Query 000829
Match_columns 1265
No_of_seqs 261 out of 1991
Neff 6.6
Searched_HMMs 46136
Date Tue Apr 2 00:14:39 2013
Command hhsearch -i /work/01045/syshi/lefta3m/000829.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/leftcdd/000829hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0261 RNA polymerase III, la 100.0 0E+00 0E+00 2866.6 70.9 1223 1-1251 127-1364(1386)
2 PRK14977 bifunctional DNA-dire 100.0 9E-285 2E-289 2693.9 95.2 1126 27-1250 152-1318(1321)
3 KOG0262 RNA polymerase I, larg 100.0 2E-277 5E-282 2443.0 67.1 1189 4-1251 182-1638(1640)
4 KOG0260 RNA polymerase II, lar 100.0 2E-264 3E-269 2322.0 68.1 1182 13-1250 133-1421(1605)
5 TIGR02390 RNA_pol_rpoA1 DNA-di 100.0 1E-202 2E-207 1898.8 62.2 735 12-796 128-867 (868)
6 PRK08566 DNA-directed RNA poly 100.0 3E-202 6E-207 1901.3 63.6 747 8-803 128-879 (882)
7 TIGR02386 rpoC_TIGR DNA-direct 100.0 9E-183 2E-187 1703.9 49.5 857 110-1243 214-1136(1140)
8 PRK00566 DNA-directed RNA poly 100.0 2E-181 4E-186 1693.2 55.2 856 110-1244 222-1139(1156)
9 PRK14906 DNA-directed RNA poly 100.0 9E-175 2E-179 1626.1 54.3 854 110-1243 310-1237(1460)
10 PRK09603 bifunctional DNA-dire 100.0 5E-169 1E-173 1632.2 54.0 673 110-936 1621-2308(2890)
11 PRK14844 bifunctional DNA-dire 100.0 5E-167 1E-171 1607.5 54.5 671 110-937 1664-2365(2836)
12 COG0086 RpoC DNA-directed RNA 100.0 1E-135 3E-140 1266.4 31.2 664 30-785 128-795 (808)
13 smart00663 RPOLA_N RNA polymer 100.0 1.9E-95 4E-100 815.1 26.9 293 113-413 1-295 (295)
14 TIGR02389 RNA_pol_rpoA2 DNA-di 100.0 4.9E-91 1.1E-95 798.3 27.0 348 879-1248 17-367 (367)
15 cd02584 RNAP_II_Rpb1_C Largest 100.0 1.8E-89 4E-94 796.8 27.8 362 880-1248 2-410 (410)
16 cd06528 RNAP_A'' A'' subunit o 100.0 7.1E-89 1.5E-93 782.0 26.6 351 875-1248 10-362 (363)
17 PRK14897 unknown domain/DNA-di 100.0 6.7E-89 1.5E-93 793.4 25.7 352 876-1251 153-506 (509)
18 PRK04309 DNA-directed RNA poly 100.0 8.9E-88 1.9E-92 777.8 29.2 347 879-1250 33-381 (383)
19 PRK02625 rpoC1 DNA-directed RN 100.0 2.6E-87 5.7E-92 791.8 23.3 287 110-421 240-527 (627)
20 cd02736 RNAP_III_Rpc1_C Larges 100.0 2.4E-87 5.3E-92 751.5 19.9 300 896-1243 1-300 (300)
21 CHL00018 rpoC1 RNA polymerase 100.0 4.4E-87 9.5E-92 797.6 20.8 286 110-420 259-547 (663)
22 TIGR02387 rpoC1_cyan DNA-direc 100.0 1E-86 2.2E-91 786.0 20.5 286 110-420 233-519 (619)
23 cd02735 RNAP_I_Rpa1_C Largest 100.0 1.6E-85 3.4E-90 742.8 18.2 307 896-1246 1-309 (309)
24 PF04998 RNA_pol_Rpb1_5: RNA p 100.0 1E-73 2.2E-78 647.2 4.5 273 712-1200 1-276 (277)
25 cd02737 RNAP_IV_NRPD1_C Larges 100.0 3.5E-71 7.6E-76 637.4 16.0 336 905-1247 1-381 (381)
26 PRK02597 rpoC2 DNA-directed RN 100.0 2.5E-70 5.4E-75 692.3 24.0 342 520-949 7-362 (1331)
27 TIGR02388 rpoC2_cyan DNA-direc 100.0 6.5E-70 1.4E-74 683.2 24.0 330 520-939 6-343 (1227)
28 PRK14898 DNA-directed RNA poly 100.0 1.1E-65 2.3E-70 650.7 23.3 317 911-1251 534-852 (858)
29 CHL00117 rpoC2 RNA polymerase 100.0 6.6E-65 1.4E-69 650.4 28.5 333 519-947 12-364 (1364)
30 PF00623 RNA_pol_Rpb1_2: RNA p 100.0 9.6E-64 2.1E-68 518.5 6.4 165 222-388 1-166 (166)
31 cd00630 RNAP_largest_subunit_C 100.0 5.9E-47 1.3E-51 387.8 7.5 110 1133-1242 49-158 (158)
32 cd02655 RNAP_beta'_C Largest s 100.0 6.9E-46 1.5E-50 393.3 9.1 109 1132-1242 54-204 (204)
33 PF04983 RNA_pol_Rpb1_3: RNA p 100.0 3.5E-31 7.7E-36 276.1 1.5 158 391-574 1-158 (158)
34 PF04997 RNA_pol_Rpb1_1: RNA p 100.0 1E-29 2.2E-34 294.3 8.8 200 10-220 124-337 (337)
35 PF05000 RNA_pol_Rpb1_4: RNA p 99.9 5.5E-24 1.2E-28 207.5 2.8 105 601-705 3-108 (108)
36 COG0086 RpoC DNA-directed RNA 99.8 8.9E-21 1.9E-25 238.5 -2.0 338 897-1251 406-748 (808)
37 PRK14898 DNA-directed RNA poly 98.8 1.6E-09 3.5E-14 139.6 4.6 51 877-927 29-79 (858)
38 PF04992 RNA_pol_Rpb1_6: RNA p 84.5 1.2 2.5E-05 48.4 4.5 95 789-900 87-187 (187)
39 PF04990 RNA_pol_Rpb1_7: RNA p 77.6 0.74 1.6E-05 47.2 0.0 50 983-1032 1-78 (135)
40 PF05183 RdRP: RNA dependent R 66.8 4.5 9.8E-05 51.5 3.5 54 315-371 364-429 (579)
41 PF14952 zf-tcix: Putative tre 54.8 6.3 0.00014 32.2 1.1 14 27-40 9-22 (44)
42 KOG0988 RNA-directed RNA polym 32.9 46 0.00099 44.6 4.4 53 317-372 771-835 (1145)
43 PF05094 LEF-9: Late expressio 32.3 53 0.0011 39.4 4.3 66 322-388 212-281 (487)
44 COG3688 Predicted RNA-binding 32.1 59 0.0013 34.3 4.1 41 1107-1159 5-45 (173)
45 KOG0571 Asparagine synthase (g 29.5 58 0.0013 39.3 4.1 47 514-582 229-275 (543)
46 PHA03396 lef-9 late expression 24.9 83 0.0018 38.1 4.3 65 322-387 215-283 (493)
47 PF02362 B3: B3 DNA binding do 22.7 86 0.0019 29.7 3.4 76 232-328 4-85 (100)
48 COG4306 Uncharacterized protei 21.9 1.1E+02 0.0023 30.9 3.7 36 9-46 21-57 (160)
No 1
>KOG0261 consensus RNA polymerase III, large subunit [Transcription]
Probab=100.00 E-value=0 Score=2866.60 Aligned_cols=1223 Identities=58% Similarity=0.940 Sum_probs=1157.3
Q ss_pred CCCCchhHHHHHHHHHHHHHHhhhcCCCCCcCCCCCCCCCcEEecceeeeEEEeccc--------chhhHHHHhhhhhcc
Q 000829 1 MRNPKMEALRKTDLMKSIVKKCSTMASKAVKCPRCGYINGMVKKAVAVLGIIHDRSK--------VTESLQEFASAITHT 72 (1265)
Q Consensus 1 ~~~~~~~~~~r~~~~k~i~~~c~~~~k~~~~C~~Cg~~~p~Vrk~~~~~ki~~~~~~--------~~~~~~~~~~~~~~~ 72 (1265)
||+|.++++.|+.+.|+|+++| |+..+|.|||+.||.|||....++|+|+.|+ .+.+..+|+.+.+.+
T Consensus 127 lr~p~~~~l~k~~l~kri~~~C----kK~~~C~hCg~~NG~VKK~~~~lkIiHd~~~~~~k~~~~~~~~~~~~~~~~~~n 202 (1386)
T KOG0261|consen 127 LRNPGLDNLRKKALLKRIVAKC----KKVNTCSHCGALNGTVKKAAALLKIIHDRFKLVKKSDPLVTNERGEFKTAISHN 202 (1386)
T ss_pred hhCCCCChHHHHHHHHHHHHHh----hccccccccCCcCceeeccccceeEeeehhhccccccchhhhhHHHHHHHhhcC
Confidence 6899999999999999999999 8999999999999999994432799999885 225667778888888
Q ss_pred hhhhhhhhccccccCHHHHHHHHHhcChhhHHhhcCC---CCcceEEEeeeeeCCCCCCCceecCC-CCcCCchhHHHHH
Q 000829 73 KESKAAVNVATYILNPVNVLFLFKRMTDTDCEVLYLS---ERPEKLIITNIAVPPIAIRPSVIMDG-SQSNENDITERLK 148 (1265)
Q Consensus 73 ~e~~~~~~~~~~~L~P~~v~~ifk~I~~ed~~lL~~~---~~p~~~~l~~lpVpP~~~RP~~~~~~-~~~~~ddlt~~l~ 148 (1265)
++.+.+.....+.|+|+.|+++|+.|++.||+||++. .||+.++++++||||.|+|||+.+++ .+++|||||.+++
T Consensus 203 ~e~~~~~~~~~~~LnPl~vLnLFk~i~~~D~eLLg~~~~~~~P~~Li~t~~~vPP~cIRPSV~~~~k~gtnEDDlT~Klt 282 (1386)
T KOG0261|consen 203 KELEGHLSSCCEELNPLVVLNLFKQIKEDDCELLGMDSEEGRPENLIITRVPVPPVCIRPSVMSEDKAGTNEDDLTMKLT 282 (1386)
T ss_pred cchHhHHHHHHhhcChHHHHHHHhhCCccccceeeeccCcCCchheEEEeccCCccccccceeecCCCCCCccchhhhhh
Confidence 9988888777899999999999999999999999998 49999999999999999999999987 4699999999999
Q ss_pred HHHHHHHHHHHHHHHhccchhhhHHHHHHHHHHHHHhccCCCCCCccccCCCCchhhhhhhcCccccccccccCCCCCCc
Q 000829 149 RIIQTNASLQQELVEANSAFKSLAGWETLQVEVAQYINSDVRGVPFSMQVARPLSGFVQRLKGKQGRFRGNLSGKRVEYT 228 (1265)
Q Consensus 149 ~Ii~~n~~l~~~~~~~~~~~~~~~~~~~lq~~v~~~~~~~~~~~~~~~~~~~~~~~i~q~l~gK~G~fR~nl~GKRvd~s 228 (1265)
+|+..|..|++.+..|.+.+.+++.|+.||.+|+.||||+.+|.|..+.+++|++||.||||||+||||+||.|||||||
T Consensus 283 EIi~tn~vik~~~~~g~~~~~imE~Wd~lQl~~AlyINSEl~g~~~~~~p~kp~RGf~QRLKGKqGRFRgNLSGKRVDFS 362 (1386)
T KOG0261|consen 283 EIILTNDVIKKHLSKGTPINLIMEDWDFLQLQVALYINSELPGIPINMAPKKPTRGFVQRLKGKQGRFRGNLSGKRVDFS 362 (1386)
T ss_pred hhhhHHHHHHHHhhcCCCchhhhhhhHHHHHHHHHhhcccCCCCCCCCCCCCchHHHHHHhcccCCceeccccCceeecc
Confidence 99999999999999999999999999999999999999999999988877999999999999999999999999999999
Q ss_pred cceEEcCCCCCCCCcccccHHHHhhcCcceeechHHHHHHHHHHHcCCCCCCCceEEE-CCCCCeEEe-ccccchhhhhc
Q 000829 229 GRTVISPDPNLKITEVAIPIRMARILTYPERVSDHNIEKLRQCIQNGPDKYPGARMIR-YPDGTARVL-YGKFRNQLAVE 306 (1265)
Q Consensus 229 aRsVIspDp~l~~~evGvP~~~A~~Lt~pe~Vt~~Ni~~l~~lv~ng~~~~pGa~~i~-~~~g~~~~l-~~~~r~~~~~~ 306 (1265)
|||||||||||+|||||||..||+.|||||+||.+|+++||+||+|||++|||||||+ +.+|.++.| |+ +|.++|.+
T Consensus 363 GRTVISPDPNL~IdeVgVP~rvAkiLTfpE~Vt~~Ni~klr~lV~NGP~vhPGANyv~~r~~~~kr~L~yg-~R~kiA~e 441 (1386)
T KOG0261|consen 363 GRTVISPDPNLRIDEVGVPIRVAKILTFPERVTRANIRKLRQLVRNGPNVHPGANYVVQRGEGFKRFLKYG-NRDKIADE 441 (1386)
T ss_pred CceeeCCCCCcceeeccchHHHHHHhcchhhccHHHHHHHHHHHhcCCCCCCCcchhhhcccchhhHhhcC-cHHHHHHh
Confidence 9999999999999999999999999999999999999999999999999999999998 456778888 99 99999999
Q ss_pred ccccceeecccccCCeEEEecCCCccccceeeEEEEEecCCeeeeecccCCCCCCCCcccccccccCChHHHHHHHHHHc
Q 000829 307 LKSGCIVDRHLEDGDVVLFNRQPSLHRMSIMCHRARIMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLM 386 (1265)
Q Consensus 307 L~~g~iV~Rhl~dgD~VL~NRQPSLHk~Simah~vkv~~~kt~rln~~vc~~yNADFDGDEMN~h~PQs~~araEa~~Lm 386 (1265)
|++||+|||||+|||+|||||||||||||||+|+|||+||+|||||.|||+||||||||||||+||||++||||||.+||
T Consensus 442 Lk~GdvVERHL~DgDvVLFNRQPSLHkmSIM~H~akV~p~RTfRFNEcvCtPYNADFDGDEMNlHvPQTEEAraEA~~LM 521 (1386)
T KOG0261|consen 442 LKIGDVVERHLMDGDVVLFNRQPSLHKMSIMSHRAKVMPWRTFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEALVLM 521 (1386)
T ss_pred hccchHHHhhcccCCEEEEcCCchHHHHHHHHHHhhcccCceeeccccccCCcCCCCCcccccccCCchHHHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCcccccCCCCCccEeecccceeeeeeeeccCccCCHHHHHHHHHHhcCCCceeecCCCceeCcccccccceeeeeeec
Q 000829 387 GVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDRAAFSLMCCYMGDGMDRVDLPTPAILKPVELWTGKQLFSVLIR 466 (1265)
Q Consensus 387 ~~~~~~~sp~~g~pi~gliQD~l~g~~llT~~d~f~~~~~~~~l~~~~~~~~~~~~lp~Pai~kp~~lwTGKql~s~~l~ 466 (1265)
.+++|+++|++|+|+++.+||+++|+||||.+|+||+|++++|+++++.++...+++|||||+||..||||||+||.+++
T Consensus 522 gvknNlvTPr~GEpiiAAtQDFiTg~YLlt~KDtF~dRa~~~ql~s~~~d~~~~i~lppPaI~KP~~LwTGKQ~fsvlir 601 (1386)
T KOG0261|consen 522 GVKNNLVTPRNGEPIIAATQDFITGGYLLTHKDTFLDRAEFSQLCSYMSDAMTHIDLPPPAILKPVELWTGKQLFSVLIR 601 (1386)
T ss_pred ccccccccCCCCCceeehhhhhhhcceeeecccccccHHHHHHHHHHHhccccccCCCChhhcCceeeeccCEEEEEEec
Confidence 99999999999999999999999999999999999999999999999999988999999999999999999999999999
Q ss_pred CCCCcceEEEEeecccccccccccccCCccccccccCCCCCeeEEecCcceecccccccccCCCcccHHHHHHHHhChhh
Q 000829 467 PHANMRVYVNLTVKEKTYSNKLIRTEGDEEIRIETMCPNDGFVYFRNSELISGQLGKATLGNGNKDGLYSVLLRDYGAHA 546 (1265)
Q Consensus 467 ~~~~~~~~in~~~~~k~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~gell~G~ldK~~lG~~~~~~Li~~i~~~yG~~~ 546 (1265)
|+....+.+|+..|++.|+.. ++.. +++|++||+|+|+|++|++|++||+.+|+|++.+||+.|.++||+.+
T Consensus 602 pn~~s~v~~Nl~~k~k~~~~~----~~k~----~~mc~nDg~v~irns~l~sG~ldKs~lG~g~k~~lfy~llrDyg~~a 673 (1386)
T KOG0261|consen 602 PNDDSPVRVNLDAKNKNFSLV----KGKS----FEMCPNDGYVIIRNSELISGVLDKSTLGSGKKDSLFYILLRDYGSMA 673 (1386)
T ss_pred cCCCCceEEeeccccceeecc----cCCC----cccCCCCCeEEEecchhhhcccccccccCCCccceEeeehhhcchHH
Confidence 999999999999999998542 2322 68999999999999999999999999999999999999999999999
Q ss_pred HHHHHhHHHHHHHHHHHhccceeeeccCCCCccchHHHHHHHHHHHHHHHHHHHHHHcCCCccCCCCCHHHHHHHHHHHH
Q 000829 547 TSGCMNRLAKLSARWIGNHGFSIGIDDVQPKKELSDKKGKLISENYEVCNVKIKEYNEGKLQLKPGCDAAQTLEAVITDI 626 (1265)
Q Consensus 547 a~~~l~~~~~l~~~~L~~~GFSigi~D~~~~~~~~~~~~~~i~~a~~~~~~~i~~~~~g~l~~~~~~~~~~~le~~i~~~ 626 (1265)
|++.|+++.+|+.+||.++||||||+|+.|.+.+.++|+++++.+|++|++.|.+|++|+++.+|||+.+++||+.|..+
T Consensus 674 Aa~am~rlaklc~r~lgnrGFSIGi~DVqPg~~L~~~k~~lv~~gY~kc~~~I~e~~kG~L~~qpg~~~eetLEa~I~~~ 753 (1386)
T KOG0261|consen 674 AADAMNRLAKLCARFLGNRGFSIGIDDVQPGEILSQEKEELVNRGYAKCDEKIEEYNKGKLQLQPGCNEEETLEAEILSE 753 (1386)
T ss_pred HHHHHHHHHHhhhhhccccccccccCCCCccHHHHHHHHHHHHhHHHHHHHHHHHHhccccccCCCCCHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhcCCCCCCcceeeeccCCCCChhcHhHHhhcccccccCCCCCCCCCCCcccCCCCCCCCCCCccceec
Q 000829 627 LNRIREDAGKACMGSLPWRNSPLIMSQCGSKGSPINISQMVACVGQQSVGGRRAPNGFIDRSLPHFPRKAKEPAAKGFVA 706 (1265)
Q Consensus 627 l~~~~~~~~~~~~~~l~~~N~~~~M~~sGsKGS~~Ni~Qi~~~lGQQ~~~G~Rip~~~~~rtLP~f~~~~~~~~a~GfV~ 706 (1265)
||.+|+++|++|+.+|.+.|++++|+.||||||.+|+|||+||||||.+.|.|+|+||.+|+||||++++..|+|+|||.
T Consensus 754 Ls~IRe~~G~~C~~eL~~~NsPliMa~CGSKGS~INiSQMvACVGQQ~ISG~RvPdGf~dRsLPHF~r~Sk~P~aKGFV~ 833 (1386)
T KOG0261|consen 754 LSTIREEAGKICIRELHPRNSPLIMALCGSKGSKINISQMVACVGQQIISGHRVPDGFEDRSLPHFERHSKTPAAKGFVA 833 (1386)
T ss_pred HHHHHHHHHHHHHHhcCcccChHHHHHhcCCCCcccHHHHHHHhhhhhhcCCcCCCccccccCccccccCCCccccchhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccCCChhhhhhhhccccccchhcccccCcCChhHHHHHHHhhheEeeecCeEEcCCCcEEEEEecCCCcccccccCC
Q 000829 707 NSFYSGLSATEFFFHTMGGREGLVDTAVKTADTGYMSRRLIKALEDLSIQYDNSVRNAGGCIVQFLYGDDGMDPANMEGK 786 (1265)
Q Consensus 707 ~sf~~GL~p~EfFfH~m~GReGLiDTAvKTa~sGYlqRrLvk~lEdl~v~YD~TVR~s~g~iiQf~YGeDG~d~~~~~~~ 786 (1265)
|||++||||+|||||+|||||||||||||||+||||||||||+||||.++||||||+|.|.||||.||+||+||..||++
T Consensus 834 NSFySGLTptEFfFHtm~GREGLVDTAVKTAETGYMqRRLmK~LEDL~~~YDgTVR~s~~~vvqF~YG~DglDPa~mEg~ 913 (1386)
T KOG0261|consen 834 NSFYSGLTPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKSLEDLSVQYDGTVRNSNGDVVQFTYGGDGLDPAMMEGK 913 (1386)
T ss_pred hhcccCCCchhhheeecccccchhhhhhhhhhhhhHHHHHHHHHHHHHHhhcCceecCCCcEEEEeecCCCCChhhhcCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred CCCCchhHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHhhcCCCcchHHHHHHHHHHHHHhhhhhhhhhhcccccCCCc
Q 000829 787 SGEPLNFDRLLMKVKATCPPAGQRYLSPQQVSEIVEKQLAAYGKESCSEAFLNSLRKFFEGQQDKLDKKIKFVEDIGWDD 866 (1265)
Q Consensus 787 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~~~~~~l~~~~~~~~~~~l~~ 866 (1265)
+ .|+||+++|.+++++.+...+..+.++++.+..+..+.+ +|..+...|.+.+++|+.....++.+. ...++.+.
T Consensus 914 ~-~pv~f~r~~~~~~~~~~~~~~~~l~~~el~e~~~~~l~~-~f~~~~~~F~~~~~~~i~~~~~~~~~~---~~~~~d~~ 988 (1386)
T KOG0261|consen 914 D-QPVNFNRVFDHAKAIFPHRHDPPLSSEELDETLEEELLR-KFTEKGDPFVHELREFIASLSKKIKKL---QDKYGDEC 988 (1386)
T ss_pred C-CchhHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHH-HhhhhhhHHHHHHHHHHHHHHHHHHHH---hhhccccc
Confidence 8 999999999999999877788889999999888877654 454567788888899886544444333 22333333
Q ss_pred cchhhhhhhhhccCCCHHHHHHHHHHHHHhhhcccCCcCccceeecccccCCccccccccccccccccccceecccchhH
Q 000829 867 KSQILEEVTHKTSGITEKQLEVFIQTCFSRYRVKRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIK 946 (1265)
Q Consensus 867 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ky~~slv~PGEaVG~IAAQSIGEPsTQMTLnTFH~AGv~~~NVTlGvPRLk 946 (1265)
........+.+.+++|+++++.|+..|..||+++.++||+|||+|||||||||+|||||+|||||||++||+||||||+|
T Consensus 989 ~~~~~~~~~~~~~~~t~kql~~f~~~~~~ky~~a~~EpGTavGAi~aQSIGEPGTQMTLKTFHFAGVASMNiTlGVPRIk 1068 (1386)
T KOG0261|consen 989 GPKFCPDLLYQISRLTEKQLEKFVERCLDKYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIK 1068 (1386)
T ss_pred CCccCccceeeeeeccHHHHHHHHHHHHHHHHhhhcCCcchhhhhhcccCCCCCceeeeeeeeecceeeeeeccCcchHH
Confidence 22333446778899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhcccccccceEEEEccCCCcHHHHHHHhcceeEEeccccceeEEEEEeCCccEEEEEeChhhHHHhhcccCHHHHHH
Q 000829 947 EIINGAKRISTPIITAELECNDNENAARVVKGRIEKTLLGQVAKSIKIVMTSRLASIVIALDMETIQDAHLCINADIVKE 1026 (1265)
Q Consensus 947 EIinask~ikTP~~ti~l~~~~~~~~a~~v~~~le~~~L~di~~~i~~~y~~~~~~~~i~ld~~~i~~~~~~i~~~~i~~ 1026 (1265)
|||||+|+|+||+|+..|.++.|+..|+.||+|||+++|+||+++|+++|.|+.+++.|.+|.+.|..++++|+.++|..
T Consensus 1069 EIINAsk~ISTPIItA~L~n~~d~~~Ar~VKgRiEKt~L~dv~~yieeV~~p~~~fl~i~vd~~~I~~l~L~i~~~~I~~ 1148 (1386)
T KOG0261|consen 1069 EIINASKTISTPIITAELENPHDERSARVVKGRIEKTTLGDVCSYIEEVYGPDSCFLLIRVDLKRISLLQLEITIESIAY 1148 (1386)
T ss_pred HHHhhhcccCccceeeeecCchhHHHHHHHhhhhhhhhHHHHHHHHHHHhCCcceEEEEEecHhHHhhhhccccHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhcCcccccccCceeeeccceEEEeCCC-CCCcceeehHHHhhhcCCcEEecccCceEEEEeccccccchhhccCCccc
Q 000829 1027 SIVQTPKIKLKQQHIKVLDFRKLEIFPPV-DKSKIHFELYSLKNVLPMVIVKGIKTVERVVIAEKEKEKRKVKENGEKKK 1105 (1265)
Q Consensus 1027 ~i~~~~k~k~~~~~i~~~~~~~~~i~~~~-~~~~~~~~l~~l~~~l~~~~v~Gi~~I~r~~i~~~~~~~~~~~~~~~~~~ 1105 (1265)
+|....+.++++.++.+.++..++|.+.. .+.+.+|.|+.++..|++++|+|+|.|.|++|+.++ ..+.
T Consensus 1149 sI~~s~~~k~~~~~v~v~~~~~~~v~~~~~~~~S~~~~lq~lk~~L~~Vvv~gip~vnr~vi~~de----------~~~~ 1218 (1386)
T KOG0261|consen 1149 SILKSPKRKVKPNDVRVVGETTLRVTPVSDTKSSVYYNLQRLKRSLPNVVVKGIPEVNRAVINIDE----------KRGL 1218 (1386)
T ss_pred HHhcCCccccCCcceEEecceeEEEeecccccchhhhhHHHHHhhCCceEEecCcchhhhheeecc----------cCCc
Confidence 99999888888999999888777777753 334468999999999999999999999999998643 2344
Q ss_pred EEEEEeCccHHHhhccCCccccccccCCHHHHHHHhCHHHHHHHHHHHHHHHhhccccccCcccceeeecccccccEEEe
Q 000829 1106 YRLLVEGTGLQAVMGAEGIDGCKTKSNHIFEVQQTLGIEAARICIIDEINETMKAHGMSIDKRHMMLLADLMTFRGEVLG 1185 (1265)
Q Consensus 1106 ~~l~teG~nl~~~~~~~~VD~~~~~sNdI~ev~~~lGIEAAR~~Iv~Ei~~v~~~~Gi~Vd~RHl~LlAD~MT~~G~~~~ 1185 (1265)
|.|.+||.+|++||..+||+..+|+||+|.||.++|||||||.+||+||.++|+.||++||+||++||||+|||+|+++|
T Consensus 1219 y~L~vEG~gLr~Vm~t~GV~g~~TtsNnv~Ev~~vLGIEAAR~~II~EI~ytM~~HGmsiD~RHiMLLaDvMTyrGEVlG 1298 (1386)
T KOG0261|consen 1219 YKLLVEGTGLRAVMNTDGVKGRRTTSNNVLEVEKVLGIEAARTTIISEIGYTMSNHGMSIDPRHIMLLADVMTYRGEVLG 1298 (1386)
T ss_pred eEEEEeccchHHHhccCCccccccccCceEEeehhhchHHHHHHHHHHHHHHHHhcCcccCHHHHHHHHHHhhhcceeee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eccccccccCCcHhhHhcchHHHHHHHHhhhcCCcccccccccceeccCCCCCCccceEeeecCCC
Q 000829 1186 ITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDDRIEGVSECIIMGIPMPLGTGILKIRQRDAV 1251 (1265)
Q Consensus 1186 i~R~Gi~~~~~Spl~~aSFE~T~~~L~~AA~~g~~D~l~gvS~~Ii~Gk~~~~GTG~fdll~~~~~ 1251 (1265)
|||+|+++|++|+|+.||||+|.|||++||.+|+.|.+.|||||||+|.++++|||.|+|++..+.
T Consensus 1299 ITRfGl~KM~~SVL~lASFEkT~DhLF~AA~~~k~D~I~GVSEcIIlG~pm~iGTG~fkl~~~~~~ 1364 (1386)
T KOG0261|consen 1299 ITRFGLAKMKDSVLMLASFEKTADHLFDAAAYGKKDAIEGVSECIILGIPMCIGTGIFKLLQRTDD 1364 (1386)
T ss_pred eeehhhHHHHHHHHHHHhhhhhhHHHHHHHHhcCcccccchhhheecccceeccccHHHHHHhcCC
Confidence 999999999999999999999999999999999999999999999999999999999999998765
No 2
>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Probab=100.00 E-value=8.9e-285 Score=2693.94 Aligned_cols=1126 Identities=35% Similarity=0.593 Sum_probs=1005.7
Q ss_pred CCCCcCCCCCCCCCcEEecceeeeEEEecccchhhHHHHhhhhhcchhhhhhhhccccccCHHHHHHHHHhcChhhHHhh
Q 000829 27 SKAVKCPRCGYINGMVKKAVAVLGIIHDRSKVTESLQEFASAITHTKESKAAVNVATYILNPVNVLFLFKRMTDTDCEVL 106 (1265)
Q Consensus 27 k~~~~C~~Cg~~~p~Vrk~~~~~ki~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~L~P~~v~~ifk~I~~ed~~lL 106 (1265)
++.++|||||+.||+|++.+. ..+.+. .+ ...++|+|++|+++|++||++|+++|
T Consensus 152 k~~~~C~~C~~~~~~i~~~~~--~~~~~~-----------------~~------~~~~~l~p~~v~~if~~i~~~d~~ll 206 (1321)
T PRK14977 152 KKAKECPHCGAPQHELEFEEP--TIFIEK-----------------TE------IEEHRLLPIEIRDIFEKIIDDDLELI 206 (1321)
T ss_pred ccCCcCCCCCCCCCeEEEeec--eeeeec-----------------cc------ccCcccCHHHHHHHHHhcCHHHHHHh
Confidence 778999999999999998763 222210 00 11368999999999999999999999
Q ss_pred cCC---CCcceEEEeeeeeCCCCCCCceecCCCCcCCchhHHHHHHHHHHHHHHHHHHHHhccchhhhHHHHHHHHHHHH
Q 000829 107 YLS---ERPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQQELVEANSAFKSLAGWETLQVEVAQ 183 (1265)
Q Consensus 107 ~~~---~~p~~~~l~~lpVpP~~~RP~~~~~~~~~~~ddlt~~l~~Ii~~n~~l~~~~~~~~~~~~~~~~~~~lq~~v~~ 183 (1265)
|++ +||+||||++|||||+++||++.++++.++|||||.+|++||+.|+.|++....|++...+.+.|+.||.+|++
T Consensus 207 g~~~~~~~p~~~il~~lpVpP~~~RP~v~~~~~~~~eddlt~~l~~Ii~~N~~l~~~~~~g~~~~~~~~~~~~LQ~~v~~ 286 (1321)
T PRK14977 207 GFDPKKARPEWAVLQAFLVPPLTARPSIILETGERSEDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTST 286 (1321)
T ss_pred CCCCCCCCcceEEEeccccCCCCCcCcEEeCCCcccCCcHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHH
Confidence 987 69999999999999999999999988779999999999999999999999999999999999999999999999
Q ss_pred HhccCCCCCCccccC--CCCchhhhhhhcCccccccccccCCCCCCccceEEcCCCCCCCCcccccHHHHhhcCcceeec
Q 000829 184 YINSDVRGVPFSMQV--ARPLSGFVQRLKGKQGRFRGNLSGKRVEYTGRTVISPDPNLKITEVAIPIRMARILTYPERVS 261 (1265)
Q Consensus 184 ~~~~~~~~~~~~~~~--~~~~~~i~q~l~gK~G~fR~nl~GKRvd~saRsVIspDp~l~~~evGvP~~~A~~Lt~pe~Vt 261 (1265)
||||+.+|.|.+.++ ++|++||+||||||+||||+|||||||||||||||||||||++||||||..||++|||||+||
T Consensus 287 ~~dn~~~~~~~~~~~~~~rp~k~i~qrLkgKeGrfR~nlmGKRVdfSaRtVIspDP~L~i~EVGvP~~iA~~LT~Pe~Vt 366 (1321)
T PRK14977 287 FFDNATAGIPQAHHKGSGRPLKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVN 366 (1321)
T ss_pred HhcccccCCCccccccCCCchhHHHHHhccccccccccccccccccccceeEeCCCCcccccccCHHHHHHhCCCCEEEc
Confidence 999999998876553 789999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHcCCCCCCCceEEECCCCCeEEe-ccccc-----hhhhhcccccceeecccccCCeEEEecCCCccccc
Q 000829 262 DHNIEKLRQCIQNGPDKYPGARMIRYPDGTARVL-YGKFR-----NQLAVELKSGCIVDRHLEDGDVVLFNRQPSLHRMS 335 (1265)
Q Consensus 262 ~~Ni~~l~~lv~ng~~~~pGa~~i~~~~g~~~~l-~~~~r-----~~~~~~L~~g~iV~Rhl~dgD~VL~NRQPSLHk~S 335 (1265)
+||+++||++|+|||+.||||+||++++|+++.| +..++ .++|.+|++||+|||||+|||+|||||||||||||
T Consensus 367 ~~Ni~~l~~lv~nG~~~~pGA~~i~~~~g~~~~l~~~~~~~~~~~~~~a~~L~~g~iV~Rhl~dGD~VL~NRQPSLHk~S 446 (1321)
T PRK14977 367 ENNIEKMKELVINGPDEFPGANAIRKGDGTKIRLDFLEDKGKDALREAAEQLEIGDIVERHLADGDIVIFNRQPSLHKLS 446 (1321)
T ss_pred hhhHHHHHHHHHcCCcccCCcceEEcCCCceeeehhhhhccchhHHHHHHhcccCcEEEEEeecCcEEEeccCCcccccc
Confidence 9999999999999999999999999999998888 54222 24789999999999999999999999999999999
Q ss_pred eeeEEEEEecCCeeeeecccCCCCCCCCcccccccccCChHHHHHHHHHHcCCCcccccCCCCCccEeecccceeeeeee
Q 000829 336 IMCHRARIMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILVASTQDFLTSSFLI 415 (1265)
Q Consensus 336 imah~vkv~~~kt~rln~~vc~~yNADFDGDEMN~h~PQs~~araEa~~Lm~~~~~~~sp~~g~pi~gliQD~l~g~~ll 415 (1265)
||||+|||+|++|||||||||+||||||||||||+|+|||++|||||++||++++||+||++|+|++|++||+|+|+|+|
T Consensus 447 imah~vkvl~~kT~Rln~~vC~pyNADFDGDEMNlHvPQS~eArAEa~~Lm~v~~niisP~~G~Pi~gliQD~l~g~~lL 526 (1321)
T PRK14977 447 ILAHRVKVLPGATFRLHPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLI 526 (1321)
T ss_pred ceEEEEEEecCceEEecccccCcccCCcccceeeeecCCCHHHHHHHHHHHhhhhcEecCCCCCeeEEeehhhhhhhhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eccCccCCHHHHHHHHHHhcCCCceeecCCCcee-CcccccccceeeeeeecCCCCcceEEEEeecccccccccccccCC
Q 000829 416 TRKDTFYDRAAFSLMCCYMGDGMDRVDLPTPAIL-KPVELWTGKQLFSVLIRPHANMRVYVNLTVKEKTYSNKLIRTEGD 494 (1265)
Q Consensus 416 T~~d~f~~~~~~~~l~~~~~~~~~~~~lp~Pai~-kp~~lwTGKql~s~~l~~~~~~~~~in~~~~~k~~~~~~~~~~~~ 494 (1265)
|++|+||+|++++||+++... ...+|+|||+ ||.+|||||||||++||+. +|+..+++.+... ++.
T Consensus 527 T~~d~fl~~~e~~~l~~~~~~---~~~lp~PaI~~kp~~lwTGKQi~s~iLp~~------~n~~~~~~~~~~~----~~~ 593 (1321)
T PRK14977 527 TKDDALFDKNEASNIAMLAGI---TDPLPEPAIKTKDGPAWTGKQLFSLFLPKD------FNFEGIAKWSAGK----AGE 593 (1321)
T ss_pred ccCcccCCHHHHHHHHHhCCC---ccccCCCceecCCCCeeeHHHHHHHHcCCC------CCceecccccccc----ccc
Confidence 999999999999999997542 2358999999 9999999999999999763 6777776654321 121
Q ss_pred ccccccccCCCCCeeEEecCcceecccccccccC--CCcccHHHHHHHHhChhhHHHHHhHHHHHHHHHHHhccceeeec
Q 000829 495 EEIRIETMCPNDGFVYFRNSELISGQLGKATLGN--GNKDGLYSVLLRDYGAHATSGCMNRLAKLSARWIGNHGFSIGID 572 (1265)
Q Consensus 495 ~~~~~~~~~~~d~~v~i~~gell~G~ldK~~lG~--~~~~~Li~~i~~~yG~~~a~~~l~~~~~l~~~~L~~~GFSigi~ 572 (1265)
. ..++|++|++|+|+||||++|+|||+++|+ ++++||+|.++++||+++|++||+++|+|+++||+.+|||||++
T Consensus 594 ~---~~~~~~~d~~v~I~~geLl~G~ldK~~~G~~~~~~~~Lih~i~~~yG~~~a~~fL~~l~~l~~~~L~~~GFSigi~ 670 (1321)
T PRK14977 594 A---KDPSCLGDGYVLIKEGELISGVIDDNIIGALVEEPESLIDRIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPG 670 (1321)
T ss_pred c---cccCCCCcceEEeecCeEEeeecchHhhccccCCCCcHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhCCEEEeeC
Confidence 1 133688999999999999999999999998 47889999999999999999999999999999999999999999
Q ss_pred cCCCCccchHHHHHHHHHHHHHHHHHHHHHH--------cCCCccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Q 000829 573 DVQPKKELSDKKGKLISENYEVCNVKIKEYN--------EGKLQLKPGCDAAQTLEAVITDILNRIREDAGKACMGSLPW 644 (1265)
Q Consensus 573 D~~~~~~~~~~~~~~i~~a~~~~~~~i~~~~--------~g~l~~~~~~~~~~~le~~i~~~l~~~~~~~~~~~~~~l~~ 644 (1265)
|+++++++.+++.+.+++++++|.++++.|. .|+++..+|++.++++|..+++.|+++++++++.+.+.+++
T Consensus 671 D~~~~~~~~~~i~~~i~~~~~~v~~l~~~~~~~~~i~~~~~~~~~~~G~~~~~~~e~~i~~~l~~~r~~~~~~~~~~l~~ 750 (1321)
T PRK14977 671 DLIIPDEAKQEIEDDIQGMKDEVSDLIDQRKITRKITIYKGKEELLRGMKEEEALEADIVNELDKARDKAGSSANDCIDA 750 (1321)
T ss_pred cEecCHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccchhcCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 9999999999999999999999999999888 88899999999999999999999999999999999999999
Q ss_pred CCcceeeeccCCCCChhcHhHHhhcccccccC--------CCCCCCCCCCcccCCCCCCCCCCCccceeccccccCCChh
Q 000829 645 RNSPLIMSQCGSKGSPINISQMVACVGQQSVG--------GRRAPNGFIDRSLPHFPRKAKEPAAKGFVANSFYSGLSAT 716 (1265)
Q Consensus 645 ~N~~~~M~~sGsKGS~~Ni~Qi~~~lGQQ~~~--------G~Rip~~~~~rtLP~f~~~~~~~~a~GfV~~sf~~GL~p~ 716 (1265)
+|++++|+.||||||++|++||+||||||+++ |+|||.||++||||||.++|.+|+|+|||.|||++||+|+
T Consensus 751 ~N~l~~Mv~SGAKGS~~Ni~Qi~~~lGQQ~ve~~~~~~~~G~Ri~~~~~~RtLPhF~~~d~~p~a~GfV~nsFl~GL~P~ 830 (1321)
T PRK14977 751 DNAGKIMAKTGARGSMANLAQIAGALGQQKRKTRIGFVLTGGRLHEGYKDRALSHFQEGDDNPDAHGFVKNNYREGLNAA 830 (1321)
T ss_pred CCcHHHHhhcccccCHHHHHHHHhccccccccccccccCCCCCCcCCCCCCcCCCCCCCCCCcccccchhhhhcCCCCHH
Confidence 99999999999999999999999999999999 9999999999999999999999999999999999999999
Q ss_pred hhhhhhccccccchhcccccCcCChhHHHHHHHhhheEeeecCeEEcCCCcEEEEEecCCCcccccccCCCCCCchhHHH
Q 000829 717 EFFFHTMGGREGLVDTAVKTADTGYMSRRLIKALEDLSIQYDNSVRNAGGCIVQFLYGDDGMDPANMEGKSGEPLNFDRL 796 (1265)
Q Consensus 717 EfFfH~m~GReGLiDTAvKTa~sGYlqRrLvk~lEdl~v~YD~TVR~s~g~iiQf~YGeDG~d~~~~~~~~~~~~~~~~~ 796 (1265)
|||||||||||||||||||||+||||||||||+||||+|+||+||||++|+||||.|||||+||++++.. .|+|++++
T Consensus 831 EfFFHaM~GREGLiDTAVKTA~SGYLQRrLvk~lEDl~v~YD~TVR~s~g~iiQF~YGeDG~d~~~~~~~--~~~n~~~~ 908 (1321)
T PRK14977 831 EFFFHAMGGREGLIDKARRTEDSGYFQRRLANALEDIRLEYDETVRDPHGHIIQFKFGEDGIDPQKLDHG--EAFNLERI 908 (1321)
T ss_pred HHHHHhhcccccccccccccCcCchhHHHHHHHhcceEEecCCeEEeCCCCEEEEeecCCCcCHHHhccC--CcccHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999998743 68999999
Q ss_pred HHHHHhcCCCCCCCCCCHHHHHHHHHHHHhhcCCCcchHHHHHHHHHHHHHhhhhhhhhhhcccccCCCccchhhhhhhh
Q 000829 797 LMKVKATCPPAGQRYLSPQQVSEIVEKQLAAYGKESCSEAFLNSLRKFFEGQQDKLDKKIKFVEDIGWDDKSQILEEVTH 876 (1265)
Q Consensus 797 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~~~~~~l~~~~~~~~~~~l~~~~~~~~~~~~ 876 (1265)
+.++.... ....+.|.++...++.+.. .+...++..+. ...
T Consensus 909 ~~~~~~~~---~~~~~~~~~~~~~~~~~~~---------~~~~~~~~~~~---------------------------~~~ 949 (1321)
T PRK14977 909 IEKQKIED---RGKGASKDEIEELAKEYTK---------TFNANLPKLLA---------------------------DAI 949 (1321)
T ss_pred HHHhhhhc---cccCCCHHHHHHHHHHHHH---------hhhhhhHHHHH---------------------------HHH
Confidence 87765432 1223445544444443211 01111111110 111
Q ss_pred hccCCCHHHHHHHHHHHHHhhhcccCCcCccceeecccccCCccccccccccccccccccceecccchhHhhhhcccccc
Q 000829 877 KTSGITEKQLEVFIQTCFSRYRVKRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINGAKRIS 956 (1265)
Q Consensus 877 ~~~~~~~~~~~~~~~~~~~ky~~slv~PGEaVG~IAAQSIGEPsTQMTLnTFH~AGv~~~NVTlGvPRLkEIinask~ik 956 (1265)
...+++++++++|+.++..+|.+++|+||||||+|||||||||+|||||||||+||++++|||+|||||+||+||+|+++
T Consensus 950 ~~~~~~~~~~~~~~~~~~~~~~~~~~~pGe~VG~iaAQSiGEP~TQmTLnTFH~AGv~~~nvt~GvpRl~Eii~a~k~~~ 1029 (1321)
T PRK14977 950 HGAELKEDELEAICAEGKEGFEKAKVEPGQAIGIISAQSIAEPGTQMTLRTFHAAGIKAMDVTHGLERFIELVDARAKPS 1029 (1321)
T ss_pred HHcCCCHHHHHHHHHHHHHHHHhcccCCcccchhhhhhhccCceeeecccccccccccccCcccCccchHHhhhcccCCC
Confidence 23468889999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cceEEEEccCC--CcHHHHHHHhcceeEEeccccceeEEEEEeCCccEEEEEeChhhHHHhhcccCHHHHHHHHhcCccc
Q 000829 957 TPIITAELECN--DNENAARVVKGRIEKTLLGQVAKSIKIVMTSRLASIVIALDMETIQDAHLCINADIVKESIVQTPKI 1034 (1265)
Q Consensus 957 TP~~ti~l~~~--~~~~~a~~v~~~le~~~L~di~~~i~~~y~~~~~~~~i~ld~~~i~~~~~~i~~~~i~~~i~~~~k~ 1034 (1265)
||+|+++|.++ .+.+.|+.++.+||+++|++++.++.+.|+|.. ..+.+|.+.++++. +++++|.+.+....+.
T Consensus 1030 tp~m~~~l~~~~~~~~~~a~~v~~~ie~~~l~~~~~~~~i~~~~~~--~~i~~d~~~i~~~~--i~~~~i~~~i~~~~~~ 1105 (1321)
T PRK14977 1030 TPTMDIYLDDECKEDIEKAIEIARNLKELKVRALIADSAIDNANEI--KLIKPDKRALENGC--IPMERFAEIEAALAKG 1105 (1321)
T ss_pred CCeEEEEeCCcccchHHHHHHHHhheeeeEHHHhhhheEeeccCCc--eEEecCHHHHHhcC--CCHHHHHHHHHHhhcC
Confidence 99999999976 457889999999999999999999999998863 45788998888864 7787777766554311
Q ss_pred ccccCceee-eccceEEEeCCC--CCCcceeehHHHhhhcCCcEEecccCceEEEEeccccccchhhccCCcccEEEEEe
Q 000829 1035 KLKQQHIKV-LDFRKLEIFPPV--DKSKIHFELYSLKNVLPMVIVKGIKTVERVVIAEKEKEKRKVKENGEKKKYRLLVE 1111 (1265)
Q Consensus 1035 k~~~~~i~~-~~~~~~~i~~~~--~~~~~~~~l~~l~~~l~~~~v~Gi~~I~r~~i~~~~~~~~~~~~~~~~~~~~l~te 1111 (1265)
+ ...+ ..++.+.+.+.+ +....++.++.++..+++++|+|+++|+|++|...++ .+.++|.|+||
T Consensus 1106 ~----~~~~~~~~~~i~~~~~~~~~~~~~~~~l~~l~~~l~~~~i~Gi~~I~r~~i~~~~~--------~~~~e~~l~te 1173 (1321)
T PRK14977 1106 K----KFEMELEDDLIILDLVEAADRDKPLATLIAIRNKILDKPVKGVPDIERAWVELVEK--------DGRDEWIIQTS 1173 (1321)
T ss_pred C----ceEEeecCCEEEEecCcccccchHHHHHHHHHHhcCCcEEecCCCceEEEEEeecc--------CCCeeEEEEec
Confidence 0 1111 112344444421 1122345678888889999999999999998864221 23367999999
Q ss_pred CccHHHhhccCCccccccccCCHHHHHHHhCHHHHHHHHHHHHHHHhhccccccCcccceeeecccccccEEEeec----
Q 000829 1112 GTGLQAVMGAEGIDGCKTKSNHIFEVQQTLGIEAARICIIDEINETMKAHGMSIDKRHMMLLADLMTFRGEVLGIT---- 1187 (1265)
Q Consensus 1112 G~nl~~~~~~~~VD~~~~~sNdI~ev~~~lGIEAAR~~Iv~Ei~~v~~~~Gi~Vd~RHl~LlAD~MT~~G~~~~i~---- 1187 (1265)
|+||+++|.+++||+.+|+||||+||+++|||||||++|++||++||+.||++||+|||+||||+||++|++++||
T Consensus 1174 G~nl~~vl~~~~Vd~~rt~sN~i~ei~~~lGIEAaR~~ii~Ei~~v~~~~G~~V~~rHi~LlaD~MT~~G~~~~i~~~~~ 1253 (1321)
T PRK14977 1174 GSNLAAVLEMKCIDIANTITNDCFEIAGTLGIEAARNAIFNELASILEDQGLEVDNRYIMLVADIMCSRGTIEAIGLQAA 1253 (1321)
T ss_pred CcCHHHHhCCCCCcccccEECCHHHHHHhhhHHHHHHHHHHHHHHHHHHcCCccCHHHHHHHHHHHccCceEEecccccc
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred --cccccccCCcHhhHhcchHHHHHHHHhhhcCCcccccccccceeccCCCCCCccceEeeecCC
Q 000829 1188 --RFGIQKMDKSVLMLASFEKTADHLFNASVNGRDDRIEGVSECIIMGIPMPLGTGILKIRQRDA 1250 (1265)
Q Consensus 1188 --R~Gi~~~~~Spl~~aSFE~T~~~L~~AA~~g~~D~l~gvS~~Ii~Gk~~~~GTG~fdll~~~~ 1250 (1265)
||||+++++|||++||||+|+++|++||++|+.|.|+|||||||+|+++|+|||+|||+++..
T Consensus 1254 ~~R~Gi~~~~~s~l~~asFE~t~~~L~~AA~~g~~D~l~gvsenii~G~~~~~GTG~~~Ll~~~~ 1318 (1321)
T PRK14977 1254 GVRHGFAGEKDSPLAKAAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIPIGSGKVDLLMDFS 1318 (1321)
T ss_pred ccccccccCCCCHHHhcCHHHHHHHHHHHHHhcCcCccCChHHhhhcCCCccCccceEEEEeccc
Confidence 999999889999999999999999999999999999999999999999999999999999754
No 3
>KOG0262 consensus RNA polymerase I, large subunit [Transcription]
Probab=100.00 E-value=2.3e-277 Score=2442.98 Aligned_cols=1189 Identities=31% Similarity=0.487 Sum_probs=978.1
Q ss_pred CchhHHHHHHHHHHHHHHhhhcCCCCCcCCCCCCCCCcEEecceeeeEEEeccc--------chh-hHHH-----Hh---
Q 000829 4 PKMEALRKTDLMKSIVKKCSTMASKAVKCPRCGYINGMVKKAVAVLGIIHDRSK--------VTE-SLQE-----FA--- 66 (1265)
Q Consensus 4 ~~~~~~~r~~~~k~i~~~c~~~~k~~~~C~~Cg~~~p~Vrk~~~~~ki~~~~~~--------~~~-~~~~-----~~--- 66 (1265)
.+...+.+++++.+|++.. ...++|++|+..+|++||+++ .||+..... +.. .... ++
T Consensus 182 t~~~~~~~~~lv~~f~k~~----l~~kkC~~C~~~~p~~rk~~~-~kv~~~~~~~~~~~~~~~~~~i~~~~~~~~~~d~~ 256 (1640)
T KOG0262|consen 182 TKNSTELKKKLVTAFLKNA----LSRKKCPRCKHSNPKLRKDGF-RKVFIDALSSKVGANVIRGAKIKKDVGSKGFEDSG 256 (1640)
T ss_pred chhhHHHHHHHHHHHHHHh----hccccCCcccCCCchhhcccc-ceeeeehhcccccccchhheeeehhcccccccccc
Confidence 4556788999999999998 568999999999999999998 488875431 000 0000 00
Q ss_pred -hhhhcchh-----------hhhhhhccccccCHHHHHHHHHhcChhhHHhhcCC----------CCcc-eEEEeeeeeC
Q 000829 67 -SAITHTKE-----------SKAAVNVATYILNPVNVLFLFKRMTDTDCEVLYLS----------ERPE-KLIITNIAVP 123 (1265)
Q Consensus 67 -~~~~~~~e-----------~~~~~~~~~~~L~P~~v~~ifk~I~~ed~~lL~~~----------~~p~-~~~l~~lpVp 123 (1265)
....+.++ .....+...++|+|.+|+++|+.+|.+|.++|... ..|. .|||..||||
T Consensus 257 ~~G~~E~~~~g~d~~e~~~~~~~~~~t~~~~l~~tevR~~l~~lf~ne~~~l~~lf~l~~~~~~k~~p~d~FFld~l~Vp 336 (1640)
T KOG0262|consen 257 IDGSNEVEEDGKDLFEKSTEPAEFEKTGKKYLLPTEVREHLRDLFKNEGELLSYLFPLWDSGSGKIDPSDMFFLDNLLVP 336 (1640)
T ss_pred cCCccccccccccccccccccccccccccccccHHHHHHHHHHHHhhhHHHHHHhhccccccccccCccceeeeeccccC
Confidence 00000000 00111123579999999999999999998887643 2365 8999999999
Q ss_pred CCCCCCceecCCCCcCCchhHHHHHHHHHHHHHHHHHHHH--h-c-------------cchhhhHHHHHHHHHHHHHhcc
Q 000829 124 PIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQQELVE--A-N-------------SAFKSLAGWETLQVEVAQYINS 187 (1265)
Q Consensus 124 P~~~RP~~~~~~~~~~~ddlt~~l~~Ii~~n~~l~~~~~~--~-~-------------~~~~~~~~~~~lq~~v~~~~~~ 187 (1265)
|+++||...+++. ..||.+|..|.+|++.|..|+..... | . -..+++..|..||.+|+.+||+
T Consensus 337 PtrfRP~s~~gd~-~~en~Qt~~L~kVle~s~~i~~~~~~m~~kl~~~~k~~l~~~~g~~~kl~~aw~~LQ~~vn~lfDs 415 (1640)
T KOG0262|consen 337 PTRFRPPSMLGDE-VHENPQTLNLNKVLESSVLIRKLLKDMKGKLDEELKLILERLRGIFSKLINAWLQLQASVNVLFDS 415 (1640)
T ss_pred CcccCCchhcchh-hhcChHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhcc
Confidence 9999999999988 99999999999999999999987622 1 1 1245778999999999999999
Q ss_pred CCCCCCccccCCCCchhhhhhhcCccccccccccCCCCCCccceEEcCCCCCCCCcccccHHHHhhcCcceeechHHHHH
Q 000829 188 DVRGVPFSMQVARPLSGFVQRLKGKQGRFRGNLSGKRVEYTGRTVISPDPNLKITEVAIPIRMARILTYPERVSDHNIEK 267 (1265)
Q Consensus 188 ~~~~~~~~~~~~~~~~~i~q~l~gK~G~fR~nl~GKRvd~saRsVIspDp~l~~~evGvP~~~A~~Lt~pe~Vt~~Ni~~ 267 (1265)
+..+.. .+.. ..||+|.|++|+|+||++||||||||+|||||||||||.+||||||..||++|||||+||+||+++
T Consensus 416 ~~~~k~---~r~~-~pGikQiLEKKeGLFRkhMMGKRVN~AaRSVIsPDPnI~tnEIGIP~vFA~KLTyPepVt~~NV~e 491 (1640)
T KOG0262|consen 416 KMASKW---SRDS-PPGIKQILEKKEGLFRKHMMGKRVNYAARSVISPDPNIETNEIGIPPVFAKKLTYPEPVTPWNVNE 491 (1640)
T ss_pred cccccc---ccCC-CchHHHHHHHhhhhHHHHhhccccchhhccccCCCCCccccccCCchHHHhhccCCCcCCcccHHH
Confidence 875321 1122 389999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHcCCCCCCCceEEECCCCCeEEec---cccchhhhhcccc----------cceeecccccCCeEEEecCCCcccc
Q 000829 268 LRQCIQNGPDKYPGARMIRYPDGTARVLY---GKFRNQLAVELKS----------GCIVDRHLEDGDVVLFNRQPSLHRM 334 (1265)
Q Consensus 268 l~~lv~ng~~~~pGa~~i~~~~g~~~~l~---~~~r~~~~~~L~~----------g~iV~Rhl~dgD~VL~NRQPSLHk~ 334 (1265)
||++|+|||++||||+|++++||....|. ..+|.++|++|.. +.+|+||++|||+||+||||||||+
T Consensus 492 lr~aViNGP~~hPGA~~iqd~dg~~t~l~~~~~~qR~alA~qLLtpst~~~~~~~~K~V~RHvknGDvvlmNRQPTLHKP 571 (1640)
T KOG0262|consen 492 LRKAVINGPDVHPGATYIQDEDGTLTLLSPMTDEQREALANQLLTPSTGNPTEFGTKKVHRHVKNGDVVLMNRQPTLHKP 571 (1640)
T ss_pred HHHHHhcCCCCCCCcceeecCCCceeecCCCCHHHHHHHHHHhhccccCCCcccCCceeeeeccCCcEEEEcCCCccccc
Confidence 99999999999999999999999988772 2379999999864 4799999999999999999999999
Q ss_pred ceeeEEEEEecC-CeeeeecccCCCCCCCCcccccccccCChHHHHHHHHHHcCCCcccccCCCCCccEeecccceeeee
Q 000829 335 SIMCHRARIMPW-RTLRFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILVASTQDFLTSSF 413 (1265)
Q Consensus 335 Simah~vkv~~~-kt~rln~~vc~~yNADFDGDEMN~h~PQs~~araEa~~Lm~~~~~~~sp~~g~pi~gliQD~l~g~~ 413 (1265)
|||||+|||+|+ |||||||++|++|||||||||||+|+|||+.|||||++|++++.||+.|++|.|++||||||++++.
T Consensus 572 SimaHkaRVL~gEktlRlHYANCkaYNADFDGDEMN~HfPQse~araEa~~ian~dsqYLvPt~G~PlrGLIQDHiVsgv 651 (1640)
T KOG0262|consen 572 SIMAHKARVLPGEKTLRLHYANCKAYNADFDGDEMNVHFPQSEIARAEAYNIANTDSQYLVPTDGTPLRGLIQDHIVSGV 651 (1640)
T ss_pred hhhhhhheecCCcceeeeeecccccccCCCCcchhcccCCchhhHHHHHHHHhccCCceeccCCCCchhhhhhhheeeeE
Confidence 999999999998 9999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeccCccCCHHHHHHHHHHhc-CCCceeecCCCceeCcccccccceeeeeeecCC-CCcceEEEEeecccccccccccc
Q 000829 414 LITRKDTFYDRAAFSLMCCYMG-DGMDRVDLPTPAILKPVELWTGKQLFSVLIRPH-ANMRVYVNLTVKEKTYSNKLIRT 491 (1265)
Q Consensus 414 llT~~d~f~~~~~~~~l~~~~~-~~~~~~~lp~Pai~kp~~lwTGKql~s~~l~~~-~~~~~~in~~~~~k~~~~~~~~~ 491 (1265)
+||.||+||+|++|+||+.... ....++.+++|+|+||.+|||||||+|++|.+. +.+.+.||+++++|...
T Consensus 652 ~LT~rd~Fftre~y~qLv~~~l~~~~~rI~~lpPtIlkP~~LWTGKQVIsTil~Ni~P~~~p~iNl~~kaKip~------ 725 (1640)
T KOG0262|consen 652 LLTMRDSFFTREDYQQLVFAGLSDTFKRIKLLPPTILKPAPLWTGKQVISTILKNIIPEGHPPINLESKAKIPG------ 725 (1640)
T ss_pred EEEecccccCHHHHHHHHHHhhhhhccceeccCccccccccccccchHHHHHHHhcCCCCCCcccchhcccCch------
Confidence 9999999999999999997533 334678999999999999999999999999776 46788999999998753
Q ss_pred cCCcccc-ccccCCCCCeeEEecCcceecccccccccCCCcccHHHHHHHHhChhhHHHHHhHHHHHHHHHHHhccceee
Q 000829 492 EGDEEIR-IETMCPNDGFVYFRNSELISGQLGKATLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLSARWIGNHGFSIG 570 (1265)
Q Consensus 492 ~~~~~~~-~~~~~~~d~~v~i~~gell~G~ldK~~lG~~~~~~Li~~i~~~yG~~~a~~~l~~~~~l~~~~L~~~GFSig 570 (1265)
+.|.- .++-..+++.|+|++||||||+|||+++|+ +.+||+|+++|.||+++++++|+.++||++.||+.+|||||
T Consensus 726 --~~W~~~s~e~~l~Es~v~ir~GellcGVLDKa~~Ga-t~yGLvH~~~ElYG~~~s~~lLs~~srlFT~ylq~~GFT~G 802 (1640)
T KOG0262|consen 726 --KAWRVHSEEPKLNESQVLIREGELLCGVLDKAQFGA-TAYGLVHCCHELYGGETSGKLLSVFSRLFTAYLQMHGFTLG 802 (1640)
T ss_pred --hhcCCCCCcccCCcceEEEecCceEEEeechhhcCc-hhhhhhhhhhhhhCccchhhHHHHHHHHHHHHHHHhccccc
Confidence 22210 011123567899999999999999999999 89999999999999999999999999999999999999999
Q ss_pred eccCCCCccchHHHHHHHHHHHHHHHHHHHHHHcCCCccC-------------CCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 000829 571 IDDVQPKKELSDKKGKLISENYEVCNVKIKEYNEGKLQLK-------------PGCDAAQTLEAVITDILNRIREDAGKA 637 (1265)
Q Consensus 571 i~D~~~~~~~~~~~~~~i~~a~~~~~~~i~~~~~g~l~~~-------------~~~~~~~~le~~i~~~l~~~~~~~~~~ 637 (1265)
++|+++.++++.+++++++++.....+..+++..-..+.. .+.+....|+..+.+.+|.+.+++.+.
T Consensus 803 vdDlll~~~~D~kR~~il~e~~~vG~qa~~~~~~l~~da~~del~~~le~~y~~d~~~~~~LD~~~k~~~n~~ts~I~~~ 882 (1640)
T KOG0262|consen 803 VDDLLLDKDADKKRREILRESRNVGNQAAKEAFGLDVDAPPDELRSRLEAIYLKDADKLAMLDRVMKSELNGYTSEIVKK 882 (1640)
T ss_pred cceeeechhhhHHHHHHHHhhhcccHHHHHHHhCCCCCCCHHHHHHHHHHHHhcchhHHHHHHHHHHHHHhhhhHHHHhh
Confidence 9999999999999999999988777777665543222211 123455778999999999999999999
Q ss_pred Hhc-C---CCCCCcceeeeccCCCCChhcHhHHhhcccccccCCCCCCCCCCCcccCCCCCCCCCCCccceeccccccCC
Q 000829 638 CMG-S---LPWRNSPLIMSQCGSKGSPINISQMVACVGQQSVGGRRAPNGFIDRSLPHFPRKAKEPAAKGFVANSFYSGL 713 (1265)
Q Consensus 638 ~~~-~---l~~~N~~~~M~~sGsKGS~~Ni~Qi~~~lGQQ~~~G~Rip~~~~~rtLP~f~~~~~~~~a~GfV~~sf~~GL 713 (1265)
|+. . ..|.|++..|+.||||||++|++||+||||||++||+|+|.|.+|||||+|.++|.+|+|+|||.++|++|+
T Consensus 883 cvP~GLlk~FP~N~mqlM~~SGAKGS~VN~~QISclLGQqeLEGkRvPlMvSGKtLPsF~p~e~spraGGfI~~RFlTGi 962 (1640)
T KOG0262|consen 883 CVPDGLLKKFPENNMQLMIQSGAKGSNVNTSQISCLLGQQELEGKRVPLMVSGKTLPSFAPYETSPRAGGFIDGRFLTGI 962 (1640)
T ss_pred hccchhhhcCCcchHHHHHHhcCCcccccHHHHHHhhhhHhhcCCccceeecCCccCCcCCCCCCCCCCCcccceeecCC
Confidence 984 2 338899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ChhhhhhhhccccccchhcccccCcCChhHHHHHHHhhheEeeecCeEEcCCCcEEEEEecCCCcccccccCCCCCCchh
Q 000829 714 SATEFFFHTMGGREGLVDTAVKTADTGYMSRRLIKALEDLSIQYDNSVRNAGGCIVQFLYGDDGMDPANMEGKSGEPLNF 793 (1265)
Q Consensus 714 ~p~EfFfH~m~GReGLiDTAvKTa~sGYlqRrLvk~lEdl~v~YD~TVR~s~g~iiQf~YGeDG~d~~~~~~~~~~~~~~ 793 (1265)
.|+|||||||||||||||||||||+|||||||||||||+|+|+||.||||+||+||||.|||||+|.+|.. ...++
T Consensus 963 ~PqeyfFHCMAGREGLIDTAVKTSRSGYLQRCLiKhLEgl~V~YD~TVRDsDgsvVQF~YGEDglDitKss----fl~~~ 1038 (1640)
T KOG0262|consen 963 KPQEYFFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLKVHYDLTVRDSDGSVVQFMYGEDGLDITKSS----FLNKK 1038 (1640)
T ss_pred CchHHhhhhhccccchhhhHHhcccchHHHHHHHHhhhhcEEeccceEEcCCCcEEEEeecCccccccHHh----hcchh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999865 33344
Q ss_pred HHHHHHHHhcCCCCCCC----CCCHHHHHHHHHHHH-------------------------hhcC-CCcchHHHHHHHHH
Q 000829 794 DRLLMKVKATCPPAGQR----YLSPQQVSEIVEKQL-------------------------AAYG-KESCSEAFLNSLRK 843 (1265)
Q Consensus 794 ~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~-------------------------~~~~-~~~~~~~~~~~i~~ 843 (1265)
++...++.++....... ...+.......+.++ ++.. ++.++++|...+..
T Consensus 1039 ~f~~~Ny~avl~~~~~~~v~s~~d~~~a~~~~k~i~kw~kk~~w~~~~k~~~cpdpv~~k~~p~~y~gsvsekf~~~i~~ 1118 (1640)
T KOG0262|consen 1039 EFPTDNYEAVLLKYKSESVLSAFDIKKASKYIKKILKWKKKHMWFELDKKIACPDPVLAKYNPDKYLGSVSEKFRKKIDD 1118 (1640)
T ss_pred hhhhhhHHHHHhhhChHHHhhhhhhHHHHHHHHHHHHHHhhhccchhhcccCCCChhhhhcchhhhhccccHHHHHHHHH
Confidence 44444544432111000 011111111111110 1111 26678888888888
Q ss_pred HHHHhhhhhhhhhhcccccCCCccchhhhhhhhhccCCCHHHHHHHHHHHHHhhhcccCCcCccceeecccccCCccccc
Q 000829 844 FFEGQQDKLDKKIKFVEDIGWDDKSQILEEVTHKTSGITEKQLEVFIQTCFSRYRVKRVEAGTAIGAIGAQSIGEPGTQM 923 (1265)
Q Consensus 844 ~i~~~~~~l~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ky~~slv~PGEaVG~IAAQSIGEPsTQM 923 (1265)
|.++++++... ..- ..+.|..+++.||.+|+++|||+||+|||||||||||||
T Consensus 1119 f~~~~~k~~~s------------------------~~~---~~~~lr~ll~~K~~~SLa~PGE~VGvlAAQSIGEPSTQM 1171 (1640)
T KOG0262|consen 1119 FDDENAKKEKS------------------------EEP---SEEKLRRLLQLKYIRSLADPGEPVGVLAAQSIGEPSTQM 1171 (1640)
T ss_pred HHHHhhhhhcc------------------------ccc---hHHHHHHHHHHHHHHHhcCCCCcceeeeecccCCCccee
Confidence 87665332211 001 135677788999999999999999999999999999999
Q ss_pred cccccccccccccceecccchhHhhh-hcccccccceEEEEccCCCcHHHHHHHhcceeEEeccccceeEEEEE----eC
Q 000829 924 TLKTFHFAGVASMNITQGVPRIKEII-NGAKRISTPIITAELECNDNENAARVVKGRIEKTLLGQVAKSIKIVM----TS 998 (1265)
Q Consensus 924 TLnTFH~AGv~~~NVTlGvPRLkEIi-nask~ikTP~~ti~l~~~~~~~~a~~v~~~le~~~L~di~~~i~~~y----~~ 998 (1265)
|||||||||+|+||||||||||+||| +||++|+||+||+|+.++.+.+.|..++..|.+++|+|+++++.+.- .+
T Consensus 1172 TLNTFHfAGrGemNVTLGIPRLREIlMtASanIkTP~mt~pi~~g~s~~ra~~i~~~l~rV~L~evlk~v~vte~~t~~~ 1251 (1640)
T KOG0262|consen 1172 TLNTFHFAGRGEMNVTLGIPRLREILMTASANIKTPSMTVPIKNGVSDERADDITKELRRVTLKEVLKKVGVTEKITMVE 1251 (1640)
T ss_pred ehhheeeccccceeeeecchHHHHHHHHHhhccCCCceeeeccCCccHHHHHHHHHHHHHHHHHHHHhheeeeEEEEeec
Confidence 99999999999999999999999999 99999999999999999988899999999999999999999876642 22
Q ss_pred Cc--cEEEEEeChhhHHHhh--cccCHHHHHHHHhcCc-------------ccc----c---------------------
Q 000829 999 RL--ASIVIALDMETIQDAH--LCINADIVKESIVQTP-------------KIK----L--------------------- 1036 (1265)
Q Consensus 999 ~~--~~~~i~ld~~~i~~~~--~~i~~~~i~~~i~~~~-------------k~k----~--------------------- 1036 (1265)
.. ..+.++++...-+.|+ ..+..++|.+.+...| +.+ .
T Consensus 1252 ~~~~~~y~lr~~~~~~~~y~~e~~v~~e~i~~~m~~~Flk~L~~aI~k~~~k~~~~~~~~~dd~~~~~~~~~~~~~~~~~ 1331 (1640)
T KOG0262|consen 1252 NQSCKKYKLRFDLLPREEYQEEYDVRPEDIEEVMENRFLKLLERAIKKKLKKAKYTRGMSNDDADPDDGNEVDNNDEVGG 1331 (1640)
T ss_pred cccceEEEEEEeecCHHHhhhhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhhccccccCCccccccCCccccccC
Confidence 22 3456666544333332 2455555554333221 000 0
Q ss_pred ---ccCc------------------------eeeeccce---EE------------------EeC---------------
Q 000829 1037 ---KQQH------------------------IKVLDFRK---LE------------------IFP--------------- 1053 (1265)
Q Consensus 1037 ---~~~~------------------------i~~~~~~~---~~------------------i~~--------------- 1053 (1265)
.+++ .++.+++. .. +..
T Consensus 1332 ~~~~~~~~e~~~~~ddddas~~k~~~k~~~~~dYe~~de~e~~~~~~~e~~~~~e~~e~d~e~g~dg~~~~~~~~~e~~~ 1411 (1640)
T KOG0262|consen 1332 EDNEDSDDESEDDEDDDDASDAKLHKKTEEEADYESEDEDERVEEREDEGDEDEESDEDDEEVGLDGTPEPEEEDQEGQP 1411 (1640)
T ss_pred CccccccccccccCcccchhHHHHhhhhccccCcCCCchhhhhhhhhcccccccccccchhhcccCCCCCcccccccCCc
Confidence 0000 00000000 00 000
Q ss_pred ------------------------C-CCCCcc-----------eeeh-HHHhhhcCCcEEecccCceEEEEeccccccch
Q 000829 1054 ------------------------P-VDKSKI-----------HFEL-YSLKNVLPMVIVKGIKTVERVVIAEKEKEKRK 1096 (1265)
Q Consensus 1054 ------------------------~-~~~~~~-----------~~~l-~~l~~~l~~~~v~Gi~~I~r~~i~~~~~~~~~ 1096 (1265)
+ .+..|. .+.+ ..+++.++.++|+.+|||+||++...+.
T Consensus 1412 ~~~~~er~~qs~~~~~~fi~~y~fd~~~~~wcev~~~lp~~~~k~~mssiVe~~~~~~vI~q~~gIeRc~~~~~~~---- 1487 (1640)
T KOG0262|consen 1412 EVNAVERREQSVKKRHDFISRYTFDKESGKWCEVELKLPLDKEKLDMSSIVESIAPKSVIHQVPGIERCVVSEPQD---- 1487 (1640)
T ss_pred hhhHHHHHHHHHHHHHHHhhhhccccccCcEEEEEEEecCCCcchHHHHHHHHHhcceeeeccCCceeeeccCCcc----
Confidence 0 000111 0111 2346778899999999999999875431
Q ss_pred hhccCCcccEEEEEeCccHHHhhccC-CccccccccCCHHHHHHHhCHHHHHHHHHHHHHHHhhccccccCcccceeeec
Q 000829 1097 VKENGEKKKYRLLVEGTGLQAVMGAE-GIDGCKTKSNHIFEVQQTLGIEAARICIIDEINETMKAHGMSIDKRHMMLLAD 1175 (1265)
Q Consensus 1097 ~~~~~~~~~~~l~teG~nl~~~~~~~-~VD~~~~~sNdI~ev~~~lGIEAAR~~Iv~Ei~~v~~~~Gi~Vd~RHl~LlAD 1175 (1265)
..++.-.|+|+|+||.++|.+. .+|++++|||||++|+++|||||||++|++||.+||..|||+||+|||+||||
T Consensus 1488 ----~~k~~~~l~TeGVnl~a~~~~~d~LDv~~lySNDI~ail~tyGVEAar~~Iv~Ev~~VF~vYGIsVd~RHLsLiAD 1563 (1640)
T KOG0262|consen 1488 ----DVKEKSVLLTEGVNLPALFDHADILDVNRLYSNDIHAILNTYGVEAARNAIVNEVNNVFKVYGISVDIRHLSLIAD 1563 (1640)
T ss_pred ----cccccceehhcCccHHHHHHHHhhhhhhhhccchHHHHHHHhhHHHHHHHHHHHHHHhhhheeeeecHHHHHHHHH
Confidence 1223338999999999999976 45999999999999999999999999999999999999999999999999999
Q ss_pred ccccccEEEeeccccccccCCcHhhHhcchHHHHHHHHhhhcCCcccccccccceeccCCCCCCccceEeeecCCC
Q 000829 1176 LMTFRGEVLGITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDDRIEGVSECIIMGIPMPLGTGILKIRQRDAV 1251 (1265)
Q Consensus 1176 ~MT~~G~~~~i~R~Gi~~~~~Spl~~aSFE~T~~~L~~AA~~g~~D~l~gvS~~Ii~Gk~~~~GTG~fdll~~~~~ 1251 (1265)
||||+|.|.|+||+||.. ++|||++||||+|+.||..||.+|+.|.|++||++|++|+++..|||+|||+++.+.
T Consensus 1564 YMTf~G~y~pfnR~Gm~~-ssSP~qkMsFETt~~Fl~~Aa~~g~~D~L~sPSArLvvG~~~r~GTG~Fdll~~v~~ 1638 (1640)
T KOG0262|consen 1564 YMTFEGGYQPFNRMGMES-SSSPLQKMSFETTCQFLKQAALFGEEDELSSPSARLVVGLPVRGGTGSFDLLQKVDF 1638 (1640)
T ss_pred HHhhcccccccccccccc-CCChhHhhhHHHHHHHHHHHHhcCcccccCCCcceeEeccccCCCcceeeeeccCCC
Confidence 999999999999999975 899999999999999999999999999999999999999999999999999998875
No 4
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=100.00 E-value=1.6e-264 Score=2321.99 Aligned_cols=1182 Identities=36% Similarity=0.563 Sum_probs=1023.1
Q ss_pred HHHHHHHHHhhhcCCCCCcCC-----------CCCCCCCcEEecceeeeEEEecccchhhHHHHhhhhhcchhhhhhhhc
Q 000829 13 DLMKSIVKKCSTMASKAVKCP-----------RCGYINGMVKKAVAVLGIIHDRSKVTESLQEFASAITHTKESKAAVNV 81 (1265)
Q Consensus 13 ~~~k~i~~~c~~~~k~~~~C~-----------~Cg~~~p~Vrk~~~~~ki~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~ 81 (1265)
.++..+|..| |++..|. .||..||.|++.| ++++.. |+.... +.. .
T Consensus 133 ~rl~~v~~vc----k~k~~ce~g~~~e~~g~sgcg~kqP~i~r~g--l~l~a~----------~k~~~e---~~~----e 189 (1605)
T KOG0260|consen 133 GRLLMVLDVC----KGKVVCEGGIDVESDGRSGCGLKQPSIRRLG--LDLWAF----------WKQGDE---DSQ----E 189 (1605)
T ss_pred chHHHHHHhh----ccceeeeccccccccccccccccCCceeccC--chhhhh----------hhccCc---cCC----c
Confidence 4688999999 8889995 6999999999999 466543 222111 111 1
Q ss_pred cccccCHHHHHHHHHhcChhhHHhhcCC---CCcceEEEeeeeeCCCCCCCceecCCCCcCCchhHHHHHHHHHHHHHHH
Q 000829 82 ATYILNPVNVLFLFKRMTDTDCEVLYLS---ERPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQ 158 (1265)
Q Consensus 82 ~~~~L~P~~v~~ifk~I~~ed~~lL~~~---~~p~~~~l~~lpVpP~~~RP~~~~~~~~~~~ddlt~~l~~Ii~~n~~l~ 158 (1265)
.+..|++++|+++|+.|.++|+..||++ .+|+||+||+|||||+.+||++.++++.+++||||++|.+|++.|..|+
T Consensus 190 ~k~~ls~e~V~~i~k~Isded~~~lg~~~~~arpewmIlTvLPVPP~~vrP~iv~~~s~rg~DdlthkLadIiK~n~~l~ 269 (1605)
T KOG0260|consen 190 SKRKLSAERVLEIFKRISDEDIDQLGFKPKIARPEWMILTVLPVPPPAVRPEIVMQGSARGEDDLTHKLADIIKKNIGLK 269 (1605)
T ss_pred ccccCcHHHHHHHHHhhchhhhhhhcCCCCcCCCceeEEEEecCCCCcccceeeecccccCcchhHHHHHHHHHHHHHHh
Confidence 2468999999999999999999999998 8999999999999999999999999988999999999999999999999
Q ss_pred HHHHHhccchhhhHHHHHHHHHHHHHhccCCCCCCccccC-CCCchhhhhhhcCccccccccccCCCCCCccceEEcCCC
Q 000829 159 QELVEANSAFKSLAGWETLQVEVAQYINSDVRGVPFSMQV-ARPLSGFVQRLKGKQGRFRGNLSGKRVEYTGRTVISPDP 237 (1265)
Q Consensus 159 ~~~~~~~~~~~~~~~~~~lq~~v~~~~~~~~~~~~~~~~~-~~~~~~i~q~l~gK~G~fR~nl~GKRvd~saRsVIspDp 237 (1265)
+..+.|++...+.+...+||.||++|+||+.+|.|.+.++ ++|+|+|++||||||||+|+|||||||||||||||+|||
T Consensus 270 r~e~~ga~~H~i~e~~~LlqfhVat~~Dn~~pgqp~a~qksGrplkSi~arlKgkegriRgnLmGKRvDFSaRTVItgDP 349 (1605)
T KOG0260|consen 270 RNEENGAPAHIIEEYEQLLQFHVATYVDNDIPGQPQADQKSGRPLKSISARLKGKEGRIRGNLMGKRVDFSARTVITGDP 349 (1605)
T ss_pred hhhhcCCchhhHHHHHhHhhhhhhheecccccCCcccccccCCcccchhhhhccccchhhhcccccccCcceeeeecCCC
Confidence 9999999999999999999999999999999999999877 899999999999999999999999999999999999999
Q ss_pred CCCCCcccccHHHHhhcCcceeechHHHHHHHHHHHcCCCCCCCceEEECCCCCeEEe-ccccchhhhhcccccceeecc
Q 000829 238 NLKITEVAIPIRMARILTYPERVSDHNIEKLRQCIQNGPDKYPGARMIRYPDGTARVL-YGKFRNQLAVELKSGCIVDRH 316 (1265)
Q Consensus 238 ~l~~~evGvP~~~A~~Lt~pe~Vt~~Ni~~l~~lv~ng~~~~pGa~~i~~~~g~~~~l-~~~~r~~~~~~L~~g~iV~Rh 316 (1265)
||++||||||.+||++|||||.||+|||++|++||.+|+..||||+||++.+|++++| |. +.+....|++||+||||
T Consensus 350 nl~ldevGVP~sIAk~lTfpE~Vtp~NidrLqeLV~~g~~~~pgakyiird~G~Ridlr~~--~~~~d~~Lq~G~kVeRh 427 (1605)
T KOG0260|consen 350 NLSLDEVGVPRSIAKRLTFPEHVTPFNIDRLQELVRRGLLEHPGAKYIIRDNGDRIDLRYH--KRAGDIHLQPGYKVERH 427 (1605)
T ss_pred CcchhcccCcHHHHhhccCcceeccccHHHHHHHhhCCCCCCCCcceeeecCCcEEEEeec--CCccccccccccEEEEe
Confidence 9999999999999999999999999999999999999999999999999999999999 66 45567799999999999
Q ss_pred cccCCeEEEecCCCccccceeeEEEEEecCCeeeeecccCCCCCCCCcccccccccCChHHHHHHHHHHcCCCcccccCC
Q 000829 317 LEDGDVVLFNRQPSLHRMSIMCHRARIMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPK 396 (1265)
Q Consensus 317 l~dgD~VL~NRQPSLHk~Simah~vkv~~~kt~rln~~vc~~yNADFDGDEMN~h~PQs~~araEa~~Lm~~~~~~~sp~ 396 (1265)
|+|||+|||||||||||||||||||||+|++|||||++||+||||||||||||+|+|||++||||+.+|+++++||+|||
T Consensus 428 l~DGD~VlfNRqPSlHKmSmmahrVrVlp~sTfrLNlsvtsPynADFDGDemnlhvPQS~etkAEl~EL~~vpkQiispQ 507 (1605)
T KOG0260|consen 428 LMDGDVVLFNRQPSLHKMSMMAHRVRVLPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSLETKAELEELAMVPKQIISPQ 507 (1605)
T ss_pred eccCCEEEEcCCCcHHHhhhhhcEEEEccCceEEeCeeecCCccCCCCCceeecccCcchhHHHHHHHHhhhhhhhcCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCccEeecccceeeeeeeeccCccCCHHHHHHHHHHhcCCCceeecC-CCceeCcccccccceeeeeeecCCCCcceEE
Q 000829 397 NGEILVASTQDFLTSSFLITRKDTFYDRAAFSLMCCYMGDGMDRVDLP-TPAILKPVELWTGKQLFSVLIRPHANMRVYV 475 (1265)
Q Consensus 397 ~g~pi~gliQD~l~g~~llT~~d~f~~~~~~~~l~~~~~~~~~~~~lp-~Pai~kp~~lwTGKql~s~~l~~~~~~~~~i 475 (1265)
+|+|++|++||+|+|++++|.+|+|++|+++|||+||+..++ ...| .|||+||++|||||||||+++|+. +
T Consensus 508 snkpvmgivQDTLta~R~~t~Rd~Fl~r~~vmnLlm~~p~~d--~~~Pa~pai~Kp~PlWTGkQifsliiP~~------i 579 (1605)
T KOG0260|consen 508 SNKPVMGIVQDTLTAVRKMTKRDVFLNRAQVMNLLMYVPDWD--GPPPAKPAILKPKPLWTGKQIFSLIIPGG------I 579 (1605)
T ss_pred CCCcceeeehhhHHHHHHHhhHhhhhcHHHHHHHHhhccccC--CCCCCCcccCCCCcccchhhheeeecCCC------c
Confidence 999999999999999999999999999999999999986554 3456 789999999999999999999865 6
Q ss_pred EEeecccccccccccccCCccccccccCCCCCeeEEecCcceecccccccccCCCcccHHHHHHHHhChhhHHHHHhHHH
Q 000829 476 NLTVKEKTYSNKLIRTEGDEEIRIETMCPNDGFVYFRNSELISGQLGKATLGNGNKDGLYSVLLRDYGAHATSGCMNRLA 555 (1265)
Q Consensus 476 n~~~~~k~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~gell~G~ldK~~lG~~~~~~Li~~i~~~yG~~~a~~~l~~~~ 555 (1265)
|+.....+.... +. ++..+.|+.|+|.+|+++.|+++|+.+|+ +.++|+|.++.+.|++.|+.|.+.+|
T Consensus 580 n~~r~~s~h~d~------~~----~~~~p~dt~~lie~g~l~~g~l~Kkt~G~-s~g~lvh~i~~e~Gp~~~~~f~~~iQ 648 (1605)
T KOG0260|consen 580 NYIRDHSTHPDS------ED----ELISPGDTRVLIEGGELLIGVLCKKTVGS-SAGGLVHVIFLEKGPKIARGFFDSIQ 648 (1605)
T ss_pred ceecccccCcCC------Cc----ccccCCCceEEEeCCceEEEEeecccccc-ccCceEEEeehhhCHHHHHHHHHHHH
Confidence 665543333211 11 35678899999999999999999999999 89999999999999999999999999
Q ss_pred HHHHHHHHhccceeeeccCCCCccchHHHHHHHHHHHHHHHHHHHHHHcCCCccCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 000829 556 KLSARWIGNHGFSIGIDDVQPKKELSDKKGKLISENYEVCNVKIKEYNEGKLQLKPGCDAAQTLEAVITDILNRIREDAG 635 (1265)
Q Consensus 556 ~l~~~~L~~~GFSigi~D~~~~~~~~~~~~~~i~~a~~~~~~~i~~~~~g~l~~~~~~~~~~~le~~i~~~l~~~~~~~~ 635 (1265)
+|.+.||...|||+||+|.+.+.++...+++.|.+|+..+..++.+.++..+++.+|++..++||.+++.+||++|+++|
T Consensus 649 ~lin~wll~~gfsigIgDtiad~~t~~~iq~~I~~ak~dv~~vi~~a~~~~L~~~pg~tlretfe~~v~~vlndArd~~g 728 (1605)
T KOG0260|consen 649 TLINSWLLREGFSIGIGDTIADAATMCVIQNTIKEAKRDVLAVIREAQNNELEPTPGRTLRETFENKVNRVLNDARDKSG 728 (1605)
T ss_pred HHHHHHHHhcCccccccccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCCcchhHHHHHHHHHHHHHHHHHHhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhcCCCCCCcceeeeccCCCCChhcHhHHhhcccccccCCCCCCCCCCCcccCCCCCCCCCCCccceeccccccCCCh
Q 000829 636 KACMGSLPWRNSPLIMSQCGSKGSPINISQMVACVGQQSVGGRRAPNGFIDRSLPHFPRKAKEPAAKGFVANSFYSGLSA 715 (1265)
Q Consensus 636 ~~~~~~l~~~N~~~~M~~sGsKGS~~Ni~Qi~~~lGQQ~~~G~Rip~~~~~rtLP~f~~~~~~~~a~GfV~~sf~~GL~p 715 (1265)
..+.+.++.+|++.+|+.+|||||.+||+|+++|+|||++||+|||+||..||||||.++|++|+++|||.|||++||+|
T Consensus 729 ssA~~sl~esNn~k~Mv~aGSKGs~inisQ~saCVGqQnVEgkrIpFGF~~Rtlphf~kDdysPesrGfVENSyL~GLtP 808 (1605)
T KOG0260|consen 729 SSAQKSLSESNNFKTMVVAGSKGSFINISQVSACVGQQNVEGKRIPFGFPKRTLPHFSKDDYSPESRGFVENSYLTGLTP 808 (1605)
T ss_pred hHHHhhhhhcccHHHHHhhcCCCcceehhhhhhhhccccccccccccCCCcccccccccCCCCccccceeecccccCCCH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhhccccccchhcccccCcCChhHHHHHHHhhheEeeecCeEEcCCCcEEEEEecCCCcccccccCCCCCCchhHH
Q 000829 716 TEFFFHTMGGREGLVDTAVKTADTGYMSRRLIKALEDLSIQYDNSVRNAGGCIVQFLYGDDGMDPANMEGKSGEPLNFDR 795 (1265)
Q Consensus 716 ~EfFfH~m~GReGLiDTAvKTa~sGYlqRrLvk~lEdl~v~YD~TVR~s~g~iiQf~YGeDG~d~~~~~~~~~~~~~~~~ 795 (1265)
+|||||+|||||||||||||||+||||||||||+|||++|+|||||||+-|++|||.|||||+|.+.+|.+.+..+++..
T Consensus 809 ~EfFfHamggREglidtavktaEtGyiqRRL~kameDimv~yDgTVRNs~gqviQf~YGeDG~d~~~vE~q~~~~l~~~~ 888 (1605)
T KOG0260|consen 809 QEFFFHAMGGREGLIDTAVKTAETGYIQRRLMKAMEDIMVAYDGTVRNSLGQVIQFKYGEDGLDGHPVEFQNGETLGSLN 888 (1605)
T ss_pred HHHHHHHhcccchhhhhhhcccccchHHHHHHHHHHHHHhhcCcceecccceeEEEEeccCccccceeeccccccccchH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999988776665431
Q ss_pred -HHHHHHhcCCCCCCCCCCHH----H------HHHHHHHH---H-hhc-------CCC----cchHHHHHHHHHHHHH--
Q 000829 796 -LLMKVKATCPPAGQRYLSPQ----Q------VSEIVEKQ---L-AAY-------GKE----SCSEAFLNSLRKFFEG-- 847 (1265)
Q Consensus 796 -~~~~~~~~~~~~~~~~~~~~----~------~~~~~~~~---~-~~~-------~~~----~~~~~~~~~i~~~i~~-- 847 (1265)
.+..-.+...-.....+... + +...++.- + .+. +++ .+.......|++-++.
T Consensus 889 a~f~~~~~~d~ld~~~~~~~~~~~~e~~~~~~l~~lle~e~~~l~~dr~~l~~i~~~g~~k~~lp~n~~r~I~Na~~~f~ 968 (1605)
T KOG0260|consen 889 ACFESEFAYDALDEPISLSSEEVVNEISELLKLQNLLECEYKKLVRDRRVLLYIFEYGDAKWPLPENLQRIIWNALKKFS 968 (1605)
T ss_pred HHHHhhhhhhhhcCcccchhhhHhhhhhhhHHHHHHHHHHHHhhhhhhhhhhhhcccCCcccccchhHHHHHHHHHhhcc
Confidence 11111111100000011100 0 11111100 0 000 001 1122222222222111
Q ss_pred ---h-------------hhhhh-hhhhcccccCC---------CccchhhhhhhhhccCCCHHHHHHHHHHHHHhhhccc
Q 000829 848 ---Q-------------QDKLD-KKIKFVEDIGW---------DDKSQILEEVTHKTSGITEKQLEVFIQTCFSRYRVKR 901 (1265)
Q Consensus 848 ---~-------------~~~l~-~~~~~~~~~~l---------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ky~~sl 901 (1265)
. .+.+. +.+.++....+ .-++..+.+.+...++++.++++|.++++..+|.++.
T Consensus 969 ~~~r~~t~l~~~~v~~g~~~l~e~l~iv~g~~~~sraqrl~~~lLrs~l~~krv~~e~rls~eaf~w~~~~Ie~~f~qa~ 1048 (1605)
T KOG0260|consen 969 IDERKPTDLIPFKVVKGVKELAEKLVIVRGEDYISRAQRLFNILLRSTLATKRVLEEYRLSSEAFEWVLGEIEARFLQAE 1048 (1605)
T ss_pred cccccccccchhhhhhhhhhhhheeEEeeCchhHHHHHHHHHHHHHhhHHHHHHHHHhcccHHHHHHHhhhhhhheeeee
Confidence 0 00000 00000110001 1133344566778899999999999999999999999
Q ss_pred CCcCccceeecccccCCccccccccccccccccccceecccchhHhhhhcccccccceEEEEccCC--CcHHHHHHHhcc
Q 000829 902 VEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINGAKRISTPIITAELECN--DNENAARVVKGR 979 (1265)
Q Consensus 902 v~PGEaVG~IAAQSIGEPsTQMTLnTFH~AGv~~~NVTlGvPRLkEIinask~ikTP~~ti~l~~~--~~~~~a~~v~~~ 979 (1265)
+.|||+||++||||||||+|||||||||+|||+++|||+||||||||+|.+|++|||.++++|... .+.+.|+.+...
T Consensus 1049 a~pgemvg~lAaqsvgePatqmTlntfh~aGVssknVt~gvprlkei~Nv~k~~ktpsLtV~l~g~~~k~~e~ak~v~~~ 1128 (1605)
T KOG0260|consen 1049 ASPGEMVGALAAQSVGEPATQMTLNTFHYAGVSSKNVTLGVPRLKEIINVAKNAKTPSLTVYLTGEAAKDNEWAKLVQCC 1128 (1605)
T ss_pred cCccchHhHHHHHHhCCchhhcccchhcccceeeeeeeccCcchhhhhhhhccCCCceEEEEecchhhcchHHHHHHhhh
Confidence 999999999999999999999999999999999999999999999999999999999999999865 678889999999
Q ss_pred eeEEeccccceeEEEEEeCCccEEEEEeChhhHHHhhc--------------------------ccCHHHHHHHHhcCcc
Q 000829 980 IEKTLLGQVAKSIKIVMTSRLASIVIALDMETIQDAHL--------------------------CINADIVKESIVQTPK 1033 (1265)
Q Consensus 980 le~~~L~di~~~i~~~y~~~~~~~~i~ld~~~i~~~~~--------------------------~i~~~~i~~~i~~~~k 1033 (1265)
||+++|.++.....++|+|+...+.|.-|.+++..+.. .++++.|..+|...+.
T Consensus 1129 le~ttl~~vt~~t~i~ydpdp~~tvI~ed~e~v~a~~e~pd~D~~~ispwlLrlelDr~~m~dk~ltm~~ia~~i~~~f~ 1208 (1605)
T KOG0260|consen 1129 LEHTTLKDVTRATEIYYDPDPQSTVIDEDREFVVAYYEMPDEDVGRISPWLLRLELDRASMTDKKLTMEQIAEKINRGFG 1208 (1605)
T ss_pred cccccHHhhhccCcceecCCCcceeeccchhhHHhhhcCcccchhhcChHHHHhhhhhhhcccccccHHHHHHHHHhhcc
Confidence 99999999999999999999888888888877765421 2455566666655431
Q ss_pred cccccCce-eeecc-----ceEEEeCCCCCCcceeehHHHh-hhcCCcEEecccCceEEEEeccc-cccchhhccCCccc
Q 000829 1034 IKLKQQHI-KVLDF-----RKLEIFPPVDKSKIHFELYSLK-NVLPMVIVKGIKTVERVVIAEKE-KEKRKVKENGEKKK 1105 (1265)
Q Consensus 1034 ~k~~~~~i-~~~~~-----~~~~i~~~~~~~~~~~~l~~l~-~~l~~~~v~Gi~~I~r~~i~~~~-~~~~~~~~~~~~~~ 1105 (1265)
++. .+.++ -.++++..+++.+..| +..++ ..+.++.++|+++|.+|+|..+. ++ .+.-++
T Consensus 1209 -----~d~~~i~~ddna~klv~r~ri~~~~e~D~~-l~~Ie~~ml~~~~l~G~~~i~kV~m~~~~~G~------f~~~~e 1276 (1605)
T KOG0260|consen 1209 -----SDLACIFSDDNAEKLVLRLRIAKEEEDDVF-LKCIEANMLGDMTLRGIPDIFKVYMSPTEDGE------FKPVDE 1276 (1605)
T ss_pred -----CCCceeecccCCcceEEEEEecCccchhHH-HHHHHHhhhhhcccCCccccceEEEeecCCCc------eeecce
Confidence 111 11111 2345555433333332 44443 56788999999999999997532 11 123478
Q ss_pred EEEEEeCccHHHhhccCCccccccccCCHHHHHHHhCHHHHHHHHHHHHHHHhhccccccCcccceeeecccccccEEEe
Q 000829 1106 YRLLVEGTGLQAVMGAEGIDGCKTKSNHIFEVQQTLGIEAARICIIDEINETMKAHGMSIDKRHMMLLADLMTFRGEVLG 1185 (1265)
Q Consensus 1106 ~~l~teG~nl~~~~~~~~VD~~~~~sNdI~ev~~~lGIEAAR~~Iv~Ei~~v~~~~Gi~Vd~RHl~LlAD~MT~~G~~~~ 1185 (1265)
|.|+|+|.+|.+++..++||..+|+|||+.||+++|||||+|.++++|+..|+..+|.+||+||+.|++|+||++|.+++
T Consensus 1277 w~LeTdg~~l~~v~s~~~vD~~rt~sn~l~ei~~vlgIea~r~a~~~e~~~vi~f~gsyVnyrhlaLl~dvmT~~g~lm~ 1356 (1605)
T KOG0260|consen 1277 WDLETDGVNLRRVLSEPDVDPARTTSNDLVEIAEVLGIEAVRKALLRELLNVISFDGSYVNYRHLALLCDVMTARGHLMA 1356 (1605)
T ss_pred eEEecCchhHHhhhccCCCCcccccccchhhhhhhhcHHHHHhhhhhhhhheEeecccchhHHHHHHHHHHHhcccceee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eccccccccCCcHhhHhcchHHHHHHHHhhhcCCcccccccccceeccCCCCCCccceEeeecCC
Q 000829 1186 ITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDDRIEGVSECIIMGIPMPLGTGILKIRQRDA 1250 (1265)
Q Consensus 1186 i~R~Gi~~~~~Spl~~aSFE~T~~~L~~AA~~g~~D~l~gvS~~Ii~Gk~~~~GTG~fdll~~~~ 1250 (1265)
|||||+++..+++|+++|||+|++.|++||++++.|.++|++|+|++|+++|.|||+|||+.|.+
T Consensus 1357 itRhg~nr~~tgaLmrcSfEetv~il~~aa~~~ekd~~rgvsEnImlgqlap~gTg~~d~~ld~e 1421 (1605)
T KOG0260|consen 1357 ITRHGINRQDTGALMRCSFEETVDILMDAAAHAEKDPCRGVSENIMLGQLAPMGTGCFDLMLDAE 1421 (1605)
T ss_pred eeccccchhhccccccccHHHHHHHHHHHHhhhccCCCccceeeeeecccccCCCcceeeeccHH
Confidence 99999999999999999999999999999999999999999999999999999999999999866
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=1.2e-202 Score=1898.81 Aligned_cols=735 Identities=41% Similarity=0.738 Sum_probs=689.8
Q ss_pred HHHHHHHHHHhhhcCCCCCcCCCCCCCCCcEEecceeeeEEEecccchhhHHHHhhhhhcchhhhhhhhccccccCHHHH
Q 000829 12 TDLMKSIVKKCSTMASKAVKCPRCGYINGMVKKAVAVLGIIHDRSKVTESLQEFASAITHTKESKAAVNVATYILNPVNV 91 (1265)
Q Consensus 12 ~~~~k~i~~~c~~~~k~~~~C~~Cg~~~p~Vrk~~~~~ki~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~L~P~~v 91 (1265)
++++++|++.| ++.++|++||+.||+||+.+. ..+.... + ...++|+|++|
T Consensus 128 ~~l~~~i~~~~----~~~~~C~~Cg~~~p~ir~~~~--~~~~~~~----------------~-------~~~~~L~p~~v 178 (868)
T TIGR02390 128 STLIEKIVKEA----AKRMKCPHCGEEQKKIKFEKP--TYFYEEG----------------K-------EGDVKLTPSEI 178 (868)
T ss_pred HHHHHHHHHHh----hcCCCCCCCCCcCceEEEeee--eeeeecc----------------C-------CCCeecCHHHH
Confidence 67899999999 677899999999999999763 2222100 0 12468999999
Q ss_pred HHHHHhcChhhHHhhcCC---CCcceEEEeeeeeCCCCCCCceecCCCCcCCchhHHHHHHHHHHHHHHHHHHHHhccch
Q 000829 92 LFLFKRMTDTDCEVLYLS---ERPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQQELVEANSAF 168 (1265)
Q Consensus 92 ~~ifk~I~~ed~~lL~~~---~~p~~~~l~~lpVpP~~~RP~~~~~~~~~~~ddlt~~l~~Ii~~n~~l~~~~~~~~~~~ 168 (1265)
+++|++||++|+++||++ .||+||||++|||||+++||++.++++.++|||||++|++||+.|++|++.+..|++..
T Consensus 179 ~~ilk~I~~eD~~lLG~~p~~~~Pe~~ilt~LPVPP~~iRPsv~~~~g~~~EDDLT~~L~~II~~N~~Lk~~~~~g~~~~ 258 (868)
T TIGR02390 179 RERLEKIPDEDAELLGINPKVARPEWMVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQL 258 (868)
T ss_pred HHHHHhCCHHHHHHhCCCCCCCCcceeeEeccccCCCCCcCeEEeCCCcccCChHHHHHHHHHHHHHHHHHHHHcCCchh
Confidence 999999999999999997 58999999999999999999999987779999999999999999999999999999999
Q ss_pred hhhHHHHHHHHHHHHHhccCCCCCCccccC-CCCchhhhhhhcCccccccccccCCCCCCccceEEcCCCCCCCCccccc
Q 000829 169 KSLAGWETLQVEVAQYINSDVRGVPFSMQV-ARPLSGFVQRLKGKQGRFRGNLSGKRVEYTGRTVISPDPNLKITEVAIP 247 (1265)
Q Consensus 169 ~~~~~~~~lq~~v~~~~~~~~~~~~~~~~~-~~~~~~i~q~l~gK~G~fR~nl~GKRvd~saRsVIspDp~l~~~evGvP 247 (1265)
.+.+.|+.||.+|+.||||+.++.|.++++ ++|++||+|||+||+||||+|||||||||||||||||||+|++||||||
T Consensus 259 ~~~~~~~~LQ~~v~~~~d~~~~~~~~~~~~~~~~~~~i~~~l~gK~G~~R~nl~GKRvd~s~RsVI~pdp~l~~~evGvP 338 (868)
T TIGR02390 259 IIEDLWELLQYHVATYFDNELPGIPPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNISINEVGVP 338 (868)
T ss_pred hhHHHHHHHHHHHHHHHcCCCCCCCccccCCCCCchhhHhhhcccccccccccccccccccCCceeeCCCCCcCCeeeCc
Confidence 899999999999999999999887765543 7899999999999999999999999999999999999999999999999
Q ss_pred HHHHhhcCcceeechHHHHHHHHHHHcCCCCCCCceEEECCCCCeEEe-ccccchhhhhcccccceeecccccCCeEEEe
Q 000829 248 IRMARILTYPERVSDHNIEKLRQCIQNGPDKYPGARMIRYPDGTARVL-YGKFRNQLAVELKSGCIVDRHLEDGDVVLFN 326 (1265)
Q Consensus 248 ~~~A~~Lt~pe~Vt~~Ni~~l~~lv~ng~~~~pGa~~i~~~~g~~~~l-~~~~r~~~~~~L~~g~iV~Rhl~dgD~VL~N 326 (1265)
..||++|||||+||+||+++|+++|.|||+.||||+||++++|+++.| +. +|.+++.+|++||+|+|||+|||+||||
T Consensus 339 ~~~A~~Lt~pe~Vt~~N~~~l~~lv~ng~~~~pga~~i~~~~g~~~~l~~~-~~~~~~~~l~~g~~v~rhl~dgd~vl~N 417 (868)
T TIGR02390 339 EQIAKELTVPERVTPWNIDELREYVLNGPDSWPGANYVIRPDGRRIKIRDE-NKEELAERLEPGWVVERHLIDGDIVLFN 417 (868)
T ss_pred HHHHHhCCCCeEEehhhHHHHHHHHHcCCccCCCceEEEcCCCcEEechhh-hHHHHHhhcccCCEEEEehhcCccceec
Confidence 999999999999999999999999999999999999999999999888 55 5778899999999999999999999999
Q ss_pred cCCCccccceeeEEEEEecCCeeeeecccCCCCCCCCcccccccccCChHHHHHHHHHHcCCCcccccCCCCCccEeecc
Q 000829 327 RQPSLHRMSIMCHRARIMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILVASTQ 406 (1265)
Q Consensus 327 RQPSLHk~Simah~vkv~~~kt~rln~~vc~~yNADFDGDEMN~h~PQs~~araEa~~Lm~~~~~~~sp~~g~pi~gliQ 406 (1265)
|||||||||||||+|||+|++||||||+||+||||||||||||+|+|||++|||||++||++.+|++||++|+|++|++|
T Consensus 418 RqPsLHr~si~a~~~~v~~~~t~r~n~~~c~~~NADFDGDeMn~h~Pqs~~a~aEa~~Lm~~~~~~~sp~~g~p~~~~~Q 497 (868)
T TIGR02390 418 RQPSLHRMSMMGHKVKVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARELMLVEEHILTPRYGGPIIGGIH 497 (868)
T ss_pred cCCccccccceeEEEEEecCceEeeccccCCccccCcccceeeEecCCCHHHHHHHHHHhhchhceecCCCCCeeEEeeh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cceeeeeeeeccCccCCHHHHHHHHHHhcCCCceeecCCCceeCcccccccceeeeeeecCCCCcceEEEEeeccccccc
Q 000829 407 DFLTSSFLITRKDTFYDRAAFSLMCCYMGDGMDRVDLPTPAILKPVELWTGKQLFSVLIRPHANMRVYVNLTVKEKTYSN 486 (1265)
Q Consensus 407 D~l~g~~llT~~d~f~~~~~~~~l~~~~~~~~~~~~lp~Pai~kp~~lwTGKql~s~~l~~~~~~~~~in~~~~~k~~~~ 486 (1265)
|+|+|+|+||.+|+||+++++++++++.. ..+.+|+|||+||.+|||||||||++||+ .+|+..+++.+..
T Consensus 498 D~l~g~~~LT~~d~f~~~~~~~~l~~~~~---~~~~~~~p~i~kp~~lwTGKqi~s~~lp~------~~n~~~~~~~~~~ 568 (868)
T TIGR02390 498 DYISGAYLLTHKSTLFTKEEVQTILGVAG---YFGDPPEPAIEKPKEYWTGKQIFSAFLPE------DLNFEGRAKICSG 568 (868)
T ss_pred hhhhheeeeeeccccCCHHHHHHHHhcCC---ccccCCCceecCCcccccHHHHHHHhcCC------CCcceeccccccc
Confidence 99999999999999999999999997632 33668999999999999999999999975 3788877776532
Q ss_pred ccccccCCccccccccCCCCCeeEEecCcceecccccccccCCCcccHHHHHHHHhChhhHHHHHhHHHHHHHHHHHhcc
Q 000829 487 KLIRTEGDEEIRIETMCPNDGFVYFRNSELISGQLGKATLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLSARWIGNHG 566 (1265)
Q Consensus 487 ~~~~~~~~~~~~~~~~~~~d~~v~i~~gell~G~ldK~~lG~~~~~~Li~~i~~~yG~~~a~~~l~~~~~l~~~~L~~~G 566 (1265)
. |....++|++|++|+|+||+|++|+|||+++|+ +++||+|.++++||+++|++|||++|+|+++||+.+|
T Consensus 569 ~--------~~~~~~~~~~d~~v~i~~g~ll~G~ldK~~lg~-~~~~li~~i~~~yG~~~a~~fl~~~~~l~~~~l~~~G 639 (868)
T TIGR02390 569 S--------DACKKEECPHDAYVVIKNGKLLKGVIDKKAIGA-EKGKILHRIVREYGPEAARRFLDSVTRLFIRFITLRG 639 (868)
T ss_pred c--------cccccccCCCcceEEEecCeEEeeeecHHHhcc-CcccHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 1 111245788999999999999999999999999 5789999999999999999999999999999999999
Q ss_pred ceeeeccCCCCccchHHHHHHHHHHHHHHHHHHHHHHcCCCccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCC
Q 000829 567 FSIGIDDVQPKKELSDKKGKLISENYEVCNVKIKEYNEGKLQLKPGCDAAQTLEAVITDILNRIREDAGKACMGSLPWRN 646 (1265)
Q Consensus 567 FSigi~D~~~~~~~~~~~~~~i~~a~~~~~~~i~~~~~g~l~~~~~~~~~~~le~~i~~~l~~~~~~~~~~~~~~l~~~N 646 (1265)
||||++|+++++++.+++++++++++++++++++.|.+|.++..++++.++++|..+++.|+++|+++++.+.+.++++|
T Consensus 640 fSigi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~e~~i~~~l~~~r~~~~~~~~~~l~~~N 719 (868)
T TIGR02390 640 FTTGIDDIDIPKEAKEEIEELIEKAEKRVDNLIERYRNGELEPLPGRTVEETLEMKIMEVLGKARDEAGEVAEKYLDPEN 719 (868)
T ss_pred EEeehhheeeCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cceeeeccCCCCChhcHhHHhhcccccccCCCCCCCCCCCcccCCCCCCCCCCCccceeccccccCCChhhhhhhhcccc
Q 000829 647 SPLIMSQCGSKGSPINISQMVACVGQQSVGGRRAPNGFIDRSLPHFPRKAKEPAAKGFVANSFYSGLSATEFFFHTMGGR 726 (1265)
Q Consensus 647 ~~~~M~~sGsKGS~~Ni~Qi~~~lGQQ~~~G~Rip~~~~~rtLP~f~~~~~~~~a~GfV~~sf~~GL~p~EfFfH~m~GR 726 (1265)
++++|+.||||||.+|++||+||||||+++|+|||.||++||||||.++|.+|+|+|||.|||++||+|+||||||||||
T Consensus 720 ~~~~M~~sGsKGS~~Ni~Qi~~~lGQQ~~~g~ri~~~~~~rtlp~f~~~d~~~~~~GfV~~sF~~GL~p~EfFfH~m~gR 799 (868)
T TIGR02390 720 HAVIMARTGARGSLLNITQMAAMVGQQSVRGGRIRRGYRNRTLPHFKKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGGR 799 (868)
T ss_pred chhhhhhccCCcccccHHHHHhccCccccCCCcCccccccCCCCCCCCCCCCcccCceecccccCCCCHHHHHHHHhhhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccchhcccccCcCChhHHHHHHHhhheEeeecCeEEcCCCcEEEEEecCCCcccccccCCCCCCchhHHH
Q 000829 727 EGLVDTAVKTADTGYMSRRLIKALEDLSIQYDNSVRNAGGCIVQFLYGDDGMDPANMEGKSGEPLNFDRL 796 (1265)
Q Consensus 727 eGLiDTAvKTa~sGYlqRrLvk~lEdl~v~YD~TVR~s~g~iiQf~YGeDG~d~~~~~~~~~~~~~~~~~ 796 (1265)
|||||||||||+||||||||||+||||+|+||+||||++|+||||.|||||+||++++.. .|+||+++
T Consensus 800 eGLiDTAvKTa~sGYLqRrLvk~lEdl~v~yD~tVR~~~g~iiQf~YG~dg~d~~~~~~~--~~~~~~~~ 867 (868)
T TIGR02390 800 EGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDTRGNLIQFKYGEDGVDPMKSDHG--KPVDVKKI 867 (868)
T ss_pred cccccccccccccchhHHHHHHHHhheEEecCCeEEeCCCcEEEEeccCCCcCHHHhccC--ccccceec
Confidence 999999999999999999999999999999999999999999999999999999999844 69988764
No 6
>PRK08566 DNA-directed RNA polymerase subunit A'; Validated
Probab=100.00 E-value=2.6e-202 Score=1901.33 Aligned_cols=747 Identities=42% Similarity=0.729 Sum_probs=698.2
Q ss_pred HHHHHHHHHHHHHHhhhcCCCCCcCCCCCCCCCcEEecceeeeEEEecccchhhHHHHhhhhhcchhhhhhhhccccccC
Q 000829 8 ALRKTDLMKSIVKKCSTMASKAVKCPRCGYINGMVKKAVAVLGIIHDRSKVTESLQEFASAITHTKESKAAVNVATYILN 87 (1265)
Q Consensus 8 ~~~r~~~~k~i~~~c~~~~k~~~~C~~Cg~~~p~Vrk~~~~~ki~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~L~ 87 (1265)
+..+++++++|++.| ++.++|++||+.||+|++++. +.+.... + ...++|+
T Consensus 128 ~~~~~~l~k~i~k~~----k~~~~C~~Cg~~~~ki~~~~~--~~~~~~~----------------~-------~~~~~L~ 178 (882)
T PRK08566 128 GSLADDLIKEVKKEA----AKRMVCPHCGEKQYKIKFEKP--TTFYEER----------------K-------EGLVKLT 178 (882)
T ss_pred hhhHHHHHHHHHHHh----cCCCCCCCcCCCCceEEEecc--eeEEEec----------------C-------CCceeCC
Confidence 345567899999999 778899999999999998764 3221100 0 1247899
Q ss_pred HHHHHHHHHhcChhhHHhhcCC---CCcceEEEeeeeeCCCCCCCceecCCCCcCCchhHHHHHHHHHHHHHHHHHHHHh
Q 000829 88 PVNVLFLFKRMTDTDCEVLYLS---ERPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQQELVEA 164 (1265)
Q Consensus 88 P~~v~~ifk~I~~ed~~lL~~~---~~p~~~~l~~lpVpP~~~RP~~~~~~~~~~~ddlt~~l~~Ii~~n~~l~~~~~~~ 164 (1265)
|++|+++|++||++|+++||++ .+|+||||++|||||+++||++.++++.++|||||.+|++||+.|++|++.+..|
T Consensus 179 p~~V~~ilk~I~~eD~~lLg~~~~~~~Pe~~il~~lPVpP~~iRPsv~~~~g~~~eDDLT~~L~~II~~N~~Lk~~~~~g 258 (882)
T PRK08566 179 PSDIRERLEKIPDEDLELLGINPEVARPEWMVLTVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAG 258 (882)
T ss_pred HHHHHHHHHhCCHHHHHHhCCCCCCCCcceeEEeeeecCCCCCcCcEEeCCCcccCchHHHHHHHHHHHHHHHHHHHHcC
Confidence 9999999999999999999997 6899999999999999999999998877999999999999999999999999999
Q ss_pred ccchhhhHHHHHHHHHHHHHhccCCCCCCccccC-CCCchhhhhhhcCccccccccccCCCCCCccceEEcCCCCCCCCc
Q 000829 165 NSAFKSLAGWETLQVEVAQYINSDVRGVPFSMQV-ARPLSGFVQRLKGKQGRFRGNLSGKRVEYTGRTVISPDPNLKITE 243 (1265)
Q Consensus 165 ~~~~~~~~~~~~lq~~v~~~~~~~~~~~~~~~~~-~~~~~~i~q~l~gK~G~fR~nl~GKRvd~saRsVIspDp~l~~~e 243 (1265)
++...+.+.|..||.+|+.|+||+.++.|.+.++ ++|++||+|||+||+||||+|||||||||||||||||||+|++||
T Consensus 259 ~~~~~~~~~~~~LQ~~v~~~~d~~~~~~~~~~~~~~~~~~~i~~~l~gK~G~fR~nl~GKRvd~s~RsVI~pdp~l~~~e 338 (882)
T PRK08566 259 APQLIIEDLWELLQYHVTTYFDNEIPGIPPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINE 338 (882)
T ss_pred CcHHHHHHHHHHHHHHHHHHhcCCccCCcccccCCCCCccchHHhcccCCCccccccccccccCcCCceeeCCCCCcCCe
Confidence 9988999999999999999999999887665443 789999999999999999999999999999999999999999999
Q ss_pred ccccHHHHhhcCcceeechHHHHHHHHHHHcCCCCCCCceEEECCCCCeEEe-ccccchhhhhcccccceeecccccCCe
Q 000829 244 VAIPIRMARILTYPERVSDHNIEKLRQCIQNGPDKYPGARMIRYPDGTARVL-YGKFRNQLAVELKSGCIVDRHLEDGDV 322 (1265)
Q Consensus 244 vGvP~~~A~~Lt~pe~Vt~~Ni~~l~~lv~ng~~~~pGa~~i~~~~g~~~~l-~~~~r~~~~~~L~~g~iV~Rhl~dgD~ 322 (1265)
||||..||++|||||+||+||+++||++|.|||+.||||+||++++|+++.| .. +|.++|.+|++||+|+|||+|||+
T Consensus 339 vGvP~~~A~~Lt~pe~v~~~N~~~l~~~v~ng~~~~pga~~i~~~~g~~~~l~~~-~~~~~~~~l~~g~~v~Rhl~dgd~ 417 (882)
T PRK08566 339 VGVPEAIAKELTVPERVTEWNIEELREYVLNGPEKHPGANYVIRPDGRRIKLTDK-NKEELAEKLEPGWIVERHLIDGDI 417 (882)
T ss_pred eeCcHHHHHhCCCCeEEchhhHHHHHHHHHcCCCcCCCceEEEcCCCceeeehhh-hHHHHHHhccccceehhhhhcCce
Confidence 9999999999999999999999999999999999999999999999998888 44 788889999999999999999999
Q ss_pred EEEecCCCccccceeeEEEEEecCCeeeeecccCCCCCCCCcccccccccCChHHHHHHHHHHcCCCcccccCCCCCccE
Q 000829 323 VLFNRQPSLHRMSIMCHRARIMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILV 402 (1265)
Q Consensus 323 VL~NRQPSLHk~Simah~vkv~~~kt~rln~~vc~~yNADFDGDEMN~h~PQs~~araEa~~Lm~~~~~~~sp~~g~pi~ 402 (1265)
|||||||||||||||||+|||+|++||||||+||+||||||||||||+|+|||++|||||++||++++|++||++|+|++
T Consensus 418 vl~NRqPsLHr~si~a~~~~v~~~~t~r~n~~~c~~~NADFDGDeMn~h~Pqs~~a~aEa~~Lm~~~~~~~sp~~g~pi~ 497 (882)
T PRK08566 418 VLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPII 497 (882)
T ss_pred eeecCCCcccccccceeEEEEecCceEeeccccCCCccCCccCcEEEEecCCCHHHHHHHHHHhcchhcEecCCCCCeeE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eecccceeeeeeeeccCccCCHHHHHHHHHHhcCCCceeecCCCceeCcccccccceeeeeeecCCCCcceEEEEeeccc
Q 000829 403 ASTQDFLTSSFLITRKDTFYDRAAFSLMCCYMGDGMDRVDLPTPAILKPVELWTGKQLFSVLIRPHANMRVYVNLTVKEK 482 (1265)
Q Consensus 403 gliQD~l~g~~llT~~d~f~~~~~~~~l~~~~~~~~~~~~lp~Pai~kp~~lwTGKql~s~~l~~~~~~~~~in~~~~~k 482 (1265)
|++||+|+|+|+||++|+||+++++++++++... ..+.+|+|||+||++|||||||||++||+. +|+..+.+
T Consensus 498 ~~~QD~l~g~~~lt~~d~f~~~~~~~~l~~~~~~--~~~~~~~pai~~p~~lwTGKqi~s~~lp~~------~~~~~~~~ 569 (882)
T PRK08566 498 GGIQDHISGAYLLTRKSTLFTKEEALDLLRAAGI--DELPEPEPAIENGKPYWTGKQIFSLFLPKD------LNLEFKAK 569 (882)
T ss_pred EeehHHHHHHHHHHhccccCCHHHHHHHHHhCCc--cccccCCcccCCCcccccHHHHHHHHcCCC------CCceeecc
Confidence 9999999999999999999999999999998642 246789999999999999999999999763 56666555
Q ss_pred ccccccccccCCccccccccCCCCCeeEEecCcceecccccccccCCCcccHHHHHHHHhChhhHHHHHhHHHHHHHHHH
Q 000829 483 TYSNKLIRTEGDEEIRIETMCPNDGFVYFRNSELISGQLGKATLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLSARWI 562 (1265)
Q Consensus 483 ~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~gell~G~ldK~~lG~~~~~~Li~~i~~~yG~~~a~~~l~~~~~l~~~~L 562 (1265)
..... ++ ...++|++|++|+|+||||++|+|||+++|+ +++||+|.+|++||+++|++||+++|+|+++||
T Consensus 570 ~~~~~----~~----~~~~~~~~d~~v~i~~gell~g~ldK~~lg~-~~~~li~~i~~~yG~~~a~~fl~~~~~l~~~~l 640 (882)
T PRK08566 570 ICSGC----DE----CKKEDCEHDAYVVIKNGKLLEGVIDKKAIGA-EQGSILDRIVKEYGPERARRFLDSVTRLAIRFI 640 (882)
T ss_pred ccccc----cc----cccccCCCCceEEEecCEEEeccccHHHhhc-ccchHHHHHHHHhCHHHHHHHHHHHHHHHHHHH
Confidence 44211 11 1134688999999999999999999999999 569999999999999999999999999999999
Q ss_pred HhccceeeeccCCCCccchHHHHHHHHHHHHHHHHHHHHHHcCCCccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 000829 563 GNHGFSIGIDDVQPKKELSDKKGKLISENYEVCNVKIKEYNEGKLQLKPGCDAAQTLEAVITDILNRIREDAGKACMGSL 642 (1265)
Q Consensus 563 ~~~GFSigi~D~~~~~~~~~~~~~~i~~a~~~~~~~i~~~~~g~l~~~~~~~~~~~le~~i~~~l~~~~~~~~~~~~~~l 642 (1265)
+.+|||||++|+++++++.++++++++++++++++++++|.+|+++..++++.++++|..+++.|+++|+++++.+.+.+
T Consensus 641 ~~~GfSigi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~e~~i~~~l~~~r~~~~~~~~~~l 720 (882)
T PRK08566 641 MLRGFTTGIDDEDIPEEAKEEIDEIIEEAEKRVEELIEAYENGELEPLPGRTLEETLEMKIMQVLGKARDEAGEIAEKYL 720 (882)
T ss_pred HhcCEEeehhhcccCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCcceeeeccCCCCChhcHhHHhhcccccccCCCCCCCCCCCcccCCCCCCCCCCCccceeccccccCCChhhhhhhh
Q 000829 643 PWRNSPLIMSQCGSKGSPINISQMVACVGQQSVGGRRAPNGFIDRSLPHFPRKAKEPAAKGFVANSFYSGLSATEFFFHT 722 (1265)
Q Consensus 643 ~~~N~~~~M~~sGsKGS~~Ni~Qi~~~lGQQ~~~G~Rip~~~~~rtLP~f~~~~~~~~a~GfV~~sf~~GL~p~EfFfH~ 722 (1265)
+++|++++|+.||||||++|++||+||||||+++|+|||+||++||||||.++|.+|+|+|||.|||++||+|+||||||
T Consensus 721 ~~~N~~~~M~~SGsKGS~~N~~Qi~~~lGqQ~~~g~ri~~~~~~rtLP~f~~~d~~~~~~GfV~~sF~~GL~p~EfffH~ 800 (882)
T PRK08566 721 GLDNPAVIMARTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTLPHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHA 800 (882)
T ss_pred CCCCcceeeeccccccCHHHHHHHHhccCceecCCCcCccCccCccCCCCCCCCCCcccCceeeccccCCCCHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccchhcccccCcCChhHHHHHHHhhheEeeecCeEEcCCCcEEEEEecCCCcccccccCCCCCCchhHHHHHHHHh
Q 000829 723 MGGREGLVDTAVKTADTGYMSRRLIKALEDLSIQYDNSVRNAGGCIVQFLYGDDGMDPANMEGKSGEPLNFDRLLMKVKA 802 (1265)
Q Consensus 723 m~GReGLiDTAvKTa~sGYlqRrLvk~lEdl~v~YD~TVR~s~g~iiQf~YGeDG~d~~~~~~~~~~~~~~~~~~~~~~~ 802 (1265)
|||||||||||||||+||||||||||+||||+|+||+|||||+|+||||.|||||+||++++.. .|+||++++.++++
T Consensus 801 m~GReGliDTAvkTa~sGYlqRrLvk~ledl~v~yD~tVR~s~g~iiQf~YG~dg~d~~~~~~~--~~~~~~~~~~~~~~ 878 (882)
T PRK08566 801 MGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDTRGNIVQFKYGEDGVDPMKSDHG--KPVDVDRIIERVLG 878 (882)
T ss_pred hhhcccccccceeeccCccchHHHHHHHhheEEeeCCceEcCCCcEEEEeccCCCcCHHHhcCC--CcccHHHHHHHHhh
Confidence 9999999999999999999999999999999999999999999999999999999999999854 69999999988775
Q ss_pred c
Q 000829 803 T 803 (1265)
Q Consensus 803 ~ 803 (1265)
.
T Consensus 879 ~ 879 (882)
T PRK08566 879 K 879 (882)
T ss_pred h
Confidence 4
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=8.6e-183 Score=1703.92 Aligned_cols=857 Identities=28% Similarity=0.460 Sum_probs=676.7
Q ss_pred CCcceEEEeeeeeCCCCCCCceecCCCCcCCchhHHHHHHHHHHHHHHHHHHHHhccchhhhHHHHHHHHHHHHHhccCC
Q 000829 110 ERPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQQELVEANSAFKSLAGWETLQVEVAQYINSDV 189 (1265)
Q Consensus 110 ~~p~~~~l~~lpVpP~~~RP~~~~~~~~~~~ddlt~~l~~Ii~~n~~l~~~~~~~~~~~~~~~~~~~lq~~v~~~~~~~~ 189 (1265)
++|+||||++||||||++||++.++++..++||||.+|++||++|++|++.+..+++...+.+.|++||.+|+.||||+.
T Consensus 214 ~~Pewmil~~lPV~Pp~lRP~v~l~gg~~~~sDLn~lyr~II~~Nn~Lk~~~~~~ap~~ii~~~~~~LQ~aV~~liDn~~ 293 (1140)
T TIGR02386 214 NRPEWMVLDVIPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGR 293 (1140)
T ss_pred CChHHhhhhcccCCCCccCCcEEeCCCccccCchHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHHhcccc
Confidence 79999999999999999999999998889999999999999999999999999999988899999999999999999999
Q ss_pred CCCCccccCCCCchhhhhhhcCccccccccccCCCCCCccceEEcCCCCCCCCcccccHHHHhhcCcceeechHHHHHHH
Q 000829 190 RGVPFSMQVARPLSGFVQRLKGKQGRFRGNLSGKRVEYTGRTVISPDPNLKITEVAIPIRMARILTYPERVSDHNIEKLR 269 (1265)
Q Consensus 190 ~~~~~~~~~~~~~~~i~q~l~gK~G~fR~nl~GKRvd~saRsVIspDp~l~~~evGvP~~~A~~Lt~pe~Vt~~Ni~~l~ 269 (1265)
++.|.....++|++||+|+||||+||||+|||||||||||||||+|||+|+++|||||..||++||+| ||+.+|+
T Consensus 294 ~g~~~~~~~~rplksls~~LkGK~GrFR~NLlGKRVDySgRSVI~pdP~L~l~e~GlP~~mA~~L~~P-----f~i~~L~ 368 (1140)
T TIGR02386 294 RGKPVVGKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKP-----FIIKRLI 368 (1140)
T ss_pred cCCCccCcCCCchhhHHHhhcCCCCcccccccccccCCCCCCeEcCCCCcccccccChHHHHHHcCch-----HHHHHHH
Confidence 88876544478999999999999999999999999999999999999999999999999999999988 4655555
Q ss_pred HHHHcCCCCCCCceEEECCCCCeEEeccccchhhhhcccccceeecccccCCeEEEecCCCccccceeeEEEEEecCCee
Q 000829 270 QCIQNGPDKYPGARMIRYPDGTARVLYGKFRNQLAVELKSGCIVDRHLEDGDVVLFNRQPSLHRMSIMCHRARIMPWRTL 349 (1265)
Q Consensus 270 ~lv~ng~~~~pGa~~i~~~~g~~~~l~~~~r~~~~~~L~~g~iV~Rhl~dgD~VL~NRQPSLHk~Simah~vkv~~~kt~ 349 (1265)
+ +|.. ..+. .. ++.-....+++|+++ ||+.+||+|||||||||||||||||+|++++++||
T Consensus 369 ~---~~~~-----~~i~---------~a-k~~i~~~~~~v~~vl-~~vi~~d~VLlNRqPTLHRlsIqAf~~~l~~gkti 429 (1140)
T TIGR02386 369 D---RELA-----ANIK---------SA-KKMIEQEDPEVWDVL-EDVIKEHPVLLNRAPTLHRLGIQAFEPVLVEGKAI 429 (1140)
T ss_pred H---cCcc-----cchH---------HH-HHHHHhcCCccceEE-EEccCCcEEEecCCCcccccccceeEEEEecCceE
Confidence 4 4421 1110 11 111112235566666 57778999999999999999999999999999999
Q ss_pred eeecccCCCCCCCCcccccccccCChHHHHHHHHHHcCCCcccccCCCCCccEeecccceeeeeeeeccC--------cc
Q 000829 350 RFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKD--------TF 421 (1265)
Q Consensus 350 rln~~vc~~yNADFDGDEMN~h~PQs~~araEa~~Lm~~~~~~~sp~~g~pi~gliQD~l~g~~llT~~d--------~f 421 (1265)
||||+||+||||||||||||+|+|||++|||||++||.+++|++||++|+|+++++||+++|+|+||.++ +|
T Consensus 430 rlhplvC~~fNADFDGDeMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~~~~~~~~~F 509 (1140)
T TIGR02386 430 RLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKPIVTPSQDMVLGLYYLTTEKPGAKGEGKIF 509 (1140)
T ss_pred EEcccccCcccCCCCcceeEeecCCCHHHHHHHHHHhCCcccEecCCCCCceEEeechhhheeeEeeeccccccCcCcee
Confidence 9999999999999999999999999999999999999999999999999999999999999999999995 79
Q ss_pred CCHHHHHHHHHHhcCCCceeecCCCceeC----ccccc--ccceeeeeeecCCCCcceEEEEeecccccccccccccCCc
Q 000829 422 YDRAAFSLMCCYMGDGMDRVDLPTPAILK----PVELW--TGKQLFSVLIRPHANMRVYVNLTVKEKTYSNKLIRTEGDE 495 (1265)
Q Consensus 422 ~~~~~~~~l~~~~~~~~~~~~lp~Pai~k----p~~lw--TGKql~s~~l~~~~~~~~~in~~~~~k~~~~~~~~~~~~~ 495 (1265)
++++++...+. .+ .+ +.|++++ ++++| +||||||.++|+.. + |.
T Consensus 510 ~~~~e~~~~~~---~~--~i--~l~~~i~~~~~g~~~~tt~Gr~if~~ilP~~~------~-------~~---------- 559 (1140)
T TIGR02386 510 SNVDEAIRAYD---NG--KV--HLHALIGVRTSGEILETTVGRVIFNEILPEGF------P-------YI---------- 559 (1140)
T ss_pred CCHHHHHHHHH---cC--Cc--cCCCceEEeccccEEEccchHHHHHHHcCCcc------c-------cc----------
Confidence 99999886432 11 23 3344443 45788 69999999997531 1 10
Q ss_pred cccccccCCCCCeeEEecCcceecccccccccCCCcccHHHHHHHHhChhhHHHHHhHHHHHHHHHHHhccceeeeccCC
Q 000829 496 EIRIETMCPNDGFVYFRNSELISGQLGKATLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLSARWIGNHGFSIGIDDVQ 575 (1265)
Q Consensus 496 ~~~~~~~~~~d~~v~i~~gell~G~ldK~~lG~~~~~~Li~~i~~~yG~~~a~~~l~~~~~l~~~~L~~~GFSigi~D~~ 575 (1265)
+.. ..+||+.+| +|+|.+|++||++.|+.|||++++|+++|++.+|||||++|+.
T Consensus 560 ---------n~~-----------~~l~Kk~lg-----~LI~~i~~~~G~~~t~~~LD~lk~Lgf~~at~~GfSigi~Dl~ 614 (1140)
T TIGR02386 560 ---------NDN-----------EPLSKKEIS-----SLIDLLYEVHGIEETAEMLDKIKALGFKYATKSGTTISASDIV 614 (1140)
T ss_pred ---------ccc-----------cccchHHHH-----HHHHHHHHHhChHHHHHHHHHHHHHHHHHHHhcCeeeeeccCC
Confidence 000 178999997 5999999999999999999999999999999999999999999
Q ss_pred CCccchHHHHHHHHHHHHHHHHHHHHHHcCCCccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC----CCcceee
Q 000829 576 PKKELSDKKGKLISENYEVCNVKIKEYNEGKLQLKPGCDAAQTLEAVITDILNRIREDAGKACMGSLPW----RNSPLIM 651 (1265)
Q Consensus 576 ~~~~~~~~~~~~i~~a~~~~~~~i~~~~~g~l~~~~~~~~~~~le~~i~~~l~~~~~~~~~~~~~~l~~----~N~~~~M 651 (1265)
+++ ++.+++++|++++.+++++|+.|.++ .+..+.++.++|+++++++++.+++.+++ .|++++|
T Consensus 615 ip~----~K~~ii~~a~~~v~~i~~~y~~G~lt-------~~er~~kvi~iw~~~~d~v~~~~~~~l~~~~~~~N~i~mM 683 (1140)
T TIGR02386 615 VPD----EKYEILKEADKEVAKIQKFYNKGLIT-------DEERYRKVVSIWSETKDKVTDAMMKLLKKDTYKFNPIFMM 683 (1140)
T ss_pred CCH----HHHHHHHHHHHHHHHHHHHHHcCCCC-------hHHHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCcHhhh
Confidence 875 47889999999999999999999875 34567899999999999999999999985 5999999
Q ss_pred eccCCCCChhcHhHHhhcccccccCCCCCCCCCCCcccCCCCCCCCCCCccceeccccccCCChhhhhhhhccccccchh
Q 000829 652 SQCGSKGSPINISQMVACVGQQSVGGRRAPNGFIDRSLPHFPRKAKEPAAKGFVANSFYSGLSATEFFFHTMGGREGLVD 731 (1265)
Q Consensus 652 ~~sGsKGS~~Ni~Qi~~~lGQQ~~~G~Rip~~~~~rtLP~f~~~~~~~~a~GfV~~sf~~GL~p~EfFfH~m~GReGLiD 731 (1265)
+.||||||.+|++||+||+|||. .|. ||++|+ ||.|||++||+|+|||||||||||||+|
T Consensus 684 a~SGARGS~~ni~QL~GmrGlma-----~p~---Grii~~------------PI~ssF~eGLtp~EyF~st~GaRkGLiD 743 (1140)
T TIGR02386 684 ADSGARGNISQFRQLAGMRGLMA-----KPS---GDIIEL------------PIKSSFREGLTVLEYFISTHGARKGLAD 743 (1140)
T ss_pred hhcccccCHHHHHHHHhCCCccc-----CCC---CCcccc------------chhhccccCCCHHHHhhhccchhccccc
Confidence 99999999999999999999986 343 478876 4999999999999999999999999999
Q ss_pred cccccCcCChhHHHHHHHhhheEeeecCeEEcCCCcEEEEEecCCCcccccccCCCCCCchhHHHHHHHH--hcCCCCCC
Q 000829 732 TAVKTADTGYMSRRLIKALEDLSIQYDNSVRNAGGCIVQFLYGDDGMDPANMEGKSGEPLNFDRLLMKVK--ATCPPAGQ 809 (1265)
Q Consensus 732 TAvKTa~sGYlqRrLvk~lEdl~v~YD~TVR~s~g~iiQf~YGeDG~d~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~ 809 (1265)
||||||+||||||||||++||++|.||.+- +..|-.|+....++| .. ++ ++. ++++..+. .+......
T Consensus 744 TAlKTAdSGYLtRRLVdv~qDviV~~dDCg-T~~gi~v~~~~~~~~-~~--i~-----~l~-~ri~GR~~~~di~~~~~~ 813 (1140)
T TIGR02386 744 TALKTADSGYLTRRLVDVAQDVVVREEDCG-TEEGIEVEAIVEGKD-EI--IE-----SLK-DRIVGRYSAEDVYDPDTG 813 (1140)
T ss_pred hheeecccceeeeehhhhhcceEEEeCCCC-CCCCEEEEEeecCCc-eE--Ee-----ehh-heeEEEEEhhheEeCCCC
Confidence 999999999999999999999999999875 456777777654332 11 11 110 11111110 01000000
Q ss_pred CCCCHHHHHHHHHHHHhhcCCCcchHHHHHHHHHHHHHhhhhhhhhhhcccccCCCccchhhhhhhhhccCCCHHHHHHH
Q 000829 810 RYLSPQQVSEIVEKQLAAYGKESCSEAFLNSLRKFFEGQQDKLDKKIKFVEDIGWDDKSQILEEVTHKTSGITEKQLEVF 889 (1265)
Q Consensus 810 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~~~~~~l~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 889 (1265)
..+ ...++ ...+...+.+. +. ++. .+..++.+||+....+
T Consensus 814 ~~i------------~~~~~--~i~~~~~~~i~-----------~~-------~i~--------~v~iRS~ltC~s~~gv 853 (1140)
T TIGR02386 814 KLI------------AEANT--LITEEIAEKIE-----------NS-------GIE--------KVKVRSVLTCESEHGV 853 (1140)
T ss_pred cEE------------EeCCC--CcCHHHHHHHH-----------Hc-------CCC--------EEEecCCeeeCCCCCC
Confidence 000 00000 01111111111 10 000 1234567888877788
Q ss_pred HHHHHHh--hhcccCCcCccceeecccccCCcccccccccccccccccc--ceecccchhHhhhhcccccccceEEEEcc
Q 000829 890 IQTCFSR--YRVKRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASM--NITQGVPRIKEIINGAKRISTPIITAELE 965 (1265)
Q Consensus 890 ~~~~~~k--y~~slv~PGEaVG~IAAQSIGEPsTQMTLnTFH~AGv~~~--NVTlGvPRLkEIinask~ikTP~~ti~l~ 965 (1265)
|+.||-. ....+|+.|||||+|||||||||+|||||+|||.+|+++. +||+|+||+.|++.|. +++.+.+..++
T Consensus 854 C~~CYG~~La~~~~V~~GeaVGiiAAQSIGEPGTQLTmRTFHtGGv~~~~~DIT~GlpRv~elfear-~p~~~a~iae~- 931 (1140)
T TIGR02386 854 CQKCYGRDLATGKLVEIGEAVGVIAAQSIGEPGTQLTMRTFHTGGVAGASGDITQGLPRVKELFEAR-TPKDKAVIAEV- 931 (1140)
T ss_pred ccccCCCcccCCcEecccccceeEeeeecCCCcchhehhheeeccccccccccccCchhhhhhhhcc-cCCCceEEEec-
Confidence 7777743 4678999999999999999999999999999999999975 9999999999999884 34444322222
Q ss_pred CCCcHHHHHHHhcceeEEeccccceeEEEE--EeCCccEEEEEeChhhHHHhhcccCHHHHHHHHhcCcccccccCceee
Q 000829 966 CNDNENAARVVKGRIEKTLLGQVAKSIKIV--MTSRLASIVIALDMETIQDAHLCINADIVKESIVQTPKIKLKQQHIKV 1043 (1265)
Q Consensus 966 ~~~~~~~a~~v~~~le~~~L~di~~~i~~~--y~~~~~~~~i~ld~~~i~~~~~~i~~~~i~~~i~~~~k~k~~~~~i~~ 1043 (1265)
-..++.. .......+.|.
T Consensus 932 -----------------------~G~v~~~~~~~~~~~~i~i~------------------------------------- 951 (1140)
T TIGR02386 932 -----------------------DGTVEIIEDIVKNKRVVVIK------------------------------------- 951 (1140)
T ss_pred -----------------------CCEEEEeecccCCcEEEEEE-------------------------------------
Confidence 1111110 00000011110
Q ss_pred eccceEEEeCCCCCCcceeehHHHhhhcCCcEEecccCceEEEEeccccccchhhccCCcccEEEEEeCccHHHhhccCC
Q 000829 1044 LDFRKLEIFPPVDKSKIHFELYSLKNVLPMVIVKGIKTVERVVIAEKEKEKRKVKENGEKKKYRLLVEGTGLQAVMGAEG 1123 (1265)
Q Consensus 1044 ~~~~~~~i~~~~~~~~~~~~l~~l~~~l~~~~v~Gi~~I~r~~i~~~~~~~~~~~~~~~~~~~~l~teG~nl~~~~~~~~ 1123 (1265)
++ ++....+. +|-=++..+...| . ...| ...+||.
T Consensus 952 -~~---------~~~~~~y~---------------ip~~~~l~v~~gd----~----V~~G--~~l~~g~---------- 986 (1140)
T TIGR02386 952 -DE---------NDEEKKYT---------------IPFGAQLRVKDGD----S----VSAG--DKLTEGS---------- 986 (1140)
T ss_pred -CC---------CCceeEEe---------------ccCCceEEecCCC----E----EccC--CcccCCC----------
Confidence 00 00000000 1111222222111 0 0111 3466773
Q ss_pred ccccccccCCHHHHHHHhCHHHHHHHHHHHHHHHhhccccccCcccceeeecccccccE---------------------
Q 000829 1124 IDGCKTKSNHIFEVQQTLGIEAARICIIDEINETMKAHGMSIDKRHMMLLADLMTFRGE--------------------- 1182 (1265)
Q Consensus 1124 VD~~~~~sNdI~ev~~~lGIEAAR~~Iv~Ei~~v~~~~Gi~Vd~RHl~LlAD~MT~~G~--------------------- 1182 (1265)
-|++++++++||||+|+.|++|+++||..||++||++|+++|++.||.+++
T Consensus 987 --------~~~~~il~v~G~~a~~~~lv~evq~vY~~QGv~I~dKHievIvrqM~~kv~i~~~gdt~~l~g~~v~~~~~~ 1058 (1140)
T TIGR02386 987 --------IDPHDLLRIKGIQAVQEYLVKEVQKVYRLQGVEINDKHIEVIVRQMLRKVRITDSGDSNLLPGELIDIHEFN 1058 (1140)
T ss_pred --------CCHHHHHHhcCHHHHHHHHHHHHHHHHHhCCccccchhHhHHHHHHhCcEEEEeCCCcCCCCCCeeeHHHHH
Confidence 378999999999999999999999999999999999999999999999853
Q ss_pred -------------------EEeeccccccccCCcHhhHhcchHHHHHHHHhhhcCCcccccccccceeccCCCCCCccce
Q 000829 1183 -------------------VLGITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDDRIEGVSECIIMGIPMPLGTGIL 1243 (1265)
Q Consensus 1183 -------------------~~~i~R~Gi~~~~~Spl~~aSFE~T~~~L~~AA~~g~~D~l~gvS~~Ii~Gk~~~~GTG~f 1243 (1265)
++||||++++ .+|+|++||||+|+++|++||+.|++|+|.|++||||+|+++|+|||..
T Consensus 1059 ~~n~~~~~~g~~~~~~~~~llGitkasl~--t~SflsaASFqeTtkvLt~Aai~gk~D~L~GlkENVIiG~liPaGTG~~ 1136 (1140)
T TIGR02386 1059 EENRKLLEQGKKPASAIPQLLGITKASLN--TESFLSAASFQETTKVLTDAAIKGKVDYLLGLKENVIIGNLIPAGTGLK 1136 (1140)
T ss_pred HHHHHHHhCCCCCccceeeeeeeeehhcc--CCCcccccchhhHHHHHHHHHhcCCCCCCCCcccceEecCcccCCCCcc
Confidence 5689999997 5899999999999999999999999999999999999999999999973
No 8
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=100.00 E-value=2e-181 Score=1693.23 Aligned_cols=856 Identities=29% Similarity=0.481 Sum_probs=671.5
Q ss_pred CCcceEEEeeeeeCCCCCCCceecCCCCcCCchhHHHHHHHHHHHHHHHHHHHHhccchhhhHHHHHHHHHHHHHhccCC
Q 000829 110 ERPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQQELVEANSAFKSLAGWETLQVEVAQYINSDV 189 (1265)
Q Consensus 110 ~~p~~~~l~~lpVpP~~~RP~~~~~~~~~~~ddlt~~l~~Ii~~n~~l~~~~~~~~~~~~~~~~~~~lq~~v~~~~~~~~ 189 (1265)
.+|+||||++||||||++||++.++++..+++|||.+|++||.+|++|++.+..++|...+.+.|++||.+|+.||||+.
T Consensus 222 ~~Pewmil~~lPV~Pp~lRP~v~l~~g~~~~sDLn~lyr~II~rNnrLk~~~~~~ap~~ii~~~~~~LQ~aV~~lidn~~ 301 (1156)
T PRK00566 222 NKPEWMILDVLPVIPPDLRPLVQLDGGRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGR 301 (1156)
T ss_pred CCccEeeEeecccCCCcccCceEeCCCcccCCchHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHHhccCc
Confidence 79999999999999999999999998889999999999999999999999999999988889999999999999999999
Q ss_pred CCCCccccCCCCchhhhhhhcCccccccccccCCCCCCccceEEcCCCCCCCCcccccHHHHhhcCcceeechHHHHHHH
Q 000829 190 RGVPFSMQVARPLSGFVQRLKGKQGRFRGNLSGKRVEYTGRTVISPDPNLKITEVAIPIRMARILTYPERVSDHNIEKLR 269 (1265)
Q Consensus 190 ~~~~~~~~~~~~~~~i~q~l~gK~G~fR~nl~GKRvd~saRsVIspDp~l~~~evGvP~~~A~~Lt~pe~Vt~~Ni~~l~ 269 (1265)
++.|.....++|++||+|+|+||+||||+|||||||||||||||+|||+|+++|||||..||++||+|+ | ++
T Consensus 302 ~g~~~~~~~~rplksls~~LkGK~GrFR~NLlGKRVDySgRSVI~pdP~L~l~e~GvP~~mA~eL~~Pf-----~---i~ 373 (1156)
T PRK00566 302 RGRPVTGPNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPF-----I---MK 373 (1156)
T ss_pred cCCCcccccCCchhHHHHhhcCCCccccccccccccCCCCCceEeCCCCcccccccChHHHHHHhCcHH-----H---HH
Confidence 887765443789999999999999999999999999999999999999999999999999999999984 4 66
Q ss_pred HHHHcCCCCCCCceEEECCCCCeEEeccccchhhhhcccccceeecccccCCeEEEecCCCccccceeeEEEEEecCCee
Q 000829 270 QCIQNGPDKYPGARMIRYPDGTARVLYGKFRNQLAVELKSGCIVDRHLEDGDVVLFNRQPSLHRMSIMCHRARIMPWRTL 349 (1265)
Q Consensus 270 ~lv~ng~~~~pGa~~i~~~~g~~~~l~~~~r~~~~~~L~~g~iV~Rhl~dgD~VL~NRQPSLHk~Simah~vkv~~~kt~ 349 (1265)
+|+.||+. ..+.. . ++.......++|++++ |+.+||+|||||||||||+|||||++++++++||
T Consensus 374 ~L~~~g~~-----~~ik~---------a-k~~~~~~~~~v~~vle-~vi~gd~VLlNRqPTLHR~sIqAf~~~l~~gkti 437 (1156)
T PRK00566 374 KLVERGLA-----TTIKS---------A-KKMVEREDPEVWDVLE-EVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAI 437 (1156)
T ss_pred HHHHcCCc-----cchHh---------h-hhhhhhhcCcceEEEE-EecCCCEEEecCCCcccccccceeEEEEecCceE
Confidence 66788862 11111 0 1111123456778775 4568999999999999999999999999999999
Q ss_pred eeecccCCCCCCCCcccccccccCChHHHHHHHHHHcCCCcccccCCCCCccEeecccceeeeeeeeccC--------cc
Q 000829 350 RFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKD--------TF 421 (1265)
Q Consensus 350 rln~~vc~~yNADFDGDEMN~h~PQs~~araEa~~Lm~~~~~~~sp~~g~pi~gliQD~l~g~~llT~~d--------~f 421 (1265)
||||+||+||||||||||||+|+|||++|||||+.||.+++|++||++|+|+++++||+++|+|+||.++ .|
T Consensus 438 rLhplvC~~fNADFDGDqMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~~~~~~~~~F 517 (1156)
T PRK00566 438 QLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPANGKPIIVPSQDMVLGLYYLTREREGAKGEGMVF 517 (1156)
T ss_pred EECccccCccccccccceeEEecCCCHHHHHHHHHHhCCcccEEecCCCCeeEEeehhhhhhhheeecccccccCCCcee
Confidence 9999999999999999999999999999999999999999999999999999999999999999999998 89
Q ss_pred CCHHHHHHHHHHhcCCCceeecCCCceeCc-----ccccccceeeeeeecCCCCcceEEEEeecccccccccccccCCcc
Q 000829 422 YDRAAFSLMCCYMGDGMDRVDLPTPAILKP-----VELWTGKQLFSVLIRPHANMRVYVNLTVKEKTYSNKLIRTEGDEE 496 (1265)
Q Consensus 422 ~~~~~~~~l~~~~~~~~~~~~lp~Pai~kp-----~~lwTGKql~s~~l~~~~~~~~~in~~~~~k~~~~~~~~~~~~~~ 496 (1265)
++++++++++..- .+.++.|..++| ...|||||+||.++|+.. + |
T Consensus 518 ~~~~e~~~~~~~~-----~i~l~~~i~~~~~~~~~i~tt~Gk~if~~ilP~~~------~-------~------------ 567 (1156)
T PRK00566 518 SSPEEALRAYENG-----EVDLHARIKVRITSKKLVETTVGRVIFNEILPEGL------P-------F------------ 567 (1156)
T ss_pred CCHHHHHHHHHcC-----CCCCCCeEEecCCCCceEEcCcHHHHHHhhccccc------e-------e------------
Confidence 9999999876421 234555555543 247999999999997531 0 1
Q ss_pred ccccccCCCCCeeEEecCcceecccccccccCCCcccHHHHHHHHhChhhHHHHHhHHHHHHHHHHHhccceeeeccCCC
Q 000829 497 IRIETMCPNDGFVYFRNSELISGQLGKATLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLSARWIGNHGFSIGIDDVQP 576 (1265)
Q Consensus 497 ~~~~~~~~~d~~v~i~~gell~G~ldK~~lG~~~~~~Li~~i~~~yG~~~a~~~l~~~~~l~~~~L~~~GFSigi~D~~~ 576 (1265)
.|. +|++||+++| +|+|.+++.||++.|+.|||++++|+++|++.+|||||++|+.+
T Consensus 568 ---------------~n~---~g~ldKk~Lg-----~LI~~i~~~yG~~~t~~~LD~ik~Lgf~yat~~GfSigi~Dl~i 624 (1156)
T PRK00566 568 ---------------INV---NKPLKKKEIS-----KIINEVYRRYGLKETVIFLDKIKDLGFKYATRSGISIGIDDIVI 624 (1156)
T ss_pred ---------------ecc---cceecHHHHH-----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCeEeehhhcCc
Confidence 010 5789999998 49999999999999999999999999999999999999999998
Q ss_pred CccchHHHHHHHHHHHHHHHHHHHHHHcCCCccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC----CCcceeee
Q 000829 577 KKELSDKKGKLISENYEVCNVKIKEYNEGKLQLKPGCDAAQTLEAVITDILNRIREDAGKACMGSLPW----RNSPLIMS 652 (1265)
Q Consensus 577 ~~~~~~~~~~~i~~a~~~~~~~i~~~~~g~l~~~~~~~~~~~le~~i~~~l~~~~~~~~~~~~~~l~~----~N~~~~M~ 652 (1265)
++ +|.+++++|+++++++.++|+.|.++. . ..+.++..+|+++++++++.+++.+.+ +|++++|+
T Consensus 625 p~----~K~~ii~~a~~~v~~i~~~y~~G~lt~------~-er~~kvi~~w~~~~d~v~~~~~~~l~~~~~~~N~i~mMa 693 (1156)
T PRK00566 625 PP----EKKEIIEEAEKEVAEIEKQYRRGLITD------G-ERYNKVIDIWSKATDEVAKAMMKNLSKDQESFNPIYMMA 693 (1156)
T ss_pred Ch----HHHHHHHHHHHHHHHHHHHHHcCCCCc------h-HHHHHHHHHHHHHHHHHHHHHHHhCccccCCCCChheee
Confidence 76 477899999999999999999998852 2 345788999999999999999999875 89999999
Q ss_pred ccCCCCChhcHhHHhhcccccccCCCCCCCCCCCcccCCCCCCCCCCCccceeccccccCCChhhhhhhhccccccchhc
Q 000829 653 QCGSKGSPINISQMVACVGQQSVGGRRAPNGFIDRSLPHFPRKAKEPAAKGFVANSFYSGLSATEFFFHTMGGREGLVDT 732 (1265)
Q Consensus 653 ~sGsKGS~~Ni~Qi~~~lGQQ~~~G~Rip~~~~~rtLP~f~~~~~~~~a~GfV~~sf~~GL~p~EfFfH~m~GReGLiDT 732 (1265)
.||||||++|++||+||+|||.. | +|+++|. ||.|||++||+|+|||||||||||||+||
T Consensus 694 ~SGARGS~~ni~QL~GmrGlma~-----p---~G~iie~------------pI~ssFreGLt~~EyFfst~GaRkGLiDT 753 (1156)
T PRK00566 694 DSGARGSASQIRQLAGMRGLMAK-----P---SGEIIET------------PIKSNFREGLTVLEYFISTHGARKGLADT 753 (1156)
T ss_pred eccCCcCHHHHHHHHhhcCcccc-----C---CCCEeeh------------hhhhhhhcCCCHHHHhhcCcchhhcccch
Confidence 99999999999999999999852 2 2344442 69999999999999999999999999999
Q ss_pred ccccCcCChhHHHHHHHhhheEeeecCeEEcCCCcEEEEEecCCCcccccccCCCCCCchhHHHHHHHH--hcCCCCCCC
Q 000829 733 AVKTADTGYMSRRLIKALEDLSIQYDNSVRNAGGCIVQFLYGDDGMDPANMEGKSGEPLNFDRLLMKVK--ATCPPAGQR 810 (1265)
Q Consensus 733 AvKTa~sGYlqRrLvk~lEdl~v~YD~TVR~s~g~iiQf~YGeDG~d~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~ 810 (1265)
|||||+|||||||||+++||++|.||.+= +..|-.+.-.. ++| .. ++ ++. ++++..+. .+.......
T Consensus 754 ALKTAdSGYLtRRLVdvaqDviV~~~DCg-T~~gi~~~~~~-~~~-~~--i~-----~l~-~~~~GR~~~~di~~~~t~~ 822 (1156)
T PRK00566 754 ALKTADSGYLTRRLVDVAQDVIVREDDCG-TDRGIEVTAII-EGG-EV--IE-----PLE-ERILGRVLAEDVVDPETGE 822 (1156)
T ss_pred heeeccceeeehhHHHhhCceEEEECCCC-CcCCEEEEEec-cCC-EE--Ee-----Ehh-heeEeEEEhhheecCCCCc
Confidence 99999999999999999999999998541 12232221110 111 00 00 000 11111100 000000000
Q ss_pred CCCHHHHHHHHHHHHhhcCCCcchHHHHHHHHHHHHHhhhhhhhhhhcccccCCCccchhhhhhhhhccCCCHHHHHHHH
Q 000829 811 YLSPQQVSEIVEKQLAAYGKESCSEAFLNSLRKFFEGQQDKLDKKIKFVEDIGWDDKSQILEEVTHKTSGITEKQLEVFI 890 (1265)
Q Consensus 811 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~~~~~~l~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ 890 (1265)
.+ ...++ ...+...+.+. +. ++. .+..++.+||+.-..+|
T Consensus 823 ~i------------~~~~~--~i~~~~~~~i~-----------~~-------~i~--------~v~iRS~ltC~s~~gvC 862 (1156)
T PRK00566 823 VI------------VPAGT--LIDEEIADKIE-----------EA-------GIE--------EVKIRSVLTCETRHGVC 862 (1156)
T ss_pred EE------------EcCCC--ccCHHHHHHHH-----------Hc-------CCC--------EEEEcCCeeecCCCccc
Confidence 00 00000 01111111111 10 110 12344678888777877
Q ss_pred HHHHHh--hhcccCCcCccceeecccccCCccccccccccccccccccceecccchhHhhhhcccccccceEEEEccCCC
Q 000829 891 QTCFSR--YRVKRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINGAKRISTPIITAELECND 968 (1265)
Q Consensus 891 ~~~~~k--y~~slv~PGEaVG~IAAQSIGEPsTQMTLnTFH~AGv~~~NVTlGvPRLkEIinask~ikTP~~ti~l~~~~ 968 (1265)
+.||-. -...+|+.|||||+|||||||||+|||||+|||.+|+ ++|.|+||+.|++.| +++|.+.+..++
T Consensus 863 ~~CYG~~La~~~~v~iGeaVGiIAAQSIGEPGTQLTmRTFHtGGv---dIT~Glprv~elfea-r~pk~~a~ise~---- 934 (1156)
T PRK00566 863 AKCYGRDLATGKLVNIGEAVGVIAAQSIGEPGTQLTMRTFHTGGV---DITGGLPRVAELFEA-RKPKGPAIIAEI---- 934 (1156)
T ss_pred HhhhCccccCCCCcccCcceeEEeeeecCCCccceeeeeeeecce---eccCCccchhhheee-ccCCCceEEEec----
Confidence 777743 3467899999999999999999999999999999999 999999999999988 445544322222
Q ss_pred cHHHHHHHhcceeEEeccccceeEEEEEeCC-ccEEEEEeChhhHHHhhcccCHHHHHHHHhcCcccccccCceeeeccc
Q 000829 969 NENAARVVKGRIEKTLLGQVAKSIKIVMTSR-LASIVIALDMETIQDAHLCINADIVKESIVQTPKIKLKQQHIKVLDFR 1047 (1265)
Q Consensus 969 ~~~~a~~v~~~le~~~L~di~~~i~~~y~~~-~~~~~i~ld~~~i~~~~~~i~~~~i~~~i~~~~k~k~~~~~i~~~~~~ 1047 (1265)
-..+++.-+.. ...+.| .++
T Consensus 935 --------------------~G~v~~~~~~~~~~~i~i--------------------------------------~~~- 955 (1156)
T PRK00566 935 --------------------DGTVSFGKETKGKRRIVI--------------------------------------TPD- 955 (1156)
T ss_pred --------------------CCEEEeccccCCceEEEE--------------------------------------eCC-
Confidence 11111100000 000111 000
Q ss_pred eEEEeCCCCCCcceeehHHHhhhcCCcEEecccCceEEEEeccccccchhhccCCcccEEEEEeCccHHHhhccCCcccc
Q 000829 1048 KLEIFPPVDKSKIHFELYSLKNVLPMVIVKGIKTVERVVIAEKEKEKRKVKENGEKKKYRLLVEGTGLQAVMGAEGIDGC 1127 (1265)
Q Consensus 1048 ~~~i~~~~~~~~~~~~l~~l~~~l~~~~v~Gi~~I~r~~i~~~~~~~~~~~~~~~~~~~~l~teG~nl~~~~~~~~VD~~ 1127 (1265)
+.....+ -+|.-.+..+...| . ...| ...|||.
T Consensus 956 --------~~~~~~y---------------~vp~~~~~~v~~gd----~----v~~G--~~l~~g~-------------- 988 (1156)
T PRK00566 956 --------DGEEREY---------------LIPKGKHLLVQEGD----H----VEAG--DKLTDGS-------------- 988 (1156)
T ss_pred --------CCceEEE---------------EccCCCeeeecCCC----E----EccC--CcccCCC--------------
Confidence 0000000 01111222222111 0 0111 3457773
Q ss_pred ccccCCHHHHHHHhCHHHHHHHHHHHHHHHhhccccccCcccceeeecccccc---------------------------
Q 000829 1128 KTKSNHIFEVQQTLGIEAARICIIDEINETMKAHGMSIDKRHMMLLADLMTFR--------------------------- 1180 (1265)
Q Consensus 1128 ~~~sNdI~ev~~~lGIEAAR~~Iv~Ei~~v~~~~Gi~Vd~RHl~LlAD~MT~~--------------------------- 1180 (1265)
=|++++++++||||+|..|++||++||..||++||++|+++|++.||.+
T Consensus 989 ----~~~~~il~v~G~~~~~~~lv~eiq~vY~~QGv~I~dKHievIvrqM~~kv~i~~~gdt~~~~g~~v~~~~~~~~n~ 1064 (1156)
T PRK00566 989 ----IDPHDILRVLGVEAVQNYLVNEVQKVYRLQGVKINDKHIEVIVRQMLRKVRITDPGDTDFLPGELVDRSEFEEENR 1064 (1156)
T ss_pred ----CCHHHHHHhcCHHHHHHHHHHHHHHHHHhCCcccccceeehHHHHHhCCeEEecCCCcCCCCCceeeHHHHHHHHH
Confidence 2688999999999999999999999999999999999999999999975
Q ss_pred -------------cEEEeeccccccccCCcHhhHhcchHHHHHHHHhhhcCCcccccccccceeccCCCCCCccceE
Q 000829 1181 -------------GEVLGITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDDRIEGVSECIIMGIPMPLGTGILK 1244 (1265)
Q Consensus 1181 -------------G~~~~i~R~Gi~~~~~Spl~~aSFE~T~~~L~~AA~~g~~D~l~gvS~~Ii~Gk~~~~GTG~fd 1244 (1265)
..++||||++++ ..|+|++||||+|+++|++||+.|++|+|.|++||||+|+++|+|||...
T Consensus 1065 ~~~~~g~~~~~~~~~llGItka~l~--t~SflsaASFQeTtkvLt~AAi~gk~D~L~GlkENVIiG~liPaGTG~~~ 1139 (1156)
T PRK00566 1065 KLIAEGKEPATGRPVLLGITKASLA--TESFLSAASFQETTRVLTEAAIKGKVDPLRGLKENVIIGRLIPAGTGLAR 1139 (1156)
T ss_pred HHHHCCCCCCcccceeeeeeecccc--cCcccccccccchHHHHHHHHhcCCCCcCCCcccceEecCcccCCCCcch
Confidence 346899999998 58999999999999999999999999999999999999999999999864
No 9
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=100.00 E-value=8.7e-175 Score=1626.09 Aligned_cols=854 Identities=27% Similarity=0.428 Sum_probs=662.5
Q ss_pred CCcceEEEeeeeeCCCCCCCceecCCCCcCCchhHHHHHHHHHHHHHHHHHHHHhccchhhhHHHHHHHHHHHHHhccCC
Q 000829 110 ERPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQQELVEANSAFKSLAGWETLQVEVAQYINSDV 189 (1265)
Q Consensus 110 ~~p~~~~l~~lpVpP~~~RP~~~~~~~~~~~ddlt~~l~~Ii~~n~~l~~~~~~~~~~~~~~~~~~~lq~~v~~~~~~~~ 189 (1265)
.+|+||||++||||||++||++.++++...+||||.+|++||.+|++|++.+..+++...+.+.|++||.+|+.||||+.
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 69999999999999999999999999889999999999999999999999999999988899999999999999999999
Q ss_pred CCCCccccCCCCchhhhhhhcCccccccccccCCCCCCccceEEcCCCCCCCCcccccHHHHhhcCcceeechHHHHHHH
Q 000829 190 RGVPFSMQVARPLSGFVQRLKGKQGRFRGNLSGKRVEYTGRTVISPDPNLKITEVAIPIRMARILTYPERVSDHNIEKLR 269 (1265)
Q Consensus 190 ~~~~~~~~~~~~~~~i~q~l~gK~G~fR~nl~GKRvd~saRsVIspDp~l~~~evGvP~~~A~~Lt~pe~Vt~~Ni~~l~ 269 (1265)
++.|.....++|+|||+|+|+||+||||+|||||||||||||||+|||+|+++|||||..||++||+|+. ++
T Consensus 390 ~g~p~~~~~~rplKsls~~LkGK~GRFRqNLlGKRVDySgRSVIspdP~L~l~e~GlP~~mA~eLf~Pf~--------i~ 461 (1460)
T PRK14906 390 RGRPVTGPGNRPLKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKPFV--------MK 461 (1460)
T ss_pred cCCCCccccCCchhHHHHHhcccCcccccccccccccCcCCceEeCCCCCccccccCcHHHHHhcCchhH--------HH
Confidence 9887654437899999999999999999999999999999999999999999999999999999999964 34
Q ss_pred HHHHcCCC-CCCCceEEECCCCCeEEeccccchhhhhcccccceeecccccCCeEEEecCCCccccceeeEEEEEecCCe
Q 000829 270 QCIQNGPD-KYPGARMIRYPDGTARVLYGKFRNQLAVELKSGCIVDRHLEDGDVVLFNRQPSLHRMSIMCHRARIMPWRT 348 (1265)
Q Consensus 270 ~lv~ng~~-~~pGa~~i~~~~g~~~~l~~~~r~~~~~~L~~g~iV~Rhl~dgD~VL~NRQPSLHk~Simah~vkv~~~kt 348 (1265)
+|+.+|.. ..++|+. .+.......+.|.||+.+||+|||||||||||||||||++++++++|
T Consensus 462 ~L~~~~~~~nik~ak~-----------------~i~~~~~~v~~vle~vi~gd~VLlNRqPTLHRlsIqAf~~~L~~gkt 524 (1460)
T PRK14906 462 RLVELEYAANIKAAKR-----------------AVDRGASYVWDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKA 524 (1460)
T ss_pred HHHHhcccccHHHHhh-----------------HHhhcCCcceeeeeeeeccceeEeccCcccchhccceeeEEecCCce
Confidence 44444421 1111211 11112233455667888999999999999999999999999999999
Q ss_pred eeeecccCCCCCCCCcccccccccCChHHHHHHHHHHcCCCcccccCCCCCccEeecccceeeeeeeecc-C-------c
Q 000829 349 LRFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRK-D-------T 420 (1265)
Q Consensus 349 ~rln~~vc~~yNADFDGDEMN~h~PQs~~araEa~~Lm~~~~~~~sp~~g~pi~gliQD~l~g~~llT~~-d-------~ 420 (1265)
|||||+||+||||||||||||+|+|||++|||||+.||++.+|++||++|+|+++++||+++|+|+||.. + .
T Consensus 525 IrLhplvC~~fNADFDGDqMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~~~~~~~~~ 604 (1460)
T PRK14906 525 IKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLTTERDGFEGEGRT 604 (1460)
T ss_pred EEecccccCccccCCcCceeeeecCCCHHHHHHHHHHhcchhcEecCCCCCeeEEeeeeeeeeeEEeeeccccccccCce
Confidence 9999999999999999999999999999999999999999999999999999999999999999999974 3 6
Q ss_pred cCCHHHHHHHHHHhcCCCceeecCCCce---------------------eCcccccccceeeeeeecCCCCcceEEEEee
Q 000829 421 FYDRAAFSLMCCYMGDGMDRVDLPTPAI---------------------LKPVELWTGKQLFSVLIRPHANMRVYVNLTV 479 (1265)
Q Consensus 421 f~~~~~~~~l~~~~~~~~~~~~lp~Pai---------------------~kp~~lwTGKql~s~~l~~~~~~~~~in~~~ 479 (1265)
|.+.+++..++.+.. .++++.|.. .++...|+||++|+.+||..
T Consensus 605 F~~~~e~~~a~~~~~----~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~tt~Gr~Ifn~ilP~d----------- 669 (1460)
T PRK14906 605 FADFDDALNAYDARA----DLDLQAKIVVRLSRDMTVRGSYGDLEETKAGERIETTVGRIIFNQVLPED----------- 669 (1460)
T ss_pred eCCHHHHHHHHhcCC----CccccccEEEecCcccccccccccccCCCCCceEECCCCEEEEecccCCC-----------
Confidence 889998887775421 122222211 22345789999999888631
Q ss_pred cccccccccccccCCccccccccCCCCCeeEEecCcceecccccccccCCCcccHHHHHHHHhChhhHHHHHhHHHHHHH
Q 000829 480 KEKTYSNKLIRTEGDEEIRIETMCPNDGFVYFRNSELISGQLGKATLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLSA 559 (1265)
Q Consensus 480 ~~k~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~gell~G~ldK~~lG~~~~~~Li~~i~~~yG~~~a~~~l~~~~~l~~ 559 (1265)
..++++.++|+.+| +|++.+|+.||...++.|||++++|++
T Consensus 670 ----------------------------------~~fvN~~l~KK~Lg-----~LI~~i~~~~G~~~t~~fLD~Ik~LGf 710 (1460)
T PRK14906 670 ----------------------------------YPYLNYKMVKKDIG-----RLVNDCCNRYSTAEVEPILDGIKKTGF 710 (1460)
T ss_pred ----------------------------------cccccceeeHHHHH-----HHHHHHHHHhCHHHHHHHHHHHHHHHH
Confidence 12345678999998 399999999999999999999999999
Q ss_pred HHHHhccceeeeccCCCCccchHHHHHHHHHHHHHHHHHHHHHHcCCCccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Q 000829 560 RWIGNHGFSIGIDDVQPKKELSDKKGKLISENYEVCNVKIKEYNEGKLQLKPGCDAAQTLEAVITDILNRIREDAGKACM 639 (1265)
Q Consensus 560 ~~L~~~GFSigi~D~~~~~~~~~~~~~~i~~a~~~~~~~i~~~~~g~l~~~~~~~~~~~le~~i~~~l~~~~~~~~~~~~ 639 (1265)
+|++.+|||||++|+.+++ .|.+++++|++++.+++++|+.|.++ ..+ .+.++.++|+++++++++.++
T Consensus 711 ~yaT~sG~SIgi~Di~ip~----~K~~iI~~A~~~V~ei~~~y~~G~iT------~~E-r~~kVi~iw~~a~d~v~~~~~ 779 (1460)
T PRK14906 711 HYATRAGLTVSVYDATIPD----DKPEILAEADEKVAAIDEDYEDGFLS------ERE-RHKQVVDIWTEATEEVGEAML 779 (1460)
T ss_pred HHHHhCCEEEeecccccCh----HHHHHHHHHHHHHHHHHHHHHcCCCc------HHH-HHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999998765 57889999999999999999999985 234 479999999999999999999
Q ss_pred cCCCCCCcceeeeccCCCCChhcHhHHhhcccccc-cCCCCCCCCCCCcccCCCCCCCCCCCccceeccccccCCChhhh
Q 000829 640 GSLPWRNSPLIMSQCGSKGSPINISQMVACVGQQS-VGGRRAPNGFIDRSLPHFPRKAKEPAAKGFVANSFYSGLSATEF 718 (1265)
Q Consensus 640 ~~l~~~N~~~~M~~sGsKGS~~Ni~Qi~~~lGQQ~-~~G~Rip~~~~~rtLP~f~~~~~~~~a~GfV~~sf~~GL~p~Ef 718 (1265)
+.+++.|++++|+.||||||..|++||+||+|||. ..|++|+ .+|.|||++||+|.||
T Consensus 780 ~~l~~~N~i~mMa~SGARGS~~QI~QLaGmRGlma~p~G~iIe---------------------~PI~SnFrEGLt~~Ey 838 (1460)
T PRK14906 780 AGFDEDNPIYMMADSGARGNIKQIRQLAGMRGLMADMKGEIID---------------------LPIKANFREGLSVLEY 838 (1460)
T ss_pred HhcccCCCeEeeeeccCcccHHHHHHHHhcccceecCCCCccc---------------------cccccccccCCCHHHH
Confidence 99999999999999999999999999999999985 5676653 1499999999999999
Q ss_pred hhhhccccccchhcccccCcCChhHHHHHHHhhheEeeecCeEEcCCCcEEEEEecCCCcccccccCCCCCCchhHHHHH
Q 000829 719 FFHTMGGREGLVDTAVKTADTGYMSRRLIKALEDLSIQYDNSVRNAGGCIVQFLYGDDGMDPANMEGKSGEPLNFDRLLM 798 (1265)
Q Consensus 719 FfH~m~GReGLiDTAvKTa~sGYlqRrLvk~lEdl~v~YD~TVR~s~g~iiQf~YGeDG~d~~~~~~~~~~~~~~~~~~~ 798 (1265)
|||||||||||+|||+|||+||||||||||++||++|..+.+ -...|-.+.-.- + . .++. ++++.
T Consensus 839 FiSt~GaRKGL~DTALKTAdSGYLTRRLVdVaQDViV~e~DC-gT~~Gi~v~~~~--~------~-----~~l~-~ri~G 903 (1460)
T PRK14906 839 FISTHGARKGLVDTALRTADSGYLTRRLVDVAQDVIVREEDC-GTDEGVTYPLVK--P------K-----GDVD-TNLIG 903 (1460)
T ss_pred HHHcccccchhhhhhhhccccchHHHHHHHhhhheEEEeccC-CCCCCEEEEEee--c------c-----cchh-heeee
Confidence 999999999999999999999999999999999999965532 112233332110 0 0 0110 11111
Q ss_pred HHHhcCCCCCCCCCCHH-HHHHHHHHHHhhcCCCcchHHHHHHHHHHHHHhhhhhhhhhhcccccCCCccchhhhhhhhh
Q 000829 799 KVKATCPPAGQRYLSPQ-QVSEIVEKQLAAYGKESCSEAFLNSLRKFFEGQQDKLDKKIKFVEDIGWDDKSQILEEVTHK 877 (1265)
Q Consensus 799 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~~~~~~l~~~~~~~~~~~l~~~~~~~~~~~~~ 877 (1265)
.+.+.. ...|. ++ +...+++ ..+.. .++++.+. |+. .+..
T Consensus 904 R~~~~d------i~~~~g~~------i~~~~~~--I~~~~----------~~~~i~~~-------gi~--------~v~i 944 (1460)
T PRK14906 904 RCLLED------VCDPNGEV------LLSAGDY--IESMD----------DLKRLVEA-------GVT--------KVQI 944 (1460)
T ss_pred EEEHhh------hcCCCCCE------EEeCCCe--eCcHH----------HHHHHHHC-------CCC--------EEEE
Confidence 110000 00000 00 0000000 00000 01111110 110 2234
Q ss_pred ccCCCHHHHHHHHHHHHHh--hhcccCCcCccceeecccccCCccccccccccccccccccceecccchhHhhhhccccc
Q 000829 878 TSGITEKQLEVFIQTCFSR--YRVKRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINGAKRI 955 (1265)
Q Consensus 878 ~~~~~~~~~~~~~~~~~~k--y~~slv~PGEaVG~IAAQSIGEPsTQMTLnTFH~AGv~~~NVTlGvPRLkEIinask~i 955 (1265)
++.+||+.-..+|+.||-. -...+|+.|||||+|||||||||+|||||+|||.+|+++.+||+|+||+.|++.|.+ +
T Consensus 945 RS~ltC~s~~gvC~kCYG~dLatg~~V~iGeaVGiIAAQSIGEPGTQLTMRTFHtGGv~~~dit~GLpRv~eLfEar~-p 1023 (1460)
T PRK14906 945 RTLMTCHAEYGVCQKCYGWDLATRRPVNIGTAVGIIAAQSIGEPGTQLTMRTFHSGGVAGDDITQGLPRVAELFEARK-P 1023 (1460)
T ss_pred eCCeeECCCCCChhhCcCCcccCCcEeccccceeeeeeeecCCCcceeeeeeeecccccccccccCcchhhhheeecc-C
Confidence 5678887767776666543 345789999999999999999999999999999999998899999999999998853 3
Q ss_pred ccceEEEEccCCCcHHHHHHHhcceeEEeccccceeEEEEEeCCccEEEEEeChhhHHHhhcccCHHHHHHHHhcCcccc
Q 000829 956 STPIITAELECNDNENAARVVKGRIEKTLLGQVAKSIKIVMTSRLASIVIALDMETIQDAHLCINADIVKESIVQTPKIK 1035 (1265)
Q Consensus 956 kTP~~ti~l~~~~~~~~a~~v~~~le~~~L~di~~~i~~~y~~~~~~~~i~ld~~~i~~~~~~i~~~~i~~~i~~~~k~k 1035 (1265)
|-+.+ +.++-..+++ ..+....++.
T Consensus 1024 k~~a~------------------------i~e~~G~v~i--~~~~~~~~i~----------------------------- 1048 (1460)
T PRK14906 1024 KGEAV------------------------LAEISGTLQI--TGDKTEKTLT----------------------------- 1048 (1460)
T ss_pred CCcee------------------------eeccCCEEEe--ccCCCceEEE-----------------------------
Confidence 33322 2222222221 1110000000
Q ss_pred cccCceeeeccceEEEeCCCCCCcceeehHHHhhhcCCcEEecccCceEEEEeccccccchhhccCCcccEEEEEeCccH
Q 000829 1036 LKQQHIKVLDFRKLEIFPPVDKSKIHFELYSLKNVLPMVIVKGIKTVERVVIAEKEKEKRKVKENGEKKKYRLLVEGTGL 1115 (1265)
Q Consensus 1036 ~~~~~i~~~~~~~~~i~~~~~~~~~~~~l~~l~~~l~~~~v~Gi~~I~r~~i~~~~~~~~~~~~~~~~~~~~l~teG~nl 1115 (1265)
|... +.....+.+..-+..+ |+|+..-.. ..| ...|+|.
T Consensus 1049 ---------------i~~~-~~~~~~y~v~~~~~~~--------~~v~~gd~v-------------~~G--~~l~~G~-- 1087 (1460)
T PRK14906 1049 ---------------IHDQ-DGNSREYVVSARVQFM--------PGVEDGVEV-------------RVG--QQITRGS-- 1087 (1460)
T ss_pred ---------------EECC-CCceeEEEccCCcccc--------cccCCCCEE-------------ccC--CCccCCC--
Confidence 0000 0000000000000000 111100000 011 2466663
Q ss_pred HHhhccCCccccccccCCHHHHHHHhCHHHHHHHHHHHHHHHhhccccccCcccceeeecccccc---------------
Q 000829 1116 QAVMGAEGIDGCKTKSNHIFEVQQTLGIEAARICIIDEINETMKAHGMSIDKRHMMLLADLMTFR--------------- 1180 (1265)
Q Consensus 1116 ~~~~~~~~VD~~~~~sNdI~ev~~~lGIEAAR~~Iv~Ei~~v~~~~Gi~Vd~RHl~LlAD~MT~~--------------- 1180 (1265)
=|.++++++.|+||+...|++|+++||..||++||++|+.+|+-.|+.+
T Consensus 1088 ----------------~~p~~il~~~g~~~~~~ylv~eVQ~VYr~QGV~InDKHiEvIvRQMl~kV~I~d~Gdt~fl~Ge 1151 (1460)
T PRK14906 1088 ----------------VNPHDLLRLTDPNTTLRYIVSQVQDVYVSQGVDINDKHIEVIARQMLRKVAVTNPGDSDYLPGR 1151 (1460)
T ss_pred ----------------CCHHHHHHhcCHHHHHHHHHHHHHHHHHhcCceeccccHHHHHHHHhceEEEecCCCcCCCCCC
Confidence 2678999999999999999999999999999999999999999999754
Q ss_pred -------------------------cEEEeeccccccccCCcHhhHhcchHHHHHHHHhhhcCCcccccccccceeccCC
Q 000829 1181 -------------------------GEVLGITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDDRIEGVSECIIMGIP 1235 (1265)
Q Consensus 1181 -------------------------G~~~~i~R~Gi~~~~~Spl~~aSFE~T~~~L~~AA~~g~~D~l~gvS~~Ii~Gk~ 1235 (1265)
-.++|||++.++ ..|+|+.|||++|+++|++||+.|++|+|.|+.||||+|++
T Consensus 1152 ~vd~~~~~~~n~~~~~~g~~pa~~~p~llGITKasL~--t~SflSaASFQeTtrVLt~AAi~gk~D~L~GLKENVIiG~l 1229 (1460)
T PRK14906 1152 QVNRYEFEDTANNLILEGKQPPVGQPLLLGITKASLA--TDSWLSAASFQETTKVLTDAAIEGKVDHLAGLKENVIIGKP 1229 (1460)
T ss_pred eeeHHHHHHHHHHHHHcCCCCceeeeEEeeeeecccc--cccccccccccchHHHHHHHHhcCCCCcCCCCccceEecce
Confidence 359999999998 58999999999999999999999999999999999999999
Q ss_pred CCCCccce
Q 000829 1236 MPLGTGIL 1243 (1265)
Q Consensus 1236 ~~~GTG~f 1243 (1265)
+|+|||..
T Consensus 1230 IPAGTG~~ 1237 (1460)
T PRK14906 1230 IPAGTGLS 1237 (1460)
T ss_pred ecCCCCcc
Confidence 99999974
No 10
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=100.00 E-value=4.9e-169 Score=1632.15 Aligned_cols=673 Identities=27% Similarity=0.417 Sum_probs=545.0
Q ss_pred CCcceEEEeeeeeCCCCCCCceecCCCCcCCchhHHHHHHHHHHHHHHHHHHHHhccchhhhHHHHHHHHHHHHHhccCC
Q 000829 110 ERPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQQELVEANSAFKSLAGWETLQVEVAQYINSDV 189 (1265)
Q Consensus 110 ~~p~~~~l~~lpVpP~~~RP~~~~~~~~~~~ddlt~~l~~Ii~~n~~l~~~~~~~~~~~~~~~~~~~lq~~v~~~~~~~~ 189 (1265)
++|+||||++||||||++||++.++++..+++|||.+|++||.+|++|++.+..++|...+.+.|++||.+|+.||||+.
T Consensus 1621 ~~PewmiL~~lPV~Pp~lRP~v~l~gg~~a~sDln~lyr~II~rNnrLk~l~~~~ap~~ii~nek~~LQ~aVd~l~DN~~ 1700 (2890)
T PRK09603 1621 NRPEWMMLTVLPVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRLMELGAPEIIVRNEKRMLQEAVDVLFDNGR 1700 (2890)
T ss_pred CChHheeeeeeccCCCcccCcEEeCCCcccCCCccHHHHHHHHHHHHHHHHHHcCCCceehHHHHHHHHHHHHHHhcccc
Confidence 79999999999999999999999998889999999999999999999999999999988899999999999999999998
Q ss_pred CCCCccccCCCCchhhhhhhcCccccccccccCCCCCCccceEEcCCCCCCCCcccccHHHHhhcCcceeechHHHHHHH
Q 000829 190 RGVPFSMQVARPLSGFVQRLKGKQGRFRGNLSGKRVEYTGRTVISPDPNLKITEVAIPIRMARILTYPERVSDHNIEKLR 269 (1265)
Q Consensus 190 ~~~~~~~~~~~~~~~i~q~l~gK~G~fR~nl~GKRvd~saRsVIspDp~l~~~evGvP~~~A~~Lt~pe~Vt~~Ni~~l~ 269 (1265)
++.|.....++|++||+|+|+||+||||+|||||||||||||||+|||+|+++|||||..||++||+|+. ++
T Consensus 1701 ~~~~~~~~~~rplKsls~~LkGK~GRFRqNLlGKRVDySgRSVI~pdP~L~l~e~GvP~~mA~eL~~P~~--------i~ 1772 (2890)
T PRK09603 1701 STNAVKGANKRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHL--------LS 1772 (2890)
T ss_pred ccccccCCCCCcchhHHHHhcCCCCccccccccccccCcCCceEeCCCCcccccccChHHHHHHhCChHH--------HH
Confidence 8776544337899999999999999999999999999999999999999999999999999999999975 67
Q ss_pred HHHHcCCCCCCCceEEECCCCCeEEeccccchhhhhcccccceeecccccCCeEEEecCCCccccceeeEEEEEecCCee
Q 000829 270 QCIQNGPDKYPGARMIRYPDGTARVLYGKFRNQLAVELKSGCIVDRHLEDGDVVLFNRQPSLHRMSIMCHRARIMPWRTL 349 (1265)
Q Consensus 270 ~lv~ng~~~~pGa~~i~~~~g~~~~l~~~~r~~~~~~L~~g~iV~Rhl~dgD~VL~NRQPSLHk~Simah~vkv~~~kt~ 349 (1265)
+|+.+|+.. .+. . .+..+......++.|+|||.+||+|||||||||||||||||+|+|++|+||
T Consensus 1773 ~L~~~G~~~-----~lk---------~--ak~~i~~~~~~v~~vlr~vi~gd~VLlNRqPTLHR~sIqAf~~~l~~gktI 1836 (2890)
T PRK09603 1773 KLEERGYAT-----TLK---------Q--AKRMIEQKSNEVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAI 1836 (2890)
T ss_pred HHHHcCCcc-----CHH---------H--HHHHHHhccCccEEEEEeeecCCeEEecCCCccccccceeeeEEEecCceE
Confidence 888898631 110 0 122222334456778899999999999999999999999999999999999
Q ss_pred eeecccCCCCCCCCcccccccccCChHHHHHHHHHHcCCCcccccCCCCCccEeecccceeeeeeeeccCccCCHH----
Q 000829 350 RFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDRA---- 425 (1265)
Q Consensus 350 rln~~vc~~yNADFDGDEMN~h~PQs~~araEa~~Lm~~~~~~~sp~~g~pi~gliQD~l~g~~llT~~d~f~~~~---- 425 (1265)
||||+||+||||||||||||+|+|||++|||||+.||++.+|++||++|+|+++++||+|+|+|+||.++.|++++
T Consensus 1837 rLhplvC~~fNADFDGDqMnvHvPqS~eA~aEa~~LM~s~~nilsP~~G~Pi~~p~QD~vlG~y~LT~~~~~~~~~~~~F 1916 (2890)
T PRK09603 1837 QLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKSGVKGEHKLF 1916 (2890)
T ss_pred EeccccCCcccCCCCCceeEEeecCCHHHHHHHHHHhcccceEEEcCCCceeEEeecceeeeeEEeeccccCCCCcccee
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999765543
Q ss_pred -HHHHHHHHhcCCCceeecCCCceeCcccccc--cceeeeeeecCCCCcceEEEEeecccccccccccccCCcccccccc
Q 000829 426 -AFSLMCCYMGDGMDRVDLPTPAILKPVELWT--GKQLFSVLIRPHANMRVYVNLTVKEKTYSNKLIRTEGDEEIRIETM 502 (1265)
Q Consensus 426 -~~~~l~~~~~~~~~~~~lp~Pai~kp~~lwT--GKql~s~~l~~~~~~~~~in~~~~~k~~~~~~~~~~~~~~~~~~~~ 502 (1265)
.+.++++++..+...+..|.|++++|..+|| |||+||.+||.. ++
T Consensus 1917 ~~~~e~~~~~~~~~~~~~~~i~~~~~p~~l~Tt~GK~ifs~ilP~~------~~-------------------------- 1964 (2890)
T PRK09603 1917 SSVNEIITAIDTKELDIHAKIRVLDQGNIIATSAGRMIIKSILPDF------IP-------------------------- 1964 (2890)
T ss_pred CCHHHHHHHHHcCCCccCCcceeecCCcEEEcCccceeeeccCccc------cc--------------------------
Confidence 2333333333333335566778889999999 999999999632 00
Q ss_pred CCCCCeeEEecCcceecccccccccCCCcccHHHHHHHHhChhhHHHHHhHHHHHHHHHHHhccceeeeccCCCCccchH
Q 000829 503 CPNDGFVYFRNSELISGQLGKATLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLSARWIGNHGFSIGIDDVQPKKELSD 582 (1265)
Q Consensus 503 ~~~d~~v~i~~gell~G~ldK~~lG~~~~~~Li~~i~~~yG~~~a~~~l~~~~~l~~~~L~~~GFSigi~D~~~~~~~~~ 582 (1265)
..++.|.+||+.+| +|+|.+|+.||+..|+.|||++++|+++|++.+|||||++|+.+++
T Consensus 1965 -----------~~~~n~~ldKK~Lg-----~LI~~i~~~yG~~~t~~fLD~lk~LGf~yat~~G~SIgI~Dl~ip~---- 2024 (2890)
T PRK09603 1965 -----------TDLWNRPMKKKDIG-----VLVDYVHKVGGIGITATFLDNLKTLGFRYATKAGISISMEDIITPK---- 2024 (2890)
T ss_pred -----------cccEeeeechHHHH-----HHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHhCCEeeeeccCcccH----
Confidence 01234679999998 4999999999999999999999999999999999999999999875
Q ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhcCCC----CCCcceeeeccCCCC
Q 000829 583 KKGKLISENYEVCNVKIKEYNEGKLQLKPGCDAAQTLEAVITDILNRIREDAGKACMGSLP----WRNSPLIMSQCGSKG 658 (1265)
Q Consensus 583 ~~~~~i~~a~~~~~~~i~~~~~g~l~~~~~~~~~~~le~~i~~~l~~~~~~~~~~~~~~l~----~~N~~~~M~~sGsKG 658 (1265)
+|.+++++|++++.+++.+|+.|.++.. ..++++.++|+++++++++.+++.+. +.||+++|+.|||||
T Consensus 2025 ~K~~iI~~A~~eV~ei~~~y~~G~it~~-------Er~~kvid~w~~~~d~v~~~~~~~l~~~~~~~N~i~mMa~SGARG 2097 (2890)
T PRK09603 2025 DKQKMVEKAKVEVKKIQQQYDQGLLTDQ-------ERYNKIIDTWTEVNDKMSKEMMTAIAKDKEGFNSIYMMADSGARG 2097 (2890)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCCcc-------HHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCcHHHHHhccccc
Confidence 4888999999999999999999998632 34678889999999999999887764 479999999999999
Q ss_pred ChhcHhHHhhcccccccCCCCCCCCCCCcccCCCCCCCCCCCccceeccccccCCChhhhhhhhccccccchhcccccCc
Q 000829 659 SPINISQMVACVGQQSVGGRRAPNGFIDRSLPHFPRKAKEPAAKGFVANSFYSGLSATEFFFHTMGGREGLVDTAVKTAD 738 (1265)
Q Consensus 659 S~~Ni~Qi~~~lGQQ~~~G~Rip~~~~~rtLP~f~~~~~~~~a~GfV~~sf~~GL~p~EfFfH~m~GReGLiDTAvKTa~ 738 (1265)
|.+|++||+||+|||.. |.| ...+ .+|.|||++||+|+|||||||||||||+|||||||+
T Consensus 2098 S~~NI~QLaGmrGqMak-----p~G---------~iie------~PI~snFrEGLtp~EyFfst~GaRKGLiDTALKTAd 2157 (2890)
T PRK09603 2098 SAAQIRQLSAMRGLMTK-----PDG---------SIIE------TPIISNFKEGLNVLEYFNSTHGARKGLADTALKTAN 2157 (2890)
T ss_pred cHHHHHHHHHcCCcEEC-----CCC---------Cccc------ChhhcCcccCCCHHHHHHhccccccchhhhhhhccc
Confidence 99999999999999753 222 1111 238999999999999999999999999999999999
Q ss_pred CChhHHHHHHHhhheEeeecCeEEcCCCcEEEEEecCCCcccccccCCCCCCchhHHHHHHHH--hcCCCCCCCCCCHHH
Q 000829 739 TGYMSRRLIKALEDLSIQYDNSVRNAGGCIVQFLYGDDGMDPANMEGKSGEPLNFDRLLMKVK--ATCPPAGQRYLSPQQ 816 (1265)
Q Consensus 739 sGYlqRrLvk~lEdl~v~YD~TVR~s~g~iiQf~YGeDG~d~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~ 816 (1265)
||||||||||++||++|..|.+-.+.+-.|-.+..|++-+.|.. ++++..+. .+........+
T Consensus 2158 SGYLTRRLVdvaQDviI~e~DCgT~~Gi~v~~~~~~~~~i~~l~-----------~ri~GR~~~~di~~p~t~~~i---- 2222 (2890)
T PRK09603 2158 AGYLTRKLIDVSQNVKVVSDDCGTHEGIEITDIAVGSELIEPLE-----------ERIFGRVLLEDVIDPITNEIL---- 2222 (2890)
T ss_pred cchhhhhHHHhhcceEEEeccCCCCCCeEEEEeecCCeeecchh-----------heeeeEEEHhheEcCCCCcEE----
Confidence 99999999999999999887664443334445545543333321 11111100 00000000000
Q ss_pred HHHHHHHHHhhcCCCcchHHHHHHHHHHHHHhhhhhhhhhhcccccCCCccchhhhhhhhhccCCCHHHHHHHHHHHHHh
Q 000829 817 VSEIVEKQLAAYGKESCSEAFLNSLRKFFEGQQDKLDKKIKFVEDIGWDDKSQILEEVTHKTSGITEKQLEVFIQTCFSR 896 (1265)
Q Consensus 817 ~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~~~~~~l~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k 896 (1265)
...++ ...+...+.+ .+. |+. .+..++.+||+.-..+|..||-.
T Consensus 2223 --------~~~~~--~I~~~~~~~i-----------~~~-------gi~--------~v~iRS~LtC~s~~gvC~~CYG~ 2266 (2890)
T PRK09603 2223 --------LYADT--LIDEEGAKKV-----------VEA-------GIK--------SITIRTPVTCKAPKGVCAKCYGL 2266 (2890)
T ss_pred --------EcCCc--CcCHHHHHHH-----------HHc-------CCC--------EEEEcCcceecCCCcChhhhcCC
Confidence 00000 0111111111 110 110 22345678888777776666532
Q ss_pred --hhcccCCcCccceeecccccCCcccccccccccccccccc
Q 000829 897 --YRVKRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASM 936 (1265)
Q Consensus 897 --y~~slv~PGEaVG~IAAQSIGEPsTQMTLnTFH~AGv~~~ 936 (1265)
-...+|+.|||||+|||||||||+|||||+|||.+|+++.
T Consensus 2267 dLa~g~~V~iGeaVGiIAAQSIGEPGTQLTMRTFHtGGvas~ 2308 (2890)
T PRK09603 2267 NLGEGKMSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTASR 2308 (2890)
T ss_pred cccCCCCccCCceeeEEeecccCCCccccchhhheecccccc
Confidence 2458899999999999999999999999999999999663
No 11
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=100.00 E-value=4.8e-167 Score=1607.54 Aligned_cols=671 Identities=27% Similarity=0.411 Sum_probs=535.9
Q ss_pred CCcceEEEeeeeeCCCCCCCceecCCCCcCCchhHHHHHHHHHHHHHHHHHHHHhccchhhhHHHHHHHHHHHHHhccCC
Q 000829 110 ERPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQQELVEANSAFKSLAGWETLQVEVAQYINSDV 189 (1265)
Q Consensus 110 ~~p~~~~l~~lpVpP~~~RP~~~~~~~~~~~ddlt~~l~~Ii~~n~~l~~~~~~~~~~~~~~~~~~~lq~~v~~~~~~~~ 189 (1265)
.+|+||||++||||||++||++.++++..++||||.+|++||.+|++|++.+..+++...+.+.|++||++|+.||||+.
T Consensus 1664 ~rPewmil~~lPV~Pp~lRP~v~l~~g~~~~sDLn~ly~~II~~NnrLk~~~~~~ap~~ii~~~~~~LQ~~V~~l~Dn~~ 1743 (2836)
T PRK14844 1664 NRPEWMILTTIPILPPDLRPLVSLESGRPAVSDLNHHYRTIINRNNRLRKLLSLNPPEIMIRNEKRMLQEAVDSLFDNSR 1743 (2836)
T ss_pred CChhheeeeccccCCCcccCcEEeCCCcccCCchHHHHHHHHHHHHHHHHHHHcCCchhhHHHHHHHHHHHHHHHhcCCC
Confidence 69999999999999999999999998889999999999999999999999999999998899999999999999999999
Q ss_pred CCCCccccCCC-CchhhhhhhcCccccccccccCCCCCCccceEEcCCCCCCCCcccccHHHHhhcCcceeechHHHHHH
Q 000829 190 RGVPFSMQVAR-PLSGFVQRLKGKQGRFRGNLSGKRVEYTGRTVISPDPNLKITEVAIPIRMARILTYPERVSDHNIEKL 268 (1265)
Q Consensus 190 ~~~~~~~~~~~-~~~~i~q~l~gK~G~fR~nl~GKRvd~saRsVIspDp~l~~~evGvP~~~A~~Lt~pe~Vt~~Ni~~l 268 (1265)
++.|.....++ +++||+|||+||+||||+|||||||||||||||+|||+|+++|||||..||++||+| ||+++|
T Consensus 1744 ~g~~~~~~~~r~~lksls~~LkGK~GRFR~NLlGKRVDySgRSVI~pdP~L~l~evGlP~~mA~eL~~P-----f~i~~L 1818 (2836)
T PRK14844 1744 RNALVNKAGAVGYKKSISDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELFKP-----FVYSKL 1818 (2836)
T ss_pred CCCCccCCCCCCccccHHHHhcCCCCcccccccccccccCCCceEeCCCCcccceeeCCHHHHHhcccH-----HHHHHH
Confidence 88766544334 589999999999999999999999999999999999999999999999999999997 577777
Q ss_pred HHHHHcCCCCCCCceEEECCCCCeEEeccccchhhhhcccccceeecccccCCeEEEecCCCccccceeeEEEEEecCCe
Q 000829 269 RQCIQNGPDKYPGARMIRYPDGTARVLYGKFRNQLAVELKSGCIVDRHLEDGDVVLFNRQPSLHRMSIMCHRARIMPWRT 348 (1265)
Q Consensus 269 ~~lv~ng~~~~pGa~~i~~~~g~~~~l~~~~r~~~~~~L~~g~iV~Rhl~dgD~VL~NRQPSLHk~Simah~vkv~~~kt 348 (1265)
+++... |..++ . ++........+|++++||+ +||+|||||||||||+|||||++++++++|
T Consensus 1819 ~~~~~~-----~~i~~------------a-~~li~~~~~~v~dile~vi-~gd~VLlNRqPTLHR~sIqAf~~~l~~gkt 1879 (2836)
T PRK14844 1819 KMYGMA-----PTIKF------------A-SKLIRAEKPEVWDMLEEVI-KEHPVLLNRAPTLHRLGIQAFEPILIEGKA 1879 (2836)
T ss_pred HHcCcc-----cchHH------------H-HHHHHhhCCcceEEEEEEe-cCCEEEecCCCccccccccceeeEeecCce
Confidence 765221 11111 1 1111123467789988776 589999999999999999999999999999
Q ss_pred eeeecccCCCCCCCCcccccccccCChHHHHHHHHHHcCCCcccccCCCCCccEeecccceeeeeeeeccCccC----CH
Q 000829 349 LRFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFY----DR 424 (1265)
Q Consensus 349 ~rln~~vc~~yNADFDGDEMN~h~PQs~~araEa~~Lm~~~~~~~sp~~g~pi~gliQD~l~g~~llT~~d~f~----~~ 424 (1265)
|||||+||+||||||||||||+|+|||++|||||+.||++.+|++||++|+|+++++||+++|+|+||.++.++ .+
T Consensus 1880 irlhp~vC~~fNADFDGDeMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pii~~~QD~ilG~y~LT~~~~~~~~~~~f 1959 (2836)
T PRK14844 1880 IQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLSPSNGRPIIVPSKDIVLGIYYLTLQEPKEDDLPSF 1959 (2836)
T ss_pred EEecccCCCcccCCCCCceeeeecCCcHHHHHHHHHHhCCcccEEecCCCceeEeehhhhhhhhhhhccccccccccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999854 55
Q ss_pred HHHHHHHHHhcCCCceeecCCCceeCccccc---------------ccceeeeeeecCCCCcceEEEEeecccccccccc
Q 000829 425 AAFSLMCCYMGDGMDRVDLPTPAILKPVELW---------------TGKQLFSVLIRPHANMRVYVNLTVKEKTYSNKLI 489 (1265)
Q Consensus 425 ~~~~~l~~~~~~~~~~~~lp~Pai~kp~~lw---------------TGKql~s~~l~~~~~~~~~in~~~~~k~~~~~~~ 489 (1265)
.+++++++++..+. ++.++.++|..+| .||++|+.+||+..
T Consensus 1960 ~~~~~~~~a~~~~~----~~i~~~i~~~~~~~~~~~~~~~~~~~tt~GR~if~~ilP~~~-------------------- 2015 (2836)
T PRK14844 1960 GAFCEVEHSLSDGT----LHIHSSIKYRMEYINSSGETHYKTICTTPGRLILWQIFPKHE-------------------- 2015 (2836)
T ss_pred CCHHHHHHHHHcCC----cccCceEEeeeccccCCCCcccceEecccHHHHHHHHcCCcc--------------------
Confidence 77888877655442 3445667777677 27777777775310
Q ss_pred cccCCccccccccCCCCCeeEEecCcceecccccccccCCCcccHHHHHHHHhChhhHHHHHhHHHHHHHHHHHhcccee
Q 000829 490 RTEGDEEIRIETMCPNDGFVYFRNSELISGQLGKATLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLSARWIGNHGFSI 569 (1265)
Q Consensus 490 ~~~~~~~~~~~~~~~~d~~v~i~~gell~G~ldK~~lG~~~~~~Li~~i~~~yG~~~a~~~l~~~~~l~~~~L~~~GFSi 569 (1265)
. .+++++.|.++|+.++ +||+.+|++||...|+.|||++++|+++|++.+|||+
T Consensus 2016 -----------~----------~~~~~~n~~l~KK~l~-----~II~~~~~~yG~~~t~~fLD~lk~LGf~yaT~~G~SI 2069 (2836)
T PRK14844 2016 -----------N----------LGFDLINQVLTVKEIT-----SIVDLVYRNCGQSATVAFSDKLMVLGFEYATFSGVSF 2069 (2836)
T ss_pred -----------c----------cCcceEeeeechhHHH-----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhccEEe
Confidence 0 0346778899999996 4999999999999999999999999999999999999
Q ss_pred eeccCCCCccchHHHHHHHHHHHHHHHHHHHHHHcCCCccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhcCC------C
Q 000829 570 GIDDVQPKKELSDKKGKLISENYEVCNVKIKEYNEGKLQLKPGCDAAQTLEAVITDILNRIREDAGKACMGSL------P 643 (1265)
Q Consensus 570 gi~D~~~~~~~~~~~~~~i~~a~~~~~~~i~~~~~g~l~~~~~~~~~~~le~~i~~~l~~~~~~~~~~~~~~l------~ 643 (1265)
|++|+.+++ ++.+++++|++++.++.++|++|.++. . ..++++..+|+++++++++.+++.+ +
T Consensus 2070 gi~Di~iP~----~K~~iI~~a~~~v~~i~~~y~~G~it~------~-Er~~kvi~iW~~~~d~v~~~~~~~l~~~~~~~ 2138 (2836)
T PRK14844 2070 SRCDMVIPE----TKATHVDHARGEIKKFSMQYQDGLITR------S-ERYNKVIDEWSKCTDMIANDMLKAISIYDGNS 2138 (2836)
T ss_pred eHhHcccCH----HHHHHHHHHHHHHHHHHHHHHcCCCCH------H-HHHHHHHHHHHHHHHHHHHHHHHhhhhccccC
Confidence 999999874 567789999999999999999999862 2 3678999999999999999998866 2
Q ss_pred CCCcceeeeccCCCCChhcHhHHhhcccccccCCCCCCCCCCCcccCCCCCCCCCCCccceeccccccCCChhhhhhhhc
Q 000829 644 WRNSPLIMSQCGSKGSPINISQMVACVGQQSVGGRRAPNGFIDRSLPHFPRKAKEPAAKGFVANSFYSGLSATEFFFHTM 723 (1265)
Q Consensus 644 ~~N~~~~M~~sGsKGS~~Ni~Qi~~~lGQQ~~~G~Rip~~~~~rtLP~f~~~~~~~~a~GfV~~sf~~GL~p~EfFfH~m 723 (1265)
+.||+++|+.||||||..|+.|++||+||+.. |.|.. ...+|.|||++||+|.|||||||
T Consensus 2139 ~~N~i~mMa~SGARGS~sQI~QLaGmRGLmak-----p~G~i---------------Ie~PI~SNFrEGLsv~EyFiSt~ 2198 (2836)
T PRK14844 2139 KYNSVYMMVNSGARGSTSQMKQLAGMRGLMTK-----PSGEI---------------IETPIISNFREGLNVFEYFNSTH 2198 (2836)
T ss_pred CCCceeeeecccCccCHHHHHHHHhcceeeec-----CCCCe---------------eecchhhhhccCCCHHHhhhhcc
Confidence 57999999999999999999999999999753 43321 11349999999999999999999
Q ss_pred cccccchhcccccCcCChhHHHHHHHhhheEeeecCeEEcCCCcEEEEE-ecCCCcccccccCCCCCCchhHHHHHHHH-
Q 000829 724 GGREGLVDTAVKTADTGYMSRRLIKALEDLSIQYDNSVRNAGGCIVQFL-YGDDGMDPANMEGKSGEPLNFDRLLMKVK- 801 (1265)
Q Consensus 724 ~GReGLiDTAvKTa~sGYlqRrLvk~lEdl~v~YD~TVR~s~g~iiQf~-YGeDG~d~~~~~~~~~~~~~~~~~~~~~~- 801 (1265)
||||||+|||+|||+|||||||||+++||++|.-+.+ -+..|-.+.-. .|++-+. ++. ++++..+.
T Consensus 2199 GaRKGL~DTALKTAdSGYLTRRLVDVaQDviI~e~DC-gT~~Gi~v~~~~~~~~~i~----------~L~-~ri~GR~~a 2266 (2836)
T PRK14844 2199 GARKGLADTALKTANSGYLTRRLVDVSQNCIVTKHDC-KTKNGLVVRATVEGSTIVA----------SLE-SVVLGRTAA 2266 (2836)
T ss_pred ccccchhhhhhhcccccchhhhhhhhhceEEEEeccc-CCCCceEEEEeccCCeEEe----------Ehh-heeEEEEEH
Confidence 9999999999999999999999999999999954321 11234444332 2211000 000 11111100
Q ss_pred -hcCCCCCCCCCCHHHHHHHHHHHHhhcCCCcchHHHHHHHHHHHHHhhhhhhhhhhcccccCCCccchhhhhhhhhccC
Q 000829 802 -ATCPPAGQRYLSPQQVSEIVEKQLAAYGKESCSEAFLNSLRKFFEGQQDKLDKKIKFVEDIGWDDKSQILEEVTHKTSG 880 (1265)
Q Consensus 802 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~~~~~~l~~~~~~~~~~~l~~~~~~~~~~~~~~~~ 880 (1265)
.+........+ ...++ ...+...+. +... |+. .+..++.
T Consensus 2267 ~di~~p~t~~~i------------~~~~~--~I~~~~~~~-----------i~~~-------gi~--------~v~IRS~ 2306 (2836)
T PRK14844 2267 NDIYNPVTKELL------------VKAGE--LIDEDKVKQ-----------INIA-------GLD--------VVKIRSP 2306 (2836)
T ss_pred hHeEcCCCCCEE------------EeCCC--ccCHHHHHH-----------HHHc-------CCC--------EEEEcCC
Confidence 00000000000 00000 011111111 1100 111 2234467
Q ss_pred CCHHHHHHHHHHHHHh--hhcccCCcCccceeecccccCCccccccccccccccccccc
Q 000829 881 ITEKQLEVFIQTCFSR--YRVKRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMN 937 (1265)
Q Consensus 881 ~~~~~~~~~~~~~~~k--y~~slv~PGEaVG~IAAQSIGEPsTQMTLnTFH~AGv~~~N 937 (1265)
+||+.-..+|+.||-. -...+|+.|||||+|||||||||+||+||+|||.+|+++..
T Consensus 2307 ltC~s~~gvC~~CYG~~La~~~~V~iGeaVGiIAAQSIGEPGTQLTMRTFHtGGvas~~ 2365 (2836)
T PRK14844 2307 LTCEISPGVCSLCYGRDLATGKIVSIGEAVGVIAAQSVGEPGTQLTMRTFHIGGVMTRG 2365 (2836)
T ss_pred eeECCCCCChhhccCccccCCCcccccccceeeeecccCCCcceeeeeheeeccccccc
Confidence 8887777777777632 35689999999999999999999999999999999997533
No 12
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]
Probab=100.00 E-value=1.4e-135 Score=1266.43 Aligned_cols=664 Identities=34% Similarity=0.487 Sum_probs=591.6
Q ss_pred CcCCCCCCCCCcEEecceeeeEEEecccchhhHHHHhhhhhcchhhhhhhhccccccCHHHHHHHHHhcChhhHHhhcCC
Q 000829 30 VKCPRCGYINGMVKKAVAVLGIIHDRSKVTESLQEFASAITHTKESKAAVNVATYILNPVNVLFLFKRMTDTDCEVLYLS 109 (1265)
Q Consensus 30 ~~C~~Cg~~~p~Vrk~~~~~ki~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~L~P~~v~~ifk~I~~ed~~lL~~~ 109 (1265)
..|++||+.++++++.+. .++.+ . + . +.++|.+++++|++|+..|+++++.
T Consensus 128 ~~~~~~Ga~~~~~~~~~~--~~~~~-------------~----~--------~-~~~~~~~~~~~~~~l~~~d~~~~~~- 178 (808)
T COG0086 128 SFCAHCGAEAIKILLEKP--DLETE-------------R----E--------E-ETLSPTKVKKLLKRLKVVDAFLLSG- 178 (808)
T ss_pred ccCCCCCchhHHHHHhCc--chhhh-------------h----h--------h-cccCHHHHHHHHhhccHHHHHHhcC-
Confidence 789999999999988774 22111 0 0 1 5789999999999999999999997
Q ss_pred CCcceEEEeeeeeCCCCCCCceecCCCCcCCchhHHHHHHHHHHHHHHHHHHHHhccchhhhHHHHHHHHHHHHHhccCC
Q 000829 110 ERPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQQELVEANSAFKSLAGWETLQVEVAQYINSDV 189 (1265)
Q Consensus 110 ~~p~~~~l~~lpVpP~~~RP~~~~~~~~~~~ddlt~~l~~Ii~~n~~l~~~~~~~~~~~~~~~~~~~lq~~v~~~~~~~~ 189 (1265)
++|+||+|++||||||++||++.++++.+++||||.+|++||+.|++|++++..+++ ..+.+.|++||++|++||||
T Consensus 179 ~~pewmil~vlpV~Pp~~RP~i~ld~g~~a~~dl~~~~~~ii~~n~rlk~~~~~~~~-~iv~~~~~~lQ~~v~~~~Dn-- 255 (808)
T COG0086 179 NRPEWMILTVLPVPPPDLRPSIQLDGGRFAESDLNDLYRRVINRNNRLKRLLELAAP-IIVRNEKRMLQEAVDALFDN-- 255 (808)
T ss_pred CCcceeEEEeeccCCCCCCcceecCCCccchhHHHHHHHHHHHHHHHhHHhhhhcch-HHHHHHHHHHHHHHHHHhhc--
Confidence 699999999999999999999999999999999999999999999999999988555 88999999999999999999
Q ss_pred CCCCccccCCCCchhhhhhhcCccccccccccCCCCCCccceEEcCCCCCCCCcccccHHHHhhcCcceeechHHHHHHH
Q 000829 190 RGVPFSMQVARPLSGFVQRLKGKQGRFRGNLSGKRVEYTGRTVISPDPNLKITEVAIPIRMARILTYPERVSDHNIEKLR 269 (1265)
Q Consensus 190 ~~~~~~~~~~~~~~~i~q~l~gK~G~fR~nl~GKRvd~saRsVIspDp~l~~~evGvP~~~A~~Lt~pe~Vt~~Ni~~l~ 269 (1265)
+.|.+.+.++|+|||+||||||+||||+|||||||||||||||||||+|+++|||||..||++||+||+||++|++.++
T Consensus 256 -~~~~~~~~~rPlksl~~~LkgK~GrFR~nL~GKRVd~SgRsVI~~~P~l~~~e~GvP~~~A~~L~~p~~v~~~~~~~~~ 334 (808)
T COG0086 256 -RRPRAVTGGRPLKSLSQRLKGKQGRFRQNLLGKRVDYSGRSVISVGPNLKLNQCGVPKKMALELFKPFVVTELNIEGLR 334 (808)
T ss_pred -CCCCCccCCCccccHHHHhcCCCceeeccccccccCCCCceeecCCCCccccccCCHHHHHHHhccCEEEEehhhhhhh
Confidence 3333323269999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHcCCCCCCCceEEECCCCCeEEeccccchhhhhcccccceeecccccCCeEEEecCCCccccceeeEEEEEec-CCe
Q 000829 270 QCIQNGPDKYPGARMIRYPDGTARVLYGKFRNQLAVELKSGCIVDRHLEDGDVVLFNRQPSLHRMSIMCHRARIMP-WRT 348 (1265)
Q Consensus 270 ~lv~ng~~~~pGa~~i~~~~g~~~~l~~~~r~~~~~~L~~g~iV~Rhl~dgD~VL~NRQPSLHk~Simah~vkv~~-~kt 348 (1265)
+ ||+|+++.+++ .+..+|.|+||+.+||+|||||||||||+|||+|++++++ ++|
T Consensus 335 ~----------~a~~~~~~~~~--------------~~~~~w~Vl~evi~gd~Vl~NR~PtLHrlsImq~~e~vl~~gkt 390 (808)
T COG0086 335 T----------GAKYAKRMVER--------------RLPEVWDVLREVIDGDPVLLNRAPTLHRLSIMQAFEPVLPEGKA 390 (808)
T ss_pred c----------CCceEEecccc--------------cccccchHHHHHhcCCccccccCChHHHHHHHhhceeeccccce
Confidence 8 89999987652 2778999999999999999999999999999999999998 899
Q ss_pred eeeecccCCCCCCCCcccccccccCChHHHHHHHHHHcCCCcccccCCCCCccEeecccceeeeeeeeccCccCCHHHHH
Q 000829 349 LRFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDRAAFS 428 (1265)
Q Consensus 349 ~rln~~vc~~yNADFDGDEMN~h~PQs~~araEa~~Lm~~~~~~~sp~~g~pi~gliQD~l~g~~llT~~d~f~~~~~~~ 428 (1265)
|||||+||.||||||||||||+|+|||.+|+|||+.||.+++|++||++|+|+++++||+|+|.||||..|+|++.++++
T Consensus 391 ~rLh~lVc~~yNADFDGDeM~~Hvp~s~ea~AEa~~lm~tq~nilsP~~Ggpiv~~~qD~v~g~ylLt~~d~~~~~~~~~ 470 (808)
T COG0086 391 IRLHPLVCEAYNADFDGDEMAVHVPASGEAAAEARGLMGTQMNILTPHYGGPIVAPIQDTVGGPYLLTIVDAKLPSTPVG 470 (808)
T ss_pred eecchhhccccccccCchhhhccccchHHHHHHHHHhhccccccccCCCCCceEeecceEEeccEEEEEecccCCCCcce
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcCCCceeecCCCceeCcccccccceeeeeeecCCCCcceEEEEeecccccccccccccCCccccccccCCC-CC
Q 000829 429 LMCCYMGDGMDRVDLPTPAILKPVELWTGKQLFSVLIRPHANMRVYVNLTVKEKTYSNKLIRTEGDEEIRIETMCPN-DG 507 (1265)
Q Consensus 429 ~l~~~~~~~~~~~~lp~Pai~kp~~lwTGKql~s~~l~~~~~~~~~in~~~~~k~~~~~~~~~~~~~~~~~~~~~~~-d~ 507 (1265)
+++.+-. .....-+.|||.+|..+|||||+++.+++........++...+.... .....+ |.
T Consensus 471 ei~l~~~--~~~~~e~~~ai~~~~~~~~~k~i~~~i~~~~~~~~i~~t~~~~~~~~---------------~~~~~~~d~ 533 (808)
T COG0086 471 EIYLKDE--YADDREKAEAIAKKIELTTGKVIVSTISPDLAELSIIVTTDGRRIFN---------------RGLPEDKDV 533 (808)
T ss_pred EEEeccc--cccchhhhHHHhcccceeeeeEEEEEeeccCCcceEEEecchhhhhh---------------ccCCcccce
Confidence 8865411 11234578999999999999999998886543222222222111100 111122 57
Q ss_pred eeEEecCcceecccccccccCCCcccHHHHHHHHhChhhHH-HHHhHHHHHHHHHHHhcc-ceeeeccCCCCccchHHHH
Q 000829 508 FVYFRNSELISGQLGKATLGNGNKDGLYSVLLRDYGAHATS-GCMNRLAKLSARWIGNHG-FSIGIDDVQPKKELSDKKG 585 (1265)
Q Consensus 508 ~v~i~~gell~G~ldK~~lG~~~~~~Li~~i~~~yG~~~a~-~~l~~~~~l~~~~L~~~G-FSigi~D~~~~~~~~~~~~ 585 (1265)
.+.|.|++++.|++||... .+++.||+..+. .+++.+.+|...|+...| |+++++|.. .++.++++
T Consensus 534 ~~~i~~~~l~~~~i~k~~~----------~i~~~~g~~~~~~~~~~~~dkl~~~~~~~~~~~~~~i~~~d--~~~~~~~~ 601 (808)
T COG0086 534 LVKIVNGKLIKGVIDKKIV----------TIYREYGPEVASKALVKLLDKLKNLGIKGIGGFGIGIGRKD--IEAEDEKD 601 (808)
T ss_pred eeEEeccccceeeehhhHH----------HHHHHhCchhhHHHHHHHHHHHHHhheeeeccceEEeeccc--ccchHHHH
Confidence 8999999999999988654 778999998888 999999999999999987 999999876 34677888
Q ss_pred HHHHHHHHHHHHHHHHHHcCCCccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcceeeeccCCCCChhcHhH
Q 000829 586 KLISENYEVCNVKIKEYNEGKLQLKPGCDAAQTLEAVITDILNRIREDAGKACMGSLPWRNSPLIMSQCGSKGSPINISQ 665 (1265)
Q Consensus 586 ~~i~~a~~~~~~~i~~~~~g~l~~~~~~~~~~~le~~i~~~l~~~~~~~~~~~~~~l~~~N~~~~M~~sGsKGS~~Ni~Q 665 (1265)
+.+.+|+.++.+++.+|+.|.++..++.+..+.+|.++++.+++++.+.++.+......+ +..|..+|++||..|++|
T Consensus 602 e~v~~ae~~v~~~i~~~~~g~lt~~~~~~i~e~~e~~~~e~l~~ai~~~~~~~~~~~g~~--~~~i~~m~~~Gs~~n~sq 679 (808)
T COG0086 602 EIVIEAEGSVLKLILQYEEGDLTRTERNNIVEIIEVLGIEALRNAIIEEIKITLEEQGLD--FVDIRHMGLSGARMNISQ 679 (808)
T ss_pred HHHHHHHHHHHHHHHHhhcCCccccCCCCeEEEeehHHHHHHHHHHHHHHhhhHHhcCCc--chhHHHHhhhhhccCHHH
Confidence 999999999999999999999999999999999999999999999999988887766665 667777778888889999
Q ss_pred HhhcccccccCCCCCCCCCCCcccCCCCCCCCCCCccceeccccccCCChhhhhhhhccccccchhcccccCcCChhHHH
Q 000829 666 MVACVGQQSVGGRRAPNGFIDRSLPHFPRKAKEPAAKGFVANSFYSGLSATEFFFHTMGGREGLVDTAVKTADTGYMSRR 745 (1265)
Q Consensus 666 i~~~lGQQ~~~G~Rip~~~~~rtLP~f~~~~~~~~a~GfV~~sf~~GL~p~EfFfH~m~GReGLiDTAvKTa~sGYlqRr 745 (1265)
|.+|+|||.+.|+|++.+ +||||.+.+..+++.|||.+||++||+|.|||||+|+||+||||||+|||+|||||||
T Consensus 680 ~~~~iG~~gv~g~r~~~~----~~~~Fe~~~~~~~a~~~i~s~f~eGLt~~e~f~~~~ggR~GlvDTA~KTa~sGYl~Rr 755 (808)
T COG0086 680 IVQLIGQQGVMGEKISVL----ARAAFEVTVKHLEAEGPGESSFLEGLTENEYFGHPIGGRTGLVDTALKTADSGYLTRR 755 (808)
T ss_pred HHHHhhhheeeccCCCcc----cccccccccccceeeeeeecccCCCCCcceEEeecCccccchHHHhhhhcccCcceEE
Confidence 999999999999999988 9999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhheEeeecCeEEcCCCcEEEEEecCCCcccccccC
Q 000829 746 LIKALEDLSIQYDNSVRNAGGCIVQFLYGDDGMDPANMEG 785 (1265)
Q Consensus 746 Lvk~lEdl~v~YD~TVR~s~g~iiQf~YGeDG~d~~~~~~ 785 (1265)
||+++|||+|+||+|||++.+.++||.|||||+|+++...
T Consensus 756 Lv~~~qdl~v~~d~~~~~g~~~~~~~~~ged~~~~~~~~~ 795 (808)
T COG0086 756 LVDVAQDLIVQEDDCVTDGIGVVIQFEYGEDGEDLTERIL 795 (808)
T ss_pred eechhcceEEEecCeEeecCceEEEEecCccccCHHHHhc
Confidence 9999999999999999998899999999999999987653
No 13
>smart00663 RPOLA_N RNA polymerase I subunit A N-terminus.
Probab=100.00 E-value=1.9e-95 Score=815.12 Aligned_cols=293 Identities=49% Similarity=0.778 Sum_probs=277.9
Q ss_pred ceEEEeeeeeCCCCCCCceecCCCCcCCchhHHHHHHHHHHHHHHHHHHHHhccchhhhHHHHHHHHHHHHHhccCCCCC
Q 000829 113 EKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQQELVEANSAFKSLAGWETLQVEVAQYINSDVRGV 192 (1265)
Q Consensus 113 ~~~~l~~lpVpP~~~RP~~~~~~~~~~~ddlt~~l~~Ii~~n~~l~~~~~~~~~~~~~~~~~~~lq~~v~~~~~~~~~~~ 192 (1265)
+||||++|||||+|+||++.++++..++||+|.+|++||+.|+.|++....|++...+.+.|..||.+|+.|+||+ +.
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 6999999999999999999998877999999999999999999999998888888888899999999999999998 33
Q ss_pred Ccccc-CCCCchhhhhhhcCccccccccccCCCCCCccceEEcCCCCCCCCcccccHHHHhhcCcceeechHHHHHHHHH
Q 000829 193 PFSMQ-VARPLSGFVQRLKGKQGRFRGNLSGKRVEYTGRTVISPDPNLKITEVAIPIRMARILTYPERVSDHNIEKLRQC 271 (1265)
Q Consensus 193 ~~~~~-~~~~~~~i~q~l~gK~G~fR~nl~GKRvd~saRsVIspDp~l~~~evGvP~~~A~~Lt~pe~Vt~~Ni~~l~~l 271 (1265)
+.... .+++++||+|||+||+|+||+|||||||||||||||||||+|++||||||..||++||+||.||.||+++|+++
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 32222 26889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHcCCCCCCCceEEECCCCCeEEe-ccccchhhhhcccccceeecccccCCeEEEecCCCccccceeeEEEEEecCCeee
Q 000829 272 IQNGPDKYPGARMIRYPDGTARVL-YGKFRNQLAVELKSGCIVDRHLEDGDVVLFNRQPSLHRMSIMCHRARIMPWRTLR 350 (1265)
Q Consensus 272 v~ng~~~~pGa~~i~~~~g~~~~l-~~~~r~~~~~~L~~g~iV~Rhl~dgD~VL~NRQPSLHk~Simah~vkv~~~kt~r 350 (1265)
|.||+ |||+||++ |++..| +. ++.+.+..|++||+|+||++|||+|||||||||||+|||||+|+|++++|||
T Consensus 159 v~ng~---pga~~i~~--g~~~~l~~~-~~~~~~~~l~~g~~v~r~l~dgd~Vl~NRqPsLHr~si~a~~v~v~~~~tir 232 (295)
T smart00663 159 VRNGP---NGAKYIIR--GKKTNLKLA-KRSKIAKHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIR 232 (295)
T ss_pred HhcCC---CCceEEEe--CcEEEchhh-hhHHHHhcCccccEeheehhcCCEEEEecCCccccccceeEEEEEecCceEE
Confidence 99999 99999997 777777 54 5666889999999999999999999999999999999999999999999999
Q ss_pred eecccCCCCCCCCcccccccccCChHHHHHHHHHHcCCCcccccCCCCCccEeecccceeeee
Q 000829 351 FNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILVASTQDFLTSSF 413 (1265)
Q Consensus 351 ln~~vc~~yNADFDGDEMN~h~PQs~~araEa~~Lm~~~~~~~sp~~g~pi~gliQD~l~g~~ 413 (1265)
|||++|+||||||||||||+|+|||++|||||.+||.+.+|++||++|+|++|++||+++|+|
T Consensus 233 ~n~~~c~~fNADFDGDeMnih~pqs~~a~aEa~~Lm~~~~~~~sp~~g~p~~~~~QD~l~g~~ 295 (295)
T smart00663 233 LNPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295 (295)
T ss_pred ecCccCCcccCCcCCCEEEEecCCCHHHHHHHHHHhhhhhccccCCCCCeeEeeecceeeecC
Confidence 999999999999999999999999999999999999999999999999999999999999987
No 14
>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=4.9e-91 Score=798.34 Aligned_cols=348 Identities=42% Similarity=0.638 Sum_probs=315.3
Q ss_pred cCCCHH-HHHHHHHHHHHhhhcccCCcCccceeecccccCCccccccccccccccccccceecccchhHhhhhccccccc
Q 000829 879 SGITEK-QLEVFIQTCFSRYRVKRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINGAKRIST 957 (1265)
Q Consensus 879 ~~~~~~-~~~~~~~~~~~ky~~slv~PGEaVG~IAAQSIGEPsTQMTLnTFH~AGv~~~NVTlGvPRLkEIinask~ikT 957 (1265)
++++.+ +++||+++|..+|.+++++||||||+|||||||||+|||||||||||||++||||+|||||+|||||+|+|||
T Consensus 17 ~~~~~~~~~~~~l~~i~~ky~~alv~PGeaVG~IAAQSIGEP~TQMTLnTFH~AGVas~nVTlGVPRlkEIINa~k~i~T 96 (367)
T TIGR02389 17 REISDKEELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDARKTPST 96 (367)
T ss_pred cCCCHHHHHHHHHHHHHHHHHHhcCCCccccchhhhhhcCCccccccccccccccccccCccccchhHHHHhhcccCCCC
Confidence 457877 9999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceEEEEccCC--CcHHHHHHHhcceeEEeccccceeEEEEEeCCccEEEEEeChhhHHHhhcccCHHHHHHHHhcCcccc
Q 000829 958 PIITAELECN--DNENAARVVKGRIEKTLLGQVAKSIKIVMTSRLASIVIALDMETIQDAHLCINADIVKESIVQTPKIK 1035 (1265)
Q Consensus 958 P~~ti~l~~~--~~~~~a~~v~~~le~~~L~di~~~i~~~y~~~~~~~~i~ld~~~i~~~~~~i~~~~i~~~i~~~~k~k 1035 (1265)
|+|+++|.++ .+.+.|+.++++||+++|+|++.+++++|. ..+++++||.+.+... .+++++|.++|.+.++.+
T Consensus 97 P~~ti~L~~~~~~~~~~a~~v~~~iE~t~l~dv~~~~~~~~~--~~~l~i~ld~~~l~~~--~i~~~~i~~~i~~~~~~~ 172 (367)
T TIGR02389 97 PSMTIYLEDEYEKDREKAEEVAKKIEATKLEDVAKDISIDLA--DMTVIIELDEEQLKER--GITVDDVEKAIKKAKLGK 172 (367)
T ss_pred CeEEEEecCcchhhHHHHHHHHHHhhheeHHHHHhhhheecc--CcEEEEEECHHHHHhc--CCCHHHHHHHHHHhcccc
Confidence 9999999875 467899999999999999999999998885 3579999999999875 589999999998764221
Q ss_pred cccCceeeeccceEEEeCCCCCCcceeehHHHhhhcCCcEEecccCceEEEEeccccccchhhccCCcccEEEEEeCccH
Q 000829 1036 LKQQHIKVLDFRKLEIFPPVDKSKIHFELYSLKNVLPMVIVKGIKTVERVVIAEKEKEKRKVKENGEKKKYRLLVEGTGL 1115 (1265)
Q Consensus 1036 ~~~~~i~~~~~~~~~i~~~~~~~~~~~~l~~l~~~l~~~~v~Gi~~I~r~~i~~~~~~~~~~~~~~~~~~~~l~teG~nl 1115 (1265)
.. .+ ...+..+++++.+ +.++.++.++..+++++|+|+|||+||++.. .+++|.|+|||.||
T Consensus 173 ~~--~~-~~~~~~i~i~~~~---~~~~~l~~l~~~l~~~~v~Gi~gI~r~~i~~------------~~~~~~l~teG~nl 234 (367)
T TIGR02389 173 VI--EI-DMDGNTITIKPPK---PSLKELRKLKEKIKNLHIKGIKGIKRVVIRK------------EGDEYVIYTEGSNL 234 (367)
T ss_pred cc--ee-ecCCCEEEEEecC---chHHHHHHHHHHhhhceEeCCCCceEEEEEC------------CCCeEEEEEeccCH
Confidence 11 11 1123456666531 2345588888899999999999999999873 24579999999999
Q ss_pred HHhhccCCccccccccCCHHHHHHHhCHHHHHHHHHHHHHHHhhccccccCcccceeeecccccccEEEeeccccccccC
Q 000829 1116 QAVMGAEGIDGCKTKSNHIFEVQQTLGIEAARICIIDEINETMKAHGMSIDKRHMMLLADLMTFRGEVLGITRFGIQKMD 1195 (1265)
Q Consensus 1116 ~~~~~~~~VD~~~~~sNdI~ev~~~lGIEAAR~~Iv~Ei~~v~~~~Gi~Vd~RHl~LlAD~MT~~G~~~~i~R~Gi~~~~ 1195 (1265)
.++|.+++||+++++||||++|+++|||||||++|++||+.||+.||++||+|||+||||+||++|+++||||+||++++
T Consensus 235 ~~v~~~~~VD~~rt~sNdI~ei~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~RHl~LiaD~MT~~G~~~~i~R~Gi~~~~ 314 (367)
T TIGR02389 235 KEVLKLEGVDKTRTTTNDIHEIAEVLGIEAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEK 314 (367)
T ss_pred HHHHcCCCCccccCccCCHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCeecHHHHHHHHHHhcCCceEEeccccccccCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999998888
Q ss_pred CcHhhHhcchHHHHHHHHhhhcCCcccccccccceeccCCCCCCccceEeeec
Q 000829 1196 KSVLMLASFEKTADHLFNASVNGRDDRIEGVSECIIMGIPMPLGTGILKIRQR 1248 (1265)
Q Consensus 1196 ~Spl~~aSFE~T~~~L~~AA~~g~~D~l~gvS~~Ii~Gk~~~~GTG~fdll~~ 1248 (1265)
+|||++||||+|+++|++||.+|+.|+|+||||||++|+++|+|||+|||+++
T Consensus 315 ~S~l~~aSFE~t~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~~~l~~~ 367 (367)
T TIGR02389 315 ASVLARAAFEVTVKHLLDAAIRGEVDELAGVIENIIVGQPIPLGTGDVDLVMD 367 (367)
T ss_pred CCHHHhcChHhHHHHHHHHhhcCCCCcCCChHHHhhcCCCcCCcCCeEEEeeC
Confidence 99999999999999999999999999999999999999999999999999874
No 15
>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=1.8e-89 Score=796.76 Aligned_cols=362 Identities=36% Similarity=0.551 Sum_probs=314.3
Q ss_pred CCCHHHHHHHHHHHHHhhhcccCCcCccceeecccccCCccccccccccccccccccceecccchhHhhhhcccccccce
Q 000829 880 GITEKQLEVFIQTCFSRYRVKRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINGAKRISTPI 959 (1265)
Q Consensus 880 ~~~~~~~~~~~~~~~~ky~~slv~PGEaVG~IAAQSIGEPsTQMTLnTFH~AGv~~~NVTlGvPRLkEIinask~ikTP~ 959 (1265)
+++.+++++|+.+|..+|.+++++||||||++||||||||+|||||||||||||+++|||+|||||||||||+|+||||+
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~ge~vg~~aaQSiGEP~TQmTLnTFH~AGVas~NVTlGVPRLkEIInasK~ikTP~ 81 (410)
T cd02584 2 RLNKEAFDWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKNIKTPS 81 (410)
T ss_pred CCCHHHHHHHHHHHHHHHHHhhcCCCCCcchhhhhhcCCchhcccccccccccccccccccCccchHHHhhcccCCCCCe
Confidence 57889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEccCC--CcHHHHHHHhcceeEEeccccceeEEEEEeCCccEEEEEeChhhHHHhh------------------c--
Q 000829 960 ITAELECN--DNENAARVVKGRIEKTLLGQVAKSIKIVMTSRLASIVIALDMETIQDAH------------------L-- 1017 (1265)
Q Consensus 960 ~ti~l~~~--~~~~~a~~v~~~le~~~L~di~~~i~~~y~~~~~~~~i~ld~~~i~~~~------------------~-- 1017 (1265)
|+++|.++ .+.+.|+.++++||+++|+|++.+++++|+|+..++.+++|.++++.++ +
T Consensus 82 ~tv~L~~~~~~d~~~A~~v~~~IE~t~l~dv~~~~~i~ydp~~~~~~i~~d~~~i~~~~~~~d~~~~~~~~~~~~lrl~l 161 (410)
T cd02584 82 LTVYLEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVESYFEFPDEDVEQDRLSPWLLRIEL 161 (410)
T ss_pred EEEEecCcccchHHHHHHHHhheeEeEHHHhhhheEEEecCcccceeecccHHHHHHhhccCcccccccccCCeeEEEEE
Confidence 99999987 6799999999999999999999999999999988888888887777654 2
Q ss_pred --------ccCHHHHHHHHhcCcccccccCceeee--ccc----eEEEeCCCCC-------CcceeehHHHhhhcCCcEE
Q 000829 1018 --------CINADIVKESIVQTPKIKLKQQHIKVL--DFR----KLEIFPPVDK-------SKIHFELYSLKNVLPMVIV 1076 (1265)
Q Consensus 1018 --------~i~~~~i~~~i~~~~k~k~~~~~i~~~--~~~----~~~i~~~~~~-------~~~~~~l~~l~~~l~~~~v 1076 (1265)
.+++++|..+|...++ +++.+. .+. .+++++.... .+..|..+.++..+++++|
T Consensus 162 d~~~~~~~~i~~~~i~~~i~~~~~-----~~~~v~~~~~~~~~~~iri~~~~~~~~~~~~~~~~~~l~~~~~~~l~~i~l 236 (410)
T cd02584 162 DRKKMTDKKLSMEQIAKKIKEEFK-----DDLNVIFSDDNAEKLVIRIRIINDDEEKEEDSEDDVFLKKIESNMLSDMTL 236 (410)
T ss_pred CHHHHHHcCCCHHHHHHHHHHhcC-----CCeEEEEcCCCcceeEEEEEecCccccccccchhHHHHHHHHHhhCCCcEE
Confidence 3456666666665321 122221 111 3555543111 1123444555688999999
Q ss_pred ecccCceEEEEeccccccchhh-c---cCCcccEEEEEeCccHHHhhccCCccccccccCCHHHHHHHhCHHHHHHHHHH
Q 000829 1077 KGIKTVERVVIAEKEKEKRKVK-E---NGEKKKYRLLVEGTGLQAVMGAEGIDGCKTKSNHIFEVQQTLGIEAARICIID 1152 (1265)
Q Consensus 1077 ~Gi~~I~r~~i~~~~~~~~~~~-~---~~~~~~~~l~teG~nl~~~~~~~~VD~~~~~sNdI~ev~~~lGIEAAR~~Iv~ 1152 (1265)
+|+|||+|+++..++ ...+. + .+++++|.|+|||+||+++|.+++||+++++||||++|+++|||||||++|++
T Consensus 237 ~Gi~~I~r~~i~~~~--~~~~~~~~g~~~~~~~~~l~teG~nl~~v~~~~~Vd~~rt~sNdI~ei~~~lGIEAaR~~ii~ 314 (410)
T cd02584 237 KGIEGIRKVFIREEN--KKKVDIETGEFKKREEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEVLGIEAARKALLK 314 (410)
T ss_pred eCCCCceEEEEEcCC--ceEecCCCCcccCCcceEEEecCcCHHHHhCCCCCccccCEeCCHHHHHHhcCHHHHHHHHHH
Confidence 999999999997432 11111 0 11345799999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhccccccCcccceeeecccccccEEEeeccccccccCCcHhhHhcchHHHHHHHHhhhcCCcccccccccceec
Q 000829 1153 EINETMKAHGMSIDKRHMMLLADLMTFRGEVLGITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDDRIEGVSECIIM 1232 (1265)
Q Consensus 1153 Ei~~v~~~~Gi~Vd~RHl~LlAD~MT~~G~~~~i~R~Gi~~~~~Spl~~aSFE~T~~~L~~AA~~g~~D~l~gvS~~Ii~ 1232 (1265)
||++||+.||++||+|||+||||+||++|+++||||+||+++++|||++||||+|+++|++||++|+.|+|+|||||||+
T Consensus 315 Ei~~v~~~~Gi~Vd~RHl~LiaD~MT~~G~~~~i~R~Gi~~~~~S~l~~aSFE~t~~~L~~AA~~g~~D~l~gvse~Ii~ 394 (410)
T cd02584 315 ELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVSENIML 394 (410)
T ss_pred HHHHHHHhcCCccCHHHHHHHHHHHhhceEEeeEeeeeeeccCCChhhhccchhHHHHHHHHHhcCCCCcCCCchHheee
Confidence 99999999999999999999999999999999999999998889999999999999999999999999999999999999
Q ss_pred cCCCCCCccceEeeec
Q 000829 1233 GIPMPLGTGILKIRQR 1248 (1265)
Q Consensus 1233 Gk~~~~GTG~fdll~~ 1248 (1265)
|+++|+|||+|||++|
T Consensus 395 G~~~~~GTG~f~l~~d 410 (410)
T cd02584 395 GQLAPIGTGCFDLLLD 410 (410)
T ss_pred cCccccccceEEEEeC
Confidence 9999999999999985
No 16
>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=7.1e-89 Score=781.99 Aligned_cols=351 Identities=40% Similarity=0.605 Sum_probs=317.4
Q ss_pred hhhccCCCHHHHHHHHHHHHHhhhcccCCcCccceeecccccCCccccccccccccccccccceecccchhHhhhhcccc
Q 000829 875 THKTSGITEKQLEVFIQTCFSRYRVKRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINGAKR 954 (1265)
Q Consensus 875 ~~~~~~~~~~~~~~~~~~~~~ky~~slv~PGEaVG~IAAQSIGEPsTQMTLnTFH~AGv~~~NVTlGvPRLkEIinask~ 954 (1265)
+...++++.++++||++++..+|.+++++||||||++||||||||+|||||||||||||++||||+|||||+|||||+|+
T Consensus 10 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~Ge~vG~iaAQSiGEP~TQMTLnTFH~AGVas~nVTlGVPRlkEIIna~K~ 89 (363)
T cd06528 10 VLKEHGLTLSEAEEIIKEVLREYLRSLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRLIEIVDARKE 89 (363)
T ss_pred HHHHcCCCHHHHHHHHHHHHHHHHHHhhccCccccceeeeecCccceecccccccccccccccCccccccHHHHhhcccC
Confidence 34556899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccceEEEEccCC--CcHHHHHHHhcceeEEeccccceeEEEEEeCCccEEEEEeChhhHHHhhcccCHHHHHHHHhcCc
Q 000829 955 ISTPIITAELECN--DNENAARVVKGRIEKTLLGQVAKSIKIVMTSRLASIVIALDMETIQDAHLCINADIVKESIVQTP 1032 (1265)
Q Consensus 955 ikTP~~ti~l~~~--~~~~~a~~v~~~le~~~L~di~~~i~~~y~~~~~~~~i~ld~~~i~~~~~~i~~~~i~~~i~~~~ 1032 (1265)
||||+|+++|.++ .+.+.|+.++++||+++|+|++.++++.+ ..++++++||.+.+.++ .+++++|.++|.+.+
T Consensus 90 i~TP~mti~L~~~~~~~~~~a~~v~~~iE~t~l~di~~~~~i~~--~~~~l~i~ld~~~l~~~--~l~~~~i~~~i~~~~ 165 (363)
T cd06528 90 PSTPTMTIYLEEEYKYDREKAEEVARKIEETTLENLAEDISIDL--FNMRITIELDEEMLEDR--GITVDDVLKAIEKLK 165 (363)
T ss_pred CCCceEEEEecCcchhhHHHHHHHHHhhceeEHHHhhhheEEec--cCcEEEEEECHHHHHHc--CCCHHHHHHHHHHhc
Confidence 9999999999976 56789999999999999999999999865 45789999999999986 489999999998765
Q ss_pred ccccccCceeeeccceEEEeCCCCCCcceeehHHHhhhcCCcEEecccCceEEEEeccccccchhhccCCcccEEEEEeC
Q 000829 1033 KIKLKQQHIKVLDFRKLEIFPPVDKSKIHFELYSLKNVLPMVIVKGIKTVERVVIAEKEKEKRKVKENGEKKKYRLLVEG 1112 (1265)
Q Consensus 1033 k~k~~~~~i~~~~~~~~~i~~~~~~~~~~~~l~~l~~~l~~~~v~Gi~~I~r~~i~~~~~~~~~~~~~~~~~~~~l~teG 1112 (1265)
+.+.. ..++..+.+... +....+.++.++..+++++|+|+|||+||++..+ +++|.|+|||
T Consensus 166 ~~~~~-----~~~~~~~~~~~~--~~~~~~~l~~l~~~l~~~~v~Gi~gI~r~~i~~~------------~~~~~l~teG 226 (363)
T cd06528 166 KGKVG-----EEGDVTLIVLKA--EEPSIKELRKLAEKILNTKIKGIKGIKRVIVRKE------------EDEYVIYTEG 226 (363)
T ss_pred CCccc-----ccCCccEEEEcC--CcchHHHHHHHHHhhcccEEeCCCCceEEEEecC------------CceEEEEecC
Confidence 33221 111112333221 1233456888889999999999999999998742 2479999999
Q ss_pred ccHHHhhccCCccccccccCCHHHHHHHhCHHHHHHHHHHHHHHHhhccccccCcccceeeecccccccEEEeecccccc
Q 000829 1113 TGLQAVMGAEGIDGCKTKSNHIFEVQQTLGIEAARICIIDEINETMKAHGMSIDKRHMMLLADLMTFRGEVLGITRFGIQ 1192 (1265)
Q Consensus 1113 ~nl~~~~~~~~VD~~~~~sNdI~ev~~~lGIEAAR~~Iv~Ei~~v~~~~Gi~Vd~RHl~LlAD~MT~~G~~~~i~R~Gi~ 1192 (1265)
.||.++|.+++||+++++||||++|+++|||||||++|++||++||+.||++||+|||+||||+||++|++.|+||+||+
T Consensus 227 ~nl~~v~~~~~Vd~~rt~sNdI~ei~~~lGIEAaR~~ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~G~~~~i~R~gi~ 306 (363)
T cd06528 227 SNLKAVLKVEGVDPTRTTTNNIHEIEEVLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVRQIGRHGIA 306 (363)
T ss_pred cCHHHHhcCCCCcccccccCCHHHHHHhCCHHHHHHHHHHHHHHHHHhcCCeecHHHHHHHHHHhccCCceecccchhhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred ccCCcHhhHhcchHHHHHHHHhhhcCCcccccccccceeccCCCCCCccceEeeec
Q 000829 1193 KMDKSVLMLASFEKTADHLFNASVNGRDDRIEGVSECIIMGIPMPLGTGILKIRQR 1248 (1265)
Q Consensus 1193 ~~~~Spl~~aSFE~T~~~L~~AA~~g~~D~l~gvS~~Ii~Gk~~~~GTG~fdll~~ 1248 (1265)
++++|||++||||+|+++|++||++|+.|+|.|||||||+|+++|+|||+|||++|
T Consensus 307 ~~~~S~L~~aSFE~t~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~~~l~~d 362 (363)
T cd06528 307 GEKPSVLARAAFEVTVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTGDVELTMD 362 (363)
T ss_pred CCCCChhhhCchhhHHHHHHHHHhcCCCCcCCCcHHHeeeCCCCCCcCCeeEEEec
Confidence 88899999999999999999999999999999999999999999999999999986
No 17
>PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Probab=100.00 E-value=6.7e-89 Score=793.36 Aligned_cols=352 Identities=36% Similarity=0.585 Sum_probs=315.8
Q ss_pred hhccCCCHHHHHHHHHHHHHhhhcccCCcCccceeecccccCCccccccccccccccccccceecccchhHhhhhccccc
Q 000829 876 HKTSGITEKQLEVFIQTCFSRYRVKRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINGAKRI 955 (1265)
Q Consensus 876 ~~~~~~~~~~~~~~~~~~~~ky~~slv~PGEaVG~IAAQSIGEPsTQMTLnTFH~AGv~~~NVTlGvPRLkEIinask~i 955 (1265)
...++++.+++++|+++|..+|.+++|+||||||+|||||||||+|||||||||||||+++|||+|||||+|||||+|+|
T Consensus 153 ~~~~~l~~~~~~~i~~ei~~~y~~~~v~pGE~VG~IAAQSIGEP~TQMTLnTFH~AGVas~NVTlGVPRLkEIINa~K~i 232 (509)
T PRK14897 153 MKKKELSDDEYEEILRRIREEYERARVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEMNVTLGLPRLIEIVDARKKP 232 (509)
T ss_pred HHHcCCCHHHHHHHHHHHHHHHHHhccCCCCCcchhhhhhhCCccccccccccccccccccccccCcchhHHHhhcccCC
Confidence 34568999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccceEEEEccCC--CcHHHHHHHhcceeEEeccccceeEEEEEeCCccEEEEEeChhhHHHhhcccCHHHHHHHHhcCcc
Q 000829 956 STPIITAELECN--DNENAARVVKGRIEKTLLGQVAKSIKIVMTSRLASIVIALDMETIQDAHLCINADIVKESIVQTPK 1033 (1265)
Q Consensus 956 kTP~~ti~l~~~--~~~~~a~~v~~~le~~~L~di~~~i~~~y~~~~~~~~i~ld~~~i~~~~~~i~~~~i~~~i~~~~k 1033 (1265)
|||+|+++|.++ .+.+.|+.++.+||+++|+|+++.+..+ ...+++++||.+.+..+ .+++++|.++|.+...
T Consensus 233 sTP~mtiyL~~~~~~d~e~A~~V~~~IE~ttL~dv~~~~~d~---~~~~i~i~Ld~~~l~~~--~l~~~~I~~~I~~~~~ 307 (509)
T PRK14897 233 STPTMTIYLKKDYREDEEKVREVAKKIENTTLIDVADIITDI---AEMSVVVELDEEKMKER--LIEYDDILAAISKLTF 307 (509)
T ss_pred CCceEEEEecCcccccHHHHHHHHhhheeeEHHHHHHHHHHh---ccceEEEEECHHHHHHc--CCCHHHHHHHHHhccc
Confidence 999999999876 4788999999999999999999866443 34568999999999986 4788999999987421
Q ss_pred cccccCceeeeccceEEEeCCCCCCcceeehHHHhhhcCCcEEecccCceEEEEeccccccchhhccCCcccEEEEEeCc
Q 000829 1034 IKLKQQHIKVLDFRKLEIFPPVDKSKIHFELYSLKNVLPMVIVKGIKTVERVVIAEKEKEKRKVKENGEKKKYRLLVEGT 1113 (1265)
Q Consensus 1034 ~k~~~~~i~~~~~~~~~i~~~~~~~~~~~~l~~l~~~l~~~~v~Gi~~I~r~~i~~~~~~~~~~~~~~~~~~~~l~teG~ 1113 (1265)
++ +. .++..+++.+.+ +.+..+..+++.+++++|+|+|||+||++..++ ++++|.|+|||+
T Consensus 308 ~~-----~~-~~~~~I~i~~~~---~~~~~L~~l~~~l~~i~I~GipgI~r~~i~~~~----------~~~~~~L~TeG~ 368 (509)
T PRK14897 308 KT-----VE-IDDGIIRLKPQQ---PSFKKLYLLAEKVKSLTIKGIKGIKRAIARKEN----------DERRWVIYTQGS 368 (509)
T ss_pred eE-----Ee-cCCCEEEEEeCc---hHHHHHHHHHHHhhccEEeCCCCccEEEEecCC----------CCceeEEEeecc
Confidence 11 11 122455665531 224467778888999999999999999998532 235699999999
Q ss_pred cHHHhhccCCccccccccCCHHHHHHHhCHHHHHHHHHHHHHHHhhccccccCcccceeeecccccccEEEeeccccccc
Q 000829 1114 GLQAVMGAEGIDGCKTKSNHIFEVQQTLGIEAARICIIDEINETMKAHGMSIDKRHMMLLADLMTFRGEVLGITRFGIQK 1193 (1265)
Q Consensus 1114 nl~~~~~~~~VD~~~~~sNdI~ev~~~lGIEAAR~~Iv~Ei~~v~~~~Gi~Vd~RHl~LlAD~MT~~G~~~~i~R~Gi~~ 1193 (1265)
||.++|.+++||++||+||||++|+++|||||||++|++||+.||+.||++||+|||+||||+||++|.+.|||||||+.
T Consensus 369 NL~~vl~~~~VD~~rt~SNdI~eI~~vlGIEAAR~~Ii~Ei~~V~~~~Gi~Vd~RHL~LIAD~MT~~G~v~~i~R~Gi~~ 448 (509)
T PRK14897 369 NLKDVLEIDEVDPTRTYTNDIIEIATVLGIEAARNAIIHEAKRTLQEQGLNVDIRHIMLVADMMTFDGSVKAIGRHGISG 448 (509)
T ss_pred CHHHHhcCCCcccccCccCCHHHHHHhcCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHhCcCCcccccccccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999988
Q ss_pred cCCcHhhHhcchHHHHHHHHhhhcCCcccccccccceeccCCCCCCccceEeeecCCC
Q 000829 1194 MDKSVLMLASFEKTADHLFNASVNGRDDRIEGVSECIIMGIPMPLGTGILKIRQRDAV 1251 (1265)
Q Consensus 1194 ~~~Spl~~aSFE~T~~~L~~AA~~g~~D~l~gvS~~Ii~Gk~~~~GTG~fdll~~~~~ 1251 (1265)
+++|||++||||+|++||++||++|+.|+|.|||||||+|+++|+|||+|||+++...
T Consensus 449 ~~~SpL~rASFE~T~~~L~~AA~~Ge~D~L~GvsenII~G~~ipvGTG~fdL~~~~~~ 506 (509)
T PRK14897 449 EKSSVLARAAFEITGKHLLRAGILGEVDKLAGVAENIIVGQPITLGTGAVSLVYKGRK 506 (509)
T ss_pred cCCCHHHhcchHhHHHHHHHHhhcCCCCcCCChHHhhhcCCccCCcCceEEEEecCCC
Confidence 8899999999999999999999999999999999999999999999999999997653
No 18
>PRK04309 DNA-directed RNA polymerase subunit A''; Validated
Probab=100.00 E-value=8.9e-88 Score=777.83 Aligned_cols=347 Identities=40% Similarity=0.638 Sum_probs=317.6
Q ss_pred cCCCHHHHHHHHHHHHHhhhcccCCcCccceeecccccCCccccccccccccccccccceecccchhHhhhhcccccccc
Q 000829 879 SGITEKQLEVFIQTCFSRYRVKRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINGAKRISTP 958 (1265)
Q Consensus 879 ~~~~~~~~~~~~~~~~~ky~~slv~PGEaVG~IAAQSIGEPsTQMTLnTFH~AGv~~~NVTlGvPRLkEIinask~ikTP 958 (1265)
.+++++++++|+.+|..+|.+++++||||||++||||||||+|||||||||||||+++|||+|||||+|||||+|+||||
T Consensus 33 ~~l~~~~~~~~~~~i~~~y~~~~v~pGe~VG~iaAQsIGEP~TQMTL~TFH~AGva~~nVTlGvPRlkEIina~K~~~TP 112 (383)
T PRK04309 33 RKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDARKEPSTP 112 (383)
T ss_pred cCCCHHHHHHHHHHHHHHHHHhhcCCCCccchhhhhhccchhhhcccccccccCccccCcccCchhHHHHHhcccCCCCC
Confidence 45899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEEEccCC--CcHHHHHHHhcceeEEeccccceeEEEEEeCCccEEEEEeChhhHHHhhcccCHHHHHHHHhcCccccc
Q 000829 959 IITAELECN--DNENAARVVKGRIEKTLLGQVAKSIKIVMTSRLASIVIALDMETIQDAHLCINADIVKESIVQTPKIKL 1036 (1265)
Q Consensus 959 ~~ti~l~~~--~~~~~a~~v~~~le~~~L~di~~~i~~~y~~~~~~~~i~ld~~~i~~~~~~i~~~~i~~~i~~~~k~k~ 1036 (1265)
+|+++|.++ .+.+.|+.++.+||+++|+|++.++++.+ ...++++++|.+.+.++ .+++++|.++|.+.++.+
T Consensus 113 ~~tv~L~~~~~~d~~~a~~v~~~iE~t~L~~v~~~i~~~~--~~~~l~i~ld~~~i~~~--~l~~~~I~~~i~~~~~~~- 187 (383)
T PRK04309 113 MMTIYLKDEYAYDREKAEEVARKIEATTLENLAKDISVDL--ANMTIIIELDEEMLEDR--GLTVDDVKEAIEKKKGGE- 187 (383)
T ss_pred eEEEEecCcccccHHHHHHHHhheeeeEHhhhhhheEecc--CCcEEEEEECHHHHHHc--CCCHHHHHHHHHHhcCcc-
Confidence 999999976 47899999999999999999999998865 45689999999999986 579999999998765332
Q ss_pred ccCceeeeccceEEEeCCCCCCcceeehHHHhhhcCCcEEecccCceEEEEeccccccchhhccCCcccEEEEEeCccHH
Q 000829 1037 KQQHIKVLDFRKLEIFPPVDKSKIHFELYSLKNVLPMVIVKGIKTVERVVIAEKEKEKRKVKENGEKKKYRLLVEGTGLQ 1116 (1265)
Q Consensus 1037 ~~~~i~~~~~~~~~i~~~~~~~~~~~~l~~l~~~l~~~~v~Gi~~I~r~~i~~~~~~~~~~~~~~~~~~~~l~teG~nl~ 1116 (1265)
+.+. ++.+.+++. ...++.+..++..+++++|+|+|||+||++..+ +++|.|.|||.||.
T Consensus 188 ----~~~~-~~~i~i~~~---~~~~~~l~~l~~~l~~~~vkGi~gI~r~~i~~~------------~~~~~l~teG~nl~ 247 (383)
T PRK04309 188 ----VEIE-GNTLIISPK---EPSYRELRKLAEKIRNIKIKGIKGIKRVIIRKE------------GDEYVIYTEGSNLK 247 (383)
T ss_pred ----eecc-CCeEEEEec---CchHHHHHHHHHHhcccEEECCCCceEEEEecC------------CCeEEEEEcccCHH
Confidence 1111 345555553 122456778888999999999999999999742 35899999999999
Q ss_pred HhhccCCccccccccCCHHHHHHHhCHHHHHHHHHHHHHHHhhccccccCcccceeeecccccccEEEeeccccccccCC
Q 000829 1117 AVMGAEGIDGCKTKSNHIFEVQQTLGIEAARICIIDEINETMKAHGMSIDKRHMMLLADLMTFRGEVLGITRFGIQKMDK 1196 (1265)
Q Consensus 1117 ~~~~~~~VD~~~~~sNdI~ev~~~lGIEAAR~~Iv~Ei~~v~~~~Gi~Vd~RHl~LlAD~MT~~G~~~~i~R~Gi~~~~~ 1196 (1265)
++|.+++||+++++|||||+|+++|||||||++|++||+.||+.||++||+|||+||||+||++|+++||||+||+++++
T Consensus 248 ~v~~~~~VD~~rt~sNdI~ei~~vlGIEAAR~~ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~G~~~~i~R~Gi~~~~~ 327 (383)
T PRK04309 248 EVLKVEGVDATRTTTNNIHEIEEVLGIEAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGVSGEKA 327 (383)
T ss_pred HHhcCCCEeeccccCCCHHHHHHHcCHHHHHHHHHHHHHHHHHHcCCeecHHHHHHHHHHhccCceEEeeechhhcCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999988889
Q ss_pred cHhhHhcchHHHHHHHHhhhcCCcccccccccceeccCCCCCCccceEeeecCC
Q 000829 1197 SVLMLASFEKTADHLFNASVNGRDDRIEGVSECIIMGIPMPLGTGILKIRQRDA 1250 (1265)
Q Consensus 1197 Spl~~aSFE~T~~~L~~AA~~g~~D~l~gvS~~Ii~Gk~~~~GTG~fdll~~~~ 1250 (1265)
|||++||||+|+++|++||++|+.|+|+|||||||+|+++|+|||+|||+++.+
T Consensus 328 S~l~~aSFE~T~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~~~l~~~~~ 381 (383)
T PRK04309 328 SVLARAAFEVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTGDVELTMDPP 381 (383)
T ss_pred CHHHhCchhhHHHHHHHHHhcCCCCCCCCcHHHhhcCCCcCCCCceEEEEcCCC
Confidence 999999999999999999999999999999999999999999999999999876
No 19
>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional
Probab=100.00 E-value=2.6e-87 Score=791.83 Aligned_cols=287 Identities=33% Similarity=0.517 Sum_probs=260.2
Q ss_pred CCcceEEEeeeeeCCCCCCCceecCCCCcCCchhHHHHHHHHHHHHHHHHHHHHhccchhhhHHHHHHHHHHHHHhccCC
Q 000829 110 ERPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQQELVEANSAFKSLAGWETLQVEVAQYINSDV 189 (1265)
Q Consensus 110 ~~p~~~~l~~lpVpP~~~RP~~~~~~~~~~~ddlt~~l~~Ii~~n~~l~~~~~~~~~~~~~~~~~~~lq~~v~~~~~~~~ 189 (1265)
++|+||||++||||||++||++.++++..+++|||.+|++||.+|++|++....+++...+.+.|++||.+|+.||||+.
T Consensus 240 ~~PewmiL~~lPV~Pp~lRP~v~l~~g~~~~sDLn~ly~~II~rNn~L~~~~~~~~p~~ii~~~~~~LQ~aVd~liDn~~ 319 (627)
T PRK02625 240 SRPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGR 319 (627)
T ss_pred CCccEEEEEeeecCCCcccCceEeCCCcccCCCHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHHhcCCC
Confidence 79999999999999999999999998878999999999999999999999999898887778899999999999999999
Q ss_pred CCCCccccCCCCchhhhhhhcCccccccccccCCCCCCccceEEcCCCCCCCCcccccHHHHhhcCcceeechHHHHHHH
Q 000829 190 RGVPFSMQVARPLSGFVQRLKGKQGRFRGNLSGKRVEYTGRTVISPDPNLKITEVAIPIRMARILTYPERVSDHNIEKLR 269 (1265)
Q Consensus 190 ~~~~~~~~~~~~~~~i~q~l~gK~G~fR~nl~GKRvd~saRsVIspDp~l~~~evGvP~~~A~~Lt~pe~Vt~~Ni~~l~ 269 (1265)
++.|.....++|++||+|+|+||+||||+|||||||||||||||||||+|++||||||.+||++||+|+ |+++|+
T Consensus 320 ~g~~~~~~~~rp~ksls~~LkGKeGRFR~NLlGKRVDySgRSVIspdP~L~l~e~GvP~~mA~eL~~Pf-----~i~~L~ 394 (627)
T PRK02625 320 RGRTVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPF-----VIHRLI 394 (627)
T ss_pred CCCCcccccCCchhhHHHHhccCCccccccccccccccCCCceEeCCCCcccccccChHHHHHhcCcHH-----hHHHHH
Confidence 887765444789999999999999999999999999999999999999999999999999999999984 666664
Q ss_pred HHHHcCC-CCCCCceEEECCCCCeEEeccccchhhhhcccccceeecccccCCeEEEecCCCccccceeeEEEEEecCCe
Q 000829 270 QCIQNGP-DKYPGARMIRYPDGTARVLYGKFRNQLAVELKSGCIVDRHLEDGDVVLFNRQPSLHRMSIMCHRARIMPWRT 348 (1265)
Q Consensus 270 ~lv~ng~-~~~pGa~~i~~~~g~~~~l~~~~r~~~~~~L~~g~iV~Rhl~dgD~VL~NRQPSLHk~Simah~vkv~~~kt 348 (1265)
.+|. ...++|++++.. .-...+.|+||+.|||+|||||||||||+|||||+|++++++|
T Consensus 395 ---~~g~~~~i~~ak~~i~~-----------------~~~~~~~Vlr~v~~gd~VLlNRqPTLHR~sIqAf~~~l~~~kt 454 (627)
T PRK02625 395 ---RQGIVNNIKAAKKLIQR-----------------ADPEVWQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRA 454 (627)
T ss_pred ---HcCchhhHHHHHHHHHh-----------------cCCcccEEEEEeecCcEEEecCCCccccccceeEeeEEcCCCe
Confidence 5554 223344433221 1122456788999999999999999999999999999999999
Q ss_pred eeeecccCCCCCCCCcccccccccCChHHHHHHHHHHcCCCcccccCCCCCccEeecccceeeeeeeeccCcc
Q 000829 349 LRFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTF 421 (1265)
Q Consensus 349 ~rln~~vc~~yNADFDGDEMN~h~PQs~~araEa~~Lm~~~~~~~sp~~g~pi~gliQD~l~g~~llT~~d~f 421 (1265)
|||||+||+||||||||||||+|+|||++|||||+.||.+++|++||++|+|+++++||+++|+|+||.++..
T Consensus 455 irlhplvC~~fNADFDGDeMnvHvPqS~~A~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~llG~y~LT~~~~~ 527 (627)
T PRK02625 455 IQLHPLVCPAFNADFDGDQMAVHVPLSLEAQAEARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLTAENPG 527 (627)
T ss_pred EEeccccCCcccCCcCCCeEEEecCCCHHHHHHHHHHhcCccceEEcCCCceeEeechhhhhheeeeeccCcc
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999854
No 20
>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=2.4e-87 Score=751.50 Aligned_cols=300 Identities=66% Similarity=0.980 Sum_probs=283.8
Q ss_pred hhhcccCCcCccceeecccccCCccccccccccccccccccceecccchhHhhhhcccccccceEEEEccCCCcHHHHHH
Q 000829 896 RYRVKRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINGAKRISTPIITAELECNDNENAARV 975 (1265)
Q Consensus 896 ky~~slv~PGEaVG~IAAQSIGEPsTQMTLnTFH~AGv~~~NVTlGvPRLkEIinask~ikTP~~ti~l~~~~~~~~a~~ 975 (1265)
+|.+++++||||||++||||||||+|||||||||+||++++|||+|||||+||+||+|+||||+|+++|.++.+.+.|+.
T Consensus 1 ky~~~~v~pGe~vG~iaaQsiGEp~TQmTL~TFH~aGv~~~nvtlGvPRlkEIinasK~~~TP~~ti~l~~~~~~~~a~~ 80 (300)
T cd02736 1 KYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNISTPIITAKLENDRDEKSARI 80 (300)
T ss_pred CchhhccCCCccchhhhhhhcCCccccccccccccccccccccccCchHHHHHHhcccCCCCCeEEEEecCcccHHHHHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999889999999
Q ss_pred HhcceeEEeccccceeEEEEEeCCccEEEEEeChhhHHHhhcccCHHHHHHHHhcCcccccccCceeeeccceEEEeCCC
Q 000829 976 VKGRIEKTLLGQVAKSIKIVMTSRLASIVIALDMETIQDAHLCINADIVKESIVQTPKIKLKQQHIKVLDFRKLEIFPPV 1055 (1265)
Q Consensus 976 v~~~le~~~L~di~~~i~~~y~~~~~~~~i~ld~~~i~~~~~~i~~~~i~~~i~~~~k~k~~~~~i~~~~~~~~~i~~~~ 1055 (1265)
++.+||+++|+|++.+++++|+|+..++.+++|.+.++++++ +.
T Consensus 81 v~~~ie~t~l~di~~~~~~~~~p~~~~~~i~~d~~~i~~~~l--~~---------------------------------- 124 (300)
T cd02736 81 VKGRIEKTYLGEVASYIEEVYSPDDCYILIKLDKKIIEKLQL--SK---------------------------------- 124 (300)
T ss_pred HHHHHhhccHHHhhhheEEEEcCCCceEEEEecHHHHHHhcC--Cc----------------------------------
Confidence 999999999999999999999999999999999999998754 10
Q ss_pred CCCcceeehHHHhhhcCCcEEecccCceEEEEeccccccchhhccCCcccEEEEEeCccHHHhhccCCccccccccCCHH
Q 000829 1056 DKSKIHFELYSLKNVLPMVIVKGIKTVERVVIAEKEKEKRKVKENGEKKKYRLLVEGTGLQAVMGAEGIDGCKTKSNHIF 1135 (1265)
Q Consensus 1056 ~~~~~~~~l~~l~~~l~~~~v~Gi~~I~r~~i~~~~~~~~~~~~~~~~~~~~l~teG~nl~~~~~~~~VD~~~~~sNdI~ 1135 (1265)
.+..+.++.++..+++++|+|+|||+||.+..++ .+++|.|+|||+||.++|.+++||+++++||||+
T Consensus 125 --~~~~~~~~~l~~~l~~~~v~Gi~gI~r~~i~~~~----------~~~~~~l~teG~nl~~v~~~~~Vd~~rt~sNdI~ 192 (300)
T cd02736 125 --SNLYFLLQSLKRKLPDVVVSGIPEVKRAVINKDK----------KKGKYKLLVEGYGLRAVMNTPGVIGTRTTSNHIM 192 (300)
T ss_pred --ccHHHHHHHHHHHhccceEeCCCCceEEEEecCC----------CCCcEEEEEecccHHHHhcCCcEeccCCccCCHH
Confidence 0123457778889999999999999999997532 2467999999999999999999999999999999
Q ss_pred HHHHHhCHHHHHHHHHHHHHHHhhccccccCcccceeeecccccccEEEeeccccccccCCcHhhHhcchHHHHHHHHhh
Q 000829 1136 EVQQTLGIEAARICIIDEINETMKAHGMSIDKRHMMLLADLMTFRGEVLGITRFGIQKMDKSVLMLASFEKTADHLFNAS 1215 (1265)
Q Consensus 1136 ev~~~lGIEAAR~~Iv~Ei~~v~~~~Gi~Vd~RHl~LlAD~MT~~G~~~~i~R~Gi~~~~~Spl~~aSFE~T~~~L~~AA 1215 (1265)
+|+++|||||||++|++||++||+.||++||+|||+||||+||++|.++||||+||+++++|||++||||+|+++|++||
T Consensus 193 ei~~~lGIEAaR~~ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~G~~~~itR~gi~~~~~S~l~~aSFE~t~~~L~~AA 272 (300)
T cd02736 193 EVEKVLGIEAARSTIINEIQYTMKSHGMSIDPRHIMLLADLMTFKGEVLGITRFGIAKMKESVLMLASFEKTTDHLFNAA 272 (300)
T ss_pred HHHHhcCHHHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHHHhccCceeeeecccccccCCCHHHhcchHhHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999988899999999999999999999
Q ss_pred hcCCcccccccccceeccCCCCCCccce
Q 000829 1216 VNGRDDRIEGVSECIIMGIPMPLGTGIL 1243 (1265)
Q Consensus 1216 ~~g~~D~l~gvS~~Ii~Gk~~~~GTG~f 1243 (1265)
++|+.|+|+|||||||+|+++|+|||+|
T Consensus 273 ~~g~~D~l~gvse~ii~G~~~~~GTG~f 300 (300)
T cd02736 273 LHGRKDSIEGVSECIIMGKPMPIGTGLF 300 (300)
T ss_pred hcCCCCcCCCcHHHeeeCCCcCCCCCCC
Confidence 9999999999999999999999999997
No 21
>CHL00018 rpoC1 RNA polymerase beta' subunit
Probab=100.00 E-value=4.4e-87 Score=797.65 Aligned_cols=286 Identities=31% Similarity=0.497 Sum_probs=264.6
Q ss_pred CCcceEEEeeeeeCCCCCCCceecCCCCcCCchhHHHHHHHHHHHHHHHHHHHH--hccchhhhHHHHHHHHHHHHHhcc
Q 000829 110 ERPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQQELVE--ANSAFKSLAGWETLQVEVAQYINS 187 (1265)
Q Consensus 110 ~~p~~~~l~~lpVpP~~~RP~~~~~~~~~~~ddlt~~l~~Ii~~n~~l~~~~~~--~~~~~~~~~~~~~lq~~v~~~~~~ 187 (1265)
.+|+||||++||||||++||++.++++..++||||..|++||.+|++|++.... +++...+.+.|.+||.+|+.|+||
T Consensus 259 ~~PewmiL~~lPV~Pp~lRP~v~l~~g~~~~sDln~lyr~II~rNn~L~~~~~~~~~~p~~~i~~~~~~LQ~aVd~lidn 338 (663)
T CHL00018 259 IEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDLLTTSRSTPGELVMCQKKLLQEAVDALLDN 338 (663)
T ss_pred CCccEEEEEeeeeCCCcccCceEcCCCcccCCChHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHHHHHHHHHhcC
Confidence 699999999999999999999999988899999999999999999999998887 778888889999999999999999
Q ss_pred CCCCCCccccCCCCchhhhhhhcCccccccccccCCCCCCccceEEcCCCCCCCCcccccHHHHhhcCcceeechHHHHH
Q 000829 188 DVRGVPFSMQVARPLSGFVQRLKGKQGRFRGNLSGKRVEYTGRTVISPDPNLKITEVAIPIRMARILTYPERVSDHNIEK 267 (1265)
Q Consensus 188 ~~~~~~~~~~~~~~~~~i~q~l~gK~G~fR~nl~GKRvd~saRsVIspDp~l~~~evGvP~~~A~~Lt~pe~Vt~~Ni~~ 267 (1265)
+.++.|.....++|++||+|+|+||+||||+|||||||||||||||||||+|+++|||||..||++||+|+.
T Consensus 339 ~~~g~~~~~~~~r~~ksls~~LkGK~GrFR~NLlGKRVDySgRSVIvpdP~L~l~e~GlP~~mA~eL~~P~~-------- 410 (663)
T CHL00018 339 GIRGQPMRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQPFV-------- 410 (663)
T ss_pred CCCCCccccCCCCCCCCccccccCcCccccccccccccccCCCceecCCCcccccccCChHHHHHHcCcHHH--------
Confidence 998877654447899999999999999999999999999999999999999999999999999999999984
Q ss_pred HHHHHHcCCC-CCCCceEEECCCCCeEEeccccchhhhhcccccceeecccccCCeEEEecCCCccccceeeEEEEEecC
Q 000829 268 LRQCIQNGPD-KYPGARMIRYPDGTARVLYGKFRNQLAVELKSGCIVDRHLEDGDVVLFNRQPSLHRMSIMCHRARIMPW 346 (1265)
Q Consensus 268 l~~lv~ng~~-~~pGa~~i~~~~g~~~~l~~~~r~~~~~~L~~g~iV~Rhl~dgD~VL~NRQPSLHk~Simah~vkv~~~ 346 (1265)
+++|+.+|+. .+.+|++++ ......++.|+||+.|||+|||||||||||+|||||+|+++++
T Consensus 411 i~~Li~~~~~~~~~~Ak~~i-----------------~~~~~~~~~Vlr~v~~gd~VLlNRqPTLHR~sIqAf~~~L~~g 473 (663)
T CHL00018 411 IRGLIRQHLASNIRAAKSKI-----------------REKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEG 473 (663)
T ss_pred HHHHHhcCccccHHHHHHHH-----------------HhcCCcccEeeeehhcCceeeecCCCcccccccceeeEEecCC
Confidence 5788888864 233443322 2233467889999999999999999999999999999999999
Q ss_pred CeeeeecccCCCCCCCCcccccccccCChHHHHHHHHHHcCCCcccccCCCCCccEeecccceeeeeeeeccCc
Q 000829 347 RTLRFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDT 420 (1265)
Q Consensus 347 kt~rln~~vc~~yNADFDGDEMN~h~PQs~~araEa~~Lm~~~~~~~sp~~g~pi~gliQD~l~g~~llT~~d~ 420 (1265)
+||||||+||+||||||||||||+|+|||++|||||+.||.+.+|++||++|+|+++++||+++|+|+||.++.
T Consensus 474 ktIrLhplvC~~fNADFDGDqMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~ 547 (663)
T CHL00018 474 RAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYVLTIGNR 547 (663)
T ss_pred CeEEeCcccCCcccCCccCcEEEEecCCCHHHHHHHHHHhcCccceeEcCCCceeEeechhhhhhhheecccCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999885
No 22
>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=1e-86 Score=785.95 Aligned_cols=286 Identities=34% Similarity=0.531 Sum_probs=260.6
Q ss_pred CCcceEEEeeeeeCCCCCCCceecCCCCcCCchhHHHHHHHHHHHHHHHHHHHHhccchhhhHHHHHHHHHHHHHhccCC
Q 000829 110 ERPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQQELVEANSAFKSLAGWETLQVEVAQYINSDV 189 (1265)
Q Consensus 110 ~~p~~~~l~~lpVpP~~~RP~~~~~~~~~~~ddlt~~l~~Ii~~n~~l~~~~~~~~~~~~~~~~~~~lq~~v~~~~~~~~ 189 (1265)
.+|+||||++||||||++||++.++++..++||||..|++||.+|++|++.+..+++...+.+.|++||.+|+.||||+.
T Consensus 233 ~~PewmiL~~lPV~Pp~lRP~v~l~~g~~~~sDln~lyr~II~rNn~L~~~~~~~~p~~i~~~~~~~LQ~aVd~lidn~~ 312 (619)
T TIGR02387 233 SRPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGR 312 (619)
T ss_pred CCcceEEEEecccCCcccCCceEeCCCcccCCCHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHHhcCCC
Confidence 79999999999999999999999998879999999999999999999999999898877778899999999999999999
Q ss_pred CCCCccccCCCCchhhhhhhcCccccccccccCCCCCCccceEEcCCCCCCCCcccccHHHHhhcCcceeechHHHHHHH
Q 000829 190 RGVPFSMQVARPLSGFVQRLKGKQGRFRGNLSGKRVEYTGRTVISPDPNLKITEVAIPIRMARILTYPERVSDHNIEKLR 269 (1265)
Q Consensus 190 ~~~~~~~~~~~~~~~i~q~l~gK~G~fR~nl~GKRvd~saRsVIspDp~l~~~evGvP~~~A~~Lt~pe~Vt~~Ni~~l~ 269 (1265)
++.|.....++|++||+|+|+||+||||+|||||||||||||||+|||+|+++|||||.+||++||+|+ |+.+|
T Consensus 313 ~g~~~~~~~~rp~ksls~~LkGKeGRFR~nLlGKRVDySgRSVI~pdP~L~l~qvGvP~~mA~eLf~Pf-----~i~~L- 386 (619)
T TIGR02387 313 RGRTVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPF-----VIHRL- 386 (619)
T ss_pred CCCCcccccCCchhhHHHHhccCCccccccccccccccCCCceecCCCCcccceecChHHHHHhcCchH-----hHHHH-
Confidence 887754444789999999999999999999999999999999999999999999999999999999975 66665
Q ss_pred HHHHcCC-CCCCCceEEECCCCCeEEeccccchhhhhcccccceeecccccCCeEEEecCCCccccceeeEEEEEecCCe
Q 000829 270 QCIQNGP-DKYPGARMIRYPDGTARVLYGKFRNQLAVELKSGCIVDRHLEDGDVVLFNRQPSLHRMSIMCHRARIMPWRT 348 (1265)
Q Consensus 270 ~lv~ng~-~~~pGa~~i~~~~g~~~~l~~~~r~~~~~~L~~g~iV~Rhl~dgD~VL~NRQPSLHk~Simah~vkv~~~kt 348 (1265)
+.+|. ...+||+.++...+ ...+.|+||+.|||+|||||||||||+|||||++++++++|
T Consensus 387 --~~~g~~~~i~~ak~~i~~~~-----------------~~v~~Vlr~v~~gd~VLlNRqPTLHR~sIqAf~~~l~~~kt 447 (619)
T TIGR02387 387 --IRQGIVNNIKAAKKLIQRAD-----------------DEIWSVLQEVITGHPVMLNRAPTLHRLGIQAFEPILVDGRA 447 (619)
T ss_pred --HhcCcccchHHHHHHHHhcC-----------------ChhHHHHHHHhcCCEEEecCCCccchhcceeeeeEEecCCe
Confidence 44664 23345554433211 12346999999999999999999999999999999999999
Q ss_pred eeeecccCCCCCCCCcccccccccCChHHHHHHHHHHcCCCcccccCCCCCccEeecccceeeeeeeeccCc
Q 000829 349 LRFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDT 420 (1265)
Q Consensus 349 ~rln~~vc~~yNADFDGDEMN~h~PQs~~araEa~~Lm~~~~~~~sp~~g~pi~gliQD~l~g~~llT~~d~ 420 (1265)
|||||+||+||||||||||||+|+|||++|||||++||.+++|++||++|+|+++++||+++|+|+||.++.
T Consensus 448 irlhplvC~~fNADFDGDeMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~llg~y~LT~~~~ 519 (619)
T TIGR02387 448 IQLHPLVCPAFNADFDGDQMAVHVPLSLEAQTEARLLMLASNNVLSPATGEPIVTPSQDMVLGCYYLTALNP 519 (619)
T ss_pred EEECcccCCcccCCCCCceeeeecCCCHHHHHHHHHHhhchhcEEecCCCceeEeechhhhhhhheeecccc
Confidence 999999999999999999999999999999999999999999999999999999999999999999999874
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=1.6e-85 Score=742.83 Aligned_cols=307 Identities=35% Similarity=0.544 Sum_probs=267.5
Q ss_pred hhhcccCCcCccceeecccccCCccccccccccccccccccceecccchhHhhh-hcccccccceEEEEccCCCcHHHHH
Q 000829 896 RYRVKRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEII-NGAKRISTPIITAELECNDNENAAR 974 (1265)
Q Consensus 896 ky~~slv~PGEaVG~IAAQSIGEPsTQMTLnTFH~AGv~~~NVTlGvPRLkEIi-nask~ikTP~~ti~l~~~~~~~~a~ 974 (1265)
||.+++|+||||||+|||||||||+|||||||||||||++|||||||||||||| +|||+||||+|+++|.++.+.+.|+
T Consensus 1 ky~~slv~PGE~VG~iaAQSIGEPsTQMTLnTFH~AGv~~~nVTlGvPRL~EIi~~Ask~i~TP~m~v~l~~~~~~~~a~ 80 (309)
T cd02735 1 KYMRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILMTASKNIKTPSMTLPLKNGKSAERAE 80 (309)
T ss_pred CchhccCCCCcccchhhhhccCCcccccccccccccCccccccccccccHHHHHhhhccCCCCCeEEEEecCchhHHHHH
Confidence 689999999999999999999999999999999999999999999999999998 7999999999999999988888999
Q ss_pred HHhcceeEEeccccceeEEEEEeCCccEEEEEeChhhHHHhhcccCHHHHHHHHhcCcccccccCceeeeccceEEEeCC
Q 000829 975 VVKGRIEKTLLGQVAKSIKIVMTSRLASIVIALDMETIQDAHLCINADIVKESIVQTPKIKLKQQHIKVLDFRKLEIFPP 1054 (1265)
Q Consensus 975 ~v~~~le~~~L~di~~~i~~~y~~~~~~~~i~ld~~~i~~~~~~i~~~~i~~~i~~~~k~k~~~~~i~~~~~~~~~i~~~ 1054 (1265)
.++++|++++|+|+++++++.| |...+...+.-+. . ....+++.+.
T Consensus 81 ~~~~~ie~~~l~dv~~~~~v~~---------------------------i~~~~~~~~~~~~-~------~~~~~~i~~~ 126 (309)
T cd02735 81 TLKKRLSRVTLSDVVEKVEVTE---------------------------ILKTIERVFKKLL-G------KWCEVTIKLP 126 (309)
T ss_pred HHHhheeEeEHHHhhhhhehhH---------------------------HHHHHHHHhhhhh-C------CEEEEEEEec
Confidence 9999999999999999988765 1111111100000 0 0012223322
Q ss_pred CCCCcceeehHHHhhhcCCcEEecccCceEEEEeccccccchhhccCCcccEEEEEeCccHHHhhcc-CCccccccccCC
Q 000829 1055 VDKSKIHFELYSLKNVLPMVIVKGIKTVERVVIAEKEKEKRKVKENGEKKKYRLLVEGTGLQAVMGA-EGIDGCKTKSNH 1133 (1265)
Q Consensus 1055 ~~~~~~~~~l~~l~~~l~~~~v~Gi~~I~r~~i~~~~~~~~~~~~~~~~~~~~l~teG~nl~~~~~~-~~VD~~~~~sNd 1133 (1265)
......+.++.++..+.+++|+|+|||+||.+..++. ....+|.|+|||.||.++|.+ ++||++|++|||
T Consensus 127 -~~~~~~~~~~~~~~~l~~~~i~gi~gI~r~~i~~~~~--------~~~~~~~l~teG~nl~~v~~~~~~vd~~r~~sNd 197 (309)
T cd02735 127 -LSSPKLLLLSIVEKLARKAVIREIPGITRCFVVEEDK--------GGKTKYLVITEGVNLAALWKFSDILDVNRIYTND 197 (309)
T ss_pred -CCchhHHHHHHHHHHhcccEEeCCCCccEEEEecCcC--------CCceEEEEEeccccHHHHHhccCccccccceeCC
Confidence 1122345567788899999999999999999985431 123468999999999999998 799999999999
Q ss_pred HHHHHHHhCHHHHHHHHHHHHHHHhhccccccCcccceeeecccccccEEEeeccccccccCCcHhhHhcchHHHHHHHH
Q 000829 1134 IFEVQQTLGIEAARICIIDEINETMKAHGMSIDKRHMMLLADLMTFRGEVLGITRFGIQKMDKSVLMLASFEKTADHLFN 1213 (1265)
Q Consensus 1134 I~ev~~~lGIEAAR~~Iv~Ei~~v~~~~Gi~Vd~RHl~LlAD~MT~~G~~~~i~R~Gi~~~~~Spl~~aSFE~T~~~L~~ 1213 (1265)
||+|+++|||||||++|++||++||+.||++||+|||+||||+||++|+++|+||+|| +.++|||++||||+|.++|++
T Consensus 198 i~ei~~~lGIEAar~~ii~Ei~~v~~~~Gi~V~~rHl~LiaD~MT~~G~~~~~nr~gi-~~~~S~l~~asFE~t~~~L~~ 276 (309)
T cd02735 198 IHAMLNTYGIEAARRAIVKEISNVFKVYGIAVDPRHLSLIADYMTFEGGYRPFNRIGM-ESSTSPLQKMSFETTLAFLKK 276 (309)
T ss_pred HHHHHHhhCHHHHHHHHHHHHHHHHHhcCCeeCHHHHHHHHHHHHhCCcEeecchhhe-ccCCCHHHhhhhhhHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999 558999999999999999999
Q ss_pred hhhcCCcccccccccceeccCCCCCCccceEee
Q 000829 1214 ASVNGRDDRIEGVSECIIMGIPMPLGTGILKIR 1246 (1265)
Q Consensus 1214 AA~~g~~D~l~gvS~~Ii~Gk~~~~GTG~fdll 1246 (1265)
||++|+.|+|+||||||++|+++|+|||+|||+
T Consensus 277 Aa~~g~~D~l~g~s~~ii~G~~~~~GTG~fdll 309 (309)
T cd02735 277 ATLNGDIDNLSSPSSRLVVGKPVNGGTGLFDLL 309 (309)
T ss_pred HhhcCCCCCCCChHHheeeCCccCccceeEEeC
Confidence 999999999999999999999999999999986
No 24
>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=1e-73 Score=647.17 Aligned_cols=273 Identities=52% Similarity=0.831 Sum_probs=220.1
Q ss_pred CCChhhhhhhhccccccchhcccccCcCChhHHHHHHHhhheEeeecCeEEcCCCcEEEEEecCCCcccccccCCCCCCc
Q 000829 712 GLSATEFFFHTMGGREGLVDTAVKTADTGYMSRRLIKALEDLSIQYDNSVRNAGGCIVQFLYGDDGMDPANMEGKSGEPL 791 (1265)
Q Consensus 712 GL~p~EfFfH~m~GReGLiDTAvKTa~sGYlqRrLvk~lEdl~v~YD~TVR~s~g~iiQf~YGeDG~d~~~~~~~~~~~~ 791 (1265)
||+|+|||||||||||||||||||||+||||||||||+|||++|.||+|||++++.|+||.||+||
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 999999999999999999999999999999999999999999999999999999999999999865
Q ss_pred hhHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHhhcCCCcchHHHHHHHHHHHHHhhhhhhhhhhcccccCCCccchhh
Q 000829 792 NFDRLLMKVKATCPPAGQRYLSPQQVSEIVEKQLAAYGKESCSEAFLNSLRKFFEGQQDKLDKKIKFVEDIGWDDKSQIL 871 (1265)
Q Consensus 792 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~~~~~~l~~~~~~~~~~~l~~~~~~~ 871 (1265)
T Consensus 67 -------------------------------------------------------------------------------- 66 (277)
T PF04998_consen 67 -------------------------------------------------------------------------------- 66 (277)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred hhhhhhccCCCHHHHHHHHHHHHHhhhcccCCcCccceeecccccCCccccccccccccccccccceecccchhHhhhhc
Q 000829 872 EEVTHKTSGITEKQLEVFIQTCFSRYRVKRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIING 951 (1265)
Q Consensus 872 ~~~~~~~~~~~~~~~~~~~~~~~~ky~~slv~PGEaVG~IAAQSIGEPsTQMTLnTFH~AGv~~~NVTlGvPRLkEIina 951 (1265)
+|+||||||+|||||||||+|||||||||+||++++|||+|+||++||+++
T Consensus 67 -----------------------------~v~~Ge~VGiiaAQSIGEP~TQ~TL~TFH~aG~~~~~vt~giprl~eii~~ 117 (277)
T PF04998_consen 67 -----------------------------LVEPGEAVGIIAAQSIGEPGTQMTLRTFHTAGVASKNVTQGIPRLKEIINA 117 (277)
T ss_dssp -----------------------------B--TTSBHHHHHHHHHHCHGCCSHHSCTSSSCSSTSSCSSSHHHHHHHHTT
T ss_pred -----------------------------ccCccccchhhhhchhcchhHHhhhcccccCceeeecccccceeecccccc
Confidence 456999999999999999999999999999999999999999999999999
Q ss_pred ccccccceEEEEccCCC--cHHHHHHHhcceeEEeccccceeEEEEEeCCccEEEEEeChhhHHHhhcccCHHHHHHHHh
Q 000829 952 AKRISTPIITAELECND--NENAARVVKGRIEKTLLGQVAKSIKIVMTSRLASIVIALDMETIQDAHLCINADIVKESIV 1029 (1265)
Q Consensus 952 sk~ikTP~~ti~l~~~~--~~~~a~~v~~~le~~~L~di~~~i~~~y~~~~~~~~i~ld~~~i~~~~~~i~~~~i~~~i~ 1029 (1265)
++++++|+++.+..... ..+.+..+....+. .
T Consensus 118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------------------------------------~ 151 (277)
T PF04998_consen 118 SKKIKTPIITVYGKKKIISEKKKIKIIRKKIKI----------------------------------------------I 151 (277)
T ss_dssp CSSSSSEEEEECSCSSECSSSHHHHHHHHTCSS----------------------------------------------S
T ss_pred ccccccceEEeecccceecccccceEEEEeeee----------------------------------------------e
Confidence 99999999988776542 12222222222111 0
Q ss_pred cCcccccccCceeeeccceEEEeCCCCCCcceeehHHHhhhcCCcEEecccCceEEEEeccccccchhhccCCcccEEEE
Q 000829 1030 QTPKIKLKQQHIKVLDFRKLEIFPPVDKSKIHFELYSLKNVLPMVIVKGIKTVERVVIAEKEKEKRKVKENGEKKKYRLL 1109 (1265)
Q Consensus 1030 ~~~k~k~~~~~i~~~~~~~~~i~~~~~~~~~~~~l~~l~~~l~~~~v~Gi~~I~r~~i~~~~~~~~~~~~~~~~~~~~l~ 1109 (1265)
... .. + ..+............. ......+|.+.
T Consensus 152 ~~~-~~-------~--------------------------------~~~~~~~~~~~~~~~~-------~~~~~~~~~l~ 184 (277)
T PF04998_consen 152 KNG-KK-------V--------------------------------KNGDKIKKGSIISKDI-------LEKKSKEYVLQ 184 (277)
T ss_dssp CST-TC-------E--------------------------------HTTCESSSSCSEHHHH-------CEECCCCCEEE
T ss_pred ecc-cc-------e--------------------------------ecceeeecceeeeecc-------ccchhHHHHHH
Confidence 000 00 0 0000000000000000 00134678999
Q ss_pred EeCccHHHhhccCC-ccccccccCCHHHHHHHhCHHHHHHHHHHHHHHHhhccccccCcccceeeecccccccEEEeecc
Q 000829 1110 VEGTGLQAVMGAEG-IDGCKTKSNHIFEVQQTLGIEAARICIIDEINETMKAHGMSIDKRHMMLLADLMTFRGEVLGITR 1188 (1265)
Q Consensus 1110 teG~nl~~~~~~~~-VD~~~~~sNdI~ev~~~lGIEAAR~~Iv~Ei~~v~~~~Gi~Vd~RHl~LlAD~MT~~G~~~~i~R 1188 (1265)
++|.+++.+|..++ +|++++++|||++|+++|||||||++|++|++.||..||++||+|||+|+||+||++|.++||||
T Consensus 185 ~~g~~l~~v~~~qgvid~~k~~sn~I~qm~~~~GIeaar~~i~~e~~~v~~~~g~~vn~rhl~llad~mt~~g~~~gitR 264 (277)
T PF04998_consen 185 TEGSNLQEVYSSQGVIDNDKHISNDIRQMLSKLGIEAARNSIIKELKNVFESYGIEVNKRHLSLLADYMTYKGVLLGITR 264 (277)
T ss_dssp CCSHHHHHHTCSTT-EETCHHECSHHHHHHHHHEHHHHHHHHHHHHHCHHHHCTSCCCHHHHHHHHHHHCCCSS---CCT
T ss_pred HHhhhchhheecccccCCCEEEeceeEeeeeeEEEEECCCceeecCcEeeHHHHHHHHHHHHHhCCCcCeeeeEEEEEEH
Confidence 99999999999999 79999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccCCcHhh
Q 000829 1189 FGIQKMDKSVLM 1200 (1265)
Q Consensus 1189 ~Gi~~~~~Spl~ 1200 (1265)
+||++.++|.|+
T Consensus 265 ~gl~~~~~S~~~ 276 (277)
T PF04998_consen 265 HGLNSNKSSFLS 276 (277)
T ss_dssp TTTSSSSSSHHH
T ss_pred HHhccCCCCccC
Confidence 999986556554
No 25
>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=3.5e-71 Score=637.39 Aligned_cols=336 Identities=20% Similarity=0.262 Sum_probs=268.0
Q ss_pred CccceeecccccCCccccccccccccccccccceecccchhHhhhhc--ccccccceEEEEccC-------CCc-HHHHH
Q 000829 905 GTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIING--AKRISTPIITAELEC-------NDN-ENAAR 974 (1265)
Q Consensus 905 GEaVG~IAAQSIGEPsTQMTLnTFH~AGv~~~NVTlGvPRLkEIina--sk~ikTP~~ti~l~~-------~~~-~~~a~ 974 (1265)
|||||+|||||||||+|||||||||+||++ +|||||||||. ++++|||.++++|.. +.. ++.|+
T Consensus 1 GE~VG~LAAqSIgEPAtQmtLntfh~agvs------~vprLKEiLn~~~~~~~ktps~~v~L~~~~~~~~~~~~~~~~a~ 74 (381)
T cd02737 1 GEPVGSLAATAISEPAYKALLDPPQSLESS------PLELLKEVLECRSKSKSKENDRRVILSLHLCKCDHGFEYERAAL 74 (381)
T ss_pred CCcchhHHHhhhcchHHHhhhccchhcCCc------cHHHHHHHhcccccCCCCCCCEEEEEeccccccccchHHHHHHH
Confidence 899999999999999999999999999996 49999999998 788999999999975 211 55799
Q ss_pred HHhcceeEEeccccceeEEEEEeCCccEEEEEeChhhHHHh--h--cccCHHHHH-HHHhcCcccccc--cCceeeeccc
Q 000829 975 VVKGRIEKTLLGQVAKSIKIVMTSRLASIVIALDMETIQDA--H--LCINADIVK-ESIVQTPKIKLK--QQHIKVLDFR 1047 (1265)
Q Consensus 975 ~v~~~le~~~L~di~~~i~~~y~~~~~~~~i~ld~~~i~~~--~--~~i~~~~i~-~~i~~~~k~k~~--~~~i~~~~~~ 1047 (1265)
.++.+||+++|++++..+.++|+|+.....+..|.+.++.. + .++-..+.. ... ..+-+++. ..........
T Consensus 75 ~Vq~~Le~~tL~~v~~~~~I~Ydp~~~~t~i~~d~~~~~~~~~~~~~~~~~~~~~~~~~-spw~~r~~l~~~~~~~~~~~ 153 (381)
T cd02737 75 EVKNHLERVTLEDLATTSMIKYSPQATEAIVGEIGDQLNTKKKGKKKAIFSTSLKITKF-SPWVCHFHLDKECQKLSDGP 153 (381)
T ss_pred HHHHHhhhccHHHhhheEEEEECCCcccccccccHHHHHhhhhhhhhcccccccccccC-CcceEEEEEehhHhcCCCCc
Confidence 99999999999999999999999998888888888775541 0 000000000 000 00000000 0000000112
Q ss_pred eEEEeCC-CCCCcc----eeehHHHhhhcCCcEEecccCceEEEEeccccccchhhc---cCCcccEEEEEe--------
Q 000829 1048 KLEIFPP-VDKSKI----HFELYSLKNVLPMVIVKGIKTVERVVIAEKEKEKRKVKE---NGEKKKYRLLVE-------- 1111 (1265)
Q Consensus 1048 ~~~i~~~-~~~~~~----~~~l~~l~~~l~~~~v~Gi~~I~r~~i~~~~~~~~~~~~---~~~~~~~~l~te-------- 1111 (1265)
++.+... +.+.+. ...++.+...+.+++|||+++|++|.|.+.+..+..|.+ ....++|+|.|+
T Consensus 154 ci~~~~~~~~~~~~~~~~~~~~~~i~~~lL~~~lkG~~~I~kv~i~~~~~~~~~~~~~~~~~~~~E~vLe~~~~~~~~~t 233 (381)
T cd02737 154 CLTFSVSKEVSKSSEELLDVLRDRIIPFLLETVIKGDERIKSVNILWEDSPSTSWVKSVGKSSRGELVLEVTVEESCKKT 233 (381)
T ss_pred eEEeecCcccccchhHHHHHHHHHHHHHHhheeecccCCeeEEEEEecCCCcccccccccccccceEEEEEEeccccccc
Confidence 3333321 111111 123555666677899999999999999875544344443 235689999988
Q ss_pred -CccHHHhhc-----cCCccccccccCCHHHHHHHhCHHHHHHHHHHHHHHHhhccccccCcccceeeecccccccEEEe
Q 000829 1112 -GTGLQAVMG-----AEGIDGCKTKSNHIFEVQQTLGIEAARICIIDEINETMKAHGMSIDKRHMMLLADLMTFRGEVLG 1185 (1265)
Q Consensus 1112 -G~nl~~~~~-----~~~VD~~~~~sNdI~ev~~~lGIEAAR~~Iv~Ei~~v~~~~Gi~Vd~RHl~LlAD~MT~~G~~~~ 1185 (1265)
|++|+.+|+ +++||++|++||||++|+++|||||||++|++||+.||+.||++||+|||+||||+||++|.++|
T Consensus 234 ~G~~~~~vl~~c~~~~~~ID~~rt~sNdI~ev~~~lGIEAAR~~ii~El~~v~~~~G~~Vd~rHL~LlAD~MT~~G~~~~ 313 (381)
T cd02737 234 RGNAWNVVMDACIPVMDLIDWERSMPYSIQQIKSVLGIDAAFEQFVQRLESAVSMTGKSVLREHLLLVADSMTYSGEFVG 313 (381)
T ss_pred cchhHHHHHHhhhcccccCcCCCcEECCHHHHHHHHhHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHhccCCceEE
Confidence 999999994 99999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eccccccccCC-----cHhhHhcchHHHHHHHHhhhcCCcccccccccceeccCCCCCCccc-eEeee
Q 000829 1186 ITRFGIQKMDK-----SVLMLASFEKTADHLFNASVNGRDDRIEGVSECIIMGIPMPLGTGI-LKIRQ 1247 (1265)
Q Consensus 1186 i~R~Gi~~~~~-----Spl~~aSFE~T~~~L~~AA~~g~~D~l~gvS~~Ii~Gk~~~~GTG~-fdll~ 1247 (1265)
|||+||+++++ |||++||||+|+++|++||.+|+.|+|+|||+||+||+++++|||+ |||++
T Consensus 314 ~nR~Gi~~~~~s~~~~spl~~asFE~t~~~l~~AA~~g~~D~l~gvs~~ii~G~~~~vGTG~~fdll~ 381 (381)
T cd02737 314 LNAKGYKAQRRSLKISAPFTEACFSSPIKCFLKAAKKGASDSLSGVLDACAWGKEAPVGTGSKFEILW 381 (381)
T ss_pred ecchhhhhcccccccCCHHHHhhHHHHHHHHHHHHhccCCCCCCChHHheeeCCcCCCcCCcceeeeC
Confidence 99999998765 8999999999999999999999999999999999999999999997 99986
No 26
>PRK02597 rpoC2 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=100.00 E-value=2.5e-70 Score=692.26 Aligned_cols=342 Identities=28% Similarity=0.474 Sum_probs=252.5
Q ss_pred ccccccccCCCcccHHHHHHHHhChhhHHHHHhHHHHHHHHHHHhccceeeeccCCCCccchHHHHHHHHHHHHHHHHHH
Q 000829 520 QLGKATLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLSARWIGNHGFSIGIDDVQPKKELSDKKGKLISENYEVCNVKI 599 (1265)
Q Consensus 520 ~ldK~~lG~~~~~~Li~~i~~~yG~~~a~~~l~~~~~l~~~~L~~~GFSigi~D~~~~~~~~~~~~~~i~~a~~~~~~~i 599 (1265)
++||+.++ +|++.+++.||+..|+.|||++++|+++|++.+|||+|++|+.+++ +|.+++++|++++.++.
T Consensus 7 ~idKk~l~-----~LI~~~~~~yG~~~t~~~lD~lk~LGf~~aT~~G~SigidDl~ip~----~K~~li~~Ae~~v~~~~ 77 (1331)
T PRK02597 7 VVDKKALK-----NLIAWAFKNYGTARTAQMADNLKDLGFRYATQAGVSISVDDLKVPP----AKRDLLEQAEEEITATE 77 (1331)
T ss_pred cccHHHHH-----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhCcEEEeecccccCH----HHHHHHHHHHHHHHHHH
Confidence 68999997 5999999999999999999999999999999999999999999876 48889999999999999
Q ss_pred HHHHcCCCccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhcCC---CCCCcceeeeccCCCCChhcHhHHhhcccccccC
Q 000829 600 KEYNEGKLQLKPGCDAAQTLEAVITDILNRIREDAGKACMGSL---PWRNSPLIMSQCGSKGSPINISQMVACVGQQSVG 676 (1265)
Q Consensus 600 ~~~~~g~l~~~~~~~~~~~le~~i~~~l~~~~~~~~~~~~~~l---~~~N~~~~M~~sGsKGS~~Ni~Qi~~~lGQQ~~~ 676 (1265)
++|..|.++. .+.+ .++..+|+++++.+.+.+++.+ ++.|++++|+.||||||..|+.|++|+.|++.
T Consensus 78 ~~y~~G~it~------~Er~-~kvi~~w~~t~e~l~~~~~~~~~~~dp~N~v~mMa~SGARGN~sQI~QLvGmRGLma-- 148 (1331)
T PRK02597 78 ERYRRGEITE------VERF-QKVIDTWNETNERLKDEVVKNFRQNDPLNSVYMMAFSGARGNMSQVRQLVGMRGLMA-- 148 (1331)
T ss_pred HHHHcCCCch------hHHH-HHHHHHHHHHHHHHHHHHHHHHhhcCCCCcHHHHhhccCCccHHHHHHHhcchhhcc--
Confidence 9999999863 3444 6777899999998888777665 56899999999999997777777777777764
Q ss_pred CCCCCCCCCCcccCCCCCCCCCCCccceeccccccCCChhhhhhhhccccccchhcccccCcCChhHHHHHHHhhheEee
Q 000829 677 GRRAPNGFIDRSLPHFPRKAKEPAAKGFVANSFYSGLSATEFFFHTMGGREGLVDTAVKTADTGYMSRRLIKALEDLSIQ 756 (1265)
Q Consensus 677 G~Rip~~~~~rtLP~f~~~~~~~~a~GfV~~sf~~GL~p~EfFfH~m~GReGLiDTAvKTa~sGYlqRrLvk~lEdl~v~ 756 (1265)
.|.|.. ..|| |.|||++||+|+|||||||||||||||||||||+|||||||||+++||++|.
T Consensus 149 ---~p~G~i-i~lP--------------I~snFrEGLs~~EyFis~~GaRKGLvDTAlKTAdSGYLTRRLVdv~QDviVr 210 (1331)
T PRK02597 149 ---NPQGEI-IDLP--------------IKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVR 210 (1331)
T ss_pred ---CCCCcE-Eecc--------------hhhhhhcCCCHHHhheeccccccchhhcceecccchhHHHHHHHhhcceEEE
Confidence 333321 2455 8999999999999999999999999999999999999999999999999997
Q ss_pred ecCeEEcCCCcEEEEEecCCCcccccccCCCCCCchhHHHHHHH--HhcCCCCCCCCCCHHHHHHHHHHHHhhcCCCcch
Q 000829 757 YDNSVRNAGGCIVQFLYGDDGMDPANMEGKSGEPLNFDRLLMKV--KATCPPAGQRYLSPQQVSEIVEKQLAAYGKESCS 834 (1265)
Q Consensus 757 YD~TVR~s~g~iiQf~YGeDG~d~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 834 (1265)
++.+ -...|-.|.-.. ||-.. ++ ++. ++++..+ ..+.... ...+ ..+++ ...
T Consensus 211 e~DC-gT~~gi~~~~~~--~~~~~--i~-----~l~-~rl~GR~~~~~i~~~~-~~~i------------~~~n~--~i~ 264 (1331)
T PRK02597 211 EEDC-GTTRGIVVEAMD--DGDRV--LI-----PLG-DRLLGRVLAEDVVDPE-GEVI------------AERNT--AID 264 (1331)
T ss_pred ecCC-CCCCCEEEEEEe--cCCEE--Ee-----Eeh-heeEEEEEhhHeeCCC-CCEE------------EeCCC--CcC
Confidence 7632 112243333221 11000 00 000 0111000 0000000 0000 00000 011
Q ss_pred HHHHHHHHHHHHHhhhhhhhhhhcccccCCCccchhhhhhhhhccCCCHHHHHHHHHHHHHh--hhcccCCcCccceeec
Q 000829 835 EAFLNSLRKFFEGQQDKLDKKIKFVEDIGWDDKSQILEEVTHKTSGITEKQLEVFIQTCFSR--YRVKRVEAGTAIGAIG 912 (1265)
Q Consensus 835 ~~~~~~i~~~i~~~~~~l~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k--y~~slv~PGEaVG~IA 912 (1265)
+...+.+.+. ++ +.+..++.+||+.-.++|+.||-. ....+|+.|||||+||
T Consensus 265 ~~~~~~i~~~------------------~~--------~~v~iRspltC~s~~gvC~~CYG~~la~~~lv~lGeaVGiiA 318 (1331)
T PRK02597 265 PDLAKKIEKA------------------GV--------EEVMVRSPLTCEAARSVCRKCYGWSLAHNHLVDLGEAVGIIA 318 (1331)
T ss_pred HHHHHHHHHc------------------CC--------CEEEEECCEEecCCCCchhhccCcchhcCcccchhhhhhhhh
Confidence 1111111110 00 023345678998888888888643 4568899999999999
Q ss_pred ccccCCcccccccccccccccccccee-------cccchhHhhh
Q 000829 913 AQSIGEPGTQMTLKTFHFAGVASMNIT-------QGVPRIKEII 949 (1265)
Q Consensus 913 AQSIGEPsTQMTLnTFH~AGv~~~NVT-------lGvPRLkEIi 949 (1265)
|||||||+|||||+|||.+||++..++ .|++++.|-+
T Consensus 319 aQSIGEPGTQLTmRTFHtGGv~~~~~~~~i~~~~~G~i~~~~~~ 362 (1331)
T PRK02597 319 AQSIGEPGTQLTMRTFHTGGVFTGEVARQVRSPFAGTVEFGKKL 362 (1331)
T ss_pred hccccCCcchhehhhhhhccccccccceeEEeccCeEEEEecCC
Confidence 999999999999999999999988888 8999999844
No 27
>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=6.5e-70 Score=683.20 Aligned_cols=330 Identities=27% Similarity=0.444 Sum_probs=240.6
Q ss_pred ccccccccCCCcccHHHHHHHHhChhhHHHHHhHHHHHHHHHHHhccceeeeccCCCCccchHHHHHHHHHHHHHHHHHH
Q 000829 520 QLGKATLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLSARWIGNHGFSIGIDDVQPKKELSDKKGKLISENYEVCNVKI 599 (1265)
Q Consensus 520 ~ldK~~lG~~~~~~Li~~i~~~yG~~~a~~~l~~~~~l~~~~L~~~GFSigi~D~~~~~~~~~~~~~~i~~a~~~~~~~i 599 (1265)
++||+.++ +|++.++.+||+..|+.|||++++|+++|++.+|||+|++|+.+++ +|.+++++|++++.+++
T Consensus 6 ~idKk~l~-----~LI~~~~~~yG~~~t~~~lD~lk~Lgf~~aT~~G~SigidDl~ip~----~K~~li~~a~~~v~~~~ 76 (1227)
T TIGR02388 6 VVDKKALK-----NLISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPP----AKQDLLEAAEKEIRATE 76 (1227)
T ss_pred ccchHHHH-----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCeEEeeccCCCCH----HHHHHHHHHHHHHHHHH
Confidence 68999996 5999999999999999999999999999999999999999999886 47889999999999999
Q ss_pred HHHHcCCCccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhcC---CCCCCcceeeeccCCCCChhcHhHHhhcccccc-c
Q 000829 600 KEYNEGKLQLKPGCDAAQTLEAVITDILNRIREDAGKACMGS---LPWRNSPLIMSQCGSKGSPINISQMVACVGQQS-V 675 (1265)
Q Consensus 600 ~~~~~g~l~~~~~~~~~~~le~~i~~~l~~~~~~~~~~~~~~---l~~~N~~~~M~~sGsKGS~~Ni~Qi~~~lGQQ~-~ 675 (1265)
++|+.|.++. .+.++ ++.++|+++++.+.+.+.+. +++.|++++|+.||||||+.|+.|++|+.|+|. .
T Consensus 77 ~~y~~G~it~------~Er~~-~ii~~w~~t~e~~~~~~~~~~~~~d~~N~v~mMa~SGARGNisQi~QLvGmrGlma~p 149 (1227)
T TIGR02388 77 ERYRRGEITE------VERFQ-KVIDTWNGTNEELKDEVVNNFRQTDPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANP 149 (1227)
T ss_pred HHHHcCCCcc------hhhHH-HHHHHHHHHHHHHHHHHHHhhhhcCCCCcHHHHhhccCcccHHHHHHHhcchheecCC
Confidence 9999999864 34454 56788999999888877765 458999999999999996666666666666654 2
Q ss_pred CCCCCCCCCCCcccCCCCCCCCCCCccceeccccccCCChhhhhhhhccccccchhcccccCcCChhHHHHHHHhhheEe
Q 000829 676 GGRRAPNGFIDRSLPHFPRKAKEPAAKGFVANSFYSGLSATEFFFHTMGGREGLVDTAVKTADTGYMSRRLIKALEDLSI 755 (1265)
Q Consensus 676 ~G~Rip~~~~~rtLP~f~~~~~~~~a~GfV~~sf~~GL~p~EfFfH~m~GReGLiDTAvKTa~sGYlqRrLvk~lEdl~v 755 (1265)
.|+++ .|| |.+||++||+|.|||||||||||||||||||||+|||||||||+++||++|
T Consensus 150 ~G~ii-------~lP--------------I~snFreGLt~~EyF~sa~GaRkGLvDTAlKTAdSGYLTRRLVdv~qDviV 208 (1227)
T TIGR02388 150 QGEII-------DLP--------------IKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIV 208 (1227)
T ss_pred CCcEe-------ecc--------------chhhhhcCCCHHHhheeccccccchhhcceeccccchHHHHHHHhhceEEE
Confidence 34333 355 899999999999999999999999999999999999999999999999999
Q ss_pred eecCeEEcCCCcEEEEEecCCCcccccccCCCCCCchhHHHHHHHH--hcCCCCCCCCCCHHHHHHHHHHHHhhcCCCcc
Q 000829 756 QYDNSVRNAGGCIVQFLYGDDGMDPANMEGKSGEPLNFDRLLMKVK--ATCPPAGQRYLSPQQVSEIVEKQLAAYGKESC 833 (1265)
Q Consensus 756 ~YD~TVR~s~g~iiQf~YGeDG~d~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 833 (1265)
.++.+ -...|-.+.-.-.++-+.+ +. ++++..+. .+.... ...+ ..+++ ..
T Consensus 209 ~~~DC-gT~~gi~v~~~~~~~~~~~----------l~-~rl~GRv~~~di~~~~-~~~i------------~~~n~--~I 261 (1227)
T TIGR02388 209 REEDC-GTERSIVVRAMTEGDKKIS----------LG-DRLLGRLVAEDVLHPE-GEVI------------VPKNT--AI 261 (1227)
T ss_pred EEcCC-CCCCCEEEEEeeCCCeEeE----------hh-heeEeeeEHhHeECCC-CcEE------------EeCCC--cc
Confidence 76632 1112322221111000101 00 11111100 000000 0000 00000 01
Q ss_pred hHHHHHHHHHHHHHhhhhhhhhhhcccccCCCccchhhhhhhhhccCCCHHHHHHHHHHHH--HhhhcccCCcCccceee
Q 000829 834 SEAFLNSLRKFFEGQQDKLDKKIKFVEDIGWDDKSQILEEVTHKTSGITEKQLEVFIQTCF--SRYRVKRVEAGTAIGAI 911 (1265)
Q Consensus 834 ~~~~~~~i~~~i~~~~~~l~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~ky~~slv~PGEaVG~I 911 (1265)
.+...+.+.++ ++ +.+..++++||+...++|+.|| ......+|+.|||||+|
T Consensus 262 ~~~~~~~i~~~------------------~~--------~~v~iRspltC~s~~~vC~~CYG~~la~~~lV~lGeaVGii 315 (1227)
T TIGR02388 262 DPDLAKTIETA------------------GI--------SEVVVRSPLTCEAARSVCRKCYGWSLAHAHLVDLGEAVGII 315 (1227)
T ss_pred CHHHHHHHHHc------------------CC--------CEEEEeCcceecchhhHhHhccCCccccCcEechhhhhhhh
Confidence 11111111110 00 1233457899999999988885 34567899999999999
Q ss_pred cccccCCcccccccccccccccccccee
Q 000829 912 GAQSIGEPGTQMTLKTFHFAGVASMNIT 939 (1265)
Q Consensus 912 AAQSIGEPsTQMTLnTFH~AGv~~~NVT 939 (1265)
||||||||+|||||+|||.+||.+..+.
T Consensus 316 AaQSIGEPGTQLTmRTFHtGGv~t~~~~ 343 (1227)
T TIGR02388 316 AAQSIGEPGTQLTMRTFHTGGVFTGEVA 343 (1227)
T ss_pred hhhccCCcchhhhhhhhhhcccccccee
Confidence 9999999999999999999999875554
No 28
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=100.00 E-value=1.1e-65 Score=650.73 Aligned_cols=317 Identities=38% Similarity=0.583 Sum_probs=275.8
Q ss_pred ecccccCCccccccccccccccccccceecccchhHhhhhcccccccceEEEEccCCC--cHHHHHHHhcceeEEecccc
Q 000829 911 IGAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINGAKRISTPIITAELECND--NENAARVVKGRIEKTLLGQV 988 (1265)
Q Consensus 911 IAAQSIGEPsTQMTLnTFH~AGv~~~NVTlGvPRLkEIinask~ikTP~~ti~l~~~~--~~~~a~~v~~~le~~~L~di 988 (1265)
++|.-| .|||||||||||||++||||||||||+|||||||+||||+|+++|.++. +.+.|+.++++|++++|+||
T Consensus 534 i~Angi---v~~~~LnTFH~AGv~~~nVTlGvPRL~EIinask~i~TP~m~i~l~~~~~~~~~~a~~v~~~ie~~~L~dv 610 (858)
T PRK14898 534 TTADGV---VTHNTMRTFHYAGVAEINVTLGLPRMIEIVDARKEPSTPIMTVHLKGEYATDREKAEEVAKKIESLTLGDV 610 (858)
T ss_pred eeeCCE---eeccccceeeccCccccccccCCchHHHHhcccCCCCCceEEEEECCCccchHHHHHHHHhheeeEEHHHH
Confidence 345555 4999999999999999999999999999999999999999999999863 56899999999999999999
Q ss_pred ceeEEEEEeCCccEEEEEeChhhHHHhhcccCHHHHHHHHhcCcccccccCceeeeccceEEEeCCCCCCcceeehHHHh
Q 000829 989 AKSIKIVMTSRLASIVIALDMETIQDAHLCINADIVKESIVQTPKIKLKQQHIKVLDFRKLEIFPPVDKSKIHFELYSLK 1068 (1265)
Q Consensus 989 ~~~i~~~y~~~~~~~~i~ld~~~i~~~~~~i~~~~i~~~i~~~~k~k~~~~~i~~~~~~~~~i~~~~~~~~~~~~l~~l~ 1068 (1265)
+.++++.+. ..+++++||.+.+..+ .+++++|..+|...++.++.. .+..+++.+.. .....+..+.
T Consensus 611 ~~~~~~~~~--~~~~~i~l~~~~~~~~--~l~~~~i~~~i~~~~~~~~~~------~~~~~~~~~~~---~~~~~~~~~~ 677 (858)
T PRK14898 611 ATSIAIDLW--TQSIKVELDEETLADR--GLTIESVEEAIEKKLGVKIDR------KGTVLYLKPKT---PSYKALRKRI 677 (858)
T ss_pred HHHhhhhcc--ccEEEEEECHHHHHHc--CCCHHHHHHHHHHhccccccC------CCCEEEEEecC---chHHHHHHHH
Confidence 999885332 2358888999988876 578999999998754332211 22445555421 1123355566
Q ss_pred hhcCCcEEecccCceEEEEeccccccchhhccCCcccEEEEEeCccHHHhhccCCccccccccCCHHHHHHHhCHHHHHH
Q 000829 1069 NVLPMVIVKGIKTVERVVIAEKEKEKRKVKENGEKKKYRLLVEGTGLQAVMGAEGIDGCKTKSNHIFEVQQTLGIEAARI 1148 (1265)
Q Consensus 1069 ~~l~~~~v~Gi~~I~r~~i~~~~~~~~~~~~~~~~~~~~l~teG~nl~~~~~~~~VD~~~~~sNdI~ev~~~lGIEAAR~ 1148 (1265)
..|++++|+|+|||+||.+..++. .+.++|.|+|||+||.++|.+++||+++|+||||++|+++|||||||+
T Consensus 678 ~~l~~~~i~gi~gI~~~~i~~~~~--------~~~~~~~l~teG~nl~~~~~~~~vd~~~~~sN~i~~i~~~lGIEAar~ 749 (858)
T PRK14898 678 PKIKNIVLKGIPGIERVLVKKEEH--------ENDEEYVLYTQGSNLREVFKIEGVDTSRTTTNNIIEIQEVLGIEAARN 749 (858)
T ss_pred HHhcCcEEECCCCccEEEEecCCC--------CCCceEEEEecCcCHHHHhcCCCCcccccccCCHHHHHHhhCHHHHHH
Confidence 678999999999999999985320 123589999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhccccccCcccceeeecccccccEEEeeccccccccCCcHhhHhcchHHHHHHHHhhhcCCccccccccc
Q 000829 1149 CIIDEINETMKAHGMSIDKRHMMLLADLMTFRGEVLGITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDDRIEGVSE 1228 (1265)
Q Consensus 1149 ~Iv~Ei~~v~~~~Gi~Vd~RHl~LlAD~MT~~G~~~~i~R~Gi~~~~~Spl~~aSFE~T~~~L~~AA~~g~~D~l~gvS~ 1228 (1265)
+|++||++||+.||++||+|||+||||+||++|+++||||+||+.+++|||++||||+|+++|++||++|++|+|+||||
T Consensus 750 ~ii~Ei~~v~~~~gi~V~~rHl~liad~MT~~G~~~~~~r~gi~~~~~s~l~~asFe~t~~~l~~Aa~~g~~D~l~g~s~ 829 (858)
T PRK14898 750 AIINEMMNTLEQQGLEVDIRHLMLVADIMTADGEVKPIGRHGVAGEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIE 829 (858)
T ss_pred HHHHHHHHHHHhcCCccCHHHHHHHHHHHccCCcEEEeccCCccCCCCCHHHhcChHhHHHHHHHHhhcCCCCcCCCchH
Confidence 99999999999999999999999999999999999999999998888999999999999999999999999999999999
Q ss_pred ceeccCCCCCCccceEeeecCCC
Q 000829 1229 CIIMGIPMPLGTGILKIRQRDAV 1251 (1265)
Q Consensus 1229 ~Ii~Gk~~~~GTG~fdll~~~~~ 1251 (1265)
|||+|+++|+|||+|||+++...
T Consensus 830 ~ii~G~~~~~GTG~~~l~~~~~~ 852 (858)
T PRK14898 830 NVIVGKPIKLGTGCVDLRIDREY 852 (858)
T ss_pred HeeeCCccCCcCceEEEEecCcc
Confidence 99999999999999999998764
No 29
>CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed
Probab=100.00 E-value=6.6e-65 Score=650.43 Aligned_cols=333 Identities=30% Similarity=0.410 Sum_probs=237.2
Q ss_pred cccccccccCCCcccHHHHHHHHhChhhHHHHHhHHHHHHHHHHHhccceeeeccCCCCccchHHHHHHHHHHHHHHHHH
Q 000829 519 GQLGKATLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLSARWIGNHGFSIGIDDVQPKKELSDKKGKLISENYEVCNVK 598 (1265)
Q Consensus 519 G~ldK~~lG~~~~~~Li~~i~~~yG~~~a~~~l~~~~~l~~~~L~~~GFSigi~D~~~~~~~~~~~~~~i~~a~~~~~~~ 598 (1265)
-++||+.++ +|++.++++||++.|+.|||++++|+++|++.+|||+|++|+.+|+ .|.+++++|++++.++
T Consensus 12 ~~~~k~~l~-----~li~~~~~~~G~~~t~~~lD~lk~lgf~~at~~G~Sigi~Dl~ip~----~K~~li~~a~~~v~~~ 82 (1364)
T CHL00117 12 KVIDKTALK-----RLISWLIDHFGMAYTSHILDQLKTLGFQQATAAGISLGIDDLLTPP----SKGWLVQDAEQQSLIL 82 (1364)
T ss_pred ccccHHHHH-----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcceEEecCcccCCH----HHHHHHHHHHHHHHHH
Confidence 368999997 4999999999999999999999999999999999999999999885 5788999999999999
Q ss_pred HHHHHcCCCccCCCCCHHHHHHHHHHHHHHHHHHHHHH---HHhcCCCCCCcceeeeccCCCCChhcHhHHhhccccccc
Q 000829 599 IKEYNEGKLQLKPGCDAAQTLEAVITDILNRIREDAGK---ACMGSLPWRNSPLIMSQCGSKGSPINISQMVACVGQQSV 675 (1265)
Q Consensus 599 i~~~~~g~l~~~~~~~~~~~le~~i~~~l~~~~~~~~~---~~~~~l~~~N~~~~M~~sGsKGS~~Ni~Qi~~~lGQQ~~ 675 (1265)
.++|+.|.++ ..|+++..+ ++|+.+.+.+.+ .+.+.+++.||+++|+.|||||| ++||.+|+|++.+
T Consensus 83 ~~~y~~G~it------~~er~~~~i-~~w~~~~~~l~~~~~~~~~~~d~~N~v~mMa~SGARGn---~sQi~qLvGmRGl 152 (1364)
T CHL00117 83 EKHYHYGNVH------AVEKLRQSI-EIWYATSEYLKQEMNPNFRMTDPLNPVYMMSFSGARGN---ASQVHQLVGMRGL 152 (1364)
T ss_pred HHHHHcCCCC------HHHHHHHHH-HHHHHHHHHHHHHHHHhhccCCCCCcHhhhhhccCccc---HHHHHHHhcccce
Confidence 9999999986 356676655 444444433333 33455678999999999999995 5555555555443
Q ss_pred ----CCCCCCCCCCCcccCCCCCCCCCCCccceeccccccCCChhhhhhhhccccccchhcccccCcCChhHHHHHHHhh
Q 000829 676 ----GGRRAPNGFIDRSLPHFPRKAKEPAAKGFVANSFYSGLSATEFFFHTMGGREGLVDTAVKTADTGYMSRRLIKALE 751 (1265)
Q Consensus 676 ----~G~Rip~~~~~rtLP~f~~~~~~~~a~GfV~~sf~~GL~p~EfFfH~m~GReGLiDTAvKTa~sGYlqRrLvk~lE 751 (1265)
.|++| .+| |.+||++||+|.|||||||||||||||||||||+|||||||||+++|
T Consensus 153 ma~p~G~iI-------~~P--------------I~snFreGLs~~EyFis~~GaRkGLvDTAlkTAdSGYLtRRLVdv~q 211 (1364)
T CHL00117 153 MSDPQGQII-------DLP--------------IQSNFREGLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRLVEVVQ 211 (1364)
T ss_pred eeCCCCcEe-------ecc--------------hhhhhhcCCCHHHhheeccccccchhhcceecccccchhhHHHhhhc
Confidence 33333 233 89999999999999999999999999999999999999999999999
Q ss_pred heEee-ec-CeEEcCCCcEEEEEecCCCcccccccCCCCCCchhHHHHHHHH--hcCCCCCCCCCCHHHHHHHHHHHHhh
Q 000829 752 DLSIQ-YD-NSVRNAGGCIVQFLYGDDGMDPANMEGKSGEPLNFDRLLMKVK--ATCPPAGQRYLSPQQVSEIVEKQLAA 827 (1265)
Q Consensus 752 dl~v~-YD-~TVR~s~g~iiQf~YGeDG~d~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~ 827 (1265)
||+|. .| ||. .|-.+.-.-|++-+.+. . ++++..+. .+.. ....+ ..+
T Consensus 212 dviV~~~dCgt~---~gi~~~~~~~~~~~~~l--~---------~rl~GRv~~~di~~--~~~~i------------~~~ 263 (1364)
T CHL00117 212 HIVVRETDCGTT---RGISVSPRNGMMIERIL--I---------QTLIGRVLADDIYI--GSRCI------------ATR 263 (1364)
T ss_pred cEEEEeccCCCC---CCEEEEEecCCeEEeEe--c---------ceeEEEEEhhhEEe--CCEEE------------EeC
Confidence 99985 44 332 23333322221100000 0 00100000 0000 00000 000
Q ss_pred cCCCcchHHHHHHHHHHHHHhhhhhhhhhhcccccCCCccchhhhhhhhhccCCCHHHHHHHHHHHH--HhhhcccCCcC
Q 000829 828 YGKESCSEAFLNSLRKFFEGQQDKLDKKIKFVEDIGWDDKSQILEEVTHKTSGITEKQLEVFIQTCF--SRYRVKRVEAG 905 (1265)
Q Consensus 828 ~~~~~~~~~~~~~i~~~i~~~~~~l~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~ky~~slv~PG 905 (1265)
++ ...+...+.+.+ . ++ +.+..++++||+...++|+.|| ......+|+.|
T Consensus 264 n~--~I~~~~~~~i~~-----------~-------~~--------~~v~iRSpltC~~~~~vC~~CYG~~la~~~lV~~G 315 (1364)
T CHL00117 264 NQ--DIGIGLANRFIT-----------F-------RA--------QPISIRSPLTCRSTSWICQLCYGWSLAHGDLVELG 315 (1364)
T ss_pred CC--CcCHHHHHHHHH-----------c-------CC--------CEEEEeCCcccccHHHHHHHHhCcccccCcccChh
Confidence 00 011111111111 0 00 1223467899999999888887 34466889999
Q ss_pred ccceeecccccCCccccccccccccccccccceec-------ccchhHh
Q 000829 906 TAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNITQ-------GVPRIKE 947 (1265)
Q Consensus 906 EaVG~IAAQSIGEPsTQMTLnTFH~AGv~~~NVTl-------GvPRLkE 947 (1265)
||||+|||||||||||||||+|||.+||++..++. |+.++.+
T Consensus 316 eaVGiiAaQSIGEPGTQLTmRTFH~GGv~t~~~~~~i~a~~~G~i~~~~ 364 (1364)
T CHL00117 316 EAVGIIAGQSIGEPGTQLTLRTFHTGGVFTGGTAEQVRAPFNGKIKFNE 364 (1364)
T ss_pred hhhhhhhhhccCCCchhhhhhhhhhcccccccceeeEEeccCeEEEEec
Confidence 99999999999999999999999999998766654 7777776
No 30
>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=9.6e-64 Score=518.52 Aligned_cols=165 Identities=59% Similarity=1.001 Sum_probs=149.1
Q ss_pred CCCCCCccceEEcCCCCCCCCcccccHHHHhhcCcceeechHHHHHHHHHHHcCCCCCCCceEEECCCCCeEEe-ccccc
Q 000829 222 GKRVEYTGRTVISPDPNLKITEVAIPIRMARILTYPERVSDHNIEKLRQCIQNGPDKYPGARMIRYPDGTARVL-YGKFR 300 (1265)
Q Consensus 222 GKRvd~saRsVIspDp~l~~~evGvP~~~A~~Lt~pe~Vt~~Ni~~l~~lv~ng~~~~pGa~~i~~~~g~~~~l-~~~~r 300 (1265)
||||||||||||||||+|+++|||||..||++||+||.||+||+++|+++|.|||+.||||+|+++.+|.++.| .. ..
T Consensus 1 GKRVnfSaRSVItpDP~L~~~EvGiP~~iA~~Lt~Pe~Vt~~N~~~l~~~v~ng~~~~pga~~i~~~~~~~~~l~~~-~~ 79 (166)
T PF00623_consen 1 GKRVNFSARSVITPDPNLKIDEVGIPIEIAKKLTFPERVTPFNIEKLRKLVINGPDKYPGANYIKRSNGNKISLRYK-KF 79 (166)
T ss_dssp CEEESSEEEEEEEEETTSCTTEEEEEHHHHHHCECCHHHHTTTHHHHHHHHHHTTTSSSSEEEEESTTCHCCCTTSS-SS
T ss_pred CCCcccCCCcEEECCCCCccceecccHHHHhhCCCcEEEHHHHHHHHHHHHhcCcccchhhhhhhcccCcceeeeec-cc
Confidence 99999999999999999999999999999999999999999999999999999999999999999998888877 33 11
Q ss_pred hhhhhcccccceeecccccCCeEEEecCCCccccceeeEEEEEecCCeeeeecccCCCCCCCCcccccccccCChHHHHH
Q 000829 301 NQLAVELKSGCIVDRHLEDGDVVLFNRQPSLHRMSIMCHRARIMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEART 380 (1265)
Q Consensus 301 ~~~~~~L~~g~iV~Rhl~dgD~VL~NRQPSLHk~Simah~vkv~~~kt~rln~~vc~~yNADFDGDEMN~h~PQs~~ara 380 (1265)
+....|++|++|+||+.|||+|||||||||||+|||||++++++++||||||++|+||||||||||||+|+|||++|+|
T Consensus 80 -~~~~~l~~~~~v~r~l~~gd~vl~nRqPtLh~~s~~a~~~~~~~~~t~~~~~~~c~~~NADFDGDem~i~~p~~~~a~~ 158 (166)
T PF00623_consen 80 -KISKKLRIGDIVERHLCDGDIVLLNRQPTLHRMSIMAHKVRVLPGKTIRINPLVCSPFNADFDGDEMNIHLPQSYEARA 158 (166)
T ss_dssp -CCCHHHHTT-EEEEEHTTT-EEEEEESS-SSGGGEEEEEEEEESSSSEEEEGGGHHHHT--TSS-EEEEE--SSHHHHH
T ss_pred -cccceecchhhHHHhhhcCceeEEeccchhccceeeeeeeeeecccEEEeeccchhhhhccCCcceEEEEecCCHHHHH
Confidence 3456788999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHcCC
Q 000829 381 EALLLMGV 388 (1265)
Q Consensus 381 Ea~~Lm~~ 388 (1265)
||.+||+|
T Consensus 159 E~~~L~~~ 166 (166)
T PF00623_consen 159 EAKELMNV 166 (166)
T ss_dssp HHHHHCBT
T ss_pred HHHHHhcC
Confidence 99999986
No 31
>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=5.9e-47 Score=387.85 Aligned_cols=110 Identities=51% Similarity=0.816 Sum_probs=107.5
Q ss_pred CHHHHHHHhCHHHHHHHHHHHHHHHhhccccccCcccceeeecccccccEEEeeccccccccCCcHhhHhcchHHHHHHH
Q 000829 1133 HIFEVQQTLGIEAARICIIDEINETMKAHGMSIDKRHMMLLADLMTFRGEVLGITRFGIQKMDKSVLMLASFEKTADHLF 1212 (1265)
Q Consensus 1133 dI~ev~~~lGIEAAR~~Iv~Ei~~v~~~~Gi~Vd~RHl~LlAD~MT~~G~~~~i~R~Gi~~~~~Spl~~aSFE~T~~~L~ 1212 (1265)
||++|+++|||||||++|++||++||+.||++||+|||+||||+||++|.++|+||+||++.++|||++||||+|.++|+
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 67899999999999999999999999999999999999999999999999999999999777899999999999999999
Q ss_pred HhhhcCCcccccccccceeccCCCCCCccc
Q 000829 1213 NASVNGRDDRIEGVSECIIMGIPMPLGTGI 1242 (1265)
Q Consensus 1213 ~AA~~g~~D~l~gvS~~Ii~Gk~~~~GTG~ 1242 (1265)
+||.+|+.|+|+|+|+||+||+++|+|||+
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 32
>cd02655 RNAP_beta'_C Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain. Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations.
Probab=100.00 E-value=6.9e-46 Score=393.30 Aligned_cols=109 Identities=28% Similarity=0.547 Sum_probs=101.5
Q ss_pred CCHHHHHHHh--CHHHHHHHHHHHHHHHhhccccccCcccceeeecccccccEE--------------------------
Q 000829 1132 NHIFEVQQTL--GIEAARICIIDEINETMKAHGMSIDKRHMMLLADLMTFRGEV-------------------------- 1183 (1265)
Q Consensus 1132 NdI~ev~~~l--GIEAAR~~Iv~Ei~~v~~~~Gi~Vd~RHl~LlAD~MT~~G~~-------------------------- 1183 (1265)
||++++++++ ||||||..|++||++||..||++||+||++||||+||+++.+
T Consensus 54 ~~~~~il~~~~~Giea~r~~iv~EIq~Vy~~qGV~I~dKHielIv~qMT~kv~i~~~g~s~~l~Ge~v~~~~~~~~N~~~ 133 (204)
T cd02655 54 INPHDLLRIKFLGPEAVQKYLVEEIQKVYRSQGVNINDKHIEIIVRQMTSKVKIIDPGDSGFLPGELVDLNEFEEENKRL 133 (204)
T ss_pred CCHHHHHHHHhHHHHHHHHHHHHHHHHHHHhcCeeecHHHHHHHHHHHhcCeEEecCCCcccCCCceeeHHHHHHHHHHH
Confidence 4556667777 999999999999999999999999999999999999999653
Q ss_pred --------------EeeccccccccCCcHhhHhcchHHHHHHHHhhhcCCcccccccccceeccCCCCCCccc
Q 000829 1184 --------------LGITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDDRIEGVSECIIMGIPMPLGTGI 1242 (1265)
Q Consensus 1184 --------------~~i~R~Gi~~~~~Spl~~aSFE~T~~~L~~AA~~g~~D~l~gvS~~Ii~Gk~~~~GTG~ 1242 (1265)
+||||++++ .+|||++||||+|+++|++||+.|++|+|+|++||||+|+++|+|||+
T Consensus 134 ~~~~~~~~~y~p~llGItk~~l~--~~Sfls~ASFqeT~kvL~~AAi~gk~D~L~GlkeNVI~G~liPaGTG~ 204 (204)
T cd02655 134 LLLGKKPAKYEPVLLGITKASLN--TESFISAASFQETTKVLTEAAIEGKIDWLRGLKENVILGRLIPAGTGL 204 (204)
T ss_pred HhCCCCcccccceeeeeeecccc--CCCccccCChHHHHHHHHHHHhcCCCCCCCCchhheEECCccCCCCCC
Confidence 589999997 589999999999999999999999999999999999999999999995
No 33
>PF04983 RNA_pol_Rpb1_3: RNA polymerase Rpb1, domain 3; InterPro: IPR007066 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1ZYR_D 1SMY_D 2A68_N 2O5J_D 3AOH_N 2O5I_D 2CW0_N 2A6H_N 2A69_D 3EQL_D ....
Probab=99.96 E-value=3.5e-31 Score=276.10 Aligned_cols=158 Identities=37% Similarity=0.601 Sum_probs=132.1
Q ss_pred ccccCCCCCccEeecccceeeeeeeeccCccCCHHHHHHHHHHhcCCCceeecCCCceeCcccccccceeeeeeecCCCC
Q 000829 391 NLCTPKNGEILVASTQDFLTSSFLITRKDTFYDRAAFSLMCCYMGDGMDRVDLPTPAILKPVELWTGKQLFSVLIRPHAN 470 (1265)
Q Consensus 391 ~~~sp~~g~pi~gliQD~l~g~~llT~~d~f~~~~~~~~l~~~~~~~~~~~~lp~Pai~kp~~lwTGKql~s~~l~~~~~ 470 (1265)
||+||++|+|+++++||+|+|+|+||++++|++++++++++++..........|.|+|++|.++|||||+||++||+.
T Consensus 1 NilSP~~G~Pii~~~QD~vlG~y~LT~~~~f~~~~e~~~~~~~~~~~~~~~~~~~~~I~~~~~~~tgk~~~s~il~~~-- 78 (158)
T PF04983_consen 1 NILSPANGKPIIGPTQDMVLGAYYLTSEDTFLSRDEAQQALMNGLIDDKKIVLLHPAILKPKELWTGKQTFSRILPNE-- 78 (158)
T ss_dssp GSEETTTTEESSS--SHHHHHHHHHSSTTTEESHHHHHHHHHCSST----CHCSSSSBSSSSSCEECHHHHHTTSHTT--
T ss_pred CccCCCCCCceEEeccceEeEEEEEEecccccchHHHHHHHHcccccccceeccchhhhccccceeeccHHHHhcccc--
Confidence 799999999999999999999999999999999999999998754322224578999999999999999999999753
Q ss_pred cceEEEEeecccccccccccccCCccccccccCCCCCeeEEecCcceecccccccccCCCcccHHHHHHHHhChhhHHHH
Q 000829 471 MRVYVNLTVKEKTYSNKLIRTEGDEEIRIETMCPNDGFVYFRNSELISGQLGKATLGNGNKDGLYSVLLRDYGAHATSGC 550 (1265)
Q Consensus 471 ~~~~in~~~~~k~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~gell~G~ldK~~lG~~~~~~Li~~i~~~yG~~~a~~~ 550 (1265)
++++... -+++|+.++|+||++++|.+||+++|+++.++|+|.++++||+++|++|
T Consensus 79 ----i~~~~~~--------------------~~~~~~~~~i~~g~~l~g~l~k~~lgk~~~~~li~~i~~~yG~~~~~~~ 134 (158)
T PF04983_consen 79 ----INPEGFS--------------------NDPDDGYVVINNGELLSGVLDKKTLGKKSLGSLIHQIYREYGPEATVQF 134 (158)
T ss_dssp ----HHEEEST--------------------SCHSSHSEEECTSSEEEC--SHHHHSCSHTTCHHHHHHHHSHHHHHHHH
T ss_pred ----ccccccc--------------------ccccccceeecCCccchhheehheecccchhhHHHHHHHHHCHHHHHHH
Confidence 3333211 0122578999999999999999999954788999999999999999999
Q ss_pred HhHHHHHHHHHHHhccceeeeccC
Q 000829 551 MNRLAKLSARWIGNHGFSIGIDDV 574 (1265)
Q Consensus 551 l~~~~~l~~~~L~~~GFSigi~D~ 574 (1265)
||++|+|+++|++.+|||||++|+
T Consensus 135 ld~i~~lg~~~~t~~GfSvgi~D~ 158 (158)
T PF04983_consen 135 LDAIKRLGFRYLTRSGFSVGIDDM 158 (158)
T ss_dssp HHHHHHHHHHHHHHHTBB-SGGGC
T ss_pred HHHHHHHHHHHHHHcCeeEecccC
Confidence 999999999999999999999996
No 34
>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=99.96 E-value=1e-29 Score=294.35 Aligned_cols=200 Identities=35% Similarity=0.561 Sum_probs=148.6
Q ss_pred HHHHHHHHHHHHhhhcCCCCCcCCCCCCCCCcEEecc---------ee-eeEEEecccchhhHHHHhhhhhcchhhhhhh
Q 000829 10 RKTDLMKSIVKKCSTMASKAVKCPRCGYINGMVKKAV---------AV-LGIIHDRSKVTESLQEFASAITHTKESKAAV 79 (1265)
Q Consensus 10 ~r~~~~k~i~~~c~~~~k~~~~C~~Cg~~~p~Vrk~~---------~~-~ki~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 79 (1265)
.+...++.+.+.| ++...|++|+..++.+++.. .. .++..+.. ..+...+... ...++ .
T Consensus 124 ~~~~~~~~i~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~i~~~i~~~-~~~~~----~ 192 (337)
T PF04997_consen 124 KKKERLKIISKEC----KKKSICSHCKAINGKIKKVEKSKKCEGCGKKNPKIRKEGA--EKIQEEIKKK-ESNKE----I 192 (337)
T ss_dssp SHHHHHHHHHHHH----HHTCSSTSTCC-SSS---SSSEETSSSSSSBSCEEEEESH--CCCCCHHHSC-CHHHH----H
T ss_pred cchhHHHHHHHhh----hhhhhhcccccccccccccccchhcccccccCcccccchh--hhcccccccc-ccccc----c
Confidence 3455677788888 66789999988888765310 00 01111100 0111111111 00111 1
Q ss_pred hccccccCHHHHHHHHHhcChhhHHhhcCC---CCcceEEEeeeeeCCCCCCCceecCCCCcCCchhHHHHHHHHHHHHH
Q 000829 80 NVATYILNPVNVLFLFKRMTDTDCEVLYLS---ERPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNAS 156 (1265)
Q Consensus 80 ~~~~~~L~P~~v~~ifk~I~~ed~~lL~~~---~~p~~~~l~~lpVpP~~~RP~~~~~~~~~~~ddlt~~l~~Ii~~n~~ 156 (1265)
....+.|+|.+|+++|++|+++|+++|++. .+|+||||++||||||++||++.++++..+|||||..|++||+.|++
T Consensus 193 ~~~~~~l~~~~v~~ilk~l~~~~~~~l~~~~~~~~P~~~~l~~lpVpP~~~RP~v~~~~~~~~eddlt~~~~~Ii~~N~~ 272 (337)
T PF04997_consen 193 KEELRILTPEEVRQILKKLSKEDKELLGFDPSGSRPEWFFLTVLPVPPPRFRPSVQLGGGRFSEDDLTSLYRKIIKRNNR 272 (337)
T ss_dssp HCHCECESHHHHHHHHHHSHHHHHHHHHHHTTTBSGGGSEEEEEEE-TGGGS-EEEESSSEEEE-HHHHHHHHHHHHHHH
T ss_pred hhhhhhhhhhhhhhcchhhhhhheeeeeccccccccceeEEeeeecCCceeeeeeeeecccccCchHHHHHHHHHHHHHH
Confidence 112347999999999999999999999976 68999999999999999999999999867999999999999999999
Q ss_pred HHHHHHHhccchhhhHHHHHHHHHHHHHhccCCCCCCccccC-CCCchhhhhhhcCccccccccc
Q 000829 157 LQQELVEANSAFKSLAGWETLQVEVAQYINSDVRGVPFSMQV-ARPLSGFVQRLKGKQGRFRGNL 220 (1265)
Q Consensus 157 l~~~~~~~~~~~~~~~~~~~lq~~v~~~~~~~~~~~~~~~~~-~~~~~~i~q~l~gK~G~fR~nl 220 (1265)
|++.+..+++...+.+.|..||.+|+.||||+.++.|.+.++ ++|++||+||||||+||||+||
T Consensus 273 L~~~~~~~~~~~~~~~~~~~LQ~~v~~~~dn~~~~~~~~~~~~~~~~k~i~q~L~gK~GrfR~NL 337 (337)
T PF04997_consen 273 LRKLLEEGAPSSIIMEEWRLLQEAVNSLIDNEKPGKPPAGQKSGRPLKGISQRLKGKEGRFRQNL 337 (337)
T ss_dssp HHHCCTSTSSSCHHHHHHHHHHHHHHHHHCTTSSSSSBCBSTTSSB--THHHHHSSTTSSHCHHT
T ss_pred HHHHHHhhCcchhhhhhhhhhhHhHhHHhhhcccCCcccccccCCCCCCHHHHccCCCCcCCCCC
Confidence 999888899999999999999999999999999988877633 7899999999999999999997
No 35
>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=99.88 E-value=5.5e-24 Score=207.50 Aligned_cols=105 Identities=47% Similarity=0.794 Sum_probs=91.3
Q ss_pred HHHc-CCCccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcceeeeccCCCCChhcHhHHhhcccccccCCCC
Q 000829 601 EYNE-GKLQLKPGCDAAQTLEAVITDILNRIREDAGKACMGSLPWRNSPLIMSQCGSKGSPINISQMVACVGQQSVGGRR 679 (1265)
Q Consensus 601 ~~~~-g~l~~~~~~~~~~~le~~i~~~l~~~~~~~~~~~~~~l~~~N~~~~M~~sGsKGS~~Ni~Qi~~~lGQQ~~~G~R 679 (1265)
++++ ++++..++.+.++.+|..++.+|+++++++++.+.+.++.+|++++|+.||||||++|++||+||+|||.++|+|
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 4444 566667788889999999999999999999999999999889999999999999999999999999999999999
Q ss_pred CCCCCCCcccCCCCCCCCCCCcccee
Q 000829 680 APNGFIDRSLPHFPRKAKEPAAKGFV 705 (1265)
Q Consensus 680 ip~~~~~rtLP~f~~~~~~~~a~GfV 705 (1265)
||.++.+||||||.+++.+|+++|||
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 36
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]
Probab=99.78 E-value=8.9e-21 Score=238.48 Aligned_cols=338 Identities=29% Similarity=0.316 Sum_probs=254.6
Q ss_pred hhcccCCcCccceeecccccCCcccccccccccccc--ccccceecccchhHhhhhcccccccceEEEEccCC--CcHHH
Q 000829 897 YRVKRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAG--VASMNITQGVPRIKEIINGAKRISTPIITAELECN--DNENA 972 (1265)
Q Consensus 897 y~~slv~PGEaVG~IAAQSIGEPsTQMTLnTFH~AG--v~~~NVTlGvPRLkEIinask~ikTP~~ti~l~~~--~~~~~ 972 (1265)
|-..++.+++++|..+|||+++|.||||+.|||+|| ++..++|.|.||+-++.++ +..+||.|++++... .+.+.
T Consensus 406 DGDeM~~Hvp~s~ea~AEa~~lm~tq~nilsP~~Ggpiv~~~qD~v~g~ylLt~~d~-~~~~~~~~ei~l~~~~~~~~e~ 484 (808)
T COG0086 406 DGDEMAVHVPASGEAAAEARGLMGTQMNILTPHYGGPIVAPIQDTVGGPYLLTIVDA-KLPSTPVGEIYLKDEYADDREK 484 (808)
T ss_pred CchhhhccccchHHHHHHHHHhhccccccccCCCCCceEeecceEEeccEEEEEecc-cCCCCcceEEEeccccccchhh
Confidence 456788999999999999999999999999999999 9999999999999999988 999999999988633 34677
Q ss_pred HHHHhcceeEEeccccceeEEEEEeCCccEEEEEeChhhHHHhhcccCHHHHHHHHhcCcccccccCceeeeccceEEEe
Q 000829 973 ARVVKGRIEKTLLGQVAKSIKIVMTSRLASIVIALDMETIQDAHLCINADIVKESIVQTPKIKLKQQHIKVLDFRKLEIF 1052 (1265)
Q Consensus 973 a~~v~~~le~~~L~di~~~i~~~y~~~~~~~~i~ld~~~i~~~~~~i~~~~i~~~i~~~~k~k~~~~~i~~~~~~~~~i~ 1052 (1265)
+..+...++.++..++++.+.... ....+.++.+...+....+..+. ++...+......+ .+.++....+.
T Consensus 485 ~~ai~~~~~~~~~k~i~~~i~~~~--~~~~i~~t~~~~~~~~~~~~~~~-d~~~~i~~~~l~~------~~i~k~~~~i~ 555 (808)
T COG0086 485 AEAIAKKIELTTGKVIVSTISPDL--AELSIIVTTDGRRIFNRGLPEDK-DVLVKIVNGKLIK------GVIDKKIVTIY 555 (808)
T ss_pred hHHHhcccceeeeeEEEEEeeccC--CcceEEEecchhhhhhccCCccc-ceeeEEeccccce------eeehhhHHHHH
Confidence 888899999999998887654321 12455666665554443211111 1111111110000 00000000000
Q ss_pred CCCCCCcceeehHHHhhhcCCcEEecccCceEEEEeccccccchhhccCCcccEEEEEeCccHHHhhccCCccccccccC
Q 000829 1053 PPVDKSKIHFELYSLKNVLPMVIVKGIKTVERVVIAEKEKEKRKVKENGEKKKYRLLVEGTGLQAVMGAEGIDGCKTKSN 1132 (1265)
Q Consensus 1053 ~~~~~~~~~~~l~~l~~~l~~~~v~Gi~~I~r~~i~~~~~~~~~~~~~~~~~~~~l~teG~nl~~~~~~~~VD~~~~~sN 1132 (1265)
-.-......+.+-.+...+.+..+++..+++..+...+. +. ...+.+|...+++.++..++..+.+|.+++.+|
T Consensus 556 ~~~g~~~~~~~~~~~~dkl~~~~~~~~~~~~~~i~~~d~-~~-----~~~~~e~v~~ae~~v~~~i~~~~~g~lt~~~~~ 629 (808)
T COG0086 556 REYGPEVASKALVKLLDKLKNLGIKGIGGFGIGIGRKDI-EA-----EDEKDEIVIEAEGSVLKLILQYEEGDLTRTERN 629 (808)
T ss_pred HHhCchhhHHHHHHHHHHHHHhheeeeccceEEeecccc-cc-----hHHHHHHHHHHHHHHHHHHHHhhcCCccccCCC
Confidence 000000000012222344555667777767766655321 00 012346788899999999999999999999999
Q ss_pred CHHHHHHHhCHHHHHHHHHHHHHHHhhccccc-cCcccceeeecccccccEEEeeccccccccCCcHhhHhcchHHHHHH
Q 000829 1133 HIFEVQQTLGIEAARICIIDEINETMKAHGMS-IDKRHMMLLADLMTFRGEVLGITRFGIQKMDKSVLMLASFEKTADHL 1211 (1265)
Q Consensus 1133 dI~ev~~~lGIEAAR~~Iv~Ei~~v~~~~Gi~-Vd~RHl~LlAD~MT~~G~~~~i~R~Gi~~~~~Spl~~aSFE~T~~~L 1211 (1265)
|+.++..++|+||+++++.+|+..+...+|.+ ++.+|+++.+|.|+.++....+.++|+...+.|++++|+||.|..+
T Consensus 630 ~i~e~~e~~~~e~l~~ai~~~~~~~~~~~g~~~~~i~~m~~~Gs~~n~sq~~~~iG~~gv~g~r~~~~~~~~Fe~~~~~- 708 (808)
T COG0086 630 NIVEIIEVLGIEALRNAIIEEIKITLEEQGLDFVDIRHMGLSGARMNISQIVQLIGQQGVMGEKISVLARAAFEVTVKH- 708 (808)
T ss_pred CeEEEeehHHHHHHHHHHHHHHhhhHHhcCCcchhHHHHhhhhhccCHHHHHHHhhhheeeccCCCccccccccccccc-
Confidence 99999999999999999999999999999999 9999999999999999999999999988778899999999999999
Q ss_pred HHhhhcCCcccccccccceeccCCCCCCccceEeeecCCC
Q 000829 1212 FNASVNGRDDRIEGVSECIIMGIPMPLGTGILKIRQRDAV 1251 (1265)
Q Consensus 1212 ~~AA~~g~~D~l~gvS~~Ii~Gk~~~~GTG~fdll~~~~~ 1251 (1265)
..|+.+++.+.+.|+++++++|+.++.|||..|.-+....
T Consensus 709 ~~a~~~i~s~f~eGLt~~e~f~~~~ggR~GlvDTA~KTa~ 748 (808)
T COG0086 709 LEAEGPGESSFLEGLTENEYFGHPIGGRTGLVDTALKTAD 748 (808)
T ss_pred ceeeeeeecccCCCCCcceEEeecCccccchHHHhhhhcc
Confidence 9999999999999999999999999999999998876553
No 37
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=98.84 E-value=1.6e-09 Score=139.57 Aligned_cols=51 Identities=47% Similarity=0.638 Sum_probs=47.3
Q ss_pred hccCCCHHHHHHHHHHHHHhhhcccCCcCccceeecccccCCccccccccc
Q 000829 877 KTSGITEKQLEVFIQTCFSRYRVKRVEAGTAIGAIGAQSIGEPGTQMTLKT 927 (1265)
Q Consensus 877 ~~~~~~~~~~~~~~~~~~~ky~~slv~PGEaVG~IAAQSIGEPsTQMTLnT 927 (1265)
...+++.++++|++..|..+|.+++++||||||++||||||||+|||||.-
T Consensus 29 ~~~~lt~~~~d~Il~~I~~~y~~a~vepge~vG~~aaqsi~~~~~~~~~~~ 79 (858)
T PRK14898 29 KRDGVTEEMVEEIIDEVVSAYLNALVEPYEAVGIVAAQSIGEPGTQMSLPY 79 (858)
T ss_pred hhcCCCHHHHHHHHHHHHHHHhhCCCCCCceeeeeeehhcCCCCccccCCC
Confidence 345789999999999999999999999999999999999999999999743
No 38
>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=84.47 E-value=1.2 Score=48.38 Aligned_cols=95 Identities=19% Similarity=0.197 Sum_probs=52.2
Q ss_pred CCchhHHHHHHHHhcCC--CCCCCCCCHHHHHHHHHHHHhhcCC----CcchHHHHHHHHHHHHHhhhhhhhhhhccccc
Q 000829 789 EPLNFDRLLMKVKATCP--PAGQRYLSPQQVSEIVEKQLAAYGK----ESCSEAFLNSLRKFFEGQQDKLDKKIKFVEDI 862 (1265)
Q Consensus 789 ~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~i~~~i~~~~~~l~~~~~~~~~~ 862 (1265)
-|+|+.|+..+++.... ......+.|..+...++.++..... +..+..- +.++.-|.+
T Consensus 87 LPVNi~RiI~nAq~~f~i~~~~~sdL~P~~Vi~~V~~L~~~L~vv~g~D~ls~Ea--------q~NAtlLf~-------- 150 (187)
T PF04992_consen 87 LPVNIQRIIWNAQKIFHIDPRKPSDLSPIYVIEKVEELLDRLVVVRGDDPLSREA--------QENATLLFK-------- 150 (187)
T ss_dssp EES-HHHHCCCCCCCTT--TTS-BS--HHHHHHHHHHHHTT--SS--SSCCCCHH--------HHCCCHHHH--------
T ss_pred CCccHHHHHHHHHHHcCCCCCCcccCCHHHHHHHHHHHHHHHhhccCCCcchHHH--------HhhHHHHHH--------
Confidence 48999998877665542 2233556777766666655432110 1011000 001111111
Q ss_pred CCCccchhhhhhhhhccCCCHHHHHHHHHHHHHhhhcc
Q 000829 863 GWDDKSQILEEVTHKTSGITEKQLEVFIQTCFSRYRVK 900 (1265)
Q Consensus 863 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ky~~s 900 (1265)
+..++.+++|.+...+++|.++|+|+++++..+|.+|
T Consensus 151 -i~lRs~LasKrvi~e~rL~~~AF~wilgEIe~rF~~a 187 (187)
T PF04992_consen 151 -ILLRSTLASKRVIEEYRLNKEAFDWILGEIESRFKKA 187 (187)
T ss_dssp -HHHCCCSSHHHHHHTSB--HHHHHHHHHHHHHHHHCC
T ss_pred -HHHHHhhhhHHHHHHhCcCHHHHHHHHHHHHHHHHcC
Confidence 1124556688899999999999999999999999875
No 39
>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=77.56 E-value=0.74 Score=47.21 Aligned_cols=50 Identities=22% Similarity=0.181 Sum_probs=34.0
Q ss_pred EeccccceeEEEEEeCCccEEEEEeChhhHHHhh----------------------------cccCHHHHHHHHhcCc
Q 000829 983 TLLGQVAKSIKIVMTSRLASIVIALDMETIQDAH----------------------------LCINADIVKESIVQTP 1032 (1265)
Q Consensus 983 ~~L~di~~~i~~~y~~~~~~~~i~ld~~~i~~~~----------------------------~~i~~~~i~~~i~~~~ 1032 (1265)
+||++|+...+|+|+|+.....|+-|..+++.|+ -++++++|+.+|.+.+
T Consensus 1 TtL~~vt~~teIyYDPdp~~Tvi~eD~e~V~~y~e~pd~~~~~~~~spWlLRieLdr~~m~dk~l~m~~I~~~I~~~f 78 (135)
T PF04990_consen 1 TTLRDVTASTEIYYDPDPRNTVIEEDREFVESYFEIPDEDDDPSRLSPWLLRIELDRKKMIDKKLTMEDIAEKIKEEF 78 (135)
T ss_dssp ECCHCHECEEEEEE-SSTTSSSSSTTHCHHHHCCCTT-SSTT-SSBESEEEEEEE-CCCCCCTT--HHHHCCCHHHCC
T ss_pred CcHHHhhhheeEEECCCCCCCcchhhHHHHHHHHhCCCcccCcccCCCeEEEEEEcHHHHHhcCCCHHHHHHHHHHhc
Confidence 6899999999999999865555555555555442 1478888888887765
No 40
>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=66.84 E-value=4.5 Score=51.49 Aligned_cols=54 Identities=33% Similarity=0.322 Sum_probs=30.5
Q ss_pred cccccCCeEEEecCCCccccceeeEEEEEecC-Ce-----------eeeecccCCCCCCCCcccccccc
Q 000829 315 RHLEDGDVVLFNRQPSLHRMSIMCHRARIMPW-RT-----------LRFNESVCNPYNADFDGDEMNMH 371 (1265)
Q Consensus 315 Rhl~dgD~VL~NRQPSLHk~Simah~vkv~~~-kt-----------~rln~~vc~~yNADFDGDEMN~h 371 (1265)
..+..| -||+-|.|++|..-|+-.++.-.|. +- =|=+++.|+. .|+|||+-.|-
T Consensus 364 ~~~~~g-~VlV~R~P~~~pgDir~~~av~~p~L~~l~~vIVF~~~G~r~~~~~lsG--gDlDGD~~~V~ 429 (579)
T PF05183_consen 364 SQVLEG-DVLVTRNPCLHPGDIRKVKAVDKPELRHLKDVIVFSTKGDRPLPSELSG--GDLDGDEYFVC 429 (579)
T ss_dssp EEEEE--EEEEE-SS--SGGGEEEEEE---GGGTT--SEEEE-S-SSS-HHHHTTT----SSS-EEEEE
T ss_pred cceeee-eEEEecCCccCcCceeEEEeeccHHHcccCCEEEeCCCCCCCchHHhcC--CCCCCceEEEE
Confidence 345567 8999999999999999999977664 11 1223334444 89999998866
No 41
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=54.78 E-value=6.3 Score=32.24 Aligned_cols=14 Identities=50% Similarity=1.113 Sum_probs=12.1
Q ss_pred CCCCcCCCCCCCCC
Q 000829 27 SKAVKCPRCGYING 40 (1265)
Q Consensus 27 k~~~~C~~Cg~~~p 40 (1265)
...++||+||+.|+
T Consensus 9 RGirkCp~CGt~NG 22 (44)
T PF14952_consen 9 RGIRKCPKCGTYNG 22 (44)
T ss_pred hccccCCcCcCccC
Confidence 35689999999997
No 42
>KOG0988 consensus RNA-directed RNA polymerase QDE-1 required for posttranscriptional gene silencing and RNA interference [RNA processing and modification]
Probab=32.88 E-value=46 Score=44.64 Aligned_cols=53 Identities=26% Similarity=0.372 Sum_probs=41.8
Q ss_pred cccCCeEEEecCCCccccceeeEEE------------EEecCCeeeeecccCCCCCCCCccccccccc
Q 000829 317 LEDGDVVLFNRQPSLHRMSIMCHRA------------RIMPWRTLRFNESVCNPYNADFDGDEMNMHV 372 (1265)
Q Consensus 317 l~dgD~VL~NRQPSLHk~Simah~v------------kv~~~kt~rln~~vc~~yNADFDGDEMN~h~ 372 (1265)
+..| .||+-|.|+||=.-|--++| .|.|.+--|=||.-|++ .||||||--|-=
T Consensus 771 vitG-~VlvtKNPcLhpGDVRVl~AV~vp~L~h~~dvVvFPQkGpRphpdE~aG--sDLDGDeYfViW 835 (1145)
T KOG0988|consen 771 VITG-KVLVTKNPCLHPGDVRVLKAVYVPALEHMVDVVVFPQKGPRPHPDEMAG--SDLDGDEYFVIW 835 (1145)
T ss_pred EEEe-eEEEecCCCCCCCceEEEEeeccHHHHhhcCEEEcCCCCCCCCcccccc--CCCCCceEEEEe
Confidence 4455 67888888888877766554 56788899999999998 999999976643
No 43
>PF05094 LEF-9: Late expression factor 9 (LEF-9); InterPro: IPR007786 The baculovirus Autographa californica nuclear polyhedrosis virus (AcMNPV) encodes a DNA-dependent RNA polymerase that is required for transcription of viral late genes. This polymerase is composed of four equimolar subunits, LEF-8, LEF-4, LEF-9, and p47. LEF-9 is homologous to the largest beta-subunit of prokaryotic DNA-directed RNA polymerase [].; GO: 0019083 viral transcription
Probab=32.26 E-value=53 Score=39.43 Aligned_cols=66 Identities=18% Similarity=0.163 Sum_probs=51.0
Q ss_pred eEEEecCCCccccceeeEEEEEecC---CeeeeecccCCCCCCCCccc-ccccccCChHHHHHHHHHHcCC
Q 000829 322 VVLFNRQPSLHRMSIMCHRARIMPW---RTLRFNESVCNPYNADFDGD-EMNMHVPQTEEARTEALLLMGV 388 (1265)
Q Consensus 322 ~VL~NRQPSLHk~Simah~vkv~~~---kt~rln~~vc~~yNADFDGD-EMN~h~PQs~~araEa~~Lm~~ 388 (1265)
-+.--|+|.+-..|=+--+|+.-.. -.++.-...+.+-|+|-||| |.--++|+ +++-.++..|+.-
T Consensus 212 raw~tRHPniSqlsTq~s~v~~~~~~~~wnvkvGlG~F~Gan~DCDGDKeviT~lP~-PNSLidlE~lLY~ 281 (487)
T PF05094_consen 212 RAWTTRHPNISQLSTQVSRVDQNDDYTDWNVKVGLGTFVGANRDCDGDKEVITYLPY-PNSLIDLESLLYG 281 (487)
T ss_pred eeeecCCCCchhhchhheEeeccccCCCcceeeeeccccCCCCCCCCCceEEEecCC-CcchhhHHHHhcC
Confidence 3555689999999998888877653 35777788899999999999 78888898 5666666666643
No 44
>COG3688 Predicted RNA-binding protein containing a PIN domain [General function prediction only]
Probab=32.11 E-value=59 Score=34.28 Aligned_cols=41 Identities=27% Similarity=0.383 Sum_probs=32.4
Q ss_pred EEEEeCccHHHhhccCCccccccccCCHHHHHHHhCHHHHHHHHHHHHHHHhh
Q 000829 1107 RLLVEGTGLQAVMGAEGIDGCKTKSNHIFEVQQTLGIEAARICIIDEINETMK 1159 (1265)
Q Consensus 1107 ~l~teG~nl~~~~~~~~VD~~~~~sNdI~ev~~~lGIEAAR~~Iv~Ei~~v~~ 1159 (1265)
.|.++|.|+-..|. ....+....|.|+||..+|.++.+-=+
T Consensus 5 iLLVDGYNmIgaWp------------~Lk~lkd~~~LE~AR~~LIe~l~~Y~s 45 (173)
T COG3688 5 ILLVDGYNMIGAWP------------ELKQLKDRNGLEAARDKLIEALAEYQS 45 (173)
T ss_pred EEEeccchhccccH------------HHHHHHhhccHHHHHHHHHHHHHHhhc
Confidence 68999999877665 345777888999999999998876333
No 45
>KOG0571 consensus Asparagine synthase (glutamine-hydrolyzing) [Amino acid transport and metabolism]
Probab=29.52 E-value=58 Score=39.33 Aligned_cols=47 Identities=21% Similarity=0.378 Sum_probs=27.5
Q ss_pred CcceecccccccccCCCcccHHHHHHHHhChhhHHHHHhHHHHHHHHHHHhccceeeeccCCCCccchH
Q 000829 514 SELISGQLGKATLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLSARWIGNHGFSIGIDDVQPKKELSD 582 (1265)
Q Consensus 514 gell~G~ldK~~lG~~~~~~Li~~i~~~yG~~~a~~~l~~~~~l~~~~L~~~GFSigi~D~~~~~~~~~ 582 (1265)
|-||+|.||.+.+.+ | |++.|-..+--. -...+.|+||++| +|++..
T Consensus 229 GvLLSGGLDSSLvAs---------i--------a~R~lk~~~~~~--~~~lhsFaIGle~---SPDL~a 275 (543)
T KOG0571|consen 229 GVLLSGGLDSSLVAS---------I--------AARELKKAQAAR--GSKLHSFAIGLED---SPDLLA 275 (543)
T ss_pred eEEeeCCchHHHHHH---------H--------HHHHHHHhhhhc--CCCceEEEecCCC---ChhHHH
Confidence 789999998766653 2 233333222111 1145899999997 455443
No 46
>PHA03396 lef-9 late expression factor 9; Provisional
Probab=24.94 E-value=83 Score=38.11 Aligned_cols=65 Identities=18% Similarity=0.202 Sum_probs=47.5
Q ss_pred eEEEecCCCccccceeeEEEEEecC---CeeeeecccCCCCCCCCccc-ccccccCChHHHHHHHHHHcC
Q 000829 322 VVLFNRQPSLHRMSIMCHRARIMPW---RTLRFNESVCNPYNADFDGD-EMNMHVPQTEEARTEALLLMG 387 (1265)
Q Consensus 322 ~VL~NRQPSLHk~Simah~vkv~~~---kt~rln~~vc~~yNADFDGD-EMN~h~PQs~~araEa~~Lm~ 387 (1265)
-+.--|+|.+-..|=+--+|+.-.. --++.=.....+-|+|-||| |.--++|+ +++--++..|+.
T Consensus 215 raw~tRHPnisqlstq~s~v~~~~~~~~wNvkvGlG~F~GanrDCDGDKeviT~lP~-PNsLidlE~lLY 283 (493)
T PHA03396 215 RAWTTRHPNISQLSTQVSRVDQNDDYTDWNVKVGLGTFPGANRDCDGDKEVITFLPY-PNSLIDLECLLY 283 (493)
T ss_pred EEeecCCCCchhhchhheEeeccccccccceeeeeccccCCCCCCCCCceEEEecCC-CcchhhHHHHhc
Confidence 3555689999999998888877542 12555566788999999999 78888898 555555555554
No 47
>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=22.68 E-value=86 Score=29.67 Aligned_cols=76 Identities=22% Similarity=0.320 Sum_probs=37.9
Q ss_pred EEcCCCCCCCCcccccHHHHhhcCcceeechHHHHHHHHHHHcCCCCCCCceEEECCCCCeEEe-c--cccchhhhhccc
Q 000829 232 VISPDPNLKITEVAIPIRMARILTYPERVSDHNIEKLRQCIQNGPDKYPGARMIRYPDGTARVL-Y--GKFRNQLAVELK 308 (1265)
Q Consensus 232 VIspDp~l~~~evGvP~~~A~~Lt~pe~Vt~~Ni~~l~~lv~ng~~~~pGa~~i~~~~g~~~~l-~--~~~r~~~~~~L~ 308 (1265)
+++|.+...-+.+.||..+|+....++ ..+-.-.+.+++|+.-.+ + ..... ..-|.
T Consensus 4 ~l~~s~~~~~~~l~iP~~f~~~~~~~~-------------------~~~~~v~l~~~~g~~W~v~~~~~~~~~--~~~l~ 62 (100)
T PF02362_consen 4 VLKPSDVSSSCRLIIPKEFAKKHGGNK-------------------RKSREVTLKDPDGRSWPVKLKYRKNSG--RYYLT 62 (100)
T ss_dssp E--TTCCCCTT-EEE-HHHHTTTS--S-------------------S--CEEEEEETTTEEEEEEEEEECCTT--EEEEE
T ss_pred EEEccCcCCCCEEEeCHHHHHHhCCCc-------------------CCCeEEEEEeCCCCEEEEEEEEEccCC--eEEEC
Confidence 556767777788999999998873211 011122345566653333 2 21111 12344
Q ss_pred ccc---eeecccccCCeEEEecC
Q 000829 309 SGC---IVDRHLEDGDVVLFNRQ 328 (1265)
Q Consensus 309 ~g~---iV~Rhl~dgD~VL~NRQ 328 (1265)
-|+ +-+..|+.||.++|-..
T Consensus 63 ~GW~~Fv~~n~L~~GD~~~F~~~ 85 (100)
T PF02362_consen 63 GGWKKFVRDNGLKEGDVCVFELI 85 (100)
T ss_dssp TTHHHHHHHCT--TT-EEEEEE-
T ss_pred CCHHHHHHHcCCCCCCEEEEEEe
Confidence 454 66788999999999865
No 48
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.87 E-value=1.1e+02 Score=30.90 Aligned_cols=36 Identities=22% Similarity=0.429 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHHhhhcCCCCCcCCCCCCCC-CcEEecc
Q 000829 9 LRKTDLMKSIVKKCSTMASKAVKCPRCGYIN-GMVKKAV 46 (1265)
Q Consensus 9 ~~r~~~~k~i~~~c~~~~k~~~~C~~Cg~~~-p~Vrk~~ 46 (1265)
.+.-.++..|+.+|++ .....||.|++.- +...-+|
T Consensus 21 dq~pel~eafcskcge--ati~qcp~csasirgd~~veg 57 (160)
T COG4306 21 DQSPELMEAFCSKCGE--ATITQCPICSASIRGDYYVEG 57 (160)
T ss_pred cCCHHHHHHHHhhhch--HHHhcCCccCCcccccceeee
Confidence 3445688899999963 4578999999843 3333344
Done!