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 39220
Date          Sun May 29 19:58:06 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780490.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR02224 recomb_XerC tyrosine 100.0 1.8E-32 4.6E-37  187.9   5.9   61    2-62    253-313 (313)
  2 TIGR02225 recomb_XerD tyrosine 100.0 3.9E-31 9.9E-36  181.0   5.9   59    2-60    247-305 (305)
  3 PRK01287 xerC site-specific ty  99.9 5.4E-26 1.4E-30  154.6   7.1   64    2-65    266-329 (361)
  4 cd01198 INT_ASSRA_C Archaeal s  99.9 4.1E-25   1E-29  150.1   7.0   60    2-61    127-186 (186)
  5 COG4974 XerD Site-specific rec  99.9   5E-25 1.3E-29  149.6   5.7   59    2-60    242-300 (300)
  6 PRK09870 tyrosine recombinase;  99.9 3.9E-24   1E-28  145.0   7.3   61    2-62    137-197 (200)
  7 PRK09871 tyrosine recombinase;  99.9   4E-24   1E-28  145.0   7.2   65    2-66    132-196 (198)
  8 PRK00283 xerD site-specific ty  99.9 3.8E-23 9.6E-28  140.0   7.1   59    2-60    238-296 (296)
  9 cd01190 INT_SG5 INT_SG5, DNA b  99.9 4.9E-23 1.3E-27  139.3   7.2   57    2-58    204-260 (260)
 10 PRK00236 xerC site-specific ty  99.9 5.2E-23 1.3E-27  139.2   7.1   59    2-60    237-295 (295)
 11 TIGR02249 integrase_gron integ  99.9 4.2E-24 1.1E-28  144.8   0.9   46    2-47    263-308 (320)
 12 cd01196 INT_VanD VanD integras  99.9 1.7E-22 4.2E-27  136.6   7.1   56    2-57    206-261 (263)
 13 PRK05084 xerS site-specific ty  99.9 2.1E-22 5.4E-27  136.1   7.1   58    1-58    301-358 (360)
 14 COG4973 XerC Site-specific rec  99.9 1.1E-22 2.8E-27  137.6   5.2   62    2-63    238-299 (299)
 15 cd01185 INT_Tn4399 Tn4399 and   99.8 1.8E-21 4.7E-26  131.3   6.4   54    2-55    245-298 (299)
 16 cd01195 INT_Tn544B_C Tn544B an  99.8   2E-20   5E-25  126.0   5.9   52    2-53    144-195 (195)
 17 cd01194 INT_Tn554A_C Tn544A an  99.8 3.2E-20 8.1E-25  124.9   6.0   55    1-55    131-186 (186)
 18 PRK02436 xerD site-specific ty  99.8 3.6E-20 9.2E-25  124.6   4.3   42    2-43    206-247 (247)
 19 cd01197 INT_FimBE_C FimB and F  99.8 1.1E-19 2.8E-24  122.1   6.2   52    2-53    129-180 (180)
 20 cd01188 INT_pAE1 pAE1 and rela  99.8 1.1E-19 2.9E-24  122.1   6.2   52    2-53    132-183 (188)
 21 cd01186 INT_SG3_C INT_SG3, DNA  99.8 1.6E-19   4E-24  121.3   6.8   56    2-57    124-179 (180)
 22 cd00798 INT_XerDC XerD and Xer  99.8 1.1E-19 2.8E-24  122.1   5.6   52    2-53    233-284 (284)
 23 cd01199 INT_Tn1545_C Tn1545-re  99.8 4.1E-19   1E-23  119.2   6.6   55    2-56    150-205 (205)
 24 cd00797 HP1_INT_C Phage HP1 in  99.7 1.4E-18 3.7E-23  116.4   6.0   54    2-55    103-156 (158)
 25 cd01192 INT_P22_C P22-like int  99.7   2E-18 5.2E-23  115.6   6.7   58    2-59    119-176 (177)
 26 cd01187 INT_SG4 INT_SG4, DNA b  99.7 1.8E-18 4.5E-23  115.9   6.1   54    2-55    237-298 (299)
 27 cd01183 INT_SG1_C INT_SG1, DNA  99.7 2.8E-18 7.2E-23  114.9   4.1   42    2-43    155-196 (196)
 28 cd01193 INT_IntI IntI (E2) int  99.7 4.5E-18 1.2E-22  113.8   4.8   43    2-44    200-242 (242)
 29 cd00796 INT_Rci Rci recombinas  99.7   8E-18   2E-22  112.6   5.5   50    2-51    156-205 (206)
 30 cd01189 INT_phiLC3_C phiLC3 ph  99.6 1.7E-16 4.2E-21  105.8   4.3   47    2-48    143-190 (191)
 31 cd00799 INT_Cre Cre recombinas  99.6 2.8E-16 7.3E-21  104.6   5.1   52    2-53    233-284 (287)
 32 pfam00589 Phage_integrase Phag  99.5 7.9E-15   2E-19   97.2   4.5   46    2-47    124-169 (170)
 33 cd00397 DNA_BRE_C DNA breaking  99.5 1.2E-14 3.1E-19   96.2   4.1   42    2-43    123-164 (164)
 34 cd01191 INT_phiCTX_C phiCTX ph  99.5 3.6E-14 9.1E-19   93.8   5.2   42    3-44    153-195 (196)
 35 cd00801 INT_P4 Bacteriophage P  99.4 1.3E-13 3.2E-18   90.9   5.4   55    2-56    299-355 (357)
 36 cd01184 INT_SG2_C INT_SG2, DNA  99.4 4.8E-14 1.2E-18   93.1   2.5   41    2-42    139-180 (181)
 37 cd00800 INT_Lambda_C Lambda in  99.1 2.9E-11 7.3E-16   78.8   3.7   40    2-44    122-161 (162)
 38 cd01182 INT_REC_C DNA breaking  99.1   3E-11 7.6E-16   78.8   3.2   42    2-43    121-162 (162)
 39 COG0582 XerC Integrase [DNA re  98.5 2.6E-07 6.8E-12   58.4   6.1   54    2-56    248-302 (309)
 40 PRK09692 integrase; Provisiona  97.9 2.5E-05 6.5E-10   48.2   5.2   58    3-60    334-393 (413)
 41 COG4688 Uncharacterized protei  90.7    0.21 5.3E-06   28.1   2.7   55    1-55    446-500 (665)
 42 pfam11917 DUF3435 Protein of u  84.0     0.9 2.3E-05   24.8   2.6   40    2-42    194-234 (414)
 43 COG4342 Uncharacterized protei  42.6      32 0.00083   16.8   6.1   58    4-62    226-284 (291)
 44 TIGR00973 leuA_bact 2-isopropy  38.1      34 0.00088   16.7   3.0   44    1-65    340-383 (514)
 45 PHA00730 int integrase          37.9      39 0.00099   16.4   5.3   55    3-58    261-316 (322)
 46 pfam07506 RepB RepB plasmid pa  36.8      41   0.001   16.3   3.3   29    9-38     10-38  (185)
 47 COG2522 Predicted transcriptio  34.8      44  0.0011   16.2   3.2   40    7-47      9-48  (119)
 48 COG1602 Uncharacterized conser  28.6      55  0.0014   15.7   2.7   20   12-31    185-204 (402)
 49 PRK09568 DNA primase large sub  21.7      78   0.002   14.9   3.2   32    4-35    228-259 (306)
 50 PRK09857 hypothetical protein;  21.3      79   0.002   14.8   2.7   23   11-33    261-283 (292)

No 1  
>TIGR02224 recomb_XerC tyrosine recombinase XerC; InterPro: IPR011931    The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This entry represents XerC, which is closely related to the other chromosomal protein XerD (IPR011932 from INTERPRO). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. XerC and XerD interact with cell division protein FtsK .; GO: 0003677 DNA binding, 0006310 DNA recombination, 0007049 cell cycle, 0007059 chromosome segregation, 0015074 DNA integration, 0051301 cell division.
Probab=99.97  E-value=1.8e-32  Score=187.88  Aligned_cols=61  Identities=54%  Similarity=0.932  Sum_probs=59.4

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       253 ~~hPH~LRHSFATHLL~~gaDLRaVQELLGH~SLSTTQiYTHv~~~~L~~~Y~~AHPRA~k  313 (313)
T TIGR02224       253 HVHPHALRHSFATHLLENGADLRAVQELLGHASLSTTQIYTHVDFQHLAKVYDKAHPRAKK  313 (313)
T ss_pred             CCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             6787531131799997468835589897444643566798884099999999973777779


No 2  
>TIGR02225 recomb_XerD tyrosine recombinase XerD; InterPro: IPR011932   Proteins in this entry are part of the wider so-called "phage" integrase fmaily which describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci.   This entry represents the chromosomally-encoded polypeptide XerD, which is closely related to, and interacts with, another chromosomally-encoded polypeptide, XerC (IPR011931 from INTERPRO). These proteins are site-specific tyrosine recombinases, which act by catalyzing the cutting and rejoining of the recombining DNA molecules . They form a cyclic heterotetrameric complex composed of two molecules of XerC and two molecules of XerD. The XerC-XerD complex is essential to convert dimers of the bacterial chromosome into monomers to permit their segregation at cell division. It also contributes to the segregational stability of plasmids.   XerD is composed of two domains, an N-terminal alpha-helical domain, and a C-terminal domain composed mostly of alpha helices, with a three-stranded antiprallel beta sheet along one edge . The active site is found at the extreme C-terminal end of the polypeptide. Most of the C-terminal domain is structurally homologous to that of other "phage" integrases, but the active site regions of these enzymes are stucturally distinct.; GO: 0003677 DNA binding, 0006310 DNA recombination, 0007049 cell cycle, 0007059 chromosome segregation, 0015074 DNA integration, 0051301 cell division.
Probab=99.97  E-value=3.9e-31  Score=181.05  Aligned_cols=59  Identities=56%  Similarity=0.902  Sum_probs=57.6

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHCHHH
Q ss_conf             21603638999999998089999999984888889999998639999999999958211
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHPSI   60 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~~~~~~~~~~~~p~~   60 (67)
                      +||||+|||+|||||+++|+|+++||+||||+||+|||+|+||+.+.++++|.++||+.
T Consensus       247 ~isPHtLRHSFATHLLenGADLR~VQeLLGHadisTTQIYTHV~~~~L~~~~~~~HPRa  305 (305)
T TIGR02225       247 PISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQIYTHVARERLKEVHKKHHPRA  305 (305)
T ss_pred             CCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             99975104679999873688276887774322147889999987999999999628899


No 3  
>PRK01287 xerC site-specific tyrosine recombinase XerC; Reviewed
Probab=99.93  E-value=5.4e-26  Score=154.57  Aligned_cols=64  Identities=44%  Similarity=0.710  Sum_probs=60.8

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHCHHHHHHHC
Q ss_conf             2160363899999999808999999998488888999999863999999999995821133310
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHPSITQKDK   65 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~~~~~~~~~~~~p~~~~k~~   65 (67)
                      .++||+|||||||+|+++|+|+.+||++|||+||+||++|+|++.+.++++|+++||++...+.
T Consensus       266 ~~~pH~LRHTfAT~lL~~GadL~~VQelLGHasi~TTqiYtHv~~~~l~~v~~~~HP~~~~~~~  329 (361)
T PRK01287        266 KGACHLFRHAMATQMLENGADLRWIQAMLGHASLETTQIYTQVSIRHLQAVHASTHPAEQMADE  329 (361)
T ss_pred             CCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCC
T ss_conf             9982105999999999869999999998689977899999847999999999981998889863


No 4  
>cd01198 INT_ASSRA_C Archaeal site-specific recombinase A (ASSRA), DNA breaking-rejoining enzymes, integrase/recombinases, C-terminal catalytic domain. Members of this CD are archael in origin. No biochemical characterization is available for the proteins of this subgroup at this point.
Probab=99.91  E-value=4.1e-25  Score=150.07  Aligned_cols=60  Identities=33%  Similarity=0.497  Sum_probs=58.2

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHCHHHH
Q ss_conf             216036389999999980899999999848888899999986399999999999582113
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHPSIT   61 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~~~~~~~~~~~~p~~~   61 (67)
                      ++|||+|||||||+|+++|+|+.+||++|||+|++||++|+|++.++++++|++++|++.
T Consensus       127 ~vtPH~lRHtfAT~Ll~~G~dl~~vq~lLGHssi~tT~~Y~h~~~~~l~e~y~k~~Pr~~  186 (186)
T cd01198         127 NFTPHCFRHFFTTWLRRRGGDRGVVQELRGDSRDEAIDTYTHIWGDELREAYLKHIPSLG  186 (186)
T ss_pred             CCCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCC
T ss_conf             758516389999999986999999999948998899999984799999999998588998


No 5  
>COG4974 XerD Site-specific recombinase XerD [DNA replication, recombination, and repair]
Probab=99.91  E-value=5e-25  Score=149.63  Aligned_cols=59  Identities=58%  Similarity=0.957  Sum_probs=57.4

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHCHHH
Q ss_conf             21603638999999998089999999984888889999998639999999999958211
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHPSI   60 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~~~~~~~~~~~~p~~   60 (67)
                      .+|||+|||+|||||+++|+|+++||+||||+||+|||+|+|++.+.+++.|.++||+.
T Consensus       242 ~isPH~LRHsFATHLL~~GADlRvVQeLLGHadisTTQIYTHV~~e~L~~~~~~~HPra  300 (300)
T COG4974         242 KISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQIYTHVTKERLRDLYAQHHPRA  300 (300)
T ss_pred             CCCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             86813657889999986785399999984866501557879988999999999738999


No 6  
>PRK09870 tyrosine recombinase; Provisional
Probab=99.90  E-value=3.9e-24  Score=145.00  Aligned_cols=61  Identities=34%  Similarity=0.459  Sum_probs=59.0

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       137 ~v~pH~LRHt~At~Ll~~G~di~~Iq~lLGHssi~TT~iYth~~~~~l~~i~~~~hpr~~~  197 (200)
T PRK09870        137 EIHPHMLRHSCGFALANMGIDTRLIQDYLGHRNIRHTVWYTASNAGRFYGIWDRARGRQRH  197 (200)
T ss_pred             CCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHCCCHHC
T ss_conf             7687602899999999869999999999489986689998817999999999984973100


No 7  
>PRK09871 tyrosine recombinase; Provisional
Probab=99.90  E-value=4e-24  Score=144.97  Aligned_cols=65  Identities=29%  Similarity=0.465  Sum_probs=61.5

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHCHHHHHHHCC
Q ss_conf             21603638999999998089999999984888889999998639999999999958211333105
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHPSITQKDKK   66 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~~~~~~~~~~~~p~~~~k~~k   66 (67)
                      +++||+|||||||+|+++|+|+..||++|||+||+||++|+|++.+.++++|++.+|..++.++.
T Consensus       132 ~~~pH~LRHTfAt~Ll~~G~dl~~Iq~lLGHssi~TT~~Yth~~~~~l~~~~~~~~p~~~~~~~~  196 (198)
T PRK09871        132 QTHPHMLRHACGYELAERGADTRLIQDYLGHRNIRHTVRYTASNAARFAGLWERNNLINEKLKRE  196 (198)
T ss_pred             CCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCC
T ss_conf             88998557999999998699999999993899778999988589999999999949610010002


No 8  
>PRK00283 xerD site-specific tyrosine recombinase XerD; Reviewed
Probab=99.88  E-value=3.8e-23  Score=139.96  Aligned_cols=59  Identities=54%  Similarity=0.882  Sum_probs=57.5

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHCHHH
Q ss_conf             21603638999999998089999999984888889999998639999999999958211
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHPSI   60 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~~~~~~~~~~~~p~~   60 (67)
                      ++|||+|||||||+|+++|+|+..||++|||+||+||++|+|++.+++++++++|+|++
T Consensus       238 ~~tpH~lRHt~at~ll~~G~~l~~i~~~LGHssi~TT~~Y~h~~~~~l~~~~~~~~p~~  296 (296)
T PRK00283        238 KLSPHVLRHAFATHLLNHGADLRVVQELLGHSDISTTQIYTHVATERLKELHAQHHPRA  296 (296)
T ss_pred             CCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHCCCC
T ss_conf             88998787999999998798999999882899889999988689999999999868499


No 9  
>cd01190 INT_SG5 INT_SG5, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 5, N- and C-terminal domains. The CD contains mainly predicted bacterial integrase/recombinases.
Probab=99.88  E-value=4.9e-23  Score=139.35  Aligned_cols=57  Identities=35%  Similarity=0.536  Sum_probs=56.0

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       204 ~~~~H~lRHt~At~ll~~G~~l~~vq~~LGH~~i~tT~~Y~hv~~~~~r~a~~k~~p  260 (260)
T cd01190         204 RISPHVLRHTTAMHLLQSGVDIVVIALWLGHASLETTNIYAEADLEMKRRALAKATP  260 (260)
T ss_pred             CCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHCC
T ss_conf             767671389999999987999999999868998899999984799999999998691


No 10 
>PRK00236 xerC site-specific tyrosine recombinase XerC; Reviewed
Probab=99.88  E-value=5.2e-23  Score=139.23  Aligned_cols=59  Identities=59%  Similarity=0.986  Sum_probs=57.5

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHCHHH
Q ss_conf             21603638999999998089999999984888889999998639999999999958211
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHPSI   60 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~~~~~~~~~~~~p~~   60 (67)
                      ++|||+|||||||.|+++|+|+..||++|||+|++||++|+|++.++++++++++||++
T Consensus       237 ~~~~H~lRHt~At~l~~~G~~l~~vq~~LGHssi~tT~~Y~h~~~~~l~~~~~~~~p~~  295 (295)
T PRK00236        237 HITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEVYDAAHPRA  295 (295)
T ss_pred             CCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHCCCC
T ss_conf             99899788999999998799999999881899889999988689999999999878399


No 11 
>TIGR02249 integrase_gron integron integrase; InterPro: IPR011946    Members of this family are integrases associated with integrons (and super-integrons), which are systems for incorporating and expressing cassettes of laterally transferred DNA. Incorporation occurs at an attI site. A super-integron, as in Vibrio sp., may include over 100 cassettes. This family belongs to the phage integrase family that also includes recombinases XerC (IPR011931 from INTERPRO) and XerD (IPR011932 from INTERPRO), which are bacterial housekeeping proteins. Within this family of integron integrases, some are designated by class, e.g. IntI4, a class 4 integron integrase from Vibrio cholerae N16961.; GO: 0003677 DNA binding, 0006310 DNA recombination, 0015074 DNA integration.
Probab=99.88  E-value=4.2e-24  Score=144.83  Aligned_cols=46  Identities=61%  Similarity=0.963  Sum_probs=43.4

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCHH
Q ss_conf             2160363899999999808999999998488888999999863999
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSK   47 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~~   47 (67)
                      .||||.|||+|||||+++|.||.+||++|||+||.|||+|+||-..
T Consensus       263 pvTcHTLRHSFATHLLe~G~DIRTVQelLGHsDVkTTqIYTHVL~r  308 (320)
T TIGR02249       263 PVTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIYTHVLNR  308 (320)
T ss_pred             CCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCCCCCCEEEEEECC
T ss_conf             6788742122443056517736789886178842246345305145


No 12 
>cd01196 INT_VanD VanD integrase, IntD, and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, N- and C-terminal domains. This CD includes various bacterial integrases including those similar to IntD, a putative integrase-like protein, a component of the vanD glycopeptide resistance cluster in Enterococcus faecium BM4339. Members of this CD are predominantly bacterial in origin.
Probab=99.87  E-value=1.7e-22  Score=136.65  Aligned_cols=56  Identities=29%  Similarity=0.497  Sum_probs=53.8

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHC
Q ss_conf             21603638999999998089999999984888889999998639999999999958
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTH   57 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~~~~~~~~~~~~   57 (67)
                      ++|||+|||||||+|+++|+|+..||++|||+||+||++|++++.+++++++++..
T Consensus       206 ~~~PH~lRHtfAt~ll~~g~dl~~vq~lLGH~si~TT~iY~~~~~~~~k~~~~k~~  261 (263)
T cd01196         206 VVYPHSFRHLFAKNFLAKYNDLALLADLMGHESIETTRIYLRKTATEQQRIVDKIV  261 (263)
T ss_pred             CCCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHC
T ss_conf             78872269999999998699999999995899878999988079999999999870


No 13 
>PRK05084 xerS site-specific tyrosine recombinase XerS; Reviewed
Probab=99.87  E-value=2.1e-22  Score=136.11  Aligned_cols=58  Identities=28%  Similarity=0.449  Sum_probs=55.3

Q ss_pred             CCCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHCH
Q ss_conf             9216036389999999980899999999848888899999986399999999999582
Q gi|254780490|r    1 MSTTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHP   58 (67)
Q Consensus         1 ~~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~~~~~~~~~~~~p   58 (67)
                      +++|||.|||||||+|+++|+|+..||++|||+|++||++|+|++++++++++++...
T Consensus       301 ~~itpH~LRHtfAT~Ll~~G~dl~~vq~lLGH~si~TT~iYthv~~~~~r~a~~~l~~  358 (360)
T PRK05084        301 VRVTPHKLRHTLATRLYDATKDQVLVADQLGHTSTQVTDLYTHIVNDEQKDALDKLEK  358 (360)
T ss_pred             CCCCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHCC
T ss_conf             9978413299999999987999999999858998799999886899999999986366


No 14 
>COG4973 XerC Site-specific recombinase XerC [DNA replication, recombination, and repair]
Probab=99.87  E-value=1.1e-22  Score=137.56  Aligned_cols=62  Identities=50%  Similarity=0.888  Sum_probs=60.1

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       238 HvhPH~LRHSFAtHmLesSgDLRaVQELLGHanlsTTQIYThLDFQHLA~vYD~AHPRAkrk  299 (299)
T COG4973         238 HVHPHKLRHSFATHMLESSGDLRAVQELLGHANLSTTQIYTHLDFQHLASVYDAAHPRAKRK  299 (299)
T ss_pred             CCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCHHHHHHHCCHHHHHHHHHHHCCCCCCC
T ss_conf             38768777788999987035489999985646512444323236899999986317411269


No 15 
>cd01185 INT_Tn4399 Tn4399 and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, N- and C-terminal domains. This CD includes various bacterial integrases, including cLV25, a Bacteroides fragilis chromosomal transfer factor integrase similar to the Bacteroides mobilizable transposon, Tn4399, integrase.
Probab=99.84  E-value=1.8e-21  Score=131.26  Aligned_cols=54  Identities=35%  Similarity=0.616  Sum_probs=52.6

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHH
Q ss_conf             216036389999999980899999999848888899999986399999999999
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQ   55 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~~~~~~~~~~   55 (67)
                      ++|||+|||||||+|+++|+|+.+||++|||+|++||++|+|++++.+++++++
T Consensus       245 ~it~H~lRHTfAt~ll~~G~~l~~vq~~LGHssi~tT~~Y~hv~~e~~~e~~~k  298 (299)
T cd01185         245 HITFHCARHTFATLQLLSGGPIETVSKMLGHTNIKTTQVYARVTDEKKSEDMNK  298 (299)
T ss_pred             CCCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHC
T ss_conf             998114099999999987989999998818998899999987798899999963


No 16 
>cd01195 INT_Tn544B_C Tn544B and related transposases, DNA breaking-rejoining enzymes, integrase/recombinases, catalytic domain. This CD includes various bacterial transposases similar to TnpB from transposon Tn554.
Probab=99.81  E-value=2e-20  Score=125.96  Aligned_cols=52  Identities=29%  Similarity=0.502  Sum_probs=50.2

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHH
Q ss_conf             2160363899999999808999999998488888999999863999999999
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIY   53 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~~~~~~~~   53 (67)
                      +++||+|||||||+|+++|+|+.+||++|||+|++||++|+|++++.++++|
T Consensus       144 ~~~~H~lRHT~aT~L~~~Gv~i~~Iq~~LGH~s~~tT~~Yahv~~e~l~~~~  195 (195)
T cd01195         144 HFHAHAFRHTVATRMINNGMPIHIIQKFLGHESPEMTSRYAHIFDETLKNEF  195 (195)
T ss_pred             CCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHC
T ss_conf             6688877489999999869999999999489998999998857989998629


No 17 
>cd01194 INT_Tn554A_C Tn544A and related transposases, DNA breaking-rejoining enzymes, integrase/recombinases, C-terminal catalytic domain. This CD includes various bacterial transposases similar to TnpA from transposon Tn554.
Probab=99.81  E-value=3.2e-20  Score=124.89  Aligned_cols=55  Identities=25%  Similarity=0.518  Sum_probs=52.1

Q ss_pred             CCCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHH-HHHHHCCHHHHHHHHHH
Q ss_conf             92160363899999999808999999998488888999-99986399999999999
Q gi|254780490|r    1 MSTTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTT-QIYTNVNSKRMMEIYDQ   55 (67)
Q Consensus         1 ~~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT-~~Y~~~~~~~~~~~~~~   55 (67)
                      ++++||+|||||||+|+++|+|+..||++|||+|++|| ++|+|+++++++++++|
T Consensus       131 ~~~~~H~lRHT~at~l~~~G~~~~~v~~~lGH~~~~tT~~~Y~h~~~e~~~~~~~k  186 (186)
T cd01194         131 IDFTPHMFRHTHATELIRAGWSIEVVADRLGHAHVQTTLNTYGHLSEEDIRREFNK  186 (186)
T ss_pred             CCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHHHCC
T ss_conf             98774575999999999879999999998289987999998456899999998658


No 18 
>PRK02436 xerD site-specific tyrosine recombinase XerD-like protein; Reviewed
Probab=99.80  E-value=3.6e-20  Score=124.62  Aligned_cols=42  Identities=24%  Similarity=0.331  Sum_probs=40.4

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             216036389999999980899999999848888899999986
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTN   43 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~   43 (67)
                      ++|||+|||+|||+|+++|+|+..||++|||+||+||++|+.
T Consensus       206 ~vtPH~LRHsFAthlL~~Gadlr~vQeLLGH~sisTTqiY~k  247 (247)
T PRK02436        206 GLTAQKLREQFILKQKEAGKSIYELARLLGLKTPVTLEKYYK  247 (247)
T ss_pred             CCCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHCC
T ss_conf             998710099999999987999999998808998788553069


No 19 
>cd01197 INT_FimBE_C FimB and FimE and related proteins, DNA breaking-rejoining enzymes, integrase/recombinases, catalytic domain. This CD includes those proteins similar to E.coli FimE and FimB regulatory proteins and Proteus mirabilis MrpI.
Probab=99.79  E-value=1.1e-19  Score=122.11  Aligned_cols=52  Identities=37%  Similarity=0.620  Sum_probs=49.8

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHH
Q ss_conf             2160363899999999808999999998488888999999863999999999
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIY   53 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~~~~~~~~   53 (67)
                      +++||+|||||||+++++|+|+.+||++|||+|++||++|+|++.+.+.+.|
T Consensus       129 ~~~~H~lRHt~At~l~~~G~~i~~Iq~~LGH~~i~tT~~Yth~~~~~l~~~~  180 (180)
T cd01197         129 KVHPHMLRHACGYALANQGADTRLIQDYLGHRNIRHTVIYTASNAARFLNLW  180 (180)
T ss_pred             CCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHC
T ss_conf             6789877899999999879999999998389987999999967999998629


No 20 
>cd01188 INT_pAE1 pAE1 and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, C-terminal domain. This CD includes various bacterial integrases, including the predicted integrase of the deletion-prone region of plasmid pAE1 of Alcaligenes eutrophus H1.
Probab=99.79  E-value=1.1e-19  Score=122.06  Aligned_cols=52  Identities=40%  Similarity=0.611  Sum_probs=50.3

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHH
Q ss_conf             2160363899999999808999999998488888999999863999999999
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIY   53 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~~~~~~~~   53 (67)
                      ++|||+|||||||+++++|+|+..||++|||+||+||++|+|++.++++++.
T Consensus       132 ~~~~H~lRHt~at~l~~~G~~l~~vq~~lGH~si~tT~~Y~h~~~e~lr~~~  183 (188)
T cd01188         132 RGGAHLLRHSLATRLLRAGAPLKEIGDVLGHRSPDSTAIYAKVDVDALRAIA  183 (188)
T ss_pred             CCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHC
T ss_conf             8787614899999999969999999998389988999998856999998664


No 21 
>cd01186 INT_SG3_C INT_SG3, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 3, catalytic domain. The CD contains various predicted bacterial and phage integrase/recombinase sequences for which not much experimental characterization is available.
Probab=99.79  E-value=1.6e-19  Score=121.33  Aligned_cols=56  Identities=25%  Similarity=0.390  Sum_probs=54.2

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHC
Q ss_conf             21603638999999998089999999984888889999998639999999999958
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTH   57 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~~~~~~~~~~~~   57 (67)
                      +++||+|||||||+++++|+|+..||++|||+|++||++|++++.+++++++++|.
T Consensus       124 ~~~~H~lRHT~at~l~~~G~~l~~iq~~LGH~si~tT~~Y~~~~~e~~~k~~~~~~  179 (180)
T cd01186         124 NIGTHTLRKTFGYHYYKQTKDIALLMEIFNHSSPAITLRYIGINQDEIDKQLDNFK  179 (180)
T ss_pred             CCCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHCC
T ss_conf             76676017899999999699999999993899989999985899999999997378


No 22 
>cd00798 INT_XerDC XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination of chromosomal replication, and stable plasmid inheritance. They share the same fold in their catalytic domain containing six conserved active site residues and the overall reaction mechanism with the DNA breaking-rejoining enzyme superfamily.  In Escherichia coli, the Xer site-specific recombination system acts to convert dimeric chromosomes, which are formed by homologous recombination to monomers. Two related recombinases, XerC and XerD, bind cooperatively to a recombination site present in the E. coli chromosome. Each recombinase catalyzes the exchange of one pair of DNA strand in a reaction that proceeds through a Holliday junction intermediate. These enzymes can bridge two different and well-separated DNA sequen
Probab=99.79  E-value=1.1e-19  Score=122.14  Aligned_cols=52  Identities=60%  Similarity=0.974  Sum_probs=50.3

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHH
Q ss_conf             2160363899999999808999999998488888999999863999999999
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIY   53 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~~~~~~~~   53 (67)
                      ++|||+|||||||.++++|+|+..||++|||+|++||++|+|++.++++++|
T Consensus       233 ~~~~H~lRHt~at~l~~~g~~~~~i~~~lGH~s~~tT~~Y~h~~~~~l~e~~  284 (284)
T cd00798         233 KISPHTLRHSFATHLLENGADLRAVQELLGHASLATTQIYTHVSFEHLKEVY  284 (284)
T ss_pred             CCCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHC
T ss_conf             9991465999999999878999999988079879999987777999998519


No 23 
>cd01199 INT_Tn1545_C Tn1545-related conjugative transposon integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes bacterial (gram positive) and phage integrases, including those similar to Tn1545, Tn5252, and Tn5276 conjugative transposon integrases and Lactobacillus phage phi adh integrase.
Probab=99.77  E-value=4.1e-19  Score=119.18  Aligned_cols=55  Identities=35%  Similarity=0.484  Sum_probs=51.9

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHH-HHHHHCCHHHHHHHHHHH
Q ss_conf             2160363899999999808999999998488888999-999863999999999995
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTT-QIYTNVNSKRMMEIYDQT   56 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT-~~Y~~~~~~~~~~~~~~~   56 (67)
                      ++|||+|||||||+|+++|+|+..||++|||+|++|| ++|+|++++..++++++.
T Consensus       150 ~~~~H~lRHT~at~l~~~G~~~~~v~~~lGHss~~tT~~iY~h~~~~~~~e~~~kl  205 (205)
T cd01199         150 HVTTHIFRHTHISFLAEEGVPLKAIMDRVGHSDGKTTLRIYSHVTEKMKDEIVKKL  205 (205)
T ss_pred             CCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHHHHCC
T ss_conf             75764559999999998699999999986799889998886616989999999609


No 24 
>cd00797 HP1_INT_C Phage HP1 integrase, C-terminal catalytic domain.  Bacteriophage HP1 and related integrases are found in eubacteria, plasmids and temperate bacteriophages of the P2 family.  They belong to the DNA breaking-rejoining enzyme superfamily, which includes tyrosine recombinases and type IB topoisomerases. These enzymes share the same fold in their C-terminal catalytic domain containing six conserved active site residues and the overall reaction mechanism. The HP1 recombinase controls phage replication by site-specific recombination between the HP1 genome and the chromosomal DNA. It is a heterobifunctional DNA-binding protein, which recognizes two different DNA sequence motifs (type I and type II binding sites). The C-terminal catalytic domain of the HP1 integrase binds to the type I site, while the less conserved N-terminal domain is largely responsible for binding to the type II site.
Probab=99.75  E-value=1.4e-18  Score=116.39  Aligned_cols=54  Identities=31%  Similarity=0.660  Sum_probs=52.1

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHH
Q ss_conf             216036389999999980899999999848888899999986399999999999
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQ   55 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~~~~~~~~~~   55 (67)
                      +++||+|||||||+++++|+|+.+||++|||+|++||++|+|++++.++++++.
T Consensus       103 ~~~~H~lRHt~At~l~~~G~~i~~v~~~lGH~s~~~T~~Y~hl~~~~l~~av~~  156 (158)
T cd00797         103 GQATHILRHTFASHFMMNGGNIATLQHILGHATIEMTMRYAHLAPDHLDDAVSL  156 (158)
T ss_pred             CCCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHCCCCCHHHHHHHHHH
T ss_conf             866227889999999984998999999848999999977748699999999985


No 25 
>cd01192 INT_P22_C P22-like integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various bacterial and phage integrases, including those similar to phage P22-like integrases, DLP12 and APSE-1.
Probab=99.75  E-value=2e-18  Score=115.60  Aligned_cols=58  Identities=26%  Similarity=0.418  Sum_probs=55.0

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHCHH
Q ss_conf             2160363899999999808999999998488888999999863999999999995821
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHPS   59 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~~~~~~~~~~~~p~   59 (67)
                      .++||+|||||||.++++|+|+..||++|||+|++||++|+|++++.+++++++....
T Consensus       119 ~~~~H~lRHt~at~l~~~G~~~~~i~~~lGH~~~~~T~~Y~h~~~~~~r~a~~~l~~~  176 (177)
T cd01192         119 DFRWHDLRHTWASWLVQSGVPLYVLQELLGHSSLQMVRRYAHLSPEHLRAAARALDAF  176 (177)
T ss_pred             CCCCCCCCHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf             9986889688999999969899999999589989999998866999999999998734


No 26 
>cd01187 INT_SG4 INT_SG4, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 4, N- and C-terminal domains. The CD contains mainly predicted bacterial integrase/recombinases for which not much biochemical characterization is available.
Probab=99.75  E-value=1.8e-18  Score=115.92  Aligned_cols=54  Identities=28%  Similarity=0.455  Sum_probs=49.7

Q ss_pred             CCCCCCHHHHHHHHHH----HHCCCHH----HHHHHHCCCCHHHHHHHHHCCHHHHHHHHHH
Q ss_conf             2160363899999999----8089999----9999848888899999986399999999999
Q gi|254780490|r    2 STTAHTLRHSFATHLL----SNGGDLR----SIQSILGHSRLSTTQIYTNVNSKRMMEIYDQ   55 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~----~~G~~~~----~vq~lLGH~~i~tT~~Y~~~~~~~~~~~~~~   55 (67)
                      .++||+||||||++++    ++|+|+.    +||++|||+||+||++|+|++++.++++++.
T Consensus       237 ~~~pH~LRHtfAt~~l~~~~~~G~di~~~L~~lq~~LGH~si~tT~~Y~h~~~e~l~~a~~r  298 (299)
T cd01187         237 GPRLHDLRHRFAVTRLTRWYRAGADVERKLPVLATYLGHANITDTYWYLHASPELMELAARR  298 (299)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHHCCHHHHHHHHHH
T ss_conf             99976571389999999998679973433999999748998688898880399999999850


No 27 
>cd01183 INT_SG1_C INT_SG1, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 1, C-terminal catalytic domain. The CD contains mainly predicted integrase/recombinase and site-specific XerD recombinases. The members of this CD are found predominantly in proteobacteria. These proteins have not been biochemically characerised as yet.
Probab=99.72  E-value=2.8e-18  Score=114.88  Aligned_cols=42  Identities=38%  Similarity=0.593  Sum_probs=40.6

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             216036389999999980899999999848888899999986
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTN   43 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~   43 (67)
                      ++|||+|||||||+++++|+|+..||++|||+||+||++|+|
T Consensus       155 ~~spH~LRHt~At~ll~~G~~l~~Vq~~LGH~si~TT~~Y~H  196 (196)
T cd01183         155 AASTHWLRHTHASHDLAAGVPLEHVQDNLGHASIDTTSRYLH  196 (196)
T ss_pred             CCCCCCCHHHHHHHHHHCCCCHHHHHHHCCCCCHHHHHHCCC
T ss_conf             678832589999999987999999998808998678734339


No 28 
>cd01193 INT_IntI IntI (E2) integrases, site-specific tyrosine recombinases, DNA breaking-rejoining enzymes, N- and C-terminal domains. This CD includes integrases which are components of multiresistant integrons and mediate recombination between a proximal attI site and a secondary target called the attC (or 59-base element) present on various mobile gene cassettes. Integron-integrases are present in many natural occurring mobile elements, including transposons and conjugative plasmids. Vibrio, Shewanella, Xanthomonas and Pseudomonas species harbor chromosomal super-integrons. All integron-integrases carry large inserts unlike the TnpF ermF-like proteins also seen in this group.
Probab=99.72  E-value=4.5e-18  Score=113.81  Aligned_cols=43  Identities=67%  Similarity=0.971  Sum_probs=41.7

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHC
Q ss_conf             2160363899999999808999999998488888999999863
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNV   44 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~   44 (67)
                      ++|||+|||||||+++++|+|+..||++|||+|++||++|+|+
T Consensus       200 ~~~~H~lRHT~at~ll~~G~~l~~v~~~lGH~si~tT~~Y~Hv  242 (242)
T cd01193         200 RVTPHTLRHSFATHLLEAGYDIRTIQELLGHSDLKTTMIYTHV  242 (242)
T ss_pred             CCCCCCCHHHHHHHHHHCCCCHHHHHHHCCCCCHHHHHHHHCC
T ss_conf             9886748999999999879999999988399888899870583


No 29 
>cd00796 INT_Rci Rci recombinase, C-terminal catalytic domain.  Rci enzymes are found in IncI1 incompatibility group plasmids such as R64.  These recombinases belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The R64 Rci recombinase mediates site specific recombination at the highly mobile DNA segments called shufflon located in the C-terminal region of the pilV gene, which determines the recipient specificity in liquid mating. This gene encodes a thin pilus component that recognizes recipient's receptors required for liquid mating. The recombination occurs between any of the seven inverted repeats that separate four DNA segments of the shufflon. The segments can be inverted independently or in groups, resulting in a complex DNA rearrangement. The catalytic domain of Rci is linked to a variable N-terminal domain, whose function is unknown.
Probab=99.71  E-value=8e-18  Score=112.56  Aligned_cols=50  Identities=26%  Similarity=0.442  Sum_probs=48.0

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       156 ~~~~H~lRHt~at~l~~~G~~~~~i~~~lGH~~~~~t~~Y~h~~~e~L~~  205 (206)
T cd00796         156 DLHFHDLRHEATSRLFEKGLSIMEVASISGHRDWRMLKRYTHLSAEDLAE  205 (206)
T ss_pred             CCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHC
T ss_conf             87532048999999998698999999985899999998846739988704


No 30 
>cd01189 INT_phiLC3_C phiLC3 phage and phage-related integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various bacterial (mainly gram positive) and phage integrases, including those similar to Lactococcus phage phiLC3, TPW22, Tuc2009, BK5-T, A2,  bIL285, bIL286, bIL311, ul36 and phi g1e; Staphylococcus aureus phage phi13 and phi42; Oenococcus oeni phage fOg44; Streptococcus thermophilus phage O1205 and Sfi21; and Streptococcus pyogenes phage T12 and T270.
Probab=99.63  E-value=1.7e-16  Score=105.78  Aligned_cols=47  Identities=34%  Similarity=0.571  Sum_probs=44.5

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHH-HHHHHCCHHH
Q ss_conf             2160363899999999808999999998488888999-9998639999
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTT-QIYTNVNSKR   48 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT-~~Y~~~~~~~   48 (67)
                      ++|||+|||||||.++++|+|+..||++|||+|++|| ++|+|+++++
T Consensus       143 ~~~~H~lRHT~aT~l~~~G~~~~~i~~~lGH~s~~~T~~~Y~h~~~~~  190 (191)
T cd01189         143 KITFHGLRHTHASLLLEAGVSIKYVSERLGHADISTTLDTYSHLLPEK  190 (191)
T ss_pred             CCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCCCCC
T ss_conf             056343599999999996999999999858998899997711669465


No 31 
>cd00799 INT_Cre Cre recombinase, C-terminal catalytic domain.  Cre-like recombinases belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism.  The bacteriophage P1 Cre recombinase maintains the circular phage replicon in a monomeric state by catalyzing a site-specific recombination between two loxP sites.  The catalytic core domain of Cre recombinase is linked to a more divergent helical N-terminal domain, which interacts primarily with the DNA major groove proximal to the crossover region.
Probab=99.63  E-value=2.8e-16  Score=104.57  Aligned_cols=52  Identities=21%  Similarity=0.133  Sum_probs=47.1

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHH
Q ss_conf             2160363899999999808999999998488888999999863999999999
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIY   53 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~~~~~~~~   53 (67)
                      .+|||+|||||||+++++|+|+..||++|||+|++||++|++..+....++.
T Consensus       233 ~~s~H~lRHt~At~ll~~G~~l~~Iq~~lGH~s~~tt~~Y~~~~d~~~~~~~  284 (287)
T cd00799         233 SWSGHSLRRGFATEAARAGYSLLEIMRQGRWRSPKMVSRYIRDADRFQGNAV  284 (287)
T ss_pred             CCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCCHHCCCHH
T ss_conf             9897513899999999879999999998589998899998537131013244


No 32 
>pfam00589 Phage_integrase Phage integrase family. Members of this family cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment. The catalytic site residues in CRE recombinase are Arg-173, His-289, Arg-292 and Tyr-324.
Probab=99.53  E-value=7.9e-15  Score=97.15  Aligned_cols=46  Identities=54%  Similarity=0.781  Sum_probs=44.2

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCHH
Q ss_conf             2160363899999999808999999998488888999999863999
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSK   47 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~~   47 (67)
                      ++|||+|||||||.++++|+|+..||++|||+|++||++|++++++
T Consensus       124 ~~s~Hs~Rht~at~l~~~g~~~~~v~~~lGH~~~~tT~~Y~~~~~~  169 (170)
T pfam00589       124 DLTPHDLRHTFATHLAENGVPLRVIQKLLGHSSISMTMRYTHVAAE  169 (170)
T ss_pred             CCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHCCCCCC
T ss_conf             6787888489999999969999999999689998999982083855


No 33 
>cd00397 DNA_BRE_C DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site residues. The best-studied members of this diverse superfamily include human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl gener
Probab=99.50  E-value=1.2e-14  Score=96.21  Aligned_cols=42  Identities=45%  Similarity=0.765  Sum_probs=40.5

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             216036389999999980899999999848888899999986
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTN   43 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~   43 (67)
                      .++||+|||||||.++++|+|+..||++|||+|++||++|+|
T Consensus       123 ~~~~H~lRht~at~l~~~g~~~~~I~~~lGHs~~~tT~~Y~h  164 (164)
T cd00397         123 GLTPHSLRHTFASALLNAGLDLEAVQDLLGHSSIAMTMRYAH  164 (164)
T ss_pred             CCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHCCC
T ss_conf             677566589999999996999999999968999889711839


No 34 
>cd01191 INT_phiCTX_C phiCTX phage and phage-related integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various phage and bacterial integrases, including those similar to phage integrases: Bordetella and Pseudomonas phiCTX;  E. coli  Rac, Qin, and Shiga toxin 2 933W; and Salmonella typhimurium LT2 Gifsy-2 and Fels-1; and a putative pore-forming cytotoxin integrase from Vibrio parahaemolyticus O3:K6.
Probab=99.48  E-value=3.6e-14  Score=93.77  Aligned_cols=42  Identities=24%  Similarity=0.441  Sum_probs=39.3

Q ss_pred             CCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHH-HHHHHC
Q ss_conf             160363899999999808999999998488888999-999863
Q gi|254780490|r    3 TTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTT-QIYTNV   44 (67)
Q Consensus         3 ~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT-~~Y~~~   44 (67)
                      .+||+|||||||.|+++|+|+.+||++|||+|++|| .+|++.
T Consensus       153 ~~~H~lRHT~aT~ll~~G~~~~~v~~~lGHss~~~T~~~Ya~~  195 (196)
T cd01191         153 RNPYQMRHTFASWMLTAGANPAFIADQMGHKSAEMVFKHYGKW  195 (196)
T ss_pred             CCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf             7777884799999998798999999996899799999998833


No 35 
>cd00801 INT_P4 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements.  They share the same fold in their catalytic domain and the overall reaction mechanism with the superfamily of DNA breaking-rejoining enzymes. The P4 integrase mediates integrative and excisive site-specific recombination between two sites, called attachment sites, located on the phage genome and the bacterial chromosome. The phage attachment site is often found adjacent to the integrase gene, while the host attachment sites are typically situated near tRNA genes.
Probab=99.44  E-value=1.3e-13  Score=90.93  Aligned_cols=55  Identities=22%  Similarity=0.121  Sum_probs=48.4

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHH-HHHHHCC-HHHHHHHHHHH
Q ss_conf             2160363899999999808999999998488888999-9998639-99999999995
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTT-QIYTNVN-SKRMMEIYDQT   56 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT-~~Y~~~~-~~~~~~~~~~~   56 (67)
                      .+|||+|||||||.|+++|+|+.+||.+|||++..+| .+|.|.. .++.+++++.-
T Consensus       299 ~~t~HdlRhT~aT~l~~~Gv~~~~i~~~LGH~~~~~t~~~Y~h~~y~~ekr~~l~~w  355 (357)
T cd00801         299 EWTPHGLRRTARTWLNELGFPPDVIERQLAHVLGGKVRAAYNRADYLEERREAMQWW  355 (357)
T ss_pred             CCEEECCHHHHHHHHHHCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             950324889999999985989999999848999981899961744899999999986


No 36 
>cd01184 INT_SG2_C INT_SG2, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 2, C-terminal catalytic domain. The CD contains mainly predicted integrase/recombinases and phage-related integrases. Some have N-terminal domains, which show little sequence similarity to each other. Members of this subgroup are predominantly found in proteobacteria.
Probab=99.43  E-value=4.8e-14  Score=93.13  Aligned_cols=41  Identities=34%  Similarity=0.501  Sum_probs=38.7

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHH-HHH
Q ss_conf             21603638999999998089999999984888889999-998
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQ-IYT   42 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~-~Y~   42 (67)
                      +++||+|||||||.|+++|+|+.+||++|||+|++||+ +|.
T Consensus       139 ~~~~H~lRHT~aT~l~~~gv~~~~v~~~lGHss~~tT~~~Yg  180 (181)
T cd01184         139 GKSFHSFRHTFITELRNAGVSRELIAAIMGHEEGTTTFGRYG  180 (181)
T ss_pred             CCCCCCCHHHHHHHHHHCCCCHHHHHHHCCCCCCCCCCCCCC
T ss_conf             897864689999999986989999999828999886425308


No 37 
>cd00800 INT_Lambda_C Lambda integrase, C-terminal catalytic domain. Lambda-type integrases catalyze site-specific integration and excision of temperate bacteriophages and other mobile genetic elements to and from the bacterial host chromosome.  They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The phage lambda integrase can bridge two different and well-separated DNA sequences called arm- and core-sites.  The C-terminal domain binds, cleaves and re-ligates DNA strands at the core-sites, while the N-terminal domain is largely responsible for high-affinity binding to the arm-type sites.
Probab=99.14  E-value=2.9e-11  Score=78.83  Aligned_cols=40  Identities=30%  Similarity=0.440  Sum_probs=35.8

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHC
Q ss_conf             2160363899999999808999999998488888999999863
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNV   44 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~   44 (67)
                      .+|+|+|||||||.+.++|.   .+|.+|||+|++||++|.+.
T Consensus       122 ~~t~H~lRht~at~~~~~g~---~~q~llGH~s~~~T~~Y~r~  161 (162)
T cd00800         122 PPTFHDIRAKAASDYEEQGK---DAQALLGHKDEKMTKIYRRK  161 (162)
T ss_pred             CCCHHHHHHHHHHHHHHCCH---HHHHHCCCCCHHHHHHHCCC
T ss_conf             66018889999999873748---89998099998997066068


No 38 
>cd01182 INT_REC_C DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family include the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many intergrase/recombinases also have N-terminal domains, which show little sequence or structure similarity.
Probab=99.13  E-value=3e-11  Score=78.76  Aligned_cols=42  Identities=52%  Similarity=0.756  Sum_probs=40.2

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             216036389999999980899999999848888899999986
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTN   43 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~   43 (67)
                      .++||+|||+|||.++++|+++..|+.++||+++.||+.|++
T Consensus       121 ~~~~h~lRh~~~t~~~~~g~~~~~i~~~~GH~~~~~t~~Y~~  162 (162)
T cd01182         121 RLTPHDLRHTFATRLLEAGVPLEVIQELLGHSSISTTERYLH  162 (162)
T ss_pred             CCCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHCCCCCC
T ss_conf             997016199999999996999999999928999898152819


No 39 
>COG0582 XerC Integrase [DNA replication, recombination, and repair]
Probab=98.51  E-value=2.6e-07  Score=58.43  Aligned_cols=54  Identities=44%  Similarity=0.605  Sum_probs=41.3

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHH-HCCHHHHHHHHHHH
Q ss_conf             21603638999999998089999999984888889999998-63999999999995
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYT-NVNSKRMMEIYDQT   56 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~-~~~~~~~~~~~~~~   56 (67)
                      .+|||.|||||++.+++.| +...++.++||+++.+|+.|. +.............
T Consensus       248 ~~~~h~lRht~~~~~~~~~-~~~~~~~~~gH~~~~~~~~~~~~~~~~~~~~~~~~~  302 (309)
T COG0582         248 KITPHGLRHTFATLLLAGG-DERVIQKLLGHASLNTTQTVYYHASDERLKEAALKL  302 (309)
T ss_pred             CCCCCCCHHHHHHHHHHCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             8787740789999998568-765899983787087899999987106678999864


No 40 
>PRK09692 integrase; Provisional
Probab=97.88  E-value=2.5e-05  Score=48.23  Aligned_cols=58  Identities=17%  Similarity=0.162  Sum_probs=43.9

Q ss_pred             CCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHH-HHHHHHHCCH-HHHHHHHHHHCHHH
Q ss_conf             1603638999999998089999999984888889-9999986399-99999999958211
Q gi|254780490|r    3 TTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLS-TTQIYTNVNS-KRMMEIYDQTHPSI   60 (67)
Q Consensus         3 ~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~-tT~~Y~~~~~-~~~~~~~~~~~p~~   60 (67)
                      .|||+||+||+|.|-+.|.+..+|-.+|||..-. +...|-+... ++.+++++..-+++
T Consensus       334 ~t~Hd~RrT~~T~l~e~g~~~~viE~~L~H~~~~~v~~~Ynr~~yl~eRr~~mq~Wadyl  393 (413)
T PRK09692        334 LVSHGLRSIASTALNEQGFPPDVIEAALAHVDKNEVRRAYNRSDYLEQRRPMMQWWADFV  393 (413)
T ss_pred             EECCCCHHHHHHHHHHCCCCHHHHHHHHCCCCCCHHHHHHCHHHHHHHHHHHHHHHHHHH
T ss_conf             658484577999899769999999998689999828999567759999999999999999


No 41 
>COG4688 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=90.68  E-value=0.21  Score=28.12  Aligned_cols=55  Identities=18%  Similarity=0.226  Sum_probs=50.5

Q ss_pred             CCCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHH
Q ss_conf             9216036389999999980899999999848888899999986399999999999
Q gi|254780490|r    1 MSTTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQ   55 (67)
Q Consensus         1 ~~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~~~~~~~~~~   55 (67)
                      +++-.|++||---|.+-+.|+|-..|+++.|-++++-.--|-|-+..++.++++.
T Consensus       446 ~rL~SH~lRHllnT~a~r~Gmde~~ia~w~gR~~Vaqn~~YDHRs~~e~s~~Ir~  500 (665)
T COG4688         446 LRLESHMLRHLLNTEAFRLGMDETIIAKWFGRRSVAQNYEYDHRSLAEQSDQIRL  500 (665)
T ss_pred             EECHHHHHHHHHHHHHHHCCCHHHHHHHHHCHHHHHHCCCCCHHHHHHHHHHHCC
T ss_conf             5443578889887888874704788887633035542124231418888654228


No 42 
>pfam11917 DUF3435 Protein of unknown function (DUF3435). This family of proteins are functionally uncharacterized. This protein is found in eukaryotes. Proteins in this family are typically between 435 to 791 amino acids in length. This family is related to pfam00589 suggesting it may be an integrase enzyme.
Probab=83.96  E-value=0.9  Score=24.83  Aligned_cols=40  Identities=28%  Similarity=0.135  Sum_probs=32.8

Q ss_pred             CCCCCCHHHHHHHHHHHHC-CCHHHHHHHHCCCCHHHHHHHH
Q ss_conf             2160363899999999808-9999999984888889999998
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNG-GDLRSIQSILGHSRLSTTQIYT   42 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G-~~~~~vq~lLGH~~i~tT~~Y~   42 (67)
                      .++||.||...|..+- +| ++-..=..+|||+++.|-..|.
T Consensus       194 ~~~~y~~R~g~a~~~n-~~~vs~a~rn~im~Ha~~~tF~k~Y  234 (414)
T pfam11917       194 PLTPYCLRYGAAKALN-SGEVSEAERNLILGHASSRTFLKHY  234 (414)
T ss_pred             CCCCHHHHHHHHHHCC-CCCCCHHHHHHHHCCCCCCHHHHHC
T ss_conf             4540023578998526-6569989997874478740577625


No 43 
>COG4342 Uncharacterized protein conserved in archaea [Function unknown]
Probab=42.57  E-value=32  Score=16.83  Aligned_cols=58  Identities=19%  Similarity=0.210  Sum_probs=45.3

Q ss_pred             CCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHH-HHHHHHHCCHHHHHHHHHHHCHHHHH
Q ss_conf             603638999999998089999999984888889-99999863999999999995821133
Q gi|254780490|r    4 TAHTLRHSFATHLLSNGGDLRSIQSILGHSRLS-TTQIYTNVNSKRMMEIYDQTHPSITQ   62 (67)
Q Consensus         4 tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~-tT~~Y~~~~~~~~~~~~~~~~p~~~~   62 (67)
                      ..--+|.-.++-|++.|+|..+|-=+-||+--. .|+.|+.+. ...++-|.+..|.+++
T Consensus       226 k~kyiRkwv~nkmlelgvP~~VvdFIqGrk~~~V~~rHY~nL~-~~Ake~Y~kyl~~L~e  284 (291)
T COG4342         226 KAKYIRKWVYNKMLELGVPEDVVDFIQGRKQSRVGTRHYANLL-GQAKEWYSKYLEWLKE  284 (291)
T ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCHHHHHHHHHHH-HHHHHHHHHHHHHHHH
T ss_conf             0999999999999980995889999874672215789999999-9999999999999877


No 44 
>TIGR00973 leuA_bact 2-isopropylmalate synthase; InterPro: IPR005671   The branched-chain amino acids are synthesised by a common pathway that leads from pyruvate and alpha-ketobutyrate to valine and isoleucine, and a branch that leads from the immediate precursor of valine, alpha-ketoisovalerate, to leucine . This pathway operates in archaea, bacteria, fungi and plants, but not mammals, making the enzymes suitable targets for the development of novel antibiotics and herbicides.   Isopropylmalate synthase is the enzyme responsible for the the first committed step in the leucine branch of this biosynthetic pathway, the conversion of alpha-ketoisovalerate to alpha-isopropylmalate. It is either dimeric or tetrameric, depending on the organism, with a monomer molecular mass of 60-70 kDa, a dependence on divalent metal ions for activity, and an alkaline pH optimum , , , . Like many other biosynthetic enzymes it is subject to feedback inhibition by the end product of the pathway, leucine.    This entry represents the isopropylmalate synthase most commonly found in bacteria. A related form of this enzyme is found mainly in eukaryotes and some other bacteria (IPR005668 from INTERPRO). A homologous family in archaea may represent isozymes and/or related enzymes (IPR005675 from INTERPRO). ; GO: 0003852 2-isopropylmalate synthase activity, 0009098 leucine biosynthetic process.
Probab=38.08  E-value=34  Score=16.70  Aligned_cols=44  Identities=14%  Similarity=0.283  Sum_probs=34.4

Q ss_pred             CCCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHCHHHHHHHC
Q ss_conf             92160363899999999808999999998488888999999863999999999995821133310
Q gi|254780490|r    1 MSTTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHPSITQKDK   65 (67)
Q Consensus         1 ~~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~~~~~~~~~~~~p~~~~k~~   65 (67)
                      |.++-|+-||.|-.+|-+=|-                     ..+++++.+.|++|-....+|++
T Consensus       340 lvLg~~SGR~A~k~rL~~lGf---------------------~~~~~~l~k~F~~F~eLADkKke  383 (514)
T TIGR00973       340 LVLGKHSGRHALKKRLEELGF---------------------KLDEEELDKLFEKFKELADKKKE  383 (514)
T ss_pred             HHHHHHHHHHHHHHHHHHHCC---------------------CCCHHHHHHHHHHHHHHHHCCCC
T ss_conf             112244468999889998287---------------------85755798999988875303785


No 45 
>PHA00730 int integrase
Probab=37.87  E-value=39  Score=16.42  Aligned_cols=55  Identities=18%  Similarity=0.192  Sum_probs=41.5

Q ss_pred             CCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHH-HHHHHHCCHHHHHHHHHHHCH
Q ss_conf             16036389999999980899999999848888899-999986399999999999582
Q gi|254780490|r    3 TTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLST-TQIYTNVNSKRMMEIYDQTHP   58 (67)
Q Consensus         3 ~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~t-T~~Y~~~~~~~~~~~~~~~~p   58 (67)
                      +-|--+|..+||-|++-|.|..+|-=+=|-..-+. |+.|+.+. .-.++.|.++..
T Consensus       261 v~~KYiRKfvatKm~elgip~dvvdFiqGR~p~~ilt~HY~dL~-~lAkk~YkkyaE  316 (322)
T PHA00730        261 VPPKYIRKFVATKMLELGIPSEVVDFIQGRTPSRILTKHYLDLL-TLAKKEYKKYAE  316 (322)
T ss_pred             CCHHHHHHHHHHHHHHHCCCHHHHHHHCCCCCCCHHHHHHHHHH-HHHHHHHHHHHH
T ss_conf             87899999999999996896889999647885504689999999-998876189999


No 46 
>pfam07506 RepB RepB plasmid partitioning protein. This family includes proteins with sequence similarity to the RepB partitioning protein of the large Ti (tumour-inducing) plasmids of Agrobacterium tumefaciens.
Probab=36.77  E-value=41  Score=16.33  Aligned_cols=29  Identities=34%  Similarity=0.437  Sum_probs=24.8

Q ss_pred             HHHHHHHHHHHCCCHHHHHHHHCCCCHHHH
Q ss_conf             899999999808999999998488888999
Q gi|254780490|r    9 RHSFATHLLSNGGDLRSIQSILGHSRLSTT   38 (67)
Q Consensus         9 RHt~at~l~~~G~~~~~vq~lLGH~~i~tT   38 (67)
                      +|.|+..+.+.|.+-..|+.-||=.. .+.
T Consensus        10 ~~~~a~rl~~~G~~~~~I~~aL~vd~-~~i   38 (185)
T pfam07506        10 RARFAARLLERGVPRAEIAAALGLDP-QTV   38 (185)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHCCCH-HHH
T ss_conf             99999999986999999999986799-999


No 47 
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=34.76  E-value=44  Score=16.15  Aligned_cols=40  Identities=20%  Similarity=0.302  Sum_probs=32.4

Q ss_pred             CHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCHH
Q ss_conf             63899999999808999999998488888999999863999
Q gi|254780490|r    7 TLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSK   47 (67)
Q Consensus         7 ~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~~   47 (67)
                      .+|-.-|-.|.+.|.+-..|+++||=+ ......|+.-...
T Consensus         9 aiRa~lA~~L~eeG~Sq~~iA~LLGlt-qaAVS~Yls~krg   48 (119)
T COG2522           9 AIRALLAKELIEEGLSQYRIAKLLGLT-QAAVSQYLSGKRG   48 (119)
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHCCC-HHHHHHHHCCCCC
T ss_conf             899999999999588699999996888-9999999736773


No 48 
>COG1602 Uncharacterized conserved protein [Function unknown]
Probab=28.63  E-value=55  Score=15.65  Aligned_cols=20  Identities=30%  Similarity=0.310  Sum_probs=17.0

Q ss_pred             HHHHHHHHCCCHHHHHHHHC
Q ss_conf             99999980899999999848
Q gi|254780490|r   12 FATHLLSNGGDLRSIQSILG   31 (67)
Q Consensus        12 ~at~l~~~G~~~~~vq~lLG   31 (67)
                      ..+.|+++|+|++.||++|-
T Consensus       185 Av~~LY~~G~d~~~I~r~LS  204 (402)
T COG1602         185 AVVELYRRGVDVYYIQRALS  204 (402)
T ss_pred             HHHHHHHCCCCHHHHHHHHH
T ss_conf             99999984998999999862


No 49 
>PRK09568 DNA primase large subunit; Reviewed
Probab=21.70  E-value=78  Score=14.87  Aligned_cols=32  Identities=13%  Similarity=0.135  Sum_probs=28.5

Q ss_pred             CCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCH
Q ss_conf             60363899999999808999999998488888
Q gi|254780490|r    4 TAHTLRHSFATHLLSNGGDLRSIQSILGHSRL   35 (67)
Q Consensus         4 tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i   35 (67)
                      -||.-|-+-||-|++-|.++..|-+++..+.-
T Consensus       228 L~H~~RFalatfL~~iG~~vd~I~~lf~~~pd  259 (306)
T PRK09568        228 LNREEARALIVYYINIGSSVDSIALVLEKNGD  259 (306)
T ss_pred             CCHHHHHHHHHHHHHCCCCHHHHHHHHHCCCC
T ss_conf             88288999999999759979999999862992


No 50 
>PRK09857 hypothetical protein; Provisional
Probab=21.28  E-value=79  Score=14.83  Aligned_cols=23  Identities=30%  Similarity=0.362  Sum_probs=12.6

Q ss_pred             HHHHHHHHHCCCHHHHHHHHCCC
Q ss_conf             99999998089999999984888
Q gi|254780490|r   11 SFATHLLSNGGDLRSIQSILGHS   33 (67)
Q Consensus        11 t~at~l~~~G~~~~~vq~lLGH~   33 (67)
                      ..|-.|+.+|.++..|+++-|=+
T Consensus       261 ~iAr~mL~~G~~~~~I~k~TGLS  283 (292)
T PRK09857        261 HIAKIMLESGVPLADIMRFTGLS  283 (292)
T ss_pred             HHHHHHHHCCCCHHHHHHHHCCC
T ss_conf             99999998699989999996979


Done!