Query gi|254780603|ref|YP_003065016.1| tRNA/rRNA methyltransferase protein [Candidatus Liberibacter asiaticus str. psy62] Match_columns 282 No_of_seqs 133 out of 4339 Neff 8.0 Searched_HMMs 39220 Date Sun May 29 23:21:54 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780603.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 COG0566 SpoU rRNA methylases [ 100.0 0 0 412.6 17.5 251 24-282 3-259 (260) 2 PRK11181 23S rRNA (guanosine-2 100.0 0 0 411.4 18.4 232 49-281 3-243 (244) 3 PRK10864 putative methyltransf 100.0 0 0 400.5 9.0 235 45-281 107-347 (348) 4 PRK11081 tRNA guanosine-2'-O-m 100.0 0 0 288.4 9.5 150 130-281 16-166 (229) 5 KOG2506 consensus 100.0 2.8E-45 0 278.4 11.2 251 25-280 103-371 (371) 6 pfam00588 SpoU_methylase SpoU 100.0 8.8E-44 0 270.3 8.7 141 133-274 1-142 (142) 7 KOG0838 consensus 100.0 2.1E-38 5.3E-43 239.5 10.0 217 46-279 40-270 (271) 8 PRK10358 putative tRNA/rRNA me 100.0 5.6E-36 1.4E-40 225.6 9.0 145 135-281 3-149 (157) 9 TIGR00186 rRNA_methyl_3 RNA me 100.0 8.9E-33 2.3E-37 207.2 6.9 231 49-280 3-271 (271) 10 COG0219 CspR Predicted rRNA me 100.0 4E-31 1E-35 197.7 9.0 147 134-281 3-150 (155) 11 TIGR00185 rRNA_methyl_2 RNA me 100.0 2.3E-31 6E-36 199.1 5.6 148 134-281 2-156 (161) 12 KOG0839 consensus 99.9 1.8E-25 4.5E-30 165.4 3.6 148 131-279 1324-1474(1477) 13 PRK10433 putative RNA methyltr 99.9 2E-23 5.2E-28 153.6 10.0 141 134-279 3-158 (228) 14 TIGR00050 rRNA_methyl_1 RNA me 99.9 1.8E-23 4.5E-28 153.9 9.1 145 133-279 4-166 (253) 15 COG0565 LasT rRNA methylase [T 99.9 4.6E-22 1.2E-26 145.8 9.3 141 133-279 4-159 (242) 16 pfam08032 SpoU_sub_bind RNA 2' 98.9 2.5E-09 6.4E-14 72.9 5.5 72 50-123 1-74 (75) 17 COG4080 SpoU rRNA Methylase fa 97.9 7.7E-05 2E-09 47.1 8.5 141 133-279 2-146 (147) 18 pfam09936 DUF2168 Uncharacteri 97.8 5.1E-05 1.3E-09 48.1 5.5 124 146-276 29-182 (185) 19 PRK03958 tRNA 2'-O-methylase; 97.2 0.0013 3.4E-08 40.0 6.9 125 142-277 14-147 (175) 20 COG1303 Uncharacterized protei 96.6 0.0022 5.7E-08 38.7 3.4 119 148-277 21-147 (179) 21 PRK12703 tRNA 2'-O-methylase; 96.0 0.014 3.5E-07 34.2 4.8 124 142-276 13-141 (339) 22 COG4752 Uncharacterized protei 95.5 0.021 5.4E-07 33.2 4.1 50 226-276 133-183 (190) 23 COG1385 Uncharacterized protei 94.7 0.27 6.8E-06 26.8 7.9 138 132-272 77-236 (246) 24 PRK11713 16S rRNA m3U1498 meth 94.5 0.29 7.4E-06 26.7 7.7 138 135-276 78-239 (243) 25 pfam09895 DUF2122 RecB-family 94.4 0.065 1.7E-06 30.4 4.2 83 188-276 21-105 (105) 26 pfam04452 Methyltrans_RNA RNA 93.8 0.21 5.3E-06 27.5 5.9 135 134-273 62-220 (225) 27 PRK02135 hypothetical protein; 93.7 0.052 1.3E-06 31.0 2.7 115 143-280 79-197 (199) 28 pfam01994 Trm56 tRNA ribose 2' 93.3 0.096 2.4E-06 29.4 3.5 81 191-277 9-93 (121) 29 pfam04407 DUF531 Protein of un 91.5 0.28 7.1E-06 26.8 4.0 136 134-273 2-164 (174) 30 pfam04013 DUF358 Protein of un 90.3 0.3 7.7E-06 26.6 3.3 118 143-279 79-197 (199) 31 KOG0838 consensus 90.3 0.078 2E-06 29.9 0.2 53 222-275 133-189 (271) 32 TIGR01362 KDO8P_synth 3-deoxy- 81.6 0.81 2.1E-05 24.1 1.6 56 139-203 200-271 (279) 33 TIGR00046 TIGR00046 conserved 77.5 4.2 0.00011 20.0 4.2 130 132-262 79-240 (258) 34 PRK04171 ribosome biogenesis p 74.1 6.5 0.00017 18.9 4.6 80 195-281 137-219 (221) 35 pfam02590 SPOUT_MTase Predicte 72.3 7.2 0.00018 18.7 5.0 73 199-279 61-145 (155) 36 COG1901 Uncharacterized conser 68.7 4.1 0.0001 20.1 2.4 114 143-280 79-196 (197) 37 PRK00103 SPOUT methyltransfera 63.6 11 0.00028 17.6 4.4 73 200-279 62-144 (156) 38 pfam04705 TSNR_N Thiostrepton- 55.5 15 0.00039 16.8 7.8 94 24-120 9-103 (115) 39 PRK13398 3-deoxy-7-phosphohept 54.0 5.6 0.00014 19.3 1.0 32 136-167 199-233 (266) 40 TIGR01456 CECR5 HAD-superfamil 53.3 3.8 9.7E-05 20.2 0.0 16 150-165 97-112 (325) 41 KOG3925 consensus 52.8 4.4 0.00011 19.9 0.3 30 206-236 277-311 (371) 42 COG3426 Butyrate kinase [Energ 51.0 7.6 0.00019 18.5 1.2 51 140-190 102-154 (358) 43 COG2106 Uncharacterized conser 47.9 12 0.0003 17.4 1.8 63 195-258 175-245 (272) 44 pfam02598 DUF171 Uncharacteriz 43.4 13 0.00033 17.2 1.5 66 189-255 180-261 (283) 45 COG3222 Uncharacterized protei 43.4 12 0.0003 17.4 1.3 77 146-230 88-167 (211) 46 COG1419 FlhF Flagellar GTP-bin 43.2 24 0.00061 15.7 3.0 120 132-258 202-342 (407) 47 pfam09837 DUF2064 Uncharacteri 40.4 27 0.00068 15.4 2.9 77 141-225 39-119 (121) 48 PRK11561 isovaleryl CoA dehydr 38.9 17 0.00042 16.6 1.4 25 218-242 266-290 (538) 49 TIGR02894 DNA_bind_RsfA transc 38.6 6.5 0.00017 18.9 -0.7 28 135-178 30-57 (163) 50 pfam07047 OPA3 Optic atrophy 3 37.7 25 0.00063 15.6 2.2 22 261-282 81-102 (134) 51 KOG2882 consensus 37.7 14 0.00035 17.0 0.9 28 47-76 36-63 (306) 52 COG1772 Uncharacterized protei 37.4 30 0.00076 15.1 3.3 135 134-272 2-163 (178) 53 COG2242 CobL Precorrin-6B meth 35.8 32 0.00081 15.0 2.8 40 131-172 57-96 (187) 54 KOG1618 consensus 35.6 24 0.00062 15.6 1.9 31 46-76 42-80 (389) 55 TIGR01855 IMP_synth_hisH imida 34.2 32 0.00082 14.9 2.3 31 135-167 1-35 (211) 56 pfam02784 Orn_Arg_deC_N Pyrido 33.7 32 0.00081 15.0 2.2 21 195-215 140-160 (245) 57 cd06840 PLPDE_III_Bif_AspK_Dap 33.4 35 0.00088 14.7 4.2 13 51-63 63-75 (368) 58 pfam05341 DUF708 Protein of un 33.3 35 0.00089 14.7 2.4 54 218-274 46-99 (105) 59 TIGR01245 trpD anthranilate ph 32.6 27 0.00068 15.4 1.7 39 135-173 184-224 (331) 60 TIGR01135 glmS glucosamine--fr 31.8 37 0.00094 14.6 5.2 76 203-281 527-612 (628) 61 TIGR01055 parE_Gneg DNA topois 30.6 39 0.00099 14.5 5.0 120 44-179 423-543 (647) 62 TIGR03565 alk_sulf_monoox alka 29.3 41 0.001 14.3 3.3 11 108-118 144-154 (346) 63 pfam00851 Peptidase_C6 Helper 28.0 34 0.00087 14.8 1.6 28 212-239 291-318 (453) 64 PRK13397 3-deoxy-7-phosphohept 27.9 40 0.001 14.4 1.9 31 143-173 134-164 (250) 65 TIGR01678 FAD_lactone_ox sugar 26.6 42 0.0011 14.3 1.9 20 219-238 217-236 (505) 66 PRK11052 malQ 4-alpha-glucanot 25.8 47 0.0012 14.0 2.7 39 140-178 160-207 (694) 67 cd06843 PLPDE_III_PvsE_like Ty 25.3 48 0.0012 13.9 4.7 55 49-105 52-107 (377) 68 TIGR00064 ftsY signal recognit 24.8 43 0.0011 14.2 1.6 78 130-216 79-175 (284) 69 COG0187 GyrB Type IIA topoisom 24.4 50 0.0013 13.8 3.4 33 41-73 414-446 (635) 70 PRK11440 hypothetical protein; 23.4 53 0.0013 13.7 2.9 65 134-200 122-186 (188) 71 TIGR02303 HpaG-C-term 4-hydrox 23.3 25 0.00064 15.6 0.2 14 134-147 159-173 (249) 72 TIGR02924 ICDH_alpha isocitrat 22.8 33 0.00083 14.9 0.7 95 145-244 291-394 (481) 73 TIGR01607 PST-A Plasmodium sub 21.1 29 0.00075 15.2 0.2 21 196-216 64-84 (379) 74 TIGR00750 lao LAO/AO transport 21.1 52 0.0013 13.7 1.4 114 145-259 123-275 (333) 75 TIGR02080 O_succ_thio_ly O-suc 20.9 27 0.0007 15.3 -0.0 37 235-272 302-341 (383) 76 TIGR01452 PGP_euk phosphoglyco 20.8 43 0.0011 14.2 0.9 32 47-80 16-47 (288) 77 pfam07075 DUF1343 Protein of u 20.5 61 0.0015 13.4 2.3 133 52-205 13-164 (359) 78 PRK13172 consensus 20.5 32 0.00081 15.0 0.2 11 157-167 125-135 (213) 79 PRK10126 tyrosine phosphatase; 20.5 19 0.00049 16.2 -0.9 13 147-159 10-22 (147) 80 pfam03308 ArgK ArgK protein. T 20.3 61 0.0016 13.3 3.1 115 144-263 107-241 (267) No 1 >COG0566 SpoU rRNA methylases [Translation, ribosomal structure and biogenesis] Probab=100.00 E-value=0 Score=412.63 Aligned_cols=251 Identities=32% Similarity=0.478 Sum_probs=221.6 Q ss_pred CCCCHHHHHHHHHHHCCCCCCCCCEEEEEEHHHHHHHHHCCCEEEEEEEECCCCCCCCCHHH--HHHCCCCEEEECHHHH Q ss_conf 22376567776543112211128819998578899999789818999997378433543455--4326996999768998 Q gi|254780603|r 24 RRNHRDYKKMQSFNQKSRHTSQPENLFLYGVHTVSAALNNPSRKIFQLLATKNALARLDWDA--NLPHPFPVKTVPPQTI 101 (282) Q Consensus 24 ~~~n~~~k~~~~l~~k~k~R~~~~~~iIeG~~~V~eaL~~~~~~i~~i~~te~~~~~~~~~~--~l~~~~~I~~v~~~~l 101 (282) ++.|+..+.+.++ |.+.+.|++||.|+|.++|.+++ .+..+|++++...+..+.. ....+++++.++.+.+ T Consensus 3 s~~n~~~~~~~~~------r~~~~~~~~~G~~~v~~al~~~~-~i~~i~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~l 75 (260) T COG0566 3 SPANPRVKALKKL------RGRAGEFLIEGEHAVLEALASGP-KIVRILVTEGRLPRFEELLALAAAKGIPVYVVSEAIL 75 (260) T ss_pred CCHHHHHHHHHHH------HCCCCCEEEECHHHHHHHHHCCC-CCEEEEEECCCCHHHHHHHHHHHHCCCCEEEECHHHH T ss_conf 7214566899986------30577089971899999996797-7069998434321378999988765992899688999 Q ss_pred HHHHCCCCCCCCCCEEEECCCCCCHHHCC---CCCEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHH Q ss_conf 77524777777442024115555401126---650688723432068899999998642001100136863200000134 Q gi|254780603|r 102 DKIVGKEAVHQGLALETAPLLSPTLDAVR---NSQLLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAK 178 (282) Q Consensus 102 ~~i~~~~~~hqGi~a~~~~~~~~~l~~~~---~~~~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~r 178 (282) +++++.. +|||+++.+.+......+.+. .++++|+||+|+||+|+|+|+|||+|||+++||++++++|+++++++| T Consensus 76 ~~~~~~~-~hqGi~a~~~~~~~~~~~~~~~~~~~~~~lvLd~V~DP~NlGaIiRtA~a~Gv~~Vi~~~~~~~~~~~~v~r 154 (260) T COG0566 76 DKLSGTE-NHQGIVAVVKKRRYPLLDDLLDAEAQPLLLVLDGVTDPHNLGAIIRTADAFGVDGVILPKRRADPLNPKVIR 154 (260) T ss_pred HHHHCCC-CCCEEEEEECCCCCCCHHHHHHCCCCCEEEEEECCCCCCCHHHHHHHHHHHCCCEEEECCCCCCCCCHHHEE T ss_conf 9875578-864057896355556524442024588699991787887124888759873898899889866774534325 Q ss_pred HHHHHHHHHCCCCCCC-CCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCEEEEECCCCCCCCHHHHHHCCCEEEECCC Q ss_conf 4433332110122232-211222222210000000123332211223689889997586789877999858939992789 Q gi|254780603|r 179 SASGALEHIPYIRISN-LTDALQKMHSWGFQTIGLSSDSKKPLEQEIKNDKIALILGAEGKGLRPKTQETATSMAHLHMP 257 (282) Q Consensus 179 as~Ga~~~l~~~~~~~-~~~~l~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~ 257 (282) +|+|++|++|++++.| ...+++.+++.|||++|++.++..++++.++++|.+||||||++|||+++++.||.+|+|||. T Consensus 155 ~s~Ga~~~vp~~~~~n~~~~~~~~~~~~G~~v~~t~~~~~~~~~~~~~~~~~aLvlG~Eg~Gls~~~~~~~D~~v~IPm~ 234 (260) T COG0566 155 ASAGAAFHVPVIRVTNLARTLLELLKEAGFWVVATSLDGEVDLYETDLPKKTALVLGNEGEGLSRLLLEHADQLVRIPMA 234 (260) T ss_pred ECCCCCCCCCEEEEECCHHHHHHHHHHCCCEEEEECCCCCCCHHHCCCCCCEEEEECCCCCCCCHHHHHHCCEEEEECCC T ss_conf 41771005735888077999999999769489998588874311026778779998789888589999517847993589 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHCC Q ss_conf 6874378999999999999876149 Q gi|254780603|r 258 GIIKALNVSNAAAVALYITQNHFAK 282 (282) Q Consensus 258 ~~~~SLNvs~a~ai~l~~~~~~~~~ 282 (282) |.++|||||||+||+|||..||+.. T Consensus 235 G~v~SLNVsvAagI~Lye~~rq~~~ 259 (260) T COG0566 235 GKVESLNVSVAAGILLYEARRQRRA 259 (260) T ss_pred CCCCCHHHHHHHHHHHHHHHHHHCC T ss_conf 9865108999999999999986445 No 2 >PRK11181 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional Probab=100.00 E-value=0 Score=411.44 Aligned_cols=232 Identities=29% Similarity=0.439 Sum_probs=209.3 Q ss_pred EEEEEHHHHHHHHHCCCEEEEEEEECCCCCCC-CCHH--HHHHCCCCEEEECHHHHHHHHCCCCCCCCCCEEEECCCCCC Q ss_conf 99985788999997898189999973784335-4345--54326996999768998775247777774420241155554 Q gi|254780603|r 49 LFLYGVHTVSAALNNPSRKIFQLLATKNALAR-LDWD--ANLPHPFPVKTVPPQTIDKIVGKEAVHQGLALETAPLLSPT 125 (282) Q Consensus 49 ~iIeG~~~V~eaL~~~~~~i~~i~~te~~~~~-~~~~--~~l~~~~~I~~v~~~~l~~i~~~~~~hqGi~a~~~~~~~~~ 125 (282) .+|||.|+|+|+|+++++.+..+|+.++...+ +... .....++++..++++.|++++.. .+|||+++.+.|..... T Consensus 3 e~IyG~haV~eaL~~~~~~i~~l~v~~~~~~~~~~~i~~~a~~~~I~v~~v~~~~l~~l~~~-~~HQGVva~v~~~~~~~ 81 (244) T PRK11181 3 EMIYGIHAVQALLERAPERFIEVFVLKGREDKRLLPLINELESQGVVIQLANRQTLDEKAEG-AVHQGIIARVKPAKQLN 81 (244) T ss_pred CEEEEHHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCEEEECHHHHHHHCCC-CCCCEEEEEEECCCCCC T ss_conf 88987999999983897646899985798776899999999976997799689999875168-87853799983245478 Q ss_pred HHHC------CCCCEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCC Q ss_conf 0112------6650688723432068899999998642001100136863200000134443333211012223221122 Q gi|254780603|r 126 LDAV------RNSQLLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYIRISNLTDAL 199 (282) Q Consensus 126 l~~~------~~~~~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l 199 (282) ..++ .+++++++||+||||+|+|+|+|||+|||+++|+++++++++++++++|+|+||.|++|++++.|+.+++ T Consensus 82 ~~~l~~~l~~~~~~lil~LD~I~DP~NlGaIiRsA~afGv~~vil~~~~~~~~~~~v~k~S~Ga~~~~pi~~~~nl~~~l 161 (244) T PRK11181 82 ENDLDDLLASTEQPFLLILDGVTDPHNLGACLRSADAAGVHAVIVPKDRSAQLTATAKKVACGAAETVPLIRVTNLARTM 161 (244) T ss_pred HHHHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCEEEECCCCCCCCCHHHHHHHHCHHHCCCEEEECCHHHHH T ss_conf 87899998357898799981887873899999999981998999789977854258888741423218816958999999 Q ss_pred CCCCCCCCHHHHCCCCCCCCCCCCCCCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 22222100000001233322112236898899975867898779998589399927896874378999999999999876 Q gi|254780603|r 200 QKMHSWGFQTIGLSSDSKKPLEQEIKNDKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVSNAAAVALYITQNH 279 (282) Q Consensus 200 ~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs~a~ai~l~~~~~~ 279 (282) +.++++|||+||++.+++.++++.+++.|.+||||||++||++.+++.||+.|+|||.|.+||||||||+||+|||+.|| T Consensus 162 ~~lk~~g~~i~g~~~~~~~~~~~~~~~~~~alvlGsE~~Gl~~~~~~~~d~~v~Ip~~g~~~SLNVsvAa~I~lyE~~RQ 241 (244) T PRK11181 162 RMLQEKNVWIVGTAGEADHTLYQSKLTGPLALVMGAEGEGMRRLTREHCDELISIPMAGSVSSLNVSVATGICLFEAVRQ 241 (244) T ss_pred HHHHHCCEEEEEECCCCCCCCCHHCCCCCEEEEECCCCCCCCHHHHHHCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHC T ss_conf 99886596999524666766410105787699987776665899997599899807999985587999999999999865 Q ss_pred HC Q ss_conf 14 Q gi|254780603|r 280 FA 281 (282) Q Consensus 280 ~~ 281 (282) |. T Consensus 242 R~ 243 (244) T PRK11181 242 RL 243 (244) T ss_pred CC T ss_conf 05 No 3 >PRK10864 putative methyltransferase; Provisional Probab=100.00 E-value=0 Score=400.49 Aligned_cols=235 Identities=23% Similarity=0.320 Sum_probs=214.2 Q ss_pred CCCEEEEEEHHHHHHHHHCCCEEEEEEEECCCCCCCCCHHH--HHHCCCCEEEECHHHHHHHHCCCCCCCCCCEEEECCC Q ss_conf 28819998578899999789818999997378433543455--4326996999768998775247777774420241155 Q gi|254780603|r 45 QPENLFLYGVHTVSAALNNPSRKIFQLLATKNALARLDWDA--NLPHPFPVKTVPPQTIDKIVGKEAVHQGLALETAPLL 122 (282) Q Consensus 45 ~~~~~iIeG~~~V~eaL~~~~~~i~~i~~te~~~~~~~~~~--~l~~~~~I~~v~~~~l~~i~~~~~~hqGi~a~~~~~~ 122 (282) ..+...|||.|+|.+++.+.++.+..+|++++...++...+ ...++..+..|+..+|+++++++ .||||++.+.+.. T Consensus 107 r~ee~~vyG~nA~~A~~~~rp~ai~Riw~t~e~~~r~~~~l~~~~a~~~~~~~V~~~eL~~~tgt~-hHqGi~l~v~~~~ 185 (348) T PRK10864 107 RAEETRVYGENACQALFQSRPDAIVRAWFIQSVTPRFKEALRWMAANRKAYHVVDEAELAKASGTE-HHGGVCFLIKKRN 185 (348) T ss_pred CHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEECHHHHHHHHCCC-CCCEEEEEECCCC T ss_conf 103431022789999997292989999988876488999999999769759984899998874888-7340689976778 Q ss_pred CCCHHHC----CCCCEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC Q ss_conf 5540112----665068872343206889999999864200110013686320000013444333321101222322112 Q gi|254780603|r 123 SPTLDAV----RNSQLLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYIRISNLTDA 198 (282) Q Consensus 123 ~~~l~~~----~~~~~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~ 198 (282) ...++.+ ..++++|+||+|+||+|||+|+|||+|||+++||+++. ..++++.++|+|+|++|++|++++.|+.++ T Consensus 186 ~~~l~~~l~~~~~~~~lL~LDgV~DP~NlGAIiRSAaafGv~gVIl~~~-~~~~s~~avr~SaGa~e~vpv~~v~nl~~a 264 (348) T PRK10864 186 GTDVQQWLAQAGAQDCVLALEDVGNPHNLGGIMRSCAHFGVKGVVVQDA-ALLESGAAIRTAEGGAEHVQPITGDSIVDV 264 (348) T ss_pred CCCHHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHHCCCEEEECCC-CCCCCHHHHHHHCCHHCCCCEEEECCHHHH T ss_conf 8799999960799985999789779715889999999858988997999-877437889663322200635997789999 Q ss_pred CCCCCCCCCHHHHCCCCCCCCCCCCCCCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHHHHH Q ss_conf 22222210000000123332211223689889997586789877999858939992789687437899999999999987 Q gi|254780603|r 199 LQKMHSWGFQTIGLSSDSKKPLEQEIKNDKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVSNAAAVALYITQN 278 (282) Q Consensus 199 l~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs~a~ai~l~~~~~ 278 (282) |+.|+++|||+|+++.++..++++.+++.+++||||+|++||++.+++.||+.|+|||.+.+||||||||+||+|||..| T Consensus 265 L~~Lk~aG~~Ivg~s~~~~~~l~~~~l~~~~vLVlGsEg~GLs~~v~~~cD~~V~IPm~g~veSLNVSVAagIlLyE~~R 344 (348) T PRK10864 265 LDDFRQAGYTIVTTSSHKGKPLFKAELPAKMVLVLGQEYDGLSDAARSPGDLSVKIDGTGNVESLNVSVATGVLLAEWWR 344 (348) T ss_pred HHHHHHCCCEEEEECCCCCCCHHHCCCCCCEEEEECCCCCCCCHHHHHHCCEEEECCCCCCCCCHHHHHHHHHHHHHHHH T ss_conf 99999889689985477886475636789889998998855069999758889982799998578899999999999987 Q ss_pred HHC Q ss_conf 614 Q gi|254780603|r 279 HFA 281 (282) Q Consensus 279 ~~~ 281 (282) |+. T Consensus 345 Q~~ 347 (348) T PRK10864 345 QNK 347 (348) T ss_pred HHC T ss_conf 316 No 4 >PRK11081 tRNA guanosine-2'-O-methyltransferase; Provisional Probab=100.00 E-value=0 Score=288.37 Aligned_cols=150 Identities=23% Similarity=0.337 Sum_probs=135.5 Q ss_pred CCCCEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHH Q ss_conf 66506887234320688999999986420011001368632000001344433332110122232211222222210000 Q gi|254780603|r 130 RNSQLLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYIRISNLTDALQKMHSWGFQT 209 (282) Q Consensus 130 ~~~~~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~~~~~i 209 (282) ..+.++|+||+|+||+|+|+|+|||+|||+++|.+.....+. ....++|+|+.+++++..+.++.+++..||+.||++ T Consensus 16 Rq~dL~vvLD~V~dP~NlGAIiRTadA~Gv~~V~~v~~~~~~--~~~~~ta~Gs~~wv~v~~~~~i~~~i~~Lk~~G~~I 93 (229) T PRK11081 16 RQPDLTVCLEQVHKPHNVSAIIRTADAVGVHEVHAVWPGSRM--RTMGSTAAGSNSWVQVKTHRTIGDAVAHLKAQGMQI 93 (229) T ss_pred CCCCEEEEECCCCCCCHHHHHHHHHHHHCCCEEEEECCCCCH--HHHHHHHHHHHCEEEEEEECCHHHHHHHHHHCCCEE T ss_conf 589869997688998509999999998389746896787520--111144303440045578478999999999749989 Q ss_pred HHCCCC-CCCCCCCCCCCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHC Q ss_conf 000123-332211223689889997586789877999858939992789687437899999999999987614 Q gi|254780603|r 210 IGLSSD-SKKPLEQEIKNDKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVSNAAAVALYITQNHFA 281 (282) Q Consensus 210 ~~~~~~-~~~~~~~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs~a~ai~l~~~~~~~~ 281 (282) ++++.. .+.++.++++++|++||||||++|||+++++.||+.|.|||.|.+|||||||||||+|||++|||. T Consensus 94 ~at~l~~~avd~~~~d~t~ptalVlGnE~~GiS~~~~~~aD~~I~IPM~G~veSLNVSVAaaIiLyEa~RQR~ 166 (229) T PRK11081 94 LATHLSDKAVDFREIDYTRPTAILMGQEKTGISQEALALADQDIIIPMIGMVQSLNVSVASALILYEAQRQRQ 166 (229) T ss_pred EEEECCCCCCCHHHHCCCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCCCCHHHHHHHHHHHHHHHHH T ss_conf 9993688864076704568769998587777599999828957996899998862599999999999999898 No 5 >KOG2506 consensus Probab=100.00 E-value=2.8e-45 Score=278.37 Aligned_cols=251 Identities=19% Similarity=0.268 Sum_probs=187.6 Q ss_pred CCCHHHHHHHHHHHCCCCCCCCCEEEEEEHHHHHHHHHCCCEEEEEEEECCCCCCCCCHHHHHHCCCCEEEECHHHHHHH Q ss_conf 23765677765431122111288199985788999997898189999973784335434554326996999768998775 Q gi|254780603|r 25 RNHRDYKKMQSFNQKSRHTSQPENLFLYGVHTVSAALNNPSRKIFQLLATKNALARLDWDANLPHPFPVKTVPPQTIDKI 104 (282) Q Consensus 25 ~~n~~~k~~~~l~~k~k~R~~~~~~iIeG~~~V~eaL~~~~~~i~~i~~te~~~~~~~~~~~l~~~~~I~~v~~~~l~~i 104 (282) -..+.+-........+++|.++...+.||+.++.++|+.+-..-..+|-+.+.......+. ..++.|+.|....+..+ T Consensus 103 lgd~~fs~~lt~v~srsf~~kqv~ii~egRrliqdaLk~g~~~ev~~Fs~~~qla~~p~e~--e~g~~i~kVks~d~K~w 180 (371) T KOG2506 103 LGDRRFSIVLTIVKSRSFREKQVRIISEGRRLIQDALKGGVHREVCMFSTNKQLATTPIEC--EAGIRIVKVKSLDMKKW 180 (371) T ss_pred CCCCCHHHHHEEEECCCCHHHCCCCCCCCHHHHHHHHHCCCCCEEEEEECCCCCCCCCHHH--HCCEEEEECCHHHHHHH T ss_conf 3763022220011014303322532223223688886246431378820444355568445--33704884238888887 Q ss_pred HCCCCCCCCCCEE-EECCCC-----CCHHH---CCCCCEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHH Q ss_conf 2477777744202-411555-----54011---26650688723432068899999998642001100136863200000 Q gi|254780603|r 105 VGKEAVHQGLALE-TAPLLS-----PTLDA---VRNSQLLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAV 175 (282) Q Consensus 105 ~~~~~~hqGi~a~-~~~~~~-----~~l~~---~~~~~~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~ 175 (282) ++-. +++|+.+- ..|... ...+. ...-++.+|||+|+||||||||+|||+||+|+++++.++|||||++| T Consensus 181 SsLv-SP~svmaIf~~P~d~hl~k~~a~~q~~~s~~lp~~lvcdnirdpgnlgti~rsaaa~~cs~v~lt~gccdpwe~k 259 (371) T KOG2506 181 SSLV-SPESVMAIFLMPIDLHLDKDIATDQNKWSPSLPRVLVCDNIRDPGNLGTIVRSAAAFNCSGVFLTPGCCDPWEDK 259 (371) T ss_pred HCCC-CCCCHHHHCCCCCHHCHHHHHHHHHHCCCCCCCEEEEECCCCCCCCHHHHHHHHHHCCCCCEEECCCCCCCCCHH T ss_conf 5156-871043321585000103537999860388887478853677885067899987507876136657767854246 Q ss_pred HHHHHHHHHHHHCCCCCCCCCCC---CCCCCCCCCHHHHCC-CCCCCC---CC--CCCCCCCEEEEECCCCCCCCHHHHH Q ss_conf 13444333321101222322112---222222100000001-233322---11--2236898899975867898779998 Q gi|254780603|r 176 LAKSASGALEHIPYIRISNLTDA---LQKMHSWGFQTIGLS-SDSKKP---LE--QEIKNDKIALILGAEGKGLRPKTQE 246 (282) Q Consensus 176 ~~ras~Ga~~~l~~~~~~~~~~~---l~~~~~~~~~i~~~~-~~~~~~---~~--~~~~~~~~~lv~G~E~~Gl~~~~~~ 246 (282) ++|+++||+|++||... +|+.. +.......+..+..+ +...++ +. .-....+.|||+|+|++|+|++-.+ T Consensus 260 alrag~ga~fr~pi~~~-~w~~l~l~~pp~~ad~c~~~~a~t~qr~~~~~k~~e~ad~~~ap~~liigge~~gvseea~~ 338 (371) T KOG2506 260 ALRAGRGASFRLPIVSG-NWNHLKLLEPPFQADLCAGHPATTTQRLKPVSKLVEFADSLAAPLCLIIGGEGNGVSEEARK 338 (371) T ss_pred HHHCCCCCCEECCEECC-CHHHHHCCCCHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHCCCCEEEEECCCCCCCCHHHHH T ss_conf 66435775066244568-65441213886677650476476665523203566777643676179974676774799998 Q ss_pred HCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 5893999278968743789999999999998761 Q gi|254780603|r 247 TATSMAHLHMPGIIKALNVSNAAAVALYITQNHF 280 (282) Q Consensus 247 ~~d~~v~Ip~~~~~~SLNvs~a~ai~l~~~~~~~ 280 (282) .| ..+.|||.+++||||||+|++|+|||.+|++ T Consensus 339 ~~-~lvgip~a~g~dslnva~a~~illfel~r~l 371 (371) T KOG2506 339 VC-VLVGIPMAGGFDSLNVAVAGGILLFELQRLL 371 (371) T ss_pred HH-HHCCCCCCCCCCHHHHHHHHHHHHHHHHHCC T ss_conf 99-9728764477213456777779998775139 No 6 >pfam00588 SpoU_methylase SpoU rRNA Methylase family. This family of proteins probably use S-AdoMet. Probab=100.00 E-value=8.8e-44 Score=270.26 Aligned_cols=141 Identities=37% Similarity=0.593 Sum_probs=134.6 Q ss_pred CEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCC-CCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHH Q ss_conf 0688723432068899999998642001100136-863200000134443333211012223221122222221000000 Q gi|254780603|r 133 QLLMVLDHVNDPHNIGAILRSAVAFSCDGIITTK-RYSPSESAVLAKSASGALEHIPYIRISNLTDALQKMHSWGFQTIG 211 (282) Q Consensus 133 ~~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~-~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~~~~~i~~ 211 (282) |++|+||+++||+|+|+|+|||++||++.|++.+ .+++++++++.|+|+|+++++|+.++.|+.++++.+++.|+++++ T Consensus 1 p~~vvL~~i~~p~NlG~i~Rta~~fG~~~v~l~~~~~~~~~~~~~~r~s~ga~~~i~~~~~~~~~~~~~~~~~~~~~i~~ 80 (142) T pfam00588 1 PLIVVLDEPQDPGNLGAIARTAAAFGADGLILVEPRCADLYNPKAIRASAGALFHLPLVIVDNLEEALKDLKEAGYWIIA 80 (142) T ss_pred CEEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCEEECCHHHHHHHHHHCCCEEEC T ss_conf 98999957988776999999999839996435578767977789999976775237832843399999998874950111 Q ss_pred CCCCCCCCCCCCCCCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHH Q ss_conf 012333221122368988999758678987799985893999278968743789999999999 Q gi|254780603|r 212 LSSDSKKPLEQEIKNDKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVSNAAAVALY 274 (282) Q Consensus 212 ~~~~~~~~~~~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs~a~ai~l~ 274 (282) ++..+ +++.+++++++.+||||+|++|||+++++.||+.|+|||.+.++|||||+|+||+|| T Consensus 81 ~~~~~-~~~~~~~~~~~~~lv~G~E~~Gls~~~l~~~d~~v~IP~~g~~~SLNvs~A~aI~ly 142 (142) T pfam00588 81 TSLKG-KPLYEIDFPKKVALVFGNEGTGLSNEVLELCDRLVRIPMSGEVESLNVAVAAAIILY 142 (142) T ss_pred CCCCC-CCHHHHCCCCCEEEEECCCCCCCCHHHHHHCCEEEEECCCCCCCCHHHHHHHHHHHC T ss_conf 34467-487781468872899778778989999986997999749889963549999999969 No 7 >KOG0838 consensus Probab=100.00 E-value=2.1e-38 Score=239.47 Aligned_cols=217 Identities=32% Similarity=0.441 Sum_probs=186.4 Q ss_pred CCEEEEEEHHHHHHHHHCCCEEEEEEEECCCCCCCC-CHHHHHHCCCCEEEECHHHHHHHHCCCCCCCCCCEEEECCCCC Q ss_conf 881999857889999978981899999737843354-3455432699699976899877524777777442024115555 Q gi|254780603|r 46 PENLFLYGVHTVSAALNNPSRKIFQLLATKNALARL-DWDANLPHPFPVKTVPPQTIDKIVGKEAVHQGLALETAPLLSP 124 (282) Q Consensus 46 ~~~~iIeG~~~V~eaL~~~~~~i~~i~~te~~~~~~-~~~~~l~~~~~I~~v~~~~l~~i~~~~~~hqGi~a~~~~~~~~ 124 (282) .+...++|.++|.++|.++.+.+...|+.....-.- .....+.+ .+..+++..|+.++... .|||+++... T Consensus 40 ~~~e~~~G~~sv~~al~~~kR~~~~~~~~~~~~~~~~e~~~v~~~--~~~~~s~h~L~~~t~~r-~h~g~~leas----- 111 (271) T KOG0838 40 LGGESVFGTHSVLAALSNGKRDCRGLLLQSATDFRSTEFELVLRR--DIEAVSKHDLNSLTDFR-PHNGILLEAS----- 111 (271) T ss_pred CCCCEEECHHHHHHHHHCCCCCCEEEEECCCCCCCCCEEEEHHHH--HHHCCCHHHHHHHHHHC-CCCCEEEEEE----- T ss_conf 653112201566888753665412555201455576413313332--43305945677887631-2232687657----- Q ss_pred CHHHCCCCCEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC Q ss_conf 40112665068872343206889999999864200110013686320000013444333321101222322112222222 Q gi|254780603|r 125 TLDAVRNSQLLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYIRISNLTDALQKMHS 204 (282) Q Consensus 125 ~l~~~~~~~~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~ 204 (282) ++++||++.||+|+|+|+|+|++||++++.+......+.++.+.++|+||.+++||.++.+..+|+...++ T Consensus 112 ---------l~vylde~tDp~n~gaI~rsA~~lg~~~v~lv~~n~s~lS~~vskss~gale~l~I~q~~~~~efl~vsva 182 (271) T KOG0838 112 ---------LCVYLDEVTDPQNIGAIIRSAYFLGADGVLLVKGNSSPLSPVVSKSSAGALEVLPIRQVDNPLEFLNVSVA 182 (271) T ss_pred ---------EEEECCCCCCCCCHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHCHHHEEEHHHCCCHHHHHHHHHH T ss_conf ---------77640575687506778776887467715897336887864677765021416638773888999899986 Q ss_pred CCCHHHHCCCCC-------CCCCCCCCCCCCEEEEECCCCCCCCHHHHHHCCCEEEECCC------CCCCHHHHHHHHHH Q ss_conf 100000001233-------32211223689889997586789877999858939992789------68743789999999 Q gi|254780603|r 205 WGFQTIGLSSDS-------KKPLEQEIKNDKIALILGAEGKGLRPKTQETATSMAHLHMP------GIIKALNVSNAAAV 271 (282) Q Consensus 205 ~~~~i~~~~~~~-------~~~~~~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~------~~~~SLNvs~a~ai 271 (282) +|++++++..-. ...+...++..|+++|+|||+.|+++.+++.||..++||++ +.++|||||+|+++ T Consensus 183 aG~~l~~t~~~~~~~~~~~~~~l~~~~~~~Pv~lv~Gneg~Gi~~~vl~~~d~~~si~~n~~~~d~~~v~SlNvSvaa~l 262 (271) T KOG0838 183 AGIRLHGTCSWAPASKTISAVSLKFIDPEEPVALVLGNEGAGIRPGVLELCDLRVSIPGNGFEKDNGAVDSLNVSVAAGL 262 (271) T ss_pred CCEEEEEEECCCCCCCCCCCHHHHHCCCCCCEEEEECCCCCCCCHHHHHCCCEEEECCCCCCCCCCCCEEECCCHHHHHH T ss_conf 75589996147677664030244301778974898546555447113424562675378762467763121110478889 Q ss_pred HHHHHHHH Q ss_conf 99999876 Q gi|254780603|r 272 ALYITQNH 279 (282) Q Consensus 272 ~l~~~~~~ 279 (282) ++|++..+ T Consensus 263 l~~~~~~~ 270 (271) T KOG0838 263 LLYHFLNE 270 (271) T ss_pred HHHHHHHC T ss_conf 88888506 No 8 >PRK10358 putative tRNA/rRNA methyltransferase YibK; Provisional Probab=100.00 E-value=5.6e-36 Score=225.56 Aligned_cols=145 Identities=19% Similarity=0.185 Sum_probs=130.1 Q ss_pred EEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCC Q ss_conf 88723432068899999998642001100136863200000134443333211012223221122222221000000012 Q gi|254780603|r 135 LMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYIRISNLTDALQKMHSWGFQTIGLSS 214 (282) Q Consensus 135 ~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~~~~~i~~~~~ 214 (282) -|||.+++.|+|+|+|+|+|++||++.+++.+.+++..++++.||++++|+++.+....++.+|++..+. -+++.++. T Consensus 3 ~IVL~~P~iP~N~G~i~R~ca~~g~~L~LV~P~gf~~~dk~lrRAgldy~~~~~~~~~~~~~~f~~~~~~--~r~~~~tt 80 (157) T PRK10358 3 NIVLYEPEIPPNTGNIIRLCANTGFRLHIIEPMGFAWDDKRLRRAGLDYHEFTAVTRHHDYAAFLEAENP--QRLFALTT 80 (157) T ss_pred EEEEECCCCCCCHHHHHHHHHHCCCEEEEEECCCCCCCCHHHHHHCCCCHHEEEEEECCCHHHHHHHCCC--CEEEEEEC T ss_conf 7999589888828999999996399899980688787426665331630212689980899999974389--72899725 Q ss_pred CCCCCCCCCCCCCCEEEEECCCCCCCCHHHHHH--CCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHC Q ss_conf 333221122368988999758678987799985--8939992789687437899999999999987614 Q gi|254780603|r 215 DSKKPLEQEIKNDKIALILGAEGKGLRPKTQET--ATSMAHLHMPGIIKALNVSNAAAVALYITQNHFA 281 (282) Q Consensus 215 ~~~~~~~~~~~~~~~~lv~G~E~~Gl~~~~~~~--~d~~v~Ip~~~~~~SLNvs~a~ai~l~~~~~~~~ 281 (282) .+...++++++....+||||+|+.|||+++++. ||..|+|||.+.++|||+|+|++|++||+.||++ T Consensus 81 ~~~~~~~~~~~~~~d~llFG~Es~GLp~e~l~~~~~~~~i~IPm~~~~rSLNLs~AvaIvlYEa~RQ~~ 149 (157) T PRK10358 81 KGTPAHSAVSYQDGDYLMFGPETRGLPASILDALPAEQKIRIPMVPDSRSMNLSNAVSVVVYEAWRQLG 149 (157) T ss_pred CCCCCCHHCCCCCCCEEEECCCCCCCCHHHHHCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHCC T ss_conf 778761002357898899777678989999951777749983089798514299999999999998369 No 9 >TIGR00186 rRNA_methyl_3 RNA methyltransferase, TrmH family, group 3; InterPro: IPR004441 The RNA methyltransferase, TrmH family, group 3 are part of the trmH (spoU) family of rRNA methylases that are involved in tRNA and rRNA base modification.; GO: 0008173 RNA methyltransferase activity, 0009451 RNA modification. Probab=99.97 E-value=8.9e-33 Score=207.19 Aligned_cols=231 Identities=32% Similarity=0.527 Sum_probs=199.2 Q ss_pred EEEEEHHHHHHHHHCCCEEEEEEEECCCCCCC-C---CHHHHHHCCCCEEEECHHHHHHHHCCCCCCCCCCEEEEC---- Q ss_conf 99985788999997898189999973784335-4---345543269969997689987752477777744202411---- Q gi|254780603|r 49 LFLYGVHTVSAALNNPSRKIFQLLATKNALAR-L---DWDANLPHPFPVKTVPPQTIDKIVGKEAVHQGLALETAP---- 120 (282) Q Consensus 49 ~iIeG~~~V~eaL~~~~~~i~~i~~te~~~~~-~---~~~~~l~~~~~I~~v~~~~l~~i~~~~~~hqGi~a~~~~---- 120 (282) .+++|.+++.+++.+.++....++........ . ........++.+..++...+++..... .|+|+++.+.+ T Consensus 3 ~~~~g~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~ 81 (271) T TIGR00186 3 EYLYGVNAVLEALLNDPRRLSRLWILKLLLSGPKLKKLLELLKKKGVTIELVDRKKLDKLAKGG-NHQGVAAEVKPPKNK 81 (271) T ss_pred CHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCEEEEECCHHHHHHHHCC-CCCCEEEEECCCCHH T ss_conf 1011257889875055357788877653112024678888887406504651303455554022-000001211221012 Q ss_pred ---CCCCCHHH-------C------CC-CCEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHH Q ss_conf ---55554011-------2------66-5068872343206889999999864200110013686320000013444333 Q gi|254780603|r 121 ---LLSPTLDA-------V------RN-SQLLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGA 183 (282) Q Consensus 121 ---~~~~~l~~-------~------~~-~~~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga 183 (282) .....++. + .. .++++++|+++||+|+|+++|||.++|+++++++.....+++..+.|+++|+ T Consensus 82 ~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~dp~~~g~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~g~ 161 (271) T TIGR00186 82 NLKYLYLDLEDENIPHELLLKTAKSKKKNPFLLLLDEITDPHNLGAILRTAEALGADGVVLPKRRSAPLTSTVLKTSAGA 161 (271) T ss_pred HHHHHHHCCCCCCCCHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHCCCEEEECCHHHCCCHHHHHHHHHHH T ss_conf 22333211343345245666665202445147886133472023467665544121102420101001001344433102 Q ss_pred HHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCC--CCCCCCCC-----------CEEEEECCCCCCCCHHHHHHCCC Q ss_conf 321101222322112222222100000001233322--11223689-----------88999758678987799985893 Q gi|254780603|r 184 LEHIPYIRISNLTDALQKMHSWGFQTIGLSSDSKKP--LEQEIKND-----------KIALILGAEGKGLRPKTQETATS 250 (282) Q Consensus 184 ~~~l~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~--~~~~~~~~-----------~~~lv~G~E~~Gl~~~~~~~~d~ 250 (282) .+++|+.++.++..++..+++.|+|+++++..+... .+...... +.++++|+|++|++..+.+.||. T Consensus 162 ~~~~~~~~~~~~~~~~~~~~~~g~w~~~~~~~~~~~~~~~~~~~~~~~~~~g~c~~~~~~~~~g~~~~g~~~~~~~~~d~ 241 (271) T TIGR00186 162 LEYLPLARVTNLSRTLTKLKELGFWTLGTDLDGEDTPELYEKLLLKLHDLNGLCNELPLALVLGNEGEGLSRLLKKNCDF 241 (271) T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHCCEEEEECCCCCCHHHHHHHHCCE T ss_conf 34300233222588999887627547861344201245666554333322212311132457637653213455530661 Q ss_pred EEEECCCCCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 999278968743789999999999998761 Q gi|254780603|r 251 MAHLHMPGIIKALNVSNAAAVALYITQNHF 280 (282) Q Consensus 251 ~v~Ip~~~~~~SLNvs~a~ai~l~~~~~~~ 280 (282) .+.||+.+.++|||+++|+++++|+..+++ T Consensus 242 ~~~~p~~~~~~~l~~~~~~g~~~~~~~~~~ 271 (271) T TIGR00186 242 LIKIPLAGKVDSLNVSVAAGILLFEIKRQR 271 (271) T ss_pred EEEECCCCCCCCHHHHHHHHHHHHHHHHCC T ss_conf 676035666320024667787877665239 No 10 >COG0219 CspR Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis] Probab=99.97 E-value=4e-31 Score=197.72 Aligned_cols=147 Identities=20% Similarity=0.234 Sum_probs=139.2 Q ss_pred EEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCC Q ss_conf 68872343206889999999864200110013686320000013444333321101222322112222222100000001 Q gi|254780603|r 134 LLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYIRISNLTDALQKMHSWGFQTIGLS 213 (282) Q Consensus 134 ~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~~~~~i~~~~ 213 (282) +.|+|.+++.|+|.|+|+|||+++|+.-.++-+-+++.-.+...||++.+|+.+.+.+.+++.+|+++.+. +-+++.++ T Consensus 3 ~~IvL~~PeIP~NTGNI~R~ca~tga~LhlI~PlGF~l~dk~lkRAGlDY~~~~~l~~h~s~e~fl~~~~~-~~rl~~~t 81 (155) T COG0219 3 LNIVLYQPEIPPNTGNIIRTCAATGAELHLIEPLGFDLDDKRLKRAGLDYHEKASLTEHDSLEAFLEAEPI-GGRLFALT 81 (155) T ss_pred CEEEEECCCCCCCHHHHHHHHHHCCCEEEEECCCCCCCCHHHHHHCCCCHHHHCCEEEECCHHHHHHHCCC-CCEEEEEE T ss_conf 07999789889845499999885297678974677765446645323451754662896889999863567-75399999 Q ss_pred CCCCCCCCCCCCCCCEEEEECCCCCCCCHHHHHHCCCE-EEECCCCCCCHHHHHHHHHHHHHHHHHHHC Q ss_conf 23332211223689889997586789877999858939-992789687437899999999999987614 Q gi|254780603|r 214 SDSKKPLEQEIKNDKIALILGAEGKGLRPKTQETATSM-AHLHMPGIIKALNVSNAAAVALYITQNHFA 281 (282) Q Consensus 214 ~~~~~~~~~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~-v~Ip~~~~~~SLNvs~a~ai~l~~~~~~~~ 281 (282) ..+...+.+..+.....|+||.|+.|||+++++..... ++|||...++|||+|+++||++||+.||.. T Consensus 82 t~~~~~~~~~~f~~~d~llFG~Es~GLP~~i~~~~~~~~irIPm~~~~RSLNLsnsvavv~yEa~RQ~~ 150 (155) T COG0219 82 TKGTTTYTDVSFQKGDYLLFGPESRGLPEEILDAAPDRCIRIPMRPGVRSLNLSNTVAVVLYEALRQLG 150 (155) T ss_pred ECCCCCCCCCCCCCCCEEEECCCCCCCCHHHHHHCCCCEEEECCCCCCCCCHHHHHHHHHHHHHHHHHC T ss_conf 436666664567888789978888899999997393355983368787631088879999999999727 No 11 >TIGR00185 rRNA_methyl_2 RNA methyltransferase, TrmH family, group 2; InterPro: IPR004440 The RNA methyltransferase, TrmH family, group 2 are part of the trmH (spoU) family of rRNA methylases that are involved in tRNA and rRNA base modification.; GO: 0008173 RNA methyltransferase activity, 0009451 RNA modification. Probab=99.97 E-value=2.3e-31 Score=199.07 Aligned_cols=148 Identities=19% Similarity=0.188 Sum_probs=135.5 Q ss_pred EEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCC Q ss_conf 68872343206889999999864200110013686320000013444333321101222322112222222100000001 Q gi|254780603|r 134 LLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYIRISNLTDALQKMHSWGFQTIGLS 213 (282) Q Consensus 134 ~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~~~~~i~~~~ 213 (282) +-|||..++-|.|.|+|+|||+|+|+.-.++.+-++.--+....||+..+|+++.+.+..++.+||+.-+..+-.+++++ T Consensus 2 ~~iVLy~PeIP~NTGNI~R~Caat~~~LHLi~PlGF~~~DK~L~RAGLdyw~fv~~~~H~s~E~fle~~~~~~~nlf~lT 81 (161) T TIGR00185 2 LNIVLYEPEIPPNTGNIVRTCAATGTRLHLIKPLGFELDDKRLKRAGLDYWEFVQLFYHKSWEEFLEAEKPQKGNLFLLT 81 (161) T ss_pred EEEEEECCCCCCCCCHHHHHHHCCCCEEEEECCCCCCCCCCEEEECCCCCCCCEEEEECCCHHHHHHHCCCCCEEEEEEE T ss_conf 15774078897884112010111586245660578620781423147874452323562556888863389971688884 Q ss_pred CCC--CCCCCCCCCCCCE--EEEECCCCCCCCHHHHHHC--CCEEEECCCC-CCCHHHHHHHHHHHHHHHHHHHC Q ss_conf 233--3221122368988--9997586789877999858--9399927896-87437899999999999987614 Q gi|254780603|r 214 SDS--KKPLEQEIKNDKI--ALILGAEGKGLRPKTQETA--TSMAHLHMPG-IIKALNVSNAAAVALYITQNHFA 281 (282) Q Consensus 214 ~~~--~~~~~~~~~~~~~--~lv~G~E~~Gl~~~~~~~~--d~~v~Ip~~~-~~~SLNvs~a~ai~l~~~~~~~~ 281 (282) ..| ..+..++.+.... -||||.|.+|||+.+++.. +..|+|||.. .++|||+|.|+||++||+.||.. T Consensus 82 ~~G~~t~~~~~~~~~~~d~~yl~fG~ET~GLP~~~~~~~P~~~~~RiPm~~s~vRSlNLsn~va~~lYEa~rQ~~ 156 (161) T TIGR00185 82 KKGDKTPDHISVTYQDGDELYLVFGQETKGLPKSLLDNLPMEQKIRIPMTNSEVRSLNLSNSVAIVLYEALRQLG 156 (161) T ss_pred ECCCCCCCCEEEEECCCCCEEEEECCCCCCCHHHHHHCCCCCCCEECCCCCCCCCCHHHHHHHHHHHHHHHHHCC T ss_conf 038877450466543786169983687755128998606321630325578884622468899999998787513 No 12 >KOG0839 consensus Probab=99.91 E-value=1.8e-25 Score=165.41 Aligned_cols=148 Identities=21% Similarity=0.317 Sum_probs=126.6 Q ss_pred CCCEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCC--CCCCCCCCCCCCCCCH Q ss_conf 65068872343206889999999864200110013686320000013444333321101222--3221122222221000 Q gi|254780603|r 131 NSQLLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYIRI--SNLTDALQKMHSWGFQ 208 (282) Q Consensus 131 ~~~~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~--~~~~~~l~~~~~~~~~ 208 (282) ...+|||-.-|..|.|+|.|+|||+.||++.+.+.+-.+- -++.---.|+-|--|+|+..+ +++..|++..|.+||. T Consensus 1324 rssLIVVASLVDKppNLgGicRTcEVFgvs~LvVad~~vi-~DkQFk~lSVtAE~W~pieeVk~~~L~~fLq~kK~EGyT 1402 (1477) T KOG0839 1324 RSSLIVVASLVDKPPNLGGICRTCEVFGVSLLVVADIKVI-NDKQFKNLSVTAERWMPIEEVKLDELASFLQEKKKEGYT 1402 (1477) T ss_pred CEEEEEEEECCCCCCCCCHHHHHHHHHCCCEEEEEEEEEE-CCHHHHHEEEEHHHCCCHHCCCHHHHHHHHHHHHHCCCE T ss_conf 6159998520158986301445666617533787423452-252042224338756202226837789999986636827 Q ss_pred HHHCCCCC-CCCCCCCCCCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 00001233-322112236898899975867898779998589399927896874378999999999999876 Q gi|254780603|r 209 TIGLSSDS-KKPLEQEIKNDKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVSNAAAVALYITQNH 279 (282) Q Consensus 209 i~~~~~~~-~~~~~~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs~a~ai~l~~~~~~ 279 (282) ++|++-.. ...+.++-||+|.+++||+|..|+|-.++...|.+|.||+.|-++||||.|++|+++||..|| T Consensus 1403 iIglEQTakSV~Ld~fqFPkKslilLG~EkEGIPvnLl~~LD~cvEIpQ~GviRSLNVHVsgAl~iweYTrQ 1474 (1477) T KOG0839 1403 IIGLEQTAKSVKLDNFQFPKKSLILLGTEKEGIPVNLLSELDLCVEIPQFGVIRSLNVHVSGALIIWEYTRQ 1474 (1477) T ss_pred EEEEHHCCCCCCCCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHEECCCCCEEEEEEEEHHHHHHHHHHHHH T ss_conf 984232055011001347753268822653588377999976761321224455664104478899998888 No 13 >PRK10433 putative RNA methyltransferase; Provisional Probab=99.90 E-value=2e-23 Score=153.57 Aligned_cols=141 Identities=21% Similarity=0.245 Sum_probs=111.5 Q ss_pred EEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCC-CCCCCCCCCCCCCCCCCHHHHC Q ss_conf 688723432068899999998642001100136863200000134443333211012-2232211222222210000000 Q gi|254780603|r 134 LLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYI-RISNLTDALQKMHSWGFQTIGL 212 (282) Q Consensus 134 ~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~-~~~~~~~~l~~~~~~~~~i~~~ 212 (282) +-+||.+++.|+|+|+++|.+..||++.+.+....+ ..++++.+.++||..-+.=. .++++.+++..+. .++|+ T Consensus 3 i~iVLvep~~p~NIGa~ARaMkN~G~~~L~LV~P~~-~~~~~a~~~A~gA~diL~~a~v~~sL~eAl~d~~----~vvgt 77 (228) T PRK10433 3 LTIILVAPARAENIGAAARAMKTMGFSELRIVDSQA-HLEPAARWVAHGSGDILDNIEVFDTLAEALHDVD----FTVAT 77 (228) T ss_pred EEEEEECCCCCCHHHHHHHHHHCCCCCCEEEECCCC-CCCHHHHHHHCCHHHHHHHCCCCCCHHHHHHCCC----EEEEE T ss_conf 999996799975199999999728998169979999-9988899983473999973733377999985489----89996 Q ss_pred CCCCCC---C----------CC-CCCCCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHHHHH Q ss_conf 123332---2----------11-223689889997586789877999858939992789687437899999999999987 Q gi|254780603|r 213 SSDSKK---P----------LE-QEIKNDKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVSNAAAVALYITQN 278 (282) Q Consensus 213 ~~~~~~---~----------~~-~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs~a~ai~l~~~~~ 278 (282) +..... + +. .....++++||||+|..||+.+-++.||..++||.+....|||+|+|++|++||+.. T Consensus 78 TaR~r~~~~~~~~p~~~~~~~~~~~~~~~~valvFG~E~~GLsneEl~~C~~~~~IPt~~~y~SLNLaqAV~i~~YEl~~ 157 (228) T PRK10433 78 TARSRAKYHYYATPAELVPLLEEKSSWMSHAALVFGREDSGLTNEELALADVLTGVPMAADYPSLNLGQAVMVYCYQLAG 157 (228) T ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCEEEEEECCCCCCCCCHHHHHHHHHHHHHH T ss_conf 45646688886899999999997323478479998886689898999867978985589998532199999999999987 Q ss_pred H Q ss_conf 6 Q gi|254780603|r 279 H 279 (282) Q Consensus 279 ~ 279 (282) . T Consensus 158 ~ 158 (228) T PRK10433 158 L 158 (228) T ss_pred H T ss_conf 5 No 14 >TIGR00050 rRNA_methyl_1 RNA methyltransferase, TrmH family, group 1; InterPro: IPR004384 These proteins are part of the trmH (spoU) family of rRNA methylases. The spoU gene of Escherichia coli codes for a protein that shows strong similarities to previously characterised 2'-O-methyltransferases . TrmH is a tRNA (guanosine-2'-O-)-methyltransferase (2.1.1.34 from EC), which specifically methylates guanosine-18 in various tRNAs using S-adenosyl-L-methionine.; GO: 0008173 RNA methyltransferase activity. Probab=99.90 E-value=1.8e-23 Score=153.93 Aligned_cols=145 Identities=21% Similarity=0.271 Sum_probs=121.0 Q ss_pred CEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHC-CCCCCCCCCCCCCCCCCCCHHHH Q ss_conf 06887234320688999999986420011001368632000001344433332110-12223221122222221000000 Q gi|254780603|r 133 QLLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIP-YIRISNLTDALQKMHSWGFQTIG 211 (282) Q Consensus 133 ~~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~-~~~~~~~~~~l~~~~~~~~~i~~ 211 (282) .+-|||=+++.|+|+|+|+|.+-.||+..++|.+.+++..+..+.-.|+||-+-|. ..-+++|.++|..+.-. .++| T Consensus 4 ~I~ivLVep~~~gNvG~~ARaMKnmGl~~L~Lv~p~~~~~~~eay~~A~~A~Di~~nA~vv~~L~Eal~sld~~--~~vg 81 (253) T TIGR00050 4 NISIVLVEPKHSGNVGSIARAMKNMGLEELILVNPRVDILEEEAYALAAHAKDILENAKVVDDLDEALDSLDCD--LVVG 81 (253) T ss_pred EEEEEEEECCCCCCHHHHHHHHHHHCCCCCEEECCCCCCCCHHHHHHHHHHHHHHCCCEEECCHHHHHHHCCCC--EEEE T ss_conf 24788861799864469999987627001256466225568789998720278658754742679998731997--0786 Q ss_pred CC-CCCC--CCC------------CCCCCCC--CEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHH Q ss_conf 01-2333--221------------1223689--88999758678987799985893999278968743789999999999 Q gi|254780603|r 212 LS-SDSK--KPL------------EQEIKND--KIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVSNAAAVALY 274 (282) Q Consensus 212 ~~-~~~~--~~~------------~~~~~~~--~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs~a~ai~l~ 274 (282) || ..|. +.+ .-..... ++++|||.|+.||+.|-++.||..|+||++...-|||+|+|++|++| T Consensus 82 TsGaRGGd~r~l~~~~~~P~el~~~~~~~~g~~~~A~vFGREd~GL~NEEL~~Ch~~v~iP~~~~YPslNL~~AV~Vi~Y 161 (253) T TIGR00050 82 TSGARGGDSRNLQRPLLTPRELADKILAKKGWMKVAIVFGREDSGLTNEELEKCHVLVSIPTSEEYPSLNLSHAVAVILY 161 (253) T ss_pred CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHHHHCCCEEECCCCCCCCHHHHHHHHHHHHH T ss_conf 26788875434467777836668764242067214788524688876688964781552257788741148999999999 Q ss_pred HHHHH Q ss_conf 99876 Q gi|254780603|r 275 ITQNH 279 (282) Q Consensus 275 ~~~~~ 279 (282) |+++. T Consensus 162 eL~~~ 166 (253) T TIGR00050 162 ELRMA 166 (253) T ss_pred HHHHH T ss_conf 99988 No 15 >COG0565 LasT rRNA methylase [Translation, ribosomal structure and biogenesis] Probab=99.87 E-value=4.6e-22 Score=145.81 Aligned_cols=141 Identities=22% Similarity=0.319 Sum_probs=113.9 Q ss_pred CEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCC-CCCCCCCCCCCCCCCCCHHHH Q ss_conf 0688723432068899999998642001100136863200000134443333211012-223221122222221000000 Q gi|254780603|r 133 QLLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYI-RISNLTDALQKMHSWGFQTIG 211 (282) Q Consensus 133 ~~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~-~~~~~~~~l~~~~~~~~~i~~ 211 (282) .+.|||-+.+.|+|+|++.|.+.-||++.+++...++. .+..+...|+||-+-+.=. .++++.++|..+. -++| T Consensus 4 ~i~iVLVep~~~gNIG~vARaMKNfGl~eL~LV~Pr~~-~~eeA~a~A~gA~dile~A~i~~tL~eAl~d~~----~v~a 78 (242) T COG0565 4 NIRIVLVEPSHPGNIGSVARAMKNFGLSELRLVNPRAG-LDEEARALAAGARDILENAKIVDTLEEALADCD----LVVA 78 (242) T ss_pred CCEEEEECCCCCCCHHHHHHHHHHCCCCEEEEECCCCC-CCHHHHHHHCCCHHHHCCCEEECCHHHHHCCCC----EEEE T ss_conf 61799975888752799999998679664899789889-889999986466666506766467999960788----7998 Q ss_pred CCCCCC---CC----------C-CCCCCCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHHHH Q ss_conf 012333---22----------1-122368988999758678987799985893999278968743789999999999998 Q gi|254780603|r 212 LSSDSK---KP----------L-EQEIKNDKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVSNAAAVALYITQ 277 (282) Q Consensus 212 ~~~~~~---~~----------~-~~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs~a~ai~l~~~~ 277 (282) ++...- .+ + .... ..+++||||.|..||+.+-+..||..++||++...-|||+|+|++|++||.+ T Consensus 79 Ttar~r~~~~~~~~P~e~~~~l~~~~~-~~~vAlvFGRE~~GLtNeEl~~c~~~v~IP~~p~Y~sLNLa~AV~ii~YEl~ 157 (242) T COG0565 79 TTARSRDLLRPLRTPREAAPELLEKAK-GGKVALVFGRERVGLTNEELALCDVLVTIPANPDYPSLNLAQAVQVILYELR 157 (242) T ss_pred ECCCCCCCCCCCCCHHHHHHHHHHHHC-CCCEEEEECCCCCCCCHHHHHHHHEEEECCCCCCCCCCCHHHHHHHHHHHHH T ss_conf 056667665565687878999998714-8976999788668978899985027873679986543659999999999999 Q ss_pred HH Q ss_conf 76 Q gi|254780603|r 278 NH 279 (282) Q Consensus 278 ~~ 279 (282) +. T Consensus 158 ~~ 159 (242) T COG0565 158 KA 159 (242) T ss_pred HH T ss_conf 86 No 16 >pfam08032 SpoU_sub_bind RNA 2'-O ribose methyltransferase substrate binding. This domain is a RNA 2'-O ribose methyltransferase substrate binding domain. Probab=98.90 E-value=2.5e-09 Score=72.86 Aligned_cols=72 Identities=24% Similarity=0.308 Sum_probs=57.7 Q ss_pred EEEEHHHHHHHHHCCCEEEEEEEECCCCCCCCC--HHHHHHCCCCEEEECHHHHHHHHCCCCCCCCCCEEEECCCC Q ss_conf 998578899999789818999997378433543--45543269969997689987752477777744202411555 Q gi|254780603|r 50 FLYGVHTVSAALNNPSRKIFQLLATKNALARLD--WDANLPHPFPVKTVPPQTIDKIVGKEAVHQGLALETAPLLS 123 (282) Q Consensus 50 iIeG~~~V~eaL~~~~~~i~~i~~te~~~~~~~--~~~~l~~~~~I~~v~~~~l~~i~~~~~~hqGi~a~~~~~~~ 123 (282) +|||.|+|.|||++++. +..+|++++...... ......+++++..++++.|+++++ +.+|||+++.+.+..+ T Consensus 1 lI~G~~~V~eAL~~~~~-i~~l~i~~~~~~~~~~i~~~a~~~~i~v~~v~~~~l~~ls~-~~~hQGvva~v~~~~~ 74 (75) T pfam08032 1 LIEGRHAVEEALKSGPE-IEKLFVTEGRRDKRKELLKLAKKRGIKVIEVSEKVLDKLSG-TVNHQGVVAVVKPPEY 74 (75) T ss_pred CEEEEHHHHHHHHCCCC-EEEEEEECCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHCC-CCCCCEEEEEECCCCC T ss_conf 97764799999977997-57999965751799999999998699856589999986469-9999848999417686 No 17 >COG4080 SpoU rRNA Methylase family enzyme [General function prediction only] Probab=97.93 E-value=7.7e-05 Score=47.13 Aligned_cols=141 Identities=19% Similarity=0.273 Sum_probs=96.5 Q ss_pred CEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCC--CC-HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHH Q ss_conf 06887234320688999999986420011001368632--00-0001344433332110122232211222222210000 Q gi|254780603|r 133 QLLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSP--SE-SAVLAKSASGALEHIPYIRISNLTDALQKMHSWGFQT 209 (282) Q Consensus 133 ~~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~--~~-~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~~~~~i 209 (282) .+++++.++..++-+=-+.|++..||++.+++++-... .- =|++.|-+--. ..|+..+.++.++++-++-.-.-. T Consensus 2 ev~vvlHN~~S~~rv~e~ariaygfg~k~lV~tka~g~AAQsGIp~~~kla~k~--G~~vlvf~dL~DAlevL~P~v~ll 79 (147) T COG4080 2 EVIVVLHNVSSVQRVLEFARIAYGFGAKRLVLTKAKGSAAQSGIPEVLKLAFKL--GKPVLVFPDLDDALEVLRPDVTLL 79 (147) T ss_pred CEEEEEECCCCHHHHHHHHHHHCCCCCCEEEEEECCCHHHHHCCHHHHHHHHHH--CCCEEEEHHHHHHHHHCCCCEEEE T ss_conf 079999427755899999999713685389997125476663568899999983--994798522778997459756998 Q ss_pred HHCCCCCCCCCCCCC-CCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 000123332211223-6898899975867898779998589399927896874378999999999999876 Q gi|254780603|r 210 IGLSSDSKKPLEQEI-KNDKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVSNAAAVALYITQNH 279 (282) Q Consensus 210 ~~~~~~~~~~~~~~~-~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs~a~ai~l~~~~~~ 279 (282) ++....+.+.+.-.+ ...++++||++-..|+++.-++.-+....| ..+.+-++ -++||+||++.+. T Consensus 80 ~~~~~~~ek~~dp~e~ie~~vliVf~ga~~gl~k~El~lg~~~~y~-ve~~VG~~---g~lAi~Lyell~~ 146 (147) T COG4080 80 VGSASEGEKKLDPNEKIEGRVLIVFSGAEPGLTKRELELGADLRYI-VEADVGEL---GALAIFLYELLKA 146 (147) T ss_pred ECCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCHHHCCCCCCEEEE-EECCCHHH---HHHHHHHHHHHCC T ss_conf 1476443234794312463379999268877586660567727999-84464178---8899999998704 No 18 >pfam09936 DUF2168 Uncharacterized protein conserved in bacteria (DUF2168). This domain, found in various hypothetical prokaryotic proteins, has no known function. It is also found in a few prokaryotic tRNA (guanine-N(1)-)-methyltransferases. Probab=97.78 E-value=5.1e-05 Score=48.15 Aligned_cols=124 Identities=22% Similarity=0.278 Sum_probs=77.4 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCC------------------CCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC--- Q ss_conf 899999998642001100136863------------------20000013444333321101222322112222222--- Q gi|254780603|r 146 NIGAILRSAVAFSCDGIITTKRYS------------------PSESAVLAKSASGALEHIPYIRISNLTDALQKMHS--- 204 (282) Q Consensus 146 NlG~I~Rta~a~g~~~vil~~~~~------------------~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~--- 204 (282) -+=-|.|+|-.+|+.+.++...-- ..+||. |.. |+..+.+ ..++.++++...+ T Consensus 29 DiHDIAR~~rTYgv~~yyiVtPl~~Q~~l~~ril~hW~~G~G~~~NP~--R~e--Al~~v~~--~~sle~ai~~i~~~~G 102 (185) T pfam09936 29 DIHDIARSARTYGVGRYYIVTPLEAQQALVERILAHWQEGYGGEYNPD--RKE--ALSLVKV--VSSLEEAIEDIEKRTG 102 (185) T ss_pred CHHHHHHHHHCCCCCCEEEECCHHHHHHHHHHHHHHHCCCCCCCCCCC--HHH--HHHHHHH--HCCHHHHHHHHHHHHC T ss_conf 477754555004776679956019999999999987325978666967--899--9857300--6029999999999619 Q ss_pred CCCHHHHCCCC-C--CCCCCC---C--CCCCCEEEEECCCCCCCCHHHHHHCCCEEE-ECCCCCCCHHHHHHHHHHHHHH Q ss_conf 10000000123-3--322112---2--368988999758678987799985893999-2789687437899999999999 Q gi|254780603|r 205 WGFQTIGLSSD-S--KKPLEQ---E--IKNDKIALILGAEGKGLRPKTQETATSMAH-LHMPGIIKALNVSNAAAVALYI 275 (282) Q Consensus 205 ~~~~i~~~~~~-~--~~~~~~---~--~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~-Ip~~~~~~SLNvs~a~ai~l~~ 275 (282) ..-.+++++.. . ..++.+ . +-.+|..|+||. |.||++++++.||..+. |--.+...-|.|=.|+||+|=. T Consensus 103 ~~p~vvaTsAr~~~~~is~~~lr~~i~~~~~P~LllFGT-GwGL~~e~~~~~D~iLePI~g~~~yNHLSVRsAaAIilDR 181 (185) T pfam09936 103 QRPLIVATSARKRPNTISYEELRKMIQEREKPVLLLFGT-GWGLAPEVLEQADYVLEPIRGAGDYNHLSVRSAAAIILDR 181 (185) T ss_pred CCCEEEEECCCCCCCCCCHHHHHHHHHCCCCCEEEEECC-CCCCCHHHHHHCCEEECCCCCCCCCCCHHHHHHHHHHHHH T ss_conf 997799804756899739999999984458818999658-7687799997468667056369997620499999999998 Q ss_pred H Q ss_conf 9 Q gi|254780603|r 276 T 276 (282) Q Consensus 276 ~ 276 (282) + T Consensus 182 L 182 (185) T pfam09936 182 L 182 (185) T ss_pred H T ss_conf 7 No 19 >PRK03958 tRNA 2'-O-methylase; Reviewed Probab=97.24 E-value=0.0013 Score=40.02 Aligned_cols=125 Identities=14% Similarity=0.061 Sum_probs=82.0 Q ss_pred CCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHH---HHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCC Q ss_conf 2068899999998642001100136863200000134---4433332110122232211222222210000000123332 Q gi|254780603|r 142 NDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAK---SASGALEHIPYIRISNLTDALQKMHSWGFQTIGLSSDSKK 218 (282) Q Consensus 142 ~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~r---as~Ga~~~l~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~ 218 (282) +|+.=.--+.=||-|||++++++... |+--...++ ..=|.-|.+.+ ..++..+++..++. -.++.+++-|.. T Consensus 14 RD~RiTTHv~LtaRAfGA~~i~l~~~--D~~~~etv~~V~~rwGG~F~~e~--~~~~~~~ir~~k~~-G~vVHLTMYG~~ 88 (175) T PRK03958 14 RDKRITTHVGLTARALGADKILFASE--DEHVKESVEDIVERWGGPFKVEV--TKSWKKYIREFKDG-GIVVHLTMYGEN 88 (175) T ss_pred CCCCHHHHHHHHHHHHCCCEEEECCC--CHHHHHHHHHHHHHCCCCEEEEE--CCCHHHHHHHHCCC-CEEEEEECCCCC T ss_conf 67631358889888726876787688--76689999999986189669997--68979998630258-889998368886 Q ss_pred ------CCCCCCCCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHHHH Q ss_conf ------21122368988999758678987799985893999278968743789999999999998 Q gi|254780603|r 219 ------PLEQEIKNDKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVSNAAAVALYITQ 277 (282) Q Consensus 219 ------~~~~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs~a~ai~l~~~~ 277 (282) .+.+..-.++..+|+|.|- +|.++-+.||+.|.|--...-| -.|.||+|..++ T Consensus 89 i~~~~~~Ir~~~~~~~ilvVVGaeK--VP~evyelADyNVaVgNQPHSE----VAALAiFLDrl~ 147 (175) T PRK03958 89 INDVMDEIREAKTCKPLLIIVGAEK--VPREVYELADYNVAVGNQPHSE----VAALAVFLDRLF 147 (175) T ss_pred HHHHHHHHHHCCCCCCEEEEECCCC--CCHHHHHHCCCCEEECCCCCHH----HHHHHHHHHHHC T ss_conf 6787767653057887899967886--9988974345415517887089----999999999860 No 20 >COG1303 Uncharacterized protein conserved in archaea [Function unknown] Probab=96.56 E-value=0.0022 Score=38.75 Aligned_cols=119 Identities=17% Similarity=0.120 Sum_probs=77.0 Q ss_pred HHHHHHHHHHHCCCCCCCCCCC---CCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCC--- Q ss_conf 9999998642001100136863---2000001344433332110122232211222222210000000123332211--- Q gi|254780603|r 148 GAILRSAVAFSCDGIITTKRYS---PSESAVLAKSASGALEHIPYIRISNLTDALQKMHSWGFQTIGLSSDSKKPLE--- 221 (282) Q Consensus 148 G~I~Rta~a~g~~~vil~~~~~---~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~~--- 221 (282) --.+=||-|||+++++++..+- ...=.++++ .=|.-|.+. ...|+...+...++ |-.++.+++-|- ++. T Consensus 21 THV~LtARAfGA~gil~~~e~De~v~esv~dVv~-rwGG~F~v~--~~~nw~~~i~~wk~-gG~vvHLTMYG~-~i~dv~ 95 (179) T COG1303 21 THVALTARAFGADGILLDGEEDEKVVESVEDVVE-RWGGPFFVK--FGVNWRKVIREWKE-GGIVVHLTMYGL-NIDDVI 95 (179) T ss_pred HHHHHHHHHHCCCEEEECCCCCHHHHHHHHHHHH-HCCCCEEEE--ECCCHHHHHHHHHC-CCEEEEEEECCC-CCHHHH T ss_conf 2333546861775479737643779999999998-549977999--72238999987404-877999996277-630341 Q ss_pred -CCCCC-CCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHHHH Q ss_conf -22368-988999758678987799985893999278968743789999999999998 Q gi|254780603|r 222 -QEIKN-DKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVSNAAAVALYITQ 277 (282) Q Consensus 222 -~~~~~-~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs~a~ai~l~~~~ 277 (282) ++.-. ....+|+|.|- +|.++-+.||..|.|--...-| | .|.||.|..+. T Consensus 96 ~ei~~~~k~~lvvVGaeK--Vp~evYelADyNV~VgnQPHSE---V-aaLAvFLDRl~ 147 (179) T COG1303 96 DEIRESKKDVLVVVGAEK--VPGEVYELADYNVSVGNQPHSE---V-AALAVFLDRLF 147 (179) T ss_pred HHHHHCCCCEEEEECCCC--CCHHHHHHCCCCEECCCCCCHH---H-HHHHHHHHHHH T ss_conf 898746872799975662--8888964234413307876089---9-99999999971 No 21 >PRK12703 tRNA 2'-O-methylase; Reviewed Probab=95.96 E-value=0.014 Score=34.21 Aligned_cols=124 Identities=15% Similarity=0.113 Sum_probs=73.9 Q ss_pred CCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCH-HHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCC-- Q ss_conf 20688999999986420011001368632000-001344433332110122232211222222210000000123332-- Q gi|254780603|r 142 NDPHNIGAILRSAVAFSCDGIITTKRYSPSES-AVLAKSASGALEHIPYIRISNLTDALQKMHSWGFQTIGLSSDSKK-- 218 (282) Q Consensus 142 ~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~-~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~-- 218 (282) +|+.=.--+.=||-|||++++++.+..-...+ -.-+-..=|.-|.+. ...++...+++.+-.++.+++.|.. T Consensus 13 RDkRITTHVaLtARAfGA~~il~~e~D~~v~etv~~V~~rwGG~F~ie-----~~~~w~~~~k~~~G~vVHLTMYG~~i~ 87 (339) T PRK12703 13 RDKRITTHVALTARAFGASSILVDERDETLENTIKKVVDNFGGSFEIK-----TGIEWKSEFKKFHGIRVHLTMYGRPIE 87 (339) T ss_pred CCCCHHHHHHHHHHHHCCCEEEECCCCHHHHHHHHHHHHHCCCCEEEE-----ECCCHHHHHHHCCCEEEEEECCCCCHH T ss_conf 676212589899987168754436887678999999997349977997-----176799998735987999831688657 Q ss_pred -CCCCCCC-CCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHHH Q ss_conf -2112236-898899975867898779998589399927896874378999999999999 Q gi|254780603|r 219 -PLEQEIK-NDKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVSNAAAVALYIT 276 (282) Q Consensus 219 -~~~~~~~-~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs~a~ai~l~~~ 276 (282) -+.++.. .++..+|+|.|- +|.++.+.+|+.|.|--...-| -.|.||+|-.+ T Consensus 88 dvi~~Ir~~~k~ilVVVGaeK--VP~evYelADyNVaVgNQPHSE----VAALAIFLDRl 141 (339) T PRK12703 88 DVIDEIRESGKDVMVLVGSEK--VPIEAYEIADYNVSVTNQPISE----VSALAIFLDRY 141 (339) T ss_pred HHHHHHHHCCCCEEEEECCCC--CCHHHHHHCCCCEEECCCCHHH----HHHHHHHHHHH T ss_conf 877776512897799975885--9989985356534327988089----99999999986 No 22 >COG4752 Uncharacterized protein conserved in bacteria [Function unknown] Probab=95.45 E-value=0.021 Score=33.17 Aligned_cols=50 Identities=20% Similarity=0.265 Sum_probs=40.5 Q ss_pred CCCEEEEECCCCCCCCHHHHHHCCCEEE-ECCCCCCCHHHHHHHHHHHHHHH Q ss_conf 8988999758678987799985893999-27896874378999999999999 Q gi|254780603|r 226 NDKIALILGAEGKGLRPKTQETATSMAH-LHMPGIIKALNVSNAAAVALYIT 276 (282) Q Consensus 226 ~~~~~lv~G~E~~Gl~~~~~~~~d~~v~-Ip~~~~~~SLNvs~a~ai~l~~~ 276 (282) .+++.++||. |.|||+++++.+|..+. |--.+...-|.|-.|+||++-.+ T Consensus 133 dkp~LilfGT-GwGlpde~m~~sDYiLEPIra~sd~NHLSVRaAvAIIlDRL 183 (190) T COG4752 133 DKPWLILFGT-GWGLPDELMNTSDYILEPIRAASDWNHLSVRAAVAIILDRL 183 (190) T ss_pred CCCEEEEECC-CCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHH T ss_conf 7867999637-88998799877667232133057753153888899999998 No 23 >COG1385 Uncharacterized protein conserved in bacteria [Function unknown] Probab=94.66 E-value=0.27 Score=26.85 Aligned_cols=138 Identities=20% Similarity=0.268 Sum_probs=76.2 Q ss_pred CCEEEEECCCCCHHHHHHHHHHHHHHHCCCC--CCCCCCCCCCHHH-------HHHHHHHHHHH-----HCCC-CCCCCC Q ss_conf 5068872343206889999999864200110--0136863200000-------13444333321-----1012-223221 Q gi|254780603|r 132 SQLLMVLDHVNDPHNIGAILRSAVAFSCDGI--ITTKRYSPSESAV-------LAKSASGALEH-----IPYI-RISNLT 196 (282) Q Consensus 132 ~~~~i~ld~i~dp~NlG~I~Rta~a~g~~~v--il~~~~~~~~~~~-------~~ras~Ga~~~-----l~~~-~~~~~~ 196 (282) +..+-+.-.+-.+..+=.|++-|.-+|+..+ +.+++|..-|..+ --+....|.++ +|-+ ...++. T Consensus 77 ~~~i~l~~~~~kg~k~d~iiqkatELGv~~i~p~~ter~~~k~~~~~~~kler~~ki~ieAaEQs~R~~vP~I~~~~~~~ 156 (246) T COG1385 77 PLKITLAQAIPKGDKLELIIQKATELGVSKIIPLITERSVVKLDGKKAAKLERWQKIAIEAAEQSGRNVVPEIKPPESLK 156 (246) T ss_pred CCEEEEEEECCCHHHHHHHHHHHHHHCCCEEEEEEECEEEEEHHCCHHHHHHHHHHHHHHHHHHCCCCCCCEEECHHHHH T ss_conf 86079999627518899999999871801179885012677200110368999999999999864998698262313099 Q ss_pred CCCCCCCCCCCHHHHCCCCCCCCCC-----CCCCCCCEEEEECCCCCCCCHHHHHHCCC--EEEECCCCCCCHHHHHHHH Q ss_conf 1222222210000000123332211-----22368988999758678987799985893--9992789687437899999 Q gi|254780603|r 197 DALQKMHSWGFQTIGLSSDSKKPLE-----QEIKNDKIALILGAEGKGLRPKTQETATS--MAHLHMPGIIKALNVSNAA 269 (282) Q Consensus 197 ~~l~~~~~~~~~i~~~~~~~~~~~~-----~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~--~v~Ip~~~~~~SLNvs~a~ 269 (282) ++++.........+.....+..... +....++..+++|.|| |++++-.+.... ...|.+..++ |=.-+|+ T Consensus 157 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iiIGPEG-Gfs~~Ei~~l~~~g~~~v~LGprI--LRtETA~ 233 (246) T COG1385 157 ELLKEIDDEDALKLIYEEKAKEGLLALPLLEALPEGKVLLIIGPEG-GFSEDEIELLREAGFTPVSLGPRI--LRTETAA 233 (246) T ss_pred HHHHHCCCHHHHHHEECCCCCCCCCCCHHHHCCCCCCEEEEECCCC-CCCHHHHHHHHHCCCEEECCCCCE--EEHHHHH T ss_conf 9998546300133222544544543330120156773899988998-999899999997798581378972--0077899 Q ss_pred HHH Q ss_conf 999 Q gi|254780603|r 270 AVA 272 (282) Q Consensus 270 ai~ 272 (282) -.+ T Consensus 234 l~a 236 (246) T COG1385 234 LAA 236 (246) T ss_pred HHH T ss_conf 999 No 24 >PRK11713 16S rRNA m3U1498 methyltransferase; Provisional Probab=94.46 E-value=0.29 Score=26.65 Aligned_cols=138 Identities=20% Similarity=0.271 Sum_probs=74.2 Q ss_pred EEEECCCCCHHHHHHHHHHHHHHHCCCC--CCCCCCCCCCHH-----H---HHHHHHHHH-----HHHC-CCCCCCCCCC Q ss_conf 8872343206889999999864200110--013686320000-----0---134443333-----2110-1222322112 Q gi|254780603|r 135 LMVLDHVNDPHNIGAILRSAVAFSCDGI--ITTKRYSPSESA-----V---LAKSASGAL-----EHIP-YIRISNLTDA 198 (282) Q Consensus 135 ~i~ld~i~dp~NlG~I~Rta~a~g~~~v--il~~~~~~~~~~-----~---~~ras~Ga~-----~~l~-~~~~~~~~~~ 198 (282) +.++-.+-.|..+=.+++-|.-+|++.+ +.++++...|.. + .-|....|. .++| +....++.++ T Consensus 78 i~L~~al~K~~~~e~il~k~tElGV~~i~p~~s~rs~~~~~~~~~~~k~eR~~~i~~eA~eQs~r~~lP~i~~~~~l~~~ 157 (243) T PRK11713 78 LTLAQALPKGDRLELIIQKATELGVSAIIPLITERSVVKLDGERADKKLERWQKIAIEAAEQSGRTRIPEIRPPVSLKEL 157 (243) T ss_pred EEEEEEECCCHHHHHHHHHHHHHCCCEEEEEEHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCEECCCCCHHHH T ss_conf 79999600755899999999872877799997000545212105666699999999999997099828776576799999 Q ss_pred CCCCCCCCCHHHHCCCCCCCC--CCCCCCCCCEEEEECCCCCCCCHHHHHHCCC--EEEECCCCCCCHHHHHH----HHH Q ss_conf 222222100000001233322--1122368988999758678987799985893--99927896874378999----999 Q gi|254780603|r 199 LQKMHSWGFQTIGLSSDSKKP--LEQEIKNDKIALILGAEGKGLRPKTQETATS--MAHLHMPGIIKALNVSN----AAA 270 (282) Q Consensus 199 l~~~~~~~~~i~~~~~~~~~~--~~~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~--~v~Ip~~~~~~SLNvs~----a~a 270 (282) ++.....+..++ ++..+... .......++.++++|.|| |.++.-++.... ...+.+..++ |=+.+ |+| T Consensus 158 l~~~~~~~~~~i-~~~~~~~~~~~~~~~~~~~i~i~IGPEG-Gfs~~E~~~l~~~g~~~vsLG~~I--LR~ETA~i~als 233 (243) T PRK11713 158 LEALADGDLRLV-LHPEANLAAALKSLKPAGKVLLLIGPEG-GFSPEEIELLREAGFTPVSLGPRI--LRTETAALAALA 233 (243) T ss_pred HHHCCCCCCEEE-ECCCCCCCCCCCCCCCCCCEEEEECCCC-CCCHHHHHHHHHCCCEEEECCCCC--CHHHHHHHHHHH T ss_conf 953867782899-8688775432011257885899987888-999999999998898898679991--357749999999 Q ss_pred HHHHHH Q ss_conf 999999 Q gi|254780603|r 271 VALYIT 276 (282) Q Consensus 271 i~l~~~ 276 (282) +++|.+ T Consensus 234 ~l~~~~ 239 (243) T PRK11713 234 ALQALL 239 (243) T ss_pred HHHHHH T ss_conf 999985 No 25 >pfam09895 DUF2122 RecB-family nuclease (DUF2122). This domain, found in various hypothetical archaeal proteins, has no known function. Probab=94.38 E-value=0.065 Score=30.38 Aligned_cols=83 Identities=14% Similarity=0.200 Sum_probs=57.0 Q ss_pred CCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCC-CCCCCCCEEEEECCCCCCCCHHHHHHCCCEEEE-CCCCCCCHHHH Q ss_conf 0122232211222222210000000123332211-223689889997586789877999858939992-78968743789 Q gi|254780603|r 188 PYIRISNLTDALQKMHSWGFQTIGLSSDSKKPLE-QEIKNDKIALILGAEGKGLRPKTQETATSMAHL-HMPGIIKALNV 265 (282) Q Consensus 188 ~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~~-~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~I-p~~~~~~SLNv 265 (282) ++....++.++++-++-. .+|.++..+..... .....+++++||+....|+|+.-++.-+ .+++ -+...+-++ T Consensus 21 ~llvl~dl~DAiEvL~P~--~v~~i~~~~~~~~~~~l~~~~rvllvf~G~e~gfsk~El~~g~-~v~~~~v~~~iG~i-- 95 (105) T pfam09895 21 SLLVLPDLKDAIELLKPD--VVYLLSRAAEGIKKEVLKVEGRVLLVFSGAEPGFSKIELELGE-AVYIKGVESDVGPI-- 95 (105) T ss_pred CEEEECCHHHHHHHHCCC--EEEEECCCCCCCCHHHHHCCCCEEEEECCCCCCCCHHHHCCCC-EEEEECCCCCCCCH-- T ss_conf 589838778899872987--7999757665620345530583899981898897965614884-47860365566628-- Q ss_pred HHHHHHHHHHH Q ss_conf 99999999999 Q gi|254780603|r 266 SNAAAVALYIT 276 (282) Q Consensus 266 s~a~ai~l~~~ 276 (282) -++||+||++ T Consensus 96 -g~~Ai~Ly~l 105 (105) T pfam09895 96 -GALAIILYLL 105 (105) T ss_pred -HHHHHHHHHC T ss_conf -8999999509 No 26 >pfam04452 Methyltrans_RNA RNA methyltransferase. RNA methyltransferases modify nucleotides during ribosomal RNA maturation in a site-specific manner. The Escherichia coli member is specific for U1498 methylation. Probab=93.79 E-value=0.21 Score=27.47 Aligned_cols=135 Identities=21% Similarity=0.343 Sum_probs=72.3 Q ss_pred EEEEECCCCCHHHHHHHHHHHHHHHCCCC--CCCCCCCCCC------------HHHHHHHHHHH-HHHHC-CCCCCCCCC Q ss_conf 68872343206889999999864200110--0136863200------------00013444333-32110-122232211 Q gi|254780603|r 134 LLMVLDHVNDPHNIGAILRSAVAFSCDGI--ITTKRYSPSE------------SAVLAKSASGA-LEHIP-YIRISNLTD 197 (282) Q Consensus 134 ~~i~ld~i~dp~NlG~I~Rta~a~g~~~v--il~~~~~~~~------------~~~~~ras~Ga-~~~l~-~~~~~~~~~ 197 (282) .+.++-.+-.|.++--+++-|.-.|++.+ +.++++...+ ..-++.|+.=+ -.++| +....++.+ T Consensus 62 ~i~l~~al~K~~~~~~il~k~tElGV~~i~p~~~ers~~k~~~~~~~~k~~R~~~i~~~A~eQs~r~~lP~I~~~~~l~~ 141 (225) T pfam04452 62 KITLAQALPKGDRLELILQKATELGVDRIVPLISERSVVKLDGKRADKKLERWQKIAIEAAEQSGRTRLPEVLPPISLKE 141 (225) T ss_pred EEEEEEEEECCHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCEECCCCCHHH T ss_conf 17999950072789999999986287657999840354544303466659999999999999719982877726689999 Q ss_pred CCCCCCCCCCHHHHCCCCCCCC---CCC---CCCCCCEEEEECCCCCCCCHHHHHHCC--CEEEECCCCCCCHHHHHHHH Q ss_conf 2222222100000001233322---112---236898899975867898779998589--39992789687437899999 Q gi|254780603|r 198 ALQKMHSWGFQTIGLSSDSKKP---LEQ---EIKNDKIALILGAEGKGLRPKTQETAT--SMAHLHMPGIIKALNVSNAA 269 (282) Q Consensus 198 ~l~~~~~~~~~i~~~~~~~~~~---~~~---~~~~~~~~lv~G~E~~Gl~~~~~~~~d--~~v~Ip~~~~~~SLNvs~a~ 269 (282) +++....... +.++.++... ... .....+.++++|.|| |.++.-.+..- ....+.+..++ |=+-+|+ T Consensus 142 ~l~~~~~~~~--~i~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPEG-Gfs~~E~~~l~~~g~~~v~LG~~I--LR~ETA~ 216 (225) T pfam04452 142 LLEELDDADK--LILHEEAAKSLGELSELLASLKGGKVLLIIGPEG-GFSPEEIELLKEAGFTPVSLGPRI--LRTETAA 216 (225) T ss_pred HHHHCCCCCE--EEEECCCCCCCCCCHHHHHCCCCCCEEEEECCCC-CCCHHHHHHHHHCCCEEEECCCCC--CCHHHHH T ss_conf 9961866888--9992665544321012321035784589988988-999999999998899898479994--6078599 Q ss_pred HHHH Q ss_conf 9999 Q gi|254780603|r 270 AVAL 273 (282) Q Consensus 270 ai~l 273 (282) -.++ T Consensus 217 i~al 220 (225) T pfam04452 217 LAAL 220 (225) T ss_pred HHHH T ss_conf 9999 No 27 >PRK02135 hypothetical protein; Provisional Probab=93.75 E-value=0.052 Score=30.95 Aligned_cols=115 Identities=17% Similarity=0.219 Sum_probs=74.7 Q ss_pred CHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCC Q ss_conf 06889999999864200110013686320000013444333321101222322112222222100000001233322112 Q gi|254780603|r 143 DPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYIRISNLTDALQKMHSWGFQTIGLSSDSKKPLEQ 222 (282) Q Consensus 143 dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~~~ 222 (282) |=.++...++.|..-... +.+ ....++.|- ++...++.+.++.+++.+ ++|-++.+|. ++.+ T Consensus 79 dERsia~~I~kaL~~~~~----~~~-------~~~e~~pGI-----~v~~~~~e~~l~e~~~~~-~~~~Ld~~G~-~i~~ 140 (199) T PRK02135 79 DERSLAALIKKALDASAG----IGE-------QEREVTPGI-----YVRTGSFEDLLQELAEDG-QLYYLHEDGE-DIRD 140 (199) T ss_pred CHHHHHHHHHHHHCCCCC----CCC-------CEEEECCCE-----EEECCCHHHHHHHHHCCC-CEEEECCCCC-CHHC T ss_conf 379999999999758899----888-------347747998-----990889999999985379-7999889999-5000 Q ss_pred CCCCCCEEEEECCCCCCCCHHHHHHC----CCEEEECCCCCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 23689889997586789877999858----93999278968743789999999999998761 Q gi|254780603|r 223 EIKNDKIALILGAEGKGLRPKTQETA----TSMAHLHMPGIIKALNVSNAAAVALYITQNHF 280 (282) Q Consensus 223 ~~~~~~~~lv~G~E~~Gl~~~~~~~~----d~~v~Ip~~~~~~SLNvs~a~ai~l~~~~~~~ 280 (282) ..++++.+||+|- ..|++++-.+.. ...|++ +-.+|=.+++.+|+-|++.++- T Consensus 141 ~~~~~~~~FILsD-h~~~~~~e~~~L~~~g~~~iSL----Gp~~L~a~~cI~iiH~~LD~~~ 197 (199) T PRK02135 141 VEFPANPVFVLGD-HIGMTKEEENLLKRLGAEKISL----GPKMLHADHCITLIHNELDRRG 197 (199) T ss_pred CCCCCCCEEEEEC-CCCCCHHHHHHHHHCCCCEEEE----CCHHHHHHHHHHHHHHHHHCCC T ss_conf 5689998799628-9998878999998708831654----7388765058999999875037 No 28 >pfam01994 Trm56 tRNA ribose 2'-O-methyltransferase, aTrm56. This family is an aTrm56 that catalyses the 2'-O-methylation of the cytidine residue in archaeal tRNA, using S-adenosyl-L-methionine. Biochemical assays showed that aTrm56 forms a dimer and prefers the L-shaped tRNA to the lambda form as its substrate. aTrm56 consists of the SPOUT domain, which contains the characteristic deep trefoil knot for AdoMet binding, and a unique C-terminal beta-hairpin. Probab=93.29 E-value=0.096 Score=29.41 Aligned_cols=81 Identities=16% Similarity=0.041 Sum_probs=58.5 Q ss_pred CCCCCCCCCCCCCCCCCHHHHCCCCCCC---CCCCCC-CCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHH Q ss_conf 2232211222222210000000123332---211223-689889997586789877999858939992789687437899 Q gi|254780603|r 191 RISNLTDALQKMHSWGFQTIGLSSDSKK---PLEQEI-KNDKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVS 266 (282) Q Consensus 191 ~~~~~~~~l~~~~~~~~~i~~~~~~~~~---~~~~~~-~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs 266 (282) ...++..+++..++.|-.++.+++-|.. -+.++. ..++..+|+|.|- +|.++-+.||+.|.|--...-| - T Consensus 9 ~~~~~~~~ir~~k~~~G~vVHLTMYG~~i~~~i~~Ir~~~~~ilvVVGaeK--VP~evye~ADyNVaVgNQPHSE----V 82 (121) T pfam01994 9 FGVNWRSYIREWKEKGGIVVHLTMYGENIDDVIPEIRESGKDILVVVGAEK--VPGEVYELADYNVAVGNQPHSE----V 82 (121) T ss_pred ECCCHHHHHHHHHHCCCEEEEEECCCCCHHHHHHHHHHCCCCEEEEECCCC--CCHHHHHHCCCCEEECCCCCHH----H T ss_conf 767989999998763988999953688668877786503886799977873--8999984355415527887089----9 Q ss_pred HHHHHHHHHHH Q ss_conf 99999999998 Q gi|254780603|r 267 NAAAVALYITQ 277 (282) Q Consensus 267 ~a~ai~l~~~~ 277 (282) .|.||+|..+. T Consensus 83 AALAiFLdrl~ 93 (121) T pfam01994 83 AALAVFLDRLF 93 (121) T ss_pred HHHHHHHHHHC T ss_conf 99999999861 No 29 >pfam04407 DUF531 Protein of unknown function (DUF531). Family of hypothetical archaeal proteins. Probab=91.52 E-value=0.28 Score=26.76 Aligned_cols=136 Identities=22% Similarity=0.197 Sum_probs=73.4 Q ss_pred EEEEECCCCCHH-----HHHHHHHH---HHHHHCCCCCCCCCCCCCCHHHHH-----HHHHHHH--HHHCCCCCCCCCCC Q ss_conf 688723432068-----89999999---864200110013686320000013-----4443333--21101222322112 Q gi|254780603|r 134 LLMVLDHVNDPH-----NIGAILRS---AVAFSCDGIITTKRYSPSESAVLA-----KSASGAL--EHIPYIRISNLTDA 198 (282) Q Consensus 134 ~~i~ld~i~dp~-----NlG~I~Rt---a~a~g~~~vil~~~~~~~~~~~~~-----ras~Ga~--~~l~~~~~~~~~~~ 198 (282) +.++|.+-.|+. ++-+|+|. |.|||++--++.=. ++......+ ..+.|.- +...++. .|-..+ T Consensus 2 lTl~LyNtYd~~k~~e~H~RaIARAapic~Af~~~LAL~~FP-~~~~~~el~~~v~~~TtIG~~G~yl~~L~~-~nr~~i 79 (174) T pfam04407 2 LTLGLYNTYDKKKVHEAHYRAIARAAPICYAFGFHLALFGFP-FDMTPKELAEYVADKTTIGESGKYLLELAE-SNKLHV 79 (174) T ss_pred EEEEEEECCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEECCC-CCCCHHHHHHHHHHCCCCCCCHHHHHHHHH-CCCEEE T ss_conf 379998446877566089999984604766417877987798-877879999997642732776799999987-496789 Q ss_pred CC----C-CCCCCCHHHHCC-CCCCCCC-----CCCCC-CCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHH Q ss_conf 22----2-222100000001-2333221-----12236-89889997586789877999858939992789687437899 Q gi|254780603|r 199 LQ----K-MHSWGFQTIGLS-SDSKKPL-----EQEIK-NDKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVS 266 (282) Q Consensus 199 l~----~-~~~~~~~i~~~~-~~~~~~~-----~~~~~-~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs 266 (282) ++ . ..+.|-.|+.++ ++.++.. .+... .++.++++|=-.+|||+++++.|++..-|- |.-=||-.. T Consensus 80 ~d~p~k~fp~qfG~~IaTT~kPd~~K~~~p~eia~~~l~~~s~~lliGLGr~GLPk~i~~~a~yHldiT--gkgIsLETc 157 (174) T pfam04407 80 IDFPKKGFPPQFGEVVATTSKPDEKKAITPEDVAREALRNKSFLLLIGLGRHGLPKELFESARYHLDIT--GKGVSLETC 157 (174) T ss_pred EECCCCCCCHHCCCEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHHCHHHEEEC--CCCEEEEEC T ss_conf 836300383320965887789984557897999998742886799994078888699986431106612--783136620 Q ss_pred HHHHHHH Q ss_conf 9999999 Q gi|254780603|r 267 NAAAVAL 273 (282) Q Consensus 267 ~a~ai~l 273 (282) +|-+.+- T Consensus 158 TAiGaI~ 164 (174) T pfam04407 158 TAIGAIP 164 (174) T ss_pred HHHHHHH T ss_conf 4561699 No 30 >pfam04013 DUF358 Protein of unknown function (DUF358). The proteins in this family are around 200 amino acids long with the exception of the Archaeoglobus fulgidus protein AF_1056 that has an additional 100 amino acids at its amino terminus. The function of these bacterial protein is unknown, however, they do contain several conserved histidines and aspartates that might form a metal binding site. Probab=90.34 E-value=0.3 Score=26.55 Aligned_cols=118 Identities=14% Similarity=0.145 Sum_probs=73.6 Q ss_pred CHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCC Q ss_conf 06889999999864200110013686320000013444333321101222322112222222100000001233322112 Q gi|254780603|r 143 DPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYIRISNLTDALQKMHSWGFQTIGLSSDSKKPLEQ 222 (282) Q Consensus 143 dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~~~ 222 (282) |-.+++.++|.|..-... +.+.+ ..++.|- ++...++.+.++++.+ ++++|-++.+|. ++.+ T Consensus 79 dERsiA~~I~kal~~~~~----~~~~~-------~e~~pGI-----~v~~~~fe~ll~e~~e-~~~~~~Ld~~G~-~i~~ 140 (199) T pfam04013 79 DERSIAILIKKALRAVKE----SGKQW-------RKVLPGI-----YVSRMGFEALIRELSE-FKPLYYLHEDGG-DISN 140 (199) T ss_pred HHHHHHHHHHHHHCCCCC----CCCCE-------EEECCCE-----EEECCCHHHHHHHHHC-CCCEEEECCCCC-CCCC T ss_conf 388999999999716788----88743-------7846998-----9949899999999855-897999978898-4323 Q ss_pred CCCC-CCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 2368-98899975867898779998589399927896874378999999999999876 Q gi|254780603|r 223 EIKN-DKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVSNAAAVALYITQNH 279 (282) Q Consensus 223 ~~~~-~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs~a~ai~l~~~~~~ 279 (282) ..++ .+.+||+|-- .|++++-.+........+.+=+-.+|=.+++.+|+-|++.|. T Consensus 141 ~~~~~~~~~FiL~Dh-~~~~~~e~~~L~~~~~~~iSLGp~~L~a~hcI~ivH~~LD~~ 197 (199) T pfam04013 141 VKIPPNNPVFILGDH-IGLPEEDEKFLERILALKVSLGPLSLHASHCITLVHNHLDRL 197 (199) T ss_pred CCCCCCCCEEEECCC-CCCCHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHHHHHHCC T ss_conf 557788976985599-998867888886448821553738888757999999987316 No 31 >KOG0838 consensus Probab=90.31 E-value=0.078 Score=29.91 Aligned_cols=53 Identities=25% Similarity=0.259 Sum_probs=42.3 Q ss_pred CCCCCCCEEEEECCCCCCCCHHHHHH---CCCEEEECCC-CCCCHHHHHHHHHHHHHH Q ss_conf 22368988999758678987799985---8939992789-687437899999999999 Q gi|254780603|r 222 QEIKNDKIALILGAEGKGLRPKTQET---ATSMAHLHMP-GIIKALNVSNAAAVALYI 275 (282) Q Consensus 222 ~~~~~~~~~lv~G~E~~Gl~~~~~~~---~d~~v~Ip~~-~~~~SLNvs~a~ai~l~~ 275 (282) .+-.-+++.++.|++ +++++.+.+. |+..+.|++- ...+||||++|+++.++. T Consensus 133 ~~lg~~~v~lv~~n~-s~lS~~vskss~gale~l~I~q~~~~~efl~vsvaaG~~l~~ 189 (271) T KOG0838 133 YFLGADGVLLVKGNS-SPLSPVVSKSSAGALEVLPIRQVDNPLEFLNVSVAAGIRLHG 189 (271) T ss_pred HHHCCCCEEEEECCC-CCCCHHHHHHHHCHHHEEEHHHCCCHHHHHHHHHHCCEEEEE T ss_conf 874677158973368-878646777650214166387738889998999867558999 No 32 >TIGR01362 KDO8P_synth 3-deoxy-8-phosphooctulonate synthase; InterPro: IPR006269 These sequences describe 2-dehydro-3-deoxyphosphooctonate aldolase. Alternate names include 3-deoxy-d-manno-octulosonic acid 8-phosphate and KDO-8 phosphate synthetase. It catalyzes the aldol condensation of phosphoenolpyruvate with D-arabinose 5-phosphate. phosphoenolpyruvate + D-arabinose 5-phosphate + H_2O = 2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate In Gram-negative bacteria, this is the first step in the biosynthesis of 3-deoxy-D-manno-octulosonate, part of the oligosaccharide core of lipopolysaccharide. ; GO: 0008676 3-deoxy-8-phosphooctulonate synthase activity, 0008152 metabolic process, 0005737 cytoplasm. Probab=81.63 E-value=0.81 Score=24.10 Aligned_cols=56 Identities=25% Similarity=0.420 Sum_probs=39.4 Q ss_pred CCCCCHH-----HHH-----------HHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC Q ss_conf 3432068-----899-----------999998642001100136863200000134443333211012223221122222 Q gi|254780603|r 139 DHVNDPH-----NIG-----------AILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYIRISNLTDALQKM 202 (282) Q Consensus 139 d~i~dp~-----NlG-----------~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~ 202 (282) +-||-|+ =.| +|+|+|.|.|++||++.-| .||-|.+. .+--.+|+. +|+.+|..+ T Consensus 200 HSvQ~PgGkkl~G~G~~SGG~refvp~LARAA~AVG~~GlF~EtH-~DP~~A~S-----DGp~mlpL~---~LE~Ll~~l 270 (279) T TIGR01362 200 HSVQQPGGKKLDGLGGKSGGQREFVPTLARAAVAVGIDGLFIETH-PDPKNAKS-----DGPNMLPLD---ELEALLEKL 270 (279) T ss_pred CCEECCCCEEECCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEECC-CCCCCCCC-----CCCCCCCHH---HHHHHHHHH T ss_conf 240376871225777767987434679999889862431466217-88777788-----884678988---999999999 Q ss_pred C Q ss_conf 2 Q gi|254780603|r 203 H 203 (282) Q Consensus 203 ~ 203 (282) . T Consensus 271 ~ 271 (279) T TIGR01362 271 L 271 (279) T ss_pred H T ss_conf 9 No 33 >TIGR00046 TIGR00046 conserved hypothetical protein TIGR00046; InterPro: IPR006700 Methyltransferases (Mtases) are responsible for the transfer of methyl groups between two molecules. The transfer of the methyl group from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms. The reaction is catalyzed by Mtases and modifies DNA, RNA, proteins or small molecules, such as catechol, for regulatory purposes. Proteins in this entry are predicted to belong to the family of Mtases, based on a crystal structure showing close structural homology to known methyltransferases .. Probab=77.49 E-value=4.2 Score=20.02 Aligned_cols=130 Identities=14% Similarity=0.167 Sum_probs=73.5 Q ss_pred CCEEEEECCCCCHHHHHHHHHHHHHHHCCCC--CCCCCCCCCCHHH-HHH------------HHHHHHHHHC-CCCCCCC Q ss_conf 5068872343206889999999864200110--0136863200000-134------------4433332110-1222322 Q gi|254780603|r 132 SQLLMVLDHVNDPHNIGAILRSAVAFSCDGI--ITTKRYSPSESAV-LAK------------SASGALEHIP-YIRISNL 195 (282) Q Consensus 132 ~~~~i~ld~i~dp~NlG~I~Rta~a~g~~~v--il~~~~~~~~~~~-~~r------------as~Ga~~~l~-~~~~~~~ 195 (282) +.-+.+.-.+-++.++=.|+|-+.-.|+..+ +.++.|..-+... +.+ +-.+.--.+| |....++ T Consensus 79 ~~~~~~~~~~~~g~~~e~ii~~~~eLGv~~~~p~~~ers~~k~~~~~~~~K~~rw~KI~~eA~eQs~r~~~P~i~~~~~l 158 (258) T TIGR00046 79 PLKIHLAIVLIKGKKMEKIIRKLTELGVSKIIPLNAERSVVKLDIERAIKKLERWQKIVIEAAEQSGRNIVPEIKVPKNL 158 (258) T ss_pred CCCEEEEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHH T ss_conf 76289999753212342565456764678998888865304855778875778889999999862779989843205678 Q ss_pred C------CCCCCCCCCCCHHHHCCCCCCCCCC--C---CCCCCCEEEEECCCCCCCCHHHHHHCC--CEEEECCCC---C Q ss_conf 1------1222222210000000123332211--2---236898899975867898779998589--399927896---8 Q gi|254780603|r 196 T------DALQKMHSWGFQTIGLSSDSKKPLE--Q---EIKNDKIALILGAEGKGLRPKTQETAT--SMAHLHMPG---I 259 (282) Q Consensus 196 ~------~~l~~~~~~~~~i~~~~~~~~~~~~--~---~~~~~~~~lv~G~E~~Gl~~~~~~~~d--~~v~Ip~~~---~ 259 (282) . ++++++....-...-...+...... . ++-.....+|+|.|| |+|+.-..... ....|+... + T Consensus 159 ~qllqr~Q~~e~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~GPEG-Gfse~E~~~~~~~~f~~~~L~~~~LR 237 (258) T TIGR00046 159 KQLLQRMQDVEKLAESEEEALKLNFHPEASPLSANLEQIEQAGKIVIIIGPEG-GFSEKEIQLLKEKGFTPVLLGPRILR 237 (258) T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHCCCCCHHHHHHHHHCCCCCEEEEEECCC-CCCHHHHHHHHHCCCEECCCCCCCCH T ss_conf 99999865687641001013232210033111200122005570489981699-96888999998829824137887021 Q ss_pred CCH Q ss_conf 743 Q gi|254780603|r 260 IKA 262 (282) Q Consensus 260 ~~S 262 (282) +|+ T Consensus 238 tET 240 (258) T TIGR00046 238 TET 240 (258) T ss_pred HHH T ss_conf 226 No 34 >PRK04171 ribosome biogenesis protein; Provisional Probab=74.07 E-value=6.5 Score=18.92 Aligned_cols=80 Identities=14% Similarity=0.146 Sum_probs=54.9 Q ss_pred CCCCCCCCCCCCCHHHHCCCCCCC-CCCCCCC-CCCEEEEECCCCCC-CCHHHHHHCCCEEEECCCCCCCHHHHHHHHHH Q ss_conf 211222222210000000123332-2112236-89889997586789-87799985893999278968743789999999 Q gi|254780603|r 195 LTDALQKMHSWGFQTIGLSSDSKK-PLEQEIK-NDKIALILGAEGKG-LRPKTQETATSMAHLHMPGIIKALNVSNAAAV 271 (282) Q Consensus 195 ~~~~l~~~~~~~~~i~~~~~~~~~-~~~~~~~-~~~~~lv~G~E~~G-l~~~~~~~~d~~v~Ip~~~~~~SLNvs~a~ai 271 (282) +.+.+.. .+-.+++++..|.. .+.++-- .++.++|+|.=.+| .+.++.+..|..++|--. +|-.+++++- T Consensus 137 l~~~l~~---~~~kii~ls~~g~~~~~~~~~~~~~~~~~vIGaf~~G~f~~~~~~~~d~~~SIs~~----~Lsa~~v~~r 209 (221) T PRK04171 137 LSELLEE---NPGKIILLSEKGEPVKPKELAKELENPVVVIGGFPHGDFSSEVLEKADKKYSIYNE----PLDAWTVVSR 209 (221) T ss_pred HHHHHCC---CCCEEEEECCCCCCCCHHHHHHHCCCCEEEEEECCCCCCCCCCHHCCCCEEEEECC----CHHHHHHHHH T ss_conf 8997065---89859998358867289999742279769983016987660000136848998488----7699999999 Q ss_pred HHHHHHHHHC Q ss_conf 9999987614 Q gi|254780603|r 272 ALYITQNHFA 281 (282) Q Consensus 272 ~l~~~~~~~~ 281 (282) +++++-+..+ T Consensus 210 i~~a~E~~~G 219 (221) T PRK04171 210 IIAAAERALG 219 (221) T ss_pred HHHHHHHHHC T ss_conf 9999999867 No 35 >pfam02590 SPOUT_MTase Predicted SPOUT methyltransferase. This family of proteins are predicted to be SPOUT methyltransferases. Probab=72.35 E-value=7.2 Score=18.67 Aligned_cols=73 Identities=19% Similarity=0.221 Sum_probs=46.2 Q ss_pred CCCCCCCCCHHHHCCCCCCCCCCCC-----------CCCCCEEEEECCCCCCCCHHHHHHCCCEEEEC-CCCCCCHHHHH Q ss_conf 2222221000000012333221122-----------36898899975867898779998589399927-89687437899 Q gi|254780603|r 199 LQKMHSWGFQTIGLSSDSKKPLEQE-----------IKNDKIALILGAEGKGLRPKTQETATSMAHLH-MPGIIKALNVS 266 (282) Q Consensus 199 l~~~~~~~~~i~~~~~~~~~~~~~~-----------~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip-~~~~~~SLNvs 266 (282) ++.++... .++.+|..|.. +... .-..+.+|++|.- .|+++.+.+.||..+++- |. +.=. T Consensus 61 ~~~i~~~~-~~I~LDe~Gk~-~sS~~fa~~i~~~~~~g~~~i~FiIGGa-~G~~~~~~~~a~~~~Sls~mT-----~pH~ 132 (155) T pfam02590 61 LAAIPPGS-YVIALDERGKE-LSSEEFAKLLEDLRLKGKSDITFVIGGS-DGLSEEVLKRANEKLSLSKMT-----LPHQ 132 (155) T ss_pred HHHCCCCC-EEEEEECCCCC-CCHHHHHHHHHHHHHCCCCCEEEEEECC-CCCCHHHHHHHHHEEECCCCC-----CCHH T ss_conf 97379999-89999379983-7879999999999833897559998379-886989997566634413676-----5089 Q ss_pred HHHHHHHHHHHHH Q ss_conf 9999999999876 Q gi|254780603|r 267 NAAAVALYITQNH 279 (282) Q Consensus 267 ~a~ai~l~~~~~~ 279 (282) .|-.|++-+++|- T Consensus 133 larv~l~EQiYRa 145 (155) T pfam02590 133 LVRLLLAEQIYRA 145 (155) T ss_pred HHHHHHHHHHHHH T ss_conf 9999999999999 No 36 >COG1901 Uncharacterized conserved protein [Function unknown] Probab=68.66 E-value=4.1 Score=20.05 Aligned_cols=114 Identities=15% Similarity=0.200 Sum_probs=69.6 Q ss_pred CHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCC Q ss_conf 06889999999864200110013686320000013444333321101222322112222222100000001233322112 Q gi|254780603|r 143 DPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYIRISNLTDALQKMHSWGFQTIGLSSDSKKPLEQ 222 (282) Q Consensus 143 dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~~~ 222 (282) |-.|+...+.-|...++.+- ..-+ +.-|- +++-..++..+..+ ..+..+|-++.+|. ++.+ T Consensus 79 dErs~a~~i~kAL~~~~~~~-----~~~~-------~~pGi-----~V~~~~~e~ll~~l-~~~~~ly~L~E~G~-DI~~ 139 (197) T COG1901 79 DERSLAILIKKALDAELGKE-----QTRE-------VTPGI-----YVRNGGFEALLAEL-AEGRSLYYLHEDGR-DISE 139 (197) T ss_pred CHHHHHHHHHHHHHHHCCCC-----CEEE-------CCCCE-----EEECCCHHHHHHHH-HCCCCEEEECCCCC-CHHH T ss_conf 06778999999997431664-----2142-------37987-----99257899999998-65584799925786-4755 Q ss_pred CCCCCCEEEEECCCCCCCCHHHH----HHCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 23689889997586789877999----85893999278968743789999999999998761 Q gi|254780603|r 223 EIKNDKIALILGAEGKGLRPKTQ----ETATSMAHLHMPGIIKALNVSNAAAVALYITQNHF 280 (282) Q Consensus 223 ~~~~~~~~lv~G~E~~Gl~~~~~----~~~d~~v~Ip~~~~~~SLNvs~a~ai~l~~~~~~~ 280 (282) .++..+.+||+|.- -|++++-. +..+..|++- --||-.+++..++-+++.+|. T Consensus 140 v~~~~np~FIlGDH-~g~t~e~~k~L~r~~~~~ISlG----P~~lha~hcit~~h~~LD~~~ 196 (197) T COG1901 140 VDLIPNPVFILGDH-IGLTEEDEKLLERHAAKKISLG----PLSLHADHCITLLHNLLDRQG 196 (197) T ss_pred CCCCCCCEEEEECC-CCCCHHHHHHHHHHHCCEEEEC----CHHHHHHHHHHHHHHHHHHCC T ss_conf 55689966996178-8989789999998648536727----668888889999998775225 No 37 >PRK00103 SPOUT methyltransferase superfamily protein; Provisional Probab=63.59 E-value=11 Score=17.62 Aligned_cols=73 Identities=15% Similarity=0.164 Sum_probs=44.2 Q ss_pred CCCCCCCCHHHHCCCCCCCCCCCCC----------CCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHHHHH Q ss_conf 2222210000000123332211223----------689889997586789877999858939992789687437899999 Q gi|254780603|r 200 QKMHSWGFQTIGLSSDSKKPLEQEI----------KNDKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVSNAA 269 (282) Q Consensus 200 ~~~~~~~~~i~~~~~~~~~~~~~~~----------~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs~a~ 269 (282) +.++... .++.+|..|.. +.... -....+||+|.- .|+++++.+.||..+++--.- +.=..|- T Consensus 62 ~~~~~~~-~~I~LDe~Gk~-~sS~~fa~~l~~~~~~g~~i~FiIGGa-~G~~~~~~~~a~~~lSlS~mT----fpH~lar 134 (156) T PRK00103 62 AAIPKGA-RVVALDIRGKP-WTSEQFAKELERWRLDGRDVTFVIGGP-EGLSPAVKKRADQSWSLSKLT----LPHQLVR 134 (156) T ss_pred HHCCCCC-EEEEEECCCCC-CCHHHHHHHHHHHHHCCCCEEEEEECC-CCCCHHHHHHHHHEEEECCCC----CCHHHHH T ss_conf 8479999-89999179980-576999999999986399669999788-876989997432288713676----6289999 Q ss_pred HHHHHHHHHH Q ss_conf 9999999876 Q gi|254780603|r 270 AVALYITQNH 279 (282) Q Consensus 270 ai~l~~~~~~ 279 (282) -|++-+++|- T Consensus 135 ~il~EQiYRa 144 (156) T PRK00103 135 LVLAEQLYRA 144 (156) T ss_pred HHHHHHHHHH T ss_conf 9999999999 No 38 >pfam04705 TSNR_N Thiostrepton-resistance methylase, N terminus. This region is found in some members of the SpoU-type rRNA methylase family (pfam00588). Probab=55.49 E-value=15 Score=16.79 Aligned_cols=94 Identities=7% Similarity=0.187 Sum_probs=63.6 Q ss_pred CCCCHHHHHHHHHHHCCCCCCCCCEEEEEEHHHHHHHHHCCCEEEEEEEECCCC-CCCCCHHHHHHCCCCEEEECHHHHH Q ss_conf 223765677765431122111288199985788999997898189999973784-3354345543269969997689987 Q gi|254780603|r 24 RRNHRDYKKMQSFNQKSRHTSQPENLFLYGVHTVSAALNNPSRKIFQLLATKNA-LARLDWDANLPHPFPVKTVPPQTID 102 (282) Q Consensus 24 ~~~n~~~k~~~~l~~k~k~R~~~~~~iIeG~~~V~eaL~~~~~~i~~i~~te~~-~~~~~~~~~l~~~~~I~~v~~~~l~ 102 (282) .+..|.++++..+-+. .|-.....+||-..+..+++.+|-. +..+|..+.. ...........+++++..++...++ T Consensus 9 ~rSDPaVQRIiDvtk~--sRs~ikT~LiED~EPL~~~i~AGve-fieVYg~~~~p~~~~ll~~c~~r~i~vrli~~~i~N 85 (115) T pfam04705 9 NRSDPAVQRIIDVTKH--SRSVIKTTLIEDIEPLMQSIRAGVE-FIEVYGSDTVPFPGDLLDLCEKRGIPVRLIDASIVN 85 (115) T ss_pred CCCCHHHHHHHHHHHC--CHHHHHEEEECCCHHHHHHHHCCCE-EEEEEECCCCCCCHHHHHHHHHCCCCEEEECHHHHH T ss_conf 3776668889988644--2656410010375578998744707-989851157879848999998659841665588999 Q ss_pred HHHCCCCCCCCCCEEEEC Q ss_conf 752477777744202411 Q gi|254780603|r 103 KIVGKEAVHQGLALETAP 120 (282) Q Consensus 103 ~i~~~~~~hqGi~a~~~~ 120 (282) ++...+.-+..+.....| T Consensus 86 qlFk~erK~kvfGiArvP 103 (115) T pfam04705 86 QLFKTERKAKVFGIARVP 103 (115) T ss_pred HHHHCCCCCCEEEEECCC T ss_conf 987323566514574179 No 39 >PRK13398 3-deoxy-7-phosphoheptulonate synthase; Provisional Probab=54.02 E-value=5.6 Score=19.27 Aligned_cols=32 Identities=16% Similarity=0.347 Sum_probs=18.6 Q ss_pred EEEC---CCCCHHHHHHHHHHHHHHHCCCCCCCCC Q ss_conf 8723---4320688999999986420011001368 Q gi|254780603|r 136 MVLD---HVNDPHNIGAILRSAVAFSCDGIITTKR 167 (282) Q Consensus 136 i~ld---~i~dp~NlG~I~Rta~a~g~~~vil~~~ 167 (282) |++| .+.+..-+-.+.|.|.++|++|+++.-+ T Consensus 199 Vi~D~SHs~G~r~~v~~la~aAva~G~dGlfiE~H 233 (266) T PRK13398 199 IIVDPSHATGRRELVIPMAKAAIAAGADGLMIEVH 233 (266) T ss_pred EEECCCCCCCCHHHHHHHHHHHHHCCCCEEEEEEC T ss_conf 89888533567999999999999839988999826 No 40 >TIGR01456 CECR5 HAD-superfamily subfamily IIA hydrolase, TIGR01456, CECR5; InterPro: IPR006353 This hypothetical equivalog is a member of the Class IIA subfamily of the haloacid dehalogenase superfamily of aspartate-nucleophile hydrolases. The sequences modelled by this equivalog are all eukaryotes. One sequence is called "Cat Eye Syndrome critical region protein 5" (CECR5) . This gene has been cloned from a pericentromere region of human chromosome 22 believed to be the location of the gene or genes responsible for Cat Eye Syndrome. This is one of a number of candidate genes. The Schizosaccharomyces pombe sequence is annotated as "phosphatidyl synthase," however this is due entirely to a C-terminal region of the protein (outside the region of similarity of this HMM) which is highly homologous to a family of CDP-alcohol phosphatidyltransferases. The physical connection of the phosphatidyl synthase and the HAD-superfamily hydrolase domain in S. pombe may, however, be an important clue to the substrate for the hydrolases in this equivalog.. Probab=53.29 E-value=3.8 Score=20.24 Aligned_cols=16 Identities=6% Similarity=0.326 Sum_probs=6.5 Q ss_pred HHHHHHHHHCCCCCCC Q ss_conf 9999864200110013 Q gi|254780603|r 150 ILRSAVAFSCDGIITT 165 (282) Q Consensus 150 I~Rta~a~g~~~vil~ 165 (282) ..-.|..+||..|+-. T Consensus 97 v~~va~gyGF~nVv~~ 112 (325) T TIGR01456 97 VAEVAEGYGFKNVVSV 112 (325) T ss_pred HHHHHCCCCCCCEEEH T ss_conf 6888516885220216 No 41 >KOG3925 consensus Probab=52.76 E-value=4.4 Score=19.90 Aligned_cols=30 Identities=20% Similarity=0.409 Sum_probs=14.2 Q ss_pred CCHH-HHCCCCCCCCCCCCC----CCCCEEEEECCC Q ss_conf 0000-000123332211223----689889997586 Q gi|254780603|r 206 GFQT-IGLSSDSKKPLEQEI----KNDKIALILGAE 236 (282) Q Consensus 206 ~~~i-~~~~~~~~~~~~~~~----~~~~~~lv~G~E 236 (282) ||-+ ++++..|. .+.+.. -+....||||.= T Consensus 277 GYD~~vg~s~rg~-~I~s~~~~~~t~~~iLlvfg~l 311 (371) T KOG3925 277 GYDFVVGTSTRGS-AIASLSLEAETPPHILLVFGGL 311 (371) T ss_pred CCCEEEEECCCCC-CCCCCCCCCCCCCCEEEEEECH T ss_conf 8446987246776-3000200258887189996030 No 42 >COG3426 Butyrate kinase [Energy production and conversion] Probab=51.00 E-value=7.6 Score=18.54 Aligned_cols=51 Identities=22% Similarity=0.192 Sum_probs=37.1 Q ss_pred CCCCHHHHHHHH--HHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCC Q ss_conf 432068899999--998642001100136863200000134443333211012 Q gi|254780603|r 140 HVNDPHNIGAIL--RSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYI 190 (282) Q Consensus 140 ~i~dp~NlG~I~--Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~ 190 (282) +-+.+-|||+|+ |.|.++|+...|+.+-.+|...+.+.=+.+--+.+=.|+ T Consensus 102 ~G~haSnLGaiiA~~ia~~~gvPayIVDPvvVDEm~~~Ar~SG~p~i~RkSiF 154 (358) T COG3426 102 QGEHASNLGAIIANRIAKALGVPAYIVDPVVVDEMEDVARFSGIPEIERKSIF 154 (358) T ss_pred CCCCHHHHHHHHHHHHHHHCCCCEEEECCEEHHHCCHHHHHCCCCCCHHHHHH T ss_conf 87551225679999876640997166675003220545510689662057788 No 43 >COG2106 Uncharacterized conserved protein [Function unknown] Probab=47.91 E-value=12 Score=17.42 Aligned_cols=63 Identities=16% Similarity=0.162 Sum_probs=34.0 Q ss_pred CCCCCCCCCCCCCHHHHCCCCCCCCCCCCC--CCCCEEEEECCCCCCCCHHHHH-----HCCCEEE-ECCCC Q ss_conf 211222222210000000123332211223--6898899975867898779998-----5893999-27896 Q gi|254780603|r 195 LTDALQKMHSWGFQTIGLSSDSKKPLEQEI--KNDKIALILGAEGKGLRPKTQE-----TATSMAH-LHMPG 258 (282) Q Consensus 195 ~~~~l~~~~~~~~~i~~~~~~~~~~~~~~~--~~~~~~lv~G~E~~Gl~~~~~~-----~~d~~v~-Ip~~~ 258 (282) +.++++.....+ .+++++-.|..+..+.. ...+..++||+=..||.+-... ..|..+. +|-.+ T Consensus 175 L~e~~~~~~~~~-vvi~tsr~g~~~~~e~~~~~~~~~~~~fg~P~~gv~~~~~~~~~~~~~d~~~N~~p~Qg 245 (272) T COG2106 175 LNELLKGFDLDV-VVIATSRYGPLDVRETEAPLKSKVTLVFGGPEKGVLEILKVGGVKLEFDIVVNFIPGQG 245 (272) T ss_pred HHHHHHCCCCCC-EEEEECCCCCCEEEECCCCCCCCCEEEECCCCCCHHEECCCCCCCCCCCEEEEECCCCC T ss_conf 887763368873-59984355865001225666776058964865570001144566643361577348755 No 44 >pfam02598 DUF171 Uncharacterized ACR, COG2106. Probab=43.40 E-value=13 Score=17.17 Aligned_cols=66 Identities=26% Similarity=0.272 Sum_probs=33.5 Q ss_pred CCCCCCCCCCCCCCCC-CCC-HHHHCCCCCCCCCCCCCC------C-CCEEEEECC--CCCCCCHH-----HHHHCCCEE Q ss_conf 1222322112222222-100-000001233322112236------8-988999758--67898779-----998589399 Q gi|254780603|r 189 YIRISNLTDALQKMHS-WGF-QTIGLSSDSKKPLEQEIK------N-DKIALILGA--EGKGLRPK-----TQETATSMA 252 (282) Q Consensus 189 ~~~~~~~~~~l~~~~~-~~~-~i~~~~~~~~~~~~~~~~------~-~~~~lv~G~--E~~Gl~~~-----~~~~~d~~v 252 (282) +....++.+.++.+.- .|| .+++++..|. ++.+... + ....+|||+ ...|.-+. ..+.-|..+ T Consensus 180 Vr~a~sl~~v~~~~~~~~gYd~~I~tS~~G~-~~~~~~~~~~~~~~~~~~lvVFG~~~~~~~~~~~~~~~~~~~~fD~~l 258 (283) T pfam02598 180 VRIASSLSDVFKKSPFPEGYDVTIGTSRRGK-DISEAELEIKLMENFKHILLVFGGWEPLKGSDEILKDQGPKELFDGYL 258 (283) T ss_pred EEEECCHHHHHHCCCCCCCCCEEEEECCCCC-CCCHHHHCCCCCCCCCCEEEEECCCHHHHHHHHHHCCCCCHHHCCEEE T ss_conf 9983689999623876788886999899996-463100011455677848999799436510344411356254378789 Q ss_pred EEC Q ss_conf 927 Q gi|254780603|r 253 HLH 255 (282) Q Consensus 253 ~Ip 255 (282) ..+ T Consensus 259 N~~ 261 (283) T pfam02598 259 NTP 261 (283) T ss_pred ECC T ss_conf 768 No 45 >COG3222 Uncharacterized protein conserved in bacteria [Function unknown] Probab=43.37 E-value=12 Score=17.44 Aligned_cols=77 Identities=21% Similarity=0.195 Sum_probs=51.7 Q ss_pred HHHHHHHHHHHHHCCC---CCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCC Q ss_conf 8999999986420011---0013686320000013444333321101222322112222222100000001233322112 Q gi|254780603|r 146 NIGAILRSAVAFSCDG---IITTKRYSPSESAVLAKSASGALEHIPYIRISNLTDALQKMHSWGFQTIGLSSDSKKPLEQ 222 (282) Q Consensus 146 NlG~I~Rta~a~g~~~---vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~~~ 222 (282) .+|.=++-+..-++++ |++....|+..+...+-.+.-++..+|.+-..- + .-||++.|+......-+.. T Consensus 88 d~gdRlars~~~a~~~~~~VliIg~DcP~lt~elLa~a~taL~~~paVLGpa----~----dGGy~llgLrr~~pe~fe~ 159 (211) T COG3222 88 DLGDRLARSHVDAFDGSYPVLIIGMDCPGLTAELLADAFTALLQIPAVLGPA----F----DGGYYLLGLRRFAPELFEA 159 (211) T ss_pred CHHHHHHHHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHHCCCCEECCC----C----CCCEEEEEEECCCHHHHHC T ss_conf 8889999999997568872799825897647999999999971476102222----2----5837899731048999950 Q ss_pred CCCCCCEE Q ss_conf 23689889 Q gi|254780603|r 223 EIKNDKIA 230 (282) Q Consensus 223 ~~~~~~~~ 230 (282) ++|..+.+ T Consensus 160 ipwg~~~v 167 (211) T COG3222 160 IPWGTPDV 167 (211) T ss_pred CCCCCCHH T ss_conf 88887459 No 46 >COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion] Probab=43.17 E-value=24 Score=15.65 Aligned_cols=120 Identities=13% Similarity=0.189 Sum_probs=76.3 Q ss_pred CCEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCC---------C---CCCCCCC Q ss_conf 506887234320688999999986420011001368632000001344433332110122---------2---3221122 Q gi|254780603|r 132 SQLLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYIR---------I---SNLTDAL 199 (282) Q Consensus 132 ~~~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~---------~---~~~~~~l 199 (282) ++.+++|-|++--|-.-|++.-|+-|. ..--...+...+-...|. ||++++.++. + .++.+++ T Consensus 202 ~~~vi~LVGPTGVGKTTTlAKLAar~~---~~~~~~kVaiITtDtYRI--GA~EQLk~Ya~im~vp~~vv~~~~el~~ai 276 (407) T COG1419 202 QKRVIALVGPTGVGKTTTLAKLAARYV---MLKKKKKVAIITTDTYRI--GAVEQLKTYADIMGVPLEVVYSPKELAEAI 276 (407) T ss_pred CCCEEEEECCCCCCHHHHHHHHHHHHH---HHCCCCCEEEEEECCCHH--HHHHHHHHHHHHHCCCEEEECCHHHHHHHH T ss_conf 685799989988758879999999997---532576068997144115--289999999998699559963999999999 Q ss_pred CCCCCCCCHHHHCCCCCCC---------CCCCCCCCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCC Q ss_conf 2222210000000123332---------2112236898899975867898779998589399927896 Q gi|254780603|r 200 QKMHSWGFQTIGLSSDSKK---------PLEQEIKNDKIALILGAEGKGLRPKTQETATSMAHLHMPG 258 (282) Q Consensus 200 ~~~~~~~~~i~~~~~~~~~---------~~~~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~ 258 (282) ..++....-++.+.+.+.. .+.+...+-.+.|||-.-.+. +++.+.-++.-.+|..+ T Consensus 277 ~~l~~~d~ILVDTaGrs~~D~~~i~el~~~~~~~~~i~~~Lvlsat~K~--~dlkei~~~f~~~~i~~ 342 (407) T COG1419 277 EALRDCDVILVDTAGRSQYDKEKIEELKELIDVSHSIEVYLVLSATTKY--EDLKEIIKQFSLFPIDG 342 (407) T ss_pred HHHHCCCEEEEECCCCCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCCH--HHHHHHHHHHCCCCCCE T ss_conf 9853188899968998833789999999997035662179998457646--88999999724588661 No 47 >pfam09837 DUF2064 Uncharacterized protein conserved in bacteria (DUF2064). This domain, found in various prokaryotic proteins, has no known function. Probab=40.36 E-value=27 Score=15.40 Aligned_cols=77 Identities=18% Similarity=0.151 Sum_probs=49.9 Q ss_pred CCCHHHHHHHHHHHHH----HHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCC Q ss_conf 3206889999999864----200110013686320000013444333321101222322112222222100000001233 Q gi|254780603|r 141 VNDPHNIGAILRSAVA----FSCDGIITTKRYSPSESAVLAKSASGALEHIPYIRISNLTDALQKMHSWGFQTIGLSSDS 216 (282) Q Consensus 141 i~dp~NlG~I~Rta~a----~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~~~~~i~~~~~~~ 216 (282) .|-.+|+|.=|+-|.. .|.+.|++....++.+++..++.+.-++.+-++ .+--..+-||+++|+.... T Consensus 39 ~Q~~gdLG~Rm~~a~~~~~~~g~~~v~lIGsD~P~l~~~~l~~A~~~L~~~d~--------VlgPa~DGGy~LiG~~~~~ 110 (121) T pfam09837 39 PQGGGDLGERMARAFRQAFAAGYRPVLLIGTDCPDLTAELLAQAFEALERHDA--------VLGPAEDGGYYLLGLRRPT 110 (121) T ss_pred ECCCCCHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCHHHHHHHHHHHHCCCE--------EEEECCCCCEEEEEECCCC T ss_conf 25999989999999999984389858998488465899999999998621997--------9997488999999747778 Q ss_pred CCCCCCCCC Q ss_conf 322112236 Q gi|254780603|r 217 KKPLEQEIK 225 (282) Q Consensus 217 ~~~~~~~~~ 225 (282) ...+.++.| T Consensus 111 ~~lF~~i~W 119 (121) T pfam09837 111 PDLFEGVPW 119 (121) T ss_pred HHHCCCCCC T ss_conf 887079998 No 48 >PRK11561 isovaleryl CoA dehydrogenase; Provisional Probab=38.85 E-value=17 Score=16.58 Aligned_cols=25 Identities=32% Similarity=0.470 Sum_probs=21.1 Q ss_pred CCCCCCCCCCCEEEEECCCCCCCCH Q ss_conf 2211223689889997586789877 Q gi|254780603|r 218 KPLEQEIKNDKIALILGAEGKGLRP 242 (282) Q Consensus 218 ~~~~~~~~~~~~~lv~G~E~~Gl~~ 242 (282) .+-.+..|.+-.++.+|.|++|+.. T Consensus 266 ~pSaEve~~gA~a~lvGeegrGv~~ 290 (538) T PRK11561 266 NASCEVEFQDAIGWLLGEEGEGIRL 290 (538) T ss_pred CCEEEEEECCCEEEEECCCCCCHHH T ss_conf 8828999888079983578857899 No 49 >TIGR02894 DNA_bind_RsfA transcription factor, RsfA family; InterPro: IPR014243 This entry represents a set of transcription factors found in some endospore-forming bacteria within the Firmicutes (low-GC Gram-positive bacteria). In some species these proteins are encoded multiple times. The best characterised protein in this entry is the prespore-specific transcription factor RsfA from Bacillus subtilis, previously known as YwfN. Expression of RsfA is controlled by sigma factor F, and it seems to improve the efficiency of sporulation by fine-tuning the expression of genes in the sigma F regulon, particularly the timing of their expression . It also negatively regulates spoIIR and its own synthesis. A paralog in B. subtilis is designated YlbO, though its function is not known. A highly variable linker region separates two very strongly conserved sequence regions within the protein. . Probab=38.58 E-value=6.5 Score=18.91 Aligned_cols=28 Identities=36% Similarity=0.425 Sum_probs=19.8 Q ss_pred EEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHH Q ss_conf 88723432068899999998642001100136863200000134 Q gi|254780603|r 135 LMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAK 178 (282) Q Consensus 135 ~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~r 178 (282) +-++|.|.|.=| ||||||||- ||..|-+ T Consensus 30 L~AFeEVG~~L~-----RT~AACGFR-----------WNa~VRk 57 (163) T TIGR02894 30 LAAFEEVGDALN-----RTAAACGFR-----------WNAVVRK 57 (163) T ss_pred HHHHHHHCCCCC-----CCCHHCCCC-----------HHHHHHH T ss_conf 778887331147-----873110253-----------3578758 No 50 >pfam07047 OPA3 Optic atrophy 3 protein (OPA3). This family consists of several optic atrophy 3 (OPA3) proteins. OPA3 deficiency causes type III 3-methylglutaconic aciduria (MGA) in humans. This disease manifests with early bilateral optic atrophy, spasticity, extrapyramidal dysfunction, ataxia, and cognitive deficits, but normal longevity. Probab=37.74 E-value=25 Score=15.58 Aligned_cols=22 Identities=27% Similarity=0.221 Sum_probs=16.9 Q ss_pred CHHHHHHHHHHHHHHHHHHHCC Q ss_conf 4378999999999999876149 Q gi|254780603|r 261 KALNVSNAAAVALYITQNHFAK 282 (282) Q Consensus 261 ~SLNvs~a~ai~l~~~~~~~~~ 282 (282) |.+=-+||+++++||..|+..| T Consensus 81 E~fIF~Va~~li~~E~~Rs~~k 102 (134) T pfam07047 81 EAFIFSVAGGLLVYEYQRSSRK 102 (134) T ss_pred HHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999999999999999998424 No 51 >KOG2882 consensus Probab=37.71 E-value=14 Score=17.04 Aligned_cols=28 Identities=14% Similarity=0.156 Sum_probs=14.5 Q ss_pred CEEEEEEHHHHHHHHHCCCEEEEEEEECCC Q ss_conf 819998578899999789818999997378 Q gi|254780603|r 47 ENLFLYGVHTVSAALNNPSRKIFQLLATKN 76 (282) Q Consensus 47 ~~~iIeG~~~V~eaL~~~~~~i~~i~~te~ 76 (282) +.-.|+|.-...++|.+.... .+|+|.+ T Consensus 36 g~~~ipGs~e~l~~L~~~gK~--i~fvTNN 63 (306) T KOG2882 36 GEKPIPGSPEALNLLKSLGKQ--IIFVTNN 63 (306) T ss_pred CCCCCCCHHHHHHHHHHCCCC--EEEEECC T ss_conf 687888859999999973982--6999678 No 52 >COG1772 Uncharacterized protein conserved in archaea [Function unknown] Probab=37.39 E-value=30 Score=15.12 Aligned_cols=135 Identities=19% Similarity=0.265 Sum_probs=71.7 Q ss_pred EEEEECCCCCHHH-----HHHHHHH---HHHHHCCCCCCCCCCCCCC----HHHHHHHHHHHH--HHHCCCCCCCCCCCC Q ss_conf 6887234320688-----9999999---8642001100136863200----000134443333--211012223221122 Q gi|254780603|r 134 LLMVLDHVNDPHN-----IGAILRS---AVAFSCDGIITTKRYSPSE----SAVLAKSASGAL--EHIPYIRISNLTDAL 199 (282) Q Consensus 134 ~~i~ld~i~dp~N-----lG~I~Rt---a~a~g~~~vil~~~~~~~~----~~~~~ras~Ga~--~~l~~~~~~~~~~~l 199 (282) +.+.|.+-.||.- +-+|.|. |.||+++-.++.=.+.+-. .-.+.++.-|.. +-+-+. -.|....+ T Consensus 2 ltiglyNtYD~~r~heaH~RaIARAAPicyAF~fhLal~~FPf~~~~~Elae~va~~TTIGesG~yl~~L~-e~n~l~~~ 80 (178) T COG1772 2 LTIGLYNTYDKKRIHEAHLRAIARAAPICYAFNFHLALIDFPFKGTEKELAEEVAEKTTIGESGKYLLVLA-ESNKLHVI 80 (178) T ss_pred EEEEEECCCCCHHHHHHHHHHHHHHCCEEEEECCEEEEECCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHH-HCCCEEEE T ss_conf 27997405683578899999987536535874242789778778987999999875170067732247568-63945885 Q ss_pred CCCCCCCC-----HHHHCCCC--CCCCC-----C-CCCCCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHH Q ss_conf 22222100-----00000123--33221-----1-223689889997586789877999858939992789687437899 Q gi|254780603|r 200 QKMHSWGF-----QTIGLSSD--SKKPL-----E-QEIKNDKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVS 266 (282) Q Consensus 200 ~~~~~~~~-----~i~~~~~~--~~~~~-----~-~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs 266 (282) +. ..+|| .+++++.. ..+-+ . ...-++...+++|=-.+|||+++++.|-+-+-|.- .++ ||--. T Consensus 81 D~-p~kgfp~qfG~vvaTTskPd~~k~i~p~dva~~~lr~ks~~~~iGLGr~GLPke~~~~~~YHLDiT~-kgv-SLETc 157 (178) T COG1772 81 DK-PKKGFPPQFGEVVATTSKPDEKKAIKPIDVAEEALRGKSFTFLIGLGRHGLPKEMFKSAKYHLDITD-KGV-SLETC 157 (178) T ss_pred CC-CCCCCCHHHCCEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCHHHHHHCEEEEEECC-CCC-EEEEH T ss_conf 16-6556971118555333689800145766679998468956999844777886999853024463136-731-02311 Q ss_pred HHHHHH Q ss_conf 999999 Q gi|254780603|r 267 NAAAVA 272 (282) Q Consensus 267 ~a~ai~ 272 (282) .|-+++ T Consensus 158 TAIGaI 163 (178) T COG1772 158 TAIGAI 163 (178) T ss_pred HHHCCH T ss_conf 243126 No 53 >COG2242 CobL Precorrin-6B methylase 2 [Coenzyme metabolism] Probab=35.80 E-value=32 Score=14.98 Aligned_cols=40 Identities=20% Similarity=0.343 Sum_probs=29.4 Q ss_pred CCCEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCC Q ss_conf 650688723432068899999998642001100136863200 Q gi|254780603|r 131 NSQLLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSE 172 (282) Q Consensus 131 ~~~~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~ 172 (282) ....++.+| +|+.=+..|-|.|+.||++.+-+....++.. T Consensus 57 p~~~v~AIe--~~~~a~~~~~~N~~~fg~~n~~vv~g~Ap~~ 96 (187) T COG2242 57 PSGRVIAIE--RDEEALELIERNAARFGVDNLEVVEGDAPEA 96 (187) T ss_pred CCCEEEEEE--CCHHHHHHHHHHHHHHCCCCEEEEECCCHHH T ss_conf 885599992--5888999999999984999679995464576 No 54 >KOG1618 consensus Probab=35.58 E-value=24 Score=15.63 Aligned_cols=31 Identities=19% Similarity=0.273 Sum_probs=17.6 Q ss_pred CCEEEEEEHHHHHHHHH--------CCCEEEEEEEECCC Q ss_conf 88199985788999997--------89818999997378 Q gi|254780603|r 46 PENLFLYGVHTVSAALN--------NPSRKIFQLLATKN 76 (282) Q Consensus 46 ~~~~iIeG~~~V~eaL~--------~~~~~i~~i~~te~ 76 (282) .+..++-|.+++-++.+ .+..+|-.+++|.. T Consensus 42 IDGVL~RG~~~i~~~~~Alr~L~~~~g~lkIP~vfLTNG 80 (389) T KOG1618 42 IDGVLFRGHRPIPGALKALRRLVDNQGQLKIPFVFLTNG 80 (389) T ss_pred CCCEEEECCCCCCCHHHHHHHHHHCCCCEECCEEEEECC T ss_conf 352798278878645889999973678710468999579 No 55 >TIGR01855 IMP_synth_hisH imidazole glycerol phosphate synthase, glutamine amidotransferase subunit; InterPro: IPR010139 Imidazole glycerol phosphate synthetase (IGPS) is a key metabolic enzyme, which links amino acid and nucleotide biosynthesis: it catalyses the closure of the imidazole ring within histidine biosynthesis (fifth step), and provides the substrate for de novo purine biosynthesis. IGPS consists of two different subunits: HisH, a glutamine amidotransferase (glutaminase), and HisF, a synthase (cyclase). HisH functions to provide a source of nitrogen, which is required for the synthesis of histidine and purines. In the HisH glutaminase reaction, the hydrolysis of glutamine yields ammonia, which is then used by HisF in the subsequent synthase reaction. The X-ray structure of the HisH/HisF heterodimer of IGPS reveals a putative tunnel for the transfer of ammonia from HisH to HisF via a (beta-alpha)8 barrel fold within HisF that abuts HisH . Ammonia tunnels connect the glutaminase and synthase active sites. HisH belongs to a large group of enzymes found in diverse and fundamental anabolic pathways. These enzymes share a common domain, referred to as the type-I glutamine amidotransferase (GATase) domain, which can occur either as single polypeptides (as with HisH) or as domains of large multifunctional proteins.; GO: 0016763 transferase activity transferring pentosyl groups, 0000105 histidine biosynthetic process, 0005737 cytoplasm. Probab=34.16 E-value=32 Score=14.95 Aligned_cols=31 Identities=13% Similarity=0.319 Sum_probs=19.1 Q ss_pred EEEECCCCCHHHHHH----HHHHHHHHHCCCCCCCCC Q ss_conf 887234320688999----999986420011001368 Q gi|254780603|r 135 LMVLDHVNDPHNIGA----ILRSAVAFSCDGIITTKR 167 (282) Q Consensus 135 ~i~ld~i~dp~NlG~----I~Rta~a~g~~~vil~~~ 167 (282) |+|+| ..+|||++ +-|.-..+|+...++.+. T Consensus 1 i~viD--YG~GNL~SlyrGV~~Al~~~G~~~~v~~~~ 35 (211) T TIGR01855 1 IVVID--YGVGNLRSLYRGVKRALKRVGAEPVVVKDS 35 (211) T ss_pred CEEEE--CCCHHHHHHHHHHHHHHHHCCCEEEEECCC T ss_conf 97874--371656889999999998449817996286 No 56 >pfam02784 Orn_Arg_deC_N Pyridoxal-dependent decarboxylase, pyridoxal binding domain. These pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates This domain has a TIM barrel fold. Probab=33.69 E-value=32 Score=14.98 Aligned_cols=21 Identities=14% Similarity=0.317 Sum_probs=10.1 Q ss_pred CCCCCCCCCCCCCHHHHCCCC Q ss_conf 211222222210000000123 Q gi|254780603|r 195 LTDALQKMHSWGFQTIGLSSD 215 (282) Q Consensus 195 ~~~~l~~~~~~~~~i~~~~~~ 215 (282) +.+.++.+++.+.++.|++.+ T Consensus 140 ~~~~~~~~~~~~~~~~GlH~H 160 (245) T pfam02784 140 AEALLKAAKELGLNVVGVHFH 160 (245) T ss_pred HHHHHHHHHHCCCCEEEEEEE T ss_conf 999999998679975475565 No 57 >cd06840 PLPDE_III_Bif_AspK_DapDC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Bifunctional Aspartate Kinase/Diaminopimelate Decarboxylase. Bifunctional aspartate kinase/diaminopimelate decarboxylase (AspK/DapDC, EC 4.1.1.20/EC 2.7.2.4) typically exists in bacteria. These proteins contain an N-terminal AspK region and a C-terminal DapDC region, which contains a PLP-binding TIM-barrel domain followed by beta-sandwich domain, characteristic of fold type III PLP-dependent enzymes. Members of this subfamily have not been fully characterized. Based on their sequence, these proteins may catalyze both reactions catalyzed by AspK and DapDC. AspK catalyzes the phosphorylation of L-aspartate to produce 4-phospho-L-aspartate while DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine. Probab=33.39 E-value=35 Score=14.75 Aligned_cols=13 Identities=8% Similarity=0.064 Sum_probs=5.8 Q ss_pred EEEHHHHHHHHHC Q ss_conf 9857889999978 Q gi|254780603|r 51 LYGVHTVSAALNN 63 (282) Q Consensus 51 IeG~~~V~eaL~~ 63 (282) +....-+..+++. T Consensus 63 vaS~~El~~al~~ 75 (368) T cd06840 63 CVSIGELDLVLKL 75 (368) T ss_pred EECHHHHHHHHHH T ss_conf 9899999999986 No 58 >pfam05341 DUF708 Protein of unknown function (DUF708). This family consists of several uncharacterized nucleopolyhedrovirus proteins of unknown function. Probab=33.33 E-value=35 Score=14.74 Aligned_cols=54 Identities=15% Similarity=0.071 Sum_probs=43.3 Q ss_pred CCCCCCCCCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHH Q ss_conf 221122368988999758678987799985893999278968743789999999999 Q gi|254780603|r 218 KPLEQEIKNDKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVSNAAAVALY 274 (282) Q Consensus 218 ~~~~~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs~a~ai~l~ 274 (282) ..+..||+.+|..+=+.+..-|+..+-+..+ ..=|..+..+++|++.+.-++.| T Consensus 46 a~~EnFDYk~PI~Y~lk~k~L~i~ne~~~~A---Ln~P~~~~~~~~ni~~~~i~~~F 99 (105) T pfam05341 46 ANLENFDYKQPIYYDLKRKQLLINNESVNKA---LNRPRYAVLDTLNISPIHIFLAF 99 (105) T ss_pred HHHHCCCCCCCEEEEECCCEEEECCHHHHHH---HCCCCCCCCCCCCCCHHHHHHHH T ss_conf 3112066889628980476887552899998---57986455675445508999999 No 59 >TIGR01245 trpD anthranilate phosphoribosyltransferase; InterPro: IPR005940 In many widely different species, including Escherichia coli, Thermotoga maritima, and Archaeoglobus fulgidus, this enzyme is a C-terminal part of a multifunctional protein together with glutamine amidotransferase; the fusion protein is designated anthranilate synthase component II (4.1.3.27 from EC).; GO: 0004048 anthranilate phosphoribosyltransferase activity, 0000162 tryptophan biosynthetic process. Probab=32.63 E-value=27 Score=15.39 Aligned_cols=39 Identities=10% Similarity=0.019 Sum_probs=29.5 Q ss_pred EEEECCCCCHHHHHHHHHHHHHHHCCCC-CCCC-CCCCCCH Q ss_conf 8872343206889999999864200110-0136-8632000 Q gi|254780603|r 135 LMVLDHVNDPHNIGAILRSAVAFSCDGI-ITTK-RYSPSES 173 (282) Q Consensus 135 ~i~ld~i~dp~NlG~I~Rta~a~g~~~v-il~~-~~~~~~~ 173 (282) -.-|=||.||.=++.+.+....+|.+.. ++.. ++-|..+ T Consensus 184 ~~qv~GVy~~~L~~~~A~aL~~LG~krAlVVhG~~GlDE~s 224 (331) T TIGR01245 184 KYQVIGVYDPDLVEVMAEALKNLGVKRALVVHGEDGLDEIS 224 (331) T ss_pred CEEEEECCCHHHHHHHHHHHHHHCCCEEEEEECCCCCCEEE T ss_conf 80278534688899999999861767089985788961453 No 60 >TIGR01135 glmS glucosamine--fructose-6-phosphate aminotransferase, isomerizing; InterPro: IPR005855 Glucosamine:fructose-6-phosphate aminotransferase (2.6.1.16 from EC) catalyses the formation of glucosamine 6-phosphate and is the first and rate-limiting enzyme of the hexosamine biosynthetic pathway. The final product of the hexosamine pathway, UDP-N-acetyl glucosamine, is an active precursor of numerous macromolecules containing amino sugars. This family of sequences belong to the MEROPS peptidase family C44 (clan PB(C)), and are classified as non-peptidase homologs.; GO: 0004360 glutamine-fructose-6-phosphate transaminase (isomerizing) activity, 0016051 carbohydrate biosynthetic process, 0005737 cytoplasm. Probab=31.76 E-value=37 Score=14.59 Aligned_cols=76 Identities=12% Similarity=0.112 Sum_probs=54.1 Q ss_pred CCCCCHHHHCCCCCC-C------CCCCCCCCCCEEEEECCC-CCCCCHHHHHHCCCEEEECCCCCCCH--HHHHHHHHHH Q ss_conf 221000000012333-2------211223689889997586-78987799985893999278968743--7899999999 Q gi|254780603|r 203 HSWGFQTIGLSSDSK-K------PLEQEIKNDKIALILGAE-GKGLRPKTQETATSMAHLHMPGIIKA--LNVSNAAAVA 272 (282) Q Consensus 203 ~~~~~~i~~~~~~~~-~------~~~~~~~~~~~~lv~G~E-~~Gl~~~~~~~~d~~v~Ip~~~~~~S--LNvs~a~ai~ 272 (282) =+.|++|++..+++. - ++.|..--+-.+++|++| +.+..+. .+|+.+.+|-.+..-+ +++.+..-++ T Consensus 527 id~~~PVva~ap~~~Gl~~K~~SNv~Ev~ARga~vi~~~~~~~~~~~~~---~~d~~i~~P~~~~~~~P~~~l~iplQLl 603 (628) T TIGR01135 527 IDEGLPVVAIAPKDSGLLEKTKSNVEEVKARGARVIVLASEDDAELIAA---IADDIIKLPEVEELLAPIVYLTIPLQLL 603 (628) T ss_pred ECCCCEEEEEECCCCCCHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCC---CCCEEEEECCCCCCCCCHHHHHHHHHHH T ss_conf 3188708998278898507778889988726963899825775324311---0545888468886304166767999999 Q ss_pred HHHHHHHHC Q ss_conf 999987614 Q gi|254780603|r 273 LYITQNHFA 281 (282) Q Consensus 273 l~~~~~~~~ 281 (282) -|+.-..++ T Consensus 604 AYhiA~~kG 612 (628) T TIGR01135 604 AYHIALAKG 612 (628) T ss_pred HHHHHHHHC T ss_conf 999999708 No 61 >TIGR01055 parE_Gneg DNA topoisomerase IV, B subunit; InterPro: IPR005737 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA . Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils . This entry represents subunit B (parE) of topoisomerase IV from Gram negative bacteria. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication . Topoisomerase IV consists of two polypeptide subunits, parC (subunit A), which is homologous to gyrA of topoisomerase II, and parE (subunit B), which is homologous to gyrB of topoisomerase II. More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0005694 chromosome. Probab=30.58 E-value=39 Score=14.47 Aligned_cols=120 Identities=16% Similarity=0.187 Sum_probs=75.5 Q ss_pred CCCCEEEEEEHHHHHHHHHCCCEEEEEEEECCCCCCCCCHHHHHHCCCCEEEECHHHHHHHHCCCCCCCC-CCEEEECCC Q ss_conf 1288199985788999997898189999973784335434554326996999768998775247777774-420241155 Q gi|254780603|r 44 SQPENLFLYGVHTVSAALNNPSRKIFQLLATKNALARLDWDANLPHPFPVKTVPPQTIDKIVGKEAVHQG-LALETAPLL 122 (282) Q Consensus 44 ~~~~~~iIeG~~~V~eaL~~~~~~i~~i~~te~~~~~~~~~~~l~~~~~I~~v~~~~l~~i~~~~~~hqG-i~a~~~~~~ 122 (282) .++++|+|||.-+==.|=.+..|+.+.|+--. .+|.-+-....+++......|.- |++.+.|.. T Consensus 423 e~TELFlVEGDSAGGSAKQAR~RE~QAilPL~---------------GKiLN~~~~~~~~vl~~~~i~D~~vAl~~~~~~ 487 (647) T TIGR01055 423 EKTELFLVEGDSAGGSAKQARDREYQAILPLK---------------GKILNTWEVSLDKVLNSQEIHDIEVALGIDPDS 487 (647) T ss_pred CCCEEEEEECCCCCCCHHHHCCCCCEEECCCC---------------CCEEEEECCCHHHHHCCCCCCEEEEEEECCCCC T ss_conf 26427898325677521343053201214456---------------647763214644553124200021022248720 Q ss_pred CCCHHHCCCCCEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHH Q ss_conf 554011266506887234320688999999986420011001368632000001344 Q gi|254780603|r 123 SPTLDAVRNSQLLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKS 179 (282) Q Consensus 123 ~~~l~~~~~~~~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ra 179 (282) ...++++.-..++++-|.=.|---+.+++=+--..-+..++-. +....--|=..|- T Consensus 488 ~~k~~~LRY~Ki~Il~DAD~DG~HIA~LL~~lF~~~~p~LV~~-GH~Y~A~PPLYR~ 543 (647) T TIGR01055 488 NDKLSQLRYGKIIILADADSDGLHIATLLCALFLKHFPKLVEE-GHVYVAKPPLYRI 543 (647) T ss_pred HHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHC-CCEEEECCCCEEE T ss_conf 0036426722288984178880789999999999988888753-9078717872021 No 62 >TIGR03565 alk_sulf_monoox alkanesulfonate monooxygenase, FMNH(2)-dependent. Members of this protein family are monooxygenases that catalyze desulfonation of aliphatic sulfonates such as methane sulfonate. This enzyme uses reduced FMN, although various others members of the same luciferase-like monooxygenase family (pfam00296) are F420-dependent enzymes. Probab=29.26 E-value=41 Score=14.34 Aligned_cols=11 Identities=9% Similarity=0.172 Sum_probs=4.9 Q ss_pred CCCCCCCCEEE Q ss_conf 77777442024 Q gi|254780603|r 108 EAVHQGLALET 118 (282) Q Consensus 108 ~~~hqGi~a~~ 118 (282) ..+|+|=-..+ T Consensus 144 ~~~~~G~~~~v 154 (346) T TIGR03565 144 TVDFDGKHIKV 154 (346) T ss_pred CCCCCCCEEEE T ss_conf 70455875773 No 63 >pfam00851 Peptidase_C6 Helper component proteinase. This protein is found in genome polyproteins of potyviruses. Probab=27.97 E-value=34 Score=14.78 Aligned_cols=28 Identities=21% Similarity=0.221 Sum_probs=20.8 Q ss_pred CCCCCCCCCCCCCCCCCEEEEECCCCCC Q ss_conf 0123332211223689889997586789 Q gi|254780603|r 212 LSSDSKKPLEQEIKNDKIALILGAEGKG 239 (282) Q Consensus 212 ~~~~~~~~~~~~~~~~~~~lv~G~E~~G 239 (282) +..+|+.-++++..|.+--||+||-|.- T Consensus 291 T~ddG~p~~S~~~~PTK~HLvIGnsgD~ 318 (453) T pfam00851 291 TLDDGKPIYSELKMPTKNHLVIGNSGDP 318 (453) T ss_pred ECCCCCEEEEECCCCCCCEEEECCCCCC T ss_conf 6688987443133787684771578985 No 64 >PRK13397 3-deoxy-7-phosphoheptulonate synthase; Provisional Probab=27.86 E-value=40 Score=14.39 Aligned_cols=31 Identities=13% Similarity=-0.073 Sum_probs=14.5 Q ss_pred CHHHHHHHHHHHHHHHCCCCCCCCCCCCCCH Q ss_conf 0688999999986420011001368632000 Q gi|254780603|r 143 DPHNIGAILRSAVAFSCDGIITTKRYSPSES 173 (282) Q Consensus 143 dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~ 173 (282) +|...-..+.-...+|.+.|+++++++..|+ T Consensus 134 s~~~~~~a~eki~~~Gn~~i~l~ERG~~gy~ 164 (250) T PRK13397 134 TIEEYLGALSYLQDTGKSNIILCERGVRGYD 164 (250) T ss_pred CHHHHHHHHHHHHHCCCCCEEEEECCCCCCC T ss_conf 9999999999999659982899828987555 No 65 >TIGR01678 FAD_lactone_ox sugar 1,4-lactone oxidases; InterPro: IPR010031 This entry identifies a family of at least two different sugar 1,4 lactone oxidases, both involved in synthesising ascorbic acid or a derivative. These include L-gulonolactone oxidase (1.1.3.8 from EC) from rat and D-arabinono-1,4-lactone oxidase (1.1.3.37 from EC) from Saccharomyces cerevisiae. Members are proposed to have the cofactor FAD covalently bound at a site specified by IPR006093 from INTERPRO.; GO: 0016899 oxidoreductase activity acting on the CH-OH group of donors oxygen as acceptor, 0009058 biosynthetic process. Probab=26.62 E-value=42 Score=14.26 Aligned_cols=20 Identities=5% Similarity=-0.069 Sum_probs=13.3 Q ss_pred CCCCCCCCCCEEEEECCCCC Q ss_conf 21122368988999758678 Q gi|254780603|r 219 PLEQEIKNDKIALILGAEGK 238 (282) Q Consensus 219 ~~~~~~~~~~~~lv~G~E~~ 238 (282) -++=+.++++++++-|+-.+ T Consensus 217 Rv~wfPyt~~~v~wr~nkt~ 236 (505) T TIGR01678 217 RVLWFPYTEKVVVWRANKTE 236 (505) T ss_pred EEEEECCCCEEEEEECCCCC T ss_conf 99871330418898447466 No 66 >PRK11052 malQ 4-alpha-glucanotransferase; Provisional Probab=25.80 E-value=47 Score=13.97 Aligned_cols=39 Identities=13% Similarity=0.020 Sum_probs=30.9 Q ss_pred CCCCHHHHHHHHHHHHHHHCCCCCCCC---------CCCCCCHHHHHH Q ss_conf 432068899999998642001100136---------863200000134 Q gi|254780603|r 140 HVNDPHNIGAILRSAVAFSCDGIITTK---------RYSPSESAVLAK 178 (282) Q Consensus 140 ~i~dp~NlG~I~Rta~a~g~~~vil~~---------~~~~~~~~~~~r 178 (282) ||.|=+.|..+++.++..|++.|.+.+ ..+.||+|..-| T Consensus 160 GiGDf~DL~~l~~~aa~~Gadfv~lNPlHA~~p~~P~~~SPYsPssRr 207 (694) T PRK11052 160 GIGDFGDLKQMLVDVAKRGGDFIGLNPIHALYPANPESASPYSPSSRR 207 (694) T ss_pred CCCCHHHHHHHHHHHHHCCCCEEEECCHHHCCCCCCCCCCCCCCCCCC T ss_conf 877899999999999976998798671320678998999997952124 No 67 >cd06843 PLPDE_III_PvsE_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme PvsE. This subfamily is composed of PvsE from Vibrio parahaemolyticus and similar proteins. PvsE is a vibrioferrin biosynthesis protein which is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. It has been suggested that PvsE may be involved in the biosynthesis of the polycarboxylate siderophore vibrioferrin. It may catalyze the decarboxylation of serine to yield ethanolamine. PvsE may require homodimer formation and the presence of the PLP cofactor for activity. Probab=25.25 E-value=48 Score=13.91 Aligned_cols=55 Identities=4% Similarity=-0.055 Sum_probs=27.5 Q ss_pred EEEEEHHHHHHHHHCCCEEEEEEEECCCCCCCCCHHHHHHCCCCEE-EECHHHHHHHH Q ss_conf 9998578899999789818999997378433543455432699699-97689987752 Q gi|254780603|r 49 LFLYGVHTVSAALNNPSRKIFQLLATKNALARLDWDANLPHPFPVK-TVPPQTIDKIV 105 (282) Q Consensus 49 ~iIeG~~~V~eaL~~~~~~i~~i~~te~~~~~~~~~~~l~~~~~I~-~v~~~~l~~i~ 105 (282) +=+....-+..++..++. ..++.+............+..++... .-+..++.++. T Consensus 52 ~DvaS~~El~~~~~~~~~--~~Iif~gp~K~~~~l~~a~~~gv~~i~~DS~~El~~i~ 107 (377) T cd06843 52 FEVASGGEIAHVRAAVPD--APLIFGGPGKTDSELAQALAQGVERIHVESELELRRLN 107 (377) T ss_pred EEEECHHHHHHHHHCCCC--CCEEECCCCCCHHHHHHHHHCCCCEEEECCHHHHHHHH T ss_conf 898299999999853999--64798899999999999998799889988999999999 No 68 >TIGR00064 ftsY signal recognition particle-docking protein FtsY; InterPro: IPR004390 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This family includes the cell division ABC transporter and the periplasmic substrate-binding protein FtsY. There is a weak division between FtsY and SRP54; both are GTPases. In Escherichia coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.; GO: 0005525 GTP binding. Probab=24.79 E-value=43 Score=14.20 Aligned_cols=78 Identities=13% Similarity=0.154 Sum_probs=50.2 Q ss_pred CCCCEEEEECCCCCHHHHHHHHHHHHHHHCCCC--CCCCCCCCCCHHHHHHHHHHHHHHHCCC------------CC-CC Q ss_conf 665068872343206889999999864200110--0136863200000134443333211012------------22-32 Q gi|254780603|r 130 RNSQLLMVLDHVNDPHNIGAILRSAVAFSCDGI--ITTKRYSPSESAVLAKSASGALEHIPYI------------RI-SN 194 (282) Q Consensus 130 ~~~~~~i~ld~i~dp~NlG~I~Rta~a~g~~~v--il~~~~~~~~~~~~~ras~Ga~~~l~~~------------~~-~~ 194 (282) .+.|.++++-||.--|=.=||.--|..|--+|- ++. .+| +.|| ||.++|..| .. +| T Consensus 79 ~~kp~Vil~VGVNG~GKTTTIaKLA~~l~~~Gk~V~la--AgD-----TFRA--AA~EQL~~Wa~R~gv~vi~~~~gn~D 149 (284) T TIGR00064 79 EKKPNVILFVGVNGVGKTTTIAKLANKLKKQGKSVLLA--AGD-----TFRA--AAIEQLEVWAKRLGVDVIKQKEGNAD 149 (284) T ss_pred CCCCEEEEEEEEECCCHHHHHHHHHHHHHHCCCEEEEE--CCC-----HHHH--HHHHHHHHHHHHHCCEEEECCCCCCC T ss_conf 78977999984408860102889999998749908998--275-----2479--99999999898838755407889887 Q ss_pred C----CCCCCCCCCCCCHHHHCCCCC Q ss_conf 2----112222222100000001233 Q gi|254780603|r 195 L----TDALQKMHSWGFQTIGLSSDS 216 (282) Q Consensus 195 ~----~~~l~~~~~~~~~i~~~~~~~ 216 (282) . .+++++.+++||=++-.|+-| T Consensus 150 PAaV~fDAi~~Ak~~niDvvliDTAG 175 (284) T TIGR00064 150 PAAVIFDAIQAAKARNIDVVLIDTAG 175 (284) T ss_pred CHHHHHHHHHHHHHCCCCEEEEECCC T ss_conf 17899998999987499789973475 No 69 >COG0187 GyrB Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), B subunit [DNA replication, recombination, and repair] Probab=24.40 E-value=50 Score=13.82 Aligned_cols=33 Identities=15% Similarity=0.239 Sum_probs=16.4 Q ss_pred CCCCCCCEEEEEEHHHHHHHHHCCCEEEEEEEE Q ss_conf 211128819998578899999789818999997 Q gi|254780603|r 41 RHTSQPENLFLYGVHTVSAALNNPSRKIFQLLA 73 (282) Q Consensus 41 k~R~~~~~~iIeG~~~V~eaL~~~~~~i~~i~~ 73 (282) +...+..+|++||.-+==.|-....|..+.|+- T Consensus 414 kd~~~~ELfiVEGDSAGGSAKqgRdR~~QAILP 446 (635) T COG0187 414 KDPEKSELFLVEGDSAGGSAKQGRDREFQAILP 446 (635) T ss_pred CCCCCCEEEEEECCCCCHHHHHCCCCCCEEEEE T ss_conf 882415599980477633244216866557720 No 70 >PRK11440 hypothetical protein; Provisional Probab=23.37 E-value=53 Score=13.70 Aligned_cols=65 Identities=14% Similarity=0.141 Sum_probs=45.1 Q ss_pred EEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCC Q ss_conf 6887234320688999999986420011001368632000001344433332110122232211222 Q gi|254780603|r 134 LLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYIRISNLTDALQ 200 (282) Q Consensus 134 ~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~ 200 (282) --|++.|+.-..=+-+-+|.|...|++-+++. +++.-+++...+++.-.++.. +..+.+..+.|. T Consensus 122 ~~lvi~G~~T~~CV~sTardA~~~gy~v~vv~-Da~a~~~~e~h~~aL~~l~~~-~a~V~tt~eil~ 186 (188) T PRK11440 122 DTIVLCGISTNIGVESTARNAWELGFNLVIAE-DACSAASAEQHQNSMNHIFPR-IARVRSVEEILN 186 (188) T ss_pred CEEEEEEECCCHHHHHHHHHHHHCCCEEEEEC-CCCCCCCHHHHHHHHHHHHHC-EEEEEEHHHHHH T ss_conf 98999322116569999999998899899810-234899999999999999854-579722999985 No 71 >TIGR02303 HpaG-C-term 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, C-terminal subunit; InterPro: IPR012684 This entry represents one of two subunits/domains of the bifunctional isomerase/decarboxylase involved in 4-hydroxyphenylacetate degradation . In Escherichia coli and some other species, this enzyme is encoded by a single polypeptide containing both this domain and the closely related N-terminal domain (IPR012686 from INTERPRO). In other species such as Pasteurella multocida, these domains are found as two separate proteins (usually as tandem genes). Together, these domains carry out the decarboxylation of 5-oxopent-3-ene-1,2,5-tricarboxylic acid (OPET) to 2-hydroxy-2,4-diene-1,7-dioate (HHDD) and the subsequent isomerization to 2-oxohept-3-ene-1,7-dioate (OHED).; GO: 0008704 5-carboxymethyl-2-hydroxymuconate delta-isomerase activity, 0018800 5-oxopent-3-ene-125-tricarboxylate decarboxylase activity. Probab=23.32 E-value=25 Score=15.56 Aligned_cols=14 Identities=36% Similarity=0.615 Sum_probs=12.1 Q ss_pred EEEE-ECCCCCHHHH Q ss_conf 6887-2343206889 Q gi|254780603|r 134 LLMV-LDHVNDPHNI 147 (282) Q Consensus 134 ~~i~-ld~i~dp~Nl 147 (282) .||| .+.|.||+|| T Consensus 159 Pw~VD~~dveDp~nL 173 (249) T TIGR02303 159 PWIVDKEDVEDPMNL 173 (249) T ss_pred CEEEEECCCCCCCCC T ss_conf 847851236785567 No 72 >TIGR02924 ICDH_alpha isocitrate dehydrogenase; InterPro: IPR014273 This entry represents a group of isocitrate dehydrogenases found mainly in the alphaproteobacteria. Many of the species containing these proteins appear to have a TCA cycle lacking only a determined isocitrate dehydrogenase. The precise identity of the cofactor (NADH -- 1.1.1.41 from EC vs. NADPH -- 1.1.1.42 from EC) is unclear.. Probab=22.76 E-value=33 Score=14.89 Aligned_cols=95 Identities=16% Similarity=0.081 Sum_probs=52.5 Q ss_pred HHHHHHHHHHHHHH-CCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCC-CCC- Q ss_conf 88999999986420-011001368632000001344433332110122232211222222210000000123332-211- Q gi|254780603|r 145 HNIGAILRSAVAFS-CDGIITTKRYSPSESAVLAKSASGALEHIPYIRISNLTDALQKMHSWGFQTIGLSSDSKK-PLE- 221 (282) Q Consensus 145 ~NlG~I~Rta~a~g-~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~-~~~- 221 (282) .++-..+-.|+-== =||| +++|.|+++.-+.=.|.-++-.=+ +.|+.+-=+.|++.-|..-+.+.+... .+. T Consensus 291 ~d~A~liynAwLKTLEdGv----HTADIy~~k~Sk~KVgTkeFA~aV-~~nlG~~P~~LP~~~~~f~~~~~~~~~~~~~~ 365 (481) T TIGR02924 291 KDIAQLIYNAWLKTLEDGV----HTADIYNEKTSKKKVGTKEFAEAV-VKNLGKKPEKLPKALISFSINSLKESKIDYER 365 (481) T ss_pred HHHHHHHHHHHHHHHHCCC----CHHHHCCCCCCCCCCCCHHHHHHH-HHHHCCCCCHHHHHHHHHHCCCEEECCCCCCC T ss_conf 4689999877644421374----313321233666666525799999-98616781023686742303210101212440 Q ss_pred CCCCC-----CCEEEEECCCCC-CCCHHH Q ss_conf 22368-----988999758678-987799 Q gi|254780603|r 222 QEIKN-----DKIALILGAEGK-GLRPKT 244 (282) Q Consensus 222 ~~~~~-----~~~~lv~G~E~~-Gl~~~~ 244 (282) ..++. +-.++|==+++. ++.+-+ T Consensus 366 ~~~~~~k~LvG~Difi~wd~~~ld~~~l~ 394 (481) T TIGR02924 366 EQSYKVKVLVGVDIFIKWDGSSLDLNQLV 394 (481) T ss_pred CCCCCEEEEEEEEEEEEECCCCCCHHHHH T ss_conf 36631148988778997367582489999 No 73 >TIGR01607 PST-A Plasmodium subtelomeric family (PST-A); InterPro: IPR006494 These proteins represent a paralogous family of genes found in Plasmodium falciparum and Plasmodium yoelii that are closely related to various phospholipases and lysophospholipases of plants as well as generally being related to the alpha/beta-fold superfamily of hydrolases. These genes are preferentially located in the subtelomeric regions of the chromosomes of both P. falciparum and P. yoelii. . Probab=21.14 E-value=29 Score=15.15 Aligned_cols=21 Identities=19% Similarity=0.404 Sum_probs=16.8 Q ss_pred CCCCCCCCCCCCHHHHCCCCC Q ss_conf 112222222100000001233 Q gi|254780603|r 196 TDALQKMHSWGFQTIGLSSDS 216 (282) Q Consensus 196 ~~~l~~~~~~~~~i~~~~~~~ 216 (282) .+|++.+-++||=|||+|.+| T Consensus 64 dSWIE~fN~~GYSVYgLDLQG 84 (379) T TIGR01607 64 DSWIEKFNKNGYSVYGLDLQG 84 (379) T ss_pred CEEEEECCCCCCEEEEEECCC T ss_conf 825651167976387534356 No 74 >TIGR00750 lao LAO/AO transport system ATPase; InterPro: IPR005129 Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components. In Escherichia coli K-12, the arginine-ornithine transport system requires an arginine-ornithine-binding protein and the lysine-arginine-ornithine (LAO) transport system includes a LAO-binding protein. Both periplasmic proteins can be phosphorylated by a single kinase, ArgK resulting in reduced levels of transport activity of the periplasmic transport systems that include each of the binding proteins. The ArgK protein acts as an ATPase enzyme and as a kinase.. Probab=21.13 E-value=52 Score=13.75 Aligned_cols=114 Identities=13% Similarity=0.114 Sum_probs=59.6 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHH-------------------HHHHHHCCCCCCCCCCCCCCC--C Q ss_conf 8899999998642001100136863200000134443-------------------333211012223221122222--2 Q gi|254780603|r 145 HNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSAS-------------------GALEHIPYIRISNLTDALQKM--H 203 (282) Q Consensus 145 ~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~-------------------Ga~~~l~~~~~~~~~~~l~~~--~ 203 (282) .-.+..++-++|||||-||+--=++=...-.++++.= |=+|-=.|+-+ |-.+-=.+- . T Consensus 123 ~at~~~~~lldA~G~DVI~vETVGVGQSEVdi~~~aDT~v~v~~pg~GDd~Q~iKaG~mEiaDI~VV-NKaD~~~a~~v~ 201 (333) T TIGR00750 123 KATRELVKLLDAAGYDVILVETVGVGQSEVDIINMADTFVVVTIPGTGDDVQGIKAGVMEIADIYVV-NKADGEGAEEVK 201 (333) T ss_pred HHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHCEEEEEECCCCCCHHHHHHHHHHEEEEEEEE-ECCCCCCHHHHH T ss_conf 9999999999863898799984157524878873415058985488783466665443023248788-168876658999 Q ss_pred CCCCHHHHCCCC----------CC-----C-CCC--CCCCCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCC Q ss_conf 210000000123----------33-----2-211--22368988999758678987799985893999278968 Q gi|254780603|r 204 SWGFQTIGLSSD----------SK-----K-PLE--QEIKNDKIALILGAEGKGLRPKTQETATSMAHLHMPGI 259 (282) Q Consensus 204 ~~~~~i~~~~~~----------~~-----~-~~~--~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~ 259 (282) ..-...|.++.+ .+ + .++ +..|.-|++=..+-||+||.+-|-..-+|.=.+--+|. T Consensus 202 ~~a~~~l~l~~esvqmlsqmthadearvq~G~~~~r~~gW~Ppv~~tsA~~G~Gi~EL~daI~eH~~~l~~~G~ 275 (333) T TIGR00750 202 TLARLMLALDLESVQMLSQMTHADEARVQKGEIYRREKGWRPPVLKTSAVEGRGIDELWDAIEEHKKFLTESGL 275 (333) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHCCC T ss_conf 99999888888899999865333344430265511010589963887335688716789999999999986360 No 75 >TIGR02080 O_succ_thio_ly O-succinylhomoserine (thiol)-lyase; InterPro: IPR011821 Proteins in this entry are important in the interconversion of the sulphur-containing amino acids L-cysteine and L-methionine in bacteria. In bacteria, inorganic sulphur is reduced to sulphide, which is then used to displace the acetyl group of O-acetyl-L-serine to form the essential amino acid L-cysteine. Biosynthesis of L-methionine then occurs via the transsulphuration pathway which involves the sequential action of two pyridoxal 5'-phosphate (PLP) enzymes, cystathionine gamma-synthase (CGS) and cystathionine beta-lyase (CBL). Firstly CGS catalyses the formation of the intermediate cystathione from a homoserine ester and L-cysteine. This intermediate is then converted by CBL to L-homoserine, which is subsequently methylated by methionine synthase to form L-methionine. For more information see . The CGS enzyme (P00935 from SWISSPROT) from Escherichia coli is, like other CGS enzymes, a homotetramer composed of two catalytically active dimers . The active site of each dimer is found at the interface between the monomers and involves residues from each monomer. Catalysis occurs by alpha,gamma-elimination/replacement reactions.. Probab=20.93 E-value=27 Score=15.33 Aligned_cols=37 Identities=19% Similarity=0.195 Sum_probs=20.8 Q ss_pred CCCCCCCHHHHHHCCC--EEEEC-CCCCCCHHHHHHHHHHH Q ss_conf 8678987799985893--99927-89687437899999999 Q gi|254780603|r 235 AEGKGLRPKTQETATS--MAHLH-MPGIIKALNVSNAAAVA 272 (282) Q Consensus 235 ~E~~Gl~~~~~~~~d~--~v~Ip-~~~~~~SLNvs~a~ai~ 272 (282) =|-+|=-+.+....+. +.++- --|+|||| ||+++.|. T Consensus 302 FEL~G~~~~v~~FL~~L~LFtLAESLGGVESL-iaHPATMT 341 (383) T TIGR02080 302 FELKGGEEAVRRFLGKLSLFTLAESLGGVESL-IAHPATMT 341 (383) T ss_pred EEECCCHHHHHHHHHHCCCHHHHHHHCCHHHH-HCHHHCCC T ss_conf 33218868999998431401212331551233-33010126 No 76 >TIGR01452 PGP_euk phosphoglycolate/pyridoxal phosphate phosphatase family; InterPro: IPR006349 This family of sequences represent 2-phosphoglycolate phosphatase which is limited to the eukaryotic lineage. PGP is an essential enzyme in the glycolate salvage pathway in higher organisms (photorespiration in plants). Phosphoglycolate results from the oxidase activity of RubisCO in the Calvin cycle when concentrations of carbon dioxide are low relative to oxygen. In mammals, PGP is found in many tissues, notably in red blood cells where P-glycolate is and important activator of the hydrolysis of 2,3-bisphosphoglycerate, a major modifier of the oxygen affinity of hemoglobin. The PGPase enzyme described here is a member of the Haloacid dehalogenase superfamily of hydrolase enzymes. Unlike the bacterial PGP equivalog (IPR006346 from INTERPRO), which is a member of class (subfamily) I, this enzyme is a member of class (subfamily) II . These two enzymes have almost certainly arisen from convergent evolution (although these two ancestors may themselves have diverged from a more distant HAD superfamily progenitor). One of the sequences in the group comes from Chlamydomonas reinhardtii, a photosynthetic alga. The enzyme has been purified and characterised and these data are fully consistent with the assignment of function as a PGPase involved in photorespiration . Another, from Homo sapiens, is supported as a member of the family indirectly. Biochemical characterization of partially purified PGP's from various tissues including red blood cells have been performed while one gene for PGP has been localized to chromosome 16p13.3 . The Homo sapiens sequence maps to chromosome 22. There is indeed a related gene on chromosome 16 (and it is expressed, since EST's are found) which shows 46 0dentity and 59603b08ositives by BLAST2 (E=1e-66). Presumably, these two genes are isoforms and have the same catalytic function while being expressed in different tissues and may be differently regulated. The sequence from Caenorhabditis elegans, is only supported by sequence similarity. This family is closely related to a family of bacterial sequences including the Escherichia coli NagD and Bacillus subtilus AraL genes which are characterised by the ability to hydrolyze para-nitrophenylphosphate (pNPPases or NPPases). The Chlamydomonas reinhardtii PGPase does not catalyze this reaction and so presumably these two groups have different functions and substrate specificities. Many of the genes in this family have been annotated as pNPPases due to this association.; GO: 0016791 phosphoric monoester hydrolase activity, 0008152 metabolic process. Probab=20.80 E-value=43 Score=14.24 Aligned_cols=32 Identities=19% Similarity=0.290 Sum_probs=18.2 Q ss_pred CEEEEEEHHHHHHHHHCCCEEEEEEEECCCCCCC Q ss_conf 8199985788999997898189999973784335 Q gi|254780603|r 47 ENLFLYGVHTVSAALNNPSRKIFQLLATKNALAR 80 (282) Q Consensus 47 ~~~iIeG~~~V~eaL~~~~~~i~~i~~te~~~~~ 80 (282) |.-.|+|.=-..+.|....+.+ +++|.|.... T Consensus 16 Ge~v~pG~Pelld~L~~~gK~~--~fvtNNstks 47 (288) T TIGR01452 16 GEKVVPGAPELLDRLAKAGKKV--LFVTNNSTKS 47 (288) T ss_pred CCEECCCCHHHHHHHHHCCCEE--EEEECCCCHH T ss_conf 8641378727899997459879--9981686410 No 77 >pfam07075 DUF1343 Protein of unknown function (DUF1343). This family consists of several hypothetical bacterial proteins of around 400 residues in length. The function of this family is unknown. Probab=20.54 E-value=61 Score=13.36 Aligned_cols=133 Identities=12% Similarity=0.082 Sum_probs=67.6 Q ss_pred EEHHHHHHHHHCCCEEEEEEEECCCCCCCCCHHHHHHCCCCEEEECHHHHHHHHCCCCCCCCCCE--EEECCCCCCHHHC Q ss_conf 85788999997898189999973784335434554326996999768998775247777774420--2411555540112 Q gi|254780603|r 52 YGVHTVSAALNNPSRKIFQLLATKNALARLDWDANLPHPFPVKTVPPQTIDKIVGKEAVHQGLAL--ETAPLLSPTLDAV 129 (282) Q Consensus 52 eG~~~V~eaL~~~~~~i~~i~~te~~~~~~~~~~~l~~~~~I~~v~~~~l~~i~~~~~~hqGi~a--~~~~~~~~~l~~~ 129 (282) .|.|.+..++++....+..+|..|.-....... +.. ++ ...+. ..|+-+ .-.....+..+.+ T Consensus 13 ~~~~~~d~L~~~~~v~l~~lF~PEHG~~G~~~a-----g~~---v~-~~~D~-------~tglpv~SLYg~~~~Pt~~~L 76 (359) T pfam07075 13 DLEHLVDLLLAAPGVNLKALFGPEHGFRGDAQA-----GEK---VG-DYVDP-------KTGLPVYSLYGKTRKPTPEML 76 (359) T ss_pred CCCCHHHHHHHCCCCCEEEEECCCCCCCCCCCC-----CCC---CC-CCCCC-------CCCCEEEECCCCCCCCCHHHH T ss_conf 987899999665698689981798787404214-----985---67-87688-------889908979899999999998 Q ss_pred CCCCEEEEECCCCCHH--------HHHHHHHHHHHHHCCCCCCCCCCCCCCHH---------HHHHHHHHHHHHHCCCCC Q ss_conf 6650688723432068--------89999999864200110013686320000---------013444333321101222 Q gi|254780603|r 130 RNSQLLMVLDHVNDPH--------NIGAILRSAVAFSCDGIITTKRYSPSESA---------VLAKSASGALEHIPYIRI 192 (282) Q Consensus 130 ~~~~~~i~ld~i~dp~--------NlG~I~Rta~a~g~~~vil~~~~~~~~~~---------~~~ras~Ga~~~l~~~~~ 192 (282) ++-. +++..|||-| -++-+|..|+..|+.-++|...+ |.+. ...+ |--+.+-+|+.+. T Consensus 77 ~~iD--vlv~DiQDvG~R~YTyi~Tm~~~meaaa~~~~~~iVLDRPN--Pl~G~~veGpvl~~~~~-SFvG~~piP~~hG 151 (359) T pfam07075 77 KGVD--VLVFDIQDVGVRFYTYISTLAYAMEAAAEAGKEFIVLDRPN--PLGGLYVEGPVLDPEFE-SFVGMYPIPVRHG 151 (359) T ss_pred HCCC--EEEEEEECCCEEEEEHHHHHHHHHHHHHHCCCCEEEECCCC--CCCCCCCCCCCCCHHHH-HCCCCCCCCCCCC T ss_conf 3699--99997422761565459999999999997499589947899--88887665786487775-1234455660047 Q ss_pred CCCCCCCCCCCCC Q ss_conf 3221122222221 Q gi|254780603|r 193 SNLTDALQKMHSW 205 (282) Q Consensus 193 ~~~~~~l~~~~~~ 205 (282) -.+.+.-...++. T Consensus 152 mTiGElA~~~n~e 164 (359) T pfam07075 152 MTIGELALLFNGE 164 (359) T ss_pred CCHHHHHHHHHHH T ss_conf 7899999999871 No 78 >PRK13172 consensus Probab=20.49 E-value=32 Score=14.98 Aligned_cols=11 Identities=9% Similarity=0.371 Sum_probs=4.5 Q ss_pred HHCCCCCCCCC Q ss_conf 20011001368 Q gi|254780603|r 157 FSCDGIITTKR 167 (282) Q Consensus 157 ~g~~~vil~~~ 167 (282) .|+..|..... T Consensus 125 ~GWn~i~~~~~ 135 (213) T PRK13172 125 IGWNELVSTSE 135 (213) T ss_pred ECHHHEECCCC T ss_conf 01445332455 No 79 >PRK10126 tyrosine phosphatase; Provisional Probab=20.48 E-value=19 Score=16.19 Aligned_cols=13 Identities=38% Similarity=0.409 Sum_probs=7.7 Q ss_pred HHHHHHHHHHHHC Q ss_conf 9999999864200 Q gi|254780603|r 147 IGAILRSAVAFSC 159 (282) Q Consensus 147 lG~I~Rta~a~g~ 159 (282) +|+|+||-.|-++ T Consensus 10 ~GNiCRSPmAE~i 22 (147) T PRK10126 10 VGNICRSPTAERL 22 (147) T ss_pred CCHHHHHHHHHHH T ss_conf 9806189999999 No 80 >pfam03308 ArgK ArgK protein. The ArgK protein acts as an ATPase enzyme and as a kinase, and phosphorylates periplasmic binding proteins involved in the LAO (lysine, arginine, ornithine)/AO transport systems. Probab=20.34 E-value=61 Score=13.34 Aligned_cols=115 Identities=15% Similarity=0.111 Sum_probs=60.4 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHH-------CCCCC Q ss_conf 68899999998642001100136863200000134443333211012223221122222221000000-------01233 Q gi|254780603|r 144 PHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYIRISNLTDALQKMHSWGFQTIG-------LSSDS 216 (282) Q Consensus 144 p~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~~~~~i~~-------~~~~~ 216 (282) +......++.|+|+|+|-||+..-++-.-.-.+... ...+=++..+...+-++..|. |.--++ .|..+ T Consensus 107 s~~t~~~i~lleaaGfD~IivETVGVGQsE~~v~~~----aD~~llv~~Pg~GDeiQ~iKa-GImEiaDi~vVNKaD~~~ 181 (267) T pfam03308 107 SRATREAILLLDAAGFDVIIIETVGVGQSEVDIANM----ADTFVLVTIPGGGDDLQGIKA-GLMEIADIYVVNKADLPG 181 (267) T ss_pred CHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHHHH----CCEEEEEECCCCCHHHHHHHH-HHHHHCCEEEEECCCHHH T ss_conf 476999999999779999999247777530355541----576899955887608889875-376535489996676476 Q ss_pred ----------CCCC---CCCCCCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHH Q ss_conf ----------3221---1223689889997586789877999858939992789687437 Q gi|254780603|r 217 ----------KKPL---EQEIKNDKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKAL 263 (282) Q Consensus 217 ----------~~~~---~~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SL 263 (282) .-.+ .+..|.-++..+-..++.|+.+-|....++.-.+-.+|..+.. T Consensus 182 A~~~~~~l~~~l~l~~~~~~~W~p~Vl~tSA~~g~Gi~el~~~I~~~~~~l~~sG~l~~r 241 (267) T pfam03308 182 AERTARELRSALHLLTPKEAGWRPPVLTTSAVTGEGIDELWDAIEEHREFLTATGLLAAR 241 (267) T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCHHHHH T ss_conf 999999999998517987789999989987478899999999999999999978869999 Done!