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!