Query 000882
Match_columns 1238
No_of_seqs 378 out of 2105
Neff 6.1
Searched_HMMs 46136
Date Tue Apr 2 00:39:45 2013
Command hhsearch -i /work/01045/syshi/lefta3m/000882.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/leftcdd/000882hhsearch_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 2E-248 5E-253 2147.2 42.9 1056 3-1103 2-1381(1386)
2 PRK14977 bifunctional DNA-dire 100.0 5E-241 1E-245 2279.4 74.4 1031 9-1084 4-1318(1321)
3 KOG0260 RNA polymerase II, lar 100.0 6E-234 1E-238 2059.8 52.8 1055 1-1092 1-1429(1605)
4 KOG0262 RNA polymerase I, larg 100.0 4E-209 9E-214 1854.7 53.5 1025 10-1082 9-1635(1640)
5 TIGR02390 RNA_pol_rpoA1 DNA-di 100.0 6E-189 1E-193 1765.1 53.4 742 11-767 1-864 (868)
6 PRK08566 DNA-directed RNA poly 100.0 3E-187 7E-192 1754.5 57.1 739 9-765 4-867 (882)
7 TIGR02386 rpoC_TIGR DNA-direct 100.0 3E-167 6E-172 1559.7 51.2 892 16-1075 1-1135(1140)
8 PRK00566 DNA-directed RNA poly 100.0 2E-166 4E-171 1553.3 53.1 898 13-1075 6-1137(1156)
9 PRK14906 DNA-directed RNA poly 100.0 4E-155 8E-160 1446.8 48.2 766 138-1075 310-1236(1460)
10 PRK14844 bifunctional DNA-dire 100.0 1E-150 2E-155 1451.9 51.3 716 9-786 1443-2357(2836)
11 PRK09603 bifunctional DNA-dire 100.0 8E-150 2E-154 1449.2 49.3 706 10-786 1392-2301(2890)
12 COG0086 RpoC DNA-directed RNA 100.0 4E-132 8E-137 1231.2 30.0 688 14-754 4-789 (808)
13 PRK02625 rpoC1 DNA-directed RN 100.0 7.3E-87 1.6E-91 787.7 28.3 408 11-441 6-525 (627)
14 TIGR02387 rpoC1_cyan DNA-direc 100.0 2.1E-86 4.6E-91 782.9 25.3 403 14-439 2-515 (619)
15 CHL00018 rpoC1 RNA polymerase 100.0 6.3E-85 1.4E-89 778.4 29.3 282 138-439 259-543 (663)
16 smart00663 RPOLA_N RNA polymer 100.0 2.9E-84 6.2E-89 724.3 20.9 290 141-436 1-295 (295)
17 TIGR02389 RNA_pol_rpoA2 DNA-di 100.0 1.2E-57 2.6E-62 522.3 14.3 332 716-1082 2-367 (367)
18 PF00623 RNA_pol_Rpb1_2: RNA p 100.0 3E-58 6.5E-63 477.6 5.1 158 253-411 1-166 (166)
19 PRK04309 DNA-directed RNA poly 100.0 1.5E-56 3.2E-61 517.3 14.4 335 716-1085 18-382 (383)
20 cd06528 RNAP_A'' A'' subunit o 100.0 2.9E-56 6.3E-61 511.7 13.0 308 742-1082 23-362 (363)
21 PRK14897 unknown domain/DNA-di 100.0 2.3E-56 5E-61 520.9 11.9 334 716-1085 141-506 (509)
22 cd02584 RNAP_II_Rpb1_C Largest 100.0 2.2E-54 4.8E-59 502.4 19.2 307 755-1082 20-410 (410)
23 cd02737 RNAP_IV_NRPD1_C Larges 100.0 4.4E-53 9.5E-58 486.9 17.9 308 762-1081 1-381 (381)
24 cd02736 RNAP_III_Rpc1_C Larges 100.0 6.4E-53 1.4E-57 473.1 17.4 279 756-1077 4-300 (300)
25 cd02735 RNAP_I_Rpa1_C Largest 100.0 6.3E-49 1.4E-53 444.1 13.7 282 755-1080 3-309 (309)
26 TIGR02388 rpoC2_cyan DNA-direc 100.0 1.2E-48 2.6E-53 490.7 14.4 245 506-786 6-333 (1227)
27 PRK02597 rpoC2 DNA-directed RN 100.0 4.3E-48 9.2E-53 489.4 16.8 245 506-786 7-335 (1331)
28 PF04998 RNA_pol_Rpb1_5: RNA p 100.0 3E-50 6.6E-55 450.9 -2.6 258 686-1027 1-275 (277)
29 CHL00117 rpoC2 RNA polymerase 100.0 3.6E-47 7.9E-52 486.1 14.2 249 506-786 13-339 (1364)
30 PF04997 RNA_pol_Rpb1_1: RNA p 100.0 2.4E-44 5.3E-49 411.2 14.2 233 12-251 2-337 (337)
31 PRK14898 DNA-directed RNA poly 100.0 1.1E-39 2.3E-44 412.3 17.4 279 777-1085 540-852 (858)
32 cd00630 RNAP_largest_subunit_C 100.0 1.4E-30 3.1E-35 267.7 3.4 98 973-1075 57-158 (158)
33 PF04983 RNA_pol_Rpb1_3: RNA p 100.0 5.7E-30 1.2E-34 265.7 3.8 144 414-559 1-158 (158)
34 cd02655 RNAP_beta'_C Largest s 99.9 4.9E-26 1.1E-30 242.4 6.5 96 966-1075 69-204 (204)
35 PF05000 RNA_pol_Rpb1_4: RNA p 99.5 8.9E-15 1.9E-19 143.0 5.0 90 584-679 15-108 (108)
36 COG0086 RpoC DNA-directed RNA 99.2 4.2E-13 9.2E-18 169.2 -9.3 346 747-1125 400-791 (808)
37 TIGR02388 rpoC2_cyan DNA-direc 99.1 2.3E-11 4.9E-16 156.0 3.5 98 973-1075 1083-1222(1227)
38 CHL00117 rpoC2 RNA polymerase 99.1 2.4E-11 5.1E-16 158.6 3.2 94 980-1081 1192-1322(1364)
39 PRK02597 rpoC2 DNA-directed RN 99.1 4E-11 8.7E-16 155.0 3.5 101 970-1075 1081-1223(1331)
40 KOG0260 RNA polymerase II, lar 98.0 1.7E-06 3.6E-11 108.5 0.2 331 760-1101 879-1281(1605)
41 PF04990 RNA_pol_Rpb1_7: RNA p 97.4 4.1E-05 8.9E-10 78.0 0.1 55 843-897 1-78 (135)
42 PRK14898 DNA-directed RNA poly 96.9 0.00011 2.5E-09 95.2 -2.8 65 716-785 15-80 (858)
43 PF05183 RdRP: RNA dependent R 62.2 4.3 9.3E-05 51.5 2.0 64 329-394 344-429 (579)
44 PF05094 LEF-9: Late expressio 34.2 47 0.001 40.0 4.3 64 345-409 212-279 (487)
45 PHA03396 lef-9 late expression 26.8 72 0.0016 38.7 4.3 72 345-416 215-291 (493)
46 TIGR01623 put_zinc_LRP1 putati 23.2 28 0.0006 28.9 0.0 20 54-73 15-34 (43)
47 KOG1999 RNA polymerase II tran 22.9 1.5E+02 0.0032 39.5 6.2 36 1131-1166 810-847 (1024)
No 1
>KOG0261 consensus RNA polymerase III, large subunit [Transcription]
Probab=100.00 E-value=2.1e-248 Score=2147.17 Aligned_cols=1056 Identities=23% Similarity=0.358 Sum_probs=918.9
Q ss_pred CCCCCcccccccceEEEecCChHHHHhccccccc-----------ccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCc
Q 000882 3 ENTSSTILEGQIVGIRFGLATQKEICTASISDCS-----------ISHASQLANPFLGLPLEFGKCESCGTSEPGKCEGH 71 (1238)
Q Consensus 3 ~~~~~~~~~~~I~~I~Fgl~S~eEI~k~Sv~~~~-----------I~~~~gl~DprlG~~~~~~~C~TCg~~~~~~CpGH 71 (1238)
+|+.....+++|++|+|+++|++||++.+++++. .+.++|++|||||++++...|+|||.+. .+|+||
T Consensus 2 k~~~e~~~~kki~~i~F~~~s~~ei~~~a~v~v~~~~LY~~~~~~~P~~~G~LD~rMGvs~K~~~C~TCg~~l-a~C~GH 80 (1386)
T KOG0261|consen 2 KQFREDEIPKKIKHIQFSILSPEEIRQQAEVEVSSKDLYDISTQRAPLPNGPLDPRMGVSNKKDKCATCGEGL-ADCIGH 80 (1386)
T ss_pred CccccccccceeeeEeeccCCHHHHHhcceEEeeccchhhhhcccCCCcCCCcCcccCCCCCCCccchhccch-hhcccc
Confidence 5778888999999999999999999999987431 1235799999999999999999999997 799999
Q ss_pred ceeEEcCcccccccChHHHHHHHHhhccccc-------------------------CchHHHHHHHhH--------h---
Q 000882 72 FGYIELPIPIYHPSHISELKLTMYAFQLQIK-------------------------NDGVAQRLLSSC--------C--- 115 (1238)
Q Consensus 72 FGhIeL~~PVfHpgf~k~i~~IL~~iCl~l~-------------------------~~~~~~~~~~~C--------C--- 115 (1238)
|||++|++||||+|||+.+++||||||..|. +.++.++++.+| |
T Consensus 81 fGy~~L~LPVFhiGyfk~ti~iLq~ICK~Cs~ilL~~~~k~~fl~~lr~p~~~~l~k~~l~kri~~~CkK~~~C~hCg~~ 160 (1386)
T KOG0261|consen 81 FGYLKLALPVFHIGYFKATIQILQCICKNCSSILLSEEDKRQFLKKLRNPGLDNLRKKALLKRIVAKCKKVNTCSHCGAL 160 (1386)
T ss_pred cceEeecceeeeehhHHHHHHHHHHHHHhhhhhhcCHHHHHHHHHHhhCCCCChHHHHHHHHHHHHHhhccccccccCCc
Confidence 9999999999999999999999999993321 224456666666 3
Q ss_pred -----------------------------------------------------------HHHHHHccCChhHHHHhccCC
Q 000882 116 -----------------------------------------------------------EVKEMLKRIPEETRKKLAGKG 136 (1238)
Q Consensus 116 -----------------------------------------------------------ev~~i~k~I~~ed~~~L~~~~ 136 (1238)
.|+++|++|++.|+++|+...
T Consensus 161 NG~VKK~~~~lkIiHd~~~~~~k~~~~~~~~~~~~~~~~~~n~e~~~~~~~~~~~LnPl~vLnLFk~i~~~D~eLLg~~~ 240 (1386)
T KOG0261|consen 161 NGTVKKAAALLKIIHDRFKLVKKSDPLVTNERGEFKTAISHNKELEGHLSSCCEELNPLVVLNLFKQIKEDDCELLGMDS 240 (1386)
T ss_pred CceeeccccceeEeeehhhccccccchhhhhHHHHHHHhhcCcchHhHHHHHHhhcChHHHHHHHhhCCccccceeeecc
Confidence 578999999999999996431
Q ss_pred -CCCCCceEEEeeccCCCCCCCccccCC-CccccchhhHHHHHHHHHHHHHHHhh-hcCCCCcchhhhhhhHHHHHHHHH
Q 000882 137 -YFPQDGYILEYLPVPPNCLSVPDISDG-VSTMSSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQY 213 (1238)
Q Consensus 137 -~~~~~~~il~~lpVpP~~~Rp~~~~~~-~~~~~~Dlt~~~l~~I~~~~~~l~~~-~~g~~~~~~~~~~~~~LQ~~v~~~ 213 (1238)
--+|+.+|++++||||.|+||++++++ ...++||+|+ +|.+|+-.|..|++. ..|+|.... ...|+.||.+|+.|
T Consensus 241 ~~~~P~~Li~t~~~vPP~cIRPSV~~~~k~gtnEDDlT~-KltEIi~tn~vik~~~~~g~~~~~i-mE~Wd~lQl~~Aly 318 (1386)
T KOG0261|consen 241 EEGRPENLIITRVPVPPVCIRPSVMSEDKAGTNEDDLTM-KLTEIILTNDVIKKHLSKGTPINLI-MEDWDFLQLQVALY 318 (1386)
T ss_pred CcCCchheEEEeccCCccccccceeecCCCCCCccchhh-hhhhhhhHHHHHHHHhhcCCCchhh-hhhhHHHHHHHHHh
Confidence 225889999999999999999999977 3467899999 699999999999986 567775554 45699999999999
Q ss_pred Hhc--cCCcccCCCcccCCCCCCCCCcchhhhhhhhhccccccCCCCCcceeEeCCCCccccccccchhhhccccccccc
Q 000882 214 LEV--RGTAKSSRDVDARFGVSQDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERV 291 (1238)
Q Consensus 214 ~~~--~~~~k~~~~~~~~~~~~k~~~~~iKgk~gr~R~nllGKRVdfSaRsVIspDP~L~i~evGvP~~iA~~LT~pE~V 291 (1238)
||+ +|.+....+... ..-..+++|||+||||+||.||||||||||||||||||+|||||||..||+.|||||+|
T Consensus 319 INSEl~g~~~~~~p~kp----~RGf~QRLKGKqGRFRgNLSGKRVDFSGRTVISPDPNL~IdeVgVP~rvAkiLTfpE~V 394 (1386)
T KOG0261|consen 319 INSELPGIPINMAPKKP----TRGFVQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDEVGVPIRVAKILTFPERV 394 (1386)
T ss_pred hcccCCCCCCCCCCCCc----hHHHHHHhcccCCceeccccCceeeccCceeeCCCCCcceeeccchHHHHHHhcchhhc
Confidence 984 444433211000 00123799999999999999999999999999999999999999999999999999999
Q ss_pred chhhHHHHHHHHHcCCcc-------ccCCCCceEEeccCCCC--cccccCcceeeeeeeccCeEeeeCCCCCCcccccce
Q 000882 292 NVHNINYLQELVDNKLCL-------TYSDGSSSYSLREGSKG--HTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQAL 362 (1238)
Q Consensus 292 t~~Ni~~l~~lV~ng~~~-------~~~~~~~~~~l~~~~~~--~~~L~~g~iV~Rhl~dgD~VL~NRqPSLHr~Simah 362 (1238)
|.+||++||+||.|||.+ +.+..+.+..|+||+|. +..|++||+|||||+|||+|||||||||||||||+|
T Consensus 395 t~~Ni~klr~lV~NGP~vhPGANyv~~r~~~~kr~L~yg~R~kiA~eLk~GdvVERHL~DgDvVLFNRQPSLHkmSIM~H 474 (1386)
T KOG0261|consen 395 TRANIRKLRQLVRNGPNVHPGANYVVQRGEGFKRFLKYGNRDKIADELKIGDVVERHLMDGDVVLFNRQPSLHKMSIMSH 474 (1386)
T ss_pred cHHHHHHHHHHHhcCCCCCCCcchhhhcccchhhHhhcCcHHHHHHhhccchHHHhhcccCCEEEEcCCchHHHHHHHHH
Confidence 999999999999999972 11222334456677654 478999999999999999999999999999999999
Q ss_pred EEEecCCCeeeecccCCCCCCCccCccccccccCCCHHHHHHHHHHhccccccccCCCCCceEeechhhhhHHHhhh-cc
Q 000882 363 SVYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF-KK 441 (1238)
Q Consensus 363 ~v~v~~~~T~rln~~vC~pyNADFDGDeMn~H~PQs~eAraEa~~Lm~~~~nilsp~~G~Piigl~QD~llg~~llt-kd 441 (1238)
++||+||+|||||.|||+||||||||||||+||||++||||||.+||.+.+|+++|+||+||++.+||+|+|+||+| ||
T Consensus 475 ~akV~p~RTfRFNEcvCtPYNADFDGDEMNlHvPQTEEAraEA~~LMgvknNlvTPr~GEpiiAAtQDFiTg~YLlt~KD 554 (1386)
T KOG0261|consen 475 RAKVMPWRTFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEALVLMGVKNNLVTPRNGEPIIAATQDFITGGYLLTHKD 554 (1386)
T ss_pred HhhcccCceeeccccccCCcCCCCCcccccccCCchHHHHHHHHHHhccccccccCCCCCceeehhhhhhhcceeeeccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999998 99
Q ss_pred ccCCHHHHHHHhcccc-----cccccccccccccccccchhhhccccCCCCcc------------------------c-c
Q 000882 442 YFLDKAFTQQLAMFAL-----SPLPRPALSKARCSARWTALQILQSVLPPGFD------------------------S-C 491 (1238)
Q Consensus 442 ~fl~~~~~~~l~~~~~-----~~lp~PaI~Kp~~~~lwTGKQi~S~~LP~~~~------------------------~-~ 491 (1238)
+||+|+++.||+.++. +.+|||||+||. .||||||+||.++.++.+ | .
T Consensus 555 tF~dRa~~~ql~s~~~d~~~~i~lppPaI~KP~--~LwTGKQ~fsvlirpn~~s~v~~Nl~~k~k~~~~~~~k~~~mc~n 632 (1386)
T KOG0261|consen 555 TFLDRAEFSQLCSYMSDAMTHIDLPPPAILKPV--ELWTGKQLFSVLIRPNDDSPVRVNLDAKNKNFSLVKGKSFEMCPN 632 (1386)
T ss_pred ccccHHHHHHHHHHHhccccccCCCChhhcCce--eeeccCEEEEEEeccCCCCceEEeeccccceeecccCCCcccCCC
Confidence 9999999999987664 469999999999 999999999999954321 1 3
Q ss_pred CcEEEEecccccccccccCCccch-HHHHHHHHHHhhCHHHHHhchhhhHHHHHHHHHhcCceeecCccccCHHHHHHHH
Q 000882 492 GDRYLIKKSEVLKGDFDRDTIPSV-INEIVTSIFFEKGPEEVLEFFDSLQPLLMENLFADGFSVSLEDFSLSKAALWNIQ 570 (1238)
Q Consensus 492 ~~~viI~~gell~G~ldK~~lG~s-~~~LI~~i~~~~G~~~a~~fLd~lqrL~~~~L~~~GFSiGi~D~~~~~~~~~~i~ 570 (1238)
++.|+|+|+++++|++||+++|.. ..+||+.+.++||+.+|++.|+++.+|+.+||..+||||||+|+.+.+...+++.
T Consensus 633 Dg~v~irns~l~sG~ldKs~lG~g~k~~lfy~llrDyg~~aAa~am~rlaklc~r~lgnrGFSIGi~DVqPg~~L~~~k~ 712 (1386)
T KOG0261|consen 633 DGYVIIRNSELISGVLDKSTLGSGKKDSLFYILLRDYGSMAAADAMNRLAKLCARFLGNRGFSIGIDDVQPGEILSQEKE 712 (1386)
T ss_pred CCeEEEecchhhhcccccccccCCCccceEeeehhhcchHHHHHHHHHHHHhhhhhccccccccccCCCCccHHHHHHHH
Confidence 567889999999999999999984 7999999999999999999999999999999999999999999999999888888
Q ss_pred HHHHHHHHHHHhhhhh-------------hHHHHHHHHHHHHHHHHHHHHHHHHh----cCCccccccccchhhhhhHHH
Q 000882 571 KEIQALYSLLYHRMST-------------QNELVDLQIENHIRHVKMLVAKFILK----SSTLGYLIDSKSDSAVSKVVQ 633 (1238)
Q Consensus 571 ~~i~~~~~~~~~~~~~-------------~~~~le~~~~~~l~~~~~~i~~~~~~----~n~l~~Mi~sGSKGS~~Ni~Q 633 (1238)
+.++..+..+.++... .++++|+.+..+|+.+|+.+++.|++ .|+..+|+.+|||||.+|++|
T Consensus 713 ~lv~~gY~kc~~~I~e~~kG~L~~qpg~~~eetLEa~I~~~Ls~IRe~~G~~C~~eL~~~NsPliMa~CGSKGS~INiSQ 792 (1386)
T KOG0261|consen 713 ELVNRGYAKCDEKIEEYNKGKLQLQPGCNEEETLEAEILSELSTIREEAGKICIRELHPRNSPLIMALCGSKGSKINISQ 792 (1386)
T ss_pred HHHHhHHHHHHHHHHHHhccccccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccChHHHHHhcCCCCcccHHH
Confidence 8888877777665443 36899999999999999999999986 588999999999999999999
Q ss_pred HHhhcccccccCCccccccccccccccccccCCCCCCCCCCCcceecccccccCCccceEEeeccccceeeecccccCCC
Q 000882 634 QAGFLGLQLSDRGKFYSKTLVEDIASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEP 713 (1238)
Q Consensus 634 i~g~lGqQ~~~ggr~~~r~l~~~~~~~f~~~~p~~~d~~~~a~GfV~ssF~~GL~P~EfFfHamagREGLiDTAvkTa~s 713 (1238)
|++|||||.+.|.| ++.++.+|.+|||+++ ...|+|+|||.|||++||+|+|||||+|+|||||||||||||+|
T Consensus 793 MvACVGQQ~ISG~R-vPdGf~dRsLPHF~r~-----Sk~P~aKGFV~NSFySGLTptEFfFHtm~GREGLVDTAVKTAET 866 (1386)
T KOG0261|consen 793 MVACVGQQIISGHR-VPDGFEDRSLPHFERH-----SKTPAAKGFVANSFYSGLTPTEFFFHTMSGREGLVDTAVKTAET 866 (1386)
T ss_pred HHHHhhhhhhcCCc-CCCccccccCcccccc-----CCCccccchhhhhcccCCCchhhheeecccccchhhhhhhhhhh
Confidence 99999999998765 6788999999999864 56789999999999999999999999999999999999999999
Q ss_pred CchhHHHHHHHheeEEEecceEeccCCCceeeeeeecccccc--------------------------------------
Q 000882 714 GTLFKNLMAVLRDVVICYDGTVRNVCSNSIIQFDYAVNARKS-------------------------------------- 755 (1238)
Q Consensus 714 GYL~RrLv~~l~d~~v~YD~tvr~~~~~~iiqf~yg~dg~~~-------------------------------------- 755 (1238)
|||||||||.|||+.++||||||+ +.+.||||.||+||+|+
T Consensus 867 GYMqRRLmK~LEDL~~~YDgTVR~-s~~~vvqF~YG~DglDPa~mEg~~~pv~f~r~~~~~~~~~~~~~~~~l~~~el~e 945 (1386)
T KOG0261|consen 867 GYMQRRLMKSLEDLSVQYDGTVRN-SNGDVVQFTYGGDGLDPAMMEGKDQPVNFNRVFDHAKAIFPHRHDPPLSSEELDE 945 (1386)
T ss_pred hhHHHHHHHHHHHHHHhhcCceec-CCCcEEEEeecCCCCChhhhcCCCCchhHHHHHHHHHhcCCCCCCCCCCHHHHHH
Confidence 999999999999999999999999 47999999999999762
Q ss_pred ---------------------------------------------------------------------------cCcCC
Q 000882 756 ---------------------------------------------------------------------------HSLFP 760 (1238)
Q Consensus 756 ---------------------------------------------------------------------------~~lv~ 760 (1238)
+..++
T Consensus 946 ~~~~~l~~~f~~~~~~F~~~~~~~i~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~t~kql~~f~~~~~~ky~~a~~E 1025 (1386)
T KOG0261|consen 946 TLEEELLRKFTEKGDPFVHELREFIASLSKKIKKLQDKYGDECGPKFCPDLLYQISRLTEKQLEKFVERCLDKYMRAKVE 1025 (1386)
T ss_pred HHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHhhhcccccCCccCccceeeeeeccHHHHHHHHHHHHHHHHhhhcC
Confidence 23469
Q ss_pred CCCeeeeeccccCCchHHHhhhccC-------CCCCCchHHHHHHHHhhccCCCCCCCceEEEEcCCCCCCCccccHHHH
Q 000882 761 AGEPVGVLAATAMSNPAYKAVLDSS-------PSSNNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERAA 833 (1238)
Q Consensus 761 ~Ge~VG~laaqsigep~tq~~l~t~-------~~~~~g~~rlkEil~~~~~~k~~~~d~~~~l~L~~~~~~~~~~~e~~a 833 (1238)
||.+||.+||||||||+|||||+|+ +|+|+|+||+|||++|.+++++| .++--|.++ .++..|
T Consensus 1026 pGTavGAi~aQSIGEPGTQMTLKTFHFAGVASMNiTlGVPRIkEIINAsk~ISTP----IItA~L~n~------~d~~~A 1095 (1386)
T KOG0261|consen 1026 PGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKTISTP----IITAELENP------HDERSA 1095 (1386)
T ss_pred CcchhhhhhcccCCCCCceeeeeeeeecceeeeeeccCcchHHHHHhhhcccCcc----ceeeeecCc------hhHHHH
Confidence 9999999999999999999999996 48999999999999999986665 566667665 488999
Q ss_pred HHHHhhhceechhhhhheeeEEecCCccccCCCceEEEEEecHHHHhhcCC--CHhhHHHHHHHh-hhhh----------
Q 000882 834 YMVKNQLKRVSLKDAAVEFLIEYKKPEIISDDEGLVGHIHLNKILLEDLRI--SMHDILPKCQET-LKSF---------- 900 (1238)
Q Consensus 834 ~~V~~~le~vtl~dv~~~i~i~y~~~~~~~~~~~~v~~i~Ld~e~L~~~~l--t~~~I~~~l~~~-~~~~---------- 900 (1238)
+.||.+||+++|+||++.+...|.++.+ ++.|.||.+.+...+| ++++|.-.+-+. ....
T Consensus 1096 r~VKgRiEKt~L~dv~~yieeV~~p~~~-------fl~i~vd~~~I~~l~L~i~~~~I~~sI~~s~~~k~~~~~v~v~~~ 1168 (1386)
T KOG0261|consen 1096 RVVKGRIEKTTLGDVCSYIEEVYGPDSC-------FLLIRVDLKRISLLQLEITIESIAYSILKSPKRKVKPNDVRVVGE 1168 (1386)
T ss_pred HHHhhhhhhhhHHHHHHHHHHHhCCcce-------EEEEEecHhHHhhhhccccHHHHHHHHhcCCccccCCcceEEecc
Confidence 9999999999999999999999999987 7889999998887765 578888655442 1110
Q ss_pred ------h-hhhh------hHHHHHhhccceeeccccccccccccccCCCcceEEEEEeecC-----Ccccccchhhcccc
Q 000882 901 ------C-KKKK------MKKVVQFFKNTSLSISECCSFQQSCADKRSNMPCLMFVLRGAS-----DSYLDKLSGVLANM 962 (1238)
Q Consensus 901 ------~-~~~~------~~~i~~~~~~~~i~~~g~~~~~~~~~~~~~~~~~lt~~~~~~~-----~~~~vd~~~~~sn~ 962 (1238)
. ..++ ...+...++++.+ +|+..+++.+++-++..--..+.++|.+ .++||..++|.+|+
T Consensus 1169 ~~~~v~~~~~~~~S~~~~lq~lk~~L~~Vvv--~gip~vnr~vi~~de~~~~y~L~vEG~gLr~Vm~t~GV~g~~TtsNn 1246 (1386)
T KOG0261|consen 1169 TTLRVTPVSDTKSSVYYNLQRLKRSLPNVVV--KGIPEVNRAVINIDEKRGLYKLLVEGTGLRAVMNTDGVKGRRTTSNN 1246 (1386)
T ss_pred eeEEEeecccccchhhhhHHHHHhhCCceEE--ecCcchhhhheeecccCCceEEEEeccchHHHhccCCccccccccCc
Confidence 0 0011 1245688888888 8999999998876442222445799987 78999999999999
Q ss_pred hhhHHHHhhhchhHHHH----HHHHHHHhhhhccccccceeeecccccccceEeeecccccccccccccccccchhhccc
Q 000882 963 IYPVLLETIIKENWWVR----QRLSASVTMVAKGVLKEHLILLANSMTCAGDLVGFNSGGYKALSRSLNVQVPFTEATLF 1038 (1238)
Q Consensus 963 I~ei~r~tiikGi~w~R----~~l~~~~~~~~~~V~~rHl~Llad~MT~~G~~~~~~r~G~~~~~~s~l~~a~Fe~~t~~ 1038 (1238)
+.||. -+.|||++| +.+..++...|.+||+||+|||||.|||+|||.||||+|+++|+.|+|++||||+
T Consensus 1247 v~Ev~---~vLGIEAAR~~II~EI~ytM~~HGmsiD~RHiMLLaDvMTyrGEVlGITRfGl~KM~~SVL~lASFEk---- 1319 (1386)
T KOG0261|consen 1247 VLEVE---KVLGIEAARTTIISEIGYTMSNHGMSIDPRHIMLLADVMTYRGEVLGITRFGLAKMKDSVLMLASFEK---- 1319 (1386)
T ss_pred eEEee---hhhchHHHHHHHHHHHHHHHHhcCcccCHHHHHHHHHHhhhcceeeeeeehhhHHHHHHHHHHHhhhh----
Confidence 99999 779999999 5567788888899999999999999999999999999999999999999999999
Q ss_pred ChHHHHHHHHhhcCCCCCCcccchhccCCcccccccceEEEEecCCCccccCCCccccccccccc
Q 000882 1039 MPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGSRFDLLWQTENEEFNQDDGVDVYDFLHMV 1103 (1238)
Q Consensus 1039 t~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~~f~l~~~~~~~~~~~~~~~~~y~~l~~~ 1103 (1238)
|. +||++||.+|.+|.+.||||+||+|+++++|||. |+|++.... +..++....|++-|+.-
T Consensus 1320 T~-DhLF~AA~~~k~D~I~GVSEcIIlG~pm~iGTG~-fkl~~~~~~-~~~~~~~~~if~~~~~~ 1381 (1386)
T KOG0261|consen 1320 TA-DHLFDAAAYGKKDAIEGVSECIILGIPMCIGTGI-FKLLQRTDD-KKVLKPKPPIFSSLNLH 1381 (1386)
T ss_pred hh-HHHHHHHHhcCcccccchhhheecccceeccccH-HHHHHhcCC-cccCCCCCCcccccccc
Confidence 44 9999999999999999999999999999999999 999997655 44444457788877654
No 2
>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Probab=100.00 E-value=4.6e-241 Score=2279.41 Aligned_cols=1031 Identities=22% Similarity=0.339 Sum_probs=889.2
Q ss_pred ccccccceEEEecCChHHHHhcccccccc---------cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeEEcCc
Q 000882 9 ILEGQIVGIRFGLATQKEICTASISDCSI---------SHASQLANPFLGLPLEFGKCESCGTSEPGKCEGHFGYIELPI 79 (1238)
Q Consensus 9 ~~~~~I~~I~Fgl~S~eEI~k~Sv~~~~I---------~~~~gl~DprlG~~~~~~~C~TCg~~~~~~CpGHFGhIeL~~ 79 (1238)
.+.++|++|+||+||||||+++||+++.. +.++||+|||||+.+++..|+|||++. .+||||||||||++
T Consensus 4 ~~~~~I~~I~Fg~~S~eeIrk~Sv~~It~~~~~d~~g~P~~gGl~DprlG~~d~~~~C~TCg~~~-~~CpGHFGHIELa~ 82 (1321)
T PRK14977 4 LAVKAIDGIIFGLISPADARKIGFAEITAPEAYDEDGLPVQGGLLDGRLGTIEPGQKCLTCGNLA-ANCPGHFGHIELAE 82 (1321)
T ss_pred CccceeceEEEecCCHHHHHHhCeEEEecccccCCCCCcCCCCCCccccCCCCCCCCCCCCCCCC-CcCCCeeEEEEccC
Confidence 56688999999999999999999964311 113699999999999999999999996 79999999999999
Q ss_pred ccccccChHHHHHHHHhhcccc-----cCc---------------------hHHH----HHH----------HhH--h--
Q 000882 80 PIYHPSHISELKLTMYAFQLQI-----KND---------------------GVAQ----RLL----------SSC--C-- 115 (1238)
Q Consensus 80 PVfHpgf~k~i~~IL~~iCl~l-----~~~---------------------~~~~----~~~----------~~C--C-- 115 (1238)
|||||+||+.|++||+|+|..| +.. .+.+ ++. +.| |
T Consensus 83 PVfHpgf~k~i~~iLr~iC~~C~rlll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~C~~C~~ 162 (1321)
T PRK14977 83 PVIHIAFIDNIKDLLNSTCHKCAKLKLPQEDLNVFKLIEEAHAAARDIPEKRIDDEIIEEVRDQVKVYAKKAKECPHCGA 162 (1321)
T ss_pred CceecccHHHHHHHHHHHHHHhchhhcCcccHHHHHHHHHHhhhcccchhhhhhHHHHHHHHhhhhhhhccCCcCCCCCC
Confidence 9999999999999999999433 110 0000 111 135 5
Q ss_pred ---------------------------HHHHHHccCChhHHHHhccC-CCCCCCceEEEeeccCCCCCCCccccCCCccc
Q 000882 116 ---------------------------EVKEMLKRIPEETRKKLAGK-GYFPQDGYILEYLPVPPNCLSVPDISDGVSTM 167 (1238)
Q Consensus 116 ---------------------------ev~~i~k~I~~ed~~~L~~~-~~~~~~~~il~~lpVpP~~~Rp~~~~~~~~~~ 167 (1238)
+|+++|++|+++|+++|+.. ...+|+||||++|||||+|+||++.++++.+.
T Consensus 163 ~~~~i~~~~~~~~~~~~~~~~~~l~p~~v~~if~~i~~~d~~llg~~~~~~~p~~~il~~lpVpP~~~RP~v~~~~~~~~ 242 (1321)
T PRK14977 163 PQHELEFEEPTIFIEKTEIEEHRLLPIEIRDIFEKIIDDDLELIGFDPKKARPEWAVLQAFLVPPLTARPSIILETGERS 242 (1321)
T ss_pred CCCeEEEeeceeeeecccccCcccCHHHHHHHHHhcCHHHHHHhCCCCCCCCcceEEEeccccCCCCCcCcEEeCCCccc
Confidence 78999999999999999632 23569999999999999999999999876678
Q ss_pred cchhhHHHHHHHHHHHHHHHhh-hcCCCCcchhhhhhhHHHHHHHHHHhcc--CCcccCCCcccCCCCCCCCCcchhhhh
Q 000882 168 SSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEVR--GTAKSSRDVDARFGVSQDPNSTTKAWL 244 (1238)
Q Consensus 168 ~~Dlt~~~l~~I~~~~~~l~~~-~~g~~~~~~~~~~~~~LQ~~v~~~~~~~--~~~k~~~~~~~~~~~~k~~~~~iKgk~ 244 (1238)
+||+|+ +|++|++.|+.|++. ..|+|.... .+.|+.||.+|++|+|+. +.+.+....++ ...|.+.+++|||+
T Consensus 243 eddlt~-~l~~Ii~~N~~l~~~~~~g~~~~~~-~~~~~~LQ~~v~~~~dn~~~~~~~~~~~~~~--rp~k~i~qrLkgKe 318 (1321)
T PRK14977 243 EDDLTH-ILVDIIKANQKLKESKDAGAPPLIV-EDEVDHLQYHTSTFFDNATAGIPQAHHKGSG--RPLKSLFQRLKGKE 318 (1321)
T ss_pred CCcHHH-HHHHHHHHHHHHHHHHHcCCcHHHH-HHHHHHHHHHHHHHhcccccCCCccccccCC--CchhHHHHHhcccc
Confidence 899999 799999999999875 567776554 578999999999999863 23222211011 12245668999999
Q ss_pred hhhhccccccCCCCCcceeEeCCCCccccccccchhhhcccccccccchhhHHHHHHHHHcCCccccC-------CCCce
Q 000882 245 EKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDNKLCLTYS-------DGSSS 317 (1238)
Q Consensus 245 gr~R~nllGKRVdfSaRsVIspDP~L~i~evGvP~~iA~~LT~pE~Vt~~Ni~~l~~lV~ng~~~~~~-------~~~~~ 317 (1238)
||||+|||||||||||||||||||||++||||||..||++|||||+||+||+++|+++|.|||. .|+ ..+.+
T Consensus 319 GrfR~nlmGKRVdfSaRtVIspDP~L~i~EVGvP~~iA~~LT~Pe~Vt~~Ni~~l~~lv~nG~~-~~pGA~~i~~~~g~~ 397 (1321)
T PRK14977 319 GRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKMKELVINGPD-EFPGANAIRKGDGTK 397 (1321)
T ss_pred ccccccccccccccccceeEeCCCCcccccccCHHHHHHhCCCCEEEchhhHHHHHHHHHcCCc-ccCCcceEEcCCCce
Confidence 9999999999999999999999999999999999999999999999999999999999999985 222 11123
Q ss_pred EEeccCC-CC-------cccccCcceeeeeeeccCeEeeeCCCCCCcccccceEEEecCCCeeeecccCCCCCCCccCcc
Q 000882 318 YSLREGS-KG-------HTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGD 389 (1238)
Q Consensus 318 ~~l~~~~-~~-------~~~L~~g~iV~Rhl~dgD~VL~NRqPSLHr~Simah~v~v~~~~T~rln~~vC~pyNADFDGD 389 (1238)
+.+++.. +. +..|++||+|||||+|||+|||||||||||||||||+|||+|++||||||+||+|||||||||
T Consensus 398 ~~l~~~~~~~~~~~~~~a~~L~~g~iV~Rhl~dGD~VL~NRQPSLHk~Simah~vkvl~~kT~Rln~~vC~pyNADFDGD 477 (1321)
T PRK14977 398 IRLDFLEDKGKDALREAAEQLEIGDIVERHLADGDIVIFNRQPSLHKLSILAHRVKVLPGATFRLHPAVCPPYNADFDGD 477 (1321)
T ss_pred eeehhhhhccchhHHHHHHhcccCcEEEEEeecCcEEEeccCCccccccceEEEEEEecCceEEecccccCcccCCcccc
Confidence 4443322 11 256899999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccCCCHHHHHHHHHHhccccccccCCCCCceEeechhhhhHHHhhh-ccccCCHHHHHHHhccccc--cccccccc
Q 000882 390 CIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF-KKYFLDKAFTQQLAMFALS--PLPRPALS 466 (1238)
Q Consensus 390 eMn~H~PQs~eAraEa~~Lm~~~~nilsp~~G~Piigl~QD~llg~~llt-kd~fl~~~~~~~l~~~~~~--~lp~PaI~ 466 (1238)
|||+|+|||++|||||++||++++||+||++|+|++|++||+|+|+|+|| +|+||++++++||+|+... .+|+|||+
T Consensus 478 EMNlHvPQS~eArAEa~~Lm~v~~niisP~~G~Pi~gliQD~l~g~~lLT~~d~fl~~~e~~~l~~~~~~~~~lp~PaI~ 557 (1321)
T PRK14977 478 EMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFDKNEASNIAMLAGITDPLPEPAIK 557 (1321)
T ss_pred eeeeecCCCHHHHHHHHHHHhhhhcEecCCCCCeeEEeehhhhhhhhhhccCcccCCHHHHHHHHHhCCCccccCCCcee
Confidence 99999999999999999999999999999999999999999999999998 7999999999999998764 37999999
Q ss_pred -ccccccccchhhhccccCCCCcccc--------------------CcEEEEecccccccccccCCccc---hHHHHHHH
Q 000882 467 -KARCSARWTALQILQSVLPPGFDSC--------------------GDRYLIKKSEVLKGDFDRDTIPS---VINEIVTS 522 (1238)
Q Consensus 467 -Kp~~~~lwTGKQi~S~~LP~~~~~~--------------------~~~viI~~gell~G~ldK~~lG~---s~~~LI~~ 522 (1238)
||. ++||||||||++||+++++. ++.|+|+||||++|++||+++|+ +.++|||.
T Consensus 558 ~kp~--~lwTGKQi~s~iLp~~~n~~~~~~~~~~~~~~~~~~~~~~d~~v~I~~geLl~G~ldK~~~G~~~~~~~~Lih~ 635 (1321)
T PRK14977 558 TKDG--PAWTGKQLFSLFLPKDFNFEGIAKWSAGKAGEAKDPSCLGDGYVLIKEGELISGVIDDNIIGALVEEPESLIDR 635 (1321)
T ss_pred cCCC--CeeeHHHHHHHHcCCCCCceecccccccccccccccCCCCcceEEeecCeEEeeecchHhhccccCCCCcHHHH
Confidence 898 99999999999999876531 45689999999999999999998 78999999
Q ss_pred HHHhhCHHHHHhchhhhHHHHHHHHHhcCceeecCccccCHHHHHHHHHHHHHHHHHHHhhhh-----------------
Q 000882 523 IFFEKGPEEVLEFFDSLQPLLMENLFADGFSVSLEDFSLSKAALWNIQKEIQALYSLLYHRMS----------------- 585 (1238)
Q Consensus 523 i~~~~G~~~a~~fLd~lqrL~~~~L~~~GFSiGi~D~~~~~~~~~~i~~~i~~~~~~~~~~~~----------------- 585 (1238)
++++||+++|.+||+.+|+|+++||+++|||||++|+++++++.+.+.+.+++++..+.++..
T Consensus 636 i~~~yG~~~a~~fL~~l~~l~~~~L~~~GFSigi~D~~~~~~~~~~i~~~i~~~~~~v~~l~~~~~~~~~i~~~~~~~~~ 715 (1321)
T PRK14977 636 IAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLIIPDEAKQEIEDDIQGMKDEVSDLIDQRKITRKITIYKGKEEL 715 (1321)
T ss_pred HHHHhCHHHHHHHHHHHHHHHHHHHHhCCEEEeeCcEecCHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccchhc
Confidence 999999999999999999999999999999999999999999877777666654433322111
Q ss_pred ----hhHHHHHHHHHHHHHHHHHHHHHHHHh----cCCccccccccchhhhhhHHHHHhhccccccc--------CCccc
Q 000882 586 ----TQNELVDLQIENHIRHVKMLVAKFILK----SSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSD--------RGKFY 649 (1238)
Q Consensus 586 ----~~~~~le~~~~~~l~~~~~~i~~~~~~----~n~l~~Mi~sGSKGS~~Ni~Qi~g~lGqQ~~~--------ggr~~ 649 (1238)
+.++.+|..+.+.|+++++.+++.+.+ .|++.+|+.||||||++|++||+||||||+++ |+ ++
T Consensus 716 ~~G~~~~~~~e~~i~~~l~~~r~~~~~~~~~~l~~~N~l~~Mv~SGAKGS~~Ni~Qi~~~lGQQ~ve~~~~~~~~G~-Ri 794 (1321)
T PRK14977 716 LRGMKEEEALEADIVNELDKARDKAGSSANDCIDADNAGKIMAKTGARGSMANLAQIAGALGQQKRKTRIGFVLTGG-RL 794 (1321)
T ss_pred CCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHhhcccccCHHHHHHHHhccccccccccccccCCCC-CC
Confidence 335677888888999999888776654 59999999999999999999999999999999 55 46
Q ss_pred cccccccccccccccCCCCCCCCCCCcceecccccccCCccceEEeeccccceeeecccccCCCCchhHHHHHHHheeEE
Q 000882 650 SKTLVEDIASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVI 729 (1238)
Q Consensus 650 ~r~l~~~~~~~f~~~~p~~~d~~~~a~GfV~ssF~~GL~P~EfFfHamagREGLiDTAvkTa~sGYL~RrLv~~l~d~~v 729 (1238)
++++..|++|||.+ ++..|+|+|||.|||++||+|+|||||||||||||||||||||+||||||||||+|||++|
T Consensus 795 ~~~~~~RtLPhF~~-----~d~~p~a~GfV~nsFl~GL~P~EfFFHaM~GREGLiDTAVKTA~SGYLQRrLvk~lEDl~v 869 (1321)
T PRK14977 795 HEGYKDRALSHFQE-----GDDNPDAHGFVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYFQRRLANALEDIRL 869 (1321)
T ss_pred cCCCCCCcCCCCCC-----CCCCcccccchhhhhcCCCCHHHHHHHhhcccccccccccccCcCchhHHHHHHHhcceEE
Confidence 77788899999964 4789999999999999999999999999999999999999999999999999999999999
Q ss_pred EecceEeccCCCceeeeeeecccccc------------------------------------------------------
Q 000882 730 CYDGTVRNVCSNSIIQFDYAVNARKS------------------------------------------------------ 755 (1238)
Q Consensus 730 ~YD~tvr~~~~~~iiqf~yg~dg~~~------------------------------------------------------ 755 (1238)
+||+|||++ +|.||||.||+||+|+
T Consensus 870 ~YD~TVR~s-~g~iiQF~YGeDG~d~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 948 (1321)
T PRK14977 870 EYDETVRDP-HGHIIQFKFGEDGIDPQKLDHGEAFNLERIIEKQKIEDRGKGASKDEIEELAKEYTKTFNANLPKLLADA 948 (1321)
T ss_pred ecCCeEEeC-CCCEEEEeecCCCcCHHHhccCCcccHHHHHHHhhhhccccCCCHHHHHHHHHHHHHhhhhhhHHHHHHH
Confidence 999999995 7899999999999662
Q ss_pred -----------------------cCcCCCCCeeeeeccccCCchHHHhhhccCC-------CCCCchHHHHHHHHhhccC
Q 000882 756 -----------------------HSLFPAGEPVGVLAATAMSNPAYKAVLDSSP-------SSNNSWELMKEILLCRVSF 805 (1238)
Q Consensus 756 -----------------------~~lv~~Ge~VG~laaqsigep~tq~~l~t~~-------~~~~g~~rlkEil~~~~~~ 805 (1238)
+++++||||||++||||||||+|||||+||+ ++|+|+|||+||++++++
T Consensus 949 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~pGe~VG~iaAQSiGEP~TQmTLnTFH~AGv~~~nvt~GvpRl~Eii~a~k~- 1027 (1321)
T PRK14977 949 IHGAELKEDELEAICAEGKEGFEKAKVEPGQAIGIISAQSIAEPGTQMTLRTFHAAGIKAMDVTHGLERFIELVDARAK- 1027 (1321)
T ss_pred HHHcCCCHHHHHHHHHHHHHHHHhcccCCcccchhhhhhhccCceeeecccccccccccccCcccCccchHHhhhcccC-
Confidence 1246799999999999999999999999974 889999999999998875
Q ss_pred CCCCCCceEEEEcCCCCCCCccccHHHHHHHHhhhceechhhhhheeeEEecCCccccCCCceEEEEEecHHHHhhcCCC
Q 000882 806 NNDPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIISDDEGLVGHIHLNKILLEDLRIS 885 (1238)
Q Consensus 806 k~~~~d~~~~l~L~~~~~~~~~~~e~~a~~V~~~le~vtl~dv~~~i~i~y~~~~~~~~~~~~v~~i~Ld~e~L~~~~lt 885 (1238)
+++|.|++||.+... .+++.|+.|+.+||+++|++++.++.+.|+++. .++++|+++|++++|+
T Consensus 1028 ---~~tp~m~~~l~~~~~----~~~~~a~~v~~~ie~~~l~~~~~~~~i~~~~~~---------~~i~~d~~~i~~~~i~ 1091 (1321)
T PRK14977 1028 ---PSTPTMDIYLDDECK----EDIEKAIEIARNLKELKVRALIADSAIDNANEI---------KLIKPDKRALENGCIP 1091 (1321)
T ss_pred ---CCCCeEEEEeCCccc----chHHHHHHHHhheeeeEHHHhhhheEeeccCCc---------eEEecCHHHHHhcCCC
Confidence 667799999987543 367889999999999999999999999999875 4789999999999999
Q ss_pred HhhHHHHHHHhhhhh-------------h---hhh------hhHHHHHhhccceeeccccccccccccc---cCC-Ccce
Q 000882 886 MHDILPKCQETLKSF-------------C---KKK------KMKKVVQFFKNTSLSISECCSFQQSCAD---KRS-NMPC 939 (1238)
Q Consensus 886 ~~~I~~~l~~~~~~~-------------~---~~~------~~~~i~~~~~~~~i~~~g~~~~~~~~~~---~~~-~~~~ 939 (1238)
+++|.+.+....... . ... ...++.+.+.++.+ +|+..+++++++ +++ ++|+
T Consensus 1092 ~~~i~~~i~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~l~~l~~~l~~~~i--~Gi~~I~r~~i~~~~~~~~~e~~ 1169 (1321)
T PRK14977 1092 MERFAEIEAALAKGKKFEMELEDDLIILDLVEAADRDKPLATLIAIRNKILDKPV--KGVPDIERAWVELVEKDGRDEWI 1169 (1321)
T ss_pred HHHHHHHHHHhhcCCceEEeecCCEEEEecCcccccchHHHHHHHHHHhcCCcEE--ecCCCceEEEEEeeccCCCeeEE
Confidence 998877655433110 0 000 01245566777666 899999997663 222 3455
Q ss_pred EEEEEeecC-----CcccccchhhcccchhhHHHHhhhchhHHHHH----HHHHHHhhhhccccccceeeecccccccce
Q 000882 940 LMFVLRGAS-----DSYLDKLSGVLANMIYPVLLETIIKENWWVRQ----RLSASVTMVAKGVLKEHLILLANSMTCAGD 1010 (1238)
Q Consensus 940 lt~~~~~~~-----~~~~vd~~~~~sn~I~ei~r~tiikGi~w~R~----~l~~~~~~~~~~V~~rHl~Llad~MT~~G~ 1010 (1238)
| .++|++ ..++||+.+|++|+|++|+ .+.|||++|+ .|..+++.+|.+||+|||+||||.||++|+
T Consensus 1170 l--~teG~nl~~vl~~~~Vd~~rt~sN~i~ei~---~~lGIEAaR~~ii~Ei~~v~~~~G~~V~~rHi~LlaD~MT~~G~ 1244 (1321)
T PRK14977 1170 I--QTSGSNLAAVLEMKCIDIANTITNDCFEIA---GTLGIEAARNAIFNELASILEDQGLEVDNRYIMLVADIMCSRGT 1244 (1321)
T ss_pred E--EecCcCHHHHhCCCCCcccccEECCHHHHH---HhhhHHHHHHHHHHHHHHHHHHcCCccCHHHHHHHHHHHccCce
Confidence 5 889987 7889999999999999999 7899999994 567788888899999999999999999999
Q ss_pred Eeeec------ccccccccccccccccchhhcccChHHHHHHHHhhcCCCCCCcccchhccCCcccccccceEEEEecCC
Q 000882 1011 LVGFN------SGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGSRFDLLWQTE 1084 (1238)
Q Consensus 1011 ~~~~~------r~G~~~~~~s~l~~a~Fe~~t~~t~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~~f~l~~~~~ 1084 (1238)
++++| ||||++++.|||++||||+ +.++|++||.+|+.|.|+||+||||||+++|+|||. |+|+++..
T Consensus 1245 ~~~i~~~~~~~R~Gi~~~~~s~l~~asFE~-----t~~~L~~AA~~g~~D~l~gvsenii~G~~~~~GTG~-~~Ll~~~~ 1318 (1321)
T PRK14977 1245 IEAIGLQAAGVRHGFAGEKDSPLAKAAFEI-----TTHTIAHAALGGEIEKIKGILDALIMGQNIPIGSGK-VDLLMDFS 1318 (1321)
T ss_pred EEeccccccccccccccCCCCHHHhcCHHH-----HHHHHHHHHHhcCcCccCChHHhhhcCCCccCccce-EEEEeccc
Confidence 99999 9999999999999999999 459999999999999999999999999999999999 99999753
No 3
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=100.00 E-value=5.8e-234 Score=2059.84 Aligned_cols=1055 Identities=26% Similarity=0.393 Sum_probs=920.1
Q ss_pred CCCCCC-CcccccccceEEEecCChHHHHhccccccc--------ccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCc
Q 000882 1 MEENTS-STILEGQIVGIRFGLATQKEICTASISDCS--------ISHASQLANPFLGLPLEFGKCESCGTSEPGKCEGH 71 (1238)
Q Consensus 1 ~~~~~~-~~~~~~~I~~I~Fgl~S~eEI~k~Sv~~~~--------I~~~~gl~DprlG~~~~~~~C~TCg~~~~~~CpGH 71 (1238)
|+++.. +++|.++|++|+||++||+||++|||.+++ ...++||+|||||++++...|+|||.++ .+||||
T Consensus 1 m~~~~~~~~~pl~~v~~vqFgi~spdeir~mSV~~i~~~e~~e~~~pk~ggl~D~RlG~idr~~~CqTC~g~~-~~CpGH 79 (1605)
T KOG0260|consen 1 MGDDCEFSQAPLRTVKSVQFGILSPDEIRRMSVAEIEFPETMEGGRPKLGGLMDPRLGTIDRDSLCQTCGGNM-FECPGH 79 (1605)
T ss_pred CCCCcccccCcceeeeEEEeeccChhhhhcceeEEeecccccccCCCCcCCccccccCCCCccchhhhhcccc-ccCCcc
Confidence 556655 789999999999999999999999997532 1234699999999999999999999986 899999
Q ss_pred ceeEEcCcccccccChHHHHHHHHhhccccc--------------------CchHHHHHHHhH-----h-----------
Q 000882 72 FGYIELPIPIYHPSHISELKLTMYAFQLQIK--------------------NDGVAQRLLSSC-----C----------- 115 (1238)
Q Consensus 72 FGhIeL~~PVfHpgf~k~i~~IL~~iCl~l~--------------------~~~~~~~~~~~C-----C----------- 115 (1238)
||||+||+|||||||+++|.+||+|+|..|. .++....++..| |
T Consensus 80 FGhieLAkPvfH~gFl~kv~kiL~cVC~~C~ki~~~~~~~~~~~~~~~~~~~k~rl~~v~~vck~k~~ce~g~~~e~~g~ 159 (1605)
T KOG0260|consen 80 FGHIELAKPVFHPGFLKKVKKILRCVCFYCSKILKDKFNPKEDQILRKRYCSKGRLLMVLDVCKGKVVCEGGIDVESDGR 159 (1605)
T ss_pred cceeeeccccccHHHHHHHHHHHHHhhhcchheeecccCcchhhhhhhhcCCcchHHHHHHhhccceeeecccccccccc
Confidence 9999999999999999999999999994441 112222344444 2
Q ss_pred --------------------------------------HHHHHHccCChhHHHHhccCC-CCCCCceEEEeeccCCCCCC
Q 000882 116 --------------------------------------EVKEMLKRIPEETRKKLAGKG-YFPQDGYILEYLPVPPNCLS 156 (1238)
Q Consensus 116 --------------------------------------ev~~i~k~I~~ed~~~L~~~~-~~~~~~~il~~lpVpP~~~R 156 (1238)
+|++||++|+++|+..|+... +..||||||++|||||+.+|
T Consensus 160 sgcg~kqP~i~r~gl~l~a~~k~~~e~~~e~k~~ls~e~V~~i~k~Isded~~~lg~~~~~arpewmIlTvLPVPP~~vr 239 (1605)
T KOG0260|consen 160 SGCGLKQPSIRRLGLDLWAFWKQGDEDSQESKRKLSAERVLEIFKRISDEDIDQLGFKPKIARPEWMILTVLPVPPPAVR 239 (1605)
T ss_pred ccccccCCceeccCchhhhhhhccCccCCcccccCcHHHHHHHHHhhchhhhhhhcCCCCcCCCceeEEEEecCCCCccc
Confidence 789999999999999997653 45689999999999999999
Q ss_pred CccccCCCccccchhhHHHHHHHHHHHHHHHhh-hcCCCCcchhhhhhhHHHHHHHHHHh--ccCCcccCCCcccCCCC-
Q 000882 157 VPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLE--VRGTAKSSRDVDARFGV- 232 (1238)
Q Consensus 157 p~~~~~~~~~~~~Dlt~~~l~~I~~~~~~l~~~-~~g~~~~~~~~~~~~~LQ~~v~~~~~--~~~~~k~~~~~~~~~~~- 232 (1238)
|.++.+|....+||+|+ +|.+|++.|..+++. ..|++.++..+ ..++||.+|++|+| ++|.+++.+ ++|.
T Consensus 240 P~iv~~~s~rg~Ddlth-kLadIiK~n~~l~r~e~~ga~~H~i~e-~~~LlqfhVat~~Dn~~pgqp~a~q----ksGrp 313 (1605)
T KOG0260|consen 240 PEIVMQGSARGEDDLTH-KLADIIKKNIGLKRNEENGAPAHIIEE-YEQLLQFHVATYVDNDIPGQPQADQ----KSGRP 313 (1605)
T ss_pred ceeeecccccCcchhHH-HHHHHHHHHHHHhhhhhcCCchhhHHH-HHhHhhhhhhheecccccCCccccc----ccCCc
Confidence 99998887777899999 699999999999864 67888777544 45899999999998 456666543 3443
Q ss_pred CCCCCcchhhhhhhhhccccccCCCCCcceeEeCCCCccccccccchhhhcccccccccchhhHHHHHHHHHcCCcc---
Q 000882 233 SQDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDNKLCL--- 309 (1238)
Q Consensus 233 ~k~~~~~iKgk~gr~R~nllGKRVdfSaRsVIspDP~L~i~evGvP~~iA~~LT~pE~Vt~~Ni~~l~~lV~ng~~~--- 309 (1238)
.|++.+++|||+||+|||||||||||||||||||||||+|||||||..||++|||||.||+|||++|++||.+|++.
T Consensus 314 lkSi~arlKgkegriRgnLmGKRvDFSaRTVItgDPnl~ldevGVP~sIAk~lTfpE~Vtp~NidrLqeLV~~g~~~~pg 393 (1605)
T KOG0260|consen 314 LKSISARLKGKEGRIRGNLMGKRVDFSARTVITGDPNLSLDEVGVPRSIAKRLTFPEHVTPFNIDRLQELVRRGLLEHPG 393 (1605)
T ss_pred ccchhhhhccccchhhhcccccccCcceeeeecCCCCcchhcccCcHHHHhhccCcceeccccHHHHHHHhhCCCCCCCC
Confidence 36677999999999999999999999999999999999999999999999999999999999999999999999862
Q ss_pred ---ccCCCCceEEeccCC-CCcccccCcceeeeeeeccCeEeeeCCCCCCcccccceEEEecCCCeeeecccCCCCCCCc
Q 000882 310 ---TYSDGSSSYSLREGS-KGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSAD 385 (1238)
Q Consensus 310 ---~~~~~~~~~~l~~~~-~~~~~L~~g~iV~Rhl~dgD~VL~NRqPSLHr~Simah~v~v~~~~T~rln~~vC~pyNAD 385 (1238)
..++.+.++++++.+ +++..|+.||+|||||+|||+|||||||||||||||||||||+|++|||||++||+|||||
T Consensus 394 akyiird~G~Ridlr~~~~~~d~~Lq~G~kVeRhl~DGD~VlfNRqPSlHKmSmmahrVrVlp~sTfrLNlsvtsPynAD 473 (1605)
T KOG0260|consen 394 AKYIIRDNGDRIDLRYHKRAGDIHLQPGYKVERHLMDGDVVLFNRQPSLHKMSMMAHRVRVLPYSTFRLNLSVTSPYNAD 473 (1605)
T ss_pred cceeeecCCcEEEEeecCCccccccccccEEEEeeccCCEEEEcCCCcHHHhhhhhcEEEEccCceEEeCeeecCCccCC
Confidence 223334455555543 4578999999999999999999999999999999999999999999999999999999999
Q ss_pred cCccccccccCCCHHHHHHHHHHhccccccccCCCCCceEeechhhhhHHHhhh-ccccCCHHHHHHHhcccc-cc--cc
Q 000882 386 FDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF-KKYFLDKAFTQQLAMFAL-SP--LP 461 (1238)
Q Consensus 386 FDGDeMn~H~PQs~eAraEa~~Lm~~~~nilsp~~G~Piigl~QD~llg~~llt-kd~fl~~~~~~~l~~~~~-~~--lp 461 (1238)
|||||||+|+|||++||||+.+|+++++||+|||+|+|++|++||+|+|+++++ ||+||+|++++||+||+. .. .|
T Consensus 474 FDGDemnlhvPQS~etkAEl~EL~~vpkQiispQsnkpvmgivQDTLta~R~~t~Rd~Fl~r~~vmnLlm~~p~~d~~~P 553 (1605)
T KOG0260|consen 474 FDGDEMNLHVPQSLETKAELEELAMVPKQIISPQSNKPVMGIVQDTLTAVRKMTKRDVFLNRAQVMNLLMYVPDWDGPPP 553 (1605)
T ss_pred CCCceeecccCcchhHHHHHHHHhhhhhhhcCCcCCCcceeeehhhHHHHHHHhhHhhhhcHHHHHHHHhhccccCCCCC
Confidence 999999999999999999999999999999999999999999999999999998 789999999999999994 43 44
Q ss_pred -cccccccccccccchhhhccccCCCCcccc-----------------CcEEEEecccccccccccCCccchHHHHHHHH
Q 000882 462 -RPALSKARCSARWTALQILQSVLPPGFDSC-----------------GDRYLIKKSEVLKGDFDRDTIPSVINEIVTSI 523 (1238)
Q Consensus 462 -~PaI~Kp~~~~lwTGKQi~S~~LP~~~~~~-----------------~~~viI~~gell~G~ldK~~lG~s~~~LI~~i 523 (1238)
.|||+||+ ||||||||||+++|.++++. +.+|+|++|+++.|+++|+.+|++.++|+|.+
T Consensus 554 a~pai~Kp~--PlWTGkQifsliiP~~in~~r~~s~h~d~~~~~~~p~dt~~lie~g~l~~g~l~Kkt~G~s~g~lvh~i 631 (1605)
T KOG0260|consen 554 AKPAILKPK--PLWTGKQIFSLIIPGGINYIRDHSTHPDSEDELISPGDTRVLIEGGELLIGVLCKKTVGSSAGGLVHVI 631 (1605)
T ss_pred CCcccCCCC--cccchhhheeeecCCCcceecccccCcCCCcccccCCCceEEEeCCceEEEEeeccccccccCceEEEe
Confidence 57999999 99999999999999988752 34899999999999999999999999999999
Q ss_pred HHhhCHHHHHhchhhhHHHHHHHHHhcCceeecCccccCHHHHHHHHHHHHHHHHHHH----hhh---------hhhHHH
Q 000882 524 FFEKGPEEVLEFFDSLQPLLMENLFADGFSVSLEDFSLSKAALWNIQKEIQALYSLLY----HRM---------STQNEL 590 (1238)
Q Consensus 524 ~~~~G~~~a~~fLd~lqrL~~~~L~~~GFSiGi~D~~~~~~~~~~i~~~i~~~~~~~~----~~~---------~~~~~~ 590 (1238)
+.+.|++.|..|++.+|+|.+.||...|||+||+|.+..++....+++.|.++..... +.. ....++
T Consensus 632 ~~e~Gp~~~~~f~~~iQ~lin~wll~~gfsigIgDtiad~~t~~~iq~~I~~ak~dv~~vi~~a~~~~L~~~pg~tlret 711 (1605)
T KOG0260|consen 632 FLEKGPKIARGFFDSIQTLINSWLLREGFSIGIGDTIADAATMCVIQNTIKEAKRDVLAVIREAQNNELEPTPGRTLRET 711 (1605)
T ss_pred ehhhCHHHHHHHHHHHHHHHHHHHHhcCccccccccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCCcchhHHHH
Confidence 9999999999999999999999999999999999999999999999988887654221 111 234678
Q ss_pred HHHHHHHHHHHHHHHHHHHHH----hcCCccccccccchhhhhhHHHHHhhcccccccCCccccccccccccccccccCC
Q 000882 591 VDLQIENHIRHVKMLVAKFIL----KSSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLVEDIASHFERIYP 666 (1238)
Q Consensus 591 le~~~~~~l~~~~~~i~~~~~----~~n~l~~Mi~sGSKGS~~Ni~Qi~g~lGqQ~~~ggr~~~r~l~~~~~~~f~~~~p 666 (1238)
+|..+..+|+++++.++..+. ++|++..|+.+|||||.+||+|+++|+|||+++|+| ++-++..|++|||.+
T Consensus 712 fe~~v~~vlndArd~~gssA~~sl~esNn~k~Mv~aGSKGs~inisQ~saCVGqQnVEgkr-IpFGF~~Rtlphf~k--- 787 (1605)
T KOG0260|consen 712 FENKVNRVLNDARDKSGSSAQKSLSESNNFKTMVVAGSKGSFINISQVSACVGQQNVEGKR-IPFGFPKRTLPHFSK--- 787 (1605)
T ss_pred HHHHHHHHHHHHHHhhhhHHHhhhhhcccHHHHHhhcCCCcceehhhhhhhhccccccccc-cccCCCccccccccc---
Confidence 888888999999988766554 479999999999999999999999999999999876 667788889999964
Q ss_pred CCCCCCCCCcceecccccccCCccceEEeeccccceeeecccccCCCCchhHHHHHHHheeEEEecceEeccCCCceeee
Q 000882 667 MDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYDGTVRNVCSNSIIQF 746 (1238)
Q Consensus 667 ~~~d~~~~a~GfV~ssF~~GL~P~EfFfHamagREGLiDTAvkTa~sGYL~RrLv~~l~d~~v~YD~tvr~~~~~~iiqf 746 (1238)
+|++|+++|||+|||++||+|+|||||||+|||||||||||||++|||||||||+|||+.|+|||||||. -|.+|||
T Consensus 788 --DdysPesrGfVENSyL~GLtP~EfFfHamggREglidtavktaEtGyiqRRL~kameDimv~yDgTVRNs-~gqviQf 864 (1605)
T KOG0260|consen 788 --DDYSPESRGFVENSYLTGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLMKAMEDIMVAYDGTVRNS-LGQVIQF 864 (1605)
T ss_pred --CCCCccccceeecccccCCCHHHHHHHHhcccchhhhhhhcccccchHHHHHHHHHHHHHhhcCcceecc-cceeEEE
Confidence 7999999999999999999999999999999999999999999999999999999999999999999996 5799999
Q ss_pred eeecccccc-----------------------------------------------------------------------
Q 000882 747 DYAVNARKS----------------------------------------------------------------------- 755 (1238)
Q Consensus 747 ~yg~dg~~~----------------------------------------------------------------------- 755 (1238)
.||+||++.
T Consensus 865 ~YGeDG~d~~~vE~q~~~~l~~~~a~f~~~~~~d~ld~~~~~~~~~~~~e~~~~~~l~~lle~e~~~l~~dr~~l~~i~~ 944 (1605)
T KOG0260|consen 865 KYGEDGLDGHPVEFQNGETLGSLNACFESEFAYDALDEPISLSSEEVVNEISELLKLQNLLECEYKKLVRDRRVLLYIFE 944 (1605)
T ss_pred EeccCccccceeeccccccccchHHHHHhhhhhhhhcCcccchhhhHhhhhhhhHHHHHHHHHHHHhhhhhhhhhhhhcc
Confidence 999999540
Q ss_pred --------------------------------------------------------------------------------
Q 000882 756 -------------------------------------------------------------------------------- 755 (1238)
Q Consensus 756 -------------------------------------------------------------------------------- 755 (1238)
T Consensus 945 ~g~~k~~lp~n~~r~I~Na~~~f~~~~r~~t~l~~~~v~~g~~~l~e~l~iv~g~~~~sraqrl~~~lLrs~l~~krv~~ 1024 (1605)
T KOG0260|consen 945 YGDAKWPLPENLQRIIWNALKKFSIDERKPTDLIPFKVVKGVKELAEKLVIVRGEDYISRAQRLFNILLRSTLATKRVLE 1024 (1605)
T ss_pred cCCcccccchhHHHHHHHHHhhcccccccccccchhhhhhhhhhhhheeEEeeCchhHHHHHHHHHHHHHhhHHHHHHHH
Confidence
Q ss_pred ---------------------cCcCCCCCeeeeeccccCCchHHHhhhccC-------CCCCCchHHHHHHHHhhccCCC
Q 000882 756 ---------------------HSLFPAGEPVGVLAATAMSNPAYKAVLDSS-------PSSNNSWELMKEILLCRVSFNN 807 (1238)
Q Consensus 756 ---------------------~~lv~~Ge~VG~laaqsigep~tq~~l~t~-------~~~~~g~~rlkEil~~~~~~k~ 807 (1238)
++.+.|||.||++||||+|||+|||||+|+ +|+|.|+||||||+|..++
T Consensus 1025 e~rls~eaf~w~~~~Ie~~f~qa~a~pgemvg~lAaqsvgePatqmTlntfh~aGVssknVt~gvprlkei~Nv~k~--- 1101 (1605)
T KOG0260|consen 1025 EYRLSSEAFEWVLGEIEARFLQAEASPGEMVGALAAQSVGEPATQMTLNTFHYAGVSSKNVTLGVPRLKEIINVAKN--- 1101 (1605)
T ss_pred HhcccHHHHHHHhhhhhhheeeeecCccchHhHHHHHHhCCchhhcccchhcccceeeeeeeccCcchhhhhhhhcc---
Confidence 245789999999999999999999999996 4899999999999998875
Q ss_pred CCCCceEEEEcCCCCCCCccccHHHHHHHHhhhceechhhhhheeeEEecCCcccc---------------------CCC
Q 000882 808 DPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIIS---------------------DDE 866 (1238)
Q Consensus 808 ~~~d~~~~l~L~~~~~~~~~~~e~~a~~V~~~le~vtl~dv~~~i~i~y~~~~~~~---------------------~~~ 866 (1238)
+++|.+++||.+..++ +.+.|+.|+++||++||++++....|.|+|+...+ ..+
T Consensus 1102 -~ktpsLtV~l~g~~~k----~~e~ak~v~~~le~ttl~~vt~~t~i~ydpdp~~tvI~ed~e~v~a~~e~pd~D~~~is 1176 (1605)
T KOG0260|consen 1102 -AKTPSLTVYLTGEAAK----DNEWAKLVQCCLEHTTLKDVTRATEIYYDPDPQSTVIDEDREFVVAYYEMPDEDVGRIS 1176 (1605)
T ss_pred -CCCceEEEEecchhhc----chHHHHHHhhhcccccHHhhhccCcceecCCCcceeeccchhhHHhhhcCcccchhhcC
Confidence 5566999999988764 67789999999999999999999999999987543 148
Q ss_pred ceEEEEEecHHHHhhcCCCHhhHHHHHHHhhhhhh------------------hhhhhHH-----H-HHhhccceeeccc
Q 000882 867 GLVGHIHLNKILLEDLRISMHDILPKCQETLKSFC------------------KKKKMKK-----V-VQFFKNTSLSISE 922 (1238)
Q Consensus 867 ~~v~~i~Ld~e~L~~~~lt~~~I~~~l~~~~~~~~------------------~~~~~~~-----i-~~~~~~~~i~~~g 922 (1238)
||+++++||...|.+++|+|++|+.+++..++.-. .+..... + .+-+-++.+ .|
T Consensus 1177 pwlLrlelDr~~m~dk~ltm~~ia~~i~~~f~~d~~~i~~ddna~klv~r~ri~~~~e~D~~l~~Ie~~ml~~~~l--~G 1254 (1605)
T KOG0260|consen 1177 PWLLRLELDRASMTDKKLTMEQIAEKINRGFGSDLACIFSDDNAEKLVLRLRIAKEEEDDVFLKCIEANMLGDMTL--RG 1254 (1605)
T ss_pred hHHHHhhhhhhhcccccccHHHHHHHHHhhccCCCceeecccCCcceEEEEEecCccchhHHHHHHHHhhhhhccc--CC
Confidence 99999999999999999999999999998775410 0010011 1 133333333 57
Q ss_pred cccccccccccCC-------CcceEEEEEeecC-----CcccccchhhcccchhhHHHHhhhchhHHHHHHHHHHHhhh-
Q 000882 923 CCSFQQSCADKRS-------NMPCLMFVLRGAS-----DSYLDKLSGVLANMIYPVLLETIIKENWWVRQRLSASVTMV- 989 (1238)
Q Consensus 923 ~~~~~~~~~~~~~-------~~~~lt~~~~~~~-----~~~~vd~~~~~sn~I~ei~r~tiikGi~w~R~~l~~~~~~~- 989 (1238)
+..+.++.++.+. ++|.| -..|.+ ..+.+|..+|++|.|++|+ .|+|||++|.++..++..+
T Consensus 1255 ~~~i~kV~m~~~~~G~f~~~~ew~L--eTdg~~l~~v~s~~~vD~~rt~sn~l~ei~---~vlgIea~r~a~~~e~~~vi 1329 (1605)
T KOG0260|consen 1255 IPDIFKVYMSPTEDGEFKPVDEWDL--ETDGVNLRRVLSEPDVDPARTTSNDLVEIA---EVLGIEAVRKALLRELLNVI 1329 (1605)
T ss_pred ccccceEEEeecCCCceeecceeEE--ecCchhHHhhhccCCCCcccccccchhhhh---hhhcHHHHHhhhhhhhhheE
Confidence 7777777665321 44555 344433 5788999999999999999 8999999997776665544
Q ss_pred ---hccccccceeeecccccccceEeeecccccccccccccccccchhhcccChHHHHHHHHhhcCCCCCCcccchhccC
Q 000882 990 ---AKGVLKEHLILLANSMTCAGDLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWG 1066 (1238)
Q Consensus 990 ---~~~V~~rHl~Llad~MT~~G~~~~~~r~G~~~~~~s~l~~a~Fe~~t~~t~~~~l~~Aa~~g~~D~l~gv~~~ii~G 1066 (1238)
|++|++||+.|++|.||+.|++++++|||+++....+|+++|||| |+ +.|.+||..++.|..+||+|||++|
T Consensus 1330 ~f~gsyVnyrhlaLl~dvmT~~g~lm~itRhg~nr~~tgaLmrcSfEe----tv-~il~~aa~~~ekd~~rgvsEnImlg 1404 (1605)
T KOG0260|consen 1330 SFDGSYVNYRHLALLCDVMTARGHLMAITRHGINRQDTGALMRCSFEE----TV-DILMDAAAHAEKDPCRGVSENIMLG 1404 (1605)
T ss_pred eecccchhHHHHHHHHHHHhcccceeeeeccccchhhccccccccHHH----HH-HHHHHHHhhhccCCCccceeeeeec
Confidence 588999999999999999999999999999999999999999999 55 9999999999999999999999999
Q ss_pred CcccccccceEEEEecCCCccccCCC
Q 000882 1067 KHVAVGTGSRFDLLWQTENEEFNQDD 1092 (1238)
Q Consensus 1067 k~~~~GTG~~f~l~~~~~~~~~~~~~ 1092 (1238)
|.+|.|||. |+|+.+.+++....+.
T Consensus 1405 qlap~gTg~-~d~~ld~e~l~~~~~~ 1429 (1605)
T KOG0260|consen 1405 QLAPMGTGC-FDLMLDAEKLKKGIEI 1429 (1605)
T ss_pred ccccCCCcc-eeeeccHHhhhccCcc
Confidence 999999999 9999999999988763
No 4
>KOG0262 consensus RNA polymerase I, large subunit [Transcription]
Probab=100.00 E-value=4.1e-209 Score=1854.68 Aligned_cols=1025 Identities=25% Similarity=0.346 Sum_probs=798.7
Q ss_pred cccccceEEEecCChHHHHhcccccc-------cccCC--CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeEEcCcc
Q 000882 10 LEGQIVGIRFGLATQKEICTASISDC-------SISHA--SQLANPFLGLPLEFGKCESCGTSEPGKCEGHFGYIELPIP 80 (1238)
Q Consensus 10 ~~~~I~~I~Fgl~S~eEI~k~Sv~~~-------~I~~~--~gl~DprlG~~~~~~~C~TCg~~~~~~CpGHFGhIeL~~P 80 (1238)
..+.+.+|+||+||++||+++||+++ .+.|| +||||++||.-+..+.|.||++.. ..||||||||||+.|
T Consensus 9 v~~~~~~v~Fg~yt~~ei~klSv~kIt~p~~~D~lGhPi~GGLYDl~LGp~~~~~~C~TC~~~~-~~CPGH~GHIeL~~p 87 (1640)
T KOG0262|consen 9 VMSFQPSVSFGSYTDQEIRKLSVKKITNPITFDNLGHPIPGGLYDLALGPLDNSDVCSTCNQDE-LNCPGHMGHIELPVP 87 (1640)
T ss_pred ccccccceeeeccCHHHHhhcceeEecCceeecccCCCCCCcccccccCCccchhhhhhhcchh-hcCCCccCeeeeccc
Confidence 34556679999999999999999642 12333 699999999555667999999986 799999999999999
Q ss_pred cccccChHHHHHHHHhhcccc-----c--------------CchH-----------------------------------
Q 000882 81 IYHPSHISELKLTMYAFQLQI-----K--------------NDGV----------------------------------- 106 (1238)
Q Consensus 81 VfHpgf~k~i~~IL~~iCl~l-----~--------------~~~~----------------------------------- 106 (1238)
||||.||+.++.+|++.|+.| + ..|+
T Consensus 88 vynPlfF~~ly~lLr~sCl~Chhf~~k~~~v~~~~cqLrll~~G~i~ea~~Le~i~~~~~~d~~d~~~~~~k~~~~~~v~ 167 (1640)
T KOG0262|consen 88 VYNPLFFDFLYNLLRGSCLFCHHFRCKNVDVHILFCQLRLLEYGLIEEAEDLESITSETVEDNEDESLNEIKSCRAQYVT 167 (1640)
T ss_pred ccCHHHHHHHHHHHHHHHHhhhhcccCcHHHHHHHHHHHHHHhchHHHHHHHHHhhhhhhccCcchhHHHHHhhhhhhcc
Confidence 999999999999999999432 1 0000
Q ss_pred ---------------------HHHH----H------HhH--h--------------------------------------
Q 000882 107 ---------------------AQRL----L------SSC--C-------------------------------------- 115 (1238)
Q Consensus 107 ---------------------~~~~----~------~~C--C-------------------------------------- 115 (1238)
.+++ + ++| |
T Consensus 168 ~~i~~~~~~~~~~~t~~~~~~~~~lv~~f~k~~l~~kkC~~C~~~~p~~rk~~~~kv~~~~~~~~~~~~~~~~~~i~~~~ 247 (1640)
T KOG0262|consen 168 EAISEALLDKSEPNTKNSTELKKKLVTAFLKNALSRKKCPRCKHSNPKLRKDGFRKVFIDALSSKVGANVIRGAKIKKDV 247 (1640)
T ss_pred HHHHHHhhcCCCccchhhHHHHHHHHHHHHHHhhccccCCcccCCCchhhccccceeeeehhcccccccchhheeeehhc
Confidence 0000 0 245 5
Q ss_pred --------------------------------------------HHHHHHccCChhHHHHhc---c------CCCCCCCc
Q 000882 116 --------------------------------------------EVKEMLKRIPEETRKKLA---G------KGYFPQDG 142 (1238)
Q Consensus 116 --------------------------------------------ev~~i~k~I~~ed~~~L~---~------~~~~~~~~ 142 (1238)
+|+++|+.++..+-..|. . ..+.|.|+
T Consensus 248 ~~~~~~d~~~~G~~E~~~~g~d~~e~~~~~~~~~~t~~~~l~~tevR~~l~~lf~ne~~~l~~lf~l~~~~~~k~~p~d~ 327 (1640)
T KOG0262|consen 248 GSKGFEDSGIDGSNEVEEDGKDLFEKSTEPAEFEKTGKKYLLPTEVREHLRDLFKNEGELLSYLFPLWDSGSGKIDPSDM 327 (1640)
T ss_pred ccccccccccCCccccccccccccccccccccccccccccccHHHHHHHHHHHHhhhHHHHHHhhccccccccccCccce
Confidence 566666666655544442 1 12456689
Q ss_pred eEEEeeccCCCCCCCccccCCCccccchhhHHHHHHHHHHHHHHHhhh---cCCCC-------------cchhhhhhhHH
Q 000882 143 YILEYLPVPPNCLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSSR---SGTPN-------------FESQEVESNDL 206 (1238)
Q Consensus 143 ~il~~lpVpP~~~Rp~~~~~~~~~~~~Dlt~~~l~~I~~~~~~l~~~~---~g~~~-------------~~~~~~~~~~L 206 (1238)
|||.+|||||+.+||+...++. ..+++++..|++|++.+..|+... .|.-+ +..+.+.|..|
T Consensus 328 FFld~l~VpPtrfRP~s~~gd~--~~en~Qt~~L~kVle~s~~i~~~~~~m~~kl~~~~k~~l~~~~g~~~kl~~aw~~L 405 (1640)
T KOG0262|consen 328 FFLDNLLVPPTRFRPPSMLGDE--VHENPQTLNLNKVLESSVLIRKLLKDMKGKLDEELKLILERLRGIFSKLINAWLQL 405 (1640)
T ss_pred eeeeccccCCcccCCchhcchh--hhcChHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHhhhhHHHHHHHHHHHH
Confidence 9999999999999998887653 356777779999999998887642 11111 11233678999
Q ss_pred HHHHHHHHhccCCcccCCCcccCCCCCCCCCcchhhhh----hhhhccccccCCCCCcceeEeCCCCccccccccchhhh
Q 000882 207 QLAVGQYLEVRGTAKSSRDVDARFGVSQDPNSTTKAWL----EKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIA 282 (1238)
Q Consensus 207 Q~~v~~~~~~~~~~k~~~~~~~~~~~~k~~~~~iKgk~----gr~R~nllGKRVdfSaRsVIspDP~L~i~evGvP~~iA 282 (1238)
|.+|+.+||+....+..|+ ...++||.+ |-||.++|||||||+|||||||||||.+||||||..||
T Consensus 406 Q~~vn~lfDs~~~~k~~r~----------~~pGikQiLEKKeGLFRkhMMGKRVN~AaRSVIsPDPnI~tnEIGIP~vFA 475 (1640)
T KOG0262|consen 406 QASVNVLFDSKMASKWSRD----------SPPGIKQILEKKEGLFRKHMMGKRVNYAARSVISPDPNIETNEIGIPPVFA 475 (1640)
T ss_pred HHHHHHHhccccccccccC----------CCchHHHHHHHhhhhHHHHhhccccchhhccccCCCCCccccccCCchHHH
Confidence 9999999997443333222 225777765 56888889999999999999999999999999999999
Q ss_pred cccccccccchhhHHHHHHHHHcCCccccCCCCceEEeccC---------C---CC---cccc-------c--Ccceeee
Q 000882 283 QRITFEERVNVHNINYLQELVDNKLCLTYSDGSSSYSLREG---------S---KG---HTFL-------R--PGQVVHR 338 (1238)
Q Consensus 283 ~~LT~pE~Vt~~Ni~~l~~lV~ng~~~~~~~~~~~~~l~~~---------~---~~---~~~L-------~--~g~iV~R 338 (1238)
++|||||+||+||+++||++|.|||++ + +++.++..+. . |. .+-| + -+.+|+|
T Consensus 476 ~KLTyPepVt~~NV~elr~aViNGP~~-h--PGA~~iqd~dg~~t~l~~~~~~qR~alA~qLLtpst~~~~~~~~K~V~R 552 (1640)
T KOG0262|consen 476 KKLTYPEPVTPWNVNELRKAVINGPDV-H--PGATYIQDEDGTLTLLSPMTDEQREALANQLLTPSTGNPTEFGTKKVHR 552 (1640)
T ss_pred hhccCCCcCCcccHHHHHHHHhcCCCC-C--CCcceeecCCCceeecCCCCHHHHHHHHHHhhccccCCCcccCCceeee
Confidence 999999999999999999999999962 2 2223322111 0 00 0111 1 4689999
Q ss_pred eeeccCeEeeeCCCCCCcccccceEEEecC-CCeeeecccCCCCCCCccCccccccccCCCHHHHHHHHHHhcccccccc
Q 000882 339 RIMDGDTVFINRPPTTHKHSLQALSVYVHD-DHTVKINPLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLS 417 (1238)
Q Consensus 339 hl~dgD~VL~NRqPSLHr~Simah~v~v~~-~~T~rln~~vC~pyNADFDGDeMn~H~PQs~eAraEa~~Lm~~~~nils 417 (1238)
|+.+||+||+||||||||+|||||+|||++ ++|+||||++|++|||||||||||+|+|||+.|||||+.|++++.||+.
T Consensus 553 HvknGDvvlmNRQPTLHKPSimaHkaRVL~gEktlRlHYANCkaYNADFDGDEMN~HfPQse~araEa~~ian~dsqYLv 632 (1640)
T KOG0262|consen 553 HVKNGDVVLMNRQPTLHKPSIMAHKARVLPGEKTLRLHYANCKAYNADFDGDEMNVHFPQSEIARAEAYNIANTDSQYLV 632 (1640)
T ss_pred eccCCcEEEEcCCCccccchhhhhhheecCCcceeeeeecccccccCCCCcchhcccCCchhhHHHHHHHHhccCCceec
Confidence 999999999999999999999999999997 5999999999999999999999999999999999999999999999999
Q ss_pred CCCCCceEeechhhhhHHHhhh-ccccCCHHHHHHHhcccc------cccccccccccccccccchhhhccccC----CC
Q 000882 418 SHNGNLNLQLATDALLSLKVMF-KKYFLDKAFTQQLAMFAL------SPLPRPALSKARCSARWTALQILQSVL----PP 486 (1238)
Q Consensus 418 p~~G~Piigl~QD~llg~~llt-kd~fl~~~~~~~l~~~~~------~~lp~PaI~Kp~~~~lwTGKQi~S~~L----P~ 486 (1238)
|++|.|++||||||+++..+|| ||+||+|++|+||++.+. +.+++|+|+||. +|||||||+|++| |+
T Consensus 633 Pt~G~PlrGLIQDHiVsgv~LT~rd~Fftre~y~qLv~~~l~~~~~rI~~lpPtIlkP~--~LWTGKQVIsTil~Ni~P~ 710 (1640)
T KOG0262|consen 633 PTDGTPLRGLIQDHIVSGVLLTMRDSFFTREDYQQLVFAGLSDTFKRIKLLPPTILKPA--PLWTGKQVISTILKNIIPE 710 (1640)
T ss_pred cCCCCchhhhhhhheeeeEEEEecccccCHHHHHHHHHHhhhhhccceeccCccccccc--cccccchHHHHHHHhcCCC
Confidence 9999999999999999876665 999999999999987653 468999999999 9999999999976 43
Q ss_pred C---cc---------------cc-----CcEEEEecccccccccccCCccchHHHHHHHHHHhhCHHHHHhchhhhHHHH
Q 000882 487 G---FD---------------SC-----GDRYLIKKSEVLKGDFDRDTIPSVINEIVTSIFFEKGPEEVLEFFDSLQPLL 543 (1238)
Q Consensus 487 ~---~~---------------~~-----~~~viI~~gell~G~ldK~~lG~s~~~LI~~i~~~~G~~~a~~fLd~lqrL~ 543 (1238)
+ ++ .. ++.|+|++||||+|+|||+++|++.+||+|++++.||++.++++|+.+.||+
T Consensus 711 ~~p~iNl~~kaKip~~~W~~~s~e~~l~Es~v~ir~GellcGVLDKa~~Gat~yGLvH~~~ElYG~~~s~~lLs~~srlF 790 (1640)
T KOG0262|consen 711 GHPPINLESKAKIPGKAWRVHSEEPKLNESQVLIREGELLCGVLDKAQFGATAYGLVHCCHELYGGETSGKLLSVFSRLF 790 (1640)
T ss_pred CCCcccchhcccCchhhcCCCCCcccCCcceEEEecCceEEEeechhhcCchhhhhhhhhhhhhCccchhhHHHHHHHHH
Confidence 2 21 11 2569999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcCceeecCccccCHHHHHHHHHHHHHHHHHHHh--------------------hhhhh------HHHHHHHHHH
Q 000882 544 MENLFADGFSVSLEDFSLSKAALWNIQKEIQALYSLLYH--------------------RMSTQ------NELVDLQIEN 597 (1238)
Q Consensus 544 ~~~L~~~GFSiGi~D~~~~~~~~~~i~~~i~~~~~~~~~--------------------~~~~~------~~~le~~~~~ 597 (1238)
+.||+++|||+|++|+++.++++..+++++++....-.+ ..+.| ...++..+.+
T Consensus 791 T~ylq~~GFT~GvdDlll~~~~D~kR~~il~e~~~vG~qa~~~~~~l~~da~~del~~~le~~y~~d~~~~~~LD~~~k~ 870 (1640)
T KOG0262|consen 791 TAYLQMHGFTLGVDDLLLDKDADKKRREILRESRNVGNQAAKEAFGLDVDAPPDELRSRLEAIYLKDADKLAMLDRVMKS 870 (1640)
T ss_pred HHHHHHhccccccceeeechhhhHHHHHHHHhhhcccHHHHHHHhCCCCCCCHHHHHHHHHHHHhcchhHHHHHHHHHHH
Confidence 999999999999999999999999888888764322111 11111 2345566677
Q ss_pred HHHHHHHHHHHHHHh--------cCCccccccccchhhhhhHHHHHhhcccccccCCcccccccccccccccc--ccCCC
Q 000882 598 HIRHVKMLVAKFILK--------SSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLVEDIASHFE--RIYPM 667 (1238)
Q Consensus 598 ~l~~~~~~i~~~~~~--------~n~l~~Mi~sGSKGS~~Ni~Qi~g~lGqQ~~~ggr~~~r~l~~~~~~~f~--~~~p~ 667 (1238)
.++...+.|.+.|++ .|++..|+.||||||++|++||+|+||||.++|+| +|.|+++.. ++.|+
T Consensus 871 ~~n~~ts~I~~~cvP~GLlk~FP~N~mqlM~~SGAKGS~VN~~QISclLGQqeLEGkR------vPlMvSGKtLPsF~p~ 944 (1640)
T KOG0262|consen 871 ELNGYTSEIVKKCVPDGLLKKFPENNMQLMIQSGAKGSNVNTSQISCLLGQQELEGKR------VPLMVSGKTLPSFAPY 944 (1640)
T ss_pred HHhhhhHHHHhhhccchhhhcCCcchHHHHHHhcCCcccccHHHHHHhhhhHhhcCCc------cceeecCCccCCcCCC
Confidence 788888888888864 48999999999999999999999999999999877 555666532 22343
Q ss_pred CCCCCCCCcceecccccccCCccceEEeeccccceeeecccccCCCCchhHHHHHHHheeEEEecceEeccCCCceeeee
Q 000882 668 DLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYDGTVRNVCSNSIIQFD 747 (1238)
Q Consensus 668 ~~d~~~~a~GfV~ssF~~GL~P~EfFfHamagREGLiDTAvkTa~sGYL~RrLv~~l~d~~v~YD~tvr~~~~~~iiqf~ 747 (1238)
|.+|+|+|||.++|++|++|+|||||||||||||||||||||+||||||||||+||.+.|+||.|||+ ++|+||||.
T Consensus 945 --e~spraGGfI~~RFlTGi~PqeyfFHCMAGREGLIDTAVKTSRSGYLQRCLiKhLEgl~V~YD~TVRD-sDgsvVQF~ 1021 (1640)
T KOG0262|consen 945 --ETSPRAGGFIDGRFLTGIKPQEYFFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLKVHYDLTVRD-SDGSVVQFM 1021 (1640)
T ss_pred --CCCCCCCCcccceeecCCCchHHhhhhhccccchhhhHHhcccchHHHHHHHHhhhhcEEeccceEEc-CCCcEEEEe
Confidence 88999999999999999999999999999999999999999999999999999999999999999999 589999999
Q ss_pred eecccccc------------------------------------------------------------------------
Q 000882 748 YAVNARKS------------------------------------------------------------------------ 755 (1238)
Q Consensus 748 yg~dg~~~------------------------------------------------------------------------ 755 (1238)
||+||+|.
T Consensus 1022 YGEDglDitKssfl~~~~f~~~Ny~avl~~~~~~~v~s~~d~~~a~~~~k~i~kw~kk~~w~~~~k~~~cpdpv~~k~~p 1101 (1640)
T KOG0262|consen 1022 YGEDGLDITKSSFLNKKEFPTDNYEAVLLKYKSESVLSAFDIKKASKYIKKILKWKKKHMWFELDKKIACPDPVLAKYNP 1101 (1640)
T ss_pred ecCccccccHHhhcchhhhhhhhHHHHHhhhChHHHhhhhhhHHHHHHHHHHHHHHhhhccchhhcccCCCChhhhhcch
Confidence 99999750
Q ss_pred ---------------------------------------------cCcCCCCCeeeeeccccCCchHHHhhhccCC----
Q 000882 756 ---------------------------------------------HSLFPAGEPVGVLAATAMSNPAYKAVLDSSP---- 786 (1238)
Q Consensus 756 ---------------------------------------------~~lv~~Ge~VG~laaqsigep~tq~~l~t~~---- 786 (1238)
+++++|||+||+|||||||||.|||||+|++
T Consensus 1102 ~~y~gsvsekf~~~i~~f~~~~~k~~~s~~~~~~~lr~ll~~K~~~SLa~PGE~VGvlAAQSIGEPSTQMTLNTFHfAGr 1181 (1640)
T KOG0262|consen 1102 DKYLGSVSEKFRKKIDDFDDENAKKEKSEEPSEEKLRRLLQLKYIRSLADPGEPVGVLAAQSIGEPSTQMTLNTFHFAGR 1181 (1640)
T ss_pred hhhhccccHHHHHHHHHHHHHhhhhhccccchHHHHHHHHHHHHHHHhcCCCCcceeeeecccCCCcceeehhheeeccc
Confidence 3578999999999999999999999999974
Q ss_pred ---CCCCchHHHHHHHHh-hccCCCCCCCceEEEEcCCCCCCCccccHHHHHHHHhhhceechhhhhheeeEEec--CCc
Q 000882 787 ---SSNNSWELMKEILLC-RVSFNNDPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYK--KPE 860 (1238)
Q Consensus 787 ---~~~~g~~rlkEil~~-~~~~k~~~~d~~~~l~L~~~~~~~~~~~e~~a~~V~~~le~vtl~dv~~~i~i~y~--~~~ 860 (1238)
|+|+|+|||+|||.. +.+ +++|.|++.+.... ..+.|..+...|.+++|++|+..+.+.=. -..
T Consensus 1182 GemNVTLGIPRLREIlMtASan----IkTP~mt~pi~~g~------s~~ra~~i~~~l~rV~L~evlk~v~vte~~t~~~ 1251 (1640)
T KOG0262|consen 1182 GEMNVTLGIPRLREILMTASAN----IKTPSMTVPIKNGV------SDERADDITKELRRVTLKEVLKKVGVTEKITMVE 1251 (1640)
T ss_pred cceeeeecchHHHHHHHHHhhc----cCCCceeeeccCCc------cHHHHHHHHHHHHHHHHHHHHhheeeeEEEEeec
Confidence 999999999999985 444 55669999987653 55789999999999999999998765411 111
Q ss_pred cccCCCceEEEEEecH--HHHhhcCCCHhhHHHHHHHhhhhh-h----h---hhh-------------------------
Q 000882 861 IISDDEGLVGHIHLNK--ILLEDLRISMHDILPKCQETLKSF-C----K---KKK------------------------- 905 (1238)
Q Consensus 861 ~~~~~~~~v~~i~Ld~--e~L~~~~lt~~~I~~~l~~~~~~~-~----~---~~~------------------------- 905 (1238)
. ....-..++|.|.. +.=++++++.++|.+.++.++-.. . + +.+
T Consensus 1252 ~-~~~~~y~lr~~~~~~~~y~~e~~v~~e~i~~~m~~~Flk~L~~aI~k~~~k~~~~~~~~~dd~~~~~~~~~~~~~~~~ 1330 (1640)
T KOG0262|consen 1252 N-QSCKKYKLRFDLLPREEYQEEYDVRPEDIEEVMENRFLKLLERAIKKKLKKAKYTRGMSNDDADPDDGNEVDNNDEVG 1330 (1640)
T ss_pred c-ccceEEEEEEeecCHHHhhhhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhhccccccCCccccccCCcccccc
Confidence 0 01133455666543 223457788777765433322100 0 0 000
Q ss_pred ----------------h-----HHH---------------------------------------H---------------
Q 000882 906 ----------------M-----KKV---------------------------------------V--------------- 910 (1238)
Q Consensus 906 ----------------~-----~~i---------------------------------------~--------------- 910 (1238)
. .++ +
T Consensus 1331 ~~~~~~~~~e~~~~~ddddas~~k~~~k~~~~~dYe~~de~e~~~~~~~e~~~~~e~~e~d~e~g~dg~~~~~~~~~e~~ 1410 (1640)
T KOG0262|consen 1331 GEDNEDSDDESEDDEDDDDASDAKLHKKTEEEADYESEDEDERVEEREDEGDEDEESDEDDEEVGLDGTPEPEEEDQEGQ 1410 (1640)
T ss_pred CCccccccccccccCcccchhHHHHhhhhccccCcCCCchhhhhhhhhcccccccccccchhhcccCCCCCcccccccCC
Confidence 0 000 0
Q ss_pred ----------------Hhh-ccceeecc-c--c--------------------ccccccccccCC-CcceE---------
Q 000882 911 ----------------QFF-KNTSLSIS-E--C--------------------CSFQQSCADKRS-NMPCL--------- 940 (1238)
Q Consensus 911 ----------------~~~-~~~~i~~~-g--~--------------------~~~~~~~~~~~~-~~~~l--------- 940 (1238)
..| ....+... | | ......+++.-+ =+.|+
T Consensus 1411 ~~~~~~er~~qs~~~~~~fi~~y~fd~~~~~wcev~~~lp~~~~k~~mssiVe~~~~~~vI~q~~gIeRc~~~~~~~~~k 1490 (1640)
T KOG0262|consen 1411 PEVNAVERREQSVKKRHDFISRYTFDKESGKWCEVELKLPLDKEKLDMSSIVESIAPKSVIHQVPGIERCVVSEPQDDVK 1490 (1640)
T ss_pred chhhHHHHHHHHHHHHHHHhhhhccccccCcEEEEEEEecCCCcchHHHHHHHHHhcceeeeccCCceeeeccCCccccc
Confidence 000 00000000 0 0 000001111000 00111
Q ss_pred ---EEEEeecC------CcccccchhhcccchhhHHHHhhhchhHHHHHH----HHHHHhhhhccccccceeeecccccc
Q 000882 941 ---MFVLRGAS------DSYLDKLSGVLANMIYPVLLETIIKENWWVRQR----LSASVTMVAKGVLKEHLILLANSMTC 1007 (1238)
Q Consensus 941 ---t~~~~~~~------~~~~vd~~~~~sn~I~ei~r~tiikGi~w~R~~----l~~~~~~~~~~V~~rHl~Llad~MT~ 1007 (1238)
.+.++|-+ ..+..|+.++++|+|+.|+ .+.|+|++|+. +.+++..+|+.||+|||.|+||+|||
T Consensus 1491 ~~~~l~TeGVnl~a~~~~~d~LDv~~lySNDI~ail---~tyGVEAar~~Iv~Ev~~VF~vYGIsVd~RHLsLiADYMTf 1567 (1640)
T KOG0262|consen 1491 EKSVLLTEGVNLPALFDHADILDVNRLYSNDIHAIL---NTYGVEAARNAIVNEVNNVFKVYGISVDIRHLSLIADYMTF 1567 (1640)
T ss_pred ccceehhcCccHHHHHHHHhhhhhhhhccchHHHHH---HHhhHHHHHHHHHHHHHHhhhheeeeecHHHHHHHHHHHhh
Confidence 01222222 2345688899999999999 56889998865 46667778899999999999999999
Q ss_pred cceEeeecccccccccccccccccchhhcccChHHHHHHHHhhcCCCCCCcccchhccCCcccccccceEEEEec
Q 000882 1008 AGDLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGSRFDLLWQ 1082 (1238)
Q Consensus 1008 ~G~~~~~~r~G~~~~~~s~l~~a~Fe~~t~~t~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~~f~l~~~ 1082 (1238)
+|.+.||||+|| +.+.||+.+.+| +|+.++|.+||.+|+.|+|+++|+++++|+++..|||+ |||+.+
T Consensus 1568 ~G~y~pfnR~Gm-~~ssSP~qkMsF-----ETt~~Fl~~Aa~~g~~D~L~sPSArLvvG~~~r~GTG~-Fdll~~ 1635 (1640)
T KOG0262|consen 1568 EGGYQPFNRMGM-ESSSSPLQKMSF-----ETTCQFLKQAALFGEEDELSSPSARLVVGLPVRGGTGS-FDLLQK 1635 (1640)
T ss_pred cccccccccccc-ccCCChhHhhhH-----HHHHHHHHHHHhcCcccccCCCcceeEeccccCCCcce-eeeecc
Confidence 999999999998 555555555555 55679999999999999999999999999999999999 999864
No 5
>TIGR02390 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit A'. This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Probab=100.00 E-value=6.2e-189 Score=1765.09 Aligned_cols=742 Identities=27% Similarity=0.420 Sum_probs=643.9
Q ss_pred ccccceEEEecCChHHHHhccccccccc---------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeEEcCccc
Q 000882 11 EGQIVGIRFGLATQKEICTASISDCSIS---------HASQLANPFLGLPLEFGKCESCGTSEPGKCEGHFGYIELPIPI 81 (1238)
Q Consensus 11 ~~~I~~I~Fgl~S~eEI~k~Sv~~~~I~---------~~~gl~DprlG~~~~~~~C~TCg~~~~~~CpGHFGhIeL~~PV 81 (1238)
+++|++|+|+++|+|||+++||+++... .++||+|||||+++++..|+|||++. .+||||||||||++||
T Consensus 1 ~~~I~~I~F~~~S~eEI~k~Sv~~It~~~~~d~~g~P~~gGL~D~RLG~~~~~~~C~TCg~~~-~~CpGHFGhIeL~~PV 79 (868)
T TIGR02390 1 PKKIGSIKFGLLSPEEIRKMSVVEVVTADTYDDDGYPIEGGLMDPRLGVIEPGLRCKTCGGKV-GECPGHFGHIELARPV 79 (868)
T ss_pred CceeeEEEEeCCCHHHHHHhCeeEEecccccCCCCCcCCCCccCcccCCCCCCCCCCCCCCCC-CcCCCcceEEeccccc
Confidence 4679999999999999999999643221 13699999999999999999999996 8999999999999999
Q ss_pred ccccChHHHHHHHHhhccccc-----C---c------------------hHHHHHHH------hH--h------------
Q 000882 82 YHPSHISELKLTMYAFQLQIK-----N---D------------------GVAQRLLS------SC--C------------ 115 (1238)
Q Consensus 82 fHpgf~k~i~~IL~~iCl~l~-----~---~------------------~~~~~~~~------~C--C------------ 115 (1238)
|||+||+.|++||+|+|..|. . . .+.+++.+ +| |
T Consensus 80 fhpgf~~~i~kiL~~vC~~C~rll~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~i~~~~~~~~~C~~Cg~~~p~ir~~~~ 159 (868)
T TIGR02390 80 VHVGFAKEIYKILRATCRKCGRITLTEEEIEQYLEKINKLKEEGGDLASTLIEKIVKEAAKRMKCPHCGEEQKKIKFEKP 159 (868)
T ss_pred cchhHHHHHHHHHHHHhhhcCceeeCccccHHHHHHHHhcccchhhhHHHHHHHHHHHhhcCCCCCCCCCcCceEEEeee
Confidence 999999999999999994441 1 0 11223333 24 5
Q ss_pred -----------------HHHHHHccCChhHHHHhccC-CCCCCCceEEEeeccCCCCCCCccccCCCccccchhhHHHHH
Q 000882 116 -----------------EVKEMLKRIPEETRKKLAGK-GYFPQDGYILEYLPVPPNCLSVPDISDGVSTMSSDLSIAMLK 177 (1238)
Q Consensus 116 -----------------ev~~i~k~I~~ed~~~L~~~-~~~~~~~~il~~lpVpP~~~Rp~~~~~~~~~~~~Dlt~~~l~ 177 (1238)
+|++||++|+++|+++|+.. ...+|+||||++|||||+|+||++..+++...+||+|+ +|+
T Consensus 160 ~~~~~~~~~~~~~L~p~~v~~ilk~I~~eD~~lLG~~p~~~~Pe~~ilt~LPVPP~~iRPsv~~~~g~~~EDDLT~-~L~ 238 (868)
T TIGR02390 160 TYFYEEGKEGDVKLTPSEIRERLEKIPDEDAELLGINPKVARPEWMVLTVLPVPPVTVRPSITLETGERSEDDLTH-KLV 238 (868)
T ss_pred eeeeeccCCCCeecCHHHHHHHHHhCCHHHHHHhCCCCCCCCcceeeEeccccCCCCCcCeEEeCCCcccCChHHH-HHH
Confidence 78999999999999999532 12469999999999999999999988766667889999 799
Q ss_pred HHHHHHHHHHhh-hcCCCCcchhhhhhhHHHHHHHHHHhccCCcccCCCcccCCC-CCCCCCcchhhhhhhhhccccccC
Q 000882 178 KVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEVRGTAKSSRDVDARFG-VSQDPNSTTKAWLEKMRTLFIRKG 255 (1238)
Q Consensus 178 ~I~~~~~~l~~~-~~g~~~~~~~~~~~~~LQ~~v~~~~~~~~~~k~~~~~~~~~~-~~k~~~~~iKgk~gr~R~nllGKR 255 (1238)
+||+.|+.|++. ..|++.... .+.|+.||.+|++|||+.....+. ..++.+ ..+.+.+++|||+||||+||||||
T Consensus 239 ~II~~N~~Lk~~~~~g~~~~~~-~~~~~~LQ~~v~~~~d~~~~~~~~--~~~~~~~~~~~i~~~l~gK~G~~R~nl~GKR 315 (868)
T TIGR02390 239 DIIRINQRLKENIEAGAPQLII-EDLWELLQYHVATYFDNELPGIPP--ARHRSGRPLKTLAQRLKGKEGRFRGNLSGKR 315 (868)
T ss_pred HHHHHHHHHHHHHHcCCchhhh-HHHHHHHHHHHHHHHcCCCCCCCc--cccCCCCCchhhHhhhccccccccccccccc
Confidence 999999999876 466666554 557999999999999863211110 011111 225567899999999999999999
Q ss_pred CCCCcceeEeCCCCccccccccchhhhcccccccccchhhHHHHHHHHHcCCcc------ccCCCCceEEeccCCCC--c
Q 000882 256 SGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDNKLCL------TYSDGSSSYSLREGSKG--H 327 (1238)
Q Consensus 256 VdfSaRsVIspDP~L~i~evGvP~~iA~~LT~pE~Vt~~Ni~~l~~lV~ng~~~------~~~~~~~~~~l~~~~~~--~ 327 (1238)
|||||||||||||||++||||||..||++|||||+||+||+++|+++|.|||+. +++..+.++.+++.++. .
T Consensus 316 vd~s~RsVI~pdp~l~~~evGvP~~~A~~Lt~pe~Vt~~N~~~l~~lv~ng~~~~pga~~i~~~~g~~~~l~~~~~~~~~ 395 (868)
T TIGR02390 316 VNFSARTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVLNGPDSWPGANYVIRPDGRRIKIRDENKEELA 395 (868)
T ss_pred ccccCCceeeCCCCCcCCeeeCcHHHHHhCCCCeEEehhhHHHHHHHHHcCCccCCCceEEEcCCCcEEechhhhHHHHH
Confidence 999999999999999999999999999999999999999999999999999852 11112224444443322 3
Q ss_pred ccccCcceeeeeeeccCeEeeeCCCCCCcccccceEEEecCCCeeeecccCCCCCCCccCccccccccCCCHHHHHHHHH
Q 000882 328 TFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQSLAAKAEVLE 407 (1238)
Q Consensus 328 ~~L~~g~iV~Rhl~dgD~VL~NRqPSLHr~Simah~v~v~~~~T~rln~~vC~pyNADFDGDeMn~H~PQs~eAraEa~~ 407 (1238)
..|++||+|+|||+|||+|||||||||||||||||+|+|++++||||||+||+||||||||||||+|+|||++|||||++
T Consensus 396 ~~l~~g~~v~rhl~dgd~vl~NRqPsLHr~si~a~~~~v~~~~t~r~n~~~c~~~NADFDGDeMn~h~Pqs~~a~aEa~~ 475 (868)
T TIGR02390 396 ERLEPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARE 475 (868)
T ss_pred hhcccCCEEEEehhcCccceeccCCccccccceeEEEEEecCceEeeccccCCccccCcccceeeEecCCCHHHHHHHHH
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhccccccccCCCCCceEeechhhhhHHHhhh-ccccCCHHHHHHHhccccc--ccccccccccccccccchhhhccccC
Q 000882 408 LFSVEKQLLSSHNGNLNLQLATDALLSLKVMF-KKYFLDKAFTQQLAMFALS--PLPRPALSKARCSARWTALQILQSVL 484 (1238)
Q Consensus 408 Lm~~~~nilsp~~G~Piigl~QD~llg~~llt-kd~fl~~~~~~~l~~~~~~--~lp~PaI~Kp~~~~lwTGKQi~S~~L 484 (1238)
||++++||+||++|+|+++++||+|+|+|+|| ||+||++++++|++++... .+|+|||+||. ++||||||||++|
T Consensus 476 Lm~~~~~~~sp~~g~p~~~~~QD~l~g~~~LT~~d~f~~~~~~~~l~~~~~~~~~~~~p~i~kp~--~lwTGKqi~s~~l 553 (868)
T TIGR02390 476 LMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQTILGVAGYFGDPPEPAIEKPK--EYWTGKQIFSAFL 553 (868)
T ss_pred HhhchhceecCCCCCeeEEeehhhhhheeeeeeccccCCHHHHHHHHhcCCccccCCCceecCCc--ccccHHHHHHHhc
Confidence 99999999999999999999999999999998 7999999999999987653 57899999998 9999999999999
Q ss_pred CCCcccc-------------------CcEEEEecccccccccccCCccchHHHHHHHHHHhhCHHHHHhchhhhHHHHHH
Q 000882 485 PPGFDSC-------------------GDRYLIKKSEVLKGDFDRDTIPSVINEIVTSIFFEKGPEEVLEFFDSLQPLLME 545 (1238)
Q Consensus 485 P~~~~~~-------------------~~~viI~~gell~G~ldK~~lG~s~~~LI~~i~~~~G~~~a~~fLd~lqrL~~~ 545 (1238)
|.++++. ++.|+|+||+|++|++||+++|++.++|||.++++||+++|++||+.+|+|+++
T Consensus 554 p~~~n~~~~~~~~~~~~~~~~~~~~~d~~v~i~~g~ll~G~ldK~~lg~~~~~li~~i~~~yG~~~a~~fl~~~~~l~~~ 633 (868)
T TIGR02390 554 PEDLNFEGRAKICSGSDACKKEECPHDAYVVIKNGKLLKGVIDKKAIGAEKGKILHRIVREYGPEAARRFLDSVTRLFIR 633 (868)
T ss_pred CCCCcceecccccccccccccccCCCcceEEEecCeEEeeeecHHHhccCcccHHHHHHHHHCHHHHHHHHHHHHHHHHH
Confidence 9866531 345889999999999999999999999999999999999999999999999999
Q ss_pred HHHhcCceeecCccccCHHHHHHHHHHHHHHHHHHHhhhhhh-------------HHHHHHHHHHHHHHHHHHHHHHHHh
Q 000882 546 NLFADGFSVSLEDFSLSKAALWNIQKEIQALYSLLYHRMSTQ-------------NELVDLQIENHIRHVKMLVAKFILK 612 (1238)
Q Consensus 546 ~L~~~GFSiGi~D~~~~~~~~~~i~~~i~~~~~~~~~~~~~~-------------~~~le~~~~~~l~~~~~~i~~~~~~ 612 (1238)
||+.+|||||++|+++++++.+.+++.++++++.+.++...| ++.+|..+.+.|+++++.+++.+.+
T Consensus 634 ~l~~~GfSigi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~e~~i~~~l~~~r~~~~~~~~~ 713 (868)
T TIGR02390 634 FITLRGFTTGIDDIDIPKEAKEEIEELIEKAEKRVDNLIERYRNGELEPLPGRTVEETLEMKIMEVLGKARDEAGEVAEK 713 (868)
T ss_pred HHHhccEEeehhheeeCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999998888888887776665543332 5677878888889998887776654
Q ss_pred ----cCCccccccccchhhhhhHHHHHhhcccccccCCccccccccccccccccccCCCCCCCCCCCcceecccccccCC
Q 000882 613 ----SSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLVEDIASHFERIYPMDLNYPTAKYGLIKGCFFHGLD 688 (1238)
Q Consensus 613 ----~n~l~~Mi~sGSKGS~~Ni~Qi~g~lGqQ~~~ggr~~~r~l~~~~~~~f~~~~p~~~d~~~~a~GfV~ssF~~GL~ 688 (1238)
.|++.+|+.||||||++|++||+||||||+++|+| +++++..+.+|||.+ ++..|+|+|||.|||++||+
T Consensus 714 ~l~~~N~~~~M~~sGsKGS~~Ni~Qi~~~lGQQ~~~g~r-i~~~~~~rtlp~f~~-----~d~~~~~~GfV~~sF~~GL~ 787 (868)
T TIGR02390 714 YLDPENHAVIMARTGARGSLLNITQMAAMVGQQSVRGGR-IRRGYRNRTLPHFKK-----GDIGAKARGFVRSSFKKGLD 787 (868)
T ss_pred hcCCCcchhhhhhccCCcccccHHHHHhccCccccCCCc-CccccccCCCCCCCC-----CCCCcccCceecccccCCCC
Confidence 59999999999999999999999999999998765 677788899999963 47889999999999999999
Q ss_pred ccceEEeeccccceeeecccccCCCCchhHHHHHHHheeEEEecceEeccCCCceeeeeeecccccccCcCCCCCeeee
Q 000882 689 PYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYDGTVRNVCSNSIIQFDYAVNARKSHSLFPAGEPVGV 767 (1238)
Q Consensus 689 P~EfFfHamagREGLiDTAvkTa~sGYL~RrLv~~l~d~~v~YD~tvr~~~~~~iiqf~yg~dg~~~~~lv~~Ge~VG~ 767 (1238)
|+|||||||||||||||||||||+||||||||||+|||++|+||+|||++ +|.||||.||+||+|+..+ +-++||.+
T Consensus 788 p~EfFfH~m~gReGLiDTAvKTa~sGYLqRrLvk~lEdl~v~yD~tVR~~-~g~iiQf~YG~dg~d~~~~-~~~~~~~~ 864 (868)
T TIGR02390 788 PTEYFFHAAGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDT-RGNLIQFKYGEDGVDPMKS-DHGKPVDV 864 (868)
T ss_pred HHHHHHHHhhhccccccccccccccchhHHHHHHHHhheEEecCCeEEeC-CCcEEEEeccCCCcCHHHh-ccCccccc
Confidence 99999999999999999999999999999999999999999999999995 7899999999999987764 46677754
No 6
>PRK08566 DNA-directed RNA polymerase subunit A'; Validated
Probab=100.00 E-value=3.1e-187 Score=1754.52 Aligned_cols=739 Identities=26% Similarity=0.406 Sum_probs=643.7
Q ss_pred ccccccceEEEecCChHHHHhcccccccc---------cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeEEcCc
Q 000882 9 ILEGQIVGIRFGLATQKEICTASISDCSI---------SHASQLANPFLGLPLEFGKCESCGTSEPGKCEGHFGYIELPI 79 (1238)
Q Consensus 9 ~~~~~I~~I~Fgl~S~eEI~k~Sv~~~~I---------~~~~gl~DprlG~~~~~~~C~TCg~~~~~~CpGHFGhIeL~~ 79 (1238)
.+.++|++|+|+++|+|||+++||+++.. +.++||+|||||++++...|+|||++. .+||||||||||++
T Consensus 4 ~~~~~I~~I~F~~~S~eEI~klSv~~It~~~~~d~~g~P~~gGL~D~RLG~~~~~~~C~TCg~~~-~~CPGHFGhIeL~~ 82 (882)
T PRK08566 4 MIPKRIGSIKFGLLSPEEIRKMSVTKIITADTYDDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRA-GECPGHFGHIELAR 82 (882)
T ss_pred CCceeeeeEEEecCCHHHHHHhCeEEEecccccCCCCCcCCCCCCCcccCCCCCCCCCCCCCCCC-CcCCCcceEEeccc
Confidence 45688999999999999999999964311 113599999999999999999999996 89999999999999
Q ss_pred ccccccChHHHHHHHHhhcccc-----cCc--------------------hHHHHHHHh------H--h-----------
Q 000882 80 PIYHPSHISELKLTMYAFQLQI-----KND--------------------GVAQRLLSS------C--C----------- 115 (1238)
Q Consensus 80 PVfHpgf~k~i~~IL~~iCl~l-----~~~--------------------~~~~~~~~~------C--C----------- 115 (1238)
|||||+||+.|++||+|+|..| ... ...+++.+. | |
T Consensus 83 PVfhpgf~~~v~~iL~~iC~~C~rll~~~~~~~~~~~~l~~~~~~~~~~~~l~k~i~k~~k~~~~C~~Cg~~~~ki~~~~ 162 (882)
T PRK08566 83 PVIHVGFAKLIYKLLRATCRECGRLKLTEEEIEEYLEKLERLKEWGSLADDLIKEVKKEAAKRMVCPHCGEKQYKIKFEK 162 (882)
T ss_pred cccchhHHHHHHHHHHHhhhhhCceeccccchHHHHHHHhchhhhhhhHHHHHHHHHHHhcCCCCCCCcCCCCceEEEec
Confidence 9999999999999999999443 111 112333443 4 5
Q ss_pred ------------------HHHHHHccCChhHHHHhccC-CCCCCCceEEEeeccCCCCCCCccccCCCccccchhhHHHH
Q 000882 116 ------------------EVKEMLKRIPEETRKKLAGK-GYFPQDGYILEYLPVPPNCLSVPDISDGVSTMSSDLSIAML 176 (1238)
Q Consensus 116 ------------------ev~~i~k~I~~ed~~~L~~~-~~~~~~~~il~~lpVpP~~~Rp~~~~~~~~~~~~Dlt~~~l 176 (1238)
+|+++|++|+++|+.+|+.. ...+|+||||++|||||+++||++..+++...+||+|. +|
T Consensus 163 ~~~~~~~~~~~~~~L~p~~V~~ilk~I~~eD~~lLg~~~~~~~Pe~~il~~lPVpP~~iRPsv~~~~g~~~eDDLT~-~L 241 (882)
T PRK08566 163 PTTFYEERKEGLVKLTPSDIRERLEKIPDEDLELLGINPEVARPEWMVLTVLPVPPVTVRPSITLETGQRSEDDLTH-KL 241 (882)
T ss_pred ceeEEEecCCCceeCCHHHHHHHHHhCCHHHHHHhCCCCCCCCcceeEEeeeecCCCCCcCcEEeCCCcccCchHHH-HH
Confidence 78999999999999999532 23469999999999999999999999776677899998 79
Q ss_pred HHHHHHHHHHHhh-hcCCCCcchhhhhhhHHHHHHHHHHhccCCcccC-CCcccCCCCCCCCCcchhhhhhhhhcccccc
Q 000882 177 KKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEVRGTAKSS-RDVDARFGVSQDPNSTTKAWLEKMRTLFIRK 254 (1238)
Q Consensus 177 ~~I~~~~~~l~~~-~~g~~~~~~~~~~~~~LQ~~v~~~~~~~~~~k~~-~~~~~~~~~~k~~~~~iKgk~gr~R~nllGK 254 (1238)
++|++.|+.|++. ..|++... ..+.|+.||.+|+.|+|+.....+. +..+++ ..+.+.+++|||+||||+|||||
T Consensus 242 ~~II~~N~~Lk~~~~~g~~~~~-~~~~~~~LQ~~v~~~~d~~~~~~~~~~~~~~~--~~~~i~~~l~gK~G~fR~nl~GK 318 (882)
T PRK08566 242 VDIIRINQRLKENIEAGAPQLI-IEDLWELLQYHVTTYFDNEIPGIPPARHRSGR--PLKTLAQRLKGKEGRFRGNLSGK 318 (882)
T ss_pred HHHHHHHHHHHHHHHcCCcHHH-HHHHHHHHHHHHHHHhcCCccCCcccccCCCC--CccchHHhcccCCCccccccccc
Confidence 9999999999875 45666544 3567999999999999863221111 110111 23456689999999999999999
Q ss_pred CCCCCcceeEeCCCCccccccccchhhhcccccccccchhhHHHHHHHHHcCCccccCCCCceEEecc---------CCC
Q 000882 255 GSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDNKLCLTYSDGSSSYSLRE---------GSK 325 (1238)
Q Consensus 255 RVdfSaRsVIspDP~L~i~evGvP~~iA~~LT~pE~Vt~~Ni~~l~~lV~ng~~~~~~~~~~~~~l~~---------~~~ 325 (1238)
||||||||||||||+|++||||||..||++|||||+||+|||++|+++|.|||+ .|+ +++|.++. .++
T Consensus 319 Rvd~s~RsVI~pdp~l~~~evGvP~~~A~~Lt~pe~v~~~N~~~l~~~v~ng~~-~~p--ga~~i~~~~g~~~~l~~~~~ 395 (882)
T PRK08566 319 RVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNGPE-KHP--GANYVIRPDGRRIKLTDKNK 395 (882)
T ss_pred cccCcCCceeeCCCCCcCCeeeCcHHHHHhCCCCeEEchhhHHHHHHHHHcCCC-cCC--CceEEEcCCCceeeehhhhH
Confidence 999999999999999999999999999999999999999999999999999986 232 33444332 222
Q ss_pred C--cccccCcceeeeeeeccCeEeeeCCCCCCcccccceEEEecCCCeeeecccCCCCCCCccCccccccccCCCHHHHH
Q 000882 326 G--HTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQSLAAKA 403 (1238)
Q Consensus 326 ~--~~~L~~g~iV~Rhl~dgD~VL~NRqPSLHr~Simah~v~v~~~~T~rln~~vC~pyNADFDGDeMn~H~PQs~eAra 403 (1238)
. +..|++||+|+|||+|||+|||||||||||||||||+|||++++||||||+||+||||||||||||+|+|||++|||
T Consensus 396 ~~~~~~l~~g~~v~Rhl~dgd~vl~NRqPsLHr~si~a~~~~v~~~~t~r~n~~~c~~~NADFDGDeMn~h~Pqs~~a~a 475 (882)
T PRK08566 396 EELAEKLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARA 475 (882)
T ss_pred HHHHHhccccceehhhhhcCceeeecCCCcccccccceeEEEEecCceEeeccccCCCccCCccCcEEEEecCCCHHHHH
Confidence 1 24689999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhccccccccCCCCCceEeechhhhhHHHhhh-ccccCCHHHHHHHhccccc---ccccccccccccccccchhhh
Q 000882 404 EVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF-KKYFLDKAFTQQLAMFALS---PLPRPALSKARCSARWTALQI 479 (1238)
Q Consensus 404 Ea~~Lm~~~~nilsp~~G~Piigl~QD~llg~~llt-kd~fl~~~~~~~l~~~~~~---~lp~PaI~Kp~~~~lwTGKQi 479 (1238)
||++||++++||+||++|+|++|++||+|+|+|+|| +|+||++++++++++++.. .+|+|||+||. ++||||||
T Consensus 476 Ea~~Lm~~~~~~~sp~~g~pi~~~~QD~l~g~~~lt~~d~f~~~~~~~~l~~~~~~~~~~~~~pai~~p~--~lwTGKqi 553 (882)
T PRK08566 476 EARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAAGIDELPEPEPAIENGK--PYWTGKQI 553 (882)
T ss_pred HHHHHhcchhcEecCCCCCeeEEeehHHHHHHHHHHhccccCCHHHHHHHHHhCCccccccCCcccCCCc--ccccHHHH
Confidence 999999999999999999999999999999999998 7999999999999998764 57899999998 99999999
Q ss_pred ccccCCCCccc-------------------cCcEEEEecccccccccccCCccchHHHHHHHHHHhhCHHHHHhchhhhH
Q 000882 480 LQSVLPPGFDS-------------------CGDRYLIKKSEVLKGDFDRDTIPSVINEIVTSIFFEKGPEEVLEFFDSLQ 540 (1238)
Q Consensus 480 ~S~~LP~~~~~-------------------~~~~viI~~gell~G~ldK~~lG~s~~~LI~~i~~~~G~~~a~~fLd~lq 540 (1238)
||++||.++++ .++.|+|+||||++|++||+++|++.++|||.++++||++.|++||+.+|
T Consensus 554 ~s~~lp~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~gell~g~ldK~~lg~~~~~li~~i~~~yG~~~a~~fl~~~~ 633 (882)
T PRK08566 554 FSLFLPKDLNLEFKAKICSGCDECKKEDCEHDAYVVIKNGKLLEGVIDKKAIGAEQGSILDRIVKEYGPERARRFLDSVT 633 (882)
T ss_pred HHHHcCCCCCceeeccccccccccccccCCCCceEEEecCEEEeccccHHHhhcccchHHHHHHHHhCHHHHHHHHHHHH
Confidence 99999976653 14568999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCceeecCccccCHHHHHHHHHHHHHHHHHHHhhhh-------------hhHHHHHHHHHHHHHHHHHHHH
Q 000882 541 PLLMENLFADGFSVSLEDFSLSKAALWNIQKEIQALYSLLYHRMS-------------TQNELVDLQIENHIRHVKMLVA 607 (1238)
Q Consensus 541 rL~~~~L~~~GFSiGi~D~~~~~~~~~~i~~~i~~~~~~~~~~~~-------------~~~~~le~~~~~~l~~~~~~i~ 607 (1238)
+|+++||+.+|||||++|+++++++.+.+++.++++++.+..+.. +.++.+|..+.+.|+++++.++
T Consensus 634 ~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~e~~i~~~l~~~r~~~~ 713 (882)
T PRK08566 634 RLAIRFIMLRGFTTGIDDEDIPEEAKEEIDEIIEEAEKRVEELIEAYENGELEPLPGRTLEETLEMKIMQVLGKARDEAG 713 (882)
T ss_pred HHHHHHHHhcCEEeehhhcccCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccccCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999988888888877665544332 2246778888889999988887
Q ss_pred HHHHh----cCCccccccccchhhhhhHHHHHhhcccccccCCccccccccccccccccccCCCCCCCCCCCcceecccc
Q 000882 608 KFILK----SSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLVEDIASHFERIYPMDLNYPTAKYGLIKGCF 683 (1238)
Q Consensus 608 ~~~~~----~n~l~~Mi~sGSKGS~~Ni~Qi~g~lGqQ~~~ggr~~~r~l~~~~~~~f~~~~p~~~d~~~~a~GfV~ssF 683 (1238)
+.+.+ .|++.+|+.||||||+.|++||+||||||+++|+| +++++.+|++|||.. ++.+|+|+|||.|||
T Consensus 714 ~~~~~~l~~~N~~~~M~~SGsKGS~~N~~Qi~~~lGqQ~~~g~r-i~~~~~~rtLP~f~~-----~d~~~~~~GfV~~sF 787 (882)
T PRK08566 714 EIAEKYLGLDNPAVIMARTGARGSMLNLTQMAACVGQQSVRGER-IRRGYRDRTLPHFKP-----GDLGAEARGFVRSSY 787 (882)
T ss_pred HHHHHhcCCCCcceeeeccccccCHHHHHHHHhccCceecCCCc-CccCccCccCCCCCC-----CCCCcccCceeeccc
Confidence 77654 59999999999999999999999999999998765 678888999999974 478999999999999
Q ss_pred cccCCccceEEeeccccceeeecccccCCCCchhHHHHHHHheeEEEecceEeccCCCceeeeeeecccccccCcCCCCC
Q 000882 684 FHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYDGTVRNVCSNSIIQFDYAVNARKSHSLFPAGE 763 (1238)
Q Consensus 684 ~~GL~P~EfFfHamagREGLiDTAvkTa~sGYL~RrLv~~l~d~~v~YD~tvr~~~~~~iiqf~yg~dg~~~~~lv~~Ge 763 (1238)
++||+|+|||||||||||||||||||||+||||||||||+|||++|+||+|||+ ++|.||||.||+||+|+... +.+.
T Consensus 788 ~~GL~p~EfffH~m~GReGliDTAvkTa~sGYlqRrLvk~ledl~v~yD~tVR~-s~g~iiQf~YG~dg~d~~~~-~~~~ 865 (882)
T PRK08566 788 KSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRD-TRGNIVQFKYGEDGVDPMKS-DHGK 865 (882)
T ss_pred cCCCCHHHHHHHHhhhcccccccceeeccCccchHHHHHHHhheEEeeCCceEc-CCCcEEEEeccCCCcCHHHh-cCCC
Confidence 999999999999999999999999999999999999999999999999999999 57999999999999887654 3445
Q ss_pred ee
Q 000882 764 PV 765 (1238)
Q Consensus 764 ~V 765 (1238)
||
T Consensus 866 ~~ 867 (882)
T PRK08566 866 PV 867 (882)
T ss_pred cc
Confidence 55
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=2.7e-167 Score=1559.70 Aligned_cols=892 Identities=20% Similarity=0.253 Sum_probs=675.2
Q ss_pred eEEEecCChHHHHhcccccccc----------cCCCCCCCCCC-CCC--------------CCCCCCCCCCCCCCCCCC-
Q 000882 16 GIRFGLATQKEICTASISDCSI----------SHASQLANPFL-GLP--------------LEFGKCESCGTSEPGKCE- 69 (1238)
Q Consensus 16 ~I~Fgl~S~eEI~k~Sv~~~~I----------~~~~gl~Dprl-G~~--------------~~~~~C~TCg~~~~~~Cp- 69 (1238)
+|+|++.|||+|++||+.++.- ++.+||.|+|. |+. .+...|++||... .+|+
T Consensus 1 ~i~i~laSPe~I~~ws~geV~~petiny~t~kPe~~GLfcerIFGp~k~~ec~Cgkyk~~~~~~~~C~~Cgve~-t~~~v 79 (1140)
T TIGR02386 1 AIKISIASPDTIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKIRYKGVVCERCGVEV-TESKV 79 (1140)
T ss_pred CeEEEecCHHHHHhhhceEEeccceecCCCCccCCCCcccchhcCCccCceeccccccccCcCCcCCCCCCCCc-ccchh
Confidence 4899999999999999864311 12359999999 654 2445799999986 7999
Q ss_pred --CcceeEEcCcccccccChHH-----------HHHHHHhhcccc-----c--CchHHH-HH---------H--------
Q 000882 70 --GHFGYIELPIPIYHPSHISE-----------LKLTMYAFQLQI-----K--NDGVAQ-RL---------L-------- 111 (1238)
Q Consensus 70 --GHFGhIeL~~PVfHpgf~k~-----------i~~IL~~iCl~l-----~--~~~~~~-~~---------~-------- 111 (1238)
+|||||+|+.||+|++|++. ..+.|.++|..+ . ...+.+ .+ .
T Consensus 80 rr~rmGhI~La~Pv~Hiwy~k~~ps~~~~ll~~~~k~le~v~y~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 159 (1140)
T TIGR02386 80 RRERMGHIELAAPVAHIWYFKGLPSRIGLLLDITAKELESVLYFENYVVLDPGDTKLDKKEVLDETEYREVLKRYGDGFR 159 (1140)
T ss_pred hhhcccceeecCCceeehhcCCCchHHHHHhCCCHHHhhheeeccceEEeCCCCCchhhhhhhchhHHHHHHHHhccCcc
Confidence 99999999999999999997 478888888221 1 110100 00 0
Q ss_pred HhH-h-----------------HHHHHHccCChh-H-HHHhc--------cCCCCCCCceEEEeeccCCCCCCCccccCC
Q 000882 112 SSC-C-----------------EVKEMLKRIPEE-T-RKKLA--------GKGYFPQDGYILEYLPVPPNCLSVPDISDG 163 (1238)
Q Consensus 112 ~~C-C-----------------ev~~i~k~I~~e-d-~~~L~--------~~~~~~~~~~il~~lpVpP~~~Rp~~~~~~ 163 (1238)
..| + +..+.++....+ . .+.+. ......|+||||++||||||++||++.++|
T Consensus 160 ~~~G~~ai~~~l~~~dl~~~~~~~~~~~~~~~~~~~~~~~~krl~~~~~f~~s~~~Pewmil~~lPV~Pp~lRP~v~l~g 239 (1140)
T TIGR02386 160 AGMGAEAIKELLEKIDLDKEIEELKIQLRESKSDQKRKKLLKRLEIVEAFKDSGNRPEWMVLDVIPVIPPELRPMVQLDG 239 (1140)
T ss_pred cccchHHHHHHHhcCCHHHHHHHHHHHHHhccchhhHHhhhhHHHHHHHHHhcCCChHHhhhhcccCCCCccCCcEEeCC
Confidence 011 1 111112111111 1 11111 013368999999999999999999999998
Q ss_pred CccccchhhHHHHHHHHHHHHHHHhh-hcCCCCcchhhhhhhHHHHHHHHHHhccCCcccCCCcccCCCCCCCCCcchhh
Q 000882 164 VSTMSSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEVRGTAKSSRDVDARFGVSQDPNSTTKA 242 (1238)
Q Consensus 164 ~~~~~~Dlt~~~l~~I~~~~~~l~~~-~~g~~~~~~~~~~~~~LQ~~v~~~~~~~~~~k~~~~~~~~~~~~k~~~~~iKg 242 (1238)
+.+.++|||. +|++||++|++|++. ..++|..+. .++|++||.+|++|||+....++......| ..|++.+++||
T Consensus 240 g~~~~sDLn~-lyr~II~~Nn~Lk~~~~~~ap~~ii-~~~~~~LQ~aV~~liDn~~~g~~~~~~~~r--plksls~~LkG 315 (1140)
T TIGR02386 240 GRFATSDLND-LYRRVINRNNRLKRLLELGAPEIIV-RNEKRMLQEAVDALFDNGRRGKPVVGKNNR--PLKSLSDMLKG 315 (1140)
T ss_pred CccccCchHH-HHHHHHHHHHHHHHHHHcCCcHHHH-HHHHHHHHHHHHHHhcccccCCCccCcCCC--chhhHHHhhcC
Confidence 8888999999 899999999999985 567776654 678999999999999975433332211111 23677899999
Q ss_pred hhhhhhccccccCCCCCcceeEeCCCCccccccccchhhhcccccccccchhhHHHHHHHHHcCCccccCCCCceEEecc
Q 000882 243 WLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDNKLCLTYSDGSSSYSLRE 322 (1238)
Q Consensus 243 k~gr~R~nllGKRVdfSaRsVIspDP~L~i~evGvP~~iA~~LT~pE~Vt~~Ni~~l~~lV~ng~~~~~~~~~~~~~l~~ 322 (1238)
|+||||+|||||||||||||||+|||+|++||||||..||++||+| ||+.+|+ .+|.....+.. +..+.
T Consensus 316 K~GrFR~NLlGKRVDySgRSVI~pdP~L~l~e~GlP~~mA~~L~~P-----f~i~~L~---~~~~~~~i~~a--k~~i~- 384 (1140)
T TIGR02386 316 KQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKP-----FIIKRLI---DRELAANIKSA--KKMIE- 384 (1140)
T ss_pred CCCcccccccccccCCCCCCeEcCCCCcccccccChHHHHHHcCch-----HHHHHHH---HcCcccchHHH--HHHHH-
Confidence 9999999999999999999999999999999999999999999987 5655444 45533111100 00000
Q ss_pred CCCCcccccCcceeeeeeeccCeEeeeCCCCCCcccccceEEEecCCCeeeecccCCCCCCCccCccccccccCCCHHHH
Q 000882 323 GSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQSLAAK 402 (1238)
Q Consensus 323 ~~~~~~~L~~g~iV~Rhl~dgD~VL~NRqPSLHr~Simah~v~v~~~~T~rln~~vC~pyNADFDGDeMn~H~PQs~eAr 402 (1238)
....++ |.|.||+++||+|||||||||||||||||+|++++++||||||+||+||||||||||||+|+|||++||
T Consensus 385 ----~~~~~v-~~vl~~vi~~d~VLlNRqPTLHRlsIqAf~~~l~~gktirlhplvC~~fNADFDGDeMnvHvPqS~eA~ 459 (1140)
T TIGR02386 385 ----QEDPEV-WDVLEDVIKEHPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQ 459 (1140)
T ss_pred ----hcCCcc-ceEEEEccCCcEEEecCCCcccccccceeEEEEecCceEEEcccccCcccCCCCcceeEeecCCCHHHH
Confidence 112334 445689999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhccccccccCCCCCceEeechhhhhHHHhhh-cc--------ccCCHHHHHHHhcccccccccccccccc--cc
Q 000882 403 AEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF-KK--------YFLDKAFTQQLAMFALSPLPRPALSKAR--CS 471 (1238)
Q Consensus 403 aEa~~Lm~~~~nilsp~~G~Piigl~QD~llg~~llt-kd--------~fl~~~~~~~l~~~~~~~lp~PaI~Kp~--~~ 471 (1238)
|||++||++++||+||++|+|+++++||+|+|+|+|| ++ +|++++++....... .++.|++++++ ..
T Consensus 460 aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~~~~~~~~~F~~~~e~~~~~~~~--~i~l~~~i~~~~~g~ 537 (1140)
T TIGR02386 460 AEARALMLASNNILNPKDGKPIVTPSQDMVLGLYYLTTEKPGAKGEGKIFSNVDEAIRAYDNG--KVHLHALIGVRTSGE 537 (1140)
T ss_pred HHHHHHhCCcccEecCCCCCceEEeechhhheeeEeeeccccccCcCceeCCHHHHHHHHHcC--CccCCCceEEecccc
Confidence 9999999999999999999999999999999999998 43 799999988754332 34455555543 12
Q ss_pred ccc--chhhhccccCCCCccccCcEEEEecccccccccccCCccchHHHHHHHHHHhhCHHHHHhchhhhHHHHHHHHHh
Q 000882 472 ARW--TALQILQSVLPPGFDSCGDRYLIKKSEVLKGDFDRDTIPSVINEIVTSIFFEKGPEEVLEFFDSLQPLLMENLFA 549 (1238)
Q Consensus 472 ~lw--TGKQi~S~~LP~~~~~~~~~viI~~gell~G~ldK~~lG~s~~~LI~~i~~~~G~~~a~~fLd~lqrL~~~~L~~ 549 (1238)
++| +|||||+.++|.++.+... . ..+||+.+| +|||.+|++||++.|+.|||.+++|+++|++.
T Consensus 538 ~~~tt~Gr~if~~ilP~~~~~~n~------~----~~l~Kk~lg----~LI~~i~~~~G~~~t~~~LD~lk~Lgf~~at~ 603 (1140)
T TIGR02386 538 ILETTVGRVIFNEILPEGFPYIND------N----EPLSKKEIS----SLIDLLYEVHGIEETAEMLDKIKALGFKYATK 603 (1140)
T ss_pred EEEccchHHHHHHHcCCccccccc------c----cccchHHHH----HHHHHHHHHhChHHHHHHHHHHHHHHHHHHHh
Confidence 788 6999999999987755321 1 157888775 79999999999999999999999999999999
Q ss_pred cCceeecCccccCHHHHHHHHHHHHHHHHHHHhhhh--hhHHHHHHHHHHHHHHHHHHHHHHHHh--------cCCcccc
Q 000882 550 DGFSVSLEDFSLSKAALWNIQKEIQALYSLLYHRMS--TQNELVDLQIENHIRHVKMLVAKFILK--------SSTLGYL 619 (1238)
Q Consensus 550 ~GFSiGi~D~~~~~~~~~~i~~~i~~~~~~~~~~~~--~~~~~le~~~~~~l~~~~~~i~~~~~~--------~n~l~~M 619 (1238)
+|||||++|+.+|+++.+.++++.+++.++..++.. ...+..+..+...|+++++.+++.+.+ .|++++|
T Consensus 604 ~GfSigi~Dl~ip~~K~~ii~~a~~~v~~i~~~y~~G~lt~~er~~kvi~iw~~~~d~v~~~~~~~l~~~~~~~N~i~mM 683 (1140)
T TIGR02386 604 SGTTISASDIVVPDEKYEILKEADKEVAKIQKFYNKGLITDEERYRKVVSIWSETKDKVTDAMMKLLKKDTYKFNPIFMM 683 (1140)
T ss_pred cCeeeeeccCCCCHHHHHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCcHhhh
Confidence 999999999999998877676666666555544432 112334455667788888888777653 2899999
Q ss_pred ccccchhhhhhHHHHHhhcccccccCCccccccccccccccccccCCCCCCCCCCCcceecccccccCCccceEEeeccc
Q 000882 620 IDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLVEDIASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSIST 699 (1238)
Q Consensus 620 i~sGSKGS~~Ni~Qi~g~lGqQ~~~ggr~~~r~l~~~~~~~f~~~~p~~~d~~~~a~GfV~ssF~~GL~P~EfFfHamag 699 (1238)
+.||||||+.|++||+||+|||+.+.|+.+ +. +|.|||++||+|+|||||||||
T Consensus 684 a~SGARGS~~ni~QL~GmrGlma~p~Grii--------------------~~------PI~ssF~eGLtp~EyF~st~Ga 737 (1140)
T TIGR02386 684 ADSGARGNISQFRQLAGMRGLMAKPSGDII--------------------EL------PIKSSFREGLTVLEYFISTHGA 737 (1140)
T ss_pred hhcccccCHHHHHHHHhCCCcccCCCCCcc--------------------cc------chhhccccCCCHHHHhhhccch
Confidence 999999999999999999999998877632 12 2999999999999999999999
Q ss_pred cceeeecccccCCCCchhHHHHHHHheeEEEec--ceE------------------------------------------
Q 000882 700 REVIVRSSRGLSEPGTLFKNLMAVLRDVVICYD--GTV------------------------------------------ 735 (1238)
Q Consensus 700 REGLiDTAvkTa~sGYL~RrLv~~l~d~~v~YD--~tv------------------------------------------ 735 (1238)
||||+|||+|||+|||||||||+++||++|.|| ||.
T Consensus 738 RkGLiDTAlKTAdSGYLtRRLVdv~qDviV~~dDCgT~~gi~v~~~~~~~~~~i~~l~~ri~GR~~~~di~~~~~~~~i~ 817 (1140)
T TIGR02386 738 RKGLADTALKTADSGYLTRRLVDVAQDVVVREEDCGTEEGIEVEAIVEGKDEIIESLKDRIVGRYSAEDVYDPDTGKLIA 817 (1140)
T ss_pred hccccchheeecccceeeeehhhhhcceEEEeCCCCCCCCEEEEEeecCCceEEeehhheeEEEEEhhheEeCCCCcEEE
Confidence 999999999999999999999999999999998 221
Q ss_pred ------------------------ecc----CCCceeeeeeecccccccCcCCCCCeeeeeccccCCchHHHhhhccCC-
Q 000882 736 ------------------------RNV----CSNSIIQFDYAVNARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDSSP- 786 (1238)
Q Consensus 736 ------------------------r~~----~~~~iiqf~yg~dg~~~~~lv~~Ge~VG~laaqsigep~tq~~l~t~~- 786 (1238)
|++ +...|||.|||+|. ....+|+.||+||++||||||||+||+|||||+
T Consensus 818 ~~~~~i~~~~~~~i~~~~i~~v~iRS~ltC~s~~gvC~~CYG~~L-a~~~~V~~GeaVGiiAAQSIGEPGTQLTmRTFHt 896 (1140)
T TIGR02386 818 EANTLITEEIAEKIENSGIEKVKVRSVLTCESEHGVCQKCYGRDL-ATGKLVEIGEAVGVIAAQSIGEPGTQLTMRTFHT 896 (1140)
T ss_pred eCCCCcCHHHHHHHHHcCCCEEEecCCeeeCCCCCCccccCCCcc-cCCcEecccccceeEeeeecCCCcchhehhheee
Confidence 111 13578999999984 577899999999999999999999999999974
Q ss_pred --------CCCCchHHHHHHHHhhccCCCCCCCceEEEEcCCCCCCCccccHHHHHHHHhhhceech-h-hhhheeeEEe
Q 000882 787 --------SSNNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSL-K-DAAVEFLIEY 856 (1238)
Q Consensus 787 --------~~~~g~~rlkEil~~~~~~k~~~~d~~~~l~L~~~~~~~~~~~e~~a~~V~~~le~vtl-~-dv~~~i~i~y 856 (1238)
++|.|+||..|+++|+. |+++.++...++.. ++ + +.-....|..
T Consensus 897 GGv~~~~~DIT~GlpRv~elfear~-----p~~~a~iae~~G~v---------------------~~~~~~~~~~~~i~i 950 (1140)
T TIGR02386 897 GGVAGASGDITQGLPRVKELFEART-----PKDKAVIAEVDGTV---------------------EIIEDIVKNKRVVVI 950 (1140)
T ss_pred ccccccccccccCchhhhhhhhccc-----CCCceEEEecCCEE---------------------EEeecccCCcEEEEE
Confidence 67899999999999977 56666555444321 10 0 0000001111
Q ss_pred cCCccccCCCceEEEEEecHHHHhhcCCCHhhHHHHHHHhhhhhhhhhhhHHHHHhhccceeeccccccccccccccCCC
Q 000882 857 KKPEIISDDEGLVGHIHLNKILLEDLRISMHDILPKCQETLKSFCKKKKMKKVVQFFKNTSLSISECCSFQQSCADKRSN 936 (1238)
Q Consensus 857 ~~~~~~~~~~~~v~~i~Ld~e~L~~~~lt~~~I~~~l~~~~~~~~~~~~~~~i~~~~~~~~i~~~g~~~~~~~~~~~~~~ 936 (1238)
.++.. + ...|.+ .+. ..+.+ ..|- . +. .
T Consensus 951 ~~~~~---------------~-~~~y~i----------------p~~----------~~l~v-~~gd----~--V~---~ 978 (1140)
T TIGR02386 951 KDEND---------------E-EKKYTI----------------PFG----------AQLRV-KDGD----S--VS---A 978 (1140)
T ss_pred ECCCC---------------c-eeEEec----------------cCC----------ceEEe-cCCC----E--Ec---c
Confidence 11100 0 000000 000 00011 0000 0 00 0
Q ss_pred cceEEEEEeecCCcccccchhhcccchhhHHHHhhhchhHHHH----HHHHHHHhhhhccccccceeeecccccccceEe
Q 000882 937 MPCLMFVLRGASDSYLDKLSGVLANMIYPVLLETIIKENWWVR----QRLSASVTMVAKGVLKEHLILLANSMTCAGDLV 1012 (1238)
Q Consensus 937 ~~~lt~~~~~~~~~~~vd~~~~~sn~I~ei~r~tiikGi~w~R----~~l~~~~~~~~~~V~~rHl~Llad~MT~~G~~~ 1012 (1238)
..-| ++|+ -++++++ -|+|+++++ +.+++++..+|..|+.+|+.++++-||.++++.
T Consensus 979 G~~l---~~g~-------------~~~~~il---~v~G~~a~~~~lv~evq~vY~~QGv~I~dKHievIvrqM~~kv~i~ 1039 (1140)
T TIGR02386 979 GDKL---TEGS-------------IDPHDLL---RIKGIQAVQEYLVKEVQKVYRLQGVEINDKHIEVIVRQMLRKVRIT 1039 (1140)
T ss_pred CCcc---cCCC-------------CCHHHHH---HhcCHHHHHHHHHHHHHHHHHhCCccccchhHhHHHHHHhCcEEEE
Confidence 1111 2232 3466777 667877777 446888889999999999999999999996554
Q ss_pred ----------------------------------------eecccccccccccccccccchhhcccChHHHHHHHHhhcC
Q 000882 1013 ----------------------------------------GFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRH 1052 (1238)
Q Consensus 1013 ----------------------------------------~~~r~G~~~~~~s~l~~a~Fe~~t~~t~~~~l~~Aa~~g~ 1052 (1238)
|||+.++ ...|++++|||+| |+ ++|.+||++|.
T Consensus 1040 ~~gdt~~l~g~~v~~~~~~~~n~~~~~~g~~~~~~~~~llGitkasl--~t~SflsaASFqe----Tt-kvLt~Aai~gk 1112 (1140)
T TIGR02386 1040 DSGDSNLLPGELIDIHEFNEENRKLLEQGKKPASAIPQLLGITKASL--NTESFLSAASFQE----TT-KVLTDAAIKGK 1112 (1140)
T ss_pred eCCCcCCCCCCeeeHHHHHHHHHHHHhCCCCCccceeeeeeeeehhc--cCCCcccccchhh----HH-HHHHHHHhcCC
Confidence 4555555 3579999999999 44 99999999999
Q ss_pred CCCCCcccchhccCCcccccccc
Q 000882 1053 TDNLSSVVAACSWGKHVAVGTGS 1075 (1238)
Q Consensus 1053 ~D~l~gv~~~ii~Gk~~~~GTG~ 1075 (1238)
+|.|.|+.||||+|+.+|+|||.
T Consensus 1113 ~D~L~GlkENVIiG~liPaGTG~ 1135 (1140)
T TIGR02386 1113 VDYLLGLKENVIIGNLIPAGTGL 1135 (1140)
T ss_pred CCCCCCcccceEecCcccCCCCc
Confidence 99999999999999999999997
No 8
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=100.00 E-value=2e-166 Score=1553.34 Aligned_cols=898 Identities=21% Similarity=0.270 Sum_probs=684.4
Q ss_pred ccceEEEecCChHHHHhcccccccc----------cCCCCCCCCCCCCCCCCCCCCCCCCCC-----CCCCC--------
Q 000882 13 QIVGIRFGLATQKEICTASISDCSI----------SHASQLANPFLGLPLEFGKCESCGTSE-----PGKCE-------- 69 (1238)
Q Consensus 13 ~I~~I~Fgl~S~eEI~k~Sv~~~~I----------~~~~gl~DprlG~~~~~~~C~TCg~~~-----~~~Cp-------- 69 (1238)
++..|++++.|||+|++||+.++.- ++.+||.|.|..+|.++..| .||+-. ...|+
T Consensus 6 ~~~~i~i~laspe~I~~ws~GeV~~petinyrt~kPe~~GLfcerIFgp~kd~eC-~Cgkyk~~~~~~~~C~~cgve~~~ 84 (1156)
T PRK00566 6 DFDAIKIGLASPEKIRSWSYGEVKKPETINYRTLKPERDGLFCERIFGPTKDYEC-LCGKYKRVRYKGIICERCGVEVTR 84 (1156)
T ss_pred CcceEEEEccCHHHHHHhhcceEccccccccCCCccCCCCcccchhcCcccCcEE-eCccccccCcCCcCCCCCCceeee
Confidence 7889999999999999999864311 12359999999999999999 999521 13799
Q ss_pred -----CcceeEEcCcccccccChHHH-----------HHHHHhhcccc-----c--Cc-----------hHH--------
Q 000882 70 -----GHFGYIELPIPIYHPSHISEL-----------KLTMYAFQLQI-----K--ND-----------GVA-------- 107 (1238)
Q Consensus 70 -----GHFGhIeL~~PVfHpgf~k~i-----------~~IL~~iCl~l-----~--~~-----------~~~-------- 107 (1238)
+|||||+|+.||.|++|++.+ .+.|.++|... . .. .+.
T Consensus 85 ~~vrr~rmGhI~La~Pv~Hiwy~k~~ps~i~~ll~~~~k~le~v~y~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 164 (1156)
T PRK00566 85 SKVRRERMGHIELAAPVAHIWFFKSLPSRIGLLLDMSLKDLERVLYFESYVVIDPGDTPLEKKQLLTEEEYREALEEYGD 164 (1156)
T ss_pred chhhhhhcceeeecCceeeeeecCCCchHHHHHhCCCHHHhhheeecceEEEeCCCCCchhhhcccCHHHHHHHHHHhcc
Confidence 999999999999999999944 77888888211 1 00 000
Q ss_pred -----------HHHHHhH-----h-HHHHHHcc-CChhHH----HHhc-----cCCCCCCCceEEEeeccCCCCCCCccc
Q 000882 108 -----------QRLLSSC-----C-EVKEMLKR-IPEETR----KKLA-----GKGYFPQDGYILEYLPVPPNCLSVPDI 160 (1238)
Q Consensus 108 -----------~~~~~~C-----C-ev~~i~k~-I~~ed~----~~L~-----~~~~~~~~~~il~~lpVpP~~~Rp~~~ 160 (1238)
+++++.. + +..+.++. -..... ++|. ...-.+|+||||++||||||++||++.
T Consensus 165 ~~~~~~Ga~ai~~ll~~~dl~~~~~~l~~~~~~~~~~~~~~~~~krl~~~~~f~~s~~~Pewmil~~lPV~Pp~lRP~v~ 244 (1156)
T PRK00566 165 EFVAKMGAEAIKELLKNIDLEAEAEELREELKETGSEQKRKKALKRLKVVEAFRKSGNKPEWMILDVLPVIPPDLRPLVQ 244 (1156)
T ss_pred cccccccHHHHHHHHHhCCHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHcCCCCccEeeEeecccCCCcccCceE
Confidence 0000000 0 11112221 111111 1111 012367999999999999999999999
Q ss_pred cCCCccccchhhHHHHHHHHHHHHHHHhh-hcCCCCcchhhhhhhHHHHHHHHHHhccCCcccCCCcccCCCCCCCCCcc
Q 000882 161 SDGVSTMSSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEVRGTAKSSRDVDARFGVSQDPNST 239 (1238)
Q Consensus 161 ~~~~~~~~~Dlt~~~l~~I~~~~~~l~~~-~~g~~~~~~~~~~~~~LQ~~v~~~~~~~~~~k~~~~~~~~~~~~k~~~~~ 239 (1238)
++|+.+.++|+|. +|++||++|++|++. ..++|..+. .++|++||.+|+.|||+....++......| ..|++.++
T Consensus 245 l~~g~~~~sDLn~-lyr~II~rNnrLk~~~~~~ap~~ii-~~~~~~LQ~aV~~lidn~~~g~~~~~~~~r--plksls~~ 320 (1156)
T PRK00566 245 LDGGRFATSDLND-LYRRVINRNNRLKRLLELGAPEIIV-RNEKRMLQEAVDALFDNGRRGRPVTGPNNR--PLKSLSDM 320 (1156)
T ss_pred eCCCcccCCchHH-HHHHHHHHHHHHHHHHHcCCcHHHH-HHHHHHHHHHHHHHhccCccCCCcccccCC--chhHHHHh
Confidence 9988888999998 899999999999985 567787654 678999999999999975443332211111 23667799
Q ss_pred hhhhhhhhhccccccCCCCCcceeEeCCCCccccccccchhhhcccccccccchhhHHHHHHHHHcCCccccCCCCceEE
Q 000882 240 TKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDNKLCLTYSDGSSSYS 319 (1238)
Q Consensus 240 iKgk~gr~R~nllGKRVdfSaRsVIspDP~L~i~evGvP~~iA~~LT~pE~Vt~~Ni~~l~~lV~ng~~~~~~~~~~~~~ 319 (1238)
+|||+||||+|||||||||||||||||||+|++||||||..||++||+| || +++|+.+|+...++... ..
T Consensus 321 LkGK~GrFR~NLlGKRVDySgRSVI~pdP~L~l~e~GvP~~mA~eL~~P-----f~---i~~L~~~g~~~~ik~ak--~~ 390 (1156)
T PRK00566 321 LKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKP-----FI---MKKLVERGLATTIKSAK--KM 390 (1156)
T ss_pred hcCCCccccccccccccCCCCCceEeCCCCcccccccChHHHHHHhCcH-----HH---HHHHHHcCCccchHhhh--hh
Confidence 9999999999999999999999999999999999999999999999988 55 56667888753332211 10
Q ss_pred eccCCCCcccccCcceeeeeeeccCeEeeeCCCCCCcccccceEEEecCCCeeeecccCCCCCCCccCccccccccCCCH
Q 000882 320 LREGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQSL 399 (1238)
Q Consensus 320 l~~~~~~~~~L~~g~iV~Rhl~dgD~VL~NRqPSLHr~Simah~v~v~~~~T~rln~~vC~pyNADFDGDeMn~H~PQs~ 399 (1238)
+. ....++|+ |.||+++||+|||||||||||||||||+|++++++||||||+||+||||||||||||+|+|||+
T Consensus 391 ~~-----~~~~~v~~-vle~vi~gd~VLlNRqPTLHR~sIqAf~~~l~~gktirLhplvC~~fNADFDGDqMnvHvPqS~ 464 (1156)
T PRK00566 391 VE-----REDPEVWD-VLEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSL 464 (1156)
T ss_pred hh-----hhcCcceE-EEEEecCCCEEEecCCCcccccccceeEEEEecCceEEECccccCccccccccceeEEecCCCH
Confidence 10 12234555 4577889999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhccccccccCCCCCceEeechhhhhHHHhhh-cc--------ccCCHHHHHHHhccccccccccccccccc
Q 000882 400 AAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF-KK--------YFLDKAFTQQLAMFALSPLPRPALSKARC 470 (1238)
Q Consensus 400 eAraEa~~Lm~~~~nilsp~~G~Piigl~QD~llg~~llt-kd--------~fl~~~~~~~l~~~~~~~lp~PaI~Kp~~ 470 (1238)
+|||||+.||++++||+||++|+|+++++||+|+|+|+|| ++ +|++++++.++.+.....++.|..++++.
T Consensus 465 eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~~~~~~~~~F~~~~e~~~~~~~~~i~l~~~i~~~~~~ 544 (1156)
T PRK00566 465 EAQAEARVLMLSSNNILSPANGKPIIVPSQDMVLGLYYLTREREGAKGEGMVFSSPEEALRAYENGEVDLHARIKVRITS 544 (1156)
T ss_pred HHHHHHHHHhCCcccEEecCCCCeeEEeehhhhhhhheeecccccccCCCceeCCHHHHHHHHHcCCCCCCCeEEecCCC
Confidence 9999999999999999999999999999999999999997 45 79999999998765554555555554421
Q ss_pred c---cccchhhhccccCCCCccccCcEEEEecccccccccccCCccchHHHHHHHHHHhhCHHHHHhchhhhHHHHHHHH
Q 000882 471 S---ARWTALQILQSVLPPGFDSCGDRYLIKKSEVLKGDFDRDTIPSVINEIVTSIFFEKGPEEVLEFFDSLQPLLMENL 547 (1238)
Q Consensus 471 ~---~lwTGKQi~S~~LP~~~~~~~~~viI~~gell~G~ldK~~lG~s~~~LI~~i~~~~G~~~a~~fLd~lqrL~~~~L 547 (1238)
. ..|||||+|+.++|.++.+... +|.+||+++| +|||.+|+.||++.|+.|||.+++|+++|+
T Consensus 545 ~~~i~tt~Gk~if~~ilP~~~~~~n~----------~g~ldKk~Lg----~LI~~i~~~yG~~~t~~~LD~ik~Lgf~ya 610 (1156)
T PRK00566 545 KKLVETTVGRVIFNEILPEGLPFINV----------NKPLKKKEIS----KIINEVYRRYGLKETVIFLDKIKDLGFKYA 610 (1156)
T ss_pred CceEEcCcHHHHHHhhccccceeecc----------cceecHHHHH----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHH
Confidence 1 3699999999999987654221 5789999886 699999999999999999999999999999
Q ss_pred HhcCceeecCccccCHHHHHHHHHHHHHHHHHHHhhhhhh--HHHHHHHHHHHHHHHHHHHHHHHHh--------cCCcc
Q 000882 548 FADGFSVSLEDFSLSKAALWNIQKEIQALYSLLYHRMSTQ--NELVDLQIENHIRHVKMLVAKFILK--------SSTLG 617 (1238)
Q Consensus 548 ~~~GFSiGi~D~~~~~~~~~~i~~~i~~~~~~~~~~~~~~--~~~le~~~~~~l~~~~~~i~~~~~~--------~n~l~ 617 (1238)
+.+|||||++|+.+|+++.+.++++.+++.++..++..-. .+..+..+...|+++++.+++.+++ .|+++
T Consensus 611 t~~GfSigi~Dl~ip~~K~~ii~~a~~~v~~i~~~y~~G~lt~~er~~kvi~~w~~~~d~v~~~~~~~l~~~~~~~N~i~ 690 (1156)
T PRK00566 611 TRSGISIGIDDIVIPPEKKEIIEEAEKEVAEIEKQYRRGLITDGERYNKVIDIWSKATDEVAKAMMKNLSKDQESFNPIY 690 (1156)
T ss_pred HhcCeEeehhhcCcChHHHHHHHHHHHHHHHHHHHHHcCCCCchHHHHHHHHHHHHHHHHHHHHHHHhCccccCCCCChh
Confidence 9999999999999999887777666666655544443210 1122234455667777776666542 48999
Q ss_pred ccccccchhhhhhHHHHHhhcccccccCCccccccccccccccccccCCCCCCCCCCCcceecccccccCCccceEEeec
Q 000882 618 YLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLVEDIASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSI 697 (1238)
Q Consensus 618 ~Mi~sGSKGS~~Ni~Qi~g~lGqQ~~~ggr~~~r~l~~~~~~~f~~~~p~~~d~~~~a~GfV~ssF~~GL~P~EfFfHam 697 (1238)
+|+.||||||+.|++||+||+|||..+.|+++ +. ||.|||++||+|+|||||||
T Consensus 691 mMa~SGARGS~~ni~QL~GmrGlma~p~G~ii--------------------e~------pI~ssFreGLt~~EyFfst~ 744 (1156)
T PRK00566 691 MMADSGARGSASQIRQLAGMRGLMAKPSGEII--------------------ET------PIKSNFREGLTVLEYFISTH 744 (1156)
T ss_pred eeeeccCCcCHHHHHHHHhhcCccccCCCCEe--------------------eh------hhhhhhhcCCCHHHHhhcCc
Confidence 99999999999999999999999987777632 11 49999999999999999999
Q ss_pred cccceeeecccccCCCCchhHHHHHHHheeEEEec--ce-----------------------------------------
Q 000882 698 STREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYD--GT----------------------------------------- 734 (1238)
Q Consensus 698 agREGLiDTAvkTa~sGYL~RrLv~~l~d~~v~YD--~t----------------------------------------- 734 (1238)
||||||+|||+|||+|||||||||+++||++|.|| ||
T Consensus 745 GaRkGLiDTALKTAdSGYLtRRLVdvaqDviV~~~DCgT~~gi~~~~~~~~~~~i~~l~~~~~GR~~~~di~~~~t~~~i 824 (1156)
T PRK00566 745 GARKGLADTALKTADSGYLTRRLVDVAQDVIVREDDCGTDRGIEVTAIIEGGEVIEPLEERILGRVLAEDVVDPETGEVI 824 (1156)
T ss_pred chhhcccchheeeccceeeehhHHHhhCceEEEECCCCCcCCEEEEEeccCCEEEeEhhheeEeEEEhhheecCCCCcEE
Confidence 99999999999999999999999999999999997 22
Q ss_pred ------------------------Eecc----CCCceeeeeeecccccccCcCCCCCeeeeeccccCCchHHHhhhccCC
Q 000882 735 ------------------------VRNV----CSNSIIQFDYAVNARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDSSP 786 (1238)
Q Consensus 735 ------------------------vr~~----~~~~iiqf~yg~dg~~~~~lv~~Ge~VG~laaqsigep~tq~~l~t~~ 786 (1238)
||++ +...|||.|||+|. ....+|+.|||||++||||||||+||+|||||+
T Consensus 825 ~~~~~~i~~~~~~~i~~~~i~~v~iRS~ltC~s~~gvC~~CYG~~L-a~~~~v~iGeaVGiIAAQSIGEPGTQLTmRTFH 903 (1156)
T PRK00566 825 VPAGTLIDEEIADKIEEAGIEEVKIRSVLTCETRHGVCAKCYGRDL-ATGKLVNIGEAVGVIAAQSIGEPGTQLTMRTFH 903 (1156)
T ss_pred EcCCCccCHHHHHHHHHcCCCEEEEcCCeeecCCCcccHhhhCccc-cCCCCcccCcceeEEeeeecCCCccceeeeeee
Confidence 1221 23578999999984 577899999999999999999999999999997
Q ss_pred ----CCCCchHHHHHHHHhhccCCCCCCCceEEEEcCCCCCCCccccHHHHHHHHhhhceechhhhhheeeEEecCCccc
Q 000882 787 ----SSNNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEII 862 (1238)
Q Consensus 787 ----~~~~g~~rlkEil~~~~~~k~~~~d~~~~l~L~~~~~~~~~~~e~~a~~V~~~le~vtl~dv~~~i~i~y~~~~~~ 862 (1238)
++|.|+||+.|+++|++ |+++.++...++... +..+. ++ ...+.| .++..
T Consensus 904 tGGvdIT~Glprv~elfear~-----pk~~a~ise~~G~v~---~~~~~-----~~----------~~~i~i--~~~~~- 957 (1156)
T PRK00566 904 TGGVDITGGLPRVAELFEARK-----PKGPAIIAEIDGTVS---FGKET-----KG----------KRRIVI--TPDDG- 957 (1156)
T ss_pred ecceeccCCccchhhheeecc-----CCCceEEEecCCEEE---ecccc-----CC----------ceEEEE--eCCCC-
Confidence 58999999999999976 556655544433210 00000 00 000111 00000
Q ss_pred cCCCceEEEEEecHHHHhhcCCCHhhHHHHHHHhhhhhhhhhhhHHHHHhhccceeeccccccccccccccCCCcceEEE
Q 000882 863 SDDEGLVGHIHLNKILLEDLRISMHDILPKCQETLKSFCKKKKMKKVVQFFKNTSLSISECCSFQQSCADKRSNMPCLMF 942 (1238)
Q Consensus 863 ~~~~~~v~~i~Ld~e~L~~~~lt~~~I~~~l~~~~~~~~~~~~~~~i~~~~~~~~i~~~g~~~~~~~~~~~~~~~~~lt~ 942 (1238)
.-.+|. +.+. ..+.+ ..- +++ . ...-|
T Consensus 958 ---------------~~~~y~----------------vp~~----------~~~~v--~~g---d~v--~---~G~~l-- 984 (1156)
T PRK00566 958 ---------------EEREYL----------------IPKG----------KHLLV--QEG---DHV--E---AGDKL-- 984 (1156)
T ss_pred ---------------ceEEEE----------------ccCC----------Ceeee--cCC---CEE--c---cCCcc--
Confidence 000000 0000 00011 000 000 0 00111
Q ss_pred EEeecCCcccccchhhcccchhhHHHHhhhchhHHHH----HHHHHHHhhhhccccccceeeecccccccc---------
Q 000882 943 VLRGASDSYLDKLSGVLANMIYPVLLETIIKENWWVR----QRLSASVTMVAKGVLKEHLILLANSMTCAG--------- 1009 (1238)
Q Consensus 943 ~~~~~~~~~~vd~~~~~sn~I~ei~r~tiikGi~w~R----~~l~~~~~~~~~~V~~rHl~Llad~MT~~G--------- 1009 (1238)
++|+ =++++++ .|.|++++| +.+++++..+|..|+.+|+.++++-||.+.
T Consensus 985 -~~g~-------------~~~~~il---~v~G~~~~~~~lv~eiq~vY~~QGv~I~dKHievIvrqM~~kv~i~~~gdt~ 1047 (1156)
T PRK00566 985 -TDGS-------------IDPHDIL---RVLGVEAVQNYLVNEVQKVYRLQGVKINDKHIEVIVRQMLRKVRITDPGDTD 1047 (1156)
T ss_pred -cCCC-------------CCHHHHH---HhcCHHHHHHHHHHHHHHHHHhCCcccccceeehHHHHHhCCeEEecCCCcC
Confidence 2232 2356666 567877777 456888899999999999999999999753
Q ss_pred -------------------------------eEeeecccccccccccccccccchhhcccChHHHHHHHHhhcCCCCCCc
Q 000882 1010 -------------------------------DLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSS 1058 (1238)
Q Consensus 1010 -------------------------------~~~~~~r~G~~~~~~s~l~~a~Fe~~t~~t~~~~l~~Aa~~g~~D~l~g 1058 (1238)
.++|||+.+++ .+|+|+.||||+ |+ ++|.+||++|.+|.|.|
T Consensus 1048 ~~~g~~v~~~~~~~~n~~~~~~g~~~~~~~~~llGItka~l~--t~SflsaASFQe----Tt-kvLt~AAi~gk~D~L~G 1120 (1156)
T PRK00566 1048 FLPGELVDRSEFEEENRKLIAEGKEPATGRPVLLGITKASLA--TESFLSAASFQE----TT-RVLTEAAIKGKVDPLRG 1120 (1156)
T ss_pred CCCCceeeHHHHHHHHHHHHHCCCCCCcccceeeeeeecccc--cCcccccccccc----hH-HHHHHHHhcCCCCcCCC
Confidence 35788888885 569999999999 44 99999999999999999
Q ss_pred ccchhccCCcccccccc
Q 000882 1059 VVAACSWGKHVAVGTGS 1075 (1238)
Q Consensus 1059 v~~~ii~Gk~~~~GTG~ 1075 (1238)
+.||||+|+.+|+|||.
T Consensus 1121 lkENVIiG~liPaGTG~ 1137 (1156)
T PRK00566 1121 LKENVIIGRLIPAGTGL 1137 (1156)
T ss_pred cccceEecCcccCCCCc
Confidence 99999999999999999
No 9
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=100.00 E-value=3.6e-155 Score=1446.82 Aligned_cols=766 Identities=19% Similarity=0.229 Sum_probs=592.5
Q ss_pred CCCCceEEEeeccCCCCCCCccccCCCccccchhhHHHHHHHHHHHHHHHhh-hcCCCCcchhhhhhhHHHHHHHHHHhc
Q 000882 138 FPQDGYILEYLPVPPNCLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEV 216 (1238)
Q Consensus 138 ~~~~~~il~~lpVpP~~~Rp~~~~~~~~~~~~Dlt~~~l~~I~~~~~~l~~~-~~g~~~~~~~~~~~~~LQ~~v~~~~~~ 216 (1238)
..|+||||++||||||++||++..+|+.+.++|||. +|++||++|++|+.. ..++|..+ ..++|++||.+|+.|||+
T Consensus 310 ~~PewmiL~vlPV~Pp~lRP~V~l~gg~~atsDLn~-lyr~II~rNnrLk~l~~~~ap~~i-i~nekr~LQeaVd~liDN 387 (1460)
T PRK14906 310 NDPADMILDVIPVIPPDLRPMVQLDGGRFATSDLND-LYRRVINRNNRLKRLLDLGAPEII-VNNEKRMLQEAVDSLFDN 387 (1460)
T ss_pred CCHHHHhhhcccCCCCCcCCcEEECCCcccCCchHH-HHHHHHHHHHHHHHHHHcCCcHHH-HHHHHHHHHHHHHHHHcC
Confidence 679999999999999999999999998888999999 899999999999985 56777655 467899999999999997
Q ss_pred cCCcccCCCcccCCCCCCCCCcchhhhhhhhhccccccCCCCCcceeEeCCCCccccccccchhhhccccccccc-----
Q 000882 217 RGTAKSSRDVDARFGVSQDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERV----- 291 (1238)
Q Consensus 217 ~~~~k~~~~~~~~~~~~k~~~~~iKgk~gr~R~nllGKRVdfSaRsVIspDP~L~i~evGvP~~iA~~LT~pE~V----- 291 (1238)
....++...... ...|++.+++|||+||||+|||||||||||||||+|||+|++||||||..||++||+|+.+
T Consensus 388 ~~~g~p~~~~~~--rplKsls~~LkGK~GRFRqNLlGKRVDySgRSVIspdP~L~l~e~GlP~~mA~eLf~Pf~i~~L~~ 465 (1460)
T PRK14906 388 GRRGRPVTGPGN--RPLKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKPFVMKRLVE 465 (1460)
T ss_pred CCcCCCCccccC--CchhHHHHHhcccCcccccccccccccCcCCceEeCCCCCccccccCcHHHHHhcCchhHHHHHHH
Confidence 433222211111 1236677999999999999999999999999999999999999999999999999999543
Q ss_pred --chhhHHHHHHHHHcCCccccCCCCceEEeccCCCCcccccCcceeeeeeeccCeEeeeCCCCCCcccccceEEEecCC
Q 000882 292 --NVHNINYLQELVDNKLCLTYSDGSSSYSLREGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDD 369 (1238)
Q Consensus 292 --t~~Ni~~l~~lV~ng~~~~~~~~~~~~~l~~~~~~~~~L~~g~iV~Rhl~dgD~VL~NRqPSLHr~Simah~v~v~~~ 369 (1238)
...|++.+++++.++ ....|.|+||+++||+|||||||||||||||||+|+++++
T Consensus 466 ~~~~~nik~ak~~i~~~-----------------------~~~v~~vle~vi~gd~VLlNRqPTLHRlsIqAf~~~L~~g 522 (1460)
T PRK14906 466 LEYAANIKAAKRAVDRG-----------------------ASYVWDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEG 522 (1460)
T ss_pred hcccccHHHHhhHHhhc-----------------------CCcceeeeeeeeccceeEeccCcccchhccceeeEEecCC
Confidence 123333333333222 1234678899999999999999999999999999999999
Q ss_pred CeeeecccCCCCCCCccCccccccccCCCHHHHHHHHHHhccccccccCCCCCceEeechhhhhHHHhhh--cc------
Q 000882 370 HTVKINPLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF--KK------ 441 (1238)
Q Consensus 370 ~T~rln~~vC~pyNADFDGDeMn~H~PQs~eAraEa~~Lm~~~~nilsp~~G~Piigl~QD~llg~~llt--kd------ 441 (1238)
+||||||+||+||||||||||||+|+|||++|||||+.||++.+||+||++|+|+++++||+|+|+|+|| ++
T Consensus 523 ktIrLhplvC~~fNADFDGDqMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~~~~~~~ 602 (1460)
T PRK14906 523 KAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLTTERDGFEGEG 602 (1460)
T ss_pred ceEEecccccCccccCCcCceeeeecCCCHHHHHHHHHHhcchhcEecCCCCCeeEEeeeeeeeeeEEeeeccccccccC
Confidence 9999999999999999999999999999999999999999999999999999999999999999999998 33
Q ss_pred -ccCCHHHHHHHhcccc-ccccccccccccc-------------------ccccchhhhccccCCCCccccCcEEEEecc
Q 000882 442 -YFLDKAFTQQLAMFAL-SPLPRPALSKARC-------------------SARWTALQILQSVLPPGFDSCGDRYLIKKS 500 (1238)
Q Consensus 442 -~fl~~~~~~~l~~~~~-~~lp~PaI~Kp~~-------------------~~lwTGKQi~S~~LP~~~~~~~~~viI~~g 500 (1238)
+|.+.+++..+..+.. ..++.|..++++. -..|+|++||+.+||.++.
T Consensus 603 ~~F~~~~e~~~a~~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~tt~Gr~Ifn~ilP~d~~----------- 671 (1460)
T PRK14906 603 RTFADFDDALNAYDARADLDLQAKIVVRLSRDMTVRGSYGDLEETKAGERIETTVGRIIFNQVLPEDYP----------- 671 (1460)
T ss_pred ceeCCHHHHHHHHhcCCCccccccEEEecCcccccccccccccCCCCCceEECCCCEEEEecccCCCcc-----------
Confidence 7899999887776532 3343332222110 0468999999999997543
Q ss_pred cccccccccCCccchHHHHHHHHHHhhCHHHHHhchhhhHHHHHHHHHhcCceeecCccccCHHHHHHHHHHHHHHHHHH
Q 000882 501 EVLKGDFDRDTIPSVINEIVTSIFFEKGPEEVLEFFDSLQPLLMENLFADGFSVSLEDFSLSKAALWNIQKEIQALYSLL 580 (1238)
Q Consensus 501 ell~G~ldK~~lG~s~~~LI~~i~~~~G~~~a~~fLd~lqrL~~~~L~~~GFSiGi~D~~~~~~~~~~i~~~i~~~~~~~ 580 (1238)
++.+.++|+.+| +||+.+|++||...|..|||.+++|+++|++.+|||||++|+.+|+++.+.++++.+++.++.
T Consensus 672 -fvN~~l~KK~Lg----~LI~~i~~~~G~~~t~~fLD~Ik~LGf~yaT~sG~SIgi~Di~ip~~K~~iI~~A~~~V~ei~ 746 (1460)
T PRK14906 672 -YLNYKMVKKDIG----RLVNDCCNRYSTAEVEPILDGIKKTGFHYATRAGLTVSVYDATIPDDKPEILAEADEKVAAID 746 (1460)
T ss_pred -cccceeeHHHHH----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhCCEEEeecccccChHHHHHHHHHHHHHHHHH
Confidence 455678888775 599999999999999999999999999999999999999999999988777777777776666
Q ss_pred Hhhhh--hhHHHHHHHHHHHHHHHHHHHHHHHHh----cCCccccccccchhhhhhHHHHHhhcccccccCCcccccccc
Q 000882 581 YHRMS--TQNELVDLQIENHIRHVKMLVAKFILK----SSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLV 654 (1238)
Q Consensus 581 ~~~~~--~~~~~le~~~~~~l~~~~~~i~~~~~~----~n~l~~Mi~sGSKGS~~Ni~Qi~g~lGqQ~~~ggr~~~r~l~ 654 (1238)
.++.. ..++..+..+..+|+++++.+++.+++ .|++++|++||||||+.|++||+||+|||..+.|+++
T Consensus 747 ~~y~~G~iT~~Er~~kVi~iw~~a~d~v~~~~~~~l~~~N~i~mMa~SGARGS~~QI~QLaGmRGlma~p~G~iI----- 821 (1460)
T PRK14906 747 EDYEDGFLSERERHKQVVDIWTEATEEVGEAMLAGFDEDNPIYMMADSGARGNIKQIRQLAGMRGLMADMKGEII----- 821 (1460)
T ss_pred HHHHcCCCcHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCeEeeeeccCcccHHHHHHHHhcccceecCCCCcc-----
Confidence 55532 112233566777889999998888775 5999999999999999999999999999988777643
Q ss_pred ccccccccccCCCCCCCCCCCcceecccccccCCccceEEeeccccceeeecccccCCCCchhHHHHHHHheeEEEec--
Q 000882 655 EDIASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYD-- 732 (1238)
Q Consensus 655 ~~~~~~f~~~~p~~~d~~~~a~GfV~ssF~~GL~P~EfFfHamagREGLiDTAvkTa~sGYL~RrLv~~l~d~~v~YD-- 732 (1238)
+. +|.|||++||+|.|||||||||||||+|||+|||+|||||||||+++||++|..+
T Consensus 822 ---------------e~------PI~SnFrEGLt~~EyFiSt~GaRKGL~DTALKTAdSGYLTRRLVdVaQDViV~e~DC 880 (1460)
T PRK14906 822 ---------------DL------PIKANFREGLSVLEYFISTHGARKGLVDTALRTADSGYLTRRLVDVAQDVIVREEDC 880 (1460)
T ss_pred ---------------cc------ccccccccCCCHHHHHHHcccccchhhhhhhhccccchHHHHHHHhhhheEEEeccC
Confidence 22 2999999999999999999999999999999999999999999999999999975
Q ss_pred ce-------------------------------------------------------------Eecc----CCCceeeee
Q 000882 733 GT-------------------------------------------------------------VRNV----CSNSIIQFD 747 (1238)
Q Consensus 733 ~t-------------------------------------------------------------vr~~----~~~~iiqf~ 747 (1238)
|| ||++ +...|||.|
T Consensus 881 gT~~Gi~v~~~~~~~~l~~ri~GR~~~~di~~~~g~~i~~~~~~I~~~~~~~~i~~~gi~~v~iRS~ltC~s~~gvC~kC 960 (1460)
T PRK14906 881 GTDEGVTYPLVKPKGDVDTNLIGRCLLEDVCDPNGEVLLSAGDYIESMDDLKRLVEAGVTKVQIRTLMTCHAEYGVCQKC 960 (1460)
T ss_pred CCCCCEEEEEeecccchhheeeeEEEHhhhcCCCCCEEEeCCCeeCcHHHHHHHHHCCCCEEEEeCCeeECCCCCChhhC
Confidence 22 1211 135789999
Q ss_pred eecccccccCcCCCCCeeeeeccccCCchHHHhhhccCC-------CCCCchHHHHHHHHhhccCCCCCCCceEEEEcCC
Q 000882 748 YAVNARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDSSP-------SSNNSWELMKEILLCRVSFNNDPIDRRVILYLND 820 (1238)
Q Consensus 748 yg~dg~~~~~lv~~Ge~VG~laaqsigep~tq~~l~t~~-------~~~~g~~rlkEil~~~~~~k~~~~d~~~~l~L~~ 820 (1238)
||+|. ....+|+.||+||++||||||||+||+|||||+ .+|.|+||+.|+++|++ |+++.++....+
T Consensus 961 YG~dL-atg~~V~iGeaVGiIAAQSIGEPGTQLTMRTFHtGGv~~~dit~GLpRv~eLfEar~-----pk~~a~i~e~~G 1034 (1460)
T PRK14906 961 YGWDL-ATRRPVNIGTAVGIIAAQSIGEPGTQLTMRTFHSGGVAGDDITQGLPRVAELFEARK-----PKGEAVLAEISG 1034 (1460)
T ss_pred cCCcc-cCCcEeccccceeeeeeeecCCCcceeeeeeeecccccccccccCcchhhhheeecc-----CCCceeeeccCC
Confidence 99984 578899999999999999999999999999985 67899999999999977 555554332222
Q ss_pred CCCCCccccHHHHHHHHhhhceechhhhhheeeEEecCCccccCCCceEEEEEecHHHHhhcCCCHhhHHHHHHHhhhhh
Q 000882 821 CGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIISDDEGLVGHIHLNKILLEDLRISMHDILPKCQETLKSF 900 (1238)
Q Consensus 821 ~~~~~~~~~e~~a~~V~~~le~vtl~dv~~~i~i~y~~~~~~~~~~~~v~~i~Ld~e~L~~~~lt~~~I~~~l~~~~~~~ 900 (1238)
. |++.+--....|.+.++.. ....|.+
T Consensus 1035 ~---------------------v~i~~~~~~~~i~i~~~~~----------------~~~~y~v---------------- 1061 (1460)
T PRK14906 1035 T---------------------LQITGDKTEKTLTIHDQDG----------------NSREYVV---------------- 1061 (1460)
T ss_pred E---------------------EEeccCCCceEEEEECCCC----------------ceeEEEc----------------
Confidence 1 1100000001111111110 0000000
Q ss_pred hhhhhhHHHHHhhccceeeccccccccccccccCCCcceEEEEEeecCCcccccchhhcccchhhHHHHhhhchhHHHH-
Q 000882 901 CKKKKMKKVVQFFKNTSLSISECCSFQQSCADKRSNMPCLMFVLRGASDSYLDKLSGVLANMIYPVLLETIIKENWWVR- 979 (1238)
Q Consensus 901 ~~~~~~~~i~~~~~~~~i~~~g~~~~~~~~~~~~~~~~~lt~~~~~~~~~~~vd~~~~~sn~I~ei~r~tiikGi~w~R- 979 (1238)
.+.. .+. .|....+.+ + ....| ++|+ =+.++++ -|+|++.+.
T Consensus 1062 ~~~~----------~~~---~~v~~gd~v--~---~G~~l---~~G~-------------~~p~~il---~~~g~~~~~~ 1104 (1460)
T PRK14906 1062 SARV----------QFM---PGVEDGVEV--R---VGQQI---TRGS-------------VNPHDLL---RLTDPNTTLR 1104 (1460)
T ss_pred cCCc----------ccc---cccCCCCEE--c---cCCCc---cCCC-------------CCHHHHH---HhcCHHHHHH
Confidence 0000 000 011100010 0 11222 3332 2234444 344544444
Q ss_pred ---HHHHHHHhhhhccccccceeeecccccc-------------cc---------------------------eEeeecc
Q 000882 980 ---QRLSASVTMVAKGVLKEHLILLANSMTC-------------AG---------------------------DLVGFNS 1016 (1238)
Q Consensus 980 ---~~l~~~~~~~~~~V~~rHl~Llad~MT~-------------~G---------------------------~~~~~~r 1016 (1238)
+.++++...||..|+..|+.+++=-|+. .| .+.|||+
T Consensus 1105 ylv~eVQ~VYr~QGV~InDKHiEvIvRQMl~kV~I~d~Gdt~fl~Ge~vd~~~~~~~n~~~~~~g~~pa~~~p~llGITK 1184 (1460)
T PRK14906 1105 YIVSQVQDVYVSQGVDINDKHIEVIARQMLRKVAVTNPGDSDYLPGRQVNRYEFEDTANNLILEGKQPPVGQPLLLGITK 1184 (1460)
T ss_pred HHHHHHHHHHHhcCceeccccHHHHHHHHhceEEEecCCCcCCCCCCeeeHHHHHHHHHHHHHcCCCCceeeeEEeeeee
Confidence 3448888999999999999998755522 13 3455555
Q ss_pred cccccccccccccccchhhcccChHHHHHHHHhhcCCCCCCcccchhccCCcccccccc
Q 000882 1017 GGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGS 1075 (1238)
Q Consensus 1017 ~G~~~~~~s~l~~a~Fe~~t~~t~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~ 1075 (1238)
..++ ..|.+..|||+| |+ ++|.+||.+|.+|.|.|..||||+|+.+|.|||.
T Consensus 1185 asL~--t~SflSaASFQe----Tt-rVLt~AAi~gk~D~L~GLKENVIiG~lIPAGTG~ 1236 (1460)
T PRK14906 1185 ASLA--TDSWLSAASFQE----TT-KVLTDAAIEGKVDHLAGLKENVIIGKPIPAGTGL 1236 (1460)
T ss_pred cccc--cccccccccccc----hH-HHHHHHHhcCCCCcCCCCccceEecceecCCCCc
Confidence 5553 359999999999 44 9999999999999999999999999999999998
No 10
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=100.00 E-value=1.1e-150 Score=1451.89 Aligned_cols=716 Identities=20% Similarity=0.258 Sum_probs=554.8
Q ss_pred ccccccceEEEecCChHHHHhcccccccccC------------CCCCCCCCCCCCCCCCCC---------------CCCC
Q 000882 9 ILEGQIVGIRFGLATQKEICTASISDCSISH------------ASQLANPFLGLPLEFGKC---------------ESCG 61 (1238)
Q Consensus 9 ~~~~~I~~I~Fgl~S~eEI~k~Sv~~~~I~~------------~~gl~DprlG~~~~~~~C---------------~TCg 61 (1238)
....++..|+.++.|||+|++||+.+ |++ .+||.+.|.-+|.++..| +.||
T Consensus 1443 ~~~~~~~~i~i~laSPe~I~~Ws~Ge--V~kpeTinyrt~kPE~dGLFcerIFGp~kd~eC~Cgkyk~~~~~g~~C~~Cg 1520 (2836)
T PRK14844 1443 NIAQSFNEVSISIASPESIKRMSYGE--IEDVSTANYRTFKVEKGGLFCPKIFGPVNDDECLCGKYKKRRHRGRICEKCG 1520 (2836)
T ss_pred hhhcccceEEEEecCHHHHHhhhcee--ECCcccccccCCCCCCCCeehhhhcCCCcCcEEecccccccccCCcCcCCCC
Confidence 34577899999999999999999864 433 358999986556665555 4444
Q ss_pred CCC--CCCCCCcceeEEcCcccccccChHHHHHHHHhhc-c-------------cc--c--CchHH--------------
Q 000882 62 TSE--PGKCEGHFGYIELPIPIYHPSHISELKLTMYAFQ-L-------------QI--K--NDGVA-------------- 107 (1238)
Q Consensus 62 ~~~--~~~CpGHFGhIeL~~PVfHpgf~k~i~~IL~~iC-l-------------~l--~--~~~~~-------------- 107 (1238)
... .+..--.+|||+|+.||.|++|++.+...|..+- + .+ . ...+.
T Consensus 1521 vevt~s~vRR~RmGhI~La~PV~HiWy~k~~ps~i~~lL~~~~k~le~v~y~~~~~v~~~~~~~~~~~~~~~~~~~~~~~ 1600 (2836)
T PRK14844 1521 VEVTSSKVRRERMGHIELASPVAHIWFLKSLPSRIGALLDMSLRDIENILYSDNYIVIDPLVSPFEKGEIISEKAYNEAK 1600 (2836)
T ss_pred cEeeechhhHhhcCceeecCcceeeecccCCcHHHHHHhCCCHHHhhheeeeeeEEEecCCCCchhhhhhccHHHHHHHH
Confidence 332 1111258999999999999999995544433222 0 00 0 00000
Q ss_pred -----------------HHHHHhH-----h-HHHHHHccCCh-hH----HHHhc-----cCCCCCCCceEEEeeccCCCC
Q 000882 108 -----------------QRLLSSC-----C-EVKEMLKRIPE-ET----RKKLA-----GKGYFPQDGYILEYLPVPPNC 154 (1238)
Q Consensus 108 -----------------~~~~~~C-----C-ev~~i~k~I~~-ed----~~~L~-----~~~~~~~~~~il~~lpVpP~~ 154 (1238)
+++++.. | +.++.++.... .. +++|. ......|+||||++||||||+
T Consensus 1601 ~~~~~~~~~~~~Gaeai~~lL~~~dl~~~~~~l~~~~~~~~~~~~~~~~~krl~~~~~f~~s~~rPewmil~~lPV~Pp~ 1680 (2836)
T PRK14844 1601 DSYGIDSFVAMQGVEAIRELLTRLDLHEIRKDLRLELESVASEIRRKKIIKRLRIVENFIKSGNRPEWMILTTIPILPPD 1680 (2836)
T ss_pred HhcCccceeecchHHHHHHHHHhCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHhcCCChhheeeeccccCCCc
Confidence 0011100 0 11222222100 11 11111 012368999999999999999
Q ss_pred CCCccccCCCccccchhhHHHHHHHHHHHHHHHhh-hcCCCCcchhhhhhhHHHHHHHHHHhccCCcccCCCcccCCCCC
Q 000882 155 LSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEVRGTAKSSRDVDARFGVS 233 (1238)
Q Consensus 155 ~Rp~~~~~~~~~~~~Dlt~~~l~~I~~~~~~l~~~-~~g~~~~~~~~~~~~~LQ~~v~~~~~~~~~~k~~~~~~~~~~~~ 233 (1238)
+||++.++|+.+.+||||. +|++||++|++|+.. ..++|..+ ..++|++||.+|+.|||+....++......+ ...
T Consensus 1681 lRP~v~l~~g~~~~sDLn~-ly~~II~~NnrLk~~~~~~ap~~i-i~~~~~~LQ~~V~~l~Dn~~~g~~~~~~~~r-~~l 1757 (2836)
T PRK14844 1681 LRPLVSLESGRPAVSDLNH-HYRTIINRNNRLRKLLSLNPPEIM-IRNEKRMLQEAVDSLFDNSRRNALVNKAGAV-GYK 1757 (2836)
T ss_pred ccCcEEeCCCcccCCchHH-HHHHHHHHHHHHHHHHHcCCchhh-HHHHHHHHHHHHHHHhcCCCCCCCccCCCCC-Ccc
Confidence 9999999988889999999 799999999999986 56777655 4678999999999999975333222211111 113
Q ss_pred CCCCcchhhhhhhhhccccccCCCCCcceeEeCCCCccccccccchhhhcccccccccchhhHHHHHHHHHcCCccccCC
Q 000882 234 QDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDNKLCLTYSD 313 (1238)
Q Consensus 234 k~~~~~iKgk~gr~R~nllGKRVdfSaRsVIspDP~L~i~evGvP~~iA~~LT~pE~Vt~~Ni~~l~~lV~ng~~~~~~~ 313 (1238)
|++.+++|||+||||+|||||||||||||||+|||+|+++|||||..||++||+| ||+++|+++.... .+.+
T Consensus 1758 ksls~~LkGK~GRFR~NLlGKRVDySgRSVI~pdP~L~l~evGlP~~mA~eL~~P-----f~i~~L~~~~~~~-~i~~-- 1829 (2836)
T PRK14844 1758 KSISDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELFKP-----FVYSKLKMYGMAP-TIKF-- 1829 (2836)
T ss_pred ccHHHHhcCCCCcccccccccccccCCCceEeCCCCcccceeeCCHHHHHhcccH-----HHHHHHHHcCccc-chHH--
Confidence 6778999999999999999999999999999999999999999999999999987 6777777653211 0000
Q ss_pred CCceEEeccCCCCcccccCcceeeeeeeccCeEeeeCCCCCCcccccceEEEecCCCeeeecccCCCCCCCccCcccccc
Q 000882 314 GSSSYSLREGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHL 393 (1238)
Q Consensus 314 ~~~~~~l~~~~~~~~~L~~g~iV~Rhl~dgD~VL~NRqPSLHr~Simah~v~v~~~~T~rln~~vC~pyNADFDGDeMn~ 393 (1238)
++..++ .....++++++ |+++||+|||||||||||||||||+|++++++||||||+||+||||||||||||+
T Consensus 1830 --a~~li~-----~~~~~v~dile-~vi~gd~VLlNRqPTLHR~sIqAf~~~l~~gktirlhp~vC~~fNADFDGDeMnv 1901 (2836)
T PRK14844 1830 --ASKLIR-----AEKPEVWDMLE-EVIKEHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAV 1901 (2836)
T ss_pred --HHHHHH-----hhCCcceEEEE-EEecCCEEEecCCCccccccccceeeEeecCceEEecccCCCcccCCCCCceeee
Confidence 011111 12345677665 5557999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCHHHHHHHHHHhccccccccCCCCCceEeechhhhhHHHhhh-ccccC----CHHHHHHHhcccc-cccccccccc
Q 000882 394 FYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF-KKYFL----DKAFTQQLAMFAL-SPLPRPALSK 467 (1238)
Q Consensus 394 H~PQs~eAraEa~~Lm~~~~nilsp~~G~Piigl~QD~llg~~llt-kd~fl----~~~~~~~l~~~~~-~~lp~PaI~K 467 (1238)
|+|||++|||||+.||++++||+||++|+|+++++||+|+|+|+|| ++.++ ...++.++++... -.++.++.++
T Consensus 1902 HvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pii~~~QD~ilG~y~LT~~~~~~~~~~~f~~~~~~~~a~~~~~~~i~~~i~ 1981 (2836)
T PRK14844 1902 HVPISLEAQLEARVLMMSTNNVLSPSNGRPIIVPSKDIVLGIYYLTLQEPKEDDLPSFGAFCEVEHSLSDGTLHIHSSIK 1981 (2836)
T ss_pred ecCCcHHHHHHHHHHhCCcccEEecCCCceeEeehhhhhhhhhhhcccccccccccccCCHHHHHHHHHcCCcccCceEE
Confidence 9999999999999999999999999999999999999999999998 56543 3455555544332 2455566677
Q ss_pred ccccccc---------------chhhhccccCCCCccccCcEEEEecccccccccccCCccchHHHHHHHHHHhhCHHHH
Q 000882 468 ARCSARW---------------TALQILQSVLPPGFDSCGDRYLIKKSEVLKGDFDRDTIPSVINEIVTSIFFEKGPEEV 532 (1238)
Q Consensus 468 p~~~~lw---------------TGKQi~S~~LP~~~~~~~~~viI~~gell~G~ldK~~lG~s~~~LI~~i~~~~G~~~a 532 (1238)
++ .+| .|||||+.+||.+.+. +++++.|.++|+.+ ++||+.+|+.||...|
T Consensus 1982 ~~--~~~~~~~~~~~~~~~~tt~GR~if~~ilP~~~~~--------~~~~~n~~l~KK~l----~~II~~~~~~yG~~~t 2047 (2836)
T PRK14844 1982 YR--MEYINSSGETHYKTICTTPGRLILWQIFPKHENL--------GFDLINQVLTVKEI----TSIVDLVYRNCGQSAT 2047 (2836)
T ss_pred ee--eccccCCCCcccceEecccHHHHHHHHcCCcccc--------CcceEeeeechhHH----HHHHHHHHHHhCHHHH
Confidence 65 444 3999999999985442 34677778888766 7799999999999999
Q ss_pred HhchhhhHHHHHHHHHhcCceeecCccccCHHHHHHHHHHHHHHHHHHHhhhhh--hHHHHHHHHHHHHHHHHHHHHHHH
Q 000882 533 LEFFDSLQPLLMENLFADGFSVSLEDFSLSKAALWNIQKEIQALYSLLYHRMST--QNELVDLQIENHIRHVKMLVAKFI 610 (1238)
Q Consensus 533 ~~fLd~lqrL~~~~L~~~GFSiGi~D~~~~~~~~~~i~~~i~~~~~~~~~~~~~--~~~~le~~~~~~l~~~~~~i~~~~ 610 (1238)
+.|||++++|+++|++.+|||+|++|+.+|+++.+.++++.+++.++..++..- ..+..+..+..+|+++++.+++.+
T Consensus 2048 ~~fLD~lk~LGf~yaT~~G~SIgi~Di~iP~~K~~iI~~a~~~v~~i~~~y~~G~it~~Er~~kvi~iW~~~~d~v~~~~ 2127 (2836)
T PRK14844 2048 VAFSDKLMVLGFEYATFSGVSFSRCDMVIPETKATHVDHARGEIKKFSMQYQDGLITRSERYNKVIDEWSKCTDMIANDM 2127 (2836)
T ss_pred HHHHHHHHHHHHHHHHhccEEeeHhHcccCHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999888777777777666555321 112234556667788888888766
Q ss_pred Hh----------cCCccccccccchhhhhhHHHHHhhcccccccCCccccccccccccccccccCCCCCCCCCCCcceec
Q 000882 611 LK----------SSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLVEDIASHFERIYPMDLNYPTAKYGLIK 680 (1238)
Q Consensus 611 ~~----------~n~l~~Mi~sGSKGS~~Ni~Qi~g~lGqQ~~~ggr~~~r~l~~~~~~~f~~~~p~~~d~~~~a~GfV~ 680 (1238)
++ .|++++|++||||||+.|++|++||+|||..+.|.++ +.| |.
T Consensus 2128 ~~~l~~~~~~~~~N~i~mMa~SGARGS~sQI~QLaGmRGLmakp~G~iI--------------------e~P------I~ 2181 (2836)
T PRK14844 2128 LKAISIYDGNSKYNSVYMMVNSGARGSTSQMKQLAGMRGLMTKPSGEII--------------------ETP------II 2181 (2836)
T ss_pred HHhhhhccccCCCCceeeeecccCccCHHHHHHHHhcceeeecCCCCee--------------------ecc------hh
Confidence 53 4899999999999999999999999999998877632 333 99
Q ss_pred ccccccCCccceEEeeccccceeeecccccCCCCchhHHHHHHHheeEEEec--ce------------------------
Q 000882 681 GCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYD--GT------------------------ 734 (1238)
Q Consensus 681 ssF~~GL~P~EfFfHamagREGLiDTAvkTa~sGYL~RrLv~~l~d~~v~YD--~t------------------------ 734 (1238)
|||++||+|.|||||||||||||+|||+|||+|||||||||+++||++|..+ ||
T Consensus 2182 SNFrEGLsv~EyFiSt~GaRKGL~DTALKTAdSGYLTRRLVDVaQDviI~e~DCgT~~Gi~v~~~~~~~~~i~~L~~ri~ 2261 (2836)
T PRK14844 2182 SNFREGLNVFEYFNSTHGARKGLADTALKTANSGYLTRRLVDVSQNCIVTKHDCKTKNGLVVRATVEGSTIVASLESVVL 2261 (2836)
T ss_pred hhhccCCCHHHhhhhccccccchhhhhhhcccccchhhhhhhhhceEEEEecccCCCCceEEEEeccCCeEEeEhhheeE
Confidence 9999999999999999999999999999999999999999999999999864 22
Q ss_pred -----------------------------------------Eecc----CCCceeeeeeecccccccCcCCCCCeeeeec
Q 000882 735 -----------------------------------------VRNV----CSNSIIQFDYAVNARKSHSLFPAGEPVGVLA 769 (1238)
Q Consensus 735 -----------------------------------------vr~~----~~~~iiqf~yg~dg~~~~~lv~~Ge~VG~la 769 (1238)
||++ +...|||.|||+|. ....+++.|||||++|
T Consensus 2262 GR~~a~di~~p~t~~~i~~~~~~I~~~~~~~i~~~gi~~v~IRS~ltC~s~~gvC~~CYG~~L-a~~~~V~iGeaVGiIA 2340 (2836)
T PRK14844 2262 GRTAANDIYNPVTKELLVKAGELIDEDKVKQINIAGLDVVKIRSPLTCEISPGVCSLCYGRDL-ATGKIVSIGEAVGVIA 2340 (2836)
T ss_pred EEEEHhHeEcCCCCCEEEeCCCccCHHHHHHHHHcCCCEEEEcCCeeECCCCCChhhccCccc-cCCCcccccccceeee
Confidence 1222 24579999999984 5788999999999999
Q ss_pred cccCCchHHHhhhccCC
Q 000882 770 ATAMSNPAYKAVLDSSP 786 (1238)
Q Consensus 770 aqsigep~tq~~l~t~~ 786 (1238)
|||||||+||+|||||+
T Consensus 2341 AQSIGEPGTQLTMRTFH 2357 (2836)
T PRK14844 2341 AQSVGEPGTQLTMRTFH 2357 (2836)
T ss_pred ecccCCCcceeeeehee
Confidence 99999999999999986
No 11
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=100.00 E-value=7.7e-150 Score=1449.24 Aligned_cols=706 Identities=22% Similarity=0.286 Sum_probs=554.6
Q ss_pred cccccceEEEecCChHHHHhcccccccccC------------CCCCCCCCCCCCCCCCCCCCCCCCC-C----C-CCC--
Q 000882 10 LEGQIVGIRFGLATQKEICTASISDCSISH------------ASQLANPFLGLPLEFGKCESCGTSE-P----G-KCE-- 69 (1238)
Q Consensus 10 ~~~~I~~I~Fgl~S~eEI~k~Sv~~~~I~~------------~~gl~DprlG~~~~~~~C~TCg~~~-~----~-~Cp-- 69 (1238)
....+..|+.++.|||+|++||+.+ |++ .+||.+.|.-+|.++..| .||+-. . . .|+
T Consensus 1392 ~~~~~~~i~i~lASpe~I~~ws~Ge--V~kpeTinyrt~kPe~dGLFcerIFGp~kd~eC-~Cgkyk~~~~~g~~~C~~C 1468 (2890)
T PRK09603 1392 RPKDFSSFQLTLASPEKIHSWSYGE--VKKPETINYRTLKPERDGLFCMKIFGPTKDYEC-LCGKYKKPRFKDIGTCEKC 1468 (2890)
T ss_pred cccCcceEEEEecCHHHHHHhhcee--EccccccccccCccCCCCEeeceeccCccCcEE-eCCCcccccCCCCEEcCCC
Confidence 4567889999999999999999864 333 258999888777777777 676310 0 1 244
Q ss_pred -----------CcceeEEcCcccccccChHHHHHHHHhhc----------c----cc-cCch-----------HHH-HH-
Q 000882 70 -----------GHFGYIELPIPIYHPSHISELKLTMYAFQ----------L----QI-KNDG-----------VAQ-RL- 110 (1238)
Q Consensus 70 -----------GHFGhIeL~~PVfHpgf~k~i~~IL~~iC----------l----~l-~~~~-----------~~~-~~- 110 (1238)
-.+|||+|+.||.|++|++.+...|..+- + .+ -..+ +.+ .+
T Consensus 1469 gvevt~s~vRR~RmGhI~La~Pv~HiWy~k~~ps~i~~ll~~~~k~le~viy~~~~~v~~~~~~~~~~~~~~~~~~~~~~ 1548 (2890)
T PRK09603 1469 GVAITHSKVRRFRMGHIELATPVAHIWYVNSLPSRIGTLLGVKMKDLERVLYYEAYIVKEPGEAAYDNEGTKLVMKYDIL 1548 (2890)
T ss_pred CcEechhHhHHHhcCceeecCcceeeeccCCCchHHHHHhCCCHHHhhhhhcceeeEEecCCccccccccccchhhhhhh
Confidence 38999999999999999994433332221 0 00 0111 000 00
Q ss_pred -----------------------------HHhH-----h-HHHHHHccCChhH-H----HHhcc-----CCCCCCCceEE
Q 000882 111 -----------------------------LSSC-----C-EVKEMLKRIPEET-R----KKLAG-----KGYFPQDGYIL 145 (1238)
Q Consensus 111 -----------------------------~~~C-----C-ev~~i~k~I~~ed-~----~~L~~-----~~~~~~~~~il 145 (1238)
++.. | +.++.++...... . ++|.. ..-..|+||||
T Consensus 1549 ~~~~~~~~~~~~~~~~f~~~~Gaeai~~lL~~~dl~~~~~~l~~~~~~~~~~~~~~~~~krl~~v~~f~~s~~~PewmiL 1628 (2890)
T PRK09603 1549 NEEQYQNISRRYEDRGFVAQMGGEAIKDLLEEIDLITLLQSLKEEVKDTNSDAKKKKLIKRLKVVESFLNSGNRPEWMML 1628 (2890)
T ss_pred hHHHHHHHHHHcCcccceechhHHHHHHHHHhCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHhcCCChHheee
Confidence 0000 0 1112222111111 1 11110 12367999999
Q ss_pred EeeccCCCCCCCccccCCCccccchhhHHHHHHHHHHHHHHHhh-hcCCCCcchhhhhhhHHHHHHHHHHhccCCcccCC
Q 000882 146 EYLPVPPNCLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEVRGTAKSSR 224 (1238)
Q Consensus 146 ~~lpVpP~~~Rp~~~~~~~~~~~~Dlt~~~l~~I~~~~~~l~~~-~~g~~~~~~~~~~~~~LQ~~v~~~~~~~~~~k~~~ 224 (1238)
++||||||++||++.++|+.+.++|+|. +|++||++|++|++. ..++|..+. .++|++||.+|+.|||+....++..
T Consensus 1629 ~~lPV~Pp~lRP~v~l~gg~~a~sDln~-lyr~II~rNnrLk~l~~~~ap~~ii-~nek~~LQ~aVd~l~DN~~~~~~~~ 1706 (2890)
T PRK09603 1629 TVLPVLPPDLRPLVALDGGKFAVSDVNE-LYRRVINRNQRLKRLMELGAPEIIV-RNEKRMLQEAVDVLFDNGRSTNAVK 1706 (2890)
T ss_pred eeeccCCCcccCcEEeCCCcccCCCccH-HHHHHHHHHHHHHHHHHcCCCceeh-HHHHHHHHHHHHHHhcccccccccc
Confidence 9999999999999999988888999998 899999999999975 667787664 6789999999999999754333322
Q ss_pred CcccCCCCCCCCCcchhhhhhhhhccccccCCCCCcceeEeCCCCccccccccchhhhcccccccccchhhHHHHHHHHH
Q 000882 225 DVDARFGVSQDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVD 304 (1238)
Q Consensus 225 ~~~~~~~~~k~~~~~iKgk~gr~R~nllGKRVdfSaRsVIspDP~L~i~evGvP~~iA~~LT~pE~Vt~~Ni~~l~~lV~ 304 (1238)
....| ..|++.+++|||+||||+|||||||||||||||+|||+|++||||||..||++||+|+. +++|+.
T Consensus 1707 ~~~~r--plKsls~~LkGK~GRFRqNLlGKRVDySgRSVI~pdP~L~l~e~GvP~~mA~eL~~P~~--------i~~L~~ 1776 (2890)
T PRK09603 1707 GANKR--PLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHL--------LSKLEE 1776 (2890)
T ss_pred CCCCC--cchhHHHHhcCCCCccccccccccccCcCCceEeCCCCcccccccChHHHHHHhCChHH--------HHHHHH
Confidence 21111 23677899999999999999999999999999999999999999999999999999954 578889
Q ss_pred cCCccccCCCCceEEeccCCCCcccccCcceeeeeeeccCeEeeeCCCCCCcccccceEEEecCCCeeeecccCCCCCCC
Q 000882 305 NKLCLTYSDGSSSYSLREGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSA 384 (1238)
Q Consensus 305 ng~~~~~~~~~~~~~l~~~~~~~~~L~~g~iV~Rhl~dgD~VL~NRqPSLHr~Simah~v~v~~~~T~rln~~vC~pyNA 384 (1238)
+|+...++.. +..+ ......+|.|+|||++||+|||||||||||||||||+|++++++||||||+||+||||
T Consensus 1777 ~G~~~~lk~a--k~~i------~~~~~~v~~vlr~vi~gd~VLlNRqPTLHR~sIqAf~~~l~~gktIrLhplvC~~fNA 1848 (2890)
T PRK09603 1777 RGYATTLKQA--KRMI------EQKSNEVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNA 1848 (2890)
T ss_pred cCCccCHHHH--HHHH------HhccCccEEEEEeeecCCeEEecCCCccccccceeeeEEEecCceEEeccccCCcccC
Confidence 9975332211 1000 1123456888999999999999999999999999999999999999999999999999
Q ss_pred ccCccccccccCCCHHHHHHHHHHhccccccccCCCCCceEeechhhhhHHHhhh-ccc--------cCCHHHHHHHhcc
Q 000882 385 DFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF-KKY--------FLDKAFTQQLAMF 455 (1238)
Q Consensus 385 DFDGDeMn~H~PQs~eAraEa~~Lm~~~~nilsp~~G~Piigl~QD~llg~~llt-kd~--------fl~~~~~~~l~~~ 455 (1238)
||||||||+|+|||++|||||+.||++.+||+||++|+|+++++||+|+|+|+|| ++. |.+.+++......
T Consensus 1849 DFDGDqMnvHvPqS~eA~aEa~~LM~s~~nilsP~~G~Pi~~p~QD~vlG~y~LT~~~~~~~~~~~~F~~~~e~~~~~~~ 1928 (2890)
T PRK09603 1849 DFDGDQMAVHVPLSQEAIAECKVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKSGVKGEHKLFSSVNEIITAIDT 1928 (2890)
T ss_pred CCCCceeEEeecCCHHHHHHHHHHhcccceEEEcCCCceeEEeecceeeeeEEeeccccCCCCccceeCCHHHHHHHHHc
Confidence 9999999999999999999999999999999999999999999999999999997 564 4455555433332
Q ss_pred cc--cccccccccccccccccc--hhhhccccCCCCccccCcEEEEecccccccccccCCccchHHHHHHHHHHhhCHHH
Q 000882 456 AL--SPLPRPALSKARCSARWT--ALQILQSVLPPGFDSCGDRYLIKKSEVLKGDFDRDTIPSVINEIVTSIFFEKGPEE 531 (1238)
Q Consensus 456 ~~--~~lp~PaI~Kp~~~~lwT--GKQi~S~~LP~~~~~~~~~viI~~gell~G~ldK~~lG~s~~~LI~~i~~~~G~~~ 531 (1238)
.. ...+.|++.+|. ++|| |||+||.+||..+.+ .++.+.+||+.+| +|||.+|+.||+..
T Consensus 1929 ~~~~~~~~i~~~~~p~--~l~Tt~GK~ifs~ilP~~~~~----------~~~n~~ldKK~Lg----~LI~~i~~~yG~~~ 1992 (2890)
T PRK09603 1929 KELDIHAKIRVLDQGN--IIATSAGRMIIKSILPDFIPT----------DLWNRPMKKKDIG----VLVDYVHKVGGIGI 1992 (2890)
T ss_pred CCCccCCcceeecCCc--EEEcCccceeeeccCcccccc----------ccEeeeechHHHH----HHHHHHHHHHCHHH
Confidence 22 234556777777 8999 999999999975432 1334668888886 69999999999999
Q ss_pred HHhchhhhHHHHHHHHHhcCceeecCccccCHHHHHHHHHHHHHHHHHHHhhh-------hhhHHHHHHHHHHHHHHHHH
Q 000882 532 VLEFFDSLQPLLMENLFADGFSVSLEDFSLSKAALWNIQKEIQALYSLLYHRM-------STQNELVDLQIENHIRHVKM 604 (1238)
Q Consensus 532 a~~fLd~lqrL~~~~L~~~GFSiGi~D~~~~~~~~~~i~~~i~~~~~~~~~~~-------~~~~~~le~~~~~~l~~~~~ 604 (1238)
|+.|||.+++|+++|++.+|||||++|+.+|+++.+.++++.+++.++..++. ++|++.+ ..|+++++
T Consensus 1993 t~~fLD~lk~LGf~yat~~G~SIgI~Dl~ip~~K~~iI~~A~~eV~ei~~~y~~G~it~~Er~~kvi-----d~w~~~~d 2067 (2890)
T PRK09603 1993 TATFLDNLKTLGFRYATKAGISISMEDIITPKDKQKMVEKAKVEVKKIQQQYDQGLLTDQERYNKII-----DTWTEVND 2067 (2890)
T ss_pred HHHHHHHHHHHHHHHHHhCCEeeeeccCcccHHHHHHHHHHHHHHHHHHHHHHcCCCCccHHHHHHH-----HHHHHHHH
Confidence 99999999999999999999999999999999887777777666666655543 2344444 44566666
Q ss_pred HHHHHHHh--------cCCccccccccchhhhhhHHHHHhhcccccccCCccccccccccccccccccCCCCCCCCCCCc
Q 000882 605 LVAKFILK--------SSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLVEDIASHFERIYPMDLNYPTAKY 676 (1238)
Q Consensus 605 ~i~~~~~~--------~n~l~~Mi~sGSKGS~~Ni~Qi~g~lGqQ~~~ggr~~~r~l~~~~~~~f~~~~p~~~d~~~~a~ 676 (1238)
.+++.+++ .|++++|+.||||||+.|++||+||+|||..+.|+.+ +.|
T Consensus 2068 ~v~~~~~~~l~~~~~~~N~i~mMa~SGARGS~~NI~QLaGmrGqMakp~G~ii--------------------e~P---- 2123 (2890)
T PRK09603 2068 KMSKEMMTAIAKDKEGFNSIYMMADSGARGSAAQIRQLSAMRGLMTKPDGSII--------------------ETP---- 2123 (2890)
T ss_pred HHHHHHHHHhhhcCCCCCcHHHHHhccccccHHHHHHHHHcCCcEECCCCCcc--------------------cCh----
Confidence 66665432 3899999999999999999999999999998876632 233
Q ss_pred ceecccccccCCccceEEeeccccceeeecccccCCCCchhHHHHHHHheeEEEec--ce--------------------
Q 000882 677 GLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYD--GT-------------------- 734 (1238)
Q Consensus 677 GfV~ssF~~GL~P~EfFfHamagREGLiDTAvkTa~sGYL~RrLv~~l~d~~v~YD--~t-------------------- 734 (1238)
|.+||++||+|+|||||||||||||+|||+|||+|||||||||+++||++|.++ ||
T Consensus 2124 --I~snFrEGLtp~EyFfst~GaRKGLiDTALKTAdSGYLTRRLVdvaQDviI~e~DCgT~~Gi~v~~~~~~~~~i~~l~ 2201 (2890)
T PRK09603 2124 --IISNFKEGLNVLEYFNSTHGARKGLADTALKTANAGYLTRKLIDVSQNVKVVSDDCGTHEGIEITDIAVGSELIEPLE 2201 (2890)
T ss_pred --hhcCcccCCCHHHHHHhccccccchhhhhhhccccchhhhhHHHhhcceEEEeccCCCCCCeEEEEeecCCeeecchh
Confidence 899999999999999999999999999999999999999999999999999986 22
Q ss_pred ---------------------------------------------Eecc----CCCceeeeeeecccccccCcCCCCCee
Q 000882 735 ---------------------------------------------VRNV----CSNSIIQFDYAVNARKSHSLFPAGEPV 765 (1238)
Q Consensus 735 ---------------------------------------------vr~~----~~~~iiqf~yg~dg~~~~~lv~~Ge~V 765 (1238)
||++ +...|||.|||+|. ....+++.||||
T Consensus 2202 ~ri~GR~~~~di~~p~t~~~i~~~~~~I~~~~~~~i~~~gi~~v~iRS~LtC~s~~gvC~~CYG~dL-a~g~~V~iGeaV 2280 (2890)
T PRK09603 2202 ERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITIRTPVTCKAPKGVCAKCYGLNL-GEGKMSYPGEAV 2280 (2890)
T ss_pred heeeeEEEHhheEcCCCCcEEEcCCcCcCHHHHHHHHHcCCCEEEEcCcceecCCCcChhhhcCCcc-cCCCCccCCcee
Confidence 1211 23568999999984 577899999999
Q ss_pred eeeccccCCchHHHhhhccCC
Q 000882 766 GVLAATAMSNPAYKAVLDSSP 786 (1238)
Q Consensus 766 G~laaqsigep~tq~~l~t~~ 786 (1238)
|++||||||||+||+|||||+
T Consensus 2281 GiIAAQSIGEPGTQLTMRTFH 2301 (2890)
T PRK09603 2281 GVVAAQSIGEPGTQLTLRTFH 2301 (2890)
T ss_pred eEEeecccCCCccccchhhhe
Confidence 999999999999999999976
No 12
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]
Probab=100.00 E-value=3.9e-132 Score=1231.19 Aligned_cols=688 Identities=23% Similarity=0.277 Sum_probs=569.0
Q ss_pred cceEEEecCChHHHHhcccccccccCC-----------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeEEcCcccc
Q 000882 14 IVGIRFGLATQKEICTASISDCSISHA-----------SQLANPFLGLPLEFGKCESCGTSEPGKCEGHFGYIELPIPIY 82 (1238)
Q Consensus 14 I~~I~Fgl~S~eEI~k~Sv~~~~I~~~-----------~gl~DprlG~~~~~~~C~TCg~~~~~~CpGHFGhIeL~~PVf 82 (1238)
+..|+||++||++|+++| . +|+.| .||+|+|||+|+++..| |||+.. ..||||||||||+.||+
T Consensus 4 ~~~i~~gl~sp~~ir~~s-~--ev~~pet~~~~~~P~~~Gl~d~ri~~~~~~~~C-~Cg~~~-~~~~~~~GhIeLa~Pv~ 78 (808)
T COG0086 4 IFDIKFGLASPEEIRSWS-G--EVKKPETINYRTKPERGGLFDERIFGPDKDYEC-TCGKYK-RICPGGFGHIELAAPVA 78 (808)
T ss_pred cceeEEecCCHHHHHhcc-e--EEcCccccCCCCcccCCCccchhhcCCCCCcee-cCCCCc-CcCCCCceeEEeecceE
Confidence 444999999999999955 4 34332 58999999999999999 999985 89999999999999999
Q ss_pred cccChHHHHHHHHhhccccc-----CchHHH-----H--HH--------HhH--h-------------------------
Q 000882 83 HPSHISELKLTMYAFQLQIK-----NDGVAQ-----R--LL--------SSC--C------------------------- 115 (1238)
Q Consensus 83 Hpgf~k~i~~IL~~iCl~l~-----~~~~~~-----~--~~--------~~C--C------------------------- 115 (1238)
||+|++.+..+|+++|..|. ...... + ++ +.| |
T Consensus 79 hi~f~k~~~~~L~~~~~~~~~v~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~Ga~~~~~~~~~~~~~~~~~~~~~~~ 158 (808)
T COG0086 79 HIWFFKSIPSLLDMTCRDCERVLYFEAYVVLGTDLEKIQLLNETEYVYDSFCAHCGAEAIKILLEKPDLETEREEETLSP 158 (808)
T ss_pred EechhhccHHHHhhhHHhhhhhhhHhHHHHhccchhhhcccchheeeccccCCCCCchhHHHHHhCcchhhhhhhcccCH
Confidence 99999999999999993221 000000 0 00 224 3
Q ss_pred -HHHHHHccCChhHHHHhccCCCCCCCceEEEeeccCCCCCCCccccCCCccccchhhHHHHHHHHHHHHHHHhhhcCCC
Q 000882 116 -EVKEMLKRIPEETRKKLAGKGYFPQDGYILEYLPVPPNCLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSSRSGTP 194 (1238)
Q Consensus 116 -ev~~i~k~I~~ed~~~L~~~~~~~~~~~il~~lpVpP~~~Rp~~~~~~~~~~~~Dlt~~~l~~I~~~~~~l~~~~~g~~ 194 (1238)
++.++|++|++.|..++ +...|+||||++||||||++||++..||+.+.+||||+ +|++||+.|++++.....+|
T Consensus 159 ~~~~~~~~~l~~~d~~~~---~~~~pewmil~vlpV~Pp~~RP~i~ld~g~~a~~dl~~-~~~~ii~~n~rlk~~~~~~~ 234 (808)
T COG0086 159 TKVKKLLKRLKVVDAFLL---SGNRPEWMILTVLPVPPPDLRPSIQLDGGRFAESDLND-LYRRVINRNNRLKRLLELAA 234 (808)
T ss_pred HHHHHHHhhccHHHHHHh---cCCCcceeEEEeeccCCCCCCcceecCCCccchhHHHH-HHHHHHHHHHHhHHhhhhcc
Confidence 67899999999999988 46789999999999999999999999999999999999 79999999999998633344
Q ss_pred CcchhhhhhhHHHHHHHHHHhccCCcccCCCcccCCCCCCCCCcchhhhhhhhhccccccCCCCCcceeEeCCCCccccc
Q 000882 195 NFESQEVESNDLQLAVGQYLEVRGTAKSSRDVDARFGVSQDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNE 274 (1238)
Q Consensus 195 ~~~~~~~~~~~LQ~~v~~~~~~~~~~k~~~~~~~~~~~~k~~~~~iKgk~gr~R~nllGKRVdfSaRsVIspDP~L~i~e 274 (1238)
. ++.+++|++||++|++|||+ +.+++... ....|++.+++|||+|||||||+||||||||||||+|||||++||
T Consensus 235 ~-~iv~~~~~~lQ~~v~~~~Dn-~~~~~~~~----~rPlksl~~~LkgK~GrFR~nL~GKRVd~SgRsVI~~~P~l~~~e 308 (808)
T COG0086 235 P-IIVRNEKRMLQEAVDALFDN-RRPRAVTG----GRPLKSLSQRLKGKQGRFRQNLLGKRVDYSGRSVISVGPNLKLNQ 308 (808)
T ss_pred h-HHHHHHHHHHHHHHHHHhhc-CCCCCccC----CCccccHHHHhcCCCceeeccccccccCCCCceeecCCCCccccc
Confidence 4 44578999999999999998 55444322 123478889999999999999999999999999999999999999
Q ss_pred cccchhhhcccccccccchhhHHHHHHHHHcCCccccCCCCceEEeccCCCCcccccCcceeeeeeeccCeEeeeCCCCC
Q 000882 275 IGVPFEIAQRITFEERVNVHNINYLQELVDNKLCLTYSDGSSSYSLREGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTT 354 (1238)
Q Consensus 275 vGvP~~iA~~LT~pE~Vt~~Ni~~l~~lV~ng~~~~~~~~~~~~~l~~~~~~~~~L~~g~iV~Rhl~dgD~VL~NRqPSL 354 (1238)
||||..||++||+|+.||++|++.+++ |. ++..+.. ...+..+|.|+||+++||+|||||||||
T Consensus 309 ~GvP~~~A~~L~~p~~v~~~~~~~~~~----~a---------~~~~~~~---~~~~~~~w~Vl~evi~gd~Vl~NR~PtL 372 (808)
T COG0086 309 CGVPKKMALELFKPFVVTELNIEGLRT----GA---------KYAKRMV---ERRLPEVWDVLREVIDGDPVLLNRAPTL 372 (808)
T ss_pred cCCHHHHHHHhccCEEEEehhhhhhhc----CC---------ceEEecc---cccccccchHHHHHhcCCccccccCChH
Confidence 999999999999999999999999987 32 3333321 1237789999999999999999999999
Q ss_pred CcccccceEEEecC-CCeeeecccCCCCCCCccCccccccccCCCHHHHHHHHHHhccccccccCCCCCceEeechhhhh
Q 000882 355 HKHSLQALSVYVHD-DHTVKINPLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALL 433 (1238)
Q Consensus 355 Hr~Simah~v~v~~-~~T~rln~~vC~pyNADFDGDeMn~H~PQs~eAraEa~~Lm~~~~nilsp~~G~Piigl~QD~ll 433 (1238)
||+|||+|.+++++ ++|||+||+||.||||||||||||+|+|||.+|+|||+.||++++|++||++|+|+++++||+|+
T Consensus 373 HrlsImq~~e~vl~~gkt~rLh~lVc~~yNADFDGDeM~~Hvp~s~ea~AEa~~lm~tq~nilsP~~Ggpiv~~~qD~v~ 452 (808)
T COG0086 373 HRLSIMQAFEPVLPEGKAIRLHPLVCEAYNADFDGDEMAVHVPASGEAAAEARGLMGTQMNILTPHYGGPIVAPIQDTVG 452 (808)
T ss_pred HHHHHHhhceeeccccceeecchhhccccccccCchhhhccccchHHHHHHHHHhhccccccccCCCCCceEeecceEEe
Confidence 99999999999987 99999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhh-ccccCCHHHHHHHhc---ccccccccccccccccccccchhhhccccCCCCcc------------------cc
Q 000882 434 SLKVMF-KKYFLDKAFTQQLAM---FALSPLPRPALSKARCSARWTALQILQSVLPPGFD------------------SC 491 (1238)
Q Consensus 434 g~~llt-kd~fl~~~~~~~l~~---~~~~~lp~PaI~Kp~~~~lwTGKQi~S~~LP~~~~------------------~~ 491 (1238)
|.|||| .|.|++..+++++.+ +.....+.||+.++. .+|||||+++.+++...+ ..
T Consensus 453 g~ylLt~~d~~~~~~~~~ei~l~~~~~~~~e~~~ai~~~~--~~~~~k~i~~~i~~~~~~~~i~~t~~~~~~~~~~~~~~ 530 (808)
T COG0086 453 GPYLLTIVDAKLPSTPVGEIYLKDEYADDREKAEAIAKKI--ELTTGKVIVSTISPDLAELSIIVTTDGRRIFNRGLPED 530 (808)
T ss_pred ccEEEEEecccCCCCcceEEEeccccccchhhhHHHhccc--ceeeeeEEEEEeeccCCcceEEEecchhhhhhccCCcc
Confidence 999997 788999999998843 444456789999988 999999999977765311 11
Q ss_pred -CcEEEEecccccccccccCCccchHHHHHHHHHHhhCHHHHH-hchhhhHHHHHHHHHhcC-ceeecCccc--cCHHHH
Q 000882 492 -GDRYLIKKSEVLKGDFDRDTIPSVINEIVTSIFFEKGPEEVL-EFFDSLQPLLMENLFADG-FSVSLEDFS--LSKAAL 566 (1238)
Q Consensus 492 -~~~viI~~gell~G~ldK~~lG~s~~~LI~~i~~~~G~~~a~-~fLd~lqrL~~~~L~~~G-FSiGi~D~~--~~~~~~ 566 (1238)
+..+.|.++++++|.+||.+. .+++.||+.++. .+++.+.+|...++...| |+++++|.. +++++.
T Consensus 531 ~d~~~~i~~~~l~~~~i~k~~~---------~i~~~~g~~~~~~~~~~~~dkl~~~~~~~~~~~~~~i~~~d~~~~~~~~ 601 (808)
T COG0086 531 KDVLVKIVNGKLIKGVIDKKIV---------TIYREYGPEVASKALVKLLDKLKNLGIKGIGGFGIGIGRKDIEAEDEKD 601 (808)
T ss_pred cceeeEEeccccceeeehhhHH---------HHHHHhCchhhHHHHHHHHHHHHHhheeeeccceEEeecccccchHHHH
Confidence 233678999999998888754 788999998888 888888888888888887 888887775 455555
Q ss_pred HHHHHHHHHHHHHHHhhhh-------hhH--HHHHHHHHHHHHHHHHHHHHHHHhcCC--ccccccccchhhhhhHHHHH
Q 000882 567 WNIQKEIQALYSLLYHRMS-------TQN--ELVDLQIENHIRHVKMLVAKFILKSST--LGYLIDSKSDSAVSKVVQQA 635 (1238)
Q Consensus 567 ~~i~~~i~~~~~~~~~~~~-------~~~--~~le~~~~~~l~~~~~~i~~~~~~~n~--l~~Mi~sGSKGS~~Ni~Qi~ 635 (1238)
+.+.++-.++.+...++.+ .|+ +.++......++++.........+... +..|..+|++|++.|++|++
T Consensus 602 e~v~~ae~~v~~~i~~~~~g~lt~~~~~~i~e~~e~~~~e~l~~ai~~~~~~~~~~~g~~~~~i~~m~~~Gs~~n~sq~~ 681 (808)
T COG0086 602 EIVIEAEGSVLKLILQYEEGDLTRTERNNIVEIIEVLGIEALRNAIIEEIKITLEEQGLDFVDIRHMGLSGARMNISQIV 681 (808)
T ss_pred HHHHHHHHHHHHHHHHhhcCCccccCCCCeEEEeehHHHHHHHHHHHHHHhhhHHhcCCcchhHHHHhhhhhccCHHHHH
Confidence 5555555555555554432 222 233444455556655554444443222 34677778888888899999
Q ss_pred hhcccccccCCccccccccccccccccccCCCCCCCCCCCcceecccccccCCccceEEeeccccceeeecccccCCCCc
Q 000882 636 GFLGLQLSDRGKFYSKTLVEDIASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGT 715 (1238)
Q Consensus 636 g~lGqQ~~~ggr~~~r~l~~~~~~~f~~~~p~~~d~~~~a~GfV~ssF~~GL~P~EfFfHamagREGLiDTAvkTa~sGY 715 (1238)
.|+|||.+.|.+. ++ .++|||.. .+..+++.|||.+||++||+|.|||||+|+||+||+|||+|||+|||
T Consensus 682 ~~iG~~gv~g~r~-~~----~~~~~Fe~-----~~~~~~a~~~i~s~f~eGLt~~e~f~~~~ggR~GlvDTA~KTa~sGY 751 (808)
T COG0086 682 QLIGQQGVMGEKI-SV----LARAAFEV-----TVKHLEAEGPGESSFLEGLTENEYFGHPIGGRTGLVDTALKTADSGY 751 (808)
T ss_pred HHhhhheeeccCC-Cc----cccccccc-----ccccceeeeeeecccCCCCCcceEEeecCccccchHHHhhhhcccCc
Confidence 9999999987652 22 27799974 35568999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHheeEEEecceEeccCCCceeeeeeeccccc
Q 000882 716 LFKNLMAVLRDVVICYDGTVRNVCSNSIIQFDYAVNARK 754 (1238)
Q Consensus 716 L~RrLv~~l~d~~v~YD~tvr~~~~~~iiqf~yg~dg~~ 754 (1238)
||||||+++||++|.||++||+ ..+.++||.||+||.+
T Consensus 752 l~RrLv~~~qdl~v~~d~~~~~-g~~~~~~~~~ged~~~ 789 (808)
T COG0086 752 LTRRLVDVAQDLIVQEDDCVTD-GIGVVIQFEYGEDGED 789 (808)
T ss_pred ceEEeechhcceEEEecCeEee-cCceEEEEecCccccC
Confidence 9999999999999999999999 6799999999999854
No 13
>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional
Probab=100.00 E-value=7.3e-87 Score=787.68 Aligned_cols=408 Identities=21% Similarity=0.310 Sum_probs=305.0
Q ss_pred ccccceEEEecCChHHHHhcc---------cccccccCC------------CCCCCCCCCCCCCCCCCCCCCCCC-----
Q 000882 11 EGQIVGIRFGLATQKEICTAS---------ISDCSISHA------------SQLANPFLGLPLEFGKCESCGTSE----- 64 (1238)
Q Consensus 11 ~~~I~~I~Fgl~S~eEI~k~S---------v~~~~I~~~------------~gl~DprlG~~~~~~~C~TCg~~~----- 64 (1238)
..++..|+.++.|||+|+++| +. +|++| +||.+.|.-+|.++..| .||+-.
T Consensus 6 ~~~~~~i~I~laSPe~I~~Ws~r~lpng~i~G--eV~kpeTinyrT~KPE~dGLFCerIFGP~k~~eC-~CGkyk~~~~~ 82 (627)
T PRK02625 6 ENRFDYVKIGLASPERIRQWGQRTLPNGQVVG--EVTKPETINYRTLKPEMDGLFCEKIFGPSKDWEC-HCGKYKRVRHR 82 (627)
T ss_pred ccccceEEEEecCHHHHHHHHHhhcCCCceee--EECCCcccccCCCCCCCCCEeechhcCCccCcEE-eCCCccccCcC
Confidence 467889999999999999999 43 34332 58888887667776666 566311
Q ss_pred CCCCC--C-----------cceeEEcCcccccccChHHHHHHHHhhc----------c----c--cc--Cc---------
Q 000882 65 PGKCE--G-----------HFGYIELPIPIYHPSHISELKLTMYAFQ----------L----Q--IK--ND--------- 104 (1238)
Q Consensus 65 ~~~Cp--G-----------HFGhIeL~~PVfHpgf~k~i~~IL~~iC----------l----~--l~--~~--------- 104 (1238)
...|+ | .+|||+|+.||-|+.|++.+...+..+- + . ++ ..
T Consensus 83 ~~~C~~CgvE~t~s~vRR~RMG~I~La~PV~HiWylk~~ps~i~~lL~~~~k~le~ivy~~~~~v~~~~~~~~~~~~~~~ 162 (627)
T PRK02625 83 GIVCERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYVAILLDMPLRDVEQIVYFNCYVVLDPGNHKNLKYKQLL 162 (627)
T ss_pred CcCCCCCCcEecchhhhHhhcCceeecCCceEeeccCCCchHHHHHhCCCHHHhhheeeeeeEEEecCCCccchhhhhhh
Confidence 01244 3 7999999999999999985433222211 0 0 00 00
Q ss_pred ---hH---HHHHHH--------h-H---h-HHHHHHc----------------cCChhH----HHHhc-----cCCCCCC
Q 000882 105 ---GV---AQRLLS--------S-C---C-EVKEMLK----------------RIPEET----RKKLA-----GKGYFPQ 140 (1238)
Q Consensus 105 ---~~---~~~~~~--------~-C---C-ev~~i~k----------------~I~~ed----~~~L~-----~~~~~~~ 140 (1238)
.. .+.++. . . . -++++|+ +..... .++|. ......|
T Consensus 163 ~~~~~~~~~~~~~~~~~~~~~~~~~~~Ga~ai~~lL~~~dl~~~~~~l~~~~~~~~~~~~~~~ikrl~~~~~f~~~~~~P 242 (627)
T PRK02625 163 TEDQWLEIEDQIYAEDSELEGEEVVGIGAEALKRLLEDLNLEEEAEQLREEIANSKGQKRAKLIKRLRVIDNFIATGSRP 242 (627)
T ss_pred hhHHHHHHHHHhcccccccccchhhhhhHHHHHHHHhhCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHhcCCCc
Confidence 00 001000 0 1 0 0111111 111111 11111 0123579
Q ss_pred CceEEEeeccCCCCCCCccccCCCccccchhhHHHHHHHHHHHHHHHhh-hcCCCCcchhhhhhhHHHHHHHHHHhccCC
Q 000882 141 DGYILEYLPVPPNCLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEVRGT 219 (1238)
Q Consensus 141 ~~~il~~lpVpP~~~Rp~~~~~~~~~~~~Dlt~~~l~~I~~~~~~l~~~-~~g~~~~~~~~~~~~~LQ~~v~~~~~~~~~ 219 (1238)
+||||++|||||+++||++.++|+.+.++|+|. +|++||++|++|+.. ..++|..+. .++|++||.+|++|||+...
T Consensus 243 ewmiL~~lPV~Pp~lRP~v~l~~g~~~~sDLn~-ly~~II~rNn~L~~~~~~~~p~~ii-~~~~~~LQ~aVd~liDn~~~ 320 (627)
T PRK02625 243 EWMVLDVIPVIPPDLRPMVQLDGGRFATSDLND-LYRRVINRNNRLARLQEILAPEIIV-RNEKRMLQEAVDALIDNGRR 320 (627)
T ss_pred cEEEEEeeecCCCcccCceEeCCCcccCCCHHH-HHHHHHHHHHHHHHHHHcCCcHHHH-HHHHHHHHHHHHHHhcCCCC
Confidence 999999999999999999999888888899998 899999999999875 556665543 56899999999999997543
Q ss_pred cccCCCcccCCCCCCCCCcchhhhhhhhhccccccCCCCCcceeEeCCCCccccccccchhhhcccccccccchhhHHHH
Q 000882 220 AKSSRDVDARFGVSQDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYL 299 (1238)
Q Consensus 220 ~k~~~~~~~~~~~~k~~~~~iKgk~gr~R~nllGKRVdfSaRsVIspDP~L~i~evGvP~~iA~~LT~pE~Vt~~Ni~~l 299 (1238)
.++......+ ..|++.+.+|||+||||+|||||||||||||||||||+|++||||||.+||++||+| |||++|
T Consensus 321 g~~~~~~~~r--p~ksls~~LkGKeGRFR~NLlGKRVDySgRSVIspdP~L~l~e~GvP~~mA~eL~~P-----f~i~~L 393 (627)
T PRK02625 321 GRTVVGANNR--PLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQP-----FVIHRL 393 (627)
T ss_pred CCCcccccCC--chhhHHHHhccCCccccccccccccccCCCceEeCCCCcccccccChHHHHHhcCcH-----HhHHHH
Confidence 3332221111 235677999999999999999999999999999999999999999999999999988 577665
Q ss_pred HHHHHcCCccccCCCCceEEeccCCCCcccccCcceeeeeeeccCeEeeeCCCCCCcccccceEEEecCCCeeeecccCC
Q 000882 300 QELVDNKLCLTYSDGSSSYSLREGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLIC 379 (1238)
Q Consensus 300 ~~lV~ng~~~~~~~~~~~~~l~~~~~~~~~L~~g~iV~Rhl~dgD~VL~NRqPSLHr~Simah~v~v~~~~T~rln~~vC 379 (1238)
+.+|.....+ .++..+... -...|.|+|||+|||+|||||||||||||||||+|++++++||||||+||
T Consensus 394 ---~~~g~~~~i~--~ak~~i~~~------~~~~~~Vlr~v~~gd~VLlNRqPTLHR~sIqAf~~~l~~~ktirlhplvC 462 (627)
T PRK02625 394 ---IRQGIVNNIK--AAKKLIQRA------DPEVWQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVC 462 (627)
T ss_pred ---HHcCchhhHH--HHHHHHHhc------CCcccEEEEEeecCcEEEecCCCccccccceeEeeEEcCCCeEEeccccC
Confidence 4555431111 011111110 12357788999999999999999999999999999999999999999999
Q ss_pred CCCCCccCccccccccCCCHHHHHHHHHHhccccccccCCCCCceEeechhhhhHHHhhh-cc
Q 000882 380 GPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF-KK 441 (1238)
Q Consensus 380 ~pyNADFDGDeMn~H~PQs~eAraEa~~Lm~~~~nilsp~~G~Piigl~QD~llg~~llt-kd 441 (1238)
+||||||||||||+|+|||++|||||+.||.+++|++||++|+|+++++||+++|+|+|| ++
T Consensus 463 ~~fNADFDGDeMnvHvPqS~~A~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~llG~y~LT~~~ 525 (627)
T PRK02625 463 PAFNADFDGDQMAVHVPLSLEAQAEARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLTAEN 525 (627)
T ss_pred CcccCCcCCCeEEEecCCCHHHHHHHHHHhcCccceEEcCCCceeEeechhhhhheeeeeccC
Confidence 999999999999999999999999999999999999999999999999999999999987 44
No 14
>TIGR02387 rpoC1_cyan DNA-directed RNA polymerase, gamma subunit. The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''.
Probab=100.00 E-value=2.1e-86 Score=782.87 Aligned_cols=403 Identities=21% Similarity=0.321 Sum_probs=303.3
Q ss_pred cceEEEecCChHHHHhcc---------cccccccCC------------CCCCCCCCCCCCCCCCCCCCCCCC-----CCC
Q 000882 14 IVGIRFGLATQKEICTAS---------ISDCSISHA------------SQLANPFLGLPLEFGKCESCGTSE-----PGK 67 (1238)
Q Consensus 14 I~~I~Fgl~S~eEI~k~S---------v~~~~I~~~------------~gl~DprlG~~~~~~~C~TCg~~~-----~~~ 67 (1238)
+..|+.++.|||+|+++| +. +|++| +||.+.|.-+|.++..| .||+-. ...
T Consensus 2 ~~~i~I~laSPe~I~~Ws~r~lpng~i~G--eV~kp~TinyrT~KPE~dGLFCerIFGP~k~~eC-~CGkyk~~~~~~~~ 78 (619)
T TIGR02387 2 FDYVKITIASPERVMEWGQRTLPNGQVVG--EVTKPETINYRTLKPEMDGLFCEKIFGPSKDWEC-HCGKYKRVRHRGIV 78 (619)
T ss_pred CceEEEEecCHHHHHHHHHhhCCCCceee--EECCCcccccCCCCCCCCCEeechhcCCCcCcEE-eCCCccccCcCCcC
Confidence 467999999999999999 43 34332 58999888777777777 677321 013
Q ss_pred CC--C-----------cceeEEcCcccccccChHHHHHHHHhhc----------cccc-----Cch----H---------
Q 000882 68 CE--G-----------HFGYIELPIPIYHPSHISELKLTMYAFQ----------LQIK-----NDG----V--------- 106 (1238)
Q Consensus 68 Cp--G-----------HFGhIeL~~PVfHpgf~k~i~~IL~~iC----------l~l~-----~~~----~--------- 106 (1238)
|+ | .+|||+|+.||-|+.|++.+...+..+- +.+. ..+ +
T Consensus 79 C~~CgvE~t~s~vRR~RMG~I~La~PV~HiWylk~~ps~i~~lL~~~~k~le~i~y~~~~~v~~~~~~~~~~~~~~~~~~ 158 (619)
T TIGR02387 79 CERCGVEVTESRVRRHRMGYIKLAAPVTHVWYLKGIPSYVSILLDMPLRDVEQIVYFNAYVVLNPGNAKNLKYKQLLTED 158 (619)
T ss_pred CCCCCCEEchhhhHHHhcCceeccCcceeeeecCCCchHHHHHhCCCHHHhhheeeeeeEEEecCCCccchhhhhhhhHH
Confidence 55 3 7999999999999999985433332221 0000 000 0
Q ss_pred -----HHH-----------------------HHHhH-----h-HHHHHHccCChhHH----HHhcc-----CCCCCCCce
Q 000882 107 -----AQR-----------------------LLSSC-----C-EVKEMLKRIPEETR----KKLAG-----KGYFPQDGY 143 (1238)
Q Consensus 107 -----~~~-----------------------~~~~C-----C-ev~~i~k~I~~ed~----~~L~~-----~~~~~~~~~ 143 (1238)
.+. +++.. + ..++.+++...... ++|.. ..-..|+||
T Consensus 159 ~~~~~~~~~~~~~~~~~~~~~~~~Ga~ai~~lL~~~dl~~~~~~l~~~~~~~~~~~~~~~~krl~~~~~f~~~~~~Pewm 238 (619)
T TIGR02387 159 QWLEIEDQIYAEDSELENEEVVGIGAEALKQLLADLNLEEVAEQLREEINGSKGQKRAKLIKRLRVIDNFIATSSRPEWM 238 (619)
T ss_pred HHHHHHHHhcccccccccceeccchHHHHHHHHHhCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcCCCcceE
Confidence 000 00000 0 11111111111111 11110 123579999
Q ss_pred EEEeeccCCCCCCCccccCCCccccchhhHHHHHHHHHHHHHHHhh-hcCCCCcchhhhhhhHHHHHHHHHHhccCCccc
Q 000882 144 ILEYLPVPPNCLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEVRGTAKS 222 (1238)
Q Consensus 144 il~~lpVpP~~~Rp~~~~~~~~~~~~Dlt~~~l~~I~~~~~~l~~~-~~g~~~~~~~~~~~~~LQ~~v~~~~~~~~~~k~ 222 (1238)
||++||||||++||++.++|+.+.++|+|. +|++||++|++|+.. ..++|..+ ..++|++||.+|+.|||+....++
T Consensus 239 iL~~lPV~Pp~lRP~v~l~~g~~~~sDln~-lyr~II~rNn~L~~~~~~~~p~~i-~~~~~~~LQ~aVd~lidn~~~g~~ 316 (619)
T TIGR02387 239 VLDVIPVIPPDLRPMVQLDGGRFATSDLND-LYRRVINRNNRLARLQEILAPEII-VRNEKRMLQEAVDALIDNGRRGRT 316 (619)
T ss_pred EEEecccCCcccCCceEeCCCcccCCCHHH-HHHHHHHHHHHHHHHHHcCCcHHH-HHHHHHHHHHHHHHHhcCCCCCCC
Confidence 999999999999999999988888999998 899999999999875 55666544 356899999999999997544333
Q ss_pred CCCcccCCCCCCCCCcchhhhhhhhhccccccCCCCCcceeEeCCCCccccccccchhhhcccccccccchhhHHHHHHH
Q 000882 223 SRDVDARFGVSQDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQEL 302 (1238)
Q Consensus 223 ~~~~~~~~~~~k~~~~~iKgk~gr~R~nllGKRVdfSaRsVIspDP~L~i~evGvP~~iA~~LT~pE~Vt~~Ni~~l~~l 302 (1238)
......+ ..|++.+.+|||+||||+|||||||||||||||||||+|++||||||.+||.+||+| |||.+|
T Consensus 317 ~~~~~~r--p~ksls~~LkGKeGRFR~nLlGKRVDySgRSVI~pdP~L~l~qvGvP~~mA~eLf~P-----f~i~~L--- 386 (619)
T TIGR02387 317 VVGANNR--PLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQP-----FVIHRL--- 386 (619)
T ss_pred cccccCC--chhhHHHHhccCCccccccccccccccCCCceecCCCCcccceecChHHHHHhcCch-----HhHHHH---
Confidence 2221111 235677999999999999999999999999999999999999999999999999987 466655
Q ss_pred HHcCCccccCCCCceEEeccCCCCcccccCcceeeeeeeccCeEeeeCCCCCCcccccceEEEecCCCeeeecccCCCCC
Q 000882 303 VDNKLCLTYSDGSSSYSLREGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPL 382 (1238)
Q Consensus 303 V~ng~~~~~~~~~~~~~l~~~~~~~~~L~~g~iV~Rhl~dgD~VL~NRqPSLHr~Simah~v~v~~~~T~rln~~vC~py 382 (1238)
+.+|.....+ +++..++... ...+.|+|||+|||+|||||||||||+|||||+|++++++||||||+||+||
T Consensus 387 ~~~g~~~~i~--~ak~~i~~~~------~~v~~Vlr~v~~gd~VLlNRqPTLHR~sIqAf~~~l~~~ktirlhplvC~~f 458 (619)
T TIGR02387 387 IRQGIVNNIK--AAKKLIQRAD------DEIWSVLQEVITGHPVMLNRAPTLHRLGIQAFEPILVDGRAIQLHPLVCPAF 458 (619)
T ss_pred HhcCcccchH--HHHHHHHhcC------ChhHHHHHHHhcCCEEEecCCCccchhcceeeeeEEecCCeEEECcccCCcc
Confidence 4466532111 1122222110 1246799999999999999999999999999999999999999999999999
Q ss_pred CCccCccccccccCCCHHHHHHHHHHhccccccccCCCCCceEeechhhhhHHHhhh
Q 000882 383 SADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF 439 (1238)
Q Consensus 383 NADFDGDeMn~H~PQs~eAraEa~~Lm~~~~nilsp~~G~Piigl~QD~llg~~llt 439 (1238)
||||||||||+|+|||++|||||++||++++|++||++|+|+++++||+|+|+|+||
T Consensus 459 NADFDGDeMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~llg~y~LT 515 (619)
T TIGR02387 459 NADFDGDQMAVHVPLSLEAQTEARLLMLASNNVLSPATGEPIVTPSQDMVLGCYYLT 515 (619)
T ss_pred cCCCCCceeeeecCCCHHHHHHHHHHhhchhcEEecCCCceeEeechhhhhhhheee
Confidence 999999999999999999999999999999999999999999999999999999987
No 15
>CHL00018 rpoC1 RNA polymerase beta' subunit
Probab=100.00 E-value=6.3e-85 Score=778.37 Aligned_cols=282 Identities=26% Similarity=0.318 Sum_probs=244.6
Q ss_pred CCCCceEEEeeccCCCCCCCccccCCCccccchhhHHHHHHHHHHHHHHHhhh-c--CCCCcchhhhhhhHHHHHHHHHH
Q 000882 138 FPQDGYILEYLPVPPNCLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSSR-S--GTPNFESQEVESNDLQLAVGQYL 214 (1238)
Q Consensus 138 ~~~~~~il~~lpVpP~~~Rp~~~~~~~~~~~~Dlt~~~l~~I~~~~~~l~~~~-~--g~~~~~~~~~~~~~LQ~~v~~~~ 214 (1238)
..|+||||++||||||++||++..+|+.+.++|+|. +|++||.+|++|+... . ++|... ..++|++||.+|++|+
T Consensus 259 ~~PewmiL~~lPV~Pp~lRP~v~l~~g~~~~sDln~-lyr~II~rNn~L~~~~~~~~~~p~~~-i~~~~~~LQ~aVd~li 336 (663)
T CHL00018 259 IEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNE-LYRRVIYRNNTLTDLLTTSRSTPGEL-VMCQKKLLQEAVDALL 336 (663)
T ss_pred CCccEEEEEeeeeCCCcccCceEcCCCcccCCChHH-HHHHHHHHHHHHHHHHhcccCCcHHH-HHHHHHHHHHHHHHHh
Confidence 579999999999999999999999888888999998 8999999999998753 2 556544 3578999999999999
Q ss_pred hccCCcccCCCcccCCCCCCCCCcchhhhhhhhhccccccCCCCCcceeEeCCCCccccccccchhhhcccccccccchh
Q 000882 215 EVRGTAKSSRDVDARFGVSQDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVH 294 (1238)
Q Consensus 215 ~~~~~~k~~~~~~~~~~~~k~~~~~iKgk~gr~R~nllGKRVdfSaRsVIspDP~L~i~evGvP~~iA~~LT~pE~Vt~~ 294 (1238)
|+....++..+...+ ..+++.+.+|||+||||+|||||||||||||||||||+|++||||||.+||++||+|+.
T Consensus 337 dn~~~g~~~~~~~~r--~~ksls~~LkGK~GrFR~NLlGKRVDySgRSVIvpdP~L~l~e~GlP~~mA~eL~~P~~---- 410 (663)
T CHL00018 337 DNGIRGQPMRDGHNK--PYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQPFV---- 410 (663)
T ss_pred cCCCCCCccccCCCC--CCCCccccccCcCccccccccccccccCCCceecCCCcccccccCChHHHHHHcCcHHH----
Confidence 975444433322111 34677899999999999999999999999999999999999999999999999999963
Q ss_pred hHHHHHHHHHcCCccccCCCCceEEeccCCCCcccccCcceeeeeeeccCeEeeeCCCCCCcccccceEEEecCCCeeee
Q 000882 295 NINYLQELVDNKLCLTYSDGSSSYSLREGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKI 374 (1238)
Q Consensus 295 Ni~~l~~lV~ng~~~~~~~~~~~~~l~~~~~~~~~L~~g~iV~Rhl~dgD~VL~NRqPSLHr~Simah~v~v~~~~T~rl 374 (1238)
+++|+.+|+...++. ++..++. ....+|.|+|||+|||+|||||||||||||||||+|++++++||||
T Consensus 411 ----i~~Li~~~~~~~~~~--Ak~~i~~------~~~~~~~Vlr~v~~gd~VLlNRqPTLHR~sIqAf~~~L~~gktIrL 478 (663)
T CHL00018 411 ----IRGLIRQHLASNIRA--AKSKIRE------KEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICL 478 (663)
T ss_pred ----HHHHHhcCccccHHH--HHHHHHh------cCCcccEeeeehhcCceeeecCCCcccccccceeeEEecCCCeEEe
Confidence 467888887532211 1222221 2246789999999999999999999999999999999999999999
Q ss_pred cccCCCCCCCccCccccccccCCCHHHHHHHHHHhccccccccCCCCCceEeechhhhhHHHhhh
Q 000882 375 NPLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF 439 (1238)
Q Consensus 375 n~~vC~pyNADFDGDeMn~H~PQs~eAraEa~~Lm~~~~nilsp~~G~Piigl~QD~llg~~llt 439 (1238)
||+||+||||||||||||||+|||++|||||+.||++++|++||++|+|+++++||+|+|+|+||
T Consensus 479 hplvC~~fNADFDGDqMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT 543 (663)
T CHL00018 479 HPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYVLT 543 (663)
T ss_pred CcccCCcccCCccCcEEEEecCCCHHHHHHHHHHhcCccceeEcCCCceeEeechhhhhhhheec
Confidence 99999999999999999999999999999999999999999999999999999999999999987
No 16
>smart00663 RPOLA_N RNA polymerase I subunit A N-terminus.
Probab=100.00 E-value=2.9e-84 Score=724.35 Aligned_cols=290 Identities=35% Similarity=0.506 Sum_probs=252.5
Q ss_pred CceEEEeeccCCCCCCCccccCCCccccchhhHHHHHHHHHHHHHHHhhh-cCCCCcchhhhhhhHHHHHHHHHHhccCC
Q 000882 141 DGYILEYLPVPPNCLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSSR-SGTPNFESQEVESNDLQLAVGQYLEVRGT 219 (1238)
Q Consensus 141 ~~~il~~lpVpP~~~Rp~~~~~~~~~~~~Dlt~~~l~~I~~~~~~l~~~~-~g~~~~~~~~~~~~~LQ~~v~~~~~~~~~ 219 (1238)
+||||++|||||+|+||++..+++.+.+||+|. +|++|++.|+.|++.. .+++... ...+|..||.+|+.|+|+.+.
T Consensus 1 e~fil~~lpVpP~~~RP~v~~~~~~~~eddlt~-~l~~Ii~~N~~L~~~~~~~~~~~~-~~~~~~~LQ~~v~~~~d~~~~ 78 (295)
T smart00663 1 EWMILTVLPVPPPCLRPSVSLDGGRFAEDDLTH-LLRDIIKRNNRLKRLLELGAPEHI-IRNEKRLLQEAVDTLFDNEGL 78 (295)
T ss_pred CeEEEeccccCCCCCCCcEEeCCCcccCCcHHH-HHHHHHHHHHHHHHHHHcCChHHH-HHHHHHHHHHHHHHHHccCCC
Confidence 699999999999999999988776677889998 7999999999999864 4555443 356799999999999998654
Q ss_pred cccCCCcccCCCCCCCCCcchhhhhhhhhccccccCCCCCcceeEeCCCCccccccccchhhhcccccccccchhhHHHH
Q 000882 220 AKSSRDVDARFGVSQDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYL 299 (1238)
Q Consensus 220 ~k~~~~~~~~~~~~k~~~~~iKgk~gr~R~nllGKRVdfSaRsVIspDP~L~i~evGvP~~iA~~LT~pE~Vt~~Ni~~l 299 (1238)
+++.... + ...+.+.++++||.|+||+|+|||||||||||||||||+|++||||||..||++||+||.||.||+++|
T Consensus 79 ~~~~~~~-~--~~~~~i~~~l~gK~G~~R~nllGKRvd~s~RsVI~pdP~l~~~evgiP~~~A~~Lt~pe~v~~~n~~~l 155 (295)
T smart00663 79 PRARQKS-G--RPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKL 155 (295)
T ss_pred cccccCC-C--CCcccccccccCcCCccccccccccccccCceEEeCCCCcceeEeeCCHHHHHhCCcCEEEhHHHHHHH
Confidence 3332110 1 123567789999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHcCCc--cccCCCCceEEeccCCC--CcccccCcceeeeeeeccCeEeeeCCCCCCcccccceEEEecCCCeeeec
Q 000882 300 QELVDNKLC--LTYSDGSSSYSLREGSK--GHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKIN 375 (1238)
Q Consensus 300 ~~lV~ng~~--~~~~~~~~~~~l~~~~~--~~~~L~~g~iV~Rhl~dgD~VL~NRqPSLHr~Simah~v~v~~~~T~rln 375 (1238)
+++|.||+. ..+.+ +..+.+++.++ ....|++||+|+||++|||+|||||||||||||||||+|+|++++|||||
T Consensus 156 ~~lv~ng~pga~~i~~-g~~~~l~~~~~~~~~~~l~~g~~v~r~l~dgd~Vl~NRqPsLHr~si~a~~v~v~~~~tir~n 234 (295)
T smart00663 156 RKLVRNGPNGAKYIIR-GKKTNLKLAKRSKIAKHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLN 234 (295)
T ss_pred HHHHhcCCCCceEEEe-CcEEEchhhhhHHHHhcCccccEeheehhcCCEEEEecCCccccccceeEEEEEecCceEEec
Confidence 999999972 11111 22344443322 24678999999999999999999999999999999999999999999999
Q ss_pred ccCCCCCCCccCccccccccCCCHHHHHHHHHHhccccccccCCCCCceEeechhhhhHHH
Q 000882 376 PLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLK 436 (1238)
Q Consensus 376 ~~vC~pyNADFDGDeMn~H~PQs~eAraEa~~Lm~~~~nilsp~~G~Piigl~QD~llg~~ 436 (1238)
|++|+||||||||||||+|+|||++|||||++||++.+|++||++|+|+++++||+|+|+|
T Consensus 235 ~~~c~~fNADFDGDeMnih~pqs~~a~aEa~~Lm~~~~~~~sp~~g~p~~~~~QD~l~g~~ 295 (295)
T smart00663 235 PLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295 (295)
T ss_pred CccCCcccCCcCCCEEEEecCCCHHHHHHHHHHhhhhhccccCCCCCeeEeeecceeeecC
Confidence 9999999999999999999999999999999999999999999999999999999999986
No 17
>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=1.2e-57 Score=522.30 Aligned_cols=332 Identities=20% Similarity=0.239 Sum_probs=284.0
Q ss_pred hhHHHHHHHheeEEEecceEe-ccCCCceeeeeeecccccccCcCCCCCeeeeeccccCCchHHHhhhccCC-------C
Q 000882 716 LFKNLMAVLRDVVICYDGTVR-NVCSNSIIQFDYAVNARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDSSP-------S 787 (1238)
Q Consensus 716 L~RrLv~~l~d~~v~YD~tvr-~~~~~~iiqf~yg~dg~~~~~lv~~Ge~VG~laaqsigep~tq~~l~t~~-------~ 787 (1238)
|+.+|.+.+++-...|..+-. .. ..++..+...+ .+++++|||+||++||||||||+|||||+||+ |
T Consensus 2 ~p~~~~~e~~~~~~~~~~~~~~~~--~~~l~~i~~ky---~~alv~PGeaVG~IAAQSIGEP~TQMTLnTFH~AGVas~n 76 (367)
T TIGR02389 2 LPEKLLKELEETVKKREISDKEEL--DEIIKRVEEEY---LRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELN 76 (367)
T ss_pred CcHHHHHHHHHHHHHcCCCHHHHH--HHHHHHHHHHH---HHhcCCCccccchhhhhhcCCccccccccccccccccccC
Confidence 567788888888777776554 32 44566666666 67889999999999999999999999999974 8
Q ss_pred CCCchHHHHHHHHhhccCCCCCCCceEEEEcCCCCCCCccccHHHHHHHHhhhceechhhhhheeeEEecCCccccCCCc
Q 000882 788 SNNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIISDDEG 867 (1238)
Q Consensus 788 ~~~g~~rlkEil~~~~~~k~~~~d~~~~l~L~~~~~~~~~~~e~~a~~V~~~le~vtl~dv~~~i~i~y~~~~~~~~~~~ 867 (1238)
+|+|+||||||++++++ +++|.|++||.+.+. .++++|++|+.+||+++|+|++..+.+.|.+
T Consensus 77 VTlGVPRlkEIINa~k~----i~TP~~ti~L~~~~~----~~~~~a~~v~~~iE~t~l~dv~~~~~~~~~~--------- 139 (367)
T TIGR02389 77 VTLGLPRLIEIVDARKT----PSTPSMTIYLEDEYE----KDREKAEEVAKKIEATKLEDVAKDISIDLAD--------- 139 (367)
T ss_pred ccccchhHHHHhhcccC----CCCCeEEEEecCcch----hhHHHHHHHHHHhhheeHHHHHhhhheeccC---------
Confidence 89999999999999886 556699999987654 3788999999999999999999999988753
Q ss_pred eEEEEEecHHHHhhcCCCHhhHHHHHHHhhhhhh--------------hh---hhhHHHHHhhccceeeccccccccccc
Q 000882 868 LVGHIHLNKILLEDLRISMHDILPKCQETLKSFC--------------KK---KKMKKVVQFFKNTSLSISECCSFQQSC 930 (1238)
Q Consensus 868 ~v~~i~Ld~e~L~~~~lt~~~I~~~l~~~~~~~~--------------~~---~~~~~i~~~~~~~~i~~~g~~~~~~~~ 930 (1238)
|+++|+||++.|++++|++++|.+++.+...... .+ ....++.+.++++.+ +|+.++.++.
T Consensus 140 ~~l~i~ld~~~l~~~~i~~~~i~~~i~~~~~~~~~~~~~~~~~i~i~~~~~~~~~l~~l~~~l~~~~v--~Gi~gI~r~~ 217 (367)
T TIGR02389 140 MTVIIELDEEQLKERGITVDDVEKAIKKAKLGKVIEIDMDGNTITIKPPKPSLKELRKLKEKIKNLHI--KGIKGIKRVV 217 (367)
T ss_pred cEEEEEECHHHHHhcCCCHHHHHHHHHHhcccccceeecCCCEEEEEecCchHHHHHHHHHHhhhceE--eCCCCceEEE
Confidence 4689999999999999999999998887542110 00 001235567777777 8999999988
Q ss_pred cccCCCcceEEEEEeecC-----CcccccchhhcccchhhHHHHhhhchhHHHH----HHHHHHHhhhhccccccceeee
Q 000882 931 ADKRSNMPCLMFVLRGAS-----DSYLDKLSGVLANMIYPVLLETIIKENWWVR----QRLSASVTMVAKGVLKEHLILL 1001 (1238)
Q Consensus 931 ~~~~~~~~~lt~~~~~~~-----~~~~vd~~~~~sn~I~ei~r~tiikGi~w~R----~~l~~~~~~~~~~V~~rHl~Ll 1001 (1238)
+++++++|++ .++|++ ..++||..++++|+|++++ .+.|||++| +.|+++++.+|.+||+|||+|+
T Consensus 218 i~~~~~~~~l--~teG~nl~~v~~~~~VD~~rt~sNdI~ei~---~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~RHl~Li 292 (367)
T TIGR02389 218 IRKEGDEYVI--YTEGSNLKEVLKLEGVDKTRTTTNDIHEIA---EVLGIEAARNAIIEEIKRTLEEQGLDVDIRHLMLV 292 (367)
T ss_pred EECCCCeEEE--EEeccCHHHHHcCCCCccccCccCCHHHHH---HhcCHHHHHHHHHHHHHHHHHHcCCeecHHHHHHH
Confidence 8766666766 789988 6789999999999999999 779999999 5578888899999999999999
Q ss_pred cccccccceEeeecccccccccccccccccchhhcccChHHHHHHHHhhcCCCCCCcccchhccCCcccccccceEEEEe
Q 000882 1002 ANSMTCAGDLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGSRFDLLW 1081 (1238)
Q Consensus 1002 ad~MT~~G~~~~~~r~G~~~~~~s~l~~a~Fe~~t~~t~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~~f~l~~ 1081 (1238)
||+||++|++.|+||+|+++.+.|||++||||+ +.++|.+||.+|+.|.|+||+|||+||+++|+|||. |+|++
T Consensus 293 aD~MT~~G~~~~i~R~Gi~~~~~S~l~~aSFE~-----t~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~-~~l~~ 366 (367)
T TIGR02389 293 ADLMTWDGEVRQIGRHGISGEKASVLARAAFEV-----TVKHLLDAAIRGEVDELAGVIENIIVGQPIPLGTGD-VDLVM 366 (367)
T ss_pred HHHhcCCceEEeccccccccCCCCHHHhcChHh-----HHHHHHHHhhcCCCCcCCChHHHhhcCCCcCCcCCe-EEEee
Confidence 999999999999999999999999999999999 459999999999999999999999999999999999 99997
Q ss_pred c
Q 000882 1082 Q 1082 (1238)
Q Consensus 1082 ~ 1082 (1238)
+
T Consensus 367 ~ 367 (367)
T TIGR02389 367 D 367 (367)
T ss_pred C
Confidence 4
No 18
>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=3e-58 Score=477.58 Aligned_cols=158 Identities=45% Similarity=0.694 Sum_probs=133.9
Q ss_pred ccCCCCCcceeEeCCCCccccccccchhhhcccccccccchhhHHHHHHHHHcCCccccC-------CCCceEEeccCC-
Q 000882 253 RKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDNKLCLTYS-------DGSSSYSLREGS- 324 (1238)
Q Consensus 253 GKRVdfSaRsVIspDP~L~i~evGvP~~iA~~LT~pE~Vt~~Ni~~l~~lV~ng~~~~~~-------~~~~~~~l~~~~- 324 (1238)
||||||||||||||||+|+++|||||.+||++||+||.||.+|+++|+++|.||+. .|+ ..+.++.|+...
T Consensus 1 GKRVnfSaRSVItpDP~L~~~EvGiP~~iA~~Lt~Pe~Vt~~N~~~l~~~v~ng~~-~~pga~~i~~~~~~~~~l~~~~~ 79 (166)
T PF00623_consen 1 GKRVNFSARSVITPDPNLKIDEVGIPIEIAKKLTFPERVTPFNIEKLRKLVINGPD-KYPGANYIKRSNGNKISLRYKKF 79 (166)
T ss_dssp CEEESSEEEEEEEEETTSCTTEEEEEHHHHHHCECCHHHHTTTHHHHHHHHHHTTT-SSSSEEEEESTTCHCCCTTSSSS
T ss_pred CCCcccCCCcEEECCCCCccceecccHHHHhhCCCcEEEHHHHHHHHHHHHhcCcc-cchhhhhhhcccCcceeeeeccc
Confidence 89999999999999999999999999999999999999999999999999999986 221 122233333322
Q ss_pred CCcccccCcceeeeeeeccCeEeeeCCCCCCcccccceEEEecCCCeeeecccCCCCCCCccCccccccccCCCHHHHHH
Q 000882 325 KGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQSLAAKAE 404 (1238)
Q Consensus 325 ~~~~~L~~g~iV~Rhl~dgD~VL~NRqPSLHr~Simah~v~v~~~~T~rln~~vC~pyNADFDGDeMn~H~PQs~eAraE 404 (1238)
+....|++|++|+||+.|||+|||||||||||+|||||++++++++||||||++|+||||||||||||+|+|||++|+||
T Consensus 80 ~~~~~l~~~~~v~r~l~~gd~vl~nRqPtLh~~s~~a~~~~~~~~~t~~~~~~~c~~~NADFDGDem~i~~p~~~~a~~E 159 (166)
T PF00623_consen 80 KISKKLRIGDIVERHLCDGDIVLLNRQPTLHRMSIMAHKVRVLPGKTIRINPLVCSPFNADFDGDEMNIHLPQSYEARAE 159 (166)
T ss_dssp CCCHHHHTT-EEEEEHTTT-EEEEEESS-SSGGGEEEEEEEEESSSSEEEEGGGHHHHT--TSS-EEEEE--SSHHHHHH
T ss_pred cccceecchhhHHHhhhcCceeEEeccchhccceeeeeeeeeecccEEEeeccchhhhhccCCcceEEEEecCCHHHHHH
Confidence 12356788999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhcc
Q 000882 405 VLELFSV 411 (1238)
Q Consensus 405 a~~Lm~~ 411 (1238)
|.+||++
T Consensus 160 ~~~L~~~ 166 (166)
T PF00623_consen 160 AKELMNV 166 (166)
T ss_dssp HHHHCBT
T ss_pred HHHHhcC
Confidence 9999985
No 19
>PRK04309 DNA-directed RNA polymerase subunit A''; Validated
Probab=100.00 E-value=1.5e-56 Score=517.31 Aligned_cols=335 Identities=19% Similarity=0.229 Sum_probs=290.2
Q ss_pred hhHHHHHHHheeEEEecceEeccCCCceeeeeeecccccccCcCCCCCeeeeeccccCCchHHHhhhccCC-------CC
Q 000882 716 LFKNLMAVLRDVVICYDGTVRNVCSNSIIQFDYAVNARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDSSP-------SS 788 (1238)
Q Consensus 716 L~RrLv~~l~d~~v~YD~tvr~~~~~~iiqf~yg~dg~~~~~lv~~Ge~VG~laaqsigep~tq~~l~t~~-------~~ 788 (1238)
|+.++.+.+++-...|..|.... ..++..++..+ .+++++||||||++||||||||+|||||+||+ ++
T Consensus 18 ~~~~~~~~~~~~~~~~~l~~~~~--~~~~~~i~~~y---~~~~v~pGe~VG~iaAQsIGEP~TQMTL~TFH~AGva~~nV 92 (383)
T PRK04309 18 LPQKLKEELREKLEERKLTEEEV--EEIIEEVVREY---LRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINV 92 (383)
T ss_pred CCHHHHHHHHHHHHHcCCCHHHH--HHHHHHHHHHH---HHhhcCCCCccchhhhhhccchhhhcccccccccCccccCc
Confidence 89999999988888877665544 55666666666 57789999999999999999999999999975 88
Q ss_pred CCchHHHHHHHHhhccCCCCCCCceEEEEcCCCCCCCccccHHHHHHHHhhhceechhhhhheeeEEecCCccccCCCce
Q 000882 789 NNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIISDDEGL 868 (1238)
Q Consensus 789 ~~g~~rlkEil~~~~~~k~~~~d~~~~l~L~~~~~~~~~~~e~~a~~V~~~le~vtl~dv~~~i~i~y~~~~~~~~~~~~ 868 (1238)
|+|+||||||++++++ +++|.|++||.++++ .++++|+.|+.+||+++|++++..+.+.|.. +
T Consensus 93 TlGvPRlkEIina~K~----~~TP~~tv~L~~~~~----~d~~~a~~v~~~iE~t~L~~v~~~i~~~~~~---------~ 155 (383)
T PRK04309 93 TLGLPRLIEIVDARKE----PSTPMMTIYLKDEYA----YDREKAEEVARKIEATTLENLAKDISVDLAN---------M 155 (383)
T ss_pred ccCchhHHHHHhcccC----CCCCeEEEEecCccc----ccHHHHHHHHhheeeeEHhhhhhheEeccCC---------c
Confidence 9999999999999885 567799999987754 4788999999999999999999999987653 2
Q ss_pred EEEEEecHHHHhhcCCCHhhHHHHHHHhhhhh----------h-hh---hhhHHHHHhhccceeeccccccccccccccC
Q 000882 869 VGHIHLNKILLEDLRISMHDILPKCQETLKSF----------C-KK---KKMKKVVQFFKNTSLSISECCSFQQSCADKR 934 (1238)
Q Consensus 869 v~~i~Ld~e~L~~~~lt~~~I~~~l~~~~~~~----------~-~~---~~~~~i~~~~~~~~i~~~g~~~~~~~~~~~~ 934 (1238)
+++|+||++.|.+++|++++|.+++.+..... . .. ....++.+.++++.+ +|+.+++++.++++
T Consensus 156 ~l~i~ld~~~i~~~~l~~~~I~~~i~~~~~~~~~~~~~~i~i~~~~~~~~~l~~l~~~l~~~~v--kGi~gI~r~~i~~~ 233 (383)
T PRK04309 156 TIIIELDEEMLEDRGLTVDDVKEAIEKKKGGEVEIEGNTLIISPKEPSYRELRKLAEKIRNIKI--KGIKGIKRVIIRKE 233 (383)
T ss_pred EEEEEECHHHHHHcCCCHHHHHHHHHHhcCcceeccCCeEEEEecCchHHHHHHHHHHhcccEE--ECCCCceEEEEecC
Confidence 58999999999999999999999888754211 0 00 011245577777777 89999999888776
Q ss_pred CCcceEEEEEeecC-----CcccccchhhcccchhhHHHHhhhchhHHHH----HHHHHHHhhhhccccccceeeecccc
Q 000882 935 SNMPCLMFVLRGAS-----DSYLDKLSGVLANMIYPVLLETIIKENWWVR----QRLSASVTMVAKGVLKEHLILLANSM 1005 (1238)
Q Consensus 935 ~~~~~lt~~~~~~~-----~~~~vd~~~~~sn~I~ei~r~tiikGi~w~R----~~l~~~~~~~~~~V~~rHl~Llad~M 1005 (1238)
+++|++ .++|.+ ..++||+.++++|+|++|+ .+.|||++| +.|.++++.+|.+||+|||+||||.|
T Consensus 234 ~~~~~l--~teG~nl~~v~~~~~VD~~rt~sNdI~ei~---~vlGIEAAR~~ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~M 308 (383)
T PRK04309 234 GDEYVI--YTEGSNLKEVLKVEGVDATRTTTNNIHEIE---EVLGIEAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMM 308 (383)
T ss_pred CCeEEE--EEcccCHHHHhcCCCEeeccccCCCHHHHH---HHcCHHHHHHHHHHHHHHHHHHcCCeecHHHHHHHHHHh
Confidence 666766 688887 6899999999999999999 789999999 56788888999999999999999999
Q ss_pred cccceEeeecccccccccccccccccchhhcccChHHHHHHHHhhcCCCCCCcccchhccCCcccccccceEEEEecCCC
Q 000882 1006 TCAGDLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGSRFDLLWQTEN 1085 (1238)
Q Consensus 1006 T~~G~~~~~~r~G~~~~~~s~l~~a~Fe~~t~~t~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~~f~l~~~~~~ 1085 (1238)
|++|++.|+||+|+++.+.|||++||||+ +.++|.+||.+|+.|+|+||+|||+|||++|+|||+ |+|+++.+.
T Consensus 309 T~~G~~~~i~R~Gi~~~~~S~l~~aSFE~-----T~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~-~~l~~~~~~ 382 (383)
T PRK04309 309 TWDGEVRQIGRHGVSGEKASVLARAAFEV-----TVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTGD-VELTMDPPL 382 (383)
T ss_pred ccCceEEeeechhhcCCCCCHHHhCchhh-----HHHHHHHHHhcCCCCCCCCcHHHhhcCCCcCCCCce-EEEEcCCCC
Confidence 99999999999999999999999999999 449999999999999999999999999999999999 999998754
No 20
>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=2.9e-56 Score=511.70 Aligned_cols=308 Identities=20% Similarity=0.244 Sum_probs=266.8
Q ss_pred ceeeeeeecccccccCcCCCCCeeeeeccccCCchHHHhhhccCC-------CCCCchHHHHHHHHhhccCCCCCCCceE
Q 000882 742 SIIQFDYAVNARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDSSP-------SSNNSWELMKEILLCRVSFNNDPIDRRV 814 (1238)
Q Consensus 742 ~iiqf~yg~dg~~~~~lv~~Ge~VG~laaqsigep~tq~~l~t~~-------~~~~g~~rlkEil~~~~~~k~~~~d~~~ 814 (1238)
.++..+.-.+ .+++++|||+||++||||||||+|||||+||+ |+|+|+||||||++++++ +++|.|
T Consensus 23 ~~~~~~~~~~---~~~~~~~Ge~vG~iaAQSiGEP~TQMTLnTFH~AGVas~nVTlGVPRlkEIIna~K~----i~TP~m 95 (363)
T cd06528 23 EIIKEVLREY---LRSLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRLIEIVDARKE----PSTPTM 95 (363)
T ss_pred HHHHHHHHHH---HHHhhccCccccceeeeecCccceecccccccccccccccCccccccHHHHhhcccC----CCCceE
Confidence 3444444444 46789999999999999999999999999975 889999999999999886 456799
Q ss_pred EEEcCCCCCCCccccHHHHHHHHhhhceechhhhhheeeEEecCCccccCCCceEEEEEecHHHHhhcCCCHhhHHHHHH
Q 000882 815 ILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIISDDEGLVGHIHLNKILLEDLRISMHDILPKCQ 894 (1238)
Q Consensus 815 ~l~L~~~~~~~~~~~e~~a~~V~~~le~vtl~dv~~~i~i~y~~~~~~~~~~~~v~~i~Ld~e~L~~~~lt~~~I~~~l~ 894 (1238)
++||.+.+. .++++|++|+++||+++|+|++..+.++|+ .|+++|+||++.|.+++|++++|++++.
T Consensus 96 ti~L~~~~~----~~~~~a~~v~~~iE~t~l~di~~~~~i~~~---------~~~l~i~ld~~~l~~~~l~~~~i~~~i~ 162 (363)
T cd06528 96 TIYLEEEYK----YDREKAEEVARKIEETTLENLAEDISIDLF---------NMRITIELDEEMLEDRGITVDDVLKAIE 162 (363)
T ss_pred EEEecCcch----hhHHHHHHHHHhhceeEHHHhhhheEEecc---------CcEEEEEECHHHHHHcCCCHHHHHHHHH
Confidence 999987654 377899999999999999999999999764 3679999999999999999999999988
Q ss_pred Hhhhhhh---h---------hh----hhHHHHHhhccceeeccccccccccccccCCCcceEEEEEeecC-----Ccccc
Q 000882 895 ETLKSFC---K---------KK----KMKKVVQFFKNTSLSISECCSFQQSCADKRSNMPCLMFVLRGAS-----DSYLD 953 (1238)
Q Consensus 895 ~~~~~~~---~---------~~----~~~~i~~~~~~~~i~~~g~~~~~~~~~~~~~~~~~lt~~~~~~~-----~~~~v 953 (1238)
+..+... . .. ....+.+.++++.+ +|+.++.++.+++++++|++ .++|++ ..+++
T Consensus 163 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~~~v--~Gi~gI~r~~i~~~~~~~~l--~teG~nl~~v~~~~~V 238 (363)
T cd06528 163 KLKKGKVGEEGDVTLIVLKAEEPSIKELRKLAEKILNTKI--KGIKGIKRVIVRKEEDEYVI--YTEGSNLKAVLKVEGV 238 (363)
T ss_pred HhcCCcccccCCccEEEEcCCcchHHHHHHHHHhhcccEE--eCCCCceEEEEecCCceEEE--EecCcCHHHHhcCCCC
Confidence 7642210 0 00 01245677778777 89999999888776666666 788987 67899
Q ss_pred cchhhcccchhhHHHHhhhchhHHHH----HHHHHHHhhhhccccccceeeecccccccceEeeeccccccccccccccc
Q 000882 954 KLSGVLANMIYPVLLETIIKENWWVR----QRLSASVTMVAKGVLKEHLILLANSMTCAGDLVGFNSGGYKALSRSLNVQ 1029 (1238)
Q Consensus 954 d~~~~~sn~I~ei~r~tiikGi~w~R----~~l~~~~~~~~~~V~~rHl~Llad~MT~~G~~~~~~r~G~~~~~~s~l~~ 1029 (1238)
|..++++|+|.+++ .+.|||++| +.|+++++.+|.+||+|||+||||+||++|++.|+||+|+.+.+.|||++
T Consensus 239 d~~rt~sNdI~ei~---~~lGIEAaR~~ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~G~~~~i~R~gi~~~~~S~L~~ 315 (363)
T cd06528 239 DPTRTTTNNIHEIE---EVLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVRQIGRHGIAGEKPSVLAR 315 (363)
T ss_pred cccccccCCHHHHH---HhCCHHHHHHHHHHHHHHHHHhcCCeecHHHHHHHHHHhccCCceecccchhhcCCCCChhhh
Confidence 99999999999999 779999999 56788888999999999999999999999999999999999999999999
Q ss_pred ccchhhcccChHHHHHHHHhhcCCCCCCcccchhccCCcccccccceEEEEec
Q 000882 1030 VPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGSRFDLLWQ 1082 (1238)
Q Consensus 1030 a~Fe~~t~~t~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~~f~l~~~ 1082 (1238)
||||+ +.++|.+||.+|+.|+|+||+|||+|||++|+|||+ |||+++
T Consensus 316 aSFE~-----t~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~-~~l~~d 362 (363)
T cd06528 316 AAFEV-----TVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTGD-VELTMD 362 (363)
T ss_pred Cchhh-----HHHHHHHHHhcCCCCcCCCcHHHeeeCCCCCCcCCe-eEEEec
Confidence 99999 449999999999999999999999999999999999 999986
No 21
>PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Probab=100.00 E-value=2.3e-56 Score=520.87 Aligned_cols=334 Identities=16% Similarity=0.188 Sum_probs=284.1
Q ss_pred hhHHHHHHHheeEEEecceEeccCCCceeeeeeecccccccCcCCCCCeeeeeccccCCchHHHhhhccCC-------CC
Q 000882 716 LFKNLMAVLRDVVICYDGTVRNVCSNSIIQFDYAVNARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDSSP-------SS 788 (1238)
Q Consensus 716 L~RrLv~~l~d~~v~YD~tvr~~~~~~iiqf~yg~dg~~~~~lv~~Ge~VG~laaqsigep~tq~~l~t~~-------~~ 788 (1238)
|+.++.+.|++....|..|.... ..++..+.-.+ .+++++|||+||++||||||||+|||||+||+ ++
T Consensus 141 lp~~~~~el~~~~~~~~l~~~~~--~~i~~ei~~~y---~~~~v~pGE~VG~IAAQSIGEP~TQMTLnTFH~AGVas~NV 215 (509)
T PRK14897 141 LPPSVIEEIAKAMKKKELSDDEY--EEILRRIREEY---ERARVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEMNV 215 (509)
T ss_pred CCHHHHHHHHHHHHHcCCCHHHH--HHHHHHHHHHH---HHhccCCCCCcchhhhhhhCCcccccccccccccccccccc
Confidence 89999999999887777665543 56666666666 67889999999999999999999999999975 88
Q ss_pred CCchHHHHHHHHhhccCCCCCCCceEEEEcCCCCCCCccccHHHHHHHHhhhceechhhhhheeeEEecCCccccCCCce
Q 000882 789 NNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIISDDEGL 868 (1238)
Q Consensus 789 ~~g~~rlkEil~~~~~~k~~~~d~~~~l~L~~~~~~~~~~~e~~a~~V~~~le~vtl~dv~~~i~i~y~~~~~~~~~~~~ 868 (1238)
|+|+|||+||++++++ +++|.|++||.+.+. .++++|++|+++||+++|+|++..+ .+| ..|
T Consensus 216 TlGVPRLkEIINa~K~----isTP~mtiyL~~~~~----~d~e~A~~V~~~IE~ttL~dv~~~~-~d~---------~~~ 277 (509)
T PRK14897 216 TLGLPRLIEIVDARKK----PSTPTMTIYLKKDYR----EDEEKVREVAKKIENTTLIDVADII-TDI---------AEM 277 (509)
T ss_pred ccCcchhHHHhhcccC----CCCceEEEEecCccc----ccHHHHHHHHhhheeeEHHHHHHHH-HHh---------ccc
Confidence 9999999999999886 556799999987654 4788999999999999999999633 223 234
Q ss_pred EEEEEecHHHHhhcCCCHhhHHHHHHHhh-hhh----------hhh---hhhHHHHHhhccceeeccccccccccccccC
Q 000882 869 VGHIHLNKILLEDLRISMHDILPKCQETL-KSF----------CKK---KKMKKVVQFFKNTSLSISECCSFQQSCADKR 934 (1238)
Q Consensus 869 v~~i~Ld~e~L~~~~lt~~~I~~~l~~~~-~~~----------~~~---~~~~~i~~~~~~~~i~~~g~~~~~~~~~~~~ 934 (1238)
.+.|+||+++|.+++|++++|.+++.+.. ... ... ....++...++++.+ +|+.++.++.++++
T Consensus 278 ~i~i~Ld~~~l~~~~l~~~~I~~~I~~~~~~~~~~~~~~I~i~~~~~~~~~L~~l~~~l~~i~I--~GipgI~r~~i~~~ 355 (509)
T PRK14897 278 SVVVELDEEKMKERLIEYDDILAAISKLTFKTVEIDDGIIRLKPQQPSFKKLYLLAEKVKSLTI--KGIKGIKRAIARKE 355 (509)
T ss_pred eEEEEECHHHHHHcCCCHHHHHHHHHhccceEEecCCCEEEEEeCchHHHHHHHHHHHhhccEE--eCCCCccEEEEecC
Confidence 58999999999999999999999987721 000 010 012345566777777 89999999888765
Q ss_pred CCc--ceEEEEEeecC-----CcccccchhhcccchhhHHHHhhhchhHHHH----HHHHHHHhhhhccccccceeeecc
Q 000882 935 SNM--PCLMFVLRGAS-----DSYLDKLSGVLANMIYPVLLETIIKENWWVR----QRLSASVTMVAKGVLKEHLILLAN 1003 (1238)
Q Consensus 935 ~~~--~~lt~~~~~~~-----~~~~vd~~~~~sn~I~ei~r~tiikGi~w~R----~~l~~~~~~~~~~V~~rHl~Llad 1003 (1238)
++. |+| .++|++ ..++||..+|+||+|++|+ .+.|||++| +.|+.+++.+|.+||+|||+||||
T Consensus 356 ~~~~~~~L--~TeG~NL~~vl~~~~VD~~rt~SNdI~eI~---~vlGIEAAR~~Ii~Ei~~V~~~~Gi~Vd~RHL~LIAD 430 (509)
T PRK14897 356 NDERRWVI--YTQGSNLKDVLEIDEVDPTRTYTNDIIEIA---TVLGIEAARNAIIHEAKRTLQEQGLNVDIRHIMLVAD 430 (509)
T ss_pred CCCceeEE--EeeccCHHHHhcCCCcccccCccCCHHHHH---HhcCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHH
Confidence 543 555 899988 6899999999999999999 789999999 457888888999999999999999
Q ss_pred cccccceEeeecccccccccccccccccchhhcccChHHHHHHHHhhcCCCCCCcccchhccCCcccccccceEEEEecC
Q 000882 1004 SMTCAGDLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGSRFDLLWQT 1083 (1238)
Q Consensus 1004 ~MT~~G~~~~~~r~G~~~~~~s~l~~a~Fe~~t~~t~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~~f~l~~~~ 1083 (1238)
+||++|++.|+||||+++.+.|||++||||+ +.++|.+||.+|+.|.|+||+|||+|||++|+|||. |+|+++.
T Consensus 431 ~MT~~G~v~~i~R~Gi~~~~~SpL~rASFE~-----T~~~L~~AA~~Ge~D~L~GvsenII~G~~ipvGTG~-fdL~~~~ 504 (509)
T PRK14897 431 MMTFDGSVKAIGRHGISGEKSSVLARAAFEI-----TGKHLLRAGILGEVDKLAGVAENIIVGQPITLGTGA-VSLVYKG 504 (509)
T ss_pred HhCcCCcccccccccccccCCCHHHhcchHh-----HHHHHHHHhhcCCCCcCCChHHhhhcCCccCCcCce-EEEEecC
Confidence 9999999999999999999999999999999 459999999999999999999999999999999999 9999976
Q ss_pred CC
Q 000882 1084 EN 1085 (1238)
Q Consensus 1084 ~~ 1085 (1238)
++
T Consensus 505 ~~ 506 (509)
T PRK14897 505 RK 506 (509)
T ss_pred CC
Confidence 54
No 22
>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=2.2e-54 Score=502.44 Aligned_cols=307 Identities=22% Similarity=0.249 Sum_probs=264.0
Q ss_pred ccCcCCCCCeeeeeccccCCchHHHhhhccCC-------CCCCchHHHHHHHHhhccCCCCCCCceEEEEcCCCCCCCcc
Q 000882 755 SHSLFPAGEPVGVLAATAMSNPAYKAVLDSSP-------SSNNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKY 827 (1238)
Q Consensus 755 ~~~lv~~Ge~VG~laaqsigep~tq~~l~t~~-------~~~~g~~rlkEil~~~~~~k~~~~d~~~~l~L~~~~~~~~~ 827 (1238)
.+++++|||+||++||||||||+|||||+||+ ++|+|+||||||++++++ +++|.|++||.+.+.
T Consensus 20 ~~~~~~~ge~vg~~aaQSiGEP~TQmTLnTFH~AGVas~NVTlGVPRLkEIInasK~----ikTP~~tv~L~~~~~---- 91 (410)
T cd02584 20 NRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKN----IKTPSLTVYLEPGFA---- 91 (410)
T ss_pred HHhhcCCCCCcchhhhhhcCCchhcccccccccccccccccccCccchHHHhhcccC----CCCCeEEEEecCccc----
Confidence 46788999999999999999999999999974 889999999999999886 556799999987754
Q ss_pred ccHHHHHHHHhhhceechhhhhheeeEEecCCcccc-----------------------CCCceEEEEEecHHHHhhcCC
Q 000882 828 CQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIIS-----------------------DDEGLVGHIHLNKILLEDLRI 884 (1238)
Q Consensus 828 ~~e~~a~~V~~~le~vtl~dv~~~i~i~y~~~~~~~-----------------------~~~~~v~~i~Ld~e~L~~~~l 884 (1238)
.++++|++|+.+||+++|+|++..+.+.|+|+...+ ..+||+++++||++.|.+++|
T Consensus 92 ~d~~~A~~v~~~IE~t~l~dv~~~~~i~ydp~~~~~~i~~d~~~i~~~~~~~d~~~~~~~~~~~~lrl~ld~~~~~~~~i 171 (410)
T cd02584 92 KDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVESYFEFPDEDVEQDRLSPWLLRIELDRKKMTDKKL 171 (410)
T ss_pred chHHHHHHHHhheeEeEHHHhhhheEEEecCcccceeecccHHHHHHhhccCcccccccccCCeeEEEEECHHHHHHcCC
Confidence 478899999999999999999999999999986532 137999999999999999999
Q ss_pred CHhhHHHHHHHhhhhh---------------h---h-hh---h--------hHH-HHHhhccceeecccccccccccccc
Q 000882 885 SMHDILPKCQETLKSF---------------C---K-KK---K--------MKK-VVQFFKNTSLSISECCSFQQSCADK 933 (1238)
Q Consensus 885 t~~~I~~~l~~~~~~~---------------~---~-~~---~--------~~~-i~~~~~~~~i~~~g~~~~~~~~~~~ 933 (1238)
++++|+.++++.++.. + . .. . ..+ +.+.++++.+ +|+.++.++++++
T Consensus 172 ~~~~i~~~i~~~~~~~~~v~~~~~~~~~~~iri~~~~~~~~~~~~~~~~~~l~~~~~~~l~~i~l--~Gi~~I~r~~i~~ 249 (410)
T cd02584 172 SMEQIAKKIKEEFKDDLNVIFSDDNAEKLVIRIRIINDDEEKEEDSEDDVFLKKIESNMLSDMTL--KGIEGIRKVFIRE 249 (410)
T ss_pred CHHHHHHHHHHhcCCCeEEEEcCCCcceeEEEEEecCccccccccchhHHHHHHHHHhhCCCcEE--eCCCCceEEEEEc
Confidence 9999999888643200 0 0 00 0 001 2356677777 8888888877754
Q ss_pred C--------------CCcceEEEEEeecC-----CcccccchhhcccchhhHHHHhhhchhHHHH----HHHHHHHhhhh
Q 000882 934 R--------------SNMPCLMFVLRGAS-----DSYLDKLSGVLANMIYPVLLETIIKENWWVR----QRLSASVTMVA 990 (1238)
Q Consensus 934 ~--------------~~~~~lt~~~~~~~-----~~~~vd~~~~~sn~I~ei~r~tiikGi~w~R----~~l~~~~~~~~ 990 (1238)
+ .+.|++ .++|++ ..++||..++++|+|++|+ .+.|||++| +.|..+++.+|
T Consensus 250 ~~~~~~~~~~g~~~~~~~~~l--~teG~nl~~v~~~~~Vd~~rt~sNdI~ei~---~~lGIEAaR~~ii~Ei~~v~~~~G 324 (410)
T cd02584 250 ENKKKVDIETGEFKKREEWVL--ETDGVNLREVLSHPGVDPTRTTSNDIVEIF---EVLGIEAARKALLKELRNVISFDG 324 (410)
T ss_pred CCceEecCCCCcccCCcceEE--EecCcCHHHHhCCCCCccccCEeCCHHHHH---HhcCHHHHHHHHHHHHHHHHHhcC
Confidence 2 124555 788987 6789999999999999999 789999999 45788888889
Q ss_pred ccccccceeeecccccccceEeeecccccccccccccccccchhhcccChHHHHHHHHhhcCCCCCCcccchhccCCccc
Q 000882 991 KGVLKEHLILLANSMTCAGDLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVA 1070 (1238)
Q Consensus 991 ~~V~~rHl~Llad~MT~~G~~~~~~r~G~~~~~~s~l~~a~Fe~~t~~t~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~ 1070 (1238)
.+||+|||+||||+||++|+++||||+|+++.+.|||++||||+ +.++|.+||.+|+.|+|+||+|||+||+++|
T Consensus 325 i~Vd~RHl~LiaD~MT~~G~~~~i~R~Gi~~~~~S~l~~aSFE~-----t~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~ 399 (410)
T cd02584 325 SYVNYRHLALLCDVMTQRGHLMAITRHGINRQDTGPLMRCSFEE-----TVDILLEAAAFGETDDLKGVSENIMLGQLAP 399 (410)
T ss_pred CccCHHHHHHHHHHHhhceEEeeEeeeeeeccCCChhhhccchh-----HHHHHHHHHhcCCCCcCCCchHheeecCccc
Confidence 99999999999999999999999999999999999999999999 4499999999999999999999999999999
Q ss_pred ccccceEEEEec
Q 000882 1071 VGTGSRFDLLWQ 1082 (1238)
Q Consensus 1071 ~GTG~~f~l~~~ 1082 (1238)
+|||+ |||++|
T Consensus 400 ~GTG~-f~l~~d 410 (410)
T cd02584 400 IGTGC-FDLLLD 410 (410)
T ss_pred cccce-EEEEeC
Confidence 99999 999985
No 23
>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=4.4e-53 Score=486.89 Aligned_cols=308 Identities=37% Similarity=0.545 Sum_probs=241.6
Q ss_pred CCeeeeeccccCCchHHHhhhccCCCCC-CchHHHHHHHHhhccCCCCCCCceEEEEcC--CCCCCCccccHHHHHHHHh
Q 000882 762 GEPVGVLAATAMSNPAYKAVLDSSPSSN-NSWELMKEILLCRVSFNNDPIDRRVILYLN--DCGCGRKYCQERAAYMVKN 838 (1238)
Q Consensus 762 Ge~VG~laaqsigep~tq~~l~t~~~~~-~g~~rlkEil~~~~~~k~~~~d~~~~l~L~--~~~~~~~~~~e~~a~~V~~ 838 (1238)
|||||+|||||||||||||||+|++... ++||||||+|+++++.+ +++|++++||. .|.|.+.|+.+++|++||+
T Consensus 1 GE~VG~LAAqSIgEPAtQmtLntfh~agvs~vprLKEiLn~~~~~~--~ktps~~v~L~~~~~~~~~~~~~~~~a~~Vq~ 78 (381)
T cd02737 1 GEPVGSLAATAISEPAYKALLDPPQSLESSPLELLKEVLECRSKSK--SKENDRRVILSLHLCKCDHGFEYERAALEVKN 78 (381)
T ss_pred CCcchhHHHhhhcchHHHhhhccchhcCCccHHHHHHHhcccccCC--CCCCCEEEEEeccccccccchHHHHHHHHHHH
Confidence 8999999999999999999999998654 58999999999977544 44556666665 4677777776789999999
Q ss_pred hhceechhhhhheeeEEecCCcccc----------------------------CCCceEEEEEecHHHHhhcCCC-HhhH
Q 000882 839 QLKRVSLKDAAVEFLIEYKKPEIIS----------------------------DDEGLVGHIHLNKILLEDLRIS-MHDI 889 (1238)
Q Consensus 839 ~le~vtl~dv~~~i~i~y~~~~~~~----------------------------~~~~~v~~i~Ld~e~L~~~~lt-~~~I 889 (1238)
+||+++|++++++++|+|+|+...+ .-+||++||+||++.-....+. +...
T Consensus 79 ~Le~~tL~~v~~~~~I~Ydp~~~~t~i~~d~~~~~~~~~~~~~~~~~~~~~~~~~spw~~r~~l~~~~~~~~~~~ci~~~ 158 (381)
T cd02737 79 HLERVTLEDLATTSMIKYSPQATEAIVGEIGDQLNTKKKGKKKAIFSTSLKITKFSPWVCHFHLDKECQKLSDGPCLTFS 158 (381)
T ss_pred HhhhccHHHhhheEEEEECCCcccccccccHHHHHhhhhhhhhcccccccccccCCcceEEEEEehhHhcCCCCceEEee
Confidence 9999999999999999999994322 1389999999998733222111 0000
Q ss_pred HH-----HHHHhhhhhhhhhhhHHHHHhhccceeeccccccccccccc--c-------------CCCcceEEEEEe----
Q 000882 890 LP-----KCQETLKSFCKKKKMKKVVQFFKNTSLSISECCSFQQSCAD--K-------------RSNMPCLMFVLR---- 945 (1238)
Q Consensus 890 ~~-----~l~~~~~~~~~~~~~~~i~~~~~~~~i~~~g~~~~~~~~~~--~-------------~~~~~~lt~~~~---- 945 (1238)
.. ........+ ...+-..+-++.+ +|+..++++.+. + ...+|+|...++
T Consensus 159 ~~~~~~~~~~~~~~~~-----~~~i~~~lL~~~l--kG~~~I~kv~i~~~~~~~~~~~~~~~~~~~~E~vLe~~~~~~~~ 231 (381)
T cd02737 159 VSKEVSKSSEELLDVL-----RDRIIPFLLETVI--KGDERIKSVNILWEDSPSTSWVKSVGKSSRGELVLEVTVEESCK 231 (381)
T ss_pred cCcccccchhHHHHHH-----HHHHHHHHhheee--cccCCeeEEEEEecCCCcccccccccccccceEEEEEEeccccc
Confidence 00 000000000 0112233334444 787777776654 1 113677755433
Q ss_pred ---ecC----------CcccccchhhcccchhhHHHHhhhchhHHHH----HHHHHHHhhhhccccccceeeeccccccc
Q 000882 946 ---GAS----------DSYLDKLSGVLANMIYPVLLETIIKENWWVR----QRLSASVTMVAKGVLKEHLILLANSMTCA 1008 (1238)
Q Consensus 946 ---~~~----------~~~~vd~~~~~sn~I~ei~r~tiikGi~w~R----~~l~~~~~~~~~~V~~rHl~Llad~MT~~ 1008 (1238)
|.+ -.+++|..|+++|+|.+|. .+.|||++| ++|..+++++|++||+|||+||||+||++
T Consensus 232 ~t~G~~~~~vl~~c~~~~~~ID~~rt~sNdI~ev~---~~lGIEAAR~~ii~El~~v~~~~G~~Vd~rHL~LlAD~MT~~ 308 (381)
T cd02737 232 KTRGNAWNVVMDACIPVMDLIDWERSMPYSIQQIK---SVLGIDAAFEQFVQRLESAVSMTGKSVLREHLLLVADSMTYS 308 (381)
T ss_pred cccchhHHHHHHhhhcccccCcCCCcEECCHHHHH---HHHhHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHhccC
Confidence 332 2689999999999999999 789999999 66888999999999999999999999999
Q ss_pred ceEeeecccccccccccccccccchhhcccChHHHHHHHHhhcCCCCCCcccchhccCCcccccccceEEEEe
Q 000882 1009 GDLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGSRFDLLW 1081 (1238)
Q Consensus 1009 G~~~~~~r~G~~~~~~s~l~~a~Fe~~t~~t~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~~f~l~~ 1081 (1238)
|+++||||+||+++++|....+||.+|||+++.++|++||.+|+.|+|+||++||+|||++|+|||++|||+|
T Consensus 309 G~~~~~nR~Gi~~~~~s~~~~spl~~asFE~t~~~l~~AA~~g~~D~l~gvs~~ii~G~~~~vGTG~~fdll~ 381 (381)
T cd02737 309 GEFVGLNAKGYKAQRRSLKISAPFTEACFSSPIKCFLKAAKKGASDSLSGVLDACAWGKEAPVGTGSKFEILW 381 (381)
T ss_pred CceEEecchhhhhcccccccCCHHHHhhHHHHHHHHHHHHhccCCCCCCChHHheeeCCcCCCcCCcceeeeC
Confidence 9999999999999999888888888888888999999999999999999999999999999999997799987
No 24
>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=6.4e-53 Score=473.14 Aligned_cols=279 Identities=19% Similarity=0.232 Sum_probs=246.9
Q ss_pred cCcCCCCCeeeeeccccCCchHHHhhhccCC-------CCCCchHHHHHHHHhhccCCCCCCCceEEEEcCCCCCCCccc
Q 000882 756 HSLFPAGEPVGVLAATAMSNPAYKAVLDSSP-------SSNNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYC 828 (1238)
Q Consensus 756 ~~lv~~Ge~VG~laaqsigep~tq~~l~t~~-------~~~~g~~rlkEil~~~~~~k~~~~d~~~~l~L~~~~~~~~~~ 828 (1238)
+++++|||+||++||||||||+|||||+||+ ++|+|+||||||++++++ +++|.|++||.+. .
T Consensus 4 ~~~v~pGe~vG~iaaQsiGEp~TQmTL~TFH~aGv~~~nvtlGvPRlkEIinasK~----~~TP~~ti~l~~~------~ 73 (300)
T cd02736 4 RAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKN----ISTPIITAKLEND------R 73 (300)
T ss_pred hhccCCCccchhhhhhhcCCccccccccccccccccccccccCchHHHHHHhcccC----CCCCeEEEEecCc------c
Confidence 5678999999999999999999999999974 889999999999999886 5566999999873 4
Q ss_pred cHHHHHHHHhhhceechhhhhheeeEEecCCccccCCCceEEEEEecHHHHhhcCCCHhhHHHHHHHhhhhhhhhhhhHH
Q 000882 829 QERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIISDDEGLVGHIHLNKILLEDLRISMHDILPKCQETLKSFCKKKKMKK 908 (1238)
Q Consensus 829 ~e~~a~~V~~~le~vtl~dv~~~i~i~y~~~~~~~~~~~~v~~i~Ld~e~L~~~~lt~~~I~~~l~~~~~~~~~~~~~~~ 908 (1238)
++++|+.|+.+||+++|+|++..+.+.|+|+.. .+.|++|++.+++++++.+...-.+ ..
T Consensus 74 ~~~~a~~v~~~ie~t~l~di~~~~~~~~~p~~~-------~~~i~~d~~~i~~~~l~~~~~~~~~-------------~~ 133 (300)
T cd02736 74 DEKSARIVKGRIEKTYLGEVASYIEEVYSPDDC-------YILIKLDKKIIEKLQLSKSNLYFLL-------------QS 133 (300)
T ss_pred cHHHHHHHHHHHhhccHHHhhhheEEEEcCCCc-------eEEEEecHHHHHHhcCCcccHHHHH-------------HH
Confidence 789999999999999999999999999999875 6799999999999999543322111 12
Q ss_pred HHHhhccceeeccccccccccccccCC--CcceEEEEEeecC-----CcccccchhhcccchhhHHHHhhhchhHHHH--
Q 000882 909 VVQFFKNTSLSISECCSFQQSCADKRS--NMPCLMFVLRGAS-----DSYLDKLSGVLANMIYPVLLETIIKENWWVR-- 979 (1238)
Q Consensus 909 i~~~~~~~~i~~~g~~~~~~~~~~~~~--~~~~lt~~~~~~~-----~~~~vd~~~~~sn~I~ei~r~tiikGi~w~R-- 979 (1238)
+.+.++++.+ +|+.++.++.+++++ +.|+| .++|++ ..++||..++++|+|.+++ .+.|||++|
T Consensus 134 l~~~l~~~~v--~Gi~gI~r~~i~~~~~~~~~~l--~teG~nl~~v~~~~~Vd~~rt~sNdI~ei~---~~lGIEAaR~~ 206 (300)
T cd02736 134 LKRKLPDVVV--SGIPEVKRAVINKDKKKGKYKL--LVEGYGLRAVMNTPGVIGTRTTSNHIMEVE---KVLGIEAARST 206 (300)
T ss_pred HHHHhccceE--eCCCCceEEEEecCCCCCcEEE--EEecccHHHHhcCCcEeccCCccCCHHHHH---HhcCHHHHHHH
Confidence 4567777777 888888887776654 45665 788987 6889999999999999999 789999999
Q ss_pred --HHHHHHHhhhhccccccceeeecccccccceEeeecccccccccccccccccchhhcccChHHHHHHHHhhcCCCCCC
Q 000882 980 --QRLSASVTMVAKGVLKEHLILLANSMTCAGDLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLS 1057 (1238)
Q Consensus 980 --~~l~~~~~~~~~~V~~rHl~Llad~MT~~G~~~~~~r~G~~~~~~s~l~~a~Fe~~t~~t~~~~l~~Aa~~g~~D~l~ 1057 (1238)
+.|+++++.+|.+||+|||+||||.||++|+++||||+|+++++.||+++||||+ +.++|.+||.+|+.|+|+
T Consensus 207 ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~G~~~~itR~gi~~~~~S~l~~aSFE~-----t~~~L~~AA~~g~~D~l~ 281 (300)
T cd02736 207 IINEIQYTMKSHGMSIDPRHIMLLADLMTFKGEVLGITRFGIAKMKESVLMLASFEK-----TTDHLFNAALHGRKDSIE 281 (300)
T ss_pred HHHHHHHHHHhcCCccCHHHHHHHHHHHhccCceeeeecccccccCCCHHHhcchHh-----HHHHHHHHhhcCCCCcCC
Confidence 4578888889999999999999999999999999999999999999999999999 459999999999999999
Q ss_pred cccchhccCCcccccccceE
Q 000882 1058 SVVAACSWGKHVAVGTGSRF 1077 (1238)
Q Consensus 1058 gv~~~ii~Gk~~~~GTG~~f 1077 (1238)
||+|||+|||++|+|||. |
T Consensus 282 gvse~ii~G~~~~~GTG~-f 300 (300)
T cd02736 282 GVSECIIMGKPMPIGTGL-F 300 (300)
T ss_pred CcHHHeeeCCCcCCCCCC-C
Confidence 999999999999999998 5
No 25
>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=6.3e-49 Score=444.13 Aligned_cols=282 Identities=23% Similarity=0.230 Sum_probs=223.1
Q ss_pred ccCcCCCCCeeeeeccccCCchHHHhhhccCC-------CCCCchHHHHHHH-HhhccCCCCCCCceEEEEcCCCCCCCc
Q 000882 755 SHSLFPAGEPVGVLAATAMSNPAYKAVLDSSP-------SSNNSWELMKEIL-LCRVSFNNDPIDRRVILYLNDCGCGRK 826 (1238)
Q Consensus 755 ~~~lv~~Ge~VG~laaqsigep~tq~~l~t~~-------~~~~g~~rlkEil-~~~~~~k~~~~d~~~~l~L~~~~~~~~ 826 (1238)
.+++++|||+||++||||||||+|||||+||+ |+|+|+|||+||+ .++++ +++|.|++||.+..
T Consensus 3 ~~slv~PGE~VG~iaAQSIGEPsTQMTLnTFH~AGv~~~nVTlGvPRL~EIi~~Ask~----i~TP~m~v~l~~~~---- 74 (309)
T cd02735 3 MRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILMTASKN----IKTPSMTLPLKNGK---- 74 (309)
T ss_pred hhccCCCCcccchhhhhccCCcccccccccccccCccccccccccccHHHHHhhhccC----CCCCeEEEEecCch----
Confidence 35789999999999999999999999999974 8999999999998 56665 56679999998764
Q ss_pred cccHHHHHHHHhhhceechhhhhheeeEEecCCcccc----CCCce-EEEEEecHHHHhhcCCCHhhHHHHHHHhhhhhh
Q 000882 827 YCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIIS----DDEGL-VGHIHLNKILLEDLRISMHDILPKCQETLKSFC 901 (1238)
Q Consensus 827 ~~~e~~a~~V~~~le~vtl~dv~~~i~i~y~~~~~~~----~~~~~-v~~i~Ld~e~L~~~~lt~~~I~~~l~~~~~~~~ 901 (1238)
.++.|+.|+.+||+++|+|+++.+.+.|-...... ....| .+++.+... .+.+.
T Consensus 75 --~~~~a~~~~~~ie~~~l~dv~~~~~v~~i~~~~~~~~~~~~~~~~~~~i~~~~~--------~~~~~----------- 133 (309)
T cd02735 75 --SAERAETLKKRLSRVTLSDVVEKVEVTEILKTIERVFKKLLGKWCEVTIKLPLS--------SPKLL----------- 133 (309)
T ss_pred --hHHHHHHHHhheeEeEHHHhhhhhehhHHHHHHHHHhhhhhCCEEEEEEEecCC--------chhHH-----------
Confidence 34589999999999999999999988772111100 00111 112222110 00000
Q ss_pred hhhhhHHHHHhhccceeeccccccccccccccCCC--cceEEEEEeecC-----Cc-ccccchhhcccchhhHHHHhhhc
Q 000882 902 KKKKMKKVVQFFKNTSLSISECCSFQQSCADKRSN--MPCLMFVLRGAS-----DS-YLDKLSGVLANMIYPVLLETIIK 973 (1238)
Q Consensus 902 ~~~~~~~i~~~~~~~~i~~~g~~~~~~~~~~~~~~--~~~lt~~~~~~~-----~~-~~vd~~~~~sn~I~ei~r~tiik 973 (1238)
....+...++++.+ +|+.++.++.++++++ .....+.++|.+ .. +++|..++++|+|++++ .+.
T Consensus 134 ---~~~~~~~~l~~~~i--~gi~gI~r~~i~~~~~~~~~~~~l~teG~nl~~v~~~~~~vd~~r~~sNdi~ei~---~~l 205 (309)
T cd02735 134 ---LLSIVEKLARKAVI--REIPGITRCFVVEEDKGGKTKYLVITEGVNLAALWKFSDILDVNRIYTNDIHAML---NTY 205 (309)
T ss_pred ---HHHHHHHHhcccEE--eCCCCccEEEEecCcCCCceEEEEEeccccHHHHHhccCccccccceeCCHHHHH---Hhh
Confidence 00113355566666 8888888877764432 112224788887 34 79999999999999999 789
Q ss_pred hhHHHH----HHHHHHHhhhhccccccceeeecccccccceEeeecccccccccccccccccchhhcccChHHHHHHHHh
Q 000882 974 ENWWVR----QRLSASVTMVAKGVLKEHLILLANSMTCAGDLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAE 1049 (1238)
Q Consensus 974 Gi~w~R----~~l~~~~~~~~~~V~~rHl~Llad~MT~~G~~~~~~r~G~~~~~~s~l~~a~Fe~~t~~t~~~~l~~Aa~ 1049 (1238)
|||++| +.|+++++.+|.+||+|||.|+||+||++|++.++||+|| +.+.|||++||||+ +.++|.+||.
T Consensus 206 GIEAar~~ii~Ei~~v~~~~Gi~V~~rHl~LiaD~MT~~G~~~~~nr~gi-~~~~S~l~~asFE~-----t~~~L~~Aa~ 279 (309)
T cd02735 206 GIEAARRAIVKEISNVFKVYGIAVDPRHLSLIADYMTFEGGYRPFNRIGM-ESSTSPLQKMSFET-----TLAFLKKATL 279 (309)
T ss_pred CHHHHHHHHHHHHHHHHHhcCCeeCHHHHHHHHHHHHhCCcEeecchhhe-ccCCCHHHhhhhhh-----HHHHHHHHhh
Confidence 999999 5678888899999999999999999999999999999999 77899999999999 4599999999
Q ss_pred hcCCCCCCcccchhccCCcccccccceEEEE
Q 000882 1050 KRHTDNLSSVVAACSWGKHVAVGTGSRFDLL 1080 (1238)
Q Consensus 1050 ~g~~D~l~gv~~~ii~Gk~~~~GTG~~f~l~ 1080 (1238)
+|+.|+|+||+|||+|||++|+|||. |||+
T Consensus 280 ~g~~D~l~g~s~~ii~G~~~~~GTG~-fdll 309 (309)
T cd02735 280 NGDIDNLSSPSSRLVVGKPVNGGTGL-FDLL 309 (309)
T ss_pred cCCCCCCCChHHheeeCCccCcccee-EEeC
Confidence 99999999999999999999999999 9985
No 26
>TIGR02388 rpoC2_cyan DNA-directed RNA polymerase, beta'' subunit. The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria.
Probab=100.00 E-value=1.2e-48 Score=490.72 Aligned_cols=245 Identities=19% Similarity=0.274 Sum_probs=206.5
Q ss_pred ccccCCccchHHHHHHHHHHhhCHHHHHhchhhhHHHHHHHHHhcCceeecCccccCHHHHHHHHHHHHHHHHHHHhhh-
Q 000882 506 DFDRDTIPSVINEIVTSIFFEKGPEEVLEFFDSLQPLLMENLFADGFSVSLEDFSLSKAALWNIQKEIQALYSLLYHRM- 584 (1238)
Q Consensus 506 ~ldK~~lG~s~~~LI~~i~~~~G~~~a~~fLd~lqrL~~~~L~~~GFSiGi~D~~~~~~~~~~i~~~i~~~~~~~~~~~- 584 (1238)
++||+.+ ++||+.++.+||+..|..|||.+++|+++|++.+|||+|++|+.+|+++.+.++++.+++....+++.
T Consensus 6 ~idKk~l----~~LI~~~~~~yG~~~t~~~lD~lk~Lgf~~aT~~G~SigidDl~ip~~K~~li~~a~~~v~~~~~~y~~ 81 (1227)
T TIGR02388 6 VVDKKAL----KNLISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPPAKQDLLEAAEKEIRATEERYRR 81 (1227)
T ss_pred ccchHHH----HHHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCeEEeeccCCCCHHHHHHHHHHHHHHHHHHHHHHc
Confidence 4666665 68999999999999999999999999999999999999999999999987777777777666655443
Q ss_pred ------hhhHHHHHHHHHHHHHHHHHHHHHHHHh-------cCCccccccccchhhhhhHHHHHhhcccccccCCccccc
Q 000882 585 ------STQNELVDLQIENHIRHVKMLVAKFILK-------SSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSK 651 (1238)
Q Consensus 585 ------~~~~~~le~~~~~~l~~~~~~i~~~~~~-------~n~l~~Mi~sGSKGS~~Ni~Qi~g~lGqQ~~~ggr~~~r 651 (1238)
+.+++.+ ..|+++++.+.+.+.+ .|++++|+.||||||+.|++|++||+|+|..++|+++
T Consensus 82 G~it~~Er~~~ii-----~~w~~t~e~~~~~~~~~~~~~d~~N~v~mMa~SGARGNisQi~QLvGmrGlma~p~G~ii-- 154 (1227)
T TIGR02388 82 GEITEVERFQKVI-----DTWNGTNEELKDEVVNNFRQTDPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEII-- 154 (1227)
T ss_pred CCCcchhhHHHHH-----HHHHHHHHHHHHHHHHhhhhcCCCCcHHHHhhccCcccHHHHHHHhcchheecCCCCcEe--
Confidence 2333333 4456666655544432 4899999999999999999999999999999888742
Q ss_pred cccccccccccccCCCCCCCCCCCcceecccccccCCccceEEeeccccceeeecccccCCCCchhHHHHHHHheeEEEe
Q 000882 652 TLVEDIASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICY 731 (1238)
Q Consensus 652 ~l~~~~~~~f~~~~p~~~d~~~~a~GfV~ssF~~GL~P~EfFfHamagREGLiDTAvkTa~sGYL~RrLv~~l~d~~v~Y 731 (1238)
+.| |.+||++||+|.|||||||||||||||||+|||+|||||||||+++||++|.+
T Consensus 155 ------------------~lP------I~snFreGLt~~EyF~sa~GaRkGLvDTAlKTAdSGYLTRRLVdv~qDviV~~ 210 (1227)
T TIGR02388 155 ------------------DLP------IKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVRE 210 (1227)
T ss_pred ------------------ecc------chhhhhcCCCHHHhheeccccccchhhcceeccccchHHHHHHHhhceEEEEE
Confidence 233 99999999999999999999999999999999999999999999999999998
Q ss_pred c--ceE---------------------------------------------------------------ecc----CCCc
Q 000882 732 D--GTV---------------------------------------------------------------RNV----CSNS 742 (1238)
Q Consensus 732 D--~tv---------------------------------------------------------------r~~----~~~~ 742 (1238)
+ ||. |+. +...
T Consensus 211 ~DCgT~~gi~v~~~~~~~~~~~l~~rl~GRv~~~di~~~~~~~i~~~n~~I~~~~~~~i~~~~~~~v~iRspltC~s~~~ 290 (1227)
T TIGR02388 211 EDCGTERSIVVRAMTEGDKKISLGDRLLGRLVAEDVLHPEGEVIVPKNTAIDPDLAKTIETAGISEVVVRSPLTCEAARS 290 (1227)
T ss_pred cCCCCCCCEEEEEeeCCCeEeEhhheeEeeeEHhHeECCCCcEEEeCCCccCHHHHHHHHHcCCCEEEEeCcceecchhh
Confidence 6 221 221 1356
Q ss_pred eeeeeeecccccccCcCCCCCeeeeeccccCCchHHHhhhccCC
Q 000882 743 IIQFDYAVNARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDSSP 786 (1238)
Q Consensus 743 iiqf~yg~dg~~~~~lv~~Ge~VG~laaqsigep~tq~~l~t~~ 786 (1238)
|||.|||++ +....+|+.|||||++||||||||+||+|||||+
T Consensus 291 vC~~CYG~~-la~~~lV~lGeaVGiiAaQSIGEPGTQLTmRTFH 333 (1227)
T TIGR02388 291 VCRKCYGWS-LAHAHLVDLGEAVGIIAAQSIGEPGTQLTMRTFH 333 (1227)
T ss_pred HhHhccCCc-cccCcEechhhhhhhhhhhccCCcchhhhhhhhh
Confidence 899999998 4578899999999999999999999999999974
No 27
>PRK02597 rpoC2 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=100.00 E-value=4.3e-48 Score=489.42 Aligned_cols=245 Identities=20% Similarity=0.299 Sum_probs=205.8
Q ss_pred ccccCCccchHHHHHHHHHHhhCHHHHHhchhhhHHHHHHHHHhcCceeecCccccCHHHHHHHHHHHHHHHHHHHhhh-
Q 000882 506 DFDRDTIPSVINEIVTSIFFEKGPEEVLEFFDSLQPLLMENLFADGFSVSLEDFSLSKAALWNIQKEIQALYSLLYHRM- 584 (1238)
Q Consensus 506 ~ldK~~lG~s~~~LI~~i~~~~G~~~a~~fLd~lqrL~~~~L~~~GFSiGi~D~~~~~~~~~~i~~~i~~~~~~~~~~~- 584 (1238)
++||+.+ ++||+.+|++||+..|+.|||.+++|+++|++.+|||+|++|+.+|+++.+.++++.+++.....++.
T Consensus 7 ~idKk~l----~~LI~~~~~~yG~~~t~~~lD~lk~LGf~~aT~~G~SigidDl~ip~~K~~li~~Ae~~v~~~~~~y~~ 82 (1331)
T PRK02597 7 VVDKKAL----KNLIAWAFKNYGTARTAQMADNLKDLGFRYATQAGVSISVDDLKVPPAKRDLLEQAEEEITATEERYRR 82 (1331)
T ss_pred cccHHHH----HHHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhCcEEEeecccccCHHHHHHHHHHHHHHHHHHHHHHc
Confidence 4566655 58999999999999999999999999999999999999999999999887777777776665555442
Q ss_pred ------hhhHHHHHHHHHHHHHHHHHHHHHHHH----h---cCCccccccccchhhhhhHHHHHhhcccccccCCccccc
Q 000882 585 ------STQNELVDLQIENHIRHVKMLVAKFIL----K---SSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSK 651 (1238)
Q Consensus 585 ------~~~~~~le~~~~~~l~~~~~~i~~~~~----~---~n~l~~Mi~sGSKGS~~Ni~Qi~g~lGqQ~~~ggr~~~r 651 (1238)
++|++.++. |+++++.+.+.+. + .|++++|+.||||||+.|++|++||+|||..++|+++
T Consensus 83 G~it~~Er~~kvi~~-----w~~t~e~l~~~~~~~~~~~dp~N~v~mMa~SGARGN~sQI~QLvGmRGLma~p~G~ii-- 155 (1331)
T PRK02597 83 GEITEVERFQKVIDT-----WNETNERLKDEVVKNFRQNDPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEII-- 155 (1331)
T ss_pred CCCchhHHHHHHHHH-----HHHHHHHHHHHHHHHHhhcCCCCcHHHHhhccCCccHHHHHHHhcchhhccCCCCcEE--
Confidence 334444444 4555544443332 2 5899999999999999999999999999999888743
Q ss_pred cccccccccccccCCCCCCCCCCCcceecccccccCCccceEEeeccccceeeecccccCCCCchhHHHHHHHheeEEEe
Q 000882 652 TLVEDIASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICY 731 (1238)
Q Consensus 652 ~l~~~~~~~f~~~~p~~~d~~~~a~GfV~ssF~~GL~P~EfFfHamagREGLiDTAvkTa~sGYL~RrLv~~l~d~~v~Y 731 (1238)
+.| |.+||++||+|+|||||||||||||+|||+|||+|||||||||++++|++|.+
T Consensus 156 ------------------~lP------I~snFrEGLs~~EyFis~~GaRKGLvDTAlKTAdSGYLTRRLVdv~QDviVre 211 (1331)
T PRK02597 156 ------------------DLP------IKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVRE 211 (1331)
T ss_pred ------------------ecc------hhhhhhcCCCHHHhheeccccccchhhcceecccchhHHHHHHHhhcceEEEe
Confidence 334 99999999999999999999999999999999999999999999999999998
Q ss_pred c--ce----------------------------------------------------------------Eecc----CCC
Q 000882 732 D--GT----------------------------------------------------------------VRNV----CSN 741 (1238)
Q Consensus 732 D--~t----------------------------------------------------------------vr~~----~~~ 741 (1238)
+ || ||++ +..
T Consensus 212 ~DCgT~~gi~~~~~~~~~~~i~~l~~rl~GR~~~~~i~~~~~~~i~~~n~~i~~~~~~~i~~~~~~~v~iRspltC~s~~ 291 (1331)
T PRK02597 212 EDCGTTRGIVVEAMDDGDRVLIPLGDRLLGRVLAEDVVDPEGEVIAERNTAIDPDLAKKIEKAGVEEVMVRSPLTCEAAR 291 (1331)
T ss_pred cCCCCCCCEEEEEEecCCEEEeEehheeEEEEEhhHeeCCCCCEEEeCCCCcCHHHHHHHHHcCCCEEEEECCEEecCCC
Confidence 6 22 1221 235
Q ss_pred ceeeeeeecccccccCcCCCCCeeeeeccccCCchHHHhhhccCC
Q 000882 742 SIIQFDYAVNARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDSSP 786 (1238)
Q Consensus 742 ~iiqf~yg~dg~~~~~lv~~Ge~VG~laaqsigep~tq~~l~t~~ 786 (1238)
.|||.|||++ +....+|+.|||||++||||||||+||+|||||+
T Consensus 292 gvC~~CYG~~-la~~~lv~lGeaVGiiAaQSIGEPGTQLTmRTFH 335 (1331)
T PRK02597 292 SVCRKCYGWS-LAHNHLVDLGEAVGIIAAQSIGEPGTQLTMRTFH 335 (1331)
T ss_pred CchhhccCcc-hhcCcccchhhhhhhhhhccccCCcchhehhhhh
Confidence 7899999998 4678899999999999999999999999999975
No 28
>PF04998 RNA_pol_Rpb1_5: RNA polymerase Rpb1, domain 5; InterPro: IPR007081 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to form the central cleft or channel where the DNA is bound [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1ZYR_D 1SMY_D 2A68_N 2O5J_D 3AOH_N 2O5I_D 2CW0_N 2A6H_N 2A69_D 3EQL_D ....
Probab=100.00 E-value=3e-50 Score=450.92 Aligned_cols=258 Identities=25% Similarity=0.315 Sum_probs=188.8
Q ss_pred cCCccceEEeeccccceeeecccccCCCCchhHHHHHHHheeEEEecceEeccCCCceeeeeeecccccccCcCCCCCee
Q 000882 686 GLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYDGTVRNVCSNSIIQFDYAVNARKSHSLFPAGEPV 765 (1238)
Q Consensus 686 GL~P~EfFfHamagREGLiDTAvkTa~sGYL~RrLv~~l~d~~v~YD~tvr~~~~~~iiqf~yg~dg~~~~~lv~~Ge~V 765 (1238)
||+|+|||||||||||||||||+|||+||||||||||+|||++|+||+|||+. ++.|+||+||+|| +++|||||
T Consensus 1 Gl~~~e~f~~~~~~R~gl~dta~kTa~sGyl~R~lv~~~~~~~v~~~~~~~~~-~~~i~~~~~~~~~-----~v~~Ge~V 74 (277)
T PF04998_consen 1 GLTPTEYFFHCMGGREGLIDTAVKTADSGYLQRRLVKVLEDLIVRYDDCVRNS-GGSIIQFIYGEDG-----LVEPGEAV 74 (277)
T ss_dssp C-THHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHTTHEEETTSEEEST-TSEEEESSCTTTS-----B--TTSBH
T ss_pred CcCHHHHHHHHhcccccccccceeeeccccchhhhhhccceEEEEEcCccccc-cceeeeccccccc-----ccCccccc
Confidence 89999999999999999999999999999999999999999999999999994 7899999999997 89999999
Q ss_pred eeeccccCCchHHHhhhccCC-------CCCCchHHHHHHHHhhccCCCCCCCceEEEEcCCCCCCCccccHHHHHHHHh
Q 000882 766 GVLAATAMSNPAYKAVLDSSP-------SSNNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERAAYMVKN 838 (1238)
Q Consensus 766 G~laaqsigep~tq~~l~t~~-------~~~~g~~rlkEil~~~~~~k~~~~d~~~~l~L~~~~~~~~~~~e~~a~~V~~ 838 (1238)
|++||||||||+||||||||+ +++.|+||++|+++++++.+ .+.+.+++..... ...+.+..++.
T Consensus 75 GiiaAQSIGEP~TQ~TL~TFH~aG~~~~~vt~giprl~eii~~~~~~~----~~~~~~~~~~~~~----~~~~~~~~~~~ 146 (277)
T PF04998_consen 75 GIIAAQSIGEPGTQMTLRTFHTAGVASKNVTQGIPRLKEIINASKKIK----TPIITVYGKKKII----SEKKKIKIIRK 146 (277)
T ss_dssp HHHHHHHHHCHGCCSHHSCTSSSCSSTSSCSSSHHHHHHHHTTCSSSS----SEEEEECSCSSEC----SSSHHHHHHHH
T ss_pred hhhhhchhcchhHHhhhcccccCceeeecccccceeeccccccccccc----cceEEeeccccee----cccccceEEEE
Confidence 999999999999999999985 67899999999999877543 4455555544332 23344555555
Q ss_pred hhceechhhhhheeeEEecCCccccCCCceEEEEEecHHHHhhcCCCHhhHHHHHHHhhhhhhhhhhhHHHHHhhcccee
Q 000882 839 QLKRVSLKDAAVEFLIEYKKPEIISDDEGLVGHIHLNKILLEDLRISMHDILPKCQETLKSFCKKKKMKKVVQFFKNTSL 918 (1238)
Q Consensus 839 ~le~vtl~dv~~~i~i~y~~~~~~~~~~~~v~~i~Ld~e~L~~~~lt~~~I~~~l~~~~~~~~~~~~~~~i~~~~~~~~i 918 (1238)
..+. .... ...... ...
T Consensus 147 ~~~~--------------~~~~-------------------------------------~~~~~~------------~~~ 163 (277)
T PF04998_consen 147 KIKI--------------IKNG-------------------------------------KKVKNG------------DKI 163 (277)
T ss_dssp TCSS--------------SCST-------------------------------------TCEHTT------------CES
T ss_pred eeee--------------eecc-------------------------------------cceecc------------eee
Confidence 5444 0000 000000 000
Q ss_pred eccccccccccccccCCCcceEEEEEeecC-----Cccc-ccchhhcccchhhHHHHhhhchhHHHHHH----HHHHHhh
Q 000882 919 SISECCSFQQSCADKRSNMPCLMFVLRGAS-----DSYL-DKLSGVLANMIYPVLLETIIKENWWVRQR----LSASVTM 988 (1238)
Q Consensus 919 ~~~g~~~~~~~~~~~~~~~~~lt~~~~~~~-----~~~~-vd~~~~~sn~I~ei~r~tiikGi~w~R~~----l~~~~~~ 988 (1238)
..+... .+....+....+++ .+.+++ ...+ +|..++++|+|.+++ ...|||++|+. ++.++..
T Consensus 164 -~~~~~~-~~~~~~~~~~~~~l--~~~g~~l~~v~~~qgvid~~k~~sn~I~qm~---~~~GIeaar~~i~~e~~~v~~~ 236 (277)
T PF04998_consen 164 -KKGSII-SKDILEKKSKEYVL--QTEGSNLQEVYSSQGVIDNDKHISNDIRQML---SKLGIEAARNSIIKELKNVFES 236 (277)
T ss_dssp -SSSCSE-HHHHCEECCCCCEE--ECCSHHHHHHTCSTT-EETCHHECSHHHHHH---HHHEHHHHHHHHHHHHHCHHHH
T ss_pred -ecceee-eeccccchhHHHHH--HHHhhhchhheecccccCCCEEEeceeEeee---eeEEEEECCCceeecCcEeeHH
Confidence 000000 00001112233444 334433 4556 899999999999999 66899999954 5666777
Q ss_pred hhccccccceeeecccccccceEeeeccccccccccccc
Q 000882 989 VAKGVLKEHLILLANSMTCAGDLVGFNSGGYKALSRSLN 1027 (1238)
Q Consensus 989 ~~~~V~~rHl~Llad~MT~~G~~~~~~r~G~~~~~~s~l 1027 (1238)
++..||+||+.|+||.||++|.++||||+||+..+.|.+
T Consensus 237 ~g~~vn~rhl~llad~mt~~g~~~gitR~gl~~~~~S~~ 275 (277)
T PF04998_consen 237 YGIEVNKRHLSLLADYMTYKGVLLGITRHGLNSNKSSFL 275 (277)
T ss_dssp CTSCCCHHHHHHHHHHHCCCSS---CCTTTTSSSSSSHH
T ss_pred HHHHHHHHHHHhCCCcCeeeeEEEEEEHHHhccCCCCcc
Confidence 778899999999999999999999999999988776543
No 29
>CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed
Probab=100.00 E-value=3.6e-47 Score=486.13 Aligned_cols=249 Identities=20% Similarity=0.287 Sum_probs=207.4
Q ss_pred ccccCCccchHHHHHHHHHHhhCHHHHHhchhhhHHHHHHHHHhcCceeecCccccCHHHHHHHHHHHHHHHHHHHhhh-
Q 000882 506 DFDRDTIPSVINEIVTSIFFEKGPEEVLEFFDSLQPLLMENLFADGFSVSLEDFSLSKAALWNIQKEIQALYSLLYHRM- 584 (1238)
Q Consensus 506 ~ldK~~lG~s~~~LI~~i~~~~G~~~a~~fLd~lqrL~~~~L~~~GFSiGi~D~~~~~~~~~~i~~~i~~~~~~~~~~~- 584 (1238)
.+||+. ..+||+.++++||+..|+.|||.+++|+++|++.+|||+|++|+.+|+++.+.++++.+++..+..++.
T Consensus 13 ~~~k~~----l~~li~~~~~~~G~~~t~~~lD~lk~lgf~~at~~G~Sigi~Dl~ip~~K~~li~~a~~~v~~~~~~y~~ 88 (1364)
T CHL00117 13 VIDKTA----LKRLISWLIDHFGMAYTSHILDQLKTLGFQQATAAGISLGIDDLLTPPSKGWLVQDAEQQSLILEKHYHY 88 (1364)
T ss_pred cccHHH----HHHHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcceEEecCcccCCHHHHHHHHHHHHHHHHHHHHHHc
Confidence 355554 478999999999999999999999999999999999999999999999988888887777776665542
Q ss_pred ------hhhHHHHHHHHHHHHHHHHHHHHHHHH---hcCCccccccccchhhhhhHHHHHhhcccccccCCccccccccc
Q 000882 585 ------STQNELVDLQIENHIRHVKMLVAKFIL---KSSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLVE 655 (1238)
Q Consensus 585 ------~~~~~~le~~~~~~l~~~~~~i~~~~~---~~n~l~~Mi~sGSKGS~~Ni~Qi~g~lGqQ~~~ggr~~~r~l~~ 655 (1238)
++|++.++.|-. ....+++.+...+. ..|++++|+.||||||+.|++|++||+|++..+.|.++
T Consensus 89 G~it~~er~~~~i~~w~~-~~~~l~~~~~~~~~~~d~~N~v~mMa~SGARGn~sQi~qLvGmRGlma~p~G~iI------ 161 (1364)
T CHL00117 89 GNVHAVEKLRQSIEIWYA-TSEYLKQEMNPNFRMTDPLNPVYMMSFSGARGNASQVHQLVGMRGLMSDPQGQII------ 161 (1364)
T ss_pred CCCCHHHHHHHHHHHHHH-HHHHHHHHHHHhhccCCCCCcHhhhhhccCcccHHHHHHHhcccceeeCCCCcEe------
Confidence 467777777621 22223333332222 25999999999999999999999999999988877643
Q ss_pred cccccccccCCCCCCCCCCCcceecccccccCCccceEEeeccccceeeecccccCCCCchhHHHHHHHheeEEEec--c
Q 000882 656 DIASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYD--G 733 (1238)
Q Consensus 656 ~~~~~f~~~~p~~~d~~~~a~GfV~ssF~~GL~P~EfFfHamagREGLiDTAvkTa~sGYL~RrLv~~l~d~~v~YD--~ 733 (1238)
+.| |.+||++||+|.|||||||||||||+|||+|||+|||||||||+++||++|..+ |
T Consensus 162 --------------~~P------I~snFreGLs~~EyFis~~GaRkGLvDTAlkTAdSGYLtRRLVdv~qdviV~~~dCg 221 (1364)
T CHL00117 162 --------------DLP------IQSNFREGLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRLVEVVQHIVVRETDCG 221 (1364)
T ss_pred --------------ecc------hhhhhhcCCCHHHhheeccccccchhhcceecccccchhhHHHhhhccEEEEeccCC
Confidence 333 999999999999999999999999999999999999999999999999999864 2
Q ss_pred e--------------------------------------------------------------Eecc----CCCceeeee
Q 000882 734 T--------------------------------------------------------------VRNV----CSNSIIQFD 747 (1238)
Q Consensus 734 t--------------------------------------------------------------vr~~----~~~~iiqf~ 747 (1238)
| ||++ +...|||.|
T Consensus 222 t~~gi~~~~~~~~~~~~~l~~rl~GRv~~~di~~~~~~i~~~n~~I~~~~~~~i~~~~~~~v~iRSpltC~~~~~vC~~C 301 (1364)
T CHL00117 222 TTRGISVSPRNGMMIERILIQTLIGRVLADDIYIGSRCIATRNQDIGIGLANRFITFRAQPISIRSPLTCRSTSWICQLC 301 (1364)
T ss_pred CCCCEEEEEecCCeEEeEecceeEEEEEhhhEEeCCEEEEeCCCCcCHHHHHHHHHcCCCEEEEeCCcccccHHHHHHHH
Confidence 2 1221 134689999
Q ss_pred eecccccccCcCCCCCeeeeeccccCCchHHHhhhccCC
Q 000882 748 YAVNARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDSSP 786 (1238)
Q Consensus 748 yg~dg~~~~~lv~~Ge~VG~laaqsigep~tq~~l~t~~ 786 (1238)
||++ +....+|+.|||||++||||||||+||+|||||+
T Consensus 302 YG~~-la~~~lV~~GeaVGiiAaQSIGEPGTQLTmRTFH 339 (1364)
T CHL00117 302 YGWS-LAHGDLVELGEAVGIIAGQSIGEPGTQLTLRTFH 339 (1364)
T ss_pred hCcc-cccCcccChhhhhhhhhhhccCCCchhhhhhhhh
Confidence 9998 5678899999999999999999999999999975
No 30
>PF04997 RNA_pol_Rpb1_1: RNA polymerase Rpb1, domain 1; InterPro: IPR007080 RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which is a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2Y0S_W 3QQC_A 1YNJ_D 1HQM_D 1YNN_D 1I6V_D 2GHO_D 2AUJ_D 1ZYR_D 1SMY_D ....
Probab=100.00 E-value=2.4e-44 Score=411.16 Aligned_cols=233 Identities=25% Similarity=0.419 Sum_probs=176.1
Q ss_pred cccceEEEecCChHHHHhcccccccccC------------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeEEcCc
Q 000882 12 GQIVGIRFGLATQKEICTASISDCSISH------------ASQLANPFLGLPLEFGKCESCGTSEPGKCEGHFGYIELPI 79 (1238)
Q Consensus 12 ~~I~~I~Fgl~S~eEI~k~Sv~~~~I~~------------~~gl~DprlG~~~~~~~C~TCg~~~~~~CpGHFGhIeL~~ 79 (1238)
++|++|+||++|+|||+++||.+ |++ ++||+|||||+.++...|+|||++. .+||||||||+|+.
T Consensus 2 ~~i~~i~f~~~s~~eI~~~Sv~~--i~~~~~~~~~~~~p~~~Gl~d~rlG~~~~~~~C~tC~~~~-~~CpGHfGhI~L~~ 78 (337)
T PF04997_consen 2 KKIKSIQFGIYSPEEIRKLSVKE--ITNPETFDNLTGKPIKGGLYDPRLGPIDKKQICSTCGLNY-TECPGHFGHIELAL 78 (337)
T ss_dssp EEEEEEEEEE--HHHHHHHEEEB----SSTSBCTSSSSCBSSSSSSSSSS-SSSSSTSSSSSSSS-SSCCCSEEEEEEEE
T ss_pred CeeeEEEEEeCCHHHHHHhCcEE--EechhhccCCCCCCccccccChhhcCCCcccccccccccc-cccCCceeEEEeCH
Confidence 68999999999999999999974 322 3699999999999999999999986 79999999999999
Q ss_pred ccccccChHHHHHHHHhhccccc------Cc--------------h---HHHHHHHh-----------------------
Q 000882 80 PIYHPSHISELKLTMYAFQLQIK------ND--------------G---VAQRLLSS----------------------- 113 (1238)
Q Consensus 80 PVfHpgf~k~i~~IL~~iCl~l~------~~--------------~---~~~~~~~~----------------------- 113 (1238)
|||||+||+.+++||+++|..|. .. . ..+.+...
T Consensus 79 PV~h~~f~~~i~~iL~~~C~~C~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~ 158 (337)
T PF04997_consen 79 PVYHPGFFKEIPKILRCICKKCSRLLLSEKEKYFYLKILLKLKKKKKKERLKIISKECKKKSICSHCKAINGKIKKVEKS 158 (337)
T ss_dssp EEETCCCHHHHHHHHTTSCTTTSCTSTCCCCHTSCHHHCHCSHSSSHHHHHHHHHHHHHHTCSSTSTCC-SSS---SSSE
T ss_pred HHHhhcccccceeeecccccccccccccccccccccccccccccccchhHHHHHHHhhhhhhhhcccccccccccccccc
Confidence 99999999999999999994431 00 0 00111110
Q ss_pred --H--h--------------------------------------HHHHHHccCChhHHHHhccC-CCCCCCceEEEeecc
Q 000882 114 --C--C--------------------------------------EVKEMLKRIPEETRKKLAGK-GYFPQDGYILEYLPV 150 (1238)
Q Consensus 114 --C--C--------------------------------------ev~~i~k~I~~ed~~~L~~~-~~~~~~~~il~~lpV 150 (1238)
| | +++++|++|+++++..|+.. ...+|+||||++|||
T Consensus 159 ~~~~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~~~~~~~l~~~~v~~ilk~l~~~~~~~l~~~~~~~~P~~~~l~~lpV 238 (337)
T PF04997_consen 159 KKCEGCGKKNPKIRKEGAEKIQEEIKKKESNKEIKEELRILTPEEVRQILKKLSKEDKELLGFDPSGSRPEWFFLTVLPV 238 (337)
T ss_dssp ETSSSSSSBSCEEEEESHCCCCCHHHSCCHHHHHHCHCECESHHHHHHHHHHSHHHHHHHHHHHTTTBSGGGSEEEEEEE
T ss_pred hhcccccccCcccccchhhhcccccccccccccchhhhhhhhhhhhhhcchhhhhhheeeeeccccccccceeEEeeeec
Confidence 1 1 67899999999999988632 235799999999999
Q ss_pred CCCCCCCccccCCCccccchhhHHHHHHHHHHHHHHHhh-hcCCCCcchhhhhhhHHHHHHHHHHhccCCcccCCCcccC
Q 000882 151 PPNCLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEVRGTAKSSRDVDAR 229 (1238)
Q Consensus 151 pP~~~Rp~~~~~~~~~~~~Dlt~~~l~~I~~~~~~l~~~-~~g~~~~~~~~~~~~~LQ~~v~~~~~~~~~~k~~~~~~~~ 229 (1238)
||+++||++.++|..+.+||+|. +|++||+.|+.|+.. ..+++... ..+.|..||.+|+.|||+.....+... ..
T Consensus 239 pP~~~RP~v~~~~~~~~eddlt~-~~~~Ii~~N~~L~~~~~~~~~~~~-~~~~~~~LQ~~v~~~~dn~~~~~~~~~--~~ 314 (337)
T PF04997_consen 239 PPPRFRPSVQLGGGRFSEDDLTS-LYRKIIKRNNRLRKLLEEGAPSSI-IMEEWRLLQEAVNSLIDNEKPGKPPAG--QK 314 (337)
T ss_dssp -TGGGS-EEEESSSEEEE-HHHH-HHHHHHHHHHHHHHCCTSTSSSCH-HHHHHHHHHHHHHHHHCTTSSSSSBCB--ST
T ss_pred CCceeeeeeeeecccccCchHHH-HHHHHHHHHHHHHHHHHhhCcchh-hhhhhhhhhHhHhHHhhhcccCCcccc--cc
Confidence 99999999999887667889998 799999999999985 44555443 467899999999999997322211110 01
Q ss_pred CC-CCCCCCcchhhhhhhhhccc
Q 000882 230 FG-VSQDPNSTTKAWLEKMRTLF 251 (1238)
Q Consensus 230 ~~-~~k~~~~~iKgk~gr~R~nl 251 (1238)
.+ ..+.+.+++|||+||||+||
T Consensus 315 ~~~~~k~i~q~L~gK~GrfR~NL 337 (337)
T PF04997_consen 315 SGRPLKGISQRLKGKEGRFRQNL 337 (337)
T ss_dssp TSSB--THHHHHSSTTSSHCHHT
T ss_pred cCCCCCCHHHHccCCCCcCCCCC
Confidence 11 23556689999999999997
No 31
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=100.00 E-value=1.1e-39 Score=412.25 Aligned_cols=279 Identities=20% Similarity=0.199 Sum_probs=237.3
Q ss_pred HHHhhhccCC-------CCCCchHHHHHHHHhhccCCCCCCCceEEEEcCCCCCCCccccHHHHHHHHhhhceechhhhh
Q 000882 777 AYKAVLDSSP-------SSNNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAA 849 (1238)
Q Consensus 777 ~tq~~l~t~~-------~~~~g~~rlkEil~~~~~~k~~~~d~~~~l~L~~~~~~~~~~~e~~a~~V~~~le~vtl~dv~ 849 (1238)
.|||||+||+ |+|+|+|||+||++++++ +++|.|++||.+.+. .++++|+.|+.+||+++|+||+
T Consensus 540 v~~~~LnTFH~AGv~~~nVTlGvPRL~EIinask~----i~TP~m~i~l~~~~~----~~~~~a~~v~~~ie~~~L~dv~ 611 (858)
T PRK14898 540 VTHNTMRTFHYAGVAEINVTLGLPRMIEIVDARKE----PSTPIMTVHLKGEYA----TDREKAEEVAKKIESLTLGDVA 611 (858)
T ss_pred eeccccceeeccCccccccccCCchHHHHhcccCC----CCCceEEEEECCCcc----chHHHHHHHHhheeeEEHHHHH
Confidence 5799999974 899999999999998886 566799999987653 3678899999999999999999
Q ss_pred heeeEEecCCccccCCCceEEEEEecHHHHhhcCCCHhhHHHHHHHhhhhh-h---------hh----hhhHHHHHhhcc
Q 000882 850 VEFLIEYKKPEIISDDEGLVGHIHLNKILLEDLRISMHDILPKCQETLKSF-C---------KK----KKMKKVVQFFKN 915 (1238)
Q Consensus 850 ~~i~i~y~~~~~~~~~~~~v~~i~Ld~e~L~~~~lt~~~I~~~l~~~~~~~-~---------~~----~~~~~i~~~~~~ 915 (1238)
..+.+.+... .++|+||++.+.+++|++++|..++.++++.. . .. ....++...+++
T Consensus 612 ~~~~~~~~~~---------~~~i~l~~~~~~~~~l~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 682 (858)
T PRK14898 612 TSIAIDLWTQ---------SIKVELDEETLADRGLTIESVEEAIEKKLGVKIDRKGTVLYLKPKTPSYKALRKRIPKIKN 682 (858)
T ss_pred HHhhhhcccc---------EEEEEECHHHHHHcCCCHHHHHHHHHHhccccccCCCCEEEEEecCchHHHHHHHHHHhcC
Confidence 9888755443 26899999999999999999999988764321 0 00 001234456677
Q ss_pred ceeeccccccccccccccCC----CcceEEEEEeecC-----CcccccchhhcccchhhHHHHhhhchhHHHH----HHH
Q 000882 916 TSLSISECCSFQQSCADKRS----NMPCLMFVLRGAS-----DSYLDKLSGVLANMIYPVLLETIIKENWWVR----QRL 982 (1238)
Q Consensus 916 ~~i~~~g~~~~~~~~~~~~~----~~~~lt~~~~~~~-----~~~~vd~~~~~sn~I~ei~r~tiikGi~w~R----~~l 982 (1238)
+.+ +|+.+++++.++++. ++|++ .++|++ ..+++|..+|+||+|++|+ .+.|||++| +.|
T Consensus 683 ~~i--~gi~gI~~~~i~~~~~~~~~~~~l--~teG~nl~~~~~~~~vd~~~~~sN~i~~i~---~~lGIEAar~~ii~Ei 755 (858)
T PRK14898 683 IVL--KGIPGIERVLVKKEEHENDEEYVL--YTQGSNLREVFKIEGVDTSRTTTNNIIEIQ---EVLGIEAARNAIINEM 755 (858)
T ss_pred cEE--ECCCCccEEEEecCCCCCCceEEE--EecCcCHHHHhcCCCCcccccccCCHHHHH---HhhCHHHHHHHHHHHH
Confidence 777 889888887776543 34555 799987 6789999999999999999 779999999 557
Q ss_pred HHHHhhhhccccccceeeecccccccceEeeecccccccccccccccccchhhcccChHHHHHHHHhhcCCCCCCcccch
Q 000882 983 SASVTMVAKGVLKEHLILLANSMTCAGDLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAA 1062 (1238)
Q Consensus 983 ~~~~~~~~~~V~~rHl~Llad~MT~~G~~~~~~r~G~~~~~~s~l~~a~Fe~~t~~t~~~~l~~Aa~~g~~D~l~gv~~~ 1062 (1238)
+++++.+|.+||+|||+||||+||++|+++++||+||++.+.|||++||||+ +.++|.+||.+|+.|.|+||++|
T Consensus 756 ~~v~~~~gi~V~~rHl~liad~MT~~G~~~~~~r~gi~~~~~s~l~~asFe~-----t~~~l~~Aa~~g~~D~l~g~s~~ 830 (858)
T PRK14898 756 MNTLEQQGLEVDIRHLMLVADIMTADGEVKPIGRHGVAGEKGSVLARAAFEE-----TVKHLYDAAEHGEVDKLKGVIEN 830 (858)
T ss_pred HHHHHhcCCccCHHHHHHHHHHHccCCcEEEeccCCccCCCCCHHHhcChHh-----HHHHHHHHhhcCCCCcCCCchHH
Confidence 8888899999999999999999999999999999999999999999999999 44999999999999999999999
Q ss_pred hccCCcccccccceEEEEecCCC
Q 000882 1063 CSWGKHVAVGTGSRFDLLWQTEN 1085 (1238)
Q Consensus 1063 ii~Gk~~~~GTG~~f~l~~~~~~ 1085 (1238)
|+||+++|+|||+ |+|+++.+-
T Consensus 831 ii~G~~~~~GTG~-~~l~~~~~~ 852 (858)
T PRK14898 831 VIVGKPIKLGTGC-VDLRIDREY 852 (858)
T ss_pred eeeCCccCCcCce-EEEEecCcc
Confidence 9999999999999 999998653
No 32
>cd00630 RNAP_largest_subunit_C Largest subunit of RNA polymerase (RNAP), C-terminal domain. RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channe
Probab=99.96 E-value=1.4e-30 Score=267.69 Aligned_cols=98 Identities=26% Similarity=0.347 Sum_probs=89.5
Q ss_pred chhHHHH----HHHHHHHhhhhccccccceeeecccccccceEeeecccccccccccccccccchhhcccChHHHHHHHH
Q 000882 973 KENWWVR----QRLSASVTMVAKGVLKEHLILLANSMTCAGDLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAA 1048 (1238)
Q Consensus 973 kGi~w~R----~~l~~~~~~~~~~V~~rHl~Llad~MT~~G~~~~~~r~G~~~~~~s~l~~a~Fe~~t~~t~~~~l~~Aa 1048 (1238)
.|||++| +.|+++++.+|.+||+|||.||||+||++|.+.|+||+|+++...|||++|+||+ +.++|.+||
T Consensus 57 lGIEAaR~~iv~El~~v~~~~Gi~V~~rHl~LIAD~MT~~G~~~ginr~g~~~~~~Spl~~aSFE~-----t~~~L~~AA 131 (158)
T cd00630 57 LGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGFRASKTSPLMRASFEK-----TTKHLLDAA 131 (158)
T ss_pred hCHHHHHHHHHHHHHHHHHhcCceecHHHHHHHHHHHhcCCcccccccccccccCCCHHHHcCHHH-----HHHHHHHHh
Confidence 4444444 3348999999999999999999999999999999999999888899999999999 569999999
Q ss_pred hhcCCCCCCcccchhccCCcccccccc
Q 000882 1049 EKRHTDNLSSVVAACSWGKHVAVGTGS 1075 (1238)
Q Consensus 1049 ~~g~~D~l~gv~~~ii~Gk~~~~GTG~ 1075 (1238)
.+|+.|+|+|+++||+|||++|+|||+
T Consensus 132 ~~g~~D~l~g~s~~ii~Gk~~~~GTG~ 158 (158)
T cd00630 132 AAGEKDELEGVSENIILGRPAPLGTGS 158 (158)
T ss_pred hcCCCCCCCCcHHhhhccCCCCCCCCC
Confidence 999999999999999999999999995
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=5.7e-30 Score=265.73 Aligned_cols=144 Identities=29% Similarity=0.496 Sum_probs=129.6
Q ss_pred ccccCCCCCceEeechhhhhHHHhhh-ccccCCHHHHHHHhcccc-----cccccccccccccccccchhhhccccCCCC
Q 000882 414 QLLSSHNGNLNLQLATDALLSLKVMF-KKYFLDKAFTQQLAMFAL-----SPLPRPALSKARCSARWTALQILQSVLPPG 487 (1238)
Q Consensus 414 nilsp~~G~Piigl~QD~llg~~llt-kd~fl~~~~~~~l~~~~~-----~~lp~PaI~Kp~~~~lwTGKQi~S~~LP~~ 487 (1238)
||+||++|+|+++++||+|+|+|+|| +++|++++++++++++.. ...+.|+|++|. ++|||||+||.+||..
T Consensus 1 NilSP~~G~Pii~~~QD~vlG~y~LT~~~~f~~~~e~~~~~~~~~~~~~~~~~~~~~I~~~~--~~~tgk~~~s~il~~~ 78 (158)
T PF04983_consen 1 NILSPANGKPIIGPTQDMVLGAYYLTSEDTFLSRDEAQQALMNGLIDDKKIVLLHPAILKPK--ELWTGKQTFSRILPNE 78 (158)
T ss_dssp GSEETTTTEESSS--SHHHHHHHHHSSTTTEESHHHHHHHHHCSST----CHCSSSSBSSSS--SCEECHHHHHTTSHTT
T ss_pred CccCCCCCCceEEeccceEeEEEEEEecccccchHHHHHHHHcccccccceeccchhhhccc--cceeeccHHHHhcccc
Confidence 79999999999999999999999998 679999999999999984 346889999997 8999999999999987
Q ss_pred ccccC-------cEEEEecccccccccccCCcc-chHHHHHHHHHHhhCHHHHHhchhhhHHHHHHHHHhcCceeecCcc
Q 000882 488 FDSCG-------DRYLIKKSEVLKGDFDRDTIP-SVINEIVTSIFFEKGPEEVLEFFDSLQPLLMENLFADGFSVSLEDF 559 (1238)
Q Consensus 488 ~~~~~-------~~viI~~gell~G~ldK~~lG-~s~~~LI~~i~~~~G~~~a~~fLd~lqrL~~~~L~~~GFSiGi~D~ 559 (1238)
+++.. +.++|++|++++|.+||+++| +..++||+.++++||+++|.+|||++|+++++|++.+|||||++|+
T Consensus 79 i~~~~~~~~~~~~~~~i~~g~~l~g~l~k~~lgk~~~~~li~~i~~~yG~~~~~~~ld~i~~lg~~~~t~~GfSvgi~D~ 158 (158)
T PF04983_consen 79 INPEGFSNDPDDGYVVINNGELLSGVLDKKTLGKKSLGSLIHQIYREYGPEATVQFLDAIKRLGFRYLTRSGFSVGIDDM 158 (158)
T ss_dssp HHEEESTSCHSSHSEEECTSSEEEC--SHHHHSCSHTTCHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHTBB-SGGGC
T ss_pred cccccccccccccceeecCCccchhheehheecccchhhHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHcCeeEecccC
Confidence 66533 579999999999999999999 7899999999999999999999999999999999999999999996
No 34
>cd02655 RNAP_beta'_C Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain. Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations.
Probab=99.92 E-value=4.9e-26 Score=242.39 Aligned_cols=96 Identities=18% Similarity=0.286 Sum_probs=83.7
Q ss_pred HHHHhhhchhHHHHHHHHHHHhhhhccccccceeeecccccccceE----------------------------------
Q 000882 966 VLLETIIKENWWVRQRLSASVTMVAKGVLKEHLILLANSMTCAGDL---------------------------------- 1011 (1238)
Q Consensus 966 i~r~tiikGi~w~R~~l~~~~~~~~~~V~~rHl~Llad~MT~~G~~---------------------------------- 1011 (1238)
..|..+|+++ ++++..+|..||+||+.|+||.||.++.+
T Consensus 69 a~r~~iv~EI-------q~Vy~~qGV~I~dKHielIv~qMT~kv~i~~~g~s~~l~Ge~v~~~~~~~~N~~~~~~~~~~~ 141 (204)
T cd02655 69 AVQKYLVEEI-------QKVYRSQGVNINDKHIEIIVRQMTSKVKIIDPGDSGFLPGELVDLNEFEEENKRLLLLGKKPA 141 (204)
T ss_pred HHHHHHHHHH-------HHHHHhcCeeecHHHHHHHHHHHhcCeEEecCCCcccCCCceeeHHHHHHHHHHHHhCCCCcc
Confidence 3355566666 89999999999999999999999999654
Q ss_pred ------eeecccccccccccccccccchhhcccChHHHHHHHHhhcCCCCCCcccchhccCCcccccccc
Q 000882 1012 ------VGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGS 1075 (1238)
Q Consensus 1012 ------~~~~r~G~~~~~~s~l~~a~Fe~~t~~t~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~ 1075 (1238)
.|+||.++. ..|++.+||||+ |. ++|.+||.+|+.|.|.|++||||+|+.+|+|||.
T Consensus 142 ~y~p~llGItk~~l~--~~Sfls~ASFqe----T~-kvL~~AAi~gk~D~L~GlkeNVI~G~liPaGTG~ 204 (204)
T cd02655 142 KYEPVLLGITKASLN--TESFISAASFQE----TT-KVLTEAAIEGKIDWLRGLKENVILGRLIPAGTGL 204 (204)
T ss_pred cccceeeeeeecccc--CCCccccCChHH----HH-HHHHHHHhcCCCCCCCCchhheEECCccCCCCCC
Confidence 367776664 479999999999 34 9999999999999999999999999999999994
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=99.51 E-value=8.9e-15 Score=142.99 Aligned_cols=90 Identities=22% Similarity=0.340 Sum_probs=70.2
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHHHh----cCCccccccccchhhhhhHHHHHhhcccccccCCccccccccccccc
Q 000882 584 MSTQNELVDLQIENHIRHVKMLVAKFILK----SSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLVEDIAS 659 (1238)
Q Consensus 584 ~~~~~~~le~~~~~~l~~~~~~i~~~~~~----~n~l~~Mi~sGSKGS~~Ni~Qi~g~lGqQ~~~ggr~~~r~l~~~~~~ 659 (1238)
...+++.++..+.++++++++.+.+.+.+ +|++.+|+.||||||+.|++||+||||||.++|+| +.+....|++|
T Consensus 15 ~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~N~l~~M~~SGaKGs~~ni~Qi~g~lGqq~~~g~r-i~~~~~~Rtlp 93 (108)
T PF05000_consen 15 GKTYEETFEQKINKILNKVRDEIGKIIKKNLPFNNSLLIMINSGAKGSMSNISQISGCLGQQSVEGKR-IPRGFSGRTLP 93 (108)
T ss_dssp TCHHHHHHHHHHHHHHHHCCHHHHHHHHHCSTTTSHHHHHHHSSSS--HHHHHHHHST-EEEEETTSE-S--SSTTCSST
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcHHhhhhccCCCCHHHHHHHHHHHHHhhccccc-cccCCCCCcCC
Confidence 34566777777788888888888888775 48999999999999999999999999999999877 44557789999
Q ss_pred cccccCCCCCCCCCCCccee
Q 000882 660 HFERIYPMDLNYPTAKYGLI 679 (1238)
Q Consensus 660 ~f~~~~p~~~d~~~~a~GfV 679 (1238)
||.+ .+..|+++|||
T Consensus 94 ~f~~-----~~~~~~~~GFI 108 (108)
T PF05000_consen 94 HFKP-----FDESPESRGFI 108 (108)
T ss_dssp TS-S-----S-SSTTTTTEE
T ss_pred CcCC-----CCCCcccCCCC
Confidence 9964 37789999998
No 36
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]
Probab=99.16 E-value=4.2e-13 Score=169.24 Aligned_cols=346 Identities=13% Similarity=0.069 Sum_probs=229.8
Q ss_pred eeecccccccCcCCCCCeeeeeccccCCchHHHhhhccCCC---------CCCchHHHHHHHHhhccCCCCCCCceEEEE
Q 000882 747 DYAVNARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDSSPS---------SNNSWELMKEILLCRVSFNNDPIDRRVILY 817 (1238)
Q Consensus 747 ~yg~dg~~~~~lv~~Ge~VG~laaqsigep~tq~~l~t~~~---------~~~g~~rlkEil~~~~~~k~~~~d~~~~l~ 817 (1238)
.|..| .|...+..++.+++..+|+|++++.+||++.|+++ .+.+.+++-++..+ ..+.++.+.++
T Consensus 400 ~yNAD-FDGDeM~~Hvp~s~ea~AEa~~lm~tq~nilsP~~Ggpiv~~~qD~v~g~ylLt~~d~-----~~~~~~~~ei~ 473 (808)
T COG0086 400 AYNAD-FDGDEMAVHVPASGEAAAEARGLMGTQMNILTPHYGGPIVAPIQDTVGGPYLLTIVDA-----KLPSTPVGEIY 473 (808)
T ss_pred ccccc-cCchhhhccccchHHHHHHHHHhhccccccccCCCCCceEeecceEEeccEEEEEecc-----cCCCCcceEEE
Confidence 56554 23445778999999999999999999999998752 23344566665544 12567789998
Q ss_pred cCCCCCCCccccHHHHHHHHhhhceechhhhhheeeEEecCCccccCCCceEEEEEecHHHHhhcCCCHh-hHHHHHHHh
Q 000882 818 LNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIISDDEGLVGHIHLNKILLEDLRISMH-DILPKCQET 896 (1238)
Q Consensus 818 L~~~~~~~~~~~e~~a~~V~~~le~vtl~dv~~~i~i~y~~~~~~~~~~~~v~~i~Ld~e~L~~~~lt~~-~I~~~l~~~ 896 (1238)
+.+.+. ...+.+.++.+.++.++.+.+++.+........ +.+.+|.+.+..+.++.+ ++...+.+.
T Consensus 474 l~~~~~----~~~e~~~ai~~~~~~~~~k~i~~~i~~~~~~~~---------i~~t~~~~~~~~~~~~~~~d~~~~i~~~ 540 (808)
T COG0086 474 LKDEYA----DDREKAEAIAKKIELTTGKVIVSTISPDLAELS---------IIVTTDGRRIFNRGLPEDKDVLVKIVNG 540 (808)
T ss_pred eccccc----cchhhhHHHhcccceeeeeEEEEEeeccCCcce---------EEEecchhhhhhccCCcccceeeEEecc
Confidence 874433 356789999999999999999987666544333 567777777777777666 332211111
Q ss_pred --------------hhhhhh--hh-hhHHHHHhhccceeeccccccccccccccCCCcc-----eEEEEEeecC-----C
Q 000882 897 --------------LKSFCK--KK-KMKKVVQFFKNTSLSISECCSFQQSCADKRSNMP-----CLMFVLRGAS-----D 949 (1238)
Q Consensus 897 --------------~~~~~~--~~-~~~~i~~~~~~~~i~~~g~~~~~~~~~~~~~~~~-----~lt~~~~~~~-----~ 949 (1238)
++.+.. .. ...++..++++.-+ ++...+...+++++...+ ++ ...++.. .
T Consensus 541 ~l~~~~i~k~~~~i~~~~g~~~~~~~~~~~~dkl~~~~~--~~~~~~~~~i~~~d~~~~~~~~e~v-~~ae~~v~~~i~~ 617 (808)
T COG0086 541 KLIKGVIDKKIVTIYREYGPEVASKALVKLLDKLKNLGI--KGIGGFGIGIGRKDIEAEDEKDEIV-IEAEGSVLKLILQ 617 (808)
T ss_pred ccceeeehhhHHHHHHHhCchhhHHHHHHHHHHHHHhhe--eeeccceEEeecccccchHHHHHHH-HHHHHHHHHHHHH
Confidence 111110 00 11123445555545 222222233333321100 11 0111211 4
Q ss_pred cccccchhhcccchhhHHHHhhhchhHHHHHHH----HHHHhhhhcc-ccccceeeecccccccceEeeecccccccccc
Q 000882 950 SYLDKLSGVLANMIYPVLLETIIKENWWVRQRL----SASVTMVAKG-VLKEHLILLANSMTCAGDLVGFNSGGYKALSR 1024 (1238)
Q Consensus 950 ~~~vd~~~~~sn~I~ei~r~tiikGi~w~R~~l----~~~~~~~~~~-V~~rHl~Llad~MT~~G~~~~~~r~G~~~~~~ 1024 (1238)
.+.++++++.+|++.+++ .+++++.+++.+ ..+...+|.. ++.+|+++.+|.||.++-+..++++|+.+.+.
T Consensus 618 ~~~g~lt~~~~~~i~e~~---e~~~~e~l~~ai~~~~~~~~~~~g~~~~~i~~m~~~Gs~~n~sq~~~~iG~~gv~g~r~ 694 (808)
T COG0086 618 YEEGDLTRTERNNIVEII---EVLGIEALRNAIIEEIKITLEEQGLDFVDIRHMGLSGARMNISQIVQLIGQQGVMGEKI 694 (808)
T ss_pred hhcCCccccCCCCeEEEe---ehHHHHHHHHHHHHHHhhhHHhcCCcchhHHHHhhhhhccCHHHHHHHhhhheeeccCC
Confidence 567789999999999988 778888888654 4445556666 99999999999999999999999999999999
Q ss_pred cccccccchhhcccChHHHHHHHHhhcCCCCCCcccchhccCCcccccccceEEEEecCCCccccCCC----cccccccc
Q 000882 1025 SLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGSRFDLLWQTENEEFNQDD----GVDVYDFL 1100 (1238)
Q Consensus 1025 s~l~~a~Fe~~t~~t~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~~f~l~~~~~~~~~~~~~----~~~~y~~l 1100 (1238)
|+++++.||+ |. .+ ..|+.+++++.++|++++.+.|++++.|||. +|.-+....-.--+-+ ..+|.--.
T Consensus 695 ~~~~~~~Fe~----~~-~~-~~a~~~i~s~f~eGLt~~e~f~~~~ggR~Gl-vDTA~KTa~sGYl~RrLv~~~qdl~v~~ 767 (808)
T COG0086 695 SVLARAAFEV----TV-KH-LEAEGPGESSFLEGLTENEYFGHPIGGRTGL-VDTALKTADSGYLTRRLVDVAQDLIVQE 767 (808)
T ss_pred Cccccccccc----cc-cc-ceeeeeeecccCCCCCcceEEeecCccccch-HHHhhhhcccCcceEEeechhcceEEEe
Confidence 9999999999 45 66 7799999999999999999999999999999 9987654322222211 11222111
Q ss_pred ccccccCCcccccccccCccchhhh
Q 000882 1101 HMVRSSTGIEELDTGCLGEEVDGLE 1125 (1238)
Q Consensus 1101 ~~~~~~~~~~~~~~~~~~~~~~~~~ 1125 (1238)
..-+.. ..+.......|+|+.+++
T Consensus 768 d~~~~~-g~~~~~~~~~ged~~~~~ 791 (808)
T COG0086 768 DDCVTD-GIGVVIQFEYGEDGEDLT 791 (808)
T ss_pred cCeEee-cCceEEEEecCccccCHH
Confidence 112222 344456666778877766
No 37
>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=99.12 E-value=2.3e-11 Score=155.99 Aligned_cols=98 Identities=19% Similarity=0.272 Sum_probs=81.6
Q ss_pred chhHHHH----HHHHHHHhhhhccccccceeeeccccccc-------------ceEeeeccc------------------
Q 000882 973 KENWWVR----QRLSASVTMVAKGVLKEHLILLANSMTCA-------------GDLVGFNSG------------------ 1017 (1238)
Q Consensus 973 kGi~w~R----~~l~~~~~~~~~~V~~rHl~Llad~MT~~-------------G~~~~~~r~------------------ 1017 (1238)
++++.+| +.++.+++.+|..|+.+|++++++-||.+ |+++.+.+.
T Consensus 1083 ~s~~~~q~~lv~eiq~vy~~QGv~I~~kHieiIvrqMtskV~i~~~G~t~~lpGeli~~~~~~~~n~~l~~~~~~~~~y~ 1162 (1227)
T TIGR02388 1083 ESLQKVQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDAGDTTLLPGELVELRQVEQVNEAMAITGGAPAQYT 1162 (1227)
T ss_pred HHHHHHHHHHHHHHHHHHHhcceEeehhhHHHHHHHHhceEEEeeCCCcccCCcceeeHHHHHHHHHHHHhcCCCccccc
Confidence 3444444 45688999999999999999999999999 885544441
Q ss_pred ----cccc---ccccccccccchhhcccChHHHHHHHHhhcCCCCCCcccchhccCCcccccccc
Q 000882 1018 ----GYKA---LSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGS 1075 (1238)
Q Consensus 1018 ----G~~~---~~~s~l~~a~Fe~~t~~t~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~ 1075 (1238)
||.+ ...|.+++|||+| |. ++|.+||.+|+.|.|+|+.||||+|+++|+|||.
T Consensus 1163 pvLlGITkasL~t~Sfis~ASFqe----Tt-rvL~~Aai~g~~D~l~glkENvI~G~liP~GTG~ 1222 (1227)
T TIGR02388 1163 PVLLGITKASLNTDSFISAASFQE----TT-RVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGF 1222 (1227)
T ss_pred eeEeeeeeccccccchhhhccHHH----HH-HHHHHHHHcCCcccccCchhheeecCccccCCCc
Confidence 2323 2369999999999 34 9999999999999999999999999999999997
No 38
>CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed
Probab=99.11 E-value=2.4e-11 Score=158.58 Aligned_cols=94 Identities=20% Similarity=0.346 Sum_probs=83.1
Q ss_pred HHHHHHHhhhhccccccceeeeccccccc--------------ceE-----------------------eeecccccccc
Q 000882 980 QRLSASVTMVAKGVLKEHLILLANSMTCA--------------GDL-----------------------VGFNSGGYKAL 1022 (1238)
Q Consensus 980 ~~l~~~~~~~~~~V~~rHl~Llad~MT~~--------------G~~-----------------------~~~~r~G~~~~ 1022 (1238)
+.++++++.+|..|+.||+.++++-||.+ |++ +||||++++
T Consensus 1192 ~eiq~vy~~qGv~i~~kHieiivrqmt~kv~i~~~g~~~v~~pge~i~~~~~~~~~~~~~~~~~~~~~llGitkasl~-- 1269 (1364)
T CHL00117 1192 NKIQKVYRSQGVQISDKHIEIIVRQMTSKVLVSEDGMSNVFLPGELIGLLRAERINRALEEAICYRPILLGITKASLN-- 1269 (1364)
T ss_pred HHHHHHHHhcCcEeehhhhhhhHHHhhCeEEEeecCccCccCCcceeeHHHHHHHhHHhhcCcceeeeeeeeeehhcc--
Confidence 55788999999999999999999999994 774 566666664
Q ss_pred cccccccccchhhcccChHHHHHHHHhhcCCCCCCcccchhccCCcccccccceEEEEe
Q 000882 1023 SRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGSRFDLLW 1081 (1238)
Q Consensus 1023 ~~s~l~~a~Fe~~t~~t~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~~f~l~~ 1081 (1238)
..|.+++|||+| |+ ++|.+||++|+.|.|+|+.||||+|+++|+|||. +++..
T Consensus 1270 t~Sfis~aSFqe----T~-rvL~~aai~g~~D~l~glkenvi~g~~ip~GTG~-~~~~~ 1322 (1364)
T CHL00117 1270 TQSFISEASFQE----TT-RVLAKAALRGRIDWLKGLKENVILGGLIPAGTGF-KGLVH 1322 (1364)
T ss_pred ccchhhhcchHH----HH-HHHHHHHHcCCcccccCchhheeecCcccCCCCc-hhhhh
Confidence 568999999999 44 9999999999999999999999999999999999 66654
No 39
>PRK02597 rpoC2 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=99.08 E-value=4e-11 Score=154.96 Aligned_cols=101 Identities=18% Similarity=0.268 Sum_probs=85.5
Q ss_pred hhhchhHHHH----HHHHHHHhhhhccccccceeeeccccccc-------------ceE------------eeecc----
Q 000882 970 TIIKENWWVR----QRLSASVTMVAKGVLKEHLILLANSMTCA-------------GDL------------VGFNS---- 1016 (1238)
Q Consensus 970 tiikGi~w~R----~~l~~~~~~~~~~V~~rHl~Llad~MT~~-------------G~~------------~~~~r---- 1016 (1238)
+.-+|++.+| +.++.+++.+|..|+.+|+.++++-||.+ |++ +.+++
T Consensus 1081 aa~~~~~~~~~~lv~evq~Vy~~QGv~I~dkHieiIvrqMt~kV~i~d~Gdt~~lpGeli~~~~~~~~N~~~~~~~~~~a 1160 (1331)
T PRK02597 1081 AALEALQKLQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDGGDTTMLPGELIELRQVEQVNEAMAITGGAPA 1160 (1331)
T ss_pred HHHHhHHHHHHHHHHHHHHHHHhcCeEechhhHHhHHHHHhCcEEEeeCCCcccCCcceeeHHHHHHHHHHHHhcCCCcc
Confidence 3346677777 55688889999999999999999999999 444 34444
Q ss_pred ------ccccccc---ccccccccchhhcccChHHHHHHHHhhcCCCCCCcccchhccCCcccccccc
Q 000882 1017 ------GGYKALS---RSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGS 1075 (1238)
Q Consensus 1017 ------~G~~~~~---~s~l~~a~Fe~~t~~t~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~ 1075 (1238)
.||.+.+ .|.+++||||| |. ++|.+||.+|+.|.|+|+.||||+|+.+|+|||.
T Consensus 1161 ~y~pvLlGItkasl~T~sfis~aSFqe----T~-rvL~~AAi~g~~D~l~GlkENVI~G~liP~GTG~ 1223 (1331)
T PRK02597 1161 EYTPVLLGITKASLNTDSFISAASFQE----TT-RVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGF 1223 (1331)
T ss_pred eeeeeeeeeeeeccccCChhhhccHHH----HH-HHHHHHHHcCCCcccCCchhheeecCccccCcCc
Confidence 5666654 49999999999 34 9999999999999999999999999999999999
No 40
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=97.97 E-value=1.7e-06 Score=108.50 Aligned_cols=331 Identities=19% Similarity=0.155 Sum_probs=207.1
Q ss_pred CCCCeeeeeccccCCchHHHhhhccCC-------CCCCchHHHHHHHHhhccCCCCCCCceEEEEcCCCCCCCccccHHH
Q 000882 760 PAGEPVGVLAATAMSNPAYKAVLDSSP-------SSNNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERA 832 (1238)
Q Consensus 760 ~~Ge~VG~laaqsigep~tq~~l~t~~-------~~~~g~~rlkEil~~~~~~k~~~~d~~~~l~L~~~~~~~~~~~e~~ 832 (1238)
+.|+++|..+|+.+.+.+|.++.+... +..++.-.++.++++ +++....|+.+.+|+..+.+.+..++++.
T Consensus 879 q~~~~l~~~~a~f~~~~~~d~ld~~~~~~~~~~~~e~~~~~~l~~lle~--e~~~l~~dr~~l~~i~~~g~~k~~lp~n~ 956 (1605)
T KOG0260|consen 879 QNGETLGSLNACFESEFAYDALDEPISLSSEEVVNEISELLKLQNLLEC--EYKKLVRDRRVLLYIFEYGDAKWPLPENL 956 (1605)
T ss_pred cccccccchHHHHHhhhhhhhhcCcccchhhhHhhhhhhhHHHHHHHHH--HHHhhhhhhhhhhhhcccCCcccccchhH
Confidence 467889999999999999988653321 123344456666665 44666789999999998888888999999
Q ss_pred HHHHHhhhceechhhhhheeeEEecCCccccCCCceEEEEEe---------------------cHHHHhhcCCCHhh---
Q 000882 833 AYMVKNQLKRVSLKDAAVEFLIEYKKPEIISDDEGLVGHIHL---------------------NKILLEDLRISMHD--- 888 (1238)
Q Consensus 833 a~~V~~~le~vtl~dv~~~i~i~y~~~~~~~~~~~~v~~i~L---------------------d~e~L~~~~lt~~~--- 888 (1238)
.+.++++++...+.+.+.+.++.+.=-..-+....- +.+-. ++.++++++++-+.
T Consensus 957 ~r~I~Na~~~f~~~~r~~t~l~~~~v~~g~~~l~e~-l~iv~g~~~~sraqrl~~~lLrs~l~~krv~~e~rls~eaf~w 1035 (1605)
T KOG0260|consen 957 QRIIWNALKKFSIDERKPTDLIPFKVVKGVKELAEK-LVIVRGEDYISRAQRLFNILLRSTLATKRVLEEYRLSSEAFEW 1035 (1605)
T ss_pred HHHHHHHHhhcccccccccccchhhhhhhhhhhhhe-eEEeeCchhHHHHHHHHHHHHHhhHHHHHHHHHhcccHHHHHH
Confidence 999999999998888765444432110000000000 11111 23334444444322
Q ss_pred HHHHHHHhhhhhhhhhh-------hHHHH--------Hhh-------ccceeec---cccccccccccccCCCcceEEEE
Q 000882 889 ILPKCQETLKSFCKKKK-------MKKVV--------QFF-------KNTSLSI---SECCSFQQSCADKRSNMPCLMFV 943 (1238)
Q Consensus 889 I~~~l~~~~~~~~~~~~-------~~~i~--------~~~-------~~~~i~~---~g~~~~~~~~~~~~~~~~~lt~~ 943 (1238)
+++.++.++........ ...++ |.| +++.... +++.++ .|...++.++++
T Consensus 1036 ~~~~Ie~~f~qa~a~pgemvg~lAaqsvgePatqmTlntfh~aGVssknVt~gvprlkei~Nv-----~k~~ktpsLtV~ 1110 (1605)
T KOG0260|consen 1036 VLGEIEARFLQAEASPGEMVGALAAQSVGEPATQMTLNTFHYAGVSSKNVTLGVPRLKEIINV-----AKNAKTPSLTVY 1110 (1605)
T ss_pred HhhhhhhheeeeecCccchHhHHHHHHhCCchhhcccchhcccceeeeeeeccCcchhhhhhh-----hccCCCceEEEE
Confidence 22222222211100000 00011 111 1111111 112111 234467899888
Q ss_pred EeecC------------CcccccchhhcccchhhHH---HHhhhch-hHHHHHHHHHHHhhhhccccccceeeecccccc
Q 000882 944 LRGAS------------DSYLDKLSGVLANMIYPVL---LETIIKE-NWWVRQRLSASVTMVAKGVLKEHLILLANSMTC 1007 (1238)
Q Consensus 944 ~~~~~------------~~~~vd~~~~~sn~I~ei~---r~tiikG-i~w~R~~l~~~~~~~~~~V~~rHl~Llad~MT~ 1007 (1238)
+.+.. ..+-.++.++.++.=+-.- ..|+|-+ -||+...++...++++ -+.+.||.|++|.-..
T Consensus 1111 l~g~~~k~~e~ak~v~~~le~ttl~~vt~~t~i~ydpdp~~tvI~ed~e~v~a~~e~pd~D~~-~ispwlLrlelDr~~m 1189 (1605)
T KOG0260|consen 1111 LTGEAAKDNEWAKLVQCCLEHTTLKDVTRATEIYYDPDPQSTVIDEDREFVVAYYEMPDEDVG-RISPWLLRLELDRASM 1189 (1605)
T ss_pred ecchhhcchHHHHHHhhhcccccHHhhhccCcceecCCCcceeeccchhhHHhhhcCcccchh-hcChHHHHhhhhhhhc
Confidence 87643 1222233333333211110 2333333 4677766666667777 7999999999999999
Q ss_pred cceEeeecccccccccccccccccchhhcccChHHHHHHHHhhcCCCCCCcccchhccCCcccccccceEEEEecCCCcc
Q 000882 1008 AGDLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGSRFDLLWQTENEE 1087 (1238)
Q Consensus 1008 ~G~~~~~~r~G~~~~~~s~l~~a~Fe~~t~~t~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~~f~l~~~~~~~~ 1087 (1238)
+|+.+.++..|.+-...=-.-.++|..+++..+..+++++|..++.|.+.+-.|+-+||+..--|++..|++++..+.+.
T Consensus 1190 ~dk~ltm~~ia~~i~~~f~~d~~~i~~ddna~klv~r~ri~~~~e~D~~l~~Ie~~ml~~~~l~G~~~i~kV~m~~~~~G 1269 (1605)
T KOG0260|consen 1190 TDKKLTMEQIAEKINRGFGSDLACIFSDDNAEKLVLRLRIAKEEEDDVFLKCIEANMLGDMTLRGIPDIFKVYMSPTEDG 1269 (1605)
T ss_pred ccccccHHHHHHHHHhhccCCCceeecccCCcceEEEEEecCccchhHHHHHHHHhhhhhcccCCccccceEEEeecCCC
Confidence 99999999988765554334456788888888999999999999999999999999999999999999999999988777
Q ss_pred ccCCCccccccccc
Q 000882 1088 FNQDDGVDVYDFLH 1101 (1238)
Q Consensus 1088 ~~~~~~~~~y~~l~ 1101 (1238)
.-++ ++.|.++-
T Consensus 1270 ~f~~--~~ew~LeT 1281 (1605)
T KOG0260|consen 1270 EFKP--VDEWDLET 1281 (1605)
T ss_pred ceee--cceeEEec
Confidence 7765 66666553
No 41
>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=97.38 E-value=4.1e-05 Score=77.96 Aligned_cols=55 Identities=22% Similarity=0.270 Sum_probs=44.3
Q ss_pred echhhhhheeeEEecCCcccc-----------------------CCCceEEEEEecHHHHhhcCCCHhhHHHHHHHhh
Q 000882 843 VSLKDAAVEFLIEYKKPEIIS-----------------------DDEGLVGHIHLNKILLEDLRISMHDILPKCQETL 897 (1238)
Q Consensus 843 vtl~dv~~~i~i~y~~~~~~~-----------------------~~~~~v~~i~Ld~e~L~~~~lt~~~I~~~l~~~~ 897 (1238)
+||++|+....|.|+|+..++ ..+||+++|+||+++|-+++|+|++|+.++.+.+
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 689999999999999998754 1389999999999999999999999998766544
No 42
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=96.89 E-value=0.00011 Score=95.16 Aligned_cols=65 Identities=23% Similarity=0.201 Sum_probs=50.1
Q ss_pred hhHHHHHHHhe-eEEEecceEeccCCCceeeeeeecccccccCcCCCCCeeeeeccccCCchHHHhhhccC
Q 000882 716 LFKNLMAVLRD-VVICYDGTVRNVCSNSIIQFDYAVNARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDSS 785 (1238)
Q Consensus 716 L~RrLv~~l~d-~~v~YD~tvr~~~~~~iiqf~yg~dg~~~~~lv~~Ge~VG~laaqsigep~tq~~l~t~ 785 (1238)
|+..+.+.+.+ +.-.|+.|-..+ ..|++.++-.+ .+++++|||+||++||||||||+|||+|...
T Consensus 15 ~p~~~~~~i~~~~~~~~~lt~~~~--d~Il~~I~~~y---~~a~vepge~vG~~aaqsi~~~~~~~~~~~D 80 (858)
T PRK14898 15 LPRSLKDELFEKLSKRDGVTEEMV--EEIIDEVVSAY---LNALVEPYEAVGIVAAQSIGEPGTQMSLPYD 80 (858)
T ss_pred CCHHHHHHHHHHHHhhcCCCHHHH--HHHHHHHHHHH---hhCCCCCCceeeeeeehhcCCCCccccCCCC
Confidence 55566666655 444556665554 67888888877 6789999999999999999999999999653
No 43
>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=62.22 E-value=4.3 Score=51.48 Aligned_cols=64 Identities=19% Similarity=0.431 Sum_probs=32.5
Q ss_pred cccCcceee-----------eeeeccCeEeeeCCCCCCcccccceEEEecCC-CeeeecccCCC----------CCCCcc
Q 000882 329 FLRPGQVVH-----------RRIMDGDTVFINRPPTTHKHSLQALSVYVHDD-HTVKINPLICG----------PLSADF 386 (1238)
Q Consensus 329 ~L~~g~iV~-----------Rhl~dgD~VL~NRqPSLHr~Simah~v~v~~~-~T~rln~~vC~----------pyNADF 386 (1238)
.|++|.+.. ..+..| .||+-|.|++|..-|+-.+++-.|. +-+ -|-.|++ -=++|+
T Consensus 344 ~L~~geV~~~~s~~~~~~~~~~~~~g-~VlV~R~P~~~pgDir~~~av~~p~L~~l-~~vIVF~~~G~r~~~~~lsGgDl 421 (579)
T PF05183_consen 344 VLKEGEVFVQFSSDEETGSQSQVLEG-DVLVTRNPCLHPGDIRKVKAVDKPELRHL-KDVIVFSTKGDRPLPSELSGGDL 421 (579)
T ss_dssp ---TTEEEEEEEEEEEETTEEEEEE--EEEEE-SS--SGGGEEEEEE---GGGTT---SEEEE-S-SSS-HHHHTTT--S
T ss_pred CCCCCEEEEEeccccccCCCcceeee-eEEEecCCccCcCceeEEEeeccHHHccc-CCEEEeCCCCCCCchHHhcCCCC
Confidence 466666554 456677 8999999999999999999876653 101 1111111 124799
Q ss_pred Cccccccc
Q 000882 387 DGDCIHLF 394 (1238)
Q Consensus 387 DGDeMn~H 394 (1238)
|||+-.|-
T Consensus 422 DGD~~~V~ 429 (579)
T PF05183_consen 422 DGDEYFVC 429 (579)
T ss_dssp SS-EEEEE
T ss_pred CCceEEEE
Confidence 99998865
No 44
>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=34.22 E-value=47 Score=40.02 Aligned_cols=64 Identities=23% Similarity=0.272 Sum_probs=48.4
Q ss_pred eEeeeCCCCCCcccccceEEEecCC---CeeeecccCCCCCCCccCcc-ccccccCCCHHHHHHHHHHh
Q 000882 345 TVFINRPPTTHKHSLQALSVYVHDD---HTVKINPLICGPLSADFDGD-CIHLFYPQSLAAKAEVLELF 409 (1238)
Q Consensus 345 ~VL~NRqPSLHr~Simah~v~v~~~---~T~rln~~vC~pyNADFDGD-eMn~H~PQs~eAraEa~~Lm 409 (1238)
.+.--|+|.+-..|-+--+|+.-+. -.+++=.-+..+-|+|-||| |.--++|+ +++-.++..|+
T Consensus 212 raw~tRHPniSqlsTq~s~v~~~~~~~~wnvkvGlG~F~Gan~DCDGDKeviT~lP~-PNSLidlE~lL 279 (487)
T PF05094_consen 212 RAWTTRHPNISQLSTQVSRVDQNDDYTDWNVKVGLGTFVGANRDCDGDKEVITYLPY-PNSLIDLESLL 279 (487)
T ss_pred eeeecCCCCchhhchhheEeeccccCCCcceeeeeccccCCCCCCCCCceEEEecCC-CcchhhHHHHh
Confidence 3556799999999999888887543 34777788889999999999 77788888 33444454444
No 45
>PHA03396 lef-9 late expression factor 9; Provisional
Probab=26.82 E-value=72 Score=38.73 Aligned_cols=72 Identities=24% Similarity=0.225 Sum_probs=49.8
Q ss_pred eEeeeCCCCCCcccccceEEEecCCC---eeeecccCCCCCCCccCcc-ccccccCC-CHHHHHHHHHHhccccccc
Q 000882 345 TVFINRPPTTHKHSLQALSVYVHDDH---TVKINPLICGPLSADFDGD-CIHLFYPQ-SLAAKAEVLELFSVEKQLL 416 (1238)
Q Consensus 345 ~VL~NRqPSLHr~Simah~v~v~~~~---T~rln~~vC~pyNADFDGD-eMn~H~PQ-s~eAraEa~~Lm~~~~nil 416 (1238)
.+.--|+|.+-..|-+--+|+.-+.- -+++=.-+..+-|+|-||| |.--++|+ +..--+|...-..+..+++
T Consensus 215 raw~tRHPnisqlstq~s~v~~~~~~~~wNvkvGlG~F~GanrDCDGDKeviT~lP~PNsLidlE~lLY~DP~y~fi 291 (493)
T PHA03396 215 RAWTTRHPNISQLSTQVSRVDQNDDYTDWNVKVGLGTFPGANRDCDGDKEVITFLPYPNSLIDLECLLYGDPRYSFI 291 (493)
T ss_pred EEeecCCCCchhhchhheEeeccccccccceeeeeccccCCCCCCCCCceEEEecCCCcchhhHHHHhcCCCcceEE
Confidence 35567999999999998888875422 2666667778999999999 78888888 4334444444333444433
No 46
>TIGR01623 put_zinc_LRP1 putative zinc finger domain, LRP1 type. This model represents a putative zinc finger domain found in plants. Arabidopsis thaliana has at least 10 distinct members. Proteins containing this domain, including LRP1, generally share the same size, about 300 amino acids, and architecture. This 43-residue domain, and a more C-terminal companion domain of similar size, appear as tightly conserved islands of sequence similarity. The remainder consists largely of low-complexity sequence. Several animal proteins have regions with matching patterns of Cys, Gly, and His residues. These are not included in the model but score between trusted and noise cutoffs.
Probab=23.24 E-value=28 Score=28.87 Aligned_cols=20 Identities=30% Similarity=0.697 Sum_probs=15.8
Q ss_pred CCCCCCCCCCCCCCCCCcce
Q 000882 54 FGKCESCGTSEPGKCEGHFG 73 (1238)
Q Consensus 54 ~~~C~TCg~~~~~~CpGHFG 73 (1238)
...|.||-+....+|+||.-
T Consensus 15 ~~~CRtCCK~r~~DC~tHv~ 34 (43)
T TIGR01623 15 FERCRTCCKSRGFHCVTHVK 34 (43)
T ss_pred hhhhhHHhcccCcCCcchhc
Confidence 45799997766679999964
No 47
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=22.88 E-value=1.5e+02 Score=39.55 Aligned_cols=36 Identities=22% Similarity=0.354 Sum_probs=21.4
Q ss_pred CCCCCcccCCCCCcccchhcchh-cc-cCCCCCCCccc
Q 000882 1131 SLSPEHNLCSDKPVFEDLVEDQS-WL-ENKQENANWDS 1166 (1238)
Q Consensus 1131 ~~~~~~~~~~~~~~~~~~~~~~~-~~-~~~~~~~~~~~ 1166 (1238)
..+|+++.....|=|+.+.--.+ |. +..+++++|.+
T Consensus 810 ~~tPa~~~~~~~~g~~g~~g~sp~~~~~a~Tpg~~~~~ 847 (1024)
T KOG1999|consen 810 GKTPARNFDNREPGFEGSGGRSPQGYYSAPTPGSNWGS 847 (1024)
T ss_pred CCCCccccCCcccCCCCCCCCCCCCCcCCCCCCCCCCc
Confidence 45566655555666665555554 66 55666666666
Done!