Query gi|254780490|ref|YP_003064903.1| site-specific tyrosine recombinase XerC [Candidatus Liberibacter asiaticus str. psy62] Match_columns 67 No_of_seqs 106 out of 4897 Neff 6.3 Searched_HMMs 33803 Date Wed Jun 1 13:48:34 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780490.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 >1aih_A HP1 integrase; DNA int 99.7 1.5E-17 4.5E-22 110.8 2.6 61 2-63 72-132 (133) 2 >2a3v_A Site-specific recombin 99.7 8.5E-18 2.5E-22 112.1 -0.0 57 2-58 71-127 (128) 3 >1a0p_A Site-specific recombin 99.5 1.8E-15 5.5E-20 100.1 -0.6 53 2-54 138-190 (190) 4 >1xo0_A Recombinase CRE; CRE r 99.4 8.6E-14 2.5E-18 91.5 3.0 45 2-46 152-196 (196) 5 >1z1b_A Integrase; protein-DNA 99.1 1.7E-10 5E-15 74.5 4.9 48 2-49 137-184 (190) 6 >1z19_A Integrase; protein-DNA 99.0 7.1E-12 2.1E-16 81.6 -2.4 52 2-53 137-189 (190) 7 >1ae9_A Lambda integrase; DNA 99.0 9.1E-12 2.7E-16 81.1 -2.4 50 2-51 127-176 (179) 8 >2v6e_A Protelemorase; hairpin 27.5 8.8 0.00026 19.4 -1.2 17 25-41 95-111 (125) 9 >1jko_C HIN recombinase, DNA-i 16.4 89 0.0026 14.2 3.8 33 12-45 13-45 (52) 10 >2vj4_A Protein MXIC, MXIC; se 11.6 65 0.0019 15.0 0.3 33 17-57 5-37 (79) No 1 >>1aih_A HP1 integrase; DNA integration, recombination; 2.50A {Bacteriophage HP1} (A:1-49,A:87-170) Probab=99.67 E-value=1.5e-17 Score=110.79 Aligned_cols=61 Identities=30% Similarity=0.557 Sum_probs=56.0 Q ss_pred CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHCHHHHHH Q ss_conf 21603638999999998089999999984888889999998639999999999958211333 Q gi|254780490|r 2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHPSITQK 63 (67) Q Consensus 2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~~~~~~~~~~~~p~~~~k 63 (67) ++|||+|||||||+++++|+|+..||++|||+|++||++|++++.++++++++. .|+.+.+ T Consensus 72 ~it~H~lRHT~At~l~~~G~d~~~Iq~~lGH~s~~tT~~Y~~~~~~~~~~~~e~-~~~~~~k 132 (133) T 1aih_A 72 GQLTHVLRHTFASHFMMNGGNILVLKEILGHSTIEMTMRYAHFAPSHLESAVKF-NPLSNPA 132 (133) T ss_dssp TCTTTHHHHHHHHHHHHTTCCHHHHHHHHTCSSHHHHGGGGGGSCCCTTHHHHH-STTTSCC T ss_pred CCCCCHHHHHHHHHHHHCCCCHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHH-CCCCCCC T ss_conf 620024688773787744730989999808998899987766799999999985-9565879 No 2 >>2a3v_A Site-specific recombinase INTI4; protein-DNA complex, recombination; HET: DNA; 2.80A {Vibrio cholerae o1 biovar eltor str} (A:95-144,A:243-320) Probab=99.66 E-value=8.5e-18 Score=112.08 Aligned_cols=57 Identities=47% Similarity=0.715 Sum_probs=54.0 Q ss_pred CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHCH Q ss_conf 216036389999999980899999999848888899999986399999999999582 Q gi|254780490|r 2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHP 58 (67) Q Consensus 2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~~~~~~~~~~~~p 58 (67) +++||+|||||||+++++|+|+..||++|||+++++|++|++++++.++++++++.+ T Consensus 71 ~~~~H~lRHT~aT~l~~~G~~~~~i~~~lGHss~~~t~~Y~h~~~~~~~~~~~~~~~ 127 (128) T 2a3v_A 71 TVTCHTLRHSFATHLLEVGADIRTVQEQLGHTDVKTTQIYTHVLDRGASGVLSPLSR 127 (128) T ss_dssp CCCHHHHHHHHHHHHHHTTCCHHHHHHHHTCSSHHHHGGGCC------CCCCCHHHH T ss_pred CCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHC T ss_conf 998711499999999987899999998848999899999884699899998617524 No 3 >>1a0p_A Site-specific recombinase XERD; DNA binding, DNA recombination; 2.50A {Escherichia coli} (A:101-290) Probab=99.49 E-value=1.8e-15 Score=100.06 Aligned_cols=53 Identities=55% Similarity=0.879 Sum_probs=50.8 Q ss_pred CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHH Q ss_conf 21603638999999998089999999984888889999998639999999999 Q gi|254780490|r 2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYD 54 (67) Q Consensus 2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~~~~~~~~~ 54 (67) +++||++||||||.++++|+|+..||++|||+|++||++|++++.++++++++ T Consensus 138 ~~~~h~~Rht~~t~~~~~~~~~~~i~~~lGH~s~~~T~~Y~~~~~~~~~~a~~ 190 (190) T 1a0p_A 138 KLSPHVLRHAFATHLLNHGADLRVVQMLLGHSDLSTTQIYTHVATERLRQLHQ 190 (190) T ss_dssp GCCHHHHHHHHHHHHHHHCSSCGGGSSCC--CCCCHHHHHHHHHHHHHHHHHC T ss_pred CCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHCC T ss_conf 87765188999999998789999999881899889999997789999998609 No 4 >>1xo0_A Recombinase CRE; CRE recombinase, holliday junction, recombination,complex (recombinase/DNA), hydrolase, ligase/DNA complex; 2.00A {Enterobacteria phage P1} (A:115-310) Probab=99.41 E-value=8.6e-14 Score=91.48 Aligned_cols=45 Identities=16% Similarity=0.172 Sum_probs=42.9 Q ss_pred CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCH Q ss_conf 216036389999999980899999999848888899999986399 Q gi|254780490|r 2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNS 46 (67) Q Consensus 2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~ 46 (67) .+|||+|||||||.+++.|+|+..||++|||+|++||++|+++.+ T Consensus 152 ~~~~h~lRht~at~l~~~g~~~~~i~~~lGH~~~~~t~~Y~~~~d 196 (196) T 1xo0_A 152 AWSGHSARVGAARDMARAGVSIPEIMQAGGWTNVNIVMNYIRNLD 196 (196) T ss_dssp SCCTTHHHHHHHHHHHHTTCCHHHHHHHHTCSSSSSHHHHSTTSG T ss_pred CCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCH T ss_conf 878861389999999987899999998819998899999972536 No 5 >>1z1b_A Integrase; protein-DNA complex, DNA binding protein/DNA complex; HET: PTR; 3.80A {Enterobacteria phage lambda} (A:167-356) Probab=99.06 E-value=1.7e-10 Score=74.52 Aligned_cols=48 Identities=13% Similarity=0.124 Sum_probs=42.7 Q ss_pred CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCHHHH Q ss_conf 216036389999999980899999999848888899999986399999 Q gi|254780490|r 2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRM 49 (67) Q Consensus 2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~~~~ 49 (67) ..++|.+||||||.++++|+|+..||++|||+|++||+.|.....+++ T Consensus 137 ~~~~~~~r~t~at~l~~~g~~~~~i~~~lGH~~~~~T~~yy~~~~~~~ 184 (190) T 1z1b_A 137 DPPTFHELRSLSARLYEKQISDKFAQHLLGHKSDTMASQXRDDRGREW 184 (190) T ss_dssp BCCCTTHHHHHHHHHHHHHTCHHHHHHHHTCSSHHHHHHHTCCTTSCC T ss_pred CCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHH T ss_conf 999748289999999986999999999838998899998832748789 No 6 >>1z19_A Integrase; protein-DNA complex, DNA binding protein/DNA complex; HET: PTR; 2.80A {Enterobacteria phage lambda} PDB: 1p7d_A* (A:94-283) Probab=99.05 E-value=7.1e-12 Score=81.63 Aligned_cols=52 Identities=12% Similarity=0.028 Sum_probs=45.6 Q ss_pred CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHH-HHHCCHHHHHHHH Q ss_conf 216036389999999980899999999848888899999-9863999999999 Q gi|254780490|r 2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQI-YTNVNSKRMMEIY 53 (67) Q Consensus 2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~-Y~~~~~~~~~~~~ 53 (67) ..++|.+||+||+.++++|+|+.+||++|||+|+++|+. |.+++.+.+++++ T Consensus 137 ~~~~~~~~r~~a~~l~~~g~~~~~i~~~lGH~~~~~T~~~Y~~~~~~~~~~a~ 189 (190) T 1z19_A 137 DPPTFHELRSLSARLYEKQISDKFAQHLLGHKSDTXASQXRDDRGREWDKIEI 189 (190) T ss_dssp SCCCGGGHHHHHHHHHHHHTCHHHHHHHHTCSSSCC----------CCCCCCC T ss_pred CCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHC T ss_conf 99973849999999998698999999994899889999985274858999864 No 7 >>1ae9_A Lambda integrase; DNA recombination, site-specific recombination; 1.90A {Bacteriophage lambda} (A:) Probab=99.03 E-value=9.1e-12 Score=81.08 Aligned_cols=50 Identities=12% Similarity=0.141 Sum_probs=45.5 Q ss_pred CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHH Q ss_conf 21603638999999998089999999984888889999998639999999 Q gi|254780490|r 2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMME 51 (67) Q Consensus 2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~~~~~~ 51 (67) ..++|.+||++++.+.++|+|+..||++|||++++||++|++++.+++++ T Consensus 127 ~~~~~~~r~~~~~~~~~~g~~~~~i~~~lGH~~~~tT~~Y~~~~~~~~~~ 176 (179) T 1ae9_A 127 DPPTFHELRSLSARLYEKQISDKFAQHLLGHKSDTMASQFRDDRGREWDK 176 (179) T ss_dssp SCCCTTHHHHHHHHHHHHHTCHHHHHHHHTC--------CEECSSCEEEE T ss_pred CHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHH T ss_conf 30268899888999999499999999993899999999987367876862 No 8 >>2v6e_A Protelemorase; hairpin telomere, hydrolase, resolvase, protelomerase, DNA distortion; 3.20A {Klebsiella phage PHIKO2} (A:250-297,A:383-459) Probab=27.45 E-value=8.8 Score=19.42 Aligned_cols=17 Identities=35% Similarity=0.448 Sum_probs=9.4 Q ss_pred HHHHHHCCCCHHHHHHH Q ss_conf 99998488888999999 Q gi|254780490|r 25 SIQSILGHSRLSTTQIY 41 (67) Q Consensus 25 ~vq~lLGH~~i~tT~~Y 41 (67) --++||||.++.|-..| T Consensus 95 F~~ElLGH~D~dTQ~~Y 111 (125) T 2v6e_A 95 FFMEILGHDDENTQLHY 111 (125) T ss_dssp HHHHHHTCSSTTGGGSS T ss_pred HHHHHHCCCCHHHHHHH T ss_conf 99998578862555566 No 9 >>1jko_C HIN recombinase, DNA-invertase HIN; water-mediated recognition, protein-DNA complex, A10G mutant, DNA binding protein/DNA complex; 2.24A {Synthetic} (C:) Probab=16.45 E-value=89 Score=14.23 Aligned_cols=33 Identities=24% Similarity=0.306 Sum_probs=25.2 Q ss_pred HHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCC Q ss_conf 9999998089999999984888889999998639 Q gi|254780490|r 12 FATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVN 45 (67) Q Consensus 12 ~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~ 45 (67) .|-.|+.+|.++..|.+.+|=+ ..|.-+|.... T Consensus 13 ~a~~l~~~G~s~~~iA~~~gVS-r~TiYr~l~~~ 45 (52) T 1jko_C 13 QISRLLEKGHPRQQLAIIFGIG-VSTLYRYFPAS 45 (52) T ss_dssp HHHHHHHTTCCHHHHHHTTSCC-HHHHHHHSCTT T ss_pred HHHHHHHCCCCHHHHHHHHCCC-HHHHHHHCCCH T ss_conf 9999998799899999998979-99999984521 No 10 >>2vj4_A Protein MXIC, MXIC; secretion regulation, transport protein, T3SS, plasmid, virulence, transport, type three secretion system; HET: MLY; 2.50A {Shigella flexneri} PDB: 2vix_A* 2vj5_A (A:92-170) Probab=11.55 E-value=65 Score=14.95 Aligned_cols=33 Identities=9% Similarity=0.169 Sum_probs=16.7 Q ss_pred HHHCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHC Q ss_conf 98089999999984888889999998639999999999958 Q gi|254780490|r 17 LSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTH 57 (67) Q Consensus 17 ~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~~~~~~~~~~~~ 57 (67) +++|.++..+.++.|-. ..++...++..|++|. T Consensus 5 ~kAGINvAl~Ak~F~~~--------l~l~a~~LR~~Yr~Fl 37 (79) T 2vj4_A 5 VNAGINSAIQAXLFGNX--------MXLEPQLLRACYRGFI 37 (79) T ss_dssp HHHHHHTHHHHHHHHHH--------HTCCHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHHHCCC--------CCCCHHHHHHHHHHHH T ss_conf 88647899999885214--------4347999999999998 Done!