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 33803
Date          Wed Jun  1 18:43:20 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 255764504.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 >2c7p_A Modification methylase  98.9 1.4E-09 4.2E-14   75.2   3.9   44    1-44    152-198 (213)
  2 >1g55_A DNA cytosine methyltra  98.7 1.2E-08 3.6E-13   69.8   5.1   58    1-58    148-207 (250)
  3 >3g7u_A Cytosine-specific meth  98.4 1.7E-07   5E-12   63.3   3.3   25    1-25    151-175 (213)
  4 >2pv0_B DNA (cytosine-5)-methy  98.3 3.6E-08 1.1E-12   67.1  -2.2   45    1-46    128-174 (205)
  5 >1dct_A Protein (modification   98.2 2.3E-06 6.7E-11   56.9   5.0   25    1-25    142-166 (324)
  6 >2c7p_A Modification methylase  98.0   6E-07 1.8E-11   60.2  -0.5   61    4-93      1-62  (82)
  7 >2qrv_A DNA (cytosine-5)-methy  97.8 7.7E-07 2.3E-11   59.6  -3.3   30    1-30    163-195 (211)
  8 >1g55_A DNA cytosine methyltra  70.9       5 0.00015   20.8   3.6   47   38-96      2-49  (93)
  9 >1uhr_A SWI/SNF related, matri  52.6     4.4 0.00013   21.1   0.6   38   28-65      7-44  (47)
 10 >3ke3_A Putative serine-pyruva  48.3      20 0.00059   17.3   3.4   44   56-99      4-47  (108)
 11 >1v31_A Hypothetical protein R  40.4     8.2 0.00024   19.6   0.4   44   28-71      7-50  (93)
 12 >1lvm_A Catalytic domain of th  29.8      42  0.0012   15.5   2.6   19    5-23      2-20  (124)
 13 >2ohw_A YUEI protein; structur  23.5      57  0.0017   14.8   2.9   71    5-83     15-98  (133)

No 1  
>>2c7p_A Modification methylase HHAI; DNA methyltransferase, methyltransferase, base flipping, restriction system, transferase; HET: 5CM A1P SAH EPE CIT; 1.7A {Haemophilus haemolyticus} (A:1-192,A:307-327)
Probab=98.87  E-value=1.4e-09  Score=75.16  Aligned_cols=44  Identities=39%  Similarity=0.812  Sum_probs=36.6

Q ss_pred             CCHHHCCCCCCCCEEEEEEEECCC--CCCCCCCCCCCC-CCHHHHHC
Q ss_conf             983435797376279999984788--875588877777-78445312
Q gi|255764504|r    1 MKACDFGVPQRRERLYIIDFLNPS--VEFKFPTPLGIK-PRLGDILE   44 (101)
Q Consensus         1 Lna~dfGvPQ~ReRvfiVg~~~~~--~~f~~P~~~~~~-~~l~diL~   44 (101)
                      |||++||+||+|+|+|+||++++.  ..|.||+|.+.. .++-++|.
T Consensus       152 l~a~~~G~PQ~R~R~flva~r~~~~~~~~~~p~P~~~~~~~~~~~~~  198 (213)
T 2c7p_A          152 LNALDYGIPQKRERIYMICFRNDLNIQNFQFPKPFELNTFVVINVLQ  198 (213)
T ss_dssp             EEGGGGTCSBCCEEEEEEEEBGGGCCCCCCCCCCCCCCCCGCHHHHH
T ss_pred             ECHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHH
T ss_conf             22899398616655621122367553311221222356534799999


No 2  
>>1g55_A DNA cytosine methyltransferase DNMT2; human DNA methyltransferase homologue; HET: DNA SAH; 1.80A {Homo sapiens} (A:1-202,A:296-343)
Probab=98.74  E-value=1.2e-08  Score=69.81  Aligned_cols=58  Identities=17%  Similarity=0.323  Sum_probs=39.1

Q ss_pred             CCHHHCCCCCCCCEEEEEEEECCC-CCCCCCCCCCCCCC-HHHHHCCCCCCCCCCCHHHH
Q ss_conf             983435797376279999984788-87558887777778-44531256774323468899
Q gi|255764504|r    1 MKACDFGVPQRRERLYIIDFLNPS-VEFKFPTPLGIKPR-LGDILEEHIDDKSTISNKLW   58 (101)
Q Consensus         1 Lna~dfGvPQ~ReRvfiVg~~~~~-~~f~~P~~~~~~~~-l~diL~~~vd~k~~ls~~~~   58 (101)
                      |||+|||+||+|+|+||||++++. ..|.+|........ ..-......+....+|++=+
T Consensus       148 lna~~yG~PQ~R~R~flia~r~~~~~~f~~p~~~~~~~p~~~~~~~~~~~~~~~~tp~e~  207 (250)
T 1g55_A          148 LSPTSLGIPNSRLRYFLIAKLQSEPLPFQAPGQVLMEFPKIEIHRKNQQDSDLSVTPKEI  207 (250)
T ss_dssp             ECGGGGTCSCCCCEEEEEEEESSSCCTTCCTTCEESSCCC------------CCCCHHHH
T ss_pred             CCHHHCCCCCEEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHH
T ss_conf             679990984104589999884797877668642234566410013454432233389999


No 3  
>>3g7u_A Cytosine-specific methyltransferase; DNA-binding, NAD-binding, structural genomics, protein structure initiative, PSI; 1.75A {Escherichia coli O157} (A:1-188,A:352-376)
Probab=98.40  E-value=1.7e-07  Score=63.29  Aligned_cols=25  Identities=32%  Similarity=0.586  Sum_probs=23.0

Q ss_pred             CCHHHCCCCCCCCEEEEEEEECCCC
Q ss_conf             9834357973762799999847888
Q gi|255764504|r    1 MKACDFGVPQRRERLYIIDFLNPSV   25 (101)
Q Consensus         1 Lna~dfGvPQ~ReRvfiVg~~~~~~   25 (101)
                      |||+|||+||+|+|+|+||++++..
T Consensus       151 lna~~yG~PQ~R~R~~lia~~~~~~  175 (213)
T 3g7u_A          151 VKASDYGAPTIRTRYFFIGVKKSLK  175 (213)
T ss_dssp             EEGGGGTCSBCCEEEEEEEEEGGGC
T ss_pred             CCCCCCCCCCHHHHHEEEEEECCCC
T ss_conf             4311101001454513455305877


No 4  
>>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* (B:182-386)
Probab=98.30  E-value=3.6e-08  Score=67.13  Aligned_cols=45  Identities=9%  Similarity=-0.228  Sum_probs=32.8

Q ss_pred             CCHHHCCCCCCCCEEEEEEEECCCCCCCCCC--CCCCCCCHHHHHCCC
Q ss_conf             9834357973762799999847888755888--777777844531256
Q gi|255764504|r    1 MKACDFGVPQRRERLYIIDFLNPSVEFKFPT--PLGIKPRLGDILEEH   46 (101)
Q Consensus         1 Lna~dfGvPQ~ReRvfiVg~~~~~~~f~~P~--~~~~~~~l~diL~~~   46 (101)
                      |||++|||||+|+|+|+||.+++. .+.+|.  ......++.++|.+.
T Consensus       128 l~a~~~G~pQ~R~R~~~i~~~~~~-~~~~~~~~~~~~~~~~~~~~~~l  174 (205)
T 2pv0_B          128 IPDVHGGSLQNAVRVWSNIPAIRS-RHWALVSEEELSLLAQNKQSSKL  174 (205)
T ss_dssp             EECCCSSSCCCEEEEEECSSSSST-TCCTTSCHHHHHHHHHHHSSSSC
T ss_pred             EECCCCCCCCCEEEEEECCCCCCC-CCCCCCCCCCHHHHHHHHHHCCC
T ss_conf             646546665620799807767455-67898763302267777753136


No 5  
>>1dct_A Protein (modification methylase HAEIII); enzyme, cytosine methylase; HET: DNA C49 5CM; 2.80A {Haemophilus aegyptus} (A:)
Probab=98.18  E-value=2.3e-06  Score=56.89  Aligned_cols=25  Identities=36%  Similarity=0.646  Sum_probs=23.0

Q ss_pred             CCHHHCCCCCCCCEEEEEEEECCCC
Q ss_conf             9834357973762799999847888
Q gi|255764504|r    1 MKACDFGVPQRRERLYIIDFLNPSV   25 (101)
Q Consensus         1 Lna~dfGvPQ~ReRvfiVg~~~~~~   25 (101)
                      |||.+|||||+|+|+|+||++++..
T Consensus       142 l~a~~~G~pq~R~R~~~i~~~~~~~  166 (324)
T 1dct_A          142 LNANDYGVAQDRKRVFYIGFRKELN  166 (324)
T ss_dssp             EEGGGGTCSBCCEEEEEEEEEGGGC
T ss_pred             EECCCCCCCHHHCEEEEEECCCCCC
T ss_conf             2033346861223156861147877


No 6  
>>2c7p_A Modification methylase HHAI; DNA methyltransferase, methyltransferase, base flipping, restriction system, transferase; HET: 5CM A1P SAH EPE CIT; 1.7A {Haemophilus haemolyticus} (A:193-274)
Probab=98.03  E-value=6e-07  Score=60.20  Aligned_cols=61  Identities=21%  Similarity=0.201  Sum_probs=40.5

Q ss_pred             HHCCCCCCCCEEEEEEEECC-CCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEECC
Q ss_conf             43579737627999998478-88755888777777844531256774323468899889978765553201355204348
Q gi|255764504|r    4 CDFGVPQRRERLYIIDFLNP-SVEFKFPTPLGIKPRLGDILEEHIDDKSTISNKLWEGHQKRKENNKIAGKGFGYGLFFE   82 (101)
Q Consensus         4 ~dfGvPQ~ReRvfiVg~~~~-~~~f~~P~~~~~~~~l~diL~~~vd~k~~ls~~~~~~l~~~~~~~k~~g~GFg~~~~~~   82 (101)
                      +||||||+||||||||-.+. .....||........++.+-.                            .|=| ..++.
T Consensus         1 KdfgvpqnreRvfiIgh~r~~~~~~vfp~~~~~~~~ig~in~----------------------------ggQG-~RVYs   51 (82)
T 2c7p_A            1 KDLLLPDSEVEHLVIDRKDLVMTNQEIEQTTPKTVRLGIVGK----------------------------GGQG-ERIYS   51 (82)
T ss_dssp             GGTCCCGGGTGGGEECCTTCEECSCCCSSCCSSCCEEEESTT----------------------------CCTT-CEEEE
T ss_pred             CCCCCCCCCHHHHCCCCCCCHHHHHHHHCCCCHHHHHCCCCC----------------------------CCCC-CCCCC
T ss_conf             320002331122124532200000022203513332010367----------------------------8887-74545


Q ss_pred             CCCCCCCEEEC
Q ss_conf             87750330104
Q gi|255764504|r   83 NSATTNTLSAR   93 (101)
Q Consensus        83 ~~~~~~Ti~ar   93 (101)
                      .+..|.||+|.
T Consensus        52 ~~Gia~TLta~   62 (82)
T 2c7p_A           52 TRGIAITLSAY   62 (82)
T ss_dssp             TTSCBCCCCSS
T ss_pred             CCCCCCCCCCC
T ss_conf             65565301146


No 7  
>>2qrv_A DNA (cytosine-5)-methyltransferase 3A; DNA methyltransferase 3A (DNMT3A) and ITS regulatory factor; HET: DNA SAH; 2.89A {Homo sapiens} (A:1-192,A:277-295)
Probab=97.80  E-value=7.7e-07  Score=59.57  Aligned_cols=30  Identities=13%  Similarity=0.238  Sum_probs=22.1

Q ss_pred             CCHHHCCCCCCCCEEEEE--EEECCCC-CCCCC
Q ss_conf             983435797376279999--9847888-75588
Q gi|255764504|r    1 MKACDFGVPQRRERLYII--DFLNPSV-EFKFP   30 (101)
Q Consensus         1 Lna~dfGvPQ~ReRvfiV--g~~~~~~-~f~~P   30 (101)
                      |||+|||+||+|+|+|+|  |++++.. .|+.|
T Consensus       163 l~a~d~G~pQ~R~R~f~v~v~~~~~~~~~~~~~  195 (211)
T 2qrv_A          163 IDAKEVSAAHRARYFWGNLPGMNRPLASTVSVP  195 (211)
T ss_dssp             EEGGGTSSBCCEEEEEECCTTSSSCCCCCSCHH
T ss_pred             ECCCEECCCCCEEEEEECCCCCCCCCCCCCCHH
T ss_conf             113470665620798614678888865444999


No 8  
>>1g55_A DNA cytosine methyltransferase DNMT2; human DNA methyltransferase homologue; HET: DNA SAH; 1.80A {Homo sapiens} (A:203-295)
Probab=70.87  E-value=5  Score=20.79  Aligned_cols=47  Identities=15%  Similarity=0.115  Sum_probs=35.5

Q ss_pred             CHHHHHCCCCC-CCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEECCCCCCCCCEEECCCC
Q ss_conf             84453125677-432346889988997876555320135520434887750330104035
Q gi|255764504|r   38 RLGDILEEHID-DKSTISNKLWEGHQKRKENNKIAGKGFGYGLFFENSATTNTLSARYYK   96 (101)
Q Consensus        38 ~l~diL~~~vd-~k~~ls~~~~~~l~~~~~~~k~~g~GFg~~~~~~~~~~~~Ti~arY~K   96 (101)
                      .|.++|+.+++ +.|.+.++++.          ..+.  ..-++.|.+..|...|++|++
T Consensus         2 ~l~~~Le~~~~~~~~~vp~~~l~----------r~~~--~lDIV~p~s~rs~CFTKgY~~   49 (93)
T 1g55_A            2 MLKDFLEDDTDVNQYLLPPKSLL----------RYAL--LLDIVQPTXRRSVCFTKGYGS   49 (93)
T ss_dssp             CGGGGCCTTCCHHHHBCCHHHHH----------HHGG--GCCEECTTCSCCCCCCTTTTT
T ss_pred             CCCCCCCCCCCHHHCCCCCCCCC----------HHHH--HHHHCCCCCCCCCCCCCCCCC
T ss_conf             12211246775001135763200----------0012--332015432223333556553


No 9  
>>1uhr_A SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily...; structural genomics, chromatin remodeling; NMR {Mus musculus} (A:1-47)
Probab=52.62  E-value=4.4  Score=21.10  Aligned_cols=38  Identities=26%  Similarity=0.517  Sum_probs=32.0

Q ss_pred             CCCCCCCCCCCHHHHHCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             58887777778445312567743234688998899787
Q gi|255764504|r   28 KFPTPLGIKPRLGDILEEHIDDKSTISNKLWEGHQKRK   65 (101)
Q Consensus        28 ~~P~~~~~~~~l~diL~~~vd~k~~ls~~~~~~l~~~~   65 (101)
                      .+|++......|.++|.......--+..++|+|++.+.
T Consensus         7 ~~~~~~~lSp~La~ilG~~~~tR~~vvk~lW~YIK~~~   44 (47)
T 1uhr_A            7 GQPPQFKLDPRLARLLGIHTQTRPVIIQALWQYIKTHK   44 (47)
T ss_dssp             SSCCEEEECTTHHHHTCCSEEEHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCHHHHHHHCCCCCCHHHHHHHHHHHHHHHC
T ss_conf             99777778999999878887689999999999999847


No 10 
>>3ke3_A Putative serine-pyruvate aminotransferase; structural genomics, joint center for structural genomics, JCSG; HET: LLP; 2.20A {Psychrobacter arcticus 273-4} (A:272-379)
Probab=48.28  E-value=20  Score=17.35  Aligned_cols=44  Identities=7%  Similarity=-0.009  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEECCCCCCCCCEEECCCCCCC
Q ss_conf             89988997876555320135520434887750330104035876
Q gi|255764504|r   56 KLWEGHQKRKENNKIAGKGFGYGLFFENSATTNTLSARYYKDGS   99 (101)
Q Consensus        56 ~~~~~l~~~~~~~k~~g~GFg~~~~~~~~~~~~Ti~arY~Kdg~   99 (101)
                      ..|+-+......-.+.-...|..++-+.+..|+|+||-|..+|-
T Consensus         4 ~~~~Rh~~~a~~~r~~~~~lGl~~~~~~~~~s~~Vtav~~P~g~   47 (108)
T 3ke3_A            4 ILRDAQWELGNRVRKVLTDKGIESVAAEGFEAPGVVVSYTERDD   47 (108)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTCCBSBCTTCBCSSEEEEECSCHH
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCCHHCCCEEEEEECCCCH
T ss_conf             66899999876654211013443034815409759998089887


No 11 
>>1v31_A Hypothetical protein RAFL11-05-P19; SWI/SNF complex subunit, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} (A:)
Probab=40.44  E-value=8.2  Score=19.55  Aligned_cols=44  Identities=20%  Similarity=0.357  Sum_probs=35.7

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~~~~sr~~v~~~lw~YIk~n~Lqd~~~   50 (93)
T 1v31_A            7 GVPEKFKLSTALMDVLGIEVETRPRIIAAIWHYVKARKLQNPND   50 (93)
T ss_dssp             SSCCCEECCHHHHHHSCCSEECSHHHHHHHHHHHHHTTCBCSSC
T ss_pred             CCCCCCCCCHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             98677048999999986787689999999999996735654667


No 12 
>>1lvm_A Catalytic domain of the nuclear inclusion protein A (NIA); beta barrel, chymotrypsin-type cystein protease, enzyme- peptide complex; 1.80A {Tobacco etch virus} (A:106-229)
Probab=29.83  E-value=42  Score=15.53  Aligned_cols=19  Identities=32%  Similarity=0.492  Sum_probs=15.7

Q ss_pred             HCCCCCCCCEEEEEEEECC
Q ss_conf             3579737627999998478
Q gi|255764504|r    5 DFGVPQRRERLYIIDFLNP   23 (101)
Q Consensus         5 dfGvPQ~ReRvfiVg~~~~   23 (101)
                      -|--|...|||+|||+.-.
T Consensus         2 ~FR~P~~~e~vclVg~~fq   20 (124)
T 1lvm_A            2 KFREPQREERICLVTTNFQ   20 (124)
T ss_dssp             CBCCCCTTCEEEEEEEECS
T ss_pred             CCCCCCCCCEEEEECCCCC
T ss_conf             3468888999999735877


No 13 
>>2ohw_A YUEI protein; structural genomics, PSI-2, protein structure initiative, NEW YORK SGX research center for structural genomics, nysgxrc; 1.40A {Bacillus subtilis} (A:)
Probab=23.50  E-value=57  Score=14.75  Aligned_cols=71  Identities=11%  Similarity=0.075  Sum_probs=36.2

Q ss_pred             HCCCCCC------------CCEEEEEEEECCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCHHH-HHHHHHHHHHHHHH
Q ss_conf             3579737------------6279999984788875588877777784453125677432346889-98899787655532
Q gi|255764504|r    5 DFGVPQR------------RERLYIIDFLNPSVEFKFPTPLGIKPRLGDILEEHIDDKSTISNKL-WEGHQKRKENNKIA   71 (101)
Q Consensus         5 dfGvPQ~------------ReRvfiVg~~~~~~~f~~P~~~~~~~~l~diL~~~vd~k~~ls~~~-~~~l~~~~~~~k~~   71 (101)
                      =||.||.            ||||++--......      .......+...|.+..+-.-.|+..+ .+.+..|..--...
T Consensus        15 ~~G~p~lkPDEqr~yLGtfrERV~lalT~~qv~------~~~~~~~~~~~l~~~~~~~l~ing~l~~~~~~~YiklA~~~   88 (133)
T 2ohw_A           15 MYGPLETKPDERHLFLGSLRERVVLALTKGQVL------RSKPYKEAEHELKNSHNVTLLINGELQYQSYSSYIQMASRY   88 (133)
T ss_dssp             CCSCCSSHHHHHHHTTTCCGGGEEEEEEHHHHT------SSSCCHHHHHHHHTCSSEEEEEETTSCHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCHHHHHHHCCCHHHHHHEEEEHHHHH------CCCHHHHHHHHHHHCCCCEEEECCCCCHHHHHHHHHHHHHC
T ss_conf             789998998899883441665610365299980------70069999999875879789984889877899999999986


Q ss_pred             HCCCCCEEECCC
Q ss_conf             013552043488
Q gi|255764504|r   72 GKGFGYGLFFEN   83 (101)
Q Consensus        72 g~GFg~~~~~~~   83 (101)
                        |-.+.+++..
T Consensus        89 --~i~fTiV~~~   98 (133)
T 2ohw_A           89 --GVPFKIVSDL   98 (133)
T ss_dssp             --TCCEEEECCC
T ss_pred             --CCCEEEECCC
T ss_conf             --9986995787


Done!