Query 000235
Match_columns 1815
No_of_seqs 523 out of 2640
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 00:40:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/000235.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/000235hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0260 RNA polymerase II, lar 100.0 0E+00 0E+00 3711.9 111.0 1386 1-1429 1-1427(1605)
2 PRK14977 bifunctional DNA-dire 100.0 4E-312 9E-317 3044.6 104.4 1227 10-1423 4-1318(1321)
3 KOG0261 RNA polymerase III, la 100.0 6E-311 1E-315 2750.2 62.5 1284 10-1424 8-1364(1386)
4 KOG0262 RNA polymerase I, larg 100.0 2E-284 4E-289 2576.5 79.6 1312 13-1423 11-1637(1640)
5 TIGR02390 RNA_pol_rpoA1 DNA-di 100.0 2E-231 4E-236 2235.5 71.8 837 13-889 2-859 (868)
6 PRK08566 DNA-directed RNA poly 100.0 3E-230 5E-235 2232.1 69.7 840 11-889 5-864 (882)
7 TIGR02386 rpoC_TIGR DNA-direct 100.0 6E-212 1E-216 2031.3 66.5 1033 17-1416 1-1136(1140)
8 PRK00566 DNA-directed RNA poly 100.0 8E-207 2E-211 1985.0 65.2 1031 14-1417 6-1139(1156)
9 PRK14906 DNA-directed RNA poly 100.0 2E-196 3E-201 1878.3 57.1 1051 13-1416 7-1237(1460)
10 PRK09603 bifunctional DNA-dire 100.0 2E-189 4E-194 1877.6 58.2 853 11-1102 1392-2309(2890)
11 PRK14844 bifunctional DNA-dire 100.0 1E-189 2E-194 1872.2 51.4 1145 12-1415 1445-2784(2836)
12 COG0086 RpoC DNA-directed RNA 100.0 7E-161 1E-165 1544.1 35.0 774 14-887 4-794 (808)
13 PRK02625 rpoC1 DNA-directed RN 100.0 6E-104 1E-108 964.5 30.2 479 13-552 7-545 (627)
14 TIGR02387 rpoC1_cyan DNA-direc 100.0 6E-103 1E-107 954.6 27.1 466 15-541 2-518 (619)
15 CHL00018 rpoC1 RNA polymerase 100.0 5E-101 1E-105 947.9 30.7 477 13-542 5-547 (663)
16 cd02584 RNAP_II_Rpb1_C Largest 100.0 6.4E-95 1.4E-99 872.4 27.4 374 1044-1421 1-410 (410)
17 smart00663 RPOLA_N RNA polymer 100.0 6.7E-93 1.5E-97 823.6 24.0 284 242-535 1-295 (295)
18 TIGR02389 RNA_pol_rpoA2 DNA-di 100.0 2.7E-87 5.9E-92 794.9 25.0 331 1042-1421 15-367 (367)
19 cd06528 RNAP_A'' A'' subunit o 100.0 3.4E-85 7.4E-90 778.7 24.5 334 1038-1421 8-362 (363)
20 PRK14897 unknown domain/DNA-di 100.0 1E-84 2.3E-89 784.2 23.1 331 1040-1423 152-505 (509)
21 PRK04309 DNA-directed RNA poly 100.0 1.3E-83 2.9E-88 769.8 24.4 331 1042-1424 31-382 (383)
22 cd02736 RNAP_III_Rpc1_C Larges 100.0 1.5E-79 3.2E-84 713.8 15.6 300 1061-1416 1-300 (300)
23 cd02735 RNAP_I_Rpa1_C Largest 100.0 1.8E-78 3.9E-83 710.4 17.0 306 1061-1419 1-309 (309)
24 PRK02597 rpoC2 DNA-directed RN 100.0 3.3E-77 7.1E-82 779.0 27.4 346 622-1115 5-363 (1331)
25 TIGR02388 rpoC2_cyan DNA-direc 100.0 4E-74 8.6E-79 744.4 30.0 334 622-1104 4-343 (1227)
26 cd02737 RNAP_IV_NRPD1_C Larges 100.0 3.2E-74 7E-79 686.3 18.2 321 1070-1420 1-381 (381)
27 CHL00117 rpoC2 RNA polymerase 100.0 4.3E-70 9.3E-75 720.9 28.1 340 621-1113 10-365 (1364)
28 PF04998 RNA_pol_Rpb1_5: RNA p 100.0 1.4E-71 3E-76 654.2 5.5 275 815-1373 1-276 (277)
29 PF04997 RNA_pol_Rpb1_1: RNA p 100.0 2.2E-64 4.8E-69 606.5 15.4 319 13-340 2-337 (337)
30 PRK14898 DNA-directed RNA poly 100.0 3.8E-61 8.2E-66 630.7 19.3 293 1077-1424 535-852 (858)
31 PF00623 RNA_pol_Rpb1_2: RNA p 100.0 5.8E-62 1.3E-66 524.5 6.7 166 342-510 1-166 (166)
32 cd00630 RNAP_largest_subunit_C 100.0 1.2E-46 2.5E-51 400.4 9.8 110 1306-1415 49-158 (158)
33 cd02655 RNAP_beta'_C Largest s 100.0 6.9E-46 1.5E-50 408.0 10.0 108 1306-1415 55-204 (204)
34 KOG0260 RNA polymerase II, lar 100.0 1.2E-40 2.6E-45 413.2 20.3 110 1311-1421 1149-1264(1605)
35 PF04992 RNA_pol_Rpb1_6: RNA p 100.0 1.9E-33 4.1E-38 309.1 4.4 185 881-1065 1-187 (187)
36 PF04983 RNA_pol_Rpb1_3: RNA p 100.0 1.6E-31 3.5E-36 289.7 6.6 155 513-677 1-158 (158)
37 PF05000 RNA_pol_Rpb1_4: RNA p 99.9 3.4E-23 7.3E-28 210.1 3.9 105 704-808 3-108 (108)
38 PF04990 RNA_pol_Rpb1_7: RNA p 99.9 9.6E-23 2.1E-27 212.4 6.7 135 1150-1284 1-135 (135)
39 COG0086 RpoC DNA-directed RNA 99.8 2.8E-20 6.1E-25 242.3 7.0 327 1063-1421 407-745 (808)
40 PRK14898 DNA-directed RNA poly 99.0 2.3E-10 5E-15 152.7 3.5 51 1041-1091 28-78 (858)
41 PHA03247 large tegument protei 98.5 0.0002 4.4E-09 99.8 38.0 18 381-398 848-865 (3151)
42 PHA03247 large tegument protei 98.4 0.00036 7.9E-09 97.5 36.2 24 1106-1132 1927-1950(3151)
43 KOG0307 Vesicle coat complex C 96.8 0.22 4.7E-06 67.1 25.9 12 1344-1355 591-602 (1049)
44 KOG0307 Vesicle coat complex C 96.3 0.87 1.9E-05 61.6 26.3 11 1147-1157 402-412 (1049)
45 KOG1999 RNA polymerase II tran 93.1 0.84 1.8E-05 60.9 13.2 9 1357-1365 669-677 (1024)
46 KOG1924 RhoA GTPase effector D 91.6 1 2.2E-05 58.5 11.0 12 848-859 157-168 (1102)
47 KOG1984 Vesicle coat complex C 91.2 51 0.0011 44.6 25.6 11 1774-1784 243-253 (1007)
48 KOG1924 RhoA GTPase effector D 91.1 1 2.2E-05 58.5 10.4 17 843-859 50-66 (1102)
49 KOG1999 RNA polymerase II tran 84.9 11 0.00025 50.9 14.3 9 1339-1347 627-635 (1024)
50 KOG2236 Uncharacterized conser 68.0 21 0.00045 45.0 9.1 20 1084-1105 38-57 (483)
51 KOG3671 Actin regulatory prote 62.0 2.3E+02 0.0049 36.6 16.2 9 1267-1275 129-137 (569)
52 KOG2236 Uncharacterized conser 61.8 46 0.001 42.1 10.4 9 1402-1410 276-284 (483)
53 PF05183 RdRP: RNA dependent R 51.0 7.8 0.00017 51.5 1.8 54 437-493 364-429 (579)
54 PF02362 B3: B3 DNA binding do 46.9 20 0.00043 35.8 3.6 76 352-450 4-85 (100)
55 PF15278 Sec3_C_2: Sec3 exocys 45.5 52 0.0011 31.5 5.5 27 743-769 59-85 (86)
56 KOG0119 Splicing factor 1/bran 42.2 9.1E+02 0.02 31.5 20.6 16 1270-1285 166-181 (554)
57 KOG1923 Rac1 GTPase effector F 38.0 1.1E+02 0.0023 41.2 8.7 9 1372-1380 154-162 (830)
58 KOG1830 Wiskott Aldrich syndro 35.4 1.1E+03 0.023 30.3 21.0 11 1295-1305 143-153 (518)
59 KOG0162 Myosin class I heavy c 34.0 4.1E+02 0.009 35.8 12.7 11 668-678 381-391 (1106)
60 PF15449 Retinal: Retinal prot 33.2 9.3E+02 0.02 34.3 16.1 15 477-491 127-141 (1287)
61 KOG0391 SNF2 family DNA-depend 31.7 1.9E+03 0.041 32.1 20.2 36 1340-1380 1499-1534(1958)
62 PRK13895 conjugal transfer pro 31.5 2.2E+02 0.0048 30.9 8.3 30 656-685 4-33 (144)
63 PF15449 Retinal: Retinal prot 31.0 1.8E+03 0.039 31.7 19.4 9 808-816 294-302 (1287)
64 KOG0119 Splicing factor 1/bran 29.5 1.4E+03 0.03 29.9 21.8 12 1317-1328 218-229 (554)
65 PHA03082 DNA-dependent RNA pol 29.5 18 0.00039 32.8 0.0 40 64-116 5-46 (63)
66 KOG3771 Amphiphysin [Intracell 29.2 1E+03 0.022 30.9 14.8 9 1323-1331 180-188 (460)
67 KOG1830 Wiskott Aldrich syndro 25.0 1.5E+03 0.034 28.9 22.4 13 1416-1429 158-170 (518)
68 KOG0566 Inositol-1,4,5-triphos 23.5 6.2E+02 0.013 35.5 12.0 26 440-468 265-290 (1080)
69 KOG2199 Signal transducing ada 23.2 2.9E+02 0.0062 34.8 8.3 84 1697-1791 378-462 (462)
No 1
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=100.00 E-value=0 Score=3711.94 Aligned_cols=1386 Identities=65% Similarity=1.042 Sum_probs=1342.0
Q ss_pred CCCCCCCCcccccccceEEEEcCCHHHHHhcceeEEeeCccccCCCCCCCCCCCCCCCCcCCCccccccccCCCCcCCcc
Q 000235 1 MDTRFPYSPAEVAKVRMVQFGILSPDEIRQMSVVQIEHGETTERGKPKPGGLSDPRLGTIDRKMKCETCTANMAECPGHF 80 (1815)
Q Consensus 1 ~~~~~~~s~~~~~~i~~i~F~~~S~eeI~~~Sv~eI~~~~~~~~~~p~~gGl~D~rlG~~~~~~~C~TCg~~~~~CpGHf 80 (1815)
|+..+.++++|+++|++|||||+|||||++|||.||..+|+++.++|+.|||.|||||++|++.+|+|||.++.+|||||
T Consensus 1 m~~~~~~~~~pl~~v~~vqFgi~spdeir~mSV~~i~~~e~~e~~~pk~ggl~D~RlG~idr~~~CqTC~g~~~~CpGHF 80 (1605)
T KOG0260|consen 1 MGDDCEFSQAPLRTVKSVQFGILSPDEIRRMSVAEIEFPETMEGGRPKLGGLMDPRLGTIDRDSLCQTCGGNMFECPGHF 80 (1605)
T ss_pred CCCCcccccCcceeeeEEEeeccChhhhhcceeEEeecccccccCCCCcCCccccccCCCCccchhhhhccccccCCccc
Confidence 77789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceeeccccccchhhhhHHHHHhcccceecceeccCCchHHHHHHHHhcC-hHHHHHHHHHHhhhccccCCCCCCCCCCCC
Q 000235 81 GHLELAKPMFHIGFMKTVLSIMRSVCFNCSKILADEDDHKFKQALKIRN-PKNRLKKILDACKNKTKCEGGDEIDVPGQD 159 (1815)
Q Consensus 81 GhIeL~~PV~h~~f~~~v~~iL~~vC~~C~~l~~~~~~~~~~~~~~~~~-~~~~~~~i~~~~~~~~~C~~~~~~~~~~~~ 159 (1815)
||||||+|||||+|+++|++||+|||++|+++++++..+++.+.++.+. +++|+..+|..|+++..|+.+.+.+
T Consensus 81 GhieLAkPvfH~gFl~kv~kiL~cVC~~C~ki~~~~~~~~~~~~~~~~~~~k~rl~~v~~vck~k~~ce~g~~~e----- 155 (1605)
T KOG0260|consen 81 GHIELAKPVFHPGFLKKVKKILRCVCFYCSKILKDKFNPKEDQILRKRYCSKGRLLMVLDVCKGKVVCEGGIDVE----- 155 (1605)
T ss_pred ceeeeccccccHHHHHHHHHHHHHhhhcchheeecccCcchhhhhhhhcCCcchHHHHHHhhccceeeecccccc-----
Confidence 9999999999999999999999999999999999998888777777665 8999999999999999998632211
Q ss_pred CCcccccccCCCCccchhhhhcccchhhhhHHhhccccccCCCCccchhcccCCHHHHHHHHhhcChhhHHHhcCCCCCC
Q 000235 160 GEEPLKKNKGGCGAQQPKLTIEGMKMIAEYKAQRKKNDDQEQLPEPVERKQTLTAERVLGVLKRISDEDCQLLGLNPKYA 239 (1815)
Q Consensus 160 ~~~~~~~~~~gCg~~~p~i~k~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~p~~v~~ilk~i~~~d~~~l~~~~~~~ 239 (1815)
...++|||..||.|++.|++++.+|+....+ .. ..++.|++++|++||++|.++|+..|||+++++
T Consensus 156 -----~~g~sgcg~kqP~i~r~gl~l~a~~k~~~e~----~~-----e~k~~ls~e~V~~i~k~Isded~~~lg~~~~~a 221 (1605)
T KOG0260|consen 156 -----SDGRSGCGLKQPSIRRLGLDLWAFWKQGDED----SQ-----ESKRKLSAERVLEIFKRISDEDIDQLGFKPKIA 221 (1605)
T ss_pred -----ccccccccccCCceeccCchhhhhhhccCcc----CC-----cccccCcHHHHHHHHHhhchhhhhhhcCCCCcC
Confidence 1267999999999999999999999872111 11 147789999999999999999999999999999
Q ss_pred CccceEEeecccCCCCCCCC----------chhHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHhhccCCCC
Q 000235 240 RPDWMILQVLPIPPPPVRPS----------DDLTHQLAMIIRHNENLRRQERNGAPAHIISEFAQLLQFHIATYFDNELP 309 (1815)
Q Consensus 240 ~Pe~~il~~lpVpP~~~RP~----------ddlT~~l~~Ii~~N~~lk~~~~~g~~~~~i~~~~~~LQ~~V~~~~dn~~~ 309 (1815)
||||||||+|||||+.+||+ ||||++|.+|||.|..|++.+++|++.|++.++.++||+||++|+||+++
T Consensus 222 rpewmIlTvLPVPP~~vrP~iv~~~s~rg~DdlthkLadIiK~n~~l~r~e~~ga~~H~i~e~~~LlqfhVat~~Dn~~p 301 (1605)
T KOG0260|consen 222 RPEWMILTVLPVPPPAVRPEIVMQGSARGEDDLTHKLADIIKKNIGLKRNEENGAPAHIIEEYEQLLQFHVATYVDNDIP 301 (1605)
T ss_pred CCceeEEEEecCCCCcccceeeecccccCcchhHHHHHHHHHHHHHHhhhhhcCCchhhHHHHHhHhhhhhhheeccccc
Confidence 99999999999999999998 99999999999999999999999999999999999999999999999999
Q ss_pred CCCcccccCCCChhhhhhhhhhcccccccccCCCCCCCCCceeecCCCCcccccccChHHHhhhccCCcccchhHHHHHH
Q 000235 310 GQPRATQRSGRPIKSICSRLKAKEGRIRGNLMGKRVDFSARTVITPDPTINIDQLGVPWSIALNLTYPETVTPYNIERLK 389 (1815)
Q Consensus 310 ~~p~~~~~~~~p~k~i~qrLkgK~Gr~R~nlmGKRVdfsaRsVIspDP~L~~~evGvP~~~A~~LT~PE~Vt~~Ni~~l~ 389 (1815)
|+|++.||+|||+|+|++||||||||+|+|||||||||||||||+|||||+|||||||++||++|||||+||+|||++|+
T Consensus 302 gqp~a~qksGrplkSi~arlKgkegriRgnLmGKRvDFSaRTVItgDPnl~ldevGVP~sIAk~lTfpE~Vtp~NidrLq 381 (1605)
T KOG0260|consen 302 GQPQADQKSGRPLKSISARLKGKEGRIRGNLMGKRVDFSARTVITGDPNLSLDEVGVPRSIAKRLTFPEHVTPFNIDRLQ 381 (1605)
T ss_pred CCcccccccCCcccchhhhhccccchhhhcccccccCcceeeeecCCCCcchhcccCcHHHHhhccCcceeccccHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHcCCCCCCCcccccEEEeCCCceeeccccccccccccccccEeeeecccCCeEEEecCCccccccccceeEEeecCC
Q 000235 390 ELVEYGPHPPPGKTGAKYIIRDDGQRLDLRYLKKSSDHHLELGYKVERHLNDGDFVLFNRQPSLHKMSIMGHRIKIMPYS 469 (1815)
Q Consensus 390 ~lv~ng~~~~pg~~~A~~i~~~~g~~~~l~~~~~~~~~~L~~g~~V~Rhl~dgD~VL~NRQPsLHk~Simah~vkv~~~~ 469 (1815)
+||++|++.||| ||||+|++|.|++|+|.++.++++|+.||+|||||+|||+|||||||||||||||||||||||++
T Consensus 382 eLV~~g~~~~pg---akyiird~G~Ridlr~~~~~~d~~Lq~G~kVeRhl~DGD~VlfNRqPSlHKmSmmahrVrVlp~s 458 (1605)
T KOG0260|consen 382 ELVRRGLLEHPG---AKYIIRDNGDRIDLRYHKRAGDIHLQPGYKVERHLMDGDVVLFNRQPSLHKMSMMAHRVRVLPYS 458 (1605)
T ss_pred HHhhCCCCCCCC---cceeeecCCcEEEEeecCCccccccccccEEEEeeccCCEEEEcCCCcHHHhhhhhcEEEEccCc
Confidence 999999999999 99999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeecccCCCCCCCCCCcCccccccCCCHhHHHHHHHHccCCCccccCCCCCCceeccccccccceecccCCCccCHHHH
Q 000235 470 TFRLNLSVTSPYNADFDGDEMNMHVPQSFETRAEVLELMMVPKCIVSPQSNRPVMGIVQDTLLGCRKITKRDTFIEKDVF 549 (1815)
Q Consensus 470 t~rln~~vc~pyNADFDGDEMn~h~Pqs~~araE~~~l~~~~~~i~sp~~g~pi~g~~QD~l~g~~~lT~~d~f~~~~~~ 549 (1815)
|||||++||+||||||||||||+|||||++||||+.+|+++++|||+||+|+|+||++||+|+|+++||.||+||+|+++
T Consensus 459 TfrLNlsvtsPynADFDGDemnlhvPQS~etkAEl~EL~~vpkQiispQsnkpvmgivQDTLta~R~~t~Rd~Fl~r~~v 538 (1605)
T KOG0260|consen 459 TFRLNLSVTSPYNADFDGDEMNLHVPQSLETKAELEELAMVPKQIISPQSNKPVMGIVQDTLTAVRKMTKRDVFLNRAQV 538 (1605)
T ss_pred eEEeCeeecCCccCCCCCceeecccCcchhHHHHHHHHhhhhhhhcCCcCCCcceeeehhhHHHHHHHhhHhhhhcHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcccCCCCCC-CCcccCccCCcchHHHHHHhcCCCceEeeecccCCCCCCCcCCCCCcEEEEecCeeeecccccc
Q 000235 550 MNILMWWEDFDGKVP-QPTILKPRPLWTGKQVFNLIIPKQINLFRTAAWHADNDKGILTAGDTLVRIEKGELLSGTLCKK 628 (1815)
Q Consensus 550 ~~l~~~~~~~~~~~~-~pai~kp~~lwtGKqi~s~~lp~~in~~~~~~~~~~~~~~~~~~~d~~v~i~~gell~g~ldK~ 628 (1815)
|||+||++.|++..| +|||+||++||||||||+++||++||+.+...|+.|.+.+++.++|+.|+|++|+|+.|+|+|+
T Consensus 539 mnLlm~~p~~d~~~Pa~pai~Kp~PlWTGkQifsliiP~~in~~r~~s~h~d~~~~~~~p~dt~~lie~g~l~~g~l~Kk 618 (1605)
T KOG0260|consen 539 MNLLMYVPDWDGPPPAKPAILKPKPLWTGKQIFSLIIPGGINYIRDHSTHPDSEDELISPGDTRVLIEGGELLIGVLCKK 618 (1605)
T ss_pred HHHHhhccccCCCCCCCcccCCCCcccchhhheeeecCCCcceecccccCcCCCcccccCCCceEEEeCCceEEEEeecc
Confidence 999999999999999 9999999999999999999999999999999999888777889999999999999999999999
Q ss_pred cccCCcccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCceeeeccCccChhhHHHHHHHHHHHHHHHHHHHHHHHcC
Q 000235 629 TLGTSTGSLIHVIWEEVGPDAARKFLGHTQWLVNYWLLQNAFSIGIGDTIADAKTMETINDTISKAKNNVKNLIKQAQDK 708 (1815)
Q Consensus 629 ~~g~s~~~Lih~i~~~~G~~~a~~~l~~~q~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~a~~~v~~~~~~~~~~ 708 (1815)
.+|++.++|+|++|.+.|++.|+.|++.+|+|+|+||+.+|||+||+|.+++.+++..+++.|.+|+++|..++++++.+
T Consensus 619 t~G~s~g~lvh~i~~e~Gp~~~~~f~~~iQ~lin~wll~~gfsigIgDtiad~~t~~~iq~~I~~ak~dv~~vi~~a~~~ 698 (1605)
T KOG0260|consen 619 TVGSSAGGLVHVIFLEKGPKIARGFFDSIQTLINSWLLREGFSIGIGDTIADAATMCVIQNTIKEAKRDVLAVIREAQNN 698 (1605)
T ss_pred ccccccCceEEEeehhhCHHHHHHHHHHHHHHHHHHHHhcCccccccccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCChHHHHHhcCCCCcccchhhhhhhccccccCCCccCCCCC
Q 000235 709 SLEPEPGRTMMESFENKVNQVLNTARDEAGSSAQKSLSESNNLKAMVTAGSKGSFINISQMTACVGQQNVEGKRIPFGFV 788 (1815)
Q Consensus 709 ~l~~~~~~~~~~~~e~~v~~~ln~~~~~~~~~~~~~l~~~N~~~~M~~sGsKGS~~N~~Qi~~~lGQQ~~eG~Rip~~~~ 788 (1815)
.|+..||+|++|+||++++.+||+||+++|..+++++++.||+++|+.+|||||++||+|+++|||||++|||||||||.
T Consensus 699 ~L~~~pg~tlretfe~~v~~vlndArd~~gssA~~sl~esNn~k~Mv~aGSKGs~inisQ~saCVGqQnVEgkrIpFGF~ 778 (1605)
T KOG0260|consen 699 ELEPTPGRTLRETFENKVNRVLNDARDKSGSSAQKSLSESNNFKTMVVAGSKGSFINISQVSACVGQQNVEGKRIPFGFP 778 (1605)
T ss_pred cccCCcchhHHHHHHHHHHHHHHHHHHhhhhHHHhhhhhcccHHHHHhhcCCCcceehhhhhhhhccccccccccccCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCCCCCccccccccCCcCCCChhhhhhhccCCCcchhhhccccCCCchhHHHHHHHhhceEEeecCeeecCC
Q 000235 789 DRTLPHFTKDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDIMVKYDGTVRNSL 868 (1815)
Q Consensus 789 ~rtLp~f~~~d~~~~~~Gfv~~sf~~GL~p~EfFfH~m~gReGLiDTAvKTa~sGYlqRrLvk~lEdl~v~YDgTVRns~ 868 (1815)
+||||||.++|++|+++|||+||||+||+|+|||||+|||||||||||||||+||||||||||+||||+|+|||||||+.
T Consensus 779 ~Rtlphf~kDdysPesrGfVENSyL~GLtP~EfFfHamggREglidtavktaEtGyiqRRL~kameDimv~yDgTVRNs~ 858 (1605)
T KOG0260|consen 779 KRTLPHFSKDDYSPESRGFVENSYLTGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLMKAMEDIMVAYDGTVRNSL 858 (1605)
T ss_pred cccccccccCCCCccccceeecccccCCCHHHHHHHHhcccchhhhhhhcccccchHHHHHHHHHHHHHhhcCcceeccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CceEEEEecCCCCCceeeecccccccccchHHHhhhhhhccccCCCCcccchHHHHHHhhhhhHHHHHHHHHHHHHHHHH
Q 000235 869 GDVIQFLYGEDGMDSVWIESQTLDSLKMKKSEFDKAFRFEMDEENWNPNYMLQEYIDDLKTIKELRDVFDAEVQKLEADR 948 (1815)
Q Consensus 869 g~iiQF~YGeDg~d~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~r 948 (1815)
|+||||.|||||+|+..+|.|..+.+..++..|++.|+++..+.+.... ..++++++..+.+++.+|+.||+++..+|
T Consensus 859 gqviQf~YGeDG~d~~~vE~q~~~~l~~~~a~f~~~~~~d~ld~~~~~~--~~~~~~e~~~~~~l~~lle~e~~~l~~dr 936 (1605)
T KOG0260|consen 859 GQVIQFKYGEDGLDGHPVEFQNGETLGSLNACFESEFAYDALDEPISLS--SEEVVNEISELLKLQNLLECEYKKLVRDR 936 (1605)
T ss_pred ceeEEEEeccCccccceeeccccccccchHHHHHhhhhhhhhcCcccch--hhhHhhhhhhhHHHHHHHHHHHHhhhhhh
Confidence 9999999999999999999999999999999999999999888665544 56777888899999999999999999999
Q ss_pred HHhHhhhccCCCCCCCccccHHHHHHHhhhhcccCCCCCCCCChHHHHHHHHHHHHhhcccCCCCcccHHHHhhhhhhhh
Q 000235 949 YQLATEIATSGDSSWPLPVNLKRLIWNAQKTFKVDPRRPSDMHPMEVVEAVDKLQERLKVVPGEDPLSVEAQKNATLFFN 1028 (1815)
Q Consensus 949 ~~l~~~~~~~~~~~~~~p~n~~r~i~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~ 1028 (1815)
..++ .++..++.+|++|+|++|+|||++++|+++.+..+++.|.+++..++++.+++++++|+|.+++ +|+ +|+
T Consensus 937 ~~l~-~i~~~g~~k~~lp~n~~r~I~Na~~~f~~~~r~~t~l~~~~v~~g~~~l~e~l~iv~g~~~~sr-aqr----l~~ 1010 (1605)
T KOG0260|consen 937 RVLL-YIFEYGDAKWPLPENLQRIIWNALKKFSIDERKPTDLIPFKVVKGVKELAEKLVIVRGEDYISR-AQR----LFN 1010 (1605)
T ss_pred hhhh-hhcccCCcccccchhHHHHHHHHHhhcccccccccccchhhhhhhhhhhhheeEEeeCchhHHH-HHH----HHH
Confidence 9999 6789999999999999999999999999999999999999999999999999999999999988 655 999
Q ss_pred hhhhhhhhhHHHHHhhccCHHHHHHHHHHHHHHhhcCcccCCCchhhHhhhccCCccccccccccccccccccccccccc
Q 000235 1029 ILLRSTFASKRVLKEHRLTREAFEWVIGEIESRFLQSLVAPGEMIGCVAAQSIGEPATQMTLNTFHYAGVSAKNVTLGVP 1108 (1815)
Q Consensus 1029 ~~lrs~l~~~~~~~~~~l~~~~~~~~l~ei~~ky~~slv~PGEaVG~iAAQSIGEPaTQMTLnTFH~AGv~~~NVTlGvP 1108 (1815)
++||+.|+.|+++.+|+++.++|+|++++|+.+|.++.|.||||||++||||||||+|||||||||+|||+++|||+|||
T Consensus 1011 ~lLrs~l~~krv~~e~rls~eaf~w~~~~Ie~~f~qa~a~pgemvg~lAaqsvgePatqmTlntfh~aGVssknVt~gvp 1090 (1605)
T KOG0260|consen 1011 ILLRSTLATKRVLEEYRLSSEAFEWVLGEIEARFLQAEASPGEMVGALAAQSVGEPATQMTLNTFHYAGVSSKNVTLGVP 1090 (1605)
T ss_pred HHHHhhHHHHHHHHHhcccHHHHHHHhhhhhhheeeeecCccchHhHHHHHHhCCchhhcccchhcccceeeeeeeccCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeeehhhcccCCCCceEEEeCCCCcchHHHHHHHHhhhccccccccceeeEEEEcCCCCceEEEcccceeheeccCCCC
Q 000235 1109 RLREIINVAKKIKTPSLSVFLKPGVNSTKERAKNVQCALEYTTLRSVTEATEVWYDPDPMGTIIEEDVEFVKSYYEMPDE 1188 (1815)
Q Consensus 1109 RLkEIin~ak~ikTP~mtv~l~~~~~~~~~~a~~v~~~le~~tL~dv~~~~~i~ydp~~~~~~i~~d~~~~~~~~~~~~~ 1188 (1815)
|||||+|++|++|||+++|+|..+.+++.+.|+.|++.||++||++|+...+|+|||++..|+|++|++|++.||+++|+
T Consensus 1091 rlkei~Nv~k~~ktpsLtV~l~g~~~k~~e~ak~v~~~le~ttl~~vt~~t~i~ydpdp~~tvI~ed~e~v~a~~e~pd~ 1170 (1605)
T KOG0260|consen 1091 RLKEIINVAKNAKTPSLTVYLTGEAAKDNEWAKLVQCCLEHTTLKDVTRATEIYYDPDPQSTVIDEDREFVVAYYEMPDE 1170 (1605)
T ss_pred chhhhhhhhccCCCceEEEEecchhhcchHHHHHHhhhcccccHHhhhccCcceecCCCcceeeccchhhHHhhhcCccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccCCcEEEEEechhhhhcccCCHHHHHHHHhhhcCCCceeeecCCCccceEEEEEEccCCCCCCCCCCCcchhHH
Q 000235 1189 DIAPEKISPWLLRIELNREMMVDKKLSMAAVAEKINQEFDDDLTCIFNDDNADKLILRIRIMNDEAPKGELNDESAEDDV 1268 (1815)
Q Consensus 1189 ~~~~~~~~~~~lrl~l~~~~~~~~~l~~~~i~~~i~~~~~~~~~~~~~~dn~~~~~~~ir~~~~~~~~~~~~~~~~~~~~ 1268 (1815)
++. ++++|+|||+||+.+|.+++|+|+.|+.+|...|++|++||++|||++++++|+|+..++ ++|.
T Consensus 1171 D~~--~ispwlLrlelDr~~m~dk~ltm~~ia~~i~~~f~~d~~~i~~ddna~klv~r~ri~~~~-----------e~D~ 1237 (1605)
T KOG0260|consen 1171 DVG--RISPWLLRLELDRASMTDKKLTMEQIAEKINRGFGSDLACIFSDDNAEKLVLRLRIAKEE-----------EDDV 1237 (1605)
T ss_pred chh--hcChHHHHhhhhhhhcccccccHHHHHHHHHhhccCCCceeecccCCcceEEEEEecCcc-----------chhH
Confidence 765 999999999999999999999999999999999999999999999999999999998743 2567
Q ss_pred HHHHHHhhccccceecc-----------------------------cchhhhhccccccccccccccHHHHHHhhcHHHH
Q 000235 1269 FLKKIESNMLTEMALRG-----------------------------VNLLAVMCHEDVDARRTTSNHLIEIIEVLGIEAV 1319 (1815)
Q Consensus 1269 ~l~~~~~~~l~~~~~~G-----------------------------~nl~~vl~~~~vD~~rt~sNdI~eI~~vlGIEAA 1319 (1815)
|++.||..+|..++++| +||.++|+.++||..||+|||+.||+++|||||+
T Consensus 1238 ~l~~Ie~~ml~~~~l~G~~~i~kV~m~~~~~G~f~~~~ew~LeTdg~~l~~v~s~~~vD~~rt~sn~l~ei~~vlgIea~ 1317 (1605)
T KOG0260|consen 1238 FLKCIEANMLGDMTLRGIPDIFKVYMSPTEDGEFKPVDEWDLETDGVNLRRVLSEPDVDPARTTSNDLVEIAEVLGIEAV 1317 (1605)
T ss_pred HHHHHHHhhhhhcccCCccccceEEEeecCCCceeecceeEEecCchhHHhhhccCCCCcccccccchhhhhhhhcHHHH
Confidence 99999998887776665 8999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhhcCcccccchhHHHHHhhhhccceecccccccccccCCccccccchHHHHHHHHHHHhhcCccccccc
Q 000235 1320 RRALLDELRVVISFDGSYVNYRHLAILCDTMTYRGHLMAITRHGINRNDTGPMMRCSFEETVDILLDAAVFAESDYLRGV 1399 (1815)
Q Consensus 1320 R~~Ii~Ei~~V~~~~Gi~Vn~RHL~LlaD~MT~~G~~~~itR~Gi~~~~~spL~~aSFEeT~~~L~~AA~~ge~D~l~gv 1399 (1815)
|.++++|+..|+.++|.||||||++||||+||++|++|+|||||+|+.++++|||||||||+++|++||+++|.|.++|+
T Consensus 1318 r~a~~~e~~~vi~f~gsyVnyrhlaLl~dvmT~~g~lm~itRhg~nr~~tgaLmrcSfEetv~il~~aa~~~ekd~~rgv 1397 (1605)
T KOG0260|consen 1318 RKALLRELLNVISFDGSYVNYRHLALLCDVMTARGHLMAITRHGINRQDTGALMRCSFEETVDILMDAAAHAEKDPCRGV 1397 (1605)
T ss_pred HhhhhhhhhheEeecccchhHHHHHHHHHHHhcccceeeeeccccchhhccccccccHHHHHHHHHHHHhhhccCCCccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccCCccccCccceeeccchhhhhhhh
Q 000235 1400 TENIMLGQLAPIGTGDCSLYLNDEMLKNAI 1429 (1815)
Q Consensus 1400 senIi~G~~~p~GTG~fdll~~~~~l~~~~ 1429 (1815)
+||||+||++|+|||+|||++|.++|+..+
T Consensus 1398 sEnImlgqlap~gTg~~d~~ld~e~l~~~~ 1427 (1605)
T KOG0260|consen 1398 SENIMLGQLAPMGTGCFDLMLDAEKLKKGI 1427 (1605)
T ss_pred eeeeeecccccCCCcceeeeccHHhhhccC
Confidence 999999999999999999999999998765
No 2
>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Probab=100.00 E-value=4.2e-312 Score=3044.58 Aligned_cols=1227 Identities=38% Similarity=0.637 Sum_probs=1080.6
Q ss_pred ccccccceEEEEcCCHHHHHhcceeEEeeCccccCC-CCCCCCCCCCCCCCcCCCccccccccCCCCcCCccceeecccc
Q 000235 10 AEVAKVRMVQFGILSPDEIRQMSVVQIEHGETTERG-KPKPGGLSDPRLGTIDRKMKCETCTANMAECPGHFGHLELAKP 88 (1815)
Q Consensus 10 ~~~~~i~~i~F~~~S~eeI~~~Sv~eI~~~~~~~~~-~p~~gGl~D~rlG~~~~~~~C~TCg~~~~~CpGHfGhIeL~~P 88 (1815)
.+.++|++|+||+||+|||+++||++|+++++||.. +|+.|||||||||+++++..|+|||++..+||||||||||++|
T Consensus 4 ~~~~~I~~I~Fg~~S~eeIrk~Sv~~It~~~~~d~~g~P~~gGl~DprlG~~d~~~~C~TCg~~~~~CpGHFGHIELa~P 83 (1321)
T PRK14977 4 LAVKAIDGIIFGLISPADARKIGFAEITAPEAYDEDGLPVQGGLLDGRLGTIEPGQKCLTCGNLAANCPGHFGHIELAEP 83 (1321)
T ss_pred CccceeceEEEecCCHHHHHHhCeEEEecccccCCCCCcCCCCCCccccCCCCCCCCCCCCCCCCCcCCCeeEEEEccCC
Confidence 467899999999999999999999999999999876 9999999999999999999999999999999999999999999
Q ss_pred ccchhhhhHHHHHhcccceecceeccCCchHHHHHHHH-hc-----ChHHHHH-----HHH----HHhhhccccCCCCCC
Q 000235 89 MFHIGFMKTVLSIMRSVCFNCSKILADEDDHKFKQALK-IR-----NPKNRLK-----KIL----DACKNKTKCEGGDEI 153 (1815)
Q Consensus 89 V~h~~f~~~v~~iL~~vC~~C~~l~~~~~~~~~~~~~~-~~-----~~~~~~~-----~i~----~~~~~~~~C~~~~~~ 153 (1815)
||||+||+.|++||+|+|++|++|++++.+.+...+++ .+ ..++++. ++. ++|++.+.|.
T Consensus 84 VfHpgf~k~i~~iLr~iC~~C~rlll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~C~----- 158 (1321)
T PRK14977 84 VIHIAFIDNIKDLLNSTCHKCAKLKLPQEDLNVFKLIEEAHAAARDIPEKRIDDEIIEEVRDQVKVYAKKAKECP----- 158 (1321)
T ss_pred ceecccHHHHHHHHHHHHHHhchhhcCcccHHHHHHHHHHhhhcccchhhhhhHHHHHHHHhhhhhhhccCCcCC-----
Confidence 99999999999999999999999999987654322221 11 1222222 211 2355555554
Q ss_pred CCCCCCCCcccccccCCCCccchhhhhcccchhhhhHHhhccccccCCCCccchhcccCCHHHHHHHHhhcChhhHHHhc
Q 000235 154 DVPGQDGEEPLKKNKGGCGAQQPKLTIEGMKMIAEYKAQRKKNDDQEQLPEPVERKQTLTAERVLGVLKRISDEDCQLLG 233 (1815)
Q Consensus 154 ~~~~~~~~~~~~~~~~gCg~~~p~i~k~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~p~~v~~ilk~i~~~d~~~l~ 233 (1815)
+||+.++++++.+...+.+.. + ..++.|+|++|+++|++||++|+++||
T Consensus 159 ----------------~C~~~~~~i~~~~~~~~~~~~---------~------~~~~~l~p~~v~~if~~i~~~d~~llg 207 (1321)
T PRK14977 159 ----------------HCGAPQHELEFEEPTIFIEKT---------E------IEEHRLLPIEIRDIFEKIIDDDLELIG 207 (1321)
T ss_pred ----------------CCCCCCCeEEEeeceeeeecc---------c------ccCcccCHHHHHHHHHhcCHHHHHHhC
Confidence 599999999876543222110 0 124579999999999999999999999
Q ss_pred CCCCCCCccceEEeecccCCCCCCCC----------chhHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHhh
Q 000235 234 LNPKYARPDWMILQVLPIPPPPVRPS----------DDLTHQLAMIIRHNENLRRQERNGAPAHIISEFAQLLQFHIATY 303 (1815)
Q Consensus 234 ~~~~~~~Pe~~il~~lpVpP~~~RP~----------ddlT~~l~~Ii~~N~~lk~~~~~g~~~~~i~~~~~~LQ~~V~~~ 303 (1815)
|++..+||+||||++|||||+++||+ ||||++|++||+.|++|++..+.|++.+++.+.|++||++|++|
T Consensus 208 ~~~~~~~p~~~il~~lpVpP~~~RP~v~~~~~~~~eddlt~~l~~Ii~~N~~l~~~~~~g~~~~~~~~~~~~LQ~~v~~~ 287 (1321)
T PRK14977 208 FDPKKARPEWAVLQAFLVPPLTARPSIILETGERSEDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTF 287 (1321)
T ss_pred CCCCCCCcceEEEeccccCCCCCcCcEEeCCCcccCCcHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999 99999999999999999999999999999999999999999999
Q ss_pred ccCCCCCCCccccc-CCCChhhhhhhhhhcccccccccCCCCCCCCCceeecCCCCcccccccChHHHhhhccCCcccch
Q 000235 304 FDNELPGQPRATQR-SGRPIKSICSRLKAKEGRIRGNLMGKRVDFSARTVITPDPTINIDQLGVPWSIALNLTYPETVTP 382 (1815)
Q Consensus 304 ~dn~~~~~p~~~~~-~~~p~k~i~qrLkgK~Gr~R~nlmGKRVdfsaRsVIspDP~L~~~evGvP~~~A~~LT~PE~Vt~ 382 (1815)
|||+.+|.|.+.++ ++||+|||+|||||||||||+|||||||||||||||||||||++||||||..||++|||||+||+
T Consensus 288 ~dn~~~~~~~~~~~~~~rp~k~i~qrLkgKeGrfR~nlmGKRVdfSaRtVIspDP~L~i~EVGvP~~iA~~LT~Pe~Vt~ 367 (1321)
T PRK14977 288 FDNATAGIPQAHHKGSGRPLKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNE 367 (1321)
T ss_pred hcccccCCCccccccCCCchhHHHHHhccccccccccccccccccccceeEeCCCCcccccccCHHHHHHhCCCCEEEch
Confidence 99999999988877 78999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHcCCCCCCCcccccEEEeCCCceeeccccccccc-------cccccccEeeeecccCCeEEEecCCcccc
Q 000235 383 YNIERLKELVEYGPHPPPGKTGAKYIIRDDGQRLDLRYLKKSSD-------HHLELGYKVERHLNDGDFVLFNRQPSLHK 455 (1815)
Q Consensus 383 ~Ni~~l~~lv~ng~~~~pg~~~A~~i~~~~g~~~~l~~~~~~~~-------~~L~~g~~V~Rhl~dgD~VL~NRQPsLHk 455 (1815)
||+++|++||+|||+.||| |+||++.+|.+++|++.+++.. ..|++||+|||||+|||+|||||||||||
T Consensus 368 ~Ni~~l~~lv~nG~~~~pG---A~~i~~~~g~~~~l~~~~~~~~~~~~~~a~~L~~g~iV~Rhl~dGD~VL~NRQPSLHk 444 (1321)
T PRK14977 368 NNIEKMKELVINGPDEFPG---ANAIRKGDGTKIRLDFLEDKGKDALREAAEQLEIGDIVERHLADGDIVIFNRQPSLHK 444 (1321)
T ss_pred hhHHHHHHHHHcCCcccCC---cceEEcCCCceeeehhhhhccchhHHHHHHhcccCcEEEEEeecCcEEEeccCCcccc
Confidence 9999999999999999999 9999999999999998765432 57899999999999999999999999999
Q ss_pred ccccceeEEeecCCeeeecccCCCCCCCCCCcCccccccCCCHhHHHHHHHHccCCCccccCCCCCCceeccccccccce
Q 000235 456 MSIMGHRIKIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFETRAEVLELMMVPKCIVSPQSNRPVMGIVQDTLLGCR 535 (1815)
Q Consensus 456 ~Simah~vkv~~~~t~rln~~vc~pyNADFDGDEMn~h~Pqs~~araE~~~l~~~~~~i~sp~~g~pi~g~~QD~l~g~~ 535 (1815)
||||||+|||+||+||||||+||+||||||||||||+|||||++|||||++||++++||++|++|+|++|++||+|+|+|
T Consensus 445 ~Simah~vkvl~~kT~Rln~~vC~pyNADFDGDEMNlHvPQS~eArAEa~~Lm~v~~niisP~~G~Pi~gliQD~l~g~~ 524 (1321)
T PRK14977 445 LSILAHRVKVLPGATFRLHPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAY 524 (1321)
T ss_pred ccceEEEEEEecCceEEecccccCcccCCcccceeeeecCCCHHHHHHHHHHHhhhhcEecCCCCCeeEEeehhhhhhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecccCCCccCHHHHHHHHHhcccCCCCCCCCccc-CccCCcchHHHHHHhcCCCceEeeecccCCCC---CCCcCCCCCc
Q 000235 536 KITKRDTFIEKDVFMNILMWWEDFDGKVPQPTIL-KPRPLWTGKQVFNLIIPKQINLFRTAAWHADN---DKGILTAGDT 611 (1815)
Q Consensus 536 ~lT~~d~f~~~~~~~~l~~~~~~~~~~~~~pai~-kp~~lwtGKqi~s~~lp~~in~~~~~~~~~~~---~~~~~~~~d~ 611 (1815)
+||++|+||+++|++||+||... ...+|+|||+ ||++|||||||||++||.++||..++++.... ...+.+.+|+
T Consensus 525 lLT~~d~fl~~~e~~~l~~~~~~-~~~lp~PaI~~kp~~lwTGKQi~s~iLp~~~n~~~~~~~~~~~~~~~~~~~~~~d~ 603 (1321)
T PRK14977 525 LITKDDALFDKNEASNIAMLAGI-TDPLPEPAIKTKDGPAWTGKQLFSLFLPKDFNFEGIAKWSAGKAGEAKDPSCLGDG 603 (1321)
T ss_pred hhccCcccCCHHHHHHHHHhCCC-ccccCCCceecCCCCeeeHHHHHHHHcCCCCCceecccccccccccccccCCCCcc
Confidence 99999999999999999998643 4468999999 99999999999999999999999877654321 1122577899
Q ss_pred EEEEecCeeeecccccccccC---CcccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCceeeeccCccChhhHHHHH
Q 000235 612 LVRIEKGELLSGTLCKKTLGT---STGSLIHVIWEEVGPDAARKFLGHTQWLVNYWLLQNAFSIGIGDTIADAKTMETIN 688 (1815)
Q Consensus 612 ~v~i~~gell~g~ldK~~~g~---s~~~Lih~i~~~~G~~~a~~~l~~~q~l~~~~l~~~GfSigi~D~~~~~~~~~~~~ 688 (1815)
.|+|+||||++|+|||+++|+ +.+||||.||++||+++|.+||+++|+|+++||+++||||||+|+++++++.+++.
T Consensus 604 ~v~I~~geLl~G~ldK~~~G~~~~~~~~Lih~i~~~yG~~~a~~fL~~l~~l~~~~L~~~GFSigi~D~~~~~~~~~~i~ 683 (1321)
T PRK14977 604 YVLIKEGELISGVIDDNIIGALVEEPESLIDRIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLIIPDEAKQEIE 683 (1321)
T ss_pred eEEeecCeEEeeecchHhhccccCCCCcHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhCCEEEeeCcEecCHHHHHHHH
Confidence 999999999999999999998 78999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHH--------cCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCChHHHHHhcCCC
Q 000235 689 DTISKAKNNVKNLIKQAQ--------DKSLEPEPGRTMMESFENKVNQVLNTARDEAGSSAQKSLSESNNLKAMVTAGSK 760 (1815)
Q Consensus 689 ~~i~~a~~~v~~~~~~~~--------~~~l~~~~~~~~~~~~e~~v~~~ln~~~~~~~~~~~~~l~~~N~~~~M~~sGsK 760 (1815)
+.++++++++.++++.++ .+.++..+|++.++++|..+++.|+++++.+++.+.+.++++|++++|+.||||
T Consensus 684 ~~i~~~~~~v~~l~~~~~~~~~i~~~~~~~~~~~G~~~~~~~e~~i~~~l~~~r~~~~~~~~~~l~~~N~l~~Mv~SGAK 763 (1321)
T PRK14977 684 DDIQGMKDEVSDLIDQRKITRKITIYKGKEELLRGMKEEEALEADIVNELDKARDKAGSSANDCIDADNAGKIMAKTGAR 763 (1321)
T ss_pred HHHHHHHHHHHHHHHHHhhhccccccccchhcCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHhhcccc
Confidence 999999999999999888 888999999999999999999999999999999999999999999999999999
Q ss_pred CcccchhhhhhhccccccC--------CCccCCCCCCCCCCCCCCCCCCCccccccccCCcCCCChhhhhhhccCCCcch
Q 000235 761 GSFINISQMTACVGQQNVE--------GKRIPFGFVDRTLPHFTKDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREGL 832 (1815)
Q Consensus 761 GS~~N~~Qi~~~lGQQ~~e--------G~Rip~~~~~rtLp~f~~~d~~~~~~Gfv~~sf~~GL~p~EfFfH~m~gReGL 832 (1815)
||++|++||+||||||+++ |+|||+||++||||||.++|.+|+|+|||.|||++||+|+|||||||||||||
T Consensus 764 GS~~Ni~Qi~~~lGQQ~ve~~~~~~~~G~Ri~~~~~~RtLPhF~~~d~~p~a~GfV~nsFl~GL~P~EfFFHaM~GREGL 843 (1321)
T PRK14977 764 GSMANLAQIAGALGQQKRKTRIGFVLTGGRLHEGYKDRALSHFQEGDDNPDAHGFVKNNYREGLNAAEFFFHAMGGREGL 843 (1321)
T ss_pred cCHHHHHHHHhccccccccccccccCCCCCCcCCCCCCcCCCCCCCCCCcccccchhhhhcCCCCHHHHHHHhhcccccc
Confidence 9999999999999999999 99999999999999999999999999999999999999999999999999999
Q ss_pred hhhccccCCCchhHHHHHHHhhceEEeecCeeecCCCceEEEEecCCCCCceeeecccccccccchHHHhhhhhhccccC
Q 000235 833 IDTAVKTSETGYIQRRLVKAMEDIMVKYDGTVRNSLGDVIQFLYGEDGMDSVWIESQTLDSLKMKKSEFDKAFRFEMDEE 912 (1815)
Q Consensus 833 iDTAvKTa~sGYlqRrLvk~lEdl~v~YDgTVRns~g~iiQF~YGeDg~d~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~ 912 (1815)
||||||||+||||||||||+||||+|+|||||||++|+||||+|||||+|+++++..
T Consensus 844 iDTAVKTA~SGYLQRrLvk~lEDl~v~YD~TVR~s~g~iiQF~YGeDG~d~~~~~~~----------------------- 900 (1321)
T PRK14977 844 IDKARRTEDSGYFQRRLANALEDIRLEYDETVRDPHGHIIQFKFGEDGIDPQKLDHG----------------------- 900 (1321)
T ss_pred cccccccCcCchhHHHHHHHhcceEEecCCeEEeCCCCEEEEeecCCCcCHHHhccC-----------------------
Confidence 999999999999999999999999999999999999999999999999999765321
Q ss_pred CCCcccchHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhHhhhccCCCCCCCccccHHHHHHHhhhhcccCCCCCCCCCh
Q 000235 913 NWNPNYMLQEYIDDLKTIKELRDVFDAEVQKLEADRYQLATEIATSGDSSWPLPVNLKRLIWNAQKTFKVDPRRPSDMHP 992 (1815)
Q Consensus 913 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~r~~l~~~~~~~~~~~~~~p~n~~r~i~~~~~~~~~~~~~~~~~~p 992 (1815)
.|+|+.|+++++..... ...+.|
T Consensus 901 ----------------------------------------------------~~~n~~~~~~~~~~~~~-----~~~~~~ 923 (1321)
T PRK14977 901 ----------------------------------------------------EAFNLERIIEKQKIEDR-----GKGASK 923 (1321)
T ss_pred ----------------------------------------------------CcccHHHHHHHhhhhcc-----ccCCCH
Confidence 12233333333222110 112234
Q ss_pred HHHHHHHHHHHHhhcccCCCCcccHHHHhhhhhhhhhhhhhhhhhHHHHHhhccCHHHHHHHHHHHHHHhhcCcccCCCc
Q 000235 993 MEVVEAVDKLQERLKVVPGEDPLSVEAQKNATLFFNILLRSTFASKRVLKEHRLTREAFEWVIGEIESRFLQSLVAPGEM 1072 (1815)
Q Consensus 993 ~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~lrs~l~~~~~~~~~~l~~~~~~~~l~ei~~ky~~slv~PGEa 1072 (1815)
.++...++++.. .+...++..++ ..+.++++++++|+|++++++.+|.+++|+||||
T Consensus 924 ~~~~~~~~~~~~---------------------~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pGe~ 980 (1321)
T PRK14977 924 DEIEELAKEYTK---------------------TFNANLPKLLA--DAIHGAELKEDELEAICAEGKEGFEKAKVEPGQA 980 (1321)
T ss_pred HHHHHHHHHHHH---------------------hhhhhhHHHHH--HHHHHcCCCHHHHHHHHHHHHHHHHhcccCCccc
Confidence 333222222111 12222333332 2456788999999999999999999999999999
Q ss_pred hhhHhhhccCCccccccccccccccccccccccccceeeeehhhcccCCCCceEEEeCCCCcchHHHHHHHHhhhccccc
Q 000235 1073 IGCVAAQSIGEPATQMTLNTFHYAGVSAKNVTLGVPRLREIINVAKKIKTPSLSVFLKPGVNSTKERAKNVQCALEYTTL 1152 (1815)
Q Consensus 1073 VG~iAAQSIGEPaTQMTLnTFH~AGv~~~NVTlGvPRLkEIin~ak~ikTP~mtv~l~~~~~~~~~~a~~v~~~le~~tL 1152 (1815)
||+|||||||||+|||||||||||||+++|||||||||+||||++|+++||+|+|+|++++..+++.|++++.+||+++|
T Consensus 981 VG~iaAQSiGEP~TQmTLnTFH~AGv~~~nvt~GvpRl~Eii~a~k~~~tp~m~~~l~~~~~~~~~~a~~v~~~ie~~~l 1060 (1321)
T PRK14977 981 IGIISAQSIAEPGTQMTLRTFHAAGIKAMDVTHGLERFIELVDARAKPSTPTMDIYLDDECKEDIEKAIEIARNLKELKV 1060 (1321)
T ss_pred chhhhhhhccCceeeecccccccccccccCcccCccchHHhhhcccCCCCCeEEEEeCCcccchHHHHHHHHhheeeeEH
Confidence 99999999999999999999999999999999999999999999999999999999999887888999999999999999
Q ss_pred cccceeeEEEEcCCCCceEEEcccceeheeccCCCCcccccccCCcEEEEEechhhhhcccCCHHHHHHHHhhhcCCCce
Q 000235 1153 RSVTEATEVWYDPDPMGTIIEEDVEFVKSYYEMPDEDIAPEKISPWLLRIELNREMMVDKKLSMAAVAEKINQEFDDDLT 1232 (1815)
Q Consensus 1153 ~dv~~~~~i~ydp~~~~~~i~~d~~~~~~~~~~~~~~~~~~~~~~~~lrl~l~~~~~~~~~l~~~~i~~~i~~~~~~~~~ 1232 (1815)
++|++.++++|||+.. .+.+|.+.+.++.|++++|.+.+...+.....
T Consensus 1061 ~~~~~~~~i~~~~~~~--------------------------------~i~~d~~~i~~~~i~~~~i~~~i~~~~~~~~~ 1108 (1321)
T PRK14977 1061 RALIADSAIDNANEIK--------------------------------LIKPDKRALENGCIPMERFAEIEAALAKGKKF 1108 (1321)
T ss_pred HHhhhheEeeccCCce--------------------------------EEecCHHHHHhcCCCHHHHHHHHHHhhcCCce
Confidence 9999999999987531 23345555666678888887777665544333
Q ss_pred eeecCCCccceEEEEEEccCCCCCCCCCCCcchhHHHHHHHHhhccc-------------------------cceecccc
Q 000235 1233 CIFNDDNADKLILRIRIMNDEAPKGELNDESAEDDVFLKKIESNMLT-------------------------EMALRGVN 1287 (1815)
Q Consensus 1233 ~~~~~dn~~~~~~~ir~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~-------------------------~~~~~G~n 1287 (1815)
.+..+++ .+++++.... +.+ ....++++++..++. .+.++|+|
T Consensus 1109 ~~~~~~~----~i~~~~~~~~------~~~--~~~~~l~~l~~~l~~~~i~Gi~~I~r~~i~~~~~~~~~e~~l~teG~n 1176 (1321)
T PRK14977 1109 EMELEDD----LIILDLVEAA------DRD--KPLATLIAIRNKILDKPVKGVPDIERAWVELVEKDGRDEWIIQTSGSN 1176 (1321)
T ss_pred EEeecCC----EEEEecCccc------ccc--hHHHHHHHHHHhcCCcEEecCCCceEEEEEeeccCCCeeEEEEecCcC
Confidence 3332222 2233332110 000 011233333332221 25667899
Q ss_pred hhhhhccccccccccccccHHHHHHhhcHHHHHHHHHHHHHHhhhcCcccccchhHHHHHhhhhccceecccc------c
Q 000235 1288 LLAVMCHEDVDARRTTSNHLIEIIEVLGIEAVRRALLDELRVVISFDGSYVNYRHLAILCDTMTYRGHLMAIT------R 1361 (1815)
Q Consensus 1288 l~~vl~~~~vD~~rt~sNdI~eI~~vlGIEAAR~~Ii~Ei~~V~~~~Gi~Vn~RHL~LlaD~MT~~G~~~~it------R 1361 (1815)
|.+||.+++||+.||+||||+||+++|||||||++|++||+.||++||++||+|||+||||+||++|++++|| |
T Consensus 1177 l~~vl~~~~Vd~~rt~sN~i~ei~~~lGIEAaR~~ii~Ei~~v~~~~G~~V~~rHi~LlaD~MT~~G~~~~i~~~~~~~R 1256 (1321)
T PRK14977 1177 LAAVLEMKCIDIANTITNDCFEIAGTLGIEAARNAIFNELASILEDQGLEVDNRYIMLVADIMCSRGTIEAIGLQAAGVR 1256 (1321)
T ss_pred HHHHhCCCCCcccccEECCHHHHHHhhhHHHHHHHHHHHHHHHHHHcCCccCHHHHHHHHHHHccCceEEeccccccccc
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999 9
Q ss_pred ccccccCCccccccchHHHHHHHHHHHhhcCcccccccccccccCCccccCccceeeccchh
Q 000235 1362 HGINRNDTGPMMRCSFEETVDILLDAAVFAESDYLRGVTENIMLGQLAPIGTGDCSLYLNDE 1423 (1815)
Q Consensus 1362 ~Gi~~~~~spL~~aSFEeT~~~L~~AA~~ge~D~l~gvsenIi~G~~~p~GTG~fdll~~~~ 1423 (1815)
|||++.++|||++||||||+++|++||++|+.|+|+|||||||+|+++|+|||+|||++|..
T Consensus 1257 ~Gi~~~~~s~l~~asFE~t~~~L~~AA~~g~~D~l~gvsenii~G~~~~~GTG~~~Ll~~~~ 1318 (1321)
T PRK14977 1257 HGFAGEKDSPLAKAAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIPIGSGKVDLLMDFS 1318 (1321)
T ss_pred cccccCCCCHHHhcCHHHHHHHHHHHHHhcCcCccCChHHhhhcCCCccCccceEEEEeccc
Confidence 99999999999999999999999999999999999999999999999999999999999864
No 3
>KOG0261 consensus RNA polymerase III, large subunit [Transcription]
Probab=100.00 E-value=5.6e-311 Score=2750.21 Aligned_cols=1284 Identities=39% Similarity=0.658 Sum_probs=1094.5
Q ss_pred ccccccceEEEEcCCHHHHHhcceeEEeeCccccCC---CCCCCCCCCCCCCCcCCCccccccccCCCCcCCccceeecc
Q 000235 10 AEVAKVRMVQFGILSPDEIRQMSVVQIEHGETTERG---KPKPGGLSDPRLGTIDRKMKCETCTANMAECPGHFGHLELA 86 (1815)
Q Consensus 10 ~~~~~i~~i~F~~~S~eeI~~~Sv~eI~~~~~~~~~---~p~~gGl~D~rlG~~~~~~~C~TCg~~~~~CpGHfGhIeL~ 86 (1815)
...++|++|+|+++|++||++.+++||.+..+||.. .|..+|++|||||+.++...|+|||++..+|.|||||++|+
T Consensus 8 ~~~kki~~i~F~~~s~~ei~~~a~v~v~~~~LY~~~~~~~P~~~G~LD~rMGvs~K~~~C~TCg~~la~C~GHfGy~~L~ 87 (1386)
T KOG0261|consen 8 EIPKKIKHIQFSILSPEEIRQQAEVEVSSKDLYDISTQRAPLPNGPLDPRMGVSNKKDKCATCGEGLADCIGHFGYLKLA 87 (1386)
T ss_pred cccceeeeEeeccCCHHHHHhcceEEeeccchhhhhcccCCCcCCCcCcccCCCCCCCccchhccchhhcccccceEeec
Confidence 345799999999999999999999999999999875 49999999999999999999999999999999999999999
Q ss_pred ccccchhhhhHHHHHhcccceecceeccCCchHHHHHHHHhcCh-------HHHHHHHHHHhhhccccCCCCCCCCCCCC
Q 000235 87 KPMFHIGFMKTVLSIMRSVCFNCSKILADEDDHKFKQALKIRNP-------KNRLKKILDACKNKTKCEGGDEIDVPGQD 159 (1815)
Q Consensus 87 ~PV~h~~f~~~v~~iL~~vC~~C~~l~~~~~~~~~~~~~~~~~~-------~~~~~~i~~~~~~~~~C~~~~~~~~~~~~ 159 (1815)
+||||+|||+.++.||+|||++|+.+++++++.+ +...++++| +...++|++.||+...|.+
T Consensus 88 LPVFhiGyfk~ti~iLq~ICK~Cs~ilL~~~~k~-~fl~~lr~p~~~~l~k~~l~kri~~~CkK~~~C~h---------- 156 (1386)
T KOG0261|consen 88 LPVFHIGYFKATIQILQCICKNCSSILLSEEDKR-QFLKKLRNPGLDNLRKKALLKRIVAKCKKVNTCSH---------- 156 (1386)
T ss_pred ceeeeehhHHHHHHHHHHHHHhhhhhhcCHHHHH-HHHHHhhCCCCChHHHHHHHHHHHHHhhccccccc----------
Confidence 9999999999999999999999999999976553 233344443 3557889999999999976
Q ss_pred CCcccccccCCCCccchhhhhc-c-cchhhh-hHHhhcccc-------c-------cCC-CCccchhcccCCHHHHHHHH
Q 000235 160 GEEPLKKNKGGCGAQQPKLTIE-G-MKMIAE-YKAQRKKND-------D-------QEQ-LPEPVERKQTLTAERVLGVL 221 (1815)
Q Consensus 160 ~~~~~~~~~~gCg~~~p~i~k~-~-~~l~~~-~~~~~~~~~-------~-------~~~-~~~~~~~~~~l~p~~v~~il 221 (1815)
||+.++.++|- + +++.++ |+..++..+ + ..+ +.........|+|..|+++|
T Consensus 157 -----------Cg~~NG~VKK~~~~lkIiHd~~~~~~k~~~~~~~~~~~~~~~~~~n~e~~~~~~~~~~~LnPl~vLnLF 225 (1386)
T KOG0261|consen 157 -----------CGALNGTVKKAAALLKIIHDRFKLVKKSDPLVTNERGEFKTAISHNKELEGHLSSCCEELNPLVVLNLF 225 (1386)
T ss_pred -----------cCCcCceeeccccceeEeeehhhccccccchhhhhHHHHHHHhhcCcchHhHHHHHHhhcChHHHHHHH
Confidence 99999999983 3 676665 222111000 0 000 00001124579999999999
Q ss_pred hhcChhhHHHhcCCCCCCCccceEEeecccCCCCCCCC-----------chhHHHHHHHHHHHHHHHHHHHcCCChhhHH
Q 000235 222 KRISDEDCQLLGLNPKYARPDWMILQVLPIPPPPVRPS-----------DDLTHQLAMIIRHNENLRRQERNGAPAHIIS 290 (1815)
Q Consensus 222 k~i~~~d~~~l~~~~~~~~Pe~~il~~lpVpP~~~RP~-----------ddlT~~l~~Ii~~N~~lk~~~~~g~~~~~i~ 290 (1815)
++|++.||++||+.+...||+.+|++++||||.|+||| ||||.+|.+||-.|..|++.+..|++...+.
T Consensus 226 k~i~~~D~eLLg~~~~~~~P~~Li~t~~~vPP~cIRPSV~~~~k~gtnEDDlT~KltEIi~tn~vik~~~~~g~~~~~im 305 (1386)
T KOG0261|consen 226 KQIKEDDCELLGMDSEEGRPENLIITRVPVPPVCIRPSVMSEDKAGTNEDDLTMKLTEIILTNDVIKKHLSKGTPINLIM 305 (1386)
T ss_pred hhCCccccceeeeccCcCCchheEEEeccCCccccccceeecCCCCCCccchhhhhhhhhhHHHHHHHHhhcCCCchhhh
Confidence 99999999999999989999999999999999999999 9999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhccCCCCCCCcccccCCCChhhhhhhhhhcccccccccCCCCCCCCCceeecCCCCcccccccChHHH
Q 000235 291 EFAQLLQFHIATYFDNELPGQPRATQRSGRPIKSICSRLKAKEGRIRGNLMGKRVDFSARTVITPDPTINIDQLGVPWSI 370 (1815)
Q Consensus 291 ~~~~~LQ~~V~~~~dn~~~~~p~~~~~~~~p~k~i~qrLkgK~Gr~R~nlmGKRVdfsaRsVIspDP~L~~~evGvP~~~ 370 (1815)
|.|+.||.+|+.||+++.+|.|..+.. ++|++||.||||||+||||+||.||||||||||||||||||+|||||||..|
T Consensus 306 E~Wd~lQl~~AlyINSEl~g~~~~~~p-~kp~RGf~QRLKGKqGRFRgNLSGKRVDFSGRTVISPDPNL~IdeVgVP~rv 384 (1386)
T KOG0261|consen 306 EDWDFLQLQVALYINSELPGIPINMAP-KKPTRGFVQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDEVGVPIRV 384 (1386)
T ss_pred hhhHHHHHHHHHhhcccCCCCCCCCCC-CCchHHHHHHhcccCCceeccccCceeeccCceeeCCCCCcceeeccchHHH
Confidence 999999999999999999999876543 5899999999999999999999999999999999999999999999999999
Q ss_pred hhhccCCcccchhHHHHHHHHHHcCCCCCCCcccccEEE-eCCCceeeccccccc-cccccccccEeeeecccCCeEEEe
Q 000235 371 ALNLTYPETVTPYNIERLKELVEYGPHPPPGKTGAKYII-RDDGQRLDLRYLKKS-SDHHLELGYKVERHLNDGDFVLFN 448 (1815)
Q Consensus 371 A~~LT~PE~Vt~~Ni~~l~~lv~ng~~~~pg~~~A~~i~-~~~g~~~~l~~~~~~-~~~~L~~g~~V~Rhl~dgD~VL~N 448 (1815)
|+.|||||+||.+||++||+||+|||+.||| ||||+ |.+|.+..|+|.+|. -+..|++|++|||||+|||+||||
T Consensus 385 AkiLTfpE~Vt~~Ni~klr~lV~NGP~vhPG---ANyv~~r~~~~kr~L~yg~R~kiA~eLk~GdvVERHL~DgDvVLFN 461 (1386)
T KOG0261|consen 385 AKILTFPERVTRANIRKLRQLVRNGPNVHPG---ANYVVQRGEGFKRFLKYGNRDKIADELKIGDVVERHLMDGDVVLFN 461 (1386)
T ss_pred HHHhcchhhccHHHHHHHHHHHhcCCCCCCC---cchhhhcccchhhHhhcCcHHHHHHhhccchHHHhhcccCCEEEEc
Confidence 9999999999999999999999999999999 99998 788899999998763 456899999999999999999999
Q ss_pred cCCccccccccceeEEeecCCeeeecccCCCCCCCCCCcCccccccCCCHhHHHHHHHHccCCCccccCCCCCCceeccc
Q 000235 449 RQPSLHKMSIMGHRIKIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFETRAEVLELMMVPKCIVSPQSNRPVMGIVQ 528 (1815)
Q Consensus 449 RQPsLHk~Simah~vkv~~~~t~rln~~vc~pyNADFDGDEMn~h~Pqs~~araE~~~l~~~~~~i~sp~~g~pi~g~~Q 528 (1815)
|||||||||||+|+|||+||+|||||.|||+||||||||||||+||||++||||||.+||.+.+|+++|++|+|+++.+|
T Consensus 462 RQPSLHkmSIM~H~akV~p~RTfRFNEcvCtPYNADFDGDEMNlHvPQTEEAraEA~~LMgvknNlvTPr~GEpiiAAtQ 541 (1386)
T KOG0261|consen 462 RQPSLHKMSIMSHRAKVMPWRTFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEALVLMGVKNNLVTPRNGEPIIAATQ 541 (1386)
T ss_pred CCchHHHHHHHHHHhhcccCceeeccccccCCcCCCCCcccccccCCchHHHHHHHHHHhccccccccCCCCCceeehhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccceecccCCCccCHHHHHHHHHhcccC--CCCCCCCcccCccCCcchHHHHHHhc-CC-----CceEeeecccCC-
Q 000235 529 DTLLGCRKITKRDTFIEKDVFMNILMWWEDF--DGKVPQPTILKPRPLWTGKQVFNLII-PK-----QINLFRTAAWHA- 599 (1815)
Q Consensus 529 D~l~g~~~lT~~d~f~~~~~~~~l~~~~~~~--~~~~~~pai~kp~~lwtGKqi~s~~l-p~-----~in~~~~~~~~~- 599 (1815)
|+|+|+||||.+|+||+|++++||+.++... .-.+|+|||+||..|||||||||.++ |+ .+|+..+.+...
T Consensus 542 DFiTg~YLlt~KDtF~dRa~~~ql~s~~~d~~~~i~lppPaI~KP~~LwTGKQ~fsvlirpn~~s~v~~Nl~~k~k~~~~ 621 (1386)
T KOG0261|consen 542 DFITGGYLLTHKDTFLDRAEFSQLCSYMSDAMTHIDLPPPAILKPVELWTGKQLFSVLIRPNDDSPVRVNLDAKNKNFSL 621 (1386)
T ss_pred hhhhcceeeecccccccHHHHHHHHHHHhccccccCCCChhhcCceeeeccCEEEEEEeccCCCCceEEeeccccceeec
Confidence 9999999999999999999999999876443 23589999999999999999999999 44 256655444221
Q ss_pred -CCCCCcCCCCCcEEEEecCeeeecccccccccCC-cccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCceeeeccC
Q 000235 600 -DNDKGILTAGDTLVRIEKGELLSGTLCKKTLGTS-TGSLIHVIWEEVGPDAARKFLGHTQWLVNYWLLQNAFSIGIGDT 677 (1815)
Q Consensus 600 -~~~~~~~~~~d~~v~i~~gell~g~ldK~~~g~s-~~~Lih~i~~~~G~~~a~~~l~~~q~l~~~~l~~~GfSigi~D~ 677 (1815)
......+|.+|++|+|+|.||++|++||+++|.+ +.+|++.|.++||..+|++.|+++.++..+||..+||||||+|+
T Consensus 622 ~~~k~~~mc~nDg~v~irns~l~sG~ldKs~lG~g~k~~lfy~llrDyg~~aAa~am~rlaklc~r~lgnrGFSIGi~DV 701 (1386)
T KOG0261|consen 622 VKGKSFEMCPNDGYVIIRNSELISGVLDKSTLGSGKKDSLFYILLRDYGSMAAADAMNRLAKLCARFLGNRGFSIGIDDV 701 (1386)
T ss_pred ccCCCcccCCCCCeEEEecchhhhcccccccccCCCccceEeeehhhcchHHHHHHHHHHHHhhhhhccccccccccCCC
Confidence 1122367999999999999999999999999974 68999999999999999999999999999999999999999999
Q ss_pred ccChhhHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCChHHHHHhc
Q 000235 678 IADAKTMETINDTISKAKNNVKNLIKQAQDKSLEPEPGRTMMESFENKVNQVLNTARDEAGSSAQKSLSESNNLKAMVTA 757 (1815)
Q Consensus 678 ~~~~~~~~~~~~~i~~a~~~v~~~~~~~~~~~l~~~~~~~~~~~~e~~v~~~ln~~~~~~~~~~~~~l~~~N~~~~M~~s 757 (1815)
.+.+...+++++.++.++.+|+++|..+.+|+|+.+||++.+|++|+.+..+|+++||++|+.|+..|.+.|+.++|+.|
T Consensus 702 qPg~~L~~~k~~lv~~gY~kc~~~I~e~~kG~L~~qpg~~~eetLEa~I~~~Ls~IRe~~G~~C~~eL~~~NsPliMa~C 781 (1386)
T KOG0261|consen 702 QPGEILSQEKEELVNRGYAKCDEKIEEYNKGKLQLQPGCNEEETLEAEILSELSTIREEAGKICIRELHPRNSPLIMALC 781 (1386)
T ss_pred CccHHHHHHHHHHHHhHHHHHHHHHHHHhccccccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccChHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCcccchhhhhhhccccccCCCccCCCCCCCCCCCCCCCCCCCccccccccCCcCCCChhhhhhhccCCCcchhhhcc
Q 000235 758 GSKGSFINISQMTACVGQQNVEGKRIPFGFVDRTLPHFTKDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAV 837 (1815)
Q Consensus 758 GsKGS~~N~~Qi~~~lGQQ~~eG~Rip~~~~~rtLp~f~~~d~~~~~~Gfv~~sf~~GL~p~EfFfH~m~gReGLiDTAv 837 (1815)
|||||++|+|||+||||||.+.|+|+|.||.+|+||||.+....|+|+|||.|||++||||.|||||+|+||||||||||
T Consensus 782 GSKGS~INiSQMvACVGQQ~ISG~RvPdGf~dRsLPHF~r~Sk~P~aKGFV~NSFySGLTptEFfFHtm~GREGLVDTAV 861 (1386)
T KOG0261|consen 782 GSKGSKINISQMVACVGQQIISGHRVPDGFEDRSLPHFERHSKTPAAKGFVANSFYSGLTPTEFFFHTMSGREGLVDTAV 861 (1386)
T ss_pred cCCCCcccHHHHHHHhhhhhhcCCcCCCccccccCccccccCCCccccchhhhhcccCCCchhhheeecccccchhhhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCchhHHHHHHHhhceEEeecCeeecCCCceEEEEecCCCCCceeeecccccccccchHHHhhhhhhcccc-CCCCc
Q 000235 838 KTSETGYIQRRLVKAMEDIMVKYDGTVRNSLGDVIQFLYGEDGMDSVWIESQTLDSLKMKKSEFDKAFRFEMDE-ENWNP 916 (1815)
Q Consensus 838 KTa~sGYlqRrLvk~lEdl~v~YDgTVRns~g~iiQF~YGeDg~d~~~~e~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~ 916 (1815)
|||+||||||||||+||||.++||||||||.|+||||.||+|||||+.+|...- ..+|.+.|.+.... +....
T Consensus 862 KTAETGYMqRRLmK~LEDL~~~YDgTVR~s~~~vvqF~YG~DglDPa~mEg~~~------pv~f~r~~~~~~~~~~~~~~ 935 (1386)
T KOG0261|consen 862 KTAETGYMQRRLMKSLEDLSVQYDGTVRNSNGDVVQFTYGGDGLDPAMMEGKDQ------PVNFNRVFDHAKAIFPHRHD 935 (1386)
T ss_pred hhhhhhhHHHHHHHHHHHHHHhhcCceecCCCcEEEEeecCCCCChhhhcCCCC------chhHHHHHHHHHhcCCCCCC
Confidence 999999999999999999999999999999999999999999999999998652 35677776554221 10001
Q ss_pred ccchHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhHhhhccCCCCCCCccccHHHHHHHhhhhcccCCCCCCCCChHHHH
Q 000235 917 NYMLQEYIDDLKTIKELRDVFDAEVQKLEADRYQLATEIATSGDSSWPLPVNLKRLIWNAQKTFKVDPRRPSDMHPMEVV 996 (1815)
Q Consensus 917 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~r~~l~~~~~~~~~~~~~~p~n~~r~i~~~~~~~~~~~~~~~~~~p~~~~ 996 (1815)
..+..+.+ ...++++ |++ .|.. .-..++
T Consensus 936 ~~l~~~el---------~e~~~~~----------l~~-------------------------~f~~--------~~~~F~ 963 (1386)
T KOG0261|consen 936 PPLSSEEL---------DETLEEE----------LLR-------------------------KFTE--------KGDPFV 963 (1386)
T ss_pred CCCCHHHH---------HHHHHHH----------HHH-------------------------Hhhh--------hhhHHH
Confidence 11111111 1111110 000 0100 001222
Q ss_pred HHHHHHHHhhcccCCCCcccHHHHhhhhhhhhhhhhhhhhhHHHHHhhccCHHHHHHHHHHHHHHhhcCcccCCCchhhH
Q 000235 997 EAVDKLQERLKVVPGEDPLSVEAQKNATLFFNILLRSTFASKRVLKEHRLTREAFEWVIGEIESRFLQSLVAPGEMIGCV 1076 (1815)
Q Consensus 997 ~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~lrs~l~~~~~~~~~~l~~~~~~~~l~ei~~ky~~slv~PGEaVG~i 1076 (1815)
..+++++..+.+..+ +.+.+-. ..--.......+...++++.+.++.++..+..||+++.++||.+||+|
T Consensus 964 ~~~~~~i~~~~~~~~------~~~~~~~----d~~~~~~~~~~~~~~~~~t~kql~~f~~~~~~ky~~a~~EpGTavGAi 1033 (1386)
T KOG0261|consen 964 HELREFIASLSKKIK------KLQDKYG----DECGPKFCPDLLYQISRLTEKQLEKFVERCLDKYMRAKVEPGTAVGAI 1033 (1386)
T ss_pred HHHHHHHHHHHHHHH------HHhhhcc----cccCCccCccceeeeeeccHHHHHHHHHHHHHHHHhhhcCCcchhhhh
Confidence 223333322211100 0000000 000000111223456889999999999999999999999999999999
Q ss_pred hhhccCCccccccccccccccccccccccccceeeeehhhcccCCCCceEEEeCCCCcchHHHHHHHHhhhccccccccc
Q 000235 1077 AAQSIGEPATQMTLNTFHYAGVSAKNVTLGVPRLREIINVAKKIKTPSLSVFLKPGVNSTKERAKNVQCALEYTTLRSVT 1156 (1815)
Q Consensus 1077 AAQSIGEPaTQMTLnTFH~AGv~~~NVTlGvPRLkEIin~ak~ikTP~mtv~l~~~~~~~~~~a~~v~~~le~~tL~dv~ 1156 (1815)
||||||||+|||||+|||||||++|||||||||+|||||++|+|+||+++..|.++. |+..|+.|+.+||+|+|+||+
T Consensus 1034 ~aQSIGEPGTQMTLKTFHFAGVASMNiTlGVPRIkEIINAsk~ISTPIItA~L~n~~--d~~~Ar~VKgRiEKt~L~dv~ 1111 (1386)
T KOG0261|consen 1034 AAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKTISTPIITAELENPH--DERSARVVKGRIEKTTLGDVC 1111 (1386)
T ss_pred hcccCCCCCceeeeeeeeecceeeeeeccCcchHHHHHhhhcccCccceeeeecCch--hHHHHHHHhhhhhhhhHHHHH
Confidence 999999999999999999999999999999999999999999999999999999874 688999999999999999999
Q ss_pred eeeEEEEcCCCCceEEEcccceeheeccCCCCcccccccCCcEEEEEechhhhhcccCCHHHHHHHHhhhc-----CCCc
Q 000235 1157 EATEVWYDPDPMGTIIEEDVEFVKSYYEMPDEDIAPEKISPWLLRIELNREMMVDKKLSMAAVAEKINQEF-----DDDL 1231 (1815)
Q Consensus 1157 ~~~~i~ydp~~~~~~i~~d~~~~~~~~~~~~~~~~~~~~~~~~lrl~l~~~~~~~~~l~~~~i~~~i~~~~-----~~~~ 1231 (1815)
++++++|.|+..... +++.+++.......+++++|+..|...- +.|+
T Consensus 1112 ~yieeV~~p~~~fl~----------------------------i~vd~~~I~~l~L~i~~~~I~~sI~~s~~~k~~~~~v 1163 (1386)
T KOG0261|consen 1112 SYIEEVYGPDSCFLL----------------------------IRVDLKRISLLQLEITIESIAYSILKSPKRKVKPNDV 1163 (1386)
T ss_pred HHHHHHhCCcceEEE----------------------------EEecHhHHhhhhccccHHHHHHHHhcCCccccCCcce
Confidence 999999988654222 3444555555666788899988875431 2344
Q ss_pred eeeecCCCccceEEEEEEccCCCCCC------------CCC--C-CcchhHHHHHHHHhhccccceecccchhhhhcccc
Q 000235 1232 TCIFNDDNADKLILRIRIMNDEAPKG------------ELN--D-ESAEDDVFLKKIESNMLTEMALRGVNLLAVMCHED 1296 (1815)
Q Consensus 1232 ~~~~~~dn~~~~~~~ir~~~~~~~~~------------~~~--~-~~~~~~~~l~~~~~~~l~~~~~~G~nl~~vl~~~~ 1296 (1815)
.++. +..+++......+... +.. . -+. ....+..-|..-+.++.++|.+|++||+.+|
T Consensus 1164 ~v~~------~~~~~v~~~~~~~~S~~~~lq~lk~~L~~Vvv~gip~v-nr~vi~~de~~~~y~L~vEG~gLr~Vm~t~G 1236 (1386)
T KOG0261|consen 1164 RVVG------ETTLRVTPVSDTKSSVYYNLQRLKRSLPNVVVKGIPEV-NRAVINIDEKRGLYKLLVEGTGLRAVMNTDG 1236 (1386)
T ss_pred EEec------ceeEEEeecccccchhhhhHHHHHhhCCceEEecCcch-hhhheeecccCCceEEEEeccchHHHhccCC
Confidence 4331 1233333322110000 000 0 000 0000000011112367789999999999999
Q ss_pred ccccccccccHHHHHHhhcHHHHHHHHHHHHHHhhhcCcccccchhHHHHHhhhhccceecccccccccccCCccccccc
Q 000235 1297 VDARRTTSNHLIEIIEVLGIEAVRRALLDELRVVISFDGSYVNYRHLAILCDTMTYRGHLMAITRHGINRNDTGPMMRCS 1376 (1815)
Q Consensus 1297 vD~~rt~sNdI~eI~~vlGIEAAR~~Ii~Ei~~V~~~~Gi~Vn~RHL~LlaD~MT~~G~~~~itR~Gi~~~~~spL~~aS 1376 (1815)
|+..||.||++.||.+||||||||..||+||..+|+.+|++||+||++||||+||++|++++|||+|+.+++.|.||.||
T Consensus 1237 V~g~~TtsNnv~Ev~~vLGIEAAR~~II~EI~ytM~~HGmsiD~RHiMLLaDvMTyrGEVlGITRfGl~KM~~SVL~lAS 1316 (1386)
T KOG0261|consen 1237 VKGRRTTSNNVLEVEKVLGIEAARTTIISEIGYTMSNHGMSIDPRHIMLLADVMTYRGEVLGITRFGLAKMKDSVLMLAS 1316 (1386)
T ss_pred ccccccccCceEEeehhhchHHHHHHHHHHHHHHHHhcCcccCHHHHHHHHHHhhhcceeeeeeehhhHHHHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHhhcCcccccccccccccCCccccCccceeeccchhh
Q 000235 1377 FEETVDILLDAAVFAESDYLRGVTENIMLGQLAPIGTGDCSLYLNDEM 1424 (1815)
Q Consensus 1377 FEeT~~~L~~AA~~ge~D~l~gvsenIi~G~~~p~GTG~fdll~~~~~ 1424 (1815)
||+|.++|++||.+|++|.+.||||+||||.++.+|||.|+|+...+.
T Consensus 1317 FEkT~DhLF~AA~~~k~D~I~GVSEcIIlG~pm~iGTG~fkl~~~~~~ 1364 (1386)
T KOG0261|consen 1317 FEKTADHLFDAAAYGKKDAIEGVSECIILGIPMCIGTGIFKLLQRTDD 1364 (1386)
T ss_pred hhhhhHHHHHHHHhcCcccccchhhheecccceeccccHHHHHHhcCC
Confidence 999999999999999999999999999999999999999999886554
No 4
>KOG0262 consensus RNA polymerase I, large subunit [Transcription]
Probab=100.00 E-value=1.8e-284 Score=2576.51 Aligned_cols=1312 Identities=32% Similarity=0.511 Sum_probs=993.6
Q ss_pred cccceEEEEcCCHHHHHhcceeEEeeCccccCC-CCCCCCCCCCCCCCcCCCccccccccCCCCcCCccceeeccccccc
Q 000235 13 AKVRMVQFGILSPDEIRQMSVVQIEHGETTERG-KPKPGGLSDPRLGTIDRKMKCETCTANMAECPGHFGHLELAKPMFH 91 (1815)
Q Consensus 13 ~~i~~i~F~~~S~eeI~~~Sv~eI~~~~~~~~~-~p~~gGl~D~rlG~~~~~~~C~TCg~~~~~CpGHfGhIeL~~PV~h 91 (1815)
+.+..|+||+|+++||+++||.+|++|.+||+. +|..|||||++||+.+....|.||++....||||||||||+.||||
T Consensus 11 ~~~~~v~Fg~yt~~ei~klSv~kIt~p~~~D~lGhPi~GGLYDl~LGp~~~~~~C~TC~~~~~~CPGH~GHIeL~~pvyn 90 (1640)
T KOG0262|consen 11 SFQPSVSFGSYTDQEIRKLSVKKITNPITFDNLGHPIPGGLYDLALGPLDNSDVCSTCNQDELNCPGHMGHIELPVPVYN 90 (1640)
T ss_pred ccccceeeeccCHHHHhhcceeEecCceeecccCCCCCCcccccccCCccchhhhhhhcchhhcCCCccCeeeecccccC
Confidence 345569999999999999999999999999996 9999999999999888888999999999999999999999999999
Q ss_pred hhhhhHHHHHhcccceecceeccCCchHH-HHHHHHhcC-----hHHHHHHHHH--Hhhh-------cccc---------
Q 000235 92 IGFMKTVLSIMRSVCFNCSKILADEDDHK-FKQALKIRN-----PKNRLKKILD--ACKN-------KTKC--------- 147 (1815)
Q Consensus 92 ~~f~~~v~~iL~~vC~~C~~l~~~~~~~~-~~~~~~~~~-----~~~~~~~i~~--~~~~-------~~~C--------- 147 (1815)
|+||+.++++|++.|++||+|++...+.. +.+.+++.. ....+..+.. .+.. .+.|
T Consensus 91 PlfF~~ly~lLr~sCl~Chhf~~k~~~v~~~~cqLrll~~G~i~ea~~Le~i~~~~~~d~~d~~~~~~k~~~~~~v~~~i 170 (1640)
T KOG0262|consen 91 PLFFDFLYNLLRGSCLFCHHFRCKNVDVHILFCQLRLLEYGLIEEAEDLESITSETVEDNEDESLNEIKSCRAQYVTEAI 170 (1640)
T ss_pred HHHHHHHHHHHHHHHHhhhhcccCcHHHHHHHHHHHHHHhchHHHHHHHHHhhhhhhccCcchhHHHHHhhhhhhccHHH
Confidence 99999999999999999999999875442 222233211 1111222211 0000 0011
Q ss_pred ----CCCCCCCCCC-CCCC-----ccc-----ccccCCCCccchhhhhcccc-hhhhhHHhh------------------
Q 000235 148 ----EGGDEIDVPG-QDGE-----EPL-----KKNKGGCGAQQPKLTIEGMK-MIAEYKAQR------------------ 193 (1815)
Q Consensus 148 ----~~~~~~~~~~-~~~~-----~~~-----~~~~~gCg~~~p~i~k~~~~-l~~~~~~~~------------------ 193 (1815)
...+.-...+ .+.. .++ .++|.+|+..+|++||++.. ++..+...+
T Consensus 171 ~~~~~~~~~~~t~~~~~~~~~lv~~f~k~~l~~kkC~~C~~~~p~~rk~~~~kv~~~~~~~~~~~~~~~~~~i~~~~~~~ 250 (1640)
T KOG0262|consen 171 SEALLDKSEPNTKNSTELKKKLVTAFLKNALSRKKCPRCKHSNPKLRKDGFRKVFIDALSSKVGANVIRGAKIKKDVGSK 250 (1640)
T ss_pred HHHhhcCCCccchhhHHHHHHHHHHHHHHhhccccCCcccCCCchhhccccceeeeehhcccccccchhheeeehhcccc
Confidence 1000000000 0000 111 57899999999999999864 333332100
Q ss_pred --c--cccc------cCCC-------C--ccchhcccCCHHHHHHHHhhcChhhHHHhcCCCC-------CCCc-cceEE
Q 000235 194 --K--KNDD------QEQL-------P--EPVERKQTLTAERVLGVLKRISDEDCQLLGLNPK-------YARP-DWMIL 246 (1815)
Q Consensus 194 --~--~~~~------~~~~-------~--~~~~~~~~l~p~~v~~ilk~i~~~d~~~l~~~~~-------~~~P-e~~il 246 (1815)
+ +.+. ++.. + .....++.|.|.+|+++|+.||.+|-++|.+... ...| +.|||
T Consensus 251 ~~~d~~~~G~~E~~~~g~d~~e~~~~~~~~~~t~~~~l~~tevR~~l~~lf~ne~~~l~~lf~l~~~~~~k~~p~d~FFl 330 (1640)
T KOG0262|consen 251 GFEDSGIDGSNEVEEDGKDLFEKSTEPAEFEKTGKKYLLPTEVREHLRDLFKNEGELLSYLFPLWDSGSGKIDPSDMFFL 330 (1640)
T ss_pred cccccccCCccccccccccccccccccccccccccccccHHHHHHHHHHHHhhhHHHHHHhhccccccccccCccceeee
Confidence 0 0000 0000 0 0011357899999999999999999887654211 2345 58999
Q ss_pred eecccCCCCCCCC---------chhHHHHHHHHHHHHHHHHHHHc--CC-C-------------hhhHHHHHHHHHHHHH
Q 000235 247 QVLPIPPPPVRPS---------DDLTHQLAMIIRHNENLRRQERN--GA-P-------------AHIISEFAQLLQFHIA 301 (1815)
Q Consensus 247 ~~lpVpP~~~RP~---------ddlT~~l~~Ii~~N~~lk~~~~~--g~-~-------------~~~i~~~~~~LQ~~V~ 301 (1815)
.+|+|||+++||. +.+|..|.+||+.|..|+++... |. + ...+-+.|..||.+|+
T Consensus 331 d~l~VpPtrfRP~s~~gd~~~en~Qt~~L~kVle~s~~i~~~~~~m~~kl~~~~k~~l~~~~g~~~kl~~aw~~LQ~~vn 410 (1640)
T KOG0262|consen 331 DNLLVPPTRFRPPSMLGDEVHENPQTLNLNKVLESSVLIRKLLKDMKGKLDEELKLILERLRGIFSKLINAWLQLQASVN 410 (1640)
T ss_pred eccccCCcccCCchhcchhhhcChHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHhhhhHHHHHHHHHHHHHHHHH
Confidence 9999999999998 77999999999999998876522 11 1 1223456889999999
Q ss_pred hhccCCCCCCCcccccCCCChhhhhhhhhhcccccccccCCCCCCCCCceeecCCCCcccccccChHHHhhhccCCcccc
Q 000235 302 TYFDNELPGQPRATQRSGRPIKSICSRLKAKEGRIRGNLMGKRVDFSARTVITPDPTINIDQLGVPWSIALNLTYPETVT 381 (1815)
Q Consensus 302 ~~~dn~~~~~p~~~~~~~~p~k~i~qrLkgK~Gr~R~nlmGKRVdfsaRsVIspDP~L~~~evGvP~~~A~~LT~PE~Vt 381 (1815)
.+||++..+. ..+ ..| .||+|.|++|||+||++||||||||+|||||||||||.+||||||..||++|||||+||
T Consensus 411 ~lfDs~~~~k---~~r-~~~-pGikQiLEKKeGLFRkhMMGKRVN~AaRSVIsPDPnI~tnEIGIP~vFA~KLTyPepVt 485 (1640)
T KOG0262|consen 411 VLFDSKMASK---WSR-DSP-PGIKQILEKKEGLFRKHMMGKRVNYAARSVISPDPNIETNEIGIPPVFAKKLTYPEPVT 485 (1640)
T ss_pred HHhccccccc---ccc-CCC-chHHHHHHHhhhhHHHHhhccccchhhccccCCCCCccccccCCchHHHhhccCCCcCC
Confidence 9999997532 111 123 69999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHcCCCCCCCcccccEEEeCCCceeeccccc--ccc--ccc-cc---------cccEeeeecccCCeEEE
Q 000235 382 PYNIERLKELVEYGPHPPPGKTGAKYIIRDDGQRLDLRYLK--KSS--DHH-LE---------LGYKVERHLNDGDFVLF 447 (1815)
Q Consensus 382 ~~Ni~~l~~lv~ng~~~~pg~~~A~~i~~~~g~~~~l~~~~--~~~--~~~-L~---------~g~~V~Rhl~dgD~VL~ 447 (1815)
+||+++||++|+|||+.||| |+||+++||.+..|.-.. ++. +.+ |. -+.+|+||++|||+||+
T Consensus 486 ~~NV~elr~aViNGP~~hPG---A~~iqd~dg~~t~l~~~~~~qR~alA~qLLtpst~~~~~~~~K~V~RHvknGDvvlm 562 (1640)
T KOG0262|consen 486 PWNVNELRKAVINGPDVHPG---ATYIQDEDGTLTLLSPMTDEQREALANQLLTPSTGNPTEFGTKKVHRHVKNGDVVLM 562 (1640)
T ss_pred cccHHHHHHHHhcCCCCCCC---cceeecCCCceeecCCCCHHHHHHHHHHhhccccCCCcccCCceeeeeccCCcEEEE
Confidence 99999999999999999999 999999999998886332 221 112 22 46899999999999999
Q ss_pred ecCCccccccccceeEEeecC-CeeeecccCCCCCCCCCCcCccccccCCCHhHHHHHHHHccCCCccccCCCCCCceec
Q 000235 448 NRQPSLHKMSIMGHRIKIMPY-STFRLNLSVTSPYNADFDGDEMNMHVPQSFETRAEVLELMMVPKCIVSPQSNRPVMGI 526 (1815)
Q Consensus 448 NRQPsLHk~Simah~vkv~~~-~t~rln~~vc~pyNADFDGDEMn~h~Pqs~~araE~~~l~~~~~~i~sp~~g~pi~g~ 526 (1815)
||||||||+|||||+||||++ |||||||++|++|||||||||||+|+|||+.|||||++|++++.|++.|++|.|++||
T Consensus 563 NRQPTLHKPSimaHkaRVL~gEktlRlHYANCkaYNADFDGDEMN~HfPQse~araEa~~ian~dsqYLvPt~G~PlrGL 642 (1640)
T KOG0262|consen 563 NRQPTLHKPSIMAHKARVLPGEKTLRLHYANCKAYNADFDGDEMNVHFPQSEIARAEAYNIANTDSQYLVPTDGTPLRGL 642 (1640)
T ss_pred cCCCccccchhhhhhheecCCcceeeeeecccccccCCCCcchhcccCCchhhHHHHHHHHhccCCceeccCCCCchhhh
Confidence 999999999999999999998 9999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccceecccCCCccCHHHHHHHHHhcc-c--CCCCCCCCcccCccCCcchHHHHHHhc----CC---CceEeeecc
Q 000235 527 VQDTLLGCRKITKRDTFIEKDVFMNILMWWE-D--FDGKVPQPTILKPRPLWTGKQVFNLII----PK---QINLFRTAA 596 (1815)
Q Consensus 527 ~QD~l~g~~~lT~~d~f~~~~~~~~l~~~~~-~--~~~~~~~pai~kp~~lwtGKqi~s~~l----p~---~in~~~~~~ 596 (1815)
||||++++++||.||+||+|++|+||++... . ..-++++|+|+||.+|||||||||.+| |+ .||+..++|
T Consensus 643 IQDHiVsgv~LT~rd~Fftre~y~qLv~~~l~~~~~rI~~lpPtIlkP~~LWTGKQVIsTil~Ni~P~~~p~iNl~~kaK 722 (1640)
T KOG0262|consen 643 IQDHIVSGVLLTMRDSFFTREDYQQLVFAGLSDTFKRIKLLPPTILKPAPLWTGKQVISTILKNIIPEGHPPINLESKAK 722 (1640)
T ss_pred hhhheeeeEEEEecccccCHHHHHHHHHHhhhhhccceeccCccccccccccccchHHHHHHHhcCCCCCCcccchhccc
Confidence 9999999999999999999999999998642 1 122578999999999999999999999 44 599998877
Q ss_pred cCCCCCCCc----CCCCCcEEEEecCeeeecccccccccCCcccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCcee
Q 000235 597 WHADNDKGI----LTAGDTLVRIEKGELLSGTLCKKTLGTSTGSLIHVIWEEVGPDAARKFLGHTQWLVNYWLLQNAFSI 672 (1815)
Q Consensus 597 ~~~~~~~~~----~~~~d~~v~i~~gell~g~ldK~~~g~s~~~Lih~i~~~~G~~~a~~~l~~~q~l~~~~l~~~GfSi 672 (1815)
...+ .|.. -..+++.|+|++||||+|||||+++|++.+||||++++.||++.+.++|+.+.||++.||+.+||||
T Consensus 723 ip~~-~W~~~s~e~~l~Es~v~ir~GellcGVLDKa~~Gat~yGLvH~~~ElYG~~~s~~lLs~~srlFT~ylq~~GFT~ 801 (1640)
T KOG0262|consen 723 IPGK-AWRVHSEEPKLNESQVLIREGELLCGVLDKAQFGATAYGLVHCCHELYGGETSGKLLSVFSRLFTAYLQMHGFTL 801 (1640)
T ss_pred Cchh-hcCCCCCcccCCcceEEEecCceEEEeechhhcCchhhhhhhhhhhhhCccchhhHHHHHHHHHHHHHHHhcccc
Confidence 4322 1110 1246788999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeccCccChhhHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCC-------------CCHHHHHHHHHHHHHHHHHHHHHH
Q 000235 673 GIGDTIADAKTMETINDTISKAKNNVKNLIKQAQDKSLEPEPG-------------RTMMESFENKVNQVLNTARDEAGS 739 (1815)
Q Consensus 673 gi~D~~~~~~~~~~~~~~i~~a~~~v~~~~~~~~~~~l~~~~~-------------~~~~~~~e~~v~~~ln~~~~~~~~ 739 (1815)
|++|++++++.+++++++|++++.-..+..+.+..-..+..+. .+-...++..+...+|...+.+.+
T Consensus 802 GvdDlll~~~~D~kR~~il~e~~~vG~qa~~~~~~l~~da~~del~~~le~~y~~d~~~~~~LD~~~k~~~n~~ts~I~~ 881 (1640)
T KOG0262|consen 802 GVDDLLLDKDADKKRREILRESRNVGNQAAKEAFGLDVDAPPDELRSRLEAIYLKDADKLAMLDRVMKSELNGYTSEIVK 881 (1640)
T ss_pred ccceeeechhhhHHHHHHHHhhhcccHHHHHHHhCCCCCCCHHHHHHHHHHHHhcchhHHHHHHHHHHHHHhhhhHHHHh
Confidence 9999999999999999999988766555555443222222211 112234555666677777777766
Q ss_pred HHH----hhcCCCChHHHHHhcCCCCcccchhhhhhhccccccCCCccCCCCCCCCCCCCCCCCCCCccccccccCCcCC
Q 000235 740 SAQ----KSLSESNNLKAMVTAGSKGSFINISQMTACVGQQNVEGKRIPFGFVDRTLPHFTKDDYGPESRGFVENSYLRG 815 (1815)
Q Consensus 740 ~~~----~~l~~~N~~~~M~~sGsKGS~~N~~Qi~~~lGQQ~~eG~Rip~~~~~rtLp~f~~~d~~~~~~Gfv~~sf~~G 815 (1815)
.|. -..+|.|++..|+.||||||+||++||+||||||++||+|+|.|.+|||||+|.++|.+|+|+|||..+|++|
T Consensus 882 ~cvP~GLlk~FP~N~mqlM~~SGAKGS~VN~~QISclLGQqeLEGkRvPlMvSGKtLPsF~p~e~spraGGfI~~RFlTG 961 (1640)
T KOG0262|consen 882 KCVPDGLLKKFPENNMQLMIQSGAKGSNVNTSQISCLLGQQELEGKRVPLMVSGKTLPSFAPYETSPRAGGFIDGRFLTG 961 (1640)
T ss_pred hhccchhhhcCCcchHHHHHHhcCCcccccHHHHHHhhhhHhhcCCccceeecCCccCCcCCCCCCCCCCCcccceeecC
Confidence 654 3468999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CChhhhhhhccCCCcchhhhccccCCCchhHHHHHHHhhceEEeecCeeecCCCceEEEEecCCCCCceeeec-cccccc
Q 000235 816 LTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDIMVKYDGTVRNSLGDVIQFLYGEDGMDSVWIES-QTLDSL 894 (1815)
Q Consensus 816 L~p~EfFfH~m~gReGLiDTAvKTa~sGYlqRrLvk~lEdl~v~YDgTVRns~g~iiQF~YGeDg~d~~~~e~-~~~~~~ 894 (1815)
+.|||||||||||||||||||||||+||||||||||+||+++|+||.||||+||+||||+|||||||..+-.. +++.+.
T Consensus 962 i~PqeyfFHCMAGREGLIDTAVKTSRSGYLQRCLiKhLEgl~V~YD~TVRDsDgsvVQF~YGEDglDitKssfl~~~~f~ 1041 (1640)
T KOG0262|consen 962 IKPQEYFFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLKVHYDLTVRDSDGSVVQFMYGEDGLDITKSSFLNKKEFP 1041 (1640)
T ss_pred CCchHHhhhhhccccchhhhHHhcccchHHHHHHHHhhhhcEEeccceEEcCCCcEEEEeecCccccccHHhhcchhhhh
Confidence 9999999999999999999999999999999999999999999999999999999999999999999975321 112222
Q ss_pred ccchHHHhhhhhhccccCCCCcccchHHHHHHhhhhhHHHHHHHHHHHHHHHHHHH-hHhhhccCCCCCCCccccHHHHH
Q 000235 895 KMKKSEFDKAFRFEMDEENWNPNYMLQEYIDDLKTIKELRDVFDAEVQKLEADRYQ-LATEIATSGDSSWPLPVNLKRLI 973 (1815)
Q Consensus 895 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~r~~-l~~~~~~~~~~~~~~p~n~~r~i 973 (1815)
..|...+...++. ..+++. ..+... ...++.+++|+++ ++....
T Consensus 1042 ~~Ny~avl~~~~~-------------~~v~s~----~d~~~a-~~~~k~i~kw~kk~~w~~~~----------------- 1086 (1640)
T KOG0262|consen 1042 TDNYEAVLLKYKS-------------ESVLSA----FDIKKA-SKYIKKILKWKKKHMWFELD----------------- 1086 (1640)
T ss_pred hhhHHHHHhhhCh-------------HHHhhh----hhhHHH-HHHHHHHHHHHhhhccchhh-----------------
Confidence 2222222222211 111111 111111 1122333333222 111000
Q ss_pred HHhhhhcccCCCCCCCCChHHHHHHHHHHHHhhcccCCCCcccHHHHhhhhhhhhhhhhhhhhhHHHHHhhccCHHHHHH
Q 000235 974 WNAQKTFKVDPRRPSDMHPMEVVEAVDKLQERLKVVPGEDPLSVEAQKNATLFFNILLRSTFASKRVLKEHRLTREAFEW 1053 (1815)
Q Consensus 974 ~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~lrs~l~~~~~~~~~~l~~~~~~~ 1053 (1815)
++. .+.........|..+++.|.+.+.+.+ +...++|+.. + ..+.-+.+.|..
T Consensus 1087 ---k~~-~cpdpv~~k~~p~~y~gsvsekf~~~i--------~~f~~~~~k~-~--------------~s~~~~~~~lr~ 1139 (1640)
T KOG0262|consen 1087 ---KKI-ACPDPVLAKYNPDKYLGSVSEKFRKKI--------DDFDDENAKK-E--------------KSEEPSEEKLRR 1139 (1640)
T ss_pred ---ccc-CCCChhhhhcchhhhhccccHHHHHHH--------HHHHHHhhhh-h--------------ccccchHHHHHH
Confidence 111 122223445677777777777655432 2223333221 1 001111334444
Q ss_pred HHHHHHHHhhcCcccCCCchhhHhhhccCCccccccccccccccccccccccccceeeeehhhc-ccCCCCceEEEeCCC
Q 000235 1054 VIGEIESRFLQSLVAPGEMIGCVAAQSIGEPATQMTLNTFHYAGVSAKNVTLGVPRLREIINVA-KKIKTPSLSVFLKPG 1132 (1815)
Q Consensus 1054 ~l~ei~~ky~~slv~PGEaVG~iAAQSIGEPaTQMTLnTFH~AGv~~~NVTlGvPRLkEIin~a-k~ikTP~mtv~l~~~ 1132 (1815)
+ +..||++||++|||+||+|||||||||+||||||||||||+|+|||||||||||||||+| +|||||+|||++.++
T Consensus 1140 l---l~~K~~~SLa~PGE~VGvlAAQSIGEPSTQMTLNTFHfAGrGemNVTLGIPRLREIlMtASanIkTP~mt~pi~~g 1216 (1640)
T KOG0262|consen 1140 L---LQLKYIRSLADPGEPVGVLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILMTASANIKTPSMTVPIKNG 1216 (1640)
T ss_pred H---HHHHHHHHhcCCCCcceeeeecccCCCcceeehhheeeccccceeeeecchHHHHHHHHHhhccCCCceeeeccCC
Confidence 4 479999999999999999999999999999999999999999999999999999999999 999999999999998
Q ss_pred CcchHHHHHHHHhhhccccccccceeeEEEEcCCCCceEEEcccceeheeccCCCCcccccccCCcEEEEEech-hhh-h
Q 000235 1133 VNSTKERAKNVQCALEYTTLRSVTEATEVWYDPDPMGTIIEEDVEFVKSYYEMPDEDIAPEKISPWLLRIELNR-EMM-V 1210 (1815)
Q Consensus 1133 ~~~~~~~a~~v~~~le~~tL~dv~~~~~i~ydp~~~~~~i~~d~~~~~~~~~~~~~~~~~~~~~~~~lrl~l~~-~~~-~ 1210 (1815)
.. .++|..++..|.+++|++|++++.+... .+ ..+... ...+.+|+.|.. +.. .
T Consensus 1217 ~s--~~ra~~i~~~l~rV~L~evlk~v~vte~----~t-~~~~~~-----------------~~~y~lr~~~~~~~~y~~ 1272 (1640)
T KOG0262|consen 1217 VS--DERADDITKELRRVTLKEVLKKVGVTEK----IT-MVENQS-----------------CKKYKLRFDLLPREEYQE 1272 (1640)
T ss_pred cc--HHHHHHHHHHHHHHHHHHHHhheeeeEE----EE-eecccc-----------------ceEEEEEEeecCHHHhhh
Confidence 64 4889999999999999999998776421 01 111100 112334444321 111 1
Q ss_pred cccCCHHHHHHHHhhh---------------------cC-----CC----------ceee--------ecCCCcc----c
Q 000235 1211 DKKLSMAAVAEKINQE---------------------FD-----DD----------LTCI--------FNDDNAD----K 1242 (1815)
Q Consensus 1211 ~~~l~~~~i~~~i~~~---------------------~~-----~~----------~~~~--------~~~dn~~----~ 1242 (1815)
++.+..++|.+-+... .. .+ +... ..+++.+ +
T Consensus 1273 e~~v~~e~i~~~m~~~Flk~L~~aI~k~~~k~~~~~~~~~dd~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ddddas~ 1352 (1640)
T KOG0262|consen 1273 EYDVRPEDIEEVMENRFLKLLERAIKKKLKKAKYTRGMSNDDADPDDGNEVDNNDEVGGEDNEDSDDESEDDEDDDDASD 1352 (1640)
T ss_pred hcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhhccccccCCccccccCCccccccCCccccccccccccCcccchhH
Confidence 2233333332211100 00 00 0000 0000001 0
Q ss_pred eEEEEEEcc----CCCCC----------C--CCC---CC-cch----------------------h--------HHHHHH
Q 000235 1243 LILRIRIMN----DEAPK----------G--ELN---DE-SAE----------------------D--------DVFLKK 1272 (1815)
Q Consensus 1243 ~~~~ir~~~----~~~~~----------~--~~~---~~-~~~----------------------~--------~~~l~~ 1272 (1815)
..++-|... +++++ + ++| ++ |.+ . ..|++.
T Consensus 1353 ~k~~~k~~~~~dYe~~de~e~~~~~~~e~~~~~e~~e~d~e~g~dg~~~~~~~~~e~~~~~~~~er~~qs~~~~~~fi~~ 1432 (1640)
T KOG0262|consen 1353 AKLHKKTEEEADYESEDEDERVEEREDEGDEDEESDEDDEEVGLDGTPEPEEEDQEGQPEVNAVERREQSVKKRHDFISR 1432 (1640)
T ss_pred HHHhhhhccccCcCCCchhhhhhhhhcccccccccccchhhcccCCCCCcccccccCCchhhHHHHHHHHHHHHHHHhhh
Confidence 111111111 00000 0 000 00 000 0 001110
Q ss_pred H----Hhhccc--------------------------------------------------cceecccchhhhhcc-ccc
Q 000235 1273 I----ESNMLT--------------------------------------------------EMALRGVNLLAVMCH-EDV 1297 (1815)
Q Consensus 1273 ~----~~~~l~--------------------------------------------------~~~~~G~nl~~vl~~-~~v 1297 (1815)
. +...|. -+.++|+||.++|.+ +.+
T Consensus 1433 y~fd~~~~~wcev~~~lp~~~~k~~mssiVe~~~~~~vI~q~~gIeRc~~~~~~~~~k~~~~l~TeGVnl~a~~~~~d~L 1512 (1640)
T KOG0262|consen 1433 YTFDKESGKWCEVELKLPLDKEKLDMSSIVESIAPKSVIHQVPGIERCVVSEPQDDVKEKSVLLTEGVNLPALFDHADIL 1512 (1640)
T ss_pred hccccccCcEEEEEEEecCCCcchHHHHHHHHHhcceeeeccCCceeeeccCCcccccccceehhcCccHHHHHHHHhhh
Confidence 0 000000 134567999999996 568
Q ss_pred cccccccccHHHHHHhhcHHHHHHHHHHHHHHhhhcCcccccchhHHHHHhhhhccceecccccccccccCCccccccch
Q 000235 1298 DARRTTSNHLIEIIEVLGIEAVRRALLDELRVVISFDGSYVNYRHLAILCDTMTYRGHLMAITRHGINRNDTGPMMRCSF 1377 (1815)
Q Consensus 1298 D~~rt~sNdI~eI~~vlGIEAAR~~Ii~Ei~~V~~~~Gi~Vn~RHL~LlaD~MT~~G~~~~itR~Gi~~~~~spL~~aSF 1377 (1815)
|.+++|||||++|+++|||||||++|++||.+||+.|||+||.|||+||||||||+|.|.++||+|| ..++|||+||||
T Consensus 1513 Dv~~lySNDI~ail~tyGVEAar~~Iv~Ev~~VF~vYGIsVd~RHLsLiADYMTf~G~y~pfnR~Gm-~~ssSP~qkMsF 1591 (1640)
T KOG0262|consen 1513 DVNRLYSNDIHAILNTYGVEAARNAIVNEVNNVFKVYGISVDIRHLSLIADYMTFEGGYQPFNRMGM-ESSSSPLQKMSF 1591 (1640)
T ss_pred hhhhhccchHHHHHHHhhHHHHHHHHHHHHHHhhhheeeeecHHHHHHHHHHHhhcccccccccccc-ccCCChhHhhhH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999 558999999999
Q ss_pred HHHHHHHHHHHhhcCcccccccccccccCCccccCccceeeccchh
Q 000235 1378 EETVDILLDAAVFAESDYLRGVTENIMLGQLAPIGTGDCSLYLNDE 1423 (1815)
Q Consensus 1378 EeT~~~L~~AA~~ge~D~l~gvsenIi~G~~~p~GTG~fdll~~~~ 1423 (1815)
|+|+.||.+||.+|+.|+|.++|++|+||+++..|||+|||+.+..
T Consensus 1592 ETt~~Fl~~Aa~~g~~D~L~sPSArLvvG~~~r~GTG~Fdll~~v~ 1637 (1640)
T KOG0262|consen 1592 ETTCQFLKQAALFGEEDELSSPSARLVVGLPVRGGTGSFDLLQKVD 1637 (1640)
T ss_pred HHHHHHHHHHHhcCcccccCCCcceeEeccccCCCcceeeeeccCC
Confidence 9999999999999999999999999999999999999999998754
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=2e-231 Score=2235.49 Aligned_cols=837 Identities=48% Similarity=0.849 Sum_probs=784.6
Q ss_pred cccceEEEEcCCHHHHHhcceeEEeeCccccCC-CCCCCCCCCCCCCCcCCCccccccccCCCCcCCccceeeccccccc
Q 000235 13 AKVRMVQFGILSPDEIRQMSVVQIEHGETTERG-KPKPGGLSDPRLGTIDRKMKCETCTANMAECPGHFGHLELAKPMFH 91 (1815)
Q Consensus 13 ~~i~~i~F~~~S~eeI~~~Sv~eI~~~~~~~~~-~p~~gGl~D~rlG~~~~~~~C~TCg~~~~~CpGHfGhIeL~~PV~h 91 (1815)
++|++|+|+++|+|||+++||+||+++++||.. +|+.|||||||||+++++..|+|||++..+||||||||||++||||
T Consensus 2 ~~I~~I~F~~~S~eEI~k~Sv~~It~~~~~d~~g~P~~gGL~D~RLG~~~~~~~C~TCg~~~~~CpGHFGhIeL~~PVfh 81 (868)
T TIGR02390 2 KKIGSIKFGLLSPEEIRKMSVVEVVTADTYDDDGYPIEGGLMDPRLGVIEPGLRCKTCGGKVGECPGHFGHIELARPVVH 81 (868)
T ss_pred ceeeEEEEeCCCHHHHHHhCeeEEecccccCCCCCcCCCCccCcccCCCCCCCCCCCCCCCCCcCCCcceEEeccccccc
Confidence 579999999999999999999999999999865 9999999999999999999999999999999999999999999999
Q ss_pred hhhhhHHHHHhcccceecceeccCCchH-HHHHHHH-hcC----h-HHHHHHHHHHhhhccccCCCCCCCCCCCCCCccc
Q 000235 92 IGFMKTVLSIMRSVCFNCSKILADEDDH-KFKQALK-IRN----P-KNRLKKILDACKNKTKCEGGDEIDVPGQDGEEPL 164 (1815)
Q Consensus 92 ~~f~~~v~~iL~~vC~~C~~l~~~~~~~-~~~~~~~-~~~----~-~~~~~~i~~~~~~~~~C~~~~~~~~~~~~~~~~~ 164 (1815)
|+||+.|++||+|||++|++|++++.+. .+.+.++ ++. . +++++++++.|++.+.|.
T Consensus 82 pgf~~~i~kiL~~vC~~C~rll~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~i~~~~~~~~~C~---------------- 145 (868)
T TIGR02390 82 VGFAKEIYKILRATCRKCGRITLTEEEIEQYLEKINKLKEEGGDLASTLIEKIVKEAAKRMKCP---------------- 145 (868)
T ss_pred hhHHHHHHHHHHHHhhhcCceeeCccccHHHHHHHHhcccchhhhHHHHHHHHHHHhhcCCCCC----------------
Confidence 9999999999999999999999986543 3443332 222 1 345677777777666675
Q ss_pred ccccCCCCccchhhhhcccchhhhhHHhhccccccCCCCccchhcccCCHHHHHHHHhhcChhhHHHhcCCCCCCCccce
Q 000235 165 KKNKGGCGAQQPKLTIEGMKMIAEYKAQRKKNDDQEQLPEPVERKQTLTAERVLGVLKRISDEDCQLLGLNPKYARPDWM 244 (1815)
Q Consensus 165 ~~~~~gCg~~~p~i~k~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~p~~v~~ilk~i~~~d~~~l~~~~~~~~Pe~~ 244 (1815)
+||+.+|+|++++...+ +... . ..++.|+|++|++||++||++|+++||+++..++||||
T Consensus 146 -----~Cg~~~p~ir~~~~~~~--~~~~-------~------~~~~~L~p~~v~~ilk~I~~eD~~lLG~~p~~~~Pe~~ 205 (868)
T TIGR02390 146 -----HCGEEQKKIKFEKPTYF--YEEG-------K------EGDVKLTPSEIRERLEKIPDEDAELLGINPKVARPEWM 205 (868)
T ss_pred -----CCCCcCceEEEeeeeee--eecc-------C------CCCeecCHHHHHHHHHhCCHHHHHHhCCCCCCCCccee
Confidence 49999999998764321 1100 0 12567999999999999999999999999999999999
Q ss_pred EEeecccCCCCCCCC----------chhHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHhhccCCCCCCCcc
Q 000235 245 ILQVLPIPPPPVRPS----------DDLTHQLAMIIRHNENLRRQERNGAPAHIISEFAQLLQFHIATYFDNELPGQPRA 314 (1815)
Q Consensus 245 il~~lpVpP~~~RP~----------ddlT~~l~~Ii~~N~~lk~~~~~g~~~~~i~~~~~~LQ~~V~~~~dn~~~~~p~~ 314 (1815)
||++|||||+++||+ ||||++|++||++|++|++.++.|++.+++.+.|++||.+|++||||+++|.+.+
T Consensus 206 ilt~LPVPP~~iRPsv~~~~g~~~EDDLT~~L~~II~~N~~Lk~~~~~g~~~~~~~~~~~~LQ~~v~~~~d~~~~~~~~~ 285 (868)
T TIGR02390 206 VLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVATYFDNELPGIPPA 285 (868)
T ss_pred eEeccccCCCCCcCeEEeCCCcccCChHHHHHHHHHHHHHHHHHHHHcCCchhhhHHHHHHHHHHHHHHHcCCCCCCCcc
Confidence 999999999999998 8999999999999999999999999999999999999999999999999998888
Q ss_pred cccCCCChhhhhhhhhhcccccccccCCCCCCCCCceeecCCCCcccccccChHHHhhhccCCcccchhHHHHHHHHHHc
Q 000235 315 TQRSGRPIKSICSRLKAKEGRIRGNLMGKRVDFSARTVITPDPTINIDQLGVPWSIALNLTYPETVTPYNIERLKELVEY 394 (1815)
Q Consensus 315 ~~~~~~p~k~i~qrLkgK~Gr~R~nlmGKRVdfsaRsVIspDP~L~~~evGvP~~~A~~LT~PE~Vt~~Ni~~l~~lv~n 394 (1815)
++++++|+|||+|||||||||||+|||||||||||||||+|||||++||||||+.||++|||||+||+||+++|++||+|
T Consensus 286 ~~~~~~~~~~i~~~l~gK~G~~R~nl~GKRvd~s~RsVI~pdp~l~~~evGvP~~~A~~Lt~pe~Vt~~N~~~l~~lv~n 365 (868)
T TIGR02390 286 RHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVLN 365 (868)
T ss_pred ccCCCCCchhhHhhhcccccccccccccccccccCCceeeCCCCCcCCeeeCcHHHHHhCCCCeEEehhhHHHHHHHHHc
Confidence 88889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCcccccEEEeCCCceeeccccccc-cccccccccEeeeecccCCeEEEecCCccccccccceeEEeecCCeeee
Q 000235 395 GPHPPPGKTGAKYIIRDDGQRLDLRYLKKS-SDHHLELGYKVERHLNDGDFVLFNRQPSLHKMSIMGHRIKIMPYSTFRL 473 (1815)
Q Consensus 395 g~~~~pg~~~A~~i~~~~g~~~~l~~~~~~-~~~~L~~g~~V~Rhl~dgD~VL~NRQPsLHk~Simah~vkv~~~~t~rl 473 (1815)
||+.||| |+||++.+|.+++|++.++. ....|++||+|||||+|||+|||||||||||||||||+|||++|+||||
T Consensus 366 g~~~~pg---a~~i~~~~g~~~~l~~~~~~~~~~~l~~g~~v~rhl~dgd~vl~NRqPsLHr~si~a~~~~v~~~~t~r~ 442 (868)
T TIGR02390 366 GPDSWPG---ANYVIRPDGRRIKIRDENKEELAERLEPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRL 442 (868)
T ss_pred CCccCCC---ceEEEcCCCcEEechhhhHHHHHhhcccCCEEEEehhcCccceeccCCccccccceeEEEEEecCceEee
Confidence 9999999 99999999999999987643 3456899999999999999999999999999999999999999999999
Q ss_pred cccCCCCCCCCCCcCccccccCCCHhHHHHHHHHccCCCccccCCCCCCceeccccccccceecccCCCccCHHHHHHHH
Q 000235 474 NLSVTSPYNADFDGDEMNMHVPQSFETRAEVLELMMVPKCIVSPQSNRPVMGIVQDTLLGCRKITKRDTFIEKDVFMNIL 553 (1815)
Q Consensus 474 n~~vc~pyNADFDGDEMn~h~Pqs~~araE~~~l~~~~~~i~sp~~g~pi~g~~QD~l~g~~~lT~~d~f~~~~~~~~l~ 553 (1815)
||+||+||||||||||||+|||||++|||||++||++.+||++|++|+|++|++||+|+|+|+||++|+||+++|+++++
T Consensus 443 n~~~c~~~NADFDGDeMn~h~Pqs~~a~aEa~~Lm~~~~~~~sp~~g~p~~~~~QD~l~g~~~LT~~d~f~~~~~~~~l~ 522 (868)
T TIGR02390 443 NLAVCPPYNADFDGDEMNLHVPQTEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQTIL 522 (868)
T ss_pred ccccCCccccCcccceeeEecCCCHHHHHHHHHHhhchhceecCCCCCeeEEeehhhhhheeeeeeccccCCHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhcccCCCCCCCCcccCccCCcchHHHHHHhcCCCceEeeecccCCCC--CCCcCCCCCcEEEEecCeeeeccccccccc
Q 000235 554 MWWEDFDGKVPQPTILKPRPLWTGKQVFNLIIPKQINLFRTAAWHADN--DKGILTAGDTLVRIEKGELLSGTLCKKTLG 631 (1815)
Q Consensus 554 ~~~~~~~~~~~~pai~kp~~lwtGKqi~s~~lp~~in~~~~~~~~~~~--~~~~~~~~d~~v~i~~gell~g~ldK~~~g 631 (1815)
++. .|...+|+|||+||++|||||||||++||.++||..++++.... ...+.+.+|+.|+|+||||++|+|||++||
T Consensus 523 ~~~-~~~~~~~~p~i~kp~~lwTGKqi~s~~lp~~~n~~~~~~~~~~~~~~~~~~~~~d~~v~i~~g~ll~G~ldK~~lg 601 (868)
T TIGR02390 523 GVA-GYFGDPPEPAIEKPKEYWTGKQIFSAFLPEDLNFEGRAKICSGSDACKKEECPHDAYVVIKNGKLLKGVIDKKAIG 601 (868)
T ss_pred hcC-CccccCCCceecCCcccccHHHHHHHhcCCCCcceecccccccccccccccCCCcceEEEecCeEEeeeecHHHhc
Confidence 864 56777899999999999999999999999999999876654321 123457889999999999999999999999
Q ss_pred CCcccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCceeeeccCccChhhHHHHHHHHHHHHHHHHHHHHHHHcCCCC
Q 000235 632 TSTGSLIHVIWEEVGPDAARKFLGHTQWLVNYWLLQNAFSIGIGDTIADAKTMETINDTISKAKNNVKNLIKQAQDKSLE 711 (1815)
Q Consensus 632 ~s~~~Lih~i~~~~G~~~a~~~l~~~q~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~a~~~v~~~~~~~~~~~l~ 711 (1815)
++.+||||.+|++||+++|++||+++|+|+++||+++||||||+|+++++++.++++++|++++++++++++.+++|.++
T Consensus 602 ~~~~~li~~i~~~yG~~~a~~fl~~~~~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~g~l~ 681 (868)
T TIGR02390 602 AEKGKILHRIVREYGPEAARRFLDSVTRLFIRFITLRGFTTGIDDIDIPKEAKEEIEELIEKAEKRVDNLIERYRNGELE 681 (868)
T ss_pred cCcccHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHhccEEeehhheeeCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCChHHHHHhcCCCCcccchhhhhhhccccccCCCccCCCCCCCC
Q 000235 712 PEPGRTMMESFENKVNQVLNTARDEAGSSAQKSLSESNNLKAMVTAGSKGSFINISQMTACVGQQNVEGKRIPFGFVDRT 791 (1815)
Q Consensus 712 ~~~~~~~~~~~e~~v~~~ln~~~~~~~~~~~~~l~~~N~~~~M~~sGsKGS~~N~~Qi~~~lGQQ~~eG~Rip~~~~~rt 791 (1815)
..+|+++.+++|..++++|+++++.+++.+.+.++++|++++|+.||||||.+|++||+||||||+++|+|||+||++||
T Consensus 682 ~~~~~~~~~~~e~~i~~~l~~~r~~~~~~~~~~l~~~N~~~~M~~sGsKGS~~Ni~Qi~~~lGQQ~~~g~ri~~~~~~rt 761 (868)
T TIGR02390 682 PLPGRTVEETLEMKIMEVLGKARDEAGEVAEKYLDPENHAVIMARTGARGSLLNITQMAAMVGQQSVRGGRIRRGYRNRT 761 (868)
T ss_pred cCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcchhhhhhccCCcccccHHHHHhccCccccCCCcCccccccCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCCccccccccCCcCCCChhhhhhhccCCCcchhhhccccCCCchhHHHHHHHhhceEEeecCeeecCCCce
Q 000235 792 LPHFTKDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDIMVKYDGTVRNSLGDV 871 (1815)
Q Consensus 792 Lp~f~~~d~~~~~~Gfv~~sf~~GL~p~EfFfH~m~gReGLiDTAvKTa~sGYlqRrLvk~lEdl~v~YDgTVRns~g~i 871 (1815)
||||.++|.+++|+|||.|||++||+|+|||||||||||||||||||||+||||||||||+||||+|+|||||||++|+|
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 EEEEecCCCCCceeeecc
Q 000235 872 IQFLYGEDGMDSVWIESQ 889 (1815)
Q Consensus 872 iQF~YGeDg~d~~~~e~~ 889 (1815)
|||+|||||+||+++|.+
T Consensus 842 iQf~YG~dg~d~~~~~~~ 859 (868)
T TIGR02390 842 IQFKYGEDGVDPMKSDHG 859 (868)
T ss_pred EEEeccCCCcCHHHhccC
Confidence 999999999999998854
No 6
>PRK08566 DNA-directed RNA polymerase subunit A'; Validated
Probab=100.00 E-value=2.5e-230 Score=2232.09 Aligned_cols=840 Identities=48% Similarity=0.821 Sum_probs=787.1
Q ss_pred cccccceEEEEcCCHHHHHhcceeEEeeCccccCC-CCCCCCCCCCCCCCcCCCccccccccCCCCcCCccceeeccccc
Q 000235 11 EVAKVRMVQFGILSPDEIRQMSVVQIEHGETTERG-KPKPGGLSDPRLGTIDRKMKCETCTANMAECPGHFGHLELAKPM 89 (1815)
Q Consensus 11 ~~~~i~~i~F~~~S~eeI~~~Sv~eI~~~~~~~~~-~p~~gGl~D~rlG~~~~~~~C~TCg~~~~~CpGHfGhIeL~~PV 89 (1815)
+.++|++|+|+++|+|||++|||+||+++++||.. +|+.|||+|||||+++++..|+|||++..+||||||||||++||
T Consensus 5 ~~~~I~~I~F~~~S~eEI~klSv~~It~~~~~d~~g~P~~gGL~D~RLG~~~~~~~C~TCg~~~~~CPGHFGhIeL~~PV 84 (882)
T PRK08566 5 IPKRIGSIKFGLLSPEEIRKMSVTKIITADTYDDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELARPV 84 (882)
T ss_pred CceeeeeEEEecCCHHHHHHhCeEEEecccccCCCCCcCCCCCCCcccCCCCCCCCCCCCCCCCCcCCCcceEEeccccc
Confidence 45789999999999999999999999999999865 99999999999999999999999999999999999999999999
Q ss_pred cchhhhhHHHHHhcccceecceeccCCchHH-HHHHHHhc-----ChHHHHHHHHHHhhhccccCCCCCCCCCCCCCCcc
Q 000235 90 FHIGFMKTVLSIMRSVCFNCSKILADEDDHK-FKQALKIR-----NPKNRLKKILDACKNKTKCEGGDEIDVPGQDGEEP 163 (1815)
Q Consensus 90 ~h~~f~~~v~~iL~~vC~~C~~l~~~~~~~~-~~~~~~~~-----~~~~~~~~i~~~~~~~~~C~~~~~~~~~~~~~~~~ 163 (1815)
|||+||+.|++||+|+|++|++|++++.+.. +...++.. ..+.+++++++.|++++.|.+
T Consensus 85 fhpgf~~~v~~iL~~iC~~C~rll~~~~~~~~~~~~l~~~~~~~~~~~~l~k~i~k~~k~~~~C~~-------------- 150 (882)
T PRK08566 85 IHVGFAKLIYKLLRATCRECGRLKLTEEEIEEYLEKLERLKEWGSLADDLIKEVKKEAAKRMVCPH-------------- 150 (882)
T ss_pred cchhHHHHHHHHHHHhhhhhCceeccccchHHHHHHHhchhhhhhhHHHHHHHHHHHhcCCCCCCC--------------
Confidence 9999999999999999999999999876543 33333321 123567788888887777764
Q ss_pred cccccCCCCccchhhhhcccchhhhhHHhhccccccCCCCccchhcccCCHHHHHHHHhhcChhhHHHhcCCCCCCCccc
Q 000235 164 LKKNKGGCGAQQPKLTIEGMKMIAEYKAQRKKNDDQEQLPEPVERKQTLTAERVLGVLKRISDEDCQLLGLNPKYARPDW 243 (1815)
Q Consensus 164 ~~~~~~gCg~~~p~i~k~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~p~~v~~ilk~i~~~d~~~l~~~~~~~~Pe~ 243 (1815)
||+.+++|++++...+... . . ..++.|+|++|+++|++||++|+++||+++...+|+|
T Consensus 151 -------Cg~~~~ki~~~~~~~~~~~--~-------~------~~~~~L~p~~V~~ilk~I~~eD~~lLg~~~~~~~Pe~ 208 (882)
T PRK08566 151 -------CGEKQYKIKFEKPTTFYEE--R-------K------EGLVKLTPSDIRERLEKIPDEDLELLGINPEVARPEW 208 (882)
T ss_pred -------cCCCCceEEEecceeEEEe--c-------C------CCceeCCHHHHHHHHHhCCHHHHHHhCCCCCCCCcce
Confidence 9999999998764322111 0 0 1356899999999999999999999999999999999
Q ss_pred eEEeecccCCCCCCCC----------chhHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHhhccCCCCCCCc
Q 000235 244 MILQVLPIPPPPVRPS----------DDLTHQLAMIIRHNENLRRQERNGAPAHIISEFAQLLQFHIATYFDNELPGQPR 313 (1815)
Q Consensus 244 ~il~~lpVpP~~~RP~----------ddlT~~l~~Ii~~N~~lk~~~~~g~~~~~i~~~~~~LQ~~V~~~~dn~~~~~p~ 313 (1815)
|||++|||||+++||+ ||||++|++||++|++|++.++.|++.+++.+.|+.||++|++||||++.|.+.
T Consensus 209 ~il~~lPVpP~~iRPsv~~~~g~~~eDDLT~~L~~II~~N~~Lk~~~~~g~~~~~~~~~~~~LQ~~v~~~~d~~~~~~~~ 288 (882)
T PRK08566 209 MVLTVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVTTYFDNEIPGIPP 288 (882)
T ss_pred eEEeeeecCCCCCcCcEEeCCCcccCchHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHHhcCCccCCcc
Confidence 9999999999999997 999999999999999999999999999999999999999999999999999887
Q ss_pred ccccCCCChhhhhhhhhhcccccccccCCCCCCCCCceeecCCCCcccccccChHHHhhhccCCcccchhHHHHHHHHHH
Q 000235 314 ATQRSGRPIKSICSRLKAKEGRIRGNLMGKRVDFSARTVITPDPTINIDQLGVPWSIALNLTYPETVTPYNIERLKELVE 393 (1815)
Q Consensus 314 ~~~~~~~p~k~i~qrLkgK~Gr~R~nlmGKRVdfsaRsVIspDP~L~~~evGvP~~~A~~LT~PE~Vt~~Ni~~l~~lv~ 393 (1815)
+.+++++|+|||+|||||||||||+|||||||||||||||+|||||++||||||..||++|||||+||+|||++|++||.
T Consensus 289 ~~~~~~~~~~~i~~~l~gK~G~fR~nl~GKRvd~s~RsVI~pdp~l~~~evGvP~~~A~~Lt~pe~v~~~N~~~l~~~v~ 368 (882)
T PRK08566 289 ARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVL 368 (882)
T ss_pred cccCCCCCccchHHhcccCCCccccccccccccCcCCceeeCCCCCcCCeeeCcHHHHHhCCCCeEEchhhHHHHHHHHH
Confidence 77788899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCCcccccEEEeCCCceeecccccccc-ccccccccEeeeecccCCeEEEecCCccccccccceeEEeecCCeee
Q 000235 394 YGPHPPPGKTGAKYIIRDDGQRLDLRYLKKSS-DHHLELGYKVERHLNDGDFVLFNRQPSLHKMSIMGHRIKIMPYSTFR 472 (1815)
Q Consensus 394 ng~~~~pg~~~A~~i~~~~g~~~~l~~~~~~~-~~~L~~g~~V~Rhl~dgD~VL~NRQPsLHk~Simah~vkv~~~~t~r 472 (1815)
|||+.||| |+||++.+|++++|.+.++.. ...|++||+|||||+|||+|||||||||||||||||+|||++++|||
T Consensus 369 ng~~~~pg---a~~i~~~~g~~~~l~~~~~~~~~~~l~~g~~v~Rhl~dgd~vl~NRqPsLHr~si~a~~~~v~~~~t~r 445 (882)
T PRK08566 369 NGPEKHPG---ANYVIRPDGRRIKLTDKNKEELAEKLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFR 445 (882)
T ss_pred cCCCcCCC---ceEEEcCCCceeeehhhhHHHHHHhccccceehhhhhcCceeeecCCCcccccccceeEEEEecCceEe
Confidence 99999999 999999999999996544322 34689999999999999999999999999999999999999999999
Q ss_pred ecccCCCCCCCCCCcCccccccCCCHhHHHHHHHHccCCCccccCCCCCCceeccccccccceecccCCCccCHHHHHHH
Q 000235 473 LNLSVTSPYNADFDGDEMNMHVPQSFETRAEVLELMMVPKCIVSPQSNRPVMGIVQDTLLGCRKITKRDTFIEKDVFMNI 552 (1815)
Q Consensus 473 ln~~vc~pyNADFDGDEMn~h~Pqs~~araE~~~l~~~~~~i~sp~~g~pi~g~~QD~l~g~~~lT~~d~f~~~~~~~~l 552 (1815)
|||+||+||||||||||||+|||||++||||+++||++++||++|++|+|++|++||+|+|+|+||++|+||+++|+++|
T Consensus 446 ~n~~~c~~~NADFDGDeMn~h~Pqs~~a~aEa~~Lm~~~~~~~sp~~g~pi~~~~QD~l~g~~~lt~~d~f~~~~~~~~l 525 (882)
T PRK08566 446 LNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDL 525 (882)
T ss_pred eccccCCCccCCccCcEEEEecCCCHHHHHHHHHHhcchhcEecCCCCCeeEEeehHHHHHHHHHHhccccCCHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhcccCCCCCCCCcccCccCCcchHHHHHHhcCCCceEeeecccCCCC--CCCcCCCCCcEEEEecCeeeecccccccc
Q 000235 553 LMWWEDFDGKVPQPTILKPRPLWTGKQVFNLIIPKQINLFRTAAWHADN--DKGILTAGDTLVRIEKGELLSGTLCKKTL 630 (1815)
Q Consensus 553 ~~~~~~~~~~~~~pai~kp~~lwtGKqi~s~~lp~~in~~~~~~~~~~~--~~~~~~~~d~~v~i~~gell~g~ldK~~~ 630 (1815)
+++...+...+|+|||+||++|||||||||++||.++||..+.+++.+. ...+++.+|+.|+|+||||++|+|||++|
T Consensus 526 ~~~~~~~~~~~~~pai~~p~~lwTGKqi~s~~lp~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~gell~g~ldK~~l 605 (882)
T PRK08566 526 LRAAGIDELPEPEPAIENGKPYWTGKQIFSLFLPKDLNLEFKAKICSGCDECKKEDCEHDAYVVIKNGKLLEGVIDKKAI 605 (882)
T ss_pred HHhCCccccccCCcccCCCcccccHHHHHHHHcCCCCCceeeccccccccccccccCCCCceEEEecCEEEeccccHHHh
Confidence 9998766667899999999999999999999999999999776544321 12345778999999999999999999999
Q ss_pred cCCcccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCceeeeccCccChhhHHHHHHHHHHHHHHHHHHHHHHHcCCC
Q 000235 631 GTSTGSLIHVIWEEVGPDAARKFLGHTQWLVNYWLLQNAFSIGIGDTIADAKTMETINDTISKAKNNVKNLIKQAQDKSL 710 (1815)
Q Consensus 631 g~s~~~Lih~i~~~~G~~~a~~~l~~~q~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~a~~~v~~~~~~~~~~~l 710 (1815)
|++.+||||.||++||+++|.+||+.+|+|+++||+.+||||||+|++++++..++++++|+++++.++++++++.+|++
T Consensus 606 g~~~~~li~~i~~~yG~~~a~~fl~~~~~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~g~l 685 (882)
T PRK08566 606 GAEQGSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDEDIPEEAKEEIDEIIEEAEKRVEELIEAYENGEL 685 (882)
T ss_pred hcccchHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCEEeehhhcccCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCChHHHHHhcCCCCcccchhhhhhhccccccCCCccCCCCCCC
Q 000235 711 EPEPGRTMMESFENKVNQVLNTARDEAGSSAQKSLSESNNLKAMVTAGSKGSFINISQMTACVGQQNVEGKRIPFGFVDR 790 (1815)
Q Consensus 711 ~~~~~~~~~~~~e~~v~~~ln~~~~~~~~~~~~~l~~~N~~~~M~~sGsKGS~~N~~Qi~~~lGQQ~~eG~Rip~~~~~r 790 (1815)
+..+|+++.+.+|.+++++|+++|+.+++.+.+.++++|++++|+.||||||++|++||+||||||+++|+|||+||++|
T Consensus 686 ~~~~~~~~~~~~e~~i~~~l~~~r~~~~~~~~~~l~~~N~~~~M~~SGsKGS~~N~~Qi~~~lGqQ~~~g~ri~~~~~~r 765 (882)
T PRK08566 686 EPLPGRTLEETLEMKIMQVLGKARDEAGEIAEKYLGLDNPAVIMARTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDR 765 (882)
T ss_pred ccccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcceeeeccccccCHHHHHHHHhccCceecCCCcCccCccCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCCCccccccccCCcCCCChhhhhhhccCCCcchhhhccccCCCchhHHHHHHHhhceEEeecCeeecCCCc
Q 000235 791 TLPHFTKDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDIMVKYDGTVRNSLGD 870 (1815)
Q Consensus 791 tLp~f~~~d~~~~~~Gfv~~sf~~GL~p~EfFfH~m~gReGLiDTAvKTa~sGYlqRrLvk~lEdl~v~YDgTVRns~g~ 870 (1815)
|||||.++|.+|+++|||.|||++||+|+|||||||||||||||||||||+||||||||||+||||+|+|||||||++|+
T Consensus 766 tLP~f~~~d~~~~~~GfV~~sF~~GL~p~EfffH~m~GReGliDTAvkTa~sGYlqRrLvk~ledl~v~yD~tVR~s~g~ 845 (882)
T PRK08566 766 TLPHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDTRGN 845 (882)
T ss_pred cCCCCCCCCCCcccCceeeccccCCCCHHHHHHHHhhhcccccccceeeccCccchHHHHHHHhheEEeeCCceEcCCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEEEecCCCCCceeeecc
Q 000235 871 VIQFLYGEDGMDSVWIESQ 889 (1815)
Q Consensus 871 iiQF~YGeDg~d~~~~e~~ 889 (1815)
||||+||||||||+++|.+
T Consensus 846 iiQf~YG~dg~d~~~~~~~ 864 (882)
T PRK08566 846 IVQFKYGEDGVDPMKSDHG 864 (882)
T ss_pred EEEEeccCCCcCHHHhcCC
Confidence 9999999999999998754
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=5.7e-212 Score=2031.35 Aligned_cols=1033 Identities=28% Similarity=0.454 Sum_probs=816.0
Q ss_pred eEEEEcCCHHHHHhcceeEEeeCccccCC--CCCCCCCCCCCC-CCc--------------CCCccccccccCCCCcC--
Q 000235 17 MVQFGILSPDEIRQMSVVQIEHGETTERG--KPKPGGLSDPRL-GTI--------------DRKMKCETCTANMAECP-- 77 (1815)
Q Consensus 17 ~i~F~~~S~eeI~~~Sv~eI~~~~~~~~~--~p~~gGl~D~rl-G~~--------------~~~~~C~TCg~~~~~Cp-- 77 (1815)
+|+|+++|||+|++||++||++|+|++++ +|+.+||||+|+ |++ ++...|++||.++.+|+
T Consensus 1 ~i~i~laSPe~I~~ws~geV~~petiny~t~kPe~~GLfcerIFGp~k~~ec~Cgkyk~~~~~~~~C~~Cgve~t~~~vr 80 (1140)
T TIGR02386 1 AIKISIASPDTIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKIRYKGVVCERCGVEVTESKVR 80 (1140)
T ss_pred CeEEEecCHHHHHhhhceEEeccceecCCCCccCCCCcccchhcCCccCceeccccccccCcCCcCCCCCCCCcccchhh
Confidence 48999999999999999999999999997 999999999999 876 45568999999999998
Q ss_pred -CccceeeccccccchhhhhH-----------HHHHhcccceecceeccCCchHHHHHHHHhcChHHHHHHHHHHhhhcc
Q 000235 78 -GHFGHLELAKPMFHIGFMKT-----------VLSIMRSVCFNCSKILADEDDHKFKQALKIRNPKNRLKKILDACKNKT 145 (1815)
Q Consensus 78 -GHfGhIeL~~PV~h~~f~~~-----------v~~iL~~vC~~C~~l~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~ 145 (1815)
+||||||||.||+|+||++. ..|.|++||++|+++.+++.+..++...-+.. ..+.++.+. ..
T Consensus 81 r~rmGhI~La~Pv~Hiwy~k~~ps~~~~ll~~~~k~le~v~y~~~~~v~~~~~~~~~~~~~~~~--~~~~~~~~~---~~ 155 (1140)
T TIGR02386 81 RERMGHIELAAPVAHIWYFKGLPSRIGLLLDITAKELESVLYFENYVVLDPGDTKLDKKEVLDE--TEYREVLKR---YG 155 (1140)
T ss_pred hhcccceeecCCceeehhcCCCchHHHHHhCCCHHHhhheeeccceEEeCCCCCchhhhhhhch--hHHHHHHHH---hc
Confidence 99999999999999999997 48999999999999999876554332211111 112222221 10
Q ss_pred ccCCCCCCCCCCCCCCcccccccCCCCccchhhhhcccchhhhhHHhhccccccCCCCccchhcccCCHHHHHHHHhhcC
Q 000235 146 KCEGGDEIDVPGQDGEEPLKKNKGGCGAQQPKLTIEGMKMIAEYKAQRKKNDDQEQLPEPVERKQTLTAERVLGVLKRIS 225 (1815)
Q Consensus 146 ~C~~~~~~~~~~~~~~~~~~~~~~gCg~~~p~i~k~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~p~~v~~ilk~i~ 225 (1815)
. ....+||+.+.+....++++..+++..+++...... ....++.+...++.+.|++
T Consensus 156 ~-------------------~~~~~~G~~ai~~~l~~~dl~~~~~~~~~~~~~~~~---~~~~~~~~krl~~~~~f~~-- 211 (1140)
T TIGR02386 156 D-------------------GFRAGMGAEAIKELLEKIDLDKEIEELKIQLRESKS---DQKRKKLLKRLEIVEAFKD-- 211 (1140)
T ss_pred c-------------------CcccccchHHHHHHHhcCCHHHHHHHHHHHHHhccc---hhhHHhhhhHHHHHHHHHh--
Confidence 0 013579999999999999988887665443221110 0011334455555555553
Q ss_pred hhhHHHhcCCCCCCCccceEEeecccCCCCCCCC----------chhHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHH
Q 000235 226 DEDCQLLGLNPKYARPDWMILQVLPIPPPPVRPS----------DDLTHQLAMIIRHNENLRRQERNGAPAHIISEFAQL 295 (1815)
Q Consensus 226 ~~d~~~l~~~~~~~~Pe~~il~~lpVpP~~~RP~----------ddlT~~l~~Ii~~N~~lk~~~~~g~~~~~i~~~~~~ 295 (1815)
..+|||||||++||||||++||+ ||||++|++||++|++|+++++.++|..++.+.|++
T Consensus 212 -----------s~~~Pewmil~~lPV~Pp~lRP~v~l~gg~~~~sDLn~lyr~II~~Nn~Lk~~~~~~ap~~ii~~~~~~ 280 (1140)
T TIGR02386 212 -----------SGNRPEWMVLDVIPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRM 280 (1140)
T ss_pred -----------cCCChHHhhhhcccCCCCccCCcEEeCCCccccCchHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHH
Confidence 35899999999999999999999 899999999999999999999999999999999999
Q ss_pred HHHHHHhhccCCCCCCCcccccCCCChhhhhhhhhhcccccccccCCCCCCCCCceeecCCCCcccccccChHHHhhhcc
Q 000235 296 LQFHIATYFDNELPGQPRATQRSGRPIKSICSRLKAKEGRIRGNLMGKRVDFSARTVITPDPTINIDQLGVPWSIALNLT 375 (1815)
Q Consensus 296 LQ~~V~~~~dn~~~~~p~~~~~~~~p~k~i~qrLkgK~Gr~R~nlmGKRVdfsaRsVIspDP~L~~~evGvP~~~A~~LT 375 (1815)
||++|++||||++.|.|. ..+++||+|||+||||||+||||+|||||||||||||||+|||+|++||||||+.||++||
T Consensus 281 LQ~aV~~liDn~~~g~~~-~~~~~rplksls~~LkGK~GrFR~NLlGKRVDySgRSVI~pdP~L~l~e~GlP~~mA~~L~ 359 (1140)
T TIGR02386 281 LQEAVDALFDNGRRGKPV-VGKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELF 359 (1140)
T ss_pred HHHHHHHHhcccccCCCc-cCcCCCchhhHHHhhcCCCCcccccccccccCCCCCCeEcCCCCcccccccChHHHHHHcC
Confidence 999999999999999875 4557899999999999999999999999999999999999999999999999999999998
Q ss_pred CCcccchhHHHHHHHHHHcCCCCCCCcccccEEEeCCCceeeccccccccccccccccEeeeecccCCeEEEecCCcccc
Q 000235 376 YPETVTPYNIERLKELVEYGPHPPPGKTGAKYIIRDDGQRLDLRYLKKSSDHHLELGYKVERHLNDGDFVLFNRQPSLHK 455 (1815)
Q Consensus 376 ~PE~Vt~~Ni~~l~~lv~ng~~~~pg~~~A~~i~~~~g~~~~l~~~~~~~~~~L~~g~~V~Rhl~dgD~VL~NRQPsLHk 455 (1815)
+| ||+++|++ +|... .++..++.-.......|.|.||+++||+|||||||||||
T Consensus 360 ~P-----f~i~~L~~---~~~~~------------------~i~~ak~~i~~~~~~v~~vl~~vi~~d~VLlNRqPTLHR 413 (1140)
T TIGR02386 360 KP-----FIIKRLID---RELAA------------------NIKSAKKMIEQEDPEVWDVLEDVIKEHPVLLNRAPTLHR 413 (1140)
T ss_pred ch-----HHHHHHHH---cCccc------------------chHHHHHHHHhcCCccceEEEEccCCcEEEecCCCcccc
Confidence 65 88877754 44311 111111110111235688899999999999999999999
Q ss_pred ccccceeEEeecCCeeeecccCCCCCCCCCCcCccccccCCCHhHHHHHHHHccCCCccccCCCCCCceeccccccccce
Q 000235 456 MSIMGHRIKIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFETRAEVLELMMVPKCIVSPQSNRPVMGIVQDTLLGCR 535 (1815)
Q Consensus 456 ~Simah~vkv~~~~t~rln~~vc~pyNADFDGDEMn~h~Pqs~~araE~~~l~~~~~~i~sp~~g~pi~g~~QD~l~g~~ 535 (1815)
||||||+|||++++||||||+||+||||||||||||||||||++||||+++||++++||+||++|+|+++++||+|+|+|
T Consensus 414 lsIqAf~~~l~~gktirlhplvC~~fNADFDGDeMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y 493 (1140)
T TIGR02386 414 LGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKPIVTPSQDMVLGLY 493 (1140)
T ss_pred cccceeEEEEecCceEEEcccccCcccCCCCcceeEeecCCCHHHHHHHHHHhCCcccEecCCCCCceEEeechhhheee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecccCC--------CccCHHHHHHHHHhcccCCCCCCCCcccCc----cCCc--chHHHHHHhcCCCceEeeecccCCCC
Q 000235 536 KITKRD--------TFIEKDVFMNILMWWEDFDGKVPQPTILKP----RPLW--TGKQVFNLIIPKQINLFRTAAWHADN 601 (1815)
Q Consensus 536 ~lT~~d--------~f~~~~~~~~l~~~~~~~~~~~~~pai~kp----~~lw--tGKqi~s~~lp~~in~~~~~~~~~~~ 601 (1815)
+||.++ +|++++++++.+ +++.++.|+++++ +.+| +|||||+.+||.+++|..+
T Consensus 494 ~LT~~~~~~~~~~~~F~~~~e~~~~~-----~~~~i~l~~~i~~~~~g~~~~tt~Gr~if~~ilP~~~~~~n~------- 561 (1140)
T TIGR02386 494 YLTTEKPGAKGEGKIFSNVDEAIRAY-----DNGKVHLHALIGVRTSGEILETTVGRVIFNEILPEGFPYIND------- 561 (1140)
T ss_pred EeeeccccccCcCceeCCHHHHHHHH-----HcCCccCCCceEEeccccEEEccchHHHHHHHcCCccccccc-------
Confidence 999995 799999999753 3456666776653 4677 6999999999998877521
Q ss_pred CCCcCCCCCcEEEEecCeeeecccccccccCCcccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCceeeeccCccCh
Q 000235 602 DKGILTAGDTLVRIEKGELLSGTLCKKTLGTSTGSLIHVIWEEVGPDAARKFLGHTQWLVNYWLLQNAFSIGIGDTIADA 681 (1815)
Q Consensus 602 ~~~~~~~~d~~v~i~~gell~g~ldK~~~g~s~~~Lih~i~~~~G~~~a~~~l~~~q~l~~~~l~~~GfSigi~D~~~~~ 681 (1815)
. ++|||+.+| +|||.+|++||++.|.+|||++++|+++|++.+||||||+|+++++
T Consensus 562 -------~-------------~~l~Kk~lg----~LI~~i~~~~G~~~t~~~LD~lk~Lgf~~at~~GfSigi~Dl~ip~ 617 (1140)
T TIGR02386 562 -------N-------------EPLSKKEIS----SLIDLLYEVHGIEETAEMLDKIKALGFKYATKSGTTISASDIVVPD 617 (1140)
T ss_pred -------c-------------cccchHHHH----HHHHHHHHHhChHHHHHHHHHHHHHHHHHHHhcCeeeeeccCCCCH
Confidence 0 179999998 8999999999999999999999999999999999999999999987
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCC----CChHHHHHhc
Q 000235 682 KTMETINDTISKAKNNVKNLIKQAQDKSLEPEPGRTMMESFENKVNQVLNTARDEAGSSAQKSLSE----SNNLKAMVTA 757 (1815)
Q Consensus 682 ~~~~~~~~~i~~a~~~v~~~~~~~~~~~l~~~~~~~~~~~~e~~v~~~ln~~~~~~~~~~~~~l~~----~N~~~~M~~s 757 (1815)
+ +.++|++|++++.+++++|++|.++. +.++.++.++|+++++++++.+++++.+ .|++++|+.|
T Consensus 618 ~----K~~ii~~a~~~v~~i~~~y~~G~lt~-------~er~~kvi~iw~~~~d~v~~~~~~~l~~~~~~~N~i~mMa~S 686 (1140)
T TIGR02386 618 E----KYEILKEADKEVAKIQKFYNKGLITD-------EERYRKVVSIWSETKDKVTDAMMKLLKKDTYKFNPIFMMADS 686 (1140)
T ss_pred H----HHHHHHHHHHHHHHHHHHHHcCCCCh-------HHHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCcHhhhhhc
Confidence 5 57899999999999999999998863 4567899999999999999999999975 5999999999
Q ss_pred CCCCcccchhhhhhhccccccCCCccCCCCCCCCCCCCCCCCCCCccccccccCCcCCCChhhhhhhccCCCcchhhhcc
Q 000235 758 GSKGSFINISQMTACVGQQNVEGKRIPFGFVDRTLPHFTKDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAV 837 (1815)
Q Consensus 758 GsKGS~~N~~Qi~~~lGQQ~~eG~Rip~~~~~rtLp~f~~~d~~~~~~Gfv~~sf~~GL~p~EfFfH~m~gReGLiDTAv 837 (1815)
|||||.+|++||+||+|||. +|. ||++|+ +|.|||++||+|+|||||||||||||+||||
T Consensus 687 GARGS~~ni~QL~GmrGlma-----~p~---Grii~~------------PI~ssF~eGLtp~EyF~st~GaRkGLiDTAl 746 (1140)
T TIGR02386 687 GARGNISQFRQLAGMRGLMA-----KPS---GDIIEL------------PIKSSFREGLTVLEYFISTHGARKGLADTAL 746 (1140)
T ss_pred ccccCHHHHHHHHhCCCccc-----CCC---CCcccc------------chhhccccCCCHHHHhhhccchhccccchhe
Confidence 99999999999999999996 232 477775 4999999999999999999999999999999
Q ss_pred ccCCCchhHHHHHHHhhceEEeecCeeecCCCceEEEEecCCCCCceeeecccccccccchHHHhhhhhhccccCCCCcc
Q 000235 838 KTSETGYIQRRLVKAMEDIMVKYDGTVRNSLGDVIQFLYGEDGMDSVWIESQTLDSLKMKKSEFDKAFRFEMDEENWNPN 917 (1815)
Q Consensus 838 KTa~sGYlqRrLvk~lEdl~v~YDgTVRns~g~iiQF~YGeDg~d~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 917 (1815)
|||+||||||||||++|||+|.||.+- ...|-.|+.+..++| ..++ .+.+..+.|....++.++..+.
T Consensus 747 KTAdSGYLtRRLVdv~qDviV~~dDCg-T~~gi~v~~~~~~~~---~~i~-------~l~~ri~GR~~~~di~~~~~~~- 814 (1140)
T TIGR02386 747 KTADSGYLTRRLVDVAQDVVVREEDCG-TEEGIEVEAIVEGKD---EIIE-------SLKDRIVGRYSAEDVYDPDTGK- 814 (1140)
T ss_pred eecccceeeeehhhhhcceEEEeCCCC-CCCCEEEEEeecCCc---eEEe-------ehhheeEEEEEhhheEeCCCCc-
Confidence 999999999999999999999999544 234667766653332 1111 1111112221111111111000
Q ss_pred cchHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhHhhhccCCCCCCCccccHHHHHHHhhhhcccCCCCCCCCChHHHHH
Q 000235 918 YMLQEYIDDLKTIKELRDVFDAEVQKLEADRYQLATEIATSGDSSWPLPVNLKRLIWNAQKTFKVDPRRPSDMHPMEVVE 997 (1815)
Q Consensus 918 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~r~~l~~~~~~~~~~~~~~p~n~~r~i~~~~~~~~~~~~~~~~~~p~~~~~ 997 (1815)
.+.. ....++. ++
T Consensus 815 ------------------------------------~i~~----------------------------~~~~i~~-~~-- 827 (1140)
T TIGR02386 815 ------------------------------------LIAE----------------------------ANTLITE-EI-- 827 (1140)
T ss_pred ------------------------------------EEEe----------------------------CCCCcCH-HH--
Confidence 0000 0011111 11
Q ss_pred HHHHHHHhhcccCCCCcccHHHHhhhhhhhhhhhhhhhhhHHHHHhhccCHHHHHHHHHHHHHHhhcCcccCCCchhhHh
Q 000235 998 AVDKLQERLKVVPGEDPLSVEAQKNATLFFNILLRSTFASKRVLKEHRLTREAFEWVIGEIESRFLQSLVAPGEMIGCVA 1077 (1815)
Q Consensus 998 ~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~lrs~l~~~~~~~~~~l~~~~~~~~l~ei~~ky~~slv~PGEaVG~iA 1077 (1815)
++++ ....+-.+.+||.|+|+ ..+++|++||+|.|+ ...+|+.|||||+||
T Consensus 828 -----~~~i---------------~~~~i~~v~iRS~ltC~---s~~gvC~~CYG~~La------~~~~V~~GeaVGiiA 878 (1140)
T TIGR02386 828 -----AEKI---------------ENSGIEKVKVRSVLTCE---SEHGVCQKCYGRDLA------TGKLVEIGEAVGVIA 878 (1140)
T ss_pred -----HHHH---------------HHcCCCEEEecCCeeeC---CCCCCccccCCCccc------CCcEecccccceeEe
Confidence 1111 01123456789999998 589999999999986 789999999999999
Q ss_pred hhccCCcccccccccccccccccc--ccccccceeeeehhhcccCCCCceEEEeCCCCcchHHHHHHHHhhhcccccccc
Q 000235 1078 AQSIGEPATQMTLNTFHYAGVSAK--NVTLGVPRLREIINVAKKIKTPSLSVFLKPGVNSTKERAKNVQCALEYTTLRSV 1155 (1815)
Q Consensus 1078 AQSIGEPaTQMTLnTFH~AGv~~~--NVTlGvPRLkEIin~ak~ikTP~mtv~l~~~~~~~~~~a~~v~~~le~~tL~dv 1155 (1815)
|||||||+|||||+|||.+||++. +||.|+||+.||+++ +++|.+.+...+...+.
T Consensus 879 AQSIGEPGTQLTmRTFHtGGv~~~~~DIT~GlpRv~elfea-r~p~~~a~iae~~G~v~--------------------- 936 (1140)
T TIGR02386 879 AQSIGEPGTQLTMRTFHTGGVAGASGDITQGLPRVKELFEA-RTPKDKAVIAEVDGTVE--------------------- 936 (1140)
T ss_pred eeecCCCcchhehhheeeccccccccccccCchhhhhhhhc-ccCCCceEEEecCCEEE---------------------
Confidence 999999999999999999999975 999999999999996 55665544333222110
Q ss_pred ceeeEEEE-cCCCCceE-EEcccceeheeccCCCCcccccccCCcEEEEEechhhhhcccCCHHHHHHHHhhhcCCCcee
Q 000235 1156 TEATEVWY-DPDPMGTI-IEEDVEFVKSYYEMPDEDIAPEKISPWLLRIELNREMMVDKKLSMAAVAEKINQEFDDDLTC 1233 (1815)
Q Consensus 1156 ~~~~~i~y-dp~~~~~~-i~~d~~~~~~~~~~~~~~~~~~~~~~~~lrl~l~~~~~~~~~l~~~~i~~~i~~~~~~~~~~ 1233 (1815)
+.- +......+ |..+.+-.. .|.+|..
T Consensus 937 -----~~~~~~~~~~~i~i~~~~~~~~-~y~ip~~--------------------------------------------- 965 (1140)
T TIGR02386 937 -----IIEDIVKNKRVVVIKDENDEEK-KYTIPFG--------------------------------------------- 965 (1140)
T ss_pred -----EeecccCCcEEEEEECCCCcee-EEeccCC---------------------------------------------
Confidence 000 00000000 110000000 0111100
Q ss_pred eecCCCccceEEEEEEccCCCCCCCCCCCcchhHHHHHHHHhhccccceecccchhhhhccccccccccccccHHHHHHh
Q 000235 1234 IFNDDNADKLILRIRIMNDEAPKGELNDESAEDDVFLKKIESNMLTEMALRGVNLLAVMCHEDVDARRTTSNHLIEIIEV 1313 (1815)
Q Consensus 1234 ~~~~dn~~~~~~~ir~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~G~nl~~vl~~~~vD~~rt~sNdI~eI~~v 1313 (1815)
.++++.+.+ .... .+.| ++| +-|++||+++
T Consensus 966 -----------~~l~v~~gd--~V~~---------------G~~l----~~g------------------~~~~~~il~v 995 (1140)
T TIGR02386 966 -----------AQLRVKDGD--SVSA---------------GDKL----TEG------------------SIDPHDLLRI 995 (1140)
T ss_pred -----------ceEEecCCC--EEcc---------------CCcc----cCC------------------CCCHHHHHHh
Confidence 011111100 0000 0011 133 5589999999
Q ss_pred hcHHHHHHHHHHHHHHhhhcCcccccchhHHHHHhhhhccceec------------------------------------
Q 000235 1314 LGIEAVRRALLDELRVVISFDGSYVNYRHLAILCDTMTYRGHLM------------------------------------ 1357 (1815)
Q Consensus 1314 lGIEAAR~~Ii~Ei~~V~~~~Gi~Vn~RHL~LlaD~MT~~G~~~------------------------------------ 1357 (1815)
+||||+|++|++||++||..||++||+|||++|+|+||.++++.
T Consensus 996 ~G~~a~~~~lv~evq~vY~~QGv~I~dKHievIvrqM~~kv~i~~~gdt~~l~g~~v~~~~~~~~n~~~~~~g~~~~~~~ 1075 (1140)
T TIGR02386 996 KGIQAVQEYLVKEVQKVYRLQGVEINDKHIEVIVRQMLRKVRITDSGDSNLLPGELIDIHEFNEENRKLLEQGKKPASAI 1075 (1140)
T ss_pred cCHHHHHHHHHHHHHHHHHhCCccccchhHhHHHHHHhCcEEEEeCCCcCCCCCCeeeHHHHHHHHHHHHhCCCCCccce
Confidence 99999999999999999999999999999999999999997544
Q ss_pred ----ccccccccccCCccccccchHHHHHHHHHHHhhcCcccccccccccccCCccccCccce
Q 000235 1358 ----AITRHGINRNDTGPMMRCSFEETVDILLDAAVFAESDYLRGVTENIMLGQLAPIGTGDC 1416 (1815)
Q Consensus 1358 ----~itR~Gi~~~~~spL~~aSFEeT~~~L~~AA~~ge~D~l~gvsenIi~G~~~p~GTG~f 1416 (1815)
+|||+.++ ..|+|++||||||+++|++||+.|++|+|+|++||||+|+++|+|||..
T Consensus 1076 ~~llGitkasl~--t~SflsaASFqeTtkvLt~Aai~gk~D~L~GlkENVIiG~liPaGTG~~ 1136 (1140)
T TIGR02386 1076 PQLLGITKASLN--TESFLSAASFQETTKVLTDAAIKGKVDYLLGLKENVIIGNLIPAGTGLK 1136 (1140)
T ss_pred eeeeeeeehhcc--CCCcccccchhhHHHHHHHHHhcCCCCCCCCcccceEecCcccCCCCcc
Confidence 56777775 4699999999999999999999999999999999999999999999963
No 8
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=100.00 E-value=8.3e-207 Score=1985.01 Aligned_cols=1031 Identities=29% Similarity=0.462 Sum_probs=802.3
Q ss_pred ccceEEEEcCCHHHHHhcceeEEeeCccccCC--CCCCCCCCCCCCCCcCCCccccccccCC------CCcC--------
Q 000235 14 KVRMVQFGILSPDEIRQMSVVQIEHGETTERG--KPKPGGLSDPRLGTIDRKMKCETCTANM------AECP-------- 77 (1815)
Q Consensus 14 ~i~~i~F~~~S~eeI~~~Sv~eI~~~~~~~~~--~p~~gGl~D~rlG~~~~~~~C~TCg~~~------~~Cp-------- 77 (1815)
+++.|+++++|||+|++||+.||++|+|+++. +|+.+||||+|++.+.+++.| .||+-. ..|+
T Consensus 6 ~~~~i~i~laspe~I~~ws~GeV~~petinyrt~kPe~~GLfcerIFgp~kd~eC-~Cgkyk~~~~~~~~C~~cgve~~~ 84 (1156)
T PRK00566 6 DFDAIKIGLASPEKIRSWSYGEVKKPETINYRTLKPERDGLFCERIFGPTKDYEC-LCGKYKRVRYKGIICERCGVEVTR 84 (1156)
T ss_pred CcceEEEEccCHHHHHHhhcceEccccccccCCCccCCCCcccchhcCcccCcEE-eCccccccCcCCcCCCCCCceeee
Confidence 78899999999999999999999999999997 999999999999877889999 798522 4688
Q ss_pred -----CccceeeccccccchhhhhHH-----------HHHhcccceecceeccCCchHHHHHHHHhcChHHHHHHHHHHh
Q 000235 78 -----GHFGHLELAKPMFHIGFMKTV-----------LSIMRSVCFNCSKILADEDDHKFKQALKIRNPKNRLKKILDAC 141 (1815)
Q Consensus 78 -----GHfGhIeL~~PV~h~~f~~~v-----------~~iL~~vC~~C~~l~~~~~~~~~~~~~~~~~~~~~~~~i~~~~ 141 (1815)
+|||||+|+.||+|+|||+.+ .|.|++||++|+++.+++.+..+.....+ . ...+.++.+..
T Consensus 85 ~~vrr~rmGhI~La~Pv~Hiwy~k~~ps~i~~ll~~~~k~le~v~y~~~~~v~~~~~~~~~~~~~~-~-~~~~~~~~~~~ 162 (1156)
T PRK00566 85 SKVRRERMGHIELAAPVAHIWFFKSLPSRIGLLLDMSLKDLERVLYFESYVVIDPGDTPLEKKQLL-T-EEEYREALEEY 162 (1156)
T ss_pred chhhhhhcceeeecCceeeeeecCCCchHHHHHhCCCHHHhhheeecceEEEeCCCCCchhhhccc-C-HHHHHHHHHHh
Confidence 999999999999999999943 79999999999999988754322221111 1 11122222211
Q ss_pred hhccccCCCCCCCCCCCCCCcccccccCCCCccchhhhhcccchhhhhHHhhccccccCCCCccchhcccCCHHHHHHHH
Q 000235 142 KNKTKCEGGDEIDVPGQDGEEPLKKNKGGCGAQQPKLTIEGMKMIAEYKAQRKKNDDQEQLPEPVERKQTLTAERVLGVL 221 (1815)
Q Consensus 142 ~~~~~C~~~~~~~~~~~~~~~~~~~~~~gCg~~~p~i~k~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~p~~v~~il 221 (1815)
. . . ...+||+...+....++++..+....+++.... -+..+..+++
T Consensus 163 ~------~--~--------------~~~~~Ga~ai~~ll~~~dl~~~~~~l~~~~~~~------------~~~~~~~~~~ 208 (1156)
T PRK00566 163 G------D--E--------------FVAKMGAEAIKELLKNIDLEAEAEELREELKET------------GSEQKRKKAL 208 (1156)
T ss_pred c------c--c--------------ccccccHHHHHHHHHhCCHHHHHHHHHHHHHhc------------ccchhHHHHH
Confidence 0 0 0 123589888888888888777665543322110 0122334455
Q ss_pred hhcChhhHHHhcCCCCCCCccceEEeecccCCCCCCCC----------chhHHHHHHHHHHHHHHHHHHHcCCChhhHHH
Q 000235 222 KRISDEDCQLLGLNPKYARPDWMILQVLPIPPPPVRPS----------DDLTHQLAMIIRHNENLRRQERNGAPAHIISE 291 (1815)
Q Consensus 222 k~i~~~d~~~l~~~~~~~~Pe~~il~~lpVpP~~~RP~----------ddlT~~l~~Ii~~N~~lk~~~~~g~~~~~i~~ 291 (1815)
|+|.--+.. .....+|+||||++||||||++||+ ||||++|++||++|++|+++.+.++|..++.+
T Consensus 209 krl~~~~~f----~~s~~~Pewmil~~lPV~Pp~lRP~v~l~~g~~~~sDLn~lyr~II~rNnrLk~~~~~~ap~~ii~~ 284 (1156)
T PRK00566 209 KRLKVVEAF----RKSGNKPEWMILDVLPVIPPDLRPLVQLDGGRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRN 284 (1156)
T ss_pred HHHHHHHHH----HcCCCCccEeeEeecccCCCcccCceEeCCCcccCCchHHHHHHHHHHHHHHHHHHHcCCcHHHHHH
Confidence 555433322 2236899999999999999999999 89999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhccCCCCCCCcccccCCCChhhhhhhhhhcccccccccCCCCCCCCCceeecCCCCcccccccChHHHh
Q 000235 292 FAQLLQFHIATYFDNELPGQPRATQRSGRPIKSICSRLKAKEGRIRGNLMGKRVDFSARTVITPDPTINIDQLGVPWSIA 371 (1815)
Q Consensus 292 ~~~~LQ~~V~~~~dn~~~~~p~~~~~~~~p~k~i~qrLkgK~Gr~R~nlmGKRVdfsaRsVIspDP~L~~~evGvP~~~A 371 (1815)
.|++||++|++||||+..|.|.. .+++||+|||+||||||+||||+|||||||||||||||+|||+|++||||||+.||
T Consensus 285 ~~~~LQ~aV~~lidn~~~g~~~~-~~~~rplksls~~LkGK~GrFR~NLlGKRVDySgRSVI~pdP~L~l~e~GvP~~mA 363 (1156)
T PRK00566 285 EKRMLQEAVDALFDNGRRGRPVT-GPNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMA 363 (1156)
T ss_pred HHHHHHHHHHHHhccCccCCCcc-cccCCchhHHHHhhcCCCccccccccccccCCCCCceEeCCCCcccccccChHHHH
Confidence 99999999999999999987654 35789999999999999999999999999999999999999999999999999999
Q ss_pred hhccCCcccchhHHHHHHHHHHcCCCCCCCcccccEEEeCCCceeeccccccccccccccccEeeeecccCCeEEEecCC
Q 000235 372 LNLTYPETVTPYNIERLKELVEYGPHPPPGKTGAKYIIRDDGQRLDLRYLKKSSDHHLELGYKVERHLNDGDFVLFNRQP 451 (1815)
Q Consensus 372 ~~LT~PE~Vt~~Ni~~l~~lv~ng~~~~pg~~~A~~i~~~~g~~~~l~~~~~~~~~~L~~g~~V~Rhl~dgD~VL~NRQP 451 (1815)
++||+| ||+++ |+.||+... ++.|+.++.. .-..+|.|.||+++||+|||||||
T Consensus 364 ~eL~~P-----f~i~~---L~~~g~~~~--ik~ak~~~~~----------------~~~~v~~vle~vi~gd~VLlNRqP 417 (1156)
T PRK00566 364 LELFKP-----FIMKK---LVERGLATT--IKSAKKMVER----------------EDPEVWDVLEEVIKEHPVLLNRAP 417 (1156)
T ss_pred HHhCcH-----HHHHH---HHHcCCccc--hHhhhhhhhh----------------hcCcceEEEEEecCCCEEEecCCC
Confidence 999865 77555 477886321 2224432210 112467788889999999999999
Q ss_pred ccccccccceeEEeecCCeeeecccCCCCCCCCCCcCccccccCCCHhHHHHHHHHccCCCccccCCCCCCceecccccc
Q 000235 452 SLHKMSIMGHRIKIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFETRAEVLELMMVPKCIVSPQSNRPVMGIVQDTL 531 (1815)
Q Consensus 452 sLHk~Simah~vkv~~~~t~rln~~vc~pyNADFDGDEMn~h~Pqs~~araE~~~l~~~~~~i~sp~~g~pi~g~~QD~l 531 (1815)
||||||||||++++++++||||||+||+||||||||||||||||||++||||+++||++.+||+||++|+|+++++||+|
T Consensus 418 TLHR~sIqAf~~~l~~gktirLhplvC~~fNADFDGDqMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~i 497 (1156)
T PRK00566 418 TLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPANGKPIIVPSQDMV 497 (1156)
T ss_pred cccccccceeEEEEecCceEEECccccCccccccccceeEEecCCCHHHHHHHHHHhCCcccEEecCCCCeeEEeehhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccceecccCC--------CccCHHHHHHHHHhcccCCCCCCCCcccCc-----cCCcchHHHHHHhcCCCceEeeecccC
Q 000235 532 LGCRKITKRD--------TFIEKDVFMNILMWWEDFDGKVPQPTILKP-----RPLWTGKQVFNLIIPKQINLFRTAAWH 598 (1815)
Q Consensus 532 ~g~~~lT~~d--------~f~~~~~~~~l~~~~~~~~~~~~~pai~kp-----~~lwtGKqi~s~~lp~~in~~~~~~~~ 598 (1815)
+|+|+||.+| +|++++|+++++... .-.++.+..+++ ..+|||||||+.+||++++|..
T Consensus 498 lG~y~LT~~~~~~~~~~~~F~~~~e~~~~~~~~---~i~l~~~i~~~~~~~~~i~tt~Gk~if~~ilP~~~~~~n----- 569 (1156)
T PRK00566 498 LGLYYLTREREGAKGEGMVFSSPEEALRAYENG---EVDLHARIKVRITSKKLVETTVGRVIFNEILPEGLPFIN----- 569 (1156)
T ss_pred hhhheeecccccccCCCceeCCHHHHHHHHHcC---CCCCCCeEEecCCCCceEEcCcHHHHHHhhccccceeec-----
Confidence 9999999998 899999999986421 112333333332 2469999999999999887652
Q ss_pred CCCCCCcCCCCCcEEEEecCeeeecccccccccCCcccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCceeeeccCc
Q 000235 599 ADNDKGILTAGDTLVRIEKGELLSGTLCKKTLGTSTGSLIHVIWEEVGPDAARKFLGHTQWLVNYWLLQNAFSIGIGDTI 678 (1815)
Q Consensus 599 ~~~~~~~~~~~d~~v~i~~gell~g~ldK~~~g~s~~~Lih~i~~~~G~~~a~~~l~~~q~l~~~~l~~~GfSigi~D~~ 678 (1815)
.+|++||+++| +|||.+|++||.++|.+|||++++|+++|++.+|||||++|++
T Consensus 570 ----------------------~~g~ldKk~Lg----~LI~~i~~~yG~~~t~~~LD~ik~Lgf~yat~~GfSigi~Dl~ 623 (1156)
T PRK00566 570 ----------------------VNKPLKKKEIS----KIINEVYRRYGLKETVIFLDKIKDLGFKYATRSGISIGIDDIV 623 (1156)
T ss_pred ----------------------ccceecHHHHH----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCeEeehhhcC
Confidence 05899999998 7999999999999999999999999999999999999999999
Q ss_pred cChhhHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCC----CChHHHH
Q 000235 679 ADAKTMETINDTISKAKNNVKNLIKQAQDKSLEPEPGRTMMESFENKVNQVLNTARDEAGSSAQKSLSE----SNNLKAM 754 (1815)
Q Consensus 679 ~~~~~~~~~~~~i~~a~~~v~~~~~~~~~~~l~~~~~~~~~~~~e~~v~~~ln~~~~~~~~~~~~~l~~----~N~~~~M 754 (1815)
++++ +.++|++|+++++++.++|++|.++. +..+.++.++|+++++.+++.+++++.+ +|++++|
T Consensus 624 ip~~----K~~ii~~a~~~v~~i~~~y~~G~lt~-------~er~~kvi~~w~~~~d~v~~~~~~~l~~~~~~~N~i~mM 692 (1156)
T PRK00566 624 IPPE----KKEIIEEAEKEVAEIEKQYRRGLITD-------GERYNKVIDIWSKATDEVAKAMMKNLSKDQESFNPIYMM 692 (1156)
T ss_pred cChH----HHHHHHHHHHHHHHHHHHHHcCCCCc-------hHHHHHHHHHHHHHHHHHHHHHHHhCccccCCCCChhee
Confidence 9875 57899999999999999999999874 2345889999999999999999999875 8999999
Q ss_pred HhcCCCCcccchhhhhhhccccc-cCCCccCCCCCCCCCCCCCCCCCCCccccccccCCcCCCChhhhhhhccCCCcchh
Q 000235 755 VTAGSKGSFINISQMTACVGQQN-VEGKRIPFGFVDRTLPHFTKDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREGLI 833 (1815)
Q Consensus 755 ~~sGsKGS~~N~~Qi~~~lGQQ~-~eG~Rip~~~~~rtLp~f~~~d~~~~~~Gfv~~sf~~GL~p~EfFfH~m~gReGLi 833 (1815)
+.||||||++|++||+||+|||. .+|+.|+ .||.+||++||+|+|||||||||||||+
T Consensus 693 a~SGARGS~~ni~QL~GmrGlma~p~G~iie---------------------~pI~ssFreGLt~~EyFfst~GaRkGLi 751 (1156)
T PRK00566 693 ADSGARGSASQIRQLAGMRGLMAKPSGEIIE---------------------TPIKSNFREGLTVLEYFISTHGARKGLA 751 (1156)
T ss_pred eeccCCcCHHHHHHHHhhcCccccCCCCEee---------------------hhhhhhhhcCCCHHHHhhcCcchhhccc
Confidence 99999999999999999999984 5565443 2699999999999999999999999999
Q ss_pred hhccccCCCchhHHHHHHHhhceEEeec--CeeecCCCceEEEEecCCCCCceeeecccccccccchHHHhhhhhhcccc
Q 000235 834 DTAVKTSETGYIQRRLVKAMEDIMVKYD--GTVRNSLGDVIQFLYGEDGMDSVWIESQTLDSLKMKKSEFDKAFRFEMDE 911 (1815)
Q Consensus 834 DTAvKTa~sGYlqRrLvk~lEdl~v~YD--gTVRns~g~iiQF~YGeDg~d~~~~e~~~~~~~~~~~~~~~~~~~~~~~~ 911 (1815)
|||||||+||||||||||++||++|.|| ||.+ |-.|--+. ++| ..++ .+.+..+.|....++.+
T Consensus 752 DTALKTAdSGYLtRRLVdvaqDviV~~~DCgT~~---gi~~~~~~-~~~---~~i~-------~l~~~~~GR~~~~di~~ 817 (1156)
T PRK00566 752 DTALKTADSGYLTRRLVDVAQDVIVREDDCGTDR---GIEVTAII-EGG---EVIE-------PLEERILGRVLAEDVVD 817 (1156)
T ss_pred chheeeccceeeehhHHHhhCceEEEECCCCCcC---CEEEEEec-cCC---EEEe-------EhhheeEeEEEhhheec
Confidence 9999999999999999999999999998 5532 31111110 111 0011 11112222222222111
Q ss_pred CCCCcccchHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhHhhhccCCCCCCCccccHHHHHHHhhhhcccCCCCCCCCC
Q 000235 912 ENWNPNYMLQEYIDDLKTIKELRDVFDAEVQKLEADRYQLATEIATSGDSSWPLPVNLKRLIWNAQKTFKVDPRRPSDMH 991 (1815)
Q Consensus 912 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~r~~l~~~~~~~~~~~~~~p~n~~r~i~~~~~~~~~~~~~~~~~~ 991 (1815)
+..+. .+... ...++
T Consensus 818 ~~t~~-------------------------------------~i~~~----------------------------~~~i~ 832 (1156)
T PRK00566 818 PETGE-------------------------------------VIVPA----------------------------GTLID 832 (1156)
T ss_pred CCCCc-------------------------------------EEEcC----------------------------CCccC
Confidence 11000 00000 00111
Q ss_pred hHHHHHHHHHHHHhhcccCCCCcccHHHHhhhhhhhhhhhhhhhhhHHHHHhhccCHHHHHHHHHHHHHHhhcCcccCCC
Q 000235 992 PMEVVEAVDKLQERLKVVPGEDPLSVEAQKNATLFFNILLRSTFASKRVLKEHRLTREAFEWVIGEIESRFLQSLVAPGE 1071 (1815)
Q Consensus 992 p~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~lrs~l~~~~~~~~~~l~~~~~~~~l~ei~~ky~~slv~PGE 1071 (1815)
. ++ ++++. ...+-++.+||+|+|+ .++++|.+||+|.|+ ...+|+.||
T Consensus 833 ~-~~-------~~~i~---------------~~~i~~v~iRS~ltC~---s~~gvC~~CYG~~La------~~~~v~iGe 880 (1156)
T PRK00566 833 E-EI-------ADKIE---------------EAGIEEVKIRSVLTCE---TRHGVCAKCYGRDLA------TGKLVNIGE 880 (1156)
T ss_pred H-HH-------HHHHH---------------HcCCCEEEEcCCeeec---CCCcccHhhhCcccc------CCCCcccCc
Confidence 1 11 11110 1123457789999998 589999999999986 788999999
Q ss_pred chhhHhhhccCCccccccccccccccccccccccccceeeeehhhcccCCCCceEEEeCCCCcchHHHHHHHHhhhcccc
Q 000235 1072 MIGCVAAQSIGEPATQMTLNTFHYAGVSAKNVTLGVPRLREIINVAKKIKTPSLSVFLKPGVNSTKERAKNVQCALEYTT 1151 (1815)
Q Consensus 1072 aVG~iAAQSIGEPaTQMTLnTFH~AGv~~~NVTlGvPRLkEIin~ak~ikTP~mtv~l~~~~~~~~~~a~~v~~~le~~t 1151 (1815)
|||+|||||||||+|||||+|||.+|| ++|.|+||+.|++++ +++|.+.+...+...+
T Consensus 881 aVGiIAAQSIGEPGTQLTmRTFHtGGv---dIT~Glprv~elfea-r~pk~~a~ise~~G~v------------------ 938 (1156)
T PRK00566 881 AVGVIAAQSIGEPGTQLTMRTFHTGGV---DITGGLPRVAELFEA-RKPKGPAIIAEIDGTV------------------ 938 (1156)
T ss_pred ceeEEeeeecCCCccceeeeeeeecce---eccCCccchhhheee-ccCCCceEEEecCCEE------------------
Confidence 999999999999999999999999999 999999999999996 6666553332222111
Q ss_pred ccccceeeEEEEcCCCCceEEEcccc-eeheeccCCCCcccccccCCcEEEEEechhhhhcccCCHHHHHHHHhhhcCCC
Q 000235 1152 LRSVTEATEVWYDPDPMGTIIEEDVE-FVKSYYEMPDEDIAPEKISPWLLRIELNREMMVDKKLSMAAVAEKINQEFDDD 1230 (1815)
Q Consensus 1152 L~dv~~~~~i~ydp~~~~~~i~~d~~-~~~~~~~~~~~~~~~~~~~~~~lrl~l~~~~~~~~~l~~~~i~~~i~~~~~~~ 1230 (1815)
++.-+......++-.+.+ ... .|.+|.
T Consensus 939 --------~~~~~~~~~~~i~i~~~~~~~~-~y~vp~------------------------------------------- 966 (1156)
T PRK00566 939 --------SFGKETKGKRRIVITPDDGEER-EYLIPK------------------------------------------- 966 (1156)
T ss_pred --------EeccccCCceEEEEeCCCCceE-EEEccC-------------------------------------------
Confidence 000000000000000000 000 000000
Q ss_pred ceeeecCCCccceEEEEEEccCCCCCCCCCCCcchhHHHHHHHHhhccccceecccchhhhhccccccccccccccHHHH
Q 000235 1231 LTCIFNDDNADKLILRIRIMNDEAPKGELNDESAEDDVFLKKIESNMLTEMALRGVNLLAVMCHEDVDARRTTSNHLIEI 1310 (1815)
Q Consensus 1231 ~~~~~~~dn~~~~~~~ir~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~G~nl~~vl~~~~vD~~rt~sNdI~eI 1310 (1815)
..++++.+.+ .... .+.| ++| +-|++||
T Consensus 967 -------------~~~~~v~~gd--~v~~---------------G~~l----~~g------------------~~~~~~i 994 (1156)
T PRK00566 967 -------------GKHLLVQEGD--HVEA---------------GDKL----TDG------------------SIDPHDI 994 (1156)
T ss_pred -------------CCeeeecCCC--EEcc---------------CCcc----cCC------------------CCCHHHH
Confidence 0001111100 0000 0001 233 4579999
Q ss_pred HHhhcHHHHHHHHHHHHHHhhhcCcccccchhHHHHHhhhhccce-----------------------------------
Q 000235 1311 IEVLGIEAVRRALLDELRVVISFDGSYVNYRHLAILCDTMTYRGH----------------------------------- 1355 (1815)
Q Consensus 1311 ~~vlGIEAAR~~Ii~Ei~~V~~~~Gi~Vn~RHL~LlaD~MT~~G~----------------------------------- 1355 (1815)
++++||||+|++||+||++||..||++||+|||++|+|+||.+++
T Consensus 995 l~v~G~~~~~~~lv~eiq~vY~~QGv~I~dKHievIvrqM~~kv~i~~~gdt~~~~g~~v~~~~~~~~n~~~~~~g~~~~ 1074 (1156)
T PRK00566 995 LRVLGVEAVQNYLVNEVQKVYRLQGVKINDKHIEVIVRQMLRKVRITDPGDTDFLPGELVDRSEFEEENRKLIAEGKEPA 1074 (1156)
T ss_pred HHhcCHHHHHHHHHHHHHHHHHhCCcccccceeehHHHHHhCCeEEecCCCcCCCCCceeeHHHHHHHHHHHHHCCCCCC
Confidence 999999999999999999999999999999999999999998754
Q ss_pred -----ecccccccccccCCccccccchHHHHHHHHHHHhhcCcccccccccccccCCccccCcccee
Q 000235 1356 -----LMAITRHGINRNDTGPMMRCSFEETVDILLDAAVFAESDYLRGVTENIMLGQLAPIGTGDCS 1417 (1815)
Q Consensus 1356 -----~~~itR~Gi~~~~~spL~~aSFEeT~~~L~~AA~~ge~D~l~gvsenIi~G~~~p~GTG~fd 1417 (1815)
+++|||++++ ..|+|++||||||+++|++||+.|++|+|+|++||||+|+++|+|||.+.
T Consensus 1075 ~~~~~llGItka~l~--t~SflsaASFQeTtkvLt~AAi~gk~D~L~GlkENVIiG~liPaGTG~~~ 1139 (1156)
T PRK00566 1075 TGRPVLLGITKASLA--TESFLSAASFQETTRVLTEAAIKGKVDPLRGLKENVIIGRLIPAGTGLAR 1139 (1156)
T ss_pred cccceeeeeeecccc--cCcccccccccchHHHHHHHHhcCCCCcCCCcccceEecCcccCCCCcch
Confidence 4678888886 46999999999999999999999999999999999999999999999763
No 9
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=100.00 E-value=1.6e-196 Score=1878.32 Aligned_cols=1051 Identities=25% Similarity=0.412 Sum_probs=781.9
Q ss_pred cccceEEEEcCCHHHHHhcceeEEeeCccccCC--CCCCCCCCCCCCCCcCCCccc---------------cccccCCCC
Q 000235 13 AKVRMVQFGILSPDEIRQMSVVQIEHGETTERG--KPKPGGLSDPRLGTIDRKMKC---------------ETCTANMAE 75 (1815)
Q Consensus 13 ~~i~~i~F~~~S~eeI~~~Sv~eI~~~~~~~~~--~p~~gGl~D~rlG~~~~~~~C---------------~TCg~~~~~ 75 (1815)
..+..|+.+++|||+|++||++||++|+|+++. ||+.+||||.|+..+.+++.| +.||..+..
T Consensus 7 ~~f~~i~I~lASPe~Ir~WS~GEV~kpeTINyrT~KPE~dGLFCerIFGP~kd~eC~CGKyk~~~~~g~~C~~CGVEvt~ 86 (1460)
T PRK14906 7 TNFDALRISLASAEDIRSWSHGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECACGKYKRIRFKGIVCERCGVEVTR 86 (1460)
T ss_pred cccceEEEEecCHHHHHhhhceeEcCccccccccCCCCCCCeeeceeccCccCcEEeCccccccCcCCeEcCCCCcEecc
Confidence 478899999999999999999999999999997 999999999999666566666 333333221
Q ss_pred ---cCCccceeeccccccchhhhhHH-----------HHHhcccceecceeccCCchH---------HHH---HHHHhcC
Q 000235 76 ---CPGHFGHLELAKPMFHIGFMKTV-----------LSIMRSVCFNCSKILADEDDH---------KFK---QALKIRN 129 (1815)
Q Consensus 76 ---CpGHfGhIeL~~PV~h~~f~~~v-----------~~iL~~vC~~C~~l~~~~~~~---------~~~---~~~~~~~ 129 (1815)
..-+||||+|+.||.|+|||+.+ .|.|+.|.++-+.+.+++... ... ...++.-
T Consensus 87 s~vRR~RMGhI~La~PV~HiWylk~~ps~i~~lL~~~~k~le~viYf~~~iv~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 166 (1460)
T PRK14906 87 AKVRRERMGHIELAAPVSHIWYFKGSPSRLGYLLDIKPKDLEKVLYFASYIITSVDKEAREEDADDLRDELAADLEELDA 166 (1460)
T ss_pred hHHHHHhcCcccccCcchhhhhccCCcHHHHHHhCCCHHHhhhhhccceeEEeccCcccccccccccccccccccccccc
Confidence 23799999999999999999954 577889998888877765210 000 0000000
Q ss_pred hHHHHHHHHHHh------h------------------------hccccCC------CCCCCCC----CCC-C-Cc-ccc-
Q 000235 130 PKNRLKKILDAC------K------------------------NKTKCEG------GDEIDVP----GQD-G-EE-PLK- 165 (1815)
Q Consensus 130 ~~~~~~~i~~~~------~------------------------~~~~C~~------~~~~~~~----~~~-~-~~-~~~- 165 (1815)
.+.++.+..... . ....+.. ...++.. ..+ . ++ ++.
T Consensus 167 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~e~~~~~~ 246 (1460)
T PRK14906 167 ERDRLIEATRRLSVDYVPEDDEFVDDIGDDERLTAEEVRAEVADIYEEYNERKALRREAFDAFMQIEPKQLISDEALYRE 246 (1460)
T ss_pred cccchhhhhhccccccccccccccccccccccccchhhhhhccccchhhhhhhhhccccchhccccchhhhhhhhhHHHH
Confidence 000000000000 0 0000000 0000000 000 0 00 000
Q ss_pred -------cccCCCCccchhhhhcccchhhhhHHhhccccccCCCCccchhcccCCHHHHHHHHhhcChhhHHHhcCCCCC
Q 000235 166 -------KNKGGCGAQQPKLTIEGMKMIAEYKAQRKKNDDQEQLPEPVERKQTLTAERVLGVLKRISDEDCQLLGLNPKY 238 (1815)
Q Consensus 166 -------~~~~gCg~~~p~i~k~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~p~~v~~ilk~i~~~d~~~l~~~~~~ 238 (1815)
.-.++.|+..-+-....+++..+....+.+.. ..+-.+..+++|+|.--+. |....
T Consensus 247 ~~~~~~~~f~~~~Gaeai~~lL~~~dl~~~~~~l~~~~~-------------~~~~~~k~k~~kRl~~v~~----f~~s~ 309 (1460)
T PRK14906 247 MRLNYSIYFKGGMGAEAVRDLLDAIDLEKEAEELRAIIA-------------NGKGQKREKAVKRLKVVDA----FLKSG 309 (1460)
T ss_pred HHHHhCCCceecchHHHHHHHHHhCCHHHHHHHHHHHHH-------------hhhHHHHHHHHHHHHHHHH----HHccC
Confidence 01223444433333334444333222221110 0122444556677765543 33346
Q ss_pred CCccceEEeecccCCCCCCCC----------chhHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHhhccCCC
Q 000235 239 ARPDWMILQVLPIPPPPVRPS----------DDLTHQLAMIIRHNENLRRQERNGAPAHIISEFAQLLQFHIATYFDNEL 308 (1815)
Q Consensus 239 ~~Pe~~il~~lpVpP~~~RP~----------ddlT~~l~~Ii~~N~~lk~~~~~g~~~~~i~~~~~~LQ~~V~~~~dn~~ 308 (1815)
.+|+||||++||||||++||+ ||||++|++||++|++|+++++.++|..++.+.|++||++|++||||++
T Consensus 310 ~~PewmiL~vlPV~Pp~lRP~V~l~gg~~atsDLn~lyr~II~rNnrLk~l~~~~ap~~ii~nekr~LQeaVd~liDN~~ 389 (1460)
T PRK14906 310 NDPADMILDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGR 389 (1460)
T ss_pred CCHHHHhhhcccCCCCCcCCcEEECCCcccCCchHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHcCCC
Confidence 899999999999999999999 8999999999999999999999999999999999999999999999999
Q ss_pred CCCCcccccCCCChhhhhhhhhhcccccccccCCCCCCCCCceeecCCCCcccccccChHHHhhhccCCcccchhHHHHH
Q 000235 309 PGQPRATQRSGRPIKSICSRLKAKEGRIRGNLMGKRVDFSARTVITPDPTINIDQLGVPWSIALNLTYPETVTPYNIERL 388 (1815)
Q Consensus 309 ~~~p~~~~~~~~p~k~i~qrLkgK~Gr~R~nlmGKRVdfsaRsVIspDP~L~~~evGvP~~~A~~LT~PE~Vt~~Ni~~l 388 (1815)
.|.|. ..+++||+|||+||||||+||||+|||||||||||||||+|||+|++||||||+.||++||+| |++++|
T Consensus 390 ~g~p~-~~~~~rplKsls~~LkGK~GRFRqNLlGKRVDySgRSVIspdP~L~l~e~GlP~~mA~eLf~P-----f~i~~L 463 (1460)
T PRK14906 390 RGRPV-TGPGNRPLKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKP-----FVMKRL 463 (1460)
T ss_pred cCCCC-ccccCCchhHHHHHhcccCcccccccccccccCcCCceEeCCCCCccccccCcHHHHHhcCch-----hHHHHH
Confidence 99876 456789999999999999999999999999999999999999999999999999999999866 666666
Q ss_pred HHHHHcCCCCCCCcccccEEEeCCCceeeccccccccccccccccEeeeecccCCeEEEecCCccccccccceeEEeecC
Q 000235 389 KELVEYGPHPPPGKTGAKYIIRDDGQRLDLRYLKKSSDHHLELGYKVERHLNDGDFVLFNRQPSLHKMSIMGHRIKIMPY 468 (1815)
Q Consensus 389 ~~lv~ng~~~~pg~~~A~~i~~~~g~~~~l~~~~~~~~~~L~~g~~V~Rhl~dgD~VL~NRQPsLHk~Simah~vkv~~~ 468 (1815)
..+ |... .++.|+.++. .....+|.|+||+++||+|||||||||||||||||+++++++
T Consensus 464 ~~~---~~~~--nik~ak~~i~----------------~~~~~v~~vle~vi~gd~VLlNRqPTLHRlsIqAf~~~L~~g 522 (1460)
T PRK14906 464 VEL---EYAA--NIKAAKRAVD----------------RGASYVWDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEG 522 (1460)
T ss_pred HHh---cccc--cHHHHhhHHh----------------hcCCcceeeeeeeeccceeEeccCcccchhccceeeEEecCC
Confidence 554 3211 1122443321 123468999999999999999999999999999999999999
Q ss_pred CeeeecccCCCCCCCCCCcCccccccCCCHhHHHHHHHHccCCCccccCCCCCCceeccccccccceeccc-CC------
Q 000235 469 STFRLNLSVTSPYNADFDGDEMNMHVPQSFETRAEVLELMMVPKCIVSPQSNRPVMGIVQDTLLGCRKITK-RD------ 541 (1815)
Q Consensus 469 ~t~rln~~vc~pyNADFDGDEMn~h~Pqs~~araE~~~l~~~~~~i~sp~~g~pi~g~~QD~l~g~~~lT~-~d------ 541 (1815)
+||||||+||+||||||||||||+|||||++||||++.||++.+||++|++|+|+++++||+|+|+|+||. +|
T Consensus 523 ktIrLhplvC~~fNADFDGDqMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~~~~~~~ 602 (1460)
T PRK14906 523 KAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLTTERDGFEGEG 602 (1460)
T ss_pred ceEEecccccCccccCCcCceeeeecCCCHHHHHHHHHHhcchhcEecCCCCCeeEEeeeeeeeeeEEeeeccccccccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999997 44
Q ss_pred -CccCHHHHHHHHHhcccCCCCCCCCc---------------------ccCccCCcchHHHHHHhcCCCceEeeecccCC
Q 000235 542 -TFIEKDVFMNILMWWEDFDGKVPQPT---------------------ILKPRPLWTGKQVFNLIIPKQINLFRTAAWHA 599 (1815)
Q Consensus 542 -~f~~~~~~~~l~~~~~~~~~~~~~pa---------------------i~kp~~lwtGKqi~s~~lp~~in~~~~~~~~~ 599 (1815)
+|.+.+++++++.+...++ ++.|. +.++...|+||+||+.+||++++|
T Consensus 603 ~~F~~~~e~~~a~~~~~~~~--l~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~tt~Gr~Ifn~ilP~d~~f-------- 672 (1460)
T PRK14906 603 RTFADFDDALNAYDARADLD--LQAKIVVRLSRDMTVRGSYGDLEETKAGERIETTVGRIIFNQVLPEDYPY-------- 672 (1460)
T ss_pred ceeCCHHHHHHHHhcCCCcc--ccccEEEecCcccccccccccccCCCCCceEECCCCEEEEecccCCCccc--------
Confidence 7999999999887532222 11111 122345799999999999985443
Q ss_pred CCCCCcCCCCCcEEEEecCeeeecccccccccCCcccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCceeeeccCcc
Q 000235 600 DNDKGILTAGDTLVRIEKGELLSGTLCKKTLGTSTGSLIHVIWEEVGPDAARKFLGHTQWLVNYWLLQNAFSIGIGDTIA 679 (1815)
Q Consensus 600 ~~~~~~~~~~d~~v~i~~gell~g~ldK~~~g~s~~~Lih~i~~~~G~~~a~~~l~~~q~l~~~~l~~~GfSigi~D~~~ 679 (1815)
++++|+|+.+| +||+.+|++||.+.+..|||++++|+++|++.+||||||+|+.+
T Consensus 673 ---------------------vN~~l~KK~Lg----~LI~~i~~~~G~~~t~~fLD~Ik~LGf~yaT~sG~SIgi~Di~i 727 (1460)
T PRK14906 673 ---------------------LNYKMVKKDIG----RLVNDCCNRYSTAEVEPILDGIKKTGFHYATRAGLTVSVYDATI 727 (1460)
T ss_pred ---------------------ccceeeHHHHH----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhCCEEEeeccccc
Confidence 45689999998 79999999999999999999999999999999999999999987
Q ss_pred ChhhHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCChHHHHHhcCC
Q 000235 680 DAKTMETINDTISKAKNNVKNLIKQAQDKSLEPEPGRTMMESFENKVNQVLNTARDEAGSSAQKSLSESNNLKAMVTAGS 759 (1815)
Q Consensus 680 ~~~~~~~~~~~i~~a~~~v~~~~~~~~~~~l~~~~~~~~~~~~e~~v~~~ln~~~~~~~~~~~~~l~~~N~~~~M~~sGs 759 (1815)
+++ +.++|++|+++|++++++|++|.++. .|+ +.+++++|+++++++++.+++++++.|++++|+.|||
T Consensus 728 p~~----K~~iI~~A~~~V~ei~~~y~~G~iT~------~Er-~~kVi~iw~~a~d~v~~~~~~~l~~~N~i~mMa~SGA 796 (1460)
T PRK14906 728 PDD----KPEILAEADEKVAAIDEDYEDGFLSE------RER-HKQVVDIWTEATEEVGEAMLAGFDEDNPIYMMADSGA 796 (1460)
T ss_pred ChH----HHHHHHHHHHHHHHHHHHHHcCCCcH------HHH-HHHHHHHHHHHHHHHHHHHHHhcccCCCeEeeeeccC
Confidence 764 58899999999999999999999863 344 7999999999999999999999999999999999999
Q ss_pred CCcccchhhhhhhcccc-ccCCCccCCCCCCCCCCCCCCCCCCCccccccccCCcCCCChhhhhhhccCCCcchhhhccc
Q 000235 760 KGSFINISQMTACVGQQ-NVEGKRIPFGFVDRTLPHFTKDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVK 838 (1815)
Q Consensus 760 KGS~~N~~Qi~~~lGQQ-~~eG~Rip~~~~~rtLp~f~~~d~~~~~~Gfv~~sf~~GL~p~EfFfH~m~gReGLiDTAvK 838 (1815)
|||..||.||+||+||| ...|++|. .+|.+||++||+|.|||||||||||||+|||||
T Consensus 797 RGS~~QI~QLaGmRGlma~p~G~iIe---------------------~PI~SnFrEGLt~~EyFiSt~GaRKGL~DTALK 855 (1460)
T PRK14906 797 RGNIKQIRQLAGMRGLMADMKGEIID---------------------LPIKANFREGLSVLEYFISTHGARKGLVDTALR 855 (1460)
T ss_pred cccHHHHHHHHhcccceecCCCCccc---------------------cccccccccCCCHHHHHHHcccccchhhhhhhh
Confidence 99999999999999997 57887763 259999999999999999999999999999999
Q ss_pred cCCCchhHHHHHHHhhceEEeec--CeeecCCCceEEEEecCCCCCceeeecccccccccchHHHhhhhhhccccCCCCc
Q 000235 839 TSETGYIQRRLVKAMEDIMVKYD--GTVRNSLGDVIQFLYGEDGMDSVWIESQTLDSLKMKKSEFDKAFRFEMDEENWNP 916 (1815)
Q Consensus 839 Ta~sGYlqRrLvk~lEdl~v~YD--gTVRns~g~iiQF~YGeDg~d~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 916 (1815)
||+||||||||||++|||+|..+ ||.+ |-.| ..+.. .. .+.+..+.|....++.++
T Consensus 856 TAdSGYLTRRLVdVaQDViV~e~DCgT~~---Gi~v-----------~~~~~--~~--~l~~ri~GR~~~~di~~~---- 913 (1460)
T PRK14906 856 TADSGYLTRRLVDVAQDVIVREEDCGTDE---GVTY-----------PLVKP--KG--DVDTNLIGRCLLEDVCDP---- 913 (1460)
T ss_pred ccccchHHHHHHHhhhheEEEeccCCCCC---CEEE-----------EEeec--cc--chhheeeeEEEHhhhcCC----
Confidence 99999999999999999999875 5532 2112 11100 00 001111111111111000
Q ss_pred ccchHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhHhhhccCCCCCCCccccHHHHHHHhhhhcccCCCCCCCCChHHHH
Q 000235 917 NYMLQEYIDDLKTIKELRDVFDAEVQKLEADRYQLATEIATSGDSSWPLPVNLKRLIWNAQKTFKVDPRRPSDMHPMEVV 996 (1815)
Q Consensus 917 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~r~~l~~~~~~~~~~~~~~p~n~~r~i~~~~~~~~~~~~~~~~~~p~~~~ 996 (1815)
.++ +.++ ....++....+
T Consensus 914 -----------------------------------------~g~--~i~~-------------------~~~~I~~~~~~ 931 (1460)
T PRK14906 914 -----------------------------------------NGE--VLLS-------------------AGDYIESMDDL 931 (1460)
T ss_pred -----------------------------------------CCC--EEEe-------------------CCCeeCcHHHH
Confidence 000 0000 00111111101
Q ss_pred HHHHHHHHhhcccCCCCcccHHHHhhhhhhhhhhhhhhhhhHHHHHhhccCHHHHHHHHHHHHHHhhcCcccCCCchhhH
Q 000235 997 EAVDKLQERLKVVPGEDPLSVEAQKNATLFFNILLRSTFASKRVLKEHRLTREAFEWVIGEIESRFLQSLVAPGEMIGCV 1076 (1815)
Q Consensus 997 ~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~lrs~l~~~~~~~~~~l~~~~~~~~l~ei~~ky~~slv~PGEaVG~i 1076 (1815)
+++ .+..+.++.+||+|+|+ .++++|++||+|.|+ ...+|+.|||||||
T Consensus 932 -------~~i---------------~~~gi~~v~iRS~ltC~---s~~gvC~kCYG~dLa------tg~~V~iGeaVGiI 980 (1460)
T PRK14906 932 -------KRL---------------VEAGVTKVQIRTLMTCH---AEYGVCQKCYGWDLA------TRRPVNIGTAVGII 980 (1460)
T ss_pred -------HHH---------------HHCCCCEEEEeCCeeEC---CCCCChhhCcCCccc------CCcEeccccceeee
Confidence 111 11234567899999998 689999999999997 78899999999999
Q ss_pred hhhccCCccccccccccccccccccccccccceeeeehhhcccCCCCceEEEeCCCCcchHHHHHHHHhhhccccccccc
Q 000235 1077 AAQSIGEPATQMTLNTFHYAGVSAKNVTLGVPRLREIINVAKKIKTPSLSVFLKPGVNSTKERAKNVQCALEYTTLRSVT 1156 (1815)
Q Consensus 1077 AAQSIGEPaTQMTLnTFH~AGv~~~NVTlGvPRLkEIin~ak~ikTP~mtv~l~~~~~~~~~~a~~v~~~le~~tL~dv~ 1156 (1815)
||||||||+|||||+|||.+||++++||.|+||+.|++.+ +++|.+.+.-.+..
T Consensus 981 AAQSIGEPGTQLTMRTFHtGGv~~~dit~GLpRv~eLfEa-r~pk~~a~i~e~~G------------------------- 1034 (1460)
T PRK14906 981 AAQSIGEPGTQLTMRTFHSGGVAGDDITQGLPRVAELFEA-RKPKGEAVLAEISG------------------------- 1034 (1460)
T ss_pred eeeecCCCcceeeeeeeecccccccccccCcchhhhheee-ccCCCceeeeccCC-------------------------
Confidence 9999999999999999999999989999999999999996 44554432211111
Q ss_pred eeeEEEEcCCC-CceE-EEcccceeheeccCCCCcccccccCCcEEEEEechhhhhcccCCHHHHHHHHhhhcCCCceee
Q 000235 1157 EATEVWYDPDP-MGTI-IEEDVEFVKSYYEMPDEDIAPEKISPWLLRIELNREMMVDKKLSMAAVAEKINQEFDDDLTCI 1234 (1815)
Q Consensus 1157 ~~~~i~ydp~~-~~~~-i~~d~~~~~~~~~~~~~~~~~~~~~~~~lrl~l~~~~~~~~~l~~~~i~~~i~~~~~~~~~~~ 1234 (1815)
.++| +.+. ...+ |..+..-.+ .|.+|..
T Consensus 1035 -~v~i--~~~~~~~~i~i~~~~~~~~-~y~v~~~---------------------------------------------- 1064 (1460)
T PRK14906 1035 -TLQI--TGDKTEKTLTIHDQDGNSR-EYVVSAR---------------------------------------------- 1064 (1460)
T ss_pred -EEEe--ccCCCceEEEEECCCCcee-EEEccCC----------------------------------------------
Confidence 0011 0000 0000 000000000 0011100
Q ss_pred ecCCCccceEEEEE--EccCCCCCCCCCCCcchhHHHHHHHHhhccccceecccchhhhhccccccccccccccHHHHHH
Q 000235 1235 FNDDNADKLILRIR--IMNDEAPKGELNDESAEDDVFLKKIESNMLTEMALRGVNLLAVMCHEDVDARRTTSNHLIEIIE 1312 (1815)
Q Consensus 1235 ~~~dn~~~~~~~ir--~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~G~nl~~vl~~~~vD~~rt~sNdI~eI~~ 1312 (1815)
.+++ +.+ . +. .. ....| ++| +-|+++|++
T Consensus 1065 ----------~~~~~~v~~-g--------d~---v~-----~G~~l----~~G------------------~~~p~~il~ 1095 (1460)
T PRK14906 1065 ----------VQFMPGVED-G--------VE---VR-----VGQQI----TRG------------------SVNPHDLLR 1095 (1460)
T ss_pred ----------cccccccCC-C--------CE---Ec-----cCCCc----cCC------------------CCCHHHHHH
Confidence 0000 000 0 00 00 00001 133 458999999
Q ss_pred hhcHHHHHHHHHHHHHHhhhcCcccccchhHHHHHhhhhccce-------------------------------------
Q 000235 1313 VLGIEAVRRALLDELRVVISFDGSYVNYRHLAILCDTMTYRGH------------------------------------- 1355 (1815)
Q Consensus 1313 vlGIEAAR~~Ii~Ei~~V~~~~Gi~Vn~RHL~LlaD~MT~~G~------------------------------------- 1355 (1815)
+.|+||+.++||+||++||..||+.||++||++|+.+|+.+-+
T Consensus 1096 ~~g~~~~~~ylv~eVQ~VYr~QGV~InDKHiEvIvRQMl~kV~I~d~Gdt~fl~Ge~vd~~~~~~~n~~~~~~g~~pa~~ 1175 (1460)
T PRK14906 1096 LTDPNTTLRYIVSQVQDVYVSQGVDINDKHIEVIARQMLRKVAVTNPGDSDYLPGRQVNRYEFEDTANNLILEGKQPPVG 1175 (1460)
T ss_pred hcCHHHHHHHHHHHHHHHHHhcCceeccccHHHHHHHHhceEEEecCCCcCCCCCCeeeHHHHHHHHHHHHHcCCCCcee
Confidence 9999999999999999999999999999999999999998864
Q ss_pred ---ecccccccccccCCccccccchHHHHHHHHHHHhhcCcccccccccccccCCccccCccce
Q 000235 1356 ---LMAITRHGINRNDTGPMMRCSFEETVDILLDAAVFAESDYLRGVTENIMLGQLAPIGTGDC 1416 (1815)
Q Consensus 1356 ---~~~itR~Gi~~~~~spL~~aSFEeT~~~L~~AA~~ge~D~l~gvsenIi~G~~~p~GTG~f 1416 (1815)
+++||+..++ ..|+|+.|||+||+++|++||+.|++|.|.|++||||+|++||+|||..
T Consensus 1176 ~p~llGITKasL~--t~SflSaASFQeTtrVLt~AAi~gk~D~L~GLKENVIiG~lIPAGTG~~ 1237 (1460)
T PRK14906 1176 QPLLLGITKASLA--TDSWLSAASFQETTKVLTDAAIEGKVDHLAGLKENVIIGKPIPAGTGLS 1237 (1460)
T ss_pred eeEEeeeeecccc--cccccccccccchHHHHHHHHhcCCCCcCCCCccceEecceecCCCCcc
Confidence 4477777775 3699999999999999999999999999999999999999999999963
No 10
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=100.00 E-value=1.7e-189 Score=1877.61 Aligned_cols=853 Identities=26% Similarity=0.402 Sum_probs=660.7
Q ss_pred cccccceEEEEcCCHHHHHhcceeEEeeCccccCC--CCCCCCCCCCCCCCcCCCccc----------------cccccC
Q 000235 11 EVAKVRMVQFGILSPDEIRQMSVVQIEHGETTERG--KPKPGGLSDPRLGTIDRKMKC----------------ETCTAN 72 (1815)
Q Consensus 11 ~~~~i~~i~F~~~S~eeI~~~Sv~eI~~~~~~~~~--~p~~gGl~D~rlG~~~~~~~C----------------~TCg~~ 72 (1815)
....+..|+.+++|||+|++||++||++|+|+++. +|+.+||||.|+..+.+++.| ..||..
T Consensus 1392 ~~~~~~~i~i~lASpe~I~~ws~GeV~kpeTinyrt~kPe~dGLFcerIFGp~kd~eC~Cgkyk~~~~~g~~~C~~Cgve 1471 (2890)
T PRK09603 1392 RPKDFSSFQLTLASPEKIHSWSYGEVKKPETINYRTLKPERDGLFCMKIFGPTKDYECLCGKYKKPRFKDIGTCEKCGVA 1471 (2890)
T ss_pred cccCcceEEEEecCHHHHHHhhceeEccccccccccCccCCCCEeeceeccCccCcEEeCCCcccccCCCCEEcCCCCcE
Confidence 35688999999999999999999999999999997 999999999999665556655 444433
Q ss_pred CCC---cCCccceeeccccccchhhhhHH-----------HHHhcccceecceeccCCchH--------HHHHHHHhcCh
Q 000235 73 MAE---CPGHFGHLELAKPMFHIGFMKTV-----------LSIMRSVCFNCSKILADEDDH--------KFKQALKIRNP 130 (1815)
Q Consensus 73 ~~~---CpGHfGhIeL~~PV~h~~f~~~v-----------~~iL~~vC~~C~~l~~~~~~~--------~~~~~~~~~~~ 130 (1815)
... ...+||||+|+.||.|+||++.+ .+.|+.|.++-..+.+++... .+.....+ .
T Consensus 1472 vt~s~vRR~RmGhI~La~Pv~HiWy~k~~ps~i~~ll~~~~k~le~viy~~~~~v~~~~~~~~~~~~~~~~~~~~~~-~- 1549 (2890)
T PRK09603 1472 ITHSKVRRFRMGHIELATPVAHIWYVNSLPSRIGTLLGVKMKDLERVLYYEAYIVKEPGEAAYDNEGTKLVMKYDIL-N- 1549 (2890)
T ss_pred echhHhHHHhcCceeecCcceeeeccCCCchHHHHHhCCCHHHhhhhhcceeeEEecCCccccccccccchhhhhhh-h-
Confidence 221 24799999999999999999954 577889998888888776421 11110001 0
Q ss_pred HHHHHHHHHHhhhccccCCCCCCCCCCCCCCcccccccCCCCccchhhhhcccchhhhhHHhhccccccCCCCccchhcc
Q 000235 131 KNRLKKILDACKNKTKCEGGDEIDVPGQDGEEPLKKNKGGCGAQQPKLTIEGMKMIAEYKAQRKKNDDQEQLPEPVERKQ 210 (1815)
Q Consensus 131 ~~~~~~i~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~gCg~~~p~i~k~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 210 (1815)
...+.++.+.. . .. .+ ..++|+..-+-....+++..+....+.+....
T Consensus 1550 ~~~~~~~~~~~---~-~~---~f--------------~~~~Gaeai~~lL~~~dl~~~~~~l~~~~~~~----------- 1597 (2890)
T PRK09603 1550 EEQYQNISRRY---E-DR---GF--------------VAQMGGEAIKDLLEEIDLITLLQSLKEEVKDT----------- 1597 (2890)
T ss_pred HHHHHHHHHHc---C-cc---cc--------------eechhHHHHHHHHHhCCHHHHHHHHHHHHHhc-----------
Confidence 01111221110 0 00 00 12355544333334455444333222211100
Q ss_pred cCCHHHHHHHHhhcChhhHHHhcCCCCCCCccceEEeecccCCCCCCCC----------chhHHHHHHHHHHHHHHHHHH
Q 000235 211 TLTAERVLGVLKRISDEDCQLLGLNPKYARPDWMILQVLPIPPPPVRPS----------DDLTHQLAMIIRHNENLRRQE 280 (1815)
Q Consensus 211 ~l~p~~v~~ilk~i~~~d~~~l~~~~~~~~Pe~~il~~lpVpP~~~RP~----------ddlT~~l~~Ii~~N~~lk~~~ 280 (1815)
-.-.+...++|+|.--+..+ ...++|+||||++||||||++||+ ||||++|++||++|++|++++
T Consensus 1598 -~~~~~~~~~~krl~~v~~f~----~s~~~PewmiL~~lPV~Pp~lRP~v~l~gg~~a~sDln~lyr~II~rNnrLk~l~ 1672 (2890)
T PRK09603 1598 -NSDAKKKKLIKRLKVVESFL----NSGNRPEWMMLTVLPVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRLM 1672 (2890)
T ss_pred -cHHHHHHHHHHHHHHHHHHH----hcCCChHheeeeeeccCCCcccCcEEeCCCcccCCCccHHHHHHHHHHHHHHHHH
Confidence 01122344567775544333 346899999999999999999999 899999999999999999999
Q ss_pred HcCCChhhHHHHHHHHHHHHHhhccCCCCCCCcccccCCCChhhhhhhhhhcccccccccCCCCCCCCCceeecCCCCcc
Q 000235 281 RNGAPAHIISEFAQLLQFHIATYFDNELPGQPRATQRSGRPIKSICSRLKAKEGRIRGNLMGKRVDFSARTVITPDPTIN 360 (1815)
Q Consensus 281 ~~g~~~~~i~~~~~~LQ~~V~~~~dn~~~~~p~~~~~~~~p~k~i~qrLkgK~Gr~R~nlmGKRVdfsaRsVIspDP~L~ 360 (1815)
+.++|..++.+.|++||++|++||||+..|.+. ..+++||+|||+||||||+||||+|||||||||||||||+|||+|+
T Consensus 1673 ~~~ap~~ii~nek~~LQ~aVd~l~DN~~~~~~~-~~~~~rplKsls~~LkGK~GRFRqNLlGKRVDySgRSVI~pdP~L~ 1751 (2890)
T PRK09603 1673 ELGAPEIIVRNEKRMLQEAVDVLFDNGRSTNAV-KGANKRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLK 1751 (2890)
T ss_pred HcCCCceehHHHHHHHHHHHHHHhccccccccc-cCCCCCcchhHHHHhcCCCCccccccccccccCcCCceEeCCCCcc
Confidence 999999999999999999999999999988754 4567899999999999999999999999999999999999999999
Q ss_pred cccccChHHHhhhccCCcccchhHHHHHHHHHHcCCCCCCCcccccEEEeCCCceeeccccccccccccccccEeeeecc
Q 000235 361 IDQLGVPWSIALNLTYPETVTPYNIERLKELVEYGPHPPPGKTGAKYIIRDDGQRLDLRYLKKSSDHHLELGYKVERHLN 440 (1815)
Q Consensus 361 ~~evGvP~~~A~~LT~PE~Vt~~Ni~~l~~lv~ng~~~~pg~~~A~~i~~~~g~~~~l~~~~~~~~~~L~~g~~V~Rhl~ 440 (1815)
+||||||+.||++||+|+ + +++|+.||+... ++.|+.+ .+.....+|.|+|||+
T Consensus 1752 l~e~GvP~~mA~eL~~P~-----~---i~~L~~~G~~~~--lk~ak~~----------------i~~~~~~v~~vlr~vi 1805 (2890)
T PRK09603 1752 MDECGLPKNMALELFKPH-----L---LSKLEERGYATT--LKQAKRM----------------IEQKSNEVWECLQEIT 1805 (2890)
T ss_pred cccccChHHHHHHhCChH-----H---HHHHHHcCCccC--HHHHHHH----------------HHhccCccEEEEEeee
Confidence 999999999999999984 4 466788886421 1112221 1223456899999999
Q ss_pred cCCeEEEecCCccccccccceeEEeecCCeeeecccCCCCCCCCCCcCccccccCCCHhHHHHHHHHccCCCccccCCCC
Q 000235 441 DGDFVLFNRQPSLHKMSIMGHRIKIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFETRAEVLELMMVPKCIVSPQSN 520 (1815)
Q Consensus 441 dgD~VL~NRQPsLHk~Simah~vkv~~~~t~rln~~vc~pyNADFDGDEMn~h~Pqs~~araE~~~l~~~~~~i~sp~~g 520 (1815)
+||+|||||||||||||||||+|||++|+||||||+||+||||||||||||||||||++|||||+.||++.+||+||++|
T Consensus 1806 ~gd~VLlNRqPTLHR~sIqAf~~~l~~gktIrLhplvC~~fNADFDGDqMnvHvPqS~eA~aEa~~LM~s~~nilsP~~G 1885 (2890)
T PRK09603 1806 EGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLSSMNILLPASG 1885 (2890)
T ss_pred cCCeEEecCCCccccccceeeeEEEecCceEEeccccCCcccCCCCCceeEEeecCCHHHHHHHHHHhcccceEEEcCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCceeccccccccceecccCCC--------ccCHHHHHHHHHhcccCCCCCCCCcccCccCCcc--hHHHHHHhcCCCce
Q 000235 521 RPVMGIVQDTLLGCRKITKRDT--------FIEKDVFMNILMWWEDFDGKVPQPTILKPRPLWT--GKQVFNLIIPKQIN 590 (1815)
Q Consensus 521 ~pi~g~~QD~l~g~~~lT~~d~--------f~~~~~~~~l~~~~~~~~~~~~~pai~kp~~lwt--GKqi~s~~lp~~in 590 (1815)
+|+++++||+|+|+|+||.+|+ |.+.++++.++.. ..++...+.+++++|+.||| ||||||.+||+.++
T Consensus 1886 ~Pi~~p~QD~vlG~y~LT~~~~~~~~~~~~F~~~~e~~~~~~~-~~~~~~~~i~~~~~p~~l~Tt~GK~ifs~ilP~~~~ 1964 (2890)
T PRK09603 1886 KAVAIPSQDMVLGLYYLSLEKSGVKGEHKLFSSVNEIITAIDT-KELDIHAKIRVLDQGNIIATSAGRMIIKSILPDFIP 1964 (2890)
T ss_pred ceeEEeecceeeeeEEeeccccCCCCccceeCCHHHHHHHHHc-CCCccCCcceeecCCcEEEcCccceeeeccCccccc
Confidence 9999999999999999999996 4556666543321 22222234567778999999 99999999998665
Q ss_pred EeeecccCCCCCCCcCCCCCcEEEEecCeeeecccccccccCCcccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCc
Q 000235 591 LFRTAAWHADNDKGILTAGDTLVRIEKGELLSGTLCKKTLGTSTGSLIHVIWEEVGPDAARKFLGHTQWLVNYWLLQNAF 670 (1815)
Q Consensus 591 ~~~~~~~~~~~~~~~~~~~d~~v~i~~gell~g~ldK~~~g~s~~~Lih~i~~~~G~~~a~~~l~~~q~l~~~~l~~~Gf 670 (1815)
+. +++|.|||+.|| +|||.+|++||.+.|+.|||++++|+++|++.+||
T Consensus 1965 ~~---------------------------~~n~~ldKK~Lg----~LI~~i~~~yG~~~t~~fLD~lk~LGf~yat~~G~ 2013 (2890)
T PRK09603 1965 TD---------------------------LWNRPMKKKDIG----VLVDYVHKVGGIGITATFLDNLKTLGFRYATKAGI 2013 (2890)
T ss_pred cc---------------------------cEeeeechHHHH----HHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHhCCE
Confidence 32 235779999998 89999999999999999999999999999999999
Q ss_pred eeeeccCccChhhHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcC----
Q 000235 671 SIGIGDTIADAKTMETINDTISKAKNNVKNLIKQAQDKSLEPEPGRTMMESFENKVNQVLNTARDEAGSSAQKSLS---- 746 (1815)
Q Consensus 671 Sigi~D~~~~~~~~~~~~~~i~~a~~~v~~~~~~~~~~~l~~~~~~~~~~~~e~~v~~~ln~~~~~~~~~~~~~l~---- 746 (1815)
||||+|++++++ ++++|++|++++.++.++|++|.++.. ..+.++.++|+++++++++.+++.+.
T Consensus 2014 SIgI~Dl~ip~~----K~~iI~~A~~eV~ei~~~y~~G~it~~-------Er~~kvid~w~~~~d~v~~~~~~~l~~~~~ 2082 (2890)
T PRK09603 2014 SISMEDIITPKD----KQKMVEKAKVEVKKIQQQYDQGLLTDQ-------ERYNKIIDTWTEVNDKMSKEMMTAIAKDKE 2082 (2890)
T ss_pred eeeeccCcccHH----HHHHHHHHHHHHHHHHHHHHcCCCCcc-------HHHHHHHHHHHHHHHHHHHHHHHHhhhcCC
Confidence 999999999865 588999999999999999999999753 23678888999999999998877663
Q ss_pred CCChHHHHHhcCCCCcccchhhhhhhccccccCCCccCCCCCCCCCCCCCCCCCCCccccccccCCcCCCChhhhhhhcc
Q 000235 747 ESNNLKAMVTAGSKGSFINISQMTACVGQQNVEGKRIPFGFVDRTLPHFTKDDYGPESRGFVENSYLRGLTPQEFFFHAM 826 (1815)
Q Consensus 747 ~~N~~~~M~~sGsKGS~~N~~Qi~~~lGQQ~~eG~Rip~~~~~rtLp~f~~~d~~~~~~Gfv~~sf~~GL~p~EfFfH~m 826 (1815)
+.|++++|+.||||||.+|++||+||+|||..-..+| . ...|.+||++||+|+|||||||
T Consensus 2083 ~~N~i~mMa~SGARGS~~NI~QLaGmrGqMakp~G~i--------------i------e~PI~snFrEGLtp~EyFfst~ 2142 (2890)
T PRK09603 2083 GFNSIYMMADSGARGSAAQIRQLSAMRGLMTKPDGSI--------------I------ETPIISNFKEGLNVLEYFNSTH 2142 (2890)
T ss_pred CCCcHHHHHhccccccHHHHHHHHHcCCcEECCCCCc--------------c------cChhhcCcccCCCHHHHHHhcc
Confidence 5799999999999999999999999999985322111 1 1248999999999999999999
Q ss_pred CCCcchhhhccccCCCchhHHHHHHHhhceEEeecCeeecCCC-ceEEEEecCCCCCceeeecccccccccchHHHhhhh
Q 000235 827 GGREGLIDTAVKTSETGYIQRRLVKAMEDIMVKYDGTVRNSLG-DVIQFLYGEDGMDSVWIESQTLDSLKMKKSEFDKAF 905 (1815)
Q Consensus 827 ~gReGLiDTAvKTa~sGYlqRrLvk~lEdl~v~YDgTVRns~g-~iiQF~YGeDg~d~~~~e~~~~~~~~~~~~~~~~~~ 905 (1815)
||||||||||||||+||||||||||++|||+|..|.+-.. .| .|-.+..|++-+.+ +.+..+.|..
T Consensus 2143 GaRKGLiDTALKTAdSGYLTRRLVdvaQDviI~e~DCgT~-~Gi~v~~~~~~~~~i~~------------l~~ri~GR~~ 2209 (2890)
T PRK09603 2143 GARKGLADTALKTANAGYLTRKLIDVSQNVKVVSDDCGTH-EGIEITDIAVGSELIEP------------LEERIFGRVL 2209 (2890)
T ss_pred ccccchhhhhhhccccchhhhhHHHhhcceEEEeccCCCC-CCeEEEEeecCCeeecc------------hhheeeeEEE
Confidence 9999999999999999999999999999999998733222 13 33333333221111 1122222222
Q ss_pred hhccccCCCCcccchHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhHhhhccCCCCCCCccccHHHHHHHhhhhcccCCC
Q 000235 906 RFEMDEENWNPNYMLQEYIDDLKTIKELRDVFDAEVQKLEADRYQLATEIATSGDSSWPLPVNLKRLIWNAQKTFKVDPR 985 (1815)
Q Consensus 906 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~r~~l~~~~~~~~~~~~~~p~n~~r~i~~~~~~~~~~~~ 985 (1815)
..++.++..+.. +...
T Consensus 2210 ~~di~~p~t~~~-------------------------------------i~~~--------------------------- 2225 (2890)
T PRK09603 2210 LEDVIDPITNEI-------------------------------------LLYA--------------------------- 2225 (2890)
T ss_pred HhheEcCCCCcE-------------------------------------EEcC---------------------------
Confidence 222211111000 0000
Q ss_pred CCCCCChHHHHHHHHHHHHhhcccCCCCcccHHHHhhhhhhhhhhhhhhhhhHHHHHhhccCHHHHHHHHHHHHHHhhcC
Q 000235 986 RPSDMHPMEVVEAVDKLQERLKVVPGEDPLSVEAQKNATLFFNILLRSTFASKRVLKEHRLTREAFEWVIGEIESRFLQS 1065 (1815)
Q Consensus 986 ~~~~~~p~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~lrs~l~~~~~~~~~~l~~~~~~~~l~ei~~ky~~s 1065 (1815)
...++. +++ +++ ....+-++.+||.|+|+ ..+++|++||+|.|+ ...
T Consensus 2226 -~~~I~~-~~~-------~~i---------------~~~gi~~v~iRS~LtC~---s~~gvC~~CYG~dLa------~g~ 2272 (2890)
T PRK09603 2226 -DTLIDE-EGA-------KKV---------------VEAGIKSITIRTPVTCK---APKGVCAKCYGLNLG------EGK 2272 (2890)
T ss_pred -CcCcCH-HHH-------HHH---------------HHcCCCEEEEcCcceec---CCCcChhhhcCCccc------CCC
Confidence 001111 111 111 01123467799999998 689999999999997 788
Q ss_pred cccCCCchhhHhhhccCCccccccccccccccccccc
Q 000235 1066 LVAPGEMIGCVAAQSIGEPATQMTLNTFHYAGVSAKN 1102 (1815)
Q Consensus 1066 lv~PGEaVG~iAAQSIGEPaTQMTLnTFH~AGv~~~N 1102 (1815)
+|+.|||||+|||||||||+|||||+|||.+||++..
T Consensus 2273 ~V~iGeaVGiIAAQSIGEPGTQLTMRTFHtGGvas~~ 2309 (2890)
T PRK09603 2273 MSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTASRS 2309 (2890)
T ss_pred CccCCceeeEEeecccCCCccccchhhheeccccccc
Confidence 9999999999999999999999999999999997753
No 11
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=100.00 E-value=1.1e-189 Score=1872.16 Aligned_cols=1145 Identities=26% Similarity=0.375 Sum_probs=799.0
Q ss_pred ccccceEEEEcCCHHHHHhcceeEEeeCccccCC--CCCCCCCCCCCCCCcCCCcc---------------ccccccCCC
Q 000235 12 VAKVRMVQFGILSPDEIRQMSVVQIEHGETTERG--KPKPGGLSDPRLGTIDRKMK---------------CETCTANMA 74 (1815)
Q Consensus 12 ~~~i~~i~F~~~S~eeI~~~Sv~eI~~~~~~~~~--~p~~gGl~D~rlG~~~~~~~---------------C~TCg~~~~ 74 (1815)
...+..|+.+++|||+|++||++||++|+|+++. +|+.+||||.|+..+.+++. |+.||....
T Consensus 1445 ~~~~~~i~i~laSPe~I~~Ws~GeV~kpeTinyrt~kPE~dGLFcerIFGp~kd~eC~Cgkyk~~~~~g~~C~~Cgvevt 1524 (2836)
T PRK14844 1445 AQSFNEVSISIASPESIKRMSYGEIEDVSTANYRTFKVEKGGLFCPKIFGPVNDDECLCGKYKKRRHRGRICEKCGVEVT 1524 (2836)
T ss_pred hcccceEEEEecCHHHHHhhhceeECCcccccccCCCCCCCCeehhhhcCCCcCcEEecccccccccCCcCcCCCCcEee
Confidence 4578899999999999999999999999999997 99999999999854444444 666665544
Q ss_pred Cc---CCccceeeccccccchhhhhHH-----------HHHhcccceecceeccCCchHHHHHHHHhcChHHHHHHHHHH
Q 000235 75 EC---PGHFGHLELAKPMFHIGFMKTV-----------LSIMRSVCFNCSKILADEDDHKFKQALKIRNPKNRLKKILDA 140 (1815)
Q Consensus 75 ~C---pGHfGhIeL~~PV~h~~f~~~v-----------~~iL~~vC~~C~~l~~~~~~~~~~~~~~~~~~~~~~~~i~~~ 140 (1815)
.+ ..+||||+|+.||.|+||++.+ .|.|+.|.++-+.+.+++....+.... +.. ...+.++.+.
T Consensus 1525 ~s~vRR~RmGhI~La~PV~HiWy~k~~ps~i~~lL~~~~k~le~v~y~~~~~v~~~~~~~~~~~~-~~~-~~~~~~~~~~ 1602 (2836)
T PRK14844 1525 SSKVRRERMGHIELASPVAHIWFLKSLPSRIGALLDMSLRDIENILYSDNYIVIDPLVSPFEKGE-IIS-EKAYNEAKDS 1602 (2836)
T ss_pred echhhHhhcCceeecCcceeeecccCCcHHHHHHhCCCHHHhhheeeeeeEEEecCCCCchhhhh-hcc-HHHHHHHHHh
Confidence 33 4899999999999999999954 577899999988888877544332211 111 1112222221
Q ss_pred hhhccccCCCCCCCCCCCCCCcccccccCCCCccchhhhhcccchhhhhHHhhccccccCCCCccchhcccCCHHHHHHH
Q 000235 141 CKNKTKCEGGDEIDVPGQDGEEPLKKNKGGCGAQQPKLTIEGMKMIAEYKAQRKKNDDQEQLPEPVERKQTLTAERVLGV 220 (1815)
Q Consensus 141 ~~~~~~C~~~~~~~~~~~~~~~~~~~~~~gCg~~~p~i~k~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~p~~v~~i 220 (1815)
. .. +. + ..+.|+..-+-....+++..+....+.+.... -+..+..++
T Consensus 1603 ---~---~~-~~----------~----~~~~Gaeai~~lL~~~dl~~~~~~l~~~~~~~------------~~~~~~~~~ 1649 (2836)
T PRK14844 1603 ---Y---GI-DS----------F----VAMQGVEAIRELLTRLDLHEIRKDLRLELESV------------ASEIRRKKI 1649 (2836)
T ss_pred ---c---Cc-cc----------e----eecchHHHHHHHHHhCCHHHHHHHHHHHHHhc------------cHHHHHHHH
Confidence 0 00 00 0 11244443333333444443332222111100 012333556
Q ss_pred HhhcChhhHHHhcCCCCCCCccceEEeecccCCCCCCCC----------chhHHHHHHHHHHHHHHHHHHHcCCChhhHH
Q 000235 221 LKRISDEDCQLLGLNPKYARPDWMILQVLPIPPPPVRPS----------DDLTHQLAMIIRHNENLRRQERNGAPAHIIS 290 (1815)
Q Consensus 221 lk~i~~~d~~~l~~~~~~~~Pe~~il~~lpVpP~~~RP~----------ddlT~~l~~Ii~~N~~lk~~~~~g~~~~~i~ 290 (1815)
+|+|.--+. |.....+|+||||++||||||++||+ ||||++|++||++|++|+++.+.++|..++.
T Consensus 1650 ~krl~~~~~----f~~s~~rPewmil~~lPV~Pp~lRP~v~l~~g~~~~sDLn~ly~~II~~NnrLk~~~~~~ap~~ii~ 1725 (2836)
T PRK14844 1650 IKRLRIVEN----FIKSGNRPEWMILTTIPILPPDLRPLVSLESGRPAVSDLNHHYRTIINRNNRLRKLLSLNPPEIMIR 1725 (2836)
T ss_pred HHHHHHHHH----HHhcCCChhheeeeccccCCCcccCcEEeCCCcccCCchHHHHHHHHHHHHHHHHHHHcCCchhhHH
Confidence 677755443 33346899999999999999999999 8999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhccCCCCCCCcccccCCC-ChhhhhhhhhhcccccccccCCCCCCCCCceeecCCCCcccccccChHH
Q 000235 291 EFAQLLQFHIATYFDNELPGQPRATQRSGR-PIKSICSRLKAKEGRIRGNLMGKRVDFSARTVITPDPTINIDQLGVPWS 369 (1815)
Q Consensus 291 ~~~~~LQ~~V~~~~dn~~~~~p~~~~~~~~-p~k~i~qrLkgK~Gr~R~nlmGKRVdfsaRsVIspDP~L~~~evGvP~~ 369 (1815)
+.|++||++|++||||+..|.+.... ++| ++|||+||||||+||||+|||||||||||||||+|||+|+++|||||+.
T Consensus 1726 ~~~~~LQ~~V~~l~Dn~~~g~~~~~~-~~r~~lksls~~LkGK~GRFR~NLlGKRVDySgRSVI~pdP~L~l~evGlP~~ 1804 (2836)
T PRK14844 1726 NEKRMLQEAVDSLFDNSRRNALVNKA-GAVGYKKSISDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKR 1804 (2836)
T ss_pred HHHHHHHHHHHHHhcCCCCCCCccCC-CCCCccccHHHHhcCCCCcccccccccccccCCCceEeCCCCcccceeeCCHH
Confidence 99999999999999999988765332 334 5899999999999999999999999999999999999999999999999
Q ss_pred HhhhccCCcccchhHHHHHHHHHHcCCCCCCCcccccEEEeCCCceeeccccccccccccccccEeeeecccCCeEEEec
Q 000235 370 IALNLTYPETVTPYNIERLKELVEYGPHPPPGKTGAKYIIRDDGQRLDLRYLKKSSDHHLELGYKVERHLNDGDFVLFNR 449 (1815)
Q Consensus 370 ~A~~LT~PE~Vt~~Ni~~l~~lv~ng~~~~pg~~~A~~i~~~~g~~~~l~~~~~~~~~~L~~g~~V~Rhl~dgD~VL~NR 449 (1815)
||++||+| ||+++|+++... +.+..|+.+++. ...+. |.|.||+++||+|||||
T Consensus 1805 mA~eL~~P-----f~i~~L~~~~~~-----~~i~~a~~li~~---------------~~~~v-~dile~vi~gd~VLlNR 1858 (2836)
T PRK14844 1805 MALELFKP-----FVYSKLKMYGMA-----PTIKFASKLIRA---------------EKPEV-WDMLEEVIKEHPVLLNR 1858 (2836)
T ss_pred HHHhcccH-----HHHHHHHHcCcc-----cchHHHHHHHHh---------------hCCcc-eEEEEEEecCCEEEecC
Confidence 99999865 899988775321 332234433321 01223 55556666899999999
Q ss_pred CCccccccccceeEEeecCCeeeecccCCCCCCCCCCcCccccccCCCHhHHHHHHHHccCCCccccCCCCCCceecccc
Q 000235 450 QPSLHKMSIMGHRIKIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFETRAEVLELMMVPKCIVSPQSNRPVMGIVQD 529 (1815)
Q Consensus 450 QPsLHk~Simah~vkv~~~~t~rln~~vc~pyNADFDGDEMn~h~Pqs~~araE~~~l~~~~~~i~sp~~g~pi~g~~QD 529 (1815)
||||||||||||++++++++||||||+||+||||||||||||+|||||++||||++.||++.+||++|++|+|+++++||
T Consensus 1859 qPTLHR~sIqAf~~~l~~gktirlhp~vC~~fNADFDGDeMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pii~~~QD 1938 (2836)
T PRK14844 1859 APTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLSPSNGRPIIVPSKD 1938 (2836)
T ss_pred CCccccccccceeeEeecCceEEecccCCCcccCCCCCceeeeecCCcHHHHHHHHHHhCCcccEEecCCCceeEeehhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccceecccCCCcc----CHHHHHHHHHhcccCCCCCCCCcccCccCCc---------------chHHHHHHhcCCCce
Q 000235 530 TLLGCRKITKRDTFI----EKDVFMNILMWWEDFDGKVPQPTILKPRPLW---------------TGKQVFNLIIPKQIN 590 (1815)
Q Consensus 530 ~l~g~~~lT~~d~f~----~~~~~~~l~~~~~~~~~~~~~pai~kp~~lw---------------tGKqi~s~~lp~~in 590 (1815)
+|+|+|+||++|.|+ .+.+++++++.. +++.+..++.++++.+| .||+||+.+||+..+
T Consensus 1939 ~ilG~y~LT~~~~~~~~~~~f~~~~~~~~a~--~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~tt~GR~if~~ilP~~~~ 2016 (2836)
T PRK14844 1939 IVLGIYYLTLQEPKEDDLPSFGAFCEVEHSL--SDGTLHIHSSIKYRMEYINSSGETHYKTICTTPGRLILWQIFPKHEN 2016 (2836)
T ss_pred hhhhhhhhcccccccccccccCCHHHHHHHH--HcCCcccCceEEeeeccccCCCCcccceEecccHHHHHHHHcCCccc
Confidence 999999999999854 456777766543 56777788888888777 499999999998443
Q ss_pred EeeecccCCCCCCCcCCCCCcEEEEecCeeeecccccccccCCcccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCc
Q 000235 591 LFRTAAWHADNDKGILTAGDTLVRIEKGELLSGTLCKKTLGTSTGSLIHVIWEEVGPDAARKFLGHTQWLVNYWLLQNAF 670 (1815)
Q Consensus 591 ~~~~~~~~~~~~~~~~~~~d~~v~i~~gell~g~ldK~~~g~s~~~Lih~i~~~~G~~~a~~~l~~~q~l~~~~l~~~Gf 670 (1815)
+ ++++++|+|+|+.++ +||+.+|++||.+.|..|||++++|+++|++.+||
T Consensus 2017 ~-------------------------~~~~~n~~l~KK~l~----~II~~~~~~yG~~~t~~fLD~lk~LGf~yaT~~G~ 2067 (2836)
T PRK14844 2017 L-------------------------GFDLINQVLTVKEIT----SIVDLVYRNCGQSATVAFSDKLMVLGFEYATFSGV 2067 (2836)
T ss_pred c-------------------------CcceEeeeechhHHH----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhccE
Confidence 2 346888999999996 89999999999999999999999999999999999
Q ss_pred eeeeccCccChhhHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhc-----
Q 000235 671 SIGIGDTIADAKTMETINDTISKAKNNVKNLIKQAQDKSLEPEPGRTMMESFENKVNQVLNTARDEAGSSAQKSL----- 745 (1815)
Q Consensus 671 Sigi~D~~~~~~~~~~~~~~i~~a~~~v~~~~~~~~~~~l~~~~~~~~~~~~e~~v~~~ln~~~~~~~~~~~~~l----- 745 (1815)
|||++|++++++. .++|++|++++.++.++|++|.++. +.+++++.++|+++++++++.+++.+
T Consensus 2068 SIgi~Di~iP~~K----~~iI~~a~~~v~~i~~~y~~G~it~-------~Er~~kvi~iW~~~~d~v~~~~~~~l~~~~~ 2136 (2836)
T PRK14844 2068 SFSRCDMVIPETK----ATHVDHARGEIKKFSMQYQDGLITR-------SERYNKVIDEWSKCTDMIANDMLKAISIYDG 2136 (2836)
T ss_pred EeeHhHcccCHHH----HHHHHHHHHHHHHHHHHHHcCCCCH-------HHHHHHHHHHHHHHHHHHHHHHHHhhhhccc
Confidence 9999999988664 6789999999999999999999874 33679999999999999999988866
Q ss_pred -CCCChHHHHHhcCCCCcccchhhhhhhcccccc-CCCccCCCCCCCCCCCCCCCCCCCccccccccCCcCCCChhhhhh
Q 000235 746 -SESNNLKAMVTAGSKGSFINISQMTACVGQQNV-EGKRIPFGFVDRTLPHFTKDDYGPESRGFVENSYLRGLTPQEFFF 823 (1815)
Q Consensus 746 -~~~N~~~~M~~sGsKGS~~N~~Qi~~~lGQQ~~-eG~Rip~~~~~rtLp~f~~~d~~~~~~Gfv~~sf~~GL~p~EfFf 823 (1815)
++.|++++|+.||||||..||.|++||+|||.. .|..| ..+|.+||++||+|.||||
T Consensus 2137 ~~~~N~i~mMa~SGARGS~sQI~QLaGmRGLmakp~G~iI---------------------e~PI~SNFrEGLsv~EyFi 2195 (2836)
T PRK14844 2137 NSKYNSVYMMVNSGARGSTSQMKQLAGMRGLMTKPSGEII---------------------ETPIISNFREGLNVFEYFN 2195 (2836)
T ss_pred cCCCCceeeeecccCccCHHHHHHHHhcceeeecCCCCee---------------------ecchhhhhccCCCHHHhhh
Confidence 357999999999999999999999999999753 34332 1348999999999999999
Q ss_pred hccCCCcchhhhccccCCCchhHHHHHHHhhceEEeec--CeeecCCCceEEEEecCCCCCceeeecccccccccchHHH
Q 000235 824 HAMGGREGLIDTAVKTSETGYIQRRLVKAMEDIMVKYD--GTVRNSLGDVIQFLYGEDGMDSVWIESQTLDSLKMKKSEF 901 (1815)
Q Consensus 824 H~m~gReGLiDTAvKTa~sGYlqRrLvk~lEdl~v~YD--gTVRns~g~iiQF~YGeDg~d~~~~e~~~~~~~~~~~~~~ 901 (1815)
|||||||||+|||+|||+||||||||||++|||+|.-+ ||-+ |-.|.-+. ||-+ .+ ..+.+..+
T Consensus 2196 St~GaRKGL~DTALKTAdSGYLTRRLVDVaQDviI~e~DCgT~~---Gi~v~~~~--~~~~--~i-------~~L~~ri~ 2261 (2836)
T PRK14844 2196 STHGARKGLADTALKTANSGYLTRRLVDVSQNCIVTKHDCKTKN---GLVVRATV--EGST--IV-------ASLESVVL 2261 (2836)
T ss_pred hccccccchhhhhhhcccccchhhhhhhhhceEEEEecccCCCC---ceEEEEec--cCCe--EE-------eEhhheeE
Confidence 99999999999999999999999999999999999764 6643 43333221 1100 01 11112222
Q ss_pred hhhhhhccccCCCCcccchHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhHhhhccCCCCCCCccccHHHHHHHhhhhcc
Q 000235 902 DKAFRFEMDEENWNPNYMLQEYIDDLKTIKELRDVFDAEVQKLEADRYQLATEIATSGDSSWPLPVNLKRLIWNAQKTFK 981 (1815)
Q Consensus 902 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~r~~l~~~~~~~~~~~~~~p~n~~r~i~~~~~~~~ 981 (1815)
.|....++.++..+. .+...
T Consensus 2262 GR~~a~di~~p~t~~-------------------------------------~i~~~----------------------- 2281 (2836)
T PRK14844 2262 GRTAANDIYNPVTKE-------------------------------------LLVKA----------------------- 2281 (2836)
T ss_pred EEEEHhHeEcCCCCC-------------------------------------EEEeC-----------------------
Confidence 222211211111000 00000
Q ss_pred cCCCCCCCCChHHHHHHHHHHHHhhcccCCCCcccHHHHhhhhhhhhhhhhhhhhhHHHHHhhccCHHHHHHHHHHHHHH
Q 000235 982 VDPRRPSDMHPMEVVEAVDKLQERLKVVPGEDPLSVEAQKNATLFFNILLRSTFASKRVLKEHRLTREAFEWVIGEIESR 1061 (1815)
Q Consensus 982 ~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~lrs~l~~~~~~~~~~l~~~~~~~~l~ei~~k 1061 (1815)
...++. ++++.+ ++..+-.+.+||.|+|+ ..+++|++||+|.|+
T Consensus 2282 -----~~~I~~-~~~~~i----------------------~~~gi~~v~IRS~ltC~---s~~gvC~~CYG~~La----- 2325 (2836)
T PRK14844 2282 -----GELIDE-DKVKQI----------------------NIAGLDVVKIRSPLTCE---ISPGVCSLCYGRDLA----- 2325 (2836)
T ss_pred -----CCccCH-HHHHHH----------------------HHcCCCEEEEcCCeeEC---CCCCChhhccCcccc-----
Confidence 000000 011111 12234567799999997 679999999999997
Q ss_pred hhcCcccCCCchhhHhhhccCCccccccccccccccccccccc--------cccceeeeehhhcccCCCCce------EE
Q 000235 1062 FLQSLVAPGEMIGCVAAQSIGEPATQMTLNTFHYAGVSAKNVT--------LGVPRLREIINVAKKIKTPSL------SV 1127 (1815)
Q Consensus 1062 y~~slv~PGEaVG~iAAQSIGEPaTQMTLnTFH~AGv~~~NVT--------lGvPRLkEIin~ak~ikTP~m------tv 1127 (1815)
...+|+.|||||+|||||||||+|||||+|||.+||++..+. .|+-++.++--+ ++-..-.+ .+
T Consensus 2326 -~~~~V~iGeaVGiIAAQSIGEPGTQLTMRTFHtGGvas~~~~~~~i~~~~~G~v~~~~~~~v-~~~~g~~iv~sr~~~~ 2403 (2836)
T PRK14844 2326 -TGKIVSIGEAVGVIAAQSVGEPGTQLTMRTFHIGGVMTRGVESSNIIASINAKIKLNNSNII-IDKNGNKIVISRSCEV 2403 (2836)
T ss_pred -CCCcccccccceeeeecccCCCcceeeeeheeeccccccccccceeEeccCceEEeccceeE-EcCCCcEEEEecccEE
Confidence 788999999999999999999999999999999999875553 477776663222 11111111 11
Q ss_pred EeCCCCcchHHHHHHHHhhhccccccccceeeEE--EEcCCCCceEEEcccceeheeccCCCC-----cc-cccccCCcE
Q 000235 1128 FLKPGVNSTKERAKNVQCALEYTTLRSVTEATEV--WYDPDPMGTIIEEDVEFVKSYYEMPDE-----DI-APEKISPWL 1199 (1815)
Q Consensus 1128 ~l~~~~~~~~~~a~~v~~~le~~tL~dv~~~~~i--~ydp~~~~~~i~~d~~~~~~~~~~~~~-----~~-~~~~~~~~~ 1199 (1815)
-+.+......+.-+......-.+.-++.+++-++ .|||... .+|.|-...+. |-++-+. +. ..+.++.++
T Consensus 2404 ~i~d~~g~~~~~~~i~yga~l~v~~g~~V~~g~~la~wdp~~~-piisE~~G~v~-f~d~~~g~t~~~~~D~~tg~~~~~ 2481 (2836)
T PRK14844 2404 VLIDSLGSEKLKHSVPYGAKLYVDEGGSVKIGDKVAEWDPYTL-PIITEKTGTVS-YQDLKDGISITEVMDESTGISSKV 2481 (2836)
T ss_pred EEEecCCcEEEEEecccccEEEecCCCEecCCCEEEEEcCCCc-ceEeecceEEE-EEEEecceeEEEEecccCCceEEE
Confidence 2211111100111111122222223333333222 3444321 22222111110 0000000 00 000000000
Q ss_pred E--------------EEEe-chh-h--------------------h--hcccCCHHHHHHHHhhhcC--CC---------
Q 000235 1200 L--------------RIEL-NRE-M--------------------M--VDKKLSMAAVAEKINQEFD--DD--------- 1230 (1815)
Q Consensus 1200 l--------------rl~l-~~~-~--------------------~--~~~~l~~~~i~~~i~~~~~--~~--------- 1230 (1815)
+ ++.| |.. . + ..-.+...+|..+|..... .|
T Consensus 2482 i~~~~~~~~~~~~~P~i~i~~~~g~~~~~~~~~~~~y~lp~ga~l~v~~g~~v~~Gdilakipr~~~~t~DIT~GLpRv~ 2561 (2836)
T PRK14844 2482 VKDWKLYSGGANLRPRIVLLDDNGKVMTLASGVEACYFIPIGAVLNVQDGQKVHAGDVITRTPRESVKTRDITGGLPRVI 2561 (2836)
T ss_pred EeeccccccccccCceEEEEcCCCceecccCCcceeeecCCCceEeeccCceecccceeecccccccccCccCCCCccch
Confidence 0 1111 000 0 0 0001222333333322110 01
Q ss_pred -ceeeecCCCc-----cceEEEEEEccCCCCCC-----CCCCCcchhHHHHHHHHhhccccceecccchhhhhccccc--
Q 000235 1231 -LTCIFNDDNA-----DKLILRIRIMNDEAPKG-----ELNDESAEDDVFLKKIESNMLTEMALRGVNLLAVMCHEDV-- 1297 (1815)
Q Consensus 1231 -~~~~~~~dn~-----~~~~~~ir~~~~~~~~~-----~~~~~~~~~~~~l~~~~~~~l~~~~~~G~nl~~vl~~~~v-- 1297 (1815)
++......+. -+.++.+ +..+..... ..++++ ....++-...++++ +-+| |.|
T Consensus 2562 eLFEar~pk~~a~isei~G~V~~-~~~~~~~~~~i~i~~~~~~~-~~~~y~vp~~~~~~---v~~g---------d~V~~ 2627 (2836)
T PRK14844 2562 ELFEARRPKEHAIVSEIDGYVAF-SEKDRRGKRSILIKPVDEQI-SPVEYLVSRSKHVI---VNEG---------DFVRK 2627 (2836)
T ss_pred heeeeecCCCceEEecCCcEEEe-cccccCCceEEEEECCCCCc-cceEEEccCCceEE---ecCC---------CEEcC
Confidence 0100000000 0001111 000000000 000000 00001000001111 0112 112
Q ss_pred -cccccccccHHHHHHhhcHHHHHHHHHHHHHHhhhcCcccccchhHHHHHhhhhcc-------------ce--------
Q 000235 1298 -DARRTTSNHLIEIIEVLGIEAVRRALLDELRVVISFDGSYVNYRHLAILCDTMTYR-------------GH-------- 1355 (1815)
Q Consensus 1298 -D~~rt~sNdI~eI~~vlGIEAAR~~Ii~Ei~~V~~~~Gi~Vn~RHL~LlaD~MT~~-------------G~-------- 1355 (1815)
|.-.--+.|++||++++||||+|++|++||++||..||++||+|||++|+++||.+ |+
T Consensus 2628 G~~l~~G~~~p~dil~v~G~ea~~~ylv~Evq~VYr~QGV~IndKHiEvIvrQMl~kV~I~d~Gdt~~l~Ge~v~~~~~~ 2707 (2836)
T PRK14844 2628 GDLLMDGDPDLHDILRVLGLEALAHYMISEIQQVYRLQGVRIDNKHLEVILKQMLQKVEITDPGDTMYLVGESIDKLEVD 2707 (2836)
T ss_pred CCCccCCCCCHHHHHHhhCHHHHHHHHHHHHHHHHHhcCeeecccEeeeehhhhhceeEEecCCCcccCCCceecHHHHH
Confidence 11112356999999999999999999999999999999999999999999999988 22
Q ss_pred -------------------ecccccccccccCCccccccchHHHHHHHHHHHhhcCcccccccccccccCCccccCccc
Q 000235 1356 -------------------LMAITRHGINRNDTGPMMRCSFEETVDILLDAAVFAESDYLRGVTENIMLGQLAPIGTGD 1415 (1815)
Q Consensus 1356 -------------------~~~itR~Gi~~~~~spL~~aSFEeT~~~L~~AA~~ge~D~l~gvsenIi~G~~~p~GTG~ 1415 (1815)
+++|||+.++ ..|+|++||||||+++|++||+.|++|+|.|++||||+|+++|+|||.
T Consensus 2708 ~~n~~~~~~g~~pa~~~pvllGITkasL~--t~SflSaASFQeTtkVLt~AAi~Gk~D~L~GlKENVIiG~lIPaGTG~ 2784 (2836)
T PRK14844 2708 RENDAMSNSGKRPAHYLPILQGITRASLE--TSSFISAASFQETTKVLTEAAFCGKSDPLSGLKENVIVGRLIPAGTGL 2784 (2836)
T ss_pred HHHHHHHhcCCCCceeeeeeeceeecccc--CCChhhcCCcccchHHHHHHHhcCCCCcCCCcccceEecCcccCCcCc
Confidence 5688888885 369999999999999999999999999999999999999999999994
No 12
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]
Probab=100.00 E-value=6.9e-161 Score=1544.15 Aligned_cols=774 Identities=36% Similarity=0.539 Sum_probs=686.6
Q ss_pred ccceEEEEcCCHHHHHhcceeEEeeCccccCC-CCCCCCCCCCCCCCcCCCccccccccCCCCcCCccceeeccccccch
Q 000235 14 KVRMVQFGILSPDEIRQMSVVQIEHGETTERG-KPKPGGLSDPRLGTIDRKMKCETCTANMAECPGHFGHLELAKPMFHI 92 (1815)
Q Consensus 14 ~i~~i~F~~~S~eeI~~~Sv~eI~~~~~~~~~-~p~~gGl~D~rlG~~~~~~~C~TCg~~~~~CpGHfGhIeL~~PV~h~ 92 (1815)
.++ |+||++||||||+|| +||++|++||++ +|+.+||+|+|||.+++++.| |||+....|||||||||||+||+|+
T Consensus 4 ~~~-i~~gl~sp~~ir~~s-~ev~~pet~~~~~~P~~~Gl~d~ri~~~~~~~~C-~Cg~~~~~~~~~~GhIeLa~Pv~hi 80 (808)
T COG0086 4 IFD-IKFGLASPEEIRSWS-GEVKKPETINYRTKPERGGLFDERIFGPDKDYEC-TCGKYKRICPGGFGHIELAAPVAHI 80 (808)
T ss_pred cce-eEEecCCHHHHHhcc-eEEcCccccCCCCcccCCCccchhhcCCCCCcee-cCCCCcCcCCCCceeEEeecceEEe
Confidence 445 999999999999966 999999999998 999999999999999999999 9999999999999999999999999
Q ss_pred hhhhHHHHHhcccceecceeccCCchHHHHHHHHhcChHHHHHHHHHHhhhccccCCCCCCCCCCCCCCcccccccCCCC
Q 000235 93 GFMKTVLSIMRSVCFNCSKILADEDDHKFKQALKIRNPKNRLKKILDACKNKTKCEGGDEIDVPGQDGEEPLKKNKGGCG 172 (1815)
Q Consensus 93 ~f~~~v~~iL~~vC~~C~~l~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~gCg 172 (1815)
||++.+..+|+|.|.+|+++++... +..+ . ..+++....++... .....|.+||
T Consensus 81 ~f~k~~~~~L~~~~~~~~~v~~~~~---~~~~---~---~~l~~~~~~~~~~~-----------------~~~~~~~~~G 134 (808)
T COG0086 81 WFFKSIPSLLDMTCRDCERVLYFEA---YVVL---G---TDLEKIQLLNETEY-----------------VYDSFCAHCG 134 (808)
T ss_pred chhhccHHHHhhhHHhhhhhhhHhH---HHHh---c---cchhhhcccchhee-----------------eccccCCCCC
Confidence 9999999999999999999998721 1111 0 11222211111100 1124578899
Q ss_pred ccchhhhhcccchhhhhHHhhccccccCCCCccchhcccCCHHHHHHHHhhcChhhHHHhcCCCCCCCccceEEeecccC
Q 000235 173 AQQPKLTIEGMKMIAEYKAQRKKNDDQEQLPEPVERKQTLTAERVLGVLKRISDEDCQLLGLNPKYARPDWMILQVLPIP 252 (1815)
Q Consensus 173 ~~~p~i~k~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~p~~v~~ilk~i~~~d~~~l~~~~~~~~Pe~~il~~lpVp 252 (1815)
+.+++++++++.++.+.+ . ..+++.+++++|++|+..|+.++| .++||||||++||||
T Consensus 135 a~~~~~~~~~~~~~~~~~-----------------~-~~~~~~~~~~~~~~l~~~d~~~~~----~~~pewmil~vlpV~ 192 (808)
T COG0086 135 AEAIKILLEKPDLETERE-----------------E-ETLSPTKVKKLLKRLKVVDAFLLS----GNRPEWMILTVLPVP 192 (808)
T ss_pred chhHHHHHhCcchhhhhh-----------------h-cccCHHHHHHHHhhccHHHHHHhc----CCCcceeEEEeeccC
Confidence 999999999988776650 1 357899999999999999999998 589999999999999
Q ss_pred CCCCCCC----------chhHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHhhccCCCCCCCcccccCCCCh
Q 000235 253 PPPVRPS----------DDLTHQLAMIIRHNENLRRQERNGAPAHIISEFAQLLQFHIATYFDNELPGQPRATQRSGRPI 322 (1815)
Q Consensus 253 P~~~RP~----------ddlT~~l~~Ii~~N~~lk~~~~~g~~~~~i~~~~~~LQ~~V~~~~dn~~~~~p~~~~~~~~p~ 322 (1815)
|+++||+ ||||++|++||++|++||++++.+++ .++++.|++||+||++|||| +.+.+.++ +||+
T Consensus 193 Pp~~RP~i~ld~g~~a~~dl~~~~~~ii~~n~rlk~~~~~~~~-~iv~~~~~~lQ~~v~~~~Dn---~~~~~~~~-~rPl 267 (808)
T COG0086 193 PPDLRPSIQLDGGRFAESDLNDLYRRVINRNNRLKRLLELAAP-IIVRNEKRMLQEAVDALFDN---RRPRAVTG-GRPL 267 (808)
T ss_pred CCCCCcceecCCCccchhHHHHHHHHHHHHHHHhHHhhhhcch-HHHHHHHHHHHHHHHHHhhc---CCCCCccC-CCcc
Confidence 9999999 99999999999999999999988555 99999999999999999999 45566666 5999
Q ss_pred hhhhhhhhhcccccccccCCCCCCCCCceeecCCCCcccccccChHHHhhhccCCcccchhHHHHHHHHHHcCCCCCCCc
Q 000235 323 KSICSRLKAKEGRIRGNLMGKRVDFSARTVITPDPTINIDQLGVPWSIALNLTYPETVTPYNIERLKELVEYGPHPPPGK 402 (1815)
Q Consensus 323 k~i~qrLkgK~Gr~R~nlmGKRVdfsaRsVIspDP~L~~~evGvP~~~A~~LT~PE~Vt~~Ni~~l~~lv~ng~~~~pg~ 402 (1815)
|||+||||||+||||+|||||||||||||||+|||||+++|||||+.||++||+|+.||+||++.|++ |
T Consensus 268 ksl~~~LkgK~GrFR~nL~GKRVd~SgRsVI~~~P~l~~~e~GvP~~~A~~L~~p~~v~~~~~~~~~~----------~- 336 (808)
T COG0086 268 KSLSQRLKGKQGRFRQNLLGKRVDYSGRSVISVGPNLKLNQCGVPKKMALELFKPFVVTELNIEGLRT----------G- 336 (808)
T ss_pred ccHHHHhcCCCceeeccccccccCCCCceeecCCCCccccccCCHHHHHHHhccCEEEEehhhhhhhc----------C-
Confidence 99999999999999999999999999999999999999999999999999999999999999999977 5
Q ss_pred ccccEEEeCCCceeeccccccccccccccccEeeeecccCCeEEEecCCccccccccceeEEeec-CCeeeecccCCCCC
Q 000235 403 TGAKYIIRDDGQRLDLRYLKKSSDHHLELGYKVERHLNDGDFVLFNRQPSLHKMSIMGHRIKIMP-YSTFRLNLSVTSPY 481 (1815)
Q Consensus 403 ~~A~~i~~~~g~~~~l~~~~~~~~~~L~~g~~V~Rhl~dgD~VL~NRQPsLHk~Simah~vkv~~-~~t~rln~~vc~py 481 (1815)
|+|+++.++.+ +..||.|+||+++||+|||||||||||+|||+|++++++ ++|||||++||.||
T Consensus 337 --a~~~~~~~~~~-------------~~~~w~Vl~evi~gd~Vl~NR~PtLHrlsImq~~e~vl~~gkt~rLh~lVc~~y 401 (808)
T COG0086 337 --AKYAKRMVERR-------------LPEVWDVLREVIDGDPVLLNRAPTLHRLSIMQAFEPVLPEGKAIRLHPLVCEAY 401 (808)
T ss_pred --CceEEeccccc-------------ccccchHHHHHhcCCccccccCChHHHHHHHhhceeeccccceeecchhhcccc
Confidence 99999877653 668999999999999999999999999999999999998 89999999999999
Q ss_pred CCCCCcCccccccCCCHhHHHHHHHHccCCCccccCCCCCCceeccccccccceecccCCCccCHHHHHHHHHhcccCCC
Q 000235 482 NADFDGDEMNMHVPQSFETRAEVLELMMVPKCIVSPQSNRPVMGIVQDTLLGCRKITKRDTFIEKDVFMNILMWWEDFDG 561 (1815)
Q Consensus 482 NADFDGDEMn~h~Pqs~~araE~~~l~~~~~~i~sp~~g~pi~g~~QD~l~g~~~lT~~d~f~~~~~~~~l~~~~~~~~~ 561 (1815)
||||||||||+|+|||.+|+||++.||++..||++|++|+||++.+||+|+|.||||..|+|++.+++++++++-...+.
T Consensus 402 NADFDGDeM~~Hvp~s~ea~AEa~~lm~tq~nilsP~~Ggpiv~~~qD~v~g~ylLt~~d~~~~~~~~~ei~l~~~~~~~ 481 (808)
T COG0086 402 NADFDGDEMAVHVPASGEAAAEARGLMGTQMNILTPHYGGPIVAPIQDTVGGPYLLTIVDAKLPSTPVGEIYLKDEYADD 481 (808)
T ss_pred ccccCchhhhccccchHHHHHHHHHhhccccccccCCCCCceEeecceEEeccEEEEEecccCCCCcceEEEeccccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999998765211122
Q ss_pred CCCCCcccCccCCcchHHHHHHhcCCC--ceEeeecccCCCCCCCcCCCC-CcEEEEecCeeeecccccccccCCcccHH
Q 000235 562 KVPQPTILKPRPLWTGKQVFNLIIPKQ--INLFRTAAWHADNDKGILTAG-DTLVRIEKGELLSGTLCKKTLGTSTGSLI 638 (1815)
Q Consensus 562 ~~~~pai~kp~~lwtGKqi~s~~lp~~--in~~~~~~~~~~~~~~~~~~~-d~~v~i~~gell~g~ldK~~~g~s~~~Li 638 (1815)
....+||.++..+|||||+++.++++. .++........ -....+..+ |..+.|.||+++.|++||...
T Consensus 482 ~e~~~ai~~~~~~~~~k~i~~~i~~~~~~~~i~~t~~~~~-~~~~~~~~~~d~~~~i~~~~l~~~~i~k~~~-------- 552 (808)
T COG0086 482 REKAEAIAKKIELTTGKVIVSTISPDLAELSIIVTTDGRR-IFNRGLPEDKDVLVKIVNGKLIKGVIDKKIV-------- 552 (808)
T ss_pred hhhhHHHhcccceeeeeEEEEEeeccCCcceEEEecchhh-hhhccCCcccceeeEEeccccceeeehhhHH--------
Confidence 356789999999999999999888874 44443211000 001112233 678999999999999998877
Q ss_pred HHHHHHhCHHHHH-HHHHHHHHHHHHHHHhcC-ceeeeccCccChhhHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCC
Q 000235 639 HVIWEEVGPDAAR-KFLGHTQWLVNYWLLQNA-FSIGIGDTIADAKTMETINDTISKAKNNVKNLIKQAQDKSLEPEPGR 716 (1815)
Q Consensus 639 h~i~~~~G~~~a~-~~l~~~q~l~~~~l~~~G-fSigi~D~~~~~~~~~~~~~~i~~a~~~v~~~~~~~~~~~l~~~~~~ 716 (1815)
.++++||+.++. .+++.+.+|.+.|+...| |+++|+|.- ..+.+++.+.+.+|+.++.+++.+++.|.++..++.
T Consensus 553 -~i~~~~g~~~~~~~~~~~~dkl~~~~~~~~~~~~~~i~~~d--~~~~~~~~e~v~~ae~~v~~~i~~~~~g~lt~~~~~ 629 (808)
T COG0086 553 -TIYREYGPEVASKALVKLLDKLKNLGIKGIGGFGIGIGRKD--IEAEDEKDEIVIEAEGSVLKLILQYEEGDLTRTERN 629 (808)
T ss_pred -HHHHHhCchhhHHHHHHHHHHHHHhheeeeccceEEeeccc--ccchHHHHHHHHHHHHHHHHHHHHhhcCCccccCCC
Confidence 689999998888 999999999999999988 999999875 334456789999999999999999999999999999
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCChHHHHHhcCCCCcccchhhhhhhccccccCCCccCCCCCCCCCCCCC
Q 000235 717 TMMESFENKVNQVLNTARDEAGSSAQKSLSESNNLKAMVTAGSKGSFINISQMTACVGQQNVEGKRIPFGFVDRTLPHFT 796 (1815)
Q Consensus 717 ~~~~~~e~~v~~~ln~~~~~~~~~~~~~l~~~N~~~~M~~sGsKGS~~N~~Qi~~~lGQQ~~eG~Rip~~~~~rtLp~f~ 796 (1815)
++.+.++.+++.++++++.+.++.+.+.+..+ +..|..+|++|+..|++||.+|+|||.+.|+|++.+ +||||.
T Consensus 630 ~i~e~~e~~~~e~l~~ai~~~~~~~~~~~g~~--~~~i~~m~~~Gs~~n~sq~~~~iG~~gv~g~r~~~~----~~~~Fe 703 (808)
T COG0086 630 NIVEIIEVLGIEALRNAIIEEIKITLEEQGLD--FVDIRHMGLSGARMNISQIVQLIGQQGVMGEKISVL----ARAAFE 703 (808)
T ss_pred CeEEEeehHHHHHHHHHHHHHHhhhHHhcCCc--chhHHHHhhhhhccCHHHHHHHhhhheeeccCCCcc----cccccc
Confidence 99999999999999999999999988888777 556666667777779999999999999999999888 999999
Q ss_pred CCCCCCccccccccCCcCCCChhhhhhhccCCCcchhhhccccCCCchhHHHHHHHhhceEEeecCeeecCCCceEEEEe
Q 000235 797 KDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDIMVKYDGTVRNSLGDVIQFLY 876 (1815)
Q Consensus 797 ~~d~~~~~~Gfv~~sf~~GL~p~EfFfH~m~gReGLiDTAvKTa~sGYlqRrLvk~lEdl~v~YDgTVRns~g~iiQF~Y 876 (1815)
+.+..+++.|||+++|++||+|.|||||+|+|||||||||+|||+||||||||||++|||+|.||+|||++.+.++||.|
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 99999999999999999999999999999999999999999999999999999999999999999999998899999999
Q ss_pred cCCCCCceeee
Q 000235 877 GEDGMDSVWIE 887 (1815)
Q Consensus 877 GeDg~d~~~~e 887 (1815)
||||+|++...
T Consensus 784 ged~~~~~~~~ 794 (808)
T COG0086 784 GEDGEDLTERI 794 (808)
T ss_pred CccccCHHHHh
Confidence 99999986543
No 13
>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional
Probab=100.00 E-value=5.7e-104 Score=964.53 Aligned_cols=479 Identities=29% Similarity=0.482 Sum_probs=370.8
Q ss_pred cccceEEEEcCCHHHHHhcc---------eeEEeeCccccCC--CCCCCCCCCCCCCCcCCCcc---------------c
Q 000235 13 AKVRMVQFGILSPDEIRQMS---------VVQIEHGETTERG--KPKPGGLSDPRLGTIDRKMK---------------C 66 (1815)
Q Consensus 13 ~~i~~i~F~~~S~eeI~~~S---------v~eI~~~~~~~~~--~p~~gGl~D~rlG~~~~~~~---------------C 66 (1815)
.++..|+.+++|||+|++|| ++||++|+|+++. +|+.+||||.|+..+.+++. |
T Consensus 7 ~~~~~i~I~laSPe~I~~Ws~r~lpng~i~GeV~kpeTinyrT~KPE~dGLFCerIFGP~k~~eC~CGkyk~~~~~~~~C 86 (627)
T PRK02625 7 NRFDYVKIGLASPERIRQWGQRTLPNGQVVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVC 86 (627)
T ss_pred cccceEEEEecCHHHHHHHHHhhcCCCceeeEECCCcccccCCCCCCCCCEeechhcCCccCcEEeCCCccccCcCCcCC
Confidence 46789999999999999999 9999999999997 99999999999955544444 5
Q ss_pred cccccCCCC---cCCccceeeccccccchhhhhHH-----------HHHhcccceecceeccCCchHHHHHHHHhcChHH
Q 000235 67 ETCTANMAE---CPGHFGHLELAKPMFHIGFMKTV-----------LSIMRSVCFNCSKILADEDDHKFKQALKIRNPKN 132 (1815)
Q Consensus 67 ~TCg~~~~~---CpGHfGhIeL~~PV~h~~f~~~v-----------~~iL~~vC~~C~~l~~~~~~~~~~~~~~~~~~~~ 132 (1815)
+.||.+..+ ..-+||||+|+.||.|+||++.+ ++.|+.+.++-..+.+++..+.......+....
T Consensus 87 ~~CgvE~t~s~vRR~RMG~I~La~PV~HiWylk~~ps~i~~lL~~~~k~le~ivy~~~~~v~~~~~~~~~~~~~~~~~~- 165 (627)
T PRK02625 87 ERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYVAILLDMPLRDVEQIVYFNCYVVLDPGNHKNLKYKQLLTED- 165 (627)
T ss_pred CCCCcEecchhhhHhhcCceeecCCceEeeccCCCchHHHHHhCCCHHHhhheeeeeeEEEecCCCccchhhhhhhhhH-
Confidence 555554433 34799999999999999999953 567888887776777765433111111111111
Q ss_pred HHHHHHHHhhhccccCCCCCCCCCCCCCCcccccccCCCCccchhhhhcccchhhhhHHhhccccccCCCCccchhcccC
Q 000235 133 RLKKILDACKNKTKCEGGDEIDVPGQDGEEPLKKNKGGCGAQQPKLTIEGMKMIAEYKAQRKKNDDQEQLPEPVERKQTL 212 (1815)
Q Consensus 133 ~~~~i~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~gCg~~~p~i~k~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l 212 (1815)
.+.++.+..-. . +. +..+ +. -.++|+..-+-....+++..+....+.+... .
T Consensus 166 ~~~~~~~~~~~----~---~~-----~~~~-~~--~~~~Ga~ai~~lL~~~dl~~~~~~l~~~~~~-------------~ 217 (627)
T PRK02625 166 QWLEIEDQIYA----E---DS-----ELEG-EE--VVGIGAEALKRLLEDLNLEEEAEQLREEIAN-------------S 217 (627)
T ss_pred HHHHHHHHhcc----c---cc-----cccc-ch--hhhhhHHHHHHHHhhCCHHHHHHHHHHHHHh-------------c
Confidence 22222222110 0 00 0000 00 0224544433333444544333222211110 1
Q ss_pred CHHHHHHHHhhcChhhHHHhcCCCCCCCccceEEeecccCCCCCCCC----------chhHHHHHHHHHHHHHHHHHHHc
Q 000235 213 TAERVLGVLKRISDEDCQLLGLNPKYARPDWMILQVLPIPPPPVRPS----------DDLTHQLAMIIRHNENLRRQERN 282 (1815)
Q Consensus 213 ~p~~v~~ilk~i~~~d~~~l~~~~~~~~Pe~~il~~lpVpP~~~RP~----------ddlT~~l~~Ii~~N~~lk~~~~~ 282 (1815)
+..+...++|+|.--+ .|.....+||||||++|||||+++||+ ||||++|++||++|++|+++...
T Consensus 218 ~~~~~~~~ikrl~~~~----~f~~~~~~PewmiL~~lPV~Pp~lRP~v~l~~g~~~~sDLn~ly~~II~rNn~L~~~~~~ 293 (627)
T PRK02625 218 KGQKRAKLIKRLRVID----NFIATGSRPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEI 293 (627)
T ss_pred chHHHHHHHHHHHHHH----HHHhcCCCccEEEEEeeecCCCcccCceEeCCCcccCCCHHHHHHHHHHHHHHHHHHHHc
Confidence 1133345566664433 233456899999999999999999999 89999999999999999999999
Q ss_pred CCChhhHHHHHHHHHHHHHhhccCCCCCCCcccccCCCChhhhhhhhhhcccccccccCCCCCCCCCceeecCCCCcccc
Q 000235 283 GAPAHIISEFAQLLQFHIATYFDNELPGQPRATQRSGRPIKSICSRLKAKEGRIRGNLMGKRVDFSARTVITPDPTINID 362 (1815)
Q Consensus 283 g~~~~~i~~~~~~LQ~~V~~~~dn~~~~~p~~~~~~~~p~k~i~qrLkgK~Gr~R~nlmGKRVdfsaRsVIspDP~L~~~ 362 (1815)
+++..++.+.|++||++|++||||++.|.|. ...++||+|||+|+||||+||||+|||||||||||||||+|||+|++|
T Consensus 294 ~~p~~ii~~~~~~LQ~aVd~liDn~~~g~~~-~~~~~rp~ksls~~LkGKeGRFR~NLlGKRVDySgRSVIspdP~L~l~ 372 (627)
T PRK02625 294 LAPEIIVRNEKRMLQEAVDALIDNGRRGRTV-VGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMH 372 (627)
T ss_pred CCcHHHHHHHHHHHHHHHHHHhcCCCCCCCc-ccccCCchhhHHHHhccCCccccccccccccccCCCceEeCCCCcccc
Confidence 9999999899999999999999999998765 344679999999999999999999999999999999999999999999
Q ss_pred cccChHHHhhhccCCcccchhHHHHHHHHHHcCCC-CCCCcccccEEEeCCCceeeccccccccccccccccEeeeeccc
Q 000235 363 QLGVPWSIALNLTYPETVTPYNIERLKELVEYGPH-PPPGKTGAKYIIRDDGQRLDLRYLKKSSDHHLELGYKVERHLND 441 (1815)
Q Consensus 363 evGvP~~~A~~LT~PE~Vt~~Ni~~l~~lv~ng~~-~~pg~~~A~~i~~~~g~~~~l~~~~~~~~~~L~~g~~V~Rhl~d 441 (1815)
|||||++||++||+| |||++|+ .+|.. ..++ |++++..+ -..+|.|+|||+|
T Consensus 373 e~GvP~~mA~eL~~P-----f~i~~L~---~~g~~~~i~~---ak~~i~~~----------------~~~~~~Vlr~v~~ 425 (627)
T PRK02625 373 QCGLPKEMAIELFQP-----FVIHRLI---RQGIVNNIKA---AKKLIQRA----------------DPEVWQVLEEVIE 425 (627)
T ss_pred cccChHHHHHhcCcH-----HhHHHHH---HcCchhhHHH---HHHHHHhc----------------CCcccEEEEEeec
Confidence 999999999999865 7888874 55542 2233 66554321 1246899999999
Q ss_pred CCeEEEecCCccccccccceeEEeecCCeeeecccCCCCCCCCCCcCccccccCCCHhHHHHHHHHccCCCccccCCCCC
Q 000235 442 GDFVLFNRQPSLHKMSIMGHRIKIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFETRAEVLELMMVPKCIVSPQSNR 521 (1815)
Q Consensus 442 gD~VL~NRQPsLHk~Simah~vkv~~~~t~rln~~vc~pyNADFDGDEMn~h~Pqs~~araE~~~l~~~~~~i~sp~~g~ 521 (1815)
||+|||||||||||||||||++++++++||||||+||+||||||||||||||||||++|||||++||++++|++||++|+
T Consensus 426 gd~VLlNRqPTLHR~sIqAf~~~l~~~ktirlhplvC~~fNADFDGDeMnvHvPqS~~A~aEa~~Lm~~~~nilsP~~G~ 505 (627)
T PRK02625 426 GHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQAEARLLMLASNNILSPATGE 505 (627)
T ss_pred CcEEEecCCCccccccceeEeeEEcCCCeEEeccccCCcccCCcCCCeEEEecCCCHHHHHHHHHHhcCccceEEcCCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CceeccccccccceecccCCC---------ccCHHHHHHH
Q 000235 522 PVMGIVQDTLLGCRKITKRDT---------FIEKDVFMNI 552 (1815)
Q Consensus 522 pi~g~~QD~l~g~~~lT~~d~---------f~~~~~~~~l 552 (1815)
|+++++||+|+|+|+||.+|. |-+.+|+...
T Consensus 506 Pi~~~~QD~llG~y~LT~~~~~~~~~~~~~f~~~~~~~~a 545 (627)
T PRK02625 506 PIVTPSQDMVLGCYYLTAENPGAQKGAGRYFASLEDVIMA 545 (627)
T ss_pred eeEeechhhhhheeeeeccCccccCCCCceeCCHHHHHHH
Confidence 999999999999999999983 4455655543
No 14
>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=5.8e-103 Score=954.62 Aligned_cols=466 Identities=28% Similarity=0.475 Sum_probs=364.0
Q ss_pred cceEEEEcCCHHHHHhcc---------eeEEeeCccccCC--CCCCCCCCCCCCCCcCCCccc---------------cc
Q 000235 15 VRMVQFGILSPDEIRQMS---------VVQIEHGETTERG--KPKPGGLSDPRLGTIDRKMKC---------------ET 68 (1815)
Q Consensus 15 i~~i~F~~~S~eeI~~~S---------v~eI~~~~~~~~~--~p~~gGl~D~rlG~~~~~~~C---------------~T 68 (1815)
+..|+.+++|||.|++|| ++||++|+|+++. +|+.+||||.|+..+.+++.| +.
T Consensus 2 ~~~i~I~laSPe~I~~Ws~r~lpng~i~GeV~kp~TinyrT~KPE~dGLFCerIFGP~k~~eC~CGkyk~~~~~~~~C~~ 81 (619)
T TIGR02387 2 FDYVKITIASPERVMEWGQRTLPNGQVVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVCER 81 (619)
T ss_pred CceEEEEecCHHHHHHHHHhhCCCCceeeEECCCcccccCCCCCCCCCEeechhcCCCcCcEEeCCCccccCcCCcCCCC
Confidence 567999999999999999 9999999999997 999999999999655555655 44
Q ss_pred cccCCCC---cCCccceeeccccccchhhhhHH-----------HHHhcccceecceeccCCchHHHHHHHHhcChHHHH
Q 000235 69 CTANMAE---CPGHFGHLELAKPMFHIGFMKTV-----------LSIMRSVCFNCSKILADEDDHKFKQALKIRNPKNRL 134 (1815)
Q Consensus 69 Cg~~~~~---CpGHfGhIeL~~PV~h~~f~~~v-----------~~iL~~vC~~C~~l~~~~~~~~~~~~~~~~~~~~~~ 134 (1815)
||.+..+ ..-+||||+|+.||.|+||++.+ ++.|+.+.++-+.+.+++.++.......+.. ...+
T Consensus 82 CgvE~t~s~vRR~RMG~I~La~PV~HiWylk~~ps~i~~lL~~~~k~le~i~y~~~~~v~~~~~~~~~~~~~~~~-~~~~ 160 (619)
T TIGR02387 82 CGVEVTESRVRRHRMGYIKLAAPVTHVWYLKGIPSYVSILLDMPLRDVEQIVYFNAYVVLNPGNAKNLKYKQLLT-EDQW 160 (619)
T ss_pred CCCEEchhhhHHHhcCceeccCcceeeeecCCCchHHHHHhCCCHHHhhheeeeeeEEEecCCCccchhhhhhhh-HHHH
Confidence 4433222 24799999999999999999953 5668888877767777664332111111111 1122
Q ss_pred HHHHHHhhhccccCCCCCCCCCCCCCCcccccccCCCCccchhhhhcccchhhhhHHhhccccccCCCCccchhcccCCH
Q 000235 135 KKILDACKNKTKCEGGDEIDVPGQDGEEPLKKNKGGCGAQQPKLTIEGMKMIAEYKAQRKKNDDQEQLPEPVERKQTLTA 214 (1815)
Q Consensus 135 ~~i~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~gCg~~~p~i~k~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~p 214 (1815)
.++.+..-. . +. +... .....+|+..-+-....+++..+....+.+... .+.
T Consensus 161 ~~~~~~~~~----~---~~-----~~~~---~~~~~~Ga~ai~~lL~~~dl~~~~~~l~~~~~~-------------~~~ 212 (619)
T TIGR02387 161 LEIEDQIYA----E---DS-----ELEN---EEVVGIGAEALKQLLADLNLEEVAEQLREEING-------------SKG 212 (619)
T ss_pred HHHHHHhcc----c---cc-----cccc---ceeccchHHHHHHHHHhCCHHHHHHHHHHHHHh-------------hhh
Confidence 222222110 0 00 0000 001235554433333444444333222211110 111
Q ss_pred HHHHHHHhhcChhhHHHhcCCCCCCCccceEEeecccCCCCCCCC----------chhHHHHHHHHHHHHHHHHHHHcCC
Q 000235 215 ERVLGVLKRISDEDCQLLGLNPKYARPDWMILQVLPIPPPPVRPS----------DDLTHQLAMIIRHNENLRRQERNGA 284 (1815)
Q Consensus 215 ~~v~~ilk~i~~~d~~~l~~~~~~~~Pe~~il~~lpVpP~~~RP~----------ddlT~~l~~Ii~~N~~lk~~~~~g~ 284 (1815)
.+...++|+|.--+. |.....+||||||++|||||+++||+ ||||.+|++||++|++|+++...++
T Consensus 213 ~~~~~~~krl~~~~~----f~~~~~~PewmiL~~lPV~Pp~lRP~v~l~~g~~~~sDln~lyr~II~rNn~L~~~~~~~~ 288 (619)
T TIGR02387 213 QKRAKLIKRLRVIDN----FIATSSRPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILA 288 (619)
T ss_pred HHHHHHHHHHHHHHH----HHhcCCCcceEEEEecccCCcccCCceEeCCCcccCCCHHHHHHHHHHHHHHHHHHHHcCC
Confidence 334556677654432 33456899999999999999999999 8999999999999999999999999
Q ss_pred ChhhHHHHHHHHHHHHHhhccCCCCCCCcccccCCCChhhhhhhhhhcccccccccCCCCCCCCCceeecCCCCcccccc
Q 000235 285 PAHIISEFAQLLQFHIATYFDNELPGQPRATQRSGRPIKSICSRLKAKEGRIRGNLMGKRVDFSARTVITPDPTINIDQL 364 (1815)
Q Consensus 285 ~~~~i~~~~~~LQ~~V~~~~dn~~~~~p~~~~~~~~p~k~i~qrLkgK~Gr~R~nlmGKRVdfsaRsVIspDP~L~~~ev 364 (1815)
+..++.+.|++||++|++||||+..|.|. ..+++||+|||+|+||||+||||+|||||||||||||||+|||+|++|||
T Consensus 289 p~~i~~~~~~~LQ~aVd~lidn~~~g~~~-~~~~~rp~ksls~~LkGKeGRFR~nLlGKRVDySgRSVI~pdP~L~l~qv 367 (619)
T TIGR02387 289 PEIIVRNEKRMLQEAVDALIDNGRRGRTV-VGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQC 367 (619)
T ss_pred cHHHHHHHHHHHHHHHHHHhcCCCCCCCc-ccccCCchhhHHHHhccCCccccccccccccccCCCceecCCCCccccee
Confidence 99999899999999999999999988764 44567999999999999999999999999999999999999999999999
Q ss_pred cChHHHhhhccCCcccchhHHHHHHHHHHcCCC-CCCCcccccEEEeCCCceeeccccccccccccccccEeeeecccCC
Q 000235 365 GVPWSIALNLTYPETVTPYNIERLKELVEYGPH-PPPGKTGAKYIIRDDGQRLDLRYLKKSSDHHLELGYKVERHLNDGD 443 (1815)
Q Consensus 365 GvP~~~A~~LT~PE~Vt~~Ni~~l~~lv~ng~~-~~pg~~~A~~i~~~~g~~~~l~~~~~~~~~~L~~g~~V~Rhl~dgD 443 (1815)
|||++||++||+ ||||++| +.+|.. ...+ |++++...+ ...|.|+|||+|||
T Consensus 368 GvP~~mA~eLf~-----Pf~i~~L---~~~g~~~~i~~---ak~~i~~~~----------------~~v~~Vlr~v~~gd 420 (619)
T TIGR02387 368 GLPKEMAIELFQ-----PFVIHRL---IRQGIVNNIKA---AKKLIQRAD----------------DEIWSVLQEVITGH 420 (619)
T ss_pred cChHHHHHhcCc-----hHhHHHH---HhcCcccchHH---HHHHHHhcC----------------ChhHHHHHHHhcCC
Confidence 999999999986 5788877 446653 2233 776653321 13588999999999
Q ss_pred eEEEecCCccccccccceeEEeecCCeeeecccCCCCCCCCCCcCccccccCCCHhHHHHHHHHccCCCccccCCCCCCc
Q 000235 444 FVLFNRQPSLHKMSIMGHRIKIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFETRAEVLELMMVPKCIVSPQSNRPV 523 (1815)
Q Consensus 444 ~VL~NRQPsLHk~Simah~vkv~~~~t~rln~~vc~pyNADFDGDEMn~h~Pqs~~araE~~~l~~~~~~i~sp~~g~pi 523 (1815)
+|||||||||||+|||||++++++++||||||+||+||||||||||||||||||++|||||++||++++||+||++|+|+
T Consensus 421 ~VLlNRqPTLHR~sIqAf~~~l~~~ktirlhplvC~~fNADFDGDeMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi 500 (619)
T TIGR02387 421 PVMLNRAPTLHRLGIQAFEPILVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQTEARLLMLASNNVLSPATGEPI 500 (619)
T ss_pred EEEecCCCccchhcceeeeeEEecCCeEEECcccCCcccCCCCCceeeeecCCCHHHHHHHHHHhhchhcEEecCCCcee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeccccccccceecccCC
Q 000235 524 MGIVQDTLLGCRKITKRD 541 (1815)
Q Consensus 524 ~g~~QD~l~g~~~lT~~d 541 (1815)
++++||+|+|+|+||.++
T Consensus 501 ~~~~QD~llg~y~LT~~~ 518 (619)
T TIGR02387 501 VTPSQDMVLGCYYLTALN 518 (619)
T ss_pred Eeechhhhhhhheeeccc
Confidence 999999999999999987
No 15
>CHL00018 rpoC1 RNA polymerase beta' subunit
Probab=100.00 E-value=5.1e-101 Score=947.85 Aligned_cols=477 Identities=26% Similarity=0.418 Sum_probs=359.3
Q ss_pred cccceEEEEcCCHHHHHhcc---------eeEEeeCccccCC--CCCCCCCCCCCCCCcCCCccc---------------
Q 000235 13 AKVRMVQFGILSPDEIRQMS---------VVQIEHGETTERG--KPKPGGLSDPRLGTIDRKMKC--------------- 66 (1815)
Q Consensus 13 ~~i~~i~F~~~S~eeI~~~S---------v~eI~~~~~~~~~--~p~~gGl~D~rlG~~~~~~~C--------------- 66 (1815)
..+..|+.+++|||+|++|| |+||++|+|+++. +|+.+||||.|+..+.+++.|
T Consensus 5 ~~~~~i~I~laSPe~I~~Ws~r~lpng~ivGeV~kp~TinyrT~KPE~dGLFCErIFGP~k~~~C~CGkyk~~~~~~~~~ 84 (663)
T CHL00018 5 YKHQQLRIGLASPQQIRAWAERILPNGEIVGEVTKPYTIHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVIGDEKEDP 84 (663)
T ss_pred cCcCeEEEEecCHHHHHHHHHhhCCCCceeeEECCCccccccCCCCCCCCEeechhcCCCcCCEEeCCCccccCccccCC
Confidence 36789999999999999999 5999999999997 999999999999655566666
Q ss_pred ---cccccCCCC---cCCccceeeccccccchhhhhHH-----------HHHhcccceecceeccCCc-hH---HHHHHH
Q 000235 67 ---ETCTANMAE---CPGHFGHLELAKPMFHIGFMKTV-----------LSIMRSVCFNCSKILADED-DH---KFKQAL 125 (1815)
Q Consensus 67 ---~TCg~~~~~---CpGHfGhIeL~~PV~h~~f~~~v-----------~~iL~~vC~~C~~l~~~~~-~~---~~~~~~ 125 (1815)
+.||.+..+ ..-+||||+|+.||.|+||++.+ ++.|+.+.++=..+..+.. .. .++..+
T Consensus 85 ~~C~~CgVE~t~s~vRR~RMG~I~La~PV~HiWylk~~ps~i~~lL~~~~k~le~~vy~~~~~~~~~~~~~~~~~~~~~~ 164 (663)
T CHL00018 85 KFCEQCGVEFTDSRVRRYRMGYIKLACPVTHVWYLKRLPSYIANLLDKPLKELEGLVYCDFSFARPIAKKPTFLRLRGLF 164 (663)
T ss_pred CccCCcCCEechhhhhHhhcCceeecCcceeehhhcCCchHHHHHhCCCHHHhhheeeeeeEEEEecCCCCChhhhhhhh
Confidence 333332221 23789999999999999999953 4567777766544444411 11 111111
Q ss_pred HhcChHHHHHHHHHHhhhccccCCCCCCCCCCCCCCcccccccCCCCccchhhhhcccchhh-------hhHHhhccccc
Q 000235 126 KIRNPKNRLKKILDACKNKTKCEGGDEIDVPGQDGEEPLKKNKGGCGAQQPKLTIEGMKMIA-------EYKAQRKKNDD 198 (1815)
Q Consensus 126 ~~~~~~~~~~~i~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~gCg~~~p~i~k~~~~l~~-------~~~~~~~~~~~ 198 (1815)
. .....+.++....... .. . .. ......++|+..-+-....+++.. +|+...++. .
T Consensus 165 ~--~~~~~~~~~~~~~~~~---~~---~-------~~-~~~~~~~~Ga~ai~~lL~~ldL~~~~~~~~~~~~~~~~~~-~ 227 (663)
T CHL00018 165 E--YEIQSWKYSIPLFFST---QG---F-------DT-FRNREISTGAGAIREQLADLDLRIIIDNSLVEWKELGEEG-S 227 (663)
T ss_pred h--hhHHHHHHHHHHHhcc---cc---c-------cc-ccchhhhHHHHHHHHHHhhCCHHHHHHHHHHHHHHhhhcc-c
Confidence 1 0011122222211000 00 0 00 000112355543333333444322 232211100 0
Q ss_pred cCCCCccchhcccCCHHHHHHHHhhcChhhHHHhcCCCCCCCccceEEeecccCCCCCCCC----------chhHHHHHH
Q 000235 199 QEQLPEPVERKQTLTAERVLGVLKRISDEDCQLLGLNPKYARPDWMILQVLPIPPPPVRPS----------DDLTHQLAM 268 (1815)
Q Consensus 199 ~~~~~~~~~~~~~l~p~~v~~ilk~i~~~d~~~l~~~~~~~~Pe~~il~~lpVpP~~~RP~----------ddlT~~l~~ 268 (1815)
.+.+ .+.+.+ -.+...++|+|.--+. |.....+||||||++|||||+++||+ ||||.+|++
T Consensus 228 ~~~~----~~~~~~-~~~~~~l~kRl~~~~~----f~~~~~~PewmiL~~lPV~Pp~lRP~v~l~~g~~~~sDln~lyr~ 298 (663)
T CHL00018 228 TGNE----WEDRKI-GRRKDFLVRRIKLAKH----FIRTNIEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRR 298 (663)
T ss_pred cccc----hhhhhh-HHHHHHHHHHHHHHHH----HHhcCCCccEEEEEeeeeCCCcccCceEcCCCcccCCChHHHHHH
Confidence 0000 001100 1122234566654443 22346899999999999999999998 899999999
Q ss_pred HHHHHHHHHHHHHc--CCChhhHHHHHHHHHHHHHhhccCCCCCCCcccccCCCChhhhhhhhhhcccccccccCCCCCC
Q 000235 269 IIRHNENLRRQERN--GAPAHIISEFAQLLQFHIATYFDNELPGQPRATQRSGRPIKSICSRLKAKEGRIRGNLMGKRVD 346 (1815)
Q Consensus 269 Ii~~N~~lk~~~~~--g~~~~~i~~~~~~LQ~~V~~~~dn~~~~~p~~~~~~~~p~k~i~qrLkgK~Gr~R~nlmGKRVd 346 (1815)
||.+|++|+++... ++|..++.+.|++||++|++||||++.|.+... .++||+|||+|+||||+||||+||||||||
T Consensus 299 II~rNn~L~~~~~~~~~~p~~~i~~~~~~LQ~aVd~lidn~~~g~~~~~-~~~r~~ksls~~LkGK~GrFR~NLlGKRVD 377 (663)
T CHL00018 299 VIYRNNTLTDLLTTSRSTPGELVMCQKKLLQEAVDALLDNGIRGQPMRD-GHNKPYKSFSDVIEGKEGRFRENLLGKRVD 377 (663)
T ss_pred HHHHHHHHHHHHhcccCCcHHHHHHHHHHHHHHHHHHhcCCCCCCcccc-CCCCCCCCccccccCcCccccccccccccc
Confidence 99999999999888 889999999999999999999999998876533 357999999999999999999999999999
Q ss_pred CCCceeecCCCCcccccccChHHHhhhccCCcccchhHHHHHHHHHHcCCCCCCCcccccEEEeCCCceeeccccccccc
Q 000235 347 FSARTVITPDPTINIDQLGVPWSIALNLTYPETVTPYNIERLKELVEYGPHPPPGKTGAKYIIRDDGQRLDLRYLKKSSD 426 (1815)
Q Consensus 347 fsaRsVIspDP~L~~~evGvP~~~A~~LT~PE~Vt~~Ni~~l~~lv~ng~~~~pg~~~A~~i~~~~g~~~~l~~~~~~~~ 426 (1815)
|||||||+|||+|++||||||..||++||+|+ + +++|+.+|+.... ..|++++...
T Consensus 378 ySgRSVIvpdP~L~l~e~GlP~~mA~eL~~P~-----~---i~~Li~~~~~~~~--~~Ak~~i~~~-------------- 433 (663)
T CHL00018 378 YSGRSVIVVGPSLSLHQCGLPREIAIELFQPF-----V---IRGLIRQHLASNI--RAAKSKIREK-------------- 433 (663)
T ss_pred cCCCceecCCCcccccccCChHHHHHHcCcHH-----H---HHHHHhcCccccH--HHHHHHHHhc--------------
Confidence 99999999999999999999999999999985 3 4667888876321 2266554321
Q ss_pred cccccccEeeeecccCCeEEEecCCccccccccceeEEeecCCeeeecccCCCCCCCCCCcCccccccCCCHhHHHHHHH
Q 000235 427 HHLELGYKVERHLNDGDFVLFNRQPSLHKMSIMGHRIKIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFETRAEVLE 506 (1815)
Q Consensus 427 ~~L~~g~~V~Rhl~dgD~VL~NRQPsLHk~Simah~vkv~~~~t~rln~~vc~pyNADFDGDEMn~h~Pqs~~araE~~~ 506 (1815)
...+|+|+|||+|||+|||||||||||||||||++++++++||||||+||+||||||||||||||||||++|||||+.
T Consensus 434 --~~~~~~Vlr~v~~gd~VLlNRqPTLHR~sIqAf~~~L~~gktIrLhplvC~~fNADFDGDqMnvHvPqS~eA~aEa~~ 511 (663)
T CHL00018 434 --EPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARL 511 (663)
T ss_pred --CCcccEeeeehhcCceeeecCCCcccccccceeeEEecCCCeEEeCcccCCcccCCccCcEEEEecCCCHHHHHHHHH
Confidence 236899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HccCCCccccCCCCCCceeccccccccceecccCCC
Q 000235 507 LMMVPKCIVSPQSNRPVMGIVQDTLLGCRKITKRDT 542 (1815)
Q Consensus 507 l~~~~~~i~sp~~g~pi~g~~QD~l~g~~~lT~~d~ 542 (1815)
||++.+||+||++|+|+++++||+|+|+|+||.+|.
T Consensus 512 Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~ 547 (663)
T CHL00018 512 LMFSHMNLLSPAIGDPISVPSQDMLLGLYVLTIGNR 547 (663)
T ss_pred HhcCccceeEcCCCceeEeechhhhhhhheecccCC
Confidence 999999999999999999999999999999999884
No 16
>cd02584 RNAP_II_Rpb1_C Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain. RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.
Probab=100.00 E-value=6.4e-95 Score=872.44 Aligned_cols=374 Identities=70% Similarity=1.112 Sum_probs=345.9
Q ss_pred hccCHHHHHHHHHHHHHHhhcCcccCCCchhhHhhhccCCccccccccccccccccccccccccceeeeehhhcccCCCC
Q 000235 1044 HRLTREAFEWVIGEIESRFLQSLVAPGEMIGCVAAQSIGEPATQMTLNTFHYAGVSAKNVTLGVPRLREIINVAKKIKTP 1123 (1815)
Q Consensus 1044 ~~l~~~~~~~~l~ei~~ky~~slv~PGEaVG~iAAQSIGEPaTQMTLnTFH~AGv~~~NVTlGvPRLkEIin~ak~ikTP 1123 (1815)
|++++++|+|++++|+.||.+++|+||||||+|||||||||+|||||||||||||++|||||||||||||||++|+||||
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~ge~vg~~aaQSiGEP~TQmTLnTFH~AGVas~NVTlGVPRLkEIInasK~ikTP 80 (410)
T cd02584 1 YRLNKEAFDWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKNIKTP 80 (410)
T ss_pred CCCCHHHHHHHHHHHHHHHHHhhcCCCCCcchhhhhhcCCchhcccccccccccccccccccCccchHHHhhcccCCCCC
Confidence 56889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceEEEeCCCCcchHHHHHHHHhhhccccccccceeeEEEEcCCCCceEEEcccceeheeccCCCCcccccccCCcEEEEE
Q 000235 1124 SLSVFLKPGVNSTKERAKNVQCALEYTTLRSVTEATEVWYDPDPMGTIIEEDVEFVKSYYEMPDEDIAPEKISPWLLRIE 1203 (1815)
Q Consensus 1124 ~mtv~l~~~~~~~~~~a~~v~~~le~~tL~dv~~~~~i~ydp~~~~~~i~~d~~~~~~~~~~~~~~~~~~~~~~~~lrl~ 1203 (1815)
+|+|+|.++++.|++.|+.++.+||+++|+||+.+++++|||+..++++++|.+|++.||+++|++......++|++|++
T Consensus 81 ~~tv~L~~~~~~d~~~A~~v~~~IE~t~l~dv~~~~~i~ydp~~~~~~i~~d~~~i~~~~~~~d~~~~~~~~~~~~lrl~ 160 (410)
T cd02584 81 SLTVYLEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVESYFEFPDEDVEQDRLSPWLLRIE 160 (410)
T ss_pred eEEEEecCcccchHHHHHHHHhheeEeEHHHhhhheEEEecCcccceeecccHHHHHHhhccCcccccccccCCeeEEEE
Confidence 99999999988899999999999999999999999999999999999999999999999999999887788999999999
Q ss_pred echhhhhcccCCHHHHHHHHhhhcCCCceeeecCCCccceEEEEEEccCCCCCCCCCCCcchhHHHHHHHHhhccc----
Q 000235 1204 LNREMMVDKKLSMAAVAEKINQEFDDDLTCIFNDDNADKLILRIRIMNDEAPKGELNDESAEDDVFLKKIESNMLT---- 1279 (1815)
Q Consensus 1204 l~~~~~~~~~l~~~~i~~~i~~~~~~~~~~~~~~dn~~~~~~~ir~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~---- 1279 (1815)
||+++|.++++++++|+.+|+..+++++.++.+++|.+++++++|+....++.. ++.+++.|+.+++..+|.
T Consensus 161 ld~~~~~~~~i~~~~i~~~i~~~~~~~~~v~~~~~~~~~~~iri~~~~~~~~~~----~~~~~~~~l~~~~~~~l~~i~l 236 (410)
T cd02584 161 LDRKKMTDKKLSMEQIAKKIKEEFKDDLNVIFSDDNAEKLVIRIRIINDDEEKE----EDSEDDVFLKKIESNMLSDMTL 236 (410)
T ss_pred ECHHHHHHcCCCHHHHHHHHHHhcCCCeEEEEcCCCcceeEEEEEecCcccccc----ccchhHHHHHHHHHhhCCCcEE
Confidence 999999999999999999999999989999888888888888988765331111 111234455554432221
Q ss_pred --------------------------------cceecccchhhhhccccccccccccccHHHHHHhhcHHHHHHHHHHHH
Q 000235 1280 --------------------------------EMALRGVNLLAVMCHEDVDARRTTSNHLIEIIEVLGIEAVRRALLDEL 1327 (1815)
Q Consensus 1280 --------------------------------~~~~~G~nl~~vl~~~~vD~~rt~sNdI~eI~~vlGIEAAR~~Ii~Ei 1327 (1815)
.+.++|+||.++|++++||++||+||||+||+++|||||||++|++||
T Consensus 237 ~Gi~~I~r~~i~~~~~~~~~~~~g~~~~~~~~~l~teG~nl~~v~~~~~Vd~~rt~sNdI~ei~~~lGIEAaR~~ii~Ei 316 (410)
T cd02584 237 KGIEGIRKVFIREENKKKVDIETGEFKKREEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEVLGIEAARKALLKEL 316 (410)
T ss_pred eCCCCceEEEEEcCCceEecCCCCcccCCcceEEEecCcCHHHHhCCCCCccccCEeCCHHHHHHhcCHHHHHHHHHHHH
Confidence 256678999999999999999999999999999999999999999999
Q ss_pred HHhhhcCcccccchhHHHHHhhhhccceecccccccccccCCccccccchHHHHHHHHHHHhhcCcccccccccccccCC
Q 000235 1328 RVVISFDGSYVNYRHLAILCDTMTYRGHLMAITRHGINRNDTGPMMRCSFEETVDILLDAAVFAESDYLRGVTENIMLGQ 1407 (1815)
Q Consensus 1328 ~~V~~~~Gi~Vn~RHL~LlaD~MT~~G~~~~itR~Gi~~~~~spL~~aSFEeT~~~L~~AA~~ge~D~l~gvsenIi~G~ 1407 (1815)
+.||+.||++||+|||+||||+||++|++++||||||++.+.|||++||||+|+++|++||++|+.|+|+|||||||+|+
T Consensus 317 ~~v~~~~Gi~Vd~RHl~LiaD~MT~~G~~~~i~R~Gi~~~~~S~l~~aSFE~t~~~L~~AA~~g~~D~l~gvse~Ii~G~ 396 (410)
T cd02584 317 RNVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVSENIMLGQ 396 (410)
T ss_pred HHHHHhcCCccCHHHHHHHHHHHhhceEEeeEeeeeeeccCCChhhhccchhHHHHHHHHHhcCCCCcCCCchHheeecC
Confidence 99999999999999999999999999999999999999988999999999999999999999999999999999999999
Q ss_pred ccccCccceeeccc
Q 000235 1408 LAPIGTGDCSLYLN 1421 (1815)
Q Consensus 1408 ~~p~GTG~fdll~~ 1421 (1815)
++|+|||+|||++|
T Consensus 397 ~~~~GTG~f~l~~d 410 (410)
T cd02584 397 LAPIGTGCFDLLLD 410 (410)
T ss_pred ccccccceEEEEeC
Confidence 99999999999986
No 17
>smart00663 RPOLA_N RNA polymerase I subunit A N-terminus.
Probab=100.00 E-value=6.7e-93 Score=823.62 Aligned_cols=284 Identities=60% Similarity=1.001 Sum_probs=273.1
Q ss_pred cceEEeecccCCCCCCCC----------chhHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHhhccCCCCCC
Q 000235 242 DWMILQVLPIPPPPVRPS----------DDLTHQLAMIIRHNENLRRQERNGAPAHIISEFAQLLQFHIATYFDNELPGQ 311 (1815)
Q Consensus 242 e~~il~~lpVpP~~~RP~----------ddlT~~l~~Ii~~N~~lk~~~~~g~~~~~i~~~~~~LQ~~V~~~~dn~~~~~ 311 (1815)
+||||++|||||+++||+ ||||.+|.+||++|+.|++..+.|++.+++.+.|..||.+|++||||+ +.
T Consensus 1 e~fil~~lpVpP~~~RP~v~~~~~~~~eddlt~~l~~Ii~~N~~L~~~~~~~~~~~~~~~~~~~LQ~~v~~~~d~~--~~ 78 (295)
T smart00663 1 EWMILTVLPVPPPCLRPSVSLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPEHIIRNEKRLLQEAVDTLFDNE--GL 78 (295)
T ss_pred CeEEEeccccCCCCCCCcEEeCCCcccCCcHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHccC--CC
Confidence 799999999999999998 899999999999999999999999999999999999999999999998 44
Q ss_pred CcccccCCCChhhhhhhhhhcccccccccCCCCCCCCCceeecCCCCcccccccChHHHhhhccCCcccchhHHHHHHHH
Q 000235 312 PRATQRSGRPIKSICSRLKAKEGRIRGNLMGKRVDFSARTVITPDPTINIDQLGVPWSIALNLTYPETVTPYNIERLKEL 391 (1815)
Q Consensus 312 p~~~~~~~~p~k~i~qrLkgK~Gr~R~nlmGKRVdfsaRsVIspDP~L~~~evGvP~~~A~~LT~PE~Vt~~Ni~~l~~l 391 (1815)
+.+.++++++++||+|||+||+||||+|||||||||||||||+|||+|++||||||..||++||+||.||.||+++|++|
T Consensus 79 ~~~~~~~~~~~~~i~~~l~gK~G~~R~nllGKRvd~s~RsVI~pdP~l~~~evgiP~~~A~~Lt~pe~v~~~n~~~l~~l 158 (295)
T smart00663 79 PRARQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKL 158 (295)
T ss_pred cccccCCCCCcccccccccCcCCccccccccccccccCceEEeCCCCcceeEeeCCHHHHHhCCcCEEEhHHHHHHHHHH
Confidence 55566778999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHcCCCCCCCcccccEEEeCCCceeeccccccc-cccccccccEeeeecccCCeEEEecCCccccccccceeEEeecCCe
Q 000235 392 VEYGPHPPPGKTGAKYIIRDDGQRLDLRYLKKS-SDHHLELGYKVERHLNDGDFVLFNRQPSLHKMSIMGHRIKIMPYST 470 (1815)
Q Consensus 392 v~ng~~~~pg~~~A~~i~~~~g~~~~l~~~~~~-~~~~L~~g~~V~Rhl~dgD~VL~NRQPsLHk~Simah~vkv~~~~t 470 (1815)
|.||+ || |+||++ |.+++|++.++. ....|++||+|+|||+|||+|||||||||||+|||||+|||++++|
T Consensus 159 v~ng~---pg---a~~i~~--g~~~~l~~~~~~~~~~~l~~g~~v~r~l~dgd~Vl~NRqPsLHr~si~a~~v~v~~~~t 230 (295)
T smart00663 159 VRNGP---NG---AKYIIR--GKKTNLKLAKRSKIAKHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKT 230 (295)
T ss_pred HhcCC---CC---ceEEEe--CcEEEchhhhhHHHHhcCccccEeheehhcCCEEEEecCCccccccceeEEEEEecCce
Confidence 99999 99 999997 888999887654 5667899999999999999999999999999999999999999999
Q ss_pred eeecccCCCCCCCCCCcCccccccCCCHhHHHHHHHHccCCCccccCCCCCCceeccccccccce
Q 000235 471 FRLNLSVTSPYNADFDGDEMNMHVPQSFETRAEVLELMMVPKCIVSPQSNRPVMGIVQDTLLGCR 535 (1815)
Q Consensus 471 ~rln~~vc~pyNADFDGDEMn~h~Pqs~~araE~~~l~~~~~~i~sp~~g~pi~g~~QD~l~g~~ 535 (1815)
|||||+||+||||||||||||+|+|||++||||+++||++.+|++||++|+|++|++||+|+|+|
T Consensus 231 ir~n~~~c~~fNADFDGDeMnih~pqs~~a~aEa~~Lm~~~~~~~sp~~g~p~~~~~QD~l~g~~ 295 (295)
T smart00663 231 IRLNPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295 (295)
T ss_pred EEecCccCCcccCCcCCCEEEEecCCCHHHHHHHHHHhhhhhccccCCCCCeeEeeecceeeecC
Confidence 99999999999999999999999999999999999999999999999999999999999999986
No 18
>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=100.00 E-value=2.7e-87 Score=794.95 Aligned_cols=331 Identities=38% Similarity=0.582 Sum_probs=297.1
Q ss_pred HhhccCHH-HHHHHHHHHHHHhhcCcccCCCchhhHhhhccCCccccccccccccccccccccccccceeeeehhhcccC
Q 000235 1042 KEHRLTRE-AFEWVIGEIESRFLQSLVAPGEMIGCVAAQSIGEPATQMTLNTFHYAGVSAKNVTLGVPRLREIINVAKKI 1120 (1815)
Q Consensus 1042 ~~~~l~~~-~~~~~l~ei~~ky~~slv~PGEaVG~iAAQSIGEPaTQMTLnTFH~AGv~~~NVTlGvPRLkEIin~ak~i 1120 (1815)
.+++++++ +|+|++++|+.||.+++|+||||||+|||||||||+|||||||||||||++|||||||||||||||++|+|
T Consensus 15 ~~~~~~~~~~~~~~l~~i~~ky~~alv~PGeaVG~IAAQSIGEP~TQMTLnTFH~AGVas~nVTlGVPRlkEIINa~k~i 94 (367)
T TIGR02389 15 KKREISDKEELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDARKTP 94 (367)
T ss_pred HHcCCCHHHHHHHHHHHHHHHHHHhcCCCccccchhhhhhcCCccccccccccccccccccCccccchhHHHHhhcccCC
Confidence 56788888 99999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCceEEEeCCCCcchHHHHHHHHhhhccccccccceeeEEEEcCCCCceEEEcccceeheeccCCCCcccccccCCcEE
Q 000235 1121 KTPSLSVFLKPGVNSTKERAKNVQCALEYTTLRSVTEATEVWYDPDPMGTIIEEDVEFVKSYYEMPDEDIAPEKISPWLL 1200 (1815)
Q Consensus 1121 kTP~mtv~l~~~~~~~~~~a~~v~~~le~~tL~dv~~~~~i~ydp~~~~~~i~~d~~~~~~~~~~~~~~~~~~~~~~~~l 1200 (1815)
|||+|+|||.++.+.+++.|++++.+||+++|+||+++++++|+ .|++
T Consensus 95 ~TP~~ti~L~~~~~~~~~~a~~v~~~iE~t~l~dv~~~~~~~~~--------------------------------~~~l 142 (367)
T TIGR02389 95 STPSMTIYLEDEYEKDREKAEEVAKKIEATKLEDVAKDISIDLA--------------------------------DMTV 142 (367)
T ss_pred CCCeEEEEecCcchhhHHHHHHHHHHhhheeHHHHHhhhheecc--------------------------------CcEE
Confidence 99999999999988889999999999999999999987775432 4689
Q ss_pred EEEechhhhhcccCCHHHHHHHHhhhcCCCceeeecCCCccceEEEEEEccCCCCCCCCCCCcchhHHHHHHHHhhcc--
Q 000235 1201 RIELNREMMVDKKLSMAAVAEKINQEFDDDLTCIFNDDNADKLILRIRIMNDEAPKGELNDESAEDDVFLKKIESNML-- 1278 (1815)
Q Consensus 1201 rl~l~~~~~~~~~l~~~~i~~~i~~~~~~~~~~~~~~dn~~~~~~~ir~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l-- 1278 (1815)
+++||+++|.++++++++|.++|.+.++....++. .++..++++...+. ...++.++..++
T Consensus 143 ~i~ld~~~l~~~~i~~~~i~~~i~~~~~~~~~~~~----~~~~~i~i~~~~~~-------------~~~l~~l~~~l~~~ 205 (367)
T TIGR02389 143 IIELDEEQLKERGITVDDVEKAIKKAKLGKVIEID----MDGNTITIKPPKPS-------------LKELRKLKEKIKNL 205 (367)
T ss_pred EEEECHHHHHhcCCCHHHHHHHHHHhcccccceee----cCCCEEEEEecCch-------------HHHHHHHHHHhhhc
Confidence 99999999999999999999999887655544331 23456777654211 112333332221
Q ss_pred -------------------ccceecccchhhhhccccccccccccccHHHHHHhhcHHHHHHHHHHHHHHhhhcCccccc
Q 000235 1279 -------------------TEMALRGVNLLAVMCHEDVDARRTTSNHLIEIIEVLGIEAVRRALLDELRVVISFDGSYVN 1339 (1815)
Q Consensus 1279 -------------------~~~~~~G~nl~~vl~~~~vD~~rt~sNdI~eI~~vlGIEAAR~~Ii~Ei~~V~~~~Gi~Vn 1339 (1815)
..+.++|+||+++|.+++||++|++||||+||+++|||||||++|++||+.||+.||++||
T Consensus 206 ~v~Gi~gI~r~~i~~~~~~~~l~teG~nl~~v~~~~~VD~~rt~sNdI~ei~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd 285 (367)
T TIGR02389 206 HIKGIKGIKRVVIRKEGDEYVIYTEGSNLKEVLKLEGVDKTRTTTNDIHEIAEVLGIEAARNAIIEEIKRTLEEQGLDVD 285 (367)
T ss_pred eEeCCCCceEEEEECCCCeEEEEEeccCHHHHHcCCCCccccCccCCHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCeec
Confidence 1367788999999999999999999999999999999999999999999999999999999
Q ss_pred chhHHHHHhhhhccceecccccccccccCCccccccchHHHHHHHHHHHhhcCcccccccccccccCCccccCccceeec
Q 000235 1340 YRHLAILCDTMTYRGHLMAITRHGINRNDTGPMMRCSFEETVDILLDAAVFAESDYLRGVTENIMLGQLAPIGTGDCSLY 1419 (1815)
Q Consensus 1340 ~RHL~LlaD~MT~~G~~~~itR~Gi~~~~~spL~~aSFEeT~~~L~~AA~~ge~D~l~gvsenIi~G~~~p~GTG~fdll 1419 (1815)
+|||+||||+||++|++++||||||++.+.|||++||||+|+++|++||++|++|+|+|||||||+|+++|+|||+|||+
T Consensus 286 ~RHl~LiaD~MT~~G~~~~i~R~Gi~~~~~S~l~~aSFE~t~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~~~l~ 365 (367)
T TIGR02389 286 IRHLMLVADLMTWDGEVRQIGRHGISGEKASVLARAAFEVTVKHLLDAAIRGEVDELAGVIENIIVGQPIPLGTGDVDLV 365 (367)
T ss_pred HHHHHHHHHHhcCCceEEeccccccccCCCCHHHhcChHhHHHHHHHHhhcCCCCcCCChHHHhhcCCCcCCcCCeEEEe
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred cc
Q 000235 1420 LN 1421 (1815)
Q Consensus 1420 ~~ 1421 (1815)
++
T Consensus 366 ~~ 367 (367)
T TIGR02389 366 MD 367 (367)
T ss_pred eC
Confidence 74
No 19
>cd06528 RNAP_A'' A'' subunit of Archaeal RNA Polymerase (RNAP). Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.
Probab=100.00 E-value=3.4e-85 Score=778.66 Aligned_cols=334 Identities=42% Similarity=0.620 Sum_probs=298.2
Q ss_pred HHHHHhhccCHHHHHHHHHHHHHHhhcCcccCCCchhhHhhhccCCccccccccccccccccccccccccceeeeehhhc
Q 000235 1038 KRVLKEHRLTREAFEWVIGEIESRFLQSLVAPGEMIGCVAAQSIGEPATQMTLNTFHYAGVSAKNVTLGVPRLREIINVA 1117 (1815)
Q Consensus 1038 ~~~~~~~~l~~~~~~~~l~ei~~ky~~slv~PGEaVG~iAAQSIGEPaTQMTLnTFH~AGv~~~NVTlGvPRLkEIin~a 1117 (1815)
++++.++++++++|+|++++++.||.+++|+||||||+|||||||||+|||||||||||||++|||||||||||||||++
T Consensus 8 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~Ge~vG~iaAQSiGEP~TQMTLnTFH~AGVas~nVTlGVPRlkEIIna~ 87 (363)
T cd06528 8 EEVLKEHGLTLSEAEEIIKEVLREYLRSLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRLIEIVDAR 87 (363)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHHHHhhccCccccceeeeecCccceecccccccccccccccCccccccHHHHhhcc
Confidence 45678899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCceEEEeCCCCcchHHHHHHHHhhhccccccccceeeEEEEcCCCCceEEEcccceeheeccCCCCcccccccCC
Q 000235 1118 KKIKTPSLSVFLKPGVNSTKERAKNVQCALEYTTLRSVTEATEVWYDPDPMGTIIEEDVEFVKSYYEMPDEDIAPEKISP 1197 (1815)
Q Consensus 1118 k~ikTP~mtv~l~~~~~~~~~~a~~v~~~le~~tL~dv~~~~~i~ydp~~~~~~i~~d~~~~~~~~~~~~~~~~~~~~~~ 1197 (1815)
|+||||+|+|+|.++.+.+++.|++++.+||+++|+||++++++.++ .
T Consensus 88 K~i~TP~mti~L~~~~~~~~~~a~~v~~~iE~t~l~di~~~~~i~~~--------------------------------~ 135 (363)
T cd06528 88 KEPSTPTMTIYLEEEYKYDREKAEEVARKIEETTLENLAEDISIDLF--------------------------------N 135 (363)
T ss_pred cCCCCceEEEEecCcchhhHHHHHHHHHhhceeEHHHhhhheEEecc--------------------------------C
Confidence 99999999999999888889999999999999999999998887421 3
Q ss_pred cEEEEEechhhhhcccCCHHHHHHHHhhhcCCCceeeecCCCccceEEEEEEccCCCCCCCCCCCcchhHHHHHHHHhhc
Q 000235 1198 WLLRIELNREMMVDKKLSMAAVAEKINQEFDDDLTCIFNDDNADKLILRIRIMNDEAPKGELNDESAEDDVFLKKIESNM 1277 (1815)
Q Consensus 1198 ~~lrl~l~~~~~~~~~l~~~~i~~~i~~~~~~~~~~~~~~dn~~~~~~~ir~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ 1277 (1815)
|+++++||+++|.++++++++|.++|.+.++.++.+ +++.. ++ +.... + .+..+|+.++..+
T Consensus 136 ~~l~i~ld~~~l~~~~l~~~~i~~~i~~~~~~~~~~---~~~~~---~~--~~~~~--~--------~~~~~l~~l~~~l 197 (363)
T cd06528 136 MRITIELDEEMLEDRGITVDDVLKAIEKLKKGKVGE---EGDVT---LI--VLKAE--E--------PSIKELRKLAEKI 197 (363)
T ss_pred cEEEEEECHHHHHHcCCCHHHHHHHHHHhcCCcccc---cCCcc---EE--EEcCC--c--------chHHHHHHHHHhh
Confidence 889999999999999999999999998877665432 11111 11 11110 0 0123444444333
Q ss_pred c---------------------ccceecccchhhhhccccccccccccccHHHHHHhhcHHHHHHHHHHHHHHhhhcCcc
Q 000235 1278 L---------------------TEMALRGVNLLAVMCHEDVDARRTTSNHLIEIIEVLGIEAVRRALLDELRVVISFDGS 1336 (1815)
Q Consensus 1278 l---------------------~~~~~~G~nl~~vl~~~~vD~~rt~sNdI~eI~~vlGIEAAR~~Ii~Ei~~V~~~~Gi 1336 (1815)
+ ..+.++|+||+++|.+++||++|++||||+||+++|||||||++|++||+.||+.||+
T Consensus 198 ~~~~v~Gi~gI~r~~i~~~~~~~~l~teG~nl~~v~~~~~Vd~~rt~sNdI~ei~~~lGIEAaR~~ii~Ei~~v~~~~Gi 277 (363)
T cd06528 198 LNTKIKGIKGIKRVIVRKEEDEYVIYTEGSNLKAVLKVEGVDPTRTTTNNIHEIEEVLGIEAARNAIINEIKRTLEEQGL 277 (363)
T ss_pred cccEEeCCCCceEEEEecCCceEEEEecCcCHHHHhcCCCCcccccccCCHHHHHHhCCHHHHHHHHHHHHHHHHHhcCC
Confidence 2 1356788999999999999999999999999999999999999999999999999999
Q ss_pred cccchhHHHHHhhhhccceecccccccccccCCccccccchHHHHHHHHHHHhhcCcccccccccccccCCccccCccce
Q 000235 1337 YVNYRHLAILCDTMTYRGHLMAITRHGINRNDTGPMMRCSFEETVDILLDAAVFAESDYLRGVTENIMLGQLAPIGTGDC 1416 (1815)
Q Consensus 1337 ~Vn~RHL~LlaD~MT~~G~~~~itR~Gi~~~~~spL~~aSFEeT~~~L~~AA~~ge~D~l~gvsenIi~G~~~p~GTG~f 1416 (1815)
+||+|||+||||+||++|+++++||+||++.+.|||++||||+|+++|++||++|+.|+|.|||||||+||++|+|||+|
T Consensus 278 ~Vd~rHl~LiaD~MT~~G~~~~i~R~gi~~~~~S~L~~aSFE~t~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~~ 357 (363)
T cd06528 278 DVDIRHIMLVADIMTYDGEVRQIGRHGIAGEKPSVLARAAFEVTVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTGDV 357 (363)
T ss_pred eecHHHHHHHHHHhccCCceecccchhhcCCCCChhhhCchhhHHHHHHHHHhcCCCCcCCCcHHHeeeCCCCCCcCCee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeccc
Q 000235 1417 SLYLN 1421 (1815)
Q Consensus 1417 dll~~ 1421 (1815)
||++|
T Consensus 358 ~l~~d 362 (363)
T cd06528 358 ELTMD 362 (363)
T ss_pred EEEec
Confidence 99987
No 20
>PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Probab=100.00 E-value=1e-84 Score=784.19 Aligned_cols=331 Identities=36% Similarity=0.555 Sum_probs=290.5
Q ss_pred HHHhhccCHHHHHHHHHHHHHHhhcCcccCCCchhhHhhhccCCccccccccccccccccccccccccceeeeehhhccc
Q 000235 1040 VLKEHRLTREAFEWVIGEIESRFLQSLVAPGEMIGCVAAQSIGEPATQMTLNTFHYAGVSAKNVTLGVPRLREIINVAKK 1119 (1815)
Q Consensus 1040 ~~~~~~l~~~~~~~~l~ei~~ky~~slv~PGEaVG~iAAQSIGEPaTQMTLnTFH~AGv~~~NVTlGvPRLkEIin~ak~ 1119 (1815)
++.+++++.++|+|++++|+.+|.+++|+||||||+|||||||||+|||||||||||||+++|||||||||+||||++|+
T Consensus 152 ~~~~~~l~~~~~~~i~~ei~~~y~~~~v~pGE~VG~IAAQSIGEP~TQMTLnTFH~AGVas~NVTlGVPRLkEIINa~K~ 231 (509)
T PRK14897 152 AMKKKELSDDEYEEILRRIREEYERARVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEMNVTLGLPRLIEIVDARKK 231 (509)
T ss_pred HHHHcCCCHHHHHHHHHHHHHHHHHhccCCCCCcchhhhhhhCCccccccccccccccccccccccCcchhHHHhhcccC
Confidence 56788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCceEEEeCCCCcchHHHHHHHHhhhccccccccceeeEEEEcCCCCceEEEcccceeheeccCCCCcccccccCCcE
Q 000235 1120 IKTPSLSVFLKPGVNSTKERAKNVQCALEYTTLRSVTEATEVWYDPDPMGTIIEEDVEFVKSYYEMPDEDIAPEKISPWL 1199 (1815)
Q Consensus 1120 ikTP~mtv~l~~~~~~~~~~a~~v~~~le~~tL~dv~~~~~i~ydp~~~~~~i~~d~~~~~~~~~~~~~~~~~~~~~~~~ 1199 (1815)
|+||+|+|+|.++++.|++.|++++.+||+++|+||+..+ .. ...|.
T Consensus 232 isTP~mtiyL~~~~~~d~e~A~~V~~~IE~ttL~dv~~~~--------------------~d-------------~~~~~ 278 (509)
T PRK14897 232 PSTPTMTIYLKKDYREDEEKVREVAKKIENTTLIDVADII--------------------TD-------------IAEMS 278 (509)
T ss_pred CCCceEEEEecCcccccHHHHHHHHhhheeeEHHHHHHHH--------------------HH-------------hccce
Confidence 9999999999999888999999999999999999997521 11 12467
Q ss_pred EEEEechhhhhcccCCHHHHHHHHhhhcCCCceeeecCCCccceEEEEEEccCCCCCCCCCCCcchhHHHHHHHHhhcc-
Q 000235 1200 LRIELNREMMVDKKLSMAAVAEKINQEFDDDLTCIFNDDNADKLILRIRIMNDEAPKGELNDESAEDDVFLKKIESNML- 1278 (1815)
Q Consensus 1200 lrl~l~~~~~~~~~l~~~~i~~~i~~~~~~~~~~~~~~dn~~~~~~~ir~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l- 1278 (1815)
++++||+++|.++++++++|.++|.+.. ...+..+++ .+++..... ....++++...+.
T Consensus 279 i~i~Ld~~~l~~~~l~~~~I~~~I~~~~---~~~~~~~~~----~I~i~~~~~-------------~~~~L~~l~~~l~~ 338 (509)
T PRK14897 279 VVVELDEEKMKERLIEYDDILAAISKLT---FKTVEIDDG----IIRLKPQQP-------------SFKKLYLLAEKVKS 338 (509)
T ss_pred EEEEECHHHHHHcCCCHHHHHHHHHhcc---ceEEecCCC----EEEEEeCch-------------HHHHHHHHHHHhhc
Confidence 9999999999999999999999997632 122223322 233333210 0111222211110
Q ss_pred ----------------------ccceecccchhhhhccccccccccccccHHHHHHhhcHHHHHHHHHHHHHHhhhcCcc
Q 000235 1279 ----------------------TEMALRGVNLLAVMCHEDVDARRTTSNHLIEIIEVLGIEAVRRALLDELRVVISFDGS 1336 (1815)
Q Consensus 1279 ----------------------~~~~~~G~nl~~vl~~~~vD~~rt~sNdI~eI~~vlGIEAAR~~Ii~Ei~~V~~~~Gi 1336 (1815)
..+.++|+||.++|++++||++||+||||+||+++|||||||++|++||+.||+.||+
T Consensus 339 i~I~GipgI~r~~i~~~~~~~~~~L~TeG~NL~~vl~~~~VD~~rt~SNdI~eI~~vlGIEAAR~~Ii~Ei~~V~~~~Gi 418 (509)
T PRK14897 339 LTIKGIKGIKRAIARKENDERRWVIYTQGSNLKDVLEIDEVDPTRTYTNDIIEIATVLGIEAARNAIIHEAKRTLQEQGL 418 (509)
T ss_pred cEEeCCCCccEEEEecCCCCceeEEEeeccCHHHHhcCCCcccccCccCCHHHHHHhcCHHHHHHHHHHHHHHHHHhcCC
Confidence 1377889999999999999999999999999999999999999999999999999999
Q ss_pred cccchhHHHHHhhhhccceecccccccccccCCccccccchHHHHHHHHHHHhhcCcccccccccccccCCccccCccce
Q 000235 1337 YVNYRHLAILCDTMTYRGHLMAITRHGINRNDTGPMMRCSFEETVDILLDAAVFAESDYLRGVTENIMLGQLAPIGTGDC 1416 (1815)
Q Consensus 1337 ~Vn~RHL~LlaD~MT~~G~~~~itR~Gi~~~~~spL~~aSFEeT~~~L~~AA~~ge~D~l~gvsenIi~G~~~p~GTG~f 1416 (1815)
+||+|||+||||+||++|.+++||||||++.+.|||++||||+|+++|++||++|++|.|+|||||||+||++|+|||+|
T Consensus 419 ~Vd~RHL~LIAD~MT~~G~v~~i~R~Gi~~~~~SpL~rASFE~T~~~L~~AA~~Ge~D~L~GvsenII~G~~ipvGTG~f 498 (509)
T PRK14897 419 NVDIRHIMLVADMMTFDGSVKAIGRHGISGEKSSVLARAAFEITGKHLLRAGILGEVDKLAGVAENIIVGQPITLGTGAV 498 (509)
T ss_pred cccHHHHHHHHHHhCcCCcccccccccccccCCCHHHhcchHhHHHHHHHHhhcCCCCcCCChHHhhhcCCccCCcCceE
Confidence 99999999999999999999999999999989999999999999999999999999999999999999999999999999
Q ss_pred eeccchh
Q 000235 1417 SLYLNDE 1423 (1815)
Q Consensus 1417 dll~~~~ 1423 (1815)
||+++..
T Consensus 499 dL~~~~~ 505 (509)
T PRK14897 499 SLVYKGR 505 (509)
T ss_pred EEEecCC
Confidence 9998764
No 21
>PRK04309 DNA-directed RNA polymerase subunit A''; Validated
Probab=100.00 E-value=1.3e-83 Score=769.80 Aligned_cols=331 Identities=41% Similarity=0.623 Sum_probs=296.1
Q ss_pred HhhccCHHHHHHHHHHHHHHhhcCcccCCCchhhHhhhccCCccccccccccccccccccccccccceeeeehhhcccCC
Q 000235 1042 KEHRLTREAFEWVIGEIESRFLQSLVAPGEMIGCVAAQSIGEPATQMTLNTFHYAGVSAKNVTLGVPRLREIINVAKKIK 1121 (1815)
Q Consensus 1042 ~~~~l~~~~~~~~l~ei~~ky~~slv~PGEaVG~iAAQSIGEPaTQMTLnTFH~AGv~~~NVTlGvPRLkEIin~ak~ik 1121 (1815)
.++++++++|+|++++|+.||.+++|+||||||+|||||||||+|||||||||||||+++||||||||||||||++|++|
T Consensus 31 ~~~~l~~~~~~~~~~~i~~~y~~~~v~pGe~VG~iaAQsIGEP~TQMTL~TFH~AGva~~nVTlGvPRlkEIina~K~~~ 110 (383)
T PRK04309 31 EERKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDARKEPS 110 (383)
T ss_pred HHcCCCHHHHHHHHHHHHHHHHHhhcCCCCccchhhhhhccchhhhcccccccccCccccCcccCchhHHHHHhcccCCC
Confidence 56789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCceEEEeCCCCcchHHHHHHHHhhhccccccccceeeEEEEcCCCCceEEEcccceeheeccCCCCcccccccCCcEEE
Q 000235 1122 TPSLSVFLKPGVNSTKERAKNVQCALEYTTLRSVTEATEVWYDPDPMGTIIEEDVEFVKSYYEMPDEDIAPEKISPWLLR 1201 (1815)
Q Consensus 1122 TP~mtv~l~~~~~~~~~~a~~v~~~le~~tL~dv~~~~~i~ydp~~~~~~i~~d~~~~~~~~~~~~~~~~~~~~~~~~lr 1201 (1815)
||+|+++|.+++..|++.|++|+.+||+++|+||+.++++.|+ .|+++
T Consensus 111 TP~~tv~L~~~~~~d~~~a~~v~~~iE~t~L~~v~~~i~~~~~--------------------------------~~~l~ 158 (383)
T PRK04309 111 TPMMTIYLKDEYAYDREKAEEVARKIEATTLENLAKDISVDLA--------------------------------NMTII 158 (383)
T ss_pred CCeEEEEecCcccccHHHHHHHHhheeeeEHhhhhhheEeccC--------------------------------CcEEE
Confidence 9999999999888889999999999999999999987775321 25799
Q ss_pred EEechhhhhcccCCHHHHHHHHhhhcCCCceeeecCCCccceEEEEEEccCCCCCCCCCCCcchhHHHHHHHHhhcc---
Q 000235 1202 IELNREMMVDKKLSMAAVAEKINQEFDDDLTCIFNDDNADKLILRIRIMNDEAPKGELNDESAEDDVFLKKIESNML--- 1278 (1815)
Q Consensus 1202 l~l~~~~~~~~~l~~~~i~~~i~~~~~~~~~~~~~~dn~~~~~~~ir~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l--- 1278 (1815)
++||++++.+++|++++|.++|...++.++.+. .+.+.++++ .. +...++++...++
T Consensus 159 i~ld~~~i~~~~l~~~~I~~~i~~~~~~~~~~~-----~~~i~i~~~--~~-------------~~~~l~~l~~~l~~~~ 218 (383)
T PRK04309 159 IELDEEMLEDRGLTVDDVKEAIEKKKGGEVEIE-----GNTLIISPK--EP-------------SYRELRKLAEKIRNIK 218 (383)
T ss_pred EEECHHHHHHcCCCHHHHHHHHHHhcCcceecc-----CCeEEEEec--Cc-------------hHHHHHHHHHHhcccE
Confidence 999999999999999999999988776654322 223334433 10 1123333332221
Q ss_pred ------------------ccceecccchhhhhccccccccccccccHHHHHHhhcHHHHHHHHHHHHHHhhhcCcccccc
Q 000235 1279 ------------------TEMALRGVNLLAVMCHEDVDARRTTSNHLIEIIEVLGIEAVRRALLDELRVVISFDGSYVNY 1340 (1815)
Q Consensus 1279 ------------------~~~~~~G~nl~~vl~~~~vD~~rt~sNdI~eI~~vlGIEAAR~~Ii~Ei~~V~~~~Gi~Vn~ 1340 (1815)
..+.++|+||.++|.+++||++|++||||+||+++|||||||++|++||+.||+.||++||+
T Consensus 219 vkGi~gI~r~~i~~~~~~~~l~teG~nl~~v~~~~~VD~~rt~sNdI~ei~~vlGIEAAR~~ii~Ei~~v~~~~Gi~Vd~ 298 (383)
T PRK04309 219 IKGIKGIKRVIIRKEGDEYVIYTEGSNLKEVLKVEGVDATRTTTNNIHEIEEVLGIEAARNAIIEEIKNTLEEQGLDVDI 298 (383)
T ss_pred EECCCCceEEEEecCCCeEEEEEcccCHHHHhcCCCEeeccccCCCHHHHHHHcCHHHHHHHHHHHHHHHHHHcCCeecH
Confidence 13667889999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHhhhhccceecccccccccccCCccccccchHHHHHHHHHHHhhcCcccccccccccccCCccccCccceeecc
Q 000235 1341 RHLAILCDTMTYRGHLMAITRHGINRNDTGPMMRCSFEETVDILLDAAVFAESDYLRGVTENIMLGQLAPIGTGDCSLYL 1420 (1815)
Q Consensus 1341 RHL~LlaD~MT~~G~~~~itR~Gi~~~~~spL~~aSFEeT~~~L~~AA~~ge~D~l~gvsenIi~G~~~p~GTG~fdll~ 1420 (1815)
|||+||||+||++|++++||||||++.+.|||++||||+|+++|++||++|++|+|+|||||||+|+++|+|||+|||++
T Consensus 299 rHl~LiaD~MT~~G~~~~i~R~Gi~~~~~S~l~~aSFE~T~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~~~l~~ 378 (383)
T PRK04309 299 RHIMLVADMMTWDGEVRQIGRHGVSGEKASVLARAAFEVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTGDVELTM 378 (383)
T ss_pred HHHHHHHHHhccCceEEeeechhhcCCCCCHHHhCchhhHHHHHHHHHhcCCCCCCCCcHHHhhcCCCcCCCCceEEEEc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chhh
Q 000235 1421 NDEM 1424 (1815)
Q Consensus 1421 ~~~~ 1424 (1815)
|..+
T Consensus 379 ~~~~ 382 (383)
T PRK04309 379 DPPL 382 (383)
T ss_pred CCCC
Confidence 8764
No 22
>cd02736 RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain. Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Probab=100.00 E-value=1.5e-79 Score=713.83 Aligned_cols=300 Identities=37% Similarity=0.591 Sum_probs=255.8
Q ss_pred HhhcCcccCCCchhhHhhhccCCccccccccccccccccccccccccceeeeehhhcccCCCCceEEEeCCCCcchHHHH
Q 000235 1061 RFLQSLVAPGEMIGCVAAQSIGEPATQMTLNTFHYAGVSAKNVTLGVPRLREIINVAKKIKTPSLSVFLKPGVNSTKERA 1140 (1815)
Q Consensus 1061 ky~~slv~PGEaVG~iAAQSIGEPaTQMTLnTFH~AGv~~~NVTlGvPRLkEIin~ak~ikTP~mtv~l~~~~~~~~~~a 1140 (1815)
||.+++|+||||||+|||||||||+|||||||||||||+++||||||||||||||++|++|||+|+++|++. .++++|
T Consensus 1 ky~~~~v~pGe~vG~iaaQsiGEp~TQmTL~TFH~aGv~~~nvtlGvPRlkEIinasK~~~TP~~ti~l~~~--~~~~~a 78 (300)
T cd02736 1 KYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNISTPIITAKLEND--RDEKSA 78 (300)
T ss_pred CchhhccCCCccchhhhhhhcCCccccccccccccccccccccccCchHHHHHHhcccCCCCCeEEEEecCc--ccHHHH
Confidence 689999999999999999999999999999999999999999999999999999999999999999999984 578999
Q ss_pred HHHHhhhccccccccceeeEEEEcCCCCceEEEcccceeheeccCCCCcccccccCCcEEEEEechhhhhcccCCHHHHH
Q 000235 1141 KNVQCALEYTTLRSVTEATEVWYDPDPMGTIIEEDVEFVKSYYEMPDEDIAPEKISPWLLRIELNREMMVDKKLSMAAVA 1220 (1815)
Q Consensus 1141 ~~v~~~le~~tL~dv~~~~~i~ydp~~~~~~i~~d~~~~~~~~~~~~~~~~~~~~~~~~lrl~l~~~~~~~~~l~~~~i~ 1220 (1815)
+.++.+||+++|+||+.+++++|||+...++|+.|.++++.++... +... .....+.
T Consensus 79 ~~v~~~ie~t~l~di~~~~~~~~~p~~~~~~i~~d~~~i~~~~l~~--------------------~~~~---~~~~~l~ 135 (300)
T cd02736 79 RIVKGRIEKTYLGEVASYIEEVYSPDDCYILIKLDKKIIEKLQLSK--------------------SNLY---FLLQSLK 135 (300)
T ss_pred HHHHHHHhhccHHHhhhheEEEEcCCCceEEEEecHHHHHHhcCCc--------------------ccHH---HHHHHHH
Confidence 9999999999999999999999999999999999988777654310 0000 0001111
Q ss_pred HHHhhhcCCCceeeecCCCccceEEEEEEccCCCCCCCCCCCcchhHHHHHHHHhhccccceecccchhhhhcccccccc
Q 000235 1221 EKINQEFDDDLTCIFNDDNADKLILRIRIMNDEAPKGELNDESAEDDVFLKKIESNMLTEMALRGVNLLAVMCHEDVDAR 1300 (1815)
Q Consensus 1221 ~~i~~~~~~~~~~~~~~dn~~~~~~~ir~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~G~nl~~vl~~~~vD~~ 1300 (1815)
..+.+ +. +..-. .+-|+.+..++ . + . .+ .+.++|+||.++|.+++||++
T Consensus 136 ~~l~~-----~~-v~Gi~----gI~r~~i~~~~--~-----~------------~-~~-~l~teG~nl~~v~~~~~Vd~~ 184 (300)
T cd02736 136 RKLPD-----VV-VSGIP----EVKRAVINKDK--K-----K------------G-KY-KLLVEGYGLRAVMNTPGVIGT 184 (300)
T ss_pred HHhcc-----ce-EeCCC----CceEEEEecCC--C-----C------------C-cE-EEEEecccHHHHhcCCcEecc
Confidence 11111 11 10000 11222222110 0 0 0 11 478999999999999999999
Q ss_pred ccccccHHHHHHhhcHHHHHHHHHHHHHHhhhcCcccccchhHHHHHhhhhccceecccccccccccCCccccccchHHH
Q 000235 1301 RTTSNHLIEIIEVLGIEAVRRALLDELRVVISFDGSYVNYRHLAILCDTMTYRGHLMAITRHGINRNDTGPMMRCSFEET 1380 (1815)
Q Consensus 1301 rt~sNdI~eI~~vlGIEAAR~~Ii~Ei~~V~~~~Gi~Vn~RHL~LlaD~MT~~G~~~~itR~Gi~~~~~spL~~aSFEeT 1380 (1815)
|++||||+||+++|||||||++|++||++||+.||++||+|||+||||+||++|.+++||||||++++.|||++||||+|
T Consensus 185 rt~sNdI~ei~~~lGIEAaR~~ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~G~~~~itR~gi~~~~~S~l~~aSFE~t 264 (300)
T cd02736 185 RTTSNHIMEVEKVLGIEAARSTIINEIQYTMKSHGMSIDPRHIMLLADLMTFKGEVLGITRFGIAKMKESVLMLASFEKT 264 (300)
T ss_pred CCccCCHHHHHHhcCHHHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHHHhccCceeeeecccccccCCCHHHhcchHhH
Confidence 99999999999999999999999999999999999999999999999999999999999999999888999999999999
Q ss_pred HHHHHHHHhhcCcccccccccccccCCccccCccce
Q 000235 1381 VDILLDAAVFAESDYLRGVTENIMLGQLAPIGTGDC 1416 (1815)
Q Consensus 1381 ~~~L~~AA~~ge~D~l~gvsenIi~G~~~p~GTG~f 1416 (1815)
+++|++||++|++|+|+|||||||+|+++|+|||+|
T Consensus 265 ~~~L~~AA~~g~~D~l~gvse~ii~G~~~~~GTG~f 300 (300)
T cd02736 265 TDHLFNAALHGRKDSIEGVSECIIMGKPMPIGTGLF 300 (300)
T ss_pred HHHHHHHhhcCCCCcCCCcHHHeeeCCCcCCCCCCC
Confidence 999999999999999999999999999999999997
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=1.8e-78 Score=710.42 Aligned_cols=306 Identities=37% Similarity=0.568 Sum_probs=243.5
Q ss_pred HhhcCcccCCCchhhHhhhccCCccccccccccccccccccccccccceeeeehhh-cccCCCCceEEEeCCCCcchHHH
Q 000235 1061 RFLQSLVAPGEMIGCVAAQSIGEPATQMTLNTFHYAGVSAKNVTLGVPRLREIINV-AKKIKTPSLSVFLKPGVNSTKER 1139 (1815)
Q Consensus 1061 ky~~slv~PGEaVG~iAAQSIGEPaTQMTLnTFH~AGv~~~NVTlGvPRLkEIin~-ak~ikTP~mtv~l~~~~~~~~~~ 1139 (1815)
||.+++|+||||||+|||||||||+|||||||||||||+++||||||||||||||. +|+||||+|+|+|+++.. .+.
T Consensus 1 ky~~slv~PGE~VG~iaAQSIGEPsTQMTLnTFH~AGv~~~nVTlGvPRL~EIi~~Ask~i~TP~m~v~l~~~~~--~~~ 78 (309)
T cd02735 1 KYMRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILMTASKNIKTPSMTLPLKNGKS--AER 78 (309)
T ss_pred CchhccCCCCcccchhhhhccCCcccccccccccccCccccccccccccHHHHHhhhccCCCCCeEEEEecCchh--HHH
Confidence 68999999999999999999999999999999999999999999999999999965 599999999999998864 468
Q ss_pred HHHHHhhhccccccccceeeEEEEcCCCCceEEEcccceeheeccCCCCcccccccCCcE-EEEEechhhhhcccCCHHH
Q 000235 1140 AKNVQCALEYTTLRSVTEATEVWYDPDPMGTIIEEDVEFVKSYYEMPDEDIAPEKISPWL-LRIELNREMMVDKKLSMAA 1218 (1815)
Q Consensus 1140 a~~v~~~le~~tL~dv~~~~~i~ydp~~~~~~i~~d~~~~~~~~~~~~~~~~~~~~~~~~-lrl~l~~~~~~~~~l~~~~ 1218 (1815)
|++++.+||+++|+||+++++++| |. +.+...|. .....|+ +++.+... ..++-+..
T Consensus 79 a~~~~~~ie~~~l~dv~~~~~v~~--------i~---~~~~~~~~--------~~~~~~~~~~i~~~~~---~~~~~~~~ 136 (309)
T cd02735 79 AETLKKRLSRVTLSDVVEKVEVTE--------IL---KTIERVFK--------KLLGKWCEVTIKLPLS---SPKLLLLS 136 (309)
T ss_pred HHHHHhheeEeEHHHhhhhhehhH--------HH---HHHHHHhh--------hhhCCEEEEEEEecCC---chhHHHHH
Confidence 999999999999999999999877 11 11111111 0112343 23333211 01111112
Q ss_pred HHHHHhhhcCCCceeeecCCCccceEEEEEEccCCCCCCCCCCCcchhHHHHHHHHhhccccceecccchhhhhcc-ccc
Q 000235 1219 VAEKINQEFDDDLTCIFNDDNADKLILRIRIMNDEAPKGELNDESAEDDVFLKKIESNMLTEMALRGVNLLAVMCH-EDV 1297 (1815)
Q Consensus 1219 i~~~i~~~~~~~~~~~~~~dn~~~~~~~ir~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~G~nl~~vl~~-~~v 1297 (1815)
+.+++.. ++. +..-. .+-|+.+..++ ++ . . ..+ .+.++|+||.++|.+ ++|
T Consensus 137 ~~~~~l~----~~~-i~gi~----gI~r~~i~~~~--~~----~---~--------~~~--~l~teG~nl~~v~~~~~~v 188 (309)
T cd02735 137 IVEKLAR----KAV-IREIP----GITRCFVVEED--KG----G---K--------TKY--LVITEGVNLAALWKFSDIL 188 (309)
T ss_pred HHHHHhc----ccE-EeCCC----CccEEEEecCc--CC----C---c--------eEE--EEEeccccHHHHHhccCcc
Confidence 2221111 111 11111 12223332211 00 0 0 011 367899999999998 799
Q ss_pred cccccccccHHHHHHhhcHHHHHHHHHHHHHHhhhcCcccccchhHHHHHhhhhccceecccccccccccCCccccccch
Q 000235 1298 DARRTTSNHLIEIIEVLGIEAVRRALLDELRVVISFDGSYVNYRHLAILCDTMTYRGHLMAITRHGINRNDTGPMMRCSF 1377 (1815)
Q Consensus 1298 D~~rt~sNdI~eI~~vlGIEAAR~~Ii~Ei~~V~~~~Gi~Vn~RHL~LlaD~MT~~G~~~~itR~Gi~~~~~spL~~aSF 1377 (1815)
|++|++||||+||+++|||||||++|++||+.||+.||++||+|||+||||+||++|+++++||+|| +.+.|||++|||
T Consensus 189 d~~r~~sNdi~ei~~~lGIEAar~~ii~Ei~~v~~~~Gi~V~~rHl~LiaD~MT~~G~~~~~nr~gi-~~~~S~l~~asF 267 (309)
T cd02735 189 DVNRIYTNDIHAMLNTYGIEAARRAIVKEISNVFKVYGIAVDPRHLSLIADYMTFEGGYRPFNRIGM-ESSTSPLQKMSF 267 (309)
T ss_pred ccccceeCCHHHHHHhhCHHHHHHHHHHHHHHHHHhcCCeeCHHHHHHHHHHHHhCCcEeecchhhe-ccCCCHHHhhhh
Confidence 9999999999999999999999999999999999999999999999999999999999999999999 678999999999
Q ss_pred HHHHHHHHHHHhhcCcccccccccccccCCccccCccceeec
Q 000235 1378 EETVDILLDAAVFAESDYLRGVTENIMLGQLAPIGTGDCSLY 1419 (1815)
Q Consensus 1378 EeT~~~L~~AA~~ge~D~l~gvsenIi~G~~~p~GTG~fdll 1419 (1815)
|+|+++|++||++|++|+|+|+|||||+||++|+|||+|||+
T Consensus 268 E~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~~~~~GTG~fdll 309 (309)
T cd02735 268 ETTLAFLKKATLNGDIDNLSSPSSRLVVGKPVNGGTGLFDLL 309 (309)
T ss_pred hhHHHHHHHHhhcCCCCCCCChHHheeeCCccCccceeEEeC
Confidence 999999999999999999999999999999999999999986
No 24
>PRK02597 rpoC2 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=100.00 E-value=3.3e-77 Score=779.03 Aligned_cols=346 Identities=25% Similarity=0.456 Sum_probs=266.8
Q ss_pred ecccccccccCCcccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCceeeeccCccChhhHHHHHHHHHHHHHHHHHH
Q 000235 622 SGTLCKKTLGTSTGSLIHVIWEEVGPDAARKFLGHTQWLVNYWLLQNAFSIGIGDTIADAKTMETINDTISKAKNNVKNL 701 (1815)
Q Consensus 622 ~g~ldK~~~g~s~~~Lih~i~~~~G~~~a~~~l~~~q~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~a~~~v~~~ 701 (1815)
+.+|||+.++ +||+.+|++||.+.|..|||++++|+++|++.+||||||+|++++++ +.++|++|++++.++
T Consensus 5 N~~idKk~l~----~LI~~~~~~yG~~~t~~~lD~lk~LGf~~aT~~G~SigidDl~ip~~----K~~li~~Ae~~v~~~ 76 (1331)
T PRK02597 5 NRVVDKKALK----NLIAWAFKNYGTARTAQMADNLKDLGFRYATQAGVSISVDDLKVPPA----KRDLLEQAEEEITAT 76 (1331)
T ss_pred cccccHHHHH----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhCcEEEeecccccCHH----HHHHHHHHHHHHHHH
Confidence 4578999997 99999999999999999999999999999999999999999998875 578999999999999
Q ss_pred HHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhc---CCCChHHHHHhcCCCCcccchhhhhhhccccc-
Q 000235 702 IKQAQDKSLEPEPGRTMMESFENKVNQVLNTARDEAGSSAQKSL---SESNNLKAMVTAGSKGSFINISQMTACVGQQN- 777 (1815)
Q Consensus 702 ~~~~~~~~l~~~~~~~~~~~~e~~v~~~ln~~~~~~~~~~~~~l---~~~N~~~~M~~sGsKGS~~N~~Qi~~~lGQQ~- 777 (1815)
+++|++|.++. .|.+ .++..+|+++++.+.+.+.+.+ ++.|++++|+.||||||..|+.|++||+|+|.
T Consensus 77 ~~~y~~G~it~------~Er~-~kvi~~w~~t~e~l~~~~~~~~~~~dp~N~v~mMa~SGARGN~sQI~QLvGmRGLma~ 149 (1331)
T PRK02597 77 EERYRRGEITE------VERF-QKVIDTWNETNERLKDEVVKNFRQNDPLNSVYMMAFSGARGNMSQVRQLVGMRGLMAN 149 (1331)
T ss_pred HHHHHcCCCch------hHHH-HHHHHHHHHHHHHHHHHHHHHHhhcCCCCcHHHHhhccCCccHHHHHHHhcchhhccC
Confidence 99999999874 3555 6788899999999888777665 67999999999999996666666666666654
Q ss_pred cCCCccCCCCCCCCCCCCCCCCCCCccccccccCCcCCCChhhhhhhccCCCcchhhhccccCCCchhHHHHHHHhhceE
Q 000235 778 VEGKRIPFGFVDRTLPHFTKDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDIM 857 (1815)
Q Consensus 778 ~eG~Rip~~~~~rtLp~f~~~d~~~~~~Gfv~~sf~~GL~p~EfFfH~m~gReGLiDTAvKTa~sGYlqRrLvk~lEdl~ 857 (1815)
..|+.| .|| |.+||++||+|+|||||||||||||||||||||+||||||||||++|||+
T Consensus 150 p~G~ii-------~lP--------------I~snFrEGLs~~EyFis~~GaRKGLvDTAlKTAdSGYLTRRLVdv~QDvi 208 (1331)
T PRK02597 150 PQGEII-------DLP--------------IKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVI 208 (1331)
T ss_pred CCCcEE-------ecc--------------hhhhhhcCCCHHHhheeccccccchhhcceecccchhHHHHHHHhhcceE
Confidence 445544 455 89999999999999999999999999999999999999999999999999
Q ss_pred Eeec--CeeecCCCceEEEEecCCCCCceeeecccccccccchHHHhhhhhhccccCCCCcccchHHHHHHhhhhhHHHH
Q 000235 858 VKYD--GTVRNSLGDVIQFLYGEDGMDSVWIESQTLDSLKMKKSEFDKAFRFEMDEENWNPNYMLQEYIDDLKTIKELRD 935 (1815)
Q Consensus 858 v~YD--gTVRns~g~iiQF~YGeDg~d~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 935 (1815)
|+++ ||.| |-.|.-+. ||-. .+ ..+.+..+.|....++.++. +
T Consensus 209 Vre~DCgT~~---gi~~~~~~--~~~~--~i-------~~l~~rl~GR~~~~~i~~~~-~-------------------- 253 (1331)
T PRK02597 209 VREEDCGTTR---GIVVEAMD--DGDR--VL-------IPLGDRLLGRVLAEDVVDPE-G-------------------- 253 (1331)
T ss_pred EEecCCCCCC---CEEEEEEe--cCCE--EE-------eEehheeEEEEEhhHeeCCC-C--------------------
Confidence 9986 6754 32332221 1100 00 01111111111111111100 0
Q ss_pred HHHHHHHHHHHHHHHhHhhhccCCCCCCCccccHHHHHHHhhhhcccCCCCCCCCChHHHHHHHHHHHHhhcccCCCCcc
Q 000235 936 VFDAEVQKLEADRYQLATEIATSGDSSWPLPVNLKRLIWNAQKTFKVDPRRPSDMHPMEVVEAVDKLQERLKVVPGEDPL 1015 (1815)
Q Consensus 936 ~l~~~~~~~~~~r~~l~~~~~~~~~~~~~~p~n~~r~i~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~d~~ 1015 (1815)
+.+.. ...++++ ++++++.
T Consensus 254 -----------------~~i~~----------------------------~n~~i~~--------~~~~~i~-------- 272 (1331)
T PRK02597 254 -----------------EVIAE----------------------------RNTAIDP--------DLAKKIE-------- 272 (1331)
T ss_pred -----------------CEEEe----------------------------CCCCcCH--------HHHHHHH--------
Confidence 00000 0011111 1111110
Q ss_pred cHHHHhhhhhhhhhhhhhhhhhHHHHHhhccCHHHHHHHHHHHHHHhhcCcccCCCchhhHhhhccCCcccccccccccc
Q 000235 1016 SVEAQKNATLFFNILLRSTFASKRVLKEHRLTREAFEWVIGEIESRFLQSLVAPGEMIGCVAAQSIGEPATQMTLNTFHY 1095 (1815)
Q Consensus 1016 ~~~~~~~~~~~~~~~lrs~l~~~~~~~~~~l~~~~~~~~l~ei~~ky~~slv~PGEaVG~iAAQSIGEPaTQMTLnTFH~ 1095 (1815)
+..+.++.+||.|+|+ ..+++|+.||+|.|+ ...+|+.|||||+|||||||||+|||||+|||.
T Consensus 273 -------~~~~~~v~iRspltC~---s~~gvC~~CYG~~la------~~~lv~lGeaVGiiAaQSIGEPGTQLTmRTFHt 336 (1331)
T PRK02597 273 -------KAGVEEVMVRSPLTCE---AARSVCRKCYGWSLA------HNHLVDLGEAVGIIAAQSIGEPGTQLTMRTFHT 336 (1331)
T ss_pred -------HcCCCEEEEECCEEec---CCCCchhhccCcchh------cCcccchhhhhhhhhhccccCCcchhehhhhhh
Confidence 1123467899999998 679999999999997 788999999999999999999999999999999
Q ss_pred ccccccccc-------cccceeeeehh
Q 000235 1096 AGVSAKNVT-------LGVPRLREIIN 1115 (1815)
Q Consensus 1096 AGv~~~NVT-------lGvPRLkEIin 1115 (1815)
+||++..++ .|++|+.|-+.
T Consensus 337 GGv~~~~~~~~i~~~~~G~i~~~~~~~ 363 (1331)
T PRK02597 337 GGVFTGEVARQVRSPFAGTVEFGKKLR 363 (1331)
T ss_pred ccccccccceeEEeccCeEEEEecCCc
Confidence 999998888 89999999553
No 25
>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=4e-74 Score=744.44 Aligned_cols=334 Identities=25% Similarity=0.436 Sum_probs=252.8
Q ss_pred ecccccccccCCcccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCceeeeccCccChhhHHHHHHHHHHHHHHHHHH
Q 000235 622 SGTLCKKTLGTSTGSLIHVIWEEVGPDAARKFLGHTQWLVNYWLLQNAFSIGIGDTIADAKTMETINDTISKAKNNVKNL 701 (1815)
Q Consensus 622 ~g~ldK~~~g~s~~~Lih~i~~~~G~~~a~~~l~~~q~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~a~~~v~~~ 701 (1815)
+.+|||+.++ +|||.+|++||.+.|.+|||++++|+++|++.+|||+||+|++++++ +.++|++|++++.++
T Consensus 4 N~~idKk~l~----~LI~~~~~~yG~~~t~~~lD~lk~Lgf~~aT~~G~SigidDl~ip~~----K~~li~~a~~~v~~~ 75 (1227)
T TIGR02388 4 NRVVDKKALK----NLISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPPA----KQDLLEAAEKEIRAT 75 (1227)
T ss_pred ccccchHHHH----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCeEEeeccCCCCHH----HHHHHHHHHHHHHHH
Confidence 4579999996 99999999999999999999999999999999999999999999875 588999999999999
Q ss_pred HHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhh---cCCCChHHHHHhcCCCCcccchhhhhhhcccc-c
Q 000235 702 IKQAQDKSLEPEPGRTMMESFENKVNQVLNTARDEAGSSAQKS---LSESNNLKAMVTAGSKGSFINISQMTACVGQQ-N 777 (1815)
Q Consensus 702 ~~~~~~~~l~~~~~~~~~~~~e~~v~~~ln~~~~~~~~~~~~~---l~~~N~~~~M~~sGsKGS~~N~~Qi~~~lGQQ-~ 777 (1815)
+++|++|.++. .|.|+ ++.++|+++++.+.+.+.+. +++.|++++|+.||||||..|+.|++||+|+| .
T Consensus 76 ~~~y~~G~it~------~Er~~-~ii~~w~~t~e~~~~~~~~~~~~~d~~N~v~mMa~SGARGNisQi~QLvGmrGlma~ 148 (1227)
T TIGR02388 76 EERYRRGEITE------VERFQ-KVIDTWNGTNEELKDEVVNNFRQTDPLNSVYMMAFSGARGNMSQVRQLVGMRGLMAN 148 (1227)
T ss_pred HHHHHcCCCcc------hhhHH-HHHHHHHHHHHHHHHHHHHhhhhcCCCCcHHHHhhccCcccHHHHHHHhcchheecC
Confidence 99999999876 36665 67789999999988877766 46899999999999999555555555555544 4
Q ss_pred cCCCccCCCCCCCCCCCCCCCCCCCccccccccCCcCCCChhhhhhhccCCCcchhhhccccCCCchhHHHHHHHhhceE
Q 000235 778 VEGKRIPFGFVDRTLPHFTKDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDIM 857 (1815)
Q Consensus 778 ~eG~Rip~~~~~rtLp~f~~~d~~~~~~Gfv~~sf~~GL~p~EfFfH~m~gReGLiDTAvKTa~sGYlqRrLvk~lEdl~ 857 (1815)
.+|++| .|| |.+||++||+|.|||||||||||||||||||||+||||||||||++|||+
T Consensus 149 p~G~ii-------~lP--------------I~snFreGLt~~EyF~sa~GaRkGLvDTAlKTAdSGYLTRRLVdv~qDvi 207 (1227)
T TIGR02388 149 PQGEII-------DLP--------------IKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVI 207 (1227)
T ss_pred CCCcEe-------ecc--------------chhhhhcCCCHHHhheeccccccchhhcceeccccchHHHHHHHhhceEE
Confidence 566655 355 89999999999999999999999999999999999999999999999999
Q ss_pred Eeec--CeeecCCCceEEEEecCCCCCceeeecccccccccchHHHhhhhhhccccCCCCcccchHHHHHHhhhhhHHHH
Q 000235 858 VKYD--GTVRNSLGDVIQFLYGEDGMDSVWIESQTLDSLKMKKSEFDKAFRFEMDEENWNPNYMLQEYIDDLKTIKELRD 935 (1815)
Q Consensus 858 v~YD--gTVRns~g~iiQF~YGeDg~d~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 935 (1815)
|.++ ||.| | +....+.... ..+.+.+..+.|....|+.++.
T Consensus 208 V~~~DCgT~~---g-----------i~v~~~~~~~-~~~~l~~rl~GRv~~~di~~~~---------------------- 250 (1227)
T TIGR02388 208 VREEDCGTER---S-----------IVVRAMTEGD-KKISLGDRLLGRLVAEDVLHPE---------------------- 250 (1227)
T ss_pred EEEcCCCCCC---C-----------EEEEEeeCCC-eEeEhhheeEeeeEHhHeECCC----------------------
Confidence 9986 6643 2 2211111000 0111111222221111111100
Q ss_pred HHHHHHHHHHHHHHHhHhhhccCCCCCCCccccHHHHHHHhhhhcccCCCCCCCCChHHHHHHHHHHHHhhcccCCCCcc
Q 000235 936 VFDAEVQKLEADRYQLATEIATSGDSSWPLPVNLKRLIWNAQKTFKVDPRRPSDMHPMEVVEAVDKLQERLKVVPGEDPL 1015 (1815)
Q Consensus 936 ~l~~~~~~~~~~r~~l~~~~~~~~~~~~~~p~n~~r~i~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~d~~ 1015 (1815)
+ ++|- ....++.+ ++++++.
T Consensus 251 -----------------------~-----------~~i~----------~~n~~I~~--------~~~~~i~-------- 270 (1227)
T TIGR02388 251 -----------------------G-----------EVIV----------PKNTAIDP--------DLAKTIE-------- 270 (1227)
T ss_pred -----------------------C-----------cEEE----------eCCCccCH--------HHHHHHH--------
Confidence 0 0000 00011111 1111110
Q ss_pred cHHHHhhhhhhhhhhhhhhhhhHHHHHhhccCHHHHHHHHHHHHHHhhcCcccCCCchhhHhhhccCCcccccccccccc
Q 000235 1016 SVEAQKNATLFFNILLRSTFASKRVLKEHRLTREAFEWVIGEIESRFLQSLVAPGEMIGCVAAQSIGEPATQMTLNTFHY 1095 (1815)
Q Consensus 1016 ~~~~~~~~~~~~~~~lrs~l~~~~~~~~~~l~~~~~~~~l~ei~~ky~~slv~PGEaVG~iAAQSIGEPaTQMTLnTFH~ 1095 (1815)
....-.+.+||.|+|+ ..+++|+.||+|.|+ ...+|+.|||||+|||||||||+|||||+|||.
T Consensus 271 -------~~~~~~v~iRspltC~---s~~~vC~~CYG~~la------~~~lV~lGeaVGiiAaQSIGEPGTQLTmRTFHt 334 (1227)
T TIGR02388 271 -------TAGISEVVVRSPLTCE---AARSVCRKCYGWSLA------HAHLVDLGEAVGIIAAQSIGEPGTQLTMRTFHT 334 (1227)
T ss_pred -------HcCCCEEEEeCcceec---chhhHhHhccCCccc------cCcEechhhhhhhhhhhccCCcchhhhhhhhhh
Confidence 0123456789999998 578999999999996 689999999999999999999999999999999
Q ss_pred ccccccccc
Q 000235 1096 AGVSAKNVT 1104 (1815)
Q Consensus 1096 AGv~~~NVT 1104 (1815)
+||.+..+.
T Consensus 335 GGv~t~~~~ 343 (1227)
T TIGR02388 335 GGVFTGEVA 343 (1227)
T ss_pred cccccccee
Confidence 999876553
No 26
>cd02737 RNAP_IV_NRPD1_C Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain. Higher plants have five multi-subunit nuclear RNA polymerases: RNAP I, RNAP II and RNAP III, which are essential for viability; plus the two isoforms of the non-essential polymerase RNAP IV (IVa and IVb), which specialize in small RNA-mediated gene silencing pathways. RNAP IVa and/or RNAP IVb might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b is the largest subunit of RNAP IVb. The full subunit compositions of RNAP IVa and RNAP IVb are not known, nor are their templates or enzymatic products. However, it has been shown that RNAP IVa and, to a lesser extent, RNAP IVb are crucial for several RNA-mediated gene silencing phenomena.
Probab=100.00 E-value=3.2e-74 Score=686.29 Aligned_cols=321 Identities=25% Similarity=0.392 Sum_probs=261.6
Q ss_pred CCchhhHhhhccCCccccccccccccccccccccccccceeeeehhh--cccCCCCceEEEeCC-------CCcchHHHH
Q 000235 1070 GEMIGCVAAQSIGEPATQMTLNTFHYAGVSAKNVTLGVPRLREIINV--AKKIKTPSLSVFLKP-------GVNSTKERA 1140 (1815)
Q Consensus 1070 GEaVG~iAAQSIGEPaTQMTLnTFH~AGv~~~NVTlGvPRLkEIin~--ak~ikTP~mtv~l~~-------~~~~~~~~a 1140 (1815)
|||||+|||||||||||||||||||+||++ +|||||||||+ ++++|||+|+|+|.. ++.. ++.|
T Consensus 1 GE~VG~LAAqSIgEPAtQmtLntfh~agvs------~vprLKEiLn~~~~~~~ktps~~v~L~~~~~~~~~~~~~-~~~a 73 (381)
T cd02737 1 GEPVGSLAATAISEPAYKALLDPPQSLESS------PLELLKEVLECRSKSKSKENDRRVILSLHLCKCDHGFEY-ERAA 73 (381)
T ss_pred CCcchhHHHhhhcchHHHhhhccchhcCCc------cHHHHHHHhcccccCCCCCCCEEEEEeccccccccchHH-HHHH
Confidence 999999999999999999999999999996 49999999999 688999999999975 3333 6789
Q ss_pred HHHHhhhccccccccceeeEEEEcCCCCceEEEcccceehe-----eccCCCCcccccccCCcEEEEEechhhhhcccCC
Q 000235 1141 KNVQCALEYTTLRSVTEATEVWYDPDPMGTIIEEDVEFVKS-----YYEMPDEDIAPEKISPWLLRIELNREMMVDKKLS 1215 (1815)
Q Consensus 1141 ~~v~~~le~~tL~dv~~~~~i~ydp~~~~~~i~~d~~~~~~-----~~~~~~~~~~~~~~~~~~lrl~l~~~~~~~~~l~ 1215 (1815)
++|++.||+++|++|+..++|+|||++..+++++|.++++. ++++++++.+...+++|++|++||++..
T Consensus 74 ~~Vq~~Le~~tL~~v~~~~~I~Ydp~~~~t~i~~d~~~~~~~~~~~~~~~~~~~~~~~~~spw~~r~~l~~~~~------ 147 (381)
T cd02737 74 LEVKNHLERVTLEDLATTSMIKYSPQATEAIVGEIGDQLNTKKKGKKKAIFSTSLKITKFSPWVCHFHLDKECQ------ 147 (381)
T ss_pred HHHHHHhhhccHHHhhheEEEEECCCcccccccccHHHHHhhhhhhhhcccccccccccCCcceEEEEEehhHh------
Confidence 99999999999999999999999999999999999999887 8888887777788899999999987521
Q ss_pred HHHHHHHHhhhcCCCceeeecCCCcc----------------------------ceEEEEEEccCCCCCCCCCCCcchhH
Q 000235 1216 MAAVAEKINQEFDDDLTCIFNDDNAD----------------------------KLILRIRIMNDEAPKGELNDESAEDD 1267 (1815)
Q Consensus 1216 ~~~i~~~i~~~~~~~~~~~~~~dn~~----------------------------~~~~~ir~~~~~~~~~~~~~~~~~~~ 1267 (1815)
++.+..|+..++|.+ ..+-++.+...++...... + .
T Consensus 148 -----------~~~~~~ci~~~~~~~~~~~~~~~~~~~~~~i~~~lL~~~lkG~~~I~kv~i~~~~~~~~~~~-~----~ 211 (381)
T cd02737 148 -----------KLSDGPCLTFSVSKEVSKSSEELLDVLRDRIIPFLLETVIKGDERIKSVNILWEDSPSTSWV-K----S 211 (381)
T ss_pred -----------cCCCCceEEeecCcccccchhHHHHHHHHHHHHHHhheeecccCCeeEEEEEecCCCccccc-c----c
Confidence 222333333222200 0011111111000000000 0 0
Q ss_pred HHHHHHHhhccccce-------ecccchhhhh-----ccccccccccccccHHHHHHhhcHHHHHHHHHHHHHHhhhcCc
Q 000235 1268 VFLKKIESNMLTEMA-------LRGVNLLAVM-----CHEDVDARRTTSNHLIEIIEVLGIEAVRRALLDELRVVISFDG 1335 (1815)
Q Consensus 1268 ~~l~~~~~~~l~~~~-------~~G~nl~~vl-----~~~~vD~~rt~sNdI~eI~~vlGIEAAR~~Ii~Ei~~V~~~~G 1335 (1815)
.-.+. +.++.-++. .+|++|+.|| .+++||++|++||||+||+++|||||||++|++||+.||++||
T Consensus 212 ~~~~~-~~E~vLe~~~~~~~~~t~G~~~~~vl~~c~~~~~~ID~~rt~sNdI~ev~~~lGIEAAR~~ii~El~~v~~~~G 290 (381)
T cd02737 212 VGKSS-RGELVLEVTVEESCKKTRGNAWNVVMDACIPVMDLIDWERSMPYSIQQIKSVLGIDAAFEQFVQRLESAVSMTG 290 (381)
T ss_pred ccccc-cceEEEEEEeccccccccchhHHHHHHhhhcccccCcCCCcEECCHHHHHHHHhHHHHHHHHHHHHHHHHHhcC
Confidence 00000 111111122 2389999999 4899999999999999999999999999999999999999999
Q ss_pred ccccchhHHHHHhhhhccceecccccccccccCC-----ccccccchHHHHHHHHHHHhhcCcccccccccccccCCccc
Q 000235 1336 SYVNYRHLAILCDTMTYRGHLMAITRHGINRNDT-----GPMMRCSFEETVDILLDAAVFAESDYLRGVTENIMLGQLAP 1410 (1815)
Q Consensus 1336 i~Vn~RHL~LlaD~MT~~G~~~~itR~Gi~~~~~-----spL~~aSFEeT~~~L~~AA~~ge~D~l~gvsenIi~G~~~p 1410 (1815)
++||+|||+||||+||++|++++||||||++.+. |||+|||||+|+++|++||.+|+.|+|+|||+||||||+++
T Consensus 291 ~~Vd~rHL~LlAD~MT~~G~~~~~nR~Gi~~~~~s~~~~spl~~asFE~t~~~l~~AA~~g~~D~l~gvs~~ii~G~~~~ 370 (381)
T cd02737 291 KSVLREHLLLVADSMTYSGEFVGLNAKGYKAQRRSLKISAPFTEACFSSPIKCFLKAAKKGASDSLSGVLDACAWGKEAP 370 (381)
T ss_pred CcccHHHHHHHHHHhccCCceEEecchhhhhcccccccCCHHHHhhHHHHHHHHHHHHhccCCCCCCChHHheeeCCcCC
Confidence 9999999999999999999999999999998765 89999999999999999999999999999999999999999
Q ss_pred cCccc-eeecc
Q 000235 1411 IGTGD-CSLYL 1420 (1815)
Q Consensus 1411 ~GTG~-fdll~ 1420 (1815)
+|||+ |||++
T Consensus 371 vGTG~~fdll~ 381 (381)
T cd02737 371 VGTGSKFEILW 381 (381)
T ss_pred CcCCcceeeeC
Confidence 99998 99975
No 27
>CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed
Probab=100.00 E-value=4.3e-70 Score=720.90 Aligned_cols=340 Identities=25% Similarity=0.371 Sum_probs=254.4
Q ss_pred eecccccccccCCcccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCceeeeccCccChhhHHHHHHHHHHHHHHHHH
Q 000235 621 LSGTLCKKTLGTSTGSLIHVIWEEVGPDAARKFLGHTQWLVNYWLLQNAFSIGIGDTIADAKTMETINDTISKAKNNVKN 700 (1815)
Q Consensus 621 l~g~ldK~~~g~s~~~Lih~i~~~~G~~~a~~~l~~~q~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~a~~~v~~ 700 (1815)
++.+|||+.++ +||+.+|++||.+.|.+|||++++|+++|++.+|||+||+|++++++ +.++|++|++++.+
T Consensus 10 ~N~~~~k~~l~----~li~~~~~~~G~~~t~~~lD~lk~lgf~~at~~G~Sigi~Dl~ip~~----K~~li~~a~~~v~~ 81 (1364)
T CHL00117 10 HNKVIDKTALK----RLISWLIDHFGMAYTSHILDQLKTLGFQQATAAGISLGIDDLLTPPS----KGWLVQDAEQQSLI 81 (1364)
T ss_pred EeccccHHHHH----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcceEEecCcccCCHH----HHHHHHHHHHHHHH
Confidence 45679999997 89999999999999999999999999999999999999999999875 57899999999999
Q ss_pred HHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH---HHhhcCCCChHHHHHhcCCCCcccchhhhhhhccccc
Q 000235 701 LIKQAQDKSLEPEPGRTMMESFENKVNQVLNTARDEAGSS---AQKSLSESNNLKAMVTAGSKGSFINISQMTACVGQQN 777 (1815)
Q Consensus 701 ~~~~~~~~~l~~~~~~~~~~~~e~~v~~~ln~~~~~~~~~---~~~~l~~~N~~~~M~~sGsKGS~~N~~Qi~~~lGQQ~ 777 (1815)
+.++|++|.++. .|+++..+. +|+.+.+.+.+. +.+.+++.|++++|+.||||| |++||.+|+|++.
T Consensus 82 ~~~~y~~G~it~------~er~~~~i~-~w~~~~~~l~~~~~~~~~~~d~~N~v~mMa~SGARG---n~sQi~qLvGmRG 151 (1364)
T CHL00117 82 LEKHYHYGNVHA------VEKLRQSIE-IWYATSEYLKQEMNPNFRMTDPLNPVYMMSFSGARG---NASQVHQLVGMRG 151 (1364)
T ss_pred HHHHHHcCCCCH------HHHHHHHHH-HHHHHHHHHHHHHHHhhccCCCCCcHhhhhhccCcc---cHHHHHHHhcccc
Confidence 999999999974 377765544 565555544433 334567899999999999999 5666666666655
Q ss_pred c----CCCccCCCCCCCCCCCCCCCCCCCccccccccCCcCCCChhhhhhhccCCCcchhhhccccCCCchhHHHHHHHh
Q 000235 778 V----EGKRIPFGFVDRTLPHFTKDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAM 853 (1815)
Q Consensus 778 ~----eG~Rip~~~~~rtLp~f~~~d~~~~~~Gfv~~sf~~GL~p~EfFfH~m~gReGLiDTAvKTa~sGYlqRrLvk~l 853 (1815)
+ .|++| .|| |.+||++||+|.|||||||||||||||||||||+||||||||||++
T Consensus 152 lma~p~G~iI-------~~P--------------I~snFreGLs~~EyFis~~GaRkGLvDTAlkTAdSGYLtRRLVdv~ 210 (1364)
T CHL00117 152 LMSDPQGQII-------DLP--------------IQSNFREGLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRLVEVV 210 (1364)
T ss_pred eeeCCCCcEe-------ecc--------------hhhhhhcCCCHHHhheeccccccchhhcceecccccchhhHHHhhh
Confidence 4 55555 233 8999999999999999999999999999999999999999999999
Q ss_pred hceEEee-c-CeeecCCCceEEEEecCCCCCceeeecccccccccchHHHhhhhhhccccCCCCcccchHHHHHHhhhhh
Q 000235 854 EDIMVKY-D-GTVRNSLGDVIQFLYGEDGMDSVWIESQTLDSLKMKKSEFDKAFRFEMDEENWNPNYMLQEYIDDLKTIK 931 (1815)
Q Consensus 854 Edl~v~Y-D-gTVRns~g~iiQF~YGeDg~d~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 931 (1815)
|||+|.- | ||.| |-.|.-+-|++ . ...+.+..+.|....|+.+ .+
T Consensus 211 qdviV~~~dCgt~~---gi~~~~~~~~~---~---------~~~l~~rl~GRv~~~di~~--~~---------------- 257 (1364)
T CHL00117 211 QHIVVRETDCGTTR---GISVSPRNGMM---I---------ERILIQTLIGRVLADDIYI--GS---------------- 257 (1364)
T ss_pred ccEEEEeccCCCCC---CEEEEEecCCe---E---------EeEecceeEEEEEhhhEEe--CC----------------
Confidence 9999975 4 6654 32222221111 0 0011111112211111100 00
Q ss_pred HHHHHHHHHHHHHHHHHHHhHhhhccCCCCCCCccccHHHHHHHhhhhcccCCCCCCCCChHHHHHHHHHHHHhhcccCC
Q 000235 932 ELRDVFDAEVQKLEADRYQLATEIATSGDSSWPLPVNLKRLIWNAQKTFKVDPRRPSDMHPMEVVEAVDKLQERLKVVPG 1011 (1815)
Q Consensus 932 ~~~~~l~~~~~~~~~~r~~l~~~~~~~~~~~~~~p~n~~r~i~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~ 1011 (1815)
+.+... ..+++. ++ ++++.
T Consensus 258 ---------------------~~i~~~----------------------------n~~I~~-~~-------~~~i~---- 276 (1364)
T CHL00117 258 ---------------------RCIATR----------------------------NQDIGI-GL-------ANRFI---- 276 (1364)
T ss_pred ---------------------EEEEeC----------------------------CCCcCH-HH-------HHHHH----
Confidence 000000 011111 11 11110
Q ss_pred CCcccHHHHhhhhhhhhhhhhhhhhhHHHHHhhccCHHHHHHHHHHHHHHhhcCcccCCCchhhHhhhccCCcccccccc
Q 000235 1012 EDPLSVEAQKNATLFFNILLRSTFASKRVLKEHRLTREAFEWVIGEIESRFLQSLVAPGEMIGCVAAQSIGEPATQMTLN 1091 (1815)
Q Consensus 1012 ~d~~~~~~~~~~~~~~~~~lrs~l~~~~~~~~~~l~~~~~~~~l~ei~~ky~~slv~PGEaVG~iAAQSIGEPaTQMTLn 1091 (1815)
+...-.+.+||+|+|+ ..+++|+.||+|.|+ ...+|+.|||||+|||||||||+|||||+
T Consensus 277 -----------~~~~~~v~iRSpltC~---~~~~vC~~CYG~~la------~~~lV~~GeaVGiiAaQSIGEPGTQLTmR 336 (1364)
T CHL00117 277 -----------TFRAQPISIRSPLTCR---STSWICQLCYGWSLA------HGDLVELGEAVGIIAGQSIGEPGTQLTLR 336 (1364)
T ss_pred -----------HcCCCEEEEeCCcccc---cHHHHHHHHhCcccc------cCcccChhhhhhhhhhhccCCCchhhhhh
Confidence 1123456789999998 678999999999997 68999999999999999999999999999
Q ss_pred cccccccccccccc-------ccceeeee
Q 000235 1092 TFHYAGVSAKNVTL-------GVPRLREI 1113 (1815)
Q Consensus 1092 TFH~AGv~~~NVTl-------GvPRLkEI 1113 (1815)
|||.+||++..++. |+.++.|-
T Consensus 337 TFH~GGv~t~~~~~~i~a~~~G~i~~~~~ 365 (1364)
T CHL00117 337 TFHTGGVFTGGTAEQVRAPFNGKIKFNED 365 (1364)
T ss_pred hhhhcccccccceeeEEeccCeEEEEecc
Confidence 99999998876654 99999883
No 28
>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=1.4e-71 Score=654.24 Aligned_cols=275 Identities=49% Similarity=0.782 Sum_probs=220.4
Q ss_pred CCChhhhhhhccCCCcchhhhccccCCCchhHHHHHHHhhceEEeecCeeecCCCceEEEEecCCCCCceeeeccccccc
Q 000235 815 GLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDIMVKYDGTVRNSLGDVIQFLYGEDGMDSVWIESQTLDSL 894 (1815)
Q Consensus 815 GL~p~EfFfH~m~gReGLiDTAvKTa~sGYlqRrLvk~lEdl~v~YDgTVRns~g~iiQF~YGeDg~d~~~~e~~~~~~~ 894 (1815)
||+|+|||||||||||||||||||||+||||||||||+||||+|+||+||||+.+.|+||+||+||
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 ccchHHHhhhhhhccccCCCCcccchHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhHhhhccCCCCCCCccccHHHHHH
Q 000235 895 KMKKSEFDKAFRFEMDEENWNPNYMLQEYIDDLKTIKELRDVFDAEVQKLEADRYQLATEIATSGDSSWPLPVNLKRLIW 974 (1815)
Q Consensus 895 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~r~~l~~~~~~~~~~~~~~p~n~~r~i~ 974 (1815)
T Consensus 67 -------------------------------------------------------------------------------- 66 (277)
T PF04998_consen 67 -------------------------------------------------------------------------------- 66 (277)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred HhhhhcccCCCCCCCCChHHHHHHHHHHHHhhcccCCCCcccHHHHhhhhhhhhhhhhhhhhhHHHHHhhccCHHHHHHH
Q 000235 975 NAQKTFKVDPRRPSDMHPMEVVEAVDKLQERLKVVPGEDPLSVEAQKNATLFFNILLRSTFASKRVLKEHRLTREAFEWV 1054 (1815)
Q Consensus 975 ~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~lrs~l~~~~~~~~~~l~~~~~~~~ 1054 (1815)
T Consensus 67 -------------------------------------------------------------------------------- 66 (277)
T PF04998_consen 67 -------------------------------------------------------------------------------- 66 (277)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred HHHHHHHhhcCcccCCCchhhHhhhccCCccccccccccccccccccccccccceeeeehhhcccCCCCceEEEeCCCCc
Q 000235 1055 IGEIESRFLQSLVAPGEMIGCVAAQSIGEPATQMTLNTFHYAGVSAKNVTLGVPRLREIINVAKKIKTPSLSVFLKPGVN 1134 (1815)
Q Consensus 1055 l~ei~~ky~~slv~PGEaVG~iAAQSIGEPaTQMTLnTFH~AGv~~~NVTlGvPRLkEIin~ak~ikTP~mtv~l~~~~~ 1134 (1815)
+|+||||||+|||||||||+|||||||||+||++++|||+|+|||+||++++++.++|+++++......
T Consensus 67 -----------~v~~Ge~VGiiaAQSIGEP~TQ~TL~TFH~aG~~~~~vt~giprl~eii~~~~~~~~~~~~~~~~~~~~ 135 (277)
T PF04998_consen 67 -----------LVEPGEAVGIIAAQSIGEPGTQMTLRTFHTAGVASKNVTQGIPRLKEIINASKKIKTPIITVYGKKKII 135 (277)
T ss_dssp -----------B--TTSBHHHHHHHHHHCHGCCSHHSCTSSSCSSTSSCSSSHHHHHHHHTTCSSSSSEEEEECSCSSEC
T ss_pred -----------ccCccccchhhhhchhcchhHHhhhcccccCceeeecccccceeeccccccccccccceEEeeccccee
Confidence 367999999999999999999999999999999999999999999999999999999999998877654
Q ss_pred chHHHHHHHHhhhccccccccceeeEEEEcCCCCceEEEcccceeheeccCCCCcccccccCCcEEEEEechhhhhcccC
Q 000235 1135 STKERAKNVQCALEYTTLRSVTEATEVWYDPDPMGTIIEEDVEFVKSYYEMPDEDIAPEKISPWLLRIELNREMMVDKKL 1214 (1815)
Q Consensus 1135 ~~~~~a~~v~~~le~~tL~dv~~~~~i~ydp~~~~~~i~~d~~~~~~~~~~~~~~~~~~~~~~~~lrl~l~~~~~~~~~l 1214 (1815)
...+.+..+....+... +..++... .......+
T Consensus 136 ~~~~~~~~~~~~~~~~~-----------------------~~~~~~~~------------------------~~~~~~~~ 168 (277)
T PF04998_consen 136 SEKKKIKIIRKKIKIIK-----------------------NGKKVKNG------------------------DKIKKGSI 168 (277)
T ss_dssp SSSHHHHHHHHTCSSSC-----------------------STTCEHTT------------------------CESSSSCS
T ss_pred cccccceEEEEeeeeee-----------------------cccceecc------------------------eeeeccee
Confidence 44444444443333300 00000000 00000000
Q ss_pred CHHHHHHHHhhhcCCCceeeecCCCccceEEEEEEccCCCCCCCCCCCcchhHHHHHHHHhhccccceecccchhhhhcc
Q 000235 1215 SMAAVAEKINQEFDDDLTCIFNDDNADKLILRIRIMNDEAPKGELNDESAEDDVFLKKIESNMLTEMALRGVNLLAVMCH 1294 (1815)
Q Consensus 1215 ~~~~i~~~i~~~~~~~~~~~~~~dn~~~~~~~ir~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~G~nl~~vl~~ 1294 (1815)
....+ .. . ......+.+.|.||..+|..
T Consensus 169 ~~~~~--------------------------------------------------~~-~-~~~~~~l~~~g~~l~~v~~~ 196 (277)
T PF04998_consen 169 ISKDI--------------------------------------------------LE-K-KSKEYVLQTEGSNLQEVYSS 196 (277)
T ss_dssp EHHHH--------------------------------------------------CE-E-CCCCCEEECCSHHHHHHTCS
T ss_pred eeecc--------------------------------------------------cc-c-hhHHHHHHHHhhhchhheec
Confidence 00000 00 0 00001356689999999999
Q ss_pred cc-ccccccccccHHHHHHhhcHHHHHHHHHHHHHHhhhcCcccccchhHHHHHhhhhccceecccccccccccCCcccc
Q 000235 1295 ED-VDARRTTSNHLIEIIEVLGIEAVRRALLDELRVVISFDGSYVNYRHLAILCDTMTYRGHLMAITRHGINRNDTGPMM 1373 (1815)
Q Consensus 1295 ~~-vD~~rt~sNdI~eI~~vlGIEAAR~~Ii~Ei~~V~~~~Gi~Vn~RHL~LlaD~MT~~G~~~~itR~Gi~~~~~spL~ 1373 (1815)
++ +|++++++|||++|+++|||||||++|++|++.||..||++||+|||+|+||+||++|.+++||||||+..++|.|+
T Consensus 197 qgvid~~k~~sn~I~qm~~~~GIeaar~~i~~e~~~v~~~~g~~vn~rhl~llad~mt~~g~~~gitR~gl~~~~~S~~~ 276 (277)
T PF04998_consen 197 QGVIDNDKHISNDIRQMLSKLGIEAARNSIIKELKNVFESYGIEVNKRHLSLLADYMTYKGVLLGITRHGLNSNKSSFLS 276 (277)
T ss_dssp TT-EETCHHECSHHHHHHHHHEHHHHHHHHHHHHHCHHHHCTSCCCHHHHHHHHHHHCCCSS---CCTTTTSSSSSSHHH
T ss_pred ccccCCCEEEeceeEeeeeeEEEEECCCceeecCcEeeHHHHHHHHHHHHHhCCCcCeeeeEEEEEEHHHhccCCCCccC
Confidence 98 99999999999999999999999999999999999999999999999999999999999999999999987666654
No 29
>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=2.2e-64 Score=606.45 Aligned_cols=319 Identities=47% Similarity=0.803 Sum_probs=259.6
Q ss_pred cccceEEEEcCCHHHHHhcceeEEeeCccccCC--CCCCCCCCCCCCCCcCCCccccccccCCCCcCCccceeecccccc
Q 000235 13 AKVRMVQFGILSPDEIRQMSVVQIEHGETTERG--KPKPGGLSDPRLGTIDRKMKCETCTANMAECPGHFGHLELAKPMF 90 (1815)
Q Consensus 13 ~~i~~i~F~~~S~eeI~~~Sv~eI~~~~~~~~~--~p~~gGl~D~rlG~~~~~~~C~TCg~~~~~CpGHfGhIeL~~PV~ 90 (1815)
++|++|+||++|+|||++|||+||+++++||.. +|+.|||||||||+.++...|+|||++..+||||||||||+.|||
T Consensus 2 ~~i~~i~f~~~s~~eI~~~Sv~~i~~~~~~~~~~~~p~~~Gl~d~rlG~~~~~~~C~tC~~~~~~CpGHfGhI~L~~PV~ 81 (337)
T PF04997_consen 2 KKIKSIQFGIYSPEEIRKLSVKEITNPETFDNLTGKPIKGGLYDPRLGPIDKKQICSTCGLNYTECPGHFGHIELALPVY 81 (337)
T ss_dssp EEEEEEEEEE--HHHHHHHEEEB--SSTSBCTSSSSCBSSSSSSSSSS-SSSSSTSSSSSSSSSSCCCSEEEEEEEEEEE
T ss_pred CeeeEEEEEeCCHHHHHHhCcEEEechhhccCCCCCCccccccChhhcCCCcccccccccccccccCCceeEEEeCHHHH
Confidence 689999999999999999999999999999997 999999999999999999999999999999999999999999999
Q ss_pred chhhhhHHHHHhcccceecceeccCCchHHH-HHH-HH--hcChHHHHHHHHHHhhhccccCCCCCCCCCCCCCCccccc
Q 000235 91 HIGFMKTVLSIMRSVCFNCSKILADEDDHKF-KQA-LK--IRNPKNRLKKILDACKNKTKCEGGDEIDVPGQDGEEPLKK 166 (1815)
Q Consensus 91 h~~f~~~v~~iL~~vC~~C~~l~~~~~~~~~-~~~-~~--~~~~~~~~~~i~~~~~~~~~C~~~~~~~~~~~~~~~~~~~ 166 (1815)
|||||+.|.+||+|+|++|++++++..+..+ ... .. ......+++.+.+.|++...|......+.. ........
T Consensus 82 h~~f~~~i~~iL~~~C~~C~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~--~~~~~~~~ 159 (337)
T PF04997_consen 82 HPGFFKEIPKILRCICKKCSRLLLSEKEKYFYLKILLKLKKKKKKERLKIISKECKKKSICSHCKAINGK--IKKVEKSK 159 (337)
T ss_dssp TCCCHHHHHHHHTTSCTTTSCTSTCCCCHTSCHHHCHCSHSSSHHHHHHHHHHHHHHTCSSTSTCC-SSS-----SSSEE
T ss_pred hhcccccceeeecccccccccccccccccccccccccccccccchhHHHHHHHhhhhhhhhccccccccc--ccccccch
Confidence 9999999999999999999999999876521 111 11 234567888999999988888753111000 00000024
Q ss_pred ccCCCCccchhhhhcc-cchhhhhHHhhccccccCCCCccchhcccCCHHHHHHHHhhcChhhHHHhcCCCCCCCccceE
Q 000235 167 NKGGCGAQQPKLTIEG-MKMIAEYKAQRKKNDDQEQLPEPVERKQTLTAERVLGVLKRISDEDCQLLGLNPKYARPDWMI 245 (1815)
Q Consensus 167 ~~~gCg~~~p~i~k~~-~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~p~~v~~ilk~i~~~d~~~l~~~~~~~~Pe~~i 245 (1815)
.+.+|+..++.+++.+ ..+...++.. +..+... ...+.|+|.+|+++|++|+++|+.+|||.+...+|+|||
T Consensus 160 ~~~~~~~~~~~~~~~~~~~i~~~i~~~-~~~~~~~------~~~~~l~~~~v~~ilk~l~~~~~~~l~~~~~~~~P~~~~ 232 (337)
T PF04997_consen 160 KCEGCGKKNPKIRKEGAEKIQEEIKKK-ESNKEIK------EELRILTPEEVRQILKKLSKEDKELLGFDPSGSRPEWFF 232 (337)
T ss_dssp TSSSSSSBSCEEEEESHCCCCCHHHSC-CHHHHHH------CHCECESHHHHHHHHHHSHHHHHHHHHHHTTTBSGGGSE
T ss_pred hcccccccCcccccchhhhcccccccc-cccccch------hhhhhhhhhhhhhcchhhhhhheeeeeccccccccceeE
Confidence 5778999888888777 4444444322 0000000 123479999999999999999999999988889999999
Q ss_pred EeecccCCCCCCCC----------chhHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHhhccCCCCCCCccc
Q 000235 246 LQVLPIPPPPVRPS----------DDLTHQLAMIIRHNENLRRQERNGAPAHIISEFAQLLQFHIATYFDNELPGQPRAT 315 (1815)
Q Consensus 246 l~~lpVpP~~~RP~----------ddlT~~l~~Ii~~N~~lk~~~~~g~~~~~i~~~~~~LQ~~V~~~~dn~~~~~p~~~ 315 (1815)
|++|||||+++||+ ||||++|++||++|++|++..+.+++...+.+.|++||++|++||||++++.|.+.
T Consensus 233 l~~lpVpP~~~RP~v~~~~~~~~eddlt~~~~~Ii~~N~~L~~~~~~~~~~~~~~~~~~~LQ~~v~~~~dn~~~~~~~~~ 312 (337)
T PF04997_consen 233 LTVLPVPPPRFRPSVQLGGGRFSEDDLTSLYRKIIKRNNRLRKLLEEGAPSSIIMEEWRLLQEAVNSLIDNEKPGKPPAG 312 (337)
T ss_dssp EEEEEE-TGGGS-EEEESSSEEEE-HHHHHHHHHHHHHHHHHHCCTSTSSSCHHHHHHHHHHHHHHHHHCTTSSSSSBCB
T ss_pred EeeeecCCceeeeeeeeecccccCchHHHHHHHHHHHHHHHHHHHHhhCcchhhhhhhhhhhHhHhHHhhhcccCCcccc
Confidence 99999999999998 89999999999999999999989999999999999999999999999999998887
Q ss_pred ccCCCChhhhhhhhhhccccccccc
Q 000235 316 QRSGRPIKSICSRLKAKEGRIRGNL 340 (1815)
Q Consensus 316 ~~~~~p~k~i~qrLkgK~Gr~R~nl 340 (1815)
++++||+|||+|||||||||||+||
T Consensus 313 ~~~~~~~k~i~q~L~gK~GrfR~NL 337 (337)
T PF04997_consen 313 QKSGRPLKGISQRLKGKEGRFRQNL 337 (337)
T ss_dssp STTSSB--THHHHHSSTTSSHCHHT
T ss_pred cccCCCCCCHHHHccCCCCcCCCCC
Confidence 7889999999999999999999997
No 30
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=100.00 E-value=3.8e-61 Score=630.74 Aligned_cols=293 Identities=35% Similarity=0.531 Sum_probs=252.7
Q ss_pred hhhccCCccccccccccccccccccccccccceeeeehhhcccCCCCceEEEeCCCCcchHHHHHHHHhhhccccccccc
Q 000235 1077 AAQSIGEPATQMTLNTFHYAGVSAKNVTLGVPRLREIINVAKKIKTPSLSVFLKPGVNSTKERAKNVQCALEYTTLRSVT 1156 (1815)
Q Consensus 1077 AAQSIGEPaTQMTLnTFH~AGv~~~NVTlGvPRLkEIin~ak~ikTP~mtv~l~~~~~~~~~~a~~v~~~le~~tL~dv~ 1156 (1815)
+|.-| .|||||||||||||++|||||||||||||||++|+||||+|+|+|.+++..+++.|+.++.+||+++|+||+
T Consensus 535 ~Angi---v~~~~LnTFH~AGv~~~nVTlGvPRL~EIinask~i~TP~m~i~l~~~~~~~~~~a~~v~~~ie~~~L~dv~ 611 (858)
T PRK14898 535 TADGV---VTHNTMRTFHYAGVAEINVTLGLPRMIEIVDARKEPSTPIMTVHLKGEYATDREKAEEVAKKIESLTLGDVA 611 (858)
T ss_pred eeCCE---eeccccceeeccCccccccccCCchHHHHhcccCCCCCceEEEEECCCccchHHHHHHHHhheeeEEHHHHH
Confidence 44444 799999999999999999999999999999999999999999999999888889999999999999999999
Q ss_pred eeeEEEEcCCCCceEEEcccceeheeccCCCCcccccccCCcEEEEEechhhhhcccCCHHHHHHHHhhhcCCCceeeec
Q 000235 1157 EATEVWYDPDPMGTIIEEDVEFVKSYYEMPDEDIAPEKISPWLLRIELNREMMVDKKLSMAAVAEKINQEFDDDLTCIFN 1236 (1815)
Q Consensus 1157 ~~~~i~ydp~~~~~~i~~d~~~~~~~~~~~~~~~~~~~~~~~~lrl~l~~~~~~~~~l~~~~i~~~i~~~~~~~~~~~~~ 1236 (1815)
+++++.+. .-.++++|+++.+.++++++++|..+|...++..+.+
T Consensus 612 ~~~~~~~~--------------------------------~~~~~i~l~~~~~~~~~l~~~~i~~~i~~~~~~~~~~--- 656 (858)
T PRK14898 612 TSIAIDLW--------------------------------TQSIKVELDEETLADRGLTIESVEEAIEKKLGVKIDR--- 656 (858)
T ss_pred HHhhhhcc--------------------------------ccEEEEEECHHHHHHcCCCHHHHHHHHHHhccccccC---
Confidence 87663110 0137788999999999999999999998776543322
Q ss_pred CCCccceEEEEEEccCCCCCCCCCCCcchhHHHHHHHHh-------------------------hccccceecccchhhh
Q 000235 1237 DDNADKLILRIRIMNDEAPKGELNDESAEDDVFLKKIES-------------------------NMLTEMALRGVNLLAV 1291 (1815)
Q Consensus 1237 ~dn~~~~~~~ir~~~~~~~~~~~~~~~~~~~~~l~~~~~-------------------------~~l~~~~~~G~nl~~v 1291 (1815)
++.+++++..... .+.+++.++. .-+ .+.++|+||+++
T Consensus 657 ----~~~~~~~~~~~~~------------~~~~~~~~~~l~~~~i~gi~gI~~~~i~~~~~~~~~~~-~l~teG~nl~~~ 719 (858)
T PRK14898 657 ----KGTVLYLKPKTPS------------YKALRKRIPKIKNIVLKGIPGIERVLVKKEEHENDEEY-VLYTQGSNLREV 719 (858)
T ss_pred ----CCCEEEEEecCch------------HHHHHHHHHHhcCcEEECCCCccEEEEecCCCCCCceE-EEEecCcCHHHH
Confidence 2345555543211 0111111110 011 377899999999
Q ss_pred hccccccccccccccHHHHHHhhcHHHHHHHHHHHHHHhhhcCcccccchhHHHHHhhhhccceecccccccccccCCcc
Q 000235 1292 MCHEDVDARRTTSNHLIEIIEVLGIEAVRRALLDELRVVISFDGSYVNYRHLAILCDTMTYRGHLMAITRHGINRNDTGP 1371 (1815)
Q Consensus 1292 l~~~~vD~~rt~sNdI~eI~~vlGIEAAR~~Ii~Ei~~V~~~~Gi~Vn~RHL~LlaD~MT~~G~~~~itR~Gi~~~~~sp 1371 (1815)
|.+++||++||+||||++|+++|||||||++|++||+.||+.||++||+|||+||||+||++|.+++|||+||++.++||
T Consensus 720 ~~~~~vd~~~~~sN~i~~i~~~lGIEAar~~ii~Ei~~v~~~~gi~V~~rHl~liad~MT~~G~~~~~~r~gi~~~~~s~ 799 (858)
T PRK14898 720 FKIEGVDTSRTTTNNIIEIQEVLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIMTADGEVKPIGRHGVAGEKGSV 799 (858)
T ss_pred hcCCCCcccccccCCHHHHHHhhCHHHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHHHccCCcEEEeccCCccCCCCCH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999889999
Q ss_pred ccccchHHHHHHHHHHHhhcCcccccccccccccCCccccCccceeeccchhh
Q 000235 1372 MMRCSFEETVDILLDAAVFAESDYLRGVTENIMLGQLAPIGTGDCSLYLNDEM 1424 (1815)
Q Consensus 1372 L~~aSFEeT~~~L~~AA~~ge~D~l~gvsenIi~G~~~p~GTG~fdll~~~~~ 1424 (1815)
|++||||+|+++|++||++|++|.|+|||||||+|+++|+|||+|||++|.+.
T Consensus 800 l~~asFe~t~~~l~~Aa~~g~~D~l~g~s~~ii~G~~~~~GTG~~~l~~~~~~ 852 (858)
T PRK14898 800 LARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTGCVDLRIDREY 852 (858)
T ss_pred HHhcChHhHHHHHHHHhhcCCCCcCCCchHHeeeCCccCCcCceEEEEecCcc
Confidence 99999999999999999999999999999999999999999999999998764
No 31
>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=5.8e-62 Score=524.51 Aligned_cols=166 Identities=59% Similarity=1.002 Sum_probs=153.2
Q ss_pred CCCCCCCCceeecCCCCcccccccChHHHhhhccCCcccchhHHHHHHHHHHcCCCCCCCcccccEEEeCCCceeecccc
Q 000235 342 GKRVDFSARTVITPDPTINIDQLGVPWSIALNLTYPETVTPYNIERLKELVEYGPHPPPGKTGAKYIIRDDGQRLDLRYL 421 (1815)
Q Consensus 342 GKRVdfsaRsVIspDP~L~~~evGvP~~~A~~LT~PE~Vt~~Ni~~l~~lv~ng~~~~pg~~~A~~i~~~~g~~~~l~~~ 421 (1815)
||||||||||||+|||+|+++|||||..||++||+||.||+||+++|+++|.||++.||| |+|+++.+|.+++|++.
T Consensus 1 GKRVnfSaRSVItpDP~L~~~EvGiP~~iA~~Lt~Pe~Vt~~N~~~l~~~v~ng~~~~pg---a~~i~~~~~~~~~l~~~ 77 (166)
T PF00623_consen 1 GKRVNFSARSVITPDPNLKIDEVGIPIEIAKKLTFPERVTPFNIEKLRKLVINGPDKYPG---ANYIKRSNGNKISLRYK 77 (166)
T ss_dssp CEEESSEEEEEEEEETTSCTTEEEEEHHHHHHCECCHHHHTTTHHHHHHHHHHTTTSSSS---EEEEESTTCHCCCTTSS
T ss_pred CCCcccCCCcEEECCCCCccceecccHHHHhhCCCcEEEHHHHHHHHHHHHhcCcccchh---hhhhhcccCcceeeeec
Confidence 999999999999999999999999999999999999999999999999999999999999 99999999999999887
Q ss_pred ccccccccccccEeeeecccCCeEEEecCCccccccccceeEEeecCCeeeecccCCCCCCCCCCcCccccccCCCHhHH
Q 000235 422 KKSSDHHLELGYKVERHLNDGDFVLFNRQPSLHKMSIMGHRIKIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFETR 501 (1815)
Q Consensus 422 ~~~~~~~L~~g~~V~Rhl~dgD~VL~NRQPsLHk~Simah~vkv~~~~t~rln~~vc~pyNADFDGDEMn~h~Pqs~~ar 501 (1815)
+.+....|+.|++|+||++|||+|||||||||||+|||||++++++++||||||++|+||||||||||||+|+|||++||
T Consensus 78 ~~~~~~~l~~~~~v~r~l~~gd~vl~nRqPtLh~~s~~a~~~~~~~~~t~~~~~~~c~~~NADFDGDem~i~~p~~~~a~ 157 (166)
T PF00623_consen 78 KFKISKKLRIGDIVERHLCDGDIVLLNRQPTLHRMSIMAHKVRVLPGKTIRINPLVCSPFNADFDGDEMNIHLPQSYEAR 157 (166)
T ss_dssp SSCCCHHHHTT-EEEEEHTTT-EEEEEESS-SSGGGEEEEEEEEESSSSEEEEGGGHHHHT--TSS-EEEEE--SSHHHH
T ss_pred cccccceecchhhHHHhhhcCceeEEeccchhccceeeeeeeeeecccEEEeeccchhhhhccCCcceEEEEecCCHHHH
Confidence 65555678999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHccC
Q 000235 502 AEVLELMMV 510 (1815)
Q Consensus 502 aE~~~l~~~ 510 (1815)
||+++||+|
T Consensus 158 ~E~~~L~~~ 166 (166)
T PF00623_consen 158 AEAKELMNV 166 (166)
T ss_dssp HHHHHHCBT
T ss_pred HHHHHHhcC
Confidence 999999986
No 32
>cd00630 RNAP_largest_subunit_C Largest subunit of RNA polymerase (RNAP), C-terminal domain. RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channe
Probab=100.00 E-value=1.2e-46 Score=400.39 Aligned_cols=110 Identities=46% Similarity=0.779 Sum_probs=107.4
Q ss_pred cHHHHHHhhcHHHHHHHHHHHHHHhhhcCcccccchhHHHHHhhhhccceecccccccccccCCccccccchHHHHHHHH
Q 000235 1306 HLIEIIEVLGIEAVRRALLDELRVVISFDGSYVNYRHLAILCDTMTYRGHLMAITRHGINRNDTGPMMRCSFEETVDILL 1385 (1815)
Q Consensus 1306 dI~eI~~vlGIEAAR~~Ii~Ei~~V~~~~Gi~Vn~RHL~LlaD~MT~~G~~~~itR~Gi~~~~~spL~~aSFEeT~~~L~ 1385 (1815)
||++|+++|||||||++|++||++||+.||++||+|||+||||+||++|.++++||+||++.++|||++||||+|+++|+
T Consensus 49 dI~~i~~~lGIEAaR~~iv~El~~v~~~~Gi~V~~rHl~LIAD~MT~~G~~~ginr~g~~~~~~Spl~~aSFE~t~~~L~ 128 (158)
T cd00630 49 SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGFRASKTSPLMRASFEKTTKHLL 128 (158)
T ss_pred cHHHHHHHhCHHHHHHHHHHHHHHHHHhcCceecHHHHHHHHHHHhcCCcccccccccccccCCCHHHHcCHHHHHHHHH
Confidence 56789999999999999999999999999999999999999999999999999999999888899999999999999999
Q ss_pred HHHhhcCcccccccccccccCCccccCccc
Q 000235 1386 DAAVFAESDYLRGVTENIMLGQLAPIGTGD 1415 (1815)
Q Consensus 1386 ~AA~~ge~D~l~gvsenIi~G~~~p~GTG~ 1415 (1815)
+||.+|++|+|+|++||||||+++|+|||+
T Consensus 129 ~AA~~g~~D~l~g~s~~ii~Gk~~~~GTG~ 158 (158)
T cd00630 129 DAAAAGEKDELEGVSENIILGRPAPLGTGS 158 (158)
T ss_pred HHhhcCCCCCCCCcHHhhhccCCCCCCCCC
Confidence 999999999999999999999999999995
No 33
>cd02655 RNAP_beta'_C Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain. Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations.
Probab=100.00 E-value=6.9e-46 Score=408.00 Aligned_cols=108 Identities=33% Similarity=0.586 Sum_probs=98.1
Q ss_pred cHHHHHHhh--cHHHHHHHHHHHHHHhhhcCcccccchhHHHHHhhhhccceec--------------------------
Q 000235 1306 HLIEIIEVL--GIEAVRRALLDELRVVISFDGSYVNYRHLAILCDTMTYRGHLM-------------------------- 1357 (1815)
Q Consensus 1306 dI~eI~~vl--GIEAAR~~Ii~Ei~~V~~~~Gi~Vn~RHL~LlaD~MT~~G~~~-------------------------- 1357 (1815)
|++++++++ ||||||++|++||++||..||++||+|||+||||+||++|+++
T Consensus 55 ~~~~il~~~~~Giea~r~~iv~EIq~Vy~~qGV~I~dKHielIv~qMT~kv~i~~~g~s~~l~Ge~v~~~~~~~~N~~~~ 134 (204)
T cd02655 55 NPHDLLRIKFLGPEAVQKYLVEEIQKVYRSQGVNINDKHIEIIVRQMTSKVKIIDPGDSGFLPGELVDLNEFEEENKRLL 134 (204)
T ss_pred CHHHHHHHHhHHHHHHHHHHHHHHHHHHHhcCeeecHHHHHHHHHHHhcCeEEecCCCcccCCCceeeHHHHHHHHHHHH
Confidence 455566666 9999999999999999999999999999999999999996644
Q ss_pred --------------ccccccccccCCccccccchHHHHHHHHHHHhhcCcccccccccccccCCccccCccc
Q 000235 1358 --------------AITRHGINRNDTGPMMRCSFEETVDILLDAAVFAESDYLRGVTENIMLGQLAPIGTGD 1415 (1815)
Q Consensus 1358 --------------~itR~Gi~~~~~spL~~aSFEeT~~~L~~AA~~ge~D~l~gvsenIi~G~~~p~GTG~ 1415 (1815)
+|||++++ ..|+|++||||||+++|++||++|++|.|+|++||||+|+++|+|||+
T Consensus 135 ~~~~~~~~y~p~llGItk~~l~--~~Sfls~ASFqeT~kvL~~AAi~gk~D~L~GlkeNVI~G~liPaGTG~ 204 (204)
T cd02655 135 LLGKKPAKYEPVLLGITKASLN--TESFISAASFQETTKVLTEAAIEGKIDWLRGLKENVILGRLIPAGTGL 204 (204)
T ss_pred hCCCCcccccceeeeeeecccc--CCCccccCChHHHHHHHHHHHhcCCCCCCCCchhheEECCccCCCCCC
Confidence 56666664 479999999999999999999999999999999999999999999994
No 34
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=100.00 E-value=1.2e-40 Score=413.16 Aligned_cols=110 Identities=16% Similarity=0.140 Sum_probs=71.4
Q ss_pred HHhhcHHHHHHHHHHHHHHhhhcCcccccchhHHHHHhhhhccceeccccccccc-----ccCCccccccchHHHHHHHH
Q 000235 1311 IEVLGIEAVRRALLDELRVVISFDGSYVNYRHLAILCDTMTYRGHLMAITRHGIN-----RNDTGPMMRCSFEETVDILL 1385 (1815)
Q Consensus 1311 ~~vlGIEAAR~~Ii~Ei~~V~~~~Gi~Vn~RHL~LlaD~MT~~G~~~~itR~Gi~-----~~~~spL~~aSFEeT~~~L~ 1385 (1815)
...++|++-|..+.-=...--+.-| .+-+-||.|.+|--...|+-+.++-.|.. ..+.-++-...|-+-..+.+
T Consensus 1149 p~~tvI~ed~e~v~a~~e~pd~D~~-~ispwlLrlelDr~~m~dk~ltm~~ia~~i~~~f~~d~~~i~~ddna~klv~r~ 1227 (1605)
T KOG0260|consen 1149 PQSTVIDEDREFVVAYYEMPDEDVG-RISPWLLRLELDRASMTDKKLTMEQIAEKINRGFGSDLACIFSDDNAEKLVLRL 1227 (1605)
T ss_pred CcceeeccchhhHHhhhcCcccchh-hcChHHHHhhhhhhhcccccccHHHHHHHHHhhccCCCceeecccCCcceEEEE
Confidence 3456666666554433322222223 67778888888887777777766655432 12334666666666666677
Q ss_pred HHHhhcCcccccccccccccCCccccCccc-eeeccc
Q 000235 1386 DAAVFAESDYLRGVTENIMLGQLAPIGTGD-CSLYLN 1421 (1815)
Q Consensus 1386 ~AA~~ge~D~l~gvsenIi~G~~~p~GTG~-fdll~~ 1421 (1815)
.+|..++.|.+.+--|+-|||++.--|++. |.|++.
T Consensus 1228 ri~~~~e~D~~l~~Ie~~ml~~~~l~G~~~i~kV~m~ 1264 (1605)
T KOG0260|consen 1228 RIAKEEEDDVFLKCIEANMLGDMTLRGIPDIFKVYMS 1264 (1605)
T ss_pred EecCccchhHHHHHHHHhhhhhcccCCccccceEEEe
Confidence 788888888888888888888888888864 555543
No 35
>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=99.97 E-value=1.9e-33 Score=309.12 Aligned_cols=185 Identities=51% Similarity=0.881 Sum_probs=156.4
Q ss_pred CCceeeecccccccccchHHHhhhhhhcc--ccCCCCcccchHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhHhhhccC
Q 000235 881 MDSVWIESQTLDSLKMKKSEFDKAFRFEM--DEENWNPNYMLQEYIDDLKTIKELRDVFDAEVQKLEADRYQLATEIATS 958 (1815)
Q Consensus 881 ~d~~~~e~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~r~~l~~~~~~~ 958 (1815)
||++++|.|+++++.+++.+|+++|+++. .+...+..++..+++++|.+|++++.+|++||++|.++|+.||..+++.
T Consensus 1 mD~~~vE~Q~l~~l~~s~~~f~~~Y~~d~~~~~~~~~~~~l~~~v~~~l~~d~~~q~~Ld~E~~qL~~dR~~Lr~~i~~~ 80 (187)
T PF04992_consen 1 MDGAHVENQKLDTLKMSDAKFEKKYRVDLMDDDPEFGRGWLDPEVIEELRNDPEVQKLLDEEYEQLLEDRELLRKEIFPS 80 (187)
T ss_dssp B-GGGEEEEE-TTSSS-HHHHCCCC---TTSTTTS-GCCTCTTH--TTTTTSHCCCHHHHHHHHHHHHHHCCCCSCCSTT
T ss_pred CCcceeccCcCCCCCCCHHHHHhhccccCCCCchhhhhhhCChHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 79999999999999999999999999999 4566777788989999999999999999999999999999999889999
Q ss_pred CCCCCCccccHHHHHHHhhhhcccCCCCCCCCChHHHHHHHHHHHHhhcccCCCCcccHHHHhhhhhhhhhhhhhhhhhH
Q 000235 959 GDSSWPLPVNLKRLIWNAQKTFKVDPRRPSDMHPMEVVEAVDKLQERLKVVPGEDPLSVEAQKNATLFFNILLRSTFASK 1038 (1815)
Q Consensus 959 ~~~~~~~p~n~~r~i~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~lrs~l~~~ 1038 (1815)
++..+++|||+.||||||++.|+|+.+..|+|+|.+|+++|++++++|+|++|+|++|+|+|+|||.||+++|||.|++|
T Consensus 81 g~~~~~LPVNi~RiI~nAq~~f~i~~~~~sdL~P~~Vi~~V~~L~~~L~vv~g~D~ls~Eaq~NAtlLf~i~lRs~LasK 160 (187)
T PF04992_consen 81 GDDKVPLPVNIQRIIWNAQKIFHIDPRKPSDLSPIYVIEKVEELLDRLVVVRGDDPLSREAQENATLLFKILLRSTLASK 160 (187)
T ss_dssp T--EEEEES-HHHHCCCCCCCTT--TTS-BS--HHHHHHHHHHHHTT--SS--SSCCCCHHHHCCCHHHHHHHCCCSSHH
T ss_pred CCcceECCccHHHHHHHHHHHcCCCCCCcccCCHHHHHHHHHHHHHHHhhccCCCcchHHHHhhHHHHHHHHHHHhhhhH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhccCHHHHHHHHHHHHHHhhcC
Q 000235 1039 RVLKEHRLTREAFEWVIGEIESRFLQS 1065 (1815)
Q Consensus 1039 ~~~~~~~l~~~~~~~~l~ei~~ky~~s 1065 (1815)
+++.+|+|+++||+|+|+||+.||.+|
T Consensus 161 rvi~e~rL~~~AF~wilgEIe~rF~~a 187 (187)
T PF04992_consen 161 RVIEEYRLNKEAFDWILGEIESRFKKA 187 (187)
T ss_dssp HHHHTSB--HHHHHHHHHHHHHHHHCC
T ss_pred HHHHHhCcCHHHHHHHHHHHHHHHHcC
Confidence 999999999999999999999999986
No 36
>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=99.97 E-value=1.6e-31 Score=289.74 Aligned_cols=155 Identities=44% Similarity=0.653 Sum_probs=137.3
Q ss_pred ccccCCCCCCceeccccccccceecccCCCccCHHHHHHHHHhcccCC--CCCCCCcccCccCCcchHHHHHHhcCCCce
Q 000235 513 CIVSPQSNRPVMGIVQDTLLGCRKITKRDTFIEKDVFMNILMWWEDFD--GKVPQPTILKPRPLWTGKQVFNLIIPKQIN 590 (1815)
Q Consensus 513 ~i~sp~~g~pi~g~~QD~l~g~~~lT~~d~f~~~~~~~~l~~~~~~~~--~~~~~pai~kp~~lwtGKqi~s~~lp~~in 590 (1815)
||+||++|+|+++++||+|+|+|+||++++|++++|+++++++...+. ...+.|+|++|+++|||||+||++||++++
T Consensus 1 NilSP~~G~Pii~~~QD~vlG~y~LT~~~~f~~~~e~~~~~~~~~~~~~~~~~~~~~I~~~~~~~tgk~~~s~il~~~i~ 80 (158)
T PF04983_consen 1 NILSPANGKPIIGPTQDMVLGAYYLTSEDTFLSRDEAQQALMNGLIDDKKIVLLHPAILKPKELWTGKQTFSRILPNEIN 80 (158)
T ss_dssp GSEETTTTEESSS--SHHHHHHHHHSSTTTEESHHHHHHHHHCSST----CHCSSSSBSSSSSCEECHHHHHTTSHTTHH
T ss_pred CccCCCCCCceEEeccceEeEEEEEEecccccchHHHHHHHHcccccccceeccchhhhccccceeeccHHHHhcccccc
Confidence 799999999999999999999999999999999999999999875543 457899999999999999999999999999
Q ss_pred EeeecccCCCCCCCcCCCCCcEEEEecCeeeeccccccccc-CCcccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcC
Q 000235 591 LFRTAAWHADNDKGILTAGDTLVRIEKGELLSGTLCKKTLG-TSTGSLIHVIWEEVGPDAARKFLGHTQWLVNYWLLQNA 669 (1815)
Q Consensus 591 ~~~~~~~~~~~~~~~~~~~d~~v~i~~gell~g~ldK~~~g-~s~~~Lih~i~~~~G~~~a~~~l~~~q~l~~~~l~~~G 669 (1815)
+.... + ..+|+.++|+||+++.|++||+++| .+.++|||.||++||+++|.+|||++|+|+++|++.+|
T Consensus 81 ~~~~~--~--------~~~~~~~~i~~g~~l~g~l~k~~lgk~~~~~li~~i~~~yG~~~~~~~ld~i~~lg~~~~t~~G 150 (158)
T PF04983_consen 81 PEGFS--N--------DPDDGYVVINNGELLSGVLDKKTLGKKSLGSLIHQIYREYGPEATVQFLDAIKRLGFRYLTRSG 150 (158)
T ss_dssp EEEST--S--------CHSSHSEEECTSSEEEC--SHHHHSCSHTTCHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred ccccc--c--------cccccceeecCCccchhheehheecccchhhHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHcC
Confidence 98642 0 1226789999999999999999999 77899999999999999999999999999999999999
Q ss_pred ceeeeccC
Q 000235 670 FSIGIGDT 677 (1815)
Q Consensus 670 fSigi~D~ 677 (1815)
||||++|+
T Consensus 151 fSvgi~D~ 158 (158)
T PF04983_consen 151 FSVGIDDM 158 (158)
T ss_dssp BB-SGGGC
T ss_pred eeEecccC
Confidence 99999996
No 37
>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=99.87 E-value=3.4e-23 Score=210.14 Aligned_cols=105 Identities=51% Similarity=0.821 Sum_probs=91.4
Q ss_pred HHHc-CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCChHHHHHhcCCCCcccchhhhhhhccccccCCCc
Q 000235 704 QAQD-KSLEPEPGRTMMESFENKVNQVLNTARDEAGSSAQKSLSESNNLKAMVTAGSKGSFINISQMTACVGQQNVEGKR 782 (1815)
Q Consensus 704 ~~~~-~~l~~~~~~~~~~~~e~~v~~~ln~~~~~~~~~~~~~l~~~N~~~~M~~sGsKGS~~N~~Qi~~~lGQQ~~eG~R 782 (1815)
++++ ++++..++++.++.+|..++++|+++++.+++.+.+++..+|++++|+.||||||++|++||+||||||.++|+|
T Consensus 3 ~~e~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~N~l~~M~~SGaKGs~~ni~Qi~g~lGqq~~~g~r 82 (108)
T PF05000_consen 3 DYERYGKLEKKWGKTYEETFEQKINKILNKVRDEIGKIIKKNLPFNNSLLIMINSGAKGSMSNISQISGCLGQQSVEGKR 82 (108)
T ss_dssp HHHCCTHHHHHCTCHHHHHHHHHHHHHHHHCCHHHHHHHHHCSTTTSHHHHHHHSSSS--HHHHHHHHST-EEEEETTSE
T ss_pred chHhhCchHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcHHhhhhccCCCCHHHHHHHHHHHHHhhccccc
Confidence 3444 566667889999999999999999999999999999998789999999999999999999999999999999999
Q ss_pred cCCCCCCCCCCCCCCCCCCCcccccc
Q 000235 783 IPFGFVDRTLPHFTKDDYGPESRGFV 808 (1815)
Q Consensus 783 ip~~~~~rtLp~f~~~d~~~~~~Gfv 808 (1815)
|+.+|.+||||||.++|.+|+++|||
T Consensus 83 i~~~~~~Rtlp~f~~~~~~~~~~GFI 108 (108)
T PF05000_consen 83 IPRGFSGRTLPHFKPFDESPESRGFI 108 (108)
T ss_dssp S--SSTTCSSTTS-SS-SSTTTTTEE
T ss_pred cccCCCCCcCCCcCCCCCCcccCCCC
Confidence 99999999999999999999999998
No 38
>PF04990 RNA_pol_Rpb1_7: RNA polymerase Rpb1, domain 7; InterPro: IPR007073 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 7, represents a mobile module of the RNA polymerase. Domain 7 interacts with the lobe domain of Rpb2 (IPR007642 from INTERPRO) [, ].; 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=99.87 E-value=9.6e-23 Score=212.37 Aligned_cols=135 Identities=61% Similarity=1.041 Sum_probs=108.6
Q ss_pred ccccccceeeEEEEcCCCCceEEEcccceeheeccCCCCcccccccCCcEEEEEechhhhhcccCCHHHHHHHHhhhcCC
Q 000235 1150 TTLRSVTEATEVWYDPDPMGTIIEEDVEFVKSYYEMPDEDIAPEKISPWLLRIELNREMMVDKKLSMAAVAEKINQEFDD 1229 (1815)
Q Consensus 1150 ~tL~dv~~~~~i~ydp~~~~~~i~~d~~~~~~~~~~~~~~~~~~~~~~~~lrl~l~~~~~~~~~l~~~~i~~~i~~~~~~ 1229 (1815)
|||++|+++++|+|||++.+|+|++|++||+.||++|+++.....++||+||++||+++|.+|+|+|++|+.+|++.|++
T Consensus 1 TtL~~vt~~teIyYDPdp~~Tvi~eD~e~V~~y~e~pd~~~~~~~~spWlLRieLdr~~m~dk~l~m~~I~~~I~~~f~~ 80 (135)
T PF04990_consen 1 TTLRDVTASTEIYYDPDPRNTVIEEDREFVESYFEIPDEDDDPSRLSPWLLRIELDRKKMIDKKLTMEDIAEKIKEEFGN 80 (135)
T ss_dssp ECCHCHECEEEEEE-SSTTSSSSSTTHCHHHHCCCTT-SSTT-SSBESEEEEEEE-CCCCCCTT--HHHHCCCHHHCCTT
T ss_pred CcHHHhhhheeEEECCCCCCCcchhhHHHHHHHHhCCCcccCcccCCCeEEEEEEcHHHHHhcCCCHHHHHHHHHHhcCC
Confidence 68999999999999999999999999999999999999878888999999999999999999999999999999999999
Q ss_pred CceeeecCCCccceEEEEEEccCCCCCCCCCCCcchhHHHHHHHHhhccccceec
Q 000235 1230 DLTCIFNDDNADKLILRIRIMNDEAPKGELNDESAEDDVFLKKIESNMLTEMALR 1284 (1815)
Q Consensus 1230 ~~~~~~~~dn~~~~~~~ir~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~ 1284 (1815)
+++|+++++|++++++|||+...++...+.+++..+++.||+++|.++|..++++
T Consensus 81 ~l~vi~sddNa~~lViRIRi~~~~~~~~~~~d~~~~dd~~Lr~~e~~lL~~~~Lr 135 (135)
T PF04990_consen 81 DLHVIYSDDNAEKLVIRIRIIKDEDKKEEDEDEQEEDDVFLRRLESNLLDDLTLR 135 (135)
T ss_dssp SEEEEE--TTSSSEEEEEEEB--S---SSSSS--S-CHHHHHHHHHHHCCS-ECC
T ss_pred CeEEEecCCCCcccEEEEEEecCcccccccccchhhHHHHHHHHHHHhhhcCcCC
Confidence 9999999999999999999988653222222222246789999999999988775
No 39
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]
Probab=99.80 E-value=2.8e-20 Score=242.30 Aligned_cols=327 Identities=26% Similarity=0.337 Sum_probs=232.7
Q ss_pred hcCcccCCCchhhHhhhccCCcccccccccccccc--ccccccccccceeeeehhhcccCCCCceEEEeCCCCcchHHHH
Q 000235 1063 LQSLVAPGEMIGCVAAQSIGEPATQMTLNTFHYAG--VSAKNVTLGVPRLREIINVAKKIKTPSLSVFLKPGVNSTKERA 1140 (1815)
Q Consensus 1063 ~~slv~PGEaVG~iAAQSIGEPaTQMTLnTFH~AG--v~~~NVTlGvPRLkEIin~ak~ikTP~mtv~l~~~~~~~~~~a 1140 (1815)
-..++.+++++|..||||+++|.|||++.|||+|| ++..++|+|.|||-++.++ +..+||.|++++...+..+.+.+
T Consensus 407 GDeM~~Hvp~s~ea~AEa~~lm~tq~nilsP~~Ggpiv~~~qD~v~g~ylLt~~d~-~~~~~~~~ei~l~~~~~~~~e~~ 485 (808)
T COG0086 407 GDEMAVHVPASGEAAAEARGLMGTQMNILTPHYGGPIVAPIQDTVGGPYLLTIVDA-KLPSTPVGEIYLKDEYADDREKA 485 (808)
T ss_pred chhhhccccchHHHHHHHHHhhccccccccCCCCCceEeecceEEeccEEEEEecc-cCCCCcceEEEeccccccchhhh
Confidence 34567899999999999999999999999999999 9999999999999999997 88999999999987777778899
Q ss_pred HHHHhhhccccccccceeeEEEEcCCCCceEEEcccceeheeccCCCC-cccccccCCcEEEEEechhhh---hcccC--
Q 000235 1141 KNVQCALEYTTLRSVTEATEVWYDPDPMGTIIEEDVEFVKSYYEMPDE-DIAPEKISPWLLRIELNREMM---VDKKL-- 1214 (1815)
Q Consensus 1141 ~~v~~~le~~tL~dv~~~~~i~ydp~~~~~~i~~d~~~~~~~~~~~~~-~~~~~~~~~~~lrl~l~~~~~---~~~~l-- 1214 (1815)
..+.+.++.++.+++++.+.... .....++..|.+.+..- .++.+ ++........+++-.+++... ...+.
T Consensus 486 ~ai~~~~~~~~~k~i~~~i~~~~--~~~~i~~t~~~~~~~~~-~~~~~~d~~~~i~~~~l~~~~i~k~~~~i~~~~g~~~ 562 (808)
T COG0086 486 EAIAKKIELTTGKVIVSTISPDL--AELSIIVTTDGRRIFNR-GLPEDKDVLVKIVNGKLIKGVIDKKIVTIYREYGPEV 562 (808)
T ss_pred HHHhcccceeeeeEEEEEeeccC--CcceEEEecchhhhhhc-cCCcccceeeEEeccccceeeehhhHHHHHHHhCchh
Confidence 99999999999999887533211 11222233333211100 00100 000000000111112221110 01111
Q ss_pred ---CHHHHHHHHhhhcCCCceeeecCCCccceEEEEEEccCCCCCCCCCCCcchhHHHHHHHHhhccccceecccchhhh
Q 000235 1215 ---SMAAVAEKINQEFDDDLTCIFNDDNADKLILRIRIMNDEAPKGELNDESAEDDVFLKKIESNMLTEMALRGVNLLAV 1291 (1815)
Q Consensus 1215 ---~~~~i~~~i~~~~~~~~~~~~~~dn~~~~~~~ir~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~G~nl~~v 1291 (1815)
...+..++++..+ ..... ...+.+.. ++ .+.. .+.+.++. ..+|.++..+
T Consensus 563 ~~~~~~~~~dkl~~~~-----~~~~~------~~~~~i~~----~d-~~~~-~~~~e~v~----------~ae~~v~~~i 615 (808)
T COG0086 563 ASKALVKLLDKLKNLG-----IKGIG------GFGIGIGR----KD-IEAE-DEKDEIVI----------EAEGSVLKLI 615 (808)
T ss_pred hHHHHHHHHHHHHHhh-----eeeec------cceEEeec----cc-ccch-HHHHHHHH----------HHHHHHHHHH
Confidence 0001111111110 00000 00011111 00 0000 00112221 2355677778
Q ss_pred hccccccccccccccHHHHHHhhcHHHHHHHHHHHHHHhhhcCccc-ccchhHHHHHhhhhccceecccccccccccCCc
Q 000235 1292 MCHEDVDARRTTSNHLIEIIEVLGIEAVRRALLDELRVVISFDGSY-VNYRHLAILCDTMTYRGHLMAITRHGINRNDTG 1370 (1815)
Q Consensus 1292 l~~~~vD~~rt~sNdI~eI~~vlGIEAAR~~Ii~Ei~~V~~~~Gi~-Vn~RHL~LlaD~MT~~G~~~~itR~Gi~~~~~s 1370 (1815)
+..+.+|.+++.+||+.+++.++|+||+|+++++|+..+...+|.. ++.+|+++.+|.|+..+....+.++|+.....|
T Consensus 616 ~~~~~g~lt~~~~~~i~e~~e~~~~e~l~~ai~~~~~~~~~~~g~~~~~i~~m~~~Gs~~n~sq~~~~iG~~gv~g~r~~ 695 (808)
T COG0086 616 LQYEEGDLTRTERNNIVEIIEVLGIEALRNAIIEEIKITLEEQGLDFVDIRHMGLSGARMNISQIVQLIGQQGVMGEKIS 695 (808)
T ss_pred HHhhcCCccccCCCCeEEEeehHHHHHHHHHHHHHHhhhHHhcCCcchhHHHHhhhhhccCHHHHHHHhhhheeeccCCC
Confidence 8899999999999999999999999999999999999999999999 999999999999999999999999999988899
Q ss_pred cccccchHHHHHHHHHHHhhcCcccccccccccccCCccccCccceeeccc
Q 000235 1371 PMMRCSFEETVDILLDAAVFAESDYLRGVTENIMLGQLAPIGTGDCSLYLN 1421 (1815)
Q Consensus 1371 pL~~aSFEeT~~~L~~AA~~ge~D~l~gvsenIi~G~~~p~GTG~fdll~~ 1421 (1815)
++++++||.|..+ .+|+.+++.+.+.|+++++++|+.+.+|||..|.-+.
T Consensus 696 ~~~~~~Fe~~~~~-~~a~~~i~s~f~eGLt~~e~f~~~~ggR~GlvDTA~K 745 (808)
T COG0086 696 VLARAAFEVTVKH-LEAEGPGESSFLEGLTENEYFGHPIGGRTGLVDTALK 745 (808)
T ss_pred ccccccccccccc-ceeeeeeecccCCCCCcceEEeecCccccchHHHhhh
Confidence 9999999999999 9999999999999999999999999999999998664
No 40
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=98.97 E-value=2.3e-10 Score=152.74 Aligned_cols=51 Identities=51% Similarity=0.683 Sum_probs=48.3
Q ss_pred HHhhccCHHHHHHHHHHHHHHhhcCcccCCCchhhHhhhccCCcccccccc
Q 000235 1041 LKEHRLTREAFEWVIGEIESRFLQSLVAPGEMIGCVAAQSIGEPATQMTLN 1091 (1815)
Q Consensus 1041 ~~~~~l~~~~~~~~l~ei~~ky~~slv~PGEaVG~iAAQSIGEPaTQMTLn 1091 (1815)
..+++|+.++|+|++++|+.+|.+++|+||||||++||||||||+|||||.
T Consensus 28 ~~~~~lt~~~~d~Il~~I~~~y~~a~vepge~vG~~aaqsi~~~~~~~~~~ 78 (858)
T PRK14898 28 SKRDGVTEEMVEEIIDEVVSAYLNALVEPYEAVGIVAAQSIGEPGTQMSLP 78 (858)
T ss_pred HhhcCCCHHHHHHHHHHHHHHHhhCCCCCCceeeeeeehhcCCCCccccCC
Confidence 356799999999999999999999999999999999999999999999874
No 41
>PHA03247 large tegument protein UL36; Provisional
Probab=98.52 E-value=0.0002 Score=99.80 Aligned_cols=18 Identities=28% Similarity=0.285 Sum_probs=14.5
Q ss_pred chhHHHHHHHHHHcCCCC
Q 000235 381 TPYNIERLKELVEYGPHP 398 (1815)
Q Consensus 381 t~~Ni~~l~~lv~ng~~~ 398 (1815)
|..+-.-|++|++.|.+.
T Consensus 848 ts~~a~LL~dLl~~G~dl 865 (3151)
T PHA03247 848 TSPQAILLRELLQRGQDL 865 (3151)
T ss_pred cchhhHHHHHHHHhCCCC
Confidence 556788899999999874
No 42
>PHA03247 large tegument protein UL36; Provisional
Probab=98.41 E-value=0.00036 Score=97.45 Aligned_cols=24 Identities=29% Similarity=0.552 Sum_probs=14.5
Q ss_pred ccceeeeehhhcccCCCCceEEEeCCC
Q 000235 1106 GVPRLREIINVAKKIKTPSLSVFLKPG 1132 (1815)
Q Consensus 1106 GvPRLkEIin~ak~ikTP~mtv~l~~~ 1132 (1815)
||--|+| +-..|..|..+.||..+
T Consensus 1927 ~v~tlRE---A~S~ID~~f~~~yLd~d 1950 (3151)
T PHA03247 1927 GPLELRE---ATSELDLPFATSYLAPD 1950 (3151)
T ss_pred cceehhh---hhhhcccccceeeecCC
Confidence 4545555 22567777777777653
No 43
>KOG0307 consensus Vesicle coat complex COPII, subunit SEC31 [Intracellular trafficking, secretion, and vesicular transport]
Probab=96.82 E-value=0.22 Score=67.05 Aligned_cols=12 Identities=25% Similarity=0.457 Sum_probs=6.8
Q ss_pred HHHHhhhhccce
Q 000235 1344 AILCDTMTYRGH 1355 (1815)
Q Consensus 1344 ~LlaD~MT~~G~ 1355 (1815)
..|+|.|...|.
T Consensus 591 ~~Lg~rl~~~g~ 602 (1049)
T KOG0307|consen 591 DMLGDRLENAGD 602 (1049)
T ss_pred HHHHHHHhhccc
Confidence 345566666664
No 44
>KOG0307 consensus Vesicle coat complex COPII, subunit SEC31 [Intracellular trafficking, secretion, and vesicular transport]
Probab=96.28 E-value=0.87 Score=61.62 Aligned_cols=11 Identities=27% Similarity=0.274 Sum_probs=4.9
Q ss_pred hccccccccce
Q 000235 1147 LEYTTLRSVTE 1157 (1815)
Q Consensus 1147 le~~tL~dv~~ 1157 (1815)
|+.-.|+++++
T Consensus 402 lk~~~l~~~c~ 412 (1049)
T KOG0307|consen 402 LKDANLGDYCE 412 (1049)
T ss_pred hccchHHHHHH
Confidence 33334555544
No 45
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=93.07 E-value=0.84 Score=60.93 Aligned_cols=9 Identities=33% Similarity=0.235 Sum_probs=4.4
Q ss_pred ccccccccc
Q 000235 1357 MAITRHGIN 1365 (1815)
Q Consensus 1357 ~~itR~Gi~ 1365 (1815)
-++.+||..
T Consensus 669 ga~g~~ggg 677 (1024)
T KOG1999|consen 669 GAFGGHGGG 677 (1024)
T ss_pred CCcCcCccC
Confidence 445555543
No 46
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=91.55 E-value=1 Score=58.49 Aligned_cols=12 Identities=25% Similarity=0.603 Sum_probs=6.2
Q ss_pred HHHHHhhceEEe
Q 000235 848 RLVKAMEDIMVK 859 (1815)
Q Consensus 848 rLvk~lEdl~v~ 859 (1815)
+|...+|.|.|+
T Consensus 157 ~l~~CleslRVs 168 (1102)
T KOG1924|consen 157 KLLECLESLRVS 168 (1102)
T ss_pred cHHHHHHHHhhh
Confidence 344455555554
No 47
>KOG1984 consensus Vesicle coat complex COPII, subunit SFB3 [Intracellular trafficking, secretion, and vesicular transport]
Probab=91.24 E-value=51 Score=44.60 Aligned_cols=11 Identities=36% Similarity=0.440 Sum_probs=6.1
Q ss_pred CCCCCCCCCCC
Q 000235 1774 AGYSPSAPGYS 1784 (1815)
Q Consensus 1774 ~~~~P~~p~~s 1784 (1815)
+..+|..+.++
T Consensus 243 p~~iPs~~qv~ 253 (1007)
T KOG1984|consen 243 PNAIPSPPQVS 253 (1007)
T ss_pred hhhCCCchhcc
Confidence 34466666663
No 48
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=91.13 E-value=1 Score=58.46 Aligned_cols=17 Identities=0% Similarity=0.016 Sum_probs=8.1
Q ss_pred chhHHHHHHHhhceEEe
Q 000235 843 GYIQRRLVKAMEDIMVK 859 (1815)
Q Consensus 843 GYlqRrLvk~lEdl~v~ 859 (1815)
|...|+..-|+.+..+.
T Consensus 50 ~~~sk~~~~H~~~ss~s 66 (1102)
T KOG1924|consen 50 DFKSKPSPAHLRSSSAS 66 (1102)
T ss_pred ccccCCCcccCCCcccc
Confidence 34444455555444443
No 49
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=84.94 E-value=11 Score=50.88 Aligned_cols=9 Identities=11% Similarity=0.180 Sum_probs=3.9
Q ss_pred cchhHHHHH
Q 000235 1339 NYRHLAILC 1347 (1815)
Q Consensus 1339 n~RHL~Lla 1347 (1815)
+.||+.|.+
T Consensus 627 k~k~~~~~g 635 (1024)
T KOG1999|consen 627 KEKNLILAG 635 (1024)
T ss_pred ecCCceecc
Confidence 444444443
No 50
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=68.02 E-value=21 Score=44.96 Aligned_cols=20 Identities=15% Similarity=0.140 Sum_probs=13.3
Q ss_pred cccccccccccccccccccccc
Q 000235 1084 PATQMTLNTFHYAGVSAKNVTL 1105 (1815)
Q Consensus 1084 PaTQMTLnTFH~AGv~~~NVTl 1105 (1815)
+.++-+++||. +|...+||-
T Consensus 38 ~~~~~~~~sen--v~~dasitv 57 (483)
T KOG2236|consen 38 VKESEPIKSEN--VVSDASITV 57 (483)
T ss_pred cCCCCCccccc--ccccccccc
Confidence 35777888888 555566653
No 51
>KOG3671 consensus Actin regulatory protein (Wiskott-Aldrich syndrome protein) [Signal transduction mechanisms; Cytoskeleton]
Probab=62.03 E-value=2.3e+02 Score=36.58 Aligned_cols=9 Identities=33% Similarity=0.582 Sum_probs=4.8
Q ss_pred HHHHHHHHh
Q 000235 1267 DVFLKKIES 1275 (1815)
Q Consensus 1267 ~~~l~~~~~ 1275 (1815)
..|.+++++
T Consensus 129 ~~F~k~V~~ 137 (569)
T KOG3671|consen 129 QKFRKKVQD 137 (569)
T ss_pred HHHHHHHHH
Confidence 456665543
No 52
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=61.80 E-value=46 Score=42.06 Aligned_cols=9 Identities=22% Similarity=0.353 Sum_probs=4.2
Q ss_pred ccccCCccc
Q 000235 1402 NIMLGQLAP 1410 (1815)
Q Consensus 1402 nIi~G~~~p 1410 (1815)
.|.+|..+-
T Consensus 276 gi~ig~~vy 284 (483)
T KOG2236|consen 276 GICIGEKVY 284 (483)
T ss_pred ccccCCeeE
Confidence 444555443
No 53
>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=51.00 E-value=7.8 Score=51.53 Aligned_cols=54 Identities=31% Similarity=0.302 Sum_probs=29.9
Q ss_pred eecccCCeEEEecCCccccccccceeEEeecC-Ce-----------eeecccCCCCCCCCCCcCccccc
Q 000235 437 RHLNDGDFVLFNRQPSLHKMSIMGHRIKIMPY-ST-----------FRLNLSVTSPYNADFDGDEMNMH 493 (1815)
Q Consensus 437 Rhl~dgD~VL~NRQPsLHk~Simah~vkv~~~-~t-----------~rln~~vc~pyNADFDGDEMn~h 493 (1815)
..+..| -||+-|.|+||.--|+-.+++-.|. +- =|=+++.|+ +.|+|||+-.|-
T Consensus 364 ~~~~~g-~VlV~R~P~~~pgDir~~~av~~p~L~~l~~vIVF~~~G~r~~~~~ls--GgDlDGD~~~V~ 429 (579)
T PF05183_consen 364 SQVLEG-DVLVTRNPCLHPGDIRKVKAVDKPELRHLKDVIVFSTKGDRPLPSELS--GGDLDGDEYFVC 429 (579)
T ss_dssp EEEEE--EEEEE-SS--SGGGEEEEEE---GGGTT--SEEEE-S-SSS-HHHHTT--T--SSS-EEEEE
T ss_pred cceeee-eEEEecCCccCcCceeEEEeeccHHHcccCCEEEeCCCCCCCchHHhc--CCCCCCceEEEE
Confidence 566778 8899999999999999888876664 11 122222233 379999998866
No 54
>PF02362 B3: B3 DNA binding domain; InterPro: IPR003340 Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species. The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see IPR001471 from INTERPRO) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors []. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1WID_A 1YEL_A.
Probab=46.86 E-value=20 Score=35.80 Aligned_cols=76 Identities=21% Similarity=0.298 Sum_probs=42.4
Q ss_pred eecCCCCcccccccChHHHhhhccCCcccchhHHHHHHHHHHcCCCCCCCcccccE-EEeCCCceeeccc--cccccccc
Q 000235 352 VITPDPTINIDQLGVPWSIALNLTYPETVTPYNIERLKELVEYGPHPPPGKTGAKY-IIRDDGQRLDLRY--LKKSSDHH 428 (1815)
Q Consensus 352 VIspDP~L~~~evGvP~~~A~~LT~PE~Vt~~Ni~~l~~lv~ng~~~~pg~~~A~~-i~~~~g~~~~l~~--~~~~~~~~ 428 (1815)
++.+.....-+.+-||..+|+.+. +... -+ .+. +.+.+|+.-.+++ .++.....
T Consensus 4 ~l~~s~~~~~~~l~iP~~f~~~~~-------------------~~~~-~~---~~v~l~~~~g~~W~v~~~~~~~~~~~~ 60 (100)
T PF02362_consen 4 VLKPSDVSSSCRLIIPKEFAKKHG-------------------GNKR-KS---REVTLKDPDGRSWPVKLKYRKNSGRYY 60 (100)
T ss_dssp E--TTCCCCTT-EEE-HHHHTTTS---------------------SS------CEEEEEETTTEEEEEEEEEECCTTEEE
T ss_pred EEEccCcCCCCEEEeCHHHHHHhC-------------------CCcC-CC---eEEEEEeCCCCEEEEEEEEEccCCeEE
Confidence 445555666677899999998761 1100 01 233 3466777655555 44434456
Q ss_pred ccccc---EeeeecccCCeEEEecC
Q 000235 429 LELGY---KVERHLNDGDFVLFNRQ 450 (1815)
Q Consensus 429 L~~g~---~V~Rhl~dgD~VL~NRQ 450 (1815)
|.-|| ..+..|+.||+++|-..
T Consensus 61 l~~GW~~Fv~~n~L~~GD~~~F~~~ 85 (100)
T PF02362_consen 61 LTGGWKKFVRDNGLKEGDVCVFELI 85 (100)
T ss_dssp EETTHHHHHHHCT--TT-EEEEEE-
T ss_pred ECCCHHHHHHHcCCCCCCEEEEEEe
Confidence 77888 57789999999999854
No 55
>PF15278 Sec3_C_2: Sec3 exocyst complex subunit
Probab=45.54 E-value=52 Score=31.46 Aligned_cols=27 Identities=26% Similarity=0.240 Sum_probs=22.9
Q ss_pred hhcCCCChHHHHHhcCCCCcccchhhh
Q 000235 743 KSLSESNNLKAMVTAGSKGSFINISQM 769 (1815)
Q Consensus 743 ~~l~~~N~~~~M~~sGsKGS~~N~~Qi 769 (1815)
++++..=|++.|..||+-|..+|+-|.
T Consensus 59 ~si~STiNL~S~~LS~~L~~VIN~EQQ 85 (86)
T PF15278_consen 59 DSIFSTINLFSMSLSTVLNDVINMEQQ 85 (86)
T ss_pred HHHHhHHHHHHHHHHHHhhcccccccC
Confidence 456666789999999999999999874
No 56
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=42.20 E-value=9.1e+02 Score=31.49 Aligned_cols=16 Identities=31% Similarity=0.567 Sum_probs=6.7
Q ss_pred HHHHHhhccccceecc
Q 000235 1270 LKKIESNMLTEMALRG 1285 (1815)
Q Consensus 1270 l~~~~~~~l~~~~~~G 1285 (1815)
+|++|++-=..|.|+|
T Consensus 166 qK~lE~etgAKI~IRG 181 (554)
T KOG0119|consen 166 QKRLERETGAKIAIRG 181 (554)
T ss_pred HHHHHHHhCCeEEEec
Confidence 3444443333344444
No 57
>KOG1923 consensus Rac1 GTPase effector FRL [Signal transduction mechanisms; Cytoskeleton]
Probab=37.95 E-value=1.1e+02 Score=41.22 Aligned_cols=9 Identities=44% Similarity=0.803 Sum_probs=3.9
Q ss_pred ccccchHHH
Q 000235 1372 MMRCSFEET 1380 (1815)
Q Consensus 1372 L~~aSFEeT 1380 (1815)
++++||..|
T Consensus 154 ll~ds~~k~ 162 (830)
T KOG1923|consen 154 LLRDSFQKT 162 (830)
T ss_pred hcccchhhh
Confidence 444444433
No 58
>KOG1830 consensus Wiskott Aldrich syndrome proteins [Cytoskeleton]
Probab=35.39 E-value=1.1e+03 Score=30.27 Aligned_cols=11 Identities=9% Similarity=0.196 Sum_probs=6.0
Q ss_pred ccccccccccc
Q 000235 1295 EDVDARRTTSN 1305 (1815)
Q Consensus 1295 ~~vD~~rt~sN 1305 (1815)
++.|.-+.|||
T Consensus 143 dgk~gLkfYTd 153 (518)
T KOG1830|consen 143 DGKDGLKFYTD 153 (518)
T ss_pred CCcccceeecC
Confidence 44555555665
No 59
>KOG0162 consensus Myosin class I heavy chain [Cytoskeleton]
Probab=33.97 E-value=4.1e+02 Score=35.81 Aligned_cols=11 Identities=45% Similarity=0.661 Sum_probs=8.6
Q ss_pred cCceeeeccCc
Q 000235 668 NAFSIGIGDTI 678 (1815)
Q Consensus 668 ~GfSigi~D~~ 678 (1815)
.-+||||-|+.
T Consensus 381 ~~~sIGiLDIY 391 (1106)
T KOG0162|consen 381 EEYSIGILDIY 391 (1106)
T ss_pred cccceeeEEee
Confidence 56888888875
No 60
>PF15449 Retinal: Retinal protein
Probab=33.15 E-value=9.3e+02 Score=34.26 Aligned_cols=15 Identities=27% Similarity=0.450 Sum_probs=8.6
Q ss_pred CCCCCCCCCCcCccc
Q 000235 477 VTSPYNADFDGDEMN 491 (1815)
Q Consensus 477 vc~pyNADFDGDEMn 491 (1815)
.|..--|||-|||=+
T Consensus 127 Sh~sq~~~f~gee~~ 141 (1287)
T PF15449_consen 127 SHGSQGAAFSGEESE 141 (1287)
T ss_pred ccccccccccccccc
Confidence 355556666666543
No 61
>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]
Probab=31.68 E-value=1.9e+03 Score=32.07 Aligned_cols=36 Identities=31% Similarity=0.202 Sum_probs=22.7
Q ss_pred chhHHHHHhhhhccceecccccccccccCCccccccchHHH
Q 000235 1340 YRHLAILCDTMTYRGHLMAITRHGINRNDTGPMMRCSFEET 1380 (1815)
Q Consensus 1340 ~RHL~LlaD~MT~~G~~~~itR~Gi~~~~~spL~~aSFEeT 1380 (1815)
.+-..=|||.|- .+.+|.||.||-...+-- -+|||-
T Consensus 1499 ~~a~ee~adl~e---qltPIe~YainfLe~~~~--~e~Eee 1534 (1958)
T KOG0391|consen 1499 PSADEELADLME---QLTPIERYAINFLELFYT--SEFEEE 1534 (1958)
T ss_pred hhhHHHHHHHHh---ccCcHHHHHHHHHHhccc--hhhhhh
Confidence 445555778876 578999999975432222 267653
No 62
>PRK13895 conjugal transfer protein TraM; Provisional
Probab=31.51 E-value=2.2e+02 Score=30.94 Aligned_cols=30 Identities=17% Similarity=0.236 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHhcCceeeeccCccChhhHH
Q 000235 656 HTQWLVNYWLLQNAFSIGIGDTIADAKTME 685 (1815)
Q Consensus 656 ~~q~l~~~~l~~~GfSigi~D~~~~~~~~~ 685 (1815)
.+..+...-...||.-+|=+|=++--.|++
T Consensus 4 ki~e~I~~IA~KHGIal~rDDPILilqTiN 33 (144)
T PRK13895 4 KIEELIKEIAAKHGIAVGRDDPILILQTIN 33 (144)
T ss_pred HHHHHHHHHHHHcCcccCCCCCchhHHHHH
Confidence 445555666679999999999776555543
No 63
>PF15449 Retinal: Retinal protein
Probab=31.01 E-value=1.8e+03 Score=31.68 Aligned_cols=9 Identities=33% Similarity=0.427 Sum_probs=5.2
Q ss_pred cccCCcCCC
Q 000235 808 VENSYLRGL 816 (1815)
Q Consensus 808 v~~sf~~GL 816 (1815)
+.++||+|-
T Consensus 294 lt~~~Le~s 302 (1287)
T PF15449_consen 294 LTSSALEGS 302 (1287)
T ss_pred hhhhhhhhh
Confidence 345666663
No 64
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=29.51 E-value=1.4e+03 Score=29.90 Aligned_cols=12 Identities=0% Similarity=0.050 Sum_probs=5.2
Q ss_pred HHHHHHHHHHHH
Q 000235 1317 EAVRRALLDELR 1328 (1815)
Q Consensus 1317 EAAR~~Ii~Ei~ 1328 (1815)
++|-++|-+=|+
T Consensus 218 ~~Ai~vienli~ 229 (554)
T KOG0119|consen 218 KKAIAVIENLIQ 229 (554)
T ss_pred HHHHHHHHHHHH
Confidence 344444444443
No 65
>PHA03082 DNA-dependent RNA polymerase subunit; Provisional
Probab=29.48 E-value=18 Score=32.76 Aligned_cols=40 Identities=20% Similarity=0.550 Sum_probs=27.5
Q ss_pred ccccccccCCCCcCCccceeeccccccchhhhh--HHHHHhcccceecceeccCC
Q 000235 64 MKCETCTANMAECPGHFGHLELAKPMFHIGFMK--TVLSIMRSVCFNCSKILADE 116 (1815)
Q Consensus 64 ~~C~TCg~~~~~CpGHfGhIeL~~PV~h~~f~~--~v~~iL~~vC~~C~~l~~~~ 116 (1815)
..|.|||.+..+=. |+ +.++ .+.++|+.+=..|.++++..
T Consensus 5 lVCsTCGrDlSeeR------------y~-Lli~~~~L~~Vl~~v~~~CCRlKLsT 46 (63)
T PHA03082 5 LVCSTCGRDLSEER------------YR-LLIKKKSLKKVLRTVKNSCCRLKLST 46 (63)
T ss_pred eeecccCcchhHHH------------HH-HHHHHhhHHHHHHHhhccceeeeeec
Confidence 47999998754321 22 2233 36788999999999998864
No 66
>KOG3771 consensus Amphiphysin [Intracellular trafficking, secretion, and vesicular transport]
Probab=29.16 E-value=1e+03 Score=30.85 Aligned_cols=9 Identities=44% Similarity=0.689 Sum_probs=4.5
Q ss_pred HHHHHHHhh
Q 000235 1323 LLDELRVVI 1331 (1815)
Q Consensus 1323 Ii~Ei~~V~ 1331 (1815)
|+.||=..|
T Consensus 180 L~eELP~L~ 188 (460)
T KOG3771|consen 180 LLEELPALY 188 (460)
T ss_pred HHHHHHHHH
Confidence 445554444
No 67
>KOG1830 consensus Wiskott Aldrich syndrome proteins [Cytoskeleton]
Probab=25.01 E-value=1.5e+03 Score=28.90 Aligned_cols=13 Identities=23% Similarity=0.452 Sum_probs=8.9
Q ss_pred eeeccchhhhhhhh
Q 000235 1416 CSLYLNDEMLKNAI 1429 (1815)
Q Consensus 1416 fdll~~~~~l~~~~ 1429 (1815)
||| +.++||+++-
T Consensus 158 FDL-WKekmLqdte 170 (518)
T KOG1830|consen 158 FDL-WKEKMLQDTE 170 (518)
T ss_pred HHH-HHHHHHHHHH
Confidence 564 6788887763
No 68
>KOG0566 consensus Inositol-1,4,5-triphosphate 5-phosphatase (synaptojanin), INP51/INP52/INP53 family [Intracellular trafficking, secretion, and vesicular transport]
Probab=23.50 E-value=6.2e+02 Score=35.47 Aligned_cols=26 Identities=31% Similarity=0.491 Sum_probs=21.7
Q ss_pred ccCCeEEEecCCccccccccceeEEeecC
Q 000235 440 NDGDFVLFNRQPSLHKMSIMGHRIKIMPY 468 (1815)
Q Consensus 440 ~dgD~VL~NRQPsLHk~Simah~vkv~~~ 468 (1815)
+.|-+=||=-||. .++-+|+|+|..+
T Consensus 265 IRGSvPlFWEQ~g---~~~~s~kv~itR~ 290 (1080)
T KOG0566|consen 265 IRGSVPLFWEQPG---VQVGSHKVKITRS 290 (1080)
T ss_pred eccceeeeEeccC---cccccceeEEecc
Confidence 4789999999994 4688999999875
No 69
>KOG2199 consensus Signal transducing adaptor protein STAM/STAM2 [Signal transduction mechanisms]
Probab=23.22 E-value=2.9e+02 Score=34.82 Aligned_cols=84 Identities=24% Similarity=0.454 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 000235 1697 QSAKYSPSLAYSPSSPRLSPASPYSPTSPNYSPTS-SSYSPTSPSYSPSSPTYSPSSPYNAGGGNPDYSPSSPQYSPSAG 1775 (1815)
Q Consensus 1697 ~~~~~~~~~~~sp~~p~~sp~~Py~p~~p~~sp~~-~~~sp~~p~~s~~s~~~sp~~p~~~~~~~~~~~ps~p~y~p~~~ 1775 (1815)
+++.+++........|..+|..-+-|. ..|||+. ...-+.||.+.+..|.+.|...|. ..+.++||..+.+
T Consensus 378 ~~~~~Y~~~~p~q~yp~qpp~~~q~~~-q~yspp~q~~pl~~Pp~~~~~~p~~~~q~~Y~-------~~~qs~p~~~Q~~ 449 (462)
T KOG2199|consen 378 QGPALYPQMTPMQNYPVQPPGRAQYPS-QSYSPPQQQQPLQQPPNSNPATPQQQPQLSYS-------VTPQSVPYPEQNQ 449 (462)
T ss_pred CCcccCCCCCccccCCCCCCcccccCc-ccCCChhhcCCCCCCCccCCCCCCCCcccccc-------CCCCCCCchhhcc
Q ss_pred CCCCCCCCCCCCCCCC
Q 000235 1776 YSPSAPGYSPSSTSQY 1791 (1815)
Q Consensus 1776 ~~P~~p~~s~~~~~~~ 1791 (1815)
+.|.+|.. ++++|
T Consensus 450 q~~pa~~a---~~~~y 462 (462)
T KOG2199|consen 450 QQPPAPTA---DPQSY 462 (462)
T ss_pred CCCCCCCC---CcCcC
Done!