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!