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 23785
Date          Tue May 31 21:54:18 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 255764504.hhm -d /home/congqian_1/database/pdb/pdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 3me5_A Cytosine-specific methy  99.7 3.1E-18 1.3E-22  123.6   8.1   99    3-101   269-376 (482)
  2 2c7p_A Modification methylase   99.2 1.3E-12 5.6E-17   91.5   0.4   96    1-96    152-257 (327)
  3 1dct_A Protein (modification m  99.1 4.7E-11   2E-15   82.7   4.8   50    1-50    142-192 (324)
  4 3g7u_A Cytosine-specific methy  98.9 9.4E-10   4E-14   75.3   4.7   45    1-45    151-199 (376)
  5 1g55_A DNA cytosine methyltran  98.9 1.1E-09 4.5E-14   75.0   4.5   57    1-57    148-224 (343)
  6 2pv0_B DNA (cytosine-5)-methyl  97.6   8E-06 3.3E-10   52.9   0.2   33    1-34    309-341 (386)
  7 2qrv_B DNA (cytosine-5)-methyl  96.6 0.00048   2E-08   42.8   1.5   31    1-32    153-183 (230)
  8 2qrv_A DNA (cytosine-5)-methyl  94.7   0.022 9.2E-07   33.3   3.5   21    3-23    164-184 (295)
  9 1v31_A Hypothetical protein RA  48.0     2.6 0.00011   21.6  -0.4   44   28-71      7-50  (93)
 10 1uhr_A SWI/SNF related, matrix  47.9     2.8 0.00012   21.4  -0.3   44   28-71      7-50  (93)
 11 2kvr_A Ubiquitin carboxyl-term  47.7      10 0.00043   18.1   2.6   29    3-31     76-105 (130)

No 1  
>3me5_A Cytosine-specific methyltransferase; structural genomics, protein structure initiative, NEW YORK structural genomix research consortium; 1.75A {Shigella flexneri 2A} PDB: 3lx6_A
Probab=99.74  E-value=3.1e-18  Score=123.61  Aligned_cols=99  Identities=32%  Similarity=0.592  Sum_probs=82.6

Q ss_pred             HHHCCCCCCCCEEEEEEEECCCC-CCCC--CCC----CCCCCCHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             34357973762799999847888-7558--887----7777784453125677432346889988997876555320135
Q gi|255764504|r    3 ACDFGVPQRRERLYIIDFLNPSV-EFKF--PTP----LGIKPRLGDILEEHIDDKSTISNKLWEGHQKRKENNKIAGKGF   75 (101)
Q Consensus         3 a~dfGvPQ~ReRvfiVg~~~~~~-~f~~--P~~----~~~~~~l~diL~~~vd~k~~ls~~~~~~l~~~~~~~k~~g~GF   75 (101)
                      +++|||||+|+|+||||++++.. .+.|  ++.    ........++|++.++.++++++.+|.++.++..++..++++|
T Consensus       269 ~a~yGVPQ~R~RvfiVG~r~dl~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  348 (482)
T 3me5_A          269 DGKHFLPQHRERIVLVGFRRDLNLKADFTLRDISECFPAQRVTLAQLLDPMVEAKYILTPVLWKYLYRYAKKHQARGNGF  348 (482)
T ss_dssp             EGGGTSSBCCEEEEEEEEEGGGCCCTTCCGGGGGGGSCSSCCCTGGGSCSSCCGGGBCCHHHHHHHHHHHHC--------
T ss_pred             CCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCC
T ss_conf             01137996677405884435767666767666554576533332223574112223567113456777877644205776


Q ss_pred             CCEEECCCC--CCCCCEEECCCCCCCCC
Q ss_conf             520434887--75033010403587639
Q gi|255764504|r   76 GYGLFFENS--ATTNTLSARYYKDGSEI  101 (101)
Q Consensus        76 g~~~~~~~~--~~~~Ti~arY~Kdg~e~  101 (101)
                      ++.++.++.  .+++|+++||+|||+++
T Consensus       349 ~~~~~~~~~~~~~~~t~~~r~~k~~~~~  376 (482)
T 3me5_A          349 GYGMVYPNNPQSVTRTLSARYYKDGAEI  376 (482)
T ss_dssp             --CEECTTSGGGGTCCBCCC---CCSSS
T ss_pred             CCCEECCCCCCCCCCCCCCEECCCCCCC
T ss_conf             7530037885344621033113799753


No 2  
>2c7p_A Modification methylase HHAI; DNA methyltransferase, methyltransferase, base flipping, restriction system, transferase; HET: 5CM A1P SAH EPE CIT; 1.7A {Haemophilus haemolyticus} SCOP: c.66.1.26 PDB: 10mh_A* 1m0e_A* 1mht_A* 1hmy_A* 1skm_A* 2c7o_A* 2c7q_A* 2hmy_B* 2hr1_A* 3eeo_A* 3mht_A* 4mht_A* 5mht_A* 6mht_A* 7mht_A* 8mht_A* 9mht_A* 2zcj_A* 2z6u_A* 2z6q_A* ...
Probab=99.20  E-value=1.3e-12  Score=91.50  Aligned_cols=96  Identities=28%  Similarity=0.411  Sum_probs=60.1

Q ss_pred             CCHHHCCCCCCCCEEEEEEEECCC--CCCCCCCCCCCCCCHHHHHCCCCCCCCCCCHHHH--------HHHHHHHHHHHH
Q ss_conf             983435797376279999984788--8755888777777844531256774323468899--------889978765553
Q gi|255764504|r    1 MKACDFGVPQRRERLYIIDFLNPS--VEFKFPTPLGIKPRLGDILEEHIDDKSTISNKLW--------EGHQKRKENNKI   70 (101)
Q Consensus         1 Lna~dfGvPQ~ReRvfiVg~~~~~--~~f~~P~~~~~~~~l~diL~~~vd~k~~ls~~~~--------~~l~~~~~~~k~   70 (101)
                      |||+||||||+|+|+||||++++.  ..+.||++........+++.+..+..+.+.+...        ........+...
T Consensus       152 l~a~~~GvPQ~R~R~fivg~r~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  231 (327)
T 2c7p_A          152 LNALDYGIPQKRERIYMICFRNDLNIQNFQFPKPFELNTFVKDLLLPDSEVEHLVIDRKDLVMTNQEIEQTTPKTVRLGI  231 (327)
T ss_dssp             EEGGGGTCSBCCEEEEEEEEBGGGCCCCCCCCCCCCCCCCGGGTCCCGGGTGGGEECCTTCEECSCCCSSCCSSCCEEEE
T ss_pred             ECHHHHCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCHHHHCCCCCCHHHCCCCCCCCCCCCHHHHHCCHHHHHHCC
T ss_conf             65999499983408888867168676656799886555423543167520111024421222110333201435553022


Q ss_pred             HHCCCCCEEECCCCCCCCCEEECCCC
Q ss_conf             20135520434887750330104035
Q gi|255764504|r   71 AGKGFGYGLFFENSATTNTLSARYYK   96 (101)
Q Consensus        71 ~g~GFg~~~~~~~~~~~~Ti~arY~K   96 (101)
                      .+.+.........+..+.|+++....
T Consensus       232 ~~~~~~~~~~~~~~~~~~t~~~~~~~  257 (327)
T 2c7p_A          232 VGKGGQGERIYSTRGIAITLSAYGGG  257 (327)
T ss_dssp             STTCCTTCEEEETTSCBCCCCSSCCS
T ss_pred             CCCCCCCCCCCCCCCCCCEEECCCCC
T ss_conf             46789876454566665201036664


No 3  
>1dct_A Protein (modification methylase HAEIII); enzyme, cytosine methylase, transferase/DNA complex; HET: DNA C49 5CM; 2.80A {Haemophilus influenzae biotypeaegyptius} SCOP: c.66.1.26
Probab=99.11  E-value=4.7e-11  Score=82.69  Aligned_cols=50  Identities=32%  Similarity=0.593  Sum_probs=40.7

Q ss_pred             CCHHHCCCCCCCCEEEEEEEECCC-CCCCCCCCCCCCCCHHHHHCCCCCCC
Q ss_conf             983435797376279999984788-87558887777778445312567743
Q gi|255764504|r    1 MKACDFGVPQRRERLYIIDFLNPS-VEFKFPTPLGIKPRLGDILEEHIDDK   50 (101)
Q Consensus         1 Lna~dfGvPQ~ReRvfiVg~~~~~-~~f~~P~~~~~~~~l~diL~~~vd~k   50 (101)
                      |||+||||||+|+|+||||++++. ..|.+|.+.....++.+++.+..+..
T Consensus       142 lna~~~GvPQ~R~R~fiv~~r~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~  192 (324)
T 1dct_A          142 LNANDYGVAQDRKRVFYIGFRKELNINYLPPIPHLIKPTFKDVIWDLKDNP  192 (324)
T ss_dssp             EEGGGGTCSBCCEEEEEEEEEGGGCCCCCCCCCCSSCCCGGGTTGGGTTCC
T ss_pred             ECHHHCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCHHHHHHHCCCCC
T ss_conf             526771899643178887133777767788632356785888766523577


No 4  
>3g7u_A Cytosine-specific methyltransferase; DNA-binding, NAD-binding, structural genomics, protein structure initiative, PSI; 1.75A {Escherichia coli O157}
Probab=98.91  E-value=9.4e-10  Score=75.28  Aligned_cols=45  Identities=24%  Similarity=0.349  Sum_probs=31.6

Q ss_pred             CCHHHCCCCCCCCEEEEEEEECCCC-CC---CCCCCCCCCCCHHHHHCC
Q ss_conf             9834357973762799999847888-75---588877777784453125
Q gi|255764504|r    1 MKACDFGVPQRRERLYIIDFLNPSV-EF---KFPTPLGIKPRLGDILEE   45 (101)
Q Consensus         1 Lna~dfGvPQ~ReRvfiVg~~~~~~-~f---~~P~~~~~~~~l~diL~~   45 (101)
                      |||+||||||+|+|+||||++++.. .+   .++.......++.++|.+
T Consensus       151 l~a~~~GvPQ~R~Rvfivg~r~~~~~~~~~~~~~~~~~~~~t~~dai~~  199 (376)
T 3g7u_A          151 VKASDYGAPTIRTRYFFIGVKKSLKLDISDEVFMPKMIDPVTVKDALYG  199 (376)
T ss_dssp             EEGGGGTCSBCCEEEEEEEEEGGGCCCCCGGGTSCCSCCCCCHHHHTTT
T ss_pred             EEHHHCCCCCEECHHHCEEECCCCCCCCCCCCCCCCCCCCCCHHHHHCC
T ss_conf             7799959851033000000115777777742247544567739997505


No 5  
>1g55_A DNA cytosine methyltransferase DNMT2; human DNA methyltransferase homologue; HET: DNA SAH; 1.80A {Homo sapiens} SCOP: c.66.1.26
Probab=98.89  E-value=1.1e-09  Score=74.96  Aligned_cols=57  Identities=25%  Similarity=0.440  Sum_probs=37.3

Q ss_pred             CCHHHCCCCCCCCEEEEEEEECCC-CCCCCCCCCCC------------------CCCHHHHHCCCCCC-CCCCCHHH
Q ss_conf             983435797376279999984788-87558887777------------------77844531256774-32346889
Q gi|255764504|r    1 MKACDFGVPQRRERLYIIDFLNPS-VEFKFPTPLGI------------------KPRLGDILEEHIDD-KSTISNKL   57 (101)
Q Consensus         1 Lna~dfGvPQ~ReRvfiVg~~~~~-~~f~~P~~~~~------------------~~~l~diL~~~vd~-k~~ls~~~   57 (101)
                      |||+||||||+|+|+||||++++. ..|.+|.+...                  ...+.++|+...+. .|.+....
T Consensus       148 lna~dyGvPQ~R~R~fivg~r~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~  224 (343)
T 1g55_A          148 LSPTSLGIPNSRLRYFLIAKLQSEPLPFQAPGQVLMEFPKIEIHRKNQQDSDLSVKMLKDFLEDDTDVNQYLLPPKS  224 (343)
T ss_dssp             ECGGGGTCSCCCCEEEEEEEESSSCCTTCCTTCEESSCCC------------CCCCCGGGGCCTTCCHHHHBCCHHH
T ss_pred             CCCCCCCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCHHCCCCHHH
T ss_conf             23120489855678999988468777767863223467621013344544444554245542356650020046266


No 6  
>2pv0_B DNA (cytosine-5)-methyltransferase 3-like; DNMT3L, unmethylated H3K4, de novo DNA methylation, transferase regulator; HET: DNA; 3.30A {Homo sapiens} PDB: 2pvc_B*
Probab=97.60  E-value=8e-06  Score=52.91  Aligned_cols=33  Identities=3%  Similarity=-0.190  Sum_probs=27.5

Q ss_pred             CCHHHCCCCCCCCEEEEEEEECCCCCCCCCCCCC
Q ss_conf             9834357973762799999847888755888777
Q gi|255764504|r    1 MKACDFGVPQRRERLYIIDFLNPSVEFKFPTPLG   34 (101)
Q Consensus         1 Lna~dfGvPQ~ReRvfiVg~~~~~~~f~~P~~~~   34 (101)
                      |||++|| ||+|+|+|++++.+....|.+|....
T Consensus       309 ina~~~g-pq~R~R~~~~nip~~~~~f~fP~~~~  341 (386)
T 2pv0_B          309 IPDVHGG-SLQNAVRVWSNIPAIRSRHWALVSEE  341 (386)
T ss_dssp             EECCCSS-SCCCEEEEEECSSSSSTTCCTTSCHH
T ss_pred             ECCCCCC-CCCCCEEEEECCCCCCCCCCCCCCCC
T ss_conf             6411077-66641799947747544578998645


No 7  
>2qrv_B DNA (cytosine-5)-methyltransferase 3-like; DNA methyltransferase 3A (DNMT3A) and ITS regulatory factor; HET: DNA SAH; 2.89A {Homo sapiens}
Probab=96.64  E-value=0.00048  Score=42.79  Aligned_cols=31  Identities=3%  Similarity=-0.164  Sum_probs=23.7

Q ss_pred             CCHHHCCCCCCCCEEEEEEEECCCCCCCCCCC
Q ss_conf             98343579737627999998478887558887
Q gi|255764504|r    1 MKACDFGVPQRRERLYIIDFLNPSVEFKFPTP   32 (101)
Q Consensus         1 Lna~dfGvPQ~ReRvfiVg~~~~~~~f~~P~~   32 (101)
                      |||++|| ||+|+|+|++++......|.+|..
T Consensus       153 ina~~~~-pq~R~R~~w~nipg~~~~f~~p~~  183 (230)
T 2qrv_B          153 IPDVHGG-SLQNAVRVWSNIPAIRSRHWALVS  183 (230)
T ss_dssp             CCCCCSC-C----CEEEECSTTSSTTCCSCSC
T ss_pred             ECCCCCC-CCCCCEEEEECCCCCCCCCCCCCC
T ss_conf             4353276-524436998567664445889985


No 8  
>2qrv_A DNA (cytosine-5)-methyltransferase 3A; DNA methyltransferase 3A (DNMT3A) and ITS regulatory factor; HET: DNA SAH; 2.89A {Homo sapiens}
Probab=94.66  E-value=0.022  Score=33.32  Aligned_cols=21  Identities=10%  Similarity=0.023  Sum_probs=16.8

Q ss_pred             HHHCCCCCCCCEEEEEEEECC
Q ss_conf             343579737627999998478
Q gi|255764504|r    3 ACDFGVPQRRERLYIIDFLNP   23 (101)
Q Consensus         3 a~dfGvPQ~ReRvfiVg~~~~   23 (101)
                      ...+++||+|+|+||+++...
T Consensus       164 ~~~~~~pq~R~R~fi~~~~~~  184 (295)
T 2qrv_A          164 DAKEVSAAHRARYFWGNLPGM  184 (295)
T ss_dssp             EGGGTSSBCCEEEEEECCTTS
T ss_pred             ECCEECCCCEEEEEEECCCCC
T ss_conf             622916453447999788787


No 9  
>1v31_A Hypothetical protein RAFL11-05-P19; SWI/SNF complex subunit, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: a.42.1.1
Probab=47.97  E-value=2.6  Score=21.56  Aligned_cols=44  Identities=20%  Similarity=0.357  Sum_probs=34.7

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         7 G~~~~~~lS~~La~~lg~~~~tR~~v~k~lw~YIk~n~Lqd~~d   50 (93)
T 1v31_A            7 GVPEKFKLSTALMDVLGIEVETRPRIIAAIWHYVKARKLQNPND   50 (93)
T ss_dssp             SSCCCEECCHHHHHHSCCSEECSHHHHHHHHHHHHHTTCBCSSC
T ss_pred             CCCCCCCCCHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             98588258999999878798689999999999999957998877


No 10 
>1uhr_A SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily...; structural genomics, chromatin remodeling; NMR {Mus musculus} SCOP: a.42.1.1
Probab=47.90  E-value=2.8  Score=21.36  Aligned_cols=44  Identities=23%  Similarity=0.426  Sum_probs=34.5

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         7 g~p~~~~lS~~La~~lg~~~~tR~~v~k~iw~YIk~n~Lqd~~d   50 (93)
T 1uhr_A            7 GQPPQFKLDPRLARLLGIHTQTRPVIIQALWQYIKTHKLQDPHE   50 (93)
T ss_dssp             SSCCEEEECTTHHHHTCCSEEEHHHHHHHHHHHHHHTTCBCSSC
T ss_pred             CCCCCCCCCHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             99877778999999878897689999999999999856878776


No 11 
>2kvr_A Ubiquitin carboxyl-terminal hydrolase 7; USP7, ubiquitin-like domain, UBL, ubiquitin specific protease, HOST-virus interaction, nucleus, protease; NMR {Homo sapiens}
Probab=47.71  E-value=10  Score=18.13  Aligned_cols=29  Identities=17%  Similarity=0.234  Sum_probs=21.0

Q ss_pred             HHHCCCCCCCCEEEEEEEECC-CCCCCCCC
Q ss_conf             343579737627999998478-88755888
Q gi|255764504|r    3 ACDFGVPQRRERLYIIDFLNP-SVEFKFPT   31 (101)
Q Consensus         3 a~dfGvPQ~ReRvfiVg~~~~-~~~f~~P~   31 (101)
                      |..||+|+.|-|++.++-|.. ......|.
T Consensus        76 a~~~g~~~~~~RlW~~~~RqN~T~Rpd~~~  105 (130)
T 2kvr_A           76 SQTMGFPQDQIRLWPMQARSNGTKRPAMLD  105 (130)
T ss_dssp             HHHHCCCGGGCEEEECCCCBTTBCCCCCCC
T ss_pred             HHHHCCCHHHEEEEEEECCCCCCCCCCCCC
T ss_conf             999597978898867554568882888638


Done!