Query gi|254780142|ref|YP_003064555.1| DNA-directed RNA polymerase subunit beta' [Candidatus Liberibacter asiaticus str. psy62] Match_columns 1398 No_of_seqs 260 out of 1941 Neff 6.5 Searched_HMMs 39220 Date Mon May 23 12:06:12 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780142.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 TIGR02386 rpoC_TIGR DNA-direct 100.0 0 0 3550.5 68.8 1337 20-1363 1-1552(1552) 2 PRK01497 DNA-directed RNA poly 100.0 0 0 3310.9 108.2 1360 7-1372 1-1365(1384) 3 PRK09603 DNA-directed RNA poly 100.0 0 0 3198.9 99.3 1331 10-1373 1388-2888(2890) 4 PRK05258 DNA-directed RNA poly 100.0 0 0 2985.9 87.8 1162 14-1376 3-1196(1204) 5 PRK02173 DNA-directed RNA poly 100.0 0 0 2931.0 81.8 1169 13-1376 8-1401(1438) 6 PRK02995 DNA-directed RNA poly 100.0 0 0 2926.5 83.2 1157 14-1378 3-1264(1291) 7 PRK00566 DNA-directed RNA poly 100.0 0 0 2798.1 85.9 1165 14-1370 2-1278(1284) 8 KOG0260 consensus 100.0 0 0 2102.0 32.5 1211 10-1359 7-1414(1605) 9 KOG0261 consensus 100.0 0 0 1998.6 35.2 1176 7-1361 2-1358(1386) 10 TIGR02390 RNA_pol_rpoA1 DNA-di 100.0 0 0 1927.4 34.0 753 15-832 1-887 (901) 11 PRK08566 DNA-directed RNA poly 100.0 0 0 1674.3 43.1 780 11-845 2-880 (881) 12 KOG0262 consensus 100.0 0 0 1674.4 30.8 1234 18-1360 13-1631(1640) 13 COG0086 RpoC DNA-directed RNA 100.0 0 0 1601.1 30.1 780 16-849 3-807 (808) 14 PRK02625 DNA-directed RNA poly 100.0 0 0 1478.3 41.4 571 13-584 4-623 (627) 15 CHL00018 rpoC1 RNA polymerase 100.0 0 0 1460.3 37.6 571 15-585 4-657 (668) 16 PRK02597 DNA-directed RNA poly 100.0 0 0 1336.2 51.2 767 590-1367 7-1236(1295) 17 TIGR02388 rpoC2_cyan DNA-direc 100.0 0 0 1272.3 30.1 759 591-1362 2-1251(1252) 18 CHL00117 rpoC2 RNA polymerase 100.0 0 0 1183.3 42.8 436 590-1036 8-456 (1350) 19 TIGR02387 rpoC1_cyan DNA-direc 100.0 0 0 1194.4 23.6 537 17-554 1-559 (625) 20 CHL00006 consensus 100.0 0 0 1144.2 42.1 432 589-1034 7-451 (1372) 21 smart00663 RPOLA_N RNA polymer 100.0 0 0 763.3 19.3 276 237-513 1-295 (295) 22 pfam04998 RNA_pol_Rpb1_5 RNA p 100.0 0 0 690.5 11.0 434 763-1317 1-447 (447) 23 PRK04309 DNA-directed RNA poly 100.0 0 0 623.4 13.3 359 855-1360 14-373 (381) 24 cd02584 RNAP_II_Rpb1_C Largest 100.0 0 0 605.9 16.7 401 882-1360 2-406 (410) 25 pfam04997 RNA_pol_Rpb1_1 RNA p 100.0 0 0 587.9 21.4 310 15-344 1-330 (330) 26 cd06528 RNAP_A'' A'' subunit o 100.0 0 0 571.4 15.9 356 860-1360 2-358 (363) 27 TIGR02389 RNA_pol_rpoA2 DNA-di 100.0 0 0 568.3 9.5 339 902-1359 38-392 (397) 28 cd02736 RNAP_III_Rpc1_C Larges 100.0 0 0 560.8 10.8 293 901-1359 2-300 (300) 29 cd02735 RNAP_I_Rpa1_C Largest 100.0 0 0 540.7 16.9 303 901-1360 2-307 (309) 30 cd02655 RNAP_beta'_C Largest s 100.0 0 0 537.3 12.0 166 1127-1358 37-204 (204) 31 cd02737 RNAP_IV_NRPD1_C Larges 100.0 0 0 485.3 8.1 351 909-1360 1-378 (381) 32 pfam00623 RNA_pol_Rpb1_2 RNA p 100.0 0 0 449.2 12.2 143 346-488 1-165 (165) 33 cd00630 RNAP_largest_subunit_C 100.0 0 0 434.7 7.6 110 1211-1358 49-158 (158) 34 pfam04983 RNA_pol_Rpb1_3 RNA p 99.9 1E-25 2.6E-30 211.5 12.2 133 491-644 1-158 (158) 35 COG0086 RpoC DNA-directed RNA 99.7 8.9E-20 2.3E-24 166.8 -8.4 121 1200-1359 619-740 (808) 36 pfam04998 RNA_pol_Rpb1_5 RNA p 99.0 2.6E-10 6.7E-15 95.5 3.1 120 1179-1298 307-426 (447) 37 pfam05000 RNA_pol_Rpb1_4 RNA p 98.8 4.7E-10 1.2E-14 93.6 -0.2 89 674-762 2-97 (108) 38 PRK02995 DNA-directed RNA poly 97.0 0.00019 4.9E-09 51.4 0.6 31 1242-1278 1166-1196(1291) 39 PRK05258 DNA-directed RNA poly 96.3 4.7E-05 1.2E-09 56.0 -6.6 30 1242-1277 1102-1131(1204) 40 TIGR02386 rpoC_TIGR DNA-direct 96.0 0.096 2.4E-06 31.1 9.1 39 977-1015 1265-1303(1552) 41 pfam05183 RdRP RNA dependent R 90.5 0.3 7.7E-06 27.3 3.4 52 417-471 228-291 (381) 42 pfam04990 RNA_pol_Rpb1_7 RNA p 87.4 0.033 8.4E-07 34.6 -3.4 71 1001-1079 1-71 (135) 43 TIGR00354 polC DNA polymerase 83.4 0.58 1.5E-05 25.2 1.5 19 790-808 727-751 (1173) 44 CHL00037 petA cytochrome f 82.7 3 7.7E-05 19.8 7.4 76 1147-1223 204-291 (320) 45 pfam01333 Apocytochr_F_C Apocy 80.8 3.5 8.9E-05 19.3 7.4 59 1150-1210 6-65 (118) 46 TIGR01343 hacA_fam homoaconita 77.0 1.4 3.6E-05 22.3 1.7 40 900-957 104-153 (432) 47 TIGR00143 hypF [NiFe] hydrogen 70.9 3.1 7.9E-05 19.7 2.2 75 84-183 103-191 (799) 48 PRK04023 DNA polymerase II lar 70.7 1.9 4.8E-05 21.3 1.1 19 264-282 153-171 (1128) 49 PRK02693 apocytochrome f; Revi 67.8 7.1 0.00018 17.0 7.4 62 1147-1210 197-259 (312) 50 KOG0988 consensus 67.2 6.3 0.00016 17.4 3.1 32 773-806 516-548 (1145) 51 TIGR00416 sms DNA repair prote 65.0 3.3 8.3E-05 19.5 1.3 27 713-739 202-228 (481) 52 pfam09567 RE_MamI MamI restric 64.3 7.4 0.00019 16.9 3.1 47 415-476 217-263 (350) 53 TIGR01369 CPSaseII_lrg carbamo 64.2 7.5 0.00019 16.8 3.0 42 840-882 635-681 (1089) 54 pfam03615 GCM GCM motif protei 63.7 3.4 8.8E-05 19.4 1.3 48 79-149 78-127 (143) 55 PRK11798 ClpXP protease specif 61.2 7.4 0.00019 16.9 2.6 80 374-474 2-85 (140) 56 pfam09538 FYDLN_acid Protein o 60.3 6.5 0.00017 17.3 2.2 25 70-94 11-37 (104) 57 PRK09001 DNA topoisomerase I; 58.4 6.1 0.00016 17.5 1.8 14 27-40 22-35 (869) 58 cd01121 Sms Sms (bacterial rad 57.5 6.1 0.00015 17.5 1.6 16 723-738 174-189 (372) 59 TIGR01995 PTS-II-ABC-beta PTS 57.4 11 0.00027 15.7 5.3 61 1141-1206 541-610 (660) 60 PRK11823 DNA repair protein Ra 57.1 5.5 0.00014 17.8 1.4 15 724-738 182-196 (454) 61 TIGR02605 CxxC_CxxC_SSSS putat 56.7 7.2 0.00018 16.9 1.9 28 65-92 2-36 (43) 62 pfam09105 SelB-wing_1 Elongati 55.9 11 0.00027 15.7 2.6 23 1318-1340 29-51 (61) 63 TIGR02487 NrdD anaerobic ribon 55.5 6.6 0.00017 17.3 1.5 37 501-549 14-50 (655) 64 smart00834 CxxC_CXXC_SSSS Puta 54.2 5.7 0.00015 17.7 1.0 29 65-93 2-36 (41) 65 COG5257 GCD11 Translation init 54.2 6.3 0.00016 17.4 1.3 18 236-253 212-229 (415) 66 COG1066 Sms Predicted ATP-depe 53.6 6.9 0.00018 17.1 1.4 14 725-738 186-199 (456) 67 KOG4275 consensus 53.3 3.7 9.4E-05 19.1 -0.1 12 772-783 46-57 (350) 68 pfam06957 COPI_C Coatomer (COP 52.9 11 0.00028 15.6 2.3 10 492-501 104-113 (421) 69 KOG0856 consensus 52.2 4.1 0.0001 18.8 0.0 14 85-108 105-118 (146) 70 KOG1618 consensus 51.6 13 0.00033 15.0 4.1 22 325-348 251-272 (389) 71 PRK06450 threonine synthase; V 49.8 7.6 0.00019 16.8 1.1 21 68-91 3-25 (336) 72 COG3813 Uncharacterized protei 49.0 5.5 0.00014 17.9 0.3 41 56-101 18-59 (84) 73 TIGR00375 TIGR00375 conserved 48.2 5 0.00013 18.1 -0.0 28 922-960 260-288 (384) 74 COG1858 MauG Cytochrome c pero 46.9 15 0.00039 14.5 2.4 10 109-118 116-125 (364) 75 PRK07562 ribonucleotide-diphos 46.1 9.5 0.00024 16.1 1.1 10 232-241 150-159 (1177) 76 CHL00077 rps18 ribosomal prote 45.6 13 0.00033 15.0 1.8 25 1241-1265 26-50 (86) 77 PRK00222 methionine sulfoxide 45.3 8.6 0.00022 16.4 0.8 75 25-111 13-110 (141) 78 TIGR00758 UDG_fam4 uracil-DNA 44.9 4.1 0.0001 18.8 -0.9 75 855-939 44-130 (185) 79 PTZ00327 eukaryotic translatio 44.7 12 0.00031 15.2 1.5 94 21-123 22-139 (460) 80 pfam09723 CxxC_CxxC_SSSS Zinc 44.6 13 0.00032 15.1 1.6 28 65-92 2-35 (42) 81 COG4307 Uncharacterized protei 44.5 7.4 0.00019 16.9 0.4 29 66-96 1-30 (349) 82 PRK08997 isocitrate dehydrogen 44.2 17 0.00042 14.2 3.1 20 1217-1236 288-307 (334) 83 TIGR02910 sulfite_red_A sulfit 43.6 10 0.00026 15.8 1.0 17 338-354 292-308 (346) 84 pfam11786 Aft1_HRA Aft1 HRA do 43.3 8.4 0.00021 16.5 0.5 17 751-767 43-59 (78) 85 KOG3993 consensus 42.7 5.9 0.00015 17.6 -0.4 30 471-516 247-276 (500) 86 TIGR01420 pilT_fam twitching m 42.3 11 0.00028 15.5 1.0 41 336-378 80-122 (350) 87 pfam01641 SelR SelR domain. Me 42.1 9.7 0.00025 16.0 0.7 75 25-111 7-104 (124) 88 COG2401 ABC-type ATPase fused 41.9 11 0.00027 15.7 0.8 21 353-375 245-265 (593) 89 TIGR02525 plasmid_TraJ plasmid 41.7 16 0.00041 14.3 1.7 18 759-778 2-22 (374) 90 PRK05508 methionine sulfoxide 40.9 10 0.00026 15.8 0.7 14 85-108 81-94 (119) 91 KOG0317 consensus 40.6 19 0.00048 13.9 2.3 25 326-350 153-177 (293) 92 TIGR00573 dnaq exonuclease, DN 40.4 17 0.00044 14.1 1.8 13 582-594 93-105 (228) 93 PRK13401 30S ribosomal protein 40.3 17 0.00042 14.2 1.6 28 1237-1264 20-48 (79) 94 PRK00391 rpsR 30S ribosomal pr 40.0 16 0.00042 14.3 1.6 29 1239-1267 21-50 (80) 95 PRK09263 anaerobic ribonucleos 40.0 19 0.00048 13.8 2.3 16 533-548 148-163 (711) 96 COG0333 RpmF Ribosomal protein 38.5 14 0.00036 14.8 1.0 19 69-90 28-47 (57) 97 pfam01084 Ribosomal_S18 Riboso 37.5 19 0.00049 13.7 1.6 26 1239-1264 3-28 (54) 98 PRK09137 DNA topoisomerase I; 37.3 20 0.00051 13.6 1.7 20 219-241 178-197 (761) 99 KOG0890 consensus 37.0 11 0.00028 15.6 0.3 31 766-796 1566-1596(2382) 100 TIGR02810 agaZ_gatZ D-tagatose 36.8 10 0.00026 15.9 0.1 20 617-637 98-117 (430) 101 pfam01139 UPF0027 Uncharacteri 36.2 20 0.00051 13.6 1.5 16 715-730 185-200 (419) 102 TIGR02974 phageshock_pspF psp 36.0 22 0.00055 13.4 2.0 14 658-671 188-201 (349) 103 KOG3430 consensus 35.4 12 0.00031 15.2 0.3 34 58-109 47-80 (90) 104 PRK05638 threonine synthase; V 35.4 20 0.0005 13.7 1.4 47 497-551 296-349 (443) 105 PRK05550 bifunctional methioni 35.2 14 0.00036 14.7 0.6 73 24-108 5-97 (284) 106 TIGR01051 topA_bact DNA topois 35.2 16 0.00042 14.3 0.9 37 629-671 576-612 (688) 107 pfam06906 DUF1272 Protein of u 35.2 12 0.00031 15.3 0.3 32 66-98 24-56 (57) 108 TIGR00875 talC transaldolase, 35.1 22 0.00057 13.3 2.2 17 1317-1334 165-181 (216) 109 TIGR00838 argH argininosuccina 35.1 8.3 0.00021 16.5 -0.6 10 366-375 110-119 (469) 110 TIGR01918 various_sel_PB selen 34.9 19 0.00048 13.8 1.2 10 868-877 333-342 (433) 111 PRK13147 consensus 34.8 9.5 0.00024 16.1 -0.3 20 760-779 140-161 (211) 112 pfam10948 DUF2635 Protein of u 34.7 23 0.00058 13.2 1.6 16 413-428 31-46 (47) 113 pfam05876 Terminase_GpA Phage 34.5 20 0.00051 13.6 1.3 18 856-873 234-251 (552) 114 pfam07829 Toxin_14 Alpha-A con 34.4 22 0.00057 13.3 1.5 21 72-97 2-22 (26) 115 TIGR01998 PTS-II-BC-nag PTS sy 34.3 16 0.00041 14.3 0.8 15 757-771 369-384 (571) 116 KOG1100 consensus 34.0 19 0.00048 13.8 1.1 15 612-626 45-59 (207) 117 COG1645 Uncharacterized Zn-fin 33.4 12 0.00031 15.3 0.0 28 63-90 23-51 (131) 118 TIGR02086 IPMI_arch 3-isopropy 33.4 21 0.00054 13.5 1.3 50 886-957 97-156 (431) 119 TIGR02002 PTS-II-BC-glcB PTS s 33.1 17 0.00042 14.2 0.7 11 759-769 327-338 (518) 120 PRK05654 acetyl-CoA carboxylas 32.6 14 0.00035 14.8 0.2 26 65-90 26-56 (288) 121 TIGR01031 rpmF_bact ribosomal 32.5 21 0.00053 13.5 1.1 18 70-90 29-47 (56) 122 PRK06556 vitamin B12-dependent 32.3 21 0.00052 13.5 1.1 44 457-502 268-319 (957) 123 TIGR02873 spore_ylxY probable 31.9 18 0.00047 13.9 0.7 16 330-345 44-59 (269) 124 COG1571 Predicted DNA-binding 31.9 25 0.00064 12.9 1.4 18 770-787 110-127 (421) 125 TIGR01161 purK phosphoribosyla 31.7 18 0.00045 14.0 0.7 78 852-938 64-144 (386) 126 TIGR01661 ELAV_HUD_SF ELAV/HuD 31.2 24 0.00062 13.0 1.3 47 594-648 112-158 (436) 127 PRK12366 replication factor A; 31.1 21 0.00053 13.5 0.9 27 929-956 305-331 (649) 128 TIGR02420 dksA RNA polymerase- 30.9 21 0.00055 13.4 1.0 15 650-664 17-31 (110) 129 COG2331 Uncharacterized protei 30.3 14 0.00035 14.8 -0.1 30 64-93 8-43 (82) 130 pfam04035 consensus 30.2 27 0.00068 12.7 1.9 48 72-132 3-50 (60) 131 pfam09290 AcetDehyd-dimer Prok 29.9 16 0.0004 14.4 0.1 33 901-934 14-46 (137) 132 TIGR01751 crot-CoA-red crotony 29.9 18 0.00047 13.9 0.5 29 903-931 192-221 (409) 133 PRK12286 rpmF 50S ribosomal pr 29.8 25 0.00065 12.8 1.2 19 69-90 28-47 (59) 134 COG1107 Archaea-specific RecJ- 29.6 21 0.00054 13.4 0.8 11 415-425 338-348 (715) 135 pfam06060 Mesothelin Pre-pro-m 29.5 9.3 0.00024 16.1 -1.1 81 264-371 136-216 (625) 136 pfam05129 Elf1 Transcription e 29.5 17 0.00044 14.1 0.3 46 66-117 15-69 (74) 137 TIGR01802 CM_pl-yst chorismate 29.4 15 0.00038 14.5 -0.0 39 88-131 147-185 (273) 138 COG5349 Uncharacterized protei 28.2 22 0.00055 13.4 0.6 11 84-94 41-51 (126) 139 COG0777 AccD Acetyl-CoA carbox 27.9 20 0.0005 13.7 0.3 10 348-357 228-237 (294) 140 pfam04502 DUF572 Family of unk 27.7 28 0.0007 12.6 1.1 28 54-82 27-57 (324) 141 PRK09588 hypothetical protein; 27.7 29 0.00074 12.4 1.4 15 716-730 160-174 (376) 142 KOG1080 consensus 27.6 29 0.00075 12.4 2.1 23 763-785 694-717 (1005) 143 PRK06319 DNA topoisomerase I/S 27.4 29 0.00075 12.4 2.0 24 218-244 175-198 (864) 144 TIGR01122 ilvE_I branched-chai 27.4 23 0.00059 13.2 0.6 21 861-881 70-91 (302) 145 COG5259 RSC8 RSC chromatin rem 27.3 26 0.00068 12.7 0.9 18 453-470 224-242 (531) 146 TIGR00280 L37a ribosomal prote 27.3 30 0.00076 12.3 1.6 28 67-94 35-65 (92) 147 TIGR02909 spore_YkwD uncharact 27.3 30 0.00076 12.3 1.5 55 475-541 31-93 (129) 148 pfam10005 DUF2248 Uncharacteri 27.1 30 0.00076 12.3 1.8 26 70-97 1-27 (340) 149 COG0229 Conserved domain frequ 27.1 23 0.0006 13.1 0.6 79 25-115 12-113 (140) 150 KOG2873 consensus 27.0 29 0.00075 12.4 1.1 14 296-309 196-209 (284) 151 COG1996 RPC10 DNA-directed RNA 26.9 26 0.00065 12.8 0.8 28 67-94 5-35 (49) 152 PRK11788 hypothetical protein; 26.7 30 0.00077 12.3 1.8 24 604-630 109-132 (389) 153 pfam10083 DUF2321 Uncharacteri 26.7 23 0.00058 13.2 0.5 42 85-131 30-76 (158) 154 TIGR00873 gnd 6-phosphoglucona 26.7 30 0.00077 12.3 4.5 28 1327-1354 398-425 (480) 155 TIGR00830 PTBA PTS system, glu 26.3 31 0.00079 12.2 6.7 64 1141-1207 30-108 (129) 156 TIGR02679 TIGR02679 conserved 26.1 26 0.00066 12.8 0.7 22 340-361 115-136 (431) 157 COG3809 Uncharacterized protei 25.9 31 0.00079 12.2 1.1 16 87-102 15-30 (88) 158 COG2805 PilT Tfp pilus assembl 25.7 28 0.00072 12.5 0.8 41 336-376 79-119 (353) 159 PRK05473 hypothetical protein; 25.5 32 0.00081 12.1 1.5 25 1260-1285 45-69 (86) 160 COG1039 RnhC Ribonuclease HIII 25.5 18 0.00045 14.0 -0.2 48 340-393 69-121 (297) 161 pfam06135 DUF965 Bacterial pro 25.5 32 0.00081 12.1 1.5 47 1228-1285 20-66 (79) 162 TIGR01018 rpsD_arch ribosomal 25.4 32 0.00081 12.1 1.0 16 730-745 126-143 (170) 163 PRK11230 glycolate oxidase sub 25.4 28 0.00071 12.6 0.7 10 1349-1358 469-478 (499) 164 KOG0396 consensus 25.3 28 0.00071 12.5 0.7 14 105-118 4-17 (389) 165 pfam00358 PTS_EIIA_1 phosphoen 25.0 32 0.00083 12.0 5.5 59 1143-1207 37-105 (133) 166 COG1379 PHP family phosphoeste 24.9 19 0.00048 13.8 -0.2 19 499-517 230-248 (403) 167 TIGR01832 kduD 2-deoxy-D-gluco 24.7 28 0.00071 12.5 0.6 87 642-742 60-147 (249) 168 pfam10080 DUF2318 Predicted me 24.6 22 0.00056 13.3 0.1 12 83-94 52-63 (102) 169 TIGR02013 rpoB DNA-directed RN 24.3 33 0.00085 12.0 6.1 22 994-1015 847-868 (1449) 170 COG5469 Predicted metal-bindin 24.1 34 0.00086 11.9 2.0 12 228-239 115-126 (143) 171 TIGR03073 release_rtcB release 24.1 34 0.00086 11.9 1.4 15 716-730 149-163 (356) 172 COG1965 CyaY Protein implicate 24.0 34 0.00086 11.9 1.2 11 1164-1174 44-54 (106) 173 pfam12151 MVL Mannan-binding p 23.9 21 0.00054 13.4 -0.1 15 452-466 8-22 (37) 174 TIGR01020 rpsE_arch ribosomal 23.7 28 0.00073 12.5 0.5 11 1213-1223 168-178 (220) 175 KOG0680 consensus 23.7 34 0.00087 11.9 2.1 72 362-438 290-371 (400) 176 pfam01939 DUF91 Protein of unk 23.6 28 0.00072 12.5 0.5 11 1244-1254 193-203 (228) 177 COG0238 RpsR Ribosomal protein 23.6 33 0.00083 12.0 0.8 27 1242-1268 27-53 (75) 178 cd00210 PTS_IIA_glc PTS_IIA, P 23.5 35 0.00088 11.8 5.3 60 1142-1207 31-100 (124) 179 PRK04338 N(2),N(2)-dimethylgua 23.4 35 0.00088 11.8 1.5 11 365-375 181-191 (376) 180 TIGR00655 PurU formyltetrahydr 23.4 18 0.00045 14.0 -0.6 28 1248-1279 177-204 (294) 181 COG1149 MinD superfamily P-loo 23.3 35 0.00088 11.8 1.2 17 223-243 207-223 (284) 182 PRK03754 DNA-directed RNA poly 23.2 31 0.00078 12.2 0.6 28 69-96 6-37 (49) 183 TIGR00201 comF comF family pro 22.8 35 0.0009 11.7 1.2 23 71-95 1-24 (207) 184 PRK00564 hypA hydrogenase nick 22.8 36 0.00091 11.7 1.1 10 15-24 23-32 (117) 185 PRK08329 threonine synthase; V 22.7 36 0.00091 11.7 1.2 19 70-91 3-23 (348) 186 TIGR00699 GABAtrns_euk 4-amino 22.7 36 0.00091 11.7 4.7 209 255-537 54-300 (469) 187 pfam07236 Phytoreo_S7 Phytoreo 22.6 36 0.00091 11.7 1.7 83 299-387 18-103 (506) 188 TIGR02283 MltB_2 lytic murein 22.6 24 0.0006 13.1 -0.1 14 603-616 83-96 (313) 189 PRK12423 LexA repressor; Provi 22.5 36 0.00091 11.7 4.2 28 413-440 125-152 (202) 190 PRK00215 LexA repressor; Valid 22.3 36 0.00092 11.7 4.1 29 413-441 128-156 (204) 191 KOG0300 consensus 22.1 36 0.00093 11.7 1.4 29 755-787 126-158 (481) 192 pfam03998 Utp11 Utp11 protein. 22.0 30 0.00076 12.3 0.4 10 98-107 11-20 (239) 193 KOG4550 consensus 21.9 36 0.00092 11.7 0.8 14 459-472 92-106 (606) 194 PRK08373 aspartate kinase; Val 21.8 32 0.00082 12.1 0.5 12 862-873 232-243 (359) 195 TIGR01843 type_I_hlyD type I s 21.7 37 0.00095 11.6 5.7 32 576-607 53-89 (434) 196 KOG0696 consensus 21.4 21 0.00052 13.5 -0.6 13 349-361 349-361 (683) 197 cd00498 Hsp33 Heat shock prote 21.2 33 0.00084 12.0 0.5 10 1214-1223 241-250 (275) 198 KOG0326 consensus 21.1 35 0.00089 11.8 0.6 11 243-253 64-74 (459) 199 KOG3002 consensus 21.1 38 0.00096 11.6 0.7 28 79-106 64-93 (299) 200 PRK06260 threonine synthase; V 20.8 39 0.00099 11.5 1.6 22 69-90 4-26 (400) 201 PRK00446 cyaY frataxin-like pr 20.8 39 0.00099 11.5 1.4 15 419-433 43-57 (104) 202 PRK07591 threonine synthase; V 20.7 39 0.00099 11.4 1.6 25 64-90 15-41 (422) 203 TIGR03215 ac_ald_DH_ac acetald 20.6 34 0.00086 11.9 0.4 32 901-933 136-167 (285) 204 COG4469 CoiA Competence protei 20.5 39 0.001 11.4 0.7 28 85-112 27-56 (342) 205 COG1001 AdeC Adenine deaminase 20.3 40 0.001 11.4 1.8 13 631-643 99-111 (584) 206 PRK08300 acetaldehyde dehydrog 20.1 37 0.00094 11.6 0.5 33 901-934 142-174 (298) 207 PRK00378 nucleoid-associated p 20.1 27 0.00068 12.7 -0.2 40 759-806 168-210 (334) 208 TIGR02016 BchX chlorophyllide 20.1 40 0.001 11.4 0.7 12 770-781 176-187 (355) No 1 >TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit; InterPro: IPR012754 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This entry represents the beta-prime subunit, RpoC, found in most bacteria. It excludes some, mainly cyanobacterial, species where RpoC is replaced by two homologous proteins that include an additional domain. One arm of the "claw" is predominantly formed by this subunit, the other being predominantly formed by the beta subunit. The active site of the enzyme is defined by three invariant aspartate residues within the beta-prime subunit .; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription. Probab=100.00 E-value=0 Score=3550.45 Aligned_cols=1337 Identities=54% Similarity=0.888 Sum_probs=1266.3 Q ss_pred EEEEECCCHHHHH-HCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC--CCCCCCCCCCCCCCCC Q ss_conf 6898458867885-014489717554254568756887336213685667721566415634--4883567578853047 Q gi|254780142|r 20 SVRISIASPAKIA-SLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRMK--YKGIICEKCGVEVTLS 96 (1398) Q Consensus 20 ~i~f~l~spe~I~-~~S~~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~Cg~~~~~~--~~g~~C~~Cg~~~~~~ 96 (1398) +|+++|||||+|| +||+|||+|||||||||+|||+||||||+||||+|||||.|||||++| |||.+|++||||+|++ T Consensus 1 ~I~I~iASpd~Ird~WS~GEVkKPETINYRTLKPEkdGLFcE~IFGPtKDwEC~CGKYK~~rPmyKGvvCerCGVEVT~s 80 (1552) T TIGR02386 1 AIKISIASPDKIRDSWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKVRPMYKGVVCERCGVEVTES 80 (1552) T ss_pred CEEEECCCCCHHHCCCCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCCCEEEECCCCEEEEE T ss_conf 91753288851310555420218752576556888778754635588876230567532237565751760178179411 Q ss_pred CCCCCCCCCCCCCCCCEEECHHHHHH--HHHHHHHCCCHHHHHHHHHHCCEEEECCCCCCHHH------HCCCCHHH--- Q ss_conf 75787677200277622013012257--89999809996563013321112321788651043------22369999--- Q gi|254780142|r 97 SVRRDRMAHIDLASPVAHPWFLKSLP--SRISTLLGMSLRDVERVLYFESYVVVDPGLSSLEK------YQILTEEE--- 165 (1398) Q Consensus 97 ~~r~ghfGhIeLa~PV~Hi~f~k~~~--~~i~~~l~~~~~~~~~v~y~~~~~~~~~~~~~~~~------~~~~~~~~--- 165 (1398) +|||.||||||||.||.||||+|.+| |+|+.+||++.+++++|+||++|+|+||+...+.+ +++|+|++ T Consensus 81 kVRRERMGHIELAaPV~HIWy~K~~PSPSRigl~LDi~~k~Le~VlYF~~YvV~d~g~~~~~~~s~f~~k~~L~e~e~k~ 160 (1552) T TIGR02386 81 KVRRERMGHIELAAPVAHIWYFKGLPSPSRIGLLLDITAKELESVLYFEKYVVIDPGDTKLDKKSAFKEKEVLDEKENKR 160 (1552) T ss_pred EEECCCCCCEECCCCCEEEEEECCCCCHHHHHHHHCCCHHHHCCEEEEEEEEEECCCCCCCCCCCCHHCCCCCCCCCCCC T ss_conf 64023245321037741453322888743588875788678050477778899878886454202200252026554530 Q ss_pred ---------------------------------HHHHHHHCC--------------CCCEEECCCHHHHHHHHHHCCHHH Q ss_conf ---------------------------------988676358--------------555061155267788877267488 Q gi|254780142|r 166 ---------------------------------YVEAVSQFG--------------QDQFIAMMGADAIYELLIALDLQN 198 (1398) Q Consensus 166 ---------------------------------~~~~~~~~~--------------~~~~~~~~g~~~i~~~l~~~~~~~ 198 (1398) |.+..+++| ++.|.++||||||+++|+++||++ T Consensus 161 ~~~~R~k~~~~~~~~~~~~~~~~~~~dy~~~~~Y~~~~~~yG~PFS~~da~~~I~Ky~~F~a~mGAEAI~~LL~~iDL~~ 240 (1552) T TIGR02386 161 SLKTREKLRRTIRDIIERLIKEKNHEDYRKAKVYREVLERYGVPFSVDDATSYIEKYDGFRAGMGAEAIKELLEKIDLDK 240 (1552) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHHHHHHCCEEEEEECHHHHHHHHHCCCHHH T ss_conf 24225788999999998654100023556656789999840898318999988653385578732489998751378689 Q ss_pred HHHHHHHHHHCCC----CCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCCEEEECCCCCCCHHHHHHHHHH Q ss_conf 9999998731032----203478864477888666634898511286304507622351388469731310037899999 Q gi|254780142|r 199 LALTLRDQLSKSS----SIFRRKKIIKRLKIVDSFITSGNNPGWMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRV 274 (1398) Q Consensus 199 ~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~f~~~~~~Pewmil~~lpV~P~~~RP~v~~~~g~~~~dDlt~~~~~I 274 (1398) +...++.+|.... +.++++|++|||+++++|..|++|||||||+++||+||++||+||||||+||+||||++||+| T Consensus 241 e~~~l~~~l~~~~kd~~~~~~~kkllKRLe~~e~F~~Sgn~PeWMvl~~~PVIPPelRPmVQLDGGRFATSDLNDLYRRV 320 (1552) T TIGR02386 241 EIEELKEELRESKKDSKSQQKRKKLLKRLEILEAFKNSGNRPEWMVLDVIPVIPPELRPMVQLDGGRFATSDLNDLYRRV 320 (1552) T ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCEECCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCEE T ss_conf 99999999862143456766888888987889999713788753035315758842267764777510122320102302 Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCEEECCCCCCCCCCCC Q ss_conf 99869999998739835677769999999888874277678772478765067899861023782000346510045774 Q gi|254780142|r 275 IGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGR 354 (1398) Q Consensus 275 i~~N~~Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~~~~~~~~~~rp~ks~~~rlkgK~GrfR~nl~GKRVdfs~R 354 (1398) |+|||||||+++.+||++|++|||||||+|||+|||||++++|+.++++|||||||++|||||||||||||||||||||| T Consensus 321 INRNNRLKrlL~l~APeIIV~NEKRMLQEAVDALfDNgRR~kPV~G~~nRpLKSLSdmLKGKQGRFRQNLLGKRVDYSGR 400 (1552) T TIGR02386 321 INRNNRLKRLLELKAPEIIVRNEKRMLQEAVDALFDNGRRGKPVVGKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGR 400 (1552) T ss_pred EECCHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCHHHHHCCCEEEECCC T ss_conf 30103788987458886887155335678888874478888631078897754324441266773003206860541552 Q ss_pred EEEECCCCCCCCCEECHHHHHHHHHHHHHHHHHHH---------CCCCCCCCCCCCEEECCCCCEEHHHHHHHCCCEEEE Q ss_conf 03412554354620034898776128999999998---------798666300010012248825013266656978997 Q gi|254780142|r 355 SVIVAGPELQLHQCGLPKLMALELFKPFLYAQLEK---------KGYVSTVKQAKKFVEKERPEVWDVLAEVVHQHVVLL 425 (1398) Q Consensus 355 sVI~pdP~l~~~evgvP~~~A~~L~~P~~~~~L~~---------~g~~~~i~~~k~~i~~~~~~v~~v~rhl~~gd~Vl~ 425 (1398) |||+++|+|+|||||+|+.||+|||+||+|++|+. .++++|||.||++|++++|+||+|+..++.++|||| T Consensus 401 SVIVVGPeLKm~QcGLPk~MALeLFKPFIi~~L~~K~DE~GNEI~~~A~NIK~Ak~~ie~~dpeVWdvLE~VIK~hPVLL 480 (1552) T TIGR02386 401 SVIVVGPELKMYQCGLPKKMALELFKPFIIKRLVDKFDELGNEIRELAANIKSAKKMIEQEDPEVWDVLEEVIKEHPVLL 480 (1552) T ss_pred EEEEECCCCCCCCCCCCHHHHHHHCCCEEEHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCC T ss_conf 78998897741136882798875167302322222102367415777776999999987428702368999852488433 Q ss_pred CCCCCCEECCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEEH Q ss_conf 57631011140123589944954797312254546787754569974689999999999876750542378878204402 Q gi|254780142|r 426 NRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPASGAPVTVPS 505 (1398) Q Consensus 426 NRqPsLHr~Simah~~~v~~~~t~rln~~vc~pyNADFDGDEMnlHvPqs~eAraEa~~Lm~~~~niisP~~g~Pi~~~~ 505 (1398) ||||||||+|||||.|++++||+|||||+||++||||||||||+||||+|.||+|||+.|||+++|||+|+||+||+.|+ T Consensus 481 NRAPTLHRLGIQAFEP~LVEGKAIrLHPLVC~AFNADFDGDQMAVHVPLS~eAq~EAr~LMLa~~NIL~P~dG~Pi~~Ps 560 (1552) T TIGR02386 481 NRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKPIVTPS 560 (1552) T ss_pred CCCCHHHHCCHHHCCCEEECCCEECCCCHHHHHHCCCCCCCCCEEECCCCHHHHHHHHHHHHCHHHCCCCCCCCEEEECC T ss_conf 67742231003334776441411106821444314788888222802788779999999984433317777885067088 Q ss_pred HHHHHHHHHHHCCC---CCCCCCC-----------------CEECCHHHHHHHHHCC----------------CCCCCCE Q ss_conf 58999999873367---8874468-----------------1417999999999888----------------9867852 Q gi|254780142|r 506 QDMVLGLCYLSTVH---EGDPGEG-----------------MLFADMGEVYHALENK----------------IVTLHSK 549 (1398) Q Consensus 506 QD~i~G~y~lT~~~---~~~~~~~-----------------~~f~~~~~~~~~~~~~----------------~~~~~a~ 549 (1398) ||||||+||||+++ ....|++ ++|.|.+||..||.++ .+.+|+. T Consensus 561 QDmvLG~YYLT~E~tyf~~~~G~g~makdPtqarvefinnf~~Fs~~~Ev~~Ay~~gGfiddvfGdrrdetGr~~~~~~~ 640 (1552) T TIGR02386 561 QDMVLGLYYLTTEKTYFPGEKGEGLMAKDPTQARVEFINNFKIFSDLEEVIRAYDNGGFIDDVFGDRRDETGRKVHLHAL 640 (1552) T ss_pred CCHHHCCHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHCCCCEEECCCCCCCCCCCEEECCCE T ss_conf 42200132115454427622478744467024566655421003588999999865880641256541225752001323 Q ss_pred EEEEECCCCCCC-C----CCCEEECCCCCCCCCCEEEECCCCCEEEE-----------------------------ECCH Q ss_conf 365204645667-6----14245217977511220554587510177-----------------------------5110 Q gi|254780142|r 550 IRGRYKSVDKDG-N----SISKIYDTTPGRMIIGEILPRHHEISFDI-----------------------------CNQE 595 (1398) Q Consensus 550 i~~~~~~~~~~~-~----~~~~~~~tt~Gr~~~~~ilp~~~~~~~~~-----------------------------~~~~ 595 (1398) |+++....+... . -.+..+.||+||++||++||++..+.... +-.. T Consensus 641 I~v~~~A~~n~~F~~~~~rlg~~l~TT~Gr~iFN~iLP~~~py~N~~~N~~~e~e~p~~fi~~~~~~i~~~i~~~~~~~p 720 (1552) T TIGR02386 641 IKVRISAFPNKKFSKENKRLGEILETTVGRVIFNEILPEGFPYINKTKNLYDEKEAPKKFIVEKGEDIKEVIEKIQVVEP 720 (1552) T ss_pred EEEEEECCCCCCCHHHHHHCCCEEEECCCEEEECCCCCCCCCCEECCCCCCHHHCCHHHHHHHCCCCHHHHHHHCCCCCC T ss_conf 78987416873200468752883662256556511157786644554466212203367763158357889974333366 Q ss_pred HCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCH Q ss_conf 02013666999999980817899987558899999998539861321232683699999999978999999886489766 Q gi|254780142|r 596 MIKKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKMVKEYENQYNDGLITR 675 (1398) Q Consensus 596 ~~k~~~~~li~~i~~~~G~~~~~~~l~~~~~l~~~~l~~~GfSigi~D~~~~~~k~~~i~~a~~~~~~~~~~~~~G~~t~ 675 (1398) +.|+.++.||..+|+.||...++.|||.++.|||+|+|.+|.|||+.|+.+|++|.+++++|+++|+.+.++|.+|+||+ T Consensus 721 ~~kK~i~~lI~~~Y~~~g~~~t~~~LD~iK~LGF~yaT~~g~t~s~~Di~~p~~K~~~~~~A~~~V~~~~~~Y~~G~iT~ 800 (1552) T TIGR02386 721 LSKKEISELIAKLYEVHGIEETVEMLDKIKDLGFKYATKAGITVSISDIVVPDEKQEILKEADKEVAKIQKDYNKGLITE 800 (1552) T ss_pred CCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCCCC T ss_conf 55036789999998760667899999888631000000101506788664387515788899999999999875286011 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC--CCCCCCCCCCCCEEEEECCCCCCCHHHEEEEEEECCCCCCCCC---- Q ss_conf 7888788642346589999999999876115--6543222246883764225555784241120010000246443---- Q gi|254780142|r 676 GEKYNKVVDLWGKTTDKVTEEMMARIKRVEF--DPETGRQKKMNSIFMMSHSGARGSIHQMRQLGGMRGLIAKPSG---- 749 (1398) Q Consensus 676 ~e~~~~i~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~N~~~~M~~SGAKGS~~qi~ql~Gqq~l~gkp~G---- 749 (1398) +|||++++++|++|+|++.++|++.+.++.. +.....++.+|+++||++||||||++||+||+||||||+||+| T Consensus 801 ~ERy~kvv~iWs~~~d~v~~~m~~~l~kd~~ylPdGsvqq~~~NpIf~MadSGARGN~sq~rQLAGMRGLMAkp~GY~~~ 880 (1552) T TIGR02386 801 EERYKKVVSIWSETKDKVTDAMMKLLKKDTYYLPDGSVQQDKFNPIFMMADSGARGNISQFRQLAGMRGLMAKPSGYDRK 880 (1552) T ss_pred CCCCCCEEEEECCCCHHHHHHHHHHHHHCCEECCCCCEEECCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCC T ss_conf 11235236653011468899999874012402688644006988279970356643578888876530124688776520 Q ss_pred -------CCCCCCCCCHHHCCCCHHHHHHCCCCCCHHHHCCCCCCCCCCEEEEHHHHHHCCCEEEEECCCCCCCCEEEEE Q ss_conf -------4445666301110888989764057610322101210156740110154230143277513887666512111 Q gi|254780142|r 750 -------EIIESPIRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHI 822 (1398) Q Consensus 750 -------~~~~~PV~~sF~~GL~p~EfFfhamgGReGLiDTAvKTA~SGYlqRrLvk~~eDl~V~~~D~~t~~g~~~~~~ 822 (1398) +|||.||+|||+||||..|||.||||+|+||+|||+|||+||||||||||++||++|++.||||.+|+.+..+ T Consensus 881 N~~g~IK~iIE~PIkssFrEGLtV~EYFiStHGARKGLADTALKTADSGYLTRRLVDv~QdVvv~e~DCGT~~Gi~v~ai 960 (1552) T TIGR02386 881 NNSGVIKDIIELPIKSSFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVVVREEDCGTEEGIEVEAI 960 (1552) T ss_pred CCCCCEEEECCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCEEEEEEEEEEECCCCCCCCEEEEEE T ss_conf 25754232047887343202772453110111200114789987426565521001254448887168788477789999 Q ss_pred EECC----EEEEEECCCCCCCCCHHHCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEECCCCCCHHHHHCCCHHHHHH Q ss_conf 0088----488650001012211442017789718851786578999999997598402023310003551865788754 Q gi|254780142|r 823 VDSG----QVVYSLGSRVLGRTALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGR 898 (1398) Q Consensus 823 ~~~~----~~~~~l~~~~~~r~~~~di~~~~~~~~i~~~~~~i~~~~~~~i~~~~i~~v~irs~lt~~~~~~v~~~cy~~ 898 (1398) .++. ..+++|.+|++||++++||++|.++++|+++|++|+++.++.|+++||++|+|||||||++++|||++|||+ T Consensus 961 ~~g~~~el~~IesL~DR~vGR~~~edv~~P~~g~~~~~~N~lI~~~~a~~i~~~Gi~~v~iRS~LTC~~~~GVC~kCYG~ 1040 (1552) T TIGR02386 961 VEGKDDELEVIESLKDRIVGRYSAEDVVDPETGKLVAKANTLITEEIAEKIENLGIEKVKIRSVLTCESKHGVCQKCYGR 1040 (1552) T ss_pred EECCCCEEEEEECCCCEEEEEEEEEEEECCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCEEECCCCCCEEECCCC T ss_conf 84788648898604211673289875312887728871577311799999985796689963421406898823100121 Q ss_pred HCCCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCC-------------------------- Q ss_conf 201785200010146021111007889877642024543222112202401487-------------------------- Q gi|254780142|r 899 DLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDG-------------------------- 952 (1398) Q Consensus 899 ~l~~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlG-------------------------- 952 (1398) |||++++|+.|||||+|||||||||||||||||||+|||||...+...+.+..| T Consensus 1041 dLat~~~v~~GEAVGvIAAQSIGEPGTQLTMRTFH~GGvA~~~~~~~~~~~~~~gI~N~I~Gl~~~~~~~~~F~R~G~~~ 1120 (1552) T TIGR02386 1041 DLATGKLVEIGEAVGVIAAQSIGEPGTQLTMRTFHTGGVAGASSEEESIKVKNGGILNGIEGLIVRVDSGILFSRKGSLK 1120 (1552) T ss_pred CCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCHHHCCCCCCCCCCCCHHECCCCEEEECCCEEEEEECCCEEEEECCEEE T ss_conf 00048521136852378864068467712020110121012332100001003605624340377632745786326078 Q ss_pred EEEE------EEEE------EEECCCCCEEEEECCCCEEEEECCCCEEEE------------EECCCHHCCCCCCCCEEE Q ss_conf 6897------2113------465178877897427604664067760000------------001100001356785532 Q gi|254780142|r 953 IVKI------KNRN------VCRNSTNDLISMGRNTTLQILDMSGQEQYS------------HRIMYGAKLFVDDGGVIE 1008 (1398) Q Consensus 953 VPRl------kEi~------~~~n~~~~~i~vs~~~~~~i~d~~~~~~~~------------~ki~~~~~~~v~~~~~v~ 1008 (1398) |-|+ .++. .-+=.++..+.+.++++..+.+..+....+ ..+.+|+.+.+.+++.|. T Consensus 1121 i~~~~~~~k~~~~~~~~V~~~Q~V~KG~~l~~~~~Ge~~v~~~~G~~~~~~~~f~i~~ee~~~~V~~G~~i~V~~g~~V~ 1200 (1552) T TIGR02386 1121 ILRYFQELKTVEISELKVLDSQKVIKGENLVVDKKGEEIVVSEEGRIKIEDKKFLIVEEEEVVPVKLGTKILVEDGDAVK 1200 (1552) T ss_pred EEEEECHHHEEECCEEEEECCCEEECCCEEEECCCCCEEEECCCCEEEEECCCEEEECCCEEEECCCCCEEEEECCCCCC T ss_conf 87620010011001256405735533713676588876770788878850585776403215642656688861586205 Q ss_pred CCEEEEECCCCCCEEEECCCCEEEEEEECCCCEEHHHHHCCCCCEEEEEEEHHHC-CCCCCCCCCEEEECCCCCEEECCC Q ss_conf 2507862135431132024636897531278320012302368602677510110-122123853477427782532247 Q gi|254780142|r 1009 CGQRISEWDPHTFPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFA-SRSQNLKPAIVVTDENGVVLKSAR 1087 (1398) Q Consensus 1009 ~~~ii~~~Dp~~~~i~~e~~~~v~~~~~~~~~~~~~~~~~~t~~~~~~~i~~~~~-~~~~~~~~~~~i~d~~~~~~~~~~ 1087 (1398) .++.+++||||+.||++|..|++.|.|++.|.++..+.++.|++....+++.... -...++.|++.+.|+.+.. T Consensus 1201 ~G~~~aefDP~~~PIIse~~Gki~~~D~~~G~~~~~~~~~~Tg~~~l~v~d~~~~~PqGr~L~PrI~i~D~~~~~----- 1275 (1552) T TIGR02386 1201 EGQRIAEFDPYNEPIISEVDGKIKYKDLVEGKSVRKEKDEETGLVELRVIDSRQEKPQGRELEPRIAILDEKGEL----- 1275 (1552) T ss_pred CCCEEEEECCCCCCEEECCCCEEEEEEEECCCCCHHHHCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEECCCCC----- T ss_conf 887578844777452711698578875003762011101424428999985357888987688748998568983----- Q ss_pred CCCCEEECCCCCEEEECCCCCCCCCCEEEECHHHHCCCCCCCCCCCHHHHHHHHHCCCC--CCEECCCCCEEEEE-EECC Q ss_conf 88420213778445413676135484222101320245543367732889887525111--10111347867863-3127 Q gi|254780142|r 1088 GTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFEARRPKN--HAILAEISGTIRIK-RNYK 1164 (1398) Q Consensus 1088 ~~~~~~~~~~~~~~~v~~~~~v~~~d~l~~~~~~~~k~~DIt~GLPrV~eLFEar~pk~--~aiisei~Giv~i~-~~~~ 1164 (1398) .+.|.+|.++...|.+|+++..||.++|+|.-+.||+|||||||||.||||||+||+ .|+|||++|+|.+. ...+ T Consensus 1276 --~a~Y~~P~~Aii~V~dG~~v~~GDIlAklp~g~~KT~DITgGLPRv~ELFEar~PK~~e~A~Iae~dG~v~~~~~~~k 1353 (1552) T TIGR02386 1276 --VATYAIPADAIISVEDGQKVKPGDILAKLPKGAEKTKDITGGLPRVKELFEARTPKDFEAAVIAEVDGVVEIIEDDVK 1353 (1552) T ss_pred --CEEEECCCCEEEEECCCCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCEEHCCCEEEEECCCCC T ss_conf --135566301078721587547474788605566455210367612577860168861121100010217885114423 Q ss_pred CCEEEEEEECCCCCCEEEEEECCCCEEEEECCCEEECCCEEECCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEEC Q ss_conf 94499998368984026898138965898419877408646438999999987527999999999999999998097006 Q gi|254780142|r 1165 NKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAIN 1244 (1398) Q Consensus 1165 ~k~~~vi~~~~~g~~~~e~~ip~~~~l~v~dgd~V~~gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN 1244 (1398) ++..++|....+..+..+|.||.++|+.|.+|+.|.+|+.||||++||||||++.||.|+|+|||+|||+||+.|||.|| T Consensus 1354 ~~r~~~i~~e~~~~e~~~Y~Ip~~~~L~V~~G~~V~~G~~ltEG~idphd~L~~~Gi~~vq~Yl~~EVQ~VYR~QGV~In 1433 (1552) T TIGR02386 1354 NKRVVVIKDENDDGEEKEYLIPFGAQLRVKDGDSVSAGDKLTEGSIDPHDLLRVKGIQAVQEYLVKEVQKVYRLQGVEIN 1433 (1552) T ss_pred CEEEEEEECCCCCCCEEEEEEECCCEEEEECCCEEECCCEECCCCCCHHHHHHHCCHHHHHHHHHHHHHHHHCCCCEEEC T ss_conf 40899983168885347876506665897218887078520168978789863417789999987523430001886786 Q ss_pred HHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHH Q ss_conf 12560124762861489418864545664106999999999999728987520121000014530231077650402589 Q gi|254780142|r 1245 HKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETT 1324 (1398) Q Consensus 1245 ~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~ 1324 (1398) |||||+|++|||+|++|+|+|||.||+|+.|+++.|..+|+.++.+|+.||.+.|+|+|||||||+|+|||||||||||| T Consensus 1434 DKHIEvIvrQMlrKV~itD~GDs~ll~Ge~i~~~~f~E~N~~~~~~Gk~Pa~a~p~l~GItKAsL~t~SFlSAASFQeTT 1513 (1552) T TIGR02386 1434 DKHIEVIVRQMLRKVRITDSGDSDLLPGELIDKHEFNEENKKLLAQGKKPASARPVLLGITKASLNTESFLSAASFQETT 1513 (1552) T ss_pred CEEEEEEEEECCCEEEEEECCCCCCCCCCEECHHHHHHHHHHHHHHCCCCCEEEEEEEEEEECCCCCCCHHHHHHHHHHH T ss_conf 71899973010506589836787563674210455688999999827998058788740044125546123320032356 Q ss_pred HHHHHHHHCCCEECCCCCCEEEECCCCCCCCCCHHHHHH Q ss_conf 999997452855236653221550730565535466533 Q gi|254780142|r 1325 KVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAILHEK 1363 (1398) Q Consensus 1325 ~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG~f~~~~ 1363 (1398) +||||||+.|++|+|.|+|||||+|+|||||||+-.|+. T Consensus 1514 kVLTdAai~GK~D~L~GLKENVIiG~lIPAGTGl~~~~~ 1552 (1552) T TIGR02386 1514 KVLTDAAIKGKVDYLLGLKENVIIGNLIPAGTGLKKYKE 1552 (1552) T ss_pred HHHHHHHHCCCCCCCCCCCCEEEECCCCCCCCCCCCCCC T ss_conf 888888644871455466213884562477888754679 No 2 >PRK01497 DNA-directed RNA polymerase subunit beta'; Provisional Probab=100.00 E-value=0 Score=3310.94 Aligned_cols=1360 Identities=62% Similarity=0.995 Sum_probs=1310.8 Q ss_pred HHHCCCCCCCCEEEEEEECCCHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 75135678640536898458867885014489717554254568756887336213685667721566415634488356 Q gi|254780142|r 7 RFFNPWTDDRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRMKYKGIIC 86 (1398) Q Consensus 7 ~~~~~~~~~~~i~~i~f~l~spe~I~~~S~~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~Cg~~~~~~~~g~~C 86 (1398) .+|++...+++|++|||||||||+||+||+|||++||||||+|+|||+|||||+|||||++||||+|||||+++|+|.+| T Consensus 1 ~~~~~~~~~~~~~~i~~~l~spe~Ir~~S~gev~~peTiny~~~kPe~~GLf~~rifg~~~d~ec~cgkyk~~~~~g~~C 80 (1384) T PRK01497 1 NLFKQQTKTEEFDAIKIGLASPEKIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGVIC 80 (1384) T ss_pred CCCCCCCCCCCCCEEEEEECCHHHHHHHHCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCEEC T ss_conf 96567787676454999715889998752589777532137889988887236201486756605156412215598056 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCEEECHHHHHHHHHHHHHCCCHHHHHHHHHHCCEEEECCCCCCHHHHCCCCHHHH Q ss_conf 75788530477578767720027762201301225789999809996563013321112321788651043223699999 Q gi|254780142|r 87 EKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRDVERVLYFESYVVVDPGLSSLEKYQILTEEEY 166 (1398) Q Consensus 87 ~~Cg~~~~~~~~r~ghfGhIeLa~PV~Hi~f~k~~~~~i~~~l~~~~~~~~~v~y~~~~~~~~~~~~~~~~~~~~~~~~~ 166 (1398) ++||+|++.|+|||+||||||||.||+||||+|++||+|+.+|++++++|++|+||++|+++||+.+.+++++++++++| T Consensus 81 ~~Cgve~~~~~vrr~rmGHIeLa~Pv~Hi~f~k~~ps~i~~ll~~~~~~l~~v~y~~~~iv~~~~~~~~~~~~~l~~~~~ 160 (1384) T PRK01497 81 EKCGVEVTLSKVRRERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFESYVVIEPGMTPLEKGQLLTEEEY 160 (1384) T ss_pred CCCCCCCCCCCCCCCCCCCEEECCCCEEEEEECCCCHHHHHHHCCCHHHHHHEEEEEEEEEECCCCCCHHHCCCCCHHHH T ss_conf 88887302064023664752436871501441588309898728998885015532126874689885134034669999 Q ss_pred HHHHHHCCCCCEEECCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCC Q ss_conf 88676358555061155267788877267488999999873103220347886447788866663489851128630450 Q gi|254780142|r 167 VEAVSQFGQDQFIAMMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMIIRKLPV 246 (1398) Q Consensus 167 ~~~~~~~~~~~~~~~~g~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~Pewmil~~lpV 246 (1398) .+..++++ +.|.+.+|++|++++|.++|++.+...++.++....+.++++++++||+++++|+.+++|||||||||||| T Consensus 161 ~~~~~~~~-~~f~~~~g~eai~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rl~~~~~f~~~~~rPewmil~vlpV 239 (1384) T PRK01497 161 LDALEEYG-DEFTAKMGAEAIRELLKSIDLDAEAEELREELKETNSETKRKKLLKRLKLVEAFRESGNKPEWMILTVLPV 239 (1384) T ss_pred HHHHHHHC-CCCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCHHEEEECCCC T ss_conf 99998737-63413657899999987478899999999987643317789999999999998875499975134303576 Q ss_pred CCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHH Q ss_conf 76223513884697313100378999999986999999873983567776999999988887427767877247876506 Q gi|254780142|r 247 LPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHKRVVTGANRRPL 326 (1398) Q Consensus 247 ~P~~~RP~v~~~~g~~~~dDlt~~~~~Ii~~N~~Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~~~~~~~~~~rp~ 326 (1398) |||++||||+||||+|++|||||+|++||++|||||++++.|||++|++|+|+||||||+|||||+++|+|++++++||| T Consensus 240 ~Pp~vRP~v~l~gg~~a~~DL~~l~~~iI~~NnrLk~~~~~~aP~~Ii~ne~~~LQ~~V~tl~dN~~~g~~~~~~~~Rpl 319 (1384) T PRK01497 240 IPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLELKAPDIIVRNEKRMLQEAVDALFDNGRRGRAITGANKRPL 319 (1384) T ss_pred CCCCCCCCEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC T ss_conf 99888878796899605665358899999987999999876995899998999999999998606787877648899823 Q ss_pred HHHHHHHCCCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCEECHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEECC Q ss_conf 78998610237820003465100457740341255435462003489877612899999999879866630001001224 Q gi|254780142|r 327 KSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKE 406 (1398) Q Consensus 327 ks~~~rlkgK~GrfR~nl~GKRVdfs~RsVI~pdP~l~~~evgvP~~~A~~L~~P~~~~~L~~~g~~~~i~~~k~~i~~~ 406 (1398) |||+|||||||||||||||||||||||||||||||||++||||||+.||++||+||++++|+++|.+.+++.++++++++ T Consensus 320 KSls~rLKGKeGRfR~NLmGKRVDfSaRSVIspDPnL~i~EvGvP~~~A~eL~~Pf~i~~L~~~g~~~~ik~akk~ie~~ 399 (1384) T PRK01497 320 KSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIYRKLEERGLATTIKAAKKMVERE 399 (1384) T ss_pred CHHHHHHCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHCCHHHHHHHHHCCCCCCCCHHHHHHHHC T ss_conf 02898847767511355676620556764751799874554378789999847467799998738766654077887624 Q ss_pred CCCEEHHHHHHHCCCEEEECCCCCCEECCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHH Q ss_conf 88250132666569789975763101114012358994495479731225454678775456997468999999999987 Q gi|254780142|r 407 RPEVWDVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLM 486 (1398) Q Consensus 407 ~~~v~~v~rhl~~gd~Vl~NRqPsLHr~Simah~~~v~~~~t~rln~~vc~pyNADFDGDEMnlHvPqs~eAraEa~~Lm 486 (1398) .+.+|+|++|+++||+|||||||||||||||||+|||+|||||||||+||+||||||||||||+|||||+||||||++|| T Consensus 400 ~~~v~dile~vi~gd~VLfNRQPTLHrmSimah~~~v~~gkT~Rln~~vc~pYNADFDGDEMNlHvPQS~eAraEa~~Lm 479 (1384) T PRK01497 400 EPEVWDILEEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAFNADFDGDQMAVHVPLSLEAQLEARALM 479 (1384) T ss_pred CCHHHHHHHHHHCCCEEEECCCCCCCCCCCCEEEEEECCCCEEEECCCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHH T ss_conf 86688999877438867882787513010250557872796687261138873688787227850679999999999987 Q ss_pred HHHHCCCCCCCCCCEEEEHHHHHHHHHHHHCCCCCCCCCCCEECCHHHHHHHHHCCCCCCCCEEEEEECCCCCCCC---- Q ss_conf 6750542378878204402589999998733678874468141799999999988898678523652046456676---- Q gi|254780142|r 487 LSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENKIVTLHSKIRGRYKSVDKDGN---- 562 (1398) Q Consensus 487 ~~~~niisP~~g~Pi~~~~QD~i~G~y~lT~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~a~i~~~~~~~~~~~~---- 562 (1398) ++++||+||++|+|++|++||+|+|+||||..+.+.+++++.|.+..+++.+|+.+.+.+|+++++++++...+.. T Consensus 480 ~v~~nilsP~~G~Piig~~QD~l~G~y~lT~~~~~~~~e~~~f~~~~e~~~~~~~~~~~l~~~i~~~~~~~~~~~~~~~~ 559 (1384) T PRK01497 480 MSTNNILSPANGEPIIVPSQDVVLGLYYLTRERVNAKGEGMVFADVEEVERAYNNGVVELHAKIKVRITEYDKDGDGEFV 559 (1384) T ss_pred HHHCCCCCCCCCCCEEECCHHHHHHHHHHHCCCCCCCCCCEEECCHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCCCCC T ss_conf 43346713789995675008999889998446556667662978999999998669876562489877756666665456 Q ss_pred CCCEEECCCCCCCCCCEEEECCCCCEEEEECCHHCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCC Q ss_conf 14245217977511220554587510177511002013666999999980817899987558899999998539861321 Q gi|254780142|r 563 SISKIYDTTPGRMIIGEILPRHHEISFDICNQEMIKKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKD 642 (1398) Q Consensus 563 ~~~~~~~tt~Gr~~~~~ilp~~~~~~~~~~~~~~~k~~~~~li~~i~~~~G~~~~~~~l~~~~~l~~~~l~~~GfSigi~ 642 (1398) ...+...||+||++||.++|++. .++++++.++|+++++|||.+|++||++.|+.|||.+|+++|+|++++|||||++ T Consensus 560 ~~~~~~~tt~Gr~if~~ilP~~~--~~~~in~~l~Kk~~g~lI~~i~~~~G~~~~~~fld~l~~l~~~~l~~~GfSigi~ 637 (1384) T PRK01497 560 PVTKIVDTTVGRAILNEILPKGL--PFSLVNKPLTKKEISKLINTVYRKCGLKETVIFADQIMYLGFRYATRAGISIGID 637 (1384) T ss_pred CCCEEEECCCHHHHHHHHCCCCC--CCEEEECCCCCCCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCCCCCCHH T ss_conf 66337863731888876568999--7146616435531789999999997979999999999999999985077657704 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEE Q ss_conf 23268369999999997899999988648976678887886423465899999999998761156543222246883764 Q gi|254780142|r 643 DIIVPESKEKIIAEADKMVKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIFMM 722 (1398) Q Consensus 643 D~~~~~~k~~~i~~a~~~~~~~~~~~~~G~~t~~e~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~N~~~~M 722 (1398) |+++|++|.++|+++++++++++++|++|++|++|+|++++++|+++++++.+++++.+.+..... .....++|++++| T Consensus 638 D~~i~~~k~~ii~~a~~~v~~i~~~y~~G~it~~er~~kvi~~~~~~~~~v~~~~~~~l~~~~~~~-~~~~~~~N~~~~M 716 (1384) T PRK01497 638 DMVIPEEKAEIIEEAEAEVKEIEQQYQSGLITAGERYNKVVDIWSKANDRVAKAMMKNLSKETVIN-EEKQESFNSIYMM 716 (1384) T ss_pred HHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC-CCCCCCCCCHHHH T ss_conf 514778999999999999999999997388863788999999999989999999999864311433-2124788767541 Q ss_pred ECCCCCCCHHHEEEEEEECCCCCCCCCCCCCCCCCCHHHCCCCHHHHHHCCCCCCHHHHCCCCCCCCCCEEEEHHHHHHC Q ss_conf 22555578424112001000024644344456663011108889897640576103221012101567401101542301 Q gi|254780142|r 723 SHSGARGSIHQMRQLGGMRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQ 802 (1398) Q Consensus 723 ~~SGAKGS~~qi~ql~Gqq~l~gkp~G~~~~~PV~~sF~~GL~p~EfFfhamgGReGLiDTAvKTA~SGYlqRrLvk~~e 802 (1398) +.||||||..||+||+||||||++|+|+++++||.+||++||+|+|||||||||||||||||||||+|||||||||||+| T Consensus 717 ~~SGAKGS~~nI~Qm~G~rGlmakp~G~~ie~Pi~s~F~eGL~p~EfFfHamgGREGLiDTAvKTA~SGYLqRRLVkv~e 796 (1384) T PRK01497 717 ADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITSNFREGLNVLEYFISTHGARKGLADTALKTANSGYLTRRLVDVAQ 796 (1384) T ss_pred HHCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHCCCCCHHHHHHCCCCCCCCCHHCCCCCCCCHHHHHHHHHHHC T ss_conf 11257889999998854567652799875567410222059999999870603133102212001000167899998742 Q ss_pred CCEEEEECCCCCCCCEEEEEEECCEEEEEECCCCCCCCCHHHCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEECCCC Q ss_conf 43277513887666512111008848865000101221144201778971885178657899999999759840202331 Q gi|254780142|r 803 NCVVNQVDCNTKKGLTITHIVDSGQVVYSLGSRVLGRTALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSA 882 (1398) Q Consensus 803 Dl~V~~~D~~t~~g~~~~~~~~~~~~~~~l~~~~~~r~~~~di~~~~~~~~i~~~~~~i~~~~~~~i~~~~i~~v~irs~ 882 (1398) |++|+++||||.+|+++..+.++++.+.+|.++++||+.++|+++|.+++.+++++++++++.++.+.+++++++++||+ T Consensus 797 Dv~V~~dDCGT~~g~~i~~~~~g~d~i~~l~eri~gR~~~~dv~~p~~~~~i~~~~~~i~e~~~~~i~~~~i~~v~iRS~ 876 (1384) T PRK01497 797 DLVVTEDDCGTLNGITMTALIEGGEVVEPLRERILGRVAAEDVVDPGTGEVLVPAGTLIDEAWADLIEEAGVDEVKVRSV 876 (1384) T ss_pred CEEEEEECCCCCCCCEEEEEEECCEEEEEHHHHHHCCEEHHHCCCCCCCCEEECCCCCCCHHHHHHHHHCCCCEEEEECC T ss_conf 75999854897577213558738855654034563520174410578875341467614999999999749973774045 Q ss_pred CCHHHHHCCCHHHHHHHCCCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCC-CEEEECCCCEEEEEEEEE Q ss_conf 0003551865788754201785200010146021111007889877642024543222112-202401487689721134 Q gi|254780142|r 883 LTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDR-SFIESPCDGIVKIKNRNV 961 (1398) Q Consensus 883 lt~~~~~~v~~~cy~~~l~~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~-~~iknvTlGVPRlkEi~~ 961 (1398) |||++++|+|.+|||++|+++++|+||||||+|||||||||||||||||||||||||+..+ +.++....|++++.+++. T Consensus 877 Ltces~~gvc~kcYgrdLa~~~lV~pGEaVGiIAAQSIGEPgTQMTLnTFH~AGVASknvt~~~i~~~~~G~~~v~~lk~ 956 (1384) T PRK01497 877 LTCETRFGVCAKCYGRDLARGHLVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIEAKNDGTVKLENLKT 956 (1384) T ss_pred CCHHHHHHHHHHHHCCCHHHCCCCCCCCCCCHHHHHCCCCCCHHHHHHHHHHCCCCCCCCCCCEEEECCCCEEEEEEEEE T ss_conf 21230452889874821452781676643004554015885312506665322312333210104623588378501258 Q ss_pred EECCCCCEEEEECCCCEEEEECCCCEEEEEECCCHHCCCCCCCCEEECCEEEEECCCCCCEEEECCCCEEEEEEECCCCE Q ss_conf 65178877897427604664067760000001100001356785532250786213543113202463689753127832 Q gi|254780142|r 962 CRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHTFPIITEVSGTVGFEDLVDGIS 1041 (1398) Q Consensus 962 ~~n~~~~~i~vs~~~~~~i~d~~~~~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp~~~~i~~e~~~~v~~~~~~~~~~ 1041 (1398) +.|..++.++++++.++.+.+....+.++++++|++++++++++.|++++++++|||++.+|+++..+.+.|.++.++.+ T Consensus 957 v~n~~~~~i~~~~~~~i~i~d~~~~~~~~~~i~~ga~l~v~~~~~v~~~~vi~~~Dp~~~~Ii~e~~g~v~~~d~~~~~t 1036 (1384) T PRK01497 957 VTNSEGKLVVISRNGELAIIDEFGRERERYKVPYGAVLLVKDGDAVKAGQVLAEWDPHTRPIITEVAGTVKFEDLIEGVT 1036 (1384) T ss_pred EECCCCCEEEECCCEEEEEECCCCHHHHHHCCCCCEEEEECCCCEEECCEEEEECCCCCCEEEEECCCEEEEEECCCCCE T ss_conf 86588977886155059952642035665114444189963786774241898505877506870256388864235744 Q ss_pred EHHHHHCCCCCEEEEEEEHHHCCCCCCCCCCEEEECCCCCEEECCCCCCCEEECCCCCEEEECCCCCCCCCCEEEECHHH Q ss_conf 00123023686026775101101221238534774277825322478842021377844541367613548422210132 Q gi|254780142|r 1042 VIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENGVVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPIS 1121 (1398) Q Consensus 1042 ~~~~~~~~t~~~~~~~i~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~v~~~d~l~~~~~~ 1121 (1398) ..++.|+.+++....+++... .....+.|++.+.++++............|+++.++..++.+++++..|+.++++|.. T Consensus 1037 ~~~~~D~~tg~~~~~i~d~~~-~~~~~l~p~i~i~d~~~~~~~~~~~~~~~y~lp~~a~~~v~d~~~v~~gd~l~rip~~ 1115 (1384) T PRK01497 1037 VKEQTDELTGLSSLVVIDRKE-RGGKDLRPAIKIVDANGEDVKIGTDVPAQYFLPVGAILSVEDGQQVKAGDVLARIPQE 1115 (1384) T ss_pred EEEEECCCCCCEEEEEEECCC-CCCCCCCCEEEEECCCCCEEEECCCCCCEEECCCCCEEEECCCCCCCCCCEEEECCHH T ss_conf 677422555624699973323-4556677318998478857750367651363588857872376731368457752413 Q ss_pred HCCCCCCCCCCCHHHHHHHHHCCCCCCEECCCCCEEEEEEECCCCEEEEEEECCCCCCEEEEEECCCCEEEEECCCEEEC Q ss_conf 02455433677328898875251111011134786786331279449999836898402689813896589841987740 Q gi|254780142|r 1122 SAKTKDITSGLPRVAELFEARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEK 1201 (1398) Q Consensus 1122 ~~k~~DIt~GLPrV~eLFEar~pk~~aiisei~Giv~i~~~~~~k~~~vi~~~~~g~~~~e~~ip~~~~l~v~dgd~V~~ 1201 (1398) ..+++|||+|||||+||||||+||++|++++++|++++++..+++.++++.. ++|.+..+|++|.+++++|.+||.|.+ T Consensus 1116 ~~kt~DItgGLPrV~eLFEar~pk~~aii~ei~G~v~~~~~~k~k~~i~i~~-~~g~~~~~~lv~~~~~l~v~~gd~V~~ 1194 (1384) T PRK01497 1116 SSKTRDITGGLPRVAELFEARRPKDPAILAEIDGTVSFGKETKGKRRLVITP-DDGSEEYEYLIPKGKHLLVFEGDVVEK 1194 (1384) T ss_pred HCCCCCCCCCCCHHHHHHHHHCCCCCCEEEEECCEEEECCCCCCCEEEEEEC-CCCCCEEEEECCCCCEEEEECCCEEEC T ss_conf 2355434478703899887405554103553044687324346743899984-899704899714784689834977732 Q ss_pred CCEEECCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHH Q ss_conf 86464389999999875279999999999999999980970061256012476286148941886454566410699999 Q gi|254780142|r 1202 GDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVE 1281 (1398) Q Consensus 1202 gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~ 1281 (1398) |+.+++|+++||||++|+||||||+||++|||.||++||+|||||||||||||||+|++|+++|||.|++|+.|+|.++. T Consensus 1195 g~~lt~g~~~~~eIl~vlGiEA~r~~lv~EIq~Vy~~qGv~In~KHieiivrqMl~Kv~I~~~GDt~~l~Ge~v~~~~~~ 1274 (1384) T PRK01497 1195 GDVISDGPPDPHDILRLLGVEALAEYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKVEITDPGDTTFLEGEQVDRSEFL 1274 (1384) T ss_pred CCEECCCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHCCCEECHHHHHHHHHHHHCCEEEEECCCCCCCCCCEEEHHHHH T ss_conf 86604799998999997699999999999999999976964306679999998850637853587655676253398999 Q ss_pred HHHHHHHHCCCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCCCCCCCCCHHHH Q ss_conf 99999997289875201210000145302310776504025899999974528552366532215507305655354665 Q gi|254780142|r 1282 ELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAILH 1361 (1398) Q Consensus 1282 ~~Nr~~~~~g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG~f~~ 1361 (1398) .+||.+..+|+.||+++|+|||||||||+|+||||+|||||||+||+|||++|++|+|+||||||||||+||+|||+..| T Consensus 1275 ~~n~~~~~~g~~pa~~~~~LlGITrasl~t~S~lsaASFeETt~vL~dAAi~gk~D~L~GvkENIIlGqliPaGTG~~~~ 1354 (1384) T PRK01497 1275 EENRRLEAEGKKPATAEPVLLGITKASLQTESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGLAYH 1354 (1384) T ss_pred HHHHHHHHCCCCCCCCCCHHCEEEHHHCCCCCHHHHCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHCCCCCCCCCCHHHH T ss_conf 99999996688775233210112010013431877601363899999999727987677702263157845677594676 Q ss_pred HHHHHHCCCHH Q ss_conf 33121025102 Q gi|254780142|r 1362 EKRRVAMNRDQ 1372 (1398) Q Consensus 1362 ~~~~~~~~~~~ 1372 (1398) +++++...++. T Consensus 1355 ~~~~~~~~~~~ 1365 (1384) T PRK01497 1355 KDRKVARARAA 1365 (1384) T ss_pred HCCCCCCCCCH T ss_conf 04224567443 No 3 >PRK09603 DNA-directed RNA polymerase subunit beta/beta'; Reviewed Probab=100.00 E-value=0 Score=3198.86 Aligned_cols=1331 Identities=50% Similarity=0.838 Sum_probs=1254.6 Q ss_pred CCCCCCCCEEEEEEECCCHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCC Q ss_conf 356786405368984588678850144897175542545687568873362136856677215664156344883-5675 Q gi|254780142|r 10 NPWTDDRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRMKYKGI-ICEK 88 (1398) Q Consensus 10 ~~~~~~~~i~~i~f~l~spe~I~~~S~~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~Cg~~~~~~~~g~-~C~~ 88 (1398) .....|+.|++|+++|||||+||+||+|||++||||||||+|||++||||+|||||+|||||+|||||+++|+|. +|++ T Consensus 1388 ~~~~~~~~f~~~~i~laspe~i~~ws~gev~kpetinyrt~kpe~dglfc~~ifgp~kd~ec~cgkyk~~~~~g~~vc~~ 1467 (2890) T PRK09603 1388 KEDDRPKDFSSFQLTLASPEKIHSWSYGEVKKPETINYRTLKPERDGLFCMKIFGPTKDYECLCGKYKKPRFKDIGTCEK 1467 (2890) T ss_pred CCCCCCCCCCCEEEEECCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEHHHCCCCCCEEECCCCCCCCCCCCCEECCC T ss_conf 56678788462589505879987503677489875035667887777523154088866355378754302589757587 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCEEECHHHHHHHHHHHHHCCCHHHHHHHHHHCCEEEECCCCC--------CHHHHCC Q ss_conf 78853047757876772002776220130122578999980999656301332111232178865--------1043223 Q gi|254780142|r 89 CGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRDVERVLYFESYVVVDPGLS--------SLEKYQI 160 (1398) Q Consensus 89 Cg~~~~~~~~r~ghfGhIeLa~PV~Hi~f~k~~~~~i~~~l~~~~~~~~~v~y~~~~~~~~~~~~--------~~~~~~~ 160 (1398) ||+|+|.+.|||.||||||||.||.||||+|++||+|+.+|+++.+++|+|+||++|++++|+.. ++.+.++ T Consensus 1468 cgvevt~~~vrr~rmghi~la~pv~hiw~~k~~ps~i~~ll~~~~~~le~v~y~~~~iv~~~~~~~~~~~~~~~~~~~~~ 1547 (2890) T PRK09603 1468 CGVAITHSKVRRFRMGHIELATPVAHIWYVNSLPSRIGTLLGVKMKDLERVLYYEAYIVKEPGEAAYDNEGTKLVMKYDI 1547 (2890) T ss_pred CCCEECCCEEEHHCCCCHHHCCCCEEEEECCCCCHHHHHHHCCCHHHHHHHHCEEEEEEECCCCCCCCCCCCCCHHHHCC T ss_conf 87286533001203576211386157767178714888884899899776240024899468843233335672065312 Q ss_pred CCHHHHHHHHHHCCCCCEEECCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEE Q ss_conf 69999988676358555061155267788877267488999999873103220347886447788866663489851128 Q gi|254780142|r 161 LTEEEYVEAVSQFGQDQFIAMMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMI 240 (1398) Q Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~g~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~Pewmi 240 (1398) +++++|.+...+++...|.+.||++|++++|.++|++.+...++.++....+.+++++++|||+++++|..+++|||||| T Consensus 1548 ~~~~~~~~~~~~~~~~~f~~~~gaeai~~ll~~~dl~~~~~~l~~~~~~~~s~~~~~~~~krl~~v~~f~~s~nrPewMi 1627 (2890) T PRK09603 1548 LNEEQYQNISRRYEDRGFVAQMGGEAIKDLLEEIDLITLLQSLKEEVKDTNSDAKKKKLIKRLKVVESFLNSGNRPEWMM 1627 (2890) T ss_pred CCHHHHHHHHHHHCCCCEEECCCHHHHHHHHHHCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCHHEE T ss_conf 68999999998717776697567999999998679899999999999865568889999999999999986699975158 Q ss_pred EEECCCCCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC Q ss_conf 63045076223513884697313100378999999986999999873983567776999999988887427767877247 Q gi|254780142|r 241 IRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHKRVVTG 320 (1398) Q Consensus 241 l~~lpV~P~~~RP~v~~~~g~~~~dDlt~~~~~Ii~~N~~Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~~~~~~~ 320 (1398) |+|||||||++||+|+||||+|++||||++|++||++|||||++++.|||++|++||++|||+|||+||||+++++|+++ T Consensus 1628 l~vlPV~Pp~lRP~v~ldggrfatsDlndlyrrvI~rNnrLkrl~~~~aP~~Ii~nekrmLQeaVdal~DN~r~~~~v~~ 1707 (2890) T PRK09603 1628 LTVLPVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRLMELGAPEIIVRNEKRMLQEAVDVLFDNGRSTNAVKG 1707 (2890) T ss_pred EEEECCCCCCCCCCEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC T ss_conf 75432489988754587897532225288899999863999999876996799988899999998897607888878869 Q ss_pred CCCCHHHHHHHHHCCCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCEECHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC Q ss_conf 87650678998610237820003465100457740341255435462003489877612899999999879866630001 Q gi|254780142|r 321 ANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAK 400 (1398) Q Consensus 321 ~~~rp~ks~~~rlkgK~GrfR~nl~GKRVdfs~RsVI~pdP~l~~~evgvP~~~A~~L~~P~~~~~L~~~g~~~~i~~~k 400 (1398) .++||||||++||||||||||||||||||||||||||||||||++||||||+.||++||+||++++|++.|.+.++|+|| T Consensus 1708 ~~~RplKSlsd~LKGKqGRFRqNLlGKRVDySgRSVIvvgP~Lkl~QcGlPk~mAleLfkPfi~~~L~~~g~~~~ik~ak 1787 (2890) T PRK09603 1708 ANKRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHLLSKLEERGYATTLKQAK 1787 (2890) T ss_pred CCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHCCCCCCHHHHH T ss_conf 99881215678647876644566676341538976365798960110578799999866554168887668714477889 Q ss_pred CEEECCCCCEEHHHHHHHCCCEEEECCCCCCEECCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCEEEEECCCCHHHHH Q ss_conf 00122488250132666569789975763101114012358994495479731225454678775456997468999999 Q gi|254780142|r 401 KFVEKERPEVWDVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQL 480 (1398) Q Consensus 401 ~~i~~~~~~v~~v~rhl~~gd~Vl~NRqPsLHr~Simah~~~v~~~~t~rln~~vc~pyNADFDGDEMnlHvPqs~eAra 480 (1398) +++++..+++|+|+||+++||||||||||||||||||||+|+|+||+|||||||||+||||||||||||||||||+|||| T Consensus 1788 ~~ve~~~~~vw~vl~~vi~~~pVLlNRaPTLHRlsIqaf~p~l~egkairLhplVC~~yNADFDGDqMavHvPlS~EAqa 1867 (2890) T PRK09603 1788 RMIEQKSNEVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIA 1867 (2890) T ss_pred HHHHHCCCCEEEEEHHHHCCCEEEECCCCCHHHCCCCEEEEEEECCCCEECCCCCCCCCCCCCCCHHHHHCCCCCHHHHH T ss_conf 99985288254311204359916887773422340020466896786602171119842558665432103779999999 Q ss_pred HHHHHHHHHHCCCCCCCCCCEEEEHHHHHHHHHHHHCCCCCCCCCCCEECCHHHHHHHHHCCCCCCCCEEEEEECCCCCC Q ss_conf 99998767505423788782044025899999987336788744681417999999999888986785236520464566 Q gi|254780142|r 481 EARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENKIVTLHSKIRGRYKSVDKD 560 (1398) Q Consensus 481 Ea~~Lm~~~~niisP~~g~Pi~~~~QD~i~G~y~lT~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~a~i~~~~~~~~~~ 560 (1398) ||+.||++++||+||++|+|+++|+||+|+|+||||..+.+..++++.|.+.++++.+|+.+.+.+|++++.... T Consensus 1868 Ea~~LMls~~NIlsP~~GkPii~p~QD~vlG~yylT~~~~~~~~e~~~f~~~~e~~~a~~~~~v~l~~~i~~~~~----- 1942 (2890) T PRK09603 1868 ECKVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKSGVKGEHKLFSSVNEIITAIDTKELDIHAKIRVLDQ----- 1942 (2890) T ss_pred HHHHHHCCCCCCCCCCCCCCEEEECHHHHHHHHHCCCCCCCCCCCCCEECCHHHHHHHHHCCCCEEECEEEEECC----- T ss_conf 999985121381258999824883118877676610467898776644289999999976799643121688659----- Q ss_pred CCCCCEEECCCCCCCCCCEEEECCCCCEEEEECCHHCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCC Q ss_conf 76142452179775112205545875101775110020136669999999808178999875588999999985398613 Q gi|254780142|r 561 GNSISKIYDTTPGRMIIGEILPRHHEISFDICNQEMIKKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFG 640 (1398) Q Consensus 561 ~~~~~~~~~tt~Gr~~~~~ilp~~~~~~~~~~~~~~~k~~~~~li~~i~~~~G~~~~~~~l~~~~~l~~~~l~~~GfSig 640 (1398) .+++.||+||++||.++|+. +.++++|+.+.|+.+++|||.+|+.||+..|+.|||.+++++|+|++++||||| T Consensus 1943 ----~~~~~Tt~Gr~i~~~ilP~~--~~~~~~n~~~~Kk~l~~lI~~~~~~~G~~~t~~~lD~lk~lgf~~at~~G~Sig 2016 (2890) T PRK09603 1943 ----GNIIATSAGRMIIKSILPDF--IPTDLWNRPMKKKDIGVLVDYVHKVGGIGITATFLDNLKTLGFRYATKAGISIS 2016 (2890) T ss_pred ----CCEEEECHHHHHHHHHCCCC--CCCCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCCEEEE T ss_conf ----93797070488999878476--874210056673149999999999729899999999999999999975767875 Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEE Q ss_conf 21232683699999999978999999886489766788878864234658999999999987611565432222468837 Q gi|254780142|r 641 KDDIIVPESKEKIIAEADKMVKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIF 720 (1398) Q Consensus 641 i~D~~~~~~k~~~i~~a~~~~~~~~~~~~~G~~t~~e~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~N~~~ 720 (1398) ++|+.+|++|.++|++|++++++++.+|++|++|++|||++++++|+++++.+.+++++.+.+. ..++|+++ T Consensus 2017 i~D~~ip~~K~~ii~~a~~~v~~i~~~y~~G~it~~Er~~kvi~~w~~~~d~v~~~~~~~~~~~--------~~~~N~v~ 2088 (2890) T PRK09603 2017 MEDIITPKDKQKMVEKAKVEVKKIQQQYDQGLLTDQERYNKIIDTWTEVNDKMSKEMMSAIAKD--------KEGFNSIY 2088 (2890) T ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--------CCCCCCHH T ss_conf 6454567589999999999999999997659872068999999999999999999999976643--------55678576 Q ss_pred EEECCCCCCCHHHEEEEEEECCCCCCCCCCCCCCCCCCHHHCCCCHHHHHHCCCCCCHHHHCCCCCCCCCCEEEEHHHHH Q ss_conf 64225555784241120010000246443444566630111088898976405761032210121015674011015423 Q gi|254780142|r 721 MMSHSGARGSIHQMRQLGGMRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDV 800 (1398) Q Consensus 721 ~M~~SGAKGS~~qi~ql~Gqq~l~gkp~G~~~~~PV~~sF~~GL~p~EfFfhamgGReGLiDTAvKTA~SGYlqRrLvk~ 800 (1398) ||+.||||||.+||+||+||||+|++|+|+++++||.+||++||+|+|||||||||||||+|||||||+||||||||||| T Consensus 2089 mMa~SGARGs~~qirQL~gmrGlmakp~G~iie~PI~sNFreGLtv~EyFist~GaRKGL~DTAlKTAdSGYLTRRLVdv 2168 (2890) T PRK09603 2089 MMADSGARGSAAQIRQLSAMRGLMTKPDGSIIETPIISNFKEGLNVLEYFNSTHGARKGLADTALKTANAGYLTRKLIDV 2168 (2890) T ss_pred HHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHCCCCHHHHHHHHCCCCCCHHHHHEECCCCCEEEHHHHHH T ss_conf 53113466679998777644374057999803542123431678899998874154213566401135566031367787 Q ss_pred HCCCEEEEECCCCCCCCEEEEEEECCEEEEEECCCCCCCCCHHHCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEECC Q ss_conf 01432775138876665121110088488650001012211442017789718851786578999999997598402023 Q gi|254780142|r 801 AQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLGSRVLGRTALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIR 880 (1398) Q Consensus 801 ~eDl~V~~~D~~t~~g~~~~~~~~~~~~~~~l~~~~~~r~~~~di~~~~~~~~i~~~~~~i~~~~~~~i~~~~i~~v~ir 880 (1398) +||++|+++||+|.+|+.+..+.++++.+++|.+|++||++++|+++|.+++.++.++++|+++.++++.+++++++.+| T Consensus 2169 aQDviV~~ddcgt~~gi~i~~~~~g~d~i~~l~eri~gR~~~~dv~~p~~~~~i~~~~~~i~~~~a~~i~~~gi~~v~iR 2248 (2890) T PRK09603 2169 SQNVKVVSDDCGTHEGIEITDIAVGSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITIR 2248 (2890) T ss_pred HCCEEEEECCCCCCCCEEEEEEEECCCCEEEHHHHHHCCHHHHHHCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEC T ss_conf 52708995267776780588775488207685564641120664127778978971885348999999997799779966 Q ss_pred CCCCHHHHHCCCHHHHHHHCCCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCC-CCEEEECCCCEEEEEEE Q ss_conf 31000355186578875420178520001014602111100788987764202454322211-22024014876897211 Q gi|254780142|r 881 SALTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMD-RSFIESPCDGIVKIKNR 959 (1398) Q Consensus 881 s~lt~~~~~~v~~~cy~~~l~~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~-~~~iknvTlGVPRlkEi 959 (1398) |||||++.+|+|++||||+|+++++|+||||||+|||||||||||||||||||+|||||... ...+.....|.+++.++ T Consensus 2249 s~ltc~~~~gvc~~cYG~~La~~~~V~~GEAVGiIAAQSIGEPGTQLTmRTFH~gGvas~~~~~~~i~a~~~G~i~f~~~ 2328 (2890) T PRK09603 2249 TPVTCKAPKGVCAKCYGLNLGEGKMSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTASRSQDEREIVASKEGFVRFYNL 2328 (2890) T ss_pred CCEEEECCCCCCHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCCEEEECCCCEEEEEEE T ss_conf 85367666773778839110168887677566654566368751103243000133236642223268356867998533 Q ss_pred EEEECCCCCEEEEECCCC-EE----------------------------------------------------------- Q ss_conf 346517887789742760-46----------------------------------------------------------- Q gi|254780142|r 960 NVCRNSTNDLISMGRNTT-LQ----------------------------------------------------------- 979 (1398) Q Consensus 960 ~~~~n~~~~~i~vs~~~~-~~----------------------------------------------------------- 979 (1398) ....+..+..+..++... +. T Consensus 2329 ~~~~~~~G~~vv~~~~~~~il~~e~~~~~~~~g~~~~e~~~~ev~~~v~~~~~~~~~~~~~~d~~~~~~l~~~~g~i~g~ 2408 (2890) T PRK09603 2329 RTYTNKEGKNIIANRRNASILVVEPKIKAPFDGELRIETVYEEVVVSVKNGEQEAKFVLRRSDIVKPSELAGVGGKIEGK 2408 (2890) T ss_pred EEEECCCCCEEEEECCCCEEEEECCCCCCCCCCCEEEECCCCCEEEEECCCCCCCEEEECCCCCCCCCHHCCCCCCCCCC T ss_conf 58875889689984145404641353112446612220134303675205643101210245432321001333410130 Q ss_pred -------------------------------------------------------------------------------- Q ss_conf -------------------------------------------------------------------------------- Q gi|254780142|r 980 -------------------------------------------------------------------------------- 979 (1398) Q Consensus 980 -------------------------------------------------------------------------------- 979 (1398) T Consensus 2409 ~~lp~~~g~~v~~g~~i~~~i~~~~~i~~~i~y~~~l~v~~n~~i~~~i~~~~~giv~~~~l~~~~i~~~~~i~~g~~v~ 2488 (2890) T PRK09603 2409 VYLPYASGHKVHKGGSIADIIQEGWNVPNRIPYASELLVKDNDPIAQDVYAKEKGIIKYYVLEANHLERTHGIKKGDMVS 2488 (2890) T ss_pred EEECCCCCCEECCCCCEEEECCCCCCCCCCCCCCCEEEECCCCHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCCCEEC T ss_conf 22024665211257601210123322356555542577506860332222113562035431144200012235564001 Q ss_pred -------EEECCCCEEEEEECCCHHCCCCCCCCEEECCE-----------EEEECCCCCCEEEECCCCEEEEEEECCCCE Q ss_conf -------64067760000001100001356785532250-----------786213543113202463689753127832 Q gi|254780142|r 980 -------ILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQ-----------RISEWDPHTFPIITEVSGTVGFEDLVDGIS 1041 (1398) Q Consensus 980 -------i~d~~~~~~~~~ki~~~~~~~v~~~~~v~~~~-----------ii~~~Dp~~~~i~~e~~~~v~~~~~~~~~~ 1041 (1398) +.+.+..+..++.+++++..++.+++.++..+ .+.+|||++.+++.+..+.+.|.++.++.+ T Consensus 2489 ~~~~~~~i~~~~gre~~r~~i~~g~~i~v~d~~~v~~~~~i~~~~~~~~~~i~~~dp~~~pIi~e~~g~v~f~dii~gvt 2568 (2890) T PRK09603 2489 EKGLFAVIADDNGREAARHYIARGSEILIDDNSEVSANSVISKPTTNTFKTIATWDPYNTPIIADFKGKVSFVDIIAGVT 2568 (2890) T ss_pred CCCCEEEEECCCCCHHHEEECCCCCEEEECCCCEEECCCEECCCCCCCCEEEECCCCCCCCEEEECCCEEEEEECCCCCE T ss_conf 35522565235663101132145736884478634126310245654411453027888725760354576343048724 Q ss_pred EHHHHHCCCCCEEEEEEEHHHCCCCCCCCCCEEEECCCCCEEECCCCCCCEEECCCCCEEEECCCCCCCCCCEEEECHHH Q ss_conf 00123023686026775101101221238534774277825322478842021377844541367613548422210132 Q gi|254780142|r 1042 VIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENGVVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPIS 1121 (1398) Q Consensus 1042 ~~~~~~~~t~~~~~~~i~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~v~~~d~l~~~~~~ 1121 (1398) ..+..++.++.....+.+. ......|.+.+.+.++... .|+++.++...+.+++.+..|+.+++++.+ T Consensus 2569 ~~e~~de~tg~~~~~i~~~----~~~~~~p~i~i~~~~g~~~--------~Y~l~~~a~l~V~dG~~V~~GdiLakl~~e 2636 (2890) T PRK09603 2569 VAEKEDENTGITSLVVNDY----IPSGYKPSLFLEGANGEEI--------RYFLEPKTSIAISDGSSVEQAEVLAKIPKA 2636 (2890) T ss_pred EEEECCCCCCCEEEEEECC----CCCCCCCEEEEECCCCCEE--------EEECCCCCEEEECCCCEECCCCEEEEECCC T ss_conf 6651146657157997314----5667784289986899788--------886599978996699996058768971022 Q ss_pred HCCCCCCCCCCCHHHHHHHHH--CCCCCCEECCCCCEEEEEEECCCCEEEEEEECCCCCCEEEEEECCCCEEEEECCCEE Q ss_conf 024554336773288988752--511110111347867863312794499998368984026898138965898419877 Q gi|254780142|r 1122 SAKTKDITSGLPRVAELFEAR--RPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHV 1199 (1398) Q Consensus 1122 ~~k~~DIt~GLPrV~eLFEar--~pk~~aiisei~Giv~i~~~~~~k~~~vi~~~~~g~~~~e~~ip~~~~l~v~dgd~V 1199 (1398) ..++.|||+|||||+|||||| +||++|++++++|++++++..+++.++++... +| ...+|++|.++++.|.+|+.| T Consensus 2637 ~~kt~DIt~GLPRV~ELfEAR~~KPK~~ailae~~G~V~~g~~~~~~~~iii~~~-dg-~~~ey~i~~g~~l~V~~Gd~V 2714 (2890) T PRK09603 2637 TVKSRDITGGLPRVSELFEARKPKPKDVAILSEVDGIVSFGKPIRNKEHIIVTSK-DG-RSMDYFVDKGKQILVHADEFV 2714 (2890) T ss_pred CCCCCCCCCCCCCHHHHHHHCCCCCCCCEEEECCCCEEEECCCCCCCEEEEEECC-CC-CEEEEECCCCCEEEECCCCEE T ss_conf 1567866488860598775134688874389536518995653478526999769-99-477775489987776799887 Q ss_pred ECCCEEECCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHH Q ss_conf 40864643899999998752799999999999999999809700612560124762861489418864545664106999 Q gi|254780142|r 1200 EKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIE 1279 (1398) Q Consensus 1200 ~~gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~ 1279 (1398) .+|+.+++|+++|||||+++|.+|++++|++|||+||++|||.||+||||+|++|||+|++|+++|||.|++|+.|++.. T Consensus 2715 ~~Ge~LtdG~inphdIL~i~g~~~lq~yLVnEVQ~VYrsQGV~InDKHIEVIVRQMtsKV~I~d~GDT~fLpGElV~~~~ 2794 (2890) T PRK09603 2715 HAGEAMTDGVVSSHDILRISGEKELYKYIVSEVQQVYRRQGVSIADKHIEIIVSQMLRQVRILDSGDSKFIEGDLVSKKL 2794 (2890) T ss_pred ECCCCCCCCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCEEEEECCCCCCCCCCCEEEHHH T ss_conf 06888237999989999840799999999999999999669855362789987513746999568888878856762999 Q ss_pred HHHHHHHHHHCCCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCCCCCCCCCHH Q ss_conf 99999999972898752012100001453023107765040258999999745285523665322155073056553546 Q gi|254780142|r 1280 VEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAI 1359 (1398) Q Consensus 1280 ~~~~Nr~~~~~g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG~f 1359 (1398) +...|+++...|+.||.|+|+|||||||||+|+||||||||||||+||++||+.|++|||+|+|||||+|+|||||||++ T Consensus 2795 ~e~~N~~~~~~g~~pA~~~PvLLGITKASL~TdSFISAASFQETTRVLTeAAI~GKvD~LrGLKENVIiGrLIPAGTGl~ 2874 (2890) T PRK09603 2795 FKEENARVIALKGEPAIAEPVLLGITRAAIGSDSIISAASFQETTKVLTEASIAMKKDFLEDLKENVVLGRMIPVGTGMY 2874 (2890) T ss_pred HHHHHHHHHHCCCCCCEEEEEHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHEEECCCEECCCCCC T ss_conf 99999999975999862666101151676624068888721308899999996689765788743312058450478837 Q ss_pred HHHHHHHHCCCHHH Q ss_conf 65331210251022 Q gi|254780142|r 1360 LHEKRRVAMNRDQM 1373 (1398) Q Consensus 1360 ~~~~~~~~~~~~~~ 1373 (1398) +|+++.+..+++.. T Consensus 2875 ~~~~~~~~~~~~~~ 2888 (2890) T PRK09603 2875 KNKKIVLRTLEDGP 2888 (2890) T ss_pred CCCEEEEEECCCCC T ss_conf 04535677446668 No 4 >PRK05258 DNA-directed RNA polymerase subunit beta'; Provisional Probab=100.00 E-value=0 Score=2985.87 Aligned_cols=1162 Identities=52% Similarity=0.872 Sum_probs=1103.3 Q ss_pred CCCCEEEEEEECCCHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 86405368984588678850144897175542545687568873362136856677215664156344883567578853 Q gi|254780142|r 14 DDRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRMKYKGIICEKCGVEV 93 (1398) Q Consensus 14 ~~~~i~~i~f~l~spe~I~~~S~~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~Cg~~~~~~~~g~~C~~Cg~~~ 93 (1398) +.++|++|||||||||+||+||+|||++||||||+|+|||+|||||||||||++||||+|||||+++|+|.+|++||+++ T Consensus 3 ~~~~f~~i~~~l~spe~Ir~~S~gev~~petiny~~~kPe~~GLf~~rifgp~~d~ec~cgkyk~~~~~g~~C~~Cgve~ 82 (1204) T PRK05258 3 DVNNFESMQIGLASPEKIRSWSYGEVKKPETINYRTLKPEKDGLFCERIFGPTKDWECHCGKYKRVRYKGIVCDRCGVEV 82 (1204) T ss_pred CCCCCCEEEEEECCHHHHHHHCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCCCCCC T ss_conf 66656649998148899986440897674442588998788982254025978675353776122035985769999864 Q ss_pred CCCCCCCCCCCCCCCCCCCEEECHHHHHHHHHHHHHCCCHHHHHHHHHHCCEEEECCCCCCHHHHCCCCHHHHHHHHHHC Q ss_conf 04775787677200277622013012257899998099965630133211123217886510432236999998867635 Q gi|254780142|r 94 TLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRDVERVLYFESYVVVDPGLSSLEKYQILTEEEYVEAVSQF 173 (1398) Q Consensus 94 ~~~~~r~ghfGhIeLa~PV~Hi~f~k~~~~~i~~~l~~~~~~~~~v~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 173 (1398) +.|+|||+||||||||.||+||||+|++||+|+.+|++++++|++|+||++|+++||+..++.+++++++.+|++..+++ T Consensus 83 ~~~~vrr~rmGHIeLa~Pv~Hiw~~k~~~s~i~~~l~~~~k~le~v~y~~~~~v~~~~~~~~~~~~~l~~~~~~~~~~~~ 162 (1204) T PRK05258 83 TRSKVRRERMGHIELAAPVSHIWYFKGIPSRMGLVLDMSPRALEEVIYFASYVVIDPGDTPLEKKQLLTEKEYREYLDKY 162 (1204) T ss_pred CCCCCCCCCCCCEEECCCEEEEEECCCCHHHHHHHHCCCHHHHHEEEEECCEEEECCCCCCCHHHHHCCHHHHHHHHHHH T ss_conf 51885588756600167726233206874689998677887750364102248766998741365445899999999984 Q ss_pred CCCCEEECCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCC Q ss_conf 85550611552677888772674889999998731032203478864477888666634898511286304507622351 Q gi|254780142|r 174 GQDQFIAMMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMIIRKLPVLPPDLRP 253 (1398) Q Consensus 174 ~~~~~~~~~g~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~Pewmil~~lpV~P~~~RP 253 (1398) + +.|.+.+|++|++++|.++|++.+..+++.++... +.+++.++++||+++++|..+++|||||||++||||||++|| T Consensus 163 ~-~~~~~~~g~e~i~~ll~~~dl~~~~~~~~~~~~~~-~~~~~~~~~~rl~~~~~f~~~~~rPewmil~vlpV~Pp~~RP 240 (1204) T PRK05258 163 G-NGFVAKMGAEAIKDLLEEIDLDKEVAELKEELKTA-TGQKRTRAIRRLEVVEAFRKSGNKPEWMILDVLPVIPPDLRP 240 (1204) T ss_pred C-CCCEECCCHHHHHHHHHHCCHHHHHHHHHHHHHHC-CHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHCCCCCCCCCCC T ss_conf 7-82033557899999998589899999999997522-358888888889999989865999663102127879998871 Q ss_pred EEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHH Q ss_conf 38846973131003789999999869999998739835677769999999888874277678772478765067899861 Q gi|254780142|r 254 LVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHKRVVTGANRRPLKSLSDML 333 (1398) Q Consensus 254 ~v~~~~g~~~~dDlt~~~~~Ii~~N~~Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~~~~~~~~~~rp~ks~~~rl 333 (1398) ||+||+|+|++|||||+|++||++|||||++++.|||++|++|+|+||||||+|||||+++|+|++++++||||||+||| T Consensus 241 ~V~ldgg~~~~~DLt~~~~~II~~N~rLk~~~~~gap~~ii~~~~~~LQ~~V~~l~dN~~~g~p~~~~~~RplKsl~~rL 320 (1204) T PRK05258 241 MVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPGIIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLKSLSHML 320 (1204) T ss_pred EEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHH T ss_conf 28968997457751789999999999999999869948889889999999999987178878876288998610399985 Q ss_pred CCCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCEECHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEECCCCCEEHH Q ss_conf 02378200034651004577403412554354620034898776128999999998798666300010012248825013 Q gi|254780142|r 334 KGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDV 413 (1398) Q Consensus 334 kgK~GrfR~nl~GKRVdfs~RsVI~pdP~l~~~evgvP~~~A~~L~~P~~~~~L~~~g~~~~i~~~k~~i~~~~~~v~~v 413 (1398) ||||||||||||||||||||||||||||||++||||||+.||++||+||++++|+.+|.+.+++.+++++++..+.+|++ T Consensus 321 KGKeGRfR~NLmGKRVDfSaRSVIspdP~L~i~EvGvP~~~A~~L~~P~~~~~Lv~~g~~~~ik~ak~~i~~~~~~v~~v 400 (1204) T PRK05258 321 KGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKEMALELFKPFVMKELVERGLAHNIKSAKRKVERVDPEVWDV 400 (1204) T ss_pred CCCCCEECCCCCCCCCCCCCCEEEECCCCCCCCEECCCHHHHHHHCCHHHHHHHHHCCCCCCCHHHHHHHHCCCCHHHHH T ss_conf 66664132456755205567536507998746700386899976278799999997587456278777776069436788 Q ss_pred HHHHHCCCEEEECCCCCCEECCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHCCC Q ss_conf 26665697899757631011140123589944954797312254546787754569974689999999999876750542 Q gi|254780142|r 414 LAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLL 493 (1398) Q Consensus 414 ~rhl~~gd~Vl~NRqPsLHr~Simah~~~v~~~~t~rln~~vc~pyNADFDGDEMnlHvPqs~eAraEa~~Lm~~~~nii 493 (1398) ++|++++|+|||||||||||||||||+|||+||||||||||||+||||||||||||||||||+||||||++||++++||+ T Consensus 401 le~vi~~~~VL~NRQPTLHr~SImah~~~v~~gkT~Rln~~vc~pYNADFDGDEMNlHvPQS~eArAEa~~LM~v~~nIl 480 (1204) T PRK05258 401 LEEVIKEHPVLLNRAPTLHRLGIQAFEPVLVEGRAIRLHPLVCTAYNADFDGDQMAVHVPLSAEAQAEARLLMLAAHNIL 480 (1204) T ss_pred HHHHHCCCCEEECCCCCCCCCCCCCCEEEEECCCEEEECCCCCCCCCCCCCCCEEEECCCCCHHHHHHHHHHHHCHHCCC T ss_conf 99874278246515863232434451268507835884510167666887762145447899999999999860340547 Q ss_pred CCCCCCCEEEEHHHHHHHHHHHHCCCCCCCCCCCEECCHHHHHHHHHCCCCCCCCEEEEEEC---CCCCCCCCCCEEECC Q ss_conf 37887820440258999999873367887446814179999999998889867852365204---645667614245217 Q gi|254780142|r 494 HPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENKIVTLHSKIRGRYK---SVDKDGNSISKIYDT 570 (1398) Q Consensus 494 sP~~g~Pi~~~~QD~i~G~y~lT~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~a~i~~~~~---~~~~~~~~~~~~~~t 570 (1398) ||++|+|++|++||+|+|+||||.++.+..++++.|.+.++++.+|..+.+.+|+.++.+.. ...|++....+.+.| T Consensus 481 sP~~G~PIig~iQD~ilG~y~LT~~d~~~~~eg~~F~~~~e~~~~~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~t 560 (1204) T PRK05258 481 NPKDGKPVVTPSQDMVLGNYYLTMEREGAEGEGMIFKDTDEALMAYQNGYVHLHTRIGVAASSMPNKPFTEEQRSKILVT 560 (1204) T ss_pred CCCCCCCEEEECHHHHHHHHHHHCCCCCCCCCCCEECCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEC T ss_conf 68899833650066765638750355455467738778999999997699656873564575678788886547615873 Q ss_pred CCCCCCCCEEEECCCCCE-----------------------------EEEECCHHCCHHHHHHHHHHHHHCCHHHHHHHH Q ss_conf 977511220554587510-----------------------------177511002013666999999980817899987 Q gi|254780142|r 571 TPGRMIIGEILPRHHEIS-----------------------------FDICNQEMIKKNISAMVDTIYRHCGQKSTVAFC 621 (1398) Q Consensus 571 t~Gr~~~~~ilp~~~~~~-----------------------------~~~~~~~~~k~~~~~li~~i~~~~G~~~~~~~l 621 (1398) |+||++||.++|++..+. ...+++.+.|+.+|+|+|.+|++||++.|+.|| T Consensus 561 t~Gk~ifs~ilP~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~g~~~K~~lg~li~~i~~~~G~~~a~~fl 640 (1204) T PRK05258 561 TVGKIIFNEIIPEDLPYINEPTNANLEEGTPDKYFLEPGQDIKEYIANLEINFPFKKKFLGNIIAEVFKRFGITETSEML 640 (1204) T ss_pred CHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCEEEEECCCEEEEEECHHHHHHHHHHHHHHHCHHHHHHHH T ss_conf 60688898876798875455564444456776400148871489864746630214357899999999997989999999 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 55889999999853986132123268369999999997899999988648976678887886423465899999999998 Q gi|254780142|r 622 DDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKMVKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARI 701 (1398) Q Consensus 622 ~~~~~l~~~~l~~~GfSigi~D~~~~~~k~~~i~~a~~~~~~~~~~~~~G~~t~~e~~~~i~~~~~~~~~~~~~~~~~~~ 701 (1398) |++++|+|+|++++|||||++|+.+|++|.++++++++++++++++|++|++|++|++++++++|+++++++++++++.+ T Consensus 641 d~l~~l~~~~l~~~GfSiGi~D~~~~~~k~eii~~a~~~v~~i~~~~~~G~~t~~e~~~~v~~~l~~~~d~v~~~~~~~l 720 (1204) T PRK05258 641 DRMKDLGYKYSTKAGITVGVADIVVLEEKQEILDEAHKKVEKITKQFRRGLITDEERYERVIEIWTDAKDKIQKKLMESL 720 (1204) T ss_pred HHHHHHHHHHHHHCCCEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 99999999999856964743104670789999999999999999999836674489999999999999999999998536 Q ss_pred HHHCCCCCCCCCCCCCCEEEEECCCCCCCHHHEEEEEEECCCCCCCCCCCCCCCCCCHHHCCCCHHHHHHCCCCCCHHHH Q ss_conf 76115654322224688376422555578424112001000024644344456663011108889897640576103221 Q gi|254780142|r 702 KRVEFDPETGRQKKMNSIFMMSHSGARGSIHQMRQLGGMRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQSCVGGRKGLL 781 (1398) Q Consensus 702 ~~~~~~~~~~~~~~~N~~~~M~~SGAKGS~~qi~ql~Gqq~l~gkp~G~~~~~PV~~sF~~GL~p~EfFfhamgGReGLi 781 (1398) +++|++++|+.||||||+.||+||+|++|++++|+|++++.||.|||++||+|+|||||||||||||| T Consensus 721 ------------~~~N~~~~M~~SGAKGS~~Ni~Qm~g~~Gl~~~~~griielPI~~sF~~GLtp~EfFfhamgGReGLi 788 (1204) T PRK05258 721 ------------DKFNPIFMMADSGARGNISNFTQLAGMRGLMAAPSGKIIELPIKSNFREGLTVLEYFISTHGARKGLA 788 (1204) T ss_pred ------------CCCCCHHHHHHHCCCCCHHHHHHHHHCCCCEECCCCCCCCCCCHHHHHCCCCHHHHHHCCHHHHCCHH T ss_conf ------------89985877755137787877999963766024699974676602243448988999980630212202 Q ss_pred CCCCCCCCCCEEEEHHHHHHCCCEEEEECCCCCCCCEEEEEEECCEEEEEECCCCCCCCCHHHCCCCCCCCEEEECCCCC Q ss_conf 01210156740110154230143277513887666512111008848865000101221144201778971885178657 Q gi|254780142|r 782 DVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLGSRVLGRTALDDIINPLTNECIVKAGQLI 861 (1398) Q Consensus 782 DTAvKTA~SGYlqRrLvk~~eDl~V~~~D~~t~~g~~~~~~~~~~~~~~~l~~~~~~r~~~~di~~~~~~~~i~~~~~~i 861 (1398) |||||||+|||||||||||+||++|+++||||.+|+++..+.++++.++++.++++||+.++|+++|.+++.++++++++ T Consensus 789 DTAvKTA~SGYLqRRLvkv~eD~~Vr~dDcgt~~g~~v~~i~~g~~~i~~l~~ri~gR~~~~di~~~~~~~~i~~~~~~i 868 (1204) T PRK05258 789 DTALKTADSGYLTRRLVDVAQDVIVREDDCGTDRGLLVSAIKEGNEVIEPLEERLVGRYTRKTVKHPETGEVIVGKNELI 868 (1204) T ss_pred HCCCCCCCCHHHHHHHHHHHCCEEEEEECCCCCCCCEEEEEEECCCCHHEHHHHHHCCHHHHHHCCCCCCCEEECCCCCC T ss_conf 22300243038999988875445999715887578068987308710105577674601354423677786765588625 Q ss_pred CHHHHHHHHHCCCCEEECCCCCCHHHHHCCCHHHHHHHCCCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCC Q ss_conf 89999999975984020233100035518657887542017852000101460211110078898776420245432221 Q gi|254780142|r 862 LESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVM 941 (1398) Q Consensus 862 ~~~~~~~i~~~~i~~v~irs~lt~~~~~~v~~~cy~~~l~~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~ 941 (1398) +++.+.++.+++++++.+||+|+|++.+|+|++||+++|+++++|+||||||+|||||||||||||||||||||||||+ T Consensus 869 ~~~~~~~i~~~gi~~v~iRS~ltc~s~~gvc~kcyg~~Lat~~~VepGEaVGiIAAQSIGEPgTQMTL~TFH~aGvas~- 947 (1204) T PRK05258 869 TEDIAKKIVDAGIEEVTIRSVFTCNTRHGVCRKCYGRNLATGDAVEVGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAGD- 947 (1204) T ss_pred CHHHHHHHHHCCCCEEEEECHHHHCCHHHHHHHHHHHHHHHCCCCCCCCEEEHHHHCCCCCCCHHHHHHHHHCCCCCCC- T ss_conf 9999999987278648874211121156499998755332114367776000110113688520142655411552434- Q ss_pred CCCEEEECCCCEEEEEEEEEEECCCCCEEEEECCCCEEEEECCCCEEEEEECCCHHCCCCCCCCEEECCEEEEECCCCCC Q ss_conf 12202401487689721134651788778974276046640677600000011000013567855322507862135431 Q gi|254780142|r 942 DRSFIESPCDGIVKIKNRNVCRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHTF 1021 (1398) Q Consensus 942 ~~~~iknvTlGVPRlkEi~~~~n~~~~~i~vs~~~~~~i~d~~~~~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp~~~ 1021 (1398) |||+ T Consensus 948 ------nIT~---------------------------------------------------------------------- 951 (1204) T PRK05258 948 ------DITQ---------------------------------------------------------------------- 951 (1204) T ss_pred ------CCCC---------------------------------------------------------------------- T ss_conf ------4446---------------------------------------------------------------------- Q ss_pred EEEECCCCEEEEEEECCCCEEHHHHHCCCCCEEEEEEEHHHCCCCCCCCCCEEEECCCCCEEECCCCCCCEEECCCCCEE Q ss_conf 13202463689753127832001230236860267751011012212385347742778253224788420213778445 Q gi|254780142|r 1022 PIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENGVVLKSARGTDARWFLPVDALL 1101 (1398) Q Consensus 1022 ~i~~e~~~~v~~~~~~~~~~~~~~~~~~t~~~~~~~i~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~ 1101 (1398) T Consensus 952 -------------------------------------------------------------------------------- 951 (1204) T PRK05258 952 -------------------------------------------------------------------------------- 951 (1204) T ss_pred -------------------------------------------------------------------------------- T ss_conf -------------------------------------------------------------------------------- Q ss_pred EECCCCCCCCCCEEEECHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCEECCCCCEEEEEEECCCCEEEEEEECCCCCCEE Q ss_conf 41367613548422210132024554336773288988752511110111347867863312794499998368984026 Q gi|254780142|r 1102 SVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFEARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPA 1181 (1398) Q Consensus 1102 ~v~~~~~v~~~d~l~~~~~~~~k~~DIt~GLPrV~eLFEar~pk~~aiisei~Giv~i~~~~~~k~~~vi~~~~~g~~~~ 1181 (1398) |+||+.|+||||+||+.+++++++|++...+..+.+....+.. .++.+.. T Consensus 952 -----------------------------GvPRl~EifeAr~pk~~aiisei~g~v~~i~~~~~~~~~~i~~-~~~~~~~ 1001 (1204) T PRK05258 952 -----------------------------GLPRVQELFEARNPKGQAVITEVDGTVVAIEEDKADRTKEVTV-KGETETR 1001 (1204) T ss_pred -----------------------------CCCCHHHHHHCCCCCCCCEEEEECCEEEEEEECCCCEEEEEEE-CCCCEEE T ss_conf -----------------------------7602899985047788612675145688745426741799997-7996489 Q ss_pred EEEECCCCEEEEECCCEEECCCEEECCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEE Q ss_conf 89813896589841987740864643899999998752799999999999999999809700612560124762861489 Q gi|254780142|r 1182 EYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEI 1261 (1398) Q Consensus 1182 e~~ip~~~~l~v~dgd~V~~gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I 1261 (1398) +|.+|.+.++.|.+|+.|..|+.+++|+++|||++++.|++|+++||++|||+||+.||+.||+||||+|++||++|+.| T Consensus 1002 ~y~ip~~~~l~v~~gd~V~~G~~l~~g~i~~~~il~v~g~~~~~~yli~Evq~vyr~qGV~i~dKhiEviirqml~kv~i 1081 (1204) T PRK05258 1002 SYTIPYTARLKVEEGDEVERGDELTEGSIDPKDLLKVKDVLSVETYLLAEVQKVYRMQGVEIGDKHVEVMVRQMLRKVRV 1081 (1204) T ss_pred EEECCCCCEEEEECCCEEECCCCCCCCCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHCCEEECCCEEEEEHHHHHHEEEE T ss_conf 99805775687705999844876257899989976634988999999999999988378764367588636514307899 Q ss_pred ECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHCCCEECCCC Q ss_conf 41886454566410699999999999972898752012100001453023107765040258999999745285523665 Q gi|254780142|r 1262 TDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDG 1341 (1398) Q Consensus 1262 ~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~G 1341 (1398) +++|||.|++|+.+++.++...|+.++..|+.||+++|+||||||+||+|+||||+||||||++||||||++|++|+|.| T Consensus 1082 ~~~gdt~~~~g~~vd~~~~~~~n~~~~~~g~~~a~~~~~llGITr~~l~t~S~LsaASFqeTt~vL~dAAi~gk~D~l~G 1161 (1204) T PRK05258 1082 MDPGDTDLLPGTLMDIFDFTDANKKVLISGGIPATARPVLLGITKASLETDSFLSAASFQETTRVLTDAAIKGKRDPLLG 1161 (1204) T ss_pred EECCCCCCCCCCEEEHHHHHHHHHHHHHCCCCCCEEEEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCC T ss_conf 82787455677685599999999999975997644545887763165233019988526637899999997179862578 Q ss_pred CCEEEECCCCCCCCCCHHHHHHHHHHCCCHHHHHH Q ss_conf 32215507305655354665331210251022211 Q gi|254780142|r 1342 FKENVIVGRSIPAGTGAILHEKRRVAMNRDQMILK 1376 (1398) Q Consensus 1342 vSENIIlGqliP~GTG~f~~~~~~~~~~~~~~~~~ 1376 (1398) |||||||||+||+|||++.|+.+++.....+...+ T Consensus 1162 lkEnII~G~liP~GTGl~~~~~~~~~~~~~~~~~~ 1196 (1204) T PRK05258 1162 LKENVIIGKLIPAGTGMARYRNIKPIEDTEEEEVE 1196 (1204) T ss_pred CCEEEECCCCCCCCCCCHHHCCEEEECCCHHHHHH T ss_conf 30103517713687585666351432240166654 No 5 >PRK02173 DNA-directed RNA polymerase subunit beta'; Provisional Probab=100.00 E-value=0 Score=2930.98 Aligned_cols=1169 Identities=41% Similarity=0.703 Sum_probs=1034.3 Q ss_pred CCCCCEEEEEEECCCHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCC------ Q ss_conf 786405368984588678850144897175542545687568873362136856677215-6641563448835------ Q gi|254780142|r 13 TDDRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECI-CGKYKRMKYKGII------ 85 (1398) Q Consensus 13 ~~~~~i~~i~f~l~spe~I~~~S~~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~-Cg~~~~~~~~g~~------ 85 (1398) -..++|++|+|||||||+||+||+|||++||||||||+|||+|||||+|||||++||||+ ||||++.+++|.+ T Consensus 8 ~~~~~f~~i~i~laspe~Ir~wS~GeV~kpeTinyrt~KPe~~GLfce~Ifgp~kd~eC~~Cgk~~~~~~~~~~c~~~~~ 87 (1438) T PRK02173 8 ISENKIQKISLALATPEDVLEWSRGEVTKPETINYKTYKPERGGLFDELIFGPLTDYKCPICGRKYKKSNENQLCIATKE 87 (1438) T ss_pred CCHHCCCEEEEEECCHHHHHHHHCEEECCCCCCCCCCCCCCCCCEEHHHHCCCCCCCCCHHCCCCCCEEECCEECCCCCC T ss_conf 37302464899831889999872840289866366889988887622032198635621100771124116855356761 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCEEECHHHHHHHHHHHHHCCCH---------HHHHHHHHHCCEEEECCCC-CCH Q ss_conf 675788530477578767720027762201301225789999809996---------5630133211123217886-510 Q gi|254780142|r 86 CEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSL---------RDVERVLYFESYVVVDPGL-SSL 155 (1398) Q Consensus 86 C~~Cg~~~~~~~~r~ghfGhIeLa~PV~Hi~f~k~~~~~i~~~l~~~~---------~~~~~v~y~~~~~~~~~~~-~~~ 155 (1398) |+.||+|++.+.|||+||||||||.||+||||+|.+||+|+.+|++++ +++|+|+||++|++++|+. ..+ T Consensus 88 C~~~gvev~~~~vrr~rmGHIeLa~PV~Hiwf~K~~ps~i~~lL~l~~~~~~~~~s~k~le~viy~~~~iv~~~~~~~~~ 167 (1438) T PRK02173 88 CKIEKPEILPKISRRSRMGHIALNAPVVHFWFFKIDHSIISKLLGLKVAESNKTVTKTDLENLIYYKSHIVLETGGLKSL 167 (1438) T ss_pred CCCCCEEECCCEECCCCCCCCEECCCCEEEEEECCCCHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCEEEEECCCCCCCC T ss_conf 78888694825450223577002686041003379603999982874434556666878787531201698558875531 Q ss_pred HHHCCCCH----------------------HHHHHHH---------------HHCCCC------------CEEECCCHHH Q ss_conf 43223699----------------------9998867---------------635855------------5061155267 Q gi|254780142|r 156 EKYQILTE----------------------EEYVEAV---------------SQFGQD------------QFIAMMGADA 186 (1398) Q Consensus 156 ~~~~~~~~----------------------~~~~~~~---------------~~~~~~------------~~~~~~g~~~ 186 (1398) .+.+++.. ++|.... ..++.+ .....+|++| T Consensus 168 ~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Gaea 247 (1438) T PRK02173 168 PKNKIIDISEAALIYKDALEEIIEFYPPGSEEYEAIAETISELADVASSKIGQDYGIDFYELNEIIEEYSSAKIATGSKA 247 (1438) T ss_pred HHCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCHHHH T ss_conf 01011221244556677889988751233488888888765444443322233305305666677776423442103999 Q ss_pred HHHHHHHCCHHHHHHHHHHHHHC-----------CCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCCEE Q ss_conf 78887726748899999987310-----------3220347886447788866663489851128630450762235138 Q gi|254780142|r 187 IYELLIALDLQNLALTLRDQLSK-----------SSSIFRRKKIIKRLKIVDSFITSGNNPGWMIIRKLPVLPPDLRPLV 255 (1398) Q Consensus 187 i~~~l~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~f~~~~~~Pewmil~~lpV~P~~~RP~v 255 (1398) |+++|.++|++.+...++.++.. ..+.+++.+++|||+++++|+.+++|||||||+|||||||++|||| T Consensus 248 i~~lL~~~dl~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~~krl~~v~~f~~s~~rPeWMil~vlPV~Pp~lRP~v 327 (1438) T PRK02173 248 IEYLLKNIDLRAEKEAIEAEIKGINKQIYKNKTSSSKNQKRDKLYKRLQVINAFINSGQDPKSMLIYNLPVIPADLRPLV 327 (1438) T ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCCCEE T ss_conf 99998566879999999999987555432211000135678889999999999986499960588613688999887208 Q ss_pred EECCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCC-CCCCCCCCCHHHHHHHHHC Q ss_conf 846973131003789999999869999998739835677769999999888874277678-7724787650678998610 Q gi|254780142|r 256 ALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHK-RVVTGANRRPLKSLSDMLK 334 (1398) Q Consensus 256 ~~~~g~~~~dDlt~~~~~Ii~~N~~Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~~-~~~~~~~~rp~ks~~~rlk 334 (1398) +||||+|++|||||||++||++|||||++++.|||++|++|||+|||+||||||||+++| .|++++++||||||+|||| T Consensus 328 ~LdgGrfatsDLn~lyrriI~rNnrLk~l~~~~aP~~Ii~nekrmLQeaVdal~DN~~~g~~~v~~~~~RPLKSLs~rLK 407 (1438) T PRK02173 328 QLDGGRHSTSDINELYRRIIIRNNRLKKWKEADAPVLIIQNELRMIQEAVDALIDNQRKSPNPVTSKDNRPLKSISDALT 407 (1438) T ss_pred EECCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHC T ss_conf 96898752665388899999987999999874998889987999999999999727877888773999895543788727 Q ss_pred CCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCEECHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEECCCCCEEHHH Q ss_conf 23782000346510045774034125543546200348987761289999999987986663000100122488250132 Q gi|254780142|r 335 GKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDVL 414 (1398) Q Consensus 335 gK~GrfR~nl~GKRVdfs~RsVI~pdP~l~~~evgvP~~~A~~L~~P~~~~~L~~~g~~~~i~~~k~~i~~~~~~v~~v~ 414 (1398) |||||||||||||||||||||||||||||++||||||+.||++||+||++++|++.+.+.+++.|++++++..+.+|+++ T Consensus 408 GKeGRFR~NLlGKRVDfSgRSVIs~dPnL~l~evGvPk~mA~eLt~P~ii~~L~~~~~~~~ik~akk~ie~~~~~vw~~l 487 (1438) T PRK02173 408 GKKGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQAGIPREMAAKLFEPWIIKELIQEEKVGSIKMAKKMIEELNPIIWPHV 487 (1438) T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCEEEEHHHHCCCCCCHHHHHHHHHHCCCCCHHHH T ss_conf 88763257788666476998715789998530035879999871977456066564774430345556662597112878 Q ss_pred HHHHCCCEEEECCCCCCEECCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHCCCC Q ss_conf 66656978997576310111401235899449547973122545467877545699746899999999998767505423 Q gi|254780142|r 415 AEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLH 494 (1398) Q Consensus 415 rhl~~gd~Vl~NRqPsLHr~Simah~~~v~~~~t~rln~~vc~pyNADFDGDEMnlHvPqs~eAraEa~~Lm~~~~niis 494 (1398) +|+++||+|||||||||||||||||+|||+||+|||||||||+||||||||||||||||||+||||||++||+|++||+| T Consensus 488 e~vi~gd~VLfNRqPTLHRmSImah~~kl~~gkTfRLhp~VC~pYNADFDGDEMNvHVPQS~EArAEA~~LM~v~~NIls 567 (1438) T PRK02173 488 AKVIQNKPVLLNRAPTLHRLSIQAFEPVLIRGKAIKLHPLVTTAFNADFDGDQMAVHVPISPEAVREAQELMFANKNILG 567 (1438) T ss_pred HHHHCCCEEEECCCCCCCCCCCCCCCEEEECCCEEEEEECCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHCCCCCCC T ss_conf 98746980575277410114333564476417358842001565568888762675167999999999998623047214 Q ss_pred CCCCCCEEEEHHHHHHHHHHHHCCCCCCCCCCCEECCHHHHHHHHHCCCCCCCCEEEEEECCCCCCC--CCCCEEECCCC Q ss_conf 7887820440258999999873367887446814179999999998889867852365204645667--61424521797 Q gi|254780142|r 495 PASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENKIVTLHSKIRGRYKSVDKDG--NSISKIYDTTP 572 (1398) Q Consensus 495 P~~g~Pi~~~~QD~i~G~y~lT~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~a~i~~~~~~~~~~~--~~~~~~~~tt~ 572 (1398) |++|+||+||+||+|+|+||||.++.+..++++.|.+.++++.+|+.+.+.+|+.+..++....+.. +.....+.||+ T Consensus 568 P~~G~PIig~iQD~IlG~Y~LT~~~~~~~geg~~F~~~~e~~~ay~~~~i~l~~~I~lp~~~I~kp~~l~~~~~~i~TT~ 647 (1438) T PRK02173 568 PKDGEPIINPSQDMILGLYYLTIEKAGAKGEGKFFSTYEAMLKAYEFKSVSLHARVALPFEQVKKPFIAKTMRGYIISTV 647 (1438) T ss_pred CCCCCCEEEEHHHHHHHHHHHEECCCCCCCCCCEECCHHHHHHHHHCCCCCCCCEEECCHHHCCCCCCCCCCCCEEEECH T ss_conf 88999547500667546565310244666876365889999999867996333235425553367656677760588471 Q ss_pred CCCCCCEEEECCCCCEEE--------------------------------EECCHHCCHHHHHHHHHHHHHCC------- Q ss_conf 751122055458751017--------------------------------75110020136669999999808------- Q gi|254780142|r 573 GRMIIGEILPRHHEISFD--------------------------------ICNQEMIKKNISAMVDTIYRHCG------- 613 (1398) Q Consensus 573 Gr~~~~~ilp~~~~~~~~--------------------------------~~~~~~~k~~~~~li~~i~~~~G------- 613 (1398) ||++||.++|++..+.++ .++..+.|+.++.+++.+|+.|+ T Consensus 648 GK~Ifn~ilP~~~~~i~~~~~~~~~~~~~~~~~~~~ip~G~~~~e~i~~~~vn~~~~kk~i~~ii~~i~d~~v~i~~~e~ 727 (1438) T PRK02173 648 GKFIFNNAFPANFPFIFDDNVDELELNYPSQIKKYVLPYGTNFREYIQNLPVNEPLNKKAIAKIVRQIFDKYVGLLTKED 727 (1438) T ss_pred HHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCE T ss_conf 99999876778788544554442112554222221256775300012444344443334577887776641152013430 Q ss_pred -------------------------------------------------------------------------------- Q ss_conf -------------------------------------------------------------------------------- Q gi|254780142|r 614 -------------------------------------------------------------------------------- 613 (1398) Q Consensus 614 -------------------------------------------------------------------------------- 613 (1398) T Consensus 728 i~gvidk~~~g~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~ll~~i~~ 807 (1438) T PRK02173 728 IASVIDQLNFGNYQNIVLLYAKLKDYKKQKLPVPHLEILSEFTIFEYSKIYKQLQQNGPGESERVWEDHEKAELLEKVWF 807 (1438) T ss_pred EEEEECCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH T ss_conf 10010122335544442011100245554221023445544444321000100002565421110010002334444544 Q ss_pred --HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHH Q ss_conf --178999875588999999985398613212326836999999999789999998864897667888788642346589 Q gi|254780142|r 614 --QKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKMVKEYENQYNDGLITRGEKYNKVVDLWGKTTD 691 (1398) Q Consensus 614 --~~~~~~~l~~~~~l~~~~l~~~GfSigi~D~~~~~~k~~~i~~a~~~~~~~~~~~~~G~~t~~e~~~~i~~~~~~~~~ 691 (1398) ...++.+||.++.++|+|++.+|||+|++|+.+|++|.+++++++++++++..+|++|++|++|+|+++++.|+++++ T Consensus 808 ~~~~~~a~~LD~ik~lGf~~at~sG~SigI~Di~~~~~k~e~I~eae~~v~~l~~~y~~Gllt~~Er~~~~i~~ws~~~d 887 (1438) T PRK02173 808 KYNNMVASVLDKIKDLGFKFSTLSGTTISISDIKTSPKKKERIKEGENYINKLKTYYAKGLITDDERYVLTIAKWTQIKN 887 (1438) T ss_pred HCCCHHHHHHHHHHHHHHHHHHHCCCEEEHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHH T ss_conf 11205788888887642577764465011513006716899999999999999999871688377899999999999999 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCHHHEEEEEEECCCCCC------CCCC-------CCCCCCCC Q ss_conf 9999999998761156543222246883764225555784241120010000246------4434-------44566630 Q gi|254780142|r 692 KVTEEMMARIKRVEFDPETGRQKKMNSIFMMSHSGARGSIHQMRQLGGMRGLIAK------PSGE-------IIESPIRS 758 (1398) Q Consensus 692 ~~~~~~~~~~~~~~~~~~~~~~~~~N~~~~M~~SGAKGS~~qi~ql~Gqq~l~gk------p~G~-------~~~~PV~~ 758 (1398) .+.+++++.+. .+++|++++|+.||||||+.||+||+||+|+++. ++++ +++.||.| T Consensus 888 ~v~~~~~k~l~----------~~~~N~i~~Ma~SGAKGS~~NIsQmaGmrG~~~~~gkrl~~~~~~eri~r~~ie~PV~s 957 (1438) T PRK02173 888 DIQEDLKKIIK----------DNPQNSLFMMMNSGARGNISNFVQLAGMRGLMANNTKALKADAENERVVRSTVEIPVKS 957 (1438) T ss_pred HHHHHHHHHHH----------CCCCCCEEEEEECCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC T ss_conf 99999999864----------28888658877046768899999986463410477764678877664545544467400 Q ss_pred HHHCCCCHHHHHHCCCCCCHHHHCCCCCCCCCCEEEEHHHHHHCCCEEEEECCCCCCCCEEEEEEE--CCEEEEEECCCC Q ss_conf 111088898976405761032210121015674011015423014327751388766651211100--884886500010 Q gi|254780142|r 759 HFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVD--SGQVVYSLGSRV 836 (1398) Q Consensus 759 sF~~GL~p~EfFfhamgGReGLiDTAvKTA~SGYlqRrLvk~~eDl~V~~~D~~t~~g~~~~~~~~--~~~~~~~l~~~~ 836 (1398) ||++||+|+|||||||||||||||||||||+||||||||||++||++|+++||+|..|+.+..+.+ ++..+.+|.+++ T Consensus 958 SF~eGLtp~EfFfHtmGGREGLiDTAVKTAeSGYLQRRLVkvleDliV~~dDcgt~~G~~v~di~d~~~~~ii~~L~eri 1037 (1438) T PRK02173 958 SFLEGLTAYEFYSSTHGARKGLTDTALNTAKSGYLTRRLVDVAQNIVVREEDCGSDFGFVVKDIIDTKTNTIIVPLLERI 1037 (1438) T ss_pred HHHCCCCHHHHEEECCCCCCCHHHHHHHHHHHCCHHHHHHHHHCCCEEEEECCCCCCCEEEEEEEECCCCCEEEEHHHHH T ss_conf 12048973661010223112315534665443225889999741248986357875886866534068983887814522 Q ss_pred CCCCCHHHCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEECCCCCCHHHHHCCCHHHHHHHCCCCCEECHHHCCCCHH Q ss_conf 12211442017789718851786578999999997598402023310003551865788754201785200010146021 Q gi|254780142|r 837 LGRTALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIA 916 (1398) Q Consensus 837 ~~r~~~~di~~~~~~~~i~~~~~~i~~~~~~~i~~~~i~~v~irs~lt~~~~~~v~~~cy~~~l~~~~lv~pGe~VG~iA 916 (1398) .||+.+++++++ +++.+++++++++++.++.+.+++++++.+||+|+|++.+|+|++|||+||+++++|+||||||+|| T Consensus 1038 ~gR~~~~~i~d~-~~~~i~~~~~li~~~~~~~i~~~~i~~v~irs~ltc~~~~gvc~~cyg~dLa~~~lV~~GEaVGiIA 1116 (1438) T PRK02173 1038 EGRFLNKDVYDS-RGKLLASAGTLITLETAKKIVAAGIKKVEIRSILSCHTKNGVCKKCYGKDLATNRLVNIGEAVGIIA 1116 (1438) T ss_pred HCCEEHHHCCCC-CCCEEEECCCCCCHHHHHHHHHCCCCEEEECCCCCCCCHHHHHHHHHCHHHHHCCCCCCCCHHHHHH T ss_conf 140002320188-8858873887079999999998699789721433311322088998474667389288875678888 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEEEEEEEEEEECCCCCEEEEECCCCEEEEECCCCEEEEEECCCH Q ss_conf 11100788987764202454322211220240148768972113465178877897427604664067760000001100 Q gi|254780142|r 917 AQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNRNVCRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYG 996 (1398) Q Consensus 917 AQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVPRlkEi~~~~n~~~~~i~vs~~~~~~i~d~~~~~~~~~ki~~~ 996 (1398) |||||||||||||||||||||||+ +|+|+|+||++||..+. T Consensus 1117 AQSIGEPgTQMTLrTFH~gGvA~~------~dIT~G~pRv~El~ea~--------------------------------- 1157 (1438) T PRK02173 1117 AQSIGEPGTQLTMRTFHTGGVAGV------EDITGGFGRLIELIDAH--------------------------------- 1157 (1438) T ss_pred HHHCCCCHHHHHHHHHHCCCCCCC------CCCCCCCCCHHHHHCCC--------------------------------- T ss_conf 882797076676870501423674------44456761376652043--------------------------------- Q ss_pred HCCCCCCCCEEECCEEEEECCCCCCEEEECCCCEEEEEEECCCCEEHHHHHCCCCCEEEEEEEHHHCCCCCCCCCCEEEE Q ss_conf 00135678553225078621354311320246368975312783200123023686026775101101221238534774 Q gi|254780142|r 997 AKLFVDDGGVIECGQRISEWDPHTFPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVT 1076 (1398) Q Consensus 997 ~~~~v~~~~~v~~~~ii~~~Dp~~~~i~~e~~~~v~~~~~~~~~~~~~~~~~~t~~~~~~~i~~~~~~~~~~~~~~~~i~ 1076 (1398) T Consensus 1158 -------------------------------------------------------------------------------- 1157 (1438) T PRK02173 1158 -------------------------------------------------------------------------------- 1157 (1438) T ss_pred -------------------------------------------------------------------------------- T ss_conf -------------------------------------------------------------------------------- Q ss_pred CCCCCEEECCCCCCCEEECCCCCEEEECCCCCCCCCCEEEECHHHHCCCCCCCCCCCHHHHHHHHHCCCC-CCEECCCCC Q ss_conf 2778253224788420213778445413676135484222101320245543367732889887525111-101113478 Q gi|254780142|r 1077 DENGVVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFEARRPKN-HAILAEISG 1155 (1398) Q Consensus 1077 d~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~v~~~d~l~~~~~~~~k~~DIt~GLPrV~eLFEar~pk~-~aiisei~G 1155 (1398) |+|+. +|++++++| T Consensus 1158 -----------------------------------------------------------------~~p~~~~a~i~~~~g 1172 (1438) T PRK02173 1158 -----------------------------------------------------------------EHPWGRPAKISPYYG 1172 (1438) T ss_pred -----------------------------------------------------------------CCCCCCCCEEEEECC T ss_conf -----------------------------------------------------------------688998655774156 Q ss_pred EEEEEEECCCCE--------EEEEEECCCCCCEEEEEECCCCEEEEECCCEEECCCEEECCCCCHHHHHHHHCHHHHHHH Q ss_conf 678633127944--------999983689840268981389658984198774086464389999999875279999999 Q gi|254780142|r 1156 TIRIKRNYKNKS--------RVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDILRIKGVEALASY 1227 (1398) Q Consensus 1156 iv~i~~~~~~k~--------~~vi~~~~~g~~~~e~~ip~~~~l~v~dgd~V~~gd~lt~Gsid~~eIl~vlGIEAAR~~ 1227 (1398) ++......+.+. .+.+....+.....+|.+|.++++.|.+||+|.+|+.+++|+++|||||++.|++|+++| T Consensus 1173 ~v~~i~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~i~~~~~~~v~~gd~v~~G~~l~~G~~~~~~il~~~g~~~~~~y 1252 (1438) T PRK02173 1173 IITKIKDLKEKNAANKGFLITIEYKTSKNEKATHIIRVEQSQKLRVKVGDKVIPGQKLVEGPIILKELLEVSDARTVQNY 1252 (1438) T ss_pred EEEEEECCCCCCCCCCCCEEEEEEECCCCCCEEEEEECCCCCEEEECCCCEECCCCCCCCCCCCHHHHHHHCCHHHHHHH T ss_conf 78786303666554455137898874789824799975479875667999976799847899998999884499999999 Q ss_pred HHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEECHHHH Q ss_conf 99999999998097006125601247628614894188645456641069999999999997289875201210000145 Q gi|254780142|r 1228 LINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKA 1307 (1398) Q Consensus 1228 Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~~~p~llGITKa 1307 (1398) |++|||+||+.|||.||+||||+|++||++|+.|+++|||.|++|+.|++.++..+|+.+..+|+.||.++|+|+||||| T Consensus 1253 l~~evq~vyr~qGv~i~dKhiEvivrqml~kv~i~~~gds~~~~g~~vd~~~~~~~n~~~~~~g~~~a~~~~~l~Gitka 1332 (1438) T PRK02173 1253 LLKEIQKIYRMQGISISDKYIEIIIRQMLSKIQIIEPGDSNFFIGSIVDIFDYQEENGQLLSQGKKPAFGKVIIKGAKQI 1332 (1438) T ss_pred HHHHHHHHHHHCCCEECCCEEEEHHHHHCCEEEEECCCCCCCCCCCEEEHHHHHHHHHHHHHCCCCCCCEEEECCCCCHH T ss_conf 99999999997597502547885365650722897288877889888459999999999998499875010000232332 Q ss_pred HHCCCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCCCCCCCCCHHHHHHHHHHCCCHHHHHH Q ss_conf 302310776504025899999974528552366532215507305655354665331210251022211 Q gi|254780142|r 1308 SLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAILHEKRRVAMNRDQMILK 1376 (1398) Q Consensus 1308 sl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG~f~~~~~~~~~~~~~~~~~ 1376 (1398) ||+|+||||||||||||+||+|||+.|++|+|+|+|||||+||+||||||+-.+.+.++.+......+. T Consensus 1333 sl~t~S~lsaASFqeTt~vLt~Aai~gk~D~L~GlkENviiG~lIPaGTg~~~~~~~~~~~~~~~~~~~ 1401 (1438) T PRK02173 1333 PLLSDSFLAAASYQETSKILVHSSISSQIDKLEGLKENIIVGHKIPAGTNSNYEPKSKYDIRNPKSYFR 1401 (1438) T ss_pred HHHHHHHHHHHHHHCHHHHHHHHHHCCCCCCCCCCCHHHHCCCEEECCCCCCCCCCCCCCCCCCHHHHC T ss_conf 342346998861214678999998758987678843676426700077782004311245448165514 No 6 >PRK02995 DNA-directed RNA polymerase subunit beta'; Provisional Probab=100.00 E-value=0 Score=2926.51 Aligned_cols=1157 Identities=51% Similarity=0.847 Sum_probs=1070.6 Q ss_pred CCCCEEEEEEECCCHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 86405368984588678850144897175542545687568873362136856677215664156344883567578853 Q gi|254780142|r 14 DDRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRMKYKGIICEKCGVEV 93 (1398) Q Consensus 14 ~~~~i~~i~f~l~spe~I~~~S~~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~Cg~~~~~~~~g~~C~~Cg~~~ 93 (1398) ....|++|||||||||+||+||+|||++||||||+|+|||+|||||||||||++||||+|||||+++|+|.+|++||+|+ T Consensus 3 ~~~~f~~i~i~laSpe~Ir~wS~geV~kpeTinyrt~kPe~~GLfce~Ifgp~kd~eC~Cgkyk~~~~kg~~C~~Cgvev 82 (1291) T PRK02995 3 DVNFFDELRIGLATADDIRQWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWECYCGKYKRVRFKGIICERCGVEV 82 (1291) T ss_pred CCCCCCEEEEEECCHHHHHHHHCEEECCCCCCCCCCCCCCCCCCCCHHHCCCCCCCEEECCCCCCCCCCCCCCCCCCCEE T ss_conf 67765728998148899998618356787652278899988883251422988587671786133246987769998650 Q ss_pred CCCCCCCCCCCCCCCCCCCEEECHHHHHHHHHHHHHCCCHHHHHHHHHHCCEEEECCCCC-------CH------H---- Q ss_conf 047757876772002776220130122578999980999656301332111232178865-------10------4---- Q gi|254780142|r 94 TLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRDVERVLYFESYVVVDPGLS-------SL------E---- 156 (1398) Q Consensus 94 ~~~~~r~ghfGhIeLa~PV~Hi~f~k~~~~~i~~~l~~~~~~~~~v~y~~~~~~~~~~~~-------~~------~---- 156 (1398) +.|+|||+||||||||.||+||||||++||+|+.+|++++++||+|+||++|+++++... .+ + T Consensus 83 t~~~vrr~rmGHIeLa~PV~Hiw~~k~~ps~i~~ll~~~~k~le~viyf~~~iv~~~~~~~~~~~~~~l~~~~~~~~~~~ 162 (1291) T PRK02995 83 TRAKVRRERMGHIELAAPVTHIWYFKGVPSRLGYLLDLAPKDLEKVIYFAAYMITSVDEEARHNDLPTLEAEMDVEKKQL 162 (1291) T ss_pred CCCCCCCCCCCCEEECCCCEEECCCCCCCHHHHHHHCCCHHHHHEEEEEECEEECCCCCCCCCCCCHHHHHHHHHHHHHH T ss_conf 55752325456740178725004127980399998698987821676520326035563211122023444554445554 Q ss_pred --------------------------------------------------------------------HHCCCC-HHHHH Q ss_conf --------------------------------------------------------------------322369-99998 Q gi|254780142|r 157 --------------------------------------------------------------------KYQILT-EEEYV 167 (1398) Q Consensus 157 --------------------------------------------------------------------~~~~~~-~~~~~ 167 (1398) ..+++. +..|+ T Consensus 163 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 242 (1291) T PRK02995 163 EDQRDADIEARAQKLEADLAELEAEGAKADARRKVRDGAEREMRQIRDRAQREIDRLDEVWDTFKKLKPKQLIGDELLYR 242 (1291) T ss_pred HHHCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHH T ss_conf 32011256665544323344432101101455542010245677776655555555666655430356322222188999 Q ss_pred HHHHHCCCCCEEECCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCC Q ss_conf 86763585550611552677888772674889999998731032203478864477888666634898511286304507 Q gi|254780142|r 168 EAVSQFGQDQFIAMMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMIIRKLPVL 247 (1398) Q Consensus 168 ~~~~~~~~~~~~~~~g~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~Pewmil~~lpV~ 247 (1398) +..++++ +.|.+.||++|++++|.++|++.+...++.++.... .+++.+++|||+++++|..+++|||||||+||||| T Consensus 243 ~~~~~~~-~~f~~~~gaeai~~ll~~~dl~~~~~~l~~~~~~~~-~~~~~~~~krl~~v~~f~~s~n~Pewmil~vlPV~ 320 (1291) T PRK02995 243 ELRDRYG-DYFTGGMGAEAIQKRLENFDLDAEAESLRETIRNGK-GQKKLRALKRLKVVAAFLTTGNSPMGMVLDAVPVI 320 (1291) T ss_pred HHHHHHH-HHHHHCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCC T ss_conf 9998640-233413429999999985799999999999986304-68999999999999999966999440210034779 Q ss_pred CCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHH Q ss_conf 62235138846973131003789999999869999998739835677769999999888874277678772478765067 Q gi|254780142|r 248 PPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHKRVVTGANRRPLK 327 (1398) Q Consensus 248 P~~~RP~v~~~~g~~~~dDlt~~~~~Ii~~N~~Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~~~~~~~~~~rp~k 327 (1398) ||++||||+||||+|++|||||||++||++|||||++++.|||++|++|+|+||||||+|||||+++|+|++++++|||| T Consensus 321 Pp~lRP~v~ldgg~~a~sDLn~ly~~II~~NnrLk~~~~~gaP~~ii~ne~~mLQ~~V~al~DN~~~g~p~~~~~~RpLK 400 (1291) T PRK02995 321 PPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLIDLGAPEIIVNNEKRMLQEAVDALFDNGRRGRPVTGPGNRPLK 400 (1291) T ss_pred CCCCCCCEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC T ss_conf 98787516968986556225889999999889999999769968999889999999999997068888876478999555 Q ss_pred HHHHHHCCCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCEECHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEECCC Q ss_conf 89986102378200034651004577403412554354620034898776128999999998798666300010012248 Q gi|254780142|r 328 SLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKER 407 (1398) Q Consensus 328 s~~~rlkgK~GrfR~nl~GKRVdfs~RsVI~pdP~l~~~evgvP~~~A~~L~~P~~~~~L~~~g~~~~i~~~k~~i~~~~ 407 (1398) ||+|||||||||||||||||||||||||||||||||++||||||+.||++||+||++++|+..+.+.+++.+++++++.+ T Consensus 401 Sls~rLKGKeGRFR~NLmGKRVDfSaRSVIspDPnL~i~EvGVP~~mA~eLt~Pfvi~rl~~~~~~~nik~ak~~v~r~~ 480 (1291) T PRK02995 401 SLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKLMALELFKPFVMKRLVDLNHAQNIKSAKRMVERQR 480 (1291) T ss_pred CHHHHHCCCCCEECCCCCCCCCCCCCCCEEECCCCCCCCCCCCCHHHHHHCCCCEEHHHHHHCCCCCCHHHHHHHHHHCC T ss_conf 38998467665120577766526589863617999865502684899987372643575776267566178999988249 Q ss_pred CCEEHHHHHHHCCCEEEECCCCCCEECCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHH Q ss_conf 82501326665697899757631011140123589944954797312254546787754569974689999999999876 Q gi|254780142|r 408 PEVWDVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLML 487 (1398) Q Consensus 408 ~~v~~v~rhl~~gd~Vl~NRqPsLHr~Simah~~~v~~~~t~rln~~vc~pyNADFDGDEMnlHvPqs~eAraEa~~Lm~ 487 (1398) +.+|+|++|++++|+|||||||||||||||||+|||+||||||||||||+||||||||||||||||||+||||||++||+ T Consensus 481 ~~v~dvle~vi~~~~VLfNRQPTLHRmSImah~~kv~~gkT~RLn~~vC~pYNADFDGDEMNlHvPQS~eAraEa~~Lm~ 560 (1291) T PRK02995 481 PQVWDVLEEVIAEHPVLLNRAPTLHRLGIQAFEPQLVEGKAIQLHPLVCEAFNADFDGDQMAVHLPLSAEAQAEARILML 560 (1291) T ss_pred CHHHHHHHHHHCCCEEEECCCCCCCCCCCCCEEEEEECCCEEEECHHCCCCCCCCCCCCEEEECCCCCHHHHHHHHHHHH T ss_conf 54778898774277146615752131533551478736845885510067666887773346427799999999999860 Q ss_pred HHHCCCCCCCCCCEEEEHHHHHHHHHHHHCCCCCCCCCCCEECCHHHHHHHHHCCCCCCCCEEEEEECCCCCCCC----- Q ss_conf 750542378878204402589999998733678874468141799999999988898678523652046456676----- Q gi|254780142|r 488 STNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENKIVTLHSKIRGRYKSVDKDGN----- 562 (1398) Q Consensus 488 ~~~niisP~~g~Pi~~~~QD~i~G~y~lT~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~a~i~~~~~~~~~~~~----- 562 (1398) +++||+||++|+|++|++||+|+|+||||..+.+..+++..|.+..++..++..+.+.++++++.++....+... T Consensus 561 v~~nilsP~~G~Piig~~QD~ilG~y~LT~~~~~~~~e~~~f~~~~~~~~~~~~~~l~l~~~i~i~~~~~~~~~~~~~~~ 640 (1291) T PRK02995 561 SSNNILKPADGRPVAMPSQDMVTGLYYLTTVKEGAKGEGRPFSSPAEAIMAFDRGELSLQAKVKIRLTQLRPPAEIEAEL 640 (1291) T ss_pred CCCCEEECCCCCCEECHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCCCC T ss_conf 33277327999821231189998889875036664456562277999997534386632672799666656776543310 Q ss_pred --------CCCEEECCCCCCCCCCEEEECCCCCEEEEECCHHCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf --------142452179775112205545875101775110020136669999999808178999875588999999985 Q gi|254780142|r 563 --------SISKIYDTTPGRMIIGEILPRHHEISFDICNQEMIKKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACS 634 (1398) Q Consensus 563 --------~~~~~~~tt~Gr~~~~~ilp~~~~~~~~~~~~~~~k~~~~~li~~i~~~~G~~~~~~~l~~~~~l~~~~l~~ 634 (1398) .......+|.||++||.++|.++. ++++.++|+.+|+|+|.+++.||+..++.|||++++++|+|+++ T Consensus 641 ~~~~~~~~~~~~~~~tt~Gr~ifn~~lp~~~~----~i~g~l~Kk~lg~li~~l~~~yg~~~~~~~ld~l~~l~~~~l~~ 716 (1291) T PRK02995 641 FGPEGWQPGDAWTAETTLGRVLFNELLPEDYP----FVNEQMDKKVLSAIVNDLAERYPMIVVAQTLDKLKDAGFYWATR 716 (1291) T ss_pred CCCCCCCCCCCEEECCCCCEEEECCCCCCCCC----EEEEEECCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 47656776763443177674764251478775----35414433148899999999839999999999999999999987 Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC Q ss_conf 39861321232683699999999978999999886489766788878864234658999999999987611565432222 Q gi|254780142|r 635 SGISFGKDDIIVPESKEKIIAEADKMVKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQK 714 (1398) Q Consensus 635 ~GfSigi~D~~~~~~k~~~i~~a~~~~~~~~~~~~~G~~t~~e~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 714 (1398) +||||||+|+++|++|.++++++++++++++.+|++|+++++|++++++++|+++++++++.+++.+ . T Consensus 717 ~GfSiGI~D~~~~~~k~eii~~~~~~~~~i~~~~~~G~lt~~e~~~~l~~il~~a~d~v~~~~~~~l------------~ 784 (1291) T PRK02995 717 SGVTVAMSDVLVPPEKQEILDGYEAQADKVEKQYERGLLTDDERRQELVEIWTEATDEVAEAMEENF------------P 784 (1291) T ss_pred CCCEEEHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC------------C T ss_conf 5865407650687789999999999999999987505565078999999999999999999999657------------8 Q ss_pred CCCCEEEEECCCCCCCHHHEEEEEEECCCCCCCCCCCCCCCCCCHHHCCCCHHHHHHCCCCCCHHHHCCCCCCCCCCEEE Q ss_conf 46883764225555784241120010000246443444566630111088898976405761032210121015674011 Q gi|254780142|r 715 KMNSIFMMSHSGARGSIHQMRQLGGMRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLS 794 (1398) Q Consensus 715 ~~N~~~~M~~SGAKGS~~qi~ql~Gqq~l~gkp~G~~~~~PV~~sF~~GL~p~EfFfhamgGReGLiDTAvKTA~SGYlq 794 (1398) ++|++++|+.||||||+.||+||+||+|++++|.|++++.||.|||++||+|+|||||||||||||||||||||+||||| T Consensus 785 ~~N~~~~Mv~SGAKGS~~NIsQm~g~rGl~~~~~G~~ip~pI~nsF~~GLtp~EfFfHamgGREGLiDTAVKTA~SGYLq 864 (1291) T PRK02995 785 DDNPIIMIVDSGARGNMMQIRQLAGMRGLVANPKGEIIPRPIKSSFREGLTVLEYFISTHGARKGLADTALRTADSGYLT 864 (1291) T ss_pred CCCCHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHCCCCHHHHHHCCCCCCCCCCCCCCCCCCCHHHH T ss_conf 88859998660576789899998640677668988847763324411169788887616132333100421025412789 Q ss_pred EHHHHHHCCCEEEEECCCCCCCCEEEEEEECCE----EEEEECCCCCCCCCHHHCCCCCCCCEEEECCCCCCHHHHHHHH Q ss_conf 015423014327751388766651211100884----8865000101221144201778971885178657899999999 Q gi|254780142|r 795 RRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQ----VVYSLGSRVLGRTALDDIINPLTNECIVKAGQLILESHVNEIE 870 (1398) Q Consensus 795 RrLvk~~eDl~V~~~D~~t~~g~~~~~~~~~~~----~~~~l~~~~~~r~~~~di~~~~~~~~i~~~~~~i~~~~~~~i~ 870 (1398) ||||||+||++|+++||||.+|+.+....++.+ ....+.+++++|+++.|++++ ++++++++++.+++..++++. T Consensus 865 RRLVkv~eDv~Vr~dDCgT~~gi~~~~~~~~~~g~~~~~~~~~~~~~~r~l~~d~~~~-~~~vi~~~~~~i~~~~~~~~~ 943 (1291) T PRK02995 865 RRLVDVSQDVIVREEDCGTERGIVVPIAERDADGTLVRDENVETSVYARTLAADAVDA-DGNVVAEAGTDLGDPLIDALL 943 (1291) T ss_pred HHHHHHHCCEEEEECCCCCCCCEEEEEEEECCCCCEEECHHHHHHHHHHHHHHHHCCC-CCCEEEECCCCCCHHHHHHHH T ss_conf 9988875555999726885068043456755887555330235557763438861388-998885488627999999999 Q ss_pred HCCCCEEECCCCCCHHHHHCCCHHHHHHHCCCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECC Q ss_conf 75984020233100035518657887542017852000101460211110078898776420245432221122024014 Q gi|254780142|r 871 KCGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPC 950 (1398) Q Consensus 871 ~~~i~~v~irs~lt~~~~~~v~~~cy~~~l~~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvT 950 (1398) .++++++++||+|||++..|+|++||+|+|+++++|+||||||+||||||||||||||||||||||||| T Consensus 944 ~~gi~~v~iRS~Ltc~s~~gvc~~cYgr~Lat~klVepGEaVGiIAAQSIGEPgTQMTLnTFH~AGvas----------- 1012 (1291) T PRK02995 944 AAGVEEVKVRSVLTCESKTGVCAKCYGRSLATGKLVDIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVGD----------- 1012 (1291) T ss_pred HCCCCEEEECCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCCHHHHHHHHCCCCCC----------- T ss_conf 759987862143354467889999998877634768888702343103368874203265642155443----------- Q ss_pred CCEEEEEEEEEEECCCCCEEEEECCCCEEEEECCCCEEEEEECCCHHCCCCCCCCEEECCEEEEECCCCCCEEEECCCCE Q ss_conf 87689721134651788778974276046640677600000011000013567855322507862135431132024636 Q gi|254780142|r 951 DGIVKIKNRNVCRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHTFPIITEVSGT 1030 (1398) Q Consensus 951 lGVPRlkEi~~~~n~~~~~i~vs~~~~~~i~d~~~~~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp~~~~i~~e~~~~ 1030 (1398) T Consensus 1013 -------------------------------------------------------------------------------- 1012 (1291) T PRK02995 1013 -------------------------------------------------------------------------------- 1012 (1291) T ss_pred -------------------------------------------------------------------------------- T ss_conf -------------------------------------------------------------------------------- Q ss_pred EEEEEECCCCEEHHHHHCCCCCEEEEEEEHHHCCCCCCCCCCEEEECCCCCEEECCCCCCCEEECCCCCEEEECCCCCCC Q ss_conf 89753127832001230236860267751011012212385347742778253224788420213778445413676135 Q gi|254780142|r 1031 VGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENGVVLKSARGTDARWFLPVDALLSVSPGQKVS 1110 (1398) Q Consensus 1031 v~~~~~~~~~~~~~~~~~~t~~~~~~~i~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~v~ 1110 (1398) T Consensus 1013 -------------------------------------------------------------------------------- 1012 (1291) T PRK02995 1013 -------------------------------------------------------------------------------- 1012 (1291) T ss_pred -------------------------------------------------------------------------------- T ss_conf -------------------------------------------------------------------------------- Q ss_pred CCCEEEECHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCEECCCCCEEEEEEECCCCEEEEEEECCCCCCEEEEEECCCCE Q ss_conf 48422210132024554336773288988752511110111347867863312794499998368984026898138965 Q gi|254780142|r 1111 TGDVLARLPISSAKTKDITSGLPRVAELFEARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKH 1190 (1398) Q Consensus 1111 ~~d~l~~~~~~~~k~~DIt~GLPrV~eLFEar~pk~~aiisei~Giv~i~~~~~~k~~~vi~~~~~g~~~~e~~ip~~~~ 1190 (1398) |||+|+||+.||||||+||..+.+++++|.+++....+ ..++++.+ +++.+..+|.++...+ T Consensus 1013 ----------------nITlGvPRlkEIfeAr~PK~~a~i~e~~g~V~ie~~~~-~~~~~i~~-dd~~~~~~y~i~~~~~ 1074 (1291) T PRK02995 1013 ----------------DITQGLPRVQELFEARTPKGKAPIAEVAGRVRIEDGER-FRKITIVP-DDGSEEVVYKVSKRQR 1074 (1291) T ss_pred ----------------CCCCCCHHHHHHHHCCCCCCCCCEEEEEEEEEEEECCC-CEEEEEEC-CCCCCEEEEECCCCCE T ss_conf ----------------32367563899985148787763133103899973377-05999977-9998357997257855 Q ss_pred EEEECCCEEECCCEEECCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCC Q ss_conf 89841987740864643899999998752799999999999999999809700612560124762861489418864545 Q gi|254780142|r 1191 FYLQDGDHVEKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYI 1270 (1398) Q Consensus 1191 l~v~dgd~V~~gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i 1270 (1398) +.+.+|++|..|+.+++|++|||+||+++|++|++.+|++|||.||+.||+.||+|||++|++||++|+.|+++|||.|+ T Consensus 1075 l~v~dgd~V~~g~~l~~g~~dp~~iLri~G~~~~~~~lv~evq~Vyr~qGV~I~dKhievIvrqml~kv~i~d~gdt~~l 1154 (1291) T PRK02995 1075 LRVSDGDHVEVGQQLVEGSADPHEVLRVLGPRAVQVHLVDEVQEVYRSQGVSIHDKHIEVIVRQMLRRVTVIDSGDTEFL 1154 (1291) T ss_pred EEEECCCEEECCCEECCCCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCEECCEEHHHHHHHHCEEEEEECCCCCCC T ss_conf 78735999964875034889989998862999999999999999999659752101007888866207899816866655 Q ss_pred CCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCC Q ss_conf 66410699999999999972898752012100001453023107765040258999999745285523665322155073 Q gi|254780142|r 1271 LGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGR 1350 (1398) Q Consensus 1271 ~g~~Inr~~~~~~Nr~~~~~g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGq 1350 (1398) +|+.|++..+..+|++.+..|+.|++++|+||||||+||+|+||||+|||||||+||+|||++|++|+|+|||||||||| T Consensus 1155 ~g~~v~~~~~~~~n~~~~~~~~~~~~~r~~llGITr~~l~t~S~Ls~ASFqeTt~vL~dAAi~gk~D~l~GlkEnIIlG~ 1234 (1291) T PRK02995 1155 PGELVDRARFEAENRRVVAEGGEPASGRPVLMGITKASLATESWLSAASFQETTRVLTDAAINGRSDKLIGLKENVIIGK 1234 (1291) T ss_pred CCCHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCCC T ss_conf 73288799999999999983997113422146640043112219998613516799999998479875778102430478 Q ss_pred CCCCCCCHHHHHHHHHHCCC--HHHHHHHH Q ss_conf 05655354665331210251--02221112 Q gi|254780142|r 1351 SIPAGTGAILHEKRRVAMNR--DQMILKER 1378 (1398) Q Consensus 1351 liP~GTG~f~~~~~~~~~~~--~~~~~~~~ 1378 (1398) +||+|||+-.|++++++-.+ ....+++. T Consensus 1235 liP~GTGl~~y~~~~~~~~~~~~~~~~~~~ 1264 (1291) T PRK02995 1235 LIPAGTGISRYRNIRVEPTEEARAAAYTIP 1264 (1291) T ss_pred CCCCCCCHHHHCCCCCCCCHHHHHHHCCCC T ss_conf 678775938864860565766774426788 No 7 >PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional Probab=100.00 E-value=0 Score=2798.08 Aligned_cols=1165 Identities=44% Similarity=0.726 Sum_probs=1039.7 Q ss_pred CCCCEEEEEEECCCHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 86405368984588678850144897175542545687568873362136856677215664156344883567578853 Q gi|254780142|r 14 DDRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRMKYKGIICEKCGVEV 93 (1398) Q Consensus 14 ~~~~i~~i~f~l~spe~I~~~S~~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~Cg~~~~~~~~g~~C~~Cg~~~ 93 (1398) ..|+|++|||||||||+||+||+|||++||||||+++||++|||||||||||++||||+|||||+++|+|.+|+|||+++ T Consensus 2 ~~k~i~~i~f~l~SPe~Ir~~S~~eV~~peT~n~~~~kP~~~GL~d~rifgp~~d~eC~cgk~k~~~~~g~~C~tCG~~~ 81 (1284) T PRK00566 2 SQKGIKSLTISIASPEQILNWSKGEVTKPETINYKSLKPEPNGLFDEAIFGPVKDYECACGKYKKIKHRGKICERCGVEI 81 (1284) T ss_pred CCCEECEEEEEECCHHHHHHHHCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCCCCCC T ss_conf 97630549999429999987605587277740088998789997477346978676342676254455985899999874 Q ss_pred CCCCCCCCCCCCCCCCCCCEEECHHHHH--HHHHHHHHCCCHHHHHHHHHHCCEEEECCCCCCHHHHCCCCHHH------ Q ss_conf 0477578767720027762201301225--78999980999656301332111232178865104322369999------ Q gi|254780142|r 94 TLSSVRRDRMAHIDLASPVAHPWFLKSL--PSRISTLLGMSLRDVERVLYFESYVVVDPGLSSLEKYQILTEEE------ 165 (1398) Q Consensus 94 ~~~~~r~ghfGhIeLa~PV~Hi~f~k~~--~~~i~~~l~~~~~~~~~v~y~~~~~~~~~~~~~~~~~~~~~~~~------ 165 (1398) ++|.||||||||||||+|||||||+|++ ||+|+.+|++++++|++|+||++|++.+++...+.+...+...+ T Consensus 82 ~~~~vr~ghfGHIeLa~PV~Higf~k~i~~ps~i~~lL~~~~k~le~v~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~ 161 (1284) T PRK00566 82 TESIVRRERMGHIELAAPVAHIWMTKELPSPSKISLVLDISYKEVEQVVYFVNYIVLDEGNNKYDKKSIFNFKEVLDLTS 161 (1284) T ss_pred CCCCCCCCCCCCCCCCCCEEECCEECCCCCHHHHHHHHCCCHHHHHHHHHCCCEEEECCCCCCCCHHCHHHHHHHHHHHH T ss_conf 50786899612513888645274635888725899986889999876640025799547876550002156899986540 Q ss_pred ---------------------------------HHHH------HHH----C----------CCCCEEECCCHHHHHHHHH Q ss_conf ---------------------------------9886------763----5----------8555061155267788877 Q gi|254780142|r 166 ---------------------------------YVEA------VSQ----F----------GQDQFIAMMGADAIYELLI 192 (1398) Q Consensus 166 ---------------------------------~~~~------~~~----~----------~~~~~~~~~g~~~i~~~l~ 192 (1398) +... ... + ....+...+|+++++++|. T Consensus 162 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~e~i~~~l~ 241 (1284) T PRK00566 162 PKGSIRTRNKLRRTLRNIQERIEKELSHEQDFDYRLAVTYYQMLKDSNLPFSVKDVFNFIEKHTGVRFGIGAEAILELLE 241 (1284) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCCCCCHHHHHHHHH T ss_conf 22013578999999999888766530231156665556676543002466422456654430145213777899999987 Q ss_pred HCCHHHHHHHHHHHHHCC--CCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCCEEEECCCCCCCHHHHHH Q ss_conf 267488999999873103--220347886447788866663489851128630450762235138846973131003789 Q gi|254780142|r 193 ALDLQNLALTLRDQLSKS--SSIFRRKKIIKRLKIVDSFITSGNNPGWMIIRKLPVLPPDLRPLVALDFGRFAASDLNDL 270 (1398) Q Consensus 193 ~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~f~~~~~~Pewmil~~lpV~P~~~RP~v~~~~g~~~~dDlt~~ 270 (1398) .+|++.+...++.++... .+.+++.++++|++++++|.++++|||||||||||||||++||||+||||+|+||||||| T Consensus 242 ~idl~~~~~~~~~~~~~~~~~~~~~~~~~~krl~~~~~~~~~~~rPewmiltvlpVpPp~vRPsv~ldgg~~~~dDLt~~ 321 (1284) T PRK00566 242 KIDLEEEHEKINQALRKSDNAEDQKTKRLLRRLETIRWIKDSGSKPEWMILTRIPVTPPDTRPIIQLDGGRFTTSDINNF 321 (1284) T ss_pred CCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCEEEEEECCCCCCCCCCHHH T ss_conf 69989999999999742676367899999988999997762699971689842478999873459968997664321889 Q ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCEEECCCCCCCC Q ss_conf 99999986999999873983567776999999988887427767877247876506789986102378200034651004 Q gi|254780142|r 271 YRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVD 350 (1398) Q Consensus 271 ~~~Ii~~N~~Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~~~~~~~~~~rp~ks~~~rlkgK~GrfR~nl~GKRVd 350 (1398) |++||++|+|||++++.|||++|++|+|+||||||+|||||+.++.|++++++||||||+|||||||||||||||||||| T Consensus 322 l~~Ii~~N~~Lk~~~~~gap~~ii~~~~~lLQ~~V~tl~dN~~~~~p~~~~s~RplKsl~qrLKGKeGRfR~NLmGKRVD 401 (1284) T PRK00566 322 YRKIIIRNERLKRIQETDAPSILLNNEKRLLQEAVDALFDNNSRKKPVLGKDKRPLKSLSDHLKGKQGLFRQNLLGKRVD 401 (1284) T ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCC T ss_conf 99999999999999875998899999999999999998707787887758899834019988466554013566766205 Q ss_pred CCCCEEEECCCCCCCCCEECHHHHHHHHHHHHHHHH----HHHCC-----CCCCCCCCCCEEECCCCCEEHHHHHHHCCC Q ss_conf 577403412554354620034898776128999999----99879-----866630001001224882501326665697 Q gi|254780142|r 351 YSGRSVIVAGPELQLHQCGLPKLMALELFKPFLYAQ----LEKKG-----YVSTVKQAKKFVEKERPEVWDVLAEVVHQH 421 (1398) Q Consensus 351 fs~RsVI~pdP~l~~~evgvP~~~A~~L~~P~~~~~----L~~~g-----~~~~i~~~k~~i~~~~~~v~~v~rhl~~gd 421 (1398) |||||||||||||++||||||+.||++||+||++++ ++.|| .+.+++.+++++.+.++.+|+|++|++++| T Consensus 402 fSaRSVIspDPnL~i~EvGVP~~~A~~Lt~P~~V~ell~~~v~nGp~~~p~a~~ik~~~~~~~~~~~~~~~i~e~~i~~~ 481 (1284) T PRK00566 402 YSGRSVIVVGPELKMYEVGIPALMILKLFKPFIIHELIRKFDENGNEIQPIAANIKLAEQMILNQDDEIWPIVEKVIKQR 481 (1284) T ss_pred CCCCEEEECCCCCCHHHCCCHHHHHHHCCCCEEHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHCCC T ss_conf 67870562699765111277088887708847799999987406986675302357778998733741457799875388 Q ss_pred EEEECCCCCCEECCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCCE Q ss_conf 89975763101114012358994495479731225454678775456997468999999999987675054237887820 Q gi|254780142|r 422 VVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPASGAPV 501 (1398) Q Consensus 422 ~Vl~NRqPsLHr~Simah~~~v~~~~t~rln~~vc~pyNADFDGDEMnlHvPqs~eAraEa~~Lm~~~~niisP~~g~Pi 501 (1398) +|||||||||||||||||||||+||+|||||||||+||||||||||||||||||+||||||++||++++||+||++|+|+ T Consensus 482 ~VLfNRQPSLHkmSiMahrvkv~~gkTfRLn~~vc~pYNADFDGDEMNlHvPQS~eArAEa~~Lm~v~~nilsP~~G~Pi 561 (1284) T PRK00566 482 PVLLNRAPTLHRLGIQAFEPKIVDGKAIRLHPLVTTAFNADFDGDQMAVHVPLSKEAVAEARAILLASWHILGPKDGKPI 561 (1284) T ss_pred EEEECCCCCCCCCEEEEEEEEEECCCEEEECCCCCCCCCCCCCCCEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCE T ss_conf 14653776212043213577983684477334456655578887424521668999999999986244157137899953 Q ss_pred EEEHHHHHHHHHHHHCCCCCCCCCCCEECCHHHHHHHHHCCCCCCCCEEEEEECCCCCCCCCCCEEECCCCCCCCCCEEE Q ss_conf 44025899999987336788744681417999999999888986785236520464566761424521797751122055 Q gi|254780142|r 502 TVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENKIVTLHSKIRGRYKSVDKDGNSISKIYDTTPGRMIIGEIL 581 (1398) Q Consensus 502 ~~~~QD~i~G~y~lT~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~a~i~~~~~~~~~~~~~~~~~~~tt~Gr~~~~~il 581 (1398) +|++||+|+|+|+||.++.+..++++.|.+..++..+|..+.+.+|+++..+................||+||++||.++ T Consensus 562 ig~iQD~i~G~y~LT~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~i~~~~~~~p~~~~~~~~~~~tt~Gk~ifs~~l 641 (1284) T PRK00566 562 ITPTQDMVLGNYYLTTEKFPQPGEGMIFSTVDEAIRAYELKKVHIHAIIGISTKAFPNKTFSKQGILITTVGKIIFNDVL 641 (1284) T ss_pred EECCHHHHHCCHHHCCCCCCCCCCCEEECCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCHHHHHHHC T ss_conf 40323354212211014467766532726899999998739842375123131337777656774498454331198765 Q ss_pred ECCCCCE----------------------EE----EECCHHCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 4587510----------------------17----751100201366699999998081789998755889999999853 Q gi|254780142|r 582 PRHHEIS----------------------FD----ICNQEMIKKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSS 635 (1398) Q Consensus 582 p~~~~~~----------------------~~----~~~~~~~k~~~~~li~~i~~~~G~~~~~~~l~~~~~l~~~~l~~~ 635 (1398) |.+..+. .+ .+.+.+.|+.+++|+|.+|++||++.++.|||++++++++|++.+ T Consensus 642 p~~~~~~~~~~~~~~~~~~~ii~~~~~~~~~i~~~~~~~~~~kk~~~~li~~l~~~~g~~~~~~~ld~i~~l~~~~~~~~ 721 (1284) T PRK00566 642 PENFPYINDGKNLYGLNQFEIVGMGEDIRDYLKAYNLKEPFTKKTLSKVIDYLYKVSEIEVVPQTMDKIKALGFKYSTIS 721 (1284) T ss_pred CCCCCCCCCCCCCCCCCCCEEEECCCCEEEEEEEEEEECCCCCCHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHC T ss_conf 89988655764334588753872698337888520650454642299999999998389999999999999999999756 Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC Q ss_conf 98613212326836999999999789999998864897667888788642346589999999999876115654322224 Q gi|254780142|r 636 GISFGKDDIIVPESKEKIIAEADKMVKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKK 715 (1398) Q Consensus 636 GfSigi~D~~~~~~k~~~i~~a~~~~~~~~~~~~~G~~t~~e~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 715 (1398) |||+|++|+..+++|.++++++++++.++.+.|++|.+++++++++++++|+.+++++.+++.+.+.. ..++ T Consensus 722 g~sigi~Di~~~~~k~~~i~~a~~~v~~~~~~~~~g~lt~~e~~~~v~~~l~~~~~~v~~~~~~~~~~--------~~~~ 793 (1284) T PRK00566 722 ATTISAFDIPSYDNKQEYFKETDELVAKLKEFYLKGLLTDDERYTKVVQAWSQVKDKVSHDIEKLINS--------PEYK 793 (1284) T ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC--------CCCC T ss_conf 87511134567257899999999999999999864688530789999999999999999999998730--------3256 Q ss_pred CCCEEEEECCCCCCCHHHEEEEEEECCCCCCCCC-----------CCCCCCCCCHHHCCCCHHHHHHCCCCCCHHHHCCC Q ss_conf 6883764225555784241120010000246443-----------44456663011108889897640576103221012 Q gi|254780142|r 716 MNSIFMMSHSGARGSIHQMRQLGGMRGLIAKPSG-----------EIIESPIRSHFKGGLCGFEFFQSCVGGRKGLLDVV 784 (1398) Q Consensus 716 ~N~~~~M~~SGAKGS~~qi~ql~Gqq~l~gkp~G-----------~~~~~PV~~sF~~GL~p~EfFfhamgGReGLiDTA 784 (1398) +|++++|+.||||||+.||+||+||||++++++| ..++.||.|||++||+|+||||||||||||||||| T Consensus 794 ~N~~~iM~~SGAKGS~~NisQm~G~~G~~~~~~~~~~~~~~~~~~~~~e~pV~nsF~~GLtP~EfFFHaMgGREGLIDTA 873 (1284) T PRK00566 794 DNSIVIMADSGARGNISNFTQLFGMRGLMSKSYNYDQKNNSKVIKDTIEVPIKHSFIEGLTVSEYFNSSYGARKGMTDTA 873 (1284) T ss_pred CCCEEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCHHHHHHCCCCCCCCHHHCC T ss_conf 77368986167766899999987423651467787667777766665550000110249973664220654233014410 Q ss_pred CCCCCCCEEEEHHHHHHCCCEEEEECCCCCCCCEEEEEEEC--CEEEEEECCCCCCCCCHHHCCCCCCCCEEEECCCCCC Q ss_conf 10156740110154230143277513887666512111008--8488650001012211442017789718851786578 Q gi|254780142|r 785 MRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDS--GQVVYSLGSRVLGRTALDDIINPLTNECIVKAGQLIL 862 (1398) Q Consensus 785 vKTA~SGYlqRrLvk~~eDl~V~~~D~~t~~g~~~~~~~~~--~~~~~~l~~~~~~r~~~~di~~~~~~~~i~~~~~~i~ 862 (1398) ||||+||||||||||+|||++|+++||++.+|..++.+.++ +..++++.+++++|+.+.++++|.+++.+++.+++++ T Consensus 874 VKTAeSGYlQRRLVKalEDl~V~ydd~~t~~g~~v~~~~~~~d~~~ie~l~~~~~~r~~~~~i~~~~~~~~~~~~~~~i~ 953 (1284) T PRK00566 874 MKTAKSGYMTRKLVDATQEVIINDDDCGTKKGIIVEEIRNTKDNSSIESLKDRIVNRYSINPIYDPKTKKLIVEADKLIT 953 (1284) T ss_pred HHCCCCCCCHHHHHHHHCCEEEEECCCCCCCCEEEEEEEECCCCCEEEEHHHHHHCCEEHHHHCCCCCCEEEECCCCCCC T ss_conf 22000146287888764647987314777788189998866997520123544415052445168566706520454002 Q ss_pred HHHHHHHHHCCCCEEECCCCCCHHHHHCCCHHHHHHHCCCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCC Q ss_conf 99999999759840202331000355186578875420178520001014602111100788987764202454322211 Q gi|254780142|r 863 ESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMD 942 (1398) Q Consensus 863 ~~~~~~i~~~~i~~v~irs~lt~~~~~~v~~~cy~~~l~~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~ 942 (1398) ++.++.+.++++.++.+||+++|++..++|++|||++|+++++|+||||||+|||||||||||||||||||||||||. T Consensus 954 ~~~~~~i~~~~i~~~~irs~l~~~~~~~~~~kc~g~dl~~~~lvepGEaVG~IAAQSIGEPgTQMTLnTFH~AGVas~-- 1031 (1284) T PRK00566 954 SELANQIQNSGIREVEVRSPLHCESENGVCQKCFGLDLSTNKLVETGTAIGVIAAQSIGEPGTQLTMRTFHTGGVAGE-- 1031 (1284) T ss_pred HHHHHHHHHCCCCEEEECCCHHHHHHHHHHHHHHCHHHHHCCCCCCCCEEEEEECCCCCCCCCHHHHHHHHHCCCCCC-- T ss_conf 999999998199789853731342154199998566556078677777210000023688622032766543433566-- Q ss_pred CCEEEECCCCEEEEEEEEEEECCCCCEEEEECCCCEEEEECCCCEEEEEECCCHHCCCCCCCCEEECCEEEEECCCCCCE Q ss_conf 22024014876897211346517887789742760466406776000000110000135678553225078621354311 Q gi|254780142|r 943 RSFIESPCDGIVKIKNRNVCRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHTFP 1022 (1398) Q Consensus 943 ~~~iknvTlGVPRlkEi~~~~n~~~~~i~vs~~~~~~i~d~~~~~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp~~~~ 1022 (1398) +|||+||||++||..+.+.+.. ... T Consensus 1032 ----~NVTlGvPRlkEIin~~~pk~~---------------------------------------------------~~~ 1056 (1284) T PRK00566 1032 ----TNITQGFERLKQLFDVIQPKEN---------------------------------------------------EKA 1056 (1284) T ss_pred ----CCCCCCCHHHHHHHHHCCCCCC---------------------------------------------------CCE T ss_conf ----7624675357988872488986---------------------------------------------------644 Q ss_pred EEECCCCEEEEEEECCCCEEHHHHHCCCCCEEEEEEEHHHCCCCCCCCCCEEEECCCCCEEECCCCCCCEEECCCCCEEE Q ss_conf 32024636897531278320012302368602677510110122123853477427782532247884202137784454 Q gi|254780142|r 1023 IITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENGVVLKSARGTDARWFLPVDALLS 1102 (1398) Q Consensus 1023 i~~e~~~~v~~~~~~~~~~~~~~~~~~t~~~~~~~i~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~ 1102 (1398) ++.+..+. T Consensus 1057 ~i~~v~g~------------------------------------------------------------------------ 1064 (1284) T PRK00566 1057 VISEVKGT------------------------------------------------------------------------ 1064 (1284) T ss_pred EEEECCEE------------------------------------------------------------------------ T ss_conf 66752729------------------------------------------------------------------------ Q ss_pred ECCCCCCCCCCEEEECHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCEECCCCCEEEEEEECCC-CEEEEEEECCCCCCEE Q ss_conf 136761354842221013202455433677328898875251111011134786786331279-4499998368984026 Q gi|254780142|r 1103 VSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFEARRPKNHAILAEISGTIRIKRNYKN-KSRVVIEPFEDGVEPA 1181 (1398) Q Consensus 1103 v~~~~~v~~~d~l~~~~~~~~k~~DIt~GLPrV~eLFEar~pk~~aiisei~Giv~i~~~~~~-k~~~vi~~~~~g~~~~ 1181 (1398) +.......+ ....++. ..+..+.. T Consensus 1065 ------------------------------------------------------i~~i~~~~~~~~~~~v~-~~~~~~~~ 1089 (1284) T PRK00566 1065 ------------------------------------------------------VESITKDSNANGYNVVI-IKNKDNEV 1089 (1284) T ss_pred ------------------------------------------------------EEEEEECCCCCCEEEEE-ECCCCCEE T ss_conf ------------------------------------------------------99999705887248999-56997179 Q ss_pred EEEECCCCEEEEECCCEEECCCEEECCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEE Q ss_conf 89813896589841987740864643899999998752799999999999999999809700612560124762861489 Q gi|254780142|r 1182 EYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEI 1261 (1398) Q Consensus 1182 e~~ip~~~~l~v~dgd~V~~gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I 1261 (1398) +|.+|....+.+.+|+.|..|+.+++|++++++++++.|++++++++++|+|+||+.||+.||+||++++++||+.+..| T Consensus 1090 ~~~i~~~~~l~v~~~d~v~~g~~lt~g~i~~~~ll~v~Gi~~~~~~~i~evq~Vy~~qGv~i~dk~ievi~rqm~~~~~i 1169 (1284) T PRK00566 1090 NYPTPFNAVLRVKTGDEVIPGSKITEGSIDVKDLLKVAGIENVRQYIIKEVQKVYRMQGIEIADKYIEVIIRQLTNKLQI 1169 (1284) T ss_pred EEECCCCCEEEECCCCEEECCCCCCCCCCCHHHHHHCCCHHHHHHHHHHHHHHHHHHCCEEEECCEEEHHHHHHCCEEEE T ss_conf 99746787788636998946986458999989987556999999999999999988448656256635267664246599 Q ss_pred ECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHCCCEECCCC Q ss_conf 41886454566410699999999999972898752012100001453023107765040258999999745285523665 Q gi|254780142|r 1262 TDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDG 1341 (1398) Q Consensus 1262 ~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~G 1341 (1398) +++|||.++.|+.|++.++..+|+.++..|+.|+.+.+.++||||++++|+||||+||||||++||+|||++|++|+|+| T Consensus 1170 ~~~gd~~~~~g~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~GIt~~~~~~~S~L~~ASFeeT~~vL~dAA~~g~~D~l~G 1249 (1284) T PRK00566 1170 TDPGDSGLFVGQTISINEFTEVNQSMLLNKKKPPSAINQVFGLDEAPSKSGSFLSAASFQDTKKILTDAAVKSQKDYLIG 1249 (1284) T ss_pred EECCCCCCCCCCEEEHHHHHHHHHHHHHCCCCCCEEECHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCC T ss_conf 95798664575375399999999999977998823221103623033554329998311316689999998479885778 Q ss_pred CCEEEECCCCCCCCCCHHHHHHHHHHCCC Q ss_conf 32215507305655354665331210251 Q gi|254780142|r 1342 FKENVIVGRSIPAGTGAILHEKRRVAMNR 1370 (1398) Q Consensus 1342 vSENIIlGqliP~GTG~f~~~~~~~~~~~ 1370 (1398) |||||||||+||+|||+|.|+++.+...+ T Consensus 1250 vsEnII~G~~iP~GTG~~~~~~~~~~~~~ 1278 (1284) T PRK00566 1250 LKENVILGNLIPAGTGFKDVEEVIAYGEE 1278 (1284) T ss_pred CCHHHCCCCCCCCCCCCCHHHEEEECCHH T ss_conf 00353038976877687413216864587 No 8 >KOG0260 consensus Probab=100.00 E-value=0 Score=2101.98 Aligned_cols=1211 Identities=25% Similarity=0.320 Sum_probs=888.6 Q ss_pred CCCCCCCCEEEEEEECCCHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 35678640536898458867885014489717554254568756887336213685667721566415634488356757 Q gi|254780142|r 10 NPWTDDRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRMKYKGIICEKC 89 (1398) Q Consensus 10 ~~~~~~~~i~~i~f~l~spe~I~~~S~~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~Cg~~~~~~~~g~~C~~C 89 (1398) ..+++.+.+++|||||+||+|||+|||.||++|||+ +.++|..|||+|+|+|.+++++ +|+|| T Consensus 7 ~~~~pl~~v~~vqFgi~spdeir~mSV~~i~~~e~~--e~~~pk~ggl~D~RlG~idr~~---------------~CqTC 69 (1605) T KOG0260 7 FSQAPLRTVKSVQFGILSPDEIRRMSVAEIEFPETM--EGGRPKLGGLMDPRLGTIDRDS---------------LCQTC 69 (1605) T ss_pred CCCCCCEEEEEEEEECCCHHHHHCCEEEEEECCCCC--CCCCCCCCCCCCCCCCCCCCCC---------------HHHHH T ss_conf 323742145688750468566420224775334201--3677776774663347777641---------------10433 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCEEECHHHH---HHHHHHHHHCCCHHHHHHHHHHCCEEEEC-CCCCCHHHHCCCCHHH Q ss_conf 8853047757876772002776220130122---57899998099965630133211123217-8865104322369999 Q gi|254780142|r 90 GVEVTLSSVRRDRMAHIDLASPVAHPWFLKS---LPSRISTLLGMSLRDVERVLYFESYVVVD-PGLSSLEKYQILTEEE 165 (1398) Q Consensus 90 g~~~~~~~~r~ghfGhIeLa~PV~Hi~f~k~---~~~~i~~~l~~~~~~~~~v~y~~~~~~~~-~~~~~~~~~~~~~~~~ 165 (1398) |.++++|| |||||||||+||||+||++. +++|+|.-|++.+++-.++...+....++ ++.....++.+++.+. T Consensus 70 ~g~~~~Cp---GHFGhieLAkPvfH~gFl~kv~kiL~cVC~~C~ki~~~~~~~~~~~~~~~~~~~k~rl~~v~~vck~k~ 146 (1605) T KOG0260 70 GGNMFECP---GHFGHIELAKPVFHPGFLKKVKKILRCVCFYCSKILKDKFNPKEDQILRKRYCSKGRLLMVLDVCKGKV 146 (1605) T ss_pred CCCCCCCC---CCCCEEEECCCCCCHHHHHHHHHHHHHHHHCCHHEEECCCCCCHHHHHHHHCCCCCHHHHHHHHHCCCE T ss_conf 35533278---655526504432238999999999988510102302044683044556640487413899987633310 Q ss_pred HHHHHHHCCCCCEEECCCHHHHHHHHHHCCHHHHHHHHHHHHHC------CCCCHHHHHHHHHH----HHHHHHHHCCCC Q ss_conf 98867635855506115526778887726748899999987310------32203478864477----888666634898 Q gi|254780142|r 166 YVEAVSQFGQDQFIAMMGADAIYELLIALDLQNLALTLRDQLSK------SSSIFRRKKIIKRL----KIVDSFITSGNN 235 (1398) Q Consensus 166 ~~~~~~~~~~~~~~~~~g~~~i~~~l~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~----~~~~~f~~~~~~ 235 (1398) .|+-......+ .-|++..++.....+..+....|+..-.. ..+..+...+++++ ....+|.+...| T Consensus 147 ~ce~g~~~e~~----g~sgcg~kqP~i~r~gl~l~a~~k~~~e~~~e~k~~ls~e~V~~i~k~Isded~~~lg~~~~~ar 222 (1605) T KOG0260 147 VCEGGIDVESD----GRSGCGLKQPSIRRLGLDLWAFWKQGDEDSQESKRKLSAERVLEIFKRISDEDIDQLGFKPKIAR 222 (1605) T ss_pred EEECCCCCCCC----CCCCCCCCCCCEECCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHCHHHHHHHCCCCCCCC T ss_conf 44045201456----65543446872342574054432115766771002475999999998613445666357877688 Q ss_pred CCEEEEEECCCCCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCC Q ss_conf 51128630450762235138846973131003789999999869999998739835677769999999888874277678 Q gi|254780142|r 236 PGWMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHK 315 (1398) Q Consensus 236 Pewmil~~lpV~P~~~RP~v~~~~g~~~~dDlt~~~~~Ii~~N~~Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~~ 315 (1398) |||||||+||||||.+||+|.+++..+++|||||++.|||+.|+.|++.++.|||.|++.+..+|||+||++|+||..+| T Consensus 223 pewmIlTvLPVPP~~vrP~iv~~~s~rg~DdlthkLadIiK~n~~l~r~e~~ga~~H~i~e~~~LlqfhVat~~Dn~~pg 302 (1605) T KOG0260 223 PEWMILTVLPVPPPAVRPEIVMQGSARGEDDLTHKLADIIKKNIGLKRNEENGAPAHIIEEYEQLLQFHVATYVDNDIPG 302 (1605) T ss_pred CCEEEEEEECCCCCCCCCEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHEECCCCCC T ss_conf 76258888437987666504532543576333789999999878875323228704668887767640131101466667 Q ss_pred CCC-CCCCCCHHHHHHHHHCCCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCEECHHHHHHHHHHH-----HHHHHH-- Q ss_conf 772-478765067899861023782000346510045774034125543546200348987761289-----999999-- Q gi|254780142|r 316 RVV-TGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKP-----FLYAQL-- 387 (1398) Q Consensus 316 ~~~-~~~~~rp~ks~~~rlkgK~GrfR~nl~GKRVdfs~RsVI~pdP~l~~~evgvP~~~A~~L~~P-----~~~~~L-- 387 (1398) .|. .++++||+||+++||||||||+|+|||||||||||||||||||||++||||||++||+.|||| ||+.+| T Consensus 303 qp~a~qksGrplkSi~arlKgkegriRgnLmGKRvDFSaRTVItgDPnl~ldevGVP~sIAk~lTfpE~Vtp~NidrLqe 382 (1605) T KOG0260 303 QPQADQKSGRPLKSISARLKGKEGRIRGNLMGKRVDFSARTVITGDPNLSLDEVGVPRSIAKRLTFPEHVTPFNIDRLQE 382 (1605) T ss_pred CCCCCCCCCCCCCCHHHHHCCCCCHHHHCCCCCCCCCCEEEEECCCCCCCHHCCCCCHHHHHHCCCCCEECCCCHHHHHH T ss_conf 75000236985200565521421022321002345764025664899865010368699996466743015203899999 Q ss_pred -HHCCCCCCCCCCCCEEEC-----------------CCCCEEHHHHHHHCCCEEEECCCCCCEECCEEEEEEEEECCCEE Q ss_conf -987986663000100122-----------------48825013266656978997576310111401235899449547 Q gi|254780142|r 388 -EKKGYVSTVKQAKKFVEK-----------------ERPEVWDVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAI 449 (1398) Q Consensus 388 -~~~g~~~~i~~~k~~i~~-----------------~~~~v~~v~rhl~~gd~Vl~NRqPsLHr~Simah~~~v~~~~t~ 449 (1398) +.+|...+ .+.|++.+ ....+|+|+|||+|||+||||||||||||||||||||||||+|| T Consensus 383 LV~~g~~~~--pgakyiird~G~Ridlr~~~~~~d~~Lq~G~kVeRhl~DGD~VlfNRqPSlHKmSmmahrVrVlp~sTf 460 (1605) T KOG0260 383 LVRRGLLEH--PGAKYIIRDNGDRIDLRYHKRAGDIHLQPGYKVERHLMDGDVVLFNRQPSLHKMSMMAHRVRVLPYSTF 460 (1605) T ss_pred HHHCCCCCC--CCCCEEEECCCCEEEEEECCCCCCCCCCCCCEEEEEECCCCEEEECCCCCHHHHHHHHCEEEECCCCEE T ss_conf 850787779--775135514785788863477566546666678886315988997489717776545307897057518 Q ss_pred EEECCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEEHHHHHHHHHHHHCCCCCCCCCCCEE Q ss_conf 97312254546787754569974689999999999876750542378878204402589999998733678874468141 Q gi|254780142|r 450 QLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLF 529 (1398) Q Consensus 450 rln~~vc~pyNADFDGDEMnlHvPqs~eAraEa~~Lm~~~~niisP~~g~Pi~~~~QD~i~G~y~lT~~~~~~~~~~~~f 529 (1398) ||||+||+||||||||||||+|||||+|||||..+|++|++||+|||+|+|+||++||+|+|+|++|.+| +| T Consensus 461 rLNlsvtsPynADFDGDemnlhvPQS~etkAEl~EL~~vpkQiispQsnkpvmgivQDTLta~R~~t~Rd--------~F 532 (1605) T KOG0260 461 RLNLSVTSPYNADFDGDEMNLHVPQSLETKAELEELAMVPKQIISPQSNKPVMGIVQDTLTAVRKMTKRD--------VF 532 (1605) T ss_pred EECEEECCCCCCCCCCCEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEHHHHHHHHHHHHHH--------HH T ss_conf 9670204776578787513012673056789999986223643377689850343256678888876676--------55 Q ss_pred CCHHHHHHHH-----HCCCCC-CCCEEEEEECCCCCCCCCCCEE-----ECC--CC----CCCCC---CEEEECCCCCEE Q ss_conf 7999999999-----888986-7852365204645667614245-----217--97----75112---205545875101 Q gi|254780142|r 530 ADMGEVYHAL-----ENKIVT-LHSKIRGRYKSVDKDGNSISKI-----YDT--TP----GRMII---GEILPRHHEISF 589 (1398) Q Consensus 530 ~~~~~~~~~~-----~~~~~~-~~a~i~~~~~~~~~~~~~~~~~-----~~t--t~----Gr~~~---~~ilp~~~~~~~ 589 (1398) .++.+++..+ |++.++ .|++.|+++.|++++.....-+ ..+ |. +-.++ +.++++++++.. T Consensus 533 l~r~~vmnLlm~~p~~d~~~Pa~pai~Kp~PlWTGkQifsliiP~~in~~r~~s~h~d~~~~~~~p~dt~~lie~g~l~~ 612 (1605) T KOG0260 533 LNRAQVMNLLMYVPDWDGPPPAKPAILKPKPLWTGKQIFSLIIPGGINYIRDHSTHPDSEDELISPGDTRVLIEGGELLI 612 (1605) T ss_pred HCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHEEEECCCCCCEECCCCCCCCCCCCCCCCCCCEEEEECCCEEE T ss_conf 06999997875136657889987556788765213101146547974233134467677764316888469995783378 Q ss_pred EEECCHHCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHH----HHHHHHHHHHHHHHHH Q ss_conf 775110020136669999999808178999875588999999985398613212326836----9999999997899999 Q gi|254780142|r 590 DICNQEMIKKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPES----KEKIIAEADKMVKEYE 665 (1398) Q Consensus 590 ~~~~~~~~k~~~~~li~~i~~~~G~~~~~~~l~~~~~l~~~~l~~~GfSigi~D~~~~~~----k~~~i~~a~~~~~~~~ 665 (1398) |.++|...|++.|+|+|.+|.+.|++.|+.|++.+|+|.+.|+++.|||+||+|.+++.+ +.+.|.+|++.+.+++ T Consensus 613 g~l~Kkt~G~s~g~lvh~i~~e~Gp~~~~~f~~~iQ~lin~wll~~gfsigIgDtiad~~t~~~iq~~I~~ak~dv~~vi 692 (1605) T KOG0260 613 GVLCKKTVGSSAGGLVHVIFLEKGPKIARGFFDSIQTLINSWLLREGFSIGIGDTIADAATMCVIQNTIKEAKRDVLAVI 692 (1605) T ss_pred EEEECCCCCCCCCCEEEEEEHHHCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 77650114554574578753121779999887878999999998627401203212588899999999999899999999 Q ss_pred HHHHCCCC-------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCC---HHHEE Q ss_conf 98864897-------667888788642346589999999999876115654322224688376422555578---42411 Q gi|254780142|r 666 NQYNDGLI-------TRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIFMMSHSGARGS---IHQMR 735 (1398) Q Consensus 666 ~~~~~G~~-------t~~e~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~N~~~~M~~SGAKGS---~~qi~ 735 (1398) ++.+.-.+ ..+.+++++..++++++++++..... .+..+||+..|+.+||||| ++|++ T Consensus 693 ~~a~~~~L~~~pg~tlretfe~~v~~vlndArd~~gssA~~------------sl~esNn~k~Mv~aGSKGs~inisQ~s 760 (1605) T KOG0260 693 REAQNNELEPTPGRTLRETFENKVNRVLNDARDKSGSSAQK------------SLSESNNFKTMVVAGSKGSFINISQVS 760 (1605) T ss_pred HHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH------------HHHHCCCHHHHHHHCCCCCCEEHHHHH T ss_conf 88765004678213578999999999999998865407876------------431020087787513777620054433 Q ss_pred EEEEECCCCCC--CCCCCC----------CCC-----CCCHHHCCCCHHHHHHCCCCCCHHHHCCCCCCCCCCEEEEHHH Q ss_conf 20010000246--443444----------566-----6301110888989764057610322101210156740110154 Q gi|254780142|r 736 QLGGMRGLIAK--PSGEII----------ESP-----IRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLV 798 (1398) Q Consensus 736 ql~Gqq~l~gk--p~G~~~----------~~P-----V~~sF~~GL~p~EfFfhamgGReGLiDTAvKTA~SGYlqRrLv 798 (1398) +|+|||+++|| |+|+.- .+| |+|||++||+|+|||||||||||||||||||||++|||||||| T Consensus 761 aCVGqQnVEgkrIpFGF~~Rtlphf~kDdysPesrGfVENSyL~GLtP~EfFfHamggREglidtavktaEtGyiqRRL~ 840 (1605) T KOG0260 761 ACVGQQNVEGKRIPFGFPKRTLPHFSKDDYSPESRGFVENSYLTGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLM 840 (1605) T ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHCCCCHHHHHHHCCCCCCHHHHHHH T ss_conf 44301000120124577754566656699982104423212025798899999874253011010011466425999999 Q ss_pred HHHCCCEEEEECCCCCCCC--EEEEEE--ECC-------EEEEEEC--CCCCCCCC------------HHHCCCCCC--- Q ss_conf 2301432775138876665--121110--088-------4886500--01012211------------442017789--- Q gi|254780142|r 799 DVAQNCVVNQVDCNTKKGL--TITHIV--DSG-------QVVYSLG--SRVLGRTA------------LDDIINPLT--- 850 (1398) Q Consensus 799 k~~eDl~V~~~D~~t~~g~--~~~~~~--~~~-------~~~~~l~--~~~~~r~~------------~~di~~~~~--- 850 (1398) |+|||++|+ ||+++++++ .+++.+ |+- +..+.++ +..+-+.. .+++++... T Consensus 841 kameDimv~-yDgTVRNs~gqviQf~YGeDG~d~~~vE~q~~~~l~~~~a~f~~~~~~d~ld~~~~~~~~~~~~e~~~~~ 919 (1605) T KOG0260 841 KAMEDIMVA-YDGTVRNSLGQVIQFKYGEDGLDGHPVEFQNGETLGSLNACFESEFAYDALDEPISLSSEEVVNEISELL 919 (1605) T ss_pred HHHHHHHHH-CCCCEECCCCEEEEEEECCCCCCCCEEECCCCCCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH T ss_conf 999988744-3754130456058987226766664010024553440588887543013331755421566766444457 Q ss_pred ----------CC---------EEEECCCC---CCHHHH----HHHHHCCCCEEE------------------------CC Q ss_conf ----------71---------88517865---789999----999975984020------------------------23 Q gi|254780142|r 851 ----------NE---------CIVKAGQL---ILESHV----NEIEKCGIRSVR------------------------IR 880 (1398) Q Consensus 851 ----------~~---------~i~~~~~~---i~~~~~----~~i~~~~i~~v~------------------------ir 880 (1398) .+ .|.+.++- ..+... +.+.++.+...+ .. T Consensus 920 ~l~~lle~e~~~l~~dr~~l~~i~~~g~~k~~lp~n~~r~I~Na~~~f~~~~r~~t~l~~~~v~~g~~~l~e~l~iv~g~ 999 (1605) T KOG0260 920 KLQNLLECEYKKLVRDRRVLLYIFEYGDAKWPLPENLQRIIWNALKKFSIDERKPTDLIPFKVVKGVKELAEKLVIVRGE 999 (1605) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHEEEEEECC T ss_conf 78999988787633114423200245775611413699999977751034433543222456544045430236886074 Q ss_pred CCCCH-------HHHHCCC-----------HHHHHHHC------CCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 31000-------3551865-----------78875420------178520001014602111100788987764202454 Q gi|254780142|r 881 SALTC-------ESSRGVC-----------VLCYGRDL------ARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGG 936 (1398) Q Consensus 881 s~lt~-------~~~~~v~-----------~~cy~~~l------~~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHfAG 936 (1398) ..++. .-+..+| ...|.|-+ ++.+.|+||||||++||||||||+|||||||||+|| T Consensus 1000 ~~~sraqrl~~~lLrs~l~~krv~~e~rls~eaf~w~~~~Ie~~f~qa~a~pgemvg~lAaqsvgePatqmTlntfh~aG 1079 (1605) T KOG0260 1000 DYISRAQRLFNILLRSTLATKRVLEEYRLSSEAFEWVLGEIEARFLQAEASPGEMVGALAAQSVGEPATQMTLNTFHYAG 1079 (1605) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHEEEEECCCCCHHHHHHHHHHCCCHHHCCCCHHCCCC T ss_conf 16788888888998766778988987035578888776434311123413762047688887717715434620001034 Q ss_pred CCCCCCCCEEEECCCCEEEEEE-EEEEECCCCCEEEEECCCCEEEEECCCCEEEEEECCCHHCCCCCCCCEEECCEEEEE Q ss_conf 3222112202401487689721-134651788778974276046640677600000011000013567855322507862 Q gi|254780142|r 937 AVTVMDRSFIESPCDGIVKIKN-RNVCRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISE 1015 (1398) Q Consensus 937 VAS~~~~~~iknvTlGVPRlkE-i~~~~n~~~~~i~vs~~~~~~i~d~~~~~~~~~ki~~~~~~~v~~~~~v~~~~ii~~ 1015 (1398) |++ ||||+||||+|| +|..++.+++.+++++ .....++.+.++.+...++++++.++....+++|+ T Consensus 1080 Vss-------knVt~gvprlkei~Nv~k~~ktpsLtV~l------~g~~~k~~e~ak~v~~~le~ttl~~vt~~t~i~yd 1146 (1605) T KOG0260 1080 VSS-------KNVTLGVPRLKEIINVAKNAKTPSLTVYL------TGEAAKDNEWAKLVQCCLEHTTLKDVTRATEIYYD 1146 (1605) T ss_pred EEE-------EEEECCCCCHHHHHHHHCCCCCCEEEEEE------CCHHHCCHHHHHHHHHHCCCCCHHHHHCCCCCEEC T ss_conf 011-------01321586513441010157996079996------42110165778777651331338765305763026 Q ss_pred CCCCCCEEEECCCCEEEEEEECCCCEEHHHHHCCCCCEEEEEEEHHHCCCCCCCCCCEEEECCCCCEEECCCCCCCEEEC Q ss_conf 13543113202463689753127832001230236860267751011012212385347742778253224788420213 Q gi|254780142|r 1016 WDPHTFPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENGVVLKSARGTDARWFL 1095 (1398) Q Consensus 1016 ~Dp~~~~i~~e~~~~v~~~~~~~~~~~~~~~~~~t~~~~~~~i~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~ 1095 (1398) +||..+.|.++.+..+.++.+.+.... ...+|..+.+.+... + .|+................. T Consensus 1147 pdp~~tvI~ed~e~v~a~~e~pd~D~~-----~ispwlLrlelDr~~-----m-------~dk~ltm~~ia~~i~~~f~~ 1209 (1605) T KOG0260 1147 PDPQSTVIDEDREFVVAYYEMPDEDVG-----RISPWLLRLELDRAS-----M-------TDKKLTMEQIAEKINRGFGS 1209 (1605) T ss_pred CCCCCEEECCCHHHHHHHHCCCCCCHH-----HCCHHHHHHHHHHHH-----C-------CCCCCCHHHHHHHHHHHCCC T ss_conf 887520334665557744407643142-----307688875330655-----0-------36533399999998742068 Q ss_pred CCCCEEEECCCCCCCCCCEEEECHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCEECC--CCCEEEEEEECCCCEEEEEEE Q ss_conf 778445413676135484222101320245543367732889887525111101113--478678633127944999983 Q gi|254780142|r 1096 PVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFEARRPKNHAILAE--ISGTIRIKRNYKNKSRVVIEP 1173 (1398) Q Consensus 1096 ~~~~~~~v~~~~~v~~~d~l~~~~~~~~k~~DIt~GLPrV~eLFEar~pk~~aiise--i~Giv~i~~~~~~k~~~vi~~ 1173 (1398) +...+.+..+.++...+..+++.. ..++|. +..+. .++.+ ..|+.. ..++++.. T Consensus 1210 d~~~i~~ddna~klv~r~ri~~~~---------------e~D~~l-~~Ie~-~ml~~~~l~G~~~-------i~kV~m~~ 1265 (1605) T KOG0260 1210 DLACIFSDDNAEKLVLRLRIAKEE---------------EDDVFL-KCIEA-NMLGDMTLRGIPD-------IFKVYMSP 1265 (1605) T ss_pred CCCEEECCCCCCCEEEEEEECCCC---------------CHHHHH-HHHHH-HHHHHCCCCCCCC-------CCEEEEEE T ss_conf 875054166776227999834764---------------066888-87887-6654143578566-------10699863 Q ss_pred CCCCCCEE-EEEECCCCEEEEECCCEEECCCEEECCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHH Q ss_conf 68984026-89813896589841987740864643899999998752799999999999999999809700612560124 Q gi|254780142|r 1174 FEDGVEPA-EYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVV 1252 (1398) Q Consensus 1174 ~~~g~~~~-e~~ip~~~~l~v~dgd~V~~gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIa 1252 (1398) ..+|.-.. ..++.......+.........|..+..+++.-||++||||||+|.+++.|+..|+.++|.||||||++|+| T Consensus 1266 ~~~G~f~~~~ew~LeTdg~~l~~v~s~~~vD~~rt~sn~l~ei~~vlgIea~r~a~~~e~~~vi~f~gsyVnyrhlaLl~ 1345 (1605) T KOG0260 1266 TEDGEFKPVDEWDLETDGVNLRRVLSEPDVDPARTTSNDLVEIAEVLGIEAVRKALLRELLNVISFDGSYVNYRHLALLC 1345 (1605) T ss_pred CCCCCEEECCEEEEECCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHCHHHHHHHHHHHHHHEEEECCCCHHHHHHHHHH T ss_conf 37786111222688328612776646678885201455333565551479887653564441676245303388899999 Q ss_pred HHHCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHH Q ss_conf 76286148941886454566410699999999999972898752012100001453023107765040258999999745 Q gi|254780142|r 1253 RHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAI 1332 (1398) Q Consensus 1253 D~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi 1332 (1398) |+||++|++| +++||||||.++++++| ||||||+++|++||+ T Consensus 1346 dvmT~~g~lm------~itRhg~nr~~tgaLmr--------------------------------cSfEetv~il~~aa~ 1387 (1605) T KOG0260 1346 DVMTARGHLM------AITRHGINRQDTGALMR--------------------------------CSFEETVDILMDAAA 1387 (1605) T ss_pred HHHHCCCCEE------EEECCCCCHHHCCCCCC--------------------------------CCHHHHHHHHHHHHH T ss_conf 9985102024------55213520430201145--------------------------------438777788987776 Q ss_pred CCCEECCCCCCEEEECCCCCCCCCCHH Q ss_conf 285523665322155073056553546 Q gi|254780142|r 1333 AGKVDTLDGFKENVIVGRSIPAGTGAI 1359 (1398) Q Consensus 1333 ~ge~D~L~GvSENIIlGqliP~GTG~f 1359 (1398) +++.|.++|++|||||||++|+|||.| T Consensus 1388 ~~ekd~~rgvsEnImlgqlap~gTg~~ 1414 (1605) T KOG0260 1388 HAEKDPCRGVSENIMLGQLAPMGTGCF 1414 (1605) T ss_pred HHCCCCCCCCEEEEEECCCCCCCCCCE T ss_conf 513377766111356536456777633 No 9 >KOG0261 consensus Probab=100.00 E-value=0 Score=1998.59 Aligned_cols=1176 Identities=25% Similarity=0.334 Sum_probs=844.8 Q ss_pred HHHCCCCCCCCEEEEEEECCCHHHHHHCCEEEEECCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 751356786405368984588678850144897175542545687-5688733621368566772156641563448835 Q gi|254780142|r 7 RFFNPWTDDRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFK-PERDGLFCARIFGPIKDYECICGKYKRMKYKGII 85 (1398) Q Consensus 7 ~~~~~~~~~~~i~~i~f~l~spe~I~~~S~~ev~~~et~n~~~~k-P~~~Gl~d~ri~g~~~d~~c~Cg~~~~~~~~g~~ 85 (1398) +.|....-+++|+.|+||+.||++|++-++.||..-+.|+-.+.+ |..+|++|+|||.+.|+ .. T Consensus 2 k~~~e~~~~kki~~i~F~~~s~~ei~~~a~v~v~~~~LY~~~~~~~P~~~G~LD~rMGvs~K~---------------~~ 66 (1386) T KOG0261 2 KQFREDEIPKKIKHIQFSILSPEEIRQQAEVEVSSKDLYDISTQRAPLPNGPLDPRMGVSNKK---------------DK 66 (1386) T ss_pred CCCCCCCCCCEEEEEEECCCCHHHHHHCCEEEEECCCHHHHHCCCCCCCCCCCCCCCCCCCCC---------------CC T ss_conf 741102244222257623699899974016776415155542144877689867345888777---------------73 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCEEECHHHHHH---HHHHHHHCCCHHHHHHHHHHCCEEEECCCCCCHHHHCCCC Q ss_conf 6757885304775787677200277622013012257---8999980999656301332111232178865104322369 Q gi|254780142|r 86 CEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLP---SRISTLLGMSLRDVERVLYFESYVVVDPGLSSLEKYQILT 162 (1398) Q Consensus 86 C~~Cg~~~~~~~~r~ghfGhIeLa~PV~Hi~f~k~~~---~~i~~~l~~~~~~~~~v~y~~~~~~~~~~~~~~~~~~~~~ 162 (1398) |+|||.++++|+ |||||++|+.|||||||||.+. .|||+.|+..+.+-+.-.+|. ..+++|+..+|.|..++. T Consensus 67 C~TCg~~la~C~---GHfGy~~L~LPVFhiGyfk~ti~iLq~ICK~Cs~ilL~~~~k~~fl-~~lr~p~~~~l~k~~l~k 142 (1386) T KOG0261 67 CATCGEGLADCI---GHFGYLKLALPVFHIGYFKATIQILQCICKNCSSILLSEEDKRQFL-KKLRNPGLDNLRKKALLK 142 (1386) T ss_pred CCHHCCCHHHCC---CCCCEEEECCEEEEEHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHH-HHHHCCCCCHHHHHHHHH T ss_conf 201105644355---4344276424045406599999999999886466556998999999-986278987477889999 Q ss_pred H----HHHHHHHHHCCCCCEEECCCHHHHHHHH------HHCC--HHHHHHHHHHHHHCCC----CCHHHHHHHHHHHHH Q ss_conf 9----9998867635855506115526778887------7267--4889999998731032----203478864477888 Q gi|254780142|r 163 E----EEYVEAVSQFGQDQFIAMMGADAIYELL------IALD--LQNLALTLRDQLSKSS----SIFRRKKIIKRLKIV 226 (1398) Q Consensus 163 ~----~~~~~~~~~~~~~~~~~~~g~~~i~~~l------~~~~--~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~ 226 (1398) . -.....+.+||.-....+-++..++-.. .+.| ...+..+++.-+.... ........++++.++ T Consensus 143 ri~~~CkK~~~C~hCg~~NG~VKK~~~~lkIiHd~~~~~~k~~~~~~~~~~~~~~~~~~n~e~~~~~~~~~~~LnPl~vL 222 (1386) T KOG0261 143 RIVAKCKKVNTCSHCGALNGTVKKAAALLKIIHDRFKLVKKSDPLVTNERGEFKTAISHNKELEGHLSSCCEELNPLVVL 222 (1386) T ss_pred HHHHHHHCCCCCCCCCCCCCEEECCCCCEEEEEEHHHCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCHHHHH T ss_conf 99998652652565677676121135410476332220455661123467888887652720576777787642859999 Q ss_pred HHHHH-------------CCCCCCEEEEEECCCCCCCCCCEEEECC-CCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHH Q ss_conf 66663-------------4898511286304507622351388469-731310037899999998699999987398356 Q gi|254780142|r 227 DSFIT-------------SGNNPGWMIIRKLPVLPPDLRPLVALDF-GRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEI 292 (1398) Q Consensus 227 ~~f~~-------------~~~~Pewmil~~lpV~P~~~RP~v~~~~-g~~~~dDlt~~~~~Ii~~N~~Lk~~~~~~ap~~ 292 (1398) +.|.. ...||+.+|||.+||||.|+||||.+++ ....|||||.++.+||..|.-|++.+..|+|-. T Consensus 223 nLFk~i~~~D~eLLg~~~~~~~P~~Li~t~~~vPP~cIRPSV~~~~k~gtnEDDlT~KltEIi~tn~vik~~~~~g~~~~ 302 (1386) T KOG0261 223 NLFKQIKEDDCELLGMDSEEGRPENLIITRVPVPPVCIRPSVMSEDKAGTNEDDLTMKLTEIILTNDVIKKHLSKGTPIN 302 (1386) T ss_pred HHHHHCCCCCCCEEEECCCCCCCHHEEEEECCCCCCCCCCCEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCH T ss_conf 99862882351403134676981134788335895114540131577777843132423555357789999861599710 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCEECHH Q ss_conf 77769999999888874277678772478765067899861023782000346510045774034125543546200348 Q gi|254780142|r 293 IIRNEKRMLQESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPK 372 (1398) Q Consensus 293 i~~~~~~lLQ~~v~~~~dn~~~~~~~~~~~~rp~ks~~~rlkgK~GrfR~nl~GKRVdfs~RsVI~pdP~l~~~evgvP~ 372 (1398) .+.+.|+.||.+|+.||+.+.+|.+.....++|++++.||||||+||||+||+||||||||||||||||||.+||||||. T Consensus 303 ~imE~Wd~lQl~~AlyINSEl~g~~~~~~p~kp~RGf~QRLKGKqGRFRgNLSGKRVDFSGRTVISPDPNL~IdeVgVP~ 382 (1386) T KOG0261 303 LIMEDWDFLQLQVALYINSELPGIPINMAPKKPTRGFVQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDEVGVPI 382 (1386) T ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCEECCCCCCEEECCCCEEECCCCCCCEEECCCHH T ss_conf 24555677777887764033779999989887418999973266771202346744402485353799985210125118 Q ss_pred HHHHHHHHHHH--------HHHHHHCCCCCCCCCCCCEEE---------------------CCCCCEEHHHHHHHCCCEE Q ss_conf 98776128999--------999998798666300010012---------------------2488250132666569789 Q gi|254780142|r 373 LMALELFKPFL--------YAQLEKKGYVSTVKQAKKFVE---------------------KERPEVWDVLAEVVHQHVV 423 (1398) Q Consensus 373 ~~A~~L~~P~~--------~~~L~~~g~~~~i~~~k~~i~---------------------~~~~~v~~v~rhl~~gd~V 423 (1398) .||+.||||+- +++|+.|| ++++++.+++. ..-+++ |+|||+|||+| T Consensus 383 rvAkiLTfpE~Vt~~Ni~klr~lV~NG--P~vhPGANyv~~r~~~~kr~L~yg~R~kiA~eLk~Gdv--VERHL~DgDvV 458 (1386) T KOG0261 383 RVAKILTFPERVTRANIRKLRQLVRNG--PNVHPGANYVVQRGEGFKRFLKYGNRDKIADELKIGDV--VERHLMDGDVV 458 (1386) T ss_pred HHHHHHCCHHHCCHHHHHHHHHHHHCC--CCCCCCCCHHHHCCCCHHHHHHCCCHHHHHHHHCCCHH--HHHHCCCCCEE T ss_conf 788770536443687799999998429--98898730032256334567634768888876124247--87641468889 Q ss_pred EECCCCCCEECCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCCEEE Q ss_conf 97576310111401235899449547973122545467877545699746899999999998767505423788782044 Q gi|254780142|r 424 LLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPASGAPVTV 503 (1398) Q Consensus 424 l~NRqPsLHr~Simah~~~v~~~~t~rln~~vc~pyNADFDGDEMnlHvPqs~eAraEa~~Lm~~~~niisP~~g~Pi~~ 503 (1398) ||||||||||||||+|++||+||+|||||.|||+|||||||||||||||||++||||||.+||.+.+|+++|++|+|+++ T Consensus 459 LFNRQPSLHkmSIM~H~akV~p~RTfRFNEcvCtPYNADFDGDEMNlHvPQTEEAraEA~~LMgvknNlvTPr~GEpiiA 538 (1386) T KOG0261 459 LFNRQPSLHKMSIMSHRAKVMPWRTFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEALVLMGVKNNLVTPRNGEPIIA 538 (1386) T ss_pred EECCCCHHHHHHHHHHHHHCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCEEE T ss_conf 98478517788888777523667434312210477678888641004688417788999998555456446888981110 Q ss_pred EHHHHHHHHHHHHCCCCCCCCCCCEECCHHHHHH--H-HHCC----CCCCCCEEEEEECCCCCCCCCCC-EE-------E Q ss_conf 0258999999873367887446814179999999--9-9888----98678523652046456676142-45-------2 Q gi|254780142|r 504 PSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYH--A-LENK----IVTLHSKIRGRYKSVDKDGNSIS-KI-------Y 568 (1398) Q Consensus 504 ~~QD~i~G~y~lT~~~~~~~~~~~~f~~~~~~~~--~-~~~~----~~~~~a~i~~~~~~~~~~~~~~~-~~-------~ 568 (1398) ++||+++|.|+||.+| +|+++.++.. + +.++ .+|+||++||...|++++..... ++ . T Consensus 539 AtQDFiTg~YLlt~KD--------tF~dRa~~~ql~s~~~d~~~~i~lppPaI~KP~~LwTGKQ~fsvlirpn~~s~v~~ 610 (1386) T KOG0261 539 ATQDFITGGYLLTHKD--------TFLDRAEFSQLCSYMSDAMTHIDLPPPAILKPVELWTGKQLFSVLIRPNDDSPVRV 610 (1386) T ss_pred HHHHHHHCCEEEECCC--------CCCCHHHHHHHHHHHHCCCCCCCCCCHHHCCCEEEECCCEEEEEEECCCCCCCEEE T ss_conf 3444321200100452--------11469999999999854443427997332374345326777899943689985388 Q ss_pred CCCC---------CCC-----CCCEEEECCCCCEEEEECCHHCCHHH-HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 1797---------751-----12205545875101775110020136-66999999980817899987558899999998 Q gi|254780142|r 569 DTTP---------GRM-----IIGEILPRHHEISFDICNQEMIKKNI-SAMVDTIYRHCGQKSTVAFCDDLMRLGFRYAC 633 (1398) Q Consensus 569 ~tt~---------Gr~-----~~~~ilp~~~~~~~~~~~~~~~k~~~-~~li~~i~~~~G~~~~~~~l~~~~~l~~~~l~ 633 (1398) ...+ ||- -.+.+++++.++..|.+||.+.|... .+|++.+.++||+.+|+..|+++.+++.+|+. T Consensus 611 Nl~~k~k~~~~~~~k~~~mc~nDg~v~irns~l~sG~ldKs~lG~g~k~~lfy~llrDyg~~aAa~am~rlaklc~r~lg 690 (1386) T KOG0261 611 NLDAKNKNFSLVKGKSFEMCPNDGYVIIRNSELISGVLDKSTLGSGKKDSLFYILLRDYGSMAAADAMNRLAKLCARFLG 690 (1386) T ss_pred EECCCCCEEECCCCCCCCCCCCCCEEEEECCHHHHCCCCCCCCCCCCCCCEEEEEHHHCCHHHHHHHHHHHHHHHHHHCC T ss_conf 40456614531468874327887769982452310333400016887463576520220617899999999985132406 Q ss_pred HCCCCCCCCCCCCC----HHHHHHHHHHHHHHHHHHHHHHCCCCC-------HHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 53986132123268----369999999997899999988648976-------6788878864234658999999999987 Q gi|254780142|r 634 SSGISFGKDDIIVP----ESKEKIIAEADKMVKEYENQYNDGLIT-------RGEKYNKVVDLWGKTTDKVTEEMMARIK 702 (1398) Q Consensus 634 ~~GfSigi~D~~~~----~~k~~~i~~a~~~~~~~~~~~~~G~~t-------~~e~~~~i~~~~~~~~~~~~~~~~~~~~ 702 (1398) .+||||||+|+.+. .+|+++++.++.++++.+.+|++|.+. ++..+..+..+++..+|++++.++. T Consensus 691 nrGFSIGi~DVqPg~~L~~~k~~lv~~gY~kc~~~I~e~~kG~L~~qpg~~~eetLEa~I~~~Ls~IRe~~G~~C~~--- 767 (1386) T KOG0261 691 NRGFSIGIDDVQPGEILSQEKEELVNRGYAKCDEKIEEYNKGKLQLQPGCNEEETLEAEILSELSTIREEAGKICIR--- 767 (1386) T ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH--- T ss_conf 66620144777854778887999998678888999998741540248999878879999998999999998889997--- Q ss_pred HHCCCCCCCCCCCCCCEEEEECCCCCCC---HHHEEEEEEECCCCCC--CCCCCCCC----------C-----CCCHHHC Q ss_conf 6115654322224688376422555578---4241120010000246--44344456----------6-----6301110 Q gi|254780142|r 703 RVEFDPETGRQKKMNSIFMMSHSGARGS---IHQMRQLGGMRGLIAK--PSGEIIES----------P-----IRSHFKG 762 (1398) Q Consensus 703 ~~~~~~~~~~~~~~N~~~~M~~SGAKGS---~~qi~ql~Gqq~l~gk--p~G~~~~~----------P-----V~~sF~~ 762 (1398) .+++.|++.+|+.|||||| ++||++|||||.+.|+ |.|+..++ | |.|||++ T Consensus 768 ---------eL~~~NsPliMa~CGSKGS~INiSQMvACVGQQ~ISG~RvPdGf~dRsLPHF~r~Sk~P~aKGFV~NSFyS 838 (1386) T KOG0261 768 ---------ELHPRNSPLIMALCGSKGSKINISQMVACVGQQIISGHRVPDGFEDRSLPHFERHSKTPAAKGFVANSFYS 838 (1386) T ss_pred ---------HCCCCCCHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHCCC T ss_conf ---------45865673799984589886669999998635430587699862013676643458993010211220135 Q ss_pred CCCHHHHHHCCCCCCHHHHCCCCCCCCCCEEEEHHHHHHCCCEEEEECCCCCCC-CEEEEEEECCEEEEEEC-------- Q ss_conf 888989764057610322101210156740110154230143277513887666-51211100884886500-------- Q gi|254780142|r 763 GLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKG-LTITHIVDSGQVVYSLG-------- 833 (1398) Q Consensus 763 GL~p~EfFfhamgGReGLiDTAvKTA~SGYlqRrLvk~~eDl~V~~~D~~t~~g-~~~~~~~~~~~~~~~l~-------- 833 (1398) ||+|.|||||||||||||+|||||||+||||||||||++||+.+. ||++++++ .++..+.++++.+++.. T Consensus 839 GLTptEFfFHtm~GREGLVDTAVKTAETGYMqRRLmK~LEDL~~~-YDgTVR~s~~~vvqF~YG~DglDPa~mEg~~~pv 917 (1386) T KOG0261 839 GLTPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKSLEDLSVQ-YDGTVRNSNGDVVQFTYGGDGLDPAMMEGKDQPV 917 (1386) T ss_pred CCCCHHHHEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HCCCEECCCCCEEEEEECCCCCCHHHHCCCCCCH T ss_conf 788545520002564311566554321116899999999998876-0673322778678985258888856634777860 Q ss_pred --CCCCCCCCHHHCCCCCCCCEEEECCC-------CCCH-------HHHHH--------------HHHC-CC-------- Q ss_conf --01012211442017789718851786-------5789-------99999--------------9975-98-------- Q gi|254780142|r 834 --SRVLGRTALDDIINPLTNECIVKAGQ-------LILE-------SHVNE--------------IEKC-GI-------- 874 (1398) Q Consensus 834 --~~~~~r~~~~di~~~~~~~~i~~~~~-------~i~~-------~~~~~--------------i~~~-~i-------- 874 (1398) +|.+-+. ..+ .|-..+.-....+ .+.. ..+.. +.+. +. T Consensus 918 ~f~r~~~~~--~~~-~~~~~~~~l~~~el~e~~~~~l~~~f~~~~~~F~~~~~~~i~~~~~~~~~~~~~~~d~~~~~~~~ 994 (1386) T KOG0261 918 NFNRVFDHA--KAI-FPHRHDPPLSSEELDETLEEELLRKFTEKGDPFVHELREFIASLSKKIKKLQDKYGDECGPKFCP 994 (1386) T ss_pred HHHHHHHHH--HHC-CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC T ss_conf 289999877--741-78978888898999999999988775540158999999999999998888765135445775674 Q ss_pred CEEECCCCCCHHHHHCCCHHHHHHHCCCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEE Q ss_conf 40202331000355186578875420178520001014602111100788987764202454322211220240148768 Q gi|254780142|r 875 RSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIV 954 (1398) Q Consensus 875 ~~v~irs~lt~~~~~~v~~~cy~~~l~~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVP 954 (1398) ..+.-++.+|++.-..--..| ++-+.++.+|||.+||+|||||||||||||||+|||||||||| |+|+||| T Consensus 995 ~~~~~~~~~t~kql~~f~~~~--~~ky~~a~~EpGTavGAi~aQSIGEPGTQMTLKTFHFAGVASM-------NiTlGVP 1065 (1386) T KOG0261 995 DLLYQISRLTEKQLEKFVERC--LDKYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASM-------NITLGVP 1065 (1386) T ss_pred CCEEEEEECCHHHHHHHHHHH--HHHHHHHHCCCCCHHHHHHCCCCCCCCCEEEEEEEEECCEEEE-------EECCCCC T ss_conf 303000013699999999999--9998765158851343443256899875124330455120211-------1025761 Q ss_pred EEEE-EEEEECCCCCEEEEECCCCEEEEECCCCEEEEEECCCHHCCCCCCCCEEECCEEEEECCCCCCEEEECCCCEEEE Q ss_conf 9721-134651788778974276046640677600000011000013567855322507862135431132024636897 Q gi|254780142|r 955 KIKN-RNVCRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHTFPIITEVSGTVGF 1033 (1398) Q Consensus 955 RlkE-i~~~~n~~~~~i~vs~~~~~~i~d~~~~~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp~~~~i~~e~~~~v~~ 1033 (1398) |+|| ||.++++.+|+|+..+ .+..+...++.++++++.++++++....+.+|-+|.....|..+.... T Consensus 1066 RIkEIINAsk~ISTPIItA~L--------~n~~d~~~Ar~VKgRiEKt~L~dv~~yieeV~~p~~~fl~i~vd~~~I--- 1134 (1386) T KOG0261 1066 RIKEIINASKTISTPIITAEL--------ENPHDERSARVVKGRIEKTTLGDVCSYIEEVYGPDSCFLLIRVDLKRI--- 1134 (1386) T ss_pred HHHHHHHHHCCCCCCCEEEEE--------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECHHHH--- T ss_conf 499997444006754013231--------583257888887643434109889999998727763589999547677--- Q ss_pred EEECCCCEEHHHHHCCCCCEEEEEEEHHHCCCCCCCCCCEEEECCCCCEEECCCCCCCEEECCCCCEEEECCCCCCCCCC Q ss_conf 53127832001230236860267751011012212385347742778253224788420213778445413676135484 Q gi|254780142|r 1034 EDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENGVVLKSARGTDARWFLPVDALLSVSPGQKVSTGD 1113 (1398) Q Consensus 1034 ~~~~~~~~~~~~~~~~t~~~~~~~i~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~v~~~d 1113 (1398) .....+.+.+ .........+...+.+....+... . T Consensus 1135 ---------~~l~L~i~~~---------~I~~sI~~s~~~k~~~~~v~v~~~---------------------------~ 1169 (1386) T KOG0261 1135 ---------SLLQLEITIE---------SIAYSILKSPKRKVKPNDVRVVGE---------------------------T 1169 (1386) T ss_pred ---------HHHHCCCCHH---------HHHHHHHCCCCCCCCCCCEEEECC---------------------------E T ss_conf ---------6662114199---------999998438730258762588433---------------------------4 Q ss_pred EEEECHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCEECCCCCEEEEEEECC-----CC-EEEEEEECCCCCCEEEEEECC Q ss_conf 222101320245543367732889887525111101113478678633127-----94-499998368984026898138 Q gi|254780142|r 1114 VLARLPISSAKTKDITSGLPRVAELFEARRPKNHAILAEISGTIRIKRNYK-----NK-SRVVIEPFEDGVEPAEYFIPK 1187 (1398) Q Consensus 1114 ~l~~~~~~~~k~~DIt~GLPrV~eLFEar~pk~~aiisei~Giv~i~~~~~-----~k-~~~vi~~~~~g~~~~e~~ip~ 1187 (1398) .+.-.+.+..+. +.-|..+..|.....-.+.|++.+.+... .+ .+++++ |..+..++.. T Consensus 1170 ~~~v~~~~~~~~----------S~~~~lq~lk~~L~~Vvv~gip~vnr~vi~~de~~~~y~L~vE----G~gLr~Vm~t- 1234 (1386) T KOG0261 1170 TLRVTPVSDTKS----------SVYYNLQRLKRSLPNVVVKGIPEVNRAVINIDEKRGLYKLLVE----GTGLRAVMNT- 1234 (1386) T ss_pred EEEEEECCCCCC----------HHHHHHHHHHHHCCCEEEECCCCHHHHHEEECCCCCCEEEEEE----CCCHHHHHCC- T ss_conf 689862345652----------0565699997447761896475431455321046874599983----4456877555- Q ss_pred CCEEEEECCCEEECCCEEECCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCC Q ss_conf 96589841987740864643899999998752799999999999999999809700612560124762861489418864 Q gi|254780142|r 1188 NKHFYLQDGDHVEKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADT 1267 (1398) Q Consensus 1188 ~~~l~v~dgd~V~~gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt 1267 (1398) +.| .-.++.+|+..|+.+||||||||..||+||..+|..||++||+|||+||+|+|||||+| T Consensus 1235 ---------~GV---~g~~TtsNnv~Ev~~vLGIEAAR~~II~EI~ytM~~HGmsiD~RHiMLLaDvMTyrGEV------ 1296 (1386) T KOG0261 1235 ---------DGV---KGRRTTSNNVLEVEKVLGIEAARTTIISEIGYTMSNHGMSIDPRHIMLLADVMTYRGEV------ 1296 (1386) T ss_pred ---------CCC---CCCCCCCCCEEEEEHHHCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCEE------ T ss_conf ---------784---55012557358740221458889999999988887258644789999988776304426------ Q ss_pred CCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHHHC--CCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEE Q ss_conf 5456641069999999999997289875201210000145302--31077650402589999997452855236653221 Q gi|254780142|r 1268 EYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQ--TKSFISAASFQETTKVLTEAAIAGKVDTLDGFKEN 1345 (1398) Q Consensus 1268 ~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~~~p~llGITKasl~--t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSEN 1345 (1398) |||||++++ ++|+|++||||+|+||||+||.+|+.|.+.||||+ T Consensus 1297 ----------------------------------lGITRfGl~KM~~SVL~lASFEkT~DhLF~AA~~~k~D~I~GVSEc 1342 (1386) T KOG0261 1297 ----------------------------------LGITRFGLAKMKDSVLMLASFEKTADHLFDAAAYGKKDAIEGVSEC 1342 (1386) T ss_pred ----------------------------------EEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHH T ss_conf ----------------------------------6564120677778899887666556788888873276423560011 Q ss_pred EECCCCCCCCCCHHHH Q ss_conf 5507305655354665 Q gi|254780142|r 1346 VIVGRSIPAGTGAILH 1361 (1398) Q Consensus 1346 IIlGqliP~GTG~f~~ 1361 (1398) ||||.++++|||.|+- T Consensus 1343 IIlG~pm~iGTG~fkl 1358 (1386) T KOG0261 1343 IILGIPMCIGTGIFKL 1358 (1386) T ss_pred EECCCCEECCCCHHHH T ss_conf 1206520204217899 No 10 >TIGR02390 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit A'; InterPro: IPR012758 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanococcus jannaschii contains an intein.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0008270 zinc ion binding, 0006350 transcription. Probab=100.00 E-value=0 Score=1927.40 Aligned_cols=753 Identities=29% Similarity=0.444 Sum_probs=610.6 Q ss_pred CCCEEEEEEECCCHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 64053689845886788501448971755425456875688733621368566772156641563448835675788530 Q gi|254780142|r 15 DRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRMKYKGIICEKCGVEVT 94 (1398) Q Consensus 15 ~~~i~~i~f~l~spe~I~~~S~~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~Cg~~~~~~~~g~~C~~Cg~~~~ 94 (1398) +|+|++|+|||||||+||+||+.+|.+|||||..++ |..|||+|+|||.+. +|..|+|||...- T Consensus 1 ~K~i~~I~FGlLSPe~IRK~Sv~~v~t~d~YD~DG~-PI~~GlmD~rlGVId---------------PGlRC~TCG~~~g 64 (901) T TIGR02390 1 PKKIKSIKFGLLSPEEIRKLSVVEVVTADTYDEDGY-PIEGGLMDPRLGVID---------------PGLRCKTCGGKVG 64 (901) T ss_pred CCCCCCCCCCCCCHHHHHHHCCCEEECCCCCCCCCC-CCCCCCCCCCCCEEC---------------CCCCCCCCCCCCC T ss_conf 973456344668847875314414761743578588-535775777572225---------------7661776778888 Q ss_pred CCCCCCCCCCCCCCCCCCEEECHHHHHHHHHHHHHCCCHHHHHHHHHH--------CCEEEE-----CCCCCCHHHHCCC Q ss_conf 477578767720027762201301225789999809996563013321--------112321-----7886510432236 Q gi|254780142|r 95 LSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRDVERVLYF--------ESYVVV-----DPGLSSLEKYQIL 161 (1398) Q Consensus 95 ~~~~r~ghfGhIeLa~PV~Hi~f~k~~~~~i~~~l~~~~~~~~~v~y~--------~~~~~~-----~~~~~~~~~~~~~ 161 (1398) +|| |||||||||+||+|+||.|. |..+|..+|..|.|++-- ..+... ++...++-...++ T Consensus 65 eCP---GHFGhIELarPV~HVgF~~~----I~~iL~ATCr~CGR~~l~e~~~~~Y~~~~~~~~~~~~~~a~~nfiq~~l~ 137 (901) T TIGR02390 65 ECP---GHFGHIELARPVVHVGFAKE----IYKILRATCRKCGRILLTEEEIEQYLEKINKLKEEGGSLALSNFIQETLI 137 (901) T ss_pred CCC---CCCCEECCCCCEEEECHHHH----HHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHH T ss_conf 687---85661215587043261478----88887610875771144778999999999999734587467888888889 Q ss_pred ----CHHHHHHHHHHCCCCCEEECCCHHHHHHHHHHCCHHHHHHHHH---HHHHCCCCCHHHHHHHHHHHHHHHHHHCCC Q ss_conf ----9999988676358555061155267788877267488999999---873103220347886447788866663489 Q gi|254780142|r 162 ----TEEEYVEAVSQFGQDQFIAMMGADAIYELLIALDLQNLALTLR---DQLSKSSSIFRRKKIIKRLKIVDSFITSGN 234 (1398) Q Consensus 162 ----~~~~~~~~~~~~~~~~~~~~~g~~~i~~~l~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~ 234 (1398) .+......|++||..++..+.- ++..-. +....-+ .+|....--++..||-..+-.+.|+++..+ T Consensus 138 ~~i~k~A~k~~~CPhCg~~q~~ik~e-----KP~~f~---e~~~~G~eeW~KLTP~eiRErLEkiPdeD~~llG~~Pk~a 209 (901) T TIGR02390 138 EKIVKEAAKRMKCPHCGEEQKKIKFE-----KPTYFY---EEDKEGKEEWVKLTPSEIRERLEKIPDEDLELLGINPKVA 209 (901) T ss_pred HHHHHHHHHCCCCCCCCCCCCCEEEE-----CCEEEE---ECCCCCCCCCEECCCHHHHHHHHCCCHHHHHHCCCCCCCC T ss_conf 99999986178798887412432452-----771577---5575555121442817999975168742444106678878 Q ss_pred CCCEEEEEECCCCCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCC Q ss_conf 85112863045076223513884697313100378999999986999999873983567776999999988887427767 Q gi|254780142|r 235 NPGWMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRH 314 (1398) Q Consensus 235 ~Pewmil~~lpV~P~~~RP~v~~~~g~~~~dDlt~~~~~Ii~~N~~Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~ 314 (1398) ||||||||||||||++|||||+|++|.|+||||||||.|||+.|+|||+.++.|||+.||.|.|+||||||+|||||+.| T Consensus 210 RPEWmvLTVLpVPPvtVRPSItLEtG~RSEDDLTHKLVDIiRiN~RL~e~~~~GAP~lIiEdLWeLLQYHV~TYFDNe~P 289 (901) T TIGR02390 210 RPEWMVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVATYFDNELP 289 (901) T ss_pred CCHHEEEECCCCCCCCCCCCEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCC T ss_conf 73010001047811854764100366752124677899998650799999753787304665578889987674314786 Q ss_pred CCCC-CCCCCCHHHHHHHHHCCCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCEECHHHHHHHHHHH-----HH---HH Q ss_conf 8772-478765067899861023782000346510045774034125543546200348987761289-----99---99 Q gi|254780142|r 315 KRVV-TGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKP-----FL---YA 385 (1398) Q Consensus 315 ~~~~-~~~~~rp~ks~~~rlkgK~GrfR~nl~GKRVdfs~RsVI~pdP~l~~~evgvP~~~A~~L~~P-----~~---~~ 385 (1398) |.|. +++||||||+|+|||||||||||+||+||||||||||||||||||++||||||..||++||+| || ++ T Consensus 290 GiPpArHRSGRPLKTLaQRLKGKEGRfR~NLSGKRVNFSARTVISPDP~iSINEVGVP~~IAk~LTvP~~VT~~Nid~~R 369 (901) T TIGR02390 290 GIPPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNISINEVGVPEEIAKELTVPERVTPWNIDELR 369 (901) T ss_pred CCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCEECCCCEECCHHHHHHH T ss_conf 46866668884034576332043554145546650042116100688854546566884770562326236804489999 Q ss_pred HHHHCCCCCCCCC-------CCCEEECC----C-----------------------CCEEHHHHHHHCCCEEEECCCCCC Q ss_conf 9998798666300-------01001224----8-----------------------825013266656978997576310 Q gi|254780142|r 386 QLEKKGYVSTVKQ-------AKKFVEKE----R-----------------------PEVWDVLAEVVHQHVVLLNRAPSL 431 (1398) Q Consensus 386 ~L~~~g~~~~i~~-------~k~~i~~~----~-----------------------~~v~~v~rhl~~gd~Vl~NRqPsL 431 (1398) ++|.|| ...+. +..||-+. + ..+|-|||||+|||+||||||||| T Consensus 370 ~yv~NG--pd~~PqfGryvtGANYVi~p~rt~dGReeeyriki~~~~Dk~~laE~L~pGw~VERHL~dGDiVLFNRQPSL 447 (901) T TIGR02390 370 EYVLNG--PDSWPQFGRYVTGANYVIRPSRTPDGREEEYRIKIRDVNDKEELAERLEPGWVVERHLIDGDIVLFNRQPSL 447 (901) T ss_pred HHHHCC--CCCCCCCCCEEEEEEEEEECCCCCCCCCCCCEEEECCCCCHHHHHHCCCCCCEEEEEECCCCEEEECCCCCH T ss_conf 996377--888764466641033366046688886544305522445378997407999789987126888766588642 Q ss_pred EECCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEEHHHHHHH Q ss_conf 11140123589944954797312254546787754569974689999999999876750542378878204402589999 Q gi|254780142|r 432 HRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPASGAPVTVPSQDMVLG 511 (1398) Q Consensus 432 Hr~Simah~~~v~~~~t~rln~~vc~pyNADFDGDEMnlHvPqs~eAraEa~~Lm~~~~niisP~~g~Pi~~~~QD~i~G 511 (1398) ||||||||+||||||||||||||||+|||||||||||||||||+|||||||+.||+|.+||+||+.|.||||.+||+|+| T Consensus 448 HRmSmMgH~VkVLPgkTFRLNLaVCPPYNADFDGDEMNlHV~Q~EEarAEA~~lM~V~~hI~tPRyGGPIIGg~~D~IsG 527 (901) T TIGR02390 448 HRMSMMGHKVKVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISG 527 (901) T ss_pred HHHHHCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHH T ss_conf 02101144546788885213667772888788876037640257335899999854111014688764011025678888 Q ss_pred HHHHHCCCCCCCCCCCEECCHHHHHHHHHCCCCCCCCEEEEEECCCCCCCCCCCEEEC----CCCCCCCCCEEEE----- Q ss_conf 9987336788744681417999999999888986785236520464566761424521----7977511220554----- Q gi|254780142|r 512 LCYLSTVHEGDPGEGMLFADMGEVYHALENKIVTLHSKIRGRYKSVDKDGNSISKIYD----TTPGRMIIGEILP----- 582 (1398) Q Consensus 512 ~y~lT~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~a~i~~~~~~~~~~~~~~~~~~~----tt~Gr~~~~~ilp----- 582 (1398) +||||... .+++.++|...+......... .....+.+..+ .|+||+|||.+|| T Consensus 528 aYLLT~k~--------~~~t~~ev~~iL~~~~~~~~~----------~~~~~ie~~~~eGrdywTGK~ifS~~LP~dLn~ 589 (901) T TIGR02390 528 AYLLTVKS--------TLFTKEEVVTILKKAGLKGEP----------EEPKAIEKPKEEGRDYWTGKQIFSAFLPEDLNF 589 (901) T ss_pred HHHHHHCC--------CCCCHHHHHHHHHHCCCCCCC----------CCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCE T ss_conf 88865047--------776889999999860767787----------666633177866753221035554207887772 Q ss_pred ---------------------------CCCCCEEEEECCHHCCHHHH-HHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf ---------------------------58751017751100201366-69999999808178999875588999999985 Q gi|254780142|r 583 ---------------------------RHHEISFDICNQEMIKKNIS-AMVDTIYRHCGQKSTVAFCDDLMRLGFRYACS 634 (1398) Q Consensus 583 ---------------------------~~~~~~~~~~~~~~~k~~~~-~li~~i~~~~G~~~~~~~l~~~~~l~~~~l~~ 634 (1398) +||.++.|++||+.+|+..| .|+|.|+++||++.|..|||.+.||+-+++++ T Consensus 590 ~~~a~~~~G~c~~C~~e~Cp~D~YvVI~NG~Ll~GViDk~a~G~e~g~~il~~i~~~yG~e~ar~~lD~~trL~i~~i~~ 669 (901) T TIGR02390 590 EFRAKVCSGKCEACKKEECPHDAYVVIKNGKLLKGVIDKKAIGAEKGDKILDRIVREYGPEAARRFLDSVTRLAIRFIEL 669 (901) T ss_pred EEECCCCCCCCCCCCCCCCCCCCEEEEECCEEEEEECCHHHCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH T ss_conf 14013678850010036799865789866804320302011274663789999987607468999999999999998755 Q ss_pred CCCCCCCCCCCCCHH----HHHHHHHHHHHHHHHHHHHHCCCC-------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 398613212326836----999999999789999998864897-------667888788642346589999999999876 Q gi|254780142|r 635 SGISFGKDDIIVPES----KEKIIAEADKMVKEYENQYNDGLI-------TRGEKYNKVVDLWGKTTDKVTEEMMARIKR 703 (1398) Q Consensus 635 ~GfSigi~D~~~~~~----k~~~i~~a~~~~~~~~~~~~~G~~-------t~~e~~~~i~~~~~~~~~~~~~~~~~~~~~ 703 (1398) .|||+|++|+.+|++ .+++|++|+++|++++++|++|.| .++..+.++.+++++++|++++-. T Consensus 670 ~GfT~g~~D~dIP~eA~~~I~~~i~~A~~~V~~LIe~Y~~GeLeplPGRt~EEtlE~~I~~~L~~~Rd~~G~va------ 743 (901) T TIGR02390 670 RGFTTGIDDIDIPKEAKEEIEELIEKAEKRVDKLIEEYRNGELEPLPGRTVEETLEMKILEVLGKARDEAGEVA------ 743 (901) T ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHH------ T ss_conf 16601336010467899999999999999999999985278230187786446558899999877766651120------ Q ss_pred HCCCCCCCCCCC-CCCEEEEECCCCCCC---HHHEEEEEEECCCCCCCC--C---CCCC-------CC-----CCCHHHC Q ss_conf 115654322224-688376422555578---424112001000024644--3---4445-------66-----6301110 Q gi|254780142|r 704 VEFDPETGRQKK-MNSIFMMSHSGARGS---IHQMRQLGGMRGLIAKPS--G---EIIE-------SP-----IRSHFKG 762 (1398) Q Consensus 704 ~~~~~~~~~~~~-~N~~~~M~~SGAKGS---~~qi~ql~Gqq~l~gkp~--G---~~~~-------~P-----V~~sF~~ 762 (1398) ...+++ .|+.++||.|||||| ++||.+|||||.+-|.+- | +++| .| |+|||.+ T Consensus 744 ------~kyld~d~n~~~iMArtGARGs~LNi~qmaA~vGQQsVRG~Ri~RGY~~RtLPHFk~GDi~a~arGFVr~sf~~ 817 (901) T TIGR02390 744 ------EKYLDPDENHAVIMARTGARGSLLNITQMAAMVGQQSVRGERIRRGYRNRTLPHFKKGDIGAKARGFVRSSFKK 817 (901) T ss_pred ------HCCCCCCCCCEEEEEECCCCHHHHHHHHHHHHCCCEEEECCHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHCC T ss_conf ------10268564662799602666136558888610040155450343035678788888888887666513431137 Q ss_pred CCCHHHHHHCCCCCCHHHHCCCCCCCCCCEEEEHHHHHHCCCEEEEECCCCCCC--CEEEEEEECCEEEEEE Q ss_conf 888989764057610322101210156740110154230143277513887666--5121110088488650 Q gi|254780142|r 763 GLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKG--LTITHIVDSGQVVYSL 832 (1398) Q Consensus 763 GL~p~EfFfhamgGReGLiDTAvKTA~SGYlqRrLvk~~eDl~V~~~D~~t~~g--~~~~~~~~~~~~~~~l 832 (1398) ||+|.|||||||||||||||||||||+|||||||||.|||||.| +||.+|+|. ..++.. .|.|.+.+. T Consensus 818 GL~P~EyFFHA~gGREGLVDTAVRTsqSGYmQRRLvNALqDl~V-~yDgtVRD~~G~liQ~~-YGEDGvdP~ 887 (901) T TIGR02390 818 GLDPTEYFFHAAGGREGLVDTAVRTSQSGYMQRRLVNALQDLRV-EYDGTVRDTRGNLIQFK-YGEDGVDPA 887 (901) T ss_pred CCCCCEEEECCCCCCCCHHHHHHCCCCCCCHHHHHHHHHCCEEE-EECCEEEECCEEEEEEE-ECCCCCCCC T ss_conf 81830011204545531021111026653047788646616057-41775884223789874-036633653 No 11 >PRK08566 DNA-directed RNA polymerase subunit alpha; Validated Probab=100.00 E-value=0 Score=1674.31 Aligned_cols=780 Identities=27% Similarity=0.395 Sum_probs=607.4 Q ss_pred CCCCCCCEEEEEEECCCHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 56786405368984588678850144897175542545687568873362136856677215664156344883567578 Q gi|254780142|r 11 PWTDDRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRMKYKGIICEKCG 90 (1398) Q Consensus 11 ~~~~~~~i~~i~f~l~spe~I~~~S~~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~Cg~~~~~~~~g~~C~~Cg 90 (1398) .++.||+|++|+||++||||||+||++||++|+|+|+. +.|++|||+|+|||... ++..|+||| T Consensus 2 ~~~~p~~I~~I~f~~~S~~eI~~~S~~eI~~~~~~~~~-~~p~~gGl~D~rmG~~~---------------~~~~C~TCg 65 (881) T PRK08566 2 MMDVPKRIGSIKFGLLSPEEIRKMSVTKIITADTYDDD-GYPIEGGLMDPRLGVID---------------PGLRCKTCG 65 (881) T ss_pred CCCCCEEECEEEEEECCHHHHHHHCEEEEECCCCCCCC-CCCCCCCCCCCCCCCCC---------------CCCCCCCCC T ss_conf 88887301459998158999986257899561238889-98588997761118999---------------729789999 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCEEECHHHHHHHHHHHHHCCCHHHHHHHHHHCC----EE--EECCCCCCHHHHCCC--- Q ss_conf 853047757876772002776220130122578999980999656301332111----23--217886510432236--- Q gi|254780142|r 91 VEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRDVERVLYFES----YV--VVDPGLSSLEKYQIL--- 161 (1398) Q Consensus 91 ~~~~~~~~r~ghfGhIeLa~PV~Hi~f~k~~~~~i~~~l~~~~~~~~~v~y~~~----~~--~~~~~~~~~~~~~~~--- 161 (1398) .+..+|| ||||||||+.||||+||++.+. .+|...|..|.+++.-.. |. ......+.....+++ T Consensus 66 ~~~~~Cp---GHfGHIeLa~PV~hp~f~~~i~----~iL~~~C~~C~rl~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 138 (881) T PRK08566 66 GRAGECP---GHFGHIELARPVIHVGFAKLIY----KLLRATCRECGRLKLTEEEIEEYLEKLERLKEWGGLAKDLIKEI 138 (881) T ss_pred CCCCCCC---CCCEEEEECCCCCCHHHHHHHH----HHHHCCCCHHCCEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9789589---9684874067510287899999----99956011230185779999999999987643115699999999 Q ss_pred -CHHHHHHHHHHCCCCCEEECCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEE Q ss_conf -9999988676358555061155267788877267488999999873103220347886447788866663489851128 Q gi|254780142|r 162 -TEEEYVEAVSQFGQDQFIAMMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMI 240 (1398) Q Consensus 162 -~~~~~~~~~~~~~~~~~~~~~g~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~Pewmi 240 (1398) .+......+..|+........- ......+.......++.......+.++|.+....+.+|.+..+|||||| T Consensus 139 ~k~~~k~~~C~~Cg~~~~~i~~~--------~~~~f~~~~~~~~~~L~p~~v~~il~~I~~ed~~~Lg~~~~~~rPe~~i 210 (881) T PRK08566 139 KKEAAKRMVCPHCGEEQYKIKFE--------KPTTFYEERKEGAVKLTPSEIRERLEKIPDEDLELLGINPEVARPEWMV 210 (881) T ss_pred HHHHHHCCCCCCCCCCCCEEEEE--------CCHHHHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHHCCCCCCCCHHHHH T ss_conf 99875245685558857203631--------5436766203230357999999999718987899848996668807834 Q ss_pred EEECCCCCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCC-C Q ss_conf 630450762235138846973131003789999999869999998739835677769999999888874277678772-4 Q gi|254780142|r 241 IRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHKRVV-T 319 (1398) Q Consensus 241 l~~lpV~P~~~RP~v~~~~g~~~~dDlt~~~~~Ii~~N~~Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~~~~~-~ 319 (1398) +++||||||++||+|.+++|.+++||||++|.+||++|++|+++++.+||+.+++++|++||+||++||||+.++.|. + T Consensus 211 l~~lpVpP~~~RP~i~~~~g~~~~ddlt~~l~~Ii~~n~~l~~~~~~~a~~~~i~~~~~~LQ~~V~~~~Dn~~~~~~~~~ 290 (881) T PRK08566 211 LTVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVTTYFDNELPGIPPAR 290 (881) T ss_pred HHCCCCCCCCCCCCEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC T ss_conf 22255799767874023787345773889999999999999999876995767899999999999999725778987434 Q ss_pred CCCCCHHHHHHHHHCCCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCEECHHHHHHHHHHHH-----HH---HHHHHCC Q ss_conf 787650678998610237820003465100457740341255435462003489877612899-----99---9999879 Q gi|254780142|r 320 GANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKPF-----LY---AQLEKKG 391 (1398) Q Consensus 320 ~~~~rp~ks~~~rlkgK~GrfR~nl~GKRVdfs~RsVI~pdP~l~~~evgvP~~~A~~L~~P~-----~~---~~L~~~g 391 (1398) .+++||+|||+||||||+||||+|||||||||||||||||||+|++||||||..||++||+|| |+ ++|+.+| T Consensus 291 ~~~~r~~k~i~q~L~gK~GrfR~nlmGKRVd~saRSVIspDP~L~~~evGvP~~~A~~Lt~pe~Vt~~N~~~l~~~v~nG 370 (881) T PRK08566 291 HRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAKELTVPERVTPWNIEELREYVLNG 370 (881) T ss_pred CCCCCCCCCHHHHHCCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCCCCCCHHHHHHCCCCEEEEHHHHHHHHHHHHCC T ss_conf 56898564188885466630100224453355430343268876367025879999757868076087899999999739 Q ss_pred CCCCCCCCCCEEE------------------CCCCCEEHHHHHHHCCCEEEECCCCCCEECCEEEEEEEEECCCEEEEEC Q ss_conf 8666300010012------------------2488250132666569789975763101114012358994495479731 Q gi|254780142|r 392 YVSTVKQAKKFVE------------------KERPEVWDVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHP 453 (1398) Q Consensus 392 ~~~~i~~~k~~i~------------------~~~~~v~~v~rhl~~gd~Vl~NRqPsLHr~Simah~~~v~~~~t~rln~ 453 (1398) .. ...+.+++. .....+|.|+|||+|||+|||||||||||||||||+|||+||+|||||| T Consensus 371 ~~--~~pga~~i~~~~g~~~~l~~~~~~~~~~~l~~g~iV~Rhl~dgD~Vl~NRqPTLHr~sima~~v~v~~gktirln~ 448 (881) T PRK08566 371 PD--KHPGANYVIRPDGRRIKLTDKNKEELAERLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNL 448 (881) T ss_pred CC--CCCCCEEEECCCCCEEEHHHHHHHHHHHHCCCCCEEEEEEECCCEEEECCCCHHHHHCCCCEEEEEEECCEEEECC T ss_conf 85--5677437882578366425756999998526786896564359667752773354420001037997434577566 Q ss_pred CCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEEHHHHHHHHHHHHCCCCCCCCCCCEECCHH Q ss_conf 22545467877545699746899999999998767505423788782044025899999987336788744681417999 Q gi|254780142|r 454 LVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMG 533 (1398) Q Consensus 454 ~vc~pyNADFDGDEMnlHvPqs~eAraEa~~Lm~~~~niisP~~g~Pi~~~~QD~i~G~y~lT~~~~~~~~~~~~f~~~~ 533 (1398) +||+||||||||||||+|||||++|||||++||++++||+||++|+|+++++||+|+|+|+||.++ .|++++ T Consensus 449 ~vc~~yNADFDGDeMn~HvPqs~~A~aEa~~Lm~~~~nilsP~~G~Pii~~~QD~vlg~y~LT~~~--------~f~~k~ 520 (881) T PRK08566 449 AVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIHDHISGAYLLTRKS--------TLFTKE 520 (881) T ss_pred CCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHCHHCCCCCCCCCCEEEEHHHHHHHHHHHHCCC--------CCCCHH T ss_conf 567870677644102331257898999999986263026337899824651188887789986487--------668999 Q ss_pred HHHHHHHC----CCCCCCCEEEEEECCCCCCCCCCCEE--------ECCC----CCC----CCCCEEEECCCCCEEEEEC Q ss_conf 99999988----89867852365204645667614245--------2179----775----1122055458751017751 Q gi|254780142|r 534 EVYHALEN----KIVTLHSKIRGRYKSVDKDGNSISKI--------YDTT----PGR----MIIGEILPRHHEISFDICN 593 (1398) Q Consensus 534 ~~~~~~~~----~~~~~~a~i~~~~~~~~~~~~~~~~~--------~~tt----~Gr----~~~~~ilp~~~~~~~~~~~ 593 (1398) +++..+.. ..++.|+++++...|++++.....-+ ..++ .+. .-.+.+++++|++..|.++ T Consensus 521 ~~~~ll~~~~~~~~~~~pai~kp~~~wTGkqi~s~iLP~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~I~~G~ll~G~ld 600 (881) T PRK08566 521 EALDLLGAVGIDELPPEPAIENGKEYWTGKQIFSLFLPKDLNLVFKAKICSKCDECKKEDCEHDAYVVIKNGKLLKGVID 600 (881) T ss_pred HHHHHHHHCCCCCCCCCCHHCCCCCCCCHHHHHHHHCCCCCCEEEEECCCCCCCCCCCCCCCCCCEEEEECCEEEEEECC T ss_conf 99999983585656775200278412538999998746887525431024675544334577876699876977762046 Q ss_pred CHHCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHH----HHHHHHHHHHHHHHHHHHHH Q ss_conf 10020136669999999808178999875588999999985398613212326836----99999999978999999886 Q gi|254780142|r 594 QEMIKKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPES----KEKIIAEADKMVKEYENQYN 669 (1398) Q Consensus 594 ~~~~k~~~~~li~~i~~~~G~~~~~~~l~~~~~l~~~~l~~~GfSigi~D~~~~~~----k~~~i~~a~~~~~~~~~~~~ 669 (1398) |...|++.++|+|.+|++||++.|+.|||.+|+|+++|++++|||||++|+.+|++ +.++++++++++.++.++|+ T Consensus 601 K~~lG~~~~~LI~~i~~~yG~~~a~~fLd~lq~L~~~~l~~~GFSvGi~Dl~i~~~~~~~i~e~i~~~~~~v~~l~~~~~ 680 (881) T PRK08566 601 KKAIGAEQGSILDRIVKEYGPERARRFLDSVTKLAIRFIMLRGFTTGIDDEDIPEEAYEEIDEIIEEAEKRVEELIEAYE 680 (881) T ss_pred HHHHCCCCCCHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCCEEEEHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 77734343439999999859799999999999999999997784766644275889999999999999999999999998 Q ss_pred CCCC-------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCC---HHHEEEEEE Q ss_conf 4897-------667888788642346589999999999876115654322224688376422555578---424112001 Q gi|254780142|r 670 DGLI-------TRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIFMMSHSGARGS---IHQMRQLGG 739 (1398) Q Consensus 670 ~G~~-------t~~e~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~N~~~~M~~SGAKGS---~~qi~ql~G 739 (1398) .|.+ +++++++++.++|+++++++.+.+++.+ .++|++++|+.|||||| ++||++|+| T Consensus 681 ~g~l~~~~~~t~~e~~E~~i~~~l~~~r~~~~~i~~~~l------------~~~N~~~~Mv~SGAKGS~~Ni~Qi~g~lG 748 (881) T PRK08566 681 NGELEPLPGRTLEETLEMKIMQVLGKARDEAGEIAEKYL------------GLDNPAVIMARTGARGSMLNITQMAACVG 748 (881) T ss_pred HCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC------------CCCCCHHHHHHCCCCCCHHHHHHHHHCCC T ss_conf 298665889867899999999999999999999998628------------99995775311367677999999995345 Q ss_pred ECCCCCCC--C---CCCCCC-------C-----CCCHHHCCCCHHHHHHCCCCCCHHHHCCCCCCCCCCEEEEHHHHHHC Q ss_conf 00002464--4---344456-------6-----63011108889897640576103221012101567401101542301 Q gi|254780142|r 740 MRGLIAKP--S---GEIIES-------P-----IRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQ 802 (1398) Q Consensus 740 qq~l~gkp--~---G~~~~~-------P-----V~~sF~~GL~p~EfFfhamgGReGLiDTAvKTA~SGYlqRrLvk~~e 802 (1398) ||.++|++ . |++++. | |.|||++||+|+|||||||||||||||||||||+||||||||||+|| T Consensus 749 QQ~~~G~Ri~~~~~~RtLP~f~~~d~~~~a~GfI~~sF~~GL~p~Efffh~m~gReGLiDTAvKTa~sGYlqRrLvk~lE 828 (881) T PRK08566 749 QQSVRGERIRRGYRDRTLPHFKPGDLGAEARGFVRSSYKSGLTPTEYFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQ 828 (881) T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCHHCCCHHHHCCCCCCCCHHHHHHHHHHHC T ss_conf 61048976746777888899988898867895161245379988999970521040186677314752099999999861 Q ss_pred CCEEEEECCCCCC--CCEEEEEEECCEEEEEEC---------CCCCCCCCHHHC Q ss_conf 4327751388766--651211100884886500---------010122114420 Q gi|254780142|r 803 NCVVNQVDCNTKK--GLTITHIVDSGQVVYSLG---------SRVLGRTALDDI 845 (1398) Q Consensus 803 Dl~V~~~D~~t~~--g~~~~~~~~~~~~~~~l~---------~~~~~r~~~~di 845 (1398) |++|. ||+++++ |-.++ +.+|++.+++.. +|+++|+.++++ T Consensus 829 dl~v~-yD~tVR~~~~~ivq-f~YG~Dg~dp~~~~~~~~~~~~~~~~~~~~~~~ 880 (881) T PRK08566 829 DLKVE-YDGTVRDTRGNIVQ-FKYGEDGVDPMKSDHGKPVDVDRIIERVLGKEV 880 (881) T ss_pred CEEEE-CCCCEECCCCCEEE-EECCCCCCCCCCCCCCCCCCHHHHHHHHHHHCC T ss_conf 86992-79973869997899-765787768000258973349999999754007 No 12 >KOG0262 consensus Probab=100.00 E-value=0 Score=1674.37 Aligned_cols=1234 Identities=22% Similarity=0.298 Sum_probs=761.8 Q ss_pred EEEEEEECCCHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 53689845886788501448971755425456875688733621368566772156641563448835675788530477 Q gi|254780142|r 18 FDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRMKYKGIICEKCGVEVTLSS 97 (1398) Q Consensus 18 i~~i~f~l~spe~I~~~S~~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~Cg~~~~~~~~g~~C~~Cg~~~~~~~ 97 (1398) ...|+||+.+++||++.|+-+|+.|-|.|. -+-|.+|||+|.+|| |.++. -.|.||+.....|| T Consensus 13 ~~~v~Fg~yt~~ei~klSv~kIt~p~~~D~-lGhPi~GGLYDl~LG-p~~~~--------------~~C~TC~~~~~~CP 76 (1640) T KOG0262 13 QPSVSFGSYTDQEIRKLSVKKITNPITFDN-LGHPIPGGLYDLALG-PLDNS--------------DVCSTCNQDELNCP 76 (1640) T ss_pred CCCEEEECCCHHHHHHCCEEEECCCEEECC-CCCCCCCCCCCCCCC-CCCCH--------------HHHHHHCCHHHCCC T ss_conf 652135026899986415467317601202-589888764231338-75432--------------34403221433199 Q ss_pred CCCCCCCCCCCCCCCEEECHHHHHHHH---HHHHHC-CCHHHHHHHHHHCCEEEECCC--------------------CC Q ss_conf 578767720027762201301225789---999809-996563013321112321788--------------------65 Q gi|254780142|r 98 VRRDRMAHIDLASPVAHPWFLKSLPSR---ISTLLG-MSLRDVERVLYFESYVVVDPG--------------------LS 153 (1398) Q Consensus 98 ~r~ghfGhIeLa~PV~Hi~f~k~~~~~---i~~~l~-~~~~~~~~v~y~~~~~~~~~~--------------------~~ 153 (1398) ||||||||+.||||+.||+.+-+. -|..|. ..|+..+.-++++..+.++-+ .. T Consensus 77 ---GH~GHIeL~~pvynPlfF~~ly~lLr~sCl~Chhf~~k~~~v~~~~cqLrll~~G~i~ea~~Le~i~~~~~~d~~d~ 153 (1640) T KOG0262 77 ---GHMGHIELPVPVYNPLFFDFLYNLLRGSCLFCHHFRCKNVDVHILFCQLRLLEYGLIEEAEDLESITSETVEDNEDE 153 (1640) T ss_pred ---CCCCEEEECCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHCCCCCH T ss_conf ---75670563431227789999999999887762210057077899999989987031888999987645541367526 Q ss_pred CH-----HHHCCCC-------------------HHH------H------HHHHHHCCCC-------CE----E----ECC Q ss_conf 10-----4322369-------------------999------9------8867635855-------50----6----115 Q gi|254780142|r 154 SL-----EKYQILT-------------------EEE------Y------VEAVSQFGQD-------QF----I----AMM 182 (1398) Q Consensus 154 ~~-----~~~~~~~-------------------~~~------~------~~~~~~~~~~-------~~----~----~~~ 182 (1398) .+ +..++.+ +.. + +..+.+|+.- .| . ++. T Consensus 154 ~~~~~k~~~~~~v~~~i~~~~~~~~~~~t~~~~~~~~~lv~~f~k~~l~~kkC~~C~~~~p~~rk~~~~kv~~~~~~~~~ 233 (1640) T KOG0262 154 SLNEIKSCRAQYVTEAISEALLDKSEPNTKNSTELKKKLVTAFLKNALSRKKCPRCKHSNPKLRKDGFRKVFIDALSSKV 233 (1640) T ss_pred HHHHHHHHHHHHCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHCCCCCEEEEEHHCCCC T ss_conf 67888765665412899988642788520006788899999999986445668754578803311343135651100233 Q ss_pred CHHHHHHH------HH------HCCHHHHHH-HHHH------HHH---C----CCCCHHHHHHHHHH-----HHHHH-HH Q ss_conf 52677888------77------267488999-9998------731---0----32203478864477-----88866-66 Q gi|254780142|r 183 GADAIYEL------LI------ALDLQNLAL-TLRD------QLS---K----SSSIFRRKKIIKRL-----KIVDS-FI 230 (1398) Q Consensus 183 g~~~i~~~------l~------~~~~~~~~~-~~~~------~~~---~----~~~~~~~~~~~~~~-----~~~~~-f~ 230 (1398) |+..++.. .. .++...+.. .-++ +.. . .......+++++.+ +++.. |. T Consensus 234 ~~~~~~~~~i~~~~~~~~~~d~~~~G~~E~~~~g~d~~e~~~~~~~~~~t~~~~l~~tevR~~l~~lf~ne~~~l~~lf~ 313 (1640) T KOG0262 234 GANVIRGAKIKKDVGSKGFEDSGIDGSNEVEEDGKDLFEKSTEPAEFEKTGKKYLLPTEVREHLRDLFKNEGELLSYLFP 313 (1640) T ss_pred CCCCHHHEEEEHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 32002200221101344433235677542134551000036552113345641206799999999998514789988621 Q ss_pred -----HCCCCCC-EEEEEECCCCCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHC---CCCH---H------ Q ss_conf -----3489851-12863045076223513884697313100378999999986999999873---9835---6------ Q gi|254780142|r 231 -----TSGNNPG-WMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSL---HAPE---I------ 292 (1398) Q Consensus 231 -----~~~~~Pe-wmil~~lpV~P~~~RP~v~~~~g~~~~dDlt~~~~~Ii~~N~~Lk~~~~~---~ap~---~------ 292 (1398) .....|. .++|..|||||+-.||...++ +...|+--|..|.+|+..|.-+..+... ..++ . T Consensus 314 l~~~~~~k~~p~d~FFld~l~VpPtrfRP~s~~g-d~~~en~Qt~~L~kVle~s~~i~~~~~~m~~kl~~~~k~~l~~~~ 392 (1640) T KOG0262 314 LWDSGSGKIDPSDMFFLDNLLVPPTRFRPPSMLG-DEVHENPQTLNLNKVLESSVLIRKLLKDMKGKLDEELKLILERLR 392 (1640) T ss_pred CCCCCCCCCCCCCEEEEECCCCCCCCCCCCHHCC-HHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH T ss_conf 2345556638421122112356874568720126-244328077889999999999999988765313788888887644 Q ss_pred ----HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCE Q ss_conf ----7776999999988887427767877247876506789986102378200034651004577403412554354620 Q gi|254780142|r 293 ----IIRNEKRMLQESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQC 368 (1398) Q Consensus 293 ----i~~~~~~lLQ~~v~~~~dn~~~~~~~~~~~~rp~ks~~~rlkgK~GrfR~nl~GKRVdfs~RsVI~pdP~l~~~ev 368 (1398) -+-|.|.-||.+|.++||+.+.++ ....+| -+|.|-|..|||+||+|||||||||+|||||||||||.+||+ T Consensus 393 g~~~kl~~aw~~LQ~~vn~lfDs~~~~k---~~r~~~-pGikQiLEKKeGLFRkhMMGKRVN~AaRSVIsPDPnI~tnEI 468 (1640) T KOG0262 393 GIFSKLINAWLQLQASVNVLFDSKMASK---WSRDSP-PGIKQILEKKEGLFRKHMMGKRVNYAARSVISPDPNIETNEI 468 (1640) T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCC---CCCCCC-CHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCCCCCCCCCCCC T ss_conf 5889999999999987788726432444---356778-129999887540688875102002433043479998663556 Q ss_pred ECHHHHHHHHHHH-----HHHHHH---HHCCCCCCCCCCCCEEECCCC-------------------------------C Q ss_conf 0348987761289-----999999---987986663000100122488-------------------------------2 Q gi|254780142|r 369 GLPKLMALELFKP-----FLYAQL---EKKGYVSTVKQAKKFVEKERP-------------------------------E 409 (1398) Q Consensus 369 gvP~~~A~~L~~P-----~~~~~L---~~~g~~~~i~~~k~~i~~~~~-------------------------------~ 409 (1398) |||..+|.+|||| ||+.+| +.|| +.++++..++..+++ . T Consensus 469 GIP~vFA~KLTyPepVt~~NV~elr~aViNG--P~~hPGA~~iqd~dg~~t~l~~~~~~qR~alA~qLLtpst~~~~~~~ 546 (1640) T KOG0262 469 GIPPVFAKKLTYPEPVTPWNVNELRKAVING--PDVHPGATYIQDEDGTLTLLSPMTDEQREALANQLLTPSTGNPTEFG 546 (1640) T ss_pred CCCHHHHHHCCCCCCCCCCCHHHHHHHHHCC--CCCCCCCCEEECCCCCEEECCCCCHHHHHHHHHHHHCCCCCCCCCCC T ss_conf 7864777523688867742699999987149--98899831356698756516878879999999986064447876567 Q ss_pred EEHHHHHHHCCCEEEECCCCCCEECCEEEEEEEEECC-CEEEEECCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHH Q ss_conf 5013266656978997576310111401235899449-547973122545467877545699746899999999998767 Q gi|254780142|r 410 VWDVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISG-KAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLS 488 (1398) Q Consensus 410 v~~v~rhl~~gd~Vl~NRqPsLHr~Simah~~~v~~~-~t~rln~~vc~pyNADFDGDEMnlHvPqs~eAraEa~~Lm~~ 488 (1398) .-+|.||+.|||+||+||||||||+||||||+||+|| ||+||||++|.+|||||||||||+|+|||+.|||||++|.++ T Consensus 547 ~K~V~RHvknGDvvlmNRQPTLHKPSimaHkaRVL~gEktlRlHYANCkaYNADFDGDEMN~HfPQse~araEa~~ian~ 626 (1640) T KOG0262 547 TKKVHRHVKNGDVVLMNRQPTLHKPSIMAHKARVLPGEKTLRLHYANCKAYNADFDGDEMNVHFPQSEIARAEAYNIANT 626 (1640) T ss_pred CCEEEEECCCCCEEEECCCCCCCCCHHHHHHHEECCCCCEEEEEECCCCCCCCCCCCCHHCCCCCCHHHHHHHHHHHHCC T ss_conf 72366540478489975787656524554443015776146631136543468888631015677135678888987505 Q ss_pred HHCCCCCCCCCCEEEEHHHHHHHHHHHHCCCCCCCCCCCEECCHHHHHHHHHCC--------CCCCCCEEEEEECCCCCC Q ss_conf 505423788782044025899999987336788744681417999999999888--------986785236520464566 Q gi|254780142|r 489 TNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENK--------IVTLHSKIRGRYKSVDKD 560 (1398) Q Consensus 489 ~~niisP~~g~Pi~~~~QD~i~G~y~lT~~~~~~~~~~~~f~~~~~~~~~~~~~--------~~~~~a~i~~~~~~~~~~ 560 (1398) ..|++.|++|.|+.|++||++....+||.+| .|+++++.+.....+ .+..|+|++|.+.|++++ T Consensus 627 dsqYLvPt~G~PlrGLIQDHiVsgv~LT~rd--------~Fftre~y~qLv~~~l~~~~~rI~~lpPtIlkP~~LWTGKQ 698 (1640) T KOG0262 627 DSQYLVPTDGTPLRGLIQDHIVSGVLLTMRD--------SFFTREDYQQLVFAGLSDTFKRIKLLPPTILKPAPLWTGKQ 698 (1640) T ss_pred CCCEECCCCCCCHHHHHHHHEEEEEEEEECC--------CCCCHHHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCCCCH T ss_conf 7744216999711556664531047887324--------33579999999987402211402126842146524546531 Q ss_pred CCCC----------------CE---EECCCCC-----CCCCCEEEECCCCCEEEEECCHHCCHHHHHHHHHHHHHCCHHH Q ss_conf 7614----------------24---5217977-----5112205545875101775110020136669999999808178 Q gi|254780142|r 561 GNSI----------------SK---IYDTTPG-----RMIIGEILPRHHEISFDICNQEMIKKNISAMVDTIYRHCGQKS 616 (1398) Q Consensus 561 ~~~~----------------~~---~~~tt~G-----r~~~~~ilp~~~~~~~~~~~~~~~k~~~~~li~~i~~~~G~~~ 616 (1398) .-.. .+ +..-|.- ++--+.+++++|++.+|++||...|++..||+|++++.||++. T Consensus 699 VIsTil~Ni~P~~~p~iNl~~kaKip~~~W~~~s~e~~l~Es~v~ir~GellcGVLDKa~~Gat~yGLvH~~~ElYG~~~ 778 (1640) T KOG0262 699 VISTILKNIIPEGHPPINLESKAKIPGKAWRVHSEEPKLNESQVLIREGELLCGVLDKAQFGATAYGLVHCCHELYGGET 778 (1640) T ss_pred HHHHHHHHCCCCCCCCCCCHHCCCCCHHHCCCCCCCCCCCCCEEEEECCCEEEEEECHHHCCCHHHHHHHHHHHHHCCCC T ss_conf 89999985288888751110004686131377887656775438984583689761154347103435664454407610 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCH----HHHHHHHHHHHHHHHHHHHHHCCCC---CHHHHHHHHHHHHH-- Q ss_conf 99987558899999998539861321232683----6999999999789999998864897---66788878864234-- Q gi|254780142|r 617 TVAFCDDLMRLGFRYACSSGISFGKDDIIVPE----SKEKIIAEADKMVKEYENQYNDGLI---TRGEKYNKVVDLWG-- 687 (1398) Q Consensus 617 ~~~~l~~~~~l~~~~l~~~GfSigi~D~~~~~----~k~~~i~~a~~~~~~~~~~~~~G~~---t~~e~~~~i~~~~~-- 687 (1398) ++++|+.+.||++.||+++|||+|++|+.+.+ ++.++|.+...--.+..+.+. |+- +-+|-..++.+++- T Consensus 779 s~~lLs~~srlFT~ylq~~GFT~GvdDlll~~~~D~kR~~il~e~~~vG~qa~~~~~-~l~~da~~del~~~le~~y~~d 857 (1640) T KOG0262 779 SGKLLSVFSRLFTAYLQMHGFTLGVDDLLLDKDADKKRREILRESRNVGNQAAKEAF-GLDVDAPPDELRSRLEAIYLKD 857 (1640) T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCEEEECHHHHHHHHHHHHHHHCCCHHHHHHHH-CCCCCCCHHHHHHHHHHHHHCC T ss_conf 216999999999999988463214320565300037899999862000289999982-9987899799999999998635 Q ss_pred ----HHHHHHH----HHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCC---HHHEEEEEEECCCCCCC-----CCCC Q ss_conf ----6589999----999999876115654322224688376422555578---42411200100002464-----4344 Q gi|254780142|r 688 ----KTTDKVT----EEMMARIKRVEFDPETGRQKKMNSIFMMSHSGARGS---IHQMRQLGGMRGLIAKP-----SGEI 751 (1398) Q Consensus 688 ----~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~N~~~~M~~SGAKGS---~~qi~ql~Gqq~l~gkp-----~G~~ 751 (1398) ...|.+. +...+.+.+.+.+.+....+|.|+++.|+.|||||| .+||++|+|||.||||+ +|++ T Consensus 858 ~~~~~~LD~~~k~~~n~~ts~I~~~cvP~GLlk~FP~N~mqlM~~SGAKGS~VN~~QISclLGQqeLEGkRvPlMvSGKt 937 (1640) T KOG0262 858 ADKLAMLDRVMKSELNGYTSEIVKKCVPDGLLKKFPENNMQLMIQSGAKGSNVNTSQISCLLGQQELEGKRVPLMVSGKT 937 (1640) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHCCCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCCEEECCCC T ss_conf 03777777999988866438888643562444308712689988725775642499987761237645775643542775 Q ss_pred CCC-------C-----CCCHHHCCCCHHHHHHCCCCCCHHHHCCCCCCCCCCEEEEHHHHHHCCCEEEEECCCCC--CCC Q ss_conf 456-------6-----63011108889897640576103221012101567401101542301432775138876--665 Q gi|254780142|r 752 IES-------P-----IRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTK--KGL 817 (1398) Q Consensus 752 ~~~-------P-----V~~sF~~GL~p~EfFfhamgGReGLiDTAvKTA~SGYlqRrLvk~~eDl~V~~~D~~t~--~g~ 817 (1398) +|. | |...|++|+.|||||||||||||||||||||||+||||||||+|.||.+.|+ |||+++ ||- T Consensus 938 LPsF~p~e~spraGGfI~~RFlTGi~PqeyfFHCMAGREGLIDTAVKTSRSGYLQRCLiKhLEgl~V~-YD~TVRDsDgs 1016 (1640) T KOG0262 938 LPSFAPYETSPRAGGFIDGRFLTGIKPQEYFFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLKVH-YDLTVRDSDGS 1016 (1640) T ss_pred CCCCCCCCCCCCCCCCCCCEEECCCCCHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHHCEEE-CCCEEECCCCC T ss_conf 67757788897778722131024888267753332464301466775041068999999864001773-23167738996 Q ss_pred EEEEEEECCEEEEEECCCCCCCC-----CHHHCCCCCCCCEEEEC-------------------------------CC-- Q ss_conf 12111008848865000101221-----14420177897188517-------------------------------86-- Q gi|254780142|r 818 TITHIVDSGQVVYSLGSRVLGRT-----ALDDIINPLTNECIVKA-------------------------------GQ-- 859 (1398) Q Consensus 818 ~~~~~~~~~~~~~~l~~~~~~r~-----~~~di~~~~~~~~i~~~-------------------------------~~-- 859 (1398) .+++.+ |.+.++-....-+... ..++++.+..-+.++.+ .+ T Consensus 1017 vVQF~Y-GEDglDitKssfl~~~~f~~~Ny~avl~~~~~~~v~s~~d~~~a~~~~k~i~kw~kk~~w~~~~k~~~cpdpv 1095 (1640) T KOG0262 1017 VVQFMY-GEDGLDITKSSFLNKKEFPTDNYEAVLLKYKSESVLSAFDIKKASKYIKKILKWKKKHMWFELDKKIACPDPV 1095 (1640) T ss_pred EEEEEE-CCCCCCCCHHHHCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCHH T ss_conf 899863-5865554377652444411223999986407487763213687899999998877651222121155788816 Q ss_pred -----------CCCHHHHHHHHHCCCCEE-ECCCC-CCHHHHHCCCHHHHHHHCCCCCEECHHHCCCCHHHHHHHHHHHH Q ss_conf -----------578999999997598402-02331-00035518657887542017852000101460211110078898 Q gi|254780142|r 860 -----------LILESHVNEIEKCGIRSV-RIRSA-LTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQ 926 (1398) Q Consensus 860 -----------~i~~~~~~~i~~~~i~~v-~irs~-lt~~~~~~v~~~cy~~~l~~~~lv~pGe~VG~iAAQSIGEP~TQ 926 (1398) .+.+....++....-+.. ++.|. =+.+..+...+.. +.++|++|||+||+|||||||||+|| T Consensus 1096 ~~k~~p~~y~gsvsekf~~~i~~f~~~~~k~~~s~~~~~~~lr~ll~~K-----~~~SLa~PGE~VGvlAAQSIGEPSTQ 1170 (1640) T KOG0262 1096 LAKYNPDKYLGSVSEKFRKKIDDFDDENAKKEKSEEPSEEKLRRLLQLK-----YIRSLADPGEPVGVLAAQSIGEPSTQ 1170 (1640) T ss_pred HHHCCHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHH-----HHHHHCCCCCCCEEEEECCCCCCCCE T ss_conf 5303624542104488999999998876654123211489999999999-----88876189874124422136887531 Q ss_pred HHHHHHCCCCCCCCCCCCEEEECCCCEEEEEEE--EEEECCCCCEEEEECCCCEEEEECCCCEEEEEECCCHHCCCCCCC Q ss_conf 776420245432221122024014876897211--346517887789742760466406776000000110000135678 Q gi|254780142|r 927 LTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNR--NVCRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDG 1004 (1398) Q Consensus 927 mTLnTFHfAGVAS~~~~~~iknvTlGVPRlkEi--~~~~n~~~~~i~vs~~~~~~i~d~~~~~~~~~ki~~~~~~~v~~~ 1004 (1398) ||||||||||.+.| |||+|+|||+|| .+.+|+++|.+++....... .+++......+-.+++. T Consensus 1171 MTLNTFHfAGrGem-------NVTLGIPRLREIlMtASanIkTP~mt~pi~~g~s--------~~ra~~i~~~l~rV~L~ 1235 (1640) T KOG0262 1171 MTLNTFHFAGRGEM-------NVTLGIPRLREILMTASANIKTPSMTVPIKNGVS--------DERADDITKELRRVTLK 1235 (1640) T ss_pred EEHHHEEECCCCCE-------EEEECCHHHHHHHHHHHHCCCCCCEEEECCCCCC--------HHHHHHHHHHHHHHHHH T ss_conf 13214010466640-------1220656899999987640489733562368864--------77899999999898999 Q ss_pred CEEECCEEEEECCCCCCEEEECCCCEEEEEEEC---CC-CEEHHHHHCCC-----------------------CCEEE-- Q ss_conf 553225078621354311320246368975312---78-32001230236-----------------------86026-- Q gi|254780142|r 1005 GVIECGQRISEWDPHTFPIITEVSGTVGFEDLV---DG-ISVIESIGEST-----------------------GIAKR-- 1055 (1398) Q Consensus 1005 ~~v~~~~ii~~~Dp~~~~i~~e~~~~v~~~~~~---~~-~~~~~~~~~~t-----------------------~~~~~-- 1055 (1398) +++++..+-..+............-...|.... +. ....+++.+.. +...+ T Consensus 1236 evlk~v~vte~~t~~~~~~~~~y~lr~~~~~~~~y~~e~~v~~e~i~~~m~~~Flk~L~~aI~k~~~k~~~~~~~~~dd~ 1315 (1640) T KOG0262 1236 EVLKKVGVTEKITMVENQSCKKYKLRFDLLPREEYQEEYDVRPEDIEEVMENRFLKLLERAIKKKLKKAKYTRGMSNDDA 1315 (1640) T ss_pred HHHHHEEEEEEEEEECCCCCEEEEEEEEECCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC T ss_conf 99866412589985046430689999860687774233077999999999999999999999999877677524665667 Q ss_pred -EEEE----HHH-------CCCCCCCCCCEEEECCCCCEEECCCCCCCEEECCCCCEEEE---CCCCCCCCCCEEEECHH Q ss_conf -7751----011-------01221238534774277825322478842021377844541---36761354842221013 Q gi|254780142|r 1056 -KVID----WRF-------ASRSQNLKPAIVVTDENGVVLKSARGTDARWFLPVDALLSV---SPGQKVSTGDVLARLPI 1120 (1398) Q Consensus 1056 -~~i~----~~~-------~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~v---~~~~~v~~~d~l~~~~~ 1120 (1398) .... ... .....+..+...-.|............+.+|..+......- .+++....++ .... T Consensus 1316 ~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ddddas~~k~~~k~~~~~dYe~~de~e~~~~~~~e~~~~~e~~---e~d~ 1392 (1640) T KOG0262 1316 DPDDGNEVDNNDEVGGEDNEDSDDESEDDEDDDDASDAKLHKKTEEEADYESEDEDERVEEREDEGDEDEESD---EDDE 1392 (1640) T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHCCCCCCCCCC---CCHH T ss_conf 8532346786533467765666421255676520367787652011267678753543202202566553222---2102 Q ss_pred HHC-------CCCCCCCCCC---HHHHH---------HH--------------------HHCCCC--CCEECCCCCEEEE Q ss_conf 202-------4554336773---28898---------87--------------------525111--1011134786786 Q gi|254780142|r 1121 SSA-------KTKDITSGLP---RVAEL---------FE--------------------ARRPKN--HAILAEISGTIRI 1159 (1398) Q Consensus 1121 ~~~-------k~~DIt~GLP---rV~eL---------FE--------------------ar~pk~--~aiisei~Giv~i 1159 (1398) +.. ..+|.+ |-| .++.. |- +++++- ..|+.++.+ ..+ T Consensus 1393 e~g~dg~~~~~~~~~e-~~~~~~~~er~~qs~~~~~~fi~~y~fd~~~~~wcev~~~lp~~~~k~~mssiVe~~~~-~~v 1470 (1640) T KOG0262 1393 EVGLDGTPEPEEEDQE-GQPEVNAVERREQSVKKRHDFISRYTFDKESGKWCEVELKLPLDKEKLDMSSIVESIAP-KSV 1470 (1640) T ss_pred HCCCCCCCCCCCCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCCCCHHHHHHHHHHHC-CEE T ss_conf 3066788873324466-77213578889988888887765411012568379999981488752179999999725-014 Q ss_pred EEECCCCEEEEEEECCCCCCEEEEEECCCC-------EEEEECCCEEECCCEEECCCCCHHHHHHHHCHHHHHHHHHHHH Q ss_conf 331279449999836898402689813896-------5898419877408646438999999987527999999999999 Q gi|254780142|r 1160 KRNYKNKSRVVIEPFEDGVEPAEYFIPKNK-------HFYLQDGDHVEKGDYILDGNPVPQDILRIKGVEALASYLINEV 1232 (1398) Q Consensus 1160 ~~~~~~k~~~vi~~~~~g~~~~e~~ip~~~-------~l~v~dgd~V~~gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~EI 1232 (1398) .+...+.+++++...++..+...++...+. +..+.|.++++ |||+|+|+++|||||||++|++|| T Consensus 1471 I~q~~gIeRc~~~~~~~~~k~~~~l~TeGVnl~a~~~~~d~LDv~~ly--------SNDI~ail~tyGVEAar~~Iv~Ev 1542 (1640) T KOG0262 1471 IHQVPGIERCVVSEPQDDVKEKSVLLTEGVNLPALFDHADILDVNRLY--------SNDIHAILNTYGVEAARNAIVNEV 1542 (1640) T ss_pred EECCCCCEEEECCCCCCCCCCCCEEHHCCCCHHHHHHHHHHHHHHHHC--------CCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 640688226640687655433401010576589999777663331101--------305999999862899999999999 Q ss_pred HHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHHHCCC Q ss_conf 99999809700612560124762861489418864545664106999999999999728987520121000014530231 Q gi|254780142|r 1233 QEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTK 1312 (1398) Q Consensus 1233 q~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~~~p~llGITKasl~t~ 1312 (1398) .+||..|||+|+.|||+||||+||+.|. |.|+||.+++. .. T Consensus 1543 ~~VF~vYGIsVd~RHLsLiADYMTf~G~-------------------y~pfnR~Gm~~--------------------ss 1583 (1640) T KOG0262 1543 NNVFKVYGISVDIRHLSLIADYMTFEGG-------------------YQPFNRMGMES--------------------SS 1583 (1640) T ss_pred HHHHHHEEEEECHHHHHHHHHHHHHCCC-------------------CCCCCCCCCCC--------------------CC T ss_conf 8766530156338898999888750565-------------------36200145555--------------------89 Q ss_pred CHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCCCCCCCCCHHH Q ss_conf 077650402589999997452855236653221550730565535466 Q gi|254780142|r 1313 SFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAIL 1360 (1398) Q Consensus 1313 S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG~f~ 1360 (1398) |.|+..|||.|..+|.+||.+|+.|.|+.+|+++++|.+...|||+|- T Consensus 1584 SP~qkMsFETt~~Fl~~Aa~~g~~D~L~sPSArLvvG~~~r~GTG~Fd 1631 (1640) T KOG0262 1584 SPLQKMSFETTCQFLKQAALFGEEDELSSPSARLVVGLPVRGGTGSFD 1631 (1640) T ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCCCCCCEEE T ss_conf 756764199999999998734750025797502583366578765111 No 13 >COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] Probab=100.00 E-value=0 Score=1601.13 Aligned_cols=780 Identities=50% Similarity=0.741 Sum_probs=704.4 Q ss_pred CCEEEEEEECCCHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 40536898458867885014489717554254568756887336213685667721566415634488356757885304 Q gi|254780142|r 16 RGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRMKYKGIICEKCGVEVTL 95 (1398) Q Consensus 16 ~~i~~i~f~l~spe~I~~~S~~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~Cg~~~~~~~~g~~C~~Cg~~~~~ 95 (1398) +.++ ||||++|||+||+|| +||++||||||++ +|++|||||+|||||.+||+|.||+|++. T Consensus 3 ~~~~-i~~gl~sp~~ir~~s-~ev~~pet~~~~~-~P~~~Gl~d~ri~~~~~~~~C~Cg~~~~~---------------- 63 (808) T COG0086 3 RIFD-IKFGLASPEEIRSWS-GEVKKPETINYRT-KPERGGLFDERIFGPDKDYECTCGKYKRI---------------- 63 (808) T ss_pred CEEE-EEEECCCHHHHHHCC-EEECCCCCCCCCC-CCCCCCCCCHHHCCCCCCCEECCCCCCCC---------------- T ss_conf 3003-798058989997443-3876702027888-51688752043169899840228885675---------------- Q ss_pred CCCCCCCCCCCCCCCCCEEECHHHHHHHHHHHHHCCCHHHHHHHHHHCCEEEECCCCCCHHHHCCCCHHHHHHHHHHCCC Q ss_conf 77578767720027762201301225789999809996563013321112321788651043223699999886763585 Q gi|254780142|r 96 SSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRDVERVLYFESYVVVDPGLSSLEKYQILTEEEYVEAVSQFGQ 175 (1398) Q Consensus 96 ~~~r~ghfGhIeLa~PV~Hi~f~k~~~~~i~~~l~~~~~~~~~v~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 175 (1398) |+ |||||||||.||+||||+|.+|| +|+.+|++|++|+||++|+++ + ..+.+.+++++.+| .. T Consensus 64 ~~---~~~GhIeLa~Pv~hi~f~k~~~~----~L~~~~~~~~~v~~~~~~~~~--~-~~l~~~~~~~~~~~-------~~ 126 (808) T COG0086 64 CP---GGFGHIELAAPVAHIWFFKSIPS----LLDMTCRDCERVLYFEAYVVL--G-TDLEKIQLLNETEY-------VY 126 (808) T ss_pred CC---CCCEEEEEECCEEEECHHHCCHH----HHHHHHHHHHHHHHHHHHHHH--C-CCHHHHCCCCHHHH-------HH T ss_conf 88---97314776263588335445799----985137744562567666662--5-62244214403331-------12 Q ss_pred CCEEECCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCCEE Q ss_conf 55061155267788877267488999999873103220347886447788866663489851128630450762235138 Q gi|254780142|r 176 DQFIAMMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMIIRKLPVLPPDLRPLV 255 (1398) Q Consensus 176 ~~~~~~~g~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~Pewmil~~lpV~P~~~RP~v 255 (1398) +.|.+.+|+++++..+...++..+. ++ ...+..+++++++++.+.+.|..+++|||||||++||||||++|||| T Consensus 127 ~~~~~~~Ga~~~~~~~~~~~~~~~~----~~--~~~~~~~~~~~~~~l~~~d~~~~~~~~pewmil~vlpV~Pp~~RP~i 200 (808) T COG0086 127 DSFCAHCGAEAIKILLEKPDLETER----EE--ETLSPTKVKKLLKRLKVVDAFLLSGNRPEWMILTVLPVPPPDLRPSI 200 (808) T ss_pred CCCCCCCCCCCHHHHHHCCCHHHHH----HH--HCCCHHHHHHHHHHCCHHHHHHHCCCCCCEEEEEEECCCCCCCCCCE T ss_conf 0447898971399887367544312----13--03587889999751665677660478865368971035998888545 Q ss_pred EECCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCC Q ss_conf 84697313100378999999986999999873983567776999999988887427767877247876506789986102 Q gi|254780142|r 256 ALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHKRVVTGANRRPLKSLSDMLKG 335 (1398) Q Consensus 256 ~~~~g~~~~dDlt~~~~~Ii~~N~~Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~~~~~~~~~~rp~ks~~~rlkg 335 (1398) +||+|+|+|||||++|++||++|||||++++.+|| +|++|+|+|||+||++|||| ..+.++++ + ||||||+||||| T Consensus 201 ~ld~g~~a~~dl~~~~~~ii~~n~rlk~~~~~~~~-~iv~~~~~~lQ~~v~~~~Dn-~~~~~~~~-~-rPlksl~~~Lkg 276 (808) T COG0086 201 QLDGGRFAESDLNDLYRRVINRNNRLKRLLELAAP-IIVRNEKRMLQEAVDALFDN-RRPRAVTG-G-RPLKSLSQRLKG 276 (808) T ss_pred ECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCH-HHHHHHHHHHHHHHHHHHHC-CCCCCCCC-C-CCCCCHHHHHCC T ss_conf 63898655668889999999998775776664545-77888999999999998616-89877658-9-764449998468 Q ss_pred CCCCEEECCCCCCCCCCCCEEEECCCCCCCCCEECHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEECCCCCEEHHHH Q ss_conf 37820003465100457740341255435462003489877612899999999879866630001001224882501326 Q gi|254780142|r 336 KQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDVLA 415 (1398) Q Consensus 336 K~GrfR~nl~GKRVdfs~RsVI~pdP~l~~~evgvP~~~A~~L~~P~~~~~L~~~g~~~~i~~~k~~i~~~~~~v~~v~r 415 (1398) |+||||||||||||||||||||+|||||++||||||+.||++||+||.+.+++..+.+..++.+++++++..+.+|+|+| T Consensus 277 K~GrFR~nL~GKRVd~SgRsVI~~~P~l~~~e~GvP~~~A~~L~~p~~v~~~~~~~~~~~a~~~~~~~~~~~~~~w~Vl~ 356 (808) T COG0086 277 KQGRFRQNLLGKRVDYSGRSVISVGPNLKLNQCGVPKKMALELFKPFVVTELNIEGLRTGAKYAKRMVERRLPEVWDVLR 356 (808) T ss_pred CCCEEECCCCCCCCCCCCCEEECCCCCCCCCCCCCHHHHHHHHCCCEEEEEHHHHHHHCCCCEEEECCCCCCCCCCHHHH T ss_conf 77545134001511787862552799863400488799988744477987332223211771688012133565404678 Q ss_pred HHHCCCEEEECCCCCCEECCEEEEEEEEEC-CCEEEEECCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHCCCC Q ss_conf 665697899757631011140123589944-9547973122545467877545699746899999999998767505423 Q gi|254780142|r 416 EVVHQHVVLLNRAPSLHRLSMQAFEPKIIS-GKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLH 494 (1398) Q Consensus 416 hl~~gd~Vl~NRqPsLHr~Simah~~~v~~-~~t~rln~~vc~pyNADFDGDEMnlHvPqs~eAraEa~~Lm~~~~niis 494 (1398) |+++||+|||||||||||+|||+|+.++++ |+||||||+||+||||||||||||+|||||++|+|||+.||++++||+| T Consensus 357 evi~gd~Vl~NR~PtLHrlsImq~~e~vl~~gkt~rLh~lVc~~yNADFDGDeM~~Hvp~s~ea~AEa~~lm~tq~nils 436 (808) T COG0086 357 EVIDGDPVLLNRAPTLHRLSIMQAFEPVLPEGKAIRLHPLVCEAYNADFDGDEMAVHVPASGEAAAEARGLMGTQMNILT 436 (808) T ss_pred HHHCCCCCCCCCCCHHHHHHHHHHCEEECCCCCEEECCHHHCCCCCCCCCCHHHHCCCCCHHHHHHHHHHHHCCCCCCCC T ss_conf 77629800015577678999986510104555335310121552456537465536575059999998864055563256 Q ss_pred CCCCCCEEEEHHHHHHHHHHHHCCCCC----CCCCC---CEECCHHHHHHHHHCCCCCCCCEEEEEECCCCCCCCCCCEE Q ss_conf 788782044025899999987336788----74468---14179999999998889867852365204645667614245 Q gi|254780142|r 495 PASGAPVTVPSQDMVLGLCYLSTVHEG----DPGEG---MLFADMGEVYHALENKIVTLHSKIRGRYKSVDKDGNSISKI 567 (1398) Q Consensus 495 P~~g~Pi~~~~QD~i~G~y~lT~~~~~----~~~~~---~~f~~~~~~~~~~~~~~~~~~a~i~~~~~~~~~~~~~~~~~ 567 (1398) |++|+|+++++||+++|.||||..+.+ ..++. ..|.+..++..++..+....++.+.......+. ..... T Consensus 437 P~~Ggpiv~~~qD~v~g~ylLt~~d~~~~~~~~~ei~l~~~~~~~~e~~~ai~~~~~~~~~k~i~~~i~~~~---~~~~i 513 (808) T COG0086 437 PHYGGPIVAPIQDTVGGPYLLTIVDAKLPSTPVGEIYLKDEYADDREKAEAIAKKIELTTGKVIVSTISPDL---AELSI 513 (808) T ss_pred CCCCCCEEEECCEEEECCEEEEEECCCCCCCCCEEEEECCCCCCCHHHHHHHHCCCCEEEEEEEEEEEECCC---CCCEE T ss_conf 789995672020588134789983266888753489721233552255677754622126458999850378---75259 Q ss_pred ECCCCCCCCCCEEEECCCCCEEEEECCHHCCHHHHHHHHHHHHHCCHHHHH-HHHHHHHHHHHHHHHHCC-CCCCCCCC- Q ss_conf 217977511220554587510177511002013666999999980817899-987558899999998539-86132123- Q gi|254780142|r 568 YDTTPGRMIIGEILPRHHEISFDICNQEMIKKNISAMVDTIYRHCGQKSTV-AFCDDLMRLGFRYACSSG-ISFGKDDI- 644 (1398) Q Consensus 568 ~~tt~Gr~~~~~ilp~~~~~~~~~~~~~~~k~~~~~li~~i~~~~G~~~~~-~~l~~~~~l~~~~l~~~G-fSigi~D~- 644 (1398) ..++.|+.+++..+|.+.++...+.++.+.++.+..++..+++.||+..+. .+++.+.++...++.+.| |+++++|. T Consensus 514 ~~t~~~~~~~~~~~~~~~d~~~~i~~~~l~~~~i~k~~~~~~~~~g~~~~~~~~~~~~dkl~~~~~~~~~~~~~~i~~~d 593 (808) T COG0086 514 IVTTDGRRIFNRGLPEDKDVLVKIVNGKLIKGVIDKKIVTIYREYGPEVASKALVKLLDKLKNLGIKGIGGFGIGIGRKD 593 (808) T ss_pred EEECCHHHHHHCCCCCCCCEEEEEECCCCCEEEEHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHEEEECCCEEEEECCC T ss_conf 99341365554068755540257731433123413458999998183055799999999998753133424207864354 Q ss_pred -CCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEE Q ss_conf -2683699999999978999999886489766788878864234658999999999987611565432222468837642 Q gi|254780142|r 645 -IVPESKEKIIAEADKMVKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIFMMS 723 (1398) Q Consensus 645 -~~~~~k~~~i~~a~~~~~~~~~~~~~G~~t~~e~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~N~~~~M~ 723 (1398) .+++++.+++.+|+.++.+++.+|+.|.+|..++++..+.+|..+.+.+.+++++.+.......... +|.+++|. T Consensus 594 ~~~~~~~~e~v~~ae~~v~~~i~~~~~g~lt~~~~~~i~e~~e~~~~e~l~~ai~~~~~~~~~~~g~~----~~~i~~m~ 669 (808) T COG0086 594 IEAEDEKDEIVIEAEGSVLKLILQYEEGDLTRTERNNIVEIIEVLGIEALRNAIIEEIKITLEEQGLD----FVDIRHMG 669 (808) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEHHHHHHHHHHHHHHHHHHHHHCCCC----HHHHHHHH T ss_conf 32057788999999999999998764587634577875687621779999999999876667752874----02399986 Q ss_pred CCCCCCCHHHEEEEEEECCCCCCCCCC-------------CCCCCCCCHHHCCCCHHHHHHCCCCCCHHHHCCCCCCCCC Q ss_conf 255557842411200100002464434-------------4456663011108889897640576103221012101567 Q gi|254780142|r 724 HSGARGSIHQMRQLGGMRGLIAKPSGE-------------IIESPIRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASS 790 (1398) Q Consensus 724 ~SGAKGS~~qi~ql~Gqq~l~gkp~G~-------------~~~~PV~~sF~~GL~p~EfFfhamgGReGLiDTAvKTA~S 790 (1398) .+||+||++||+||+|||||||+|.|. ..+.||.+||++||+|.|||||+||||+||+|||+|||+| T Consensus 670 ~~Gs~~n~sq~~~~~G~~gv~g~r~~~~~~~~Fe~~~~~~~a~~~i~s~f~eGLt~~e~f~~~~ggR~GlvDTA~KTa~s 749 (808) T COG0086 670 LSGARMNISQIVQLIGQQGVMGEKISVLARAAFEVTVKHLEAEGPGESSFLEGLTENEYFGHPIGGRTGLVDTALKTADS 749 (808) T ss_pred HHHHCCCHHHHHHHHHHHEEECCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCEEEEECCCCCCCHHHHHHHHCCC T ss_conf 43624489999998633203125788653222234665534554566455779972268750576653168876652346 Q ss_pred CEEEEHHHHHHCCCEEEEECCCCCCCCEEEEEEECCEEEEEECCCCCCCCCHHHCCCCC Q ss_conf 40110154230143277513887666512111008848865000101221144201778 Q gi|254780142|r 791 GYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLGSRVLGRTALDDIINPL 849 (1398) Q Consensus 791 GYlqRrLvk~~eDl~V~~~D~~t~~g~~~~~~~~~~~~~~~l~~~~~~r~~~~di~~~~ 849 (1398) |||||||||++||++|+++||++. |..+..+...++....+.+++.||+..+|+.++. T Consensus 750 GYl~RrLv~~~qdl~v~~d~~~~~-g~~~~~~~~~ged~~~~~~~~~~~~~~~~v~~~~ 807 (808) T COG0086 750 GYLTRRLVDVAQDLIVQEDDCVTD-GIGVVIQFEYGEDGEDLTERILGRVLEEDVLRPV 807 (808) T ss_pred CCCEEEEECHHCCEEEEECCEEEE-CCCEEEEEECCCCCCCHHHHHCCEEEHHHHCCCC T ss_conf 762577310222449995482872-6855888715764428888744847453402567 No 14 >PRK02625 DNA-directed RNA polymerase subunit gamma; Provisional Probab=100.00 E-value=0 Score=1478.32 Aligned_cols=571 Identities=56% Similarity=0.966 Sum_probs=537.7 Q ss_pred CCCCCEEEEEEECCCHHHHHHCC---------EEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 78640536898458867885014---------489717554254568756887336213685667721566415634488 Q gi|254780142|r 13 TDDRGFDSVRISIASPAKIASLS---------YGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRMKYKG 83 (1398) Q Consensus 13 ~~~~~i~~i~f~l~spe~I~~~S---------~~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~Cg~~~~~~~~g 83 (1398) ...++|++|+++|||||+||+|| ||||++||||||+|+|||+|||||+|||||++||+|+|||||+++|+| T Consensus 4 ~~~~~f~~i~I~LASPe~Ir~WS~r~lpngeivGEVtkpeTINYrT~KPE~dGLFCErIFGP~Kd~eC~CGKyk~~k~kg 83 (627) T PRK02625 4 RTENHFDYVKIGLASPERIMQWGQRTLPNGQVVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRG 83 (627) T ss_pred CCCCCCCEEEEEECCHHHHHHHHHHCCCCCCEEEEECCCCCCCCCCCCCCCCCEEEHHHCCCCCCCEEECCCCCCCCCCC T ss_conf 31057672799836989999987530677865688889742125779988888830444087758377188721303287 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECHHHHHHHHHHHHHCCCHHHHHHHHHHCCEEEECCCCCC-HHHHCCCC Q ss_conf 35675788530477578767720027762201301225789999809996563013321112321788651-04322369 Q gi|254780142|r 84 IICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRDVERVLYFESYVVVDPGLSS-LEKYQILT 162 (1398) Q Consensus 84 ~~C~~Cg~~~~~~~~r~ghfGhIeLa~PV~Hi~f~k~~~~~i~~~l~~~~~~~~~v~y~~~~~~~~~~~~~-~~~~~~~~ 162 (1398) .+|++||||++++.|||+|||||+||.||+||||+|++||+|+.+|+++.+++|+++||++|++++|+... ++..++++ T Consensus 84 ~vCe~CGVEvt~S~VRR~RMGHIeLA~PV~HIWYLK~~PS~Is~LLd~~~KeLE~ViYf~~yiV~dpg~~~~l~~k~ll~ 163 (627) T PRK02625 84 IVCERCGVEVTESRVRRHRMGYIKLAAPVSHVWYLKGIPSYVAILLDMPLRDVEQIVYFNCYVVLDPGNHKNLKYKQLLT 163 (627) T ss_pred EECCCCCCCCCCCCCCCCCCCCEEECCCCEEEEEECCCCHHHHHHCCCCHHHHHHHHHCCEEEEECCCCCCCHHHHHHCC T ss_conf 16687685734352110135644465870443340688269999808868888875612306875677686346664315 Q ss_pred HHHHHHHHHHCCC-C-----CEEECCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCC Q ss_conf 9999886763585-5-----506115526778887726748899999987310322034788644778886666348985 Q gi|254780142|r 163 EEEYVEAVSQFGQ-D-----QFIAMMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNP 236 (1398) Q Consensus 163 ~~~~~~~~~~~~~-~-----~~~~~~g~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~P 236 (1398) +++|.+..+.... + ...+.+|++|++++|.++|++.+...++.++.... .+++.+++||+++++.|..+++|| T Consensus 164 e~~~~e~~~~i~~~~~~~~~~~~~~~GaeAI~~lL~~lDL~~~~~~Lr~ei~~~k-~qkr~KliKRLkli~~Fi~S~~rP 242 (627) T PRK02625 164 EDQWLEIEDEIYAEDSELENEEVVGIGAEALKQLLEDLNLEEEAEQLREEIANSK-GQKRAKLIKRLRVIDNFIATGARP 242 (627) T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHHHHHHCCCCC T ss_conf 8999998988640221004764015449999999886798999999999976474-256899999999999998669883 Q ss_pred CEEEEEECCCCCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCC Q ss_conf 11286304507622351388469731310037899999998699999987398356777699999998888742776787 Q gi|254780142|r 237 GWMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHKR 316 (1398) Q Consensus 237 ewmil~~lpV~P~~~RP~v~~~~g~~~~dDlt~~~~~Ii~~N~~Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~~~ 316 (1398) |||||++|||+||++||+|++|+|++++||||++|++||.+||||+++.+.+||++|++|+|+|||+|||+||||+++|+ T Consensus 243 EWMIL~vLPVlPP~LRP~v~Ldggr~a~sDlN~lYrriI~rNnrLk~~~~~~ap~~ii~~ekrlLQeaVd~L~DN~~~g~ 322 (627) T PRK02625 243 EWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGR 322 (627) T ss_pred HHEEEECCCCCCCCCCCCEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCC T ss_conf 50787323558987774278668865666658999999999999999886599578888899999999888544655688 Q ss_pred CCCCCCCCHHHHHHHHHCCCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCEECHHHHHHHHHHHHHHHHHHHCCCCCCC Q ss_conf 72478765067899861023782000346510045774034125543546200348987761289999999987986663 Q gi|254780142|r 317 VVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTV 396 (1398) Q Consensus 317 ~~~~~~~rp~ks~~~rlkgK~GrfR~nl~GKRVdfs~RsVI~pdP~l~~~evgvP~~~A~~L~~P~~~~~L~~~g~~~~i 396 (1398) ++++.++||+|||+|+||||+||||||||||||||||||||+|||+|++||||+|+.||+|||+||++++|++.+.+.++ T Consensus 323 ~~~~~~~RplKSlsd~lkGK~GRfRqnLlGKRVDySgRsVIvvgP~L~l~qcGlP~~mA~elf~Pfvi~~l~~~~~~~~i 402 (627) T PRK02625 323 TVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQNIVNNI 402 (627) T ss_pred CCCCCCCCCCCCHHHHHCCCCCCHHHHCCCCCCCCCCCCEEECCCCCCHHHCCCCHHHHHHHCCHHHHHHHHHHCCCCCH T ss_conf 64279997021357662687880212146551056787068249865214308848999984418999999970664545 Q ss_pred CCCCCEEECCCCCEEHHHHHHHCCCEEEECCCCCCEECCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCEEEEECCCCH Q ss_conf 00010012248825013266656978997576310111401235899449547973122545467877545699746899 Q gi|254780142|r 397 KQAKKFVEKERPEVWDVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISP 476 (1398) Q Consensus 397 ~~~k~~i~~~~~~v~~v~rhl~~gd~Vl~NRqPsLHr~Simah~~~v~~~~t~rln~~vc~pyNADFDGDEMnlHvPqs~ 476 (1398) +.|++++++.++.+|++++|+++||+|||||||||||||||||+|++++|+||||||+||+||||||||||||+|||||. T Consensus 403 ~~ak~~i~~~~~~v~~~l~~v~~~~pVllNRaPTLHRlgiqaf~p~l~~g~ai~lhplvc~~fNADFDGDqMavhvPls~ 482 (627) T PRK02625 403 KAAKKLIQRADDEVWQVLQEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSL 482 (627) T ss_pred HHHHHHHHHCCCHHHHHHHHHHCCCEEEECCCCCCCCCEEECEEEEEECCEEEEECCCCCCCCCCCCCCCCEEECCCCCH T ss_conf 77999988668389999999973995787588521004111104688778048865545776689988721441378998 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCEEEEHHHHHHHHHHHHCCCCC-CCCCCCEECCHHHHHHHHHCCCCCCCCEEEEEEC Q ss_conf 999999998767505423788782044025899999987336788-7446814179999999998889867852365204 Q gi|254780142|r 477 EAQLEARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEG-DPGEGMLFADMGEVYHALENKIVTLHSKIRGRYK 555 (1398) Q Consensus 477 eAraEa~~Lm~~~~niisP~~g~Pi~~~~QD~i~G~y~lT~~~~~-~~~~~~~f~~~~~~~~~~~~~~~~~~a~i~~~~~ 555 (1398) ||||||+.||++++||+||++|+|++.|+||+++|+||||..+.. ..++++.|.+.+++..||..+.+++|++||+++. T Consensus 483 ea~~Ea~~lmls~~nilsPa~g~pi~~psQDmvlG~yylT~~~~~~~~~~~~~f~~~~~~~~a~~~~~i~lh~~i~~r~~ 562 (627) T PRK02625 483 EAQTEARMLMLASNNILSPATGEPIVTPSQDMVLGCYYLTAENPGAQKDAGRYFASLEDVIHAFEDGRIDLHAWVWVRFN 562 (627) T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCEECCHHHHHHHHHCCCCCCCCEEEEEEC T ss_conf 99999999853115777788899722355121103236503567764788865789999999997696024665899965 Q ss_pred CCC--------------------------------CCCCCCCEEECCCCCCCCCCEEEECC Q ss_conf 645--------------------------------66761424521797751122055458 Q gi|254780142|r 556 SVD--------------------------------KDGNSISKIYDTTPGRMIIGEILPRH 584 (1398) Q Consensus 556 ~~~--------------------------------~~~~~~~~~~~tt~Gr~~~~~ilp~~ 584 (1398) ... ..+.....++.||+||.+||+++|+. T Consensus 563 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~TT~Gri~fn~~i~~~ 623 (627) T PRK02625 563 GEVEDDDEDDEPLKTETLEDGTRIEQWNYRRDRFDEDGNLISQYILTTVGRVIMNKTIQDA 623 (627) T ss_pred CCCCCCCCCCCCCEEEECCCCCEEEEECCEEEEECCCCCEEEEEEEECCCEEEHHHHHHHH T ss_conf 7402465445650368627884377501204553367876568999477444446665887 No 15 >CHL00018 rpoC1 RNA polymerase beta' subunit Probab=100.00 E-value=0 Score=1460.35 Aligned_cols=571 Identities=43% Similarity=0.711 Sum_probs=513.6 Q ss_pred CCCEEEEEEECCCHHHHHHCCE---------EEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---CCC Q ss_conf 6405368984588678850144---------8971755425456875688733621368566772156641563---448 Q gi|254780142|r 15 DRGFDSVRISIASPAKIASLSY---------GEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRM---KYK 82 (1398) Q Consensus 15 ~~~i~~i~f~l~spe~I~~~S~---------~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~Cg~~~~~---~~~ 82 (1398) ..+|++|+++|||||+||+||. |||++||||||+|+|||+|||||||||||++||||+|||||++ +|+ T Consensus 4 ~~~f~~i~I~lASPe~Ir~WS~r~lpng~~vGEV~kpeTINYrT~KPE~dGLFCErIFGP~kd~eC~CGKYK~i~~~k~~ 83 (668) T CHL00018 4 RYKHQQLRIGLASPQQIRAWAERILPNGEIVGEVTKPYTFHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVIGDEKED 83 (668) T ss_pred CCCCCEEEEEECCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCCCCCCEEEHHHHCCCCCCEEECCCCCCCCCCCCC T ss_conf 24666379982698999998763066776031688965400577898888881003208885866758775224655657 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECHHHHHHHHHHHHHCCCHHHHHHHHHHCCEEEECCCCC----CHHHH Q ss_conf 83567578853047757876772002776220130122578999980999656301332111232178865----10432 Q gi|254780142|r 83 GIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRDVERVLYFESYVVVDPGLS----SLEKY 158 (1398) Q Consensus 83 g~~C~~Cg~~~~~~~~r~ghfGhIeLa~PV~Hi~f~k~~~~~i~~~l~~~~~~~~~v~y~~~~~~~~~~~~----~~~~~ 158 (1398) |.+|++||||+|++.|||+|||||+||.||+||||+|++||+|+.+|+++.+++|+|+||++|+++..... .++.. T Consensus 84 g~vCerCGVEvt~S~VRR~RMGHIeLAaPV~HIWYlK~~PS~Ia~LLdls~KeLEkViYf~~~iv~~~~~~~~~~~lk~~ 163 (668) T CHL00018 84 PKFCEQCGVEFVDSRIRRYRMGYIKLACPVTHVWYLKRLPSYIANLLDKPLKELEGLVYCDFSFARPIAKKPTFLRLRGL 163 (668) T ss_pred CCCCCCCCCCCCCCHHHHHCCCCEEECCCCCCHHHHCCCCHHHHHHHCCCHHHHHHEEEEEEEEEECCCCCCCHHHHHHH T ss_conf 62468778360401666750575545587130234268805999984898888754211037985246778413436777 Q ss_pred CCCCHHHHHHHHHHCCC-------CCEEECCCHHHHHHHHHHCCHHHHHHHHHHHHHCC-------------CCCHHHHH Q ss_conf 23699999886763585-------55061155267788877267488999999873103-------------22034788 Q gi|254780142|r 159 QILTEEEYVEAVSQFGQ-------DQFIAMMGADAIYELLIALDLQNLALTLRDQLSKS-------------SSIFRRKK 218 (1398) Q Consensus 159 ~~~~~~~~~~~~~~~~~-------~~~~~~~g~~~i~~~l~~~~~~~~~~~~~~~~~~~-------------~~~~~~~~ 218 (1398) ....+++|....+.+.. ......+|++|++++|.++|++.+....+.++... ...+++.+ T Consensus 164 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ei~~GaeAIkklL~~lDL~~~~~~l~~elk~l~~~~~~~~e~e~~ki~~kk~k 243 (668) T CHL00018 164 FEYEIQSWKYSIPLFFTTQGFDTFRNREISTGAGAIREQLADLDLRIIIENSLVEWKELGEEGPTGNEWEDRKIGRRKDF 243 (668) T ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHH T ss_conf 89999999987776530110032220221656999999997269999999999999975552010123445567788999 Q ss_pred HHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHH--CCCCHHHHHH Q ss_conf 64477888666634898511286304507622351388469731310037899999998699999987--3983567776 Q gi|254780142|r 219 IIKRLKIVDSFITSGNNPGWMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKS--LHAPEIIIRN 296 (1398) Q Consensus 219 ~~~~~~~~~~f~~~~~~Pewmil~~lpV~P~~~RP~v~~~~g~~~~dDlt~~~~~Ii~~N~~Lk~~~~--~~ap~~i~~~ 296 (1398) ++||+++++.|..++++||||||++|||+||++||+|+||||++++||||++|++||.+||||++++. .+||++|++| T Consensus 244 liKRLkli~~F~~SgnkPEWMILtVLPVLPPdLRPmVqLDGGrFatSDlN~lYrriI~rNnrL~~l~~~~~~~p~iIi~n 323 (668) T CHL00018 244 LVRRIELAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDLLTTSRSTPGELVMC 323 (668) T ss_pred HHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHH T ss_conf 99999999999866999424886345548987742489579841578517899999999999988775024895899999 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCEECHHHHHH Q ss_conf 99999998888742776787724787650678998610237820003465100457740341255435462003489877 Q gi|254780142|r 297 EKRMLQESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMAL 376 (1398) Q Consensus 297 ~~~lLQ~~v~~~~dn~~~~~~~~~~~~rp~ks~~~rlkgK~GrfR~nl~GKRVdfs~RsVI~pdP~l~~~evgvP~~~A~ 376 (1398) +|+|||+|||+||||+++|+|++++++||+|||+++||||+||||||||||||||||||||+|||+|++||||+|+.||. T Consensus 324 EkR~LQeaVd~lidN~~~g~~~~~~~~rplKslsd~lkGK~GrfRqnLlGKRVdySgRsVI~vgP~L~l~qcGlP~~mA~ 403 (668) T CHL00018 324 QKKLVQEAVDTLLDNGIRGQPMRDGHNKVYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAI 403 (668) T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEECCCCCCEEECCCCCHHHHH T ss_conf 99999999999872678788751889983411898854667610100366510455650332699732101288789999 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCEEECCCCCEEHHHHHHHCCCEEEECCCCCCEECCEEEEEEEEECCCEEEEECCCC Q ss_conf 61289999999987986663000100122488250132666569789975763101114012358994495479731225 Q gi|254780142|r 377 ELFKPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVC 456 (1398) Q Consensus 377 ~L~~P~~~~~L~~~g~~~~i~~~k~~i~~~~~~v~~v~rhl~~gd~Vl~NRqPsLHr~Simah~~~v~~~~t~rln~~vc 456 (1398) |||+||++++|+.+|.+.+++.||+++++..+.+|++++|+++||+|||||||||||||||||+|++++|+||||||+|| T Consensus 404 eLf~pf~i~~l~~~~~~~~~~~ak~~i~~~~~~~~~~l~~v~~~~~vllNRaPTLHrl~iqaf~p~l~~g~ai~lhplvc 483 (668) T CHL00018 404 ELFQPFVIRGLIRQHLASNIRVAKSKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVC 483 (668) T ss_pred HHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHHHHHHCCCEEEECCCCCCCCCCCEEEEEEECCCCEEEECCCCC T ss_conf 86028999999862776770788899986585999999987439847981785212132200025632783477244567 Q ss_pred CCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEEHHHHHHHHHHHHCCCC-------------CCC Q ss_conf 4546787754569974689999999999876750542378878204402589999998733678-------------874 Q gi|254780142|r 457 AGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHE-------------GDP 523 (1398) Q Consensus 457 ~pyNADFDGDEMnlHvPqs~eAraEa~~Lm~~~~niisP~~g~Pi~~~~QD~i~G~y~lT~~~~-------------~~~ 523 (1398) +||||||||||||+|||||.||||||+.||++++||+||++|+|++.|+|||++|+||||..+. ... T Consensus 484 ~~fNADFDGDqMavhvpls~ea~~Ea~~lm~s~~NilsPa~G~Pi~~psqdmvlg~yylt~~~~~~~~~~~~~~~~~~~~ 563 (668) T CHL00018 484 KGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYVLTSGNRRGICANRYNYQNDDNN 563 (668) T ss_pred CCCCCCCCCCEEEEECCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCC T ss_conf 87679988830465168998999999998644057777888997124442201143365035655432222211133546 Q ss_pred CCCCEECCHHHHHHHHHCCCCCCCCEEEEEECCCC--------------------------------CCCCCCCEEECCC Q ss_conf 46814179999999998889867852365204645--------------------------------6676142452179 Q gi|254780142|r 524 GEGMLFADMGEVYHALENKIVTLHSKIRGRYKSVD--------------------------------KDGNSISKIYDTT 571 (1398) Q Consensus 524 ~~~~~f~~~~~~~~~~~~~~~~~~a~i~~~~~~~~--------------------------------~~~~~~~~~~~tt 571 (1398) +++..|.+.++|..||..+.+.+|++||+++.... ..+.....++.|| T Consensus 564 ~~~~~f~~~~~~~~ay~~~~i~l~~~i~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~i~TT 643 (668) T CHL00018 564 TKEPYFSNSYDAIGAYRQKRINLDSPLWLRWRLDQRVIASREVPIEVQYESLGTYHEIYEHYLIVKSVKKEILSIYIRTT 643 (668) T ss_pred CCCCEECCHHHHHHHHHCCCEECCCEEEEEECCCCCCCCCCCCCEEEEECCCCCCEEECCCCEEEECCCCCEEEEEEEEC T ss_conf 78864689999999997594112560699723654444554565157751578511311011134225787556899707 Q ss_pred CCCCCCCEEEECCC Q ss_conf 77511220554587 Q gi|254780142|r 572 PGRMIIGEILPRHH 585 (1398) Q Consensus 572 ~Gr~~~~~ilp~~~ 585 (1398) +||.+||+++|++. T Consensus 644 ~Gri~fn~~i~~~l 657 (668) T CHL00018 644 VGRILFNREIEEAI 657 (668) T ss_pred CCEEEHHHHHHHHH T ss_conf 76113555659988 No 16 >PRK02597 DNA-directed RNA polymerase subunit beta'; Provisional Probab=100.00 E-value=0 Score=1336.17 Aligned_cols=767 Identities=41% Similarity=0.647 Sum_probs=634.3 Q ss_pred EEECCHHCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 77511002013666999999980817899987558899999998539861321232683699999999978999999886 Q gi|254780142|r 590 DICNQEMIKKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKMVKEYENQYN 669 (1398) Q Consensus 590 ~~~~~~~~k~~~~~li~~i~~~~G~~~~~~~l~~~~~l~~~~l~~~GfSigi~D~~~~~~k~~~i~~a~~~~~~~~~~~~ 669 (1398) .+.|+.++|+.++.||..+++.||...++.+||.++.+||+|+|.+|+|+|++|+.+|++|.+++++|++++.+++++|. T Consensus 7 ~f~N~~~~k~~l~~li~~~~~~~g~~~t~~~ld~lk~lGf~~at~ag~s~~i~D~~~p~~k~~~~~~a~~~~~~~~~~~~ 86 (1295) T PRK02597 7 PFRNRVVDKKALKKLIAWAFKNYGTARTAAMADNLKDLGFRYATQAAVSISVDDLKVPPAKRDLLEQAEEEITATEERYR 86 (1295) T ss_pred CCCCCCCCHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCCEEEEHHHCCCCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 85644156889999999999984989999999999876678762120498563255680399999999999999999865 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCHHHEEEEEEECCCCCCCCC Q ss_conf 48976678887886423465899999999998761156543222246883764225555784241120010000246443 Q gi|254780142|r 670 DGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIFMMSHSGARGSIHQMRQLGGMRGLIAKPSG 749 (1398) Q Consensus 670 ~G~~t~~e~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~N~~~~M~~SGAKGS~~qi~ql~Gqq~l~gkp~G 749 (1398) .|.+|+.|||++++++|..+.+.+.++|+.++... +++|+++||+.||||||++|++||+||||||++|+| T Consensus 87 ~g~it~~er~~~~i~~W~~~~~~~~~~~~~~~~~~---------~~~n~v~mm~~SGARGn~~qv~Ql~gmRGlma~p~g 157 (1295) T PRK02597 87 RGEITEVERFQKVIDTWNETNERLKDEVKKNFNQN---------DPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQG 157 (1295) T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC---------CCCCCEEEEECCCCCCCHHHHHHHHHCCCCCCCCCC T ss_conf 68877888777999999997999999998640012---------898765788667766788898777422103588699 Q ss_pred CCCCCCCCCHHHCCCCHHHHHHCCCCCCHHHHCCCCCCCCCCEEEEHHHHHHCCCEEEEECCCCCCCCEEEEEEECCEEE Q ss_conf 44456663011108889897640576103221012101567401101542301432775138876665121110088488 Q gi|254780142|r 750 EIIESPIRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVV 829 (1398) Q Consensus 750 ~~~~~PV~~sF~~GL~p~EfFfhamgGReGLiDTAvKTA~SGYlqRrLvk~~eDl~V~~~D~~t~~g~~~~~~~~~~~~~ 829 (1398) ++++.||++||++||+..|||.+|||+|+||+|||+|||+||||+||||+|+||++|++.||||.+|+.+..+.+++..+ T Consensus 158 ~ii~~Pi~snfreGl~v~ey~is~~GaRKGl~DTAlrTadsGYlTRrLvdvaq~vii~~~dcgt~~gi~~~~~~~~~~~~ 237 (1295) T PRK02597 158 EIIDLPIKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTTRGIVVEAMDDGDRVL 237 (1295) T ss_pred CEECCCHHHHCCCCCCHHHHHHCCCCCCCCHHHHHHHHCCCCCCHHHHHHHCCCCEEECCCCCCCCCEEEEEEECCCEEE T ss_conf 86573422203256348687553775541114536561254620005466327229966248999998998883797299 Q ss_pred EEECCCCCCCCCHHHCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEECCCCCCHHHHHCCCHHHHHHHCCCCCEECHH Q ss_conf 65000101221144201778971885178657899999999759840202331000355186578875420178520001 Q gi|254780142|r 830 YSLGSRVLGRTALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVG 909 (1398) Q Consensus 830 ~~l~~~~~~r~~~~di~~~~~~~~i~~~~~~i~~~~~~~i~~~~i~~v~irs~lt~~~~~~v~~~cy~~~l~~~~lv~pG 909 (1398) .+|.+|++||++++|+++| .+++|+.+|++|+++.++.+.++++++|.|||||||++.+|||++||||+|+++++|+.| T Consensus 238 ~~l~~r~~Gr~~~~~v~~~-~~~~i~~~~~~i~~~~~~~~~~~~~~~v~irs~ltc~~~~~vc~~cYG~~la~~~~v~~G 316 (1295) T PRK02597 238 IKLGDRLVGRVTAEDVVDP-DGEVIAERNTEIDPDLAKKIEKAGVEEVMVRSPLTCEANRSVCRKCYGWSLAHNHLVDLG 316 (1295) T ss_pred EEECCEEEEEEEHHHEECC-CCCEEEECCCCCCHHHHHHHHHCCCCEEEECCCCEECCCCCCCHHHCCCCCCCCCCCCCC T ss_conf 9810355646387567889-996899798675999999999869978997898053799737442008564588856567 Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEEEEEE---EEEEECCCCCEEEEEC-CCCEEEEECCC Q ss_conf 0146021111007889877642024543222112202401487689721---1346517887789742-76046640677 Q gi|254780142|r 910 EAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKN---RNVCRNSTNDLISMGR-NTTLQILDMSG 985 (1398) Q Consensus 910 e~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVPRlkE---i~~~~n~~~~~i~vs~-~~~~~i~d~~~ 985 (1398) ||||+||||||||||||+||||||.|||++......+.++..|..++.+ ....++..+....+.. +..+.+..... T Consensus 317 eaVGiiAaQSIGEPGTQLTmRTFHtGGvFTge~a~~vrap~~G~I~f~~~l~~~~~RTrhG~~A~~~~~~~~l~I~~~~~ 396 (1295) T PRK02597 317 EAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEVARVVRSPFAGTVEFGSKARTRPYRTRHGVEAQQAEVDFDLVLKPSGK 396 (1295) T ss_pred CEEEEEEECCCCCCHHHHHHHCCCCCCCCCCCCCEEEECCCCCEEECCCCCCCCEEECCCCCEEEEEECCCEEEEEECCC T ss_conf 72107764037886234546432417644576310550564758966766643033568995779875062899997799 Q ss_pred CEEEEEECCCHHCCCCCCCCEEECCEEEEECCCC---------CCEEEECCCCEEEEEEECCCC---------------- Q ss_conf 6000000110000135678553225078621354---------311320246368975312783---------------- Q gi|254780142|r 986 QEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPH---------TFPIITEVSGTVGFEDLVDGI---------------- 1040 (1398) Q Consensus 986 ~~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp~---------~~~i~~e~~~~v~~~~~~~~~---------------- 1040 (1398) .......++.++++++.+++.|++.++++++-.. ...+.++..|.+.|.+..... T Consensus 397 ~~~~~~~ip~~SlL~V~n~q~V~~~qvIAEi~a~~~~~~~Ek~~K~I~sd~~GEv~~~~~v~~~~~~~~gn~~~~~~~~g 476 (1295) T PRK02597 397 GKPQKIEITQGSLLFVDDGQTVEADQTLAEIAAGAVKKSTEKATKDVICDLAGEVRFADLIPEEKTDRQGNTTLKAQRLG 476 (1295) T ss_pred CCEEEEECCCCCEEEEECCCEEECCCEEEEEECCCCCCCEEEEEEEEEECCCCEEEECCCCCCCCCCCCCCEEEECCCCC T ss_conf 82689713898689998996984273899995376311126663226725775599503443443223376675225575 Q ss_pred ---------------------------------------------------------EE--------------------- Q ss_conf ---------------------------------------------------------20--------------------- Q gi|254780142|r 1041 ---------------------------------------------------------SV--------------------- 1042 (1398) Q Consensus 1041 ---------------------------------------------------------~~--------------------- 1042 (1398) .. T Consensus 477 ~lWILsG~vy~lp~~~~~~~k~~d~v~~~~~la~~~~~s~~gg~vr~~~~~~~~~e~~ii~~s~~l~~~~~~~~~~~~~~ 556 (1295) T PRK02597 477 LLWVLSGDVYNLPPGAEPVVKNGDRVEEGTVLAETSLVSEHGGVVRLRESIGDSREVEIVTASVTLDQAKVLEESTHGRE 556 (1295) T ss_pred EEEEEECCEECCCCCCCCEEECCCEECCCCEEEEEEEECCCCCEEECCCCCCCCCEEEEECCCCEECHHHHHHHHCCCCC T ss_conf 36998376014687645325147631136435775465166986753566888732443121001030112102014673 Q ss_pred ---HH-------------------------HHH----------------------------------------CCCC--- Q ss_conf ---01-------------------------230----------------------------------------2368--- Q gi|254780142|r 1043 ---IE-------------------------SIG----------------------------------------ESTG--- 1051 (1398) Q Consensus 1043 ---~~-------------------------~~~----------------------------------------~~t~--- 1051 (1398) .. ..+ +.+. T Consensus 557 ~~~l~~~~~~~~~l~~~p~~ki~n~~iiA~~~d~rYrT~t~GiiKY~~i~v~k~~~~k~~y~v~k~g~~~~IPEEth~i~ 636 (1295) T PRK02597 557 QYNLETKDGQRFRLNATPGTKVGNGEVVAELIDDRYRTKTGGLVKYAGLEVKKAGSAKNGYEVSKGGTLLWIPEETHEVN 636 (1295) T ss_pred EECCCCCCCCEEEECCCCCCCCCCCCEEEEECCCCEECCCCCCEEECCEEEEECCCCCCCCEEECCCEEEECCHHHCCCC T ss_conf 01011366624673048887323696778860675132788715665544410356566716712762897020531046 Q ss_pred --CEEEEE--------------------------EEHHHCCCCCC----------------------C------------ Q ss_conf --602677--------------------------51011012212----------------------3------------ Q gi|254780142|r 1052 --IAKRKV--------------------------IDWRFASRSQN----------------------L------------ 1069 (1398) Q Consensus 1052 --~~~~~~--------------------------i~~~~~~~~~~----------------------~------------ 1069 (1398) .+...+ .+++...+... . T Consensus 637 k~~Sli~V~ng~~I~~gTeI~kni~s~~~GlV~v~~Kn~il~EI~IkpG~i~~~~~~~~i~~~~~~li~PGe~I~~~~~~ 716 (1295) T PRK02597 637 KDISLLMVEDGQYVEAGTEVVKDIFCQTSGVVEVTQKNDILREIIVKPGELHLCDDPEALETGDGQLVNPGEEVLPGVVT 716 (1295) T ss_pred CCCCEEEEECCCEECCCCEEECCEEECCCCEEEEEECCCCEEEEEECCCCEECCCCCCHHHCCCCCEECCCCCCCCCCCC T ss_conf 65440687668354269565136040257369998716631489961572433676110010478477887543566322 Q ss_pred -------------------CC------------------------CEE------EECCCCC------------------- Q ss_conf -------------------85------------------------347------7427782------------------- Q gi|254780142|r 1070 -------------------KP------------------------AIV------VTDENGV------------------- 1081 (1398) Q Consensus 1070 -------------------~~------------------------~~~------i~d~~~~------------------- 1081 (1398) .| .+. +.-.++. T Consensus 717 ~~l~y~e~I~~~~~~~lLiRPv~~Y~I~~~~~~~~~~~~~~~~~~~i~l~~v~~i~ykdge~Iksi~gIqLvrT~LvL~~ 796 (1295) T PRK02597 717 DELVYVETVETPEGPGLLLRPVEEFTIPDEPQLPSQGSVKQEKGRSIGLRAVQRLPYKDGERVKSVEGVELLRTQLVLEI 796 (1295) T ss_pred CCEEEEEEEECCCCCEEEECCCEEEECCCCCCCCCCCCHHHCCCCCEEEEEEEEEECCCCCEEEEECCEEEEEEEEEEEE T ss_conf 52599999825877408863317986368866666552233247733688989997059966643157068988899983 Q ss_pred -------------------------------------------------------------------------------- Q ss_conf -------------------------------------------------------------------------------- Q gi|254780142|r 1082 -------------------------------------------------------------------------------- 1081 (1398) Q Consensus 1082 -------------------------------------------------------------------------------- 1081 (1398) T Consensus 797 ~~~~~~~~~die~~~~~~~~~~~rl~lviles~l~r~d~~~d~~~~s~~t~llv~~~q~I~~~~via~t~il~~~~g~ir 876 (1295) T PRK02597 797 FDTTPQLTADIELIPDKKDKTIQRLQLVILESLLVRRDTASDSSHGSTHTELLVKDGQSIKPGDVVARTQILCKEAGVVQ 876 (1295) T ss_pred CCCCCEEEEEEEEECCCCCCCCCEEEEEEEEHHEEECCCCCCCCCCCCCEEEECCCCCCCCCCCEEEEEEEEEECCEEEC T ss_conf 58874367999980487544411002553000102157777867884102453157863188876524676554160451 Q ss_pred ------------------------------------------------------EEECCC-----CCCCEEECCCCCEEE Q ss_conf ------------------------------------------------------532247-----884202137784454 Q gi|254780142|r 1082 ------------------------------------------------------VLKSAR-----GTDARWFLPVDALLS 1102 (1398) Q Consensus 1082 ------------------------------------------------------~~~~~~-----~~~~~~~~~~~~~~~ 1102 (1398) +..... .....|....++... T Consensus 877 ~i~~~~~~~r~ili~~~~d~~~i~~~~~~~v~lGqlI~~g~~I~~~~~~~~SGQVi~I~~~~ivIRlakPYL~s~gA~ih 956 (1295) T PRK02597 877 GIRVGDEPVRRLLVERDEDTITIPLSGKPVVKVGDLVVAGDELAPGVPAPESGEVEAVSGGSVTLRLGRPYMVSPGAVLH 956 (1295) T ss_pred CHHCCCCCCEEEEECCCCCCEEECCCCCCEECCCCEEECCEEECCCCCCCCCCEEEEEECCEEEEEECCEEECCCCCEEE T ss_conf 31025753006997477776565478874874888898781742898767861289984785899854617759996898 Q ss_pred ECCCCCCCCCCEEEECHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCEECCCCCEEEEEEECCCCEEEEEEECCCCCCEEE Q ss_conf 13676135484222101320245543367732889887525111101113478678633127944999983689840268 Q gi|254780142|r 1103 VSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFEARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAE 1182 (1398) Q Consensus 1103 v~~~~~v~~~d~l~~~~~~~~k~~DIt~GLPrV~eLFEar~pk~~aiisei~Giv~i~~~~~~k~~~vi~~~~~g~~~~e 1182 (1398) +.+++-+..||.++.+..+..++.||+||||||+||||||+||+.+++++.+|++.+...... ..+.+..........+ T Consensus 957 v~~GdiV~~GDtLvtLiyEr~KSGDIiQGLPKVEeLLEARkpk~~~~l~~~~G~v~~~~~~~~-~si~i~v~e~d~~~~e 1035 (1295) T PRK02597 957 VRDGDLVQRGDNLALLVFERAKTGDIIQGLPRIEELLEARKPKESCILCKKPGTVQIKYGDDD-ESVDVKVIEDDGTITE 1035 (1295) T ss_pred EECCCEEECCCEEEEEEEEHHCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCEEECCCCCC-CCEEEEEEECCCCCEE T ss_conf 426879714976788752010147745687017877543155531000035760232135666-6426787622674200 Q ss_pred EEECCCCEEEEECCCEEECCCEEECCCCCHHHHHHH----------------HCHHHHHHHHHHHHHHHHHHHCCEECHH Q ss_conf 981389658984198774086464389999999875----------------2799999999999999999809700612 Q gi|254780142|r 1183 YFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDILRI----------------KGVEALASYLINEVQEVYRLEGVAINHK 1246 (1398) Q Consensus 1183 ~~ip~~~~l~v~dgd~V~~gd~lt~Gsid~~eIl~v----------------lGIEAAR~~Ii~EIq~V~~~~Gi~IN~R 1246 (1398) |.+..+.++.+.+|+.|.+|+.+|||.++||++|++ ++++..|.+||+|||+||++|||.|++| T Consensus 1036 y~~~~g~~~~v~~g~~V~~ge~lTdg~~npH~iL~i~f~~~~~~~g~~~aA~lSi~q~Q~~LVneIQkVYrSQGV~IsDK 1115 (1295) T PRK02597 1036 YPILPGQNVMVSDGQQVDAGEPLTDGPINPHELLECFFEDLRDRKGLYEAAQEALAKLQRFLVNEVQNVYQSQGVDIDDK 1115 (1295) T ss_pred CCCCCCCCEEECCCCEEECCCCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHEECCCCCEEECC T ss_conf 13455632242257366136524578788788876566653021667889999999999999987651504489566041 Q ss_pred HHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHHHH Q ss_conf 56012476286148941886454566410699999999999972898752012100001453023107765040258999 Q gi|254780142|r 1247 HIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKV 1326 (1398) Q Consensus 1247 HIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~~v 1326 (1398) |||+||+|||+|+.|.|+|||.|+||+.|+..+++.+||.+...|+.|+.|+|+|||||||||+|+||||+||||||++| T Consensus 1116 HIEIIVRQMTSKV~IeDgg~T~FLPGELIeL~raer~Nral~~~gg~~a~Y~PILLGITKASLNT~SFISAASFQETTRV 1195 (1295) T PRK02597 1116 HIEVIVRQMTSKVRIDDGGDTTLLPGELIELRQVEQVNQAMAITGGAPAEFTPVLLGITKASLNTDSFISAASFQETTRV 1195 (1295) T ss_pred EEEEEEEECCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEEECCCCCCCHHHHHCHHHHHHH T ss_conf 79999996344189972878742872244199999998999962798774698987676021156531244321548899 Q ss_pred HHHHHHCCCEECCCCCCEEEECCCCCCCCCCHHHHHHHHHH Q ss_conf 99974528552366532215507305655354665331210 Q gi|254780142|r 1327 LTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAILHEKRRVA 1367 (1398) Q Consensus 1327 L~eAAi~ge~D~L~GvSENIIlGqliP~GTG~f~~~~~~~~ 1367 (1398) |++||+.|++|||+|+|||||+|+|||||||+..|..-.+. T Consensus 1196 LTkAAIeGRiDWLrGLKENVIiGrlIPAGTGf~~~~~~~~~ 1236 (1295) T PRK02597 1196 LTEAAIEGKSDWLRGLKENVIIGRLIPAGTGFSGFEETAVL 1236 (1295) T ss_pred HHHHHHCCCHHHHCCCCHHEEECCCEECCCCCCCCCCCCCC T ss_conf 99998727703326852215722747567681754221235 No 17 >TIGR02388 rpoC2_cyan DNA-directed RNA polymerase, beta'' subunit; InterPro: IPR012756 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription. Probab=100.00 E-value=0 Score=1272.29 Aligned_cols=759 Identities=41% Similarity=0.669 Sum_probs=609.4 Q ss_pred EECCHHCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 75110020136669999999808178999875588999999985398613212326836999999999789999998864 Q gi|254780142|r 591 ICNQEMIKKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKMVKEYENQYND 670 (1398) Q Consensus 591 ~~~~~~~k~~~~~li~~i~~~~G~~~~~~~l~~~~~l~~~~l~~~GfSigi~D~~~~~~k~~~i~~a~~~~~~~~~~~~~ 670 (1398) +.|+.++|+.+..||..-|..||...|+.+.|.++.|||+|+|+.|.||+++|+.+|++|+++|+.|+++++.-+..|.+ T Consensus 2 F~N~~vDK~~L~~Li~way~~~GtA~ta~~AD~lKdLGF~yAT~AgVSISVdDL~vP~~K~~lle~AE~~I~~te~rY~~ 81 (1252) T TIGR02388 2 FKNRVVDKKALKNLISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPPEKQDLLEAAEKEIRATEERYRR 81 (1252) T ss_pred CCEEEEEHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCHHHHHHCCEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 31005414678889999874058325788877765200011322401698705548878999999888876778876305 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCHHHEEEEEEECCCCCCCCCC Q ss_conf 89766788878864234658999999999987611565432222468837642255557842411200100002464434 Q gi|254780142|r 671 GLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIFMMSHSGARGSIHQMRQLGGMRGLIAKPSGE 750 (1398) Q Consensus 671 G~~t~~e~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~N~~~~M~~SGAKGS~~qi~ql~Gqq~l~gkp~G~ 750 (1398) |.||+-||+.|+++.|+.|.+++.+++..+|++. ++.|++|||+.||||||++|++|||||||||+.|.|+ T Consensus 82 GEITEVERf~KVIDTW~~T~E~L~d~V~~~F~~~---------dpLNSVyMMAfSGARGN~SQVRQLVGMRGLMA~PQGE 152 (1252) T TIGR02388 82 GEITEVERFQKVIDTWNGTNEELKDEVVNNFRQT---------DPLNSVYMMAFSGARGNLSQVRQLVGMRGLMADPQGE 152 (1252) T ss_pred CCEEEEECCEEEEECCCCCCHHHHHHHHHHHHCC---------CCCCEEEEECCCCCCCCHHHHHHHHCCCCCCCCCCCC T ss_conf 8613530200476455661168899999864205---------8732110002168756634565543131225689976 Q ss_pred CCCCCCCCHHHCCCCHHHHHHCCCCCCHHHHCCCCCCCCCCEEEEHHHHHHCCCEEEEECCCCCCCCEEEEEEECCEEEE Q ss_conf 44566630111088898976405761032210121015674011015423014327751388766651211100884886 Q gi|254780142|r 751 IIESPIRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVY 830 (1398) Q Consensus 751 ~~~~PV~~sF~~GL~p~EfFfhamgGReGLiDTAvKTA~SGYlqRrLvk~~eDl~V~~~D~~t~~g~~~~~~~~~~~~~~ 830 (1398) +|+.||+.||++|||..||.++++|+|+||+|||++|||||||+||||+++||++||+.||+|+.|+.+..+.++++... T Consensus 153 IIDLPIkTNFREGLTVTEYvISSYGARKGLVDTALRTADSGYLTRRLVDVsQDVIvRE~DCgT~R~i~~~~mt~g~k~~~ 232 (1252) T TIGR02388 153 IIDLPIKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTERSIVVRAMTEGDKVVI 232 (1252) T ss_pred EEECCCCCCCCCCCEEEEEEEECCCCCCCHHHHHHHHCCCCCHHHEEEEEECCEEEECCCCCCCCCEEEEEECCCCEEEE T ss_conf 78468544653685356456632354422034554312553101101333231589614688524358876247872799 Q ss_pred EECCCCCCCCCHHHCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEECCCCCCHHHHHCCCHHHHHHHCCCCCEECHHH Q ss_conf 50001012211442017789718851786578999999997598402023310003551865788754201785200010 Q gi|254780142|r 831 SLGSRVLGRTALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVGE 910 (1398) Q Consensus 831 ~l~~~~~~r~~~~di~~~~~~~~i~~~~~~i~~~~~~~i~~~~i~~v~irs~lt~~~~~~v~~~cy~~~l~~~~lv~pGe 910 (1398) .|.+|++||+.++|+++|.++++|+++|+.|++..++.|.++++.+|.||||||||+.+.||++||||.|++.++|..|| T Consensus 233 ~l~~RL~GR~~~~Dv~~p~tge~i~~~N~~I~~~Lak~i~~~~~~~V~vRSPLTCEA~rSVC~~CYGWsLAH~~~VDlGE 312 (1252) T TIGR02388 233 KLADRLLGRLVAEDVLHPETGEVIVPKNTAIDEDLAKKIEKAGIEEVVVRSPLTCEAARSVCRKCYGWSLAHAHLVDLGE 312 (1252) T ss_pred EECCCCEEEEEHHHCCCCCCCEEEECCCCCCCHHHHHHHHHHHHCEEEECCCCCCCCCCCCCCCCCCHHHHHCCCEECCC T ss_conf 86254022332100247654606611676021899999975111576871687401252210045422555356010222 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEEEEEEE---EEEECCCCCE-EEEECCCCEEEEECCCC Q ss_conf 1460211110078898776420245432221122024014876897211---3465178877-89742760466406776 Q gi|254780142|r 911 AVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNR---NVCRNSTNDL-ISMGRNTTLQILDMSGQ 986 (1398) Q Consensus 911 ~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVPRlkEi---~~~~n~~~~~-i~vs~~~~~~i~d~~~~ 986 (1398) |||+|||||||||||||||||||++||++.......++...|.+.+-.- ...+...+.- ..+-.+..+.+...... T Consensus 313 AVGIIAAQSIGEPGTQLTMRTFHTGGVfTgEva~~~r~~~~G~v~~g~kl~~R~~RTrHG~dA~~vE~~g~l~~~~~~~~ 392 (1252) T TIGR02388 313 AVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEVARQVRSKIDGTVEFGKKLRIRKYRTRHGEDAKQVEVAGLLILKPEGKK 392 (1252) T ss_pred CEEEEEEECCCCCCCCCCCEEEECCCEEECCCCEEEECCCCCEEECCCCCEECCCCCCCCCCCEEEEEEEEEEECCCCCC T ss_conf 01200210368797533220342386431332202214545337558721234556887644002333106898357654 Q ss_pred ----EEEEEECCCHHCCCCCCCCEEECCEEEEECC-----------CCCCEEEECCCCEEEEEEEC-------------- Q ss_conf ----0000001100001356785532250786213-----------54311320246368975312-------------- Q gi|254780142|r 987 ----EQYSHRIMYGAKLFVDDGGVIECGQRISEWD-----------PHTFPIITEVSGTVGFEDLV-------------- 1037 (1398) Q Consensus 987 ----~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~D-----------p~~~~i~~e~~~~v~~~~~~-------------- 1037 (1398) ....+.+..|+++++.+|+.|.+.+.+++.. ..+..+..+..|.+.|..++ T Consensus 393 ~~~~~~Q~~~~t~GS~~~v~DG~~v~~g~l~a~~~~~~r~~~~~~Eka~KDV~~DLAGeV~f~~~~~p~e~~DRQGn~T~ 472 (1252) T TIGR02388 393 TETAAAQEIEVTQGSLLFVEDGQTVKAGQLLAEIALGARAVRKSTEKATKDVASDLAGEVKFDKVVQPEEKTDRQGNTTR 472 (1252) T ss_pred CCCCCCCEEEECCCCEEEEECCCCCHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCCCCCHHH T ss_conf 45656544772377389986376100061000134410244443222222123103473353221062203367763113 Q ss_pred -------------------------------------------------------------------------------- Q ss_conf -------------------------------------------------------------------------------- Q gi|254780142|r 1038 -------------------------------------------------------------------------------- 1037 (1398) Q Consensus 1038 -------------------------------------------------------------------------------- 1037 (1398) T Consensus 473 ~A~rgGl~WvLsGeVYNLPPgA~pVV~~~~~vE~g~vlAEt~~~t~~GG~VRL~e~~~~k~~REv~IiTaSvlLd~~~v~ 552 (1252) T TIGR02388 473 IAQRGGLIWVLSGEVYNLPPGAEPVVKNGDRVEAGTVLAETKLSTEHGGVVRLPESVDSKDSREVEIITASVLLDQAKVI 552 (1252) T ss_pred HHHCCCEEEEEECCEECCCCCCEEEECCCCEECCCCEEEEEEEEECCCCEEEECCCCCCCCCCEEEEEEEEEEECCCEEE T ss_conf 32026758998332103888871164068775124266423542047875872245788876458888722100111235 Q ss_pred -------------------------------------------------------------------------------- Q ss_conf -------------------------------------------------------------------------------- Q gi|254780142|r 1038 -------------------------------------------------------------------------------- 1037 (1398) Q Consensus 1038 -------------------------------------------------------------------------------- 1037 (1398) T Consensus 553 ~es~~gre~y~i~t~~~~~f~L~a~PGtKv~~g~vvAeLiDdRyrT~TGG~~kyApg~~V~K~g~~K~GyEV~~GGTLLW 632 (1252) T TIGR02388 553 EESSQGREQYLIETADGQRFRLKAAPGTKVQNGQVVAELIDDRYRTTTGGLLKYAPGVEVAKKGKAKQGYEVVKGGTLLW 632 (1252) T ss_pred EECCCCCEEEEEECCCCCEEEEECCCCCCCCCCCEEEEECCCCCCCCCCCEEEECCCCEEEECCCCCCCCEEECCCEEEE T ss_conf 21127750478981787189986588861126646465215651014575478628732721676667707613873752 Q ss_pred -------------------------------------------------------------------------------- Q ss_conf -------------------------------------------------------------------------------- Q gi|254780142|r 1038 -------------------------------------------------------------------------------- 1037 (1398) Q Consensus 1038 -------------------------------------------------------------------------------- 1037 (1398) T Consensus 633 IP~ETHE~NKDISLL~vED~~yvEAGTEVVKDIFcQ~SG~V~V~QKNDILREi~vk~G~~~~~~D~e~~~rf~~~g~L~~ 712 (1252) T TIGR02388 633 IPEETHEINKDISLLLVEDGQYVEAGTEVVKDIFCQNSGIVEVVQKNDILREIIVKPGELHEVDDPEAVKRFLEEGTLLQ 712 (1252) T ss_pred CCCCCCCCCCCEEEEEEECCCEEEECCEEEEEEEECCCCEEEEEECCCCEEEEEEECCCEEEECCHHHHHHHHHCCCCCC T ss_conf 67532100243468775266345406347764551588669998527505788971782244358799999873684027 Q ss_pred ------------------------------------------------------------------------------CC Q ss_conf ------------------------------------------------------------------------------78 Q gi|254780142|r 1038 ------------------------------------------------------------------------------DG 1039 (1398) Q Consensus 1038 ------------------------------------------------------------------------------~~ 1039 (1398) +| T Consensus 713 PGe~~~~G~~~~~l~~~~~~E~~p~G~~lLlRpV~Ey~vp~ep~~P~~~~~~~~~G~~i~lravQRL~YKd~e~vKSVeG 792 (1252) T TIGR02388 713 PGEEVLPGVVVDELSQVQYLEDTPEGKGLLLRPVEEYKVPDEPEVPSQSSVSQEKGRSIELRAVQRLPYKDGERVKSVEG 792 (1252) T ss_pred CHHHHHCCCCHHHHHHHHHHHCCCCCCEEEECCEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCEEEEECC T ss_conf 81666288302454544654148898735533302331578756786344112578668887664134447861355448 Q ss_pred CEEH------H---HHHC---CCCCEE----------------------------------------------------- Q ss_conf 3200------1---2302---368602----------------------------------------------------- Q gi|254780142|r 1040 ISVI------E---SIGE---STGIAK----------------------------------------------------- 1054 (1398) Q Consensus 1040 ~~~~------~---~~~~---~t~~~~----------------------------------------------------- 1054 (1398) ..+. + .... .+.+.. T Consensus 793 v~LL~T~LvlE~~~~~~~~~~~s~l~~DiE~~~D~~d~~~~RL~LVILESl~~RRD~~~D~~~Gst~T~L~v~dgd~i~p 872 (1252) T TIGR02388 793 VELLRTQLVLEIEDEGPQEHNISHLAADIELIQDEEDKDIQRLQLVILESLVLRRDIASDSTQGSTKTSLLVKDGDLIKP 872 (1252) T ss_pred CHHHCEEEEEEECCCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHCCCHHCCCCCCCEEEEEECCCCEECC T ss_conf 11001024677424573000753036777764487543102555554345444302000356884125788416876167 Q ss_pred -----------------------------EEEEEHH-------------------HCCCCCCCCCCEEEECCCCCEEECC Q ss_conf -----------------------------6775101-------------------1012212385347742778253224 Q gi|254780142|r 1055 -----------------------------RKVIDWR-------------------FASRSQNLKPAIVVTDENGVVLKSA 1086 (1398) Q Consensus 1055 -----------------------------~~~i~~~-------------------~~~~~~~~~~~~~i~d~~~~~~~~~ 1086 (1398) +.+.... +......+.+. ....+.+.+.... T Consensus 873 G~V~A~T~I~~Ke~G~v~g~~~~~~E~~RR~lv~r~~D~~~~~~~g~kp~VK~Gdl~v~G~~l~~G-v~~~~~g~~~~v~ 951 (1252) T TIGR02388 873 GAVVARTQILCKEAGVVRGIKKGEGESIRRVLVERNSDRLKVNIKGAKPKVKTGDLVVAGDELAKG-VKAEESGEVLEVK 951 (1252) T ss_pred CCEEEEEEECCCCCCEEEECCCCCCCCEEEEEEEECCCEEEEEECCCCCCCCCCCEEECCCHHCCC-CCCCCCCEEEEEC T ss_conf 755873000015676685033467761358999725764898405788612467654176121277-3444662056731 Q ss_pred CCC---------CCEEECCCCCEEEECCCCCCCCCCEEEECHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCEECCCCCEE Q ss_conf 788---------42021377844541367613548422210132024554336773288988752511110111347867 Q gi|254780142|r 1087 RGT---------DARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFEARRPKNHAILAEISGTI 1157 (1398) Q Consensus 1087 ~~~---------~~~~~~~~~~~~~v~~~~~v~~~d~l~~~~~~~~k~~DIt~GLPrV~eLFEar~pk~~aiisei~Giv 1157 (1398) ... .-.|....++.+.+.+|+-+..||.++.+..+.+|+.||.||||||+||+|||+||+.++++.-.|.+ T Consensus 952 ~~~~~~~v~lR~~RPY~VSPgaVL~i~dGDLV~RGDnL~LLVFER~KTGDIvQGLPRIEELLEAR~Pke~c~La~~~G~~ 1031 (1252) T TIGR02388 952 NADDNYAVILRIARPYRVSPGAVLHIEDGDLVQRGDNLVLLVFERAKTGDIVQGLPRIEELLEARKPKEACVLAKRPGVV 1031 (1252) T ss_pred CCCCCCEEEEECCCCCEECCCCEEEEECCCEEEECCCEEEEEEECCCCCCEECCCCCHHHHHHCCCCCCCEEEECCCCEE T ss_conf 58885079996178843478654775458566517855899873046686211885068886227972113662279769 Q ss_pred EEEEECCCC--EEEEEEECCCCCCEEEEEECCCCEEEEECCCEEECCCEEECCCCCHHHHHHHH---------------- Q ss_conf 863312794--49999836898402689813896589841987740864643899999998752---------------- Q gi|254780142|r 1158 RIKRNYKNK--SRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDILRIK---------------- 1219 (1398) Q Consensus 1158 ~i~~~~~~k--~~~vi~~~~~g~~~~e~~ip~~~~l~v~dgd~V~~gd~lt~Gsid~~eIl~vl---------------- 1219 (1398) .+....... .--||+ .+| ...+|.+..+.++.+.||..|..++.||||.+||||||++| T Consensus 1032 ~v~~~~~desv~i~ViE--~dg-~~~eY~ll~GQN~~v~DG~~v~~g~~LtDGp~nPH~iL~~~F~~~~~~~g~~~aA~~ 1108 (1252) T TIGR02388 1032 QVKYGEDDESVEIKVIE--EDG-TVSEYPLLPGQNIMVSDGQKVDVGEPLTDGPINPHDILDVFFSYYKDKDGLLEAAQE 1108 (1252) T ss_pred EEEECCCCCEEEEEEEE--CCC-CEEECCCCCCCCCEEECCCEECCCCCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHH T ss_conf 99886887568999980--588-361213568785222078551367423688987378999887523575247999999 Q ss_pred CHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEE Q ss_conf 79999999999999999980970061256012476286148941886454566410699999999999972898752012 Q gi|254780142|r 1220 GVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSP 1299 (1398) Q Consensus 1220 GIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~~~p 1299 (1398) +++++|+.|+||+|.||.+|||.|.|||||+|+||||.|++|-|+|||.+|+|+.|.....+..|..+--.|+.||.|.| T Consensus 1109 ~l~k~Q~~lVNEVQ~VY~SQGv~I~DKHIEVIVRQMT~KVRIdD~GDT~lLpGEL~~LRQvE~~N~aM~iTGgApA~yTP 1188 (1252) T TIGR02388 1109 SLQKVQKFLVNEVQSVYQSQGVDISDKHIEVIVRQMTSKVRIDDAGDTTLLPGELVELRQVEQVNEAMAITGGAPAQYTP 1188 (1252) T ss_pred HHHHHHHHHHHHHHHHHHCCCEEEECCEEEEEEEECCCEEEEECCCCEEECCCCEEEEECHHCCCCCCCCCCCCCCCCCC T ss_conf 99999887635554232107814533448999962465236635887055373202200021035521013678652331 Q ss_pred EEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCCCCCCCCCHHHHH Q ss_conf 100001453023107765040258999999745285523665322155073056553546653 Q gi|254780142|r 1300 ILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAILHE 1362 (1398) Q Consensus 1300 ~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG~f~~~ 1362 (1398) +|||||||||+||||+|||||||||+||+|||+.|+.|||||+|||||+|||||||||+.-|. T Consensus 1189 VLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGf~~~~ 1251 (1252) T TIGR02388 1189 VLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGFSSYE 1251 (1252) T ss_pred EEEECHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHCCCEEEEEEEEECCCCCCCCCCC T ss_conf 320001121021013443100014566655430576023146600178863126888777577 No 18 >CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed Probab=100.00 E-value=0 Score=1183.26 Aligned_cols=436 Identities=36% Similarity=0.568 Sum_probs=398.2 Q ss_pred EEECCHHCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 77511002013666999999980817899987558899999998539861321232683699999999978999999886 Q gi|254780142|r 590 DICNQEMIKKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKMVKEYENQYN 669 (1398) Q Consensus 590 ~~~~~~~~k~~~~~li~~i~~~~G~~~~~~~l~~~~~l~~~~l~~~GfSigi~D~~~~~~k~~~i~~a~~~~~~~~~~~~ 669 (1398) -+.|+.++|+.+..||..++..||...|+.|+|.++.|||+|+|..|.|+|++|+.+|++|..++++|++++..++.+|. T Consensus 8 ~f~n~~~~k~~~~~~i~~~~~~~g~~~t~~~~d~~k~~gf~~at~~g~s~~i~dl~~~~~k~~~~~~a~~~~~~~~~~~~ 87 (1350) T CHL00117 8 VFHNKVIDKTALKRLISRLIDHFGMAYTSHILDQLKTLGFQQATAAGISLGIDDLLTPPSKGWLLQDAEQQSLILEKHYH 87 (1350) T ss_pred EEEECCCCHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHHCCEEEEHHHCCCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 38801056889999999999985979999999999876768751132587450164680499999999999999999975 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCHHHEEEEEEECCCCCCCCC Q ss_conf 48976678887886423465899999999998761156543222246883764225555784241120010000246443 Q gi|254780142|r 670 DGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIFMMSHSGARGSIHQMRQLGGMRGLIAKPSG 749 (1398) Q Consensus 670 ~G~~t~~e~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~N~~~~M~~SGAKGS~~qi~ql~Gqq~l~gkp~G 749 (1398) .|.+|+.||+++++++|..|.|.+.++|+.+++.. +++|+++||+.||||||++|++||+||||||++|.| T Consensus 88 ~g~~~~~e~~~~~i~~w~~~~~~~~~~~~~~~~~~---------~~~n~v~~m~~sgarg~~~qv~ql~gmrglm~~p~g 158 (1350) T CHL00117 88 YGNVTAVEKLQQSIETWYATSEYLKQEMNPNFRMT---------DPLNPVYMMAFSGARGNASQVHQLVGMRGLMSDPQG 158 (1350) T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC---------CCCCCEEEEECCCCCCCHHHHHHHHHCCCCCCCCCC T ss_conf 67876788777999999987999999998766316---------898871467657667888998887423214568799 Q ss_pred CCCCCCCCCHHHCCCCHHHHHHCCCCCCHHHHCCCCCCCCCCEEEEHHHHHHCCCEEEEECCCCCCCCEEEEEEECCEEE Q ss_conf 44456663011108889897640576103221012101567401101542301432775138876665121110088488 Q gi|254780142|r 750 EIIESPIRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVV 829 (1398) Q Consensus 750 ~~~~~PV~~sF~~GL~p~EfFfhamgGReGLiDTAvKTA~SGYlqRrLvk~~eDl~V~~~D~~t~~g~~~~~~~~~~~~~ 829 (1398) .+++.||.+||+|||+..|||.+|+|+|+||+|||+|||+||||+||||+|+||++|++.||||.+|+.+.. .++.... T Consensus 159 ~ii~~pi~~nfregl~~~ey~is~~garkg~~dtalrta~~gyltrrlvdv~q~~iv~~~dc~t~~gi~~~~-~~~~~~~ 237 (1350) T CHL00117 159 QIIDLPIQSNFREGLSLTEYIISCYGARKGVVDTALRTADAGYLTRRLVDVVQHIVVRRTDCGTIRGISVSP-RNGMMPE 237 (1350) T ss_pred CEECCCHHHHCCCCCCHHHHHHCCCCCCCCHHHHHHHHCCCCCCCHHHHHHCCEEEEECCCCCCCCCEEEEE-CCCCEEE T ss_conf 866743222121564776720137853311255565503646420043643363699554689988789992-6997575 Q ss_pred EEECCCCCCCCCHHHCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEECCCCCCHHHHHCCCHHHHHHHCCCCCEECHH Q ss_conf 65000101221144201778971885178657899999999759840202331000355186578875420178520001 Q gi|254780142|r 830 YSLGSRVLGRTALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVG 909 (1398) Q Consensus 830 ~~l~~~~~~r~~~~di~~~~~~~~i~~~~~~i~~~~~~~i~~~~i~~v~irs~lt~~~~~~v~~~cy~~~l~~~~lv~pG 909 (1398) ..|.+|++||++++|+++|.++++|+.+|+.|++..++.+.+++++++.|||||||++.+|+|++||||+|+++++|+.| T Consensus 238 ~~~~~~~~grv~~~~~~~~~~~~~i~~~~~~i~~~~~~~~~~~~~~~i~vrspltc~~~~~ic~~cyg~~l~~~~~v~~g 317 (1350) T CHL00117 238 RILIQTLIGRVLADDIYIPKGSRCIATRNQDIGIGLVNRFITFRIQPIYIRSPLTCRSTSWICQLCYGWSLTHGDLVELG 317 (1350) T ss_pred EEECCEEEEEEEHHHEECCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCEEECCCCCCCHHHCCCCCCCCCCCCCC T ss_conf 22001011157773578089985998399675999999999879988997898120688758653348552268876457 Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEEEEEEE--EEEECCCCCEEEEECCC-CEEEEECCCC Q ss_conf 01460211110078898776420245432221122024014876897211--34651788778974276-0466406776 Q gi|254780142|r 910 EAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNR--NVCRNSTNDLISMGRNT-TLQILDMSGQ 986 (1398) Q Consensus 910 e~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVPRlkEi--~~~~n~~~~~i~vs~~~-~~~i~d~~~~ 986 (1398) ||||+||||||||||||+||||||+|||.+...+..+.++..|+.++.+. ..+++..+....+..+. .+.+. .... T Consensus 318 eavgiia~qsigepgtqlt~rtfhtggvftge~ae~iraP~~G~I~f~~~~~~~~RTrhG~~A~l~~~~~~l~I~-~~~~ 396 (1350) T CHL00117 318 EAVGIIAGQSIGEPGTQLTMRTFHTGGVFTGGTAEQVRAPFNGKIKFNEDLVHPTRTRHGHPAFLCKIDLYVTIV-ESED 396 (1350) T ss_pred CEEEEEEEECCCCCCCCCEEEEEEECCEECCCHHHHCCCCCCCEEECCCCCCCCCCCCCCCEEEEEECCEEEEEE-CCCC T ss_conf 753588630158886420356543355003421432017767458536545543134688534887214069985-4788 Q ss_pred EEEEEECCCHHCCCCCCCCEEECCEEEEECCCC----------CCEEEECCCCEEEEEEE Q ss_conf 000000110000135678553225078621354----------31132024636897531 Q gi|254780142|r 987 EQYSHRIMYGAKLFVDDGGVIECGQRISEWDPH----------TFPIITEVSGTVGFEDL 1036 (1398) Q Consensus 987 ~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp~----------~~~i~~e~~~~v~~~~~ 1036 (1398) ......+|.++++++..++.|++.|++++.-.. ...+.++..|.+.|... T Consensus 397 ~~~~~~ip~~SlL~V~n~q~V~s~QvIAEi~~~~~~~~~~Ek~~K~i~S~~~GEv~~~~~ 456 (1350) T CHL00117 397 IIHNVNIPPKSLLLVQNDQYVESEQVIAEIRAGTSTLKFKEKVRKHIYSDSEGEMHWSTD 456 (1350) T ss_pred EEEEEEECCCCEEEEECCCEEECCCEEEEEECCCCCCCCCEEEEEEEECCCCCCEEECCC T ss_conf 179988679848999899587516189997057775545305887775488642681364 No 19 >TIGR02387 rpoC1_cyan DNA-directed RNA polymerase, gamma subunit; InterPro: IPR012755 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription. Probab=100.00 E-value=0 Score=1194.45 Aligned_cols=537 Identities=59% Similarity=1.000 Sum_probs=515.9 Q ss_pred CEEEEEEECCCHHHHHHCC---------EEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 0536898458867885014---------4897175542545687568873362136856677215664156344883567 Q gi|254780142|r 17 GFDSVRISIASPAKIASLS---------YGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRMKYKGIICE 87 (1398) Q Consensus 17 ~i~~i~f~l~spe~I~~~S---------~~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~Cg~~~~~~~~g~~C~ 87 (1398) +|+.|+++++|||.|..|. +|||++|||+||+|+|||-+||||++||||.|||||.||||||+||+|.+|+ T Consensus 1 ~fdy~ki~~asPer~~~WG~rtlPnG~vvGevtkPetinyrtlkPemdGlfCe~ifGPskdWeC~CGkykrvrhrGivCe 80 (625) T TIGR02387 1 RFDYVKIAIASPERVMEWGQRTLPNGQVVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECYCGKYKRVRHRGIVCE 80 (625) T ss_pred CCCEEEEEECCCHHHHHHCCCCCCCCCEEEEECCCCEECEEECCCCCCCEEEHHCCCCCCCCCCCCCCEEEEEECCEEEE T ss_conf 96259998528089986111238887378620377400001037321430001013788664110464015542212650 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCEEECHHHHHHHHHHHHHCCCHHHHHHHHHHCCEEEECCCC-CCHHHHCCCCHHHH Q ss_conf 57885304775787677200277622013012257899998099965630133211123217886-51043223699999 Q gi|254780142|r 88 KCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRDVERVLYFESYVVVDPGL-SSLEKYQILTEEEY 166 (1398) Q Consensus 88 ~Cg~~~~~~~~r~ghfGhIeLa~PV~Hi~f~k~~~~~i~~~l~~~~~~~~~v~y~~~~~~~~~~~-~~~~~~~~~~~~~~ 166 (1398) +||+|+|++.|||.|||||+||.||.|+||+|.+||+++.+|++.+++.+.+.||.+|++.+|+. ..|+.+++++|++| T Consensus 81 rCGvevtes~vrrhrmG~iklaaPv~hvWylkGiPsy~~~lldm~lrdveq~vyfn~yvvl~PG~~~~l~ykqllted~~ 160 (625) T TIGR02387 81 RCGVEVTESRVRRHRMGYIKLAAPVTHVWYLKGIPSYVSILLDMPLRDVEQIVYFNAYVVLNPGNAKNLKYKQLLTEDQW 160 (625) T ss_pred CCCEEEECCEEEEEECCEEEECCCCEEEEEECCHHHHHHHHHHHHHHHHHEEEEEEEEEEECCCCCCCCHHHHHHCCCCE T ss_conf 36502311200100011244315400110002516899998520023332023355578877887200013333034432 Q ss_pred HHHHHHCCC-------CCEEECCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEE Q ss_conf 886763585-------5506115526778887726748899999987310322034788644778886666348985112 Q gi|254780142|r 167 VEAVSQFGQ-------DQFIAMMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWM 239 (1398) Q Consensus 167 ~~~~~~~~~-------~~~~~~~g~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~Pewm 239 (1398) .+..+.... ......+|++|++.+|..+++++....+++++... ..+++.+++||+++++.|..+.++|||| T Consensus 161 ~e~ed~iyae~s~~e~~~~~~~~Gaea~~~ll~~~~le~~ae~lr~~~~~s-kGqkr~klikrlrv~dnf~at~~~~eWm 239 (625) T TIGR02387 161 VEIEDQIYAEDSELENEEGVVGIGAEAVKELLAELELEEVAEKLREEINES-KGQKRAKLIKRLRVIDNFIATSSRPEWM 239 (625) T ss_pred EEECCHHCCCCHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCHHHHHHHHHHHHHHHHHHCCCCCCEE T ss_conf 543001000200002454301013799999998510578899999998621-4515788999988876655326776437 Q ss_pred EEEECCCCCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCC Q ss_conf 86304507622351388469731310037899999998699999987398356777699999998888742776787724 Q gi|254780142|r 240 IIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHKRVVT 319 (1398) Q Consensus 240 il~~lpV~P~~~RP~v~~~~g~~~~dDlt~~~~~Ii~~N~~Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~~~~~~ 319 (1398) +|+++||+||++||+|++|||+|+++|||++|+++|++||||.|+-+.-||++|++|+|+|||++|++|+|||++|+.+. T Consensus 240 ~l~~iPviPPdlrPmvqldGGrfatsdlndlyrrvinrnnrlarlqeilaPeiivrnekrmlqeavdalidnGrrGrtvv 319 (625) T TIGR02387 240 VLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVV 319 (625) T ss_pred EEEEECCCCCCCCCEEEECCCEEEHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEECHHHHHHHHHHHHHHCCCCCCEEE T ss_conf 88872047887662034348611013477899998521015778887525400431025788999999982788654465 Q ss_pred CCCCCHHHHHHHHHCCCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCEECHHHHHHHHHHHHHHHHHHHCCCCCCCCCC Q ss_conf 78765067899861023782000346510045774034125543546200348987761289999999987986663000 Q gi|254780142|r 320 GANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQA 399 (1398) Q Consensus 320 ~~~~rp~ks~~~rlkgK~GrfR~nl~GKRVdfs~RsVI~pdP~l~~~evgvP~~~A~~L~~P~~~~~L~~~g~~~~i~~~ 399 (1398) |.++||||||+|-+.||+||||+||+||||||||||||+.+|+|+++|||+|++||.+||.||++.+|+..+.+++|+.| T Consensus 320 Gannr~lkslsdiieGkqGrfrqnllGkrvdysGrsvivvGP~lk~~qCGlP~emaielfqPfvih~li~~~~vnnikaa 399 (625) T TIGR02387 320 GANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKLHQCGLPKEMAIELFQPFVIHRLIKRGIVNNIKAA 399 (625) T ss_pred CCCCCCHHHHHHHHCCCCCCHHHHHCCCEEECCCCEEEEECCCEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 05763024567664166651135341340200574789987840476358855678876305899999986566677999 Q ss_pred CCEEECCCCCEEHHHHHHHCCCEEEECCCCCCEECCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCEEEEECCCCHHHH Q ss_conf 10012248825013266656978997576310111401235899449547973122545467877545699746899999 Q gi|254780142|r 400 KKFVEKERPEVWDVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQ 479 (1398) Q Consensus 400 k~~i~~~~~~v~~v~rhl~~gd~Vl~NRqPsLHr~Simah~~~v~~~~t~rln~~vc~pyNADFDGDEMnlHvPqs~eAr 479 (1398) ||+|.+.+..+|.|+.++++|+||++||+|||||++||||.|.++.|++++|||+||++||||||||||++|||.|.||+ T Consensus 400 kkli~~~d~~~~~vl~evi~GhP~~lnraPtlhrlGiqafeP~lv~GraiqlhPlvC~afnadfdGdqmavhvPl~~e~q 479 (625) T TIGR02387 400 KKLIQRADDEIWSVLEEVITGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQ 479 (625) T ss_pred HHHHHCCCHHHHHHHHHHHCCCCEEEECCCCHHHHCHHHCCCEEECCCEEEECCCCHHHHCCCCCCCEEEEEECCCCCHH T ss_conf 99874043689999998746872576267502330222227444236136640320000125667761578703100002 Q ss_pred HHHHHHHHHHHCCCCCCCCCCEEEEHHHHHHHHHHHHCCCCC-----CCCCCCEECCHHHHHHHHHCCCCCCCCEEEEEE Q ss_conf 999998767505423788782044025899999987336788-----744681417999999999888986785236520 Q gi|254780142|r 480 LEARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEG-----DPGEGMLFADMGEVYHALENKIVTLHSKIRGRY 554 (1398) Q Consensus 480 aEa~~Lm~~~~niisP~~g~Pi~~~~QD~i~G~y~lT~~~~~-----~~~~~~~f~~~~~~~~~~~~~~~~~~a~i~~~~ 554 (1398) +||+.||++++|++||+.|+|++.|+||+++|+||||..... +-+.++.|.+.+++..||..+.+++|+.+|.+. T Consensus 480 ~earllmla~~n~lsPatG~Pi~~P~qdmvlG~yylt~~~P~a~~~~~~~~~~~~~~~ed~~~a~~~~~~~lh~~~W~r~ 559 (625) T TIGR02387 480 AEARLLMLASNNVLSPATGKPIVTPSQDMVLGCYYLTAENPDAEKPEFGGAGRYFASLEDAVRAYEDGRIDLHDKIWVRH 559 (625) T ss_pred HHHHHHHHHHHHCCCCCCCCCEECCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHH T ss_conf 35788777753104766787301356110223213332388744321144432000157899864135200125444443 No 20 >CHL00006 consensus Probab=100.00 E-value=0 Score=1144.24 Aligned_cols=432 Identities=32% Similarity=0.525 Sum_probs=387.9 Q ss_pred EEEECCHHCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 17751100201366699999998081789998755889999999853986132123268369999999997899999988 Q gi|254780142|r 589 FDICNQEMIKKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKMVKEYENQY 668 (1398) Q Consensus 589 ~~~~~~~~~k~~~~~li~~i~~~~G~~~~~~~l~~~~~l~~~~l~~~GfSigi~D~~~~~~k~~~i~~a~~~~~~~~~~~ 668 (1398) .-+.|+.++|+.+..||..++..||...|+.++|.++.|||+|++..|.|+|++|+.+|+.|..++++|++++...+.+| T Consensus 7 ~~f~n~~~~k~~~~~~i~~~~~~~g~~~t~~~~d~~k~~gf~~at~~g~s~~~~dl~~~~~k~~~~~~a~~~~~~~~~~~ 86 (1372) T CHL00006 7 LVFHNKVIDGTAIKRLISRLIDHFGMAYTSHILDQVKTLGFQQATATSISLGIDDLLTIPSKGWLVQDAEQQSLILEKHH 86 (1372) T ss_pred EEEEEEECCHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHCHHHHCCCCEEEEHHHCCCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 04882124689999999999998498999999999987677865104168755132568328999999999999999997 Q ss_pred HCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCHHHEEEEEEECCCCCCCC Q ss_conf 64897667888788642346589999999999876115654322224688376422555578424112001000024644 Q gi|254780142|r 669 NDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIFMMSHSGARGSIHQMRQLGGMRGLIAKPS 748 (1398) Q Consensus 669 ~~G~~t~~e~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~N~~~~M~~SGAKGS~~qi~ql~Gqq~l~gkp~ 748 (1398) ..|.+|..||+++++++|..|.|.+.+.|+.++... +++|+++||+.||||||++|++||+||||||++|. T Consensus 87 ~~g~i~~~e~~~~~i~~w~~~~~~l~~~~~~~~~~~---------~~~n~v~~m~~sgarg~~~qv~ql~gmrglm~~p~ 157 (1372) T CHL00006 87 HYGNVHAVEKLRQSIEIWYATSEYLRQEMNPNFRMT---------DPFNPVHIMSFSGARGNASQVHQLVGMRGLMSDPQ 157 (1372) T ss_pred HCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC---------CCCCCEEEEECCCCCCCHHHHHHHHHCCCCCCCCC T ss_conf 668976788776999999987999999997665107---------99888267765767788899888742110256869 Q ss_pred CCCCCCCCCCHHHCCCCHHHHHHCCCCCCHHHHCCCCCCCCCCEEEEHHHHHHCCCEEEEECCCCCCCCEEEEEEECCEE Q ss_conf 34445666301110888989764057610322101210156740110154230143277513887666512111008848 Q gi|254780142|r 749 GEIIESPIRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQV 828 (1398) Q Consensus 749 G~~~~~PV~~sF~~GL~p~EfFfhamgGReGLiDTAvKTA~SGYlqRrLvk~~eDl~V~~~D~~t~~g~~~~~~~~~~~~ 828 (1398) |.+++.||.+||+|||+..|||.+|+|+|+||+|||||||+||||+||||+|+||++|++.||||..|+.+.... ++.. T Consensus 158 g~ii~~pi~~nfregl~~~ey~is~~garkg~~dtal~ta~~gyltrrlvdv~q~~~v~~~dc~t~~gi~~~~~~-~~~~ 236 (1372) T CHL00006 158 GQMIDLPIQSNLREGLSLTEYIISCYGARKGVVDTAVRTSDAGYLTRRLVEVVQHIVVRRTDCGTIRGISVSPRN-GMMP 236 (1372) T ss_pred CCEECCCHHHHCCCCCCHHHHHHCCCCCCCCHHHHHHHHCCCCCCCCHHHHHCCEEEEECCCCCCCCCEEEEEEC-CCCE T ss_conf 986553222202256367562013785331125546550364642004365347259962368998877999605-8832 Q ss_pred EEEECCCCCCCCCHHHCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEECCCCCCHHHHHCCCHHHHHHHCCCCCEECH Q ss_conf 86500010122114420177897188517865789999999975984020233100035518657887542017852000 Q gi|254780142|r 829 VYSLGSRVLGRTALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNV 908 (1398) Q Consensus 829 ~~~l~~~~~~r~~~~di~~~~~~~~i~~~~~~i~~~~~~~i~~~~i~~v~irs~lt~~~~~~v~~~cy~~~l~~~~lv~p 908 (1398) ...+.+|++||++++|++ .+.++|+.+|+.|++..++.+.+++++++.|||||||++.+|+|++||||+|+++++|+. T Consensus 237 ~~~~~~~~~gr~~~~~i~--~~~~~i~~~~~~i~~~~~~~~~~~~~~~~~vrspltc~~~~~ic~~cyg~~l~~~~~v~~ 314 (1372) T CHL00006 237 ERIFIQTLIGRVLADDIY--IGSRCIATRNQDIGIGLVNRFITFRAQPISIRTPFTCRSTSWICRLCYGRSPTHGDLVEL 314 (1372) T ss_pred EEEECCEEEEEEEEEEEE--ECCCEEEECCCCCCHHHHHHHHHCCCCEEEECCCEECCCCCCCCHHHCCCCCCCCCCCCC T ss_conf 431003322057814488--878389958955599999999987997799779810068873865333845226873555 Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEEEEEEE--EEEECCCCCEEEEECC-CCEEEEECCC Q ss_conf 101460211110078898776420245432221122024014876897211--3465178877897427-6046640677 Q gi|254780142|r 909 GEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNR--NVCRNSTNDLISMGRN-TTLQILDMSG 985 (1398) Q Consensus 909 Ge~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVPRlkEi--~~~~n~~~~~i~vs~~-~~~~i~d~~~ 985 (1398) |||||+||||||||||||+||||||.|||.+...+..+.++..|+.++.+- ..+++..+....+..+ ..+.+ ... T Consensus 315 geavgiiaaqsigepgtqlt~rtfhtggvf~~~~~~~~~~~~~g~i~f~~~l~~ptRTrhG~~A~l~~~~~~v~i--~~~ 392 (1372) T CHL00006 315 GEAVGIIAGQSIGEPGTQLTLRTFHTGGVFTGGTAEHVRAPSNGKIKFNEDLVHPTRTRHGHPAFLCYIDLYVTI--ESE 392 (1372) T ss_pred CCEEEEEEEECCCCCCCCCEEEEEECCCCCCCCCHHHCCCCCCCEEECCCCCCCCCCCCCCCEEEEEECCCEEEE--CCC T ss_conf 753347742015887643124421016521342011012776744752655676765779953599740307998--349 Q ss_pred CEEEEEECCCHHCCCCCCCCEEECCEEEEECCCC----------CCEEEECCCCEEEEE Q ss_conf 6000000110000135678553225078621354----------311320246368975 Q gi|254780142|r 986 QEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPH----------TFPIITEVSGTVGFE 1034 (1398) Q Consensus 986 ~~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp~----------~~~i~~e~~~~v~~~ 1034 (1398) .......++.++++++..++.|++.|++++.-.. ...+.++..|.+.|. T Consensus 393 ~~~~~~~ip~~SlL~V~n~q~V~s~QvIAEi~a~~~~~~~kEk~~K~i~s~~~GE~~~~ 451 (1372) T CHL00006 393 DIIHNVNIPPKSFLLVQNDQYVESEQVIAEIRAGTSTFNFKERVRKHIYSDSEGEMHWS 451 (1372) T ss_pred CEEEEEEECCCCEEEEECCCEEECCCEEEEEECCCCCCCCEEEEEEEEECCCCCCCCCC T ss_conf 86899887898389998995885052899982577666630258767752776412124 No 21 >smart00663 RPOLA_N RNA polymerase I subunit A N-terminus. Probab=100.00 E-value=0 Score=763.31 Aligned_cols=276 Identities=54% Similarity=0.796 Sum_probs=248.6 Q ss_pred CEEEEEECCCCCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCC Q ss_conf 11286304507622351388469731310037899999998699999987398356777699999998888742776787 Q gi|254780142|r 237 GWMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHKR 316 (1398) Q Consensus 237 ewmil~~lpV~P~~~RP~v~~~~g~~~~dDlt~~~~~Ii~~N~~Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~~~ 316 (1398) ||||+++||||||++||++.+++|.+++||||++|++||++|++|+++.+.++|+.++.++|.+||+||++|+||+.... T Consensus 1 ew~il~~lpVpP~~~RP~~~~~~~~~~~ddlt~~y~~II~~N~~L~~~~~~~~~~~~~~~~~~~LQ~~V~~~~dn~~~~~ 80 (295) T smart00663 1 EWMILTVLPVPPPCLRPSVSLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPEHIIRNEKRLLQEAVDTLFDNEGLPR 80 (295) T ss_pred CEEEEECCCCCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCC T ss_conf 94699612439987186089699987348478999999999999999986599177899999999999999954889876 Q ss_pred CCCCCCCCHHHHHHHHHCCCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCEECHHHHHHHHHHHH-----HH---HHHH Q ss_conf 724787650678998610237820003465100457740341255435462003489877612899-----99---9999 Q gi|254780142|r 317 VVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKPF-----LY---AQLE 388 (1398) Q Consensus 317 ~~~~~~~rp~ks~~~rlkgK~GrfR~nl~GKRVdfs~RsVI~pdP~l~~~evgvP~~~A~~L~~P~-----~~---~~L~ 388 (1398) ....++||+|||+|||+||+||||+|||||||||||||||||||+|++||||||..||++||+|| |+ ++|+ T Consensus 81 -~~~~~~~~~k~i~~rL~gK~Gr~R~nl~GKRvd~s~RsVItpdP~L~~~evGvP~~~A~~Lt~pe~V~~~n~~~l~~~v 159 (295) T smart00663 81 -ARQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKLV 159 (295) T ss_pred -CCCCCCCCCCCHHHHHCCCCCEECCCCCCCCCCCCCCCEEECCCCCCCCEECCCHHHHHHCCCCEEEEHHHHHHHHHHH T ss_conf -7677898575689884587731211336554476576436369876358764889999737834797277899999998 Q ss_pred HCCC--CCCCCCCCC-E--------EECCCCCEEHHHHHHHCCCEEEECCCCCCEECCEEEEEEEEECCCEEEEECCCCC Q ss_conf 8798--666300010-0--------1224882501326665697899757631011140123589944954797312254 Q gi|254780142|r 389 KKGY--VSTVKQAKK-F--------VEKERPEVWDVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCA 457 (1398) Q Consensus 389 ~~g~--~~~i~~~k~-~--------i~~~~~~v~~v~rhl~~gd~Vl~NRqPsLHr~Simah~~~v~~~~t~rln~~vc~ 457 (1398) .+|. +..+...++ . .......+|.|+||++|||+|||||||||||+|||||+|+++||+||||||+||+ T Consensus 160 ~~g~~ga~~~~~~~~~~~~~~~~~~~~~~l~~g~~v~r~l~~gd~vl~NRqPtLHr~si~a~~~~i~~~~tir~n~~~c~ 239 (295) T smart00663 160 RNGPNGAKYIIRGKKTNLKLAKRSKIAKHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLVCS 239 (295) T ss_pred HCCCCCCEEEECCCEEEHHHHHHHHHHHCCCCCCEEEEEEECCCEEEECCCCHHHHCCCEEEEEEEECCCEEEECCCCCC T ss_conf 52997744896186014055454566640576769865644597899737740211031036899976957898854578 Q ss_pred CCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEEHHHHHHHHH Q ss_conf 54678775456997468999999999987675054237887820440258999999 Q gi|254780142|r 458 GYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPASGAPVTVPSQDMVLGLC 513 (1398) Q Consensus 458 pyNADFDGDEMnlHvPqs~eAraEa~~Lm~~~~niisP~~g~Pi~~~~QD~i~G~y 513 (1398) ||||||||||||+|||||++|||||++||.+++|++||++|+|++|++||+|+|+| T Consensus 240 ~~NADFDGDeMnih~pqs~~a~aEa~~L~~~~~~~~sp~~g~p~~~~~QD~~~g~y 295 (295) T smart00663 240 PYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295 (295) T ss_pred CCCCCCCCCEEEEECCCCHHHHHHHHHHHHCHHCEEECCCCCEEEEEEHHHEEECC T ss_conf 70688776126764579989999999985032137507999805884215304349 No 22 >pfam04998 RNA_pol_Rpb1_5 RNA polymerase Rpb1, domain 5. RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound. Probab=100.00 E-value=0 Score=690.53 Aligned_cols=434 Identities=28% Similarity=0.386 Sum_probs=269.1 Q ss_pred CCCHHHHHHCCCCCCHHHHCCCCCCCCCCEEEEHHHHHHCCCEEEEECCCCCCCCEEEEEEECCEEEEEECCCCCCCCCH Q ss_conf 88898976405761032210121015674011015423014327751388766651211100884886500010122114 Q gi|254780142|r 763 GLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLGSRVLGRTAL 842 (1398) Q Consensus 763 GL~p~EfFfhamgGReGLiDTAvKTA~SGYlqRrLvk~~eDl~V~~~D~~t~~g~~~~~~~~~~~~~~~l~~~~~~r~~~ 842 (1398) ||+|+|||||||||||||||||||||+||||||||||+|||++|+++||++..+..+..+.++++.+++...+..++... T Consensus 1 GL~p~EfFfh~m~gReGLiDTAvKTa~SGYlqRrLvk~ledl~V~yD~tvr~~~g~ivqf~yG~Dg~d~~~~~~~~~~~~ 80 (447) T pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAETGYLQRRLVKALEDLVVQYDDTVRNSGGEIVQFLYGEDGLDPLKIEGQGRFTI 80 (447) T ss_pred CCCHHHHHHCCCHHCCHHHHCCHHHHHHHHHHHHHHHHHCEEEEEECCCCCCCCEEEEEEEECCCCEECCEEEEECCEEE T ss_conf 96878998768401233876731565554689998887174799945982389906999898885665126896264356 Q ss_pred HHCCCCC--------CCCEEEECCCCCCHHHHHHHHHCCCCEEECCCCCCHHHHHCCCHHHHHHHCCCCCEECHHHCCCC Q ss_conf 4201778--------97188517865789999999975984020233100035518657887542017852000101460 Q gi|254780142|r 843 DDIINPL--------TNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVGEAVGV 914 (1398) Q Consensus 843 ~di~~~~--------~~~~i~~~~~~i~~~~~~~i~~~~i~~v~irs~lt~~~~~~v~~~cy~~~l~~~~lv~pGe~VG~ 914 (1398) .+...+. .+..+..............+...++.++++||+++|+...++|.+||+++++++++|+||||||+ T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~slv~pGEaVGi 160 (447) T pfam04998 81 EDSDLKLEKKFKIDLNDVLLLLSEFSLSTLLFEILLRSGIESKRVRSELTCNSKAGVCFLCYGRDKYRRSLVEPGEAVGI 160 (447) T ss_pred EECCCCCCCCEEECCCCCEEECCCHHHHHHHHHHHHHHCCCEEEEEEEEECCCHHHHHHHHHHHHHHHHCCCCCCCCHHH T ss_conf 76257223747745998554002214558899999972767378865530261889999999987542132478741102 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEEEEEEEEE-EECCCCCEEEEECCCCEEEEECCCCEEEEEEC Q ss_conf 21111007889877642024543222112202401487689721134-65178877897427604664067760000001 Q gi|254780142|r 915 IAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNRNV-CRNSTNDLISMGRNTTLQILDMSGQEQYSHRI 993 (1398) Q Consensus 915 iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVPRlkEi~~-~~n~~~~~i~vs~~~~~~i~d~~~~~~~~~ki 993 (1398) |||||||||||||||||||||||||+ |||+||||++|+.. .++.++|.+++.+.... ..+...... T Consensus 161 IAAQSIGEP~TQmTLnTFH~AGvas~-------nvT~GvPRl~Eil~~~~~~~tp~~~~~~~~~~------~~~~~~~~~ 227 (447) T pfam04998 161 IAAQSIGEPGTQMTLNTFHFAGVASK-------NVTLGVPRLKEIINVAKNNKKPVITVLLIKNI------VSDKARVKK 227 (447) T ss_pred HHHCCCCCCHHHHHHHHHHHCCCCCC-------CCCCCCEEEEEEEEEEEECCEEEEECCCCEEE------ECCCCEEEE T ss_conf 33202467035564776543331012-------33226349985249996154357853785444------323450687 Q ss_pred CCHHCCCCCCCCEEECCEEEEECCCCCCEEEECCCCEEEEEEECCCCEEHHHHHCCCCCEEEEEEEHHHCCCCCCCCCCE Q ss_conf 10000135678553225078621354311320246368975312783200123023686026775101101221238534 Q gi|254780142|r 994 MYGAKLFVDDGGVIECGQRISEWDPHTFPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAI 1073 (1398) Q Consensus 994 ~~~~~~~v~~~~~v~~~~ii~~~Dp~~~~i~~e~~~~v~~~~~~~~~~~~~~~~~~t~~~~~~~i~~~~~~~~~~~~~~~ 1073 (1398) ......++..........+.++++........+......+....+... +...... ........ T Consensus 228 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~------------~~~~~~~~ 290 (447) T pfam04998 228 QREEKTLLLLKKVTIIIVIYYDDDSESTVIKKDRIWVLAYFVIPEEVA-----EEVALAI------------IIIGKRKS 290 (447) T ss_pred EECCCEEEEEEEECEEEEEEECCCCEEEECCEEEEECCCCCCCCHHHH-----CHHHHHH------------HCCCEEEE T ss_conf 722674999998330589997589656623300133331266531221-----2123344------------15616530 Q ss_pred EEECCCC-CEEECCCCCCCEEECCCCCEEEECCCCCCCCCCEEEECHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCEECC Q ss_conf 7742778-253224788420213778445413676135484222101320245543367732889887525111101113 Q gi|254780142|r 1074 VVTDENG-VVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFEARRPKNHAILAE 1152 (1398) Q Consensus 1074 ~i~d~~~-~~~~~~~~~~~~~~~~~~~~~~v~~~~~v~~~d~l~~~~~~~~k~~DIt~GLPrV~eLFEar~pk~~aiise 1152 (1398) ....... ............+..+......+..+..+..+..+. T Consensus 291 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------------------------------ 334 (447) T pfam04998 291 RKRKKNNLGVAKDEKGLEEEELLLLNKILLVIPGIKVKYGVILT------------------------------------ 334 (447) T ss_pred EEECCCEEEEEECCCCCHHHHCCCCCCHHEECCCCEEEECCCCC------------------------------------ T ss_conf 68336407998537751112125212102001386897223256------------------------------------ Q ss_pred CCCEEEE-EEECCCCEEEEEEECCCCCCEEEEEECCCCEEEEECCCEEECCCEEECCCCCHHHHHHHHCHHHHHHHHHHH Q ss_conf 4786786-331279449999836898402689813896589841987740864643899999998752799999999999 Q gi|254780142|r 1153 ISGTIRI-KRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDILRIKGVEALASYLINE 1231 (1398) Q Consensus 1153 i~Giv~i-~~~~~~k~~~vi~~~~~g~~~~e~~ip~~~~l~v~dgd~V~~gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~E 1231 (1398) .|.+.. ......+.++++. +.|.++.+.+-.. .+.+.++.. +||+++|+++|||||||++|++| T Consensus 335 -~~~~~~~~~~~~~~~~~~l~--t~G~nl~~v~~~~----gvid~~k~~--------sn~I~em~~~lGIEAAr~~i~~E 399 (447) T pfam04998 335 -DGRVDPHTILEKLGKEWLLK--TEGNNLQAVMRLQ----GVIDNDKTY--------SNDIREMLKKLGIEAARDSILLE 399 (447) T ss_pred -CCCCCCHHHHCCCCCEEEEE--EEHHHHHHHHHCC----CCCCCCCEE--------EEEHHHHHHHEEEEECCCCHHHH T ss_conf -57776213201368376664--4058999999728----935478168--------98299665225999885121353 Q ss_pred HHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHHHCC Q ss_conf 99999980970061256012476286148941886454566410699999999999972898752012100001453023 Q gi|254780142|r 1232 VQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQT 1311 (1398) Q Consensus 1232 Iq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~~~p~llGITKasl~t 1311 (1398) ++.|+++||++||+|||+|+||+||++|.++ ||||+|+++ T Consensus 400 ~~~V~~~~g~~vn~RHl~llaD~MT~~G~l~----------------------------------------gitR~Gl~~ 439 (447) T pfam04998 400 IRNVFKFDGIYVNRRHLALLADLMTFKGELL----------------------------------------GITRAGLNR 439 (447) T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCEECCEEE----------------------------------------EECHHHHCC T ss_conf 8999988778876999985897462356176----------------------------------------330645166 Q ss_pred --CCHHHH Q ss_conf --107765 Q gi|254780142|r 1312 --KSFISA 1317 (1398) Q Consensus 1312 --~S~Ls~ 1317 (1398) +|||++ T Consensus 440 ~~~s~l~~ 447 (447) T pfam04998 440 EKSSFILM 447 (447) T ss_pred CCCCCCCC T ss_conf 99886157 No 23 >PRK04309 DNA-directed RNA polymerase subunit A''; Validated Probab=100.00 E-value=0 Score=623.41 Aligned_cols=359 Identities=26% Similarity=0.339 Sum_probs=253.2 Q ss_pred EECCCCCCHHHHHHHHHCCCCEEECCCCCCHHHHHCCCHHHHHHHCCCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCC Q ss_conf 51786578999999997598402023310003551865788754201785200010146021111007889877642024 Q gi|254780142|r 855 VKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHL 934 (1398) Q Consensus 855 ~~~~~~i~~~~~~~i~~~~i~~v~irs~lt~~~~~~v~~~cy~~~l~~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHf 934 (1398) +.-.+.|+|+.+++|++++++++++||+|+ +|.+||+|+| |+||||||+|||||||||||||||||||+ T Consensus 14 ~~~~~~i~e~~~~~i~~~gi~~~~irsvlt------~~~~~Y~rsL-----V~~GEaVGiIAAQSIGEPgTQLTLrTFH~ 82 (381) T PRK04309 14 SELPESLKEELEEKVKKYGLTEEEVEEIIK------EVVREYLRSL-----IEPGEAVGIVAAQSIGEPGTQMTMRTFHY 82 (381) T ss_pred CCCCHHHHHHHHHHHHHCCCCHHHHHHHHH------HHHHHHCCCC-----CCCCCHHHHHHHHHCCCHHHHHHHHHHHH T ss_conf 799878999999999886998999999999------9999857157-----67874688887773284788888987635 Q ss_pred CCCCCCCCCCEEEECCCCEEEEEEEEEEE-CCCCCEEEEECCCCEEEEECCCCEEEEEECCCHHCCCCCCCCEEECCEEE Q ss_conf 54322211220240148768972113465-17887789742760466406776000000110000135678553225078 Q gi|254780142|r 935 GGAVTVMDRSFIESPCDGIVKIKNRNVCR-NSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRI 1013 (1398) Q Consensus 935 AGVAS~~~~~~iknvTlGVPRlkEi~~~~-n~~~~~i~vs~~~~~~i~d~~~~~~~~~ki~~~~~~~v~~~~~v~~~~ii 1013 (1398) ||||++ |+|+|+||++|+..++ +.++|.+++. +.+....+.+.++.....++.++..++++..+ T Consensus 83 gGva~~-------~vT~G~pRl~Ei~~a~k~~~tp~~~i~------l~~~~~~~~~~~~~v~~~i~~~~~~dv~~~~~-- 147 (381) T PRK04309 83 AGVAEI-------NVTLGLPRLIEIVDARKTPSTPMMTIY------LKEEYAYDREKAEEVAKKIEATTLEDLAKDIS-- 147 (381) T ss_pred HCEEEE-------EEECCCCEEEEEEECCCCCCCCEEEEE------ECCCCCCCHHHHHHHHHHCCEEEEEEEEEEEE-- T ss_conf 211000-------055377628999862356664318999------33433443899999875303499573036999-- Q ss_pred EECCCCCCEEEECCCCEEEEEEECCCCEEHHHHHCCCCCEEEEEEEHHHCCCCCCCCCCEEEECCCCCEEECCCCCCCEE Q ss_conf 62135431132024636897531278320012302368602677510110122123853477427782532247884202 Q gi|254780142|r 1014 SEWDPHTFPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENGVVLKSARGTDARW 1093 (1398) Q Consensus 1014 ~~~Dp~~~~i~~e~~~~v~~~~~~~~~~~~~~~~~~t~~~~~~~i~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~ 1093 (1398) +|+.+..+..+. + .......+.....+. ........ T Consensus 148 --~d~~~~~i~i~~----------~-----~~~~~~~~i~~~~i~------------------------~~i~~~~~--- 183 (381) T PRK04309 148 --VDLANMTIIIEL----------D-----EEQLEERGLTVDKVV------------------------EKIKSKLG--- 183 (381) T ss_pred --EECCCCEEEEEE----------C-----HHHHHHCCCCHHHHH------------------------HHHHHCCC--- T ss_conf --936897699998----------8-----677856389889999------------------------99862158--- Q ss_pred ECCCCCEEEECCCCCCCCCCEEEECHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCEECCCCCEEEEEEECCCCEEEEEEE Q ss_conf 13778445413676135484222101320245543367732889887525111101113478678633127944999983 Q gi|254780142|r 1094 FLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFEARRPKNHAILAEISGTIRIKRNYKNKSRVVIEP 1173 (1398) Q Consensus 1094 ~~~~~~~~~v~~~~~v~~~d~l~~~~~~~~k~~DIt~GLPrV~eLFEar~pk~~aiisei~Giv~i~~~~~~k~~~vi~~ 1173 (1398) ........+.+++.+.|++.+||+++.+...+.+++++|+.++.....+ .++++. T Consensus 184 -----------------------~~~~~~~~~~~i~~~~~~v~el~~~~~~~~~~~i~gi~gi~r~~i~~~~-~e~~i~- 238 (381) T PRK04309 184 -----------------------LKVEIEGNTIIVTPKEPSIRELRKLAEKIKDIKIKGIKGIKRVIIRKEG-DEYVIY- 238 (381) T ss_pred -----------------------CEEECCCCEEEEECCCCCHHHHHHHHHCCCCCEEECCCCCEEEEEECCC-CEEEEE- T ss_conf -----------------------4683379879981799888999997630357168457992699997589-789999- Q ss_pred CCCCCCEEEEEECCCCEEEEECCCEEECCCEEECCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHH Q ss_conf 68984026898138965898419877408646438999999987527999999999999999998097006125601247 Q gi|254780142|r 1174 FEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVR 1253 (1398) Q Consensus 1174 ~~~g~~~~e~~ip~~~~l~v~dgd~V~~gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD 1253 (1398) ++|.+..+.+ . +...|....+++|||||+++|||||||++|++|+|+||+.||++||+|||+||+| T Consensus 239 -t~G~~l~~~~-------~------~~~vD~~~~~sndi~dIl~i~GiEAar~~iv~Eiq~Vy~~qGv~IndkHIelI~d 304 (381) T PRK04309 239 -TEGSNLKEVL-------K------IEGVDPTRTTTNNIHEIAEVLGIEAARNAIIEEIKRTLEEQGLDVDIRHLMLVAD 304 (381) T ss_pred -ECCCCHHHEE-------E------ECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEE T ss_conf -4474545526-------5------2563344522486899998860999999999998878862886435203103200 Q ss_pred HHCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHC Q ss_conf 62861489418864545664106999999999999728987520121000014530231077650402589999997452 Q gi|254780142|r 1254 HMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIA 1333 (1398) Q Consensus 1254 ~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ 1333 (1398) |||++|.+++ +.|+++ + ..++||||+||||||++||++||++ T Consensus 305 ~Mt~~G~~~~------i~r~gi-----------------------------~---~~~~S~lsaASFqeTt~VLt~AAi~ 346 (381) T PRK04309 305 MMTWDGEVRQ------IGRHGI-----------------------------S---GEKASVLARAAFEVTVKHLLDAAIR 346 (381) T ss_pred EHHCCCEEEE------CCCCCC-----------------------------C---CCCCCHHHHHHHHHHHHHHHHHHHC T ss_conf 0303780530------550112-----------------------------6---7887899982227499999999850 Q ss_pred CCEECCCCCCEEEECCCCCCCCCCHHH Q ss_conf 855236653221550730565535466 Q gi|254780142|r 1334 GKVDTLDGFKENVIVGRSIPAGTGAIL 1360 (1398) Q Consensus 1334 ge~D~L~GvSENIIlGqliP~GTG~f~ 1360 (1398) |++|+|+|+|||||+||+||+|||+|. T Consensus 347 Gk~D~L~GlkeNVIvG~liPaGTG~~~ 373 (381) T PRK04309 347 GEVDELKGVVENIIVGQPIPLGTGDVE 373 (381) T ss_pred CCCCCCCCCHHHEECCCCCCCCCCCEE T ss_conf 897778880887334897568866678 No 24 >cd02584 RNAP_II_Rpb1_C Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain. RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures. Probab=100.00 E-value=0 Score=605.91 Aligned_cols=401 Identities=21% Similarity=0.228 Sum_probs=259.6 Q ss_pred CCCHHHHHCCCHHHHHHHCCCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEEEEEEEE- Q ss_conf 1000355186578875420178520001014602111100788987764202454322211220240148768972113- Q gi|254780142|r 882 ALTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNRN- 960 (1398) Q Consensus 882 ~lt~~~~~~v~~~cy~~~l~~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVPRlkEi~- 960 (1398) .||.+++.+++.++ +..+.+++|+||||||+|||||||||||||||||||+||+||+ |||+|+||++||. T Consensus 2 ~~s~~~~~~~~~~~--~~ky~rslV~pGEaVGiIAAQSIGEPgTQlTLrTFH~gG~as~-------~vT~GipRl~Ei~~ 72 (410) T cd02584 2 RLNKEAFDWILGEI--ETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAK-------NVTLGVPRLKEIIN 72 (410) T ss_pred CCCHHHHHHHHHHH--HHHHHHHCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHCCHHHH-------CEECCCHHHHHHHH T ss_conf 77889999999999--9999983879875889998873473698898874604013101-------04457405676765 Q ss_pred EEECCCCCEEEEECCCCEEEEECCCCEEEEEECCCHHCCCCCCCCEEECCEEEEECCCCCCEEEECCCCEEEEEEECCCC Q ss_conf 46517887789742760466406776000000110000135678553225078621354311320246368975312783 Q gi|254780142|r 961 VCRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHTFPIITEVSGTVGFEDLVDGI 1040 (1398) Q Consensus 961 ~~~n~~~~~i~vs~~~~~~i~d~~~~~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp~~~~i~~e~~~~v~~~~~~~~~ 1040 (1398) ..++.++|.+++. +.+....+.+.++.+...+++++++++++..+++|+|++....+..+......+.++.+.. T Consensus 73 ~~k~~kt~~~~i~------l~~~~~~~~~~~~~~~~~i~~~~l~d~~~~~~i~~~~~~~~~~i~~~~~~i~~~~~~~~~~ 146 (410) T cd02584 73 VAKNIKTPSLTVY------LEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVESYFEFPDED 146 (410) T ss_pred HCCCCCCCEEEEE------ECCCCCCCHHHHHHHHHEEEEEEHHHEEEEEEEEECCCCCCEEEEECCEEEEEEEEECCCC T ss_conf 4057777607999------7577542188887776500155444511245899627777427873140388768833410 Q ss_pred EEHHHHHCCCCCEEEEEEEHHHCCCCCCCCCCEEEECCCCCEEECCCCCCCEEECCCCCEEEECCCCCCCCCCEEEECHH Q ss_conf 20012302368602677510110122123853477427782532247884202137784454136761354842221013 Q gi|254780142|r 1041 SVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENGVVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPI 1120 (1398) Q Consensus 1041 ~~~~~~~~~t~~~~~~~i~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~v~~~d~l~~~~~ 1120 (1398) . .......+..+...+... .....+...+..... ...+..+........+..+ .....+.+. T Consensus 147 ~---~~~~~~~~~~~~~~~~~~-----~~~~~i~~~~~~~~i-------~~~~~~~~~~~~~~~~~~~---~~~~~r~~~ 208 (410) T cd02584 147 V---EQDRLSPWLLRIELDRKK-----MTDKKLSMEQIAKKI-------KEEFKDDLNVIFSDDNAEK---LVIRIRIIN 208 (410) T ss_pred C---CCCCCCCEEEEEEECHHH-----HCCCCCCHHHHHHHH-------HHHCCCCCEEEECCCCCCE---EEEEEECCC T ss_conf 2---213335437999953355-----303787788889999-------8752898469841577653---699998047 Q ss_pred HHCCCCCCCCCCCHHHHHHHHHCCCCCCEECCCCCEEEEEEECCCCEEEEEEECCCCCCEEEEEE-CCCCEEEEECCCEE Q ss_conf 20245543367732889887525111101113478678633127944999983689840268981-38965898419877 Q gi|254780142|r 1121 SSAKTKDITSGLPRVAELFEARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFI-PKNKHFYLQDGDHV 1199 (1398) Q Consensus 1121 ~~~k~~DIt~GLPrV~eLFEar~pk~~aiisei~Giv~i~~~~~~k~~~vi~~~~~g~~~~e~~i-p~~~~l~v~dgd~V 1199 (1398) .....+.+.+.++..+.|+++.+.+.++.....+...+.. ..++.+........+ ...+|.+ ..+.. +.+.-.+ T Consensus 209 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~-~~~~~~l~t~g~n--l~~il~~ 283 (410) T cd02584 209 -DDEEKEEDSEDDVFLKKIESNMLSDMTLKGIEGIRKVFIR-EENKKKVDIETGEFK-KREEWVLETDGVN--LREVLSH 283 (410) T ss_pred -CCCCCCCCCCCHHHHHHHHHCCCCCCEEECCCCEEEEEEE-ECCCEEEEECCCCCC-CCEEEEEECCCCC--HHHEECC T ss_conf -7655555676245535666336666469764665999989-717279980378767-6507998048832--6333243 Q ss_pred ECCCEEECCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHH Q ss_conf 40864643899999998752799999999999999999809700612560124762861489418864545664106999 Q gi|254780142|r 1200 EKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIE 1279 (1398) Q Consensus 1200 ~~gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~ 1279 (1398) ...|.....+||+|||+++|||||||++|++|||.||+.||++||+|||+|||||||++|.++ T Consensus 284 ~~vd~~~~~sNdi~eil~~~GiEAar~~iv~Ei~~V~~~~Gv~In~rHi~lI~d~Mt~~G~~~----------------- 346 (410) T cd02584 284 PGVDPTRTTSNDIVEIFEVLGIEAARKALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLM----------------- 346 (410) T ss_pred CCCCCCCCCCCCCCHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCEE----------------- T ss_conf 575333002576314666414999999988888899984595516999999888872178265----------------- Q ss_pred HHHHHHHHHHCCCCCCCEEEEEECHHHHHH--CCCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCCCCCCCCC Q ss_conf 999999999728987520121000014530--231077650402589999997452855236653221550730565535 Q gi|254780142|r 1280 VEELNRSLAQQGKKLVSFSPILQGITKASL--QTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTG 1357 (1398) Q Consensus 1280 ~~~~Nr~~~~~g~~pa~~~p~llGITKasl--~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG 1357 (1398) ||||+++ ++.||||+||||||++||++||++|++|+|+|+|||||+||+||+||| T Consensus 347 -----------------------~itR~gi~k~s~S~isaASFqeTt~vLt~AAi~G~~D~L~GlkenVIvG~lipaGTG 403 (410) T cd02584 347 -----------------------AITRHGINRQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVSENIMLGQLAPIGTG 403 (410) T ss_pred -----------------------EECHHHCCCCCCCHHHHHHCHHHHHHHHHHHHCCCCCCCCCCHHHEECCCCCCCCCC T ss_conf -----------------------401764466986888872046289999999862896667780887445897578777 Q ss_pred HHH Q ss_conf 466 Q gi|254780142|r 1358 AIL 1360 (1398) Q Consensus 1358 ~f~ 1360 (1398) +|- T Consensus 404 ~fd 406 (410) T cd02584 404 CFD 406 (410) T ss_pred CEE T ss_conf 378 No 25 >pfam04997 RNA_pol_Rpb1_1 RNA polymerase Rpb1, domain 1. RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand. Probab=100.00 E-value=0 Score=587.93 Aligned_cols=310 Identities=41% Similarity=0.581 Sum_probs=235.3 Q ss_pred CCCEEEEEEECCCHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 64053689845886788501448971755425456875688733621368566772156641563448835675788530 Q gi|254780142|r 15 DRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRMKYKGIICEKCGVEVT 94 (1398) Q Consensus 15 ~~~i~~i~f~l~spe~I~~~S~~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~Cg~~~~~~~~g~~C~~Cg~~~~ 94 (1398) .|+|++|+||++|||||++|||+||++|+||||.+++|++|||||+|||++.++ ..|+|||++.+ T Consensus 1 ~k~i~~i~f~l~S~eeI~k~Sv~eVt~~~t~~~~~~~P~~gGL~D~rlG~~~~~---------------~~C~TCg~~~~ 65 (330) T pfam04997 1 LKKIKEIQFGIASPEEIRKWSVGEVTKPETYNYGSLKPEPGGLLDERMGTIKKK---------------SICETCGVEVT 65 (330) T ss_pred CCCCCEEEEEECCHHHHHHHCEEEECCCCCEECCCCCCCCCCCCCCCCCCCCCC---------------CCCCCCCCCCC T ss_conf 974163899817899999744799837566638999747899865001799999---------------86889999877 Q ss_pred CCCCCCCCCCCCCCCCCCEEECHHHHHHH---HHHHHHCCCHHHHHHHHHHCCEEEECC-CCCCHHHHCCCCHHH-HHHH Q ss_conf 47757876772002776220130122578---999980999656301332111232178-865104322369999-9886 Q gi|254780142|r 95 LSSVRRDRMAHIDLASPVAHPWFLKSLPS---RISTLLGMSLRDVERVLYFESYVVVDP-GLSSLEKYQILTEEE-YVEA 169 (1398) Q Consensus 95 ~~~~r~ghfGhIeLa~PV~Hi~f~k~~~~---~i~~~l~~~~~~~~~v~y~~~~~~~~~-~~~~~~~~~~~~~~~-~~~~ 169 (1398) +|| |||||||||.||||+|||+.+++ ++|..|+..+..-+...|+ ...+..+ ......+.+.+.+.. .... T Consensus 66 ~Cp---GHfGhIeL~~PV~h~~f~~~i~~iL~~iC~~C~~~ll~~~~~~~~-~~~~~~~~~~~~~~~~~~i~~~~~~~~~ 141 (330) T pfam04997 66 ECP---GHFGHIELAKPVFHIGFFKKILSILRCVCKLCSSLLLNESVKYFF-LKVVIDPKGKNSKKRLKKINNLCKKKSI 141 (330) T ss_pred CCC---CCCEEEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHH-HHHHHCCCCCCHHHHHHHHHHHHHHHHH T ss_conf 179---856268865312019899999999999875065503656678899-9988621678878999999999977654 Q ss_pred HHHCCC--------------CCEEECCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 763585--------------550611552677888772674889999998731032203478864477888666634898 Q gi|254780142|r 170 VSQFGQ--------------DQFIAMMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNN 235 (1398) Q Consensus 170 ~~~~~~--------------~~~~~~~g~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~ 235 (1398) +..++. ..+....|..++...+.....+. ..+....+.........+++.+++..+.+|.+..+| T Consensus 142 c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~ilk~I~~~d~~llg~~~~~~~ 220 (330) T pfam04997 142 CSKCGEDNGGLKAFEGCGKYQPKISKDGAEAIKALLKNIEIEE-LKEKLRKLNPEKVLQIFKKISKEDEEILGFNPSGNR 220 (330) T ss_pred HHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCHH-HHHHHHHCCHHHHHHHHHHCCHHHHHHHCCCCCCCC T ss_conf 0146601343110378666787045507999999986275166-678875358999999998556989998577677999 Q ss_pred CCEEEEEECCCCCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCC Q ss_conf 51128630450762235138846973131003789999999869999998739835677769999999888874277678 Q gi|254780142|r 236 PGWMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHK 315 (1398) Q Consensus 236 Pewmil~~lpV~P~~~RP~v~~~~g~~~~dDlt~~~~~Ii~~N~~Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~~ 315 (1398) ||||||++||||||++||+|++++|.++|||||++|++||++|++|+++++.++|+.++.++|++||+||++||||+.++ T Consensus 221 Pe~mil~~lPVpPp~~RP~v~~~~~~~~edDlt~~~~~Ii~~N~~L~~~~~~~~~~~~i~~~~~~LQ~~V~~lidn~~~~ 300 (330) T pfam04997 221 PEWMILTVLPVPPPCIRPSVQLDGGRFAEDDLTHKLRDIIKRNNRLKKMLEEGAPSHIIREEKRLLQEHVATLFDNDIPG 300 (330) T ss_pred CCEEEEEECCCCCCCCCCCEECCCCCEECCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCC T ss_conf 77688775358989999977719985206831799999999999999999749968899999999999999995499889 Q ss_pred CCC-CCCCCCHHHHHHHHHCCCCCCEEECC Q ss_conf 772-47876506789986102378200034 Q gi|254780142|r 316 RVV-TGANRRPLKSLSDMLKGKQGRFRTNL 344 (1398) Q Consensus 316 ~~~-~~~~~rp~ks~~~rlkgK~GrfR~nl 344 (1398) .+. ..+++||+|||+|||||||||||+|| T Consensus 301 ~~~~~~~~~kp~k~i~qrLkgKeGrfR~NL 330 (330) T pfam04997 301 QPPALQKSGRPLKSISQRLKGKEGRFRGNL 330 (330) T ss_pred CCCCCCCCCCCCCCHHHHHCCCCCCCCCCC T ss_conf 986668897914329999678877578899 No 26 >cd06528 RNAP_A'' A'' subunit of Archaeal RNA Polymerase (RNAP). Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. Probab=100.00 E-value=0 Score=571.44 Aligned_cols=356 Identities=25% Similarity=0.320 Sum_probs=239.6 Q ss_pred CCCHHHHHHHHHCCCCEEECCCCCCHHHHHCCCHHHHHHHCCCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCC Q ss_conf 57899999999759840202331000355186578875420178520001014602111100788987764202454322 Q gi|254780142|r 860 LILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVT 939 (1398) Q Consensus 860 ~i~~~~~~~i~~~~i~~v~irs~lt~~~~~~v~~~cy~~~l~~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHfAGVAS 939 (1398) +++|++++.+.++++..+..++.+. .|..||.++| |+||||||+|||||||||||||||||||+||+|+ T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~y~~sl-----V~pGEaVGiIAAQSIGEPgTQLTLrTFH~aG~a~ 70 (363) T cd06528 2 LLKEKLEEVLKEHGLTLSEAEEIIK------EVLREYLRSL-----IEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAE 70 (363) T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHH------HHHHHHHHCC-----CCCCCHHHHHHHHHCCCHHHHHHHHHHHHHCEEE T ss_conf 5578999999982999999999999------9999987607-----7987388999887327669888898764510001 Q ss_pred CCCCCEEEECCCCEEEEEEEEEEE-CCCCCEEEEECCCCEEEEECCCCEEEEEECCCHHCCCCCCCCEEECCEEEEECCC Q ss_conf 211220240148768972113465-1788778974276046640677600000011000013567855322507862135 Q gi|254780142|r 940 VMDRSFIESPCDGIVKIKNRNVCR-NSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDP 1018 (1398) Q Consensus 940 ~~~~~~iknvTlGVPRlkEi~~~~-n~~~~~i~vs~~~~~~i~d~~~~~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp 1018 (1398) .|+|+|+||++|+..++ +.++|.+++.+. +....+...+......++.++..+.++..+ +|+ T Consensus 71 -------~~vt~G~pRl~Ei~~a~k~~~tp~~~i~l~------~~~~~~~~~~~~v~~~i~~~~~~~~~~~i~----id~ 133 (363) T cd06528 71 -------INVTLGLPRLIEIVDARKEPSTPTMTIYLE------EEYKYDREKAEEVARKIEETTLENLAEDIS----IDL 133 (363) T ss_pred -------EEEECCCCEEEEEEECCCCCCCCEEEEEEC------CCCCCCHHHHHHHHHHCCEEEEEEEEEEEE----ECC T ss_conf -------006537432699886004766756999960------544551899998886435189870068999----917 Q ss_pred CCCEEEECCCCEEEEEEECCCCEEHHHHHCCCCCEEEEEEEHHHCCCCCCCCCCEEEECCCCCEEECCCCCCCEEECCCC Q ss_conf 43113202463689753127832001230236860267751011012212385347742778253224788420213778 Q gi|254780142|r 1019 HTFPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENGVVLKSARGTDARWFLPVD 1098 (1398) Q Consensus 1019 ~~~~i~~e~~~~v~~~~~~~~~~~~~~~~~~t~~~~~~~i~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~ 1098 (1398) .+..+..+... ...+..+ .. +.+........ . T Consensus 134 ~~~~i~i~l~~---------------~~~~~~~-----------------i~----~~~i~~~i~~~-~----------- 165 (363) T cd06528 134 FNMRITIELDE---------------EMLEDRG-----------------IT----VDDVLKAIEKL-K----------- 165 (363) T ss_pred CCCEEEEEECH---------------HHHHHCC-----------------CC----HHHHHHHHHHH-C----------- T ss_conf 87079999884---------------6764249-----------------98----89999998764-3----------- Q ss_pred CEEEECCCCCCCCCCEEEECHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCEECCCCCEEEEEEECCCCEEEEEEECCCCC Q ss_conf 44541367613548422210132024554336773288988752511110111347867863312794499998368984 Q gi|254780142|r 1099 ALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFEARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGV 1178 (1398) Q Consensus 1099 ~~~~v~~~~~v~~~d~l~~~~~~~~k~~DIt~GLPrV~eLFEar~pk~~aiisei~Giv~i~~~~~~k~~~vi~~~~~g~ 1178 (1398) ....... ..........+.|++.++++++.+...+.+++++|+.++.-...++ ++++. ++|. T Consensus 166 ------~~~~~~~---------~~~~~~~~~~~~~~~~~l~~~~~~~~~~~i~gi~gi~~~~i~~~~~-e~~i~--t~G~ 227 (363) T cd06528 166 ------KGKVGEE---------GDVTLIVLKAEEPSIKELRKLAEKILNTKIKGIKGIKRVIVRKEED-EYVIY--TEGS 227 (363) T ss_pred ------CCCEEEC---------CCCCEEEECCCCCCHHHHHHHHHHCCCEEEECCCCEEEEEEEECCC-EEEEE--ECCC T ss_conf ------8877664---------9952797069999989999987442674793679858999996399-99999--5475 Q ss_pred CEEEEEECCCCEEEEECCCEEECCCEEECCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCE Q ss_conf 02689813896589841987740864643899999998752799999999999999999809700612560124762861 Q gi|254780142|r 1179 EPAEYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQK 1258 (1398) Q Consensus 1179 ~~~e~~ip~~~~l~v~dgd~V~~gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~k 1258 (1398) ++.+.+ ..+.| |.....++|+|||+++|||||||++|++|+|+||++||++||+|||+||||+||++ T Consensus 228 nl~~~l----------~~~~v---D~~~~~tndi~dI~~i~GiEAar~~lv~Ei~~v~~~qGv~In~rHi~li~d~Mt~~ 294 (363) T cd06528 228 NLKAVL----------KVEGV---DPTRTTTNNIHEIEEVLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYD 294 (363) T ss_pred CHHHHE----------ECCCC---CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCC T ss_conf 567723----------00661---35323358789999886088899999999988886078632057787765344046 Q ss_pred EEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHCCCEEC Q ss_conf 48941886454566410699999999999972898752012100001453023107765040258999999745285523 Q gi|254780142|r 1259 VEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDT 1338 (1398) Q Consensus 1259 g~I~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~ 1338 (1398) |.+++ +.|++ ++..+.||||+||||||++||++||++|+.|+ T Consensus 295 G~~~~------i~r~g--------------------------------~~~~~~S~ls~ASFqeT~~vLt~AAi~g~~D~ 336 (363) T cd06528 295 GEVRQ------IGRHG--------------------------------IAGEKPSVLARAAFEVTVKHLLDAAVRGEVDE 336 (363) T ss_pred CCEEE------CCHHH--------------------------------HCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCC T ss_conf 71420------45132--------------------------------23799889997210638999999985389676 Q ss_pred CCCCCEEEECCCCCCCCCCHHH Q ss_conf 6653221550730565535466 Q gi|254780142|r 1339 LDGFKENVIVGRSIPAGTGAIL 1360 (1398) Q Consensus 1339 L~GvSENIIlGqliP~GTG~f~ 1360 (1398) |+|+|||||+||+||+|||+|. T Consensus 337 L~GlkenVi~G~~ipaGTG~~~ 358 (363) T cd06528 337 LRGVIENIIVGQPIPLGTGDVE 358 (363) T ss_pred CCCCHHHEECCCCCCCCCCCEE T ss_conf 7880888335897568868779 No 27 >TIGR02389 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit A''; InterPro: IPR012757 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanococcus jannaschii contains an intein.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription. Probab=100.00 E-value=0 Score=568.27 Aligned_cols=339 Identities=27% Similarity=0.364 Sum_probs=224.6 Q ss_pred CCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEEEEEEEEEEECC-CCCEEEEECCCCEEE Q ss_conf 7852000101460211110078898776420245432221122024014876897211346517-887789742760466 Q gi|254780142|r 902 RGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNRNVCRNS-TNDLISMGRNTTLQI 980 (1398) Q Consensus 902 ~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVPRlkEi~~~~n~-~~~~i~vs~~~~~~i 980 (1398) .+++|+||||||+||||||||||||||||||||||||-+ |||+|.|||=||..+++. ++|.|++ ++ T Consensus 38 ~~~li~P~EAvGiVAAQSiGEPGTQMTmRTFHYAGv~El-------nVTlGLPRLIEIVDArk~PSTP~MtI------YL 104 (397) T TIGR02389 38 LRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEL-------NVTLGLPRLIEIVDARKTPSTPLMTI------YL 104 (397) T ss_pred HHHHCCCCCCCEEEEEEEECCCHHHHHHHHHHHHHHHHH-------HHHCCCCCCEEEECCCCCCCCCEEEE------EE T ss_conf 764106688610388442188454787776657766788-------76447840145450666789863799------62 Q ss_pred EECCCC----EEEEEECCCHHCCCCCCCCEEECCEEEEECCCCCCEEEECCCCEEEEEEECCCCEEHHHHHCCCCCEEEE Q ss_conf 406776----0000001100001356785532250786213543113202463689753127832001230236860267 Q gi|254780142|r 981 LDMSGQ----EQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHTFPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRK 1056 (1398) Q Consensus 981 ~d~~~~----~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp~~~~i~~e~~~~v~~~~~~~~~~~~~~~~~~t~~~~~~ 1056 (1398) .+++.. +.+.+..+...+++|+..++.+...+ |..+..+.-+.. ++..+.-+...+. T Consensus 105 ~~ey~~dyaydrE~a~~va~kie~t~l~~v~~~i~~----D~~~~~v~i~Ld---------------~~~~~~r~~t~d~ 165 (397) T TIGR02389 105 EDEYEKDYAYDREKAEEVAKKIEATKLEDVAKDISI----DLADMTVIIELD---------------EEKLKERGITVDD 165 (397) T ss_pred CCCCCCCCCCCHHHHHHHHHHHHHCCHHHHHCEEEE----EEECEEEEEEEC---------------HHHHHHCCCCHHH T ss_conf 788632245667899999987520333252241248----875308999417---------------4886306986689 Q ss_pred EEEHHHCCCCCCCCCCEEEE----CCCCCEEECCCCCCCEEECCCCCEEEECCCCCCCCCCEEEECHHHHCCCCCCCCCC Q ss_conf 75101101221238534774----27782532247884202137784454136761354842221013202455433677 Q gi|254780142|r 1057 VIDWRFASRSQNLKPAIVVT----DENGVVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGL 1132 (1398) Q Consensus 1057 ~i~~~~~~~~~~~~~~~~i~----d~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~v~~~d~l~~~~~~~~k~~DIt~GL 1132 (1398) +.+. -...+....+. +..+ + ..+....+--. ..+. ..+- ... T Consensus 166 v~~a-----~~~~~~~~~~~~~~~~~~~-v-------------seGGvkkvivy------~~i~---~~~~------~~~ 211 (397) T TIGR02389 166 VLKA-----IKKAKLGKVIEEVSEDVDN-V-------------SEGGVKKVIVY------STIT---IKAP------PKE 211 (397) T ss_pred HHHH-----HHHHHCCEEEEEECCCCCC-C-------------CCCCEEEEEEE------EEEE---ECCC------CCC T ss_conf 9999-----9987464255664368676-5-------------34761489999------8897---1578------899 Q ss_pred CHHH--HHHHHHCCCCCCEECCCCCEEEEE--EECCCCE--EEEEEECCCCCCEEEEEECCCCEEEEECCCEEECCCEEE Q ss_conf 3288--988752511110111347867863--3127944--999983689840268981389658984198774086464 Q gi|254780142|r 1133 PRVA--ELFEARRPKNHAILAEISGTIRIK--RNYKNKS--RVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYIL 1206 (1398) Q Consensus 1133 PrV~--eLFEar~pk~~aiisei~Giv~i~--~~~~~k~--~~vi~~~~~g~~~~e~~ip~~~~l~v~dgd~V~~gd~lt 1206 (1398) |... +||-.+.-=-..-|++|.|+-++. ++.+... +|++. ++|+++++++ .+...|... T Consensus 212 p~~~sneL~~l~~ki~~~~iKGikgIkrvvir~E~~k~dsyEy~i~--TeGSNL~~VL-------------~~eGVD~tR 276 (397) T TIGR02389 212 PSLKSNELRKLKEKIKNLKIKGIKGIKRVVIRREEEKGDSYEYVIY--TEGSNLKEVL-------------KLEGVDKTR 276 (397) T ss_pred CCCCHHHHHHHHHHHCCEEEEEEECCEEEEEEEECCCCCEEEEEEE--ECCCCHHHHC-------------CCCCCCCCC T ss_conf 8622267898887570415334504328999986688842799998--6063317650-------------889847742 Q ss_pred CCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCE-ECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHHHHH Q ss_conf 389999999875279999999999999999980970-0612560124762861489418864545664106999999999 Q gi|254780142|r 1207 DGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVA-INHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNR 1285 (1398) Q Consensus 1207 ~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~-IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~~Nr 1285 (1398) +.+||+|||.+||||||||++||+|++.|++.||.. ||-|||+|+||.||+.|.|-+ |-|||| T Consensus 277 T~TNdI~EI~~VLGIEAAR~AII~E~~~tL~EQGL~dVDiRHlmLvAD~MT~~G~V~~------IGRHGi---------- 340 (397) T TIGR02389 277 TTTNDIHEIEEVLGIEAARNAIIEEIKRTLEEQGLDDVDIRHLMLVADLMTWDGEVRQ------IGRHGI---------- 340 (397) T ss_pred CEECCHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCEEEE------EEEEEC---------- T ss_conf 0015614455530668999999999999986428860248989888651078854841------012000---------- Q ss_pred HHHHCCCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCCCCCCCCCHH Q ss_conf 99972898752012100001453023107765040258999999745285523665322155073056553546 Q gi|254780142|r 1286 SLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAI 1359 (1398) Q Consensus 1286 ~~~~~g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG~f 1359 (1398) +-.+.|+|++|+||.|++||++||+.|+.|.|.||-||||+||+||+|||+- T Consensus 341 ----------------------~GeK~SVLARAAFEvTvKhLl~Aa~rGe~d~L~GV~ENIIvG~Pi~lGTG~V 392 (397) T TIGR02389 341 ----------------------SGEKASVLARAAFEVTVKHLLDAAIRGEVDELKGVVENIIVGQPIRLGTGSV 392 (397) T ss_pred ----------------------CCCCCCHHHHCCCCCCHHHHHHHHHCCCHHHCCCEEEEEECCCCCCCCCCEE T ss_conf ----------------------3547853420012022346887520371214676799997077852154258 No 28 >cd02736 RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain. Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role. Probab=100.00 E-value=0 Score=560.80 Aligned_cols=293 Identities=27% Similarity=0.380 Sum_probs=203.6 Q ss_pred CCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEEEEEEEE-EEECCCCCEEEEECCCCEE Q ss_conf 178520001014602111100788987764202454322211220240148768972113-4651788778974276046 Q gi|254780142|r 901 ARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNRN-VCRNSTNDLISMGRNTTLQ 979 (1398) Q Consensus 901 ~~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVPRlkEi~-~~~n~~~~~i~vs~~~~~~ 979 (1398) +.+++|+||||||+|||||||||||||||||||+|||||+ |+|+|+||++|+. ..++.++|.+++... T Consensus 2 y~~slv~pGEaVGiIAAQSIGEPgTQlTLrTFH~aGvas~-------~vT~GvpRl~El~~a~k~~~tp~i~~~l~---- 70 (300) T cd02736 2 YMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASM-------NITLGVPRIKEIINASKNISTPIITAKLE---- 70 (300) T ss_pred CCCCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHCCCCE-------EEECCCCEEEEEEECCCCCCCCEEEEEEE---- T ss_conf 5415279986378776773386488888885635220030-------35437651799886555677877999974---- Q ss_pred EEECCCCEEEEEECCCHHCCCCCCCCEEECCEEEEECCCCCCEEEECCCCEEEEEEECCCCEEHHHHHCCCCCEEEEEEE Q ss_conf 64067760000001100001356785532250786213543113202463689753127832001230236860267751 Q gi|254780142|r 980 ILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHTFPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVID 1059 (1398) Q Consensus 980 i~d~~~~~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp~~~~i~~e~~~~v~~~~~~~~~~~~~~~~~~t~~~~~~~i~ 1059 (1398) + ..+.+.++.+.+.++.+++++++...+++++++.....+..+. T Consensus 71 --~--~~~~~~~~~v~~~i~k~~l~~v~~~~~~~~~~~~~~~~i~~~~-------------------------------- 114 (300) T cd02736 71 --N--DRDEKSARIVKGRIEKTYLGEVASYIEEVYSPDDCYILIKLDK-------------------------------- 114 (300) T ss_pred --C--CCCHHHHHEECCEEEEEEEECCCCEEEEEECCCCEEEEEEECH-------------------------------- T ss_conf --2--5325432201146889985201122799988983489998467-------------------------------- Q ss_pred HHHCCCCCCCCCCEEEECCCCCEEECCCCCCCEEECCCCCEEEECCCCCCCCCCEEEECHHHHCCCCCCCCCCCHHHHHH Q ss_conf 01101221238534774277825322478842021377844541367613548422210132024554336773288988 Q gi|254780142|r 1060 WRFASRSQNLKPAIVVTDENGVVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELF 1139 (1398) Q Consensus 1060 ~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~v~~~d~l~~~~~~~~k~~DIt~GLPrV~eLF 1139 (1398) ..... . +++.....| T Consensus 115 -~~i~~-~---------------------------------------------------------------~l~~~~~~~ 129 (300) T cd02736 115 -KIIEK-L---------------------------------------------------------------QLSKSNLYF 129 (300) T ss_pred -HHHHH-C---------------------------------------------------------------CCCHHHHHH T ss_conf -67753-3---------------------------------------------------------------787477888 Q ss_pred HHHCCCC---CCEECCCCCEEEEEEECCCCEEEEEEECCCCCCEEEEEECCCCEEEEECCCEEECCCEEECCCCCHHHHH Q ss_conf 7525111---1011134786786331279449999836898402689813896589841987740864643899999998 Q gi|254780142|r 1140 EARRPKN---HAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDIL 1216 (1398) Q Consensus 1140 Ear~pk~---~aiisei~Giv~i~~~~~~k~~~vi~~~~~g~~~~e~~ip~~~~l~v~dgd~V~~gd~lt~Gsid~~eIl 1216 (1398) ..+..+. ..+++.+.|+.+ .++.. .++....++.+.......+...+.|+..... ++|++||+ T Consensus 130 ~~~~~~~~l~~v~i~Gi~~i~~----------~~i~~-~~~~~~~~~~~~g~~l~~v~~~~~vd~~~~~---sn~i~~i~ 195 (300) T cd02736 130 LLQSLKRKLPDVVVSGIPEVKR----------AVINK-DKKKGKYKLLVEGYGLRAVMNTPGVIGTRTT---SNHIMEVE 195 (300) T ss_pred HHHHHHHHCCCEEEECCCCCCE----------EEEEE-CCCCCEEEEEECCCCCEEEECCCCEECCEEC---CCCHHHHH T ss_conf 8888884458559946678547----------99960-2788538999538771024313867323412---37888888 Q ss_pred HHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCC Q ss_conf 75279999999999999999980970061256012476286148941886454566410699999999999972898752 Q gi|254780142|r 1217 RIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVS 1296 (1398) Q Consensus 1217 ~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~ 1296 (1398) ++|||||||++|++|+++||+.||++||+|||+||+|+||++|++ T Consensus 196 ~~lGiEAar~~ii~Ei~~v~~~~Gv~in~rHi~li~d~Mt~~g~~----------------------------------- 240 (300) T cd02736 196 KVLGIEAARSTIINEIQYTMKSHGMSIDPRHIMLLADLMTFKGEV----------------------------------- 240 (300) T ss_pred HHHHHHHHHEEEEECCCEEEECCCCEECHHHHHHHCCEEEECCEE----------------------------------- T ss_conf 774366532156411520330365100034476534430574789----------------------------------- Q ss_pred EEEEEECHHHHHHC--CCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCCCCCCCCCHH Q ss_conf 01210000145302--3107765040258999999745285523665322155073056553546 Q gi|254780142|r 1297 FSPILQGITKASLQ--TKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAI 1359 (1398) Q Consensus 1297 ~~p~llGITKasl~--t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG~f 1359 (1398) +||||++++ ++||||+||||||++||++||++|++|+|+|+|||||+||+||+|||+| T Consensus 241 -----~~itr~gl~~~~~S~ls~ASFeeT~~vLt~AAi~g~~D~L~GlkenVi~G~~ip~GTG~F 300 (300) T cd02736 241 -----LGITRFGIAKMKESVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIGTGLF 300 (300) T ss_pred -----EEECHHHCCCCCCCHHHHCCCHHHHHHHHHHHHHCCCCCCCCHHHHEECCCCCCCCCCCC T ss_conf -----610143176799998897031879999999997189776788288665289767886889 No 29 >cd02735 RNAP_I_Rpa1_C Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain. RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role. Probab=100.00 E-value=0 Score=540.69 Aligned_cols=303 Identities=22% Similarity=0.313 Sum_probs=195.8 Q ss_pred CCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEEEEEEE--EEEECCCCCEEEEECCCCE Q ss_conf 17852000101460211110078898776420245432221122024014876897211--3465178877897427604 Q gi|254780142|r 901 ARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNR--NVCRNSTNDLISMGRNTTL 978 (1398) Q Consensus 901 ~~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVPRlkEi--~~~~n~~~~~i~vs~~~~~ 978 (1398) +.+++|+||||||+|||||||||+|||||||||+||+|+ +|+|+|+||++|| +..++.++|.+++... T Consensus 2 y~~slV~pGEaVGiIAAQSIGEPgTQlTLrTFH~aGv~~-------~~vT~GvpRl~EIl~~~sk~~ktp~~~v~l~--- 71 (309) T cd02735 2 YMRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGE-------MNVTLGIPRLREILMTASKNIKTPSMTLPLK--- 71 (309) T ss_pred CCCCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHCCCCCC-------EEEEECCCCEEEEEEECCCCCCCCEEEEEEE--- T ss_conf 200447997689999988638558888887663076045-------1145156631677752378887876999961--- Q ss_pred EEEECCCCEEEEEECCCHHCCCCCCCCEEECCEEEEECCCCCCEEEECCCCEEEEEEECCCCEEHHHHHCCCCCEEEEEE Q ss_conf 66406776000000110000135678553225078621354311320246368975312783200123023686026775 Q gi|254780142|r 979 QILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHTFPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVI 1058 (1398) Q Consensus 979 ~i~d~~~~~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp~~~~i~~e~~~~v~~~~~~~~~~~~~~~~~~t~~~~~~~i 1058 (1398) +.. ....++.....+..+++.++++..++.+..+. .... T Consensus 72 ---~~~--~~~~~~~~~~~~~~~~l~dv~~~i~i~~i~~~------------------------------~~~~------ 110 (309) T cd02735 72 ---NGK--SAERAETLKKRLSRVTLSDVVEKVEVTEILKT------------------------------IERV------ 110 (309) T ss_pred ---CCC--CHHHHHHHHHHCCCEEEEEECCCEEEEEEHHH------------------------------HHHH------ T ss_conf ---783--07899999862373999871472799995232------------------------------0001------ Q ss_pred EHHHCCCCCCCCCCEEEECCCCCEEECCCCCCCEEECCCCCEEEECCCCCCCCCCEEEECHHHHCCCCCCCCCCCHHHHH Q ss_conf 10110122123853477427782532247884202137784454136761354842221013202455433677328898 Q gi|254780142|r 1059 DWRFASRSQNLKPAIVVTDENGVVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAEL 1138 (1398) Q Consensus 1059 ~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~v~~~d~l~~~~~~~~k~~DIt~GLPrV~eL 1138 (1398) ..+. .. .. ..+. . +.+ ..-|++..+ T Consensus 111 ----------~~~~---~~---~~--------~~~~--------~-------------~~~----------~~~~~~~~~ 135 (309) T cd02735 111 ----------FKKL---LG---KW--------CEVT--------I-------------KLP----------LSSPKLLLL 135 (309) T ss_pred ----------EECC---CC---CE--------EEEE--------E-------------EEC----------CCCCHHHHH T ss_conf ----------0013---48---53--------8999--------9-------------816----------888402677 Q ss_pred HHHHCCCCCCEECCCCCEEEEEEECCCCE-EEEEEECCCCCCEEEEEECCCCEEEEECCCEEECCCEEECCCCCHHHHHH Q ss_conf 87525111101113478678633127944-99998368984026898138965898419877408646438999999987 Q gi|254780142|r 1139 FEARRPKNHAILAEISGTIRIKRNYKNKS-RVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDILR 1217 (1398) Q Consensus 1139 FEar~pk~~aiisei~Giv~i~~~~~~k~-~~vi~~~~~g~~~~e~~ip~~~~l~v~dgd~V~~gd~lt~Gsid~~eIl~ 1217 (1398) +...+....+++++++|+.+......... .......++|.+..+.+ ...+.++..... ++|+|||++ T Consensus 136 ~~~~~~~~~~~i~~i~gI~~~~~~~~~~~~~~~~~~~t~g~n~~~~~---------~~~~~id~~~~~---sndi~di~~ 203 (309) T cd02735 136 SIVEKLARKAVIREIPGITRCFVVEEDKGGKTKYLVITEGVNLAALW---------KFSDILDVNRIY---TNDIHAMLN 203 (309) T ss_pred HHHHHHHHHCEEECCCCEEEEEEEECCCCCEEEEEECCCCCCHHHHC---------CCCCEECCCCCC---CCCHHHHHH T ss_conf 88876541038967899179999703798138999546872276610---------137767677555---688999998 Q ss_pred HHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCE Q ss_conf 52799999999999999999809700612560124762861489418864545664106999999999999728987520 Q gi|254780142|r 1218 IKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSF 1297 (1398) Q Consensus 1218 vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~~ 1297 (1398) +|||||||++|++|+|+||+.||++||+|||+||||+||++|.+++ ++|+| T Consensus 204 ~~GIEAar~~li~Ei~~V~~~~Gv~in~rHi~li~d~Mt~~G~~~~------~~R~g----------------------- 254 (309) T cd02735 204 TYGIEAARRAIVKEISNVFKVYGIAVDPRHLSLIADYMTFEGGYRP------FNRIG----------------------- 254 (309) T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCCEEE------CCHHC----------------------- T ss_conf 7579999999999999997435865674776657665000685731------01221----------------------- Q ss_pred EEEEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCCCCCCCCCHHH Q ss_conf 121000014530231077650402589999997452855236653221550730565535466 Q gi|254780142|r 1298 SPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAIL 1360 (1398) Q Consensus 1298 ~p~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG~f~ 1360 (1398) |++ .+||||+||||||++||++||++|++|.|+|||||||+||++|+|||+|. T Consensus 255 ------i~~----~~s~L~~aSFeet~~vL~~AAi~g~~D~l~Gl~enVi~G~~ip~GTG~~~ 307 (309) T cd02735 255 ------MES----STSPLQKMSFETTLAFLKKATLNGDIDNLSSPSSRLVVGKPVNGGTGLFD 307 (309) T ss_pred ------CCC----CCCHHHHHHCHHHHHHHHHHHHCCCCCCCCCCHHHEECCCCCCCCCCCEE T ss_conf ------025----98898984267599999999863896777880776442898778776435 No 30 >cd02655 RNAP_beta'_C Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain. Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations. Probab=100.00 E-value=0 Score=537.33 Aligned_cols=166 Identities=63% Similarity=0.929 Sum_probs=158.2 Q ss_pred CCCCCCCHHHHHHHHHCCCCCCEECCCCCEEEEEEECCCCEEEEEEECCCCCCEEEEEECCCCEEEEECCCEEECCCEEE Q ss_conf 43367732889887525111101113478678633127944999983689840268981389658984198774086464 Q gi|254780142|r 1127 DITSGLPRVAELFEARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYIL 1206 (1398) Q Consensus 1127 DIt~GLPrV~eLFEar~pk~~aiisei~Giv~i~~~~~~k~~~vi~~~~~g~~~~e~~ip~~~~l~v~dgd~V~~gd~lt 1206 (1398) |||+||||+.|+||||++ T Consensus 37 ~it~Glpri~ei~~ar~~-------------------------------------------------------------- 54 (204) T cd02655 37 DITQGLPRVEELFEARKI-------------------------------------------------------------- 54 (204) T ss_pred CCCCCCCCHHHHHHCCCC-------------------------------------------------------------- T ss_conf 233575208999864189-------------------------------------------------------------- Q ss_pred CCCCCHHHHHHH--HCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHHHH Q ss_conf 389999999875--279999999999999999980970061256012476286148941886454566410699999999 Q gi|254780142|r 1207 DGNPVPQDILRI--KGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELN 1284 (1398) Q Consensus 1207 ~Gsid~~eIl~v--lGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~~N 1284 (1398) ++|+++++ .|+++++++|++|||+||+.||+.||+||+|+|++|||.|+.|.++|||.|++|+.+++..+...| T Consensus 55 ----~~~~il~~~~~~~~~~~~~iv~eIq~vY~~qGV~I~dKHiEiIvrqm~~kV~I~~~Gdt~~l~Ge~v~~~~i~~~n 130 (204) T cd02655 55 ----NPHDLLRIKFLGPEAVQKYLVEEIQKVYRSQGVNINDKHIEIIVRQMTSKVKIIDPGDSGFLPGELVDLNEFEEEN 130 (204) T ss_pred ----CCHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCEECCCEEEEEEEEECCEEEEEECCCCCCCCCCEEEHHHHHHHH T ss_conf ----9478777651069999999999999999986970245778988544023489975898635777635199999999 Q ss_pred HHHHHCCCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCCCCCCCCCH Q ss_conf 99997289875201210000145302310776504025899999974528552366532215507305655354 Q gi|254780142|r 1285 RSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGA 1358 (1398) Q Consensus 1285 r~~~~~g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG~ 1358 (1398) +.+...++.|++|+|++|||||+||+++||||+||||||++||++||++|+.|+|+|||||||+||+||+|||+ T Consensus 131 ~~~~~~~~~~~~~~~~vLGITr~~l~~~S~Ls~ASFeeT~~~L~~AAi~g~~D~L~Gv~EnIIiG~~Ip~GTGl 204 (204) T cd02655 131 KRLLLLGKKPAKYEPVLLGITKASLNTESFISAASFQETTKVLTEAAIEGKIDWLRGLKENVILGRLIPAGTGL 204 (204) T ss_pred HHHHHCCCCCCCCCHHHHHHHHHHHCCCCHHHHCCHHHHHHHHHHHHHCCCCCCCCCCHHHHCCCCCCCCCCCC T ss_conf 99997058885411143301045424788054311799999999998638975348823440207854688798 No 31 >cd02737 RNAP_IV_NRPD1_C Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain. Higher plants have five multi-subunit nuclear RNA polymerases: RNAP I, RNAP II and RNAP III, which are essential for viability; plus the two isoforms of the non-essential polymerase RNAP IV (IVa and IVb), which specialize in small RNA-mediated gene silencing pathways. RNAP IVa and/or RNAP IVb might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b is the largest subunit of RNAP IVb. The full subunit compositions of RNAP IVa and RNAP IVb are not known, nor are their templates or enzymatic products. However, it has been shown that RNAP IVa and, to a lesser extent, RNAP IVb are crucial for several RNA-mediated gene silencing phenomena. Probab=100.00 E-value=0 Score=485.27 Aligned_cols=351 Identities=16% Similarity=0.109 Sum_probs=200.0 Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEEEEEEEEEE-ECCCCCE--EEEECCCCEEEEECCC Q ss_conf 101460211110078898776420245432221122024014876897211346-5178877--8974276046640677 Q gi|254780142|r 909 GEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNRNVC-RNSTNDL--ISMGRNTTLQILDMSG 985 (1398) Q Consensus 909 Ge~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVPRlkEi~~~-~n~~~~~--i~vs~~~~~~i~d~~~ 985 (1398) |||||+|||||||||+||||||||||||++ |+||++|+..+ ++.+.+. .++.+.....-.+... T Consensus 1 GE~VG~IAAQSIGEPaTQMTLnTFH~agts-------------~vpRlkEIl~~~~~~~~~~~t~~~~l~~~~~~~~~~~ 67 (381) T cd02737 1 GEPVGSLAATAISEPAYKALLDPPQSLESS-------------PLELLKEVLECRSKSKSKENDRRVILSLHLCKCDHGF 67 (381) T ss_pred CCCCHHHHHHHCCCHHHCCCCCCCCCCCCC-------------CCHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCHHH T ss_conf 972126676744727754112251336456-------------6277888863102678999873589840323320116 Q ss_pred CEEEEEECCCHHCCCCCCCCEEECCEEEEECCCCCCEEEECCCCEEEEEEEC--CCCEEHHHHHCCCCCEEEEEEEHHHC Q ss_conf 6000000110000135678553225078621354311320246368975312--78320012302368602677510110 Q gi|254780142|r 986 QEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHTFPIITEVSGTVGFEDLV--DGISVIESIGESTGIAKRKVIDWRFA 1063 (1398) Q Consensus 986 ~~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp~~~~i~~e~~~~v~~~~~~--~~~~~~~~~~~~t~~~~~~~i~~~~~ 1063 (1398) +..++++.++..++++++++++...+++|+|++....+.........+.... .............+|......+.... T Consensus 68 e~~~~A~~Vk~~IE~ttL~div~~~~I~y~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~d~~~~ 147 (381) T cd02737 68 EYERAALEVKNHLERVTLEDLATTSMIKYSPQATEAIVGEIGDQLNTKKKGKKKAIFSTSLKITKFSPWVCHFHLDKECQ 147 (381) T ss_pred HHHHHHHHHHHHHHHEEHHHHHEEEEEEECCCCCCEEEECCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHEEEEECHHHH T ss_conf 78999999998764137984010899999488662244031889998875555566776653313673021356405451 Q ss_pred CCCCCCCCCEEEECCCCCEEECCCCCCCEEECCCCCEEEECCCCCCCCCCEEEECHHHHCCCCCCCCCCCHHHHHHHHHC Q ss_conf 12212385347742778253224788420213778445413676135484222101320245543367732889887525 Q gi|254780142|r 1064 SRSQNLKPAIVVTDENGVVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFEARR 1143 (1398) Q Consensus 1064 ~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~v~~~d~l~~~~~~~~k~~DIt~GLPrV~eLFEar~ 1143 (1398) . ..... + ..+...... ..+ ....+...+. T Consensus 148 ~--------------------~~~~~---------~-i~~~~~~~~---------------~~~------~~~~l~~l~~ 176 (381) T cd02737 148 K--------------------LSDGP---------C-LTFSVSKEV---------------SKS------SEELLDVLRD 176 (381) T ss_pred C--------------------CCCCC---------E-EEEEECCCC---------------CCH------HHHHHHHHHH T ss_conf 0--------------------24563---------5-999836555---------------700------8999999999 Q ss_pred ---CC-CCCEECCCCCEEEEEE--EC------------CCCEEEEEEECCCCCCEEEEEECCCCEEE-EECCC--EEECC Q ss_conf ---11-1101113478678633--12------------79449999836898402689813896589-84198--77408 Q gi|254780142|r 1144 ---PK-NHAILAEISGTIRIKR--NY------------KNKSRVVIEPFEDGVEPAEYFIPKNKHFY-LQDGD--HVEKG 1202 (1398) Q Consensus 1144 ---pk-~~aiisei~Giv~i~~--~~------------~~k~~~vi~~~~~g~~~~e~~ip~~~~l~-v~dgd--~V~~g 1202 (1398) |. ....+.++.|+.++.- .. ....++++.....+... ...+..|. +.++. -.+.- T Consensus 177 ~i~~~ll~~~ikGi~~i~~v~i~~~~~~~~~~~~~~~~~~~~e~~l~v~~~~~~~----~~~~~~~~~v~~~cl~~ld~V 252 (381) T cd02737 177 RIIPFLLETVIKGDERIKSVNILWEDSPSTSWVKSVGKSSRGELVLEVTVEESCK----KTRGNAWNVVMDACIPVMDLI 252 (381) T ss_pred HHHHHHHCCEECCCCCCCEEEEEEECCCCCCCCCCCCCCCCCEEEEEEEEECCCC----CCCCCHHHHHHHHCCCCCCCC T ss_conf 9875652033458766556999840576543112334577754999998403433----014303566654121223443 Q ss_pred CEEECCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHH Q ss_conf 64643899999998752799999999999999999809700612560124762861489418864545664106999999 Q gi|254780142|r 1203 DYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEE 1282 (1398) Q Consensus 1203 d~lt~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~ 1282 (1398) |...+-+||++||+++|||||||++|++|+++|++++|++||+|||+||||.||++|.+++ ++|||+++.. T Consensus 253 D~~RT~sn~i~ei~~~lGIEaar~~i~~e~~~~~~~~g~~v~~rHl~llad~mt~~G~~~~------i~r~G~~~~~--- 323 (381) T cd02737 253 DWERSMPYSIQQIKSVLGIDAAFEQFVQRLESAVSMTGKSVLREHLLLVADSMTYSGEFVG------LNAKGYKAQR--- 323 (381) T ss_pred CCCCCEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCEEE------EECCCCCCCC--- T ss_conf 5775230879999997709999999999999999852764218889898887335781677------5330201445--- Q ss_pred HHHHHHHCCCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCCCCCCCCCH-HH Q ss_conf 9999997289875201210000145302310776504025899999974528552366532215507305655354-66 Q gi|254780142|r 1283 LNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGA-IL 1360 (1398) Q Consensus 1283 ~Nr~~~~~g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG~-f~ 1360 (1398) .|....|+|++||||+|+++|++||.+|+.|+|+|||||||+||++|+|||+ |. T Consensus 324 ------------------------~sv~~~~pl~~asfe~t~~~l~~Aa~~~~~d~~~gvs~~i~~G~~~~~GTG~~Fd 378 (381) T cd02737 324 ------------------------RSLKISAPFTEACFSSPIKCFLKAAKKGASDSLSGVLDACAWGKEAPVGTGSKFE 378 (381) T ss_pred ------------------------CCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHCCCCCCCCCCCCEE T ss_conf ------------------------5554468888854465999999999847977778989987659988888887641 No 32 >pfam00623 RNA_pol_Rpb1_2 RNA polymerase Rpb1, domain 2. RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion. Probab=100.00 E-value=0 Score=449.16 Aligned_cols=143 Identities=50% Similarity=0.711 Sum_probs=121.5 Q ss_pred CCCCCCCCCEEEECCCCCCCCCEECHHHHHHHHHHHHH--------HHHHHHCCCCCC-----CC---CCCCEEE----- Q ss_conf 51004577403412554354620034898776128999--------999998798666-----30---0010012----- Q gi|254780142|r 346 GKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKPFL--------YAQLEKKGYVST-----VK---QAKKFVE----- 404 (1398) Q Consensus 346 GKRVdfs~RsVI~pdP~l~~~evgvP~~~A~~L~~P~~--------~~~L~~~g~~~~-----i~---~~k~~i~----- 404 (1398) ||||||||||||||||+|++||||||..||++||+|+. +++++.+|.... +. ..+..+. T Consensus 1 GKRvd~saRsVItpdP~L~i~evGiP~~iA~~Lt~pe~V~~~N~~~l~~~v~~g~~~~~~~~~~~~~~~~~~~l~~~~~~ 80 (165) T pfam00623 1 GKRVDFSGRSVITPDPNLKLDEVGVPIEMALELTKPEIVTKLNIKKLRKLVSNGPNVPPGAKYIKRIKGAKRDLEYKKRI 80 (165) T ss_pred CCCCCCCCCCCCCCCCCCCCCEEECCHHHHHHCCCHHEEHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCEEEEEECCCC T ss_conf 99877489754617998838874697999986281032379899999999972986566650677178858887505631 Q ss_pred -CCCCCEEHHHHHHHCCCEEEECCCCCCEECCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCEEEEECCCCHHHHHHHH Q ss_conf -2488250132666569789975763101114012358994495479731225454678775456997468999999999 Q gi|254780142|r 405 -KERPEVWDVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEAR 483 (1398) Q Consensus 405 -~~~~~v~~v~rhl~~gd~Vl~NRqPsLHr~Simah~~~v~~~~t~rln~~vc~pyNADFDGDEMnlHvPqs~eAraEa~ 483 (1398) .....+|.|+|||+|||+|||||||||||+|||||+|++++++||||||++|+||||||||||||+|||||++|||||+ T Consensus 81 ~~~l~~g~~v~R~l~dGD~Vl~NRqPTLHr~si~a~~v~i~~~~tirlnp~vc~~fNADFDGDeMnih~pqs~~a~~E~~ 160 (165) T pfam00623 81 AIELWYGDIVLRHVIDGDVVLLNRQPTLHRMSIMAHRPRVLEGKTIRLNPSVCSPYNADFDGDEMNLHVPQSEEARAEAR 160 (165) T ss_pred CHHHCCCHHHHHHHHCCCEEEEECCCCCCCCEEEEEEEEEECCCEEEECCCCCCCCCCCCCCCEEEEECCCCHHHHHHHH T ss_conf 11212351156576479889992785225142036688996897058776546770588787247876689999999999 Q ss_pred HHHHH Q ss_conf 98767 Q gi|254780142|r 484 VLMLS 488 (1398) Q Consensus 484 ~Lm~~ 488 (1398) +||+| T Consensus 161 ~Lm~v 165 (165) T pfam00623 161 ELMLV 165 (165) T ss_pred HHHCC T ss_conf 87249 No 33 >cd00630 RNAP_largest_subunit_C Largest subunit of RNA polymerase (RNAP), C-terminal domain. RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channe Probab=100.00 E-value=0 Score=434.70 Aligned_cols=110 Identities=35% Similarity=0.547 Sum_probs=100.3 Q ss_pred CHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHC Q ss_conf 99999875279999999999999999980970061256012476286148941886454566410699999999999972 Q gi|254780142|r 1211 VPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQ 1290 (1398) Q Consensus 1211 d~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~ 1290 (1398) |+|||+++|||||||++|++||++||++||++||+|||+||||+||++|.+++ ++|||+++ T Consensus 49 di~eil~vlGIEAaR~~Ii~Ei~~V~~~~Gi~Id~RHi~LIaD~MT~~G~i~~------i~R~Gi~~------------- 109 (158) T cd00630 49 SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRG------VTRSGFRA------------- 109 (158) T ss_pred CHHHHHHHCCHHHHHHHHHHHHHHHHHHCCEEECHHHHHHHHHHHHCCCCCCC------CCHHHHCC------------- T ss_conf 99999995199999999999999999965935439999999999854786666------72565104------------- Q ss_pred CCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCCCCCCCCCH Q ss_conf 89875201210000145302310776504025899999974528552366532215507305655354 Q gi|254780142|r 1291 GKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGA 1358 (1398) Q Consensus 1291 g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG~ 1358 (1398) +++|||++||||+|+++|++||++|+.|+|+|||||||+||++|+|||+ T Consensus 110 -------------------~~~S~L~~ASFE~T~~~L~~AAi~g~~D~L~gvsenIiiG~~ip~GTGs 158 (158) T cd00630 110 -------------------SKTSPLMRASFEKTTKHLLDAAAAGEKDELEGVSENIILGRPAPLGTGS 158 (158) T ss_pred -------------------CCCCHHHHCCHHHHHHHHHHHHHCCCCCCCCCHHHHHCCCCCCCCCCCC T ss_conf -------------------6757888716599999999999818978787819873058987899896 No 34 >pfam04983 RNA_pol_Rpb1_3 RNA polymerase Rpb1, domain 3. RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking. Probab=99.93 E-value=1e-25 Score=211.53 Aligned_cols=133 Identities=37% Similarity=0.574 Sum_probs=114.9 Q ss_pred CCCCCCCCCCEEEEHHHHHHHHHHHHCCCCCCCCCCCEECCHHHHHHHHHCCCCCCCCEEEEEECCCCCCCCCCCEEECC Q ss_conf 54237887820440258999999873367887446814179999999998889867852365204645667614245217 Q gi|254780142|r 491 NLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENKIVTLHSKIRGRYKSVDKDGNSISKIYDT 570 (1398) Q Consensus 491 niisP~~g~Pi~~~~QD~i~G~y~lT~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~a~i~~~~~~~~~~~~~~~~~~~t 570 (1398) ||+||++|+|+++|+||+|+|+|+||..+ .|.++++++.++..+.+.+|+.+..+.. . . T Consensus 1 NiisP~~G~Pii~~~QD~ilG~y~LT~~~--------~f~~~~e~~~~~~~~~~~~~~~i~~~~~-~------------~ 59 (158) T pfam04983 1 NILSPQNGKPIIGPSQDMVLGLYLLTRRD--------TFFDREEVMQLLMYGIVLPHPAILKPIK-P------------L 59 (158) T ss_pred CCCCCCCCCCEEEEHHHHHHHHHHHHCCC--------CCCCHHHHHHHHHHCCCCCCCCEEECCC-C------------C T ss_conf 93268998936764028989989972898--------6699999999998379877870576376-6------------7 Q ss_pred CCCCCCCCE-------------------------EEECCCCCEEEEECCHHCCHHHHHHHHHHHHHCCHHHHHHHHHHHH Q ss_conf 977511220-------------------------5545875101775110020136669999999808178999875588 Q gi|254780142|r 571 TPGRMIIGE-------------------------ILPRHHEISFDICNQEMIKKNISAMVDTIYRHCGQKSTVAFCDDLM 625 (1398) Q Consensus 571 t~Gr~~~~~-------------------------ilp~~~~~~~~~~~~~~~k~~~~~li~~i~~~~G~~~~~~~l~~~~ 625 (1398) |.|+++|+. +++++|++..|.+||.+.|++.++|+|.++++||+++|+.|||++| T Consensus 60 ~tgkq~~s~il~~~~~~~~~~~~~~~~~~~~~~~v~I~~G~l~~G~idk~~~~~~~~~Li~~i~~~~G~~~~~~~ld~i~ 139 (158) T pfam04983 60 WTGKQTFSRLLPNEINPKGKPKTNEETLCENDSYVLINNGELISGVIDKKLGGKSLGSLIHIIYKEYGPEETVKFLDRLQ 139 (158) T ss_pred CEEEEEHHHCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCEEEEEEECCHHCCCCHHHHHHHHHHHCCHHHHHHHHHHHH T ss_conf 23103131102266454757766764457777748985781787453311126528889999999829899999999999 Q ss_pred HHHHHHHHHCCCCCCCCCC Q ss_conf 9999999853986132123 Q gi|254780142|r 626 RLGFRYACSSGISFGKDDI 644 (1398) Q Consensus 626 ~l~~~~l~~~GfSigi~D~ 644 (1398) +++++|++.+|||||++|+ T Consensus 140 ~l~~~~l~~~GfSvgi~Dl 158 (158) T pfam04983 140 KLGFRYLTKSGFSIGIDDI 158 (158) T ss_pred HHHHHHHHHCCEEEEECCC T ss_conf 9999999977867952059 No 35 >COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] Probab=99.68 E-value=8.9e-20 Score=166.75 Aligned_cols=121 Identities=25% Similarity=0.337 Sum_probs=96.8 Q ss_pred ECCCEEECCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCE-ECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHH Q ss_conf 4086464389999999875279999999999999999980970-061256012476286148941886454566410699 Q gi|254780142|r 1200 EKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVA-INHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRI 1278 (1398) Q Consensus 1200 ~~gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~-IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~ 1278 (1398) ..|+...+-.+|.++++.++|+||+|+++++|+..+...+|.. ++.+|++.-++.|+.-+.+-..| +||+ T Consensus 619 ~~g~lt~~~~~~i~e~~e~~~~e~l~~ai~~~~~~~~~~~g~~~~~i~~m~~~Gs~~n~sq~~~~~G------~~gv--- 689 (808) T COG0086 619 EEGDLTRTERNNIVEIIEVLGIEALRNAIIEEIKITLEEQGLDFVDIRHMGLSGARMNISQIVQLIG------QQGV--- 689 (808) T ss_pred HCCCCCCCCCCCEEEEEEHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHHH------HHEE--- T ss_conf 4587634577875687621779999999999876667752874023999864362448999999863------3203--- Q ss_pred HHHHHHHHHHHCCCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCCCCCCCCCH Q ss_conf 99999999997289875201210000145302310776504025899999974528552366532215507305655354 Q gi|254780142|r 1279 EVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGA 1358 (1398) Q Consensus 1279 ~~~~~Nr~~~~~g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG~ 1358 (1398) .-...|.+++|+||.|..+ .+|+.+++.+.++|+++|+++|+.+++|||+ T Consensus 690 -----------------------------~g~r~~~~~~~~Fe~~~~~-~~a~~~i~s~f~eGLt~~e~f~~~~ggR~Gl 739 (808) T COG0086 690 -----------------------------MGEKISVLARAAFEVTVKH-LEAEGPGESSFLEGLTENEYFGHPIGGRTGL 739 (808) T ss_pred -----------------------------ECCCCCCCCCCCCCCCCCC-CEEEEEEECCCCCCCCCCEEEEECCCCCCCH T ss_conf -----------------------------1257886532222346655-3455456645577997226875057665316 Q ss_pred H Q ss_conf 6 Q gi|254780142|r 1359 I 1359 (1398) Q Consensus 1359 f 1359 (1398) - T Consensus 740 v 740 (808) T COG0086 740 V 740 (808) T ss_pred H T ss_conf 8 No 36 >pfam04998 RNA_pol_Rpb1_5 RNA polymerase Rpb1, domain 5. RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound. Probab=98.98 E-value=2.6e-10 Score=95.50 Aligned_cols=120 Identities=29% Similarity=0.286 Sum_probs=110.6 Q ss_pred CEEEEEECCCCEEEEECCCEEECCCEEECCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCE Q ss_conf 02689813896589841987740864643899999998752799999999999999999809700612560124762861 Q gi|254780142|r 1179 EPAEYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQK 1258 (1398) Q Consensus 1179 ~~~e~~ip~~~~l~v~dgd~V~~gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~k 1258 (1398) ...++.++...++.+..++.+..+..++++++++++++...|.|++..+..++++.||..||+.+++||++..+.+|..+ T Consensus 307 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~t~G~nl~~v~~~~gvid~~k~~sn~I~em~~~ 386 (447) T pfam04998 307 LEEEELLLLNKILLVIPGIKVKYGVILTDGRVDPHTILEKLGKEWLLKTEGNNLQAVMRLQGVIDNDKTYSNDIREMLKK 386 (447) T ss_pred CHHHHCCCCCCHHEECCCCEEEECCCCCCCCCCCHHHHCCCCCEEEEEEEHHHHHHHHHCCCCCCCCCEEEEEHHHHHHH T ss_conf 11121252121020013868972232565777621320136837666440589999997289354781689829966522 Q ss_pred EEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEE Q ss_conf 4894188645456641069999999999997289875201 Q gi|254780142|r 1259 VEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFS 1298 (1398) Q Consensus 1259 g~I~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~~~ 1298 (1398) ..|..++++.+.+.+.|.....-..|.+.+..+.-+++++ T Consensus 387 lGIEAAr~~i~~E~~~V~~~~g~~vn~RHl~llaD~MT~~ 426 (447) T pfam04998 387 LGIEAARDSILLEIRNVFKFDGIYVNRRHLALLADLMTFK 426 (447) T ss_pred EEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEC T ss_conf 5999885121353899998877887699998589746235 No 37 >pfam05000 RNA_pol_Rpb1_4 RNA polymerase Rpb1, domain 4. RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors. Probab=98.83 E-value=4.7e-10 Score=93.59 Aligned_cols=89 Identities=31% Similarity=0.435 Sum_probs=57.1 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----CCCCCCCCCCCCCCEEEEECCCCCCC---HHHEEEEEEECCCCCC Q ss_conf 6678887886423465899999999998761----15654322224688376422555578---4241120010000246 Q gi|254780142|r 674 TRGEKYNKVVDLWGKTTDKVTEEMMARIKRV----EFDPETGRQKKMNSIFMMSHSGARGS---IHQMRQLGGMRGLIAK 746 (1398) Q Consensus 674 t~~e~~~~i~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~N~~~~M~~SGAKGS---~~qi~ql~Gqq~l~gk 746 (1398) ++.+++.++...|+.+.+++.+..+..+.+. ........+..+|++++|+.|||||| +.||+.|+|||.++|+ T Consensus 2 ~~~~~~~~~~~~~~~s~~~~~E~~i~~~l~~~~~~~~~~~~~~~~~~N~~~~Mv~SGsKGs~~Ni~Qi~g~~GQQ~v~g~ 81 (108) T pfam05000 2 TDAERYGKLEDIWGMTLEEVFEALINNILNKARDPAGNIASKSLDLNNSIYMMADSGAKGSIINISQIAGCRGQQNVEGK 81 (108) T ss_pred CCHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCCHHHHHHHHHHHCCEEECCC T ss_conf 16544885347999988999999999999999999999999865866659999883377654529999986352147782 Q ss_pred CCCCCCCCCCCCHHHC Q ss_conf 4434445666301110 Q gi|254780142|r 747 PSGEIIESPIRSHFKG 762 (1398) Q Consensus 747 p~G~~~~~PV~~sF~~ 762 (1398) +.-..+..+...+|.. T Consensus 82 Ri~~~~~~Rtlp~f~~ 97 (108) T pfam05000 82 RIPFGFSGRTLPHFKK 97 (108) T ss_pred CCCCCCCCCCCCCCCC T ss_conf 1678989987999999 No 38 >PRK02995 DNA-directed RNA polymerase subunit beta'; Provisional Probab=96.99 E-value=0.00019 Score=51.36 Aligned_cols=31 Identities=10% Similarity=-0.030 Sum_probs=25.6 Q ss_pred EECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHH Q ss_conf 0061256012476286148941886454566410699 Q gi|254780142|r 1242 AINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRI 1278 (1398) Q Consensus 1242 ~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~ 1278 (1398) .+|.||++...+.||+|+.|+. |||++++.. T Consensus 1166 ~~n~~~~~~~~~~~~~r~~llG------ITr~~l~t~ 1196 (1291) T PRK02995 1166 AENRRVVAEGGEPASGRPVLMG------ITKASLATE 1196 (1291) T ss_pred HHHHHHHHCCCCCCEEEEEEEE------EEECCCCCC T ss_conf 9999999839971134221466------400431122 No 39 >PRK05258 DNA-directed RNA polymerase subunit beta'; Provisional Probab=96.26 E-value=4.7e-05 Score=55.96 Aligned_cols=30 Identities=10% Similarity=-0.015 Sum_probs=25.6 Q ss_pred EECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCH Q ss_conf 006125601247628614894188645456641069 Q gi|254780142|r 1242 AINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDR 1277 (1398) Q Consensus 1242 ~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr 1277 (1398) .+|.||++...+.||+++.++. |||++++. T Consensus 1102 ~~n~~~~~~g~~~a~~~~~llG------ITr~~l~t 1131 (1204) T PRK05258 1102 DANKKVLISGGIPATARPVLLG------ITKASLET 1131 (1204) T ss_pred HHHHHHHHCCCCCCEEEEEEEE------EECCCCCC T ss_conf 9999999759976445458877------63165233 No 40 >TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit; InterPro: IPR012754 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This entry represents the beta-prime subunit, RpoC, found in most bacteria. It excludes some, mainly cyanobacterial, species where RpoC is replaced by two homologous proteins that include an additional domain. One arm of the "claw" is predominantly formed by this subunit, the other being predominantly formed by the beta subunit. The active site of the enzyme is defined by three invariant aspartate residues within the beta-prime subunit .; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription. Probab=95.95 E-value=0.096 Score=31.08 Aligned_cols=39 Identities=26% Similarity=0.340 Sum_probs=21.5 Q ss_pred CEEEEECCCCEEEEEECCCHHCCCCCCCCEEECCEEEEE Q ss_conf 046640677600000011000013567855322507862 Q gi|254780142|r 977 TLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISE 1015 (1398) Q Consensus 977 ~~~i~d~~~~~~~~~ki~~~~~~~v~~~~~v~~~~ii~~ 1015 (1398) .+.+.|........|.+|+++++.|.+|+.|+.+.+++. T Consensus 1265 rI~i~D~~~~~~a~Y~~P~~Aii~V~dG~~v~~GDIlAk 1303 (1552) T TIGR02386 1265 RIAILDEKGELVATYAIPADAIISVEDGQKVKPGDILAK 1303 (1552) T ss_pred EEEEEECCCCCCEEEECCCCEEEEECCCCCCCCCCEEEE T ss_conf 489985689831355663010787215875474747886 No 41 >pfam05183 RdRP RNA dependent RNA polymerase. This family of proteins are eukaryotic RNA dependent RNA polymerases. These proteins are involved in post transcriptional gene silencing where they are thought to amplify dsRNA templates. Probab=90.52 E-value=0.3 Score=27.34 Aligned_cols=52 Identities=27% Similarity=0.379 Sum_probs=31.7 Q ss_pred HHCCCEEEECCCCCCEECCEEEEEEEEECC------------CEEEEECCCCCCCCCCCCCCEEEEE Q ss_conf 656978997576310111401235899449------------5479731225454678775456997 Q gi|254780142|r 417 VVHQHVVLLNRAPSLHRLSMQAFEPKIISG------------KAIQLHPLVCAGYNADFDGDQMAVY 471 (1398) Q Consensus 417 l~~gd~Vl~NRqPsLHr~Simah~~~v~~~------------~t~rln~~vc~pyNADFDGDEMnlH 471 (1398) ++.|+ ||.-|.|.||.--|+-++++-.|. +-=|=+++-|+ ..|+|||+.++- T Consensus 228 ~~~g~-VlV~RnP~lhPGDiq~~~AV~~p~L~hl~dvIVFp~kG~rpl~~~lS--GgDlDGD~y~V~ 291 (381) T pfam05183 228 VIGGD-VLVTRNPCLHPGDIRVLKAVDVPELRHLKDVIVFPQKGDRPLPSELS--GGDLDGDLYFVI 291 (381) T ss_pred EEEEE-EEEEECCCCCCCCEEEEECCCCHHHHCCCCEEEECCCCCCCCHHHHC--CCCCCCCEEEEE T ss_conf 55003-99983676688854788626765564138789948989988557735--778788657997 No 42 >pfam04990 RNA_pol_Rpb1_7 RNA polymerase Rpb1, domain 7. RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 7, represents a mobile module of the RNA polymerase. Domain 7 forms a substantial interaction with the lobe domain of Rpb2 (pfam04561). Probab=87.39 E-value=0.033 Score=34.57 Aligned_cols=71 Identities=11% Similarity=0.037 Sum_probs=46.1 Q ss_pred CCCCCEEECCEEEEECCCCCCEEEECCCCEEEEEEECCCCEEHHHHHCCCCCEEEEEEEHHHCCCCCCCCCCEEEECCC Q ss_conf 5678553225078621354311320246368975312783200123023686026775101101221238534774277 Q gi|254780142|r 1001 VDDGGVIECGQRISEWDPHTFPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDEN 1079 (1398) Q Consensus 1001 v~~~~~v~~~~ii~~~Dp~~~~i~~e~~~~v~~~~~~~~~~~~~~~~~~t~~~~~~~i~~~~~~~~~~~~~~~~i~d~~ 1079 (1398) |+++++|.+.+++|+|++.++.+.++......|+.+.+. .......++|..+...+.. .++.+.+.+.+.. T Consensus 1 T~L~div~~~~IyyDPd~~~T~ieeD~~~l~~y~ef~d~---~~~~~~~S~WvlR~~ldk~-----~m~~k~itm~dI~ 71 (135) T pfam04990 1 TTLRSVTASTEIYYDPDPRNTVIEEDREWVESYFEIPDE---DDDPSRLSPWLLRLELDRE-----KMTDKKLTMKDIA 71 (135) T ss_pred CCHHHHHHHEEEEECCCCCCCCCHHHHHHHHHHHHCCCC---CCCCCCCCCEEEEEEECHH-----HHHHCCCCHHHHH T ss_conf 946782412379989998777606059999999956464---4463456872899998699-----9987799899999 No 43 >TIGR00354 polC DNA polymerase II, large subunit DP2; InterPro: IPR004475 This family represents the large subunit, DP2, of a two subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0006308 DNA catabolic process. Probab=83.39 E-value=0.58 Score=25.16 Aligned_cols=19 Identities=26% Similarity=0.567 Sum_probs=14.5 Q ss_pred CCEEEEHH------HHHHCCCEEEE Q ss_conf 74011015------42301432775 Q gi|254780142|r 790 SGYLSRRL------VDVAQNCVVNQ 808 (1398) Q Consensus 790 SGYlqRrL------vk~~eDl~V~~ 808 (1398) -|||.|+. -.|++.+-|+. T Consensus 727 eGymkrk~~L~~l~~~A~~nlg~~k 751 (1173) T TIGR00354 727 EGYMKRKVDLKELYKEALKNLGVRK 751 (1173) T ss_pred CCCEEECCCHHHHHHHHHHHCCCCC T ss_conf 5311211438999999998575205 No 44 >CHL00037 petA cytochrome f Probab=82.68 E-value=3 Score=19.79 Aligned_cols=76 Identities=22% Similarity=0.315 Sum_probs=51.9 Q ss_pred CCEECCCCCEEE-EEEECCCCEEEEEEECCCCCCEEEEEECCCCEEEEECCCEEECCCEEECCCCC-----------HHH Q ss_conf 101113478678-63312794499998368984026898138965898419877408646438999-----------999 Q gi|254780142|r 1147 HAILAEISGTIR-IKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYILDGNPV-----------PQD 1214 (1398) Q Consensus 1147 ~aiisei~Giv~-i~~~~~~k~~~vi~~~~~g~~~~e~~ip~~~~l~v~dgd~V~~gd~lt~Gsid-----------~~e 1214 (1398) ....+...|.+. |.+..++..++.+....+|... ...||.+-.+.|.+|+.|..++.||...|. .++ T Consensus 204 ~~~~as~~G~i~~I~~~ekgg~~itI~~~~dG~~v-~~~iP~Gpel~V~eG~~vk~dqpLT~nPNVGGFGQ~e~EIVLQ~ 282 (320) T CHL00037 204 TVYNATAAGIVSKIIRKEKGGYEITIVDASDGRQV-VDIIPPGPELLVSEGESIKLDQPLTSNPNVGGFGQGDAEIVLQD 282 (320) T ss_pred CEECCCCCCEEEEEEECCCCCEEEEEEECCCCCEE-EEECCCCCEEEECCCCEEECCCCCCCCCCCCCCCCCCEEEEECC T ss_conf 26605577278887765789569999865899788-87449997589727988856985556998676676614899418 Q ss_pred HHHHHCHHH Q ss_conf 987527999 Q gi|254780142|r 1215 ILRIKGVEA 1223 (1398) Q Consensus 1215 Il~vlGIEA 1223 (1398) =.++.|.=| T Consensus 283 P~Rv~gll~ 291 (320) T CHL00037 283 PLRVQGLLF 291 (320) T ss_pred HHHHHHHHH T ss_conf 358465799 No 45 >pfam01333 Apocytochr_F_C Apocytochrome F, C-terminal. This is a sub-family of cytochrome C. See pfam00034. Probab=80.81 E-value=3.5 Score=19.33 Aligned_cols=59 Identities=29% Similarity=0.363 Sum_probs=41.5 Q ss_pred ECCCCCEEE-EEEECCCCEEEEEEECCCCCCEEEEEECCCCEEEEECCCEEECCCEEECCCC Q ss_conf 113478678-6331279449999836898402689813896589841987740864643899 Q gi|254780142|r 1150 LAEISGTIR-IKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYILDGNP 1210 (1398) Q Consensus 1150 isei~Giv~-i~~~~~~k~~~vi~~~~~g~~~~e~~ip~~~~l~v~dgd~V~~gd~lt~Gsi 1210 (1398) .+...|.+. |....++...+.|. ..+|.. ....||.+-.+.|.+|+.|.+++.||..+| T Consensus 6 ~as~~G~I~~I~~~ekg~~~vtI~-t~dG~~-v~~~IP~GpeliV~~G~~V~~dqpLT~nPN 65 (118) T pfam01333 6 NASAAGTITKITRNEKGGYEVTIE-TADGET-VVETIPAGPELIVSEGQTVKADQPLTNNPN 65 (118) T ss_pred ECCCCEEEEEEEECCCCCEEEEEE-CCCCCE-EEEECCCCCEEEECCCCEEECCCCCCCCCC T ss_conf 166770899977567885799998-699989-988539997489738988866984445998 No 46 >TIGR01343 hacA_fam homoaconitate hydratase family protein; InterPro: IPR006251 3-isopropylmalate dehydratase (or isopropylmalate isomerase; 4.2.1.33 from EC) catalyses the stereo-specific isomerisation of 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. This enzyme performs the second step in the biosynthesis of leucine, and is present in most prokaryotes and many fungal species. The prokaryotic enzyme is a heterodimer composed of a large (LeuC) and small (LeuD) subunit, while the fungal form is a monomeric enzyme. Both forms of isopropylmalate are related and are part of the larger aconitase family . Aconitases are mostly monomeric proteins which share four domains in common and contain a single, labile [4Fe-4S] cluster. Three structural domains (1, 2 and 3) are tightly packed around the iron-sulphur cluster, while a fourth domain (4) forms a deep active-site cleft. The prokaryotic enzyme is encoded by two adjacent genes, leuC and leuD, corresponding to aconitase domains 1-3 and 4 respectively , . LeuC does not bind an iron-sulphur cluster. It is thought that some prokaryotic isopropylamalate dehydrogenases can also function as homoaconitase 4.2.1.36 from EC, converting cis-homoaconitate to homoisocitric acid in lysine biosynthesis . Homoaconitase has been identified in higher fungi (mitochondria) and several archaea and one thermophilic species of bacteria, Thermus thermophilus . This entry represents the large subunit of 3-isopropylmalate dehydratase (LeuC), as well as homoaconitase, certain aconitases and uncharacterised proteins, and is a subgroup of those represented in IPR012095. Homoaconitase, aconitase and 3-isopropylmalate dehydratase have similar overall structures and domain organisation . All are dehydratases that bind a [4Fe-4S]-cluster. The majority of the members of this family have been designated as 3-isopropylmalate dehydratase large subunit (LeuC) in microbial genome annotation, but the only characterised member is T. thermophilus homoaconitase, an enzyme of a non-aspartate pathway of lysine biosynthesis. Information about related proteins can be found at Protein of the Month: Aconitase .; GO: 0016836 hydro-lyase activity, 0051539 4 iron 4 sulfur cluster binding, 0008652 amino acid biosynthetic process. Probab=77.00 E-value=1.4 Score=22.31 Aligned_cols=40 Identities=28% Similarity=0.415 Sum_probs=28.7 Q ss_pred CCCCCEECHHHCC----------CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEEEEE Q ss_conf 0178520001014----------602111100788987764202454322211220240148768972 Q gi|254780142|r 900 LARGSLVNVGEAV----------GVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIK 957 (1398) Q Consensus 900 l~~~~lv~pGe~V----------G~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVPRlk 957 (1398) |..+.+|.||+-| |+++|=|=|==||=|-+ ...+|...|| T Consensus 104 L~E~glv~PG~~vvGaDSHTCTyGA~GAFaTG~GsTD~A~------------------a~A~Gk~W~r 153 (432) T TIGR01343 104 LPEEGLVKPGDLVVGADSHTCTYGALGAFATGVGSTDIAY------------------AIATGKVWFR 153 (432) T ss_pred ECCCCEECCCCEEEECCCCHHHHHHHHHHHCCCCHHHHHH------------------HHHHCCCEEE T ss_conf 3268700678779934731223455765413744589999------------------9982861021 No 47 >TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF; InterPro: IPR004421 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesized as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins , , . Members of the HypF family are accessory proteins involved in hydrogenase maturation. They contain the following domains: acylphosphatase, zinc fingers (2 repeats), a YrdC-like domain, and a C-terminal domain with a putative O-carbamoyltransferase motif. The presence of CO and CN- ligands of the active site iron atoms is essential for [NiFe]-hydrogenase enzyme activity . Both ligands have been suggested to originate from carbamoylphosphate , which is required for maturation of [NiFe]-hydrogenases . Escherichia coli HypF interacts with carbamoylphosphate as a substrate and releases inorganic phosphate . In addition, HypF also cleaves ATP into AMP and pyrophosphate in the presence of carbamoylphosphate. This, and the fact that HypF catalyzes a carbamoylphosphate-dependent pyrophosphate ATP exchange reaction, suggest that the protein catalyzes the activation of carbamoylphosphate . The mechanism of action of HypF, as well as of its individual domains, is not yet clear. Mutations in any of the three major signature motifs, the acylphosphatase, the zinc fingers, and the O-carbamoyltransferase motif, can block carbamoylphosphate phosphatase activity. This indicates an integrated cooperativity between these domains in the cleavage reaction . The N-terminal acylphosphatase (ACP) domain is thought to support the conversion of carbamoylphosphate into CO and CN- , . Biochemical results demonstrating its ACP activity are not available , . ACPs are small enzymes that specifically catalyze the hydrolysis of carboxylphosphate bonds in acylphosphates, including carbamoylphosphate . Zinc fingers have been implicated in bivalent cation binding or as part of a chaperone domain interacting with the large subunit precursor, but experimental studies on such a function are lacking thus far. The YrdC-like domain is present in protein families with regulatory functions (IPR012200 from INTERPRO, IPR010923 from INTERPRO) and has been implicated in RNA binding . It is not clear what function it may have in members of the HypF family. A C-terminal domain is distantly related to peptidase M22, but contains a conserved O-carbamoyltransferase motif required for the carbamoylphosphate phosphatase activity . The function of this domain is not clear. Nomenclature note: the following names are used as synonyms of HypF: HupY in Azotobacter chroococcum, HupN in Rhizobium leguminosarum, HydA in Escherichia coli. In other organisms, these names are used to designate various "hydrogenase cluster" proteins unrelated to the members of this family. ; GO: 0030528 transcription regulator activity. Probab=70.92 E-value=3.1 Score=19.71 Aligned_cols=75 Identities=23% Similarity=0.394 Sum_probs=41.3 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECHHHHHHHHHHHHHCCCHHHHHHHHHHCCEEEECCCCCCHHHHCCC-- Q ss_conf 356757885304775787677200277622013012257899998099965630133211123217886510432236-- Q gi|254780142|r 84 IICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRDVERVLYFESYVVVDPGLSSLEKYQIL-- 161 (1398) Q Consensus 84 ~~C~~Cg~~~~~~~~r~ghfGhIeLa~PV~Hi~f~k~~~~~i~~~l~~~~~~~~~v~y~~~~~~~~~~~~~~~~~~~~-- 161 (1398) .+|+.|=.|+.+...||||+-.|. |+-||=--.-++.+-| + -..+.++...+| T Consensus 103 a~C~~CL~E~~D~~~RRY~YPF~~------------------CT~CGPRfTi~~aLPY-D------Re~T~m~~FpLC~~ 157 (799) T TIGR00143 103 ATCDDCLEEMLDKNDRRYLYPFIS------------------CTDCGPRFTIIEALPY-D------RENTSMADFPLCPD 157 (799) T ss_pred CCCHHHHHHHCCCCCCCCCCCCCC------------------CCCCCCCHHHHHCCCC-C------CCCCCCCCCCCCHH T ss_conf 026155775077868811274324------------------3556752567642788-8------87433457898846 Q ss_pred CHHHHHHH-----------HHHCCCC-CEEECCC Q ss_conf 99999886-----------7635855-5061155 Q gi|254780142|r 162 TEEEYVEA-----------VSQFGQD-QFIAMMG 183 (1398) Q Consensus 162 ~~~~~~~~-----------~~~~~~~-~~~~~~g 183 (1398) |++||.+. +++||.. .|...-| T Consensus 158 C~~EY~dP~DRRFHAQ~~aCP~CGP~L~f~~~~~ 191 (799) T TIGR00143 158 CEKEYKDPLDRRFHAQAIACPRCGPKLEFVSRGG 191 (799) T ss_pred HHHHCCCCCCCEEEECCCCCCCCCCCCCEECCCC T ss_conf 8997078876304644627733578653021687 No 48 >PRK04023 DNA polymerase II large subunit; Validated Probab=70.69 E-value=1.9 Score=21.33 Aligned_cols=19 Identities=21% Similarity=0.146 Sum_probs=13.8 Q ss_pred CHHHHHHHHHHHHHHHHHH Q ss_conf 1003789999999869999 Q gi|254780142|r 264 ASDLNDLYRRVIGRNNRLM 282 (1398) Q Consensus 264 ~dDlt~~~~~Ii~~N~~Lk 282 (1398) ..-|..+..|.++++-.|- T Consensus 153 aqAlsVLiaD~vR~~~g~~ 171 (1128) T PRK04023 153 AQALSVLVGDYVRRKLGID 171 (1128) T ss_pred HHHHHHHHHHHHHHHCCCC T ss_conf 9999999999999975987 No 49 >PRK02693 apocytochrome f; Reviewed Probab=67.78 E-value=7.1 Score=17.01 Aligned_cols=62 Identities=27% Similarity=0.384 Sum_probs=43.2 Q ss_pred CCEECCCCCEEE-EEEECCCCEEEEEEECCCCCCEEEEEECCCCEEEEECCCEEECCCEEECCCC Q ss_conf 101113478678-6331279449999836898402689813896589841987740864643899 Q gi|254780142|r 1147 HAILAEISGTIR-IKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYILDGNP 1210 (1398) Q Consensus 1147 ~aiisei~Giv~-i~~~~~~k~~~vi~~~~~g~~~~e~~ip~~~~l~v~dgd~V~~gd~lt~Gsi 1210 (1398) ....+...|.+. |....++...+.|.. .+|.. ....||.+-.+.|.+|+.|.+++.||...| T Consensus 197 ~~~~as~~G~I~~I~~~e~G~~~v~I~t-~~G~~-v~~~iP~Gp~liV~~G~~v~~~qpLT~nPN 259 (312) T PRK02693 197 NVFTASAAGTITSIETGEDGSYVVTITT-EDGEV-VTETIPAGPELIVKEGDAVEAGAPLTNDPN 259 (312) T ss_pred CEECCCCCEEEEEEEECCCCCEEEEEEC-CCCCE-EEEECCCCCEEEECCCCEEECCCCCCCCCC T ss_conf 2553667727888776688867999988-99999-988529998589727988856986667998 No 50 >KOG0988 consensus Probab=67.16 E-value=6.3 Score=17.39 Aligned_cols=32 Identities=19% Similarity=0.214 Sum_probs=18.0 Q ss_pred CCCCCHHHHCCCCCCCCCCEEEEHHHHHHC-CCEE Q ss_conf 576103221012101567401101542301-4327 Q gi|254780142|r 773 CVGGRKGLLDVVMRTASSGYLSRRLVDVAQ-NCVV 806 (1398) Q Consensus 773 amgGReGLiDTAvKTA~SGYlqRrLvk~~e-Dl~V 806 (1398) -|++|-|..=|+ |-.|||.-||+.-... |+.. T Consensus 516 K~aARmGqCFs~--Sr~T~~~~~~~~~~~~~DI~~ 548 (1145) T KOG0988 516 KLAARMGQCFSQ--SRGTGYVLERLDRMCPPDIEG 548 (1145) T ss_pred HHHHHCCCCEEC--CCCCCCCCCCCCCCCCCCCCC T ss_conf 998646864000--255201145324024776202 No 51 >TIGR00416 sms DNA repair protein RadA; InterPro: IPR004504 RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC .; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0006281 DNA repair. Probab=65.01 E-value=3.3 Score=19.54 Aligned_cols=27 Identities=22% Similarity=0.426 Sum_probs=20.0 Q ss_pred CCCCCCEEEEECCCCCCCHHHEEEEEE Q ss_conf 224688376422555578424112001 Q gi|254780142|r 713 QKKMNSIFMMSHSGARGSIHQMRQLGG 739 (1398) Q Consensus 713 ~~~~N~~~~M~~SGAKGS~~qi~ql~G 739 (1398) .++.=.+|.-.-+=|=||++|++-|.+ T Consensus 202 iDSIQ~ly~~di~SaPGSVsQVRE~t~ 228 (481) T TIGR00416 202 IDSIQTLYLPDISSAPGSVSQVRECTA 228 (481) T ss_pred EECCCCCCCHHHCCCCCCHHHHHHHHH T ss_conf 914210000000258884238889999 No 52 >pfam09567 RE_MamI MamI restriction endonuclease. This family includes the MamI (recognizes and cleaves GATNN^NNATC) restriction endonuclease. Probab=64.29 E-value=7.4 Score=16.86 Aligned_cols=47 Identities=30% Similarity=0.386 Sum_probs=29.4 Q ss_pred HHHHCCCEEEECCCCCCEECCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCEEEEECCCCH Q ss_conf 66656978997576310111401235899449547973122545467877545699746899 Q gi|254780142|r 415 AEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISP 476 (1398) Q Consensus 415 rhl~~gd~Vl~NRqPsLHr~Simah~~~v~~~~t~rln~~vc~pyNADFDGDEMnlHvPqs~ 476 (1398) +.+--.|-|..|- |-. .-|.-.+++..++++ |||||-|.+-|||.+- T Consensus 217 ~P~gydddvvvnt---lgn---l~~~~~i~~d~~i~~---------~~~~~~~~~~h~pl~t 263 (350) T pfam09567 217 PPLGYDDDVVVNT---LGN---LDFQNFILFDARIQL---------ADFDGHEIAEHVPLPT 263 (350) T ss_pred CCCCCCCCEEECC---CCC---CCEEEEEEECCEEEE---------CCCCCCCCCCCCCCCC T ss_conf 7757775400023---243---111336641452451---------2478887433346875 No 53 >TIGR01369 CPSaseII_lrg carbamoyl-phosphate synthase, large subunit; InterPro: IPR006275 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates , . CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate . The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain . CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites . The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein . The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP . There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia . CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains . This entry represents glutamine-dependent CPSase (6.3.5.5 from EC) from prokaryotes and eukaryotes (CPSase II). ; GO: 0004086 carbamoyl-phosphate synthase activity, 0006807 nitrogen compound metabolic process. Probab=64.18 E-value=7.5 Score=16.84 Aligned_cols=42 Identities=21% Similarity=0.337 Sum_probs=23.8 Q ss_pred CCHHHCCCCCC----CCEEEECCCCCCHHHHHHHHHCC-CCEEECCCC Q ss_conf 11442017789----71885178657899999999759-840202331 Q gi|254780142|r 840 TALDDIINPLT----NECIVKAGQLILESHVNEIEKCG-IRSVRIRSA 882 (1398) Q Consensus 840 ~~~~di~~~~~----~~~i~~~~~~i~~~~~~~i~~~~-i~~v~irs~ 882 (1398) ...++|.|=.. .-+|++-|=-+--..+.+|.+++ +. +-.-|+ T Consensus 635 lt~E~Vm~I~e~E~~~GVIVq~GGQtp~nlA~~L~~~GG~~-iLGTS~ 681 (1089) T TIGR01369 635 LTFEDVMNIIELEKPEGVIVQFGGQTPLNLAKELEEAGGVP-ILGTSP 681 (1089) T ss_pred CCCCCCEEHEEECCCCEEEEECCCHHHHHHHHHHHHCCCCE-EECCCH T ss_conf 35031001100058667999748732678999999708931-736885 No 54 >pfam03615 GCM GCM motif protein. Probab=63.65 E-value=3.4 Score=19.36 Aligned_cols=48 Identities=25% Similarity=0.418 Sum_probs=31.5 Q ss_pred CCCCCCCCCC--CCCCCCCCCCCCCCCCCCCCCCCCEEECHHHHHHHHHHHHHCCCHHHHHHHHHHCCEEEEC Q ss_conf 3448835675--7885304775787677200277622013012257899998099965630133211123217 Q gi|254780142|r 79 MKYKGIICEK--CGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRDVERVLYFESYVVVD 149 (1398) Q Consensus 79 ~~~~g~~C~~--Cg~~~~~~~~r~ghfGhIeLa~PV~Hi~f~k~~~~~i~~~l~~~~~~~~~v~y~~~~~~~~ 149 (1398) .+..|..|.+ |.... +-.-||||-|| ||.|.|-.. ...+||++.-+.| T Consensus 78 ~KQqgk~Cpn~~C~g~L-~~~~CrGh~GY-----PVThFWR~~-----------------~~aIfFqaKG~HD 127 (143) T pfam03615 78 RKQQGKQCPNRGCNGRL-ELIPCRGHCGY-----PVTHFWRHD-----------------GNAIFFQAKGVHD 127 (143) T ss_pred HHHCCCCCCCCCCCCCE-EEEECCCCCCC-----CCEEEEEEC-----------------CCEEEEECCCCCC T ss_conf 87626889898987626-88745787898-----640478856-----------------9889997357658 No 55 >PRK11798 ClpXP protease specificity-enhancing factor; Provisional Probab=61.24 E-value=7.4 Score=16.87 Aligned_cols=80 Identities=26% Similarity=0.406 Sum_probs=47.0 Q ss_pred HHHHHHHHHHHHHH----HHCCCCCCCCCCCCEEECCCCCEEHHHHHHHCCCEEEECCCCCCEECCEEEEEEEEECCCEE Q ss_conf 87761289999999----98798666300010012248825013266656978997576310111401235899449547 Q gi|254780142|r 374 MALELFKPFLYAQL----EKKGYVSTVKQAKKFVEKERPEVWDVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAI 449 (1398) Q Consensus 374 ~A~~L~~P~~~~~L----~~~g~~~~i~~~k~~i~~~~~~v~~v~rhl~~gd~Vl~NRqPsLHr~Simah~~~v~~~~t~ 449 (1398) |.+.-+.||+++-+ +.+|....| +++-..+.+.--..|+.||.+| ||=.|+--+- -.+....+ T Consensus 2 m~m~s~rPYLiRA~yeW~~Dn~~TPyi-----~V~a~~~~v~VP~~~v~dg~Iv-LNIsp~Av~~-------L~i~nd~i 68 (140) T PRK11798 2 MQMTSTRPYLLRALYEWLVDNGLTPHL-----LVDATYPGVQVPMEYVKDGQIV-LNISPRAVGN-------LQLDNDAI 68 (140) T ss_pred CCCCCCCCHHHHHHHHHHHHCCCCCEE-----EEEECCCCCCCCHHHCCCCEEE-EECCHHHHHC-------EEECCCEE T ss_conf 777588426899999999728998549-----9981799966898880199899-9779888603-------07758789 Q ss_pred EEECCCCCCCCCCCCCCEEEEECCC Q ss_conf 9731225454678775456997468 Q gi|254780142|r 450 QLHPLVCAGYNADFDGDQMAVYAVI 474 (1398) Q Consensus 450 rln~~vc~pyNADFDGDEMnlHvPq 474 (1398) .|+|-|.|=.|.+.||- T Consensus 69 --------sF~ARF~G~~~~i~vP~ 85 (140) T PRK11798 69 --------SFNARFGGVPRQIYVPI 85 (140) T ss_pred --------EEEEEECCEEEEEEEEH T ss_conf --------99879799158999778 No 56 >pfam09538 FYDLN_acid Protein of unknown function (FYDLN_acid). Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown. Probab=60.28 E-value=6.5 Score=17.29 Aligned_cols=25 Identities=44% Similarity=1.063 Sum_probs=11.2 Q ss_pred CC-CCCC-CCCCCCCCCCCCCCCCCCC Q ss_conf 21-5664-1563448835675788530 Q gi|254780142|r 70 EC-ICGK-YKRMKYKGIICEKCGVEVT 94 (1398) Q Consensus 70 ~c-~Cg~-~~~~~~~g~~C~~Cg~~~~ 94 (1398) .| .||+ |.-.+..-.+|..||.++. T Consensus 11 ~c~~c~~~fydl~k~p~~cp~cg~~~~ 37 (104) T pfam09538 11 TCPTCGKRFYDLNKDPIVCPKCGEEVP 37 (104) T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCEEC T ss_conf 478888821127989871899888746 No 57 >PRK09001 DNA topoisomerase I; Validated Probab=58.41 E-value=6.1 Score=17.51 Aligned_cols=14 Identities=21% Similarity=0.313 Sum_probs=9.8 Q ss_pred CHHHHHHCCEEEEE Q ss_conf 86788501448971 Q gi|254780142|r 27 SPAKIASLSYGEIK 40 (1398) Q Consensus 27 spe~I~~~S~~ev~ 40 (1398) ..+=|-.||+|+|. T Consensus 22 G~~y~V~aS~GHir 35 (869) T PRK09001 22 GNDYVVKSSVGHIR 35 (869) T ss_pred CCCCEEEECCCCEE T ss_conf 98978997167025 No 58 >cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules. Probab=57.49 E-value=6.1 Score=17.51 Aligned_cols=16 Identities=31% Similarity=0.449 Sum_probs=9.3 Q ss_pred ECCCCCCCHHHEEEEE Q ss_conf 2255557842411200 Q gi|254780142|r 723 SHSGARGSIHQMRQLG 738 (1398) Q Consensus 723 ~~SGAKGS~~qi~ql~ 738 (1398) -..++-||++|++.|+ T Consensus 174 ~~~s~pGsvsQVReca 189 (372) T cd01121 174 ELTSAPGSVSQVRECT 189 (372) T ss_pred CCCCCCCCHHHHHHHH T ss_conf 7677998789999999 No 59 >TIGR01995 PTS-II-ABC-beta PTS system, beta-glucoside-specific IIABC component; InterPro: IPR011297 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) , is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC . These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose , , , . This entry represents a family of PTS enzyme II proteins in which all three domains are found in the same polypeptide chain and which appear to have a broad specificity for beta-glucosides including salicin (beta-D-glucose-1-salicylate) and arbutin (hydroquinone-O-beta-D-glucopyranoside) . These are distinct from the closely related sucrose-specific and trehalose-specific PTS transporters.; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system. Probab=57.36 E-value=11 Score=15.69 Aligned_cols=61 Identities=30% Similarity=0.443 Sum_probs=37.4 Q ss_pred HHCCCCCCEECCCCCEEEEEE--------ECCCCEEEEEEECCCCCCEE-EEEECCCCEEEEECCCEEECCCEEE Q ss_conf 525111101113478678633--------12794499998368984026-8981389658984198774086464 Q gi|254780142|r 1141 ARRPKNHAILAEISGTIRIKR--------NYKNKSRVVIEPFEDGVEPA-EYFIPKNKHFYLQDGDHVEKGDYIL 1206 (1398) Q Consensus 1141 ar~pk~~aiisei~Giv~i~~--------~~~~k~~~vi~~~~~g~~~~-e~~ip~~~~l~v~dgd~V~~gd~lt 1206 (1398) |-.|++-.++|.++|.+.... ..+++-++.|.-.-|.++++ +|+ ...|..||+|.+||.|- T Consensus 541 Ai~P~eG~~~AP~dG~v~~VF~T~HAiGi~~~nG~E~LIHvGIDTV~L~G~~F-----e~~V~~Gd~v~~Gq~L~ 610 (660) T TIGR01995 541 AILPSEGEVVAPVDGTVTAVFPTKHAIGIRSDNGVEILIHVGIDTVELKGEYF-----EILVKVGDKVKAGQLLL 610 (660) T ss_pred EEEECCCEEECCCCCEEEEEECCCCEEEECCCCCEEEEEEEEEEEEEECCEEE-----EEEEEECCEEEECCCCC T ss_conf 89715877882337789999748622741268972899984123456545012-----22145667875066312 No 60 >PRK11823 DNA repair protein RadA; Provisional Probab=57.12 E-value=5.5 Score=17.84 Aligned_cols=15 Identities=33% Similarity=0.481 Sum_probs=9.1 Q ss_pred CCCCCCCHHHEEEEE Q ss_conf 255557842411200 Q gi|254780142|r 724 HSGARGSIHQMRQLG 738 (1398) Q Consensus 724 ~SGAKGS~~qi~ql~ 738 (1398) ..|+-||++|++.|. T Consensus 182 ~~s~pGsvsQVre~a 196 (454) T PRK11823 182 LESAPGSVSQVRECA 196 (454) T ss_pred CCCCCCCHHHHHHHH T ss_conf 677899789999999 No 61 >TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB . Most proteins in this entry have a C-terminal region containing highly degenerate sequence.. Probab=56.72 E-value=7.2 Score=16.94 Aligned_cols=28 Identities=32% Similarity=0.852 Sum_probs=17.7 Q ss_pred CCCCCCC-CCCCC----CCCCCC--CCCCCCCCCC Q ss_conf 5667721-56641----563448--8356757885 Q gi|254780142|r 65 PIKDYEC-ICGKY----KRMKYK--GIICEKCGVE 92 (1398) Q Consensus 65 ~~~d~~c-~Cg~~----~~~~~~--g~~C~~Cg~~ 92 (1398) |+.+|.| .||+- -++... -..|..||.+ T Consensus 2 P~Y~Y~C~~Cg~~fe~~Qk~sD~~pl~~CP~C~~~ 36 (43) T TIGR02605 2 PIYEYRCTSCGHQFEVLQKISDEEPLTTCPACGGP 36 (43) T ss_pred CCCCCEECCCCCCEEEEECCCCCCCCCCCCCCCCC T ss_conf 97740346899814566504775534478767876 No 62 >pfam09105 SelB-wing_1 Elongation factor SelB, winged helix. Members of this family adopt a winged-helix fold, with an alpha/beta structure consisting of three alpha-helices and a twisted three-stranded antiparallel beta-sheet, with an alpha-beta-alpha-alpha-beta-beta connectivity. They are involved in both DNA and RNA binding. Probab=55.89 E-value=11 Score=15.72 Aligned_cols=23 Identities=43% Similarity=0.537 Sum_probs=18.3 Q ss_pred CCCHHHHHHHHHHHHCCCEECCC Q ss_conf 04025899999974528552366 Q gi|254780142|r 1318 ASFQETTKVLTEAAIAGKVDTLD 1340 (1398) Q Consensus 1318 ASFEeT~~vL~eAAi~ge~D~L~ 1340 (1398) -|.|||-+.|..-|..|++--|+ T Consensus 29 lsleetrkllqsmaaagqvtllr 51 (61) T pfam09105 29 LSLEETRKLLQSMAAAGQVTLLR 51 (61) T ss_pred CCHHHHHHHHHHHHHCCCEEEEE T ss_conf 34899999999998557537888 No 63 >TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase; InterPro: IPR012833 This entry is found in the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centred radical , a C-terminal zinc binding site , and a set of conserved active site cysteines and asparagines . This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (IPR012837 from INTERPRO). Together the two form an alpha-2/beta-2 heterodimer.; GO: 0008998 ribonucleoside-triphosphate reductase activity, 0016491 oxidoreductase activity. Probab=55.45 E-value=6.6 Score=17.26 Aligned_cols=37 Identities=14% Similarity=-0.028 Sum_probs=20.5 Q ss_pred EEEEHHHHHHHHHHHHCCCCCCCCCCCEECCHHHHHHHHHCCCCCCCCE Q ss_conf 0440258999999873367887446814179999999998889867852 Q gi|254780142|r 501 VTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENKIVTLHSK 549 (1398) Q Consensus 501 i~~~~QD~i~G~y~lT~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~a~ 549 (1398) ++..++|.+.=.|+|.. ++ ..++..|+.+|.|.+|.. T Consensus 14 ~~~~~a~e~~K~~~l~~-----------~l-p~~~~~AH~~GdIHiHDL 50 (655) T TIGR02487 14 QRKLIASEVSKDYALKK-----------LL-PKDIARAHLNGDIHIHDL 50 (655) T ss_pred HHHHHHHHHHHHHHHHH-----------CC-CHHHHHHHHCCCCCCCCC T ss_conf 89999999999998863-----------18-888999987488420245 No 64 >smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence. Probab=54.22 E-value=5.7 Score=17.73 Aligned_cols=29 Identities=34% Similarity=0.911 Sum_probs=18.4 Q ss_pred CCCCCCC-CCCC-CCCCC----CCCCCCCCCCCCC Q ss_conf 5667721-5664-15634----4883567578853 Q gi|254780142|r 65 PIKDYEC-ICGK-YKRMK----YKGIICEKCGVEV 93 (1398) Q Consensus 65 ~~~d~~c-~Cg~-~~~~~----~~g~~C~~Cg~~~ 93 (1398) |+.||.| .||+ +..++ .....|..||.++ T Consensus 2 P~Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~ 36 (41) T smart00834 2 PIYEYRCEDCGHTFEVLQKISDDPLATCPECGGDV 36 (41) T ss_pred CCEEEEECCCCCEEEEEEECCCCCCCCCCCCCCCC T ss_conf 98848968999979999865788788586899922 No 65 >COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis] Probab=54.17 E-value=6.3 Score=17.41 Aligned_cols=18 Identities=28% Similarity=0.495 Sum_probs=7.2 Q ss_pred CCEEEEEECCCCCCCCCC Q ss_conf 511286304507622351 Q gi|254780142|r 236 PGWMIIRKLPVLPPDLRP 253 (1398) Q Consensus 236 Pewmil~~lpV~P~~~RP 253 (1398) |-..++.-+-|-+|..+| T Consensus 212 p~m~v~RSFDVNkPGt~~ 229 (415) T COG5257 212 PRMYVARSFDVNKPGTPP 229 (415) T ss_pred CEEEEEEECCCCCCCCCH T ss_conf 669998640358998997 No 66 >COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones] Probab=53.59 E-value=6.9 Score=17.07 Aligned_cols=14 Identities=36% Similarity=0.669 Sum_probs=7.4 Q ss_pred CCCCCCHHHEEEEE Q ss_conf 55557842411200 Q gi|254780142|r 725 SGARGSIHQMRQLG 738 (1398) Q Consensus 725 SGAKGS~~qi~ql~ 738 (1398) ++|-||.+|++.|. T Consensus 186 ~SapGsVsQVRe~t 199 (456) T COG1066 186 TSAPGSVSQVREVA 199 (456) T ss_pred CCCCCCHHHHHHHH T ss_conf 57998589999999 No 67 >KOG4275 consensus Probab=53.25 E-value=3.7 Score=19.15 Aligned_cols=12 Identities=17% Similarity=0.321 Sum_probs=4.1 Q ss_pred CCCCCCHHHHCC Q ss_conf 057610322101 Q gi|254780142|r 772 SCVGGRKGLLDV 783 (1398) Q Consensus 772 hamgGReGLiDT 783 (1398) ||-+--+-.-|+ T Consensus 46 ~ckacg~~f~~~ 57 (350) T KOG4275 46 HCKACGEEFEDA 57 (350) T ss_pred HHHHHCHHHHHH T ss_conf 345402167665 No 68 >pfam06957 COPI_C Coatomer (COPI) alpha subunit C-terminus. This family represents the C-terminus (approximately 500 residues) of the eukaryotic coatomer alpha subunit. Coatomer (COPI) is a large cytosolic protein complex which forms a coat around vesicles budding from the Golgi apparatus. Such coatomer-coated vesicles have been proposed to play a role in many distinct steps of intracellular transport. Note that many family members also contain the pfam04053 domain. Probab=52.93 E-value=11 Score=15.56 Aligned_cols=10 Identities=30% Similarity=0.680 Sum_probs=4.1 Q ss_pred CCCCCCCCCE Q ss_conf 4237887820 Q gi|254780142|r 492 LLHPASGAPV 501 (1398) Q Consensus 492 iisP~~g~Pi 501 (1398) ++.|+-|.|. T Consensus 104 fv~P~~G~s~ 113 (421) T pfam06957 104 FVAPNPGMSV 113 (421) T ss_pred EECCCCCCCH T ss_conf 5689999887 No 69 >KOG0856 consensus Probab=52.25 E-value=4.1 Score=18.81 Aligned_cols=14 Identities=29% Similarity=0.819 Sum_probs=10.7 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 567578853047757876772002 Q gi|254780142|r 85 ICEKCGVEVTLSSVRRDRMAHIDL 108 (1398) Q Consensus 85 ~C~~Cg~~~~~~~~r~ghfGhIeL 108 (1398) .|.+|| +|+|||-. T Consensus 105 ~Ca~C~----------~HLGHVF~ 118 (146) T KOG0856 105 SCATCG----------GHLGHVFK 118 (146) T ss_pred EEEECC----------CCEEEEEC T ss_conf 876228----------81320564 No 70 >KOG1618 consensus Probab=51.55 E-value=13 Score=15.04 Aligned_cols=22 Identities=41% Similarity=0.534 Sum_probs=16.3 Q ss_pred HHHHHHHHHCCCCCCEEECCCCCC Q ss_conf 067899861023782000346510 Q gi|254780142|r 325 PLKSLSDMLKGKQGRFRTNLLGKR 348 (1398) Q Consensus 325 p~ks~~~rlkgK~GrfR~nl~GKR 348 (1398) -+.||-++|.||.=|++ .|||- T Consensus 251 ~lesiy~kltGk~L~~~--t~GKP 272 (389) T KOG1618 251 CLESIYQKLTGKPLRYT--TLGKP 272 (389) T ss_pred HHHHHHHHHCCCCCCCC--CCCCC T ss_conf 99999998538744220--26898 No 71 >PRK06450 threonine synthase; Validated Probab=49.79 E-value=7.6 Score=16.77 Aligned_cols=21 Identities=38% Similarity=0.934 Sum_probs=12.8 Q ss_pred CCCC-CCCC-CCCCCCCCCCCCCCCC Q ss_conf 7721-5664-1563448835675788 Q gi|254780142|r 68 DYEC-ICGK-YKRMKYKGIICEKCGV 91 (1398) Q Consensus 68 d~~c-~Cg~-~~~~~~~g~~C~~Cg~ 91 (1398) .++| .||+ |.... ..|..||. T Consensus 3 ~l~C~~CG~~~~~~~---~~C~~Cgg 25 (336) T PRK06450 3 KVRCIRCGKEREGEE---LRCKKCGG 25 (336) T ss_pred EEECCCCCCCCCCCC---EECCCCCC T ss_conf 588785588889887---58899998 No 72 >COG3813 Uncharacterized protein conserved in bacteria [Function unknown] Probab=48.96 E-value=5.5 Score=17.87 Aligned_cols=41 Identities=29% Similarity=0.669 Sum_probs=25.2 Q ss_pred CCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 7336213685667721-566415634488356757885304775787 Q gi|254780142|r 56 GLFCARIFGPIKDYEC-ICGKYKRMKYKGIICEKCGVEVTLSSVRRD 101 (1398) Q Consensus 56 Gl~d~ri~g~~~d~~c-~Cg~~~~~~~~g~~C~~Cg~~~~~~~~r~g 101 (1398) +--|.+| -.||| .|-.+-..+..|. |..||.+...-|+|+- T Consensus 18 ~s~dA~I----CtfEcTFCadCae~~l~g~-CPnCGGelv~RP~RPa 59 (84) T COG3813 18 DSTDARI----CTFECTFCADCAENRLHGL-CPNCGGELVARPIRPA 59 (84) T ss_pred CCCCEEE----EEEEEEHHHHHHHHHHCCC-CCCCCCHHHCCCCCHH T ss_conf 9875147----8876002575787764584-8898751321767859 No 73 >TIGR00375 TIGR00375 conserved hypothetical protein TIGR00375; InterPro: IPR005287 This family of conserved hypothetical proteins has no known function. . Probab=48.21 E-value=5 Score=18.13 Aligned_cols=28 Identities=14% Similarity=0.309 Sum_probs=14.2 Q ss_pred HHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEE-EEEEEE Q ss_conf 788987764202454322211220240148768-972113 Q gi|254780142|r 922 EPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIV-KIKNRN 960 (1398) Q Consensus 922 EP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVP-RlkEi~ 960 (1398) |-|..|-+|==.=+| .++-||- |+.||- T Consensus 260 E~a~~~~~~CpkCgg-----------~ikKGV~~R~~ELS 288 (384) T TIGR00375 260 EDAKKADAKCPKCGG-----------KIKKGVSDRVRELS 288 (384) T ss_pred CCHHHHHCCCCCCCC-----------EEECCHHHHHHHCC T ss_conf 002555246979786-----------05537356776336 No 74 >COG1858 MauG Cytochrome c peroxidase [Inorganic ion transport and metabolism] Probab=46.89 E-value=15 Score=14.53 Aligned_cols=10 Identities=10% Similarity=-0.160 Sum_probs=6.3 Q ss_pred CCCCEEECHH Q ss_conf 7762201301 Q gi|254780142|r 109 ASPVAHPWFL 118 (1398) Q Consensus 109 a~PV~Hi~f~ 118 (1398) -.||||+||| T Consensus 116 ~n~~F~ggqF 125 (364) T COG1858 116 FNSVFNGGQF 125 (364) T ss_pred CCCCCCCCCC T ss_conf 1466566546 No 75 >PRK07562 ribonucleotide-diphosphate reductase subunit alpha; Validated Probab=46.14 E-value=9.5 Score=16.06 Aligned_cols=10 Identities=30% Similarity=0.773 Sum_probs=6.4 Q ss_pred CCCCCCEEEE Q ss_conf 4898511286 Q gi|254780142|r 232 SGNNPGWMII 241 (1398) Q Consensus 232 ~~~~Pewmil 241 (1398) ..+.|.|+=. T Consensus 150 a~nsp~wfn~ 159 (1177) T PRK07562 150 APNSPQWFNT 159 (1177) T ss_pred CCCCCCEEEC T ss_conf 7899832786 No 76 >CHL00077 rps18 ribosomal protein S18 Probab=45.61 E-value=13 Score=15.04 Aligned_cols=25 Identities=16% Similarity=0.242 Sum_probs=21.8 Q ss_pred CEECHHHHHHHHHHHCCEEEEECCC Q ss_conf 7006125601247628614894188 Q gi|254780142|r 1241 VAINHKHIEVVVRHMLQKVEITDPA 1265 (1398) Q Consensus 1241 i~IN~RHIeLIaD~MT~kg~I~~~G 1265 (1398) -.||||++++|-..+|..|.|++.= T Consensus 26 ~~IDYKnv~lL~~Fise~GKIlprR 50 (86) T CHL00077 26 DRIDYKNMSLLSRFISEQGKILSRR 50 (86) T ss_pred CCCCCCCHHHHHHHCCCCCEEECCC T ss_conf 8677668899998758888280852 No 77 >PRK00222 methionine sulfoxide reductase B; Provisional Probab=45.30 E-value=8.6 Score=16.37 Aligned_cols=75 Identities=20% Similarity=0.441 Sum_probs=36.1 Q ss_pred CCCHHHHHHCCEEEEECCCCCCCCCCCCCCCCCC-----CCCCCCCCCCCCCCCCCC---CC-----CCC-----CC--- Q ss_conf 5886788501448971755425456875688733-----621368566772156641---56-----344-----88--- Q gi|254780142|r 25 IASPAKIASLSYGEIKKPETINYRTFKPERDGLF-----CARIFGPIKDYECICGKY---KR-----MKY-----KG--- 83 (1398) Q Consensus 25 l~spe~I~~~S~~ev~~~et~n~~~~kP~~~Gl~-----d~ri~g~~~d~~c~Cg~~---~~-----~~~-----~g--- 83 (1398) .+||++-+-.--.--+-|-|=.|... .+.|.+ +..||.....|++-||=. +- +.+ -| T Consensus 13 ~Lt~~~y~V~r~~gTE~pfsg~y~~~--~~~G~Y~C~~Cg~~LF~S~~KfdSg~GWPSF~~~i~~~~v~~~~D~s~gm~R 90 (141) T PRK00222 13 QLTPEQYRVTQEHGTERPFTGEYLDN--KRKGIYVCIVCGEPLFSSDTKFDSGCGWPSFTKPIDEEAIRELRDTSHGMVR 90 (141) T ss_pred HCCHHHHHHHHHCCCCCCCCCCCCCC--CCCEEEEECCCCCEEEECCCCCCCCCCCCHHHHHCCCCCCEEECCCCCCCEE T ss_conf 58999999998659889988777588--8998998469989844115514799987203122465620697689888016 Q ss_pred --CCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf --3567578853047757876772002776 Q gi|254780142|r 84 --IICEKCGVEVTLSSVRRDRMAHIDLASP 111 (1398) Q Consensus 84 --~~C~~Cg~~~~~~~~r~ghfGhIeLa~P 111 (1398) ..|..|| +|.||+----| T Consensus 91 ~Ev~C~~Cg----------~HLGHVF~DGP 110 (141) T PRK00222 91 TEVRCANCD----------SHLGHVFPDGP 110 (141) T ss_pred EEEECCCCC----------CCCCCCCCCCC T ss_conf 899868999----------85674269898 No 78 >TIGR00758 UDG_fam4 uracil-DNA glycosylase, family 4; InterPro: IPR005273 This well-conserved family of proteins is about 200 residues in length and homologous to the N-terminus of the DNA polymerase of phage SPO1 of Bacillus subtilis. The function of these proteins is unknown. . Probab=44.91 E-value=4.1 Score=18.83 Aligned_cols=75 Identities=24% Similarity=0.330 Sum_probs=34.3 Q ss_pred EECCCCCCHHHHHHHHHCCCC-EEECCCCCCHH---------HHHCCCHHHHHHHCCCCCEECHHH--CCCCHHHHHHHH Q ss_conf 517865789999999975984-02023310003---------551865788754201785200010--146021111007 Q gi|254780142|r 855 VKAGQLILESHVNEIEKCGIR-SVRIRSALTCE---------SSRGVCVLCYGRDLARGSLVNVGE--AVGVIAAQSIGE 922 (1398) Q Consensus 855 ~~~~~~i~~~~~~~i~~~~i~-~v~irs~lt~~---------~~~~v~~~cy~~~l~~~~lv~pGe--~VG~iAAQSIGE 922 (1398) -++|.++++-..+.| -..-. .|.|-.++-|. .+..+|.-.--+.+ +++.|== .||..|||+| T Consensus 44 G~aGkLLd~lL~e~i-Gl~R~q~vYITNvvKCRPP~NR~PT~eE~~~C~pyL~~~i---~lI~Pkvi~~lGr~Aa~~~-- 117 (185) T TIGR00758 44 GRAGKLLDELLEEAI-GLSREQNVYITNVVKCRPPNNRDPTPEEVEACAPYLVKQI---ELIRPKVIICLGRTAAQSI-- 117 (185) T ss_pred CHHHHHHHHHHHHHH-CCCCCCCEEEEEEEEECCCCCCCCCHHHHHHHHHHHHHHH---HHCCCCEEEEECHHHHHHH-- T ss_conf 400568999999983-7443786235225654685222389899985157889999---7509806899602788988-- Q ss_pred HHHHHHHHHHCCCCCCC Q ss_conf 88987764202454322 Q gi|254780142|r 923 PGTQLTMRTFHLGGAVT 939 (1398) Q Consensus 923 P~TQmTLnTFHfAGVAS 939 (1398) |-++-|.++|++- T Consensus 118 ----l~~~gl~~~~I~k 130 (185) T TIGR00758 118 ----LGKAGLEFEGITK 130 (185) T ss_pred ----HHHCCCCCCCCCE T ss_conf ----7652876267301 No 79 >PTZ00327 eukaryotic translation initiation factor 2 gamma subunit; Provisional Probab=44.67 E-value=12 Score=15.21 Aligned_cols=94 Identities=21% Similarity=0.422 Sum_probs=44.2 Q ss_pred EEEECCCHHHHHHCC------EEEEECCCCCC--------CCCCC--CCCCCCCCCCCC-CCCCCCCC-CCCC---CCC- Q ss_conf 898458867885014------48971755425--------45687--568873362136-85667721-5664---156- Q gi|254780142|r 21 VRISIASPAKIASLS------YGEIKKPETIN--------YRTFK--PERDGLFCARIF-GPIKDYEC-ICGK---YKR- 78 (1398) Q Consensus 21 i~f~l~spe~I~~~S------~~ev~~~et~n--------~~~~k--P~~~Gl~d~ri~-g~~~d~~c-~Cg~---~~~- 78 (1398) =++.-.|||-|.+-+ .|+|-+-.|-= -.+++ -+||=.. ++| ...+-|+| .|.. |.. T Consensus 22 ~~~~~~~~e~~~~q~~vNIGtiGHVDHGKTTLvkALTgv~t~r~~eE~~RgiTI--~LGya~~kiykc~~~~~p~~y~~~ 99 (460) T PTZ00327 22 DKLTPLTPEVISRQATINIGTIGHVAHGKSTVVKALSGVKTVRFHREKVRNITI--KLGYANAKIYKCTKCPPPACYKSY 99 (460) T ss_pred HHCCCCCHHHHHCCCCEEEEEECCCCCCHHHHHHHHHCCCHHHCHHHHHCCCEE--EECCCCEEEECCCCCCCCCCEECC T ss_conf 224789988962588218988746289899999998677501065678758721--205433011136567763101014 Q ss_pred --CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECHHHHHHH Q ss_conf --344883567578853047757876772002776220130122578 Q gi|254780142|r 79 --MKYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPS 123 (1398) Q Consensus 79 --~~~~g~~C~~Cg~~~~~~~~r~ghfGhIeLa~PV~Hi~f~k~~~~ 123 (1398) .......|++||.+.+... |+.||+- | =|--|+++..+ T Consensus 100 ~s~~~~~~~c~~c~~~~t~~R----h~s~VDc--P-GH~~l~~nmi~ 139 (460) T PTZ00327 100 PSSKPDNPQCPGCGHKMTLKR----HVSFVDC--P-GHDILMATMLN 139 (460) T ss_pred CCCCCCCCCCCCCCCCCCCCE----EEEEEEC--C-CHHHHHHHHHH T ss_conf 666655544555565431220----4899868--9-87999999874 No 80 >pfam09723 CxxC_CxxC_SSSS Zinc ribbon domain. This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence. Probab=44.56 E-value=13 Score=15.14 Aligned_cols=28 Identities=32% Similarity=0.877 Sum_probs=17.2 Q ss_pred CCCCCCC-CCCC-CCC---CCC-CCCCCCCCCCC Q ss_conf 5667721-5664-156---344-88356757885 Q gi|254780142|r 65 PIKDYEC-ICGK-YKR---MKY-KGIICEKCGVE 92 (1398) Q Consensus 65 ~~~d~~c-~Cg~-~~~---~~~-~g~~C~~Cg~~ 92 (1398) |+.+|.| .||+ +.. +.. .-..|..||.. T Consensus 2 PiYey~C~~Cg~~fe~~~~~~~~~~~~CP~C~~~ 35 (42) T pfam09723 2 PIYEYRCEDCGHTFEVLQKISDAPLATCPECGST 35 (42) T ss_pred CCEEEEECCCCCEEEEEEECCCCCCCCCCCCCCC T ss_conf 9887894889998999986579988769799998 No 81 >COG4307 Uncharacterized protein conserved in bacteria [Function unknown] Probab=44.55 E-value=7.4 Score=16.88 Aligned_cols=29 Identities=34% Similarity=0.976 Sum_probs=20.7 Q ss_pred CCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 667721-5664156344883567578853047 Q gi|254780142|r 66 IKDYEC-ICGKYKRMKYKGIICEKCGVEVTLS 96 (1398) Q Consensus 66 ~~d~~c-~Cg~~~~~~~~g~~C~~Cg~~~~~~ 96 (1398) .|+|-| .||. ++-|....|..||.-...+ T Consensus 1 mk~FhC~~CgQ--~v~FeN~~C~~Cg~~Lg~~ 30 (349) T COG4307 1 MKDFHCPNCGQ--RVAFENSACLSCGSALGFS 30 (349) T ss_pred CCCCCCCCCCC--EEEECCHHHHHHHHHHHHC T ss_conf 97555787788--3244323887513676430 No 82 >PRK08997 isocitrate dehydrogenase; Provisional Probab=44.18 E-value=17 Score=14.24 Aligned_cols=20 Identities=15% Similarity=0.155 Sum_probs=7.5 Q ss_pred HHHCHHHHHHHHHHHHHHHH Q ss_conf 75279999999999999999 Q gi|254780142|r 1217 RIKGVEALASYLINEVQEVY 1236 (1398) Q Consensus 1217 ~vlGIEAAR~~Ii~EIq~V~ 1236 (1398) +-||-.++.+.|-+-|..|+ T Consensus 288 ~~lg~~~~A~~i~~Av~~~l 307 (334) T PRK08997 288 EYLGMPDKAERIRKAIVAVI 307 (334) T ss_pred HHCCCHHHHHHHHHHHHHHH T ss_conf 98699789999999999999 No 83 >TIGR02910 sulfite_red_A sulfite reductase, subunit A; InterPro: IPR014259 This entry represents subunit A, one of the three subunits of the anaerobic sulphite reductase of Salmonella, and close homologues from various Clostridium species, where the three-gene neighbourhood is preserved. Two such gene clusters are found in Clostridium perfringens, but it may be that these sets of genes correspond to the distinct assimilatory and dissimilatory forms seen in Clostridium pasteurianum. Note that any one of these enzymes may have secondary substrates such as NH2OH, SeO3(2-), and SO3(2-). Heterologous expression of the anaerobic sulphite reductase of Salmonella confers on Escherichia coli the ability to produce hydrogen sulphide gas from sulphite.. Probab=43.62 E-value=10 Score=15.81 Aligned_cols=17 Identities=35% Similarity=0.530 Sum_probs=7.5 Q ss_pred CCEEECCCCCCCCCCCC Q ss_conf 82000346510045774 Q gi|254780142|r 338 GRFRTNLLGKRVDYSGR 354 (1398) Q Consensus 338 GrfR~nl~GKRVdfs~R 354 (1398) -|+|=..|-|=-||-+| T Consensus 292 ~RmRfkvmHKv~DYkkR 308 (346) T TIGR02910 292 QRMRFKVMHKVNDYKKR 308 (346) T ss_pred CCEEEEEEEEEECCCCC T ss_conf 61123431021100001 No 84 >pfam11786 Aft1_HRA Aft1 HRA domain. This domain is found in the transcription factor Aft1 which is required for a wide range of stress responses. The HRA domain is involved in meiotic recombination. It has been shown to be necessary and sufficient to activate recombination. Probab=43.29 E-value=8.4 Score=16.46 Aligned_cols=17 Identities=24% Similarity=0.229 Sum_probs=14.2 Q ss_pred CCCCCCCCHHHCCCCHH Q ss_conf 44566630111088898 Q gi|254780142|r 751 IIESPIRSHFKGGLCGF 767 (1398) Q Consensus 751 ~~~~PV~~sF~~GL~p~ 767 (1398) .+++|.++||++||+|- T Consensus 43 GFptpnesslRtglTPg 59 (78) T pfam11786 43 GFPTPNESSLRTGLTPG 59 (78) T ss_pred CCCCCCHHHHHCCCCCC T ss_conf 77887601222043668 No 85 >KOG3993 consensus Probab=42.66 E-value=5.9 Score=17.61 Aligned_cols=30 Identities=17% Similarity=0.152 Sum_probs=17.8 Q ss_pred ECCCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEEHHHHHHHHHHHH Q ss_conf 7468999999999987675054237887820440258999999873 Q gi|254780142|r 471 YAVISPEAQLEARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLS 516 (1398) Q Consensus 471 HvPqs~eAraEa~~Lm~~~~niisP~~g~Pi~~~~QD~i~G~y~lT 516 (1398) -|+-++|+|+++-.+ -..+-|+|+-+...- T Consensus 247 ~vEiteesr~~l~~i----------------~n~iGdyiCqLCK~k 276 (500) T KOG3993 247 EVEITEESRAKLAGI----------------PNVIGDYICQLCKEK 276 (500) T ss_pred EECCCCHHHHHHCCC----------------CCCHHHHHHHHHHHH T ss_conf 420461555554157----------------630889999987776 No 86 >TIGR01420 pilT_fam twitching motility protein; InterPro: IPR006321 These represent the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction . Members of this family may be found in some species that do not have type IV pili but have related structures for DNA uptake and natural transformation. ; GO: 0005524 ATP binding, 0006810 transport. Probab=42.32 E-value=11 Score=15.53 Aligned_cols=41 Identities=27% Similarity=0.360 Sum_probs=32.3 Q ss_pred CCCCEEECCCCCCCCCCC--CEEEECCCCCCCCCEECHHHHHHHH Q ss_conf 378200034651004577--4034125543546200348987761 Q gi|254780142|r 336 KQGRFRTNLLGKRVDYSG--RSVIVAGPELQLHQCGLPKLMALEL 378 (1398) Q Consensus 336 K~GrfR~nl~GKRVdfs~--RsVI~pdP~l~~~evgvP~~~A~~L 378 (1398) +-||||.|++--|-.+++ |.+ |-.=..+.|.|+|..+-+++ T Consensus 80 ~~~RfRvN~f~QRg~~a~vlR~i--p~~Ip~fe~LGLP~~v~~~~ 122 (350) T TIGR01420 80 GLARFRVNAFKQRGGVALVLRLI--PSKIPTFEELGLPRPVLREL 122 (350) T ss_pred CCCEEEEHHHHHCCHHHHHHHHC--CCCCCCHHHCCCCHHHHHHH T ss_conf 73221220323500064232311--53462166637987899999 No 87 >pfam01641 SelR SelR domain. Methionine sulfoxide reduction is an important process, by which cells regulate biological processes and cope with oxidative stress. MsrA, a protein involved in the reduction of methionine sulfoxides in proteins, has been known for four decades and has been extensively characterized with respect to structure and function. However, recent studies revealed that MsrA is only specific for methionine-S-sulfoxides. Because oxidized methionines occur in a mixture of R and S isomers in vivo, it was unclear how stereo-specific MsrA could be responsible for the reduction of all protein methionine sulfoxides. It appears that a second methionine sulfoxide reductase, SelR, evolved that is specific for methionine-R-sulfoxides, the activity that is different but complementary to that of MsrA. Thus, these proteins, working together, could reduce both stereoisomers of methionine sulfoxide. This domain is found both in SelR proteins and fused with the peptide methionine sulfo Probab=42.11 E-value=9.7 Score=15.99 Aligned_cols=75 Identities=21% Similarity=0.469 Sum_probs=37.9 Q ss_pred CCCHHHHHHCCEEEEECCCCCCCCCCCCCCCCCC-----CCCCCCCCCCCCCCCCCC---CCCCCC----------C--- Q ss_conf 5886788501448971755425456875688733-----621368566772156641---563448----------8--- Q gi|254780142|r 25 IASPAKIASLSYGEIKKPETINYRTFKPERDGLF-----CARIFGPIKDYECICGKY---KRMKYK----------G--- 83 (1398) Q Consensus 25 l~spe~I~~~S~~ev~~~et~n~~~~kP~~~Gl~-----d~ri~g~~~d~~c~Cg~~---~~~~~~----------g--- 83 (1398) .|||++-+-.--.--+.|-|=.|.. ..+.|.| +..||.....|+.-||=. +-+... | T Consensus 7 ~Lt~~~y~Vlr~~gTE~pfsg~y~~--~~~~G~Y~C~~C~~~LF~S~~KfdSg~GWPSF~~~i~~~~v~~~~D~s~g~~R 84 (124) T pfam01641 7 VLSPEQYRVLRNKGTEKPFTGEYDD--HFEEGIYVCIGCGEPLFSSTTKFDSGCGWPSFFEPISGDAIKYTEDRSHGMRR 84 (124) T ss_pred HCCHHHHHHHHHCCCCCCCCCCCCC--CCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCEE T ss_conf 4899999999856888998777768--88988998168998374328603489998431311687750899963579478 Q ss_pred --CCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf --3567578853047757876772002776 Q gi|254780142|r 84 --IICEKCGVEVTLSSVRRDRMAHIDLASP 111 (1398) Q Consensus 84 --~~C~~Cg~~~~~~~~r~ghfGhIeLa~P 111 (1398) ..|..|| +|.||+----| T Consensus 85 ~Ev~C~~C~----------~HLGHvF~DGp 104 (124) T pfam01641 85 TEVRCANCD----------GHLGHVFKDGP 104 (124) T ss_pred EEEEECCCC----------CCCCCCCCCCC T ss_conf 888826899----------81682008899 No 88 >COG2401 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only] Probab=41.88 E-value=11 Score=15.72 Aligned_cols=21 Identities=24% Similarity=0.434 Sum_probs=11.4 Q ss_pred CCEEEECCCCCCCCCEECHHHHH Q ss_conf 74034125543546200348987 Q gi|254780142|r 353 GRSVIVAGPELQLHQCGLPKLMA 375 (1398) Q Consensus 353 ~RsVI~pdP~l~~~evgvP~~~A 375 (1398) ||-|. -|.-.-|-+|+--.+| T Consensus 245 arvvv--hpdyr~dglg~~sv~~ 265 (593) T COG2401 245 ARVVV--HPDYRADGLGQLSVIA 265 (593) T ss_pred EEEEE--CCCCCCCCCCHHHHHH T ss_conf 67885--6654567610637999 No 89 >TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ; InterPro: IPR013364 Proteins in this entry are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase (IPR013363 from INTERPRO) of a type-IV secretion-like system of the obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii.. Probab=41.66 E-value=16 Score=14.32 Aligned_cols=18 Identities=44% Similarity=0.844 Sum_probs=14.6 Q ss_pred HHHCCCCHH---HHHHCCCCCCH Q ss_conf 111088898---97640576103 Q gi|254780142|r 759 HFKGGLCGF---EFFQSCVGGRK 778 (1398) Q Consensus 759 sF~~GL~p~---EfFfhamgGRe 778 (1398) .|..||||+ +||.||. |. T Consensus 2 ~F~~gltA~~Lr~FfvhC~--r~ 22 (374) T TIGR02525 2 DFEDGLTADTLREFFVHCE--RH 22 (374) T ss_pred CCCCCCCHHHHHHHHHHHC--CC T ss_conf 9877889889998866111--68 No 90 >PRK05508 methionine sulfoxide reductase B; Provisional Probab=40.92 E-value=10 Score=15.77 Aligned_cols=14 Identities=21% Similarity=0.788 Sum_probs=9.7 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 567578853047757876772002 Q gi|254780142|r 85 ICEKCGVEVTLSSVRRDRMAHIDL 108 (1398) Q Consensus 85 ~C~~Cg~~~~~~~~r~ghfGhIeL 108 (1398) .|..|| +|.||+-- T Consensus 81 ~C~~C~----------~HLGHVF~ 94 (119) T PRK05508 81 VCANCN----------GHLGHVFE 94 (119) T ss_pred EECCCC----------CCCCCCCC T ss_conf 812789----------84675439 No 91 >KOG0317 consensus Probab=40.56 E-value=19 Score=13.85 Aligned_cols=25 Identities=24% Similarity=0.315 Sum_probs=12.3 Q ss_pred HHHHHHHHCCCCCCEEECCCCCCCC Q ss_conf 6789986102378200034651004 Q gi|254780142|r 326 LKSLSDMLKGKQGRFRTNLLGKRVD 350 (1398) Q Consensus 326 ~ks~~~rlkgK~GrfR~nl~GKRVd 350 (1398) ..||+.|+.|=.=.|-..|.|+-.+ T Consensus 153 ~y~IskRltgI~yv~~~~~~~~~~~ 177 (293) T KOG0317 153 FYSISKRLTGIRYVLARTLKGHEAN 177 (293) T ss_pred HHHHHHHHCCCEEEEEECCCCCCCC T ss_conf 5888886405258887313543234 No 92 >TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family; InterPro: IPR006054 All proteins in this entry for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the N-terminal region of DinG from some low GC Gram-positive bacteria. ; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication. Probab=40.43 E-value=17 Score=14.08 Aligned_cols=13 Identities=8% Similarity=0.051 Sum_probs=5.3 Q ss_pred ECCCCCEEEEECC Q ss_conf 4587510177511 Q gi|254780142|r 582 PRHHEISFDICNQ 594 (1398) Q Consensus 582 p~~~~~~~~~~~~ 594 (1398) .-+-.++.|++|. T Consensus 93 ~HNA~FD~GFl~~ 105 (228) T TIGR00573 93 IHNASFDVGFLNY 105 (228) T ss_pred EEHHHCCHHHHHH T ss_conf 5200305778999 No 93 >PRK13401 30S ribosomal protein S18; Provisional Probab=40.33 E-value=17 Score=14.23 Aligned_cols=28 Identities=14% Similarity=0.181 Sum_probs=23.1 Q ss_pred HHHCC-EECHHHHHHHHHHHCCEEEEECC Q ss_conf 98097-00612560124762861489418 Q gi|254780142|r 1237 RLEGV-AINHKHIEVVVRHMLQKVEITDP 1264 (1398) Q Consensus 1237 ~~~Gi-~IN~RHIeLIaD~MT~kg~I~~~ 1264 (1398) ...|+ +||||.+++|-..+|.+|.|++. T Consensus 20 ~~~~i~~iDYKdv~lL~~Fis~~GkI~~r 48 (79) T PRK13401 20 DSLGVESVDYKDTATLRVFISDRGKIRSR 48 (79) T ss_pred CCCCCCCCCCCCHHHHHHHCCCCCEEECC T ss_conf 55898856765889999874888858686 No 94 >PRK00391 rpsR 30S ribosomal protein S18; Reviewed Probab=40.03 E-value=16 Score=14.27 Aligned_cols=29 Identities=21% Similarity=0.279 Sum_probs=22.8 Q ss_pred HCC-EECHHHHHHHHHHHCCEEEEECCCCC Q ss_conf 097-00612560124762861489418864 Q gi|254780142|r 1239 EGV-AINHKHIEVVVRHMLQKVEITDPADT 1267 (1398) Q Consensus 1239 ~Gi-~IN~RHIeLIaD~MT~kg~I~~~Gdt 1267 (1398) .++ +||||.+++|-..|+..|.|++.-.| T Consensus 21 ~~~~~IDYKdv~lL~~Fis~~GkI~prr~T 50 (80) T PRK00391 21 EKIEYIDYKDVELLKKFISERGKILPRRIT 50 (80) T ss_pred CCCCCCCCCCHHHHHHHCCCCCEECCCCCC T ss_conf 999827876999999875888758276337 No 95 >PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional Probab=39.96 E-value=19 Score=13.79 Aligned_cols=16 Identities=25% Similarity=0.279 Sum_probs=10.1 Q ss_pred HHHHHHHHCCCCCCCC Q ss_conf 9999999888986785 Q gi|254780142|r 533 GEVYHALENKIVTLHS 548 (1398) Q Consensus 533 ~~~~~~~~~~~~~~~a 548 (1398) .++..|..+|.+.+|. T Consensus 148 ~~i~~AH~~GdiHiHD 163 (711) T PRK09263 148 KDVAQAHEKGDIHYHD 163 (711) T ss_pred HHHHHHHHCCCEEEEC T ss_conf 9999998649878833 No 96 >COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis] Probab=38.54 E-value=14 Score=14.78 Aligned_cols=19 Identities=47% Similarity=1.081 Sum_probs=10.7 Q ss_pred CCC-CCCCCCCCCCCCCCCCCCC Q ss_conf 721-5664156344883567578 Q gi|254780142|r 69 YEC-ICGKYKRMKYKGIICEKCG 90 (1398) Q Consensus 69 ~~c-~Cg~~~~~~~~g~~C~~Cg 90 (1398) -+| .||+|+. ..-+|..|| T Consensus 28 ~~c~~cG~~~l---~Hrvc~~cg 47 (57) T COG0333 28 SVCPNCGEYKL---PHRVCLKCG 47 (57) T ss_pred EECCCCCCEEC---CCEECCCCC T ss_conf 03567886015---754748677 No 97 >pfam01084 Ribosomal_S18 Ribosomal protein S18. Probab=37.53 E-value=19 Score=13.74 Aligned_cols=26 Identities=19% Similarity=0.218 Sum_probs=22.5 Q ss_pred HCCEECHHHHHHHHHHHCCEEEEECC Q ss_conf 09700612560124762861489418 Q gi|254780142|r 1239 EGVAINHKHIEVVVRHMLQKVEITDP 1264 (1398) Q Consensus 1239 ~Gi~IN~RHIeLIaD~MT~kg~I~~~ 1264 (1398) ...+||||++.+|...++..|.|.+. T Consensus 3 ~~~~idYKn~~lL~~fis~~GkI~pr 28 (54) T pfam01084 3 KIEYIDYKDVELLRRFISERGKILPR 28 (54) T ss_pred CCCCCCCCCHHHHHHHCCCCCEEECC T ss_conf 88872888969999876999828397 No 98 >PRK09137 DNA topoisomerase I; Validated Probab=37.31 E-value=20 Score=13.64 Aligned_cols=20 Identities=25% Similarity=0.411 Sum_probs=9.0 Q ss_pred HHHHHHHHHHHHHCCCCCCEEEE Q ss_conf 64477888666634898511286 Q gi|254780142|r 219 IIKRLKIVDSFITSGNNPGWMII 241 (1398) Q Consensus 219 ~~~~~~~~~~f~~~~~~Pewmil 241 (1398) +..|.+-+..|.+ .|-|-|. T Consensus 178 IveRE~EI~~F~p---~~Yw~i~ 197 (761) T PRK09137 178 ICEREIEIEAFEA---QEYWTIH 197 (761) T ss_pred HHHHHHHHHCCCC---CCEEEEE T ss_conf 9999999971788---4058999 No 99 >KOG0890 consensus Probab=36.98 E-value=11 Score=15.61 Aligned_cols=31 Identities=10% Similarity=0.112 Sum_probs=14.5 Q ss_pred HHHHHHCCCCCCHHHHCCCCCCCCCCEEEEH Q ss_conf 9897640576103221012101567401101 Q gi|254780142|r 766 GFEFFQSCVGGRKGLLDVVMRTASSGYLSRR 796 (1398) Q Consensus 766 p~EfFfhamgGReGLiDTAvKTA~SGYlqRr 796 (1398) +.+|.=...+.|+-.||-.---|-.|=.||. T Consensus 1566 ~~~~~~~i~~~r~~~i~~lsa~s~~~Sy~~~ 1596 (2382) T KOG0890 1566 EIATLDLIENSRELVIENLSACSIEGSYVRS 1596 (2382) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCHHHHH T ss_conf 3567789878899863667875411118878 No 100 >TIGR02810 agaZ_gatZ D-tagatose-bisphosphate aldolase, class II, non-catalytic subunit; InterPro: IPR012062 Escherichia coli and other enteric bacteria contain two closely related D-tagatose 1,6-bisphosphate (TagBP)-specific aldolases involved in catabolism of galactitol (genes gatY gatZ) and of N-acetyl-galactosamine and D-galactosamine (genes kbaY, kbaZ, also called agaY, agaZ). The catalytic subunits GatY/KbaY alone are sufficient to show aldolase activity and contain most or all of the residues that have been identified as essential in substrate/product recognition and catalysis for class II aldolases , . However, these aldolases differ from other Class II aldolases (which are homodimeric enzymes) in that they require subunits GatZ/KbaZ for full activity and for good in vivo and in vitro stability. The Z subunits alone do not show any aldolase activity . It should be noted that the previous suggestion of a tagatose 6P-kinase function for AgaZ and other members of this family turned out to be erroneous , .; GO: 0009024 tagatose-6-phosphate kinase activity, 0019402 galactitol metabolic process. Probab=36.84 E-value=10 Score=15.87 Aligned_cols=20 Identities=15% Similarity=0.144 Sum_probs=9.4 Q ss_pred HHHHHHHHHHHHHHHHHHCCC Q ss_conf 999875588999999985398 Q gi|254780142|r 617 TVAFCDDLMRLGFRYACSSGI 637 (1398) Q Consensus 617 ~~~~l~~~~~l~~~~l~~~Gf 637 (1398) |..-|..-+.|...|. ..|| T Consensus 98 A~~AM~~A~~lv~aYv-~AGF 117 (430) T TIGR02810 98 AEEAMEKAEALVKAYV-EAGF 117 (430) T ss_pred HHHHHHHHHHHHHHHH-HHCC T ss_conf 7999999999999999-8588 No 101 >pfam01139 UPF0027 Uncharacterized protein family UPF0027. Probab=36.23 E-value=20 Score=13.61 Aligned_cols=16 Identities=38% Similarity=0.756 Sum_probs=13.4 Q ss_pred CCCCEEEEECCCCCCC Q ss_conf 4688376422555578 Q gi|254780142|r 715 KMNSIFMMSHSGARGS 730 (1398) Q Consensus 715 ~~N~~~~M~~SGAKGS 730 (1398) ..+.+++|+.|||||= T Consensus 185 ~~g~v~l~vHSGSRgl 200 (419) T pfam01139 185 EKGQVWVMIHSGSRGL 200 (419) T ss_pred CCCEEEEEEECCCCCC T ss_conf 6886999996288535 No 102 >TIGR02974 phageshock_pspF psp operon transcriptional activator PspF; InterPro: IPR014317 Members of this protein are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, found in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol and filamentous phage infection.. Probab=36.02 E-value=22 Score=13.35 Aligned_cols=14 Identities=21% Similarity=0.202 Sum_probs=5.2 Q ss_pred HHHHHHHHHHHHCC Q ss_conf 97899999988648 Q gi|254780142|r 658 DKMVKEYENQYNDG 671 (1398) Q Consensus 658 ~~~~~~~~~~~~~G 671 (1398) .+++.|+.-.+=.| T Consensus 188 ~~Ma~EL~~~~F~G 201 (349) T TIGR02974 188 IRMARELGLPLFPG 201 (349) T ss_pred HHHHHHHCCCCCHH T ss_conf 99999707865511 No 103 >KOG3430 consensus Probab=35.44 E-value=12 Score=15.20 Aligned_cols=34 Identities=29% Similarity=0.613 Sum_probs=19.3 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 3621368566772156641563448835675788530477578767720027 Q gi|254780142|r 58 FCARIFGPIKDYECICGKYKRMKYKGIICEKCGVEVTLSSVRRDRMAHIDLA 109 (1398) Q Consensus 58 ~d~ri~g~~~d~~c~Cg~~~~~~~~g~~C~~Cg~~~~~~~~r~ghfGhIeLa 109 (1398) ||.+ |||. |.|.||+. =|..+|.+. |||=|+.+. T Consensus 47 fDkk-yG~~--WhcivG~~------------FGs~vThe~---g~Fiyf~~g 80 (90) T KOG3430 47 FDKK-YGPT--WHCIVGRN------------FGSYVTHET---GHFIYFYLG 80 (90) T ss_pred HHHH-CCCC--CEEEECCC------------CCEEEEEEC---CCEEEEEEC T ss_conf 7541-2995--18998686------------232788603---828999963 No 104 >PRK05638 threonine synthase; Validated Probab=35.35 E-value=20 Score=13.69 Aligned_cols=47 Identities=21% Similarity=0.451 Sum_probs=20.9 Q ss_pred CCCCEEEEHHH-HHHHHHHHHCCCCCCCCCCCEECCHHHH------HHHHHCCCCCCCCEEE Q ss_conf 87820440258-9999998733678874468141799999------9999888986785236 Q gi|254780142|r 497 SGAPVTVPSQD-MVLGLCYLSTVHEGDPGEGMLFADMGEV------YHALENKIVTLHSKIR 551 (1398) Q Consensus 497 ~g~Pi~~~~QD-~i~G~y~lT~~~~~~~~~~~~f~~~~~~------~~~~~~~~~~~~a~i~ 551 (1398) +|.-.+..+-| ++-+..++.. +| +|....-+ ..+...|.+.....+- T Consensus 296 sgG~~vaVsD~EI~~a~~lla~-------eG-if~EPasAaa~Agl~kl~e~G~I~~~e~VV 349 (443) T PRK05638 296 SGGTAVVVNEEEIMAGEKLLAN-------EG-IFAELSSAVVMPALLKLVETGFIEKGDRVV 349 (443) T ss_pred HCCEEEECCHHHHHHHHHHHHH-------CC-CEECHHHHHHHHHHHHHHHCCCCCCCCEEE T ss_conf 3998998289999999999996-------89-147757899999999999769989999299 No 105 >PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional Probab=35.24 E-value=14 Score=14.74 Aligned_cols=73 Identities=19% Similarity=0.429 Sum_probs=36.6 Q ss_pred ECCCHHHHHHCCEEEEECCCCCCCCCCCCCCCCCC-----CCCCCCCCCCCCCCCCCCC----------CCCCCC----- Q ss_conf 45886788501448971755425456875688733-----6213685667721566415----------634488----- Q gi|254780142|r 24 SIASPAKIASLSYGEIKKPETINYRTFKPERDGLF-----CARIFGPIKDYECICGKYK----------RMKYKG----- 83 (1398) Q Consensus 24 ~l~spe~I~~~S~~ev~~~et~n~~~~kP~~~Gl~-----d~ri~g~~~d~~c~Cg~~~----------~~~~~g----- 83 (1398) .-|||++-+-.-..--+.|-|=.|...+ +.|.+ +..||.+...|.+-||=.- .....| T Consensus 5 ~~Lt~~~y~v~r~~gTE~pfsg~y~~~~--~~G~y~C~~C~~~LF~s~~KfdSg~GWPSF~~~i~~~v~~~~d~~m~R~E 82 (284) T PRK05550 5 KSLTPFEYRVIEDKGTERPFSGEYYDHD--EKGVYLCKKCGAPLFRSEDKFNSGCGWPSFDDEIPGAVKRLPDADGRRTE 82 (284) T ss_pred CCCCHHHHHHHHHCCCCCCCCCCCCCCC--CCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCEEEE T ss_conf 4599999999973688999877554898--98799945899704556651479988866564167755897489931878 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 3567578853047757876772002 Q gi|254780142|r 84 IICEKCGVEVTLSSVRRDRMAHIDL 108 (1398) Q Consensus 84 ~~C~~Cg~~~~~~~~r~ghfGhIeL 108 (1398) ..|.+|| +|.||+-- T Consensus 83 v~C~~C~----------~HLGHvF~ 97 (284) T PRK05550 83 IVCANCG----------AHLGHVFE 97 (284) T ss_pred EEECCCC----------CCCCCCCC T ss_conf 8955899----------84573159 No 106 >TIGR01051 topA_bact DNA topoisomerase I; InterPro: IPR005733 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 I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry describes topoisomerase I from bacteria, which is more closely related to archaeal than to eukaryotic topoisomerase I . Topoisomerase I is the major enzyme for relaxing negatively supercoiled DNA, and its presence is balanced by reverse gyrase, which can introduce negative supercoils. Prokaryotic topoisomerase I folds in an unusual way to give 4 distinct domains, enclosing a hole large enough to accommodate a double-stranded DNA segment. A tyrosine at the active site, which lies at the interface of 2 domains, is involved in transient breakage of a DNA strand, and the formation of a covalent protein-DNA intermediate through a 5-phosphotyrosine linkage. The structure reveals a plausible mechanism by which this and related enzymes could catalyse the passage of one DNA strand through a transient break in another strand . Topoisomerase I require Mg2+ as a cofactor for catalysis to take place. More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003917 DNA topoisomerase type I activity, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome. Probab=35.20 E-value=16 Score=14.27 Aligned_cols=37 Identities=16% Similarity=0.139 Sum_probs=15.4 Q ss_pred HHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 9999853986132123268369999999997899999988648 Q gi|254780142|r 629 FRYACSSGISFGKDDIIVPESKEKIIAEADKMVKEYENQYNDG 671 (1398) Q Consensus 629 ~~~l~~~GfSigi~D~~~~~~k~~~i~~a~~~~~~~~~~~~~G 671 (1398) |.=+....||=.|..= + +-|++.+.+-..+.++|=.| T Consensus 576 F~~~Vd~~FTA~ME~~-L-----DeiA~gk~~w~~~L~~Fy~~ 612 (688) T TIGR01051 576 FGELVDYDFTAKMEKE-L-----DEIAEGKAEWKPVLKNFYTG 612 (688) T ss_pred CCCCCCCHHHHHHHHH-H-----HHHHCCCHHHHHHHHHHCCC T ss_conf 2643355023764344-6-----78850515679999610686 No 107 >pfam06906 DUF1272 Protein of unknown function (DUF1272). This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown. Probab=35.16 E-value=12 Score=15.26 Aligned_cols=32 Identities=25% Similarity=0.721 Sum_probs=16.6 Q ss_pred CCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 667721-566415634488356757885304775 Q gi|254780142|r 66 IKDYEC-ICGKYKRMKYKGIICEKCGVEVTLSSV 98 (1398) Q Consensus 66 ~~d~~c-~Cg~~~~~~~~g~~C~~Cg~~~~~~~~ 98 (1398) +=.||| .|-.+--.... -+|..||.+...-|+ T Consensus 24 ICsfECTFC~~C~~~~l~-~~CPNCgGelv~RP~ 56 (57) T pfam06906 24 ICSFECTFCADCAETRLH-GVCPNCGGELVPRPI 56 (57) T ss_pred EEEEECEECHHHHHHHHC-CCCCCCCCCCCCCCC T ss_conf 887856126789978866-848499881255889 No 108 >TIGR00875 talC transaldolase, putative; InterPro: IPR004731 Transaldolase (2.2.1.2 from EC) catalyzes the reversible transfer of a three-carbon ketol unit from sedoheptulose 7-phosphate to glyceraldehyde 3-phosphate to form erythrose 4-phosphate and fructose 6-phosphate. This enzyme, together with transketolase, provides a link between the glycolytic and pentose-phosphate pathways. Transaldolase is an enzyme of about 34 Kd whose sequence has been well conserved throughout evolution. A lysine has been implicated in the catalytic mechanism of the enzyme; it acts as a nucleophilic group that attacks the carbonyl group of fructose-6-phosphate. Transaldolase is evolutionary related to a bacterial protein of about 20 Kd (known as talC in Escherichia coli), whose exact function is not yet known.; GO: 0005975 carbohydrate metabolic process. Probab=35.13 E-value=22 Score=13.26 Aligned_cols=17 Identities=41% Similarity=0.501 Sum_probs=10.8 Q ss_pred HCCCHHHHHHHHHHHHCC Q ss_conf 504025899999974528 Q gi|254780142|r 1317 AASFQETTKVLTEAAIAG 1334 (1398) Q Consensus 1317 ~ASFEeT~~vL~eAAi~g 1334 (1398) +||| .|..|-+|||..| T Consensus 165 ~AS~-rhP~hvle~al~G 181 (216) T TIGR00875 165 AASV-RHPRHVLEAALIG 181 (216) T ss_pred EEEC-CCHHHHHHHHHHC T ss_conf 5402-3717899999706 No 109 >TIGR00838 argH argininosuccinate lyase; InterPro: IPR009049 This entry represents argininosuccinate lyase, but may include examples of avian delta crystallins, in which argininosuccinate lyase activity may or may not be present and the biological role is to provide the optically clear cellular protein of the eye lens. ; GO: 0004056 argininosuccinate lyase activity, 0042450 arginine biosynthetic process via ornithine. Probab=35.06 E-value=8.3 Score=16.51 Aligned_cols=10 Identities=10% Similarity=-0.067 Sum_probs=4.2 Q ss_pred CCEECHHHHH Q ss_conf 6200348987 Q gi|254780142|r 366 HQCGLPKLMA 375 (1398) Q Consensus 366 ~evgvP~~~A 375 (1398) |||+.=..|+ T Consensus 110 DQVATDlrl~ 119 (469) T TIGR00838 110 DQVATDLRLY 119 (469) T ss_pred CHHHHHHHHH T ss_conf 1789989999 No 110 >TIGR01918 various_sel_PB selenoprotein B, glycine/betaine/sarcosine/D-proline reductase family; InterPro: IPR010187 This entry represents selenoprotein B of glycine reductase, sarcosine reductase, betaine reductase, D-proline reductase, and perhaps others. All members are expected to contain an internal UGA codon, encoding selenocysteine, which may be misinterpreted as a stop codon.; GO: 0030699 glycine reductase activity, 0050485 oxidoreductase activity acting on X-H and Y-H to form an X-Y bond with a disulfide as acceptor, 0030700 glycine reductase complex. Probab=34.90 E-value=19 Score=13.82 Aligned_cols=10 Identities=30% Similarity=0.557 Sum_probs=3.8 Q ss_pred HHHHCCCCEE Q ss_conf 9997598402 Q gi|254780142|r 868 EIEKCGIRSV 877 (1398) Q Consensus 868 ~i~~~~i~~v 877 (1398) ++...+++.| T Consensus 333 ~L~~~~VDaV 342 (433) T TIGR01918 333 ELLEGGVDAV 342 (433) T ss_pred HHHHCCCCEE T ss_conf 9982798889 No 111 >PRK13147 consensus Probab=34.80 E-value=9.5 Score=16.05 Aligned_cols=20 Identities=25% Similarity=0.416 Sum_probs=12.3 Q ss_pred HHCCCCHHH--HHHCCCCCCHH Q ss_conf 110888989--76405761032 Q gi|254780142|r 760 FKGGLCGFE--FFQSCVGGRKG 779 (1398) Q Consensus 760 F~~GL~p~E--fFfhamgGReG 779 (1398) +.+|+.... ||.|+++-... T Consensus 140 ~~~~~~~~~~fYFvHSY~~~~~ 161 (211) T PRK13147 140 LTDGLIPGDHGYFVHSYALRDG 161 (211) T ss_pred HHCCCCCCCEEEEECCCCCCCC T ss_conf 3247676886999612340688 No 112 >pfam10948 DUF2635 Protein of unknown function (DUF2635). This is a family of phage proteins with unknown function. Probab=34.71 E-value=23 Score=13.21 Aligned_cols=16 Identities=25% Similarity=0.316 Sum_probs=12.7 Q ss_pred HHHHHHCCCEEEECCC Q ss_conf 3266656978997576 Q gi|254780142|r 413 VLAEVVHQHVVLLNRA 428 (1398) Q Consensus 413 v~rhl~~gd~Vl~NRq 428 (1398) -+|+|.|||+|+.+-+ T Consensus 31 W~RRl~dGDVv~v~~~ 46 (47) T pfam10948 31 WLRRLADGDVVLVEPK 46 (47) T ss_pred HHHHHCCCCEEEECCC T ss_conf 8743216988984468 No 113 >pfam05876 Terminase_GpA Phage terminase large subunit (GpA). This family consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities. Probab=34.46 E-value=20 Score=13.62 Aligned_cols=18 Identities=28% Similarity=0.479 Sum_probs=9.4 Q ss_pred ECCCCCCHHHHHHHHHCC Q ss_conf 178657899999999759 Q gi|254780142|r 856 KAGQLILESHVNEIEKCG 873 (1398) Q Consensus 856 ~~~~~i~~~~~~~i~~~~ 873 (1398) ..+..|++..-..+...| T Consensus 234 ~Cg~~i~e~~k~~m~~~G 251 (552) T pfam05876 234 HCGCVIEEHHKRAMLRAG 251 (552) T ss_pred CCCCCCCHHHHHHHHHCC T ss_conf 898888999999887689 No 114 >pfam07829 Toxin_14 Alpha-A conotoxin PIVA-like protein. Alpha-A conotoxin PIVA is the major paralytic toxin found in the venom produced by the piscivorous snail Conus purpurascens. This peptide acts by blocking the acetylcholine binding site of the nicotinic acetylcholine receptor at the neuromuscular junction. The overall shape of the peptide is described as an "iron" with a highly charged hydrophilic loop of 15S-19R forming the "handle" domain that is exposed to the exterior of the protein. The stability of the conotoxin is primarily governed by three disulphide bonds. A triangular structural motif formed by residues 19R, 12H and 6Y is thought to constitute a "binding core" that is important in binding to the acetylcholine receptor. Probab=34.36 E-value=22 Score=13.28 Aligned_cols=21 Identities=38% Similarity=0.933 Sum_probs=14.3 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 56641563448835675788530477 Q gi|254780142|r 72 ICGKYKRMKYKGIICEKCGVEVTLSS 97 (1398) Q Consensus 72 ~Cg~~~~~~~~g~~C~~Cg~~~~~~~ 97 (1398) .|||| +...|.-||..+...+ T Consensus 2 ccg~y-----pnaachpc~c~v~rp~ 22 (26) T pfam07829 2 CCGKY-----PNAACHPCGCKVDRPP 22 (26) T ss_pred CCCCC-----CCCCCCCCCCCCCCCC T ss_conf 65667-----8744245553158888 No 115 >TIGR01998 PTS-II-BC-nag PTS system, N-acetylglucosamine-specific IIBC component; InterPro: IPR010974 This entry represents the combined B and C domains of the PTS transport system enzyme II specific for N-acetylglucosamine transport . Many of the genes in this family also include an A domain as part of the same polypeptide and thus should be given the name 'PTS system, N-acetylglucosamine-specific IIABC component'. This family is most closely related to the glucose-specific PTS enzymes.; GO: 0005351 sugar:hydrogen ion symporter activity, 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016021 integral to membrane, 0019866 organelle inner membrane. Probab=34.32 E-value=16 Score=14.33 Aligned_cols=15 Identities=27% Similarity=0.335 Sum_probs=11.9 Q ss_pred CCHHHCCCC-HHHHHH Q ss_conf 301110888-989764 Q gi|254780142|r 757 RSHFKGGLC-GFEFFQ 771 (1398) Q Consensus 757 ~~sF~~GL~-p~EfFf 771 (1398) -.||++|.| |.||-| T Consensus 369 ~asFlTGVTEPlEF~F 384 (571) T TIGR01998 369 FASFLTGVTEPLEFSF 384 (571) T ss_pred HHHHHCCCCCCHHHHH T ss_conf 9986326743257779 No 116 >KOG1100 consensus Probab=33.98 E-value=19 Score=13.81 Aligned_cols=15 Identities=7% Similarity=0.005 Sum_probs=4.9 Q ss_pred CCHHHHHHHHHHHHH Q ss_conf 081789998755889 Q gi|254780142|r 612 CGQKSTVAFCDDLMR 626 (1398) Q Consensus 612 ~G~~~~~~~l~~~~~ 626 (1398) |-+-....++..+.. T Consensus 45 ~~~~~~~~~l~~~e~ 59 (207) T KOG1100 45 NRQRELRNLLKAVEE 59 (207) T ss_pred HCHHHHHHHHHHHHH T ss_conf 470888878999999 No 117 >COG1645 Uncharacterized Zn-finger containing protein [General function prediction only] Probab=33.42 E-value=12 Score=15.27 Aligned_cols=28 Identities=25% Similarity=0.484 Sum_probs=13.7 Q ss_pred CCCCCCCCC-CCCCCCCCCCCCCCCCCCC Q ss_conf 685667721-5664156344883567578 Q gi|254780142|r 63 FGPIKDYEC-ICGKYKRMKYKGIICEKCG 90 (1398) Q Consensus 63 ~g~~~d~~c-~Cg~~~~~~~~g~~C~~Cg 90 (1398) |+...+.-| .||.....+..-.+|..|| T Consensus 23 GAkML~~hCp~Cg~PLF~KdG~v~CPvC~ 51 (131) T COG1645 23 GAKMLAKHCPKCGTPLFRKDGEVFCPVCG 51 (131) T ss_pred HHHHHHHHCCCCCCCCEEECCEEECCCCC T ss_conf 46788744865588316308958777777 No 118 >TIGR02086 IPMI_arch 3-isopropylmalate dehydratase, large subunit; InterPro: IPR011826 3-isopropylmalate dehydratase (or isopropylmalate isomerase; 4.2.1.33 from EC) catalyses the stereo-specific isomerisation of 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. This enzyme performs the second step in the biosynthesis of leucine, and is present in most prokaryotes and many fungal species. The prokaryotic enzyme is a heterodimer composed of a large (LeuC) and small (LeuD) subunit, while the fungal form is a monomeric enzyme. Both forms of isopropylmalate are related and are part of the larger aconitase family . Aconitases are mostly monomeric proteins which share four domains in common and contain a single, labile [4Fe-4S] cluster. Three structural domains (1, 2 and 3) are tightly packed around the iron-sulphur cluster, while a fourth domain (4) forms a deep active-site cleft. The prokaryotic enzyme is encoded by two adjacent genes, leuC and leuD, corresponding to aconitase domains 1-3 and 4 respectively , . LeuC does not bind an iron-sulphur cluster. It is thought that some prokaryotic isopropylamalate dehydrogenases can also function as homoaconitase 4.2.1.36 from EC, converting cis-homoaconitate to homoisocitric acid in lysine biosynthesis . Homoaconitase has been identified in higher fungi (mitochondria) and several archaea and one thermophilic species of bacteria, Thermus thermophilus . This entry represents the large subunit of 3-isopropylmalate dehydratase (LeuC), as well as homoaconitase enzymes, from prokaryotes. Homoaconitase, aconitase and 3-isopropylmalate dehydratase have similar overall structures and domain organisation . All are dehydratases that bind a [4Fe-4S]-cluster. Information about related proteins can be found at Protein of the Month: Aconitase .; GO: 0003861 3-isopropylmalate dehydratase activity, 0051539 4 iron 4 sulfur cluster binding, 0009098 leucine biosynthetic process. Probab=33.35 E-value=21 Score=13.45 Aligned_cols=50 Identities=22% Similarity=0.379 Sum_probs=27.3 Q ss_pred HHHHCCCHHHHHHHCCCCCEECHHHCC----------CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEEE Q ss_conf 355186578875420178520001014----------6021111007889877642024543222112202401487689 Q gi|254780142|r 886 ESSRGVCVLCYGRDLARGSLVNVGEAV----------GVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVK 955 (1398) Q Consensus 886 ~~~~~v~~~cy~~~l~~~~lv~pGe~V----------G~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVPR 955 (1398) +.-.|||=. -|..+=+|+||.-| |++.|=..|==+|=|-+ ..-+|--+ T Consensus 97 ~~g~GIcHQ----~L~E~Gya~PG~vvvG~DSHT~T~GA~GAFA~GmGATDvA~------------------a~~~G~~W 154 (431) T TIGR02086 97 DVGEGICHQ----VLVEKGYAEPGMVVVGADSHTCTSGALGAFATGMGATDVAI------------------ALATGKTW 154 (431) T ss_pred ECCCEEEEE----EEEECCCCCCCEEEEECCCCCCHHHCHHHEEECCCHHHHHH------------------HHHHCCCE T ss_conf 879802778----86530624776189952677400000023042578689999------------------99828613 Q ss_pred EE Q ss_conf 72 Q gi|254780142|r 956 IK 957 (1398) Q Consensus 956 lk 957 (1398) +| T Consensus 155 ~~ 156 (431) T TIGR02086 155 LK 156 (431) T ss_pred EE T ss_conf 64 No 119 >TIGR02002 PTS-II-BC-glcB PTS system, glucose-specific IIBC component; InterPro: IPR011299 This entry represents the combined B and C domains of the PTS transport system enzyme II specific for glucose transport . Many of the genes in this family also include an A domain as part of the same polypeptide and thus should be given the name 'PTS system, glucose-specific IIABC component' while the Bacillus subtilus enzyme also contains an enzyme III domain which appears to act independently of the enzyme II domains . This group is most closely related to the N-acetylglucosamine-specific PTS enzymes (IPR010974 from INTERPRO).; GO: 0005355 glucose transmembrane transporter activity, 0015758 glucose transport, 0016021 integral to membrane. Probab=33.10 E-value=17 Score=14.23 Aligned_cols=11 Identities=36% Similarity=0.712 Sum_probs=4.9 Q ss_pred HHHCCCC-HHHH Q ss_conf 1110888-9897 Q gi|254780142|r 759 HFKGGLC-GFEF 769 (1398) Q Consensus 759 sF~~GL~-p~Ef 769 (1398) ||+||+| |.|| T Consensus 327 SFLTGITEPlEF 338 (518) T TIGR02002 327 SFLTGITEPLEF 338 (518) T ss_pred HHHHCCCCCHHH T ss_conf 543125452477 No 120 >PRK05654 acetyl-CoA carboxylase subunit beta; Validated Probab=32.56 E-value=14 Score=14.82 Aligned_cols=26 Identities=31% Similarity=0.829 Sum_probs=12.5 Q ss_pred CCCCC-CC-CCCCC--CCC-CCCCCCCCCCC Q ss_conf 56677-21-56641--563-44883567578 Q gi|254780142|r 65 PIKDY-EC-ICGKY--KRM-KYKGIICEKCG 90 (1398) Q Consensus 65 ~~~d~-~c-~Cg~~--~~~-~~~g~~C~~Cg 90 (1398) |.--| +| .||+. +.. ...-.+|..|| T Consensus 26 P~glW~kCp~C~~~i~~~dL~~n~~VCp~C~ 56 (288) T PRK05654 26 PEGLWTKCPSCGQVLYRKELEANLNVCPKCG 56 (288) T ss_pred CCCCCCCCCCCCHHHHHHHHHHHCCCCCCCC T ss_conf 9884222877650350999998387892997 No 121 >TIGR01031 rpmF_bact ribosomal protein L32; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene }.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit. Probab=32.47 E-value=21 Score=13.51 Aligned_cols=18 Identities=44% Similarity=1.147 Sum_probs=9.7 Q ss_pred CC-CCCCCCCCCCCCCCCCCCC Q ss_conf 21-5664156344883567578 Q gi|254780142|r 70 EC-ICGKYKRMKYKGIICEKCG 90 (1398) Q Consensus 70 ~c-~Cg~~~~~~~~g~~C~~Cg 90 (1398) +| .||.|+. .| -+|..|| T Consensus 29 ~C~~CGe~~~-pH--rvC~~CG 47 (56) T TIGR01031 29 VCPNCGEYKL-PH--RVCPSCG 47 (56) T ss_pred CCCCCCCCCC-CE--EECCCCC T ss_conf 2677888535-50--2028888 No 122 >PRK06556 vitamin B12-dependent ribonucleotide reductase; Validated Probab=32.30 E-value=21 Score=13.54 Aligned_cols=44 Identities=25% Similarity=0.282 Sum_probs=20.7 Q ss_pred CCCCCCCCCCE--------EEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCCEE Q ss_conf 45467877545--------69974689999999999876750542378878204 Q gi|254780142|r 457 AGYNADFDGDQ--------MAVYAVISPEAQLEARVLMLSTNNLLHPASGAPVT 502 (1398) Q Consensus 457 ~pyNADFDGDE--------MnlHvPqs~eAraEa~~Lm~~~~niisP~~g~Pi~ 502 (1398) .+|..||||+- -|+-|-.|.+= -+|- .-.-...+..|.+|+++- T Consensus 268 ~g~d~~~~~~~~~~v~~qNfN~SV~vtd~F-M~Av-~~d~~~~L~~~~~g~v~~ 319 (957) T PRK06556 268 AGYDMDLGGEAYASVQYQNANNSVRVSDEF-MRAV-EDDETFGLRARTDGSVIE 319 (957) T ss_pred CCCCCCCCCCCEEECCCCCCEEEEEECHHH-HHHH-HCCCCEEEEECCCCCEEE T ss_conf 156667675310000413032369747999-9998-669962678147896404 No 123 >TIGR02873 spore_ylxY probable sporulation protein, polysaccharide deacetylase family; InterPro: IPR014228 Members of this entry include YlxY, and are related to IPR014132 from INTERPRO, which represents a subset of the polysaccharide deacetylase family found in a species if, and only if, the species forms endospores e.g. Bacillus subtilis or Clostridium tetani. Proteins in this entry are likewise restricted to spore-formers, but are not universally found among endospore-forming species.. Probab=31.93 E-value=18 Score=13.92 Aligned_cols=16 Identities=31% Similarity=0.650 Sum_probs=6.3 Q ss_pred HHHHCCCCCCEEECCC Q ss_conf 9861023782000346 Q gi|254780142|r 330 SDMLKGKQGRFRTNLL 345 (1398) Q Consensus 330 ~~rlkgK~GrfR~nl~ 345 (1398) -.+.|-++||||+.+| T Consensus 44 Y~~MKd~~~kF~~~~L 59 (269) T TIGR02873 44 YKKMKDQEGKFDEKLL 59 (269) T ss_pred HHHHHHHHCCCCCHHC T ss_conf 5564566268551001 No 124 >COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only] Probab=31.91 E-value=25 Score=12.89 Aligned_cols=18 Identities=17% Similarity=0.183 Sum_probs=7.9 Q ss_pred HHCCCCCCHHHHCCCCCC Q ss_conf 640576103221012101 Q gi|254780142|r 770 FQSCVGGRKGLLDVVMRT 787 (1398) Q Consensus 770 FfhamgGReGLiDTAvKT 787 (1398) |.|+-=++.|-+|+|-|- T Consensus 110 ~~~~aL~~~~~~~~a~r~ 127 (421) T COG1571 110 FYHAALAGVGVIAEAERG 127 (421) T ss_pred HHHHHHHCCCCHHHHHHH T ss_conf 999998445789999988 No 125 >TIGR01161 purK phosphoribosylaminoimidazole carboxylase, ATPase subunit; InterPro: IPR005875 Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. This family represents PurK, N5-carboxyaminoimidazole ribonucleotide (N5_CAIR) synthetase, which catalyzes the conversion of 5-aminoimidazole ribonucleotide (AIR), ATP, and bicarbonate to N5-CAIR, ADP, and Pi. PurE converts N5-CAIR to CAIR. In the presence of high concentrations of bicarbonate, PurE is reported able to convert AIR to CAIR directly and without ATP. PurK belongs to the ATP grasp superfamily of C-N ligase enzymes. Each subunit of PurK is composed of three domains (A, B, and C). The B domain contains a flexible, glycine-rich loop (B loop, T123-G130) that is disordered in the sulphate-PurK structure and becomes ordered in the MgADP-PurK structure. MgADP is wedged between the B and C domains, as with all members of the ATP grasp superfamily. Other enzymes in this superfamily contain a conserved Omega loop proposed to interact with the B loop, define the specificity of their nonnucleotide substrate, and protect the acyl phosphate intermediate formed from this substrate. PurK contains a minimal Omega loop without conserved residues. In the reaction catalyzed by PurK, carboxyphosphate is the putative acyl phosphate intermediate. The sulphate of the sulphate ion-liganded PurK interacts electrostatically with Arg 242 and the backbone amide group of Asn 245, components of the J loop of the C domain. This sulphate may reveal the location of the carboxyphosphate binding site. Conserved residues within the C-terminus of the C domain define a pocket that is proposed to bind AIR in collaboration with an N-terminal strand loop helix motif in the A domain (P loop, G8-L1). The P loop is proposed to bind the phosphate of AIR on the basis of similar binding sites observed in PurN and PurE and proposed in PurD and PurT, four other enzymes in the purine pathway .; GO: 0004638 phosphoribosylaminoimidazole carboxylase activity, 0006189 'de novo' IMP biosynthetic process, 0009320 phosphoribosylaminoimidazole carboxylase complex. Probab=31.66 E-value=18 Score=14.00 Aligned_cols=78 Identities=10% Similarity=0.085 Sum_probs=33.6 Q ss_pred CEEEECCCCCCHHHHHHHHHCC--CCEEECCCCCCHHHHHCCCHHHHHHHCCCCCEECHHHCCCCHHH-HHHHHHHHHHH Q ss_conf 1885178657899999999759--84020233100035518657887542017852000101460211-11007889877 Q gi|254780142|r 852 ECIVKAGQLILESHVNEIEKCG--IRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAA-QSIGEPGTQLT 928 (1398) Q Consensus 852 ~~i~~~~~~i~~~~~~~i~~~~--i~~v~irs~lt~~~~~~v~~~cy~~~l~~~~lv~pGe~VG~iAA-QSIGEP~TQmT 928 (1398) .+|--+.|.++...++++...+ ++-..-...|-+...+ ..+|-+. -+-|=+|===.+ +-=.+...--- T Consensus 64 DviT~E~Ehv~~~~L~~L~~~g~~~~~~P~~~~l~~~~dk-~~qK~~L--------~~~g~~vp~f~~~~~~~~~~~~~~ 134 (386) T TIGR01161 64 DVITFEFEHVDVEALEKLEARGDKVKVRPSPEALAIIQDK-LTQKQFL--------QKLGLPVPPFVVIEIKDEEELDSA 134 (386) T ss_pred CEEEEEECCCCCHHHHHHHHCCCEEEEECCHHHHHHHHCH-HHHHHHH--------HHCCCCCCCCCEEECCCHHHHHHH T ss_conf 6554310137856789998359847760388999988365-8999999--------966899884120223684257899 Q ss_pred HHHHCCCCCC Q ss_conf 6420245432 Q gi|254780142|r 929 MRTFHLGGAV 938 (1398) Q Consensus 929 LnTFHfAGVA 938 (1398) +..|-|-+|- T Consensus 135 ~~~~g~p~Vl 144 (386) T TIGR01161 135 LQELGFPVVL 144 (386) T ss_pred HHHCCCCEEE T ss_conf 9873984799 No 126 >TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor; InterPro: IPR006548 These sequences represent the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human . ELAV stands for the Drosophila Embryonic lethal abnormalvisual protein . ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (IPR006546 from INTERPRO). ; GO: 0003723 RNA binding. Probab=31.24 E-value=24 Score=12.96 Aligned_cols=47 Identities=17% Similarity=0.200 Sum_probs=26.1 Q ss_pred CHHCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCH Q ss_conf 1002013666999999980817899987558899999998539861321232683 Q gi|254780142|r 594 QEMIKKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPE 648 (1398) Q Consensus 594 ~~~~k~~~~~li~~i~~~~G~~~~~~~l~~~~~l~~~~l~~~GfSigi~D~~~~~ 648 (1398) |.+..++ +..||.-||.-.|.+.|.+- +.-.+ -.|.|=|++=+--|+ T Consensus 112 K~MTq~e----LE~lF~pfG~IITSRIL~d~--vtgeh--a~~~skGVGFiRFDk 158 (436) T TIGR01661 112 KTMTQKE----LESLFSPFGKIITSRILSDN--VTGEH--ADTLSKGVGFIRFDK 158 (436) T ss_pred CCCCHHH----HHHHHCCCCCEEEEHEECCC--CCCHH--HCCCCCCCEEEECCC T ss_conf 6523689----99983202752410000036--67500--154115711476176 No 127 >PRK12366 replication factor A; Reviewed Probab=31.07 E-value=21 Score=13.46 Aligned_cols=27 Identities=22% Similarity=0.182 Sum_probs=12.1 Q ss_pred HHHHCCCCCCCCCCCCEEEECCCCEEEE Q ss_conf 6420245432221122024014876897 Q gi|254780142|r 929 MRTFHLGGAVTVMDRSFIESPCDGIVKI 956 (1398) Q Consensus 929 LnTFHfAGVAS~~~~~~iknvTlGVPRl 956 (1398) .|||-+..-.+ ...+-..+--.|-+|+ T Consensus 305 ~Refe~~Dgsg-~Vq~i~l~D~TG~VRv 331 (649) T PRK12366 305 SREVQFDDRSA-EVQDIYLSDGTGRVKI 331 (649) T ss_pred CCEEECCCCCE-EEEEEEEECCCCCEEE T ss_conf 51586389856-9999999558881899 No 128 >TIGR02420 dksA RNA polymerase-binding protein DksA; InterPro: IPR012784 This entry describes a small, pleiotropic protein family, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants . DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the proteobacteria. Whether the closest homologues outside the proteobacteria function equivalently is unknown. The entry also contains possible DksA proteins from outside the proteobacteria while IPR012783 from INTERPRO describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage.; GO: 0008270 zinc ion binding. Probab=30.87 E-value=21 Score=13.38 Aligned_cols=15 Identities=33% Similarity=0.632 Sum_probs=5.8 Q ss_pred HHHHHHHHHHHHHHH Q ss_conf 999999999789999 Q gi|254780142|r 650 KEKIIAEADKMVKEY 664 (1398) Q Consensus 650 k~~~i~~a~~~~~~~ 664 (1398) |.+++.++.+.+..+ T Consensus 17 k~~l~~e~~~t~~~l 31 (110) T TIGR02420 17 KQELLEEADKTLEHL 31 (110) T ss_pred HHHHHHHHHHHHHHH T ss_conf 999999999998666 No 129 >COG2331 Uncharacterized protein conserved in bacteria [Function unknown] Probab=30.27 E-value=14 Score=14.84 Aligned_cols=30 Identities=33% Similarity=0.722 Sum_probs=16.0 Q ss_pred CCCCCCCC-CCCCCCC-C---C-CCCCCCCCCCCCC Q ss_conf 85667721-5664156-3---4-4883567578853 Q gi|254780142|r 64 GPIKDYEC-ICGKYKR-M---K-YKGIICEKCGVEV 93 (1398) Q Consensus 64 g~~~d~~c-~Cg~~~~-~---~-~~g~~C~~Cg~~~ 93 (1398) -|+..|+| .||.-.- + + .+-..|+.||..+ T Consensus 8 MPtY~Y~c~~cg~~~dvvq~~~ddplt~ce~c~a~~ 43 (82) T COG2331 8 MPTYSYECTECGNRFDVVQAMTDDPLTTCEECGARL 43 (82) T ss_pred CCCEEEEECCCCHHHHHHHHCCCCCCCCCHHHCHHH T ss_conf 640688641334088998861268454385557279 No 130 >pfam04035 consensus Probab=30.23 E-value=27 Score=12.69 Aligned_cols=48 Identities=25% Similarity=0.473 Sum_probs=29.4 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECHHHHHHHHHHHHHCCC Q ss_conf 5664156344883567578853047757876772002776220130122578999980999 Q gi|254780142|r 72 ICGKYKRMKYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMS 132 (1398) Q Consensus 72 ~Cg~~~~~~~~g~~C~~Cg~~~~~~~~r~ghfGhIeLa~PV~Hi~f~k~~~~~i~~~l~~~ 132 (1398) +|..++++-.....|..||..-. -....|+|-..-|- -|.|+..|++. T Consensus 3 AC~~C~~i~~~~~~Cp~Cgs~~~----s~dW~G~viI~dpe---------~SeIAk~l~i~ 50 (60) T pfam04035 3 ACKNCKRLTEEDTTCPVCGSEDL----TEEWFGLVIIIDPE---------KSEIAKRLGAK 50 (60) T ss_pred CHHHCCCCCCCCCCCCCCCCCCC----CCCCCEEEEEECCH---------HHHHHHHHCCC T ss_conf 44239727899981889839878----77613599996770---------77999984999 No 131 >pfam09290 AcetDehyd-dimer Prokaryotic acetaldehyde dehydrogenase, dimerization. Members of this family are found in prokaryotic acetaldehyde dehydrogenase (acylating), and adopt a structure consisting of an alpha-beta-alpha-beta(3) core. They mediate dimerization of the protein. Probab=29.94 E-value=16 Score=14.44 Aligned_cols=33 Identities=36% Similarity=0.531 Sum_probs=27.4 Q ss_pred CCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCC Q ss_conf 1785200010146021111007889877642024 Q gi|254780142|r 901 ARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHL 934 (1398) Q Consensus 901 ~~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHf 934 (1398) ++...|+-+|-|-.||..|+| |||-..++-|-. T Consensus 14 srv~~v~Y~EiVasiaS~SaG-pgTR~NIDEy~~ 46 (137) T pfam09290 14 SRVAPVDYAEIVASIASKSAG-PGTRANIDEFTE 46 (137) T ss_pred HHCCCEEEEEEEEHHHHCCCC-CHHHCCHHHHHH T ss_conf 601531257755112442479-333314378899 No 132 >TIGR01751 crot-CoA-red crotonyl-CoA reductase; InterPro: IPR010085 Crotonyl-CoA reductase is responsible for the conversion of crotonyl-CoA to butyryl-CoA. In serine cycle methylotrophic bacteria this enzyme is involved in the process of acetyl-CoA to glyoxylate , . In other bacteria the enzyme is used to produce butyrate for incorporation into polyketides such as tylosin from Streptomyces fradiae and coronatine from Pseudomonas syringae .. Probab=29.87 E-value=18 Score=13.89 Aligned_cols=29 Identities=28% Similarity=0.265 Sum_probs=22.9 Q ss_pred CCEECHHHCCCCH-HHHHHHHHHHHHHHHH Q ss_conf 8520001014602-1111007889877642 Q gi|254780142|r 903 GSLVNVGEAVGVI-AAQSIGEPGTQLTMRT 931 (1398) Q Consensus 903 ~~lv~pGe~VG~i-AAQSIGEP~TQmTLnT 931 (1398) .+-+.||.+|=+= ||=-.|==+||+|.+- T Consensus 192 p~~~KpGD~VLIWGAaGGLGs~A~Ql~~a~ 221 (409) T TIGR01751 192 PAEVKPGDNVLIWGAAGGLGSYAIQLARAG 221 (409) T ss_pred CCCCCCCCCEEEECCCCCHHHHHHHHHHHC T ss_conf 776688883798426662568999999954 No 133 >PRK12286 rpmF 50S ribosomal protein L32; Reviewed Probab=29.80 E-value=25 Score=12.84 Aligned_cols=19 Identities=42% Similarity=1.009 Sum_probs=9.4 Q ss_pred CCC-CCCCCCCCCCCCCCCCCCC Q ss_conf 721-5664156344883567578 Q gi|254780142|r 69 YEC-ICGKYKRMKYKGIICEKCG 90 (1398) Q Consensus 69 ~~c-~Cg~~~~~~~~g~~C~~Cg 90 (1398) .+| .||.++.- --+|..|| T Consensus 28 ~~C~~CG~~~~~---H~vC~~CG 47 (59) T PRK12286 28 VECPNCGELKLP---HRVCPSCG 47 (59) T ss_pred EECCCCCCCCCC---CEECCCCC T ss_conf 578899986547---77889898 No 134 >COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair] Probab=29.63 E-value=21 Score=13.44 Aligned_cols=11 Identities=9% Similarity=0.350 Sum_probs=5.8 Q ss_pred HHHHCCCEEEE Q ss_conf 66656978997 Q gi|254780142|r 415 AEVVHQHVVLL 425 (1398) Q Consensus 415 rhl~~gd~Vl~ 425 (1398) |-+.+|.||++ T Consensus 338 rAV~egRPIii 348 (715) T COG1107 338 RAVLEGRPIII 348 (715) T ss_pred HHHHCCCCEEE T ss_conf 98734783699 No 135 >pfam06060 Mesothelin Pre-pro-megakaryocyte potentiating factor precursor (Mesothelin). This family consists of several mammalian pre-pro-megakaryocyte potentiating factor precursor (MPF) or mesothelin proteins. Mesothelin is a glycosylphosphatidylinositol-linked glycoprotein highly expressed in mesothelial cells, mesotheliomas, and ovarian cancer, but the biological function of the protein is not known. Probab=29.53 E-value=9.3 Score=16.12 Aligned_cols=81 Identities=22% Similarity=0.314 Sum_probs=42.8 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCEEEC Q ss_conf 10037899999998699999987398356777699999998888742776787724787650678998610237820003 Q gi|254780142|r 264 ASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQGRFRTN 343 (1398) Q Consensus 264 ~dDlt~~~~~Ii~~N~~Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~~~~~~~~~~rp~ks~~~rlkgK~GrfR~n 343 (1398) .---+|..+.|-++|-. ++..++++ -+|||-++.+.+ +.+|-.+...+-|.+ |-.--. T Consensus 136 ~~aC~hfFs~v~kaNvd---~L~r~s~e-----RqRLL~~AL~C~---gv~g~~vse~dvraL-----------G~LaCD 193 (625) T pfam06060 136 QQACAHFFSLISKANVD---VLPRRSLE-----RQRLLPAALKCQ---GVYGFQVSEADVRAL-----------GGLACD 193 (625) T ss_pred CCHHHHHHHHHHHCCCC---CCCCCCHH-----HHHHHHHHHHHC---CCCCCCCCHHHHHHH-----------CCCCCC T ss_conf 42689999886441334---14565578-----887778767552---766631267778885-----------363316 Q ss_pred CCCCCCCCCCCEEEECCCCCCCCCEECH Q ss_conf 4651004577403412554354620034 Q gi|254780142|r 344 LLGKRVDYSGRSVIVAGPELQLHQCGLP 371 (1398) Q Consensus 344 l~GKRVdfs~RsVI~pdP~l~~~evgvP 371 (1398) |-|+-|.-|+-.+. |. +-+|+=| T Consensus 194 L~g~fva~SaevlL---p~--L~~C~gp 216 (625) T pfam06060 194 LPGRFVAESSEVLL---PW--LASCPGP 216 (625) T ss_pred CCHHHHHCCHHHHH---HH--HHHCCCC T ss_conf 86066650245667---99--9747998 No 136 >pfam05129 Elf1 Transcription elongation factor Elf1 like. This family of short proteins contains a putative zinc binding domain with four conserved cysteines. Elf1 has been identified as a transcription elongation factor in Saccharomyces cerevisiae. Probab=29.53 E-value=17 Score=14.11 Aligned_cols=46 Identities=15% Similarity=0.505 Sum_probs=24.0 Q ss_pred CCCCCC-CCCC-------CCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECH Q ss_conf 667721-5664-------15634488-3567578853047757876772002776220130 Q gi|254780142|r 66 IKDYEC-ICGK-------YKRMKYKG-IICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWF 117 (1398) Q Consensus 66 ~~d~~c-~Cg~-------~~~~~~~g-~~C~~Cg~~~~~~~~r~ghfGhIeLa~PV~Hi~f 117 (1398) .+.|.| .||- .++..-.| ..|..||.... -...++.=+.=||+-|. T Consensus 15 ~~~F~CpfC~h~~sv~vkidk~~~~g~l~C~vCg~~~~------~~i~~L~epIDVYs~wi 69 (74) T pfam05129 15 PTVFDCPFCNHKKSVSVKIDKKTGIAKLHCRVCGLSFQ------TEINALSEPIDVYSDWI 69 (74) T ss_pred CCEEECCCCCCCCEEEEEEECCCCEEEEEEECCCCEEE------ECCCCCCCCEEEHHHHH T ss_conf 85674786799875999998147989999621788578------66766675600046666 No 137 >TIGR01802 CM_pl-yst chorismate mutase; InterPro: IPR008238 Chorismate mutase (CM; 5.4.99.5 from EC) catalyses the reaction at the branch point of the biosynthetic pathway leading to the three aromatic amino acids, phenylalanine, tryptophan and tyrosine (chorismic acid is the last common intermediate, and CM leads to the L-phenylalanine/L-tyrosine branch). It is part of the shikimate pathway, which is present only in bacteria, fungi and plants. Members of this family, which are restricted to plants and fungi, contain a chorismate mutase domain of the AroQ class (eukaryotic type) and have an all-helical structure. The monomer consists of a catalytic and a regulatory domain covalently linked by a loop, which functions as a molecular hinge. They are monofunctional, allosteric enzymes and are subject to allosteric inhibition by tyrosine and activation by tryptophan. The three types of CM are AroQ class, prokaryotic type (e.g., IPR008239 from INTERPRO and others); AroQ class, eukaryotic type; and AroH class (IPR008243 from INTERPRO). They fall into two structural folds (AroQ class and AroH class) which are completely unrelated . The two types of the AroQ structural class (the Escherichia coli CM dimer and the yeast CM monomer) can be structurally superimposed, and the topology of the four-helix bundle forming the active site is conserved . For additional information please see , , , , , , , .; GO: 0004106 chorismate mutase activity, 0009073 aromatic amino acid family biosynthetic process. Probab=29.40 E-value=15 Score=14.54 Aligned_cols=39 Identities=23% Similarity=0.216 Sum_probs=15.6 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCEEECHHHHHHHHHHHHHCC Q ss_conf 57885304775787677200277622013012257899998099 Q gi|254780142|r 88 KCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGM 131 (1398) Q Consensus 88 ~Cg~~~~~~~~r~ghfGhIeLa~PV~Hi~f~k~~~~~i~~~l~~ 131 (1398) ||-++|..|-.||=|||-- |.=-=|.+........++.. T Consensus 147 tcD~~CLQ~LSRRIHfGKF-----VAEaKFqa~pe~y~~lIkA~ 185 (273) T TIGR01802 147 TCDVECLQSLSRRIHFGKF-----VAEAKFQAEPEKYKKLIKAK 185 (273) T ss_pred EHHHHHHHHHCCCCCCCCH-----HHHHHHHCCCHHHHHHHCCC T ss_conf 3243575333011025623-----66645422834458876078 No 138 >COG5349 Uncharacterized protein conserved in bacteria [Function unknown] Probab=28.24 E-value=22 Score=13.36 Aligned_cols=11 Identities=36% Similarity=0.960 Sum_probs=7.9 Q ss_pred CCCCCCCCCCC Q ss_conf 35675788530 Q gi|254780142|r 84 IICEKCGVEVT 94 (1398) Q Consensus 84 ~~C~~Cg~~~~ 94 (1398) ..|+.||.++. T Consensus 41 p~C~aCG~dyg 51 (126) T COG5349 41 PACEACGLDYG 51 (126) T ss_pred CHHHHCCCCCC T ss_conf 43666064115 No 139 >COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism] Probab=27.89 E-value=20 Score=13.69 Aligned_cols=10 Identities=30% Similarity=0.670 Sum_probs=4.9 Q ss_pred CCCCCCCEEE Q ss_conf 0045774034 Q gi|254780142|r 348 RVDYSGRSVI 357 (1398) Q Consensus 348 RVdfs~RsVI 357 (1398) ++-|.||-|| T Consensus 228 lIGFAGpRVI 237 (294) T COG0777 228 LIGFAGPRVI 237 (294) T ss_pred CCCCCCCHHH T ss_conf 0015763244 No 140 >pfam04502 DUF572 Family of unknown function (DUF572). Family of eukaryotic proteins with undetermined function. Probab=27.73 E-value=28 Score=12.58 Aligned_cols=28 Identities=32% Similarity=0.929 Sum_probs=15.3 Q ss_pred CCCCCCCCCCCCCCCCCC-CCCC--CCCCCCC Q ss_conf 887336213685667721-5664--1563448 Q gi|254780142|r 54 RDGLFCARIFGPIKDYEC-ICGK--YKRMKYK 82 (1398) Q Consensus 54 ~~Gl~d~ri~g~~~d~~c-~Cg~--~~~~~~~ 82 (1398) ++|.+--|+--|-. -.| .||. |++.+|. T Consensus 27 ~~~~~~vR~m~Pf~-i~C~~C~~~i~kG~kFN 57 (324) T pfam04502 27 KNGQLVVRFMAPFN-MRCNTCGEYIYKGTKFN 57 (324) T ss_pred CCCCEEEEEECCEE-EECCCCCCCCCCCEECC T ss_conf 58824899836701-35278842001535503 No 141 >PRK09588 hypothetical protein; Reviewed Probab=27.69 E-value=29 Score=12.38 Aligned_cols=15 Identities=33% Similarity=0.795 Sum_probs=13.0 Q ss_pred CCCEEEEECCCCCCC Q ss_conf 688376422555578 Q gi|254780142|r 716 MNSIFMMSHSGARGS 730 (1398) Q Consensus 716 ~N~~~~M~~SGAKGS 730 (1398) .+.+++|+.|||||= T Consensus 160 ~g~v~l~iHSGSRgl 174 (376) T PRK09588 160 ADHLLLLVHSGSRGL 174 (376) T ss_pred CCCEEEEEECCCCHH T ss_conf 785899994257154 No 142 >KOG1080 consensus Probab=27.59 E-value=29 Score=12.37 Aligned_cols=23 Identities=13% Similarity=0.184 Sum_probs=10.0 Q ss_pred CCCHHHHHHCCCCCCH-HHHCCCC Q ss_conf 8889897640576103-2210121 Q gi|254780142|r 763 GLCGFEFFQSCVGGRK-GLLDVVM 785 (1398) Q Consensus 763 GL~p~EfFfhamgGRe-GLiDTAv 785 (1398) ++.-.|=-+|+|.+=- |-.++++ T Consensus 694 ~~~~~~~~~~~~~a~~~~~~~e~~ 717 (1005) T KOG1080 694 QCCKCETGSHAMCASRAGYIMEAV 717 (1005) T ss_pred HCCHHHCCCEEHHHCCCCCHHHHH T ss_conf 013021073423333656615655 No 143 >PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated Probab=27.43 E-value=29 Score=12.35 Aligned_cols=24 Identities=25% Similarity=0.457 Sum_probs=13.1 Q ss_pred HHHHHHHHHHHHHHCCCCCCEEEEEEC Q ss_conf 864477888666634898511286304 Q gi|254780142|r 218 KIIKRLKIVDSFITSGNNPGWMIIRKL 244 (1398) Q Consensus 218 ~~~~~~~~~~~f~~~~~~Pewmil~~l 244 (1398) -|..|.+-+..|.+ .|=|-|--.+ T Consensus 175 LIVeRE~EI~~FvP---~~Yw~I~a~~ 198 (864) T PRK06319 175 LVVDREKAIEAFVP---VEYWNIRVLL 198 (864) T ss_pred HHHHHHHHHHHCCC---CCEEEEEEEE T ss_conf 99999999982588---6438999998 No 144 >TIGR01122 ilvE_I branched-chain amino acid aminotransferase; InterPro: IPR005785 Aminotransferases share certain mechanistic features with other pyridoxal-phosphate dependent enzymes, such as the covalent binding of the pyridoxal-phosphate group to a lysine residue. On the basis of sequence similarity, these various enzymes can be grouped into subfamilies. One of these, called class-IV, currently consists of proteins of about 270 to 415 amino-acid residues that share a few regions of sequence similarity. Surprisingly, the best conserved region does not include the lysine residue to which the pyridoxal-phosphate group is known to be attached, in ilvE, but is located some 40 residues at the C-terminus side of the PlP-lysine. Among the class IV aminotransferases are two phylogenetically separable groups of branched-chain amino acid aminotransferase (IlvE) (2.6.1.42 from EC). The last common ancestor of the two lineages appears also to have given rise to a family of D-amino acid aminotransferases (DAAT). This model represents the IlvE family more strongly similar to the DAAT family. ; GO: 0004084 branched-chain-amino-acid transaminase activity, 0009081 branched chain family amino acid metabolic process. Probab=27.36 E-value=23 Score=13.16 Aligned_cols=21 Identities=29% Similarity=0.491 Sum_probs=12.9 Q ss_pred CCHHHHHHHHHCCCCE-EECCC Q ss_conf 7899999999759840-20233 Q gi|254780142|r 861 ILESHVNEIEKCGIRS-VRIRS 881 (1398) Q Consensus 861 i~~~~~~~i~~~~i~~-v~irs 881 (1398) |.+...+.|.++++++ +-||= T Consensus 70 l~ea~~E~lR~NnL~sdaYIRP 91 (302) T TIGR01122 70 LMEATRETLRKNNLRSDAYIRP 91 (302) T ss_pred HHHHHHHHHHHCCCCCCEEEEE T ss_conf 9999999987338736703611 No 145 >COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription] Probab=27.35 E-value=26 Score=12.70 Aligned_cols=18 Identities=22% Similarity=0.396 Sum_probs=7.3 Q ss_pred CCCCC-CCCCCCCCCEEEE Q ss_conf 12254-5467877545699 Q gi|254780142|r 453 PLVCA-GYNADFDGDQMAV 470 (1398) Q Consensus 453 ~~vc~-pyNADFDGDEMnl 470 (1398) |.+|. .=|+-|-+--||+ T Consensus 224 ~~~C~~cG~~~~~t~y~nl 242 (531) T COG5259 224 PSSCSCCGNKSFNTRYHNL 242 (531) T ss_pred CCEEECCCCCCCCHHHHHH T ss_conf 7421056744320355530 No 146 >TIGR00280 L37a ribosomal protein L37a; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . This ribosomal protein is found in archaebacteria and eukaryotes . Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type .; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome. Probab=27.30 E-value=30 Score=12.34 Aligned_cols=28 Identities=43% Similarity=0.992 Sum_probs=15.1 Q ss_pred CCCCC-CCCCCCCCCC-CCC-CCCCCCCCCC Q ss_conf 67721-5664156344-883-5675788530 Q gi|254780142|r 67 KDYEC-ICGKYKRMKY-KGI-ICEKCGVEVT 94 (1398) Q Consensus 67 ~d~~c-~Cg~~~~~~~-~g~-~C~~Cg~~~~ 94 (1398) +-|.| .||+..=-|. .|+ .|..||..++ T Consensus 35 ~kY~C~~CG~k~vKR~s~GIW~C~~Cg~~~A 65 (92) T TIGR00280 35 KKYVCPVCGKKAVKRESTGIWKCRKCGAKFA 65 (92) T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCEEC T ss_conf 1678888758973406653340267897522 No 147 >TIGR02909 spore_YkwD uncharacterized protein, YkwD family; InterPro: IPR014258 This entry represents a subgroup of the SCP-like extracellular domain which is found only in bacteria capable of endospore formation. Proteins in this entry include YkwD of Bacillus subtilis. This domain is generally found at the C-terminal region of these proteins, while the N-terminal region sometimes contains a domain homologous to the spore coat assembly protein SafA (IPR014248 from INTERPRO).. Probab=27.27 E-value=30 Score=12.33 Aligned_cols=55 Identities=29% Similarity=0.446 Sum_probs=29.5 Q ss_pred CHHHHHHHHHHHHHHHCC---CCCCCCCCEEEEHHHHH--HHH-HHHHCCCCCCCCCCCE--ECCHHHHHHHHHC Q ss_conf 999999999987675054---23788782044025899--999-9873367887446814--1799999999988 Q gi|254780142|r 475 SPEAQLEARVLMLSTNNL---LHPASGAPVTVPSQDMV--LGL-CYLSTVHEGDPGEGML--FADMGEVYHALEN 541 (1398) Q Consensus 475 s~eAraEa~~Lm~~~~ni---isP~~g~Pi~~~~QD~i--~G~-y~lT~~~~~~~~~~~~--f~~~~~~~~~~~~ 541 (1398) +--||.=|+-. .++|+ .||+.|.|= ||+ -|+ -|- ...||+.- ..+.+.|..|+++ T Consensus 31 ~~vARlKs~DM--~d~nYFsH~SPTYGSPF-----~Mmk~FGik~Y~-----W~AGENIA~G~~T~~~v~~awMN 93 (129) T TIGR02909 31 SKVARLKSEDM--IDKNYFSHTSPTYGSPF-----DMMKKFGIKSYR-----WAAGENIAAGNSTVEAVHQAWMN 93 (129) T ss_pred HHHHHHHHHHH--HCCCCCCCCCCCCCCCH-----HHHHHCCCCCCH-----HHHHHHHHHCCCCHHHHHHHHCC T ss_conf 88863746851--00789988888999716-----899864664310-----23235433048778899853058 No 148 >pfam10005 DUF2248 Uncharacterized protein conserved in bacteria (DUF2248). Members of this family of hypothetical bacterial proteins have no known function. Probab=27.13 E-value=30 Score=12.32 Aligned_cols=26 Identities=23% Similarity=0.788 Sum_probs=19.5 Q ss_pred CC-CCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 21-56641563448835675788530477 Q gi|254780142|r 70 EC-ICGKYKRMKYKGIICEKCGVEVTLSS 97 (1398) Q Consensus 70 ~c-~Cg~~~~~~~~g~~C~~Cg~~~~~~~ 97 (1398) .| .||- .+-|....|..||..+.-.| T Consensus 1 ~C~~Cg~--~vfFeN~~C~~Cg~~LGf~p 27 (340) T pfam10005 1 HCPNCGQ--PVFFENTACLACGAALGFDP 27 (340) T ss_pred CCCCCCC--CEEECCCCCCCCCCCCCCCC T ss_conf 9877899--02677875366895302476 No 149 >COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones] Probab=27.09 E-value=23 Score=13.11 Aligned_cols=79 Identities=19% Similarity=0.430 Sum_probs=35.8 Q ss_pred CCCHHHHHHCCEEEEECCCCCCCCCCCCCCCCCC-----CCCCCCCCCCCCCCCCCC---CCC-----CC-----CC--- Q ss_conf 5886788501448971755425456875688733-----621368566772156641---563-----44-----88--- Q gi|254780142|r 25 IASPAKIASLSYGEIKKPETINYRTFKPERDGLF-----CARIFGPIKDYECICGKY---KRM-----KY-----KG--- 83 (1398) Q Consensus 25 l~spe~I~~~S~~ev~~~et~n~~~~kP~~~Gl~-----d~ri~g~~~d~~c~Cg~~---~~~-----~~-----~g--- 83 (1398) .++|+|-+-.-...-+.|-|=.|-.. .+.|++ ++-+|.+...|+--||=. +-+ .+ -| T Consensus 12 ~Lt~~qy~Vtq~~gTE~pft~~y~~~--~~~GiY~c~~cg~pLF~S~~KfdSgcGWPSF~~pi~~~~I~~~~D~S~gM~R 89 (140) T COG0229 12 KLTPEQYRVTQNHGTERPFTGEYLDN--KEKGIYVCIVCGEPLFSSEDKFDSGCGWPSFTKPISPDAITYKEDRSHGMVR 89 (140) T ss_pred HCCHHHHHHHHHCCCCCCCCCHHHCC--CCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCEE T ss_conf 55999999998458879987700126--6885698614797043545423479998453555781511674135788488 Q ss_pred --CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEE Q ss_conf --35675788530477578767720027762201 Q gi|254780142|r 84 --IICEKCGVEVTLSSVRRDRMAHIDLASPVAHP 115 (1398) Q Consensus 84 --~~C~~Cg~~~~~~~~r~ghfGhIeLa~PV~Hi 115 (1398) ..|.+|+ +|.||+-=--|--.- T Consensus 90 tEVrc~~c~----------sHLGHVF~DGP~~tg 113 (140) T COG0229 90 TEVRCANCD----------SHLGHVFPDGPPPTG 113 (140) T ss_pred EEEEECCCC----------CCCCCCCCCCCCCCC T ss_conf 899844888----------734644589998989 No 150 >KOG2873 consensus Probab=27.01 E-value=29 Score=12.35 Aligned_cols=14 Identities=21% Similarity=0.266 Sum_probs=5.3 Q ss_pred HHHHHHHHHHHHHH Q ss_conf 69999999888874 Q gi|254780142|r 296 NEKRMLQESVDALF 309 (1398) Q Consensus 296 ~~~~lLQ~~v~~~~ 309 (1398) +-|.|-+.+-.++| T Consensus 196 ~mk~l~~qf~gaif 209 (284) T KOG2873 196 YMKDLERQFYGAIF 209 (284) T ss_pred HHHHHHHHHHHHHH T ss_conf 99999999988898 No 151 >COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription] Probab=26.93 E-value=26 Score=12.81 Aligned_cols=28 Identities=32% Similarity=0.876 Sum_probs=17.8 Q ss_pred CCCCC-CCCCCCC--CCCCCCCCCCCCCCCC Q ss_conf 67721-5664156--3448835675788530 Q gi|254780142|r 67 KDYEC-ICGKYKR--MKYKGIICEKCGVEVT 94 (1398) Q Consensus 67 ~d~~c-~Cg~~~~--~~~~g~~C~~Cg~~~~ 94 (1398) ..|.| .||+--. +.+.+..|..||-.+. T Consensus 5 ~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~rIl 35 (49) T COG1996 5 MEYKCARCGREVELDQETRGIRCPYCGSRIL 35 (49) T ss_pred EEEEHHHCCCEEEHHHCCCCEECCCCCCEEE T ss_conf 8999345588500010357445798885799 No 152 >PRK11788 hypothetical protein; Provisional Probab=26.72 E-value=30 Score=12.26 Aligned_cols=24 Identities=8% Similarity=0.073 Sum_probs=10.8 Q ss_pred HHHHHHHHCCHHHHHHHHHHHHHHHHH Q ss_conf 999999980817899987558899999 Q gi|254780142|r 604 MVDTIYRHCGQKSTVAFCDDLMRLGFR 630 (1398) Q Consensus 604 li~~i~~~~G~~~~~~~l~~~~~l~~~ 630 (1398) ....+.++| ..+.++|+...+... T Consensus 109 a~~ELa~Dy---~~aGllDRAE~~f~~ 132 (389) T PRK11788 109 ALQELGQDY---LKAGLLDRAEELFLQ 132 (389) T ss_pred HHHHHHHHH---HHCCCHHHHHHHHHH T ss_conf 999999999---867749999999999 No 153 >pfam10083 DUF2321 Uncharacterized protein conserved in bacteria (DUF2321). Members of this family of hypothetical bacterial proteins have no known function. Probab=26.68 E-value=23 Score=13.17 Aligned_cols=42 Identities=24% Similarity=0.228 Sum_probs=17.9 Q ss_pred CCCCCCCC-CCCCCCC----CCCCCCCCCCCCCEEECHHHHHHHHHHHHHCC Q ss_conf 56757885-3047757----87677200277622013012257899998099 Q gi|254780142|r 85 ICEKCGVE-VTLSSVR----RDRMAHIDLASPVAHPWFLKSLPSRISTLLGM 131 (1398) Q Consensus 85 ~C~~Cg~~-~~~~~~r----~ghfGhIeLa~PV~Hi~f~k~~~~~i~~~l~~ 131 (1398) +|+.||.+ ++.||.| ||++ |. --|+-+|+-...|++ |.-||+ T Consensus 30 fC~kCG~~TI~~Cp~C~t~IrG~y-~v---~GV~~lg~~y~~Psy-C~nCG~ 76 (158) T pfam10083 30 FCSKCGAATITSCPHCSTPIRGFY-YV---DGVLGLGSDYDAPSY-CHNCGK 76 (158) T ss_pred HHHHHHHHHHHHCCCCCCCCCCCC-CC---CCEEECCCCCCCCHH-HHHCCC T ss_conf 998766899975868999867750-26---873644888999546-874799 No 154 >TIGR00873 gnd 6-phosphogluconate dehydrogenase, decarboxylating; InterPro: IPR006113 6-Phosphogluconate dehydrogenase (1.1.1.44 from EC) (6PGD) is an oxidative carboxylase that catalyses the decarboxylating reduction of 6-phosphogluconate into ribulose 5-phosphate in the presence of NADP. This reaction is a component of the hexose mono-phosphate shunt and pentose phosphate pathways (PPP) , . Prokaryotic and eukaryotic 6PGD are proteins of about 470 amino acids whose sequence are highly conserved . The protein is a homodimer in which the monomers act independently : each contains a large, mainly alpha-helical domain and a smaller beta-alpha-beta domain, containing a mixed parallel and anti-parallel 6-stranded beta sheet . NADP is bound in a cleft in the small domain, the substrate binding in an adjacent pocket . This model does not specify whether the cofactor is NADP only, NAD only, or both.; GO: 0004616 phosphogluconate dehydrogenase (decarboxylating) activity, 0050661 NADP binding, 0006098 pentose-phosphate shunt. Probab=26.67 E-value=30 Score=12.26 Aligned_cols=28 Identities=14% Similarity=0.191 Sum_probs=17.6 Q ss_pred HHHHHHCCCEECCCCCCEEEECCCCCCC Q ss_conf 9997452855236653221550730565 Q gi|254780142|r 1327 LTEAAIAGKVDTLDGFKENVIVGRSIPA 1354 (1398) Q Consensus 1327 L~eAAi~ge~D~L~GvSENIIlGqliP~ 1354 (1398) +.++.-..+.++=+=|++.|=+|=++|+ T Consensus 398 F~~~l~~~~~gwR~vv~~A~~~GIP~Pa 425 (480) T TIGR00873 398 FKDALKDAQSGWRRVVAKAIELGIPVPA 425 (480) T ss_pred HHHHHHHHCCCHHHHHHHHHHHCCCHHH T ss_conf 9999986215188999999853023578 No 155 >TIGR00830 PTBA PTS system, glucose subfamily, IIA component; InterPro: IPR001127 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) , is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC . These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose , , , . ; GO: 0005351 sugar:hydrogen ion symporter activity, 0006810 transport, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016020 membrane. Probab=26.25 E-value=31 Score=12.20 Aligned_cols=64 Identities=28% Similarity=0.479 Sum_probs=37.6 Q ss_pred HHCCCCCCEECCCCC--EEEEEEECCCCEEEEEEECCCCCCEEEEE----E-CCCCE--------EEEECCCEEECCCEE Q ss_conf 525111101113478--67863312794499998368984026898----1-38965--------898419877408646 Q gi|254780142|r 1141 ARRPKNHAILAEISG--TIRIKRNYKNKSRVVIEPFEDGVEPAEYF----I-PKNKH--------FYLQDGDHVEKGDYI 1205 (1398) Q Consensus 1141 ar~pk~~aiisei~G--iv~i~~~~~~k~~~vi~~~~~g~~~~e~~----i-p~~~~--------l~v~dgd~V~~gd~l 1205 (1398) |-+|.+..+.|..+| ++. ..++.++-+.++. ++|.+.--+. | ..++. ..+.+|++|.+||.| T Consensus 30 AI~P~~g~v~AP~dGGv~i~--~~F~T~HA~gi~s-~~G~EiLiH~GIDTV~L~G~GPGELEvF~~~v~~G~~V~~Gd~l 106 (129) T TIGR00830 30 AILPTDGEVVAPVDGGVKIT--KIFPTKHAIGIES-DSGVEILIHIGIDTVKLNGEGPGELEVFTSHVEEGDKVKKGDPL 106 (129) T ss_pred EEECCCCCEECCCCCCEEEE--EECCCCCEEEEEE-CCCEEEEEECCCCEEEECCCCCCEEEEEEEEEEECCEECCCCEE T ss_conf 87408981782421652898--9738984799982-89839999824235887874896131247876438787179779 Q ss_pred EC Q ss_conf 43 Q gi|254780142|r 1206 LD 1207 (1398) Q Consensus 1206 t~ 1207 (1398) -+ T Consensus 107 ~e 108 (129) T TIGR00830 107 LE 108 (129) T ss_pred EE T ss_conf 99 No 156 >TIGR02679 TIGR02679 conserved hypothetical protein TIGR02679; InterPro: IPR013495 Proteins in this entry are encoded within a conserved gene four-gene neighbourhood found sporadically in a phylogenetically broad range of bacteria including: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria). . Probab=26.06 E-value=26 Score=12.77 Aligned_cols=22 Identities=14% Similarity=0.197 Sum_probs=8.3 Q ss_pred EEECCCCCCCCCCCCEEEECCC Q ss_conf 0003465100457740341255 Q gi|254780142|r 340 FRTNLLGKRVDYSGRSVIVAGP 361 (1398) Q Consensus 340 fR~nl~GKRVdfs~RsVI~pdP 361 (1398) +=+-+.|.+-+-..|-|+..|- T Consensus 115 ~~~r~~~~~~e~a~~ll~~vg~ 136 (431) T TIGR02679 115 LVRRLYGADTEAAAALLRDVGA 136 (431) T ss_pred HHHHHHCCCHHHHHHHHHHHHH T ss_conf 9999844798899999999999 No 157 >COG3809 Uncharacterized protein conserved in bacteria [Function unknown] Probab=25.94 E-value=31 Score=12.18 Aligned_cols=16 Identities=25% Similarity=0.349 Sum_probs=10.4 Q ss_pred CCCCCCCCCCCCCCCC Q ss_conf 7578853047757876 Q gi|254780142|r 87 EKCGVEVTLSSVRRDR 102 (1398) Q Consensus 87 ~~Cg~~~~~~~~r~gh 102 (1398) ++-|+|+--||-|||- T Consensus 15 ~rs~vEiD~CPrCrGV 30 (88) T COG3809 15 VRSGVEIDYCPRCRGV 30 (88) T ss_pred EECCCEEEECCCCCCE T ss_conf 3238324307765617 No 158 >COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion] Probab=25.71 E-value=28 Score=12.49 Aligned_cols=41 Identities=24% Similarity=0.354 Sum_probs=33.7 Q ss_pred CCCCEEECCCCCCCCCCCCEEEECCCCCCCCCEECHHHHHH Q ss_conf 37820003465100457740341255435462003489877 Q gi|254780142|r 336 KQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMAL 376 (1398) Q Consensus 336 K~GrfR~nl~GKRVdfs~RsVI~pdP~l~~~evgvP~~~A~ 376 (1398) +-+|||.|.---|-.+++===+-|-.-+.+.|.|+|..+-. T Consensus 79 ~~~RfRvN~f~qr~~~a~vlR~Ip~~i~~~e~LglP~i~~~ 119 (353) T COG2805 79 GVARFRVNAFKQRGGYALVLRLIPSKIPTLEELGLPPIVRE 119 (353) T ss_pred CCCEEEEEHHHHCCCCEEEEECCCCCCCCHHHCCCCHHHHH T ss_conf 75168864555468837997616766899878199779999 No 159 >PRK05473 hypothetical protein; Provisional Probab=25.54 E-value=32 Score=12.11 Aligned_cols=25 Identities=28% Similarity=0.367 Sum_probs=13.5 Q ss_pred EEECCCCCCCCCCCCCCHHHHHHHHH Q ss_conf 89418864545664106999999999 Q gi|254780142|r 1260 EITDPADTEYILGDNVDRIEVEELNR 1285 (1398) Q Consensus 1260 ~I~~~Gdt~~i~g~~Inr~~~~~~Nr 1285 (1398) +|+ +||..+||+|-=.|.-.+.+.| T Consensus 45 Yll-SGDPaYItsh~~AR~lIrk~eR 69 (86) T PRK05473 45 YLL-SGDPAYIPRHNDARNLIRKLER 69 (86) T ss_pred HHC-CCCCCCCCCCCCHHHHHHHHHH T ss_conf 512-4897631674029999999868 No 160 >COG1039 RnhC Ribonuclease HIII [DNA replication, recombination, and repair] Probab=25.53 E-value=18 Score=14.01 Aligned_cols=48 Identities=15% Similarity=0.227 Sum_probs=28.8 Q ss_pred EEECCCCCCCCCCCCEEEECCCCCCCCCEEC-----HHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 0003465100457740341255435462003-----48987761289999999987986 Q gi|254780142|r 340 FRTNLLGKRVDYSGRSVIVAGPELQLHQCGL-----PKLMALELFKPFLYAQLEKKGYV 393 (1398) Q Consensus 340 fR~nl~GKRVdfs~RsVI~pdP~l~~~evgv-----P~~~A~~L~~P~~~~~L~~~g~~ 393 (1398) .-+-++-++++.+++.+| ..||+|. |..++--...|+++..|.+.|.. T Consensus 69 ~~~~~~~~~~~~~~~~~I------GsDEvG~GDyFGpl~v~av~v~~e~~~~L~~lgV~ 121 (297) T COG1039 69 IAQTVLEANVNQDAKNLI------GSDEVGKGDYFGPLVVCAVYVSKENLPKLKELGVK 121 (297) T ss_pred HHHHHHHHHHHHCCCCCC------CCCCCCCCCCCCCCEEEEEECCHHHHHHHHHCCCC T ss_conf 653310444431146314------77787888755771689997389997999863985 No 161 >pfam06135 DUF965 Bacterial protein of unknown function (DUF965). This family consists of several hypothetical bacterial proteins. The function of the family is unknown. Probab=25.50 E-value=32 Score=12.11 Aligned_cols=47 Identities=23% Similarity=0.358 Sum_probs=23.4 Q ss_pred HHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHHHHH Q ss_conf 9999999999809700612560124762861489418864545664106999999999 Q gi|254780142|r 1228 LINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNR 1285 (1398) Q Consensus 1228 Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~~Nr 1285 (1398) ++..|...++.-|= | -+-=|| |+|+ +||..+||+|-=.|.-.+.+.| T Consensus 20 iL~~Vy~AL~EKGY--N--PiNQiV------GYll-SgDPtYItsh~nAR~lIrkiER 66 (79) T pfam06135 20 ILTTVYQALEEKGY--N--PINQIV------GYLL-SGDPAYITRHNDARNLIRKIER 66 (79) T ss_pred HHHHHHHHHHHCCC--C--HHHHHH------HHHC-CCCCCCCCCCCCHHHHHHHHHH T ss_conf 99999999998589--8--087788------4412-4897752775259999999858 No 162 >TIGR01018 rpsD_arch ribosomal protein S4; InterPro: IPR005710 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . The S4 domain is a small domain consisting of 60-65 amino acid residues that probably mediates binding to RNA. This model finds eukaryotic ribosomal protein S9 as well as eukaryotic and archaeal ribosomal protein S4.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit. Probab=25.43 E-value=32 Score=12.12 Aligned_cols=16 Identities=38% Similarity=0.353 Sum_probs=9.1 Q ss_pred CHHHEEEEE--EECCCCC Q ss_conf 842411200--1000024 Q gi|254780142|r 730 SIHQMRQLG--GMRGLIA 745 (1398) Q Consensus 730 S~~qi~ql~--Gqq~l~g 745 (1398) |+-|-+||+ |-..|.| T Consensus 126 Ti~~ARqLi~hGHI~v~G 143 (170) T TIGR01018 126 TIKQARQLIVHGHIAVDG 143 (170) T ss_pred CHHHCCEEEEECEEEECC T ss_conf 632343023203388768 No 163 >PRK11230 glycolate oxidase subunit GlcD; Provisional Probab=25.39 E-value=28 Score=12.56 Aligned_cols=10 Identities=30% Similarity=0.574 Sum_probs=4.3 Q ss_pred CCCCCCCCCH Q ss_conf 7305655354 Q gi|254780142|r 1349 GRSIPAGTGA 1358 (1398) Q Consensus 1349 GqliP~GTG~ 1358 (1398) ||++|-|-+. T Consensus 469 GKviP~~~~~ 478 (499) T PRK11230 469 GKNIPTLHRC 478 (499) T ss_pred CCCCCCCCCC T ss_conf 9356997742 No 164 >KOG0396 consensus Probab=25.30 E-value=28 Score=12.53 Aligned_cols=14 Identities=14% Similarity=0.145 Sum_probs=10.2 Q ss_pred CCCCCCCCEEECHH Q ss_conf 20027762201301 Q gi|254780142|r 105 HIDLASPVAHPWFL 118 (1398) Q Consensus 105 hIeLa~PV~Hi~f~ 118 (1398) |.+|.-+.|||.|. T Consensus 4 ~l~l~y~l~ripye 17 (389) T KOG0396 4 HLKLEYQLFRIPYE 17 (389) T ss_pred HHHHHCHHHCCCHH T ss_conf 46441204127799 No 165 >pfam00358 PTS_EIIA_1 phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1. Probab=24.97 E-value=32 Score=12.04 Aligned_cols=59 Identities=31% Similarity=0.523 Sum_probs=32.4 Q ss_pred CCCCCCEECCCCCEEEEEEECCCCEEEEEEECCCCCCEEEEEEC----------CCCEEEEECCCEEECCCEEEC Q ss_conf 51111011134786786331279449999836898402689813----------896589841987740864643 Q gi|254780142|r 1143 RPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIP----------KNKHFYLQDGDHVEKGDYILD 1207 (1398) Q Consensus 1143 ~pk~~aiisei~Giv~i~~~~~~k~~~vi~~~~~g~~~~e~~ip----------~~~~l~v~dgd~V~~gd~lt~ 1207 (1398) .|.+..+.|.++|.+.... ..+.-+.+.. .+|.+ .+++ .+=...+.+|+.|.+|+.|.+ T Consensus 37 ~P~~~~v~AP~~G~V~~v~--~T~HAigi~~-~~G~e---iLiHiGiDTV~L~G~gF~~~v~~Gd~V~~G~~L~~ 105 (133) T pfam00358 37 KPSDGKVVAPVDGTIVQIF--PTKHAIGIES-DGGVE---ILIHVGIDTVKLNGEGFESHVEEGDRVKQGDKLLE 105 (133) T ss_pred ECCCCEEEECCCEEEEEEC--CCCCEEEEEE-CCCCE---EEEEECCCCEECCCCCEEEEECCCCEECCCCEEEE T ss_conf 8479979907897999986--8997999996-89989---99998645223389631899758999989999999 No 166 >COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only] Probab=24.86 E-value=19 Score=13.79 Aligned_cols=19 Identities=26% Similarity=0.120 Sum_probs=9.1 Q ss_pred CCEEEEHHHHHHHHHHHHC Q ss_conf 8204402589999998733 Q gi|254780142|r 499 APVTVPSQDMVLGLCYLST 517 (1398) Q Consensus 499 ~Pi~~~~QD~i~G~y~lT~ 517 (1398) +++...--|-.+|-|++|. T Consensus 230 ~ivaNyGLdP~LGKY~~TA 248 (403) T COG1379 230 KIVANYGLDPRLGKYHLTA 248 (403) T ss_pred EEEEECCCCCCCCCHHHHH T ss_conf 1787337671113064788 No 167 >TIGR01832 kduD 2-deoxy-D-gluconate 3-dehydrogenase; InterPro: IPR011286 This entry describes 2-deoxy-D-gluconate 3-dehydrogenase (also called 2-keto-3-deoxygluconate oxidoreductase), a member of the family of short-chain-alcohol dehydrogenases (IPR002198 from INTERPRO). This protein has been characterised in Erwinia chrysanthemi as an enzyme of pectin degradation .; GO: 0008678 2-deoxy-D-gluconate 3-dehydrogenase activity, 0051287 NAD binding. Probab=24.68 E-value=28 Score=12.53 Aligned_cols=87 Identities=15% Similarity=0.199 Sum_probs=41.7 Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHH-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEE Q ss_conf 1232683699999999978999999886-489766788878864234658999999999987611565432222468837 Q gi|254780142|r 642 DDIIVPESKEKIIAEADKMVKEYENQYN-DGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIF 720 (1398) Q Consensus 642 ~D~~~~~~k~~~i~~a~~~~~~~~~~~~-~G~~t~~e~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~N~~~ 720 (1398) -|+.-++..+.+++++.++...+.-..+ -|+|-.++-..--..-|.++.+-=.++++--.+. --. T Consensus 60 ~Dl~~~~~~~~~~~~~~~~~g~~DiLVNNAGIIrR~da~~f~e~dWd~V~nvNlk~vF~l~q~--------------~a~ 125 (249) T TIGR01832 60 ADLSDIEAIKALVDSAVEEFGKIDILVNNAGIIRREDAVEFSEKDWDDVMNVNLKSVFFLTQA--------------AAK 125 (249) T ss_pred HHHHCHHHHHHHHHHHHHHHCCCCEEEECCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHH--------------HHH T ss_conf 212232137899999998618865676074221045775156144579998668999999999--------------999 Q ss_pred EEECCCCCCCHHHEEEEEEECC Q ss_conf 6422555578424112001000 Q gi|254780142|r 721 MMSHSGARGSIHQMRQLGGMRG 742 (1398) Q Consensus 721 ~M~~SGAKGS~~qi~ql~Gqq~ 742 (1398) .|+..|..|.+.||..|+-.|| T Consensus 126 ~~l~~G~~GkiiNIAS~LSFQG 147 (249) T TIGR01832 126 QFLKQGRGGKIINIASLLSFQG 147 (249) T ss_pred HHHHCCCCCCEEEEHHHHHHCC T ss_conf 9996489950575142344226 No 168 >pfam10080 DUF2318 Predicted membrane protein (DUF2318). Members of this family of hypothetical bacterial proteins have no known function. Probab=24.58 E-value=22 Score=13.32 Aligned_cols=12 Identities=42% Similarity=1.082 Sum_probs=6.8 Q ss_pred CCCCCCCCCCCC Q ss_conf 835675788530 Q gi|254780142|r 83 GIICEKCGVEVT 94 (1398) Q Consensus 83 g~~C~~Cg~~~~ 94 (1398) ..+|..||+.+. T Consensus 52 ~~vC~~C~~~~~ 63 (102) T pfam10080 52 KLICKNCGVRFF 63 (102) T ss_pred EEEEECCCCEEE T ss_conf 998852896975 No 169 >TIGR02013 rpoB DNA-directed RNA polymerase, beta subunit; InterPro: IPR010243 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This entry describes orthologues of the beta subunit of bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription. Probab=24.33 E-value=33 Score=11.96 Aligned_cols=22 Identities=18% Similarity=0.380 Sum_probs=15.8 Q ss_pred CCHHCCCCCCCCEEECCEEEEE Q ss_conf 1000013567855322507862 Q gi|254780142|r 994 MYGAKLFVDDGGVIECGQRISE 1015 (1398) Q Consensus 994 ~~~~~~~v~~~~~v~~~~ii~~ 1015 (1398) .+.+.=.|..||.|..++|++| T Consensus 847 C~nQ~PiV~~GDrV~~GdvlAD 868 (1449) T TIGR02013 847 CINQRPIVSVGDRVEAGDVLAD 868 (1449) T ss_pred EECCEEECCCCCEECCCCEEEC T ss_conf 0145355014868102127734 No 170 >COG5469 Predicted metal-binding protein [Function unknown] Probab=24.13 E-value=34 Score=11.93 Aligned_cols=12 Identities=8% Similarity=0.196 Sum_probs=5.6 Q ss_pred HHHHCCCCCCEE Q ss_conf 666348985112 Q gi|254780142|r 228 SFITSGNNPGWM 239 (1398) Q Consensus 228 ~f~~~~~~Pewm 239 (1398) |+.+-..|||-+ T Consensus 115 G~~pw~~rPe~L 126 (143) T COG5469 115 GLVPWRKRPEPL 126 (143) T ss_pred CCCCCCCCCHHH T ss_conf 755424298667 No 171 >TIGR03073 release_rtcB release factor H-coupled RctB family protein. Members of this family are related to RctB. RctB a protein of known structure but unknown function that often is encoded near RNA cyclase and therefore is suggested to be a tRNA or mRNA processing enzyme. This family of RctB-like proteins in encoded upstream of, and apparently is translationally coupled to, the putative peptide chain release factor RF-H (TIGR03072), product of the prfH gene. Note that a large deletion at the junction between this gene and the prfH gene in Escherichia coli K-12 marks both as probable pseudogenes. Probab=24.13 E-value=34 Score=11.93 Aligned_cols=15 Identities=33% Similarity=0.773 Sum_probs=12.8 Q ss_pred CCCEEEEECCCCCCC Q ss_conf 688376422555578 Q gi|254780142|r 716 MNSIFMMSHSGARGS 730 (1398) Q Consensus 716 ~N~~~~M~~SGAKGS 730 (1398) .+.+++|+.|||||= T Consensus 149 ~~~v~l~iHsGSRgl 163 (356) T TIGR03073 149 AKQLLLLVHSGSRGL 163 (356) T ss_pred CCEEEEEEECCCCCC T ss_conf 770899996377643 No 172 >COG1965 CyaY Protein implicated in iron transport, frataxin homolog [Inorganic ion transport and metabolism] Probab=23.99 E-value=34 Score=11.91 Aligned_cols=11 Identities=27% Similarity=0.450 Sum_probs=4.6 Q ss_pred CCCEEEEEEEC Q ss_conf 79449999836 Q gi|254780142|r 1164 KNKSRVVIEPF 1174 (1398) Q Consensus 1164 ~~k~~~vi~~~ 1174 (1398) .++..+||... T Consensus 44 ~ngs~iiINkQ 54 (106) T COG1965 44 DNGSQIIINKQ 54 (106) T ss_pred CCCCEEEEECC T ss_conf 89858999279 No 173 >pfam12151 MVL Mannan-binding protein. This domain family is found in bacteria, and is approximately 40 amino acids in length, There is a single completely conserved residue G that may be functionally important. The domain occurs in two types of proteins. In mannan binding proteins, it forms a homodimeric molecule which complexes into a homo-octamer. In thiamidases it occurs without repeats but in the presence of other domains. MVL is distinct amongst other oligomannoside binding proteins in that it exhibits specificity for certain tetrasaccharides. Each molecule of MVL has four distinct carbohydrate binding sites. Probab=23.85 E-value=21 Score=13.40 Aligned_cols=15 Identities=33% Similarity=0.835 Sum_probs=10.8 Q ss_pred ECCCCCCCCCCCCCC Q ss_conf 312254546787754 Q gi|254780142|r 452 HPLVCAGYNADFDGD 466 (1398) Q Consensus 452 n~~vc~pyNADFDGD 466 (1398) =|.+|..+.+||||- T Consensus 8 cp~~c~~~gg~W~GQ 22 (37) T pfam12151 8 CPSFCAALGGDWNGQ 22 (37) T ss_pred CCHHHHHHCCCCCCE T ss_conf 506789748954661 No 174 >TIGR01020 rpsE_arch ribosomal protein S5; InterPro: IPR005711 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . This model finds eukaryotic ribosomal protein S2 as well as archaeal ribosomal protein S5.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit. Probab=23.69 E-value=28 Score=12.47 Aligned_cols=11 Identities=27% Similarity=0.812 Sum_probs=6.2 Q ss_pred HHHHHHHCHHH Q ss_conf 99987527999 Q gi|254780142|r 1213 QDILRIKGVEA 1223 (1398) Q Consensus 1213 ~eIl~vlGIEA 1223 (1398) ..||++=||+= T Consensus 168 K~~L~LAGI~D 178 (220) T TIGR01020 168 KKVLRLAGIKD 178 (220) T ss_pred HHHHHHCCCCE T ss_conf 68877459623 No 175 >KOG0680 consensus Probab=23.66 E-value=34 Score=11.86 Aligned_cols=72 Identities=19% Similarity=0.186 Sum_probs=37.8 Q ss_pred CCCCCCEECHHHHHHHHH-HHHHHHHHHHC-----CCCCCCCC----CCCEEECCCCCEEHHHHHHHCCCEEEECCCCCC Q ss_conf 435462003489877612-89999999987-----98666300----010012248825013266656978997576310 Q gi|254780142|r 362 ELQLHQCGLPKLMALELF-KPFLYAQLEKK-----GYVSTVKQ----AKKFVEKERPEVWDVLAEVVHQHVVLLNRAPSL 431 (1398) Q Consensus 362 ~l~~~evgvP~~~A~~L~-~P~~~~~L~~~-----g~~~~i~~----~k~~i~~~~~~v~~v~rhl~~gd~Vl~NRqPsL 431 (1398) .+.+.|+|||+.++--|. .||+++.+-.. |...+... .++-++...|.-|+|-- ...+|++.|- - T Consensus 290 di~I~q~GIpEAV~esl~~~Pe~~~p~l~~NIv~iGGn~~fPgF~~RL~~Elr~l~P~d~~v~V-~~p~dp~~~~----W 364 (400) T KOG0680 290 DIGIQQPGIPEAVLESLSMLPEEVRPLLLENIVCIGGNSNFPGFRQRLARELRSLLPADWEVSV-SVPEDPITFA----W 364 (400) T ss_pred HCCCCCCCCHHHHHHHHHHCHHHHHHHHHHCEEEECCCCCCCCHHHHHHHHHHHHCCCCCEEEE-ECCCCCCEEE----E T ss_conf 4385647916999999986979778998746899347667864689999999853886524788-5489862444----0 Q ss_pred EECCEEE Q ss_conf 1114012 Q gi|254780142|r 432 HRLSMQA 438 (1398) Q Consensus 432 Hr~Sima 438 (1398) |.+|-+| T Consensus 365 ~~g~~~~ 371 (400) T KOG0680 365 EGGSEFA 371 (400) T ss_pred HHCCCCC T ss_conf 0002146 No 176 >pfam01939 DUF91 Protein of unknown function DUF91. The function of this prokaryotic protein is unknown. Probab=23.65 E-value=28 Score=12.47 Aligned_cols=11 Identities=0% Similarity=0.021 Sum_probs=4.4 Q ss_pred CHHHHHHHHHH Q ss_conf 61256012476 Q gi|254780142|r 1244 NHKHIEVVVRH 1254 (1398) Q Consensus 1244 N~RHIeLIaD~ 1254 (1398) -++-..|+.|. T Consensus 193 t~~Ar~Ll~d~ 203 (228) T pfam01939 193 TEGAKKLLEEE 203 (228) T ss_pred CHHHHHHHHHC T ss_conf 98899999975 No 177 >COG0238 RpsR Ribosomal protein S18 [Translation, ribosomal structure and biogenesis] Probab=23.56 E-value=33 Score=12.01 Aligned_cols=27 Identities=22% Similarity=0.272 Sum_probs=21.3 Q ss_pred EECHHHHHHHHHHHCCEEEEECCCCCC Q ss_conf 006125601247628614894188645 Q gi|254780142|r 1242 AINHKHIEVVVRHMLQKVEITDPADTE 1268 (1398) Q Consensus 1242 ~IN~RHIeLIaD~MT~kg~I~~~Gdt~ 1268 (1398) .|||+-+++|-+.-|-+|.|.+...|. T Consensus 27 ~iDYKd~~~Lkrfise~GKI~prRiTG 53 (75) T COG0238 27 EIDYKDVELLKRFISERGKILPRRITG 53 (75) T ss_pred CCCCCCHHHHHHHHCCCCCCCCCCCCC T ss_conf 467248999999856267656541235 No 178 >cd00210 PTS_IIA_glc PTS_IIA, PTS system, glucose/sucrose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. Probab=23.45 E-value=35 Score=11.84 Aligned_cols=60 Identities=28% Similarity=0.478 Sum_probs=33.8 Q ss_pred HCCCCCCEECCCCCEEEEEEECCCCEEEEEEECCCCCCEEEEEEC----------CCCEEEEECCCEEECCCEEEC Q ss_conf 251111011134786786331279449999836898402689813----------896589841987740864643 Q gi|254780142|r 1142 RRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIP----------KNKHFYLQDGDHVEKGDYILD 1207 (1398) Q Consensus 1142 r~pk~~aiisei~Giv~i~~~~~~k~~~vi~~~~~g~~~~e~~ip----------~~~~l~v~dgd~V~~gd~lt~ 1207 (1398) -.|.+..+.|.++|.+.... ..+..+.+.. .+|.+ .++. .+=...+.+|+.|.+|+.|.+ T Consensus 31 I~P~~~~v~AP~~G~V~~v~--~T~HAigi~t-~~G~e---vLiHiGiDTV~L~G~gF~~~v~~Gd~V~~G~~L~~ 100 (124) T cd00210 31 IKPSDGKVVAPVDGTIVQIF--PTKHAIGIES-DSGVE---ILIHIGIDTVKLNGEGFTSHVEEGQRVKQGDKLLE 100 (124) T ss_pred EECCCCEEECCCCEEEEEEC--CCCCEEEEEE-CCCCE---EEEEEEECCCCCCCCCEEEEECCCCEECCCCEEEE T ss_conf 98479989907897999986--7896999996-89989---99997304201489531899748899989999999 No 179 >PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional Probab=23.41 E-value=35 Score=11.83 Aligned_cols=11 Identities=36% Similarity=0.649 Sum_probs=5.3 Q ss_pred CCCEECHHHHH Q ss_conf 46200348987 Q gi|254780142|r 365 LHQCGLPKLMA 375 (1398) Q Consensus 365 ~~evgvP~~~A 375 (1398) .+|.|+=..++ T Consensus 181 ~hE~glRiLl~ 191 (376) T PRK04338 181 YHEMGLRILIG 191 (376) T ss_pred HHHHHHHHHHH T ss_conf 57788999999 No 180 >TIGR00655 PurU formyltetrahydrofolate deformylase; InterPro: IPR004810 An Escherichia coli gene designated purU has been identified and characterised. The gene codes for a 280-amino-acid protein, PurU (P37051 from SWISSPROT, 3.5.1.10 from EC). PurU is an enzyme that catalyses the hydrolysis of 10-formyltetrahydrofolate (formyl-FH4) to FH4 and formate ,.10-formyltetrahydrofolate + H(2)O = formate +tetrahydrofolate Formyl-FH4 hydrolase generates the formate that is used by purT-encoded 5'-phosphoribosylglycinamide transformylase for step three of de novo purine nucleotide synthesis. Formyl-FH4 hydrolase, a hexamer of 32kDa subunits, is activated by methionine and inhibited by glycine. Heterotropic cooperativity is observed for activation by methionine in the presence of glycine and for inhibition by glycine in the presence of methionine. These results suggest that formyl-FH4 hydrolase is a regulatory enzyme whose main function is to balance the pools of FH4 and C1-FH4 in response to changing growth conditions. The enzyme uses methionine and glycine to sense the pools of C1-FH4 and FH4, respectively. ; GO: 0008864 formyltetrahydrofolate deformylase activity, 0006189 'de novo' IMP biosynthetic process. Probab=23.40 E-value=18 Score=14.04 Aligned_cols=28 Identities=14% Similarity=0.172 Sum_probs=15.6 Q ss_pred HHHHHHHHCCEEEEECCCCCCCCCCCCCCHHH Q ss_conf 60124762861489418864545664106999 Q gi|254780142|r 1248 IEVVVRHMLQKVEITDPADTEYILGDNVDRIE 1279 (1398) Q Consensus 1248 IeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~ 1279 (1398) +=+||+|| +|.+|+....++...||.+. T Consensus 177 lvVLAkYM----qIL~p~Fv~~~pN~iINIHH 204 (294) T TIGR00655 177 LVVLAKYM----QILSPDFVKRYPNKIINIHH 204 (294) T ss_pred EEEEEHHC----CCCCHHHHHHCCCCEEECCC T ss_conf 69821010----21783577445793121123 No 181 >COG1149 MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Energy production and conversion] Probab=23.34 E-value=35 Score=11.82 Aligned_cols=17 Identities=29% Similarity=0.659 Sum_probs=8.3 Q ss_pred HHHHHHHHHCCCCCCEEEEEE Q ss_conf 788866663489851128630 Q gi|254780142|r 223 LKIVDSFITSGNNPGWMIIRK 243 (1398) Q Consensus 223 ~~~~~~f~~~~~~Pewmil~~ 243 (1398) +++++-| .-|-|.++-. T Consensus 207 ~el~~~f----~ip~~iViNr 223 (284) T COG1149 207 LELVEHF----GIPTGIVINR 223 (284) T ss_pred HHHHHHH----CCCEEEEEEC T ss_conf 9999983----9954999966 No 182 >PRK03754 DNA-directed RNA polymerase subunit P; Provisional Probab=23.20 E-value=31 Score=12.22 Aligned_cols=28 Identities=25% Similarity=0.833 Sum_probs=12.9 Q ss_pred CCC-CCCCCCCC---CCCCCCCCCCCCCCCCC Q ss_conf 721-56641563---44883567578853047 Q gi|254780142|r 69 YEC-ICGKYKRM---KYKGIICEKCGVEVTLS 96 (1398) Q Consensus 69 ~~c-~Cg~~~~~---~~~g~~C~~Cg~~~~~~ 96 (1398) |.| .|||--.. .-+...|.-||..+.-. T Consensus 6 yrcakcgkev~ldl~~~revrcpycgskilyk 37 (49) T PRK03754 6 YRCAKCGREVKLDLSTTRDLRCPYCGSKILYK 37 (49) T ss_pred HHHHHCCCEEEEEHHHHHHCCCCCCCCEEEEC T ss_conf 57765383036412323310377767754545 No 183 >TIGR00201 comF comF family protein; InterPro: IPR005222 Proteins in this family are found in bacterial species which posses systems for natural transformation with exogenous DNA (eg Bacillus subtilis, Haemophilus influenzae), and also species without these systems (eg Escherichia coli). Competence protein F has been shown to be important for the uptake of exogenous DNA in naturally competent bacteria, though the precise role of this protein is not yet known , . GntX is a periplasmic gluconate binding protein thought to be part of a high-affinity gluconate transport system .. Probab=22.81 E-value=35 Score=11.75 Aligned_cols=23 Identities=48% Similarity=1.084 Sum_probs=14.8 Q ss_pred C-CCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 1-566415634488356757885304 Q gi|254780142|r 71 C-ICGKYKRMKYKGIICEKCGVEVTL 95 (1398) Q Consensus 71 c-~Cg~~~~~~~~g~~C~~Cg~~~~~ 95 (1398) | .|||-- +....+|..||++.+. T Consensus 1 C~~C~k~~--~S~~a~C~~C~~~~t~ 24 (207) T TIGR00201 1 CSLCGKRI--KSSKALCDQCGSERTL 24 (207) T ss_pred CCCCCCCC--CCCCCCCCCCCCHHHH T ss_conf 98888873--0077624666624666 No 184 >PRK00564 hypA hydrogenase nickel incorporation protein; Provisional Probab=22.77 E-value=36 Score=11.74 Aligned_cols=10 Identities=10% Similarity=0.255 Sum_probs=4.9 Q ss_pred CCCEEEEEEE Q ss_conf 6405368984 Q gi|254780142|r 15 DRGFDSVRIS 24 (1398) Q Consensus 15 ~~~i~~i~f~ 24 (1398) -++|.+|... T Consensus 23 ~~~V~~v~l~ 32 (117) T PRK00564 23 AHKIERVVVG 32 (117) T ss_pred CCEEEEEEEE T ss_conf 9779999999 No 185 >PRK08329 threonine synthase; Validated Probab=22.73 E-value=36 Score=11.74 Aligned_cols=19 Identities=42% Similarity=1.298 Sum_probs=8.0 Q ss_pred CC-CCCC-CCCCCCCCCCCCCCCC Q ss_conf 21-5664-1563448835675788 Q gi|254780142|r 70 EC-ICGK-YKRMKYKGIICEKCGV 91 (1398) Q Consensus 70 ~c-~Cg~-~~~~~~~g~~C~~Cg~ 91 (1398) +| .||+ |.. .+ -..| .||. T Consensus 3 ~C~~CG~~y~~-~~-~~~C-~cg~ 23 (348) T PRK08329 3 RCTKCGRTYEE-KF-RLRC-TCGG 23 (348) T ss_pred CCCCCCCCCCC-CC-CEEC-CCCC T ss_conf 88878793699-99-7789-9999 No 186 >TIGR00699 GABAtrns_euk 4-aminobutyrate aminotransferase; InterPro: IPR004631 4-aminobutyrate aminotransferase eukaryotic (2.6.1.19 from EC) is a class III pyridoxal-phosphate-dependent aminotransferase. The enzyme catalyses the conversion of 4-aminobutanoate and 2-oxoglutarate into succinate semialdehyde and L-glutamate. The degree of sequence difference between this set and known bacterial examples is greater than the distance between either set the most similar enzyme with distinct function, and so the prokaryotic and eukaryotic sets have been placed into separate families. This family describes known eukaryotic examples of the enzyme. Alternate names include GABA transaminase, gamma-amino-N-butyrate transaminase, and beta-alanine--oxoglutarate aminotransferase.; GO: 0003867 4-aminobutyrate transaminase activity, 0009448 gamma-aminobutyric acid metabolic process. Probab=22.70 E-value=36 Score=11.73 Aligned_cols=209 Identities=27% Similarity=0.400 Sum_probs=108.7 Q ss_pred EEECCCCCCCHHHHHHHHHH----HHHHHH-HHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHH Q ss_conf 88469731310037899999----998699-9999873983567776999999988887427767877247876506789 Q gi|254780142|r 255 VALDFGRFAASDLNDLYRRV----IGRNNR-LMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHKRVVTGANRRPLKSL 329 (1398) Q Consensus 255 v~~~~g~~~~dDlt~~~~~I----i~~N~~-Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~~~~~~~~~~rp~ks~ 329 (1398) |-+||.. |=++|+.| |=-||- |-|+.+ .||. ..+||| +|.-| +=|-|.+ T Consensus 54 ~DvDGN~-----lLDlYsQIsSiPiGYNnP~L~K~a~--sPe~------------a~~Lin-----RPALG--nfp~~~l 107 (469) T TIGR00699 54 VDVDGNV-----LLDLYSQISSIPIGYNNPALLKAAQ--SPEM------------ATTLIN-----RPALG--NFPSKDL 107 (469) T ss_pred EEECCCH-----HHHHHHHHHHCCCCCCCHHHHHHHC--CHHH------------HHHHHC-----CCCCC--CCCHHHH T ss_conf 6314304-----7888877752122466878998651--7245------------788644-----73014--6766799 Q ss_pred HHHHCCCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCEECHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEECCCCC Q ss_conf 98610237820003465100457740341255435462003489877612899999999879866630001001224882 Q gi|254780142|r 330 SDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKERPE 409 (1398) Q Consensus 330 ~~rlkgK~GrfR~nl~GKRVdfs~RsVI~pdP~l~~~evgvP~~~A~~L~~P~~~~~L~~~g~~~~i~~~k~~i~~~~~~ 409 (1398) ..-+ |+|-+| .+=|-.|++-+..=-+||| +||-++- |...+-.++|.- -+.+-+.+ T Consensus 108 ~~~~--~~g~~k--~aPKg~~~v~~~~aG~dan----------e~AfK~a--f~yYr~~~RGGp-----~~~Fs~eE--- 163 (469) T TIGR00699 108 AKIL--KSGILK--VAPKGQDSVYRAMAGSDAN----------ELAFKAA--FMYYRSKQRGGP-----ERDFSEEE--- 163 (469) T ss_pred HHHH--CCCCHH--HCCCCCCCCCCCCCCCCHH----------HHHHHHH--HHHHHHCCCCCC-----CCCCCHHH--- T ss_conf 9985--488123--2452103011446664267----------8999999--999983589888-----75311788--- Q ss_pred EEHHHHHHHCCCEEEECCCCCCEECCEEEEEEEEECCCEEE---------EECCCCCCC---CCCCCCCEEEEECCCCH- Q ss_conf 50132666569789975763101114012358994495479---------731225454---67877545699746899- Q gi|254780142|r 410 VWDVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQ---------LHPLVCAGY---NADFDGDQMAVYAVISP- 476 (1398) Q Consensus 410 v~~v~rhl~~gd~Vl~NRqPsLHr~Simah~~~v~~~~t~r---------ln~~vc~py---NADFDGDEMnlHvPqs~- 476 (1398) + .-+|.|-+|===.+|||.|+.=- +||+|- +|=+--++| -|||= .+--|+-| T Consensus 164 -------~---~s~m~N~~PG~P~~siLSF~~aF-HGRlfGsLsTT~SKpiHKlD~PaF~WP~A~FP----~LkYPLeE~ 228 (469) T TIGR00699 164 -------N---ESCMVNQAPGSPDLSILSFKAAF-HGRLFGSLSTTRSKPIHKLDIPAFDWPQAPFP----SLKYPLEEH 228 (469) T ss_pred -------H---HHHHCCCCCCCCHHHHHHHCCCC-HHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC----CCCCCCHHH T ss_conf -------7---76431687558507888523431-03444420003477603178657774677787----667870232 Q ss_pred ---HHHHHHHHHHHHHHCCCCCCCCCC---EEE----EHH----------HHHHHHHHHHCCCCCCCCCCCEECCHHHHH Q ss_conf ---999999998767505423788782---044----025----------899999987336788744681417999999 Q gi|254780142|r 477 ---EAQLEARVLMLSTNNLLHPASGAP---VTV----PSQ----------DMVLGLCYLSTVHEGDPGEGMLFADMGEVY 536 (1398) Q Consensus 477 ---eAraEa~~Lm~~~~niisP~~g~P---i~~----~~Q----------D~i~G~y~lT~~~~~~~~~~~~f~~~~~~~ 536 (1398) .++=|.+-|--|..=|. +.-.| |.+ ||| |++=++.=.|++.. +.+-.+||+ T Consensus 229 ~~~N~~Ee~rCL~~vE~L~~--~~~~pkrtVaA~IvEPIQSEGGDNHAS~~Ff~KLr~i~~k~~-------v~FivDEVQ 299 (469) T TIGR00699 229 VEENAKEEQRCLEEVEDLIK--KWHKPKRTVAAIIVEPIQSEGGDNHASPDFFRKLRDITKKHN-------VAFIVDEVQ 299 (469) T ss_pred HHHHHHHHHHHHHHHHHHHH--HCCCCCCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHCC-------CEEEEEEEE T ss_conf 57545588899999999997--317986158888862434788853433788899999998859-------568996455 Q ss_pred H Q ss_conf 9 Q gi|254780142|r 537 H 537 (1398) Q Consensus 537 ~ 537 (1398) . T Consensus 300 T 300 (469) T TIGR00699 300 T 300 (469) T ss_pred E T ss_conf 0 No 187 >pfam07236 Phytoreo_S7 Phytoreovirus S7 protein. This family consists of several Phytoreovirus S7 proteins which are thought to be viral core proteins. Probab=22.56 E-value=36 Score=11.71 Aligned_cols=83 Identities=24% Similarity=0.304 Sum_probs=35.6 Q ss_pred HHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCEEECCCCCCC--CCCCCEEEECCCCCCC-CCEECHHHHH Q ss_conf 999998888742776787724787650678998610237820003465100--4577403412554354-6200348987 Q gi|254780142|r 299 RMLQESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRV--DYSGRSVIVAGPELQL-HQCGLPKLMA 375 (1398) Q Consensus 299 ~lLQ~~v~~~~dn~~~~~~~~~~~~rp~ks~~~rlkgK~GrfR~nl~GKRV--dfs~RsVI~pdP~l~~-~evgvP~~~A 375 (1398) |+|--||..|+ |...|+.+ -|-+++++|+.+-.=-.|.-.----| ||-.-+-|.-.|++++ |-||-|-.+| T Consensus 18 R~LnD~vk~fY-~~i~G~~~-----~~~~~it~k~~~~si~~rk~vP~~TviLD~kdE~fI~~Np~~SlmDI~gSpsNtA 91 (506) T pfam07236 18 RNLTDHVKAFY-NAIIGRFV-----SGPDTITEKLGMDSIILRKIVPTSTVILDFKDESFIRENPNASLMDICGSPSNTA 91 (506) T ss_pred HHHHHHHHHHH-HHHCCCCC-----CCCCCHHHHCCCCCEEEEEECCCCEEEEECCCHHHHHCCCCCHHHHHHCCCCCCC T ss_conf 44368899999-97328757-----8964243331567046787246515898426667775188741777627988878 Q ss_pred HHHHHHHHHHHH Q ss_conf 761289999999 Q gi|254780142|r 376 LELFKPFLYAQL 387 (1398) Q Consensus 376 ~~L~~P~~~~~L 387 (1398) .+-||--+|..| T Consensus 92 PKTtfqSiMPSL 103 (506) T pfam07236 92 PKTTFQSIMPSL 103 (506) T ss_pred CHHHHHHHHHHH T ss_conf 612587775779 No 188 >TIGR02283 MltB_2 lytic murein transglycosylase; InterPro: IPR011970 Proteins of this entries are closely related to the MltB family lytic murein transglycosylases described by IPR011757 from INTERPRO and are likewise all proteobacterial, although that family and this one form clearly distinct clades. Several species have one member of each family. Many proteins of this entry(unlike the MltB family) contain an additional C-terminal domain, a putative peptidoglycan binding domain (IPR002477 from INTERPRO), not included in region described by this model. Many sequences appear to contain N-terminal lipoprotein attachment sites, as does Esherichia coli MltB in IPR011757 from INTERPRO.. Probab=22.56 E-value=24 Score=13.07 Aligned_cols=14 Identities=21% Similarity=0.387 Sum_probs=5.8 Q ss_pred HHHHHHHHHCCHHH Q ss_conf 69999999808178 Q gi|254780142|r 603 AMVDTIYRHCGQKS 616 (1398) Q Consensus 603 ~li~~i~~~~G~~~ 616 (1398) .++..|=++||-.. T Consensus 83 ~~L~~iE~~yGVp~ 96 (313) T TIGR02283 83 ALLARIEKRYGVPA 96 (313) T ss_pred HHHHHHHHHCCCCC T ss_conf 99999875238881 No 189 >PRK12423 LexA repressor; Provisional Probab=22.55 E-value=36 Score=11.71 Aligned_cols=28 Identities=11% Similarity=0.171 Sum_probs=20.8 Q ss_pred HHHHHHCCCEEEECCCCCCEECCEEEEE Q ss_conf 3266656978997576310111401235 Q gi|254780142|r 413 VLAEVVHQHVVLLNRAPSLHRLSMQAFE 440 (1398) Q Consensus 413 v~rhl~~gd~Vl~NRqPsLHr~Simah~ 440 (1398) +..++.|||+|+..||++-+---|-+-. T Consensus 125 i~~gI~dGD~viV~~~~~~~~GdIVvA~ 152 (202) T PRK12423 125 IDDGILDGDLVGVHRSPEARDGQIVVAR 152 (202) T ss_pred CCCCCCCCCEEEEECCCCCCCCCEEEEE T ss_conf 4489689999999636878999699999 No 190 >PRK00215 LexA repressor; Validated Probab=22.26 E-value=36 Score=11.67 Aligned_cols=29 Identities=7% Similarity=0.096 Sum_probs=22.0 Q ss_pred HHHHHHCCCEEEECCCCCCEECCEEEEEE Q ss_conf 32666569789975763101114012358 Q gi|254780142|r 413 VLAEVVHQHVVLLNRAPSLHRLSMQAFEP 441 (1398) Q Consensus 413 v~rhl~~gd~Vl~NRqPsLHr~Simah~~ 441 (1398) +...+.|||+|+..+|++.+--.|-+..+ T Consensus 128 i~~~I~dGD~viV~~~~~~~~G~Ivva~i 156 (204) T PRK00215 128 IDAGILDGDLVIVRKQQTARNGQIVVALI 156 (204) T ss_pred CCCCCCCCCEEEEECCCCCCCCCEEEEEE T ss_conf 65798999999995789688996999997 No 191 >KOG0300 consensus Probab=22.13 E-value=36 Score=11.66 Aligned_cols=29 Identities=31% Similarity=0.431 Sum_probs=18.6 Q ss_pred CCCCHHHCCCC----HHHHHHCCCCCCHHHHCCCCCC Q ss_conf 66301110888----9897640576103221012101 Q gi|254780142|r 755 PIRSHFKGGLC----GFEFFQSCVGGRKGLLDVVMRT 787 (1398) Q Consensus 755 PV~~sF~~GL~----p~EfFfhamgGReGLiDTAvKT 787 (1398) .|-+||+.|-- ..|| -|-|+|+-+-|++- T Consensus 126 rivssFk~~t~~~~lvre~----~GHkDGiW~Vaa~~ 158 (481) T KOG0300 126 RIVSSFKDGTVKFRLVREL----EGHKDGIWHVAADS 158 (481) T ss_pred HHEEEECCCCEEEEEHHHH----CCCCCCEEEEHHHC T ss_conf 0000110771147652544----36656526552224 No 192 >pfam03998 Utp11 Utp11 protein. This protein is found to be part of a large ribonucleoprotein complex containing the U3 snoRNA. Depletion of the Utp proteins impedes production of the 18S rRNA, indicating that they are part of the active pre-rRNA processing complex. This large RNP complex has been termed the small subunit (SSU) processome. Probab=22.01 E-value=30 Score=12.30 Aligned_cols=10 Identities=10% Similarity=0.355 Sum_probs=4.5 Q ss_pred CCCCCCCCCC Q ss_conf 5787677200 Q gi|254780142|r 98 VRRDRMAHID 107 (1398) Q Consensus 98 ~r~ghfGhIe 107 (1398) ..|-|||+.| T Consensus 11 ~~R~~lGlLE 20 (239) T pfam03998 11 ESRKHLGLLE 20 (239) T ss_pred HHHHHCCCCC T ss_conf 6641347530 No 193 >KOG4550 consensus Probab=21.93 E-value=36 Score=11.69 Aligned_cols=14 Identities=57% Similarity=0.866 Sum_probs=8.6 Q ss_pred CCCCCCCC-EEEEEC Q ss_conf 46787754-569974 Q gi|254780142|r 459 YNADFDGD-QMAVYA 472 (1398) Q Consensus 459 yNADFDGD-EMnlHv 472 (1398) --.||||| +|-+-| T Consensus 92 ~pGDfdGDs~mDVLv 106 (606) T KOG4550 92 VPGDFDGDSQMDVLV 106 (606) T ss_pred CCCCCCCCCEEEEEE T ss_conf 666778850345788 No 194 >PRK08373 aspartate kinase; Validated Probab=21.78 E-value=32 Score=12.07 Aligned_cols=12 Identities=17% Similarity=0.135 Sum_probs=4.2 Q ss_pred CHHHHHHHHHCC Q ss_conf 899999999759 Q gi|254780142|r 862 LESHVNEIEKCG 873 (1398) Q Consensus 862 ~~~~~~~i~~~~ 873 (1398) +-+.+.++..+| T Consensus 232 SY~EA~ELA~~G 243 (359) T PRK08373 232 SYDEIKIAAKLG 243 (359) T ss_pred CHHHHHHHHHCC T ss_conf 899999999779 No 195 >TIGR01843 type_I_hlyD type I secretion membrane fusion protein, HlyD family; InterPro: IPR010129 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). Type I secretion is an ABC transporter that exports proteins, without cleavage of any signal sequence, from the cytosol to extracellular medium across both inner and outer membranes. The secretion signal is found in the C terminus of the transported protein. This entry represents the adaptor protein between the ATP-binding cassette (ABC) protein of the inner membrane and the outer membrane protein, and is called the membrane fusion protein. This entry selects a group of sequences closely related to HlyD; it is defined narrowly and excludes, for example, colicin V secretion protein CvaA and multidrug efflux proteins.; GO: 0015031 protein transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane. Probab=21.69 E-value=37 Score=11.59 Aligned_cols=32 Identities=16% Similarity=0.208 Sum_probs=14.5 Q ss_pred CCCEEEECCCCCEE-E----EECCHHCCHHHHHHHHH Q ss_conf 12205545875101-7----75110020136669999 Q gi|254780142|r 576 IIGEILPRHHEISF-D----ICNQEMIKKNISAMVDT 607 (1398) Q Consensus 576 ~~~~ilp~~~~~~~-~----~~~~~~~k~~~~~li~~ 607 (1398) ++..|+.++|+..- | -+|.....+....+-.. T Consensus 53 i~~~I~V~EG~~V~~Gq~L~~Ld~t~~~A~~~~~~~~ 89 (434) T TIGR01843 53 IVREILVREGDRVKAGQVLVELDATSVEADAAELESQ 89 (434) T ss_pred EEEEEEECCCCEECCCCCCEEECHHHHHHHHHHHHHH T ss_conf 4413552258642037701354135789999999999 No 196 >KOG0696 consensus Probab=21.41 E-value=21 Score=13.53 Aligned_cols=13 Identities=23% Similarity=0.294 Sum_probs=6.0 Q ss_pred CCCCCCEEEECCC Q ss_conf 0457740341255 Q gi|254780142|r 349 VDYSGRSVIVAGP 361 (1398) Q Consensus 349 Vdfs~RsVI~pdP 361 (1398) .||+--.|+.-+. T Consensus 349 tDFnFl~VlGKGS 361 (683) T KOG0696 349 TDFNFLMVLGKGS 361 (683) T ss_pred CCCCEEEEECCCC T ss_conf 2530478861676 No 197 >cd00498 Hsp33 Heat shock protein 33 (Hsp33): Cytosolic protein that acts as a molecular chaperone under oxidative conditions. In normal (reducing) cytosolic conditions, four conserved Cys residues are coordinated by a Zn ion. Under oxidative stress (such as heat shock), the Cys are reversibly oxidized to disulfide bonds, which causes the chaperone activity to be turned on. Hsp33 is homodimeric in its functional form. Probab=21.22 E-value=33 Score=11.97 Aligned_cols=10 Identities=30% Similarity=0.219 Sum_probs=4.4 Q ss_pred HHHHHHCHHH Q ss_conf 9987527999 Q gi|254780142|r 1214 DILRIKGVEA 1223 (1398) Q Consensus 1214 eIl~vlGIEA 1223 (1398) +.+..||.+. T Consensus 241 ~~L~~L~~~E 250 (275) T cd00498 241 AALLTLGKEE 250 (275) T ss_pred HHHHHCCHHH T ss_conf 9998379999 No 198 >KOG0326 consensus Probab=21.08 E-value=35 Score=11.79 Aligned_cols=11 Identities=36% Similarity=0.455 Sum_probs=5.1 Q ss_pred ECCCCCCCCCC Q ss_conf 04507622351 Q gi|254780142|r 243 KLPVLPPDLRP 253 (1398) Q Consensus 243 ~lpV~P~~~RP 253 (1398) .|..||.+.|+ T Consensus 64 ~l~lpp~d~R~ 74 (459) T KOG0326 64 TLKLPPKDTRY 74 (459) T ss_pred HCCCCCCCCCC T ss_conf 50589877631 No 199 >KOG3002 consensus Probab=21.08 E-value=38 Score=11.56 Aligned_cols=28 Identities=18% Similarity=0.302 Sum_probs=20.3 Q ss_pred CCCCC-CCCCCCC-CCCCCCCCCCCCCCCC Q ss_conf 34488-3567578-8530477578767720 Q gi|254780142|r 79 MKYKG-IICEKCG-VEVTLSSVRRDRMAHI 106 (1398) Q Consensus 79 ~~~~g-~~C~~Cg-~~~~~~~~r~ghfGhI 106 (1398) +...| .+|..|- .--..||.||+-||+| T Consensus 64 QC~nGHlaCssC~~~~~~~CP~Cr~~~g~~ 93 (299) T KOG3002 64 QCDNGHLACSSCRTKVSNKCPTCRLPIGNI 93 (299) T ss_pred ECCCCCEEHHHHHHHHCCCCCCCCCCCCCH T ss_conf 248886756543345405598654556527 No 200 >PRK06260 threonine synthase; Validated Probab=20.81 E-value=39 Score=11.46 Aligned_cols=22 Identities=27% Similarity=0.612 Sum_probs=9.6 Q ss_pred CCC-CCCCCCCCCCCCCCCCCCC Q ss_conf 721-5664156344883567578 Q gi|254780142|r 69 YEC-ICGKYKRMKYKGIICEKCG 90 (1398) Q Consensus 69 ~~c-~Cg~~~~~~~~g~~C~~Cg 90 (1398) .+| .||+--.....-..|..|| T Consensus 4 L~C~~CG~~~~~~~~~~~Cp~Cg 26 (400) T PRK06260 4 LKCIECGAEYDPDEIIYTCPECG 26 (400) T ss_pred EECCCCCCCCCCCCCCCCCCCCC T ss_conf 99799989589977675688789 No 201 >PRK00446 cyaY frataxin-like protein; Provisional Probab=20.77 E-value=39 Score=11.46 Aligned_cols=15 Identities=27% Similarity=0.569 Sum_probs=6.4 Q ss_pred CCCEEEECCCCCCEE Q ss_conf 697899757631011 Q gi|254780142|r 419 HQHVVLLNRAPSLHR 433 (1398) Q Consensus 419 ~gd~Vl~NRqPsLHr 433 (1398) +|.-+++||||-+|. T Consensus 43 ~~~~~ViNrQ~p~~q 57 (104) T PRK00446 43 NGSKIIINRQEPLHE 57 (104) T ss_pred CCCEEEECCCCCHHH T ss_conf 998899857970255 No 202 >PRK07591 threonine synthase; Validated Probab=20.65 E-value=39 Score=11.44 Aligned_cols=25 Identities=36% Similarity=0.841 Sum_probs=12.7 Q ss_pred CCCCCCCC-CCCC-CCCCCCCCCCCCCCC Q ss_conf 85667721-5664-156344883567578 Q gi|254780142|r 64 GPIKDYEC-ICGK-YKRMKYKGIICEKCG 90 (1398) Q Consensus 64 g~~~d~~c-~Cg~-~~~~~~~g~~C~~Cg 90 (1398) ||....+| .||+ |.- .. -..|..|| T Consensus 15 ~~~t~L~C~~CG~~y~~-~~-~~~C~~Cg 41 (422) T PRK07591 15 GPATALKCRECGAEYPL-EP-LHVCEECF 41 (422) T ss_pred CCCCEEECCCCCCCCCC-CC-CCCCCCCC T ss_conf 89646587664791698-65-46677799 No 203 >TIGR03215 ac_ald_DH_ac acetaldehyde dehydrogenase (acetylating). Members of this protein family are acetaldehyde dehydrogenase (acetylating), EC 1.2.1.10. This enzyme oxidizes acetaldehyde, using NAD(+), and attaches coenzyme A (CoA), yielding acetyl-CoA. It occurs as a late step in the meta-cleavage pathways of a variety of compounds, including catechol, biphenyl, toluene, salicylate, etc. Probab=20.63 E-value=34 Score=11.92 Aligned_cols=32 Identities=38% Similarity=0.566 Sum_probs=27.7 Q ss_pred CCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHC Q ss_conf 178520001014602111100788987764202 Q gi|254780142|r 901 ARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFH 933 (1398) Q Consensus 901 ~~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFH 933 (1398) ++...|+-.|-|-.||..|.| |||-..++-|- T Consensus 136 srv~~V~Y~EiVasiaS~SaG-PgTR~NIDEf~ 167 (285) T TIGR03215 136 SRVAPVHYAEIVASIASRSAG-PGTRANIDEFT 167 (285) T ss_pred HHCCCCCEEEEEEEEECCCCC-HHHHHHHHHHH T ss_conf 503543279988764003678-25665368889 No 204 >COG4469 CoiA Competence protein CoiA-like family, contains a predicted nuclease domain [General function prediction only] Probab=20.49 E-value=39 Score=11.42 Aligned_cols=28 Identities=21% Similarity=0.497 Sum_probs=19.1 Q ss_pred CCCCCCCCCC--CCCCCCCCCCCCCCCCCC Q ss_conf 5675788530--477578767720027762 Q gi|254780142|r 85 ICEKCGVEVT--LSSVRRDRMAHIDLASPV 112 (1398) Q Consensus 85 ~C~~Cg~~~~--~~~~r~ghfGhIeLa~PV 112 (1398) .|.-||.++. .-..++-||.|-.|+.=- T Consensus 27 fCPaC~~~l~lK~G~~k~pHFAHk~l~~C~ 56 (342) T COG4469 27 FCPACGSQLILKQGLIKIPHFAHKSLKACA 56 (342) T ss_pred CCCCCCCEEEEECCCCCCCHHHHHHHHHCC T ss_conf 267789841453375106406454265452 No 205 >COG1001 AdeC Adenine deaminase [Nucleotide transport and metabolism] Probab=20.30 E-value=40 Score=11.39 Aligned_cols=13 Identities=15% Similarity=0.056 Sum_probs=5.5 Q ss_pred HHHHCCCCCCCCC Q ss_conf 9985398613212 Q gi|254780142|r 631 YACSSGISFGKDD 643 (1398) Q Consensus 631 ~l~~~GfSigi~D 643 (1398) +..-+|.|-=+.| T Consensus 99 ~Vlp~GtTtvV~D 111 (584) T COG1001 99 AVLPHGTTTVVSD 111 (584) T ss_pred HHHCCCCEEEEEC T ss_conf 8651785589617 No 206 >PRK08300 acetaldehyde dehydrogenase; Validated Probab=20.10 E-value=37 Score=11.64 Aligned_cols=33 Identities=36% Similarity=0.521 Sum_probs=27.9 Q ss_pred CCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCC Q ss_conf 1785200010146021111007889877642024 Q gi|254780142|r 901 ARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHL 934 (1398) Q Consensus 901 ~~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHf 934 (1398) ++...|+-.|-|-.||..|.| |||-..++-|-. T Consensus 142 srv~~V~YaEiVasiaS~SaG-PgTR~NIDEf~~ 174 (298) T PRK08300 142 SRVAPVHYAEIVASIASKSAG-PGTRANIDEFTE 174 (298) T ss_pred HHCCCCCEEEEEEEEHHCCCC-HHHHHHHHHHHH T ss_conf 742763179988653122578-467655799999 No 207 >PRK00378 nucleoid-associated protein NdpA; Validated Probab=20.09 E-value=27 Score=12.66 Aligned_cols=40 Identities=25% Similarity=0.390 Sum_probs=28.2 Q ss_pred HHHCCC---CHHHHHHCCCCCCHHHHCCCCCCCCCCEEEEHHHHHHCCCEE Q ss_conf 111088---898976405761032210121015674011015423014327 Q gi|254780142|r 759 HFKGGL---CGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVV 806 (1398) Q Consensus 759 sF~~GL---~p~EfFfhamgGReGLiDTAvKTA~SGYlqRrLvk~~eDl~V 806 (1398) ||..|- ...+||...+|.-||+.-++ -+++|+++.+|-.- T Consensus 168 sFikgr~grkvsdyF~~flGc~e~~~~~~--------~t~~Ll~av~df~~ 210 (334) T PRK00378 168 SFIKGRVGRKVADFFLDFLGAEEGLNTKA--------QNRTLLQAVSDFVA 210 (334) T ss_pred EEECCCCCCHHHHHHHHHHCCCCCCCHHH--------HHHHHHHHHHHHHH T ss_conf 99857787619999999728744576499--------99999999999997 No 208 >TIGR02016 BchX chlorophyllide reductase iron protein subunit X; InterPro: IPR010246 This entry represents the X subunit of the three-subunit enzyme, (bacterio)chlorophyllide reductase , . This enzyme is responsible for the reduction of the chlorin B-ring and is closely related to the protochlorophyllide reductase complex which reduces the D-ring. Both of these complexes in turn are homologous to nitrogenase. This subunit is homologous to the nitrogenase component II, or 'iron' protein.; GO: 0005524 ATP binding, 0016628 oxidoreductase activity acting on the CH-CH group of donors NAD or NADP as acceptor, 0051539 4 iron 4 sulfur cluster binding, 0015979 photosynthesis, 0030494 bacteriochlorophyll biosynthetic process. Probab=20.08 E-value=40 Score=11.36 Aligned_cols=12 Identities=42% Similarity=0.728 Sum_probs=7.4 Q ss_pred HHCCCCCCHHHH Q ss_conf 640576103221 Q gi|254780142|r 770 FQSCVGGRKGLL 781 (1398) Q Consensus 770 FfhamgGReGLi 781 (1398) ||-+||||-+|. T Consensus 176 YFr~~GGr~~ll 187 (355) T TIGR02016 176 YFRKLGGRSKLL 187 (355) T ss_pred HHHHCCCCEEEE T ss_conf 998618860467 Done!