Query gi|254780882|ref|YP_003065295.1| site-specific tyrosine recombinase XerC [Candidatus Liberibacter asiaticus str. psy62] Match_columns 328 No_of_seqs 176 out of 10042 Neff 8.9 Searched_HMMs 39220 Date Mon May 30 00:45:23 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780882.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 0 0 609.8 18.6 300 19-323 1-313 (313) 2 TIGR02225 recomb_XerD tyrosine 100.0 0 0 598.6 18.9 293 19-321 1-305 (305) 3 COG4974 XerD Site-specific rec 100.0 0 0 518.4 19.3 294 14-321 5-300 (300) 4 PRK01287 xerC site-specific ty 100.0 0 0 501.2 22.0 299 13-326 22-329 (361) 5 PRK00236 xerC site-specific ty 100.0 0 0 486.0 22.0 294 10-321 2-295 (295) 6 PRK00283 xerD site-specific ty 100.0 0 0 475.2 21.7 291 16-321 4-296 (296) 7 COG4973 XerC Site-specific rec 100.0 0 0 461.0 19.9 294 14-324 6-299 (299) 8 cd00798 INT_XerDC XerD and Xer 100.0 0 0 446.2 20.1 281 18-308 1-282 (284) 9 PRK05084 xerS site-specific ty 100.0 0 0 438.4 18.7 300 11-313 14-356 (360) 10 cd01196 INT_VanD VanD integras 100.0 0 0 395.7 16.7 260 21-314 1-261 (263) 11 cd01187 INT_SG4 INT_SG4, DNA b 100.0 0 0 390.7 18.2 284 14-312 1-298 (299) 12 PRK02436 xerD site-specific ty 100.0 0 0 391.6 15.1 247 18-300 1-247 (247) 13 cd01185 INT_Tn4399 Tn4399 and 100.0 0 0 383.7 19.9 284 8-312 9-298 (299) 14 cd01190 INT_SG5 INT_SG5, DNA b 100.0 0 0 376.5 15.2 247 61-319 3-260 (260) 15 TIGR02249 integrase_gron integ 100.0 0 0 379.5 11.2 253 29-302 12-306 (320) 16 cd01193 INT_IntI IntI (E2) int 100.0 0 0 358.1 12.7 229 60-301 4-242 (242) 17 PRK09870 tyrosine recombinase; 100.0 0 0 338.5 11.1 195 118-323 2-197 (200) 18 PRK09871 tyrosine recombinase; 100.0 0 0 324.9 10.3 189 127-325 5-194 (198) 19 cd00799 INT_Cre Cre recombinas 100.0 0 0 314.9 15.5 258 33-306 1-280 (287) 20 cd00801 INT_P4 Bacteriophage P 100.0 2.8E-45 0 302.5 18.1 275 10-311 69-353 (357) 21 cd00796 INT_Rci Rci recombinas 100.0 1.4E-45 0 305.5 11.2 202 87-308 1-205 (206) 22 cd01198 INT_ASSRA_C Archaeal s 100.0 4.6E-44 0 294.6 9.7 176 128-321 1-185 (186) 23 cd01188 INT_pAE1 pAE1 and rela 100.0 8.5E-44 0 292.9 10.4 177 125-309 1-182 (188) 24 cd01197 INT_FimBE_C FimB and F 100.0 1.3E-43 0 291.7 9.7 174 127-307 3-177 (180) 25 cd01186 INT_SG3_C INT_SG3, DNA 100.0 1.9E-39 4.8E-44 265.7 10.4 169 130-317 8-178 (180) 26 cd01194 INT_Tn554A_C Tn544A an 100.0 1.3E-39 3.2E-44 266.9 8.8 170 129-311 1-185 (186) 27 cd01183 INT_SG1_C INT_SG1, DNA 100.0 5.5E-40 1.4E-44 269.1 6.7 172 128-300 1-196 (196) 28 cd01199 INT_Tn1545_C Tn1545-re 100.0 5.4E-38 1.4E-42 256.7 9.9 179 128-312 1-204 (205) 29 cd01192 INT_P22_C P22-like int 100.0 1.9E-37 4.7E-42 253.3 9.3 167 126-313 4-173 (177) 30 pfam00589 Phage_integrase Phag 100.0 1.1E-37 2.8E-42 254.7 7.9 169 127-305 1-170 (170) 31 cd01189 INT_phiLC3_C phiLC3 ph 100.0 4.4E-37 1.1E-41 250.9 6.9 171 127-305 1-190 (191) 32 cd01195 INT_Tn544B_C Tn544B an 100.0 1.6E-36 4.2E-41 247.4 8.8 175 127-309 1-194 (195) 33 cd00397 DNA_BRE_C DNA breaking 100.0 4.8E-33 1.2E-37 225.7 8.1 159 133-300 1-164 (164) 34 cd01191 INT_phiCTX_C phiCTX ph 100.0 2.1E-32 5.3E-37 221.8 8.2 166 126-301 1-195 (196) 35 PRK09692 integrase; Provisiona 100.0 3.3E-30 8.4E-35 208.0 17.2 280 12-317 105-392 (413) 36 cd00797 HP1_INT_C Phage HP1 in 100.0 4.1E-32 1E-36 219.9 7.3 154 132-311 1-155 (158) 37 cd01184 INT_SG2_C INT_SG2, DNA 100.0 1.7E-32 4.2E-37 222.4 5.0 163 129-300 1-181 (181) 38 cd00800 INT_Lambda_C Lambda in 100.0 6.6E-31 1.7E-35 212.4 6.8 155 127-301 2-161 (162) 39 cd01182 INT_REC_C DNA breaking 99.9 3.9E-27 9.8E-32 188.8 6.8 146 153-300 14-162 (162) 40 COG0582 XerC Integrase [DNA re 99.9 4.1E-22 1.1E-26 157.4 18.1 208 84-312 84-301 (309) 41 pfam02899 Phage_integr_N Phage 99.6 7.6E-16 1.9E-20 118.3 8.8 83 18-106 1-83 (83) 42 PHA00730 int integrase 98.6 1E-06 2.6E-11 61.3 11.8 198 43-301 98-303 (322) 43 COG4342 Uncharacterized protei 98.5 9.6E-07 2.4E-11 61.4 7.8 205 68-302 57-268 (291) 44 pfam11917 DUF3435 Protein of u 97.8 3.8E-05 9.7E-10 51.4 4.8 64 235-299 170-235 (414) 45 pfam01028 Topoisom_I Eukaryoti 96.9 0.0023 5.8E-08 40.3 5.3 115 173-300 84-224 (244) 46 cd00659 Topo_IB_C DNA topoisom 96.9 0.00074 1.9E-08 43.4 2.6 114 173-300 71-207 (218) 47 cd01190 INT_SG5 INT_SG5, DNA b 96.2 0.018 4.7E-07 34.7 6.3 62 16-77 11-86 (260) 48 cd01193 INT_IntI IntI (E2) int 95.6 0.034 8.8E-07 33.0 5.7 71 5-78 5-83 (242) 49 cd01185 INT_Tn4399 Tn4399 and 95.0 0.067 1.7E-06 31.2 5.6 39 16-54 69-107 (299) 50 PRK01287 xerC site-specific ty 94.9 0.028 7.2E-07 33.5 3.5 39 69-107 25-63 (361) 51 PRK05084 xerS site-specific ty 94.6 0.037 9.4E-07 32.8 3.5 41 68-108 18-58 (360) 52 PRK00283 xerD site-specific ty 93.8 0.073 1.9E-06 30.9 3.5 38 16-54 51-88 (296) 53 PRK00236 xerC site-specific ty 92.9 0.12 3.1E-06 29.5 3.5 37 16-53 56-92 (295) 54 COG4688 Uncharacterized protei 92.1 0.22 5.7E-06 27.9 4.0 66 246-311 432-499 (665) 55 pfam02899 Phage_integr_N Phage 91.3 0.59 1.5E-05 25.3 5.4 34 71-104 1-35 (83) 56 TIGR01108 oadA oxaloacetate de 73.5 3.2 8.1E-05 20.7 2.7 91 207-299 146-245 (616) 57 smart00435 TOPEUc DNA Topoisom 59.5 5.2 0.00013 19.4 1.6 92 164-272 124-231 (391) 58 TIGR01983 UbiG ubiquinone bios 49.4 15 0.00038 16.5 2.5 11 278-288 229-239 (275) 59 PRK11582 flagella biosynthesis 48.4 19 0.00048 15.9 6.7 68 33-107 58-126 (179) 60 pfam08849 DUF1819 Putative inn 47.4 19 0.0005 15.8 4.1 20 128-147 116-135 (191) 61 TIGR00802 nico transition meta 43.3 15 0.00039 16.5 1.8 26 146-178 151-176 (290) 62 TIGR00016 ackA acetate kinase; 39.8 12 0.00031 17.0 0.9 14 169-182 204-217 (416) 63 COG0282 ackA Acetate kinase [E 39.4 16 0.00042 16.3 1.5 13 169-181 188-200 (396) 64 cd00569 HTH_Hin_like Helix-tur 36.2 29 0.00074 14.7 3.2 32 257-290 3-34 (42) 65 COG4565 CitB Response regulato 35.9 29 0.00075 14.7 4.8 20 279-299 175-194 (224) 66 TIGR01304 IMP_DH_rel_2 IMP deh 34.4 17 0.00042 16.2 0.9 24 260-284 140-163 (376) 67 pfam05202 Flp_C Recombinase Fl 34.1 31 0.0008 14.5 3.7 132 167-302 53-211 (244) 68 KOG0440 consensus 31.1 26 0.00066 15.0 1.4 81 162-254 99-182 (243) 69 TIGR01822 2am3keto_CoA 2-amino 29.6 37 0.00095 14.0 2.5 34 245-278 305-348 (395) 70 pfam07506 RepB RepB plasmid pa 29.1 38 0.00097 14.0 3.3 19 74-92 13-31 (185) 71 PRK10046 dpiA two-component re 29.0 38 0.00097 14.0 4.6 44 255-300 154-199 (225) 72 pfam04852 DUF640 Protein of un 27.6 40 0.001 13.8 4.2 39 40-82 25-63 (133) 73 TIGR02810 agaZ_gatZ D-tagatose 27.2 39 0.001 13.9 1.8 35 276-317 383-425 (430) 74 PRK02615 thiamine-phosphate py 26.4 42 0.0011 13.7 3.7 67 225-297 263-334 (345) 75 PRK00043 thiE thiamine-phospha 25.8 44 0.0011 13.6 4.9 65 226-295 129-198 (210) 76 TIGR02057 PAPS_reductase phosp 25.3 34 0.00088 14.2 1.2 46 163-217 144-192 (239) 77 TIGR01262 maiA maleylacetoacet 24.5 46 0.0012 13.4 3.0 37 245-288 115-151 (218) 78 pfam09968 DUF2202 Uncharacteri 23.9 47 0.0012 13.4 3.5 16 128-143 65-80 (162) 79 PRK02249 DNA primase large sub 22.7 50 0.0013 13.2 4.9 51 241-296 223-276 (333) 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=100.00 E-value=0 Score=609.80 Aligned_cols=300 Identities=35% Similarity=0.565 Sum_probs=278.0 Q ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCC---CCCCCCCCHHHCCHHHHHHHHHHHHH--HHHHHHHHHHHHH Q ss_conf 999999998625488999999999999999998512---14788789689899999999999986--1210133211234 Q gi|254780882|r 19 QNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYT---EEKITIQTIRQLSYTEIRAFISKRRT--QKIGDRSLKRSLS 93 (328) Q Consensus 19 e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~---~~~~~~~~~~~i~~~~i~~~l~~l~~--~~~s~~T~~~~ls 93 (328) ++||+||+.||++|++|+++|+.||+.|..|+..+. ...+ +.++.+++..+|+.|+..+.. +|+|++|++|.|| T Consensus 1 ~~fl~yL~~er~~S~hT~~aY~~DL~~f~~fl~~~~~~~~~~~-~~~~~~~~~~d~R~~la~l~~~~~g~s~rS~~R~LS 79 (313) T TIGR02224 1 EAFLEYLRVERNYSPHTLRAYRRDLEAFLEFLEEHKQEEGGPL-LASLAEVTAADLRSFLAELHAKERGLSRRSLARKLS 79 (313) T ss_pred CHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCHH-HCCHHHCCHHHHHHHHHHHHHCCCCCCHHHHHHHHH T ss_conf 8678999988500089999999999999999999877520111-015762488999999999984657876768999999 Q ss_pred HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCC Q ss_conf 44222233321012322222222222222121111111015678776531013567757753201222100112332222 Q gi|254780882|r 94 GIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEA 173 (328) Q Consensus 94 ~lr~f~~~~~~~~~i~~np~~~i~~~k~~~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El 173 (328) +||+||+||+++++++.||+..|+.||.++++|++|+++|+..+++...........|.++||+|||+|||.||||+||+ T Consensus 80 alRsFy~~L~~~~~~~~nPa~~~~~PK~~~~LP~~L~~~~~~~ll~~~~~~~~~~~~~~~~RDrA~lEllYssGlRvSEl 159 (313) T TIGR02224 80 ALRSFYRFLLRRGLIDANPAAGVRAPKKPKKLPKFLSEDEMEALLDAPEEDAEDREDWLALRDRAILELLYSSGLRVSEL 159 (313) T ss_pred HHHHHHHHHHHCCCCCCCHHHHHHCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999987287402238872267544679988898999999601234666677789998999999998746899998 Q ss_pred CCCCCC-CCCCCC--CCEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCC-----CCCCCCCCCCCCCCCCHHH Q ss_conf 211222-223323--22033237853100011221002343221110012344665-----5432111122111000123 Q gi|254780882|r 174 LSLTPQ-NIMDDQ--STLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQ-----LPLFRGIRGKPLNPGVFQR 245 (328) Q Consensus 174 ~~L~~~-did~~~--~~i~v~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~-----~~lF~~~~g~~ls~~~i~~ 245 (328) ++|+++ |||++. ++|+|+|||+|||+||+++.+.++|.+|++.++........ ++||+|.+|+||++++|++ T Consensus 160 ~~L~~~~D~d~~~~~~~vrV~GKG~KeR~VP~G~~A~~al~~YL~~~r~~~~~~~~~~~~~~~LF~~~~G~rL~~R~v~~ 239 (313) T TIGR02224 160 VGLDLSEDLDLDFSLGLVRVRGKGNKERIVPFGSYARDALQAYLEERREPLLAKEPPAQDHDALFLNRRGGRLTPRGVRY 239 (313) T ss_pred HCCCCCCCCCCHHCCCEEEEEECCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHH T ss_conf 24771336473221476777414881353031489999999998644721145667777522300178887257778999 Q ss_pred HHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHCHHHHHHHHHHHHHHHCCCHHC Q ss_conf 567899976869998805417999999998489988999983788878979999619899999999999981730001 Q gi|254780882|r 246 YIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQTHPSITQ 323 (328) Q Consensus 246 ~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~~l~~~~~~~~~~~~~ 323 (328) +++++..++|++.++|||+||||||||||++|+|+++|||||||+|++|||||||||.++. +++|++||||++| T Consensus 240 ~l~~~~~~~~l~~~~hPH~LRHSFATHLL~~gaDLRaVQELLGH~SLSTTQiYTHv~~~~L----~~~Y~~AHPRA~k 313 (313) T TIGR02224 240 RLQQLVAKAGLPKHVHPHALRHSFATHLLENGADLRAVQELLGHASLSTTQIYTHVDFQHL----AKVYDKAHPRAKK 313 (313) T ss_pred HHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHH----HHHHHHHCCCCCC T ss_conf 9999998568888678753113179999746883558989744464356679888409999----9999973777779 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=100.00 E-value=0 Score=598.55 Aligned_cols=293 Identities=32% Similarity=0.515 Sum_probs=272.0 Q ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999862548899999999999999999851214788789689899999999999986121013321123444222 Q gi|254780882|r 19 QNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLSGIKSF 98 (328) Q Consensus 19 e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~~~s~~T~~~~ls~lr~f 98 (328) ++||+++..|||+|+||+.+|++||..|..|+.... .. .+.+++..+|.+|+.++.++|.|++|++|.||+||+| T Consensus 1 ~~Fl~~L~~E~GLs~NT~~aYrrDL~~f~~~L~~~~----~g-~~~~~~~~~i~~fl~~l~~~g~~~~S~AR~lsalR~F 75 (305) T TIGR02225 1 DDFLDYLWVERGLSQNTLEAYRRDLEKFLEYLEESE----RG-DLAEVDRGDIEDFLAELKEAGLSARSIARALSALRSF 75 (305) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC----CC-CHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH T ss_conf 948899999863538889999999999999862224----78-7641687899999999986687700288999999999 Q ss_pred HHHHHHHCCCCCCCCCC-CCCCCCCCCCCCCCCCCHHHHHHHHH-HHCCCCC-CCHHHHHHHCCCCCCCCCCCCCCCCCC Q ss_conf 23332101232222222-22222221211111110156787765-3101356-775775320122210011233222221 Q gi|254780882|r 99 LKYLKKRKITTESNILN-MRNLKKSNSLPRALNEKQALTLVDNV-LLHTSHE-TKWIDARNSAILYLLYGCGLRISEALS 175 (328) Q Consensus 99 ~~~~~~~~~i~~np~~~-i~~~k~~~~~p~~lt~~e~~~ll~~~-~~~~~~~-~~~~~~Rd~~i~~ll~~TGlR~~El~~ 175 (328) |+||..+++++.||+.. |+.||..+++|++||++||.+||+++ ....+.. ... .+||+||+++||+||||+||+|+ T Consensus 76 y~fL~~e~~~~~dP~~~~~~~PK~~~~LP~vLt~~EV~~LL~~p~~~~~~~g~kr~-~lRDrAmLElLYATGlRVSELv~ 154 (305) T TIGR02225 76 YRFLLREGLREDDPSALRIETPKVARKLPKVLTVEEVEALLAAPIDVDTPLGGKRP-ALRDRAMLELLYATGLRVSELVG 154 (305) T ss_pred HHHHHHCCCCCCCCHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCH-HHHHHHHHHHHHHCCCCEEEEEC T ss_conf 99998688745573366420342245788837989999998500246776767640-16547999999864883553305 Q ss_pred CCCCCCCCCCCC-EE-ECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCC-CCC--CCCC---CCCCCC-CCCCCCCCHHHH Q ss_conf 122222332322-03-32378531000112210023432211100123-446--6554---321111-221110001235 Q gi|254780882|r 176 LTPQNIMDDQST-LR-IQGKGDKIRIVPLLPSVRKAILEYYDLCPFDL-NLN--IQLP---LFRGIR-GKPLNPGVFQRY 246 (328) Q Consensus 176 L~~~did~~~~~-i~-v~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~-~~~--~~~~---lF~~~~-g~~ls~~~i~~~ 246 (328) |+.+||+++.++ |. |.|||+|||.|||++.+++.|..|++.+|... ..+ ..++ ||+|.+ |++||+++|+++ T Consensus 155 L~~~d~~l~~g~~~~~v~GKG~KERlVP~G~~A~~~l~~Yl~~~R~~~~~~~~~~~d~~~~LFln~~~G~~lsRQ~~W~~ 234 (305) T TIGR02225 155 LRLEDVNLDEGVKVRKVRGKGSKERLVPLGEEAIEALERYLKEARPLLLKKKKKSSDAKSALFLNRREGGPLSRQGFWKI 234 (305) T ss_pred CCHHHHHCCCCEEEEEEEECCCCEEECCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHH T ss_conf 61665200277379998616884120220289999999999874067641778887554311246888888788999999 Q ss_pred HHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHCHHHHHHHHHHHHHHHCCCH Q ss_conf 678999768699988054179999999984899889999837888789799996198999999999999817300 Q gi|254780882|r 247 IRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQTHPSI 321 (328) Q Consensus 247 ~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~~l~~~~~~~~~~~ 321 (328) ++++++++||.++||||.|||+||||||++|+|+++||+||||+||+||||||||+ ++.|+++|.++|||+ T Consensus 235 ~K~~A~~aGI~k~isPHtLRHSFATHLLenGADLR~VQeLLGHadisTTQIYTHV~----~~~L~~~~~~~HPRa 305 (305) T TIGR02225 235 LKEYAKRAGIEKPISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQIYTHVA----RERLKEVHKKHHPRA 305 (305) T ss_pred HHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHH----HHHHHHHHHHHCCCC T ss_conf 99999981889899975104679999873688276887774322147889999987----999999999628899 No 3 >COG4974 XerD Site-specific recombinase XerD [DNA replication, recombination, and repair] Probab=100.00 E-value=0 Score=518.43 Aligned_cols=294 Identities=33% Similarity=0.505 Sum_probs=273.6 Q ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999998625488999999999999999998512147887896898999999999999861210133211234 Q gi|254780882|r 14 LLKERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLS 93 (328) Q Consensus 14 l~~~~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~~~s~~T~~~~ls 93 (328) ....+++||+++..|||+|.||+.+|+.||..|..|+... ++..+.+++..++..|+.++.++|+|++|++|.+| T Consensus 5 ~~~~i~~fL~~l~~Er~ls~nTl~sYrrDL~~f~~~L~~~-----~~~~l~~~~~~di~~yl~~l~~~g~s~~S~aR~ls 79 (300) T COG4974 5 DEALIEQFLEYLWIERGLSANTLSSYRRDLEDFREWLEER-----GITDLADATEADIREYLTELAEQGLSATSIARALS 79 (300) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-----CCCCHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHH T ss_conf 7899999999999975432644999999999999998762-----79884546899999999999857867224889999 Q ss_pred HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCC Q ss_conf 44222233321012322222222222222121111111015678776531013567757753201222100112332222 Q gi|254780882|r 94 GIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEA 173 (328) Q Consensus 94 ~lr~f~~~~~~~~~i~~np~~~i~~~k~~~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El 173 (328) ++|+||.|+..++++..||+..+..||.++++|++|+++|+..+++ .++.....++||+||++|||+||||+||+ T Consensus 80 alR~fy~fl~~E~~~~~dP~~~l~~PK~~~~LPk~Ls~~eve~Ll~-----~~~~~~p~~LRdrAmlELLYATGlRVSEl 154 (300) T COG4974 80 ALRSFYQFLIREGLREDDPTRLLDSPKLPKRLPKFLSEEEVEALLE-----APDEDTPLGLRDRAMLELLYATGLRVSEL 154 (300) T ss_pred HHHHHHHHHHHCCCCCCCCHHHHCCCCCCCCCCCCCCHHHHHHHHH-----CCCCCCCHHHHHHHHHHHHHHCCCHHHHH T ss_conf 9999999999779853382444247877776776259999999981-----88889807579999999999827759998 Q ss_pred CCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCC-CC-CCCCCCCCCCCCCCCCCHHHHHHHHH Q ss_conf 21122222332322033237853100011221002343221110012344-66-55432111122111000123567899 Q gi|254780882|r 174 LSLTPQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNL-NI-QLPLFRGIRGKPLNPGVFQRYIRQLR 251 (328) Q Consensus 174 ~~L~~~did~~~~~i~v~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~-~~-~~~lF~~~~g~~ls~~~i~~~~~~~~ 251 (328) ++|+..||++..+.+.|+|||+|+|+||+++.+...|..|+...|..... .. .++||+|.+|++||+++|++.++.+. T Consensus 155 v~L~l~dv~~~~~~v~V~GKG~KeR~VP~g~~A~~~l~~Yl~~~R~~l~~~~~~~~~LF~n~~g~~ltrq~~w~~lk~~a 234 (300) T COG4974 155 VGLTLSDVDLRQGVVRVRGKGNKERLVPFGEEAVEALEKYLEEARPKLLKGKSSTDALFPNQRGGGLTRQGFWKRLKDYA 234 (300) T ss_pred HCCCHHHHCCCCCEEEEECCCCCEEEEECHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCCHHHHHHHHHHHH T ss_conf 56757651324686899715882555213399999999999986598842578898564548999877999999999999 Q ss_pred HHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHCHHHHHHHHHHHHHHHCCCH Q ss_conf 9768699988054179999999984899889999837888789799996198999999999999817300 Q gi|254780882|r 252 RYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQTHPSI 321 (328) Q Consensus 252 ~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~~l~~~~~~~~~~~ 321 (328) ..+|+.+.+|||.|||+|||+|+++|+|+++||++|||+|++||||||||+ .+.|+++|.++|||+ T Consensus 235 ~~Agi~~~isPH~LRHsFATHLL~~GADlRvVQeLLGHadisTTQIYTHV~----~e~L~~~~~~~HPra 300 (300) T COG4974 235 ERAGIDKKISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQIYTHVT----KERLRDLYAQHHPRA 300 (300) T ss_pred HHHCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCHHHHHHHHH----HHHHHHHHHHHCCCC T ss_conf 981888786813657889999986785399999984866501557879988----999999999738999 No 4 >PRK01287 xerC site-specific tyrosine recombinase XerC; Reviewed Probab=100.00 E-value=0 Score=501.25 Aligned_cols=299 Identities=25% Similarity=0.361 Sum_probs=269.5 Q ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHH------HHHHHH Q ss_conf 99999999999999862548899999999999999999851214788789689899999999999986------121013 Q gi|254780882|r 13 ELLKERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRT------QKIGDR 86 (328) Q Consensus 13 ~l~~~~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~------~~~s~~ 86 (328) .+...+++|++||+ +||+|++|+++|+.+|+.|+.||... ++..+.+++..++..|..++.. .++|++ T Consensus 22 ~~~~ll~~Fl~yL~-er~~S~~Ti~aY~~dL~~F~~fl~~~-----g~~~~~~vt~~~l~~y~~~L~~~r~~~g~~ls~~ 95 (361) T PRK01287 22 SLYALLLRFVEWLQ-ERNWSERTLKVQTHHTYHFILWCEER-----GLYYAADVTRPVLERYQRYLYQYRKTNGEPLSQG 95 (361) T ss_pred HHHHHHHHHHHHHH-HCCCCHHHHHHHHHHHHHHHHHHHHC-----CCCCHHHCCHHHHHHHHHHHHHHHHCCCCCCCHH T ss_conf 79999999999999-83998999999999999999999984-----8999375899999999999998654068877999 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC-CCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCC Q ss_conf 32112344422223332101232222222222222212111-11110156787765310135677577532012221001 Q gi|254780882|r 87 SLKRSLSGIKSFLKYLKKRKITTESNILNMRNLKKSNSLPR-ALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYG 165 (328) Q Consensus 87 T~~~~ls~lr~f~~~~~~~~~i~~np~~~i~~~k~~~~~p~-~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~ 165 (328) |+++++++||+||+|+++++++..||+..|..||.++++|+ +++.+|+.++++++ +...+.+.||+||+.|||. T Consensus 96 T~~r~LsalrsFf~~l~~~~~i~~nP~~~i~~PK~~k~lP~~~Ls~~Ev~~LL~~~-----~~~~~~g~RDrAil~LLy~ 170 (361) T PRK01287 96 TQRTQLTPLRVWFKWLTKQNLILYNPAADIELPKLEKRLPRYILSIDETEAILAAP-----DPTTLQGLRDRALLELLWS 170 (361) T ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCHHHHCCCCCCCCCCCCCCCCHHHHHHHHHCC-----CCCCCHHHHHHHHHHHHHH T ss_conf 99999999999999999879935375876327776555777679999999998474-----5588065999999999999 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCEEE-CCCCCCCCCCCCCCCCHHHHHHHHHHHCCCC-CCCCCCCCCCCCCCCCCCCCCH Q ss_conf 1233222221122222332322033-2378531000112210023432211100123-4466554321111221110001 Q gi|254780882|r 166 CGLRISEALSLTPQNIMDDQSTLRI-QGKGDKIRIVPLLPSVRKAILEYYDLCPFDL-NLNIQLPLFRGIRGKPLNPGVF 243 (328) Q Consensus 166 TGlR~~El~~L~~~did~~~~~i~v-~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~-~~~~~~~lF~~~~g~~ls~~~i 243 (328) ||||+||+++|+|+|||++.+.+.| .|||+|+|+|||++.+..+|.+|++..+... .....++||++.+|++|+++++ T Consensus 171 tGLRvsEl~~L~~~DId~~~~~i~v~~GKG~KeR~VPl~~~~~~~L~~Yl~~~r~~~~~~~~~~~lFvs~~G~~ls~~~v 250 (361) T PRK01287 171 TGIRRSELARLDLYDVDGSRKTVTVRQGKGNKDRVVPLGERALVWLQRYLQQVRPQLIVNPDSGALFVAMDGDGLQRNGI 250 (361) T ss_pred HCCHHHHHHHCCCCCCCCCCCEEEEECCCCCCEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCEEECCCCCCCCHHHH T ss_conf 37779888716664667888838873488874002027699999999999986176412788775212889995878999 Q ss_pred HHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHCHHHHHHHHHHHHHHHCCCHHC Q ss_conf 23567899976869998805417999999998489988999983788878979999619899999999999981730001 Q gi|254780882|r 244 QRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQTHPSITQ 323 (328) Q Consensus 244 ~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~~l~~~~~~~~~~~~~ 323 (328) +++++++++.+|+++.++||+|||||||+|+++|+|+.+||++|||+|++||||||||+.++ |+++|+++||+..+ T Consensus 251 ~~~vk~~~~~agi~k~~~pH~LRHTfAT~lL~~GadL~~VQelLGHasi~TTqiYtHv~~~~----l~~v~~~~HP~~~~ 326 (361) T PRK01287 251 TNLVGRYIRAAGIEKKGACHLFRHAMATQMLENGADLRWIQAMLGHASLETTQIYTQVSIRH----LQAVHASTHPAEQM 326 (361) T ss_pred HHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHH----HHHHHHHHCCCCCC T ss_conf 99999999980899999821059999999998699999999986899778999998479999----99999981998889 Q ss_pred CCC Q ss_conf 223 Q gi|254780882|r 324 KDK 326 (328) Q Consensus 324 ~~~ 326 (328) ..+ T Consensus 327 ~~~ 329 (361) T PRK01287 327 ADE 329 (361) T ss_pred CCC T ss_conf 863 No 5 >PRK00236 xerC site-specific tyrosine recombinase XerC; Reviewed Probab=100.00 E-value=0 Score=485.95 Aligned_cols=294 Identities=40% Similarity=0.620 Sum_probs=271.4 Q ss_pred CCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 49899999999999999862548899999999999999999851214788789689899999999999986121013321 Q gi|254780882|r 10 VSFELLKERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLK 89 (328) Q Consensus 10 ~~~~l~~~~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~~~s~~T~~ 89 (328) .+.+|.+++++||+|++.++|+||+|+++|+.+++.|+.||... +..++.+++..+|..|+.++..+|+|++|++ T Consensus 2 ~~~~~~~~i~~fl~~l~~~r~lS~~Ti~~Y~~~l~~f~~~~~~~-----~~~~l~~i~~~~i~~~~~~l~~~g~s~~Ti~ 76 (295) T PRK00236 2 ADADLPAALEAFLEYLRVERGLSPHTLRAYRRDLRAFLAFLEEV-----GLADLQQLDLADLRAFLARLRRQGLSARSLA 76 (295) T ss_pred CCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHC-----CCCCHHHCCHHHHHHHHHHHHHCCCCHHHHH T ss_conf 80778999999999999885907999999999999999999875-----9999476999999999999987699999999 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCC Q ss_conf 12344422223332101232222222222222212111111101567877653101356775775320122210011233 Q gi|254780882|r 90 RSLSGIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLR 169 (328) Q Consensus 90 ~~ls~lr~f~~~~~~~~~i~~np~~~i~~~k~~~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR 169 (328) +++++|++||+||+.+++++.||+..|+.||..++.|++++.+|+.++++.... ...+.||++|+.|||.|||| T Consensus 77 ~~l~~lr~~~~~a~~~~~i~~nP~~~i~~~k~~~~~~~~lt~~e~~~ll~~~~~------~~~~~Rd~~i~~ll~~tGlR 150 (295) T PRK00236 77 RRLSALRSFYRWLVRRGLLKANPAAGLRAPKAPKRLPKPLDVDQAKRLLDADAD------DPLALRDRAILELLYGSGLR 150 (295) T ss_pred HHHHHHHHHHHHHHHCCCCCCCHHHHCCCCCCCCCCCCCHHHHHHHHHHHCCCC------CCHHHHHHHHHHHHHHHCCC T ss_conf 999999999998876286145778751277766568850018999999971325------80658999999999981978 Q ss_pred CCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHH Q ss_conf 22222112222233232203323785310001122100234322111001234466554321111221110001235678 Q gi|254780882|r 170 ISEALSLTPQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQ 249 (328) Q Consensus 170 ~~El~~L~~~did~~~~~i~v~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g~~ls~~~i~~~~~~ 249 (328) +||+++|+|+|||++.++|+|.|||+|+|+|||++.+.+.|..|++.++. ...+++||++.+|++++++++++.|++ T Consensus 151 ~~E~~~L~~~did~~~~~i~i~~Kg~K~R~Vpl~~~~~~~L~~yl~~~~~---~~~~~~lF~~~~g~~l~~~~i~~~~~~ 227 (295) T PRK00236 151 LSELVGLDIDDLDLASGTVRVLGKGNKERTVPVGSAALEALEAYLARPLA---EEDDDALFLGARGGRLSPRVVQRRVKK 227 (295) T ss_pred HHHHCCCCHHHCCCCCCEEEEECCCCEEEEEECCHHHHHHHHHHHHHCCC---CCCCCEEEECCCCCCCCHHHHHHHHHH T ss_conf 33120563977277789898817898168986599999999999996776---789983775689995878899999999 Q ss_pred HHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHCHHHHHHHHHHHHHHHCCCH Q ss_conf 999768699988054179999999984899889999837888789799996198999999999999817300 Q gi|254780882|r 250 LRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQTHPSI 321 (328) Q Consensus 250 ~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~~l~~~~~~~~~~~ 321 (328) +++++|++.+++||+|||||||+|+++|+|+.+||++|||+|++||++|+|++.++ |+++|+++|||+ T Consensus 228 ~~~~~gi~~~~~~H~lRHt~At~l~~~G~~l~~vq~~LGHssi~tT~~Y~h~~~~~----l~~~~~~~~p~~ 295 (295) T PRK00236 228 LRKKAGLPEHITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQH----LAEVYDAAHPRA 295 (295) T ss_pred HHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHH----HHHHHHHHCCCC T ss_conf 99985999999899788999999998799999999881899889999988689999----999999878399 No 6 >PRK00283 xerD site-specific tyrosine recombinase XerD; Reviewed Probab=100.00 E-value=0 Score=475.22 Aligned_cols=291 Identities=33% Similarity=0.478 Sum_probs=267.2 Q ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999862548899999999999999999851214788789689899999999999986121013321123444 Q gi|254780882|r 16 KERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLSGI 95 (328) Q Consensus 16 ~~~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~~~s~~T~~~~ls~l 95 (328) +.+++||+||..+||+|++|+++|+.+++.|..|+.... .++.+++..+|..|+.++.+.++|++|+|+++++| T Consensus 4 ~~i~~fl~~L~~erg~S~~Ti~~Y~~~l~~f~~~l~~~~------~~~~~it~~~i~~y~~~L~~~~~s~~Tin~~l~~l 77 (296) T PRK00283 4 ALIEQFLDALWVERGLAENTLSSYRRDLELFAEWLAARG------LSLAEATRDDLQAFLAELAEGGYKATSSARRLSAL 77 (296) T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCC------CCHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHH T ss_conf 999999999999879079999999999999999998759------99477999999999999987799999999999999 Q ss_pred HHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCC Q ss_conf 22223332101232222222222222212111111101567877653101356775775320122210011233222221 Q gi|254780882|r 96 KSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALS 175 (328) Q Consensus 96 r~f~~~~~~~~~i~~np~~~i~~~k~~~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~ 175 (328) ++||+||+.+++++.||+..|+.||.+++.|++++.+|+.++++++.. ....+.||++|+.+||.||||+||+++ T Consensus 78 r~~~~~a~~~~~i~~np~~~i~~~k~~~~~~~~lt~eei~~ll~~~~~-----~~~~~~Rd~ail~ll~~tGlR~~El~~ 152 (296) T PRK00283 78 RRFFQFLLREGLREDDPTALLDSPKLPRRLPKTLSEAQVEALLDAPDI-----DTPLGLRDRAMLELLYATGLRVSELVG 152 (296) T ss_pred HHHHHHHHHCCCCCCCHHHHCCCCCCCCCCCCHHHHHHHHHHHHCCCC-----CCHHHHHHHHHHHHHHHHCCCHHHHCC T ss_conf 974799987074334878636677888889741437899998732377-----865768999999999983876120217 Q ss_pred CCCCCCCCCCCCEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCC-CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHC Q ss_conf 1222223323220332378531000112210023432211100123-446655432111122111000123567899976 Q gi|254780882|r 176 LTPQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDL-NLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYL 254 (328) Q Consensus 176 L~~~did~~~~~i~v~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~-~~~~~~~lF~~~~g~~ls~~~i~~~~~~~~~~~ 254 (328) |+|+|||++.+.|.|.|||+|+|+|||++.+.++|.+|+...+... ....+++||++.+|++++++++++.++++++.+ T Consensus 153 L~~~di~~~~~~i~v~~Kg~K~R~vpl~~~~~~~l~~yl~~~r~~~~~~~~~~~lF~~~~g~~l~~~~~~~~~~~~~~~a 232 (296) T PRK00283 153 LTLDDVSLRQGVVRVTGKGNKERLVPLGEEAVYAIERYLERGRPALLGGRSSDALFPSARGGQLTRQTFWHRIKHYAKRA 232 (296) T ss_pred CCHHHCCCCCCCEEEECCCCEEEEEECCHHHHHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCCHHHHHHHHHHHHHHC T ss_conf 85999235779557717898036997088999999999998657751489997475428898467999999999999980 Q ss_pred CCC-CCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHCHHHHHHHHHHHHHHHCCCH Q ss_conf 869-9988054179999999984899889999837888789799996198999999999999817300 Q gi|254780882|r 255 GLP-LSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQTHPSI 321 (328) Q Consensus 255 gi~-~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~~l~~~~~~~~~~~ 321 (328) |++ .++|||+|||||||+|+++|+|+.+||++|||+|++||++|+|+++++. +++|++|||++ T Consensus 233 gi~~~~~tpH~lRHt~at~ll~~G~~l~~i~~~LGHssi~TT~~Y~h~~~~~l----~~~~~~~~p~~ 296 (296) T PRK00283 233 GIDPKKLSPHVLRHAFATHLLNHGADLRVVQELLGHSDISTTQIYTHVATERL----KELHAQHHPRA 296 (296) T ss_pred CCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHH----HHHHHHHCCCC T ss_conf 89999889987879999999987989999998828998899999886899999----99999868499 No 7 >COG4973 XerC Site-specific recombinase XerC [DNA replication, recombination, and repair] Probab=100.00 E-value=0 Score=461.02 Aligned_cols=294 Identities=32% Similarity=0.518 Sum_probs=274.5 Q ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999998625488999999999999999998512147887896898999999999999861210133211234 Q gi|254780882|r 14 LLKERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLS 93 (328) Q Consensus 14 l~~~~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~~~s~~T~~~~ls 93 (328) +...+++|++|+..||++|++|+.+|+.+|...+.+.... ++.+|..+++.+++.++.....+|++++++.+++| T Consensus 6 ~~~~~~~yl~~L~~Er~lS~hTl~~Y~rqL~~l~~~~~q~-----~~~~w~~ld~~~vr~~~a~~~~~Gl~a~SlA~rLS 80 (299) T COG4973 6 MAADLDAYLRYLRVERQLSPHTLANYRRQLEALIALLAQM-----GLGSWQQLDPADVRAFVARSHRRGLSARSLARRLS 80 (299) T ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHC-----CCCCHHHCCHHHHHHHHHHHHCCCCCHHHHHHHHH T ss_conf 6788999999999861468888999999999999999972-----76566656999999999998318855778999999 Q ss_pred HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCC Q ss_conf 44222233321012322222222222222121111111015678776531013567757753201222100112332222 Q gi|254780882|r 94 GIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEA 173 (328) Q Consensus 94 ~lr~f~~~~~~~~~i~~np~~~i~~~k~~~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El 173 (328) ++|+||.|++++|.+..||+.+|+.||.++++|+.++.||+.++++ + +....++.||+||+++||.+|+|.||+ T Consensus 81 a~R~f~~wLv~~g~l~~nPa~GvsaPK~~r~LPk~ld~d~~~~ll~-~-----d~~dPlavRDrAllElmY~sGLRLSEL 154 (299) T COG4973 81 ALRSFYDWLVKQGELKANPAKGVSAPKQPRHLPKNLDVDEANRLLD-I-----DGDDPLAVRDRALLELMYGSGLRLSEL 154 (299) T ss_pred HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHC-C-----CCCCCHHHHHHHHHHHHHHCCCCHHHH T ss_conf 9999999998727646686456889887443777689999999966-7-----899933478999999998437008988 Q ss_pred CCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH Q ss_conf 21122222332322033237853100011221002343221110012344665543211112211100012356789997 Q gi|254780882|r 174 LSLTPQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRY 253 (328) Q Consensus 174 ~~L~~~did~~~~~i~v~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g~~ls~~~i~~~~~~~~~~ 253 (328) ++|+++|||++.+.++|.|||+|+|.||++..+.++|..|+..+.. ....++.||++..|++||.+.|.+.+..+..+ T Consensus 155 vgLd~~~vdl~~geV~V~GKGnKeR~vP~g~~A~~al~~WL~lR~~--~a~~d~AlF~s~~G~Ris~R~iQkR~~~wgik 232 (299) T COG4973 155 VGLDLKHVDLDEGEVRVMGKGNKERRVPVGRKAVEALEHWLALRGL--FASEDDALFLSRLGKRISARAIQKRLAQWGIK 232 (299) T ss_pred HCCCCCCCCCCCCEEEEECCCCCEEECCCHHHHHHHHHHHHHHHHC--CCCCCCEEEECCCCCCCCHHHHHHHHHHHHHH T ss_conf 4788444545542589962787346535217799999999865510--37987605310368816488999999999986 Q ss_pred CCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHCHHHHHHHHHHHHHHHCCCHHCC Q ss_conf 68699988054179999999984899889999837888789799996198999999999999817300012 Q gi|254780882|r 254 LGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQTHPSITQK 324 (328) Q Consensus 254 ~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~~l~~~~~~~~~~~~~~ 324 (328) .|+..+++||.|||+|||+|+|+..|++.||++|||+|++|||||||+|-++ |.++||.+|||+||| T Consensus 233 qg~~~HvhPH~LRHSFAtHmLesSgDLRaVQELLGHanlsTTQIYThLDFQH----LA~vYD~AHPRAkrk 299 (299) T COG4973 233 QGLNSHVHPHKLRHSFATHMLESSGDLRAVQELLGHANLSTTQIYTHLDFQH----LASVYDAAHPRAKRK 299 (299) T ss_pred CCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCHHHHHHHCCHHH----HHHHHHHHCCCCCCC T ss_conf 0322138768777788999987035489999985646512444323236899----999986317411269 No 8 >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=100.00 E-value=0 Score=446.21 Aligned_cols=281 Identities=35% Similarity=0.506 Sum_probs=258.3 Q ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999986254889999999999999999985121478878968989999999999998612101332112344422 Q gi|254780882|r 18 RQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLSGIKS 97 (328) Q Consensus 18 ~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~~~s~~T~~~~ls~lr~ 97 (328) +|+|++||..+||+||+|+++|+.+++.|..||... +...+.+++..+|..|+.++.+.++|++|+++++++|++ T Consensus 1 i~~fl~~l~~~r~lS~~T~~~Y~~~l~~f~~~~~~~-----~~~~~~~i~~~~i~~~~~~L~~~~~s~~Ti~~~~~~l~~ 75 (284) T cd00798 1 IERFLDYLAVERGLSENTLAAYRRDLERFLEFLEER-----GILFPADVTPDDIRRFLAELKDQGLSARSIARKLSALRS 75 (284) T ss_pred CHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHC-----CCCCHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH T ss_conf 978999999985907999999999999999999982-----999948799999999999998769999999999999999 Q ss_pred HHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCC Q ss_conf 22333210123222222222222221211111110156787765310135677577532012221001123322222112 Q gi|254780882|r 98 FLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLT 177 (328) Q Consensus 98 f~~~~~~~~~i~~np~~~i~~~k~~~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~ 177 (328) ||+||+++++++.||+..++.|+..+..|++++.+|+.++++++. .....+.||++|+.+++.||||++|+++|+ T Consensus 76 ~~~~~~~~~~i~~np~~~i~~~k~~~~~~~~l~~~ei~~ll~~~~-----~~~~~~~Rd~~i~~ll~~tGlR~~E~~~L~ 150 (284) T cd00798 76 FFKFLLREGLILANPAELIEPPKLKRSLPKVLTIEEVERLLAAPD-----GDTPLGLRDRALLELLYSTGLRVSELVGLK 150 (284) T ss_pred HHHHHHHCCCCCCCCHHHCCCCCCCCCCCCCCCHHHHHHHHHHHC-----CCCHHHHHHHHHHHHHHHHCCCHHHHHCCC T ss_conf 999998658765682320257886877888679999899998632-----377677999999999999679924461696 Q ss_pred CCCCCCCCCCEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCC-CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCC Q ss_conf 22223323220332378531000112210023432211100123-44665543211112211100012356789997686 Q gi|254780882|r 178 PQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDL-NLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGL 256 (328) Q Consensus 178 ~~did~~~~~i~v~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~-~~~~~~~lF~~~~g~~ls~~~i~~~~~~~~~~~gi 256 (328) |+|||++.+++.|.|||+|+|+|||++.+.++|..|+..++... .....+++|++.+|++++++++++.++++++++|+ T Consensus 151 ~~did~~~~~i~v~~K~~k~r~vpl~~~~~~~l~~~~~~~~~~~~~~~~~~~lF~~~~g~~~~~~~~~~~~~~~~~~~g~ 230 (284) T cd00798 151 LSDVDLSRGLIRVRGKGNKERIVPLGETAVEALQRYLEVRRPLLLKVGDSDALFLNQRGKRLSRRGVWKILKEYARRAGI 230 (284) T ss_pred HHHCCCCCCEEEEECCCCCEEEEECCHHHHHHHHHHHHHHHHHCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHHHHCC T ss_conf 99947667779996479944788649999999999999833420367877633223689826579999999999999099 Q ss_pred CCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHCHHHHHH Q ss_conf 9998805417999999998489988999983788878979999619899999 Q gi|254780882|r 257 PLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGD 308 (328) Q Consensus 257 ~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~ 308 (328) +.+++||+|||||||+|+++|+|+..||++|||+|++||++|+|++.++.++ T Consensus 231 ~~~~~~H~lRHt~at~l~~~g~~~~~i~~~lGH~s~~tT~~Y~h~~~~~l~e 282 (284) T cd00798 231 EKKISPHTLRHSFATHLLENGADLRAVQELLGHASLATTQIYTHVSFEHLKE 282 (284) T ss_pred CCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHH T ss_conf 9999914659999999998789999999880798799999877779999985 No 9 >PRK05084 xerS site-specific tyrosine recombinase XerS; Reviewed Probab=100.00 E-value=0 Score=438.39 Aligned_cols=300 Identities=22% Similarity=0.315 Sum_probs=251.5 Q ss_pred CHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCC------CCCCCCCHHHCCHHHHHHHHHHHHH---- Q ss_conf 989999999999999986254889999999999999999985121------4788789689899999999999986---- Q gi|254780882|r 11 SFELLKERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTE------EKITIQTIRQLSYTEIRAFISKRRT---- 80 (328) Q Consensus 11 ~~~l~~~~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~------~~~~~~~~~~i~~~~i~~~l~~l~~---- 80 (328) ..+|+..+++|++++. ++++||+|+.+|..||+.|+.|+..... ..+++..+.+++..||..|+.||.. T Consensus 14 ~~~~P~~i~ey~~~~~-~~~~Sp~Ti~~Y~~DL~~F~~fL~~~~~~~~~~~~~i~~~~l~~l~~~di~~y~~~L~~~~~~ 92 (360) T PRK05084 14 KAEMPWYVLEYYQSKL-ATPYSPTTLYEYLTEYRRFFNWLIDEGLTVATKIKDIPLSTLENLTKKDVELFILYLRERPSL 92 (360) T ss_pred HHHCHHHHHHHHHHHH-HCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHCCHHHHHHHHHHHHHCCCC T ss_conf 8867099999999886-059898999999999999999998649875556332778999756699999999999852223 Q ss_pred ------HHHHHHHHHHHHHHHHHHHHHHHHHC-------CCCCCCCCCCCCCCCCCC--------CCCCCCCCHHHHHHH Q ss_conf ------12101332112344422223332101-------232222222222222212--------111111101567877 Q gi|254780882|r 81 ------QKIGDRSLKRSLSGIKSFLKYLKKRK-------ITTESNILNMRNLKKSNS--------LPRALNEKQALTLVD 139 (328) Q Consensus 81 ------~~~s~~T~~~~ls~lr~f~~~~~~~~-------~i~~np~~~i~~~k~~~~--------~p~~lt~~e~~~ll~ 139 (328) .++|++|+||++++|++||+|+.+++ ++..||...+..|+.... .|+.++.+|+..+++ T Consensus 93 ~~~~~~~~~s~~tinRklsaLrsFfkyL~~~~~~~~~~~y~~~n~~~~i~~~k~~~~~~~r~~~~~~~~l~~~e~~~ll~ 172 (360) T PRK05084 93 NGHLTGEGVSQTTINRTLSALKSLFKYLTEETENEDGEPYFYRNVMKKISLKKKKETLAARAENLKQKLFLGDETVEFLD 172 (360) T ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHCCHHHHCCCCCCCCCCCCCCHHCCCCCCCHHHHHHHHH T ss_conf 43212257678899999999999999999852022322133115265257776532122310000120055678999997 Q ss_pred HHHHCCCCCCC--------HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCHHHHH Q ss_conf 65310135677--------5775320122210011233222221122222332322033237853100011221002343 Q gi|254780882|r 140 NVLLHTSHETK--------WIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKAIL 211 (328) Q Consensus 140 ~~~~~~~~~~~--------~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~gKg~K~R~Vpi~~~~~~~l~ 211 (328) .+......... ....||+||+.|||.||||+||+++|+|+|||++.+.|.|.|||+|+|.||+++.+.++|. T Consensus 173 ~i~~~~~~~l~~~~~~~~~~~~~RD~aIi~ll~~tGlRvsEl~~L~~~DId~~~~~i~V~~Kg~K~r~vpi~~~~~~~l~ 252 (360) T PRK05084 173 FIDNEYEQKLSNRALSSFKKNKERDLAIIALLLGSGIRVSELVNLDLKDLNLKQMTIDVTRKGGKRDSVPIAPFALPYLE 252 (360) T ss_pred HHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCHHHHHHCCCHHHCCCCCCEEEEEECCCCEEEEECCHHHHHHHH T ss_conf 65244341202555443012367999999999985879999976979985878997999847984468877899999999 Q ss_pred HHHHHHCCCCC-CCCCCCCCCCCCC---CCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHH Q ss_conf 22111001234-4665543211112---2111000123567899976869998805417999999998489988999983 Q gi|254780882|r 212 EYYDLCPFDLN-LNIQLPLFRGIRG---KPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSIL 287 (328) Q Consensus 212 ~yl~~~~~~~~-~~~~~~lF~~~~g---~~ls~~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~l 287 (328) +|++.+..... ....+++|++..| ++++.++|.+++++++..+|+ ++|||+|||||||+|+++|+|+..||++| T Consensus 253 ~yl~~r~~~~~~~~~~~~lF~~~~~~~~~rls~~~i~~~v~k~~~~~~~--~itpH~LRHtfAT~Ll~~G~dl~~vq~lL 330 (360) T PRK05084 253 EYLKIRAQRYKAEKNDTALFLTKYRGKPNRISASAIEKMVAKYSEAFGV--RVTPHKLRHTLATRLYDATKDQVLVADQL 330 (360) T ss_pred HHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCHHHHHHHHHHHHHHCCC--CCCCCHHHHHHHHHHHHCCCCHHHHHHHH T ss_conf 9999708743577888815764689988822499999999999986799--97841329999999998799999999985 Q ss_pred CCCCHHHHHHHHHHCHHHHHHHHHHH Q ss_conf 78887897999961989999999999 Q gi|254780882|r 288 GHFRLSTTQIYTNVNSKNGGDWMMEI 313 (328) Q Consensus 288 GH~s~~tT~~Y~h~~~~~~~~~l~~~ 313 (328) ||+|++||++|+|++.++.++++.++ T Consensus 331 GH~si~TT~iYthv~~~~~r~a~~~l 356 (360) T PRK05084 331 GHTSTQVTDLYTHIVNDEQKDALDKL 356 (360) T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH T ss_conf 89987999998868999999999863 No 10 >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=100.00 E-value=0 Score=395.73 Aligned_cols=260 Identities=18% Similarity=0.287 Sum_probs=218.0 Q ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999986254889999999999999999985121478878968989999999999998612101332112344422223 Q gi|254780882|r 21 WLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLSGIKSFLK 100 (328) Q Consensus 21 ~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~~~s~~T~~~~ls~lr~f~~ 100 (328) |.+||. ++|+|++|+++|..++.+|+ +. ..+++..++.+|+.++.+ +++++|+|+++++|++||+ T Consensus 1 F~~yL~-e~g~S~~Ti~sY~~dl~~ff--~~-----------~~~i~~~~i~~y~~~L~~-~~~~~Tin~~lsalr~F~~ 65 (263) T cd01196 1 FEEYLY-KNNLSKNTVSSYLRTVVQYF--LN-----------GKELTKPNLLEYKGYLQE-NFKAQTVNLRLQGINKYLE 65 (263) T ss_pred CHHHHH-HCCCCHHHHHHHHHHHHHHH--CC-----------CCCCCHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHH T ss_conf 958796-76978999999999999997--15-----------588999999999999996-8989999999999999999 Q ss_pred HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 33210123222222222222221211111110156787765310135677577532012221001123322222112222 Q gi|254780882|r 101 YLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQN 180 (328) Q Consensus 101 ~~~~~~~i~~np~~~i~~~k~~~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~d 180 (328) |+..+++. .. ...++....+|.+++.+|+..+++++.... ..||++|+.+||.||||+||+++|+++| T Consensus 66 fl~~~~~~----~k-~~k~~~~~~l~~~l~~~e~~~l~~~~~~~~-------~~r~~~ii~lL~~tGlRvsEl~~L~~~d 133 (263) T cd01196 66 FIGWHDLK----LK-FVKVQQKAFLENVISDADYKFLKTALKADG-------NEEWYFVVWFLAATGARVSELIHIKVEH 133 (263) T ss_pred HHHHCCCC----CC-CCCCCCCCCCCCCCCHHHHHHHHHHHCCCC-------CHHHHHHHHHHHHHCCHHHHHHCCCHHH T ss_conf 96554786----55-678888899999899999999997631366-------7769999999998499999998368988 Q ss_pred CCCCCCCEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCC-CC Q ss_conf 23323220332378531000112210023432211100123446655432111122111000123567899976869-99 Q gi|254780882|r 181 IMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLP-LS 259 (328) Q Consensus 181 id~~~~~i~v~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g~~ls~~~i~~~~~~~~~~~gi~-~~ 259 (328) |+++ .+.|.|||+|+|.|||++.+...+.+|++.+. ..+++||++..|+|++++++++.++++++++|++ .. T Consensus 134 i~~~--~~~i~~KG~K~R~v~i~~~~~~~l~~y~~~~~-----~~~~~lF~~~~g~~l~~~~i~~~~k~~~~~agi~~~~ 206 (263) T cd01196 134 VQTG--YADIYSKGGKIRRLYIPKNLRVEALKWLKELN-----LDSGYIFLNRFGKPITARGIAQQLKNYAAKYKMNPRV 206 (263) T ss_pred HCCC--CEEEEECCCCEEEEEECHHHHHHHHHHHHHCC-----CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCC T ss_conf 2668--64999559937887307999999999999728-----8657716699949888999999999999985999877 Q ss_pred CCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHCHHHHHHHHHHHH Q ss_conf 8805417999999998489988999983788878979999619899999999999 Q gi|254780882|r 260 TTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIY 314 (328) Q Consensus 260 ~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~~l~~~~ 314 (328) ++||+|||||||+|+++|+|+..||++|||+|++||++|+|++.++.++++.+++ T Consensus 207 ~~PH~lRHtfAt~ll~~g~dl~~vq~lLGH~si~TT~iY~~~~~~~~k~~~~k~~ 261 (263) T cd01196 207 VYPHSFRHLFAKNFLAKYNDLALLADLMGHESIETTRIYLRKTATEQQRIVDKIV 261 (263) T ss_pred CCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHC T ss_conf 8872269999999998699999999995899878999988079999999999870 No 11 >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=100.00 E-value=0 Score=390.72 Aligned_cols=284 Identities=20% Similarity=0.189 Sum_probs=237.9 Q ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999998625488999999999999999998512147887896898999999999999861210133211234 Q gi|254780882|r 14 LLKERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLS 93 (328) Q Consensus 14 l~~~~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~~~s~~T~~~~ls 93 (328) |.+++++||++.+. .|+|.+| |..+|+.|..||.... ...++.+++..|+.. ..+.+++|++++++ T Consensus 1 l~~~i~~yl~~~r~-~G~~~~t---~~~~L~~F~~fl~~~~--------~~~~~~~~~~~w~~~--~~~~s~~t~~~rls 66 (299) T cd01187 1 LRQALEEYIALRRA-LGYKYRT---PARLLRDFVRFLERHG--------AGFITTDLALRWAAS--PPSAQPATWAGRLG 66 (299) T ss_pred CHHHHHHHHHHHHH-CCCCHHH---HHHHHHHHHHHHHHCC--------CCCCCHHHHHHHHHH--CCCCCHHHHHHHHH T ss_conf 96999999999998-7998156---8999999999998679--------988899999999987--79998899999999 Q ss_pred HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCC Q ss_conf 44222233321012322222222222222121111111015678776531013567757753201222100112332222 Q gi|254780882|r 94 GIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEA 173 (328) Q Consensus 94 ~lr~f~~~~~~~~~i~~np~~~i~~~k~~~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El 173 (328) +||+||+|+..+|++..||...+..|+..+..|.++|++|+.++++++.... ......+.|+++||.|||.||||+||+ T Consensus 67 ~lr~F~~~l~~~g~~~~~P~~~~~~~k~~~~~P~~lt~~Ei~~Ll~a~~~~~-~~~~~~~~~~~~l~~Lly~tGlR~sEl 145 (299) T cd01187 67 VVRRFARHRRRADPRTEVPPADLFPRRPRRPTPYIYTDEEIQRLLAAALQLP-PTSGLRPWTYRTLFGLLAVTGLRLGEA 145 (299) T ss_pred HHHHHHHHHHHCCCCCCCCHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHCCC-CCCHHHHHHHHHHHHHHHHHCCHHHHH T ss_conf 9999999999869956690765457899999999999999999984110169-961057689999999999958889998 Q ss_pred CCCCCCCCCCCCCCEEEC-CCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHH---HHHHH Q ss_conf 211222223323220332-37853100011221002343221110012344665543211112211100012---35678 Q gi|254780882|r 174 LSLTPQNIMDDQSTLRIQ-GKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQ---RYIRQ 249 (328) Q Consensus 174 ~~L~~~did~~~~~i~v~-gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g~~ls~~~i~---~~~~~ 249 (328) ++|+++|||++++.|.|. |||+|+|+|||++.+.++|.+|++.++.......+++||++.+|++++..+.. ..++. T Consensus 146 ~~L~~~Dvd~~~~~i~v~~gKg~K~R~Vpl~~~~~~~L~~yl~~r~~~~~~~~~~~lF~~~~g~~l~~~~~~~~~~~~r~ 225 (299) T cd01187 146 LRLRLSDVDLDSGILTVRDSKFGKSRLVPLHASTRAALRDYLARRDRLLPAPDSSAFFVSSRGGRLSYGGHRVFYALSRE 225 (299) T ss_pred HCCCCCCCCCCCCEEEEECCCCCCEEEEECCHHHHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCCHHHHHHHHHHHHH T ss_conf 03343305676784765418899707985669999999999998476426898986745899897877789999999999 Q ss_pred HHHHCCC--CCCCCCCCCHHHHHHHHH----HCCCCHH----HHHHHHCCCCHHHHHHHHHHCHHHHHHHHHH Q ss_conf 9997686--999880541799999999----8489988----9999837888789799996198999999999 Q gi|254780882|r 250 LRRYLGL--PLSTTAHTLRHSFATHLL----SNGGDLR----SIQSILGHFRLSTTQIYTNVNSKNGGDWMME 312 (328) Q Consensus 250 ~~~~~gi--~~~~spH~lRHtfAt~ll----~~G~~~~----~v~~~lGH~s~~tT~~Y~h~~~~~~~~~l~~ 312 (328) +....+. ....+||+|||||||+++ ++|+|+. +||++|||+|++||++|+|+++|..+++.++ T Consensus 226 ~~~~~~~~~~~~~~pH~LRHtfAt~~l~~~~~~G~di~~~L~~lq~~LGH~si~tT~~Y~h~~~e~l~~a~~r 298 (299) T cd01187 226 IGLRGWAQRGRGPRLHDLRHRFAVTRLTRWYRAGADVERKLPVLATYLGHANITDTYWYLHASPELMELAARR 298 (299) T ss_pred HHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHHCCHHHHHHHHHH T ss_conf 9986066668999976571389999999998679973433999999748998688898880399999999850 No 12 >PRK02436 xerD site-specific tyrosine recombinase XerD-like protein; Reviewed Probab=100.00 E-value=0 Score=391.64 Aligned_cols=247 Identities=21% Similarity=0.263 Sum_probs=208.8 Q ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999986254889999999999999999985121478878968989999999999998612101332112344422 Q gi|254780882|r 18 RQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLSGIKS 97 (328) Q Consensus 18 ~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~~~s~~T~~~~ls~lr~ 97 (328) +++||+++..|||+|+||+++|+.||+.|..|+.. +++..++..|..++. +++++|++|++++|++ T Consensus 1 l~~fl~~l~~ek~lS~nTi~aY~~DL~~F~~fl~~------------~i~~~~i~~y~~~L~--~~~~st~~Rklsslr~ 66 (247) T PRK02436 1 MKNYIEPFLASKALSVNSQKSYRYDLQQFCQLVGE------------RVNQTSLKLYQNSLA--NLKLSAQKRKLSAVNQ 66 (247) T ss_pred CHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH------------HCCHHHHHHHHHHHH--CCCHHHHHHHHHHHHH T ss_conf 98899999998691499999999999999999873------------589999999999987--1679999999999999 Q ss_pred HHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCC Q ss_conf 22333210123222222222222221211111110156787765310135677577532012221001123322222112 Q gi|254780882|r 98 FLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLT 177 (328) Q Consensus 98 f~~~~~~~~~i~~np~~~i~~~k~~~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~ 177 (328) ||+|+.++++++..+- ....|+.++..|..++..++..+++.. ...|+++|+.+||.||||+||+++|+ T Consensus 67 F~~fL~~~~~i~~~~~-~~~~~k~~~~~~~~~~~~~~~~~~~~~----------~~~~~r~i~~ll~~tGlRvSEl~~L~ 135 (247) T PRK02436 67 FLYFLYQKKYLDSFFK-LKETAKVMRSEKQQPEILDLSSFYQET----------PFPEGQLIALLILELGLTPSEIAGLK 135 (247) T ss_pred HHHHHHHCCCCCCCCC-HHCCCCCCCCCCCCCHHHHHHHHHCCC----------CCHHHHHHHHHHHHHCCHHHHHHCCC T ss_conf 9999997687667520-420588988765413186799885646----------78568999999999694799997891 Q ss_pred CCCCCCCCCCEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCC Q ss_conf 22223323220332378531000112210023432211100123446655432111122111000123567899976869 Q gi|254780882|r 178 PQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLP 257 (328) Q Consensus 178 ~~did~~~~~i~v~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g~~ls~~~i~~~~~~~~~~~gi~ 257 (328) |+|||++.+.|.| |||+|+|.|||++.+.+.|..|++. ...++| +.+|+|++++++++.++++++.+|++ T Consensus 136 ~~Did~~~~~i~v-~kg~k~R~Vpl~~~~~~~l~~y~~~--------~~~~l~-~~~g~~lsr~~~~~~lk~~~~~~g~~ 205 (247) T PRK02436 136 VADIDLDFQVLTI-EKAGGKRVLPLPEALLPFLEQILNG--------KEVYLF-EHKGKPYSRQWFFNQLKSFVNSIGYP 205 (247) T ss_pred HHHHCCCCCEEEE-ECCCEEEEEECCHHHHHHHHHHHHC--------CCCEEE-CCCCCCCCHHHHHHHHHHHHHHCCCC T ss_conf 9991988787999-0799078754679999999998715--------865011-68999667999999999999974999 Q ss_pred CCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHH Q ss_conf 9988054179999999984899889999837888789799996 Q gi|254780882|r 258 LSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTN 300 (328) Q Consensus 258 ~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h 300 (328) ++|||.|||||||+|+++|+|+.+||++|||+|++|||||++ 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 13 >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=100.00 E-value=0 Score=383.75 Aligned_cols=284 Identities=20% Similarity=0.256 Sum_probs=237.4 Q ss_pred HHCCHHHHHHHHHHHHHH-HHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHH-HHHHHH Q ss_conf 314989999999999999-986254889999999999999999985121478878968989999999999998-612101 Q gi|254780882|r 8 EIVSFELLKERQNWLQNL-EIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRR-TQKIGD 85 (328) Q Consensus 8 ~~~~~~l~~~~e~~L~~l-~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~-~~~~s~ 85 (328) +...-++++.+++|++.+ +.++++|++|+++|..+++.|..|+...... ....+.+++..+|.+|+.++. +.++|+ T Consensus 9 ~~~~~tf~~~~~~~~e~~~~~~k~~S~~Ti~~Y~~~l~~f~~Fl~~~~~~--~di~~~~i~~~~i~~f~~~L~~~k~~s~ 86 (299) T cd01185 9 KEMQQTFLAYFDKHNDERERVGKDKAQSTWKRYRTHLKNLREFIECTYKE--IDIALLELTREFILEFKLFLRKEKKLSR 86 (299) T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHCCC--CCCCHHHCCHHHHHHHHHHHHHCCCCCH T ss_conf 78899999999999999998677567999999999999999999982887--7788788479999999999987579888 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCC Q ss_conf 33211234442222333210123222222222222221211111110156787765310135677577532012221001 Q gi|254780882|r 86 RSLKRSLSGIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYG 165 (328) Q Consensus 86 ~T~~~~ls~lr~f~~~~~~~~~i~~np~~~i~~~k~~~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~ 165 (328) +|+++++++|++||+||++++++..||+..++.|+.++..|++|+.+|+.++++... ........||.++|.+ . T Consensus 87 ~Ti~~~l~~lr~~~~~a~~~~~i~~nP~~~i~~~k~~~~~~~~Lt~eEi~~ll~~~~----~~~~~~~~r~~~l~~~--~ 160 (299) T cd01185 87 NTAVHYLSWLKKLLKIAYRDKGLRDNPFAKFKCKKEEETDREYLTPDELQKLAETPC----KDPRLELVRRAFLFSC--F 160 (299) T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCCHHHCCCCCCCCCCCCCCCHHHHHHHHHCCC----CCCCHHHHHHHHHHHH--H T ss_conf 899999999999999999889921192965617888998999999999999982714----7874699999999998--8 Q ss_pred CCCCCCCCCCCCCCCCCCCCCC---EEE-CCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 1233222221122222332322---033-237853100011221002343221110012344665543211112211100 Q gi|254780882|r 166 CGLRISEALSLTPQNIMDDQST---LRI-QGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPG 241 (328) Q Consensus 166 TGlR~~El~~L~~~did~~~~~---i~v-~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g~~ls~~ 241 (328) ||||+||+++|+|+||+++... +.+ .+|+++.+.|||++.+.++|..|.. ...+++|+. ++.. T Consensus 161 TGlR~~El~~L~~~dI~~~~~~~~~i~~~~~Kt~~~~~ipl~~~~~~~l~~~~~--------~~~~~lF~~-----~~~~ 227 (299) T cd01185 161 TGLRYSDIKKLTWEEIVEDSDGEKWIRKRRQKTKVEVYIPLLDEALQILGKYPD--------EKEGLVFPL-----LKNS 227 (299) T ss_pred HCCCHHHHHHCCHHHHHHCCCCEEEEEECCCCCCEEEEEECHHHHHHHHHHHHC--------CCCCCCCCC-----CCHH T ss_conf 098899998396998213369648998516744224320015999999998522--------675440688-----8756 Q ss_pred CHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHCHHHHHHHHHH Q ss_conf 01235678999768699988054179999999984899889999837888789799996198999999999 Q gi|254780882|r 242 VFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMME 312 (328) Q Consensus 242 ~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~~l~~ 312 (328) .+++.++++++.+|+++++|||+|||||||+|+++|+|+.+||++|||+|++||++|+|++++++.+++.+ T Consensus 228 ~~~~~lk~~~~~agi~~~it~H~lRHTfAt~ll~~G~~l~~vq~~LGHssi~tT~~Y~hv~~e~~~e~~~k 298 (299) T cd01185 228 NMNKPLKEWAKLAGIKKHITFHCARHTFATLQLLSGGPIETVSKMLGHTNIKTTQVYARVTDEKKSEDMNK 298 (299) T ss_pred HHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHC T ss_conf 89999999999828899998114099999999987989999998818998899999987798899999963 No 14 >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=100.00 E-value=0 Score=376.54 Aligned_cols=247 Identities=26% Similarity=0.374 Sum_probs=213.2 Q ss_pred CCHHHCCHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC---CCCCCCCCCCCCCCCCCCCCCCHHHH Q ss_conf 8968989999999999998-6121013321123444222233321012322---22222222222212111111101567 Q gi|254780882|r 61 QTIRQLSYTEIRAFISKRR-TQKIGDRSLKRSLSGIKSFLKYLKKRKITTE---SNILNMRNLKKSNSLPRALNEKQALT 136 (328) Q Consensus 61 ~~~~~i~~~~i~~~l~~l~-~~~~s~~T~~~~ls~lr~f~~~~~~~~~i~~---np~~~i~~~k~~~~~p~~lt~~e~~~ 136 (328) .++.+|+..+|.+|+.+|. ++|+|++|+|+++++|++||+||..++.... +|+..++..+..+..+.+++.+|+.+ T Consensus 3 l~l~dI~~~~i~~y~~~L~~~rg~s~~Tin~~l~~L~~f~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~l~~eei~~ 82 (260) T cd01190 3 LEIEDIDAPLILAFLDHLENDRGNSIRTRNARLAALHSFFRYAAREVPEHLPTIQRVLAIPMKRFKRPLVTYLTREEVQA 82 (260) T ss_pred CCHHHCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHH T ss_conf 87587999999999999998469999999999999999999999808401455371014887888999998899999999 Q ss_pred HHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CEEECCCCCCCCCCCCCCCCHHHHHHHHH Q ss_conf 87765310135677577532012221001123322222112222233232-20332378531000112210023432211 Q gi|254780882|r 137 LVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQS-TLRIQGKGDKIRIVPLLPSVRKAILEYYD 215 (328) Q Consensus 137 ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~-~i~v~gKg~K~R~Vpi~~~~~~~l~~yl~ 215 (328) +++.. ....+.+.||++|+.+++.||||+||+++|+|+|||++.+ .+.+.|||+|+|.|||++.+.++|.+|++ T Consensus 83 ll~~~-----~~~~~~~~rd~~i~~ll~~tGlR~sEl~~L~~~did~~~~~~~~~~~K~~k~r~vpi~~~~~~~L~~~~~ 157 (260) T cd01190 83 LLAAP-----DRRTWSGRRDRAMLLFLYNTGARVSEATGLKVDDLQLDPPAQVRLIGKGRKERTVPLWRSTAAALRAWLR 157 (260) T ss_pred HHHCC-----CCCCCCCHHHHHHHHHHHHHCCCHHHHHCCCHHHCCCCCCEEEEEECCCCEEEEEECCHHHHHHHHHHHH T ss_conf 98186-----6567303689999999999575589786286976178998089996899804135468999999999999 Q ss_pred HHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCC------CCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCC Q ss_conf 10012344665543211112211100012356789997686------999880541799999999848998899998378 Q gi|254780882|r 216 LCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGL------PLSTTAHTLRHSFATHLLSNGGDLRSIQSILGH 289 (328) Q Consensus 216 ~~~~~~~~~~~~~lF~~~~g~~ls~~~i~~~~~~~~~~~gi------~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH 289 (328) .++. ...+++||++..|++++..++.+.++++...+|. .++++||+|||||||+|+++|+|+..||++||| T Consensus 158 ~~~~---~~~~~~lF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~H~lRHt~At~ll~~G~~l~~vq~~LGH 234 (260) T cd01190 158 ERGL---HAEDEPLFVNRRGEPMTRFGVTYLLRKHAAKAAATAPTLATKRISPHVLRHTTAMHLLQSGVDIVVIALWLGH 234 (260) T ss_pred HCCC---CCCCCEEEECCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCC T ss_conf 7544---6876615127899947868899999999999724164324677676713899999999879999999998689 Q ss_pred CCHHHHHHHHHHCHHHHHHHHHHHHHHHCC Q ss_conf 887897999961989999999999998173 Q gi|254780882|r 290 FRLSTTQIYTNVNSKNGGDWMMEIYDQTHP 319 (328) Q Consensus 290 ~s~~tT~~Y~h~~~~~~~~~l~~~~~~~~~ 319 (328) +|++||++|+|++.++. +++++++|| T Consensus 235 ~~i~tT~~Y~hv~~~~~----r~a~~k~~p 260 (260) T cd01190 235 ASLETTNIYAEADLEMK----RRALAKATP 260 (260) T ss_pred CCHHHHHHHHCCCHHHH----HHHHHHHCC T ss_conf 98899999984799999----999998691 No 15 >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=100.00 E-value=0 Score=379.55 Aligned_cols=253 Identities=32% Similarity=0.448 Sum_probs=212.1 Q ss_pred HCCCHHHHHHHHHHHHHHHHH--HHHCCCCCCCCCCHHHCCHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 254889999999999999999--985121478878968989999999999998-61210133211234442222333210 Q gi|254780882|r 29 RGLSKLTLQSYECDTRQFLIF--LAFYTEEKITIQTIRQLSYTEIRAFISKRR-TQKIGDRSLKRSLSGIKSFLKYLKKR 105 (328) Q Consensus 29 r~~s~~T~~~Y~~~l~~f~~~--~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~-~~~~s~~T~~~~ls~lr~f~~~~~~~ 105 (328) ++||..|+.+|-.-+++|+.| -.. ..+++.+...+|++|+.+|. +.+.|++|.|..|++|.-||+-.... T Consensus 12 ~hYs~~T~~aY~~Wi~rfI~frG~~C-------~~hp~~~g~~eVeaFLs~LAv~~~Vs~sTQ~QAL~ALlFLY~~iL~~ 84 (320) T TIGR02249 12 RHYSKRTEEAYLHWIKRFIRFRGHNC-------LRHPSTLGDTEVEAFLSDLAVDGKVSASTQNQALAALLFLYKEILKL 84 (320) T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCC-------CCCHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCC T ss_conf 88789999999999999998850510-------13853307567888856776425747657999999999999998468 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHH-HCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 1232222222222222212111111101567877653-101356775775320122210011233222221122222332 Q gi|254780882|r 106 KITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVL-LHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDD 184 (328) Q Consensus 106 ~~i~~np~~~i~~~k~~~~~p~~lt~~e~~~ll~~~~-~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~ 184 (328) ++-. ...+-.++.++++|-+||+||+.++++.+. ... +++..|||+||||+.|++.|+++||||+ T Consensus 85 ~L~~---~~~~~Ra~~~~kLPvVLT~eEV~~~l~~l~eg~y-----------~L~a~LLYGsGMRlmE~LRLRikDiDF~ 150 (320) T TIGR02249 85 ELSL---MENFVRAKRPRKLPVVLTREEVARLLEHLEEGKY-----------RLIAKLLYGSGMRLMECLRLRIKDIDFD 150 (320) T ss_pred CCCC---HHHCCCCCCCCCCCEECCHHHHHHHHHHCCCCCH-----------HHHHHHHCCCHHHHHHHHHCCCCEEEEC T ss_conf 8874---2222067888737733598899999842578613-----------1122231255158988875101103433 Q ss_pred CCCEEEC-CCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCC--------------------------CCCCCCCCCC--- Q ss_conf 3220332-378531000112210023432211100123446--------------------------6554321111--- Q gi|254780882|r 185 QSTLRIQ-GKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLN--------------------------IQLPLFRGIR--- 234 (328) Q Consensus 185 ~~~i~v~-gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~~--------------------------~~~~lF~~~~--- 234 (328) .+.|.|+ |||+|.|.|||+.++.+-|+..++..+.-...+ ..-||||+.+ T Consensus 151 ~~~I~vr~GKG~KdR~v~Lp~~L~~~L~~q~~~~~~~h~~Dl~~~G~g~V~LP~AL~rKYPnA~~~~~WqylFPs~~~S~ 230 (320) T TIGR02249 151 YGEIRVRDGKGGKDRVVTLPKSLAPPLREQLERARALHEKDLLAEGYGGVYLPHALARKYPNASKEWGWQYLFPSARLSR 230 (320) T ss_pred CCEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEHHHHHHCCCCCCCCCCCCEEECCCCCCCC T ss_conf 76689973668988612681755799999999999999986405885301004554215787356678766537750155 Q ss_pred ----CC----CCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHC Q ss_conf ----22----111000123567899976869998805417999999998489988999983788878979999619 Q gi|254780882|r 235 ----GK----PLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVN 302 (328) Q Consensus 235 ----g~----~ls~~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~ 302 (328) |. .|+..+|.+.++++..+|||+|.+|||+|||||||+||++|.||++||++|||+|++||||||||- T Consensus 231 DPrsG~~~RHH~~e~~~QRav~~Av~~AGI~KpvTcHTLRHSFATHLLe~G~DIRTVQelLGHsDVkTTqIYTHVL 306 (320) T TIGR02249 231 DPRSGRIRRHHIDEKTIQRAVRRAVERAGIEKPVTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIYTHVL 306 (320) T ss_pred CCCCCCCEEEECCCCHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCCCCCCEEEEEE T ss_conf 7777852001067004328999999957898867887421224430565177367898861788422463453051 No 16 >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=100.00 E-value=0 Score=358.12 Aligned_cols=229 Identities=33% Similarity=0.478 Sum_probs=203.8 Q ss_pred CCCHHHCCHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHH Q ss_conf 78968989999999999998612-10133211234442222333210123222222222222221211111110156787 Q gi|254780882|r 60 IQTIRQLSYTEIRAFISKRRTQK-IGDRSLKRSLSGIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLV 138 (328) Q Consensus 60 ~~~~~~i~~~~i~~~l~~l~~~~-~s~~T~~~~ls~lr~f~~~~~~~~~i~~np~~~i~~~k~~~~~p~~lt~~e~~~ll 138 (328) ..++++|+..||++|+.++..++ +|++|+|+++++|++||+|+...++ +|+..++.++.+++.|+++|.+|+.+++ T Consensus 4 ~k~~~~it~~dI~~y~~~L~~~~~~s~~Tin~~l~~l~~~~~~~~~~~~---~~~~~~~~~k~~~~~~~~lt~eEi~~ll 80 (242) T cd01193 4 GRSPDELGEEDVRAFLTLLAVEGNVSASTQNQALSALLFFYRHTLKRDL---PWLQRIRRPRKPRKLPVVLSPEEVRRLL 80 (242) T ss_pred CCCHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCC---CHHHHCCCCCCCCCCCCCCCHHHHHHHH T ss_conf 9895889999999999999984898999999999999999999987689---6566565578999899889999999999 Q ss_pred HHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEE-CCCCCCCCCCCCCCCCHHHHHHHHHHH Q ss_conf 7653101356775775320122210011233222221122222332322033-237853100011221002343221110 Q gi|254780882|r 139 DNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRI-QGKGDKIRIVPLLPSVRKAILEYYDLC 217 (328) Q Consensus 139 ~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v-~gKg~K~R~Vpi~~~~~~~l~~yl~~~ 217 (328) +++. +.|+++++.+++.||||+||+++|+|+|||+++++|.| .|||+|+|.|||++.+.++|.+|++.. T Consensus 81 ~~~~----------~~r~~~~~~ll~~tGlR~~El~~L~~~did~~~~~i~i~~~K~~k~R~vpl~~~~~~~l~~~l~~~ 150 (242) T cd01193 81 GALT----------GLKHRLILSLLYGCGLRLSECLRLRVKDIDFDRGQIRVRQGKGGKDRYVMLPEALLELLRAYWKRA 150 (242) T ss_pred HCCC----------CCHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCEEEEEEECCCCCCEEEECCHHHHHHHHHHHHHH T ss_conf 7387----------767999999999828988889878663167675179986188996058875999999999999984 Q ss_pred CCCCCCCCCCCCCCCCCC--------CCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCC Q ss_conf 012344665543211112--------211100012356789997686999880541799999999848998899998378 Q gi|254780882|r 218 PFDLNLNIQLPLFRGIRG--------KPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGH 289 (328) Q Consensus 218 ~~~~~~~~~~~lF~~~~g--------~~ls~~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH 289 (328) +........+++|++.+| .+++.+++++.++++++.+|++++++||+|||||||+|+++|+|+..||++||| T Consensus 151 ~~~~~~~~~~~lF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gi~~~~~~H~lRHT~at~ll~~G~~l~~v~~~lGH 230 (242) T cd01193 151 RALGRERPWQWLFPSTRRSRDPVERRHHLSERTLQRALKKAVEQAGIDKRVTPHTLRHSFATHLLEAGYDIRTIQELLGH 230 (242) T ss_pred HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHCCC T ss_conf 65300365210135667775755367767599999999999998499999886748999999999879999999988399 Q ss_pred CCHHHHHHHHHH Q ss_conf 887897999961 Q gi|254780882|r 290 FRLSTTQIYTNV 301 (328) Q Consensus 290 ~s~~tT~~Y~h~ 301 (328) +|++|||+|+|| T Consensus 231 ~si~tT~~Y~Hv 242 (242) T cd01193 231 SDLKTTMIYTHV 242 (242) T ss_pred CCHHHHHHHHCC T ss_conf 888899870583 No 17 >PRK09870 tyrosine recombinase; Provisional Probab=100.00 E-value=0 Score=338.54 Aligned_cols=195 Identities=25% Similarity=0.243 Sum_probs=174.5 Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEC-CCCCC Q ss_conf 22222121111111015678776531013567757753201222100112332222211222223323220332-37853 Q gi|254780882|r 118 NLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQ-GKGDK 196 (328) Q Consensus 118 ~~k~~~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~-gKg~K 196 (328) ++|.+++.|++||.+|+.++++++.. . ..+.||++|+.+||.||||+||+++|+|+|||++++.+.|. +|+|+ T Consensus 2 k~K~~~k~~~~LT~~Ev~~lL~~~~~-----~-~~~~Rd~aii~ll~~tGlRvsEl~~L~~~DId~~~~~i~i~~~k~g~ 75 (200) T PRK09870 2 KNKADNKKRNFLTHSEIESLLKAANT-----G-PHAARNYCLTLLCFIHGFRASEICRLRISDIDLKAKCIYIHRLKKGF 75 (200) T ss_pred CCCCCCCCCCCCCHHHHHHHHHCCCC-----C-CHHHHHHHHHHHHHHHCCHHHHHHCCCHHHCCCCCCEEEEEECCCCC T ss_conf 98778888998899999999827799-----9-37589999999999968689999769598718779979999767897 Q ss_pred CCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHC Q ss_conf 10001122100234322111001234466554321111221110001235678999768699988054179999999984 Q gi|254780882|r 197 IRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSN 276 (328) Q Consensus 197 ~R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g~~ls~~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~ 276 (328) .|.+|+.+....+|.+|++.+... ....+++||+|.+|+|++++++++.++++++++|++.+++||+|||||||+|+++ T Consensus 76 ~~~~pl~~~~~~~l~~~l~~r~~~-~~~~~~~lF~s~~G~~ls~~~i~~~~~~~~~~agi~~~v~pH~LRHt~At~Ll~~ 154 (200) T PRK09870 76 STTHPLLNKEIQALKNWLSIRTSY-PHAESEWVFLSRKGNPLSRQQFYHIISTSGGNAGLSLEIHPHMLRHSCGFALANM 154 (200) T ss_pred EEEEECHHHHHHHHHHHHHHHHHC-CCCCCCEECCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHC T ss_conf 578876799999999999987524-5888871425799997779999999999999859997768760289999999986 Q ss_pred CCCHHHHHHHHCCCCHHHHHHHHHHCHHHHHHHHHHHHHHHCCCHHC Q ss_conf 89988999983788878979999619899999999999981730001 Q gi|254780882|r 277 GGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQTHPSITQ 323 (328) Q Consensus 277 G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~~l~~~~~~~~~~~~~ 323 (328) |+|+.+||++|||+|++|||+|+|++.+ .|+++|+++|||.++ T Consensus 155 G~di~~Iq~lLGHssi~TT~iYth~~~~----~l~~i~~~~hpr~~~ 197 (200) T PRK09870 155 GIDTRLIQDYLGHRNIRHTVWYTASNAG----RFYGIWDRARGRQRH 197 (200) T ss_pred CCCHHHHHHHHCCCCHHHHHHHHHCCHH----HHHHHHHHHCCCHHC T ss_conf 9999999999489986689998817999----999999984973100 No 18 >PRK09871 tyrosine recombinase; Provisional Probab=100.00 E-value=0 Score=324.95 Aligned_cols=189 Identities=25% Similarity=0.298 Sum_probs=169.6 Q ss_pred CCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECC-CCCCCCCCCCCCC Q ss_conf 111110156787765310135677577532012221001123322222112222233232203323-7853100011221 Q gi|254780882|r 127 RALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQG-KGDKIRIVPLLPS 205 (328) Q Consensus 127 ~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~g-Kg~K~R~Vpi~~~ 205 (328) ++||.+|+.++++++.. ...+.||+||+.+||.||||+||+++|+|+|||++++.|.|.+ ||++.+++|+.+. T Consensus 5 ryLt~~Ev~~Ll~a~~~------~~~~~Rd~aii~ll~~tGlR~sEl~~L~~~Did~~~~~i~i~~~k~g~~~~~pl~~~ 78 (198) T PRK09871 5 RYLTGKEVQAMMQAVCY------GATGARDYCLILLAYRHGMRISELLDLHYQDLDLNEGRINIRRLKNGFSTVHPLRFD 78 (198) T ss_pred CCCCHHHHHHHHHCCCC------CCCCHHHHHHHHHHHHHCCHHHHHHCCCHHHCCCCCCEEEEEECCCCEEEEEECCHH T ss_conf 76999999999844143------985448999999999978689999788887758779969999789974898748699 Q ss_pred CHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHH Q ss_conf 00234322111001234466554321111221110001235678999768699988054179999999984899889999 Q gi|254780882|r 206 VRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQS 285 (328) Q Consensus 206 ~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g~~ls~~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~ 285 (328) +.+++..|+..+.........+++|++.+|.+++++++++++++++.++|+..+++||+|||||||+|+++|+|+..||+ T Consensus 79 ~~~~l~~~~~~r~~~~~~~~~~~lF~s~~G~~ls~~~~~~~ik~~~~~aG~~~~~~pH~LRHTfAt~Ll~~G~dl~~Iq~ 158 (198) T PRK09871 79 EREAVERWTQERANWKGADRTDAIFISRRGSRLSRQQAYRIIRDAGIEAGTVTQTHPHMLRHACGYELAERGADTRLIQD 158 (198) T ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHH T ss_conf 99999999998777512677884143588994799999999999999849998889985579999999986999999999 Q ss_pred HHCCCCHHHHHHHHHHCHHHHHHHHHHHHHHHCCCHHCCC Q ss_conf 8378887897999961989999999999998173000122 Q gi|254780882|r 286 ILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQTHPSITQKD 325 (328) Q Consensus 286 ~lGH~s~~tT~~Y~h~~~~~~~~~l~~~~~~~~~~~~~~~ 325 (328) +|||+|++||++|+|++.+ .|+++|+++||.+.+.. T Consensus 159 lLGHssi~TT~~Yth~~~~----~l~~~~~~~~p~~~~~~ 194 (198) T PRK09871 159 YLGHRNIRHTVRYTASNAA----RFAGLWERNNLINEKLK 194 (198) T ss_pred HHCCCCHHHHHHHHCCCHH----HHHHHHHHHCCCCCCCC T ss_conf 9389977899998858999----99999999496100100 No 19 >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=100.00 E-value=0 Score=314.87 Aligned_cols=258 Identities=19% Similarity=0.199 Sum_probs=201.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC Q ss_conf 89999999999999999985121478878968989999999999998612101332112344422223332101232222 Q gi|254780882|r 33 KLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLSGIKSFLKYLKKRKITTESN 112 (328) Q Consensus 33 ~~T~~~Y~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~~~s~~T~~~~ls~lr~f~~~~~~~~~i~~np 112 (328) +||+++|.++++.|..||...... + ..++..+|..|+.++. ++++++|+++++++|++||.|+...+....+| T Consensus 1 enT~~aY~~~l~~f~~wc~~~~~~-----~-~~~t~~~v~~yl~~L~-~~~~~~Ti~~~lsalr~~~~~~~~~~~~~~~~ 73 (287) T cd00799 1 DNTRKAYLSDWRRFAAWCQAHGRT-----P-LPASPETVTLYLTDLA-DSLAPSTISRRLSALSQLHRRSGLPSPADSPL 73 (287) T ss_pred CCHHHHHHHHHHHHHHHHHHCCCC-----C-CCCCHHHHHHHHHHHH-HCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCH T ss_conf 905999999999999999974999-----7-8899999999999998-47787699999999999999970588654714 Q ss_pred CCCC-C---CCC-CCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC- Q ss_conf 2222-2---222-221211111110156787765310135677577532012221001123322222112222233232- Q gi|254780882|r 113 ILNM-R---NLK-KSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQS- 186 (328) Q Consensus 113 ~~~i-~---~~k-~~~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~- 186 (328) +..+ + .+. ..++.+.+++.+++.++++.+ +......++||++|+.++|.||||++|+++|+|+||+++.+ T Consensus 74 ~~~~~~~~~r~~~~~~~~~~~~~~~~l~~ll~~~----~~~~~~~~~Rd~ail~ll~~tGlR~~El~~L~~~di~~~~~~ 149 (287) T cd00799 74 VRLVLRGIRREEARPKRQALAILPEDLDKLRSLL----DESDTLRDLRDLALLLLGFAGLLRRSELVRLRWEDLTFTDGG 149 (287) T ss_pred HHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHCC----CCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCC T ss_conf 8887532112368876578989999999998625----557875879999999999986238999971839871857897 Q ss_pred C--EEE-CCCCCCC------CCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC------CCCCCCCCCHHHHHHHHH Q ss_conf 2--033-2378531------000112210023432211100123446655432111------122111000123567899 Q gi|254780882|r 187 T--LRI-QGKGDKI------RIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGI------RGKPLNPGVFQRYIRQLR 251 (328) Q Consensus 187 ~--i~v-~gKg~K~------R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~------~g~~ls~~~i~~~~~~~~ 251 (328) . |.+ .+|+++. +.+|.......++..|+... ....+++|++. .+++++.+++++++++++ T Consensus 150 ~~~i~~~~~K~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-----~~~~~~lF~~~~~~~~~~~~~ls~~~v~~~~~~~~ 224 (287) T cd00799 150 GLLVTLRRSKTDQSGLGVLKLIPPLTTCPVRALERWLEAA-----RIPKGPLFRRIDRWGVLGPGALSDNSLNRILKRLA 224 (287) T ss_pred EEEEEECCCCEEECCCCCEEEECCCHHHHHHHHHHHHHHC-----CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHH T ss_conf 1799955874035487836750621589999999999872-----56766430244446775788787899999999999 Q ss_pred HHCCCCC-CCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHCHHHH Q ss_conf 9768699-988054179999999984899889999837888789799996198999 Q gi|254780882|r 252 RYLGLPL-STTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNG 306 (328) Q Consensus 252 ~~~gi~~-~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~ 306 (328) +.+|++. .+|||+|||||||+|+++|+|+..||++|||+|++||++|.|..+.-. T Consensus 225 ~~ag~~~~~~s~H~lRHt~At~ll~~G~~l~~Iq~~lGH~s~~tt~~Y~~~~d~~~ 280 (287) T cd00799 225 EAAGLRSGSWSGHSLRRGFATEAARAGYSLLEIMRQGRWRSPKMVSRYIRDADRFQ 280 (287) T ss_pred HHCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCCHHC T ss_conf 98599999989751389999999987999999999858999889999853713101 No 20 >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=100.00 E-value=2.8e-45 Score=302.48 Aligned_cols=275 Identities=17% Similarity=0.188 Sum_probs=214.6 Q ss_pred CCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH-HHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 4989999999999999986254889999999999999-999985121478878968989999999999998612101332 Q gi|254780882|r 10 VSFELLKERQNWLQNLEIERGLSKLTLQSYECDTRQF-LIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSL 88 (328) Q Consensus 10 ~~~~l~~~~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f-~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~~~s~~T~ 88 (328) ...++.+++++|++... ...+++|.+.|+..++.. ..++ +..++.+|+..++..|+..+... .+++|+ T Consensus 69 ~~~T~~~~~e~~~~~~~--~~~~~~t~~~~~~~l~~~i~p~~--------g~~~l~~It~~~i~~~~~~l~~~-~~~~ta 137 (357) T cd00801 69 AANTFAEVAEEWLAAKK--PRWSEKHARQWRRTLEKHVLPVL--------GKKPITEITARDLLDVLRRIEAR-GALETA 137 (357) T ss_pred HHCHHHHHHHHHHHHHC--CCCCHHHHHHHHHHHHHHHHHHH--------CCCCHHHCCHHHHHHHHHHHHHC-CCHHHH T ss_conf 45549999999999731--02476899999999997758987--------78748991889999999999856-989999 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC--CCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCC Q ss_conf 112344422223332101232222222222222212--111111101567877653101356775775320122210011 Q gi|254780882|r 89 KRSLSGIKSFLKYLKKRKITTESNILNMRNLKKSNS--LPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGC 166 (328) Q Consensus 89 ~~~ls~lr~f~~~~~~~~~i~~np~~~i~~~k~~~~--~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~T 166 (328) ++.++.|+++|+||+..++++.||+..++.++..+. ..++++.+|+..+++++...... . +...++.|++.| T Consensus 138 ~~~~~~l~~~~~~A~~~~~i~~NP~~~i~~~~~~~~~~r~r~lt~ee~~~l~~~l~~~~~~-~-----~~~~~~~l~l~T 211 (357) T cd00801 138 RRVRQRLKQVFRYAIARGLIEANPAADLRGADGAPKKQHDRALSPDELPEFLQALDAASGS-P-----VTRLALKLLLLT 211 (357) T ss_pred HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCC-H-----HHHHHHHHHHHH T ss_conf 9999999999999998277443657654441067887766678999999999999857788-3-----799999999997 Q ss_pred CCCCCCCCCCCCCCCCCCCCCEEE---CCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCC--CCCCCC Q ss_conf 233222221122222332322033---237853100011221002343221110012344665543211112--211100 Q gi|254780882|r 167 GLRISEALSLTPQNIMDDQSTLRI---QGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRG--KPLNPG 241 (328) Q Consensus 167 GlR~~El~~L~~~did~~~~~i~v---~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g--~~ls~~ 241 (328) |||+||+++|+|+|||++.++++| ..|+++.+.|||++.+.++|+.+... ...+++||++..| .+++.. T Consensus 212 G~R~gE~~~L~w~diD~~~~~~~Ip~~~tK~~~~~~vPL~~~~~~~L~~~~~~------~~~~~~vF~~~~~~~~~~~~~ 285 (357) T cd00801 212 GVRPGELRGARWSEIDLENALWTIPAERMKTRRPHRVPLSDQALALLEELREL------SGHSEYVFPSRRDRGKPLSEN 285 (357) T ss_pred CCCHHHHHCCCHHHEECCCCEEEEECCCCCCCCCEEEECCHHHHHHHHHHHHH------CCCCCEEECCCCCCCCCCCHH T ss_conf 77888886387998777788489620236589936983989999999999886------499945825799999977489 Q ss_pred CHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHH-HHHHHC-HHHHHHHHH Q ss_conf 0123567899976869998805417999999998489988999983788878979-999619-899999999 Q gi|254780882|r 242 VFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQ-IYTNVN-SKNGGDWMM 311 (328) Q Consensus 242 ~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~-~Y~h~~-~~~~~~~l~ 311 (328) ++++.++ ++|...+++||+|||||||.|+++|+|+.+||++|||++.++|+ +|+|.+ .++.+++|+ T Consensus 286 ~~~~~~~----~~~~~~~~t~HdlRhT~aT~l~~~Gv~~~~i~~~LGH~~~~~t~~~Y~h~~y~~ekr~~l~ 353 (357) T cd00801 286 TLNKALK----RMGYLGEWTPHGLRRTARTWLNELGFPPDVIERQLAHVLGGKVRAAYNRADYLEERREAMQ 353 (357) T ss_pred HHHHHHH----HHCCCCCCEEECCHHHHHHHHHHCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 9999999----9659999503248899999999859899999998489999818999617448999999999 No 21 >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=100.00 E-value=1.4e-45 Score=305.49 Aligned_cols=202 Identities=19% Similarity=0.255 Sum_probs=175.0 Q ss_pred HHHHHHHHHHHHHHHHHHH--CCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCC Q ss_conf 3211234442222333210--12322222222222222121111111015678776531013567757753201222100 Q gi|254780882|r 87 SLKRSLSGIKSFLKYLKKR--KITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLY 164 (328) Q Consensus 87 T~~~~ls~lr~f~~~~~~~--~~i~~np~~~i~~~k~~~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~ 164 (328) |+|+++++|+++|+||+++ .++..||+.+|+.|+.++..+++++.+|+.++++++..... ..+.++++.|++ T Consensus 1 Tinr~l~~L~~~f~~A~~~~~~~~~~NP~~~i~~pk~~~~r~r~lt~eE~~~ll~~~~~~~~------~~~~~~~~~l~~ 74 (206) T cd00796 1 TVRRELALLSHLFTVARKEWGLDVLTNPVELVRKPPVGKGRDRRLTEEEEERLLRAFGEEEG------SPRLPVIILLAL 74 (206) T ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCC------CHHHHHHHHHHH T ss_conf 98899999999999999978887677927748588999999887999999999996764545------766999999999 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCEEE-CCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCH Q ss_conf 11233222221122222332322033-23785310001122100234322111001234466554321111221110001 Q gi|254780882|r 165 GCGLRISEALSLTPQNIMDDQSTLRI-QGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVF 243 (328) Q Consensus 165 ~TGlR~~El~~L~~~did~~~~~i~v-~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g~~ls~~~i 243 (328) +||||+||+++|+|+|||++.+.+.| .+|+++.|.|||++.+.++|..|... ..++++| |++..++ T Consensus 75 ~TG~R~~Ei~~L~~~did~~~~~i~i~~~K~~~~r~vpl~~~~~~~l~~~~~~-------~~~~~vf------~~~~~~~ 141 (206) T cd00796 75 ETAMRRGEILSLRWEQVDLKKRVAHLPDTKNGTSRDVPLSKRAVALLQMLPKV-------PDDGPVF------PITSDSV 141 (206) T ss_pred HHCCCHHHHHHCCCCCCCCCCCEEEEEECCCCCEEEEECCHHHHHHHHHHHHC-------CCCCCCC------CCCHHHH T ss_conf 90998899942857334533584898636789656852889999999999861-------4777667------8861789 Q ss_pred HHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHCHHHHHH Q ss_conf 23567899976869998805417999999998489988999983788878979999619899999 Q gi|254780882|r 244 QRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGD 308 (328) Q Consensus 244 ~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~ 308 (328) ++.|+++++++|++ +++||+|||||||.|+++|+|+.+||++|||+|++||++|+|+++|+..+ T Consensus 142 ~~~~~~~~~~~gi~-~~~~H~lRHt~at~l~~~G~~~~~i~~~lGH~~~~~t~~Y~h~~~e~L~~ 205 (206) T cd00796 142 DAAFRRAKERAGLE-DLHFHDLRHEATSRLFEKGLSIMEVASISGHRDWRMLKRYTHLSAEDLAE 205 (206) T ss_pred HHHHHHHHHHHCCC-CCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHC T ss_conf 99999999982777-87532048999999998698999999985899999998846739988704 No 22 >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=100.00 E-value=4.6e-44 Score=294.56 Aligned_cols=176 Identities=20% Similarity=0.209 Sum_probs=146.3 Q ss_pred CCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCC-CCCCCCCCCC Q ss_conf 111101567877653101356775775320122210011233222221122222332322033237853-1000112210 Q gi|254780882|r 128 ALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDK-IRIVPLLPSV 206 (328) Q Consensus 128 ~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~gKg~K-~R~Vpi~~~~ 206 (328) +||.||+.++++++. ..||+||+.+||.||||+||+++|+|+|||++.+++.|.++++| .+.++++... T Consensus 1 iLt~eev~~li~~~~----------~~rdraii~lL~~TGlRvsEl~~L~~~DId~~~~~i~V~~~~~k~~~~~~~~~~~ 70 (186) T cd01198 1 LISVEAMRELIADIT----------HPLERAVIVGLAKTGIRRGELINLDRRDVNLDKPTLYLKPASNKRSNRTLFPDLE 70 (186) T ss_pred CCCHHHHHHHHHCCC----------CHHHHHHHHHHHHHCCHHHHHHCCCHHHCCCCCCEEEECCCCCCCCEEECCCHHH T ss_conf 989999999998379----------8799999999999587999997792877686578788527889866055583899 Q ss_pred HHH-HHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCC-------CCCCCCCCHHHHHHHHHHCCC Q ss_conf 023-432211100123446655432111122111000123567899976869-------998805417999999998489 Q gi|254780882|r 207 RKA-ILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLP-------LSTTAHTLRHSFATHLLSNGG 278 (328) Q Consensus 207 ~~~-l~~yl~~~~~~~~~~~~~~lF~~~~g~~ls~~~i~~~~~~~~~~~gi~-------~~~spH~lRHtfAt~ll~~G~ 278 (328) .+. +..|+..+ .....+++|++.+|++++...++..++++++++|++ +++|||+|||||||+|+++|+ T Consensus 71 ~~~~~~~~~~~r----~~~~~~~lF~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~vtPH~lRHtfAT~Ll~~G~ 146 (186) T cd01198 71 TELFRWLAIRPR----TTSPADALFIGTQDGWGCRRLVYEMVTGMARRHGEHRPWGDLEENFTPHCFRHFFTTWLRRRGG 146 (186) T ss_pred HHHHHHHHHHHH----HCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCC T ss_conf 999999998775----3589982676179997768689999999999977643212114675851638999999998699 Q ss_pred CHHHHHHHHCCCCHHHHHHHHHHCHHHHHHHHHHHHHHHCCCH Q ss_conf 9889999837888789799996198999999999999817300 Q gi|254780882|r 279 DLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQTHPSI 321 (328) Q Consensus 279 ~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~~l~~~~~~~~~~~ 321 (328) |+.+||++|||+|++||++|+|++.+ .++++|+++|||. T Consensus 147 dl~~vq~lLGHssi~tT~~Y~h~~~~----~l~e~y~k~~Pr~ 185 (186) T cd01198 147 DRGVVQELRGDSRDEAIDTYTHIWGD----ELREAYLKHIPSL 185 (186) T ss_pred CHHHHHHHHCCCCHHHHHHHHCCCHH----HHHHHHHHHCCCC T ss_conf 99999999489988999999847999----9999999858899 No 23 >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=100.00 E-value=8.5e-44 Score=292.87 Aligned_cols=177 Identities=30% Similarity=0.382 Sum_probs=155.9 Q ss_pred CCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEC-CCCCCCCCCCCC Q ss_conf 1111111015678776531013567757753201222100112332222211222223323220332-378531000112 Q gi|254780882|r 125 LPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQ-GKGDKIRIVPLL 203 (328) Q Consensus 125 ~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~-gKg~K~R~Vpi~ 203 (328) +|++||+||+.++++++.. ....++||++||.++++||||+||+++|+|+|||++.++|.|. +||+|.|.||++ T Consensus 1 lpr~Ls~eEi~~Ll~a~~~-----~~~~~~Rd~ali~ll~~tGlR~~El~~L~~~Did~~~~~i~i~~~K~~k~r~vpl~ 75 (188) T cd01188 1 LPRALPWEDVERLLASCDR-----STPVGRRDYAILLLLARLGLRAGEVAALRLDDIDWRTGTIRVRQGKGGRVTRLPLP 75 (188) T ss_pred CCCCCCHHHHHHHHHCCCC-----CCCHHHHHHHHHHHHHHHCHHHHHHHHCCCCCCCCCCCCEEEECCCCCCCCCCCCH T ss_conf 9699999999999957576-----88451799999999999881599998569835565689778863899853344684 Q ss_pred CCCHHHHHHHHHHHCCCCCCCCCCCCCCCCC---CCCCCCCCHHHHHHHHHHHCCCC-CCCCCCCCHHHHHHHHHHCCCC Q ss_conf 2100234322111001234466554321111---22111000123567899976869-9988054179999999984899 Q gi|254780882|r 204 PSVRKAILEYYDLCPFDLNLNIQLPLFRGIR---GKPLNPGVFQRYIRQLRRYLGLP-LSTTAHTLRHSFATHLLSNGGD 279 (328) Q Consensus 204 ~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~---g~~ls~~~i~~~~~~~~~~~gi~-~~~spH~lRHtfAt~ll~~G~~ 279 (328) +++.+.|.+|+...+.. ...+++|++.+ +.+.+..+++++++++++++|++ .+++||+|||||||+|+++|+| T Consensus 76 ~~~~~~l~~~l~~~~~~---~~~~~lf~~~~~~~~~~~~~~~i~~~~~~~~~~ag~~~~~~~~H~lRHt~at~l~~~G~~ 152 (188) T cd01188 76 AEVGAALADYLRDGRPA---TDSRRVFLRMRAPFRPFAGHSAVSNIVRRALRRAGISPRRGGAHLLRHSLATRLLRAGAP 152 (188) T ss_pred HHHHHHHHHHHHHHCCC---CCCCCEEEECCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCC T ss_conf 99999999999980767---887644350588888876699999999999998499889878761489999999996999 Q ss_pred HHHHHHHHCCCCHHHHHHHHHHCHHHHHHH Q ss_conf 889999837888789799996198999999 Q gi|254780882|r 280 LRSIQSILGHFRLSTTQIYTNVNSKNGGDW 309 (328) Q Consensus 280 ~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~~ 309 (328) +..||++|||+|++||++|+|++.|+.+++ T Consensus 153 l~~vq~~lGH~si~tT~~Y~h~~~e~lr~~ 182 (188) T cd01188 153 LKEIGDVLGHRSPDSTAIYAKVDVDALRAI 182 (188) T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHH T ss_conf 999999838998899999885699999866 No 24 >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=100.00 E-value=1.3e-43 Score=291.68 Aligned_cols=174 Identities=28% Similarity=0.375 Sum_probs=156.4 Q ss_pred CCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEC-CCCCCCCCCCCCCC Q ss_conf 11111015678776531013567757753201222100112332222211222223323220332-37853100011221 Q gi|254780882|r 127 RALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQ-GKGDKIRIVPLLPS 205 (328) Q Consensus 127 ~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~-gKg~K~R~Vpi~~~ 205 (328) ++||+||+.++++++... ..+.||++||.+++.||||+||+++|+|+|||++++.+.|. .||++.+.+|+.+. T Consensus 3 ~~Lt~eEi~~ll~~~~~~------~~~~Rd~~i~~ll~~tGlR~~El~~L~~~did~~~~~i~i~~~K~~~~~~~pl~~~ 76 (180) T cd01197 3 KYLTPSEVRSLLKAALDG------RYSARDYCLMLLMFRHGLRVSEACGLKLSDIDLESRQIYIRRLKGGFSTTHPLRDD 76 (180) T ss_pred CCCCHHHHHHHHHCCCCC------CCCHHHHHHHHHHHHHCCCHHHHHHCCHHHCCCCCCEEEEEEECCCCEEEECCCHH T ss_conf 899999999999651507------64389999999999959529999518176561788848999704773036338289 Q ss_pred CHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHH Q ss_conf 00234322111001234466554321111221110001235678999768699988054179999999984899889999 Q gi|254780882|r 206 VRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQS 285 (328) Q Consensus 206 ~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g~~ls~~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~ 285 (328) +.+++.+|++.+... ..+..+++|++.+|+|++.+++++.++++++.+|++.+++||+|||||||+|+++|+|+.+||+ T Consensus 77 ~~~~l~~~~~~~~~~-~~~~~~~lF~s~~g~~l~~~~i~~~~~~~~~~agl~~~~~~H~lRHt~At~l~~~G~~i~~Iq~ 155 (180) T cd01197 77 ELEALKNWLEIRAWK-GLPDSDWIFLSRRGGPLSRQQVYKLIRRLGAQAGLSIKVHPHMLRHACGYALANQGADTRLIQD 155 (180) T ss_pred HHHHHHHHHHHHHHC-CCCCCCCEEECCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHH T ss_conf 999999999986620-4775411222688884218889999999999828876678987789999999987999999999 Q ss_pred HHCCCCHHHHHHHHHHCHHHHH Q ss_conf 8378887897999961989999 Q gi|254780882|r 286 ILGHFRLSTTQIYTNVNSKNGG 307 (328) Q Consensus 286 ~lGH~s~~tT~~Y~h~~~~~~~ 307 (328) +|||+|++||++|+|++.++.. T Consensus 156 ~LGH~~i~tT~~Yth~~~~~l~ 177 (180) T cd01197 156 YLGHRNIRHTVIYTASNAARFL 177 (180) T ss_pred HHCCCCHHHHHHHHHCCHHHHH T ss_conf 8389987999999967999998 No 25 >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=100.00 E-value=1.9e-39 Score=265.74 Aligned_cols=169 Identities=22% Similarity=0.336 Sum_probs=147.5 Q ss_pred CCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCHHH Q ss_conf 11015678776531013567757753201222100112332222211222223323220332378531000112210023 Q gi|254780882|r 130 NEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKA 209 (328) Q Consensus 130 t~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~gKg~K~R~Vpi~~~~~~~ 209 (328) ++||+.++++++.... .||++||.+++.||||+||+++|+|+||+.+.....+.+||+|.|.|||++.+.++ T Consensus 8 ~~eei~~i~~~l~~~~--------~Rd~~l~~l~~~TGlR~sEl~~Lk~~Di~~~~~i~i~~~K~~k~r~v~l~~~~~~~ 79 (180) T cd01186 8 DKEQIKAIKDYLKNHS--------ERNYLLFLIGINTGLRISDILALKVKDVRGDERISIKEKKTGKRKRIYLNPILKEE 79 (180) T ss_pred CHHHHHHHHHHHHCCC--------HHHHHHHHHHHHCCCCHHHHHCCCHHHCCCCCEEEEEECCCCCCCCCCCCHHHHHH T ss_conf 9999999999987569--------88999999999839239999637648727998299997878844651188999999 Q ss_pred HHHHHHHHCCCCCCCCCCCCCCCCCC--CCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHH Q ss_conf 43221110012344665543211112--2111000123567899976869998805417999999998489988999983 Q gi|254780882|r 210 ILEYYDLCPFDLNLNIQLPLFRGIRG--KPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSIL 287 (328) Q Consensus 210 l~~yl~~~~~~~~~~~~~~lF~~~~g--~~ls~~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~l 287 (328) |..|+... ..++++|++.+| .+++...+++.++++++.+|++ +++||+|||||||+|+++|+|+.+||++| T Consensus 80 l~~y~~~~------~~~~~lF~s~~~~~~~is~~~~~~~~~~~~~~~gi~-~~~~H~lRHT~at~l~~~G~~l~~iq~~L 152 (180) T cd01186 80 LLYYIKDL------EENEYLFQSRKGGNRPITRQQAYRILKKAAEQVGID-NIGTHTLRKTFGYHYYKQTKDIALLMEIF 152 (180) T ss_pred HHHHHHHC------CCCCEEEECCCCCCCCCCHHHHHHHHHHHHHHCCCC-CCCCCHHHHHHHHHHHHCCCCHHHHHHHH T ss_conf 99998843------877514323888998978999999999999980898-76676017899999999699999999993 Q ss_pred CCCCHHHHHHHHHHCHHHHHHHHHHHHHHH Q ss_conf 788878979999619899999999999981 Q gi|254780882|r 288 GHFRLSTTQIYTNVNSKNGGDWMMEIYDQT 317 (328) Q Consensus 288 GH~s~~tT~~Y~h~~~~~~~~~l~~~~~~~ 317 (328) ||+|++||++|+|++.+.. ++++++| T Consensus 153 GH~si~tT~~Y~~~~~e~~----~k~~~~~ 178 (180) T cd01186 153 NHSSPAITLRYIGINQDEI----DKQLDNF 178 (180) T ss_pred CCCCHHHHHHHHCCCHHHH----HHHHHHC T ss_conf 8999899999858999999----9999737 No 26 >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=100.00 E-value=1.3e-39 Score=266.86 Aligned_cols=170 Identities=25% Similarity=0.374 Sum_probs=147.0 Q ss_pred CCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEC----------CCCCCCC Q ss_conf 111015678776531013567757753201222100112332222211222223323220332----------3785310 Q gi|254780882|r 129 LNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQ----------GKGDKIR 198 (328) Q Consensus 129 lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~----------gKg~K~R 198 (328) ||++|+.++++++. ..||++||.+|+.||||+||+++|+|+|||++++.++|. .|++++| T Consensus 1 LT~~Ev~~ll~a~~----------~~Rd~~i~~ll~~TGlR~gE~~~L~~~Did~~~~~i~i~~~~~~~~~~~~K~~~~r 70 (186) T cd01194 1 LTPSEVQRLINACG----------NLRDKFLFALLYETGLRIGEALGLRIEDIDLAENQIWLVPREDNANGARAKSGRER 70 (186) T ss_pred CCHHHHHHHHHHCC----------HHHHHHHHHHHHHHCCCHHHHHHCCHHHCCCCCCEEEEEECCCCCCCCCCCCCCEE T ss_conf 99899999998154----------03899999999996989888970889872576998999854455555203688425 Q ss_pred CCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCC----CCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHH Q ss_conf 0011221002343221110012344665543211112----211100012356789997686999880541799999999 Q gi|254780882|r 199 IVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRG----KPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLL 274 (328) Q Consensus 199 ~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g----~~ls~~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll 274 (328) .||+++.+.+.+.+|+...... .....+++|++..| .|++..+++..++++++.+|+ +++||+|||||||+|+ T Consensus 71 ~vpi~~~l~~~~~~~~~~~~~~-~~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~--~~~~H~lRHT~at~l~ 147 (186) T cd01194 71 RIPVSQYLIDLYVDYVTEIYYL-EELESDYVFVNVKGGNQGKPLNYTDVYDLVRRLKKKTGI--DFTPHMFRHTHATELI 147 (186) T ss_pred EEECCHHHHHHHHHHHHHHHHH-HCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHHHHHCCC--CCCCCCCHHHHHHHHH T ss_conf 8877799999999999997633-215777445633577568877799999999999998499--8774575999999999 Q ss_pred HCCCCHHHHHHHHCCCCHHHH-HHHHHHCHHHHHHHHH Q ss_conf 848998899998378887897-9999619899999999 Q gi|254780882|r 275 SNGGDLRSIQSILGHFRLSTT-QIYTNVNSKNGGDWMM 311 (328) Q Consensus 275 ~~G~~~~~v~~~lGH~s~~tT-~~Y~h~~~~~~~~~l~ 311 (328) ++|+|+..||++|||+|++|| ++|+|+++++.++++. T Consensus 148 ~~G~~~~~v~~~lGH~~~~tT~~~Y~h~~~e~~~~~~~ 185 (186) T cd01194 148 RAGWSIEVVADRLGHAHVQTTLNTYGHLSEEDIRREFN 185 (186) T ss_pred HCCCCHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHHHC T ss_conf 87999999999828998799999845689999999865 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=100.00 E-value=5.5e-40 Score=269.10 Aligned_cols=172 Identities=29% Similarity=0.331 Sum_probs=142.1 Q ss_pred CCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC----CEEE-CCCCCCCCCCCC Q ss_conf 11110156787765310135677577532012221001123322222112222233232----2033-237853100011 Q gi|254780882|r 128 ALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQS----TLRI-QGKGDKIRIVPL 202 (328) Q Consensus 128 ~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~----~i~v-~gKg~K~R~Vpi 202 (328) .||.+|+.++++++.. .|+...+.+.||++||.|||.||||+||+++|+|+||+++.+ ++.| .|||+|+|+||| T Consensus 1 ~lt~~~~~~~~~~~~~-~p~~~~~~~~Rd~ail~ll~~tGlR~sEl~~L~~~Di~~~~~~~~~~l~i~~gKg~k~R~vpl 79 (196) T cd01183 1 ALTEDQWAFVIDTVAS-LPAQDPEHAARLLFLLALLYSTGLRISELAAATGPDLEAFVQGGGWWLYVPVGKGGKERRVPV 79 (196) T ss_pred CCCHHHHHHHHHHHHH-CCCCCCCHHHHHHHHHHHHHHHCCHHHHHHCCCHHHHCHHCCCCCEEEEEEECCCCCEEEECC T ss_conf 9799999999999985-777897076999999999999666299998398887023116786059988588985003018 Q ss_pred CCCCHHHHHHHHHHHCCCC--CCCCCCCCCCCC----CCCCCCCCCHHHHHHHHHHHCC-------------CCCCCCCC Q ss_conf 2210023432211100123--446655432111----1221110001235678999768-------------69998805 Q gi|254780882|r 203 LPSVRKAILEYYDLCPFDL--NLNIQLPLFRGI----RGKPLNPGVFQRYIRQLRRYLG-------------LPLSTTAH 263 (328) Q Consensus 203 ~~~~~~~l~~yl~~~~~~~--~~~~~~~lF~~~----~g~~ls~~~i~~~~~~~~~~~g-------------i~~~~spH 263 (328) ++.+.+.|++|+..+.... ......++|++. .|++++.++++..++++...++ ..+++||| T Consensus 80 ~~~~~~~L~~yl~~r~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~~~v~~~~~~a~~~~~~~~~~~~~~~~~~~spH 159 (196) T cd01183 80 SDELLAALARYRQARGLPPEPAAGEAVPLLGRHKSAGGGGGLSSAQLYRIVKRVFGAAADRLQADGFEEDAAQLRAASTH 159 (196) T ss_pred CHHHHHHHHHHHHHCCCCCCCCCCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHCCCCCCC T ss_conf 89999999999998477655554667640103677766787519999999999999999997641217675103767883 Q ss_pred CCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHH Q ss_conf 4179999999984899889999837888789799996 Q gi|254780882|r 264 TLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTN 300 (328) Q Consensus 264 ~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h 300 (328) +|||||||+|+++|+|+..||++|||+|++||++|+| T Consensus 160 ~LRHt~At~ll~~G~~l~~Vq~~LGH~si~TT~~Y~H 196 (196) T cd01183 160 WLRHTHASHDLAAGVPLEHVQDNLGHASIDTTSRYLH 196 (196) T ss_pred CCHHHHHHHHHHCCCCHHHHHHHCCCCCHHHHHHCCC T ss_conf 2589999999987999999998808998678734339 No 28 >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=100.00 E-value=5.4e-38 Score=256.67 Aligned_cols=179 Identities=26% Similarity=0.381 Sum_probs=145.9 Q ss_pred CCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECC--------------- Q ss_conf 11110156787765310135677577532012221001123322222112222233232203323--------------- Q gi|254780882|r 128 ALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQG--------------- 192 (328) Q Consensus 128 ~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~g--------------- 192 (328) +||.||+.++++++..... ..|+++|+.+++.||||+||+++|+|+|||+++++|.|.+ T Consensus 1 yLt~eEi~~ll~~~~~~~~------~~~~~~ii~ll~~TGlR~~Ei~~L~~~did~~~~~i~i~~~~~~~~~~~~~~~~~ 74 (205) T cd01199 1 YLEKNELKALLDVLNSYKN------NQLYADILEFLFLTGMRIGELLALQEKDIDFENKLINIDGTLDSHTGKEENGYKD 74 (205) T ss_pred CCCHHHHHHHHHHHHHCCC------CHHHHHHHHHHHHHCCCHHHHHCCCHHHCCCCCCEEEEEEEEEEECCCCCCCEEC T ss_conf 9398999999970514778------7699999999999773488897590988065589899977886412566662434 Q ss_pred --CCC-CCCCCCCCCCCHHHHHHHHHHHCCCC---CCCCCCCCCCCCCCCCCCCCCH-HHHHHHHHHHCCCC--CCCCCC Q ss_conf --785-31000112210023432211100123---4466554321111221110001-23567899976869--998805 Q gi|254780882|r 193 --KGD-KIRIVPLLPSVRKAILEYYDLCPFDL---NLNIQLPLFRGIRGKPLNPGVF-QRYIRQLRRYLGLP--LSTTAH 263 (328) Q Consensus 193 --Kg~-K~R~Vpi~~~~~~~l~~yl~~~~~~~---~~~~~~~lF~~~~g~~ls~~~i-~~~~~~~~~~~gi~--~~~spH 263 (328) |+. ..|.|||++.+.++|.+|++...... .....+++|++..|.++....+ ...++++.+.+|.+ .+++|| T Consensus 75 ~~Kt~~~~R~vpl~~~~~~~l~~~~~~~~~~~~~~~~~~~~~lf~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~H 154 (205) T cd01199 75 TPKTKSSIRTISLSERAVEIIKRFIKRNKFDKFNPDYKDSDFLFTNKKGNPLDLGPINSKILSKFLKDLGSQSKKHVTTH 154 (205) T ss_pred CCCCCCCEEEEECCHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC T ss_conf 57788863686179999999999999714410354568776377616898476408999999999998575546775764 Q ss_pred CCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHH-HHHHHHCHHHHHHHHHH Q ss_conf 41799999999848998899998378887897-99996198999999999 Q gi|254780882|r 264 TLRHSFATHLLSNGGDLRSIQSILGHFRLSTT-QIYTNVNSKNGGDWMME 312 (328) Q Consensus 264 ~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT-~~Y~h~~~~~~~~~l~~ 312 (328) +|||||||+|+++|+|+..||++|||+|++|| ++|+|++++.+++++.+ T Consensus 155 ~lRHT~at~l~~~G~~~~~v~~~lGHss~~tT~~iY~h~~~~~~~e~~~k 204 (205) T cd01199 155 IFRHTHISFLAEEGVPLKAIMDRVGHSDGKTTLRIYSHVTEKMKDEIVKK 204 (205) T ss_pred CCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHHHHC T ss_conf 55999999999869999999998679988999888661698999999960 No 29 >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=100.00 E-value=1.9e-37 Score=253.30 Aligned_cols=167 Identities=23% Similarity=0.264 Sum_probs=143.8 Q ss_pred CCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEC---CCCCCCCCCCC Q ss_conf 111111015678776531013567757753201222100112332222211222223323220332---37853100011 Q gi|254780882|r 126 PRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQ---GKGDKIRIVPL 202 (328) Q Consensus 126 p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~---gKg~K~R~Vpi 202 (328) .++||++|+.++++++.. .. +.++.+++.||||+||+++|+|+|||++++.++|. +||++.|.||+ T Consensus 4 ~r~Lt~eE~~~ll~~~~~---------~~--r~~i~l~~~TG~R~~El~~L~~~did~~~~~i~i~~~~~K~~~~r~vpl 72 (177) T cd01192 4 VRWLTPEEAERLIAELPP---------HL--KPAVLFALNTGLRRSEILGLEWSQVDLDNRVAWVRPATSKGGRAIRVPL 72 (177) T ss_pred CCCCCHHHHHHHHHHCCH---------HH--HHHHHHHHHHCCCHHHHHHCCCHHHHHHCCHHCCCCCCCCCCCEEECCC T ss_conf 789999999999982898---------79--9999999997834999983878666630111011445688885442613 Q ss_pred CCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHH Q ss_conf 22100234322111001234466554321111221110001235678999768699988054179999999984899889 Q gi|254780882|r 203 LPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRS 282 (328) Q Consensus 203 ~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g~~ls~~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~ 282 (328) ++.+.++|..|... ....++|++..|.+.. ...+.|+++++++|++ +++||+|||||||+|+++|+|+.+ T Consensus 73 ~~~~~~~l~~~~~~-------~~~~~vf~~~~~~~~~--~~~~~~~~~~~~agi~-~~~~H~lRHt~at~l~~~G~~~~~ 142 (177) T cd01192 73 NDEALQVLKRQKAG-------AHKPWVFAGAGGDPRI--DSKTAWRQALQRAGIS-DFRWHDLRHTWASWLVQSGVPLYV 142 (177) T ss_pred HHHHHHHHHHHHHC-------CCCCCEECCCCCCCCC--HHHHHHHHHHHHCCCC-CCCCCCCCHHHHHHHHHCCCCHHH T ss_conf 09999999998723-------5775141158998510--1789999999973799-998688968899999996989999 Q ss_pred HHHHHCCCCHHHHHHHHHHCHHHHHHHHHHH Q ss_conf 9998378887897999961989999999999 Q gi|254780882|r 283 IQSILGHFRLSTTQIYTNVNSKNGGDWMMEI 313 (328) Q Consensus 283 v~~~lGH~s~~tT~~Y~h~~~~~~~~~l~~~ 313 (328) ||++|||+|++||++|+|++++..++++.++ T Consensus 143 i~~~lGH~~~~~T~~Y~h~~~~~~r~a~~~l 173 (177) T cd01192 143 LQELLGHSSLQMVRRYAHLSPEHLRAAARAL 173 (177) T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH T ss_conf 9999589989999998866999999999998 No 30 >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=100.00 E-value=1.1e-37 Score=254.72 Aligned_cols=169 Identities=38% Similarity=0.464 Sum_probs=152.6 Q ss_pred CCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEC-CCCCCCCCCCCCCC Q ss_conf 11111015678776531013567757753201222100112332222211222223323220332-37853100011221 Q gi|254780882|r 127 RALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQ-GKGDKIRIVPLLPS 205 (328) Q Consensus 127 ~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~-gKg~K~R~Vpi~~~ 205 (328) ++||++|+.++++++.. ..++||++||.+++.||||++|+++|+|+||+++.+.++|. +|+++.|.+|+++. T Consensus 1 ~~lt~~e~~~ll~~~~~-------~~~lR~~~l~~l~~~tG~R~~El~~L~~~di~~~~~~i~i~~~K~~~~r~i~i~~~ 73 (170) T pfam00589 1 RRLTEDEVERLLAALEE-------PLNIRDRALVELLLLTGLRISELLSLRWSDIDLDNGTIRIPQTKTRKSRTVPLSDA 73 (170) T ss_pred CCCCHHHHHHHHHHHCC-------CCCHHHHHHHHHHHHHCCCHHHHHHHCCCCCCCCCEEEEECCCCCCCCEECCCCHH T ss_conf 98999999999986463-------45977999999999968698889742130046765178730441133100146777 Q ss_pred CHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHH Q ss_conf 00234322111001234466554321111221110001235678999768699988054179999999984899889999 Q gi|254780882|r 206 VRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQS 285 (328) Q Consensus 206 ~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g~~ls~~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~ 285 (328) +...+.+|+..... ....+++|++..|++++.+.+++.|++++..+|++.+++||+|||||||+|+++|+|+..||+ T Consensus 74 ~~~~l~~~~~~~~~---~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~s~Hs~Rht~at~l~~~g~~~~~v~~ 150 (170) T pfam00589 74 ALEALKEWLGDRKE---AEESEFLFVSRRGKPLSRSTVNRAFRRAGKRAGIEKDLTPHDLRHTFATHLAENGVPLRVIQK 150 (170) T ss_pred HHHHHHHHHHHHCC---CCCCCEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHH T ss_conf 99999999997314---677761432016885531346788888888607787678788848999999996999999999 Q ss_pred HHCCCCHHHHHHHHHHCHHH Q ss_conf 83788878979999619899 Q gi|254780882|r 286 ILGHFRLSTTQIYTNVNSKN 305 (328) Q Consensus 286 ~lGH~s~~tT~~Y~h~~~~~ 305 (328) +|||+|++||++|+|+++|+ T Consensus 151 ~lGH~~~~tT~~Y~~~~~~~ 170 (170) T pfam00589 151 LLGHSSISMTMRYTHVAAER 170 (170) T ss_pred HHCCCCHHHHHHHCCCCCCC T ss_conf 96899989999820838559 No 31 >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=100.00 E-value=4.4e-37 Score=250.93 Aligned_cols=171 Identities=27% Similarity=0.374 Sum_probs=146.3 Q ss_pred CCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEC--------------C Q ss_conf 11111015678776531013567757753201222100112332222211222223323220332--------------3 Q gi|254780882|r 127 RALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQ--------------G 192 (328) Q Consensus 127 ~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~--------------g 192 (328) ++||++|+.++++++.... ..|++++|.+++.||||++|+++|+|+|||++++.+.|. . T Consensus 1 ~yLt~~Ei~~ll~~~~~~~-------~~~~~~~~~l~~~tGlR~~Ei~~L~~~did~~~~~i~v~~~~~~~~~~~~~~~~ 73 (191) T cd01189 1 KFLTKEELKKLLEYLKKHE-------NSFSKLLILLLAYTGLRIGEALALTWSDIDFENNTITINKTWDYKTGGYIFKPP 73 (191) T ss_pred CCCCHHHHHHHHHHHHHCC-------CHHHHHHHHHHHHHCCCHHHHHHCCHHHCCCCCCEEEEECCEEECCCCEEECCC T ss_conf 9899999999999875668-------978999999999978149999728999946555858984101211353033577 Q ss_pred CCCC-CCCCCCCCCCHHHHHHHHHHHCCC---CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHH Q ss_conf 7853-100011221002343221110012---344665543211112211100012356789997686999880541799 Q gi|254780882|r 193 KGDK-IRIVPLLPSVRKAILEYYDLCPFD---LNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHS 268 (328) Q Consensus 193 Kg~K-~R~Vpi~~~~~~~l~~yl~~~~~~---~~~~~~~~lF~~~~g~~ls~~~i~~~~~~~~~~~gi~~~~spH~lRHt 268 (328) |++. .|.|||++++.+.|..|+...... .......++|.+..|.+++.++++..++++++++|++ +++||+|||| T Consensus 74 Kt~~~~R~v~i~~~~~~~L~~~~~~~~~~~~~~~~~~~~~if~~~~~~~~~~~~~~~~~~~~~~~~gi~-~~~~H~lRHT 152 (191) T cd01189 74 KTKSSIRTIPLDKKTIAILKEYKKEQKKYLLGEINNDDELVFTNKGGKISTPSTINKRLKRICKKAGIP-KITFHGLRHT 152 (191) T ss_pred CCCCCCEEEECCHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCCCCHHHHHHHHHHHHHHCCCC-CCCHHHHHHH T ss_conf 788872488479999999999999977764035789874376469999178889999999999980898-0563435999 Q ss_pred HHHHHHHCCCCHHHHHHHHCCCCHHHH-HHHHHHCHHH Q ss_conf 999999848998899998378887897-9999619899 Q gi|254780882|r 269 FATHLLSNGGDLRSIQSILGHFRLSTT-QIYTNVNSKN 305 (328) Q Consensus 269 fAt~ll~~G~~~~~v~~~lGH~s~~tT-~~Y~h~~~~~ 305 (328) |||.|+++|+|+..||++|||+|++|| ++|+|+++|+ T Consensus 153 ~aT~l~~~G~~~~~i~~~lGH~s~~~T~~~Y~h~~~~~ 190 (191) T cd01189 153 HASLLLEAGVSIKYVSERLGHADISTTLDTYSHLLPEK 190 (191) T ss_pred HHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCCCCC T ss_conf 99999996999999999858998899997711669465 No 32 >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=100.00 E-value=1.6e-36 Score=247.39 Aligned_cols=175 Identities=23% Similarity=0.235 Sum_probs=136.3 Q ss_pred CCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC------CEEE-CCCCCCCCC Q ss_conf 111110156787765310135677577532012221001123322222112222233232------2033-237853100 Q gi|254780882|r 127 RALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQS------TLRI-QGKGDKIRI 199 (328) Q Consensus 127 ~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~------~i~v-~gKg~K~R~ 199 (328) ++++.+++.++.+++....+. .+.|+.+++.||||+||+++|+|+||+.+.. .+.. .++|.|+|. T Consensus 1 ~~i~~~~~~~l~~~l~~l~~~--------~~~~~~ll~~TGlRisE~l~L~~~~i~~~~~~~~~~~~~~~~~k~~~k~r~ 72 (195) T cd01195 1 RFIPEFVLEQLNSHIDKLPEY--------IIPMTMIVQETGMRISDLLTLKKNCLLEDKDGDFFYKYYQCIWKTKIKEHI 72 (195) T ss_pred CCCCHHHHHHHHHHHHHCCHH--------HHHHHHHHHHCCCHHHHHHCCCHHHHHHHCCCCCEEEEEEEECCCCCEEEE T ss_conf 989989999999999868998--------999999999808739999638611455503655526799996798874368 Q ss_pred CCCCCCCHHHHHHHHHHHCCCC--CCCCCCCCCCCCCCC----CCCCCCHHHHHHHHHHHCCCC------CCCCCCCCHH Q ss_conf 0112210023432211100123--446655432111122----111000123567899976869------9988054179 Q gi|254780882|r 200 VPLLPSVRKAILEYYDLCPFDL--NLNIQLPLFRGIRGK----PLNPGVFQRYIRQLRRYLGLP------LSTTAHTLRH 267 (328) Q Consensus 200 Vpi~~~~~~~l~~yl~~~~~~~--~~~~~~~lF~~~~g~----~ls~~~i~~~~~~~~~~~gi~------~~~spH~lRH 267 (328) |||++++.+.|..|++..+... ..+.+++||++..|+ +++...++..+++++++.|+. .+++||+||| T Consensus 73 ipi~~~~~~~l~~~~~~~~~~~~~~~~~~~~lF~~~~g~~~~~~~~~~~~~~~~~~~~~~~~i~~~~g~~~~~~~H~lRH 152 (195) T cd01195 73 IPISKKVALLIKVREDKTKELSTEDNNPSEYLFPRYDGKPKGQPTNKQAFRGELNKLAYEKNIVDKSGEIYHFHAHAFRH 152 (195) T ss_pred EECCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHH T ss_conf 86789999999999999898730206988548767889808887619999999999999818653347725668887748 Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHCHHHHHHH Q ss_conf 999999984899889999837888789799996198999999 Q gi|254780882|r 268 SFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDW 309 (328) Q Consensus 268 tfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~~ 309 (328) ||||+|+++|+|+.+||++|||+|++||++|+|++++..+++ T Consensus 153 T~aT~L~~~Gv~i~~Iq~~LGH~s~~tT~~Yahv~~e~l~~~ 194 (195) T cd01195 153 TVATRMINNGMPIHIIQKFLGHESPEMTSRYAHIFDETLKNE 194 (195) T ss_pred HHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH T ss_conf 999999986999999999948999899999885798999862 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=99.98 E-value=4.8e-33 Score=225.74 Aligned_cols=159 Identities=33% Similarity=0.401 Sum_probs=135.7 Q ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEC-CCCCCCCCCCCCCCCHHHHH Q ss_conf 15678776531013567757753201222100112332222211222223323220332-37853100011221002343 Q gi|254780882|r 133 QALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQ-GKGDKIRIVPLLPSVRKAIL 211 (328) Q Consensus 133 e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~-gKg~K~R~Vpi~~~~~~~l~ 211 (328) |+.++++++....+ .|++++|.+++.||||++|+++|+|+||+++++++.|. +|+++.|.||+++.+...|. T Consensus 1 e~~~~~~~~~~~~~-------~r~r~~~~l~~~tGlR~~Ei~~L~~~di~~~~~~i~i~~~K~~~~r~vpi~~~~~~~l~ 73 (164) T cd00397 1 EIERLLAAAEASTP-------ERLYLALLLLLATGLRISELCALRWSDIDLDKRVIHITGTKTKKERTVPLSEEALKLLK 73 (164) T ss_pred CHHHHHHHHHHCCC-------HHHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCHHHHHHH T ss_conf 98999976514679-------88999999999978199999638462056776479983564665333667601234688 Q ss_pred HHHHHHCCCCCCCCCCCCCCCCCCCC---CCCCCHHHHHHHHHHHCCCC-CCCCCCCCHHHHHHHHHHCCCCHHHHHHHH Q ss_conf 22111001234466554321111221---11000123567899976869-998805417999999998489988999983 Q gi|254780882|r 212 EYYDLCPFDLNLNIQLPLFRGIRGKP---LNPGVFQRYIRQLRRYLGLP-LSTTAHTLRHSFATHLLSNGGDLRSIQSIL 287 (328) Q Consensus 212 ~yl~~~~~~~~~~~~~~lF~~~~g~~---ls~~~i~~~~~~~~~~~gi~-~~~spH~lRHtfAt~ll~~G~~~~~v~~~l 287 (328) +|....... ....+++|++..+.+ .+...+...+++++..+|+. .+++||+|||||||+|+++|+|+..||++| T Consensus 74 ~~~~~~~~~--~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~H~lRht~at~l~~~g~~~~~I~~~l 151 (164) T cd00397 74 EYLKKRRPA--NGDEEYLFPSRRGGPAATLSRRNVKRIFKAAGRRAGIDKEGLTPHSLRHTFASALLNAGLDLEAVQDLL 151 (164) T ss_pred HHHHHHCCC--CCCCCCEEECCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHH T ss_conf 889885014--687541211368986652046789999789999833676567756658999999999699999999996 Q ss_pred CCCCHHHHHHHHH Q ss_conf 7888789799996 Q gi|254780882|r 288 GHFRLSTTQIYTN 300 (328) Q Consensus 288 GH~s~~tT~~Y~h 300 (328) ||+|++||++|+| T Consensus 152 GHs~~~tT~~Y~h 164 (164) T cd00397 152 GHSSIAMTMRYAH 164 (164) T ss_pred CCCCHHHHHHCCC T ss_conf 8999889711839 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=99.97 E-value=2.1e-32 Score=221.78 Aligned_cols=166 Identities=19% Similarity=0.254 Sum_probs=127.5 Q ss_pred CCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECC----------CC- Q ss_conf 1111110156787765310135677577532012221001123322222112222233232203323----------78- Q gi|254780882|r 126 PRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQG----------KG- 194 (328) Q Consensus 126 p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~g----------Kg- 194 (328) |+|||.||+.++++++... .+++.++.|+++||||.||+++|+|+|||++.++|.|.. |+ T Consensus 1 p~plT~eE~~~ll~a~~~~---------~~~~~~~~l~~~TGlR~gE~~~L~w~dId~~~~~i~v~~~~~~~~~~~~Kt~ 71 (196) T cd01191 1 PDPFTRDEFAALIEAARVC---------QQEQNLWEFAVFTGLRPSELIALAWEDVDLERGTVYVRRALVRGIFKVPKTK 71 (196) T ss_pred CCCCCHHHHHHHHHHCCCC---------HHHHHHHHHHHHHCCHHHHHHHCCHHHCCCCCCEEEEEEEEEECCCCCCCCC T ss_conf 9898999999999806606---------4189999999997916999970779984756898999961684565688778 Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHCC--------------CCCCCCCCCCCCCCC-CCCC--CCCCHHHHHHHHHHHCCCC Q ss_conf 5310001122100234322111001--------------234466554321111-2211--1000123567899976869 Q gi|254780882|r 195 DKIRIVPLLPSVRKAILEYYDLCPF--------------DLNLNIQLPLFRGIR-GKPL--NPGVFQRYIRQLRRYLGLP 257 (328) Q Consensus 195 ~K~R~Vpi~~~~~~~l~~yl~~~~~--------------~~~~~~~~~lF~~~~-g~~l--s~~~i~~~~~~~~~~~gi~ 257 (328) +..|.||+++.+.++|.++....+. ........++|.+.. |.+. +.....+.+.++++++|++ T Consensus 72 ~~~R~v~l~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vf~~~~~~~~~~~~~~~~~~~~~~~~~~~gi~ 151 (196) T cd01191 72 AGTRDVDLNPPALAALKEQAKLTRLSRPHQITVLEREYGRTEKQKGTFVFHDPKTGEPWTYAVASRKSFWDPALKRAGIR 151 (196) T ss_pred CCCCEECCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCCCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHCCCC T ss_conf 85312218999999999999985010102456665311444566774584378778886506899999999999982999 Q ss_pred CCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHH-HHHHH Q ss_conf 998805417999999998489988999983788878979-99961 Q gi|254780882|r 258 LSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQ-IYTNV 301 (328) Q Consensus 258 ~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~-~Y~h~ 301 (328) .++||+|||||||.|+++|+|+.+||++|||+|++||+ +|+|. T Consensus 152 -~~~~H~lRHT~aT~ll~~G~~~~~v~~~lGHss~~~T~~~Ya~~ 195 (196) T cd01191 152 -YRNPYQMRHTFASWMLTAGANPAFIADQMGHKSAEMVFKHYGKW 195 (196) T ss_pred -CCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHH T ss_conf -67777884799999998798999999996899799999998833 No 35 >PRK09692 integrase; Provisional Probab=99.97 E-value=3.3e-30 Score=208.01 Aligned_cols=280 Identities=13% Similarity=0.105 Sum_probs=196.7 Q ss_pred HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 89999999999999986254889999999999999999985121478878968989999999999998612101332112 Q gi|254780882|r 12 FELLKERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRS 91 (328) Q Consensus 12 ~~l~~~~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~~~s~~T~~~~ 91 (328) .++....++|+...+. +.+..+.+.+...++ .++ .+.++..++.+|+..++...+.....++ +..|.++. T Consensus 105 ~tf~~va~~w~~~~~~--~~~~~~~~~~~r~le---~~v----~p~iG~~~i~~I~~~di~~~l~~i~~rg-~~~~a~r~ 174 (413) T PRK09692 105 NTFQLVAERWWNVKKA--SVTEDYAEDIWRSLE---RDV----FPAIGDVSVTDIKAHTLVQAVQPVQARG-ALETVRRL 174 (413) T ss_pred HHHHHHHHHHHHHHHH--HCCHHHHHHHHHHHH---HHH----HHHHCCCCCCCCCHHHHHHHHHHHHHCC-HHHHHHHH T ss_conf 1999999999998754--325779999999999---888----7985888410078999999987999739-89999999 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCCC--CCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCC Q ss_conf 3444222233321012322222222222--22212111111101567877653101356775775320122210011233 Q gi|254780882|r 92 LSGIKSFLKYLKKRKITTESNILNMRNL--KKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLR 169 (328) Q Consensus 92 ls~lr~f~~~~~~~~~i~~np~~~i~~~--k~~~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR 169 (328) +..++.+|+||+..++++.||+..+... +..++--..++.+|+..++..+...... ...| +++.|++.||+| T Consensus 175 ~~~l~~i~~~A~~~gli~~nP~~~~~~~~~~p~~~~~~~l~~~el~~l~~~l~~~~~~----~~~~--~~l~l~lLt~~R 248 (413) T PRK09692 175 CQRINEVMIYAQNTGLIDAVPSVNIGKAFEKPQKKNMPSIRPDQLPQLMQTMRTASIS----LSTR--CLFMWQLLTITR 248 (413) T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCC----HHHH--HHHHHHHHHCCC T ss_conf 9999999999996586445854343452568754577768989999999999857997----3578--999999997232 Q ss_pred CCCCCCCCCCCCCCCCCCEEE---CCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC--CCCCCCCCCHH Q ss_conf 222221122222332322033---2378531000112210023432211100123446655432111--12211100012 Q gi|254780882|r 170 ISEALSLTPQNIMDDQSTLRI---QGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGI--RGKPLNPGVFQ 244 (328) Q Consensus 170 ~~El~~L~~~did~~~~~i~v---~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~--~g~~ls~~~i~ 244 (328) .+|+++++|++||++.+.++| +.|+++...|||++.++++|+.-... ....+|||++. .++|++..+++ T Consensus 249 ~~Ev~~arW~eiD~~~~~W~IPaer~K~~~~h~VPLs~qA~~iL~~l~~~------~~~~~~vFps~~~~~~~~s~~t~~ 322 (413) T PRK09692 249 PAEAAEARWEEVDIEAQEWKIPAARMKMNRDHTVPLSDEAIAILEMMKPL------SGNREFIFPSRIKPNQPMNSQTVN 322 (413) T ss_pred HHHHHCCCHHHEECCCCEEEECHHHCCCCCCCEECCCHHHHHHHHHHHHH------CCCCEEECCCCCCCCCCCCHHHHH T ss_conf 68773677999557888799756884898871527869999999999986------199769803699999978889999 Q ss_pred HHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHH-HHHHHHHHCHHHHHHHHHHHHHHH Q ss_conf 3567899976869998805417999999998489988999983788878-979999619899999999999981 Q gi|254780882|r 245 RYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLS-TTQIYTNVNSKNGGDWMMEIYDQT 317 (328) Q Consensus 245 ~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~-tT~~Y~h~~~~~~~~~l~~~~~~~ 317 (328) ..+ +.+|.....+||+||+||+|.|-+.|++..+|-.+|||..-. +..+|-+-+--..+-.+.+.+..| T Consensus 323 ~al----~~~~~~~~~t~Hd~RrT~~T~l~e~g~~~~viE~~L~H~~~~~v~~~Ynr~~yl~eRr~~mq~Wady 392 (413) T PRK09692 323 ASL----KRAGFGGVLVSHGLRSIASTALNEQGFPPDVIEAALAHVDKNEVRRAYNRSDYLEQRRPMMQWWADF 392 (413) T ss_pred HHH----HHCCCCCCEECCCCHHHHHHHHHHCCCCHHHHHHHHCCCCCCHHHHHHCHHHHHHHHHHHHHHHHHH T ss_conf 999----9669999765848457799989976999999999868999982899956775999999999999999 No 36 >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=99.97 E-value=4.1e-32 Score=219.94 Aligned_cols=154 Identities=27% Similarity=0.398 Sum_probs=120.4 Q ss_pred CHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEE-CCCCCCCCCCCCCCCCHHHH Q ss_conf 01567877653101356775775320122210011233222221122222332322033-23785310001122100234 Q gi|254780882|r 132 KQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRI-QGKGDKIRIVPLLPSVRKAI 210 (328) Q Consensus 132 ~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v-~gKg~K~R~Vpi~~~~~~~l 210 (328) ||+.++++++.... ..++||.++ |+++||||+||+++|+|+||+ .+.+.+ .+|+++.|.|||++.+.++| T Consensus 1 eE~~rLl~~~~~~~-----~~~~r~~~~--l~~~TGlR~sEi~~L~~~di~--~~~i~~~~~K~~~~r~ipl~~~~~~~l 71 (158) T cd00797 1 DEEERLLAALDALG-----SGDLKDVAI--LCLDTGARWGEALGLKAEDIQ--EGRVTFWKTKSGKSRTVPISERVAAML 71 (158) T ss_pred CHHHHHHHHHHHCC-----CHHHHHHHH--HHHHHCCCHHHHHHHHHHHCC--CCEEEEEECCCCCEEEECCCHHHHHHH T ss_conf 98999998730557-----863999999--999948888886262797726--885898875799754733419999999 Q ss_pred HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCC Q ss_conf 32211100123446655432111122111000123567899976869998805417999999998489988999983788 Q gi|254780882|r 211 LEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHF 290 (328) Q Consensus 211 ~~yl~~~~~~~~~~~~~~lF~~~~g~~ls~~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~ 290 (328) ..+. ...++|++.. ...+.+.++++... ++.+++||+|||||||+|+++|+|+.+||++|||+ T Consensus 72 ~~~~----------~~~~~f~~~~-----~~~~~~~~~~~~~~--~~~~~~~H~lRHt~At~l~~~G~~i~~v~~~lGH~ 134 (158) T cd00797 72 KRRR----------MRGGLFPDLY-----YESFRHIWKRAKIE--LPKGQATHILRHTFASHFMMNGGNIATLQHILGHA 134 (158) T ss_pred HHHH----------HCCCCCCCCC-----HHHHHHHHHHHHHC--CCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHCCC T ss_conf 9615----------4178888854-----78999999999824--79886622788999999998499899999984899 Q ss_pred CHHHHHHHHHHCHHHHHHHHH Q ss_conf 878979999619899999999 Q gi|254780882|r 291 RLSTTQIYTNVNSKNGGDWMM 311 (328) Q Consensus 291 s~~tT~~Y~h~~~~~~~~~l~ 311 (328) |++||++|+|++++..++++. T Consensus 135 s~~~T~~Y~hl~~~~l~~av~ 155 (158) T cd00797 135 TIEMTMRYAHLAPDHLDDAVS 155 (158) T ss_pred CHHHHHHCCCCCHHHHHHHHH T ss_conf 999997774869999999998 No 37 >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=99.97 E-value=1.7e-32 Score=222.38 Aligned_cols=163 Identities=21% Similarity=0.301 Sum_probs=126.6 Q ss_pred CCCCHHHHHHHHHHHCCCCCCCHHHHHH---HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEE--C-------CCCCC Q ss_conf 1110156787765310135677577532---0122210011233222221122222332322033--2-------37853 Q gi|254780882|r 129 LNEKQALTLVDNVLLHTSHETKWIDARN---SAILYLLYGCGLRISEALSLTPQNIMDDQSTLRI--Q-------GKGDK 196 (328) Q Consensus 129 lt~~e~~~ll~~~~~~~~~~~~~~~~Rd---~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v--~-------gKg~K 196 (328) +|++|+..++.+... ..|.+.|| +.++.|+++||||+||+++|+|+|||++++.+.| . .|++. T Consensus 1 f~~~e~~~ll~~~~~-----~~~~~~~~~~~y~~~ll~~~TGlR~~Ei~~L~~~Di~~~~g~~~i~i~~~~~~~~~Kt~~ 75 (181) T cd01184 1 FTTEELKAIFASPAY-----TGWASQKDPHRYWLPLLGLYTGARVNEIAQLQVDDIREEDGVPCIDITNDDEDQSLKNAA 75 (181) T ss_pred CCHHHHHHHHCCCCC-----CCCCCCCCCHHHHHHHHHHHHCCCHHHHHCCCHHHEEEECCEEEEEEECCCCCCCCCCCC T ss_conf 998999999678000-----345467980599999999996907999971979897135998999996378776567877 Q ss_pred -CCCCCCCCCCHHH-HHHHHHHHCCCCCCCCCCCCCCCCC--CCCCCCCCHHHHHHHHHHHCCCC-CCCCCCCCHHHHHH Q ss_conf -1000112210023-4322111001234466554321111--22111000123567899976869-99880541799999 Q gi|254780882|r 197 -IRIVPLLPSVRKA-ILEYYDLCPFDLNLNIQLPLFRGIR--GKPLNPGVFQRYIRQLRRYLGLP-LSTTAHTLRHSFAT 271 (328) Q Consensus 197 -~R~Vpi~~~~~~~-l~~yl~~~~~~~~~~~~~~lF~~~~--g~~ls~~~i~~~~~~~~~~~gi~-~~~spH~lRHtfAt 271 (328) .|.|||++.+.++ +.+|++..+ ....+++|++.. +.+.+...+.+.++++++++|++ .+++||+||||||| T Consensus 76 s~R~vPl~~~l~~~~~~~~~~~~~----~~~~~~lF~~~~~~~~~~~~~~~~~~~~~~~~~~gi~~~~~~~H~lRHT~aT 151 (181) T cd01184 76 SRRTIPVHPELIELGFLDYVEARR----AAGHKRLFPDLPAGKTGGYGSAVSKWFSRYLKKLGLKDKGKSFHSFRHTFIT 151 (181) T ss_pred CEEEECCCHHHHHHHHHHHHHHHH----HCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHH T ss_conf 536416889999999999999987----1599612444447888861057999999999984999788978646899999 Q ss_pred HHHHCCCCHHHHHHHHCCCCHHHHH-HHHH Q ss_conf 9998489988999983788878979-9996 Q gi|254780882|r 272 HLLSNGGDLRSIQSILGHFRLSTTQ-IYTN 300 (328) Q Consensus 272 ~ll~~G~~~~~v~~~lGH~s~~tT~-~Y~h 300 (328) +|+++|+|+.+||++|||+|++||+ +|.+ T Consensus 152 ~l~~~gv~~~~v~~~lGHss~~tT~~~Ygk 181 (181) T cd01184 152 ELRNAGVSRELIAAIMGHEEGTTTFGRYGK 181 (181) T ss_pred HHHHCCCCHHHHHHHCCCCCCCCCCCCCCC T ss_conf 999869899999998289998864253081 No 38 >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=99.97 E-value=6.6e-31 Score=212.38 Aligned_cols=155 Identities=25% Similarity=0.336 Sum_probs=128.4 Q ss_pred CCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEE-CCCCCCCCCCCCCCC Q ss_conf 1111101567877653101356775775320122210011233222221122222332322033-237853100011221 Q gi|254780882|r 127 RALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRI-QGKGDKIRIVPLLPS 205 (328) Q Consensus 127 ~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v-~gKg~K~R~Vpi~~~ 205 (328) ++||.+|+.++++++.. .+ .++++.|++.||||+||+++|+|+||+ .+.+.| .+|+++.+.|||+++ T Consensus 2 R~Lt~eE~~~l~~~~~~------~~----~~~~~~l~~~TGlR~~Ei~~L~w~di~--~~~i~i~~~Ktg~~~~ipl~~~ 69 (162) T cd00800 2 RYLTDEEYRAIYEAADA------PW----LRCAMDLALLTGQRVGDVLRMKWSDID--DDGLHIEQSKTGAKLAIPLSPS 69 (162) T ss_pred CCCCHHHHHHHHHHCCC------HH----HHHHHHHHHHHCCCHHHHHCCCHHHCC--CCEEEEEECCCCCEEEEECCHH T ss_conf 98999999999985788------66----899999999978899999719197645--6879998478870467657899 Q ss_pred CHHHHHHHHHHHCCCCCCCCCCCCCCCCC-CCCCCCCCHHHHHHHHHHHCCCCC---CCCCCCCHHHHHHHHHHCCCCHH Q ss_conf 00234322111001234466554321111-221110001235678999768699---98805417999999998489988 Q gi|254780882|r 206 VRKAILEYYDLCPFDLNLNIQLPLFRGIR-GKPLNPGVFQRYIRQLRRYLGLPL---STTAHTLRHSFATHLLSNGGDLR 281 (328) Q Consensus 206 ~~~~l~~yl~~~~~~~~~~~~~~lF~~~~-g~~ls~~~i~~~~~~~~~~~gi~~---~~spH~lRHtfAt~ll~~G~~~~ 281 (328) +.++|+.+.+.. ...++++|++.. |.|++..++++.|+++++++|++. ++++|+|||||||.+.++|. T Consensus 70 l~~~l~~~~~~~-----~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~agi~~~~~~~t~H~lRht~at~~~~~g~--- 141 (162) T cd00800 70 LREVIERCRDLS-----RVSSPYLVHTRPGGKQVSAKTLSRAFRKARKAAGVKWGGDPPTFHDIRAKAASDYEEQGK--- 141 (162) T ss_pred HHHHHHHHHHHC-----CCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCCH--- T ss_conf 999999999843-----677860763179999778679999999999984997687766018889999999873748--- Q ss_pred HHHHHHCCCCHHHHHHHHHH Q ss_conf 99998378887897999961 Q gi|254780882|r 282 SIQSILGHFRLSTTQIYTNV 301 (328) Q Consensus 282 ~v~~~lGH~s~~tT~~Y~h~ 301 (328) .+|++|||+|++||++|.+. T Consensus 142 ~~q~llGH~s~~~T~~Y~r~ 161 (162) T cd00800 142 DAQALLGHKDEKMTKIYRRK 161 (162) T ss_pred HHHHHCCCCCHHHHHHHCCC T ss_conf 89998099998997066068 No 39 >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=99.94 E-value=3.9e-27 Score=188.84 Aligned_cols=146 Identities=36% Similarity=0.514 Sum_probs=126.2 Q ss_pred HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEC-CCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCC Q ss_conf 753201222100112332222211222223323220332-3785310001122100234322111001234466554321 Q gi|254780882|r 153 DARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQ-GKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFR 231 (328) Q Consensus 153 ~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~-gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~ 231 (328) ..|+++++.+++.||||++|+++|+|+||+++.+.+.|. .||++.|.||+++.+...|..|...... .....++||+ T Consensus 14 ~~~~~~~~~l~~~tG~R~~El~~l~~~di~~~~~~i~i~~~K~~~~~~i~i~~~~~~~l~~~~~~~~~--~~~~~~~lF~ 91 (162) T cd01182 14 APRDRALILLLLYTGLRVSELLALRWSDIDLDKGTITVRRTKTGKERTVPLSPELAELLREYLELRRP--APKPDDYLFP 91 (162) T ss_pred CHHHHHHHHHHHHHCCCHHHHHHCCHHEEECCCCEEEECCCCCCCEEEEECCHHHHHHHHHHHHHHCC--CCCCCCEEEE T ss_conf 99999999999997849888984431108067986873378776203762563776799999998422--3688771554 Q ss_pred CCCCC--CCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHH Q ss_conf 11122--1110001235678999768699988054179999999984899889999837888789799996 Q gi|254780882|r 232 GIRGK--PLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTN 300 (328) Q Consensus 232 ~~~g~--~ls~~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h 300 (328) +..+. +.+...++..++++....|.+.+++||+|||||||.|+++|+++..|+++|||+++.||++|.+ T Consensus 92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~lRh~~~t~~~~~g~~~~~i~~~~GH~~~~~t~~Y~~ 162 (162) T cd01182 92 SRRGGPKRLTRRAVRRLLKKAGKRAGIPERLTPHDLRHTFATRLLEAGVPLEVIQELLGHSSISTTERYLH 162 (162) T ss_pred ECCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHCCCCCC T ss_conf 26899765103567776665554137878997016199999999996999999999928999898152819 No 40 >COG0582 XerC Integrase [DNA replication, recombination, and repair] Probab=99.90 E-value=4.1e-22 Score=157.42 Aligned_cols=208 Identities=29% Similarity=0.387 Sum_probs=150.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC-CCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCC Q ss_conf 0133211234442222333210123222222222-222221211111110156787765310135677577532012221 Q gi|254780882|r 84 GDRSLKRSLSGIKSFLKYLKKRKITTESNILNMR-NLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYL 162 (328) Q Consensus 84 s~~T~~~~ls~lr~f~~~~~~~~~i~~np~~~i~-~~k~~~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~l 162 (328) +..+.+.....++.++.|+.... +|...+. .++.....++.++.+++..+++++... ....++.+++. T Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~------~~~~~~~~~~~- 152 (309) T COG0582 84 STLTRVFRLAALRGFFAYLDNPG----APLKALREKPKRRKKLPKALTAEEVEALLEALDRY------RDALRLALLIL- 152 (309) T ss_pred HHHHHHHHHHHHHHHHHHHCCCC----CHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHH------HHHHHHHHHHH- T ss_conf 47779999999988888621631----04666531134454454548999999999998750------57899999998- Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCEEECC---CCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC- Q ss_conf 001123322222112222233232203323---7853100011221002343221110012344665543211112211- Q gi|254780882|r 163 LYGCGLRISEALSLTPQNIMDDQSTLRIQG---KGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPL- 238 (328) Q Consensus 163 l~~TGlR~~El~~L~~~did~~~~~i~v~g---Kg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g~~l- 238 (328) .||||.+|+++|+|+||++....+.+.+ |+++.|.||+++.+...+..|....+... ++|+...|... T Consensus 153 --~tG~R~~E~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~------~~~~~~~~~~~~ 224 (309) T COG0582 153 --LTGLRVSELLGLRWSDIDLENGTIWIRGTKTKGRKERRVPLSEQALEALKKYLLIRRPRE------YLFLSLRGPRLS 224 (309) T ss_pred --HHCCCHHHHHHCCHHHCCCCCCEEEEEECCCCCCCCEEEEECHHHHHHHHHHHHHCCCCC------CCCCCCCCCCCC T ss_conf --718779999827666505456727996135556651589605999999999998544433------006532356533 Q ss_pred ----CCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHH-HHCHHHHHHHHHH Q ss_conf ----1000123567899976869998805417999999998489988999983788878979999-6198999999999 Q gi|254780882|r 239 ----NPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYT-NVNSKNGGDWMME 312 (328) Q Consensus 239 ----s~~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~-h~~~~~~~~~l~~ 312 (328) +...+...+...+...|++ .++||.|||||++.+++.| +...|++++||++..+|+.|. +...+........ T Consensus 225 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~h~lRht~~~~~~~~~-~~~~~~~~~gH~~~~~~~~~~~~~~~~~~~~~~~~ 301 (309) T COG0582 225 RSALTINRLLRARAKAAKEAGIR-KITPHGLRHTFATLLLAGG-DERVIQKLLGHASLNTTQTVYYHASDERLKEAALK 301 (309) T ss_pred CCHHHHHHHHHHHHHHHHHCCCC-CCCCCCCHHHHHHHHHHCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 10367999999999973222788-8787740789999998568-76589998378708789999998710667899986 No 41 >pfam02899 Phage_integr_N Phage integrase, N-terminal SAM-like domain. Probab=99.65 E-value=7.6e-16 Score=118.28 Aligned_cols=83 Identities=35% Similarity=0.570 Sum_probs=77.1 Q ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999986254889999999999999999985121478878968989999999999998612101332112344422 Q gi|254780882|r 18 RQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLSGIKS 97 (328) Q Consensus 18 ~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~~~s~~T~~~~ls~lr~ 97 (328) +|+|++||+.|||+|++|+.+|+.||+.|..|+... ..++.+++..+|..|+.++..+|++++|+++++++||+ T Consensus 1 i~~fl~~L~~er~~S~~Ti~aY~~dL~~f~~~l~~~------~~~~~~i~~~~i~~yl~~l~~~~~s~~Ti~r~lsalr~ 74 (83) T pfam02899 1 IDQFLEYLSLERGLSPNTVRAYRRDLKAFLKFLAEG------GLSLDQLTTDDVRAFLAELLREGLSAASLARRLSALRS 74 (83) T ss_pred CHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHC------CCCHHHCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH T ss_conf 988899999885849999999999999999999874------99988868998999999987089889999999999999 Q ss_pred HHHHHHHHC Q ss_conf 223332101 Q gi|254780882|r 98 FLKYLKKRK 106 (328) Q Consensus 98 f~~~~~~~~ 106 (328) ||+|+.++| T Consensus 75 F~~~l~~eG 83 (83) T pfam02899 75 FFQFLKREG 83 (83) T ss_pred HHHHHHHHC T ss_conf 999999719 No 42 >PHA00730 int integrase Probab=98.62 E-value=1e-06 Score=61.26 Aligned_cols=198 Identities=18% Similarity=0.246 Sum_probs=111.0 Q ss_pred HHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC Q ss_conf 99999999851214788789689899999999999986121013321123444222233321012322222222222222 Q gi|254780882|r 43 TRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLSGIKSFLKYLKKRKITTESNILNMRNLKKS 122 (328) Q Consensus 43 l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~~~s~~T~~~~ls~lr~f~~~~~~~~~i~~np~~~i~~~k~~ 122 (328) +..|++||-... .++...+..|+.++... +..+ |.-+.++|.|++|....+.++ .++..|.. T Consensus 98 ~~effe~~l~~k----------~ise~T~K~Yv~~l~kp-~~~s--n~~~kA~r~f~~~~~~r~~~~-----~lK~kK~~ 159 (322) T PHA00730 98 NSEFFELTLRQR----------KISEKTIKDYINCIKQP-RKES--NNCIKAYRLFYRFLLNRDPPK-----ELKVKKTK 159 (322) T ss_pred HHHHHHHHHHHC----------CCCHHHHHHHHHHHHHH-HHHH--HHHHHHHHHHHHHHHCCCCHH-----HHHHCCCC T ss_conf 899999998752----------67688999999998756-5540--214999999999972246377-----65220368 Q ss_pred CCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCC-----CCCCCCCCCEEECCCCCCC Q ss_conf 12111111101567877653101356775775320122210011233222221122-----2223323220332378531 Q gi|254780882|r 123 NSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTP-----QNIMDDQSTLRIQGKGDKI 197 (328) Q Consensus 123 ~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~-----~did~~~~~i~v~gKg~K~ 197 (328) ..+ ++-|.+|+.+.++.+....+- +++..|+..+|+|.+|++.+-- .||+.++-.+. T Consensus 160 pDl-~VPT~eeVk~tL~~~key~~v---------y~vYrllLESG~RlsEaLkvLn~y~p~~dv~e~~~~~y-------- 221 (322) T PHA00730 160 PDL-RIPTLEEIKRTLQLVKEYENL---------YLLYRLLLESGSRLSEALKVLNNYNPQNDIREDGFSIY-------- 221 (322) T ss_pred CCC-CCCCHHHHHHHHHHHCCCCCH---------HHHHHHHHHHCHHHHHHHHHHHCCCHHHHCCCCCEEEE-------- T ss_conf 862-478889999999875047641---------46899998713028999999741480543035876999-------- Q ss_pred CCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC--CCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHH Q ss_conf 000112210023432211100123446655432111--122111000123567899976869998805417999999998 Q gi|254780882|r 198 RIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGI--RGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLS 275 (328) Q Consensus 198 R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~--~g~~ls~~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~ 275 (328) |+ +|.. +....-++|.-. +--.++..++...+ .+.+ -+.|--+|.-+||-|++ T Consensus 222 ---~L---------~w~R------g~K~~fy~fhit~Lk~~~It~~~i~~~~----~~~~---~v~~KYiRKfvatKm~e 276 (322) T PHA00730 222 ---IL---------NWTR------GQKKSFYLFHITPLKQIKITKAYIDKYV----RRLN---LVPPKYIRKFVATKMLE 276 (322) T ss_pred ---EE---------HHHC------CCCCEEEEEEECCCEEEEECHHHHHHHH----HCCC---CCCHHHHHHHHHHHHHH T ss_conf ---83---------2221------6775699999425424566188886665----4046---68789999999999999 Q ss_pred CCCCHHHHHHHHCCCCHHH-HHHHHHH Q ss_conf 4899889999837888789-7999961 Q gi|254780882|r 276 NGGDLRSIQSILGHFRLST-TQIYTNV 301 (328) Q Consensus 276 ~G~~~~~v~~~lGH~s~~t-T~~Y~h~ 301 (328) -|.|..+|--+=|-..-+. |++|+.+ T Consensus 277 lgip~dvvdFiqGR~p~~ilt~HY~dL 303 (322) T PHA00730 277 LGIPSEVVDFIQGRTPSRILTKHYLDL 303 (322) T ss_pred HCCCHHHHHHHCCCCCCCHHHHHHHHH T ss_conf 689688999964788550468999999 No 43 >COG4342 Uncharacterized protein conserved in archaea [Function unknown] Probab=98.45 E-value=9.6e-07 Score=61.44 Aligned_cols=205 Identities=18% Similarity=0.182 Sum_probs=113.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC-CCCCCCC--CCC-CCCHHHHHHHHHHH Q ss_conf 9999999999986121013321123444222233321012322222222222-2221211--111-11015678776531 Q gi|254780882|r 68 YTEIRAFISKRRTQKIGDRSLKRSLSGIKSFLKYLKKRKITTESNILNMRNL-KKSNSLP--RAL-NEKQALTLVDNVLL 143 (328) Q Consensus 68 ~~~i~~~l~~l~~~~~s~~T~~~~ls~lr~f~~~~~~~~~i~~np~~~i~~~-k~~~~~p--~~l-t~~e~~~ll~~~~~ 143 (328) .....+|+..+...=-+...-..+-.+.|.|.+||...|+|..+-+..+..+ |..+..+ -++ +.+++.+-++.... T Consensus 57 ~k~ardyls~l~r~ig~~~~kdKy~kA~R~f~~fl~~rgiise~~Ae~lrk~lk~k~~~g~dlyIp~de~ir~~~~l~r~ 136 (291) T COG4342 57 GKTARDYLSALNRPIGSVREKDKYQKAYRLFIKFLTSRGIISEEFAEKLRKPLKVKKSNGVDLYIPSDEEIRATEELARE 136 (291) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCEECCCHHHHHHHHHHHHH T ss_conf 78999999998876443110057999999999999870413399999999986457678863324987999889999988 Q ss_pred CCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCC Q ss_conf 01356775775320122210011233222221122222332322033237853100011221002343221110012344 Q gi|254780882|r 144 HTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNL 223 (328) Q Consensus 144 ~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~ 223 (328) .. .|-++++.++..+|+|++|++.+-.+ +|-+.-.-.+.||+ -+.-|+ .|.. +. T Consensus 137 ~~--------e~~y~v~~ll~~SGaRLse~v~~L~~-~D~s~~~~~~ng~~--icyy~l---------~w~r------g~ 190 (291) T COG4342 137 YS--------ERAYLVYLLLLFSGARLSEAVAVLRN-LDHSRLYCVVNGKV--ICYYPL---------SWSR------GH 190 (291) T ss_pred HC--------CHHHHHHHHHHHCCCHHHHHHHHHHC-CCHHHHEEECCCEE--EEEECC---------CHHH------CC T ss_conf 54--------01899999998634309999999967-14312023128737--885011---------0320------45 Q ss_pred CCCCCCC-CCCCCCCCCCCCH-HHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHH-HHHHHH Q ss_conf 6655432-1111221110001-235678999768699988054179999999984899889999837888789-799996 Q gi|254780882|r 224 NIQLPLF-RGIRGKPLNPGVF-QRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLST-TQIYTN 300 (328) Q Consensus 224 ~~~~~lF-~~~~g~~ls~~~i-~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~t-T~~Y~h 300 (328) ...-++| |...+.++-.-.+ +..++......| +..--+|.-.++-|++.|+|..+|--+-||+.-.. |++|+. T Consensus 191 K~afyif~P~~~~~~l~kidisy~~vq~~~~~~~----Vk~kyiRkwv~nkmlelgvP~~VvdFIqGrk~~~V~~rHY~n 266 (291) T COG4342 191 KRAFYIFHPKDFAESLRKIDISYHRVQRFENRRG----VKAKYIRKWVYNKMLELGVPEDVVDFIQGRKQSRVGTRHYAN 266 (291) T ss_pred CCEEEEECCHHHHHHCHHCCCHHHHHHHHHHCCC----CHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCHHHHHHHHH T ss_conf 4115686636652001101112999999986058----209999999999999809958899998746722157899999 Q ss_pred HC Q ss_conf 19 Q gi|254780882|r 301 VN 302 (328) Q Consensus 301 ~~ 302 (328) +. T Consensus 267 L~ 268 (291) T COG4342 267 LL 268 (291) T ss_pred HH T ss_conf 99 No 44 >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=97.78 E-value=3.8e-05 Score=51.45 Aligned_cols=64 Identities=23% Similarity=0.279 Sum_probs=51.7 Q ss_pred CCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCC-CCHHHHHHHHCCCCHHHHHH-HH Q ss_conf 2211100012356789997686999880541799999999848-99889999837888789799-99 Q gi|254780882|r 235 GKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNG-GDLRSIQSILGHFRLSTTQI-YT 299 (328) Q Consensus 235 g~~ls~~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G-~~~~~v~~~lGH~s~~tT~~-Y~ 299 (328) ..||+..+++.+++++++.+|+...+++|.||.+.|..+ ++| ++-..=..+|||++..|=.. |. T Consensus 170 ~~~lt~st~~~~lk~lgei~Gf~~~~~~y~~R~g~a~~~-n~~~vs~a~rn~im~Ha~~~tF~k~Y~ 235 (414) T pfam11917 170 DQALTASTLNSWLKRLGEIAGFEDPLTPYCLRYGAAKAL-NSGEVSEAERNLILGHASSRTFLKHYL 235 (414) T ss_pred CCCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHC-CCCCCCHHHHHHHHCCCCCCHHHHHCC T ss_conf 778898999999999988841111454002357899852-665699899978744787405776256 No 45 >pfam01028 Topoisom_I Eukaryotic DNA topoisomerase I, catalytic core. Topoisomerase I promotes the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex DNA and are vital for the processes of replication, transcription, and recombination. Probab=96.88 E-value=0.0023 Score=40.35 Aligned_cols=115 Identities=18% Similarity=0.236 Sum_probs=68.9 Q ss_pred CCCCCCCCCCCCCCCEEE--CCCCCCCCCCCCCCC-CHHHHHHHHHHHCCCCCCCCCCCCCCCC-CC--CCCCCCCHHHH Q ss_conf 221122222332322033--237853100011221-0023432211100123446655432111-12--21110001235 Q gi|254780882|r 173 ALSLTPQNIMDDQSTLRI--QGKGDKIRIVPLLPS-VRKAILEYYDLCPFDLNLNIQLPLFRGI-RG--KPLNPGVFQRY 246 (328) Q Consensus 173 l~~L~~~did~~~~~i~v--~gKg~K~R~Vpi~~~-~~~~l~~yl~~~~~~~~~~~~~~lF~~~-~g--~~ls~~~i~~~ 246 (328) ++.|+.+||.+..+.|.+ .||+|+.+.+-|.+. +...|.... ...++..||.-. .| .+++...++.+ T Consensus 84 ltTLr~~Hv~i~~~~i~~~F~GK~gv~~~~~v~d~~l~~~l~~l~-------~~~pg~~LF~y~~~g~~~~v~s~dvN~y 156 (244) T pfam01028 84 LTTLRNRHVTLEGDVIRFDFLGKDGIRHENTVRDKRLAKNLKRLK-------QKLPGDELFQYLDDGERDRVSSSDLNAY 156 (244) T ss_pred EEECCCCCEEEECCEEEEEEECCCCCEEEEEECCHHHHHHHHHHH-------HCCCCCHHEEEECCCCEEECCHHHHHHH T ss_conf 010010447898998999987798747898868889999999998-------5299732168716996342788999999 Q ss_pred HHHHHHHCCCCCCCCCCCCHHHHHHH-----HHHCCCC--------------HHHHHHHHCCCCHHHH-HHHHH Q ss_conf 67899976869998805417999999-----9984899--------------8899998378887897-99996 Q gi|254780882|r 247 IRQLRRYLGLPLSTTAHTLRHSFATH-----LLSNGGD--------------LRSIQSILGHFRLSTT-QIYTN 300 (328) Q Consensus 247 ~~~~~~~~gi~~~~spH~lRHtfAt~-----ll~~G~~--------------~~~v~~~lGH~s~~tT-~~Y~h 300 (328) ++.+. | ..+|+.+||--.||. |.+.+.+ +..|++.|||.- ++. .-|.| T Consensus 157 Lk~~~---g--~~~TaKdFRTw~at~~a~~~L~~~~~~~~~~~~~k~~i~~a~~~vA~~LgnTp-aV~R~sYi~ 224 (244) T pfam01028 157 LRELM---G--EGFTAKDFRTWNASVTALEALAELGKSLESVAEKKKAINAANKEVAILLGNTP-AVSRKSYIH 224 (244) T ss_pred HHHHH---C--CCCCHHHHHHHCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCC-CCHHHHCCC T ss_conf 99983---5--88752122221207999999996589988999999999999999999858984-113774458 No 46 >cd00659 Topo_IB_C DNA topoisomerase IB, C-terminal catalytic domain. Topoisomerase I promotes the relaxation of both positive and negative DNA superhelical tension by introducing a transient single-stranded break in duplex DNA. This function is vital for the processes of replication, transcription, and recombination. Unlike Topo IA enzymes, Topo IB enzymes do not require a single-stranded region of DNA or metal ions for their function. The type IB family of DNA topoisomerases includes eukaryotic nuclear topoisomerase I, topoisomerases of poxviruses and bacterial versions of Topo IB. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their C-terminal catalytic domain and the overall reaction mechanism with tyrosine recombinases. The C-terminal catalytic domain in topoisomerases is linked to a divergent N-terminal domain that shows no sequence or structure similarity to the N-terminal domains of tyrosine recombinases. Probab=96.85 E-value=0.00074 Score=43.40 Aligned_cols=114 Identities=17% Similarity=0.159 Sum_probs=68.4 Q ss_pred CCCCCCCCCCCCCCCEEE--CCCCCCCCCCCCCC--CCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHH Q ss_conf 221122222332322033--23785310001122--10023432211100123446655432111122111000123567 Q gi|254780882|r 173 ALSLTPQNIMDDQSTLRI--QGKGDKIRIVPLLP--SVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIR 248 (328) Q Consensus 173 l~~L~~~did~~~~~i~v--~gKg~K~R~Vpi~~--~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g~~ls~~~i~~~~~ 248 (328) ++.|+.+||.+..+.|.+ .||+|+.+..-|.+ .+...+.... ...++..||.-..+.+++...++.+++ T Consensus 71 ltTLr~~Hv~~~~~~i~~~F~GK~gv~~~~~i~d~~~l~~~~~~~~-------~~~pg~~LF~y~~~~~v~s~~vN~yLk 143 (218) T cd00659 71 LCTLRKEHVTLKPNVVRFDFLGKDSIRYENEVEVEPRLFKNLRKFL-------DKLPGDDLFQYLQVDRLNSSKLNAYLR 143 (218) T ss_pred EEEECHHHEEEECCEEEEEEECCCCCEEEEEEECCHHHHHHHHHHH-------HCCCCHHHEECCCCCCCCHHHHHHHHH T ss_conf 5540131165769989999856888289999706599999999997-------369906640346788669899999999 Q ss_pred HHHHHCCCCCCCCCCCCHHHHHHHHHH-----CCCC-------------HHHHHHHHCCCCHHHH-HHHHH Q ss_conf 899976869998805417999999998-----4899-------------8899998378887897-99996 Q gi|254780882|r 249 QLRRYLGLPLSTTAHTLRHSFATHLLS-----NGGD-------------LRSIQSILGHFRLSTT-QIYTN 300 (328) Q Consensus 249 ~~~~~~gi~~~~spH~lRHtfAt~ll~-----~G~~-------------~~~v~~~lGH~s~~tT-~~Y~h 300 (328) .+ + .++|+-+||--.||.++. ...+ +..|++.|||.- .+. .-|.| T Consensus 144 ~~----~--~~~TaKdFRTw~at~~~~~~L~~~~~~~s~~~~k~~i~~a~~~vA~~LgnTp-aV~r~sYi~ 207 (218) T cd00659 144 EF----M--EGLTAKVFRTYNASLTALEQLARLPASLSLAEKKKAYNDANREVAILLNHTP-AISKINYID 207 (218) T ss_pred HH----C--CCCCHHCEEEHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCCCC-CCCHHHCCC T ss_conf 97----5--9997002331378999999998668877889999999999999999968986-562230588 No 47 >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=96.18 E-value=0.018 Score=34.67 Aligned_cols=62 Identities=21% Similarity=0.236 Sum_probs=44.0 Q ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCC--------------CCCCHHHCCHHHHHHHHHH Q ss_conf 9999999999986254889999999999999999985121478--------------8789689899999999999 Q gi|254780882|r 16 KERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKI--------------TIQTIRQLSYTEIRAFISK 77 (328) Q Consensus 16 ~~~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~~~~--------------~~~~~~~i~~~~i~~~l~~ 77 (328) +.+++|+.||..++|+|++|+..|...|+.|+.|+........ ......-++.+++..+++. T Consensus 11 ~~i~~y~~~L~~~rg~s~~Tin~~l~~L~~f~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~l~~eei~~ll~~ 86 (260) T cd01190 11 PLILAFLDHLENDRGNSIRTRNARLAALHSFFRYAAREVPEHLPTIQRVLAIPMKRFKRPLVTYLTREEVQALLAA 86 (260) T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHC T ss_conf 9999999999984699999999999999999999998084014553710148878889999988999999999818 No 48 >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=95.61 E-value=0.034 Score=32.98 Aligned_cols=71 Identities=15% Similarity=0.073 Sum_probs=47.2 Q ss_pred CCHHHCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCC--------CCCCHHHCCHHHHHHHHH Q ss_conf 304314989999999999999986254889999999999999999985121478--------878968989999999999 Q gi|254780882|r 5 NLPEIVSFELLKERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKI--------TIQTIRQLSYTEIRAFIS 76 (328) Q Consensus 5 ~~~~~~~~~l~~~~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~~~~--------~~~~~~~i~~~~i~~~l~ 76 (328) +-|+.+.. +.+++|+.||..++++|++|+..|...|+.|+.|+........ ......-++.+++...++ T Consensus 5 k~~~~it~---~dI~~y~~~L~~~~~~s~~Tin~~l~~l~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~lt~eEi~~ll~ 81 (242) T cd01193 5 RSPDELGE---EDVRAFLTLLAVEGNVSASTQNQALSALLFFYRHTLKRDLPWLQRIRRPRKPRKLPVVLSPEEVRRLLG 81 (242) T ss_pred CCHHHCCH---HHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHCCCCCCCCCCCCCCCHHHHHHHHH T ss_conf 89588999---999999999998489899999999999999999998768965665655789998998899999999997 Q ss_pred HH Q ss_conf 99 Q gi|254780882|r 77 KR 78 (328) Q Consensus 77 ~l 78 (328) .+ T Consensus 82 ~~ 83 (242) T cd01193 82 AL 83 (242) T ss_pred CC T ss_conf 38 No 49 >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=95.02 E-value=0.067 Score=31.16 Aligned_cols=39 Identities=18% Similarity=0.023 Sum_probs=33.2 Q ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 999999999998625488999999999999999998512 Q gi|254780882|r 16 KERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYT 54 (328) Q Consensus 16 ~~~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~ 54 (328) +.+++|+.||..++|+|++|+..|...++.|+.|+.... T Consensus 69 ~~i~~f~~~L~~~k~~s~~Ti~~~l~~lr~~~~~a~~~~ 107 (299) T cd01185 69 EFILEFKLFLRKEKKLSRNTAVHYLSWLKKLLKIAYRDK 107 (299) T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCC T ss_conf 999999999987579888899999999999999999889 No 50 >PRK01287 xerC site-specific tyrosine recombinase XerC; Reviewed Probab=94.92 E-value=0.028 Score=33.50 Aligned_cols=39 Identities=15% Similarity=0.278 Sum_probs=25.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 999999999986121013321123444222233321012 Q gi|254780882|r 69 TEIRAFISKRRTQKIGDRSLKRSLSGIKSFLKYLKKRKI 107 (328) Q Consensus 69 ~~i~~~l~~l~~~~~s~~T~~~~ls~lr~f~~~~~~~~~ 107 (328) ..+..|+.||.++++|+.|+..|...|+.|+.||.+.|. T Consensus 25 ~ll~~Fl~yL~er~~S~~Ti~aY~~dL~~F~~fl~~~g~ 63 (361) T PRK01287 25 ALLLRFVEWLQERNWSERTLKVQTHHTYHFILWCEERGL 63 (361) T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCC T ss_conf 999999999998399899999999999999999998489 No 51 >PRK05084 xerS site-specific tyrosine recombinase XerS; Reviewed Probab=94.63 E-value=0.037 Score=32.78 Aligned_cols=41 Identities=12% Similarity=0.204 Sum_probs=24.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 99999999999861210133211234442222333210123 Q gi|254780882|r 68 YTEIRAFISKRRTQKIGDRSLKRSLSGIKSFLKYLKKRKIT 108 (328) Q Consensus 68 ~~~i~~~l~~l~~~~~s~~T~~~~ls~lr~f~~~~~~~~~i 108 (328) +.-|.+|+.++...++|++|+..|..-|+.||+|+..++.. T Consensus 18 P~~i~ey~~~~~~~~~Sp~Ti~~Y~~DL~~F~~fL~~~~~~ 58 (360) T PRK05084 18 PWYVLEYYQSKLATPYSPTTLYEYLTEYRRFFNWLIDEGLT 58 (360) T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 09999999988605989899999999999999999864987 No 52 >PRK00283 xerD site-specific tyrosine recombinase XerD; Reviewed Probab=93.78 E-value=0.073 Score=30.93 Aligned_cols=38 Identities=21% Similarity=0.230 Sum_probs=30.5 Q ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 999999999998625488999999999999999998512 Q gi|254780882|r 16 KERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYT 54 (328) Q Consensus 16 ~~~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~ 54 (328) +.+++|+.++.. +|+|++|+..|...++.|+.|+.... T Consensus 51 ~~i~~y~~~L~~-~~~s~~Tin~~l~~lr~~~~~a~~~~ 88 (296) T PRK00283 51 DDLQAFLAELAE-GGYKATSSARRLSALRRFFQFLLREG 88 (296) T ss_pred HHHHHHHHHHHH-CCCCHHHHHHHHHHHHHHHHHHHHCC T ss_conf 999999999987-79999999999999997479998707 No 53 >PRK00236 xerC site-specific tyrosine recombinase XerC; Reviewed Probab=92.89 E-value=0.12 Score=29.55 Aligned_cols=37 Identities=24% Similarity=0.307 Sum_probs=26.6 Q ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHC Q ss_conf 99999999999862548899999999999999999851 Q gi|254780882|r 16 KERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFY 53 (328) Q Consensus 16 ~~~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~ 53 (328) +.++.|+.++.. +|+|++|+..|...++.|+.|+... T Consensus 56 ~~i~~~~~~l~~-~g~s~~Ti~~~l~~lr~~~~~a~~~ 92 (295) T PRK00236 56 ADLRAFLARLRR-QGLSARSLARRLSALRSFYRWLVRR 92 (295) T ss_pred HHHHHHHHHHHH-CCCCHHHHHHHHHHHHHHHHHHHHC T ss_conf 999999999987-6999999999999999999988762 No 54 >COG4688 Uncharacterized protein conserved in bacteria [Function unknown] Probab=92.10 E-value=0.22 Score=27.93 Aligned_cols=66 Identities=18% Similarity=0.191 Sum_probs=49.5 Q ss_pred HHHHHHHHCC--CCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHCHHHHHHHHH Q ss_conf 5678999768--69998805417999999998489988999983788878979999619899999999 Q gi|254780882|r 246 YIRQLRRYLG--LPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMM 311 (328) Q Consensus 246 ~~~~~~~~~g--i~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~~l~ 311 (328) .|++++..+. -.-++-.|.+||-.-|.+-..|+|-..|+.+.|-+++.----|-|=+.+++-+.++ T Consensus 432 lferhg~~~edG~~~rL~SH~lRHllnT~a~r~Gmde~~ia~w~gR~~Vaqn~~YDHRs~~e~s~~Ir 499 (665) T COG4688 432 LFERHGQSAEDGKQLRLESHMLRHLLNTEAFRLGMDETIIAKWFGRRSVAQNYEYDHRSLAEQSDQIR 499 (665) T ss_pred HHHHHCCCCCCCCEEECHHHHHHHHHHHHHHHCCCHHHHHHHHHCHHHHHHCCCCCHHHHHHHHHHHC T ss_conf 89874755568865544357888988788887470478888763303554212423141888865422 No 55 >pfam02899 Phage_integr_N Phage integrase, N-terminal SAM-like domain. Probab=91.28 E-value=0.59 Score=25.28 Aligned_cols=34 Identities=21% Similarity=0.437 Sum_probs=28.9 Q ss_pred HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999998-6121013321123444222233321 Q gi|254780882|r 71 IRAFISKRR-TQKIGDRSLKRSLSGIKSFLKYLKK 104 (328) Q Consensus 71 i~~~l~~l~-~~~~s~~T~~~~ls~lr~f~~~~~~ 104 (328) |+.|+.++. ++++|+.|+..|..-|+.|++|+.. T Consensus 1 i~~fl~~L~~er~~S~~Ti~aY~~dL~~f~~~l~~ 35 (83) T pfam02899 1 IDQFLEYLSLERGLSPNTVRAYRRDLKAFLKFLAE 35 (83) T ss_pred CHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 98889999988584999999999999999999987 No 56 >TIGR01108 oadA oxaloacetate decarboxylase alpha subunit; InterPro: IPR005776 This family describes the bacterial oxaloacetate decarboxylase alpha subunit and its equivalents in archaea . The oxaloacetate decarboxylase Na+ pump is the paradigm of the family of Na+ transport decarboxylases that present in bacteria and archaea. It a multi subunit enzyme consisting of a peripheral alpha-subunit and integral membrane subunits beta and gamma. The energy released by the decarboxylation reaction of oxaloacetate is coupled to Na+ ion pumping across the membrane.; GO: 0008948 oxaloacetate decarboxylase activity, 0006814 sodium ion transport. Probab=73.50 E-value=3.2 Score=20.72 Aligned_cols=91 Identities=20% Similarity=0.284 Sum_probs=61.1 Q ss_pred HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCC-CCCCCCCCCCHHHHHHH----HHHCCCCH- Q ss_conf 0234322111001234466554321111221110001235678999768-69998805417999999----99848998- Q gi|254780882|r 207 RKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLG-LPLSTTAHTLRHSFATH----LLSNGGDL- 280 (328) Q Consensus 207 ~~~l~~yl~~~~~~~~~~~~~~lF~~~~g~~ls~~~i~~~~~~~~~~~g-i~~~~spH~lRHtfAt~----ll~~G~~~- 280 (328) +.-|+.|++..+...... -|-+.+-.-.+=|||..-+..++.+.++.| ++-++|.|+- -.+|.. .+|+|+|. T Consensus 146 vHTl~~yl~la~~L~~~G-~DSI~IKDMaGlLTP~~AYELV~alK~~~~n~pvhLH~H~T-tGmA~~AllkA~EAG~d~i 223 (616) T TIGR01108 146 VHTLEKYLELAKELLEMG-VDSICIKDMAGLLTPKVAYELVSALKKEFGNLPVHLHSHAT-TGMAEMALLKAIEAGADMI 223 (616) T ss_pred HHHHHHHHHHHHHHHHHC-CCEEEEECCCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCC-HHHHHHHHHHHHHCCCCCC T ss_conf 367888999999999818-86055202004644158999999997423974688632472-3379999998887078800 Q ss_pred -HHHHHHHCCCCHHH--HHHHH Q ss_conf -89999837888789--79999 Q gi|254780882|r 281 -RSIQSILGHFRLST--TQIYT 299 (328) Q Consensus 281 -~~v~~~lGH~s~~t--T~~Y~ 299 (328) ..|+-+-|-.|--. ||+|+ T Consensus 224 DTAisS~S~gtSHPptE~lv~~ 245 (616) T TIGR01108 224 DTAISSMSGGTSHPPTETLVAA 245 (616) T ss_pred HHCCCCCCCCCCCCHHHHHHHH T ss_conf 2005523478888747999999 No 57 >smart00435 TOPEUc DNA Topoisomerase I (eukaryota). DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras Probab=59.50 E-value=5.2 Score=19.37 Aligned_cols=92 Identities=21% Similarity=0.175 Sum_probs=52.0 Q ss_pred CCCCCCCC-C----------CCCCCCCCCCCCC-CCEE--ECCCCC--CCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCC Q ss_conf 01123322-2----------2211222223323-2203--323785--31000112210023432211100123446655 Q gi|254780882|r 164 YGCGLRIS-E----------ALSLTPQNIMDDQ-STLR--IQGKGD--KIRIVPLLPSVRKAILEYYDLCPFDLNLNIQL 227 (328) Q Consensus 164 ~~TGlR~~-E----------l~~L~~~did~~~-~~i~--v~gKg~--K~R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~ 227 (328) .-.+||.| | +|+|+++||.+.. ..|. ..||-+ -.-.||+.+.+...|..+.. +..+++ T Consensus 124 DklALRaGnEKdedeADTVGcCSLRvEHI~l~~~n~v~fDFLGKDSIRy~n~V~V~~~VfkNL~~F~k------~Kk~~D 197 (391) T smart00435 124 DKLALRAGNEKGEDEADTVGCCSLRVEHVTLKPPNKVIFDFLGKDSIRYYNEVEVDKQVFKNLKIFMK------PKKPGD 197 (391) T ss_pred HHHHHHCCCCCCCCCCCCCCCCCEEEEEEEECCCCEEEEEECCCCCEEEECCEECCHHHHHHHHHHHC------CCCCCC T ss_conf 78887406766766576311010157655864898068875167642554104448999999999942------899843 Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHH Q ss_conf 432111122111000123567899976869998805417999999 Q gi|254780882|r 228 PLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATH 272 (328) Q Consensus 228 ~lF~~~~g~~ls~~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ 272 (328) .||- +|++..++..++.+- ..+|+-.||-.-||. T Consensus 198 dlFD-----rl~ts~LN~hL~~~M------~GLTAKVFRTYNAS~ 231 (391) T smart00435 198 DLFD-----RLNTSKLNKHLKELM------PGLTAKVFRTYNASI 231 (391) T ss_pred HHHH-----CCCHHHHHHHHHHHC------CCCCEEEEEEECCCH T ss_conf 1010-----368899988799755------675213465204777 No 58 >TIGR01983 UbiG ubiquinone biosynthesis O-methyltransferase; InterPro: IPR010233 This entry represents an O-methyltransferase, which is believed to act at two points in the ubiquinone biosynthetic pathway in bacteria (UbiG) and mitochondria (COQ3) , . A separate methylase (MenG/UbiE) catalyses the single C-methylation step. The most commonly used names for genes in this family do not indicate whether this gene is an O-methyl, or C-methyl transferase.; GO: 0008425 2-polyprenyl-6-methoxy-14-benzoquinone methyltransferase activity, 0006744 ubiquinone biosynthetic process. Probab=49.39 E-value=15 Score=16.53 Aligned_cols=11 Identities=18% Similarity=0.006 Sum_probs=5.0 Q ss_pred CCHHHHHHHHC Q ss_conf 99889999837 Q gi|254780882|r 278 GDLRSIQSILG 288 (328) Q Consensus 278 ~~~~~v~~~lG 288 (328) +.+..+..+|. T Consensus 229 i~P~EL~~~l~ 239 (275) T TIGR01983 229 IKPSELTSWLE 239 (275) T ss_pred CCHHHHHHHHH T ss_conf 38799999985 No 59 >PRK11582 flagella biosynthesis protein FliZ; Provisional Probab=48.39 E-value=19 Score=15.88 Aligned_cols=68 Identities=13% Similarity=0.123 Sum_probs=39.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 8999999999999999998512147887896898999999999999861-21013321123444222233321012 Q gi|254780882|r 33 KLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQ-KIGDRSLKRSLSGIKSFLKYLKKRKI 107 (328) Q Consensus 33 ~~T~~~Y~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~-~~s~~T~~~~ls~lr~f~~~~~~~~~ 107 (328) +.+...+...|..+++||+...-.. +-+.=||..|-.++.++ .+|.+|++-|..-||.+=..+...++ T Consensus 58 d~~W~~~Q~~l~aLCRFCs~i~c~~-------~~~yFDI~gFkQyL~eQTeMshsTvrEYVVRLRRLd~~L~~~n~ 126 (179) T PRK11582 58 DNGWQKEQKEWAALCRFCGDLHCKT-------QSDYFDIIGFKQYLFEQTEMSHSTVREYVVRLRRLGNHLHEQNI 126 (179) T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCC-------CCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCC T ss_conf 8889999999999999988875178-------87601089999999985015221299999999999888763358 No 60 >pfam08849 DUF1819 Putative inner membrane protein (DUF1819). These proteins are functionally uncharacterized. Several are annotated as putative inner membrane proteins. Probab=47.41 E-value=19 Score=15.78 Aligned_cols=20 Identities=5% Similarity=-0.032 Sum_probs=9.8 Q ss_pred CCCCCHHHHHHHHHHHCCCC Q ss_conf 11110156787765310135 Q gi|254780882|r 128 ALNEKQALTLVDNVLLHTSH 147 (328) Q Consensus 128 ~lt~~e~~~ll~~~~~~~~~ 147 (328) .|+.+++..+++......+. T Consensus 116 ~L~~~d~~~F~~~k~~~~~~ 135 (191) T pfam08849 116 DLPKEDWDAFFEAKAEWDPE 135 (191) T ss_pred CCCHHHHHHHHHHHHHCCCC T ss_conf 88999999999987665910 No 61 >TIGR00802 nico transition metal uptake transporter, Ni2+-Co2+ transporter (NiCoT) family; InterPro: IPR004688 This family is found in both Gram-negative and Gram-positive bacteria. The functionally characterised members of the family catalyze uptake of either Ni2+ or Co2+ in a proton motive force-dependent process. Topological analyses with the HoxN Ni2+ transporter of Ralstonia eutropha suggest that it possesses 8 TMSs with its N- and C-termini in the cytoplasm.; GO: 0015099 nickel ion transmembrane transporter activity, 0015675 nickel ion transport, 0016021 integral to membrane. Probab=43.33 E-value=15 Score=16.47 Aligned_cols=26 Identities=15% Similarity=0.042 Sum_probs=12.0 Q ss_pred CCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCC Q ss_conf 356775775320122210011233222221122 Q gi|254780882|r 146 SHETKWIDARNSAILYLLYGCGLRISEALSLTP 178 (328) Q Consensus 146 ~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~ 178 (328) ++-..++|. +|-|.++|. +|+.=|-. T Consensus 151 SWHMYPvGf----LFGLGFDTA---tEvaLL~l 176 (290) T TIGR00802 151 SWHMYPVGF----LFGLGFDTA---TEVALLGL 176 (290) T ss_pred CHHHHHHHH----HHHCCCHHH---HHHHHHHH T ss_conf 524313588----762121189---99999999 No 62 >TIGR00016 ackA acetate kinase; InterPro: IPR004372 Acetate kinase is involved in the activation of acetate to acetyl CoA and in the secretion of acetate. It catalyzes the reaction ATP + acetate = ADP + acetyl phosphate.; GO: 0016301 kinase activity, 0016774 phosphotransferase activity carboxyl group as acceptor, 0006082 organic acid metabolic process. Probab=39.82 E-value=12 Score=17.05 Aligned_cols=14 Identities=14% Similarity=0.223 Sum_probs=7.3 Q ss_pred CCCCCCCCCCCCCC Q ss_conf 32222211222223 Q gi|254780882|r 169 RISEALSLTPQNIM 182 (328) Q Consensus 169 R~~El~~L~~~did 182 (328) |..|+++...+|+. T Consensus 204 ~~~~~Lnkp~~~l~ 217 (416) T TIGR00016 204 RAAKLLNKPLDDLN 217 (416) T ss_pred HHHHHHCCCHHHCC T ss_conf 99997178101368 No 63 >COG0282 ackA Acetate kinase [Energy production and conversion] Probab=39.41 E-value=16 Score=16.26 Aligned_cols=13 Identities=23% Similarity=0.376 Sum_probs=5.2 Q ss_pred CCCCCCCCCCCCC Q ss_conf 3222221122222 Q gi|254780882|r 169 RISEALSLTPQNI 181 (328) Q Consensus 169 R~~El~~L~~~di 181 (328) |..|+++-..+|+ T Consensus 188 ~aa~~L~k~~~~l 200 (396) T COG0282 188 RAAEILGKPLEDL 200 (396) T ss_pred HHHHHHCCCCCCC T ss_conf 9999868975334 No 64 >cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D Probab=36.20 E-value=29 Score=14.70 Aligned_cols=32 Identities=28% Similarity=0.389 Sum_probs=23.9 Q ss_pred CCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCC Q ss_conf 9998805417999999998489988999983788 Q gi|254780882|r 257 PLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHF 290 (328) Q Consensus 257 ~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~ 290 (328) +..+|+...+. |..|+++|.+...|+..+|=+ T Consensus 3 ~~~lt~~q~~~--ar~l~~~G~~~~~iA~~~GVs 34 (42) T cd00569 3 PPKLTPEQIEE--ARRLLAAGESVAEIARRLGVS 34 (42) T ss_pred CCCCCHHHHHH--HHHHHHCCCCHHHHHHHHCCC T ss_conf 98699999999--999999789899999997979 No 65 >COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms] Probab=35.94 E-value=29 Score=14.67 Aligned_cols=20 Identities=25% Similarity=0.325 Sum_probs=8.4 Q ss_pred CHHHHHHHHCCCCHHHHHHHH Q ss_conf 988999983788878979999 Q gi|254780882|r 279 DLRSIQSILGHFRLSTTQIYT 299 (328) Q Consensus 279 ~~~~v~~~lGH~s~~tT~~Y~ 299 (328) ....+++.+|=|- .|-.+|. T Consensus 175 Taeela~~~giSR-vTaRRYL 194 (224) T COG4565 175 TAEELAQALGISR-VTARRYL 194 (224) T ss_pred CHHHHHHHHCCCH-HHHHHHH T ss_conf 7999998837219-9999999 No 66 >TIGR01304 IMP_DH_rel_2 IMP dehydrogenase family protein; InterPro: IPR005992 This family of proteins, often annotated as a putative IMP dehydrogenase, are related to IMP dehydrogenase and GMP reductase. Most species with a member of this family belong to the high GC Gram-positive bacteria.. Probab=34.39 E-value=17 Score=16.21 Aligned_cols=24 Identities=25% Similarity=0.372 Sum_probs=9.1 Q ss_pred CCCCCCHHHHHHHHHHCCCCHHHHH Q ss_conf 8805417999999998489988999 Q gi|254780882|r 260 TTAHTLRHSFATHLLSNGGDLRSIQ 284 (328) Q Consensus 260 ~spH~lRHtfAt~ll~~G~~~~~v~ 284 (328) +||-..+. ||.-++++|+|+.+|| T Consensus 140 lsPq~~~~-~a~~vv~AG~DLLvIq 163 (376) T TIGR01304 140 LSPQNASK-LAPVVVEAGADLLVIQ 163 (376) T ss_pred ECCHHHHH-HHHHHHHHCCCEEEEH T ss_conf 66531678-8899997173004200 No 67 >pfam05202 Flp_C Recombinase Flp protein. Probab=34.05 E-value=31 Score=14.48 Aligned_cols=132 Identities=17% Similarity=0.112 Sum_probs=57.0 Q ss_pred CCCCCCCCCCCCCCCCCCCC-----CEE--E-CCCCCCCCCCCC---CCCC--HHHHHHHHHHHCCCCCCCCCCCCCCCC Q ss_conf 23322222112222233232-----203--3-237853100011---2210--023432211100123446655432111 Q gi|254780882|r 167 GLRISEALSLTPQNIMDDQS-----TLR--I-QGKGDKIRIVPL---LPSV--RKAILEYYDLCPFDLNLNIQLPLFRGI 233 (328) Q Consensus 167 GlR~~El~~L~~~did~~~~-----~i~--v-~gKg~K~R~Vpi---~~~~--~~~l~~yl~~~~~~~~~~~~~~lF~~~ 233 (328) -||-+++-+++.+-+..-.. .|+ | ..|++|+|.|.. ...+ .-+|.+|+.......+...++- .+. T Consensus 53 CcR~sDLkN~DP~TFeiv~nk~lG~ilra~V~eTKTr~~R~IyFfPv~gr~DpllaL~d~l~~~~Pv~Ksrts~~--~s~ 130 (244) T pfam05202 53 CCRHSDLKNADPKTFEIVKNKFLGRILRALVTETKTRKSRFIYFFPVNGRCDPLLALHDYLRETEPVPKSRTSNR--ESN 130 (244) T ss_pred HHCCHHCCCCCCCCEEEECCCHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCCC--CHH T ss_conf 521000145894315762452054577642022556651049997448987646879999874288764434564--115 Q ss_pred CCCCCCCCCHHHHHHHHH-HHC-----CCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCC-----HH-H-H-HHHH Q ss_conf 122111000123567899-976-----8699988054179999999984899889999837888-----78-9-7-9999 Q gi|254780882|r 234 RGKPLNPGVFQRYIRQLR-RYL-----GLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFR-----LS-T-T-QIYT 299 (328) Q Consensus 234 ~g~~ls~~~i~~~~~~~~-~~~-----gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s-----~~-t-T-~~Y~ 299 (328) +--+|-+.++-.-..+.. +.+ +|+-.--.|-=||-.||.|-.++.+-. ...+|..| ++ - - ..|+ T Consensus 131 q~~Qllrdslv~~YdrFl~k~~~e~iF~I~nGPKSHlGRHLM~SyLs~~~l~~~--vs~~GNWsa~~~~~~S~vARs~Y~ 208 (244) T pfam05202 131 QEYQLLRDSLVRSYDRFLAKHAPEPIFAIKNGPKSHLGRHLMASYLSNNELGEW--VSPYGNWSAGDDEIESAVARSKYT 208 (244) T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCEEECCCCCHHHHHHHHHHHHHCCCCCCCE--ECCCCCCCCCCCHHHHHHHHHCCC T ss_conf 678888988888899999737987645147896678878999988530567751--114666243444146566542034 Q ss_pred HHC Q ss_conf 619 Q gi|254780882|r 300 NVN 302 (328) Q Consensus 300 h~~ 302 (328) |.. T Consensus 209 H~~ 211 (244) T pfam05202 209 HGQ 211 (244) T ss_pred CCC T ss_conf 566 No 68 >KOG0440 consensus Probab=31.12 E-value=26 Score=15.03 Aligned_cols=81 Identities=22% Similarity=0.333 Sum_probs=41.8 Q ss_pred CCCCCCCCCCCCCCCCCCC-CCCC--CCCEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC Q ss_conf 1001123322222112222-2332--322033237853100011221002343221110012344665543211112211 Q gi|254780882|r 162 LLYGCGLRISEALSLTPQN-IMDD--QSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPL 238 (328) Q Consensus 162 ll~~TGlR~~El~~L~~~d-id~~--~~~i~v~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g~~l 238 (328) ++|+| ++|.|.-.-.- ...+ ..++|.-.+|.+. .|| .+..++.+..|.+.. -.+.-|||++.|.+. T Consensus 99 ~lYGt---itEfCT~~sCp~Msag~~yeY~W~D~~~kp~-~~s-ApqYId~lmtw~q~~------~dde~iFPtK~g~~F 167 (243) T KOG0440 99 LLYGT---ITEFCTQQSCPHMSAGPNYEYLWADEKGKPV-RVS-APQYIDYLMTWCQNQ------LDDENIFPTKYGNPF 167 (243) T ss_pred HHHHH---HHHHHCCCCCCCCCCCCCCEEEEECCCCCCC-CCC-CHHHHHHHHHHHHHH------CCCCCCCCCCCCCCC T ss_conf 98878---8877074458654678861156100258852-147-158999999999873------453002764357879 Q ss_pred CCCCHHHHHHHHHHHC Q ss_conf 1000123567899976 Q gi|254780882|r 239 NPGVFQRYIRQLRRYL 254 (328) Q Consensus 239 s~~~i~~~~~~~~~~~ 254 (328) - ..+...++++.+++ T Consensus 168 P-~nF~~~vk~Ilr~l 182 (243) T KOG0440 168 P-GNFESVVKKILRRL 182 (243) T ss_pred C-CHHHHHHHHHHHHH T ss_conf 8-00899999999999 No 69 >TIGR01822 2am3keto_CoA 2-amino-3-ketobutyrate coenzyme A ligase; InterPro: IPR011282 This entry represents a narrowly defined clade of animal and bacterial (almost exclusively proteobacterial) 2-amino-3-ketobutyrate--CoA ligase. This enzyme can act in threonine catabolism. The closest homologue from Bacillus subtilis, and sequences like it, may be functionally equivalent but were not included in the model because of difficulty in finding reports of function.; GO: 0008890 glycine C-acetyltransferase activity. Probab=29.65 E-value=37 Score=14.03 Aligned_cols=34 Identities=26% Similarity=0.426 Sum_probs=20.6 Q ss_pred HHHHHHHHHCCCCCC-----CCC---CCCH--HHHHHHHHHCCC Q ss_conf 356789997686999-----880---5417--999999998489 Q gi|254780882|r 245 RYIRQLRRYLGLPLS-----TTA---HTLR--HSFATHLLSNGG 278 (328) Q Consensus 245 ~~~~~~~~~~gi~~~-----~sp---H~lR--HtfAt~ll~~G~ 278 (328) ++|+.-...+|++-+ |.| ++.+ -.||..|++.|+ T Consensus 305 ~~FR~~m~AaGFd~~p~~hpI~pvMlyDA~~Aq~~A~~Ll~~Gi 348 (395) T TIGR01822 305 RYFRERMEAAGFDVKPAEHPIIPVMLYDAKLAQRFAERLLEEGI 348 (395) T ss_pred HHHHHHHHHCCCCCCCCCCCCEEEECCCHHHHHHHHHHHHHCCE T ss_conf 98787534247401789885102321147899999999987792 No 70 >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=29.08 E-value=38 Score=13.97 Aligned_cols=19 Identities=11% Similarity=0.240 Sum_probs=7.2 Q ss_pred HHHHHHHHHHHHHHHHHHH Q ss_conf 9999986121013321123 Q gi|254780882|r 74 FISKRRTQKIGDRSLKRSL 92 (328) Q Consensus 74 ~l~~l~~~~~s~~T~~~~l 92 (328) |+..+.+.|++..+|...+ T Consensus 13 ~a~rl~~~G~~~~~I~~aL 31 (185) T pfam07506 13 FAARLLERGVPRAEIAAAL 31 (185) T ss_pred HHHHHHHCCCCHHHHHHHH T ss_conf 9999998699999999998 No 71 >PRK10046 dpiA two-component response regulator DpiA; Provisional Probab=29.00 E-value=38 Score=13.96 Aligned_cols=44 Identities=18% Similarity=0.188 Sum_probs=25.9 Q ss_pred CCCCCCCCCCCHHHHHHHHHHCC--CCHHHHHHHHCCCCHHHHHHHHH Q ss_conf 86999880541799999999848--99889999837888789799996 Q gi|254780882|r 255 GLPLSTTAHTLRHSFATHLLSNG--GDLRSIQSILGHFRLSTTQIYTN 300 (328) Q Consensus 255 gi~~~~spH~lRHtfAt~ll~~G--~~~~~v~~~lGH~s~~tT~~Y~h 300 (328) .+|+.+++.+|..-. ..+-++| .....|++.+|= |-.|..+|.- T Consensus 154 ~lpKGl~~~Tl~~v~-~~l~~~~~~~ta~eva~~~gi-SrvTaRRYLe 199 (225) T PRK10046 154 ELPTGIDPLTLNAVR-KLFKEPGVQHTAETVAQALTI-SRTTARRYLE 199 (225) T ss_pred CCCCCCCHHHHHHHH-HHHHCCCCCCCHHHHHHHHCC-CHHHHHHHHH T ss_conf 589999989999999-999717998689999998585-1999999999 No 72 >pfam04852 DUF640 Protein of unknown function (DUF640). This family represents a conserved region found in plant proteins including Resistance protein-like protein. Probab=27.57 E-value=40 Score=13.80 Aligned_cols=39 Identities=13% Similarity=0.031 Sum_probs=30.1 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHH Q ss_conf 9999999999985121478878968989999999999998612 Q gi|254780882|r 40 ECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQK 82 (328) Q Consensus 40 ~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~~ 82 (328) ++|+..|..|+..+.+ ...+...+..||.+|+.++..-| T Consensus 25 rrdw~tf~qyL~n~rP----Pl~l~~csg~hvl~FL~~~d~fG 63 (133) T pfam04852 25 RRDWNTFGQYLRNQRP----PLNLSKCSGNHVLDFLRYLDQFG 63 (133) T ss_pred HHHHHHHHHHHHCCCC----CCCHHHCCHHHHHHHHHHHHHCC T ss_conf 5308999999871699----98612068389999999876127 No 73 >TIGR02810 agaZ_gatZ D-tagatose-bisphosphate aldolase, class II, non-catalytic subunit; InterPro: IPR012062 Escherichia coli and other enteric bacteria contain two closely related D-tagatose 1,6-bisphosphate (TagBP)-specific aldolases involved in catabolism of galactitol (genes gatY gatZ) and of N-acetyl-galactosamine and D-galactosamine (genes kbaY, kbaZ, also called agaY, agaZ). The catalytic subunits GatY/KbaY alone are sufficient to show aldolase activity and contain most or all of the residues that have been identified as essential in substrate/product recognition and catalysis for class II aldolases , . However, these aldolases differ from other Class II aldolases (which are homodimeric enzymes) in that they require subunits GatZ/KbaZ for full activity and for good in vivo and in vitro stability. The Z subunits alone do not show any aldolase activity . It should be noted that the previous suggestion of a tagatose 6P-kinase function for AgaZ and other members of this family turned out to be erroneous , .; GO: 0009024 tagatose-6-phosphate kinase activity, 0019402 galactitol metabolic process. Probab=27.20 E-value=39 Score=13.88 Aligned_cols=35 Identities=14% Similarity=0.088 Sum_probs=20.7 Q ss_pred CCCCHHHHHHHHCCCCHHHHHHHHHHCH--------HHHHHHHHHHHHHH Q ss_conf 4899889999837888789799996198--------99999999999981 Q gi|254780882|r 276 NGGDLRSIQSILGHFRLSTTQIYTNVNS--------KNGGDWMMEIYDQT 317 (328) Q Consensus 276 ~G~~~~~v~~~lGH~s~~tT~~Y~h~~~--------~~~~~~l~~~~~~~ 317 (328) .-+|+..|++.|+ .-|..|.. +=..+.++++...| T Consensus 383 ~~iPl~LlSQYLP-------~qy~av~~G~l~p~P~~l~~~~i~~VL~~Y 425 (430) T TIGR02810 383 QPIPLTLLSQYLP-------EQYAAVRAGELAPKPRELILDKIRDVLADY 425 (430) T ss_pred CCCCHHHHHHHHH-------HHHHHHHCCCCCCCHHHHHHHHHHHHHHHH T ss_conf 8896477999858-------999999718888764899999999999999 No 74 >PRK02615 thiamine-phosphate pyrophosphorylase; Provisional Probab=26.38 E-value=42 Score=13.67 Aligned_cols=67 Identities=15% Similarity=0.248 Sum_probs=41.9 Q ss_pred CCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCC----CCCCCCCCHHHHHHHHHHCCCC-HHHHHHHHCCCCHHHHHH Q ss_conf 655432111122111000123567899976869----9988054179999999984899-889999837888789799 Q gi|254780882|r 225 IQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLP----LSTTAHTLRHSFATHLLSNGGD-LRSIQSILGHFRLSTTQI 297 (328) Q Consensus 225 ~~~~lF~~~~g~~ls~~~i~~~~~~~~~~~gi~----~~~spH~lRHtfAt~ll~~G~~-~~~v~~~lGH~s~~tT~~ 297 (328) .-+|+|++..-.-..+.++ ..++.+++.+.+| ..|+++.+ ..++++|++ +-+|+.+|+..++..+-. T Consensus 263 g~Gpvf~T~TK~~~~p~Gl-~~l~~~~~~~~iPvvAIGGI~~~N~-----~~v~~aGa~gvAVisAI~~A~DP~~aa~ 334 (345) T PRK02615 263 GVGPVFPTPTKPGKAPAGL-EYLKYARKEANIPWFAIGGIDKSNI-----SEVLQAGADRVAVVRAIMNAEDPKQATQ 334 (345) T ss_pred EECCEEECCCCCCCCCCCH-HHHHHHHHHCCCCEEEECCCCHHHH-----HHHHHCCCCEEEEEHHHHCCCCHHHHHH T ss_conf 9887742588888887899-9999999837999999999699999-----9999859999998228557999999999 No 75 >PRK00043 thiE thiamine-phosphate pyrophosphorylase; Reviewed Probab=25.75 E-value=44 Score=13.60 Aligned_cols=65 Identities=20% Similarity=0.290 Sum_probs=37.9 Q ss_pred CCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCC----CCCCCCCCHHHHHHHHHHCCCC-HHHHHHHHCCCCHHHH Q ss_conf 55432111122111000123567899976869----9988054179999999984899-8899998378887897 Q gi|254780882|r 226 QLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLP----LSTTAHTLRHSFATHLLSNGGD-LRSIQSILGHFRLSTT 295 (328) Q Consensus 226 ~~~lF~~~~g~~ls~~~i~~~~~~~~~~~gi~----~~~spH~lRHtfAt~ll~~G~~-~~~v~~~lGH~s~~tT 295 (328) -+++|++.......+..=...++.+++...+| ..+++..+ ..+++.|++ +-+++.++++.+++.+ T Consensus 129 ~Gpvf~T~tK~~~~~~~g~~~l~~~~~~~~iPvvAIGGI~~~ni-----~~~~~~Ga~giAvis~I~~a~dp~~a 198 (210) T PRK00043 129 VGPIFPTPTKKDAKPAVGLELLREAREAIDIPIVAIGGITPENA-----AEVLEAGADGVAVVSAITAAEDPAAA 198 (210) T ss_pred ECCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCEEEECCCCHHHH-----HHHHHCCCCEEEEEHHHHCCCCHHHH T ss_conf 74521479888887778999999999847999899808899999-----99998099999970897769999999 No 76 >TIGR02057 PAPS_reductase phosphoadenosine phosphosulfate reductase; InterPro: IPR011800 Requiring thioredoxin as an electron donor, phosphoadenosine phosphosulphate reductase catalyzes the reduction of 3'-phosphoadenylylsulphate (PAPS) to sulphite and phospho-adenosine-phosphate (PAP). Found in enterobacteria, cyanobacteria, and yeast, PAPS reductase is related to a group of plant (IPR004508 from INTERPRO) and bacterial (IPR011798 from INTERPRO) enzymes preferring 5'-adenylylsulphate (APS) over PAPS as a substrate for reduction to sulphite.; GO: 0004604 phosphoadenylyl-sulfate reductase (thioredoxin) activity, 0019344 cysteine biosynthetic process. Probab=25.27 E-value=34 Score=14.24 Aligned_cols=46 Identities=22% Similarity=0.303 Sum_probs=35.3 Q ss_pred CCCCCCCCCCCC---CCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCHHHHHHHHHHH Q ss_conf 001123322222---1122222332322033237853100011221002343221110 Q gi|254780882|r 163 LYGCGLRISEAL---SLTPQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLC 217 (328) Q Consensus 163 l~~TGlR~~El~---~L~~~did~~~~~i~v~gKg~K~R~Vpi~~~~~~~l~~yl~~~ 217 (328) .+-||+|.+-.. +|.+=+||..+|.++| .||-+.-.+.+.+|+... T Consensus 144 Aw~tG~Rr~Q~~~R~nL~v~~~D~~~G~lKv---------~Pl~~W~~~~~~~Y~~~h 192 (239) T TIGR02057 144 AWFTGRRRDQASARANLPVLELDLQNGILKV---------NPLIDWTRKQVYQYLAAH 192 (239) T ss_pred HHHHCCCHHHHCCCCCCCCEEEECCCCCCEE---------CCCCCCCHHHHHHHHHHC T ss_conf 9874255434202236861000014781032---------021026502279999867 No 77 >TIGR01262 maiA maleylacetoacetate isomerase; InterPro: IPR005955 Maleylacetoacetate isomerase is an enzyme of tyrosine and phenylalanine catabolism. It requires glutathione and belongs by homology to the zeta family of glutathione S-transferases. The enzyme (5.2.1.2 from EC) is described as active also on maleylpyruvate.; GO: 0003824 catalytic activity, 0009072 aromatic amino acid family metabolic process, 0005737 cytoplasm. Probab=24.47 E-value=46 Score=13.45 Aligned_cols=37 Identities=27% Similarity=0.462 Sum_probs=21.8 Q ss_pred HHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHC Q ss_conf 35678999768699988054179999999984899889999837 Q gi|254780882|r 245 RYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILG 288 (328) Q Consensus 245 ~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lG 288 (328) ++++.+.++.|++. ..|+.++-+++.+|-. .+=++|+ T Consensus 115 ~Vl~~L~~~~g~~~-----~~~~~W~~~wI~~Gl~--A~E~lL~ 151 (218) T TIGR01262 115 RVLQYLREKLGVDE-----EERRRWYQHWISKGLA--ALEALLQ 151 (218) T ss_pred HHHHHHHHHCCCCH-----HHHHHHHHHHHHHHHH--HHHHHHH T ss_conf 99988865328998-----8888899999998899--9999860 No 78 >pfam09968 DUF2202 Uncharacterized protein domain (DUF2202). This domain, found in various hypothetical archaeal proteins, has no known function. Probab=23.89 E-value=47 Score=13.38 Aligned_cols=16 Identities=6% Similarity=0.158 Sum_probs=8.1 Q ss_pred CCCCCHHHHHHHHHHH Q ss_conf 1111015678776531 Q gi|254780882|r 128 ALNEKQALTLVDNVLL 143 (328) Q Consensus 128 ~lt~~e~~~ll~~~~~ 143 (328) .++..++..+.+.+.. T Consensus 65 ~F~npelQ~LYn~L~~ 80 (162) T pfam09968 65 VFTNPDLQELYNQLVE 80 (162) T ss_pred CCCCHHHHHHHHHHHH T ss_conf 5288779999999999 No 79 >PRK02249 DNA primase large subunit; Validated Probab=22.71 E-value=50 Score=13.23 Aligned_cols=51 Identities=20% Similarity=0.282 Sum_probs=36.7 Q ss_pred CCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCC---CHHHHH Q ss_conf 00123567899976869998805417999999998489988999983788---878979 Q gi|254780882|r 241 GVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHF---RLSTTQ 296 (328) Q Consensus 241 ~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~---s~~tT~ 296 (328) --+...+..+. .| .++ ||.-|=+.||-|+.-|++...|-++...+ +.++|. T Consensus 223 PCmk~~i~~l~--~G--~Nl-~H~~Rf~Lasfl~~iG~~~d~i~~lf~~aPDf~e~~t~ 276 (333) T PRK02249 223 PCMKALLSALQ--AG--ENL-PHTARFAITSFLHNIGMDVDEIVELFRNAPDFDEEITR 276 (333) T ss_pred HHHHHHHHHHH--CC--CCC-CHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCHHHH T ss_conf 07999999986--69--987-71789999999997699889999998419986602467 Done!