Query psy16766
Match_columns 621
No_of_seqs 309 out of 2327
Neff 7.1
Searched_HMMs 46136
Date Fri Aug 16 21:27:17 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16766.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16766hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0262|consensus 100.0 5E-114 1E-118 962.4 33.6 498 116-620 7-540 (1640)
2 PRK08566 DNA-directed RNA poly 100.0 1.5E-94 3.3E-99 841.1 36.3 393 117-616 5-404 (882)
3 TIGR02390 RNA_pol_rpoA1 DNA-di 100.0 3.1E-94 6.6E-99 836.3 34.7 392 119-616 2-400 (868)
4 PRK14977 bifunctional DNA-dire 100.0 5.5E-94 1.2E-98 851.9 34.7 406 116-616 4-420 (1321)
5 KOG0261|consensus 100.0 5.5E-88 1.2E-92 737.5 24.5 413 119-615 11-443 (1386)
6 KOG0260|consensus 100.0 2.6E-80 5.7E-85 689.0 25.1 395 115-602 9-410 (1605)
7 COG0086 RpoC DNA-directed RNA 100.0 8.1E-68 1.8E-72 606.1 20.2 343 119-596 3-347 (808)
8 PF04997 RNA_pol_Rpb1_1: RNA p 100.0 6.6E-61 1.4E-65 505.5 16.5 310 119-524 2-337 (337)
9 TIGR02386 rpoC_TIGR DNA-direct 100.0 1.6E-54 3.5E-59 503.0 14.8 358 123-592 1-400 (1140)
10 PRK00566 DNA-directed RNA poly 100.0 6.1E-51 1.3E-55 473.7 23.2 338 120-580 6-380 (1156)
11 smart00663 RPOLA_N RNA polymer 100.0 1.4E-49 3.1E-54 408.6 17.2 188 401-616 1-191 (295)
12 PRK02625 rpoC1 DNA-directed RN 100.0 1.4E-46 3E-51 410.8 25.2 151 397-573 239-394 (627)
13 TIGR02387 rpoC1_cyan DNA-direc 100.0 4.6E-47 9.9E-52 414.1 20.2 166 397-591 232-403 (619)
14 CHL00018 rpoC1 RNA polymerase 100.0 2.7E-46 5.8E-51 412.4 21.5 166 398-590 259-430 (663)
15 PRK14906 DNA-directed RNA poly 100.0 4.2E-45 9.1E-50 424.9 22.4 164 397-581 309-484 (1460)
16 PRK14844 bifunctional DNA-dire 100.0 1.2E-43 2.6E-48 427.7 23.0 154 397-576 1663-1822(2836)
17 PRK09603 bifunctional DNA-dire 100.0 1.9E-43 4.2E-48 427.4 23.4 156 397-581 1620-1780(2890)
18 KOG0261|consensus 100.0 5.9E-39 1.3E-43 352.9 4.3 189 11-203 358-589 (1386)
19 KOG0262|consensus 100.0 9.8E-38 2.1E-42 350.9 4.7 192 11-203 448-693 (1640)
20 PRK14977 bifunctional DNA-dire 100.0 1.6E-37 3.5E-42 370.2 6.8 196 10-209 328-572 (1321)
21 TIGR02390 RNA_pol_rpoA1 DNA-di 100.0 3.1E-36 6.6E-41 351.3 7.3 197 10-211 314-550 (868)
22 PRK08566 DNA-directed RNA poly 100.0 4.1E-36 8.9E-41 351.2 6.4 185 9-198 317-541 (882)
23 KOG0260|consensus 100.0 4.5E-36 9.8E-41 336.2 4.7 208 9-220 334-584 (1605)
24 smart00663 RPOLA_N RNA polymer 100.0 1.6E-33 3.4E-38 290.0 8.1 150 9-167 109-295 (295)
25 PF00623 RNA_pol_Rpb1_2: RNA p 100.0 1.6E-32 3.4E-37 261.2 0.5 123 11-133 3-153 (166)
26 PF00623 RNA_pol_Rpb1_2: RNA p 99.9 1.7E-27 3.7E-32 226.7 1.9 79 526-604 1-79 (166)
27 CHL00018 rpoC1 RNA polymerase 99.9 9.7E-26 2.1E-30 249.8 3.0 148 10-172 374-545 (663)
28 PRK02625 rpoC1 DNA-directed RN 99.9 2.3E-25 5.1E-30 244.5 2.1 148 9-172 352-524 (627)
29 TIGR02387 rpoC1_cyan DNA-direc 99.9 3.5E-25 7.7E-30 242.8 2.3 147 9-173 345-518 (619)
30 TIGR02386 rpoC_TIGR DNA-direct 99.9 5.6E-24 1.2E-28 248.7 4.7 141 10-172 327-498 (1140)
31 PRK00566 DNA-directed RNA poly 99.9 5.6E-24 1.2E-28 249.0 2.1 149 9-173 334-507 (1156)
32 PRK14906 DNA-directed RNA poly 99.9 2.9E-23 6.3E-28 243.3 5.2 141 10-171 423-593 (1460)
33 PRK09603 bifunctional DNA-dire 99.9 1.3E-22 2.9E-27 247.7 3.6 152 10-177 1734-1910(2890)
34 COG0086 RpoC DNA-directed RNA 99.9 2.8E-22 6.1E-27 231.1 5.7 145 10-171 288-459 (808)
35 PRK14844 bifunctional DNA-dire 99.8 1.2E-21 2.6E-26 238.7 3.7 149 10-173 1778-1950(2836)
36 PF04983 RNA_pol_Rpb1_3: RNA p 64.3 1.1 2.3E-05 42.5 -2.2 29 141-173 1-29 (158)
37 PF14952 zf-tcix: Putative tre 42.1 13 0.00029 27.4 1.0 14 308-321 10-23 (44)
38 KOG0856|consensus 26.7 27 0.00058 32.4 0.6 16 171-193 103-118 (146)
39 PF02044 Bombesin: Bombesin-li 25.3 23 0.00049 19.6 -0.1 7 522-528 7-13 (14)
No 1
>KOG0262|consensus
Probab=100.00 E-value=4.6e-114 Score=962.42 Aligned_cols=498 Identities=36% Similarity=0.609 Sum_probs=420.2
Q ss_pred ccccCcce-EEEecCChHHHHhhcccccccccccCCCCCccccCccCCCCCccccCCCccCCCCCCccccCCcccccCCC
Q psy16766 116 RQEVVPEI-LKLKYYTDQEVKQLSVVKVFSPITFNSLGHTIPGGLYDLAMGPISERGDPCTTCGNNYTKCKGHIGHIELP 194 (621)
Q Consensus 116 ~p~~~~~g-~ef~~~s~eei~~lSv~~I~~~~~~d~~g~Pi~ggl~D~~lG~~~~~~~~C~tC~~~~~~C~GhfGhI~L~ 194 (621)
+|+..|-. ++|++|+++||+++||++|++|.+||+.|+|+.|||||++||+ .+..+.|.||++...+||||||||+||
T Consensus 7 ~pv~~~~~~v~Fg~yt~~ei~klSv~kIt~p~~~D~lGhPi~GGLYDl~LGp-~~~~~~C~TC~~~~~~CPGH~GHIeL~ 85 (1640)
T KOG0262|consen 7 MPVMSFQPSVSFGSYTDQEIRKLSVKKITNPITFDNLGHPIPGGLYDLALGP-LDNSDVCSTCNQDELNCPGHMGHIELP 85 (1640)
T ss_pred CcccccccceeeeccCHHHHhhcceeEecCceeecccCCCCCCcccccccCC-ccchhhhhhhcchhhcCCCccCeeeec
Confidence 57766655 9999999999999999999999999999999999999999997 788899999999999999999999999
Q ss_pred cccccchhhHhHHHHHhhccccccCcccCcchHHHHHHHHhhccccchHHHHhHHHhh--hhccccCcChHHHHHHHHHH
Q psy16766 195 VPVINTLFFRDVQLLLKLSCFLCHKINIPATSQLLFINQIKLLDAGYVTQAKDLEETL--FNEENLRLHPAQLVQLVDSH 272 (621)
Q Consensus 195 ~Pv~hp~f~~~v~~lL~~iC~~C~~l~~~~~~~~~~~~~Lkll~~G~l~~a~~L~~~~--~~~~~~~~~~~~~~~~~~~~ 272 (621)
.|||||+||+.+|++||+.|++||+|+++..+.+.+.+||++++.|++.+|.+|+.+. ..+++.+.+..++......+
T Consensus 86 ~pvynPlfF~~ly~lLr~sCl~Chhf~~k~~~v~~~~cqLrll~~G~i~ea~~Le~i~~~~~~d~~d~~~~~~k~~~~~~ 165 (1640)
T KOG0262|consen 86 VPVYNPLFFDFLYNLLRGSCLFCHHFRCKNVDVHILFCQLRLLEYGLIEEAEDLESITSETVEDNEDESLNEIKSCRAQY 165 (1640)
T ss_pred ccccCHHHHHHHHHHHHHHHHhhhhcccCcHHHHHHHHHHHHHHhchHHHHHHHHHhhhhhhccCcchhHHHHHhhhhhh
Confidence 9999999999999999999999999999999999999999999999999999999987 46666654444444444445
Q ss_pred HHHHHhhccccccCCCCcchHHHHHHHHHHHHhhh-cCCCCCCCCCCCceeecccceEEEEeeccc--------------
Q psy16766 273 VQSILAHGTKICDINDYKGGEELRSAFVAQVLSRH-VKRKCIFCATPINAISYQQRKIIKSFKIDK-------------- 337 (621)
Q Consensus 273 ~~~~~~~~~~~~~~~~~k~~~~~r~~i~~~~~~~~-~~kkC~~C~~~~p~irk~~~~~i~~~~~~~-------------- 337 (621)
+.+.+.+.........+++..+.+++++.+|++.+ ..++|+||+..+|.+||+++.++++.....
T Consensus 166 v~~~i~~~~~~~~~~~t~~~~~~~~~lv~~f~k~~l~~kkC~~C~~~~p~~rk~~~~kv~~~~~~~~~~~~~~~~~~i~~ 245 (1640)
T KOG0262|consen 166 VTEAISEALLDKSEPNTKNSTELKKKLVTAFLKNALSRKKCPRCKHSNPKLRKDGFRKVFIDALSSKVGANVIRGAKIKK 245 (1640)
T ss_pred ccHHHHHHhhcCCCccchhhHHHHHHHHHHHHHHhhccccCCcccCCCchhhccccceeeeehhcccccccchhheeeeh
Confidence 44444433333333347788999999999999988 889999999999999999999998632210
Q ss_pred ccc-chhhhh----hhccc--chh---------hhhhccccccCHHHHHHHHhhcchhhHHHHhhhcccCCC-cccCCCC
Q psy16766 338 DNL-DQSLDK----SLNKS--SNQ---------IIRKREQGYVMASEVEADFKKLWTNEHLFLKCLIPVLDT-TKELIAT 400 (621)
Q Consensus 338 ~~~-~~~~d~----~~e~~--~~~---------~~~~~~~~~l~p~ev~~~lk~i~~~d~~~L~~l~~~~~~-~~~~~~~ 400 (621)
+.. .+.+|+ +.|.. +.+ +.......||+|.|||+||+.||.+|.++|..||+..+. .+...|.
T Consensus 246 ~~~~~~~~d~~~~G~~E~~~~g~d~~e~~~~~~~~~~t~~~~l~~tevR~~l~~lf~ne~~~l~~lf~l~~~~~~k~~p~ 325 (1640)
T KOG0262|consen 246 DVGSKGFEDSGIDGSNEVEEDGKDLFEKSTEPAEFEKTGKKYLLPTEVREHLRDLFKNEGELLSYLFPLWDSGSGKIDPS 325 (1640)
T ss_pred hcccccccccccCCccccccccccccccccccccccccccccccHHHHHHHHHHHHhhhHHHHHHhhccccccccccCcc
Confidence 000 001111 00100 000 011123469999999999999999999999999993331 1234578
Q ss_pred ceEEEEeeecCCCCCccccccCCCccccchhHHHHHHHHHHHHHHHHHHHhhhhchhhhhHHHhhcccCCchhhHHHHHH
Q psy16766 401 DIMFIRSLVVPPNNLRPLSMEQMPPVEHSRNKLYQSILYSCGSLKSVIMAMKNKEQSDLLSEALKGIRGDTLNNKLQNSW 480 (621)
Q Consensus 401 d~ffl~~lpVpP~~~RP~~~~~~~~~ed~~t~~l~~Il~~N~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~l~~~w 480 (621)
|+|||+.|||||++|||++++||...||+||..|.+||+.|..|++++..+. +.-....+..++..+| +.++++++|
T Consensus 326 d~FFld~l~VpPtrfRP~s~~gd~~~en~Qt~~L~kVle~s~~i~~~~~~m~-~kl~~~~k~~l~~~~g--~~~kl~~aw 402 (1640)
T KOG0262|consen 326 DMFFLDNLLVPPTRFRPPSMLGDEVHENPQTLNLNKVLESSVLIRKLLKDMK-GKLDEELKLILERLRG--IFSKLINAW 402 (1640)
T ss_pred ceeeeeccccCCcccCCchhcchhhhcChHHHHHHHHHHHHHHHHHHHHHhh-hccCHHHHHHHHhhhh--HHHHHHHHH
Confidence 8999999999999999999999999999999999999999999999886655 3222222445566677 678999999
Q ss_pred HHHHHHHHHhhcccccC-CCCCCCCCccchHHhhccCccccccccCCCccCcccceeecCCCCCccccccchHHHHhhCC
Q psy16766 481 HELQYNVDLLMDAKLNI-NKTTGAHQIDGLKQMLDGKTGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLT 559 (621)
Q Consensus 481 ~~LQ~~V~~~~d~~~~~-~~~~~~k~~~gi~q~L~gKeG~fR~nlmGKRVnfsaRSVIsPDP~l~idevGvP~~fAk~LT 559 (621)
.+||.+||.+||++ + ++.+... .+||||+||||||+||+|||||||||||||||||||||++||||||+.||++||
T Consensus 403 ~~LQ~~vn~lfDs~--~~~k~~r~~-~pGikQiLEKKeGLFRkhMMGKRVN~AaRSVIsPDPnI~tnEIGIP~vFA~KLT 479 (1640)
T KOG0262|consen 403 LQLQASVNVLFDSK--MASKWSRDS-PPGIKQILEKKEGLFRKHMMGKRVNYAARSVISPDPNIETNEIGIPPVFAKKLT 479 (1640)
T ss_pred HHHHHHHHHHhccc--cccccccCC-CchHHHHHHHhhhhHHHHhhccccchhhccccCCCCCccccccCCchHHHhhcc
Confidence 99999999999999 6 4444443 489999999999999999999999999999999999999999999999999999
Q ss_pred cCcccCHHHHHHHHHHHHcCCCCCCcceEEEcCCCcEEEeCCCchHhHHHHHHHhcCCCCC
Q psy16766 560 YPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRISSSQAVQRESLAKRLITPEGN 620 (621)
Q Consensus 560 ~PE~VT~~Ni~~Lr~lV~NGp~~~PGA~~i~~~~G~~~~L~~~~~~~R~~~A~~L~~~~~~ 620 (621)
||||||+||+++||++|+|||++||||+||+++||+++.|..++.++|+|+|+|||||+.|
T Consensus 480 yPepVt~~NV~elr~aViNGP~~hPGA~~iqd~dg~~t~l~~~~~~qR~alA~qLLtpst~ 540 (1640)
T KOG0262|consen 480 YPEPVTPWNVNELRKAVINGPDVHPGATYIQDEDGTLTLLSPMTDEQREALANQLLTPSTG 540 (1640)
T ss_pred CCCcCCcccHHHHHHHHhcCCCCCCCcceeecCCCceeecCCCCHHHHHHHHHHhhccccC
Confidence 9999999999999999999999999999999999999999999999999999999998765
No 2
>PRK08566 DNA-directed RNA polymerase subunit A'; Validated
Probab=100.00 E-value=1.5e-94 Score=841.15 Aligned_cols=393 Identities=29% Similarity=0.490 Sum_probs=339.2
Q ss_pred cccCcceEEEecCChHHHHhhcccccccccccCCCCCccccCccCCCCCccccCCCccCCCCCCccccCCcccccCCCcc
Q psy16766 117 QEVVPEILKLKYYTDQEVKQLSVVKVFSPITFNSLGHTIPGGLYDLAMGPISERGDPCTTCGNNYTKCKGHIGHIELPVP 196 (621)
Q Consensus 117 p~~~~~g~ef~~~s~eei~~lSv~~I~~~~~~d~~g~Pi~ggl~D~~lG~~~~~~~~C~tC~~~~~~C~GhfGhI~L~~P 196 (621)
+.+.+++++|+++|+|||+++||++|+++.+||..|+|+.||++|+|||+ .++...|.|||++..+||||||||+|+.|
T Consensus 5 ~~~~I~~I~F~~~S~eEI~klSv~~It~~~~~d~~g~P~~gGL~D~RLG~-~~~~~~C~TCg~~~~~CPGHFGhIeL~~P 83 (882)
T PRK08566 5 IPKRIGSIKFGLLSPEEIRKMSVTKIITADTYDDDGYPIDGGLMDPRLGV-IDPGLRCKTCGGRAGECPGHFGHIELARP 83 (882)
T ss_pred CceeeeeEEEecCCHHHHHHhCeEEEecccccCCCCCcCCCCCCCcccCC-CCCCCCCCCCCCCCCcCCCcceEEecccc
Confidence 45779999999999999999999999999999999999999999999999 78889999999999999999999999999
Q ss_pred cccchhhHhHHHHHhhccccccCcccCcchHHHHHHHHhhccccchHHHHhHHHhhhhccccCcChHHHHHHHHHHHHHH
Q psy16766 197 VINTLFFRDVQLLLKLSCFLCHKINIPATSQLLFINQIKLLDAGYVTQAKDLEETLFNEENLRLHPAQLVQLVDSHVQSI 276 (621)
Q Consensus 197 v~hp~f~~~v~~lL~~iC~~C~~l~~~~~~~~~~~~~Lkll~~G~l~~a~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 276 (621)
||||+||+.+++||+|+|++||++++++++.+.|..+++.++...
T Consensus 84 Vfhpgf~~~v~~iL~~iC~~C~rll~~~~~~~~~~~~l~~~~~~~----------------------------------- 128 (882)
T PRK08566 84 VIHVGFAKLIYKLLRATCRECGRLKLTEEEIEEYLEKLERLKEWG----------------------------------- 128 (882)
T ss_pred ccchhHHHHHHHHHHHhhhhhCceeccccchHHHHHHHhchhhhh-----------------------------------
Confidence 999999999999999999999999999988888877777543100
Q ss_pred HhhccccccCCCCcchHHHHHHHHHHHHhhh-cCCCCCCCCCCCceeecccceEEEEeeccccccchhhhhhhcccchhh
Q psy16766 277 LAHGTKICDINDYKGGEELRSAFVAQVLSRH-VKRKCIFCATPINAISYQQRKIIKSFKIDKDNLDQSLDKSLNKSSNQI 355 (621)
Q Consensus 277 ~~~~~~~~~~~~~k~~~~~r~~i~~~~~~~~-~~kkC~~C~~~~p~irk~~~~~i~~~~~~~~~~~~~~d~~~e~~~~~~ 355 (621)
..++++++++++.+ +.++|+||++.+|+|+++...... ...+
T Consensus 129 -----------------~~~~~l~k~i~k~~k~~~~C~~Cg~~~~ki~~~~~~~~~--~~~~------------------ 171 (882)
T PRK08566 129 -----------------SLADDLIKEVKKEAAKRMVCPHCGEKQYKIKFEKPTTFY--EERK------------------ 171 (882)
T ss_pred -----------------hhHHHHHHHHHHHhcCCCCCCCcCCCCceEEEecceeEE--EecC------------------
Confidence 00124556666665 557899999999999987543221 1000
Q ss_pred hhhccccccCHHHHHHHHhhcchhhHHHHhhhcccCCCcccCCCCceEEEEeeecCCCCCccccccCC-CccccchhHHH
Q psy16766 356 IRKREQGYVMASEVEADFKKLWTNEHLFLKCLIPVLDTTKELIATDIMFIRSLVVPPNNLRPLSMEQM-PPVEHSRNKLY 434 (621)
Q Consensus 356 ~~~~~~~~l~p~ev~~~lk~i~~~d~~~L~~l~~~~~~~~~~~~~d~ffl~~lpVpP~~~RP~~~~~~-~~~ed~~t~~l 434 (621)
....+|+|.+|+++|++||++|+++|++- + ...+|+||||++|||||+++||++.+++ ...|||+|.+|
T Consensus 172 ---~~~~~L~p~~V~~ilk~I~~eD~~lLg~~-----~--~~~~Pe~~il~~lPVpP~~iRPsv~~~~g~~~eDDLT~~L 241 (882)
T PRK08566 172 ---EGLVKLTPSDIRERLEKIPDEDLELLGIN-----P--EVARPEWMVLTVLPVPPVTVRPSITLETGQRSEDDLTHKL 241 (882)
T ss_pred ---CCceeCCHHHHHHHHHhCCHHHHHHhCCC-----C--CCCCcceeEEeeeecCCCCCcCcEEeCCCcccCchHHHHH
Confidence 12358999999999999999999999741 1 1246899999999999999999999965 58899999999
Q ss_pred HHHHHHHHHHHHHHHHhhhhchhhhhHHHhhcccCCchhhHHHHHHHHHHHHHHHhhcccccCCCCC-----CCCCccch
Q psy16766 435 QSILYSCGSLKSVIMAMKNKEQSDLLSEALKGIRGDTLNNKLQNSWHELQYNVDLLMDAKLNINKTT-----GAHQIDGL 509 (621)
Q Consensus 435 ~~Il~~N~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~l~~~w~~LQ~~V~~~~d~~~~~~~~~-----~~k~~~gi 509 (621)
.+||+.|+.|++.+.. +. ....+.+.|..||.+|+.|+||+ .++.+ .+++.+||
T Consensus 242 ~~II~~N~~Lk~~~~~---g~----------------~~~~~~~~~~~LQ~~v~~~~d~~--~~~~~~~~~~~~~~~~~i 300 (882)
T PRK08566 242 VDIIRINQRLKENIEA---GA----------------PQLIIEDLWELLQYHVTTYFDNE--IPGIPPARHRSGRPLKTL 300 (882)
T ss_pred HHHHHHHHHHHHHHHc---CC----------------cHHHHHHHHHHHHHHHHHHhcCC--ccCCcccccCCCCCccch
Confidence 9999999999986532 11 12356789999999999999999 54421 23567899
Q ss_pred HHhhccCccccccccCCCccCcccceeecCCCCCccccccchHHHHhhCCcCcccCHHHHHHHHHHHHcCCCCCCcceEE
Q psy16766 510 KQMLDGKTGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMI 589 (621)
Q Consensus 510 ~q~L~gKeG~fR~nlmGKRVnfsaRSVIsPDP~l~idevGvP~~fAk~LT~PE~VT~~Ni~~Lr~lV~NGp~~~PGA~~i 589 (621)
+|||+||+||||+|||||||||||||||||||||++||||||..||++|||||+||+||+++||++|+|||+.||||+||
T Consensus 301 ~~~l~gK~G~fR~nl~GKRvd~s~RsVI~pdp~l~~~evGvP~~~A~~Lt~pe~v~~~N~~~l~~~v~ng~~~~pga~~i 380 (882)
T PRK08566 301 AQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNGPEKHPGANYV 380 (882)
T ss_pred HHhcccCCCccccccccccccCcCCceeeCCCCCcCCeeeCcHHHHHhCCCCeEEchhhHHHHHHHHHcCCCcCCCceEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EcCCCcEEEeCCCchHhHHHHHHHhcC
Q psy16766 590 QNEDGSVVRISSSQAVQRESLAKRLIT 616 (621)
Q Consensus 590 ~~~~G~~~~L~~~~~~~R~~~A~~L~~ 616 (621)
++++|+++.|. ..+|+++|++|..
T Consensus 381 ~~~~g~~~~l~---~~~~~~~~~~l~~ 404 (882)
T PRK08566 381 IRPDGRRIKLT---DKNKEELAEKLEP 404 (882)
T ss_pred EcCCCceeeeh---hhhHHHHHHhccc
Confidence 99999998884 3579999998864
No 3
>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=3.1e-94 Score=836.32 Aligned_cols=392 Identities=30% Similarity=0.542 Sum_probs=335.1
Q ss_pred cCcceEEEecCChHHHHhhcccccccccccCCCCCccccCccCCCCCccccCCCccCCCCCCccccCCcccccCCCcccc
Q psy16766 119 VVPEILKLKYYTDQEVKQLSVVKVFSPITFNSLGHTIPGGLYDLAMGPISERGDPCTTCGNNYTKCKGHIGHIELPVPVI 198 (621)
Q Consensus 119 ~~~~g~ef~~~s~eei~~lSv~~I~~~~~~d~~g~Pi~ggl~D~~lG~~~~~~~~C~tC~~~~~~C~GhfGhI~L~~Pv~ 198 (621)
++|++++|+++|+|||+++||++|+++.+||..|+|+.||++|+|||+ .++...|.|||++..+||||||||+|+.|||
T Consensus 2 ~~I~~I~F~~~S~eEI~k~Sv~~It~~~~~d~~g~P~~gGL~D~RLG~-~~~~~~C~TCg~~~~~CpGHFGhIeL~~PVf 80 (868)
T TIGR02390 2 KKIGSIKFGLLSPEEIRKMSVVEVVTADTYDDDGYPIEGGLMDPRLGV-IEPGLRCKTCGGKVGECPGHFGHIELARPVV 80 (868)
T ss_pred ceeeEEEEeCCCHHHHHHhCeeEEecccccCCCCCcCCCCccCcccCC-CCCCCCCCCCCCCCCcCCCcceEEecccccc
Confidence 468999999999999999999999999999999999999999999999 7888899999999999999999999999999
Q ss_pred cchhhHhHHHHHhhccccccCcccCcchHHHHHHHHhhccccchHHHHhHHHhhhhccccCcChHHHHHHHHHHHHHHHh
Q psy16766 199 NTLFFRDVQLLLKLSCFLCHKINIPATSQLLFINQIKLLDAGYVTQAKDLEETLFNEENLRLHPAQLVQLVDSHVQSILA 278 (621)
Q Consensus 199 hp~f~~~v~~lL~~iC~~C~~l~~~~~~~~~~~~~Lkll~~G~l~~a~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 278 (621)
||+||+.+++||+|+|++|+|+++++++.+.|..+++.++...
T Consensus 81 hpgf~~~i~kiL~~vC~~C~rll~~~~~~~~~~~~l~~~~~~~------------------------------------- 123 (868)
T TIGR02390 81 HVGFAKEIYKILRATCRKCGRITLTEEEIEQYLEKINKLKEEG------------------------------------- 123 (868)
T ss_pred chhHHHHHHHHHHHHhhhcCceeeCccccHHHHHHHHhcccch-------------------------------------
Confidence 9999999999999999999999999888777776665433100
Q ss_pred hccccccCCCCcchHHHHHHHHHHHHhhh-cCCCCCCCCCCCceeecccceEEEEeeccccccchhhhhhhcccchhhhh
Q psy16766 279 HGTKICDINDYKGGEELRSAFVAQVLSRH-VKRKCIFCATPINAISYQQRKIIKSFKIDKDNLDQSLDKSLNKSSNQIIR 357 (621)
Q Consensus 279 ~~~~~~~~~~~k~~~~~r~~i~~~~~~~~-~~kkC~~C~~~~p~irk~~~~~i~~~~~~~~~~~~~~d~~~e~~~~~~~~ 357 (621)
...++++++++++.+ ..++|+||++.+|.|++.+...++ ...+
T Consensus 124 --------------~~~~~~l~~~i~~~~~~~~~C~~Cg~~~p~ir~~~~~~~~--~~~~-------------------- 167 (868)
T TIGR02390 124 --------------GDLASTLIEKIVKEAAKRMKCPHCGEEQKKIKFEKPTYFY--EEGK-------------------- 167 (868)
T ss_pred --------------hhhHHHHHHHHHHHhhcCCCCCCCCCcCceEEEeeeeeee--eccC--------------------
Confidence 001134555566555 557899999999999987532211 1000
Q ss_pred hccccccCHHHHHHHHhhcchhhHHHHhhhcccCCCcccCCCCceEEEEeeecCCCCCccccccCC-CccccchhHHHHH
Q psy16766 358 KREQGYVMASEVEADFKKLWTNEHLFLKCLIPVLDTTKELIATDIMFIRSLVVPPNNLRPLSMEQM-PPVEHSRNKLYQS 436 (621)
Q Consensus 358 ~~~~~~l~p~ev~~~lk~i~~~d~~~L~~l~~~~~~~~~~~~~d~ffl~~lpVpP~~~RP~~~~~~-~~~ed~~t~~l~~ 436 (621)
.....|+|.+|+++|++||++|+++|++ .+ ...+|+||||++|||||+++||++.+++ ...|||+|++|.+
T Consensus 168 -~~~~~L~p~~v~~ilk~I~~eD~~lLG~-----~p--~~~~Pe~~ilt~LPVPP~~iRPsv~~~~g~~~EDDLT~~L~~ 239 (868)
T TIGR02390 168 -EGDVKLTPSEIRERLEKIPDEDAELLGI-----NP--KVARPEWMVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVD 239 (868)
T ss_pred -CCCeecCHHHHHHHHHhCCHHHHHHhCC-----CC--CCCCcceeeEeccccCCCCCcCeEEeCCCcccCChHHHHHHH
Confidence 1135799999999999999999999974 11 1236899999999999999999999975 5889999999999
Q ss_pred HHHHHHHHHHHHHHhhhhchhhhhHHHhhcccCCchhhHHHHHHHHHHHHHHHhhcccccCCCCC-----CCCCccchHH
Q psy16766 437 ILYSCGSLKSVIMAMKNKEQSDLLSEALKGIRGDTLNNKLQNSWHELQYNVDLLMDAKLNINKTT-----GAHQIDGLKQ 511 (621)
Q Consensus 437 Il~~N~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~l~~~w~~LQ~~V~~~~d~~~~~~~~~-----~~k~~~gi~q 511 (621)
||+.|+.|++.+.. +. ....+.+.|..||.+|+.|||++ .++.+ .+++.+||+|
T Consensus 240 II~~N~~Lk~~~~~---g~----------------~~~~~~~~~~~LQ~~v~~~~d~~--~~~~~~~~~~~~~~~~~i~~ 298 (868)
T TIGR02390 240 IIRINQRLKENIEA---GA----------------PQLIIEDLWELLQYHVATYFDNE--LPGIPPARHRSGRPLKTLAQ 298 (868)
T ss_pred HHHHHHHHHHHHHc---CC----------------chhhhHHHHHHHHHHHHHHHcCC--CCCCCccccCCCCCchhhHh
Confidence 99999999886532 11 12346678999999999999998 54321 2356789999
Q ss_pred hhccCccccccccCCCccCcccceeecCCCCCccccccchHHHHhhCCcCcccCHHHHHHHHHHHHcCCCCCCcceEEEc
Q psy16766 512 MLDGKTGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQN 591 (621)
Q Consensus 512 ~L~gKeG~fR~nlmGKRVnfsaRSVIsPDP~l~idevGvP~~fAk~LT~PE~VT~~Ni~~Lr~lV~NGp~~~PGA~~i~~ 591 (621)
||+||+||||+|||||||||||||||||||||++||||||..||++|||||+||+||+++||++|+|||+.||||+||++
T Consensus 299 ~l~gK~G~~R~nl~GKRvd~s~RsVI~pdp~l~~~evGvP~~~A~~Lt~pe~Vt~~N~~~l~~lv~ng~~~~pga~~i~~ 378 (868)
T TIGR02390 299 RLKGKEGRFRGNLSGKRVNFSARTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVLNGPDSWPGANYVIR 378 (868)
T ss_pred hhcccccccccccccccccccCCceeeCCCCCcCCeeeCcHHHHHhCCCCeEEehhhHHHHHHHHHcCCccCCCceEEEc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCcEEEeCCCchHhHHHHHHHhcC
Q psy16766 592 EDGSVVRISSSQAVQRESLAKRLIT 616 (621)
Q Consensus 592 ~~G~~~~L~~~~~~~R~~~A~~L~~ 616 (621)
++|+++.|... +|.++|++|..
T Consensus 379 ~~g~~~~l~~~---~~~~~~~~l~~ 400 (868)
T TIGR02390 379 PDGRRIKIRDE---NKEELAERLEP 400 (868)
T ss_pred CCCcEEechhh---hHHHHHhhccc
Confidence 99999999876 48899998853
No 4
>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Probab=100.00 E-value=5.5e-94 Score=851.94 Aligned_cols=406 Identities=26% Similarity=0.470 Sum_probs=330.1
Q ss_pred ccccCcceEEEecCChHHHHhhcccccccccccCCCCCccccCccCCCCCccccCCCccCCCCCCccccCCcccccCCCc
Q psy16766 116 RQEVVPEILKLKYYTDQEVKQLSVVKVFSPITFNSLGHTIPGGLYDLAMGPISERGDPCTTCGNNYTKCKGHIGHIELPV 195 (621)
Q Consensus 116 ~p~~~~~g~ef~~~s~eei~~lSv~~I~~~~~~d~~g~Pi~ggl~D~~lG~~~~~~~~C~tC~~~~~~C~GhfGhI~L~~ 195 (621)
.+.+++++++|+++|||||+++||++|+++.+||..|+|+.||++|||||+ .++...|.||+++..+||||||||||+.
T Consensus 4 ~~~~~I~~I~Fg~~S~eeIrk~Sv~~It~~~~~d~~g~P~~gGl~DprlG~-~d~~~~C~TCg~~~~~CpGHFGHIELa~ 82 (1321)
T PRK14977 4 LAVKAIDGIIFGLISPADARKIGFAEITAPEAYDEDGLPVQGGLLDGRLGT-IEPGQKCLTCGNLAANCPGHFGHIELAE 82 (1321)
T ss_pred CccceeceEEEecCCHHHHHHhCeEEEecccccCCCCCcCCCCCCccccCC-CCCCCCCCCCCCCCCcCCCeeEEEEccC
Confidence 356789999999999999999999999999999999999999999999999 7888999999999999999999999999
Q ss_pred ccccchhhHhHHHHHhhccccccCcccCcchHHHHHHHHhhccccchHHHHhHHHhhhhccccCcChHHHHHHHHHHHHH
Q psy16766 196 PVINTLFFRDVQLLLKLSCFLCHKINIPATSQLLFINQIKLLDAGYVTQAKDLEETLFNEENLRLHPAQLVQLVDSHVQS 275 (621)
Q Consensus 196 Pv~hp~f~~~v~~lL~~iC~~C~~l~~~~~~~~~~~~~Lkll~~G~l~~a~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~ 275 (621)
|||||+||+.+++||+|+|++|||+++++++.+.|....+ +.++... . ....+.
T Consensus 83 PVfHpgf~k~i~~iLr~iC~~C~rlll~~~~~~~~~~~~~---------~~~~~~~--------~----~~~~~~----- 136 (1321)
T PRK14977 83 PVIHIAFIDNIKDLLNSTCHKCAKLKLPQEDLNVFKLIEE---------AHAAARD--------I----PEKRID----- 136 (1321)
T ss_pred CceecccHHHHHHHHHHHHHHhchhhcCcccHHHHHHHHH---------Hhhhccc--------c----hhhhhh-----
Confidence 9999999999999999999999999999988876631111 1000000 0 000000
Q ss_pred HHhhccccccCCCCcchHHHHHHHHHHHHhhh-cCCCCCCCCCCCceeecccceEEEEeeccccccchhhhhhhcccchh
Q psy16766 276 ILAHGTKICDINDYKGGEELRSAFVAQVLSRH-VKRKCIFCATPINAISYQQRKIIKSFKIDKDNLDQSLDKSLNKSSNQ 354 (621)
Q Consensus 276 ~~~~~~~~~~~~~~k~~~~~r~~i~~~~~~~~-~~kkC~~C~~~~p~irk~~~~~i~~~~~~~~~~~~~~d~~~e~~~~~ 354 (621)
..+..++.......+ +.++|+||++.+|.|++.....+... .
T Consensus 137 -----------------~~~~~~~~~~~~~~~k~~~~C~~C~~~~~~i~~~~~~~~~~~---~----------------- 179 (1321)
T PRK14977 137 -----------------DEIIEEVRDQVKVYAKKAKECPHCGAPQHELEFEEPTIFIEK---T----------------- 179 (1321)
T ss_pred -----------------HHHHHHHHhhhhhhhccCCcCCCCCCCCCeEEEeeceeeeec---c-----------------
Confidence 000000110000112 56789999999999987643321110 0
Q ss_pred hhhhccccccCHHHHHHHHhhcchhhHHHHhhhcccCCCcccCCCCceEEEEeeecCCCCCccccccCC-CccccchhHH
Q psy16766 355 IIRKREQGYVMASEVEADFKKLWTNEHLFLKCLIPVLDTTKELIATDIMFIRSLVVPPNNLRPLSMEQM-PPVEHSRNKL 433 (621)
Q Consensus 355 ~~~~~~~~~l~p~ev~~~lk~i~~~d~~~L~~l~~~~~~~~~~~~~d~ffl~~lpVpP~~~RP~~~~~~-~~~ed~~t~~ 433 (621)
.....+|+|.+|+++|++||++|+++|++ ++ ...+|+||||++|||||+++||++.+++ ...|||+|.+
T Consensus 180 ---~~~~~~l~p~~v~~if~~i~~~d~~llg~-----~~--~~~~p~~~il~~lpVpP~~~RP~v~~~~~~~~eddlt~~ 249 (1321)
T PRK14977 180 ---EIEEHRLLPIEIRDIFEKIIDDDLELIGF-----DP--KKARPEWAVLQAFLVPPLTARPSIILETGERSEDDLTHI 249 (1321)
T ss_pred ---cccCcccCHHHHHHHHHhcCHHHHHHhCC-----CC--CCCCcceEEEeccccCCCCCcCcEEeCCCcccCCcHHHH
Confidence 01125799999999999999999999983 11 1347999999999999999999999975 5889999999
Q ss_pred HHHHHHHHHHHHHHHHHhhhhchhhhhHHHhhcccCCchhhHHHHHHHHHHHHHHHhhcccccCCCCC------CCCCcc
Q psy16766 434 YQSILYSCGSLKSVIMAMKNKEQSDLLSEALKGIRGDTLNNKLQNSWHELQYNVDLLMDAKLNINKTT------GAHQID 507 (621)
Q Consensus 434 l~~Il~~N~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~l~~~w~~LQ~~V~~~~d~~~~~~~~~------~~k~~~ 507 (621)
|.+||+.|+.|++.... +. ....+.+.|..||.+|++||||+ .++.+ .+++.+
T Consensus 250 l~~Ii~~N~~l~~~~~~---g~----------------~~~~~~~~~~~LQ~~v~~~~dn~--~~~~~~~~~~~~~rp~k 308 (1321)
T PRK14977 250 LVDIIKANQKLKESKDA---GA----------------PPLIVEDEVDHLQYHTSTFFDNA--TAGIPQAHHKGSGRPLK 308 (1321)
T ss_pred HHHHHHHHHHHHHHHHc---CC----------------cHHHHHHHHHHHHHHHHHHhccc--ccCCCccccccCCCchh
Confidence 99999999999986532 11 12457789999999999999999 55432 235678
Q ss_pred chHHhhccCccccccccCCCccCcccceeecCCCCCccccccchHHHHhhCCcCcccCHHHHHHHHHHHHcCCCCCCcce
Q psy16766 508 GLKQMLDGKTGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGAN 587 (621)
Q Consensus 508 gi~q~L~gKeG~fR~nlmGKRVnfsaRSVIsPDP~l~idevGvP~~fAk~LT~PE~VT~~Ni~~Lr~lV~NGp~~~PGA~ 587 (621)
||+|||||||||||+|||||||||||||||||||||++||||||..||++|||||+||+||+++||++|+|||++||||+
T Consensus 309 ~i~qrLkgKeGrfR~nlmGKRVdfSaRtVIspDP~L~i~EVGvP~~iA~~LT~Pe~Vt~~Ni~~l~~lv~nG~~~~pGA~ 388 (1321)
T PRK14977 309 SLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKMKELVINGPDEFPGAN 388 (1321)
T ss_pred HHHHHhccccccccccccccccccccceeEeCCCCcccccccCHHHHHHhCCCCEEEchhhHHHHHHHHHcCCcccCCcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEcCCCcEEEeCCCchH---hHHHHHHHhcC
Q psy16766 588 MIQNEDGSVVRISSSQAV---QRESLAKRLIT 616 (621)
Q Consensus 588 ~i~~~~G~~~~L~~~~~~---~R~~~A~~L~~ 616 (621)
||++++|+++.|.+.+.. .+.++|++|..
T Consensus 389 ~i~~~~g~~~~l~~~~~~~~~~~~~~a~~L~~ 420 (1321)
T PRK14977 389 AIRKGDGTKIRLDFLEDKGKDALREAAEQLEI 420 (1321)
T ss_pred eEEcCCCceeeehhhhhccchhHHHHHHhccc
Confidence 999999999999764322 24568999874
No 5
>KOG0261|consensus
Probab=100.00 E-value=5.5e-88 Score=737.53 Aligned_cols=413 Identities=26% Similarity=0.430 Sum_probs=346.1
Q ss_pred cCcceEEEecCChHHHHhhcccccccccccCCCCC--ccccCccCCCCCccccCCCccCCCCCCccccCCcccccCCCcc
Q psy16766 119 VVPEILKLKYYTDQEVKQLSVVKVFSPITFNSLGH--TIPGGLYDLAMGPISERGDPCTTCGNNYTKCKGHIGHIELPVP 196 (621)
Q Consensus 119 ~~~~g~ef~~~s~eei~~lSv~~I~~~~~~d~~g~--Pi~ggl~D~~lG~~~~~~~~C~tC~~~~~~C~GhfGhI~L~~P 196 (621)
.++.+++|++.+|+||++.++++|.+...||.... |..+|..||+||+ +.+...|.|||++..+|+|||||++|++|
T Consensus 11 kki~~i~F~~~s~~ei~~~a~v~v~~~~LY~~~~~~~P~~~G~LD~rMGv-s~K~~~C~TCg~~la~C~GHfGy~~L~LP 89 (1386)
T KOG0261|consen 11 KKIKHIQFSILSPEEIRQQAEVEVSSKDLYDISTQRAPLPNGPLDPRMGV-SNKKDKCATCGEGLADCIGHFGYLKLALP 89 (1386)
T ss_pred ceeeeEeeccCCHHHHHhcceEEeeccchhhhhcccCCCcCCCcCcccCC-CCCCCccchhccchhhcccccceEeecce
Confidence 56899999999999999999999999999977633 9999999999999 88999999999999999999999999999
Q ss_pred cccchhhHhHHHHHhhccccccCcccCcchHHHHHHHHhhccccchHHHHhHHHhhhhccccCcChHHHHHHHHHHHHHH
Q psy16766 197 VINTLFFRDVQLLLKLSCFLCHKINIPATSQLLFINQIKLLDAGYVTQAKDLEETLFNEENLRLHPAQLVQLVDSHVQSI 276 (621)
Q Consensus 197 v~hp~f~~~v~~lL~~iC~~C~~l~~~~~~~~~~~~~Lkll~~G~l~~a~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 276 (621)
|||.|||+.+++||+|+|+.|+++++++++.+.|..+|+....+++.+
T Consensus 90 VFhiGyfk~ti~iLq~ICK~Cs~ilL~~~~k~~fl~~lr~p~~~~l~k-------------------------------- 137 (1386)
T KOG0261|consen 90 VFHIGYFKATIQILQCICKNCSSILLSEEDKRQFLKKLRNPGLDNLRK-------------------------------- 137 (1386)
T ss_pred eeeehhHHHHHHHHHHHHHhhhhhhcCHHHHHHHHHHhhCCCCChHHH--------------------------------
Confidence 999999999999999999999999999999999999888765444322
Q ss_pred HhhccccccCCCCcchHHHHHHHHHHHHhhh-cCCCCCCCCCCCceeecccc-eEEEEeecc--c--ccc-chhhhh---
Q psy16766 277 LAHGTKICDINDYKGGEELRSAFVAQVLSRH-VKRKCIFCATPINAISYQQR-KIIKSFKID--K--DNL-DQSLDK--- 346 (621)
Q Consensus 277 ~~~~~~~~~~~~~k~~~~~r~~i~~~~~~~~-~~kkC~~C~~~~p~irk~~~-~~i~~~~~~--~--~~~-~~~~d~--- 346 (621)
+.+.+.+..+| +...|.|||+.|+.|+|... .+|++.... + +.. .++.++
T Consensus 138 --------------------~~l~kri~~~CkK~~~C~hCg~~NG~VKK~~~~lkIiHd~~~~~~k~~~~~~~~~~~~~~ 197 (1386)
T KOG0261|consen 138 --------------------KALLKRIVAKCKKVNTCSHCGALNGTVKKAAALLKIIHDRFKLVKKSDPLVTNERGEFKT 197 (1386)
T ss_pred --------------------HHHHHHHHHHhhccccccccCCcCceeeccccceeEeeehhhccccccchhhhhHHHHHH
Confidence 23333444444 56789999999999999543 566542211 1 000 111111
Q ss_pred hhcccc-hhhhhhccccccCHHHHHHHHhhcchhhHHHHhhhcccCCCcccCCCCceEEEEeeecCCCCCccccccCC--
Q psy16766 347 SLNKSS-NQIIRKREQGYVMASEVEADFKKLWTNEHLFLKCLIPVLDTTKELIATDIMFIRSLVVPPNNLRPLSMEQM-- 423 (621)
Q Consensus 347 ~~e~~~-~~~~~~~~~~~l~p~ev~~~lk~i~~~d~~~L~~l~~~~~~~~~~~~~d~ffl~~lpVpP~~~RP~~~~~~-- 423 (621)
+.+..+ .+.........|+|..|+++|++|.+.|+++|++.. ...+|+.++++++||||.|+||++++++
T Consensus 198 ~~~~n~e~~~~~~~~~~~LnPl~vLnLFk~i~~~D~eLLg~~~-------~~~~P~~Li~t~~~vPP~cIRPSV~~~~k~ 270 (1386)
T KOG0261|consen 198 AISHNKELEGHLSSCCEELNPLVVLNLFKQIKEDDCELLGMDS-------EEGRPENLIITRVPVPPVCIRPSVMSEDKA 270 (1386)
T ss_pred HhhcCcchHhHHHHHHhhcChHHHHHHHhhCCccccceeeecc-------CcCCchheEEEeccCCccccccceeecCCC
Confidence 011111 111222344579999999999999999999998521 1236788899999999999999999988
Q ss_pred CccccchhHHHHHHHHHHHHHHHHHHHhhhhchhhhhHHHhhcccCCchhhHHHHHHHHHHHHHHHhhcccccCCCCC--
Q psy16766 424 PPVEHSRNKLYQSILYSCGSLKSVIMAMKNKEQSDLLSEALKGIRGDTLNNKLQNSWHELQYNVDLLMDAKLNINKTT-- 501 (621)
Q Consensus 424 ~~~ed~~t~~l~~Il~~N~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~l~~~w~~LQ~~V~~~~d~~~~~~~~~-- 501 (621)
+..|||+|+++.+||..|..|++.+.. | +....+++.|+.||.+|+.||+|. +++.+
T Consensus 271 gtnEDDlT~KltEIi~tn~vik~~~~~------------------g-~~~~~imE~Wd~lQl~~AlyINSE--l~g~~~~ 329 (1386)
T KOG0261|consen 271 GTNEDDLTMKLTEIILTNDVIKKHLSK------------------G-TPINLIMEDWDFLQLQVALYINSE--LPGIPIN 329 (1386)
T ss_pred CCCccchhhhhhhhhhHHHHHHHHhhc------------------C-CCchhhhhhhHHHHHHHHHhhccc--CCCCCCC
Confidence 589999999999999999999987632 2 124568899999999999999999 77643
Q ss_pred --CCCCccchHHhhccCccccccccCCCccCcccceeecCCCCCccccccchHHHHhhCCcCcccCHHHHHHHHHHHHcC
Q psy16766 502 --GAHQIDGLKQMLDGKTGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVING 579 (621)
Q Consensus 502 --~~k~~~gi~q~L~gKeG~fR~nlmGKRVnfsaRSVIsPDP~l~idevGvP~~fAk~LT~PE~VT~~Ni~~Lr~lV~NG 579 (621)
..++.+||.||||||+||||+||.|||||||+||||||||||.|||||||..+|+.|||||+||.+|+++||+||+||
T Consensus 330 ~~p~kp~RGf~QRLKGKqGRFRgNLSGKRVDFSGRTVISPDPNL~IdeVgVP~rvAkiLTfpE~Vt~~Ni~klr~lV~NG 409 (1386)
T KOG0261|consen 330 MAPKKPTRGFVQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDEVGVPIRVAKILTFPERVTRANIRKLRQLVRNG 409 (1386)
T ss_pred CCCCCchHHHHHHhcccCCceeccccCceeeccCceeeCCCCCcceeeccchHHHHHHhcchhhccHHHHHHHHHHHhcC
Confidence 246788999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCcceEEE-cCCCcEEEeCCCchHhHHHHHHHhc
Q psy16766 580 PNVYPGANMIQ-NEDGSVVRISSSQAVQRESLAKRLI 615 (621)
Q Consensus 580 p~~~PGA~~i~-~~~G~~~~L~~~~~~~R~~~A~~L~ 615 (621)
|++|||||||+ ...|.++.|.++ +|..+|+.|.
T Consensus 410 P~vhPGANyv~~r~~~~kr~L~yg---~R~kiA~eLk 443 (1386)
T KOG0261|consen 410 PNVHPGANYVVQRGEGFKRFLKYG---NRDKIADELK 443 (1386)
T ss_pred CCCCCCcchhhhcccchhhHhhcC---cHHHHHHhhc
Confidence 99999999999 567889999998 7999999986
No 6
>KOG0260|consensus
Probab=100.00 E-value=2.6e-80 Score=689.04 Aligned_cols=395 Identities=27% Similarity=0.378 Sum_probs=330.9
Q ss_pred cccccCcceEEEecCChHHHHhhcccccccccccCCCCCccccCccCCCCCccccCCCccCCCCCCccccCCcccccCCC
Q psy16766 115 TRQEVVPEILKLKYYTDQEVKQLSVVKVFSPITFNSLGHTIPGGLYDLAMGPISERGDPCTTCGNNYTKCKGHIGHIELP 194 (621)
Q Consensus 115 ~~p~~~~~g~ef~~~s~eei~~lSv~~I~~~~~~d~~g~Pi~ggl~D~~lG~~~~~~~~C~tC~~~~~~C~GhfGhI~L~ 194 (621)
..|.+++..++|++++|+|+++|||.+|.-|++.+. |.|-.|||.|+|+|. .++...|.||+.+...||||||||+|+
T Consensus 9 ~~pl~~v~~vqFgi~spdeir~mSV~~i~~~e~~e~-~~pk~ggl~D~RlG~-idr~~~CqTC~g~~~~CpGHFGhieLA 86 (1605)
T KOG0260|consen 9 QAPLRTVKSVQFGILSPDEIRRMSVAEIEFPETMEG-GRPKLGGLMDPRLGT-IDRDSLCQTCGGNMFECPGHFGHIELA 86 (1605)
T ss_pred cCcceeeeEEEeeccChhhhhcceeEEeeccccccc-CCCCcCCccccccCC-CCccchhhhhccccccCCcccceeeec
Confidence 457788999999999999999999999999998775 799999999999999 899999999999999999999999999
Q ss_pred cccccchhhHhHHHHHhhccccccCcccCcchHHHHHHHHhh-ccccchHHHHhHHHhhhhccccCcChHHHHHHHHHHH
Q psy16766 195 VPVINTLFFRDVQLLLKLSCFLCHKINIPATSQLLFINQIKL-LDAGYVTQAKDLEETLFNEENLRLHPAQLVQLVDSHV 273 (621)
Q Consensus 195 ~Pv~hp~f~~~v~~lL~~iC~~C~~l~~~~~~~~~~~~~Lkl-l~~G~l~~a~~L~~~~~~~~~~~~~~~~~~~~~~~~~ 273 (621)
.|||||+|++++.+||+|+|++|+++++++..........+. -..|++...++++.....|+.+..
T Consensus 87 kPvfH~gFl~kv~kiL~cVC~~C~ki~~~~~~~~~~~~~~~~~~~k~rl~~v~~vck~k~~ce~g~~------------- 153 (1605)
T KOG0260|consen 87 KPVFHPGFLKKVKKILRCVCFYCSKILKDKFNPKEDQILRKRYCSKGRLLMVLDVCKGKVVCEGGID------------- 153 (1605)
T ss_pred cccccHHHHHHHHHHHHHhhhcchheeecccCcchhhhhhhhcCCcchHHHHHHhhccceeeecccc-------------
Confidence 999999999999999999999999999987765433221111 145666666655543322211100
Q ss_pred HHHHhhccccccCCCCcchHHHHHHHHHHHHhhhcCCCCCCCCCCCceeecccceEEEEeeccccccchhhhhhhcccch
Q psy16766 274 QSILAHGTKICDINDYKGGEELRSAFVAQVLSRHVKRKCIFCATPINAISYQQRKIIKSFKIDKDNLDQSLDKSLNKSSN 353 (621)
Q Consensus 274 ~~~~~~~~~~~~~~~~k~~~~~r~~i~~~~~~~~~~kkC~~C~~~~p~irk~~~~~i~~~~~~~~~~~~~~d~~~e~~~~ 353 (621)
. ....-..||..+|.|++.+...+.+|+...+
T Consensus 154 ---------------------------~------e~~g~sgcg~kqP~i~r~gl~l~a~~k~~~e--------------- 185 (1605)
T KOG0260|consen 154 ---------------------------V------ESDGRSGCGLKQPSIRRLGLDLWAFWKQGDE--------------- 185 (1605)
T ss_pred ---------------------------c------cccccccccccCCceeccCchhhhhhhccCc---------------
Confidence 0 1123468999999999999988888765221
Q ss_pred hhhhhccccccCHHHHHHHHhhcchhhHHHHhhhcccCCCcccCCCCceEEEEeeecCCCCCccccccCCC-ccccchhH
Q psy16766 354 QIIRKREQGYVMASEVEADFKKLWTNEHLFLKCLIPVLDTTKELIATDIMFIRSLVVPPNNLRPLSMEQMP-PVEHSRNK 432 (621)
Q Consensus 354 ~~~~~~~~~~l~p~ev~~~lk~i~~~d~~~L~~l~~~~~~~~~~~~~d~ffl~~lpVpP~~~RP~~~~~~~-~~ed~~t~ 432 (621)
........+++++|.++|+.|.++|+..|++ ++ .-.+||||++++|||||+.+||++.+++. +.+||+|+
T Consensus 186 --~~~e~k~~ls~e~V~~i~k~Isded~~~lg~-----~~--~~arpewmIlTvLPVPP~~vrP~iv~~~s~rg~Ddlth 256 (1605)
T KOG0260|consen 186 --DSQESKRKLSAERVLEIFKRISDEDIDQLGF-----KP--KIARPEWMILTVLPVPPPAVRPEIVMQGSARGEDDLTH 256 (1605)
T ss_pred --cCCcccccCcHHHHHHHHHhhchhhhhhhcC-----CC--CcCCCceeEEEEecCCCCcccceeeecccccCcchhHH
Confidence 0112345799999999999999999999874 21 23478999999999999999999999876 78999999
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhchhhhhHHHhhcccCCchhhHHHHHHHHHHHHHHHhhcccccCCCCCC-----CCCcc
Q psy16766 433 LYQSILYSCGSLKSVIMAMKNKEQSDLLSEALKGIRGDTLNNKLQNSWHELQYNVDLLMDAKLNINKTTG-----AHQID 507 (621)
Q Consensus 433 ~l~~Il~~N~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~l~~~w~~LQ~~V~~~~d~~~~~~~~~~-----~k~~~ 507 (621)
.|.+|++.|..|++..+. |. ....+.+....||.||++++||+ .++.++ ..+.+
T Consensus 257 kLadIiK~n~~l~r~e~~---ga----------------~~H~i~e~~~LlqfhVat~~Dn~--~pgqp~a~qksGrplk 315 (1605)
T KOG0260|consen 257 KLADIIKKNIGLKRNEEN---GA----------------PAHIIEEYEQLLQFHVATYVDND--IPGQPQADQKSGRPLK 315 (1605)
T ss_pred HHHHHHHHHHHHhhhhhc---CC----------------chhhHHHHHhHhhhhhhheeccc--ccCCcccccccCCccc
Confidence 999999999999865421 11 23456677789999999999999 665433 24567
Q ss_pred chHHhhccCccccccccCCCccCcccceeecCCCCCccccccchHHHHhhCCcCcccCHHHHHHHHHHHHcCCCCCCcce
Q psy16766 508 GLKQMLDGKTGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGAN 587 (621)
Q Consensus 508 gi~q~L~gKeG~fR~nlmGKRVnfsaRSVIsPDP~l~idevGvP~~fAk~LT~PE~VT~~Ni~~Lr~lV~NGp~~~PGA~ 587 (621)
+|++|||||||++|+|||||||||||||||+|||||++||||||..+|++|||||.||+|||++|+++|.+||+.||||+
T Consensus 316 Si~arlKgkegriRgnLmGKRvDFSaRTVItgDPnl~ldevGVP~sIAk~lTfpE~Vtp~NidrLqeLV~~g~~~~pgak 395 (1605)
T KOG0260|consen 316 SISARLKGKEGRIRGNLMGKRVDFSARTVITGDPNLSLDEVGVPRSIAKRLTFPEHVTPFNIDRLQELVRRGLLEHPGAK 395 (1605)
T ss_pred chhhhhccccchhhhcccccccCcceeeeecCCCCcchhcccCcHHHHhhccCcceeccccHHHHHHHhhCCCCCCCCcc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEcCCCcEEEeCCC
Q psy16766 588 MIQNEDGSVVRISSS 602 (621)
Q Consensus 588 ~i~~~~G~~~~L~~~ 602 (621)
||+..+|.+++|.+.
T Consensus 396 yiird~G~Ridlr~~ 410 (1605)
T KOG0260|consen 396 YIIRDNGDRIDLRYH 410 (1605)
T ss_pred eeeecCCcEEEEeec
Confidence 999999999999875
No 7
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]
Probab=100.00 E-value=8.1e-68 Score=606.12 Aligned_cols=343 Identities=28% Similarity=0.434 Sum_probs=290.4
Q ss_pred cCcceEEEecCChHHHHhhcccccccccccCCCCCccccCccCCCCCccccCCCccCCCCCCccccCCcccccCCCcccc
Q psy16766 119 VVPEILKLKYYTDQEVKQLSVVKVFSPITFNSLGHTIPGGLYDLAMGPISERGDPCTTCGNNYTKCKGHIGHIELPVPVI 198 (621)
Q Consensus 119 ~~~~g~ef~~~s~eei~~lSv~~I~~~~~~d~~g~Pi~ggl~D~~lG~~~~~~~~C~tC~~~~~~C~GhfGhI~L~~Pv~ 198 (621)
..|+ ++|+++||++|++ |+.+|+.|++||..++|..+||+|++||. .+++..| |||+....||||||||||+.||+
T Consensus 3 ~~~~-i~~gl~sp~~ir~-~s~ev~~pet~~~~~~P~~~Gl~d~ri~~-~~~~~~C-~Cg~~~~~~~~~~GhIeLa~Pv~ 78 (808)
T COG0086 3 RIFD-IKFGLASPEEIRS-WSGEVKKPETINYRTKPERGGLFDERIFG-PDKDYEC-TCGKYKRICPGGFGHIELAAPVA 78 (808)
T ss_pred ccce-eEEecCCHHHHHh-cceEEcCccccCCCCcccCCCccchhhcC-CCCCcee-cCCCCcCcCCCCceeEEeecceE
Confidence 3578 9999999999999 55999999999999999999999999999 7899999 99999999999999999999999
Q ss_pred cchhhHhHHHHHhhccccccCcccCcchHHHHHHHHhhccccchHHHHhHHHhhhhccccCcChHHHHHHHHHHHHHHHh
Q psy16766 199 NTLFFRDVQLLLKLSCFLCHKINIPATSQLLFINQIKLLDAGYVTQAKDLEETLFNEENLRLHPAQLVQLVDSHVQSILA 278 (621)
Q Consensus 199 hp~f~~~v~~lL~~iC~~C~~l~~~~~~~~~~~~~Lkll~~G~l~~a~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 278 (621)
|++||+.+.++|+++|.+|+++++. +...+. + ..++ ..+ .+.
T Consensus 79 hi~f~k~~~~~L~~~~~~~~~v~~~--~~~~~~-~-~~l~-----~~~-----------------------------~~~ 120 (808)
T COG0086 79 HIWFFKSIPSLLDMTCRDCERVLYF--EAYVVL-G-TDLE-----KIQ-----------------------------LLN 120 (808)
T ss_pred EechhhccHHHHhhhHHhhhhhhhH--hHHHHh-c-cchh-----hhc-----------------------------ccc
Confidence 9999999999999999999999987 222222 1 0000 000 000
Q ss_pred hccccccCCCCcchHHHHHHHHHHHHhhhcCCCCCCCCCCCceeecccceEEEEeeccccccchhhhhhhcccchhhhhh
Q psy16766 279 HGTKICDINDYKGGEELRSAFVAQVLSRHVKRKCIFCATPINAISYQQRKIIKSFKIDKDNLDQSLDKSLNKSSNQIIRK 358 (621)
Q Consensus 279 ~~~~~~~~~~~k~~~~~r~~i~~~~~~~~~~kkC~~C~~~~p~irk~~~~~i~~~~~~~~~~~~~~d~~~e~~~~~~~~~ 358 (621)
+ +.. + ....|+|||+.++.+++++...+...
T Consensus 121 ------~---~~~-----------~----~~~~~~~~Ga~~~~~~~~~~~~~~~~------------------------- 151 (808)
T COG0086 121 ------E---TEY-----------V----YDSFCAHCGAEAIKILLEKPDLETER------------------------- 151 (808)
T ss_pred ------h---hee-----------e----ccccCCCCCchhHHHHHhCcchhhhh-------------------------
Confidence 0 000 0 23679999999999988766544311
Q ss_pred ccccccCHHHHHHHHhhcchhhHHHHhhhcccCCCcccCCCCceEEEEeeecCCCCCccccccCCC-ccccchhHHHHHH
Q psy16766 359 REQGYVMASEVEADFKKLWTNEHLFLKCLIPVLDTTKELIATDIMFIRSLVVPPNNLRPLSMEQMP-PVEHSRNKLYQSI 437 (621)
Q Consensus 359 ~~~~~l~p~ev~~~lk~i~~~d~~~L~~l~~~~~~~~~~~~~d~ffl~~lpVpP~~~RP~~~~~~~-~~ed~~t~~l~~I 437 (621)
. ...++|.+++++|++|...|..+++ ..+|+||+|+++||||+++||++.++|+ ..|||+|.+|++|
T Consensus 152 ~-~~~~~~~~~~~~~~~l~~~d~~~~~-----------~~~pewmil~vlpV~Pp~~RP~i~ld~g~~a~~dl~~~~~~i 219 (808)
T COG0086 152 E-EETLSPTKVKKLLKRLKVVDAFLLS-----------GNRPEWMILTVLPVPPPDLRPSIQLDGGRFAESDLNDLYRRV 219 (808)
T ss_pred h-hcccCHHHHHHHHhhccHHHHHHhc-----------CCCcceeEEEeeccCCCCCCcceecCCCccchhHHHHHHHHH
Confidence 0 1578999999999999999998886 2479999999999999999999999875 7899999999999
Q ss_pred HHHHHHHHHHHHHhhhhchhhhhHHHhhcccCCchhhHHHHHHHHHHHHHHHhhcccccCCCC-CCCCCccchHHhhccC
Q psy16766 438 LYSCGSLKSVIMAMKNKEQSDLLSEALKGIRGDTLNNKLQNSWHELQYNVDLLMDAKLNINKT-TGAHQIDGLKQMLDGK 516 (621)
Q Consensus 438 l~~N~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~l~~~w~~LQ~~V~~~~d~~~~~~~~-~~~k~~~gi~q~L~gK 516 (621)
|..|+.|+..+.. . ....+.+.|..||.+|++||||. .++. ..++|.+||.||||||
T Consensus 220 i~~n~rlk~~~~~-~-------------------~~~iv~~~~~~lQ~~v~~~~Dn~--~~~~~~~~rPlksl~~~LkgK 277 (808)
T COG0086 220 INRNNRLKRLLEL-A-------------------APIIVRNEKRMLQEAVDALFDNR--RPRAVTGGRPLKSLSQRLKGK 277 (808)
T ss_pred HHHHHHhHHhhhh-c-------------------chHHHHHHHHHHHHHHHHHhhcC--CCCCccCCCccccHHHHhcCC
Confidence 9999999987643 1 11357889999999999999994 3332 1247788999999999
Q ss_pred ccccccccCCCccCcccceeecCCCCCccccccchHHHHhhCCcCcccCHHHHHHHHHHHHcCCCCCCcceEEEcCCCcE
Q psy16766 517 TGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSV 596 (621)
Q Consensus 517 eG~fR~nlmGKRVnfsaRSVIsPDP~l~idevGvP~~fAk~LT~PE~VT~~Ni~~Lr~lV~NGp~~~PGA~~i~~~~G~~ 596 (621)
+||||+|||||||||||||||||||+|+++|+|||..||++||+|+.||+||++.|++ ||+++++.+|+.
T Consensus 278 ~GrFR~nL~GKRVd~SgRsVI~~~P~l~~~e~GvP~~~A~~L~~p~~v~~~~~~~~~~----------~a~~~~~~~~~~ 347 (808)
T COG0086 278 QGRFRQNLLGKRVDYSGRSVISVGPNLKLNQCGVPKKMALELFKPFVVTELNIEGLRT----------GAKYAKRMVERR 347 (808)
T ss_pred CceeeccccccccCCCCceeecCCCCccccccCCHHHHHHHhccCEEEEehhhhhhhc----------CCceEEeccccc
Confidence 9999999999999999999999999999999999999999999999999999999999 899999987765
No 8
>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=6.6e-61 Score=505.49 Aligned_cols=310 Identities=27% Similarity=0.483 Sum_probs=223.2
Q ss_pred cCcceEEEecCChHHHHhhcccccccccccCCC-CCccccCccCCCCCccccCCCccCCCCCCccccCCcccccCCCccc
Q psy16766 119 VVPEILKLKYYTDQEVKQLSVVKVFSPITFNSL-GHTIPGGLYDLAMGPISERGDPCTTCGNNYTKCKGHIGHIELPVPV 197 (621)
Q Consensus 119 ~~~~g~ef~~~s~eei~~lSv~~I~~~~~~d~~-g~Pi~ggl~D~~lG~~~~~~~~C~tC~~~~~~C~GhfGhI~L~~Pv 197 (621)
+.|.+++|+++|+|||+++||.+|+++.+||.. |+|+.|||+|++||+ .+....|.|||+...+||||||||+|+.||
T Consensus 2 ~~i~~i~f~~~s~~eI~~~Sv~~i~~~~~~~~~~~~p~~~Gl~d~rlG~-~~~~~~C~tC~~~~~~CpGHfGhI~L~~PV 80 (337)
T PF04997_consen 2 KKIKSIQFGIYSPEEIRKLSVKEITNPETFDNLTGKPIKGGLYDPRLGP-IDKKQICSTCGLNYTECPGHFGHIELALPV 80 (337)
T ss_dssp EEEEEEEEEE--HHHHHHHEEEB--SSTSBCTSSSSCBSSSSSSSSSS--SSSSSTSSSSSSSSSSCCCSEEEEEEEEEE
T ss_pred CeeeEEEEEeCCHHHHHHhCcEEEechhhccCCCCCCccccccChhhcC-CCcccccccccccccccCCceeEEEeCHHH
Confidence 458899999999999999999999999999998 999999999999999 788899999999999999999999999999
Q ss_pred ccchhhHhHHHHHhhccccccCcccCcchHHHHHHHHhhccccchHHHHhHHHhhhhccccCcChHHHHHHHHHHHHHHH
Q psy16766 198 INTLFFRDVQLLLKLSCFLCHKINIPATSQLLFINQIKLLDAGYVTQAKDLEETLFNEENLRLHPAQLVQLVDSHVQSIL 277 (621)
Q Consensus 198 ~hp~f~~~v~~lL~~iC~~C~~l~~~~~~~~~~~~~Lkll~~G~l~~a~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 277 (621)
|||+||+.++++|+++|++|+++++++.+...+...+..+. .......+
T Consensus 81 ~h~~f~~~i~~iL~~~C~~C~~l~~~~~~~~~~~~~~~~~~--~~~~~~~~----------------------------- 129 (337)
T PF04997_consen 81 YHPGFFKEIPKILRCICKKCSRLLLSEKEKYFYLKILLKLK--KKKKKERL----------------------------- 129 (337)
T ss_dssp ETCCCHHHHHHHHTTSCTTTSCTSTCCCCHTSCHHHCHCSH--SSSHHHHH-----------------------------
T ss_pred Hhhcccccceeeecccccccccccccccccccccccccccc--cccchhHH-----------------------------
Confidence 99999999999999999999999999887643322222111 00011000
Q ss_pred hhccccccCCCCcchHHHHHHHHHHHHhhhcCCCCCCCCCCCc-------------------eeecccceEEEEeecccc
Q psy16766 278 AHGTKICDINDYKGGEELRSAFVAQVLSRHVKRKCIFCATPIN-------------------AISYQQRKIIKSFKIDKD 338 (621)
Q Consensus 278 ~~~~~~~~~~~~k~~~~~r~~i~~~~~~~~~~kkC~~C~~~~p-------------------~irk~~~~~i~~~~~~~~ 338 (621)
+.+....+ ....|.+|+..++ .++..+...+..
T Consensus 130 --------------------~~i~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~------ 181 (337)
T PF04997_consen 130 --------------------KIISKECK--KKSICSHCKAINGKIKKVEKSKKCEGCGKKNPKIRKEGAEKIQE------ 181 (337)
T ss_dssp --------------------HHHHHHHH--HTCSSTSTCC-SSS---SSSEETSSSSSSBSCEEEEESHCCCCC------
T ss_pred --------------------HHHHHhhh--hhhhhcccccccccccccccchhcccccccCcccccchhhhccc------
Confidence 11111111 2344555554444 443332111100
Q ss_pred ccchhhhhhhcccchhhhhhccccccCHHHHHHHHhhcchhhHHHHhhhcccCCCcccCCCCceEEEEeeecCCCCCccc
Q psy16766 339 NLDQSLDKSLNKSSNQIIRKREQGYVMASEVEADFKKLWTNEHLFLKCLIPVLDTTKELIATDIMFIRSLVVPPNNLRPL 418 (621)
Q Consensus 339 ~~~~~~d~~~e~~~~~~~~~~~~~~l~p~ev~~~lk~i~~~d~~~L~~l~~~~~~~~~~~~~d~ffl~~lpVpP~~~RP~ 418 (621)
..+ .............+++|.+|+++|++||+++.++|++.. ...+|+||||++|||||+++||+
T Consensus 182 ----~i~----~~~~~~~~~~~~~~l~~~~v~~ilk~l~~~~~~~l~~~~-------~~~~P~~~~l~~lpVpP~~~RP~ 246 (337)
T PF04997_consen 182 ----EIK----KKESNKEIKEELRILTPEEVRQILKKLSKEDKELLGFDP-------SGSRPEWFFLTVLPVPPPRFRPS 246 (337)
T ss_dssp ----HHH----SCCHHHHHHCHCECESHHHHHHHHHHSHHHHHHHHHHHT-------TTBSGGGSEEEEEEE-TGGGS-E
T ss_pred ----ccc----cccccccchhhhhhhhhhhhhhcchhhhhhheeeeeccc-------cccccceeEEeeeecCCceeeee
Confidence 000 000011111222379999999999999999999998632 12368999999999999999999
Q ss_pred cccCCCc-cccchhHHHHHHHHHHHHHHHHHHHhhhhchhhhhHHHhhcccCCchhhHHHHHHHHHHHHHHHhhcccccC
Q psy16766 419 SMEQMPP-VEHSRNKLYQSILYSCGSLKSVIMAMKNKEQSDLLSEALKGIRGDTLNNKLQNSWHELQYNVDLLMDAKLNI 497 (621)
Q Consensus 419 ~~~~~~~-~ed~~t~~l~~Il~~N~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~l~~~w~~LQ~~V~~~~d~~~~~ 497 (621)
+.++|+. .|||+|..|++||+.|+.|+..+.. + .....+.+.|..||.+|+.||||+ .
T Consensus 247 v~~~~~~~~eddlt~~~~~Ii~~N~~L~~~~~~---~----------------~~~~~~~~~~~~LQ~~v~~~~dn~--~ 305 (337)
T PF04997_consen 247 VQLGGGRFSEDDLTSLYRKIIKRNNRLRKLLEE---G----------------APSSIIMEEWRLLQEAVNSLIDNE--K 305 (337)
T ss_dssp EEESSSEEEE-HHHHHHHHHHHHHHHHHHCCTS---T----------------SSSCHHHHHHHHHHHHHHHHHCTT--S
T ss_pred eeeecccccCchHHHHHHHHHHHHHHHHHHHHh---h----------------CcchhhhhhhhhhhHhHhHHhhhc--c
Confidence 9999875 8999999999999999999875421 1 112467889999999999999998 4
Q ss_pred CCCC-----CCCCccchHHhhccCcccccccc
Q psy16766 498 NKTT-----GAHQIDGLKQMLDGKTGMIRQNM 524 (621)
Q Consensus 498 ~~~~-----~~k~~~gi~q~L~gKeG~fR~nl 524 (621)
++.+ .+++.+||+|||||||||||+||
T Consensus 306 ~~~~~~~~~~~~~~k~i~q~L~gK~GrfR~NL 337 (337)
T PF04997_consen 306 PGKPPAGQKSGRPLKGISQRLKGKEGRFRQNL 337 (337)
T ss_dssp SSSSBCBSTTSSB--THHHHHSSTTSSHCHHT
T ss_pred cCCcccccccCCCCCCHHHHccCCCCcCCCCC
Confidence 4432 23567899999999999999997
No 9
>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-54 Score=503.03 Aligned_cols=358 Identities=22% Similarity=0.316 Sum_probs=251.9
Q ss_pred eEEEecCChHHHHhhcccccccccccCCC-CCccccCccCCCC-Cccc-------------cCCCccCCCCCCccccC--
Q psy16766 123 ILKLKYYTDQEVKQLSVVKVFSPITFNSL-GHTIPGGLYDLAM-GPIS-------------ERGDPCTTCGNNYTKCK-- 185 (621)
Q Consensus 123 g~ef~~~s~eei~~lSv~~I~~~~~~d~~-g~Pi~ggl~D~~l-G~~~-------------~~~~~C~tC~~~~~~C~-- 185 (621)
++++++.|||+|+++|+-+|++|++++.. .+|..+||.|.++ ||.- .+...|.+||-....|+
T Consensus 1 ~i~i~laSPe~I~~ws~geV~~petiny~t~kPe~~GLfcerIFGp~k~~ec~Cgkyk~~~~~~~~C~~Cgve~t~~~vr 80 (1140)
T TIGR02386 1 AIKISIASPDTIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKIRYKGVVCERCGVEVTESKVR 80 (1140)
T ss_pred CeEEEecCHHHHHhhhceEEeccceecCCCCccCCCCcccchhcCCccCceeccccccccCcCCcCCCCCCCCcccchhh
Confidence 37899999999999999999999999774 7999999999888 9831 22357999999999999
Q ss_pred -CcccccCCCcccccchhhHh-----------HHHHHhhccccccCcccCcchHHHHHHHHhhccccchHHHHhHHHhhh
Q psy16766 186 -GHIGHIELPVPVINTLFFRD-----------VQLLLKLSCFLCHKINIPATSQLLFINQIKLLDAGYVTQAKDLEETLF 253 (621)
Q Consensus 186 -GhfGhI~L~~Pv~hp~f~~~-----------v~~lL~~iC~~C~~l~~~~~~~~~~~~~Lkll~~G~l~~a~~L~~~~~ 253 (621)
+|||||+|+.||+|.+|++. ..+.|.++|.+|+.+.+.+....+...+ ++. +
T Consensus 81 r~rmGhI~La~Pv~Hiwy~k~~ps~~~~ll~~~~k~le~v~y~~~~~v~~~~~~~~~~~~--~~~-----~--------- 144 (1140)
T TIGR02386 81 RERMGHIELAAPVAHIWYFKGLPSRIGLLLDITAKELESVLYFENYVVLDPGDTKLDKKE--VLD-----E--------- 144 (1140)
T ss_pred hhcccceeecCCceeehhcCCCchHHHHHhCCCHHHhhheeeccceEEeCCCCCchhhhh--hhc-----h---------
Confidence 99999999999999999997 4788999999999987765322111111 000 0
Q ss_pred hccccCcChHHHHHHHHHHHHHHHhhccccccCCCCcchHHHHHHHHHHHHhhhcCCCCCCCCCCCceeecccceEEEEe
Q psy16766 254 NEENLRLHPAQLVQLVDSHVQSILAHGTKICDINDYKGGEELRSAFVAQVLSRHVKRKCIFCATPINAISYQQRKIIKSF 333 (621)
Q Consensus 254 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~r~~i~~~~~~~~~~kkC~~C~~~~p~irk~~~~~i~~~ 333 (621)
++..+ +...| ....-..||+...+....+....
T Consensus 145 ---------~~~~~-------------------------------~~~~~----~~~~~~~~G~~ai~~~l~~~dl~--- 177 (1140)
T TIGR02386 145 ---------TEYRE-------------------------------VLKRY----GDGFRAGMGAEAIKELLEKIDLD--- 177 (1140)
T ss_pred ---------hHHHH-------------------------------HHHHh----ccCcccccchHHHHHHHhcCCHH---
Confidence 00000 00000 00000113322221111110000
Q ss_pred eccccccchhhhhhhcccchhhhhhccccccCHHHHHHHHhhcchhhHHHHhhhcccCCCcccCCCCceEEEEeeecCCC
Q psy16766 334 KIDKDNLDQSLDKSLNKSSNQIIRKREQGYVMASEVEADFKKLWTNEHLFLKCLIPVLDTTKELIATDIMFIRSLVVPPN 413 (621)
Q Consensus 334 ~~~~~~~~~~~d~~~e~~~~~~~~~~~~~~l~p~ev~~~lk~i~~~d~~~L~~l~~~~~~~~~~~~~d~ffl~~lpVpP~ 413 (621)
.+.+...+..............+...++.+.|++ ...+|+||||++|||||+
T Consensus 178 --------~~~~~~~~~~~~~~~~~~~~~~~krl~~~~~f~~--------------------s~~~Pewmil~~lPV~Pp 229 (1140)
T TIGR02386 178 --------KEIEELKIQLRESKSDQKRKKLLKRLEIVEAFKD--------------------SGNRPEWMVLDVIPVIPP 229 (1140)
T ss_pred --------HHHHHHHHHHHhccchhhHHhhhhHHHHHHHHHh--------------------cCCChHHhhhhcccCCCC
Confidence 0000000000000000000123344444444443 134799999999999999
Q ss_pred CCccccccCCC-ccccchhHHHHHHHHHHHHHHHHHHHhhhhchhhhhHHHhhcccCCchhhHHHHHHHHHHHHHHHhhc
Q psy16766 414 NLRPLSMEQMP-PVEHSRNKLYQSILYSCGSLKSVIMAMKNKEQSDLLSEALKGIRGDTLNNKLQNSWHELQYNVDLLMD 492 (621)
Q Consensus 414 ~~RP~~~~~~~-~~ed~~t~~l~~Il~~N~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~l~~~w~~LQ~~V~~~~d 492 (621)
++||++.++|+ ..+||+|.+|+.||+.|+.|++.+... . ....+.+.|..||.+|+.|||
T Consensus 230 ~lRP~v~l~gg~~~~sDLn~lyr~II~~Nn~Lk~~~~~~---a----------------p~~ii~~~~~~LQ~aV~~liD 290 (1140)
T TIGR02386 230 ELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLELG---A----------------PEIIVRNEKRMLQEAVDALFD 290 (1140)
T ss_pred ccCCcEEeCCCccccCchHHHHHHHHHHHHHHHHHHHcC---C----------------cHHHHHHHHHHHHHHHHHHhc
Confidence 99999999775 789999999999999999999876421 1 112456899999999999999
Q ss_pred ccccCCCC----CCCCCccchHHhhccCccccccccCCCccCcccceeecCCCCCccccccchHHHHhhCCcCcccC---
Q psy16766 493 AKLNINKT----TGAHQIDGLKQMLDGKTGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVT--- 565 (621)
Q Consensus 493 ~~~~~~~~----~~~k~~~gi~q~L~gKeG~fR~nlmGKRVnfsaRSVIsPDP~l~idevGvP~~fAk~LT~PE~VT--- 565 (621)
|+ ..+. ..+++.+||+|+|+||+||||+|||||||||||||||+|||+|++||||||..||++||+|+.|+
T Consensus 291 n~--~~g~~~~~~~~rplksls~~LkGK~GrFR~NLlGKRVDySgRSVI~pdP~L~l~e~GlP~~mA~~L~~Pf~i~~L~ 368 (1140)
T TIGR02386 291 NG--RRGKPVVGKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKPFIIKRLI 368 (1140)
T ss_pred cc--ccCCCccCcCCCchhhHHHhhcCCCCcccccccccccCCCCCCeEcCCCCcccccccChHHHHHHcCchHHHHHHH
Confidence 98 4332 23466789999999999999999999999999999999999999999999999999999998876
Q ss_pred ----HHHHHHHHHHHHcC-CCCCCcceEEEcC
Q psy16766 566 ----PWNVTLLRKMVING-PNVYPGANMIQNE 592 (621)
Q Consensus 566 ----~~Ni~~Lr~lV~NG-p~~~PGA~~i~~~ 592 (621)
.+|+...++++.++ |.+|.-...+++.
T Consensus 369 ~~~~~~~i~~ak~~i~~~~~~v~~vl~~vi~~ 400 (1140)
T TIGR02386 369 DRELAANIKSAKKMIEQEDPEVWDVLEDVIKE 400 (1140)
T ss_pred HcCcccchHHHHHHHHhcCCccceEEEEccCC
Confidence 36777777788876 5578766666654
No 10
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=100.00 E-value=6.1e-51 Score=473.70 Aligned_cols=338 Identities=25% Similarity=0.375 Sum_probs=231.6
Q ss_pred CcceEEEecCChHHHHhhcccccccccccCC-CCCccccCccCCCC-CccccCCCccCCCCCCc------cccC------
Q psy16766 120 VPEILKLKYYTDQEVKQLSVVKVFSPITFNS-LGHTIPGGLYDLAM-GPISERGDPCTTCGNNY------TKCK------ 185 (621)
Q Consensus 120 ~~~g~ef~~~s~eei~~lSv~~I~~~~~~d~-~g~Pi~ggl~D~~l-G~~~~~~~~C~tC~~~~------~~C~------ 185 (621)
+|+.+++++.|||.|+++|+-+|++|++++. +.+|..+||++.+. || .++..| .||... ..|+
T Consensus 6 ~~~~i~i~laspe~I~~ws~GeV~~petinyrt~kPe~~GLfcerIFgp--~kd~eC-~Cgkyk~~~~~~~~C~~cgve~ 82 (1156)
T PRK00566 6 DFDAIKIGLASPEKIRSWSYGEVKKPETINYRTLKPERDGLFCERIFGP--TKDYEC-LCGKYKRVRYKGIICERCGVEV 82 (1156)
T ss_pred CcceEEEEccCHHHHHHhhcceEccccccccCCCccCCCCcccchhcCc--ccCcEE-eCccccccCcCCcCCCCCCcee
Confidence 7999999999999999999999999999866 48999999999766 66 578999 998533 4788
Q ss_pred -------CcccccCCCcccccchhhHhH-----------HHHHhhccccccCcccCcchHHHHHHHHhhccccchHHHHh
Q psy16766 186 -------GHIGHIELPVPVINTLFFRDV-----------QLLLKLSCFLCHKINIPATSQLLFINQIKLLDAGYVTQAKD 247 (621)
Q Consensus 186 -------GhfGhI~L~~Pv~hp~f~~~v-----------~~lL~~iC~~C~~l~~~~~~~~~~~~~Lkll~~G~l~~a~~ 247 (621)
+|||||+|+.||.|++||+.+ .+.|.++|.+|+.+.+.+.... + .+..++.
T Consensus 83 ~~~~vrr~rmGhI~La~Pv~Hiwy~k~~ps~i~~ll~~~~k~le~v~y~~~~~v~~~~~~~-~-~~~~~~~--------- 151 (1156)
T PRK00566 83 TRSKVRRERMGHIELAAPVAHIWFFKSLPSRIGLLLDMSLKDLERVLYFESYVVIDPGDTP-L-EKKQLLT--------- 151 (1156)
T ss_pred eechhhhhhcceeeecCceeeeeecCCCchHHHHHhCCCHHHhhheeecceEEEeCCCCCc-h-hhhcccC---------
Confidence 999999999999999999943 7889999999998877653311 1 0101110
Q ss_pred HHHhhhhccccCcChHHHHHHHHHHHHHHHhhccccccCCCCcchHHHHHHHHHHHHhhhcCCCCCCCCCCCceeecccc
Q psy16766 248 LEETLFNEENLRLHPAQLVQLVDSHVQSILAHGTKICDINDYKGGEELRSAFVAQVLSRHVKRKCIFCATPINAISYQQR 327 (621)
Q Consensus 248 L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~r~~i~~~~~~~~~~kkC~~C~~~~p~irk~~~ 327 (621)
++++.+..+.| ... .. .....+ .+.+.++..
T Consensus 152 --------------~~~~~~~~~~~-----~~~-----~~-~~~Ga~----ai~~ll~~~-------------------- 182 (1156)
T PRK00566 152 --------------EEEYREALEEY-----GDE-----FV-AKMGAE----AIKELLKNI-------------------- 182 (1156)
T ss_pred --------------HHHHHHHHHHh-----ccc-----cc-ccccHH----HHHHHHHhC--------------------
Confidence 00000000000 000 00 000000 000000000
Q ss_pred eEEEEeeccccccchhhhhhhcccchhhhhhccccccCHHHHHHHHhhcchhhHHHHhhhcccCCCcccCCCCceEEEEe
Q psy16766 328 KIIKSFKIDKDNLDQSLDKSLNKSSNQIIRKREQGYVMASEVEADFKKLWTNEHLFLKCLIPVLDTTKELIATDIMFIRS 407 (621)
Q Consensus 328 ~~i~~~~~~~~~~~~~~d~~~e~~~~~~~~~~~~~~l~p~ev~~~lk~i~~~d~~~L~~l~~~~~~~~~~~~~d~ffl~~ 407 (621)
+ -..+.. ....+-.. .-+...-..++++| +++..+. ....+|+||||++
T Consensus 183 ---------d--l~~~~~----~l~~~~~~-----~~~~~~~~~~~krl-----~~~~~f~------~s~~~Pewmil~~ 231 (1156)
T PRK00566 183 ---------D--LEAEAE----ELREELKE-----TGSEQKRKKALKRL-----KVVEAFR------KSGNKPEWMILDV 231 (1156)
T ss_pred ---------C--HHHHHH----HHHHHHHh-----cccchhHHHHHHHH-----HHHHHHH------cCCCCccEeeEee
Confidence 0 000000 00000000 00001111222332 1221111 1134799999999
Q ss_pred eecCCCCCccccccCCC-ccccchhHHHHHHHHHHHHHHHHHHHhhhhchhhhhHHHhhcccCCchhhHHHHHHHHHHHH
Q psy16766 408 LVVPPNNLRPLSMEQMP-PVEHSRNKLYQSILYSCGSLKSVIMAMKNKEQSDLLSEALKGIRGDTLNNKLQNSWHELQYN 486 (621)
Q Consensus 408 lpVpP~~~RP~~~~~~~-~~ed~~t~~l~~Il~~N~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~l~~~w~~LQ~~ 486 (621)
|||||+++||++.++|+ ..++|+|.+|+.||..|+.|++.+.. +. +...+.+.|..||.+
T Consensus 232 lPV~Pp~lRP~v~l~~g~~~~sDLn~lyr~II~rNnrLk~~~~~---~a----------------p~~ii~~~~~~LQ~a 292 (1156)
T PRK00566 232 LPVIPPDLRPLVQLDGGRFATSDLNDLYRRVINRNNRLKRLLEL---GA----------------PEIIVRNEKRMLQEA 292 (1156)
T ss_pred cccCCCcccCceEeCCCcccCCchHHHHHHHHHHHHHHHHHHHc---CC----------------cHHHHHHHHHHHHHH
Confidence 99999999999999875 67899999999999999999987632 11 112456899999999
Q ss_pred HHHhhcccccCCCC----CCCCCccchHHhhccCccccccccCCCccCcccceeecCCCCCccccccchHHHHhhCCcCc
Q psy16766 487 VDLLMDAKLNINKT----TGAHQIDGLKQMLDGKTGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYPV 562 (621)
Q Consensus 487 V~~~~d~~~~~~~~----~~~k~~~gi~q~L~gKeG~fR~nlmGKRVnfsaRSVIsPDP~l~idevGvP~~fAk~LT~PE 562 (621)
|+.||||+ ..+. ..+++.+||+|+|+||+||||+|||||||||||||||+|||+|+++|||||..||++||+|
T Consensus 293 V~~lidn~--~~g~~~~~~~~rplksls~~LkGK~GrFR~NLlGKRVDySgRSVI~pdP~L~l~e~GvP~~mA~eL~~P- 369 (1156)
T PRK00566 293 VDALFDNG--RRGRPVTGPNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKP- 369 (1156)
T ss_pred HHHHhccC--ccCCCcccccCCchhHHHHhhcCCCccccccccccccCCCCCceEeCCCCcccccccChHHHHHHhCcH-
Confidence 99999998 4332 2345678999999999999999999999999999999999999999999999999999998
Q ss_pred ccCHHHHHHHHHHHHcCC
Q psy16766 563 PVTPWNVTLLRKMVINGP 580 (621)
Q Consensus 563 ~VT~~Ni~~Lr~lV~NGp 580 (621)
|| +++|+.||+
T Consensus 370 ----f~---i~~L~~~g~ 380 (1156)
T PRK00566 370 ----FI---MKKLVERGL 380 (1156)
T ss_pred ----HH---HHHHHHcCC
Confidence 45 566677886
No 11
>smart00663 RPOLA_N RNA polymerase I subunit A N-terminus.
Probab=100.00 E-value=1.4e-49 Score=408.63 Aligned_cols=188 Identities=37% Similarity=0.569 Sum_probs=164.4
Q ss_pred ceEEEEeeecCCCCCccccccCC-CccccchhHHHHHHHHHHHHHHHHHHHhhhhchhhhhHHHhhcccCCchhhHHHHH
Q psy16766 401 DIMFIRSLVVPPNNLRPLSMEQM-PPVEHSRNKLYQSILYSCGSLKSVIMAMKNKEQSDLLSEALKGIRGDTLNNKLQNS 479 (621)
Q Consensus 401 d~ffl~~lpVpP~~~RP~~~~~~-~~~ed~~t~~l~~Il~~N~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~l~~~ 479 (621)
+||||++|||||+|+||++.+++ ...+||+|..|.+||+.|+.|++.+.. +. ....+.+.
T Consensus 1 e~fil~~lpVpP~~~RP~v~~~~~~~~eddlt~~l~~Ii~~N~~L~~~~~~---~~----------------~~~~~~~~ 61 (295)
T smart00663 1 EWMILTVLPVPPPCLRPSVSLDGGRFAEDDLTHLLRDIIKRNNRLKRLLEL---GA----------------PEHIIRNE 61 (295)
T ss_pred CeEEEeccccCCCCCCCcEEeCCCcccCCcHHHHHHHHHHHHHHHHHHHHc---CC----------------hHHHHHHH
Confidence 69999999999999999999976 588999999999999999999986532 11 12345678
Q ss_pred HHHHHHHHHHhhcccccCCCC--CCCCCccchHHhhccCccccccccCCCccCcccceeecCCCCCccccccchHHHHhh
Q psy16766 480 WHELQYNVDLLMDAKLNINKT--TGAHQIDGLKQMLDGKTGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVPLEFAKT 557 (621)
Q Consensus 480 w~~LQ~~V~~~~d~~~~~~~~--~~~k~~~gi~q~L~gKeG~fR~nlmGKRVnfsaRSVIsPDP~l~idevGvP~~fAk~ 557 (621)
|..||.+|+.|+|++ ...+. ..+++.+||+|+|+||+|+||+|||||||||||||||||||+|++||||||..||++
T Consensus 62 ~~~LQ~~v~~~~d~~-~~~~~~~~~~~~~~~i~~~l~gK~G~~R~nllGKRvd~s~RsVI~pdP~l~~~evgiP~~~A~~ 140 (295)
T smart00663 62 KRLLQEAVDTLFDNE-GLPRARQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALE 140 (295)
T ss_pred HHHHHHHHHHHHccC-CCcccccCCCCCcccccccccCcCCccccccccccccccCceEEeCCCCcceeEeeCCHHHHHh
Confidence 999999999999997 22221 123557899999999999999999999999999999999999999999999999999
Q ss_pred CCcCcccCHHHHHHHHHHHHcCCCCCCcceEEEcCCCcEEEeCCCchHhHHHHHHHhcC
Q psy16766 558 LTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRISSSQAVQRESLAKRLIT 616 (621)
Q Consensus 558 LT~PE~VT~~Ni~~Lr~lV~NGp~~~PGA~~i~~~~G~~~~L~~~~~~~R~~~A~~L~~ 616 (621)
|||||.||.||+++|++||.||| |||+||++ |.++.|... +|.++|++|..
T Consensus 141 Lt~pe~v~~~n~~~l~~lv~ng~---pga~~i~~--g~~~~l~~~---~~~~~~~~l~~ 191 (295)
T smart00663 141 LTFPEIVTPLNIDKLRKLVRNGP---NGAKYIIR--GKKTNLKLA---KRSKIAKHLKI 191 (295)
T ss_pred CCcCEEEhHHHHHHHHHHHhcCC---CCceEEEe--CcEEEchhh---hhHHHHhcCcc
Confidence 99999999999999999999999 99999997 888888764 67778888763
No 12
>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional
Probab=100.00 E-value=1.4e-46 Score=410.84 Aligned_cols=151 Identities=28% Similarity=0.414 Sum_probs=129.5
Q ss_pred CCCCceEEEEeeecCCCCCccccccCCC-ccccchhHHHHHHHHHHHHHHHHHHHhhhhchhhhhHHHhhcccCCchhhH
Q psy16766 397 LIATDIMFIRSLVVPPNNLRPLSMEQMP-PVEHSRNKLYQSILYSCGSLKSVIMAMKNKEQSDLLSEALKGIRGDTLNNK 475 (621)
Q Consensus 397 ~~~~d~ffl~~lpVpP~~~RP~~~~~~~-~~ed~~t~~l~~Il~~N~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~ 475 (621)
..+|+||||++|||||+++||++.++|+ ..++|+|.+|++||..|+.|++..... . ....
T Consensus 239 ~~~PewmiL~~lPV~Pp~lRP~v~l~~g~~~~sDLn~ly~~II~rNn~L~~~~~~~---~----------------p~~i 299 (627)
T PRK02625 239 GSRPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEIL---A----------------PEII 299 (627)
T ss_pred CCCccEEEEEeeecCCCcccCceEeCCCcccCCCHHHHHHHHHHHHHHHHHHHHcC---C----------------cHHH
Confidence 3479999999999999999999999875 679999999999999999999865321 1 1123
Q ss_pred HHHHHHHHHHHHHHhhcccccCCCC----CCCCCccchHHhhccCccccccccCCCccCcccceeecCCCCCccccccch
Q psy16766 476 LQNSWHELQYNVDLLMDAKLNINKT----TGAHQIDGLKQMLDGKTGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVP 551 (621)
Q Consensus 476 l~~~w~~LQ~~V~~~~d~~~~~~~~----~~~k~~~gi~q~L~gKeG~fR~nlmGKRVnfsaRSVIsPDP~l~idevGvP 551 (621)
+.+.|..||.+|+.||||+ ..+. ..+++.+||+|+|+||+||||+|||||||||||||||||||+|++||||||
T Consensus 300 i~~~~~~LQ~aVd~liDn~--~~g~~~~~~~~rp~ksls~~LkGKeGRFR~NLlGKRVDySgRSVIspdP~L~l~e~GvP 377 (627)
T PRK02625 300 VRNEKRMLQEAVDALIDNG--RRGRTVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLP 377 (627)
T ss_pred HHHHHHHHHHHHHHHhcCC--CCCCCcccccCCchhhHHHHhccCCccccccccccccccCCCceEeCCCCcccccccCh
Confidence 4578999999999999999 4332 234567899999999999999999999999999999999999999999999
Q ss_pred HHHHhhCCcCcccCHHHHHHHH
Q psy16766 552 LEFAKTLTYPVPVTPWNVTLLR 573 (621)
Q Consensus 552 ~~fAk~LT~PE~VT~~Ni~~Lr 573 (621)
..||++||+|+ |+++|+
T Consensus 378 ~~mA~eL~~Pf-----~i~~L~ 394 (627)
T PRK02625 378 KEMAIELFQPF-----VIHRLI 394 (627)
T ss_pred HHHHHhcCcHH-----hHHHHH
Confidence 99999999985 555554
No 13
>TIGR02387 rpoC1_cyan DNA-directed RNA polymerase, gamma subunit. The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''.
Probab=100.00 E-value=4.6e-47 Score=414.15 Aligned_cols=166 Identities=27% Similarity=0.393 Sum_probs=137.1
Q ss_pred CCCCceEEEEeeecCCCCCccccccCCC-ccccchhHHHHHHHHHHHHHHHHHHHhhhhchhhhhHHHhhcccCCchhhH
Q psy16766 397 LIATDIMFIRSLVVPPNNLRPLSMEQMP-PVEHSRNKLYQSILYSCGSLKSVIMAMKNKEQSDLLSEALKGIRGDTLNNK 475 (621)
Q Consensus 397 ~~~~d~ffl~~lpVpP~~~RP~~~~~~~-~~ed~~t~~l~~Il~~N~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~ 475 (621)
..+|+||||++|||||+++||++.++|+ ..+||+|.+|+.||..|+.|++.+.... ....
T Consensus 232 ~~~PewmiL~~lPV~Pp~lRP~v~l~~g~~~~sDln~lyr~II~rNn~L~~~~~~~~-------------------p~~i 292 (619)
T TIGR02387 232 SSRPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILA-------------------PEII 292 (619)
T ss_pred CCCcceEEEEecccCCcccCCceEeCCCcccCCCHHHHHHHHHHHHHHHHHHHHcCC-------------------cHHH
Confidence 3479999999999999999999999875 6799999999999999999998653211 1123
Q ss_pred HHHHHHHHHHHHHHhhcccccCCCC----CCCCCccchHHhhccCccccccccCCCccCcccceeecCCCCCccccccch
Q psy16766 476 LQNSWHELQYNVDLLMDAKLNINKT----TGAHQIDGLKQMLDGKTGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVP 551 (621)
Q Consensus 476 l~~~w~~LQ~~V~~~~d~~~~~~~~----~~~k~~~gi~q~L~gKeG~fR~nlmGKRVnfsaRSVIsPDP~l~idevGvP 551 (621)
+.+.|..||.+|+.||||+ ..+. ..+++.+||+|+|+||+||||+|||||||||||||||+|||+|++||||||
T Consensus 293 ~~~~~~~LQ~aVd~lidn~--~~g~~~~~~~~rp~ksls~~LkGKeGRFR~nLlGKRVDySgRSVI~pdP~L~l~qvGvP 370 (619)
T TIGR02387 293 VRNEKRMLQEAVDALIDNG--RRGRTVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLP 370 (619)
T ss_pred HHHHHHHHHHHHHHHhcCC--CCCCCcccccCCchhhHHHHhccCCccccccccccccccCCCceecCCCCcccceecCh
Confidence 4578999999999999999 4332 234567899999999999999999999999999999999999999999999
Q ss_pred HHHHhhCCcCcccCHHHHHHHHHHHHcCC-CCCCcceEEEc
Q psy16766 552 LEFAKTLTYPVPVTPWNVTLLRKMVINGP-NVYPGANMIQN 591 (621)
Q Consensus 552 ~~fAk~LT~PE~VT~~Ni~~Lr~lV~NGp-~~~PGA~~i~~ 591 (621)
..||++||+|+ |+.+|+ .+|. ...+||+.++.
T Consensus 371 ~~mA~eLf~Pf-----~i~~L~---~~g~~~~i~~ak~~i~ 403 (619)
T TIGR02387 371 KEMAIELFQPF-----VIHRLI---RQGIVNNIKAAKKLIQ 403 (619)
T ss_pred HHHHHhcCchH-----hHHHHH---hcCcccchHHHHHHHH
Confidence 99999999875 666654 4554 23356655543
No 14
>CHL00018 rpoC1 RNA polymerase beta' subunit
Probab=100.00 E-value=2.7e-46 Score=412.41 Aligned_cols=166 Identities=27% Similarity=0.420 Sum_probs=140.3
Q ss_pred CCCceEEEEeeecCCCCCccccccCCC-ccccchhHHHHHHHHHHHHHHHHHHHhhhhchhhhhHHHhhcccCCchhhHH
Q psy16766 398 IATDIMFIRSLVVPPNNLRPLSMEQMP-PVEHSRNKLYQSILYSCGSLKSVIMAMKNKEQSDLLSEALKGIRGDTLNNKL 476 (621)
Q Consensus 398 ~~~d~ffl~~lpVpP~~~RP~~~~~~~-~~ed~~t~~l~~Il~~N~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~l 476 (621)
..|+||||++|||||+++||++.++|+ ..+||+|..|+.||..|+.|++...... ......+
T Consensus 259 ~~PewmiL~~lPV~Pp~lRP~v~l~~g~~~~sDln~lyr~II~rNn~L~~~~~~~~-----------------~~p~~~i 321 (663)
T CHL00018 259 IEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDLLTTSR-----------------STPGELV 321 (663)
T ss_pred CCccEEEEEeeeeCCCcccCceEcCCCcccCCChHHHHHHHHHHHHHHHHHHhccc-----------------CCcHHHH
Confidence 469999999999999999999999764 7899999999999999999998653210 0112356
Q ss_pred HHHHHHHHHHHHHhhcccccCCCC----CCCCCccchHHhhccCccccccccCCCccCcccceeecCCCCCccccccchH
Q psy16766 477 QNSWHELQYNVDLLMDAKLNINKT----TGAHQIDGLKQMLDGKTGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVPL 552 (621)
Q Consensus 477 ~~~w~~LQ~~V~~~~d~~~~~~~~----~~~k~~~gi~q~L~gKeG~fR~nlmGKRVnfsaRSVIsPDP~l~idevGvP~ 552 (621)
.++|..||.+|+.|+||+ ..+. ..+++.+||+|+|+||+||||+|||||||||||||||+|||+|+++|||||.
T Consensus 322 ~~~~~~LQ~aVd~lidn~--~~g~~~~~~~~r~~ksls~~LkGK~GrFR~NLlGKRVDySgRSVIvpdP~L~l~e~GlP~ 399 (663)
T CHL00018 322 MCQKKLLQEAVDALLDNG--IRGQPMRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPR 399 (663)
T ss_pred HHHHHHHHHHHHHHhcCC--CCCCccccCCCCCCCCccccccCcCccccccccccccccCCCceecCCCcccccccCChH
Confidence 789999999999999999 4432 2345678999999999999999999999999999999999999999999999
Q ss_pred HHHhhCCcCcccCHHHHHHHHHHHHcCCC-CCCcceEEE
Q psy16766 553 EFAKTLTYPVPVTPWNVTLLRKMVINGPN-VYPGANMIQ 590 (621)
Q Consensus 553 ~fAk~LT~PE~VT~~Ni~~Lr~lV~NGp~-~~PGA~~i~ 590 (621)
.||++||+|+. +++|+.+|+. ...+|+.++
T Consensus 400 ~mA~eL~~P~~--------i~~Li~~~~~~~~~~Ak~~i 430 (663)
T CHL00018 400 EIAIELFQPFV--------IRGLIRQHLASNIRAAKSKI 430 (663)
T ss_pred HHHHHcCcHHH--------HHHHHhcCccccHHHHHHHH
Confidence 99999999984 5678888876 445666543
No 15
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=100.00 E-value=4.2e-45 Score=424.87 Aligned_cols=164 Identities=29% Similarity=0.395 Sum_probs=143.1
Q ss_pred CCCCceEEEEeeecCCCCCccccccCCC-ccccchhHHHHHHHHHHHHHHHHHHHhhhhchhhhhHHHhhcccCCchhhH
Q psy16766 397 LIATDIMFIRSLVVPPNNLRPLSMEQMP-PVEHSRNKLYQSILYSCGSLKSVIMAMKNKEQSDLLSEALKGIRGDTLNNK 475 (621)
Q Consensus 397 ~~~~d~ffl~~lpVpP~~~RP~~~~~~~-~~ed~~t~~l~~Il~~N~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~ 475 (621)
...|+||||++|||||+++||++.++|+ ..+||+|.+|+.||..|+.|++.+.... ....
T Consensus 309 ~~~PewmiL~vlPV~Pp~lRP~V~l~gg~~atsDLn~lyr~II~rNnrLk~l~~~~a-------------------p~~i 369 (1460)
T PRK14906 309 GNDPADMILDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGA-------------------PEII 369 (1460)
T ss_pred CCCHHHHhhhcccCCCCCcCCcEEECCCcccCCchHHHHHHHHHHHHHHHHHHHcCC-------------------cHHH
Confidence 3479999999999999999999999775 6799999999999999999998764211 1124
Q ss_pred HHHHHHHHHHHHHHhhcccccCCCC----CCCCCccchHHhhccCccccccccCCCccCcccceeecCCCCCccccccch
Q psy16766 476 LQNSWHELQYNVDLLMDAKLNINKT----TGAHQIDGLKQMLDGKTGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVP 551 (621)
Q Consensus 476 l~~~w~~LQ~~V~~~~d~~~~~~~~----~~~k~~~gi~q~L~gKeG~fR~nlmGKRVnfsaRSVIsPDP~l~idevGvP 551 (621)
+.+.|..||.+|+.||||. ..+. ..+++.+||+|+|+||+||||+|||||||||||||||+|||+|+++|||||
T Consensus 370 i~nekr~LQeaVd~liDN~--~~g~p~~~~~~rplKsls~~LkGK~GRFRqNLlGKRVDySgRSVIspdP~L~l~e~GlP 447 (1460)
T PRK14906 370 VNNEKRMLQEAVDSLFDNG--RRGRPVTGPGNRPLKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLP 447 (1460)
T ss_pred HHHHHHHHHHHHHHHHcCC--CcCCCCccccCCchhHHHHHhcccCcccccccccccccCcCCceEeCCCCCccccccCc
Confidence 6689999999999999999 4332 234567899999999999999999999999999999999999999999999
Q ss_pred HHHHhhCCcCccc-------CHHHHHHHHHHHHcCCC
Q psy16766 552 LEFAKTLTYPVPV-------TPWNVTLLRKMVINGPN 581 (621)
Q Consensus 552 ~~fAk~LT~PE~V-------T~~Ni~~Lr~lV~NGp~ 581 (621)
..||++||+|+.+ ...|+..++++|.++..
T Consensus 448 ~~mA~eLf~Pf~i~~L~~~~~~~nik~ak~~i~~~~~ 484 (1460)
T PRK14906 448 SAMALELFKPFVMKRLVELEYAANIKAAKRAVDRGAS 484 (1460)
T ss_pred HHHHHhcCchhHHHHHHHhcccccHHHHhhHHhhcCC
Confidence 9999999999988 45789999999998743
No 16
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=100.00 E-value=1.2e-43 Score=427.71 Aligned_cols=154 Identities=29% Similarity=0.448 Sum_probs=131.7
Q ss_pred CCCCceEEEEeeecCCCCCccccccCCC-ccccchhHHHHHHHHHHHHHHHHHHHhhhhchhhhhHHHhhcccCCchhhH
Q psy16766 397 LIATDIMFIRSLVVPPNNLRPLSMEQMP-PVEHSRNKLYQSILYSCGSLKSVIMAMKNKEQSDLLSEALKGIRGDTLNNK 475 (621)
Q Consensus 397 ~~~~d~ffl~~lpVpP~~~RP~~~~~~~-~~ed~~t~~l~~Il~~N~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~ 475 (621)
..+|+||||++|||||+++||++.++|+ ..+||+|.+|+.||..|+.|++.+.... +...
T Consensus 1663 ~~rPewmil~~lPV~Pp~lRP~v~l~~g~~~~sDLn~ly~~II~~NnrLk~~~~~~a-------------------p~~i 1723 (2836)
T PRK14844 1663 GNRPEWMILTTIPILPPDLRPLVSLESGRPAVSDLNHHYRTIINRNNRLRKLLSLNP-------------------PEIM 1723 (2836)
T ss_pred CCChhheeeeccccCCCcccCcEEeCCCcccCCchHHHHHHHHHHHHHHHHHHHcCC-------------------chhh
Confidence 3479999999999999999999999764 7899999999999999999998764211 1124
Q ss_pred HHHHHHHHHHHHHHhhcccccCCCC----CCCCC-ccchHHhhccCccccccccCCCccCcccceeecCCCCCccccccc
Q psy16766 476 LQNSWHELQYNVDLLMDAKLNINKT----TGAHQ-IDGLKQMLDGKTGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGV 550 (621)
Q Consensus 476 l~~~w~~LQ~~V~~~~d~~~~~~~~----~~~k~-~~gi~q~L~gKeG~fR~nlmGKRVnfsaRSVIsPDP~l~idevGv 550 (621)
+.+.|..||.+|+.||||+ ..+. ..+++ .+||+|+|+||+||||+|||||||||||||||+|||+|+++||||
T Consensus 1724 i~~~~~~LQ~~V~~l~Dn~--~~g~~~~~~~~r~~lksls~~LkGK~GRFR~NLlGKRVDySgRSVI~pdP~L~l~evGl 1801 (2836)
T PRK14844 1724 IRNEKRMLQEAVDSLFDNS--RRNALVNKAGAVGYKKSISDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGL 1801 (2836)
T ss_pred HHHHHHHHHHHHHHHhcCC--CCCCCccCCCCCCccccHHHHhcCCCCcccccccccccccCCCceEeCCCCcccceeeC
Confidence 6789999999999999999 4332 11223 579999999999999999999999999999999999999999999
Q ss_pred hHHHHhhCCcCcccCHHHHHHHHHHH
Q psy16766 551 PLEFAKTLTYPVPVTPWNVTLLRKMV 576 (621)
Q Consensus 551 P~~fAk~LT~PE~VT~~Ni~~Lr~lV 576 (621)
|..||++||+| ||+++|+++.
T Consensus 1802 P~~mA~eL~~P-----f~i~~L~~~~ 1822 (2836)
T PRK14844 1802 PKRMALELFKP-----FVYSKLKMYG 1822 (2836)
T ss_pred CHHHHHhcccH-----HHHHHHHHcC
Confidence 99999999997 5677776653
No 17
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=100.00 E-value=1.9e-43 Score=427.40 Aligned_cols=156 Identities=31% Similarity=0.429 Sum_probs=134.7
Q ss_pred CCCCceEEEEeeecCCCCCccccccCCC-ccccchhHHHHHHHHHHHHHHHHHHHhhhhchhhhhHHHhhcccCCchhhH
Q psy16766 397 LIATDIMFIRSLVVPPNNLRPLSMEQMP-PVEHSRNKLYQSILYSCGSLKSVIMAMKNKEQSDLLSEALKGIRGDTLNNK 475 (621)
Q Consensus 397 ~~~~d~ffl~~lpVpP~~~RP~~~~~~~-~~ed~~t~~l~~Il~~N~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~ 475 (621)
..+|+||||++|||||+++||++.++|+ ..++|+|.+|+.||..|+.|++.+.... +...
T Consensus 1620 ~~~PewmiL~~lPV~Pp~lRP~v~l~gg~~a~sDln~lyr~II~rNnrLk~l~~~~a-------------------p~~i 1680 (2890)
T PRK09603 1620 GNRPEWMMLTVLPVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRLMELGA-------------------PEII 1680 (2890)
T ss_pred CCChHheeeeeeccCCCcccCcEEeCCCcccCCCccHHHHHHHHHHHHHHHHHHcCC-------------------Ccee
Confidence 3579999999999999999999999865 6899999999999999999998764211 1123
Q ss_pred HHHHHHHHHHHHHHhhcccccCCCC----CCCCCccchHHhhccCccccccccCCCccCcccceeecCCCCCccccccch
Q psy16766 476 LQNSWHELQYNVDLLMDAKLNINKT----TGAHQIDGLKQMLDGKTGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVP 551 (621)
Q Consensus 476 l~~~w~~LQ~~V~~~~d~~~~~~~~----~~~k~~~gi~q~L~gKeG~fR~nlmGKRVnfsaRSVIsPDP~l~idevGvP 551 (621)
+.+.|..||.+|+.||||+ ..+. ..+++.+||+|+|+||+||||+|||||||||||||||+|||+|+++|||||
T Consensus 1681 i~nek~~LQ~aVd~l~DN~--~~~~~~~~~~~rplKsls~~LkGK~GRFRqNLlGKRVDySgRSVI~pdP~L~l~e~GvP 1758 (2890)
T PRK09603 1681 VRNEKRMLQEAVDVLFDNG--RSTNAVKGANKRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLP 1758 (2890)
T ss_pred hHHHHHHHHHHHHHHhccc--cccccccCCCCCcchhHHHHhcCCCCccccccccccccCcCCceEeCCCCcccccccCh
Confidence 5688999999999999998 4321 234667899999999999999999999999999999999999999999999
Q ss_pred HHHHhhCCcCcccCHHHHHHHHHHHHcCCC
Q psy16766 552 LEFAKTLTYPVPVTPWNVTLLRKMVINGPN 581 (621)
Q Consensus 552 ~~fAk~LT~PE~VT~~Ni~~Lr~lV~NGp~ 581 (621)
..||++||+|+. +++|+.||+.
T Consensus 1759 ~~mA~eL~~P~~--------i~~L~~~G~~ 1780 (2890)
T PRK09603 1759 KNMALELFKPHL--------LSKLEERGYA 1780 (2890)
T ss_pred HHHHHHhCChHH--------HHHHHHcCCc
Confidence 999999999966 4677788863
No 18
>KOG0261|consensus
Probab=100.00 E-value=5.9e-39 Score=352.93 Aligned_cols=189 Identities=27% Similarity=0.412 Sum_probs=149.6
Q ss_pred CCCCCCceeecCCCCCCcccccccHHHHhcCCcceEechhhHHHHHHHHHcCCCCCCCcceeEcCCCcEEEEcc------
Q psy16766 11 AHVFPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRISS------ 84 (621)
Q Consensus 11 ~~~fsaRsVIspDP~l~~~evgvP~~~A~~lt~pe~vt~~N~~~l~~~v~ng~~~~pga~~~~~~~g~~~~~~~------ 84 (621)
+-+||+||||||||||+|||||||..+|+.|||||+||.+|+++||+||+|||++||||||+++.+....+...
T Consensus 358 RVDFSGRTVISPDPNL~IdeVgVP~rvAkiLTfpE~Vt~~Ni~klr~lV~NGP~vhPGANyv~~r~~~~kr~L~yg~R~k 437 (1386)
T KOG0261|consen 358 RVDFSGRTVISPDPNLRIDEVGVPIRVAKILTFPERVTRANIRKLRQLVRNGPNVHPGANYVVQRGEGFKRFLKYGNRDK 437 (1386)
T ss_pred eeeccCceeeCCCCCcceeeccchHHHHHHhcchhhccHHHHHHHHHHHhcCCCCCCCcchhhhcccchhhHhhcCcHHH
Confidence 34899999999999999999999999999999999999999999999999999999999999954322223321
Q ss_pred -cccchhhhhhhhccC--------Ccchhhh-hhhhhhhhcccc--------------cCcceEEEecCCh--HHHH---
Q psy16766 85 -SQAVQRESLAKRLIT--------PEDQQHR-AIMKEKIITRQE--------------VVPEILKLKYYTD--QEVK--- 135 (621)
Q Consensus 85 -~~~~~~~~~~~~ll~--------~~~slhr-sim~~~~~~~p~--------------~~~~g~ef~~~s~--eei~--- 135 (621)
...++.|++++|+|. ++||||| |||+|+++++|| +|||||||++|.| ||++
T Consensus 438 iA~eLk~GdvVERHL~DgDvVLFNRQPSLHkmSIM~H~akV~p~RTfRFNEcvCtPYNADFDGDEMNlHvPQTEEAraEA 517 (1386)
T KOG0261|consen 438 IADELKIGDVVERHLMDGDVVLFNRQPSLHKMSIMSHRAKVMPWRTFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEA 517 (1386)
T ss_pred HHHhhccchHHHhhcccCCEEEEcCCchHHHHHHHHHHhhcccCceeeccccccCCcCCCCCcccccccCCchHHHHHHH
Confidence 246788999999775 5579999 999999999998 5799999999998 4554
Q ss_pred --hhccc-ccccccccCCCCCccccCccCCCCCccccCCCccCCCCCCccccCCc----ccccCCCcccc-cchhh
Q psy16766 136 --QLSVV-KVFSPITFNSLGHTIPGGLYDLAMGPISERGDPCTTCGNNYTKCKGH----IGHIELPVPVI-NTLFF 203 (621)
Q Consensus 136 --~lSv~-~I~~~~~~d~~g~Pi~ggl~D~~lG~~~~~~~~C~tC~~~~~~C~Gh----fGhI~L~~Pv~-hp~f~ 203 (621)
.|.++ ++.+|+. |+|++..+||.+.|.|+++...-+.....+.+.... .-||+||.|++ .|...
T Consensus 518 ~~LMgvknNlvTPr~----GEpiiAAtQDFiTg~YLlt~KDtF~dRa~~~ql~s~~~d~~~~i~lppPaI~KP~~L 589 (1386)
T KOG0261|consen 518 LVLMGVKNNLVTPRN----GEPIIAATQDFITGGYLLTHKDTFLDRAEFSQLCSYMSDAMTHIDLPPPAILKPVEL 589 (1386)
T ss_pred HHHhccccccccCCC----CCceeehhhhhhhcceeeecccccccHHHHHHHHHHHhccccccCCCChhhcCceee
Confidence 34454 6888986 999999999999999987742211222212111111 45899999988 55544
No 19
>KOG0262|consensus
Probab=100.00 E-value=9.8e-38 Score=350.93 Aligned_cols=192 Identities=34% Similarity=0.502 Sum_probs=153.0
Q ss_pred CCCCCCceeecCCCCCCcccccccHHHHhcCCcceEechhhHHHHHHHHHcCCCCCCCcceeEcCCCcEEEEcccccchh
Q psy16766 11 AHVFPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRISSSQAVQR 90 (621)
Q Consensus 11 ~~~fsaRsVIspDP~l~~~evgvP~~~A~~lt~pe~vt~~N~~~l~~~v~ng~~~~pga~~~~~~~g~~~~~~~~~~~~~ 90 (621)
+-+|+|||||||||||.+||||||..||++|||||+||+||+++||++|+|||++||||+|+++++|.++.+......+|
T Consensus 448 RVN~AaRSVIsPDPnI~tnEIGIP~vFA~KLTyPepVt~~NV~elr~aViNGP~~hPGA~~iqd~dg~~t~l~~~~~~qR 527 (1640)
T KOG0262|consen 448 RVNYAARSVISPDPNIETNEIGIPPVFAKKLTYPEPVTPWNVNELRKAVINGPDVHPGATYIQDEDGTLTLLSPMTDEQR 527 (1640)
T ss_pred ccchhhccccCCCCCccccccCCchHHHhhccCCCcCCcccHHHHHHHHhcCCCCCCCcceeecCCCceeecCCCCHHHH
Confidence 45799999999999999999999999999999999999999999999999999999999999999999988876777788
Q ss_pred hhhhhhcc---------------------------CCcchhhh-hhhhhhhhcccc---------------cCcceEEEe
Q psy16766 91 ESLAKRLI---------------------------TPEDQQHR-AIMKEKIITRQE---------------VVPEILKLK 127 (621)
Q Consensus 91 ~~~~~~ll---------------------------~~~~slhr-sim~~~~~~~p~---------------~~~~g~ef~ 127 (621)
+++|++|| ||+||||| |||||+++++|. +||||||||
T Consensus 528 ~alA~qLLtpst~~~~~~~~K~V~RHvknGDvvlmNRQPTLHKPSimaHkaRVL~gEktlRlHYANCkaYNADFDGDEMN 607 (1640)
T KOG0262|consen 528 EALANQLLTPSTGNPTEFGTKKVHRHVKNGDVVLMNRQPTLHKPSIMAHKARVLPGEKTLRLHYANCKAYNADFDGDEMN 607 (1640)
T ss_pred HHHHHHhhccccCCCcccCCceeeeeccCCcEEEEcCCCccccchhhhhhheecCCcceeeeeecccccccCCCCcchhc
Confidence 88888876 35689999 999999999984 699999999
Q ss_pred cCChH-HHHhhcccccccc--ccc-CCCCCccccCccCC-CCCccccCCCccCCCCCCcc----cc-CCcccccCCCccc
Q psy16766 128 YYTDQ-EVKQLSVVKVFSP--ITF-NSLGHTIPGGLYDL-AMGPISERGDPCTTCGNNYT----KC-KGHIGHIELPVPV 197 (621)
Q Consensus 128 ~~s~e-ei~~lSv~~I~~~--~~~-d~~g~Pi~ggl~D~-~lG~~~~~~~~C~tC~~~~~----~C-~GhfGhI~L~~Pv 197 (621)
+|.|| |+.+.-..+|.+. ++. ..+|.|+.|.+||. .+|+++..++.++|- .++. .| --.++.|.|..|.
T Consensus 608 ~HfPQse~araEa~~ian~dsqYLvPt~G~PlrGLIQDHiVsgv~LT~rd~Fftr-e~y~qLv~~~l~~~~~rI~~lpPt 686 (1640)
T KOG0262|consen 608 VHFPQSEIARAEAYNIANTDSQYLVPTDGTPLRGLIQDHIVSGVLLTMRDSFFTR-EDYQQLVFAGLSDTFKRIKLLPPT 686 (1640)
T ss_pred ccCCchhhHHHHHHHHhccCCceeccCCCCchhhhhhhheeeeEEEEecccccCH-HHHHHHHHHhhhhhccceeccCcc
Confidence 99996 4433333344332 222 44699999999995 557744334544442 2222 11 1256999999999
Q ss_pred c-cchhh
Q psy16766 198 I-NTLFF 203 (621)
Q Consensus 198 ~-hp~f~ 203 (621)
| -|.-+
T Consensus 687 IlkP~~L 693 (1640)
T KOG0262|consen 687 ILKPAPL 693 (1640)
T ss_pred ccccccc
Confidence 8 44444
No 20
>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Probab=100.00 E-value=1.6e-37 Score=370.23 Aligned_cols=196 Identities=28% Similarity=0.415 Sum_probs=155.3
Q ss_pred CCCCCCCceeecCCCCCCcccccccHHHHhcCCcceEechhhHHHHHHHHHcCCCCCCCcceeEcCCCcEEEEccc----
Q psy16766 10 HAHVFPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRISSS---- 85 (621)
Q Consensus 10 ~~~~fsaRsVIspDP~l~~~evgvP~~~A~~lt~pe~vt~~N~~~l~~~v~ng~~~~pga~~~~~~~g~~~~~~~~---- 85 (621)
-+.+|||||||||||||++||||||..||++|||||+||+||+++||++|.|||+.||||+||++++|+++.+...
T Consensus 328 KRVdfSaRtVIspDP~L~i~EVGvP~~iA~~LT~Pe~Vt~~Ni~~l~~lv~nG~~~~pGA~~i~~~~g~~~~l~~~~~~~ 407 (1321)
T PRK14977 328 KRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKMKELVINGPDEFPGANAIRKGDGTKIRLDFLEDKG 407 (1321)
T ss_pred cccccccceeEeCCCCcccccccCHHHHHHhCCCCEEEchhhHHHHHHHHHcCCcccCCcceEEcCCCceeeehhhhhcc
Confidence 4678999999999999999999999999999999999999999999999999999999999999999988777421
Q ss_pred --------ccchhhhhhhhcc--------CCcchhhh-hhhhhhhhcccc--------------cCcceEEEecCChH--
Q psy16766 86 --------QAVQRESLAKRLI--------TPEDQQHR-AIMKEKIITRQE--------------VVPEILKLKYYTDQ-- 132 (621)
Q Consensus 86 --------~~~~~~~~~~~ll--------~~~~slhr-sim~~~~~~~p~--------------~~~~g~ef~~~s~e-- 132 (621)
..+..|++++|+| ||+||||| |||+|+++++|+ ||||||||++|.||
T Consensus 408 ~~~~~~~a~~L~~g~iV~Rhl~dGD~VL~NRQPSLHk~Simah~vkvl~~kT~Rln~~vC~pyNADFDGDEMNlHvPQS~ 487 (1321)
T PRK14977 408 KDALREAAEQLEIGDIVERHLADGDIVIFNRQPSLHKLSILAHRVKVLPGATFRLHPAVCPPYNADFDGDEMNLHVPQIE 487 (1321)
T ss_pred chhHHHHHHhcccCcEEEEEeecCcEEEeccCCccccccceEEEEEEecCceEEecccccCcccCCcccceeeeecCCCH
Confidence 2345788999954 67789999 999999998885 68999999999985
Q ss_pred ----HHHhhc-c-cccccccccCCCCCccccCccCCCCCccccCCCccCCCCCCccccCCcccc-cCCCccccc--c--h
Q psy16766 133 ----EVKQLS-V-VKVFSPITFNSLGHTIPGGLYDLAMGPISERGDPCTTCGNNYTKCKGHIGH-IELPVPVIN--T--L 201 (621)
Q Consensus 133 ----ei~~lS-v-~~I~~~~~~d~~g~Pi~ggl~D~~lG~~~~~~~~C~tC~~~~~~C~GhfGh-I~L~~Pv~h--p--~ 201 (621)
|++.++ + .+|.+|+. |+|+.|.+||.++|+|.++....+.-..++.+.....|. +.||.|++- | +
T Consensus 488 eArAEa~~Lm~v~~niisP~~----G~Pi~gliQD~l~g~~lLT~~d~fl~~~e~~~l~~~~~~~~~lp~PaI~~kp~~l 563 (1321)
T PRK14977 488 DARAEAIELMGVKDNLISPRT----GGPIIGALQDFITAAYLITKDDALFDKNEASNIAMLAGITDPLPEPAIKTKDGPA 563 (1321)
T ss_pred HHHHHHHHHHhhhhcEecCCC----CCeeEEeehhhhhhhhhhccCcccCCHHHHHHHHHhCCCccccCCCceecCCCCe
Confidence 444444 3 58999986 999999999999999987743222222223332222333 458888774 3 3
Q ss_pred hh-HhHHHH
Q psy16766 202 FF-RDVQLL 209 (621)
Q Consensus 202 f~-~~v~~l 209 (621)
|. |+|+.+
T Consensus 564 wTGKQi~s~ 572 (1321)
T PRK14977 564 WTGKQLFSL 572 (1321)
T ss_pred eeHHHHHHH
Confidence 32 555554
No 21
>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=3.1e-36 Score=351.34 Aligned_cols=197 Identities=28% Similarity=0.443 Sum_probs=154.5
Q ss_pred CCCCCCCceeecCCCCCCcccccccHHHHhcCCcceEechhhHHHHHHHHHcCCCCCCCcceeEcCCCcEEEEccc----
Q psy16766 10 HAHVFPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRISSS---- 85 (621)
Q Consensus 10 ~~~~fsaRsVIspDP~l~~~evgvP~~~A~~lt~pe~vt~~N~~~l~~~v~ng~~~~pga~~~~~~~g~~~~~~~~---- 85 (621)
.+.+|||||||||||+|++||||||..||++|||||+||+||+++|+++|.|||+.||||+|+++++|+++.+...
T Consensus 314 KRvd~s~RsVI~pdp~l~~~evGvP~~~A~~Lt~pe~Vt~~N~~~l~~lv~ng~~~~pga~~i~~~~g~~~~l~~~~~~~ 393 (868)
T TIGR02390 314 KRVNFSARTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVLNGPDSWPGANYVIRPDGRRIKIRDENKEE 393 (868)
T ss_pred ccccccCCceeeCCCCCcCCeeeCcHHHHHhCCCCeEEehhhHHHHHHHHHcCCccCCCceEEEcCCCcEEechhhhHHH
Confidence 4679999999999999999999999999999999999999999999999999999999999999999998877632
Q ss_pred --ccchhhhhhhhcc--------CCcchhhh-hhhhhhhhcccc--------------cCcceEEEecCChH------HH
Q psy16766 86 --QAVQRESLAKRLI--------TPEDQQHR-AIMKEKIITRQE--------------VVPEILKLKYYTDQ------EV 134 (621)
Q Consensus 86 --~~~~~~~~~~~ll--------~~~~slhr-sim~~~~~~~p~--------------~~~~g~ef~~~s~e------ei 134 (621)
..++.|++++|++ ||+||||| |||||+++++|+ ||||||||++|.|+ |+
T Consensus 394 ~~~~l~~g~~v~rhl~dgd~vl~NRqPsLHr~si~a~~~~v~~~~t~r~n~~~c~~~NADFDGDeMn~h~Pqs~~a~aEa 473 (868)
T TIGR02390 394 LAERLEPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEA 473 (868)
T ss_pred HHhhcccCCEEEEehhcCccceeccCCccccccceeEEEEEecCceEeeccccCCccccCcccceeeEecCCCHHHHHHH
Confidence 2356678888854 67789999 999999988885 68999999999884 44
Q ss_pred Hhhc-c-cccccccccCCCCCccccCccCCCCCccccCC-CccCCCCCCccccCCc-ccccCCCcccc-cchhhHhHHHH
Q psy16766 135 KQLS-V-VKVFSPITFNSLGHTIPGGLYDLAMGPISERG-DPCTTCGNNYTKCKGH-IGHIELPVPVI-NTLFFRDVQLL 209 (621)
Q Consensus 135 ~~lS-v-~~I~~~~~~d~~g~Pi~ggl~D~~lG~~~~~~-~~C~tC~~~~~~C~Gh-fGhI~L~~Pv~-hp~f~~~v~~l 209 (621)
+.++ + .++.+|+. |+|+.|.+||.++|+|.++. +...+- .++.+..+. .-.+++|.|++ .|.-+++=.+|
T Consensus 474 ~~Lm~~~~~~~sp~~----g~p~~~~~QD~l~g~~~LT~~d~f~~~-~~~~~l~~~~~~~~~~~~p~i~kp~~lwTGKqi 548 (868)
T TIGR02390 474 RELMLVEEHILTPRY----GGPIIGGIHDYISGAYLLTHKSTLFTK-EEVQTILGVAGYFGDPPEPAIEKPKEYWTGKQI 548 (868)
T ss_pred HHHhhchhceecCCC----CCeeEEeehhhhhheeeeeeccccCCH-HHHHHHHhcCCccccCCCceecCCcccccHHHH
Confidence 4444 2 58899986 99999999999999998774 333332 222222111 11355777876 34444444444
Q ss_pred Hh
Q psy16766 210 LK 211 (621)
Q Consensus 210 L~ 211 (621)
+.
T Consensus 549 ~s 550 (868)
T TIGR02390 549 FS 550 (868)
T ss_pred HH
Confidence 43
No 22
>PRK08566 DNA-directed RNA polymerase subunit A'; Validated
Probab=100.00 E-value=4.1e-36 Score=351.20 Aligned_cols=185 Identities=30% Similarity=0.458 Sum_probs=150.7
Q ss_pred CCCCCCCCceeecCCCCCCcccccccHHHHhcCCcceEechhhHHHHHHHHHcCCCCCCCcceeEcCCCcEEEEccc---
Q psy16766 9 NHAHVFPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRISSS--- 85 (621)
Q Consensus 9 ~~~~~fsaRsVIspDP~l~~~evgvP~~~A~~lt~pe~vt~~N~~~l~~~v~ng~~~~pga~~~~~~~g~~~~~~~~--- 85 (621)
..+.+|||||||||||+|++||||||..||++|||||+||+||+++|+++|.|||+.||||+|+++++|+++.+...
T Consensus 317 GKRvd~s~RsVI~pdp~l~~~evGvP~~~A~~Lt~pe~v~~~N~~~l~~~v~ng~~~~pga~~i~~~~g~~~~l~~~~~~ 396 (882)
T PRK08566 317 GKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNGPEKHPGANYVIRPDGRRIKLTDKNKE 396 (882)
T ss_pred cccccCcCCceeeCCCCCcCCeeeCcHHHHHhCCCCeEEchhhHHHHHHHHHcCCCcCCCceEEEcCCCceeeehhhhHH
Confidence 35779999999999999999999999999999999999999999999999999999999999999999988777421
Q ss_pred ---ccchhhhhhhhc--------cCCcchhhh-hhhhhhhhcccc--------------cCcceEEEecCChH------H
Q psy16766 86 ---QAVQRESLAKRL--------ITPEDQQHR-AIMKEKIITRQE--------------VVPEILKLKYYTDQ------E 133 (621)
Q Consensus 86 ---~~~~~~~~~~~l--------l~~~~slhr-sim~~~~~~~p~--------------~~~~g~ef~~~s~e------e 133 (621)
..+..|++++|+ ++|+||||| |||||+++++|+ ||||||||++|.|+ |
T Consensus 397 ~~~~~l~~g~~v~Rhl~dgd~vl~NRqPsLHr~si~a~~~~v~~~~t~r~n~~~c~~~NADFDGDeMn~h~Pqs~~a~aE 476 (882)
T PRK08566 397 ELAEKLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAE 476 (882)
T ss_pred HHHHhccccceehhhhhcCceeeecCCCcccccccceeEEEEecCceEeeccccCCCccCCccCcEEEEecCCCHHHHHH
Confidence 234567888885 467789999 999999998885 68999999999884 4
Q ss_pred HHhhc-c-cccccccccCCCCCccccCccCCCCCccccCC-CccCCCCCCccccCCccc--ccCCCcccc
Q psy16766 134 VKQLS-V-VKVFSPITFNSLGHTIPGGLYDLAMGPISERG-DPCTTCGNNYTKCKGHIG--HIELPVPVI 198 (621)
Q Consensus 134 i~~lS-v-~~I~~~~~~d~~g~Pi~ggl~D~~lG~~~~~~-~~C~tC~~~~~~C~GhfG--hI~L~~Pv~ 198 (621)
++.++ + .++.+|+. |+|+.|.+||.++|+|.++. +...+ ..++.+....++ .+++|.|++
T Consensus 477 a~~Lm~~~~~~~sp~~----g~pi~~~~QD~l~g~~~lt~~d~f~~-~~~~~~l~~~~~~~~~~~~~pai 541 (882)
T PRK08566 477 ARILMLVQEHILSPRY----GGPIIGGIQDHISGAYLLTRKSTLFT-KEEALDLLRAAGIDELPEPEPAI 541 (882)
T ss_pred HHHHhcchhcEecCCC----CCeeEEeehHHHHHHHHHHhccccCC-HHHHHHHHHhCCccccccCCccc
Confidence 44444 2 58899986 99999999999999988774 33323 233333333333 367788876
No 23
>KOG0260|consensus
Probab=100.00 E-value=4.5e-36 Score=336.18 Aligned_cols=208 Identities=22% Similarity=0.279 Sum_probs=167.8
Q ss_pred CCCCCCCCceeecCCCCCCcccccccHHHHhcCCcceEechhhHHHHHHHHHcCCCCCCCcceeEcCCCcEEEEcccc--
Q psy16766 9 NHAHVFPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRISSSQ-- 86 (621)
Q Consensus 9 ~~~~~fsaRsVIspDP~l~~~evgvP~~~A~~lt~pe~vt~~N~~~l~~~v~ng~~~~pga~~~~~~~g~~~~~~~~~-- 86 (621)
..+++|||||||+|||||++||||||+.||++|||||.||+|||++|++||.+|+..||||+|+++.+|.+++++...
T Consensus 334 GKRvDFSaRTVItgDPnl~ldevGVP~sIAk~lTfpE~Vtp~NidrLqeLV~~g~~~~pgakyiird~G~Ridlr~~~~~ 413 (1605)
T KOG0260|consen 334 GKRVDFSARTVITGDPNLSLDEVGVPRSIAKRLTFPEHVTPFNIDRLQELVRRGLLEHPGAKYIIRDNGDRIDLRYHKRA 413 (1605)
T ss_pred ccccCcceeeeecCCCCcchhcccCcHHHHhhccCcceeccccHHHHHHHhhCCCCCCCCcceeeecCCcEEEEeecCCc
Confidence 457899999999999999999999999999999999999999999999999999999999999999999999987543
Q ss_pred ---cchhhhhhhhccCCc--------chhhh-hhhhhhhhcccc--------------cCcceEEEecCChH------HH
Q psy16766 87 ---AVQRESLAKRLITPE--------DQQHR-AIMKEKIITRQE--------------VVPEILKLKYYTDQ------EV 134 (621)
Q Consensus 87 ---~~~~~~~~~~ll~~~--------~slhr-sim~~~~~~~p~--------------~~~~g~ef~~~s~e------ei 134 (621)
+++.|+.++|++.|| ||||+ |||||+|+++|+ +|||||||++|.|| |+
T Consensus 414 ~d~~Lq~G~kVeRhl~DGD~VlfNRqPSlHKmSmmahrVrVlp~sTfrLNlsvtsPynADFDGDemnlhvPQS~etkAEl 493 (1605)
T KOG0260|consen 414 GDIHLQPGYKVERHLMDGDVVLFNRQPSLHKMSMMAHRVRVLPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSLETKAEL 493 (1605)
T ss_pred cccccccccEEEEeeccCCEEEEcCCCcHHHhhhhhcEEEEccCceEEeCeeecCCccCCCCCceeecccCcchhHHHHH
Confidence 789999999987554 69999 999999999997 58999999999996 44
Q ss_pred Hhhc-c-cccccccccCCCCCccccCccCCCCCccccCCCccCCCCCCccccCCcccccCCCcc---cc-cchhhHhHHH
Q psy16766 135 KQLS-V-VKVFSPITFNSLGHTIPGGLYDLAMGPISERGDPCTTCGNNYTKCKGHIGHIELPVP---VI-NTLFFRDVQL 208 (621)
Q Consensus 135 ~~lS-v-~~I~~~~~~d~~g~Pi~ggl~D~~lG~~~~~~~~C~tC~~~~~~C~GhfGhI~L~~P---v~-hp~f~~~v~~ 208 (621)
.++. | ++|.+|++ |+|+.|.+||.++|.+..+...|+.-...+.+..-..--.+++.| ++ .|.-.+.-.|
T Consensus 494 ~EL~~vpkQiispQs----nkpvmgivQDTLta~R~~t~Rd~Fl~r~~vmnLlm~~p~~d~~~Pa~pai~Kp~PlWTGkQ 569 (1605)
T KOG0260|consen 494 EELAMVPKQIISPQS----NKPVMGIVQDTLTAVRKMTKRDVFLNRAQVMNLLMYVPDWDGPPPAKPAILKPKPLWTGKQ 569 (1605)
T ss_pred HHHhhhhhhhcCCcC----CCcceeeehhhHHHHHHHhhHhhhhcHHHHHHHHhhccccCCCCCCCcccCCCCcccchhh
Confidence 4554 3 68999997 999999999999999765544465544333322211113455555 44 5666667777
Q ss_pred HHhhcc---ccccCc
Q psy16766 209 LLKLSC---FLCHKI 220 (621)
Q Consensus 209 lL~~iC---~~C~~l 220 (621)
||..+= ++|-+.
T Consensus 570 ifsliiP~~in~~r~ 584 (1605)
T KOG0260|consen 570 IFSLIIPGGINYIRD 584 (1605)
T ss_pred heeeecCCCcceecc
Confidence 776554 355554
No 24
>smart00663 RPOLA_N RNA polymerase I subunit A N-terminus.
Probab=100.00 E-value=1.6e-33 Score=289.98 Aligned_cols=150 Identities=31% Similarity=0.491 Sum_probs=128.0
Q ss_pred CCCCCCCCceeecCCCCCCcccccccHHHHhcCCcceEechhhHHHHHHHHHcCCCCCCCcceeEcCCCcEEEEcc----
Q psy16766 9 NHAHVFPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRISS---- 84 (621)
Q Consensus 9 ~~~~~fsaRsVIspDP~l~~~evgvP~~~A~~lt~pe~vt~~N~~~l~~~v~ng~~~~pga~~~~~~~g~~~~~~~---- 84 (621)
..+.+|||||||||||+|++||||||..||++||+||.||.||+++|+++|.||+ |||+|+++ |....+..
T Consensus 109 GKRvd~s~RsVI~pdP~l~~~evgiP~~~A~~Lt~pe~v~~~n~~~l~~lv~ng~---pga~~i~~--g~~~~l~~~~~~ 183 (295)
T smart00663 109 GKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKLVRNGP---NGAKYIIR--GKKTNLKLAKRS 183 (295)
T ss_pred cccccccCceEEeCCCCcceeEeeCCHHHHHhCCcCEEEhHHHHHHHHHHHhcCC---CCceEEEe--CcEEEchhhhhH
Confidence 4678999999999999999999999999999999999999999999999999998 99999996 66666542
Q ss_pred --cccchhhhhhhhc--------cCCcchhhh-hhhhhhhhcccc--------------cCcceEEEecCChH------H
Q psy16766 85 --SQAVQRESLAKRL--------ITPEDQQHR-AIMKEKIITRQE--------------VVPEILKLKYYTDQ------E 133 (621)
Q Consensus 85 --~~~~~~~~~~~~l--------l~~~~slhr-sim~~~~~~~p~--------------~~~~g~ef~~~s~e------e 133 (621)
...+..+++++|+ ++|+||||| |||||+++++++ ||||||||++|.|+ |
T Consensus 184 ~~~~~l~~g~~v~r~l~dgd~Vl~NRqPsLHr~si~a~~v~v~~~~tir~n~~~c~~fNADFDGDeMnih~pqs~~a~aE 263 (295)
T smart00663 184 KIAKHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLVCSPYNADFDGDEMNLHVPQSLEARAE 263 (295)
T ss_pred HHHhcCccccEeheehhcCCEEEEecCCccccccceeEEEEEecCceEEecCccCCcccCCcCCCEEEEecCCCHHHHHH
Confidence 1234567888884 467789999 999999887764 78999999999883 4
Q ss_pred HHhhc--ccccccccccCCCCCccccCccCCCCCcc
Q psy16766 134 VKQLS--VVKVFSPITFNSLGHTIPGGLYDLAMGPI 167 (621)
Q Consensus 134 i~~lS--v~~I~~~~~~d~~g~Pi~ggl~D~~lG~~ 167 (621)
++.++ ..++.+|.+ |+|+.|.+||.++|+|
T Consensus 264 a~~Lm~~~~~~~sp~~----g~p~~~~~QD~l~g~~ 295 (295)
T smart00663 264 ARELMLVPNNILSPKN----GKPIIGPIQDMLLGLY 295 (295)
T ss_pred HHHHhhhhhccccCCC----CCeeEeeecceeeecC
Confidence 54444 258889886 9999999999999974
No 25
>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=99.97 E-value=1.6e-32 Score=261.19 Aligned_cols=123 Identities=37% Similarity=0.625 Sum_probs=100.6
Q ss_pred CCCCCCceeecCCCCCCcccccccHHHHhcCCcceEechhhHHHHHHHHHcCCCCCCCcceeEcCCCcEEEEccc-----
Q psy16766 11 AHVFPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRISSS----- 85 (621)
Q Consensus 11 ~~~fsaRsVIspDP~l~~~evgvP~~~A~~lt~pe~vt~~N~~~l~~~v~ng~~~~pga~~~~~~~g~~~~~~~~----- 85 (621)
+-+|||||||+|||+|+++|||||..||++||+||.||+||+++|+++|.||++.||||+|+++.+|....+...
T Consensus 3 RVnfSaRSVItpDP~L~~~EvGiP~~iA~~Lt~Pe~Vt~~N~~~l~~~v~ng~~~~pga~~i~~~~~~~~~l~~~~~~~~ 82 (166)
T PF00623_consen 3 RVNFSARSVITPDPNLKIDEVGIPIEIAKKLTFPERVTPFNIEKLRKLVINGPDKYPGANYIKRSNGNKISLRYKKFKIS 82 (166)
T ss_dssp EESSEEEEEEEEETTSCTTEEEEEHHHHHHCECCHHHHTTTHHHHHHHHHHTTTSSSSEEEEESTTCHCCCTTSSSSCCC
T ss_pred CcccCCCcEEECCCCCccceecccHHHHhhCCCcEEEHHHHHHHHHHHHhcCcccchhhhhhhcccCcceeeeecccccc
Confidence 357999999999999999999999999999999999999999999999999999999999999888887777643
Q ss_pred ccchhhhhhhhc--------cCCcchhhh-hhhhhhhhcccc--------------cCcceEEEecCChHH
Q psy16766 86 QAVQRESLAKRL--------ITPEDQQHR-AIMKEKIITRQE--------------VVPEILKLKYYTDQE 133 (621)
Q Consensus 86 ~~~~~~~~~~~l--------l~~~~slhr-sim~~~~~~~p~--------------~~~~g~ef~~~s~ee 133 (621)
..++.+++++|+ ++|+||||| |||+|++++.+. +|||||||++|.|+.
T Consensus 83 ~~l~~~~~v~r~l~~gd~vl~nRqPtLh~~s~~a~~~~~~~~~t~~~~~~~c~~~NADFDGDem~i~~p~~ 153 (166)
T PF00623_consen 83 KKLRIGDIVERHLCDGDIVLLNRQPTLHRMSIMAHKVRVLPGKTIRINPLVCSPFNADFDGDEMNIHLPQS 153 (166)
T ss_dssp HHHHTT-EEEEEHTTT-EEEEEESS-SSGGGEEEEEEEEESSSSEEEEGGGHHHHT--TSS-EEEEE--SS
T ss_pred ceecchhhHHHhhhcCceeEEeccchhccceeeeeeeeeecccEEEeeccchhhhhccCCcceEEEEecCC
Confidence 233445677774 466789999 999999876553 789999999998853
No 26
>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=99.93 E-value=1.7e-27 Score=226.67 Aligned_cols=79 Identities=56% Similarity=0.997 Sum_probs=76.4
Q ss_pred CCccCcccceeecCCCCCccccccchHHHHhhCCcCcccCHHHHHHHHHHHHcCCCCCCcceEEEcCCCcEEEeCCCch
Q psy16766 526 GKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRISSSQA 604 (621)
Q Consensus 526 GKRVnfsaRSVIsPDP~l~idevGvP~~fAk~LT~PE~VT~~Ni~~Lr~lV~NGp~~~PGA~~i~~~~G~~~~L~~~~~ 604 (621)
||||||||||||||||+|++||||||..||++||+||.||+||+++|+++|.|||+.||||+++++.+|.++.|...+.
T Consensus 1 GKRVnfSaRSVItpDP~L~~~EvGiP~~iA~~Lt~Pe~Vt~~N~~~l~~~v~ng~~~~pga~~i~~~~~~~~~l~~~~~ 79 (166)
T PF00623_consen 1 GKRVNFSARSVITPDPNLKIDEVGIPIEIAKKLTFPERVTPFNIEKLRKLVINGPDKYPGANYIKRSNGNKISLRYKKF 79 (166)
T ss_dssp CEEESSEEEEEEEEETTSCTTEEEEEHHHHHHCECCHHHHTTTHHHHHHHHHHTTTSSSSEEEEESTTCHCCCTTSSSS
T ss_pred CCCcccCCCcEEECCCCCccceecccHHHHhhCCCcEEEHHHHHHHHHHHHhcCcccchhhhhhhcccCcceeeeeccc
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999987643
No 27
>CHL00018 rpoC1 RNA polymerase beta' subunit
Probab=99.91 E-value=9.7e-26 Score=249.82 Aligned_cols=148 Identities=21% Similarity=0.194 Sum_probs=114.7
Q ss_pred CCCCCCCceeecCCCCCCcccccccHHHHhcCCcceEechhhHHHHHHHHHcCCC-CCCCcceeEcCCCcEEEEcccccc
Q psy16766 10 HAHVFPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPN-VYPGANMIQNEDGSVVRISSSQAV 88 (621)
Q Consensus 10 ~~~~fsaRsVIspDP~l~~~evgvP~~~A~~lt~pe~vt~~N~~~l~~~v~ng~~-~~pga~~~~~~~g~~~~~~~~~~~ 88 (621)
.+-+|||||||||||+|++||||||..||++||+|+. +++|+.+|+. .+.+|+..+.+++..+..- ..+.
T Consensus 374 KRVDySgRSVIvpdP~L~l~e~GlP~~mA~eL~~P~~--------i~~Li~~~~~~~~~~Ak~~i~~~~~~~~~V-lr~v 444 (663)
T CHL00018 374 KRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQPFV--------IRGLIRQHLASNIRAAKSKIREKEPIVWEI-LQEV 444 (663)
T ss_pred cccccCCCceecCCCcccccccCChHHHHHHcCcHHH--------HHHHHhcCccccHHHHHHHHHhcCCcccEe-eeeh
Confidence 4678999999999999999999999999999999985 6889999964 5678888776544322111 0112
Q ss_pred hhhhhhhhccCCcchhhh-hhhhhhhhccc--------------ccCcceEEEecCChH------HHHhhc--ccccccc
Q psy16766 89 QRESLAKRLITPEDQQHR-AIMKEKIITRQ--------------EVVPEILKLKYYTDQ------EVKQLS--VVKVFSP 145 (621)
Q Consensus 89 ~~~~~~~~ll~~~~slhr-sim~~~~~~~p--------------~~~~~g~ef~~~s~e------ei~~lS--v~~I~~~ 145 (621)
..|++| |+||+||||| |||||+++..+ .||||||||++|.|+ |++.++ ..++.+|
T Consensus 445 ~~gd~V--LlNRqPTLHR~sIqAf~~~L~~gktIrLhplvC~~fNADFDGDqMnvHvPqS~eA~aEa~~Lm~~~~nilsP 522 (663)
T CHL00018 445 MQGHPV--LLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSP 522 (663)
T ss_pred hcCcee--eecCCCcccccccceeeEEecCCCeEEeCcccCCcccCCccCcEEEEecCCCHHHHHHHHHHhcCccceeEc
Confidence 222222 6899999999 99999876544 379999999999984 444443 3588888
Q ss_pred cccCCCCCccccCccCCCCCccccCCC
Q psy16766 146 ITFNSLGHTIPGGLYDLAMGPISERGD 172 (621)
Q Consensus 146 ~~~d~~g~Pi~ggl~D~~lG~~~~~~~ 172 (621)
.+ |+|+.+..||.++|.|.++..
T Consensus 523 ~~----G~Pi~~~~QD~ilG~y~LT~~ 545 (663)
T CHL00018 523 AI----GDPISVPSQDMLLGLYVLTIG 545 (663)
T ss_pred CC----CceeEeechhhhhhhheeccc
Confidence 86 999999999999999887643
No 28
>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional
Probab=99.90 E-value=2.3e-25 Score=244.53 Aligned_cols=148 Identities=21% Similarity=0.224 Sum_probs=110.5
Q ss_pred CCCCCCCCceeecCCCCCCcccccccHHHHhcCCcceEechhhHHHHHHHHHcCC-CCCCCcceeEcCCCcE-EEEcccc
Q psy16766 9 NHAHVFPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGP-NVYPGANMIQNEDGSV-VRISSSQ 86 (621)
Q Consensus 9 ~~~~~fsaRsVIspDP~l~~~evgvP~~~A~~lt~pe~vt~~N~~~l~~~v~ng~-~~~pga~~~~~~~g~~-~~~~~~~ 86 (621)
..+-+|||||||||||+|++||||||..||.+||+|+ |+.+| +.+|. ...++|+.++..++.. ..+. .
T Consensus 352 GKRVDySgRSVIspdP~L~l~e~GvP~~mA~eL~~Pf-----~i~~L---~~~g~~~~i~~ak~~i~~~~~~~~~Vl--r 421 (627)
T PRK02625 352 GKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPF-----VIHRL---IRQGIVNNIKAAKKLIQRADPEVWQVL--E 421 (627)
T ss_pred ccccccCCCceEeCCCCcccccccChHHHHHhcCcHH-----hHHHH---HHcCchhhHHHHHHHHHhcCCcccEEE--E
Confidence 3567999999999999999999999999999999995 55544 56664 3456777776543321 1111 0
Q ss_pred cchhhhhhhhccCCcchhhh-hhhhhhhhcccc--------------cCcceEEEecCChH------HHHhhc--ccccc
Q psy16766 87 AVQRESLAKRLITPEDQQHR-AIMKEKIITRQE--------------VVPEILKLKYYTDQ------EVKQLS--VVKVF 143 (621)
Q Consensus 87 ~~~~~~~~~~ll~~~~slhr-sim~~~~~~~p~--------------~~~~g~ef~~~s~e------ei~~lS--v~~I~ 143 (621)
+..-|+.+ |++|+||||| |||||+++..++ ||||||||++|.|+ |++.++ ..++.
T Consensus 422 ~v~~gd~V--LlNRqPTLHR~sIqAf~~~l~~~ktirlhplvC~~fNADFDGDeMnvHvPqS~~A~aEa~~Lm~~~~nil 499 (627)
T PRK02625 422 EVIEGHPV--LLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQAEARLLMLASNNIL 499 (627)
T ss_pred EeecCcEE--EecCCCccccccceeEeeEEcCCCeEEeccccCCcccCCcCCCeEEEecCCCHHHHHHHHHHhcCccceE
Confidence 12223332 7899999999 999999765553 79999999999884 444433 35788
Q ss_pred cccccCCCCCccccCccCCCCCccccCCC
Q psy16766 144 SPITFNSLGHTIPGGLYDLAMGPISERGD 172 (621)
Q Consensus 144 ~~~~~d~~g~Pi~ggl~D~~lG~~~~~~~ 172 (621)
+|.+ |+|+.+..||.++|.|.++..
T Consensus 500 sP~~----G~Pi~~~~QD~llG~y~LT~~ 524 (627)
T PRK02625 500 SPAT----GEPIVTPSQDMVLGCYYLTAE 524 (627)
T ss_pred EcCC----CceeEeechhhhhheeeeecc
Confidence 8886 999999999999999877643
No 29
>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=99.90 E-value=3.5e-25 Score=242.82 Aligned_cols=147 Identities=20% Similarity=0.212 Sum_probs=111.0
Q ss_pred CCCCCCCCceeecCCCCCCcccccccHHHHhcCCcceEechhhHHHHHHHHHcCC-CCCCCcceeEcCCCcEEEEccccc
Q psy16766 9 NHAHVFPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGP-NVYPGANMIQNEDGSVVRISSSQA 87 (621)
Q Consensus 9 ~~~~~fsaRsVIspDP~l~~~evgvP~~~A~~lt~pe~vt~~N~~~l~~~v~ng~-~~~pga~~~~~~~g~~~~~~~~~~ 87 (621)
..+.+|||||||+|||+|++||||||..||.+||+|+ |+.+ |+.+|. ...+||+.++..++..+..
T Consensus 345 GKRVDySgRSVI~pdP~L~l~qvGvP~~mA~eLf~Pf-----~i~~---L~~~g~~~~i~~ak~~i~~~~~~v~~----- 411 (619)
T TIGR02387 345 GKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPF-----VIHR---LIRQGIVNNIKAAKKLIQRADDEIWS----- 411 (619)
T ss_pred ccccccCCCceecCCCCcccceecChHHHHHhcCchH-----hHHH---HHhcCcccchHHHHHHHHhcCChhHH-----
Confidence 3577999999999999999999999999999999986 5544 456774 4456788777544322110
Q ss_pred chhhhhhhh---ccCCcchhhh-hhhhhhhhccc--------------ccCcceEEEecCChH------HHHhhc--ccc
Q psy16766 88 VQRESLAKR---LITPEDQQHR-AIMKEKIITRQ--------------EVVPEILKLKYYTDQ------EVKQLS--VVK 141 (621)
Q Consensus 88 ~~~~~~~~~---ll~~~~slhr-sim~~~~~~~p--------------~~~~~g~ef~~~s~e------ei~~lS--v~~ 141 (621)
. ...+... |++|+||||| |||||+++..+ .||||||||++|.|+ |++.++ ..+
T Consensus 412 V-lr~v~~gd~VLlNRqPTLHR~sIqAf~~~l~~~ktirlhplvC~~fNADFDGDeMnvHvPqS~eA~aEa~~Lm~~~~n 490 (619)
T TIGR02387 412 V-LQEVITGHPVMLNRAPTLHRLGIQAFEPILVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQTEARLLMLASNN 490 (619)
T ss_pred H-HHHHhcCCEEEecCCCccchhcceeeeeEEecCCeEEECcccCCcccCCCCCceeeeecCCCHHHHHHHHHHhhchhc
Confidence 0 0122222 6799999999 99999876544 379999999999984 444443 358
Q ss_pred cccccccCCCCCccccCccCCCCCccccCCCc
Q psy16766 142 VFSPITFNSLGHTIPGGLYDLAMGPISERGDP 173 (621)
Q Consensus 142 I~~~~~~d~~g~Pi~ggl~D~~lG~~~~~~~~ 173 (621)
+.+|.+ |+|+.+..||.++|.|.++...
T Consensus 491 ilsP~~----G~Pi~~~~QD~llg~y~LT~~~ 518 (619)
T TIGR02387 491 VLSPAT----GEPIVTPSQDMVLGCYYLTALN 518 (619)
T ss_pred EEecCC----CceeEeechhhhhhhheeeccc
Confidence 889886 9999999999999999876543
No 30
>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=99.89 E-value=5.6e-24 Score=248.74 Aligned_cols=141 Identities=20% Similarity=0.235 Sum_probs=104.4
Q ss_pred CCCCCCCceeecCCCCCCcccccccHHHHhcCCcceEec-------hhhHHHHHHHHHcC-CCCCCCcceeEcCCCcEEE
Q psy16766 10 HAHVFPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVT-------PWNVTLLRKMVING-PNVYPGANMIQNEDGSVVR 81 (621)
Q Consensus 10 ~~~~fsaRsVIspDP~l~~~evgvP~~~A~~lt~pe~vt-------~~N~~~l~~~v~ng-~~~~pga~~~~~~~g~~~~ 81 (621)
.+-+|||||||+|||+|++||||||..||++||+|+.|+ .+|+...++++.++ |.+|.-...++
T Consensus 327 KRVDySgRSVI~pdP~L~l~e~GlP~~mA~~L~~Pf~i~~L~~~~~~~~i~~ak~~i~~~~~~v~~vl~~vi-------- 398 (1140)
T TIGR02386 327 KRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKPFIIKRLIDRELAANIKSAKKMIEQEDPEVWDVLEDVI-------- 398 (1140)
T ss_pred cccCCCCCCeEcCCCCcccccccChHHHHHHcCchHHHHHHHHcCcccchHHHHHHHHhcCCccceEEEEcc--------
Confidence 467899999999999999999999999999999996653 12333333333332 12222111111
Q ss_pred EcccccchhhhhhhhccCCcchhhh-hhhhhhhhcccc--------------cCcceEEEecCChH------HHHhhc--
Q psy16766 82 ISSSQAVQRESLAKRLITPEDQQHR-AIMKEKIITRQE--------------VVPEILKLKYYTDQ------EVKQLS-- 138 (621)
Q Consensus 82 ~~~~~~~~~~~~~~~ll~~~~slhr-sim~~~~~~~p~--------------~~~~g~ef~~~s~e------ei~~lS-- 138 (621)
.++. -|+||+||||| |||||++++.++ ||||||||++|.|+ |++.++
T Consensus 399 --------~~d~--VLlNRqPTLHRlsIqAf~~~l~~gktirlhplvC~~fNADFDGDeMnvHvPqS~eA~aEa~~Lm~~ 468 (1140)
T TIGR02386 399 --------KEHP--VLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLA 468 (1140)
T ss_pred --------CCcE--EEecCCCcccccccceeEEEEecCceEEEcccccCcccCCCCcceeEeecCCCHHHHHHHHHHhCC
Confidence 1222 17899999999 999999876653 79999999999883 444443
Q ss_pred ccccccccccCCCCCccccCccCCCCCccccCCC
Q psy16766 139 VVKVFSPITFNSLGHTIPGGLYDLAMGPISERGD 172 (621)
Q Consensus 139 v~~I~~~~~~d~~g~Pi~ggl~D~~lG~~~~~~~ 172 (621)
..+|.+|.+ |+|+.+..||.++|.|.++..
T Consensus 469 ~~nilsP~~----G~Pi~~~~QD~ilG~y~LT~~ 498 (1140)
T TIGR02386 469 SNNILNPKD----GKPIVTPSQDMVLGLYYLTTE 498 (1140)
T ss_pred cccEecCCC----CCceEEeechhhheeeEeeec
Confidence 368999986 999999999999999977754
No 31
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=99.88 E-value=5.6e-24 Score=248.99 Aligned_cols=149 Identities=20% Similarity=0.227 Sum_probs=109.4
Q ss_pred CCCCCCCCceeecCCCCCCcccccccHHHHhcCCcceEechhhHHHHHHHHHcCC-CCCCCcceeEcCC-CcEEEEcccc
Q psy16766 9 NHAHVFPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGP-NVYPGANMIQNED-GSVVRISSSQ 86 (621)
Q Consensus 9 ~~~~~fsaRsVIspDP~l~~~evgvP~~~A~~lt~pe~vt~~N~~~l~~~v~ng~-~~~pga~~~~~~~-g~~~~~~~~~ 86 (621)
..+-+|||||||+|||+|++||||||..||++||+|+ | +++|+.||+ .....|+..+... ....++..
T Consensus 334 GKRVDySgRSVI~pdP~L~l~e~GvP~~mA~eL~~Pf-----~---i~~L~~~g~~~~ik~ak~~~~~~~~~v~~vle-- 403 (1156)
T PRK00566 334 GKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPF-----I---MKKLVERGLATTIKSAKKMVEREDPEVWDVLE-- 403 (1156)
T ss_pred ccccCCCCCceEeCCCCcccccccChHHHHHHhCcHH-----H---HHHHHHcCCccchHhhhhhhhhhcCcceEEEE--
Confidence 3567999999999999999999999999999999995 3 677888986 2333444433221 11111110
Q ss_pred cchhhhhhhhccCCcchhhh-hhhhhhhhcccc--------------cCcceEEEecCChH------HHHhhc--ccccc
Q psy16766 87 AVQRESLAKRLITPEDQQHR-AIMKEKIITRQE--------------VVPEILKLKYYTDQ------EVKQLS--VVKVF 143 (621)
Q Consensus 87 ~~~~~~~~~~ll~~~~slhr-sim~~~~~~~p~--------------~~~~g~ef~~~s~e------ei~~lS--v~~I~ 143 (621)
..-.++. -|+||+||||| |||||+++..++ ||||||||++|.|+ |++.++ ..+|.
T Consensus 404 ~vi~gd~--VLlNRqPTLHR~sIqAf~~~l~~gktirLhplvC~~fNADFDGDqMnvHvPqS~eA~aEa~~Lm~~~~nil 481 (1156)
T PRK00566 404 EVIKEHP--VLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNIL 481 (1156)
T ss_pred EecCCCE--EEecCCCcccccccceeEEEEecCceEEECccccCccccccccceeEEecCCCHHHHHHHHHHhCCcccEE
Confidence 0011222 16899999999 999999765553 79999999999883 444443 35889
Q ss_pred cccccCCCCCccccCccCCCCCccccCCCc
Q psy16766 144 SPITFNSLGHTIPGGLYDLAMGPISERGDP 173 (621)
Q Consensus 144 ~~~~~d~~g~Pi~ggl~D~~lG~~~~~~~~ 173 (621)
+|.+ |+|+.+..||.++|.|.++...
T Consensus 482 sP~~----G~Pi~~~~QD~ilG~y~LT~~~ 507 (1156)
T PRK00566 482 SPAN----GKPIIVPSQDMVLGLYYLTRER 507 (1156)
T ss_pred ecCC----CCeeEEeehhhhhhhheeeccc
Confidence 9986 9999999999999999876543
No 32
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=99.87 E-value=2.9e-23 Score=243.26 Aligned_cols=141 Identities=18% Similarity=0.205 Sum_probs=106.9
Q ss_pred CCCCCCCceeecCCCCCCcccccccHHHHhcCCcceEec-------hhhHHHHHHHHHcCCCCCCCcceeEcCCCcEEEE
Q psy16766 10 HAHVFPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVT-------PWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRI 82 (621)
Q Consensus 10 ~~~~fsaRsVIspDP~l~~~evgvP~~~A~~lt~pe~vt-------~~N~~~l~~~v~ng~~~~pga~~~~~~~g~~~~~ 82 (621)
.+-+|||||||+|||+|++||||||..||++||+|+.+. ..|+..+++++.++.. ++ ..+
T Consensus 423 KRVDySgRSVIspdP~L~l~e~GlP~~mA~eLf~Pf~i~~L~~~~~~~nik~ak~~i~~~~~------~v-------~~v 489 (1460)
T PRK14906 423 KRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKPFVMKRLVELEYAANIKAAKRAVDRGAS------YV-------WDV 489 (1460)
T ss_pred ccccCcCCceEeCCCCCccccccCcHHHHHhcCchhHHHHHHHhcccccHHHHhhHHhhcCC------cc-------eee
Confidence 466899999999999999999999999999999998763 3566666666666421 11 011
Q ss_pred cccccchhhhhhhhccCCcchhhh-hhhhhhhhcccc--------------cCcceEEEecCChH------HHHhhc--c
Q psy16766 83 SSSQAVQRESLAKRLITPEDQQHR-AIMKEKIITRQE--------------VVPEILKLKYYTDQ------EVKQLS--V 139 (621)
Q Consensus 83 ~~~~~~~~~~~~~~ll~~~~slhr-sim~~~~~~~p~--------------~~~~g~ef~~~s~e------ei~~lS--v 139 (621)
.. ..-.++. -|+||+||||| |||||+++..++ ||||||||++|.|+ |++.++ .
T Consensus 490 le--~vi~gd~--VLlNRqPTLHRlsIqAf~~~L~~gktIrLhplvC~~fNADFDGDqMnvHvPqS~eA~aEa~~Lm~~~ 565 (1460)
T PRK14906 490 LE--EVIQDHP--VLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSS 565 (1460)
T ss_pred ee--eeeccce--eEeccCcccchhccceeeEEecCCceEEecccccCccccCCcCceeeeecCCCHHHHHHHHHHhcch
Confidence 10 0111232 27899999999 999998765543 79999999999884 444443 3
Q ss_pred cccccccccCCCCCccccCccCCCCCccccCC
Q psy16766 140 VKVFSPITFNSLGHTIPGGLYDLAMGPISERG 171 (621)
Q Consensus 140 ~~I~~~~~~d~~g~Pi~ggl~D~~lG~~~~~~ 171 (621)
.+|.+|.+ |+|+.+.+||.++|.|.++.
T Consensus 566 ~nilsP~~----G~Pi~~~~QD~ilG~y~LT~ 593 (1460)
T PRK14906 566 NNIKSPAH----GRPLTVPTQDMIIGVYYLTT 593 (1460)
T ss_pred hcEecCCC----CCeeEEeeeeeeeeeEEeee
Confidence 58899986 99999999999999998774
No 33
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=99.85 E-value=1.3e-22 Score=247.71 Aligned_cols=152 Identities=20% Similarity=0.181 Sum_probs=113.5
Q ss_pred CCCCCCCceeecCCCCCCcccccccHHHHhcCCcceEechhhHHHHHHHHHcCCC-CCCCcceeEc-CCCcEEEEccccc
Q psy16766 10 HAHVFPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPN-VYPGANMIQN-EDGSVVRISSSQA 87 (621)
Q Consensus 10 ~~~~fsaRsVIspDP~l~~~evgvP~~~A~~lt~pe~vt~~N~~~l~~~v~ng~~-~~pga~~~~~-~~g~~~~~~~~~~ 87 (621)
.+-+|||||||+|||+|++||||||..||++||+|+. +++|+.+|+. ....|+.... ..+..+.+. .+
T Consensus 1734 KRVDySgRSVI~pdP~L~l~e~GvP~~mA~eL~~P~~--------i~~L~~~G~~~~lk~ak~~i~~~~~~v~~vl--r~ 1803 (2890)
T PRK09603 1734 KRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHL--------LSKLEERGYATTLKQAKRMIEQKSNEVWECL--QE 1803 (2890)
T ss_pred ccccCcCCceEeCCCCcccccccChHHHHHHhCChHH--------HHHHHHcCCccCHHHHHHHHHhccCccEEEE--Ee
Confidence 4678999999999999999999999999999999976 6888999963 2223333322 223223221 01
Q ss_pred chhhhhhhhccCCcchhhh-hhhhhhhhcccc--------------cCcceEEEecCChH------HHHhh--ccccccc
Q psy16766 88 VQRESLAKRLITPEDQQHR-AIMKEKIITRQE--------------VVPEILKLKYYTDQ------EVKQL--SVVKVFS 144 (621)
Q Consensus 88 ~~~~~~~~~ll~~~~slhr-sim~~~~~~~p~--------------~~~~g~ef~~~s~e------ei~~l--Sv~~I~~ 144 (621)
...++.+ |+||+||||| |||||+++++++ ||||||||++|.|+ |++.+ |..+|.+
T Consensus 1804 vi~gd~V--LlNRqPTLHR~sIqAf~~~l~~gktIrLhplvC~~fNADFDGDqMnvHvPqS~eA~aEa~~LM~s~~nils 1881 (2890)
T PRK09603 1804 ITEGYPV--LLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLSSMNILL 1881 (2890)
T ss_pred eecCCeE--EecCCCccccccceeeeEEEecCceEEeccccCCcccCCCCCceeEEeecCCHHHHHHHHHHhcccceEEE
Confidence 1122222 6899999999 999999876553 79999999999884 44443 3468999
Q ss_pred ccccCCCCCccccCccCCCCCccccCCCccCCC
Q psy16766 145 PITFNSLGHTIPGGLYDLAMGPISERGDPCTTC 177 (621)
Q Consensus 145 ~~~~d~~g~Pi~ggl~D~~lG~~~~~~~~C~tC 177 (621)
|.+ |+|+.+..||.++|.|.++...+...
T Consensus 1882 P~~----G~Pi~~p~QD~vlG~y~LT~~~~~~~ 1910 (2890)
T PRK09603 1882 PAS----GKAVAIPSQDMVLGLYYLSLEKSGVK 1910 (2890)
T ss_pred cCC----CceeEEeecceeeeeEEeeccccCCC
Confidence 986 99999999999999998886554433
No 34
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]
Probab=99.85 E-value=2.8e-22 Score=231.14 Aligned_cols=145 Identities=22% Similarity=0.219 Sum_probs=115.0
Q ss_pred CCCCCCCceeecCCCCCCcccccccHHHHhcCCcceEechhhHHHHHHHHHcCCCCCCCcceeEcCCCcEEEEcccccch
Q psy16766 10 HAHVFPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRISSSQAVQ 89 (621)
Q Consensus 10 ~~~~fsaRsVIspDP~l~~~evgvP~~~A~~lt~pe~vt~~N~~~l~~~v~ng~~~~pga~~~~~~~g~~~~~~~~~~~~ 89 (621)
.+-+|||||||||||+|++||||||..||++||+||+||+||++.+++ ||+++++..++....- ...-
T Consensus 288 KRVd~SgRsVI~~~P~l~~~e~GvP~~~A~~L~~p~~v~~~~~~~~~~----------~a~~~~~~~~~~~~~~--w~Vl 355 (808)
T COG0086 288 KRVDYSGRSVISVGPNLKLNQCGVPKKMALELFKPFVVTELNIEGLRT----------GAKYAKRMVERRLPEV--WDVL 355 (808)
T ss_pred cccCCCCceeecCCCCccccccCCHHHHHHHhccCEEEEehhhhhhhc----------CCceEEeccccccccc--chHH
Confidence 356899999999999999999999999999999999999999999998 8999998777641110 0000
Q ss_pred hhhhhhh---ccCCcchhhh-hhhhhhhhccc---------------ccCcceEEEecCChH--HHHhhc------cccc
Q psy16766 90 RESLAKR---LITPEDQQHR-AIMKEKIITRQ---------------EVVPEILKLKYYTDQ--EVKQLS------VVKV 142 (621)
Q Consensus 90 ~~~~~~~---ll~~~~slhr-sim~~~~~~~p---------------~~~~~g~ef~~~s~e--ei~~lS------v~~I 142 (621)
.++... |++++||||| |||+|...+++ ++|||||||++|.|+ |+++-| -.+|
T Consensus 356 -~evi~gd~Vl~NR~PtLHrlsImq~~e~vl~~gkt~rLh~lVc~~yNADFDGDeM~~Hvp~s~ea~AEa~~lm~tq~ni 434 (808)
T COG0086 356 -REVIDGDPVLLNRAPTLHRLSIMQAFEPVLPEGKAIRLHPLVCEAYNADFDGDEMAVHVPASGEAAAEARGLMGTQMNI 434 (808)
T ss_pred -HHHhcCCccccccCChHHHHHHHhhceeeccccceeecchhhccccccccCchhhhccccchHHHHHHHHHhhcccccc
Confidence 112222 6789999999 99988766555 278999999999983 443332 2478
Q ss_pred ccccccCCCCCccccCccCCCCCccccCC
Q psy16766 143 FSPITFNSLGHTIPGGLYDLAMGPISERG 171 (621)
Q Consensus 143 ~~~~~~d~~g~Pi~ggl~D~~lG~~~~~~ 171 (621)
.+|.. |.|+.+..||.++|+|.++.
T Consensus 435 lsP~~----Ggpiv~~~qD~v~g~ylLt~ 459 (808)
T COG0086 435 LTPHY----GGPIVAPIQDTVGGPYLLTI 459 (808)
T ss_pred ccCCC----CCceEeecceEEeccEEEEE
Confidence 88886 99999999999999987763
No 35
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=99.83 E-value=1.2e-21 Score=238.73 Aligned_cols=149 Identities=19% Similarity=0.181 Sum_probs=108.5
Q ss_pred CCCCCCCceeecCCCCCCcccccccHHHHhcCCcceEechhhHHHHHHHHHcCCCCCCCcceeEcC-CCcEEEEcccccc
Q psy16766 10 HAHVFPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNE-DGSVVRISSSQAV 88 (621)
Q Consensus 10 ~~~~fsaRsVIspDP~l~~~evgvP~~~A~~lt~pe~vt~~N~~~l~~~v~ng~~~~pga~~~~~~-~g~~~~~~~~~~~ 88 (621)
.+-+|||||||+|||+|+++|||||..||++||+| ||+++|+++... .....|+..+.. +....++.. ...
T Consensus 1778 KRVDySgRSVI~pdP~L~l~evGlP~~mA~eL~~P-----f~i~~L~~~~~~--~~i~~a~~li~~~~~~v~dile-~vi 1849 (2836)
T PRK14844 1778 KRVDYSGRSVIVVGPTLKLNQCGLPKRMALELFKP-----FVYSKLKMYGMA--PTIKFASKLIRAEKPEVWDMLE-EVI 1849 (2836)
T ss_pred cccccCCCceEeCCCCcccceeeCCHHHHHhcccH-----HHHHHHHHcCcc--cchHHHHHHHHhhCCcceEEEE-EEe
Confidence 46789999999999999999999999999999998 467777765332 122344444332 222222211 011
Q ss_pred hhhhhhhhccCCcchhhh-hhhhhhhhcccc--------------cCcceEEEecCChH------HHHhhc--ccccccc
Q psy16766 89 QRESLAKRLITPEDQQHR-AIMKEKIITRQE--------------VVPEILKLKYYTDQ------EVKQLS--VVKVFSP 145 (621)
Q Consensus 89 ~~~~~~~~ll~~~~slhr-sim~~~~~~~p~--------------~~~~g~ef~~~s~e------ei~~lS--v~~I~~~ 145 (621)
.++. -|+||+||||| |||||+++..++ ||||||||++|.|+ |++.++ ..+|.+|
T Consensus 1850 -~gd~--VLlNRqPTLHR~sIqAf~~~l~~gktirlhp~vC~~fNADFDGDeMnvHvPqS~eA~aEa~~Lm~~~~nilsP 1926 (2836)
T PRK14844 1850 -KEHP--VLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLSP 1926 (2836)
T ss_pred -cCCE--EEecCCCccccccccceeeEeecCceEEecccCCCcccCCCCCceeeeecCCcHHHHHHHHHHhCCcccEEec
Confidence 1332 27899999999 999999766553 79999999999884 444333 3588999
Q ss_pred cccCCCCCccccCccCCCCCccccCCCc
Q psy16766 146 ITFNSLGHTIPGGLYDLAMGPISERGDP 173 (621)
Q Consensus 146 ~~~d~~g~Pi~ggl~D~~lG~~~~~~~~ 173 (621)
.+ |+|+.+..||.++|.|.++...
T Consensus 1927 ~~----G~Pii~~~QD~ilG~y~LT~~~ 1950 (2836)
T PRK14844 1927 SN----GRPIIVPSKDIVLGIYYLTLQE 1950 (2836)
T ss_pred CC----CceeEeehhhhhhhhhhhcccc
Confidence 86 9999999999999999877544
No 36
>PF04983 RNA_pol_Rpb1_3: RNA polymerase Rpb1, domain 3; InterPro: IPR007066 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1ZYR_D 1SMY_D 2A68_N 2O5J_D 3AOH_N 2O5I_D 2CW0_N 2A6H_N 2A69_D 3EQL_D ....
Probab=64.32 E-value=1.1 Score=42.48 Aligned_cols=29 Identities=24% Similarity=0.463 Sum_probs=22.7
Q ss_pred ccccccccCCCCCccccCccCCCCCccccCCCc
Q psy16766 141 KVFSPITFNSLGHTIPGGLYDLAMGPISERGDP 173 (621)
Q Consensus 141 ~I~~~~~~d~~g~Pi~ggl~D~~lG~~~~~~~~ 173 (621)
+|.+|++ |+|+.+..||..+|.|.++...
T Consensus 1 NilSP~~----G~Pii~~~QD~vlG~y~LT~~~ 29 (158)
T PF04983_consen 1 NILSPAN----GKPIIGPTQDMVLGAYYLTSED 29 (158)
T ss_dssp GSEETTT----TEESSS--SHHHHHHHHHSSTT
T ss_pred CccCCCC----CCceEEeccceEeEEEEEEecc
Confidence 4677875 9999999999999999887544
No 37
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=42.14 E-value=13 Score=27.39 Aligned_cols=14 Identities=36% Similarity=0.422 Sum_probs=11.5
Q ss_pred cCCCCCCCCCCCce
Q psy16766 308 VKRKCIFCATPINA 321 (621)
Q Consensus 308 ~~kkC~~C~~~~p~ 321 (621)
-.++||+||+.++.
T Consensus 10 GirkCp~CGt~NG~ 23 (44)
T PF14952_consen 10 GIRKCPKCGTYNGT 23 (44)
T ss_pred ccccCCcCcCccCc
Confidence 56899999999843
No 38
>KOG0856|consensus
Probab=26.66 E-value=27 Score=32.42 Aligned_cols=16 Identities=44% Similarity=0.974 Sum_probs=11.0
Q ss_pred CCccCCCCCCccccCCcccccCC
Q psy16766 171 GDPCTTCGNNYTKCKGHIGHIEL 193 (621)
Q Consensus 171 ~~~C~tC~~~~~~C~GhfGhI~L 193 (621)
.-.|.+| -||.||+=.
T Consensus 103 Ev~Ca~C-------~~HLGHVF~ 118 (146)
T KOG0856|consen 103 EVSCATC-------GGHLGHVFK 118 (146)
T ss_pred EEEEeec-------CCceeeeec
Confidence 4556666 489999755
No 39
>PF02044 Bombesin: Bombesin-like peptide; InterPro: IPR000874 Bombesin-like peptides comprise a large family of peptides which were initially isolated from amphibian skin, where they stimulate smooth muscle contraction. They were later found to be widely distributed in mammalian neural and endocrine cells. The amphibian peptides which belong to this family are currently classified into three subfamilies [, ]; the Bombesin group, which includes bombesin and alytesin; the Ranatensin group, which includes ranatensins, litorin, and Rohdei litorin; and the Phyllolitorin group, which includes Leu(8)- and Phe(8)-phyllolitorins. In mammals and birds two categories of bombesin-like peptides are known [, ], gastrin-releasing peptide (GRP), which stimulates the release of gastrin as well as other gastrointestinal hormones, and neuromedin B (NMB), a neuropeptide whose function is not yet clear. Bombesin-like peptides, like many other active peptides, are synthesized as larger protein precursors that are enzymatically converted to their mature forms. The final peptides are eight to fourteen residues long.; GO: 0007218 neuropeptide signaling pathway; PDB: 1C9A_A 1C98_A.
Probab=25.31 E-value=23 Score=19.65 Aligned_cols=7 Identities=43% Similarity=0.885 Sum_probs=2.1
Q ss_pred cccCCCc
Q psy16766 522 QNMMGKR 528 (621)
Q Consensus 522 ~nlmGKR 528 (621)
+++|||+
T Consensus 7 Gh~Mgkk 13 (14)
T PF02044_consen 7 GHFMGKK 13 (14)
T ss_dssp HCT----
T ss_pred eeeeccC
Confidence 5778886
Done!