.350  Sum_probs=34.3

Q ss_pred             CCCCCCCCCCCHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             58887777778445312567743234688998899787655532
Q gi|255764504|r   28 KFPTPLGIKPRLGDILEEHIDDKSTISNKLWEGHQKRKENNKIA   71 (101)
Q Consensus        28 ~~P~~~~~~~~l~diL~~~vd~k~~ls~~~~~~l~~~~~~~k~~   71 (101)
                      -||++......+..+|.......-.++..+|+|++.+...+-..
T Consensus         8 g~~~~~~ls~~L~~~lG~~~~sR~~v~k~iw~YIK~~nLqdp~n   51 (85)
T LOAD_swib         8 GFPKKFKLSPALARVLGISELTRPEIVKALWQYIKEHNLQDPKN   51 (85)
T ss_pred             CCCCCCCCCHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             98888778999999868887779999999999999827988767


No 9  
>pfam02201 SWIB SWIB/MDM2 domain. This family includes the SWIB domain and the MDM2 domain. The p53-associated protein (MDM2) is an inhibitor of the p53 tumour suppressor gene binding the transactivation domain and down regulating the ability of p53 to activate transcription. This family contains the p53 binding domain of MDM2.
Probab=38.79  E-value=13  Score=18.75  Aligned_cols=44  Identities=16%  Similarity=0.350  Sum_probs=31.9

Q ss_pred             CCCCCCCCCCHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             88877777784453125677432346889988997876555320
Q gi|255764504|r   29 FPTPLGIKPRLGDILEEHIDDKSTISNKLWEGHQKRKENNKIAG   72 (101)
Q Consensus        29 ~P~~~~~~~~l~diL~~~vd~k~~ls~~~~~~l~~~~~~~k~~g   72 (101)
                      |++|......+..+|........-++..+|+|++.+...+...+
T Consensus         1 ~~kp~~lS~eL~~~lG~~~~sR~~v~k~iw~YIK~n~Lqdp~~k   44 (76)
T pfam02201         1 LTKPFPLSPDLAKFLGAGELSRTEVVKKLWQYIKEHNLQDPKNK   44 (76)
T ss_pred             CCCCCCCCHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             99986799999998688866799999999999998279987677


No 10 
>COG4386 Mu-like prophage tail sheath protein gpL [General function prediction only]
Probab=33.94  E-value=27  Score=16.94  Aligned_cols=17  Identities=29%  Similarity=0.602  Sum_probs=14.2

Q ss_pred             CCCCCCCCEEEEEEEEC
Q ss_conf             57973762799999847
Q gi|255764504|r    6 FGVPQRRERLYIIDFLN   22 (101)
Q Consensus         6 fGvPQ~ReRvfiVg~~~   22 (101)
                      =|.||+|.||.|||-..
T Consensus        28 tg~pt~~qrvLivgq~~   44 (487)
T COG4386          28 TGLPTNRQRVLIVGQAR   44 (487)
T ss_pred             CCCCCCCEEEEEEECCC
T ss_conf             58998744799996034


No 11 
>TIGR01289 LPOR light-dependent protochlorophyllide reductase; InterPro: IPR005979    This family contains the light-dependent, NADPH-dependent form of protochlorophyllide reductase (1.3.1.33 from EC) which catalyses the reaction  chlorophyllide A + NADP+ = protochlorophyllide + NADPH.  The enzyme belongs to the short chain alcohol dehydrogenase family. ; GO: 0016630 protochlorophyllide reductase activity, 0015995 chlorophyll biosynthetic process, 0019685 photosynthesis dark reaction, 0009507 chloroplast.
Probab=27.36  E-value=24  Score=17.28  Aligned_cols=35  Identities=26%  Similarity=0.496  Sum_probs=21.3

Q ss_pred             CCCCCCEEEEEEEECCCCC-CCCCCCCCCCCCHHHH
Q ss_conf             9737627999998478887-5588877777784453
Q gi|255764504|r    8 VPQRRERLYIIDFLNPSVE-FKFPTPLGIKPRLGDI   42 (101)
Q Consensus         8 vPQ~ReRvfiVg~~~~~~~-f~~P~~~~~~~~l~di   42 (101)
                      .|+.-+|++|||.--.+.+ .-=.-|.+.+.+|+|+
T Consensus       131 ~~~~~~RlII~G~~T~N~~~L~G~~P~Pa~a~LGdl  166 (321)
T TIGR01289       131 SPDKDKRLIILGSVTANSKELAGKVPIPAKADLGDL  166 (321)
T ss_pred             CCCCCCCEEEEEECCCCHHHCCCCCCCCCCCCCCCC
T ss_conf             677778679983010450014778853468776763


No 12 
>pfam00863 Peptidase_C4 Peptidase family C4. This peptidase is present in the nuclear inclusion protein of potyviruses.
Probab=22.97  E-value=68  Score=14.69  Aligned_cols=18  Identities=22%  Similarity=0.418  Sum_probs=15.0

Q ss_pred             HHCCCCCCCCEEEEEEEE
Q ss_conf             435797376279999984
Q gi|255764504|r    4 CDFGVPQRRERLYIIDFL   21 (101)
Q Consensus         4 ~dfGvPQ~ReRvfiVg~~   21 (101)
                      .-|-.|+..|||+|||..
T Consensus        98 l~FR~P~~~ervclVg~n  115 (233)
T pfam00863        98 LKFRAPTEGERVCLVGTN  115 (233)
T ss_pred             CCCCCCCCCCEEEEEEEE
T ss_conf             225899988869999656


No 13 
>COG0400 Predicted esterase [General function prediction only]
Probab=22.16  E-value=45  Score=15.68  Aligned_cols=20  Identities=25%  Similarity=0.531  Sum_probs=16.6

Q ss_pred             CHHHCCCCCCCCEEEEEEEECC
Q ss_conf             8343579737627999998478
Q gi|255764504|r    2 KACDFGVPQRRERLYIIDFLNP   23 (101)
Q Consensus         2 na~dfGvPQ~ReRvfiVg~~~~   23 (101)
                      .+.++|++  ++|++++||.++
T Consensus        90 ~~~~~gi~--~~~ii~~GfSqG  109 (207)
T COG0400          90 LAEEYGID--SSRIILIGFSQG  109 (207)
T ss_pred             HHHHHCCC--HHHEEEEECCHH
T ss_conf             99983998--122689851707


Done!