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!