Query 001771
Match_columns 1015
No_of_seqs 291 out of 467
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 08:57:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001771.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001771hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0988 RNA-directed RNA polym 100.0 2E-150 4E-155 1345.2 52.1 877 6-1001 58-1129(1145)
2 PF05183 RdRP: RNA dependent R 100.0 6E-116 1E-120 1045.7 26.4 551 235-876 2-575 (579)
3 KOG0988 RNA-directed RNA polym 96.4 0.0047 1E-07 78.1 6.7 193 765-959 868-1142(1145)
4 smart00663 RPOLA_N RNA polymer 83.8 1.4 3E-05 50.0 4.9 53 659-727 199-253 (295)
5 PF00623 RNA_pol_Rpb1_2: RNA p 83.4 1.1 2.3E-05 46.9 3.5 53 659-727 95-149 (166)
6 CHL00018 rpoC1 RNA polymerase 66.9 5.1 0.00011 49.9 3.7 54 658-727 443-498 (663)
7 PRK02625 rpoC1 DNA-directed RN 66.6 7 0.00015 48.3 4.8 54 658-727 422-477 (627)
8 TIGR02387 rpoC1_cyan DNA-direc 66.1 5.3 0.00011 49.3 3.6 54 658-727 415-470 (619)
9 TIGR02390 RNA_pol_rpoA1 DNA-di 52.9 17 0.00037 47.2 5.1 53 659-727 408-462 (868)
10 TIGR02386 rpoC_TIGR DNA-direct 49.6 15 0.00032 48.7 3.8 54 658-727 396-451 (1140)
11 PRK00566 DNA-directed RNA poly 47.5 18 0.00039 48.0 4.1 53 659-727 405-459 (1156)
12 PRK08566 DNA-directed RNA poly 47.5 19 0.00042 46.8 4.4 53 659-727 412-466 (882)
13 PRK09603 bifunctional DNA-dire 45.0 23 0.0005 50.5 4.6 54 658-727 1803-1858(2890)
14 PRK14906 DNA-directed RNA poly 44.8 22 0.00047 48.0 4.2 53 659-727 493-547 (1460)
15 PRK14844 bifunctional DNA-dire 33.9 36 0.00078 48.6 3.8 53 659-727 1848-1902(2836)
16 PRK14977 bifunctional DNA-dire 28.0 61 0.0013 44.1 4.4 53 659-727 428-482 (1321)
17 PF10664 NdhM: Cyanobacterial 25.1 74 0.0016 30.8 3.2 47 20-79 41-87 (108)
No 1
>KOG0988 consensus RNA-directed RNA polymerase QDE-1 required for posttranscriptional gene silencing and RNA interference [RNA processing and modification]
Probab=100.00 E-value=1.7e-150 Score=1345.24 Aligned_cols=877 Identities=28% Similarity=0.391 Sum_probs=715.5
Q ss_pred ccccccccccchh-HHHHHHHHHHHhCC-C-CCChhh-hhhhhc---cChHHHHHHHHHhhcccc--ccchhHHHHHHhh
Q 001771 6 VVSQQGVVSLPLS-VEQLISKIYTEQNK-L-PPDDGA-RRSLAS---LGEDAALDVLRTIASDKI--KYSFSGYINYLVK 76 (1015)
Q Consensus 6 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~-~-~~~~~~-~~~~~~---~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~ 76 (1015)
.+++...++|+++ +++.+++||-+.++ . +.++++ |+.|++ ..|.++..++++++.... .++|++|+.+.++
T Consensus 58 ~~~~f~~i~l~~~~~~~~~a~v~f~~~~~~~~~e~~~~~~~l~~~a~~~~~l~~i~~~~~F~~~~~~t~~~~~~~~~~v~ 137 (1145)
T KOG0988|consen 58 HGSDFTSIALDCSGIETPLAKVYFKHNQGLNPWEVETSRRILSSLAVIRESLNQIVLEKVFDKPDGITKTFDCLESYKVN 137 (1145)
T ss_pred ccccccccccccccchhhHHHHhhccCCCCCccchhhhhhhccccccchHHHhhHHHhhccCcccceeeeecceEEEeec
Confidence 4677888999999 99999999999997 3 899999 999999 889999999999999985 9999999999999
Q ss_pred hccC-CCCCccccccCCCCCCCCCCC---CcceeeeeccCCCCCcccccCCcccccCCCCC----CcchhhhhcCCCCC-
Q 001771 77 KRNN-NGSPLKRVCFSPSSPQQNRSP---VTVTTVRLLNLPQGTDYVVKQSPVADQQPRGS----PMSSISHAMRHRAS- 147 (1015)
Q Consensus 77 ~~~~-~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~- 147 (1015)
+.++ +|+|.++. +.+|++.+-. +..++|+.+ |+.+++|...|| |+..+...+|.|++
T Consensus 138 ~~v~V~~~~~~~~---~~~p~~~~~~~~v~f~~~~~~~-----------i~~~~~D~~~~s~~~~~~~~~~~~~G~~k~~ 203 (1145)
T KOG0988|consen 138 DQVTVRGSPVRRI---VESPVVEYCKLCVPFEHSCRVL-----------IETVSLDLDKPSIIRYPKSRRYLDNGGSKYF 203 (1145)
T ss_pred ceEEEeccceeee---eecccccccccccchhhcchhh-----------eeeEEeccCcchhccCcchhhhhhcCcccee
Confidence 9998 99999887 7888887644 677777777 999999999999 99999999999988
Q ss_pred ----chHHHHhc--CchhhHHHH-HhhhcccCcch-------hhhhHHHHhh--ccccccccc------ch--HHHHHhc
Q 001771 148 ----IPQYVALG--ELEFRKAFL-ILSYIGENSLE-------EVITADEIRG--MRDLQMARF------ES--EVWEKLG 203 (1015)
Q Consensus 148 ----~~~~~~l~--~l~~~k~~~-~l~~~~~~~~~-------~~~~~~~ir~--~~~~~m~~~------e~--~~w~~~~ 203 (1015)
+|...||| ++||+|.++ .+.|+....+- ++.+..||+. |+++||-.+ +. .+|+.+|
T Consensus 204 ~~~~~p~~~~~~~~~~Ef~k~~~~~~~~i~~~~~~~~~~v~~eta~~~eI~~~i~~~lP~~r~~~~~~~~~~~s~~ir~~ 283 (1145)
T KOG0988|consen 204 RFAFSPLLLALGDSELEFKKDFLADLLYIRTTDLRSRTGVGIETASCDEIRVPIWKDLPYNRYNGSTAEEFRLSVWIRLG 283 (1145)
T ss_pred ecccccHHHhhccceeeeecccccccceeeecceeccccccceeeccceecchhhccCCcccccccchhhhhhhhheecc
Confidence 99999999 999999999 99999987773 4778999999 999999877 34 7898888
Q ss_pred ccccchhh----------------------h------------------------------c------------------
Q 001771 204 RKNISQED----------------------R------------------------------R------------------ 213 (1015)
Q Consensus 204 ~~~~~~~~----------------------~------------------------------~------------------ 213 (1015)
.+|...+. + .
T Consensus 284 ~~~~~~~~~~~~l~~~~~~git~~~e~l~~r~slv~dq~~~~~~~~~~f~~l~~~~~~~d~~v~~a~LekL~~~~~~cfd 363 (1145)
T KOG0988|consen 284 SKYDVSSAQLVPLNDERDFGITHLYECLVSRGSLVKDQVLLEEAHLLEFLGLLRHKVLGDDNVLEAKLEKLLKLSTKCFD 363 (1145)
T ss_pred cccccccceeeeccccccccceeehhhhhcccchhhhhHHhhhhHHHHHHHHHhhhhccchhHHHHHHHHHhhhhhhhhh
Confidence 75541000 0 0
Q ss_pred -------c------ccc------cCCCceEEEEEEEecCCeEEecCCeeccCCceEecccC-CCcEEEEEEecCCCC-CC
Q 001771 214 -------M------SLK------WDSGKTHMYHCHISTKGNCTFKGPYLNQTRTHLQRELG-DDNILLVKFDEELGG-HR 272 (1015)
Q Consensus 214 -------~------~~~------~~~g~~~v~~~~vtp~~~~~~~gP~le~snr~lrr~~g-~d~FLrV~F~de~~~-~~ 272 (1015)
. +-. ...|.++++++.||||+ ++|.+||++++|||+|||.. .++||||+|.||+.+ +.
T Consensus 364 ~~~~~k~i~~~~~~ng~~~~~~~~~~g~~~vrk~v~TPtr-v~~~~PE~~~gNRVlR~f~~~~t~~lRvtF~De~~~~~i 442 (1145)
T KOG0988|consen 364 PYCQYKKIAKLNPSNGKLVTTKEIMEGLRRVRKVVFTPTR-VYLLAPEVEMGNRVLRKFDKDSTRFLRVTFRDEDNKLKI 442 (1145)
T ss_pred HHHHHHHHHHHhcccCccccchhhhhcceeEEEEEEcCce-eEecCchhhhcchhheeccccCceEEEEEEEcccccccc
Confidence 0 011 35678999999999995 77999999999999999764 699999999888774 32
Q ss_pred CCCCc---cchHHHHHHHHHcCeEEcCeEEEEEEEecCCccccCCCCCCCCcEEEEEecCChhhhccccccccchhcHHH
Q 001771 273 SSNNW---NDSYSKYNEIAREGILVGLRCYHFFVFKDGGKEEKKKDPSTSPVKCYFVRMESSAFIDMGYQYILSGKTVHE 349 (1015)
Q Consensus 273 ~~~~~---~~~~~r~~~~L~~Gi~I~gR~y~FLa~s~S~~re~~k~~S~s~~~~~F~r~~s~w~~~~~~P~~~~~~ti~~ 349 (1015)
+.... ..++.++..+|.+||.||+|+|+|||||+||+|+| +.||++.. ...+|.+
T Consensus 443 r~~S~~~~t~l~~rv~~~L~~Gi~v~~r~y~FL~~s~sQlRdn---------gy~m~~~s-------------~~~~i~~ 500 (1145)
T KOG0988|consen 443 RTLSTGSRTKLDMRVNSYLTDGISVANRRYEFLAFSNSQLRDN---------GYFMARFS-------------DKTKIED 500 (1145)
T ss_pred ccCCcchhhHHHHHHHHHHhcccEEccceeEEEEecccccccC---------ceEEeecC-------------CCccHHH
Confidence 22222 34788999999999999999999999999999998 75555421 2257899
Q ss_pred HHhhccCCCCCCchhHHHHhhhccccCcccceeeccceeEEEecCccCCCCCCCccccCCCccccccccccccHHHHHhh
Q 001771 350 ARYMFMHVRTVSSVANYMSRLSLILSKTMKLEVDFSRINIERIEDEPCRDKDGNVVYKDGEALIHTDGTGFISEDLALKC 429 (1015)
Q Consensus 350 ~r~~f~~i~~~~~vaK~aARlgq~FSsT~~~~V~~~~~~i~~I~DI~~~d~~g~dv~~~g~~y~FTDGvG~IS~~lA~~I 429 (1015)
+|.||++|+.+.+++|||||||||||+|....+-+....+..+|||+.. ++|..||||||||+||.++|++|
T Consensus 501 iR~wmG~F~~i~nv~K~aARmGqCFs~Sr~T~~~~~~~~~~~~~DI~~g--------~~g~~y~FSDGvG~iS~~~a~~v 572 (1145)
T KOG0988|consen 501 IREWMGDFRDIDNVPKLAARMGQCFSQSRGTGYVLERLDRMCPPDIEGG--------KRGNNYCFSDGVGMISLQFAREV 572 (1145)
T ss_pred HHHHhcchhhccCHHHHHhhcCcceeccccccccccccccccCCccccc--------ccCCceeecCCcccccHHHHHHH
Confidence 9999999999999999999999999999853333567788899999742 46777999999999999999999
Q ss_pred chhhcccccCCCCccccchhhhhhhhccccccccCCCCCCCCceEEEEecCCCCcceeEEEecCCCCCCeeeeCCCceee
Q 001771 430 PTYVYKEKCTNDDSTERSIDRKELEANFSDVARTESHYGEPPLLMQVRLFYNGTAVKGTLLLNKKLPPQTIQIRPSMIKV 509 (1015)
Q Consensus 430 ~~~i~k~~~l~~~~~~~k~~~~~~~~~f~~~~~~~~~~~~~PSAfQiR~~y~G~GaKGvL~vdp~l~~~~I~lRpSm~KF 509 (1015)
.+.+ . ....+|||||||+ || +||||+|||.++. .+.+|.||.||
T Consensus 573 sq~~------~-------------------------~~~~vPsaFQiR~--~G--~KGVvav~Ps~~~-~~~~~~~~~~s 616 (1145)
T KOG0988|consen 573 SQKR------K-------------------------FGKAVPSAFQIRY--GG--YKGVVAVDPSMDK-VLKLRDSMNKS 616 (1145)
T ss_pred HHHH------c-------------------------ccccCChheeeec--cC--CcceEEeCccHhh-hhhhhhhhhhh
Confidence 8742 1 1146999999995 77 7999999999764 88999999999
Q ss_pred ecCCCCCCCCCcceEEEEeecCCCccccccHHHHHHHhCCCCCHHHHHHHHHHHHHHHHhHhcCHHH-HHHHHhhcCC-C
Q 001771 510 KADRDLSDGQTFNSLEVVKTSNQPRKTYLSRNLIALLSYGGVPEIFFLDILRNALDDARGVFSNKRN-ALKVSFNYGG-M 587 (1015)
Q Consensus 510 ~~~~~~~~~~~~~~LEIv~~S~~~~~~~LNRqlI~lL~~lGVp~evF~~Lq~~~l~~l~~~~~~~~~-Al~~l~~~~~-~ 587 (1015)
.+. +..+||+.|+ ++.+++||||+|.+|+.+||++++|+++|+..+++-+....-.+. +.++..+++. +
T Consensus 617 ~S~--------n~~~~v~~~~-~f~~~~lnr~lI~Lls~~gv~n~~F~~il~~vle~~r~~~n~~e~~~~~~~l~~~~~m 687 (1145)
T KOG0988|consen 617 QSF--------NSLLEVTPSS-KFQPAFLNRQLITLLSYLGVLNKPFINILDQVLEKQRRITNRIEELLDRAALNYGEQM 687 (1145)
T ss_pred hhh--------cceeeeeecc-CCccccccHHHHHHHHhcCccchHHHHHHHHHHHHHHhhhhhhhHHHHHHHhhhhhhc
Confidence 764 3456776666 689999999999999999999999999999999965433322222 2333445554 4
Q ss_pred ChhHHHHHHHHcCCC-CC-cHHHHHHHHHHHHHHHHhhh-ccCeecCCcceeEeecCCCCCCCCCeEEEEecc-------
Q 001771 588 DYDFTSARMILSGIS-LD-EPYLQHRLSILMKEEKKSLQ-AGKLPVTESYYLMGTVDPTGILKSNEVCIILKD------- 657 (1015)
Q Consensus 588 d~~~~~~~ml~aGfp-~~-epfl~~~L~~~~~~~l~~Lk-k~rIpV~~s~~L~GV~DetG~L~eGEVfv~~s~------- 657 (1015)
+ +++.++|++.|+| .+ ||||+++|+..++..++.+| +.||||+.|++||||+||||+||+||||||++.
T Consensus 688 ~-~en~a~~~l~~~~~~D~EPflr~mL~~~~k~~~~~~kek~ripv~~Gr~lmGvvDETG~L~ygQVfVq~t~~~~~~~~ 766 (1145)
T KOG0988|consen 688 D-DENIAAMILKGFPRIDSEPFLRSMLSSLLKFTLQLLKEKIRIPVDLGRSLMGVVDETGILKYGQVFVQYTKTIRNSDS 766 (1145)
T ss_pred c-chHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHhcccccCcCCceeEeeeccccccccCeEEEEEccccccccc
Confidence 5 6778899999996 55 99999999999999888888 599999999999999999999999999999985
Q ss_pred c---eeeceeEEEEeCCCCCCCCeeEEEEeecCcccccccCcceEEEeCCCCCCCccccccCCCCCCCeEEEEeCccccc
Q 001771 658 G---QVSWEKVLVYRNPGLHFGDIHVLKATYVKELEDFVGTSKYAIFFPCNGPRSLADEIAGGDFDGDMYFVSRNPELLK 734 (1015)
Q Consensus 658 ~---~l~G~~VlV~RnP~lHPGDVr~v~AV~~P~L~~~~~~lkdVIVFp~kG~Rplps~lSGGDLDGD~y~ViWD~~Lv~ 734 (1015)
+ +|+| +|||||||||||||||+++||++|+|+|+ .|||||||||+||||+||||||||||+|||||||+|||
T Consensus 767 ~~~~vitG-~VlvtKNPcLhpGDVRVl~AV~vp~L~h~----~dvVvFPQkGpRphpdE~aGsDLDGDeYfViWDqkLL~ 841 (1145)
T KOG0988|consen 767 GRKEVITG-KVLVTKNPCLHPGDVRVLKAVYVPALEHM----VDVVVFPQKGPRPHPDEMAGSDLDGDEYFVIWDQKLLP 841 (1145)
T ss_pred CCceEEEe-eEEEecCCCCCCCceEEEEeeccHHHHhh----cCEEEcCCCCCCCCccccccCCCCCceEEEEeChhhcc
Confidence 2 5999 99999999999999999999999999954 56999999999999999999999999999999999999
Q ss_pred cccccccccccCCCCcccccCccCChHHHHHHHHHHHHhcccCCCCchhhhhhHHHHHHHHhccCCCchhHHHHhccHHH
Q 001771 735 HFKESERWMSTSKNLSANKRLIDFSLEELESELFKLFLNTRFCPSNAKSLAADCWQAVMDRFLTLGDESAEEKAAMKENM 814 (1015)
Q Consensus 735 ~f~~~~p~~~~~~P~~~~~~p~~~~~~~~~~~~f~~Fl~~~y~~~d~LG~isn~Hl~~aD~~~~~g~~~~~~~g~~~~~C 814 (1015)
++++ +||.. .+.++..+...+..+++.++|+ +|+.+|+||+|+|+|+++||++ |+++..|
T Consensus 842 ~~~~-epmd~------~~~~sk~~~~~~~~~~m~effv--~yL~~DslG~isnAhl~~aD~~-----------G~~~~~C 901 (1145)
T KOG0988|consen 842 PRNE-EPMDS------SSEKSKILDGRVPLDEMSEFFV--EYLKEDSLGLISNAHLANADVY-----------GLFSDVC 901 (1145)
T ss_pred CcCC-Ccccc------CccccccccCCCCHHHHHHHHH--HHHHHHHHHHHhhccccchhhc-----------chhhHHH
Confidence 9877 67754 3333333332222224444555 3556799999999999999984 5788999
Q ss_pred HHHHHHHhhcccCCCCCCCcccCCCCCCCCCCCCCcCCCCCCcccccCchhhhhhhccccccccc-cc--ccccc---Cc
Q 001771 815 LRLINIYYDALDAPKKSGIKVEVPEDLKVEKFPCYMRRDESVSFESTSVLGTIYNTVKSYEAVDR-SV--TEIWK---LP 888 (1015)
Q Consensus 815 l~LA~L~S~AVD~pK~TG~~v~lp~~L~~~~~PdFM~k~~~~~Y~S~kiLGkLYr~v~~~~~~~~-~~--~~~~~---~~ 888 (1015)
+.||++||+|||||| ||..+.+|..++|++|||||++.++++|.|++++|||||+++.+..... .+ ++... .+
T Consensus 902 l~LA~k~~~AVDF~K-sG~d~~~~~~ek~e~~PDfm~~~d~p~Y~S~~l~GkLfR~~~aid~~~~~~e~~~~~~~i~yD~ 980 (1145)
T KOG0988|consen 902 LELAKKHSQAVDFPK-SGADESMPEKEKPERYPDFMEKTDKPTYYSERLCGKLFREAKAIDAPLKGSEERSEQVEVEYDE 980 (1145)
T ss_pred HHHHHhhcccccccc-cCCcccccchhchhhcchhhhCCCCceeecchhhhHHHHHHHhhcchhhcCccccCcccccCCc
Confidence 999999999999999 9999999999999999999999999999999999999998876543222 11 11111 12
Q ss_pred cCCCCCChHHHHHHHHHHHHHHHHHHHHHHhhhhhH------------HH-----------HHHHHHHHHHHHHHhh---
Q 001771 889 CFDDGVPEACMTKWKGYYDQYRWEMKEAIDKCTVER------------EE-----------AAELVIEKYKQILYGA--- 942 (1015)
Q Consensus 889 ~f~~~v~~~~~~~a~~~~~~Y~~~l~~lm~~~k~~~------------~~-----------~~~~l~~~yr~~~~~~--- 942 (1015)
+...+.++.+++.|..+...|+.+|++||++++.+. ++ +++.+...||+.|++.
T Consensus 981 ~l~v~gFe~yme~a~~~~~~y~~qL~slm~~ygi~~E~eI~sG~~~~ddms~~~t~~~~e~~~~~l~~~~r~~~~qef~~ 1060 (1145)
T KOG0988|consen 981 DLEVDGFEHYMERAKKQVASYNGQLRSLMDFYGISTEGEIFSGILDQDDMSFYNTERMIELKLERLVLKLREKFFQEFGA 1060 (1145)
T ss_pred ccCcCCcHHHHHHHHHHHhhhhhHHHHHHHHhCccchhhhhccCccccchhhhcccccchhhhHHHHHHHHHHHHHHhhh
Confidence 222556899999999999999999999999854322 22 2334555555443331
Q ss_pred --------hhhhhccCCHHHHHHHhHHhhh-hccccccccCCCCccccchhhhHHHHHHHHHH---hhCCC
Q 001771 943 --------AEFEQSTRTLEEIYNEALAIYN-ITYDLAASRRQVSYCSFAWRVAGSALRKFYAR---RQGDR 1001 (1015)
Q Consensus 943 --------~~f~~~~~~~~~~~~~A~AwY~-VtY~~a~~~~~~~~lSFpWiv~~~~L~~ik~~---~~~~~ 1001 (1015)
.+|++. ...+.+.+||+|||+ ++|+.+...+..+++||||+++ ++||+||.. +.+++
T Consensus 1061 y~~~~e~l~~fe~~-~~eE~~~kKa~aWY~v~~ye~~~~~~~~~~~SF~wia~-Dvl~~iK~~~~~~~g~a 1129 (1145)
T KOG0988|consen 1061 YKLEIEKLSCFEDS-PEEEFIMKKASAWYRVYRYEMAQAMRETRKLSFAWIAY-DVLARIKQTFLGAIGGA 1129 (1145)
T ss_pred hcchhhhccccccC-chhHHHHHHHHHHHHHHHhhhhcccccCcccchHHHHH-HHHHHHHHHHHHhhccc
Confidence 123221 223448899999999 9999998877888999999977 699999998 55554
No 2
>PF05183 RdRP: RNA dependent RNA polymerase; InterPro: IPR007855 This entry represents various eukaryotic RNA-dependent RNA polymerases (RDRP; 2.7.7.48 from EC), such as RCRP-1, RDRP-2 and RDRP-6. These enzymes are involved in the amplification of regulatory microRNAs during post-transcriptional gene silencing []; they are also required for transcriptional gene silencing. Double-stranded RNA has been shown to induce gene silencing in diverse eukaryotes and by a variety of pathways []. These enzymes also play a role in the RNA interference (RNAi) pathway, which is important for heterochromatin formation, accurate chromosome segregation, centromere cohesion and telomere function during mitosis and meiosis. RDRP enzymes are highly conserved in most eukaryotes, but are missing in archaea and bacteria. The core catalytic domain of RDRP enzymes is structurally similar to the beta' subunit of DNA-dependent RNA polymerases (DDRP), however the other domains of DDRP show no similarity to those of RDRP.; GO: 0003968 RNA-directed RNA polymerase activity; PDB: 2J7O_A 2J7N_A.
Probab=100.00 E-value=5.8e-116 Score=1045.73 Aligned_cols=551 Identities=32% Similarity=0.503 Sum_probs=362.2
Q ss_pred eEEecCCeeccCCceEecccCCCcEEEEEEecCCCCCCCCCCccchHHHHHHHHHcCeEEcCeEEEEEEEecCCccccCC
Q 001771 235 NCTFKGPYLNQTRTHLQRELGDDNILLVKFDEELGGHRSSNNWNDSYSKYNEIAREGILVGLRCYHFFVFKDGGKEEKKK 314 (1015)
Q Consensus 235 ~~~~~gP~le~snr~lrr~~g~d~FLrV~F~de~~~~~~~~~~~~~~~r~~~~L~~Gi~I~gR~y~FLa~s~S~~re~~k 314 (1015)
+++|++|+++.|||++|+| |+|+||||+|+|++......... .+..+++++|++||.|+||+|+||++|+||+|++
T Consensus 2 r~~l~~p~~~~snr~~R~f-g~~~Flrv~f~d~~~~~~~~~~~-~~~~~~~~~l~~gi~i~~~~y~fl~~S~sqlr~~-- 77 (579)
T PF05183_consen 2 RIILEPPELEKSNRVLRRF-GSDRFLRVSFPDENSSSLRFSPR-VLGRRIRKFLKNGIKIGGRHYRFLGFSNSQLRDH-- 77 (579)
T ss_dssp -EEE---EEEE-BHHHHHH--GGGEEEEEEE-TT---SSS-TT-STTEEEEEEEEEE-------------------EE--
T ss_pred eEEEECCEecCCCceeEEe-CCCCEEEEEEEcCCCCcccccch-hHHHHHHHHHhccceECcEEEEEeecCCccccCC--
Confidence 5789999999999999996 99999999999888654322211 1456778899999999999999999999999998
Q ss_pred CCCCCCcEEEEEecCChhhhccccccccchhcHHHHHhhccCCCCCCch-hHHHHhhhccccCcccceeeccceeEEEec
Q 001771 315 DPSTSPVKCYFVRMESSAFIDMGYQYILSGKTVHEARYMFMHVRTVSSV-ANYMSRLSLILSKTMKLEVDFSRINIERIE 393 (1015)
Q Consensus 315 ~~S~s~~~~~F~r~~s~w~~~~~~P~~~~~~ti~~~r~~f~~i~~~~~v-aK~aARlgq~FSsT~~~~V~~~~~~i~~I~ 393 (1015)
+|||++++.. .....++.+++.|++++..++++ +||+||||||||+|.+ ++.+...++..|+
T Consensus 78 -------~~~f~~~~~~---------~~~~~~~~~i~~~~g~~~~~~~~~~K~~aRl~l~fS~T~~-~~~i~~~~~~~i~ 140 (579)
T PF05183_consen 78 -------SCWFFAEDDG---------DRPPLTVEDIRNWMGDFSNIQSIPAKYAARLGLCFSSTVP-TVVIPPDEIEVIP 140 (579)
T ss_dssp -------EEEEEEEE-------------B---HHHHHHHHH-GGGTSBH-HHHHHTTHHHHSB-EE-EEE--GGGEE-SS
T ss_pred -------eEEEEecCCc---------cCCcccHHHHHHhcccccccccHHHHHHHHHHHhccCccc-eEEecccceEEcC
Confidence 9999997611 02346677777777777766676 9999999999999997 3346677789999
Q ss_pred CccCCCCCCCccccCCCccccccccccccHHHHHhhchhhcccccCCCCccccchhhhhhhhccccccccCCCCCCCCce
Q 001771 394 DEPCRDKDGNVVYKDGEALIHTDGTGFISEDLALKCPTYVYKEKCTNDDSTERSIDRKELEANFSDVARTESHYGEPPLL 473 (1015)
Q Consensus 394 DI~~~d~~g~dv~~~g~~y~FTDGvG~IS~~lA~~I~~~i~k~~~l~~~~~~~k~~~~~~~~~f~~~~~~~~~~~~~PSA 473 (1015)
||.. .+| |+||||||+||++||++|++.+. ...+|||
T Consensus 141 Di~~---------~~~--~~ftDG~G~IS~~la~~I~~~l~--------------------------------~~~~PsA 177 (579)
T PF05183_consen 141 DITS---------RNG--YVFTDGCGRISPDLARKIAEKLG--------------------------------LDYVPSA 177 (579)
T ss_dssp --TT---------SS----BSSTTEEEE-HHHHHHHHHHHT---------------------------------SS--SE
T ss_pred CcCC---------CCC--ccccCCchhhCHHHHHHHHHHcC--------------------------------CCCCCeE
Confidence 9821 234 89999999999999999987641 2468999
Q ss_pred EEEEecCCCCcceeEEEecCCCCCCeeeeCCCceeeecCCCCCCCCCcceEEEEeecCCCccccccHHHHHHHhCCCCCH
Q 001771 474 MQVRLFYNGTAVKGTLLLNKKLPPQTIQIRPSMIKVKADRDLSDGQTFNSLEVVKTSNQPRKTYLSRNLIALLSYGGVPE 553 (1015)
Q Consensus 474 fQiR~~y~G~GaKGvL~vdp~l~~~~I~lRpSm~KF~~~~~~~~~~~~~~LEIv~~S~~~~~~~LNRqlI~lL~~lGVp~ 553 (1015)
||||| || +||||+|||+++|.+|+|||||+|| .. ..++.+++||||++|+++.+++||||+|++|+++|||+
T Consensus 178 ~QiR~--~G--~KGml~vdp~~~~~~I~lr~Sm~Kf-~~---~~~~~~~~lei~~~s~~~~~~~LN~q~I~iL~~~gv~~ 249 (579)
T PF05183_consen 178 FQIRI--GG--AKGMLVVDPTLDGPWIQLRPSMIKF-DE---PWDSEHRTLEIVKYSRPPRPAYLNRQLITILEDLGVPD 249 (579)
T ss_dssp EEEEE--TT--EEEEEEE-TT-----EEE-TTTB-S--------SGGGSEEEEEEE--------B-TTTHHHHHHTBSS-
T ss_pred EEEec--cC--ceeEEEECCCCCcceEEEehhhhhh-cc---CcccccCeEEecccCCCCCcccccHHHHHHHHhcCCCH
Confidence 99998 66 8999999999988999999999999 11 13567899999999998899999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhHhcCHHHHHHHHhhcCCCChhHHH--HHHHHcCC-CCCcHHHHHHHHHHHHHHHHhhh-ccCee
Q 001771 554 IFFLDILRNALDDARGVFSNKRNALKVSFNYGGMDYDFTS--ARMILSGI-SLDEPYLQHRLSILMKEEKKSLQ-AGKLP 629 (1015)
Q Consensus 554 evF~~Lq~~~l~~l~~~~~~~~~Al~~l~~~~~~d~~~~~--~~ml~aGf-p~~epfl~~~L~~~~~~~l~~Lk-k~rIp 629 (1015)
++|+++|+++|+++.+++.+...|++.+..+.... .... .+|+.+|| +.++||++++++.+++..++.+| ++|||
T Consensus 250 ~~f~~l~~~~l~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~~~~ll~~g~~~~~~pfl~~~l~~~~~~~l~~~~~~~ri~ 328 (579)
T PF05183_consen 250 EVFLELQDEALEELRNILTDPDAARDLLSNQSRDG-DFRLIRRQLLDAGFDPLNDPFLRSLLKALIKKKLKELKKKARIP 328 (579)
T ss_dssp HHHHHHHHHHHHHHHHHTTSHHHHHHHHHHHS--H-HHHHHHTHHHHTT--TTTBHHHHHHHHHHHHHHHHHHHHC--B-
T ss_pred HHHHHHHHHHHHHHHHHhhCHHHHHHHHHhcCCCc-chhHHHHHHHHcCCCcccCHHHHHHHHHHHHHHHHhccceEEEE
Confidence 99999999999999999999988998887665433 2222 28999999 89999999999999999999999 79999
Q ss_pred cCCcceeEeecCCCCCCCCCeEEEEecc--------ceeeceeEEEEeCCCCCCCCeeEEEEeecCcccccccCcceEEE
Q 001771 630 VTESYYLMGTVDPTGILKSNEVCIILKD--------GQVSWEKVLVYRNPGLHFGDIHVLKATYVKELEDFVGTSKYAIF 701 (1015)
Q Consensus 630 V~~s~~L~GV~DetG~L~eGEVfv~~s~--------~~l~G~~VlV~RnP~lHPGDVr~v~AV~~P~L~~~~~~lkdVIV 701 (1015)
||+|++||||+||||+|+||||||+++. .+++| +|+|+||||+||||||+|+||+.|+|+ |++||||
T Consensus 329 v~~s~~l~gv~D~~g~L~~geV~~~~s~~~~~~~~~~~~~g-~VlV~R~P~~~pgDir~~~av~~p~L~----~l~~vIV 403 (579)
T PF05183_consen 329 VPKSRYLMGVPDPTGVLKEGEVFVQFSSDEETGSQSQVLEG-DVLVTRNPCLHPGDIRKVKAVDKPELR----HLKDVIV 403 (579)
T ss_dssp -SSEEEEEEEE-TTS---TTEEEEEEEEEEEETTEEEEEE--EEEEE-SS--SGGGEEEEEE---GGGT----T--SEEE
T ss_pred cCCCcEEEEeeCCcCCCCCCEEEEEeccccccCCCcceeee-eEEEecCCccCcCceeEEEeeccHHHc----ccCCEEE
Confidence 9999999999999999999999999821 47999 999999999999999999999999998 5799999
Q ss_pred eCCCCCCCccccccCCCCCCCeEEEEeCccccccccccccccccCCC-Ccccc-------cCccCChHHHHHHHHHHHHh
Q 001771 702 FPCNGPRSLADEIAGGDFDGDMYFVSRNPELLKHFKESERWMSTSKN-LSANK-------RLIDFSLEELESELFKLFLN 773 (1015)
Q Consensus 702 Fp~kG~Rplps~lSGGDLDGD~y~ViWD~~Lv~~f~~~~p~~~~~~P-~~~~~-------~p~~~~~~~~~~~~f~~Fl~ 773 (1015)
||++|+||+|++|||||||||+||||||++||++|++.+|... .+| .+... .+..+..+....++.++|+.
T Consensus 404 F~~~G~r~~~~~lsGgDlDGD~~~V~wd~~lv~~~~~~~~~~~-~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~ 482 (579)
T PF05183_consen 404 FSTKGDRPLPSELSGGDLDGDEYFVCWDPRLVEPFKNPPPPKS-EEPMNYESEKVSDSSGDPKPLSRPVTEEDIQDFFLE 482 (579)
T ss_dssp E-S-SSS-HHHHTTT--SSS-EEEEE--HHHHHTB------------TTTSEE---BHHHHTT-SSHHHHHHHHHHHHHH
T ss_pred eCCCCCCCchHHhcCCCCCCceEEEEeCHhhhhhhhccCcccC-CCccccccccccccccCccccCccccHHHHHHHHHH
Confidence 9999999999999999999999999999999999988755433 333 42221 22334454555555555553
Q ss_pred cccCCCCchhhhhhHHHHHHHHhccCCCchhHHHHhccHHHHHHHHHHhhcccCCCCCCCcccCCCC-CCCCCCCCCcCC
Q 001771 774 TRFCPSNAKSLAADCWQAVMDRFLTLGDESAEEKAAMKENMLRLINIYYDALDAPKKSGIKVEVPED-LKVEKFPCYMRR 852 (1015)
Q Consensus 774 ~~y~~~d~LG~isn~Hl~~aD~~~~~g~~~~~~~g~~~~~Cl~LA~L~S~AVD~pK~TG~~v~lp~~-L~~~~~PdFM~k 852 (1015)
.|+.++.||+|+|+|++++|+.. |+.++.|++||+|||+||||+| ||+++.++.. ++++.|||||++
T Consensus 483 -~~~~~~~lG~~s~~h~~~~d~~~----------g~~~~~~~~La~l~s~~vD~~K-tG~~~~~~~~~~~~~~~P~~~~~ 550 (579)
T PF05183_consen 483 -FYINNDNLGLISNAHLAIADQSS----------GIDSPECLKLAQLHSQAVDAPK-TGVPVKLPRWPLKPPEYPDFMEK 550 (579)
T ss_dssp -HHTS--HHHHHHHHHHHHHHHHT-----------SSSHHHHHHHHHHHHHTTHHH-HTEE--HHHHHSS-----GGGSS
T ss_pred -hhcccCcHHHHHHHHHHHHHhcC----------CCCCHHHHHHHHHHHHHhCccc-cCCCccccchhhcCCCCChhhcc
Confidence 47889999999999999999852 4678999999999999999999 9999999988 899999999999
Q ss_pred CCCCc-ccccCchhhhhhhcccccc
Q 001771 853 DESVS-FESTSVLGTIYNTVKSYEA 876 (1015)
Q Consensus 853 ~~~~~-Y~S~kiLGkLYr~v~~~~~ 876 (1015)
..++. |+|++|||+|||+|+....
T Consensus 551 ~~~~~~y~S~~ilg~ly~~v~~~~~ 575 (579)
T PF05183_consen 551 EDKKSYYKSTSILGQLYREVKEIVK 575 (579)
T ss_dssp -----SSS--SHHHHHHHTTH----
T ss_pred ccccccCCCccHHHHHHHHHHhhcc
Confidence 86665 7999999999999997643
No 3
>KOG0988 consensus RNA-directed RNA polymerase QDE-1 required for posttranscriptional gene silencing and RNA interference [RNA processing and modification]
Probab=96.42 E-value=0.0047 Score=78.12 Aligned_cols=193 Identities=31% Similarity=0.429 Sum_probs=123.3
Q ss_pred HHHHHHHHhc---------ccCCCCchhhhhhHHHHHHHH------hccCC-Cchh--HHHHh--------------ccH
Q 001771 765 SELFKLFLNT---------RFCPSNAKSLAADCWQAVMDR------FLTLG-DESA--EEKAA--------------MKE 812 (1015)
Q Consensus 765 ~~~f~~Fl~~---------~y~~~d~LG~isn~Hl~~aD~------~~~~g-~~~~--~~~g~--------------~~~ 812 (1015)
.+||.+||++ .+...|..|.-+..++.+|+. +...| ++.. .++-- .|+
T Consensus 868 ~effv~yL~~DslG~isnAhl~~aD~~G~~~~~Cl~LA~k~~~AVDF~KsG~d~~~~~~ek~e~~PDfm~~~d~p~Y~S~ 947 (1145)
T KOG0988|consen 868 SEFFVEYLKEDSLGLISNAHLANADVYGLFSDVCLELAKKHSQAVDFPKSGADESMPEKEKPERYPDFMEKTDKPTYYSE 947 (1145)
T ss_pred HHHHHHHHHHHHHHHHhhccccchhhcchhhHHHHHHHHhhcccccccccCCcccccchhchhhcchhhhCCCCceeecc
Confidence 3566666665 345678999999999999999 65566 2211 11111 111
Q ss_pred -HHHHHHHHHhhcccCCCCCCCc-------ccCCCCCCCCCCCCCcCCCC------------CCcccccCchhhhh----
Q 001771 813 -NMLRLINIYYDALDAPKKSGIK-------VEVPEDLKVEKFPCYMRRDE------------SVSFESTSVLGTIY---- 868 (1015)
Q Consensus 813 -~Cl~LA~L~S~AVD~pK~TG~~-------v~lp~~L~~~~~PdFM~k~~------------~~~Y~S~kiLGkLY---- 868 (1015)
.|=+|=.-+ +|+|.++ .|.+ +..+..++++.|||||+... -.-|.+-+..|.+|
T Consensus 948 ~l~GkLfR~~-~aid~~~-~~~e~~~~~~~i~yD~~l~v~gFe~yme~a~~~~~~y~~qL~slm~~ygi~~E~eI~sG~~ 1025 (1145)
T KOG0988|consen 948 RLCGKLFREA-KAIDAPL-KGSEERSEQVEVEYDEDLEVDGFEHYMERAKKQVASYNGQLRSLMDFYGISTEGEIFSGIL 1025 (1145)
T ss_pred hhhhHHHHHH-Hhhcchh-hcCccccCcccccCCcccCcCCcHHHHHHHHHHHhhhhhHHHHHHHHhCccchhhhhccCc
Confidence 344444433 6999999 9999 88899999999999998752 13455667778888
Q ss_pred --hhccccccccccc----------------------cccccCccCC-CCCChHHHHHHHHHHHHHHHHHHHHHHhh-hh
Q 001771 869 --NTVKSYEAVDRSV----------------------TEIWKLPCFD-DGVPEACMTKWKGYYDQYRWEMKEAIDKC-TV 922 (1015)
Q Consensus 869 --r~v~~~~~~~~~~----------------------~~~~~~~~f~-~~v~~~~~~~a~~~~~~Y~~~l~~lm~~~-k~ 922 (1015)
+.+...+.+...+ .++..+++|+ .+..|.+++.|..+|..|.-.+.+.|... +.
T Consensus 1026 ~~ddms~~~t~~~~e~~~~~l~~~~r~~~~qef~~y~~~~e~l~~fe~~~~eE~~~kKa~aWY~v~~ye~~~~~~~~~~~ 1105 (1145)
T KOG0988|consen 1026 DQDDMSFYNTERMIELKLERLVLKLREKFFQEFGAYKLEIEKLSCFEDSPEEEFIMKKASAWYRVYRYEMAQAMRETRKL 1105 (1145)
T ss_pred cccchhhhcccccchhhhHHHHHHHHHHHHHHhhhhcchhhhccccccCchhHHHHHHHHHHHHHHHhhhhcccccCccc
Confidence 3333332221111 1244566776 55667789999999987888888888552 23
Q ss_pred hHHHHHHHHHHHHHHHHHhhhhhhhccCCHHHHHHHh
Q 001771 923 EREEAAELVIEKYKQILYGAAEFEQSTRTLEEIYNEA 959 (1015)
Q Consensus 923 ~~~~~~~~l~~~yr~~~~~~~~f~~~~~~~~~~~~~A 959 (1015)
.-+..+..+..++|+.++++.++.....+..+....+
T Consensus 1106 SF~wia~Dvl~~iK~~~~~~~g~a~p~~tl~e~~~~~ 1142 (1145)
T KOG0988|consen 1106 SFAWIAYDVLARIKQTFLGAIGGANPVYTLEELHRQR 1142 (1145)
T ss_pred chHHHHHHHHHHHHHHHHHhhcccCchHHHHHhhHHh
Confidence 3344566788889888666544433323334444433
No 4
>smart00663 RPOLA_N RNA polymerase I subunit A N-terminus.
Probab=83.78 E-value=1.4 Score=49.99 Aligned_cols=53 Identities=26% Similarity=0.333 Sum_probs=38.9
Q ss_pred eeeceeEEEEeCCCCCCCCeeEEEEeecCcccccccCcceEEEeCCCCCCCcccccc--CCCCCCCeEEEE
Q 001771 659 QVSWEKVLVYRNPGLHFGDIHVLKATYVKELEDFVGTSKYAIFFPCNGPRSLADEIA--GGDFDGDMYFVS 727 (1015)
Q Consensus 659 ~l~G~~VlV~RnP~lHPGDVr~v~AV~~P~L~~~~~~lkdVIVFp~kG~Rplps~lS--GGDLDGD~y~Vi 727 (1015)
.+.|..||+-|.|+||..-||-+++.-.|. + +| |=+|..|+ +.|+|||+..+.
T Consensus 199 l~dgd~Vl~NRqPsLHr~si~a~~v~v~~~-~--------ti-------r~n~~~c~~fNADFDGDeMnih 253 (295)
T smart00663 199 VIDGDVVLFNRQPTLHRMSIQAHRVRVLEG-K--------TI-------RLNPLVCSPYNADFDGDEMNLH 253 (295)
T ss_pred hhcCCEEEEecCCccccccceeEEEEEecC-c--------eE-------EecCccCCcccCCcCCCEEEEe
Confidence 467768999999999999999998876664 1 11 22233333 489999999865
No 5
>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=83.39 E-value=1.1 Score=46.87 Aligned_cols=53 Identities=26% Similarity=0.255 Sum_probs=34.6
Q ss_pred eeeceeEEEEeCCCCCCCCeeEEEEeecCcccccccCcceEEEeCCCCCCCcccccc--CCCCCCCeEEEE
Q 001771 659 QVSWEKVLVYRNPGLHFGDIHVLKATYVKELEDFVGTSKYAIFFPCNGPRSLADEIA--GGDFDGDMYFVS 727 (1015)
Q Consensus 659 ~l~G~~VlV~RnP~lHPGDVr~v~AV~~P~L~~~~~~lkdVIVFp~kG~Rplps~lS--GGDLDGD~y~Vi 727 (1015)
...|..||+-|.|+||..-++-++++-.+. . -=|=+|..|+ +.|+|||+..|.
T Consensus 95 l~~gd~vl~nRqPtLh~~s~~a~~~~~~~~-~---------------t~~~~~~~c~~~NADFDGDem~i~ 149 (166)
T PF00623_consen 95 LCDGDIVLLNRQPTLHRMSIMAHKVRVLPG-K---------------TIRINPLVCSPFNADFDGDEMNIH 149 (166)
T ss_dssp HTTT-EEEEEESS-SSGGGEEEEEEEEESS-S---------------SEEEEGGGHHHHT--TSS-EEEEE
T ss_pred hhcCceeEEeccchhccceeeeeeeeeecc-c---------------EEEeeccchhhhhccCCcceEEEE
Confidence 346767999999999999999999876665 1 1122334444 599999999876
No 6
>CHL00018 rpoC1 RNA polymerase beta' subunit
Probab=66.87 E-value=5.1 Score=49.90 Aligned_cols=54 Identities=30% Similarity=0.298 Sum_probs=39.1
Q ss_pred ceeeceeEEEEeCCCCCCCCeeEEEEeecCcccccccCcceEEEeCCCCCCCcccccc--CCCCCCCeEEEE
Q 001771 658 GQVSWEKVLVYRNPGLHFGDIHVLKATYVKELEDFVGTSKYAIFFPCNGPRSLADEIA--GGDFDGDMYFVS 727 (1015)
Q Consensus 658 ~~l~G~~VlV~RnP~lHPGDVr~v~AV~~P~L~~~~~~lkdVIVFp~kG~Rplps~lS--GGDLDGD~y~Vi 727 (1015)
.++.|..||+-|-|+||.--||-+++|-.+.- +| |=+|..|+ +.|+|||+..|-
T Consensus 443 ~v~~gd~VLlNRqPTLHR~sIqAf~~~L~~gk---------tI-------rLhplvC~~fNADFDGDqMnvH 498 (663)
T CHL00018 443 EVMQGHPVLLNRAPTLHRLGIQAFQPILVEGR---------AI-------CLHPLVCKGFNADFDGDQMAVH 498 (663)
T ss_pred ehhcCceeeecCCCcccccccceeeEEecCCC---------eE-------EeCcccCCcccCCccCcEEEEe
Confidence 46778899999999999999999988765531 01 12233333 489999998874
No 7
>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional
Probab=66.61 E-value=7 Score=48.33 Aligned_cols=54 Identities=26% Similarity=0.280 Sum_probs=39.4
Q ss_pred ceeeceeEEEEeCCCCCCCCeeEEEEeecCcccccccCcceEEEeCCCCCCCcccccc--CCCCCCCeEEEE
Q 001771 658 GQVSWEKVLVYRNPGLHFGDIHVLKATYVKELEDFVGTSKYAIFFPCNGPRSLADEIA--GGDFDGDMYFVS 727 (1015)
Q Consensus 658 ~~l~G~~VlV~RnP~lHPGDVr~v~AV~~P~L~~~~~~lkdVIVFp~kG~Rplps~lS--GGDLDGD~y~Vi 727 (1015)
..+.|..||.-|-|+||.--||-++++-.+.- -=|=+|..|+ +.|+|||+..|-
T Consensus 422 ~v~~gd~VLlNRqPTLHR~sIqAf~~~l~~~k----------------tirlhplvC~~fNADFDGDeMnvH 477 (627)
T PRK02625 422 EVIEGHPVLLNRAPTLHRLGIQAFEPILVEGR----------------AIQLHPLVCPAFNADFDGDQMAVH 477 (627)
T ss_pred EeecCcEEEecCCCccccccceeEeeEEcCCC----------------eEEeccccCCcccCCcCCCeEEEe
Confidence 36778789999999999999999988765541 1122333343 489999998874
No 8
>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=66.15 E-value=5.3 Score=49.29 Aligned_cols=54 Identities=24% Similarity=0.276 Sum_probs=39.1
Q ss_pred ceeeceeEEEEeCCCCCCCCeeEEEEeecCcccccccCcceEEEeCCCCCCCcccccc--CCCCCCCeEEEE
Q 001771 658 GQVSWEKVLVYRNPGLHFGDIHVLKATYVKELEDFVGTSKYAIFFPCNGPRSLADEIA--GGDFDGDMYFVS 727 (1015)
Q Consensus 658 ~~l~G~~VlV~RnP~lHPGDVr~v~AV~~P~L~~~~~~lkdVIVFp~kG~Rplps~lS--GGDLDGD~y~Vi 727 (1015)
.++.|..||.-|-|+||.--||-++++-.+.- -=|=+|..|+ +.|+|||+..|-
T Consensus 415 ~v~~gd~VLlNRqPTLHR~sIqAf~~~l~~~k----------------tirlhplvC~~fNADFDGDeMnvH 470 (619)
T TIGR02387 415 EVITGHPVMLNRAPTLHRLGIQAFEPILVDGR----------------AIQLHPLVCPAFNADFDGDQMAVH 470 (619)
T ss_pred HHhcCCEEEecCCCccchhcceeeeeEEecCC----------------eEEECcccCCcccCCCCCceeeee
Confidence 35778789999999999999999988755431 1122333344 489999998874
No 9
>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=52.89 E-value=17 Score=47.20 Aligned_cols=53 Identities=25% Similarity=0.236 Sum_probs=38.7
Q ss_pred eeeceeEEEEeCCCCCCCCeeEEEEeecCcccccccCcceEEEeCCCCCCCcccccc--CCCCCCCeEEEE
Q 001771 659 QVSWEKVLVYRNPGLHFGDIHVLKATYVKELEDFVGTSKYAIFFPCNGPRSLADEIA--GGDFDGDMYFVS 727 (1015)
Q Consensus 659 ~l~G~~VlV~RnP~lHPGDVr~v~AV~~P~L~~~~~~lkdVIVFp~kG~Rplps~lS--GGDLDGD~y~Vi 727 (1015)
.+.|..||+-|-|+||.--|+-.++.-.|. + -=|=+|+.|+ +.|+|||+.++-
T Consensus 408 l~dgd~vl~NRqPsLHr~si~a~~~~v~~~-~---------------t~r~n~~~c~~~NADFDGDeMn~h 462 (868)
T TIGR02390 408 LIDGDIVLFNRQPSLHRMSMMGHKVKVLPG-K---------------TFRLNLAVCPPYNADFDGDEMNLH 462 (868)
T ss_pred hhcCccceeccCCccccccceeEEEEEecC-c---------------eEeeccccCCccccCcccceeeEe
Confidence 467878999999999999999888876653 1 1122333343 489999999876
No 10
>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=49.62 E-value=15 Score=48.74 Aligned_cols=54 Identities=28% Similarity=0.327 Sum_probs=39.0
Q ss_pred ceeeceeEEEEeCCCCCCCCeeEEEEeecCcccccccCcceEEEeCCCCCCCcccccc--CCCCCCCeEEEE
Q 001771 658 GQVSWEKVLVYRNPGLHFGDIHVLKATYVKELEDFVGTSKYAIFFPCNGPRSLADEIA--GGDFDGDMYFVS 727 (1015)
Q Consensus 658 ~~l~G~~VlV~RnP~lHPGDVr~v~AV~~P~L~~~~~~lkdVIVFp~kG~Rplps~lS--GGDLDGD~y~Vi 727 (1015)
..+.|..||.-|-|+||.--||=++++-.|. +-=|=||..|+ +.|+|||+..|-
T Consensus 396 ~vi~~d~VLlNRqPTLHRlsIqAf~~~l~~g----------------ktirlhplvC~~fNADFDGDeMnvH 451 (1140)
T TIGR02386 396 DVIKEHPVLLNRAPTLHRLGIQAFEPVLVEG----------------KAIRLHPLVCTAFNADFDGDQMAVH 451 (1140)
T ss_pred EccCCcEEEecCCCcccccccceeEEEEecC----------------ceEEEcccccCcccCCCCcceeEee
Confidence 3567779999999999999999988876653 11122233333 489999998875
No 11
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=47.52 E-value=18 Score=48.04 Aligned_cols=53 Identities=26% Similarity=0.330 Sum_probs=38.9
Q ss_pred eeeceeEEEEeCCCCCCCCeeEEEEeecCcccccccCcceEEEeCCCCCCCcccccc--CCCCCCCeEEEE
Q 001771 659 QVSWEKVLVYRNPGLHFGDIHVLKATYVKELEDFVGTSKYAIFFPCNGPRSLADEIA--GGDFDGDMYFVS 727 (1015)
Q Consensus 659 ~l~G~~VlV~RnP~lHPGDVr~v~AV~~P~L~~~~~~lkdVIVFp~kG~Rplps~lS--GGDLDGD~y~Vi 727 (1015)
++.|..||.-|-|.||.--||=++++-.|.-- | |=||..|+ +.|+|||+..|-
T Consensus 405 vi~gd~VLlNRqPTLHR~sIqAf~~~l~~gkt---------i-------rLhplvC~~fNADFDGDqMnvH 459 (1156)
T PRK00566 405 VIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKA---------I-------QLHPLVCTAFNADFDGDQMAVH 459 (1156)
T ss_pred ecCCCEEEecCCCcccccccceeEEEEecCce---------E-------EECccccCccccccccceeEEe
Confidence 56788999999999999999999987665410 1 22233333 489999998875
No 12
>PRK08566 DNA-directed RNA polymerase subunit A'; Validated
Probab=47.46 E-value=19 Score=46.80 Aligned_cols=53 Identities=25% Similarity=0.261 Sum_probs=39.1
Q ss_pred eeeceeEEEEeCCCCCCCCeeEEEEeecCcccccccCcceEEEeCCCCCCCcccccc--CCCCCCCeEEEE
Q 001771 659 QVSWEKVLVYRNPGLHFGDIHVLKATYVKELEDFVGTSKYAIFFPCNGPRSLADEIA--GGDFDGDMYFVS 727 (1015)
Q Consensus 659 ~l~G~~VlV~RnP~lHPGDVr~v~AV~~P~L~~~~~~lkdVIVFp~kG~Rplps~lS--GGDLDGD~y~Vi 727 (1015)
.+.|..||+-|-|+||.--|+-.+++-.|. + -=|=+|..|+ +.|+|||+..+-
T Consensus 412 l~dgd~vl~NRqPsLHr~si~a~~~~v~~~-~---------------t~r~n~~~c~~~NADFDGDeMn~h 466 (882)
T PRK08566 412 LIDGDIVLFNRQPSLHRMSIMAHRVRVLPG-K---------------TFRLNLAVCPPYNADFDGDEMNLH 466 (882)
T ss_pred hhcCceeeecCCCcccccccceeEEEEecC-c---------------eEeeccccCCCccCCccCcEEEEe
Confidence 467878999999999999999888876664 1 1122333343 499999999875
No 13
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=44.97 E-value=23 Score=50.55 Aligned_cols=54 Identities=24% Similarity=0.280 Sum_probs=39.5
Q ss_pred ceeeceeEEEEeCCCCCCCCeeEEEEeecCcccccccCcceEEEeCCCCCCCcccccc--CCCCCCCeEEEE
Q 001771 658 GQVSWEKVLVYRNPGLHFGDIHVLKATYVKELEDFVGTSKYAIFFPCNGPRSLADEIA--GGDFDGDMYFVS 727 (1015)
Q Consensus 658 ~~l~G~~VlV~RnP~lHPGDVr~v~AV~~P~L~~~~~~lkdVIVFp~kG~Rplps~lS--GGDLDGD~y~Vi 727 (1015)
..+.|..||.-|.|.||.--||-++++-.|. +-=|=||..|+ +.|+|||+..|-
T Consensus 1803 ~vi~gd~VLlNRqPTLHR~sIqAf~~~l~~g----------------ktIrLhplvC~~fNADFDGDqMnvH 1858 (2890)
T PRK09603 1803 EITEGYPVLLNRAPTLHKQSIQAFHPKLIDG----------------KAIQLHPLVCSAFNADFDGDQMAVH 1858 (2890)
T ss_pred eeecCCeEEecCCCccccccceeeeEEEecC----------------ceEEeccccCCcccCCCCCceeEEe
Confidence 3678878999999999999999988876553 11122333343 489999998875
No 14
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=44.84 E-value=22 Score=47.96 Aligned_cols=53 Identities=26% Similarity=0.315 Sum_probs=38.5
Q ss_pred eeeceeEEEEeCCCCCCCCeeEEEEeecCcccccccCcceEEEeCCCCCCCcccccc--CCCCCCCeEEEE
Q 001771 659 QVSWEKVLVYRNPGLHFGDIHVLKATYVKELEDFVGTSKYAIFFPCNGPRSLADEIA--GGDFDGDMYFVS 727 (1015)
Q Consensus 659 ~l~G~~VlV~RnP~lHPGDVr~v~AV~~P~L~~~~~~lkdVIVFp~kG~Rplps~lS--GGDLDGD~y~Vi 727 (1015)
.+.|..||+-|-|.||.--||=++++-.+. +-=|=||.-|+ +.|+|||+..|-
T Consensus 493 vi~gd~VLlNRqPTLHRlsIqAf~~~L~~g----------------ktIrLhplvC~~fNADFDGDqMnvH 547 (1460)
T PRK14906 493 VIQDHPVLLNRAPTLHRLGIQAFEPVLVEG----------------KAIKLHPLVCTAFNADFDGDQMAVH 547 (1460)
T ss_pred eeccceeEeccCcccchhccceeeEEecCC----------------ceEEecccccCccccCCcCceeeee
Confidence 567879999999999999999988776553 11122233333 489999998875
No 15
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=33.93 E-value=36 Score=48.63 Aligned_cols=53 Identities=25% Similarity=0.307 Sum_probs=38.6
Q ss_pred eeeceeEEEEeCCCCCCCCeeEEEEeecCcccccccCcceEEEeCCCCCCCcccccc--CCCCCCCeEEEE
Q 001771 659 QVSWEKVLVYRNPGLHFGDIHVLKATYVKELEDFVGTSKYAIFFPCNGPRSLADEIA--GGDFDGDMYFVS 727 (1015)
Q Consensus 659 ~l~G~~VlV~RnP~lHPGDVr~v~AV~~P~L~~~~~~lkdVIVFp~kG~Rplps~lS--GGDLDGD~y~Vi 727 (1015)
.+.|..||.-|-|+||.--||=++++-.+. +-=|=||..|+ +.|+|||+..|-
T Consensus 1848 vi~gd~VLlNRqPTLHR~sIqAf~~~l~~g----------------ktirlhp~vC~~fNADFDGDeMnvH 1902 (2836)
T PRK14844 1848 VIKEHPVLLNRAPTLHRLGIQAFEPILIEG----------------KAIQLHPLVCTAFNADFDGDQMAVH 1902 (2836)
T ss_pred EecCCEEEecCCCccccccccceeeEeecC----------------ceEEecccCCCcccCCCCCceeeee
Confidence 466779999999999999999888765553 11123334444 489999999875
No 16
>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Probab=27.99 E-value=61 Score=44.12 Aligned_cols=53 Identities=23% Similarity=0.236 Sum_probs=37.7
Q ss_pred eeeceeEEEEeCCCCCCCCeeEEEEeecCcccccccCcceEEEeCCCCCCCcccccc--CCCCCCCeEEEE
Q 001771 659 QVSWEKVLVYRNPGLHFGDIHVLKATYVKELEDFVGTSKYAIFFPCNGPRSLADEIA--GGDFDGDMYFVS 727 (1015)
Q Consensus 659 ~l~G~~VlV~RnP~lHPGDVr~v~AV~~P~L~~~~~~lkdVIVFp~kG~Rplps~lS--GGDLDGD~y~Vi 727 (1015)
.+.|..||+-|-|+||.--|+=.++.-.|. + ==|=++..|+ ..|+|||+..+-
T Consensus 428 l~dGD~VL~NRQPSLHk~Simah~vkvl~~-k---------------T~Rln~~vC~pyNADFDGDEMNlH 482 (1321)
T PRK14977 428 LADGDIVIFNRQPSLHKLSILAHRVKVLPG-A---------------TFRLHPAVCPPYNADFDGDEMNLH 482 (1321)
T ss_pred eecCcEEEeccCCccccccceEEEEEEecC-c---------------eEEecccccCcccCCcccceeeee
Confidence 457878999999999999998888876664 1 1111222222 489999998865
No 17
>PF10664 NdhM: Cyanobacterial and plastid NDH-1 subunit M; InterPro: IPR018922 The NADH dehydrogenase I complex shuttles electrons from an unknown electron donor, via FMN and iron-sulphur (Fe-S) centres, to quinones in the respiratory and/or the photosynthetic chain. The immediate electron acceptor for the enzyme in plants is believed to be plastoquinone. The NADH dehydrogenase I complex couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. This entry represents subunit M of the NADH dehydrogenase I complex in cyanobacteria and plant chloroplasts []. ; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0055114 oxidation-reduction process
Probab=25.07 E-value=74 Score=30.82 Aligned_cols=47 Identities=28% Similarity=0.426 Sum_probs=37.1
Q ss_pred HHHHHHHHHHhCCCCCChhhhhhhhccChHHHHHHHHHhhccccccchhHHHHHHhhhcc
Q 001771 20 EQLISKIYTEQNKLPPDDGARRSLASLGEDAALDVLRTIASDKIKYSFSGYINYLVKKRN 79 (1015)
Q Consensus 20 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (1015)
++.|+|+|+++.. ..+ +.-|+++.-=.||+|.+. |.+||+.|..+-.
T Consensus 41 ~~~l~kVy~~F~e-LVe-------~~~G~~LtdYnLRrIGSd-----LE~~iR~LLq~Ge 87 (108)
T PF10664_consen 41 EEALQKVYRKFDE-LVE-------SYAGEDLTDYNLRRIGSD-----LEHFIRSLLQAGE 87 (108)
T ss_pred HHHHHHHHHHHHH-HHH-------hhcCCCchhhhHHHhccH-----HHHHHHHHHHCCc
Confidence 5778999999987 222 345788888899999987 8999999987643
Done!