Query 000291
Match_columns 1714
No_of_seqs 526 out of 2129
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 03:04:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/000291.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/000291hhsearch_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 3E-240 7E-245 2129.3 42.0 1052 4-1102 3-1380(1386)
2 PRK14977 bifunctional DNA-dire 100.0 1E-232 3E-237 2266.0 72.3 1031 9-1084 4-1318(1321)
3 KOG0260 RNA polymerase II, lar 100.0 2E-228 5E-233 2061.3 51.9 1058 1-1093 1-1430(1605)
4 KOG0262 RNA polymerase I, larg 100.0 6E-204 1E-208 1855.5 51.0 1031 9-1082 8-1635(1640)
5 TIGR02390 RNA_pol_rpoA1 DNA-di 100.0 1E-183 3E-188 1769.6 52.1 740 11-767 1-864 (868)
6 PRK08566 DNA-directed RNA poly 100.0 4E-182 8E-187 1761.6 54.6 737 8-765 3-867 (882)
7 TIGR02386 rpoC_TIGR DNA-direct 100.0 2E-162 5E-167 1558.9 46.3 890 16-1075 1-1135(1140)
8 PRK00566 DNA-directed RNA poly 100.0 2E-161 4E-166 1551.7 46.0 900 13-1075 6-1137(1156)
9 PRK14906 DNA-directed RNA poly 100.0 3E-152 6E-157 1459.7 44.8 770 138-1075 310-1236(1460)
10 PRK14844 bifunctional DNA-dire 100.0 6E-147 1E-151 1454.7 51.5 717 8-786 1442-2357(2836)
11 PRK09603 bifunctional DNA-dire 100.0 2E-146 5E-151 1455.0 49.6 707 10-786 1392-2301(2890)
12 COG0086 RpoC DNA-directed RNA 100.0 8E-129 2E-133 1238.0 31.1 688 14-754 4-789 (808)
13 PRK02625 rpoC1 DNA-directed RN 100.0 1.7E-84 3.7E-89 789.8 28.9 408 10-439 5-522 (627)
14 TIGR02387 rpoC1_cyan DNA-direc 100.0 4.2E-84 9E-89 785.6 26.6 403 14-439 2-515 (619)
15 CHL00018 rpoC1 RNA polymerase 100.0 4.5E-83 9.7E-88 784.7 25.7 282 138-439 259-543 (663)
16 smart00663 RPOLA_N RNA polymer 100.0 9.3E-81 2E-85 718.2 19.5 290 141-436 1-295 (295)
17 PF00623 RNA_pol_Rpb1_2: RNA p 100.0 4.3E-56 9.3E-61 476.7 5.1 159 253-411 1-166 (166)
18 TIGR02389 RNA_pol_rpoA2 DNA-di 100.0 8.4E-54 1.8E-58 506.1 12.6 334 716-1082 2-367 (367)
19 cd06528 RNAP_A'' A'' subunit o 100.0 5.5E-53 1.2E-57 500.1 11.9 329 722-1083 5-363 (363)
20 PRK04309 DNA-directed RNA poly 100.0 9.6E-53 2.1E-57 501.1 13.5 337 716-1085 18-382 (383)
21 PRK14897 unknown domain/DNA-di 100.0 7.1E-53 1.5E-57 506.3 10.0 338 716-1085 141-506 (509)
22 cd02584 RNAP_II_Rpb1_C Largest 100.0 2.4E-51 5.3E-56 492.0 17.4 309 755-1082 20-410 (410)
23 cd02737 RNAP_IV_NRPD1_C Larges 100.0 2E-49 4.4E-54 471.0 15.3 311 762-1081 1-381 (381)
24 cd02736 RNAP_III_Rpc1_C Larges 100.0 4.8E-49 1E-53 456.0 15.2 277 756-1077 4-300 (300)
25 TIGR02388 rpoC2_cyan DNA-direc 100.0 7E-47 1.5E-51 488.5 14.2 245 506-786 6-333 (1227)
26 PRK02597 rpoC2 DNA-directed RN 100.0 1.9E-46 4.2E-51 488.1 16.4 245 506-786 7-335 (1331)
27 PF04998 RNA_pol_Rpb1_5: RNA p 100.0 1.3E-47 2.7E-52 445.3 -4.2 258 686-1027 1-275 (277)
28 cd02735 RNAP_I_Rpa1_C Largest 100.0 1E-45 2.2E-50 431.6 11.5 280 755-1080 3-309 (309)
29 CHL00117 rpoC2 RNA polymerase 100.0 1.7E-45 3.8E-50 484.5 13.5 249 506-786 13-339 (1364)
30 PF04997 RNA_pol_Rpb1_1: RNA p 100.0 1.9E-42 4.1E-47 410.2 12.9 234 12-251 2-337 (337)
31 PRK14898 DNA-directed RNA poly 100.0 4.7E-38 1E-42 410.0 15.9 281 777-1085 540-852 (858)
32 PF04983 RNA_pol_Rpb1_3: RNA p 99.9 6.3E-29 1.4E-33 267.1 3.2 144 414-559 1-158 (158)
33 cd00630 RNAP_largest_subunit_C 99.9 4.4E-28 9.5E-33 257.6 2.9 100 964-1075 59-158 (158)
34 PF11523 DUF3223: Protein of u 99.9 1E-27 2.3E-32 225.4 1.8 76 1592-1669 1-76 (76)
35 cd02655 RNAP_beta'_C Largest s 99.9 3.9E-24 8.6E-29 235.3 6.1 97 965-1075 68-204 (204)
36 PF05000 RNA_pol_Rpb1_4: RNA p 99.5 2.3E-14 5E-19 145.1 5.1 91 583-679 14-108 (108)
37 TIGR02388 rpoC2_cyan DNA-direc 99.1 1.6E-11 3.5E-16 162.0 3.5 89 980-1075 1094-1222(1227)
38 CHL00117 rpoC2 RNA polymerase 99.1 1.5E-11 3.3E-16 165.2 3.2 94 980-1081 1192-1322(1364)
39 PRK02597 rpoC2 DNA-directed RN 99.1 5.4E-11 1.2E-15 158.5 3.7 91 980-1075 1095-1223(1331)
40 COG0086 RpoC DNA-directed RNA 98.9 1.9E-11 4.2E-16 159.4 -8.3 322 722-1083 379-746 (808)
41 KOG0260 RNA polymerase II, lar 98.0 1.5E-06 3.2E-11 111.9 -0.5 336 760-1103 879-1283(1605)
42 PF04990 RNA_pol_Rpb1_7: RNA p 97.5 2.8E-05 6.1E-10 82.0 0.5 55 843-897 1-78 (135)
43 COG5164 SPT5 Transcription elo 96.2 0.02 4.4E-07 69.2 10.1 30 1227-1256 463-492 (607)
44 PRK14898 DNA-directed RNA poly 94.6 0.0047 1E-07 83.3 -2.8 65 716-785 15-80 (858)
45 KOG1999 RNA polymerase II tran 93.3 1.1 2.5E-05 59.5 14.8 27 832-861 452-478 (1024)
46 KOG1999 RNA polymerase II tran 92.5 3.4 7.4E-05 55.3 17.4 11 993-1003 626-636 (1024)
47 COG5164 SPT5 Transcription elo 88.8 3.2 6.8E-05 51.3 11.4 16 1110-1125 394-409 (607)
48 PF05183 RdRP: RNA dependent R 59.5 4.4 9.5E-05 53.4 1.5 56 338-394 364-429 (579)
49 PF05094 LEF-9: Late expressio 35.2 43 0.00094 41.7 4.4 74 345-418 212-290 (487)
50 smart00157 PRP Major prion pro 28.4 2.1E+02 0.0046 32.3 7.8 25 1567-1603 112-136 (217)
51 PHA03396 lef-9 late expression 28.0 66 0.0014 40.4 4.3 74 345-418 215-293 (493)
52 PF07023 DUF1315: Protein of u 20.1 99 0.0022 31.3 3.1 47 1587-1633 11-62 (93)
No 1
>KOG0261 consensus RNA polymerase III, large subunit [Transcription]
Probab=100.00 E-value=3.2e-240 Score=2129.27 Aligned_cols=1052 Identities=24% Similarity=0.356 Sum_probs=908.3
Q ss_pred CCCCcccccceeeEEEecCCHHHHHHhcccccc------cc-----cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcc
Q 000291 4 NTSSTILEGQIVGIRFGLATQKEICTASISDCS------IS-----HASQLANPFLGLPLEFGKCESCGTSEPGKCEGHF 72 (1714)
Q Consensus 4 ~~~~~~~~~~I~~I~F~l~S~eEI~k~Sv~~~~------I~-----~~~gl~DprLG~~~~~~~C~TCg~~~~~~CpGHF 72 (1714)
|-.....+.+|++|+|+++|++||++.+++++. +. .++|++|||||++++...|+|||.++ .+|+|||
T Consensus 3 ~~~e~~~~kki~~i~F~~~s~~ei~~~a~v~v~~~~LY~~~~~~~P~~~G~LD~rMGvs~K~~~C~TCg~~l-a~C~GHf 81 (1386)
T KOG0261|consen 3 QFREDEIPKKIKHIQFSILSPEEIRQQAEVEVSSKDLYDISTQRAPLPNGPLDPRMGVSNKKDKCATCGEGL-ADCIGHF 81 (1386)
T ss_pred ccccccccceeeeEeeccCCHHHHHhcceEEeeccchhhhhcccCCCcCCCcCcccCCCCCCCccchhccch-hhccccc
Confidence 345667889999999999999999999987541 11 14799999999999999999999996 7999999
Q ss_pred eeEEcCcccccccchHHHHHHHHHHHhhhc-------------------------cchHHHHHHHHH--------H----
Q 000291 73 GYIELPIPIYHPSHISELKLTMYAFQLQIK-------------------------NDGVAQRLLSSC--------C---- 115 (1714)
Q Consensus 73 GhIeL~~PVfHpgf~k~I~~IL~~iC~ri~-------------------------~~g~~kri~~~C--------C---- 115 (1714)
||++|++||||+|||+.+++||||||+.|- +.++.++|+.+| |
T Consensus 82 Gy~~L~LPVFhiGyfk~ti~iLq~ICK~Cs~ilL~~~~k~~fl~~lr~p~~~~l~k~~l~kri~~~CkK~~~C~hCg~~N 161 (1386)
T KOG0261|consen 82 GYLKLALPVFHIGYFKATIQILQCICKNCSSILLSEEDKRQFLKKLRNPGLDNLRKKALLKRIVAKCKKVNTCSHCGALN 161 (1386)
T ss_pred ceEeecceeeeehhHHHHHHHHHHHHHhhhhhhcCHHHHHHHHHHhhCCCCChHHHHHHHHHHHHHhhccccccccCCcC
Confidence 999999999999999999999999987552 123456666666 3
Q ss_pred ----------------------------------------------------------HHHHHHhcCChHHHHhhccC-C
Q 000291 116 ----------------------------------------------------------EVKEMLKRIPEETRKKLAGK-G 136 (1714)
Q Consensus 116 ----------------------------------------------------------eV~~IfkkI~~ed~~~L~~~-~ 136 (1714)
.|+++|++|++.|+++|++. .
T Consensus 162 G~VKK~~~~lkIiHd~~~~~~k~~~~~~~~~~~~~~~~~~n~e~~~~~~~~~~~LnPl~vLnLFk~i~~~D~eLLg~~~~ 241 (1386)
T KOG0261|consen 162 GTVKKAAALLKIIHDRFKLVKKSDPLVTNERGEFKTAISHNKELEGHLSSCCEELNPLVVLNLFKQIKEDDCELLGMDSE 241 (1386)
T ss_pred ceeeccccceeEeeehhhccccccchhhhhHHHHHHHhhcCcchHhHHHHHHhhcChHHHHHHHhhCCccccceeeeccC
Confidence 67899999999999999653 2
Q ss_pred CCCCCcEEEeeccCCCCCCCCCcccCC-CccccchhHHHHHHHHHHHHHHHHhh-hcCCCCccchhhhhhHHHHHHHHHH
Q 000291 137 YFPQDGYILEYLPVPPNCLSVPDISDG-VSTMSSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYL 214 (1714)
Q Consensus 137 ~~~pe~~il~~lpVPP~~~Rp~~~~~g-~~~~~~Dlt~~~l~~Il~~n~~lk~~-~~g~p~~~~~~~~~~~LQ~~v~~~~ 214 (1714)
.-+|+.+|++++||||.|+||++++++ ....+||+|+ +|.+|+-.|..|++. ..|.|.... ...|+.||.+|+.||
T Consensus 242 ~~~P~~Li~t~~~vPP~cIRPSV~~~~k~gtnEDDlT~-KltEIi~tn~vik~~~~~g~~~~~i-mE~Wd~lQl~~AlyI 319 (1386)
T KOG0261|consen 242 EGRPENLIITRVPVPPVCIRPSVMSEDKAGTNEDDLTM-KLTEIILTNDVIKKHLSKGTPINLI-MEDWDFLQLQVALYI 319 (1386)
T ss_pred cCCchheEEEeccCCccccccceeecCCCCCCccchhh-hhhhhhhHHHHHHHHhhcCCCchhh-hhhhHHHHHHHHHhh
Confidence 346889999999999999999999877 3567899999 699999999999975 567765554 456999999999999
Q ss_pred hh--cCCCcCCCCCCCCCCCCCCCCchhhhhHhhhhhcccccCCCCccceeEeCCCCCccccccchhhcccccccccccc
Q 000291 215 EV--RGTAKSSRDVDARFGVSQDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVN 292 (1714)
Q Consensus 215 ~~--~~~~~~~~~~~~~~~~~k~~~~~ik~k~gr~R~~l~GKRvdfSaRsVI~pdP~l~~~evgvP~~~A~~Lt~pe~vt 292 (1714)
++ +|.+....+. .......+++|||+||||+||.||||||||||||||||||+|+|||||..||+.|||||+||
T Consensus 320 NSEl~g~~~~~~p~----kp~RGf~QRLKGKqGRFRgNLSGKRVDFSGRTVISPDPNL~IdeVgVP~rvAkiLTfpE~Vt 395 (1386)
T KOG0261|consen 320 NSELPGIPINMAPK----KPTRGFVQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDEVGVPIRVAKILTFPERVT 395 (1386)
T ss_pred cccCCCCCCCCCCC----CchHHHHHHhcccCCceeccccCceeeccCceeeCCCCCcceeeccchHHHHHHhcchhhcc
Confidence 84 4544321110 00011237899999999999999999999999999999999999999999999999999999
Q ss_pred hhhHHHHHHHHHccCcc-------ccCCCCceEEeccCCCC--ccccCCcceeeheeeccceEEEeCCCcccccccccee
Q 000291 293 VHNINYLQELVDNKLCL-------TYSDGSSSYSLREGSKG--HTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALS 363 (1714)
Q Consensus 293 ~~Ni~~l~~lv~~g~~~-------~~~~~~~~~~l~~~~~~--~~~l~~g~iV~Rhl~dgd~VL~NRqPsLHr~Sima~~ 363 (1714)
.+||++||+||+|||.+ +.+..+.+..|+|++|. +..|++||+|||||+|||+|||||||||||||||+|+
T Consensus 396 ~~Ni~klr~lV~NGP~vhPGANyv~~r~~~~kr~L~yg~R~kiA~eLk~GdvVERHL~DgDvVLFNRQPSLHkmSIM~H~ 475 (1386)
T KOG0261|consen 396 RANIRKLRQLVRNGPNVHPGANYVVQRGEGFKRFLKYGNRDKIADELKIGDVVERHLMDGDVVLFNRQPSLHKMSIMSHR 475 (1386)
T ss_pred HHHHHHHHHHHhcCCCCCCCcchhhhcccchhhHhhcCcHHHHHHhhccchHHHhhcccCCEEEEcCCchHHHHHHHHHH
Confidence 99999999999999962 11233345557777654 4689999999999999999999999999999999999
Q ss_pred eEecCCCeEEecccccCCCCCccccccccccCCCCHHHHHHHHHhcccccccccCCCCCceEeechhhHhHHHhhh-ccc
Q 000291 364 VYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF-KKY 442 (1714)
Q Consensus 364 ~~v~~~~t~rln~~vC~pyNADFDGDeMnlHvPQS~eAraEa~~Lm~~~~nilsp~~G~Piigl~QD~llg~~llt-kd~ 442 (1714)
+||+|++|||||.|||+||||||||||||+||||++||||||.+||.+++||++|++|+|||+++||||+|+|||| ||+
T Consensus 476 akV~p~RTfRFNEcvCtPYNADFDGDEMNlHvPQTEEAraEA~~LMgvknNlvTPr~GEpiiAAtQDFiTg~YLlt~KDt 555 (1386)
T KOG0261|consen 476 AKVMPWRTFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEALVLMGVKNNLVTPRNGEPIIAATQDFITGGYLLTHKDT 555 (1386)
T ss_pred hhcccCceeeccccccCCcCCCCCcccccccCCchHHHHHHHHHHhccccccccCCCCCceeehhhhhhhcceeeecccc
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999997 999
Q ss_pred cCCHHHHHHhhcccc-----cccccccccccccccccceeeeccccCCCCcc------------------------c-cC
Q 000291 443 FLDKAFTQQLAMFAL-----SPLPRPALSKARCSARWTALQILQSVLPPGFD------------------------S-CG 492 (1714)
Q Consensus 443 fl~~~~~~~l~~~~~-----~~lp~PaI~Kp~~~~lWTGKQl~s~~LP~~~~------------------------~-~~ 492 (1714)
||+|+++.||+.++. +.+|||||+||. .|||||||||+++.++.+ | .+
T Consensus 556 F~dRa~~~ql~s~~~d~~~~i~lppPaI~KP~--~LwTGKQ~fsvlirpn~~s~v~~Nl~~k~k~~~~~~~k~~~mc~nD 633 (1386)
T KOG0261|consen 556 FLDRAEFSQLCSYMSDAMTHIDLPPPAILKPV--ELWTGKQLFSVLIRPNDDSPVRVNLDAKNKNFSLVKGKSFEMCPND 633 (1386)
T ss_pred cccHHHHHHHHHHHhccccccCCCChhhcCce--eeeccCEEEEEEeccCCCCceEEeeccccceeecccCCCcccCCCC
Confidence 999999999986653 579999999999 999999999999954321 1 36
Q ss_pred CEEEEEcceecccccccCcccch-HHHHHHHHHHhhCHHHHHhchhhhHHHHHHHHHhcCceeeeCCcccCHHHHHHHHH
Q 000291 493 DRYLIKKSEVLKGDFDRDTIPSV-INEIVTSIFFEKGPEEVLEFFDSLQPLLMENLFADGFSVSLEDFSLSKAALWNIQK 571 (1714)
Q Consensus 493 ~~viI~~Gell~G~ldK~~lg~s-~~~Li~~i~~~~G~~~a~~fLd~lqrL~~~~L~~~GFSiGi~Dl~~~~~~~~~i~~ 571 (1714)
+.|+|+|++|+.|.+||+++|.. ..+||+.|.++||+.+|++.|+++.+|+.+||..+||||||+|+.+.+.+.+++.+
T Consensus 634 g~v~irns~l~sG~ldKs~lG~g~k~~lfy~llrDyg~~aAa~am~rlaklc~r~lgnrGFSIGi~DVqPg~~L~~~k~~ 713 (1386)
T KOG0261|consen 634 GYVIIRNSELISGVLDKSTLGSGKKDSLFYILLRDYGSMAAADAMNRLAKLCARFLGNRGFSIGIDDVQPGEILSQEKEE 713 (1386)
T ss_pred CeEEEecchhhhcccccccccCCCccceEeeehhhcchHHHHHHHHHHHHhhhhhccccccccccCCCCccHHHHHHHHH
Confidence 77899999999999999999985 68999999999999999999999999999999999999999999999999998888
Q ss_pred HHHHHHHHHHHhhh-------------hhHHHHHHHHHHHHHHHHHHHHHHHHh----cCCcccccccccchhhhhHHHH
Q 000291 572 EIQALYSLLYHRMS-------------TQNELVDLQIENHIRHVKMLVAKFILK----SSTLGYLIDSKSDSAVSKVVQQ 634 (1714)
Q Consensus 572 ~i~~~~~~~~~~~~-------------~~~e~le~~i~~~l~~~~~~i~~~~~~----~n~l~~Mi~SGSKGS~~Ni~Qi 634 (1714)
.++..|..+.++.. ..+++||+.+..+|+.+|+.+++.|++ .|+..+|+.||||||.+||+||
T Consensus 714 lv~~gY~kc~~~I~e~~kG~L~~qpg~~~eetLEa~I~~~Ls~IRe~~G~~C~~eL~~~NsPliMa~CGSKGS~INiSQM 793 (1386)
T KOG0261|consen 714 LVNRGYAKCDEKIEEYNKGKLQLQPGCNEEETLEAEILSELSTIREEAGKICIRELHPRNSPLIMALCGSKGSKINISQM 793 (1386)
T ss_pred HHHhHHHHHHHHHHHHhccccccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccChHHHHHhcCCCCcccHHHH
Confidence 88888877766543 336899999999999999999999996 4888999999999999999999
Q ss_pred hHhccceecCCCccccccccccccccccccCCCCCCCCCCccceecCcccccCCccceEEeeccccceeeecccccCCCC
Q 000291 635 AGFLGLQLSDRGKFYSKTLVEDIASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPG 714 (1714)
Q Consensus 635 ~g~lGQQ~~~g~r~~~r~l~~~~~~~f~~~~p~~~d~~~~a~GfV~ssF~~GL~P~EfFfHamagREGLiDTAvkTA~sG 714 (1714)
++|||||.+.|.| ++.++.+|.+|||+++ ...|+|+|||.||||+||+|.|||||+|+|||||||||||||+||
T Consensus 794 vACVGQQ~ISG~R-vPdGf~dRsLPHF~r~-----Sk~P~aKGFV~NSFySGLTptEFfFHtm~GREGLVDTAVKTAETG 867 (1386)
T KOG0261|consen 794 VACVGQQIISGHR-VPDGFEDRSLPHFERH-----SKTPAAKGFVANSFYSGLTPTEFFFHTMSGREGLVDTAVKTAETG 867 (1386)
T ss_pred HHHhhhhhhcCCc-CCCccccccCcccccc-----CCCccccchhhhhcccCCCchhhheeecccccchhhhhhhhhhhh
Confidence 9999999999776 6788999999999864 567899999999999999999999999999999999999999999
Q ss_pred chhHHHHHHHhceEEEeccccccccCCceeEEEeccccccc---------------------------------------
Q 000291 715 TLFKNLMAVLRDVVICYDGTVRNVCSNSIIQFDYAVNARKS--------------------------------------- 755 (1714)
Q Consensus 715 YLqRrLvk~ledl~v~YD~Tvr~~~~~~IiQf~yg~dg~~~--------------------------------------- 755 (1714)
||||||||.||||.++||+|||++ .+.||||+||+||+|+
T Consensus 868 YMqRRLmK~LEDL~~~YDgTVR~s-~~~vvqF~YG~DglDPa~mEg~~~pv~f~r~~~~~~~~~~~~~~~~l~~~el~e~ 946 (1386)
T KOG0261|consen 868 YMQRRLMKSLEDLSVQYDGTVRNS-NGDVVQFTYGGDGLDPAMMEGKDQPVNFNRVFDHAKAIFPHRHDPPLSSEELDET 946 (1386)
T ss_pred hHHHHHHHHHHHHHHhhcCceecC-CCcEEEEeecCCCCChhhhcCCCCchhHHHHHHHHHhcCCCCCCCCCCHHHHHHH
Confidence 999999999999999999999995 7999999999999762
Q ss_pred --------------------------------------------------------------------------cCcCCC
Q 000291 756 --------------------------------------------------------------------------HSLFPA 761 (1714)
Q Consensus 756 --------------------------------------------------------------------------~~lv~~ 761 (1714)
+..++|
T Consensus 947 ~~~~l~~~f~~~~~~F~~~~~~~i~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~t~kql~~f~~~~~~ky~~a~~Ep 1026 (1386)
T KOG0261|consen 947 LEEELLRKFTEKGDPFVHELREFIASLSKKIKKLQDKYGDECGPKFCPDLLYQISRLTEKQLEKFVERCLDKYMRAKVEP 1026 (1386)
T ss_pred HHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHhhhcccccCCccCccceeeeeeccHHHHHHHHHHHHHHHHhhhcCC
Confidence 124699
Q ss_pred CceeEEeccccCChhHHHHhhcCCC-------CCCCchHHHHHHHHhhccCCCCCCCceEEEEcCCCCCCCccccHHHHH
Q 000291 762 GEPVGVLAATAMSNPAYKAVLDSSP-------SSNNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERAAY 834 (1714)
Q Consensus 762 GepVG~laaqsigepatq~~L~t~~-------~~~~g~~rlkEil~~~~~~k~~~~d~~~~l~L~~~~~~~~~~~e~~a~ 834 (1714)
|.+||++||||||||+|||||+||| |+|+|+||+||||++.++++|+ .++-.|..++ ++..|+
T Consensus 1027 GTavGAi~aQSIGEPGTQMTLKTFHFAGVASMNiTlGVPRIkEIINAsk~ISTP----IItA~L~n~~------d~~~Ar 1096 (1386)
T KOG0261|consen 1027 GTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKTISTP----IITAELENPH------DERSAR 1096 (1386)
T ss_pred cchhhhhhcccCCCCCceeeeeeeeecceeeeeeccCcchHHHHHhhhcccCcc----ceeeeecCch------hHHHHH
Confidence 9999999999999999999999987 8999999999999999987766 4555565543 888999
Q ss_pred HHHhhhccccHhhhhheeEEEecCCccccCCCceEEEEEecHHHHHHhcC--ChhhhHHHHHHhh-hhh-----------
Q 000291 835 MVKNQLKRVSLKDAAVEFLIEYKKPEIISDDEGLVGHIHLNKILLEDLRI--SMHDILPKCQETL-KSF----------- 900 (1714)
Q Consensus 835 ~V~~~le~vtl~dv~~~i~I~y~~~~~~~~~~~wv~~i~Ld~e~L~~~~l--t~~~I~~k~~~~~-~~~----------- 900 (1714)
.||.+||+++|.||++.|...|.++.. .+.|.||.+.+...+| ++++|...|-+.- ...
T Consensus 1097 ~VKgRiEKt~L~dv~~yieeV~~p~~~-------fl~i~vd~~~I~~l~L~i~~~~I~~sI~~s~~~k~~~~~v~v~~~~ 1169 (1386)
T KOG0261|consen 1097 VVKGRIEKTTLGDVCSYIEEVYGPDSC-------FLLIRVDLKRISLLQLEITIESIAYSILKSPKRKVKPNDVRVVGET 1169 (1386)
T ss_pred HHhhhhhhhhHHHHHHHHHHHhCCcce-------EEEEEecHhHHhhhhccccHHHHHHHHhcCCccccCCcceEEecce
Confidence 999999999999999999999999976 7889999988877665 4778887655421 110
Q ss_pred -----hhcchh---hHHHHHhhccccccccccc--ccccccccCCCcceEEEEEcccC-----CcccccceecccccchH
Q 000291 901 -----CKKKKM---KKVVQFFKNTSLSISECCS--FQQSCADKRSNMPCLMFVLRGAS-----DSYLDKLSGVLANMIYP 965 (1714)
Q Consensus 901 -----~~~~~~---~~i~~~~~~~~~~~~~~gi--~~~~~~~~~~~~~~l~~~~~~~~-----~~~~vd~~~~~~n~I~~ 965 (1714)
....++ +--.+.+++.+..+.+||+ +++.+++-++..-...+.++|.+ .++||.-++|.+|++.+
T Consensus 1170 ~~~v~~~~~~~~S~~~~lq~lk~~L~~Vvv~gip~vnr~vi~~de~~~~y~L~vEG~gLr~Vm~t~GV~g~~TtsNnv~E 1249 (1386)
T KOG0261|consen 1170 TLRVTPVSDTKSSVYYNLQRLKRSLPNVVVKGIPEVNRAVINIDEKRGLYKLLVEGTGLRAVMNTDGVKGRRTTSNNVLE 1249 (1386)
T ss_pred eEEEeecccccchhhhhHHHHHhhCCceEEecCcchhhhheeecccCCceEEEEeccchHHHhccCCccccccccCceEE
Confidence 000000 1126777777778888999 78888776422221334799987 78999999999999988
Q ss_pred HH--------HHHhhhhhHHHHHHHHHHHHHhhcccccceeeeeccceeeeceEeeeccccccccccCcccccccccccc
Q 000291 966 VL--------LETIIKENWWVRQRLSASVTMVAKGVLKEHLILLANSMTCAGDLVGFNSGGYKALSRSLNVQVPFTEATL 1037 (1714)
Q Consensus 966 i~--------r~~IIkgi~w~r~~l~~~~~~~~~~V~~rHl~LlAd~MT~~G~~~~~~r~G~~~~~~s~l~~a~Fe~~t~ 1037 (1714)
|. |.+||.||. .++..-|.+||+||+|||||.|||.|+|+||||+|++++++|+|+.||||+|
T Consensus 1250 v~~vLGIEAAR~~II~EI~-------ytM~~HGmsiD~RHiMLLaDvMTyrGEVlGITRfGl~KM~~SVL~lASFEkT-- 1320 (1386)
T KOG0261|consen 1250 VEKVLGIEAARTTIISEIG-------YTMSNHGMSIDPRHIMLLADVMTYRGEVLGITRFGLAKMKDSVLMLASFEKT-- 1320 (1386)
T ss_pred eehhhchHHHHHHHHHHHH-------HHHHhcCcccCHHHHHHHHHHhhhcceeeeeeehhhHHHHHHHHHHHhhhhh--
Confidence 76 666666655 6667777889999999999999999999999999999999999999999998
Q ss_pred cCcHHHHHHHHhhcCCCCCCchhhhhhcCCcccccccceEEEEeccCCcccccCCccchhhcccc
Q 000291 1038 FMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGSRFDLLWQTENEEFNQDDGVDVYDFLHM 1102 (1714)
Q Consensus 1038 ~~~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~~~~l~~~~~~~~~~~~~~~~~y~~l~~ 1102 (1714)
.+||++||.++.+|.+.||+|+||+|+|+++|||. |+|++..+. +..++....|++-|..
T Consensus 1321 ---~DhLF~AA~~~k~D~I~GVSEcIIlG~pm~iGTG~-fkl~~~~~~-~~~~~~~~~if~~~~~ 1380 (1386)
T KOG0261|consen 1321 ---ADHLFDAAAYGKKDAIEGVSECIILGIPMCIGTGI-FKLLQRTDD-KKVLKPKPPIFSSLNL 1380 (1386)
T ss_pred ---hHHHHHHHHhcCcccccchhhheecccceeccccH-HHHHHhcCC-cccCCCCCCccccccc
Confidence 89999999999999999999999999999999999 999997655 3333334556665543
No 2
>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Probab=100.00 E-value=1.4e-232 Score=2265.98 Aligned_cols=1031 Identities=23% Similarity=0.343 Sum_probs=885.6
Q ss_pred ccccceeeEEEecCCHHHHHHhccccccccc-----------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeEEc
Q 000291 9 ILEGQIVGIRFGLATQKEICTASISDCSISH-----------ASQLANPFLGLPLEFGKCESCGTSEPGKCEGHFGYIEL 77 (1714)
Q Consensus 9 ~~~~~I~~I~F~l~S~eEI~k~Sv~~~~I~~-----------~~gl~DprLG~~~~~~~C~TCg~~~~~~CpGHFGhIeL 77 (1714)
.+.++|++|+|++||+|||+++||++ |++ ++||+|||||+.++...|+|||+++ .+||||||||||
T Consensus 4 ~~~~~I~~I~Fg~~S~eeIrk~Sv~~--It~~~~~d~~g~P~~gGl~DprlG~~d~~~~C~TCg~~~-~~CpGHFGHIEL 80 (1321)
T PRK14977 4 LAVKAIDGIIFGLISPADARKIGFAE--ITAPEAYDEDGLPVQGGLLDGRLGTIEPGQKCLTCGNLA-ANCPGHFGHIEL 80 (1321)
T ss_pred CccceeceEEEecCCHHHHHHhCeEE--EecccccCCCCCcCCCCCCccccCCCCCCCCCCCCCCCC-CcCCCeeEEEEc
Confidence 46788999999999999999999964 432 3599999999999999999999996 899999999999
Q ss_pred CcccccccchHHHHHHHHHHHhhh---c--cc--hH-------------------HH----HHH----------HHH--H
Q 000291 78 PIPIYHPSHISELKLTMYAFQLQI---K--ND--GV-------------------AQ----RLL----------SSC--C 115 (1714)
Q Consensus 78 ~~PVfHpgf~k~I~~IL~~iC~ri---~--~~--g~-------------------~k----ri~----------~~C--C 115 (1714)
++|||||+||+.|++||+|+|.+| + .. .. .+ ++. +.| |
T Consensus 81 a~PVfHpgf~k~i~~iLr~iC~~C~rlll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~C~~C 160 (1321)
T PRK14977 81 AEPVIHIAFIDNIKDLLNSTCHKCAKLKLPQEDLNVFKLIEEAHAAARDIPEKRIDDEIIEEVRDQVKVYAKKAKECPHC 160 (1321)
T ss_pred cCCceecccHHHHHHHHHHHHHHhchhhcCcccHHHHHHHHHHhhhcccchhhhhhHHHHHHHHhhhhhhhccCCcCCCC
Confidence 999999999999999999998655 2 00 00 00 111 134 5
Q ss_pred -----------------------------HHHHHHhcCChHHHHhhccC-CCCCCCcEEEeeccCCCCCCCCCcccCCCc
Q 000291 116 -----------------------------EVKEMLKRIPEETRKKLAGK-GYFPQDGYILEYLPVPPNCLSVPDISDGVS 165 (1714)
Q Consensus 116 -----------------------------eV~~IfkkI~~ed~~~L~~~-~~~~pe~~il~~lpVPP~~~Rp~~~~~g~~ 165 (1714)
+|++||++|+++|+++|+.. ...+|+||||++|||||+|+||++.+++..
T Consensus 161 ~~~~~~i~~~~~~~~~~~~~~~~~~l~p~~v~~if~~i~~~d~~llg~~~~~~~p~~~il~~lpVpP~~~RP~v~~~~~~ 240 (1321)
T PRK14977 161 GAPQHELEFEEPTIFIEKTEIEEHRLLPIEIRDIFEKIIDDDLELIGFDPKKARPEWAVLQAFLVPPLTARPSIILETGE 240 (1321)
T ss_pred CCCCCeEEEeeceeeeecccccCcccCHHHHHHHHHhcCHHHHHHhCCCCCCCCcceEEEeccccCCCCCcCcEEeCCCc
Confidence 78999999999999998642 235799999999999999999999987766
Q ss_pred cccchhHHHHHHHHHHHHHHHHhh-hcCCCCccchhhhhhHHHHHHHHHHhhc--CCCcCCCCCCCCCCCCCCCCchhhh
Q 000291 166 TMSSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEVR--GTAKSSRDVDARFGVSQDPNSTTKA 242 (1714)
Q Consensus 166 ~~~~Dlt~~~l~~Il~~n~~lk~~-~~g~p~~~~~~~~~~~LQ~~v~~~~~~~--~~~~~~~~~~~~~~~~k~~~~~ik~ 242 (1714)
..+||+|+ +|++||+.|+.|++. ..++|..+. ...|++||.+|++|||+. +.+.+.....+ ...+.+.+++|+
T Consensus 241 ~~eddlt~-~l~~Ii~~N~~l~~~~~~g~~~~~~-~~~~~~LQ~~v~~~~dn~~~~~~~~~~~~~~--rp~k~i~qrLkg 316 (1321)
T PRK14977 241 RSEDDLTH-ILVDIIKANQKLKESKDAGAPPLIV-EDEVDHLQYHTSTFFDNATAGIPQAHHKGSG--RPLKSLFQRLKG 316 (1321)
T ss_pred ccCCcHHH-HHHHHHHHHHHHHHHHHcCCcHHHH-HHHHHHHHHHHHHHhcccccCCCccccccCC--CchhHHHHHhcc
Confidence 78899998 799999999999875 567776553 568999999999999863 33322111011 123456689999
Q ss_pred hHhhhhhcccccCCCCccceeEeCCCCCccccccchhhcccccccccccchhhHHHHHHHHHccCccccC-------CCC
Q 000291 243 WLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDNKLCLTYS-------DGS 315 (1714)
Q Consensus 243 k~gr~R~~l~GKRvdfSaRsVI~pdP~l~~~evgvP~~~A~~Lt~pe~vt~~Ni~~l~~lv~~g~~~~~~-------~~~ 315 (1714)
|+||||+|||||||||||||||||||+|.+||||||..||++|||||+||+|||++|++||.|||. .|+ ..+
T Consensus 317 KeGrfR~nlmGKRVdfSaRtVIspDP~L~i~EVGvP~~iA~~LT~Pe~Vt~~Ni~~l~~lv~nG~~-~~pGA~~i~~~~g 395 (1321)
T PRK14977 317 KEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKMKELVINGPD-EFPGANAIRKGDG 395 (1321)
T ss_pred ccccccccccccccccccceeEeCCCCcccccccCHHHHHHhCCCCEEEchhhHHHHHHHHHcCCc-ccCCcceEEcCCC
Confidence 999999999999999999999999999999999999999999999999999999999999999985 222 122
Q ss_pred ceEEeccCC-C-------CccccCCcceeeheeeccceEEEeCCCccccccccceeeEecCCCeEEecccccCCCCCccc
Q 000291 316 SSYSLREGS-K-------GHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFD 387 (1714)
Q Consensus 316 ~~~~l~~~~-~-------~~~~l~~g~iV~Rhl~dgd~VL~NRqPsLHr~Sima~~~~v~~~~t~rln~~vC~pyNADFD 387 (1714)
.++.|++.. + .+..|++||+|||||+|||+|||||||||||||||||+|+|+|++||||||+||+|||||||
T Consensus 396 ~~~~l~~~~~~~~~~~~~~a~~L~~g~iV~Rhl~dGD~VL~NRQPSLHk~Simah~vkvl~~kT~Rln~~vC~pyNADFD 475 (1321)
T PRK14977 396 TKIRLDFLEDKGKDALREAAEQLEIGDIVERHLADGDIVIFNRQPSLHKLSILAHRVKVLPGATFRLHPAVCPPYNADFD 475 (1321)
T ss_pred ceeeehhhhhccchhHHHHHHhcccCcEEEEEeecCcEEEeccCCccccccceEEEEEEecCceEEecccccCcccCCcc
Confidence 234444322 1 12568999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccCCCCHHHHHHHHHhcccccccccCCCCCceEeechhhHhHHHhhh-ccccCCHHHHHHhhccccc--cccccc
Q 000291 388 GDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF-KKYFLDKAFTQQLAMFALS--PLPRPA 464 (1714)
Q Consensus 388 GDeMnlHvPQS~eAraEa~~Lm~~~~nilsp~~G~Piigl~QD~llg~~llt-kd~fl~~~~~~~l~~~~~~--~lp~Pa 464 (1714)
|||||+|||||++|||||++||++++||++|++|+|+++++||+|+|+|+|| +|+||+++++++|+|+... .+|+||
T Consensus 476 GDEMNlHvPQS~eArAEa~~Lm~v~~niisP~~G~Pi~gliQD~l~g~~lLT~~d~fl~~~e~~~l~~~~~~~~~lp~Pa 555 (1321)
T PRK14977 476 GDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFDKNEASNIAMLAGITDPLPEPA 555 (1321)
T ss_pred cceeeeecCCCHHHHHHHHHHHhhhhcEecCCCCCeeEEeehhhhhhhhhhccCcccCCHHHHHHHHHhCCCccccCCCc
Confidence 9999999999999999999999999999999999999999999999999997 7999999999999998764 379999
Q ss_pred cc-ccccccccceeeeccccCCCCcccc--------------------CCEEEEEcceecccccccCcccc---hHHHHH
Q 000291 465 LS-KARCSARWTALQILQSVLPPGFDSC--------------------GDRYLIKKSEVLKGDFDRDTIPS---VINEIV 520 (1714)
Q Consensus 465 I~-Kp~~~~lWTGKQl~s~~LP~~~~~~--------------------~~~viI~~Gell~G~ldK~~lg~---s~~~Li 520 (1714)
|+ ||. +|||||||||++||+++++. ++.|+|+||||++|+|||+++|+ +.++||
T Consensus 556 I~~kp~--~lwTGKQi~s~iLp~~~n~~~~~~~~~~~~~~~~~~~~~~d~~v~I~~geLl~G~ldK~~~G~~~~~~~~Li 633 (1321)
T PRK14977 556 IKTKDG--PAWTGKQLFSLFLPKDFNFEGIAKWSAGKAGEAKDPSCLGDGYVLIKEGELISGVIDDNIIGALVEEPESLI 633 (1321)
T ss_pred eecCCC--CeeeHHHHHHHHcCCCCCceecccccccccccccccCCCCcceEEeecCeEEeeecchHhhccccCCCCcHH
Confidence 99 898 99999999999999877541 45689999999999999999998 789999
Q ss_pred HHHHHhhCHHHHHhchhhhHHHHHHHHHhcCceeeeCCcccCHHHHHHHHHHHHHHHHHHHHh----h------------
Q 000291 521 TSIFFEKGPEEVLEFFDSLQPLLMENLFADGFSVSLEDFSLSKAALWNIQKEIQALYSLLYHR----M------------ 584 (1714)
Q Consensus 521 ~~i~~~~G~~~a~~fLd~lqrL~~~~L~~~GFSiGi~Dl~~~~~~~~~i~~~i~~~~~~~~~~----~------------ 584 (1714)
|.|+++||+++|.+||+.+++|+++||+++||||||+|+++++++.+.+.+.+++++..+.++ .
T Consensus 634 h~i~~~yG~~~a~~fL~~l~~l~~~~L~~~GFSigi~D~~~~~~~~~~i~~~i~~~~~~v~~l~~~~~~~~~i~~~~~~~ 713 (1321)
T PRK14977 634 DRIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLIIPDEAKQEIEDDIQGMKDEVSDLIDQRKITRKITIYKGKE 713 (1321)
T ss_pred HHHHHHhCHHHHHHHHHHHHHHHHHHHHhCCEEEeeCcEecCHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccch
Confidence 999999999999999999999999999999999999999999998877777666554333221 1
Q ss_pred -----hhhHHHHHHHHHHHHHHHHHHHHHHHHh----cCCcccccccccchhhhhHHHHhHhccceecC--------CCc
Q 000291 585 -----STQNELVDLQIENHIRHVKMLVAKFILK----SSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSD--------RGK 647 (1714)
Q Consensus 585 -----~~~~e~le~~i~~~l~~~~~~i~~~~~~----~n~l~~Mi~SGSKGS~~Ni~Qi~g~lGQQ~~~--------g~r 647 (1714)
.+.++++|..+.+.|+++++.+++.+.+ .|++.+|+.||||||++|++||+||||||+++ |+|
T Consensus 714 ~~~~G~~~~~~~e~~i~~~l~~~r~~~~~~~~~~l~~~N~l~~Mv~SGAKGS~~Ni~Qi~~~lGQQ~ve~~~~~~~~G~R 793 (1321)
T PRK14977 714 ELLRGMKEEEALEADIVNELDKARDKAGSSANDCIDADNAGKIMAKTGARGSMANLAQIAGALGQQKRKTRIGFVLTGGR 793 (1321)
T ss_pred hcCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHhhcccccCHHHHHHHHhccccccccccccccCCCCC
Confidence 1345678888888999999888876654 59999999999999999999999999999999 554
Q ss_pred cccccccccccccccccCCCCCCCCCCccceecCcccccCCccceEEeeccccceeeecccccCCCCchhHHHHHHHhce
Q 000291 648 FYSKTLVEDIASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDV 727 (1714)
Q Consensus 648 ~~~r~l~~~~~~~f~~~~p~~~d~~~~a~GfV~ssF~~GL~P~EfFfHamagREGLiDTAvkTA~sGYLqRrLvk~ledl 727 (1714)
+++++..|++|||.+ +++.|+|+|||.|||++||+|+|||||||||||||||||||||+||||||||||+||||
T Consensus 794 -i~~~~~~RtLPhF~~-----~d~~p~a~GfV~nsFl~GL~P~EfFFHaM~GREGLiDTAVKTA~SGYLQRrLvk~lEDl 867 (1321)
T PRK14977 794 -LHEGYKDRALSHFQE-----GDDNPDAHGFVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYFQRRLANALEDI 867 (1321)
T ss_pred -CcCCCCCCcCCCCCC-----CCCCcccccchhhhhcCCCCHHHHHHHhhcccccccccccccCcCchhHHHHHHHhcce
Confidence 677788899999963 48899999999999999999999999999999999999999999999999999999999
Q ss_pred EEEeccccccccCCceeEEEecccccccc---------------------------------------------------
Q 000291 728 VICYDGTVRNVCSNSIIQFDYAVNARKSH--------------------------------------------------- 756 (1714)
Q Consensus 728 ~v~YD~Tvr~~~~~~IiQf~yg~dg~~~~--------------------------------------------------- 756 (1714)
+|+||+|||++ +|+||||+||+||+|+.
T Consensus 868 ~v~YD~TVR~s-~g~iiQF~YGeDG~d~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 946 (1321)
T PRK14977 868 RLEYDETVRDP-HGHIIQFKFGEDGIDPQKLDHGEAFNLERIIEKQKIEDRGKGASKDEIEELAKEYTKTFNANLPKLLA 946 (1321)
T ss_pred EEecCCeEEeC-CCCEEEEeecCCCcCHHHhccCCcccHHHHHHHhhhhccccCCCHHHHHHHHHHHHHhhhhhhHHHHH
Confidence 99999999995 78999999999996631
Q ss_pred --------------------------CcCCCCceeEEeccccCChhHHHHhhcCCC-------CCCCchHHHHHHHHhhc
Q 000291 757 --------------------------SLFPAGEPVGVLAATAMSNPAYKAVLDSSP-------SSNNSWELMKEILLCRV 803 (1714)
Q Consensus 757 --------------------------~lv~~GepVG~laaqsigepatq~~L~t~~-------~~~~g~~rlkEil~~~~ 803 (1714)
++++|||+||++||||||||+|||||+||| ++|+|+|||+||+++++
T Consensus 947 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pGe~VG~iaAQSiGEP~TQmTLnTFH~AGv~~~nvt~GvpRl~Eii~a~k 1026 (1321)
T PRK14977 947 DAIHGAELKEDELEAICAEGKEGFEKAKVEPGQAIGIISAQSIAEPGTQMTLRTFHAAGIKAMDVTHGLERFIELVDARA 1026 (1321)
T ss_pred HHHHHcCCCHHHHHHHHHHHHHHHHhcccCCcccchhhhhhhccCceeeecccccccccccccCcccCccchHHhhhccc
Confidence 246799999999999999999999999998 89999999999999877
Q ss_pred cCCCCCCCceEEEEcCCCCCCCccccHHHHHHHHhhhccccHhhhhheeEEEecCCccccCCCceEEEEEecHHHHHHhc
Q 000291 804 SFNNDPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIISDDEGLVGHIHLNKILLEDLR 883 (1714)
Q Consensus 804 ~~k~~~~d~~~~l~L~~~~~~~~~~~e~~a~~V~~~le~vtl~dv~~~i~I~y~~~~~~~~~~~wv~~i~Ld~e~L~~~~ 883 (1714)
+ +++|.|++||.+.+.. ++++|++|+.+||+++|++|+.++.|.|+++ +.+|++|+++|++++
T Consensus 1027 ~----~~tp~m~~~l~~~~~~----~~~~a~~v~~~ie~~~l~~~~~~~~i~~~~~---------~~~i~~d~~~i~~~~ 1089 (1321)
T PRK14977 1027 K----PSTPTMDIYLDDECKE----DIEKAIEIARNLKELKVRALIADSAIDNANE---------IKLIKPDKRALENGC 1089 (1321)
T ss_pred C----CCCCeEEEEeCCcccc----hHHHHHHHHhheeeeEHHHhhhheEeeccCC---------ceEEecCHHHHHhcC
Confidence 5 6677999999876443 7788999999999999999999999999988 357899999999999
Q ss_pred CChhhhHHHHHHhhhhh--h--------------hcc--hhhHHHHHhhccccccccccc--ccccccc---cCC-Ccce
Q 000291 884 ISMHDILPKCQETLKSF--C--------------KKK--KMKKVVQFFKNTSLSISECCS--FQQSCAD---KRS-NMPC 939 (1714)
Q Consensus 884 lt~~~I~~k~~~~~~~~--~--------------~~~--~~~~i~~~~~~~~~~~~~~gi--~~~~~~~---~~~-~~~~ 939 (1714)
|++++|.+.+....... . ... ......+.+++.++.+.++|+ |.+++++ +++ .+|+
T Consensus 1090 i~~~~i~~~i~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~l~~l~~~l~~~~i~Gi~~I~r~~i~~~~~~~~~e~~ 1169 (1321)
T PRK14977 1090 IPMERFAEIEAALAKGKKFEMELEDDLIILDLVEAADRDKPLATLIAIRNKILDKPVKGVPDIERAWVELVEKDGRDEWI 1169 (1321)
T ss_pred CCHHHHHHHHHHhhcCCceEEeecCCEEEEecCcccccchHHHHHHHHHHhcCCcEEecCCCceEEEEEeeccCCCeeEE
Confidence 99998877655443210 0 000 001124455555667778998 6776553 222 2444
Q ss_pred EEEEEcccC-----CcccccceecccccchHHHHHHhhhhhHHHH----HHHHHHHHHhhcccccceeeeeccceeeece
Q 000291 940 LMFVLRGAS-----DSYLDKLSGVLANMIYPVLLETIIKENWWVR----QRLSASVTMVAKGVLKEHLILLANSMTCAGD 1010 (1714)
Q Consensus 940 l~~~~~~~~-----~~~~vd~~~~~~n~I~~i~r~~IIkgi~w~r----~~l~~~~~~~~~~V~~rHl~LlAd~MT~~G~ 1010 (1714)
| .++|++ ..++||..+|++|+|++|+. +.|||+.| ++|..+++.+|.+||+|||+||||+||++|+
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--QTSGSNLAAVLEMKCIDIANTITNDCFEIAG---TLGIEAARNAIFNELASILEDQGLEVDNRYIMLVADIMCSRGT 1244 (1321)
T ss_pred E--EecCcCHHHHhCCCCCcccccEECCHHHHHH---hhhHHHHHHHHHHHHHHHHHHcCCccCHHHHHHHHHHHccCce
Confidence 4 788887 78899999999999999982 34777766 4455777777789999999999999999999
Q ss_pred Eeeec------cccccccccCcccccccccccccCcHHHHHHHHhhcCCCCCCchhhhhhcCCcccccccceEEEEeccC
Q 000291 1011 LVGFN------SGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGSRFDLLWQTE 1084 (1714)
Q Consensus 1011 ~~~~~------r~G~~~~~~s~l~~a~Fe~~t~~~~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~~~~l~~~~~ 1084 (1714)
+++|| ||||++.+.|+|++|+||+| +++|++||.+|+.|.|+||+||||+|+++|+|||+ |||+++..
T Consensus 1245 ~~~i~~~~~~~R~Gi~~~~~s~l~~asFE~t-----~~~L~~AA~~g~~D~l~gvsenii~G~~~~~GTG~-~~Ll~~~~ 1318 (1321)
T PRK14977 1245 IEAIGLQAAGVRHGFAGEKDSPLAKAAFEIT-----THTIAHAALGGEIEKIKGILDALIMGQNIPIGSGK-VDLLMDFS 1318 (1321)
T ss_pred EEeccccccccccccccCCCCHHHhcCHHHH-----HHHHHHHHHhcCcCccCChHHhhhcCCCccCccce-EEEEeccc
Confidence 99999 99999999999999999998 89999999999999999999999999999999999 99999753
No 3
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=100.00 E-value=2.5e-228 Score=2061.35 Aligned_cols=1058 Identities=26% Similarity=0.384 Sum_probs=917.7
Q ss_pred CCCCCC-CcccccceeeEEEecCCHHHHHHhccccccc------c--cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCc
Q 000291 1 MEENTS-STILEGQIVGIRFGLATQKEICTASISDCSI------S--HASQLANPFLGLPLEFGKCESCGTSEPGKCEGH 71 (1714)
Q Consensus 1 ~~~~~~-~~~~~~~I~~I~F~l~S~eEI~k~Sv~~~~I------~--~~~gl~DprLG~~~~~~~C~TCg~~~~~~CpGH 71 (1714)
|+++-. +++|.++|++|+||++||+||++|||.++.. . .+.||+|||||++++..+|.|||.++ .+||||
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 444433 6899999999999999999999999975321 1 24689999999999999999999985 899999
Q ss_pred ceeEEcCcccccccchHHHHHHHHHHHhhhc---c-----------------chHHHHHHHHH-----H-----------
Q 000291 72 FGYIELPIPIYHPSHISELKLTMYAFQLQIK---N-----------------DGVAQRLLSSC-----C----------- 115 (1714)
Q Consensus 72 FGhIeL~~PVfHpgf~k~I~~IL~~iC~ri~---~-----------------~g~~kri~~~C-----C----------- 115 (1714)
||||+||+|||||||+++|++||+|||..|. . .+....++..| |
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 9999999999999999999999999987553 0 12223445555 3
Q ss_pred --------------------------------------HHHHHHhcCChHHHHhhccC-CCCCCCcEEEeeccCCCCCCC
Q 000291 116 --------------------------------------EVKEMLKRIPEETRKKLAGK-GYFPQDGYILEYLPVPPNCLS 156 (1714)
Q Consensus 116 --------------------------------------eV~~IfkkI~~ed~~~L~~~-~~~~pe~~il~~lpVPP~~~R 156 (1714)
+|++||++|+++++..|++. .+.+||||||++|||||+.+|
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 88999999999999999765 466789999999999999999
Q ss_pred CCcccCCCccccchhHHHHHHHHHHHHHHHHhh-hcCCCCccchhhhhhHHHHHHHHHHhh--cCCCcCCCCCCCCCC-C
Q 000291 157 VPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEV--RGTAKSSRDVDARFG-V 232 (1714)
Q Consensus 157 p~~~~~g~~~~~~Dlt~~~l~~Il~~n~~lk~~-~~g~p~~~~~~~~~~~LQ~~v~~~~~~--~~~~~~~~~~~~~~~-~ 232 (1714)
|.+++++....+||||+ +|.+||+.|..|+.. ..|++.++.. ...++||.||++|+|+ .+.+++.+ +.+ .
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-KLADIIKKNIGLKRNEENGAPAHIIE-EYEQLLQFHVATYVDNDIPGQPQADQ----KSGRP 313 (1605)
T ss_pred ceeeecccccCcchhHH-HHHHHHHHHHHHhhhhhcCCchhhHH-HHHhHhhhhhhheecccccCCccccc----ccCCc
Confidence 99888887667899999 699999999999864 6788877753 3457999999999984 55555543 333 3
Q ss_pred CCCCCchhhhhHhhhhhcccccCCCCccceeEeCCCCCccccccchhhcccccccccccchhhHHHHHHHHHccCcc---
Q 000291 233 SQDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDNKLCL--- 309 (1714)
Q Consensus 233 ~k~~~~~ik~k~gr~R~~l~GKRvdfSaRsVI~pdP~l~~~evgvP~~~A~~Lt~pe~vt~~Ni~~l~~lv~~g~~~--- 309 (1714)
.|++..++|+|+||+|+|||||||||||||||||||||+|||||||..||++|||||+||+|||++|++||++|++.
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 36677899999999999999999999999999999999999999999999999999999999999999999999862
Q ss_pred ---ccCCCCceEEeccCC-CCccccCCcceeeheeeccceEEEeCCCccccccccceeeEecCCCeEEecccccCCCCCc
Q 000291 310 ---TYSDGSSSYSLREGS-KGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSAD 385 (1714)
Q Consensus 310 ---~~~~~~~~~~l~~~~-~~~~~l~~g~iV~Rhl~dgd~VL~NRqPsLHr~Sima~~~~v~~~~t~rln~~vC~pyNAD 385 (1714)
+.++.+.+++|++.+ .++..|+.|++|||||+|||+|||||||||||||||||+|||+|+.|||||++||+|||||
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 233444556666544 4578999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccccCCCCHHHHHHHHHhcccccccccCCCCCceEeechhhHhHHHhhh-ccccCCHHHHHHhhccc-ccc--cc
Q 000291 386 FDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF-KKYFLDKAFTQQLAMFA-LSP--LP 461 (1714)
Q Consensus 386 FDGDeMnlHvPQS~eAraEa~~Lm~~~~nilsp~~G~Piigl~QD~llg~~llt-kd~fl~~~~~~~l~~~~-~~~--lp 461 (1714)
|||||||+|||||++||||+.+|+++++|||+||+|+|++|++||+|+|+|+|+ ||+||+|+++++|+|++ .+. .|
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 999999999999999999999999999999999999999999999999999997 78999999999999999 444 44
Q ss_pred -cccccccccccccceeeeccccCCCCcccc-----------------CCEEEEEcceecccccccCcccchHHHHHHHH
Q 000291 462 -RPALSKARCSARWTALQILQSVLPPGFDSC-----------------GDRYLIKKSEVLKGDFDRDTIPSVINEIVTSI 523 (1714)
Q Consensus 462 -~PaI~Kp~~~~lWTGKQl~s~~LP~~~~~~-----------------~~~viI~~Gell~G~ldK~~lg~s~~~Li~~i 523 (1714)
.|||+||. |||||||||++++|.+|++. +.+|+|.+|+|+.|+++|+.+|++.++|+|.+
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 99999999999999988762 34899999999999999999999999999999
Q ss_pred HHhhCHHHHHhchhhhHHHHHHHHHhcCceeeeCCcccCHHHHHHHHHHHHHHHHHHH----Hh---------hhhhHHH
Q 000291 524 FFEKGPEEVLEFFDSLQPLLMENLFADGFSVSLEDFSLSKAALWNIQKEIQALYSLLY----HR---------MSTQNEL 590 (1714)
Q Consensus 524 ~~~~G~~~a~~fLd~lqrL~~~~L~~~GFSiGi~Dl~~~~~~~~~i~~~i~~~~~~~~----~~---------~~~~~e~ 590 (1714)
+.+.|++.|..|++.||+|.+.||...|||+||+|.+...+....|+++|.++..-.. +. ..+..++
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 9999999999999999999999999999999999999999999999998887654221 11 1245788
Q ss_pred HHHHHHHHHHHHHHHHHHHHH----hcCCcccccccccchhhhhHHHHhHhccceecCCCccccccccccccccccccCC
Q 000291 591 VDLQIENHIRHVKMLVAKFIL----KSSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLVEDIASHFERIYP 666 (1714)
Q Consensus 591 le~~i~~~l~~~~~~i~~~~~----~~n~l~~Mi~SGSKGS~~Ni~Qi~g~lGQQ~~~g~r~~~r~l~~~~~~~f~~~~p 666 (1714)
+|..+..+|+++++.++..+. ++|++..|+.+|||||.+||+|+++|+|||+++|+| |+.+++.|++|||.+
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 899999999999988765554 469999999999999999999999999999999876 678889999999974
Q ss_pred CCCCCCCCccceecCcccccCCccceEEeeccccceeeecccccCCCCchhHHHHHHHhceEEEeccccccccCCceeEE
Q 000291 667 MDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYDGTVRNVCSNSIIQF 746 (1714)
Q Consensus 667 ~~~d~~~~a~GfV~ssF~~GL~P~EfFfHamagREGLiDTAvkTA~sGYLqRrLvk~ledl~v~YD~Tvr~~~~~~IiQf 746 (1714)
++++|+++|||+|||++||+|+|||||+|+|||||||||||||++|||||||||+|||++|+|||||||. -|+||||
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 6999999999999999999999999999999999999999999999999999999999999999999996 5799999
Q ss_pred Eeccccccc-----------------------------------------------------------------------
Q 000291 747 DYAVNARKS----------------------------------------------------------------------- 755 (1714)
Q Consensus 747 ~yg~dg~~~----------------------------------------------------------------------- 755 (1714)
.||+||++.
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 999999530
Q ss_pred --------------------------------------------------------------------------------
Q 000291 756 -------------------------------------------------------------------------------- 755 (1714)
Q Consensus 756 -------------------------------------------------------------------------------- 755 (1714)
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 ---------------------cCcCCCCceeEEeccccCChhHHHHhhcCCC-------CCCCchHHHHHHHHhhccCCC
Q 000291 756 ---------------------HSLFPAGEPVGVLAATAMSNPAYKAVLDSSP-------SSNNSWELMKEILLCRVSFNN 807 (1714)
Q Consensus 756 ---------------------~~lv~~GepVG~laaqsigepatq~~L~t~~-------~~~~g~~rlkEil~~~~~~k~ 807 (1714)
+..+.|||.||++|||++|||||||+|+||| |+|.|+||||||++..++
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 2256799999999999999999999999987 999999999999998875
Q ss_pred CCCCceEEEEcCCCCCCCccccHHHHHHHHhhhccccHhhhhheeEEEecCCcccc---------------------CCC
Q 000291 808 DPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIIS---------------------DDE 866 (1714)
Q Consensus 808 ~~~d~~~~l~L~~~~~~~~~~~e~~a~~V~~~le~vtl~dv~~~i~I~y~~~~~~~---------------------~~~ 866 (1714)
+++|.+++||.+...+ +.+.|+.|+++||++||++++....|.|+|+...+ ..+
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 5667999999988766 67889999999999999999999999999987643 159
Q ss_pred ceEEEEEecHHHHHHhcCChhhhHHHHHHhhhhhh------------------hcchhhH-HHHHh-hccccccccccc-
Q 000291 867 GLVGHIHLNKILLEDLRISMHDILPKCQETLKSFC------------------KKKKMKK-VVQFF-KNTSLSISECCS- 925 (1714)
Q Consensus 867 ~wv~~i~Ld~e~L~~~~lt~~~I~~k~~~~~~~~~------------------~~~~~~~-i~~~~-~~~~~~~~~~gi- 925 (1714)
||.++++||+.+|.+++|+|++|.++++..+..-. .+..... +...+ .+.+......|+
T Consensus 1177 pwlLrlelDr~~m~dk~ltm~~ia~~i~~~f~~d~~~i~~ddna~klv~r~ri~~~~e~D~~l~~Ie~~ml~~~~l~G~~ 1256 (1605)
T KOG0260|consen 1177 PWLLRLELDRASMTDKKLTMEQIAEKINRGFGSDLACIFSDDNAEKLVLRLRIAKEEEDDVFLKCIEANMLGDMTLRGIP 1256 (1605)
T ss_pred hHHHHhhhhhhhcccccccHHHHHHHHHhhccCCCceeecccCCcceEEEEEecCccchhHHHHHHHHhhhhhcccCCcc
Confidence 99999999999999999999999999988764320 0000000 00000 011112223455
Q ss_pred -ccccccccC-------CCcceEEEEEcccC-----CcccccceecccccchHHHHHHhhhhhHHHHHHHHHHHHHhh--
Q 000291 926 -FQQSCADKR-------SNMPCLMFVLRGAS-----DSYLDKLSGVLANMIYPVLLETIIKENWWVRQRLSASVTMVA-- 990 (1714)
Q Consensus 926 -~~~~~~~~~-------~~~~~l~~~~~~~~-----~~~~vd~~~~~~n~I~~i~r~~IIkgi~w~r~~l~~~~~~~~-- 990 (1714)
+.+++++.+ .++|.| -..+.+ ....+|..+|++|.|++++ -++||+.+|..|.+++..|.
T Consensus 1257 ~i~kV~m~~~~~G~f~~~~ew~L--eTdg~~l~~v~s~~~vD~~rt~sn~l~ei~---~vlgIea~r~a~~~e~~~vi~f 1331 (1605)
T KOG0260|consen 1257 DIFKVYMSPTEDGEFKPVDEWDL--ETDGVNLRRVLSEPDVDPARTTSNDLVEIA---EVLGIEAVRKALLRELLNVISF 1331 (1605)
T ss_pred ccceEEEeecCCCceeecceeEE--ecCchhHHhhhccCCCCcccccccchhhhh---hhhcHHHHHhhhhhhhhheEee
Confidence 445544422 134444 233332 5788999999999999997 47899999987777777665
Q ss_pred --cccccceeeeeccceeeeceEeeeccccccccccCcccccccccccccCcHHHHHHHHhhcCCCCCCchhhhhhcCCc
Q 000291 991 --KGVLKEHLILLANSMTCAGDLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKH 1068 (1714)
Q Consensus 991 --~~V~~rHl~LlAd~MT~~G~~~~~~r~G~~~~~~s~l~~a~Fe~~t~~~~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~ 1068 (1714)
++|++||+.|++|+||+.|+++.|+|||+++....+|++++|||| +..|.+||..++.|.++||+|||++||.
T Consensus 1332 ~gsyVnyrhlaLl~dvmT~~g~lm~itRhg~nr~~tgaLmrcSfEet-----v~il~~aa~~~ekd~~rgvsEnImlgql 1406 (1605)
T KOG0260|consen 1332 DGSYVNYRHLALLCDVMTARGHLMAITRHGINRQDTGALMRCSFEET-----VDILMDAAAHAEKDPCRGVSENIMLGQL 1406 (1605)
T ss_pred cccchhHHHHHHHHHHHhcccceeeeeccccchhhccccccccHHHH-----HHHHHHHHhhhccCCCccceeeeeeccc
Confidence 789999999999999999999999999999999999999999998 9999999999999999999999999999
Q ss_pred ccccccceEEEEeccCCcccccCCc
Q 000291 1069 VAVGTGSRFDLLWQTENEEFNQDDG 1093 (1714)
Q Consensus 1069 ~~~GTG~~~~l~~~~~~~~~~~~~~ 1093 (1714)
+|+|||+ ||||++.|++....+.+
T Consensus 1407 ap~gTg~-~d~~ld~e~l~~~~~~~ 1430 (1605)
T KOG0260|consen 1407 APMGTGC-FDLMLDAEKLKKGIEIP 1430 (1605)
T ss_pred ccCCCcc-eeeeccHHhhhccCccC
Confidence 9999999 99999999999988733
No 4
>KOG0262 consensus RNA polymerase I, large subunit [Transcription]
Probab=100.00 E-value=5.5e-204 Score=1855.48 Aligned_cols=1031 Identities=25% Similarity=0.338 Sum_probs=800.9
Q ss_pred ccccceeeEEEecCCHHHHHHhccccc-------ccccC--CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeEEcCc
Q 000291 9 ILEGQIVGIRFGLATQKEICTASISDC-------SISHA--SQLANPFLGLPLEFGKCESCGTSEPGKCEGHFGYIELPI 79 (1714)
Q Consensus 9 ~~~~~I~~I~F~l~S~eEI~k~Sv~~~-------~I~~~--~gl~DprLG~~~~~~~C~TCg~~~~~~CpGHFGhIeL~~ 79 (1714)
...+.+..|+|++||++||+++||+.+ .+.|| .||||++||+-+....|.||++.. ..||||||||+|+.
T Consensus 8 pv~~~~~~v~Fg~yt~~ei~klSv~kIt~p~~~D~lGhPi~GGLYDl~LGp~~~~~~C~TC~~~~-~~CPGH~GHIeL~~ 86 (1640)
T KOG0262|consen 8 PVMSFQPSVSFGSYTDQEIRKLSVKKITNPITFDNLGHPIPGGLYDLALGPLDNSDVCSTCNQDE-LNCPGHMGHIELPV 86 (1640)
T ss_pred cccccccceeeeccCHHHHhhcceeEecCceeecccCCCCCCcccccccCCccchhhhhhhcchh-hcCCCccCeeeecc
Confidence 345566679999999999999999642 12333 589999999555567999999985 79999999999999
Q ss_pred ccccccchHHHHHHHHHHHhhhc-------------------cchHH---------------------------------
Q 000291 80 PIYHPSHISELKLTMYAFQLQIK-------------------NDGVA--------------------------------- 107 (1714)
Q Consensus 80 PVfHpgf~k~I~~IL~~iC~ri~-------------------~~g~~--------------------------------- 107 (1714)
|||||+||+.++.+|++.|+.|. ..|+.
T Consensus 87 pvynPlfF~~ly~lLr~sCl~Chhf~~k~~~v~~~~cqLrll~~G~i~ea~~Le~i~~~~~~d~~d~~~~~~k~~~~~~v 166 (1640)
T KOG0262|consen 87 PVYNPLFFDFLYNLLRGSCLFCHHFRCKNVDVHILFCQLRLLEYGLIEEAEDLESITSETVEDNEDESLNEIKSCRAQYV 166 (1640)
T ss_pred cccCHHHHHHHHHHHHHHHHhhhhcccCcHHHHHHHHHHHHHHhchHHHHHHHHHhhhhhhccCcchhHHHHHhhhhhhc
Confidence 99999999999999999986441 00100
Q ss_pred -----------------------HHH----H------HHH--H-------------------------------------
Q 000291 108 -----------------------QRL----L------SSC--C------------------------------------- 115 (1714)
Q Consensus 108 -----------------------kri----~------~~C--C------------------------------------- 115 (1714)
+++ + ++| |
T Consensus 167 ~~~i~~~~~~~~~~~t~~~~~~~~~lv~~f~k~~l~~kkC~~C~~~~p~~rk~~~~kv~~~~~~~~~~~~~~~~~~i~~~ 246 (1640)
T KOG0262|consen 167 TEAISEALLDKSEPNTKNSTELKKKLVTAFLKNALSRKKCPRCKHSNPKLRKDGFRKVFIDALSSKVGANVIRGAKIKKD 246 (1640)
T ss_pred cHHHHHHhhcCCCccchhhHHHHHHHHHHHHHHhhccccCCcccCCCchhhccccceeeeehhcccccccchhheeeehh
Confidence 000 0 245 5
Q ss_pred ---------------------------------------------HHHHHHhcCChHHHHhhc---cC------CCCCCC
Q 000291 116 ---------------------------------------------EVKEMLKRIPEETRKKLA---GK------GYFPQD 141 (1714)
Q Consensus 116 ---------------------------------------------eV~~IfkkI~~ed~~~L~---~~------~~~~pe 141 (1714)
+|+++|+.+...+-.+|. .. .+.|.|
T Consensus 247 ~~~~~~~d~~~~G~~E~~~~g~d~~e~~~~~~~~~~t~~~~l~~tevR~~l~~lf~ne~~~l~~lf~l~~~~~~k~~p~d 326 (1640)
T KOG0262|consen 247 VGSKGFEDSGIDGSNEVEEDGKDLFEKSTEPAEFEKTGKKYLLPTEVREHLRDLFKNEGELLSYLFPLWDSGSGKIDPSD 326 (1640)
T ss_pred cccccccccccCCccccccccccccccccccccccccccccccHHHHHHHHHHHHhhhHHHHHHhhccccccccccCccc
Confidence 566666665554433332 11 234558
Q ss_pred cEEEeeccCCCCCCCCCcccCCCccccchhHHHHHHHHHHHHHHHHhhh-c--CC-C------------CccchhhhhhH
Q 000291 142 GYILEYLPVPPNCLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSSR-S--GT-P------------NFESQEVESND 205 (1714)
Q Consensus 142 ~~il~~lpVPP~~~Rp~~~~~g~~~~~~Dlt~~~l~~Il~~n~~lk~~~-~--g~-p------------~~~~~~~~~~~ 205 (1714)
+|||.+|||||+.+||+..+++. ..+++++..|.+||+.+..|+... . +. + .+....+.|..
T Consensus 327 ~FFld~l~VpPtrfRP~s~~gd~--~~en~Qt~~L~kVle~s~~i~~~~~~m~~kl~~~~k~~l~~~~g~~~kl~~aw~~ 404 (1640)
T KOG0262|consen 327 MFFLDNLLVPPTRFRPPSMLGDE--VHENPQTLNLNKVLESSVLIRKLLKDMKGKLDEELKLILERLRGIFSKLINAWLQ 404 (1640)
T ss_pred eeeeeccccCCcccCCchhcchh--hhcChHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHhhhhHHHHHHHHHHH
Confidence 99999999999999998887653 345777778999999988887532 1 10 0 11223467889
Q ss_pred HHHHHHHHHhhcCCCcCCCCCCCCCCCCCCCCchhhhhHh----hhhhcccccCCCCccceeEeCCCCCccccccchhhc
Q 000291 206 LQLAVGQYLEVRGTAKSSRDVDARFGVSQDPNSTTKAWLE----KMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEI 281 (1714)
Q Consensus 206 LQ~~v~~~~~~~~~~~~~~~~~~~~~~~k~~~~~ik~k~g----r~R~~l~GKRvdfSaRsVI~pdP~l~~~evgvP~~~ 281 (1714)
||.+|+.+||+....+..++ ...+|||.++ .||.++|||||||+|||||+|||||.+||||||..|
T Consensus 405 LQ~~vn~lfDs~~~~k~~r~----------~~pGikQiLEKKeGLFRkhMMGKRVN~AaRSVIsPDPnI~tnEIGIP~vF 474 (1640)
T KOG0262|consen 405 LQASVNVLFDSKMASKWSRD----------SPPGIKQILEKKEGLFRKHMMGKRVNYAARSVISPDPNIETNEIGIPPVF 474 (1640)
T ss_pred HHHHHHHHhccccccccccC----------CCchHHHHHHHhhhhHHHHhhccccchhhccccCCCCCccccccCCchHH
Confidence 99999999997443333222 2257777765 588889999999999999999999999999999999
Q ss_pred ccccccccccchhhHHHHHHHHHccCcc-------ccCCCCceEEeccCC---CC---cccc---------CCcceeehe
Q 000291 282 AQRITFEERVNVHNINYLQELVDNKLCL-------TYSDGSSSYSLREGS---KG---HTFL---------RPGQVVHRR 339 (1714)
Q Consensus 282 A~~Lt~pe~vt~~Ni~~l~~lv~~g~~~-------~~~~~~~~~~l~~~~---~~---~~~l---------~~g~iV~Rh 339 (1714)
|++|||||+||+||+++||++|+|||.. +-+++..++ |-... |. ...| .-+.+|+||
T Consensus 475 A~KLTyPepVt~~NV~elr~aViNGP~~hPGA~~iqd~dg~~t~-l~~~~~~qR~alA~qLLtpst~~~~~~~~K~V~RH 553 (1640)
T KOG0262|consen 475 AKKLTYPEPVTPWNVNELRKAVINGPDVHPGATYIQDEDGTLTL-LSPMTDEQREALANQLLTPSTGNPTEFGTKKVHRH 553 (1640)
T ss_pred HhhccCCCcCCcccHHHHHHHHhcCCCCCCCcceeecCCCceee-cCCCCHHHHHHHHHHhhccccCCCcccCCceeeee
Confidence 9999999999999999999999999962 112222111 11100 00 0111 146899999
Q ss_pred eeccceEEEeCCCccccccccceeeEecC-CCeEEecccccCCCCCccccccccccCCCCHHHHHHHHHhcccccccccC
Q 000291 340 IMDGDTVFINRPPTTHKHSLQALSVYVHD-DHTVKINPLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSS 418 (1714)
Q Consensus 340 l~dgd~VL~NRqPsLHr~Sima~~~~v~~-~~t~rln~~vC~pyNADFDGDeMnlHvPQS~eAraEa~~Lm~~~~nilsp 418 (1714)
+.+||+||+||||||||+|||||+|||++ +|||||||++|++|||||||||||+|+|||+.|||||+.|+++..||+.|
T Consensus 554 vknGDvvlmNRQPTLHKPSimaHkaRVL~gEktlRlHYANCkaYNADFDGDEMN~HfPQse~araEa~~ian~dsqYLvP 633 (1640)
T KOG0262|consen 554 VKNGDVVLMNRQPTLHKPSIMAHKARVLPGEKTLRLHYANCKAYNADFDGDEMNVHFPQSEIARAEAYNIANTDSQYLVP 633 (1640)
T ss_pred ccCCcEEEEcCCCccccchhhhhhheecCCcceeeeeecccccccCCCCcchhcccCCchhhHHHHHHHHhccCCceecc
Confidence 99999999999999999999999999997 59999999999999999999999999999999999999999999999999
Q ss_pred CCCCceEeechhhHhHHHhh-hccccCCHHHHHHhhcccc------cccccccccccccccccceeeeccccC----CCC
Q 000291 419 HNGNLNLQLATDALLSLKVM-FKKYFLDKAFTQQLAMFAL------SPLPRPALSKARCSARWTALQILQSVL----PPG 487 (1714)
Q Consensus 419 ~~G~Piigl~QD~llg~~ll-tkd~fl~~~~~~~l~~~~~------~~lp~PaI~Kp~~~~lWTGKQl~s~~L----P~~ 487 (1714)
++|.|++|||||||++..+| +||+||+|++|+||++.+. +.+++|+|+||. +|||||||||++| |++
T Consensus 634 t~G~PlrGLIQDHiVsgv~LT~rd~Fftre~y~qLv~~~l~~~~~rI~~lpPtIlkP~--~LWTGKQVIsTil~Ni~P~~ 711 (1640)
T KOG0262|consen 634 TDGTPLRGLIQDHIVSGVLLTMRDSFFTREDYQQLVFAGLSDTFKRIKLLPPTILKPA--PLWTGKQVISTILKNIIPEG 711 (1640)
T ss_pred CCCCchhhhhhhheeeeEEEEecccccCHHHHHHHHHHhhhhhccceeccCccccccc--cccccchHHHHHHHhcCCCC
Confidence 99999999999999976666 5999999999999987653 568999999999 9999999999977 432
Q ss_pred ---ccc---------------cC-----CEEEEEcceecccccccCcccchHHHHHHHHHHhhCHHHHHhchhhhHHHHH
Q 000291 488 ---FDS---------------CG-----DRYLIKKSEVLKGDFDRDTIPSVINEIVTSIFFEKGPEEVLEFFDSLQPLLM 544 (1714)
Q Consensus 488 ---~~~---------------~~-----~~viI~~Gell~G~ldK~~lg~s~~~Li~~i~~~~G~~~a~~fLd~lqrL~~ 544 (1714)
+|. .+ ..|+|++||||+|+|||+++|++.+||+|++++.||++.+.++|..+.||++
T Consensus 712 ~p~iNl~~kaKip~~~W~~~s~e~~l~Es~v~ir~GellcGVLDKa~~Gat~yGLvH~~~ElYG~~~s~~lLs~~srlFT 791 (1640)
T KOG0262|consen 712 HPPINLESKAKIPGKAWRVHSEEPKLNESQVLIREGELLCGVLDKAQFGATAYGLVHCCHELYGGETSGKLLSVFSRLFT 791 (1640)
T ss_pred CCcccchhcccCchhhcCCCCCcccCCcceEEEecCceEEEeechhhcCchhhhhhhhhhhhhCccchhhHHHHHHHHHH
Confidence 221 12 5699999999999999999999999999999999999999999999999999
Q ss_pred HHHHhcCceeeeCCcccCHHHHHHHHHHHHHHHHHHHH----------------hh----hhh------HHHHHHHHHHH
Q 000291 545 ENLFADGFSVSLEDFSLSKAALWNIQKEIQALYSLLYH----------------RM----STQ------NELVDLQIENH 598 (1714)
Q Consensus 545 ~~L~~~GFSiGi~Dl~~~~~~~~~i~~~i~~~~~~~~~----------------~~----~~~------~e~le~~i~~~ 598 (1714)
.||+++|||||++|+++.++.+..+++++++....-.+ ++ ..| ...|+..+...
T Consensus 792 ~ylq~~GFT~GvdDlll~~~~D~kR~~il~e~~~vG~qa~~~~~~l~~da~~del~~~le~~y~~d~~~~~~LD~~~k~~ 871 (1640)
T KOG0262|consen 792 AYLQMHGFTLGVDDLLLDKDADKKRREILRESRNVGNQAAKEAFGLDVDAPPDELRSRLEAIYLKDADKLAMLDRVMKSE 871 (1640)
T ss_pred HHHHHhccccccceeeechhhhHHHHHHHHhhhcccHHHHHHHhCCCCCCCHHHHHHHHHHHHhcchhHHHHHHHHHHHH
Confidence 99999999999999999999999998888865432111 11 111 23355556667
Q ss_pred HHHHHHHHHHHHHh--------cCCcccccccccchhhhhHHHHhHhccceecCCCccccccccccccccccccCCCCCC
Q 000291 599 IRHVKMLVAKFILK--------SSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLVEDIASHFERIYPMDLN 670 (1714)
Q Consensus 599 l~~~~~~i~~~~~~--------~n~l~~Mi~SGSKGS~~Ni~Qi~g~lGQQ~~~g~r~~~r~l~~~~~~~f~~~~p~~~d 670 (1714)
++.+.+.|.+.|+. .|++..|+.||||||++|++||+|+||||.++|+| +|.|+++.+.+++.+.|
T Consensus 872 ~n~~ts~I~~~cvP~GLlk~FP~N~mqlM~~SGAKGS~VN~~QISclLGQqeLEGkR------vPlMvSGKtLPsF~p~e 945 (1640)
T KOG0262|consen 872 LNGYTSEIVKKCVPDGLLKKFPENNMQLMIQSGAKGSNVNTSQISCLLGQQELEGKR------VPLMVSGKTLPSFAPYE 945 (1640)
T ss_pred HhhhhHHHHhhhccchhhhcCCcchHHHHHHhcCCcccccHHHHHHhhhhHhhcCCc------cceeecCCccCCcCCCC
Confidence 77777788887764 48999999999999999999999999999999887 56777776544433459
Q ss_pred CCCCccceecCcccccCCccceEEeeccccceeeecccccCCCCchhHHHHHHHhceEEEeccccccccCCceeEEEecc
Q 000291 671 YPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYDGTVRNVCSNSIIQFDYAV 750 (1714)
Q Consensus 671 ~~~~a~GfV~ssF~~GL~P~EfFfHamagREGLiDTAvkTA~sGYLqRrLvk~ledl~v~YD~Tvr~~~~~~IiQf~yg~ 750 (1714)
.+|+|+|||..+|++|+.|+||||||||||||||||||||++||||||||||+||.|+|+||.|||++ +|+||||.|||
T Consensus 946 ~spraGGfI~~RFlTGi~PqeyfFHCMAGREGLIDTAVKTSRSGYLQRCLiKhLEgl~V~YD~TVRDs-DgsvVQF~YGE 1024 (1640)
T KOG0262|consen 946 TSPRAGGFIDGRFLTGIKPQEYFFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLKVHYDLTVRDS-DGSVVQFMYGE 1024 (1640)
T ss_pred CCCCCCCcccceeecCCCchHHhhhhhccccchhhhHHhcccchHHHHHHHHhhhhcEEeccceEEcC-CCcEEEEeecC
Confidence 99999999999999999999999999999999999999999999999999999999999999999995 89999999999
Q ss_pred ccccc---------------------------------------------------------------------------
Q 000291 751 NARKS--------------------------------------------------------------------------- 755 (1714)
Q Consensus 751 dg~~~--------------------------------------------------------------------------- 755 (1714)
||+|.
T Consensus 1025 DglDitKssfl~~~~f~~~Ny~avl~~~~~~~v~s~~d~~~a~~~~k~i~kw~kk~~w~~~~k~~~cpdpv~~k~~p~~y 1104 (1640)
T KOG0262|consen 1025 DGLDITKSSFLNKKEFPTDNYEAVLLKYKSESVLSAFDIKKASKYIKKILKWKKKHMWFELDKKIACPDPVLAKYNPDKY 1104 (1640)
T ss_pred ccccccHHhhcchhhhhhhhHHHHHhhhChHHHhhhhhhHHHHHHHHHHHHHHhhhccchhhcccCCCChhhhhcchhhh
Confidence 99751
Q ss_pred ------------------------------------------cCcCCCCceeEEeccccCChhHHHHhhcCCC-------
Q 000291 756 ------------------------------------------HSLFPAGEPVGVLAATAMSNPAYKAVLDSSP------- 786 (1714)
Q Consensus 756 ------------------------------------------~~lv~~GepVG~laaqsigepatq~~L~t~~------- 786 (1714)
++|+.|||+||+|||||||||.|||||+|||
T Consensus 1105 ~gsvsekf~~~i~~f~~~~~k~~~s~~~~~~~lr~ll~~K~~~SLa~PGE~VGvlAAQSIGEPSTQMTLNTFHfAGrGem 1184 (1640)
T KOG0262|consen 1105 LGSVSEKFRKKIDDFDDENAKKEKSEEPSEEKLRRLLQLKYIRSLADPGEPVGVLAAQSIGEPSTQMTLNTFHFAGRGEM 1184 (1640)
T ss_pred hccccHHHHHHHHHHHHHhhhhhccccchHHHHHHHHHHHHHHHhcCCCCcceeeeecccCCCcceeehhheeeccccce
Confidence 3478999999999999999999999999998
Q ss_pred CCCCchHHHHHHHHhhccCCCCCCCceEEEEcCCCCCCCccccHHHHHHHHhhhccccHhhhhheeEEEec--CCccccC
Q 000291 787 SSNNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYK--KPEIISD 864 (1714)
Q Consensus 787 ~~~~g~~rlkEil~~~~~~k~~~~d~~~~l~L~~~~~~~~~~~e~~a~~V~~~le~vtl~dv~~~i~I~y~--~~~~~~~ 864 (1714)
|+|+|+|||+|||+..+. .+++|.|++.+.... ..+.|..+...|.+|+|++|+..+.+.-. -... ..
T Consensus 1185 NVTLGIPRLREIlMtASa---nIkTP~mt~pi~~g~------s~~ra~~i~~~l~rV~L~evlk~v~vte~~t~~~~-~~ 1254 (1640)
T KOG0262|consen 1185 NVTLGIPRLREILMTASA---NIKTPSMTVPIKNGV------SDERADDITKELRRVTLKEVLKKVGVTEKITMVEN-QS 1254 (1640)
T ss_pred eeeecchHHHHHHHHHhh---ccCCCceeeeccCCc------cHHHHHHHHHHHHHHHHHHHHhheeeeEEEEeecc-cc
Confidence 999999999999996442 255668999987653 44789999999999999999998876411 1100 01
Q ss_pred CCceEEEEEecH--HHHHHhcCChhhhHHHHHHhhhhh-h-------hcch-----------------------------
Q 000291 865 DEGLVGHIHLNK--ILLEDLRISMHDILPKCQETLKSF-C-------KKKK----------------------------- 905 (1714)
Q Consensus 865 ~~~wv~~i~Ld~--e~L~~~~lt~~~I~~k~~~~~~~~-~-------~~~~----------------------------- 905 (1714)
.....+||.|.. +.=++++|+-++|.+.++.+|-+. . ++.+
T Consensus 1255 ~~~y~lr~~~~~~~~y~~e~~v~~e~i~~~m~~~Flk~L~~aI~k~~~k~~~~~~~~~dd~~~~~~~~~~~~~~~~~~~~ 1334 (1640)
T KOG0262|consen 1255 CKKYKLRFDLLPREEYQEEYDVRPEDIEEVMENRFLKLLERAIKKKLKKAKYTRGMSNDDADPDDGNEVDNNDEVGGEDN 1334 (1640)
T ss_pred ceEEEEEEeecCHHHhhhhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhhccccccCCccccccCCccccccCCcc
Confidence 133456666643 223457777777765433322110 0 0000
Q ss_pred ------------h-----hH------------------------------------------------------------
Q 000291 906 ------------M-----KK------------------------------------------------------------ 908 (1714)
Q Consensus 906 ------------~-----~~------------------------------------------------------------ 908 (1714)
. .+
T Consensus 1335 ~~~~~e~~~~~ddddas~~k~~~k~~~~~dYe~~de~e~~~~~~~e~~~~~e~~e~d~e~g~dg~~~~~~~~~e~~~~~~ 1414 (1640)
T KOG0262|consen 1335 EDSDDESEDDEDDDDASDAKLHKKTEEEADYESEDEDERVEEREDEGDEDEESDEDDEEVGLDGTPEPEEEDQEGQPEVN 1414 (1640)
T ss_pred ccccccccccCcccchhHHHHhhhhccccCcCCCchhhhhhhhhcccccccccccchhhcccCCCCCcccccccCCchhh
Confidence 0 00
Q ss_pred -H---------HHHhhc-ccccc---ccccc----------------c----cccccccC-CCcceE------------E
Q 000291 909 -V---------VQFFKN-TSLSI---SECCS----------------F----QQSCADKR-SNMPCL------------M 941 (1714)
Q Consensus 909 -i---------~~~~~~-~~~~~---~~~gi----------------~----~~~~~~~~-~~~~~l------------~ 941 (1714)
+ ...|.+ ..+.. .-|-+ + ..++|++- +=+.|+ .
T Consensus 1415 ~~er~~qs~~~~~~fi~~y~fd~~~~~wcev~~~lp~~~~k~~mssiVe~~~~~~vI~q~~gIeRc~~~~~~~~~k~~~~ 1494 (1640)
T KOG0262|consen 1415 AVERREQSVKKRHDFISRYTFDKESGKWCEVELKLPLDKEKLDMSSIVESIAPKSVIHQVPGIERCVVSEPQDDVKEKSV 1494 (1640)
T ss_pred HHHHHHHHHHHHHHHhhhhccccccCcEEEEEEEecCCCcchHHHHHHHHHhcceeeeccCCceeeeccCCcccccccce
Confidence 0 000100 00000 00000 0 11112211 011111 0
Q ss_pred EEEcccC------CcccccceecccccchHHHHHHhhhhhHHHHHH----HHHHHHHhhcccccceeeeeccceeeeceE
Q 000291 942 FVLRGAS------DSYLDKLSGVLANMIYPVLLETIIKENWWVRQR----LSASVTMVAKGVLKEHLILLANSMTCAGDL 1011 (1714)
Q Consensus 942 ~~~~~~~------~~~~vd~~~~~~n~I~~i~r~~IIkgi~w~r~~----l~~~~~~~~~~V~~rHl~LlAd~MT~~G~~ 1011 (1714)
+.+++.+ ..+..|+.++++|+|..|++ + -|+++.|+. +..++.-+|+.||+|||.||||||||+|.+
T Consensus 1495 l~TeGVnl~a~~~~~d~LDv~~lySNDI~ail~-t--yGVEAar~~Iv~Ev~~VF~vYGIsVd~RHLsLiADYMTf~G~y 1571 (1640)
T KOG0262|consen 1495 LLTEGVNLPALFDHADILDVNRLYSNDIHAILN-T--YGVEAARNAIVNEVNNVFKVYGISVDIRHLSLIADYMTFEGGY 1571 (1640)
T ss_pred ehhcCccHHHHHHHHhhhhhhhhccchHHHHHH-H--hhHHHHHHHHHHHHHHhhhheeeeecHHHHHHHHHHHhhcccc
Confidence 1223322 24567889999999998882 2 244444422 336677778999999999999999999999
Q ss_pred eeeccccccccccCcccccccccccccCcHHHHHHHHhhcCCCCCCchhhhhhcCCcccccccceEEEEec
Q 000291 1012 VGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGSRFDLLWQ 1082 (1714)
Q Consensus 1012 ~~~~r~G~~~~~~s~l~~a~Fe~~t~~~~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~~~~l~~~ 1082 (1714)
.+|||+|| +...||+.+++||.+ .++|.+||.+|+.|+|+++|++|++|+++..|||+ |||+-+
T Consensus 1572 ~pfnR~Gm-~~ssSP~qkMsFETt-----~~Fl~~Aa~~g~~D~L~sPSArLvvG~~~r~GTG~-Fdll~~ 1635 (1640)
T KOG0262|consen 1572 QPFNRMGM-ESSSSPLQKMSFETT-----CQFLKQAALFGEEDELSSPSARLVVGLPVRGGTGS-FDLLQK 1635 (1640)
T ss_pred cccccccc-ccCCChhHhhhHHHH-----HHHHHHHHhcCcccccCCCcceeEeccccCCCcce-eeeecc
Confidence 99999998 778898888888887 79999999999999999999999999999999999 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=1.5e-183 Score=1769.62 Aligned_cols=740 Identities=27% Similarity=0.423 Sum_probs=645.2
Q ss_pred ccceeeEEEecCCHHHHHHhccccccccc---------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeEEcCccc
Q 000291 11 EGQIVGIRFGLATQKEICTASISDCSISH---------ASQLANPFLGLPLEFGKCESCGTSEPGKCEGHFGYIELPIPI 81 (1714)
Q Consensus 11 ~~~I~~I~F~l~S~eEI~k~Sv~~~~I~~---------~~gl~DprLG~~~~~~~C~TCg~~~~~~CpGHFGhIeL~~PV 81 (1714)
+++|++|+|++||+|||+++||+++...+ ++||+|||||++++...|+|||++. .+||||||||||++||
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 46799999999999999999997532211 3589999999999999999999995 8999999999999999
Q ss_pred ccccchHHHHHHHHHHHhhhc-----c---c------------------hHHHHHHHH------H--H------------
Q 000291 82 YHPSHISELKLTMYAFQLQIK-----N---D------------------GVAQRLLSS------C--C------------ 115 (1714)
Q Consensus 82 fHpgf~k~I~~IL~~iC~ri~-----~---~------------------g~~kri~~~------C--C------------ 115 (1714)
|||+||+.|++||+|+|.+|- . . .+.+++.+. | |
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 999999999999999987653 0 0 111233332 4 5
Q ss_pred -----------------HHHHHHhcCChHHHHhhccC-CCCCCCcEEEeeccCCCCCCCCCcccCCCccccchhHHHHHH
Q 000291 116 -----------------EVKEMLKRIPEETRKKLAGK-GYFPQDGYILEYLPVPPNCLSVPDISDGVSTMSSDLSIAMLK 177 (1714)
Q Consensus 116 -----------------eV~~IfkkI~~ed~~~L~~~-~~~~pe~~il~~lpVPP~~~Rp~~~~~g~~~~~~Dlt~~~l~ 177 (1714)
+|++||++|+++|+++|+.. ...+|+||||++|||||+|+||++.+++....+||+|+ +|+
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 78999999999999998642 23579999999999999999999988766677899998 799
Q ss_pred HHHHHHHHHHhh-hcCCCCccchhhhhhHHHHHHHHHHhhcC--CCcCCCCCCCCCC-CCCCCCchhhhhHhhhhhcccc
Q 000291 178 KVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEVRG--TAKSSRDVDARFG-VSQDPNSTTKAWLEKMRTLFIR 253 (1714)
Q Consensus 178 ~Il~~n~~lk~~-~~g~p~~~~~~~~~~~LQ~~v~~~~~~~~--~~~~~~~~~~~~~-~~k~~~~~ik~k~gr~R~~l~G 253 (1714)
+||+.|+.|++. ..+++..+. ...|++||.+|++|||+.. .+.+. ++.+ ..+.+.+++++|+||||+||||
T Consensus 239 ~II~~N~~Lk~~~~~g~~~~~~-~~~~~~LQ~~v~~~~d~~~~~~~~~~----~~~~~~~~~i~~~l~gK~G~~R~nl~G 313 (868)
T TIGR02390 239 DIIRINQRLKENIEAGAPQLII-EDLWELLQYHVATYFDNELPGIPPAR----HRSGRPLKTLAQRLKGKEGRFRGNLSG 313 (868)
T ss_pred HHHHHHHHHHHHHHcCCchhhh-HHHHHHHHHHHHHHHcCCCCCCCccc----cCCCCCchhhHhhhccccccccccccc
Confidence 999999999875 466666543 4578999999999998632 21111 1111 2355668899999999999999
Q ss_pred cCCCCccceeEeCCCCCccccccchhhcccccccccccchhhHHHHHHHHHccCcc------ccCCCCceEEeccCCCC-
Q 000291 254 KGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDNKLCL------TYSDGSSSYSLREGSKG- 326 (1714)
Q Consensus 254 KRvdfSaRsVI~pdP~l~~~evgvP~~~A~~Lt~pe~vt~~Ni~~l~~lv~~g~~~------~~~~~~~~~~l~~~~~~- 326 (1714)
|||||||||||+|||+|++||||||..||++|||||+||+|||++|++||.||++. +++..+.++.|++.++.
T Consensus 314 KRvd~s~RsVI~pdp~l~~~evGvP~~~A~~Lt~pe~Vt~~N~~~l~~lv~ng~~~~pga~~i~~~~g~~~~l~~~~~~~ 393 (868)
T TIGR02390 314 KRVNFSARTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVLNGPDSWPGANYVIRPDGRRIKIRDENKEE 393 (868)
T ss_pred ccccccCCceeeCCCCCcCCeeeCcHHHHHhCCCCeEEehhhHHHHHHHHHcCCccCCCceEEEcCCCcEEechhhhHHH
Confidence 99999999999999999999999999999999999999999999999999999852 12222234445443322
Q ss_pred -ccccCCcceeeheeeccceEEEeCCCccccccccceeeEecCCCeEEecccccCCCCCccccccccccCCCCHHHHHHH
Q 000291 327 -HTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQSLAAKAEV 405 (1714)
Q Consensus 327 -~~~l~~g~iV~Rhl~dgd~VL~NRqPsLHr~Sima~~~~v~~~~t~rln~~vC~pyNADFDGDeMnlHvPQS~eAraEa 405 (1714)
...|++||+|+|||+|||+|||||||||||||||||+|+|++++||||||+||+||||||||||||||||||++|||||
T Consensus 394 ~~~~l~~g~~v~rhl~dgd~vl~NRqPsLHr~si~a~~~~v~~~~t~r~n~~~c~~~NADFDGDeMn~h~Pqs~~a~aEa 473 (868)
T TIGR02390 394 LAERLEPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEA 473 (868)
T ss_pred HHhhcccCCEEEEehhcCccceeccCCccccccceeEEEEEecCceEeeccccCCccccCcccceeeEecCCCHHHHHHH
Confidence 3468999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhcccccccccCCCCCceEeechhhHhHHHhhh-ccccCCHHHHHHhhccccc--ccccccccccccccccceeeeccc
Q 000291 406 LELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF-KKYFLDKAFTQQLAMFALS--PLPRPALSKARCSARWTALQILQS 482 (1714)
Q Consensus 406 ~~Lm~~~~nilsp~~G~Piigl~QD~llg~~llt-kd~fl~~~~~~~l~~~~~~--~lp~PaI~Kp~~~~lWTGKQl~s~ 482 (1714)
++||++.+||++|++|+|+++++||+|+|+|+|| +|+||+++++++|++.... .+|+|||+||. +|||||||||+
T Consensus 474 ~~Lm~~~~~~~sp~~g~p~~~~~QD~l~g~~~LT~~d~f~~~~~~~~l~~~~~~~~~~~~p~i~kp~--~lwTGKqi~s~ 551 (868)
T TIGR02390 474 RELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQTILGVAGYFGDPPEPAIEKPK--EYWTGKQIFSA 551 (868)
T ss_pred HHHhhchhceecCCCCCeeEEeehhhhhheeeeeeccccCCHHHHHHHHhcCCccccCCCceecCCc--ccccHHHHHHH
Confidence 9999999999999999999999999999999998 7999999999999987653 47899999998 99999999999
Q ss_pred cCCCCcccc-------------------CCEEEEEcceecccccccCcccchHHHHHHHHHHhhCHHHHHhchhhhHHHH
Q 000291 483 VLPPGFDSC-------------------GDRYLIKKSEVLKGDFDRDTIPSVINEIVTSIFFEKGPEEVLEFFDSLQPLL 543 (1714)
Q Consensus 483 ~LP~~~~~~-------------------~~~viI~~Gell~G~ldK~~lg~s~~~Li~~i~~~~G~~~a~~fLd~lqrL~ 543 (1714)
+||.++++. ++.|+|+||+|++|+|||+++|++.++|||.|+++||+++|++||+.+|+|+
T Consensus 552 ~lp~~~n~~~~~~~~~~~~~~~~~~~~~d~~v~i~~g~ll~G~ldK~~lg~~~~~li~~i~~~yG~~~a~~fl~~~~~l~ 631 (868)
T TIGR02390 552 FLPEDLNFEGRAKICSGSDACKKEECPHDAYVVIKNGKLLKGVIDKKAIGAEKGKILHRIVREYGPEAARRFLDSVTRLF 631 (868)
T ss_pred hcCCCCcceecccccccccccccccCCCcceEEEecCeEEeeeecHHHhccCcccHHHHHHHHHCHHHHHHHHHHHHHHH
Confidence 999876541 3458999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcCceeeeCCcccCHHHHHHHHHHHHHHHHHHHHhhhh-------------hHHHHHHHHHHHHHHHHHHHHHHH
Q 000291 544 MENLFADGFSVSLEDFSLSKAALWNIQKEIQALYSLLYHRMST-------------QNELVDLQIENHIRHVKMLVAKFI 610 (1714)
Q Consensus 544 ~~~L~~~GFSiGi~Dl~~~~~~~~~i~~~i~~~~~~~~~~~~~-------------~~e~le~~i~~~l~~~~~~i~~~~ 610 (1714)
++||+++||||||+|+++++++.+.+++.++++++.+.++... .++.+|..+...|+++++.+++.+
T Consensus 632 ~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~e~~i~~~l~~~r~~~~~~~ 711 (868)
T TIGR02390 632 IRFITLRGFTTGIDDIDIPKEAKEEIEELIEKAEKRVDNLIERYRNGELEPLPGRTVEETLEMKIMEVLGKARDEAGEVA 711 (868)
T ss_pred HHHHHhccEEeehhheeeCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCcCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999988888888877665544332 356778888888999998877766
Q ss_pred Hh----cCCcccccccccchhhhhHHHHhHhccceecCCCccccccccccccccccccCCCCCCCCCCccceecCccccc
Q 000291 611 LK----SSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLVEDIASHFERIYPMDLNYPTAKYGLIKGCFFHG 686 (1714)
Q Consensus 611 ~~----~n~l~~Mi~SGSKGS~~Ni~Qi~g~lGQQ~~~g~r~~~r~l~~~~~~~f~~~~p~~~d~~~~a~GfV~ssF~~G 686 (1714)
.+ .|++.+|+.||||||++|++||+||||||.++|+| +++++..|++|||.. +++.|+|+|||.|||++|
T Consensus 712 ~~~l~~~N~~~~M~~sGsKGS~~Ni~Qi~~~lGQQ~~~g~r-i~~~~~~rtlp~f~~-----~d~~~~~~GfV~~sF~~G 785 (868)
T TIGR02390 712 EKYLDPENHAVIMARTGARGSLLNITQMAAMVGQQSVRGGR-IRRGYRNRTLPHFKK-----GDIGAKARGFVRSSFKKG 785 (868)
T ss_pred HHhcCCCcchhhhhhccCCcccccHHHHHhccCccccCCCc-CccccccCCCCCCCC-----CCCCcccCceecccccCC
Confidence 54 59999999999999999999999999999999775 677788889999963 478899999999999999
Q ss_pred CCccceEEeeccccceeeecccccCCCCchhHHHHHHHhceEEEeccccccccCCceeEEEeccccccccCcCCCCceeE
Q 000291 687 LDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYDGTVRNVCSNSIIQFDYAVNARKSHSLFPAGEPVG 766 (1714)
Q Consensus 687 L~P~EfFfHamagREGLiDTAvkTA~sGYLqRrLvk~ledl~v~YD~Tvr~~~~~~IiQf~yg~dg~~~~~lv~~GepVG 766 (1714)
|+|+|||||||||||||||||||||+||||||||||+||||+|+||+|||++ +|+||||.||+||+|+..+ +-++||.
T Consensus 786 L~p~EfFfH~m~gReGLiDTAvKTa~sGYLqRrLvk~lEdl~v~yD~tVR~~-~g~iiQf~YG~dg~d~~~~-~~~~~~~ 863 (868)
T TIGR02390 786 LDPTEYFFHAAGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDT-RGNLIQFKYGEDGVDPMKS-DHGKPVD 863 (868)
T ss_pred CCHHHHHHHHhhhccccccccccccccchhHHHHHHHHhheEEecCCeEEeC-CCcEEEEeccCCCcCHHHh-ccCcccc
Confidence 9999999999999999999999999999999999999999999999999995 7899999999999987764 3667765
Q ss_pred E
Q 000291 767 V 767 (1714)
Q Consensus 767 ~ 767 (1714)
+
T Consensus 864 ~ 864 (868)
T TIGR02390 864 V 864 (868)
T ss_pred c
Confidence 4
No 6
>PRK08566 DNA-directed RNA polymerase subunit A'; Validated
Probab=100.00 E-value=3.8e-182 Score=1761.55 Aligned_cols=737 Identities=26% Similarity=0.400 Sum_probs=645.2
Q ss_pred cccccceeeEEEecCCHHHHHHhccccccccc-----------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeEE
Q 000291 8 TILEGQIVGIRFGLATQKEICTASISDCSISH-----------ASQLANPFLGLPLEFGKCESCGTSEPGKCEGHFGYIE 76 (1714)
Q Consensus 8 ~~~~~~I~~I~F~l~S~eEI~k~Sv~~~~I~~-----------~~gl~DprLG~~~~~~~C~TCg~~~~~~CpGHFGhIe 76 (1714)
+...++|.+|+|++||+|||+++||++ |++ ++||+|||||++++...|+|||++. .+|||||||||
T Consensus 3 ~~~~~~I~~I~F~~~S~eEI~klSv~~--It~~~~~d~~g~P~~gGL~D~RLG~~~~~~~C~TCg~~~-~~CPGHFGhIe 79 (882)
T PRK08566 3 MMIPKRIGSIKFGLLSPEEIRKMSVTK--IITADTYDDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRA-GECPGHFGHIE 79 (882)
T ss_pred CCCceeeeeEEEecCCHHHHHHhCeEE--EecccccCCCCCcCCCCCCCcccCCCCCCCCCCCCCCCC-CcCCCcceEEe
Confidence 446789999999999999999999965 432 3599999999999999999999996 89999999999
Q ss_pred cCcccccccchHHHHHHHHHHHhhhc-----cc--------------------hHHHHHHHHH--------H--------
Q 000291 77 LPIPIYHPSHISELKLTMYAFQLQIK-----ND--------------------GVAQRLLSSC--------C-------- 115 (1714)
Q Consensus 77 L~~PVfHpgf~k~I~~IL~~iC~ri~-----~~--------------------g~~kri~~~C--------C-------- 115 (1714)
|++|||||+||+.|++||+|+|.+|- .. .+.+++.+.| |
T Consensus 80 L~~PVfhpgf~~~v~~iL~~iC~~C~rll~~~~~~~~~~~~l~~~~~~~~~~~~l~k~i~k~~k~~~~C~~Cg~~~~ki~ 159 (882)
T PRK08566 80 LARPVIHVGFAKLIYKLLRATCRECGRLKLTEEEIEEYLEKLERLKEWGSLADDLIKEVKKEAAKRMVCPHCGEKQYKIK 159 (882)
T ss_pred ccccccchhHHHHHHHHHHHhhhhhCceeccccchHHHHHHHhchhhhhhhHHHHHHHHHHHhcCCCCCCCcCCCCceEE
Confidence 99999999999999999999987652 10 0123334434 5
Q ss_pred ---------------------HHHHHHhcCChHHHHhhccC-CCCCCCcEEEeeccCCCCCCCCCcccCCCccccchhHH
Q 000291 116 ---------------------EVKEMLKRIPEETRKKLAGK-GYFPQDGYILEYLPVPPNCLSVPDISDGVSTMSSDLSI 173 (1714)
Q Consensus 116 ---------------------eV~~IfkkI~~ed~~~L~~~-~~~~pe~~il~~lpVPP~~~Rp~~~~~g~~~~~~Dlt~ 173 (1714)
+|++||++|+++|+++|+.. ...+|+||||++|||||+|+||++.+++....+||+|.
T Consensus 160 ~~~~~~~~~~~~~~~~~L~p~~V~~ilk~I~~eD~~lLg~~~~~~~Pe~~il~~lPVpP~~iRPsv~~~~g~~~eDDLT~ 239 (882)
T PRK08566 160 FEKPTTFYEERKEGLVKLTPSDIRERLEKIPDEDLELLGINPEVARPEWMVLTVLPVPPVTVRPSITLETGQRSEDDLTH 239 (882)
T ss_pred EecceeEEEecCCCceeCCHHHHHHHHHhCCHHHHHHhCCCCCCCCcceeEEeeeecCCCCCcCcEEeCCCcccCchHHH
Confidence 88999999999999998642 33579999999999999999999998776677899998
Q ss_pred HHHHHHHHHHHHHHhh-hcCCCCccchhhhhhHHHHHHHHHHhhcCC--CcCCCCCCCCCCCCCCCCchhhhhHhhhhhc
Q 000291 174 AMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEVRGT--AKSSRDVDARFGVSQDPNSTTKAWLEKMRTL 250 (1714)
Q Consensus 174 ~~l~~Il~~n~~lk~~-~~g~p~~~~~~~~~~~LQ~~v~~~~~~~~~--~~~~~~~~~~~~~~k~~~~~ik~k~gr~R~~ 250 (1714)
+|++||+.|+.|++. ..+++... ....|..||.+|+.|+|+... +.+. ...+ ...+.+.+++|+|+||||+|
T Consensus 240 -~L~~II~~N~~Lk~~~~~g~~~~~-~~~~~~~LQ~~v~~~~d~~~~~~~~~~-~~~~--~~~~~i~~~l~gK~G~fR~n 314 (882)
T PRK08566 240 -KLVDIIRINQRLKENIEAGAPQLI-IEDLWELLQYHVTTYFDNEIPGIPPAR-HRSG--RPLKTLAQRLKGKEGRFRGN 314 (882)
T ss_pred -HHHHHHHHHHHHHHHHHcCCcHHH-HHHHHHHHHHHHHHHhcCCccCCcccc-cCCC--CCccchHHhcccCCCccccc
Confidence 799999999999875 45666544 356789999999999986321 1111 1011 12355668899999999999
Q ss_pred ccccCCCCccceeEeCCCCCccccccchhhcccccccccccchhhHHHHHHHHHccCccccCCCCceEEecc--------
Q 000291 251 FIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDNKLCLTYSDGSSSYSLRE-------- 322 (1714)
Q Consensus 251 l~GKRvdfSaRsVI~pdP~l~~~evgvP~~~A~~Lt~pe~vt~~Ni~~l~~lv~~g~~~~~~~~~~~~~l~~-------- 322 (1714)
||||||||||||||+|||+|.++|||||..||++|||||+||+|||++|++||.|||. .|+ +++|+++.
T Consensus 315 l~GKRvd~s~RsVI~pdp~l~~~evGvP~~~A~~Lt~pe~v~~~N~~~l~~~v~ng~~-~~p--ga~~i~~~~g~~~~l~ 391 (882)
T PRK08566 315 LSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNGPE-KHP--GANYVIRPDGRRIKLT 391 (882)
T ss_pred cccccccCcCCceeeCCCCCcCCeeeCcHHHHHhCCCCeEEchhhHHHHHHHHHcCCC-cCC--CceEEEcCCCceeeeh
Confidence 9999999999999999999999999999999999999999999999999999999986 232 33444332
Q ss_pred -CCCC--ccccCCcceeeheeeccceEEEeCCCccccccccceeeEecCCCeEEecccccCCCCCccccccccccCCCCH
Q 000291 323 -GSKG--HTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQSL 399 (1714)
Q Consensus 323 -~~~~--~~~l~~g~iV~Rhl~dgd~VL~NRqPsLHr~Sima~~~~v~~~~t~rln~~vC~pyNADFDGDeMnlHvPQS~ 399 (1714)
..+. +..|++||+|+|||+|||+|||||||||||||||||+|+|++++||||||+||+||||||||||||+|||||+
T Consensus 392 ~~~~~~~~~~l~~g~~v~Rhl~dgd~vl~NRqPsLHr~si~a~~~~v~~~~t~r~n~~~c~~~NADFDGDeMn~h~Pqs~ 471 (882)
T PRK08566 392 DKNKEELAEKLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTE 471 (882)
T ss_pred hhhHHHHHHhccccceehhhhhcCceeeecCCCcccccccceeEEEEecCceEeeccccCCCccCCccCcEEEEecCCCH
Confidence 2221 2468899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcccccccccCCCCCceEeechhhHhHHHhhh-ccccCCHHHHHHhhccccc---ccccccccccccccccc
Q 000291 400 AAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF-KKYFLDKAFTQQLAMFALS---PLPRPALSKARCSARWT 475 (1714)
Q Consensus 400 eAraEa~~Lm~~~~nilsp~~G~Piigl~QD~llg~~llt-kd~fl~~~~~~~l~~~~~~---~lp~PaI~Kp~~~~lWT 475 (1714)
+|||||++||++.+||++|++|+|+++++||+|+|+|+|| +|+||+++++++|++++.+ .+|+|||+||. +|||
T Consensus 472 ~a~aEa~~Lm~~~~~~~sp~~g~pi~~~~QD~l~g~~~lt~~d~f~~~~~~~~l~~~~~~~~~~~~~pai~~p~--~lwT 549 (882)
T PRK08566 472 EARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAAGIDELPEPEPAIENGK--PYWT 549 (882)
T ss_pred HHHHHHHHHhcchhcEecCCCCCeeEEeehHHHHHHHHHHhccccCCHHHHHHHHHhCCccccccCCcccCCCc--cccc
Confidence 9999999999999999999999999999999999999998 7999999999999998763 57899999998 9999
Q ss_pred eeeeccccCCCCcccc-------------------CCEEEEEcceecccccccCcccchHHHHHHHHHHhhCHHHHHhch
Q 000291 476 ALQILQSVLPPGFDSC-------------------GDRYLIKKSEVLKGDFDRDTIPSVINEIVTSIFFEKGPEEVLEFF 536 (1714)
Q Consensus 476 GKQl~s~~LP~~~~~~-------------------~~~viI~~Gell~G~ldK~~lg~s~~~Li~~i~~~~G~~~a~~fL 536 (1714)
||||||++||.++++. ++.|+|+||||++|+|||++||++.++|||.|+++||+++|+.||
T Consensus 550 GKqi~s~~lp~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~gell~g~ldK~~lg~~~~~li~~i~~~yG~~~a~~fl 629 (882)
T PRK08566 550 GKQIFSLFLPKDLNLEFKAKICSGCDECKKEDCEHDAYVVIKNGKLLEGVIDKKAIGAEQGSILDRIVKEYGPERARRFL 629 (882)
T ss_pred HHHHHHHHcCCCCCceeeccccccccccccccCCCCceEEEecCEEEeccccHHHhhcccchHHHHHHHHhCHHHHHHHH
Confidence 9999999999866531 457899999999999999999999999999999999999999999
Q ss_pred hhhHHHHHHHHHhcCceeeeCCcccCHHHHHHHHHHHHHHHHHHHHhhh-------------hhHHHHHHHHHHHHHHHH
Q 000291 537 DSLQPLLMENLFADGFSVSLEDFSLSKAALWNIQKEIQALYSLLYHRMS-------------TQNELVDLQIENHIRHVK 603 (1714)
Q Consensus 537 d~lqrL~~~~L~~~GFSiGi~Dl~~~~~~~~~i~~~i~~~~~~~~~~~~-------------~~~e~le~~i~~~l~~~~ 603 (1714)
+.+++|+++||+.+||||||+|+++++++.+.++++++++++.+.++.. +.++.+|..+.+.|++++
T Consensus 630 ~~~~~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~e~~i~~~l~~~r 709 (882)
T PRK08566 630 DSVTRLAIRFIMLRGFTTGIDDEDIPEEAKEEIDEIIEEAEKRVEELIEAYENGELEPLPGRTLEETLEMKIMQVLGKAR 709 (882)
T ss_pred HHHHHHHHHHHHhcCEEeehhhcccCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccccCCCHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999998888888877765543322 234678888888999999
Q ss_pred HHHHHHHHh----cCCcccccccccchhhhhHHHHhHhccceecCCCccccccccccccccccccCCCCCCCCCCcccee
Q 000291 604 MLVAKFILK----SSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLVEDIASHFERIYPMDLNYPTAKYGLI 679 (1714)
Q Consensus 604 ~~i~~~~~~----~n~l~~Mi~SGSKGS~~Ni~Qi~g~lGQQ~~~g~r~~~r~l~~~~~~~f~~~~p~~~d~~~~a~GfV 679 (1714)
+.+++.+.+ .|++.+|+.||||||++|++||+||||||+++|+| +++++..|++|||.. ++..|+++|||
T Consensus 710 ~~~~~~~~~~l~~~N~~~~M~~SGsKGS~~N~~Qi~~~lGqQ~~~g~r-i~~~~~~rtLP~f~~-----~d~~~~~~GfV 783 (882)
T PRK08566 710 DEAGEIAEKYLGLDNPAVIMARTGARGSMLNLTQMAACVGQQSVRGER-IRRGYRDRTLPHFKP-----GDLGAEARGFV 783 (882)
T ss_pred HHHHHHHHHhcCCCCcceeeeccccccCHHHHHHHHhccCceecCCCc-CccCccCccCCCCCC-----CCCCcccCcee
Confidence 888777665 59999999999999999999999999999999765 678888999999963 48899999999
Q ss_pred cCcccccCCccceEEeeccccceeeecccccCCCCchhHHHHHHHhceEEEeccccccccCCceeEEEeccccccccCcC
Q 000291 680 KGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYDGTVRNVCSNSIIQFDYAVNARKSHSLF 759 (1714)
Q Consensus 680 ~ssF~~GL~P~EfFfHamagREGLiDTAvkTA~sGYLqRrLvk~ledl~v~YD~Tvr~~~~~~IiQf~yg~dg~~~~~lv 759 (1714)
.+||++||+|+|||||||||||||||||||||+||||||||||+||||+|+||+|||+ ++|+||||+||+||+|+..+
T Consensus 784 ~~sF~~GL~p~EfffH~m~GReGliDTAvkTa~sGYlqRrLvk~ledl~v~yD~tVR~-s~g~iiQf~YG~dg~d~~~~- 861 (882)
T PRK08566 784 RSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRD-TRGNIVQFKYGEDGVDPMKS- 861 (882)
T ss_pred eccccCCCCHHHHHHHHhhhcccccccceeeccCccchHHHHHHHhheEEeeCCceEc-CCCcEEEEeccCCCcCHHHh-
Confidence 9999999999999999999999999999999999999999999999999999999999 47999999999999887654
Q ss_pred CCCcee
Q 000291 760 PAGEPV 765 (1714)
Q Consensus 760 ~~GepV 765 (1714)
+.+.||
T Consensus 862 ~~~~~~ 867 (882)
T PRK08566 862 DHGKPV 867 (882)
T ss_pred cCCCcc
Confidence 244555
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=2.3e-162 Score=1558.93 Aligned_cols=890 Identities=20% Similarity=0.255 Sum_probs=669.7
Q ss_pred eEEEecCCHHHHHHhcccccccccC------------CCCCCCCC-CCC--------------CCCCCCCCCCCCCCCCC
Q 000291 16 GIRFGLATQKEICTASISDCSISHA------------SQLANPFL-GLP--------------LEFGKCESCGTSEPGKC 68 (1714)
Q Consensus 16 ~I~F~l~S~eEI~k~Sv~~~~I~~~------------~gl~DprL-G~~--------------~~~~~C~TCg~~~~~~C 68 (1714)
+|+|++.|||+|+++|+.| |++| .||+|+|+ |+. .+...|++||... .+|
T Consensus 1 ~i~i~laSPe~I~~ws~ge--V~~petiny~t~kPe~~GLfcerIFGp~k~~ec~Cgkyk~~~~~~~~C~~Cgve~-t~~ 77 (1140)
T TIGR02386 1 AIKISIASPDTIRNWSYGE--VKKPETINYRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKIRYKGVVCERCGVEV-TES 77 (1140)
T ss_pred CeEEEecCHHHHHhhhceE--EeccceecCCCCccCCCCcccchhcCCccCceeccccccccCcCCcCCCCCCCCc-ccc
Confidence 4899999999999999865 4332 58999999 754 2455899999986 699
Q ss_pred C---CcceeEEcCcccccccchHH-----------HHHHHHHHHhhh---c-cc---hHH----------HHHH------
Q 000291 69 E---GHFGYIELPIPIYHPSHISE-----------LKLTMYAFQLQI---K-ND---GVA----------QRLL------ 111 (1714)
Q Consensus 69 p---GHFGhIeL~~PVfHpgf~k~-----------I~~IL~~iC~ri---~-~~---g~~----------kri~------ 111 (1714)
+ +|||||+|+.||+|++||+. ..+.|.++|..+ . +. .+. ..+.
T Consensus 78 ~vrr~rmGhI~La~Pv~Hiwy~k~~ps~~~~ll~~~~k~le~v~y~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (1140)
T TIGR02386 78 KVRRERMGHIELAAPVAHIWYFKGLPSRIGLLLDITAKELESVLYFENYVVLDPGDTKLDKKEVLDETEYREVLKRYGDG 157 (1140)
T ss_pred hhhhhcccceeecCCceeehhcCCCchHHHHHhCCCHHHhhheeeccceEEeCCCCCchhhhhhhchhHHHHHHHHhccC
Confidence 9 99999999999999999998 467777776422 1 11 010 0000
Q ss_pred --HHH-H-----------------HHHHHHhcCChHHH-H-hhc--------cCCCCCCCcEEEeeccCCCCCCCCCccc
Q 000291 112 --SSC-C-----------------EVKEMLKRIPEETR-K-KLA--------GKGYFPQDGYILEYLPVPPNCLSVPDIS 161 (1714)
Q Consensus 112 --~~C-C-----------------eV~~IfkkI~~ed~-~-~L~--------~~~~~~pe~~il~~lpVPP~~~Rp~~~~ 161 (1714)
..| + ++.+.++....+.. . ++. .....+|+||||++|||||||+||++.+
T Consensus 158 ~~~~~G~~ai~~~l~~~dl~~~~~~~~~~~~~~~~~~~~~~~~krl~~~~~f~~s~~~Pewmil~~lPV~Pp~lRP~v~l 237 (1140)
T TIGR02386 158 FRAGMGAEAIKELLEKIDLDKEIEELKIQLRESKSDQKRKKLLKRLEIVEAFKDSGNRPEWMVLDVIPVIPPELRPMVQL 237 (1140)
T ss_pred cccccchHHHHHHHhcCCHHHHHHHHHHHHHhccchhhHHhhhhHHHHHHHHHhcCCChHHhhhhcccCCCCccCCcEEe
Confidence 011 0 11222222111111 1 111 0134689999999999999999999999
Q ss_pred CCCccccchhHHHHHHHHHHHHHHHHhh-hcCCCCccchhhhhhHHHHHHHHHHhhcCCCcCCCCCCCCCCCCCCCCchh
Q 000291 162 DGVSTMSSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEVRGTAKSSRDVDARFGVSQDPNSTT 240 (1714)
Q Consensus 162 ~g~~~~~~Dlt~~~l~~Il~~n~~lk~~-~~g~p~~~~~~~~~~~LQ~~v~~~~~~~~~~~~~~~~~~~~~~~k~~~~~i 240 (1714)
+|..+.++|||. +|++||++|++|+.. ..++|..+. .+++++||++|++|||+....++.....+ ...|++.+.+
T Consensus 238 ~gg~~~~sDLn~-lyr~II~~Nn~Lk~~~~~~ap~~ii-~~~~~~LQ~aV~~liDn~~~g~~~~~~~~--rplksls~~L 313 (1140)
T TIGR02386 238 DGGRFATSDLND-LYRRVINRNNRLKRLLELGAPEIIV-RNEKRMLQEAVDALFDNGRRGKPVVGKNN--RPLKSLSDML 313 (1140)
T ss_pred CCCccccCchHH-HHHHHHHHHHHHHHHHHcCCcHHHH-HHHHHHHHHHHHHHhcccccCCCccCcCC--CchhhHHHhh
Confidence 988888999998 899999999999875 567776653 57899999999999997443333221111 1346677899
Q ss_pred hhhHhhhhhcccccCCCCccceeEeCCCCCccccccchhhcccccccccccchhhHHHHHHHHHccCccccCCCCceEEe
Q 000291 241 KAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDNKLCLTYSDGSSSYSL 320 (1714)
Q Consensus 241 k~k~gr~R~~l~GKRvdfSaRsVI~pdP~l~~~evgvP~~~A~~Lt~pe~vt~~Ni~~l~~lv~~g~~~~~~~~~~~~~l 320 (1714)
|||+||||+|||||||||||||||+|||+|++||||||..||++||+| ||+.+| +.+|....++.. +..+
T Consensus 314 kGK~GrFR~NLlGKRVDySgRSVI~pdP~L~l~e~GlP~~mA~~L~~P-----f~i~~L---~~~~~~~~i~~a--k~~i 383 (1140)
T TIGR02386 314 KGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKP-----FIIKRL---IDRELAANIKSA--KKMI 383 (1140)
T ss_pred cCCCCcccccccccccCCCCCCeEcCCCCcccccccChHHHHHHcCch-----HHHHHH---HHcCcccchHHH--HHHH
Confidence 999999999999999999999999999999999999999999999987 555544 445533221111 0001
Q ss_pred ccCCCCccccCCcceeeheeeccceEEEeCCCccccccccceeeEecCCCeEEecccccCCCCCccccccccccCCCCHH
Q 000291 321 REGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQSLA 400 (1714)
Q Consensus 321 ~~~~~~~~~l~~g~iV~Rhl~dgd~VL~NRqPsLHr~Sima~~~~v~~~~t~rln~~vC~pyNADFDGDeMnlHvPQS~e 400 (1714)
. ...+.+++ |.||+++||+|||||||||||||||||+|++++++||||||+||+||||||||||||||||||++
T Consensus 384 ~-----~~~~~v~~-vl~~vi~~d~VLlNRqPTLHRlsIqAf~~~l~~gktirlhplvC~~fNADFDGDeMnvHvPqS~e 457 (1140)
T TIGR02386 384 E-----QEDPEVWD-VLEDVIKEHPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPE 457 (1140)
T ss_pred H-----hcCCccce-EEEEccCCcEEEecCCCcccccccceeEEEEecCceEEEcccccCcccCCCCcceeEeecCCCHH
Confidence 0 12234555 55788899999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhcccccccccCCCCCceEeechhhHhHHHhhhcc---------ccCCHHHHHHhhcccccccccccccccc--
Q 000291 401 AKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMFKK---------YFLDKAFTQQLAMFALSPLPRPALSKAR-- 469 (1714)
Q Consensus 401 AraEa~~Lm~~~~nilsp~~G~Piigl~QD~llg~~lltkd---------~fl~~~~~~~l~~~~~~~lp~PaI~Kp~-- 469 (1714)
|||||++||++++||+||++|+|+++++||+|+|+|+||+. +|++++++........ ++.|+++++.
T Consensus 458 A~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~~~~~~~~~F~~~~e~~~~~~~~~--i~l~~~i~~~~~ 535 (1140)
T TIGR02386 458 AQAEARALMLASNNILNPKDGKPIVTPSQDMVLGLYYLTTEKPGAKGEGKIFSNVDEAIRAYDNGK--VHLHALIGVRTS 535 (1140)
T ss_pred HHHHHHHHhCCcccEecCCCCCceEEeechhhheeeEeeeccccccCcCceeCCHHHHHHHHHcCC--ccCCCceEEecc
Confidence 99999999999999999999999999999999999999732 7999999887543332 4445555543
Q ss_pred ccccc--ceeeeccccCCCCccccCCEEEEEcceecccccccCcccchHHHHHHHHHHhhCHHHHHhchhhhHHHHHHHH
Q 000291 470 CSARW--TALQILQSVLPPGFDSCGDRYLIKKSEVLKGDFDRDTIPSVINEIVTSIFFEKGPEEVLEFFDSLQPLLMENL 547 (1714)
Q Consensus 470 ~~~lW--TGKQl~s~~LP~~~~~~~~~viI~~Gell~G~ldK~~lg~s~~~Li~~i~~~~G~~~a~~fLd~lqrL~~~~L 547 (1714)
..++| +|||||+.+||.++.+... . ..+||+.+| +|||.+|++||++.|+.|||.+++|+++|+
T Consensus 536 g~~~~tt~Gr~if~~ilP~~~~~~n~------~----~~l~Kk~lg----~LI~~i~~~~G~~~t~~~LD~lk~Lgf~~a 601 (1140)
T TIGR02386 536 GEILETTVGRVIFNEILPEGFPYIND------N----EPLSKKEIS----SLIDLLYEVHGIEETAEMLDKIKALGFKYA 601 (1140)
T ss_pred ccEEEccchHHHHHHHcCCccccccc------c----cccchHHHH----HHHHHHHHHhChHHHHHHHHHHHHHHHHHH
Confidence 22677 6999999999987765321 0 157888875 799999999999999999999999999999
Q ss_pred HhcCceeeeCCcccCHHHHHHHHHHHHHHHHHHHHhhh--hhHHHHHHHHHHHHHHHHHHHHHHHHh--------cCCcc
Q 000291 548 FADGFSVSLEDFSLSKAALWNIQKEIQALYSLLYHRMS--TQNELVDLQIENHIRHVKMLVAKFILK--------SSTLG 617 (1714)
Q Consensus 548 ~~~GFSiGi~Dl~~~~~~~~~i~~~i~~~~~~~~~~~~--~~~e~le~~i~~~l~~~~~~i~~~~~~--------~n~l~ 617 (1714)
+.+||||||+|+++|+++.+.++++.+++..+..++.. ...+..+..+..+|+++++.+++.+++ .|+++
T Consensus 602 t~~GfSigi~Dl~ip~~K~~ii~~a~~~v~~i~~~y~~G~lt~~er~~kvi~iw~~~~d~v~~~~~~~l~~~~~~~N~i~ 681 (1140)
T TIGR02386 602 TKSGTTISASDIVVPDEKYEILKEADKEVAKIQKFYNKGLITDEERYRKVVSIWSETKDKVTDAMMKLLKKDTYKFNPIF 681 (1140)
T ss_pred HhcCeeeeeccCCCCHHHHHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCcHh
Confidence 99999999999999998877776666666555554432 112334455666778888887776653 28999
Q ss_pred cccccccchhhhhHHHHhHhccceecCCCccccccccccccccccccCCCCCCCCCCccceecCcccccCCccceEEeec
Q 000291 618 YLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLVEDIASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSI 697 (1714)
Q Consensus 618 ~Mi~SGSKGS~~Ni~Qi~g~lGQQ~~~g~r~~~r~l~~~~~~~f~~~~p~~~d~~~~a~GfV~ssF~~GL~P~EfFfHam 697 (1714)
+|+.||||||+.|++||+||||||+.+.|+.+ + . ||.+||++||+|+|||||||
T Consensus 682 mMa~SGARGS~~ni~QL~GmrGlma~p~Grii---------~-----------~------PI~ssF~eGLtp~EyF~st~ 735 (1140)
T TIGR02386 682 MMADSGARGNISQFRQLAGMRGLMAKPSGDII---------E-----------L------PIKSSFREGLTVLEYFISTH 735 (1140)
T ss_pred hhhhcccccCHHHHHHHHhCCCcccCCCCCcc---------c-----------c------chhhccccCCCHHHHhhhcc
Confidence 99999999999999999999999998877632 1 1 39999999999999999999
Q ss_pred cccceeeecccccCCCCchhHHHHHHHhceEEEec--cccccc-------------------------------------
Q 000291 698 STREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYD--GTVRNV------------------------------------- 738 (1714)
Q Consensus 698 agREGLiDTAvkTA~sGYLqRrLvk~ledl~v~YD--~Tvr~~------------------------------------- 738 (1714)
+|||||+|||||||+|||||||||+++||++|.|| +|.+.+
T Consensus 736 GaRkGLiDTAlKTAdSGYLtRRLVdv~qDviV~~dDCgT~~gi~v~~~~~~~~~~i~~l~~ri~GR~~~~di~~~~~~~~ 815 (1140)
T TIGR02386 736 GARKGLADTALKTADSGYLTRRLVDVAQDVVVREEDCGTEEGIEVEAIVEGKDEIIESLKDRIVGRYSAEDVYDPDTGKL 815 (1140)
T ss_pred chhccccchheeecccceeeeehhhhhcceEEEeCCCCCCCCEEEEEeecCCceEEeehhheeEEEEEhhheEeCCCCcE
Confidence 99999999999999999999999999999999998 332110
Q ss_pred ---------------------------------cCCceeEEEeccccccccCcCCCCceeEEeccccCChhHHHHhhcCC
Q 000291 739 ---------------------------------CSNSIIQFDYAVNARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDSS 785 (1714)
Q Consensus 739 ---------------------------------~~~~IiQf~yg~dg~~~~~lv~~GepVG~laaqsigepatq~~L~t~ 785 (1714)
+...|||.|||.+. ....+|+.||+||+|||||||||+||+||+||
T Consensus 816 i~~~~~~i~~~~~~~i~~~~i~~v~iRS~ltC~s~~gvC~~CYG~~L-a~~~~V~~GeaVGiiAAQSIGEPGTQLTmRTF 894 (1140)
T TIGR02386 816 IAEANTLITEEIAEKIENSGIEKVKVRSVLTCESEHGVCQKCYGRDL-ATGKLVEIGEAVGVIAAQSIGEPGTQLTMRTF 894 (1140)
T ss_pred EEeCCCCcCHHHHHHHHHcCCCEEEecCCeeeCCCCCCccccCCCcc-cCCcEecccccceeEeeeecCCCcchhehhhe
Confidence 12369999999983 56889999999999999999999999999999
Q ss_pred C---------CCCCchHHHHHHHHhhccCCCCCCCceEEEEcCCCCCCCccccHHHHHHHHhhhccccH-h-hhhheeEE
Q 000291 786 P---------SSNNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSL-K-DAAVEFLI 854 (1714)
Q Consensus 786 ~---------~~~~g~~rlkEil~~~~~~k~~~~d~~~~l~L~~~~~~~~~~~e~~a~~V~~~le~vtl-~-dv~~~i~I 854 (1714)
| .+|.|+||+.|+++++. |+++.++..++... ++ + +.-....|
T Consensus 895 HtGGv~~~~~DIT~GlpRv~elfear~-----p~~~a~iae~~G~v---------------------~~~~~~~~~~~~i 948 (1140)
T TIGR02386 895 HTGGVAGASGDITQGLPRVKELFEART-----PKDKAVIAEVDGTV---------------------EIIEDIVKNKRVV 948 (1140)
T ss_pred eeccccccccccccCchhhhhhhhccc-----CCCceEEEecCCEE---------------------EEeecccCCcEEE
Confidence 7 57789999999999876 66666665544321 10 0 00000011
Q ss_pred EecCCccccCCCceEEEEEecHHHHHHhcCChhhhHHHHHHhhhhhhhcchhhHHHHHhhcccccccccccccccccccC
Q 000291 855 EYKKPEIISDDEGLVGHIHLNKILLEDLRISMHDILPKCQETLKSFCKKKKMKKVVQFFKNTSLSISECCSFQQSCADKR 934 (1714)
Q Consensus 855 ~y~~~~~~~~~~~wv~~i~Ld~e~L~~~~lt~~~I~~k~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~gi~~~~~~~~~ 934 (1714)
...++.. + ...+.| +..+ .+.+ .-| +.+ ..
T Consensus 949 ~i~~~~~---------------~-~~~y~i-----------------p~~~---------~l~v---~~g---d~V-~~- 978 (1140)
T TIGR02386 949 VIKDEND---------------E-EKKYTI-----------------PFGA---------QLRV---KDG---DSV-SA- 978 (1140)
T ss_pred EEECCCC---------------c-eeEEec-----------------cCCc---------eEEe---cCC---CEE-cc-
Confidence 1111100 0 000000 0000 0000 001 000 00
Q ss_pred CCcceEEEEEcccCCcccccceecccccchHHHHHHhhhhhHHHH----HHHHHHHHHhhcccccceeeeeccceeeece
Q 000291 935 SNMPCLMFVLRGASDSYLDKLSGVLANMIYPVLLETIIKENWWVR----QRLSASVTMVAKGVLKEHLILLANSMTCAGD 1010 (1714)
Q Consensus 935 ~~~~~l~~~~~~~~~~~~vd~~~~~~n~I~~i~r~~IIkgi~w~r----~~l~~~~~~~~~~V~~rHl~LlAd~MT~~G~ 1010 (1714)
...| ++|+ -+++++++ |.|++.++ +.++++++.+|..|+.+|+.+|++-||.+++
T Consensus 979 --G~~l---~~g~-------------~~~~~il~---v~G~~a~~~~lv~evq~vY~~QGv~I~dKHievIvrqM~~kv~ 1037 (1140)
T TIGR02386 979 --GDKL---TEGS-------------IDPHDLLR---IKGIQAVQEYLVKEVQKVYRLQGVEINDKHIEVIVRQMLRKVR 1037 (1140)
T ss_pred --CCcc---cCCC-------------CCHHHHHH---hcCHHHHHHHHHHHHHHHHHhCCccccchhHhHHHHHHhCcEE
Confidence 0111 2222 12233332 33444333 3345888889999999999999999999964
Q ss_pred Ee----------------------------------------eeccccccccccCcccccccccccccCcHHHHHHHHhh
Q 000291 1011 LV----------------------------------------GFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEK 1050 (1714)
Q Consensus 1011 ~~----------------------------------------~~~r~G~~~~~~s~l~~a~Fe~~t~~~~~~~l~~Aa~~ 1050 (1714)
+. |||+..+ ..+|+|+.|||++| .++|.+||++
T Consensus 1038 i~~~gdt~~l~g~~v~~~~~~~~n~~~~~~g~~~~~~~~~llGitkasl--~t~SflsaASFqeT-----tkvLt~Aai~ 1110 (1140)
T TIGR02386 1038 ITDSGDSNLLPGELIDIHEFNEENRKLLEQGKKPASAIPQLLGITKASL--NTESFLSAASFQET-----TKVLTDAAIK 1110 (1140)
T ss_pred EEeCCCcCCCCCCeeeHHHHHHHHHHHHhCCCCCccceeeeeeeeehhc--cCCCcccccchhhH-----HHHHHHHHhc
Confidence 44 5666666 46799999999998 7999999999
Q ss_pred cCCCCCCchhhhhhcCCcccccccc
Q 000291 1051 RHTDNLSSVVAACSWGKHVAVGTGS 1075 (1714)
Q Consensus 1051 g~~D~l~gv~~~ii~Gk~~~~GTG~ 1075 (1714)
|.+|.|.|+.||||+|+.+|+|||.
T Consensus 1111 gk~D~L~GlkENVIiG~liPaGTG~ 1135 (1140)
T TIGR02386 1111 GKVDYLLGLKENVIIGNLIPAGTGL 1135 (1140)
T ss_pred CCCCCCCCcccceEecCcccCCCCc
Confidence 9999999999999999999999998
No 8
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=100.00 E-value=2e-161 Score=1551.67 Aligned_cols=900 Identities=21% Similarity=0.267 Sum_probs=679.6
Q ss_pred ceeeEEEecCCHHHHHHhccccccccc------------CCCCCCCCCCCCCCCCCCCCCCCCC-----CCCCC------
Q 000291 13 QIVGIRFGLATQKEICTASISDCSISH------------ASQLANPFLGLPLEFGKCESCGTSE-----PGKCE------ 69 (1714)
Q Consensus 13 ~I~~I~F~l~S~eEI~k~Sv~~~~I~~------------~~gl~DprLG~~~~~~~C~TCg~~~-----~~~Cp------ 69 (1714)
++..|++++.|||+|+++|+.| |++ ..||+|.|...|.++..| .||+-. ...|+
T Consensus 6 ~~~~i~i~laspe~I~~ws~Ge--V~~petinyrt~kPe~~GLfcerIFgp~kd~eC-~Cgkyk~~~~~~~~C~~cgve~ 82 (1156)
T PRK00566 6 DFDAIKIGLASPEKIRSWSYGE--VKKPETINYRTLKPERDGLFCERIFGPTKDYEC-LCGKYKRVRYKGIICERCGVEV 82 (1156)
T ss_pred CcceEEEEccCHHHHHHhhcce--EccccccccCCCccCCCCcccchhcCcccCcEE-eCccccccCcCCcCCCCCCcee
Confidence 7889999999999999999865 433 259999999889999999 999521 13798
Q ss_pred -------CcceeEEcCcccccccchHHH-----------HHHHHHHHhhh---c-cch---H----------HHHHHH--
Q 000291 70 -------GHFGYIELPIPIYHPSHISEL-----------KLTMYAFQLQI---K-NDG---V----------AQRLLS-- 112 (1714)
Q Consensus 70 -------GHFGhIeL~~PVfHpgf~k~I-----------~~IL~~iC~ri---~-~~g---~----------~kri~~-- 112 (1714)
+|||||+|+.||+|++||+.+ ++.|.++|... . ..+ + ...+..
T Consensus 83 ~~~~vrr~rmGhI~La~Pv~Hiwy~k~~ps~i~~ll~~~~k~le~v~y~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~ 162 (1156)
T PRK00566 83 TRSKVRRERMGHIELAAPVAHIWFFKSLPSRIGLLLDMSLKDLERVLYFESYVVIDPGDTPLEKKQLLTEEEYREALEEY 162 (1156)
T ss_pred eechhhhhhcceeeecCceeeeeecCCCchHHHHHhCCCHHHhhheeecceEEEeCCCCCchhhhcccCHHHHHHHHHHh
Confidence 999999999999999999954 67777775422 1 110 0 000000
Q ss_pred ------HH-----------------H-HHHHHHhc-CChHHHHh----hcc-----CCCCCCCcEEEeeccCCCCCCCCC
Q 000291 113 ------SC-----------------C-EVKEMLKR-IPEETRKK----LAG-----KGYFPQDGYILEYLPVPPNCLSVP 158 (1714)
Q Consensus 113 ------~C-----------------C-eV~~Ifkk-I~~ed~~~----L~~-----~~~~~pe~~il~~lpVPP~~~Rp~ 158 (1714)
.| + +..+.++. .....+.+ |.. ..-.+|+||||++|||||||+||+
T Consensus 163 ~~~~~~~~Ga~ai~~ll~~~dl~~~~~~l~~~~~~~~~~~~~~~~~krl~~~~~f~~s~~~Pewmil~~lPV~Pp~lRP~ 242 (1156)
T PRK00566 163 GDEFVAKMGAEAIKELLKNIDLEAEAEELREELKETGSEQKRKKALKRLKVVEAFRKSGNKPEWMILDVLPVIPPDLRPL 242 (1156)
T ss_pred cccccccccHHHHHHHHHhCCHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHcCCCCccEeeEeecccCCCcccCc
Confidence 00 0 11122221 11111111 110 123579999999999999999999
Q ss_pred cccCCCccccchhHHHHHHHHHHHHHHHHhh-hcCCCCccchhhhhhHHHHHHHHHHhhcCCCcCCCCCCCCCCCCCCCC
Q 000291 159 DISDGVSTMSSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEVRGTAKSSRDVDARFGVSQDPN 237 (1714)
Q Consensus 159 ~~~~g~~~~~~Dlt~~~l~~Il~~n~~lk~~-~~g~p~~~~~~~~~~~LQ~~v~~~~~~~~~~~~~~~~~~~~~~~k~~~ 237 (1714)
+.+++..+.++|||. +|++||++|++|+.. ..++|..+. .+++++||.+|+.|||+....++.....+| ..|++.
T Consensus 243 v~l~~g~~~~sDLn~-lyr~II~rNnrLk~~~~~~ap~~ii-~~~~~~LQ~aV~~lidn~~~g~~~~~~~~r--plksls 318 (1156)
T PRK00566 243 VQLDGGRFATSDLND-LYRRVINRNNRLKRLLELGAPEIIV-RNEKRMLQEAVDALFDNGRRGRPVTGPNNR--PLKSLS 318 (1156)
T ss_pred eEeCCCcccCCchHH-HHHHHHHHHHHHHHHHHcCCcHHHH-HHHHHHHHHHHHHHhccCccCCCcccccCC--chhHHH
Confidence 999988888999998 899999999999875 667777654 578999999999999975433332221111 236677
Q ss_pred chhhhhHhhhhhcccccCCCCccceeEeCCCCCccccccchhhcccccccccccchhhHHHHHHHHHccCccccCCCCce
Q 000291 238 STTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDNKLCLTYSDGSSS 317 (1714)
Q Consensus 238 ~~ik~k~gr~R~~l~GKRvdfSaRsVI~pdP~l~~~evgvP~~~A~~Lt~pe~vt~~Ni~~l~~lv~~g~~~~~~~~~~~ 317 (1714)
+.+|||+||||+|||||||||||||||+|||+|++||||||..||++||+| || +++|+.+|+...++...
T Consensus 319 ~~LkGK~GrFR~NLlGKRVDySgRSVI~pdP~L~l~e~GvP~~mA~eL~~P-----f~---i~~L~~~g~~~~ik~ak-- 388 (1156)
T PRK00566 319 DMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKP-----FI---MKKLVERGLATTIKSAK-- 388 (1156)
T ss_pred HhhcCCCccccccccccccCCCCCceEeCCCCcccccccChHHHHHHhCcH-----HH---HHHHHHcCCccchHhhh--
Confidence 899999999999999999999999999999999999999999999999888 45 56678888754333221
Q ss_pred EEeccCCCCccccCCcceeeheeeccceEEEeCCCccccccccceeeEecCCCeEEecccccCCCCCccccccccccCCC
Q 000291 318 YSLREGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQ 397 (1714)
Q Consensus 318 ~~l~~~~~~~~~l~~g~iV~Rhl~dgd~VL~NRqPsLHr~Sima~~~~v~~~~t~rln~~vC~pyNADFDGDeMnlHvPQ 397 (1714)
..+. ....++|+++ ||+++||+|||||||||||||||||+|++++++||||||+||+|||||||||||||||||
T Consensus 389 ~~~~-----~~~~~v~~vl-e~vi~gd~VLlNRqPTLHR~sIqAf~~~l~~gktirLhplvC~~fNADFDGDqMnvHvPq 462 (1156)
T PRK00566 389 KMVE-----REDPEVWDVL-EEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPL 462 (1156)
T ss_pred hhhh-----hhcCcceEEE-EEecCCCEEEecCCCcccccccceeEEEEecCceEEECccccCccccccccceeEEecCC
Confidence 1111 1234566654 678899999999999999999999999999999999999999999999999999999999
Q ss_pred CHHHHHHHHHhcccccccccCCCCCceEeechhhHhHHHhhh-cc--------ccCCHHHHHHhhccccccccccccccc
Q 000291 398 SLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF-KK--------YFLDKAFTQQLAMFALSPLPRPALSKA 468 (1714)
Q Consensus 398 S~eAraEa~~Lm~~~~nilsp~~G~Piigl~QD~llg~~llt-kd--------~fl~~~~~~~l~~~~~~~lp~PaI~Kp 468 (1714)
|++|||||++||++.+||+||++|+|+++++||+|+|+|+|| ++ +|++++++.++++...+.++.|..+++
T Consensus 463 S~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~~~~~~~~~F~~~~e~~~~~~~~~i~l~~~i~~~~ 542 (1156)
T PRK00566 463 SLEAQAEARVLMLSSNNILSPANGKPIIVPSQDMVLGLYYLTREREGAKGEGMVFSSPEEALRAYENGEVDLHARIKVRI 542 (1156)
T ss_pred CHHHHHHHHHHhCCcccEEecCCCCeeEEeehhhhhhhheeecccccccCCCceeCCHHHHHHHHHcCCCCCCCeEEecC
Confidence 999999999999999999999999999999999999999997 44 799999999987665555555555544
Q ss_pred ccc---cccceeeeccccCCCCccccCCEEEEEcceecccccccCcccchHHHHHHHHHHhhCHHHHHhchhhhHHHHHH
Q 000291 469 RCS---ARWTALQILQSVLPPGFDSCGDRYLIKKSEVLKGDFDRDTIPSVINEIVTSIFFEKGPEEVLEFFDSLQPLLME 545 (1714)
Q Consensus 469 ~~~---~lWTGKQl~s~~LP~~~~~~~~~viI~~Gell~G~ldK~~lg~s~~~Li~~i~~~~G~~~a~~fLd~lqrL~~~ 545 (1714)
+.. ..|||||||+.+||.++.+... +|.+||+.|| +|||.+|+.||+++|+.|||.+++|+++
T Consensus 543 ~~~~~i~tt~Gk~if~~ilP~~~~~~n~----------~g~ldKk~Lg----~LI~~i~~~yG~~~t~~~LD~ik~Lgf~ 608 (1156)
T PRK00566 543 TSKKLVETTVGRVIFNEILPEGLPFINV----------NKPLKKKEIS----KIINEVYRRYGLKETVIFLDKIKDLGFK 608 (1156)
T ss_pred CCCceEEcCcHHHHHHhhccccceeecc----------cceecHHHHH----HHHHHHHHHhCHHHHHHHHHHHHHHHHH
Confidence 211 4699999999999987654221 5789999986 5999999999999999999999999999
Q ss_pred HHHhcCceeeeCCcccCHHHHHHHHHHHHHHHHHHHHhhhhh--HHHHHHHHHHHHHHHHHHHHHHHHh--------cCC
Q 000291 546 NLFADGFSVSLEDFSLSKAALWNIQKEIQALYSLLYHRMSTQ--NELVDLQIENHIRHVKMLVAKFILK--------SST 615 (1714)
Q Consensus 546 ~L~~~GFSiGi~Dl~~~~~~~~~i~~~i~~~~~~~~~~~~~~--~e~le~~i~~~l~~~~~~i~~~~~~--------~n~ 615 (1714)
|++.+||||||+|+++|+++.+.+++..+++.++..++..-. .+..+..+...|+++++.+.+.+++ .|+
T Consensus 609 yat~~GfSigi~Dl~ip~~K~~ii~~a~~~v~~i~~~y~~G~lt~~er~~kvi~~w~~~~d~v~~~~~~~l~~~~~~~N~ 688 (1156)
T PRK00566 609 YATRSGISIGIDDIVIPPEKKEIIEEAEKEVAEIEKQYRRGLITDGERYNKVIDIWSKATDEVAKAMMKNLSKDQESFNP 688 (1156)
T ss_pred HHHhcCeEeehhhcCcChHHHHHHHHHHHHHHHHHHHHHcCCCCchHHHHHHHHHHHHHHHHHHHHHHHhCccccCCCCC
Confidence 999999999999999999887777776666665555443210 1112234455667777766665542 489
Q ss_pred cccccccccchhhhhHHHHhHhccceecCCCccccccccccccccccccCCCCCCCCCCccceecCcccccCCccceEEe
Q 000291 616 LGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLVEDIASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTH 695 (1714)
Q Consensus 616 l~~Mi~SGSKGS~~Ni~Qi~g~lGQQ~~~g~r~~~r~l~~~~~~~f~~~~p~~~d~~~~a~GfV~ssF~~GL~P~EfFfH 695 (1714)
+++|+.||||||+.|++||+||||||..+.|+++ +. ||.+||++||+|+|||||
T Consensus 689 i~mMa~SGARGS~~ni~QL~GmrGlma~p~G~ii--------------------e~------pI~ssFreGLt~~EyFfs 742 (1156)
T PRK00566 689 IYMMADSGARGSASQIRQLAGMRGLMAKPSGEII--------------------ET------PIKSNFREGLTVLEYFIS 742 (1156)
T ss_pred hheeeeccCCcCHHHHHHHHhhcCccccCCCCEe--------------------eh------hhhhhhhcCCCHHHHhhc
Confidence 9999999999999999999999999987777642 11 499999999999999999
Q ss_pred eccccceeeecccccCCCCchhHHHHHHHhceEEEec--cccccc-----------------------------------
Q 000291 696 SISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYD--GTVRNV----------------------------------- 738 (1714)
Q Consensus 696 amagREGLiDTAvkTA~sGYLqRrLvk~ledl~v~YD--~Tvr~~----------------------------------- 738 (1714)
||||||||+|||||||+|||||||||+++||++|.|| ||.+.+
T Consensus 743 t~GaRkGLiDTALKTAdSGYLtRRLVdvaqDviV~~~DCgT~~gi~~~~~~~~~~~i~~l~~~~~GR~~~~di~~~~t~~ 822 (1156)
T PRK00566 743 THGARKGLADTALKTADSGYLTRRLVDVAQDVIVREDDCGTDRGIEVTAIIEGGEVIEPLEERILGRVLAEDVVDPETGE 822 (1156)
T ss_pred CcchhhcccchheeeccceeeehhHHHhhCceEEEECCCCCcCCEEEEEeccCCEEEeEhhheeEeEEEhhheecCCCCc
Confidence 9999999999999999999999999999999999997 442210
Q ss_pred ----------------------------------cCCceeEEEeccccccccCcCCCCceeEEeccccCChhHHHHhhcC
Q 000291 739 ----------------------------------CSNSIIQFDYAVNARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDS 784 (1714)
Q Consensus 739 ----------------------------------~~~~IiQf~yg~dg~~~~~lv~~GepVG~laaqsigepatq~~L~t 784 (1714)
+...|||.|||.|. ....+|+.||+||+|||||||||+||+||+|
T Consensus 823 ~i~~~~~~i~~~~~~~i~~~~i~~v~iRS~ltC~s~~gvC~~CYG~~L-a~~~~v~iGeaVGiIAAQSIGEPGTQLTmRT 901 (1156)
T PRK00566 823 VIVPAGTLIDEEIADKIEEAGIEEVKIRSVLTCETRHGVCAKCYGRDL-ATGKLVNIGEAVGVIAAQSIGEPGTQLTMRT 901 (1156)
T ss_pred EEEcCCCccCHHHHHHHHHcCCCEEEEcCCeeecCCCcccHhhhCccc-cCCCCcccCcceeEEeeeecCCCccceeeee
Confidence 13469999999983 5678999999999999999999999999999
Q ss_pred CC----CCCCchHHHHHHHHhhccCCCCCCCceEEEEcCCCCCCCccccHHHHHHHHhhhccccHhhhhheeEEEecCCc
Q 000291 785 SP----SSNNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPE 860 (1714)
Q Consensus 785 ~~----~~~~g~~rlkEil~~~~~~k~~~~d~~~~l~L~~~~~~~~~~~e~~a~~V~~~le~vtl~dv~~~i~I~y~~~~ 860 (1714)
|| .+|.|+||+.|+++++. |+++.++-.++..... . ++.-..-.|...+..
T Consensus 902 FHtGGvdIT~Glprv~elfear~-----pk~~a~ise~~G~v~~---~-----------------~~~~~~~~i~i~~~~ 956 (1156)
T PRK00566 902 FHTGGVDITGGLPRVAELFEARK-----PKGPAIIAEIDGTVSF---G-----------------KETKGKRRIVITPDD 956 (1156)
T ss_pred eeecceeccCCccchhhheeecc-----CCCceEEEecCCEEEe---c-----------------cccCCceEEEEeCCC
Confidence 99 58999999999999866 5666655544432100 0 000000000000000
Q ss_pred cccCCCceEEEEEecHHHHHHhcCChhhhHHHHHHhhhhhhhcchhhHHHHHhhcccccccccccccccccccCCCcceE
Q 000291 861 IISDDEGLVGHIHLNKILLEDLRISMHDILPKCQETLKSFCKKKKMKKVVQFFKNTSLSISECCSFQQSCADKRSNMPCL 940 (1714)
Q Consensus 861 ~~~~~~~wv~~i~Ld~e~L~~~~lt~~~I~~k~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~l 940 (1714)
. ...++. + ...+ .+. + .-|. ++ .. + ..|
T Consensus 957 ~----------------~~~~y~----------------v-p~~~---------~~~--v-~~gd--~v--~~-G--~~l 984 (1156)
T PRK00566 957 G----------------EEREYL----------------I-PKGK---------HLL--V-QEGD--HV--EA-G--DKL 984 (1156)
T ss_pred C----------------ceEEEE----------------c-cCCC---------eee--e-cCCC--EE--cc-C--Ccc
Confidence 0 000000 0 0000 000 0 0010 00 00 0 111
Q ss_pred EEEEcccCCcccccceecccccchHHHHHHhhhhhHHHHHHHHHHHHHhhcccccceeeeeccceeeec-----------
Q 000291 941 MFVLRGASDSYLDKLSGVLANMIYPVLLETIIKENWWVRQRLSASVTMVAKGVLKEHLILLANSMTCAG----------- 1009 (1714)
Q Consensus 941 ~~~~~~~~~~~~vd~~~~~~n~I~~i~r~~IIkgi~w~r~~l~~~~~~~~~~V~~rHl~LlAd~MT~~G----------- 1009 (1714)
++|+ ++..+++.-.=++..++.||+| ++++++.+|..|+.+|+.+|++-||...
T Consensus 985 ---~~g~-----~~~~~il~v~G~~~~~~~lv~e-------iq~vY~~QGv~I~dKHievIvrqM~~kv~i~~~gdt~~~ 1049 (1156)
T PRK00566 985 ---TDGS-----IDPHDILRVLGVEAVQNYLVNE-------VQKVYRLQGVKINDKHIEVIVRQMLRKVRITDPGDTDFL 1049 (1156)
T ss_pred ---cCCC-----CCHHHHHHhcCHHHHHHHHHHH-------HHHHHHhCCcccccceeehHHHHHhCCeEEecCCCcCCC
Confidence 2222 1111111111122224444454 4488999999999999999999999753
Q ss_pred -----------------------------eEeeeccccccccccCcccccccccccccCcHHHHHHHHhhcCCCCCCchh
Q 000291 1010 -----------------------------DLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVV 1060 (1714)
Q Consensus 1010 -----------------------------~~~~~~r~G~~~~~~s~l~~a~Fe~~t~~~~~~~l~~Aa~~g~~D~l~gv~ 1060 (1714)
.|+|||+++++ .+|+|+.|||++| .++|.+||++|++|.|.|+.
T Consensus 1050 ~g~~v~~~~~~~~n~~~~~~g~~~~~~~~~llGItka~l~--t~SflsaASFQeT-----tkvLt~AAi~gk~D~L~Glk 1122 (1156)
T PRK00566 1050 PGELVDRSEFEEENRKLIAEGKEPATGRPVLLGITKASLA--TESFLSAASFQET-----TRVLTEAAIKGKVDPLRGLK 1122 (1156)
T ss_pred CCceeeHHHHHHHHHHHHHCCCCCCcccceeeeeeecccc--cCcccccccccch-----HHHHHHHHhcCCCCcCCCcc
Confidence 35788888884 6799999999998 79999999999999999999
Q ss_pred hhhhcCCcccccccc
Q 000291 1061 AACSWGKHVAVGTGS 1075 (1714)
Q Consensus 1061 ~~ii~Gk~~~~GTG~ 1075 (1714)
||||+|+.+|+|||.
T Consensus 1123 ENVIiG~liPaGTG~ 1137 (1156)
T PRK00566 1123 ENVIIGRLIPAGTGL 1137 (1156)
T ss_pred cceEecCcccCCCCc
Confidence 999999999999999
No 9
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=100.00 E-value=2.8e-152 Score=1459.71 Aligned_cols=770 Identities=19% Similarity=0.226 Sum_probs=593.9
Q ss_pred CCCCcEEEeeccCCCCCCCCCcccCCCccccchhHHHHHHHHHHHHHHHHhh-hcCCCCccchhhhhhHHHHHHHHHHhh
Q 000291 138 FPQDGYILEYLPVPPNCLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEV 216 (1714)
Q Consensus 138 ~~pe~~il~~lpVPP~~~Rp~~~~~g~~~~~~Dlt~~~l~~Il~~n~~lk~~-~~g~p~~~~~~~~~~~LQ~~v~~~~~~ 216 (1714)
.+|+||||++||||||++||++.++|..+.++|||. +|++||++|++|+.. ..++|..+ ..+++++||.+|+.|||+
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 579999999999999999999999988888999998 899999999999875 56777655 357899999999999996
Q ss_pred cCCCcCCCCCCCCCCCCCCCCchhhhhHhhhhhcccccCCCCccceeEeCCCCCccccccchhhcccccccccccc----
Q 000291 217 RGTAKSSRDVDARFGVSQDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVN---- 292 (1714)
Q Consensus 217 ~~~~~~~~~~~~~~~~~k~~~~~ik~k~gr~R~~l~GKRvdfSaRsVI~pdP~l~~~evgvP~~~A~~Lt~pe~vt---- 292 (1714)
....++.....+ ...|++.+.+|||+||||+|||||||||||||||+|||+|+++|||||..||++||+|+.+.
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 432222211111 12366778999999999999999999999999999999999999999999999999996431
Q ss_pred ---hhhHHHHHHHHHccCccccCCCCceEEeccCCCCccccCCcceeeheeeccceEEEeCCCccccccccceeeEecCC
Q 000291 293 ---VHNINYLQELVDNKLCLTYSDGSSSYSLREGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDD 369 (1714)
Q Consensus 293 ---~~Ni~~l~~lv~~g~~~~~~~~~~~~~l~~~~~~~~~l~~g~iV~Rhl~dgd~VL~NRqPsLHr~Sima~~~~v~~~ 369 (1714)
..||+.+++++.++ ....+.|+||+++||+|||||||||||||||||+|+++++
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 12333333332221 1234567889999999999999999999999999999999
Q ss_pred CeEEecccccCCCCCccccccccccCCCCHHHHHHHHHhcccccccccCCCCCceEeechhhHhHHHhhh--cc------
Q 000291 370 HTVKINPLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF--KK------ 441 (1714)
Q Consensus 370 ~t~rln~~vC~pyNADFDGDeMnlHvPQS~eAraEa~~Lm~~~~nilsp~~G~Piigl~QD~llg~~llt--kd------ 441 (1714)
+||||||+||+||||||||||||||||||++|||||+.||++.+||++|++|+|+++++||+|+|+|+|| ++
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-------------------ccccceeeeccccCCCCccccCCEEEEEcc
Q 000291 442 -YFLDKAFTQQLAMFAL-SPLPRPALSKARC-------------------SARWTALQILQSVLPPGFDSCGDRYLIKKS 500 (1714)
Q Consensus 442 -~fl~~~~~~~l~~~~~-~~lp~PaI~Kp~~-------------------~~lWTGKQl~s~~LP~~~~~~~~~viI~~G 500 (1714)
+|++.+++..+.+... +.++.|..++++. -..|+|++||+.+||.++.
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 7899999888776532 3444333322110 0468999999999998653
Q ss_pred eecccccccCcccchHHHHHHHHHHhhCHHHHHhchhhhHHHHHHHHHhcCceeeeCCcccCHHHHHHHHHHHHHHHHHH
Q 000291 501 EVLKGDFDRDTIPSVINEIVTSIFFEKGPEEVLEFFDSLQPLLMENLFADGFSVSLEDFSLSKAALWNIQKEIQALYSLL 580 (1714)
Q Consensus 501 ell~G~ldK~~lg~s~~~Li~~i~~~~G~~~a~~fLd~lqrL~~~~L~~~GFSiGi~Dl~~~~~~~~~i~~~i~~~~~~~ 580 (1714)
++.+.++|+.|| .||+.+|++||...|..|||.+++|+++|++.+||||||+|+.+|+++.+.++++.+++.++.
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 445678888875 599999999999999999999999999999999999999999999988777777777777666
Q ss_pred HHhhh--hhHHHHHHHHHHHHHHHHHHHHHHHHh----cCCcccccccccchhhhhHHHHhHhccceecCCCcccccccc
Q 000291 581 YHRMS--TQNELVDLQIENHIRHVKMLVAKFILK----SSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLV 654 (1714)
Q Consensus 581 ~~~~~--~~~e~le~~i~~~l~~~~~~i~~~~~~----~n~l~~Mi~SGSKGS~~Ni~Qi~g~lGQQ~~~g~r~~~r~l~ 654 (1714)
.++.. ...+..+..+..+|+++++.+++.+++ .|++++|++||||||+.||+||+||||||..+.|+++
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 65542 112223556677889999998888875 4999999999999999999999999999988777643
Q ss_pred ccccccccccCCCCCCCCCCccceecCcccccCCccceEEeeccccceeeecccccCCCCchhHHHHHHHhceEEEec--
Q 000291 655 EDIASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYD-- 732 (1714)
Q Consensus 655 ~~~~~~f~~~~p~~~d~~~~a~GfV~ssF~~GL~P~EfFfHamagREGLiDTAvkTA~sGYLqRrLvk~ledl~v~YD-- 732 (1714)
+. ||.+||++||+|.|||||||+|||||+|||+|||+|||||||||+++|||+|..+
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 11 3999999999999999999999999999999999999999999999999999875
Q ss_pred cccccc-----------------------------------------------------------------cCCceeEEE
Q 000291 733 GTVRNV-----------------------------------------------------------------CSNSIIQFD 747 (1714)
Q Consensus 733 ~Tvr~~-----------------------------------------------------------------~~~~IiQf~ 747 (1714)
||.+++ +...|||.|
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 332110 134699999
Q ss_pred eccccccccCcCCCCceeEEeccccCChhHHHHhhcCCC-------CCCCchHHHHHHHHhhccCCCCCCCceEEEEcCC
Q 000291 748 YAVNARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDSSP-------SSNNSWELMKEILLCRVSFNNDPIDRRVILYLND 820 (1714)
Q Consensus 748 yg~dg~~~~~lv~~GepVG~laaqsigepatq~~L~t~~-------~~~~g~~rlkEil~~~~~~k~~~~d~~~~l~L~~ 820 (1714)
||.|. ....+|..||+||+|||||||||+||+||+||| .+|.|+||+.|++.++. |+++.++-..+.
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 578899999999999999999999999999998 77899999999999876 555554433222
Q ss_pred CCCCCccccHHHHHHHHhhhccccHhhhhheeEEEecCCccccCCCceEEEEEecHHHHHHhcCChhhhHHHHHHhhhhh
Q 000291 821 CGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIISDDEGLVGHIHLNKILLEDLRISMHDILPKCQETLKSF 900 (1714)
Q Consensus 821 ~~~~~~~~~e~~a~~V~~~le~vtl~dv~~~i~I~y~~~~~~~~~~~wv~~i~Ld~e~L~~~~lt~~~I~~k~~~~~~~~ 900 (1714)
. |++.+--....|.+.+... ....+.+
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 1100000001111111100 0000000
Q ss_pred hhcchhhHHHHHhhcccccccccccccccccccCCCcceEEEEEcccCCcccccceecccccchHHHHHHhhhhhHHHHH
Q 000291 901 CKKKKMKKVVQFFKNTSLSISECCSFQQSCADKRSNMPCLMFVLRGASDSYLDKLSGVLANMIYPVLLETIIKENWWVRQ 980 (1714)
Q Consensus 901 ~~~~~~~~i~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~l~~~~~~~~~~~~vd~~~~~~n~I~~i~r~~IIkgi~w~r~ 980 (1714)
...+ ++ . -++.+...+. ....| ++|+ .+..+++++. =++....-+|+|
T Consensus 1062 -~~~~--~~---~---------~~v~~gd~v~---~G~~l---~~G~--~~p~~il~~~---g~~~~~~ylv~e------ 1109 (1460)
T PRK14906 1062 -SARV--QF---M---------PGVEDGVEVR---VGQQI---TRGS--VNPHDLLRLT---DPNTTLRYIVSQ------ 1109 (1460)
T ss_pred -cCCc--cc---c---------cccCCCCEEc---cCCCc---cCCC--CCHHHHHHhc---CHHHHHHHHHHH------
Confidence 0000 00 0 0110000000 01112 2232 1222222211 111112333444
Q ss_pred HHHHHHHHhhcccccceeeeeccce----------------------------------------eeeceEeeecccccc
Q 000291 981 RLSASVTMVAKGVLKEHLILLANSM----------------------------------------TCAGDLVGFNSGGYK 1020 (1714)
Q Consensus 981 ~l~~~~~~~~~~V~~rHl~LlAd~M----------------------------------------T~~G~~~~~~r~G~~ 1020 (1714)
++++++.+|..|+..|+.+|+=-| ++.=.++|||+..+
T Consensus 1110 -VQ~VYr~QGV~InDKHiEvIvRQMl~kV~I~d~Gdt~fl~Ge~vd~~~~~~~n~~~~~~g~~pa~~~p~llGITKasL- 1187 (1460)
T PRK14906 1110 -VQDVYVSQGVDINDKHIEVIARQMLRKVAVTNPGDSDYLPGRQVNRYEFEDTANNLILEGKQPPVGQPLLLGITKASL- 1187 (1460)
T ss_pred -HHHHHHhcCceeccccHHHHHHHHhceEEEecCCCcCCCCCCeeeHHHHHHHHHHHHHcCCCCceeeeEEeeeeeccc-
Confidence 448888999999999999988666 44456788888887
Q ss_pred ccccCcccccccccccccCcHHHHHHHHhhcCCCCCCchhhhhhcCCcccccccc
Q 000291 1021 ALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGS 1075 (1714)
Q Consensus 1021 ~~~~s~l~~a~Fe~~t~~~~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~ 1075 (1714)
...|.++.|||++| .++|.+||++|.+|.|.|..||||+|+.||+|||.
T Consensus 1188 -~t~SflSaASFQeT-----trVLt~AAi~gk~D~L~GLKENVIiG~lIPAGTG~ 1236 (1460)
T PRK14906 1188 -ATDSWLSAASFQET-----TKVLTDAAIEGKVDHLAGLKENVIIGKPIPAGTGL 1236 (1460)
T ss_pred -ccccccccccccch-----HHHHHHHHhcCCCCcCCCCccceEecceecCCCCc
Confidence 35699999999998 69999999999999999999999999999999998
No 10
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=100.00 E-value=6e-147 Score=1454.69 Aligned_cols=717 Identities=20% Similarity=0.246 Sum_probs=558.6
Q ss_pred cccccceeeEEEecCCHHHHHHhcccccccccC------------CCCCCCCCCCCCCCC---------------CCCCC
Q 000291 8 TILEGQIVGIRFGLATQKEICTASISDCSISHA------------SQLANPFLGLPLEFG---------------KCESC 60 (1714)
Q Consensus 8 ~~~~~~I~~I~F~l~S~eEI~k~Sv~~~~I~~~------------~gl~DprLG~~~~~~---------------~C~TC 60 (1714)
.....++..|+.++.|||.|+++|+.| |++| .||+|.|.-.|.++. .|+.|
T Consensus 1442 ~~~~~~~~~i~i~laSPe~I~~Ws~Ge--V~kpeTinyrt~kPE~dGLFcerIFGp~kd~eC~Cgkyk~~~~~g~~C~~C 1519 (2836)
T PRK14844 1442 TNIAQSFNEVSISIASPESIKRMSYGE--IEDVSTANYRTFKVEKGGLFCPKIFGPVNDDECLCGKYKKRRHRGRICEKC 1519 (2836)
T ss_pred hhhhcccceEEEEecCHHHHHhhhcee--ECCcccccccCCCCCCCCeehhhhcCCCcCcEEecccccccccCCcCcCCC
Confidence 445778999999999999999999865 4433 589998864455433 56666
Q ss_pred CCCC--CCCCCCcceeEEcCcccccccchHHHHHHHHHHHh-------hhc--------cch---HH-------------
Q 000291 61 GTSE--PGKCEGHFGYIELPIPIYHPSHISELKLTMYAFQL-------QIK--------NDG---VA------------- 107 (1714)
Q Consensus 61 g~~~--~~~CpGHFGhIeL~~PVfHpgf~k~I~~IL~~iC~-------ri~--------~~g---~~------------- 107 (1714)
|... .+...-++|||+|+.||.|++||+.+...|..+-. ++. +.+ +.
T Consensus 1520 gvevt~s~vRR~RmGhI~La~PV~HiWy~k~~ps~i~~lL~~~~k~le~v~y~~~~~v~~~~~~~~~~~~~~~~~~~~~~ 1599 (2836)
T PRK14844 1520 GVEVTSSKVRRERMGHIELASPVAHIWFLKSLPSRIGALLDMSLRDIENILYSDNYIVIDPLVSPFEKGEIISEKAYNEA 1599 (2836)
T ss_pred CcEeeechhhHhhcCceeecCcceeeecccCCcHHHHHHhCCCHHHhhheeeeeeEEEecCCCCchhhhhhccHHHHHHH
Confidence 6432 22334699999999999999999977665554410 110 110 00
Q ss_pred ------------------HHHHHHH-----H-HHHHHHhcC-ChHHH----Hhhcc-----CCCCCCCcEEEeeccCCCC
Q 000291 108 ------------------QRLLSSC-----C-EVKEMLKRI-PEETR----KKLAG-----KGYFPQDGYILEYLPVPPN 153 (1714)
Q Consensus 108 ------------------kri~~~C-----C-eV~~IfkkI-~~ed~----~~L~~-----~~~~~pe~~il~~lpVPP~ 153 (1714)
++++... | ++++.++.. ....+ ++|.. ..-.+|+||||++||||||
T Consensus 1600 ~~~~~~~~~~~~~Gaeai~~lL~~~dl~~~~~~l~~~~~~~~~~~~~~~~~krl~~~~~f~~s~~rPewmil~~lPV~Pp 1679 (2836)
T PRK14844 1600 KDSYGIDSFVAMQGVEAIRELLTRLDLHEIRKDLRLELESVASEIRRKKIIKRLRIVENFIKSGNRPEWMILTTIPILPP 1679 (2836)
T ss_pred HHhcCccceeecchHHHHHHHHHhCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHhcCCChhheeeeccccCCC
Confidence 0000000 0 222222221 11111 11110 1235899999999999999
Q ss_pred CCCCCcccCCCccccchhHHHHHHHHHHHHHHHHhh-hcCCCCccchhhhhhHHHHHHHHHHhhcCCCcCCCCCCCCCCC
Q 000291 154 CLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEVRGTAKSSRDVDARFGV 232 (1714)
Q Consensus 154 ~~Rp~~~~~g~~~~~~Dlt~~~l~~Il~~n~~lk~~-~~g~p~~~~~~~~~~~LQ~~v~~~~~~~~~~~~~~~~~~~~~~ 232 (1714)
|+||++.+++.++.++|||. +|++||++|++|+.. ..++|..+ ..++|++||++|+.|||+.....+.....+| ..
T Consensus 1680 ~lRP~v~l~~g~~~~sDLn~-ly~~II~~NnrLk~~~~~~ap~~i-i~~~~~~LQ~~V~~l~Dn~~~g~~~~~~~~r-~~ 1756 (2836)
T PRK14844 1680 DLRPLVSLESGRPAVSDLNH-HYRTIINRNNRLRKLLSLNPPEIM-IRNEKRMLQEAVDSLFDNSRRNALVNKAGAV-GY 1756 (2836)
T ss_pred cccCcEEeCCCcccCCchHH-HHHHHHHHHHHHHHHHHcCCchhh-HHHHHHHHHHHHHHHhcCCCCCCCccCCCCC-Cc
Confidence 99999999888889999998 899999999999975 56677655 4678999999999999964332222211111 11
Q ss_pred CCCCCchhhhhHhhhhhcccccCCCCccceeEeCCCCCccccccchhhcccccccccccchhhHHHHHHHHHccCccccC
Q 000291 233 SQDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDNKLCLTYS 312 (1714)
Q Consensus 233 ~k~~~~~ik~k~gr~R~~l~GKRvdfSaRsVI~pdP~l~~~evgvP~~~A~~Lt~pe~vt~~Ni~~l~~lv~~g~~~~~~ 312 (1714)
.|++.+.+|||+||||+|||||||||||||||+|||+|+++|||||..||++||+| ||+++|+++.... ..+
T Consensus 1757 lksls~~LkGK~GRFR~NLlGKRVDySgRSVI~pdP~L~l~evGlP~~mA~eL~~P-----f~i~~L~~~~~~~---~i~ 1828 (2836)
T PRK14844 1757 KKSISDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELFKP-----FVYSKLKMYGMAP---TIK 1828 (2836)
T ss_pred cccHHHHhcCCCCcccccccccccccCCCceEeCCCCcccceeeCCHHHHHhcccH-----HHHHHHHHcCccc---chH
Confidence 36677999999999999999999999999999999999999999999999999987 6777777653211 100
Q ss_pred CCCceEEeccCCCCccccCCcceeeheeeccceEEEeCCCccccccccceeeEecCCCeEEecccccCCCCCcccccccc
Q 000291 313 DGSSSYSLREGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIH 392 (1714)
Q Consensus 313 ~~~~~~~l~~~~~~~~~l~~g~iV~Rhl~dgd~VL~NRqPsLHr~Sima~~~~v~~~~t~rln~~vC~pyNADFDGDeMn 392 (1714)
.++..++ .....++++|+|| ++||+|||||||||||||||||+|++++++||||||+||+||||||||||||
T Consensus 1829 --~a~~li~-----~~~~~v~dile~v-i~gd~VLlNRqPTLHR~sIqAf~~~l~~gktirlhp~vC~~fNADFDGDeMn 1900 (2836)
T PRK14844 1829 --FASKLIR-----AEKPEVWDMLEEV-IKEHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMA 1900 (2836)
T ss_pred --HHHHHHH-----hhCCcceEEEEEE-ecCCEEEecCCCccccccccceeeEeecCceEEecccCCCcccCCCCCceee
Confidence 0011111 1234567776655 5699999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCHHHHHHHHHhcccccccccCCCCCceEeechhhHhHHHhhh-ccccC----CHHHHHHhhcccc-ccccccccc
Q 000291 393 LFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF-KKYFL----DKAFTQQLAMFAL-SPLPRPALS 466 (1714)
Q Consensus 393 lHvPQS~eAraEa~~Lm~~~~nilsp~~G~Piigl~QD~llg~~llt-kd~fl----~~~~~~~l~~~~~-~~lp~PaI~ 466 (1714)
||||||++|||||++||++.+||++|++|+|+++++||+|+|+|+|| ++.++ ...+++++++... -.++.++.+
T Consensus 1901 vHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pii~~~QD~ilG~y~LT~~~~~~~~~~~f~~~~~~~~a~~~~~~~i~~~i 1980 (2836)
T PRK14844 1901 VHVPISLEAQLEARVLMMSTNNVLSPSNGRPIIVPSKDIVLGIYYLTLQEPKEDDLPSFGAFCEVEHSLSDGTLHIHSSI 1980 (2836)
T ss_pred eecCCcHHHHHHHHHHhCCcccEEecCCCceeEeehhhhhhhhhhhcccccccccccccCCHHHHHHHHHcCCcccCceE
Confidence 99999999999999999999999999999999999999999999997 55543 3455556544332 234556666
Q ss_pred cccccccc---------------ceeeeccccCCCCccccCCEEEEEcceecccccccCcccchHHHHHHHHHHhhCHHH
Q 000291 467 KARCSARW---------------TALQILQSVLPPGFDSCGDRYLIKKSEVLKGDFDRDTIPSVINEIVTSIFFEKGPEE 531 (1714)
Q Consensus 467 Kp~~~~lW---------------TGKQl~s~~LP~~~~~~~~~viI~~Gell~G~ldK~~lg~s~~~Li~~i~~~~G~~~ 531 (1714)
+++ .+| .||+||+.+||..++. +++++.+.++|+.+ .+||+.+|+.||...
T Consensus 1981 ~~~--~~~~~~~~~~~~~~~~tt~GR~if~~ilP~~~~~--------~~~~~n~~l~KK~l----~~II~~~~~~yG~~~ 2046 (2836)
T PRK14844 1981 KYR--MEYINSSGETHYKTICTTPGRLILWQIFPKHENL--------GFDLINQVLTVKEI----TSIVDLVYRNCGQSA 2046 (2836)
T ss_pred Eee--eccccCCCCcccceEecccHHHHHHHHcCCcccc--------CcceEeeeechhHH----HHHHHHHHHHhCHHH
Confidence 665 344 4999999999985443 34677788888776 779999999999999
Q ss_pred HHhchhhhHHHHHHHHHhcCceeeeCCcccCHHHHHHHHHHHHHHHHHHHHhhhh--hHHHHHHHHHHHHHHHHHHHHHH
Q 000291 532 VLEFFDSLQPLLMENLFADGFSVSLEDFSLSKAALWNIQKEIQALYSLLYHRMST--QNELVDLQIENHIRHVKMLVAKF 609 (1714)
Q Consensus 532 a~~fLd~lqrL~~~~L~~~GFSiGi~Dl~~~~~~~~~i~~~i~~~~~~~~~~~~~--~~e~le~~i~~~l~~~~~~i~~~ 609 (1714)
|+.|||+|++|+++|++.+||||||+|+.+|+++.+.+++..+++.++..+|..- ..+..+..+..+|+++++.+++.
T Consensus 2047 t~~fLD~lk~LGf~yaT~~G~SIgi~Di~iP~~K~~iI~~a~~~v~~i~~~y~~G~it~~Er~~kvi~iW~~~~d~v~~~ 2126 (2836)
T PRK14844 2047 TVAFSDKLMVLGFEYATFSGVSFSRCDMVIPETKATHVDHARGEIKKFSMQYQDGLITRSERYNKVIDEWSKCTDMIAND 2126 (2836)
T ss_pred HHHHHHHHHHHHHHHHHhccEEeeHhHcccCHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999888877777777766665421 11223455666778888888876
Q ss_pred HHh----------cCCcccccccccchhhhhHHHHhHhccceecCCCccccccccccccccccccCCCCCCCCCCcccee
Q 000291 610 ILK----------SSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLVEDIASHFERIYPMDLNYPTAKYGLI 679 (1714)
Q Consensus 610 ~~~----------~n~l~~Mi~SGSKGS~~Ni~Qi~g~lGQQ~~~g~r~~~r~l~~~~~~~f~~~~p~~~d~~~~a~GfV 679 (1714)
+++ .|++++|++||||||+.|+.|++||+|||..+.|.++ +. +|
T Consensus 2127 ~~~~l~~~~~~~~~N~i~mMa~SGARGS~sQI~QLaGmRGLmakp~G~iI--------------------e~------PI 2180 (2836)
T PRK14844 2127 MLKAISIYDGNSKYNSVYMMVNSGARGSTSQMKQLAGMRGLMTKPSGEII--------------------ET------PI 2180 (2836)
T ss_pred HHHhhhhccccCCCCceeeeecccCccCHHHHHHHHhcceeeecCCCCee--------------------ec------ch
Confidence 653 4899999999999999999999999999998877632 22 29
Q ss_pred cCcccccCCccceEEeeccccceeeecccccCCCCchhHHHHHHHhceEEEec--cccccc-------------------
Q 000291 680 KGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYD--GTVRNV------------------- 738 (1714)
Q Consensus 680 ~ssF~~GL~P~EfFfHamagREGLiDTAvkTA~sGYLqRrLvk~ledl~v~YD--~Tvr~~------------------- 738 (1714)
.+||++||+|.|||||||+|||||+|||+|||+|||||||||+++||++|..+ ||.+++
T Consensus 2181 ~SNFrEGLsv~EyFiSt~GaRKGL~DTALKTAdSGYLTRRLVDVaQDviI~e~DCgT~~Gi~v~~~~~~~~~i~~L~~ri 2260 (2836)
T PRK14844 2181 ISNFREGLNVFEYFNSTHGARKGLADTALKTANSGYLTRRLVDVSQNCIVTKHDCKTKNGLVVRATVEGSTIVASLESVV 2260 (2836)
T ss_pred hhhhccCCCHHHhhhhccccccchhhhhhhcccccchhhhhhhhhceEEEEecccCCCCceEEEEeccCCeEEeEhhhee
Confidence 99999999999999999999999999999999999999999999999999764 332110
Q ss_pred --------------------------------------------------cCCceeEEEeccccccccCcCCCCceeEEe
Q 000291 739 --------------------------------------------------CSNSIIQFDYAVNARKSHSLFPAGEPVGVL 768 (1714)
Q Consensus 739 --------------------------------------------------~~~~IiQf~yg~dg~~~~~lv~~GepVG~l 768 (1714)
+...|||.|||.+. ....+|..||+||+|
T Consensus 2261 ~GR~~a~di~~p~t~~~i~~~~~~I~~~~~~~i~~~gi~~v~IRS~ltC~s~~gvC~~CYG~~L-a~~~~V~iGeaVGiI 2339 (2836)
T PRK14844 2261 LGRTAANDIYNPVTKELLVKAGELIDEDKVKQINIAGLDVVKIRSPLTCEISPGVCSLCYGRDL-ATGKIVSIGEAVGVI 2339 (2836)
T ss_pred EEEEEHhHeEcCCCCCEEEeCCCccCHHHHHHHHHcCCCEEEEcCCeeECCCCCChhhccCccc-cCCCcccccccceee
Confidence 23479999999984 578899999999999
Q ss_pred ccccCChhHHHHhhcCCC
Q 000291 769 AATAMSNPAYKAVLDSSP 786 (1714)
Q Consensus 769 aaqsigepatq~~L~t~~ 786 (1714)
||||||||+||+||+|||
T Consensus 2340 AAQSIGEPGTQLTMRTFH 2357 (2836)
T PRK14844 2340 AAQSVGEPGTQLTMRTFH 2357 (2836)
T ss_pred eecccCCCcceeeeehee
Confidence 999999999999999998
No 11
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=100.00 E-value=2.1e-146 Score=1454.97 Aligned_cols=707 Identities=22% Similarity=0.271 Sum_probs=555.2
Q ss_pred cccceeeEEEecCCHHHHHHhcccccccccC------------CCCCCCCCCCCCCCCCC----------------CCCC
Q 000291 10 LEGQIVGIRFGLATQKEICTASISDCSISHA------------SQLANPFLGLPLEFGKC----------------ESCG 61 (1714)
Q Consensus 10 ~~~~I~~I~F~l~S~eEI~k~Sv~~~~I~~~------------~gl~DprLG~~~~~~~C----------------~TCg 61 (1714)
....+..|+.++.|||.|+++|+.| |++| .||++.|.-.|.++..| +.||
T Consensus 1392 ~~~~~~~i~i~lASpe~I~~ws~Ge--V~kpeTinyrt~kPe~dGLFcerIFGp~kd~eC~Cgkyk~~~~~g~~~C~~Cg 1469 (2890)
T PRK09603 1392 RPKDFSSFQLTLASPEKIHSWSYGE--VKKPETINYRTLKPERDGLFCMKIFGPTKDYECLCGKYKKPRFKDIGTCEKCG 1469 (2890)
T ss_pred cccCcceEEEEecCHHHHHHhhcee--EccccccccccCccCCCCEeeceeccCccCcEEeCCCcccccCCCCEEcCCCC
Confidence 4567889999999999999999865 4433 58999888667665555 4444
Q ss_pred CCC--CCCCCCcceeEEcCcccccccchHHHHHHHHHH-------------Hhh--hccch-----------HHH-----
Q 000291 62 TSE--PGKCEGHFGYIELPIPIYHPSHISELKLTMYAF-------------QLQ--IKNDG-----------VAQ----- 108 (1714)
Q Consensus 62 ~~~--~~~CpGHFGhIeL~~PVfHpgf~k~I~~IL~~i-------------C~r--i~~~g-----------~~k----- 108 (1714)
... .+...-.+|||+|+.||.|++||+.+...|..+ |.. +.+.+ +.+
T Consensus 1470 vevt~s~vRR~RmGhI~La~Pv~HiWy~k~~ps~i~~ll~~~~k~le~viy~~~~~v~~~~~~~~~~~~~~~~~~~~~~~ 1549 (2890)
T PRK09603 1470 VAITHSKVRRFRMGHIELATPVAHIWYVNSLPSRIGTLLGVKMKDLERVLYYEAYIVKEPGEAAYDNEGTKLVMKYDILN 1549 (2890)
T ss_pred cEechhHhHHHhcCceeecCcceeeeccCCCchHHHHHhCCCHHHhhhhhcceeeEEecCCccccccccccchhhhhhhh
Confidence 221 112234899999999999999999665544433 110 00111 000
Q ss_pred --------------------------HHHHHH-----H-HHHHHHhcCChHHH-H----hhcc-----CCCCCCCcEEEe
Q 000291 109 --------------------------RLLSSC-----C-EVKEMLKRIPEETR-K----KLAG-----KGYFPQDGYILE 146 (1714)
Q Consensus 109 --------------------------ri~~~C-----C-eV~~IfkkI~~ed~-~----~L~~-----~~~~~pe~~il~ 146 (1714)
++++.. | ++++.++......+ + +|.. ..-.+|+||||+
T Consensus 1550 ~~~~~~~~~~~~~~~f~~~~Gaeai~~lL~~~dl~~~~~~l~~~~~~~~~~~~~~~~~krl~~v~~f~~s~~~PewmiL~ 1629 (2890)
T PRK09603 1550 EEQYQNISRRYEDRGFVAQMGGEAIKDLLEEIDLITLLQSLKEEVKDTNSDAKKKKLIKRLKVVESFLNSGNRPEWMMLT 1629 (2890)
T ss_pred HHHHHHHHHHcCcccceechhHHHHHHHHHhCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHhcCCChHheeee
Confidence 000000 0 12222222111111 1 1111 123589999999
Q ss_pred eccCCCCCCCCCcccCCCccccchhHHHHHHHHHHHHHHHHhh-hcCCCCccchhhhhhHHHHHHHHHHhhcCCCcCCCC
Q 000291 147 YLPVPPNCLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEVRGTAKSSRD 225 (1714)
Q Consensus 147 ~lpVPP~~~Rp~~~~~g~~~~~~Dlt~~~l~~Il~~n~~lk~~-~~g~p~~~~~~~~~~~LQ~~v~~~~~~~~~~~~~~~ 225 (1714)
+|||||||+||++.+++..+.++|+|. +|++||++|++|+.. ..++|..+. .+++++||.+|+.|||+.....+...
T Consensus 1630 ~lPV~Pp~lRP~v~l~gg~~a~sDln~-lyr~II~rNnrLk~l~~~~ap~~ii-~nek~~LQ~aVd~l~DN~~~~~~~~~ 1707 (2890)
T PRK09603 1630 VLPVLPPDLRPLVALDGGKFAVSDVNE-LYRRVINRNQRLKRLMELGAPEIIV-RNEKRMLQEAVDVLFDNGRSTNAVKG 1707 (2890)
T ss_pred eeccCCCcccCcEEeCCCcccCCCccH-HHHHHHHHHHHHHHHHHcCCCceeh-HHHHHHHHHHHHHHhccccccccccC
Confidence 999999999999999988888999998 899999999999975 667777654 57899999999999987543322222
Q ss_pred CCCCCCCCCCCCchhhhhHhhhhhcccccCCCCccceeEeCCCCCccccccchhhcccccccccccchhhHHHHHHHHHc
Q 000291 226 VDARFGVSQDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDN 305 (1714)
Q Consensus 226 ~~~~~~~~k~~~~~ik~k~gr~R~~l~GKRvdfSaRsVI~pdP~l~~~evgvP~~~A~~Lt~pe~vt~~Ni~~l~~lv~~ 305 (1714)
..+| ..|++.+.+|||+||||+|||||||||||||||+|||+|+++|||||..||++||+|+. +++|+.+
T Consensus 1708 ~~~r--plKsls~~LkGK~GRFRqNLlGKRVDySgRSVI~pdP~L~l~e~GvP~~mA~eL~~P~~--------i~~L~~~ 1777 (2890)
T PRK09603 1708 ANKR--PLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHL--------LSKLEER 1777 (2890)
T ss_pred CCCC--cchhHHHHhcCCCCccccccccccccCcCCceEeCCCCcccccccChHHHHHHhCChHH--------HHHHHHc
Confidence 1111 34677899999999999999999999999999999999999999999999999999964 5788899
Q ss_pred cCccccCCCCceEEeccCCCCccccCCcceeeheeeccceEEEeCCCccccccccceeeEecCCCeEEecccccCCCCCc
Q 000291 306 KLCLTYSDGSSSYSLREGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSAD 385 (1714)
Q Consensus 306 g~~~~~~~~~~~~~l~~~~~~~~~l~~g~iV~Rhl~dgd~VL~NRqPsLHr~Sima~~~~v~~~~t~rln~~vC~pyNAD 385 (1714)
|+...++.. +..+ .......+.|+|||++||+|||||||||||||||||+|+|++++||||||+||+|||||
T Consensus 1778 G~~~~lk~a--k~~i------~~~~~~v~~vlr~vi~gd~VLlNRqPTLHR~sIqAf~~~l~~gktIrLhplvC~~fNAD 1849 (2890)
T PRK09603 1778 GYATTLKQA--KRMI------EQKSNEVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNAD 1849 (2890)
T ss_pred CCccCHHHH--HHHH------HhccCccEEEEEeeecCCeEEecCCCccccccceeeeEEEecCceEEeccccCCcccCC
Confidence 976433211 1101 11233457788999999999999999999999999999999999999999999999999
Q ss_pred cccccccccCCCCHHHHHHHHHhcccccccccCCCCCceEeechhhHhHHHhhh-ccc--------cCCHHHHHHhhccc
Q 000291 386 FDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF-KKY--------FLDKAFTQQLAMFA 456 (1714)
Q Consensus 386 FDGDeMnlHvPQS~eAraEa~~Lm~~~~nilsp~~G~Piigl~QD~llg~~llt-kd~--------fl~~~~~~~l~~~~ 456 (1714)
|||||||||||||++|||||++||++.+||+||++|+|+++++||+|+|+|+|| ++. |.+.+++...+...
T Consensus 1850 FDGDqMnvHvPqS~eA~aEa~~LM~s~~nilsP~~G~Pi~~p~QD~vlG~y~LT~~~~~~~~~~~~F~~~~e~~~~~~~~ 1929 (2890)
T PRK09603 1850 FDGDQMAVHVPLSQEAIAECKVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKSGVKGEHKLFSSVNEIITAIDTK 1929 (2890)
T ss_pred CCCceeEEeecCCHHHHHHHHHHhcccceEEEcCCCceeEEeecceeeeeEEeeccccCCCCccceeCCHHHHHHHHHcC
Confidence 999999999999999999999999999999999999999999999999999997 554 45555554433322
Q ss_pred c--cccccccccccccccccc--eeeeccccCCCCccccCCEEEEEcceecccccccCcccchHHHHHHHHHHhhCHHHH
Q 000291 457 L--SPLPRPALSKARCSARWT--ALQILQSVLPPGFDSCGDRYLIKKSEVLKGDFDRDTIPSVINEIVTSIFFEKGPEEV 532 (1714)
Q Consensus 457 ~--~~lp~PaI~Kp~~~~lWT--GKQl~s~~LP~~~~~~~~~viI~~Gell~G~ldK~~lg~s~~~Li~~i~~~~G~~~a 532 (1714)
. +..+.|++++|. .||| |||||+.+||..+.+ .++.+.+||+.|| +|||.+|+.||+..|
T Consensus 1930 ~~~~~~~i~~~~~p~--~l~Tt~GK~ifs~ilP~~~~~----------~~~n~~ldKK~Lg----~LI~~i~~~yG~~~t 1993 (2890)
T PRK09603 1930 ELDIHAKIRVLDQGN--IIATSAGRMIIKSILPDFIPT----------DLWNRPMKKKDIG----VLVDYVHKVGGIGIT 1993 (2890)
T ss_pred CCccCCcceeecCCc--EEEcCccceeeeccCcccccc----------ccEeeeechHHHH----HHHHHHHHHHCHHHH
Confidence 2 234566777777 8999 999999999976532 2334678888876 699999999999999
Q ss_pred HhchhhhHHHHHHHHHhcCceeeeCCcccCHHHHHHHHHHHHHHHHHHHHhhh-------hhHHHHHHHHHHHHHHHHHH
Q 000291 533 LEFFDSLQPLLMENLFADGFSVSLEDFSLSKAALWNIQKEIQALYSLLYHRMS-------TQNELVDLQIENHIRHVKML 605 (1714)
Q Consensus 533 ~~fLd~lqrL~~~~L~~~GFSiGi~Dl~~~~~~~~~i~~~i~~~~~~~~~~~~-------~~~e~le~~i~~~l~~~~~~ 605 (1714)
+.|||.+++|+++|++.+||||||+|+.+|+++.+.+++..+++.++..++.. +|++.++ .|+++++.
T Consensus 1994 ~~fLD~lk~LGf~yat~~G~SIgI~Dl~ip~~K~~iI~~A~~eV~ei~~~y~~G~it~~Er~~kvid-----~w~~~~d~ 2068 (2890)
T PRK09603 1994 ATFLDNLKTLGFRYATKAGISISMEDIITPKDKQKMVEKAKVEVKKIQQQYDQGLLTDQERYNKIID-----TWTEVNDK 2068 (2890)
T ss_pred HHHHHHHHHHHHHHHHhCCEeeeeccCcccHHHHHHHHHHHHHHHHHHHHHHcCCCCccHHHHHHHH-----HHHHHHHH
Confidence 99999999999999999999999999999998877777776666666655532 3444444 45566666
Q ss_pred HHHHHH----h----cCCcccccccccchhhhhHHHHhHhccceecCCCccccccccccccccccccCCCCCCCCCCccc
Q 000291 606 VAKFIL----K----SSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLVEDIASHFERIYPMDLNYPTAKYG 677 (1714)
Q Consensus 606 i~~~~~----~----~n~l~~Mi~SGSKGS~~Ni~Qi~g~lGQQ~~~g~r~~~r~l~~~~~~~f~~~~p~~~d~~~~a~G 677 (1714)
+.+.++ + .|++++|+.||||||+.|++||+||||||..+.|+.+ +.
T Consensus 2069 v~~~~~~~l~~~~~~~N~i~mMa~SGARGS~~NI~QLaGmrGqMakp~G~ii--------------------e~------ 2122 (2890)
T PRK09603 2069 MSKEMMTAIAKDKEGFNSIYMMADSGARGSAAQIRQLSAMRGLMTKPDGSII--------------------ET------ 2122 (2890)
T ss_pred HHHHHHHHhhhcCCCCCcHHHHHhccccccHHHHHHHHHcCCcEECCCCCcc--------------------cC------
Confidence 655543 2 3899999999999999999999999999998876632 22
Q ss_pred eecCcccccCCccceEEeeccccceeeecccccCCCCchhHHHHHHHhceEEEec--cccccc-----------------
Q 000291 678 LIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYD--GTVRNV----------------- 738 (1714)
Q Consensus 678 fV~ssF~~GL~P~EfFfHamagREGLiDTAvkTA~sGYLqRrLvk~ledl~v~YD--~Tvr~~----------------- 738 (1714)
+|.+||++||+|+|||||||||||||+|||||||+|||||||||+++|||+|.++ ||.+++
T Consensus 2123 PI~snFrEGLtp~EyFfst~GaRKGLiDTALKTAdSGYLTRRLVdvaQDviI~e~DCgT~~Gi~v~~~~~~~~~i~~l~~ 2202 (2890)
T PRK09603 2123 PIISNFKEGLNVLEYFNSTHGARKGLADTALKTANAGYLTRKLIDVSQNVKVVSDDCGTHEGIEITDIAVGSELIEPLEE 2202 (2890)
T ss_pred hhhcCcccCCCHHHHHHhccccccchhhhhhhccccchhhhhHHHhhcceEEEeccCCCCCCeEEEEeecCCeeecchhh
Confidence 2899999999999999999999999999999999999999999999999999876 332210
Q ss_pred ----------------------------------------------------cCCceeEEEeccccccccCcCCCCceeE
Q 000291 739 ----------------------------------------------------CSNSIIQFDYAVNARKSHSLFPAGEPVG 766 (1714)
Q Consensus 739 ----------------------------------------------------~~~~IiQf~yg~dg~~~~~lv~~GepVG 766 (1714)
+...|||.|||.|. ....+|..||+||
T Consensus 2203 ri~GR~~~~di~~p~t~~~i~~~~~~I~~~~~~~i~~~gi~~v~iRS~LtC~s~~gvC~~CYG~dL-a~g~~V~iGeaVG 2281 (2890)
T PRK09603 2203 RIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITIRTPVTCKAPKGVCAKCYGLNL-GEGKMSYPGEAVG 2281 (2890)
T ss_pred eeeeEEEHhheEcCCCCcEEEcCCcCcCHHHHHHHHHcCCCEEEEcCcceecCCCcChhhhcCCcc-cCCCCccCCceee
Confidence 13469999999984 5788999999999
Q ss_pred EeccccCChhHHHHhhcCCC
Q 000291 767 VLAATAMSNPAYKAVLDSSP 786 (1714)
Q Consensus 767 ~laaqsigepatq~~L~t~~ 786 (1714)
+|||||||||+||+||+|||
T Consensus 2282 iIAAQSIGEPGTQLTMRTFH 2301 (2890)
T PRK09603 2282 VVAAQSIGEPGTQLTLRTFH 2301 (2890)
T ss_pred EEeecccCCCccccchhhhe
Confidence 99999999999999999998
No 12
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]
Probab=100.00 E-value=8.3e-129 Score=1238.01 Aligned_cols=688 Identities=23% Similarity=0.277 Sum_probs=570.5
Q ss_pred eeeEEEecCCHHHHHHhcccccccccC-----------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeEEcCcccc
Q 000291 14 IVGIRFGLATQKEICTASISDCSISHA-----------SQLANPFLGLPLEFGKCESCGTSEPGKCEGHFGYIELPIPIY 82 (1714)
Q Consensus 14 I~~I~F~l~S~eEI~k~Sv~~~~I~~~-----------~gl~DprLG~~~~~~~C~TCg~~~~~~CpGHFGhIeL~~PVf 82 (1714)
+..|+|+++||++|++ |+.+ |+.| .||+|+|||+|.++..| |||+.. ..||||||||||+.||+
T Consensus 4 ~~~i~~gl~sp~~ir~-~s~e--v~~pet~~~~~~P~~~Gl~d~ri~~~~~~~~C-~Cg~~~-~~~~~~~GhIeLa~Pv~ 78 (808)
T COG0086 4 IFDIKFGLASPEEIRS-WSGE--VKKPETINYRTKPERGGLFDERIFGPDKDYEC-TCGKYK-RICPGGFGHIELAAPVA 78 (808)
T ss_pred cceeEEecCCHHHHHh-cceE--EcCccccCCCCcccCCCccchhhcCCCCCcee-cCCCCc-CcCCCCceeEEeecceE
Confidence 3449999999999999 5443 4432 48999999999999999 999985 89999999999999999
Q ss_pred cccchHHHHHHHHHHHh---hhc--cchHH-----HH--HH--------HHH--H-------------------------
Q 000291 83 HPSHISELKLTMYAFQL---QIK--NDGVA-----QR--LL--------SSC--C------------------------- 115 (1714)
Q Consensus 83 Hpgf~k~I~~IL~~iC~---ri~--~~g~~-----kr--i~--------~~C--C------------------------- 115 (1714)
||+|++.+..+|++.|. +++ ...+. ++ ++ ..| |
T Consensus 79 hi~f~k~~~~~L~~~~~~~~~v~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~Ga~~~~~~~~~~~~~~~~~~~~~~~ 158 (808)
T COG0086 79 HIWFFKSIPSLLDMTCRDCERVLYFEAYVVLGTDLEKIQLLNETEYVYDSFCAHCGAEAIKILLEKPDLETEREEETLSP 158 (808)
T ss_pred EechhhccHHHHhhhHHhhhhhhhHhHHHHhccchhhhcccchheeeccccCCCCCchhHHHHHhCcchhhhhhhcccCH
Confidence 99999999999999975 433 00000 00 00 234 3
Q ss_pred -HHHHHHhcCChHHHHhhccCCCCCCCcEEEeeccCCCCCCCCCcccCCCccccchhHHHHHHHHHHHHHHHHhhhcCCC
Q 000291 116 -EVKEMLKRIPEETRKKLAGKGYFPQDGYILEYLPVPPNCLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSSRSGTP 194 (1714)
Q Consensus 116 -eV~~IfkkI~~ed~~~L~~~~~~~pe~~il~~lpVPP~~~Rp~~~~~g~~~~~~Dlt~~~l~~Il~~n~~lk~~~~g~p 194 (1714)
+++++|++|+..|..++. ..+|+||||++||||||++||++.++|+.+.++|||+ +|++||++|++|+.....+|
T Consensus 159 ~~~~~~~~~l~~~d~~~~~---~~~pewmil~vlpV~Pp~~RP~i~ld~g~~a~~dl~~-~~~~ii~~n~rlk~~~~~~~ 234 (808)
T COG0086 159 TKVKKLLKRLKVVDAFLLS---GNRPEWMILTVLPVPPPDLRPSIQLDGGRFAESDLND-LYRRVINRNNRLKRLLELAA 234 (808)
T ss_pred HHHHHHHhhccHHHHHHhc---CCCcceeEEEeeccCCCCCCcceecCCCccchhHHHH-HHHHHHHHHHHhHHhhhhcc
Confidence 678899999999988874 7789999999999999999999999999999999998 79999999999987633344
Q ss_pred CccchhhhhhHHHHHHHHHHhhcCCCcCCCCCCCCCCCCCCCCchhhhhHhhhhhcccccCCCCccceeEeCCCCCcccc
Q 000291 195 NFESQEVESNDLQLAVGQYLEVRGTAKSSRDVDARFGVSQDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNE 274 (1714)
Q Consensus 195 ~~~~~~~~~~~LQ~~v~~~~~~~~~~~~~~~~~~~~~~~k~~~~~ik~k~gr~R~~l~GKRvdfSaRsVI~pdP~l~~~e 274 (1714)
. +...++|++||++|++|||+ +.+.+... ....|++.+++|||+||||+||+||||||||||||+|||+|+++|
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 55544322 123478889999999999999999999999999999999999999
Q ss_pred ccchhhcccccccccccchhhHHHHHHHHHccCccccCCCCceEEeccCCCCccccCCcceeeheeeccceEEEeCCCcc
Q 000291 275 IGVPFEIAQRITFEERVNVHNINYLQELVDNKLCLTYSDGSSSYSLREGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTT 354 (1714)
Q Consensus 275 vgvP~~~A~~Lt~pe~vt~~Ni~~l~~lv~~g~~~~~~~~~~~~~l~~~~~~~~~l~~g~iV~Rhl~dgd~VL~NRqPsL 354 (1714)
||||..||++||+|+.|+++|++.|++ | ++|..+.. ...+..+|.|+||+++||+|||||||||
T Consensus 309 ~GvP~~~A~~L~~p~~v~~~~~~~~~~----~---------a~~~~~~~---~~~~~~~w~Vl~evi~gd~Vl~NR~PtL 372 (808)
T COG0086 309 CGVPKKMALELFKPFVVTELNIEGLRT----G---------AKYAKRMV---ERRLPEVWDVLREVIDGDPVLLNRAPTL 372 (808)
T ss_pred cCCHHHHHHHhccCEEEEehhhhhhhc----C---------CceEEecc---cccccccchHHHHHhcCCccccccCChH
Confidence 999999999999999999999999987 2 23333321 1236789999999999999999999999
Q ss_pred ccccccceeeEecC-CCeEEecccccCCCCCccccccccccCCCCHHHHHHHHHhcccccccccCCCCCceEeechhhHh
Q 000291 355 HKHSLQALSVYVHD-DHTVKINPLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALL 433 (1714)
Q Consensus 355 Hr~Sima~~~~v~~-~~t~rln~~vC~pyNADFDGDeMnlHvPQS~eAraEa~~Lm~~~~nilsp~~G~Piigl~QD~ll 433 (1714)
||+|||+|++++++ ++||||||+||.||||||||||||+|+|||.+|+|||+.||++++||++|++|+||++++||+|+
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---ccccccccccccccccccccceeeeccccCCCCc--c----------------cc
Q 000291 434 SLKVMF-KKYFLDKAFTQQLAM---FALSPLPRPALSKARCSARWTALQILQSVLPPGF--D----------------SC 491 (1714)
Q Consensus 434 g~~llt-kd~fl~~~~~~~l~~---~~~~~lp~PaI~Kp~~~~lWTGKQl~s~~LP~~~--~----------------~~ 491 (1714)
|.|||| .|.|++..+++++++ +.....++|||.++. .+||+||+++.+++... . ..
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 688999999998843 344456789999888 99999999998777531 1 01
Q ss_pred -CCEEEEEcceecccccccCcccchHHHHHHHHHHhhCHHHHH-hchhhhHHHHHHHHHhcC-ceeeeCCcc--cCHHHH
Q 000291 492 -GDRYLIKKSEVLKGDFDRDTIPSVINEIVTSIFFEKGPEEVL-EFFDSLQPLLMENLFADG-FSVSLEDFS--LSKAAL 566 (1714)
Q Consensus 492 -~~~viI~~Gell~G~ldK~~lg~s~~~Li~~i~~~~G~~~a~-~fLd~lqrL~~~~L~~~G-FSiGi~Dl~--~~~~~~ 566 (1714)
+..+.|.+++++.|.+||.+. .+++.||+.++. .+++.+.+|...++...| |+++|+|.. +++++.
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 233578899998888888664 789999998888 888888888888888887 888887775 555555
Q ss_pred HHHHHHHHHHHHHHHHhhh-------hh--HHHHHHHHHHHHHHHHHHHHHHHHhcCC--cccccccccchhhhhHHHHh
Q 000291 567 WNIQKEIQALYSLLYHRMS-------TQ--NELVDLQIENHIRHVKMLVAKFILKSST--LGYLIDSKSDSAVSKVVQQA 635 (1714)
Q Consensus 567 ~~i~~~i~~~~~~~~~~~~-------~~--~e~le~~i~~~l~~~~~~i~~~~~~~n~--l~~Mi~SGSKGS~~Ni~Qi~ 635 (1714)
+.+.++-.++.++..++.. .| .+.++......+++++........+... +..|..+|++|++.|++||+
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 5555555555555555432 22 2334455556666666555554443322 34677788888888899999
Q ss_pred HhccceecCCCccccccccccccccccccCCCCCCCCCCccceecCcccccCCccceEEeeccccceeeecccccCCCCc
Q 000291 636 GFLGLQLSDRGKFYSKTLVEDIASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGT 715 (1714)
Q Consensus 636 g~lGQQ~~~g~r~~~r~l~~~~~~~f~~~~p~~~d~~~~a~GfV~ssF~~GL~P~EfFfHamagREGLiDTAvkTA~sGY 715 (1714)
.|+|||.+.|.+. ++ .++|||.. .+..+++.|||.++|++||+|.|||||+|+||+||||||+|||++||
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 9999999997762 22 27799974 35668999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHhceEEEeccccccccCCceeEEEecccccc
Q 000291 716 LFKNLMAVLRDVVICYDGTVRNVCSNSIIQFDYAVNARK 754 (1714)
Q Consensus 716 LqRrLvk~ledl~v~YD~Tvr~~~~~~IiQf~yg~dg~~ 754 (1714)
||||||+++|||+|.||++||+ ..+.++||.||+|+.+
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 6789999999999854
No 13
>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional
Probab=100.00 E-value=1.7e-84 Score=789.79 Aligned_cols=408 Identities=20% Similarity=0.294 Sum_probs=305.1
Q ss_pred cccceeeEEEecCCHHHHHHhc---------ccccccccC------------CCCCCCCCCCCCCCCC------------
Q 000291 10 LEGQIVGIRFGLATQKEICTAS---------ISDCSISHA------------SQLANPFLGLPLEFGK------------ 56 (1714)
Q Consensus 10 ~~~~I~~I~F~l~S~eEI~k~S---------v~~~~I~~~------------~gl~DprLG~~~~~~~------------ 56 (1714)
...++..|+.++.|||.|+++| +.| |++| .||++.|.-.|.++..
T Consensus 5 ~~~~~~~i~I~laSPe~I~~Ws~r~lpng~i~Ge--V~kpeTinyrT~KPE~dGLFCerIFGP~k~~eC~CGkyk~~~~~ 82 (627)
T PRK02625 5 TENRFDYVKIGLASPERIRQWGQRTLPNGQVVGE--VTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHR 82 (627)
T ss_pred cccccceEEEEecCHHHHHHHHHhhcCCCceeeE--ECCCcccccCCCCCCCCCEeechhcCCccCcEEeCCCccccCcC
Confidence 3567889999999999999999 533 4433 4899988755665554
Q ss_pred ---CCCCCCCC--CCCCCCcceeEEcCcccccccchHHHHHHHHHH-------------Hhh--hccch--------H--
Q 000291 57 ---CESCGTSE--PGKCEGHFGYIELPIPIYHPSHISELKLTMYAF-------------QLQ--IKNDG--------V-- 106 (1714)
Q Consensus 57 ---C~TCg~~~--~~~CpGHFGhIeL~~PVfHpgf~k~I~~IL~~i-------------C~r--i~~~g--------~-- 106 (1714)
|+.||... .....=.+|||+|+.||.|++|++.+...|..+ |.. +.+.+ .
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 44554322 111234899999999999999999665444433 220 00110 0
Q ss_pred --------HHHHHH--------H-H-------------------H-HHHHHHhcCChHHHHhh----cc-----CCCCCC
Q 000291 107 --------AQRLLS--------S-C-------------------C-EVKEMLKRIPEETRKKL----AG-----KGYFPQ 140 (1714)
Q Consensus 107 --------~kri~~--------~-C-------------------C-eV~~IfkkI~~ed~~~L----~~-----~~~~~p 140 (1714)
.+++.. . . + .++..++......+.++ .. ....+|
T Consensus 163 ~~~~~~~~~~~~~~~~~~~~~~~~~~~Ga~ai~~lL~~~dl~~~~~~l~~~~~~~~~~~~~~~ikrl~~~~~f~~~~~~P 242 (627)
T PRK02625 163 TEDQWLEIEDQIYAEDSELEGEEVVGIGAEALKRLLEDLNLEEEAEQLREEIANSKGQKRAKLIKRLRVIDNFIATGSRP 242 (627)
T ss_pred hhHHHHHHHHHhcccccccccchhhhhhHHHHHHHHhhCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHhcCCCc
Confidence 000000 0 1 0 11112222111111111 10 123579
Q ss_pred CcEEEeeccCCCCCCCCCcccCCCccccchhHHHHHHHHHHHHHHHHhh-hcCCCCccchhhhhhHHHHHHHHHHhhcCC
Q 000291 141 DGYILEYLPVPPNCLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEVRGT 219 (1714)
Q Consensus 141 e~~il~~lpVPP~~~Rp~~~~~g~~~~~~Dlt~~~l~~Il~~n~~lk~~-~~g~p~~~~~~~~~~~LQ~~v~~~~~~~~~ 219 (1714)
+||||++|||||+|+||++.++++.+.++|+|. +|++||++|++|+.. ..++|..+. .+++++||.+|++|||+...
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 999999999999999999999887888899998 899999999999875 556665443 46789999999999997543
Q ss_pred CcCCCCCCCCCCCCCCCCchhhhhHhhhhhcccccCCCCccceeEeCCCCCccccccchhhcccccccccccchhhHHHH
Q 000291 220 AKSSRDVDARFGVSQDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYL 299 (1714)
Q Consensus 220 ~~~~~~~~~~~~~~k~~~~~ik~k~gr~R~~l~GKRvdfSaRsVI~pdP~l~~~evgvP~~~A~~Lt~pe~vt~~Ni~~l 299 (1714)
.++..+..+| ..+++.+.+|||+||||+|||||||||||||||+|||+|++||||||.+||++||+| |||++|
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 3222221111 335677899999999999999999999999999999999999999999999999888 566655
Q ss_pred HHHHHccCccccCCCCceEEeccCCCCccccCCcceeeheeeccceEEEeCCCccccccccceeeEecCCCeEEeccccc
Q 000291 300 QELVDNKLCLTYSDGSSSYSLREGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLIC 379 (1714)
Q Consensus 300 ~~lv~~g~~~~~~~~~~~~~l~~~~~~~~~l~~g~iV~Rhl~dgd~VL~NRqPsLHr~Sima~~~~v~~~~t~rln~~vC 379 (1714)
+.+|....++ .++..+... . ...+.|+|||+|||+|||||||||||||||||+|++++++||||||+||
T Consensus 394 ---~~~g~~~~i~--~ak~~i~~~-----~-~~~~~Vlr~v~~gd~VLlNRqPTLHR~sIqAf~~~l~~~ktirlhplvC 462 (627)
T PRK02625 394 ---IRQGIVNNIK--AAKKLIQRA-----D-PEVWQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVC 462 (627)
T ss_pred ---HHcCchhhHH--HHHHHHHhc-----C-CcccEEEEEeecCcEEEecCCCccccccceeEeeEEcCCCeEEeccccC
Confidence 4555432111 111112111 1 1245688999999999999999999999999999999999999999999
Q ss_pred CCCCCccccccccccCCCCHHHHHHHHHhcccccccccCCCCCceEeechhhHhHHHhhh
Q 000291 380 GPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF 439 (1714)
Q Consensus 380 ~pyNADFDGDeMnlHvPQS~eAraEa~~Lm~~~~nilsp~~G~Piigl~QD~llg~~llt 439 (1714)
+||||||||||||||||||++|||||++||++++||+||++|+|+++++||+|+|+|+||
T Consensus 463 ~~fNADFDGDeMnvHvPqS~~A~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~llG~y~LT 522 (627)
T PRK02625 463 PAFNADFDGDQMAVHVPLSLEAQAEARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLT 522 (627)
T ss_pred CcccCCcCCCeEEEecCCCHHHHHHHHHHhcCccceEEcCCCceeEeechhhhhheeeee
Confidence 999999999999999999999999999999999999999999999999999999999987
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=4.2e-84 Score=785.55 Aligned_cols=403 Identities=20% Similarity=0.296 Sum_probs=303.3
Q ss_pred eeeEEEecCCHHHHHHhc---------ccccccccC------------CCCCCCCCCCCCCCCCCCCCCCCC-----CCC
Q 000291 14 IVGIRFGLATQKEICTAS---------ISDCSISHA------------SQLANPFLGLPLEFGKCESCGTSE-----PGK 67 (1714)
Q Consensus 14 I~~I~F~l~S~eEI~k~S---------v~~~~I~~~------------~gl~DprLG~~~~~~~C~TCg~~~-----~~~ 67 (1714)
+..|+.++.|||.|+++| +.| |++| .||++.|.-.|.++..| .||+-. ...
T Consensus 2 ~~~i~I~laSPe~I~~Ws~r~lpng~i~Ge--V~kp~TinyrT~KPE~dGLFCerIFGP~k~~eC-~CGkyk~~~~~~~~ 78 (619)
T TIGR02387 2 FDYVKITIASPERVMEWGQRTLPNGQVVGE--VTKPETINYRTLKPEMDGLFCEKIFGPSKDWEC-HCGKYKRVRHRGIV 78 (619)
T ss_pred CceEEEEecCHHHHHHHHHhhCCCCceeeE--ECCCcccccCCCCCCCCCEeechhcCCCcCcEE-eCCCccccCcCCcC
Confidence 567999999999999999 543 4433 48999888667766666 565210 012
Q ss_pred CC-------------CcceeEEcCcccccccchHHHHHHHHHH-------------Hhh--hccch--------HH----
Q 000291 68 CE-------------GHFGYIELPIPIYHPSHISELKLTMYAF-------------QLQ--IKNDG--------VA---- 107 (1714)
Q Consensus 68 Cp-------------GHFGhIeL~~PVfHpgf~k~I~~IL~~i-------------C~r--i~~~g--------~~---- 107 (1714)
|+ =.+|||+|+.||.|++|++.+...|..+ |.. +.+.+ ..
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 44 3899999999999999999665554443 220 00110 00
Q ss_pred --HHHHH--------------H-----H-------------H-HHHHHHhcCChHHHHhh----cc-----CCCCCCCcE
Q 000291 108 --QRLLS--------------S-----C-------------C-EVKEMLKRIPEETRKKL----AG-----KGYFPQDGY 143 (1714)
Q Consensus 108 --kri~~--------------~-----C-------------C-eV~~IfkkI~~ed~~~L----~~-----~~~~~pe~~ 143 (1714)
..+.. . + + .++..++......+.++ .. ..-.+|+||
T Consensus 159 ~~~~~~~~~~~~~~~~~~~~~~~~Ga~ai~~lL~~~dl~~~~~~l~~~~~~~~~~~~~~~~krl~~~~~f~~~~~~Pewm 238 (619)
T TIGR02387 159 QWLEIEDQIYAEDSELENEEVVGIGAEALKQLLADLNLEEVAEQLREEINGSKGQKRAKLIKRLRVIDNFIATSSRPEWM 238 (619)
T ss_pred HHHHHHHHhcccccccccceeccchHHHHHHHHHhCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcCCCcceE
Confidence 00000 0 0 0 11112222111111111 10 123579999
Q ss_pred EEeeccCCCCCCCCCcccCCCccccchhHHHHHHHHHHHHHHHHhh-hcCCCCccchhhhhhHHHHHHHHHHhhcCCCcC
Q 000291 144 ILEYLPVPPNCLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEVRGTAKS 222 (1714)
Q Consensus 144 il~~lpVPP~~~Rp~~~~~g~~~~~~Dlt~~~l~~Il~~n~~lk~~-~~g~p~~~~~~~~~~~LQ~~v~~~~~~~~~~~~ 222 (1714)
||++|||||+|+||++.+++..+.++|+|. +|++||++|++|+.. ..++|..+ ..++|++||.+|+.|||+....++
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 999999999999999999888888999998 899999999999875 55666544 346799999999999997543332
Q ss_pred CCCCCCCCCCCCCCCchhhhhHhhhhhcccccCCCCccceeEeCCCCCccccccchhhcccccccccccchhhHHHHHHH
Q 000291 223 SRDVDARFGVSQDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQEL 302 (1714)
Q Consensus 223 ~~~~~~~~~~~k~~~~~ik~k~gr~R~~l~GKRvdfSaRsVI~pdP~l~~~evgvP~~~A~~Lt~pe~vt~~Ni~~l~~l 302 (1714)
.....+| ..+++.+.+|||+||||+|||||||||||||||+|||+|++||||||.+||.+||+| |||++|
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 235677899999999999999999999999999999999999999999999999887 466655
Q ss_pred HHccCccccCCCCceEEeccCCCCccccCCcceeeheeeccceEEEeCCCccccccccceeeEecCCCeEEecccccCCC
Q 000291 303 VDNKLCLTYSDGSSSYSLREGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPL 382 (1714)
Q Consensus 303 v~~g~~~~~~~~~~~~~l~~~~~~~~~l~~g~iV~Rhl~dgd~VL~NRqPsLHr~Sima~~~~v~~~~t~rln~~vC~py 382 (1714)
+.+|....++ .++..++... ...+.|+|||+|||+|||||||||||+|||||+|++++++||||||+||+||
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 4456432211 1122222110 1235699999999999999999999999999999999999999999999999
Q ss_pred CCccccccccccCCCCHHHHHHHHHhcccccccccCCCCCceEeechhhHhHHHhhh
Q 000291 383 SADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF 439 (1714)
Q Consensus 383 NADFDGDeMnlHvPQS~eAraEa~~Lm~~~~nilsp~~G~Piigl~QD~llg~~llt 439 (1714)
||||||||||||||||++|||||++||++.+||+||++|+|+++++||+|+|+|+||
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 999999999999999999999999999999999999999999999999999999997
No 15
>CHL00018 rpoC1 RNA polymerase beta' subunit
Probab=100.00 E-value=4.5e-83 Score=784.74 Aligned_cols=282 Identities=26% Similarity=0.316 Sum_probs=244.1
Q ss_pred CCCCcEEEeeccCCCCCCCCCcccCCCccccchhHHHHHHHHHHHHHHHHhhh-c--CCCCccchhhhhhHHHHHHHHHH
Q 000291 138 FPQDGYILEYLPVPPNCLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSSR-S--GTPNFESQEVESNDLQLAVGQYL 214 (1714)
Q Consensus 138 ~~pe~~il~~lpVPP~~~Rp~~~~~g~~~~~~Dlt~~~l~~Il~~n~~lk~~~-~--g~p~~~~~~~~~~~LQ~~v~~~~ 214 (1714)
.+|+||||++|||||+++||++.+++..+.++|+|. +|++||.+|++|+... . ++|..+ ...++++||.+|+.|+
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 579999999999999999999999887888999998 8999999999998753 2 556544 3567899999999999
Q ss_pred hhcCCCcCCCCCCCCCCCCCCCCchhhhhHhhhhhcccccCCCCccceeEeCCCCCccccccchhhcccccccccccchh
Q 000291 215 EVRGTAKSSRDVDARFGVSQDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVH 294 (1714)
Q Consensus 215 ~~~~~~~~~~~~~~~~~~~k~~~~~ik~k~gr~R~~l~GKRvdfSaRsVI~pdP~l~~~evgvP~~~A~~Lt~pe~vt~~ 294 (1714)
|+....++..+..+ ...+++.+.+|||+||||+|||||||||||||||+|||+|+++|||||.+||++||+|+.
T Consensus 337 dn~~~g~~~~~~~~--r~~ksls~~LkGK~GrFR~NLlGKRVDySgRSVIvpdP~L~l~e~GlP~~mA~eL~~P~~---- 410 (663)
T CHL00018 337 DNGIRGQPMRDGHN--KPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQPFV---- 410 (663)
T ss_pred cCCCCCCccccCCC--CCCCCccccccCcCccccccccccccccCCCceecCCCcccccccCChHHHHHHcCcHHH----
Confidence 97544333332222 234677889999999999999999999999999999999999999999999999999973
Q ss_pred hHHHHHHHHHccCccccCCCCceEEeccCCCCccccCCcceeeheeeccceEEEeCCCccccccccceeeEecCCCeEEe
Q 000291 295 NINYLQELVDNKLCLTYSDGSSSYSLREGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKI 374 (1714)
Q Consensus 295 Ni~~l~~lv~~g~~~~~~~~~~~~~l~~~~~~~~~l~~g~iV~Rhl~dgd~VL~NRqPsLHr~Sima~~~~v~~~~t~rl 374 (1714)
+++|+.+++...++ .+++.++. ...++++|+|||+|||+|||||||||||||||||+|++++++||||
T Consensus 411 ----i~~Li~~~~~~~~~--~Ak~~i~~------~~~~~~~Vlr~v~~gd~VLlNRqPTLHR~sIqAf~~~L~~gktIrL 478 (663)
T CHL00018 411 ----IRGLIRQHLASNIR--AAKSKIRE------KEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICL 478 (663)
T ss_pred ----HHHHHhcCccccHH--HHHHHHHh------cCCcccEeeeehhcCceeeecCCCcccccccceeeEEecCCCeEEe
Confidence 56788888753322 11222221 1235788999999999999999999999999999999999999999
Q ss_pred cccccCCCCCccccccccccCCCCHHHHHHHHHhcccccccccCCCCCceEeechhhHhHHHhhh
Q 000291 375 NPLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF 439 (1714)
Q Consensus 375 n~~vC~pyNADFDGDeMnlHvPQS~eAraEa~~Lm~~~~nilsp~~G~Piigl~QD~llg~~llt 439 (1714)
||+||+||||||||||||||||||++|||||+.||++.+||+||++|+|+++++||+|+|+|+||
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=9.3e-81 Score=718.24 Aligned_cols=290 Identities=35% Similarity=0.500 Sum_probs=252.1
Q ss_pred CcEEEeeccCCCCCCCCCcccCCCccccchhHHHHHHHHHHHHHHHHhhh-cCCCCccchhhhhhHHHHHHHHHHhhcCC
Q 000291 141 DGYILEYLPVPPNCLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSSR-SGTPNFESQEVESNDLQLAVGQYLEVRGT 219 (1714)
Q Consensus 141 e~~il~~lpVPP~~~Rp~~~~~g~~~~~~Dlt~~~l~~Il~~n~~lk~~~-~g~p~~~~~~~~~~~LQ~~v~~~~~~~~~ 219 (1714)
+||||++|||||+|+||++..++..+.++|+|. +|++||+.|+.|+... .+++... ...+|..||.+|+.|+|+.+.
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 589999999999999999888776677899998 7999999999998764 4555443 345689999999999998654
Q ss_pred CcCCCCCCCCCCCCCCCCchhhhhHhhhhhcccccCCCCccceeEeCCCCCccccccchhhcccccccccccchhhHHHH
Q 000291 220 AKSSRDVDARFGVSQDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYL 299 (1714)
Q Consensus 220 ~~~~~~~~~~~~~~k~~~~~ik~k~gr~R~~l~GKRvdfSaRsVI~pdP~l~~~evgvP~~~A~~Lt~pe~vt~~Ni~~l 299 (1714)
++..... ....+.+.+++++|.|+||+|||||||||||||||+|||+|.++|||||..||++|||||.||.||+++|
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---GRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKL 155 (295)
T ss_pred cccccCC---CCCcccccccccCcCCccccccccccccccCceEEeCCCCcceeEeeCCHHHHHhCCcCEEEhHHHHHHH
Confidence 3322111 1123567789999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHccCc--cccCCCCceEEeccCCC--CccccCCcceeeheeeccceEEEeCCCccccccccceeeEecCCCeEEec
Q 000291 300 QELVDNKLC--LTYSDGSSSYSLREGSK--GHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKIN 375 (1714)
Q Consensus 300 ~~lv~~g~~--~~~~~~~~~~~l~~~~~--~~~~l~~g~iV~Rhl~dgd~VL~NRqPsLHr~Sima~~~~v~~~~t~rln 375 (1714)
++||.||+. ..+.+ +..+.|+..++ ....|++|++|+|||+|||+|||||||||||+|||||+|+|++++|||||
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 22344444322 24678999999999999999999999999999999999999999999999
Q ss_pred ccccCCCCCccccccccccCCCCHHHHHHHHHhcccccccccCCCCCceEeechhhHhHHH
Q 000291 376 PLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLK 436 (1714)
Q Consensus 376 ~~vC~pyNADFDGDeMnlHvPQS~eAraEa~~Lm~~~~nilsp~~G~Piigl~QD~llg~~ 436 (1714)
|+||+||||||||||||+|+|||++|||||++||.+.+||+||++|+|+++++||+|+|+|
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
>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=4.3e-56 Score=476.68 Aligned_cols=159 Identities=44% Similarity=0.659 Sum_probs=134.0
Q ss_pred ccCCCCccceeEeCCCCCccccccchhhcccccccccccchhhHHHHHHHHHccCccc------cCCCCceEEeccCC-C
Q 000291 253 RKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDNKLCLT------YSDGSSSYSLREGS-K 325 (1714)
Q Consensus 253 GKRvdfSaRsVI~pdP~l~~~evgvP~~~A~~Lt~pe~vt~~Ni~~l~~lv~~g~~~~------~~~~~~~~~l~~~~-~ 325 (1714)
||||||||||||+|||+|+++|||||.+||++||+||+||.+|+++|+++|.||+... +...+.++.|+... +
T Consensus 1 GKRVnfSaRSVItpDP~L~~~EvGiP~~iA~~Lt~Pe~Vt~~N~~~l~~~v~ng~~~~pga~~i~~~~~~~~~l~~~~~~ 80 (166)
T PF00623_consen 1 GKRVNFSARSVITPDPNLKIDEVGIPIEIAKKLTFPERVTPFNIEKLRKLVINGPDKYPGANYIKRSNGNKISLRYKKFK 80 (166)
T ss_dssp CEEESSEEEEEEEEETTSCTTEEEEEHHHHHHCECCHHHHTTTHHHHHHHHHHTTTSSSSEEEEESTTCHCCCTTSSSSC
T ss_pred CCCcccCCCcEEECCCCCccceecccHHHHhhCCCcEEEHHHHHHHHHHHHhcCcccchhhhhhhcccCcceeeeecccc
Confidence 8999999999999999999999999999999999999999999999999999998521 11222233333322 1
Q ss_pred CccccCCcceeeheeeccceEEEeCCCccccccccceeeEecCCCeEEecccccCCCCCccccccccccCCCCHHHHHHH
Q 000291 326 GHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQSLAAKAEV 405 (1714)
Q Consensus 326 ~~~~l~~g~iV~Rhl~dgd~VL~NRqPsLHr~Sima~~~~v~~~~t~rln~~vC~pyNADFDGDeMnlHvPQS~eAraEa 405 (1714)
....|++|++|+|||.|||+|||||||||||+|||||++++++++||||||++|+||||||||||||||+|||++|+|||
T Consensus 81 ~~~~l~~~~~v~r~l~~gd~vl~nRqPtLh~~s~~a~~~~~~~~~t~~~~~~~c~~~NADFDGDem~i~~p~~~~a~~E~ 160 (166)
T PF00623_consen 81 ISKKLRIGDIVERHLCDGDIVLLNRQPTLHRMSIMAHKVRVLPGKTIRINPLVCSPFNADFDGDEMNIHLPQSYEARAEA 160 (166)
T ss_dssp CCHHHHTT-EEEEEHTTT-EEEEEESS-SSGGGEEEEEEEEESSSSEEEEGGGHHHHT--TSS-EEEEE--SSHHHHHHH
T ss_pred ccceecchhhHHHhhhcCceeEEeccchhccceeeeeeeeeecccEEEeeccchhhhhccCCcceEEEEecCCHHHHHHH
Confidence 23467889999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhccc
Q 000291 406 LELFSV 411 (1714)
Q Consensus 406 ~~Lm~~ 411 (1714)
++||+|
T Consensus 161 ~~L~~~ 166 (166)
T PF00623_consen 161 KELMNV 166 (166)
T ss_dssp HHHCBT
T ss_pred HHHhcC
Confidence 999985
No 18
>TIGR02389 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit A''. This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Probab=100.00 E-value=8.4e-54 Score=506.13 Aligned_cols=334 Identities=19% Similarity=0.219 Sum_probs=276.3
Q ss_pred hhHHHHHHHhceEEEeccccc-cccCCceeEEEeccccccccCcCCCCceeEEeccccCChhHHHHhhcCCC-------C
Q 000291 716 LFKNLMAVLRDVVICYDGTVR-NVCSNSIIQFDYAVNARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDSSP-------S 787 (1714)
Q Consensus 716 LqRrLvk~ledl~v~YD~Tvr-~~~~~~IiQf~yg~dg~~~~~lv~~GepVG~laaqsigepatq~~L~t~~-------~ 787 (1714)
|..+|.+.+++-...|..|.. .. ..++..+.-.| .+++++|||+||++||||||||+|||||+||| +
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 456777777777777766555 32 44566666555 57899999999999999999999999999998 9
Q ss_pred CCCchHHHHHHHHhhccCCCCCCCceEEEEcCCCCCCCccccHHHHHHHHhhhccccHhhhhheeEEEecCCccccCCCc
Q 000291 788 SNNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIISDDEG 867 (1714)
Q Consensus 788 ~~~g~~rlkEil~~~~~~k~~~~d~~~~l~L~~~~~~~~~~~e~~a~~V~~~le~vtl~dv~~~i~I~y~~~~~~~~~~~ 867 (1714)
+|+|+||||||++++++ +++|.|++||.+.+.. ++++|++|+.+||+++|+||+..+.+.|.+
T Consensus 77 VTlGVPRlkEIINa~k~----i~TP~~ti~L~~~~~~----~~~~a~~v~~~iE~t~l~dv~~~~~~~~~~--------- 139 (367)
T TIGR02389 77 VTLGLPRLIEIVDARKT----PSTPSMTIYLEDEYEK----DREKAEEVAKKIEATKLEDVAKDISIDLAD--------- 139 (367)
T ss_pred ccccchhHHHHhhcccC----CCCCeEEEEecCcchh----hHHHHHHHHHHhhheeHHHHHhhhheeccC---------
Confidence 99999999999999886 5566999999977654 788999999999999999999999988753
Q ss_pred eEEEEEecHHHHHHhcCChhhhHHHHHHhhhhhh-h---c---------chhhHHHHHhhccccccccccc--ccccccc
Q 000291 868 LVGHIHLNKILLEDLRISMHDILPKCQETLKSFC-K---K---------KKMKKVVQFFKNTSLSISECCS--FQQSCAD 932 (1714)
Q Consensus 868 wv~~i~Ld~e~L~~~~lt~~~I~~k~~~~~~~~~-~---~---------~~~~~i~~~~~~~~~~~~~~gi--~~~~~~~ 932 (1714)
|+++|+||++.|++++|++++|.+++.+...... . + .......+.+++.+..+.++|+ |.++.++
T Consensus 140 ~~l~i~ld~~~l~~~~i~~~~i~~~i~~~~~~~~~~~~~~~~~i~i~~~~~~~~~l~~l~~~l~~~~v~Gi~gI~r~~i~ 219 (367)
T TIGR02389 140 MTVIIELDEEQLKERGITVDDVEKAIKKAKLGKVIEIDMDGNTITIKPPKPSLKELRKLKEKIKNLHIKGIKGIKRVVIR 219 (367)
T ss_pred cEEEEEECHHHHHhcCCCHHHHHHHHHHhcccccceeecCCCEEEEEecCchHHHHHHHHHHhhhceEeCCCCceEEEEE
Confidence 3799999999999999999999999887542210 0 0 0001123444445556667888 6777776
Q ss_pred cCCCcceEEEEEcccC-----CcccccceecccccchHHHHHHhhhhhHHHH----HHHHHHHHHhhcccccceeeeecc
Q 000291 933 KRSNMPCLMFVLRGAS-----DSYLDKLSGVLANMIYPVLLETIIKENWWVR----QRLSASVTMVAKGVLKEHLILLAN 1003 (1714)
Q Consensus 933 ~~~~~~~l~~~~~~~~-----~~~~vd~~~~~~n~I~~i~r~~IIkgi~w~r----~~l~~~~~~~~~~V~~rHl~LlAd 1003 (1714)
+++++++| .++|++ ..+++|..++++|+|.+++. +.||+..| +.|.++++.+|..||+|||+||||
T Consensus 220 ~~~~~~~l--~teG~nl~~v~~~~~VD~~rt~sNdI~ei~~---~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~RHl~LiaD 294 (367)
T TIGR02389 220 KEGDEYVI--YTEGSNLKEVLKLEGVDKTRTTTNDIHEIAE---VLGIEAARNAIIEEIKRTLEEQGLDVDIRHLMLVAD 294 (367)
T ss_pred CCCCeEEE--EEeccCHHHHHcCCCCccccCccCCHHHHHH---hcCHHHHHHHHHHHHHHHHHHcCCeecHHHHHHHHH
Confidence 65566666 788887 67899999999999999982 33666655 445588888889999999999999
Q ss_pred ceeeeceEeeeccccccccccCcccccccccccccCcHHHHHHHHhhcCCCCCCchhhhhhcCCcccccccceEEEEec
Q 000291 1004 SMTCAGDLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGSRFDLLWQ 1082 (1714)
Q Consensus 1004 ~MT~~G~~~~~~r~G~~~~~~s~l~~a~Fe~~t~~~~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~~~~l~~~ 1082 (1714)
+||++|++++|||+||++.+.|||++|+||+| .++|++||.+|+.|.|+||+||||+|+++|+|||+ |||+++
T Consensus 295 ~MT~~G~~~~i~R~Gi~~~~~S~l~~aSFE~t-----~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~-~~l~~~ 367 (367)
T TIGR02389 295 LMTWDGEVRQIGRHGISGEKASVLARAAFEVT-----VKHLLDAAIRGEVDELAGVIENIIVGQPIPLGTGD-VDLVMD 367 (367)
T ss_pred HhcCCceEEeccccccccCCCCHHHhcChHhH-----HHHHHHHhhcCCCCcCCChHHHhhcCCCcCCcCCe-EEEeeC
Confidence 99999999999999999999999999999997 89999999999999999999999999999999999 999974
No 19
>cd06528 RNAP_A'' A'' subunit of Archaeal RNA Polymerase (RNAP). Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.
Probab=100.00 E-value=5.5e-53 Score=500.05 Aligned_cols=329 Identities=19% Similarity=0.216 Sum_probs=268.6
Q ss_pred HHHhceEEEeccccccccCCceeEEEeccccccccCcCCCCceeEEeccccCChhHHHHhhcCCC-------CCCCchHH
Q 000291 722 AVLRDVVICYDGTVRNVCSNSIIQFDYAVNARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDSSP-------SSNNSWEL 794 (1714)
Q Consensus 722 k~ledl~v~YD~Tvr~~~~~~IiQf~yg~dg~~~~~lv~~GepVG~laaqsigepatq~~L~t~~-------~~~~g~~r 794 (1714)
+.++.+...|..|.... ..++..+.-.+ .+++++|||+||++||||||||+|||||+||| |+|+|+||
T Consensus 5 ~~~~~~~~~~~l~~~~~--~~~~~~~~~~~---~~~~~~~Ge~vG~iaAQSiGEP~TQMTLnTFH~AGVas~nVTlGVPR 79 (363)
T cd06528 5 EKLEEVLKEHGLTLSEA--EEIIKEVLREY---LRSLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPR 79 (363)
T ss_pred HHHHHHHHHcCCCHHHH--HHHHHHHHHHH---HHHhhccCccccceeeeecCccceecccccccccccccccCcccccc
Confidence 33444444444444322 33444444334 46789999999999999999999999999998 88999999
Q ss_pred HHHHHHhhccCCCCCCCceEEEEcCCCCCCCccccHHHHHHHHhhhccccHhhhhheeEEEecCCccccCCCceEEEEEe
Q 000291 795 MKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIISDDEGLVGHIHL 874 (1714)
Q Consensus 795 lkEil~~~~~~k~~~~d~~~~l~L~~~~~~~~~~~e~~a~~V~~~le~vtl~dv~~~i~I~y~~~~~~~~~~~wv~~i~L 874 (1714)
||||++++++ +++|.|++||.+.+.. ++++|++|+.+||+++|+|++..+.|.|. .|+++|+|
T Consensus 80 lkEIIna~K~----i~TP~mti~L~~~~~~----~~~~a~~v~~~iE~t~l~di~~~~~i~~~---------~~~l~i~l 142 (363)
T cd06528 80 LIEIVDARKE----PSTPTMTIYLEEEYKY----DREKAEEVARKIEETTLENLAEDISIDLF---------NMRITIEL 142 (363)
T ss_pred HHHHhhcccC----CCCceEEEEecCcchh----hHHHHHHHHHhhceeEHHHhhhheEEecc---------CcEEEEEE
Confidence 9999999886 4567999999976544 77899999999999999999999999764 35899999
Q ss_pred cHHHHHHhcCChhhhHHHHHHhhhhhh---h---------cchhhHHHHHhhccccccccccc--ccccccccCCCcceE
Q 000291 875 NKILLEDLRISMHDILPKCQETLKSFC---K---------KKKMKKVVQFFKNTSLSISECCS--FQQSCADKRSNMPCL 940 (1714)
Q Consensus 875 d~e~L~~~~lt~~~I~~k~~~~~~~~~---~---------~~~~~~i~~~~~~~~~~~~~~gi--~~~~~~~~~~~~~~l 940 (1714)
|+++|++++|++++|++++.+.++... . ........+.+++.+..+.++|+ +.++.++++.++++|
T Consensus 143 d~~~l~~~~l~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~~~v~Gi~gI~r~~i~~~~~~~~l 222 (363)
T cd06528 143 DEEMLEDRGITVDDVLKAIEKLKKGKVGEEGDVTLIVLKAEEPSIKELRKLAEKILNTKIKGIKGIKRVIVRKEEDEYVI 222 (363)
T ss_pred CHHHHHHcCCCHHHHHHHHHHhcCCcccccCCccEEEEcCCcchHHHHHHHHHhhcccEEeCCCCceEEEEecCCceEEE
Confidence 999999999999999999887653211 0 00111234555555666778888 777777766555665
Q ss_pred EEEEcccC-----CcccccceecccccchHHHHHHhhhhhHHHH----HHHHHHHHHhhcccccceeeeeccceeeeceE
Q 000291 941 MFVLRGAS-----DSYLDKLSGVLANMIYPVLLETIIKENWWVR----QRLSASVTMVAKGVLKEHLILLANSMTCAGDL 1011 (1714)
Q Consensus 941 ~~~~~~~~-----~~~~vd~~~~~~n~I~~i~r~~IIkgi~w~r----~~l~~~~~~~~~~V~~rHl~LlAd~MT~~G~~ 1011 (1714)
.++|++ ..+++|..++++|+|.+++ + +.||+..| +.|..+++.+|.+||+|||+||||+||++|++
T Consensus 223 --~teG~nl~~v~~~~~Vd~~rt~sNdI~ei~-~--~lGIEAaR~~ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~G~~ 297 (363)
T cd06528 223 --YTEGSNLKAVLKVEGVDPTRTTTNNIHEIE-E--VLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEV 297 (363)
T ss_pred --EecCcCHHHHhcCCCCcccccccCCHHHHH-H--hCCHHHHHHHHHHHHHHHHHhcCCeecHHHHHHHHHHhccCCce
Confidence 788887 6789999999999999998 2 23666655 44558888888999999999999999999999
Q ss_pred eeeccccccccccCcccccccccccccCcHHHHHHHHhhcCCCCCCchhhhhhcCCcccccccceEEEEecc
Q 000291 1012 VGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGSRFDLLWQT 1083 (1714)
Q Consensus 1012 ~~~~r~G~~~~~~s~l~~a~Fe~~t~~~~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~~~~l~~~~ 1083 (1714)
+++||+|+.+.+.|+|++|+||+| .++|++||.+|+.|+|+||+|||||||++|+|||+ |||++|.
T Consensus 298 ~~i~R~gi~~~~~S~L~~aSFE~t-----~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~-~~l~~d~ 363 (363)
T cd06528 298 RQIGRHGIAGEKPSVLARAAFEVT-----VKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTGD-VELTMDP 363 (363)
T ss_pred ecccchhhcCCCCChhhhCchhhH-----HHHHHHHHhcCCCCcCCCcHHHeeeCCCCCCcCCe-eEEEecC
Confidence 999999999999999999999997 89999999999999999999999999999999999 9999863
No 20
>PRK04309 DNA-directed RNA polymerase subunit A''; Validated
Probab=100.00 E-value=9.6e-53 Score=501.07 Aligned_cols=337 Identities=19% Similarity=0.198 Sum_probs=283.4
Q ss_pred hhHHHHHHHhceEEEeccccccccCCceeEEEeccccccccCcCCCCceeEEeccccCChhHHHHhhcCCC-------CC
Q 000291 716 LFKNLMAVLRDVVICYDGTVRNVCSNSIIQFDYAVNARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDSSP-------SS 788 (1714)
Q Consensus 716 LqRrLvk~ledl~v~YD~Tvr~~~~~~IiQf~yg~dg~~~~~lv~~GepVG~laaqsigepatq~~L~t~~-------~~ 788 (1714)
|.++|.+.|++-...|..|.... ..++..++-.| .+++++|||+||++||||||||+|||||+||| ++
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 78888888888777777776654 45666666666 57789999999999999999999999999998 89
Q ss_pred CCchHHHHHHHHhhccCCCCCCCceEEEEcCCCCCCCccccHHHHHHHHhhhccccHhhhhheeEEEecCCccccCCCce
Q 000291 789 NNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIISDDEGL 868 (1714)
Q Consensus 789 ~~g~~rlkEil~~~~~~k~~~~d~~~~l~L~~~~~~~~~~~e~~a~~V~~~le~vtl~dv~~~i~I~y~~~~~~~~~~~w 868 (1714)
|+|+||||||++++++ +++|.|++||.++++. ++++|+.|+.+||+++|++|+..+.+.|...
T Consensus 93 TlGvPRlkEIina~K~----~~TP~~tv~L~~~~~~----d~~~a~~v~~~iE~t~L~~v~~~i~~~~~~~--------- 155 (383)
T PRK04309 93 TLGLPRLIEIVDARKE----PSTPMMTIYLKDEYAY----DREKAEEVARKIEATTLENLAKDISVDLANM--------- 155 (383)
T ss_pred ccCchhHHHHHhcccC----CCCCeEEEEecCcccc----cHHHHHHHHhheeeeEHhhhhhheEeccCCc---------
Confidence 9999999999999875 6677999999987654 7899999999999999999999999876543
Q ss_pred EEEEEecHHHHHHhcCChhhhHHHHHHhhhhh----------hhcchhhHHHHHhhccccccccccc--ccccccccCCC
Q 000291 869 VGHIHLNKILLEDLRISMHDILPKCQETLKSF----------CKKKKMKKVVQFFKNTSLSISECCS--FQQSCADKRSN 936 (1714)
Q Consensus 869 v~~i~Ld~e~L~~~~lt~~~I~~k~~~~~~~~----------~~~~~~~~i~~~~~~~~~~~~~~gi--~~~~~~~~~~~ 936 (1714)
+++|+||+++|.+++|++++|++++.+..... ............++..+..+.++|+ +.+++++++++
T Consensus 156 ~l~i~ld~~~i~~~~l~~~~I~~~i~~~~~~~~~~~~~~i~i~~~~~~~~~l~~l~~~l~~~~vkGi~gI~r~~i~~~~~ 235 (383)
T PRK04309 156 TIIIELDEEMLEDRGLTVDDVKEAIEKKKGGEVEIEGNTLIISPKEPSYRELRKLAEKIRNIKIKGIKGIKRVIIRKEGD 235 (383)
T ss_pred EEEEEECHHHHHHcCCCHHHHHHHHHHhcCcceeccCCeEEEEecCchHHHHHHHHHHhcccEEECCCCceEEEEecCCC
Confidence 79999999999999999999999988754211 0000001123444555556677888 67777776656
Q ss_pred cceEEEEEcccC-----CcccccceecccccchHHHHHHhhhhhHHHH----HHHHHHHHHhhcccccceeeeeccceee
Q 000291 937 MPCLMFVLRGAS-----DSYLDKLSGVLANMIYPVLLETIIKENWWVR----QRLSASVTMVAKGVLKEHLILLANSMTC 1007 (1714)
Q Consensus 937 ~~~l~~~~~~~~-----~~~~vd~~~~~~n~I~~i~r~~IIkgi~w~r----~~l~~~~~~~~~~V~~rHl~LlAd~MT~ 1007 (1714)
+++| .++|.+ ..+++|..++++|+|.+++ + +.||+..| +.|..+++.+|.+||+|||+||||+||+
T Consensus 236 ~~~l--~teG~nl~~v~~~~~VD~~rt~sNdI~ei~-~--vlGIEAAR~~ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~ 310 (383)
T PRK04309 236 EYVI--YTEGSNLKEVLKVEGVDATRTTTNNIHEIE-E--VLGIEAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTW 310 (383)
T ss_pred eEEE--EEcccCHHHHhcCCCEeeccccCCCHHHHH-H--HcCHHHHHHHHHHHHHHHHHHcCCeecHHHHHHHHHHhcc
Confidence 6666 688887 6789999999999999998 2 33666666 4556888888899999999999999999
Q ss_pred eceEeeeccccccccccCcccccccccccccCcHHHHHHHHhhcCCCCCCchhhhhhcCCcccccccceEEEEeccCC
Q 000291 1008 AGDLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGSRFDLLWQTEN 1085 (1714)
Q Consensus 1008 ~G~~~~~~r~G~~~~~~s~l~~a~Fe~~t~~~~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~~~~l~~~~~~ 1085 (1714)
+|++++|||+||.+.+.|||++|+||+| .++|++||.+|++|+|.||+||||||+++|+|||+ |+|+++.++
T Consensus 311 ~G~~~~i~R~Gi~~~~~S~l~~aSFE~T-----~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~-~~l~~~~~~ 382 (383)
T PRK04309 311 DGEVRQIGRHGVSGEKASVLARAAFEVT-----VKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTGD-VELTMDPPL 382 (383)
T ss_pred CceEEeeechhhcCCCCCHHHhCchhhH-----HHHHHHHHhcCCCCCCCCcHHHhhcCCCcCCCCce-EEEEcCCCC
Confidence 9999999999999999999999999997 89999999999999999999999999999999999 999998764
No 21
>PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Probab=100.00 E-value=7.1e-53 Score=506.35 Aligned_cols=338 Identities=16% Similarity=0.176 Sum_probs=276.1
Q ss_pred hhHHHHHHHhceEEEeccccccccCCceeEEEeccccccccCcCCCCceeEEeccccCChhHHHHhhcCCC-------CC
Q 000291 716 LFKNLMAVLRDVVICYDGTVRNVCSNSIIQFDYAVNARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDSSP-------SS 788 (1714)
Q Consensus 716 LqRrLvk~ledl~v~YD~Tvr~~~~~~IiQf~yg~dg~~~~~lv~~GepVG~laaqsigepatq~~L~t~~-------~~ 788 (1714)
|..+|.+.|+.....|..|.... ..|+..+.-.| .+++++|||+||++||||||||+|||||+||| ++
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 78888888888777777766654 56677676666 67889999999999999999999999999998 99
Q ss_pred CCchHHHHHHHHhhccCCCCCCCceEEEEcCCCCCCCccccHHHHHHHHhhhccccHhhhhheeEEEecCCccccCCCce
Q 000291 789 NNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIISDDEGL 868 (1714)
Q Consensus 789 ~~g~~rlkEil~~~~~~k~~~~d~~~~l~L~~~~~~~~~~~e~~a~~V~~~le~vtl~dv~~~i~I~y~~~~~~~~~~~w 868 (1714)
|+|+|||+||++++++ +++|.|++||.+.+.. ++++|++|+.+||+++|+||+..+ .+| ..|
T Consensus 216 TlGVPRLkEIINa~K~----isTP~mtiyL~~~~~~----d~e~A~~V~~~IE~ttL~dv~~~~-~d~---------~~~ 277 (509)
T PRK14897 216 TLGLPRLIEIVDARKK----PSTPTMTIYLKKDYRE----DEEKVREVAKKIENTTLIDVADII-TDI---------AEM 277 (509)
T ss_pred ccCcchhHHHhhcccC----CCCceEEEEecCcccc----cHHHHHHHHhhheeeEHHHHHHHH-HHh---------ccc
Confidence 9999999999999886 5567999999877654 788999999999999999999633 223 234
Q ss_pred EEEEEecHHHHHHhcCChhhhHHHHHHhh-hhh-------h--hcchhhHHHHHhhccccccccccc--ccccccccCCC
Q 000291 869 VGHIHLNKILLEDLRISMHDILPKCQETL-KSF-------C--KKKKMKKVVQFFKNTSLSISECCS--FQQSCADKRSN 936 (1714)
Q Consensus 869 v~~i~Ld~e~L~~~~lt~~~I~~k~~~~~-~~~-------~--~~~~~~~i~~~~~~~~~~~~~~gi--~~~~~~~~~~~ 936 (1714)
.++|+||+++|.+++|++++|++++.+.. ... + ...........+.+.+..+.++|+ |.+++++++.+
T Consensus 278 ~i~i~Ld~~~l~~~~l~~~~I~~~I~~~~~~~~~~~~~~I~i~~~~~~~~~L~~l~~~l~~i~I~GipgI~r~~i~~~~~ 357 (509)
T PRK14897 278 SVVVELDEEKMKERLIEYDDILAAISKLTFKTVEIDDGIIRLKPQQPSFKKLYLLAEKVKSLTIKGIKGIKRAIARKEND 357 (509)
T ss_pred eEEEEECHHHHHHcCCCHHHHHHHHHhccceEEecCCCEEEEEeCchHHHHHHHHHHHhhccEEeCCCCccEEEEecCCC
Confidence 79999999999999999999999987621 000 0 000001113333444455567888 67777776543
Q ss_pred cceEEEEEcccC-----CcccccceecccccchHHHHHHhhhhhHHHH----HHHHHHHHHhhcccccceeeeeccceee
Q 000291 937 MPCLMFVLRGAS-----DSYLDKLSGVLANMIYPVLLETIIKENWWVR----QRLSASVTMVAKGVLKEHLILLANSMTC 1007 (1714)
Q Consensus 937 ~~~l~~~~~~~~-----~~~~vd~~~~~~n~I~~i~r~~IIkgi~w~r----~~l~~~~~~~~~~V~~rHl~LlAd~MT~ 1007 (1714)
.....+.++|++ ..++||..+|++|+|.+++. +.||+..| +.|..+++.+|.+||+|||+||||+||+
T Consensus 358 ~~~~~L~TeG~NL~~vl~~~~VD~~rt~SNdI~eI~~---vlGIEAAR~~Ii~Ei~~V~~~~Gi~Vd~RHL~LIAD~MT~ 434 (509)
T PRK14897 358 ERRWVIYTQGSNLKDVLEIDEVDPTRTYTNDIIEIAT---VLGIEAARNAIIHEAKRTLQEQGLNVDIRHIMLVADMMTF 434 (509)
T ss_pred CceeEEEeeccCHHHHhcCCCcccccCccCCHHHHHH---hcCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHhCc
Confidence 322234899987 78999999999999999982 33566555 3455888888899999999999999999
Q ss_pred eceEeeeccccccccccCcccccccccccccCcHHHHHHHHhhcCCCCCCchhhhhhcCCcccccccceEEEEeccCC
Q 000291 1008 AGDLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGSRFDLLWQTEN 1085 (1714)
Q Consensus 1008 ~G~~~~~~r~G~~~~~~s~l~~a~Fe~~t~~~~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~~~~l~~~~~~ 1085 (1714)
.|++.+||||||+..+.|||++|+||+| +++|++||.+|++|.|.||+||||+|+++|+|||+ |+|+++.++
T Consensus 435 ~G~v~~i~R~Gi~~~~~SpL~rASFE~T-----~~~L~~AA~~Ge~D~L~GvsenII~G~~ipvGTG~-fdL~~~~~~ 506 (509)
T PRK14897 435 DGSVKAIGRHGISGEKSSVLARAAFEIT-----GKHLLRAGILGEVDKLAGVAENIIVGQPITLGTGA-VSLVYKGRK 506 (509)
T ss_pred CCcccccccccccccCCCHHHhcchHhH-----HHHHHHHhhcCCCCcCCChHHhhhcCCccCCcCce-EEEEecCCC
Confidence 9999999999999999999999999998 89999999999999999999999999999999999 999998754
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=2.4e-51 Score=492.04 Aligned_cols=309 Identities=21% Similarity=0.219 Sum_probs=258.6
Q ss_pred ccCcCCCCceeEEeccccCChhHHHHhhcCCC-------CCCCchHHHHHHHHhhccCCCCCCCceEEEEcCCCCCCCcc
Q 000291 755 SHSLFPAGEPVGVLAATAMSNPAYKAVLDSSP-------SSNNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKY 827 (1714)
Q Consensus 755 ~~~lv~~GepVG~laaqsigepatq~~L~t~~-------~~~~g~~rlkEil~~~~~~k~~~~d~~~~l~L~~~~~~~~~ 827 (1714)
.+++++|||+||++||||||||+|||||+||| ++|+|+||||||++++++ +++|.|++||.+.+..
T Consensus 20 ~~~~~~~ge~vg~~aaQSiGEP~TQmTLnTFH~AGVas~NVTlGVPRLkEIInasK~----ikTP~~tv~L~~~~~~--- 92 (410)
T cd02584 20 NRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKN----IKTPSLTVYLEPGFAK--- 92 (410)
T ss_pred HHhhcCCCCCcchhhhhhcCCchhcccccccccccccccccccCccchHHHhhcccC----CCCCeEEEEecCcccc---
Confidence 46788999999999999999999999999998 899999999999999886 5567999999987544
Q ss_pred ccHHHHHHHHhhhccccHhhhhheeEEEecCCcccc-----------------------CCCceEEEEEecHHHHHHhcC
Q 000291 828 CQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIIS-----------------------DDEGLVGHIHLNKILLEDLRI 884 (1714)
Q Consensus 828 ~~e~~a~~V~~~le~vtl~dv~~~i~I~y~~~~~~~-----------------------~~~~wv~~i~Ld~e~L~~~~l 884 (1714)
++++|++|+.+||+++|+||+..+.|.|+|+...+ ..+||+++++||+++|.+++|
T Consensus 93 -d~~~A~~v~~~IE~t~l~dv~~~~~i~ydp~~~~~~i~~d~~~i~~~~~~~d~~~~~~~~~~~~lrl~ld~~~~~~~~i 171 (410)
T cd02584 93 -DEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVESYFEFPDEDVEQDRLSPWLLRIELDRKKMTDKKL 171 (410)
T ss_pred -hHHHHHHHHhheeEeEHHHhhhheEEEecCcccceeecccHHHHHHhhccCcccccccccCCeeEEEEECHHHHHHcCC
Confidence 78999999999999999999999999999976521 138999999999999999999
Q ss_pred ChhhhHHHHHHhhhhh---------------h---h-cc---h-----hhHHHHHhhccccccccccc--ccccccccC-
Q 000291 885 SMHDILPKCQETLKSF---------------C---K-KK---K-----MKKVVQFFKNTSLSISECCS--FQQSCADKR- 934 (1714)
Q Consensus 885 t~~~I~~k~~~~~~~~---------------~---~-~~---~-----~~~i~~~~~~~~~~~~~~gi--~~~~~~~~~- 934 (1714)
++++|+.++.+.++.. + . .. . ..-+.+.+++.+....++|+ +.+++++++
T Consensus 172 ~~~~i~~~i~~~~~~~~~v~~~~~~~~~~~iri~~~~~~~~~~~~~~~~~~l~~~~~~~l~~i~l~Gi~~I~r~~i~~~~ 251 (410)
T cd02584 172 SMEQIAKKIKEEFKDDLNVIFSDDNAEKLVIRIRIINDDEEKEEDSEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREEN 251 (410)
T ss_pred CHHHHHHHHHHhcCCCeEEEEcCCCcceeEEEEEecCccccccccchhHHHHHHHHHhhCCCcEEeCCCCceEEEEEcCC
Confidence 9999999988643210 0 0 00 0 00123333455556677888 566665532
Q ss_pred -------------CCcceEEEEEcccC-----CcccccceecccccchHHHHHHhhhhhHHHH----HHHHHHHHHhhcc
Q 000291 935 -------------SNMPCLMFVLRGAS-----DSYLDKLSGVLANMIYPVLLETIIKENWWVR----QRLSASVTMVAKG 992 (1714)
Q Consensus 935 -------------~~~~~l~~~~~~~~-----~~~~vd~~~~~~n~I~~i~r~~IIkgi~w~r----~~l~~~~~~~~~~ 992 (1714)
.+.++| .++|++ ..++||..+|++|+|.+++. +.||+..| +.|..+++.+|.+
T Consensus 252 ~~~~~~~~g~~~~~~~~~l--~teG~nl~~v~~~~~Vd~~rt~sNdI~ei~~---~lGIEAaR~~ii~Ei~~v~~~~Gi~ 326 (410)
T cd02584 252 KKKVDIETGEFKKREEWVL--ETDGVNLREVLSHPGVDPTRTTSNDIVEIFE---VLGIEAARKALLKELRNVISFDGSY 326 (410)
T ss_pred ceEecCCCCcccCCcceEE--EecCcCHHHHhCCCCCccccCEeCCHHHHHH---hcCHHHHHHHHHHHHHHHHHhcCCc
Confidence 123444 788887 67899999999999999983 33666666 4455777788889
Q ss_pred cccceeeeeccceeeeceEeeeccccccccccCcccccccccccccCcHHHHHHHHhhcCCCCCCchhhhhhcCCccccc
Q 000291 993 VLKEHLILLANSMTCAGDLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVG 1072 (1714)
Q Consensus 993 V~~rHl~LlAd~MT~~G~~~~~~r~G~~~~~~s~l~~a~Fe~~t~~~~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~G 1072 (1714)
||+|||+||||+||++|++++|||+||++.+.|+|++|+||+| .++|++||.+|+.|+|+||+||||+|+++|+|
T Consensus 327 Vd~RHl~LiaD~MT~~G~~~~i~R~Gi~~~~~S~l~~aSFE~t-----~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~G 401 (410)
T cd02584 327 VNYRHLALLCDVMTQRGHLMAITRHGINRQDTGPLMRCSFEET-----VDILLEAAAFGETDDLKGVSENIMLGQLAPIG 401 (410)
T ss_pred cCHHHHHHHHHHHhhceEEeeEeeeeeeccCCChhhhccchhH-----HHHHHHHHhcCCCCcCCCchHheeecCccccc
Confidence 9999999999999999999999999999999999999999997 89999999999999999999999999999999
Q ss_pred ccceEEEEec
Q 000291 1073 TGSRFDLLWQ 1082 (1714)
Q Consensus 1073 TG~~~~l~~~ 1082 (1714)
||+ |||++|
T Consensus 402 TG~-f~l~~d 410 (410)
T cd02584 402 TGC-FDLLLD 410 (410)
T ss_pred cce-EEEEeC
Confidence 999 999986
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=2e-49 Score=470.96 Aligned_cols=311 Identities=36% Similarity=0.496 Sum_probs=234.7
Q ss_pred CceeEEeccccCChhHHHHhhcCCCCCC-CchHHHHHHHHhhccCCCCCCCceEEEEcC--CCCCCCccccHHHHHHHHh
Q 000291 762 GEPVGVLAATAMSNPAYKAVLDSSPSSN-NSWELMKEILLCRVSFNNDPIDRRVILYLN--DCGCGRKYCQERAAYMVKN 838 (1714)
Q Consensus 762 GepVG~laaqsigepatq~~L~t~~~~~-~g~~rlkEil~~~~~~k~~~~d~~~~l~L~--~~~~~~~~~~e~~a~~V~~ 838 (1714)
|||||+|||||||||||||||+|||... +++|||||||+++++.+ +++|.+++||. .|.|...|+.+++|++|++
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 8999999999999999999999999655 48999999999976544 44556666664 4777777777789999999
Q ss_pred hhccccHhhhhheeEEEecCCcccc----------------------------CCCceEEEEEecHHHHHHhcCC-hhhh
Q 000291 839 QLKRVSLKDAAVEFLIEYKKPEIIS----------------------------DDEGLVGHIHLNKILLEDLRIS-MHDI 889 (1714)
Q Consensus 839 ~le~vtl~dv~~~i~I~y~~~~~~~----------------------------~~~~wv~~i~Ld~e~L~~~~lt-~~~I 889 (1714)
+||+++|++++.+++|+|+|+...+ ..+||++||+||++.-....+. +...
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 2399999999999833222111 0000
Q ss_pred HHHHHHhhhhhhhcchhhHHHHHhhccccccccccc--ccccccc--c-------------CCCcceEEEEEcc------
Q 000291 890 LPKCQETLKSFCKKKKMKKVVQFFKNTSLSISECCS--FQQSCAD--K-------------RSNMPCLMFVLRG------ 946 (1714)
Q Consensus 890 ~~k~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~gi--~~~~~~~--~-------------~~~~~~l~~~~~~------ 946 (1714)
....... .. ......+...+...++.+.++|+ |+++.+. + ...+++|.+.++.
T Consensus 159 ~~~~~~~--~~--~~~~~~~~~~i~~~lL~~~lkG~~~I~kv~i~~~~~~~~~~~~~~~~~~~~E~vLe~~~~~~~~~t~ 234 (381)
T cd02737 159 VSKEVSK--SS--EELLDVLRDRIIPFLLETVIKGDERIKSVNILWEDSPSTSWVKSVGKSSRGELVLEVTVEESCKKTR 234 (381)
T ss_pred cCccccc--ch--hHHHHHHHHHHHHHHhheeecccCCeeEEEEEecCCCcccccccccccccceEEEEEEecccccccc
Confidence 0000000 00 00000123333333344567787 5555443 1 1235666554333
Q ss_pred -cC----------CcccccceecccccchHHHHHHhhhhhHHHH----HHHHHHHHHhhcccccceeeeeccceeeeceE
Q 000291 947 -AS----------DSYLDKLSGVLANMIYPVLLETIIKENWWVR----QRLSASVTMVAKGVLKEHLILLANSMTCAGDL 1011 (1714)
Q Consensus 947 -~~----------~~~~vd~~~~~~n~I~~i~r~~IIkgi~w~r----~~l~~~~~~~~~~V~~rHl~LlAd~MT~~G~~ 1011 (1714)
.+ -.+++|..++++|+|.+|. + +.||+..| ++|..+++.+|++||+|||+||||+||++|++
T Consensus 235 G~~~~~vl~~c~~~~~~ID~~rt~sNdI~ev~-~--~lGIEAAR~~ii~El~~v~~~~G~~Vd~rHL~LlAD~MT~~G~~ 311 (381)
T cd02737 235 GNAWNVVMDACIPVMDLIDWERSMPYSIQQIK-S--VLGIDAAFEQFVQRLESAVSMTGKSVLREHLLLVADSMTYSGEF 311 (381)
T ss_pred chhHHHHHHhhhcccccCcCCCcEECCHHHHH-H--HHhHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHhccCCce
Confidence 22 2689999999999999998 2 33777776 56778888899999999999999999999999
Q ss_pred eeeccccccccccCcccccccccccccCcHHHHHHHHhhcCCCCCCchhhhhhcCCcccccccceEEEEe
Q 000291 1012 VGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGSRFDLLW 1081 (1714)
Q Consensus 1012 ~~~~r~G~~~~~~s~l~~a~Fe~~t~~~~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~~~~l~~ 1081 (1714)
+||||+||+++++|+.+.+||.++||++|+++|++||.+|++|+|+||+++|+|||++|+|||++|||+|
T Consensus 312 ~~~nR~Gi~~~~~s~~~~spl~~asFE~t~~~l~~AA~~g~~D~l~gvs~~ii~G~~~~vGTG~~fdll~ 381 (381)
T cd02737 312 VGLNAKGYKAQRRSLKISAPFTEACFSSPIKCFLKAAKKGASDSLSGVLDACAWGKEAPVGTGSKFEILW 381 (381)
T ss_pred EEecchhhhhcccccccCCHHHHhhHHHHHHHHHHHHhccCCCCCCChHHheeeCCcCCCcCCcceeeeC
Confidence 9999999999998776777777777777799999999999999999999999999999999997799986
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=4.8e-49 Score=456.03 Aligned_cols=277 Identities=19% Similarity=0.234 Sum_probs=236.4
Q ss_pred cCcCCCCceeEEeccccCChhHHHHhhcCCC-------CCCCchHHHHHHHHhhccCCCCCCCceEEEEcCCCCCCCccc
Q 000291 756 HSLFPAGEPVGVLAATAMSNPAYKAVLDSSP-------SSNNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYC 828 (1714)
Q Consensus 756 ~~lv~~GepVG~laaqsigepatq~~L~t~~-------~~~~g~~rlkEil~~~~~~k~~~~d~~~~l~L~~~~~~~~~~ 828 (1714)
+++++|||+||++||||||||+|||||+||| ++|+|+||||||++++++ +++|.|++||.+. .
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 5689999999999999999999999999998 899999999999999886 5566999999863 3
Q ss_pred cHHHHHHHHhhhccccHhhhhheeEEEecCCccccCCCceEEEEEecHHHHHHhcCChhhhHHHHHHhhhhhhhcchhhH
Q 000291 829 QERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIISDDEGLVGHIHLNKILLEDLRISMHDILPKCQETLKSFCKKKKMKK 908 (1714)
Q Consensus 829 ~e~~a~~V~~~le~vtl~dv~~~i~I~y~~~~~~~~~~~wv~~i~Ld~e~L~~~~lt~~~I~~k~~~~~~~~~~~~~~~~ 908 (1714)
++++|+.|+.+||+++|+||+..+.+.|+++.. .+.|++|++.|++++|+.+...-.
T Consensus 74 ~~~~a~~v~~~ie~t~l~di~~~~~~~~~p~~~-------~~~i~~d~~~i~~~~l~~~~~~~~---------------- 130 (300)
T cd02736 74 DEKSARIVKGRIEKTYLGEVASYIEEVYSPDDC-------YILIKLDKKIIEKLQLSKSNLYFL---------------- 130 (300)
T ss_pred cHHHHHHHHHHHhhccHHHhhhheEEEEcCCCc-------eEEEEecHHHHHHhcCCcccHHHH----------------
Confidence 789999999999999999999999999999866 789999999999999854332211
Q ss_pred HHHHhhccccccccccc--ccccccccCC--CcceEEEEEcccC-----CcccccceecccccchHHHHHHhhhhhHHHH
Q 000291 909 VVQFFKNTSLSISECCS--FQQSCADKRS--NMPCLMFVLRGAS-----DSYLDKLSGVLANMIYPVLLETIIKENWWVR 979 (1714)
Q Consensus 909 i~~~~~~~~~~~~~~gi--~~~~~~~~~~--~~~~l~~~~~~~~-----~~~~vd~~~~~~n~I~~i~r~~IIkgi~w~r 979 (1714)
...+++.+....++|+ +.++.++++. +.++| .++|++ ..++||..++++|+|.+++. +.||+..|
T Consensus 131 -~~~l~~~l~~~~v~Gi~gI~r~~i~~~~~~~~~~l--~teG~nl~~v~~~~~Vd~~rt~sNdI~ei~~---~lGIEAaR 204 (300)
T cd02736 131 -LQSLKRKLPDVVVSGIPEVKRAVINKDKKKGKYKL--LVEGYGLRAVMNTPGVIGTRTTSNHIMEVEK---VLGIEAAR 204 (300)
T ss_pred -HHHHHHHhccceEeCCCCceEEEEecCCCCCcEEE--EEecccHHHHhcCCcEeccCCccCCHHHHHH---hcCHHHHH
Confidence 1222233333446777 5666665543 45555 788887 67899999999999999982 33666666
Q ss_pred ----HHHHHHHHHhhcccccceeeeeccceeeeceEeeeccccccccccCcccccccccccccCcHHHHHHHHhhcCCCC
Q 000291 980 ----QRLSASVTMVAKGVLKEHLILLANSMTCAGDLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDN 1055 (1714)
Q Consensus 980 ----~~l~~~~~~~~~~V~~rHl~LlAd~MT~~G~~~~~~r~G~~~~~~s~l~~a~Fe~~t~~~~~~~l~~Aa~~g~~D~ 1055 (1714)
+.|.++++.+|.+||+|||+||||+||++|+++||||+|+.+++.|+|++|+||+| .++|++||.+|+.|+
T Consensus 205 ~~ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~G~~~~itR~gi~~~~~S~l~~aSFE~t-----~~~L~~AA~~g~~D~ 279 (300)
T cd02736 205 STIINEIQYTMKSHGMSIDPRHIMLLADLMTFKGEVLGITRFGIAKMKESVLMLASFEKT-----TDHLFNAALHGRKDS 279 (300)
T ss_pred HHHHHHHHHHHHhcCCccCHHHHHHHHHHHhccCceeeeecccccccCCCHHHhcchHhH-----HHHHHHHhhcCCCCc
Confidence 44557788888999999999999999999999999999999999999999999997 899999999999999
Q ss_pred CCchhhhhhcCCcccccccceE
Q 000291 1056 LSSVVAACSWGKHVAVGTGSRF 1077 (1714)
Q Consensus 1056 l~gv~~~ii~Gk~~~~GTG~~~ 1077 (1714)
|+||+||||+|+++|+|||+ |
T Consensus 280 l~gvse~ii~G~~~~~GTG~-f 300 (300)
T cd02736 280 IEGVSECIIMGKPMPIGTGL-F 300 (300)
T ss_pred CCCcHHHeeeCCCcCCCCCC-C
Confidence 99999999999999999998 5
No 25
>TIGR02388 rpoC2_cyan DNA-directed RNA polymerase, beta'' subunit. The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria.
Probab=100.00 E-value=7e-47 Score=488.46 Aligned_cols=245 Identities=19% Similarity=0.281 Sum_probs=206.9
Q ss_pred ccccCcccchHHHHHHHHHHhhCHHHHHhchhhhHHHHHHHHHhcCceeeeCCcccCHHHHHHHHHHHHHHHHHHHHhh-
Q 000291 506 DFDRDTIPSVINEIVTSIFFEKGPEEVLEFFDSLQPLLMENLFADGFSVSLEDFSLSKAALWNIQKEIQALYSLLYHRM- 584 (1714)
Q Consensus 506 ~ldK~~lg~s~~~Li~~i~~~~G~~~a~~fLd~lqrL~~~~L~~~GFSiGi~Dl~~~~~~~~~i~~~i~~~~~~~~~~~- 584 (1714)
++||+.+ ..||+.++.+||++.|.+|||.+++|+++|++.+|||+||+|+.+|+++.+.++++.+++..+..++.
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 4566665 68999999999999999999999999999999999999999999999988777777777766655543
Q ss_pred ------hhhHHHHHHHHHHHHHHHHHHHHHHHHh-------cCCcccccccccchhhhhHHHHhHhccceecCCCccccc
Q 000291 585 ------STQNELVDLQIENHIRHVKMLVAKFILK-------SSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSK 651 (1714)
Q Consensus 585 ------~~~~e~le~~i~~~l~~~~~~i~~~~~~-------~n~l~~Mi~SGSKGS~~Ni~Qi~g~lGQQ~~~g~r~~~r 651 (1714)
+.+++.+ ..|+++++.+.+.+.+ .|++++|+.||||||+.|+.||+||+|||..++|+++
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 3455555555444432 4899999999999999999999999999999988743
Q ss_pred cccccccccccccCCCCCCCCCCccceecCcccccCCccceEEeeccccceeeecccccCCCCchhHHHHHHHhceEEEe
Q 000291 652 TLVEDIASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICY 731 (1714)
Q Consensus 652 ~l~~~~~~~f~~~~p~~~d~~~~a~GfV~ssF~~GL~P~EfFfHamagREGLiDTAvkTA~sGYLqRrLvk~ledl~v~Y 731 (1714)
+.| |++||++||+|.|||||||||||||||||||||+|||||||||+++||++|.+
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 222 99999999999999999999999999999999999999999999999999987
Q ss_pred c--cccccc-------------------------------------------------------------------cCCc
Q 000291 732 D--GTVRNV-------------------------------------------------------------------CSNS 742 (1714)
Q Consensus 732 D--~Tvr~~-------------------------------------------------------------------~~~~ 742 (1714)
+ ||.+++ +...
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 443211 1236
Q ss_pred eeEEEeccccccccCcCCCCceeEEeccccCChhHHHHhhcCCC
Q 000291 743 IIQFDYAVNARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDSSP 786 (1714)
Q Consensus 743 IiQf~yg~dg~~~~~lv~~GepVG~laaqsigepatq~~L~t~~ 786 (1714)
|||.|||.+ +....+|+.||+||++||||||||+||+||+|||
T Consensus 291 vC~~CYG~~-la~~~lV~lGeaVGiiAaQSIGEPGTQLTmRTFH 333 (1227)
T TIGR02388 291 VCRKCYGWS-LAHAHLVDLGEAVGIIAAQSIGEPGTQLTMRTFH 333 (1227)
T ss_pred HhHhccCCc-cccCcEechhhhhhhhhhhccCCcchhhhhhhhh
Confidence 999999998 4578899999999999999999999999999998
No 26
>PRK02597 rpoC2 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=100.00 E-value=1.9e-46 Score=488.06 Aligned_cols=245 Identities=20% Similarity=0.300 Sum_probs=206.3
Q ss_pred ccccCcccchHHHHHHHHHHhhCHHHHHhchhhhHHHHHHHHHhcCceeeeCCcccCHHHHHHHHHHHHHHHHHHHHhh-
Q 000291 506 DFDRDTIPSVINEIVTSIFFEKGPEEVLEFFDSLQPLLMENLFADGFSVSLEDFSLSKAALWNIQKEIQALYSLLYHRM- 584 (1714)
Q Consensus 506 ~ldK~~lg~s~~~Li~~i~~~~G~~~a~~fLd~lqrL~~~~L~~~GFSiGi~Dl~~~~~~~~~i~~~i~~~~~~~~~~~- 584 (1714)
++||+.+ .+||+.+|++||+..|..|||.+++|+++|++.+||||||+|+.+|+++.+.++++.+++..+..++.
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 4566665 58999999999999999999999999999999999999999999999988777777777666555543
Q ss_pred ------hhhHHHHHHHHHHHHHHHHHHHHHHHH----h---cCCcccccccccchhhhhHHHHhHhccceecCCCccccc
Q 000291 585 ------STQNELVDLQIENHIRHVKMLVAKFIL----K---SSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSK 651 (1714)
Q Consensus 585 ------~~~~e~le~~i~~~l~~~~~~i~~~~~----~---~n~l~~Mi~SGSKGS~~Ni~Qi~g~lGQQ~~~g~r~~~r 651 (1714)
+++++.++. |+++++.+.+.++ + .|+++||+.||||||+.||.|++||+|||..+.|+++
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 234444444 3444444433332 2 4899999999999999999999999999999888743
Q ss_pred cccccccccccccCCCCCCCCCCccceecCcccccCCccceEEeeccccceeeecccccCCCCchhHHHHHHHhceEEEe
Q 000291 652 TLVEDIASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICY 731 (1714)
Q Consensus 652 ~l~~~~~~~f~~~~p~~~d~~~~a~GfV~ssF~~GL~P~EfFfHamagREGLiDTAvkTA~sGYLqRrLvk~ledl~v~Y 731 (1714)
+.| |.+||++||+|+|||||||||||||||||||||+|||||||||++++|++|.+
T Consensus 156 ------------------~lP------I~snFrEGLs~~EyFis~~GaRKGLvDTAlKTAdSGYLTRRLVdv~QDviVre 211 (1331)
T PRK02597 156 ------------------DLP------IKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVRE 211 (1331)
T ss_pred ------------------ecc------hhhhhhcCCCHHHhheeccccccchhhcceecccchhHHHHHHHhhcceEEEe
Confidence 222 99999999999999999999999999999999999999999999999999988
Q ss_pred c--cccccc--------------------------------------------------------------------cCC
Q 000291 732 D--GTVRNV--------------------------------------------------------------------CSN 741 (1714)
Q Consensus 732 D--~Tvr~~--------------------------------------------------------------------~~~ 741 (1714)
+ ||.+++ +..
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 443211 134
Q ss_pred ceeEEEeccccccccCcCCCCceeEEeccccCChhHHHHhhcCCC
Q 000291 742 SIIQFDYAVNARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDSSP 786 (1714)
Q Consensus 742 ~IiQf~yg~dg~~~~~lv~~GepVG~laaqsigepatq~~L~t~~ 786 (1714)
.|||+|||++ +....+|+.||+||+|||||||||+||+||+|||
T Consensus 292 gvC~~CYG~~-la~~~lv~lGeaVGiiAaQSIGEPGTQLTmRTFH 335 (1331)
T PRK02597 292 SVCRKCYGWS-LAHNHLVDLGEAVGIIAAQSIGEPGTQLTMRTFH 335 (1331)
T ss_pred CchhhccCcc-hhcCcccchhhhhhhhhhccccCCcchhehhhhh
Confidence 6999999998 4578899999999999999999999999999998
No 27
>PF04998 RNA_pol_Rpb1_5: RNA polymerase Rpb1, domain 5; InterPro: IPR007081 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to form the central cleft or channel where the DNA is bound [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1ZYR_D 1SMY_D 2A68_N 2O5J_D 3AOH_N 2O5I_D 2CW0_N 2A6H_N 2A69_D 3EQL_D ....
Probab=100.00 E-value=1.3e-47 Score=445.34 Aligned_cols=258 Identities=26% Similarity=0.333 Sum_probs=181.7
Q ss_pred cCCccceEEeeccccceeeecccccCCCCchhHHHHHHHhceEEEeccccccccCCceeEEEeccccccccCcCCCCcee
Q 000291 686 GLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYDGTVRNVCSNSIIQFDYAVNARKSHSLFPAGEPV 765 (1714)
Q Consensus 686 GL~P~EfFfHamagREGLiDTAvkTA~sGYLqRrLvk~ledl~v~YD~Tvr~~~~~~IiQf~yg~dg~~~~~lv~~GepV 765 (1714)
||+|+|||||||||||||||||||||+||||||||||+|||++|+||+|||+. ++.|+||+||+|+ +++|||||
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 89999999999999999999999999999999999999999999999999995 7899999999997 89999999
Q ss_pred EEeccccCChhHHHHhhcCCC-------CCCCchHHHHHHHHhhccCCCCCCCceEEEEcCCCCCCCccccHHHHHHHHh
Q 000291 766 GVLAATAMSNPAYKAVLDSSP-------SSNNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERAAYMVKN 838 (1714)
Q Consensus 766 G~laaqsigepatq~~L~t~~-------~~~~g~~rlkEil~~~~~~k~~~~d~~~~l~L~~~~~~~~~~~e~~a~~V~~ 838 (1714)
|+|||||||||+|||||+||| +++.|+||++|+++++++.+ .+.+.+++...... .++.+..++.
T Consensus 75 GiiaAQSIGEP~TQ~TL~TFH~aG~~~~~vt~giprl~eii~~~~~~~----~~~~~~~~~~~~~~----~~~~~~~~~~ 146 (277)
T PF04998_consen 75 GIIAAQSIGEPGTQMTLRTFHTAGVASKNVTQGIPRLKEIINASKKIK----TPIITVYGKKKIIS----EKKKIKIIRK 146 (277)
T ss_dssp HHHHHHHHHCHGCCSHHSCTSSSCSSTSSCSSSHHHHHHHHTTCSSSS----SEEEEECSCSSECS----SSHHHHHHHH
T ss_pred hhhhhchhcchhHHhhhcccccCceeeecccccceeeccccccccccc----cceEEeecccceec----ccccceEEEE
Confidence 999999999999999999998 67889999999999877543 44555655544322 3344555555
Q ss_pred hhccccHhhhhheeEEEecCCccccCCCceEEEEEecHHHHHHhcCChhhhHHHHHHhhhhhhhcchhhHHHHHhhcccc
Q 000291 839 QLKRVSLKDAAVEFLIEYKKPEIISDDEGLVGHIHLNKILLEDLRISMHDILPKCQETLKSFCKKKKMKKVVQFFKNTSL 918 (1714)
Q Consensus 839 ~le~vtl~dv~~~i~I~y~~~~~~~~~~~wv~~i~Ld~e~L~~~~lt~~~I~~k~~~~~~~~~~~~~~~~i~~~~~~~~~ 918 (1714)
..+. .... ..+.. .. ...+
T Consensus 147 ~~~~--------------~~~~---------------------------~~~~~------~~-~~~~------------- 165 (277)
T PF04998_consen 147 KIKI--------------IKNG---------------------------KKVKN------GD-KIKK------------- 165 (277)
T ss_dssp TCSS--------------SCST---------------------------TCEHT------TC-ESSS-------------
T ss_pred eeee--------------eecc---------------------------cceec------ce-eeec-------------
Confidence 5444 0000 00000 00 0000
Q ss_pred cccccccccccccccCCCcceEEEEEcccC-----Cccc-ccceecccccchHHHHHHhhhhhHHHHH----HHHHHHHH
Q 000291 919 SISECCSFQQSCADKRSNMPCLMFVLRGAS-----DSYL-DKLSGVLANMIYPVLLETIIKENWWVRQ----RLSASVTM 988 (1714)
Q Consensus 919 ~~~~~gi~~~~~~~~~~~~~~l~~~~~~~~-----~~~~-vd~~~~~~n~I~~i~r~~IIkgi~w~r~----~l~~~~~~ 988 (1714)
..+..+.........+++ .+.+++ ...+ +|..++++|.|.+++ +++ ||+..|+ .+..++..
T Consensus 166 ----~~~~~~~~~~~~~~~~~l--~~~g~~l~~v~~~qgvid~~k~~sn~I~qm~-~~~--GIeaar~~i~~e~~~v~~~ 236 (277)
T PF04998_consen 166 ----GSIISKDILEKKSKEYVL--QTEGSNLQEVYSSQGVIDNDKHISNDIRQML-SKL--GIEAARNSIIKELKNVFES 236 (277)
T ss_dssp ----SCSEHHHHCEECCCCCEE--ECCSHHHHHHTCSTT-EETCHHECSHHHHHH-HHH--EHHHHHHHHHHHHHCHHHH
T ss_pred ----ceeeeeccccchhHHHHH--HHHhhhchhheecccccCCCEEEeceeEeee-eeE--EEEECCCceeecCcEeeHH
Confidence 000000000111222333 233332 3445 788999999998887 222 4454442 23466677
Q ss_pred hhcccccceeeeeccceeeeceEeeeccccccccccCcc
Q 000291 989 VAKGVLKEHLILLANSMTCAGDLVGFNSGGYKALSRSLN 1027 (1714)
Q Consensus 989 ~~~~V~~rHl~LlAd~MT~~G~~~~~~r~G~~~~~~s~l 1027 (1714)
.+..||+|||.|+||+||++|.++||||+||+..+.|.+
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 778899999999999999999999999999988776644
No 28
>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=1e-45 Score=431.63 Aligned_cols=280 Identities=23% Similarity=0.207 Sum_probs=215.4
Q ss_pred ccCcCCCCceeEEeccccCChhHHHHhhcCCC-------CCCCchHHHHHHHH-hhccCCCCCCCceEEEEcCCCCCCCc
Q 000291 755 SHSLFPAGEPVGVLAATAMSNPAYKAVLDSSP-------SSNNSWELMKEILL-CRVSFNNDPIDRRVILYLNDCGCGRK 826 (1714)
Q Consensus 755 ~~~lv~~GepVG~laaqsigepatq~~L~t~~-------~~~~g~~rlkEil~-~~~~~k~~~~d~~~~l~L~~~~~~~~ 826 (1714)
.+++++|||+||++||||||||+|||||+||| |+|+|+|||+|||+ ++++ +++|.|++||.+.+
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 35789999999999999999999999999998 99999999999985 5664 56779999998764
Q ss_pred cccHHHHHHHHhhhccccHhhhhheeEEEecCCcccc----CCCce-EEEEEecHHHHHHhcCChhhhHHHHHHhhhhhh
Q 000291 827 YCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIIS----DDEGL-VGHIHLNKILLEDLRISMHDILPKCQETLKSFC 901 (1714)
Q Consensus 827 ~~~e~~a~~V~~~le~vtl~dv~~~i~I~y~~~~~~~----~~~~w-v~~i~Ld~e~L~~~~lt~~~I~~k~~~~~~~~~ 901 (1714)
.+++|+.|+.+||+++|+||+..+.|.|-...... ....| .++|.+...
T Consensus 75 --~~~~a~~~~~~ie~~~l~dv~~~~~v~~i~~~~~~~~~~~~~~~~~~~i~~~~~------------------------ 128 (309)
T cd02735 75 --SAERAETLKKRLSRVTLSDVVEKVEVTEILKTIERVFKKLLGKWCEVTIKLPLS------------------------ 128 (309)
T ss_pred --hHHHHHHHHhheeEeEHHHhhhhhehhHHHHHHHHHhhhhhCCEEEEEEEecCC------------------------
Confidence 34589999999999999999999988761111000 00111 112221100
Q ss_pred hcchhhHHHHHhhccccccccccc--ccccccccCCC--cceEEEEEcccC-----Cc-ccccceecccccchHHHHHHh
Q 000291 902 KKKKMKKVVQFFKNTSLSISECCS--FQQSCADKRSN--MPCLMFVLRGAS-----DS-YLDKLSGVLANMIYPVLLETI 971 (1714)
Q Consensus 902 ~~~~~~~i~~~~~~~~~~~~~~gi--~~~~~~~~~~~--~~~l~~~~~~~~-----~~-~~vd~~~~~~n~I~~i~r~~I 971 (1714)
....-+...+++.+..+.++|+ |.++.++++.+ .....+.++|.+ .. +++|..++++|+|.+++.
T Consensus 129 --~~~~~~~~~~~~~l~~~~i~gi~gI~r~~i~~~~~~~~~~~~l~teG~nl~~v~~~~~~vd~~r~~sNdi~ei~~--- 203 (309)
T cd02735 129 --SPKLLLLSIVEKLARKAVIREIPGITRCFVVEEDKGGKTKYLVITEGVNLAALWKFSDILDVNRIYTNDIHAMLN--- 203 (309)
T ss_pred --chhHHHHHHHHHHhcccEEeCCCCccEEEEecCcCCCceEEEEEeccccHHHHHhccCccccccceeCCHHHHHH---
Confidence 0000122333333344456777 56665554321 112224778876 33 789999999999999982
Q ss_pred hhhhHHHH----HHHHHHHHHhhcccccceeeeeccceeeeceEeeeccccccccccCcccccccccccccCcHHHHHHH
Q 000291 972 IKENWWVR----QRLSASVTMVAKGVLKEHLILLANSMTCAGDLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKA 1047 (1714)
Q Consensus 972 Ikgi~w~r----~~l~~~~~~~~~~V~~rHl~LlAd~MT~~G~~~~~~r~G~~~~~~s~l~~a~Fe~~t~~~~~~~l~~A 1047 (1714)
+.||+..| +.|..+++.+|.+||+|||.||||+||++|++++|||+|| +...|||++|+||+| .++|.+|
T Consensus 204 ~lGIEAar~~ii~Ei~~v~~~~Gi~V~~rHl~LiaD~MT~~G~~~~~nr~gi-~~~~S~l~~asFE~t-----~~~L~~A 277 (309)
T cd02735 204 TYGIEAARRAIVKEISNVFKVYGIAVDPRHLSLIADYMTFEGGYRPFNRIGM-ESSTSPLQKMSFETT-----LAFLKKA 277 (309)
T ss_pred hhCHHHHHHHHHHHHHHHHHhcCCeeCHHHHHHHHHHHHhCCcEeecchhhe-ccCCCHHHhhhhhhH-----HHHHHHH
Confidence 33666666 4556788888899999999999999999999999999999 778999999999997 8999999
Q ss_pred HhhcCCCCCCchhhhhhcCCcccccccceEEEE
Q 000291 1048 AEKRHTDNLSSVVAACSWGKHVAVGTGSRFDLL 1080 (1714)
Q Consensus 1048 a~~g~~D~l~gv~~~ii~Gk~~~~GTG~~~~l~ 1080 (1714)
|.+|++|+|+||+|||+|||++|+|||+ |||+
T Consensus 278 a~~g~~D~l~g~s~~ii~G~~~~~GTG~-fdll 309 (309)
T cd02735 278 TLNGDIDNLSSPSSRLVVGKPVNGGTGL-FDLL 309 (309)
T ss_pred hhcCCCCCCCChHHheeeCCccCcccee-EEeC
Confidence 9999999999999999999999999999 9985
No 29
>CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed
Probab=100.00 E-value=1.7e-45 Score=484.49 Aligned_cols=249 Identities=20% Similarity=0.288 Sum_probs=208.1
Q ss_pred ccccCcccchHHHHHHHHHHhhCHHHHHhchhhhHHHHHHHHHhcCceeeeCCcccCHHHHHHHHHHHHHHHHHHHHhh-
Q 000291 506 DFDRDTIPSVINEIVTSIFFEKGPEEVLEFFDSLQPLLMENLFADGFSVSLEDFSLSKAALWNIQKEIQALYSLLYHRM- 584 (1714)
Q Consensus 506 ~ldK~~lg~s~~~Li~~i~~~~G~~~a~~fLd~lqrL~~~~L~~~GFSiGi~Dl~~~~~~~~~i~~~i~~~~~~~~~~~- 584 (1714)
.+||+. ...||+.++++||+++|+.|||++++|+++|++.+|||+||+|+.+|+++.+.++++.+++..+..++.
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 355555 477999999999999999999999999999999999999999999999988888888777776665543
Q ss_pred ------hhhHHHHHHHHHHHHHHHHHHHHHHHH---hcCCcccccccccchhhhhHHHHhHhccceecCCCccccccccc
Q 000291 585 ------STQNELVDLQIENHIRHVKMLVAKFIL---KSSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLVE 655 (1714)
Q Consensus 585 ------~~~~e~le~~i~~~l~~~~~~i~~~~~---~~n~l~~Mi~SGSKGS~~Ni~Qi~g~lGQQ~~~g~r~~~r~l~~ 655 (1714)
++|++.++.|- .....+++.+...+. ..|+++||+.||||||+.|+.|++||+|+|..+.|.++
T Consensus 89 G~it~~er~~~~i~~w~-~~~~~l~~~~~~~~~~~d~~N~v~mMa~SGARGn~sQi~qLvGmRGlma~p~G~iI------ 161 (1364)
T CHL00117 89 GNVHAVEKLRQSIEIWY-ATSEYLKQEMNPNFRMTDPLNPVYMMSFSGARGNASQVHQLVGMRGLMSDPQGQII------ 161 (1364)
T ss_pred CCCCHHHHHHHHHHHHH-HHHHHHHHHHHHhhccCCCCCcHhhhhhccCcccHHHHHHHhcccceeeCCCCcEe------
Confidence 46777777762 122333333333222 25999999999999999999999999999998877654
Q ss_pred cccccccccCCCCCCCCCCccceecCcccccCCccceEEeeccccceeeecccccCCCCchhHHHHHHHhceEEEec--c
Q 000291 656 DIASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYD--G 733 (1714)
Q Consensus 656 ~~~~~f~~~~p~~~d~~~~a~GfV~ssF~~GL~P~EfFfHamagREGLiDTAvkTA~sGYLqRrLvk~ledl~v~YD--~ 733 (1714)
+.| |.+||++||+|.|||||||||||||||||||||+|||||||||+++|||+|..+ |
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 222 999999999999999999999999999999999999999999999999999764 4
Q ss_pred ccccc------------------------------------------------------------------cCCceeEEE
Q 000291 734 TVRNV------------------------------------------------------------------CSNSIIQFD 747 (1714)
Q Consensus 734 Tvr~~------------------------------------------------------------------~~~~IiQf~ 747 (1714)
|.+++ +...|||.|
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 43211 123589999
Q ss_pred eccccccccCcCCCCceeEEeccccCChhHHHHhhcCCC
Q 000291 748 YAVNARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDSSP 786 (1714)
Q Consensus 748 yg~dg~~~~~lv~~GepVG~laaqsigepatq~~L~t~~ 786 (1714)
||++ +....+|+.||+||+|||||||||+||+||+|||
T Consensus 302 YG~~-la~~~lV~~GeaVGiiAaQSIGEPGTQLTmRTFH 339 (1364)
T CHL00117 302 YGWS-LAHGDLVELGEAVGIIAGQSIGEPGTQLTLRTFH 339 (1364)
T ss_pred hCcc-cccCcccChhhhhhhhhhhccCCCchhhhhhhhh
Confidence 9998 4678899999999999999999999999999998
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=1.9e-42 Score=410.17 Aligned_cols=234 Identities=25% Similarity=0.396 Sum_probs=176.3
Q ss_pred cceeeEEEecCCHHHHHHhccccccccc------------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeEEcCc
Q 000291 12 GQIVGIRFGLATQKEICTASISDCSISH------------ASQLANPFLGLPLEFGKCESCGTSEPGKCEGHFGYIELPI 79 (1714)
Q Consensus 12 ~~I~~I~F~l~S~eEI~k~Sv~~~~I~~------------~~gl~DprLG~~~~~~~C~TCg~~~~~~CpGHFGhIeL~~ 79 (1714)
++|++|+|++||+|||+++||.+ |++ ++||+|||||+.++...|+|||++. .+||||||||+|++
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 68999999999999999999975 332 3589999999999999999999986 79999999999999
Q ss_pred ccccccchHHHHHHHHHHHhhhc------cc-----------------hHHHHHHHHH----------------------
Q 000291 80 PIYHPSHISELKLTMYAFQLQIK------ND-----------------GVAQRLLSSC---------------------- 114 (1714)
Q Consensus 80 PVfHpgf~k~I~~IL~~iC~ri~------~~-----------------g~~kri~~~C---------------------- 114 (1714)
|||||+||+.|++||+++|..|. .. ...+.+...|
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 99999999999999999986542 00 0001111111
Q ss_pred -----H--------------------------------------HHHHHHhcCChHHHHhhccC-CCCCCCcEEEeeccC
Q 000291 115 -----C--------------------------------------EVKEMLKRIPEETRKKLAGK-GYFPQDGYILEYLPV 150 (1714)
Q Consensus 115 -----C--------------------------------------eV~~IfkkI~~ed~~~L~~~-~~~~pe~~il~~lpV 150 (1714)
| +|+++|++|+++++.+|++. ...+|+||||++|||
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 68899999999999988643 245799999999999
Q ss_pred CCCCCCCCcccCCCccccchhHHHHHHHHHHHHHHHHhh-hcCCCCccchhhhhhHHHHHHHHHHhhcCCCcCCCCCCCC
Q 000291 151 PPNCLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEVRGTAKSSRDVDAR 229 (1714)
Q Consensus 151 PP~~~Rp~~~~~g~~~~~~Dlt~~~l~~Il~~n~~lk~~-~~g~p~~~~~~~~~~~LQ~~v~~~~~~~~~~~~~~~~~~~ 229 (1714)
||+++||++.+++..+.++|+|. +|++||+.|+.|+.. ..+++... ....|.+||.+|+.|||+.....+.... ..
T Consensus 239 pP~~~RP~v~~~~~~~~eddlt~-~~~~Ii~~N~~L~~~~~~~~~~~~-~~~~~~~LQ~~v~~~~dn~~~~~~~~~~-~~ 315 (337)
T PF04997_consen 239 PPPRFRPSVQLGGGRFSEDDLTS-LYRKIIKRNNRLRKLLEEGAPSSI-IMEEWRLLQEAVNSLIDNEKPGKPPAGQ-KS 315 (337)
T ss_dssp -TGGGS-EEEESSSEEEE-HHHH-HHHHHHHHHHHHHHCCTSTSSSCH-HHHHHHHHHHHHHHHHCTTSSSSSBCBS-TT
T ss_pred CCceeeeeeeeecccccCchHHH-HHHHHHHHHHHHHHHHHhhCcchh-hhhhhhhhhHhHhHHhhhcccCCccccc-cc
Confidence 99999999998887667889998 899999999999985 44555443 4567899999999999973222211110 01
Q ss_pred CCCCCCCCchhhhhHhhhhhcc
Q 000291 230 FGVSQDPNSTTKAWLEKMRTLF 251 (1714)
Q Consensus 230 ~~~~k~~~~~ik~k~gr~R~~l 251 (1714)
....+.+.+++|||+||||+||
T Consensus 316 ~~~~k~i~q~L~gK~GrfR~NL 337 (337)
T PF04997_consen 316 GRPLKGISQRLKGKEGRFRQNL 337 (337)
T ss_dssp SSB--THHHHHSSTTSSHCHHT
T ss_pred CCCCCCHHHHccCCCCcCCCCC
Confidence 1123556689999999999997
No 31
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=100.00 E-value=4.7e-38 Score=410.03 Aligned_cols=281 Identities=19% Similarity=0.160 Sum_probs=230.6
Q ss_pred HHHHhhcCCC-------CCCCchHHHHHHHHhhccCCCCCCCceEEEEcCCCCCCCccccHHHHHHHHhhhccccHhhhh
Q 000291 777 AYKAVLDSSP-------SSNNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAA 849 (1714)
Q Consensus 777 atq~~L~t~~-------~~~~g~~rlkEil~~~~~~k~~~~d~~~~l~L~~~~~~~~~~~e~~a~~V~~~le~vtl~dv~ 849 (1714)
.+||+|+||| |+|+|+|||+|||+++++ +++|.|++||.+.+.. ++++|++|+.+||+++|+||+
T Consensus 540 v~~~~LnTFH~AGv~~~nVTlGvPRL~EIinask~----i~TP~m~i~l~~~~~~----~~~~a~~v~~~ie~~~L~dv~ 611 (858)
T PRK14898 540 VTHNTMRTFHYAGVAEINVTLGLPRMIEIVDARKE----PSTPIMTVHLKGEYAT----DREKAEEVAKKIESLTLGDVA 611 (858)
T ss_pred eeccccceeeccCccccccccCCchHHHHhcccCC----CCCceEEEEECCCccc----hHHHHHHHHhheeeEEHHHHH
Confidence 5799999998 999999999999998775 5667999999987543 678899999999999999999
Q ss_pred heeEEEecCCccccCCCceEEEEEecHHHHHHhcCChhhhHHHHHHhhhhh-h---------hcchhhHHHHHhhccccc
Q 000291 850 VEFLIEYKKPEIISDDEGLVGHIHLNKILLEDLRISMHDILPKCQETLKSF-C---------KKKKMKKVVQFFKNTSLS 919 (1714)
Q Consensus 850 ~~i~I~y~~~~~~~~~~~wv~~i~Ld~e~L~~~~lt~~~I~~k~~~~~~~~-~---------~~~~~~~i~~~~~~~~~~ 919 (1714)
..+.+.+... .++|+||++.|.+++|++++|+.++..+++.. . ...........+...+..
T Consensus 612 ~~~~~~~~~~---------~~~i~l~~~~~~~~~l~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 682 (858)
T PRK14898 612 TSIAIDLWTQ---------SIKVELDEETLADRGLTIESVEEAIEKKLGVKIDRKGTVLYLKPKTPSYKALRKRIPKIKN 682 (858)
T ss_pred HHhhhhcccc---------EEEEEECHHHHHHcCCCHHHHHHHHHHhccccccCCCCEEEEEecCchHHHHHHHHHHhcC
Confidence 9988755443 48999999999999999999999988765321 0 000001112223333445
Q ss_pred cccccc--ccccccccCC----CcceEEEEEcccC-----CcccccceecccccchHHHHHHhhhhhHHHH----HHHHH
Q 000291 920 ISECCS--FQQSCADKRS----NMPCLMFVLRGAS-----DSYLDKLSGVLANMIYPVLLETIIKENWWVR----QRLSA 984 (1714)
Q Consensus 920 ~~~~gi--~~~~~~~~~~----~~~~l~~~~~~~~-----~~~~vd~~~~~~n~I~~i~r~~IIkgi~w~r----~~l~~ 984 (1714)
+.++|+ |.++.+.++. ++++| .++|++ ..+++|..+|++|+|.+|+. +.||+..| +.|.+
T Consensus 683 ~~i~gi~gI~~~~i~~~~~~~~~~~~l--~teG~nl~~~~~~~~vd~~~~~sN~i~~i~~---~lGIEAar~~ii~Ei~~ 757 (858)
T PRK14898 683 IVLKGIPGIERVLVKKEEHENDEEYVL--YTQGSNLREVFKIEGVDTSRTTTNNIIEIQE---VLGIEAARNAIINEMMN 757 (858)
T ss_pred cEEECCCCccEEEEecCCCCCCceEEE--EecCcCHHHHhcCCCCcccccccCCHHHHHH---hhCHHHHHHHHHHHHHH
Confidence 567888 6777666532 34454 789987 67899999999999999982 23666666 44558
Q ss_pred HHHHhhcccccceeeeeccceeeeceEeeeccccccccccCcccccccccccccCcHHHHHHHHhhcCCCCCCchhhhhh
Q 000291 985 SVTMVAKGVLKEHLILLANSMTCAGDLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACS 1064 (1714)
Q Consensus 985 ~~~~~~~~V~~rHl~LlAd~MT~~G~~~~~~r~G~~~~~~s~l~~a~Fe~~t~~~~~~~l~~Aa~~g~~D~l~gv~~~ii 1064 (1714)
+++.+|..||+|||+||||+||++|.+++|||+||+..+.|||++|+||+| .++|++||.+|++|+|+||++|||
T Consensus 758 v~~~~gi~V~~rHl~liad~MT~~G~~~~~~r~gi~~~~~s~l~~asFe~t-----~~~l~~Aa~~g~~D~l~g~s~~ii 832 (858)
T PRK14898 758 TLEQQGLEVDIRHLMLVADIMTADGEVKPIGRHGVAGEKGSVLARAAFEET-----VKHLYDAAEHGEVDKLKGVIENVI 832 (858)
T ss_pred HHHhcCCccCHHHHHHHHHHHccCCcEEEeccCCccCCCCCHHHhcChHhH-----HHHHHHHhhcCCCCcCCCchHHee
Confidence 888888999999999999999999999999999999899999999999997 899999999999999999999999
Q ss_pred cCCcccccccceEEEEeccCC
Q 000291 1065 WGKHVAVGTGSRFDLLWQTEN 1085 (1714)
Q Consensus 1065 ~Gk~~~~GTG~~~~l~~~~~~ 1085 (1714)
||+++|+|||+ |||+++.+.
T Consensus 833 ~G~~~~~GTG~-~~l~~~~~~ 852 (858)
T PRK14898 833 VGKPIKLGTGC-VDLRIDREY 852 (858)
T ss_pred eCCccCCcCce-EEEEecCcc
Confidence 99999999999 999998654
No 32
>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=99.95 E-value=6.3e-29 Score=267.11 Aligned_cols=144 Identities=29% Similarity=0.496 Sum_probs=129.7
Q ss_pred ccccCCCCCceEeechhhHhHHHhhh-ccccCCHHHHHHhhcccc-----cccccccccccccccccceeeeccccCCCC
Q 000291 414 QLLSSHNGNLNLQLATDALLSLKVMF-KKYFLDKAFTQQLAMFAL-----SPLPRPALSKARCSARWTALQILQSVLPPG 487 (1714)
Q Consensus 414 nilsp~~G~Piigl~QD~llg~~llt-kd~fl~~~~~~~l~~~~~-----~~lp~PaI~Kp~~~~lWTGKQl~s~~LP~~ 487 (1714)
||+||++|+|+++++||+|+|+|+|| +++|++++|++++++... ...+.|+|++|. ++|||||+|+++||..
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 579999999999999985 347889999997 8999999999999987
Q ss_pred ccccC-------CEEEEEcceecccccccCccc-chHHHHHHHHHHhhCHHHHHhchhhhHHHHHHHHHhcCceeeeCCc
Q 000291 488 FDSCG-------DRYLIKKSEVLKGDFDRDTIP-SVINEIVTSIFFEKGPEEVLEFFDSLQPLLMENLFADGFSVSLEDF 559 (1714)
Q Consensus 488 ~~~~~-------~~viI~~Gell~G~ldK~~lg-~s~~~Li~~i~~~~G~~~a~~fLd~lqrL~~~~L~~~GFSiGi~Dl 559 (1714)
+++.. +.++|++|+++.|.+||+++| +..++||+.++++||+++|++|||++|+|+++|++.+|||||++|+
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 76533 579999999999999999999 7899999999999999999999999999999999999999999996
No 33
>cd00630 RNAP_largest_subunit_C Largest subunit of RNA polymerase (RNAP), C-terminal domain. RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channe
Probab=99.94 E-value=4.4e-28 Score=257.55 Aligned_cols=100 Identities=29% Similarity=0.389 Sum_probs=95.0
Q ss_pred hHHHHHHhhhhhHHHHHHHHHHHHHhhcccccceeeeeccceeeeceEeeeccccccccccCcccccccccccccCcHHH
Q 000291 964 YPVLLETIIKENWWVRQRLSASVTMVAKGVLKEHLILLANSMTCAGDLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKC 1043 (1714)
Q Consensus 964 ~~i~r~~IIkgi~w~r~~l~~~~~~~~~~V~~rHl~LlAd~MT~~G~~~~~~r~G~~~~~~s~l~~a~Fe~~t~~~~~~~ 1043 (1714)
||..|++||+|+. ++++.+|..||+|||.||||+||++|.+++|||+||++...|+|++|+||++ .++
T Consensus 59 IEAaR~~iv~El~-------~v~~~~Gi~V~~rHl~LIAD~MT~~G~~~ginr~g~~~~~~Spl~~aSFE~t-----~~~ 126 (158)
T cd00630 59 IEAARETIIREIQ-------KVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGFRASKTSPLMRASFEKT-----TKH 126 (158)
T ss_pred HHHHHHHHHHHHH-------HHHHhcCceecHHHHHHHHHHHhcCCcccccccccccccCCCHHHHcCHHHH-----HHH
Confidence 3667888999966 9999999999999999999999999999999999998888999999999997 899
Q ss_pred HHHHHhhcCCCCCCchhhhhhcCCcccccccc
Q 000291 1044 FEKAAEKRHTDNLSSVVAACSWGKHVAVGTGS 1075 (1714)
Q Consensus 1044 l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~ 1075 (1714)
|++||.+|+.|+|+||++||||||++|+|||+
T Consensus 127 L~~AA~~g~~D~l~g~s~~ii~Gk~~~~GTG~ 158 (158)
T cd00630 127 LLDAAAAGEKDELEGVSENIILGRPAPLGTGS 158 (158)
T ss_pred HHHHhhcCCCCCCCCcHHhhhccCCCCCCCCC
Confidence 99999999999999999999999999999995
No 34
>PF11523 DUF3223: Protein of unknown function (DUF3223); InterPro: IPR021602 This family of proteins has no known function. ; PDB: 2K0M_A.
Probab=99.93 E-value=1e-27 Score=225.41 Aligned_cols=76 Identities=54% Similarity=1.081 Sum_probs=63.5
Q ss_pred HHHHhcccCCCCCCccCCcchhhHHHHHhccCCCccccccCCcceEEEecCCCCCCccEEEEEecCCCcccccHHHHH
Q 000291 1592 IRRIMHQSGYNDGDRLSADDKSFIFDNVFNYHPDKAMKMGAGIDHFKVDKHGSFQDSRCLFVVSTDGSQQDFSYRKCL 1669 (1714)
Q Consensus 1592 ~~~il~~~~y~~g~~l~~~d~~~~l~~ll~~Hp~~~~Kig~gi~~~~v~~~p~~~~srcf~vvr~Dg~~~dFSy~kC~ 1669 (1714)
||+||| +|++|++|+++|++++|+.||.|||++++||||||++|+|+.||.|++||||||||+|||.+||||+|||
T Consensus 1 ~k~iL~--~y~~g~~l~~~d~~~~l~~ll~~HP~~~~KiG~Gi~~i~V~~hp~~~~srCF~vvR~DGs~~DFSy~KCi 76 (76)
T PF11523_consen 1 FKRILH--RYPDGERLSEEDEKSVLEALLKYHPEAEEKIGCGIDHIMVRKHPEFKDSRCFFVVRTDGSEEDFSYRKCI 76 (76)
T ss_dssp HHHHHH--HS-TTEE--HHH-HHHHHHHHHTSTTHHHHHTT-EEEEEEEESSSS---EEEEEEETTS-EEE--GGGSS
T ss_pred ChhHHh--hCCCcCCcCHHHHHHHHHHHHHhCCcHHHhhcCCeeeEEEeecCCCCcceEEEEEEeCCCeeeeEhhhhC
Confidence 689999 9999999999999999999999999999999999999999999999889999999999999999999996
No 35
>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=99.89 E-value=3.9e-24 Score=235.32 Aligned_cols=97 Identities=18% Similarity=0.275 Sum_probs=86.4
Q ss_pred HHHHHHhhhhhHHHHHHHHHHHHHhhcccccceeeeeccceeeeceE---------------------------------
Q 000291 965 PVLLETIIKENWWVRQRLSASVTMVAKGVLKEHLILLANSMTCAGDL--------------------------------- 1011 (1714)
Q Consensus 965 ~i~r~~IIkgi~w~r~~l~~~~~~~~~~V~~rHl~LlAd~MT~~G~~--------------------------------- 1011 (1714)
+..|..||+||. ++++.+|..|++||+.||||.||+++.+
T Consensus 68 ea~r~~iv~EIq-------~Vy~~qGV~I~dKHielIv~qMT~kv~i~~~g~s~~l~Ge~v~~~~~~~~N~~~~~~~~~~ 140 (204)
T cd02655 68 EAVQKYLVEEIQ-------KVYRSQGVNINDKHIEIIVRQMTSKVKIIDPGDSGFLPGELVDLNEFEEENKRLLLLGKKP 140 (204)
T ss_pred HHHHHHHHHHHH-------HHHHhcCeeecHHHHHHHHHHHhcCeEEecCCCcccCCCceeeHHHHHHHHHHHHhCCCCc
Confidence 445667788866 9999999999999999999999999653
Q ss_pred -------eeeccccccccccCcccccccccccccCcHHHHHHHHhhcCCCCCCchhhhhhcCCcccccccc
Q 000291 1012 -------VGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGS 1075 (1714)
Q Consensus 1012 -------~~~~r~G~~~~~~s~l~~a~Fe~~t~~~~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~ 1075 (1714)
+||||.++. ..|+|++||||+| .++|.+||.+|++|.|.|++||||+|+++|+|||.
T Consensus 141 ~~y~p~llGItk~~l~--~~Sfls~ASFqeT-----~kvL~~AAi~gk~D~L~GlkeNVI~G~liPaGTG~ 204 (204)
T cd02655 141 AKYEPVLLGITKASLN--TESFISAASFQET-----TKVLTEAAIEGKIDWLRGLKENVILGRLIPAGTGL 204 (204)
T ss_pred ccccceeeeeeecccc--CCCccccCChHHH-----HHHHHHHHhcCCCCCCCCchhheEECCccCCCCCC
Confidence 477777774 5799999999998 79999999999999999999999999999999995
No 36
>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=99.48 E-value=2.3e-14 Score=145.10 Aligned_cols=91 Identities=22% Similarity=0.330 Sum_probs=71.5
Q ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHHHHHh----cCCcccccccccchhhhhHHHHhHhccceecCCCcccccccccccc
Q 000291 583 RMSTQNELVDLQIENHIRHVKMLVAKFILK----SSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLVEDIA 658 (1714)
Q Consensus 583 ~~~~~~e~le~~i~~~l~~~~~~i~~~~~~----~n~l~~Mi~SGSKGS~~Ni~Qi~g~lGQQ~~~g~r~~~r~l~~~~~ 658 (1714)
....+++.++..+..+++++++.+.+.+.+ +|++++|+.||||||+.|++||+||||||.++|+| +.+....|++
T Consensus 14 ~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~N~l~~M~~SGaKGs~~ni~Qi~g~lGqq~~~g~r-i~~~~~~Rtl 92 (108)
T PF05000_consen 14 WGKTYEETFEQKINKILNKVRDEIGKIIKKNLPFNNSLLIMINSGAKGSMSNISQISGCLGQQSVEGKR-IPRGFSGRTL 92 (108)
T ss_dssp CTCHHHHHHHHHHHHHHHHCCHHHHHHHHHCSTTTSHHHHHHHSSSS--HHHHHHHHST-EEEEETTSE-S--SSTTCSS
T ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcHHhhhhccCCCCHHHHHHHHHHHHHhhccccc-cccCCCCCcC
Confidence 334567777877888888888888888875 48999999999999999999999999999999877 4555778999
Q ss_pred ccccccCCCCCCCCCCcccee
Q 000291 659 SHFERIYPMDLNYPTAKYGLI 679 (1714)
Q Consensus 659 ~~f~~~~p~~~d~~~~a~GfV 679 (1714)
|||.. .+..|+++|||
T Consensus 93 p~f~~-----~~~~~~~~GFI 108 (108)
T PF05000_consen 93 PHFKP-----FDESPESRGFI 108 (108)
T ss_dssp TTS-S-----S-SSTTTTTEE
T ss_pred CCcCC-----CCCCcccCCCC
Confidence 99963 37789999998
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=99.14 E-value=1.6e-11 Score=162.04 Aligned_cols=89 Identities=19% Similarity=0.327 Sum_probs=79.3
Q ss_pred HHHHHHHHHhhcccccceeeeeccceeee-------------ceE---------------------------eeeccccc
Q 000291 980 QRLSASVTMVAKGVLKEHLILLANSMTCA-------------GDL---------------------------VGFNSGGY 1019 (1714)
Q Consensus 980 ~~l~~~~~~~~~~V~~rHl~LlAd~MT~~-------------G~~---------------------------~~~~r~G~ 1019 (1714)
+.++.+++.+|..|+.||++||++.||.+ |++ +||||+.+
T Consensus 1094 ~eiq~vy~~QGv~I~~kHieiIvrqMtskV~i~~~G~t~~lpGeli~~~~~~~~n~~l~~~~~~~~~y~pvLlGITkasL 1173 (1227)
T TIGR02388 1094 NEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDAGDTTLLPGELVELRQVEQVNEAMAITGGAPAQYTPVLLGITKASL 1173 (1227)
T ss_pred HHHHHHHHhcceEeehhhHHHHHHHHhceEEEeeCCCcccCCcceeeHHHHHHHHHHHHhcCCCccccceeEeeeeeccc
Confidence 44568999999999999999999999999 885 44445444
Q ss_pred cccccCcccccccccccccCcHHHHHHHHhhcCCCCCCchhhhhhcCCcccccccc
Q 000291 1020 KALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGS 1075 (1714)
Q Consensus 1020 ~~~~~s~l~~a~Fe~~t~~~~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~ 1075 (1714)
...|.+++|||+|| .++|.+||++|+.|.|+|+.||||+|+++|+|||.
T Consensus 1174 --~t~Sfis~ASFqeT-----trvL~~Aai~g~~D~l~glkENvI~G~liP~GTG~ 1222 (1227)
T TIGR02388 1174 --NTDSFISAASFQET-----TRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGF 1222 (1227)
T ss_pred --cccchhhhccHHHH-----HHHHHHHHHcCCcccccCchhheeecCccccCCCc
Confidence 34699999999998 79999999999999999999999999999999998
No 38
>CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed
Probab=99.14 E-value=1.5e-11 Score=165.20 Aligned_cols=94 Identities=20% Similarity=0.349 Sum_probs=84.1
Q ss_pred HHHHHHHHHhhcccccceeeeeccceeee--------------ce-----------------------Eeeecccccccc
Q 000291 980 QRLSASVTMVAKGVLKEHLILLANSMTCA--------------GD-----------------------LVGFNSGGYKAL 1022 (1714)
Q Consensus 980 ~~l~~~~~~~~~~V~~rHl~LlAd~MT~~--------------G~-----------------------~~~~~r~G~~~~ 1022 (1714)
+.++++++.+|..|+.||+.+|++.||.+ |+ |+||||++++
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 56778899999999999999999999994 77 4577777774
Q ss_pred ccCcccccccccccccCcHHHHHHHHhhcCCCCCCchhhhhhcCCcccccccceEEEEe
Q 000291 1023 SRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGSRFDLLW 1081 (1714)
Q Consensus 1023 ~~s~l~~a~Fe~~t~~~~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~~~~l~~ 1081 (1714)
..|.+++|||+|| .++|.+||++|++|.|+|+.||||+|+++|+|||. +++..
T Consensus 1270 t~Sfis~aSFqeT-----~rvL~~aai~g~~D~l~glkenvi~g~~ip~GTG~-~~~~~ 1322 (1364)
T CHL00117 1270 TQSFISEASFQET-----TRVLAKAALRGRIDWLKGLKENVILGGLIPAGTGF-KGLVH 1322 (1364)
T ss_pred ccchhhhcchHHH-----HHHHHHHHHcCCcccccCchhheeecCcccCCCCc-hhhhh
Confidence 6799999999998 79999999999999999999999999999999999 66643
No 39
>PRK02597 rpoC2 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=99.07 E-value=5.4e-11 Score=158.46 Aligned_cols=91 Identities=20% Similarity=0.308 Sum_probs=79.3
Q ss_pred HHHHHHHHHhhcccccceeeeeccceeee-------------ceE------------eeecc----------ccccccc-
Q 000291 980 QRLSASVTMVAKGVLKEHLILLANSMTCA-------------GDL------------VGFNS----------GGYKALS- 1023 (1714)
Q Consensus 980 ~~l~~~~~~~~~~V~~rHl~LlAd~MT~~-------------G~~------------~~~~r----------~G~~~~~- 1023 (1714)
+.++++++.+|..|+.+||.+|++.||.+ |++ +.+++ +||.+..
T Consensus 1095 ~evq~Vy~~QGv~I~dkHieiIvrqMt~kV~i~d~Gdt~~lpGeli~~~~~~~~N~~~~~~~~~~a~y~pvLlGItkasl 1174 (1331)
T PRK02597 1095 NEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDGGDTTMLPGELIELRQVEQVNEAMAITGGAPAEYTPVLLGITKASL 1174 (1331)
T ss_pred HHHHHHHHhcCeEechhhHHhHHHHHhCcEEEeeCCCcccCCcceeeHHHHHHHHHHHHhcCCCcceeeeeeeeeeeecc
Confidence 56678888899999999999999999999 444 33344 4665543
Q ss_pred --cCcccccccccccccCcHHHHHHHHhhcCCCCCCchhhhhhcCCcccccccc
Q 000291 1024 --RSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGS 1075 (1714)
Q Consensus 1024 --~s~l~~a~Fe~~t~~~~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~ 1075 (1714)
.|++++|||+|| +++|.+||++|++|.|+|+.||||+|+++|+|||.
T Consensus 1175 ~T~sfis~aSFqeT-----~rvL~~AAi~g~~D~l~GlkENVI~G~liP~GTG~ 1223 (1331)
T PRK02597 1175 NTDSFISAASFQET-----TRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGF 1223 (1331)
T ss_pred ccCChhhhccHHHH-----HHHHHHHHHcCCCcccCCchhheeecCccccCcCc
Confidence 499999999998 79999999999999999999999999999999999
No 40
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]
Probab=98.93 E-value=1.9e-11 Score=159.36 Aligned_cols=322 Identities=14% Similarity=0.074 Sum_probs=212.9
Q ss_pred HHHhceEEEeccccccccCCceeEEEeccccccccCcCCCCceeEEeccccCChhHHHHhhcCCCC---------CCCch
Q 000291 722 AVLRDVVICYDGTVRNVCSNSIIQFDYAVNARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDSSPS---------SNNSW 792 (1714)
Q Consensus 722 k~ledl~v~YD~Tvr~~~~~~IiQf~yg~dg~~~~~lv~~GepVG~laaqsigepatq~~L~t~~~---------~~~g~ 792 (1714)
.+.+.+.+.+ -|.|= +.++--.|..| .|...+..++..++..+|+|++++.+|+.+.++|+ .+.+.
T Consensus 379 q~~e~vl~~g-kt~rL---h~lVc~~yNAD-FDGDeM~~Hvp~s~ea~AEa~~lm~tq~nilsP~~Ggpiv~~~qD~v~g 453 (808)
T COG0086 379 QAFEPVLPEG-KAIRL---HPLVCEAYNAD-FDGDEMAVHVPASGEAAAEARGLMGTQMNILTPHYGGPIVAPIQDTVGG 453 (808)
T ss_pred hhceeecccc-ceeec---chhhccccccc-cCchhhhccccchHHHHHHHHHhhccccccccCCCCCceEeecceEEec
Confidence 5666665544 22221 23333366654 23455677899999999999999999999998873 23355
Q ss_pred HHHHHHHHhhccCCCCCCCceEEEEcCCCCCCCccccHHHHHHHHhhhccccHhhhhheeEEEecCCccccCCCceEEEE
Q 000291 793 ELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIISDDEGLVGHI 872 (1714)
Q Consensus 793 ~rlkEil~~~~~~k~~~~d~~~~l~L~~~~~~~~~~~e~~a~~V~~~le~vtl~dv~~~i~I~y~~~~~~~~~~~wv~~i 872 (1714)
+++-++..+ ..+.++.|.+||...+.. ..+.+.++.+.++.++.+.+++.+....... .+.+
T Consensus 454 ~ylLt~~d~-----~~~~~~~~ei~l~~~~~~----~~e~~~ai~~~~~~~~~k~i~~~i~~~~~~~---------~i~~ 515 (808)
T COG0086 454 PYLLTIVDA-----KLPSTPVGEIYLKDEYAD----DREKAEAIAKKIELTTGKVIVSTISPDLAEL---------SIIV 515 (808)
T ss_pred cEEEEEecc-----cCCCCcceEEEecccccc----chhhhHHHhcccceeeeeEEEEEeeccCCcc---------eEEE
Confidence 666666544 126677899988744332 5678999999999999999998766554333 4678
Q ss_pred EecHHHHHHhcCChh-hhHHHHHH--------------hhhhhhh--cc-hhhHHHHHhhcccccccccccccccccccC
Q 000291 873 HLNKILLEDLRISMH-DILPKCQE--------------TLKSFCK--KK-KMKKVVQFFKNTSLSISECCSFQQSCADKR 934 (1714)
Q Consensus 873 ~Ld~e~L~~~~lt~~-~I~~k~~~--------------~~~~~~~--~~-~~~~i~~~~~~~~~~~~~~gi~~~~~~~~~ 934 (1714)
.+|.+.+..+.+..+ ++...+.+ .++.+.. .. ...++...+++.-+... +.+...++.++
T Consensus 516 t~~~~~~~~~~~~~~~d~~~~i~~~~l~~~~i~k~~~~i~~~~g~~~~~~~~~~~~dkl~~~~~~~~--~~~~~~i~~~d 593 (808)
T COG0086 516 TTDGRRIFNRGLPEDKDVLVKIVNGKLIKGVIDKKIVTIYREYGPEVASKALVKLLDKLKNLGIKGI--GGFGIGIGRKD 593 (808)
T ss_pred ecchhhhhhccCCcccceeeEEeccccceeeehhhHHHHHHHhCchhhHHHHHHHHHHHHHhheeee--ccceEEeeccc
Confidence 888888888888776 33322111 1111110 00 11123344433332111 10111222221
Q ss_pred CCcc-----eEEEEEcccC-----CcccccceecccccchHHH--------HHHhhhhhHHHHHHHHHHHHHhhcc-ccc
Q 000291 935 SNMP-----CLMFVLRGAS-----DSYLDKLSGVLANMIYPVL--------LETIIKENWWVRQRLSASVTMVAKG-VLK 995 (1714)
Q Consensus 935 ~~~~-----~l~~~~~~~~-----~~~~vd~~~~~~n~I~~i~--------r~~IIkgi~w~r~~l~~~~~~~~~~-V~~ 995 (1714)
...+ ++ ...++.. ..+.++++++.+|++.+++ ++++++++. .++..++.. ++.
T Consensus 594 ~~~~~~~~e~v-~~ae~~v~~~i~~~~~g~lt~~~~~~i~e~~e~~~~e~l~~ai~~~~~-------~~~~~~g~~~~~i 665 (808)
T COG0086 594 IEAEDEKDEIV-IEAEGSVLKLILQYEEGDLTRTERNNIVEIIEVLGIEALRNAIIEEIK-------ITLEEQGLDFVDI 665 (808)
T ss_pred ccchHHHHHHH-HHHHHHHHHHHHHhhcCCccccCCCCeEEEeehHHHHHHHHHHHHHHh-------hhHHhcCCcchhH
Confidence 0000 00 0111111 3445667777777665444 555555433 666777777 999
Q ss_pred ceeeeeccceeeeceEeeeccccccccccCcccccccccccccCcHHHHHHHHhhcCCCCCCchhhhhhcCCcccccccc
Q 000291 996 EHLILLANSMTCAGDLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGS 1075 (1714)
Q Consensus 996 rHl~LlAd~MT~~G~~~~~~r~G~~~~~~s~l~~a~Fe~~t~~~~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~ 1075 (1714)
+|+++.+|.|+.++.+..++++|+.+.+.++++++.|+.+ .++ .+|+.+++++.++|++++++.|++++.|||.
T Consensus 666 ~~m~~~Gs~~n~sq~~~~iG~~gv~g~r~~~~~~~~Fe~~-----~~~-~~a~~~i~s~f~eGLt~~e~f~~~~ggR~Gl 739 (808)
T COG0086 666 RHMGLSGARMNISQIVQLIGQQGVMGEKISVLARAAFEVT-----VKH-LEAEGPGESSFLEGLTENEYFGHPIGGRTGL 739 (808)
T ss_pred HHHhhhhhccCHHHHHHHhhhheeeccCCCcccccccccc-----ccc-ceeeeeeecccCCCCCcceEEeecCccccch
Confidence 9999999999999999999999999999999999999998 788 8899999999999999999999999999999
Q ss_pred eEEEEecc
Q 000291 1076 RFDLLWQT 1083 (1714)
Q Consensus 1076 ~~~l~~~~ 1083 (1714)
+|..+..
T Consensus 740 -vDTA~KT 746 (808)
T COG0086 740 -VDTALKT 746 (808)
T ss_pred -HHHhhhh
Confidence 9987654
No 41
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=97.96 E-value=1.5e-06 Score=111.89 Aligned_cols=336 Identities=18% Similarity=0.150 Sum_probs=207.8
Q ss_pred CCCceeEEeccccCChhHHHHhhcCCCCC-------CCchHHHHHHHHhhccCCCCCCCceEEEEcCCCCCCCccccHHH
Q 000291 760 PAGEPVGVLAATAMSNPAYKAVLDSSPSS-------NNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERA 832 (1714)
Q Consensus 760 ~~GepVG~laaqsigepatq~~L~t~~~~-------~~g~~rlkEil~~~~~~k~~~~d~~~~l~L~~~~~~~~~~~e~~ 832 (1714)
+.++++|.++|+.+.+.+|.++.+..... .++.-.++.+|+ .++++-..|+.+.+||.++.+.+..+.++.
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 QNGETLGSLNACFESEFAYDALDEPISLSSEEVVNEISELLKLQNLLE--CEYKKLVRDRRVLLYIFEYGDAKWPLPENL 956 (1605)
T ss_pred cccccccchHHHHHhhhhhhhhcCcccchhhhHhhhhhhhHHHHHHHH--HHHHhhhhhhhhhhhhcccCCcccccchhH
Confidence 35788888899999999998875443221 223334555554 455666789999999999998889999999
Q ss_pred HHHHHhhhccccHhhhhheeEEEecCCccccCCCceEEEEE----e----------------cHHHHHHhcCChhh---h
Q 000291 833 AYMVKNQLKRVSLKDAAVEFLIEYKKPEIISDDEGLVGHIH----L----------------NKILLEDLRISMHD---I 889 (1714)
Q Consensus 833 a~~V~~~le~vtl~dv~~~i~I~y~~~~~~~~~~~wv~~i~----L----------------d~e~L~~~~lt~~~---I 889 (1714)
.+.|+++++.+.+.+.+....+.+.=-........-++.+. | ++.+++.++|+-+. +
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~ 1036 (1605)
T KOG0260|consen 957 QRIIWNALKKFSIDERKPTDLIPFKVVKGVKELAEKLVIVRGEDYISRAQRLFNILLRSTLATKRVLEEYRLSSEAFEWV 1036 (1605)
T ss_pred HHHHHHHHhhcccccccccccchhhhhhhhhhhhheeEEeeCchhHHHHHHHHHHHHHhhHHHHHHHHHhcccHHHHHHH
Confidence 99999999988888775443332210000000000011111 1 23334444444322 2
Q ss_pred HHHHHHhhhhhhhcch-h-----hH-H--------HHHhh-------cccccc-cccccccccccccCCCcceEEEEEcc
Q 000291 890 LPKCQETLKSFCKKKK-M-----KK-V--------VQFFK-------NTSLSI-SECCSFQQSCADKRSNMPCLMFVLRG 946 (1714)
Q Consensus 890 ~~k~~~~~~~~~~~~~-~-----~~-i--------~~~~~-------~~~~~~-~~~gi~~~~~~~~~~~~~~l~~~~~~ 946 (1714)
+..++.++..+..... + .+ + .+.|. |+++.+ +.+-|++ +.+...++.|++++.+
T Consensus 1037 ~~~Ie~~f~qa~a~pgemvg~lAaqsvgePatqmTlntfh~aGVssknVt~gvprlkei~N---v~k~~ktpsLtV~l~g 1113 (1605)
T KOG0260|consen 1037 LGEIEARFLQAEASPGEMVGALAAQSVGEPATQMTLNTFHYAGVSSKNVTLGVPRLKEIIN---VAKNAKTPSLTVYLTG 1113 (1605)
T ss_pred hhhhhhheeeeecCccchHhHHHHHHhCCchhhcccchhcccceeeeeeeccCcchhhhhh---hhccCCCceEEEEecc
Confidence 2222222211110000 0 00 0 11111 111100 0111111 1234567888887766
Q ss_pred cC------------Ccccccceecccccch---HHHHHHhhhh-hHHHHHHHHHHHHHhhcccccceeeeeccceeeece
Q 000291 947 AS------------DSYLDKLSGVLANMIY---PVLLETIIKE-NWWVRQRLSASVTMVAKGVLKEHLILLANSMTCAGD 1010 (1714)
Q Consensus 947 ~~------------~~~~vd~~~~~~n~I~---~i~r~~IIkg-i~w~r~~l~~~~~~~~~~V~~rHl~LlAd~MT~~G~ 1010 (1714)
.. ..+-.++.++.++.=+ |=-..++|.+ -+|+...++...++++ .+.+.||.|++|.-..+|+
T Consensus 1114 ~~~k~~e~ak~v~~~le~ttl~~vt~~t~i~ydpdp~~tvI~ed~e~v~a~~e~pd~D~~-~ispwlLrlelDr~~m~dk 1192 (1605)
T KOG0260|consen 1114 EAAKDNEWAKLVQCCLEHTTLKDVTRATEIYYDPDPQSTVIDEDREFVVAYYEMPDEDVG-RISPWLLRLELDRASMTDK 1192 (1605)
T ss_pred hhhcchHHHHHHhhhcccccHHhhhccCcceecCCCcceeeccchhhHHhhhcCcccchh-hcChHHHHhhhhhhhcccc
Confidence 42 1112222222222111 1113344444 5677766666667777 8999999999999999999
Q ss_pred EeeeccccccccccCcccccccccccccCcHHHHHHHHhhcCCCCCCchhhhhhcCCcccccccceEEEEeccCCccccc
Q 000291 1011 LVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGSRFDLLWQTENEEFNQ 1090 (1714)
Q Consensus 1011 ~~~~~r~G~~~~~~s~l~~a~Fe~~t~~~~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~~~~l~~~~~~~~~~~ 1090 (1714)
.+.++-.|.+-...--.-.++|-..+|..+..+++++|..++.|.+.+-.|+.+||+..--|++..|++++..+.+..-+
T Consensus 1193 ~ltm~~ia~~i~~~f~~d~~~i~~ddna~klv~r~ri~~~~e~D~~l~~Ie~~ml~~~~l~G~~~i~kV~m~~~~~G~f~ 1272 (1605)
T KOG0260|consen 1193 KLTMEQIAEKINRGFGSDLACIFSDDNAEKLVLRLRIAKEEEDDVFLKCIEANMLGDMTLRGIPDIFKVYMSPTEDGEFK 1272 (1605)
T ss_pred cccHHHHHHHHHhhccCCCceeecccCCcceEEEEEecCccchhHHHHHHHHhhhhhcccCCccccceEEEeecCCCcee
Confidence 99999888755554444456788889999999999999999999999999999999999999999999999998888888
Q ss_pred CCccchhhccccc
Q 000291 1091 DDGVDVYDFLHMV 1103 (1714)
Q Consensus 1091 ~~~~~~y~~l~~~ 1103 (1714)
+ ++.|+++-..
T Consensus 1273 ~--~~ew~LeTdg 1283 (1605)
T KOG0260|consen 1273 P--VDEWDLETDG 1283 (1605)
T ss_pred e--cceeEEecCc
Confidence 7 7888776544
No 42
>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=97.49 E-value=2.8e-05 Score=81.99 Aligned_cols=55 Identities=22% Similarity=0.270 Sum_probs=44.6
Q ss_pred ccHhhhhheeEEEecCCcccc-----------------------CCCceEEEEEecHHHHHHhcCChhhhHHHHHHhh
Q 000291 843 VSLKDAAVEFLIEYKKPEIIS-----------------------DDEGLVGHIHLNKILLEDLRISMHDILPKCQETL 897 (1714)
Q Consensus 843 vtl~dv~~~i~I~y~~~~~~~-----------------------~~~~wv~~i~Ld~e~L~~~~lt~~~I~~k~~~~~ 897 (1714)
+||++|+..+.|.|+|+...+ ..+||++||+||+++|.+++|+|++|++++.+.+
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 689999999999999998755 1499999999999999999999999998866544
No 43
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=96.22 E-value=0.02 Score=69.24 Aligned_cols=30 Identities=7% Similarity=0.017 Sum_probs=19.5
Q ss_pred CCCCCccccCCCCCCCCCCCCCCCCCCCCC
Q 000291 1227 ESSCDKWENVGSPAAKSFSEWGTEASWGKS 1256 (1714)
Q Consensus 1227 ~~k~~~w~~~~~~~~~~~~~WG~~ssw~~s 1256 (1714)
+.|+++|+.++-......+.|+.+|.|..-
T Consensus 463 g~ktpA~n~pg~~~g~~~~~w~~gs~~~a~ 492 (607)
T COG5164 463 GPKTPALNDPGIDWGDEKDNWYKGSLIHAL 492 (607)
T ss_pred CCCCccccCCCccCCCCCCCCCcccccccc
Confidence 466777776665555666777766666543
No 44
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=94.59 E-value=0.0047 Score=83.31 Aligned_cols=65 Identities=23% Similarity=0.201 Sum_probs=47.7
Q ss_pred hhHHHHHHHhc-eEEEeccccccccCCceeEEEeccccccccCcCCCCceeEEeccccCChhHHHHhhcCC
Q 000291 716 LFKNLMAVLRD-VVICYDGTVRNVCSNSIIQFDYAVNARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDSS 785 (1714)
Q Consensus 716 LqRrLvk~led-l~v~YD~Tvr~~~~~~IiQf~yg~dg~~~~~lv~~GepVG~laaqsigepatq~~L~t~ 785 (1714)
|..++.+.+.. |.-.|+.|...+ ..|++.++-.+ .+++++|||+||++||||||||+|||+|...
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 33444444443 333455665554 56888888777 5789999999999999999999999998653
No 45
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=93.30 E-value=1.1 Score=59.54 Aligned_cols=27 Identities=11% Similarity=-0.023 Sum_probs=17.0
Q ss_pred HHHHHHhhhccccHhhhhheeEEEecCCcc
Q 000291 832 AAYMVKNQLKRVSLKDAAVEFLIEYKKPEI 861 (1714)
Q Consensus 832 ~a~~V~~~le~vtl~dv~~~i~I~y~~~~~ 861 (1714)
.+.+++. ++...|.++.++-.|..+..
T Consensus 452 ~~~eLrK---yF~~GDhVKVi~G~~eG~tG 478 (1024)
T KOG1999|consen 452 PASELRK---YFEPGDHVKVIAGRYEGDTG 478 (1024)
T ss_pred chHhhhh---hccCCCeEEEEeccccCCcc
Confidence 3455544 44567777777777777653
No 46
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=92.48 E-value=3.4 Score=55.34 Aligned_cols=11 Identities=27% Similarity=0.401 Sum_probs=6.3
Q ss_pred cccceeeeecc
Q 000291 993 VLKEHLILLAN 1003 (1714)
Q Consensus 993 V~~rHl~LlAd 1003 (1714)
...+|+.|.+-
T Consensus 626 ck~k~~~~~g~ 636 (1024)
T KOG1999|consen 626 CKEKNLILAGG 636 (1024)
T ss_pred EecCCceeccc
Confidence 45566666554
No 47
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=88.77 E-value=3.2 Score=51.28 Aligned_cols=16 Identities=31% Similarity=0.509 Sum_probs=9.7
Q ss_pred cccccccccccccccc
Q 000291 1110 EELDTGCLGEEVDGLE 1125 (1714)
Q Consensus 1110 ~~~~~~~~~~~~~~~~ 1125 (1714)
+-+-+++++.+++.++
T Consensus 394 ~K~~l~y~~reGe~it 409 (607)
T COG5164 394 EKSRLAYLGREGEGIT 409 (607)
T ss_pred ehhheEEecccccccc
Confidence 3355677777774444
No 48
>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=59.47 E-value=4.4 Score=53.38 Aligned_cols=56 Identities=20% Similarity=0.414 Sum_probs=29.5
Q ss_pred heeeccceEEEeCCCccccccccceeeEecCC-C----e--EEe---cccccCCCCCcccccccccc
Q 000291 338 RRIMDGDTVFINRPPTTHKHSLQALSVYVHDD-H----T--VKI---NPLICGPLSADFDGDCIHLF 394 (1714)
Q Consensus 338 Rhl~dgd~VL~NRqPsLHr~Sima~~~~v~~~-~----t--~rl---n~~vC~pyNADFDGDeMnlH 394 (1714)
..++.| .||+-|.|+||..-|+-++++-.|. + + |-. +|+...-=++|||||+..|-
T Consensus 364 ~~~~~g-~VlV~R~P~~~pgDir~~~av~~p~L~~l~~vIVF~~~G~r~~~~~lsGgDlDGD~~~V~ 429 (579)
T PF05183_consen 364 SQVLEG-DVLVTRNPCLHPGDIRKVKAVDKPELRHLKDVIVFSTKGDRPLPSELSGGDLDGDEYFVC 429 (579)
T ss_dssp EEEEE--EEEEE-SS--SGGGEEEEEE---GGGTT--SEEEE-S-SSS-HHHHTTT--SSS-EEEEE
T ss_pred cceeee-eEEEecCCccCcCceeEEEeeccHHHcccCCEEEeCCCCCCCchHHhcCCCCCCceEEEE
Confidence 356677 8999999999999999999876553 1 1 111 22222223479999998865
No 49
>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=35.17 E-value=43 Score=41.68 Aligned_cols=74 Identities=22% Similarity=0.193 Sum_probs=54.5
Q ss_pred eEEEeCCCccccccccceeeEecCC---CeEEecccccCCCCCccccc-cccccCCC-CHHHHHHHHHhcccccccccC
Q 000291 345 TVFINRPPTTHKHSLQALSVYVHDD---HTVKINPLICGPLSADFDGD-CIHLFYPQ-SLAAKAEVLELFSVEKQLLSS 418 (1714)
Q Consensus 345 ~VL~NRqPsLHr~Sima~~~~v~~~---~t~rln~~vC~pyNADFDGD-eMnlHvPQ-S~eAraEa~~Lm~~~~nilsp 418 (1714)
.+.--|+|.+-.+|-|--+|+.-+. -.+++=.-++..-|+|.||| |.--++|+ +..--+|...-..+..++|.=
T Consensus 212 raw~tRHPniSqlsTq~s~v~~~~~~~~wnvkvGlG~F~Gan~DCDGDKeviT~lP~PNSLidlE~lLY~DP~ysficF 290 (487)
T PF05094_consen 212 RAWTTRHPNISQLSTQVSRVDQNDDYTDWNVKVGLGTFVGANRDCDGDKEVITYLPYPNSLIDLESLLYGDPRYSFICF 290 (487)
T ss_pred eeeecCCCCchhhchhheEeeccccCCCcceeeeeccccCCCCCCCCCceEEEecCCCcchhhHHHHhcCCCcceEEEE
Confidence 4667799999999999999888543 35788888899999999999 66677887 444555555555555555443
No 50
>smart00157 PRP Major prion protein. The prion protein is a major component of scrapie-associated fibrils in Creutzfeldt-Jakob disease, kuru, Gerstmann-Straussler syndrome and bovine spongiform encephalopathy.
Probab=28.38 E-value=2.1e+02 Score=32.30 Aligned_cols=25 Identities=28% Similarity=0.442 Sum_probs=13.9
Q ss_pred cccccccCcchhhhhhhchHHHHHHHHHHhcccCCCC
Q 000291 1567 TRQRLDMFTSEEQDILSDVEPIMRSIRRIMHQSGYND 1603 (1714)
Q Consensus 1567 ~~~~~~~~~~~e~~i~~~~~~~~~~~~~il~~~~y~~ 1603 (1714)
+|.+| .|.+.|++ ++.++-+. ||.+
T Consensus 112 ~rp~~-~F~np~Ee---------ryYne~my--rYpn 136 (217)
T smart00157 112 SRPLI-HFGNDYED---------RYYRENMY--RYPN 136 (217)
T ss_pred CCCcc-ccCChHHH---------HHHHHHHH--hCCC
Confidence 56666 56655544 35566666 5543
No 51
>PHA03396 lef-9 late expression factor 9; Provisional
Probab=27.98 E-value=66 Score=40.43 Aligned_cols=74 Identities=23% Similarity=0.207 Sum_probs=54.2
Q ss_pred eEEEeCCCccccccccceeeEecCCC---eEEecccccCCCCCccccc-cccccCCC-CHHHHHHHHHhcccccccccC
Q 000291 345 TVFINRPPTTHKHSLQALSVYVHDDH---TVKINPLICGPLSADFDGD-CIHLFYPQ-SLAAKAEVLELFSVEKQLLSS 418 (1714)
Q Consensus 345 ~VL~NRqPsLHr~Sima~~~~v~~~~---t~rln~~vC~pyNADFDGD-eMnlHvPQ-S~eAraEa~~Lm~~~~nilsp 418 (1714)
.+.--|+|.+-.+|-|--+|+.-+.- -+++=.-+...-|+|.||| |.--++|+ +..--+|...-..+..++|.=
T Consensus 215 raw~tRHPnisqlstq~s~v~~~~~~~~wNvkvGlG~F~GanrDCDGDKeviT~lP~PNsLidlE~lLY~DP~y~ficF 293 (493)
T PHA03396 215 RAWTTRHPNISQLSTQVSRVDQNDDYTDWNVKVGLGTFPGANRDCDGDKEVITFLPYPNSLIDLECLLYGDPRYSFICF 293 (493)
T ss_pred EEeecCCCCchhhchhheEeeccccccccceeeeeccccCCCCCCCCCceEEEecCCCcchhhHHHHhcCCCcceEEEE
Confidence 46678999999999999888875432 2666667788999999999 66778888 555556666555555555443
No 52
>PF07023 DUF1315: Protein of unknown function (DUF1315); InterPro: IPR009749 This family consists of several bacterial proteins of around 90 residues in length. The function of this family is unknown.
Probab=20.07 E-value=99 Score=31.29 Aligned_cols=47 Identities=15% Similarity=0.368 Sum_probs=37.4
Q ss_pred HHHHHHHHHhcccCCCCCCccCCcchhhHHHHHhc---c--CCCccccccCC
Q 000291 1587 PIMRSIRRIMHQSGYNDGDRLSADDKSFIFDNVFN---Y--HPDKAMKMGAG 1633 (1714)
Q Consensus 1587 ~~~~~~~~il~~~~y~~g~~l~~~d~~~~l~~ll~---~--Hp~~~~Kig~g 1633 (1714)
.+..-|+.-+..++|+||.+|+++....-|.+++. . +|+-+..||.|
T Consensus 11 evY~rL~~AVElGKWpDG~~LT~eQre~~mQaVm~yq~~~n~~~e~~ti~~~ 62 (93)
T PF07023_consen 11 EVYERLKQAVELGKWPDGRALTPEQRESCMQAVMLYQARHNLPEEHRTIGAD 62 (93)
T ss_pred HHHHHHHHHHHhCcCCCCCCCCHHHHHHHHHHHHHHHHHcCCCHHHcccCCC
Confidence 46677788888899999999999998888887775 3 47777788743
Done!