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 13730
Date          Wed Jun  1 06:30:29 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780490.hhm -d /home/congqian_1/database/scop/scop70_1_75.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 d1aiha_ d.163.1.1 (A:) Integra  99.6 3.6E-16 2.6E-20  101.7   2.7   60    2-62    109-168 (170)
  2 d1a0pa2 d.163.1.1 (A:111-292)   99.6 1.2E-16 8.5E-21  104.2  -0.6   53    2-54    130-182 (182)
  3 d1f44a2 d.163.1.1 (A:130-343)   99.4 1.6E-14 1.2E-18   93.2   3.4   53    2-54    156-208 (214)
  4 d1ae9a_ d.163.1.1 (A:) Integra  98.8   9E-10 6.5E-14   68.8   2.3   43    2-45    128-170 (179)
  5 d1ijwc_ a.4.1.2 (C:) HIN recom  15.3      39  0.0028   14.1   4.0   32   11-43     12-43  (47)
  6 d1k78a1 a.4.1.5 (A:19-81) Pax-   7.1      79  0.0057   12.5   3.0   30    4-34     15-44  (63)
  7 d1a9xa1 a.92.1.1 (A:403-555) C   6.4      86  0.0062   12.3   3.7   31    4-34     28-58  (153)
  8 d2odgc1 a.140.1.1 (C:2-47) Inn   6.0      91  0.0067   12.2   1.9   18   40-57      2-19  (46)
  9 d1bl0a2 a.4.1.8 (A:63-124) Mar   4.8 1.1E+02   0.008   11.8   3.8   42   11-52      4-50  (62)
 10 d1d5ya2 a.4.1.8 (A:57-121) Rob   4.2 1.2E+02  0.0089   11.5   6.3   44   10-53      3-51  (65)

No 1  
>d1aiha_ d.163.1.1 (A:) Integrase {Bacteriophage HP1 [TaxId: 10690]}
Probab=99.56  E-value=3.6e-16  Score=101.69  Aligned_cols=60  Identities=30%  Similarity=0.577  Sum_probs=55.9

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHCHHHHH
Q ss_conf             2160363899999999808999999998488888999999863999999999995821133
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHPSITQ   62 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~~~~~~~~~~~~p~~~~   62 (67)
                      .++||+|||||||.++++|+|+..|+++|||+++.+|++|++++.+++++++ +++|+.+.
T Consensus       109 ~~~~H~lRht~at~l~~~g~~~~~i~~~lGH~~~~~t~~Y~~~~~~~~~~a~-~~~p~~~~  168 (170)
T d1aiha_         109 GQLTHVLRHTFASHFMMNGGNILVLKEILGHSTIEMTMRYAHFAPSHLESAV-KFNPLSNP  168 (170)
T ss_dssp             TCTTTHHHHHHHHHHHHTTCCHHHHHHHHTCSSHHHHGGGGGGSCCCTTHHH-HHSTTTSC
T ss_pred             CCEEEECHHHHHHHHHCCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH-HHCCCCCC
T ss_conf             6101110465514552169899999998089998999988767999999999-86857687


No 2  
>d1a0pa2 d.163.1.1 (A:111-292) Recombinase XerD {Escherichia coli [TaxId: 562]}
Probab=99.55  E-value=1.2e-16  Score=104.21  Aligned_cols=53  Identities=55%  Similarity=0.879  Sum_probs=50.4

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       130 ~~t~H~~Rht~at~l~~~G~~~~~I~~~lGH~s~~tt~~Y~~~~~e~~re~~~  182 (182)
T d1a0pa2         130 KLSPHVLRHAFATHLLNHGADLRVVQMLLGHSDLSTTQIYTHVATERLRQLHQ  182 (182)
T ss_dssp             GCCHHHHHHHHHHHHHHHCSSCGGGSSCC--CCCCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHC
T ss_conf             83614146589996556499999999995899889999876879999998609


No 3  
>d1f44a2 d.163.1.1 (A:130-343) Cre recombinase {Bacteriophage P1 [TaxId: 10678]}
Probab=99.45  E-value=1.6e-14  Score=93.24  Aligned_cols=53  Identities=11%  Similarity=0.114  Sum_probs=47.2

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       156 ~~t~HslRht~at~l~~~G~~~~~i~~~~GH~s~~~~~~Y~~~~~~~~~~~~~  208 (214)
T d1f44a2         156 AWSGHSARVGAARDMARAGVSIPEIMQAGGWTNVNIVMNFIRNLDSETGAMVR  208 (214)
T ss_dssp             SCCTTHHHHHHHHHHHHTTCCHHHHHHHHTCCCHHHHHHHTTTCCSCCCHHHH
T ss_pred             CCCHHHHHCCCCHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHH
T ss_conf             78666641330027977799999999996899989999986033477999999


No 4  
>d1ae9a_ d.163.1.1 (A:) Integrase (Int) {Bacteriophage lambda [TaxId: 10710]}
Probab=98.78  E-value=9e-10  Score=68.79  Aligned_cols=43  Identities=21%  Similarity=0.285  Sum_probs=38.3

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCC
Q ss_conf             21603638999999998089999999984888889999998639
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVN   45 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~   45 (67)
                      ..++|+||| ||+.++++|+|+..||.+|||+|++||++|....
T Consensus       128 ~~~~h~lR~-~~t~~~~~g~~~~~i~~~lGH~s~~~t~~Y~~~~  170 (179)
T d1ae9a_         128 PPTFHELRS-LSARLYEKQISDKFAQHLLGHKSDTMASQFRDDR  170 (179)
T ss_dssp             CCCTTHHHH-HHHHHHHHHTCHHHHHHHHTC--------CEECS
T ss_pred             CCHHHHHHH-HHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCC
T ss_conf             103778888-8889998499999999995899999999987367


No 5  
>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}
Probab=15.28  E-value=39  Score=14.06  Aligned_cols=32  Identities=25%  Similarity=0.307  Sum_probs=24.6

Q ss_pred             HHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             999999980899999999848888899999986
Q gi|254780490|r   11 SFATHLLSNGGDLRSIQSILGHSRLSTTQIYTN   43 (67)
Q Consensus        11 t~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~   43 (67)
                      .-|-.|+.+|.++..|.+.+|=+ ..|.-+|.-
T Consensus        12 ~~a~~l~~~G~s~~~iA~~~gVS-r~TiYry~p   43 (47)
T d1ijwc_          12 EQISRLLEKGHPRQQLAIIFGIG-VSTLYRYFP   43 (47)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHTCC-HHHHHHHSC
T ss_pred             HHHHHHHHCCCCHHHHHHHHCCC-HHHHHHHCC
T ss_conf             99999998899799999997969-999985577


No 6  
>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [TaxId: 9606]}
Probab=7.09  E-value=79  Score=12.49  Aligned_cols=30  Identities=20%  Similarity=0.186  Sum_probs=24.2

Q ss_pred             CCCCHHHHHHHHHHHHCCCHHHHHHHHCCCC
Q ss_conf             6036389999999980899999999848888
Q gi|254780490|r    4 TAHTLRHSFATHLLSNGGDLRSIQSILGHSR   34 (67)
Q Consensus         4 tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~   34 (67)
                      -|.+||.-.. .+++.|.+...+++.++=+-
T Consensus        15 ls~DLR~Riv-~~~~~G~s~r~aA~rf~VS~   44 (63)
T d1k78a1          15 LPDVVRQRIV-ELAHQGVRPCDISRQLRVSH   44 (63)
T ss_dssp             CCHHHHHHHH-HHHHTTCCHHHHHHHHTCCH
T ss_pred             CCHHHHHHHH-HHHHCCCCHHHHHHHHCCCH
T ss_conf             9999999999-99995998999999959779


No 7  
>d1a9xa1 a.92.1.1 (A:403-555) Carbamoyl phosphate synthetase, large subunit connection domain {Escherichia coli [TaxId: 562]}
Probab=6.42  E-value=86  Score=12.30  Aligned_cols=31  Identities=13%  Similarity=0.145  Sum_probs=26.2

Q ss_pred             CCCCHHHHHHHHHHHHCCCHHHHHHHHCCCC
Q ss_conf             6036389999999980899999999848888
Q gi|254780490|r    4 TAHTLRHSFATHLLSNGGDLRSIQSILGHSR   34 (67)
Q Consensus         4 tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~   34 (67)
                      .|..-|=.+....++.|.++..|.++-|=--
T Consensus        28 ~Pt~~Ri~~i~eAlr~G~sveeI~elTkID~   58 (153)
T d1a9xa1          28 DAGADRIWYIADAFRAGLSVDGVFNLTNIDR   58 (153)
T ss_dssp             TCBTTHHHHHHHHHHTTBCHHHHHHHHCCCH
T ss_pred             CCCCHHHHHHHHHHHCCCCHHHHHHHHCEEE
T ss_conf             6995499999999982999999988618200


No 8  
>d2odgc1 a.140.1.1 (C:2-47) Inner nuclear membrane protein emerin {Human (Homo sapiens) [TaxId: 9606]}
Probab=5.96  E-value=91  Score=12.16  Aligned_cols=18  Identities=6%  Similarity=0.314  Sum_probs=12.6

Q ss_pred             HHHHCCHHHHHHHHHHHC
Q ss_conf             998639999999999958
Q gi|254780490|r   40 IYTNVNSKRMMEIYDQTH   57 (67)
Q Consensus        40 ~Y~~~~~~~~~~~~~~~~   57 (67)
                      -|..+|++++.+..+++.
T Consensus         2 ~y~~lSd~El~~lL~~y~   19 (46)
T d2odgc1           2 NYADLSDTELTTLLRRYN   19 (46)
T ss_dssp             GGGGSCHHHHHHHHHHTT
T ss_pred             CHHHHCHHHHHHHHHHHC
T ss_conf             265606899999999928


No 9  
>d1bl0a2 a.4.1.8 (A:63-124) MarA {Escherichia coli [TaxId: 562]}
Probab=4.80  E-value=1.1e+02  Score=11.75  Aligned_cols=42  Identities=12%  Similarity=0.113  Sum_probs=30.4

Q ss_pred             HHHHHHHH-HCCCHHHHHHHHCCCCHHHH----HHHHHCCHHHHHHH
Q ss_conf             99999998-08999999998488888999----99986399999999
Q gi|254780490|r   11 SFATHLLS-NGGDLRSIQSILGHSRLSTT----QIYTNVNSKRMMEI   52 (67)
Q Consensus        11 t~at~l~~-~G~~~~~vq~lLGH~~i~tT----~~Y~~~~~~~~~~~   52 (67)
                      ..|..++. ...+|..|...+|-+|.+.-    ..+..+++.+.++.
T Consensus         4 ~~a~~lL~~t~~~i~~IA~~~Gf~~~~~F~r~Fk~~~g~tP~~~R~~   50 (62)
T d1bl0a2           4 TEIAQKLKESNEPILYLAERYGFESQQTLTRTFKNYFDVPPHKYRMT   50 (62)
T ss_dssp             HHHHHHHHHCCCCHHHHHHHTTCSCHHHHHHHHHHHHSSCHHHHHTC
T ss_pred             HHHHHHHHCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHH
T ss_conf             99999988369999999999879988999999998889099999976


No 10 
>d1d5ya2 a.4.1.8 (A:57-121) Rob transcription factor, N-terminal domain {Escherichia coli [TaxId: 562]}
Probab=4.23  E-value=1.2e+02  Score=11.52  Aligned_cols=44  Identities=9%  Similarity=-0.151  Sum_probs=32.9

Q ss_pred             HHHHHHHHHH-CCCHHHHHHHHCCCCHHHH----HHHHHCCHHHHHHHH
Q ss_conf             9999999980-8999999998488888999----999863999999999
Q gi|254780490|r   10 HSFATHLLSN-GGDLRSIQSILGHSRLSTT----QIYTNVNSKRMMEIY   53 (67)
Q Consensus        10 Ht~at~l~~~-G~~~~~vq~lLGH~~i~tT----~~Y~~~~~~~~~~~~   53 (67)
                      =..|..++.. ..++..|...+|-+|.+.-    ..+..++..+.++..
T Consensus         3 l~~A~~lL~~t~~~i~~IA~~~Gf~~~~~F~r~Fk~~~G~tP~~yRk~~   51 (65)
T d1d5ya2           3 LSKSAVALRLTARPILDIALQYRFDSQQTFTRAFKKQFAQTPALYRRSP   51 (65)
T ss_dssp             HHHHHHHHHHCCCCHHHHHHHTTCSCHHHHHHHHHHHHSSCHHHHHHCS
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHCC
T ss_conf             9999999886899999999997899879999999988890999998582


Done!