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!