Query 002586
Match_columns 904
No_of_seqs 288 out of 488
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 03:00:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002586.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002586hhsearch_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 4E-178 9E-183 1566.0 63.2 852 12-894 257-1136(1145)
2 PF05183 RdRP: RNA dependent R 100.0 5E-127 1E-131 1135.4 20.7 545 151-728 1-574 (579)
3 smart00663 RPOLA_N RNA polymer 81.7 2 4.3E-05 48.0 5.0 52 536-599 199-253 (295)
4 PF00623 RNA_pol_Rpb1_2: RNA p 73.1 2.5 5.5E-05 43.3 2.6 52 536-599 95-149 (166)
5 CHL00018 rpoC1 RNA polymerase 64.3 6.5 0.00014 48.2 3.9 53 535-599 443-498 (663)
6 TIGR02387 rpoC1_cyan DNA-direc 63.0 6.9 0.00015 47.5 3.7 52 535-598 415-469 (619)
7 PRK02625 rpoC1 DNA-directed RN 59.0 11 0.00025 45.8 4.6 53 535-599 422-477 (627)
8 TIGR02386 rpoC_TIGR DNA-direct 46.2 19 0.00042 47.0 4.0 52 536-599 397-451 (1140)
9 PRK09603 bifunctional DNA-dire 43.2 28 0.0006 49.1 4.9 53 535-599 1803-1858(2890)
10 PRK08566 DNA-directed RNA poly 42.4 25 0.00055 45.2 4.3 53 535-599 411-466 (882)
11 PRK00566 DNA-directed RNA poly 42.1 24 0.00053 46.2 4.0 52 536-599 405-459 (1156)
12 TIGR02390 RNA_pol_rpoA1 DNA-di 40.7 27 0.00058 44.9 4.1 53 535-599 407-462 (868)
13 PRK14906 DNA-directed RNA poly 39.0 29 0.00062 46.2 4.0 52 536-599 493-547 (1460)
14 PRK14844 bifunctional DNA-dire 31.0 48 0.001 46.8 4.2 52 536-599 1848-1902(2836)
15 PRK14977 bifunctional DNA-dire 28.1 67 0.0014 43.2 4.8 53 535-599 427-482 (1321)
16 TIGR00489 aEF-1_beta translati 26.1 1.7E+02 0.0036 27.1 5.6 59 206-267 18-76 (88)
17 cd01213 tensin Tensin Phosphot 26.0 3.5E+02 0.0076 27.1 8.3 86 145-262 47-133 (138)
18 PRK00435 ef1B elongation facto 24.5 1.8E+02 0.0038 26.9 5.5 59 206-267 18-76 (88)
19 cd00292 EF1B Elongation factor 22.5 1.8E+02 0.004 26.8 5.2 53 207-262 19-71 (88)
20 PHA02770 hypothetical protein; 22.0 80 0.0017 27.3 2.5 20 221-244 45-65 (81)
21 KOG0260 RNA polymerase II, lar 21.7 67 0.0015 41.9 2.8 58 542-599 383-482 (1605)
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=4.1e-178 Score=1566.03 Aligned_cols=852 Identities=41% Similarity=0.615 Sum_probs=742.6
Q ss_pred hhccccccccc-----cC--eeEEeeCCccc-cCCCcccccC-CCCCCCCCcchHHHHHHHHHhCcCCcccccHHHHHhh
Q 002586 12 FKENFAYYKES-----ED--RFVLETGSAYS-RSLDLVPIVG-PPDGIALPYEILFKINLLVQNGCVAGPLLDSNFYRLV 82 (904)
Q Consensus 12 ~~~~~~~~~~~-----~~--~~~~~~~~~~~-~~~~~~~~~~-~~~~~~lpf~v~fql~~l~~~g~l~~~~~~~~f~~~l 82 (904)
+..++||+.++ .- .+.++.|+.|. ++..++||++ ...++..+++++++.++||+.|.+.......+|+.++
T Consensus 257 i~~~lP~~r~~~~~~~~~~~s~~ir~~~~~~~~~~~~~~l~~~~~~git~~~e~l~~r~slv~dq~~~~~~~~~~f~~l~ 336 (1145)
T KOG0988|consen 257 IWKDLPYNRYNGSTAEEFRLSVWIRLGSKYDVSSAQLVPLNDERDFGITHLYECLVSRGSLVKDQVLLEEAHLLEFLGLL 336 (1145)
T ss_pred hhccCCcccccccchhhhhhhhheecccccccccceeeeccccccccceeehhhhhcccchhhhhHHhhhhHHHHHHHHH
Confidence 67888888875 33 67888999998 5777999988 4567889999999999999999999999999999999
Q ss_pred CCCCCCCChHHHHHHHHHHHhccccccCcchhHHHHHHHhhhcCCCCCCCCccCCCCcEEEEEEEEcCCeeeeccccccc
Q 002586 83 DPYRAPVSISCIEHALDKLYHLKECCYEPSRWLTDQYRKYMTSRSKPSSPAISLDDGLVYVHRVQVTPSRVYFCGPEINV 162 (904)
Q Consensus 83 ~~~~~~~~~~~~~~~l~~l~~~~~~~~dp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~v~vTPtri~~~~P~~e~ 162 (904)
..... .....++..||+|.+...+|+||.-+....++....++.+ .....+.+|+++|+||.|||||||+.+||+++
T Consensus 337 ~~~~~-~d~~v~~a~LekL~~~~~~cfd~~~~~k~i~~~~~~ng~~--~~~~~~~~g~~~vrk~v~TPtrv~~~~PE~~~ 413 (1145)
T KOG0988|consen 337 RHKVL-GDDNVLEAKLEKLLKLSTKCFDPYCQYKKIAKLNPSNGKL--VTTKEIMEGLRRVRKVVFTPTRVYLLAPEVEM 413 (1145)
T ss_pred hhhhc-cchhHHHHHHHHHhhhhhhhhhHHHHHHHHHHHhcccCcc--ccchhhhhcceeEEEEEEcCceeEecCchhhh
Confidence 76332 1225667789999999999999999888877765445442 23345678999999999999999999999999
Q ss_pred cCchhcccCcCCCcEEEEEEeeCCCCccccCCCCCCCCCCccchhhhHHHHHHHHHhcCeEEcceeEEEeeecCCCCCcC
Q 002586 163 SNRVLRHFRRDIDNFLRISFIDEDLDKIHSTDLSPRGSSATDITRTRIYTRILSTLRNGILIGDRKFEFLAFSSSQLRES 242 (904)
Q Consensus 163 sNRvlR~f~~~~d~FlRV~F~DE~~~~l~~~~~~~r~~~~~~~~~~~i~~rv~~~L~~Gi~I~gr~y~FLa~S~SqlR~~ 242 (904)
+|||+|+|..+.++||||+|+||+++ +..++.+++ .++.+|.||..+|++||+||+|.|+||||||||||+|
T Consensus 414 gNRVlR~f~~~~t~~lRvtF~De~~~-~~ir~~S~~-------~~t~l~~rv~~~L~~Gi~v~~r~y~FL~~s~sQlRdn 485 (1145)
T KOG0988|consen 414 GNRVLRKFDKDSTRFLRVTFRDEDNK-LKIRTLSTG-------SRTKLDMRVNSYLTDGISVANRRYEFLAFSNSQLRDN 485 (1145)
T ss_pred cchhheeccccCceEEEEEEEccccc-cccccCCcc-------hhhHHHHHHHHHHhcccEEccceeEEEEecccccccC
Confidence 99999999999999999999999986 444333221 1689999999999999999999999999999999999
Q ss_pred eEEEEEcCCCCCHHHHHHHhCCCCcccCHHHHHHHHcccccCCccceee-eCCcEEEccCcccccCCccccccccccccc
Q 002586 243 SAWMFASRYGLTAAEIREWMGNFREIRNVAKYAARLGQSFSSSKETLSV-HMDEIEIIPDVKIEIGKTKYVFSDGIGKVS 321 (904)
Q Consensus 243 s~wf~a~~~~~t~~~Ir~~mG~F~~i~~~aK~aARlgq~FSsT~~t~~i-~~~~i~~i~Di~~~~~g~~~~fTDG~G~IS 321 (904)
|.||++.....++++||.|||+|++|.|++|||||||||||+|++|..+ +...+..+|||+.+++|++||||||||+||
T Consensus 486 gy~m~~~s~~~~i~~iR~wmG~F~~i~nv~K~aARmGqCFs~Sr~T~~~~~~~~~~~~~DI~~g~~g~~y~FSDGvG~iS 565 (1145)
T KOG0988|consen 486 GYFMARFSDKTKIEDIREWMGDFRDIDNVPKLAARMGQCFSQSRGTGYVLERLDRMCPPDIEGGKRGNNYCFSDGVGMIS 565 (1145)
T ss_pred ceEEeecCCCccHHHHHHHhcchhhccCHHHHHhhcCcceeccccccccccccccccCCcccccccCCceeecCCccccc
Confidence 9888887777899999999999999999999999999999999999877 667788999999887889999999999999
Q ss_pred HHHHHHHHHHcCCCCCCCceEEEeccCceEEEEeCCCCCcceeecccccccccCCCceeEeeecCcccccccHHHHHHHh
Q 002586 322 AEFARKVASKCGLKDNPPSAFQIRYGGYKGVVAADPTSSKKLSLRDSMRKYESELTKLDVLAWSKYQPCFLNRQLISLLS 401 (904)
Q Consensus 322 ~~la~~I~~~l~l~~~~PSafQiR~gG~KGvL~vdp~~~~~I~lR~Sm~KF~s~~~~leI~~~S~~~p~~LNrQ~I~iL~ 401 (904)
.++|++|++++++...+|||||||++|+||||+|||.....+.+|.||.||.|.+..++|+.|++++||+||||+|.+|+
T Consensus 566 ~~~a~~vsq~~~~~~~vPsaFQiR~~G~KGVvav~Ps~~~~~~~~~~~~~s~S~n~~~~v~~~~~f~~~~lnr~lI~Lls 645 (1145)
T KOG0988|consen 566 LQFAREVSQKRKFGKAVPSAFQIRYGGYKGVVAVDPSMDKVLKLRDSMNKSQSFNSLLEVTPSSKFQPAFLNRQLITLLS 645 (1145)
T ss_pred HHHHHHHHHHHcccccCChheeeeccCCcceEEeCccHhhhhhhhhhhhhhhhhcceeeeeeccCCccccccHHHHHHHH
Confidence 99999999999998889999999999999999999999889999999999999999999999999999999999999999
Q ss_pred hCCCCHHHHHHHHHHHHHH--HHHHhcCHHHHHHHHHhcCCCCcHHHHHHHHHCCCCCCCchHHHHHHHHHHHHHHHHhc
Q 002586 402 TLGIWDEIFEKKQREAVRQ--LDAILTDPLKAQEALELMSPGENTNILKELLICGYKPDAEPFLSMMLQTFRASKLLELR 479 (904)
Q Consensus 402 ~lGV~~evF~~lq~~~l~~--l~~~l~d~~~a~~~L~~~~~~~~~~~l~~ll~~Gf~~~~epfl~~~L~~~~~~~l~~lk 479 (904)
.+||++++|+++|+..++. ....+.....+.++|......+..+.++.++..++.++.|||+++||..++++.++.+|
T Consensus 646 ~~gv~n~~F~~il~~vle~~r~~~n~~e~~~~~~~l~~~~~m~~en~a~~~l~~~~~~D~EPflr~mL~~~~k~~~~~~k 725 (1145)
T KOG0988|consen 646 YLGVLNKPFINILDQVLEKQRRITNRIEELLDRAALNYGEQMDDENIAAMILKGFPRIDSEPFLRSMLSSLLKFTLQLLK 725 (1145)
T ss_pred hcCccchHHHHHHHHHHHHHHhhhhhhhHHHHHHHhhhhhhccchHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999983 33444555555666665544566676666666666688899999999999999999999
Q ss_pred cccceeccCceeeeeecCCCCCCCCCcEEEEEcCCcccccCCCcccccccccccceEEeeeEEEEeCCCCCCCCeeEEEE
Q 002586 480 TKTRIFIPNGRSMMGCLDETRTLNYGQVFVQISGAGYRQLHGESSLFSSSRSRQRFIVQGLVVVAKNPCLHPGDVRVLKA 559 (904)
Q Consensus 480 ~K~rI~Vp~s~~l~GV~DetG~L~~gEVfvq~s~~~~~~~~~~~~~~~~~~~~~~~vi~G~VlV~RnP~lhPGDIr~v~A 559 (904)
+|.|||||.||+||||+||||+|||||||||++.+.... ......|++|+|+|||||||||||||+++|
T Consensus 726 ek~ripv~~Gr~lmGvvDETG~L~ygQVfVq~t~~~~~~-----------~~~~~~vitG~VlvtKNPcLhpGDVRVl~A 794 (1145)
T KOG0988|consen 726 EKIRIPVDLGRSLMGVVDETGILKYGQVFVQYTKTIRNS-----------DSGRKEVITGKVLVTKNPCLHPGDVRVLKA 794 (1145)
T ss_pred hcccccCcCCceeEeeeccccccccCeEEEEEccccccc-----------ccCCceEEEeeEEEecCCCCCCCceEEEEe
Confidence 999999999999999999999999999999999863211 112347999999999999999999999999
Q ss_pred ecCCCCCCCCCeEEecCCCCCCCCCCcCCCCCCCCeEEEeecCCCCCCCCCCCCCCCCCcccCCCCccCHHHHHHHHHHh
Q 002586 560 VNVPALHHMVDCVVFPQKGMRPHPNECSGSDLDGDIYFVCWDDELIPPQQDPPMDYTPAQSMQLDHDVQIEDVEEYFTNY 639 (904)
Q Consensus 560 V~~P~L~hl~dvIVFp~kG~Rplps~lsGGDLDGD~y~ViWD~~Lv~~~~~~P~~y~~~~~~~l~~~vt~~di~~ffv~y 639 (904)
|++|+|+||+|||||||||+||||+||||||||||+|||||||+|+|+.+++||+|++++++.+++.++.++|.+||++|
T Consensus 795 V~vp~L~h~~dvVvFPQkGpRphpdE~aGsDLDGDeYfViWDqkLL~~~~~epmd~~~~~sk~~~~~~~~~~m~effv~y 874 (1145)
T KOG0988|consen 795 VYVPALEHMVDVVVFPQKGPRPHPDEMAGSDLDGDEYFVIWDQKLLPPRNEEPMDSSSEKSKILDGRVPLDEMSEFFVEY 874 (1145)
T ss_pred eccHHHHhhcCEEEcCCCCCCCCccccccCCCCCceEEEEeChhhccCcCCCccccCccccccccCCCCHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hccCcHHHHHHHHHHHhccCCCCCCChhHHHHHHHHhhcccCCCCCCcccCCCCCCCCCCCCCCCCCCCCCccccchhcH
Q 002586 640 IVNDSLGIIANAHTVFADREPRKARSEPCLQLAEKFSIAVDFPKTGVPAEIPPHLYVKEYPDFMEKPDKPTYESQNVIGK 719 (904)
Q Consensus 640 m~~d~LG~isn~Hl~~aD~~~~g~~~~~Cl~LA~l~s~AVD~~KTG~~v~ip~~l~~~~~Pdfm~k~~~~~Y~S~~iLG~ 719 (904)
|++|+||+|+|||+++||+ .|+.+..|+.||++||+||||||||+.+.||..++++++||||++.++|+|.|++++||
T Consensus 875 L~~DslG~isnAhl~~aD~--~G~~~~~Cl~LA~k~~~AVDF~KsG~d~~~~~~ek~e~~PDfm~~~d~p~Y~S~~l~Gk 952 (1145)
T KOG0988|consen 875 LKEDSLGLISNAHLANADV--YGLFSDVCLELAKKHSQAVDFPKSGADESMPEKEKPERYPDFMEKTDKPTYYSERLCGK 952 (1145)
T ss_pred HHHHHHHHHhhccccchhh--cchhhHHHHHHHHhhcccccccccCCcccccchhchhhcchhhhCCCCceeecchhhhH
Confidence 9999999999999999999 59999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhhhhcCCccccccchhhhhhccCCCCCccCChHHHHHHHHHHHHhHHHHHHHHHhhcCCCChhhhhhh--hhcccc
Q 002586 720 LFRAVKDIAPHTSCIRLFTKEVARRSYDPDMEVDGFEDHIDDAIYHKGNYDYKLGNLMDYYGIKTEAEILTG--SIMKMS 797 (904)
Q Consensus 720 Lyr~v~~~~~~~~~~~~~~~~~~~~~~d~~l~~~g~~~~~~~A~~~k~~Y~~~l~~lm~~y~i~tE~Ev~sG--~i~~~~ 797 (904)
|||+++.+.............+. ..||++++++||++|+++|..+++.|+.+|++||++|||.+|+||+|| .+..|+
T Consensus 953 LfR~~~aid~~~~~~e~~~~~~~-i~yD~~l~v~gFe~yme~a~~~~~~y~~qL~slm~~ygi~~E~eI~sG~~~~ddms 1031 (1145)
T KOG0988|consen 953 LFREAKAIDAPLKGSEERSEQVE-VEYDEDLEVDGFEHYMERAKKQVASYNGQLRSLMDFYGISTEGEIFSGILDQDDMS 1031 (1145)
T ss_pred HHHHHHhhcchhhcCccccCccc-ccCCcccCcCCcHHHHHHHHHHHhhhhhHHHHHHHHhCccchhhhhccCccccchh
Confidence 99988766544333233334444 789999999999999999999999999999999999999999999999 555677
Q ss_pred chhhhhhhHHHHHHHHHHHHHHHHHHHhh-h----c----CCCC-hhhHHHHHHHHhh-hccccccccccccCCCCCccc
Q 002586 798 KSFTKRRDAEAIGMAVRALRKEARAWFKE-K----S----GSDT-EDDAYAKASAWYH-VTYHPDYWGCYNQGMNRDHFL 866 (904)
Q Consensus 798 ~~~~~~~~~e~i~~~~~~l~~~~r~~f~~-~----~----~~~~-~~~~~~~a~A~Y~-Vty~~~~~~~~~~~~~~~~~l 866 (904)
.+.+.+...+++...+..||+.|.+.|.. . . .+.+ .+.+.+||+|||+ ++|+... .++..+.+
T Consensus 1032 ~~~t~~~~e~~~~~l~~~~r~~~~qef~~y~~~~e~l~~fe~~~~eE~~~kKa~aWY~v~~ye~~~------~~~~~~~~ 1105 (1145)
T KOG0988|consen 1032 FYNTERMIELKLERLVLKLREKFFQEFGAYKLEIEKLSCFEDSPEEEFIMKKASAWYRVYRYEMAQ------AMRETRKL 1105 (1145)
T ss_pred hhcccccchhhhHHHHHHHHHHHHHHhhhhcchhhhccccccCchhHHHHHHHHHHHHHHHhhhhc------ccccCccc
Confidence 77776666667777888888777777741 1 0 1223 3338899999999 7776542 23566778
Q ss_pred ccccchhHHHHHHHhh---ccccCCCchhHH
Q 002586 867 SFPWCVYDRLVEIKKD---KTSIGNAFPALE 894 (904)
Q Consensus 867 SFpWi~~d~l~~ik~~---~~~~~~~~~~~~ 894 (904)
|||||++|+|++||++ +....+.+.+|+
T Consensus 1106 SF~wia~Dvl~~iK~~~~~~~g~a~p~~tl~ 1136 (1145)
T KOG0988|consen 1106 SFAWIAYDVLARIKQTFLGAIGGANPVYTLE 1136 (1145)
T ss_pred chHHHHHHHHHHHHHHHHHhhcccCchHHHH
Confidence 9999999999999999 555444444443
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=5.3e-127 Score=1135.39 Aligned_cols=545 Identities=47% Similarity=0.811 Sum_probs=389.1
Q ss_pred CeeeeccccccccCchhcccCcCCCcEEEEEEeeCCCCccccCCCCCCCCCCccchhhhHHHHHHHHHhcCeEEcceeEE
Q 002586 151 SRVYFCGPEINVSNRVLRHFRRDIDNFLRISFIDEDLDKIHSTDLSPRGSSATDITRTRIYTRILSTLRNGILIGDRKFE 230 (904)
Q Consensus 151 tri~~~~P~~e~sNRvlR~f~~~~d~FlRV~F~DE~~~~l~~~~~~~r~~~~~~~~~~~i~~rv~~~L~~Gi~I~gr~y~ 230 (904)
||++|.+|+++.||||+|+|++ ++||||+|+||++..++... ..++++++++|++||.|+||+|+
T Consensus 1 ~r~~l~~p~~~~snr~~R~fg~--~~Flrv~f~d~~~~~~~~~~-------------~~~~~~~~~~l~~gi~i~~~~y~ 65 (579)
T PF05183_consen 1 TRIILEPPELEKSNRVLRRFGS--DRFLRVSFPDENSSSLRFSP-------------RVLGRRIRKFLKNGIKIGGRHYR 65 (579)
T ss_dssp --EEE---EEEE-BHHHHHH-G--GGEEEEEEE-TT---SSS-T-------------TSTTEEEEEEEEEE---------
T ss_pred CeEEEECCEecCCCceeEEeCC--CCEEEEEEEcCCCCcccccc-------------hhHHHHHHHHHhccceECcEEEE
Confidence 7899999999999999999966 67999999999988765421 11567788999999999999999
Q ss_pred EeeecCCCCCcCeEEEEEcC----CCCCHHHHHHHhCCCCcccCH-HHHHHHHcccccCCccceeeeCCcEEEccCcccc
Q 002586 231 FLAFSSSQLRESSAWMFASR----YGLTAAEIREWMGNFREIRNV-AKYAARLGQSFSSSKETLSVHMDEIEIIPDVKIE 305 (904)
Q Consensus 231 FLa~S~SqlR~~s~wf~a~~----~~~t~~~Ir~~mG~F~~i~~~-aK~aARlgq~FSsT~~t~~i~~~~i~~i~Di~~~ 305 (904)
|||+|+||+|+++||||++. ..+++++|++|||+|++++++ +||+||+|||||+|.+++.+++++|..||||.
T Consensus 66 fl~~S~sqlr~~~~~f~~~~~~~~~~~~~~~i~~~~g~~~~~~~~~~K~~aRl~l~fS~T~~~~~i~~~~~~~i~Di~-- 143 (579)
T PF05183_consen 66 FLGFSNSQLRDHSCWFFAEDDGDRPPLTVEDIRNWMGDFSNIQSIPAKYAARLGLCFSSTVPTVVIPPDEIEVIPDIT-- 143 (579)
T ss_dssp ----------EEEEEEEEEE----B---HHHHHHHHH-GGGTSBH-HHHHHTTHHHHSB-EEEEE--GGGEE-SS--T--
T ss_pred EeecCCccccCCeEEEEecCCccCCcccHHHHHHhcccccccccHHHHHHHHHHHhccCccceEEecccceEEcCCcC--
Confidence 99999999999999999987 679999999999999998886 99999999999999999999999999999993
Q ss_pred cCCcccccccccccccHHHHHHHHHHcCCCCCCCceEEEeccCceEEEEeCCCC-Ccceeeccccccc----ccCCCcee
Q 002586 306 IGKTKYVFSDGIGKVSAEFARKVASKCGLKDNPPSAFQIRYGGYKGVVAADPTS-SKKLSLRDSMRKY----ESELTKLD 380 (904)
Q Consensus 306 ~~g~~~~fTDG~G~IS~~la~~I~~~l~l~~~~PSafQiR~gG~KGvL~vdp~~-~~~I~lR~Sm~KF----~s~~~~le 380 (904)
++++|+||||||+||+++|++||+++++ ..+|||||||+|||||||+|||+. +.+|+||+||+|| .+.+++||
T Consensus 144 -~~~~~~ftDG~G~IS~~la~~I~~~l~~-~~~PsA~QiR~~G~KGml~vdp~~~~~~I~lr~Sm~Kf~~~~~~~~~~le 221 (579)
T PF05183_consen 144 -SRNGYVFTDGCGRISPDLARKIAEKLGL-DYVPSAFQIRIGGAKGMLVVDPTLDGPWIQLRPSMIKFDEPWDSEHRTLE 221 (579)
T ss_dssp -TSS--BSSTTEEEE-HHHHHHHHHHHT--SS--SEEEEEETTEEEEEEE-TT-----EEE-TTTB-S----SGGGSEEE
T ss_pred -CCCCccccCCchhhCHHHHHHHHHHcCC-CCCCeEEEEeccCceeEEEECCCCCcceEEEehhhhhhccCcccccCeEE
Confidence 3678999999999999999999999998 889999999999999999999998 5799999999999 67789999
Q ss_pred EeeecC-cccccccHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHhcCCCCcHHHHH-HHHHCCCCCC
Q 002586 381 VLAWSK-YQPCFLNRQLISLLSTLGIWDEIFEKKQREAVRQLDAILTDPLKAQEALELMSPGENTNILK-ELLICGYKPD 458 (904)
Q Consensus 381 I~~~S~-~~p~~LNrQ~I~iL~~lGV~~evF~~lq~~~l~~l~~~l~d~~~a~~~L~~~~~~~~~~~l~-~ll~~Gf~~~ 458 (904)
|+++|+ +.+++||||+|++|+++|||+++|+++|+++++++..+++++..|..++............. .|+.+||++.
T Consensus 222 i~~~s~~~~~~~LN~q~I~iL~~~gv~~~~f~~l~~~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ll~~g~~~~ 301 (579)
T PF05183_consen 222 IVKYSRPPRPAYLNRQLITILEDLGVPDEVFLELQDEALEELRNILTDPDAARDLLSNQSRDGDFRLIRRQLLDAGFDPL 301 (579)
T ss_dssp EEEE--------B-TTTHHHHHHTBSS-HHHHHHHHHHHHHHHHHTTSHHHHHHHHHHHS--HHHHHHHTHHHHTT--TT
T ss_pred ecccCCCCCcccccHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHhhCHHHHHHHHHhcCCCcchhHHHHHHHHcCCCcc
Confidence 999999 89999999999999999999999999999999999999999999999998766544443333 8999999999
Q ss_pred CchHHHHHHHHHHHHHHHHhccccceeccCceeeeeecCCCCCCCCCcEEEEEcCCcccccCCCcccccccccccceEEe
Q 002586 459 AEPFLSMMLQTFRASKLLELRTKTRIFIPNGRSMMGCLDETRTLNYGQVFVQISGAGYRQLHGESSLFSSSRSRQRFIVQ 538 (904)
Q Consensus 459 ~epfl~~~L~~~~~~~l~~lk~K~rI~Vp~s~~l~GV~DetG~L~~gEVfvq~s~~~~~~~~~~~~~~~~~~~~~~~vi~ 538 (904)
++||++.+++.+.++.+.++|+|+||+||+|++||||+||||+|+|||||||+|... ..+....+++
T Consensus 302 ~~pfl~~~l~~~~~~~l~~~~~~~ri~v~~s~~l~gv~D~~g~L~~geV~~~~s~~~-------------~~~~~~~~~~ 368 (579)
T PF05183_consen 302 NDPFLRSLLKALIKKKLKELKKKARIPVPKSRYLMGVPDPTGVLKEGEVFVQFSSDE-------------ETGSQSQVLE 368 (579)
T ss_dssp TBHHHHHHHHHHHHHHHHHHHHC--B--SSEEEEEEEE-TTS---TTEEEEEEEEEE-------------EETTEEEEEE
T ss_pred cCHHHHHHHHHHHHHHHHhccceEEEEcCCCcEEEEeeCCcCCCCCCEEEEEecccc-------------ccCCCcceee
Confidence 999999999999999999999999999999999999999999999999999997221 1123467899
Q ss_pred eeEEEEeCCCCCCCCeeEEEEecCCCCCCCCCeEEecCCCCCCCCCCcCCCCCCCCeEEEeecCCCCCC-------CCCC
Q 002586 539 GLVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRPHPNECSGSDLDGDIYFVCWDDELIPP-------QQDP 611 (904)
Q Consensus 539 G~VlV~RnP~lhPGDIr~v~AV~~P~L~hl~dvIVFp~kG~Rplps~lsGGDLDGD~y~ViWD~~Lv~~-------~~~~ 611 (904)
|+|+|+||||+||||||+|+||++|+|+||+||||||++|+||+|++|||||||||+|||||||+||.+ ...+
T Consensus 369 g~VlV~R~P~~~pgDir~~~av~~p~L~~l~~vIVF~~~G~r~~~~~lsGgDlDGD~~~V~wd~~lv~~~~~~~~~~~~~ 448 (579)
T PF05183_consen 369 GDVLVTRNPCLHPGDIRKVKAVDKPELRHLKDVIVFSTKGDRPLPSELSGGDLDGDEYFVCWDPRLVEPFKNPPPPKSEE 448 (579)
T ss_dssp -EEEEE-SS--SGGGEEEEEE---GGGTT--SEEEE-S-SSS-HHHHTTT--SSS-EEEEE--HHHHHTB----------
T ss_pred eeEEEecCCccCcCceeEEEeeccHHHcccCCEEEeCCCCCCCchHHhcCCCCCCceEEEEeCHhhhhhhhccCcccCCC
Confidence 999999999999999999999999999999999999999999999999999999999999999999444 4456
Q ss_pred CCCCCCCc-------ccCCCCccCHHHHHHHHHH-hhccCcHHHHHHHHHHHhccCCCCCCChhHHHHHHHHhhcccCCC
Q 002586 612 PMDYTPAQ-------SMQLDHDVQIEDVEEYFTN-YIVNDSLGIIANAHTVFADREPRKARSEPCLQLAEKFSIAVDFPK 683 (904)
Q Consensus 612 P~~y~~~~-------~~~l~~~vt~~di~~ffv~-ym~~d~LG~isn~Hl~~aD~~~~g~~~~~Cl~LA~l~s~AVD~~K 683 (904)
|+.|...+ +..+.++++.+++++||++ ||.++.||+|+|+|+++||+++ |+.++.|++||++||+||||+|
T Consensus 449 p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~lG~~s~~h~~~~d~~~-g~~~~~~~~La~l~s~~vD~~K 527 (579)
T PF05183_consen 449 PMNYESEKVSDSSGDPKPLSRPVTEEDIQDFFLEFYINNDNLGLISNAHLAIADQSS-GIDSPECLKLAQLHSQAVDAPK 527 (579)
T ss_dssp -TTTSEE---BHHHHTT-SSHHHHHHHHHHHHHHHHTS--HHHHHHHHHHHHHHHHT--SSSHHHHHHHHHHHHHTTHHH
T ss_pred ccccccccccccccCccccCccccHHHHHHHHHHhhcccCcHHHHHHHHHHHHHhcC-CCCCHHHHHHHHHHHHHhCccc
Confidence 66653322 2345667889999999999 9999999999999999999987 9999999999999999999999
Q ss_pred CCCcccCCCC-CCCCCCCCCCCCCCCCC-ccccchhcHHHHhhhhhc
Q 002586 684 TGVPAEIPPH-LYVKEYPDFMEKPDKPT-YESQNVIGKLFRAVKDIA 728 (904)
Q Consensus 684 TG~~v~ip~~-l~~~~~Pdfm~k~~~~~-Y~S~~iLG~Lyr~v~~~~ 728 (904)
||+++.++.. ++++.+||||++..++. |+|++|||+|||+|++..
T Consensus 528 tG~~~~~~~~~~~~~~~P~~~~~~~~~~~y~S~~ilg~ly~~v~~~~ 574 (579)
T PF05183_consen 528 TGVPVKLPRWPLKPPEYPDFMEKEDKKSYYKSTSILGQLYREVKEIV 574 (579)
T ss_dssp HTEE--HHHHHSS-----GGGSS-----SSS--SHHHHHHHTTH---
T ss_pred cCCCccccchhhcCCCCChhhccccccccCCCccHHHHHHHHHHhhc
Confidence 9999998877 88999999999877665 799999999999998864
No 3
>smart00663 RPOLA_N RNA polymerase I subunit A N-terminus.
Probab=81.71 E-value=2 Score=47.99 Aligned_cols=52 Identities=27% Similarity=0.537 Sum_probs=38.3
Q ss_pred EEee-eEEEEeCCCCCCCCeeEEEEecCCCCCCCCCeEEecCCCCCCCCCCcC--CCCCCCCeEEEe
Q 002586 536 IVQG-LVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRPHPNECS--GSDLDGDIYFVC 599 (904)
Q Consensus 536 vi~G-~VlV~RnP~lhPGDIr~v~AV~~P~L~hl~dvIVFp~kG~Rplps~ls--GGDLDGD~y~Vi 599 (904)
+..| -|++-|.|+||..-|+-+++.-.|. +-=|=+|..|+ +.|+|||+..+.
T Consensus 199 l~dgd~Vl~NRqPsLHr~si~a~~v~v~~~------------~tir~n~~~c~~fNADFDGDeMnih 253 (295)
T smart00663 199 VIDGDVVLFNRQPTLHRMSIQAHRVRVLEG------------KTIRLNPLVCSPYNADFDGDEMNLH 253 (295)
T ss_pred hhcCCEEEEecCCccccccceeEEEEEecC------------ceEEecCccCCcccCCcCCCEEEEe
Confidence 5677 6999999999999999999876654 22222344444 479999998864
No 4
>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=73.12 E-value=2.5 Score=43.27 Aligned_cols=52 Identities=31% Similarity=0.573 Sum_probs=34.0
Q ss_pred EEee-eEEEEeCCCCCCCCeeEEEEecCCCCCCCCCeEEecCCCCCCCCCCcC--CCCCCCCeEEEe
Q 002586 536 IVQG-LVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRPHPNECS--GSDLDGDIYFVC 599 (904)
Q Consensus 536 vi~G-~VlV~RnP~lhPGDIr~v~AV~~P~L~hl~dvIVFp~kG~Rplps~ls--GGDLDGD~y~Vi 599 (904)
+..| .|++-|.|+||..-++-++++-.+. +-=|=+|..|+ +.|+|||+..|.
T Consensus 95 l~~gd~vl~nRqPtLh~~s~~a~~~~~~~~------------~t~~~~~~~c~~~NADFDGDem~i~ 149 (166)
T PF00623_consen 95 LCDGDIVLLNRQPTLHRMSIMAHKVRVLPG------------KTIRINPLVCSPFNADFDGDEMNIH 149 (166)
T ss_dssp HTTT-EEEEEESS-SSGGGEEEEEEEEESS------------SSEEEEGGGHHHHT--TSS-EEEEE
T ss_pred hhcCceeEEeccchhccceeeeeeeeeecc------------cEEEeeccchhhhhccCCcceEEEE
Confidence 3466 5999999999999999999876555 11122334443 689999998875
No 5
>CHL00018 rpoC1 RNA polymerase beta' subunit
Probab=64.34 E-value=6.5 Score=48.24 Aligned_cols=53 Identities=28% Similarity=0.530 Sum_probs=37.6
Q ss_pred eEEee-eEEEEeCCCCCCCCeeEEEEecCCCCCCCCCeEEecCCCCCCCCCCcC--CCCCCCCeEEEe
Q 002586 535 FIVQG-LVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRPHPNECS--GSDLDGDIYFVC 599 (904)
Q Consensus 535 ~vi~G-~VlV~RnP~lhPGDIr~v~AV~~P~L~hl~dvIVFp~kG~Rplps~ls--GGDLDGD~y~Vi 599 (904)
.++.| .|+.-|.|+||.--||-+++|-.+. +-=|=+|..|+ ..|+|||+..|-
T Consensus 443 ~v~~gd~VLlNRqPTLHR~sIqAf~~~L~~g------------ktIrLhplvC~~fNADFDGDqMnvH 498 (663)
T CHL00018 443 EVMQGHPVLLNRAPTLHRLGIQAFQPILVEG------------RAICLHPLVCKGFNADFDGDQMAVH 498 (663)
T ss_pred ehhcCceeeecCCCcccccccceeeEEecCC------------CeEEeCcccCCcccCCccCcEEEEe
Confidence 35677 6899999999999999988765543 11222344444 379999998763
No 6
>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=62.95 E-value=6.9 Score=47.55 Aligned_cols=52 Identities=27% Similarity=0.562 Sum_probs=37.3
Q ss_pred eEEee-eEEEEeCCCCCCCCeeEEEEecCCCCCCCCCeEEecCCCCCCCCCCcC--CCCCCCCeEEE
Q 002586 535 FIVQG-LVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRPHPNECS--GSDLDGDIYFV 598 (904)
Q Consensus 535 ~vi~G-~VlV~RnP~lhPGDIr~v~AV~~P~L~hl~dvIVFp~kG~Rplps~ls--GGDLDGD~y~V 598 (904)
.++.| .|+.-|.|+||.--||-++++-.+. +-=|=+|..|+ ..|+|||+..|
T Consensus 415 ~v~~gd~VLlNRqPTLHR~sIqAf~~~l~~~------------ktirlhplvC~~fNADFDGDeMnv 469 (619)
T TIGR02387 415 EVITGHPVMLNRAPTLHRLGIQAFEPILVDG------------RAIQLHPLVCPAFNADFDGDQMAV 469 (619)
T ss_pred HHhcCCEEEecCCCccchhcceeeeeEEecC------------CeEEECcccCCcccCCCCCceeee
Confidence 35667 6999999999999999988765442 22233444454 37999999776
No 7
>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional
Probab=59.04 E-value=11 Score=45.81 Aligned_cols=53 Identities=26% Similarity=0.557 Sum_probs=37.9
Q ss_pred eEEee-eEEEEeCCCCCCCCeeEEEEecCCCCCCCCCeEEecCCCCCCCCCCcC--CCCCCCCeEEEe
Q 002586 535 FIVQG-LVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRPHPNECS--GSDLDGDIYFVC 599 (904)
Q Consensus 535 ~vi~G-~VlV~RnP~lhPGDIr~v~AV~~P~L~hl~dvIVFp~kG~Rplps~ls--GGDLDGD~y~Vi 599 (904)
.++.| .|+.-|.|+||.--||-++++-.+. +-=|=+|..|+ ..|+|||+..|-
T Consensus 422 ~v~~gd~VLlNRqPTLHR~sIqAf~~~l~~~------------ktirlhplvC~~fNADFDGDeMnvH 477 (627)
T PRK02625 422 EVIEGHPVLLNRAPTLHRLGIQAFEPILVEG------------RAIQLHPLVCPAFNADFDGDQMAVH 477 (627)
T ss_pred EeecCcEEEecCCCccccccceeEeeEEcCC------------CeEEeccccCCcccCCcCCCeEEEe
Confidence 36677 6999999999999999998766553 11222344444 379999998763
No 8
>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=46.19 E-value=19 Score=47.03 Aligned_cols=52 Identities=31% Similarity=0.576 Sum_probs=37.5
Q ss_pred EEee-eEEEEeCCCCCCCCeeEEEEecCCCCCCCCCeEEecCCCCCCCCCCcC--CCCCCCCeEEEe
Q 002586 536 IVQG-LVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRPHPNECS--GSDLDGDIYFVC 599 (904)
Q Consensus 536 vi~G-~VlV~RnP~lhPGDIr~v~AV~~P~L~hl~dvIVFp~kG~Rplps~ls--GGDLDGD~y~Vi 599 (904)
++.| .|+.-|.|.||.--||=++++-.|. +-=|=||..|+ ..|+|||+..|-
T Consensus 397 vi~~d~VLlNRqPTLHRlsIqAf~~~l~~g------------ktirlhplvC~~fNADFDGDeMnvH 451 (1140)
T TIGR02386 397 VIKEHPVLLNRAPTLHRLGIQAFEPVLVEG------------KAIRLHPLVCTAFNADFDGDQMAVH 451 (1140)
T ss_pred ccCCcEEEecCCCcccccccceeEEEEecC------------ceEEEcccccCcccCCCCcceeEee
Confidence 4556 7999999999999999998776543 22223344444 479999998875
No 9
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=43.20 E-value=28 Score=49.11 Aligned_cols=53 Identities=30% Similarity=0.546 Sum_probs=38.8
Q ss_pred eEEee-eEEEEeCCCCCCCCeeEEEEecCCCCCCCCCeEEecCCCCCCCCCCcC--CCCCCCCeEEEe
Q 002586 535 FIVQG-LVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRPHPNECS--GSDLDGDIYFVC 599 (904)
Q Consensus 535 ~vi~G-~VlV~RnP~lhPGDIr~v~AV~~P~L~hl~dvIVFp~kG~Rplps~ls--GGDLDGD~y~Vi 599 (904)
.++.| .|+.-|.|.||.--||-++++-.|. +-=|=||..|+ ..|+|||+..|-
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 46678 6899999999999999998765543 22233444454 479999998875
No 10
>PRK08566 DNA-directed RNA polymerase subunit A'; Validated
Probab=42.44 E-value=25 Score=45.18 Aligned_cols=53 Identities=23% Similarity=0.486 Sum_probs=38.7
Q ss_pred eEEee-eEEEEeCCCCCCCCeeEEEEecCCCCCCCCCeEEecCCCCCCCCCCcC--CCCCCCCeEEEe
Q 002586 535 FIVQG-LVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRPHPNECS--GSDLDGDIYFVC 599 (904)
Q Consensus 535 ~vi~G-~VlV~RnP~lhPGDIr~v~AV~~P~L~hl~dvIVFp~kG~Rplps~ls--GGDLDGD~y~Vi 599 (904)
.+..| .|++-|.|+||.--|+-.++.-.|. + -=|=+|+.|+ ..|+|||+.++-
T Consensus 411 hl~dgd~vl~NRqPsLHr~si~a~~~~v~~~-~-----------t~r~n~~~c~~~NADFDGDeMn~h 466 (882)
T PRK08566 411 HLIDGDIVLFNRQPSLHRMSIMAHRVRVLPG-K-----------TFRLNLAVCPPYNADFDGDEMNLH 466 (882)
T ss_pred hhhcCceeeecCCCcccccccceeEEEEecC-c-----------eEeeccccCCCccCCccCcEEEEe
Confidence 35677 5899999999999999998877664 1 1123444444 479999998865
No 11
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=42.06 E-value=24 Score=46.17 Aligned_cols=52 Identities=27% Similarity=0.554 Sum_probs=37.4
Q ss_pred EEee-eEEEEeCCCCCCCCeeEEEEecCCCCCCCCCeEEecCCCCCCCCCCcC--CCCCCCCeEEEe
Q 002586 536 IVQG-LVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRPHPNECS--GSDLDGDIYFVC 599 (904)
Q Consensus 536 vi~G-~VlV~RnP~lhPGDIr~v~AV~~P~L~hl~dvIVFp~kG~Rplps~ls--GGDLDGD~y~Vi 599 (904)
++.| .|+.-|.|.||.--||-++++-.|. +-=|=||..|+ ..|+|||+..|-
T Consensus 405 vi~gd~VLlNRqPTLHR~sIqAf~~~l~~g------------ktirLhplvC~~fNADFDGDqMnvH 459 (1156)
T PRK00566 405 VIKEHPVLLNRAPTLHRLGIQAFEPVLIEG------------KAIQLHPLVCTAFNADFDGDQMAVH 459 (1156)
T ss_pred ecCCCEEEecCCCcccccccceeEEEEecC------------ceEEECccccCccccccccceeEEe
Confidence 4567 6999999999999999998776553 11122333343 369999998875
No 12
>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=40.69 E-value=27 Score=44.87 Aligned_cols=53 Identities=26% Similarity=0.477 Sum_probs=38.4
Q ss_pred eEEee-eEEEEeCCCCCCCCeeEEEEecCCCCCCCCCeEEecCCCCCCCCCCcC--CCCCCCCeEEEe
Q 002586 535 FIVQG-LVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRPHPNECS--GSDLDGDIYFVC 599 (904)
Q Consensus 535 ~vi~G-~VlV~RnP~lhPGDIr~v~AV~~P~L~hl~dvIVFp~kG~Rplps~ls--GGDLDGD~y~Vi 599 (904)
.++.| .|++-|.|+||.--|+-.++.-.|. +-=|=+|+.|+ ..|+|||+.++-
T Consensus 407 hl~dgd~vl~NRqPsLHr~si~a~~~~v~~~------------~t~r~n~~~c~~~NADFDGDeMn~h 462 (868)
T TIGR02390 407 HLIDGDIVLFNRQPSLHRMSMMGHKVKVLPG------------KTFRLNLAVCPPYNADFDGDEMNLH 462 (868)
T ss_pred ehhcCccceeccCCccccccceeEEEEEecC------------ceEeeccccCCccccCcccceeeEe
Confidence 35677 5899999999999999988776653 11222444444 479999998875
No 13
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=38.99 E-value=29 Score=46.16 Aligned_cols=52 Identities=31% Similarity=0.577 Sum_probs=37.4
Q ss_pred EEee-eEEEEeCCCCCCCCeeEEEEecCCCCCCCCCeEEecCCCCCCCCCCcC--CCCCCCCeEEEe
Q 002586 536 IVQG-LVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRPHPNECS--GSDLDGDIYFVC 599 (904)
Q Consensus 536 vi~G-~VlV~RnP~lhPGDIr~v~AV~~P~L~hl~dvIVFp~kG~Rplps~ls--GGDLDGD~y~Vi 599 (904)
++.| .|+.-|.|.||.--||-++++-.|. +-=|=||.-|+ ..|+|||+..|-
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 5567 6999999999999999998766553 22222333343 369999998875
No 14
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=30.98 E-value=48 Score=46.81 Aligned_cols=52 Identities=25% Similarity=0.552 Sum_probs=37.4
Q ss_pred EEee-eEEEEeCCCCCCCCeeEEEEecCCCCCCCCCeEEecCCCCCCCCCCcC--CCCCCCCeEEEe
Q 002586 536 IVQG-LVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRPHPNECS--GSDLDGDIYFVC 599 (904)
Q Consensus 536 vi~G-~VlV~RnP~lhPGDIr~v~AV~~P~L~hl~dvIVFp~kG~Rplps~ls--GGDLDGD~y~Vi 599 (904)
++.| .|+.-|.|+||.--||-++++-.|. +-=|=+|..|+ ..|+|||+..|-
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 4567 7999999999999999887665443 22233444454 369999998875
No 15
>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Probab=28.14 E-value=67 Score=43.16 Aligned_cols=53 Identities=26% Similarity=0.559 Sum_probs=37.5
Q ss_pred eEEee-eEEEEeCCCCCCCCeeEEEEecCCCCCCCCCeEEecCCCCCCCCCCcC--CCCCCCCeEEEe
Q 002586 535 FIVQG-LVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRPHPNECS--GSDLDGDIYFVC 599 (904)
Q Consensus 535 ~vi~G-~VlV~RnP~lhPGDIr~v~AV~~P~L~hl~dvIVFp~kG~Rplps~ls--GGDLDGD~y~Vi 599 (904)
.+..| -|++-|.|+||.--|+=.++.-.|. +- =|=+|+-|+ ..|+|||+..+-
T Consensus 427 hl~dGD~VL~NRQPSLHk~Simah~vkvl~~-kT-----------~Rln~~vC~pyNADFDGDEMNlH 482 (1321)
T PRK14977 427 HLADGDIVIFNRQPSLHKLSILAHRVKVLPG-AT-----------FRLHPAVCPPYNADFDGDEMNLH 482 (1321)
T ss_pred EeecCcEEEeccCCccccccceEEEEEEecC-ce-----------EEecccccCcccCCcccceeeee
Confidence 45677 5899999999999999888777664 21 122233333 479999998764
No 16
>TIGR00489 aEF-1_beta translation elongation factor aEF-1 beta. This model describes the archaeal translation elongation factor aEF-1 beta. The member from Sulfolobus solfataricus was demonstrated experimentally. It is a dimer that catalyzes the exchange of GDP for GTP on aEF-1 alpha.
Probab=26.13 E-value=1.7e+02 Score=27.11 Aligned_cols=59 Identities=14% Similarity=0.113 Sum_probs=44.6
Q ss_pred hhhhHHHHHHHHHhcCeEEcceeEEEeeecCCCCCcCeEEEEEcCCCCCHHHHHHHhCCCCc
Q 002586 206 TRTRIYTRILSTLRNGILIGDRKFEFLAFSSSQLRESSAWMFASRYGLTAAEIREWMGNFRE 267 (904)
Q Consensus 206 ~~~~i~~rv~~~L~~Gi~I~gr~y~FLa~S~SqlR~~s~wf~a~~~~~t~~~Ir~~mG~F~~ 267 (904)
..+.+.+.++.++..|..+++-..+.+||+ |+.=.+.+.-+......++|-+-+..+..
T Consensus 18 Dle~L~~~ik~~~~~g~~~~~~~~ePiaFG---LkaL~~~~vv~D~~g~td~lee~i~~ve~ 76 (88)
T TIGR00489 18 DLEALKEKIKERIPEGVEIRKIDEEPIAFG---LVAINVMVVMGDAEGGTEAAEESLSGIEG 76 (88)
T ss_pred CHHHHHHHHHHhCcCCcEEeeeEEEeeecc---ceeeEEEEEEecCCcChHHHHHHHhcCCC
Confidence 367889999999999999999999999998 55555556555554555777666665554
No 17
>cd01213 tensin Tensin Phosphotyrosine-binding (PTB) domain. Tensin Phosphotyrosine-binding (PTB) domain. Tensin is a a focal adhesion protein, which contains a C-terminal SH2 domain followed by a PTB domain. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether.
Probab=25.95 E-value=3.5e+02 Score=27.11 Aligned_cols=86 Identities=17% Similarity=0.245 Sum_probs=54.7
Q ss_pred EEEEcCCeeeeccccccccCchhcccCcCCCcEEEEEEeeCCCCccccCCCCCCCCCCccchhhhHHHHHHHHHhcCeEE
Q 002586 145 RVQVTPSRVYFCGPEINVSNRVLRHFRRDIDNFLRISFIDEDLDKIHSTDLSPRGSSATDITRTRIYTRILSTLRNGILI 224 (904)
Q Consensus 145 ~v~vTPtri~~~~P~~e~sNRvlR~f~~~~d~FlRV~F~DE~~~~l~~~~~~~r~~~~~~~~~~~i~~rv~~~L~~Gi~I 224 (904)
++.|+..+|.+..|.-. .-..|+|+.+ .|+|+.-+.+.-+ ++..|-..
T Consensus 47 h~kVS~qGItLtDn~rk--~ffrrhypl~-----~Vs~ca~dp~n~~-------------------------~~~~~~~~ 94 (138)
T cd01213 47 HFKVSSQGITLTDNTRK--KFFRRHYKVD-----SVIFCAIDPEERM-------------------------WENEGAIA 94 (138)
T ss_pred EEEEEcCCeeeeccccc--eeehhhCCcC-----eEEEEeeCCcccc-------------------------cccccccc
Confidence 77888888888765421 1123446543 6888875543211 12222223
Q ss_pred cceeEEEeeecCCCCCcCeEEEEEcC-CCCCHHHHHHHh
Q 002586 225 GDRKFEFLAFSSSQLRESSAWMFASR-YGLTAAEIREWM 262 (904)
Q Consensus 225 ~gr~y~FLa~S~SqlR~~s~wf~a~~-~~~t~~~Ir~~m 262 (904)
..|.|-|.+-...+..++.|+-|++- ....+..|.+..
T Consensus 95 ~kriFgFVar~~~~~~~~~ChvF~e~~~~qpa~~iv~~~ 133 (138)
T cd01213 95 KARIFAFVARIPHSSTDNACHVFAELEPEQPASAIVNFA 133 (138)
T ss_pred ccEEEEEEEecCCCCCCeeEEEeccCCCCCCHHHHHHHH
Confidence 67889999887666678999999974 457788887654
No 18
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=24.50 E-value=1.8e+02 Score=26.92 Aligned_cols=59 Identities=17% Similarity=0.188 Sum_probs=44.3
Q ss_pred hhhhHHHHHHHHHhcCeEEcceeEEEeeecCCCCCcCeEEEEEcCCCCCHHHHHHHhCCCCc
Q 002586 206 TRTRIYTRILSTLRNGILIGDRKFEFLAFSSSQLRESSAWMFASRYGLTAAEIREWMGNFRE 267 (904)
Q Consensus 206 ~~~~i~~rv~~~L~~Gi~I~gr~y~FLa~S~SqlR~~s~wf~a~~~~~t~~~Ir~~mG~F~~ 267 (904)
....+.+.|+.++..|+.+++-..+.+||+ |+.=.+.+.-+......+++-+-+..|..
T Consensus 18 Dl~~L~~~ik~~~~~g~~~~~~~~ePIaFG---LkaL~i~~vv~D~~~~td~lee~i~~~e~ 76 (88)
T PRK00435 18 DLDELKEKIKEVLPEGYKINGIEEEPIAFG---LKALKLYVIMPDEEGGTEPVEEAFANVEG 76 (88)
T ss_pred CHHHHHHHHHHhCcCCcEEeEeEEEEeecc---ceeEEEEEEEEcCCcCcHHHHHHHhccCC
Confidence 367888999999999999999999999998 55555556555555555777666555544
No 19
>cd00292 EF1B Elongation factor 1 beta (EF1B) guanine nucleotide exchange domain. EF1B catalyzes the exchange of GDP bound to the G-protein, EF1A, for GTP, an important step in the elongation cycle of the protein biosynthesis. EF1A binds to and delivers the aminoacyl tRNA to the ribosome. The guanine nucleotide exchange domain of EF1B, which is the alpha subunit in yeast, is responsible for the catalysis of this exchange reaction.
Probab=22.49 E-value=1.8e+02 Score=26.77 Aligned_cols=53 Identities=23% Similarity=0.326 Sum_probs=39.8
Q ss_pred hhhHHHHHHHHHhcCeEEcceeEEEeeecCCCCCcCeEEEEEcCCCCCHHHHHHHh
Q 002586 207 RTRIYTRILSTLRNGILIGDRKFEFLAFSSSQLRESSAWMFASRYGLTAAEIREWM 262 (904)
Q Consensus 207 ~~~i~~rv~~~L~~Gi~I~gr~y~FLa~S~SqlR~~s~wf~a~~~~~t~~~Ir~~m 262 (904)
.+.+.+.|+.++.+|+.+++...+.+||+ |+.=.+.+.-+......+++-+-+
T Consensus 19 l~~l~~~Ik~~~~~gl~~~~~~~epiaFG---lk~L~i~~vv~D~~~~td~lee~i 71 (88)
T cd00292 19 LDELEEKIRAILMDGLLWGKSKLEPIAFG---LKALQIYCVVEDDEGGTDELEEAI 71 (88)
T ss_pred HHHHHHHHHHhCcCCcEEEEEEEEEeeeE---eeEEEEEEEEEeCCcCcHHHHHHH
Confidence 67888999999999999999999999998 444444454455445556665544
No 20
>PHA02770 hypothetical protein; Provisional
Probab=22.04 E-value=80 Score=27.28 Aligned_cols=20 Identities=30% Similarity=0.640 Sum_probs=15.4
Q ss_pred CeEEcceeEEE-eeecCCCCCcCeE
Q 002586 221 GILIGDRKFEF-LAFSSSQLRESSA 244 (904)
Q Consensus 221 Gi~I~gr~y~F-La~S~SqlR~~s~ 244 (904)
=+.|+||||+| |-|| +++|+
T Consensus 45 ylei~~~hyrfelifs----kdnsv 65 (81)
T PHA02770 45 YLEVNGRHYRFELIFS----KDNSV 65 (81)
T ss_pred EEEEcCceEEEEEEEe----cCCcE
Confidence 35699999999 7777 56665
No 21
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=21.67 E-value=67 Score=41.85 Aligned_cols=58 Identities=26% Similarity=0.391 Sum_probs=37.6
Q ss_pred EEEeCCCCCCC-------CeeEEEEecCC-----CC-------CCCC--CeEEecCCC-------------------CCC
Q 002586 542 VVAKNPCLHPG-------DVRVLKAVNVP-----AL-------HHMV--DCVVFPQKG-------------------MRP 581 (904)
Q Consensus 542 lV~RnP~lhPG-------DIr~v~AV~~P-----~L-------~hl~--dvIVFp~kG-------------------~Rp 581 (904)
+|-+-|+.||| +-+.+.+..++ .| |||. |+|+|..+- =|=
T Consensus 383 LV~~g~~~~pgakyiird~G~Ridlr~~~~~~d~~Lq~G~kVeRhl~DGD~VlfNRqPSlHKmSmmahrVrVlp~sTfrL 462 (1605)
T KOG0260|consen 383 LVRRGLLEHPGAKYIIRDNGDRIDLRYHKRAGDIHLQPGYKVERHLMDGDVVLFNRQPSLHKMSMMAHRVRVLPYSTFRL 462 (1605)
T ss_pred HhhCCCCCCCCcceeeecCCcEEEEeecCCccccccccccEEEEeeccCCEEEEcCCCcHHHhhhhhcEEEEccCceEEe
Confidence 56677788888 66667676666 23 5775 478886531 122
Q ss_pred CCCCcC--CCCCCCCeEEEe
Q 002586 582 HPNECS--GSDLDGDIYFVC 599 (904)
Q Consensus 582 lps~ls--GGDLDGD~y~Vi 599 (904)
-+++|| .+|+|||+...-
T Consensus 463 NlsvtsPynADFDGDemnlh 482 (1605)
T KOG0260|consen 463 NLSVTSPYNADFDGDEMNLH 482 (1605)
T ss_pred CeeecCCccCCCCCceeecc
Confidence 345555 689999998754
Done!