Query 003789
Match_columns 795
No_of_seqs 250 out of 485
Neff 6.4
Searched_HMMs 46136
Date Thu Mar 28 12:04:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003789.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003789hhsearch_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 9E-172 2E-176 1490.7 60.2 761 3-791 346-1121(1145)
2 PF05183 RdRP: RNA dependent R 100.0 1E-127 2E-132 1126.0 20.9 546 61-636 1-575 (579)
3 smart00663 RPOLA_N RNA polymer 76.4 2.7 5.9E-05 46.0 4.0 52 443-506 199-253 (295)
4 PF00623 RNA_pol_Rpb1_2: RNA p 57.7 5 0.00011 40.3 1.2 52 443-506 95-149 (166)
5 CHL00018 rpoC1 RNA polymerase 56.7 9.9 0.00021 45.9 3.6 52 442-505 443-497 (663)
6 PRK02625 rpoC1 DNA-directed RN 56.4 13 0.00028 44.6 4.4 52 442-505 422-476 (627)
7 TIGR02387 rpoC1_cyan DNA-direc 55.1 9.7 0.00021 45.5 3.2 52 442-505 415-469 (619)
8 PRK00566 DNA-directed RNA poly 39.5 27 0.00059 45.0 3.8 52 443-506 405-459 (1156)
9 TIGR02390 RNA_pol_rpoA1 DNA-di 38.4 44 0.00096 42.2 5.4 53 442-506 407-462 (868)
10 TIGR00489 aEF-1_beta translati 36.8 87 0.0019 28.2 5.6 59 116-177 18-76 (88)
11 PRK00435 ef1B elongation facto 36.6 84 0.0018 28.4 5.4 59 116-177 18-76 (88)
12 PRK14906 DNA-directed RNA poly 36.2 32 0.0007 45.0 3.7 53 442-506 492-547 (1460)
13 TIGR02386 rpoC_TIGR DNA-direct 35.9 32 0.00069 44.3 3.6 52 443-506 397-451 (1140)
14 PRK09603 bifunctional DNA-dire 33.9 46 0.001 46.3 4.7 53 442-506 1803-1858(2890)
15 cd00292 EF1B Elongation factor 33.6 89 0.0019 28.1 5.1 55 116-173 18-72 (88)
16 PRK08566 DNA-directed RNA poly 31.1 41 0.00089 42.6 3.5 53 442-506 411-466 (882)
17 PHA02770 hypothetical protein; 28.7 51 0.0011 27.7 2.5 22 129-154 43-65 (81)
18 KOG1547 Septin CDC10 and relat 27.8 45 0.00097 35.7 2.5 64 15-79 120-184 (336)
19 KOG0260 RNA polymerase II, lar 23.6 59 0.0013 41.6 2.9 58 448-505 382-481 (1605)
20 PF14538 Raptor_N: Raptor N-te 23.5 88 0.0019 31.1 3.6 38 137-174 93-135 (154)
21 PRK14844 bifunctional DNA-dire 22.7 71 0.0015 44.5 3.6 52 443-506 1848-1902(2836)
22 PRK14977 bifunctional DNA-dire 22.0 84 0.0018 41.5 3.9 54 442-506 427-482 (1321)
23 cd01213 tensin Tensin Phosphot 21.1 5.2E+02 0.011 25.3 8.3 86 55-173 47-134 (138)
24 COG5207 UBP14 Isopeptidase T [ 21.0 5.4E+02 0.012 30.6 9.5 101 300-417 555-669 (749)
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=8.8e-172 Score=1490.70 Aligned_cols=761 Identities=43% Similarity=0.655 Sum_probs=666.8
Q ss_pred HHHHHHHHhhhccccccchhHHHHHHHHHHHhhcccCCCCccccCCCcEEEEEEEEecCceeecCccccccCccccccCC
Q 003789 3 YIEHALETLFHLRECCYEPVRWLEEQYRKYVLSRRFLTSPAVALDDGLIYVNKVLVTPSKVYFSGPEISLSNRVVRSYPD 82 (795)
Q Consensus 3 ~~~~~l~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~v~vTPt~i~~~~P~~~~sNRvlR~f~~ 82 (795)
.+++.||+|.++..+||||+.+.+..+.....+.+ .....++.+|+..|++|.|||||+|+.+||++++|||+|+|..
T Consensus 346 v~~a~LekL~~~~~~cfd~~~~~k~i~~~~~~ng~--~~~~~~~~~g~~~vrk~v~TPtrv~~~~PE~~~gNRVlR~f~~ 423 (1145)
T KOG0988|consen 346 VLEAKLEKLLKLSTKCFDPYCQYKKIAKLNPSNGK--LVTTKEIMEGLRRVRKVVFTPTRVYLLAPEVEMGNRVLRKFDK 423 (1145)
T ss_pred HHHHHHHHHhhhhhhhhhHHHHHHHHHHHhcccCc--cccchhhhhcceeEEEEEEcCceeEecCchhhhcchhheeccc
Confidence 47888999999999999999999998876655555 2345678899999999999999999999999999999999999
Q ss_pred CCCcEEEEEEeeCCCccccccccCCCccCCcchhhhHHHHHHHHHHhcCeEEcceeEEEeeecCCCCcCCeEEEEecCCC
Q 003789 83 EIDNFLRLSFVDEDLDKLYSTVLSPLISSTNEERHTTIYERVLSTLRNGIVIGDKKFETLAFSNSQVKDNSMWMFASRPE 162 (795)
Q Consensus 83 ~~d~FlRV~F~DE~~~~l~~~~~~p~~~~~~~~~~~~~~~rv~~~L~~Gi~I~gr~y~fL~~S~SqlR~~s~wf~~~~~~ 162 (795)
+.++||||+|+|||++ +..++++. + .++.+|.||...|++||.|++|.|+||||||||||+||.||++....
T Consensus 424 ~~t~~lRvtF~De~~~-~~ir~~S~-----~--~~t~l~~rv~~~L~~Gi~v~~r~y~FL~~s~sQlRdngy~m~~~s~~ 495 (1145)
T KOG0988|consen 424 DSTRFLRVTFRDEDNK-LKIRTLST-----G--SRTKLDMRVNSYLTDGISVANRRYEFLAFSNSQLRDNGYFMARFSDK 495 (1145)
T ss_pred cCceEEEEEEEccccc-cccccCCc-----c--hhhHHHHHHHHHHhcccEEccceeEEEEecccccccCceEEeecCCC
Confidence 9999999999999996 44433322 1 16889999999999999999999999999999999999888877666
Q ss_pred CCHHHHHHHhCCCCCccCHHHHHHHHcccccCCcceeee-cCCCeEEcCCccccCCCcccccccccccccHHHHHHHHHH
Q 003789 163 LTAADIRESMGDFRDIKNVAKYAARLGQSFGSSREALHV-DSSDIEIIPDVEVEDDGITYCFSDGIGKISAELAEIVAKN 241 (795)
Q Consensus 163 ~~~~~Ir~~lG~f~~i~~~aK~aARlgq~FS~T~~tv~i-~~~~i~~i~Di~~~~~g~~~~fTDG~G~IS~~la~~I~~~ 241 (795)
.++++||.|||+|+++.|++|||||||||||+|+.|..+ +...+..+|||+.+++|++||||||||+||.++|++|+++
T Consensus 496 ~~i~~iR~wmG~F~~i~nv~K~aARmGqCFs~Sr~T~~~~~~~~~~~~~DI~~g~~g~~y~FSDGvG~iS~~~a~~vsq~ 575 (1145)
T KOG0988|consen 496 TKIEDIREWMGDFRDIDNVPKLAARMGQCFSQSRGTGYVLERLDRMCPPDIEGGKRGNNYCFSDGVGMISLQFAREVSQK 575 (1145)
T ss_pred ccHHHHHHHhcchhhccCHHHHHhhcCcceeccccccccccccccccCCcccccccCCceeecCCcccccHHHHHHHHHH
Confidence 899999999999999999999999999999999999877 6677889999998778889999999999999999999999
Q ss_pred cCCCCCCCceEEEeecCceEEEEeCCCCCceEEeccccccCCCCCCcEEEEeccCCccccccHHHHHHHhcCCCChHHHH
Q 003789 242 CGFTIYTPSAFQIRYGGYKGVVAVDPTSSTKLSLRKSMLKYKSESTSLDILANSKYQPCFLNRQLITLLSTLGIRDHVFE 321 (795)
Q Consensus 242 l~l~~~~PSafQiR~~G~KGvl~vdp~~~~~i~lR~Sm~KF~~~~~~leI~~~S~~~~~~LNrq~I~iL~~lGV~~~vF~ 321 (795)
+++...+|||||||++|+||||+|||.....+.+|.||.||.|.+..++|+.|+++.|++||||+|.+|+.+||++++|+
T Consensus 576 ~~~~~~vPsaFQiR~~G~KGVvav~Ps~~~~~~~~~~~~~s~S~n~~~~v~~~~~f~~~~lnr~lI~Lls~~gv~n~~F~ 655 (1145)
T KOG0988|consen 576 RKFGKAVPSAFQIRYGGYKGVVAVDPSMDKVLKLRDSMNKSQSFNSLLEVTPSSKFQPAFLNRQLITLLSYLGVLNKPFI 655 (1145)
T ss_pred HcccccCChheeeeccCCcceEEeCccHhhhhhhhhhhhhhhhhcceeeeeeccCCccccccHHHHHHHHhcCccchHHH
Confidence 99988899999999999999999999998899999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHH--HHHhcCHHHHHHHHHhcCCCCcHHHHHHHHHCCCCCCCcHHHHHHHHHHHHHHHHHhhcceeEEecCc
Q 003789 322 KKQREGVAQL--DAILTDPLKAHEALELMSSGENTNVLKELLMCGYKPDVEPFLLMMLQTFRASNLLELRTRTRIFIQNG 399 (795)
Q Consensus 322 ~lq~~~l~~l--~~~~~d~~~a~~~l~~~~~~~~~~~l~~ll~~Gf~~~~epfl~~~l~~~~~~~l~~lk~k~rI~Vp~s 399 (795)
++|+..++.- ...+..+..+..+|......+..+.++.++..++.++.|||++++|..++++.++.+|+|.||||+.|
T Consensus 656 ~il~~vle~~r~~~n~~e~~~~~~~l~~~~~m~~en~a~~~l~~~~~~D~EPflr~mL~~~~k~~~~~~kek~ripv~~G 735 (1145)
T KOG0988|consen 656 NILDQVLEKQRRITNRIEELLDRAALNYGEQMDDENIAAMILKGFPRIDSEPFLRSMLSSLLKFTLQLLKEKIRIPVDLG 735 (1145)
T ss_pred HHHHHHHHHHHhhhhhhhHHHHHHHhhhhhhccchHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHhcccccCcCC
Confidence 9999999843 33344454555666554434555655555555566878999999999999999999999999999999
Q ss_pred eeeeeecCCCCCCCCCCEEEEeccccccccccCcCCCCCCCceeeeeeEEEeeCCCCCCCCeeEEEeecCCCCCCCCCeE
Q 003789 400 RAMMGCLDETGTLESGQVFVQCSASRRREFLDNSCNNRSGELGVVEGKVVVAKNPCLHPGDMRVLRAVDVPSLHHMVDCV 479 (795)
Q Consensus 400 ~~l~GV~DetG~L~~gEVfvq~s~~~~~~~~~~~~~~~~~~~~~i~G~VlV~RnP~lhPgDIr~v~AV~~P~L~hl~dvI 479 (795)
|+||||+||||.||+||||||++.+.. +...++..+++|+|+|||||||||||||+++||++|+|+||+|||
T Consensus 736 r~lmGvvDETG~L~ygQVfVq~t~~~~--------~~~~~~~~vitG~VlvtKNPcLhpGDVRVl~AV~vp~L~h~~dvV 807 (1145)
T KOG0988|consen 736 RSLMGVVDETGILKYGQVFVQYTKTIR--------NSDSGRKEVITGKVLVTKNPCLHPGDVRVLKAVYVPALEHMVDVV 807 (1145)
T ss_pred ceeEeeeccccccccCeEEEEEccccc--------ccccCCceEEEeeEEEecCCCCCCCceEEEEeeccHHHHhhcCEE
Confidence 999999999999999999999998632 012344589999999999999999999999999999999999999
Q ss_pred EecCCCCCCCCCcccCCCCCCCeEEEEecCCCCCCCCCCCCCCCCCcccccCCCCCHHHHHHHHHHhhccChhhhHHHHH
Q 003789 480 VFPAKGKRPHTNECSGSDLDGDVYFVCWDHELIPPLQFPPMDYTPAPEKVLARDMTIEDVEEYFADYIVNDSLGVICNAH 559 (795)
Q Consensus 480 VFp~~G~rplps~lsGgDlDGD~y~ViWD~~Lv~~~~~~P~~y~~~~~~~l~~~~~~~di~~ff~~y~~~d~LG~isn~h 559 (795)
||||||+||||+||||||||||+|||||||+|+|+++.+||+|++++++.+.+.++.++|.+||++||++|+||+|+|||
T Consensus 808 vFPQkGpRphpdE~aGsDLDGDeYfViWDqkLL~~~~~epmd~~~~~sk~~~~~~~~~~m~effv~yL~~DslG~isnAh 887 (1145)
T KOG0988|consen 808 VFPQKGPRPHPDEMAGSDLDGDEYFVIWDQKLLPPRNEEPMDSSSEKSKILDGRVPLDEMSEFFVEYLKEDSLGLISNAH 887 (1145)
T ss_pred EcCCCCCCCCccccccCCCCCceEEEEeChhhccCcCCCccccCccccccccCCCCHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhccCCCCCCCHHHHHHHHHHhhcccccCCCCccccCCCCCCCCCCCccCCCCCCcccccchhhHHHHhhhhcCCCCc
Q 003789 560 VVHADLEPDKARSNQCLELAKLSTIAVDFSKTGVAATIPSGLRVEIYPDFMEKQDKTCYESQRVIGKLYRAVKDIAPPTA 639 (795)
Q Consensus 560 l~~aD~~~~g~~~~~cl~LA~l~s~aVD~~KtG~~~~~p~~l~~~~~Pdfm~k~~~~~Y~S~~ilG~Lyr~v~~~~~~~~ 639 (795)
+++||+ .|+++..|+.||++||+||||||||..+.+|..++++.+||||++.++|+|.|++++|||||+++.+.....
T Consensus 888 l~~aD~--~G~~~~~Cl~LA~k~~~AVDF~KsG~d~~~~~~ek~e~~PDfm~~~d~p~Y~S~~l~GkLfR~~~aid~~~~ 965 (1145)
T KOG0988|consen 888 LANADV--YGLFSDVCLELAKKHSQAVDFPKSGADESMPEKEKPERYPDFMEKTDKPTYYSERLCGKLFREAKAIDAPLK 965 (1145)
T ss_pred ccchhh--cchhhHHHHHHHHhhcccccccccCCcccccchhchhhcchhhhCCCCceeecchhhhHHHHHHHhhcchhh
Confidence 999999 599999999999999999999999999999999999999999999999999999999999998876654332
Q ss_pred ccccchhhhhhcccCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcceeeee--hhhcccchhhhHhhHHHHH
Q 003789 640 TIKSFTKEVAMQSYDTDMEVDGFEDYITDAFKYKTEYDNRLGNLMDYYGIKTEAEILSG--CIMEMAKSFDKKRDLEAII 717 (795)
Q Consensus 640 ~~~~~~~~~~~~~~d~~l~~~g~~~~~~~A~~~~~~Y~~~l~~lm~~y~i~tE~Ev~sG--~i~~~~~~~~~~~~~~~i~ 717 (795)
......... ...||++++++||++|+++|.++++.|+.+|++||++|||.+|+||+|| .+..|+...+++...+.+.
T Consensus 966 ~~e~~~~~~-~i~yD~~l~v~gFe~yme~a~~~~~~y~~qL~slm~~ygi~~E~eI~sG~~~~ddms~~~t~~~~e~~~~ 1044 (1145)
T KOG0988|consen 966 GSEERSEQV-EVEYDEDLEVDGFEHYMERAKKQVASYNGQLRSLMDFYGISTEGEIFSGILDQDDMSFYNTERMIELKLE 1044 (1145)
T ss_pred cCccccCcc-cccCCcccCcCCcHHHHHHHHHHHhhhhhHHHHHHHHhCccchhhhhccCccccchhhhcccccchhhhH
Confidence 222222222 3689999999999999999999999999999999999999999999999 4445666666555555666
Q ss_pred HHHHHHHHHHHHHHhh------cCC--CCCc-hhhHhHHHHHHhH-hhccccccccccccCCCcCcccccccchHHHHHH
Q 003789 718 FAVKSLKKEARAWFNK------KNE--SDSS-HEDVYAKASAWYH-VAYHPSYWGRYKEEGMNRTHFLSFPWCIHDKLIE 787 (795)
Q Consensus 718 ~~~~~l~~~~r~~f~~------~~~--~~~~-~~~~~~~a~A~Y~-vty~~~~~~~~~~~~~~~~~~lSFpWi~~d~l~~ 787 (795)
..+..||+.+.+.|.. .-+ .+.. .+.+.+||+|||+ ++|+.... .+..+.+|||||++|+|++
T Consensus 1045 ~l~~~~r~~~~qef~~y~~~~e~l~~fe~~~~eE~~~kKa~aWY~v~~ye~~~~-------~~~~~~~SF~wia~Dvl~~ 1117 (1145)
T KOG0988|consen 1045 RLVLKLREKFFQEFGAYKLEIEKLSCFEDSPEEEFIMKKASAWYRVYRYEMAQA-------MRETRKLSFAWIAYDVLAR 1117 (1145)
T ss_pred HHHHHHHHHHHHHhhhhcchhhhccccccCchhHHHHHHHHHHHHHHHhhhhcc-------cccCcccchHHHHHHHHHH
Confidence 7777777665444421 001 1223 3348899999999 77775422 2345778999999999999
Q ss_pred HHhh
Q 003789 788 IKRG 791 (795)
Q Consensus 788 ik~~ 791 (795)
||++
T Consensus 1118 iK~~ 1121 (1145)
T KOG0988|consen 1118 IKQT 1121 (1145)
T ss_pred HHHH
Confidence 9998
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=1.1e-127 Score=1125.99 Aligned_cols=546 Identities=45% Similarity=0.780 Sum_probs=388.4
Q ss_pred CceeecCccccccCccccccCCCCCcEEEEEEeeCCCccccccccCCCccCCcchhhhHHHHHHHHHHhcCeEEcceeEE
Q 003789 61 SKVYFSGPEISLSNRVVRSYPDEIDNFLRLSFVDEDLDKLYSTVLSPLISSTNEERHTTIYERVLSTLRNGIVIGDKKFE 140 (795)
Q Consensus 61 t~i~~~~P~~~~sNRvlR~f~~~~d~FlRV~F~DE~~~~l~~~~~~p~~~~~~~~~~~~~~~rv~~~L~~Gi~I~gr~y~ 140 (795)
||++|.+|+++.|||++|+|+. |+||||+|+||++..++... ..++++++++|++||.|+||+|+
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 7899999999999999999965 67999999999988765421 01567788999999999999999
Q ss_pred EeeecCCCCcCCeEEEEecC----CCCCHHHHHHHhCCCCCccCH-HHHHHHHcccccCCcceeeecCCCeEEcCCcccc
Q 003789 141 TLAFSNSQVKDNSMWMFASR----PELTAADIRESMGDFRDIKNV-AKYAARLGQSFGSSREALHVDSSDIEIIPDVEVE 215 (795)
Q Consensus 141 fL~~S~SqlR~~s~wf~~~~----~~~~~~~Ir~~lG~f~~i~~~-aK~aARlgq~FS~T~~tv~i~~~~i~~i~Di~~~ 215 (795)
|||+|+||+|+++||||+++ ..+++++|++|+|+|++++++ +||+||||||||+|.+++.+++++|..|+||.
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 789999999999999998886 99999999999999999999999999999993
Q ss_pred CCCcccccccccccccHHHHHHHHHHcCCCCCCCceEEEeecCceEEEEeCCCC-CceEEeccccccC----CCCCCcEE
Q 003789 216 DDGITYCFSDGIGKISAELAEIVAKNCGFTIYTPSAFQIRYGGYKGVVAVDPTS-STKLSLRKSMLKY----KSESTSLD 290 (795)
Q Consensus 216 ~~g~~~~fTDG~G~IS~~la~~I~~~l~l~~~~PSafQiR~~G~KGvl~vdp~~-~~~i~lR~Sm~KF----~~~~~~le 290 (795)
++++|+||||||+||++||++||+++++ ..+|||||||++||||||+|||+. +.+|+||+||+|| .+.+++||
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 4799999999999 66789999
Q ss_pred EEeccC-CccccccHHHHHHHhcCCCChHHHHHHHHHHHHHHHHHhcCHHHHHHHHHhcCCCCcHHHHH-HHHHCCCCCC
Q 003789 291 ILANSK-YQPCFLNRQLITLLSTLGIRDHVFEKKQREGVAQLDAILTDPLKAHEALELMSSGENTNVLK-ELLMCGYKPD 368 (795)
Q Consensus 291 I~~~S~-~~~~~LNrq~I~iL~~lGV~~~vF~~lq~~~l~~l~~~~~d~~~a~~~l~~~~~~~~~~~l~-~ll~~Gf~~~ 368 (795)
|+++|+ +.+++||||+|.+|+++|||+++|+++|+++++++..++.++..|..++............. +|+.+||++.
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 89999999999999999999999999999999999999999999999988765544433333 8999999999
Q ss_pred CcHHHHHHHHHHHHHHHHHhhcceeEEecCceeeeeecCCCCCCCCCCEEEEeccccccccccCcCCCCCCCceeeeeeE
Q 003789 369 VEPFLLMMLQTFRASNLLELRTRTRIFIQNGRAMMGCLDETGTLESGQVFVQCSASRRREFLDNSCNNRSGELGVVEGKV 448 (795)
Q Consensus 369 ~epfl~~~l~~~~~~~l~~lk~k~rI~Vp~s~~l~GV~DetG~L~~gEVfvq~s~~~~~~~~~~~~~~~~~~~~~i~G~V 448 (795)
++||++++++.+.++.+.++|+|+||+||+|++||||+||||+|+|||||||++... .......+++|+|
T Consensus 302 ~~pfl~~~l~~~~~~~l~~~~~~~ri~v~~s~~l~gv~D~~g~L~~geV~~~~s~~~----------~~~~~~~~~~g~V 371 (579)
T PF05183_consen 302 NDPFLRSLLKALIKKKLKELKKKARIPVPKSRYLMGVPDPTGVLKEGEVFVQFSSDE----------ETGSQSQVLEGDV 371 (579)
T ss_dssp TBHHHHHHHHHHHHHHHHHHHHC--B--SSEEEEEEEE-TTS---TTEEEEEEEEEE----------EETTEEEEEE-EE
T ss_pred cCHHHHHHHHHHHHHHHHhccceEEEEcCCCcEEEEeeCCcCCCCCCEEEEEecccc----------ccCCCcceeeeeE
Confidence 999999999999999999999999999999999999999999999999999996221 1234557999999
Q ss_pred EEeeCCCCCCCCeeEEEeecCCCCCCCCCeEEecCCCCCCCCCcccCCCCCCCeEEEEecCCCCCCC-------CCCCCC
Q 003789 449 VVAKNPCLHPGDMRVLRAVDVPSLHHMVDCVVFPAKGKRPHTNECSGSDLDGDVYFVCWDHELIPPL-------QFPPMD 521 (795)
Q Consensus 449 lV~RnP~lhPgDIr~v~AV~~P~L~hl~dvIVFp~~G~rplps~lsGgDlDGD~y~ViWD~~Lv~~~-------~~~P~~ 521 (795)
+|+||||+||||||+|+||++|+|+||+||||||++|+||+|++|||||||||+|||||||+||.++ ..+|+.
T Consensus 372 lV~R~P~~~pgDir~~~av~~p~L~~l~~vIVF~~~G~r~~~~~lsGgDlDGD~~~V~wd~~lv~~~~~~~~~~~~~p~~ 451 (579)
T PF05183_consen 372 LVTRNPCLHPGDIRKVKAVDKPELRHLKDVIVFSTKGDRPLPSELSGGDLDGDEYFVCWDPRLVEPFKNPPPPKSEEPMN 451 (579)
T ss_dssp EEE-SS--SGGGEEEEEE---GGGTT--SEEEE-S-SSS-HHHHTTT--SSS-EEEEE--HHHHHTB-----------TT
T ss_pred EEecCCccCcCceeEEEeeccHHHcccCCEEEeCCCCCCCchHHhcCCCCCCceEEEEeCHhhhhhhhccCcccCCCccc
Confidence 9999999999999999999999999999999999999999999999999999999999999995554 345555
Q ss_pred CCCCc-------ccccCCCCCHHHHHHHHHH-hhccChhhhHHHHHHHHhccCCCCCCCHHHHHHHHHHhhcccccCCCC
Q 003789 522 YTPAP-------EKVLARDMTIEDVEEYFAD-YIVNDSLGVICNAHVVHADLEPDKARSNQCLELAKLSTIAVDFSKTGV 593 (795)
Q Consensus 522 y~~~~-------~~~l~~~~~~~di~~ff~~-y~~~d~LG~isn~hl~~aD~~~~g~~~~~cl~LA~l~s~aVD~~KtG~ 593 (795)
|...+ +..+.++.+.+++++||++ |+.++.||+|+|+|+++||+++ |+.++.|++||++||+||||+|||+
T Consensus 452 ~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~lG~~s~~h~~~~d~~~-g~~~~~~~~La~l~s~~vD~~KtG~ 530 (579)
T PF05183_consen 452 YESEKVSDSSGDPKPLSRPVTEEDIQDFFLEFYINNDNLGLISNAHLAIADQSS-GIDSPECLKLAQLHSQAVDAPKTGV 530 (579)
T ss_dssp TSEE---BHHHHTT-SSHHHHHHHHHHHHHHHHTS--HHHHHHHHHHHHHHHHT--SSSHHHHHHHHHHHHHTTHHHHTE
T ss_pred cccccccccccCccccCccccHHHHHHHHHHhhcccCcHHHHHHHHHHHHHhcC-CCCCHHHHHHHHHHHHHhCccccCC
Confidence 43222 1234456778999999999 9999999999999999999987 9999999999999999999999999
Q ss_pred ccccCCC-CCCCCCCCccCCCCCCc-ccccchhhHHHHhhhhcCC
Q 003789 594 AATIPSG-LRVEIYPDFMEKQDKTC-YESQRVIGKLYRAVKDIAP 636 (795)
Q Consensus 594 ~~~~p~~-l~~~~~Pdfm~k~~~~~-Y~S~~ilG~Lyr~v~~~~~ 636 (795)
++.++.. ++++.+||||++..++. |+|++|||+|||+|++...
T Consensus 531 ~~~~~~~~~~~~~~P~~~~~~~~~~~y~S~~ilg~ly~~v~~~~~ 575 (579)
T PF05183_consen 531 PVKLPRWPLKPPEYPDFMEKEDKKSYYKSTSILGQLYREVKEIVK 575 (579)
T ss_dssp E--HHHHHSS-----GGGSS-----SSS--SHHHHHHHTTH----
T ss_pred CccccchhhcCCCCChhhccccccccCCCccHHHHHHHHHHhhcc
Confidence 9999887 88999999999876665 7999999999999988653
No 3
>smart00663 RPOLA_N RNA polymerase I subunit A N-terminus.
Probab=76.38 E-value=2.7 Score=46.02 Aligned_cols=52 Identities=27% Similarity=0.479 Sum_probs=37.4
Q ss_pred eeee-eEEEeeCCCCCCCCeeEEEeecCCCCCCCCCeEEecCCCCCCCCCccc--CCCCCCCeEEEE
Q 003789 443 VVEG-KVVVAKNPCLHPGDMRVLRAVDVPSLHHMVDCVVFPAKGKRPHTNECS--GSDLDGDVYFVC 506 (795)
Q Consensus 443 ~i~G-~VlV~RnP~lhPgDIr~v~AV~~P~L~hl~dvIVFp~~G~rplps~ls--GgDlDGD~y~Vi 506 (795)
+.+| -|++-|.|+||..-||-+++.-.|. .+| |=+|..|+ ..|+|||+-.+.
T Consensus 199 l~dgd~Vl~NRqPsLHr~si~a~~v~v~~~-----~ti-------r~n~~~c~~fNADFDGDeMnih 253 (295)
T smart00663 199 VIDGDVVLFNRQPTLHRMSIQAHRVRVLEG-----KTI-------RLNPLVCSPYNADFDGDEMNLH 253 (295)
T ss_pred hhcCCEEEEecCCccccccceeEEEEEecC-----ceE-------EecCccCCcccCCcCCCEEEEe
Confidence 5567 6999999999999999999887664 111 11233333 479999998764
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=57.66 E-value=5 Score=40.30 Aligned_cols=52 Identities=25% Similarity=0.482 Sum_probs=33.6
Q ss_pred eeee-eEEEeeCCCCCCCCeeEEEeecCCCCCCCCCeEEecCCCCCCCCCccc--CCCCCCCeEEEE
Q 003789 443 VVEG-KVVVAKNPCLHPGDMRVLRAVDVPSLHHMVDCVVFPAKGKRPHTNECS--GSDLDGDVYFVC 506 (795)
Q Consensus 443 ~i~G-~VlV~RnP~lhPgDIr~v~AV~~P~L~hl~dvIVFp~~G~rplps~ls--GgDlDGD~y~Vi 506 (795)
+..| .|++-|.|+||..-++-++++-.+. .+| |=+|..|+ +.|+|||+-.|.
T Consensus 95 l~~gd~vl~nRqPtLh~~s~~a~~~~~~~~-----~t~-------~~~~~~c~~~NADFDGDem~i~ 149 (166)
T PF00623_consen 95 LCDGDIVLLNRQPTLHRMSIMAHKVRVLPG-----KTI-------RINPLVCSPFNADFDGDEMNIH 149 (166)
T ss_dssp HTTT-EEEEEESS-SSGGGEEEEEEEEESS-----SSE-------EEEGGGHHHHT--TSS-EEEEE
T ss_pred hhcCceeEEeccchhccceeeeeeeeeecc-----cEE-------EeeccchhhhhccCCcceEEEE
Confidence 3456 5999999999999999999876655 111 11333333 689999998875
No 5
>CHL00018 rpoC1 RNA polymerase beta' subunit
Probab=56.69 E-value=9.9 Score=45.87 Aligned_cols=52 Identities=27% Similarity=0.458 Sum_probs=36.6
Q ss_pred eeeee-eEEEeeCCCCCCCCeeEEEeecCCCCCCCCCeEEecCCCCCCCCCccc--CCCCCCCeEEE
Q 003789 442 GVVEG-KVVVAKNPCLHPGDMRVLRAVDVPSLHHMVDCVVFPAKGKRPHTNECS--GSDLDGDVYFV 505 (795)
Q Consensus 442 ~~i~G-~VlV~RnP~lhPgDIr~v~AV~~P~L~hl~dvIVFp~~G~rplps~ls--GgDlDGD~y~V 505 (795)
.++.| .|+.-|.|+||.--||-+++|-.+.- -=|=+|..|+ ..|+|||+-.|
T Consensus 443 ~v~~gd~VLlNRqPTLHR~sIqAf~~~L~~gk------------tIrLhplvC~~fNADFDGDqMnv 497 (663)
T CHL00018 443 EVMQGHPVLLNRAPTLHRLGIQAFQPILVEGR------------AICLHPLVCKGFNADFDGDQMAV 497 (663)
T ss_pred ehhcCceeeecCCCcccccccceeeEEecCCC------------eEEeCcccCCcccCCccCcEEEE
Confidence 36677 68999999999999999988765531 1111233333 47999999775
No 6
>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional
Probab=56.42 E-value=13 Score=44.59 Aligned_cols=52 Identities=29% Similarity=0.498 Sum_probs=36.9
Q ss_pred eeeee-eEEEeeCCCCCCCCeeEEEeecCCCCCCCCCeEEecCCCCCCCCCccc--CCCCCCCeEEE
Q 003789 442 GVVEG-KVVVAKNPCLHPGDMRVLRAVDVPSLHHMVDCVVFPAKGKRPHTNECS--GSDLDGDVYFV 505 (795)
Q Consensus 442 ~~i~G-~VlV~RnP~lhPgDIr~v~AV~~P~L~hl~dvIVFp~~G~rplps~ls--GgDlDGD~y~V 505 (795)
.++.| .|+.-|.|+||.--||-++++-.+.- -=|=+|..|+ ..|+|||+-.|
T Consensus 422 ~v~~gd~VLlNRqPTLHR~sIqAf~~~l~~~k------------tirlhplvC~~fNADFDGDeMnv 476 (627)
T PRK02625 422 EVIEGHPVLLNRAPTLHRLGIQAFEPILVEGR------------AIQLHPLVCPAFNADFDGDQMAV 476 (627)
T ss_pred EeecCcEEEecCCCccccccceeEeeEEcCCC------------eEEeccccCCcccCCcCCCeEEE
Confidence 36677 69999999999999999988765531 1112333333 47999999775
No 7
>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=55.13 E-value=9.7 Score=45.48 Aligned_cols=52 Identities=27% Similarity=0.503 Sum_probs=36.5
Q ss_pred eeeee-eEEEeeCCCCCCCCeeEEEeecCCCCCCCCCeEEecCCCCCCCCCccc--CCCCCCCeEEE
Q 003789 442 GVVEG-KVVVAKNPCLHPGDMRVLRAVDVPSLHHMVDCVVFPAKGKRPHTNECS--GSDLDGDVYFV 505 (795)
Q Consensus 442 ~~i~G-~VlV~RnP~lhPgDIr~v~AV~~P~L~hl~dvIVFp~~G~rplps~ls--GgDlDGD~y~V 505 (795)
.++.| .|+.-|.|+||.--||-++++-.+. +-=|=+|..|+ ..|+|||+-.|
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 35677 6999999999999999998765543 11122333443 47999999765
No 8
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=39.47 E-value=27 Score=45.00 Aligned_cols=52 Identities=25% Similarity=0.440 Sum_probs=36.8
Q ss_pred eeee-eEEEeeCCCCCCCCeeEEEeecCCCCCCCCCeEEecCCCCCCCCCccc--CCCCCCCeEEEE
Q 003789 443 VVEG-KVVVAKNPCLHPGDMRVLRAVDVPSLHHMVDCVVFPAKGKRPHTNECS--GSDLDGDVYFVC 506 (795)
Q Consensus 443 ~i~G-~VlV~RnP~lhPgDIr~v~AV~~P~L~hl~dvIVFp~~G~rplps~ls--GgDlDGD~y~Vi 506 (795)
++.| .|+.-|.|.||.--||-++++-.|.- -=|=||..|+ ..|+|||+-.|-
T Consensus 405 vi~gd~VLlNRqPTLHR~sIqAf~~~l~~gk------------tirLhplvC~~fNADFDGDqMnvH 459 (1156)
T PRK00566 405 VIKEHPVLLNRAPTLHRLGIQAFEPVLIEGK------------AIQLHPLVCTAFNADFDGDQMAVH 459 (1156)
T ss_pred ecCCCEEEecCCCcccccccceeEEEEecCc------------eEEECccccCccccccccceeEEe
Confidence 5567 69999999999999999988766541 1112233333 469999998764
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=38.45 E-value=44 Score=42.21 Aligned_cols=53 Identities=25% Similarity=0.420 Sum_probs=37.8
Q ss_pred eeeee-eEEEeeCCCCCCCCeeEEEeecCCCCCCCCCeEEecCCCCCCCCCccc--CCCCCCCeEEEE
Q 003789 442 GVVEG-KVVVAKNPCLHPGDMRVLRAVDVPSLHHMVDCVVFPAKGKRPHTNECS--GSDLDGDVYFVC 506 (795)
Q Consensus 442 ~~i~G-~VlV~RnP~lhPgDIr~v~AV~~P~L~hl~dvIVFp~~G~rplps~ls--GgDlDGD~y~Vi 506 (795)
.++.| -|++-|.|+||.--|+-.++.-.|. + . =|=+|+.|+ ..|+|||+-.+-
T Consensus 407 hl~dgd~vl~NRqPsLHr~si~a~~~~v~~~-~----t-------~r~n~~~c~~~NADFDGDeMn~h 462 (868)
T TIGR02390 407 HLIDGDIVLFNRQPSLHRMSMMGHKVKVLPG-K----T-------FRLNLAVCPPYNADFDGDEMNLH 462 (868)
T ss_pred ehhcCccceeccCCccccccceeEEEEEecC-c----e-------EeeccccCCccccCcccceeeEe
Confidence 46678 5899999999999999988877663 1 1 122333333 479999998765
No 10
>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=36.80 E-value=87 Score=28.25 Aligned_cols=59 Identities=15% Similarity=0.226 Sum_probs=46.0
Q ss_pred hhhHHHHHHHHHHhcCeEEcceeEEEeeecCCCCcCCeEEEEecCCCCCHHHHHHHhCCCCC
Q 003789 116 RHTTIYERVLSTLRNGIVIGDKKFETLAFSNSQVKDNSMWMFASRPELTAADIRESMGDFRD 177 (795)
Q Consensus 116 ~~~~~~~rv~~~L~~Gi~I~gr~y~fL~~S~SqlR~~s~wf~~~~~~~~~~~Ir~~lG~f~~ 177 (795)
+.+.+.++++..+..|+.+++-..+.+||+ |+.=.+.++-++.....+.+-+-+..+..
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 66666666665554556777666666554
No 11
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=36.62 E-value=84 Score=28.36 Aligned_cols=59 Identities=17% Similarity=0.292 Sum_probs=46.1
Q ss_pred hhhHHHHHHHHHHhcCeEEcceeEEEeeecCCCCcCCeEEEEecCCCCCHHHHHHHhCCCCC
Q 003789 116 RHTTIYERVLSTLRNGIVIGDKKFETLAFSNSQVKDNSMWMFASRPELTAADIRESMGDFRD 177 (795)
Q Consensus 116 ~~~~~~~rv~~~L~~Gi~I~gr~y~fL~~S~SqlR~~s~wf~~~~~~~~~~~Ir~~lG~f~~ 177 (795)
..+.+.+.|+.++..|+.+++-..+.+||+ |+.=.+.++-++.....+.+-+-+..|..
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 367788999999999999999999999998 77666666666555666777666665554
No 12
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=36.19 E-value=32 Score=44.95 Aligned_cols=53 Identities=26% Similarity=0.445 Sum_probs=37.2
Q ss_pred eeeee-eEEEeeCCCCCCCCeeEEEeecCCCCCCCCCeEEecCCCCCCCCCccc--CCCCCCCeEEEE
Q 003789 442 GVVEG-KVVVAKNPCLHPGDMRVLRAVDVPSLHHMVDCVVFPAKGKRPHTNECS--GSDLDGDVYFVC 506 (795)
Q Consensus 442 ~~i~G-~VlV~RnP~lhPgDIr~v~AV~~P~L~hl~dvIVFp~~G~rplps~ls--GgDlDGD~y~Vi 506 (795)
.++.| .|+.-|.|.||.--||-++++-.+.- -=|=||.-|+ ..|+|||+-.|-
T Consensus 492 ~vi~gd~VLlNRqPTLHRlsIqAf~~~L~~gk------------tIrLhplvC~~fNADFDGDqMnvH 547 (1460)
T PRK14906 492 EVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGK------------AIKLHPLVCTAFNADFDGDQMAVH 547 (1460)
T ss_pred eeeccceeEeccCcccchhccceeeEEecCCc------------eEEecccccCccccCCcCceeeee
Confidence 35667 79999999999999999987765541 1112233333 469999998765
No 13
>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=35.93 E-value=32 Score=44.33 Aligned_cols=52 Identities=31% Similarity=0.496 Sum_probs=36.8
Q ss_pred eeee-eEEEeeCCCCCCCCeeEEEeecCCCCCCCCCeEEecCCCCCCCCCccc--CCCCCCCeEEEE
Q 003789 443 VVEG-KVVVAKNPCLHPGDMRVLRAVDVPSLHHMVDCVVFPAKGKRPHTNECS--GSDLDGDVYFVC 506 (795)
Q Consensus 443 ~i~G-~VlV~RnP~lhPgDIr~v~AV~~P~L~hl~dvIVFp~~G~rplps~ls--GgDlDGD~y~Vi 506 (795)
++.| .|+.-|.|.||.--||=++++-.|. +-=|=+|..|+ ..|+|||+-.|-
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 5566 7999999999999999998876653 11112233333 479999998764
No 14
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=33.90 E-value=46 Score=46.34 Aligned_cols=53 Identities=28% Similarity=0.498 Sum_probs=37.8
Q ss_pred eeeee-eEEEeeCCCCCCCCeeEEEeecCCCCCCCCCeEEecCCCCCCCCCccc--CCCCCCCeEEEE
Q 003789 442 GVVEG-KVVVAKNPCLHPGDMRVLRAVDVPSLHHMVDCVVFPAKGKRPHTNECS--GSDLDGDVYFVC 506 (795)
Q Consensus 442 ~~i~G-~VlV~RnP~lhPgDIr~v~AV~~P~L~hl~dvIVFp~~G~rplps~ls--GgDlDGD~y~Vi 506 (795)
.++.| .|+.-|.|.||.--||-++++-.|. +-=|=||..|+ ..|+|||+-.|-
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 36678 6899999999999999998876553 11122333343 479999998764
No 15
>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=33.58 E-value=89 Score=28.14 Aligned_cols=55 Identities=20% Similarity=0.407 Sum_probs=42.1
Q ss_pred hhhHHHHHHHHHHhcCeEEcceeEEEeeecCCCCcCCeEEEEecCCCCCHHHHHHHhC
Q 003789 116 RHTTIYERVLSTLRNGIVIGDKKFETLAFSNSQVKDNSMWMFASRPELTAADIRESMG 173 (795)
Q Consensus 116 ~~~~~~~rv~~~L~~Gi~I~gr~y~fL~~S~SqlR~~s~wf~~~~~~~~~~~Ir~~lG 173 (795)
..+.+.+.|+.++.+|+.+++...+.+||+ |+.=.+.++-++...+.+++-+-+.
T Consensus 18 Dl~~l~~~Ik~~~~~gl~~~~~~~epiaFG---lk~L~i~~vv~D~~~~td~lee~i~ 72 (88)
T cd00292 18 DLDELEEKIRAILMDGLLWGKSKLEPIAFG---LKALQIYCVVEDDEGGTDELEEAIS 72 (88)
T ss_pred CHHHHHHHHHHhCcCCcEEEEEEEEEeeeE---eeEEEEEEEEEeCCcCcHHHHHHHh
Confidence 367788999999999999999999999998 6665555655555556666665543
No 16
>PRK08566 DNA-directed RNA polymerase subunit A'; Validated
Probab=31.07 E-value=41 Score=42.56 Aligned_cols=53 Identities=25% Similarity=0.462 Sum_probs=38.2
Q ss_pred eeeee-eEEEeeCCCCCCCCeeEEEeecCCCCCCCCCeEEecCCCCCCCCCccc--CCCCCCCeEEEE
Q 003789 442 GVVEG-KVVVAKNPCLHPGDMRVLRAVDVPSLHHMVDCVVFPAKGKRPHTNECS--GSDLDGDVYFVC 506 (795)
Q Consensus 442 ~~i~G-~VlV~RnP~lhPgDIr~v~AV~~P~L~hl~dvIVFp~~G~rplps~ls--GgDlDGD~y~Vi 506 (795)
.++.| -|++-|.|+||.--|+-.++.-.|. + +| |=+|+.|+ ..|+|||+-.+-
T Consensus 411 hl~dgd~vl~NRqPsLHr~si~a~~~~v~~~-~----t~-------r~n~~~c~~~NADFDGDeMn~h 466 (882)
T PRK08566 411 HLIDGDIVLFNRQPSLHRMSIMAHRVRVLPG-K----TF-------RLNLAVCPPYNADFDGDEMNLH 466 (882)
T ss_pred hhhcCceeeecCCCcccccccceeEEEEecC-c----eE-------eeccccCCCccCCccCcEEEEe
Confidence 46678 5899999999999999998887664 1 11 22333333 479999998764
No 17
>PHA02770 hypothetical protein; Provisional
Probab=28.72 E-value=51 Score=27.71 Aligned_cols=22 Identities=32% Similarity=0.534 Sum_probs=16.4
Q ss_pred hcCeEEcceeEEE-eeecCCCCcCCeE
Q 003789 129 RNGIVIGDKKFET-LAFSNSQVKDNSM 154 (795)
Q Consensus 129 ~~Gi~I~gr~y~f-L~~S~SqlR~~s~ 154 (795)
..=+.|+||||+| |-|| +++|+
T Consensus 43 ~gylei~~~hyrfelifs----kdnsv 65 (81)
T PHA02770 43 TGYLEVNGRHYRFELIFS----KDNSV 65 (81)
T ss_pred EEEEEEcCceEEEEEEEe----cCCcE
Confidence 3445699999999 7777 66664
No 18
>KOG1547 consensus Septin CDC10 and related P-loop GTPases [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms; Cytoskeleton]
Probab=27.81 E-value=45 Score=35.67 Aligned_cols=64 Identities=17% Similarity=0.423 Sum_probs=46.7
Q ss_pred cccccchh-HHHHHHHHHHHhhcccCCCCccccCCCcEEEEEEEEecCceeecCccccccCccccc
Q 003789 15 RECCYEPV-RWLEEQYRKYVLSRRFLTSPAVALDDGLIYVNKVLVTPSKVYFSGPEISLSNRVVRS 79 (795)
Q Consensus 15 ~~~~~~p~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~v~vTPt~i~~~~P~~~~sNRvlR~ 79 (795)
++.||+|. +.+.+||.+|++....- .-...+|+--+.|.=-.|.||+--|.+=.+|---|+.+-
T Consensus 120 N~ncWePI~kyIneQye~yL~eElni-~R~kripDTRVHcclyFi~ptGhsLrplDieflkrLt~v 184 (336)
T KOG1547|consen 120 NDNCWEPIEKYINEQYEQYLREELNI-AREKRIPDTRVHCCLYFIPPTGHSLRPLDIEFLKRLTEV 184 (336)
T ss_pred ccchhHHHHHHHHHHHHHHHHHHHhH-HhhhcCCCceEEEEEEEeCCCCCccCcccHHHHHHHhhh
Confidence 46899995 78999999998753322 223466788888888889999988877667665555543
No 19
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=23.64 E-value=59 Score=41.56 Aligned_cols=58 Identities=26% Similarity=0.348 Sum_probs=36.4
Q ss_pred EEEeeCCCCCCC-------CeeEEEeecCC-----CC-------CCCC--CeEEecCCC-------------------CC
Q 003789 448 VVVAKNPCLHPG-------DMRVLRAVDVP-----SL-------HHMV--DCVVFPAKG-------------------KR 487 (795)
Q Consensus 448 VlV~RnP~lhPg-------DIr~v~AV~~P-----~L-------~hl~--dvIVFp~~G-------------------~r 487 (795)
-+|-+-|+.||| +-+++.+..++ .| |||. |+|+|..+- =|
T Consensus 382 eLV~~g~~~~pgakyiird~G~Ridlr~~~~~~d~~Lq~G~kVeRhl~DGD~VlfNRqPSlHKmSmmahrVrVlp~sTfr 461 (1605)
T KOG0260|consen 382 ELVRRGLLEHPGAKYIIRDNGDRIDLRYHKRAGDIHLQPGYKVERHLMDGDVVLFNRQPSLHKMSMMAHRVRVLPYSTFR 461 (1605)
T ss_pred HHhhCCCCCCCCcceeeecCCcEEEEeecCCccccccccccEEEEeeccCCEEEEcCCCcHHHhhhhhcEEEEccCceEE
Confidence 356667777777 66667676666 23 5665 477775431 12
Q ss_pred CCCCccc--CCCCCCCeEEE
Q 003789 488 PHTNECS--GSDLDGDVYFV 505 (795)
Q Consensus 488 plps~ls--GgDlDGD~y~V 505 (795)
=.++++| .+|+|||+...
T Consensus 462 LNlsvtsPynADFDGDemnl 481 (1605)
T KOG0260|consen 462 LNLSVTSPYNADFDGDEMNL 481 (1605)
T ss_pred eCeeecCCccCCCCCceeec
Confidence 2344444 68999999764
No 20
>PF14538 Raptor_N: Raptor N-terminal CASPase like domain
Probab=23.53 E-value=88 Score=31.08 Aligned_cols=38 Identities=16% Similarity=0.381 Sum_probs=31.1
Q ss_pred eeEEEeeecCCC-CcCCeEEEEecCC----CCCHHHHHHHhCC
Q 003789 137 KKFETLAFSNSQ-VKDNSMWMFASRP----ELTAADIRESMGD 174 (795)
Q Consensus 137 r~y~fL~~S~Sq-lR~~s~wf~~~~~----~~~~~~Ir~~lG~ 174 (795)
.-|.|.|++--. ..++.+|+|..+. .+++.++.+|+|.
T Consensus 93 vLFHYnGhGvP~Pt~~GeIw~f~~~~tqyip~si~dL~~~lg~ 135 (154)
T PF14538_consen 93 VLFHYNGHGVPRPTENGEIWVFNKNYTQYIPLSIYDLQSWLGS 135 (154)
T ss_pred EEEEECCCCCCCCCCCCeEEEEcCCCCcceEEEHHHHHHhcCC
Confidence 348888988776 7888999998653 4889999999995
No 21
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=22.71 E-value=71 Score=44.53 Aligned_cols=52 Identities=25% Similarity=0.472 Sum_probs=36.7
Q ss_pred eeee-eEEEeeCCCCCCCCeeEEEeecCCCCCCCCCeEEecCCCCCCCCCccc--CCCCCCCeEEEE
Q 003789 443 VVEG-KVVVAKNPCLHPGDMRVLRAVDVPSLHHMVDCVVFPAKGKRPHTNECS--GSDLDGDVYFVC 506 (795)
Q Consensus 443 ~i~G-~VlV~RnP~lhPgDIr~v~AV~~P~L~hl~dvIVFp~~G~rplps~ls--GgDlDGD~y~Vi 506 (795)
++.| .|+.-|.|+||.--||-++++-.|. +-=|=+|..|+ ..|+|||+-.|-
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 7999999999999999888765543 11122344443 369999998764
No 22
>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Probab=22.01 E-value=84 Score=41.54 Aligned_cols=54 Identities=24% Similarity=0.391 Sum_probs=37.0
Q ss_pred eeeee-eEEEeeCCCCCCCCeeEEEeecCCCCCCCC-CeEEecCCCCCCCCCcccCCCCCCCeEEEE
Q 003789 442 GVVEG-KVVVAKNPCLHPGDMRVLRAVDVPSLHHMV-DCVVFPAKGKRPHTNECSGSDLDGDVYFVC 506 (795)
Q Consensus 442 ~~i~G-~VlV~RnP~lhPgDIr~v~AV~~P~L~hl~-dvIVFp~~G~rplps~lsGgDlDGD~y~Vi 506 (795)
.+..| -|++-|.|+||.--|+=.++.-.|. +-++ |-.|++. =..|+|||+-.+-
T Consensus 427 hl~dGD~VL~NRQPSLHk~Simah~vkvl~~-kT~Rln~~vC~p----------yNADFDGDEMNlH 482 (1321)
T PRK14977 427 HLADGDIVIFNRQPSLHKLSILAHRVKVLPG-ATFRLHPAVCPP----------YNADFDGDEMNLH 482 (1321)
T ss_pred EeecCcEEEeccCCccccccceEEEEEEecC-ceEEecccccCc----------ccCCcccceeeee
Confidence 45678 5899999999999999988887764 2111 1122221 1479999997754
No 23
>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=21.06 E-value=5.2e+02 Score=25.34 Aligned_cols=86 Identities=19% Similarity=0.249 Sum_probs=54.3
Q ss_pred EEEEecCceeecCccccccCccccc-cCCCCCcEEEEEEeeCCCccccccccCCCccCCcchhhhHHHHHHHHHHhcCeE
Q 003789 55 KVLVTPSKVYFSGPEISLSNRVVRS-YPDEIDNFLRLSFVDEDLDKLYSTVLSPLISSTNEERHTTIYERVLSTLRNGIV 133 (795)
Q Consensus 55 ~v~vTPt~i~~~~P~~~~sNRvlR~-f~~~~d~FlRV~F~DE~~~~l~~~~~~p~~~~~~~~~~~~~~~rv~~~L~~Gi~ 133 (795)
++.|+.-+|.+..|.- .-+.|+ |+.+ .|+|+.-+.+.-+ ++..|-.
T Consensus 47 h~kVS~qGItLtDn~r---k~ffrrhypl~-----~Vs~ca~dp~n~~-------------------------~~~~~~~ 93 (138)
T cd01213 47 HFKVSSQGITLTDNTR---KKFFRRHYKVD-----SVIFCAIDPEERM-------------------------WENEGAI 93 (138)
T ss_pred EEEEEcCCeeeecccc---ceeehhhCCcC-----eEEEEeeCCcccc-------------------------ccccccc
Confidence 7888888888877542 222443 5543 6888865543211 1122112
Q ss_pred EcceeEEEeeecCCCCcCCeEEEEec-CCCCCHHHHHHHhC
Q 003789 134 IGDKKFETLAFSNSQVKDNSMWMFAS-RPELTAADIRESMG 173 (795)
Q Consensus 134 I~gr~y~fL~~S~SqlR~~s~wf~~~-~~~~~~~~Ir~~lG 173 (795)
...|.|.|.+=......++.|+-|++ ++...+..|.+..+
T Consensus 94 ~~kriFgFVar~~~~~~~~~ChvF~e~~~~qpa~~iv~~~~ 134 (138)
T cd01213 94 AKARIFAFVARIPHSSTDNACHVFAELEPEQPASAIVNFAN 134 (138)
T ss_pred cccEEEEEEEecCCCCCCeeEEEeccCCCCCCHHHHHHHHH
Confidence 36788899887655667899999997 45667888876543
No 24
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=20.97 E-value=5.4e+02 Score=30.57 Aligned_cols=101 Identities=20% Similarity=0.327 Sum_probs=51.6
Q ss_pred ccccHHHHHHHhcCCCChHHHHHH--------HHHHHHHHHHHhcCHHHHHHHH--HhcC---CCCcHHHHHHHHHCCCC
Q 003789 300 CFLNRQLITLLSTLGIRDHVFEKK--------QREGVAQLDAILTDPLKAHEAL--ELMS---SGENTNVLKELLMCGYK 366 (795)
Q Consensus 300 ~~LNrq~I~iL~~lGV~~~vF~~l--------q~~~l~~l~~~~~d~~~a~~~l--~~~~---~~~~~~~l~~ll~~Gf~ 366 (795)
..=|+-.|.-|.++|.|.+.-.+. .+.++++|-.-|.||+--.-+. ..++ ..-+..-+..|+..||.
T Consensus 555 ~t~Nqs~I~qL~~mGfp~~~~~rAL~~tgNqDaEsAMNWLFqHMdDPdlndP~~~~~~vPKkDkeVdE~~~~Slle~Gln 634 (749)
T COG5207 555 FTDNQSLIRQLVDMGFPEEDAARALGITGNQDAESAMNWLFQHMDDPDLNDPFVPPPNVPKKDKEVDESKARSLLENGLN 634 (749)
T ss_pred cCchHHHHHHHHHcCCCHHHHHHHHhhccCcchHHHHHHHHhhccCcccCCCCCCCCCCCcccccccHHHHHHHHHcCCC
Confidence 456889999999999996543221 1223344433333332100000 0000 00123347889999998
Q ss_pred CCCcHHHHHHHHHHHHHHHHHhhcceeEEecCceeeeeec-CCCCCCCCCCE
Q 003789 367 PDVEPFLLMMLQTFRASNLLELRTRTRIFIQNGRAMMGCL-DETGTLESGQV 417 (795)
Q Consensus 367 ~~~epfl~~~l~~~~~~~l~~lk~k~rI~Vp~s~~l~GV~-DetG~L~~gEV 417 (795)
|..+ ++.|.+.....+ |.+.+|. |+.|+.+|.||
T Consensus 635 ~n~~-----------Rkal~~~n~d~~------r~V~w~~N~~D~tF~EP~v 669 (749)
T COG5207 635 PNLC-----------RKALMDMNTDSK------RRVVWCINDDDGTFPEPEV 669 (749)
T ss_pred HHHH-----------HHHHHHccCCch------heEEEEEeCCCCCCCCCCC
Confidence 7421 223333332211 3334443 89999998887
Done!