Query 046825
Match_columns 1208
No_of_seqs 234 out of 1866
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 04:50:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046825.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046825hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0262 RNA polymerase I, larg 100.0 1E-280 3E-285 2464.2 65.5 1079 1-1207 65-1217(1640)
2 KOG0261 RNA polymerase III, la 100.0 1E-249 2E-254 2151.9 57.1 981 1-1207 67-1090(1386)
3 PRK14977 bifunctional DNA-dire 100.0 2E-243 4E-248 2298.7 76.8 949 1-1206 61-1040(1321)
4 KOG0260 RNA polymerase II, lar 100.0 9E-226 2E-230 1984.3 58.2 960 1-1206 66-1114(1605)
5 TIGR02390 RNA_pol_rpoA1 DNA-di 100.0 7E-213 1E-217 1980.3 64.1 794 1-1048 56-860 (868)
6 PRK08566 DNA-directed RNA poly 100.0 4E-212 9E-217 1978.6 64.4 794 1-1048 61-865 (882)
7 TIGR02386 rpoC_TIGR DNA-direct 100.0 5E-165 1E-169 1536.5 38.8 690 276-1203 213-931 (1140)
8 PRK00566 DNA-directed RNA poly 100.0 3E-162 7E-167 1512.7 43.1 692 276-1203 221-934 (1156)
9 PRK14906 DNA-directed RNA poly 100.0 1E-152 2E-157 1422.3 39.4 689 274-1203 307-1032(1460)
10 PRK09603 bifunctional DNA-dire 100.0 1E-147 2E-152 1427.1 40.3 668 275-1175 1619-2309(2890)
11 PRK14844 bifunctional DNA-dire 100.0 8E-145 2E-149 1395.2 35.7 691 275-1186 1662-2384(2836)
12 COG0086 RpoC DNA-directed RNA 100.0 2E-142 3E-147 1321.8 31.2 736 1-1047 55-796 (808)
13 smart00663 RPOLA_N RNA polymer 100.0 2.1E-91 4.5E-96 779.7 22.8 290 280-594 1-295 (295)
14 PRK02625 rpoC1 DNA-directed RN 100.0 6E-84 1.3E-88 760.8 22.9 282 275-601 238-526 (627)
15 CHL00018 rpoC1 RNA polymerase 100.0 1.2E-83 2.6E-88 765.4 20.4 284 275-601 257-547 (663)
16 TIGR02387 rpoC1_cyan DNA-direc 100.0 1.8E-83 3.9E-88 755.9 20.5 282 275-601 231-519 (619)
17 PF00623 RNA_pol_Rpb1_2: RNA p 100.0 2.1E-61 4.6E-66 499.4 8.4 166 384-569 1-166 (166)
18 PRK02597 rpoC2 DNA-directed RN 100.0 5.6E-60 1.2E-64 595.8 14.9 341 762-1187 6-362 (1331)
19 TIGR02388 rpoC2_cyan DNA-direc 100.0 1.8E-59 3.9E-64 586.7 18.0 331 762-1177 5-343 (1227)
20 CHL00117 rpoC2 RNA polymerase 100.0 9.3E-59 2E-63 591.2 18.4 344 760-1187 10-366 (1364)
21 PF04998 RNA_pol_Rpb1_5: RNA p 100.0 8.1E-53 1.7E-57 472.2 3.3 132 973-1205 1-132 (277)
22 PF04997 RNA_pol_Rpb1_1: RNA p 100.0 3.7E-48 8.1E-53 443.5 10.2 274 1-382 57-337 (337)
23 cd02735 RNAP_I_Rpa1_C Largest 100.0 2.7E-34 5.9E-39 324.4 4.9 73 1134-1206 1-73 (309)
24 TIGR02389 RNA_pol_rpoA2 DNA-di 100.0 4.3E-33 9.2E-38 319.3 7.7 86 1120-1206 17-106 (367)
25 PRK14897 unknown domain/DNA-di 100.0 8E-32 1.7E-36 314.6 7.7 87 1119-1206 155-244 (509)
26 cd02584 RNAP_II_Rpb1_C Largest 100.0 1.1E-31 2.4E-36 312.1 6.0 80 1126-1206 10-89 (410)
27 cd06528 RNAP_A'' A'' subunit o 100.0 1.5E-31 3.3E-36 307.0 5.5 87 1119-1206 13-102 (363)
28 PRK04309 DNA-directed RNA poly 100.0 1.5E-30 3.1E-35 300.9 7.6 87 1119-1206 32-121 (383)
29 cd02736 RNAP_III_Rpc1_C Larges 100.0 1.3E-30 2.8E-35 292.5 4.7 72 1134-1206 1-72 (300)
30 PF04983 RNA_pol_Rpb1_3: RNA p 100.0 5.6E-30 1.2E-34 265.4 4.8 155 572-814 1-158 (158)
31 PF05000 RNA_pol_Rpb1_4: RNA p 99.8 8.7E-21 1.9E-25 184.5 4.9 95 867-966 14-108 (108)
32 cd02655 RNAP_beta'_C Largest s 99.7 2.7E-18 5.7E-23 182.7 2.9 50 1138-1188 1-50 (204)
33 cd02737 RNAP_IV_NRPD1_C Larges 99.7 2.8E-18 6E-23 198.6 2.3 57 1143-1205 1-58 (381)
34 PRK14898 DNA-directed RNA poly 99.5 1.7E-15 3.6E-20 193.0 3.6 48 1158-1206 540-587 (858)
35 cd00630 RNAP_largest_subunit_C 99.4 1.4E-13 3.1E-18 141.7 1.4 46 1143-1188 1-46 (158)
36 PRK14898 DNA-directed RNA poly 98.7 9.9E-09 2.1E-13 131.7 4.3 46 1119-1164 30-78 (858)
37 COG0086 RpoC DNA-directed RNA 97.5 2.1E-05 4.6E-10 100.3 -0.5 68 1135-1204 406-475 (808)
38 PRK02625 rpoC1 DNA-directed RN 64.0 3.1 6.7E-05 52.1 1.1 20 14-33 102-121 (627)
39 PRK09603 bifunctional DNA-dire 46.9 7.8 0.00017 55.8 0.8 32 1172-1203 2639-2670(2890)
40 TIGR02387 rpoC1_cyan DNA-direc 46.3 8.5 0.00019 48.3 0.9 20 14-33 95-114 (619)
41 CHL00018 rpoC1 RNA polymerase 45.9 9.3 0.0002 48.4 1.2 20 14-33 103-122 (663)
42 PF05183 RdRP: RNA dependent R 44.2 10 0.00023 47.9 1.3 54 496-552 365-429 (579)
43 PRK14906 DNA-directed RNA poly 41.2 11 0.00024 51.3 0.9 19 14-32 93-111 (1460)
44 PF14952 zf-tcix: Putative tre 32.1 23 0.00051 29.2 1.1 13 137-149 11-23 (44)
45 PF04992 RNA_pol_Rpb1_6: RNA p 31.4 38 0.00082 36.8 2.9 78 1061-1138 71-187 (187)
46 PF05094 LEF-9: Late expressio 29.5 84 0.0018 37.8 5.3 65 502-567 212-279 (487)
47 PHA03396 lef-9 late expression 23.9 1.2E+02 0.0026 36.8 5.3 64 502-567 215-282 (493)
48 PF12234 Rav1p_C: RAVE protein 22.6 47 0.001 42.4 1.9 37 21-65 184-220 (631)
49 PF05864 Chordopox_RPO7: Chord 22.3 59 0.0013 28.4 1.8 19 32-50 27-45 (63)
No 1
>KOG0262 consensus RNA polymerase I, large subunit [Transcription]
Probab=100.00 E-value=1.4e-280 Score=2464.20 Aligned_cols=1079 Identities=48% Similarity=0.775 Sum_probs=914.0
Q ss_pred CCCCCCCCCCCCCccceeeccccccchhcHHHHHHHHHHhhhhccccccChhhHHHHHHHHHHhhcCChHHHhhhhcccC
Q 046825 1 CKTCGQRQFLCPGHFGHIDLVVPVYNPLLFNLLYTLLKRICFFCHHFKASRREVEKCVRKLELIIKGDIIAAKSLDLDLP 80 (1208)
Q Consensus 1 C~TCg~~~~~CPGHFGHIELa~PVynP~ff~~l~kLLr~iC~~C~rfll~~~~~~~~~~kL~ll~~G~~~~a~~L~~i~~ 80 (1208)
|.||++...+||||||||||++|||||+||+.+|++||+.|++||||++++.+++.+.|+||+|++|++.+|.+|+.+..
T Consensus 65 C~TC~~~~~~CPGH~GHIeL~~pvynPlfF~~ly~lLr~sCl~Chhf~~k~~~v~~~~cqLrll~~G~i~ea~~Le~i~~ 144 (1640)
T KOG0262|consen 65 CSTCNQDELNCPGHMGHIELPVPVYNPLFFDFLYNLLRGSCLFCHHFRCKNVDVHILFCQLRLLEYGLIEEAEDLESITS 144 (1640)
T ss_pred hhhhcchhhcCCCccCeeeecccccCHHHHHHHHHHHHHHHHhhhhcccCcHHHHHHHHHHHHHHhchHHHHHHHHHhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999998776
Q ss_pred CCCCCCCCcc--ccccccccccCCCCCCCCccCCCCcccchhhHHHHHHHHHHHHHhc--ccCCCCCCCCCCceecccce
Q 046825 81 SESSNPEDSD--VSNKSSCSMVTPRGNYDNVRNLKPQEWTSLQFAEAKLALLQFLKIE--TTKCGNCKAKNPRISKPTFG 156 (1208)
Q Consensus 81 ~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~ii~eflk~~--~~kC~~Cg~~~p~Irk~g~~ 156 (1208)
...++.+|.. +....+++++.. +..+..... ...-++...+.+++++.+|++.. .++|++|+..+|++||+++.
T Consensus 145 ~~~~d~~d~~~~~~k~~~~~~v~~-~i~~~~~~~-~~~~t~~~~~~~~~lv~~f~k~~l~~kkC~~C~~~~p~~rk~~~~ 222 (1640)
T KOG0262|consen 145 ETVEDNEDESLNEIKSCRAQYVTE-AISEALLDK-SEPNTKNSTELKKKLVTAFLKNALSRKKCPRCKHSNPKLRKDGFR 222 (1640)
T ss_pred hhhccCcchhHHHHHhhhhhhccH-HHHHHhhcC-CCccchhhHHHHHHHHHHHHHHhhccccCCcccCCCchhhccccc
Confidence 3322212110 111122223332 101100000 11113445678999999999986 78999999999999999999
Q ss_pred EEEEecCCchhhhhhhhccCCcCCCcCCCccccccCCCCC-CCCCCCCCCCCCCCCCcchhhhhcccCCCCCCCCccccc
Q 046825 157 WIHMNGMPHADIRANLIRGCNLGETFSGGEEEKDLGASSD-VDAPETHSFNGTFPGTQDTAARRHQKGSGAVPSGFKKQK 235 (1208)
Q Consensus 157 ki~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ed~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 235 (1208)
|++...++.+....+...+....+...... +..+-++ .++.++. .+.+ +++.+.....+..+.
T Consensus 223 kv~~~~~~~~~~~~~~~~~~i~~~~~~~~~---~d~~~~G~~E~~~~g--~d~~------e~~~~~~~~~~t~~~----- 286 (1640)
T KOG0262|consen 223 KVFIDALSSKVGANVIRGAKIKKDVGSKGF---EDSGIDGSNEVEEDG--KDLF------EKSTEPAEFEKTGKK----- 286 (1640)
T ss_pred eeeeehhcccccccchhheeeehhcccccc---cccccCCcccccccc--cccc------ccccccccccccccc-----
Confidence 999998875544333333222222221000 0000000 0000000 0000 011111111122233
Q ss_pred cccCCCCCHHHHHHHHHhcCHhHHHHccccccccccCCCCCCCCceEEEeeeecCCCcccCCcccCCCccCchhHHHHHH
Q 046825 236 DLFSGPLLPSDVKDIIEKLWENEFELCSFISDMQQQGFGKKAGHSIFFLGVVLVPPIKFRLPSKGGDSVMEHPQTVLLSK 315 (1208)
Q Consensus 236 ~~~~~~L~P~eV~~iLkkI~~~d~~lL~ll~~~~~~~~~~~~~Pe~ffL~~lpVpP~~~RP~~~~~~~~~eddlt~~l~~ 315 (1208)
+|+|.+|+++|+.||.+|.++|.++|+.......+..+-++|||+.|||||+++||+.++++...|+++|..|.+
T Consensus 287 -----~l~~tevR~~l~~lf~ne~~~l~~lf~l~~~~~~k~~p~d~FFld~l~VpPtrfRP~s~~gd~~~en~Qt~~L~k 361 (1640)
T KOG0262|consen 287 -----YLLPTEVREHLRDLFKNEGELLSYLFPLWDSGSGKIDPSDMFFLDNLLVPPTRFRPPSMLGDEVHENPQTLNLNK 361 (1640)
T ss_pred -----cccHHHHHHHHHHHHhhhHHHHHHhhccccccccccCccceeeeeccccCCcccCCchhcchhhhcChHHHHHHH
Confidence 999999999999999999999999998321111334555699999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHcC--CCC-------------HHHHHHHHhhHHHHHHhhhcCCCCCc-CCCChhhHHHHhhccccccc
Q 046825 316 VLQANIYLANAYVNQ--PDN-------------AKVIVARWMNLQQSVNVLFDGKNAAG-QRDMASGICQLLEKKEGLFR 379 (1208)
Q Consensus 316 Ii~~n~~l~~~~~~~--~~~-------------~~~i~~~~~~LQ~~v~~~~d~~~~~~-~~~~~~~i~q~L~gK~G~fR 379 (1208)
||+.|..|..+.... +.+ ...++..|.+||.+||.+||+..... +.....||+|.||+|+|+||
T Consensus 362 Vle~s~~i~~~~~~m~~kl~~~~k~~l~~~~g~~~kl~~aw~~LQ~~vn~lfDs~~~~k~~r~~~pGikQiLEKKeGLFR 441 (1640)
T KOG0262|consen 362 VLESSVLIRKLLKDMKGKLDEELKLILERLRGIFSKLINAWLQLQASVNVLFDSKMASKWSRDSPPGIKQILEKKEGLFR 441 (1640)
T ss_pred HHHHHHHHHHHHHHhhhccCHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccccccccccCCCchHHHHHHHhhhhHH
Confidence 999999999876331 111 23477899999999999999998532 24445899999999999999
Q ss_pred ccccCccCCccceeeecCCCCccccccCchHHHHhhcCcccccchHHHHHHHHHHHcCCCCCCCceEEecCCCCcccCCC
Q 046825 380 QKLMGKRVNYACRSVISPDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLPPN 459 (1208)
Q Consensus 380 ~nlmGKRvd~saRsVIspDP~l~~~evgvP~~~A~~Lt~pe~Vt~~Ni~~L~~lv~nG~~~~pGa~~i~~~~g~~~~~l~ 459 (1208)
+|||||||||+|||||||||||.+||||||..||++|||||+||+||+++||++|+|||++||||++|++++| .++.|.
T Consensus 442 khMMGKRVN~AaRSVIsPDPnI~tnEIGIP~vFA~KLTyPepVt~~NV~elr~aViNGP~~hPGA~~iqd~dg-~~t~l~ 520 (1640)
T KOG0262|consen 442 KHMMGKRVNYAARSVISPDPNIETNEIGIPPVFAKKLTYPEPVTPWNVNELRKAVINGPDVHPGATYIQDEDG-TLTLLS 520 (1640)
T ss_pred HHhhccccchhhccccCCCCCccccccCCchHHHhhccCCCcCCcccHHHHHHHHhcCCCCCCCcceeecCCC-ceeecC
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999 677776
Q ss_pred ccccccccchhhhcccccccCCCCCCCcccCceeehhhcccceEEEecCCCCCcCcccceeEEEeCCCCeEEEeccCCCC
Q 046825 460 KKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQPTLHKPSIMAHVVRVLKGEKTLRMHYANCST 539 (1208)
Q Consensus 460 ~~~~~~~~~r~~~a~~l~l~~~~~~~~~~~g~~v~Rhl~dgD~Vl~NRqPsLHk~simah~v~vl~~~~t~rln~~~c~~ 539 (1208)
.. +.++|.++|++| |.|+...+..+.+++||||+++||+||+||||||||+|||||+|||||++|||||||++|++
T Consensus 521 ~~---~~~qR~alA~qL-Ltpst~~~~~~~~K~V~RHvknGDvvlmNRQPTLHKPSimaHkaRVL~gEktlRlHYANCka 596 (1640)
T KOG0262|consen 521 PM---TDEQREALANQL-LTPSTGNPTEFGTKKVHRHVKNGDVVLMNRQPTLHKPSIMAHKARVLPGEKTLRLHYANCKA 596 (1640)
T ss_pred CC---CHHHHHHHHHHh-hccccCCCcccCCceeeeeccCCcEEEEcCCCccccchhhhhhheecCCcceeeeeeccccc
Confidence 44 678999999999 99887776777899999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCceecccCCCHHHHHHHHHhcccCCceecCCCCCCcccchhhhhhhhhhcccCccccCHHHHHHHHHhcCccC
Q 046825 540 YNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQDHIVSAALLTKKDTFLNRDEFCQLLYSSGVSS 619 (1208)
Q Consensus 540 yNADFDGDemn~h~pqs~~a~~Ea~~L~~~~~~~~sp~~g~pi~gl~QD~l~g~~lLT~~d~f~~~~~~~~l~~~~~~~~ 619 (1208)
|||||||||||+|+|||+.|||||++|++++.||++|++|+|++|||||||+++++||.||+||+|++|+||+|.++.
T Consensus 597 YNADFDGDEMN~HfPQse~araEa~~ian~dsqYLvPt~G~PlrGLIQDHiVsgv~LT~rd~Fftre~y~qLv~~~l~-- 674 (1640)
T KOG0262|consen 597 YNADFDGDEMNVHFPQSEIARAEAYNIANTDSQYLVPTDGTPLRGLIQDHIVSGVLLTMRDSFFTREDYQQLVFAGLS-- 674 (1640)
T ss_pred ccCCCCcchhcccCCchhhHHHHHHHHhccCCceeccCCCCchhhhhhhheeeeEEEEecccccCHHHHHHHHHHhhh--
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999998773
Q ss_pred CCCCCCCCCCCceeeeecccceeeccCCCccCCCCCCCCCeEEEEeecccc-CCCcceeeccCCCCCccccccccccccc
Q 046825 620 SGLGSFTGKPGQRVLISRSEQEVLPLLPAIWKPEPLWTGKQVITAVLNHIT-RGRPPFVVERGGKLPQDFFKTRFNADKQ 698 (1208)
Q Consensus 620 ~~~~~~~~~~~~~~~~~~~~~~~~~~~PaIlkp~~lwTGKqv~s~~l~~~~-~~~~~~n~~~~~k~~~~~~~~~~~~~~~ 698 (1208)
+...+|.++||+|+||.+|||||||||++|.+++ .|+++||+++++|+|.++|+..
T Consensus 675 -----------------~~~~rI~~lpPtIlkP~~LWTGKQVIsTil~Ni~P~~~p~iNl~~kaKip~~~W~~~------ 731 (1640)
T KOG0262|consen 675 -----------------DTFKRIKLLPPTILKPAPLWTGKQVISTILKNIIPEGHPPINLESKAKIPGKAWRVH------ 731 (1640)
T ss_pred -----------------hhccceeccCccccccccccccchHHHHHHHhcCCCCCCcccchhcccCchhhcCCC------
Confidence 3345789999999999999999999999999987 5799999999999999999520
Q ss_pred ccccccccCccccccccccccCCCccccccCCCCchhhhhhhcccccccCCceEEEecceeeeeecCccccC--CccHHH
Q 046825 699 SDRKKNDKGKLSKTNKMHKDKSGKKKEVVEGKPGEEKEAEKNKSKEKELSEEKLLIYKNDLVRGVIDKAQFA--DYGLVH 776 (1208)
Q Consensus 699 ~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~gell~G~ldK~~iG--~~~Lih 776 (1208)
++ +...+|+.|+||+||||+|||||++|| .+||||
T Consensus 732 ---------------------------------s~----------e~~l~Es~v~ir~GellcGVLDKa~~Gat~yGLvH 768 (1640)
T KOG0262|consen 732 ---------------------------------SE----------EPKLNESQVLIREGELLCGVLDKAQFGATAYGLVH 768 (1640)
T ss_pred ---------------------------------CC----------cccCCcceEEEecCceEEEeechhhcCchhhhhhh
Confidence 00 011678999999999999999999999 899999
Q ss_pred HHHHHhCHHHHHHHHHHHHHHHHHHHHHcCceeeecccccChHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCChhhH
Q 046825 777 TVQELYGSNTAGTLLSALSRLFTVFLQMHGFTCGVDDLLILKDKERERKNHLHGSEEIGKRVHLEALELEDGAEIDPIKL 856 (1208)
Q Consensus 777 ~i~~~yG~~~a~~~l~~l~~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~l 856 (1208)
++||.||+++++++|+.++|||+.||+++|||||++|+++.++++.+|+++++++...+.++.++++++... .+++++
T Consensus 769 ~~~ElYG~~~s~~lLs~~srlFT~ylq~~GFT~GvdDlll~~~~D~kR~~il~e~~~vG~qa~~~~~~l~~d--a~~del 846 (1640)
T KOG0262|consen 769 CCHELYGGETSGKLLSVFSRLFTAYLQMHGFTLGVDDLLLDKDADKKRREILRESRNVGNQAAKEAFGLDVD--APPDEL 846 (1640)
T ss_pred hhhhhhCccchhhHHHHHHHHHHHHHHHhccccccceeeechhhhHHHHHHHHhhhcccHHHHHHHhCCCCC--CCHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999999999988765 356789
Q ss_pred HHHHHHHhcCCcchhhHHHHHHHHHHHHhhhhhHHHHHHhhcCCCCCCCCCcchhhhhcCCCCCcccHHHHHhhcccccc
Q 046825 857 KSEIEKAMRGGGDAAVAYFDMKMTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQEL 936 (1208)
Q Consensus 857 ~~~~~~~l~~~~~~~~~~~~~~~~~~ln~~~~~~~~~~~~~~~l~~~~~~N~~~~M~~SGaKGS~vN~~Qi~~~lGQQ~l 936 (1208)
..+++.+...+. ...+.||..+++.+|.++++ |++.|+|.||.+.||.|++..|+.||||||+||++||||+||||++
T Consensus 847 ~~~le~~y~~d~-~~~~~LD~~~k~~~n~~ts~-I~~~cvP~GLlk~FP~N~mqlM~~SGAKGS~VN~~QISclLGQqeL 924 (1640)
T KOG0262|consen 847 RSRLEAIYLKDA-DKLAMLDRVMKSELNGYTSE-IVKKCVPDGLLKKFPENNMQLMIQSGAKGSNVNTSQISCLLGQQEL 924 (1640)
T ss_pred HHHHHHHHhcch-hHHHHHHHHHHHHHhhhhHH-HHhhhccchhhhcCCcchHHHHHHhcCCcccccHHHHHHhhhhHhh
Confidence 999999888332 22389999999999999999 9999999999999999999999999999999999999999999999
Q ss_pred cCcccCCCCCCccccCCCCCCCCccccccccccccCCCCchhhhhhcccccccchhccccccCCchhhHHHHhhhceeee
Q 046825 937 EGKRVPRMVSGKTLPSFHPWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKI 1016 (1208)
Q Consensus 937 eG~Rip~~~~grtLP~f~~~d~~~~a~GfI~~sF~~GL~p~EfFfH~maGReGLiDTAvKTa~SGYLqRrLvK~lEdl~V 1016 (1208)
||+|||.|+||||||||.++|++|+|+|||.++|++|+.|+|||||||||||||||||||||+|||||||||||||+|+|
T Consensus 925 EGkRvPlMvSGKtLPsF~p~e~spraGGfI~~RFlTGi~PqeyfFHCMAGREGLIDTAVKTSRSGYLQRCLiKhLEgl~V 1004 (1640)
T KOG0262|consen 925 EGKRVPLMVSGKTLPSFAPYETSPRAGGFIDGRFLTGIKPQEYFFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLKV 1004 (1640)
T ss_pred cCCccceeecCCccCCcCCCCCCCCCCCcccceeecCCCchHHhhhhhccccchhhhHHhcccchHHHHHHHHhhhhcEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecccEEEcCCCCEEEeeecCCcceeccccccccchhhhhhhccccccccccccCCCceeeechhHHHHHhhhcchh----
Q 046825 1017 SYDYSVRDADGSIVQFCYGEDGVDVHQTSFISKFDALAARERGRGRGRNKFCDKGSHTFVMGRNQEMIYKKCSGQL---- 1092 (1208)
Q Consensus 1017 ~YD~TVR~~~g~IvQF~YGedGld~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~~~~---- 1092 (1208)
+||.||||+||+||||.|||||+|++|++++++|++..+ |++.+...++++.
T Consensus 1005 ~YD~TVRDsDgsvVQF~YGEDglDitKssfl~~~~f~~~------------------------Ny~avl~~~~~~~v~s~ 1060 (1640)
T KOG0262|consen 1005 HYDLTVRDSDGSVVQFMYGEDGLDITKSSFLNKKEFPTD------------------------NYEAVLLKYKSESVLSA 1060 (1640)
T ss_pred eccceEEcCCCcEEEEeecCccccccHHhhcchhhhhhh------------------------hHHHHHhhhChHHHhhh
Confidence 999999999999999999999999999999999998876 4444444333320
Q ss_pred ---hhHHHHHHh-------------------------------------------HHHHHHHhHHHHHHhhhcchhHHHH
Q 046825 1093 ---DASNAYIME-------------------------------------------LPDALKDNAEKFADKFLSNEMAKQD 1126 (1208)
Q Consensus 1093 ---~~~~~~~~~-------------------------------------------~~~~~~~~~~~~~~~~~~~~l~~~~ 1126 (1208)
.++..++++ +..|.+++ .+..+ .+.-+.+.
T Consensus 1061 ~d~~~a~~~~k~i~kw~kk~~w~~~~k~~~cpdpv~~k~~p~~y~gsvsekf~~~i~~f~~~~-~k~~~---s~~~~~~~ 1136 (1640)
T KOG0262|consen 1061 FDIKKASKYIKKILKWKKKHMWFELDKKIACPDPVLAKYNPDKYLGSVSEKFRKKIDDFDDEN-AKKEK---SEEPSEEK 1136 (1640)
T ss_pred hhhHHHHHHHHHHHHHHhhhccchhhcccCCCChhhhhcchhhhhccccHHHHHHHHHHHHHh-hhhhc---cccchHHH
Confidence 112222222 22232222 11111 12233678
Q ss_pred HHHHHHHHhhhcCCCCCCchhhhhhccCCCcccccccccccccCccccccccccchHHHHHHHhhcCCCCCeEEEecCCC
Q 046825 1127 FLKLVKHKFVLSLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIKTPVITCPLLVG 1206 (1208)
Q Consensus 1127 f~~l~~~~y~~slv~pGeaVGiIAAQSIGEP~TQMTLnTFH~AGv~~~nVTlGvPRlkEIi~~ask~ikTP~~~~~l~~~ 1206 (1208)
|+.+++.||++|+++|||+||+||||||||||||||||||||||+|+|||||||||||||||+||++||||+||+|+.++
T Consensus 1137 lr~ll~~K~~~SLa~PGE~VGvlAAQSIGEPSTQMTLNTFHfAGrGemNVTLGIPRLREIlMtASanIkTP~mt~pi~~g 1216 (1640)
T KOG0262|consen 1137 LRRLLQLKYIRSLADPGEPVGVLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILMTASANIKTPSMTVPIKNG 1216 (1640)
T ss_pred HHHHHHHHHHHHhcCCCCcceeeeecccCCCcceeehhheeeccccceeeeecchHHHHHHHHHhhccCCCceeeeccCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999876
Q ss_pred C
Q 046825 1207 K 1207 (1208)
Q Consensus 1207 ~ 1207 (1208)
.
T Consensus 1217 ~ 1217 (1640)
T KOG0262|consen 1217 V 1217 (1640)
T ss_pred c
Confidence 4
No 2
>KOG0261 consensus RNA polymerase III, large subunit [Transcription]
Probab=100.00 E-value=1.1e-249 Score=2151.87 Aligned_cols=981 Identities=33% Similarity=0.507 Sum_probs=826.9
Q ss_pred CCCCCCCCCCCCCccceeeccccccchhcHHHHHHHHHHhhhhccccccChhhHHHHHHHHHHhhcCChHHHhhhhcccC
Q 046825 1 CKTCGQRQFLCPGHFGHIDLVVPVYNPLLFNLLYTLLKRICFFCHHFKASRREVEKCVRKLELIIKGDIIAAKSLDLDLP 80 (1208)
Q Consensus 1 C~TCg~~~~~CPGHFGHIELa~PVynP~ff~~l~kLLr~iC~~C~rfll~~~~~~~~~~kL~ll~~G~~~~a~~L~~i~~ 80 (1208)
|.|||++..+|+|||||++|++||||+|||+.++.||+|+|+.|++++|++++.+.|..+|+.- .
T Consensus 67 C~TCg~~la~C~GHfGy~~L~LPVFhiGyfk~ti~iLq~ICK~Cs~ilL~~~~k~~fl~~lr~p---------~------ 131 (1386)
T KOG0261|consen 67 CATCGEGLADCIGHFGYLKLALPVFHIGYFKATIQILQCICKNCSSILLSEEDKRQFLKKLRNP---------G------ 131 (1386)
T ss_pred cchhccchhhcccccceEeecceeeeehhHHHHHHHHHHHHHhhhhhhcCHHHHHHHHHHhhCC---------C------
Confidence 9999999999999999999999999999999999999999999999999999998898887731 0
Q ss_pred CCCCCCCCccccccccccccCCCCCCCCccCCCCcccchhhHHHHHHHHHHHHHhc--ccCCCCCCCCCCceecc-cceE
Q 046825 81 SESSNPEDSDVSNKSSCSMVTPRGNYDNVRNLKPQEWTSLQFAEAKLALLQFLKIE--TTKCGNCKAKNPRISKP-TFGW 157 (1208)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~ii~eflk~~--~~kC~~Cg~~~p~Irk~-g~~k 157 (1208)
..+..|+.|.+.++++| .++|.|||+.|+.++|. +..+
T Consensus 132 ---------------------------------------~~~l~k~~l~kri~~~CkK~~~C~hCg~~NG~VKK~~~~lk 172 (1386)
T KOG0261|consen 132 ---------------------------------------LDNLRKKALLKRIVAKCKKVNTCSHCGALNGTVKKAAALLK 172 (1386)
T ss_pred ---------------------------------------CChHHHHHHHHHHHHHhhccccccccCCcCceeecccccee
Confidence 12345667888888888 67899999999999995 4477
Q ss_pred EEEecCCchhhhhhhhccCCcCCCcCCCccccccCCCCCCCCCCCC-CCCCCCCCCcchhhhhcccCCCCCCCCcccccc
Q 046825 158 IHMNGMPHADIRANLIRGCNLGETFSGGEEEKDLGASSDVDAPETH-SFNGTFPGTQDTAARRHQKGSGAVPSGFKKQKD 236 (1208)
Q Consensus 158 i~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ed~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 236 (1208)
|++....-.. ++ +++. .+...+. .......+..........
T Consensus 173 IiHd~~~~~~-------------------------k~-----~~~~~~~~~~~~--~~~~~n~e~~~~~~~~~~------ 214 (1386)
T KOG0261|consen 173 IIHDRFKLVK-------------------------KS-----DPLVTNERGEFK--TAISHNKELEGHLSSCCE------ 214 (1386)
T ss_pred Eeeehhhccc-------------------------cc-----cchhhhhHHHHH--HHhhcCcchHhHHHHHHh------
Confidence 8776321100 00 0000 0000000 000000001111112223
Q ss_pred ccCCCCCHHHHHHHHHhcCHhHHHHccccccccccCCCCCCCCceEEEeeeecCCCcccCCcccCC--CccCchhHHHHH
Q 046825 237 LFSGPLLPSDVKDIIEKLWENEFELCSFISDMQQQGFGKKAGHSIFFLGVVLVPPIKFRLPSKGGD--SVMEHPQTVLLS 314 (1208)
Q Consensus 237 ~~~~~L~P~eV~~iLkkI~~~d~~lL~ll~~~~~~~~~~~~~Pe~ffL~~lpVpP~~~RP~~~~~~--~~~eddlt~~l~ 314 (1208)
.|+|..|+++|++|.+.|+++|++.. ...+|+.+|++++||||.|+|||+++++ .+.|||+|.++.
T Consensus 215 ----~LnPl~vLnLFk~i~~~D~eLLg~~~--------~~~~P~~Li~t~~~vPP~cIRPSV~~~~k~gtnEDDlT~Klt 282 (1386)
T KOG0261|consen 215 ----ELNPLVVLNLFKQIKEDDCELLGMDS--------EEGRPENLIITRVPVPPVCIRPSVMSEDKAGTNEDDLTMKLT 282 (1386)
T ss_pred ----hcChHHHHHHHhhCCccccceeeecc--------CcCCchheEEEeccCCccccccceeecCCCCCCccchhhhhh
Confidence 79999999999999999999998742 3569999999999999999999999887 789999999999
Q ss_pred HHHHHHHHHHHHHHcCCCCHHHHHHHHhhHHHHHHhhhcCCCCC----c-CCCChhhHHHHhhcccccccccccCccCCc
Q 046825 315 KVLQANIYLANAYVNQPDNAKVIVARWMNLQQSVNVLFDGKNAA----G-QRDMASGICQLLEKKEGLFRQKLMGKRVNY 389 (1208)
Q Consensus 315 ~Ii~~n~~l~~~~~~~~~~~~~i~~~~~~LQ~~v~~~~d~~~~~----~-~~~~~~~i~q~L~gK~G~fR~nlmGKRvd~ 389 (1208)
+||-.|..|++.+..+ .+.+.+++.|+.||.+|+.||+|+.+. . .++|.+|+.||||||+||||+||.||||||
T Consensus 283 EIi~tn~vik~~~~~g-~~~~~imE~Wd~lQl~~AlyINSEl~g~~~~~~p~kp~RGf~QRLKGKqGRFRgNLSGKRVDF 361 (1386)
T KOG0261|consen 283 EIILTNDVIKKHLSKG-TPINLIMEDWDFLQLQVALYINSELPGIPINMAPKKPTRGFVQRLKGKQGRFRGNLSGKRVDF 361 (1386)
T ss_pred hhhhHHHHHHHHhhcC-CCchhhhhhhHHHHHHHHHhhcccCCCCCCCCCCCCchHHHHHHhcccCCceeccccCceeec
Confidence 9999999999999986 788889999999999999999999873 1 288999999999999999999999999999
Q ss_pred cceeeecCCCCccccccCchHHHHhhcCcccccchHHHHHHHHHHHcCCCCCCCceEEec-CCCCcccCCCccccccccc
Q 046825 390 ACRSVISPDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLD-KLSTMRLPPNKKMRISIGR 468 (1208)
Q Consensus 390 saRsVIspDP~l~~~evgvP~~~A~~Lt~pe~Vt~~Ni~~L~~lv~nG~~~~pGa~~i~~-~~g~~~~~l~~~~~~~~~~ 468 (1208)
||||||||||||+|||||||..||+.|||||+||..|+++||+||.|||++|||||||++ ..| .+..|.+ .+
T Consensus 362 SGRTVISPDPNL~IdeVgVP~rvAkiLTfpE~Vt~~Ni~klr~lV~NGP~vhPGANyv~~r~~~-~kr~L~y------g~ 434 (1386)
T KOG0261|consen 362 SGRTVISPDPNLRIDEVGVPIRVAKILTFPERVTRANIRKLRQLVRNGPNVHPGANYVVQRGEG-FKRFLKY------GN 434 (1386)
T ss_pred cCceeeCCCCCcceeeccchHHHHHHhcchhhccHHHHHHHHHHHhcCCCCCCCcchhhhcccc-hhhHhhc------Cc
Confidence 999999999999999999999999999999999999999999999999999999999984 444 4455544 58
Q ss_pred hhhhcccccccCCCCCCCcccCceeehhhcccceEEEecCCCCCcCcccceeEEEeCCCCeEEEeccCCCCCCCCCCCCc
Q 046825 469 KLDTSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDE 548 (1208)
Q Consensus 469 r~~~a~~l~l~~~~~~~~~~~g~~v~Rhl~dgD~Vl~NRqPsLHk~simah~v~vl~~~~t~rln~~~c~~yNADFDGDe 548 (1208)
|.++|+.| ++|++|+|||.|||+|||||||||||+|||+|+|||+|| +|||||.|+|+||||||||||
T Consensus 435 R~kiA~eL-----------k~GdvVERHL~DgDvVLFNRQPSLHkmSIM~H~akV~p~-RTfRFNEcvCtPYNADFDGDE 502 (1386)
T KOG0261|consen 435 RDKIADEL-----------KIGDVVERHLMDGDVVLFNRQPSLHKMSIMSHRAKVMPW-RTFRFNECVCTPYNADFDGDE 502 (1386)
T ss_pred HHHHHHhh-----------ccchHHHhhcccCCEEEEcCCchHHHHHHHHHHhhcccC-ceeeccccccCCcCCCCCccc
Confidence 88899887 689999999999999999999999999999999999998 999999999999999999999
Q ss_pred eecccCCCHHHHHHHHHhcccCCceecCCCCCCcccchhhhhhhhhhcccCccccCHHHHHHHHHhcCccCCCCCCCCCC
Q 046825 549 MNVHFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQDHIVSAALLTKKDTFLNRDEFCQLLYSSGVSSSGLGSFTGK 628 (1208)
Q Consensus 549 mn~h~pqs~~a~~Ea~~L~~~~~~~~sp~~g~pi~gl~QD~l~g~~lLT~~d~f~~~~~~~~l~~~~~~~~~~~~~~~~~ 628 (1208)
||+||||++||||||.+||.+.+|+++|+||+||++.+||+|+|+||||.+|+||+|++++||+....
T Consensus 503 MNlHvPQTEEAraEA~~LMgvknNlvTPr~GEpiiAAtQDFiTg~YLlt~KDtF~dRa~~~ql~s~~~------------ 570 (1386)
T KOG0261|consen 503 MNLHVPQTEEARAEALVLMGVKNNLVTPRNGEPIIAATQDFITGGYLLTHKDTFLDRAEFSQLCSYMS------------ 570 (1386)
T ss_pred ccccCCchHHHHHHHHHHhccccccccCCCCCceeehhhhhhhcceeeecccccccHHHHHHHHHHHh------------
Confidence 99999999999999999999999999999999999999999999999999999999999999987432
Q ss_pred CCceeeeecccceeeccCCCccCCCCCCCCCeEEEEeeccccCCCcceeeccCCCCCcccccccccccccccccccccCc
Q 046825 629 PGQRVLISRSEQEVLPLLPAIWKPEPLWTGKQVITAVLNHITRGRPPFVVERGGKLPQDFFKTRFNADKQSDRKKNDKGK 708 (1208)
Q Consensus 629 ~~~~~~~~~~~~~~~~~~PaIlkp~~lwTGKqv~s~~l~~~~~~~~~~n~~~~~k~~~~~~~~~~~~~~~~~~~~~~~g~ 708 (1208)
+....+.+|||||+||..||||||+||.++++.......+|+..+++. +.. . +|
T Consensus 571 --------d~~~~i~lppPaI~KP~~LwTGKQ~fsvlirpn~~s~v~~Nl~~k~k~---~~~------------~--~~- 624 (1386)
T KOG0261|consen 571 --------DAMTHIDLPPPAILKPVELWTGKQLFSVLIRPNDDSPVRVNLDAKNKN---FSL------------V--KG- 624 (1386)
T ss_pred --------ccccccCCCChhhcCceeeeccCEEEEEEeccCCCCceEEeeccccce---eec------------c--cC-
Confidence 223468899999999999999999999999876555555666544332 100 0 01
Q ss_pred cccccccccccCCCccccccCCCCchhhhhhhcccccccCCceEEEecceeeeeecCccccC---CccHHHHHHHHhCHH
Q 046825 709 LSKTNKMHKDKSGKKKEVVEGKPGEEKEAEKNKSKEKELSEEKLLIYKNDLVRGVIDKAQFA---DYGLVHTVQELYGSN 785 (1208)
Q Consensus 709 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~gell~G~ldK~~iG---~~~Lih~i~~~yG~~ 785 (1208)
...++|.+|++|+|+|++|++|++||+.+| +.+|++.|.++||+.
T Consensus 625 --------------------------------k~~~mc~nDg~v~irns~l~sG~ldKs~lG~g~k~~lfy~llrDyg~~ 672 (1386)
T KOG0261|consen 625 --------------------------------KSFEMCPNDGYVIIRNSELISGVLDKSTLGSGKKDSLFYILLRDYGSM 672 (1386)
T ss_pred --------------------------------CCcccCCCCCeEEEecchhhhcccccccccCCCccceEeeehhhcchH
Confidence 123689999999999999999999999999 789999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHcCceeeecccccChHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCChhhHHHHHHHHhc
Q 046825 786 TAGTLLSALSRLFTVFLQMHGFTCGVDDLLILKDKERERKNHLHGSEEIGKRVHLEALELEDGAEIDPIKLKSEIEKAMR 865 (1208)
Q Consensus 786 ~a~~~l~~l~~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~ 865 (1208)
+|++.|+++.+|..+||..+||||||+|+.+.+...++++++++.++.+|.+.+.+|.. .+|+ .
T Consensus 673 aAa~am~rlaklc~r~lgnrGFSIGi~DVqPg~~L~~~k~~lv~~gY~kc~~~I~e~~k---------G~L~-------~ 736 (1386)
T KOG0261|consen 673 AAADAMNRLAKLCARFLGNRGFSIGIDDVQPGEILSQEKEELVNRGYAKCDEKIEEYNK---------GKLQ-------L 736 (1386)
T ss_pred HHHHHHHHHHHhhhhhccccccccccCCCCccHHHHHHHHHHHHhHHHHHHHHHHHHhc---------cccc-------c
Confidence 99999999999999999999999999999999999999999999999999998888743 1221 3
Q ss_pred CCcchhhHHHHHHHHHHHHhhhhhHHHHHHhhcCCCCCCCCCcchhhhhcCCCCCcccHHHHHhhcccccccCcccCCCC
Q 046825 866 GGGDAAVAYFDMKMTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMV 945 (1208)
Q Consensus 866 ~~~~~~~~~~~~~~~~~ln~~~~~~~~~~~~~~~l~~~~~~N~~~~M~~SGaKGS~vN~~Qi~~~lGQQ~leG~Rip~~~ 945 (1208)
++++..+++||+.+.++|+.++++ +++.|+. +..+.|++++|+.||||||.+|+|||.+|||||.++|.|||.||
T Consensus 737 qpg~~~eetLEa~I~~~Ls~IRe~-~G~~C~~----eL~~~NsPliMa~CGSKGS~INiSQMvACVGQQ~ISG~RvPdGf 811 (1386)
T KOG0261|consen 737 QPGCNEEETLEAEILSELSTIREE-AGKICIR----ELHPRNSPLIMALCGSKGSKINISQMVACVGQQIISGHRVPDGF 811 (1386)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHH-HHHHHHH----hcCcccChHHHHHhcCCCCcccHHHHHHHhhhhhhcCCcCCCcc
Confidence 466666699999999999999999 9999994 44789999999999999999999999999999999999999999
Q ss_pred CCccccCCCCCCCCccccccccccccCCCCchhhhhhcccccccchhccccccCCchhhHHHHhhhceeeeecccEEEcC
Q 046825 946 SGKTLPSFHPWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDA 1025 (1208)
Q Consensus 946 ~grtLP~f~~~d~~~~a~GfI~~sF~~GL~p~EfFfH~maGReGLiDTAvKTa~SGYLqRrLvK~lEdl~V~YD~TVR~~ 1025 (1208)
..|+||||++.+..|.|+|||.|||++||+|+|||||+|||||||||||||||+||||||||||+||||.++||+|||++
T Consensus 812 ~dRsLPHF~r~Sk~P~aKGFV~NSFySGLTptEFfFHtm~GREGLVDTAVKTAETGYMqRRLmK~LEDL~~~YDgTVR~s 891 (1386)
T KOG0261|consen 812 EDRSLPHFERHSKTPAAKGFVANSFYSGLTPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKSLEDLSVQYDGTVRNS 891 (1386)
T ss_pred ccccCccccccCCCccccchhhhhcccCCCchhhheeecccccchhhhhhhhhhhhhHHHHHHHHHHHHHHhhcCceecC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCEEEeeecCCcceeccccc---cccchhhhhhhccccccccccccCCCceeeechhHHHHHhhhcchh-----hhHHH
Q 046825 1026 DGSIVQFCYGEDGVDVHQTSF---ISKFDALAARERGRGRGRNKFCDKGSHTFVMGRNQEMIYKKCSGQL-----DASNA 1097 (1208)
Q Consensus 1026 ~g~IvQF~YGedGld~~k~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~~~~-----~~~~~ 1097 (1208)
.|.||||.||+||+||...+- ..+|...+++..... ... .++. + +.+.+.+.....+ .....
T Consensus 892 ~~~vvqF~YG~DglDPa~mEg~~~pv~f~r~~~~~~~~~------~~~-~~~~-l--~~~el~e~~~~~l~~~f~~~~~~ 961 (1386)
T KOG0261|consen 892 NGDVVQFTYGGDGLDPAMMEGKDQPVNFNRVFDHAKAIF------PHR-HDPP-L--SSEELDETLEEELLRKFTEKGDP 961 (1386)
T ss_pred CCcEEEEeecCCCCChhhhcCCCCchhHHHHHHHHHhcC------CCC-CCCC-C--CHHHHHHHHHHHHHHHhhhhhhH
Confidence 999999999999999986532 234555554332211 010 1110 1 1111222111111 11223
Q ss_pred HHHhHHHHHHHhHHHH--HHh---------------hhcchhHH---HHHHHHHHHHhhhcCCCCCCchhhhhhccCCCc
Q 046825 1098 YIMELPDALKDNAEKF--ADK---------------FLSNEMAK---QDFLKLVKHKFVLSLAQPGEPVGLLASQSVGEP 1157 (1208)
Q Consensus 1098 ~~~~~~~~~~~~~~~~--~~~---------------~~~~~l~~---~~f~~l~~~~y~~slv~pGeaVGiIAAQSIGEP 1157 (1208)
+...+++|+.....+. ++. ...+++++ +.|.+.|+.+|+++.+|||+|||+|||||||||
T Consensus 962 F~~~~~~~i~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~t~kql~~f~~~~~~ky~~a~~EpGTavGAi~aQSIGEP 1041 (1386)
T KOG0261|consen 962 FVHELREFIASLSKKIKKLQDKYGDECGPKFCPDLLYQISRLTEKQLEKFVERCLDKYMRAKVEPGTAVGAIAAQSIGEP 1041 (1386)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhcccccCCccCccceeeeeeccHHHHHHHHHHHHHHHHhhhcCCcchhhhhhcccCCCC
Confidence 3334555554332221 110 01345555 568888999999999999999999999999999
Q ss_pred ccccccccccccCccccccccccchHHHHHHHhhcCCCCCeEEEecCCCC
Q 046825 1158 STQMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIKTPVITCPLLVGK 1207 (1208)
Q Consensus 1158 ~TQMTLnTFH~AGv~~~nVTlGvPRlkEIi~~ask~ikTP~~~~~l~~~~ 1207 (1208)
||||||+|||||||++||+|||||||+||| ||||+|+||+|+..|.++.
T Consensus 1042 GTQMTLKTFHFAGVASMNiTlGVPRIkEII-NAsk~ISTPIItA~L~n~~ 1090 (1386)
T KOG0261|consen 1042 GTQMTLKTFHFAGVASMNITLGVPRIKEII-NASKTISTPIITAELENPH 1090 (1386)
T ss_pred CceeeeeeeeecceeeeeeccCcchHHHHH-hhhcccCccceeeeecCch
Confidence 999999999999999999999999999999 7999999999999998753
No 3
>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Probab=100.00 E-value=1.8e-243 Score=2298.73 Aligned_cols=949 Identities=30% Similarity=0.474 Sum_probs=776.8
Q ss_pred CCCCCCCCCCCCCccceeeccccccchhcHHHHHHHHHHhhhhccccccChhhHHHHHHHHHHhhcCChHHHhhhhcccC
Q 046825 1 CKTCGQRQFLCPGHFGHIDLVVPVYNPLLFNLLYTLLKRICFFCHHFKASRREVEKCVRKLELIIKGDIIAAKSLDLDLP 80 (1208)
Q Consensus 1 C~TCg~~~~~CPGHFGHIELa~PVynP~ff~~l~kLLr~iC~~C~rfll~~~~~~~~~~kL~ll~~G~~~~a~~L~~i~~ 80 (1208)
|+|||+++.+||||||||||++|||||+||+.+++||||+|++||||++++++.+.|.. ++. ++++.....
T Consensus 61 C~TCg~~~~~CpGHFGHIELa~PVfHpgf~k~i~~iLr~iC~~C~rlll~~~~~~~~~~-~~~--------~~~~~~~~~ 131 (1321)
T PRK14977 61 CLTCGNLAANCPGHFGHIELAEPVIHIAFIDNIKDLLNSTCHKCAKLKLPQEDLNVFKL-IEE--------AHAAARDIP 131 (1321)
T ss_pred CCCCCCCCCcCCCeeEEEEccCCceecccHHHHHHHHHHHHHHhchhhcCcccHHHHHH-HHH--------Hhhhcccch
Confidence 99999999999999999999999999999999999999999999999999988866532 211 111110000
Q ss_pred CCCCCCCCccccccccccccCCCCCCCCccCCCCcccchhhHHHHHHHHHHHHHhcccCCCCCCCCCCceecccceEEEE
Q 046825 81 SESSNPEDSDVSNKSSCSMVTPRGNYDNVRNLKPQEWTSLQFAEAKLALLQFLKIETTKCGNCKAKNPRISKPTFGWIHM 160 (1208)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~ii~eflk~~~~kC~~Cg~~~p~Irk~g~~ki~~ 160 (1208)
...+. ....+...+.+..+ .+..++|+|||+.+|.|++++...+..
T Consensus 132 ------------~~~~~---------------------~~~~~~~~~~~~~~-~k~~~~C~~C~~~~~~i~~~~~~~~~~ 177 (1321)
T PRK14977 132 ------------EKRID---------------------DEIIEEVRDQVKVY-AKKAKECPHCGAPQHELEFEEPTIFIE 177 (1321)
T ss_pred ------------hhhhh---------------------HHHHHHHHhhhhhh-hccCCcCCCCCCCCCeEEEeeceeeee
Confidence 00000 00000000011111 112578999999999998764432211
Q ss_pred ecCCchhhhhhhhccCCcCCCcCCCccccccCCCCCCCCCCCCCCCCCCCCCcchhhhhcccCCCCCCCCccccccccCC
Q 046825 161 NGMPHADIRANLIRGCNLGETFSGGEEEKDLGASSDVDAPETHSFNGTFPGTQDTAARRHQKGSGAVPSGFKKQKDLFSG 240 (1208)
Q Consensus 161 ~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ed~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 240 (1208)
. .+. .+.
T Consensus 178 ~--------------------------------------~~~-------------------------~~~---------- 184 (1321)
T PRK14977 178 K--------------------------------------TEI-------------------------EEH---------- 184 (1321)
T ss_pred c--------------------------------------ccc-------------------------cCc----------
Confidence 0 000 012
Q ss_pred CCCHHHHHHHHHhcCHhHHHHccccccccccCCCCCCCCceEEEeeeecCCCcccCCcccCC-CccCchhHHHHHHHHHH
Q 046825 241 PLLPSDVKDIIEKLWENEFELCSFISDMQQQGFGKKAGHSIFFLGVVLVPPIKFRLPSKGGD-SVMEHPQTVLLSKVLQA 319 (1208)
Q Consensus 241 ~L~P~eV~~iLkkI~~~d~~lL~ll~~~~~~~~~~~~~Pe~ffL~~lpVpP~~~RP~~~~~~-~~~eddlt~~l~~Ii~~ 319 (1208)
+|+|.+|+++|++||++|+++|++. +...+|+||||++|||||+++||++.+++ .++|||+|.+|++||+.
T Consensus 185 ~l~p~~v~~if~~i~~~d~~llg~~--------~~~~~p~~~il~~lpVpP~~~RP~v~~~~~~~~eddlt~~l~~Ii~~ 256 (1321)
T PRK14977 185 RLLPIEIRDIFEKIIDDDLELIGFD--------PKKARPEWAVLQAFLVPPLTARPSIILETGERSEDDLTHILVDIIKA 256 (1321)
T ss_pred ccCHHHHHHHHHhcCHHHHHHhCCC--------CCCCCcceEEEeccccCCCCCcCcEEeCCCcccCCcHHHHHHHHHHH
Confidence 8999999999999999999999953 34679999999999999999999999875 68999999999999999
Q ss_pred HHHHHHHHHcCCCCHHHHHHHHhhHHHHHHhhhcCCCCCc-------CCCChhhHHHHhhcccccccccccCccCCccce
Q 046825 320 NIYLANAYVNQPDNAKVIVARWMNLQQSVNVLFDGKNAAG-------QRDMASGICQLLEKKEGLFRQKLMGKRVNYACR 392 (1208)
Q Consensus 320 n~~l~~~~~~~~~~~~~i~~~~~~LQ~~v~~~~d~~~~~~-------~~~~~~~i~q~L~gK~G~fR~nlmGKRvd~saR 392 (1208)
|++|++....+ ++...+.+.|..||.+|+.||||+.+.. .++|++||+||||||+||||+||||||||||||
T Consensus 257 N~~l~~~~~~g-~~~~~~~~~~~~LQ~~v~~~~dn~~~~~~~~~~~~~~rp~k~i~qrLkgKeGrfR~nlmGKRVdfSaR 335 (1321)
T PRK14977 257 NQKLKESKDAG-APPLIVEDEVDHLQYHTSTFFDNATAGIPQAHHKGSGRPLKSLFQRLKGKEGRFRGNLIGKRVDFSAR 335 (1321)
T ss_pred HHHHHHHHHcC-CcHHHHHHHHHHHHHHHHHHhcccccCCCccccccCCCchhHHHHHhccccccccccccccccccccc
Confidence 99999988875 6677788999999999999999997621 268999999999999999999999999999999
Q ss_pred eeecCCCCccccccCchHHHHhhcCcccccchHHHHHHHHHHHcCCCCCCCceEEecCCCCcccCCCccccccccchhhh
Q 046825 393 SVISPDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLPPNKKMRISIGRKLDT 472 (1208)
Q Consensus 393 sVIspDP~l~~~evgvP~~~A~~Lt~pe~Vt~~Ni~~L~~lv~nG~~~~pGa~~i~~~~g~~~~~l~~~~~~~~~~r~~~ 472 (1208)
|||||||+|++||||||..||++|||||+||+||+++||++|.|||+.||||+||++.+| .+++|.+........+..+
T Consensus 336 tVIspDP~L~i~EVGvP~~iA~~LT~Pe~Vt~~Ni~~l~~lv~nG~~~~pGA~~i~~~~g-~~~~l~~~~~~~~~~~~~~ 414 (1321)
T PRK14977 336 TVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKMKELVINGPDEFPGANAIRKGDG-TKIRLDFLEDKGKDALREA 414 (1321)
T ss_pred eeEeCCCCcccccccCHHHHHHhCCCCEEEchhhHHHHHHHHHcCCcccCCcceEEcCCC-ceeeehhhhhccchhHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999 6787765411111123346
Q ss_pred cccccccCCCCCCCcccCceeehhhcccceEEEecCCCCCcCcccceeEEEeCCCCeEEEeccCCCCCCCCCCCCceecc
Q 046825 473 SRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVH 552 (1208)
Q Consensus 473 a~~l~l~~~~~~~~~~~g~~v~Rhl~dgD~Vl~NRqPsLHk~simah~v~vl~~~~t~rln~~~c~~yNADFDGDemn~h 552 (1208)
|.+| .+||+|||||+|||+|||||||||||||||||+|||+|+ +||||||+||+||||||||||||+|
T Consensus 415 a~~L-----------~~g~iV~Rhl~dGD~VL~NRQPSLHk~Simah~vkvl~~-kT~Rln~~vC~pyNADFDGDEMNlH 482 (1321)
T PRK14977 415 AEQL-----------EIGDIVERHLADGDIVIFNRQPSLHKLSILAHRVKVLPG-ATFRLHPAVCPPYNADFDGDEMNLH 482 (1321)
T ss_pred HHhc-----------ccCcEEEEEeecCcEEEeccCCccccccceEEEEEEecC-ceEEecccccCcccCCcccceeeee
Confidence 6666 579999999999999999999999999999999999998 9999999999999999999999999
Q ss_pred cCCCHHHHHHHHHhcccCCceecCCCCCCcccchhhhhhhhhhcccCccccCHHHHHHHHHhcCccCCCCCCCCCCCCce
Q 046825 553 FPQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQDHIVSAALLTKKDTFLNRDEFCQLLYSSGVSSSGLGSFTGKPGQR 632 (1208)
Q Consensus 553 ~pqs~~a~~Ea~~L~~~~~~~~sp~~g~pi~gl~QD~l~g~~lLT~~d~f~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~ 632 (1208)
+|||++|||||++||++++||+||++|+|++|++||+|+|+|+||++|+||++++|++|+|....
T Consensus 483 vPQS~eArAEa~~Lm~v~~niisP~~G~Pi~gliQD~l~g~~lLT~~d~fl~~~e~~~l~~~~~~--------------- 547 (1321)
T PRK14977 483 VPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFDKNEASNIAMLAGI--------------- 547 (1321)
T ss_pred cCCCHHHHHHHHHHHhhhhcEecCCCCCeeEEeehhhhhhhhhhccCcccCCHHHHHHHHHhCCC---------------
Confidence 99999999999999999999999999999999999999999999999999999999999994321
Q ss_pred eeeecccceeeccCCCcc-CCCCCCCCCeEEEEeeccccCCCcceeeccCCCCCcccccccccccccccccccccCcccc
Q 046825 633 VLISRSEQEVLPLLPAIW-KPEPLWTGKQVITAVLNHITRGRPPFVVERGGKLPQDFFKTRFNADKQSDRKKNDKGKLSK 711 (1208)
Q Consensus 633 ~~~~~~~~~~~~~~PaIl-kp~~lwTGKqv~s~~l~~~~~~~~~~n~~~~~k~~~~~~~~~~~~~~~~~~~~~~~g~~~~ 711 (1208)
...+|+|||+ ||.+|||||||||++||+ .+|+..+.+++...|. .
T Consensus 548 --------~~~lp~PaI~~kp~~lwTGKQi~s~iLp~------~~n~~~~~~~~~~~~~-----------------~--- 593 (1321)
T PRK14977 548 --------TDPLPEPAIKTKDGPAWTGKQLFSLFLPK------DFNFEGIAKWSAGKAG-----------------E--- 593 (1321)
T ss_pred --------ccccCCCceecCCCCeeeHHHHHHHHcCC------CCCceecccccccccc-----------------c---
Confidence 1257999999 999999999999999985 4677766554433331 0
Q ss_pred ccccccccCCCccccccCCCCchhhhhhhcccccccCCceEEEecceeeeeecCccccCC-----ccHHHHHHHHhCHHH
Q 046825 712 TNKMHKDKSGKKKEVVEGKPGEEKEAEKNKSKEKELSEEKLLIYKNDLVRGVIDKAQFAD-----YGLVHTVQELYGSNT 786 (1208)
Q Consensus 712 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~gell~G~ldK~~iG~-----~~Lih~i~~~yG~~~ 786 (1208)
...+.|.+|+.|+|+||||++|+|||+++|. +||||.+|++||+++
T Consensus 594 -----------------------------~~~~~~~~d~~v~I~~geLl~G~ldK~~~G~~~~~~~~Lih~i~~~yG~~~ 644 (1321)
T PRK14977 594 -----------------------------AKDPSCLGDGYVLIKEGELISGVIDDNIIGALVEEPESLIDRIAKDYGEAV 644 (1321)
T ss_pred -----------------------------ccccCCCCcceEEeecCeEEeeecchHhhccccCCCCcHHHHHHHHhCHHH
Confidence 0112457899999999999999999999984 689999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHcCceeeecccccChHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCChhhHHHHHHHHhcC
Q 046825 787 AGTLLSALSRLFTVFLQMHGFTCGVDDLLILKDKERERKNHLHGSEEIGKRVHLEALELEDGAEIDPIKLKSEIEKAMRG 866 (1208)
Q Consensus 787 a~~~l~~l~~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~ 866 (1208)
|++||+++++|+++||+++|||||++|+++++++.+++.+.++++.+++.+.+..|..-... .....++ -..
T Consensus 645 a~~fL~~l~~l~~~~L~~~GFSigi~D~~~~~~~~~~i~~~i~~~~~~v~~l~~~~~~~~~i-~~~~~~~-------~~~ 716 (1321)
T PRK14977 645 AIEFLNKILIIAKKEILHYGFSNGPGDLIIPDEAKQEIEDDIQGMKDEVSDLIDQRKITRKI-TIYKGKE-------ELL 716 (1321)
T ss_pred HHHHHHHHHHHHHHHHHhCCEEEeeCcEecCHHHHHHHHHHHHHHHHHHHHHHHHHhhhccc-cccccch-------hcC
Confidence 99999999999999999999999999999999998888888888888777666554310000 0000011 011
Q ss_pred CcchhhHHHHHHHHHHHHhhhhhHHHHHHhhcCCCCCCCCCcchhhhhcCCCCCcccHHHHHhhccccccc--------C
Q 046825 867 GGDAAVAYFDMKMTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQELE--------G 938 (1208)
Q Consensus 867 ~~~~~~~~~~~~~~~~ln~~~~~~~~~~~~~~~l~~~~~~N~~~~M~~SGaKGS~vN~~Qi~~~lGQQ~le--------G 938 (1208)
++...+++++..+.+.|++++++ +.+.+. .. ..|+|++++|+.||||||++|++||+||||||+++ |
T Consensus 717 ~G~~~~~~~e~~i~~~l~~~r~~-~~~~~~-~~---l~~~N~l~~Mv~SGAKGS~~Ni~Qi~~~lGQQ~ve~~~~~~~~G 791 (1321)
T PRK14977 717 RGMKEEEALEADIVNELDKARDK-AGSSAN-DC---IDADNAGKIMAKTGARGSMANLAQIAGALGQQKRKTRIGFVLTG 791 (1321)
T ss_pred CCCcHHHHHHHHHHHHHHHHHHH-HHHHHH-Hh---cCCCCcHHHHhhcccccCHHHHHHHHhccccccccccccccCCC
Confidence 23333477888888899888877 555443 22 24789999999999999999999999999999999 9
Q ss_pred cccCCCCCCccccCCCCCCCCccccccccccccCCCCchhhhhhcccccccchhccccccCCchhhHHHHhhhceeeeec
Q 046825 939 KRVPRMVSGKTLPSFHPWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISY 1018 (1208)
Q Consensus 939 ~Rip~~~~grtLP~f~~~d~~~~a~GfI~~sF~~GL~p~EfFfH~maGReGLiDTAvKTa~SGYLqRrLvK~lEdl~V~Y 1018 (1208)
+|||+||+|||||||.++|.+|+|+|||.|||++||+|+|||||||||||||||||||||+||||||||||+||||+|+|
T Consensus 792 ~Ri~~~~~~RtLPhF~~~d~~p~a~GfV~nsFl~GL~P~EfFFHaM~GREGLiDTAVKTA~SGYLQRrLvk~lEDl~v~Y 871 (1321)
T PRK14977 792 GRLHEGYKDRALSHFQEGDDNPDAHGFVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYFQRRLANALEDIRLEY 871 (1321)
T ss_pred CCCcCCCCCCcCCCCCCCCCCcccccchhhhhcCCCCHHHHHHHhhcccccccccccccCcCchhHHHHHHHhcceEEec
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccEEEcCCCCEEEeeecCCcceeccccccccch--hhhhhhccccccccccccCCCceeeechhHHHHHhhhcchhhhHH
Q 046825 1019 DYSVRDADGSIVQFCYGEDGVDVHQTSFISKFD--ALAARERGRGRGRNKFCDKGSHTFVMGRNQEMIYKKCSGQLDASN 1096 (1208)
Q Consensus 1019 D~TVR~~~g~IvQF~YGedGld~~k~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~~~~~~~~ 1096 (1208)
|+||||++|+||||.|||||+||++.+....+. .+..+.. .. .. ... . .-+. ..
T Consensus 872 D~TVR~s~g~iiQF~YGeDG~d~~~~~~~~~~n~~~~~~~~~----~~----~~-~~~-~---~~~~-----------~~ 927 (1321)
T PRK14977 872 DETVRDPHGHIIQFKFGEDGIDPQKLDHGEAFNLERIIEKQK----IE----DR-GKG-A---SKDE-----------IE 927 (1321)
T ss_pred CCeEEeCCCCEEEEeecCCCcCHHHhccCCcccHHHHHHHhh----hh----cc-ccC-C---CHHH-----------HH
Confidence 999999999999999999999999876543332 2221100 00 00 000 0 0000 00
Q ss_pred HHHHhHHHHHHHhHH---HHHH-hhhcchhHHHHHHHHH---HHHhhhcCCCCCCchhhhhhccCCCccccccccccccc
Q 046825 1097 AYIMELPDALKDNAE---KFAD-KFLSNEMAKQDFLKLV---KHKFVLSLAQPGEPVGLLASQSVGEPSTQMTLNTFHLA 1169 (1208)
Q Consensus 1097 ~~~~~~~~~~~~~~~---~~~~-~~~~~~l~~~~f~~l~---~~~y~~slv~pGeaVGiIAAQSIGEP~TQMTLnTFH~A 1169 (1208)
+. +++|+..... ..+. .....+++++.|.+++ +.+|.+++|+||||||+|||||||||+|||||||||+|
T Consensus 928 ~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pGe~VG~iaAQSiGEP~TQmTLnTFH~A 1004 (1321)
T PRK14977 928 EL---AKEYTKTFNANLPKLLADAIHGAELKEDELEAICAEGKEGFEKAKVEPGQAIGIISAQSIAEPGTQMTLRTFHAA 1004 (1321)
T ss_pred HH---HHHHHHhhhhhhHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccCCcccchhhhhhhccCceeeecccccccc
Confidence 01 1222211111 1111 1113456777776666 88999999999999999999999999999999999999
Q ss_pred CccccccccccchHHHHHHHhhcCCCCCeEEEecCCC
Q 046825 1170 GRGEMNVTLGIPRLQEILTIASKDIKTPVITCPLLVG 1206 (1208)
Q Consensus 1170 Gv~~~nVTlGvPRlkEIi~~ask~ikTP~~~~~l~~~ 1206 (1208)
|++++|||+|||||+||| +|+|+|+||+|+++|.++
T Consensus 1005 Gv~~~nvt~GvpRl~Eii-~a~k~~~tp~m~~~l~~~ 1040 (1321)
T PRK14977 1005 GIKAMDVTHGLERFIELV-DARAKPSTPTMDIYLDDE 1040 (1321)
T ss_pred cccccCcccCccchHHhh-hcccCCCCCeEEEEeCCc
Confidence 999999999999999999 799999999999999865
No 4
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=100.00 E-value=9.2e-226 Score=1984.27 Aligned_cols=960 Identities=33% Similarity=0.501 Sum_probs=799.6
Q ss_pred CCCCCCCCCCCCCccceeeccccccchhcHHHHHHHHHHhhhhccccccChhhHHHHHHHHHHhhcCChHHHhhhhcccC
Q 046825 1 CKTCGQRQFLCPGHFGHIDLVVPVYNPLLFNLLYTLLKRICFFCHHFKASRREVEKCVRKLELIIKGDIIAAKSLDLDLP 80 (1208)
Q Consensus 1 C~TCg~~~~~CPGHFGHIELa~PVynP~ff~~l~kLLr~iC~~C~rfll~~~~~~~~~~kL~ll~~G~~~~a~~L~~i~~ 80 (1208)
|.|||.+..+|||||||||||+|||||+|++++.+||+|+|++|++++.++..+ .....++. .++ ..+++..+|.
T Consensus 66 CqTC~g~~~~CpGHFGhieLAkPvfH~gFl~kv~kiL~cVC~~C~ki~~~~~~~-~~~~~~~~-~~~---~k~rl~~v~~ 140 (1605)
T KOG0260|consen 66 CQTCGGNMFECPGHFGHIELAKPVFHPGFLKKVKKILRCVCFYCSKILKDKFNP-KEDQILRK-RYC---SKGRLLMVLD 140 (1605)
T ss_pred hhhhccccccCCcccceeeeccccccHHHHHHHHHHHHHhhhcchheeecccCc-chhhhhhh-hcC---CcchHHHHHH
Confidence 999999999999999999999999999999999999999999999999987665 22223332 222 3455665555
Q ss_pred CCCCCCCCccccccccccccCCCCCCCCccCCCCcccchhhHHHHHHHHHHHHHhcccCCCCCCCCCCceecccceEEEE
Q 046825 81 SESSNPEDSDVSNKSSCSMVTPRGNYDNVRNLKPQEWTSLQFAEAKLALLQFLKIETTKCGNCKAKNPRISKPTFGWIHM 160 (1208)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~ii~eflk~~~~kC~~Cg~~~p~Irk~g~~ki~~ 160 (1208)
.|+. ...|+.-+.. ......+||..||.|++.|+..+-+
T Consensus 141 vck~--------k~~ce~g~~~---------------------------------e~~g~sgcg~kqP~i~r~gl~l~a~ 179 (1605)
T KOG0260|consen 141 VCKG--------KVVCEGGIDV---------------------------------ESDGRSGCGLKQPSIRRLGLDLWAF 179 (1605)
T ss_pred hhcc--------ceeeeccccc---------------------------------cccccccccccCCceeccCchhhhh
Confidence 5432 1112111100 0124579999999999999987765
Q ss_pred ecCCchhhhhhhhccCCcCCCcCCCccccccCCCCCCCCCCCCCCCCCCCCCcchhhhhcccCCCCCCCCccccccccCC
Q 046825 161 NGMPHADIRANLIRGCNLGETFSGGEEEKDLGASSDVDAPETHSFNGTFPGTQDTAARRHQKGSGAVPSGFKKQKDLFSG 240 (1208)
Q Consensus 161 ~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ed~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 240 (1208)
++. . +++..+ .+.
T Consensus 180 ~k~----------------------------~-------~e~~~e----------------------~k~---------- 192 (1605)
T KOG0260|consen 180 WKQ----------------------------G-------DEDSQE----------------------SKR---------- 192 (1605)
T ss_pred hhc----------------------------c-------CccCCc----------------------ccc----------
Confidence 521 0 111100 023
Q ss_pred CCCHHHHHHHHHhcCHhHHHHccccccccccCCCCCCCCceEEEeeeecCCCcccCCcccCC-CccCchhHHHHHHHHHH
Q 046825 241 PLLPSDVKDIIEKLWENEFELCSFISDMQQQGFGKKAGHSIFFLGVVLVPPIKFRLPSKGGD-SVMEHPQTVLLSKVLQA 319 (1208)
Q Consensus 241 ~L~P~eV~~iLkkI~~~d~~lL~ll~~~~~~~~~~~~~Pe~ffL~~lpVpP~~~RP~~~~~~-~~~eddlt~~l~~Ii~~ 319 (1208)
.|++++|.++|+.|.++|+..|++- ++..+|+||||++|||||+.+||++.+++ .+.+||+|++|.+||+.
T Consensus 193 ~ls~e~V~~i~k~Isded~~~lg~~--------~~~arpewmIlTvLPVPP~~vrP~iv~~~s~rg~DdlthkLadIiK~ 264 (1605)
T KOG0260|consen 193 KLSAERVLEIFKRISDEDIDQLGFK--------PKIARPEWMILTVLPVPPPAVRPEIVMQGSARGEDDLTHKLADIIKK 264 (1605)
T ss_pred cCcHHHHHHHHHhhchhhhhhhcCC--------CCcCCCceeEEEEecCCCCcccceeeecccccCcchhHHHHHHHHHH
Confidence 7999999999999999999999763 56889999999999999999999999877 57999999999999999
Q ss_pred HHHHHHHHHcCCCCHHHHHHHHhhHHHHHHhhhcCCCCC--c----CCCChhhHHHHhhcccccccccccCccCCcccee
Q 046825 320 NIYLANAYVNQPDNAKVIVARWMNLQQSVNVLFDGKNAA--G----QRDMASGICQLLEKKEGLFRQKLMGKRVNYACRS 393 (1208)
Q Consensus 320 n~~l~~~~~~~~~~~~~i~~~~~~LQ~~v~~~~d~~~~~--~----~~~~~~~i~q~L~gK~G~fR~nlmGKRvd~saRs 393 (1208)
|..|++..+++ ++++.+.+...+||.||++|+||+.+. . .++|+++|++||||||||+|+|||||||||||||
T Consensus 265 n~~l~r~e~~g-a~~H~i~e~~~LlqfhVat~~Dn~~pgqp~a~qksGrplkSi~arlKgkegriRgnLmGKRvDFSaRT 343 (1605)
T KOG0260|consen 265 NIGLKRNEENG-APAHIIEEYEQLLQFHVATYVDNDIPGQPQADQKSGRPLKSISARLKGKEGRIRGNLMGKRVDFSART 343 (1605)
T ss_pred HHHHhhhhhcC-CchhhHHHHHhHhhhhhhheecccccCCcccccccCCcccchhhhhccccchhhhcccccccCcceee
Confidence 99999888875 888888888889999999999999873 1 2889999999999999999999999999999999
Q ss_pred eecCCCCccccccCchHHHHhhcCcccccchHHHHHHHHHHHcCCCCCCCceEEecCCCCcccCCCccccccccchhhhc
Q 046825 394 VISPDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLPPNKKMRISIGRKLDTS 473 (1208)
Q Consensus 394 VIspDP~l~~~evgvP~~~A~~Lt~pe~Vt~~Ni~~L~~lv~nG~~~~pGa~~i~~~~g~~~~~l~~~~~~~~~~r~~~a 473 (1208)
||+|||||++||||||..||++|||||.||+|||++|++||.+|+..||||+||++.+| .|++|++.. | +
T Consensus 344 VItgDPnl~ldevGVP~sIAk~lTfpE~Vtp~NidrLqeLV~~g~~~~pgakyiird~G-~Ridlr~~~------~---~ 413 (1605)
T KOG0260|consen 344 VITGDPNLSLDEVGVPRSIAKRLTFPEHVTPFNIDRLQELVRRGLLEHPGAKYIIRDNG-DRIDLRYHK------R---A 413 (1605)
T ss_pred eecCCCCcchhcccCcHHHHhhccCcceeccccHHHHHHHhhCCCCCCCCcceeeecCC-cEEEEeecC------C---c
Confidence 99999999999999999999999999999999999999999999999999999999999 899987751 1 1
Q ss_pred ccccccCCCCCCCcccCceeehhhcccceEEEecCCCCCcCcccceeEEEeCCCCeEEEeccCCCCCCCCCCCCceeccc
Q 046825 474 RGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHF 553 (1208)
Q Consensus 474 ~~l~l~~~~~~~~~~~g~~v~Rhl~dgD~Vl~NRqPsLHk~simah~v~vl~~~~t~rln~~~c~~yNADFDGDemn~h~ 553 (1208)
..+ .++.|++|+|||+|||+|||||||||||||||||||||+|+ .|||||++||+||||||||||||+|+
T Consensus 414 ~d~---------~Lq~G~kVeRhl~DGD~VlfNRqPSlHKmSmmahrVrVlp~-sTfrLNlsvtsPynADFDGDemnlhv 483 (1605)
T KOG0260|consen 414 GDI---------HLQPGYKVERHLMDGDVVLFNRQPSLHKMSMMAHRVRVLPY-STFRLNLSVTSPYNADFDGDEMNLHV 483 (1605)
T ss_pred ccc---------ccccccEEEEeeccCCEEEEcCCCcHHHhhhhhcEEEEccC-ceEEeCeeecCCccCCCCCceeeccc
Confidence 111 23679999999999999999999999999999999999998 89999999999999999999999999
Q ss_pred CCCHHHHHHHHHhcccCCceecCCCCCCcccchhhhhhhhhhcccCccccCHHHHHHHHHhcCccCCCCCCCCCCCCcee
Q 046825 554 PQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQDHIVSAALLTKKDTFLNRDEFCQLLYSSGVSSSGLGSFTGKPGQRV 633 (1208)
Q Consensus 554 pqs~~a~~Ea~~L~~~~~~~~sp~~g~pi~gl~QD~l~g~~lLT~~d~f~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~ 633 (1208)
|||.+||||+.+|+.++.||++|++|+|++|++||.|+|++++|.+|+|++++++|||+|.. .+|+|
T Consensus 484 PQS~etkAEl~EL~~vpkQiispQsnkpvmgivQDTLta~R~~t~Rd~Fl~r~~vmnLlm~~-------p~~d~------ 550 (1605)
T KOG0260|consen 484 PQSLETKAELEELAMVPKQIISPQSNKPVMGIVQDTLTAVRKMTKRDVFLNRAQVMNLLMYV-------PDWDG------ 550 (1605)
T ss_pred CcchhHHHHHHHHhhhhhhhcCCcCCCcceeeehhhHHHHHHHhhHhhhhcHHHHHHHHhhc-------cccCC------
Confidence 99999999999999999999999999999999999999999999999999999999999943 24666
Q ss_pred eeecccceeecc-CCCccCCCCCCCCCeEEEEeeccccCCCcceeeccCCCCCcccccccccccccccccccccCccccc
Q 046825 634 LISRSEQEVLPL-LPAIWKPEPLWTGKQVITAVLNHITRGRPPFVVERGGKLPQDFFKTRFNADKQSDRKKNDKGKLSKT 712 (1208)
Q Consensus 634 ~~~~~~~~~~~~-~PaIlkp~~lwTGKqv~s~~l~~~~~~~~~~n~~~~~k~~~~~~~~~~~~~~~~~~~~~~~g~~~~~ 712 (1208)
..| .|||+||+||||||||||+++|. +||+.+......+ +.+
T Consensus 551 ---------~~Pa~pai~Kp~PlWTGkQifsliiP~------~in~~r~~s~h~d-----------------~~~----- 593 (1605)
T KOG0260|consen 551 ---------PPPAKPAILKPKPLWTGKQIFSLIIPG------GINYIRDHSTHPD-----------------SED----- 593 (1605)
T ss_pred ---------CCCCCcccCCCCcccchhhheeeecCC------CcceecccccCcC-----------------CCc-----
Confidence 456 89999999999999999999984 5776543221111 000
Q ss_pred cccccccCCCccccccCCCCchhhhhhhcccccccCCceEEEecceeeeeecCccccC--CccHHHHHHHHhCHHHHHHH
Q 046825 713 NKMHKDKSGKKKEVVEGKPGEEKEAEKNKSKEKELSEEKLLIYKNDLVRGVIDKAQFA--DYGLVHTVQELYGSNTAGTL 790 (1208)
Q Consensus 713 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~gell~G~ldK~~iG--~~~Lih~i~~~yG~~~a~~~ 790 (1208)
++..+.|..|+|.+|+++.|+|+|+.+| .++|+|++|.+.|++.|+.|
T Consensus 594 ------------------------------~~~~p~dt~~lie~g~l~~g~l~Kkt~G~s~g~lvh~i~~e~Gp~~~~~f 643 (1605)
T KOG0260|consen 594 ------------------------------ELISPGDTRVLIEGGELLIGVLCKKTVGSSAGGLVHVIFLEKGPKIARGF 643 (1605)
T ss_pred ------------------------------ccccCCCceEEEeCCceEEEEeeccccccccCceEEEeehhhCHHHHHHH
Confidence 1223678999999999999999999999 78999999999999999999
Q ss_pred HHHHHHHHHHHHHHcCceeeecccccChHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCChhhHHHHHHHHhcCCcch
Q 046825 791 LSALSRLFTVFLQMHGFTCGVDDLLILKDKERERKNHLHGSEEIGKRVHLEALELEDGAEIDPIKLKSEIEKAMRGGGDA 870 (1208)
Q Consensus 791 l~~l~~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~ 870 (1208)
++.+|+|.+.||...|||+||+|.+...+....+++.|.+|+..+...+++..+.. | -.+++..
T Consensus 644 ~~~iQ~lin~wll~~gfsigIgDtiad~~t~~~iq~~I~~ak~dv~~vi~~a~~~~---------L-------~~~pg~t 707 (1605)
T KOG0260|consen 644 FDSIQTLINSWLLREGFSIGIGDTIADAATMCVIQNTIKEAKRDVLAVIREAQNNE---------L-------EPTPGRT 707 (1605)
T ss_pred HHHHHHHHHHHHHhcCccccccccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcc---------c-------cCCcchh
Confidence 99999999999999999999999999999999999999999999888887764311 1 1123333
Q ss_pred hhHHHHHHHHHHHHhhhhhHHHHHHhhcCCCCCCCCCcchhhhhcCCCCCcccHHHHHhhcccccccCcccCCCCCCccc
Q 046825 871 AVAYFDMKMTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGKTL 950 (1208)
Q Consensus 871 ~~~~~~~~~~~~ln~~~~~~~~~~~~~~~l~~~~~~N~~~~M~~SGaKGS~vN~~Qi~~~lGQQ~leG~Rip~~~~grtL 950 (1208)
..++|+..++.++|+.+++ .....- . .....||+.+|+.+|||||.+|++|+++|+|||++||+|||+||..|||
T Consensus 708 lretfe~~v~~vlndArd~-~gssA~-~---sl~esNn~k~Mv~aGSKGs~inisQ~saCVGqQnVEgkrIpFGF~~Rtl 782 (1605)
T KOG0260|consen 708 LRETFENKVNRVLNDARDK-SGSSAQ-K---SLSESNNFKTMVVAGSKGSFINISQVSACVGQQNVEGKRIPFGFPKRTL 782 (1605)
T ss_pred HHHHHHHHHHHHHHHHHHh-hhhHHH-h---hhhhcccHHHHHhhcCCCcceehhhhhhhhccccccccccccCCCcccc
Confidence 3478999999999999887 443221 1 2246899999999999999999999999999999999999999999999
Q ss_pred cCCCCCCCCccccccccccccCCCCchhhhhhcccccccchhccccccCCchhhHHHHhhhceeeeecccEEEcCCCCEE
Q 046825 951 PSFHPWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSIV 1030 (1208)
Q Consensus 951 P~f~~~d~~~~a~GfI~~sF~~GL~p~EfFfH~maGReGLiDTAvKTa~SGYLqRrLvK~lEdl~V~YD~TVR~~~g~Iv 1030 (1208)
|||.++|++|+++|||+|||++||+|+|||||+|||||||||||||||++|||||||||+|||++|+|||||||+-|++|
T Consensus 783 phf~kDdysPesrGfVENSyL~GLtP~EfFfHamggREglidtavktaEtGyiqRRL~kameDimv~yDgTVRNs~gqvi 862 (1605)
T KOG0260|consen 783 PHFSKDDYSPESRGFVENSYLTGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLMKAMEDIMVAYDGTVRNSLGQVI 862 (1605)
T ss_pred cccccCCCCccccceeecccccCCCHHHHHHHHhcccchhhhhhhcccccchHHHHHHHHHHHHHhhcCcceecccceeE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EeeecCCcceecccccc-------------ccchhhhhh--------------------------hc-----cccccccc
Q 046825 1031 QFCYGEDGVDVHQTSFI-------------SKFDALAAR--------------------------ER-----GRGRGRNK 1066 (1208)
Q Consensus 1031 QF~YGedGld~~k~~~~-------------~~~~~~~~~--------------------------~~-----~~~~~~~~ 1066 (1208)
||.|||||+|.+-.++. ..|.+.+.+ +. .|.... .
T Consensus 863 Qf~YGeDG~d~~~vE~q~~~~l~~~~a~f~~~~~~d~ld~~~~~~~~~~~~e~~~~~~l~~lle~e~~~l~~dr~~l~-~ 941 (1605)
T KOG0260|consen 863 QFKYGEDGLDGHPVEFQNGETLGSLNACFESEFAYDALDEPISLSSEEVVNEISELLKLQNLLECEYKKLVRDRRVLL-Y 941 (1605)
T ss_pred EEEeccCccccceeeccccccccchHHHHHhhhhhhhhcCcccchhhhHhhhhhhhHHHHHHHHHHHHhhhhhhhhhh-h
Confidence 99999999997643321 112111100 00 000000 1
Q ss_pred cccCCCceeeechhHHHHHhhhcchh------------hh----HHHHHHh-----HHHHHHHhHHH----HHHhhh---
Q 046825 1067 FCDKGSHTFVMGRNQEMIYKKCSGQL------------DA----SNAYIME-----LPDALKDNAEK----FADKFL--- 1118 (1208)
Q Consensus 1067 ~~~~~~~~~~~~~n~~~~~~~~~~~~------------~~----~~~~~~~-----~~~~~~~~~~~----~~~~~~--- 1118 (1208)
+...+...+.++.|..+++.+....+ .+ ..+..++ -++++.. ++. ++++.+
T Consensus 942 i~~~g~~k~~lp~n~~r~I~Na~~~f~~~~r~~t~l~~~~v~~g~~~l~e~l~iv~g~~~~sr-aqrl~~~lLrs~l~~k 1020 (1605)
T KOG0260|consen 942 IFEYGDAKWPLPENLQRIIWNALKKFSIDERKPTDLIPFKVVKGVKELAEKLVIVRGEDYISR-AQRLFNILLRSTLATK 1020 (1605)
T ss_pred hcccCCcccccchhHHHHHHHHHhhcccccccccccchhhhhhhhhhhhheeEEeeCchhHHH-HHHHHHHHHHhhHHHH
Confidence 11233445667777777665532110 00 1111111 1345544 333 333322
Q ss_pred ----cchhHHHHHHHHH---HHHhhhcCCCCCCchhhhhhccCCCcccccccccccccCccccccccccchHHHHHHHhh
Q 046825 1119 ----SNEMAKQDFLKLV---KHKFVLSLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTIAS 1191 (1208)
Q Consensus 1119 ----~~~l~~~~f~~l~---~~~y~~slv~pGeaVGiIAAQSIGEP~TQMTLnTFH~AGv~~~nVTlGvPRlkEIi~~as 1191 (1208)
.++++.++|.|++ ..+|.++.+.|||+||++||||||||+|||||||||+|||+++|||+|||||+||++ .+
T Consensus 1021 rv~~e~rls~eaf~w~~~~Ie~~f~qa~a~pgemvg~lAaqsvgePatqmTlntfh~aGVssknVt~gvprlkei~N-v~ 1099 (1605)
T KOG0260|consen 1021 RVLEEYRLSSEAFEWVLGEIEARFLQAEASPGEMVGALAAQSVGEPATQMTLNTFHYAGVSSKNVTLGVPRLKEIIN-VA 1099 (1605)
T ss_pred HHHHHhcccHHHHHHHhhhhhhheeeeecCccchHhHHHHHHhCCchhhcccchhcccceeeeeeeccCcchhhhhh-hh
Confidence 6788999999886 788999999999999999999999999999999999999999999999999999995 57
Q ss_pred cCCCCCeEEEecCCC
Q 046825 1192 KDIKTPVITCPLLVG 1206 (1208)
Q Consensus 1192 k~ikTP~~~~~l~~~ 1206 (1208)
|++|||+++|+|..+
T Consensus 1100 k~~ktpsLtV~l~g~ 1114 (1605)
T KOG0260|consen 1100 KNAKTPSLTVYLTGE 1114 (1605)
T ss_pred ccCCCceEEEEecch
Confidence 999999999999754
No 5
>TIGR02390 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit A'. This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Probab=100.00 E-value=6.6e-213 Score=1980.32 Aligned_cols=794 Identities=35% Similarity=0.541 Sum_probs=703.2
Q ss_pred CCCCCCCCCCCCCccceeeccccccchhcHHHHHHHHHHhhhhccccccChhhHHHHHHHHHHhhcCChHHHhhhhcccC
Q 046825 1 CKTCGQRQFLCPGHFGHIDLVVPVYNPLLFNLLYTLLKRICFFCHHFKASRREVEKCVRKLELIIKGDIIAAKSLDLDLP 80 (1208)
Q Consensus 1 C~TCg~~~~~CPGHFGHIELa~PVynP~ff~~l~kLLr~iC~~C~rfll~~~~~~~~~~kL~ll~~G~~~~a~~L~~i~~ 80 (1208)
|+|||++..+||||||||||++|||||+||+.+++||+|+|++||||++++++...|..++++++..
T Consensus 56 C~TCg~~~~~CpGHFGhIeL~~PVfhpgf~~~i~kiL~~vC~~C~rll~~~~~~~~~~~~l~~~~~~------------- 122 (868)
T TIGR02390 56 CKTCGGKVGECPGHFGHIELARPVVHVGFAKEIYKILRATCRKCGRITLTEEEIEQYLEKINKLKEE------------- 122 (868)
T ss_pred CCCCCCCCCcCCCcceEEeccccccchhHHHHHHHHHHHHhhhcCceeeCccccHHHHHHHHhcccc-------------
Confidence 9999999999999999999999999999999999999999999999999988887888777653210
Q ss_pred CCCCCCCCccccccccccccCCCCCCCCccCCCCcccchhhHHHHHHHHHHHHHhc--ccCCCCCCCCCCceecccceEE
Q 046825 81 SESSNPEDSDVSNKSSCSMVTPRGNYDNVRNLKPQEWTSLQFAEAKLALLQFLKIE--TTKCGNCKAKNPRISKPTFGWI 158 (1208)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~ii~eflk~~--~~kC~~Cg~~~p~Irk~g~~ki 158 (1208)
....++++++++++.| .++|+|||+.+|+|++++...+
T Consensus 123 ----------------------------------------~~~~~~~l~~~i~~~~~~~~~C~~Cg~~~p~ir~~~~~~~ 162 (868)
T TIGR02390 123 ----------------------------------------GGDLASTLIEKIVKEAAKRMKCPHCGEEQKKIKFEKPTYF 162 (868)
T ss_pred ----------------------------------------hhhhHHHHHHHHHHHhhcCCCCCCCCCcCceEEEeeeeee
Confidence 0001256677777766 4689999999999998753321
Q ss_pred EEecCCchhhhhhhhccCCcCCCcCCCccccccCCCCCCCCCCCCCCCCCCCCCcchhhhhcccCCCCCCCCcccccccc
Q 046825 159 HMNGMPHADIRANLIRGCNLGETFSGGEEEKDLGASSDVDAPETHSFNGTFPGTQDTAARRHQKGSGAVPSGFKKQKDLF 238 (1208)
Q Consensus 159 ~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ed~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 238 (1208)
+.. .++ .++
T Consensus 163 ~~~--------------------------------------~~~-------------------------~~~-------- 171 (868)
T TIGR02390 163 YEE--------------------------------------GKE-------------------------GDV-------- 171 (868)
T ss_pred eec--------------------------------------cCC-------------------------CCe--------
Confidence 100 000 012
Q ss_pred CCCCCHHHHHHHHHhcCHhHHHHccccccccccCCCCCCCCceEEEeeeecCCCcccCCcccCC-CccCchhHHHHHHHH
Q 046825 239 SGPLLPSDVKDIIEKLWENEFELCSFISDMQQQGFGKKAGHSIFFLGVVLVPPIKFRLPSKGGD-SVMEHPQTVLLSKVL 317 (1208)
Q Consensus 239 ~~~L~P~eV~~iLkkI~~~d~~lL~ll~~~~~~~~~~~~~Pe~ffL~~lpVpP~~~RP~~~~~~-~~~eddlt~~l~~Ii 317 (1208)
.|+|.+|+++|++||++|+++|++. +...+|+||||++|||||+++||++.+++ .+.|||||.+|++||
T Consensus 172 --~L~p~~v~~ilk~I~~eD~~lLG~~--------p~~~~Pe~~ilt~LPVPP~~iRPsv~~~~g~~~EDDLT~~L~~II 241 (868)
T TIGR02390 172 --KLTPSEIRERLEKIPDEDAELLGIN--------PKVARPEWMVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDII 241 (868)
T ss_pred --ecCHHHHHHHHHhCCHHHHHHhCCC--------CCCCCcceeeEeccccCCCCCcCeEEeCCCcccCChHHHHHHHHH
Confidence 7999999999999999999999863 34578999999999999999999999875 789999999999999
Q ss_pred HHHHHHHHHHHcCCCCHHHHHHHHhhHHHHHHhhhcCCCCC--c----CCCChhhHHHHhhcccccccccccCccCCccc
Q 046825 318 QANIYLANAYVNQPDNAKVIVARWMNLQQSVNVLFDGKNAA--G----QRDMASGICQLLEKKEGLFRQKLMGKRVNYAC 391 (1208)
Q Consensus 318 ~~n~~l~~~~~~~~~~~~~i~~~~~~LQ~~v~~~~d~~~~~--~----~~~~~~~i~q~L~gK~G~fR~nlmGKRvd~sa 391 (1208)
+.|++|++.+..+ ++...+.+.|..||.+|+.||||+.+. . .+++.+||+|||+||+||||+|||||||||||
T Consensus 242 ~~N~~Lk~~~~~g-~~~~~~~~~~~~LQ~~v~~~~d~~~~~~~~~~~~~~~~~~~i~~~l~gK~G~~R~nl~GKRvd~s~ 320 (868)
T TIGR02390 242 RINQRLKENIEAG-APQLIIEDLWELLQYHVATYFDNELPGIPPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSA 320 (868)
T ss_pred HHHHHHHHHHHcC-CchhhhHHHHHHHHHHHHHHHcCCCCCCCccccCCCCCchhhHhhhcccccccccccccccccccC
Confidence 9999999988775 566667789999999999999998762 1 16889999999999999999999999999999
Q ss_pred eeeecCCCCccccccCchHHHHhhcCcccccchHHHHHHHHHHHcCCCCCCCceEEecCCCCcccCCCccccccccchhh
Q 046825 392 RSVISPDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLPPNKKMRISIGRKLD 471 (1208)
Q Consensus 392 RsVIspDP~l~~~evgvP~~~A~~Lt~pe~Vt~~Ni~~L~~lv~nG~~~~pGa~~i~~~~g~~~~~l~~~~~~~~~~r~~ 471 (1208)
||||||||+|++||||||..||++|||||+||+||+++|+++|.|||+.||||++|++++| .+++|... +|.+
T Consensus 321 RsVI~pdp~l~~~evGvP~~~A~~Lt~pe~Vt~~N~~~l~~lv~ng~~~~pga~~i~~~~g-~~~~l~~~------~~~~ 393 (868)
T TIGR02390 321 RTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVLNGPDSWPGANYVIRPDG-RRIKIRDE------NKEE 393 (868)
T ss_pred CceeeCCCCCcCCeeeCcHHHHHhCCCCeEEehhhHHHHHHHHHcCCccCCCceEEEcCCC-cEEechhh------hHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999 68887654 4666
Q ss_pred hcccccccCCCCCCCcccCceeehhhcccceEEEecCCCCCcCcccceeEEEeCCCCeEEEeccCCCCCCCCCCCCceec
Q 046825 472 TSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNV 551 (1208)
Q Consensus 472 ~a~~l~l~~~~~~~~~~~g~~v~Rhl~dgD~Vl~NRqPsLHk~simah~v~vl~~~~t~rln~~~c~~yNADFDGDemn~ 551 (1208)
+|.+| .+||+|+|||+|||+|||||||||||+|||||+|+|+++ +||||||++|+||||||||||||+
T Consensus 394 ~~~~l-----------~~g~~v~rhl~dgd~vl~NRqPsLHr~si~a~~~~v~~~-~t~r~n~~~c~~~NADFDGDeMn~ 461 (868)
T TIGR02390 394 LAERL-----------EPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPG-KTFRLNLAVCPPYNADFDGDEMNL 461 (868)
T ss_pred HHhhc-----------ccCCEEEEehhcCccceeccCCccccccceeEEEEEecC-ceEeeccccCCccccCcccceeeE
Confidence 67666 579999999999999999999999999999999999998 999999999999999999999999
Q ss_pred ccCCCHHHHHHHHHhcccCCceecCCCCCCcccchhhhhhhhhhcccCccccCHHHHHHHHHhcCccCCCCCCCCCCCCc
Q 046825 552 HFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQDHIVSAALLTKKDTFLNRDEFCQLLYSSGVSSSGLGSFTGKPGQ 631 (1208)
Q Consensus 552 h~pqs~~a~~Ea~~L~~~~~~~~sp~~g~pi~gl~QD~l~g~~lLT~~d~f~~~~~~~~l~~~~~~~~~~~~~~~~~~~~ 631 (1208)
|+|||++|||||++||++++||+||++|+|++|++||+|+|+|+||.+|+||++++++++++.+.+
T Consensus 462 h~Pqs~~a~aEa~~Lm~~~~~~~sp~~g~p~~~~~QD~l~g~~~LT~~d~f~~~~~~~~l~~~~~~-------------- 527 (868)
T TIGR02390 462 HVPQTEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQTILGVAGY-------------- 527 (868)
T ss_pred ecCCCHHHHHHHHHHhhchhceecCCCCCeeEEeehhhhhheeeeeeccccCCHHHHHHHHhcCCc--------------
Confidence 999999999999999999999999999999999999999999999999999999999999985442
Q ss_pred eeeeecccceeeccCCCccCCCCCCCCCeEEEEeeccccCCCcceeeccCCCCCcccccccccccccccccccccCcccc
Q 046825 632 RVLISRSEQEVLPLLPAIWKPEPLWTGKQVITAVLNHITRGRPPFVVERGGKLPQDFFKTRFNADKQSDRKKNDKGKLSK 711 (1208)
Q Consensus 632 ~~~~~~~~~~~~~~~PaIlkp~~lwTGKqv~s~~l~~~~~~~~~~n~~~~~k~~~~~~~~~~~~~~~~~~~~~~~g~~~~ 711 (1208)
.+.+|+|||+||+++||||||||++||. .+|+..+++++...|.
T Consensus 528 ---------~~~~~~p~i~kp~~lwTGKqi~s~~lp~------~~n~~~~~~~~~~~~~--------------------- 571 (868)
T TIGR02390 528 ---------FGDPPEPAIEKPKEYWTGKQIFSAFLPE------DLNFEGRAKICSGSDA--------------------- 571 (868)
T ss_pred ---------cccCCCceecCCcccccHHHHHHHhcCC------CCcceecccccccccc---------------------
Confidence 1357899999999999999999999974 4777766655443331
Q ss_pred ccccccccCCCccccccCCCCchhhhhhhcccccccCCceEEEecceeeeeecCccccC--CccHHHHHHHHhCHHHHHH
Q 046825 712 TNKMHKDKSGKKKEVVEGKPGEEKEAEKNKSKEKELSEEKLLIYKNDLVRGVIDKAQFA--DYGLVHTVQELYGSNTAGT 789 (1208)
Q Consensus 712 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~gell~G~ldK~~iG--~~~Lih~i~~~yG~~~a~~ 789 (1208)
...+.|.+|+.|+|+||+|++|+|||+++| .+||||.+|++||+.+|++
T Consensus 572 -----------------------------~~~~~~~~d~~v~i~~g~ll~G~ldK~~lg~~~~~li~~i~~~yG~~~a~~ 622 (868)
T TIGR02390 572 -----------------------------CKKEECPHDAYVVIKNGKLLKGVIDKKAIGAEKGKILHRIVREYGPEAARR 622 (868)
T ss_pred -----------------------------cccccCCCcceEEEecCeEEeeeecHHHhccCcccHHHHHHHHHCHHHHHH
Confidence 112345789999999999999999999999 7899999999999999999
Q ss_pred HHHHHHHHHHHHHHHcCceeeecccccChHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCChhhHHHHHHHHhcCCcc
Q 046825 790 LLSALSRLFTVFLQMHGFTCGVDDLLILKDKERERKNHLHGSEEIGKRVHLEALELEDGAEIDPIKLKSEIEKAMRGGGD 869 (1208)
Q Consensus 790 ~l~~l~~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~ 869 (1208)
||+++|+|+++||+++|||||++|+++++++.++++++++++++++.+++++|...... ..++.
T Consensus 623 fl~~~~~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~g~l~----------------~~~~~ 686 (868)
T TIGR02390 623 FLDSVTRLFIRFITLRGFTTGIDDIDIPKEAKEEIEELIEKAEKRVDNLIERYRNGELE----------------PLPGR 686 (868)
T ss_pred HHHHHHHHHHHHHHhccEEeehhheeeCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCc----------------cCcCC
Confidence 99999999999999999999999999999999999999999999998887777531100 01222
Q ss_pred hhhHHHHHHHHHHHHhhhhhHHHHHHhhcCCCCCCCCCcchhhhhcCCCCCcccHHHHHhhcccccccCcccCCCCCCcc
Q 046825 870 AAVAYFDMKMTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGKT 949 (1208)
Q Consensus 870 ~~~~~~~~~~~~~ln~~~~~~~~~~~~~~~l~~~~~~N~~~~M~~SGaKGS~vN~~Qi~~~lGQQ~leG~Rip~~~~grt 949 (1208)
..++.+|..+.+.|++++++ +.+.+. .. ..|+|++++|+.||||||.+|++||++|||||+++|+|||+|++|||
T Consensus 687 ~~~~~~e~~i~~~l~~~r~~-~~~~~~-~~---l~~~N~~~~M~~sGsKGS~~Ni~Qi~~~lGQQ~~~g~ri~~~~~~rt 761 (868)
T TIGR02390 687 TVEETLEMKIMEVLGKARDE-AGEVAE-KY---LDPENHAVIMARTGARGSLLNITQMAAMVGQQSVRGGRIRRGYRNRT 761 (868)
T ss_pred CHHHHHHHHHHHHHHHHHHH-HHHHHH-Hh---cCCCcchhhhhhccCCcccccHHHHHhccCccccCCCcCccccccCC
Confidence 23367787888888888877 544443 22 24799999999999999999999999999999999999999999999
Q ss_pred ccCCCCCCCCccccccccccccCCCCchhhhhhcccccccchhccccccCCchhhHHHHhhhceeeeecccEEEcCCCCE
Q 046825 950 LPSFHPWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSI 1029 (1208)
Q Consensus 950 LP~f~~~d~~~~a~GfI~~sF~~GL~p~EfFfH~maGReGLiDTAvKTa~SGYLqRrLvK~lEdl~V~YD~TVR~~~g~I 1029 (1208)
||||.++|.+|+|+|||.|||++||+|+|||||||||||||||||||||+||||||||||+||||+|+||+||||++|+|
T Consensus 762 lp~f~~~d~~~~~~GfV~~sF~~GL~p~EfFfH~m~gReGLiDTAvKTa~sGYLqRrLvk~lEdl~v~yD~tVR~~~g~i 841 (868)
T TIGR02390 762 LPHFKKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDTRGNL 841 (868)
T ss_pred CCCCCCCCCCcccCceecccccCCCCHHHHHHHHhhhccccccccccccccchhHHHHHHHHhheEEecCCeEEeCCCcE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeeecCCcceeccccccc
Q 046825 1030 VQFCYGEDGVDVHQTSFIS 1048 (1208)
Q Consensus 1030 vQF~YGedGld~~k~~~~~ 1048 (1208)
|||.|||||+||++.++..
T Consensus 842 iQf~YG~dg~d~~~~~~~~ 860 (868)
T TIGR02390 842 IQFKYGEDGVDPMKSDHGK 860 (868)
T ss_pred EEEeccCCCcCHHHhccCc
Confidence 9999999999999877654
No 6
>PRK08566 DNA-directed RNA polymerase subunit A'; Validated
Probab=100.00 E-value=4.3e-212 Score=1978.62 Aligned_cols=794 Identities=36% Similarity=0.545 Sum_probs=706.3
Q ss_pred CCCCCCCCCCCCCccceeeccccccchhcHHHHHHHHHHhhhhccccccChhhHHHHHHHHHHhhcCChHHHhhhhcccC
Q 046825 1 CKTCGQRQFLCPGHFGHIDLVVPVYNPLLFNLLYTLLKRICFFCHHFKASRREVEKCVRKLELIIKGDIIAAKSLDLDLP 80 (1208)
Q Consensus 1 C~TCg~~~~~CPGHFGHIELa~PVynP~ff~~l~kLLr~iC~~C~rfll~~~~~~~~~~kL~ll~~G~~~~a~~L~~i~~ 80 (1208)
|+|||++..+||||||||||++|||||+||+.+++||+|+|++||||++++++...|..+|+++...
T Consensus 61 C~TCg~~~~~CPGHFGhIeL~~PVfhpgf~~~v~~iL~~iC~~C~rll~~~~~~~~~~~~l~~~~~~------------- 127 (882)
T PRK08566 61 CKTCGGRAGECPGHFGHIELARPVIHVGFAKLIYKLLRATCRECGRLKLTEEEIEEYLEKLERLKEW------------- 127 (882)
T ss_pred CCCCCCCCCcCCCcceEEeccccccchhHHHHHHHHHHHhhhhhCceeccccchHHHHHHHhchhhh-------------
Confidence 9999999999999999999999999999999999999999999999999998887888887753210
Q ss_pred CCCCCCCCccccccccccccCCCCCCCCccCCCCcccchhhHHHHHHHHHHHHHhc--ccCCCCCCCCCCceecccceEE
Q 046825 81 SESSNPEDSDVSNKSSCSMVTPRGNYDNVRNLKPQEWTSLQFAEAKLALLQFLKIE--TTKCGNCKAKNPRISKPTFGWI 158 (1208)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~ii~eflk~~--~~kC~~Cg~~~p~Irk~g~~ki 158 (1208)
....+++++++++.| .++|+|||+.+|+|+++++..+
T Consensus 128 -----------------------------------------~~~~~~l~k~i~k~~k~~~~C~~Cg~~~~ki~~~~~~~~ 166 (882)
T PRK08566 128 -----------------------------------------GSLADDLIKEVKKEAAKRMVCPHCGEKQYKIKFEKPTTF 166 (882)
T ss_pred -----------------------------------------hhhHHHHHHHHHHHhcCCCCCCCcCCCCceEEEecceeE
Confidence 012245677888877 4689999999999998765422
Q ss_pred EEecCCchhhhhhhhccCCcCCCcCCCccccccCCCCCCCCCCCCCCCCCCCCCcchhhhhcccCCCCCCCCcccccccc
Q 046825 159 HMNGMPHADIRANLIRGCNLGETFSGGEEEKDLGASSDVDAPETHSFNGTFPGTQDTAARRHQKGSGAVPSGFKKQKDLF 238 (1208)
Q Consensus 159 ~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ed~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 238 (1208)
... .++ .++
T Consensus 167 ~~~--------------------------------------~~~-------------------------~~~-------- 175 (882)
T PRK08566 167 YEE--------------------------------------RKE-------------------------GLV-------- 175 (882)
T ss_pred EEe--------------------------------------cCC-------------------------Cce--------
Confidence 211 000 012
Q ss_pred CCCCCHHHHHHHHHhcCHhHHHHccccccccccCCCCCCCCceEEEeeeecCCCcccCCcccCC-CccCchhHHHHHHHH
Q 046825 239 SGPLLPSDVKDIIEKLWENEFELCSFISDMQQQGFGKKAGHSIFFLGVVLVPPIKFRLPSKGGD-SVMEHPQTVLLSKVL 317 (1208)
Q Consensus 239 ~~~L~P~eV~~iLkkI~~~d~~lL~ll~~~~~~~~~~~~~Pe~ffL~~lpVpP~~~RP~~~~~~-~~~eddlt~~l~~Ii 317 (1208)
+|+|.+|+++|++||++|+++|++. +...+|+||||++|||||+++||++.+++ .+.|||+|.+|++||
T Consensus 176 --~L~p~~V~~ilk~I~~eD~~lLg~~--------~~~~~Pe~~il~~lPVpP~~iRPsv~~~~g~~~eDDLT~~L~~II 245 (882)
T PRK08566 176 --KLTPSDIRERLEKIPDEDLELLGIN--------PEVARPEWMVLTVLPVPPVTVRPSITLETGQRSEDDLTHKLVDII 245 (882)
T ss_pred --eCCHHHHHHHHHhCCHHHHHHhCCC--------CCCCCcceeEEeeeecCCCCCcCcEEeCCCcccCchHHHHHHHHH
Confidence 8999999999999999999999863 34679999999999999999999999865 689999999999999
Q ss_pred HHHHHHHHHHHcCCCCHHHHHHHHhhHHHHHHhhhcCCCCCc------CCCChhhHHHHhhcccccccccccCccCCccc
Q 046825 318 QANIYLANAYVNQPDNAKVIVARWMNLQQSVNVLFDGKNAAG------QRDMASGICQLLEKKEGLFRQKLMGKRVNYAC 391 (1208)
Q Consensus 318 ~~n~~l~~~~~~~~~~~~~i~~~~~~LQ~~v~~~~d~~~~~~------~~~~~~~i~q~L~gK~G~fR~nlmGKRvd~sa 391 (1208)
+.|++|++.+..+ ++...+.+.|..||.+|+.||||+.+.. .+++++||+|||+||+||||+|||||||||||
T Consensus 246 ~~N~~Lk~~~~~g-~~~~~~~~~~~~LQ~~v~~~~d~~~~~~~~~~~~~~~~~~~i~~~l~gK~G~fR~nl~GKRvd~s~ 324 (882)
T PRK08566 246 RINQRLKENIEAG-APQLIIEDLWELLQYHVTTYFDNEIPGIPPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSA 324 (882)
T ss_pred HHHHHHHHHHHcC-CcHHHHHHHHHHHHHHHHHHhcCCccCCcccccCCCCCccchHHhcccCCCccccccccccccCcC
Confidence 9999999988875 5666678899999999999999988631 16789999999999999999999999999999
Q ss_pred eeeecCCCCccccccCchHHHHhhcCcccccchHHHHHHHHHHHcCCCCCCCceEEecCCCCcccCCCccccccccchhh
Q 046825 392 RSVISPDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLPPNKKMRISIGRKLD 471 (1208)
Q Consensus 392 RsVIspDP~l~~~evgvP~~~A~~Lt~pe~Vt~~Ni~~L~~lv~nG~~~~pGa~~i~~~~g~~~~~l~~~~~~~~~~r~~ 471 (1208)
||||||||+|++||||||..||++|||||+||+||+++|+++|.|||+.||||+||++++| .+++|.. .+|.+
T Consensus 325 RsVI~pdp~l~~~evGvP~~~A~~Lt~pe~v~~~N~~~l~~~v~ng~~~~pga~~i~~~~g-~~~~l~~------~~~~~ 397 (882)
T PRK08566 325 RTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNGPEKHPGANYVIRPDG-RRIKLTD------KNKEE 397 (882)
T ss_pred CceeeCCCCCcCCeeeCcHHHHHhCCCCeEEchhhHHHHHHHHHcCCCcCCCceEEEcCCC-ceeeehh------hhHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999 6777743 35777
Q ss_pred hcccccccCCCCCCCcccCceeehhhcccceEEEecCCCCCcCcccceeEEEeCCCCeEEEeccCCCCCCCCCCCCceec
Q 046825 472 TSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNV 551 (1208)
Q Consensus 472 ~a~~l~l~~~~~~~~~~~g~~v~Rhl~dgD~Vl~NRqPsLHk~simah~v~vl~~~~t~rln~~~c~~yNADFDGDemn~ 551 (1208)
+|+.| .+||+|+|||+|||+|||||||||||+|||||+|||+++ +||||||++|+||||||||||||+
T Consensus 398 ~~~~l-----------~~g~~v~Rhl~dgd~vl~NRqPsLHr~si~a~~~~v~~~-~t~r~n~~~c~~~NADFDGDeMn~ 465 (882)
T PRK08566 398 LAEKL-----------EPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPG-KTFRLNLAVCPPYNADFDGDEMNL 465 (882)
T ss_pred HHHhc-----------cccceehhhhhcCceeeecCCCcccccccceeEEEEecC-ceEeeccccCCCccCCccCcEEEE
Confidence 77776 569999999999999999999999999999999999998 999999999999999999999999
Q ss_pred ccCCCHHHHHHHHHhcccCCceecCCCCCCcccchhhhhhhhhhcccCccccCHHHHHHHHHhcCccCCCCCCCCCCCCc
Q 046825 552 HFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQDHIVSAALLTKKDTFLNRDEFCQLLYSSGVSSSGLGSFTGKPGQ 631 (1208)
Q Consensus 552 h~pqs~~a~~Ea~~L~~~~~~~~sp~~g~pi~gl~QD~l~g~~lLT~~d~f~~~~~~~~l~~~~~~~~~~~~~~~~~~~~ 631 (1208)
|+|||++|||||++||++++||+||++|+|++|++||+|+|+|+||++|+||++++++++++.+..
T Consensus 466 h~Pqs~~a~aEa~~Lm~~~~~~~sp~~g~pi~~~~QD~l~g~~~lt~~d~f~~~~~~~~l~~~~~~-------------- 531 (882)
T PRK08566 466 HVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAAGI-------------- 531 (882)
T ss_pred ecCCCHHHHHHHHHHhcchhcEecCCCCCeeEEeehHHHHHHHHHHhccccCCHHHHHHHHHhCCc--------------
Confidence 999999999999999999999999999999999999999999999999999999999999995432
Q ss_pred eeeeecccceeeccCCCccCCCCCCCCCeEEEEeeccccCCCcceeeccCCCCCcccccccccccccccccccccCcccc
Q 046825 632 RVLISRSEQEVLPLLPAIWKPEPLWTGKQVITAVLNHITRGRPPFVVERGGKLPQDFFKTRFNADKQSDRKKNDKGKLSK 711 (1208)
Q Consensus 632 ~~~~~~~~~~~~~~~PaIlkp~~lwTGKqv~s~~l~~~~~~~~~~n~~~~~k~~~~~~~~~~~~~~~~~~~~~~~g~~~~ 711 (1208)
..+.+|+|||++|+++||||||||++||. .+|+..+.+++.+.|..
T Consensus 532 --------~~~~~~~pai~~p~~lwTGKqi~s~~lp~------~~~~~~~~~~~~~~~~~-------------------- 577 (882)
T PRK08566 532 --------DELPEPEPAIENGKPYWTGKQIFSLFLPK------DLNLEFKAKICSGCDEC-------------------- 577 (882)
T ss_pred --------cccccCCcccCCCcccccHHHHHHHHcCC------CCCceeecccccccccc--------------------
Confidence 12568999999999999999999999974 46777766665555420
Q ss_pred ccccccccCCCccccccCCCCchhhhhhhcccccccCCceEEEecceeeeeecCccccC--CccHHHHHHHHhCHHHHHH
Q 046825 712 TNKMHKDKSGKKKEVVEGKPGEEKEAEKNKSKEKELSEEKLLIYKNDLVRGVIDKAQFA--DYGLVHTVQELYGSNTAGT 789 (1208)
Q Consensus 712 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~gell~G~ldK~~iG--~~~Lih~i~~~yG~~~a~~ 789 (1208)
..+.|.+|+.|+|+||+|++|+|||+++| ++||||.+|++||++.|++
T Consensus 578 ------------------------------~~~~~~~d~~v~i~~gell~g~ldK~~lg~~~~~li~~i~~~yG~~~a~~ 627 (882)
T PRK08566 578 ------------------------------KKEDCEHDAYVVIKNGKLLEGVIDKKAIGAEQGSILDRIVKEYGPERARR 627 (882)
T ss_pred ------------------------------ccccCCCCceEEEecCEEEeccccHHHhhcccchHHHHHHHHhCHHHHHH
Confidence 12245779999999999999999999999 7899999999999999999
Q ss_pred HHHHHHHHHHHHHHHcCceeeecccccChHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCChhhHHHHHHHHhcCCcc
Q 046825 790 LLSALSRLFTVFLQMHGFTCGVDDLLILKDKERERKNHLHGSEEIGKRVHLEALELEDGAEIDPIKLKSEIEKAMRGGGD 869 (1208)
Q Consensus 790 ~l~~l~~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~ 869 (1208)
||+++++|+++||+.+|||||++|+++++++.++++++++++++.+.+++++|...... ..++.
T Consensus 628 fl~~~~~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~g~l~----------------~~~~~ 691 (882)
T PRK08566 628 FLDSVTRLAIRFIMLRGFTTGIDDEDIPEEAKEEIDEIIEEAEKRVEELIEAYENGELE----------------PLPGR 691 (882)
T ss_pred HHHHHHHHHHHHHHhcCEEeehhhcccCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCc----------------cccCC
Confidence 99999999999999999999999999999999999999999999988888877541110 11222
Q ss_pred hhhHHHHHHHHHHHHhhhhhHHHHHHhhcCCCCCCCCCcchhhhhcCCCCCcccHHHHHhhcccccccCcccCCCCCCcc
Q 046825 870 AAVAYFDMKMTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGKT 949 (1208)
Q Consensus 870 ~~~~~~~~~~~~~ln~~~~~~~~~~~~~~~l~~~~~~N~~~~M~~SGaKGS~vN~~Qi~~~lGQQ~leG~Rip~~~~grt 949 (1208)
...+++|..+...|++++++ +.+.+. .. ..|+|++++|+.||||||.+|++||++|||||+++|+|||+||+|||
T Consensus 692 ~~~~~~e~~i~~~l~~~r~~-~~~~~~-~~---l~~~N~~~~M~~SGsKGS~~N~~Qi~~~lGqQ~~~g~ri~~~~~~rt 766 (882)
T PRK08566 692 TLEETLEMKIMQVLGKARDE-AGEIAE-KY---LGLDNPAVIMARTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDRT 766 (882)
T ss_pred CHHHHHHHHHHHHHHHHHHH-HHHHHH-Hh---cCCCCcceeeeccccccCHHHHHHHHhccCceecCCCcCccCccCcc
Confidence 23366777888888888776 554443 21 24799999999999999999999999999999999999999999999
Q ss_pred ccCCCCCCCCccccccccccccCCCCchhhhhhcccccccchhccccccCCchhhHHHHhhhceeeeecccEEEcCCCCE
Q 046825 950 LPSFHPWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSI 1029 (1208)
Q Consensus 950 LP~f~~~d~~~~a~GfI~~sF~~GL~p~EfFfH~maGReGLiDTAvKTa~SGYLqRrLvK~lEdl~V~YD~TVR~~~g~I 1029 (1208)
||||.++|.+|+|+|||.|||++||+|+|||||||||||||||||||||+||||||||||+||||+|+||+||||++|+|
T Consensus 767 LP~f~~~d~~~~~~GfV~~sF~~GL~p~EfffH~m~GReGliDTAvkTa~sGYlqRrLvk~ledl~v~yD~tVR~s~g~i 846 (882)
T PRK08566 767 LPHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDTRGNI 846 (882)
T ss_pred CCCCCCCCCCcccCceeeccccCCCCHHHHHHHHhhhcccccccceeeccCccchHHHHHHHhheEEeeCCceEcCCCcE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeeecCCcceeccccccc
Q 046825 1030 VQFCYGEDGVDVHQTSFIS 1048 (1208)
Q Consensus 1030 vQF~YGedGld~~k~~~~~ 1048 (1208)
|||.|||||+||++.++..
T Consensus 847 iQf~YG~dg~d~~~~~~~~ 865 (882)
T PRK08566 847 VQFKYGEDGVDPMKSDHGK 865 (882)
T ss_pred EEEeccCCCcCHHHhcCCC
Confidence 9999999999999877553
No 7
>TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit, predominant form. Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain.
Probab=100.00 E-value=5.2e-165 Score=1536.48 Aligned_cols=690 Identities=25% Similarity=0.362 Sum_probs=550.3
Q ss_pred CCCCceEEEeeeecCCCcccCCcccCC-CccCchhHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHhhHHHHHHhhhcC
Q 046825 276 KAGHSIFFLGVVLVPPIKFRLPSKGGD-SVMEHPQTVLLSKVLQANIYLANAYVNQPDNAKVIVARWMNLQQSVNVLFDG 354 (1208)
Q Consensus 276 ~~~Pe~ffL~~lpVpP~~~RP~~~~~~-~~~eddlt~~l~~Ii~~n~~l~~~~~~~~~~~~~i~~~~~~LQ~~v~~~~d~ 354 (1208)
.++|+||||++|||||+++||++.+++ .+++||+|.+|++||+.|++|++++..+ ++...+.++|.+||.+|+.||||
T Consensus 213 ~~~Pewmil~~lPV~Pp~lRP~v~l~gg~~~~sDLn~lyr~II~~Nn~Lk~~~~~~-ap~~ii~~~~~~LQ~aV~~liDn 291 (1140)
T TIGR02386 213 GNRPEWMVLDVIPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLELG-APEIIVRNEKRMLQEAVDALFDN 291 (1140)
T ss_pred CCChHHhhhhcccCCCCccCCcEEeCCCccccCchHHHHHHHHHHHHHHHHHHHcC-CcHHHHHHHHHHHHHHHHHHhcc
Confidence 478999999999999999999999976 6899999999999999999999998875 66666778999999999999999
Q ss_pred CCCCc-----CCCChhhHHHHhhcccccccccccCccCCccceeeecCCCCccccccCchHHHHhhcCcccccchHHHHH
Q 046825 355 KNAAG-----QRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVISPDPYLAVNEIGIPPYFALRLTYPERVTPWNVVK 429 (1208)
Q Consensus 355 ~~~~~-----~~~~~~~i~q~L~gK~G~fR~nlmGKRvd~saRsVIspDP~l~~~evgvP~~~A~~Lt~pe~Vt~~Ni~~ 429 (1208)
+.... .++|++||+|+||||+||||+|||||||||||||||+|||+|+++|||||..||++||+| ||+.+
T Consensus 292 ~~~g~~~~~~~~rplksls~~LkGK~GrFR~NLlGKRVDySgRSVI~pdP~L~l~e~GlP~~mA~~L~~P-----f~i~~ 366 (1140)
T TIGR02386 292 GRRGKPVVGKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKP-----FIIKR 366 (1140)
T ss_pred cccCCCccCcCCCchhhHHHhhcCCCCcccccccccccCCCCCCeEcCCCCcccccccChHHHHHHcCch-----HHHHH
Confidence 87631 278999999999999999999999999999999999999999999999999999999988 77766
Q ss_pred HHHHHHcCCCCCCCceEEecCCCCcccCCCccccccccchhhhcccccccCCCCCCCcccCceeehhhcccceEEEecCC
Q 046825 430 LRDSIINGAEIHPGATHYLDKLSTMRLPPNKKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQP 509 (1208)
Q Consensus 430 L~~lv~nG~~~~pGa~~i~~~~g~~~~~l~~~~~~~~~~r~~~a~~l~l~~~~~~~~~~~g~~v~Rhl~dgD~Vl~NRqP 509 (1208)
|++ +|.. .++ +.|+.+ +... ....|.|.+|+.+||+|||||||
T Consensus 367 L~~---~~~~----------------~~i------------~~ak~~-i~~~-----~~~v~~vl~~vi~~d~VLlNRqP 409 (1140)
T TIGR02386 367 LID---RELA----------------ANI------------KSAKKM-IEQE-----DPEVWDVLEDVIKEHPVLLNRAP 409 (1140)
T ss_pred HHH---cCcc----------------cch------------HHHHHH-HHhc-----CCccceEEEEccCCcEEEecCCC
Confidence 665 4321 111 112222 2211 12345566899999999999999
Q ss_pred CCCcCcccceeEEEeCCCCeEEEeccCCCCCCCCCCCCceecccCCCHHHHHHHHHhcccCCceecCCCCCCcccchhhh
Q 046825 510 TLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQDH 589 (1208)
Q Consensus 510 sLHk~simah~v~vl~~~~t~rln~~~c~~yNADFDGDemn~h~pqs~~a~~Ea~~L~~~~~~~~sp~~g~pi~gl~QD~ 589 (1208)
||||+|||||+++++++ +||||||+||+||||||||||||+|+|||++|++||++||.+++|++||++|+|+++++||+
T Consensus 410 TLHRlsIqAf~~~l~~g-ktirlhplvC~~fNADFDGDeMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ 488 (1140)
T TIGR02386 410 TLHRLGIQAFEPVLVEG-KAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKPIVTPSQDM 488 (1140)
T ss_pred cccccccceeEEEEecC-ceEEEcccccCcccCCCCcceeEeecCCCHHHHHHHHHHhCCcccEecCCCCCceEEeechh
Confidence 99999999999999987 99999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhcccCc--------cccCHHHHHHHHHhcCccCCCCCCCCCCCCceeeeecccceeeccCCCcc----CCCCCC-
Q 046825 590 IVSAALLTKKD--------TFLNRDEFCQLLYSSGVSSSGLGSFTGKPGQRVLISRSEQEVLPLLPAIW----KPEPLW- 656 (1208)
Q Consensus 590 l~g~~lLT~~d--------~f~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~PaIl----kp~~lw- 656 (1208)
++|+|+||.++ +|+++++++..+... .++.|+++ +++++|
T Consensus 489 ilG~y~LT~~~~~~~~~~~~F~~~~e~~~~~~~~---------------------------~i~l~~~i~~~~~g~~~~t 541 (1140)
T TIGR02386 489 VLGLYYLTTEKPGAKGEGKIFSNVDEAIRAYDNG---------------------------KVHLHALIGVRTSGEILET 541 (1140)
T ss_pred hheeeEeeeccccccCcCceeCCHHHHHHHHHcC---------------------------CccCCCceEEeccccEEEc
Confidence 99999999995 799999988643311 12223333 345677
Q ss_pred -CCCeEEEEeeccccCCCcceeeccCCCCCcccccccccccccccccccccCccccccccccccCCCccccccCCCCchh
Q 046825 657 -TGKQVITAVLNHITRGRPPFVVERGGKLPQDFFKTRFNADKQSDRKKNDKGKLSKTNKMHKDKSGKKKEVVEGKPGEEK 735 (1208)
Q Consensus 657 -TGKqv~s~~l~~~~~~~~~~n~~~~~k~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 735 (1208)
+|||||+.++|.- ++ |.+
T Consensus 542 t~Gr~if~~ilP~~------~~----------~~n--------------------------------------------- 560 (1140)
T TIGR02386 542 TVGRVIFNEILPEG------FP----------YIN--------------------------------------------- 560 (1140)
T ss_pred cchHHHHHHHcCCc------cc----------ccc---------------------------------------------
Confidence 5999998887631 11 100
Q ss_pred hhhhhcccccccCCceEEEecceeeeeecCccccCCccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHcCceeeecccc
Q 046825 736 EAEKNKSKEKELSEEKLLIYKNDLVRGVIDKAQFADYGLVHTVQELYGSNTAGTLLSALSRLFTVFLQMHGFTCGVDDLL 815 (1208)
Q Consensus 736 ~~~~~~~~~~~~~d~~v~i~~gell~G~ldK~~iG~~~Lih~i~~~yG~~~a~~~l~~l~~l~~~~l~~~GfSigi~D~~ 815 (1208)
.. .+|||+.+| +|||.+|++||++.|+.|||.+++|+++|++.+|||||++|+.
T Consensus 561 -----------~~-------------~~l~Kk~lg--~LI~~i~~~~G~~~t~~~LD~lk~Lgf~~at~~GfSigi~Dl~ 614 (1140)
T TIGR02386 561 -----------DN-------------EPLSKKEIS--SLIDLLYEVHGIEETAEMLDKIKALGFKYATKSGTTISASDIV 614 (1140)
T ss_pred -----------cc-------------cccchHHHH--HHHHHHHHHhChHHHHHHHHHHHHHHHHHHHhcCeeeeeccCC
Confidence 00 178999998 9999999999999999999999999999999999999999999
Q ss_pred cChHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCChhhHHHHHHHHhcCCcchhhHHHHHHHHHHHHhhhhhHHHHHH
Q 046825 816 ILKDKERERKNHLHGSEEIGKRVHLEALELEDGAEIDPIKLKSEIEKAMRGGGDAAVAYFDMKMTSQLNKHTSSSVINEL 895 (1208)
Q Consensus 816 ~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~ln~~~~~~~~~~~ 895 (1208)
+++++ .+++++|++++.++.++|.. + .+++.+ ....+...|++.+++ +.+.+
T Consensus 615 ip~~K----~~ii~~a~~~v~~i~~~y~~---G-~lt~~e-------------------r~~kvi~iw~~~~d~-v~~~~ 666 (1140)
T TIGR02386 615 VPDEK----YEILKEADKEVAKIQKFYNK---G-LITDEE-------------------RYRKVVSIWSETKDK-VTDAM 666 (1140)
T ss_pred CCHHH----HHHHHHHHHHHHHHHHHHHc---C-CCChHH-------------------HHHHHHHHHHHHHHH-HHHHH
Confidence 99864 58899999888888777743 1 112111 122333455555555 44444
Q ss_pred hhcCCCC-CCCCCcchhhhhcCCCCCcccHHHHHhhcccccccCcccCCCCCCccccCCCCCCCCccccccccccccCCC
Q 046825 896 LSEGLLK-PTGKNWISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGKTLPSFHPWDWAPRAGGFIIDRFLTGL 974 (1208)
Q Consensus 896 ~~~~l~~-~~~~N~~~~M~~SGaKGS~vN~~Qi~~~lGQQ~leG~Rip~~~~grtLP~f~~~d~~~~a~GfI~~sF~~GL 974 (1208)
+ ..+.+ ..+.|++++|+.||||||.+|++||+||+|||. ..+||++|+ ||.|||++||
T Consensus 667 ~-~~l~~~~~~~N~i~mMa~SGARGS~~ni~QL~GmrGlma--------~p~Grii~~------------PI~ssF~eGL 725 (1140)
T TIGR02386 667 M-KLLKKDTYKFNPIFMMADSGARGNISQFRQLAGMRGLMA--------KPSGDIIEL------------PIKSSFREGL 725 (1140)
T ss_pred H-HhcccccCCCCcHhhhhhcccccCHHHHHHHHhCCCccc--------CCCCCcccc------------chhhccccCC
Confidence 3 22321 125799999999999999999999999999987 345788885 5999999999
Q ss_pred CchhhhhhcccccccchhccccccCCchhhHHHHhhhceeeeecccEEEcCCCCEEEeeecCCcceeccccccccchhhh
Q 046825 975 RPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSIVQFCYGEDGVDVHQTSFISKFDALA 1054 (1208)
Q Consensus 975 ~p~EfFfH~maGReGLiDTAvKTa~SGYLqRrLvK~lEdl~V~YD~TVR~~~g~IvQF~YGedGld~~k~~~~~~~~~~~ 1054 (1208)
+|+|||||||||||||+|||||||+||||||||||++||+.|.||--- ...|-.|+....++| +..+.+.
T Consensus 726 tp~EyF~st~GaRkGLiDTAlKTAdSGYLtRRLVdv~qDviV~~dDCg-T~~gi~v~~~~~~~~---------~~i~~l~ 795 (1140)
T TIGR02386 726 TVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVVVREEDCG-TEEGIEVEAIVEGKD---------EIIESLK 795 (1140)
T ss_pred CHHHHhhhccchhccccchheeecccceeeeehhhhhcceEEEeCCCC-CCCCEEEEEeecCCc---------eEEeehh
Confidence 999999999999999999999999999999999999999999987432 223444554443221 2234456
Q ss_pred hhhccccccccccccCCCceeeechhHHHHHhhhcchhhhHHHHHHhHHHHHHHhHHHHHHh-hhcchhHHHHHHHHHHH
Q 046825 1055 ARERGRGRGRNKFCDKGSHTFVMGRNQEMIYKKCSGQLDASNAYIMELPDALKDNAEKFADK-FLSNEMAKQDFLKLVKH 1133 (1208)
Q Consensus 1055 ~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~l~~~~f~~l~~~ 1133 (1208)
+++.||+.+.+.+. +....+.+.+|...- . +..+++ .+.. ++. ..++.+||+.-..+|..
T Consensus 796 ~ri~GR~~~~di~~-~~~~~~i~~~~~~i~-~----------~~~~~i---~~~~----i~~v~iRS~ltC~s~~gvC~~ 856 (1140)
T TIGR02386 796 DRIVGRYSAEDVYD-PDTGKLIAEANTLIT-E----------EIAEKI---ENSG----IEKVKVRSVLTCESEHGVCQK 856 (1140)
T ss_pred heeEEEEEhhheEe-CCCCcEEEeCCCCcC-H----------HHHHHH---HHcC----CCEEEecCCeeeCCCCCCccc
Confidence 78889987766543 333445555553210 0 000000 0000 001 23789999999999999
Q ss_pred Hhhh-----cCCCCCCchhhhhhccCCCcccccccccccccCcccc--ccccccchHHHHHHHhhcCCCCCeEEEec
Q 046825 1134 KFVL-----SLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEM--NVTLGIPRLQEILTIASKDIKTPVITCPL 1203 (1208)
Q Consensus 1134 ~y~~-----slv~pGeaVGiIAAQSIGEP~TQMTLnTFH~AGv~~~--nVTlGvPRlkEIi~~ask~ikTP~~~~~l 1203 (1208)
||++ .+|+.|||||||||||||||||||||||||++|+++. +||+|+||+.||+. | .++|.|.+-.++
T Consensus 857 CYG~~La~~~~V~~GeaVGiiAAQSIGEPGTQLTmRTFHtGGv~~~~~DIT~GlpRv~elfe-a-r~p~~~a~iae~ 931 (1140)
T TIGR02386 857 CYGRDLATGKLVEIGEAVGVIAAQSIGEPGTQLTMRTFHTGGVAGASGDITQGLPRVKELFE-A-RTPKDKAVIAEV 931 (1140)
T ss_pred cCCCcccCCcEecccccceeEeeeecCCCcchhehhheeeccccccccccccCchhhhhhhh-c-ccCCCceEEEec
Confidence 9986 5789999999999999999999999999999999875 99999999999995 4 678877776554
No 8
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=100.00 E-value=3.3e-162 Score=1512.72 Aligned_cols=692 Identities=26% Similarity=0.376 Sum_probs=547.0
Q ss_pred CCCCceEEEeeeecCCCcccCCcccCC-CccCchhHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHhhHHHHHHhhhcC
Q 046825 276 KAGHSIFFLGVVLVPPIKFRLPSKGGD-SVMEHPQTVLLSKVLQANIYLANAYVNQPDNAKVIVARWMNLQQSVNVLFDG 354 (1208)
Q Consensus 276 ~~~Pe~ffL~~lpVpP~~~RP~~~~~~-~~~eddlt~~l~~Ii~~n~~l~~~~~~~~~~~~~i~~~~~~LQ~~v~~~~d~ 354 (1208)
.++|+||||++|||||+++||++.+++ ..++||+|.+|++||+.|++|++.+..+ ++...+.++|.+||.+|+.||||
T Consensus 221 ~~~Pewmil~~lPV~Pp~lRP~v~l~~g~~~~sDLn~lyr~II~rNnrLk~~~~~~-ap~~ii~~~~~~LQ~aV~~lidn 299 (1156)
T PRK00566 221 GNKPEWMILDVLPVIPPDLRPLVQLDGGRFATSDLNDLYRRVINRNNRLKRLLELG-APEIIVRNEKRMLQEAVDALFDN 299 (1156)
T ss_pred CCCccEeeEeecccCCCcccCceEeCCCcccCCchHHHHHHHHHHHHHHHHHHHcC-CcHHHHHHHHHHHHHHHHHHhcc
Confidence 479999999999999999999999976 6789999999999999999999998875 56665678999999999999999
Q ss_pred CCCCc-----CCCChhhHHHHhhcccccccccccCccCCccceeeecCCCCccccccCchHHHHhhcCcccccchHHHHH
Q 046825 355 KNAAG-----QRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVISPDPYLAVNEIGIPPYFALRLTYPERVTPWNVVK 429 (1208)
Q Consensus 355 ~~~~~-----~~~~~~~i~q~L~gK~G~fR~nlmGKRvd~saRsVIspDP~l~~~evgvP~~~A~~Lt~pe~Vt~~Ni~~ 429 (1208)
+.... .++|++||+|+||||+||||+|||||||||||||||+|||+|+++|||||..||++||+| ||
T Consensus 300 ~~~g~~~~~~~~rplksls~~LkGK~GrFR~NLlGKRVDySgRSVI~pdP~L~l~e~GvP~~mA~eL~~P-----f~--- 371 (1156)
T PRK00566 300 GRRGRPVTGPNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKP-----FI--- 371 (1156)
T ss_pred CccCCCcccccCCchhHHHHhhcCCCccccccccccccCCCCCceEeCCCCcccccccChHHHHHHhCcH-----HH---
Confidence 97631 268999999999999999999999999999999999999999999999999999999998 56
Q ss_pred HHHHHHcCCCCCCCceEEecCCCCcccCCCccccccccchhhhcccccccCCCCCCCcccCceeehhhcccceEEEecCC
Q 046825 430 LRDSIINGAEIHPGATHYLDKLSTMRLPPNKKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQP 509 (1208)
Q Consensus 430 L~~lv~nG~~~~pGa~~i~~~~g~~~~~l~~~~~~~~~~r~~~a~~l~l~~~~~~~~~~~g~~v~Rhl~dgD~Vl~NRqP 509 (1208)
+++|+.||+. .. +. .|+.+ +... . ...|.|.||+++||+|||||||
T Consensus 372 i~~L~~~g~~-----~~-----------ik------------~ak~~-~~~~----~-~~v~~vle~vi~gd~VLlNRqP 417 (1156)
T PRK00566 372 MKKLVERGLA-----TT-----------IK------------SAKKM-VERE----D-PEVWDVLEEVIKEHPVLLNRAP 417 (1156)
T ss_pred HHHHHHcCCc-----cc-----------hH------------hhhhh-hhhh----c-CcceEEEEEecCCCEEEecCCC
Confidence 5556778753 11 10 01111 1100 1 1234455778899999999999
Q ss_pred CCCcCcccceeEEEeCCCCeEEEeccCCCCCCCCCCCCceecccCCCHHHHHHHHHhcccCCceecCCCCCCcccchhhh
Q 046825 510 TLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQDH 589 (1208)
Q Consensus 510 sLHk~simah~v~vl~~~~t~rln~~~c~~yNADFDGDemn~h~pqs~~a~~Ea~~L~~~~~~~~sp~~g~pi~gl~QD~ 589 (1208)
||||+|||||+++++++ +||||||+||+||||||||||||+|+|||++|++||+.||.+++|++||++|+|+++++||+
T Consensus 418 TLHR~sIqAf~~~l~~g-ktirLhplvC~~fNADFDGDqMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ 496 (1156)
T PRK00566 418 TLHRLGIQAFEPVLIEG-KAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPANGKPIIVPSQDM 496 (1156)
T ss_pred cccccccceeEEEEecC-ceEEECccccCccccccccceeEEecCCCHHHHHHHHHHhCCcccEEecCCCCeeEEeehhh
Confidence 99999999999999886 99999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhcccCc--------cccCHHHHHHHHHhcCccCCCCCCCCCCCCceeeeecccceeeccCCCccCCCCCCCCCeE
Q 046825 590 IVSAALLTKKD--------TFLNRDEFCQLLYSSGVSSSGLGSFTGKPGQRVLISRSEQEVLPLLPAIWKPEPLWTGKQV 661 (1208)
Q Consensus 590 l~g~~lLT~~d--------~f~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~PaIlkp~~lwTGKqv 661 (1208)
|+|+|+||.++ +|+++++++++++...+ +.+..+.+++|.. +....|||||+
T Consensus 497 ilG~y~LT~~~~~~~~~~~~F~~~~e~~~~~~~~~i-------------------~l~~~i~~~~~~~-~~i~tt~Gk~i 556 (1156)
T PRK00566 497 VLGLYYLTREREGAKGEGMVFSSPEEALRAYENGEV-------------------DLHARIKVRITSK-KLVETTVGRVI 556 (1156)
T ss_pred hhhhheeecccccccCCCceeCCHHHHHHHHHcCCC-------------------CCCCeEEecCCCC-ceEEcCcHHHH
Confidence 99999999998 89999999987653221 1122333333310 12347999999
Q ss_pred EEEeeccccCCCcceeeccCCCCCcccccccccccccccccccccCccccccccccccCCCccccccCCCCchhhhhhhc
Q 046825 662 ITAVLNHITRGRPPFVVERGGKLPQDFFKTRFNADKQSDRKKNDKGKLSKTNKMHKDKSGKKKEVVEGKPGEEKEAEKNK 741 (1208)
Q Consensus 662 ~s~~l~~~~~~~~~~n~~~~~k~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 741 (1208)
|+.++|.- ++ |
T Consensus 557 f~~ilP~~------~~-----------~---------------------------------------------------- 567 (1156)
T PRK00566 557 FNEILPEG------LP-----------F---------------------------------------------------- 567 (1156)
T ss_pred HHhhcccc------ce-----------e----------------------------------------------------
Confidence 99988731 11 0
Q ss_pred ccccccCCceEEEecceeeeeecCccccCCccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHcCceeeecccccChHHH
Q 046825 742 SKEKELSEEKLLIYKNDLVRGVIDKAQFADYGLVHTVQELYGSNTAGTLLSALSRLFTVFLQMHGFTCGVDDLLILKDKE 821 (1208)
Q Consensus 742 ~~~~~~~d~~v~i~~gell~G~ldK~~iG~~~Lih~i~~~yG~~~a~~~l~~l~~l~~~~l~~~GfSigi~D~~~~~~~~ 821 (1208)
. +. +|++||+++| +|||.+|+.||++.|+.|||.+++|+++|++.+|||||++|+.+++++
T Consensus 568 -----~--------n~---~g~ldKk~Lg--~LI~~i~~~yG~~~t~~~LD~ik~Lgf~yat~~GfSigi~Dl~ip~~K- 628 (1156)
T PRK00566 568 -----I--------NV---NKPLKKKEIS--KIINEVYRRYGLKETVIFLDKIKDLGFKYATRSGISIGIDDIVIPPEK- 628 (1156)
T ss_pred -----e--------cc---cceecHHHHH--HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCeEeehhhcCcChHH-
Confidence 0 00 5899999999 899999999999999999999999999999999999999999999864
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhccCCCCChhhHHHHHHHHhcCCcchhhHHHHHHHHHHHHhhhhhHHHHHHhhcCCC
Q 046825 822 RERKNHLHGSEEIGKRVHLEALELEDGAEIDPIKLKSEIEKAMRGGGDAAVAYFDMKMTSQLNKHTSSSVINELLSEGLL 901 (1208)
Q Consensus 822 ~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~ln~~~~~~~~~~~~~~~l~ 901 (1208)
.++++++++++.++.++|.. + ..+.. +++ ..+...|++++++ +.+.++ +.+.
T Consensus 629 ---~~ii~~a~~~v~~i~~~y~~---G-~lt~~---er~----------------~kvi~~w~~~~d~-v~~~~~-~~l~ 680 (1156)
T PRK00566 629 ---KEIIEEAEKEVAEIEKQYRR---G-LITDG---ERY----------------NKVIDIWSKATDE-VAKAMM-KNLS 680 (1156)
T ss_pred ---HHHHHHHHHHHHHHHHHHHc---C-CCCch---HHH----------------HHHHHHHHHHHHH-HHHHHH-HhCc
Confidence 57888998888877777643 1 11111 111 1223334444444 444433 2232
Q ss_pred -CCCCCCcchhhhhcCCCCCcccHHHHHhhcccccccCcccCCCCCCccccCCCCCCCCccccccccccccCCCCchhhh
Q 046825 902 -KPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGKTLPSFHPWDWAPRAGGFIIDRFLTGLRPQEYY 980 (1208)
Q Consensus 902 -~~~~~N~~~~M~~SGaKGS~vN~~Qi~~~lGQQ~leG~Rip~~~~grtLP~f~~~d~~~~a~GfI~~sF~~GL~p~EfF 980 (1208)
+.+|+|++++|+.||||||.+|++||+||+|||. ..+|+++| .||.|||++||+|+|||
T Consensus 681 ~~~~~~N~i~mMa~SGARGS~~ni~QL~GmrGlma--------~p~G~iie------------~pI~ssFreGLt~~EyF 740 (1156)
T PRK00566 681 KDQESFNPIYMMADSGARGSASQIRQLAGMRGLMA--------KPSGEIIE------------TPIKSNFREGLTVLEYF 740 (1156)
T ss_pred cccCCCCChheeeeccCCcCHHHHHHHHhhcCccc--------cCCCCEee------------hhhhhhhhcCCCHHHHh
Confidence 3578999999999999999999999999999986 34677776 27999999999999999
Q ss_pred hhcccccccchhccccccCCchhhHHHHhhhceeeeecccEEEcCCCCEEEeeecCCcceecccc-ccccchhhhhhhcc
Q 046825 981 FHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSIVQFCYGEDGVDVHQTS-FISKFDALAARERG 1059 (1208)
Q Consensus 981 fH~maGReGLiDTAvKTa~SGYLqRrLvK~lEdl~V~YD~TVR~~~g~IvQF~YGedGld~~k~~-~~~~~~~~~~~~~~ 1059 (1208)
||||||||||+|||||||+|||||||||+ |++|.+||..||.. ..|+.+.... ..+..+.+.+++.|
T Consensus 741 fst~GaRkGLiDTALKTAdSGYLtRRLVd------vaqDviV~~~DCgT------~~gi~~~~~~~~~~~i~~l~~~~~G 808 (1156)
T PRK00566 741 ISTHGARKGLADTALKTADSGYLTRRLVD------VAQDVIVREDDCGT------DRGIEVTAIIEGGEVIEPLEERILG 808 (1156)
T ss_pred hcCcchhhcccchheeeccceeeehhHHH------hhCceEEEECCCCC------cCCEEEEEeccCCEEEeEhhheeEe
Confidence 99999999999999999999999999998 55555677777643 3454432211 11233456678889
Q ss_pred ccccccccccCCCceeeechhHHHHHhhhcchhhhHHHHHHhHHHHHHHhHHHHHHh-hhcchhHHHHHHHHHHHHhhhc
Q 046825 1060 RGRGRNKFCDKGSHTFVMGRNQEMIYKKCSGQLDASNAYIMELPDALKDNAEKFADK-FLSNEMAKQDFLKLVKHKFVLS 1138 (1208)
Q Consensus 1060 ~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~l~~~~f~~l~~~~y~~s 1138 (1208)
|+.+.+.+.. ....+.+.+|...- . +..+++ .+.. +++ ..++.+||+.-..+|..||++.
T Consensus 809 R~~~~di~~~-~t~~~i~~~~~~i~-~----------~~~~~i---~~~~----i~~v~iRS~ltC~s~~gvC~~CYG~~ 869 (1156)
T PRK00566 809 RVLAEDVVDP-ETGEVIVPAGTLID-E----------EIADKI---EEAG----IEEVKIRSVLTCETRHGVCAKCYGRD 869 (1156)
T ss_pred EEEhhheecC-CCCcEEEcCCCccC-H----------HHHHHH---HHcC----CCEEEEcCCeeecCCCcccHhhhCcc
Confidence 9887665543 23445555553210 0 000000 0000 011 1278999999999999999874
Q ss_pred -----CCCCCCchhhhhhccCCCcccccccccccccCccccccccccchHHHHHHHhhcCCCCCeEEEec
Q 046825 1139 -----LAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIKTPVITCPL 1203 (1208)
Q Consensus 1139 -----lv~pGeaVGiIAAQSIGEP~TQMTLnTFH~AGv~~~nVTlGvPRlkEIi~~ask~ikTP~~~~~l 1203 (1208)
+|+.|||||||||||||||||||||||||++|+ ++|.|+||+.|++. | .++|.+.+-.++
T Consensus 870 La~~~~v~iGeaVGiIAAQSIGEPGTQLTmRTFHtGGv---dIT~Glprv~elfe-a-r~pk~~a~ise~ 934 (1156)
T PRK00566 870 LATGKLVNIGEAVGVIAAQSIGEPGTQLTMRTFHTGGV---DITGGLPRVAELFE-A-RKPKGPAIIAEI 934 (1156)
T ss_pred ccCCCCcccCcceeEEeeeecCCCccceeeeeeeecce---eccCCccchhhhee-e-ccCCCceEEEec
Confidence 699999999999999999999999999999999 99999999999995 4 788888766554
No 9
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=100.00 E-value=9.5e-153 Score=1422.28 Aligned_cols=689 Identities=25% Similarity=0.340 Sum_probs=547.0
Q ss_pred CCCCCCceEEEeeeecCCCcccCCcccCC-CccCchhHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHhhHHHHHHhhh
Q 046825 274 GKKAGHSIFFLGVVLVPPIKFRLPSKGGD-SVMEHPQTVLLSKVLQANIYLANAYVNQPDNAKVIVARWMNLQQSVNVLF 352 (1208)
Q Consensus 274 ~~~~~Pe~ffL~~lpVpP~~~RP~~~~~~-~~~eddlt~~l~~Ii~~n~~l~~~~~~~~~~~~~i~~~~~~LQ~~v~~~~ 352 (1208)
...++|+||||++||||||++||++.+++ .+.+||||.+|++||+.|++|++++..+ ++...+.+.|.+||.+|+.||
T Consensus 307 ~s~~~PewmiL~vlPV~Pp~lRP~V~l~gg~~atsDLn~lyr~II~rNnrLk~l~~~~-ap~~ii~nekr~LQeaVd~li 385 (1460)
T PRK14906 307 KSGNDPADMILDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLG-APEIIVNNEKRMLQEAVDSLF 385 (1460)
T ss_pred ccCCCHHHHhhhcccCCCCCcCCcEEECCCcccCCchHHHHHHHHHHHHHHHHHHHcC-CcHHHHHHHHHHHHHHHHHHH
Confidence 34579999999999999999999999976 6789999999999999999999998875 666667789999999999999
Q ss_pred cCCCCCc-----CCCChhhHHHHhhcccccccccccCccCCccceeeecCCCCccccccCchHHHHhhcCcccccchHHH
Q 046825 353 DGKNAAG-----QRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVISPDPYLAVNEIGIPPYFALRLTYPERVTPWNV 427 (1208)
Q Consensus 353 d~~~~~~-----~~~~~~~i~q~L~gK~G~fR~nlmGKRvd~saRsVIspDP~l~~~evgvP~~~A~~Lt~pe~Vt~~Ni 427 (1208)
||+.... .++|++||+|+|+||+||||+|||||||||||||||+|||+|+++|||||..||.+||+| |++
T Consensus 386 DN~~~g~p~~~~~~rplKsls~~LkGK~GRFRqNLlGKRVDySgRSVIspdP~L~l~e~GlP~~mA~eLf~P-----f~i 460 (1460)
T PRK14906 386 DNGRRGRPVTGPGNRPLKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKP-----FVM 460 (1460)
T ss_pred cCCCcCCCCccccCCchhHHHHHhcccCcccccccccccccCcCCceEeCCCCCccccccCcHHHHHhcCch-----hHH
Confidence 9998631 278999999999999999999999999999999999999999999999999999999999 455
Q ss_pred HHHHHHHHcCCCCCCCceEEecCCCCcccCCCccccccccchhhhcccccccCCCCCCCcccCceeehhhcccceEEEec
Q 046825 428 VKLRDSIINGAEIHPGATHYLDKLSTMRLPPNKKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNR 507 (1208)
Q Consensus 428 ~~L~~lv~nG~~~~pGa~~i~~~~g~~~~~l~~~~~~~~~~r~~~a~~l~l~~~~~~~~~~~g~~v~Rhl~dgD~Vl~NR 507 (1208)
.+|.. +|.. .++.. |+.+ +.. .....|.|+||+++||+|||||
T Consensus 461 ~~L~~---~~~~----------------~nik~------------ak~~-i~~-----~~~~v~~vle~vi~gd~VLlNR 503 (1460)
T PRK14906 461 KRLVE---LEYA----------------ANIKA------------AKRA-VDR-----GASYVWDVLEEVIQDHPVLLNR 503 (1460)
T ss_pred HHHHH---hccc----------------ccHHH------------HhhH-Hhh-----cCCcceeeeeeeeccceeEecc
Confidence 44444 4321 01100 1111 110 0124677889999999999999
Q ss_pred CCCCCcCcccceeEEEeCCCCeEEEeccCCCCCCCCCCCCceecccCCCHHHHHHHHHhcccCCceecCCCCCCcccchh
Q 046825 508 QPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQ 587 (1208)
Q Consensus 508 qPsLHk~simah~v~vl~~~~t~rln~~~c~~yNADFDGDemn~h~pqs~~a~~Ea~~L~~~~~~~~sp~~g~pi~gl~Q 587 (1208)
||||||+|||||+++++++ +||||||+||+||||||||||||+|+|||++|++||+.||++++|++||++|+|+++++|
T Consensus 504 qPTLHRlsIqAf~~~L~~g-ktIrLhplvC~~fNADFDGDqMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~Q 582 (1460)
T PRK14906 504 APTLHRLGIQAFEPVLVEG-KAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSSNNIKSPAHGRPLTVPTQ 582 (1460)
T ss_pred CcccchhccceeeEEecCC-ceEEecccccCccccCCcCceeeeecCCCHHHHHHHHHHhcchhcEecCCCCCeeEEeee
Confidence 9999999999999988776 999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhhhcccC-c-------cccCHHHHHHHHHhcC-ccCCCCCCCCCCCCceeeeecccceeeccCC-----------
Q 046825 588 DHIVSAALLTKK-D-------TFLNRDEFCQLLYSSG-VSSSGLGSFTGKPGQRVLISRSEQEVLPLLP----------- 647 (1208)
Q Consensus 588 D~l~g~~lLT~~-d-------~f~~~~~~~~l~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P----------- 647 (1208)
|+|+|+|+||.. + .|.+.++++.++.... + +.+..+.+..|
T Consensus 583 D~ilG~y~LT~~~~~~~~~~~~F~~~~e~~~a~~~~~~~-------------------~l~~~i~~~~~~~~~~~~~~~~ 643 (1460)
T PRK14906 583 DMIIGVYYLTTERDGFEGEGRTFADFDDALNAYDARADL-------------------DLQAKIVVRLSRDMTVRGSYGD 643 (1460)
T ss_pred eeeeeeEEeeeccccccccCceeCCHHHHHHHHhcCCCc-------------------cccccEEEecCccccccccccc
Confidence 999999999974 3 7999999887766321 1 01111111111
Q ss_pred ----CccCCCCCCCCCeEEEEeeccccCCCcceeeccCCCCCcccccccccccccccccccccCccccccccccccCCCc
Q 046825 648 ----AIWKPEPLWTGKQVITAVLNHITRGRPPFVVERGGKLPQDFFKTRFNADKQSDRKKNDKGKLSKTNKMHKDKSGKK 723 (1208)
Q Consensus 648 ----aIlkp~~lwTGKqv~s~~l~~~~~~~~~~n~~~~~k~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ 723 (1208)
+..++...|+|+++|+.+||.
T Consensus 644 ~~~~~~~~~~~tt~Gr~Ifn~ilP~------------------------------------------------------- 668 (1460)
T PRK14906 644 LEETKAGERIETTVGRIIFNQVLPE------------------------------------------------------- 668 (1460)
T ss_pred ccCCCCCceEECCCCEEEEecccCC-------------------------------------------------------
Confidence 112334568888888877652
Q ss_pred cccccCCCCchhhhhhhcccccccCCceEEEecceeeeeecCccccCCccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHH
Q 046825 724 KEVVEGKPGEEKEAEKNKSKEKELSEEKLLIYKNDLVRGVIDKAQFADYGLVHTVQELYGSNTAGTLLSALSRLFTVFLQ 803 (1208)
Q Consensus 724 ~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~gell~G~ldK~~iG~~~Lih~i~~~yG~~~a~~~l~~l~~l~~~~l~ 803 (1208)
+..+++++++|+.+| +||+.+|+.||...++.|||.+++|+++|++
T Consensus 669 --------------------------------d~~fvN~~l~KK~Lg--~LI~~i~~~~G~~~t~~fLD~Ik~LGf~yaT 714 (1460)
T PRK14906 669 --------------------------------DYPYLNYKMVKKDIG--RLVNDCCNRYSTAEVEPILDGIKKTGFHYAT 714 (1460)
T ss_pred --------------------------------CcccccceeeHHHHH--HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHH
Confidence 012345689999998 8999999999999999999999999999999
Q ss_pred HcCceeeecccccChHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCChhhHHHHHHHHhcCCcchhhHHHHHHHHHHH
Q 046825 804 MHGFTCGVDDLLILKDKERERKNHLHGSEEIGKRVHLEALELEDGAEIDPIKLKSEIEKAMRGGGDAAVAYFDMKMTSQL 883 (1208)
Q Consensus 804 ~~GfSigi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~l 883 (1208)
.+|||||++|+.+|+++ .+++++|++++.++.++|.. + .++.. ..+..+...|
T Consensus 715 ~sG~SIgi~Di~ip~~K----~~iI~~A~~~V~ei~~~y~~---G-~iT~~-------------------Er~~kVi~iw 767 (1460)
T PRK14906 715 RAGLTVSVYDATIPDDK----PEILAEADEKVAAIDEDYED---G-FLSER-------------------ERHKQVVDIW 767 (1460)
T ss_pred hCCEEEeecccccChHH----HHHHHHHHHHHHHHHHHHHc---C-CCcHH-------------------HHHHHHHHHH
Confidence 99999999999998864 57899999998888887743 2 11111 1134455677
Q ss_pred HhhhhhHHHHHHhhcCCCCCCCCCcchhhhhcCCCCCcccHHHHHhhccccc-ccCcccCCCCCCccccCCCCCCCCccc
Q 046825 884 NKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQE-LEGKRVPRMVSGKTLPSFHPWDWAPRA 962 (1208)
Q Consensus 884 n~~~~~~~~~~~~~~~l~~~~~~N~~~~M~~SGaKGS~vN~~Qi~~~lGQQ~-leG~Rip~~~~grtLP~f~~~d~~~~a 962 (1208)
++++++ +.+.++. .+ .+.|++++|+.||||||..|+.||+||+|||. ..|++|+
T Consensus 768 ~~a~d~-v~~~~~~-~l---~~~N~i~mMa~SGARGS~~QI~QLaGmRGlma~p~G~iIe-------------------- 822 (1460)
T PRK14906 768 TEATEE-VGEAMLA-GF---DEDNPIYMMADSGARGNIKQIRQLAGMRGLMADMKGEIID-------------------- 822 (1460)
T ss_pred HHHHHH-HHHHHHH-hc---ccCCCeEeeeeccCcccHHHHHHHHhcccceecCCCCccc--------------------
Confidence 777777 6666652 33 36899999999999999999999999999975 4555442
Q ss_pred cccccccccCCCCchhhhhhcccccccchhccccccCCchhhHHHHhhhceeeeecccEEEcCCCCEEEeeecCCcceec
Q 046825 963 GGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSIVQFCYGEDGVDVH 1042 (1208)
Q Consensus 963 ~GfI~~sF~~GL~p~EfFfH~maGReGLiDTAvKTa~SGYLqRrLvK~lEdl~V~YD~TVR~~~g~IvQF~YGedGld~~ 1042 (1208)
.||.|||++||+|.|||||||||||||+|||+|||+||||||||||.+||| .||..||.. ..|+.+.
T Consensus 823 -~PI~SnFrEGLt~~EyFiSt~GaRKGL~DTALKTAdSGYLTRRLVdVaQDV------iV~e~DCgT------~~Gi~v~ 889 (1460)
T PRK14906 823 -LPIKANFREGLSVLEYFISTHGARKGLVDTALRTADSGYLTRRLVDVAQDV------IVREEDCGT------DEGVTYP 889 (1460)
T ss_pred -cccccccccCCCHHHHHHHcccccchhhhhhhhccccchHHHHHHHhhhhe------EEEeccCCC------CCCEEEE
Confidence 269999999999999999999999999999999999999999999977666 577777743 5676654
Q ss_pred cccccccchhhhhhhccccccccccccCCCceeeechhHHHHHhhhcchhhhHHHHHHhHHHHHHHhHHHHHHh-hhcch
Q 046825 1043 QTSFISKFDALAARERGRGRGRNKFCDKGSHTFVMGRNQEMIYKKCSGQLDASNAYIMELPDALKDNAEKFADK-FLSNE 1121 (1208)
Q Consensus 1043 k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~ 1121 (1208)
... ....+.+++.||+.+.+.+... ..+.+..|...-.. ...+ ...+.. +.+ ..++.
T Consensus 890 ~~~---~~~~l~~ri~GR~~~~di~~~~--g~~i~~~~~~I~~~----------~~~~---~i~~~g----i~~v~iRS~ 947 (1460)
T PRK14906 890 LVK---PKGDVDTNLIGRCLLEDVCDPN--GEVLLSAGDYIESM----------DDLK---RLVEAG----VTKVQIRTL 947 (1460)
T ss_pred Eee---cccchhheeeeEEEHhhhcCCC--CCEEEeCCCeeCcH----------HHHH---HHHHCC----CCEEEEeCC
Confidence 321 1345677888998776655332 34444445321000 0000 000000 011 23789
Q ss_pred hHHHHHHHHHHHHhhh-----cCCCCCCchhhhhhccCCCcccccccccccccCccccccccccchHHHHHHHhhcCCCC
Q 046825 1122 MAKQDFLKLVKHKFVL-----SLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIKT 1196 (1208)
Q Consensus 1122 l~~~~f~~l~~~~y~~-----slv~pGeaVGiIAAQSIGEP~TQMTLnTFH~AGv~~~nVTlGvPRlkEIi~~ask~ikT 1196 (1208)
+||+.-..+|..||++ .+|+.|||||||||||||||||||||||||++|++..+||+|+||+.|+|. | .++|.
T Consensus 948 ltC~s~~gvC~kCYG~dLatg~~V~iGeaVGiIAAQSIGEPGTQLTMRTFHtGGv~~~dit~GLpRv~eLfE-a-r~pk~ 1025 (1460)
T PRK14906 948 MTCHAEYGVCQKCYGWDLATRRPVNIGTAVGIIAAQSIGEPGTQLTMRTFHSGGVAGDDITQGLPRVAELFE-A-RKPKG 1025 (1460)
T ss_pred eeECCCCCChhhCcCCcccCCcEeccccceeeeeeeecCCCcceeeeeeeecccccccccccCcchhhhhee-e-ccCCC
Confidence 9999999999999987 468999999999999999999999999999999988899999999999995 4 56777
Q ss_pred CeEEEec
Q 046825 1197 PVITCPL 1203 (1208)
Q Consensus 1197 P~~~~~l 1203 (1208)
|.+-.+.
T Consensus 1026 ~a~i~e~ 1032 (1460)
T PRK14906 1026 EAVLAEI 1032 (1460)
T ss_pred ceeeecc
Confidence 6664443
No 10
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=100.00 E-value=1.1e-147 Score=1427.11 Aligned_cols=668 Identities=25% Similarity=0.366 Sum_probs=525.6
Q ss_pred CCCCCceEEEeeeecCCCcccCCcccCC-CccCchhHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHhhHHHHHHhhhc
Q 046825 275 KKAGHSIFFLGVVLVPPIKFRLPSKGGD-SVMEHPQTVLLSKVLQANIYLANAYVNQPDNAKVIVARWMNLQQSVNVLFD 353 (1208)
Q Consensus 275 ~~~~Pe~ffL~~lpVpP~~~RP~~~~~~-~~~eddlt~~l~~Ii~~n~~l~~~~~~~~~~~~~i~~~~~~LQ~~v~~~~d 353 (1208)
..++|+||||++||||||++||++.+++ .+++||+|.+|++||+.|++|++++..+ ++...+.+.|.+||.+|+.|||
T Consensus 1619 s~~~PewmiL~~lPV~Pp~lRP~v~l~gg~~a~sDln~lyr~II~rNnrLk~l~~~~-ap~~ii~nek~~LQ~aVd~l~D 1697 (2890)
T PRK09603 1619 SGNRPEWMMLTVLPVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRLMELG-APEIIVRNEKRMLQEAVDVLFD 1697 (2890)
T ss_pred cCCChHheeeeeeccCCCcccCcEEeCCCcccCCCccHHHHHHHHHHHHHHHHHHcC-CCceehHHHHHHHHHHHHHHhc
Confidence 4579999999999999999999999976 6789999999999999999999998875 5555567889999999999999
Q ss_pred CCCCCc-----CCCChhhHHHHhhcccccccccccCccCCccceeeecCCCCccccccCchHHHHhhcCcccccchHHHH
Q 046825 354 GKNAAG-----QRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVISPDPYLAVNEIGIPPYFALRLTYPERVTPWNVV 428 (1208)
Q Consensus 354 ~~~~~~-----~~~~~~~i~q~L~gK~G~fR~nlmGKRvd~saRsVIspDP~l~~~evgvP~~~A~~Lt~pe~Vt~~Ni~ 428 (1208)
|+.... .++|++||+|+|+||+||||+|||||||||||||||+|||+|+++|||||..||.+||+|+.
T Consensus 1698 N~~~~~~~~~~~~rplKsls~~LkGK~GRFRqNLlGKRVDySgRSVI~pdP~L~l~e~GvP~~mA~eL~~P~~------- 1770 (2890)
T PRK09603 1698 NGRSTNAVKGANKRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHL------- 1770 (2890)
T ss_pred cccccccccCCCCCcchhHHHHhcCCCCccccccccccccCcCCceEeCCCCcccccccChHHHHHHhCChHH-------
Confidence 998631 27899999999999999999999999999999999999999999999999999999999953
Q ss_pred HHHHHHHcCCCCCCCceEEecCCCCcccCCCccccccccchhhhcccccccCCCCCCCcccCceeehhhcccceEEEecC
Q 046825 429 KLRDSIINGAEIHPGATHYLDKLSTMRLPPNKKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQ 508 (1208)
Q Consensus 429 ~L~~lv~nG~~~~pGa~~i~~~~g~~~~~l~~~~~~~~~~r~~~a~~l~l~~~~~~~~~~~g~~v~Rhl~dgD~Vl~NRq 508 (1208)
+++|+.+|+.. .+.. |+.+ +.. .....|.|+|||.+||+||||||
T Consensus 1771 -i~~L~~~G~~~----------------~lk~------------ak~~-i~~-----~~~~v~~vlr~vi~gd~VLlNRq 1815 (2890)
T PRK09603 1771 -LSKLEERGYAT----------------TLKQ------------AKRM-IEQ-----KSNEVWECLQEITEGYPVLLNRA 1815 (2890)
T ss_pred -HHHHHHcCCcc----------------CHHH------------HHHH-HHh-----ccCccEEEEEeeecCCeEEecCC
Confidence 57788888631 1111 1111 110 11346788899999999999999
Q ss_pred CCCCcCcccceeEEEeCCCCeEEEeccCCCCCCCCCCCCceecccCCCHHHHHHHHHhcccCCceecCCCCCCcccchhh
Q 046825 509 PTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQD 588 (1208)
Q Consensus 509 PsLHk~simah~v~vl~~~~t~rln~~~c~~yNADFDGDemn~h~pqs~~a~~Ea~~L~~~~~~~~sp~~g~pi~gl~QD 588 (1208)
|||||+|||||+++++++ +||||||+||+||||||||||||+|+|||++|++||+.||++++|++||++|+|+++++||
T Consensus 1816 PTLHR~sIqAf~~~l~~g-ktIrLhplvC~~fNADFDGDqMnvHvPqS~eA~aEa~~LM~s~~nilsP~~G~Pi~~p~QD 1894 (2890)
T PRK09603 1816 PTLHKQSIQAFHPKLIDG-KAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLSSMNILLPASGKAVAIPSQD 1894 (2890)
T ss_pred CccccccceeeeEEEecC-ceEEeccccCCcccCCCCCceeEEeecCCHHHHHHHHHHhcccceEEEcCCCceeEEeecc
Confidence 999999999999999997 9999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhhcccCcccc--------CHHHHHHHHHhcCccCCCCCCCCCCCCceeeeecccceeeccCCCccCCCCCCC--C
Q 046825 589 HIVSAALLTKKDTFL--------NRDEFCQLLYSSGVSSSGLGSFTGKPGQRVLISRSEQEVLPLLPAIWKPEPLWT--G 658 (1208)
Q Consensus 589 ~l~g~~lLT~~d~f~--------~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~PaIlkp~~lwT--G 658 (1208)
+|+|+|+||.+++|+ +.+++...+.... . .+..+.|++++|+++|| |
T Consensus 1895 ~vlG~y~LT~~~~~~~~~~~~F~~~~e~~~~~~~~~-------------------~----~~~~~i~~~~~p~~l~Tt~G 1951 (2890)
T PRK09603 1895 MVLGLYYLSLEKSGVKGEHKLFSSVNEIITAIDTKE-------------------L----DIHAKIRVLDQGNIIATSAG 1951 (2890)
T ss_pred eeeeeEEeeccccCCCCccceeCCHHHHHHHHHcCC-------------------C----ccCCcceeecCCcEEEcCcc
Confidence 999999999999654 4445443222111 0 12345566678999999 9
Q ss_pred CeEEEEeeccccCCCcceeeccCCCCCcccccccccccccccccccccCccccccccccccCCCccccccCCCCchhhhh
Q 046825 659 KQVITAVLNHITRGRPPFVVERGGKLPQDFFKTRFNADKQSDRKKNDKGKLSKTNKMHKDKSGKKKEVVEGKPGEEKEAE 738 (1208)
Q Consensus 659 Kqv~s~~l~~~~~~~~~~n~~~~~k~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 738 (1208)
||+|+.+||.. ++ .
T Consensus 1952 K~ifs~ilP~~------~~--------~---------------------------------------------------- 1965 (2890)
T PRK09603 1952 RMIIKSILPDF------IP--------T---------------------------------------------------- 1965 (2890)
T ss_pred ceeeeccCccc------cc--------c----------------------------------------------------
Confidence 99999998731 00 0
Q ss_pred hhcccccccCCceEEEecceeeeeecCccccCCccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHcCceeeecccccCh
Q 046825 739 KNKSKEKELSEEKLLIYKNDLVRGVIDKAQFADYGLVHTVQELYGSNTAGTLLSALSRLFTVFLQMHGFTCGVDDLLILK 818 (1208)
Q Consensus 739 ~~~~~~~~~~d~~v~i~~gell~G~ldK~~iG~~~Lih~i~~~yG~~~a~~~l~~l~~l~~~~l~~~GfSigi~D~~~~~ 818 (1208)
.++.|+|||+.+| +|||.+|+.||+..|+.|||.+++|+++|++.+|||||++|+.+++
T Consensus 1966 -------------------~~~n~~ldKK~Lg--~LI~~i~~~yG~~~t~~fLD~lk~LGf~yat~~G~SIgI~Dl~ip~ 2024 (2890)
T PRK09603 1966 -------------------DLWNRPMKKKDIG--VLVDYVHKVGGIGITATFLDNLKTLGFRYATKAGISISMEDIITPK 2024 (2890)
T ss_pred -------------------ccEeeeechHHHH--HHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHhCCEeeeeccCcccH
Confidence 1223679999999 8999999999999999999999999999999999999999999997
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCChhhHHHHHHHHhcCCcchhhHHHHHHHHHHHHhhhhhHHHHHHhhc
Q 046825 819 DKERERKNHLHGSEEIGKRVHLEALELEDGAEIDPIKLKSEIEKAMRGGGDAAVAYFDMKMTSQLNKHTSSSVINELLSE 898 (1208)
Q Consensus 819 ~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~ln~~~~~~~~~~~~~~ 898 (1208)
+ +.+++++|.+++.++..+|.. + .++.. ++++++ ++ .|.++.++++++ +.+.+.
T Consensus 2025 ~----K~~iI~~A~~eV~ei~~~y~~---G-~it~~---Er~~kv-----------id-~w~~~~d~v~~~-~~~~l~-- 2078 (2890)
T PRK09603 2025 D----KQKMVEKAKVEVKKIQQQYDQ---G-LLTDQ---ERYNKI-----------ID-TWTEVNDKMSKE-MMTAIA-- 2078 (2890)
T ss_pred H----HHHHHHHHHHHHHHHHHHHHc---C-CCCcc---HHHHHH-----------HH-HHHHHHHHHHHH-HHHHhh--
Confidence 6 457899999888888777743 1 11111 122221 11 233333333333 333321
Q ss_pred CCCCCCCCCcchhhhhcCCCCCcccHHHHHhhcccccccCcccCCCCCCccccCCCCCCCCccccccccccccCCCCchh
Q 046825 899 GLLKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGKTLPSFHPWDWAPRAGGFIIDRFLTGLRPQE 978 (1208)
Q Consensus 899 ~l~~~~~~N~~~~M~~SGaKGS~vN~~Qi~~~lGQQ~leG~Rip~~~~grtLP~f~~~d~~~~a~GfI~~sF~~GL~p~E 978 (1208)
...++.|++++|+.||||||.+|++||+||+||+. .|.+...+ .+|.|||++||+|+|
T Consensus 2079 --~~~~~~N~i~mMa~SGARGS~~NI~QLaGmrGqMa--------------kp~G~iie------~PI~snFrEGLtp~E 2136 (2890)
T PRK09603 2079 --KDKEGFNSIYMMADSGARGSAAQIRQLSAMRGLMT--------------KPDGSIIE------TPIISNFKEGLNVLE 2136 (2890)
T ss_pred --hcCCCCCcHHHHHhccccccHHHHHHHHHcCCcEE--------------CCCCCccc------ChhhcCcccCCCHHH
Confidence 12357899999999999999999999999999965 23333332 359999999999999
Q ss_pred hhhhcccccccchhccccccCCchhhHHHHhhhceeeeecccEEEcCCCCEEEeeecCCcceeccccc-cccchhhhhhh
Q 046825 979 YYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSIVQFCYGEDGVDVHQTSF-ISKFDALAARE 1057 (1208)
Q Consensus 979 fFfH~maGReGLiDTAvKTa~SGYLqRrLvK~lEdl~V~YD~TVR~~~g~IvQF~YGedGld~~k~~~-~~~~~~~~~~~ 1057 (1208)
||||||||||||+|||||||+||||||||||++||+.|. ..||.. ..|+.+..... .+....+.+++
T Consensus 2137 yFfst~GaRKGLiDTALKTAdSGYLTRRLVdvaQDviI~------e~DCgT------~~Gi~v~~~~~~~~~i~~l~~ri 2204 (2890)
T PRK09603 2137 YFNSTHGARKGLADTALKTANAGYLTRKLIDVSQNVKVV------SDDCGT------HEGIEITDIAVGSELIEPLEERI 2204 (2890)
T ss_pred HHHhccccccchhhhhhhccccchhhhhHHHhhcceEEE------eccCCC------CCCeEEEEeecCCeeecchhhee
Confidence 999999999999999999999999999999988888654 444422 33444332111 12234467788
Q ss_pred ccccccccccccCCCceeeechhHHHHHhhhcchhhhHHHHHHhHHHHHHHhHHHHHHh-hhcchhHHHHHHHHHHHHhh
Q 046825 1058 RGRGRGRNKFCDKGSHTFVMGRNQEMIYKKCSGQLDASNAYIMELPDALKDNAEKFADK-FLSNEMAKQDFLKLVKHKFV 1136 (1208)
Q Consensus 1058 ~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~l~~~~f~~l~~~~y~ 1136 (1208)
.||+.+.+.+ ++....+.+.+|...- + +..+++ .+.. +++ ..++.+||+.-..+|..||+
T Consensus 2205 ~GR~~~~di~-~p~t~~~i~~~~~~I~-~----------~~~~~i---~~~g----i~~v~iRS~LtC~s~~gvC~~CYG 2265 (2890)
T PRK09603 2205 FGRVLLEDVI-DPITNEILLYADTLID-E----------EGAKKV---VEAG----IKSITIRTPVTCKAPKGVCAKCYG 2265 (2890)
T ss_pred eeEEEHhheE-cCCCCcEEEcCCcCcC-H----------HHHHHH---HHcC----CCEEEEcCcceecCCCcChhhhcC
Confidence 8998776554 3334445555553210 0 000000 0000 011 13889999999999999998
Q ss_pred h-----cCCCCCCchhhhhhccCCCcccccccccccccCccccc
Q 046825 1137 L-----SLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMN 1175 (1208)
Q Consensus 1137 ~-----slv~pGeaVGiIAAQSIGEP~TQMTLnTFH~AGv~~~n 1175 (1208)
+ .+|+.|||||||||||||||||||||||||++|+++..
T Consensus 2266 ~dLa~g~~V~iGeaVGiIAAQSIGEPGTQLTMRTFHtGGvas~~ 2309 (2890)
T PRK09603 2266 LNLGEGKMSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTASRS 2309 (2890)
T ss_pred CcccCCCCccCCceeeEEeecccCCCccccchhhheeccccccc
Confidence 7 46799999999999999999999999999999997643
No 11
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=100.00 E-value=8.3e-145 Score=1395.20 Aligned_cols=691 Identities=25% Similarity=0.334 Sum_probs=527.8
Q ss_pred CCCCCceEEEeeeecCCCcccCCcccCC-CccCchhHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHhhHHHHHHhhhc
Q 046825 275 KKAGHSIFFLGVVLVPPIKFRLPSKGGD-SVMEHPQTVLLSKVLQANIYLANAYVNQPDNAKVIVARWMNLQQSVNVLFD 353 (1208)
Q Consensus 275 ~~~~Pe~ffL~~lpVpP~~~RP~~~~~~-~~~eddlt~~l~~Ii~~n~~l~~~~~~~~~~~~~i~~~~~~LQ~~v~~~~d 353 (1208)
..++|+||||++|||||+++||++.+++ .+.+||||.+|++||+.|++|++++..+ ++...+.+.|.+||.+|+.|||
T Consensus 1662 s~~rPewmil~~lPV~Pp~lRP~v~l~~g~~~~sDLn~ly~~II~~NnrLk~~~~~~-ap~~ii~~~~~~LQ~~V~~l~D 1740 (2836)
T PRK14844 1662 SGNRPEWMILTTIPILPPDLRPLVSLESGRPAVSDLNHHYRTIINRNNRLRKLLSLN-PPEIMIRNEKRMLQEAVDSLFD 1740 (2836)
T ss_pred cCCChhheeeeccccCCCcccCcEEeCCCcccCCchHHHHHHHHHHHHHHHHHHHcC-CchhhHHHHHHHHHHHHHHHhc
Confidence 3579999999999999999999999875 7899999999999999999999998875 6666677899999999999999
Q ss_pred CCCCCc----C-CC-ChhhHHHHhhcccccccccccCccCCccceeeecCCCCccccccCchHHHHhhcCcccccchHHH
Q 046825 354 GKNAAG----Q-RD-MASGICQLLEKKEGLFRQKLMGKRVNYACRSVISPDPYLAVNEIGIPPYFALRLTYPERVTPWNV 427 (1208)
Q Consensus 354 ~~~~~~----~-~~-~~~~i~q~L~gK~G~fR~nlmGKRvd~saRsVIspDP~l~~~evgvP~~~A~~Lt~pe~Vt~~Ni 427 (1208)
|+.... . ++ +++||+|+|+||+||||+|||||||||||||||+|||+|+++|||||..||++||+| ||+
T Consensus 1741 n~~~g~~~~~~~~r~~lksls~~LkGK~GRFR~NLlGKRVDySgRSVI~pdP~L~l~evGlP~~mA~eL~~P-----f~i 1815 (2836)
T PRK14844 1741 NSRRNALVNKAGAVGYKKSISDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELFKP-----FVY 1815 (2836)
T ss_pred CCCCCCCccCCCCCCccccHHHHhcCCCCcccccccccccccCCCceEeCCCCcccceeeCCHHHHHhcccH-----HHH
Confidence 998631 1 33 479999999999999999999999999999999999999999999999999999997 788
Q ss_pred HHHHHHHHcCCCCCCCceEEecCCCCcccCCCccccccccchhhhcccccccCCCCCCCcccCceeehhhcccceEEEec
Q 046825 428 VKLRDSIINGAEIHPGATHYLDKLSTMRLPPNKKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNR 507 (1208)
Q Consensus 428 ~~L~~lv~nG~~~~pGa~~i~~~~g~~~~~l~~~~~~~~~~r~~~a~~l~l~~~~~~~~~~~g~~v~Rhl~dgD~Vl~NR 507 (1208)
++|+++... |.++ .|+.+ +... ...++++|+ |+++||+|||||
T Consensus 1816 ~~L~~~~~~-----~~i~--------------------------~a~~l-i~~~----~~~v~dile-~vi~gd~VLlNR 1858 (2836)
T PRK14844 1816 SKLKMYGMA-----PTIK--------------------------FASKL-IRAE----KPEVWDMLE-EVIKEHPVLLNR 1858 (2836)
T ss_pred HHHHHcCcc-----cchH--------------------------HHHHH-HHhh----CCcceEEEE-EEecCCEEEecC
Confidence 888875221 1110 11122 1110 113456555 455799999999
Q ss_pred CCCCCcCcccceeEEEeCCCCeEEEeccCCCCCCCCCCCCceecccCCCHHHHHHHHHhcccCCceecCCCCCCcccchh
Q 046825 508 QPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQ 587 (1208)
Q Consensus 508 qPsLHk~simah~v~vl~~~~t~rln~~~c~~yNADFDGDemn~h~pqs~~a~~Ea~~L~~~~~~~~sp~~g~pi~gl~Q 587 (1208)
||||||+|||||+++++++ +||||||+||+||||||||||||+|+|||++|+|||+.||++++|++||++|+|+++++|
T Consensus 1859 qPTLHR~sIqAf~~~l~~g-ktirlhp~vC~~fNADFDGDeMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pii~~~Q 1937 (2836)
T PRK14844 1859 APTLHRLGIQAFEPILIEG-KAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLSPSNGRPIIVPSK 1937 (2836)
T ss_pred CCccccccccceeeEeecC-ceEEecccCCCcccCCCCCceeeeecCCcHHHHHHHHHHhCCcccEEecCCCceeEeehh
Confidence 9999999999999998876 999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhhhcccCcccc----CHHHHHHHHHhcCccCCCCCCCCCCCCceeeeecccceeeccCCCccCCCCCC---CCCe
Q 046825 588 DHIVSAALLTKKDTFL----NRDEFCQLLYSSGVSSSGLGSFTGKPGQRVLISRSEQEVLPLLPAIWKPEPLW---TGKQ 660 (1208)
Q Consensus 588 D~l~g~~lLT~~d~f~----~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~PaIlkp~~lw---TGKq 660 (1208)
|+|+|+|+||.++.++ .+.+++++++... +| .+..++.++|..+| +|..
T Consensus 1938 D~ilG~y~LT~~~~~~~~~~~f~~~~~~~~a~~---------~~---------------~~~i~~~i~~~~~~~~~~~~~ 1993 (2836)
T PRK14844 1938 DIVLGIYYLTLQEPKEDDLPSFGAFCEVEHSLS---------DG---------------TLHIHSSIKYRMEYINSSGET 1993 (2836)
T ss_pred hhhhhhhhhcccccccccccccCCHHHHHHHHH---------cC---------------CcccCceEEeeeccccCCCCc
Confidence 9999999999999754 4566777555322 11 23445667777777 4431
Q ss_pred EEEEeeccccCCCcceeeccCCCCCcccccccccccccccccccccCccccccccccccCCCccccccCCCCchhhhhhh
Q 046825 661 VITAVLNHITRGRPPFVVERGGKLPQDFFKTRFNADKQSDRKKNDKGKLSKTNKMHKDKSGKKKEVVEGKPGEEKEAEKN 740 (1208)
Q Consensus 661 v~s~~l~~~~~~~~~~n~~~~~k~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 740 (1208)
....+. .+.|+..||.. +|
T Consensus 1994 ~~~~~~--tt~GR~if~~i----lP------------------------------------------------------- 2012 (2836)
T PRK14844 1994 HYKTIC--TTPGRLILWQI----FP------------------------------------------------------- 2012 (2836)
T ss_pred ccceEe--cccHHHHHHHH----cC-------------------------------------------------------
Confidence 110000 12222222210 00
Q ss_pred cccccccCCceEEEecceeeeeecCccccCCccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHcCceeeecccccChHH
Q 046825 741 KSKEKELSEEKLLIYKNDLVRGVIDKAQFADYGLVHTVQELYGSNTAGTLLSALSRLFTVFLQMHGFTCGVDDLLILKDK 820 (1208)
Q Consensus 741 ~~~~~~~~d~~v~i~~gell~G~ldK~~iG~~~Lih~i~~~yG~~~a~~~l~~l~~l~~~~l~~~GfSigi~D~~~~~~~ 820 (1208)
.... .++++++|+|+|+.++ +||+.+|+.||...++.|||.+++|+++|++.+|||+|++|+.+|+++
T Consensus 2013 ------~~~~----~~~~~~n~~l~KK~l~--~II~~~~~~yG~~~t~~fLD~lk~LGf~yaT~~G~SIgi~Di~iP~~K 2080 (2836)
T PRK14844 2013 ------KHEN----LGFDLINQVLTVKEIT--SIVDLVYRNCGQSATVAFSDKLMVLGFEYATFSGVSFSRCDMVIPETK 2080 (2836)
T ss_pred ------Cccc----cCcceEeeeechhHHH--HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhccEEeeHhHcccCHHH
Confidence 0000 1457889999999998 999999999999999999999999999999999999999999999876
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhccCCCCChhhHHHHHHHHhcCCcchhhHHHHHHHHHHHHhhhhhHHHHHHhhcCC
Q 046825 821 ERERKNHLHGSEEIGKRVHLEALELEDGAEIDPIKLKSEIEKAMRGGGDAAVAYFDMKMTSQLNKHTSSSVINELLSEGL 900 (1208)
Q Consensus 821 ~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~ln~~~~~~~~~~~~~~~l 900 (1208)
. +++++|++++.++.++|.. + .++.. ++ ...+...|++++++ +.+.++. .+
T Consensus 2081 ~----~iI~~a~~~v~~i~~~y~~---G-~it~~---Er----------------~~kvi~iW~~~~d~-v~~~~~~-~l 2131 (2836)
T PRK14844 2081 A----THVDHARGEIKKFSMQYQD---G-LITRS---ER----------------YNKVIDEWSKCTDM-IANDMLK-AI 2131 (2836)
T ss_pred H----HHHHHHHHHHHHHHHHHHc---C-CCCHH---HH----------------HHHHHHHHHHHHHH-HHHHHHH-hh
Confidence 4 6888999888888887743 2 11111 12 23444566666666 6655542 22
Q ss_pred C---CCCCCCcchhhhhcCCCCCcccHHHHHhhcccccccCcccCCCCCCccccCCCCCCCCccccccccccccCCCCch
Q 046825 901 L---KPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGKTLPSFHPWDWAPRAGGFIIDRFLTGLRPQ 977 (1208)
Q Consensus 901 ~---~~~~~N~~~~M~~SGaKGS~vN~~Qi~~~lGQQ~leG~Rip~~~~grtLP~f~~~d~~~~a~GfI~~sF~~GL~p~ 977 (1208)
. ...+.|++++|+.||||||..|+.|++||+||+.. | +|... ..+|.|||++||+|.
T Consensus 2132 ~~~~~~~~~N~i~mMa~SGARGS~sQI~QLaGmRGLmak-----p---~G~iI------------e~PI~SNFrEGLsv~ 2191 (2836)
T PRK14844 2132 SIYDGNSKYNSVYMMVNSGARGSTSQMKQLAGMRGLMTK-----P---SGEII------------ETPIISNFREGLNVF 2191 (2836)
T ss_pred hhccccCCCCceeeeecccCccCHHHHHHHHhcceeeec-----C---CCCee------------ecchhhhhccCCCHH
Confidence 1 11257999999999999999999999999999652 2 22221 245999999999999
Q ss_pred hhhhhcccccccchhccccccCCchhhHHHHhhhceeeeecccEEEcCCCCEEEeeecCCcceecccc-ccccchhhhhh
Q 046825 978 EYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSIVQFCYGEDGVDVHQTS-FISKFDALAAR 1056 (1208)
Q Consensus 978 EfFfH~maGReGLiDTAvKTa~SGYLqRrLvK~lEdl~V~YD~TVR~~~g~IvQF~YGedGld~~k~~-~~~~~~~~~~~ 1056 (1208)
|||||||||||||+|||+|||+|||||||||+.+||+ .||..||.. ..|+.+.... -......+.++
T Consensus 2192 EyFiSt~GaRKGL~DTALKTAdSGYLTRRLVDVaQDv------iI~e~DCgT------~~Gi~v~~~~~~~~~i~~L~~r 2259 (2836)
T PRK14844 2192 EYFNSTHGARKGLADTALKTANSGYLTRRLVDVSQNC------IVTKHDCKT------KNGLVVRATVEGSTIVASLESV 2259 (2836)
T ss_pred HhhhhccccccchhhhhhhcccccchhhhhhhhhceE------EEEecccCC------CCceEEEEeccCCeEEeEhhhe
Confidence 9999999999999999999999999999999866655 577777743 4565554321 11234456788
Q ss_pred hccccccccccccCCCceeeechhHHHHHhhhcchhhhHHHHHHhHHHHHHHhHHHHHHh-hhcchhHHHHHHHHHHHHh
Q 046825 1057 ERGRGRGRNKFCDKGSHTFVMGRNQEMIYKKCSGQLDASNAYIMELPDALKDNAEKFADK-FLSNEMAKQDFLKLVKHKF 1135 (1208)
Q Consensus 1057 ~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~l~~~~f~~l~~~~y 1135 (1208)
+.||+.+.+.+.+ ....+.+.+|... .. +..+.+. ... +++ ..++.+||+.-..+|..||
T Consensus 2260 i~GR~~a~di~~p-~t~~~i~~~~~~I-~~----------~~~~~i~---~~g----i~~v~IRS~ltC~s~~gvC~~CY 2320 (2836)
T PRK14844 2260 VLGRTAANDIYNP-VTKELLVKAGELI-DE----------DKVKQIN---IAG----LDVVKIRSPLTCEISPGVCSLCY 2320 (2836)
T ss_pred eEEEEEHhHeEcC-CCCCEEEeCCCcc-CH----------HHHHHHH---HcC----CCEEEEcCCeeECCCCCChhhcc
Confidence 8999877655433 3334444444321 00 0000000 000 011 2278999999999999999
Q ss_pred hh-----cCCCCCCchhhhhhccCCCcccccccccccccCccccccc--------cccchHHHH
Q 046825 1136 VL-----SLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVT--------LGIPRLQEI 1186 (1208)
Q Consensus 1136 ~~-----slv~pGeaVGiIAAQSIGEP~TQMTLnTFH~AGv~~~nVT--------lGvPRlkEI 1186 (1208)
++ .+|+.|||||||||||||||||||||||||++|+++..+. .|+-++..+
T Consensus 2321 G~~La~~~~V~iGeaVGiIAAQSIGEPGTQLTMRTFHtGGvas~~~~~~~i~~~~~G~v~~~~~ 2384 (2836)
T PRK14844 2321 GRDLATGKIVSIGEAVGVIAAQSVGEPGTQLTMRTFHIGGVMTRGVESSNIIASINAKIKLNNS 2384 (2836)
T ss_pred CccccCCCcccccccceeeeecccCCCcceeeeeheeeccccccccccceeEeccCceEEeccc
Confidence 87 5789999999999999999999999999999999765443 466665553
No 12
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]
Probab=100.00 E-value=1.6e-142 Score=1321.83 Aligned_cols=736 Identities=29% Similarity=0.400 Sum_probs=603.8
Q ss_pred CCCCCCCCCCCCCccceeeccccccchhcHHHHHHHHHHhhhhccccccChhhHHHHHHHHHHhhcCChHHHhhhhcccC
Q 046825 1 CKTCGQRQFLCPGHFGHIDLVVPVYNPLLFNLLYTLLKRICFFCHHFKASRREVEKCVRKLELIIKGDIIAAKSLDLDLP 80 (1208)
Q Consensus 1 C~TCg~~~~~CPGHFGHIELa~PVynP~ff~~l~kLLr~iC~~C~rfll~~~~~~~~~~kL~ll~~G~~~~a~~L~~i~~ 80 (1208)
| |||+....|||||||||||.||+||+||+.+..+|+|+|.+|+++++. +...+. . . .|+....
T Consensus 55 C-~Cg~~~~~~~~~~GhIeLa~Pv~hi~f~k~~~~~L~~~~~~~~~v~~~--~~~~~~-~-~-----------~l~~~~~ 118 (808)
T COG0086 55 C-TCGKYKRICPGGFGHIELAAPVAHIWFFKSIPSLLDMTCRDCERVLYF--EAYVVL-G-T-----------DLEKIQL 118 (808)
T ss_pred e-cCCCCcCcCCCCceeEEeecceEEechhhccHHHHhhhHHhhhhhhhH--hHHHHh-c-c-----------chhhhcc
Confidence 9 999999999999999999999999999999999999999999999998 222222 1 0 1110000
Q ss_pred CCCCCCCCccccccccccccCCCCCCCCccCCCCcccchhhHHHHHHHHHHHHHhcccCCCCCCCCCCceecccceEEEE
Q 046825 81 SESSNPEDSDVSNKSSCSMVTPRGNYDNVRNLKPQEWTSLQFAEAKLALLQFLKIETTKCGNCKAKNPRISKPTFGWIHM 160 (1208)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~ii~eflk~~~~kC~~Cg~~~p~Irk~g~~ki~~ 160 (1208)
.. ...+ +. ...|+|||+.+++++++++.++.+
T Consensus 119 ~~------------------------------------~~~~---------~~---~~~~~~~Ga~~~~~~~~~~~~~~~ 150 (808)
T COG0086 119 LN------------------------------------ETEY---------VY---DSFCAHCGAEAIKILLEKPDLETE 150 (808)
T ss_pred cc------------------------------------hhee---------ec---cccCCCCCchhHHHHHhCcchhhh
Confidence 00 0000 00 268999999999999887665532
Q ss_pred ecCCchhhhhhhhccCCcCCCcCCCccccccCCCCCCCCCCCCCCCCCCCCCcchhhhhcccCCCCCCCCccccccccCC
Q 046825 161 NGMPHADIRANLIRGCNLGETFSGGEEEKDLGASSDVDAPETHSFNGTFPGTQDTAARRHQKGSGAVPSGFKKQKDLFSG 240 (1208)
Q Consensus 161 ~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ed~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 240 (1208)
. ++ .
T Consensus 151 ~--------------------------------------~~----------------------------~---------- 154 (808)
T COG0086 151 R--------------------------------------EE----------------------------E---------- 154 (808)
T ss_pred h--------------------------------------hh----------------------------c----------
Confidence 1 00 1
Q ss_pred CCCHHHHHHHHHhcCHhHHHHccccccccccCCCCCCCCceEEEeeeecCCCcccCCcccCC-CccCchhHHHHHHHHHH
Q 046825 241 PLLPSDVKDIIEKLWENEFELCSFISDMQQQGFGKKAGHSIFFLGVVLVPPIKFRLPSKGGD-SVMEHPQTVLLSKVLQA 319 (1208)
Q Consensus 241 ~L~P~eV~~iLkkI~~~d~~lL~ll~~~~~~~~~~~~~Pe~ffL~~lpVpP~~~RP~~~~~~-~~~eddlt~~l~~Ii~~ 319 (1208)
.++|.+++++|++|+..|..+++ .++|+||||++|||||+++||++.+++ .+++||+|++|++||+.
T Consensus 155 ~~~~~~~~~~~~~l~~~d~~~~~------------~~~pewmil~vlpV~Pp~~RP~i~ld~g~~a~~dl~~~~~~ii~~ 222 (808)
T COG0086 155 TLSPTKVKKLLKRLKVVDAFLLS------------GNRPEWMILTVLPVPPPDLRPSIQLDGGRFAESDLNDLYRRVINR 222 (808)
T ss_pred ccCHHHHHHHHhhccHHHHHHhc------------CCCcceeEEEeeccCCCCCCcceecCCCccchhHHHHHHHHHHHH
Confidence 78899999999999999999987 368999999999999999999999986 78999999999999999
Q ss_pred HHHHHHHHHcCCCCHHHHHHHHhhHHHHHHhhhcCCCCCc--CCCChhhHHHHhhcccccccccccCccCCccceeeecC
Q 046825 320 NIYLANAYVNQPDNAKVIVARWMNLQQSVNVLFDGKNAAG--QRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVISP 397 (1208)
Q Consensus 320 n~~l~~~~~~~~~~~~~i~~~~~~LQ~~v~~~~d~~~~~~--~~~~~~~i~q~L~gK~G~fR~nlmGKRvd~saRsVIsp 397 (1208)
|++|+.++.. +++..+.++|..||++|++||||..++. .++|++||+||||||+||||+|||||||||||||||+|
T Consensus 223 n~rlk~~~~~--~~~~iv~~~~~~lQ~~v~~~~Dn~~~~~~~~~rPlksl~~~LkgK~GrFR~nL~GKRVd~SgRsVI~~ 300 (808)
T COG0086 223 NNRLKRLLEL--AAPIIVRNEKRMLQEAVDALFDNRRPRAVTGGRPLKSLSQRLKGKQGRFRQNLLGKRVDYSGRSVISV 300 (808)
T ss_pred HHHhHHhhhh--cchHHHHHHHHHHHHHHHHHhhcCCCCCccCCCccccHHHHhcCCCceeeccccccccCCCCceeecC
Confidence 9999998876 3446678899999999999999943321 16999999999999999999999999999999999999
Q ss_pred CCCccccccCchHHHHhhcCcccccchHHHHHHHHHHHcCCCCCCCceEEecCCCCcccCCCccccccccchhhhccccc
Q 046825 398 DPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLPPNKKMRISIGRKLDTSRGAI 477 (1208)
Q Consensus 398 DP~l~~~evgvP~~~A~~Lt~pe~Vt~~Ni~~L~~lv~nG~~~~pGa~~i~~~~g~~~~~l~~~~~~~~~~r~~~a~~l~ 477 (1208)
||+|+++|||||..||++||+|+.||++|++.|++ ||+++++..+ .+ +
T Consensus 301 ~P~l~~~e~GvP~~~A~~L~~p~~v~~~~~~~~~~----------~a~~~~~~~~-~~--------------------~- 348 (808)
T COG0086 301 GPNLKLNQCGVPKKMALELFKPFVVTELNIEGLRT----------GAKYAKRMVE-RR--------------------L- 348 (808)
T ss_pred CCCccccccCCHHHHHHHhccCEEEEehhhhhhhc----------CCceEEeccc-cc--------------------c-
Confidence 99999999999999999999999999999999998 8999987766 11 1
Q ss_pred ccCCCCCCCcccCceeehhhcccceEEEecCCCCCcCcccceeEEEeCCCCeEEEeccCCCCCCCCCCCCceecccCCCH
Q 046825 478 VQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDE 557 (1208)
Q Consensus 478 l~~~~~~~~~~~g~~v~Rhl~dgD~Vl~NRqPsLHk~simah~v~vl~~~~t~rln~~~c~~yNADFDGDemn~h~pqs~ 557 (1208)
..+|.|+||+++||+|||||||||||+|||+|.+++++.++|||+||++|.||||||||||||+|+|||.
T Consensus 349 ----------~~~w~Vl~evi~gd~Vl~NR~PtLHrlsImq~~e~vl~~gkt~rLh~lVc~~yNADFDGDeM~~Hvp~s~ 418 (808)
T COG0086 349 ----------PEVWDVLREVIDGDPVLLNRAPTLHRLSIMQAFEPVLPEGKAIRLHPLVCEAYNADFDGDEMAVHVPASG 418 (808)
T ss_pred ----------cccchHHHHHhcCCccccccCChHHHHHHHhhceeeccccceeecchhhccccccccCchhhhccccchH
Confidence 3589999999999999999999999999999999999977999999999999999999999999999999
Q ss_pred HHHHHHHHhcccCCceecCCCCCCcccchhhhhhhhhhcccCccccCHHHHHHHHHhcCccCCCCCCCCCCCCceeeeec
Q 046825 558 VSRAEAYNIVNANNQYVRPSNGDPLRSLIQDHIVSAALLTKKDTFLNRDEFCQLLYSSGVSSSGLGSFTGKPGQRVLISR 637 (1208)
Q Consensus 558 ~a~~Ea~~L~~~~~~~~sp~~g~pi~gl~QD~l~g~~lLT~~d~f~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ 637 (1208)
+|+|||+.||.+.+|++||++|+|+++.+||+|+|.||||..|+|++..+++++++... +
T Consensus 419 ea~AEa~~lm~tq~nilsP~~Ggpiv~~~qD~v~g~ylLt~~d~~~~~~~~~ei~l~~~--------~------------ 478 (808)
T COG0086 419 EAAAEARGLMGTQMNILTPHYGGPIVAPIQDTVGGPYLLTIVDAKLPSTPVGEIYLKDE--------Y------------ 478 (808)
T ss_pred HHHHHHHHhhccccccccCCCCCceEeecceEEeccEEEEEecccCCCCcceEEEeccc--------c------------
Confidence 99999999999999999999999999999999999999999999999999888766311 0
Q ss_pred ccceeeccCCCccCCCCCCCCCeEEEEeeccccCCCcceeeccCCCCCcccccccccccccccccccccCcccccccccc
Q 046825 638 SEQEVLPLLPAIWKPEPLWTGKQVITAVLNHITRGRPPFVVERGGKLPQDFFKTRFNADKQSDRKKNDKGKLSKTNKMHK 717 (1208)
Q Consensus 638 ~~~~~~~~~PaIlkp~~lwTGKqv~s~~l~~~~~~~~~~n~~~~~k~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~ 717 (1208)
.....+.|||.+|..+|||||++++++++.. ..++.... .|.
T Consensus 479 --~~~~e~~~ai~~~~~~~~~k~i~~~i~~~~~----~~~i~~t~-----------------------~~~--------- 520 (808)
T COG0086 479 --ADDREKAEAIAKKIELTTGKVIVSTISPDLA----ELSIIVTT-----------------------DGR--------- 520 (808)
T ss_pred --ccchhhhHHHhcccceeeeeEEEEEeeccCC----cceEEEec-----------------------chh---------
Confidence 1134577899999999999999998776431 11111000 000
Q ss_pred ccCCCccccccCCCCchhhhhhhcccccccC-CceEEEecceeeeeecCccccCCccHHHHHHHHhCHHHHH-HHHHHHH
Q 046825 718 DKSGKKKEVVEGKPGEEKEAEKNKSKEKELS-EEKLLIYKNDLVRGVIDKAQFADYGLVHTVQELYGSNTAG-TLLSALS 795 (1208)
Q Consensus 718 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-d~~v~i~~gell~G~ldK~~iG~~~Lih~i~~~yG~~~a~-~~l~~l~ 795 (1208)
.. .+ +....+ |..+.|.++.++.|++||.+. .+++.||+..+. .+++.+.
T Consensus 521 -----~~------------~~----~~~~~~~d~~~~i~~~~l~~~~i~k~~~-------~i~~~~g~~~~~~~~~~~~d 572 (808)
T COG0086 521 -----RI------------FN----RGLPEDKDVLVKIVNGKLIKGVIDKKIV-------TIYREYGPEVASKALVKLLD 572 (808)
T ss_pred -----hh------------hh----ccCCcccceeeEEeccccceeeehhhHH-------HHHHHhCchhhHHHHHHHHH
Confidence 00 00 000022 577899999999999997554 789999998888 9999999
Q ss_pred HHHHHHHHHcC-ceeeecccccChHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCChhhHHHHHHHHhcCCcchhhHH
Q 046825 796 RLFTVFLQMHG-FTCGVDDLLILKDKERERKNHLHGSEEIGKRVHLEALELEDGAEIDPIKLKSEIEKAMRGGGDAAVAY 874 (1208)
Q Consensus 796 ~l~~~~l~~~G-fSigi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~ 874 (1208)
+|...|+...| |+++++|.. .++.+++.+++.+|+..+.+.+.+|....- +.. .+......
T Consensus 573 kl~~~~~~~~~~~~~~i~~~d--~~~~~~~~e~v~~ae~~v~~~i~~~~~g~l----t~~------------~~~~i~e~ 634 (808)
T COG0086 573 KLKNLGIKGIGGFGIGIGRKD--IEAEDEKDEIVIEAEGSVLKLILQYEEGDL----TRT------------ERNNIVEI 634 (808)
T ss_pred HHHHhheeeeccceEEeeccc--ccchHHHHHHHHHHHHHHHHHHHHhhcCCc----ccc------------CCCCeEEE
Confidence 99999999888 999998876 233445568888898888888877754111 100 00001122
Q ss_pred HHHHHHHHHHhhhhhHHHHHHhhcCCCCCCCCCcchhhhhcCCCCCcccHHHHHhhcccccccCcccCCCCCCccccCCC
Q 046825 875 FDMKMTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGKTLPSFH 954 (1208)
Q Consensus 875 ~~~~~~~~ln~~~~~~~~~~~~~~~l~~~~~~N~~~~M~~SGaKGS~vN~~Qi~~~lGQQ~leG~Rip~~~~grtLP~f~ 954 (1208)
++.....++++...+ .++.+. ....++ +..|..+|++||..|++||++|+|||.+.|+|++.+ |||||.
T Consensus 635 ~e~~~~e~l~~ai~~-~~~~~~----~~~g~~--~~~i~~m~~~Gs~~n~sq~~~~iG~~gv~g~r~~~~----~~~~Fe 703 (808)
T COG0086 635 IEVLGIEALRNAIIE-EIKITL----EEQGLD--FVDIRHMGLSGARMNISQIVQLIGQQGVMGEKISVL----ARAAFE 703 (808)
T ss_pred eehHHHHHHHHHHHH-HHhhhH----HhcCCc--chhHHHHhhhhhccCHHHHHHHhhhheeeccCCCcc----cccccc
Confidence 333444444444433 233222 222333 566677777777789999999999999999999998 999999
Q ss_pred CCCCCccccccccccccCCCCchhhhhhcccccccchhccccccCCchhhHHHHhhhceeeeecccEEEcCCCCEEEeee
Q 046825 955 PWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSIVQFCY 1034 (1208)
Q Consensus 955 ~~d~~~~a~GfI~~sF~~GL~p~EfFfH~maGReGLiDTAvKTa~SGYLqRrLvK~lEdl~V~YD~TVR~~~g~IvQF~Y 1034 (1208)
+.+.++.+.|||.+||++||+|.|||||+|+||+||||||+|||+|||||||||+++|||+|.||++||++.+.++||.|
T Consensus 704 ~~~~~~~a~~~i~s~f~eGLt~~e~f~~~~ggR~GlvDTA~KTa~sGYl~RrLv~~~qdl~v~~d~~~~~g~~~~~~~~~ 783 (808)
T COG0086 704 VTVKHLEAEGPGESSFLEGLTENEYFGHPIGGRTGLVDTALKTADSGYLTRRLVDVAQDLIVQEDDCVTDGIGVVIQFEY 783 (808)
T ss_pred cccccceeeeeeecccCCCCCcceEEeecCccccchHHHhhhhcccCcceEEeechhcceEEEecCeEeecCceEEEEec
Confidence 99999999999999999999999999999999999999999999999999999999999999999999998889999999
Q ss_pred cCCcceecccccc
Q 046825 1035 GEDGVDVHQTSFI 1047 (1208)
Q Consensus 1035 GedGld~~k~~~~ 1047 (1208)
||||+|++.....
T Consensus 784 ged~~~~~~~~~~ 796 (808)
T COG0086 784 GEDGEDLTERILG 796 (808)
T ss_pred CccccCHHHHhcC
Confidence 9999998765443
No 13
>smart00663 RPOLA_N RNA polymerase I subunit A N-terminus.
Probab=100.00 E-value=2.1e-91 Score=779.71 Aligned_cols=290 Identities=41% Similarity=0.597 Sum_probs=267.9
Q ss_pred ceEEEeeeecCCCcccCCcccCC-CccCchhHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHhhHHHHHHhhhcCCCCC
Q 046825 280 SIFFLGVVLVPPIKFRLPSKGGD-SVMEHPQTVLLSKVLQANIYLANAYVNQPDNAKVIVARWMNLQQSVNVLFDGKNAA 358 (1208)
Q Consensus 280 e~ffL~~lpVpP~~~RP~~~~~~-~~~eddlt~~l~~Ii~~n~~l~~~~~~~~~~~~~i~~~~~~LQ~~v~~~~d~~~~~ 358 (1208)
+||||++|||||+|+||++.+++ .+.+||+|.+|++||+.|+.|++....+ ++...+.+.|..||.+|+.|+||+..+
T Consensus 1 e~fil~~lpVpP~~~RP~v~~~~~~~~eddlt~~l~~Ii~~N~~L~~~~~~~-~~~~~~~~~~~~LQ~~v~~~~d~~~~~ 79 (295)
T smart00663 1 EWMILTVLPVPPPCLRPSVSLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELG-APEHIIRNEKRLLQEAVDTLFDNEGLP 79 (295)
T ss_pred CeEEEeccccCCCCCCCcEEeCCCcccCCcHHHHHHHHHHHHHHHHHHHHcC-ChHHHHHHHHHHHHHHHHHHHccCCCc
Confidence 69999999999999999999876 7889999999999999999999988764 566667788999999999999998322
Q ss_pred -c---CCCChhhHHHHhhcccccccccccCccCCccceeeecCCCCccccccCchHHHHhhcCcccccchHHHHHHHHHH
Q 046825 359 -G---QRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVISPDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSI 434 (1208)
Q Consensus 359 -~---~~~~~~~i~q~L~gK~G~fR~nlmGKRvd~saRsVIspDP~l~~~evgvP~~~A~~Lt~pe~Vt~~Ni~~L~~lv 434 (1208)
. .+++++||+|||+||+|+||+|||||||||||||||||||+|++||||||..||++||+||.||.||+++|+++|
T Consensus 80 ~~~~~~~~~~~~i~~~l~gK~G~~R~nllGKRvd~s~RsVI~pdP~l~~~evgiP~~~A~~Lt~pe~v~~~n~~~l~~lv 159 (295)
T smart00663 80 RARQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKLV 159 (295)
T ss_pred ccccCCCCCcccccccccCcCCccccccccccccccCceEEeCCCCcceeEeeCCHHHHHhCCcCEEEhHHHHHHHHHHH
Confidence 1 257899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HcCCCCCCCceEEecCCCCcccCCCccccccccchhhhcccccccCCCCCCCcccCceeehhhcccceEEEecCCCCCcC
Q 046825 435 INGAEIHPGATHYLDKLSTMRLPPNKKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQPTLHKP 514 (1208)
Q Consensus 435 ~nG~~~~pGa~~i~~~~g~~~~~l~~~~~~~~~~r~~~a~~l~l~~~~~~~~~~~g~~v~Rhl~dgD~Vl~NRqPsLHk~ 514 (1208)
.||+ |||++|++ | .+++|... +|.+++..| .+|++|+|||+|||+|||||||||||+
T Consensus 160 ~ng~---pga~~i~~--g-~~~~l~~~------~~~~~~~~l-----------~~g~~v~r~l~dgd~Vl~NRqPsLHr~ 216 (295)
T smart00663 160 RNGP---NGAKYIIR--G-KKTNLKLA------KRSKIAKHL-----------KIGDIVERHVIDGDVVLFNRQPTLHRM 216 (295)
T ss_pred hcCC---CCceEEEe--C-cEEEchhh------hhHHHHhcC-----------ccccEeheehhcCCEEEEecCCccccc
Confidence 9999 99999997 6 56666443 344455555 579999999999999999999999999
Q ss_pred cccceeEEEeCCCCeEEEeccCCCCCCCCCCCCceecccCCCHHHHHHHHHhcccCCceecCCCCCCcccchhhhhhhhh
Q 046825 515 SIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQDHIVSAA 594 (1208)
Q Consensus 515 simah~v~vl~~~~t~rln~~~c~~yNADFDGDemn~h~pqs~~a~~Ea~~L~~~~~~~~sp~~g~pi~gl~QD~l~g~~ 594 (1208)
|||||+|+|+++ +||||||++|+||||||||||||+|+|||++|+|||.+||.+.+|++||++|+|++|++||+++|+|
T Consensus 217 si~a~~v~v~~~-~tir~n~~~c~~fNADFDGDeMnih~pqs~~a~aEa~~Lm~~~~~~~sp~~g~p~~~~~QD~l~g~~ 295 (295)
T smart00663 217 SIQAHRVRVLEG-KTIRLNPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295 (295)
T ss_pred cceeEEEEEecC-ceEEecCccCCcccCCcCCCEEEEecCCCHHHHHHHHHHhhhhhccccCCCCCeeEeeecceeeecC
Confidence 999999999998 9999999999999999999999999999999999999999999999999999999999999999987
No 14
>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional
Probab=100.00 E-value=6e-84 Score=760.84 Aligned_cols=282 Identities=28% Similarity=0.423 Sum_probs=249.8
Q ss_pred CCCCCceEEEeeeecCCCcccCCcccCC-CccCchhHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHhhHHHHHHhhhc
Q 046825 275 KKAGHSIFFLGVVLVPPIKFRLPSKGGD-SVMEHPQTVLLSKVLQANIYLANAYVNQPDNAKVIVARWMNLQQSVNVLFD 353 (1208)
Q Consensus 275 ~~~~Pe~ffL~~lpVpP~~~RP~~~~~~-~~~eddlt~~l~~Ii~~n~~l~~~~~~~~~~~~~i~~~~~~LQ~~v~~~~d 353 (1208)
...+|+||||++|||||+++||++.+++ ..++||+|.+|++||+.|++|++....+ ++...+.+.|.+||.+|++|||
T Consensus 238 ~~~~PewmiL~~lPV~Pp~lRP~v~l~~g~~~~sDLn~ly~~II~rNn~L~~~~~~~-~p~~ii~~~~~~LQ~aVd~liD 316 (627)
T PRK02625 238 TGSRPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEIL-APEIIVRNEKRMLQEAVDALID 316 (627)
T ss_pred cCCCccEEEEEeeecCCCcccCceEeCCCcccCCCHHHHHHHHHHHHHHHHHHHHcC-CcHHHHHHHHHHHHHHHHHHhc
Confidence 4579999999999999999999999976 6789999999999999999999988775 5555456799999999999999
Q ss_pred CCCCCc-----CCCChhhHHHHhhcccccccccccCccCCccceeeecCCCCccccccCchHHHHhhcCcccccchHHHH
Q 046825 354 GKNAAG-----QRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVISPDPYLAVNEIGIPPYFALRLTYPERVTPWNVV 428 (1208)
Q Consensus 354 ~~~~~~-----~~~~~~~i~q~L~gK~G~fR~nlmGKRvd~saRsVIspDP~l~~~evgvP~~~A~~Lt~pe~Vt~~Ni~ 428 (1208)
|+.... .+++.+||+|+|+||+||||+|||||||||||||||||||+|++||||||.+||.+||+| ||++
T Consensus 317 n~~~g~~~~~~~~rp~ksls~~LkGKeGRFR~NLlGKRVDySgRSVIspdP~L~l~e~GvP~~mA~eL~~P-----f~i~ 391 (627)
T PRK02625 317 NGRRGRTVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQP-----FVIH 391 (627)
T ss_pred CCCCCCCcccccCCchhhHHHHhccCCccccccccccccccCCCceEeCCCCcccccccChHHHHHhcCcH-----HhHH
Confidence 998631 278999999999999999999999999999999999999999999999999999999998 6877
Q ss_pred HHHHHHHcCCC-CCCCceEEecCCCCcccCCCccccccccchhhhcccccccCCCCCCCcccCceeehhhcccceEEEec
Q 046825 429 KLRDSIINGAE-IHPGATHYLDKLSTMRLPPNKKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNR 507 (1208)
Q Consensus 429 ~L~~lv~nG~~-~~pGa~~i~~~~g~~~~~l~~~~~~~~~~r~~~a~~l~l~~~~~~~~~~~g~~v~Rhl~dgD~Vl~NR 507 (1208)
+|+ .+|.. ..++ |+.+ +... ....+.|+|||+|||+|||||
T Consensus 392 ~L~---~~g~~~~i~~-----------------------------ak~~-i~~~-----~~~~~~Vlr~v~~gd~VLlNR 433 (627)
T PRK02625 392 RLI---RQGIVNNIKA-----------------------------AKKL-IQRA-----DPEVWQVLEEVIEGHPVLLNR 433 (627)
T ss_pred HHH---HcCchhhHHH-----------------------------HHHH-HHhc-----CCcccEEEEEeecCcEEEecC
Confidence 764 45532 0111 2222 2111 124678899999999999999
Q ss_pred CCCCCcCcccceeEEEeCCCCeEEEeccCCCCCCCCCCCCceecccCCCHHHHHHHHHhcccCCceecCCCCCCcccchh
Q 046825 508 QPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQ 587 (1208)
Q Consensus 508 qPsLHk~simah~v~vl~~~~t~rln~~~c~~yNADFDGDemn~h~pqs~~a~~Ea~~L~~~~~~~~sp~~g~pi~gl~Q 587 (1208)
||||||+|||||+++++++ +||||||+||+||||||||||||+|+|||++|+|||+.||.+++|++||++|+|+++++|
T Consensus 434 qPTLHR~sIqAf~~~l~~~-ktirlhplvC~~fNADFDGDeMnvHvPqS~~A~aEa~~Lm~~~~nilsP~~G~Pi~~~~Q 512 (627)
T PRK02625 434 APTLHRLGIQAFEPILVEG-RAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQAEARLLMLASNNILSPATGEPIVTPSQ 512 (627)
T ss_pred CCccccccceeEeeEEcCC-CeEEeccccCCcccCCcCCCeEEEecCCCHHHHHHHHHHhcCccceEEcCCCceeEeech
Confidence 9999999999999987765 999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhhhcccCcc
Q 046825 588 DHIVSAALLTKKDT 601 (1208)
Q Consensus 588 D~l~g~~lLT~~d~ 601 (1208)
|+++|+|+||.++.
T Consensus 513 D~llG~y~LT~~~~ 526 (627)
T PRK02625 513 DMVLGCYYLTAENP 526 (627)
T ss_pred hhhhheeeeeccCc
Confidence 99999999999984
No 15
>CHL00018 rpoC1 RNA polymerase beta' subunit
Probab=100.00 E-value=1.2e-83 Score=765.37 Aligned_cols=284 Identities=27% Similarity=0.407 Sum_probs=252.7
Q ss_pred CCCCCceEEEeeeecCCCcccCCcccCC-CccCchhHHHHHHHHHHHHHHHHHHHcC-CCCHHHHHHHHhhHHHHHHhhh
Q 046825 275 KKAGHSIFFLGVVLVPPIKFRLPSKGGD-SVMEHPQTVLLSKVLQANIYLANAYVNQ-PDNAKVIVARWMNLQQSVNVLF 352 (1208)
Q Consensus 275 ~~~~Pe~ffL~~lpVpP~~~RP~~~~~~-~~~eddlt~~l~~Ii~~n~~l~~~~~~~-~~~~~~i~~~~~~LQ~~v~~~~ 352 (1208)
...+|+||||++|||||+++||++.+++ ..++||+|.+|++||..|++|++..... .++...+.++|..||.+|+.||
T Consensus 257 ~~~~PewmiL~~lPV~Pp~lRP~v~l~~g~~~~sDln~lyr~II~rNn~L~~~~~~~~~~p~~~i~~~~~~LQ~aVd~li 336 (663)
T CHL00018 257 TNIEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDLLTTSRSTPGELVMCQKKLLQEAVDALL 336 (663)
T ss_pred cCCCccEEEEEeeeeCCCcccCceEcCCCcccCCChHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHHHHHHHHHh
Confidence 3578999999999999999999999976 6899999999999999999999988762 1455567789999999999999
Q ss_pred cCCCCCc-----CCCChhhHHHHhhcccccccccccCccCCccceeeecCCCCccccccCchHHHHhhcCcccccchHHH
Q 046825 353 DGKNAAG-----QRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVISPDPYLAVNEIGIPPYFALRLTYPERVTPWNV 427 (1208)
Q Consensus 353 d~~~~~~-----~~~~~~~i~q~L~gK~G~fR~nlmGKRvd~saRsVIspDP~l~~~evgvP~~~A~~Lt~pe~Vt~~Ni 427 (1208)
||+.... .+++.+||+|+|+||+||||+|||||||||||||||||||+|+++|||||.+||++||+|+.
T Consensus 337 dn~~~g~~~~~~~~r~~ksls~~LkGK~GrFR~NLlGKRVDySgRSVIvpdP~L~l~e~GlP~~mA~eL~~P~~------ 410 (663)
T CHL00018 337 DNGIRGQPMRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQPFV------ 410 (663)
T ss_pred cCCCCCCccccCCCCCCCCccccccCcCccccccccccccccCCCceecCCCcccccccCChHHHHHHcCcHHH------
Confidence 9998631 27899999999999999999999999999999999999999999999999999999999963
Q ss_pred HHHHHHHHcCCCCCCCceEEecCCCCcccCCCccccccccchhhhcccccccCCCCCCCcccCceeehhhcccceEEEec
Q 046825 428 VKLRDSIINGAEIHPGATHYLDKLSTMRLPPNKKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNR 507 (1208)
Q Consensus 428 ~~L~~lv~nG~~~~pGa~~i~~~~g~~~~~l~~~~~~~~~~r~~~a~~l~l~~~~~~~~~~~g~~v~Rhl~dgD~Vl~NR 507 (1208)
+++|+.+|+... ...|+.+ ++.. ...++.|+|||+|||+|||||
T Consensus 411 --i~~Li~~~~~~~----------------------------~~~Ak~~-i~~~-----~~~~~~Vlr~v~~gd~VLlNR 454 (663)
T CHL00018 411 --IRGLIRQHLASN----------------------------IRAAKSK-IREK-----EPIVWEILQEVMQGHPVLLNR 454 (663)
T ss_pred --HHHHHhcCcccc----------------------------HHHHHHH-HHhc-----CCcccEeeeehhcCceeeecC
Confidence 567888876410 1112222 2211 246789999999999999999
Q ss_pred CCCCCcCcccceeEEEeCCCCeEEEeccCCCCCCCCCCCCceecccCCCHHHHHHHHHhcccCCceecCCCCCCcccchh
Q 046825 508 QPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQ 587 (1208)
Q Consensus 508 qPsLHk~simah~v~vl~~~~t~rln~~~c~~yNADFDGDemn~h~pqs~~a~~Ea~~L~~~~~~~~sp~~g~pi~gl~Q 587 (1208)
||||||+|||||+++++++ +||||||+||+||||||||||||+|+|||++|+|||+.||.+++|++||++|+|+++++|
T Consensus 455 qPTLHR~sIqAf~~~L~~g-ktIrLhplvC~~fNADFDGDqMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~Q 533 (663)
T CHL00018 455 APTLHRLGIQAFQPILVEG-RAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQ 533 (663)
T ss_pred CCcccccccceeeEEecCC-CeEEeCcccCCcccCCccCcEEEEecCCCHHHHHHHHHHhcCccceeEcCCCceeEeech
Confidence 9999999999999977665 999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhhhcccCcc
Q 046825 588 DHIVSAALLTKKDT 601 (1208)
Q Consensus 588 D~l~g~~lLT~~d~ 601 (1208)
|+|+|+|+||.++.
T Consensus 534 D~ilG~y~LT~~~~ 547 (663)
T CHL00018 534 DMLLGLYVLTIGNR 547 (663)
T ss_pred hhhhhhheecccCC
Confidence 99999999999885
No 16
>TIGR02387 rpoC1_cyan DNA-directed RNA polymerase, gamma subunit. 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''.
Probab=100.00 E-value=1.8e-83 Score=755.90 Aligned_cols=282 Identities=28% Similarity=0.415 Sum_probs=249.6
Q ss_pred CCCCCceEEEeeeecCCCcccCCcccCC-CccCchhHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHhhHHHHHHhhhc
Q 046825 275 KKAGHSIFFLGVVLVPPIKFRLPSKGGD-SVMEHPQTVLLSKVLQANIYLANAYVNQPDNAKVIVARWMNLQQSVNVLFD 353 (1208)
Q Consensus 275 ~~~~Pe~ffL~~lpVpP~~~RP~~~~~~-~~~eddlt~~l~~Ii~~n~~l~~~~~~~~~~~~~i~~~~~~LQ~~v~~~~d 353 (1208)
...+|+||||++|||||+++||++.+++ ..++||+|.+|++||..|++|++....+ ++...+.+.|.+||.+|+.|||
T Consensus 231 ~~~~PewmiL~~lPV~Pp~lRP~v~l~~g~~~~sDln~lyr~II~rNn~L~~~~~~~-~p~~i~~~~~~~LQ~aVd~lid 309 (619)
T TIGR02387 231 TSSRPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEIL-APEIIVRNEKRMLQEAVDALID 309 (619)
T ss_pred cCCCcceEEEEecccCCcccCCceEeCCCcccCCCHHHHHHHHHHHHHHHHHHHHcC-CcHHHHHHHHHHHHHHHHHHhc
Confidence 4679999999999999999999999976 6789999999999999999999988775 5555456789999999999999
Q ss_pred CCCCCc-----CCCChhhHHHHhhcccccccccccCccCCccceeeecCCCCccccccCchHHHHhhcCcccccchHHHH
Q 046825 354 GKNAAG-----QRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVISPDPYLAVNEIGIPPYFALRLTYPERVTPWNVV 428 (1208)
Q Consensus 354 ~~~~~~-----~~~~~~~i~q~L~gK~G~fR~nlmGKRvd~saRsVIspDP~l~~~evgvP~~~A~~Lt~pe~Vt~~Ni~ 428 (1208)
|+.... .+++.+||+|+|+||+||||+|||||||||||||||+|||+|+++|||||.+||.+||+| ||++
T Consensus 310 n~~~g~~~~~~~~rp~ksls~~LkGKeGRFR~nLlGKRVDySgRSVI~pdP~L~l~qvGvP~~mA~eLf~P-----f~i~ 384 (619)
T TIGR02387 310 NGRRGRTVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQP-----FVIH 384 (619)
T ss_pred CCCCCCCcccccCCchhhHHHHhccCCccccccccccccccCCCceecCCCCcccceecChHHHHHhcCch-----HhHH
Confidence 998631 278999999999999999999999999999999999999999999999999999999997 6777
Q ss_pred HHHHHHHcCCC-CCCCceEEecCCCCcccCCCccccccccchhhhcccccccCCCCCCCcccCceeehhhcccceEEEec
Q 046825 429 KLRDSIINGAE-IHPGATHYLDKLSTMRLPPNKKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNR 507 (1208)
Q Consensus 429 ~L~~lv~nG~~-~~pGa~~i~~~~g~~~~~l~~~~~~~~~~r~~~a~~l~l~~~~~~~~~~~g~~v~Rhl~dgD~Vl~NR 507 (1208)
+|++ +|.. ..+|| +.+ +... ....+.|+|||+|||+|||||
T Consensus 385 ~L~~---~g~~~~i~~a-----------------------------k~~-i~~~-----~~~v~~Vlr~v~~gd~VLlNR 426 (619)
T TIGR02387 385 RLIR---QGIVNNIKAA-----------------------------KKL-IQRA-----DDEIWSVLQEVITGHPVMLNR 426 (619)
T ss_pred HHHh---cCcccchHHH-----------------------------HHH-HHhc-----CChhHHHHHHHhcCCEEEecC
Confidence 7654 5542 11122 222 2211 123567999999999999999
Q ss_pred CCCCCcCcccceeEEEeCCCCeEEEeccCCCCCCCCCCCCceecccCCCHHHHHHHHHhcccCCceecCCCCCCcccchh
Q 046825 508 QPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQ 587 (1208)
Q Consensus 508 qPsLHk~simah~v~vl~~~~t~rln~~~c~~yNADFDGDemn~h~pqs~~a~~Ea~~L~~~~~~~~sp~~g~pi~gl~Q 587 (1208)
||||||+|||||+++++++ +||||||+||+||||||||||||+|+|||++|+|||+.||++++|++||++|+|+++++|
T Consensus 427 qPTLHR~sIqAf~~~l~~~-ktirlhplvC~~fNADFDGDeMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~Q 505 (619)
T TIGR02387 427 APTLHRLGIQAFEPILVDG-RAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQTEARLLMLASNNVLSPATGEPIVTPSQ 505 (619)
T ss_pred CCccchhcceeeeeEEecC-CeEEECcccCCcccCCCCCceeeeecCCCHHHHHHHHHHhhchhcEEecCCCceeEeech
Confidence 9999999999999987765 999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhhhcccCcc
Q 046825 588 DHIVSAALLTKKDT 601 (1208)
Q Consensus 588 D~l~g~~lLT~~d~ 601 (1208)
|+|+|+|+||.++.
T Consensus 506 D~llg~y~LT~~~~ 519 (619)
T TIGR02387 506 DMVLGCYYLTALNP 519 (619)
T ss_pred hhhhhhheeecccc
Confidence 99999999999874
No 17
>PF00623 RNA_pol_Rpb1_2: RNA polymerase Rpb1, domain 2; InterPro: IPR000722 RNA polymerases catalyse the DNA dependent polymerisation of RNA from DNA, using the four ribonucleoside triphosphates as substrates. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Eukaryotic RNA polymerase I is essentially used to transcribe ribosomal RNA units, polymerase II is used for mRNA precursors, and III is used to transcribe 5S and tRNA genes. Each class of RNA polymerase is assembled from nine to fourteen different polypeptides. Members of the family include the largest subunit from eukaryotes; the gamma subunit from Cyanobacteria; the beta' subunit from bacteria; the A' subunit from archaea; and the B'' subunit from chloroplast RNA polymerases.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_M 2PMZ_Q 3HKZ_I 1ZYR_D 1SMY_D 2A68_N 2O5J_D 3AOH_N 2O5I_D 2CW0_N ....
Probab=100.00 E-value=2.1e-61 Score=499.41 Aligned_cols=166 Identities=53% Similarity=0.835 Sum_probs=146.2
Q ss_pred CccCCccceeeecCCCCccccccCchHHHHhhcCcccccchHHHHHHHHHHHcCCCCCCCceEEecCCCCcccCCCcccc
Q 046825 384 GKRVNYACRSVISPDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLPPNKKMR 463 (1208)
Q Consensus 384 GKRvd~saRsVIspDP~l~~~evgvP~~~A~~Lt~pe~Vt~~Ni~~L~~lv~nG~~~~pGa~~i~~~~g~~~~~l~~~~~ 463 (1208)
||||||||||||||||+|+++|||||.+||++||+||.||+||+++|+++|.||++.||||+++++.+| .++.|...
T Consensus 1 GKRVnfSaRSVItpDP~L~~~EvGiP~~iA~~Lt~Pe~Vt~~N~~~l~~~v~ng~~~~pga~~i~~~~~-~~~~l~~~-- 77 (166)
T PF00623_consen 1 GKRVNFSARSVITPDPNLKIDEVGIPIEIAKKLTFPERVTPFNIEKLRKLVINGPDKYPGANYIKRSNG-NKISLRYK-- 77 (166)
T ss_dssp CEEESSEEEEEEEEETTSCTTEEEEEHHHHHHCECCHHHHTTTHHHHHHHHHHTTTSSSSEEEEESTTC-HCCCTTSS--
T ss_pred CCCcccCCCcEEECCCCCccceecccHHHHhhCCCcEEEHHHHHHHHHHHHhcCcccchhhhhhhcccC-cceeeeec--
Confidence 999999999999999999999999999999999999999999999999999999999999999999988 77777654
Q ss_pred ccccchhhhcccccccCCCCCCCcccCceeehhhcccceEEEecCCCCCcCcccceeEEEeCCCCeEEEeccCCCCCCCC
Q 046825 464 ISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNAD 543 (1208)
Q Consensus 464 ~~~~~r~~~a~~l~l~~~~~~~~~~~g~~v~Rhl~dgD~Vl~NRqPsLHk~simah~v~vl~~~~t~rln~~~c~~yNAD 543 (1208)
.. +....+ ..|++|+||+.|||+|||||||||||+|||||+++++++ +||||||++|+|||||
T Consensus 78 -~~----~~~~~l-----------~~~~~v~r~l~~gd~vl~nRqPtLh~~s~~a~~~~~~~~-~t~~~~~~~c~~~NAD 140 (166)
T PF00623_consen 78 -KF----KISKKL-----------RIGDIVERHLCDGDIVLLNRQPTLHRMSIMAHKVRVLPG-KTIRINPLVCSPFNAD 140 (166)
T ss_dssp -SS----CCCHHH-----------HTT-EEEEEHTTT-EEEEEESS-SSGGGEEEEEEEEESS-SSEEEEGGGHHHHT--
T ss_pred -cc----ccccee-----------cchhhHHHhhhcCceeEEeccchhccceeeeeeeeeecc-cEEEeeccchhhhhcc
Confidence 11 111222 468999999999999999999999999999999999998 9999999999999999
Q ss_pred CCCCceecccCCCHHHHHHHHHhccc
Q 046825 544 FDGDEMNVHFPQDEVSRAEAYNIVNA 569 (1208)
Q Consensus 544 FDGDemn~h~pqs~~a~~Ea~~L~~~ 569 (1208)
|||||||+|+|||++|++||++||++
T Consensus 141 FDGDem~i~~p~~~~a~~E~~~L~~~ 166 (166)
T PF00623_consen 141 FDGDEMNIHLPQSYEARAEAKELMNV 166 (166)
T ss_dssp TSS-EEEEE--SSHHHHHHHHHHCBT
T ss_pred CCcceEEEEecCCHHHHHHHHHHhcC
Confidence 99999999999999999999999985
No 18
>PRK02597 rpoC2 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=100.00 E-value=5.6e-60 Score=595.79 Aligned_cols=341 Identities=27% Similarity=0.371 Sum_probs=250.0
Q ss_pred eecCccccCCccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHcCceeeecccccChHHHHHHHHHHHHHHHHHHHHHHH
Q 046825 762 GVIDKAQFADYGLVHTVQELYGSNTAGTLLSALSRLFTVFLQMHGFTCGVDDLLILKDKERERKNHLHGSEEIGKRVHLE 841 (1208)
Q Consensus 762 G~ldK~~iG~~~Lih~i~~~yG~~~a~~~l~~l~~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~ 841 (1208)
-++||+.+| +||+.+|++||...|+.|||.+++|+++|++.+|||+|++|+.+|+++ .+++++|++++.++.++
T Consensus 6 ~~idKk~l~--~LI~~~~~~yG~~~t~~~lD~lk~LGf~~aT~~G~SigidDl~ip~~K----~~li~~Ae~~v~~~~~~ 79 (1331)
T PRK02597 6 RVVDKKALK--NLIAWAFKNYGTARTAQMADNLKDLGFRYATQAGVSISVDDLKVPPAK----RDLLEQAEEEITATEER 79 (1331)
T ss_pred ccccHHHHH--HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhCcEEEeecccccCHHH----HHHHHHHHHHHHHHHHH
Confidence 478999998 999999999999999999999999999999999999999999999864 57999999999888887
Q ss_pred HHhhccCCCCChhhHHHHHHHHhcCCcchhhHHHHHHHHHHHHhhhhhHHHHHHhhcCCCCCCCCCcchhhhhcCCCCCc
Q 046825 842 ALELEDGAEIDPIKLKSEIEKAMRGGGDAAVAYFDMKMTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSK 921 (1208)
Q Consensus 842 ~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~ln~~~~~~~~~~~~~~~l~~~~~~N~~~~M~~SGaKGS~ 921 (1208)
|.. + .++. .+++++++ ..|..+.+.++++ +.+ .+.+.+|.|++++|+.|||||
T Consensus 80 y~~---G-~it~---~Er~~kvi------------~~w~~t~e~l~~~-~~~-----~~~~~dp~N~v~mMa~SGARG-- 132 (1331)
T PRK02597 80 YRR---G-EITE---VERFQKVI------------DTWNETNERLKDE-VVK-----NFRQNDPLNSVYMMAFSGARG-- 132 (1331)
T ss_pred HHc---C-CCch---hHHHHHHH------------HHHHHHHHHHHHH-HHH-----HHhhcCCCCcHHHHhhccCCc--
Confidence 743 1 1111 12222221 1333333333333 222 233456899999999999999
Q ss_pred ccHHHHHhhcccccccCcccCCCCCCc--cccCCCCCCCCccccccccccccCCCCchhhhhhcccccccchhccccccC
Q 046825 922 VNFQQISSHLGQQELEGKRVPRMVSGK--TLPSFHPWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSR 999 (1208)
Q Consensus 922 vN~~Qi~~~lGQQ~leG~Rip~~~~gr--tLP~f~~~d~~~~a~GfI~~sF~~GL~p~EfFfH~maGReGLiDTAvKTa~ 999 (1208)
|++||.+|+|||.+. +. .+|+ .|| |.+||++||+|+|||||||||||||||||||||+
T Consensus 133 -N~sQI~QLvGmRGLm--a~---p~G~ii~lP--------------I~snFrEGLs~~EyFis~~GaRKGLvDTAlKTAd 192 (1331)
T PRK02597 133 -NMSQVRQLVGMRGLM--AN---PQGEIIDLP--------------IKTNFREGLTVTEYVISSYGARKGLVDTALRTAD 192 (1331)
T ss_pred -cHHHHHHHhcchhhc--cC---CCCcEEecc--------------hhhhhhcCCCHHHhheeccccccchhhcceeccc
Confidence 555555555555431 11 2233 344 9999999999999999999999999999999999
Q ss_pred CchhhHHHHhhhceeeeecccEEEcCCCCEEEeeecCCcceeccccc-cccchhhhhhhccccccccccccCCCceeeec
Q 046825 1000 SGYLQRCLIKNLECLKISYDYSVRDADGSIVQFCYGEDGVDVHQTSF-ISKFDALAARERGRGRGRNKFCDKGSHTFVMG 1078 (1208)
Q Consensus 1000 SGYLqRrLvK~lEdl~V~YD~TVR~~~g~IvQF~YGedGld~~k~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1078 (1208)
|||||||||+ |++|.+||..||.. ..|+.+..... ......+.+++.||+.+.+.+... ..+.+.
T Consensus 193 SGYLTRRLVd------v~QDviVre~DCgT------~~gi~~~~~~~~~~~i~~l~~rl~GR~~~~~i~~~~--~~~i~~ 258 (1331)
T PRK02597 193 SGYLTRRLVD------VSQDVIVREEDCGT------TRGIVVEAMDDGDRVLIPLGDRLLGRVLAEDVVDPE--GEVIAE 258 (1331)
T ss_pred chhHHHHHHH------hhcceEEEecCCCC------CCCEEEEEEecCCEEEeEehheeEEEEEhhHeeCCC--CCEEEe
Confidence 9999999998 45555677777744 34555433211 112334667888998877665543 445556
Q ss_pred hhHHHHHhhhcchhhhHHHHHHhHHHHHHHhHHHHHHh-hhcchhHHHHHHHHHHHHhhhc-----CCCCCCchhhhhhc
Q 046825 1079 RNQEMIYKKCSGQLDASNAYIMELPDALKDNAEKFADK-FLSNEMAKQDFLKLVKHKFVLS-----LAQPGEPVGLLASQ 1152 (1208)
Q Consensus 1079 ~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~l~~~~f~~l~~~~y~~s-----lv~pGeaVGiIAAQ 1152 (1208)
+|...- . +...++ .+.. +++ ..++.+||+.-.++|..||+++ +|+.||||||||||
T Consensus 259 ~n~~i~-~----------~~~~~i---~~~~----~~~v~iRspltC~s~~gvC~~CYG~~la~~~lv~lGeaVGiiAaQ 320 (1331)
T PRK02597 259 RNTAID-P----------DLAKKI---EKAG----VEEVMVRSPLTCEAARSVCRKCYGWSLAHNHLVDLGEAVGIIAAQ 320 (1331)
T ss_pred CCCCcC-H----------HHHHHH---HHcC----CCEEEEECCEEecCCCCchhhccCcchhcCcccchhhhhhhhhhc
Confidence 664321 0 000101 1000 011 2389999999999999999874 68999999999999
Q ss_pred cCCCcccccccccccccCccccccc-------cccchHHHHH
Q 046825 1153 SVGEPSTQMTLNTFHLAGRGEMNVT-------LGIPRLQEIL 1187 (1208)
Q Consensus 1153 SIGEP~TQMTLnTFH~AGv~~~nVT-------lGvPRlkEIi 1187 (1208)
|||||||||||||||++||+...++ .|++|+.|-+
T Consensus 321 SIGEPGTQLTmRTFHtGGv~~~~~~~~i~~~~~G~i~~~~~~ 362 (1331)
T PRK02597 321 SIGEPGTQLTMRTFHTGGVFTGEVARQVRSPFAGTVEFGKKL 362 (1331)
T ss_pred cccCCcchhehhhhhhccccccccceeEEeccCeEEEEecCC
Confidence 9999999999999999999988898 9999999854
No 19
>TIGR02388 rpoC2_cyan DNA-directed RNA polymerase, beta'' subunit. 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.
Probab=100.00 E-value=1.8e-59 Score=586.73 Aligned_cols=331 Identities=26% Similarity=0.374 Sum_probs=240.1
Q ss_pred eecCccccCCccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHcCceeeecccccChHHHHHHHHHHHHHHHHHHHHHHH
Q 046825 762 GVIDKAQFADYGLVHTVQELYGSNTAGTLLSALSRLFTVFLQMHGFTCGVDDLLILKDKERERKNHLHGSEEIGKRVHLE 841 (1208)
Q Consensus 762 G~ldK~~iG~~~Lih~i~~~yG~~~a~~~l~~l~~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~ 841 (1208)
-++||+.++ +|||.+|.+||+..|+.|||.+++|+++|++.+|||+|++|+.+|+++ .+++++|++++.+..++
T Consensus 5 ~~idKk~l~--~LI~~~~~~yG~~~t~~~lD~lk~Lgf~~aT~~G~SigidDl~ip~~K----~~li~~a~~~v~~~~~~ 78 (1227)
T TIGR02388 5 RVVDKKALK--NLISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPPAK----QDLLEAAEKEIRATEER 78 (1227)
T ss_pred cccchHHHH--HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCeEEeeccCCCCHHH----HHHHHHHHHHHHHHHHH
Confidence 478999997 999999999999999999999999999999999999999999999874 58999999998888887
Q ss_pred HHhhccCCCCChhhHHHHHHHHhcCCcchhhHHHHHHHHHHHHhhhhhHHHHHHhhcCCCCCCCCCcchhhhhcCCCCCc
Q 046825 842 ALELEDGAEIDPIKLKSEIEKAMRGGGDAAVAYFDMKMTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSK 921 (1208)
Q Consensus 842 ~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~ln~~~~~~~~~~~~~~~l~~~~~~N~~~~M~~SGaKGS~ 921 (1208)
|.. + .+++ .+++++ +...|++.++. +.+.+. ..+...+|.|++++|+.|||||
T Consensus 79 y~~---G-~it~---~Er~~~----------------ii~~w~~t~e~-~~~~~~-~~~~~~d~~N~v~mMa~SGARG-- 131 (1227)
T TIGR02388 79 YRR---G-EITE---VERFQK----------------VIDTWNGTNEE-LKDEVV-NNFRQTDPLNSVYMMAFSGARG-- 131 (1227)
T ss_pred HHc---C-CCcc---hhhHHH----------------HHHHHHHHHHH-HHHHHH-HhhhhcCCCCcHHHHhhccCcc--
Confidence 743 1 1111 111111 12234444333 222222 2223456899999999999999
Q ss_pred ccHHHHHhhcccccccCcccCCCCCCcc--ccCCCCCCCCccccccccccccCCCCchhhhhhcccccccchhccccccC
Q 046825 922 VNFQQISSHLGQQELEGKRVPRMVSGKT--LPSFHPWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSR 999 (1208)
Q Consensus 922 vN~~Qi~~~lGQQ~leG~Rip~~~~grt--LP~f~~~d~~~~a~GfI~~sF~~GL~p~EfFfH~maGReGLiDTAvKTa~ 999 (1208)
|++||.+|+|||.+. +.| .|+. || |.+||++||+|.|||||||||||||||||||||+
T Consensus 132 -NisQi~QLvGmrGlm--a~p---~G~ii~lP--------------I~snFreGLt~~EyF~sa~GaRkGLvDTAlKTAd 191 (1227)
T TIGR02388 132 -NMSQVRQLVGMRGLM--ANP---QGEIIDLP--------------IKTNFREGLTVTEYVISSYGARKGLVDTALRTAD 191 (1227)
T ss_pred -cHHHHHHHhcchhee--cCC---CCcEeecc--------------chhhhhcCCCHHHhheeccccccchhhcceeccc
Confidence 666666666666442 122 2222 44 9999999999999999999999999999999999
Q ss_pred CchhhHHHHhhhceeeeecccEEEcCCCCEEEeeecCCcceeccccccccchhhhhhhccccccccccccCCCceeeech
Q 046825 1000 SGYLQRCLIKNLECLKISYDYSVRDADGSIVQFCYGEDGVDVHQTSFISKFDALAARERGRGRGRNKFCDKGSHTFVMGR 1079 (1208)
Q Consensus 1000 SGYLqRrLvK~lEdl~V~YD~TVR~~~g~IvQF~YGedGld~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1079 (1208)
|||||||||+++||+ .||..||. ...|+.+...........+.+++.||+.+.+.+... ......+
T Consensus 192 SGYLTRRLVdv~qDv------iV~~~DCg------T~~gi~v~~~~~~~~~~~l~~rl~GRv~~~di~~~~--~~~i~~~ 257 (1227)
T TIGR02388 192 SGYLTRRLVDVSQDV------IVREEDCG------TERSIVVRAMTEGDKKISLGDRLLGRLVAEDVLHPE--GEVIVPK 257 (1227)
T ss_pred cchHHHHHHHhhceE------EEEEcCCC------CCCCEEEEEeeCCCeEeEhhheeEeeeEHhHeECCC--CcEEEeC
Confidence 999999999977766 47777764 356666643211112334677888998776655433 3455555
Q ss_pred hHHHHHhhhcchhhhHHHHHHhHHHHHHHhHHHHHHh-hhcchhHHHHHHHHHHHHhhhc-----CCCCCCchhhhhhcc
Q 046825 1080 NQEMIYKKCSGQLDASNAYIMELPDALKDNAEKFADK-FLSNEMAKQDFLKLVKHKFVLS-----LAQPGEPVGLLASQS 1153 (1208)
Q Consensus 1080 n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~l~~~~f~~l~~~~y~~s-----lv~pGeaVGiIAAQS 1153 (1208)
|...-. +..+++ .... ++. ..++++||+.-.++|..||+++ +|+.|||||+|||||
T Consensus 258 n~~I~~-----------~~~~~i---~~~~----~~~v~iRspltC~s~~~vC~~CYG~~la~~~lV~lGeaVGiiAaQS 319 (1227)
T TIGR02388 258 NTAIDP-----------DLAKTI---ETAG----ISEVVVRSPLTCEAARSVCRKCYGWSLAHAHLVDLGEAVGIIAAQS 319 (1227)
T ss_pred CCccCH-----------HHHHHH---HHcC----CCEEEEeCcceecchhhHhHhccCCccccCcEechhhhhhhhhhhc
Confidence 643210 001101 0000 011 1279999999999999999875 578999999999999
Q ss_pred CCCcccccccccccccCccccccc
Q 046825 1154 VGEPSTQMTLNTFHLAGRGEMNVT 1177 (1208)
Q Consensus 1154 IGEP~TQMTLnTFH~AGv~~~nVT 1177 (1208)
||||||||||||||++||....+.
T Consensus 320 IGEPGTQLTmRTFHtGGv~t~~~~ 343 (1227)
T TIGR02388 320 IGEPGTQLTMRTFHTGGVFTGEVA 343 (1227)
T ss_pred cCCcchhhhhhhhhhcccccccee
Confidence 999999999999999999765443
No 20
>CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed
Probab=100.00 E-value=9.3e-59 Score=591.18 Aligned_cols=344 Identities=25% Similarity=0.311 Sum_probs=254.4
Q ss_pred eeeecCccccCCccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHcCceeeecccccChHHHHHHHHHHHHHHHHHHHHH
Q 046825 760 VRGVIDKAQFADYGLVHTVQELYGSNTAGTLLSALSRLFTVFLQMHGFTCGVDDLLILKDKERERKNHLHGSEEIGKRVH 839 (1208)
Q Consensus 760 l~G~ldK~~iG~~~Lih~i~~~yG~~~a~~~l~~l~~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~~~~~~~~~~ 839 (1208)
++-++||+.++ +||+.+|.+||+..|+.|||.+++|+++|++.+|||+|++|+.+|+++ .+++++|++++..+.
T Consensus 10 ~N~~~~k~~l~--~li~~~~~~~G~~~t~~~lD~lk~lgf~~at~~G~Sigi~Dl~ip~~K----~~li~~a~~~v~~~~ 83 (1364)
T CHL00117 10 HNKVIDKTALK--RLISWLIDHFGMAYTSHILDQLKTLGFQQATAAGISLGIDDLLTPPSK----GWLVQDAEQQSLILE 83 (1364)
T ss_pred EeccccHHHHH--HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcceEEecCcccCCHHH----HHHHHHHHHHHHHHH
Confidence 34579999998 999999999999999999999999999999999999999999999875 489999999998888
Q ss_pred HHHHhhccCCCCChhhHHHHHHHHhcCCcchhhHHHHHHHHHHHHhhhhhHHHHHHhhcCCCCCCCCCcchhhhhcCCCC
Q 046825 840 LEALELEDGAEIDPIKLKSEIEKAMRGGGDAAVAYFDMKMTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKG 919 (1208)
Q Consensus 840 ~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~ln~~~~~~~~~~~~~~~l~~~~~~N~~~~M~~SGaKG 919 (1208)
++|.. + .++. .+++++.+. .|..+.+.++++ +. .+ +....|.|++++|+.|||||
T Consensus 84 ~~y~~---G-~it~---~er~~~~i~------------~w~~~~~~l~~~-~~-~~----~~~~d~~N~v~mMa~SGARG 138 (1364)
T CHL00117 84 KHYHY---G-NVHA---VEKLRQSIE------------IWYATSEYLKQE-MN-PN----FRMTDPLNPVYMMSFSGARG 138 (1364)
T ss_pred HHHHc---C-CCCH---HHHHHHHHH------------HHHHHHHHHHHH-HH-Hh----hccCCCCCcHhhhhhccCcc
Confidence 87753 2 1111 123333222 333344444444 32 22 23346899999999999999
Q ss_pred CcccHHHHHhhcccccccCcccCCCCCCccccCCCCCCCCccccccccccccCCCCchhhhhhcccccccchhccccccC
Q 046825 920 SKVNFQQISSHLGQQELEGKRVPRMVSGKTLPSFHPWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSR 999 (1208)
Q Consensus 920 S~vN~~Qi~~~lGQQ~leG~Rip~~~~grtLP~f~~~d~~~~a~GfI~~sF~~GL~p~EfFfH~maGReGLiDTAvKTa~ 999 (1208)
|++||.+|+|++.+. ..|+....| -+|.+||++||+|.|||||||||||||||||||||+
T Consensus 139 ---n~sQi~qLvGmRGlm-----------a~p~G~iI~------~PI~snFreGLs~~EyFis~~GaRkGLvDTAlkTAd 198 (1364)
T CHL00117 139 ---NASQVHQLVGMRGLM-----------SDPQGQIID------LPIQSNFREGLSLTEYIISCYGARKGVVDTAVRTAD 198 (1364)
T ss_pred ---cHHHHHHHhccccee-----------eCCCCcEee------cchhhhhhcCCCHHHhheeccccccchhhcceeccc
Confidence 678888888877662 122222111 139999999999999999999999999999999999
Q ss_pred CchhhHHHHhhhceeeeecccEEEcCCCCEEEeeecCCcceeccccccccchhhhhhhccccccccccccCCCceeeech
Q 046825 1000 SGYLQRCLIKNLECLKISYDYSVRDADGSIVQFCYGEDGVDVHQTSFISKFDALAARERGRGRGRNKFCDKGSHTFVMGR 1079 (1208)
Q Consensus 1000 SGYLqRrLvK~lEdl~V~YD~TVR~~~g~IvQF~YGedGld~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1079 (1208)
|||||||||+++||| .||..||. ...|+.+...........+.+++.||+.+.+.+. .....+.+
T Consensus 199 SGYLtRRLVdv~qdv------iV~~~dCg------t~~gi~~~~~~~~~~~~~l~~rl~GRv~~~di~~---~~~~i~~~ 263 (1364)
T CHL00117 199 AGYLTRRLVEVVQHI------VVRETDCG------TTRGISVSPRNGMMIERILIQTLIGRVLADDIYI---GSRCIATR 263 (1364)
T ss_pred ccchhhHHHhhhccE------EEEeccCC------CCCCEEEEEecCCeEEeEecceeEEEEEhhhEEe---CCEEEEeC
Confidence 999999999977766 47777874 3567766433211234456788899988776654 33445555
Q ss_pred hHHHHHhhhcchhhhHHHHHHhHHHHHHHhHHHHHHh-hhcchhHHHHHHHHHHHHhhhc-----CCCCCCchhhhhhcc
Q 046825 1080 NQEMIYKKCSGQLDASNAYIMELPDALKDNAEKFADK-FLSNEMAKQDFLKLVKHKFVLS-----LAQPGEPVGLLASQS 1153 (1208)
Q Consensus 1080 n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~l~~~~f~~l~~~~y~~s-----lv~pGeaVGiIAAQS 1153 (1208)
|...- . +..+++. ... +++ ..++++||+.-.++|..||+++ +|+.|||||||||||
T Consensus 264 n~~I~-~----------~~~~~i~---~~~----~~~v~iRSpltC~~~~~vC~~CYG~~la~~~lV~~GeaVGiiAaQS 325 (1364)
T CHL00117 264 NQDIG-I----------GLANRFI---TFR----AQPISIRSPLTCRSTSWICQLCYGWSLAHGDLVELGEAVGIIAGQS 325 (1364)
T ss_pred CCCcC-H----------HHHHHHH---HcC----CCEEEEeCCcccccHHHHHHHHhCcccccCcccChhhhhhhhhhhc
Confidence 64321 0 0000010 000 111 1289999999999999999885 589999999999999
Q ss_pred CCCcccccccccccccCcccccccc-------ccchHHHHH
Q 046825 1154 VGEPSTQMTLNTFHLAGRGEMNVTL-------GIPRLQEIL 1187 (1208)
Q Consensus 1154 IGEP~TQMTLnTFH~AGv~~~nVTl-------GvPRlkEIi 1187 (1208)
||||||||||||||++||++..++. |+.++.+-+
T Consensus 326 IGEPGTQLTmRTFH~GGv~t~~~~~~i~a~~~G~i~~~~~~ 366 (1364)
T CHL00117 326 IGEPGTQLTLRTFHTGGVFTGGTAEQVRAPFNGKIKFNEDL 366 (1364)
T ss_pred cCCCchhhhhhhhhhcccccccceeeEEeccCeEEEEecce
Confidence 9999999999999999998766665 999888843
No 21
>PF04998 RNA_pol_Rpb1_5: RNA polymerase Rpb1, domain 5; InterPro: IPR007081 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 form the central cleft or channel where the DNA is bound [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1ZYR_D 1SMY_D 2A68_N 2O5J_D 3AOH_N 2O5I_D 2CW0_N 2A6H_N 2A69_D 3EQL_D ....
Probab=100.00 E-value=8.1e-53 Score=472.16 Aligned_cols=132 Identities=65% Similarity=1.019 Sum_probs=124.4
Q ss_pred CCCchhhhhhcccccccchhccccccCCchhhHHHHhhhceeeeecccEEEcCCCCEEEeeecCCcceeccccccccchh
Q 046825 973 GLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSIVQFCYGEDGVDVHQTSFISKFDA 1052 (1208)
Q Consensus 973 GL~p~EfFfH~maGReGLiDTAvKTa~SGYLqRrLvK~lEdl~V~YD~TVR~~~g~IvQF~YGedGld~~k~~~~~~~~~ 1052 (1208)
||+|+|||||||||||||||||||||+||||||||||+||||.|.||+|||++++.|+||.||+||
T Consensus 1 Gl~~~e~f~~~~~~R~gl~dta~kTa~sGyl~R~lv~~~~~~~v~~~~~~~~~~~~i~~~~~~~~~-------------- 66 (277)
T PF04998_consen 1 GLTPTEYFFHCMGGREGLIDTAVKTADSGYLQRRLVKVLEDLIVRYDDCVRNSGGSIIQFIYGEDG-------------- 66 (277)
T ss_dssp C-THHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHTTHEEETTSEEESTTSEEEESSCTTTS--------------
T ss_pred CcCHHHHHHHHhcccccccccceeeeccccchhhhhhccceEEEEEcCccccccceeeeccccccc--------------
Confidence 999999999999999999999999999999999999999999999999999999999999999876
Q ss_pred hhhhhccccccccccccCCCceeeechhHHHHHhhhcchhhhHHHHHHhHHHHHHHhHHHHHHhhhcchhHHHHHHHHHH
Q 046825 1053 LAARERGRGRGRNKFCDKGSHTFVMGRNQEMIYKKCSGQLDASNAYIMELPDALKDNAEKFADKFLSNEMAKQDFLKLVK 1132 (1208)
Q Consensus 1053 ~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~f~~l~~ 1132 (1208)
T Consensus 67 -------------------------------------------------------------------------------- 66 (277)
T PF04998_consen 67 -------------------------------------------------------------------------------- 66 (277)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred HHhhhcCCCCCCchhhhhhccCCCcccccccccccccCccccccccccchHHHHHHHhhcCCCCCeEEEecCC
Q 046825 1133 HKFVLSLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIKTPVITCPLLV 1205 (1208)
Q Consensus 1133 ~~y~~slv~pGeaVGiIAAQSIGEP~TQMTLnTFH~AGv~~~nVTlGvPRlkEIi~~ask~ikTP~~~~~l~~ 1205 (1208)
+|+||||||+|||||||||+|||||||||+||++++|||+|+|||+||+ +++++++||+++++...
T Consensus 67 ------~v~~Ge~VGiiaAQSIGEP~TQ~TL~TFH~aG~~~~~vt~giprl~eii-~~~~~~~~~~~~~~~~~ 132 (277)
T PF04998_consen 67 ------LVEPGEAVGIIAAQSIGEPGTQMTLRTFHTAGVASKNVTQGIPRLKEII-NASKKIKTPIITVYGKK 132 (277)
T ss_dssp ------B--TTSBHHHHHHHHHHCHGCCSHHSCTSSSCSSTSSCSSSHHHHHHHH-TTCSSSSSEEEEECSCS
T ss_pred ------ccCccccchhhhhchhcchhHHhhhcccccCceeeecccccceeecccc-ccccccccceEEeeccc
Confidence 5678999999999999999999999999999999999999999999999 57899999999988754
No 22
>PF04997 RNA_pol_Rpb1_1: RNA polymerase Rpb1, domain 1; InterPro: IPR007080 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 is a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2Y0S_W 3QQC_A 1YNJ_D 1HQM_D 1YNN_D 1I6V_D 2GHO_D 2AUJ_D 1ZYR_D 1SMY_D ....
Probab=100.00 E-value=3.7e-48 Score=443.46 Aligned_cols=274 Identities=30% Similarity=0.435 Sum_probs=184.3
Q ss_pred CCCCCCCCCCCCCccceeeccccccchhcHHHHHHHHHHhhhhccccccChhhHHHHHHHHHHhhcCChHHHhhhhcccC
Q 046825 1 CKTCGQRQFLCPGHFGHIDLVVPVYNPLLFNLLYTLLKRICFFCHHFKASRREVEKCVRKLELIIKGDIIAAKSLDLDLP 80 (1208)
Q Consensus 1 C~TCg~~~~~CPGHFGHIELa~PVynP~ff~~l~kLLr~iC~~C~rfll~~~~~~~~~~kL~ll~~G~~~~a~~L~~i~~ 80 (1208)
|+|||++..+|||||||||||+|||||+||+.+++||+|+|++|++++++.++...+...++.+. .
T Consensus 57 C~tC~~~~~~CpGHfGhI~L~~PV~h~~f~~~i~~iL~~~C~~C~~l~~~~~~~~~~~~~~~~~~--~------------ 122 (337)
T PF04997_consen 57 CSTCGLNYTECPGHFGHIELALPVYHPGFFKEIPKILRCICKKCSRLLLSEKEKYFYLKILLKLK--K------------ 122 (337)
T ss_dssp SSSSSSSSSSCCCSEEEEEEEEEEETCCCHHHHHHHHTTSCTTTSCTSTCCCCHTSCHHHCHCSH--S------------
T ss_pred cccccccccccCCceeEEEeCHHHHhhcccccceeeecccccccccccccccccccccccccccc--c------------
Confidence 99999999999999999999999999999999999999999999999999887633322221110 0
Q ss_pred CCCCCCCCccccccccccccCCCCCCCCccCCCCcccchhhHHHHHHHHHHHHHhcccCCCCCCCCCCceecccceEEEE
Q 046825 81 SESSNPEDSDVSNKSSCSMVTPRGNYDNVRNLKPQEWTSLQFAEAKLALLQFLKIETTKCGNCKAKNPRISKPTFGWIHM 160 (1208)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~ii~eflk~~~~kC~~Cg~~~p~Irk~g~~ki~~ 160 (1208)
.....+.+.+.+..+. ...|.+|+..++.+++........
T Consensus 123 ---------------------------------------~~~~~~~~~i~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~ 162 (337)
T PF04997_consen 123 ---------------------------------------KKKKERLKIISKECKK-KSICSHCKAINGKIKKVEKSKKCE 162 (337)
T ss_dssp ---------------------------------------SSHHHHHHHHHHHHHH-TCSSTSTCC-SSS---SSSEETSS
T ss_pred ---------------------------------------ccchhHHHHHHHhhhh-hhhhcccccccccccccccchhcc
Confidence 0011122222222221 567888887777665200000000
Q ss_pred ecCCchhhhhhhhccCCcCCCcCCCccccccCCCCCCCCCCCCCCCCCCCCCcchhhhhcccCCCCCCCCccccccccCC
Q 046825 161 NGMPHADIRANLIRGCNLGETFSGGEEEKDLGASSDVDAPETHSFNGTFPGTQDTAARRHQKGSGAVPSGFKKQKDLFSG 240 (1208)
Q Consensus 161 ~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ed~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 240 (1208)
...+. ... .... . .+.... ..+.. ..... ......
T Consensus 163 -~~~~~-------------~~~----~~~~-~-------~~~i~~--~i~~~-~~~~~------~~~~~~---------- 197 (337)
T PF04997_consen 163 -GCGKK-------------NPK----IRKE-G-------AEKIQE--EIKKK-ESNKE------IKEELR---------- 197 (337)
T ss_dssp -SSSSB-------------SCE----EEEE-S-------HCCCCC--HHHSC-CHHHH------HHCHCE----------
T ss_pred -ccccc-------------Ccc----cccc-h-------hhhccc--ccccc-ccccc------chhhhh----------
Confidence 00000 000 0000 0 000000 00000 00000 000011
Q ss_pred CCCHHHHHHHHHhcCHhHHHHccccccccccCCCCCCCCceEEEeeeecCCCcccCCcccCCCc-cCchhHHHHHHHHHH
Q 046825 241 PLLPSDVKDIIEKLWENEFELCSFISDMQQQGFGKKAGHSIFFLGVVLVPPIKFRLPSKGGDSV-MEHPQTVLLSKVLQA 319 (1208)
Q Consensus 241 ~L~P~eV~~iLkkI~~~d~~lL~ll~~~~~~~~~~~~~Pe~ffL~~lpVpP~~~RP~~~~~~~~-~eddlt~~l~~Ii~~ 319 (1208)
+|+|.+|+++|++||++|.++|++. ....+|+||||++|||||+++||++.+++.. ++||+|.+|++||+.
T Consensus 198 ~l~~~~v~~ilk~l~~~~~~~l~~~--------~~~~~P~~~~l~~lpVpP~~~RP~v~~~~~~~~eddlt~~~~~Ii~~ 269 (337)
T PF04997_consen 198 ILTPEEVRQILKKLSKEDKELLGFD--------PSGSRPEWFFLTVLPVPPPRFRPSVQLGGGRFSEDDLTSLYRKIIKR 269 (337)
T ss_dssp CESHHHHHHHHHHSHHHHHHHHHHH--------TTTBSGGGSEEEEEEE-TGGGS-EEEESSSEEEE-HHHHHHHHHHHH
T ss_pred hhhhhhhhhcchhhhhhheeeeecc--------ccccccceeEEeeeecCCceeeeeeeeecccccCchHHHHHHHHHHH
Confidence 6999999999999999999999874 2357999999999999999999999998854 899999999999999
Q ss_pred HHHHHHHHHcCCCCHHHHHHHHhhHHHHHHhhhcCCCCCc------CCCChhhHHHHhhcccccccccc
Q 046825 320 NIYLANAYVNQPDNAKVIVARWMNLQQSVNVLFDGKNAAG------QRDMASGICQLLEKKEGLFRQKL 382 (1208)
Q Consensus 320 n~~l~~~~~~~~~~~~~i~~~~~~LQ~~v~~~~d~~~~~~------~~~~~~~i~q~L~gK~G~fR~nl 382 (1208)
|++|+.....+ ++...+.+.|..||.+|+.||||+.+.. .++|++||+||||||+||||+||
T Consensus 270 N~~L~~~~~~~-~~~~~~~~~~~~LQ~~v~~~~dn~~~~~~~~~~~~~~~~k~i~q~L~gK~GrfR~NL 337 (337)
T PF04997_consen 270 NNRLRKLLEEG-APSSIIMEEWRLLQEAVNSLIDNEKPGKPPAGQKSGRPLKGISQRLKGKEGRFRQNL 337 (337)
T ss_dssp HHHHHHCCTST-SSSCHHHHHHHHHHHHHHHHHCTTSSSSSBCBSTTSSB--THHHHHSSTTSSHCHHT
T ss_pred HHHHHHHHHhh-CcchhhhhhhhhhhHhHhHHhhhcccCCcccccccCCCCCCHHHHccCCCCcCCCCC
Confidence 99999987764 5666788999999999999999987521 16899999999999999999997
No 23
>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=2.7e-34 Score=324.39 Aligned_cols=73 Identities=75% Similarity=1.117 Sum_probs=71.3
Q ss_pred HhhhcCCCCCCchhhhhhccCCCcccccccccccccCccccccccccchHHHHHHHhhcCCCCCeEEEecCCC
Q 046825 1134 KFVLSLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIKTPVITCPLLVG 1206 (1208)
Q Consensus 1134 ~y~~slv~pGeaVGiIAAQSIGEP~TQMTLnTFH~AGv~~~nVTlGvPRlkEIi~~ask~ikTP~~~~~l~~~ 1206 (1208)
||.+++|+||||||+|||||||||+||||||||||||+|+||||||||||+||||+|||+||||+|+++|.++
T Consensus 1 ky~~slv~PGE~VG~iaAQSIGEPsTQMTLnTFH~AGv~~~nVTlGvPRL~EIi~~Ask~i~TP~m~v~l~~~ 73 (309)
T cd02735 1 KYMRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILMTASKNIKTPSMTLPLKNG 73 (309)
T ss_pred CchhccCCCCcccchhhhhccCCcccccccccccccCccccccccccccHHHHHhhhccCCCCCeEEEEecCc
Confidence 5899999999999999999999999999999999999999999999999999999999999999999999875
No 24
>TIGR02389 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit A''. This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Probab=99.97 E-value=4.3e-33 Score=319.35 Aligned_cols=86 Identities=49% Similarity=0.731 Sum_probs=77.9
Q ss_pred chhHHH-HHH---HHHHHHhhhcCCCCCCchhhhhhccCCCcccccccccccccCccccccccccchHHHHHHHhhcCCC
Q 046825 1120 NEMAKQ-DFL---KLVKHKFVLSLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIK 1195 (1208)
Q Consensus 1120 ~~l~~~-~f~---~l~~~~y~~slv~pGeaVGiIAAQSIGEP~TQMTLnTFH~AGv~~~nVTlGvPRlkEIi~~ask~ik 1195 (1208)
++++.+ +|. ..++.+|.+++|+||||||+|||||||||+|||||||||+|||++||||+|||||+||| +|+|+||
T Consensus 17 ~~~~~~~~~~~~l~~i~~ky~~alv~PGeaVG~IAAQSIGEP~TQMTLnTFH~AGVas~nVTlGVPRlkEII-Na~k~i~ 95 (367)
T TIGR02389 17 REISDKEELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIV-DARKTPS 95 (367)
T ss_pred cCCCHHHHHHHHHHHHHHHHHHhcCCCccccchhhhhhcCCccccccccccccccccccCccccchhHHHHh-hcccCCC
Confidence 344555 555 45589999999999999999999999999999999999999999999999999999999 7899999
Q ss_pred CCeEEEecCCC
Q 046825 1196 TPVITCPLLVG 1206 (1208)
Q Consensus 1196 TP~~~~~l~~~ 1206 (1208)
||+|+++|.++
T Consensus 96 TP~~ti~L~~~ 106 (367)
T TIGR02389 96 TPSMTIYLEDE 106 (367)
T ss_pred CCeEEEEecCc
Confidence 99999999865
No 25
>PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Probab=99.97 E-value=8e-32 Score=314.57 Aligned_cols=87 Identities=44% Similarity=0.695 Sum_probs=80.4
Q ss_pred cchhHHHHHHHHH---HHHhhhcCCCCCCchhhhhhccCCCcccccccccccccCccccccccccchHHHHHHHhhcCCC
Q 046825 1119 SNEMAKQDFLKLV---KHKFVLSLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIK 1195 (1208)
Q Consensus 1119 ~~~l~~~~f~~l~---~~~y~~slv~pGeaVGiIAAQSIGEP~TQMTLnTFH~AGv~~~nVTlGvPRlkEIi~~ask~ik 1195 (1208)
.++++.+.|.+++ ..+|.+++|+||||||+|||||||||+|||||||||+|||+++|||+|||||+||| +|+|+||
T Consensus 155 ~~~l~~~~~~~i~~ei~~~y~~~~v~pGE~VG~IAAQSIGEP~TQMTLnTFH~AGVas~NVTlGVPRLkEII-Na~K~is 233 (509)
T PRK14897 155 KKELSDDEYEEILRRIREEYERARVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEMNVTLGLPRLIEIV-DARKKPS 233 (509)
T ss_pred HcCCCHHHHHHHHHHHHHHHHHhccCCCCCcchhhhhhhCCccccccccccccccccccccccCcchhHHHh-hcccCCC
Confidence 4567777776665 88899999999999999999999999999999999999999999999999999999 7899999
Q ss_pred CCeEEEecCCC
Q 046825 1196 TPVITCPLLVG 1206 (1208)
Q Consensus 1196 TP~~~~~l~~~ 1206 (1208)
||+|+++|.++
T Consensus 234 TP~mtiyL~~~ 244 (509)
T PRK14897 234 TPTMTIYLKKD 244 (509)
T ss_pred CceEEEEecCc
Confidence 99999999864
No 26
>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=99.97 E-value=1.1e-31 Score=312.11 Aligned_cols=80 Identities=55% Similarity=0.805 Sum_probs=75.1
Q ss_pred HHHHHHHHHhhhcCCCCCCchhhhhhccCCCcccccccccccccCccccccccccchHHHHHHHhhcCCCCCeEEEecCC
Q 046825 1126 DFLKLVKHKFVLSLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIKTPVITCPLLV 1205 (1208)
Q Consensus 1126 ~f~~l~~~~y~~slv~pGeaVGiIAAQSIGEP~TQMTLnTFH~AGv~~~nVTlGvPRlkEIi~~ask~ikTP~~~~~l~~ 1205 (1208)
.|...++.+|.+++|+||||||+|||||||||+|||||||||+|||+++|||||||||+||| +|+|+||||+|+++|.+
T Consensus 10 ~~~~~~~~~~~~~~~~~ge~vg~~aaQSiGEP~TQmTLnTFH~AGVas~NVTlGVPRLkEII-nasK~ikTP~~tv~L~~ 88 (410)
T cd02584 10 WILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEII-NVAKNIKTPSLTVYLEP 88 (410)
T ss_pred HHHHHHHHHHHHhhcCCCCCcchhhhhhcCCchhcccccccccccccccccccCccchHHHh-hcccCCCCCeEEEEecC
Confidence 34455688999999999999999999999999999999999999999999999999999999 78999999999999987
Q ss_pred C
Q 046825 1206 G 1206 (1208)
Q Consensus 1206 ~ 1206 (1208)
+
T Consensus 89 ~ 89 (410)
T cd02584 89 G 89 (410)
T ss_pred c
Confidence 5
No 27
>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=99.97 E-value=1.5e-31 Score=307.02 Aligned_cols=87 Identities=46% Similarity=0.706 Sum_probs=79.6
Q ss_pred cchhHHHHHHHHH---HHHhhhcCCCCCCchhhhhhccCCCcccccccccccccCccccccccccchHHHHHHHhhcCCC
Q 046825 1119 SNEMAKQDFLKLV---KHKFVLSLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIK 1195 (1208)
Q Consensus 1119 ~~~l~~~~f~~l~---~~~y~~slv~pGeaVGiIAAQSIGEP~TQMTLnTFH~AGv~~~nVTlGvPRlkEIi~~ask~ik 1195 (1208)
..+++.+.|.+++ ..+|.+++|+||||||+|||||||||+|||||||||||||++||||+|||||+||| +|+|+||
T Consensus 13 ~~~l~~~~~~~~~~~~~~~~~~~~~~~Ge~vG~iaAQSiGEP~TQMTLnTFH~AGVas~nVTlGVPRlkEII-na~K~i~ 91 (363)
T cd06528 13 EHGLTLSEAEEIIKEVLREYLRSLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRLIEIV-DARKEPS 91 (363)
T ss_pred HcCCCHHHHHHHHHHHHHHHHHHhhccCccccceeeeecCccceecccccccccccccccCccccccHHHHh-hcccCCC
Confidence 4566776666554 78999999999999999999999999999999999999999999999999999999 6999999
Q ss_pred CCeEEEecCCC
Q 046825 1196 TPVITCPLLVG 1206 (1208)
Q Consensus 1196 TP~~~~~l~~~ 1206 (1208)
||+|+++|.++
T Consensus 92 TP~mti~L~~~ 102 (363)
T cd06528 92 TPTMTIYLEEE 102 (363)
T ss_pred CceEEEEecCc
Confidence 99999999864
No 28
>PRK04309 DNA-directed RNA polymerase subunit A''; Validated
Probab=99.96 E-value=1.5e-30 Score=300.88 Aligned_cols=87 Identities=46% Similarity=0.719 Sum_probs=78.7
Q ss_pred cchhHHHHHHH---HHHHHhhhcCCCCCCchhhhhhccCCCcccccccccccccCccccccccccchHHHHHHHhhcCCC
Q 046825 1119 SNEMAKQDFLK---LVKHKFVLSLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIK 1195 (1208)
Q Consensus 1119 ~~~l~~~~f~~---l~~~~y~~slv~pGeaVGiIAAQSIGEP~TQMTLnTFH~AGv~~~nVTlGvPRlkEIi~~ask~ik 1195 (1208)
..+++++.|.+ .+..+|.+++|+||||||+|||||||||+|||||||||+||++++|||+|||||+||| +|+|+||
T Consensus 32 ~~~l~~~~~~~~~~~i~~~y~~~~v~pGe~VG~iaAQsIGEP~TQMTL~TFH~AGva~~nVTlGvPRlkEIi-na~K~~~ 110 (383)
T PRK04309 32 ERKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIV-DARKEPS 110 (383)
T ss_pred HcCCCHHHHHHHHHHHHHHHHHhhcCCCCccchhhhhhccchhhhcccccccccCccccCcccCchhHHHHH-hcccCCC
Confidence 34566655554 4578999999999999999999999999999999999999999999999999999999 7999999
Q ss_pred CCeEEEecCCC
Q 046825 1196 TPVITCPLLVG 1206 (1208)
Q Consensus 1196 TP~~~~~l~~~ 1206 (1208)
||+|+++|.++
T Consensus 111 TP~~tv~L~~~ 121 (383)
T PRK04309 111 TPMMTIYLKDE 121 (383)
T ss_pred CCeEEEEecCc
Confidence 99999999864
No 29
>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=99.96 E-value=1.3e-30 Score=292.54 Aligned_cols=72 Identities=54% Similarity=0.882 Sum_probs=69.5
Q ss_pred HhhhcCCCCCCchhhhhhccCCCcccccccccccccCccccccccccchHHHHHHHhhcCCCCCeEEEecCCC
Q 046825 1134 KFVLSLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIKTPVITCPLLVG 1206 (1208)
Q Consensus 1134 ~y~~slv~pGeaVGiIAAQSIGEP~TQMTLnTFH~AGv~~~nVTlGvPRlkEIi~~ask~ikTP~~~~~l~~~ 1206 (1208)
+|.+++|+||||||+|||||||||+|||||||||+||++++|||+|||||+||| +|||+||||+|+++|.++
T Consensus 1 ky~~~~v~pGe~vG~iaaQsiGEp~TQmTL~TFH~aGv~~~nvtlGvPRlkEIi-nasK~~~TP~~ti~l~~~ 72 (300)
T cd02736 1 KYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEII-NASKNISTPIITAKLEND 72 (300)
T ss_pred CchhhccCCCccchhhhhhhcCCccccccccccccccccccccccCchHHHHHH-hcccCCCCCeEEEEecCc
Confidence 589999999999999999999999999999999999999999999999999999 799999999999999764
No 30
>PF04983 RNA_pol_Rpb1_3: RNA polymerase Rpb1, domain 3; InterPro: IPR007066 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 [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1ZYR_D 1SMY_D 2A68_N 2O5J_D 3AOH_N 2O5I_D 2CW0_N 2A6H_N 2A69_D 3EQL_D ....
Probab=99.96 E-value=5.6e-30 Score=265.41 Aligned_cols=155 Identities=34% Similarity=0.563 Sum_probs=129.0
Q ss_pred ceecCCCCCCcccchhhhhhhhhhcccCccccCHHHHHHHHHhcCccCCCCCCCCCCCCceeeeecccceeeccCCCccC
Q 046825 572 QYVRPSNGDPLRSLIQDHIVSAALLTKKDTFLNRDEFCQLLYSSGVSSSGLGSFTGKPGQRVLISRSEQEVLPLLPAIWK 651 (1208)
Q Consensus 572 ~~~sp~~g~pi~gl~QD~l~g~~lLT~~d~f~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~PaIlk 651 (1208)
||+||++|+|+++++||+|+|+|+||++++|++++|++++++..... . .....+.|+|++
T Consensus 1 NilSP~~G~Pii~~~QD~vlG~y~LT~~~~f~~~~e~~~~~~~~~~~-------~-------------~~~~~~~~~I~~ 60 (158)
T PF04983_consen 1 NILSPANGKPIIGPTQDMVLGAYYLTSEDTFLSRDEAQQALMNGLID-------D-------------KKIVLLHPAILK 60 (158)
T ss_dssp GSEETTTTEESSS--SHHHHHHHHHSSTTTEESHHHHHHHHHCSST------------------------CHCSSSSBSS
T ss_pred CccCCCCCCceEEeccceEeEEEEEEecccccchHHHHHHHHccccc-------c-------------cceeccchhhhc
Confidence 79999999999999999999999999999999999999999965421 0 023578999999
Q ss_pred CCCCCCCCeEEEEeeccccCCCcceeeccCCCCCcccccccccccccccccccccCccccccccccccCCCccccccCCC
Q 046825 652 PEPLWTGKQVITAVLNHITRGRPPFVVERGGKLPQDFFKTRFNADKQSDRKKNDKGKLSKTNKMHKDKSGKKKEVVEGKP 731 (1208)
Q Consensus 652 p~~lwTGKqv~s~~l~~~~~~~~~~n~~~~~k~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~ 731 (1208)
|+++|||||++|.+||+ .+++....
T Consensus 61 ~~~~~tgk~~~s~il~~------~i~~~~~~------------------------------------------------- 85 (158)
T PF04983_consen 61 PKELWTGKQTFSRILPN------EINPEGFS------------------------------------------------- 85 (158)
T ss_dssp SSSCEECHHHHHTTSHT------THHEEEST-------------------------------------------------
T ss_pred cccceeeccHHHHhccc------cccccccc-------------------------------------------------
Confidence 99999999999999985 23322100
Q ss_pred CchhhhhhhcccccccCCceEEEecceeeeeecCccccC---CccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHcCce
Q 046825 732 GEEKEAEKNKSKEKELSEEKLLIYKNDLVRGVIDKAQFA---DYGLVHTVQELYGSNTAGTLLSALSRLFTVFLQMHGFT 808 (1208)
Q Consensus 732 ~~~~~~~~~~~~~~~~~d~~v~i~~gell~G~ldK~~iG---~~~Lih~i~~~yG~~~a~~~l~~l~~l~~~~l~~~GfS 808 (1208)
.+.+|+.|+|++|++++|++||+++| .++|+|.+|++||+++|++|||++++|+++|++.+|||
T Consensus 86 -------------~~~~~~~~~i~~g~~l~g~l~k~~lgk~~~~~li~~i~~~yG~~~~~~~ld~i~~lg~~~~t~~GfS 152 (158)
T PF04983_consen 86 -------------NDPDDGYVVINNGELLSGVLDKKTLGKKSLGSLIHQIYREYGPEATVQFLDAIKRLGFRYLTRSGFS 152 (158)
T ss_dssp -------------SCHSSHSEEECTSSEEEC--SHHHHSCSHTTCHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHTBB
T ss_pred -------------ccccccceeecCCccchhheehheecccchhhHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHcCee
Confidence 01236789999999999999999998 67999999999999999999999999999999999999
Q ss_pred eeeccc
Q 046825 809 CGVDDL 814 (1208)
Q Consensus 809 igi~D~ 814 (1208)
||++|+
T Consensus 153 vgi~D~ 158 (158)
T PF04983_consen 153 VGIDDM 158 (158)
T ss_dssp -SGGGC
T ss_pred EecccC
Confidence 999996
No 31
>PF05000 RNA_pol_Rpb1_4: RNA polymerase Rpb1, domain 4; InterPro: IPR007083 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 entry, domain 4, represents the funnel domain. The funnel domain contains the binding site for some elongation factors [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Q 3HKZ_I 1YNJ_D 1HQM_D 1YNN_D 1I6V_D 2GHO_D 2Y0S_W 3IYD_D 3LU0_D ....
Probab=99.81 E-value=8.7e-21 Score=184.45 Aligned_cols=95 Identities=43% Similarity=0.634 Sum_probs=74.6
Q ss_pred CcchhhHHHHHHHHHHHHhhhhhHHHHHHhhcCCCCCCCCCcchhhhhcCCCCCcccHHHHHhhcccccccCcccCCCCC
Q 046825 867 GGDAAVAYFDMKMTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMVS 946 (1208)
Q Consensus 867 ~~~~~~~~~~~~~~~~ln~~~~~~~~~~~~~~~l~~~~~~N~~~~M~~SGaKGS~vN~~Qi~~~lGQQ~leG~Rip~~~~ 946 (1208)
++....+.++..++..+++++++ +.+.+. ..+ ..+|++++|+.||||||.+|++||++|||||.++|+|||.+++
T Consensus 14 ~~~~~~~~~e~~~~~~~~~~~~~-~~~~~~-~~~---~~~N~l~~M~~SGaKGs~~ni~Qi~g~lGqq~~~g~ri~~~~~ 88 (108)
T PF05000_consen 14 WGKTYEETFEQKINKILNKVRDE-IGKIIK-KNL---PFNNSLLIMINSGAKGSMSNISQISGCLGQQSVEGKRIPRGFS 88 (108)
T ss_dssp CTCHHHHHHHHHHHHHHHHCCHH-HHHHHH-HCS---TTTSHHHHHHHSSSS--HHHHHHHHST-EEEEETTSES--SST
T ss_pred hhhhHHHHHHHHHHHHHHHHHHH-HHHHHH-HhC---CCCCcHHhhhhccCCCCHHHHHHHHHHHHHhhccccccccCCC
Confidence 44444477888888888888887 555544 222 1369999999999999999999999999999999999999999
Q ss_pred CccccCCCCCCCCccccccc
Q 046825 947 GKTLPSFHPWDWAPRAGGFI 966 (1208)
Q Consensus 947 grtLP~f~~~d~~~~a~GfI 966 (1208)
|||||||.++|.+|+|+|||
T Consensus 89 ~Rtlp~f~~~~~~~~~~GFI 108 (108)
T PF05000_consen 89 GRTLPHFKPFDESPESRGFI 108 (108)
T ss_dssp TCSSTTS-SS-SSTTTTTEE
T ss_pred CCcCCCcCCCCCCcccCCCC
Confidence 99999999999999999998
No 32
>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=99.71 E-value=2.7e-18 Score=182.75 Aligned_cols=50 Identities=46% Similarity=0.882 Sum_probs=47.6
Q ss_pred cCCCCCCchhhhhhccCCCcccccccccccccCccccccccccchHHHHHH
Q 046825 1138 SLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILT 1188 (1208)
Q Consensus 1138 slv~pGeaVGiIAAQSIGEP~TQMTLnTFH~AGv~~~nVTlGvPRlkEIi~ 1188 (1208)
.+|+||||||+|||||||||+|||||||||+||+++ ++|+|+||++||+.
T Consensus 1 ~~~~~g~~vg~~aaqsigep~tq~t~~tfh~~g~~~-dIt~Glprv~el~e 50 (204)
T cd02655 1 KLVELGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAT-DITQGLPRVEELFE 50 (204)
T ss_pred CccCcccccchhhhhhcCCCccccccchhhhccccc-ccccccHHHHHHHH
Confidence 378999999999999999999999999999999976 99999999999995
No 33
>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=99.70 E-value=2.8e-18 Score=198.57 Aligned_cols=57 Identities=26% Similarity=0.345 Sum_probs=52.2
Q ss_pred CCchhhhhhccCCCcccccccccccccCccccccccccchHHHHHHH-hhcCCCCCeEEEecCC
Q 046825 1143 GEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTI-ASKDIKTPVITCPLLV 1205 (1208)
Q Consensus 1143 GeaVGiIAAQSIGEP~TQMTLnTFH~AGv~~~nVTlGvPRlkEIi~~-ask~ikTP~~~~~l~~ 1205 (1208)
|||||+|||||||||+|||||||||+||++ +||||||||+. +++++|||.++|+|..
T Consensus 1 GE~VG~LAAqSIgEPAtQmtLntfh~agvs------~vprLKEiLn~~~~~~~ktps~~v~L~~ 58 (381)
T cd02737 1 GEPVGSLAATAISEPAYKALLDPPQSLESS------PLELLKEVLECRSKSKSKENDRRVILSL 58 (381)
T ss_pred CCcchhHHHhhhcchHHHhhhccchhcCCc------cHHHHHHHhcccccCCCCCCCEEEEEec
Confidence 899999999999999999999999999996 49999999953 1688999999999974
No 34
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=99.54 E-value=1.7e-15 Score=192.96 Aligned_cols=48 Identities=48% Similarity=0.678 Sum_probs=46.0
Q ss_pred ccccccccccccCccccccccccchHHHHHHHhhcCCCCCeEEEecCCC
Q 046825 1158 STQMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIKTPVITCPLLVG 1206 (1208)
Q Consensus 1158 ~TQMTLnTFH~AGv~~~nVTlGvPRlkEIi~~ask~ikTP~~~~~l~~~ 1206 (1208)
.||||||||||||||+||||||||||+||| +|||+||||+|+++|.++
T Consensus 540 v~~~~LnTFH~AGv~~~nVTlGvPRL~EIi-nask~i~TP~m~i~l~~~ 587 (858)
T PRK14898 540 VTHNTMRTFHYAGVAEINVTLGLPRMIEIV-DARKEPSTPIMTVHLKGE 587 (858)
T ss_pred eeccccceeeccCccccccccCCchHHHHh-cccCCCCCceEEEEECCC
Confidence 599999999999999999999999999999 799999999999999865
No 35
>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=99.36 E-value=1.4e-13 Score=141.72 Aligned_cols=46 Identities=72% Similarity=1.120 Sum_probs=44.7
Q ss_pred CCchhhhhhccCCCcccccccccccccCccccccccccchHHHHHH
Q 046825 1143 GEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILT 1188 (1208)
Q Consensus 1143 GeaVGiIAAQSIGEP~TQMTLnTFH~AGv~~~nVTlGvPRlkEIi~ 1188 (1208)
|||||+|||||||||+|||||.|||+.|..+.++|+|.||++|++.
T Consensus 1 g~~~g~~a~~~~~~p~~~~tl~t~~~~~~~~~~~t~~~pk~~~~~~ 46 (158)
T cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVASMNVTLGLPRLKEILN 46 (158)
T ss_pred CCcchhhhhhhcCCCccchhhhhhhhccccccccccCCccchhhcc
Confidence 8999999999999999999999999999999999999999999984
No 36
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=98.68 E-value=9.9e-09 Score=131.72 Aligned_cols=46 Identities=33% Similarity=0.595 Sum_probs=41.8
Q ss_pred cchhHHHHHHHHH---HHHhhhcCCCCCCchhhhhhccCCCcccccccc
Q 046825 1119 SNEMAKQDFLKLV---KHKFVLSLAQPGEPVGLLASQSVGEPSTQMTLN 1164 (1208)
Q Consensus 1119 ~~~l~~~~f~~l~---~~~y~~slv~pGeaVGiIAAQSIGEP~TQMTLn 1164 (1208)
..+++.+.|.+++ ..+|.+++|+||||||+|||||||||+|||||.
T Consensus 30 ~~~lt~~~~d~Il~~I~~~y~~a~vepge~vG~~aaqsi~~~~~~~~~~ 78 (858)
T PRK14898 30 RDGVTEEMVEEIIDEVVSAYLNALVEPYEAVGIVAAQSIGEPGTQMSLP 78 (858)
T ss_pred hcCCCHHHHHHHHHHHHHHHhhCCCCCCceeeeeeehhcCCCCccccCC
Confidence 4578888898887 688999999999999999999999999999874
No 37
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]
Probab=97.49 E-value=2.1e-05 Score=100.31 Aligned_cols=68 Identities=31% Similarity=0.185 Sum_probs=63.1
Q ss_pred hhhcCCCCCCchhhhhhccCCCcccccccccccccC--ccccccccccchHHHHHHHhhcCCCCCeEEEecC
Q 046825 1135 FVLSLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAG--RGEMNVTLGIPRLQEILTIASKDIKTPVITCPLL 1204 (1208)
Q Consensus 1135 y~~slv~pGeaVGiIAAQSIGEP~TQMTLnTFH~AG--v~~~nVTlGvPRlkEIi~~ask~ikTP~~~~~l~ 1204 (1208)
|...++.+++++|..+|||+|+|.||||+.|||+|| ++..++|.|.||+-++. .| +-.+||.|++.+.
T Consensus 406 DGDeM~~Hvp~s~ea~AEa~~lm~tq~nilsP~~Ggpiv~~~qD~v~g~ylLt~~-d~-~~~~~~~~ei~l~ 475 (808)
T COG0086 406 DGDEMAVHVPASGEAAAEARGLMGTQMNILTPHYGGPIVAPIQDTVGGPYLLTIV-DA-KLPSTPVGEIYLK 475 (808)
T ss_pred CchhhhccccchHHHHHHHHHhhccccccccCCCCCceEeecceEEeccEEEEEe-cc-cCCCCcceEEEec
Confidence 567889999999999999999999999999999999 99999999999999997 45 8999999999664
No 38
>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional
Probab=64.01 E-value=3.1 Score=52.10 Aligned_cols=20 Identities=25% Similarity=0.441 Sum_probs=17.8
Q ss_pred ccceeeccccccchhcHHHH
Q 046825 14 HFGHIDLVVPVYNPLLFNLL 33 (1208)
Q Consensus 14 HFGHIELa~PVynP~ff~~l 33 (1208)
-+|||+|+.||-|+-|++.+
T Consensus 102 RMG~I~La~PV~HiWylk~~ 121 (627)
T PRK02625 102 RMGFIKLAAPVTHVWYLKGI 121 (627)
T ss_pred hcCceeecCCceEeeccCCC
Confidence 59999999999999998743
No 39
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=46.92 E-value=7.8 Score=55.76 Aligned_cols=32 Identities=22% Similarity=0.360 Sum_probs=23.1
Q ss_pred cccccccccchHHHHHHHhhcCCCCCeEEEec
Q 046825 1172 GEMNVTLGIPRLQEILTIASKDIKTPVITCPL 1203 (1208)
Q Consensus 1172 ~~~nVTlGvPRlkEIi~~ask~ikTP~~~~~l 1203 (1208)
...++|.|+||+.||+...-.++|-|.+..+.
T Consensus 2639 ~t~DITgGLprv~eLfear~~~pk~~a~i~ei 2670 (2890)
T PRK09603 2639 KSRDITGGLPRVSELFEARKPKPKDVAILSEV 2670 (2890)
T ss_pred ccccccCCcccchhheEeecCCCCCceEEecc
Confidence 34589999999999995222377877776554
No 40
>TIGR02387 rpoC1_cyan DNA-directed RNA polymerase, gamma subunit. 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''.
Probab=46.31 E-value=8.5 Score=48.28 Aligned_cols=20 Identities=25% Similarity=0.406 Sum_probs=17.9
Q ss_pred ccceeeccccccchhcHHHH
Q 046825 14 HFGHIDLVVPVYNPLLFNLL 33 (1208)
Q Consensus 14 HFGHIELa~PVynP~ff~~l 33 (1208)
-+|||+|+.||-|+-|++.+
T Consensus 95 RMG~I~La~PV~HiWylk~~ 114 (619)
T TIGR02387 95 RMGYIKLAAPVTHVWYLKGI 114 (619)
T ss_pred hcCceeccCcceeeeecCCC
Confidence 58999999999999998744
No 41
>CHL00018 rpoC1 RNA polymerase beta' subunit
Probab=45.85 E-value=9.3 Score=48.44 Aligned_cols=20 Identities=30% Similarity=0.461 Sum_probs=17.9
Q ss_pred ccceeeccccccchhcHHHH
Q 046825 14 HFGHIDLVVPVYNPLLFNLL 33 (1208)
Q Consensus 14 HFGHIELa~PVynP~ff~~l 33 (1208)
-+|||+|+.||-|+-|++.+
T Consensus 103 RMG~I~La~PV~HiWylk~~ 122 (663)
T CHL00018 103 RMGYIKLACPVTHVWYLKRL 122 (663)
T ss_pred hcCceeecCcceeehhhcCC
Confidence 48999999999999999744
No 42
>PF05183 RdRP: RNA dependent RNA polymerase; InterPro: IPR007855 This entry represents various eukaryotic RNA-dependent RNA polymerases (RDRP; 2.7.7.48 from EC), such as RCRP-1, RDRP-2 and RDRP-6. These enzymes are involved in the amplification of regulatory microRNAs during post-transcriptional gene silencing []; they are also required for transcriptional gene silencing. Double-stranded RNA has been shown to induce gene silencing in diverse eukaryotes and by a variety of pathways []. These enzymes also play a role in the RNA interference (RNAi) pathway, which is important for heterochromatin formation, accurate chromosome segregation, centromere cohesion and telomere function during mitosis and meiosis. RDRP enzymes are highly conserved in most eukaryotes, but are missing in archaea and bacteria. The core catalytic domain of RDRP enzymes is structurally similar to the beta' subunit of DNA-dependent RNA polymerases (DDRP), however the other domains of DDRP show no similarity to those of RDRP.; GO: 0003968 RNA-directed RNA polymerase activity; PDB: 2J7O_A 2J7N_A.
Probab=44.17 E-value=10 Score=47.94 Aligned_cols=54 Identities=33% Similarity=0.368 Sum_probs=27.7
Q ss_pred hhcccceEEEecCCCCCcCcccceeEEEeCCCCeE-----------EEeccCCCCCCCCCCCCceecc
Q 046825 496 HLQDGDVVLVNRQPTLHKPSIMAHVVRVLKGEKTL-----------RMHYANCSTYNADFDGDEMNVH 552 (1208)
Q Consensus 496 hl~dgD~Vl~NRqPsLHk~simah~v~vl~~~~t~-----------rln~~~c~~yNADFDGDemn~h 552 (1208)
.+..| .||+-|.|++|..-|+-.++.-.|.-+-+ |=++..|+ ++|+|||+-.|-
T Consensus 365 ~~~~g-~VlV~R~P~~~pgDir~~~av~~p~L~~l~~vIVF~~~G~r~~~~~ls--GgDlDGD~~~V~ 429 (579)
T PF05183_consen 365 QVLEG-DVLVTRNPCLHPGDIRKVKAVDKPELRHLKDVIVFSTKGDRPLPSELS--GGDLDGDEYFVC 429 (579)
T ss_dssp EEEE--EEEEE-SS--SGGGEEEEEE---GGGTT--SEEEE-S-SSS-HHHHTT--T--SSS-EEEEE
T ss_pred ceeee-eEEEecCCccCcCceeEEEeeccHHHcccCCEEEeCCCCCCCchHHhc--CCCCCCceEEEE
Confidence 34566 79999999999999998887544431111 11111222 379999999876
No 43
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=41.22 E-value=11 Score=51.27 Aligned_cols=19 Identities=37% Similarity=0.634 Sum_probs=17.6
Q ss_pred ccceeeccccccchhcHHH
Q 046825 14 HFGHIDLVVPVYNPLLFNL 32 (1208)
Q Consensus 14 HFGHIELa~PVynP~ff~~ 32 (1208)
.+|||||+.||-|+-||+.
T Consensus 93 RMGhI~La~PV~HiWylk~ 111 (1460)
T PRK14906 93 RMGHIELAAPVSHIWYFKG 111 (1460)
T ss_pred hcCcccccCcchhhhhccC
Confidence 6999999999999999983
No 44
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=32.14 E-value=23 Score=29.18 Aligned_cols=13 Identities=31% Similarity=0.616 Sum_probs=11.1
Q ss_pred ccCCCCCCCCCCc
Q 046825 137 TTKCGNCKAKNPR 149 (1208)
Q Consensus 137 ~~kC~~Cg~~~p~ 149 (1208)
.++||+||++++.
T Consensus 11 irkCp~CGt~NG~ 23 (44)
T PF14952_consen 11 IRKCPKCGTYNGT 23 (44)
T ss_pred cccCCcCcCccCc
Confidence 5799999999954
No 45
>PF04992 RNA_pol_Rpb1_6: RNA polymerase Rpb1, domain 6; InterPro: IPR007075 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 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module [, ]. This family appears to be specific to the largest subunit of RNA polymerase II.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_M 1Y77_A 3CQZ_A 3GTM_A 1TWA_A 4A3I_A 2NVY_A 2NVT_A 1I6H_A 1TWF_A ....
Probab=31.37 E-value=38 Score=36.75 Aligned_cols=78 Identities=13% Similarity=0.135 Sum_probs=40.9
Q ss_pred cccccccccCCCceeeechhHHHHHhhhcchh----------------hhHHHHHHhH---------HHHHHHhHHHHHH
Q 046825 1061 GRGRNKFCDKGSHTFVMGRNQEMIYKKCSGQL----------------DASNAYIMEL---------PDALKDNAEKFAD 1115 (1208)
Q Consensus 1061 ~~~~~~~~~~~~~~~~~~~n~~~~~~~~~~~~----------------~~~~~~~~~~---------~~~~~~~~~~~~~ 1115 (1208)
...+..+...+...+.+|+|+.+++.+.+... ..+.++++++ ..-.+.|+..+++
T Consensus 71 ~~Lr~~i~~~g~~~~~LPVNi~RiI~nAq~~f~i~~~~~sdL~P~~Vi~~V~~L~~~L~vv~g~D~ls~Eaq~NAtlLf~ 150 (187)
T PF04992_consen 71 ELLRKEIFPSGDDKVPLPVNIQRIIWNAQKIFHIDPRKPSDLSPIYVIEKVEELLDRLVVVRGDDPLSREAQENATLLFK 150 (187)
T ss_dssp CCCCSCCSTTT--EEEEES-HHHHCCCCCCCTT--TTS-BS--HHHHHHHHHHHHTT--SS--SSCCCCHHHHCCCHHHH
T ss_pred HHHHHHhccCCCcceECCccHHHHHHHHHHHcCCCCCCcccCCHHHHHHHHHHHHHHHhhccCCCcchHHHHhhHHHHHH
Confidence 33444455666789999999999987654321 1222222221 0112334444433
Q ss_pred h----h-------hcchhHHHHHHHHH---HHHhhhc
Q 046825 1116 K----F-------LSNEMAKQDFLKLV---KHKFVLS 1138 (1208)
Q Consensus 1116 ~----~-------~~~~l~~~~f~~l~---~~~y~~s 1138 (1208)
. . ..++++.++|.|++ +.+|.+|
T Consensus 151 i~lRs~LasKrvi~e~rL~~~AF~wilgEIe~rF~~a 187 (187)
T PF04992_consen 151 ILLRSTLASKRVIEEYRLNKEAFDWILGEIESRFKKA 187 (187)
T ss_dssp HHHCCCSSHHHHHHTSB--HHHHHHHHHHHHHHHHCC
T ss_pred HHHHHhhhhHHHHHHhCcCHHHHHHHHHHHHHHHHcC
Confidence 2 1 16899999999997 6777764
No 46
>PF05094 LEF-9: Late expression factor 9 (LEF-9); InterPro: IPR007786 The baculovirus Autographa californica nuclear polyhedrosis virus (AcMNPV) encodes a DNA-dependent RNA polymerase that is required for transcription of viral late genes. This polymerase is composed of four equimolar subunits, LEF-8, LEF-4, LEF-9, and p47. LEF-9 is homologous to the largest beta-subunit of prokaryotic DNA-directed RNA polymerase [].; GO: 0019083 viral transcription
Probab=29.50 E-value=84 Score=37.78 Aligned_cols=65 Identities=17% Similarity=0.207 Sum_probs=46.6
Q ss_pred eEEEecCCCCCcCcccceeEEEeC--CCCeEEEeccCCCCCCCCCCCCc-eecccCCCHHHHHHHHHhc
Q 046825 502 VVLVNRQPTLHKPSIMAHVVRVLK--GEKTLRMHYANCSTYNADFDGDE-MNVHFPQDEVSRAEAYNIV 567 (1208)
Q Consensus 502 ~Vl~NRqPsLHk~simah~v~vl~--~~~t~rln~~~c~~yNADFDGDe-mn~h~pqs~~a~~Ea~~L~ 567 (1208)
.+.--|+|.+-..|-+--+|+.-. .+-.+++=......-|+|-|||- .--++|+ |++..++..|+
T Consensus 212 raw~tRHPniSqlsTq~s~v~~~~~~~~wnvkvGlG~F~Gan~DCDGDKeviT~lP~-PNSLidlE~lL 279 (487)
T PF05094_consen 212 RAWTTRHPNISQLSTQVSRVDQNDDYTDWNVKVGLGTFVGANRDCDGDKEVITYLPY-PNSLIDLESLL 279 (487)
T ss_pred eeeecCCCCchhhchhheEeeccccCCCcceeeeeccccCCCCCCCCCceEEEecCC-CcchhhHHHHh
Confidence 466679999999999988876522 12367777888899999999995 5556665 44455555554
No 47
>PHA03396 lef-9 late expression factor 9; Provisional
Probab=23.87 E-value=1.2e+02 Score=36.81 Aligned_cols=64 Identities=17% Similarity=0.238 Sum_probs=44.0
Q ss_pred eEEEecCCCCCcCcccceeEEEeCC---CCeEEEeccCCCCCCCCCCCCc-eecccCCCHHHHHHHHHhc
Q 046825 502 VVLVNRQPTLHKPSIMAHVVRVLKG---EKTLRMHYANCSTYNADFDGDE-MNVHFPQDEVSRAEAYNIV 567 (1208)
Q Consensus 502 ~Vl~NRqPsLHk~simah~v~vl~~---~~t~rln~~~c~~yNADFDGDe-mn~h~pqs~~a~~Ea~~L~ 567 (1208)
-+.--|+|.+-..|-+--+|+. +. .--+++=......-|+|-|||- .--++|+ |++..++..|+
T Consensus 215 raw~tRHPnisqlstq~s~v~~-~~~~~~wNvkvGlG~F~GanrDCDGDKeviT~lP~-PNsLidlE~lL 282 (493)
T PHA03396 215 RAWTTRHPNISQLSTQVSRVDQ-NDDYTDWNVKVGLGTFPGANRDCDGDKEVITFLPY-PNSLIDLECLL 282 (493)
T ss_pred EEeecCCCCchhhchhheEeec-cccccccceeeeeccccCCCCCCCCCceEEEecCC-CcchhhHHHHh
Confidence 4666799999999998888764 32 1135566677889999999995 5556666 34444444443
No 48
>PF12234 Rav1p_C: RAVE protein 1 C terminal; InterPro: IPR022033 This domain family is found in eukaryotes, and is typically between 621 and 644 amino acids in length. This family is the C-terminal region of the protein RAVE (regulator of the ATPase of vacuolar and endosomal membranes). Rav1p is involved in regulating the glucose dependent assembly and disassembly of vacuolar ATPase V1 and V0 subunits.
Probab=22.57 E-value=47 Score=42.40 Aligned_cols=37 Identities=19% Similarity=0.373 Sum_probs=28.1
Q ss_pred cccccchhcHHHHHHHHHHhhhhccccccChhhHHHHHHHHHHhh
Q 046825 21 VVPVYNPLLFNLLYTLLKRICFFCHHFKASRREVEKCVRKLELII 65 (1208)
Q Consensus 21 a~PVynP~ff~~l~kLLr~iC~~C~rfll~~~~~~~~~~kL~ll~ 65 (1208)
|+|||||-|+- .|..|+++.+-+.-+..+...|+...
T Consensus 184 pLPvYHPqfL~--------q~l~~Gk~~lv~~IL~~L~~~L~~~~ 220 (631)
T PF12234_consen 184 PLPVYHPQFLI--------QLLLSGKFKLVKKILLHLFKCLRFLD 220 (631)
T ss_pred CCCCcCHHHHH--------HHHHcCCHHHHHHHHHHHHHHHHhhc
Confidence 79999999874 47889999888777666666666543
No 49
>PF05864 Chordopox_RPO7: Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7); InterPro: IPR008448 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 kDa, 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 several Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide sequences. DNA-dependent RNA polymerase catalyses the transcription of DNA into RNA [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=22.33 E-value=59 Score=28.38 Aligned_cols=19 Identities=26% Similarity=0.345 Sum_probs=14.1
Q ss_pred HHHHHHHHhhhhccccccC
Q 046825 32 LLYTLLKRICFFCHHFKAS 50 (1208)
Q Consensus 32 ~l~kLLr~iC~~C~rfll~ 50 (1208)
.+.++|+.+=..|.|++++
T Consensus 27 ~Lk~Vl~~v~n~CCRlKLs 45 (63)
T PF05864_consen 27 SLKKVLRTVKNSCCRLKLS 45 (63)
T ss_pred hHHHHHHHhhccceeeeec
Confidence 4567777777888888776
Done!