Query psy13846
Match_columns 1423
No_of_seqs 469 out of 2805
Neff 6.6
Searched_HMMs 46136
Date Fri Aug 16 21:55:49 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13846.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13846hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0261|consensus 100.0 3E-223 7E-228 1951.6 48.8 1001 76-1418 10-1384(1386)
2 PRK14977 bifunctional DNA-dire 100.0 1E-191 3E-196 1851.7 58.3 880 77-1398 7-1318(1321)
3 KOG0262|consensus 100.0 7E-189 1E-193 1696.8 45.0 986 79-1399 13-1638(1640)
4 KOG0260|consensus 100.0 1E-179 3E-184 1608.1 38.5 996 76-1401 12-1424(1605)
5 TIGR02390 RNA_pol_rpoA1 DNA-di 100.0 2E-128 4E-133 1238.2 31.9 533 77-682 2-852 (868)
6 PRK08566 DNA-directed RNA poly 100.0 4E-128 8E-133 1239.0 30.1 534 76-681 6-856 (882)
7 TIGR02386 rpoC_TIGR DNA-direct 100.0 3E-125 6E-130 1198.3 33.7 476 83-668 2-770 (1140)
8 PRK00566 DNA-directed RNA poly 100.0 2E-123 5E-128 1181.3 33.4 481 78-668 6-779 (1156)
9 PRK14906 DNA-directed RNA poly 100.0 1E-112 2E-117 1079.1 31.0 272 341-667 495-877 (1460)
10 PRK14844 bifunctional DNA-dire 100.0 3E-111 6E-116 1101.3 31.2 278 341-667 1850-2232(2836)
11 PRK09603 bifunctional DNA-dire 100.0 2E-109 4E-114 1088.6 36.0 264 341-667 1806-2176(2890)
12 KOG0261|consensus 100.0 1E-110 2E-115 994.1 9.4 759 11-999 509-1300(1386)
13 COG0086 RpoC DNA-directed RNA 100.0 8.8E-84 1.9E-88 812.2 17.1 497 79-674 4-774 (808)
14 KOG0260|consensus 100.0 8.1E-75 1.7E-79 701.1 10.3 796 12-999 486-1358(1605)
15 TIGR02389 RNA_pol_rpoA2 DNA-di 100.0 2.6E-72 5.6E-77 651.6 23.6 294 1086-1396 17-367 (367)
16 cd02584 RNAP_II_Rpb1_C Largest 100.0 9.9E-71 2.1E-75 647.7 27.1 369 690-1396 19-410 (410)
17 PRK14897 unknown domain/DNA-di 100.0 1E-70 2.2E-75 648.3 21.7 300 1084-1399 154-506 (509)
18 cd06528 RNAP_A'' A'' subunit o 100.0 7.8E-70 1.7E-74 632.1 21.6 296 1083-1396 11-362 (363)
19 PRK04309 DNA-directed RNA poly 100.0 2E-69 4.3E-74 632.8 24.6 294 1086-1399 33-382 (383)
20 cd02736 RNAP_III_Rpc1_C Larges 100.0 3.4E-68 7.4E-73 604.1 22.6 170 1220-1391 131-300 (300)
21 cd02735 RNAP_I_Rpa1_C Largest 100.0 4E-66 8.7E-71 591.9 22.6 177 1217-1394 132-309 (309)
22 KOG0262|consensus 100.0 3.9E-63 8.4E-68 602.7 10.6 782 8-999 609-1575(1640)
23 PRK14977 bifunctional DNA-dire 100.0 3.1E-60 6.8E-65 620.3 15.0 370 12-471 486-893 (1321)
24 cd02737 RNAP_IV_NRPD1_C Larges 100.0 1.2E-57 2.7E-62 531.4 15.0 177 1219-1395 174-381 (381)
25 PRK14898 DNA-directed RNA poly 100.0 1.6E-54 3.5E-59 555.8 25.7 182 1218-1399 671-852 (858)
26 TIGR02389 RNA_pol_rpoA2 DNA-di 100.0 1.3E-52 2.9E-57 487.2 14.6 269 690-999 36-306 (367)
27 TIGR02388 rpoC2_cyan DNA-direc 100.0 1E-52 2.2E-57 534.3 14.2 111 1279-1391 1057-1223(1227)
28 PF04998 RNA_pol_Rpb1_5: RNA p 100.0 1.6E-53 3.5E-58 489.1 2.7 252 622-999 1-263 (277)
29 PRK14897 unknown domain/DNA-di 100.0 8.2E-51 1.8E-55 479.9 13.6 300 652-999 141-442 (509)
30 cd06528 RNAP_A'' A'' subunit o 100.0 2.5E-50 5.3E-55 469.1 14.5 268 690-999 32-301 (363)
31 PRK04309 DNA-directed RNA poly 100.0 7.1E-50 1.5E-54 468.2 14.5 266 690-999 51-318 (383)
32 PRK02597 rpoC2 DNA-directed RN 100.0 1.4E-49 3E-54 509.7 10.8 113 1279-1393 1058-1226(1331)
33 CHL00117 rpoC2 RNA polymerase 100.0 2.4E-48 5.3E-53 504.1 13.1 108 1288-1397 1180-1324(1364)
34 TIGR02386 rpoC_TIGR DNA-direct 100.0 1.6E-48 3.5E-53 497.3 11.2 627 10-1054 453-1102(1140)
35 PRK02625 rpoC1 DNA-directed RN 100.0 1.3E-47 2.7E-52 459.8 16.9 103 341-457 425-527 (627)
36 TIGR02387 rpoC1_cyan DNA-direc 100.0 7.9E-48 1.7E-52 461.0 10.9 102 341-456 418-519 (619)
37 PRK00566 DNA-directed RNA poly 100.0 6.6E-47 1.4E-51 483.1 10.7 620 10-1052 461-1102(1156)
38 CHL00018 rpoC1 RNA polymerase 100.0 2.4E-46 5.3E-51 453.1 14.9 103 341-457 446-548 (663)
39 PRK14906 DNA-directed RNA poly 100.0 1.2E-43 2.6E-48 451.6 11.3 617 11-1052 550-1201(1460)
40 cd00630 RNAP_largest_subunit_C 100.0 7.4E-44 1.6E-48 369.4 6.1 110 1281-1390 49-158 (158)
41 cd02655 RNAP_beta'_C Largest s 100.0 1.4E-42 3.1E-47 372.4 9.8 109 1280-1390 54-204 (204)
42 PF04997 RNA_pol_Rpb1_1: RNA p 100.0 2.4E-41 5.2E-46 397.2 5.6 249 77-339 2-252 (337)
43 PRK14844 bifunctional DNA-dire 100.0 2E-40 4.3E-45 437.1 12.4 114 933-1046 2625-2745(2836)
44 PRK09603 bifunctional DNA-dire 100.0 9.9E-40 2.1E-44 432.2 8.6 111 936-1046 2717-2834(2890)
45 cd02737 RNAP_IV_NRPD1_C Larges 100.0 2.8E-37 6E-42 360.9 10.4 265 698-999 1-315 (381)
46 smart00663 RPOLA_N RNA polymer 100.0 2.1E-36 4.5E-41 343.8 9.5 95 341-449 201-295 (295)
47 TIGR02390 RNA_pol_rpoA1 DNA-di 100.0 9.6E-37 2.1E-41 392.5 4.4 361 12-471 466-852 (868)
48 PF04998 RNA_pol_Rpb1_5: RNA p 100.0 1.3E-36 2.8E-41 349.2 4.8 99 1250-1348 177-276 (277)
49 PRK08566 DNA-directed RNA poly 100.0 2.5E-36 5.4E-41 389.8 4.3 363 11-471 469-857 (882)
50 PF00623 RNA_pol_Rpb1_2: RNA p 99.9 7.3E-26 1.6E-30 238.6 3.6 66 340-405 96-161 (166)
51 cd02736 RNAP_III_Rpc1_C Larges 99.9 4.1E-24 8.8E-29 244.1 9.2 243 690-999 2-244 (300)
52 cd02584 RNAP_II_Rpb1_C Largest 99.9 1.4E-23 3.1E-28 248.6 9.0 176 824-999 153-349 (410)
53 cd02655 RNAP_beta'_C Largest s 99.9 1.9E-23 4.2E-28 225.0 7.3 109 944-1054 54-171 (204)
54 PF04983 RNA_pol_Rpb1_3: RNA p 99.9 2.3E-23 5.1E-28 220.3 -0.1 158 427-608 1-158 (158)
55 cd02735 RNAP_I_Rpa1_C Largest 99.8 1E-21 2.3E-26 226.1 7.5 247 690-999 2-251 (309)
56 PRK14898 DNA-directed RNA poly 99.8 5.9E-21 1.3E-25 246.7 9.6 246 714-999 541-788 (858)
57 cd00630 RNAP_largest_subunit_C 99.8 8E-21 1.7E-25 197.8 5.5 55 945-999 49-103 (158)
58 COG0086 RpoC DNA-directed RNA 99.7 3.8E-20 8.1E-25 235.7 -8.2 120 311-469 668-787 (808)
59 TIGR02388 rpoC2_cyan DNA-direc 99.5 4.3E-15 9.4E-20 191.9 2.3 192 167-446 13-208 (1227)
60 CHL00117 rpoC2 RNA polymerase 99.5 1.5E-14 3.3E-19 190.5 2.0 194 167-447 20-216 (1364)
61 PF04983 RNA_pol_Rpb1_3: RNA p 99.1 5.7E-12 1.2E-16 133.6 -5.0 146 28-214 1-156 (158)
62 PRK02597 rpoC2 DNA-directed RN 98.9 1.2E-09 2.6E-14 143.5 8.7 118 937-1056 1052-1192(1331)
63 PRK02625 rpoC1 DNA-directed RN 98.2 5.5E-07 1.2E-11 110.8 3.7 49 10-58 479-527 (627)
64 TIGR02387 rpoC1_cyan DNA-direc 98.2 5.5E-07 1.2E-11 110.7 3.3 49 10-58 472-520 (619)
65 CHL00018 rpoC1 RNA polymerase 98.2 8.1E-07 1.8E-11 110.5 3.6 49 10-58 500-548 (663)
66 PF05000 RNA_pol_Rpb1_4: RNA p 91.1 0.024 5.3E-07 56.5 -2.9 62 301-386 47-108 (108)
67 PF04992 RNA_pol_Rpb1_6: RNA p 87.9 0.14 3E-06 56.2 -0.4 88 1000-1113 87-187 (187)
68 PF04990 RNA_pol_Rpb1_7: RNA p 57.7 2.9 6.2E-05 43.6 -0.5 53 806-858 1-81 (135)
69 PF04990 RNA_pol_Rpb1_7: RNA p 44.8 21 0.00045 37.3 3.3 86 1146-1233 5-135 (135)
70 PF14952 zf-tcix: Putative tre 41.0 14 0.0003 30.7 1.1 14 218-231 9-22 (44)
71 COG3688 Predicted RNA-binding 39.3 38 0.00081 36.1 4.1 44 1255-1310 5-48 (173)
72 PF05183 RdRP: RNA dependent R 25.6 35 0.00075 44.3 1.6 50 344-393 370-429 (579)
No 1
>KOG0261|consensus
Probab=100.00 E-value=3.2e-223 Score=1951.60 Aligned_cols=1001 Identities=53% Similarity=0.880 Sum_probs=909.2
Q ss_pred ccceeeeEEEecCCHHHHhhcceeeeecCcccccCCCCC-CcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEcc
Q psy13846 76 KVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRT-PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLP 154 (1423)
Q Consensus 76 ~~~i~~~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~g~-P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~ 154 (1423)
+.+|.. |+|++.||+||++.+++||.+..+|+ ...++ |.++|++|||||+++++..|+|||++..+|+|||||+.|+
T Consensus 10 ~kki~~-i~F~~~s~~ei~~~a~v~v~~~~LY~-~~~~~~P~~~G~LD~rMGvs~K~~~C~TCg~~la~C~GHfGy~~L~ 87 (1386)
T KOG0261|consen 10 PKKIKH-IQFSILSPEEIRQQAEVEVSSKDLYD-ISTQRAPLPNGPLDPRMGVSNKKDKCATCGEGLADCIGHFGYLKLA 87 (1386)
T ss_pred cceeee-EeeccCCHHHHHhcceEEeeccchhh-hhcccCCCcCCCcCcccCCCCCCCccchhccchhhcccccceEeec
Confidence 467889 99999999999999999999999994 22233 9999999999999999999999999999999999999999
Q ss_pred CceeEEeeeccHHHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCcee
Q psy13846 155 LPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVK 234 (1423)
Q Consensus 155 ~PV~h~gffd~v~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~ir 234 (1423)
+||||+|||+.+.+||+|+|+. |+.+|+++++++.|+.++++|..+++.++++.++|.+.|++..+|.|||+.||.|+
T Consensus 88 LPVFhiGyfk~ti~iLq~ICK~--Cs~ilL~~~~k~~fl~~lr~p~~~~l~k~~l~kri~~~CkK~~~C~hCg~~NG~VK 165 (1386)
T KOG0261|consen 88 LPVFHIGYFKATIQILQCICKN--CSSILLSEEDKRQFLKKLRNPGLDNLRKKALLKRIVAKCKKVNTCSHCGALNGTVK 165 (1386)
T ss_pred ceeeeehhHHHHHHHHHHHHHh--hhhhhcCHHHHHHHHHHhhCCCCChHHHHHHHHHHHHHhhccccccccCCcCceee
Confidence 9999999999999999999999 99999999999999999999999999999999999999999999999999999999
Q ss_pred ec-CcceehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHHHhhccCCCcccccccccCCC
Q psy13846 235 KC-GLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELS 313 (1423)
Q Consensus 235 k~-~~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~eiLe~I~~~d~~lL~m~~~~a 313 (1423)
|. +.++|.|+.++...+ .++..+.+..+|+.+...+++++.++. ...+.|+|..|+++|++|.+.|+++|+|++..+
T Consensus 166 K~~~~lkIiHd~~~~~~k-~~~~~~~~~~~~~~~~~~n~e~~~~~~-~~~~~LnPl~vLnLFk~i~~~D~eLLg~~~~~~ 243 (1386)
T KOG0261|consen 166 KAAALLKIIHDRFKLVKK-SDPLVTNERGEFKTAISHNKELEGHLS-SCCEELNPLVVLNLFKQIKEDDCELLGMDSEEG 243 (1386)
T ss_pred ccccceeEeeehhhcccc-ccchhhhhHHHHHHHhhcCcchHhHHH-HHHhhcChHHHHHHHhhCCccccceeeeccCcC
Confidence 94 558999998754443 577777888999999999999998886 567889999999999999999999999999889
Q ss_pred CCcceEEEEecCCCCCCCCcEEcCCCC-----------------------------------------------------
Q psy13846 314 KPSDLILTRLLVPPNCIRPSVISDLKS----------------------------------------------------- 340 (1423)
Q Consensus 314 rPe~liLt~lpVPP~~vRPsv~~g~~~----------------------------------------------------- 340 (1423)
||+.++|++|||||.|+|||+++++..
T Consensus 244 ~P~~Li~t~~~vPP~cIRPSV~~~~k~gtnEDDlT~KltEIi~tn~vik~~~~~g~~~~~imE~Wd~lQl~~AlyINSEl 323 (1386)
T KOG0261|consen 244 RPENLIITRVPVPPVCIRPSVMSEDKAGTNEDDLTMKLTEIILTNDVIKKHLSKGTPINLIMEDWDFLQLQVALYINSEL 323 (1386)
T ss_pred CchheEEEeccCCccccccceeecCCCCCCccchhhhhhhhhhHHHHHHHHhhcCCCchhhhhhhHHHHHHHHHhhcccC
Confidence 999999999999999999999998842
Q ss_pred --------------------------------------------------------------------------------
Q psy13846 341 -------------------------------------------------------------------------------- 340 (1423)
Q Consensus 341 -------------------------------------------------------------------------------- 340 (1423)
T Consensus 324 ~g~~~~~~p~kp~RGf~QRLKGKqGRFRgNLSGKRVDFSGRTVISPDPNL~IdeVgVP~rvAkiLTfpE~Vt~~Ni~klr 403 (1386)
T KOG0261|consen 324 PGIPINMAPKKPTRGFVQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDEVGVPIRVAKILTFPERVTRANIRKLR 403 (1386)
T ss_pred CCCCCCCCCCCchHHHHHHhcccCCceeccccCceeeccCceeeCCCCCcceeeccchHHHHHHhcchhhccHHHHHHHH
Confidence
Q ss_pred --------------------------------------------------CCeEEEEecCccccccccceeeeEEecCCc
Q psy13846 341 --------------------------------------------------DNDVVLFNRQPSLHKLSIMAHRAKVLPHRT 370 (1423)
Q Consensus 341 --------------------------------------------------~~d~Vl~nRqPsLHk~Simah~~~~~~~~t 370 (1423)
+||+|||||||||||+|||+|++|+.||+|
T Consensus 404 ~lV~NGP~vhPGANyv~~r~~~~kr~L~yg~R~kiA~eLk~GdvVERHL~DgDvVLFNRQPSLHkmSIM~H~akV~p~RT 483 (1386)
T KOG0261|consen 404 QLVRNGPNVHPGANYVVQRGEGFKRFLKYGNRDKIADELKIGDVVERHLMDGDVVLFNRQPSLHKMSIMSHRAKVMPWRT 483 (1386)
T ss_pred HHHhcCCCCCCCcchhhhcccchhhHhhcCcHHHHHHhhccchHHHhhcccCCEEEEcCCchHHHHHHHHHHhhcccCce
Confidence 999999999999999999999999999999
Q ss_pred eeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEe
Q psy13846 371 FRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYL 450 (1423)
Q Consensus 371 ir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~ 450 (1423)
||||+|+|+||||||||||||+||||+|||||||. .||++.+|+++|++|+|+|+++|||++|+|+
T Consensus 484 fRFNEcvCtPYNADFDGDEMNlHvPQTEEAraEA~--------------~LMgvknNlvTPr~GEpiiAAtQDFiTg~YL 549 (1386)
T KOG0261|consen 484 FRFNECVCTPYNADFDGDEMNLHVPQTEEARAEAL--------------VLMGVKNNLVTPRNGEPIIAATQDFITGGYL 549 (1386)
T ss_pred eeccccccCCcCCCCCcccccccCCchHHHHHHHH--------------HHhccccccccCCCCCceeehhhhhhhccee
Confidence 99999999999999999999999999999999999 9999999999999999999999999999999
Q ss_pred ecccccCCCHHHHHHHHHhhccCCccccceEeeeeccccCCceeecceeeeecceeeeecccCCCCcccccceeeccccc
Q psy13846 451 LTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAY 530 (1423)
Q Consensus 451 ~t~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~kp~~~wtGKqi~s~il~~~~~~~~~~~~~~~~~~~ 530 (1423)
+|.+|+|+++.++.+++.++. +...+| .+|||||+||..||||||+|+.+++|+...++..|+..+++.|
T Consensus 550 lt~KDtF~dRa~~~ql~s~~~----d~~~~i------~lppPaI~KP~~LwTGKQ~fsvlirpn~~s~v~~Nl~~k~k~~ 619 (1386)
T KOG0261|consen 550 LTHKDTFLDRAEFSQLCSYMS----DAMTHI------DLPPPAILKPVELWTGKQLFSVLIRPNDDSPVRVNLDAKNKNF 619 (1386)
T ss_pred eecccccccHHHHHHHHHHHh----cccccc------CCCChhhcCceeeeccCEEEEEEeccCCCCceEEeecccccee
Confidence 999999999999999999886 444556 8999999999999999999999999999999999999888887
Q ss_pred cc----CcccccCCcEEEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceecC
Q psy13846 531 TA----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIG 606 (1423)
Q Consensus 531 ~~----~~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~ 606 (1423)
+. +.++|++|++|+|+|+++++|++||+.+|++++.++++.+.++||+.+|+..|+++.++..+||.++||||||+
T Consensus 620 ~~~~~k~~~mc~nDg~v~irns~l~sG~ldKs~lG~g~k~~lfy~llrDyg~~aAa~am~rlaklc~r~lgnrGFSIGi~ 699 (1386)
T KOG0261|consen 620 SLVKGKSFEMCPNDGYVIIRNSELISGVLDKSTLGSGKKDSLFYILLRDYGSMAAADAMNRLAKLCARFLGNRGFSIGID 699 (1386)
T ss_pred ecccCCCcccCCCCCeEEEecchhhhcccccccccCCCccceEeeehhhcchHHHHHHHHHHHHhhhhhccccccccccC
Confidence 43 56899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCc--------------------------------------------------------------------------
Q psy13846 607 DVTPGQ-------------------------------------------------------------------------- 612 (1423)
Q Consensus 607 D~~~~~-------------------------------------------------------------------------- 612 (1423)
|+.|.+
T Consensus 700 DVqPg~~L~~~k~~lv~~gY~kc~~~I~e~~kG~L~~qpg~~~eetLEa~I~~~Ls~IRe~~G~~C~~eL~~~NsPliMa 779 (1386)
T KOG0261|consen 700 DVQPGEILSQEKEELVNRGYAKCDEKIEEYNKGKLQLQPGCNEEETLEAEILSELSTIREEAGKICIRELHPRNSPLIMA 779 (1386)
T ss_pred CCCccHHHHHHHHHHHHhHHHHHHHHHHHHhccccccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccChHHHH
Confidence 999876
Q ss_pred --------------------------------------------------cccccccccCCCceeeeeecccccccchhc
Q psy13846 613 --------------------------------------------------GFVQNSFFSGLTPTEFFFHTMGGREGLVDT 642 (1423)
Q Consensus 613 --------------------------------------------------GfI~~sf~~GL~p~Efffh~maGReGLiDT 642 (1423)
|||.|||++||+|.|||||+||||||||||
T Consensus 780 ~CGSKGS~INiSQMvACVGQQ~ISG~RvPdGf~dRsLPHF~r~Sk~P~aKGFV~NSFySGLTptEFfFHtm~GREGLVDT 859 (1386)
T KOG0261|consen 780 LCGSKGSKINISQMVACVGQQIISGHRVPDGFEDRSLPHFERHSKTPAAKGFVANSFYSGLTPTEFFFHTMSGREGLVDT 859 (1386)
T ss_pred HhcCCCCcccHHHHHHHhhhhhhcCCcCCCccccccCccccccCCCccccchhhhhcccCCCchhhheeecccccchhhh
Confidence 999999999999999999999999999999
Q ss_pred ccccCCCCcchHHHHHHHhhhhhcccceeeccccCCCccCCCcchheecCCCcccchhHHHHhhhcCCCCCCccccccCC
Q psy13846 643 AVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDN 722 (1423)
Q Consensus 643 AvKTa~sGYlqRrLvk~ledl~v~yD~tVR~s~yG~~~~~~~~~~~~~~~~~~~~g~~vg~i~aqsige~~tq~tL~~~~ 722 (1423)
|||||+||||||||||+|||+.++||+|||||. +
T Consensus 860 AVKTAETGYMqRRLmK~LEDL~~~YDgTVR~s~-------~--------------------------------------- 893 (1386)
T KOG0261|consen 860 AVKTAETGYMQRRLMKSLEDLSVQYDGTVRNSN-------G--------------------------------------- 893 (1386)
T ss_pred hhhhhhhhhHHHHHHHHHHHHHHhhcCceecCC-------C---------------------------------------
Confidence 999999999999999999999999999999761 0
Q ss_pred CCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhHHHHhhhcCCCCceeeeecccCChHHHHHHHhhh
Q psy13846 723 PEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGR 802 (1423)
Q Consensus 723 ~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlkEIinaSk~ikTPiitv~L~~~~~~e~a~~v~~r 802 (1423)
T Consensus 894 -------------------------------------------------------------------------------- 893 (1386)
T KOG0261|consen 894 -------------------------------------------------------------------------------- 893 (1386)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred hcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhhhHHhhhcccccCcccccccccccccCCCCccccch
Q psy13846 803 LERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNS 882 (1423)
Q Consensus 803 ie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I~~~i~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~ 882 (1423)
+++|+
T Consensus 894 -------~vvqF-------------------------------------------------------------------- 898 (1386)
T KOG0261|consen 894 -------DVVQF-------------------------------------------------------------------- 898 (1386)
T ss_pred -------cEEEE--------------------------------------------------------------------
Confidence 11111
Q ss_pred hhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCccccccceeecccceeeccCchHHHHHHhchHHHHHHH
Q psy13846 883 KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTI 962 (1423)
Q Consensus 883 ~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~nL~~vl~~~gvD~~~t~SN~i~eV~~~LGIEAAR~~I 962 (1423)
++|.|+.. +.
T Consensus 899 --------------------------------------------------~YG~DglD----Pa---------------- 908 (1386)
T KOG0261|consen 899 --------------------------------------------------TYGGDGLD----PA---------------- 908 (1386)
T ss_pred --------------------------------------------------eecCCCCC----hh----------------
Confidence 22223322 11
Q ss_pred HHHHHHHHHhcCccccCCchhhHhhhhccccccccCCcchhhHHHHHHHHHhccCCCCCCCCHHHHHHHhhhhcCcchhh
Q psy13846 963 MTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFL 1042 (1423)
Q Consensus 963 i~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~ 1042 (1423)
.|| |...||+|.+.|+++++....+.++.++++++....++.|.. +|.
T Consensus 909 ------~mE-------------------------g~~~pv~f~r~~~~~~~~~~~~~~~~l~~~el~e~~~~~l~~-~f~ 956 (1386)
T KOG0261|consen 909 ------MME-------------------------GKDQPVNFNRVFDHAKAIFPHRHDPPLSSEELDETLEEELLR-KFT 956 (1386)
T ss_pred ------hhc-------------------------CCCCchhHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHH-Hhh
Confidence 233 455788999999999998888899999999999888887765 343
Q ss_pred hhhhHHHHHHHHHHHHHhhhccccccccccC--CchhhhhhhccccccCcccCCCCCChhHHHHHHHHHhhhccCCCCcc
Q psy13846 1043 QDTSENFVRDIKKFLEEFSKKESVTSHQDKV--SQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATA 1120 (1423)
Q Consensus 1043 ~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~s~v~PGea 1120 (1423)
.+...|...+++|+..-.++..+.+...+. ........+.+.+++|++++ + .|++.|+.+|+++.+|||+|
T Consensus 957 -~~~~~F~~~~~~~i~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~t~kql----~--~f~~~~~~ky~~a~~EpGTa 1029 (1386)
T KOG0261|consen 957 -EKGDPFVHELREFIASLSKKIKKLQDKYGDECGPKFCPDLLYQISRLTEKQL----E--KFVERCLDKYMRAKVEPGTA 1029 (1386)
T ss_pred -hhhhHHHHHHHHHHHHHHHHHHHHhhhcccccCCccCccceeeeeeccHHHH----H--HHHHHHHHHHHhhhcCCcch
Confidence 355678888888876544443322221111 11233457888899999988 7 99999999999999999999
Q ss_pred hhhhhhcccCCcccccccccccccc------------------------------------------------------c
Q psy13846 1121 VGALAAQSIGEPGTQMTLKTFHFAG------------------------------------------------------E 1146 (1423)
Q Consensus 1121 VG~iAAQSIGEP~TQmTLnTFH~AG------------------------------------------------------~ 1146 (1423)
||+|||||||||+|||||+|||||| |
T Consensus 1030 vGAi~aQSIGEPGTQMTLKTFHFAGVASMNiTlGVPRIkEIINAsk~ISTPIItA~L~n~~d~~~Ar~VKgRiEKt~L~d 1109 (1386)
T KOG0261|consen 1030 VGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKTISTPIITAELENPHDERSARVVKGRIEKTTLGD 1109 (1386)
T ss_pred hhhhhcccCCCCCceeeeeeeeecceeeeeeccCcchHHHHHhhhcccCccceeeeecCchhHHHHHHHhhhhhhhhHHH
Confidence 9999999999999999999999999 6
Q ss_pred ccceeEEEEccCCcEEEEEEchHHHHHhcccCCHHHHHHHHH---hccccCCceEEecCcEEEEEeCCCC-chhhhHHHH
Q psy13846 1147 VCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIE---RTRGISGHLTVSGHSFLILKPKDSS-KSFNSKMYQ 1222 (1423)
Q Consensus 1147 i~~~i~~~~~~~~~~~~i~l~~~~~~~~~~~i~~~~i~~~i~---~~k~~~~~~~~~~~~~i~i~~~~~~-~~~~~~l~~ 1222 (1423)
|+++|+++|.|+.+++.|++|+++++++++++++++|..+|- +.+.++.++.+.++..+++.+.... .+.++.|+.
T Consensus 1110 v~~yieeV~~p~~~fl~i~vd~~~I~~l~L~i~~~~I~~sI~~s~~~k~~~~~v~v~~~~~~~v~~~~~~~~S~~~~lq~ 1189 (1386)
T KOG0261|consen 1110 VCSYIEEVYGPDSCFLLIRVDLKRISLLQLEITIESIAYSILKSPKRKVKPNDVRVVGETTLRVTPVSDTKSSVYYNLQR 1189 (1386)
T ss_pred HHHHHHHHhCCcceEEEEEecHhHHhhhhccccHHHHHHHHhcCCccccCCcceEEecceeEEEeecccccchhhhhHHH
Confidence 788999999999999999999999999999999999999994 4456788898888888888876533 345889999
Q ss_pred HHhccCCcEEcccCCccEEEEecccccceeeEEEEecCccHHHHhhcccccceecccccHHHHHHHhCHHHHHHHHHHHH
Q psy13846 1223 MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEI 1302 (1423)
Q Consensus 1223 l~~~l~~~~v~Gi~~i~r~~i~~~~~~~~~~~~l~teG~nl~~~~~~~~vd~~~~~sN~i~~i~~~lGIEAar~~ii~Ei 1302 (1423)
++..|++++|+|+|.|.|++|+.++. .+.|.|.+||++|++||+.+||+..||+||++.||.++|||||||.+||+||
T Consensus 1190 lk~~L~~Vvv~gip~vnr~vi~~de~--~~~y~L~vEG~gLr~Vm~t~GV~g~~TtsNnv~Ev~~vLGIEAAR~~II~EI 1267 (1386)
T KOG0261|consen 1190 LKRSLPNVVVKGIPEVNRAVINIDEK--RGLYKLLVEGTGLRAVMNTDGVKGRRTTSNNVLEVEKVLGIEAARTTIISEI 1267 (1386)
T ss_pred HHhhCCceEEecCcchhhhheeeccc--CCceEEEEeccchHHHhccCCccccccccCceEEeehhhchHHHHHHHHHHH
Confidence 99999999999999999999988653 2349999999999999999999999999999999999999999999999999
Q ss_pred HHHhhcCCccccCCchhhhhccccceeEEEeeecccccccccchhhhccchhhHHHHHhhcccCCcccccccccceeecc
Q psy13846 1303 KLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGL 1382 (1423)
Q Consensus 1303 ~~v~~~~Gi~v~~rHl~LiaD~Mt~~G~~~~i~r~g~~~~~~S~l~~aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~ 1382 (1423)
..+|++||++||+||++||||+|||+|+++||||+|+++|++|+|+.||||+|.+||++||.+|++|.+.|||||||+|.
T Consensus 1268 ~ytM~~HGmsiD~RHiMLLaDvMTyrGEVlGITRfGl~KM~~SVL~lASFEkT~DhLF~AA~~~k~D~I~GVSEcIIlG~ 1347 (1386)
T KOG0261|consen 1268 GYTMSNHGMSIDPRHIMLLADVMTYRGEVLGITRFGLAKMKDSVLMLASFEKTADHLFDAAAYGKKDAIEGVSECIILGI 1347 (1386)
T ss_pred HHHHHhcCcccCHHHHHHHHHHhhhcceeeeeeehhhHHHHHHHHHHHhhhhhhHHHHHHHHhcCcccccchhhheeccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccceEEEeecCCCCC-CCCcccccCCCcccccc
Q psy13846 1383 PMNVGTGLIKLLQAVPRSE-PVPRTLLFDNPEFHTNT 1418 (1423)
Q Consensus 1383 ~~~~GTG~~~l~~~~~~~~-~~~~~~~~~~~~~~~~~ 1418 (1423)
++++|||.|+|++..+..+ +++++++|+....+++.
T Consensus 1348 pm~iGTG~fkl~~~~~~~~~~~~~~~if~~~~~~~~~ 1384 (1386)
T KOG0261|consen 1348 PMCIGTGIFKLLQRTDDKKVLKPKPPIFSSLNLHLSL 1384 (1386)
T ss_pred ceeccccHHHHHHhcCCcccCCCCCCccccccccccc
Confidence 9999999999999887765 77789999999988765
No 2
>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Probab=100.00 E-value=1.3e-191 Score=1851.74 Aligned_cols=880 Identities=33% Similarity=0.540 Sum_probs=742.9
Q ss_pred cceeeeEEEecCCHHHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccCc
Q psy13846 77 VFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156 (1423)
Q Consensus 77 ~~i~~~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~P 156 (1423)
.+|.+ |+|++||||||+++||++|+++++| |.+|+|++|||||||||+++++..|+|||++..+||||||||+|++|
T Consensus 7 ~~I~~-I~Fg~~S~eeIrk~Sv~~It~~~~~--d~~g~P~~gGl~DprlG~~d~~~~C~TCg~~~~~CpGHFGHIELa~P 83 (1321)
T PRK14977 7 KAIDG-IIFGLISPADARKIGFAEITAPEAY--DEDGLPVQGGLLDGRLGTIEPGQKCLTCGNLAANCPGHFGHIELAEP 83 (1321)
T ss_pred ceece-EEEecCCHHHHHHhCeEEEeccccc--CCCCCcCCCCCCccccCCCCCCCCCCCCCCCCCcCCCeeEEEEccCC
Confidence 56888 9999999999999999999999999 77999999999999999999999999999999999999999999999
Q ss_pred eeEEeeeccHHHHhhhccccccccccccChhhHHHHH--HHhcCCchhHHHH---HHHHHH----HHHHccCCccCCCCC
Q psy13846 157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFR--AKLRNPALSYLVR---KSLKKK----ILETTKKVSVCPHCG 227 (1423)
Q Consensus 157 V~h~gffd~v~~iL~~iC~~~~C~~ll~~~~~~~~~~--~kl~~~~~~~~~~---~~~~~~----i~~~~kk~k~C~~Cg 227 (1423)
|||||||+.++++|+|+|++ ||+|++++++...|. .+..++......+ ..+..+ +...|++.++|||||
T Consensus 84 VfHpgf~k~i~~iLr~iC~~--C~rlll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~C~~C~ 161 (1321)
T PRK14977 84 VIHIAFIDNIKDLLNSTCHK--CAKLKLPQEDLNVFKLIEEAHAAARDIPEKRIDDEIIEEVRDQVKVYAKKAKECPHCG 161 (1321)
T ss_pred ceecccHHHHHHHHHHHHHH--hchhhcCcccHHHHHHHHHHhhhcccchhhhhhHHHHHHHHhhhhhhhccCCcCCCCC
Confidence 99999999999999999999 999999998877663 2222211111111 111122 223488899999999
Q ss_pred CCCCceeecCcceehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHHHhhccCCCcccccc
Q psy13846 228 EINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLL 307 (1423)
Q Consensus 228 ~~~~~irk~~~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~eiLe~I~~~d~~lL~ 307 (1423)
+.+|.+++.+...... . ++ .....|+|.+|+++|++||++|+++|+
T Consensus 162 ~~~~~i~~~~~~~~~~-------~--------------------~~-------~~~~~l~p~~v~~if~~i~~~d~~llg 207 (1321)
T PRK14977 162 APQHELEFEEPTIFIE-------K--------------------TE-------IEEHRLLPIEIRDIFEKIIDDDLELIG 207 (1321)
T ss_pred CCCCeEEEeeceeeee-------c--------------------cc-------ccCcccCHHHHHHHHHhcCHHHHHHhC
Confidence 9999998764221100 0 00 113578999999999999999999999
Q ss_pred cccCCCCCcceEEEEecCCCCCCCCcEEcCCC--C---------------------------------------------
Q psy13846 308 MNAELSKPSDLILTRLLVPPNCIRPSVISDLK--S--------------------------------------------- 340 (1423)
Q Consensus 308 m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~--~--------------------------------------------- 340 (1423)
+++..+||+||||+++||||+|+||++.+++. .
T Consensus 208 ~~~~~~~p~~~il~~lpVpP~~~RP~v~~~~~~~~eddlt~~l~~Ii~~N~~l~~~~~~g~~~~~~~~~~~~LQ~~v~~~ 287 (1321)
T PRK14977 208 FDPKKARPEWAVLQAFLVPPLTARPSIILETGERSEDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTF 287 (1321)
T ss_pred CCCCCCCcceEEEeccccCCCCCcCcEEeCCCcccCCcHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHH
Confidence 99988999999999999999999999999753 1
Q ss_pred --------------------------------------------------------------------------------
Q psy13846 341 -------------------------------------------------------------------------------- 340 (1423)
Q Consensus 341 -------------------------------------------------------------------------------- 340 (1423)
T Consensus 288 ~dn~~~~~~~~~~~~~~rp~k~i~qrLkgKeGrfR~nlmGKRVdfSaRtVIspDP~L~i~EVGvP~~iA~~LT~Pe~Vt~ 367 (1321)
T PRK14977 288 FDNATAGIPQAHHKGSGRPLKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNE 367 (1321)
T ss_pred hcccccCCCccccccCCCchhHHHHHhccccccccccccccccccccceeEeCCCCcccccccCHHHHHHhCCCCEEEch
Confidence
Q ss_pred --------------------------------------------------------------CCeEEEEecCcccccccc
Q psy13846 341 --------------------------------------------------------------DNDVVLFNRQPSLHKLSI 358 (1423)
Q Consensus 341 --------------------------------------------------------------~~d~Vl~nRqPsLHk~Si 358 (1423)
+||+|||||||||||+||
T Consensus 368 ~Ni~~l~~lv~nG~~~~pGA~~i~~~~g~~~~l~~~~~~~~~~~~~~a~~L~~g~iV~Rhl~dGD~VL~NRQPSLHk~Si 447 (1321)
T PRK14977 368 NNIEKMKELVINGPDEFPGANAIRKGDGTKIRLDFLEDKGKDALREAAEQLEIGDIVERHLADGDIVIFNRQPSLHKLSI 447 (1321)
T ss_pred hhHHHHHHHHHcCCcccCCcceEEcCCCceeeehhhhhccchhHHHHHHhcccCcEEEEEeecCcEEEeccCCccccccc
Confidence 889999999999999999
Q ss_pred ceeeeEEecCCceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCcccc
Q psy13846 359 MAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLI 438 (1423)
Q Consensus 359 mah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~ 438 (1423)
|||++|++|++||||||++|+||||||||||||+|+|||++|||||. .||.+.+|++||++|+|++
T Consensus 448 mah~vkvl~~kT~Rln~~vC~pyNADFDGDEMNlHvPQS~eArAEa~--------------~Lm~v~~niisP~~G~Pi~ 513 (1321)
T PRK14977 448 LAHRVKVLPGATFRLHPAVCPPYNADFDGDEMNLHVPQIEDARAEAI--------------ELMGVKDNLISPRTGGPII 513 (1321)
T ss_pred eEEEEEEecCceEEecccccCcccCCcccceeeeecCCCHHHHHHHH--------------HHHhhhhcEecCCCCCeeE
Confidence 99999999999999999999999999999999999999999999999 9999999999999999999
Q ss_pred ccccceEEEEEeecccccCCCHHHHHHHHHhhccCCccccceEeeeeccccCCceee-cceeeeecceeeeecccCCCCc
Q psy13846 439 AATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFV-RTAVIWTGKQIFSLILKPNRDC 517 (1423)
Q Consensus 439 ~~~qD~~~~~~~~t~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~-kp~~~wtGKqi~s~il~~~~~~ 517 (1423)
+++||+|+|+|+||.+|+|++++|+++++++... . ..+|+|||+ ||.++||||||||++||++
T Consensus 514 gliQD~l~g~~lLT~~d~fl~~~e~~~l~~~~~~-----~--------~~lp~PaI~~kp~~lwTGKQi~s~iLp~~--- 577 (1321)
T PRK14977 514 GALQDFITAAYLITKDDALFDKNEASNIAMLAGI-----T--------DPLPEPAIKTKDGPAWTGKQLFSLFLPKD--- 577 (1321)
T ss_pred EeehhhhhhhhhhccCcccCCHHHHHHHHHhCCC-----c--------cccCCCceecCCCCeeeHHHHHHHHcCCC---
Confidence 9999999999999999999999999999997531 1 158999999 9999999999999999875
Q ss_pred ccccceeeccccccc-----CcccccCCcEEEeccccccccccccCCcCC--CCCCchHHHHHHHhCHHHHHHHHHHhhh
Q psy13846 518 PVNANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGS--GGKANVFYILLRDFGEDVAVTAMWRLSR 590 (1423)
Q Consensus 518 ~~~~~~~~~~~~~~~-----~~~~~~~d~~v~i~~~ell~g~ldK~~~g~--~~~~~li~~i~~~~G~~~a~~~l~~l~~ 590 (1423)
+|+..+.+.+.. ...+|++|++|+|+||||++|++||+++|+ +++++++|.+|++||+++|..||+++++
T Consensus 578 ---~n~~~~~~~~~~~~~~~~~~~~~~d~~v~I~~geLl~G~ldK~~~G~~~~~~~~Lih~i~~~yG~~~a~~fL~~l~~ 654 (1321)
T PRK14977 578 ---FNFEGIAKWSAGKAGEAKDPSCLGDGYVLIKEGELISGVIDDNIIGALVEEPESLIDRIAKDYGEAVAIEFLNKILI 654 (1321)
T ss_pred ---CCceecccccccccccccccCCCCcceEEeecCeEEeeecchHhhccccCCCCcHHHHHHHHhCHHHHHHHHHHHHH
Confidence 344433332221 223678899999999999999999999997 4679999999999999999999999999
Q ss_pred hhhHHHhhcCcceecCCCCCCc----------------------------------------------------------
Q psy13846 591 MTSFYLMNRGFSIGIGDVTPGQ---------------------------------------------------------- 612 (1423)
Q Consensus 591 l~~~~L~~~GfsiGi~D~~~~~---------------------------------------------------------- 612 (1423)
++++||+.+|||+|++|+++++
T Consensus 655 l~~~~L~~~GFSigi~D~~~~~~~~~~i~~~i~~~~~~v~~l~~~~~~~~~i~~~~~~~~~~~G~~~~~~~e~~i~~~l~ 734 (1321)
T PRK14977 655 IAKKEILHYGFSNGPGDLIIPDEAKQEIEDDIQGMKDEVSDLIDQRKITRKITIYKGKEELLRGMKEEEALEADIVNELD 734 (1321)
T ss_pred HHHHHHHhCCEEEeeCcEecCHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccchhcCCCCcHHHHHHHHHHHHHH
Confidence 9999999999999999996332
Q ss_pred --------------------------------------------------------------------------------
Q psy13846 613 -------------------------------------------------------------------------------- 612 (1423)
Q Consensus 613 -------------------------------------------------------------------------------- 612 (1423)
T Consensus 735 ~~r~~~~~~~~~~l~~~N~l~~Mv~SGAKGS~~Ni~Qi~~~lGQQ~ve~~~~~~~~G~Ri~~~~~~RtLPhF~~~d~~p~ 814 (1321)
T PRK14977 735 KARDKAGSSANDCIDADNAGKIMAKTGARGSMANLAQIAGALGQQKRKTRIGFVLTGGRLHEGYKDRALSHFQEGDDNPD 814 (1321)
T ss_pred HHHHHHHHHHHHhcCCCCcHHHHhhcccccCHHHHHHHHhccccccccccccccCCCCCCcCCCCCCcCCCCCCCCCCcc
Confidence
Q ss_pred --cccccccccCCCceeeeeecccccccchhcccccCCCCcchHHHHHHHhhhhhcccceeecc-------ccCCCccCC
Q psy13846 613 --GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAA-------FYGQTDCIS 683 (1423)
Q Consensus 613 --GfI~~sf~~GL~p~Efffh~maGReGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~tVR~s-------~yG~~~~~~ 683 (1423)
|||.|||++||+|+|||||||||||||||||||||+||||||||||+|||++|+||+||||+ .||+|+.+.
T Consensus 815 a~GfV~nsFl~GL~P~EfFFHaM~GREGLiDTAVKTA~SGYLQRrLvk~lEDl~v~YD~TVR~s~g~iiQF~YGeDG~d~ 894 (1321)
T PRK14977 815 AHGFVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYFQRRLANALEDIRLEYDETVRDPHGHIIQFKFGEDGIDP 894 (1321)
T ss_pred cccchhhhhcCCCCHHHHHHHhhcccccccccccccCcCchhHHHHHHHhcceEEecCCeEEeCCCCEEEEeecCCCcCH
Confidence 89999999999999999999999999999999999999999999999999999999999998 499987762
Q ss_pred Ccc---------------------------------------------------------------------hheecCCC
Q psy13846 684 GVS---------------------------------------------------------------------ECIIMGLP 694 (1423)
Q Consensus 684 ~~~---------------------------------------------------------------------~~~~~~~~ 694 (1423)
.-. ...|.+++
T Consensus 895 ~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 974 (1321)
T PRK14977 895 QKLDHGEAFNLERIIEKQKIEDRGKGASKDEIEELAKEYTKTFNANLPKLLADAIHGAELKEDELEAICAEGKEGFEKAK 974 (1321)
T ss_pred HHhccCCcccHHHHHHHhhhhccccCCCHHHHHHHHHHHHHhhhhhhHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcc
Confidence 110 01256678
Q ss_pred cccchhHHHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhHHHHhh
Q psy13846 695 MNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINA 774 (1423)
Q Consensus 695 ~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlkEIina 774 (1423)
++|||+||.+||||||||+||||| +|||+||+ +++|+|+ |||||+||+||
T Consensus 975 ~~pGe~VG~iaAQSiGEP~TQmTL----nTFH~AGv-------------~~~nvt~-------------GvpRl~Eii~a 1024 (1321)
T PRK14977 975 VEPGQAIGIISAQSIAEPGTQMTL----RTFHAAGI-------------KAMDVTH-------------GLERFIELVDA 1024 (1321)
T ss_pred cCCcccchhhhhhhccCceeeecc----cccccccc-------------cccCccc-------------CccchHHhhhc
Confidence 999999999999999999999999 99999999 8999999 99999999999
Q ss_pred hcCCCCceeeeecccC--ChHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhhhHHhh
Q psy13846 775 SRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIE 852 (1423)
Q Consensus 775 Sk~ikTPiitv~L~~~--~~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I~~~i~ 852 (1423)
||+|+||+|+++|.++ .+.+.|+.++.+||+++++++++.++..|+++.. ++.+|..
T Consensus 1025 ~k~~~tp~m~~~l~~~~~~~~~~a~~v~~~ie~~~l~~~~~~~~i~~~~~~~--~i~~d~~------------------- 1083 (1321)
T PRK14977 1025 RAKPSTPTMDIYLDDECKEDIEKAIEIARNLKELKVRALIADSAIDNANEIK--LIKPDKR------------------- 1083 (1321)
T ss_pred ccCCCCCeEEEEeCCcccchHHHHHHHHhheeeeEHHHhhhheEeeccCCce--EEecCHH-------------------
Confidence 9999999999999986 4678999999999999999999876544432200 0000000
Q ss_pred hcccccCcccccccccccccCCCCccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCccccccce
Q psy13846 853 RTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMA 932 (1423)
Q Consensus 853 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~nL~~vl~ 932 (1423)
T Consensus 1084 -------------------------------------------------------------------------------- 1083 (1321)
T PRK14977 1084 -------------------------------------------------------------------------------- 1083 (1321)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred eecccceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCCcchhhHHHHHHHH
Q psy13846 933 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDII 1012 (1423)
Q Consensus 933 ~~gvD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~~~~~~~~~~~~~~ 1012 (1423)
.++.++
T Consensus 1084 ------------------------------------~i~~~~-------------------------------------- 1089 (1321)
T PRK14977 1084 ------------------------------------ALENGC-------------------------------------- 1089 (1321)
T ss_pred ------------------------------------HHHhcC--------------------------------------
Confidence 011000
Q ss_pred HhccCCCCCCCCHHHHHHHhhhhcCcchhhhhhhHHHHHHHHHHHHHhhhccccccccccCCchhhhhhhccccccCccc
Q psy13846 1013 AKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGR 1092 (1423)
Q Consensus 1013 ~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1092 (1423)
+....|. +.+.... . . ..
T Consensus 1090 ----------i~~~~i~---------------------~~i~~~~--------------------------~-~----~~ 1107 (1321)
T PRK14977 1090 ----------IPMERFA---------------------EIEAALA--------------------------K-G----KK 1107 (1321)
T ss_pred ----------CCHHHHH---------------------HHHHHhh--------------------------c-C----Cc
Confidence 0000000 0000000 0 0 00
Q ss_pred CCCCCChhHHHHHHHHHhhhccCCCCcchhhhhhcccCCcccccccccccccccccceeEEEEccCCcEEEEEEchHHHH
Q psy13846 1093 ESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEVCEYIEEVFVPDDSFILIKLDMDRIR 1172 (1423)
Q Consensus 1093 ~~~~~~~~~~~~~~~~~y~~s~v~PGeaVG~iAAQSIGEP~TQmTLnTFH~AG~i~~~i~~~~~~~~~~~~i~l~~~~~~ 1172 (1423)
+ .+..
T Consensus 1108 ~---------------------------------------------------------------------~~~~------ 1112 (1321)
T PRK14977 1108 F---------------------------------------------------------------------EMEL------ 1112 (1321)
T ss_pred e---------------------------------------------------------------------EEee------
Confidence 0 0000
Q ss_pred HhcccCCHHHHHHHHHhccccCCceEEecCcEEEEEeCC--CCchhhhHHHHHHhccCCcEEcccCCccEEEEecccccc
Q psy13846 1173 LLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKD--SSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEG 1250 (1423)
Q Consensus 1173 ~~~~~i~~~~i~~~i~~~k~~~~~~~~~~~~~i~i~~~~--~~~~~~~~l~~l~~~l~~~~v~Gi~~i~r~~i~~~~~~~ 1250 (1423)
+++.+.+.+.+ ..+...+.|+.++..+.+++|+|+|||+|++|...+..+
T Consensus 1113 ----------------------------~~~~i~~~~~~~~~~~~~~~~l~~l~~~l~~~~i~Gi~~I~r~~i~~~~~~~ 1164 (1321)
T PRK14977 1113 ----------------------------EDDLIILDLVEAADRDKPLATLIAIRNKILDKPVKGVPDIERAWVELVEKDG 1164 (1321)
T ss_pred ----------------------------cCCEEEEecCcccccchHHHHHHHHHHhcCCcEEecCCCceEEEEEeeccCC
Confidence 00112222211 111235678889998999999999999999886432223
Q ss_pred eeeEEEEecCccHHHHhhcccccceecccccHHHHHHHhCHHHHHHHHHHHHHHHhhcCCccccCCchhhhhccccceeE
Q psy13846 1251 VTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGE 1330 (1423)
Q Consensus 1251 ~~~~~l~teG~nl~~~~~~~~vd~~~~~sN~i~~i~~~lGIEAar~~ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~G~ 1330 (1423)
.++|+|.|||+||.++|.+++||+.||+||||+||+++|||||||++|++||++||+.||++||+|||+||||+||++|.
T Consensus 1165 ~~e~~l~teG~nl~~vl~~~~Vd~~rt~sN~i~ei~~~lGIEAaR~~ii~Ei~~v~~~~G~~V~~rHi~LlaD~MT~~G~ 1244 (1321)
T PRK14977 1165 RDEWIIQTSGSNLAAVLEMKCIDIANTITNDCFEIAGTLGIEAARNAIFNELASILEDQGLEVDNRYIMLVADIMCSRGT 1244 (1321)
T ss_pred CeeEEEEecCcCHHHHhCCCCCcccccEECCHHHHHHhhhHHHHHHHHHHHHHHHHHHcCCccCHHHHHHHHHHHccCce
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeee------cccccccccchhhhccchhhHHHHHhhcccCCcccccccccceeeccccccccceEEEeecCC
Q psy13846 1331 VLGIT------RHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 1398 (1423)
Q Consensus 1331 ~~~i~------r~g~~~~~~S~l~~aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~~~~~GTG~~~l~~~~~ 1398 (1423)
++++| ||||+++++|||++||||+|+++|++||++|+.|+++|||||||+|+++|+|||+|+|+++..
T Consensus 1245 ~~~i~~~~~~~R~Gi~~~~~s~l~~asFE~t~~~L~~AA~~g~~D~l~gvsenii~G~~~~~GTG~~~Ll~~~~ 1318 (1321)
T PRK14977 1245 IEAIGLQAAGVRHGFAGEKDSPLAKAAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIPIGSGKVDLLMDFS 1318 (1321)
T ss_pred EEeccccccccccccccCCCCHHHhcCHHHHHHHHHHHHHhcCcCccCChHHhhhcCCCccCccceEEEEeccc
Confidence 99999 999999899999999999999999999999999999999999999999999999999999854
No 3
>KOG0262|consensus
Probab=100.00 E-value=6.6e-189 Score=1696.77 Aligned_cols=986 Identities=32% Similarity=0.487 Sum_probs=749.4
Q ss_pred eeeeEEEecCCHHHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccCcee
Q psy13846 79 FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVF 158 (1423)
Q Consensus 79 i~~~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~PV~ 158 (1423)
... ++|++|+++||+++||++|++|.+| |+.|||++|||||++|||-+....|.||++....||||||||+|+.|||
T Consensus 13 ~~~-v~Fg~yt~~ei~klSv~kIt~p~~~--D~lGhPi~GGLYDl~LGp~~~~~~C~TC~~~~~~CPGH~GHIeL~~pvy 89 (1640)
T KOG0262|consen 13 QPS-VSFGSYTDQEIRKLSVKKITNPITF--DNLGHPIPGGLYDLALGPLDNSDVCSTCNQDELNCPGHMGHIELPVPVY 89 (1640)
T ss_pred ccc-eeeeccCHHHHhhcceeEecCceee--cccCCCCCCcccccccCCccchhhhhhhcchhhcCCCccCeeeeccccc
Confidence 445 9999999999999999999999999 8899999999999999999888899999999999999999999999999
Q ss_pred EEeeeccHHHHhhhccccccccccccChhhHHHHHHHhcCCc--------------------------------------
Q psy13846 159 HIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA-------------------------------------- 200 (1423)
Q Consensus 159 h~gffd~v~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~-------------------------------------- 200 (1423)
||.||+.++++|++.|.+ ||+|.+.+.+++.++++++...
T Consensus 90 nPlfF~~ly~lLr~sCl~--Chhf~~k~~~v~~~~cqLrll~~G~i~ea~~Le~i~~~~~~d~~d~~~~~~k~~~~~~v~ 167 (1640)
T KOG0262|consen 90 NPLFFDFLYNLLRGSCLF--CHHFRCKNVDVHILFCQLRLLEYGLIEEAEDLESITSETVEDNEDESLNEIKSCRAQYVT 167 (1640)
T ss_pred CHHHHHHHHHHHHHHHHh--hhhcccCcHHHHHHHHHHHHHHhchHHHHHHHHHhhhhhhccCcchhHHHHHhhhhhhcc
Confidence 999999999999999999 9999999999988888877410
Q ss_pred ----------------hhHHHHHHHHHHHHHHccCCccCCCCCCCCCceeecCcceehhhhhcccccc----hhhHHHHH
Q psy13846 201 ----------------LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKK----KDAIVEDL 260 (1423)
Q Consensus 201 ----------------~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk~~~~ki~~e~~~~~~~~----~~~~~~~~ 260 (1423)
.....++.+..+|++.....++|++|+..+|.+||++..+++......+... ......+.
T Consensus 168 ~~i~~~~~~~~~~~t~~~~~~~~~lv~~f~k~~l~~kkC~~C~~~~p~~rk~~~~kv~~~~~~~~~~~~~~~~~~i~~~~ 247 (1640)
T KOG0262|consen 168 EAISEALLDKSEPNTKNSTELKKKLVTAFLKNALSRKKCPRCKHSNPKLRKDGFRKVFIDALSSKVGANVIRGAKIKKDV 247 (1640)
T ss_pred HHHHHHhhcCCCccchhhHHHHHHHHHHHHHHhhccccCCcccCCCchhhccccceeeeehhcccccccchhheeeehhc
Confidence 0012345667777777778899999999999999999988876543111000 00000000
Q ss_pred H------HHh---hhh-------hccChhhhhhhccCccccCCHHHHHHHhhccCCCccccccc--c--c----CCCCCc
Q psy13846 261 L------AEY---NEA-------VKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLM--N--A----ELSKPS 316 (1423)
Q Consensus 261 ~------~~~---~~~-------~~~~~~~~~~~~~~~~~~L~p~~V~eiLe~I~~~d~~lL~m--~--~----~~arPe 316 (1423)
. +++ .++ .....+.....+ ....+|.|.+|+++|+.+|.+|..+|.. . . ..+..+
T Consensus 248 ~~~~~~d~~~~G~~E~~~~g~d~~e~~~~~~~~~~-t~~~~l~~tevR~~l~~lf~ne~~~l~~lf~l~~~~~~k~~p~d 326 (1640)
T KOG0262|consen 248 GSKGFEDSGIDGSNEVEEDGKDLFEKSTEPAEFEK-TGKKYLLPTEVREHLRDLFKNEGELLSYLFPLWDSGSGKIDPSD 326 (1640)
T ss_pred ccccccccccCCccccccccccccccccccccccc-cccccccHHHHHHHHHHHHhhhHHHHHHhhccccccccccCccc
Confidence 0 000 000 000001111111 2357899999999999999998766542 1 1 112235
Q ss_pred ceEEEEecCCCCCCCCcEEcCCCC--------------------------------------------------------
Q psy13846 317 DLILTRLLVPPNCIRPSVISDLKS-------------------------------------------------------- 340 (1423)
Q Consensus 317 ~liLt~lpVPP~~vRPsv~~g~~~-------------------------------------------------------- 340 (1423)
+|||..++|||.++||.+++|+..
T Consensus 327 ~FFld~l~VpPtrfRP~s~~gd~~~en~Qt~~L~kVle~s~~i~~~~~~m~~kl~~~~k~~l~~~~g~~~kl~~aw~~LQ 406 (1640)
T KOG0262|consen 327 MFFLDNLLVPPTRFRPPSMLGDEVHENPQTLNLNKVLESSVLIRKLLKDMKGKLDEELKLILERLRGIFSKLINAWLQLQ 406 (1640)
T ss_pred eeeeeccccCCcccCCchhcchhhhcChHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHhhhhHHHHHHHHHHHHH
Confidence 999999999999999999988863
Q ss_pred --------------------------------------------------------------------------------
Q psy13846 341 -------------------------------------------------------------------------------- 340 (1423)
Q Consensus 341 -------------------------------------------------------------------------------- 340 (1423)
T Consensus 407 ~~vn~lfDs~~~~k~~r~~~pGikQiLEKKeGLFRkhMMGKRVN~AaRSVIsPDPnI~tnEIGIP~vFA~KLTyPepVt~ 486 (1640)
T KOG0262|consen 407 ASVNVLFDSKMASKWSRDSPPGIKQILEKKEGLFRKHMMGKRVNYAARSVISPDPNIETNEIGIPPVFAKKLTYPEPVTP 486 (1640)
T ss_pred HHHHHHhccccccccccCCCchHHHHHHHhhhhHHHHhhccccchhhccccCCCCCccccccCCchHHHhhccCCCcCCc
Confidence
Q ss_pred ---------------------------------------------------------------------CCeEEEEecCc
Q psy13846 341 ---------------------------------------------------------------------DNDVVLFNRQP 351 (1423)
Q Consensus 341 ---------------------------------------------------------------------~~d~Vl~nRqP 351 (1423)
+||+||+||||
T Consensus 487 ~NV~elr~aViNGP~~hPGA~~iqd~dg~~t~l~~~~~~qR~alA~qLLtpst~~~~~~~~K~V~RHvknGDvvlmNRQP 566 (1640)
T KOG0262|consen 487 WNVNELRKAVINGPDVHPGATYIQDEDGTLTLLSPMTDEQREALANQLLTPSTGNPTEFGTKKVHRHVKNGDVVLMNRQP 566 (1640)
T ss_pred ccHHHHHHHHhcCCCCCCCcceeecCCCceeecCCCCHHHHHHHHHHhhccccCCCcccCCceeeeeccCCcEEEEcCCC
Confidence 99999999999
Q ss_pred cccccccceeeeEEecC-CceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhcccccccc
Q psy13846 352 SLHKLSIMAHRAKVLPH-RTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVT 430 (1423)
Q Consensus 352 sLHk~Simah~~~~~~~-~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s 430 (1423)
||||+|||||++||||+ ||+|+|+++|++|||||||||||+|+||++.|||||+ .|.++..|++.
T Consensus 567 TLHKPSimaHkaRVL~gEktlRlHYANCkaYNADFDGDEMN~HfPQse~araEa~--------------~ian~dsqYLv 632 (1640)
T KOG0262|consen 567 TLHKPSIMAHKARVLPGEKTLRLHYANCKAYNADFDGDEMNVHFPQSEIARAEAY--------------NIANTDSQYLV 632 (1640)
T ss_pred ccccchhhhhhheecCCcceeeeeecccccccCCCCcchhcccCCchhhHHHHHH--------------HHhccCCceec
Confidence 99999999999999999 9999999999999999999999999999999999999 99999999999
Q ss_pred CCCCccccccccceEEEEEeecccccCCCHHHHHHHHHhhccCCccccceEeeeeccccCCceeecceeeeecceeeeec
Q psy13846 431 PRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLI 510 (1423)
Q Consensus 431 ~~~~~~~~~~~qD~~~~~~~~t~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~kp~~~wtGKqi~s~i 510 (1423)
|++|.||.+++|||+++...||.||+||++++|+++++.... +..++| .++||+|+||.+|||||||+|.+
T Consensus 633 Pt~G~PlrGLIQDHiVsgv~LT~rd~Fftre~y~qLv~~~l~---~~~~rI------~~lpPtIlkP~~LWTGKQVIsTi 703 (1640)
T KOG0262|consen 633 PTDGTPLRGLIQDHIVSGVLLTMRDSFFTREDYQQLVFAGLS---DTFKRI------KLLPPTILKPAPLWTGKQVISTI 703 (1640)
T ss_pred cCCCCchhhhhhhheeeeEEEEecccccCHHHHHHHHHHhhh---hhccce------eccCccccccccccccchHHHHH
Confidence 999999999999999999999999999999999999998764 344666 79999999999999999999998
Q ss_pred ccCCC-Ccccccceeeccccccc-----CcccccCCcEEEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHH
Q psy13846 511 LKPNR-DCPVNANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTA 584 (1423)
Q Consensus 511 l~~~~-~~~~~~~~~~~~~~~~~-----~~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~ 584 (1423)
|.... .....+|+.++.+.... +.+-..+++.|+|++||||+|+|||.++|+ +.+||+|.+++.||+++++++
T Consensus 704 l~Ni~P~~~p~iNl~~kaKip~~~W~~~s~e~~l~Es~v~ir~GellcGVLDKa~~Ga-t~yGLvH~~~ElYG~~~s~~l 782 (1640)
T KOG0262|consen 704 LKNIIPEGHPPINLESKAKIPGKAWRVHSEEPKLNESQVLIREGELLCGVLDKAQFGA-TAYGLVHCCHELYGGETSGKL 782 (1640)
T ss_pred HHhcCCCCCCcccchhcccCchhhcCCCCCcccCCcceEEEecCceEEEeechhhcCc-hhhhhhhhhhhhhCccchhhH
Confidence 64332 22345667666554332 111123457799999999999999999999 789999999999999999999
Q ss_pred HHHhhhhhhHHHhhcCcceecCCCCCCc----------------------------------------------------
Q psy13846 585 MWRLSRMTSFYLMNRGFSIGIGDVTPGQ---------------------------------------------------- 612 (1423)
Q Consensus 585 l~~l~~l~~~~L~~~GfsiGi~D~~~~~---------------------------------------------------- 612 (1423)
|+.++|+++.||++||||+|++|+...+
T Consensus 783 Ls~~srlFT~ylq~~GFT~GvdDlll~~~~D~kR~~il~e~~~vG~qa~~~~~~l~~da~~del~~~le~~y~~d~~~~~ 862 (1640)
T KOG0262|consen 783 LSVFSRLFTAYLQMHGFTLGVDDLLLDKDADKKRREILRESRNVGNQAAKEAFGLDVDAPPDELRSRLEAIYLKDADKLA 862 (1640)
T ss_pred HHHHHHHHHHHHHHhccccccceeeechhhhHHHHHHHHhhhcccHHHHHHHhCCCCCCCHHHHHHHHHHHHhcchhHHH
Confidence 9999999999999999999999997655
Q ss_pred --------------------------------------------------------------------------------
Q psy13846 613 -------------------------------------------------------------------------------- 612 (1423)
Q Consensus 613 -------------------------------------------------------------------------------- 612 (1423)
T Consensus 863 ~LD~~~k~~~n~~ts~I~~~cvP~GLlk~FP~N~mqlM~~SGAKGS~VN~~QISclLGQqeLEGkRvPlMvSGKtLPsF~ 942 (1640)
T KOG0262|consen 863 MLDRVMKSELNGYTSEIVKKCVPDGLLKKFPENNMQLMIQSGAKGSNVNTSQISCLLGQQELEGKRVPLMVSGKTLPSFA 942 (1640)
T ss_pred HHHHHHHHHHhhhhHHHHhhhccchhhhcCCcchHHHHHHhcCCcccccHHHHHHhhhhHhhcCCccceeecCCccCCcC
Confidence
Q ss_pred ---------cccccccccCCCceeeeeecccccccchhcccccCCCCcchHHHHHHHhhhhhcccceeeccccCCCccCC
Q psy13846 613 ---------GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAFYGQTDCIS 683 (1423)
Q Consensus 613 ---------GfI~~sf~~GL~p~Efffh~maGReGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~tVR~s~yG~~~~~~ 683 (1423)
|||..||++|++|+|||||||||||||||||||||+||||||||+|+||+++|+||.|||++ ++
T Consensus 943 p~e~spraGGfI~~RFlTGi~PqeyfFHCMAGREGLIDTAVKTSRSGYLQRCLiKhLEgl~V~YD~TVRDs-------Dg 1015 (1640)
T KOG0262|consen 943 PYETSPRAGGFIDGRFLTGIKPQEYFFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLKVHYDLTVRDS-------DG 1015 (1640)
T ss_pred CCCCCCCCCCcccceeecCCCchHHhhhhhccccchhhhHHhcccchHHHHHHHHhhhhcEEeccceEEcC-------CC
Confidence 99999999999999999999999999999999999999999999999999999999999965 23
Q ss_pred CcchheecCCCcccchhHHHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCC
Q psy13846 684 GVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQD 763 (1423)
Q Consensus 684 ~~~~~~~~~~~~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~ 763 (1423)
.++|++|+ |+
T Consensus 1016 svVQF~YG-------------------ED--------------------------------------------------- 1025 (1640)
T KOG0262|consen 1016 SVVQFMYG-------------------ED--------------------------------------------------- 1025 (1640)
T ss_pred cEEEEeec-------------------Cc---------------------------------------------------
Confidence 33333321 11
Q ss_pred CchhhHHHHhhhcCCCCceeeeecccCChHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccc
Q psy13846 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVD 843 (1423)
Q Consensus 764 GvPRlkEIinaSk~ikTPiitv~L~~~~~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~ 843 (1423)
|++-.|+ -+|+ ++++. . .-+..++..
T Consensus 1026 glDitKs--------------sfl~---~~~f~---~-----~Ny~avl~~----------------------------- 1051 (1640)
T KOG0262|consen 1026 GLDITKS--------------SFLN---KKEFP---T-----DNYEAVLLK----------------------------- 1051 (1640)
T ss_pred cccccHH--------------hhcc---hhhhh---h-----hhHHHHHhh-----------------------------
Confidence 1110000 0000 00000 0 000000000
Q ss_pred hhhhhHHhhhcccccCcccccccccccccCCCCccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeecc
Q psy13846 844 IDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVE 923 (1423)
Q Consensus 844 ~~~I~~~i~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~e 923 (1423)
.
T Consensus 1052 ----------~--------------------------------------------------------------------- 1052 (1640)
T KOG0262|consen 1052 ----------Y--------------------------------------------------------------------- 1052 (1640)
T ss_pred ----------h---------------------------------------------------------------------
Confidence 0
Q ss_pred CccccccceeecccceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCCcchh
Q psy13846 924 GDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVE 1003 (1423)
Q Consensus 924 G~nL~~vl~~~gvD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~~~~~ 1003 (1423)
....|..-++++.|-..+- -+.++-. +|
T Consensus 1053 ---------------------~~~~v~s~~d~~~a~~~~k-~i~kw~k--------k~---------------------- 1080 (1640)
T KOG0262|consen 1053 ---------------------KSESVLSAFDIKKASKYIK-KILKWKK--------KH---------------------- 1080 (1640)
T ss_pred ---------------------ChHHHhhhhhhHHHHHHHH-HHHHHHh--------hh----------------------
Confidence 0111222233333322211 1111111 01
Q ss_pred hHHHHHHHHHhccCCCCCCCCHHHHHHHhhhhcCcchhhhhhhHHHHHHHHHHHHHhhhccccccccccCCchhhhhhhc
Q psy13846 1004 LKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILS 1083 (1423)
Q Consensus 1004 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1083 (1423)
.|....+.. ...+|.++ .+.++.++++.||+|.+.+..|..+++++.....
T Consensus 1081 ---~w~~~~k~~-~cpdpv~~----------k~~p~~y~gsvsekf~~~i~~f~~~~~k~~~s~~--------------- 1131 (1640)
T KOG0262|consen 1081 ---MWFELDKKI-ACPDPVLA----------KYNPDKYLGSVSEKFRKKIDDFDDENAKKEKSEE--------------- 1131 (1640)
T ss_pred ---ccchhhccc-CCCChhhh----------hcchhhhhccccHHHHHHHHHHHHHhhhhhcccc---------------
Confidence 111111111 12233332 4667889999999999999999977643322110
Q ss_pred cccccCcccCCCCCChhHHHHHHHHHhhhccCCCCcchhhhhhcccCCcccccccccccccc------------------
Q psy13846 1084 HQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG------------------ 1145 (1423)
Q Consensus 1084 ~~~~~~~~~~~~~~~~~~~~~~~~~~y~~s~v~PGeaVG~iAAQSIGEP~TQmTLnTFH~AG------------------ 1145 (1423)
-++ + .|...++.||.+|+++|||+||+||||||||||||||||||||||
T Consensus 1132 ----~~~-------~--~lr~ll~~K~~~SLa~PGE~VGvlAAQSIGEPSTQMTLNTFHfAGrGemNVTLGIPRLREIlM 1198 (1640)
T KOG0262|consen 1132 ----PSE-------E--KLRRLLQLKYIRSLADPGEPVGVLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILM 1198 (1640)
T ss_pred ----chH-------H--HHHHHHHHHHHHHhcCCCCcceeeeecccCCCcceeehhheeeccccceeeeecchHHHHHHH
Confidence 011 3 789999999999999999999999999999999999999999999
Q ss_pred -------------------------------------cccceeE--EEEc--c-CC-cEEEEEEchHHHHHh--cccCCH
Q psy13846 1146 -------------------------------------EVCEYIE--EVFV--P-DD-SFILIKLDMDRIRLL--HLEVDI 1180 (1423)
Q Consensus 1146 -------------------------------------~i~~~i~--~~~~--~-~~-~~~~i~l~~~~~~~~--~~~i~~ 1180 (1423)
++.+++. +.+. + .. ..+.+++++..-+.+ .+.+..
T Consensus 1199 tASanIkTP~mt~pi~~g~s~~ra~~i~~~l~rV~L~evlk~v~vte~~t~~~~~~~~~y~lr~~~~~~~~y~~e~~v~~ 1278 (1640)
T KOG0262|consen 1199 TASANIKTPSMTVPIKNGVSDERADDITKELRRVTLKEVLKKVGVTEKITMVENQSCKKYKLRFDLLPREEYQEEYDVRP 1278 (1640)
T ss_pred HHhhccCCCceeeeccCCccHHHHHHHHHHHHHHHHHHHHhheeeeEEEEeeccccceEEEEEEeecCHHHhhhhcCCCH
Confidence 1111111 1111 1 12 335666666554444 446677
Q ss_pred HHHHHHHH------------h----cc---ccC-----Cce--------EEe---------------cC-----------
Q psy13846 1181 DSIRYCIE------------R----TR---GIS-----GHL--------TVS---------------GH----------- 1202 (1423)
Q Consensus 1181 ~~i~~~i~------------~----~k---~~~-----~~~--------~~~---------------~~----------- 1202 (1423)
++|.+.++ + .+ ... .++ .+. ++
T Consensus 1279 e~i~~~m~~~Flk~L~~aI~k~~~k~~~~~~~~~dd~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ddddas~~k~~~k 1358 (1640)
T KOG0262|consen 1279 EDIEEVMENRFLKLLERAIKKKLKKAKYTRGMSNDDADPDDGNEVDNNDEVGGEDNEDSDDESEDDEDDDDASDAKLHKK 1358 (1640)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhHHhhccccccCCccccccCCccccccCCccccccccccccCcccchhHHHHhhh
Confidence 77665431 1 00 000 000 000 00
Q ss_pred -------------cEEEEEeC----------------------------------------------------------C
Q psy13846 1203 -------------SFLILKPK----------------------------------------------------------D 1211 (1423)
Q Consensus 1203 -------------~~i~i~~~----------------------------------------------------------~ 1211 (1423)
..+..+-. .
T Consensus 1359 ~~~~~dYe~~de~e~~~~~~~e~~~~~e~~e~d~e~g~dg~~~~~~~~~e~~~~~~~~er~~qs~~~~~~fi~~y~fd~~ 1438 (1640)
T KOG0262|consen 1359 TEEEADYESEDEDERVEEREDEGDEDEESDEDDEEVGLDGTPEPEEEDQEGQPEVNAVERREQSVKKRHDFISRYTFDKE 1438 (1640)
T ss_pred hccccCcCCCchhhhhhhhhcccccccccccchhhcccCCCCCcccccccCCchhhHHHHHHHHHHHHHHHhhhhccccc
Confidence 00000000 0
Q ss_pred CCc------------hhhhHHHHHHhccCCcEEcccCCccEEEEecccccceeeEEEEecCccHHHHhhccc-ccceecc
Q psy13846 1212 SSK------------SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYG-VKGVKCS 1278 (1423)
Q Consensus 1212 ~~~------------~~~~~l~~l~~~l~~~~v~Gi~~i~r~~i~~~~~~~~~~~~l~teG~nl~~~~~~~~-vd~~~~~ 1278 (1423)
..+ ....+.+.++..+++++|+.+|||+||++...+...++.-++.|+|+||.++|++.. +|.+++|
T Consensus 1439 ~~~wcev~~~lp~~~~k~~mssiVe~~~~~~vI~q~~gIeRc~~~~~~~~~k~~~~l~TeGVnl~a~~~~~d~LDv~~ly 1518 (1640)
T KOG0262|consen 1439 SGKWCEVELKLPLDKEKLDMSSIVESIAPKSVIHQVPGIERCVVSEPQDDVKEKSVLLTEGVNLPALFDHADILDVNRLY 1518 (1640)
T ss_pred cCcEEEEEEEecCCCcchHHHHHHHHHhcceeeeccCCceeeeccCCcccccccceehhcCccHHHHHHHHhhhhhhhhc
Confidence 000 012345667889999999999999999997653222223389999999999999765 5999999
Q ss_pred cccHHHHHHHhCHHHHHHHHHHHHHHHhhcCCccccCCchhhhhccccceeEEEeeecccccccccchhhhccchhhHHH
Q psy13846 1279 SNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDH 1358 (1423)
Q Consensus 1279 sN~i~~i~~~lGIEAar~~ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~G~~~~i~r~g~~~~~~S~l~~aSFE~t~~~ 1358 (1423)
||||++|+++|||||||++|++|+.+||..|||+||.|||+||||||||+|.+.|+||+||.. ++|||++||||+|.+|
T Consensus 1519 SNDI~ail~tyGVEAar~~Iv~Ev~~VF~vYGIsVd~RHLsLiADYMTf~G~y~pfnR~Gm~~-ssSP~qkMsFETt~~F 1597 (1640)
T KOG0262|consen 1519 SNDIHAILNTYGVEAARNAIVNEVNNVFKVYGISVDIRHLSLIADYMTFEGGYQPFNRMGMES-SSSPLQKMSFETTCQF 1597 (1640)
T ss_pred cchHHHHHHHhhHHHHHHHHHHHHHHhhhheeeeecHHHHHHHHHHHhhcccccccccccccc-CCChhHhhhHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999965 8999999999999999
Q ss_pred HHhhcccCCcccccccccceeeccccccccceEEEeecCCC
Q psy13846 1359 LFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPR 1399 (1423)
Q Consensus 1359 L~~Aa~~g~~D~l~g~s~~ii~G~~~~~GTG~~~l~~~~~~ 1399 (1423)
|.+||.+|+.|.|++||++|++|+++..|||+|||+++.+.
T Consensus 1598 l~~Aa~~g~~D~L~sPSArLvvG~~~r~GTG~Fdll~~v~~ 1638 (1640)
T KOG0262|consen 1598 LKQAALFGEEDELSSPSARLVVGLPVRGGTGSFDLLQKVDF 1638 (1640)
T ss_pred HHHHHhcCcccccCCCcceeEeccccCCCcceeeeeccCCC
Confidence 99999999999999999999999999999999999998765
No 4
>KOG0260|consensus
Probab=100.00 E-value=1.5e-179 Score=1608.07 Aligned_cols=996 Identities=33% Similarity=0.522 Sum_probs=773.8
Q ss_pred ccceeeeEEEecCCHHHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccC
Q psy13846 76 KVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPL 155 (1423)
Q Consensus 76 ~~~i~~~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~ 155 (1423)
...+.+ |+||++||+|||+|||.+|..|++++ .|+|..|||.|||||..++...|.|||.++.+||||||||+|+.
T Consensus 12 l~~v~~-vqFgi~spdeir~mSV~~i~~~e~~e---~~~pk~ggl~D~RlG~idr~~~CqTC~g~~~~CpGHFGhieLAk 87 (1605)
T KOG0260|consen 12 LRTVKS-VQFGILSPDEIRRMSVAEIEFPETME---GGRPKLGGLMDPRLGTIDRDSLCQTCGGNMFECPGHFGHIELAK 87 (1605)
T ss_pred ceeeeE-EEeeccChhhhhcceeEEeecccccc---cCCCCcCCccccccCCCCccchhhhhccccccCCcccceeeecc
Confidence 356888 99999999999999999999999995 68999999999999999999999999999999999999999999
Q ss_pred ceeEEeeeccHHHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCC-----------
Q psy13846 156 PVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCP----------- 224 (1423)
Q Consensus 156 PV~h~gffd~v~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~----------- 224 (1423)
|||||||++++.++|+|+|++ |++++.++...........+.+ .+++...+++.|+++..|.
T Consensus 88 PvfH~gFl~kv~kiL~cVC~~--C~ki~~~~~~~~~~~~~~~~~~-----~k~rl~~v~~vck~k~~ce~g~~~e~~g~s 160 (1605)
T KOG0260|consen 88 PVFHPGFLKKVKKILRCVCFY--CSKILKDKFNPKEDQILRKRYC-----SKGRLLMVLDVCKGKVVCEGGIDVESDGRS 160 (1605)
T ss_pred ccccHHHHHHHHHHHHHhhhc--chheeecccCcchhhhhhhhcC-----CcchHHHHHHhhccceeeeccccccccccc
Confidence 999999999999999999999 9999987654322111111111 2467888999999999996
Q ss_pred CCCCCCCceeecCcceehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHHHhhccCCCccc
Q psy13846 225 HCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIP 304 (1423)
Q Consensus 225 ~Cg~~~~~irk~~~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~eiLe~I~~~d~~ 304 (1423)
+||..+|.+++.+ ++.+.. ++.. ++ +.. ..+..+++++|.++|+.|.++|+.
T Consensus 161 gcg~kqP~i~r~g-l~l~a~-~k~~----~e-----------------~~~-----e~k~~ls~e~V~~i~k~Isded~~ 212 (1605)
T KOG0260|consen 161 GCGLKQPSIRRLG-LDLWAF-WKQG----DE-----------------DSQ-----ESKRKLSAERVLEIFKRISDEDID 212 (1605)
T ss_pred cccccCCceeccC-chhhhh-hhcc----Cc-----------------cCC-----cccccCcHHHHHHHHHhhchhhhh
Confidence 5999999999988 454432 1110 00 000 235578999999999999999999
Q ss_pred ccccccCCCCCcceEEEEecCCCCCCCCcEEcCCCC--------------------------------------------
Q psy13846 305 LLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKS-------------------------------------------- 340 (1423)
Q Consensus 305 lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~~-------------------------------------------- 340 (1423)
.++|++..+||+||+||++||||+.+||++++++..
T Consensus 213 ~lg~~~~~arpewmIlTvLPVPP~~vrP~iv~~~s~rg~DdlthkLadIiK~n~~l~r~e~~ga~~H~i~e~~~LlqfhV 292 (1605)
T KOG0260|consen 213 QLGFKPKIARPEWMILTVLPVPPPAVRPEIVMQGSARGEDDLTHKLADIIKKNIGLKRNEENGAPAHIIEEYEQLLQFHV 292 (1605)
T ss_pred hhcCCCCcCCCceeEEEEecCCCCcccceeeecccccCcchhHHHHHHHHHHHHHHhhhhhcCCchhhHHHHHhHhhhhh
Confidence 999999999999999999999999999999987652
Q ss_pred --------------------------------------------------------------------------------
Q psy13846 341 -------------------------------------------------------------------------------- 340 (1423)
Q Consensus 341 -------------------------------------------------------------------------------- 340 (1423)
T Consensus 293 at~~Dn~~pgqp~a~qksGrplkSi~arlKgkegriRgnLmGKRvDFSaRTVItgDPnl~ldevGVP~sIAk~lTfpE~V 372 (1605)
T KOG0260|consen 293 ATYVDNDIPGQPQADQKSGRPLKSISARLKGKEGRIRGNLMGKRVDFSARTVITGDPNLSLDEVGVPRSIAKRLTFPEHV 372 (1605)
T ss_pred hheecccccCCcccccccCCcccchhhhhccccchhhhcccccccCcceeeeecCCCCcchhcccCcHHHHhhccCccee
Confidence
Q ss_pred ---------------------------------------------------------CCeEEEEecCccccccccceeee
Q psy13846 341 ---------------------------------------------------------DNDVVLFNRQPSLHKLSIMAHRA 363 (1423)
Q Consensus 341 ---------------------------------------------------------~~d~Vl~nRqPsLHk~Simah~~ 363 (1423)
|||+|||||||||||||||||++
T Consensus 373 tp~NidrLqeLV~~g~~~~pgakyiird~G~Ridlr~~~~~~d~~Lq~G~kVeRhl~DGD~VlfNRqPSlHKmSmmahrV 452 (1605)
T KOG0260|consen 373 TPFNIDRLQELVRRGLLEHPGAKYIIRDNGDRIDLRYHKRAGDIHLQPGYKVERHLMDGDVVLFNRQPSLHKMSMMAHRV 452 (1605)
T ss_pred ccccHHHHHHHhhCCCCCCCCcceeeecCCcEEEEeecCCccccccccccEEEEeeccCCEEEEcCCCcHHHhhhhhcEE
Confidence 99999999999999999999999
Q ss_pred EEecCCceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccc
Q psy13846 364 KVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQD 443 (1423)
Q Consensus 364 ~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD 443 (1423)
||+|++|||+|+.+|+||||||||||||+|+|||++||||.. +|+.+.+|++||++|+|+++++||
T Consensus 453 rVlp~sTfrLNlsvtsPynADFDGDemnlhvPQS~etkAEl~--------------EL~~vpkQiispQsnkpvmgivQD 518 (1605)
T KOG0260|consen 453 RVLPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSLETKAELE--------------ELAMVPKQIISPQSNKPVMGIVQD 518 (1605)
T ss_pred EEccCceEEeCeeecCCccCCCCCceeecccCcchhHHHHHH--------------HHhhhhhhhcCCcCCCcceeeehh
Confidence 999999999999999999999999999999999999999999 999999999999999999999999
Q ss_pred eEEEEEeecccccCCCHHHHHHHHHhhccCCccccceEeeeeccccC-CceeecceeeeecceeeeecccCCCCcccccc
Q psy13846 444 FITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWN-PVVFVRTAVIWTGKQIFSLILKPNRDCPVNAN 522 (1423)
Q Consensus 444 ~~~~~~~~t~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~-~p~i~kp~~~wtGKqi~s~il~~~~~~~~~~~ 522 (1423)
+|+|.+.+|.||.|+++.|++++++++. +|.+ ..| +|+|+||.++|||||||++++|++. |
T Consensus 519 TLta~R~~t~Rd~Fl~r~~vmnLlm~~p----~~d~--------~~Pa~pai~Kp~PlWTGkQifsliiP~~i------n 580 (1605)
T KOG0260|consen 519 TLTAVRKMTKRDVFLNRAQVMNLLMYVP----DWDG--------PPPAKPAILKPKPLWTGKQIFSLIIPGGI------N 580 (1605)
T ss_pred hHHHHHHHhhHhhhhcHHHHHHHHhhcc----ccCC--------CCCCCcccCCCCcccchhhheeeecCCCc------c
Confidence 9999999999999999999999999984 4444 345 6899999999999999999999763 3
Q ss_pred eeeccccccc--CcccccCCcEEEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcC
Q psy13846 523 LKTKGRAYTA--NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRG 600 (1423)
Q Consensus 523 ~~~~~~~~~~--~~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~G 600 (1423)
+......... ++...++|..++|.+|+++.|+++|+.+|+ +.++++|.+|.+.|++.|+.|.+.+|++.+.||..+|
T Consensus 581 ~~r~~s~h~d~~~~~~~p~dt~~lie~g~l~~g~l~Kkt~G~-s~g~lvh~i~~e~Gp~~~~~f~~~iQ~lin~wll~~g 659 (1605)
T KOG0260|consen 581 YIRDHSTHPDSEDELISPGDTRVLIEGGELLIGVLCKKTVGS-SAGGLVHVIFLEKGPKIARGFFDSIQTLINSWLLREG 659 (1605)
T ss_pred eecccccCcCCCcccccCCCceEEEeCCceEEEEeecccccc-ccCceEEEeehhhCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 3333222222 446688999999999999999999999998 7799999999999999999999999999999999999
Q ss_pred cceecCCCCCCc--------------------------------------------------------------------
Q psy13846 601 FSIGIGDVTPGQ-------------------------------------------------------------------- 612 (1423)
Q Consensus 601 fsiGi~D~~~~~-------------------------------------------------------------------- 612 (1423)
||+||+|++++.
T Consensus 660 fsigIgDtiad~~t~~~iq~~I~~ak~dv~~vi~~a~~~~L~~~pg~tlretfe~~v~~vlndArd~~gssA~~sl~esN 739 (1605)
T KOG0260|consen 660 FSIGIGDTIADAATMCVIQNTIKEAKRDVLAVIREAQNNELEPTPGRTLRETFENKVNRVLNDARDKSGSSAQKSLSESN 739 (1605)
T ss_pred ccccccccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCCcchhHHHHHHHHHHHHHHHHHHhhhhHHHhhhhhcc
Confidence 999999999877
Q ss_pred --------------------------------------------------------cccccccccCCCceeeeeeccccc
Q psy13846 613 --------------------------------------------------------GFVQNSFFSGLTPTEFFFHTMGGR 636 (1423)
Q Consensus 613 --------------------------------------------------------GfI~~sf~~GL~p~Efffh~maGR 636 (1423)
|||.|||++||+|+|||||+||||
T Consensus 740 n~k~Mv~aGSKGs~inisQ~saCVGqQnVEgkrIpFGF~~Rtlphf~kDdysPesrGfVENSyL~GLtP~EfFfHamggR 819 (1605)
T KOG0260|consen 740 NFKTMVVAGSKGSFINISQVSACVGQQNVEGKRIPFGFPKRTLPHFSKDDYSPESRGFVENSYLTGLTPQEFFFHAMGGR 819 (1605)
T ss_pred cHHHHHhhcCCCcceehhhhhhhhccccccccccccCCCcccccccccCCCCccccceeecccccCCCHHHHHHHHhccc
Confidence 999999999999999999999999
Q ss_pred ccchhcccccCCCCcchHHHHHHHhhhhhcccceeeccc-------cCCCccCCCcchheecCCCcccchhHHHHhhhcC
Q psy13846 637 EGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAF-------YGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 709 (1423)
Q Consensus 637 eGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~tVR~s~-------yG~~~~~~~~~~~~~~~~~~~~g~~vg~i~aqsi 709 (1423)
|||||||||||++|||||||||+|||++|+|||||||++ ||+|+.++-.+|.. -|++++...|...
T Consensus 820 EglidtavktaEtGyiqRRL~kameDimv~yDgTVRNs~gqviQf~YGeDG~d~~~vE~q-------~~~~l~~~~a~f~ 892 (1605)
T KOG0260|consen 820 EGLIDTAVKTAETGYIQRRLMKAMEDIMVAYDGTVRNSLGQVIQFKYGEDGLDGHPVEFQ-------NGETLGSLNACFE 892 (1605)
T ss_pred chhhhhhhcccccchHHHHHHHHHHHHHhhcCcceecccceeEEEEeccCccccceeecc-------ccccccchHHHHH
Confidence 999999999999999999999999999999999999993 99987655444432 2334443333321
Q ss_pred CCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhHHHHhhhcCCCCceeeeeccc
Q psy13846 710 RSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINASRNISTPIITAYLDK 789 (1423)
Q Consensus 710 ge~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlkEIinaSk~ikTPiitv~L~~ 789 (1423)
++|.+.-. ..++.+ .-..-++|+-+. ..+++
T Consensus 893 -------------~~~~~d~l--------------d~~~~~------------~~~~~~~e~~~~----------~~l~~ 923 (1605)
T KOG0260|consen 893 -------------SEFAYDAL--------------DEPISL------------SSEEVVNEISEL----------LKLQN 923 (1605)
T ss_pred -------------hhhhhhhh--------------cCcccc------------hhhhHhhhhhhh----------HHHHH
Confidence 11110000 000111 000011111111 01222
Q ss_pred CChHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhhhHHhhhcccccCcccccccccc
Q psy13846 790 DTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFL 869 (1423)
Q Consensus 790 ~~~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I~~~i~~~~~~~~~i~~~~~~~~ 869 (1423)
..+.|+.+.+++|-. + ..++...+..+++..+..++ |..+.++...
T Consensus 924 lle~e~~~l~~dr~~---l-------~~i~~~g~~k~~lp~n~~r~-----------I~Na~~~f~~------------- 969 (1605)
T KOG0260|consen 924 LLECEYKKLVRDRRV---L-------LYIFEYGDAKWPLPENLQRI-----------IWNALKKFSI------------- 969 (1605)
T ss_pred HHHHHHHhhhhhhhh---h-------hhhcccCCcccccchhHHHH-----------HHHHHhhccc-------------
Confidence 234455544444421 1 11223344455555555443 1111111100
Q ss_pred cccCCCCccccchhhhhhhhcCCceEEccccccc-eeeeecccccceeEEeeeccCccccccceeecccceeeccCchHH
Q psy13846 870 ILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGIN-RAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYE 948 (1423)
Q Consensus 870 ~~~~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~-r~~i~~~~~~~~~~~~l~~eG~nL~~vl~~~gvD~~~t~SN~i~e 948 (1423)
.......+.+.-+++|.+... ++++ +.|.|.... .|.
T Consensus 970 -------------~~r~~t~l~~~~v~~g~~~l~e~l~i-------------------------v~g~~~~sr-aqr--- 1007 (1605)
T KOG0260|consen 970 -------------DERKPTDLIPFKVVKGVKELAEKLVI-------------------------VRGEDYISR-AQR--- 1007 (1605)
T ss_pred -------------ccccccccchhhhhhhhhhhhheeEE-------------------------eeCchhHHH-HHH---
Confidence 000001111222222222210 1110 001111000 000
Q ss_pred HHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCCcchhhHHHHHHHHHhccCCCCCCCCHHHH
Q psy13846 949 VYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDPSLSAQEI 1028 (1423)
Q Consensus 949 V~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~ 1028 (1423)
-+
T Consensus 1008 ------------------------------------------------------------------------------l~ 1009 (1605)
T KOG0260|consen 1008 ------------------------------------------------------------------------------LF 1009 (1605)
T ss_pred ------------------------------------------------------------------------------HH
Confidence 01
Q ss_pred HHHhhhhcCcchhhhhhhHHHHHHHHHHHHHhhhccccccccccCCchhhhhhhccccccCcccCCCCCChhHHHHHHHH
Q psy13846 1029 LALSNETLDSKEFLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACRE 1108 (1423)
Q Consensus 1029 ~~~~~~~l~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1108 (1423)
..++|+.|++ +.+..+++++.+++ + |+.+++..
T Consensus 1010 ~~lLrs~l~~-----------------------------------------krv~~e~rls~eaf----~--w~~~~Ie~ 1042 (1605)
T KOG0260|consen 1010 NILLRSTLAT-----------------------------------------KRVLEEYRLSSEAF----E--WVLGEIEA 1042 (1605)
T ss_pred HHHHHhhHHH-----------------------------------------HHHHHHhcccHHHH----H--HHhhhhhh
Confidence 1223333332 22335567888776 7 99999999
Q ss_pred HhhhccCCCCcchhhhhhcccCCcccccccccccccc-------------------------------------------
Q psy13846 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG------------------------------------------- 1145 (1423)
Q Consensus 1109 ~y~~s~v~PGeaVG~iAAQSIGEP~TQmTLnTFH~AG------------------------------------------- 1145 (1423)
++.++.+.|||+||++||||||||+|||||||||+||
T Consensus 1043 ~f~qa~a~pgemvg~lAaqsvgePatqmTlntfh~aGVssknVt~gvprlkei~Nv~k~~ktpsLtV~l~g~~~k~~e~a 1122 (1605)
T KOG0260|consen 1043 RFLQAEASPGEMVGALAAQSVGEPATQMTLNTFHYAGVSSKNVTLGVPRLKEIINVAKNAKTPSLTVYLTGEAAKDNEWA 1122 (1605)
T ss_pred heeeeecCccchHhHHHHHHhCCchhhcccchhcccceeeeeeeccCcchhhhhhhhccCCCceEEEEecchhhcchHHH
Confidence 9999999999999999999999999999999999999
Q ss_pred -------------cccceeEEEEccCCcEEEE--------------------------EEchHHHHHhcccCCHHHHHHH
Q psy13846 1146 -------------EVCEYIEEVFVPDDSFILI--------------------------KLDMDRIRLLHLEVDIDSIRYC 1186 (1423)
Q Consensus 1146 -------------~i~~~i~~~~~~~~~~~~i--------------------------~l~~~~~~~~~~~i~~~~i~~~ 1186 (1423)
+++...+++|+|+...+.| +|.+++..+.+..+++++|...
T Consensus 1123 k~v~~~le~ttl~~vt~~t~i~ydpdp~~tvI~ed~e~v~a~~e~pd~D~~~ispwlLrlelDr~~m~dk~ltm~~ia~~ 1202 (1605)
T KOG0260|consen 1123 KLVQCCLEHTTLKDVTRATEIYYDPDPQSTVIDEDREFVVAYYEMPDEDVGRISPWLLRLELDRASMTDKKLTMEQIAEK 1202 (1605)
T ss_pred HHHhhhcccccHHhhhccCcceecCCCcceeeccchhhHHhhhcCcccchhhcChHHHHhhhhhhhcccccccHHHHHHH
Confidence 2334445678887655444 4455555555666778888777
Q ss_pred HHhccccCCceEEecC----cEEEEEeCCCCchhhhHHHHH-HhccCCcEEcccCCccEEEEecccc---cceeeEEEEe
Q psy13846 1187 IERTRGISGHLTVSGH----SFLILKPKDSSKSFNSKMYQM-KQLLPSVVIKGVQGINRAVIHEEDV---EGVTKYKLLV 1258 (1423)
Q Consensus 1187 i~~~k~~~~~~~~~~~----~~i~i~~~~~~~~~~~~l~~l-~~~l~~~~v~Gi~~i~r~~i~~~~~---~~~~~~~l~t 1258 (1423)
|.+--..+-.....++ ..++++.-..+++ ...+..+ .+.|.++.++|++.|.++++...+. +..++|.|+|
T Consensus 1203 i~~~f~~d~~~i~~ddna~klv~r~ri~~~~e~-D~~l~~Ie~~ml~~~~l~G~~~i~kV~m~~~~~G~f~~~~ew~LeT 1281 (1605)
T KOG0260|consen 1203 INRGFGSDLACIFSDDNAEKLVLRLRIAKEEED-DVFLKCIEANMLGDMTLRGIPDIFKVYMSPTEDGEFKPVDEWDLET 1281 (1605)
T ss_pred HHhhccCCCceeecccCCcceEEEEEecCccch-hHHHHHHHHhhhhhcccCCccccceEEEeecCCCceeecceeEEec
Confidence 7431111111111111 2455555433222 2344555 4678899999999999999975432 2347999999
Q ss_pred cCccHHHHhhcccccceecccccHHHHHHHhCHHHHHHHHHHHHHHHhhcCCccccCCchhhhhccccceeEEEeeeccc
Q psy13846 1259 EGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHG 1338 (1423)
Q Consensus 1259 eG~nl~~~~~~~~vd~~~~~sN~i~~i~~~lGIEAar~~ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~G~~~~i~r~g 1338 (1423)
+|+||.+++..++||..||+|||+.+|+++|||||+|.++++|+..|....|.+||+||+.|++|.||++|.+++|+|||
T Consensus 1282 dg~~l~~v~s~~~vD~~rt~sn~l~ei~~vlgIea~r~a~~~e~~~vi~f~gsyVnyrhlaLl~dvmT~~g~lm~itRhg 1361 (1605)
T KOG0260|consen 1282 DGVNLRRVLSEPDVDPARTTSNDLVEIAEVLGIEAVRKALLRELLNVISFDGSYVNYRHLALLCDVMTARGHLMAITRHG 1361 (1605)
T ss_pred CchhHHhhhccCCCCcccccccchhhhhhhhcHHHHHhhhhhhhhheEeecccchhHHHHHHHHHHHhcccceeeeeccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccchhhhccchhhHHHHHhhcccCCcccccccccceeeccccccccceEEEeecCCCCC
Q psy13846 1339 LAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSE 1401 (1423)
Q Consensus 1339 ~~~~~~S~l~~aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~~~~~GTG~~~l~~~~~~~~ 1401 (1423)
+++...++|+++|||||+++|.+||++++.|.++|++|+|++|++.|.|||+|+|+.+.+...
T Consensus 1362 ~nr~~tgaLmrcSfEetv~il~~aa~~~ekd~~rgvsEnImlgqlap~gTg~~d~~ld~e~l~ 1424 (1605)
T KOG0260|consen 1362 INRQDTGALMRCSFEETVDILMDAAAHAEKDPCRGVSENIMLGQLAPMGTGCFDLMLDAEKLK 1424 (1605)
T ss_pred cchhhccccccccHHHHHHHHHHHHhhhccCCCccceeeeeecccccCCCcceeeeccHHhhh
Confidence 999899999999999999999999999999999999999999999999999999999977643
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=1.7e-128 Score=1238.18 Aligned_cols=533 Identities=39% Similarity=0.689 Sum_probs=480.3
Q ss_pred cceeeeEEEecCCHHHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccCc
Q psy13846 77 VFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156 (1423)
Q Consensus 77 ~~i~~~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~P 156 (1423)
.+|.+ |+|++||+|||+++||++|+++++| |.+|+|++|||||||||+.++...|+|||++..+||||||||+|+.|
T Consensus 2 ~~I~~-I~F~~~S~eEI~k~Sv~~It~~~~~--d~~g~P~~gGL~D~RLG~~~~~~~C~TCg~~~~~CpGHFGhIeL~~P 78 (868)
T TIGR02390 2 KKIGS-IKFGLLSPEEIRKMSVVEVVTADTY--DDDGYPIEGGLMDPRLGVIEPGLRCKTCGGKVGECPGHFGHIELARP 78 (868)
T ss_pred ceeeE-EEEeCCCHHHHHHhCeeEEeccccc--CCCCCcCCCCccCcccCCCCCCCCCCCCCCCCCcCCCcceEEecccc
Confidence 35788 9999999999999999999999999 77999999999999999999999999999999999999999999999
Q ss_pred eeEEeeeccHHHHhhhccccccccccccChhhHHHHHHHhcCCchh-HHHHHHHHHHHHHHccCCccCCCCCCCCCceee
Q psy13846 157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALS-YLVRKSLKKKILETTKKVSVCPHCGEINGVVKK 235 (1423)
Q Consensus 157 V~h~gffd~v~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~-~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk 235 (1423)
|||||||+.++++|+|+|++ |++|++++++...|.+++++.... ...++.+.+++.+.|++.++|++||+.+|.+|+
T Consensus 79 Vfhpgf~~~i~kiL~~vC~~--C~rll~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~i~~~~~~~~~C~~Cg~~~p~ir~ 156 (868)
T TIGR02390 79 VVHVGFAKEIYKILRATCRK--CGRITLTEEEIEQYLEKINKLKEEGGDLASTLIEKIVKEAAKRMKCPHCGEEQKKIKF 156 (868)
T ss_pred ccchhHHHHHHHHHHHHhhh--cCceeeCccccHHHHHHHHhcccchhhhHHHHHHHHHHHhhcCCCCCCCCCcCceEEE
Confidence 99999999999999999999 999999988888888877654321 112257788899999988999999999999998
Q ss_pred cCcceehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHHHhhccCCCcccccccccCCCCC
Q psy13846 236 CGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKP 315 (1423)
Q Consensus 236 ~~~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~eiLe~I~~~d~~lL~m~~~~arP 315 (1423)
.+.... .. .. + ...+.|+|.+|+++|++||++|+++|++++..++|
T Consensus 157 ~~~~~~-~~----~~----------------------------~-~~~~~L~p~~v~~ilk~I~~eD~~lLG~~p~~~~P 202 (868)
T TIGR02390 157 EKPTYF-YE----EG----------------------------K-EGDVKLTPSEIRERLEKIPDEDAELLGINPKVARP 202 (868)
T ss_pred eeeeee-ee----cc----------------------------C-CCCeecCHHHHHHHHHhCCHHHHHHhCCCCCCCCc
Confidence 752211 00 00 0 12356899999999999999999999999988999
Q ss_pred cceEEEEecCCCCCCCCcEEcCCC-C------------------------------------------------------
Q psy13846 316 SDLILTRLLVPPNCIRPSVISDLK-S------------------------------------------------------ 340 (1423)
Q Consensus 316 e~liLt~lpVPP~~vRPsv~~g~~-~------------------------------------------------------ 340 (1423)
+||||++|||||+|+||++.+++. .
T Consensus 203 e~~ilt~LPVPP~~iRPsv~~~~g~~~EDDLT~~L~~II~~N~~Lk~~~~~g~~~~~~~~~~~~LQ~~v~~~~d~~~~~~ 282 (868)
T TIGR02390 203 EWMVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVATYFDNELPGI 282 (868)
T ss_pred ceeeEeccccCCCCCcCeEEeCCCcccCChHHHHHHHHHHHHHHHHHHHHcCCchhhhHHHHHHHHHHHHHHHcCCCCCC
Confidence 999999999999999999998753 1
Q ss_pred --------------------------------------------------------------------------------
Q psy13846 341 -------------------------------------------------------------------------------- 340 (1423)
Q Consensus 341 -------------------------------------------------------------------------------- 340 (1423)
T Consensus 283 ~~~~~~~~~~~~~i~~~l~gK~G~~R~nl~GKRvd~s~RsVI~pdp~l~~~evGvP~~~A~~Lt~pe~Vt~~N~~~l~~l 362 (868)
T TIGR02390 283 PPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREY 362 (868)
T ss_pred CccccCCCCCchhhHhhhcccccccccccccccccccCCceeeCCCCCcCCeeeCcHHHHHhCCCCeEEehhhHHHHHHH
Confidence
Q ss_pred -----------------------------------------------CCeEEEEecCccccccccceeeeEEecCCceee
Q psy13846 341 -----------------------------------------------DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRF 373 (1423)
Q Consensus 341 -----------------------------------------------~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~ 373 (1423)
+||+|||||||||||+|||||++|++|++||||
T Consensus 363 v~ng~~~~pga~~i~~~~g~~~~l~~~~~~~~~~~l~~g~~v~rhl~dgd~vl~NRqPsLHr~si~a~~~~v~~~~t~r~ 442 (868)
T TIGR02390 363 VLNGPDSWPGANYVIRPDGRRIKIRDENKEELAERLEPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRL 442 (868)
T ss_pred HHcCCccCCCceEEEcCCCcEEechhhhHHHHHhhcccCCEEEEehhcCccceeccCCccccccceeEEEEEecCceEee
Confidence 789999999999999999999999999999999
Q ss_pred ccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecc
Q psy13846 374 NECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453 (1423)
Q Consensus 374 ~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~ 453 (1423)
||++|+||||||||||||+|+|||++|||||+ +||.+.+|++||++|+|+++++||+++|+|.||.
T Consensus 443 n~~~c~~~NADFDGDeMn~h~Pqs~~a~aEa~--------------~Lm~~~~~~~sp~~g~p~~~~~QD~l~g~~~LT~ 508 (868)
T TIGR02390 443 NLAVCPPYNADFDGDEMNLHVPQTEEARAEAR--------------ELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTH 508 (868)
T ss_pred ccccCCccccCcccceeeEecCCCHHHHHHHH--------------HHhhchhceecCCCCCeeEEeehhhhhheeeeee
Confidence 99999999999999999999999999999999 9999999999999999999999999999999999
Q ss_pred cccCCCHHHHHHHHHhhccCCccccceEeeeeccccCCceeecceeeeecceeeeecccCCCCcccccceeeccccccc-
Q psy13846 454 KNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTA- 532 (1423)
Q Consensus 454 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~kp~~~wtGKqi~s~il~~~~~~~~~~~~~~~~~~~~~- 532 (1423)
+|+|+++++++++++... +. + .+|+|+|++|.++||||||||++||+. +|+..+.+.+..
T Consensus 509 ~d~f~~~~~~~~l~~~~~-----~~--~------~~~~p~i~kp~~lwTGKqi~s~~lp~~------~n~~~~~~~~~~~ 569 (868)
T TIGR02390 509 KSTLFTKEEVQTILGVAG-----YF--G------DPPEPAIEKPKEYWTGKQIFSAFLPED------LNFEGRAKICSGS 569 (868)
T ss_pred ccccCCHHHHHHHHhcCC-----cc--c------cCCCceecCCcccccHHHHHHHhcCCC------Ccceecccccccc
Confidence 999999999999987643 11 1 678999999999999999999999864 444444443321
Q ss_pred ---CcccccCCcEEEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceecCCCC
Q psy13846 533 ---NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609 (1423)
Q Consensus 533 ---~~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~D~~ 609 (1423)
..+++++|+.|+|+|||+++|++||+++|+ ++++++|.+|++||++.|+.||+++++++++||+.+|||+|++|++
T Consensus 570 ~~~~~~~~~~d~~v~i~~g~ll~G~ldK~~lg~-~~~~li~~i~~~yG~~~a~~fl~~~~~l~~~~l~~~GfSigi~D~~ 648 (868)
T TIGR02390 570 DACKKEECPHDAYVVIKNGKLLKGVIDKKAIGA-EKGKILHRIVREYGPEAARRFLDSVTRLFIRFITLRGFTTGIDDID 648 (868)
T ss_pred cccccccCCCcceEEEecCeEEeeeecHHHhcc-CcccHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHhccEEeehhhee
Confidence 345688999999999999999999999998 5789999999999999999999999999999999999999999998
Q ss_pred CCc-----------------------------------------------------------------------------
Q psy13846 610 PGQ----------------------------------------------------------------------------- 612 (1423)
Q Consensus 610 ~~~----------------------------------------------------------------------------- 612 (1423)
+++
T Consensus 649 ~~~~~~~~~~~~i~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~e~~i~~~l~~~r~~~~~~~~~~l~~~N~~~~M~~sG 728 (868)
T TIGR02390 649 IPKEAKEEIEELIEKAEKRVDNLIERYRNGELEPLPGRTVEETLEMKIMEVLGKARDEAGEVAEKYLDPENHAVIMARTG 728 (868)
T ss_pred eCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcchhhhhhcc
Confidence 654
Q ss_pred -----------------------------------------------cccccccccCCCceeeeeecccccccchhcccc
Q psy13846 613 -----------------------------------------------GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVK 645 (1423)
Q Consensus 613 -----------------------------------------------GfI~~sf~~GL~p~Efffh~maGReGLiDTAvK 645 (1423)
|||.+||++||+|+|||||||||||||||||||
T Consensus 729 sKGS~~Ni~Qi~~~lGQQ~~~g~ri~~~~~~rtlp~f~~~d~~~~~~GfV~~sF~~GL~p~EfFfH~m~gReGLiDTAvK 808 (868)
T TIGR02390 729 ARGSLLNITQMAAMVGQQSVRGGRIRRGYRNRTLPHFKKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGGREGLVDTAVR 808 (868)
T ss_pred CCcccccHHHHHhccCccccCCCcCccccccCCCCCCCCCCCCcccCceecccccCCCCHHHHHHHHhhhcccccccccc
Confidence 899999999999999999999999999999999
Q ss_pred cCCCCcchHHHHHHHhhhhhcccceeecc-------ccCCCccC
Q psy13846 646 TAETGYMQRRLVKSLEDLCVQYDMSFDAA-------FYGQTDCI 682 (1423)
Q Consensus 646 Ta~sGYlqRrLvk~ledl~v~yD~tVR~s-------~yG~~~~~ 682 (1423)
||+||||||||||+|||++|+||+||||+ .||+|+.+
T Consensus 809 Ta~sGYLqRrLvk~lEdl~v~yD~tVR~~~g~iiQf~YG~dg~d 852 (868)
T TIGR02390 809 TSQSGYMQRRLINALQDLYVEYDGTVRDTRGNLIQFKYGEDGVD 852 (868)
T ss_pred ccccchhHHHHHHHHhheEEecCCeEEeCCCcEEEEeccCCCcC
Confidence 99999999999999999999999999987 37776443
No 6
>PRK08566 DNA-directed RNA polymerase subunit A'; Validated
Probab=100.00 E-value=3.6e-128 Score=1238.97 Aligned_cols=534 Identities=40% Similarity=0.705 Sum_probs=483.9
Q ss_pred ccceeeeEEEecCCHHHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccC
Q psy13846 76 KVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPL 155 (1423)
Q Consensus 76 ~~~i~~~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~ 155 (1423)
..+|.+ |+|++||++||+++||++|+++++| |.+|+|++|||||||||++++...|+|||++..+||||||||+|+.
T Consensus 6 ~~~I~~-I~F~~~S~eEI~klSv~~It~~~~~--d~~g~P~~gGL~D~RLG~~~~~~~C~TCg~~~~~CPGHFGhIeL~~ 82 (882)
T PRK08566 6 PKRIGS-IKFGLLSPEEIRKMSVTKIITADTY--DDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELAR 82 (882)
T ss_pred ceeeee-EEEecCCHHHHHHhCeEEEeccccc--CCCCCcCCCCCCCcccCCCCCCCCCCCCCCCCCcCCCcceEEeccc
Confidence 356889 9999999999999999999999999 7799999999999999999999999999999999999999999999
Q ss_pred ceeEEeeeccHHHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCceee
Q psy13846 156 PVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKK 235 (1423)
Q Consensus 156 PV~h~gffd~v~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk 235 (1423)
||||||||+.+++||+|+|++ |++|++++++...|..+++.+...+...+.+.+++.+.|++.++|+|||+.+|.+++
T Consensus 83 PVfhpgf~~~v~~iL~~iC~~--C~rll~~~~~~~~~~~~l~~~~~~~~~~~~l~k~i~k~~k~~~~C~~Cg~~~~ki~~ 160 (882)
T PRK08566 83 PVIHVGFAKLIYKLLRATCRE--CGRLKLTEEEIEEYLEKLERLKEWGSLADDLIKEVKKEAAKRMVCPHCGEKQYKIKF 160 (882)
T ss_pred cccchhHHHHHHHHHHHhhhh--hCceeccccchHHHHHHHhchhhhhhhHHHHHHHHHHHhcCCCCCCCcCCCCceEEE
Confidence 999999999999999999999 999999998888899988876644445567888999999999999999999999987
Q ss_pred cCcceehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHHHhhccCCCcccccccccCCCCC
Q psy13846 236 CGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKP 315 (1423)
Q Consensus 236 ~~~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~eiLe~I~~~d~~lL~m~~~~arP 315 (1423)
++....... . + ...+.++|.+|+++|++||++|+++|++++..++|
T Consensus 161 ~~~~~~~~~-----~----------------------------~-~~~~~L~p~~V~~ilk~I~~eD~~lLg~~~~~~~P 206 (882)
T PRK08566 161 EKPTTFYEE-----R----------------------------K-EGLVKLTPSDIRERLEKIPDEDLELLGINPEVARP 206 (882)
T ss_pred ecceeEEEe-----c----------------------------C-CCceeCCHHHHHHHHHhCCHHHHHHhCCCCCCCCc
Confidence 642111000 0 0 12457899999999999999999999999999999
Q ss_pred cceEEEEecCCCCCCCCcEEcCCC-C------------------------------------------------------
Q psy13846 316 SDLILTRLLVPPNCIRPSVISDLK-S------------------------------------------------------ 340 (1423)
Q Consensus 316 e~liLt~lpVPP~~vRPsv~~g~~-~------------------------------------------------------ 340 (1423)
+||||++|||||+|+||++.+++. .
T Consensus 207 e~~il~~lPVpP~~iRPsv~~~~g~~~eDDLT~~L~~II~~N~~Lk~~~~~g~~~~~~~~~~~~LQ~~v~~~~d~~~~~~ 286 (882)
T PRK08566 207 EWMVLTVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVTTYFDNEIPGI 286 (882)
T ss_pred ceeEEeeeecCCCCCcCcEEeCCCcccCchHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHHhcCCccCC
Confidence 999999999999999999998653 1
Q ss_pred --------------------------------------------------------------------------------
Q psy13846 341 -------------------------------------------------------------------------------- 340 (1423)
Q Consensus 341 -------------------------------------------------------------------------------- 340 (1423)
T Consensus 287 ~~~~~~~~~~~~~i~~~l~gK~G~fR~nl~GKRvd~s~RsVI~pdp~l~~~evGvP~~~A~~Lt~pe~v~~~N~~~l~~~ 366 (882)
T PRK08566 287 PPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREY 366 (882)
T ss_pred cccccCCCCCccchHHhcccCCCccccccccccccCcCCceeeCCCCCcCCeeeCcHHHHHhCCCCeEEchhhHHHHHHH
Confidence
Q ss_pred -----------------------------------------------CCeEEEEecCccccccccceeeeEEecCCceee
Q psy13846 341 -----------------------------------------------DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRF 373 (1423)
Q Consensus 341 -----------------------------------------------~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~ 373 (1423)
+||+|||||||||||+|||||++|++|++||||
T Consensus 367 v~ng~~~~pga~~i~~~~g~~~~l~~~~~~~~~~~l~~g~~v~Rhl~dgd~vl~NRqPsLHr~si~a~~~~v~~~~t~r~ 446 (882)
T PRK08566 367 VLNGPEKHPGANYVIRPDGRRIKLTDKNKEELAEKLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRL 446 (882)
T ss_pred HHcCCCcCCCceEEEcCCCceeeehhhhHHHHHHhccccceehhhhhcCceeeecCCCcccccccceeEEEEecCceEee
Confidence 789999999999999999999999999999999
Q ss_pred ccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecc
Q psy13846 374 NECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453 (1423)
Q Consensus 374 ~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~ 453 (1423)
||++|+||||||||||||+|+|||++|||||+ .||.+.+|++||++|+|+++++||+++|+|+||.
T Consensus 447 n~~~c~~~NADFDGDeMn~h~Pqs~~a~aEa~--------------~Lm~~~~~~~sp~~g~pi~~~~QD~l~g~~~lt~ 512 (882)
T PRK08566 447 NLAVCPPYNADFDGDEMNLHVPQTEEARAEAR--------------ILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTR 512 (882)
T ss_pred ccccCCCccCCccCcEEEEecCCCHHHHHHHH--------------HHhcchhcEecCCCCCeeEEeehHHHHHHHHHHh
Confidence 99999999999999999999999999999999 9999999999999999999999999999999999
Q ss_pred cccCCCHHHHHHHHHhhccCCccccceEeeeeccccCCceeecceeeeecceeeeecccCCCCcccccceeecccccc--
Q psy13846 454 KNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYT-- 531 (1423)
Q Consensus 454 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~kp~~~wtGKqi~s~il~~~~~~~~~~~~~~~~~~~~-- 531 (1423)
+|+|++++|+++++++... ..+ .+|+|+|++|.++||||||||++||++. ++..+.+...
T Consensus 513 ~d~f~~~~~~~~l~~~~~~------~~~------~~~~pai~~p~~lwTGKqi~s~~lp~~~------~~~~~~~~~~~~ 574 (882)
T PRK08566 513 KSTLFTKEEALDLLRAAGI------DEL------PEPEPAIENGKPYWTGKQIFSLFLPKDL------NLEFKAKICSGC 574 (882)
T ss_pred ccccCCHHHHHHHHHhCCc------ccc------ccCCcccCCCcccccHHHHHHHHcCCCC------Cceeeccccccc
Confidence 9999999999999998741 112 6889999999999999999999998753 3333222221
Q ss_pred --cCcccccCCcEEEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceecCCCC
Q psy13846 532 --ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609 (1423)
Q Consensus 532 --~~~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~D~~ 609 (1423)
....++++|+.|+|+||||++|++||+.+|+ +.++++|.+|++||++.|+.||+++++++++||+.+|||||++|++
T Consensus 575 ~~~~~~~~~~d~~v~i~~gell~g~ldK~~lg~-~~~~li~~i~~~yG~~~a~~fl~~~~~l~~~~l~~~GfSigi~D~~ 653 (882)
T PRK08566 575 DECKKEDCEHDAYVVIKNGKLLEGVIDKKAIGA-EQGSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDED 653 (882)
T ss_pred cccccccCCCCceEEEecCEEEeccccHHHhhc-ccchHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCEEeehhhcc
Confidence 1234678899999999999999999999998 4599999999999999999999999999999999999999999998
Q ss_pred CCc-----------------------------------------------------------------------------
Q psy13846 610 PGQ----------------------------------------------------------------------------- 612 (1423)
Q Consensus 610 ~~~----------------------------------------------------------------------------- 612 (1423)
+++
T Consensus 654 ~~~~~~~~~~~~i~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~e~~i~~~l~~~r~~~~~~~~~~l~~~N~~~~M~~SG 733 (882)
T PRK08566 654 IPEEAKEEIDEIIEEAEKRVEELIEAYENGELEPLPGRTLEETLEMKIMQVLGKARDEAGEIAEKYLGLDNPAVIMARTG 733 (882)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcceeeeccc
Confidence 655
Q ss_pred -----------------------------------------------cccccccccCCCceeeeeecccccccchhcccc
Q psy13846 613 -----------------------------------------------GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVK 645 (1423)
Q Consensus 613 -----------------------------------------------GfI~~sf~~GL~p~Efffh~maGReGLiDTAvK 645 (1423)
|||.+||++||+|+|||||||||||||||||||
T Consensus 734 sKGS~~N~~Qi~~~lGqQ~~~g~ri~~~~~~rtLP~f~~~d~~~~~~GfV~~sF~~GL~p~EfffH~m~GReGliDTAvk 813 (882)
T PRK08566 734 ARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTLPHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAVR 813 (882)
T ss_pred cccCHHHHHHHHhccCceecCCCcCccCccCccCCCCCCCCCCcccCceeeccccCCCCHHHHHHHHhhhccccccccee
Confidence 899999999999999999999999999999999
Q ss_pred cCCCCcchHHHHHHHhhhhhcccceeecc-------ccCCCcc
Q psy13846 646 TAETGYMQRRLVKSLEDLCVQYDMSFDAA-------FYGQTDC 681 (1423)
Q Consensus 646 Ta~sGYlqRrLvk~ledl~v~yD~tVR~s-------~yG~~~~ 681 (1423)
||+||||||||||+|||++|+||+||||| .||+|+.
T Consensus 814 Ta~sGYlqRrLvk~ledl~v~yD~tVR~s~g~iiQf~YG~dg~ 856 (882)
T PRK08566 814 TSQSGYMQRRLINALQDLKVEYDGTVRDTRGNIVQFKYGEDGV 856 (882)
T ss_pred eccCccchHHHHHHHhheEEeeCCceEcCCCcEEEEeccCCCc
Confidence 99999999999999999999999999987 3776643
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=2.5e-125 Score=1198.33 Aligned_cols=476 Identities=26% Similarity=0.421 Sum_probs=370.1
Q ss_pred EEEecCCHHHHhhcceeeeecCcccccCCCCCCcCCccccCCC-CCC--------------CCCCccCCCCCCCcccC--
Q psy13846 83 IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRM-GTN--------------QKEANCTTCGQNLSDCV-- 145 (1423)
Q Consensus 83 i~F~~~S~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rL-G~~--------------~~~~~C~TCg~~~~eCp-- 145 (1423)
+++++.|||+|+++|+.||++|++++ +.+.+|..+||+|+|+ ||. ++...|.+||....+|+
T Consensus 2 i~i~laSPe~I~~ws~geV~~petin-y~t~kPe~~GLfcerIFGp~k~~ec~Cgkyk~~~~~~~~C~~Cgve~t~~~vr 80 (1140)
T TIGR02386 2 IKISIASPDTIRNWSYGEVKKPETIN-YRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKIRYKGVVCERCGVEVTESKVR 80 (1140)
T ss_pred eEEEecCHHHHHhhhceEEeccceec-CCCCccCCCCcccchhcCCccCceeccccccccCcCCcCCCCCCCCcccchhh
Confidence 79999999999999999999999997 6799999999999998 997 46678999999999999
Q ss_pred -CccceEEccCceeEEeeecc-----------HHHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHH
Q psy13846 146 -GHFGYIDLPLPVFHIGYFRC-----------VINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKI 213 (1423)
Q Consensus 146 -GHfGhIeL~~PV~h~gffd~-----------v~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i 213 (1423)
+|||||+|+.||+|+|||+. ..+.|+++|++ |+.+.+.+.........+... .++. ++
T Consensus 81 r~rmGhI~La~Pv~Hiwy~k~~ps~~~~ll~~~~k~le~v~y~--~~~~v~~~~~~~~~~~~~~~~-------~~~~-~~ 150 (1140)
T TIGR02386 81 RERMGHIELAAPVAHIWYFKGLPSRIGLLLDITAKELESVLYF--ENYVVLDPGDTKLDKKEVLDE-------TEYR-EV 150 (1140)
T ss_pred hhcccceeecCCceeehhcCCCchHHHHHhCCCHHHhhheeec--cceEEeCCCCCchhhhhhhch-------hHHH-HH
Confidence 99999999999999999998 38999999999 999887663211101111000 0111 11
Q ss_pred HHHccCCccCCCCCCCCCceeecCcceehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHH
Q psy13846 214 LETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQ 293 (1423)
Q Consensus 214 ~~~~kk~k~C~~Cg~~~~~irk~~~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~e 293 (1423)
.+... ...=..||+........+ +.+ +.....+.+++.. ... .. +..+.+...++.+
T Consensus 151 ~~~~~-~~~~~~~G~~ai~~~l~~-~dl------------~~~~~~~~~~~~~----~~~----~~-~~~~~~krl~~~~ 207 (1140)
T TIGR02386 151 LKRYG-DGFRAGMGAEAIKELLEK-IDL------------DKEIEELKIQLRE----SKS----DQ-KRKKLLKRLEIVE 207 (1140)
T ss_pred HHHhc-cCcccccchHHHHHHHhc-CCH------------HHHHHHHHHHHHh----ccc----hh-hHHhhhhHHHHHH
Confidence 11110 000112343221111000 000 0111111111111 000 00 1123455666666
Q ss_pred HhhccCCCcccccccccCCCCCcceEEEEecCCCCCCCCcEEcCCCC---------------------------------
Q psy13846 294 LFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKS--------------------------------- 340 (1423)
Q Consensus 294 iLe~I~~~d~~lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~~--------------------------------- 340 (1423)
.|.. +++||+||+|++|||||+++||++.+++..
T Consensus 208 ~f~~-------------s~~~Pewmil~~lPV~Pp~lRP~v~l~gg~~~~sDLn~lyr~II~~Nn~Lk~~~~~~ap~~ii 274 (1140)
T TIGR02386 208 AFKD-------------SGNRPEWMVLDVIPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIV 274 (1140)
T ss_pred HHHh-------------cCCChHHhhhhcccCCCCccCCcEEeCCCccccCchHHHHHHHHHHHHHHHHHHHcCCcHHHH
Confidence 6665 357999999999999999999999997641
Q ss_pred --------------------------------------------------------------------------------
Q psy13846 341 -------------------------------------------------------------------------------- 340 (1423)
Q Consensus 341 -------------------------------------------------------------------------------- 340 (1423)
T Consensus 275 ~~~~~~LQ~aV~~liDn~~~g~~~~~~~~rplksls~~LkGK~GrFR~NLlGKRVDySgRSVI~pdP~L~l~e~GlP~~m 354 (1140)
T TIGR02386 275 RNEKRMLQEAVDALFDNGRRGKPVVGKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKM 354 (1140)
T ss_pred HHHHHHHHHHHHHHhcccccCCCccCcCCCchhhHHHhhcCCCCcccccccccccCCCCCCeEcCCCCcccccccChHHH
Confidence
Q ss_pred --------------------------------------------CCeEEEEecCccccccccceeeeEEecCCceeeccC
Q psy13846 341 --------------------------------------------DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNEC 376 (1423)
Q Consensus 341 --------------------------------------------~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~ 376 (1423)
++|+|||||||||||+|||||++++++++|||+||+
T Consensus 355 A~~L~~Pf~i~~L~~~~~~~~i~~ak~~i~~~~~~v~~vl~~vi~~d~VLlNRqPTLHRlsIqAf~~~l~~gktirlhpl 434 (1140)
T TIGR02386 355 ALELFKPFIIKRLIDRELAANIKSAKKMIEQEDPEVWDVLEDVIKEHPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPL 434 (1140)
T ss_pred HHHcCchHHHHHHHHcCcccchHHHHHHHHhcCCccceEEEEccCCcEEEecCCCcccccccceeEEEEecCceEEEccc
Confidence 789999999999999999999999999999999999
Q ss_pred CCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecccc-
Q psy13846 377 VCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKN- 455 (1423)
Q Consensus 377 ~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~- 455 (1423)
+|+||||||||||||+|+|||++|||||+ .||.+.+|++||++|+|+++++||+++|+|.||.++
T Consensus 435 vC~~fNADFDGDeMnvHvPqS~eA~aEa~--------------~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~ 500 (1140)
T TIGR02386 435 VCTAFNADFDGDQMAVHVPLSPEAQAEAR--------------ALMLASNNILNPKDGKPIVTPSQDMVLGLYYLTTEKP 500 (1140)
T ss_pred ccCcccCCCCcceeEeecCCCHHHHHHHH--------------HHhCCcccEecCCCCCceEEeechhhheeeEeeeccc
Confidence 99999999999999999999999999999 999999999999999999999999999999999996
Q ss_pred -------cCCCHHHHHHHHHhhccCCccccceEeeeeccccCCceeecceeee--ecceeeeecccCCCCcccccceeec
Q psy13846 456 -------AFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIW--TGKQIFSLILKPNRDCPVNANLKTK 526 (1423)
Q Consensus 456 -------~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~kp~~~w--tGKqi~s~il~~~~~~~~~~~~~~~ 526 (1423)
.|++++++...... +....+..++ ...++..+| +|||+|+.++|++... .
T Consensus 501 ~~~~~~~~F~~~~e~~~~~~~---~~i~l~~~i~----------~~~~g~~~~tt~Gr~if~~ilP~~~~~------~-- 559 (1140)
T TIGR02386 501 GAKGEGKIFSNVDEAIRAYDN---GKVHLHALIG----------VRTSGEILETTVGRVIFNEILPEGFPY------I-- 559 (1140)
T ss_pred cccCcCceeCCHHHHHHHHHc---CCccCCCceE----------EeccccEEEccchHHHHHHHcCCcccc------c--
Confidence 68999998764321 1112222220 001234566 6999999999864210 0
Q ss_pred ccccccCcccccCCcEEEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceecC
Q psy13846 527 GRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIG 606 (1423)
Q Consensus 527 ~~~~~~~~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~ 606 (1423)
+ . .+.++|+.+| ++++.+|++||++.|+.||++++++..+|++.+|||+|++
T Consensus 560 ------------n-------~----~~~l~Kk~lg-----~LI~~i~~~~G~~~t~~~LD~lk~Lgf~~at~~GfSigi~ 611 (1140)
T TIGR02386 560 ------------N-------D----NEPLSKKEIS-----SLIDLLYEVHGIEETAEMLDKIKALGFKYATKSGTTISAS 611 (1140)
T ss_pred ------------c-------c----ccccchHHHH-----HHHHHHHHHhChHHHHHHHHHHHHHHHHHHHhcCeeeeec
Confidence 0 0 0167888875 7999999999999999999999999999999999999999
Q ss_pred CCCCCc--------------------------------------------------------------------------
Q psy13846 607 DVTPGQ-------------------------------------------------------------------------- 612 (1423)
Q Consensus 607 D~~~~~-------------------------------------------------------------------------- 612 (1423)
|+.+++
T Consensus 612 Dl~ip~~K~~ii~~a~~~v~~i~~~y~~G~lt~~er~~kvi~iw~~~~d~v~~~~~~~l~~~~~~~N~i~mMa~SGARGS 691 (1140)
T TIGR02386 612 DIVVPDEKYEILKEADKEVAKIQKFYNKGLITDEERYRKVVSIWSETKDKVTDAMMKLLKKDTYKFNPIFMMADSGARGN 691 (1140)
T ss_pred cCCCCHHHHHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCcHhhhhhcccccC
Confidence 996554
Q ss_pred -----------------------cccccccccCCCceeeeeecccccccchhcccccCCCCcchHHHHHHHhhhhhccc
Q psy13846 613 -----------------------GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668 (1423)
Q Consensus 613 -----------------------GfI~~sf~~GL~p~Efffh~maGReGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD 668 (1423)
-||.+||++||+|+|||||||||||||+|||+|||+||||||||||++||++|.||
T Consensus 692 ~~ni~QL~GmrGlma~p~Grii~~PI~ssF~eGLtp~EyF~st~GaRkGLiDTAlKTAdSGYLtRRLVdv~qDviV~~d 770 (1140)
T TIGR02386 692 ISQFRQLAGMRGLMAKPSGDIIELPIKSSFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVVVREE 770 (1140)
T ss_pred HHHHHHHHhCCCcccCCCCCccccchhhccccCCCHHHHhhhccchhccccchheeecccceeeeehhhhhcceEEEeC
Confidence 47999999999999999999999999999999999999999999999999999995
No 8
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=100.00 E-value=2.5e-123 Score=1181.28 Aligned_cols=481 Identities=29% Similarity=0.444 Sum_probs=368.5
Q ss_pred ceeeeEEEecCCHHHHhhcceeeeecCcccccCCCCCCcCCccccCCC-CCCCCCCccCCCCCCC------cccC-----
Q psy13846 78 FFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRM-GTNQKEANCTTCGQNL------SDCV----- 145 (1423)
Q Consensus 78 ~i~~~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rL-G~~~~~~~C~TCg~~~------~eCp----- 145 (1423)
.+.. ++.++.|||+|+++|+-||++|++.+ +.+.+|..+||+|.|+ || .++..| .||+.. ..|+
T Consensus 6 ~~~~-i~i~laspe~I~~ws~GeV~~petin-yrt~kPe~~GLfcerIFgp-~kd~eC-~Cgkyk~~~~~~~~C~~cgve 81 (1156)
T PRK00566 6 DFDA-IKIGLASPEKIRSWSYGEVKKPETIN-YRTLKPERDGLFCERIFGP-TKDYEC-LCGKYKRVRYKGIICERCGVE 81 (1156)
T ss_pred Ccce-EEEEccCHHHHHHhhcceEccccccc-cCCCccCCCCcccchhcCc-ccCcEE-eCccccccCcCCcCCCCCCce
Confidence 4677 99999999999999999999999997 6799999999999997 66 467788 888532 4788
Q ss_pred --------CccceEEccCceeEEeeeccH-----------HHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHH
Q psy13846 146 --------GHFGYIDLPLPVFHIGYFRCV-----------INILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR 206 (1423)
Q Consensus 146 --------GHfGhIeL~~PV~h~gffd~v-----------~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~ 206 (1423)
+|||||+|+.||.|+|||+.. .+.|+++|+. |+.+...+... . +.+.... .....
T Consensus 82 ~~~~~vrr~rmGhI~La~Pv~Hiwy~k~~ps~i~~ll~~~~k~le~v~y~--~~~~v~~~~~~-~-~~~~~~~--~~~~~ 155 (1156)
T PRK00566 82 VTRSKVRRERMGHIELAAPVAHIWFFKSLPSRIGLLLDMSLKDLERVLYF--ESYVVIDPGDT-P-LEKKQLL--TEEEY 155 (1156)
T ss_pred eeechhhhhhcceeeecCceeeeeecCCCchHHHHHhCCCHHHhhheeec--ceEEEeCCCCC-c-hhhhccc--CHHHH
Confidence 999999999999999999944 9999999999 99887766431 1 1100000 00011
Q ss_pred HHHHHHHHHHccCCccCCCCCCCCCceeecCcceehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccC
Q psy13846 207 KSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTL 286 (1423)
Q Consensus 207 ~~~~~~i~~~~kk~k~C~~Cg~~~~~irk~~~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L 286 (1423)
+ ++.+... ...=..||+ +...+.+.... -+.....+.+++... ... . +..+.+
T Consensus 156 ~----~~~~~~~-~~~~~~~Ga-----------~ai~~ll~~~d--l~~~~~~l~~~~~~~---~~~----~--~~~~~~ 208 (1156)
T PRK00566 156 R----EALEEYG-DEFVAKMGA-----------EAIKELLKNID--LEAEAEELREELKET---GSE----Q--KRKKAL 208 (1156)
T ss_pred H----HHHHHhc-ccccccccH-----------HHHHHHHHhCC--HHHHHHHHHHHHHhc---ccc----h--hHHHHH
Confidence 1 1111110 000001111 11111110000 011111111111110 000 0 112223
Q ss_pred CHHHHHHHhhccCCCcccccccccCCCCCcceEEEEecCCCCCCCCcEEcCCCC--------------------------
Q psy13846 287 NPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKS-------------------------- 340 (1423)
Q Consensus 287 ~p~~V~eiLe~I~~~d~~lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~~-------------------------- 340 (1423)
...++.+.|.. +++||+||+|++|||||+|+||++.+++..
T Consensus 209 krl~~~~~f~~-------------s~~~Pewmil~~lPV~Pp~lRP~v~l~~g~~~~sDLn~lyr~II~rNnrLk~~~~~ 275 (1156)
T PRK00566 209 KRLKVVEAFRK-------------SGNKPEWMILDVLPVIPPDLRPLVQLDGGRFATSDLNDLYRRVINRNNRLKRLLEL 275 (1156)
T ss_pred HHHHHHHHHHc-------------CCCCccEeeEeecccCCCcccCceEeCCCcccCCchHHHHHHHHHHHHHHHHHHHc
Confidence 34444444443 357999999999999999999999998642
Q ss_pred --------------------------------------------------------------------------------
Q psy13846 341 -------------------------------------------------------------------------------- 340 (1423)
Q Consensus 341 -------------------------------------------------------------------------------- 340 (1423)
T Consensus 276 ~ap~~ii~~~~~~LQ~aV~~lidn~~~g~~~~~~~~rplksls~~LkGK~GrFR~NLlGKRVDySgRSVI~pdP~L~l~e 355 (1156)
T PRK00566 276 GAPEIIVRNEKRMLQEAVDALFDNGRRGRPVTGPNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQ 355 (1156)
T ss_pred CCcHHHHHHHHHHHHHHHHHHhccCccCCCcccccCCchhHHHHhhcCCCccccccccccccCCCCCceEeCCCCccccc
Confidence
Q ss_pred ---------------------------------------------------CCeEEEEecCccccccccceeeeEEecCC
Q psy13846 341 ---------------------------------------------------DNDVVLFNRQPSLHKLSIMAHRAKVLPHR 369 (1423)
Q Consensus 341 ---------------------------------------------------~~d~Vl~nRqPsLHk~Simah~~~~~~~~ 369 (1423)
+||+|||||||||||+|||||++++++++
T Consensus 356 ~GvP~~mA~eL~~Pf~i~~L~~~g~~~~ik~ak~~~~~~~~~v~~vle~vi~gd~VLlNRqPTLHR~sIqAf~~~l~~gk 435 (1156)
T PRK00566 356 CGLPKKMALELFKPFIMKKLVERGLATTIKSAKKMVEREDPEVWDVLEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGK 435 (1156)
T ss_pred ccChHHHHHHhCcHHHHHHHHHcCCccchHhhhhhhhhhcCcceEEEEEecCCCEEEecCCCcccccccceeEEEEecCc
Confidence 89999999999999999999999999999
Q ss_pred ceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEE
Q psy13846 370 TFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGY 449 (1423)
Q Consensus 370 tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~ 449 (1423)
||||||++|+||||||||||||+|+|||++|||||+ .||.+.+|++||++|+|+++++||+++|+|
T Consensus 436 tirLhplvC~~fNADFDGDqMnvHvPqS~eA~aEa~--------------~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y 501 (1156)
T PRK00566 436 AIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEAR--------------VLMLSSNNILSPANGKPIIVPSQDMVLGLY 501 (1156)
T ss_pred eEEECccccCccccccccceeEEecCCCHHHHHHHH--------------HHhCCcccEEecCCCCeeEEeehhhhhhhh
Confidence 999999999999999999999999999999999999 999999999999999999999999999999
Q ss_pred eecccc--------cCCCHHHHHHHHHhhccCCccccceEeeeeccccCCceeecceeeeecceeeeecccCCCCccccc
Q psy13846 450 LLTQKN--------AFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNA 521 (1423)
Q Consensus 450 ~~t~~~--------~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~kp~~~wtGKqi~s~il~~~~~~~~~~ 521 (1423)
.||.++ .|++.+++.++.+.. ..+.+..+ .+++|. .+..+.|+|||+|+.++|++..
T Consensus 502 ~LT~~~~~~~~~~~~F~~~~e~~~~~~~~---~i~l~~~i------~~~~~~-~~~i~tt~Gk~if~~ilP~~~~----- 566 (1156)
T PRK00566 502 YLTREREGAKGEGMVFSSPEEALRAYENG---EVDLHARI------KVRITS-KKLVETTVGRVIFNEILPEGLP----- 566 (1156)
T ss_pred eeecccccccCCCceeCCHHHHHHHHHcC---CCCCCCeE------EecCCC-CceEEcCcHHHHHHhhccccce-----
Confidence 999998 789999998875432 12333333 122221 1234679999999999986410
Q ss_pred ceeecccccccCcccccCCcEEEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCc
Q psy13846 522 NLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGF 601 (1423)
Q Consensus 522 ~~~~~~~~~~~~~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~Gf 601 (1423)
| + + ..|.+||+.+| +++|.+|++||.+.|+.||++++++..+|++.+||
T Consensus 567 --------~------------~---n---~~g~ldKk~Lg-----~LI~~i~~~yG~~~t~~~LD~ik~Lgf~yat~~Gf 615 (1156)
T PRK00566 567 --------F------------I---N---VNKPLKKKEIS-----KIINEVYRRYGLKETVIFLDKIKDLGFKYATRSGI 615 (1156)
T ss_pred --------e------------e---c---ccceecHHHHH-----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCe
Confidence 0 0 0 05789999986 59999999999999999999999999999999999
Q ss_pred ceecCCCCCCc---------------------------------------------------------------------
Q psy13846 602 SIGIGDVTPGQ--------------------------------------------------------------------- 612 (1423)
Q Consensus 602 siGi~D~~~~~--------------------------------------------------------------------- 612 (1423)
|+|++|+++.+
T Consensus 616 Sigi~Dl~ip~~K~~ii~~a~~~v~~i~~~y~~G~lt~~er~~kvi~~w~~~~d~v~~~~~~~l~~~~~~~N~i~mMa~S 695 (1156)
T PRK00566 616 SIGIDDIVIPPEKKEIIEEAEKEVAEIEKQYRRGLITDGERYNKVIDIWSKATDEVAKAMMKNLSKDQESFNPIYMMADS 695 (1156)
T ss_pred EeehhhcCcChHHHHHHHHHHHHHHHHHHHHHcCCCCchHHHHHHHHHHHHHHHHHHHHHHHhCccccCCCCChheeeec
Confidence 99999997644
Q ss_pred ----------------------------cccccccccCCCceeeeeecccccccchhcccccCCCCcchHHHHHHHhhhh
Q psy13846 613 ----------------------------GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664 (1423)
Q Consensus 613 ----------------------------GfI~~sf~~GL~p~Efffh~maGReGLiDTAvKTa~sGYlqRrLvk~ledl~ 664 (1423)
.||.+||++||+|+|||||||||||||+|||||||+||||||||||++||++
T Consensus 696 GARGS~~ni~QL~GmrGlma~p~G~iie~pI~ssFreGLt~~EyFfst~GaRkGLiDTALKTAdSGYLtRRLVdvaqDvi 775 (1156)
T PRK00566 696 GARGSASQIRQLAGMRGLMAKPSGEIIETPIKSNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVI 775 (1156)
T ss_pred cCCcCHHHHHHHHhhcCccccCCCCEeehhhhhhhhcCCCHHHHhhcCcchhhcccchheeeccceeeehhHHHhhCceE
Confidence 4899999999999999999999999999999999999999999999999988
Q ss_pred hccc
Q psy13846 665 VQYD 668 (1423)
Q Consensus 665 v~yD 668 (1423)
|.||
T Consensus 776 V~~~ 779 (1156)
T PRK00566 776 VRED 779 (1156)
T ss_pred EEEC
Confidence 8773
No 9
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=100.00 E-value=1.1e-112 Score=1079.08 Aligned_cols=272 Identities=31% Similarity=0.488 Sum_probs=233.7
Q ss_pred CCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhh
Q psy13846 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKV 420 (1423)
Q Consensus 341 ~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~ 420 (1423)
++|+|||||||||||+|||||++++++++||||||++|+||||||||||||+|+|||++|||||+ .
T Consensus 495 ~gd~VLlNRqPTLHRlsIqAf~~~L~~gktIrLhplvC~~fNADFDGDqMnvHvPqS~eA~aEa~--------------~ 560 (1460)
T PRK14906 495 QDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEAR--------------V 560 (1460)
T ss_pred ccceeEeccCcccchhccceeeEEecCCceEEecccccCccccCCcCceeeeecCCCHHHHHHHH--------------H
Confidence 79999999999999999999999999999999999999999999999999999999999999999 9
Q ss_pred hhccccccccCCCCccccccccceEEEEEeecc-cc-------cCCCHHHHHHHHHhhccCCccccceEe-eeecccc--
Q psy13846 421 LMANKSNLVTPRNGELLIAATQDFITGGYLLTQ-KN-------AFFNRAQTMRIASTLIADTSDICGIIK-RFSWRSW-- 489 (1423)
Q Consensus 421 l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~-~~-------~~~~~~~~~~l~~~~~~~~~~~~~~~~-~~~~~~l-- 489 (1423)
||.+.+|++||++|+|+++++||+++|.|.||. ++ .|.+..++..+.++.. ..+.+..+. ++.. .+
T Consensus 561 Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~~~~~~~~~F~~~~e~~~a~~~~~--~~~l~~~i~~~~~~-~~~~ 637 (1460)
T PRK14906 561 LMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLTTERDGFEGEGRTFADFDDALNAYDARA--DLDLQAKIVVRLSR-DMTV 637 (1460)
T ss_pred HhcchhcEecCCCCCeeEEeeeeeeeeeEEeeeccccccccCceeCCHHHHHHHHhcCC--CccccccEEEecCc-cccc
Confidence 999999999999999999999999999999997 43 6788888877766421 113343332 1100 00
Q ss_pred -------CCceeecceeeeecceeeeecccCCCCcccccceeecccccccCcccccCCcEEEeccccccccccccCCcCC
Q psy13846 490 -------NPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGS 562 (1423)
Q Consensus 490 -------~~p~i~kp~~~wtGKqi~s~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~~ell~g~ldK~~~g~ 562 (1423)
..+...++...|+||++|+.+||.+. .++.+.++|+.+|
T Consensus 638 ~~~~~~~~~~~~~~~~~tt~Gr~Ifn~ilP~d~---------------------------------~fvN~~l~KK~Lg- 683 (1460)
T PRK14906 638 RGSYGDLEETKAGERIETTVGRIIFNQVLPEDY---------------------------------PYLNYKMVKKDIG- 683 (1460)
T ss_pred ccccccccCCCCCceEECCCCEEEEecccCCCc---------------------------------ccccceeeHHHHH-
Confidence 00112235567999999999998531 1334578888886
Q ss_pred CCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceecCCCCCCc------------------------------
Q psy13846 563 GGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ------------------------------ 612 (1423)
Q Consensus 563 ~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~D~~~~~------------------------------ 612 (1423)
++++.+|++||...+..|+++++++..+|++.+|||+|++|++..+
T Consensus 684 ----~LI~~i~~~~G~~~t~~fLD~Ik~LGf~yaT~sG~SIgi~Di~ip~~K~~iI~~A~~~V~ei~~~y~~G~iT~~Er 759 (1460)
T PRK14906 684 ----RLVNDCCNRYSTAEVEPILDGIKKTGFHYATRAGLTVSVYDATIPDDKPEILAEADEKVAAIDEDYEDGFLSERER 759 (1460)
T ss_pred ----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhCCEEEeecccccChHHHHHHHHHHHHHHHHHHHHHcCCCcHHHH
Confidence 5999999999999999999999999999999999999999984433
Q ss_pred ---------------------------------------------------------------cccccccccCCCceeee
Q psy13846 613 ---------------------------------------------------------------GFVQNSFFSGLTPTEFF 629 (1423)
Q Consensus 613 ---------------------------------------------------------------GfI~~sf~~GL~p~Eff 629 (1423)
.||.+||.+||+|.|||
T Consensus 760 ~~kVi~iw~~a~d~v~~~~~~~l~~~N~i~mMa~SGARGS~~QI~QLaGmRGlma~p~G~iIe~PI~SnFrEGLt~~EyF 839 (1460)
T PRK14906 760 HKQVVDIWTEATEEVGEAMLAGFDEDNPIYMMADSGARGNIKQIRQLAGMRGLMADMKGEIIDLPIKANFREGLSVLEYF 839 (1460)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcccCCCeEeeeeccCcccHHHHHHHHhcccceecCCCCccccccccccccCCCHHHHH
Confidence 68999999999999999
Q ss_pred eecccccccchhcccccCCCCcchHHHHHHHhhhhhcc
Q psy13846 630 FHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667 (1423)
Q Consensus 630 fh~maGReGLiDTAvKTa~sGYlqRrLvk~ledl~v~y 667 (1423)
||||||||||+|||+|||+||||||||||++||++|..
T Consensus 840 iSt~GaRKGL~DTALKTAdSGYLTRRLVdVaQDViV~e 877 (1460)
T PRK14906 840 ISTHGARKGLVDTALRTADSGYLTRRLVDVAQDVIVRE 877 (1460)
T ss_pred HHcccccchhhhhhhhccccchHHHHHHHhhhheEEEe
Confidence 99999999999999999999999999999999998765
No 10
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=100.00 E-value=2.8e-111 Score=1101.32 Aligned_cols=278 Identities=29% Similarity=0.443 Sum_probs=231.8
Q ss_pred CCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhh
Q psy13846 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKV 420 (1423)
Q Consensus 341 ~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~ 420 (1423)
++|+|||||||||||+|||||++++++++||||||++|+||||||||||||+|+|||++|||||+ .
T Consensus 1850 ~gd~VLlNRqPTLHR~sIqAf~~~l~~gktirlhp~vC~~fNADFDGDeMnvHvPqS~eA~aEa~--------------~ 1915 (2836)
T PRK14844 1850 KEHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEAR--------------V 1915 (2836)
T ss_pred cCCEEEecCCCccccccccceeeEeecCceEEecccCCCcccCCCCCceeeeecCCcHHHHHHHH--------------H
Confidence 79999999999999999999999999999999999999999999999999999999999999999 9
Q ss_pred hhccccccccCCCCccccccccceEEEEEeecccccCC----CHHHHHHHHHhhccCCccccceEe-eeeccccCCceee
Q psy13846 421 LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFF----NRAQTMRIASTLIADTSDICGIIK-RFSWRSWNPVVFV 495 (1423)
Q Consensus 421 l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~~~----~~~~~~~l~~~~~~~~~~~~~~~~-~~~~~~l~~p~i~ 495 (1423)
||.+.+|++||++|+|+++++||+++|+|.||.++.+. ...++...+..+..+....+..++ ++.|-... ..-.
T Consensus 1916 Lm~~~~nilsP~~G~Pii~~~QD~ilG~y~LT~~~~~~~~~~~f~~~~~~~~a~~~~~~~i~~~i~~~~~~~~~~-~~~~ 1994 (2836)
T PRK14844 1916 LMMSTNNVLSPSNGRPIIVPSKDIVLGIYYLTLQEPKEDDLPSFGAFCEVEHSLSDGTLHIHSSIKYRMEYINSS-GETH 1994 (2836)
T ss_pred HhCCcccEEecCCCceeEeehhhhhhhhhhhcccccccccccccCCHHHHHHHHHcCCcccCceEEeeeccccCC-CCcc
Confidence 99999999999999999999999999999999999754 335556666655433333444332 11110000 0000
Q ss_pred cce-eeeecceeeeecccCCCCcccccceeecccccccCcccccCCcEEEeccccccccccccCCcCCCCCCchHHHHHH
Q psy13846 496 RTA-VIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574 (1423)
Q Consensus 496 kp~-~~wtGKqi~s~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~ 574 (1423)
.+. ....||++|+.+||.... -+++++.|.++|+.+ .++|+.+|+
T Consensus 1995 ~~~~~tt~GR~if~~ilP~~~~-----------------------------~~~~~~n~~l~KK~l-----~~II~~~~~ 2040 (2836)
T PRK14844 1995 YKTICTTPGRLILWQIFPKHEN-----------------------------LGFDLINQVLTVKEI-----TSIVDLVYR 2040 (2836)
T ss_pred cceEecccHHHHHHHHcCCccc-----------------------------cCcceEeeeechhHH-----HHHHHHHHH
Confidence 000 111599999999975311 023566778888877 469999999
Q ss_pred HhCHHHHHHHHHHhhhhhhHHHhhcCcceecCCCCCCc------------------------------------------
Q psy13846 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ------------------------------------------ 612 (1423)
Q Consensus 575 ~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~D~~~~~------------------------------------------ 612 (1423)
+||...++.||++++++..+|++.+|||+|++|+...+
T Consensus 2041 ~yG~~~t~~fLD~lk~LGf~yaT~~G~SIgi~Di~iP~~K~~iI~~a~~~v~~i~~~y~~G~it~~Er~~kvi~iW~~~~ 2120 (2836)
T PRK14844 2041 NCGQSATVAFSDKLMVLGFEYATFSGVSFSRCDMVIPETKATHVDHARGEIKKFSMQYQDGLITRSERYNKVIDEWSKCT 2120 (2836)
T ss_pred HhCHHHHHHHHHHHHHHHHHHHHhccEEeeHhHcccCHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999995443
Q ss_pred ---------------------------------------------------------cccccccccCCCceeeeeecccc
Q psy13846 613 ---------------------------------------------------------GFVQNSFFSGLTPTEFFFHTMGG 635 (1423)
Q Consensus 613 ---------------------------------------------------------GfI~~sf~~GL~p~Efffh~maG 635 (1423)
.+|.+||.+||+|.|||||||||
T Consensus 2121 d~v~~~~~~~l~~~~~~~~~N~i~mMa~SGARGS~sQI~QLaGmRGLmakp~G~iIe~PI~SNFrEGLsv~EyFiSt~Ga 2200 (2836)
T PRK14844 2121 DMIANDMLKAISIYDGNSKYNSVYMMVNSGARGSTSQMKQLAGMRGLMTKPSGEIIETPIISNFREGLNVFEYFNSTHGA 2200 (2836)
T ss_pred HHHHHHHHHhhhhccccCCCCceeeeecccCccCHHHHHHHHhcceeeecCCCCeeecchhhhhccCCCHHHhhhhcccc
Confidence 67999999999999999999999
Q ss_pred cccchhcccccCCCCcchHHHHHHHhhhhhcc
Q psy13846 636 REGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667 (1423)
Q Consensus 636 ReGLiDTAvKTa~sGYlqRrLvk~ledl~v~y 667 (1423)
||||+|||+|||+|||||||||+++||++|.-
T Consensus 2201 RKGL~DTALKTAdSGYLTRRLVDVaQDviI~e 2232 (2836)
T PRK14844 2201 RKGLADTALKTANSGYLTRRLVDVSQNCIVTK 2232 (2836)
T ss_pred ccchhhhhhhcccccchhhhhhhhhceEEEEe
Confidence 99999999999999999999999999998653
No 11
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=100.00 E-value=1.8e-109 Score=1088.61 Aligned_cols=264 Identities=31% Similarity=0.480 Sum_probs=232.2
Q ss_pred CCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhh
Q psy13846 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKV 420 (1423)
Q Consensus 341 ~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~ 420 (1423)
+||+|||||||||||+|||||++++++++||||||++|+||||||||||||+|+|||++|+|||+ .
T Consensus 1806 ~gd~VLlNRqPTLHR~sIqAf~~~l~~gktIrLhplvC~~fNADFDGDqMnvHvPqS~eA~aEa~--------------~ 1871 (2890)
T PRK09603 1806 EGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECK--------------V 1871 (2890)
T ss_pred cCCeEEecCCCccccccceeeeEEEecCceEEeccccCCcccCCCCCceeEEeecCCHHHHHHHH--------------H
Confidence 89999999999999999999999999999999999999999999999999999999999999999 9
Q ss_pred hhccccccccCCCCccccccccceEEEEEeecccccCC--------CHHHHHHHHHhhccCCccccceEeeeeccccCCc
Q psy13846 421 LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFF--------NRAQTMRIASTLIADTSDICGIIKRFSWRSWNPV 492 (1423)
Q Consensus 421 l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~~~--------~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p 492 (1423)
||.+.+|++||++|+|+++++||+++|.|.||.+|.++ +..++.. ++..+....+. +.|
T Consensus 1872 LM~s~~nilsP~~G~Pi~~p~QD~vlG~y~LT~~~~~~~~~~~~F~~~~e~~~---~~~~~~~~~~~----------~i~ 1938 (2890)
T PRK09603 1872 LMLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKSGVKGEHKLFSSVNEIIT---AIDTKELDIHA----------KIR 1938 (2890)
T ss_pred HhcccceEEEcCCCceeEEeecceeeeeEEeeccccCCCCccceeCCHHHHHH---HHHcCCCccCC----------cce
Confidence 99999999999999999999999999999999999643 4444432 22212112222 234
Q ss_pred eeecceeeee--cceeeeecccCCCCcccccceeecccccccCcccccCCcEEEeccccccccccccCCcCCCCCCchHH
Q psy13846 493 VFVRTAVIWT--GKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFY 570 (1423)
Q Consensus 493 ~i~kp~~~wt--GKqi~s~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~~~~li~ 570 (1423)
.+.+|..+|| |||+|+.+||.... ..++.+.++|+.+| ++++
T Consensus 1939 ~~~~p~~l~Tt~GK~ifs~ilP~~~~-------------------------------~~~~n~~ldKK~Lg-----~LI~ 1982 (2890)
T PRK09603 1939 VLDQGNIIATSAGRMIIKSILPDFIP-------------------------------TDLWNRPMKKKDIG-----VLVD 1982 (2890)
T ss_pred eecCCcEEEcCccceeeeccCccccc-------------------------------cccEeeeechHHHH-----HHHH
Confidence 5557899999 99999999974310 01223568899886 5999
Q ss_pred HHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceecCCCCCCc--------------------------------------
Q psy13846 571 ILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ-------------------------------------- 612 (1423)
Q Consensus 571 ~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~D~~~~~-------------------------------------- 612 (1423)
.+|++||...|+.||++++++..+|++.+|||+|++|+.+.+
T Consensus 1983 ~i~~~yG~~~t~~fLD~lk~LGf~yat~~G~SIgI~Dl~ip~~K~~iI~~A~~eV~ei~~~y~~G~it~~Er~~kvid~w 2062 (2890)
T PRK09603 1983 YVHKVGGIGITATFLDNLKTLGFRYATKAGISISMEDIITPKDKQKMVEKAKVEVKKIQQQYDQGLLTDQERYNKIIDTW 2062 (2890)
T ss_pred HHHHHHCHHHHHHHHHHHHHHHHHHHHhCCEeeeeccCcccHHHHHHHHHHHHHHHHHHHHHHcCCCCccHHHHHHHHHH
Confidence 999999999999999999999999999999999999996654
Q ss_pred -----------------------------------------------------------cccccccccCCCceeeeeecc
Q psy13846 613 -----------------------------------------------------------GFVQNSFFSGLTPTEFFFHTM 633 (1423)
Q Consensus 613 -----------------------------------------------------------GfI~~sf~~GL~p~Efffh~m 633 (1423)
.+|.+||++||+|+|||||||
T Consensus 2063 ~~~~d~v~~~~~~~l~~~~~~~N~i~mMa~SGARGS~~NI~QLaGmrGqMakp~G~iie~PI~snFrEGLtp~EyFfst~ 2142 (2890)
T PRK09603 2063 TEVNDKMSKEMMTAIAKDKEGFNSIYMMADSGARGSAAQIRQLSAMRGLMTKPDGSIIETPIISNFKEGLNVLEYFNSTH 2142 (2890)
T ss_pred HHHHHHHHHHHHHHhhhcCCCCCcHHHHHhccccccHHHHHHHHHcCCcEECCCCCcccChhhcCcccCCCHHHHHHhcc
Confidence 578999999999999999999
Q ss_pred cccccchhcccccCCCCcchHHHHHHHhhhhhcc
Q psy13846 634 GGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667 (1423)
Q Consensus 634 aGReGLiDTAvKTa~sGYlqRrLvk~ledl~v~y 667 (1423)
||||||+|||||||+||||||||||++||++|..
T Consensus 2143 GaRKGLiDTALKTAdSGYLTRRLVdvaQDviI~e 2176 (2890)
T PRK09603 2143 GARKGLADTALKTANAGYLTRKLIDVSQNVKVVS 2176 (2890)
T ss_pred ccccchhhhhhhccccchhhhhHHHhhcceEEEe
Confidence 9999999999999999999999999999998876
No 12
>KOG0261|consensus
Probab=100.00 E-value=1e-110 Score=994.13 Aligned_cols=759 Identities=33% Similarity=0.434 Sum_probs=598.8
Q ss_pred hHHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeecccCCcccCHHHHHHHHHHhhcccccceeeeEEEecCCH
Q psy13846 11 LYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFFRGLIEGTVTKE 90 (1423)
Q Consensus 11 ~~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~F~~~S~ 90 (1423)
--|||||||.+||+|++|+||||+|+|+|+++||||||.||||+|||||+|+++++|+++++.+. ..+.+..|
T Consensus 509 QTEEAraEA~~LMgvknNlvTPr~GEpiiAAtQDFiTg~YLlt~KDtF~dRa~~~ql~s~~~d~~-------~~i~lppP 581 (1386)
T KOG0261|consen 509 QTEEARAEALVLMGVKNNLVTPRNGEPIIAATQDFITGGYLLTHKDTFLDRAEFSQLCSYMSDAM-------THIDLPPP 581 (1386)
T ss_pred chHHHHHHHHHHhccccccccCCCCCceeehhhhhhhcceeeecccccccHHHHHHHHHHHhccc-------cccCCCCh
Confidence 35999999999999999999999999999999999999999999999999999999999988761 33444444
Q ss_pred HHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCC----CCCccCC---CCCCCcccCCccceEEccCceeEEeee
Q psy13846 91 DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQ----KEANCTT---CGQNLSDCVGHFGYIDLPLPVFHIGYF 163 (1423)
Q Consensus 91 eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~----~~~~C~T---Cg~~~~eCpGHfGhIeL~~PV~h~gff 163 (1423)
..+ ...++| |||++.+-|+-|--+..- ....|.- |+++. +.|..+||+-+.+.++-.|.+
T Consensus 582 aI~--------KP~~Lw----TGKQ~fsvlirpn~~s~v~~Nl~~k~k~~~~~~~k~~-~mc~nDg~v~irns~l~sG~l 648 (1386)
T KOG0261|consen 582 AIL--------KPVELW----TGKQLFSVLIRPNDDSPVRVNLDAKNKNFSLVKGKSF-EMCPNDGYVIIRNSELISGVL 648 (1386)
T ss_pred hhc--------Cceeee----ccCEEEEEEeccCCCCceEEeeccccceeecccCCCc-ccCCCCCeEEEecchhhhccc
Confidence 433 455778 899999888877654321 1112322 77777 556689999999999999999
Q ss_pred ccHHHHhhhccccccccccc--cChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCceeecCccee
Q psy13846 164 RCVINILQSICKNPTCARVL--LGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKI 241 (1423)
Q Consensus 164 d~v~~iL~~iC~~~~C~~ll--~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk~~~~ki 241 (1423)
| +.+|...-+.++.+.+| +++.++...++++.+.+..++-.++|+.+|.|..+.. .+.+.
T Consensus 649 d--Ks~lG~g~k~~lfy~llrDyg~~aAa~am~rlaklc~r~lgnrGFSIGi~DVqPg~----------------~L~~~ 710 (1386)
T KOG0261|consen 649 D--KSTLGSGKKDSLFYILLRDYGSMAAADAMNRLAKLCARFLGNRGFSIGIDDVQPGE----------------ILSQE 710 (1386)
T ss_pred c--cccccCCCccceEeeehhhcchHHHHHHHHHHHHhhhhhccccccccccCCCCccH----------------HHHHH
Confidence 9 88999999998999988 8899999999999999989999999999999885322 22222
Q ss_pred hhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHHHhhccCCCcc------------------
Q psy13846 242 SHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDI------------------ 303 (1423)
Q Consensus 242 ~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~eiLe~I~~~d~------------------ 303 (1423)
..+.....+.+|++. +.+|+. |.++..|++.-+++||.....++
T Consensus 711 k~~lv~~gY~kc~~~----I~e~~k--------------G~L~~qpg~~~eetLEa~I~~~Ls~IRe~~G~~C~~eL~~~ 772 (1386)
T KOG0261|consen 711 KEELVNRGYAKCDEK----IEEYNK--------------GKLQLQPGCNEEETLEAEILSELSTIREEAGKICIRELHPR 772 (1386)
T ss_pred HHHHHHhHHHHHHHH----HHHHhc--------------cccccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcc
Confidence 222233334444433 333432 66777888888888887433222
Q ss_pred -cccccccCCCCCcceEEEEecCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEEecCCceeeccCCCCccc
Q psy13846 304 -PLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYN 382 (1423)
Q Consensus 304 -~lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~n 382 (1423)
+-|.|+.+|++++.++++||. +||+||+++|.|.+++| ..|.||| |+.....|.+
T Consensus 773 NsPliMa~CGSKGS~INiSQMv---ACVGQQ~ISG~RvPdGf-----------------~dRsLPH----F~r~Sk~P~a 828 (1386)
T KOG0261|consen 773 NSPLIMALCGSKGSKINISQMV---ACVGQQIISGHRVPDGF-----------------EDRSLPH----FERHSKTPAA 828 (1386)
T ss_pred cChHHHHHhcCCCCcccHHHHH---HHhhhhhhcCCcCCCcc-----------------ccccCcc----ccccCCCccc
Confidence 347788899999999999999 99999999999999999 9999999 9999999999
Q ss_pred CCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecccccCCCHHH
Q psy13846 383 ADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 462 (1423)
Q Consensus 383 adFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~~~~~~~ 462 (1423)
.+|+-+++..+|.++| ||||+|+||||+++++++|+.+|||+|+|+.+++| |++.|++|+|++.++..|
T Consensus 829 KGFV~NSFySGLTptE----------FfFHtm~GREGLVDTAVKTAETGYMqRRLmK~LED-L~~~YDgTVR~s~~~vvq 897 (1386)
T KOG0261|consen 829 KGFVANSFYSGLTPTE----------FFFHTMSGREGLVDTAVKTAETGYMQRRLMKSLED-LSVQYDGTVRNSNGDVVQ 897 (1386)
T ss_pred cchhhhhcccCCCchh----------hheeecccccchhhhhhhhhhhhhHHHHHHHHHHH-HHHhhcCceecCCCcEEE
Confidence 9999999999999998 99999999999999999999999999999999999 999999999999999999
Q ss_pred HHHHHHhhccCCccccceEeeeeccccCCceeecceeeeec-ceeeeecccCCCCcccccceeecccccccCcccccCCc
Q psy13846 463 TMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTG-KQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDS 541 (1423)
Q Consensus 463 ~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~kp~~~wtG-Kqi~s~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~ 541 (1423)
|.|+.++++ +..++++.. |..+. ..|.- |.+ .|+....+ +.+++
T Consensus 898 F~YG~DglD--Pa~mEg~~~--------pv~f~---r~~~~~~~~----~~~~~~~~-----------------l~~~e- 942 (1386)
T KOG0261|consen 898 FTYGGDGLD--PAMMEGKDQ--------PVNFN---RVFDHAKAI----FPHRHDPP-----------------LSSEE- 942 (1386)
T ss_pred EeecCCCCC--hhhhcCCCC--------chhHH---HHHHHHHhc----CCCCCCCC-----------------CCHHH-
Confidence 999988874 446666531 22221 12211 111 11100000 00000
Q ss_pred EEEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceecCCCCCCcccccccccc
Q psy13846 542 YVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSFFS 621 (1423)
Q Consensus 542 ~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~D~~~~~GfI~~sf~~ 621 (1423)
+ .|-+...+.+..... ....++. -.+|+..+.+-....-..+|--++-. ..++
T Consensus 943 --l---~e~~~~~l~~~f~~~--~~~F~~~---------~~~~i~~~~~~~~~~~~~~~d~~~~~-~~~~---------- 995 (1386)
T KOG0261|consen 943 --L---DETLEEELLRKFTEK--GDPFVHE---------LREFIASLSKKIKKLQDKYGDECGPK-FCPD---------- 995 (1386)
T ss_pred --H---HHHHHHHHHHHhhhh--hhHHHHH---------HHHHHHHHHHHHHHHhhhcccccCCc-cCcc----------
Confidence 0 000111122222111 0111211 23344444333221111222211100 0000
Q ss_pred CCCceeeeeecccccccchhcccccCCCCcchHHHHHHHhhhhhcccceeeccccCCCccCCCcchheecCCCcccchhH
Q psy13846 622 GLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGL 701 (1423)
Q Consensus 622 GL~p~Efffh~maGReGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~tVR~s~yG~~~~~~~~~~~~~~~~~~~~g~~v 701 (1423)
+.+-.++-....|-++++.+.-+| +++.+|||+||
T Consensus 996 ----------------------~~~~~~~~t~kql~~f~~~~~~ky-----------------------~~a~~EpGTav 1030 (1386)
T KOG0261|consen 996 ----------------------LLYQISRLTEKQLEKFVERCLDKY-----------------------MRAKVEPGTAV 1030 (1386)
T ss_pred ----------------------ceeeeeeccHHHHHHHHHHHHHHH-----------------------HhhhcCCcchh
Confidence 111122223345777777777666 67889999999
Q ss_pred HHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhHHHHhhhcCCCCc
Q psy13846 702 IKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINASRNISTP 781 (1423)
Q Consensus 702 g~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlkEIinaSk~ikTP 781 (1423)
|+++|||||||+||||| +||||||| ||||||| |||||||||||+|+||||
T Consensus 1031 GAi~aQSIGEPGTQMTL----KTFHFAGV-------------ASMNiTl-------------GVPRIkEIINAsk~ISTP 1080 (1386)
T KOG0261|consen 1031 GAIAAQSIGEPGTQMTL----KTFHFAGV-------------ASMNITL-------------GVPRIKEIINASKTISTP 1080 (1386)
T ss_pred hhhhcccCCCCCceeee----eeeeecce-------------eeeeecc-------------CcchHHHHHhhhcccCcc
Confidence 99999999999999999 99999999 9999999 999999999999999999
Q ss_pred eeeeecccCChHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhhhHHhhhc---cccc
Q psy13846 782 IITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERT---RGIS 858 (1423)
Q Consensus 782 iitv~L~~~~~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I~~~i~~~---~~~~ 858 (1423)
+|++.|.++.|...||.++.|||+|+|+|+++||+++|.|+++|+.|++|++++++++|++++++|.++|.+. +..+
T Consensus 1081 IItA~L~n~~d~~~Ar~VKgRiEKt~L~dv~~yieeV~~p~~~fl~i~vd~~~I~~l~L~i~~~~I~~sI~~s~~~k~~~ 1160 (1386)
T KOG0261|consen 1081 IITAELENPHDERSARVVKGRIEKTTLGDVCSYIEEVYGPDSCFLLIRVDLKRISLLQLEITIESIAYSILKSPKRKVKP 1160 (1386)
T ss_pred ceeeeecCchhHHHHHHHhhhhhhhhHHHHHHHHHHHhCCcceEEEEEecHhHHhhhhccccHHHHHHHHhcCCccccCC
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999543 3456
Q ss_pred CcccccccccccccCC-CCccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCccccccceeeccc
Q psy13846 859 GHLTVSGHSFLILKPK-DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK 937 (1423)
Q Consensus 859 ~~i~~~~~~~~~~~~~-~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~nL~~vl~~~gvD 937 (1423)
.+|.+.++..+.+.|. +++.+.++.++.++..+|+|+|+|+|.|+|++|+.+++.+. |.|++||.+|+++|+++||+
T Consensus 1161 ~~v~v~~~~~~~v~~~~~~~~S~~~~lq~lk~~L~~Vvv~gip~vnr~vi~~de~~~~--y~L~vEG~gLr~Vm~t~GV~ 1238 (1386)
T KOG0261|consen 1161 NDVRVVGETTLRVTPVSDTKSSVYYNLQRLKRSLPNVVVKGIPEVNRAVINIDEKRGL--YKLLVEGTGLRAVMNTDGVK 1238 (1386)
T ss_pred cceEEecceeEEEeecccccchhhhhHHHHHhhCCceEEecCcchhhhheeecccCCc--eEEEEeccchHHHhccCCcc
Confidence 7888888766666664 34445577899999999999999999999999998765433 99999999999999999999
Q ss_pred ceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC
Q psy13846 938 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG 999 (1423)
Q Consensus 938 ~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~ 999 (1423)
+.+|+||+++||+++|||||||.+||+||.++|.+||++||+||||||||+||++|+|+|+.
T Consensus 1239 g~~TtsNnv~Ev~~vLGIEAAR~~II~EI~ytM~~HGmsiD~RHiMLLaDvMTyrGEVlGIT 1300 (1386)
T KOG0261|consen 1239 GRRTTSNNVLEVEKVLGIEAARTTIISEIGYTMSNHGMSIDPRHIMLLADVMTYRGEVLGIT 1300 (1386)
T ss_pred ccccccCceEEeehhhchHHHHHHHHHHHHHHHHhcCcccCHHHHHHHHHHhhhcceeeeee
Confidence 99999999999999999999999999999999999999999999999999999999999984
No 13
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]
Probab=100.00 E-value=8.8e-84 Score=812.15 Aligned_cols=497 Identities=33% Similarity=0.489 Sum_probs=415.9
Q ss_pred eeeeEEEecCCHHHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccCcee
Q psy13846 79 FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVF 158 (1423)
Q Consensus 79 i~~~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~PV~ 158 (1423)
+.+ ++|+++||++||+ |+.+|+.|++| |..++|..+||+|+|||..+++..| |||+....||||||||||+.||+
T Consensus 4 ~~~-i~~gl~sp~~ir~-~s~ev~~pet~--~~~~~P~~~Gl~d~ri~~~~~~~~C-~Cg~~~~~~~~~~GhIeLa~Pv~ 78 (808)
T COG0086 4 IFD-IKFGLASPEEIRS-WSGEVKKPETI--NYRTKPERGGLFDERIFGPDKDYEC-TCGKYKRICPGGFGHIELAAPVA 78 (808)
T ss_pred cce-eEEecCCHHHHHh-cceEEcCcccc--CCCCcccCCCccchhhcCCCCCcee-cCCCCcCcCCCCceeEEeecceE
Confidence 456 9999999999999 77999999999 5556999999999999999999999 99999999999999999999999
Q ss_pred EEeeeccHHHHhhhccccccccccccChhhHHHHH-HHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCceeecC
Q psy13846 159 HIGYFRCVINILQSICKNPTCARVLLGEEKAAGFR-AKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCG 237 (1423)
Q Consensus 159 h~gffd~v~~iL~~iC~~~~C~~ll~~~~~~~~~~-~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk~~ 237 (1423)
|+|||+.+.++|++.|.. |+++++. ++..++ ..+..... +....+ -....|+|||+.++.+++.+
T Consensus 79 hi~f~k~~~~~L~~~~~~--~~~v~~~--~~~~~~~~~l~~~~~--~~~~~~--------~~~~~~~~~Ga~~~~~~~~~ 144 (808)
T COG0086 79 HIWFFKSIPSLLDMTCRD--CERVLYF--EAYVVLGTDLEKIQL--LNETEY--------VYDSFCAHCGAEAIKILLEK 144 (808)
T ss_pred EechhhccHHHHhhhHHh--hhhhhhH--hHHHHhccchhhhcc--cchhee--------eccccCCCCCchhHHHHHhC
Confidence 999999999999999999 9999988 333333 11111110 000011 22378999999998777665
Q ss_pred cceehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHHHhhccCCCcccccccccCCCCCcc
Q psy13846 238 LLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSD 317 (1423)
Q Consensus 238 ~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~eiLe~I~~~d~~lL~m~~~~arPe~ 317 (1423)
...+... + . +.++|.++.++|++|...|+.+++ ++||+|
T Consensus 145 ~~~~~~~----------------------------------~-~--~~~~~~~~~~~~~~l~~~d~~~~~----~~~pew 183 (808)
T COG0086 145 PDLETER----------------------------------E-E--ETLSPTKVKKLLKRLKVVDAFLLS----GNRPEW 183 (808)
T ss_pred cchhhhh----------------------------------h-h--cccCHHHHHHHHhhccHHHHHHhc----CCCcce
Confidence 3222110 0 1 356899999999999999988888 589999
Q ss_pred eEEEEecCCCCCCCCcEEcCCCC---------------------------------------------------------
Q psy13846 318 LILTRLLVPPNCIRPSVISDLKS--------------------------------------------------------- 340 (1423)
Q Consensus 318 liLt~lpVPP~~vRPsv~~g~~~--------------------------------------------------------- 340 (1423)
|+|+++||||+++||++.+++..
T Consensus 184 mil~vlpV~Pp~~RP~i~ld~g~~a~~dl~~~~~~ii~~n~rlk~~~~~~~~~iv~~~~~~lQ~~v~~~~Dn~~~~~~~~ 263 (808)
T COG0086 184 MILTVLPVPPPDLRPSIQLDGGRFAESDLNDLYRRVINRNNRLKRLLELAAPIIVRNEKRMLQEAVDALFDNRRPRAVTG 263 (808)
T ss_pred eEEEeeccCCCCCCcceecCCCccchhHHHHHHHHHHHHHHHhHHhhhhcchHHHHHHHHHHHHHHHHHhhcCCCCCccC
Confidence 99999999999999999988742
Q ss_pred --------------------------------------------------------------------------------
Q psy13846 341 -------------------------------------------------------------------------------- 340 (1423)
Q Consensus 341 -------------------------------------------------------------------------------- 340 (1423)
T Consensus 264 ~rPlksl~~~LkgK~GrFR~nL~GKRVd~SgRsVI~~~P~l~~~e~GvP~~~A~~L~~p~~v~~~~~~~~~~~a~~~~~~ 343 (808)
T COG0086 264 GRPLKSLSQRLKGKQGRFRQNLLGKRVDYSGRSVISVGPNLKLNQCGVPKKMALELFKPFVVTELNIEGLRTGAKYAKRM 343 (808)
T ss_pred CCccccHHHHhcCCCceeeccccccccCCCCceeecCCCCccccccCCHHHHHHHhccCEEEEehhhhhhhcCCceEEec
Confidence
Q ss_pred ----------------CCeEEEEecCccccccccceeeeEEec-CCceeeccCCCCcccCCCcccccccccCCCHHHHhc
Q psy13846 341 ----------------DNDVVLFNRQPSLHKLSIMAHRAKVLP-HRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAE 403 (1423)
Q Consensus 341 ----------------~~d~Vl~nRqPsLHk~Simah~~~~~~-~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE 403 (1423)
++|.|||||||||||+|||+|..++++ ++|||+|+++|.||||||||||||+|+||+++|+||
T Consensus 344 ~~~~~~~~w~Vl~evi~gd~Vl~NR~PtLHrlsImq~~e~vl~~gkt~rLh~lVc~~yNADFDGDeM~~Hvp~s~ea~AE 423 (808)
T COG0086 344 VERRLPEVWDVLREVIDGDPVLLNRAPTLHRLSIMQAFEPVLPEGKAIRLHPLVCEAYNADFDGDEMAVHVPASGEAAAE 423 (808)
T ss_pred ccccccccchHHHHHhcCCccccccCChHHHHHHHhhceeeccccceeecchhhccccccccCchhhhccccchHHHHHH
Confidence 899999999999999999999999999 799999999999999999999999999999999999
Q ss_pred ccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecccccCCCHHHHHHHHHhhccCCccccceEee
Q psy13846 404 ALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKR 483 (1423)
Q Consensus 404 ~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~ 483 (1423)
|+ .+|.+.+|+.||..|+|+++.+||++.|.|+||..|+++...+.++++..-. . ..+
T Consensus 424 a~--------------~lm~tq~nilsP~~Ggpiv~~~qD~v~g~ylLt~~d~~~~~~~~~ei~l~~~----~--~~~-- 481 (808)
T COG0086 424 AR--------------GLMGTQMNILTPHYGGPIVAPIQDTVGGPYLLTIVDAKLPSTPVGEIYLKDE----Y--ADD-- 481 (808)
T ss_pred HH--------------HhhccccccccCCCCCceEeecceEEeccEEEEEecccCCCCcceEEEeccc----c--ccc--
Confidence 99 9999999999999999999999999999999999999988888777654310 0 111
Q ss_pred eeccccCCceeecceeeeecceeeeecccCCCCcccccceeecccccccCcccccC-CcEEEeccccccccccccCCcCC
Q psy13846 484 FSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHR-DSYVILRNSELLAGSMDKSTLGS 562 (1423)
Q Consensus 484 ~~~~~l~~p~i~kp~~~wtGKqi~s~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~-d~~v~i~~~ell~g~ldK~~~g~ 562 (1423)
..+++++.++..+|+||++++.+++......+..+........ .....+ |..+.+.|++++.|.++|...
T Consensus 482 ----~e~~~ai~~~~~~~~~k~i~~~i~~~~~~~~i~~t~~~~~~~~---~~~~~~~d~~~~i~~~~l~~~~i~k~~~-- 552 (808)
T COG0086 482 ----REKAEAIAKKIELTTGKVIVSTISPDLAELSIIVTTDGRRIFN---RGLPEDKDVLVKIVNGKLIKGVIDKKIV-- 552 (808)
T ss_pred ----hhhhHHHhcccceeeeeEEEEEeeccCCcceEEEecchhhhhh---ccCCcccceeeEEeccccceeeehhhHH--
Confidence 3457899999999999999998776543222222221111111 111122 577899999999999988764
Q ss_pred CCCCchHHHHHHHhCHHHHH-HHHHHhhhhhhHHHhhcC-cceecCCCC---CCc-------------------------
Q psy13846 563 GGKANVFYILLRDFGEDVAV-TAMWRLSRMTSFYLMNRG-FSIGIGDVT---PGQ------------------------- 612 (1423)
Q Consensus 563 ~~~~~li~~i~~~~G~~~a~-~~l~~l~~l~~~~L~~~G-fsiGi~D~~---~~~------------------------- 612 (1423)
.++++||+.++. .+++.+.++.+.+++..| |+++++|.- +..
T Consensus 553 --------~i~~~~g~~~~~~~~~~~~dkl~~~~~~~~~~~~~~i~~~d~~~~~~~~e~v~~ae~~v~~~i~~~~~g~lt 624 (808)
T COG0086 553 --------TIYREYGPEVASKALVKLLDKLKNLGIKGIGGFGIGIGRKDIEAEDEKDEIVIEAEGSVLKLILQYEEGDLT 624 (808)
T ss_pred --------HHHHHhCchhhHHHHHHHHHHHHHhheeeeccceEEeecccccchHHHHHHHHHHHHHHHHHHHHhhcCCcc
Confidence 678999998888 999999999999999988 988888763 211
Q ss_pred --------------------------------------------------------------------------------
Q psy13846 613 -------------------------------------------------------------------------------- 612 (1423)
Q Consensus 613 -------------------------------------------------------------------------------- 612 (1423)
T Consensus 625 ~~~~~~i~e~~e~~~~e~l~~ai~~~~~~~~~~~g~~~~~i~~m~~~Gs~~n~sq~~~~iG~~gv~g~r~~~~~~~~Fe~ 704 (808)
T COG0086 625 RTERNNIVEIIEVLGIEALRNAIIEEIKITLEEQGLDFVDIRHMGLSGARMNISQIVQLIGQQGVMGEKISVLARAAFEV 704 (808)
T ss_pred ccCCCCeEEEeehHHHHHHHHHHHHHHhhhHHhcCCcchhHHHHhhhhhccCHHHHHHHhhhheeeccCCCccccccccc
Confidence
Q ss_pred --------cccccccccCCCceeeeeecccccccchhcccccCCCCcchHHHHHHHhhhhhcccceeecc
Q psy13846 613 --------GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAA 674 (1423)
Q Consensus 613 --------GfI~~sf~~GL~p~Efffh~maGReGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~tVR~s 674 (1423)
|||.++|++||+|.|||||+||||+||+|||+|||+|||||||||+++|||+|.||++||++
T Consensus 705 ~~~~~~a~~~i~s~f~eGLt~~e~f~~~~ggR~GlvDTA~KTa~sGYl~RrLv~~~qdl~v~~d~~~~~g 774 (808)
T COG0086 705 TVKHLEAEGPGESSFLEGLTENEYFGHPIGGRTGLVDTALKTADSGYLTRRLVDVAQDLIVQEDDCVTDG 774 (808)
T ss_pred ccccceeeeeeecccCCCCCcceEEeecCccccchHHHhhhhcccCcceEEeechhcceEEEecCeEeec
Confidence 88999999999999999999999999999999999999999999999999999999999975
No 14
>KOG0260|consensus
Probab=100.00 E-value=8.1e-75 Score=701.10 Aligned_cols=796 Identities=20% Similarity=0.258 Sum_probs=533.1
Q ss_pred HHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeecccCCcccCHHHHHHHHHHhhcccccceeeeEEEecCCHH
Q psy13846 12 YYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFFRGLIEGTVTKED 91 (1423)
Q Consensus 12 ~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~F~~~S~e 91 (1423)
-+|||||+.||++||+||||||+|+|+||++||+|||+|++|.||+||+|+++|||+||+- . |+....-
T Consensus 486 S~etkAEl~EL~~vpkQiispQsnkpvmgivQDTLta~R~~t~Rd~Fl~r~~vmnLlm~~p-~--------~d~~~Pa-- 554 (1605)
T KOG0260|consen 486 SLETKAELEELAMVPKQIISPQSNKPVMGIVQDTLTAVRKMTKRDVFLNRAQVMNLLMYVP-D--------WDGPPPA-- 554 (1605)
T ss_pred chhHHHHHHHHhhhhhhhcCCcCCCcceeeehhhHHHHHHHhhHhhhhcHHHHHHHHhhcc-c--------cCCCCCC--
Confidence 4799999999999999999999999999999999999999999999999999999999961 1 1111110
Q ss_pred HHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccCceeEEeeeccH--HHH
Q psy13846 92 RVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCV--INI 169 (1423)
Q Consensus 92 eIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~PV~h~gffd~v--~~i 169 (1423)
--.......+| +|+++.+-++++.+........-.--+ ...--||--+ +-+....++.|.+.+. .+.
T Consensus 555 -----~pai~Kp~PlW----TGkQifsliiP~~in~~r~~s~h~d~~-~~~~~p~dt~-~lie~g~l~~g~l~Kkt~G~s 623 (1605)
T KOG0260|consen 555 -----KPAILKPKPLW----TGKQIFSLIIPGGINYIRDHSTHPDSE-DELISPGDTR-VLIEGGELLIGVLCKKTVGSS 623 (1605)
T ss_pred -----CcccCCCCccc----chhhheeeecCCCcceecccccCcCCC-cccccCCCce-EEEeCCceEEEEeeccccccc
Confidence 00023566788 999999999998876543211111011 1133455444 3445566667766532 334
Q ss_pred hhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCceeecCcceehhhhhccc
Q psy13846 170 LQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNR 249 (1423)
Q Consensus 170 L~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk~~~~ki~~e~~~~~ 249 (1423)
+..+.+- |.. ..+++..+.|...++..-...+.+.+|+.+|.+..... ..++.+++.+.+.
T Consensus 624 ~g~lvh~--i~~-e~Gp~~~~~f~~~iQ~lin~wll~~gfsigIgDtiad~----------------~t~~~iq~~I~~a 684 (1605)
T KOG0260|consen 624 AGGLVHV--IFL-EKGPKIARGFFDSIQTLINSWLLREGFSIGIGDTIADA----------------ATMCVIQNTIKEA 684 (1605)
T ss_pred cCceEEE--eeh-hhCHHHHHHHHHHHHHHHHHHHHhcCccccccccccCH----------------HHHHHHHHHHHHH
Confidence 4444333 322 25677777888777665555566778888887764322 1122222222111
Q ss_pred ccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHHHhhcc-------------------CCCccccccccc
Q psy13846 250 TKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAI-------------------PLEDIPLLLMNA 310 (1423)
Q Consensus 250 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~eiLe~I-------------------~~~d~~lL~m~~ 310 (1423)
+ ..+-+.+++.. . ..++..++.+.+++|++. -.+-+.++.|..
T Consensus 685 k----~dv~~vi~~a~-------------~-~~L~~~pg~tlretfe~~v~~vlndArd~~gssA~~sl~esNn~k~Mv~ 746 (1605)
T KOG0260|consen 685 K----RDVLAVIREAQ-------------N-NELEPTPGRTLRETFENKVNRVLNDARDKSGSSAQKSLSESNNFKTMVV 746 (1605)
T ss_pred H----HHHHHHHHHHh-------------h-ccccCCcchhHHHHHHHHHHHHHHHHHHhhhhHHHhhhhhcccHHHHHh
Confidence 1 01111111110 1 346677888888888872 122246677777
Q ss_pred CCCCCcceEEEEecCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCccccc
Q psy13846 311 ELSKPSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEM 390 (1423)
Q Consensus 311 ~~arPe~liLt~lpVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m 390 (1423)
.|++++.++|+|+. +||+||.+.|.+++.+| .-|++|| |-..+-+|...+|+.+++
T Consensus 747 aGSKGs~inisQ~s---aCVGqQnVEgkrIpFGF-----------------~~Rtlph----f~kDdysPesrGfVENSy 802 (1605)
T KOG0260|consen 747 AGSKGSFINISQVS---ACVGQQNVEGKRIPFGF-----------------PKRTLPH----FSKDDYSPESRGFVENSY 802 (1605)
T ss_pred hcCCCcceehhhhh---hhhccccccccccccCC-----------------Ccccccc----cccCCCCccccceeeccc
Confidence 88999999999999 99999999999999999 9999999 999999999999999999
Q ss_pred ccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecccccCCCHHHHHHHHHhh
Q psy13846 391 NVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 470 (1423)
Q Consensus 391 ~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~~~~~~~~~~l~~~~ 470 (1423)
-.+|.|.| |||||||||||++++++++..+||-+|+|+.+++| +++.||.|+|+++++..||.|+.+++
T Consensus 803 L~GLtP~E----------fFfHamggREglidtavktaEtGyiqRRL~kameD-imv~yDgTVRNs~gqviQf~YGeDG~ 871 (1605)
T KOG0260|consen 803 LTGLTPQE----------FFFHAMGGREGLIDTAVKTAETGYIQRRLMKAMED-IMVAYDGTVRNSLGQVIQFKYGEDGL 871 (1605)
T ss_pred ccCCCHHH----------HHHHHhcccchhhhhhhcccccchHHHHHHHHHHH-HHhhcCcceecccceeEEEEeccCcc
Confidence 99999665 99999999999999999999999999999999999 99999999999999999999999987
Q ss_pred ccCCccccceEeeeeccccCCceeecc-eeeeecceeeeecccCCCCc--cc----c--cceeec-ccccccCcccccCC
Q psy13846 471 IADTSDICGIIKRFSWRSWNPVVFVRT-AVIWTGKQIFSLILKPNRDC--PV----N--ANLKTK-GRAYTANEEFCHRD 540 (1423)
Q Consensus 471 ~~~~~~~~~~~~~~~~~~l~~p~i~kp-~~~wtGKqi~s~il~~~~~~--~~----~--~~~~~~-~~~~~~~~~~~~~d 540 (1423)
++..+... .++. +++ ...+-.+.-++.+..+.... .+ . .++... ...|.. ...|
T Consensus 872 d~~~vE~q---------~~~~---l~~~~a~f~~~~~~d~ld~~~~~~~~~~~~e~~~~~~l~~lle~e~~~----l~~d 935 (1605)
T KOG0260|consen 872 DGHPVEFQ---------NGET---LGSLNACFESEFAYDALDEPISLSSEEVVNEISELLKLQNLLECEYKK----LVRD 935 (1605)
T ss_pred ccceeecc---------cccc---ccchHHHHHhhhhhhhhcCcccchhhhHhhhhhhhHHHHHHHHHHHHh----hhhh
Confidence 64321111 1111 010 00011111111111000000 00 0 000000 000000 0000
Q ss_pred cEEEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceecCCCCCCccccccccc
Q psy13846 541 SYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSFF 620 (1423)
Q Consensus 541 ~~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~D~~~~~GfI~~sf~ 620 (1423)
..+. -.+....++++.+ +......+.+.++.+.... .-..|+++
T Consensus 936 r~~l----~~i~~~g~~k~~l----------------p~n~~r~I~Na~~~f~~~~------r~~t~l~~---------- 979 (1605)
T KOG0260|consen 936 RRVL----LYIFEYGDAKWPL----------------PENLQRIIWNALKKFSIDE------RKPTDLIP---------- 979 (1605)
T ss_pred hhhh----hhhcccCCccccc----------------chhHHHHHHHHHhhccccc------ccccccch----------
Confidence 0000 0001111222221 1222222222222211100 01112222
Q ss_pred cCCCceeeeeecccccccchhcccccCCCCcchH--HHHHHHhhhhhcccceeecc-----ccCCC-ccCCCcchheecC
Q psy13846 621 SGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQR--RLVKSLEDLCVQYDMSFDAA-----FYGQT-DCISGVSECIIMG 692 (1423)
Q Consensus 621 ~GL~p~Efffh~maGReGLiDTAvKTa~sGYlqR--rLvk~ledl~v~yD~tVR~s-----~yG~~-~~~~~~~~~~~~~ 692 (1423)
|++.-|-..+.-.-+--.-.-|+.| ||.. +-++-+..+++. +-.++ +|..|.++..+.+
T Consensus 980 ---------~~v~~g~~~l~e~l~iv~g~~~~sraqrl~~----~lLrs~l~~krv~~e~rls~eaf~w~~~~Ie~~f~q 1046 (1605)
T KOG0260|consen 980 ---------FKVVKGVKELAEKLVIVRGEDYISRAQRLFN----ILLRSTLATKRVLEEYRLSSEAFEWVLGEIEARFLQ 1046 (1605)
T ss_pred ---------hhhhhhhhhhhheeEEeeCchhHHHHHHHHH----HHHHhhHHHHHHHHHhcccHHHHHHHhhhhhhheee
Confidence 1233333333333332233335555 2111 111111111111 11111 3445666667788
Q ss_pred CCcccchhHHHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhHHHH
Q psy13846 693 LPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEII 772 (1423)
Q Consensus 693 ~~~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlkEIi 772 (1423)
+...||+-||.+||||+|||.||||| +|||+||| ++.|+|+ ||||+|||+
T Consensus 1047 a~a~pgemvg~lAaqsvgePatqmTl----ntfh~aGV-------------ssknVt~-------------gvprlkei~ 1096 (1605)
T KOG0260|consen 1047 AEASPGEMVGALAAQSVGEPATQMTL----NTFHYAGV-------------SSKNVTL-------------GVPRLKEII 1096 (1605)
T ss_pred eecCccchHhHHHHHHhCCchhhccc----chhcccce-------------eeeeeec-------------cCcchhhhh
Confidence 99999999999999999999999999 99999999 7889999 999999999
Q ss_pred hhhcCCCCceeeeecccC--ChHHHHHHHhhhhcccchhhhhhhheeeecCCC--------------------------c
Q psy13846 773 NASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD--------------------------S 824 (1423)
Q Consensus 773 naSk~ikTPiitv~L~~~--~~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~--------------------------~ 824 (1423)
|.+|++|||.+++||..+ .+.|+|+.+..+||++++.++...-+++|+|+. .
T Consensus 1097 Nv~k~~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 1097 NVAKNAKTPSLTVYLTGEAAKDNEWAKLVQCCLEHTTLKDVTRATEIYYDPDPQSTVIDEDREFVVAYYEMPDEDVGRIS 1176 (1605)
T ss_pred hhhccCCCceEEEEecchhhcchHHHHHHhhhcccccHHhhhccCcceecCCCcceeeccchhhHHhhhcCcccchhhcC
Confidence 999999999999999887 578999999999999999999988788887752 2
Q ss_pred ceeeehhhhHHHhhccccchhhhhHHhhhcccccCccccccc----ccccccCCCC--ccccchhhhhh-hhcCCceEEc
Q psy13846 825 FILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGH----SFLILKPKDS--SKSFNSKMYQM-KQLLPSVVIK 897 (1423)
Q Consensus 825 ~~~i~ld~~r~~~~~l~i~~~~I~~~i~~~~~~~~~i~~~~~----~~~~~~~~~~--~~~~~~~l~~l-~~~l~~v~Ik 897 (1423)
.|+++|.+||.++.+..+.+..|.+.|.+.++.+.....+.+ ..+.++..+. ++.| +..+ ...+.++...
T Consensus 1177 pwlLrlelDr~~m~dk~ltm~~ia~~i~~~f~~d~~~i~~ddna~klv~r~ri~~~~e~D~~---l~~Ie~~ml~~~~l~ 1253 (1605)
T KOG0260|consen 1177 PWLLRLELDRASMTDKKLTMEQIAEKINRGFGSDLACIFSDDNAEKLVLRLRIAKEEEDDVF---LKCIEANMLGDMTLR 1253 (1605)
T ss_pred hHHHHhhhhhhhcccccccHHHHHHHHHhhccCCCceeecccCCcceEEEEEecCccchhHH---HHHHHHhhhhhcccC
Confidence 245677777777777788888888888776654333222221 1222332211 1122 2233 3457788899
Q ss_pred cccccceeeeeccccc---ceeEEeeeccCccccccceeecccceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcC
Q psy13846 898 GVQGINRAVIHEEDVE---GVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHG 974 (1423)
Q Consensus 898 Gi~~I~r~~i~~~~~~---~~~~~~l~~eG~nL~~vl~~~gvD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~G 974 (1423)
|+++|.+++|+.+... ...+|.|.++|.+|+.++..+++|..+|+||++.|++.+|||||+|..++.|+..+....|
T Consensus 1254 G~~~i~kV~m~~~~~G~f~~~~ew~LeTdg~~l~~v~s~~~vD~~rt~sn~l~ei~~vlgIea~r~a~~~e~~~vi~f~g 1333 (1605)
T KOG0260|consen 1254 GIPDIFKVYMSPTEDGEFKPVDEWDLETDGVNLRRVLSEPDVDPARTTSNDLVEIAEVLGIEAVRKALLRELLNVISFDG 1333 (1605)
T ss_pred CccccceEEEeecCCCceeecceeEEecCchhHHhhhccCCCCcccccccchhhhhhhhcHHHHHhhhhhhhhheEeecc
Confidence 9999999999865432 3478999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCCchhhHhhhhccccccccCC
Q psy13846 975 MSIDFRHPMLVADLMTSKGEVLGNG 999 (1423)
Q Consensus 975 i~Id~RHi~LLAD~MT~~G~i~g~~ 999 (1423)
.+||+||+.||+|+||++|.++++.
T Consensus 1334 syVnyrhlaLl~dvmT~~g~lm~it 1358 (1605)
T KOG0260|consen 1334 SYVNYRHLALLCDVMTARGHLMAIT 1358 (1605)
T ss_pred cchhHHHHHHHHHHHhcccceeeee
Confidence 9999999999999999999999864
No 15
>TIGR02389 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit A''. This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Probab=100.00 E-value=2.6e-72 Score=651.56 Aligned_cols=294 Identities=39% Similarity=0.608 Sum_probs=253.2
Q ss_pred cccCcc-cCCCCCChhHHHHHHHHHhhhccCCCCcchhhhhhcccCCcccccccccccccc--------------c----
Q psy13846 1086 DKIGHG-RESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------E---- 1146 (1423)
Q Consensus 1086 ~~~~~~-~~~~~~~~~~~~~~~~~~y~~s~v~PGeaVG~iAAQSIGEP~TQmTLnTFH~AG--------------~---- 1146 (1423)
++++++ ++ + ||+++|+.+|.+++++||||||+|||||||||+|||||||||||| |
T Consensus 17 ~~~~~~~~~----~--~~l~~i~~ky~~alv~PGeaVG~IAAQSIGEP~TQMTLnTFH~AGVas~nVTlGVPRlkEIINa 90 (367)
T TIGR02389 17 REISDKEEL----D--EIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDA 90 (367)
T ss_pred cCCCHHHHH----H--HHHHHHHHHHHHhcCCCccccchhhhhhcCCccccccccccccccccccCccccchhHHHHhhc
Confidence 346666 66 7 999999999999999999999999999999999999999999999 1
Q ss_pred --------------------------------------ccceeEEEEccCCcEEEEEEchHHHHHhcccCCHHHHHHHHH
Q psy13846 1147 --------------------------------------VCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIE 1188 (1423)
Q Consensus 1147 --------------------------------------i~~~i~~~~~~~~~~~~i~l~~~~~~~~~~~i~~~~i~~~i~ 1188 (1423)
|+.+++..+. ...+.++||.+.++.. .+++++|..+|.
T Consensus 91 ~k~i~TP~~ti~L~~~~~~~~~~a~~v~~~iE~t~l~dv~~~~~~~~~--~~~l~i~ld~~~l~~~--~i~~~~i~~~i~ 166 (367)
T TIGR02389 91 RKTPSTPSMTIYLEDEYEKDREKAEEVAKKIEATKLEDVAKDISIDLA--DMTVIIELDEEQLKER--GITVDDVEKAIK 166 (367)
T ss_pred ccCCCCCeEEEEecCcchhhHHHHHHHHHHhhheeHHHHHhhhheecc--CcEEEEEECHHHHHhc--CCCHHHHHHHHH
Confidence 1222222222 3356778888877665 689999999986
Q ss_pred hccccCCceEEecCcEEEEEeCCCCchhhhHHHHHHhccCCcEEcccCCccEEEEecccccceeeEEEEecCccHHHHhh
Q psy13846 1189 RTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMA 1268 (1423)
Q Consensus 1189 ~~k~~~~~~~~~~~~~i~i~~~~~~~~~~~~l~~l~~~l~~~~v~Gi~~i~r~~i~~~~~~~~~~~~l~teG~nl~~~~~ 1268 (1423)
+.+.........++..+++++.. +....|+.+++.+.+++|+|+|||+||++.++ +++|+|.|||+||.++|+
T Consensus 167 ~~~~~~~~~~~~~~~~i~i~~~~---~~~~~l~~l~~~l~~~~v~Gi~gI~r~~i~~~----~~~~~l~teG~nl~~v~~ 239 (367)
T TIGR02389 167 KAKLGKVIEIDMDGNTITIKPPK---PSLKELRKLKEKIKNLHIKGIKGIKRVVIRKE----GDEYVIYTEGSNLKEVLK 239 (367)
T ss_pred HhcccccceeecCCCEEEEEecC---chHHHHHHHHHHhhhceEeCCCCceEEEEECC----CCeEEEEEeccCHHHHHc
Confidence 54321111111233567777642 23456888999999999999999999999843 358999999999999999
Q ss_pred cccccceecccccHHHHHHHhCHHHHHHHHHHHHHHHhhcCCccccCCchhhhhccccceeEEEeeecccccccccchhh
Q psy13846 1269 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLN 1348 (1423)
Q Consensus 1269 ~~~vd~~~~~sN~i~~i~~~lGIEAar~~ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~G~~~~i~r~g~~~~~~S~l~ 1348 (1423)
+++||++|++||||++|+++|||||||++|++|+++||+.||++||+|||+||||+||++|.+.|+||+|+++++.|||+
T Consensus 240 ~~~VD~~rt~sNdI~ei~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~RHl~LiaD~MT~~G~~~~i~R~Gi~~~~~S~l~ 319 (367)
T TIGR02389 240 LEGVDKTRTTTNDIHEIAEVLGIEAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKASVLA 319 (367)
T ss_pred CCCCccccCccCCHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCeecHHHHHHHHHHhcCCceEEeccccccccCCCCHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999888999999
Q ss_pred hccchhhHHHHHhhcccCCcccccccccceeeccccccccceEEEeec
Q psy13846 1349 LASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA 1396 (1423)
Q Consensus 1349 ~aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~~~~~GTG~~~l~~~ 1396 (1423)
+||||+|+++|++||.+|+.|+|+|||||||+|+++|+|||+|+|+++
T Consensus 320 ~aSFE~t~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~~~l~~~ 367 (367)
T TIGR02389 320 RAAFEVTVKHLLDAAIRGEVDELAGVIENIIVGQPIPLGTGDVDLVMD 367 (367)
T ss_pred hcChHhHHHHHHHHhhcCCCCcCCChHHHhhcCCCcCCcCCeEEEeeC
Confidence 999999999999999999999999999999999999999999999874
No 16
>cd02584 RNAP_II_Rpb1_C Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain. RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.
Probab=100.00 E-value=9.9e-71 Score=647.67 Aligned_cols=369 Identities=31% Similarity=0.476 Sum_probs=300.3
Q ss_pred ecCCCcccchhHHHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhH
Q psy13846 690 IMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIK 769 (1423)
Q Consensus 690 ~~~~~~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlk 769 (1423)
|.++.++||++||.+||||||||+||||| +||||||| ||+|+|| ||||||
T Consensus 19 ~~~~~~~~ge~vg~~aaQSiGEP~TQmTL----nTFH~AGV-------------as~NVTl-------------GVPRLk 68 (410)
T cd02584 19 FNRSLVHPGEMVGTIAAQSIGEPATQMTL----NTFHFAGV-------------SAKNVTL-------------GVPRLK 68 (410)
T ss_pred HHHhhcCCCCCcchhhhhhcCCchhcccc----cccccccc-------------ccccccc-------------CccchH
Confidence 36678999999999999999999999999 99999999 9999999 999999
Q ss_pred HHHhhhcCCCCceeeeecccC--ChHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhh
Q psy13846 770 EIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSI 847 (1423)
Q Consensus 770 EIinaSk~ikTPiitv~L~~~--~~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I 847 (1423)
|||||+|+||||+|++||.++ .|.+.|+.++.+||+++|+|++.+++++|+|+.++..++.|.+.++.+
T Consensus 69 EIInasK~ikTP~~tv~L~~~~~~d~~~A~~v~~~IE~t~l~dv~~~~~i~ydp~~~~~~i~~d~~~i~~~--------- 139 (410)
T cd02584 69 EIINVAKNIKTPSLTVYLEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVESY--------- 139 (410)
T ss_pred HHhhcccCCCCCeEEEEecCcccchHHHHHHHHhheeEeEHHHhhhheEEEecCcccceeecccHHHHHHh---------
Confidence 999999999999999999998 679999999999999999999999999999988776665555443110
Q ss_pred hHHhhhcccccCcccccccccccccCCCCccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCccc
Q psy13846 848 RYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927 (1423)
Q Consensus 848 ~~~i~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~nL 927 (1423)
T Consensus 140 -------------------------------------------------------------------------------- 139 (410)
T cd02584 140 -------------------------------------------------------------------------------- 139 (410)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred cccceeecccceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCCcchhhHHH
Q psy13846 928 RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRL 1007 (1423)
Q Consensus 928 ~~vl~~~gvD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~~~~~~~~~ 1007 (1423)
++ ..+
T Consensus 140 ------------------------------------------~~--------------------------~~d------- 144 (410)
T cd02584 140 ------------------------------------------FE--------------------------FPD------- 144 (410)
T ss_pred ------------------------------------------hc--------------------------cCc-------
Confidence 00 000
Q ss_pred HHHHHHhccCCCCCCCCHHHHHHHhhhhcCcchhhhhhhHHHHHHHHHHHHHhhhccccccccccCCchhhhhhhccccc
Q psy13846 1008 LDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDK 1087 (1423)
Q Consensus 1008 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1087 (1423)
...
T Consensus 145 -------------~~~---------------------------------------------------------------- 147 (410)
T cd02584 145 -------------EDV---------------------------------------------------------------- 147 (410)
T ss_pred -------------ccc----------------------------------------------------------------
Confidence 000
Q ss_pred cCcccCCCCCChhHHHHHHHHHhhhccCCCCcchhhhhhcccCCcccccccccccccccccceeEEEEccCCcEEEEEEc
Q psy13846 1088 IGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEVCEYIEEVFVPDDSFILIKLD 1167 (1423)
Q Consensus 1088 ~~~~~~~~~~~~~~~~~~~~~~y~~s~v~PGeaVG~iAAQSIGEP~TQmTLnTFH~AG~i~~~i~~~~~~~~~~~~i~l~ 1167 (1423)
..+. ...+.+++.
T Consensus 148 -~~~~------------------------------------------------------------------~~~~~lrl~ 160 (410)
T cd02584 148 -EQDR------------------------------------------------------------------LSPWLLRIE 160 (410)
T ss_pred -cccc------------------------------------------------------------------cCCeeEEEE
Confidence 0000 001133344
Q ss_pred hHHHHHhcccCCHHHHHHHHHhccccCCceEEecCc----EEEEEeCCCC-------chhhhHHHHHHhccCCcEEcccC
Q psy13846 1168 MDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHS----FLILKPKDSS-------KSFNSKMYQMKQLLPSVVIKGVQ 1236 (1423)
Q Consensus 1168 ~~~~~~~~~~i~~~~i~~~i~~~k~~~~~~~~~~~~----~i~i~~~~~~-------~~~~~~l~~l~~~l~~~~v~Gi~ 1236 (1423)
++..+.....+++++|..+|++.......+..++++ .+++++.... +...+..+.++..+++++|+|+|
T Consensus 161 ld~~~~~~~~i~~~~i~~~i~~~~~~~~~v~~~~~~~~~~~iri~~~~~~~~~~~~~~~~~~l~~~~~~~l~~i~l~Gi~ 240 (410)
T cd02584 161 LDRKKMTDKKLSMEQIAKKIKEEFKDDLNVIFSDDNAEKLVIRIRIINDDEEKEEDSEDDVFLKKIESNMLSDMTLKGIE 240 (410)
T ss_pred ECHHHHHHcCCCHHHHHHHHHHhcCCCeEEEEcCCCcceeEEEEEecCccccccccchhHHHHHHHHHhhCCCcEEeCCC
Confidence 444444455778888888776432111122222222 4555543211 11233445557889999999999
Q ss_pred CccEEEEecccc----------cceeeEEEEecCccHHHHhhcccccceecccccHHHHHHHhCHHHHHHHHHHHHHHHh
Q psy13846 1237 GINRAVIHEEDV----------EGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVM 1306 (1423)
Q Consensus 1237 ~i~r~~i~~~~~----------~~~~~~~l~teG~nl~~~~~~~~vd~~~~~sN~i~~i~~~lGIEAar~~ii~Ei~~v~ 1306 (1423)
||+|+++..++. ++.++|+|+|||+||+++|++++||++|++||||++|+++|||||||++|++||++||
T Consensus 241 ~I~r~~i~~~~~~~~~~~~g~~~~~~~~~l~teG~nl~~v~~~~~Vd~~rt~sNdI~ei~~~lGIEAaR~~ii~Ei~~v~ 320 (410)
T cd02584 241 GIRKVFIREENKKKVDIETGEFKKREEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEVLGIEAARKALLKELRNVI 320 (410)
T ss_pred CceEEEEEcCCceEecCCCCcccCCcceEEEecCcCHHHHhCCCCCccccCEeCCHHHHHHhcCHHHHHHHHHHHHHHHH
Confidence 999999975321 1245799999999999999999999999999999999999999999999999999999
Q ss_pred hcCCccccCCchhhhhccccceeEEEeeecccccccccchhhhccchhhHHHHHhhcccCCcccccccccceeecccccc
Q psy13846 1307 ENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNV 1386 (1423)
Q Consensus 1307 ~~~Gi~v~~rHl~LiaD~Mt~~G~~~~i~r~g~~~~~~S~l~~aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~~~~~ 1386 (1423)
+.||++||+|||+||||+||++|.++||||+||++++.|||++||||+|+++|++||++|+.|+|+|||||||+|+++|+
T Consensus 321 ~~~Gi~Vd~RHl~LiaD~MT~~G~~~~i~R~Gi~~~~~S~l~~aSFE~t~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~ 400 (410)
T cd02584 321 SFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVSENIMLGQLAPI 400 (410)
T ss_pred HhcCCccCHHHHHHHHHHHhhceEEeeEeeeeeeccCCChhhhccchhHHHHHHHHHhcCCCCcCCCchHheeecCcccc
Confidence 99999999999999999999999999999999998889999999999999999999999999999999999999999999
Q ss_pred ccceEEEeec
Q psy13846 1387 GTGLIKLLQA 1396 (1423)
Q Consensus 1387 GTG~~~l~~~ 1396 (1423)
|||+|+|++|
T Consensus 401 GTG~f~l~~d 410 (410)
T cd02584 401 GTGCFDLLLD 410 (410)
T ss_pred ccceEEEEeC
Confidence 9999999975
No 17
>PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Probab=100.00 E-value=1e-70 Score=648.33 Aligned_cols=300 Identities=35% Similarity=0.589 Sum_probs=254.8
Q ss_pred cccccCcccCCCCCChhHHHHHHHHHhhhccCCCCcchhhhhhcccCCcccccccccccccc--------------cccc
Q psy13846 1084 HQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE 1149 (1423)
Q Consensus 1084 ~~~~~~~~~~~~~~~~~~~~~~~~~~y~~s~v~PGeaVG~iAAQSIGEP~TQmTLnTFH~AG--------------~i~~ 1149 (1423)
..++++.+++ + +|+++|..+|.+++|+||||||+|||||||||+|||||||||||| ||.+
T Consensus 154 ~~~~l~~~~~----~--~i~~ei~~~y~~~~v~pGE~VG~IAAQSIGEP~TQMTLnTFH~AGVas~NVTlGVPRLkEIIN 227 (509)
T PRK14897 154 KKKELSDDEY----E--EILRRIREEYERARVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEMNVTLGLPRLIEIVD 227 (509)
T ss_pred HHcCCCHHHH----H--HHHHHHHHHHHHhccCCCCCcchhhhhhhCCccccccccccccccccccccccCcchhHHHhh
Confidence 3456777776 7 999999999999999999999999999999999999999999999 2211
Q ss_pred e--------eEEEEcc-------------------------------CCcEEEEEEchHHHHHhcccCCHHHHHHHHHhc
Q psy13846 1150 Y--------IEEVFVP-------------------------------DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERT 1190 (1423)
Q Consensus 1150 ~--------i~~~~~~-------------------------------~~~~~~i~l~~~~~~~~~~~i~~~~i~~~i~~~ 1190 (1423)
. +..+..+ ....+.++||.+.+... .+++++|..+|.+.
T Consensus 228 a~K~isTP~mtiyL~~~~~~d~e~A~~V~~~IE~ttL~dv~~~~~d~~~~~i~i~Ld~~~l~~~--~l~~~~I~~~I~~~ 305 (509)
T PRK14897 228 ARKKPSTPTMTIYLKKDYREDEEKVREVAKKIENTTLIDVADIITDIAEMSVVVELDEEKMKER--LIEYDDILAAISKL 305 (509)
T ss_pred cccCCCCceEEEEecCcccccHHHHHHHHhhheeeEHHHHHHHHHHhccceEEEEECHHHHHHc--CCCHHHHHHHHHhc
Confidence 1 1111111 12335666777666654 67889999998763
Q ss_pred cccCCceEEecCcEEEEEeCCCCchhhhHHHHHHhccCCcEEcccCCccEEEEecccccceeeEEEEecCccHHHHhhcc
Q psy13846 1191 RGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATY 1270 (1423)
Q Consensus 1191 k~~~~~~~~~~~~~i~i~~~~~~~~~~~~l~~l~~~l~~~~v~Gi~~i~r~~i~~~~~~~~~~~~l~teG~nl~~~~~~~ 1270 (1423)
+. ..+ ..+++.+++.+.. +.+..|..+++.+++++|+|+|||+||+++.++ ++++|+|.|||+||+++|+++
T Consensus 306 ~~--~~~-~~~~~~I~i~~~~---~~~~~L~~l~~~l~~i~I~GipgI~r~~i~~~~--~~~~~~L~TeG~NL~~vl~~~ 377 (509)
T PRK14897 306 TF--KTV-EIDDGIIRLKPQQ---PSFKKLYLLAEKVKSLTIKGIKGIKRAIARKEN--DERRWVIYTQGSNLKDVLEID 377 (509)
T ss_pred cc--eEE-ecCCCEEEEEeCc---hHHHHHHHHHHHhhccEEeCCCCccEEEEecCC--CCceeEEEeeccCHHHHhcCC
Confidence 21 111 1233556666642 224578888899999999999999999998653 235799999999999999999
Q ss_pred cccceecccccHHHHHHHhCHHHHHHHHHHHHHHHhhcCCccccCCchhhhhccccceeEEEeeecccccccccchhhhc
Q psy13846 1271 GVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLA 1350 (1423)
Q Consensus 1271 ~vd~~~~~sN~i~~i~~~lGIEAar~~ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~G~~~~i~r~g~~~~~~S~l~~a 1350 (1423)
+||++||+||||++|+++|||||||++|++|++.||+.||++||+|||+||||+||++|.+.|+|||||+.++.|||++|
T Consensus 378 ~VD~~rt~SNdI~eI~~vlGIEAAR~~Ii~Ei~~V~~~~Gi~Vd~RHL~LIAD~MT~~G~v~~i~R~Gi~~~~~SpL~rA 457 (509)
T PRK14897 378 EVDPTRTYTNDIIEIATVLGIEAARNAIIHEAKRTLQEQGLNVDIRHIMLVADMMTFDGSVKAIGRHGISGEKSSVLARA 457 (509)
T ss_pred CcccccCccCCHHHHHHhcCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHhCcCCcccccccccccccCCCHHHhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999988899999999
Q ss_pred cchhhHHHHHhhcccCCcccccccccceeeccccccccceEEEeecCCC
Q psy13846 1351 SFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPR 1399 (1423)
Q Consensus 1351 SFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~~~~~GTG~~~l~~~~~~ 1399 (1423)
|||+|+++|++||++|+.|+|+|||||||+|+++|+|||+|+|+++...
T Consensus 458 SFE~T~~~L~~AA~~Ge~D~L~GvsenII~G~~ipvGTG~fdL~~~~~~ 506 (509)
T PRK14897 458 AFEITGKHLLRAGILGEVDKLAGVAENIIVGQPITLGTGAVSLVYKGRK 506 (509)
T ss_pred chHhHHHHHHHHhhcCCCCcCCChHHhhhcCCccCCcCceEEEEecCCC
Confidence 9999999999999999999999999999999999999999999998554
No 18
>cd06528 RNAP_A'' A'' subunit of Archaeal RNA Polymerase (RNAP). Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.
Probab=100.00 E-value=7.8e-70 Score=632.14 Aligned_cols=296 Identities=39% Similarity=0.591 Sum_probs=255.8
Q ss_pred ccccccCcccCCCCCChhHHHHHHHHHhhhccCCCCcchhhhhhcccCCcccccccccccccc-----------------
Q psy13846 1083 SHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG----------------- 1145 (1423)
Q Consensus 1083 ~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~s~v~PGeaVG~iAAQSIGEP~TQmTLnTFH~AG----------------- 1145 (1423)
...++++++++ + ||+++++.+|.+++++||||||++||||||||+||||||||||||
T Consensus 11 ~~~~~l~~~~~----~--~~~~~~~~~~~~~~~~~Ge~vG~iaAQSiGEP~TQMTLnTFH~AGVas~nVTlGVPRlkEII 84 (363)
T cd06528 11 LKEHGLTLSEA----E--EIIKEVLREYLRSLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRLIEIV 84 (363)
T ss_pred HHHcCCCHHHH----H--HHHHHHHHHHHHHhhccCccccceeeeecCccceecccccccccccccccCccccccHHHHh
Confidence 35567888877 7 999999999999999999999999999999999999999999999
Q ss_pred ---------------------------------------cccceeEEEEccCCcEEEEEEchHHHHHhcccCCHHHHHHH
Q psy13846 1146 ---------------------------------------EVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYC 1186 (1423)
Q Consensus 1146 ---------------------------------------~i~~~i~~~~~~~~~~~~i~l~~~~~~~~~~~i~~~~i~~~ 1186 (1423)
+|+.++++ +++.+.+.++||.+.++.. .+++++|..+
T Consensus 85 na~K~i~TP~mti~L~~~~~~~~~~a~~v~~~iE~t~l~di~~~~~i--~~~~~~l~i~ld~~~l~~~--~l~~~~i~~~ 160 (363)
T cd06528 85 DARKEPSTPTMTIYLEEEYKYDREKAEEVARKIEETTLENLAEDISI--DLFNMRITIELDEEMLEDR--GITVDDVLKA 160 (363)
T ss_pred hcccCCCCceEEEEecCcchhhHHHHHHHHHhhceeEHHHhhhheEE--eccCcEEEEEECHHHHHHc--CCCHHHHHHH
Confidence 12222222 2445667778888887775 5799999999
Q ss_pred HHhccccCCceEEecCcEEEEEeCCCCchhhhHHHHHHhccCCcEEcccCCccEEEEecccccceeeEEEEecCccHHHH
Q psy13846 1187 IERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDV 1266 (1423)
Q Consensus 1187 i~~~k~~~~~~~~~~~~~i~i~~~~~~~~~~~~l~~l~~~l~~~~v~Gi~~i~r~~i~~~~~~~~~~~~l~teG~nl~~~ 1266 (1423)
|.+... ..+...++..+++... ++.....|+.+++.+.+++|+|+|||+||++.+++ ++|+|.|||+||+++
T Consensus 161 i~~~~~--~~~~~~~~~~~~~~~~--~~~~~~~l~~l~~~l~~~~v~Gi~gI~r~~i~~~~----~~~~l~teG~nl~~v 232 (363)
T cd06528 161 IEKLKK--GKVGEEGDVTLIVLKA--EEPSIKELRKLAEKILNTKIKGIKGIKRVIVRKEE----DEYVIYTEGSNLKAV 232 (363)
T ss_pred HHHhcC--CcccccCCccEEEEcC--CcchHHHHHHHHHhhcccEEeCCCCceEEEEecCC----ceEEEEecCcCHHHH
Confidence 865321 1122222222333332 22335688999999999999999999999998653 489999999999999
Q ss_pred hhcccccceecccccHHHHHHHhCHHHHHHHHHHHHHHHhhcCCccccCCchhhhhccccceeEEEeeecccccccccch
Q psy13846 1267 MATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESV 1346 (1423)
Q Consensus 1267 ~~~~~vd~~~~~sN~i~~i~~~lGIEAar~~ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~G~~~~i~r~g~~~~~~S~ 1346 (1423)
|.+++||++|++||||++|+++|||||||++|++||++||+.||++||+|||+||||+||++|++.|+||+|+++++.||
T Consensus 233 ~~~~~Vd~~rt~sNdI~ei~~~lGIEAaR~~ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~G~~~~i~R~gi~~~~~S~ 312 (363)
T cd06528 233 LKVEGVDPTRTTTNNIHEIEEVLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVRQIGRHGIAGEKPSV 312 (363)
T ss_pred hcCCCCcccccccCCHHHHHHhCCHHHHHHHHHHHHHHHHHhcCCeecHHHHHHHHHHhccCCceecccchhhcCCCCCh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999998888999
Q ss_pred hhhccchhhHHHHHhhcccCCcccccccccceeeccccccccceEEEeec
Q psy13846 1347 LNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA 1396 (1423)
Q Consensus 1347 l~~aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~~~~~GTG~~~l~~~ 1396 (1423)
|++||||+|+++|++||.+|+.|+|+|||||||+|+++|+|||+|+|+++
T Consensus 313 L~~aSFE~t~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~~~l~~d 362 (363)
T cd06528 313 LARAAFEVTVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTGDVELTMD 362 (363)
T ss_pred hhhCchhhHHHHHHHHHhcCCCCcCCCcHHHeeeCCCCCCcCCeeEEEec
Confidence 99999999999999999999999999999999999999999999999986
No 19
>PRK04309 DNA-directed RNA polymerase subunit A''; Validated
Probab=100.00 E-value=2e-69 Score=632.76 Aligned_cols=294 Identities=40% Similarity=0.653 Sum_probs=256.7
Q ss_pred cccCcccCCCCCChhHHHHHHHHHhhhccCCCCcchhhhhhcccCCcccccccccccccc--------------cc----
Q psy13846 1086 DKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EV---- 1147 (1423)
Q Consensus 1086 ~~~~~~~~~~~~~~~~~~~~~~~~y~~s~v~PGeaVG~iAAQSIGEP~TQmTLnTFH~AG--------------~i---- 1147 (1423)
++++++++ + +|++.|..+|.+++++||||||++||||||||+|||||||||||| ||
T Consensus 33 ~~l~~~~~----~--~~~~~i~~~y~~~~v~pGe~VG~iaAQsIGEP~TQMTL~TFH~AGva~~nVTlGvPRlkEIina~ 106 (383)
T PRK04309 33 RKLTEEEV----E--EIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDAR 106 (383)
T ss_pred cCCCHHHH----H--HHHHHHHHHHHHhhcCCCCccchhhhhhccchhhhcccccccccCccccCcccCchhHHHHHhcc
Confidence 45788776 7 999999999999999999999999999999999999999999999 11
Q ss_pred --------------------------------------cceeEEEEccCCcEEEEEEchHHHHHhcccCCHHHHHHHHHh
Q psy13846 1148 --------------------------------------CEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIER 1189 (1423)
Q Consensus 1148 --------------------------------------~~~i~~~~~~~~~~~~i~l~~~~~~~~~~~i~~~~i~~~i~~ 1189 (1423)
+.+++. +++...+.++||...++.+ .+++++|..+|.+
T Consensus 107 K~~~TP~~tv~L~~~~~~d~~~a~~v~~~iE~t~L~~v~~~i~~--~~~~~~l~i~ld~~~i~~~--~l~~~~I~~~i~~ 182 (383)
T PRK04309 107 KEPSTPMMTIYLKDEYAYDREKAEEVARKIEATTLENLAKDISV--DLANMTIIIELDEEMLEDR--GLTVDDVKEAIEK 182 (383)
T ss_pred cCCCCCeEEEEecCcccccHHHHHHHHhheeeeEHhhhhhheEe--ccCCcEEEEEECHHHHHHc--CCCHHHHHHHHHH
Confidence 111111 2334556778888777765 6799999999865
Q ss_pred ccccCCceEEecCcEEEEEeCCCCchhhhHHHHHHhccCCcEEcccCCccEEEEecccccceeeEEEEecCccHHHHhhc
Q psy13846 1190 TRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMAT 1269 (1423)
Q Consensus 1190 ~k~~~~~~~~~~~~~i~i~~~~~~~~~~~~l~~l~~~l~~~~v~Gi~~i~r~~i~~~~~~~~~~~~l~teG~nl~~~~~~ 1269 (1423)
... ..+.+. .+.+.+++.. +....|+.++..+++++|+|+|||+||++.++ +++|+|.|||+||.++|++
T Consensus 183 ~~~--~~~~~~-~~~i~i~~~~---~~~~~l~~l~~~l~~~~vkGi~gI~r~~i~~~----~~~~~l~teG~nl~~v~~~ 252 (383)
T PRK04309 183 KKG--GEVEIE-GNTLIISPKE---PSYRELRKLAEKIRNIKIKGIKGIKRVIIRKE----GDEYVIYTEGSNLKEVLKV 252 (383)
T ss_pred hcC--cceecc-CCeEEEEecC---chHHHHHHHHHHhcccEEECCCCceEEEEecC----CCeEEEEEcccCHHHHhcC
Confidence 321 223333 3556666652 23467888999999999999999999999864 3589999999999999999
Q ss_pred ccccceecccccHHHHHHHhCHHHHHHHHHHHHHHHhhcCCccccCCchhhhhccccceeEEEeeecccccccccchhhh
Q psy13846 1270 YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNL 1349 (1423)
Q Consensus 1270 ~~vd~~~~~sN~i~~i~~~lGIEAar~~ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~G~~~~i~r~g~~~~~~S~l~~ 1349 (1423)
++||++|++||||++|+++|||||||++|++|++.||+.||++||+|||+||||+||++|++.|+||+|+++++.|||++
T Consensus 253 ~~VD~~rt~sNdI~ei~~vlGIEAAR~~ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~G~~~~i~R~Gi~~~~~S~l~~ 332 (383)
T PRK04309 253 EGVDATRTTTNNIHEIEEVLGIEAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGVSGEKASVLAR 332 (383)
T ss_pred CCEeeccccCCCHHHHHHHcCHHHHHHHHHHHHHHHHHHcCCeecHHHHHHHHHHhccCceEEeeechhhcCCCCCHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999998889999999
Q ss_pred ccchhhHHHHHhhcccCCcccccccccceeeccccccccceEEEeecCCC
Q psy13846 1350 ASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPR 1399 (1423)
Q Consensus 1350 aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~~~~~GTG~~~l~~~~~~ 1399 (1423)
||||+|+++|++||++|+.|+++|||||||+|+++|+|||+|+|+++.+.
T Consensus 333 aSFE~T~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~~~l~~~~~~ 382 (383)
T PRK04309 333 AAFEVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTGDVELTMDPPL 382 (383)
T ss_pred CchhhHHHHHHHHHhcCCCCCCCCcHHHhhcCCCcCCCCceEEEEcCCCC
Confidence 99999999999999999999999999999999999999999999998764
No 20
>cd02736 RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain. Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Probab=100.00 E-value=3.4e-68 Score=604.08 Aligned_cols=170 Identities=63% Similarity=0.922 Sum_probs=161.5
Q ss_pred HHHHHhccCCcEEcccCCccEEEEecccccceeeEEEEecCccHHHHhhcccccceecccccHHHHHHHhCHHHHHHHHH
Q psy13846 1220 MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIM 1299 (1423)
Q Consensus 1220 l~~l~~~l~~~~v~Gi~~i~r~~i~~~~~~~~~~~~l~teG~nl~~~~~~~~vd~~~~~sN~i~~i~~~lGIEAar~~ii 1299 (1423)
++.+++.|++++|+|+|||+||++.+++. .++|.|.|||+||.++|++++||++|++||||++|+++|||||||++|+
T Consensus 131 ~~~l~~~l~~~~v~Gi~gI~r~~i~~~~~--~~~~~l~teG~nl~~v~~~~~Vd~~rt~sNdI~ei~~~lGIEAaR~~ii 208 (300)
T cd02736 131 LQSLKRKLPDVVVSGIPEVKRAVINKDKK--KGKYKLLVEGYGLRAVMNTPGVIGTRTTSNHIMEVEKVLGIEAARSTII 208 (300)
T ss_pred HHHHHHHhccceEeCCCCceEEEEecCCC--CCcEEEEEecccHHHHhcCCcEeccCCccCCHHHHHHhcCHHHHHHHHH
Confidence 34456678899999999999999986532 3589999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhcCCccccCCchhhhhccccceeEEEeeecccccccccchhhhccchhhHHHHHhhcccCCccccccccccee
Q psy13846 1300 TEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECII 1379 (1423)
Q Consensus 1300 ~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~G~~~~i~r~g~~~~~~S~l~~aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ii 1379 (1423)
+||++||+.||++||+|||+||||+||++|.++||||+|++++++|||++||||+|.++|++||.+|+.|+|+|||||||
T Consensus 209 ~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~G~~~~itR~gi~~~~~S~l~~aSFE~t~~~L~~AA~~g~~D~l~gvse~ii 288 (300)
T cd02736 209 NEIQYTMKSHGMSIDPRHIMLLADLMTFKGEVLGITRFGIAKMKESVLMLASFEKTTDHLFNAALHGRKDSIEGVSECII 288 (300)
T ss_pred HHHHHHHHhcCCccCHHHHHHHHHHHhccCceeeeecccccccCCCHHHhcchHhHHHHHHHHhhcCCCCcCCCcHHHee
Confidence 99999999999999999999999999999999999999999888999999999999999999999999999999999999
Q ss_pred eccccccccceE
Q psy13846 1380 MGLPMNVGTGLI 1391 (1423)
Q Consensus 1380 ~G~~~~~GTG~~ 1391 (1423)
+|+++|+|||+|
T Consensus 289 ~G~~~~~GTG~f 300 (300)
T cd02736 289 MGKPMPIGTGLF 300 (300)
T ss_pred eCCCcCCCCCCC
Confidence 999999999987
No 21
>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=4e-66 Score=591.95 Aligned_cols=177 Identities=35% Similarity=0.463 Sum_probs=166.8
Q ss_pred hhHHHHHHhccCCcEEcccCCccEEEEecccccceeeEEEEecCccHHHHhhc-ccccceecccccHHHHHHHhCHHHHH
Q psy13846 1217 NSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMAT-YGVKGVKCSSNNTYEVYKTLGIEAAR 1295 (1423)
Q Consensus 1217 ~~~l~~l~~~l~~~~v~Gi~~i~r~~i~~~~~~~~~~~~l~teG~nl~~~~~~-~~vd~~~~~sN~i~~i~~~lGIEAar 1295 (1423)
.+.++.+++.+.+++|+|+|||+||++.+++..+..+|.+.|||+||.++|.+ ++||++|++||||++|+++|||||||
T Consensus 132 ~~~~~~~~~~l~~~~i~gi~gI~r~~i~~~~~~~~~~~~l~teG~nl~~v~~~~~~vd~~r~~sNdi~ei~~~lGIEAar 211 (309)
T cd02735 132 LLLLSIVEKLARKAVIREIPGITRCFVVEEDKGGKTKYLVITEGVNLAALWKFSDILDVNRIYTNDIHAMLNTYGIEAAR 211 (309)
T ss_pred HHHHHHHHHHhcccEEeCCCCccEEEEecCcCCCceEEEEEeccccHHHHHhccCccccccceeCCHHHHHHhhCHHHHH
Confidence 35667788899999999999999999987643334579999999999999998 78999999999999999999999999
Q ss_pred HHHHHHHHHHhhcCCccccCCchhhhhccccceeEEEeeecccccccccchhhhccchhhHHHHHhhcccCCcccccccc
Q psy13846 1296 STIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVS 1375 (1423)
Q Consensus 1296 ~~ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~G~~~~i~r~g~~~~~~S~l~~aSFE~t~~~L~~Aa~~g~~D~l~g~s 1375 (1423)
++|++|+++||+.||++||+|||+||||+||++|.+.|+||+|| +.+.|||++||||+|.++|++||.+|+.|+|+|||
T Consensus 212 ~~ii~Ei~~v~~~~Gi~V~~rHl~LiaD~MT~~G~~~~~nr~gi-~~~~S~l~~asFE~t~~~L~~Aa~~g~~D~l~g~s 290 (309)
T cd02735 212 RAIVKEISNVFKVYGIAVDPRHLSLIADYMTFEGGYRPFNRIGM-ESSTSPLQKMSFETTLAFLKKATLNGDIDNLSSPS 290 (309)
T ss_pred HHHHHHHHHHHHhcCCeeCHHHHHHHHHHHHhCCcEeecchhhe-ccCCCHHHhhhhhhHHHHHHHHhhcCCCCCCCChH
Confidence 99999999999999999999999999999999999999999999 56899999999999999999999999999999999
Q ss_pred cceeeccccccccceEEEe
Q psy13846 1376 ECIIMGLPMNVGTGLIKLL 1394 (1423)
Q Consensus 1376 ~~ii~G~~~~~GTG~~~l~ 1394 (1423)
|||++|+++|+|||+|||+
T Consensus 291 ~~ii~G~~~~~GTG~fdll 309 (309)
T cd02735 291 SRLVVGKPVNGGTGLFDLL 309 (309)
T ss_pred HheeeCCccCccceeEEeC
Confidence 9999999999999999985
No 22
>KOG0262|consensus
Probab=100.00 E-value=3.9e-63 Score=602.67 Aligned_cols=782 Identities=20% Similarity=0.236 Sum_probs=478.4
Q ss_pred hhhhHHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeecccCCcccCHHHHHHHHHHhhcccccceeeeEEEec
Q psy13846 8 TLTLYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFFRGLIEGTV 87 (1423)
Q Consensus 8 ~~~~~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~F~~ 87 (1423)
-|---|.|||||..|..+-.|.+.|.+|.|+-|.||||+...-+||.||+||+||+.|+|+.. +-.....
T Consensus 609 HfPQse~araEa~~ian~dsqYLvPt~G~PlrGLIQDHiVsgv~LT~rd~Fftre~y~qLv~~---~l~~~~~------- 678 (1640)
T KOG0262|consen 609 HFPQSEIARAEAYNIANTDSQYLVPTDGTPLRGLIQDHIVSGVLLTMRDSFFTREDYQQLVFA---GLSDTFK------- 678 (1640)
T ss_pred cCCchhhHHHHHHHHhccCCceeccCCCCchhhhhhhheeeeEEEEecccccCHHHHHHHHHH---hhhhhcc-------
Confidence 455568999999999999999999999999999999999999999999999999999999983 3221111
Q ss_pred CCHHHHhhcceeeeecCcccccCCCCCCcCCccc----cCCCCCCCCCCccCCCCCCCcccCCcc-----ceEEccCcee
Q psy13846 88 TKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLL----DRRMGTNQKEANCTTCGQNLSDCVGHF-----GYIDLPLPVF 158 (1423)
Q Consensus 88 ~S~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLl----D~rLG~~~~~~~C~TCg~~~~eCpGHf-----GhIeL~~PV~ 158 (1423)
+|.-+.-.=.....+| +||++.+.++ ++..-+.+-...-.+-| ..+.|++-- .|+.+..+.+
T Consensus 679 ----rI~~lpPtIlkP~~LW----TGKQVIsTil~Ni~P~~~p~iNl~~kaKip~-~~W~~~s~e~~l~Es~v~ir~Gel 749 (1640)
T KOG0262|consen 679 ----RIKLLPPTILKPAPLW----TGKQVISTILKNIIPEGHPPINLESKAKIPG-KAWRVHSEEPKLNESQVLIREGEL 749 (1640)
T ss_pred ----ceeccCcccccccccc----ccchHHHHHHHhcCCCCCCcccchhcccCch-hhcCCCCCcccCCcceEEEecCce
Confidence 1111111122455677 8988876544 22222221111111111 123333333 6799999999
Q ss_pred EEeeeccH------HHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccC----------Ccc
Q psy13846 159 HIGYFRCV------INILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKK----------VSV 222 (1423)
Q Consensus 159 h~gffd~v------~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk----------~k~ 222 (1423)
.+|.+|+- +-|.+ |-+=+++.+.....+--+.+....|++.++|.-++.|..-. ..-
T Consensus 750 lcGVLDKa~~Gat~yGLvH-------~~~ElYG~~~s~~lLs~~srlFT~ylq~~GFT~GvdDlll~~~~D~kR~~il~e 822 (1640)
T KOG0262|consen 750 LCGVLDKAQFGATAYGLVH-------CCHELYGGETSGKLLSVFSRLFTAYLQMHGFTLGVDDLLLDKDADKKRREILRE 822 (1640)
T ss_pred EEEeechhhcCchhhhhhh-------hhhhhhCccchhhHHHHHHHHHHHHHHHhccccccceeeechhhhHHHHHHHHh
Confidence 99999976 33333 33335787777666666666666777777777776664210 123
Q ss_pred CCCCCCCCCceeec-CcceehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHH--------HHH
Q psy13846 223 CPHCGEINGVVKKC-GLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLE--------VLQ 293 (1423)
Q Consensus 223 C~~Cg~~~~~irk~-~~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~--------V~e 293 (1423)
|.+||... ++.. ++.... ..++....+.+.|. ...+....++.+....+++.+ -.-
T Consensus 823 ~~~vG~qa--~~~~~~l~~da---------~~del~~~le~~y~----~d~~~~~~LD~~~k~~~n~~ts~I~~~cvP~G 887 (1640)
T KOG0262|consen 823 SRNVGNQA--AKEAFGLDVDA---------PPDELRSRLEAIYL----KDADKLAMLDRVMKSELNGYTSEIVKKCVPDG 887 (1640)
T ss_pred hhcccHHH--HHHHhCCCCCC---------CHHHHHHHHHHHHh----cchhHHHHHHHHHHHHHhhhhHHHHhhhccch
Confidence 45554321 0000 000000 00111111111111 000000000000001111111 112
Q ss_pred HhhccCCCcccccccccCCCCCcceEEEEecCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEEecCCceee
Q psy13846 294 LFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRF 373 (1423)
Q Consensus 294 iLe~I~~~d~~lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~ 373 (1423)
+++..+.+.+. .|..+|++++..|..||. .+.+|+...|.|.+-=+ ..|.||- |
T Consensus 888 Llk~FP~N~mq--lM~~SGAKGS~VN~~QIS---clLGQqeLEGkRvPlMv-----------------SGKtLPs----F 941 (1640)
T KOG0262|consen 888 LLKKFPENNMQ--LMIQSGAKGSNVNTSQIS---CLLGQQELEGKRVPLMV-----------------SGKTLPS----F 941 (1640)
T ss_pred hhhcCCcchHH--HHHHhcCCcccccHHHHH---HhhhhHhhcCCccceee-----------------cCCccCC----c
Confidence 33333433222 344578999999999998 88999998887765555 7889998 9
Q ss_pred ccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecc
Q psy13846 374 NECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453 (1423)
Q Consensus 374 ~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~ 453 (1423)
.|-..+|-..+|.-+.+-.++-| ++||||.|+||||+++|+++|.-|||-||.||.-++- +.+.|++|+
T Consensus 942 ~p~e~spraGGfI~~RFlTGi~P----------qeyfFHCMAGREGLIDTAVKTSRSGYLQRCLiKhLEg-l~V~YD~TV 1010 (1640)
T KOG0262|consen 942 APYETSPRAGGFIDGRFLTGIKP----------QEYFFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEG-LKVHYDLTV 1010 (1640)
T ss_pred CCCCCCCCCCCcccceeecCCCc----------hHHhhhhhccccchhhhHHhcccchHHHHHHHHhhhh-cEEeccceE
Confidence 99999999999999999999984 4599999999999999999999999999999999999 999999999
Q ss_pred cccCCCHHHHHHHHHhhccCCccccceEeeeeccccCCceeecceeeeecceeeeecccCCCCcccccceeecccccccC
Q psy13846 454 KNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTAN 533 (1423)
Q Consensus 454 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~kp~~~wtGKqi~s~il~~~~~~~~~~~~~~~~~~~~~~ 533 (1423)
||+.++..||+|+.++++... -.++.+ |+-. ..|++.--..+
T Consensus 1011 RDsDgsvVQF~YGEDglDitK-----------------ssfl~~------~~f~------------~~Ny~avl~~~--- 1052 (1640)
T KOG0262|consen 1011 RDSDGSVVQFMYGEDGLDITK-----------------SSFLNK------KEFP------------TDNYEAVLLKY--- 1052 (1640)
T ss_pred EcCCCcEEEEeecCccccccH-----------------Hhhcch------hhhh------------hhhHHHHHhhh---
Confidence 999999999999998875211 111111 1100 00100000000
Q ss_pred cccccCCcEEEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceecCCCCCCcc
Q psy13846 534 EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQG 613 (1423)
Q Consensus 534 ~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~D~~~~~G 613 (1423)
+. .+++ ...+.+.|......+-+--..- |..-++.++. .+++
T Consensus 1053 -------------~~---~~v~------------------s~~d~~~a~~~~k~i~kw~kk~-~w~~~~k~~~--cpdp- 1094 (1640)
T KOG0262|consen 1053 -------------KS---ESVL------------------SAFDIKKASKYIKKILKWKKKH-MWFELDKKIA--CPDP- 1094 (1640)
T ss_pred -------------Ch---HHHh------------------hhhhhHHHHHHHHHHHHHHhhh-ccchhhcccC--CCCh-
Confidence 00 0111 1112222222221111100000 2222223332 2221
Q ss_pred ccccccccCCCceeeeeecccccccchhcccccCCCCcchHHHHHHHhhhhhcccceeeccccCCCccCCCcchheecCC
Q psy13846 614 FVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAFYGQTDCISGVSECIIMGL 693 (1423)
Q Consensus 614 fI~~sf~~GL~p~Efffh~maGReGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~tVR~s~yG~~~~~~~~~~~~~~~~ 693 (1423)
|...| +.+-|+-+++-+ ..+.-++|.+|+ .|- + -.|+.+ - +-..-+.+.-|.+.
T Consensus 1095 -v~~k~-----~p~~y~gsvsek-------f~~~i~~f~~~~-~k~-~---~s~~~~-~-------~~lr~ll~~K~~~S 1148 (1640)
T KOG0262|consen 1095 -VLAKY-----NPDKYLGSVSEK-------FRKKIDDFDDEN-AKK-E---KSEEPS-E-------EKLRRLLQLKYIRS 1148 (1640)
T ss_pred -hhhhc-----chhhhhccccHH-------HHHHHHHHHHHh-hhh-h---ccccch-H-------HHHHHHHHHHHHHH
Confidence 00000 011111111111 112334566665 211 0 011111 0 00000112234677
Q ss_pred CcccchhHHHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhHHHH-
Q psy13846 694 PMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEII- 772 (1423)
Q Consensus 694 ~~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlkEIi- 772 (1423)
+.+|||+||.|||||||||.||||| +||||||. +.||+|| |+|||+||+
T Consensus 1149 La~PGE~VGvlAAQSIGEPSTQMTL----NTFHfAGr-------------GemNVTL-------------GIPRLREIlM 1198 (1640)
T KOG0262|consen 1149 LADPGEPVGVLAAQSIGEPSTQMTL----NTFHFAGR-------------GEMNVTL-------------GIPRLREILM 1198 (1640)
T ss_pred hcCCCCcceeeeecccCCCcceeeh----hheeeccc-------------cceeeee-------------cchHHHHHHH
Confidence 8999999999999999999999999 99999998 8899999 999999999
Q ss_pred hhhcCCCCceeeeecccCChHHHHHHHhhhhcccchhhhhhhhee--eec--CCCc-c-eeeehhhh-HHHh-hccccch
Q psy13846 773 NASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEE--VFV--PDDS-F-ILIKLDMD-RIRL-LHLEVDI 844 (1423)
Q Consensus 773 naSk~ikTPiitv~L~~~~~~e~a~~v~~rie~~~l~dii~~i~~--~~~--~~~~-~-~~i~ld~~-r~~~-~~l~i~~ 844 (1423)
.||++|+||+|++.+.+..+.+-|..+..++.+++|+++++++.. .+. ++.. . ..|++++- +... .++.+..
T Consensus 1199 tASanIkTP~mt~pi~~g~s~~ra~~i~~~l~rV~L~evlk~v~vte~~t~~~~~~~~~y~lr~~~~~~~~y~~e~~v~~ 1278 (1640)
T KOG0262|consen 1199 TASANIKTPSMTVPIKNGVSDERADDITKELRRVTLKEVLKKVGVTEKITMVENQSCKKYKLRFDLLPREEYQEEYDVRP 1278 (1640)
T ss_pred HHhhccCCCceeeeccCCccHHHHHHHHHHHHHHHHHHHHhheeeeEEEEeeccccceEEEEEEeecCHHHhhhhcCCCH
Confidence 999999999999999999888999999999999999999998642 222 2222 1 23444431 1111 1111111
Q ss_pred hh------------hhHHhhh----cc---cc-----c----------Ccc-----------------------------
Q psy13846 845 DS------------IRYCIER----TR---GI-----S----------GHL----------------------------- 861 (1423)
Q Consensus 845 ~~------------I~~~i~~----~~---~~-----~----------~~i----------------------------- 861 (1423)
+. +..+|++ .+ .. + .++
T Consensus 1279 e~i~~~m~~~Flk~L~~aI~k~~~k~~~~~~~~~dd~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ddddas~~k~~~k 1358 (1640)
T KOG0262|consen 1279 EDIEEVMENRFLKLLERAIKKKLKKAKYTRGMSNDDADPDDGNEVDNNDEVGGEDNEDSDDESEDDEDDDDASDAKLHKK 1358 (1640)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhHHhhccccccCCccccccCCccccccCCccccccccccccCcccchhHHHHhhh
Confidence 11 2222211 10 00 0 000
Q ss_pred -----cccccc---ccccc----C--CCC-------c---------------c----------------------ccch-
Q psy13846 862 -----TVSGHS---FLILK----P--KDS-------S---------------K----------------------SFNS- 882 (1423)
Q Consensus 862 -----~~~~~~---~~~~~----~--~~~-------~---------------~----------------------~~~~- 882 (1423)
+..+.. ....+ + .++ . + .|.+
T Consensus 1359 ~~~~~dYe~~de~e~~~~~~~e~~~~~e~~e~d~e~g~dg~~~~~~~~~e~~~~~~~~er~~qs~~~~~~fi~~y~fd~~ 1438 (1640)
T KOG0262|consen 1359 TEEEADYESEDEDERVEEREDEGDEDEESDEDDEEVGLDGTPEPEEEDQEGQPEVNAVERREQSVKKRHDFISRYTFDKE 1438 (1640)
T ss_pred hccccCcCCCchhhhhhhhhcccccccccccchhhcccCCCCCcccccccCCchhhHHHHHHHHHHHHHHHhhhhccccc
Confidence 000000 00000 0 000 0 0 0000
Q ss_pred ------------------hh-hhhhhcCCceEEccccccceeeeecccccceeEEeeeccCccccccceeecc-cceeec
Q psy13846 883 ------------------KM-YQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGV-KGVKCS 942 (1423)
Q Consensus 883 ------------------~l-~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~nL~~vl~~~gv-D~~~t~ 942 (1423)
.+ ..+.+..+..+|..++||.|+++....+.++..-.+.|+|.||..+..+..+ |..+.+
T Consensus 1439 ~~~wcev~~~lp~~~~k~~mssiVe~~~~~~vI~q~~gIeRc~~~~~~~~~k~~~~l~TeGVnl~a~~~~~d~LDv~~ly 1518 (1640)
T KOG0262|consen 1439 SGKWCEVELKLPLDKEKLDMSSIVESIAPKSVIHQVPGIERCVVSEPQDDVKEKSVLLTEGVNLPALFDHADILDVNRLY 1518 (1640)
T ss_pred cCcEEEEEEEecCCCcchHHHHHHHHHhcceeeeccCCceeeeccCCcccccccceehhcCccHHHHHHHHhhhhhhhhc
Confidence 01 1134467889999999999999987654444445899999999998888765 899999
Q ss_pred cCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC
Q psy13846 943 SNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG 999 (1423)
Q Consensus 943 SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~ 999 (1423)
||||+.|++++||||||++|++|+..||..+||+||.||+.|+|||||+.|.+...+
T Consensus 1519 SNDI~ail~tyGVEAar~~Iv~Ev~~VF~vYGIsVd~RHLsLiADYMTf~G~y~pfn 1575 (1640)
T KOG0262|consen 1519 SNDIHAILNTYGVEAARNAIVNEVNNVFKVYGISVDIRHLSLIADYMTFEGGYQPFN 1575 (1640)
T ss_pred cchHHHHHHHhhHHHHHHHHHHHHHHhhhheeeeecHHHHHHHHHHHhhcccccccc
Confidence 999999999999999999999999999999999999999999999999999987653
No 23
>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Probab=100.00 E-value=3.1e-60 Score=620.30 Aligned_cols=370 Identities=18% Similarity=0.162 Sum_probs=273.5
Q ss_pred HHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeecccCCcccCHHHHHHHHHHhhcccccceeeeEEEecCCHH
Q psy13846 12 YYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFFRGLIEGTVTKED 91 (1423)
Q Consensus 12 ~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~F~~~S~e 91 (1423)
-+||||||++||+|++||+||++|+|+||++||+|+|+|+||.||+||+|+++++|++|. +....+ ..|.
T Consensus 486 S~eArAEa~~Lm~v~~niisP~~G~Pi~gliQD~l~g~~lLT~~d~fl~~~e~~~l~~~~--~~~~~l--------p~Pa 555 (1321)
T PRK14977 486 IEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFDKNEASNIAMLA--GITDPL--------PEPA 555 (1321)
T ss_pred CHHHHHHHHHHHhhhhcEecCCCCCeeEEeehhhhhhhhhhccCcccCCHHHHHHHHHhC--CCcccc--------CCCc
Confidence 479999999999999999999999999999999999999999999999999999999972 211111 1111
Q ss_pred HHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccC-CCCCCCcccCCccceEEccCceeEEeeeccHH---
Q psy13846 92 RVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCT-TCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVI--- 167 (1423)
Q Consensus 92 eIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~-TCg~~~~eCpGHfGhIeL~~PV~h~gffd~v~--- 167 (1423)
.+ .....+| |||++.+.++++.+....+...+. .|+.+....|...|++.+...++..|.+|+-.
T Consensus 556 I~-------~kp~~lw----TGKQi~s~iLp~~~n~~~~~~~~~~~~~~~~~~~~~~d~~v~I~~geLl~G~ldK~~~G~ 624 (1321)
T PRK14977 556 IK-------TKDGPAW----TGKQLFSLFLPKDFNFEGIAKWSAGKAGEAKDPSCLGDGYVLIKEGELISGVIDDNIIGA 624 (1321)
T ss_pred ee-------cCCCCee----eHHHHHHHHcCCCCCceecccccccccccccccCCCCcceEEeecCeEEeeecchHhhcc
Confidence 11 0234688 999999999988775543332222 23333333455799999999999999999531
Q ss_pred ------HHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCceeecCccee
Q psy13846 168 ------NILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKI 241 (1423)
Q Consensus 168 ------~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk~~~~ki 241 (1423)
.+++.+... ++++....|++++.+....++...+|+.++.|..... .
T Consensus 625 ~~~~~~~Lih~i~~~-------yG~~~a~~fL~~l~~l~~~~L~~~GFSigi~D~~~~~--------------------~ 677 (1321)
T PRK14977 625 LVEEPESLIDRIAKD-------YGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLIIPD--------------------E 677 (1321)
T ss_pred ccCCCCcHHHHHHHH-------hCHHHHHHHHHHHHHHHHHHHHhCCEEEeeCcEecCH--------------------H
Confidence 244444444 8889999999999988888888888888887764211 0
Q ss_pred hhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHHHhh--------------------ccCCC
Q psy13846 242 SHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFE--------------------AIPLE 301 (1423)
Q Consensus 242 ~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~eiLe--------------------~I~~~ 301 (1423)
..++..+..++......++.+.|... +.+... + +..+.+++...++.|+ .++ .
T Consensus 678 ~~~~i~~~i~~~~~~v~~l~~~~~~~----~~i~~~-~-~~~~~~~G~~~~~~~e~~i~~~l~~~r~~~~~~~~~~l~-~ 750 (1321)
T PRK14977 678 AKQEIEDDIQGMKDEVSDLIDQRKIT----RKITIY-K-GKEELLRGMKEEEALEADIVNELDKARDKAGSSANDCID-A 750 (1321)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhh----cccccc-c-cchhcCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-C
Confidence 00001000000111122222222200 000000 0 1112222222222221 132 3
Q ss_pred cccccccccCCCCCcceEEEEecCCCCCCCCcEEc--------CCCCCCeEEEEecCccccccccceeeeEEecCCceee
Q psy13846 302 DIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVIS--------DLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRF 373 (1423)
Q Consensus 302 d~~lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~--------g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~ 373 (1423)
+++++.|..+|||+++++++||. +|++||... |.++..++ ..|+||| |
T Consensus 751 ~N~l~~Mv~SGAKGS~~Ni~Qi~---~~lGQQ~ve~~~~~~~~G~Ri~~~~-----------------~~RtLPh----F 806 (1321)
T PRK14977 751 DNAGKIMAKTGARGSMANLAQIA---GALGQQKRKTRIGFVLTGGRLHEGY-----------------KDRALSH----F 806 (1321)
T ss_pred CCcHHHHhhcccccCHHHHHHHH---hccccccccccccccCCCCCCcCCC-----------------CCCcCCC----C
Confidence 57888899999999999999999 999999998 77777777 9999999 9
Q ss_pred ccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecc
Q psy13846 374 NECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453 (1423)
Q Consensus 374 ~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~ 453 (1423)
.+.+.+|...+|+-+++..+|.+.| ||||+||||||++++|++|+.|||.+|+|+.++|| +.+.||.|+
T Consensus 807 ~~~d~~p~a~GfV~nsFl~GL~P~E----------fFFHaM~GREGLiDTAVKTA~SGYLQRrLvk~lED-l~v~YD~TV 875 (1321)
T PRK14977 807 QEGDDNPDAHGFVKNNYREGLNAAE----------FFFHAMGGREGLIDKARRTEDSGYFQRRLANALED-IRLEYDETV 875 (1321)
T ss_pred CCCCCCcccccchhhhhcCCCCHHH----------HHHHhhcccccccccccccCcCchhHHHHHHHhcc-eEEecCCeE
Confidence 9999999999999999999999766 99999999999999999999999999999999999 999999999
Q ss_pred cccCCCHHHHHHHHHhhc
Q psy13846 454 KNAFFNRAQTMRIASTLI 471 (1423)
Q Consensus 454 ~~~~~~~~~~~~l~~~~~ 471 (1423)
||+.+++.||.|+.++++
T Consensus 876 R~s~g~iiQF~YGeDG~d 893 (1321)
T PRK14977 876 RDPHGHIIQFKFGEDGID 893 (1321)
T ss_pred EeCCCCEEEEeecCCCcC
Confidence 999999999999988875
No 24
>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=1.2e-57 Score=531.44 Aligned_cols=177 Identities=25% Similarity=0.319 Sum_probs=164.2
Q ss_pred HHHHHHhccCCcEEcccCCccEEEEe--ccc---------ccceeeEEEEec---------CccHHHHhh-----ccccc
Q psy13846 1219 KMYQMKQLLPSVVIKGVQGINRAVIH--EED---------VEGVTKYKLLVE---------GDNLRDVMA-----TYGVK 1273 (1423)
Q Consensus 1219 ~l~~l~~~l~~~~v~Gi~~i~r~~i~--~~~---------~~~~~~~~l~te---------G~nl~~~~~-----~~~vd 1273 (1423)
+++.+...|.+++|||+|+|++|.|. +.. .+.+++|+|.|+ |.+|..+|+ +++||
T Consensus 174 ~~~~i~~~lL~~~lkG~~~I~kv~i~~~~~~~~~~~~~~~~~~~~E~vLe~~~~~~~~~t~G~~~~~vl~~c~~~~~~ID 253 (381)
T cd02737 174 LRDRIIPFLLETVIKGDERIKSVNILWEDSPSTSWVKSVGKSSRGELVLEVTVEESCKKTRGNAWNVVMDACIPVMDLID 253 (381)
T ss_pred HHHHHHHHHhheeecccCCeeEEEEEecCCCcccccccccccccceEEEEEEeccccccccchhHHHHHHhhhcccccCc
Confidence 56667776778999999999999997 221 124579999988 999999995 89999
Q ss_pred ceecccccHHHHHHHhCHHHHHHHHHHHHHHHhhcCCccccCCchhhhhccccceeEEEeeeccccccccc-----chhh
Q psy13846 1274 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKE-----SVLN 1348 (1423)
Q Consensus 1274 ~~~~~sN~i~~i~~~lGIEAar~~ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~G~~~~i~r~g~~~~~~-----S~l~ 1348 (1423)
++|++||||++|+++|||||||++|++||+.||+.||++||+|||+||||+||++|.++||||+||+++.. |||+
T Consensus 254 ~~rt~sNdI~ev~~~lGIEAAR~~ii~El~~v~~~~G~~Vd~rHL~LlAD~MT~~G~~~~~nR~Gi~~~~~s~~~~spl~ 333 (381)
T cd02737 254 WERSMPYSIQQIKSVLGIDAAFEQFVQRLESAVSMTGKSVLREHLLLVADSMTYSGEFVGLNAKGYKAQRRSLKISAPFT 333 (381)
T ss_pred CCCcEECCHHHHHHHHhHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHhccCCceEEecchhhhhcccccccCCHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999997654 8999
Q ss_pred hccchhhHHHHHhhcccCCcccccccccceeeccccccccce-EEEee
Q psy13846 1349 LASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGL-IKLLQ 1395 (1423)
Q Consensus 1349 ~aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~~~~~GTG~-~~l~~ 1395 (1423)
+||||+|+++|++||.+|+.|+|+|||++|+||+++|+|||+ |||++
T Consensus 334 ~asFE~t~~~l~~AA~~g~~D~l~gvs~~ii~G~~~~vGTG~~fdll~ 381 (381)
T cd02737 334 EACFSSPIKCFLKAAKKGASDSLSGVLDACAWGKEAPVGTGSKFEILW 381 (381)
T ss_pred HhhHHHHHHHHHHHHhccCCCCCCChHHheeeCCcCCCcCCcceeeeC
Confidence 999999999999999999999999999999999999999997 99985
No 25
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=100.00 E-value=1.6e-54 Score=555.80 Aligned_cols=182 Identities=41% Similarity=0.648 Sum_probs=170.7
Q ss_pred hHHHHHHhccCCcEEcccCCccEEEEecccccceeeEEEEecCccHHHHhhcccccceecccccHHHHHHHhCHHHHHHH
Q psy13846 1218 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297 (1423)
Q Consensus 1218 ~~l~~l~~~l~~~~v~Gi~~i~r~~i~~~~~~~~~~~~l~teG~nl~~~~~~~~vd~~~~~sN~i~~i~~~lGIEAar~~ 1297 (1423)
..+..+...|.+++|+|+|||+||++.+++..+.++|+|.|||+||+++|++++||++||+||||++|+++|||||||++
T Consensus 671 ~~~~~~~~~l~~~~i~gi~gI~~~~i~~~~~~~~~~~~l~teG~nl~~~~~~~~vd~~~~~sN~i~~i~~~lGIEAar~~ 750 (858)
T PRK14898 671 KALRKRIPKIKNIVLKGIPGIERVLVKKEEHENDEEYVLYTQGSNLREVFKIEGVDTSRTTTNNIIEIQEVLGIEAARNA 750 (858)
T ss_pred HHHHHHHHHhcCcEEECCCCccEEEEecCCCCCCceEEEEecCcCHHHHhcCCCCcccccccCCHHHHHHhhCHHHHHHH
Confidence 34555556799999999999999999865432336899999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhcCCccccCCchhhhhccccceeEEEeeecccccccccchhhhccchhhHHHHHhhcccCCcccccccccc
Q psy13846 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSEC 1377 (1423)
Q Consensus 1298 ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~G~~~~i~r~g~~~~~~S~l~~aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ 1377 (1423)
|++||++||+.||++||+|||+||||+||++|.++|+||+||+.++.|||++||||+|+++|++||++|++|+|+|||||
T Consensus 751 ii~Ei~~v~~~~gi~V~~rHl~liad~MT~~G~~~~~~r~gi~~~~~s~l~~asFe~t~~~l~~Aa~~g~~D~l~g~s~~ 830 (858)
T PRK14898 751 IINEMMNTLEQQGLEVDIRHLMLVADIMTADGEVKPIGRHGVAGEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIEN 830 (858)
T ss_pred HHHHHHHHHHhcCCccCHHHHHHHHHHHccCCcEEEeccCCccCCCCCHHHhcChHhHHHHHHHHhhcCCCCcCCCchHH
Confidence 99999999999999999999999999999999999999999988889999999999999999999999999999999999
Q ss_pred eeeccccccccceEEEeecCCC
Q psy13846 1378 IIMGLPMNVGTGLIKLLQAVPR 1399 (1423)
Q Consensus 1378 ii~G~~~~~GTG~~~l~~~~~~ 1399 (1423)
||+|+++|+|||+|+|+++...
T Consensus 831 ii~G~~~~~GTG~~~l~~~~~~ 852 (858)
T PRK14898 831 VIVGKPIKLGTGCVDLRIDREY 852 (858)
T ss_pred eeeCCccCCcCceEEEEecCcc
Confidence 9999999999999999998654
No 26
>TIGR02389 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit A''. This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Probab=100.00 E-value=1.3e-52 Score=487.18 Aligned_cols=269 Identities=32% Similarity=0.500 Sum_probs=230.9
Q ss_pred ecCCCcccchhHHHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhH
Q psy13846 690 IMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIK 769 (1423)
Q Consensus 690 ~~~~~~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlk 769 (1423)
|.+++++|||+||++||||||||+||||| +||||||| ||||+|| |||||+
T Consensus 36 y~~alv~PGeaVG~IAAQSIGEP~TQMTL----nTFH~AGV-------------as~nVTl-------------GVPRlk 85 (367)
T TIGR02389 36 YLRSLIDPGEAVGIVAAQSIGEPGTQMTM----RTFHYAGV-------------AELNVTL-------------GLPRLI 85 (367)
T ss_pred HHHhcCCCccccchhhhhhcCCccccccc----cccccccc-------------cccCccc-------------cchhHH
Confidence 57789999999999999999999999999 99999999 9999999 999999
Q ss_pred HHHhhhcCCCCceeeeecccCC--hHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhh
Q psy13846 770 EIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSI 847 (1423)
Q Consensus 770 EIinaSk~ikTPiitv~L~~~~--~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I 847 (1423)
|||||+|+||||+|++||.++. +.++|+.++.+||+++|+|++.+++++|. ++.+.+++|.+++. .+.++++.|
T Consensus 86 EIINa~k~i~TP~~ti~L~~~~~~~~~~a~~v~~~iE~t~l~dv~~~~~~~~~--~~~l~i~ld~~~l~--~~~i~~~~i 161 (367)
T TIGR02389 86 EIVDARKTPSTPSMTIYLEDEYEKDREKAEEVAKKIEATKLEDVAKDISIDLA--DMTVIIELDEEQLK--ERGITVDDV 161 (367)
T ss_pred HHhhcccCCCCCeEEEEecCcchhhHHHHHHHHHHhhheeHHHHHhhhheecc--CcEEEEEECHHHHH--hcCCCHHHH
Confidence 9999999999999999999764 67899999999999999999999987764 44566677777664 446788899
Q ss_pred hHHhhhcccccCcccccccccccccCCCCccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCccc
Q psy13846 848 RYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927 (1423)
Q Consensus 848 ~~~i~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~nL 927 (1423)
+.++.+.+.........+...+.+++.. .. ...++.+++.+++++|+|+|||+|+++.++ .++|.+.|+|+||
T Consensus 162 ~~~i~~~~~~~~~~~~~~~~~i~i~~~~--~~-~~~l~~l~~~l~~~~v~Gi~gI~r~~i~~~----~~~~~l~teG~nl 234 (367)
T TIGR02389 162 EKAIKKAKLGKVIEIDMDGNTITIKPPK--PS-LKELRKLKEKIKNLHIKGIKGIKRVVIRKE----GDEYVIYTEGSNL 234 (367)
T ss_pred HHHHHHhcccccceeecCCCEEEEEecC--ch-HHHHHHHHHHhhhceEeCCCCceEEEEECC----CCeEEEEEeccCH
Confidence 9988765432221111122333333321 11 235888889999999999999999999743 2479999999999
Q ss_pred cccceeecccceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC
Q psy13846 928 RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG 999 (1423)
Q Consensus 928 ~~vl~~~gvD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~ 999 (1423)
++++.+++||+.+|+||||++|+++|||||||++|++|++.+|+.||++||+|||+||||+||++|++.+.+
T Consensus 235 ~~v~~~~~VD~~rt~sNdI~ei~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~RHl~LiaD~MT~~G~~~~i~ 306 (367)
T TIGR02389 235 KEVLKLEGVDKTRTTTNDIHEIAEVLGIEAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIG 306 (367)
T ss_pred HHHHcCCCCccccCccCCHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCeecHHHHHHHHHHhcCCceEEecc
Confidence 999999999999999999999999999999999999999999999999999999999999999999999864
No 27
>TIGR02388 rpoC2_cyan DNA-directed RNA polymerase, beta'' subunit. The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria.
Probab=100.00 E-value=1e-52 Score=534.29 Aligned_cols=111 Identities=31% Similarity=0.521 Sum_probs=104.6
Q ss_pred cccHHHHHHH----------------hCHHHHHHHHHHHHHHHhhcCCccccCCchhhhhccccce-------------e
Q psy13846 1279 SNNTYEVYKT----------------LGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK-------------G 1329 (1423)
Q Consensus 1279 sN~i~~i~~~----------------lGIEAar~~ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~-------------G 1329 (1423)
+.|.|+++.+ +|+||+|..|++|+++||+.||+.|++|||++|+|+||.+ |
T Consensus 1057 ~~~ph~iL~~~~~~~~~~~g~~~aa~~s~~~~q~~lv~eiq~vy~~QGv~I~~kHieiIvrqMtskV~i~~~G~t~~lpG 1136 (1227)
T TIGR02388 1057 PINPHDILDVFFSYYKDQDGLYEAAQESLQKVQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDAGDTTLLPG 1136 (1227)
T ss_pred CCCHHHHHhhhhhhhcccchhHHHHHHHHHHHHHHHHHHHHHHHHhcceEeehhhHHHHHHHHhceEEEeeCCCcccCCc
Confidence 5678888887 4999999999999999999999999999999999999987 5
Q ss_pred E---------------------------EEeeecccccccccchhhhccchhhHHHHHhhcccCCcccccccccceeecc
Q psy13846 1330 E---------------------------VLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGL 1382 (1423)
Q Consensus 1330 ~---------------------------~~~i~r~g~~~~~~S~l~~aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~ 1382 (1423)
+ ++||||++++ ..|+|++||||+|+++|++||++|+.|+|+|++||||+|+
T Consensus 1137 eli~~~~~~~~n~~l~~~~~~~~~y~pvLlGITkasL~--t~Sfis~ASFqeTtrvL~~Aai~g~~D~l~glkENvI~G~ 1214 (1227)
T TIGR02388 1137 ELVELRQVEQVNEAMAITGGAPAQYTPVLLGITKASLN--TDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGR 1214 (1227)
T ss_pred ceeeHHHHHHHHHHHHhcCCCccccceeEeeeeecccc--ccchhhhccHHHHHHHHHHHHHcCCcccccCchhheeecC
Confidence 4 7999999997 5899999999999999999999999999999999999999
Q ss_pred ccccccceE
Q psy13846 1383 PMNVGTGLI 1391 (1423)
Q Consensus 1383 ~~~~GTG~~ 1391 (1423)
++|+|||..
T Consensus 1215 liP~GTG~~ 1223 (1227)
T TIGR02388 1215 LIPAGTGFS 1223 (1227)
T ss_pred ccccCCCcc
Confidence 999999974
No 28
>PF04998 RNA_pol_Rpb1_5: RNA polymerase Rpb1, domain 5; InterPro: IPR007081 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to form the central cleft or channel where the DNA is bound [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1ZYR_D 1SMY_D 2A68_N 2O5J_D 3AOH_N 2O5I_D 2CW0_N 2A6H_N 2A69_D 3EQL_D ....
Probab=100.00 E-value=1.6e-53 Score=489.14 Aligned_cols=252 Identities=43% Similarity=0.628 Sum_probs=199.0
Q ss_pred CCCceeeeeecccccccchhcccccCCCCcchHHHHHHHhhhhhcccceeecc-------ccCCCccCCCcchheecCCC
Q psy13846 622 GLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAA-------FYGQTDCISGVSECIIMGLP 694 (1423)
Q Consensus 622 GL~p~Efffh~maGReGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~tVR~s-------~yG~~~~~~~~~~~~~~~~~ 694 (1423)
||+|.|||||||||||||||||||||+||||||||||++||++|+||+|||++ .||+|+ +
T Consensus 1 Gl~~~e~f~~~~~~R~gl~dta~kTa~sGyl~R~lv~~~~~~~v~~~~~~~~~~~~i~~~~~~~~~-------------~ 67 (277)
T PF04998_consen 1 GLTPTEYFFHCMGGREGLIDTAVKTADSGYLQRRLVKVLEDLIVRYDDCVRNSGGSIIQFIYGEDG-------------L 67 (277)
T ss_dssp C-THHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHTTHEEETTSEEESTTSEEEESSCTTTS-------------B
T ss_pred CcCHHHHHHHHhcccccccccceeeeccccchhhhhhccceEEEEEcCccccccceeeeccccccc-------------c
Confidence 89999999999999999999999999999999999999999999999999987 366552 7
Q ss_pred cccchhHHHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhHHHHhh
Q psy13846 695 MNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINA 774 (1423)
Q Consensus 695 ~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlkEIina 774 (1423)
++|||+||.|||||||||+||||| +|||+||+ +++++|+ |+||++||+++
T Consensus 68 v~~Ge~VGiiaAQSIGEP~TQ~TL----~TFH~aG~-------------~~~~vt~-------------giprl~eii~~ 117 (277)
T PF04998_consen 68 VEPGEAVGIIAAQSIGEPGTQMTL----RTFHTAGV-------------ASKNVTQ-------------GIPRLKEIINA 117 (277)
T ss_dssp --TTSBHHHHHHHHHHCHGCCSHH----SCTSSSCS-------------STSSCSS-------------SHHHHHHHHTT
T ss_pred cCccccchhhhhchhcchhHHhhh----cccccCce-------------eeecccc-------------cceeecccccc
Confidence 899999999999999999999999 99999999 7778888 99999999999
Q ss_pred hcCCCCceeeeecccCCh--HHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhhhHHhh
Q psy13846 775 SRNISTPIITAYLDKDTD--LDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIE 852 (1423)
Q Consensus 775 Sk~ikTPiitv~L~~~~~--~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I~~~i~ 852 (1423)
++++++|+++.+...... .+....+............
T Consensus 118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------------------------------- 156 (277)
T PF04998_consen 118 SKKIKTPIITVYGKKKIISEKKKIKIIRKKIKIIKNGKK----------------------------------------- 156 (277)
T ss_dssp CSSSSSEEEEECSCSSECSSSHHHHHHHHTCSSSCSTTC-----------------------------------------
T ss_pred ccccccceEEeecccceecccccceEEEEeeeeeecccc-----------------------------------------
Confidence 999999999988865432 1222122111111000000
Q ss_pred hcccccCcccccccccccccCCCCccccchhhhhhhhcCCceEEccccccceeeee-cccccceeEEeeeccCccccccc
Q psy13846 853 RTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIH-EEDVEGVTKYKLLVEGDNLRDVM 931 (1423)
Q Consensus 853 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~-~~~~~~~~~~~l~~eG~nL~~vl 931 (1423)
+..+.......... ........+|.+.++|+++..++
T Consensus 157 ------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~l~~v~ 194 (277)
T PF04998_consen 157 ------------------------------------------VKNGDKIKKGSIISKDILEKKSKEYVLQTEGSNLQEVY 194 (277)
T ss_dssp ------------------------------------------EHTTCESSSSCSEHHHHCEECCCCCEEECCSHHHHHHT
T ss_pred ------------------------------------------eecceeeecceeeeeccccchhHHHHHHHHhhhchhhe
Confidence 00000000000000 00011235789999999999999
Q ss_pred eeec-ccceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC
Q psy13846 932 ATYG-VKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG 999 (1423)
Q Consensus 932 ~~~g-vD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~ 999 (1423)
..+| +|+.++.+|+|++|++++||||||++|++|++.+++.+|++||+||++|+||.||++|.++|+.
T Consensus 195 ~~qgvid~~k~~sn~I~qm~~~~GIeaar~~i~~e~~~v~~~~g~~vn~rhl~llad~mt~~g~~~git 263 (277)
T PF04998_consen 195 SSQGVIDNDKHISNDIRQMLSKLGIEAARNSIIKELKNVFESYGIEVNKRHLSLLADYMTYKGVLLGIT 263 (277)
T ss_dssp CSTT-EETCHHECSHHHHHHHHHEHHHHHHHHHHHHHCHHHHCTSCCCHHHHHHHHHHHCCCSS---CC
T ss_pred ecccccCCCEEEeceeEeeeeeEEEEECCCceeecCcEeeHHHHHHHHHHHHHhCCCcCeeeeEEEEEE
Confidence 9999 8999999999999999999999999999999999999999999999999999999999999975
No 29
>PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Probab=100.00 E-value=8.2e-51 Score=479.85 Aligned_cols=300 Identities=29% Similarity=0.447 Sum_probs=241.6
Q ss_pred chHHHHHHHhhhhhcccceeeccccCCCccCCCcchheecCCCcccchhHHHHhhhcCCCCCCccccccCCCCcccCccc
Q psy13846 652 MQRRLVKSLEDLCVQYDMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVY 731 (1423)
Q Consensus 652 lqRrLvk~ledl~v~yD~tVR~s~yG~~~~~~~~~~~~~~~~~~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~ 731 (1423)
|-.++.+-|..+...|..|-..- +..-+.....|.+++++||++||.+||||||||+||||| +|||||||
T Consensus 141 lp~~~~~el~~~~~~~~l~~~~~-----~~i~~ei~~~y~~~~v~pGE~VG~IAAQSIGEP~TQMTL----nTFH~AGV- 210 (509)
T PRK14897 141 LPPSVIEEIAKAMKKKELSDDEY-----EEILRRIREEYERARVDPYEAVGIVAAQSIGEPGTQMTM----RTFHYAGV- 210 (509)
T ss_pred CCHHHHHHHHHHHHHcCCCHHHH-----HHHHHHHHHHHHHhccCCCCCcchhhhhhhCCccccccc----cccccccc-
Confidence 66667776666666664332210 000011122367889999999999999999999999999 99999999
Q ss_pred cccccccccccccccceeecccCCCCCccCCCCchhhHHHHhhhcCCCCceeeeecccCC--hHHHHHHHhhhhcccchh
Q psy13846 732 YERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLG 809 (1423)
Q Consensus 732 ~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlkEIinaSk~ikTPiitv~L~~~~--~~e~a~~v~~rie~~~l~ 809 (1423)
|++|+|| |||||+|||||+|+||||+|++||.++. |.++|+.++.+||+++|+
T Consensus 211 ------------as~NVTl-------------GVPRLkEIINa~K~isTP~mtiyL~~~~~~d~e~A~~V~~~IE~ttL~ 265 (509)
T PRK14897 211 ------------AEMNVTL-------------GLPRLIEIVDARKKPSTPTMTIYLKKDYREDEEKVREVAKKIENTTLI 265 (509)
T ss_pred ------------ccccccc-------------CcchhHHHhhcccCCCCceEEEEecCcccccHHHHHHHHhhheeeEHH
Confidence 9999999 9999999999999999999999999774 788999999999999999
Q ss_pred hhhhhheeeecCCCcceeeehhhhHHHhhccccchhhhhHHhhhcccccCcccccccccccccCCCCccccchhhhhhhh
Q psy13846 810 EVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQ 889 (1423)
Q Consensus 810 dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I~~~i~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~l~~ 889 (1423)
|+++++..+ .++.+.+++|.+++ ..+.++++.|..+|.+... ..+.. +++.+.+.+.. .. ...++++.+
T Consensus 266 dv~~~~~d~---~~~~i~i~Ld~~~l--~~~~l~~~~I~~~I~~~~~--~~~~~-~~~~I~i~~~~--~~-~~~L~~l~~ 334 (509)
T PRK14897 266 DVADIITDI---AEMSVVVELDEEKM--KERLIEYDDILAAISKLTF--KTVEI-DDGIIRLKPQQ--PS-FKKLYLLAE 334 (509)
T ss_pred HHHHHHHHh---ccceEEEEECHHHH--HHcCCCHHHHHHHHHhccc--eEEec-CCCEEEEEeCc--hH-HHHHHHHHH
Confidence 999876544 34445556666555 5566777889988876321 11221 22233343321 12 236778888
Q ss_pred cCCceEEccccccceeeeecccccceeEEeeeccCccccccceeecccceeeccCchHHHHHHhchHHHHHHHHHHHHHH
Q psy13846 890 LLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLV 969 (1423)
Q Consensus 890 ~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~nL~~vl~~~gvD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v 969 (1423)
.+++++|+|+|||+|+++..+++ ...|.|.|+|+||++++.++|||+.+|+||||+||+++|||||||++|++|++.+
T Consensus 335 ~l~~i~I~GipgI~r~~i~~~~~--~~~~~L~TeG~NL~~vl~~~~VD~~rt~SNdI~eI~~vlGIEAAR~~Ii~Ei~~V 412 (509)
T PRK14897 335 KVKSLTIKGIKGIKRAIARKEND--ERRWVIYTQGSNLKDVLEIDEVDPTRTYTNDIIEIATVLGIEAARNAIIHEAKRT 412 (509)
T ss_pred HhhccEEeCCCCccEEEEecCCC--CceeEEEeeccCHHHHhcCCCcccccCccCCHHHHHHhcCHHHHHHHHHHHHHHH
Confidence 99999999999999999986543 3469999999999999999999999999999999999999999999999999999
Q ss_pred HHhcCccccCCchhhHhhhhccccccccCC
Q psy13846 970 MENHGMSIDFRHPMLVADLMTSKGEVLGNG 999 (1423)
Q Consensus 970 ~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~ 999 (1423)
|+.||++||+|||+||||+||++|++.+.+
T Consensus 413 ~~~~Gi~Vd~RHL~LIAD~MT~~G~v~~i~ 442 (509)
T PRK14897 413 LQEQGLNVDIRHIMLVADMMTFDGSVKAIG 442 (509)
T ss_pred HHhcCCcccHHHHHHHHHHhCcCCcccccc
Confidence 999999999999999999999999998875
No 30
>cd06528 RNAP_A'' A'' subunit of Archaeal RNA Polymerase (RNAP). Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.
Probab=100.00 E-value=2.5e-50 Score=469.13 Aligned_cols=268 Identities=32% Similarity=0.482 Sum_probs=229.3
Q ss_pred ecCCCcccchhHHHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhH
Q psy13846 690 IMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIK 769 (1423)
Q Consensus 690 ~~~~~~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlk 769 (1423)
|.++.++||++||.+||||+|||+||||| +||||||| ||||+|| |||||+
T Consensus 32 ~~~~~~~~Ge~vG~iaAQSiGEP~TQMTL----nTFH~AGV-------------as~nVTl-------------GVPRlk 81 (363)
T cd06528 32 YLRSLIEPGEAVGIVAAQSIGEPGTQMTL----RTFHYAGV-------------AEINVTL-------------GLPRLI 81 (363)
T ss_pred HHHHhhccCccccceeeeecCccceeccc----cccccccc-------------ccccCcc-------------ccccHH
Confidence 46778999999999999999999999999 99999999 9999999 999999
Q ss_pred HHHhhhcCCCCceeeeecccC--ChHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhh
Q psy13846 770 EIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSI 847 (1423)
Q Consensus 770 EIinaSk~ikTPiitv~L~~~--~~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I 847 (1423)
|||||+|+||||+|++||.++ .+.+.|+.++.+||+++|+|++.++++. ++++.+.+++|.+++.. +.++++.|
T Consensus 82 EIIna~K~i~TP~mti~L~~~~~~~~~~a~~v~~~iE~t~l~di~~~~~i~--~~~~~l~i~ld~~~l~~--~~l~~~~i 157 (363)
T cd06528 82 EIVDARKEPSTPTMTIYLEEEYKYDREKAEEVARKIEETTLENLAEDISID--LFNMRITIELDEEMLED--RGITVDDV 157 (363)
T ss_pred HHhhcccCCCCceEEEEecCcchhhHHHHHHHHHhhceeEHHHhhhheEEe--ccCcEEEEEECHHHHHH--cCCCHHHH
Confidence 999999999999999999977 4678999999999999999999998875 34566677777776654 45788899
Q ss_pred hHHhhhcccccCcccccccccccccCCCCccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCccc
Q psy13846 848 RYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927 (1423)
Q Consensus 848 ~~~i~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~nL 927 (1423)
..++.+....... ..++..+.+.... +.....++.+++.+++++|+|+|||+|+.++.++ ++|.+.|+|+||
T Consensus 158 ~~~i~~~~~~~~~--~~~~~~~~~~~~~--~~~~~~l~~l~~~l~~~~v~Gi~gI~r~~i~~~~----~~~~l~teG~nl 229 (363)
T cd06528 158 LKAIEKLKKGKVG--EEGDVTLIVLKAE--EPSIKELRKLAEKILNTKIKGIKGIKRVIVRKEE----DEYVIYTEGSNL 229 (363)
T ss_pred HHHHHHhcCCccc--ccCCccEEEEcCC--cchHHHHHHHHHhhcccEEeCCCCceEEEEecCC----ceEEEEecCcCH
Confidence 9998765432221 1121111111111 1222467888899999999999999999998654 379999999999
Q ss_pred cccceeecccceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC
Q psy13846 928 RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG 999 (1423)
Q Consensus 928 ~~vl~~~gvD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~ 999 (1423)
++++.+++||+.+|+|||++||+++|||||||++|++|++.+|+.||++||+|||+||||+||++|++.+.+
T Consensus 230 ~~v~~~~~Vd~~rt~sNdI~ei~~~lGIEAaR~~ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~G~~~~i~ 301 (363)
T cd06528 230 KAVLKVEGVDPTRTTTNNIHEIEEVLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVRQIG 301 (363)
T ss_pred HHHhcCCCCcccccccCCHHHHHHhCCHHHHHHHHHHHHHHHHHhcCCeecHHHHHHHHHHhccCCceeccc
Confidence 999999999999999999999999999999999999999999999999999999999999999999998865
No 31
>PRK04309 DNA-directed RNA polymerase subunit A''; Validated
Probab=100.00 E-value=7.1e-50 Score=468.24 Aligned_cols=266 Identities=33% Similarity=0.538 Sum_probs=230.1
Q ss_pred ecCCCcccchhHHHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhH
Q psy13846 690 IMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIK 769 (1423)
Q Consensus 690 ~~~~~~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlk 769 (1423)
|.++.++|||+||.+||||||||+||||| +||||||+ +++|+|| |||||+
T Consensus 51 y~~~~v~pGe~VG~iaAQsIGEP~TQMTL----~TFH~AGv-------------a~~nVTl-------------GvPRlk 100 (383)
T PRK04309 51 YLRSLVEPGEAVGVVAAQSIGEPGTQMTM----RTFHYAGV-------------AEINVTL-------------GLPRLI 100 (383)
T ss_pred HHHhhcCCCCccchhhhhhccchhhhccc----ccccccCc-------------cccCccc-------------CchhHH
Confidence 56788999999999999999999999999 99999999 8999999 999999
Q ss_pred HHHhhhcCCCCceeeeecccCC--hHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhh
Q psy13846 770 EIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSI 847 (1423)
Q Consensus 770 EIinaSk~ikTPiitv~L~~~~--~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I 847 (1423)
|||||+|+||||+|++||.++. |.++|+.++.+||+++|+++++++++. ++++.+.+++|.+++. .++++++.|
T Consensus 101 EIina~K~~~TP~~tv~L~~~~~~d~~~a~~v~~~iE~t~L~~v~~~i~~~--~~~~~l~i~ld~~~i~--~~~l~~~~I 176 (383)
T PRK04309 101 EIVDARKEPSTPMMTIYLKDEYAYDREKAEEVARKIEATTLENLAKDISVD--LANMTIIIELDEEMLE--DRGLTVDDV 176 (383)
T ss_pred HHHhcccCCCCCeEEEEecCcccccHHHHHHHHhheeeeEHhhhhhheEec--cCCcEEEEEECHHHHH--HcCCCHHHH
Confidence 9999999999999999999874 789999999999999999999998864 3456667777777765 456688899
Q ss_pred hHHhhhcccccCcccccccccccccCCCCccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCccc
Q psy13846 848 RYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927 (1423)
Q Consensus 848 ~~~i~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~nL 927 (1423)
+..|.+.+..... +. ...+.+++.. .....++.+...+++++|+|++||+|+++.+++ ++|.+.|+|+||
T Consensus 177 ~~~i~~~~~~~~~--~~-~~~i~i~~~~---~~~~~l~~l~~~l~~~~vkGi~gI~r~~i~~~~----~~~~l~teG~nl 246 (383)
T PRK04309 177 KEAIEKKKGGEVE--IE-GNTLIISPKE---PSYRELRKLAEKIRNIKIKGIKGIKRVIIRKEG----DEYVIYTEGSNL 246 (383)
T ss_pred HHHHHHhcCccee--cc-CCeEEEEecC---chHHHHHHHHHHhcccEEECCCCceEEEEecCC----CeEEEEEcccCH
Confidence 9998766543221 11 1222333321 112467788899999999999999999997542 479999999999
Q ss_pred cccceeecccceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC
Q psy13846 928 RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG 999 (1423)
Q Consensus 928 ~~vl~~~gvD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~ 999 (1423)
++++.+++||+.+|+||||++|+++|||||||++|++|++.+|+.||++||+|||+||||+||++|++.+.+
T Consensus 247 ~~v~~~~~VD~~rt~sNdI~ei~~vlGIEAAR~~ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~G~~~~i~ 318 (383)
T PRK04309 247 KEVLKVEGVDATRTTTNNIHEIEEVLGIEAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIG 318 (383)
T ss_pred HHHhcCCCEeeccccCCCHHHHHHHcCHHHHHHHHHHHHHHHHHHcCCeecHHHHHHHHHHhccCceEEeee
Confidence 999999999999999999999999999999999999999999999999999999999999999999999864
No 32
>PRK02597 rpoC2 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=100.00 E-value=1.4e-49 Score=509.72 Aligned_cols=113 Identities=29% Similarity=0.472 Sum_probs=105.7
Q ss_pred cccHHHHHHH----------------hCHHHHHHHHHHHHHHHhhcCCccccCCchhhhhccccceeE------------
Q psy13846 1279 SNNTYEVYKT----------------LGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGE------------ 1330 (1423)
Q Consensus 1279 sN~i~~i~~~----------------lGIEAar~~ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~G~------------ 1330 (1423)
+.|.|+++.+ +|+||+|..+++|+++||+.||++||+|||++|+|+||.++.
T Consensus 1058 ~~~ph~iL~~~f~~~~~~~g~~~aa~~~~~~~~~~lv~evq~Vy~~QGv~I~dkHieiIvrqMt~kV~i~d~Gdt~~lpG 1137 (1331)
T PRK02597 1058 PINPHELLEIFFEDLRDRKGLYEAALEALQKLQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDGGDTTMLPG 1137 (1331)
T ss_pred CCCHHHHHhhhhhhhcccchhhHHHHHhHHHHHHHHHHHHHHHHHhcCeEechhhHHhHHHHHhCcEEEeeCCCcccCCc
Confidence 5788999998 899999999999999999999999999999999999998843
Q ss_pred ----------------------------EEeeecccccccccchhhhccchhhHHHHHhhcccCCcccccccccceeecc
Q psy13846 1331 ----------------------------VLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGL 1382 (1423)
Q Consensus 1331 ----------------------------~~~i~r~g~~~~~~S~l~~aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~ 1382 (1423)
++||||..++ ..|+|++||||+|+++|++||++|+.|+|+|++||||+|+
T Consensus 1138 eli~~~~~~~~N~~~~~~~~~~a~y~pvLlGItkasl~--T~sfis~aSFqeT~rvL~~AAi~g~~D~l~GlkENVI~G~ 1215 (1331)
T PRK02597 1138 ELIELRQVEQVNEAMAITGGAPAEYTPVLLGITKASLN--TDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGR 1215 (1331)
T ss_pred ceeeHHHHHHHHHHHHhcCCCcceeeeeeeeeeeeccc--cCChhhhccHHHHHHHHHHHHHcCCCcccCCchhheeecC
Confidence 3888998887 5899999999999999999999999999999999999999
Q ss_pred ccccccceEEE
Q psy13846 1383 PMNVGTGLIKL 1393 (1423)
Q Consensus 1383 ~~~~GTG~~~l 1393 (1423)
++|+|||++.+
T Consensus 1216 liP~GTG~~~~ 1226 (1331)
T PRK02597 1216 LIPAGTGFSGF 1226 (1331)
T ss_pred ccccCcCchhh
Confidence 99999999744
No 33
>CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed
Probab=100.00 E-value=2.4e-48 Score=504.08 Aligned_cols=108 Identities=33% Similarity=0.536 Sum_probs=100.6
Q ss_pred HhCHHHHHHHHHHHHHHHhhcCCccccCCchhhhhccccce--------------eE-----------------------
Q psy13846 1288 TLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK--------------GE----------------------- 1330 (1423)
Q Consensus 1288 ~lGIEAar~~ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~--------------G~----------------------- 1330 (1423)
-+.|||+|..|++|+++||+.||+.|++|||++|+|+||.+ |+
T Consensus 1180 ~lS~~~~~~~lv~eiq~vy~~qGv~i~~kHieiivrqmt~kv~i~~~g~~~v~~pge~i~~~~~~~~~~~~~~~~~~~~~ 1259 (1364)
T CHL00117 1180 ELSIAQSQISLVNKIQKVYRSQGVQISDKHIEIIVRQMTSKVLVSEDGMSNVFLPGELIGLLRAERINRALEEAICYRPI 1259 (1364)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCcEeehhhhhhhHHHhhCeEEEeecCccCccCCcceeeHHHHHHHhHHhhcCcceeee
Confidence 44599999999999999999999999999999999999985 44
Q ss_pred EEeeecccccccccchhhhccchhhHHHHHhhcccCCcccccccccceeeccccccccceEEEeecC
Q psy13846 1331 VLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 1397 (1423)
Q Consensus 1331 ~~~i~r~g~~~~~~S~l~~aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~~~~~GTG~~~l~~~~ 1397 (1423)
++||||++++ .+|+|++||||+|+++|++||++|++|+|+|++||||+|+++|+|||..++....
T Consensus 1260 llGitkasl~--t~Sfis~aSFqeT~rvL~~aai~g~~D~l~glkenvi~g~~ip~GTG~~~~~~~~ 1324 (1364)
T CHL00117 1260 LLGITKASLN--TQSFISEASFQETTRVLAKAALRGRIDWLKGLKENVILGGLIPAGTGFKGLVHRS 1324 (1364)
T ss_pred eeeeeehhcc--ccchhhhcchHHHHHHHHHHHHcCCcccccCchhheeecCcccCCCCchhhhhhh
Confidence 6799999998 5899999999999999999999999999999999999999999999998776543
No 34
>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=1.6e-48 Score=497.30 Aligned_cols=627 Identities=16% Similarity=0.185 Sum_probs=379.7
Q ss_pred hhHHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeecccCC--------cccCHHHHHHHHHHhhcccccceee
Q psy13846 10 TLYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKN--------AFFNRAQTMRIASTLIAGRKVFFRG 81 (1423)
Q Consensus 10 ~~~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~~~--------~~~~~~~~~~~~~~~~~~~~~~i~~ 81 (1423)
-.-+||||||++||++++||+||++|+|++|.+||+++|+|+||.+| +|++++++++.+. . +...+..
T Consensus 453 PqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~~~~~~~~~F~~~~e~~~~~~---~-~~i~l~~ 528 (1140)
T TIGR02386 453 PLSPEAQAEARALMLASNNILNPKDGKPIVTPSQDMVLGLYYLTTEKPGAKGEGKIFSNVDEAIRAYD---N-GKVHLHA 528 (1140)
T ss_pred CCCHHHHHHHHHHhCCcccEecCCCCCceEEeechhhheeeEeeeccccccCcCceeCCHHHHHHHHH---c-CCccCCC
Confidence 34579999999999999999999999999999999999999999996 7999999987542 2 2222333
Q ss_pred eEEEecCCHHHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccCceeEEe
Q psy13846 82 LIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIG 161 (1423)
Q Consensus 82 ~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~PV~h~g 161 (1423)
.+... .....+| ..+|+.+.+-++++.++..+...
T Consensus 529 ~i~~~--------------~~g~~~~--tt~Gr~if~~ilP~~~~~~n~~~----------------------------- 563 (1140)
T TIGR02386 529 LIGVR--------------TSGEILE--TTVGRVIFNEILPEGFPYINDNE----------------------------- 563 (1140)
T ss_pred ceEEe--------------ccccEEE--ccchHHHHHHHcCCccccccccc-----------------------------
Confidence 11111 0111223 12688888878776665443210
Q ss_pred eec--cHHHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCceeecCcc
Q psy13846 162 YFR--CVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLL 239 (1423)
Q Consensus 162 ffd--~v~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk~~~~ 239 (1423)
.++ .+.+++..+... ++.+....|++++++....+..+.+++.++.|...... | .
T Consensus 564 ~l~Kk~lg~LI~~i~~~-------~G~~~t~~~LD~lk~Lgf~~at~~GfSigi~Dl~ip~~-------------K---~ 620 (1140)
T TIGR02386 564 PLSKKEISSLIDLLYEV-------HGIEETAEMLDKIKALGFKYATKSGTTISASDIVVPDE-------------K---Y 620 (1140)
T ss_pred ccchHHHHHHHHHHHHH-------hChHHHHHHHHHHHHHHHHHHHhcCeeeeeccCCCCHH-------------H---H
Confidence 222 123555555555 77888899999999988888888888888887632110 0 0
Q ss_pred eehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhcc--CccccCCHHHHHHHhhccCCCcccccccccCCCCCcc
Q psy13846 240 KISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKF--GLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSD 317 (1423)
Q Consensus 240 ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~L~p~~V~eiLe~I~~~d~~lL~m~~~~arPe~ 317 (1423)
+++. +.+..+.+..+.|..-.....+....... ......-...+.+.|..-.+..++++.|..+|||++.
T Consensus 621 ~ii~--------~a~~~v~~i~~~y~~G~lt~~er~~kvi~iw~~~~d~v~~~~~~~l~~~~~~~N~i~mMa~SGARGS~ 692 (1140)
T TIGR02386 621 EILK--------EADKEVAKIQKFYNKGLITDEERYRKVVSIWSETKDKVTDAMMKLLKKDTYKFNPIFMMADSGARGNI 692 (1140)
T ss_pred HHHH--------HHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCcHhhhhhcccccCH
Confidence 1111 11111222222222110000000000000 0000001222223332110124789999999999999
Q ss_pred eEEEEecCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCcccccccccCCC
Q psy13846 318 LILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQT 397 (1423)
Q Consensus 318 liLt~lpVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~ 397 (1423)
.++.||. .|.++++...+ +++|. |.-+++..+|.+.
T Consensus 693 ~ni~QL~---GmrGlma~p~G-------------------------rii~~----------------PI~ssF~eGLtp~ 728 (1140)
T TIGR02386 693 SQFRQLA---GMRGLMAKPSG-------------------------DIIEL----------------PIKSSFREGLTVL 728 (1140)
T ss_pred HHHHHHH---hCCCcccCCCC-------------------------Ccccc----------------chhhccccCCCHH
Confidence 9999999 88887643221 22222 4677788899866
Q ss_pred HHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecccccCCCHHHHHHHHHhhccCCccc
Q psy13846 398 EEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDI 477 (1423)
Q Consensus 398 ~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~~~~~~~~~~l~~~~~~~~~~~ 477 (1423)
| ||||+||||+|+++++.+|+.|||.+|+|+...|| +...|+=+..+..+.... +. +.
T Consensus 729 E----------yF~st~GaRkGLiDTAlKTAdSGYLtRRLVdv~qD-viV~~dDCgT~~gi~v~~-------~~----~~ 786 (1140)
T TIGR02386 729 E----------YFISTHGARKGLADTALKTADSGYLTRRLVDVAQD-VVVREEDCGTEEGIEVEA-------IV----EG 786 (1140)
T ss_pred H----------Hhhhccchhccccchheeecccceeeeehhhhhcc-eEEEeCCCCCCCCEEEEE-------ee----cC
Confidence 6 99999999999999999999999999999999999 666654332111000000 00 00
Q ss_pred cceEeeeeccccCCceeecceeeeecceeeeecccCCCCcccccceeecccccccCcccccCCcEEEecccccccccccc
Q psy13846 478 CGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDK 557 (1423)
Q Consensus 478 ~~~~~~~~~~~l~~p~i~kp~~~wtGKqi~s~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~~ell~g~ldK 557 (1423)
.+++ +....+-..|+.+...+. .+..+.++...++++...+
T Consensus 787 ~~~~------------i~~l~~ri~GR~~~~di~-------------------------~~~~~~~i~~~~~~i~~~~-- 827 (1140)
T TIGR02386 787 KDEI------------IESLKDRIVGRYSAEDVY-------------------------DPDTGKLIAEANTLITEEI-- 827 (1140)
T ss_pred CceE------------EeehhheeEEEEEhhheE-------------------------eCCCCcEEEeCCCCcCHHH--
Confidence 0000 000011112332211111 1222334444444432211
Q ss_pred CCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceecCCCCCCccccccccccCCCceeeeeecccccc
Q psy13846 558 STLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSFFSGLTPTEFFFHTMGGRE 637 (1423)
Q Consensus 558 ~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~D~~~~~GfI~~sf~~GL~p~Efffh~maGRe 637 (1423)
...+.. .| +.-+...+ - + +|-++.
T Consensus 828 -----------~~~i~~------------------------~~----i~~v~iRS-----~-----------l-tC~s~~ 851 (1140)
T TIGR02386 828 -----------AEKIEN------------------------SG----IEKVKVRS-----V-----------L-TCESEH 851 (1140)
T ss_pred -----------HHHHHH------------------------cC----CCEEEecC-----C-----------e-eeCCCC
Confidence 111111 01 11111000 0 0 000011
Q ss_pred cchhcccccCCCCcchHHHHHHHhhhhhcccceeeccccCCCccCCCcchheecCCCcccchhHHHHhhhcCCCCCCccc
Q psy13846 638 GLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRT 717 (1423)
Q Consensus 638 GLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~tVR~s~yG~~~~~~~~~~~~~~~~~~~~g~~vg~i~aqsige~~tq~t 717 (1423)
+ |=..|||.| ++++.+++.|+|||++||||||||+||+|
T Consensus 852 ------------------------g--------vC~~CYG~~---------La~~~~V~~GeaVGiiAAQSIGEPGTQLT 890 (1140)
T TIGR02386 852 ------------------------G--------VCQKCYGRD---------LATGKLVEIGEAVGVIAAQSIGEPGTQLT 890 (1140)
T ss_pred ------------------------C--------CccccCCCc---------ccCCcEecccccceeEeeeecCCCcchhe
Confidence 1 112268887 56788999999999999999999999999
Q ss_pred cccCCCCcccCcccccccccccccccccc--ceeecccCCCCCccCCCCchhhHHHHhhhcCCCCceeeeecccCChHHH
Q psy13846 718 LLFDNPEFHFPQVYYERRRDYSVKVTASV--KVTLELWNPGDYKLSQDGVPRIKEIINASRNISTPIITAYLDKDTDLDY 795 (1423)
Q Consensus 718 L~~~~~tFh~agv~~~~~~~~~~~~~as~--~itl~~~~~g~~~~~~~GvPRlkEIinaSk~ikTPiitv~L~~~~~~e~ 795 (1423)
| +|||.+|+ |+. +||+ |+||+.|+++|++ +|.+.+-......
T Consensus 891 m----RTFHtGGv-------------~~~~~DIT~-------------GlpRv~elfear~-p~~~a~iae~~G~----- 934 (1140)
T TIGR02386 891 M----RTFHTGGV-------------AGASGDITQ-------------GLPRVKELFEART-PKDKAVIAEVDGT----- 934 (1140)
T ss_pred h----hheeeccc-------------ccccccccc-------------Cchhhhhhhhccc-CCCceEEEecCCE-----
Confidence 9 99999999 554 8998 9999999999953 4444433322210
Q ss_pred HHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhhhHHhhhcccccCcccccccccccccCCC
Q psy13846 796 ARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKD 875 (1423)
Q Consensus 796 a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I~~~i~~~~~~~~~i~~~~~~~~~~~~~~ 875 (1423)
+++++ ..
T Consensus 935 ----------------v~~~~---~~------------------------------------------------------ 941 (1140)
T TIGR02386 935 ----------------VEIIE---DI------------------------------------------------------ 941 (1140)
T ss_pred ----------------EEEee---cc------------------------------------------------------
Confidence 00000 00
Q ss_pred CccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCc--cccccceeecccceeeccCchHHHHHHh
Q psy13846 876 SSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD--NLRDVMATYGVKGVKCSSNNTYEVYKTL 953 (1423)
Q Consensus 876 ~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~--nL~~vl~~~gvD~~~t~SN~i~eV~~~L 953 (1423)
.+|-.+++|..+++ ...+|.+-. |. ...+...+...|...-.+-|++||++++
T Consensus 942 -----------------------~~~~~~i~i~~~~~-~~~~y~ip~-~~~l~v~~gd~V~~G~~l~~g~~~~~~il~v~ 996 (1140)
T TIGR02386 942 -----------------------VKNKRVVVIKDEND-EEKKYTIPF-GAQLRVKDGDSVSAGDKLTEGSIDPHDLLRIK 996 (1140)
T ss_pred -----------------------cCCcEEEEEECCCC-ceeEEeccC-CceEEecCCCEEccCCcccCCCCCHHHHHHhc
Confidence 00000111111100 000111100 00 0011111223344445567999999999
Q ss_pred chHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC-------cchhhHHHHHHHHHhccCCCCCCCCHH
Q psy13846 954 GIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG-------TPVELKRLLDDIIAKNSSRSDPSLSAQ 1026 (1423)
Q Consensus 954 GIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~-------~~~~~~~~~~~~~~~~~~~~~~~l~~~ 1026 (1423)
||||+|+.|++|+++++..||++||++||++++++||++++|...| ..|+...+.+.++....++..|+...+
T Consensus 997 G~~a~~~~lv~evq~vY~~QGv~I~dKHievIvrqM~~kv~i~~~gdt~~l~g~~v~~~~~~~~n~~~~~~g~~~~~~~~ 1076 (1140)
T TIGR02386 997 GIQAVQEYLVKEVQKVYRLQGVEINDKHIEVIVRQMLRKVRITDSGDSNLLPGELIDIHEFNEENRKLLEQGKKPASAIP 1076 (1140)
T ss_pred CHHHHHHHHHHHHHHHHHhCCccccchhHhHHHHHHhCcEEEEeCCCcCCCCCCeeeHHHHHHHHHHHHhCCCCCcccee
Confidence 9999999999999999999999999999999999999999999655 567778888888887788888998888
Q ss_pred HHHHHhhhhcCcchhhhhhhHHHHHHHH
Q psy13846 1027 EILALSNETLDSKEFLQDTSENFVRDIK 1054 (1423)
Q Consensus 1027 ~~~~~~~~~l~~~~~~~~~~~~f~~~~~ 1054 (1423)
.+++++++.|++++|+++|| |++-.+
T Consensus 1077 ~llGitkasl~t~SflsaAS--FqeTtk 1102 (1140)
T TIGR02386 1077 QLLGITKASLNTESFLSAAS--FQETTK 1102 (1140)
T ss_pred eeeeeeehhccCCCcccccc--hhhHHH
Confidence 99999999999999998776 655433
No 35
>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional
Probab=100.00 E-value=1.3e-47 Score=459.80 Aligned_cols=103 Identities=41% Similarity=0.720 Sum_probs=101.0
Q ss_pred CCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhh
Q psy13846 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKV 420 (1423)
Q Consensus 341 ~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~ 420 (1423)
+||+|||||||||||+|||||++++++++||||||++|+||||||||||||+|+|||++|||||+ .
T Consensus 425 ~gd~VLlNRqPTLHR~sIqAf~~~l~~~ktirlhplvC~~fNADFDGDeMnvHvPqS~~A~aEa~--------------~ 490 (627)
T PRK02625 425 EGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQAEAR--------------L 490 (627)
T ss_pred cCcEEEecCCCccccccceeEeeEEcCCCeEEeccccCCcccCCcCCCeEEEecCCCHHHHHHHH--------------H
Confidence 79999999999999999999999999999999999999999999999999999999999999999 9
Q ss_pred hhccccccccCCCCccccccccceEEEEEeecccccC
Q psy13846 421 LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAF 457 (1423)
Q Consensus 421 l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~~ 457 (1423)
||.+.+|++||++|+|+++++||+++|+|.||.+|..
T Consensus 491 Lm~~~~nilsP~~G~Pi~~~~QD~llG~y~LT~~~~~ 527 (627)
T PRK02625 491 LMLASNNILSPATGEPIVTPSQDMVLGCYYLTAENPG 527 (627)
T ss_pred HhcCccceEEcCCCceeEeechhhhhheeeeeccCcc
Confidence 9999999999999999999999999999999999843
No 36
>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=7.9e-48 Score=461.00 Aligned_cols=102 Identities=39% Similarity=0.711 Sum_probs=100.4
Q ss_pred CCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhh
Q psy13846 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKV 420 (1423)
Q Consensus 341 ~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~ 420 (1423)
+||+|||||||||||+|||||++++++++||||||++|+||||||||||||+|+|||++|||||+ +
T Consensus 418 ~gd~VLlNRqPTLHR~sIqAf~~~l~~~ktirlhplvC~~fNADFDGDeMnvHvPqS~eA~aEa~--------------~ 483 (619)
T TIGR02387 418 TGHPVMLNRAPTLHRLGIQAFEPILVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQTEAR--------------L 483 (619)
T ss_pred cCCEEEecCCCccchhcceeeeeEEecCCeEEECcccCCcccCCCCCceeeeecCCCHHHHHHHH--------------H
Confidence 69999999999999999999999999999999999999999999999999999999999999999 9
Q ss_pred hhccccccccCCCCccccccccceEEEEEeeccccc
Q psy13846 421 LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNA 456 (1423)
Q Consensus 421 l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~ 456 (1423)
||.+.+|++||++|+|+++++||+++|+|.||.++.
T Consensus 484 Lm~~~~nilsP~~G~Pi~~~~QD~llg~y~LT~~~~ 519 (619)
T TIGR02387 484 LMLASNNVLSPATGEPIVTPSQDMVLGCYYLTALNP 519 (619)
T ss_pred HhhchhcEEecCCCceeEeechhhhhhhheeecccc
Confidence 999999999999999999999999999999999884
No 37
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=100.00 E-value=6.6e-47 Score=483.06 Aligned_cols=620 Identities=17% Similarity=0.199 Sum_probs=372.8
Q ss_pred hhHHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeecccCC--------cccCHHHHHHHHHHhhcccccceee
Q psy13846 10 TLYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKN--------AFFNRAQTMRIASTLIAGRKVFFRG 81 (1423)
Q Consensus 10 ~~~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~~~--------~~~~~~~~~~~~~~~~~~~~~~i~~ 81 (1423)
-.-+||||||+.||++++||+||++|+|++|.+||+++|+|+||.+| +|++++++++++.+ + ...+..
T Consensus 461 PqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~~~~~~~~~F~~~~e~~~~~~~---~-~i~l~~ 536 (1156)
T PRK00566 461 PLSLEAQAEARVLMLSSNNILSPANGKPIIVPSQDMVLGLYYLTREREGAKGEGMVFSSPEEALRAYEN---G-EVDLHA 536 (1156)
T ss_pred CCCHHHHHHHHHHhCCcccEEecCCCCeeEEeehhhhhhhheeecccccccCCCceeCCHHHHHHHHHc---C-CCCCCC
Confidence 34579999999999999999999999999999999999999999999 89999999988652 2 222222
Q ss_pred eEEEecCCHHHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccCceeEEe
Q psy13846 82 LIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIG 161 (1423)
Q Consensus 82 ~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~PV~h~g 161 (1423)
.+.... + ..++ -++| +|+.+.+-++++.++..+. .+
T Consensus 537 ~i~~~~--~-------~~~~--i~tt----~Gk~if~~ilP~~~~~~n~-----------------------------~g 572 (1156)
T PRK00566 537 RIKVRI--T-------SKKL--VETT----VGRVIFNEILPEGLPFINV-----------------------------NK 572 (1156)
T ss_pred eEEecC--C-------CCce--EEcC----cHHHHHHhhccccceeecc-----------------------------cc
Confidence 122211 0 0011 1234 7888888887665432211 13
Q ss_pred eecc--HHHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCceeecCcc
Q psy13846 162 YFRC--VINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLL 239 (1423)
Q Consensus 162 ffd~--v~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk~~~~ 239 (1423)
.+++ +.+++..++.. ++.+....|++++++....+..+.+++.++.|...... |.
T Consensus 573 ~ldKk~Lg~LI~~i~~~-------yG~~~t~~~LD~ik~Lgf~yat~~GfSigi~Dl~ip~~-------------K~--- 629 (1156)
T PRK00566 573 PLKKKEISKIINEVYRR-------YGLKETVIFLDKIKDLGFKYATRSGISIGIDDIVIPPE-------------KK--- 629 (1156)
T ss_pred eecHHHHHHHHHHHHHH-------hCHHHHHHHHHHHHHHHHHHHHhcCeEeehhhcCcChH-------------HH---
Confidence 4442 13444444444 78888999999999988888888899998888732110 00
Q ss_pred eehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhcc---CccccCCHHHHHHHhhccCCCcccccccccCCCCCc
Q psy13846 240 KISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKF---GLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS 316 (1423)
Q Consensus 240 ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~L~p~~V~eiLe~I~~~d~~lL~m~~~~arPe 316 (1423)
+++. +.+..+++..+.|+.-.-...+....... ...+ .-...+.+.|..-...+++++.|..+|||++
T Consensus 630 ~ii~--------~a~~~v~~i~~~y~~G~lt~~er~~kvi~~w~~~~d-~v~~~~~~~l~~~~~~~N~i~mMa~SGARGS 700 (1156)
T PRK00566 630 EIIE--------EAEKEVAEIEKQYRRGLITDGERYNKVIDIWSKATD-EVAKAMMKNLSKDQESFNPIYMMADSGARGS 700 (1156)
T ss_pred HHHH--------HHHHHHHHHHHHHHcCCCCchHHHHHHHHHHHHHHH-HHHHHHHHhCccccCCCCChheeeeccCCcC
Confidence 1111 01111222222222211000000000000 0000 0122222333211123688999999999999
Q ss_pred ceEEEEecCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCcccccccccCC
Q psy13846 317 DLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQ 396 (1423)
Q Consensus 317 ~liLt~lpVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~ 396 (1423)
..++.||. .+.++++.. +|.. ++ .|.-+.+..+|.+
T Consensus 701 ~~ni~QL~---GmrGlma~p----~G~i---------------------ie----------------~pI~ssFreGLt~ 736 (1156)
T PRK00566 701 ASQIRQLA---GMRGLMAKP----SGEI---------------------IE----------------TPIKSNFREGLTV 736 (1156)
T ss_pred HHHHHHHH---hhcCccccC----CCCE---------------------ee----------------hhhhhhhhcCCCH
Confidence 99999999 888775422 1221 11 1566778889986
Q ss_pred CHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecccccCCCHHHHHHHHHhhccCCcc
Q psy13846 397 TEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSD 476 (1423)
Q Consensus 397 ~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~~~~~~~~~~l~~~~~~~~~~ 476 (1423)
.| ||||+||||+|+++++.+|+.|||.+|+|+...|| +...++=. ++.. ++......
T Consensus 737 ~E----------yFfst~GaRkGLiDTALKTAdSGYLtRRLVdvaqD-viV~~~DC-----gT~~-------gi~~~~~~ 793 (1156)
T PRK00566 737 LE----------YFISTHGARKGLADTALKTADSGYLTRRLVDVAQD-VIVREDDC-----GTDR-------GIEVTAII 793 (1156)
T ss_pred HH----------HhhcCcchhhcccchheeeccceeeehhHHHhhCc-eEEEECCC-----CCcC-------CEEEEEec
Confidence 66 99999999999999999999999999999999999 44443211 1100 00000000
Q ss_pred ccceEeeeeccccCCceeecceeeeecceeeeecccCCCCcccccceeecccccccCcccccCCcEEEeccccccccccc
Q psy13846 477 ICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMD 556 (1423)
Q Consensus 477 ~~~~~~~~~~~~l~~p~i~kp~~~wtGKqi~s~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~~ell~g~ld 556 (1423)
..+++ +..-.+...|+-+...+. .+..+.++...++++...
T Consensus 794 ~~~~~------------i~~l~~~~~GR~~~~di~-------------------------~~~t~~~i~~~~~~i~~~-- 834 (1156)
T PRK00566 794 EGGEV------------IEPLEERILGRVLAEDVV-------------------------DPETGEVIVPAGTLIDEE-- 834 (1156)
T ss_pred cCCEE------------EeEhhheeEeEEEhhhee-------------------------cCCCCcEEEcCCCccCHH--
Confidence 00000 000011112222211111 122233444444432211
Q ss_pred cCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceecCCCCCCccccccccccCCCceeeeeeccccc
Q psy13846 557 KSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSFFSGLTPTEFFFHTMGGR 636 (1423)
Q Consensus 557 K~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~D~~~~~GfI~~sf~~GL~p~Efffh~maGR 636 (1423)
+...+.. . |+..+...+
T Consensus 835 -----------~~~~i~~------------------------~----~i~~v~iRS------------------------ 851 (1156)
T PRK00566 835 -----------IADKIEE------------------------A----GIEEVKIRS------------------------ 851 (1156)
T ss_pred -----------HHHHHHH------------------------c----CCCEEEEcC------------------------
Confidence 1111100 0 111111000
Q ss_pred ccchhcccccCCCCcchHHHHHHHhhhhhcccceeeccccCCCccCCCcchheecCCCcccchhHHHHhhhcCCCCCCcc
Q psy13846 637 EGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPR 716 (1423)
Q Consensus 637 eGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~tVR~s~yG~~~~~~~~~~~~~~~~~~~~g~~vg~i~aqsige~~tq~ 716 (1423)
+-| | .-...|=..|||.| ++++.+++.|||||+|||||||||+||+
T Consensus 852 -------~lt----------------C--~s~~gvC~~CYG~~---------La~~~~v~iGeaVGiIAAQSIGEPGTQL 897 (1156)
T PRK00566 852 -------VLT----------------C--ETRHGVCAKCYGRD---------LATGKLVNIGEAVGVIAAQSIGEPGTQL 897 (1156)
T ss_pred -------Cee----------------e--cCCCcccHhhhCcc---------ccCCCCcccCcceeEEeeeecCCCccce
Confidence 000 0 00001111268887 5678899999999999999999999999
Q ss_pred ccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhHHHHhhhcCCCCceeeeecccCChHHHH
Q psy13846 717 TLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINASRNISTPIITAYLDKDTDLDYA 796 (1423)
Q Consensus 717 tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlkEIinaSk~ikTPiitv~L~~~~~~e~a 796 (1423)
|| +|||.+|+ +||+ |+||+.|++.| +++|.+.+-......
T Consensus 898 Tm----RTFHtGGv----------------dIT~-------------Glprv~elfea-r~pk~~a~ise~~G~------ 937 (1156)
T PRK00566 898 TM----RTFHTGGV----------------DITG-------------GLPRVAELFEA-RKPKGPAIIAEIDGT------ 937 (1156)
T ss_pred ee----eeeeecce----------------eccC-------------Cccchhhheee-ccCCCceEEEecCCE------
Confidence 99 99999997 5777 99999999999 455555433322210
Q ss_pred HHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhhhHHhhhcccccCcccccccccccccCCCC
Q psy13846 797 RIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDS 876 (1423)
Q Consensus 797 ~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I~~~i~~~~~~~~~i~~~~~~~~~~~~~~~ 876 (1423)
+++++.
T Consensus 938 ---------------v~~~~~----------------------------------------------------------- 943 (1156)
T PRK00566 938 ---------------VSFGKE----------------------------------------------------------- 943 (1156)
T ss_pred ---------------EEeccc-----------------------------------------------------------
Confidence 000000
Q ss_pred ccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCc--cccccceeecccceeeccCchHHHHHHhc
Q psy13846 877 SKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD--NLRDVMATYGVKGVKCSSNNTYEVYKTLG 954 (1423)
Q Consensus 877 ~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~--nL~~vl~~~gvD~~~t~SN~i~eV~~~LG 954 (1423)
.+|-.+++|..++. ...+|.+ -.+. ...+...+...|...-.+-|++||++++|
T Consensus 944 ----------------------~~~~~~i~i~~~~~-~~~~y~v-p~~~~~~v~~gd~v~~G~~l~~g~~~~~~il~v~G 999 (1156)
T PRK00566 944 ----------------------TKGKRRIVITPDDG-EEREYLI-PKGKHLLVQEGDHVEAGDKLTDGSIDPHDILRVLG 999 (1156)
T ss_pred ----------------------cCCceEEEEeCCCC-ceEEEEc-cCCCeeeecCCCEEccCCcccCCCCCHHHHHHhcC
Confidence 00000011110000 0011110 0000 00111112223444445668999999999
Q ss_pred hHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC-------cchhhHHHHHHHHHhccCCCCCCCCHHH
Q psy13846 955 IEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG-------TPVELKRLLDDIIAKNSSRSDPSLSAQE 1027 (1423)
Q Consensus 955 IEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~-------~~~~~~~~~~~~~~~~~~~~~~~l~~~~ 1027 (1423)
+||+|..|++|+++++..||++||++||++++++||.+++|...| ..|+..++.+.+++...++..|+.....
T Consensus 1000 ~~~~~~~lv~eiq~vY~~QGv~I~dKHievIvrqM~~kv~i~~~gdt~~~~g~~v~~~~~~~~n~~~~~~g~~~~~~~~~ 1079 (1156)
T PRK00566 1000 VEAVQNYLVNEVQKVYRLQGVKINDKHIEVIVRQMLRKVRITDPGDTDFLPGELVDRSEFEEENRKLIAEGKEPATGRPV 1079 (1156)
T ss_pred HHHHHHHHHHHHHHHHHhCCcccccceeehHHHHHhCCeEEecCCCcCCCCCceeeHHHHHHHHHHHHHCCCCCCcccce
Confidence 999999999999999999999999999999999999999998655 5677888888888877888888888889
Q ss_pred HHHHhhhhcCcchhhhhhhHHHHHH
Q psy13846 1028 ILALSNETLDSKEFLQDTSENFVRD 1052 (1423)
Q Consensus 1028 ~~~~~~~~l~~~~~~~~~~~~f~~~ 1052 (1423)
+++++++.|++++|+++|| |++-
T Consensus 1080 llGItka~l~t~SflsaAS--FQeT 1102 (1156)
T PRK00566 1080 LLGITKASLATESFLSAAS--FQET 1102 (1156)
T ss_pred eeeeeecccccCccccccc--ccch
Confidence 9999999999999998776 5443
No 38
>CHL00018 rpoC1 RNA polymerase beta' subunit
Probab=100.00 E-value=2.4e-46 Score=453.14 Aligned_cols=103 Identities=41% Similarity=0.655 Sum_probs=101.3
Q ss_pred CCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhh
Q psy13846 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKV 420 (1423)
Q Consensus 341 ~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~ 420 (1423)
+||+|||||||||||+|||||++++.+++||||||++|+||||||||||||+|+|||++|||||+ .
T Consensus 446 ~gd~VLlNRqPTLHR~sIqAf~~~L~~gktIrLhplvC~~fNADFDGDqMnvHvPqS~eA~aEa~--------------~ 511 (663)
T CHL00018 446 QGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEAR--------------L 511 (663)
T ss_pred cCceeeecCCCcccccccceeeEEecCCCeEEeCcccCCcccCCccCcEEEEecCCCHHHHHHHH--------------H
Confidence 89999999999999999999999999999999999999999999999999999999999999999 9
Q ss_pred hhccccccccCCCCccccccccceEEEEEeecccccC
Q psy13846 421 LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAF 457 (1423)
Q Consensus 421 l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~~ 457 (1423)
||.+.+|++||++|+|+++++||+++|+|.||.+|..
T Consensus 512 Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~~ 548 (663)
T CHL00018 512 LMFSHMNLLSPAIGDPISVPSQDMLLGLYVLTIGNRR 548 (663)
T ss_pred HhcCccceeEcCCCceeEeechhhhhhhheecccCCC
Confidence 9999999999999999999999999999999999863
No 39
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=100.00 E-value=1.2e-43 Score=451.65 Aligned_cols=617 Identities=16% Similarity=0.175 Sum_probs=362.4
Q ss_pred hHHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeeccc-CC-------cccCHHHHHHHHHHhhcccccceeee
Q psy13846 11 LYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ-KN-------AFFNRAQTMRIASTLIAGRKVFFRGL 82 (1423)
Q Consensus 11 ~~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~-~~-------~~~~~~~~~~~~~~~~~~~~~~i~~~ 82 (1423)
.-+||||||+.||++++||+||++|+|++|.+||+++|+|+||. +| .|.+.+++++++.|. ....+...
T Consensus 550 qS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~~~~~~~~~F~~~~e~~~a~~~~---~~~~l~~~ 626 (1460)
T PRK14906 550 LSTQAQAEARVLMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLTTERDGFEGEGRTFADFDDALNAYDAR---ADLDLQAK 626 (1460)
T ss_pred CCHHHHHHHHHHhcchhcEecCCCCCeeEEeeeeeeeeeEEeeeccccccccCceeCCHHHHHHHHhcC---CCcccccc
Confidence 45799999999999999999999999999999999999999996 55 799999999888742 11112210
Q ss_pred EEEecCCHHHHhh-cceeeeec---CcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccCcee
Q psy13846 83 IEGTVTKEDRVQQ-QSHIQIVS---KNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVF 158 (1423)
Q Consensus 83 i~F~~~S~eeIrk-lSv~eIt~---~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~PV~ 158 (1423)
|...+ +.++.- .+...... ...+. ...|+.+.+.+ ||-.++++.
T Consensus 627 i~~~~--~~~~~~~~~~~~~~~~~~~~~~~-tt~Gr~Ifn~i-----------------------lP~d~~fvN------ 674 (1460)
T PRK14906 627 IVVRL--SRDMTVRGSYGDLEETKAGERIE-TTVGRIIFNQV-----------------------LPEDYPYLN------ 674 (1460)
T ss_pred EEEec--CcccccccccccccCCCCCceEE-CCCCEEEEecc-----------------------cCCCccccc------
Confidence 11110 000000 00000000 00000 00222222222 333333221
Q ss_pred EEeeecc--HHHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCceeec
Q psy13846 159 HIGYFRC--VINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKC 236 (1423)
Q Consensus 159 h~gffd~--v~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk~ 236 (1423)
+.+++ +..|++.+... ++......|+++++.....+..+.+++.++.|..... - |.
T Consensus 675 --~~l~KK~Lg~LI~~i~~~-------~G~~~t~~fLD~Ik~LGf~yaT~sG~SIgi~Di~ip~------------~-K~ 732 (1460)
T PRK14906 675 --YKMVKKDIGRLVNDCCNR-------YSTAEVEPILDGIKKTGFHYATRAGLTVSVYDATIPD------------D-KP 732 (1460)
T ss_pred --ceeeHHHHHHHHHHHHHH-------hCHHHHHHHHHHHHHHHHHHHHhCCEEEeecccccCh------------H-HH
Confidence 12331 13344444444 6778888999999988777777778887777752100 0 00
Q ss_pred CcceehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHHHhhccCCCcccccccccCCCCCc
Q psy13846 237 GLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS 316 (1423)
Q Consensus 237 ~~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~eiLe~I~~~d~~lL~m~~~~arPe 316 (1423)
+++. +.+..+.+..+.|+.-.-...+....+. ..+....-.-...+.+.+. ..++++.|+.+|||++
T Consensus 733 ---~iI~--------~A~~~V~ei~~~y~~G~iT~~Er~~kVi-~iw~~a~d~v~~~~~~~l~-~~N~i~mMa~SGARGS 799 (1460)
T PRK14906 733 ---EILA--------EADEKVAAIDEDYEDGFLSERERHKQVV-DIWTEATEEVGEAMLAGFD-EDNPIYMMADSGARGN 799 (1460)
T ss_pred ---HHHH--------HHHHHHHHHHHHHHcCCCcHHHHHHHHH-HHHHHHHHHHHHHHHHhcc-cCCCeEeeeeccCccc
Confidence 1111 1111222222222211000000000000 0000000011122233332 3688999999999999
Q ss_pred ceEEEEecCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCcccccccccCC
Q psy13846 317 DLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQ 396 (1423)
Q Consensus 317 ~liLt~lpVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~ 396 (1423)
+.++.||. .+.++++...+ .+ +.. |.-.++..+|.+
T Consensus 800 ~~QI~QLa---GmRGlma~p~G----~i--------------------------Ie~-----------PI~SnFrEGLt~ 835 (1460)
T PRK14906 800 IKQIRQLA---GMRGLMADMKG----EI--------------------------IDL-----------PIKANFREGLSV 835 (1460)
T ss_pred HHHHHHHH---hcccceecCCC----Cc--------------------------ccc-----------ccccccccCCCH
Confidence 99999999 88888653222 11 000 244567788886
Q ss_pred CHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEee-cccccCCCHHHHHHHHHhhccCCc
Q psy13846 397 TEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLL-TQKNAFFNRAQTMRIASTLIADTS 475 (1423)
Q Consensus 397 ~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~-t~~~~~~~~~~~~~l~~~~~~~~~ 475 (1423)
.| ||||+||||+|+++|+.+|+.|||..|+|+...||.++...+- |.+...
T Consensus 836 ~E----------yFiSt~GaRKGL~DTALKTAdSGYLTRRLVdVaQDViV~e~DCgT~~Gi~------------------ 887 (1460)
T PRK14906 836 LE----------YFISTHGARKGLVDTALRTADSGYLTRRLVDVAQDVIVREEDCGTDEGVT------------------ 887 (1460)
T ss_pred HH----------HHHHcccccchhhhhhhhccccchHHHHHHHhhhheEEEeccCCCCCCEE------------------
Confidence 66 9999999999999999999999999999999999955443221 111000
Q ss_pred cccceEeeeeccccCCceeec--c-eeeeecceeeeecccCCCCcccccceeecccccccCcccccCCcEEEeccccccc
Q psy13846 476 DICGIIKRFSWRSWNPVVFVR--T-AVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLA 552 (1423)
Q Consensus 476 ~~~~~~~~~~~~~l~~p~i~k--p-~~~wtGKqi~s~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~~ell~ 552 (1423)
+ .++.. + .+-.-|+-+...+. .+. +.+++..++++.
T Consensus 888 -----v----------~~~~~~~~l~~ri~GR~~~~di~-------------------------~~~-g~~i~~~~~~I~ 926 (1460)
T PRK14906 888 -----Y----------PLVKPKGDVDTNLIGRCLLEDVC-------------------------DPN-GEVLLSAGDYIE 926 (1460)
T ss_pred -----E----------EEeecccchhheeeeEEEHhhhc-------------------------CCC-CCEEEeCCCeeC
Confidence 0 00000 0 00011221111111 121 334444444432
Q ss_pred cccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceecCCCCCCccccccccccCCCceeeeeec
Q psy13846 553 GSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSFFSGLTPTEFFFHT 632 (1423)
Q Consensus 553 g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~D~~~~~GfI~~sf~~GL~p~Efffh~ 632 (1423)
... +...+. ..| +.
T Consensus 927 ~~~------------~~~~i~------------------------~~g----i~-------------------------- 940 (1460)
T PRK14906 927 SMD------------DLKRLV------------------------EAG----VT-------------------------- 940 (1460)
T ss_pred cHH------------HHHHHH------------------------HCC----CC--------------------------
Confidence 110 000000 000 00
Q ss_pred ccccccchhcccccCCCCcchHHHHHHHhhhhhcccceee------ccccCCCccCCCcchheecCCCcccchhHHHHhh
Q psy13846 633 MGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFD------AAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706 (1423)
Q Consensus 633 maGReGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~tVR------~s~yG~~~~~~~~~~~~~~~~~~~~g~~vg~i~a 706 (1423)
.|.|..=.|.. ..|||.| ++++.+++.|+|||+|||
T Consensus 941 -----------------------------~v~iRS~ltC~s~~gvC~kCYG~d---------Latg~~V~iGeaVGiIAA 982 (1460)
T PRK14906 941 -----------------------------KVQIRTLMTCHAEYGVCQKCYGWD---------LATRRPVNIGTAVGIIAA 982 (1460)
T ss_pred -----------------------------EEEEeCCeeECCCCCChhhCcCCc---------ccCCcEeccccceeeeee
Confidence 11111111111 1268987 668889999999999999
Q ss_pred hcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhHHHHhhhcCCCCceeeee
Q psy13846 707 AVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINASRNISTPIITAY 786 (1423)
Q Consensus 707 qsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlkEIinaSk~ikTPiitv~ 786 (1423)
||||||+||+|| +|||.+|+ ++.+||+ |+||+.|++.|++ ||.+-+-..
T Consensus 983 QSIGEPGTQLTM----RTFHtGGv-------------~~~dit~-------------GLpRv~eLfEar~-pk~~a~i~e 1031 (1460)
T PRK14906 983 QSIGEPGTQLTM----RTFHSGGV-------------AGDDITQ-------------GLPRVAELFEARK-PKGEAVLAE 1031 (1460)
T ss_pred eecCCCcceeee----eeeecccc-------------ccccccc-------------Ccchhhhheeecc-CCCceeeec
Confidence 999999999999 99999998 5578888 9999999999964 233321111
Q ss_pred cccCChHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhhhHHhhhcccccCccccccc
Q psy13846 787 LDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGH 866 (1423)
Q Consensus 787 L~~~~~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I~~~i~~~~~~~~~i~~~~~ 866 (1423)
.. ..
T Consensus 1032 ~~-----------------------------------G~----------------------------------------- 1035 (1460)
T PRK14906 1032 IS-----------------------------------GT----------------------------------------- 1035 (1460)
T ss_pred cC-----------------------------------CE-----------------------------------------
Confidence 10 00
Q ss_pred ccccccCCCCccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCcccc----ccceeecccceeec
Q psy13846 867 SFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLR----DVMATYGVKGVKCS 942 (1423)
Q Consensus 867 ~~~~~~~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~nL~----~vl~~~gvD~~~t~ 942 (1423)
|.|..-+|-.+++|..++.+ ..+|. .-.+..|. +.-.+...|...-.
T Consensus 1036 ---------------------------v~i~~~~~~~~i~i~~~~~~-~~~y~-v~~~~~~~~~v~~gd~v~~G~~l~~G 1086 (1460)
T PRK14906 1036 ---------------------------LQITGDKTEKTLTIHDQDGN-SREYV-VSARVQFMPGVEDGVEVRVGQQITRG 1086 (1460)
T ss_pred ---------------------------EEeccCCCceEEEEECCCCc-eeEEE-ccCCcccccccCCCCEEccCCCccCC
Confidence 00100011112222222110 01221 11121111 11223334555566
Q ss_pred cCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC-------cchhhHHHHHHHHHhc
Q psy13846 943 SNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG-------TPVELKRLLDDIIAKN 1015 (1423)
Q Consensus 943 SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~-------~~~~~~~~~~~~~~~~ 1015 (1423)
+-|.++++++.|+||++.+|++|+++|+..||+.||.+||++++.+|+.+-+|...| ..|+...+.+.+.+..
T Consensus 1087 ~~~p~~il~~~g~~~~~~ylv~eVQ~VYr~QGV~InDKHiEvIvRQMl~kV~I~d~Gdt~fl~Ge~vd~~~~~~~n~~~~ 1166 (1460)
T PRK14906 1087 SVNPHDLLRLTDPNTTLRYIVSQVQDVYVSQGVDINDKHIEVIARQMLRKVAVTNPGDSDYLPGRQVNRYEFEDTANNLI 1166 (1460)
T ss_pred CCCHHHHHHhcCHHHHHHHHHHHHHHHHHhcCceeccccHHHHHHHHhceEEEecCCCcCCCCCCeeeHHHHHHHHHHHH
Confidence 779999999999999999999999999999999999999999999999999998765 5577788888887777
Q ss_pred cCCCCCCCCHHHHHHHhhhhcCcchhhhhhhHHHHHH
Q psy13846 1016 SSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRD 1052 (1423)
Q Consensus 1016 ~~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~f~~~ 1052 (1423)
.++..|+...+.+++++++.|++++|+++|| |++.
T Consensus 1167 ~~g~~pa~~~p~llGITKasL~t~SflSaAS--FQeT 1201 (1460)
T PRK14906 1167 LEGKQPPVGQPLLLGITKASLATDSWLSAAS--FQET 1201 (1460)
T ss_pred HcCCCCceeeeEEeeeeeccccccccccccc--ccch
Confidence 8888888888889999999999999998876 5543
No 40
>cd00630 RNAP_largest_subunit_C Largest subunit of RNA polymerase (RNAP), C-terminal domain. RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channe
Probab=100.00 E-value=7.4e-44 Score=369.38 Aligned_cols=110 Identities=49% Similarity=0.703 Sum_probs=108.2
Q ss_pred cHHHHHHHhCHHHHHHHHHHHHHHHhhcCCccccCCchhhhhccccceeEEEeeecccccccccchhhhccchhhHHHHH
Q psy13846 1281 NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLF 1360 (1423)
Q Consensus 1281 ~i~~i~~~lGIEAar~~ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~G~~~~i~r~g~~~~~~S~l~~aSFE~t~~~L~ 1360 (1423)
||++|+++|||||||++|++||++||+.||++||+|||+||||+||++|.++|+||+||++.+.|||++||||+|.++|+
T Consensus 49 dI~~i~~~lGIEAaR~~iv~El~~v~~~~Gi~V~~rHl~LIAD~MT~~G~~~ginr~g~~~~~~Spl~~aSFE~t~~~L~ 128 (158)
T cd00630 49 SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGFRASKTSPLMRASFEKTTKHLL 128 (158)
T ss_pred cHHHHHHHhCHHHHHHHHHHHHHHHHHhcCceecHHHHHHHHHHHhcCCcccccccccccccCCCHHHHcCHHHHHHHHH
Confidence 89999999999999999999999999999999999999999999999999999999999877899999999999999999
Q ss_pred hhcccCCcccccccccceeeccccccccce
Q psy13846 1361 DAAFYGQTDCISGVSECIIMGLPMNVGTGL 1390 (1423)
Q Consensus 1361 ~Aa~~g~~D~l~g~s~~ii~G~~~~~GTG~ 1390 (1423)
+||.+|+.|+|+|+|+||+||+++|+|||+
T Consensus 129 ~AA~~g~~D~l~g~s~~ii~Gk~~~~GTG~ 158 (158)
T cd00630 129 DAAAAGEKDELEGVSENIILGRPAPLGTGS 158 (158)
T ss_pred HHhhcCCCCCCCCcHHhhhccCCCCCCCCC
Confidence 999999999999999999999999999995
No 41
>cd02655 RNAP_beta'_C Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain. Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations.
Probab=100.00 E-value=1.4e-42 Score=372.38 Aligned_cols=109 Identities=35% Similarity=0.534 Sum_probs=105.0
Q ss_pred ccHHHHHHHh--CHHHHHHHHHHHHHHHhhcCCccccCCchhhhhccccceeE---------------------------
Q psy13846 1280 NNTYEVYKTL--GIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGE--------------------------- 1330 (1423)
Q Consensus 1280 N~i~~i~~~l--GIEAar~~ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~G~--------------------------- 1330 (1423)
||++++++++ ||||||++|++|+++||+.||++||+||++||||+||+++.
T Consensus 54 ~~~~~il~~~~~Giea~r~~iv~EIq~Vy~~qGV~I~dKHielIv~qMT~kv~i~~~g~s~~l~Ge~v~~~~~~~~N~~~ 133 (204)
T cd02655 54 INPHDLLRIKFLGPEAVQKYLVEEIQKVYRSQGVNINDKHIEIIVRQMTSKVKIIDPGDSGFLPGELVDLNEFEEENKRL 133 (204)
T ss_pred CCHHHHHHHHhHHHHHHHHHHHHHHHHHHHhcCeeecHHHHHHHHHHHhcCeEEecCCCcccCCCceeeHHHHHHHHHHH
Confidence 8999999999 99999999999999999999999999999999999999955
Q ss_pred -------------EEeeecccccccccchhhhccchhhHHHHHhhcccCCcccccccccceeeccccccccce
Q psy13846 1331 -------------VLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGL 1390 (1423)
Q Consensus 1331 -------------~~~i~r~g~~~~~~S~l~~aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~~~~~GTG~ 1390 (1423)
++||||++++ ++|||++||||+|+++|++||++|++|+|+|++||||+|+++|+|||+
T Consensus 134 ~~~~~~~~~y~p~llGItk~~l~--~~Sfls~ASFqeT~kvL~~AAi~gk~D~L~GlkeNVI~G~liPaGTG~ 204 (204)
T cd02655 134 LLLGKKPAKYEPVLLGITKASLN--TESFISAASFQETTKVLTEAAIEGKIDWLRGLKENVILGRLIPAGTGL 204 (204)
T ss_pred HhCCCCcccccceeeeeeecccc--CCCccccCChHHHHHHHHHHHhcCCCCCCCCchhheEECCccCCCCCC
Confidence 4599999997 589999999999999999999999999999999999999999999995
No 42
>PF04997 RNA_pol_Rpb1_1: RNA polymerase Rpb1, domain 1; InterPro: IPR007080 RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which is a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2Y0S_W 3QQC_A 1YNJ_D 1HQM_D 1YNN_D 1I6V_D 2GHO_D 2AUJ_D 1ZYR_D 1SMY_D ....
Probab=100.00 E-value=2.4e-41 Score=397.24 Aligned_cols=249 Identities=33% Similarity=0.511 Sum_probs=178.5
Q ss_pred cceeeeEEEecCCHHHHhhcceeeeecCcccccCCC-CCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccC
Q psy13846 77 VFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQ-RTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPL 155 (1423)
Q Consensus 77 ~~i~~~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~-g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~ 155 (1423)
.+|.+ |+|++|||+||+++||++|+++.+| |.. |+|+.|||||||||+.++...|+|||+...+||||||||+|+.
T Consensus 2 ~~i~~-i~f~~~s~~eI~~~Sv~~i~~~~~~--~~~~~~p~~~Gl~d~rlG~~~~~~~C~tC~~~~~~CpGHfGhI~L~~ 78 (337)
T PF04997_consen 2 KKIKS-IQFGIYSPEEIRKLSVKEITNPETF--DNLTGKPIKGGLYDPRLGPIDKKQICSTCGLNYTECPGHFGHIELAL 78 (337)
T ss_dssp EEEEE-EEEEE--HHHHHHHEEEB--SSTSB--CTSSSSCBSSSSSSSSSS-SSSSSTSSSSSSSSSSCCCSEEEEEEEE
T ss_pred CeeeE-EEEEeCCHHHHHHhCcEEEechhhc--cCCCCCCccccccChhhcCCCcccccccccccccccCCceeEEEeCH
Confidence 46888 9999999999999999999999999 555 9999999999999999999999999999999999999999999
Q ss_pred ceeEEeeeccHHHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCceee
Q psy13846 156 PVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKK 235 (1423)
Q Consensus 156 PV~h~gffd~v~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk 235 (1423)
||||||||+.++++|+++|+. |+++++.+++...+...+.... ...+......+.+.|++...|++|+..++.+++
T Consensus 79 PV~h~~f~~~i~~iL~~~C~~--C~~l~~~~~~~~~~~~~~~~~~--~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~ 154 (337)
T PF04997_consen 79 PVYHPGFFKEIPKILRCICKK--CSRLLLSEKEKYFYLKILLKLK--KKKKKERLKIISKECKKKSICSHCKAINGKIKK 154 (337)
T ss_dssp EEETCCCHHHHHHHHTTSCTT--TSCTSTCCCCHTSCHHHCHCSH--SSSHHHHHHHHHHHHHHTCSSTSTCC-SSS---
T ss_pred HHHhhcccccceeeecccccc--cccccccccccccccccccccc--cccchhHHHHHHHhhhhhhhhcccccccccccc
Confidence 999999999999999999999 9999999887644443333321 223345667778888888999999988877653
Q ss_pred cCcceehhhhhccccc-chhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHHHhhccCCCcccccccccCCCC
Q psy13846 236 CGLLKISHEKYKNRTK-KKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSK 314 (1423)
Q Consensus 236 ~~~~ki~~e~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~eiLe~I~~~d~~lL~m~~~~ar 314 (1423)
....+... ....... ........ +...+... +.....+ ...+.++|.+++++|+++++++..++++.+..++
T Consensus 155 ~~~~~~~~-~~~~~~~~~~~~~~~~----i~~~i~~~-~~~~~~~-~~~~~l~~~~v~~ilk~l~~~~~~~l~~~~~~~~ 227 (337)
T PF04997_consen 155 VEKSKKCE-GCGKKNPKIRKEGAEK----IQEEIKKK-ESNKEIK-EELRILTPEEVRQILKKLSKEDKELLGFDPSGSR 227 (337)
T ss_dssp SSSEETSS-SSSSBSCEEEEESHCC----CCCHHHSC-CHHHHHH-CHCECESHHHHHHHHHHSHHHHHHHHHHHTTTBS
T ss_pred cccchhcc-cccccCcccccchhhh----cccccccc-cccccch-hhhhhhhhhhhhhcchhhhhhheeeeeccccccc
Confidence 10000000 0000000 00000000 00000000 0001111 2234689999999999999999999999988899
Q ss_pred CcceEEEEecCCCCCCCCcEEcCCC
Q psy13846 315 PSDLILTRLLVPPNCIRPSVISDLK 339 (1423)
Q Consensus 315 Pe~liLt~lpVPP~~vRPsv~~g~~ 339 (1423)
|+||||++|||||+++||++.+|+.
T Consensus 228 P~~~~l~~lpVpP~~~RP~v~~~~~ 252 (337)
T PF04997_consen 228 PEWFFLTVLPVPPPRFRPSVQLGGG 252 (337)
T ss_dssp GGGSEEEEEEE-TGGGS-EEEESSS
T ss_pred cceeEEeeeecCCceeeeeeeeecc
Confidence 9999999999999999999999875
No 43
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=100.00 E-value=2e-40 Score=437.08 Aligned_cols=114 Identities=18% Similarity=0.264 Sum_probs=100.9
Q ss_pred eecccceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC-------cchhhH
Q psy13846 933 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG-------TPVELK 1005 (1423)
Q Consensus 933 ~~gvD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~-------~~~~~~ 1005 (1423)
+...|...-.+.+++|+++++|+||+|++|++|+++++..||++||.+||++++++||++-+|...| ..|+..
T Consensus 2625 V~~G~~l~~G~~~p~dil~v~G~ea~~~ylv~Evq~VYr~QGV~IndKHiEvIvrQMl~kV~I~d~Gdt~~l~Ge~v~~~ 2704 (2836)
T PRK14844 2625 VRKGDLLMDGDPDLHDILRVLGLEALAHYMISEIQQVYRLQGVRIDNKHLEVILKQMLQKVEITDPGDTMYLVGESIDKL 2704 (2836)
T ss_pred EcCCCCccCCCCCHHHHHHhhCHHHHHHHHHHHHHHHHHhcCeeecccEeeeehhhhhceeEEecCCCcccCCCceecHH
Confidence 4445666777889999999999999999999999999999999999999999999999998888765 456777
Q ss_pred HHHHHHHHhccCCCCCCCCHHHHHHHhhhhcCcchhhhhhh
Q psy13846 1006 RLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTS 1046 (1423)
Q Consensus 1006 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~ 1046 (1423)
.+.+.+.....++..|+...+.+++++++.|++++|+++||
T Consensus 2705 ~~~~~n~~~~~~g~~pa~~~pvllGITkasL~t~SflSaAS 2745 (2836)
T PRK14844 2705 EVDRENDAMSNSGKRPAHYLPILQGITRASLETSSFISAAS 2745 (2836)
T ss_pred HHHHHHHHHHhcCCCCceeeeeeeceeeccccCCChhhcCC
Confidence 78777777777788899888889999999999999998877
No 44
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=100.00 E-value=9.9e-40 Score=432.17 Aligned_cols=111 Identities=15% Similarity=0.274 Sum_probs=99.6
Q ss_pred ccceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC-------cchhhHHHH
Q psy13846 936 VKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG-------TPVELKRLL 1008 (1423)
Q Consensus 936 vD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~-------~~~~~~~~~ 1008 (1423)
.|...-.+-+.+|+++++|++|...+|++|+++|+..||+.||.+||++++.+|+.+-+|...| ..|+...+.
T Consensus 2717 G~~l~~G~~~p~dil~~~g~~~~~~ylv~EVQ~VYr~QGV~InDKHIEvIvrQMl~kV~I~d~GDt~fl~Ge~vd~~~~~ 2796 (2890)
T PRK09603 2717 GEAMTDGVVSSHDILRISGEKELYKYIVSEVQQVYRRQGVSIADKHIEIIVSQMLRQVRILDSGDSKFIEGDLVSKKLFK 2796 (2890)
T ss_pred CCCcCCCCCCHHHHHHhcCHHHHHHHHHHHHHHHHHhcCEEeccceehhhHhhhheeEEEEcCCCcccCCCceeeHHHHH
Confidence 3455555668999999999999999999999999999999999999999999999999998766 556777888
Q ss_pred HHHHHhccCCCCCCCCHHHHHHHhhhhcCcchhhhhhh
Q psy13846 1009 DDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTS 1046 (1423)
Q Consensus 1009 ~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~ 1046 (1423)
+.+.+....+..|+...+.+++++++.|.+++|+++||
T Consensus 2797 ~~n~~~~~~g~~pa~~~p~LlGITKAsL~t~SfiSAAS 2834 (2890)
T PRK09603 2797 EENARVIALKGEPAIAEPVLLGITRAAIGSDSIISAAS 2834 (2890)
T ss_pred HHHHHHHHcCCCCceeeeeeeeeehhhhcccchhhccc
Confidence 88888888888899988889999999999999998887
No 45
>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=2.8e-37 Score=360.92 Aligned_cols=265 Identities=19% Similarity=0.155 Sum_probs=197.0
Q ss_pred chhHHHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhHHHHhh--h
Q psy13846 698 GTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINA--S 775 (1423)
Q Consensus 698 g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlkEIina--S 775 (1423)
|+.||.|||||||||.||||| ++||++|+. +|||||||||. +
T Consensus 1 GE~VG~LAAqSIgEPAtQmtL----ntfh~agvs--------------------------------~vprLKEiLn~~~~ 44 (381)
T cd02737 1 GEPVGSLAATAISEPAYKALL----DPPQSLESS--------------------------------PLELLKEVLECRSK 44 (381)
T ss_pred CCcchhHHHhhhcchHHHhhh----ccchhcCCc--------------------------------cHHHHHHHhccccc
Confidence 688999999999999999999 999999972 79999999999 7
Q ss_pred cCCCCceeeeeccc-------CCh-HHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhcc-------
Q psy13846 776 RNISTPIITAYLDK-------DTD-LDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHL------- 840 (1423)
Q Consensus 776 k~ikTPiitv~L~~-------~~~-~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l------- 840 (1423)
+++|||.++++|.. +.. .+.|+.++++||+++|+++++..+++|+|+....++..|.+.++...+
T Consensus 45 ~~~ktps~~v~L~~~~~~~~~~~~~~~~a~~Vq~~Le~~tL~~v~~~~~I~Ydp~~~~t~i~~d~~~~~~~~~~~~~~~~ 124 (381)
T cd02737 45 SKSKENDRRVILSLHLCKCDHGFEYERAALEVKNHLERVTLEDLATTSMIKYSPQATEAIVGEIGDQLNTKKKGKKKAIF 124 (381)
T ss_pred CCCCCCCEEEEEeccccccccchHHHHHHHHHHHHhhhccHHHhhheEEEEECCCcccccccccHHHHHhhhhhhhhccc
Confidence 88999999999975 221 457999999999999999999999999999777777776665432110
Q ss_pred ccchhh--hhHHhhhcccccCcccccccc-cccccCC-CCccc----cchhhhhhhhcCCceEEccccccceeeeecccc
Q psy13846 841 EVDIDS--IRYCIERTRGISGHLTVSGHS-FLILKPK-DSSKS----FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDV 912 (1423)
Q Consensus 841 ~i~~~~--I~~~i~~~~~~~~~i~~~~~~-~~~~~~~-~~~~~----~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~ 912 (1423)
..+.+. .-..+.+... +.......+. .+.+... ..+.. ....+..+...+.+++|||+++|+++.|...+.
T Consensus 125 ~~~~~~~~~spw~~r~~l-~~~~~~~~~~~ci~~~~~~~~~~~~~~~~~~~~~~i~~~lL~~~lkG~~~I~kv~i~~~~~ 203 (381)
T cd02737 125 STSLKITKFSPWVCHFHL-DKECQKLSDGPCLTFSVSKEVSKSSEELLDVLRDRIIPFLLETVIKGDERIKSVNILWEDS 203 (381)
T ss_pred ccccccccCCcceEEEEE-ehhHhcCCCCceEEeecCcccccchhHHHHHHHHHHHHHHhheeecccCCeeEEEEEecCC
Confidence 001100 0000000000 0000000000 0000010 11111 111233444445579999999999999973221
Q ss_pred -----------cceeEEeeecc---------Cccccccc-----eeecccceeeccCchHHHHHHhchHHHHHHHHHHHH
Q psy13846 913 -----------EGVTKYKLLVE---------GDNLRDVM-----ATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIK 967 (1423)
Q Consensus 913 -----------~~~~~~~l~~e---------G~nL~~vl-----~~~gvD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~ 967 (1423)
....+|+|.|+ |.+++.+| .+++||+.+++||||++|+++|||||||++|++|++
T Consensus 204 ~~~~~~~~~~~~~~~E~vLe~~~~~~~~~t~G~~~~~vl~~c~~~~~~ID~~rt~sNdI~ev~~~lGIEAAR~~ii~El~ 283 (381)
T cd02737 204 PSTSWVKSVGKSSRGELVLEVTVEESCKKTRGNAWNVVMDACIPVMDLIDWERSMPYSIQQIKSVLGIDAAFEQFVQRLE 283 (381)
T ss_pred CcccccccccccccceEEEEEEeccccccccchhHHHHHHhhhcccccCcCCCcEECCHHHHHHHHhHHHHHHHHHHHHH
Confidence 23468999987 99999999 589999999999999999999999999999999999
Q ss_pred HHHHhcCccccCCchhhHhhhhccccccccCC
Q psy13846 968 LVMENHGMSIDFRHPMLVADLMTSKGEVLGNG 999 (1423)
Q Consensus 968 ~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~ 999 (1423)
.+++.||++||+|||+||||+||++|++.+.+
T Consensus 284 ~v~~~~G~~Vd~rHL~LlAD~MT~~G~~~~~n 315 (381)
T cd02737 284 SAVSMTGKSVLREHLLLVADSMTYSGEFVGLN 315 (381)
T ss_pred HHHHhcCCcccHHHHHHHHHHhccCCceEEec
Confidence 99999999999999999999999999999975
No 46
>smart00663 RPOLA_N RNA polymerase I subunit A N-terminus.
Probab=100.00 E-value=2.1e-36 Score=343.76 Aligned_cols=95 Identities=59% Similarity=0.974 Sum_probs=93.5
Q ss_pred CCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhh
Q psy13846 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKV 420 (1423)
Q Consensus 341 ~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~ 420 (1423)
+||+|||||||||||+|||||++++++++||||||++|+||||||||||||+|+|||++|||||. .
T Consensus 201 dgd~Vl~NRqPsLHr~si~a~~v~v~~~~tir~n~~~c~~fNADFDGDeMnih~pqs~~a~aEa~--------------~ 266 (295)
T smart00663 201 DGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLVCSPYNADFDGDEMNLHVPQSLEARAEAR--------------E 266 (295)
T ss_pred cCCEEEEecCCccccccceeEEEEEecCceEEecCccCCcccCCcCCCEEEEecCCCHHHHHHHH--------------H
Confidence 67899999999999999999999999999999999999999999999999999999999999999 9
Q ss_pred hhccccccccCCCCccccccccceEEEEE
Q psy13846 421 LMANKSNLVTPRNGELLIAATQDFITGGY 449 (1423)
Q Consensus 421 l~~~~~~~~s~~~~~~~~~~~qD~~~~~~ 449 (1423)
||.+.+|++||++|+|+++++||+++|+|
T Consensus 267 Lm~~~~~~~sp~~g~p~~~~~QD~l~g~~ 295 (295)
T smart00663 267 LMLVPNNILSPKNGKPIIGPIQDMLLGLY 295 (295)
T ss_pred HhhhhhccccCCCCCeeEeeecceeeecC
Confidence 99999999999999999999999999986
No 47
>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=9.6e-37 Score=392.50 Aligned_cols=361 Identities=19% Similarity=0.219 Sum_probs=274.7
Q ss_pred HHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeecccCCcccCHHHHHHHHHHhhcccccceeeeEEEecCCHH
Q psy13846 12 YYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFFRGLIEGTVTKED 91 (1423)
Q Consensus 12 ~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~F~~~S~e 91 (1423)
-+||||||++||+|++||+||++|+|++|++||+|+|+|+||.||+||+++++++++++-. ++..+..|.
T Consensus 466 s~~a~aEa~~Lm~~~~~~~sp~~g~p~~~~~QD~l~g~~~LT~~d~f~~~~~~~~l~~~~~----------~~~~~~~p~ 535 (868)
T TIGR02390 466 TEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQTILGVAG----------YFGDPPEPA 535 (868)
T ss_pred CHHHHHHHHHHhhchhceecCCCCCeeEEeehhhhhheeeeeeccccCCHHHHHHHHhcCC----------ccccCCCce
Confidence 4799999999999999999999999999999999999999999999999999999998521 111111121
Q ss_pred HHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCC-CCCCcccCCccceEEccCceeEEeeeccH----
Q psy13846 92 RVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTC-GQNLSDCVGHFGYIDLPLPVFHIGYFRCV---- 166 (1423)
Q Consensus 92 eIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TC-g~~~~eCpGHfGhIeL~~PV~h~gffd~v---- 166 (1423)
| +....+| ||+++.+.++++.+....+...+..+ +.....|+ ..++|.+.+.++..|.+|+-
T Consensus 536 -i-------~kp~~lw----TGKqi~s~~lp~~~n~~~~~~~~~~~~~~~~~~~~-~d~~v~i~~g~ll~G~ldK~~lg~ 602 (868)
T TIGR02390 536 -I-------EKPKEYW----TGKQIFSAFLPEDLNFEGRAKICSGSDACKKEECP-HDAYVVIKNGKLLKGVIDKKAIGA 602 (868)
T ss_pred -e-------cCCcccc----cHHHHHHHhcCCCCcceecccccccccccccccCC-CcceEEEecCeEEeeeecHHHhcc
Confidence 1 2356788 99999999998766654433333322 11223454 58899999999999999843
Q ss_pred --HHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCceeecCcceehhh
Q psy13846 167 --INILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHE 244 (1423)
Q Consensus 167 --~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk~~~~ki~~e 244 (1423)
..|++.+... ++++....|++++.+....++...+|+.++.|...... ..+
T Consensus 603 ~~~~li~~i~~~-------yG~~~a~~fl~~~~~l~~~~l~~~GfSigi~D~~~~~~--------------------~~~ 655 (868)
T TIGR02390 603 EKGKILHRIVRE-------YGPEAARRFLDSVTRLFIRFITLRGFTTGIDDIDIPKE--------------------AKE 655 (868)
T ss_pred CcccHHHHHHHH-------HCHHHHHHHHHHHHHHHHHHHHhccEEeehhheeeCHH--------------------HHH
Confidence 1344444444 78889999999999988888888999999888753210 111
Q ss_pred hhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHH-------------------HHhhccCCCcccc
Q psy13846 245 KYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVL-------------------QLFEAIPLEDIPL 305 (1423)
Q Consensus 245 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~-------------------eiLe~I~~~d~~l 305 (1423)
...+..++..+...++.+.|.. +..+.+++.+++ +...+.-+.++.+
T Consensus 656 ~~~~~i~~~~~~~~~~~~~~~~--------------g~l~~~~~~~~~~~~e~~i~~~l~~~r~~~~~~~~~~l~~~N~~ 721 (868)
T TIGR02390 656 EIEELIEKAEKRVDNLIERYRN--------------GELEPLPGRTVEETLEMKIMEVLGKARDEAGEVAEKYLDPENHA 721 (868)
T ss_pred HHHHHHHHHHHHHHHHHHHHHc--------------CCCccCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcch
Confidence 1111111111222233333322 111112221111 1222222235788
Q ss_pred cccccCCCCCcceEEEEecCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCC
Q psy13846 306 LLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADF 385 (1423)
Q Consensus 306 L~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadF 385 (1423)
+.|..+||+++.++++||. +|++||...|.|++.++ ..|+||| |.+.+..|...+|
T Consensus 722 ~~M~~sGsKGS~~Ni~Qi~---~~lGQQ~~~g~ri~~~~-----------------~~rtlp~----f~~~d~~~~~~Gf 777 (868)
T TIGR02390 722 VIMARTGARGSLLNITQMA---AMVGQQSVRGGRIRRGY-----------------RNRTLPH----FKKGDIGAKARGF 777 (868)
T ss_pred hhhhhccCCcccccHHHHH---hccCccccCCCcCcccc-----------------ccCCCCC----CCCCCCCcccCce
Confidence 8999999999999999999 99999999999998888 8999999 8899999999999
Q ss_pred cccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecccccCCCHHHHHH
Q psy13846 386 DGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMR 465 (1423)
Q Consensus 386 dgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~~~~~~~~~~ 465 (1423)
+-+++..+|.+.| ||||+||||||+++++++|+.|||.+|+|+.++|| +.+.||.|+||+.+++.||.|
T Consensus 778 V~~sF~~GL~p~E----------fFfH~m~gReGLiDTAvKTa~sGYLqRrLvk~lEd-l~v~yD~tVR~~~g~iiQf~Y 846 (868)
T TIGR02390 778 VRSSFKKGLDPTE----------YFFHAAGGREGLVDTAVRTSQSGYMQRRLINALQD-LYVEYDGTVRDTRGNLIQFKY 846 (868)
T ss_pred ecccccCCCCHHH----------HHHHHhhhccccccccccccccchhHHHHHHHHhh-eEEecCCeEEeCCCcEEEEec
Confidence 9999999999776 99999999999999999999999999999999999 999999999999999999999
Q ss_pred HHHhhc
Q psy13846 466 IASTLI 471 (1423)
Q Consensus 466 l~~~~~ 471 (1423)
+.++++
T Consensus 847 G~dg~d 852 (868)
T TIGR02390 847 GEDGVD 852 (868)
T ss_pred cCCCcC
Confidence 988875
No 48
>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-36 Score=349.18 Aligned_cols=99 Identities=44% Similarity=0.656 Sum_probs=90.5
Q ss_pred ceeeEEEEecCccHHHHhhccc-ccceecccccHHHHHHHhCHHHHHHHHHHHHHHHhhcCCccccCCchhhhhccccce
Q psy13846 1250 GVTKYKLLVEGDNLRDVMATYG-VKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 1328 (1423)
Q Consensus 1250 ~~~~~~l~teG~nl~~~~~~~~-vd~~~~~sN~i~~i~~~lGIEAar~~ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~ 1328 (1423)
...+|.+.++|.||+.+|..++ +|++++++|||++|+++|||||||++|++|+..|+..||++||+|||+|+||+||++
T Consensus 177 ~~~~~~l~~~g~~l~~v~~~qgvid~~k~~sn~I~qm~~~~GIeaar~~i~~e~~~v~~~~g~~vn~rhl~llad~mt~~ 256 (277)
T PF04998_consen 177 KSKEYVLQTEGSNLQEVYSSQGVIDNDKHISNDIRQMLSKLGIEAARNSIIKELKNVFESYGIEVNKRHLSLLADYMTYK 256 (277)
T ss_dssp CCCCCEEECCSHHHHHHTCSTT-EETCHHECSHHHHHHHHHEHHHHHHHHHHHHHCHHHHCTSCCCHHHHHHHHHHHCCC
T ss_pred hhHHHHHHHHhhhchhheecccccCCCEEEeceeEeeeeeEEEEECCCceeecCcEeeHHHHHHHHHHHHHhCCCcCeee
Confidence 3468899999999999999999 799999999999999999999999999999999999999999999999999999999
Q ss_pred eEEEeeecccccccccchhh
Q psy13846 1329 GEVLGITRHGLAKMKESVLN 1348 (1423)
Q Consensus 1329 G~~~~i~r~g~~~~~~S~l~ 1348 (1423)
|.++||||+||+++++|+++
T Consensus 257 g~~~gitR~gl~~~~~S~~~ 276 (277)
T PF04998_consen 257 GVLLGITRHGLNSNKSSFLS 276 (277)
T ss_dssp SS---CCTTTTSSSSSSHHH
T ss_pred eEEEEEEHHHhccCCCCccC
Confidence 99999999999986566554
No 49
>PRK08566 DNA-directed RNA polymerase subunit A'; Validated
Probab=100.00 E-value=2.5e-36 Score=389.83 Aligned_cols=363 Identities=21% Similarity=0.252 Sum_probs=277.7
Q ss_pred hHHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeecccCCcccCHHHHHHHHHHhhcccccceeeeEEEecCCH
Q psy13846 11 LYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFFRGLIEGTVTKE 90 (1423)
Q Consensus 11 ~~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~F~~~S~ 90 (1423)
.-+||||||++||+|++||+||++|+|++|.+||+|+|+|+||.||+||+|++++++++|.. ...+ .+..|
T Consensus 469 qs~~a~aEa~~Lm~~~~~~~sp~~g~pi~~~~QD~l~g~~~lt~~d~f~~~~~~~~l~~~~~---~~~~------~~~~p 539 (882)
T PRK08566 469 QTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAAG---IDEL------PEPEP 539 (882)
T ss_pred CCHHHHHHHHHHhcchhcEecCCCCCeeEEeehHHHHHHHHHHhccccCCHHHHHHHHHhCC---cccc------ccCCc
Confidence 35799999999999999999999999999999999999999999999999999999999741 1100 01111
Q ss_pred HHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCC-CcccCCccceEEccCceeEEeeeccH---
Q psy13846 91 DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN-LSDCVGHFGYIDLPLPVFHIGYFRCV--- 166 (1423)
Q Consensus 91 eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~-~~eCpGHfGhIeL~~PV~h~gffd~v--- 166 (1423)
. -.....+| |||++.+.++.+.+....+...+..+... ...|+ ..|++.+...++..|.+++-
T Consensus 540 a--------i~~p~~lw----TGKqi~s~~lp~~~~~~~~~~~~~~~~~~~~~~~~-~d~~v~i~~gell~g~ldK~~lg 606 (882)
T PRK08566 540 A--------IENGKPYW----TGKQIFSLFLPKDLNLEFKAKICSGCDECKKEDCE-HDAYVVIKNGKLLEGVIDKKAIG 606 (882)
T ss_pred c--------cCCCcccc----cHHHHHHHHcCCCCCceeeccccccccccccccCC-CCceEEEecCEEEeccccHHHhh
Confidence 0 11334788 99999999998766554444444444332 23455 48999999999999999954
Q ss_pred ---HHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCceeecCcceehh
Q psy13846 167 ---INILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISH 243 (1423)
Q Consensus 167 ---~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk~~~~ki~~ 243 (1423)
..|++.++.. ++++....|++++.+....++...+|+.++.|.+.... ..
T Consensus 607 ~~~~~li~~i~~~-------yG~~~a~~fl~~~~~l~~~~l~~~GfSigi~D~~~~~~--------------------~~ 659 (882)
T PRK08566 607 AEQGSILDRIVKE-------YGPERARRFLDSVTRLAIRFIMLRGFTTGIDDEDIPEE--------------------AK 659 (882)
T ss_pred cccchHHHHHHHH-------hCHHHHHHHHHHHHHHHHHHHHhcCEEeehhhcccCHH--------------------HH
Confidence 3466666666 88889999999999988889999999999988753220 00
Q ss_pred hhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHH-------------------HHHHHhhccCCCccc
Q psy13846 244 EKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPL-------------------EVLQLFEAIPLEDIP 304 (1423)
Q Consensus 244 e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~-------------------~V~eiLe~I~~~d~~ 304 (1423)
++..+..++......++.++|.. +..+.+++. .+.+...+--+.+++
T Consensus 660 ~~~~~~i~~~~~~~~~~~~~~~~--------------g~l~~~~~~~~~~~~e~~i~~~l~~~r~~~~~~~~~~l~~~N~ 725 (882)
T PRK08566 660 EEIDEIIEEAEKRVEELIEAYEN--------------GELEPLPGRTLEETLEMKIMQVLGKARDEAGEIAEKYLGLDNP 725 (882)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHc--------------CCCccccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCc
Confidence 00111111111122233333322 111111111 111122221233578
Q ss_pred ccccccCCCCCcceEEEEecCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCC
Q psy13846 305 LLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNAD 384 (1423)
Q Consensus 305 lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nad 384 (1423)
++.|..+||+++..+++||. +|++||...|.+++.++ ..|+||| |.+.+.+|...+
T Consensus 726 ~~~M~~SGsKGS~~N~~Qi~---~~lGqQ~~~g~ri~~~~-----------------~~rtLP~----f~~~d~~~~~~G 781 (882)
T PRK08566 726 AVIMARTGARGSMLNLTQMA---ACVGQQSVRGERIRRGY-----------------RDRTLPH----FKPGDLGAEARG 781 (882)
T ss_pred ceeeeccccccCHHHHHHHH---hccCceecCCCcCccCc-----------------cCccCCC----CCCCCCCcccCc
Confidence 89999999999999999999 99999999999888888 8899999 889999999999
Q ss_pred CcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecccccCCCHHHHH
Q psy13846 385 FDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 464 (1423)
Q Consensus 385 Fdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~~~~~~~~~ 464 (1423)
|+-+++-.+|.+.| ||||+||||||++++|++|+.|||.+|+|+..+|| +.+.||.|+||+.+++.||.
T Consensus 782 fV~~sF~~GL~p~E----------fffH~m~GReGliDTAvkTa~sGYlqRrLvk~led-l~v~yD~tVR~s~g~iiQf~ 850 (882)
T PRK08566 782 FVRSSYKSGLTPTE----------FFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQD-LKVEYDGTVRDTRGNIVQFK 850 (882)
T ss_pred eeeccccCCCCHHH----------HHHHHhhhcccccccceeeccCccchHHHHHHHhh-eEEeeCCceEcCCCcEEEEe
Confidence 99999999999776 99999999999999999999999999999999999 99999999999999999999
Q ss_pred HHHHhhc
Q psy13846 465 RIASTLI 471 (1423)
Q Consensus 465 ~l~~~~~ 471 (1423)
|+.++++
T Consensus 851 YG~dg~d 857 (882)
T PRK08566 851 YGEDGVD 857 (882)
T ss_pred ccCCCcC
Confidence 9988875
No 50
>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=99.91 E-value=7.3e-26 Score=238.56 Aligned_cols=66 Identities=67% Similarity=1.129 Sum_probs=58.2
Q ss_pred CCCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCcccccccccCCCHHHHhccc
Q psy13846 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEAL 405 (1423)
Q Consensus 340 ~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~ 405 (1423)
.+||+|||||||||||+|||||++++++++|||+||++|+||||||||||||+|+||+++|++|+.
T Consensus 96 ~~gd~vl~nRqPtLh~~s~~a~~~~~~~~~t~~~~~~~c~~~NADFDGDem~i~~p~~~~a~~E~~ 161 (166)
T PF00623_consen 96 CDGDIVLLNRQPTLHRMSIMAHKVRVLPGKTIRINPLVCSPFNADFDGDEMNIHLPQSYEARAEAK 161 (166)
T ss_dssp TTT-EEEEEESS-SSGGGEEEEEEEEESSSSEEEEGGGHHHHT--TSS-EEEEE--SSHHHHHHHH
T ss_pred hcCceeEEeccchhccceeeeeeeeeecccEEEeeccchhhhhccCCcceEEEEecCCHHHHHHHH
Confidence 499999999999999999999999999999999999999999999999999999999999999999
No 51
>cd02736 RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain. Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Probab=99.90 E-value=4.1e-24 Score=244.08 Aligned_cols=243 Identities=54% Similarity=0.751 Sum_probs=223.1
Q ss_pred ecCCCcccchhHHHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhH
Q psy13846 690 IMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIK 769 (1423)
Q Consensus 690 ~~~~~~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlk 769 (1423)
|.+++++||++||.+||||||||+||||| +|||+||+ +++|+|| |||||+
T Consensus 2 y~~~~v~pGe~vG~iaaQsiGEp~TQmTL----~TFH~aGv-------------~~~nvtl-------------GvPRlk 51 (300)
T cd02736 2 YMRAKVEPGTAVGAIAAQSIGEPGTQMTL----KTFHFAGV-------------ASMNITL-------------GVPRIK 51 (300)
T ss_pred chhhccCCCccchhhhhhhcCCccccccc----cccccccc-------------ccccccc-------------CchHHH
Confidence 35678999999999999999999999999 99999999 8999999 999999
Q ss_pred HHHhhhcCCCCceeeeecccCChHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhhhH
Q psy13846 770 EIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRY 849 (1423)
Q Consensus 770 EIinaSk~ikTPiitv~L~~~~~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I~~ 849 (1423)
|||||||+||||+|++||.++.+.+.|+.++.+||+++|+|++.+++++|+|+.+++.+++|.+.+..+++. .
T Consensus 52 EIinasK~~~TP~~ti~l~~~~~~~~a~~v~~~ie~t~l~di~~~~~~~~~p~~~~~~i~~d~~~i~~~~l~--~----- 124 (300)
T cd02736 52 EIINASKNISTPIITAKLENDRDEKSARIVKGRIEKTYLGEVASYIEEVYSPDDCYILIKLDKKIIEKLQLS--K----- 124 (300)
T ss_pred HHHhcccCCCCCeEEEEecCcccHHHHHHHHHHHhhccHHHhhhheEEEEcCCCceEEEEecHHHHHHhcCC--c-----
Confidence 999999999999999999998899999999999999999999999999999999999999999887544330 0
Q ss_pred HhhhcccccCcccccccccccccCCCCccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCccccc
Q psy13846 850 CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRD 929 (1423)
Q Consensus 850 ~i~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~nL~~ 929 (1423)
+.....++.+++.+++++|+|+|||+|+.+.+++. .++|.|.|+|+||++
T Consensus 125 ----------------------------~~~~~~~~~l~~~l~~~~v~Gi~gI~r~~i~~~~~--~~~~~l~teG~nl~~ 174 (300)
T cd02736 125 ----------------------------SNLYFLLQSLKRKLPDVVVSGIPEVKRAVINKDKK--KGKYKLLVEGYGLRA 174 (300)
T ss_pred ----------------------------ccHHHHHHHHHHHhccceEeCCCCceEEEEecCCC--CCcEEEEEecccHHH
Confidence 01223466788899999999999999999986543 247999999999999
Q ss_pred cceeecccceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC
Q psy13846 930 VMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG 999 (1423)
Q Consensus 930 vl~~~gvD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~ 999 (1423)
++.+++||+.+|+||||++|+++|||||||++|++|++++|+.||++||+|||+||||+||++|.+.|..
T Consensus 175 v~~~~~Vd~~rt~sNdI~ei~~~lGIEAaR~~ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~G~~~~it 244 (300)
T cd02736 175 VMNTPGVIGTRTTSNHIMEVEKVLGIEAARSTIINEIQYTMKSHGMSIDPRHIMLLADLMTFKGEVLGIT 244 (300)
T ss_pred HhcCCcEeccCCccCCHHHHHHhcCHHHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHHHhccCceeeee
Confidence 9999999999999999999999999999999999999999999999999999999999999999999874
No 52
>cd02584 RNAP_II_Rpb1_C Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain. RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.
Probab=99.89 E-value=1.4e-23 Score=248.55 Aligned_cols=176 Identities=24% Similarity=0.431 Sum_probs=138.4
Q ss_pred cceeeehhhhHHHhhccccchhhhhHHhhhcccccCcccccccc----cccccCCCCc-------cccchhhhhhhhcCC
Q psy13846 824 SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHS----FLILKPKDSS-------KSFNSKMYQMKQLLP 892 (1423)
Q Consensus 824 ~~~~i~ld~~r~~~~~l~i~~~~I~~~i~~~~~~~~~i~~~~~~----~~~~~~~~~~-------~~~~~~l~~l~~~l~ 892 (1423)
+.|.+++.+++.++....++++.|...|++.++....+..+.++ .+.+++.... .......+.++..++
T Consensus 153 ~~~~lrl~ld~~~~~~~~i~~~~i~~~i~~~~~~~~~v~~~~~~~~~~~iri~~~~~~~~~~~~~~~~~~l~~~~~~~l~ 232 (410)
T cd02584 153 SPWLLRIELDRKKMTDKKLSMEQIAKKIKEEFKDDLNVIFSDDNAEKLVIRIRIINDDEEKEEDSEDDVFLKKIESNMLS 232 (410)
T ss_pred CCeeEEEEECHHHHHHcCCCHHHHHHHHHHhcCCCeEEEEcCCCcceeEEEEEecCccccccccchhHHHHHHHHHhhCC
Confidence 56788888888888888899988888887654433333222222 2233322111 011122344568899
Q ss_pred ceEEccccccceeeeecccc------c----ceeEEeeeccCccccccceeecccceeeccCchHHHHHHhchHHHHHHH
Q psy13846 893 SVVIKGVQGINRAVIHEEDV------E----GVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTI 962 (1423)
Q Consensus 893 ~v~IkGi~~I~r~~i~~~~~------~----~~~~~~l~~eG~nL~~vl~~~gvD~~~t~SN~i~eV~~~LGIEAAR~~I 962 (1423)
+++|+|++||+|+++..++. . ...+|.+.|+|+||++++.++|||+.+|+||||+||+++|||||||++|
T Consensus 233 ~i~l~Gi~~I~r~~i~~~~~~~~~~~~g~~~~~~~~~l~teG~nl~~v~~~~~Vd~~rt~sNdI~ei~~~lGIEAaR~~i 312 (410)
T cd02584 233 DMTLKGIEGIRKVFIREENKKKVDIETGEFKKREEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEVLGIEAARKAL 312 (410)
T ss_pred CcEEeCCCCceEEEEEcCCceEecCCCCcccCCcceEEEecCcCHHHHhCCCCCccccCEeCCHHHHHHhcCHHHHHHHH
Confidence 99999999999999975421 1 2357999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhcCccccCCchhhHhhhhccccccccCC
Q psy13846 963 MTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG 999 (1423)
Q Consensus 963 i~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~ 999 (1423)
++|++.+|+.||++||+|||+||||+||++|++.+++
T Consensus 313 i~Ei~~v~~~~Gi~Vd~RHl~LiaD~MT~~G~~~~i~ 349 (410)
T cd02584 313 LKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAIT 349 (410)
T ss_pred HHHHHHHHHhcCCccCHHHHHHHHHHHhhceEEeeEe
Confidence 9999999999999999999999999999999999875
No 53
>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=99.88 E-value=1.9e-23 Score=225.03 Aligned_cols=109 Identities=22% Similarity=0.356 Sum_probs=93.4
Q ss_pred CchHHHHHHh--chHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC-------cchhhHHHHHHHHHh
Q psy13846 944 NNTYEVYKTL--GIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG-------TPVELKRLLDDIIAK 1014 (1423)
Q Consensus 944 N~i~eV~~~L--GIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~-------~~~~~~~~~~~~~~~ 1014 (1423)
||++++.+++ ||||||..|++|++++++.||++||+|||+|+||+||+++++...+ ..+++.++...++..
T Consensus 54 ~~~~~il~~~~~Giea~r~~iv~EIq~Vy~~qGV~I~dKHielIv~qMT~kv~i~~~g~s~~l~Ge~v~~~~~~~~N~~~ 133 (204)
T cd02655 54 INPHDLLRIKFLGPEAVQKYLVEEIQKVYRSQGVNINDKHIEIIVRQMTSKVKIIDPGDSGFLPGELVDLNEFEEENKRL 133 (204)
T ss_pred CCHHHHHHHHhHHHHHHHHHHHHHHHHHHHhcCeeecHHHHHHHHHHHhcCeEEecCCCcccCCCceeeHHHHHHHHHHH
Confidence 4778888888 9999999999999999999999999999999999999999998654 667777777777776
Q ss_pred ccCCCCCCCCHHHHHHHhhhhcCcchhhhhhhHHHHHHHH
Q psy13846 1015 NSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIK 1054 (1423)
Q Consensus 1015 ~~~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~f~~~~~ 1054 (1423)
...+..+....+.+++++++.|.+++|+++|| |.+..+
T Consensus 134 ~~~~~~~~~y~p~llGItk~~l~~~Sfls~AS--FqeT~k 171 (204)
T cd02655 134 LLLGKKPAKYEPVLLGITKASLNTESFISAAS--FQETTK 171 (204)
T ss_pred HhCCCCcccccceeeeeeeccccCCCccccCC--hHHHHH
Confidence 66677777777778999999999999998776 655444
No 54
>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=99.86 E-value=2.3e-23 Score=220.28 Aligned_cols=158 Identities=32% Similarity=0.529 Sum_probs=131.5
Q ss_pred ccccCCCCccccccccceEEEEEeecccccCCCHHHHHHHHHhhccCCccccceEeeeeccccCCceeecceeeeeccee
Q psy13846 427 NLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQI 506 (1423)
Q Consensus 427 ~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~kp~~~wtGKqi 506 (1423)
|++||++|+|+++++||+++|+|.||.++.|++++|+.++++..... .. +...+.|+|.+|.++|||||+
T Consensus 1 NilSP~~G~Pii~~~QD~vlG~y~LT~~~~f~~~~e~~~~~~~~~~~----~~------~~~~~~~~I~~~~~~~tgk~~ 70 (158)
T PF04983_consen 1 NILSPANGKPIIGPTQDMVLGAYYLTSEDTFLSRDEAQQALMNGLID----DK------KIVLLHPAILKPKELWTGKQT 70 (158)
T ss_dssp GSEETTTTEESSS--SHHHHHHHHHSSTTTEESHHHHHHHHHCSST--------------CHCSSSSBSSSSSCEECHHH
T ss_pred CccCCCCCCceEEeccceEeEEEEEEecccccchHHHHHHHHccccc----cc------ceeccchhhhccccceeeccH
Confidence 68999999999999999999999999999999999999999987421 00 115678999999999999999
Q ss_pred eeecccCCCCcccccceeecccccccCcccccCCcEEEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHH
Q psy13846 507 FSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMW 586 (1423)
Q Consensus 507 ~s~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~ 586 (1423)
++.+||.+ ++..... -+++++.++|++|+++.|.+||+++|.++.+++++.+|++||++.+..||+
T Consensus 71 ~s~il~~~------i~~~~~~--------~~~~~~~~~i~~g~~l~g~l~k~~lgk~~~~~li~~i~~~yG~~~~~~~ld 136 (158)
T PF04983_consen 71 FSRILPNE------INPEGFS--------NDPDDGYVVINNGELLSGVLDKKTLGKKSLGSLIHQIYREYGPEATVQFLD 136 (158)
T ss_dssp HHTTSHTT------HHEEEST--------SCHSSHSEEECTSSEEEC--SHHHHSCSHTTCHHHHHHHHSHHHHHHHHHH
T ss_pred HHHhcccc------ccccccc--------ccccccceeecCCccchhheehheecccchhhHHHHHHHHHCHHHHHHHHH
Confidence 99999853 3333221 012367899999999999999999995578899999999999999999999
Q ss_pred HhhhhhhHHHhhcCcceecCCC
Q psy13846 587 RLSRMTSFYLMNRGFSIGIGDV 608 (1423)
Q Consensus 587 ~l~~l~~~~L~~~GfsiGi~D~ 608 (1423)
+++++..+|++.+|||+|++|+
T Consensus 137 ~i~~lg~~~~t~~GfSvgi~D~ 158 (158)
T PF04983_consen 137 AIKRLGFRYLTRSGFSVGIDDM 158 (158)
T ss_dssp HHHHHHHHHHHHHTBB-SGGGC
T ss_pred HHHHHHHHHHHHcCeeEecccC
Confidence 9999999999999999999996
No 55
>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=99.84 E-value=1e-21 Score=226.13 Aligned_cols=247 Identities=33% Similarity=0.424 Sum_probs=206.8
Q ss_pred ecCCCcccchhHHHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhH
Q psy13846 690 IMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIK 769 (1423)
Q Consensus 690 ~~~~~~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlk 769 (1423)
|.+++++|||+||.+||||||||+||||| +||||||+ +++|+|| |||||+
T Consensus 2 y~~slv~PGE~VG~iaAQSIGEPsTQMTL----nTFH~AGv-------------~~~nVTl-------------GvPRL~ 51 (309)
T cd02735 2 YMRSLVEPGEAVGLLAAQSIGEPSTQMTL----NTFHFAGR-------------GEMNVTL-------------GIPRLR 51 (309)
T ss_pred chhccCCCCcccchhhhhccCCccccccc----ccccccCc-------------ccccccc-------------ccccHH
Confidence 45678999999999999999999999999 99999999 8999999 999999
Q ss_pred HHH-hhhcCCCCceeeeecccCChHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhhh
Q psy13846 770 EII-NASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIR 848 (1423)
Q Consensus 770 EIi-naSk~ikTPiitv~L~~~~~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I~ 848 (1423)
||| +|||+||||+|+++|.++.+.+.|+.++++|++++|+|+++++++.| +...++......+
T Consensus 52 EIi~~Ask~i~TP~m~v~l~~~~~~~~a~~~~~~ie~~~l~dv~~~~~v~~------i~~~~~~~~~~~~---------- 115 (309)
T cd02735 52 EILMTASKNIKTPSMTLPLKNGKSAERAETLKKRLSRVTLSDVVEKVEVTE------ILKTIERVFKKLL---------- 115 (309)
T ss_pred HHHhhhccCCCCCeEEEEecCchhHHHHHHHHhheeEeEHHHhhhhhehhH------HHHHHHHHhhhhh----------
Confidence 998 89999999999999999988899999999999999999999987654 1111111111000
Q ss_pred HHhhhcccccCccccccccccccc-CCCCccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCccc
Q psy13846 849 YCIERTRGISGHLTVSGHSFLILK-PKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927 (1423)
Q Consensus 849 ~~i~~~~~~~~~i~~~~~~~~~~~-~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~nL 927 (1423)
. ....+.+. +.+..+ ...++.+++.+++++|+|+|||+|+.+.++++.+..+|.+.++|.||
T Consensus 116 -------~--------~~~~~~i~~~~~~~~--~~~~~~~~~~l~~~~i~gi~gI~r~~i~~~~~~~~~~~~l~teG~nl 178 (309)
T cd02735 116 -------G--------KWCEVTIKLPLSSPK--LLLLSIVEKLARKAVIREIPGITRCFVVEEDKGGKTKYLVITEGVNL 178 (309)
T ss_pred -------C--------CEEEEEEEecCCchh--HHHHHHHHHHhcccEEeCCCCccEEEEecCcCCCceEEEEEeccccH
Confidence 0 00001111 111111 12345678889999999999999999987765555679999999999
Q ss_pred ccccee-ecccceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC
Q psy13846 928 RDVMAT-YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG 999 (1423)
Q Consensus 928 ~~vl~~-~gvD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~ 999 (1423)
++++.+ +++|+.+++|||+++|+++|||||||+.|++|++.+++.||++||+|||+||||+||++|++.+.+
T Consensus 179 ~~v~~~~~~vd~~r~~sNdi~ei~~~lGIEAar~~ii~Ei~~v~~~~Gi~V~~rHl~LiaD~MT~~G~~~~~n 251 (309)
T cd02735 179 AALWKFSDILDVNRIYTNDIHAMLNTYGIEAARRAIVKEISNVFKVYGIAVDPRHLSLIADYMTFEGGYRPFN 251 (309)
T ss_pred HHHHhccCccccccceeCCHHHHHHhhCHHHHHHHHHHHHHHHHHhcCCeeCHHHHHHHHHHHHhCCcEeecc
Confidence 999999 699999999999999999999999999999999999999999999999999999999999998864
No 56
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=99.83 E-value=5.9e-21 Score=246.70 Aligned_cols=246 Identities=36% Similarity=0.564 Sum_probs=203.7
Q ss_pred CccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhHHHHhhhcCCCCceeeeecccCC--
Q psy13846 714 VPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINASRNISTPIITAYLDKDT-- 791 (1423)
Q Consensus 714 tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlkEIinaSk~ikTPiitv~L~~~~-- 791 (1423)
||+|| +||||||+ ++||+|| |||||+|||||||+||||+|+++|.++.
T Consensus 541 ~~~~L----nTFH~AGv-------------~~~nVTl-------------GvPRL~EIinask~i~TP~m~i~l~~~~~~ 590 (858)
T PRK14898 541 THNTM----RTFHYAGV-------------AEINVTL-------------GLPRMIEIVDARKEPSTPIMTVHLKGEYAT 590 (858)
T ss_pred ecccc----ceeeccCc-------------ccccccc-------------CCchHHHHhcccCCCCCceEEEEECCCccc
Confidence 78999 99999999 8999999 9999999999999999999999999875
Q ss_pred hHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhhhHHhhhcccccCcccccccccccc
Q psy13846 792 DLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLIL 871 (1423)
Q Consensus 792 ~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I~~~i~~~~~~~~~i~~~~~~~~~~ 871 (1423)
+.+.|+.++++|++++|+|++++++.... ...+.+.| ++..+..+.++++.|...|++.+... +.. ....+.+
T Consensus 591 ~~~~a~~v~~~ie~~~L~dv~~~~~~~~~--~~~~~i~l--~~~~~~~~~l~~~~i~~~i~~~~~~~--~~~-~~~~~~~ 663 (858)
T PRK14898 591 DREKAEEVAKKIESLTLGDVATSIAIDLW--TQSIKVEL--DEETLADRGLTIESVEEAIEKKLGVK--IDR-KGTVLYL 663 (858)
T ss_pred hHHHHHHHHhheeeEEHHHHHHHhhhhcc--ccEEEEEE--CHHHHHHcCCCHHHHHHHHHHhcccc--ccC-CCCEEEE
Confidence 56899999999999999999998773211 11244444 44445566778889999887654321 111 2233333
Q ss_pred cCCCCccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCccccccceeecccceeeccCchHHHHH
Q psy13846 872 KPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYK 951 (1423)
Q Consensus 872 ~~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~nL~~vl~~~gvD~~~t~SN~i~eV~~ 951 (1423)
.+... ....++.+...+++++|+|+|||+|+.+.+++..+..+|.+.|+|+||++++.+++||+.+|+||||++|++
T Consensus 664 ~~~~~---~~~~~~~~~~~l~~~~i~gi~gI~~~~i~~~~~~~~~~~~l~teG~nl~~~~~~~~vd~~~~~sN~i~~i~~ 740 (858)
T PRK14898 664 KPKTP---SYKALRKRIPKIKNIVLKGIPGIERVLVKKEEHENDEEYVLYTQGSNLREVFKIEGVDTSRTTTNNIIEIQE 740 (858)
T ss_pred EecCc---hHHHHHHHHHHhcCcEEECCCCccEEEEecCCCCCCceEEEEecCcCHHHHhcCCCCcccccccCCHHHHHH
Confidence 33211 123466677789999999999999999987664444689999999999999999999999999999999999
Q ss_pred HhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC
Q psy13846 952 TLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG 999 (1423)
Q Consensus 952 ~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~ 999 (1423)
+|||||||++|++|++++|+.||++||+|||+||||+||++|++.+.+
T Consensus 741 ~lGIEAar~~ii~Ei~~v~~~~gi~V~~rHl~liad~MT~~G~~~~~~ 788 (858)
T PRK14898 741 VLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIMTADGEVKPIG 788 (858)
T ss_pred hhCHHHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHHHccCCcEEEec
Confidence 999999999999999999999999999999999999999999999864
No 57
>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=99.82 E-value=8e-21 Score=197.83 Aligned_cols=55 Identities=45% Similarity=0.654 Sum_probs=53.2
Q ss_pred chHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC
Q psy13846 945 NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG 999 (1423)
Q Consensus 945 ~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~ 999 (1423)
||++|+++|||||||..|++|++++++.||++||+|||+||||+||++|.+.+.+
T Consensus 49 dI~~i~~~lGIEAaR~~iv~El~~v~~~~Gi~V~~rHl~LIAD~MT~~G~~~gin 103 (158)
T cd00630 49 SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVT 103 (158)
T ss_pred cHHHHHHHhCHHHHHHHHHHHHHHHHHhcCceecHHHHHHHHHHHhcCCcccccc
Confidence 7899999999999999999999999999999999999999999999999999864
No 58
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]
Probab=99.73 E-value=3.8e-20 Score=235.71 Aligned_cols=120 Identities=9% Similarity=-0.108 Sum_probs=106.4
Q ss_pred CCCCCcceEEEEecCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCccccc
Q psy13846 311 ELSKPSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEM 390 (1423)
Q Consensus 311 ~~arPe~liLt~lpVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m 390 (1423)
.+.+++.+++++|. .|++++.++|.+.... .+|| |++.+-.+..+.|.-.++
T Consensus 668 m~~~Gs~~n~sq~~---~~iG~~gv~g~r~~~~---------------------~~~~----Fe~~~~~~~a~~~i~s~f 719 (808)
T COG0086 668 MGLSGARMNISQIV---QLIGQQGVMGEKISVL---------------------ARAA----FEVTVKHLEAEGPGESSF 719 (808)
T ss_pred HhhhhhccCHHHHH---HHhhhheeeccCCCcc---------------------cccc----cccccccceeeeeeeccc
Confidence 45789999999999 9999999999763221 7899 999999999999999999
Q ss_pred ccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecccccCCCHHHHHHHHHh
Q psy13846 391 NVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAST 469 (1423)
Q Consensus 391 ~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~~~~~~~~~~l~~~ 469 (1423)
.-+|.+++ ||||+||||+|+++++.+++.|+|.+|+|+...|| +.+.|+.|+++......|+.|..+.
T Consensus 720 ~eGLt~~e----------~f~~~~ggR~GlvDTA~KTa~sGYl~RrLv~~~qd-l~v~~d~~~~~g~~~~~~~~~ged~ 787 (808)
T COG0086 720 LEGLTENE----------YFGHPIGGRTGLVDTALKTADSGYLTRRLVDVAQD-LIVQEDDCVTDGIGVVIQFEYGEDG 787 (808)
T ss_pred CCCCCcce----------EEeecCccccchHHHhhhhcccCcceEEeechhcc-eEEEecCeEeecCceEEEEecCccc
Confidence 99999777 99999999999999999999999999999999999 9999999999977666776664443
No 59
>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=99.50 E-value=4.3e-15 Score=191.88 Aligned_cols=192 Identities=14% Similarity=0.115 Sum_probs=111.5
Q ss_pred HHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCceeecCcceehhhhh
Q psy13846 167 INILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKY 246 (1423)
Q Consensus 167 ~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk~~~~ki~~e~~ 246 (1423)
.+++..+... ++......|+++++.....+..+.+++.++.|..... .|. .++
T Consensus 13 ~~LI~~~~~~-------yG~~~t~~~lD~lk~Lgf~~aT~~G~SigidDl~ip~-------------~K~---~li---- 65 (1227)
T TIGR02388 13 KNLISWAYKT-------YGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPP-------------AKQ---DLL---- 65 (1227)
T ss_pred HHHHHHHHHH-------hCHHHHHHHHHHHHHHHHHHHHhcCeEEeeccCCCCH-------------HHH---HHH----
Confidence 5566666666 7888889999999988888888888888888763211 000 011
Q ss_pred cccccchhhHHHHHHHHhhhhhcc-Chh---hhhhhccCccccCCHHHHHHHhhccCCCcccccccccCCCCCcceEEEE
Q psy13846 247 KNRTKKKDAIVEDLLAEYNEAVKF-NPE---IEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTR 322 (1423)
Q Consensus 247 ~~~~~~~~~~~~~~~~~~~~~~~~-~~~---~~~~~~~~~~~~L~p~~V~eiLe~I~~~d~~lL~m~~~~arPe~liLt~ 322 (1423)
++++....+..+.|+.-.-. .+. +..... ...+. -..++...|+...+ .+++..|+.+|||++..-+.+
T Consensus 66 ----~~a~~~v~~~~~~y~~G~it~~Er~~~ii~~w~-~t~e~-~~~~~~~~~~~~d~-~N~v~mMa~SGARGNisQi~Q 138 (1227)
T TIGR02388 66 ----EAAEKEIRATEERYRRGEITEVERFQKVIDTWN-GTNEE-LKDEVVNNFRQTDP-LNSVYMMAFSGARGNMSQVRQ 138 (1227)
T ss_pred ----HHHHHHHHHHHHHHHcCCCcchhhHHHHHHHHH-HHHHH-HHHHHHHhhhhcCC-CCcHHHHhhccCcccHHHHHH
Confidence 01111122222222210000 000 000000 00000 12233444444333 478999999999994444444
Q ss_pred ecCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCcccccccccCCCHHHHh
Q psy13846 323 LLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARA 402 (1423)
Q Consensus 323 lpVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~ara 402 (1423)
| ++.+-.|-. ..|.. ..+| .-..+..+|.+.|
T Consensus 139 L------vGmrGlma~-p~G~i-------------------i~lP------------------I~snFreGLt~~E---- 170 (1227)
T TIGR02388 139 L------VGMRGLMAN-PQGEI-------------------IDLP------------------IKTNFREGLTVTE---- 170 (1227)
T ss_pred H------hcchheecC-CCCcE-------------------eecc------------------chhhhhcCCCHHH----
Confidence 4 344432211 11211 1123 3345778888777
Q ss_pred cccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEE
Q psy13846 403 EALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFIT 446 (1423)
Q Consensus 403 E~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~ 446 (1423)
||||+||||+|++|+|.+|+.|||.+|+|+...||.++
T Consensus 171 ------yF~sa~GaRkGLvDTAlKTAdSGYLTRRLVdv~qDviV 208 (1227)
T TIGR02388 171 ------YVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIV 208 (1227)
T ss_pred ------hheeccccccchhhcceeccccchHHHHHHHhhceEEE
Confidence 99999999999999999999999999999999999443
No 60
>CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed
Probab=99.45 E-value=1.5e-14 Score=190.49 Aligned_cols=194 Identities=10% Similarity=0.057 Sum_probs=109.8
Q ss_pred HHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCceeecCcceehhhhh
Q psy13846 167 INILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKY 246 (1423)
Q Consensus 167 ~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk~~~~ki~~e~~ 246 (1423)
.+|+..+... ++.+....|+++++.....+..+.+++.++.|..... - |. +++.
T Consensus 20 ~~li~~~~~~-------~G~~~t~~~lD~lk~lgf~~at~~G~Sigi~Dl~ip~------------~-K~---~li~--- 73 (1364)
T CHL00117 20 KRLISWLIDH-------FGMAYTSHILDQLKTLGFQQATAAGISLGIDDLLTPP------------S-KG---WLVQ--- 73 (1364)
T ss_pred HHHHHHHHHH-------hCHHHHHHHHHHHHHHHHHHHHhcceEEecCcccCCH------------H-HH---HHHH---
Confidence 4455555555 7888889999999988888888888888887763110 0 00 1111
Q ss_pred cccccchhhHHHHHHHHhhhhhccC-hhhhhhhcc--CccccCCHHHHHHHhhccCCCcccccccccCCCCCcceEEEEe
Q psy13846 247 KNRTKKKDAIVEDLLAEYNEAVKFN-PEIEAHKKF--GLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRL 323 (1423)
Q Consensus 247 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~--~~~~~L~p~~V~eiLe~I~~~d~~lL~m~~~~arPe~liLt~l 323 (1423)
+++..+..+.+.|..-.-.. .......+. ...+.+ ..++...|+... ..++++.|+.+|||++ ++||
T Consensus 74 -----~a~~~v~~~~~~y~~G~it~~er~~~~i~~w~~~~~~l-~~~~~~~~~~~d-~~N~v~mMa~SGARGn---~sQi 143 (1364)
T CHL00117 74 -----DAEQQSLILEKHYHYGNVHAVEKLRQSIEIWYATSEYL-KQEMNPNFRMTD-PLNPVYMMSFSGARGN---ASQV 143 (1364)
T ss_pred -----HHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHH-HHHHHHhhccCC-CCCcHhhhhhccCccc---HHHH
Confidence 11111122222221100000 000000000 001111 112333444433 3589999999999994 5555
Q ss_pred cCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCcccccccccCCCHHHHhc
Q psy13846 324 LVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAE 403 (1423)
Q Consensus 324 pVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE 403 (1423)
- .+++....|- ...|. .|.++ .-..+..+|.+.|
T Consensus 144 ~---qLvGmRGlma-~p~G~--------------------------iI~~P-----------I~snFreGLs~~E----- 177 (1364)
T CHL00117 144 H---QLVGMRGLMS-DPQGQ--------------------------IIDLP-----------IQSNFREGLSLTE----- 177 (1364)
T ss_pred H---HHhcccceee-CCCCc--------------------------Eeecc-----------hhhhhhcCCCHHH-----
Confidence 4 4444211110 01111 11111 3456778888777
Q ss_pred ccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEE
Q psy13846 404 ALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITG 447 (1423)
Q Consensus 404 ~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~ 447 (1423)
||||+||||+|++|||.+|+.|||.+|+|+...||.++.
T Consensus 178 -----yFis~~GaRkGLvDTAlkTAdSGYLtRRLVdv~qdviV~ 216 (1364)
T CHL00117 178 -----YIISCYGARKGVVDTAVRTADAGYLTRRLVEVVQHIVVR 216 (1364)
T ss_pred -----hheeccccccchhhcceecccccchhhHHHhhhccEEEE
Confidence 999999999999999999999999999999999995543
No 61
>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=99.06 E-value=5.7e-12 Score=133.57 Aligned_cols=146 Identities=21% Similarity=0.356 Sum_probs=102.5
Q ss_pred ccccCCCCCceEeeehhhhhheeecccCCcccCHHHHHHHHHHhhccc--ccceeeeEEEecCCHHHHhhcceeeeecC-
Q psy13846 28 NLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR--KVFFRGLIEGTVTKEDRVQQQSHIQIVSK- 104 (1423)
Q Consensus 28 ~i~sp~~~~p~~g~~qd~~~g~~~lt~~~~~~~~~~~~~~~~~~~~~~--~~~i~~~i~F~~~S~eeIrklSv~eIt~~- 104 (1423)
||+||++|+|++|.+||+++|+|+||++++|++++|++++++|..... ...+.. .|..+
T Consensus 1 NilSP~~G~Pii~~~QD~vlG~y~LT~~~~f~~~~e~~~~~~~~~~~~~~~~~~~~------------------~I~~~~ 62 (158)
T PF04983_consen 1 NILSPANGKPIIGPTQDMVLGAYYLTSEDTFLSRDEAQQALMNGLIDDKKIVLLHP------------------AILKPK 62 (158)
T ss_dssp GSEETTTTEESSS--SHHHHHHHHHSSTTTEESHHHHHHHHHCSST----CHCSSS------------------SBSSSS
T ss_pred CccCCCCCCceEEeccceEeEEEEEEecccccchHHHHHHHHcccccccceeccch------------------hhhccc
Confidence 799999999999999999999999999999999999999999643221 111222 23322
Q ss_pred cccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccCceeEEeeeccH-------HHHhhhccccc
Q psy13846 105 NLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCV-------INILQSICKNP 177 (1423)
Q Consensus 105 ~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~PV~h~gffd~v-------~~iL~~iC~~~ 177 (1423)
+.| +|+.+.|-++...+-+.... .|.. .+.+.+...+...|.+++. .+|++.++..
T Consensus 63 ~~~----tgk~~~s~il~~~i~~~~~~-~~~~-----------~~~~~i~~g~~l~g~l~k~~lgk~~~~~li~~i~~~- 125 (158)
T PF04983_consen 63 ELW----TGKQTFSRILPNEINPEGFS-NDPD-----------DGYVVINNGELLSGVLDKKTLGKKSLGSLIHQIYRE- 125 (158)
T ss_dssp SCE----ECHHHHHTTSHTTHHEEEST-SCHS-----------SHSEEECTSSEEEC--SHHHHSCSHTTCHHHHHHHH-
T ss_pred cce----eeccHHHHhccccccccccc-cccc-----------ccceeecCCccchhheehheecccchhhHHHHHHHH-
Confidence 356 78888888877644333222 1111 6788899999999998743 3566666666
Q ss_pred cccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHH
Q psy13846 178 TCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKIL 214 (1423)
Q Consensus 178 ~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~ 214 (1423)
+++++...|++++++....+..+.+++.++.
T Consensus 126 ------yG~~~~~~~ld~i~~lg~~~~t~~GfSvgi~ 156 (158)
T PF04983_consen 126 ------YGPEATVQFLDAIKRLGFRYLTRSGFSVGID 156 (158)
T ss_dssp ------SHHHHHHHHHHHHHHHHHHHHHHHTBB-SGG
T ss_pred ------HCHHHHHHHHHHHHHHHHHHHHHcCeeEecc
Confidence 7888899999999988877777777765543
No 62
>PRK02597 rpoC2 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=98.94 E-value=1.2e-09 Score=143.53 Aligned_cols=118 Identities=18% Similarity=0.288 Sum_probs=96.1
Q ss_pred cceeeccCchHHHHHH----------------hchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC-
Q psy13846 937 KGVKCSSNNTYEVYKT----------------LGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG- 999 (1423)
Q Consensus 937 D~~~t~SN~i~eV~~~----------------LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~- 999 (1423)
+.....+.|.|+++.+ +|+||+|..+++|++++++.||++||+|||++++|+||+++.+...|
T Consensus 1052 ~~lt~g~~~ph~iL~~~f~~~~~~~g~~~aa~~~~~~~~~~lv~evq~Vy~~QGv~I~dkHieiIvrqMt~kV~i~d~Gd 1131 (1331)
T PRK02597 1052 EPLTDGPINPHELLEIFFEDLRDRKGLYEAALEALQKLQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDGGD 1131 (1331)
T ss_pred ccccCCCCCHHHHHhhhhhhhcccchhhHHHHHhHHHHHHHHHHHHHHHHHhcCeEechhhHHhHHHHHhCcEEEeeCCC
Confidence 3334445678888887 89999999999999999999999999999999999999999886544
Q ss_pred ------cchhhHHHHHHHHHhccCCCCCCCCHHHHHHHhhhhcCcchhhhhhhHHHHHHHHHH
Q psy13846 1000 ------TPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056 (1423)
Q Consensus 1000 ------~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~f~~~~~~~ 1056 (1423)
..|++.++...++.....+..|+...+.+++++++.|.+++|+++|| |.+-.+-.
T Consensus 1132 t~~lpGeli~~~~~~~~N~~~~~~~~~~a~y~pvLlGItkasl~T~sfis~aS--FqeT~rvL 1192 (1331)
T PRK02597 1132 TTMLPGELIELRQVEQVNEAMAITGGAPAEYTPVLLGITKASLNTDSFISAAS--FQETTRVL 1192 (1331)
T ss_pred cccCCcceeeHHHHHHHHHHHHhcCCCcceeeeeeeeeeeeccccCChhhhcc--HHHHHHHH
Confidence 56777888777777666666667666778899999999999998776 66654443
No 63
>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional
Probab=98.24 E-value=5.5e-07 Score=110.83 Aligned_cols=49 Identities=29% Similarity=0.489 Sum_probs=46.2
Q ss_pred hhHHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeecccCCcc
Q psy13846 10 TLYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAF 58 (1423)
Q Consensus 10 ~~~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~~~~~ 58 (1423)
-.-+||||||+.||.+++|++||++|+|++|.+||+++|+|+||.+|..
T Consensus 479 PqS~~A~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~llG~y~LT~~~~~ 527 (627)
T PRK02625 479 PLSLEAQAEARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLTAENPG 527 (627)
T ss_pred CCCHHHHHHHHHHhcCccceEEcCCCceeEeechhhhhheeeeeccCcc
Confidence 3458999999999999999999999999999999999999999999865
No 64
>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=98.23 E-value=5.5e-07 Score=110.69 Aligned_cols=49 Identities=29% Similarity=0.465 Sum_probs=45.8
Q ss_pred hhHHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeecccCCcc
Q psy13846 10 TLYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAF 58 (1423)
Q Consensus 10 ~~~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~~~~~ 58 (1423)
-.-+||||||++||.+++|++||++|+|++|.+||+++|+|+||.+|.-
T Consensus 472 PqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~llg~y~LT~~~~~ 520 (619)
T TIGR02387 472 PLSLEAQTEARLLMLASNNVLSPATGEPIVTPSQDMVLGCYYLTALNPG 520 (619)
T ss_pred CCCHHHHHHHHHHhhchhcEEecCCCceeEeechhhhhhhheeeccccc
Confidence 3457999999999999999999999999999999999999999999853
No 65
>CHL00018 rpoC1 RNA polymerase beta' subunit
Probab=98.19 E-value=8.1e-07 Score=110.46 Aligned_cols=49 Identities=29% Similarity=0.394 Sum_probs=45.9
Q ss_pred hhHHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeecccCCcc
Q psy13846 10 TLYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAF 58 (1423)
Q Consensus 10 ~~~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~~~~~ 58 (1423)
-.-+||||||+.||++.+|++||++|+|++|.+||+++|+|+||.+|.-
T Consensus 500 PqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~~ 548 (663)
T CHL00018 500 PLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYVLTIGNRR 548 (663)
T ss_pred CCCHHHHHHHHHHhcCccceeEcCCCceeEeechhhhhhhheecccCCC
Confidence 3457999999999999999999999999999999999999999999863
No 66
>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=91.13 E-value=0.024 Score=56.53 Aligned_cols=62 Identities=19% Similarity=0.287 Sum_probs=49.5
Q ss_pred CcccccccccCCCCCcceEEEEecCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEEecCCceeeccCCCCc
Q psy13846 301 EDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTP 380 (1423)
Q Consensus 301 ~d~~lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~ 380 (1423)
.+++++.|..+|+|++++++.||. .|+++|...|.++...+ ..|+||| |.+..-.|
T Consensus 47 ~~N~l~~M~~SGaKGs~~ni~Qi~---g~lGqq~~~g~ri~~~~-----------------~~Rtlp~----f~~~~~~~ 102 (108)
T PF05000_consen 47 FNNSLLIMINSGAKGSMSNISQIS---GCLGQQSVEGKRIPRGF-----------------SGRTLPH----FKPFDESP 102 (108)
T ss_dssp TTSHHHHHHHSSSS--HHHHHHHH---ST-EEEEETTSES--SS-----------------TTCSSTT----S-SS-SST
T ss_pred CCCcHHhhhhccCCCCHHHHHHHH---HHHHHhhccccccccCC-----------------CCCcCCC----cCCCCCCc
Confidence 468899999999999999999999 99999999999877767 8999999 88888888
Q ss_pred ccCCCc
Q psy13846 381 YNADFD 386 (1423)
Q Consensus 381 ~nadFd 386 (1423)
...+|.
T Consensus 103 ~~~GFI 108 (108)
T PF05000_consen 103 ESRGFI 108 (108)
T ss_dssp TTTTEE
T ss_pred ccCCCC
Confidence 888884
No 67
>PF04992 RNA_pol_Rpb1_6: RNA polymerase Rpb1, domain 6; InterPro: IPR007075 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module [, ]. This family appears to be specific to the largest subunit of RNA polymerase II.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_M 1Y77_A 3CQZ_A 3GTM_A 1TWA_A 4A3I_A 2NVY_A 2NVT_A 1I6H_A 1TWF_A ....
Probab=87.94 E-value=0.14 Score=56.20 Aligned_cols=88 Identities=14% Similarity=0.177 Sum_probs=58.3
Q ss_pred cchhhHHHHHHHHHhcc--CCCCCCCCHHHHHHHhhhhcCcchhhh-----------hhhHHHHHHHHHHHHHhhhcccc
Q psy13846 1000 TPVELKRLLDDIIAKNS--SRSDPSLSAQEILALSNETLDSKEFLQ-----------DTSENFVRDIKKFLEEFSKKESV 1066 (1423)
Q Consensus 1000 ~~~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~l~~~~~~~-----------~~~~~f~~~~~~~~~~~~~~~~~ 1066 (1423)
.||++.|++.+++.... .+....+.|.+++..+++.++.-..+. .|.-.|.-.|++
T Consensus 87 LPVNi~RiI~nAq~~f~i~~~~~sdL~P~~Vi~~V~~L~~~L~vv~g~D~ls~Eaq~NAtlLf~i~lRs----------- 155 (187)
T PF04992_consen 87 LPVNIQRIIWNAQKIFHIDPRKPSDLSPIYVIEKVEELLDRLVVVRGDDPLSREAQENATLLFKILLRS----------- 155 (187)
T ss_dssp EES-HHHHCCCCCCCTT--TTS-BS--HHHHHHHHHHHHTT--SS--SSCCCCHHHHCCCHHHHHHHCC-----------
T ss_pred CCccHHHHHHHHHHHcCCCCCCcccCCHHHHHHHHHHHHHHHhhccCCCcchHHHHhhHHHHHHHHHHH-----------
Confidence 89999999888776532 455578999999999998876421110 122344433332
Q ss_pred ccccccCCchhhhhhhccccccCcccCCCCCChhHHHHHHHHHhhhc
Q psy13846 1067 TSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRA 1113 (1423)
Q Consensus 1067 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~s 1113 (1423)
.++.|.+..++++|++++ + |++++++.+|.+|
T Consensus 156 ---------~LasKrvi~e~rL~~~AF----~--wilgEIe~rF~~a 187 (187)
T PF04992_consen 156 ---------TLASKRVIEEYRLNKEAF----D--WILGEIESRFKKA 187 (187)
T ss_dssp ---------CSSHHHHHHTSB--HHHH----H--HHHHHHHHHHHCC
T ss_pred ---------hhhhHHHHHHhCcCHHHH----H--HHHHHHHHHHHcC
Confidence 356788889999999998 8 9999999999886
No 68
>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=57.75 E-value=2.9 Score=43.56 Aligned_cols=53 Identities=26% Similarity=0.417 Sum_probs=34.2
Q ss_pred cchhhhhhhheeeecCCC----------------------------cceeeehhhhHHHhhccccchhhhhHHhhhcccc
Q psy13846 806 TTLGEVCEYIEEVFVPDD----------------------------SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI 857 (1423)
Q Consensus 806 ~~l~dii~~i~~~~~~~~----------------------------~~~~i~ld~~r~~~~~l~i~~~~I~~~i~~~~~~ 857 (1423)
|||++|+...+++|+|+. +.|++++.++|-++...++++..|...|.+.++.
T Consensus 1 TtL~~vt~~teIyYDPdp~~Tvi~eD~e~V~~y~e~pd~~~~~~~~spWlLRieLdr~~m~dk~l~m~~I~~~I~~~f~~ 80 (135)
T PF04990_consen 1 TTLRDVTASTEIYYDPDPRNTVIEEDREFVESYFEIPDEDDDPSRLSPWLLRIELDRKKMIDKKLTMEDIAEKIKEEFGN 80 (135)
T ss_dssp ECCHCHECEEEEEE-SSTTSSSSSTTHCHHHHCCCTT-SSTT-SSBESEEEEEEE-CCCCCCTT--HHHHCCCHHHCCTT
T ss_pred CcHHHhhhheeEEECCCCCCCcchhhHHHHHHHHhCCCcccCcccCCCeEEEEEEcHHHHHhcCCCHHHHHHHHHHhcCC
Confidence 456666666666666652 3467788888877777888888888888776654
Q ss_pred c
Q psy13846 858 S 858 (1423)
Q Consensus 858 ~ 858 (1423)
.
T Consensus 81 ~ 81 (135)
T PF04990_consen 81 D 81 (135)
T ss_dssp S
T ss_pred C
Confidence 3
No 69
>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=44.77 E-value=21 Score=37.35 Aligned_cols=86 Identities=16% Similarity=0.312 Sum_probs=48.6
Q ss_pred cccceeEEEEccCCc----------------------------EEEEEEchHHHHHhcccCCHHHHHHHHHhccccCCce
Q psy13846 1146 EVCEYIEEVFVPDDS----------------------------FILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHL 1197 (1423)
Q Consensus 1146 ~i~~~i~~~~~~~~~----------------------------~~~i~l~~~~~~~~~~~i~~~~i~~~i~~~k~~~~~~ 1197 (1423)
+|+...+++|+|+.. .+.+++.+++-++...++++++|..+|.+.. +.++
T Consensus 5 ~vt~~teIyYDPdp~~Tvi~eD~e~V~~y~e~pd~~~~~~~~spWlLRieLdr~~m~dk~l~m~~I~~~I~~~f--~~~l 82 (135)
T PF04990_consen 5 DVTASTEIYYDPDPRNTVIEEDREFVESYFEIPDEDDDPSRLSPWLLRIELDRKKMIDKKLTMEDIAEKIKEEF--GNDL 82 (135)
T ss_dssp CHECEEEEEE-SSTTSSSSSTTHCHHHHCCCTT-SSTT-SSBESEEEEEEE-CCCCCCTT--HHHHCCCHHHCC--TTSE
T ss_pred HhhhheeEEECCCCCCCcchhhHHHHHHHHhCCCcccCcccCCCeEEEEEEcHHHHHhcCCCHHHHHHHHHHhc--CCCe
Confidence 678888999998632 2477888888778888999999998886532 1233
Q ss_pred EE--ecC----cEEEEEeCCCC------c----hhhhHHHHHH-hccCCcEEc
Q psy13846 1198 TV--SGH----SFLILKPKDSS------K----SFNSKMYQMK-QLLPSVVIK 1233 (1423)
Q Consensus 1198 ~~--~~~----~~i~i~~~~~~------~----~~~~~l~~l~-~~l~~~~v~ 1233 (1423)
.+ +++ -++|||+.... . .....|+.++ +.|.++.+|
T Consensus 83 ~vi~sddNa~~lViRIRi~~~~~~~~~~~d~~~~dd~~Lr~~e~~lL~~~~Lr 135 (135)
T PF04990_consen 83 HVIYSDDNAEKLVIRIRIIKDEDKKEEDEDEQEEDDVFLRRLESNLLDDLTLR 135 (135)
T ss_dssp EEEE--TTSSSEEEEEEEB--S---SSSSS--S-CHHHHHHHHHHHCCS-ECC
T ss_pred EEEecCCCCcccEEEEEEecCcccccccccchhhHHHHHHHHHHHhhhcCcCC
Confidence 22 222 35677764211 0 1235677775 556555543
No 70
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=41.00 E-value=14 Score=30.75 Aligned_cols=14 Identities=43% Similarity=1.194 Sum_probs=12.0
Q ss_pred cCCccCCCCCCCCC
Q psy13846 218 KKVSVCPHCGEING 231 (1423)
Q Consensus 218 kk~k~C~~Cg~~~~ 231 (1423)
+..++||+||.+|+
T Consensus 9 RGirkCp~CGt~NG 22 (44)
T PF14952_consen 9 RGIRKCPKCGTYNG 22 (44)
T ss_pred hccccCCcCcCccC
Confidence 46789999999986
No 71
>COG3688 Predicted RNA-binding protein containing a PIN domain [General function prediction only]
Probab=39.34 E-value=38 Score=36.11 Aligned_cols=44 Identities=25% Similarity=0.342 Sum_probs=34.2
Q ss_pred EEEecCccHHHHhhcccccceecccccHHHHHHHhCHHHHHHHHHHHHHHHhhcCC
Q psy13846 1255 KLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHG 1310 (1423)
Q Consensus 1255 ~l~teG~nl~~~~~~~~vd~~~~~sN~i~~i~~~lGIEAar~~ii~Ei~~v~~~~G 1310 (1423)
.|+++|.|+-..|. ....+.+..|.|+||..+|+.|.+-=+..|
T Consensus 5 iLLVDGYNmIgaWp------------~Lk~lkd~~~LE~AR~~LIe~l~~Y~s~~g 48 (173)
T COG3688 5 ILLVDGYNMIGAWP------------ELKQLKDRNGLEAARDKLIEALAEYQSFTG 48 (173)
T ss_pred EEEeccchhccccH------------HHHHHHhhccHHHHHHHHHHHHHHhhcccC
Confidence 68899999777664 366788889999999999999866443333
No 72
>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=25.57 E-value=35 Score=44.26 Aligned_cols=50 Identities=32% Similarity=0.357 Sum_probs=26.3
Q ss_pred EEEEecCccccccccceeeeEEecC-----Cceeecc-CC----CCcccCCCcccccccc
Q psy13846 344 VVLFNRQPSLHKLSIMAHRAKVLPH-----RTFRFNE-CV----CTPYNADFDGDEMNVH 393 (1423)
Q Consensus 344 ~Vl~nRqPsLHk~Simah~~~~~~~-----~tir~~~-~~----~~~~nadFdgd~m~~~ 393 (1423)
-||+-|.|++|..-|+-.++.-.|. ..|=|+. +. ..--..|+|||.+.+-
T Consensus 370 ~VlV~R~P~~~pgDir~~~av~~p~L~~l~~vIVF~~~G~r~~~~~lsGgDlDGD~~~V~ 429 (579)
T PF05183_consen 370 DVLVTRNPCLHPGDIRKVKAVDKPELRHLKDVIVFSTKGDRPLPSELSGGDLDGDEYFVC 429 (579)
T ss_dssp EEEEE-SS--SGGGEEEEEE---GGGTT--SEEEE-S-SSS-HHHHTTT--SSS-EEEEE
T ss_pred eEEEecCCccCcCceeEEEeeccHHHcccCCEEEeCCCCCCCchHHhcCCCCCCceEEEE
Confidence 8899999999999999888876664 1122221 00 0012369999999866
Done!