Query 002545
Match_columns 910
No_of_seqs 174 out of 1738
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 02:09:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002545.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002545hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0216 RNA polymerase I, seco 100.0 2E-226 5E-231 1891.8 63.3 867 2-909 5-916 (1111)
2 PRK08565 DNA-directed RNA poly 100.0 2E-200 4E-205 1853.5 79.0 824 9-909 8-916 (1103)
3 KOG0214 RNA polymerase II, sec 100.0 1E-192 2E-197 1630.6 44.3 841 8-909 11-956 (1141)
4 KOG0215 RNA polymerase III, se 100.0 3E-178 6E-183 1493.4 38.6 832 9-909 53-971 (1153)
5 COG0085 RpoB DNA-directed RNA 100.0 6E-170 1E-174 1512.5 54.4 785 7-909 19-889 (1060)
6 cd00653 RNA_pol_B_RPB2 RNA pol 100.0 1E-162 3E-167 1487.5 56.5 629 15-909 1-690 (866)
7 TIGR02013 rpoB DNA-directed RN 100.0 8E-158 2E-162 1451.4 60.5 708 8-909 13-897 (1065)
8 PRK00405 rpoB DNA-directed RNA 100.0 5E-156 1E-160 1442.5 62.7 722 10-909 22-940 (1112)
9 CHL00001 rpoB RNA polymerase b 100.0 8E-153 2E-157 1399.8 59.6 728 8-909 8-874 (1070)
10 CHL00207 rpoB RNA polymerase b 100.0 6E-141 1E-145 1287.9 60.9 730 9-909 4-870 (1077)
11 PRK09603 bifunctional DNA-dire 100.0 3E-129 7E-134 1221.1 56.7 750 10-909 22-1148(2890)
12 PRK14844 bifunctional DNA-dire 100.0 4E-127 8E-132 1198.4 58.7 748 10-909 27-1141(2836)
13 PRK07225 DNA-directed RNA poly 100.0 2E-109 3E-114 970.9 35.8 374 516-909 4-418 (605)
14 TIGR03670 rpoB_arch DNA-direct 100.0 1E-109 3E-114 970.6 32.8 371 519-909 1-412 (599)
15 PRK09606 DNA-directed RNA poly 100.0 4.5E-97 1E-101 862.2 45.4 437 9-504 12-492 (494)
16 PF00562 RNA_pol_Rpb2_6: RNA p 100.0 3E-78 6.5E-83 683.1 15.3 264 639-909 1-296 (386)
17 PF04563 RNA_pol_Rpb2_1: RNA p 100.0 2.3E-36 5.1E-41 314.8 13.7 107 14-122 1-149 (203)
18 PF04565 RNA_pol_Rpb2_3: RNA p 99.9 1.1E-27 2.4E-32 204.6 4.7 67 407-473 1-68 (68)
19 PF04561 RNA_pol_Rpb2_2: RNA p 99.9 3.7E-22 8E-27 205.2 5.8 174 123-322 1-190 (190)
20 PF04566 RNA_pol_Rpb2_4: RNA p 99.5 1.8E-13 3.9E-18 115.1 9.5 63 519-590 1-63 (63)
21 PF06883 RNA_pol_Rpa2_4: RNA p 99.1 7.8E-11 1.7E-15 97.2 5.5 58 526-583 1-58 (58)
22 PF04567 RNA_pol_Rpb2_5: RNA p 98.5 4.3E-08 9.3E-13 78.2 2.5 40 595-634 7-48 (48)
23 COG0085 RpoB DNA-directed RNA 97.6 6E-05 1.3E-09 93.6 6.5 73 627-719 526-598 (1060)
24 KOG0215 RNA polymerase III, se 97.2 0.00017 3.7E-09 85.3 2.2 350 68-478 190-552 (1153)
25 KOG0214 RNA polymerase II, sec 95.6 0.0062 1.4E-07 73.6 2.5 233 650-903 680-933 (1141)
26 PHA03394 lef-8 DNA-directed RN 93.8 0.096 2.1E-06 63.4 6.1 60 836-898 696-756 (865)
27 PF14251 DUF4346: Domain of un 52.8 6.7 0.00015 37.3 1.1 14 97-110 10-23 (119)
28 PF04941 LEF-8: Late expressio 49.2 21 0.00046 43.6 4.7 31 311-341 211-241 (748)
29 PF13375 RnfC_N: RnfC Barrel s 28.4 1.8E+02 0.0038 27.2 6.4 52 784-840 45-96 (101)
30 PF13533 Biotin_lipoyl_2: Biot 21.9 55 0.0012 26.2 1.5 16 784-799 17-32 (50)
No 1
>KOG0216 consensus RNA polymerase I, second largest subunit [Transcription]
Probab=100.00 E-value=2.3e-226 Score=1891.78 Aligned_cols=867 Identities=53% Similarity=0.891 Sum_probs=819.3
Q ss_pred CCCCcCCccCchhhHHHHHHHHHHHHHHhHHHHH--------------------------------------------HH
Q 002545 2 ARKKSADFEPLRELVRHHIESFDYMLDEGLSEMF--------------------------------------------DH 37 (910)
Q Consensus 2 ~~~~~~~~~~~~~Lv~~hi~SFn~Fi~~gl~~i~--------------------------------------------~e 37 (910)
|+.+...+..+++++++|++|||...+.||.... .|
T Consensus 5 ~~k~~p~fp~l~~a~~pHi~sfnal~~~gll~~~v~~~~ek~~~~~g~kis~~ve~i~iakP~l~~~~~ss~~r~lyPaE 84 (1111)
T KOG0216|consen 5 PPKDYPSFPELQDAASPHIDSFNALTNGGLLNAGVAGIAEKVPLKAGDKISMKVESIQIAKPMLSDKVHSSDTRKLYPAE 84 (1111)
T ss_pred CcccCccchhhhhhhhhhhccccchhhhhHHHHHhhchhhhcccccCCceeEEEEEEEecCCCCCccccccccccccchh
Confidence 4555566778999999999999999998887664 89
Q ss_pred HHHcCCeeeeEEEEEEEEEEecCCCceeeeEeeecccceeecCCCccCCCCChHHHHhcccccccCCcEEEEcCceeEEE
Q 002545 38 CRQAKISYTGKLMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFR 117 (910)
Q Consensus 38 cR~r~~TY~~~l~v~i~~~~~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~~~~~el~~~~E~~~D~GGYFIInG~EKVIr 117 (910)
||+|.+||+|.+.|++.|.+| ++........+|.+||||+|++|||.|++++||++.+|++.|+||||||||+|||||
T Consensus 85 cRqR~~TY~Gkl~v~v~wsVN--g~~~~~e~~dlG~vPIMlrSklChL~g~sp~eLV~hkEe~~EmGGYFIvNGIEKvIR 162 (1111)
T KOG0216|consen 85 CRQRGLTYKGKLVVRVSWSVN--GGHVVIEKRDLGHVPIMLRSKLCHLNGASPKELVKHKEESSEMGGYFIVNGIEKVIR 162 (1111)
T ss_pred HhhccceecceEEEEEEEEEC--CeeeeeeeeecCccceEEeccccccCCCChHHHhhccCchhhcCcEEEEcChHHhhh
Confidence 999999999999999999999 888878889999999999999999999999999999999999999999999999999
Q ss_pred EEEeecCCccEEEEeccccCCCCcceeeEEEEEeeecCCCceEEEEEEEeCCeEEEEEEeecccccccHHHHHHhccCCC
Q 002545 118 SVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTN 197 (910)
Q Consensus 118 ~qi~~~~N~~~~~~r~~~~~~~~~~t~~~v~~r~~~~~~~~~~~~l~y~~~g~~~l~~~~~~~~~~IPi~ilLkALg~~s 197 (910)
++|+++||+|+++.|++|++||..||+|++++|||++|+++.+++|||+.||.+.++|.++|.+|.+|++++||||...|
T Consensus 163 mLIm~RRNHPiAiIR~Sfk~RG~~yS~yGVsmRcVReDqSsvtn~LHYLnnGtv~~~F~~rK~eylvPv~lILKAL~~ts 242 (1111)
T KOG0216|consen 163 MLIMPRRNHPIAIIRPSFKDRGSSYSDYGVSMRCVREDQSSVTNVLHYLNNGTVMFRFSHRKREYLVPVVLILKALTNTT 242 (1111)
T ss_pred hheeccCCCceEEechhhhhcCCCccccceEEEEeccccccceeEEEEecCCcEEEEEEEeeeeehhhHHHHHHHHhccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhcccccchhhcccCCCCChhhHHHHHHHHHHHHhcccccHHHHHHHHhhcccccccCCCCccHHHHHHHHHHh
Q 002545 198 DLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRD 277 (910)
Q Consensus 198 D~EI~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i~t~~~al~yLg~~fr~~~~~~~~~~~~~~g~~~L~~ 277 (910)
|+|||+.++ +++..++|+.++++.||+++++++++|+++|++|||++||+.+...+.+++.++|+++|++
T Consensus 243 DeEIf~~lv----------~g~~gdqfl~~rv~~mLr~v~ee~l~trtqcl~yLGs~FRaVl~~v~~~~D~evg~fILr~ 312 (1111)
T KOG0216|consen 243 DEEIFEGLV----------GGDEGDQFLTSRVELMLREVQEENLFTRTQCLQYLGSRFRAVLDFVPEQPDLEVGRFILRE 312 (1111)
T ss_pred HHHHHHHHh----------CCccCceeHHHHHHHHHHHHhhcccccHHHHHHHHhhhhhhhhcCCCCCchHHHHHHHHHh
Confidence 999999997 4778899999999999999999999999999999999999877655569999999999999
Q ss_pred HhccCCCCCcchHHHHHHHHHHHHhhcCCCCCCCCcccccccEEcccchhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCc
Q 002545 278 YIFVHLNDNNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKK 357 (910)
Q Consensus 278 ~ll~Hl~~~~~K~~~L~~Mi~kLl~~~~g~~~~Dd~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~~~~i~~~~~~~~~~ 357 (910)
+++.||+++.+||.+|++|++||++++.|+|.+||+|+.+|||++++|+|++.+|+|++++|+..++.++++.+.+.+.+
T Consensus 313 ~VlvHLd~~~DKF~lLifmiqKL~slv~ge~~~dnpDs~q~qEil~~ghl~~~~LkEriEe~l~~~~~~vr~~l~~~~~~ 392 (1111)
T KOG0216|consen 313 YVLVHLDSDEDKFNLLIFMIQKLYSLVDGECTPDNPDSPQNQEILLPGHLYGSILKERIEEWLRFISAQVRRDLYKLGFK 392 (1111)
T ss_pred heEEEecccHHHHHHHHHHHHHHHHHhcCCcCCCCCCChhhhhcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhcCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999886667
Q ss_pred ccccchHHHHHHHhcCCCcchHHHHHhHhcccCcccccccccccccceEEEccccchhhHhhhhcccccCCccccccccc
Q 002545 358 FDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTS 437 (910)
Q Consensus 358 ~~~~~~~~~~~~~~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~sGvsqvleRln~~~~lSH~Rrv~rg~~~~~~k~t~ 437 (910)
.++.+..++.+++.+.+ ..|+++|++||||||++++++++++|++|++++|||+|++|||||||.||||++|++|++|+
T Consensus 393 ~~~~~~~~i~~~~~r~~-~~Ig~~me~fLsTGnl~s~sgldLqQ~sG~tv~AEriNf~RflShFRavhRGa~f~~mrTTt 471 (1111)
T KOG0216|consen 393 EDFLDISAIRKVFMRTN-GNIGRKMEYFLSTGNLVSRSGLDLQQTSGYTVVAERINFYRFLSHFRAVHRGAFFAEMRTTT 471 (1111)
T ss_pred chhHhHHHHHHHHhhcc-ccHHHHHHHHHhcCCeeeccchhhHhhcCcEEehhhhhHHHHHHHHHHHhcccchhheeehh
Confidence 77777788888998876 49999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCCCCccccccCCCCCCccccccccccceeEEeeecCCCCcccccchhhHHHHHHHHhcCCeecCCccccCCCCcee
Q 002545 438 VRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVL 517 (910)
Q Consensus 438 vR~Lhps~wG~iCPveTPEG~~cGLv~~LA~~~~Is~~~~~~~~~~~~~~~~~~i~~~L~~lG~~~~~~~~~~~~~~~~~ 517 (910)
+|||.|++|||+||||||||+||||+||||..|+|++..++.+ .+..+|.++||.|... .... ....|
T Consensus 472 vRKLlPEsWGFlCPVHTPDG~PCGlLnH~t~~c~I~t~~dd~s----------~ip~~L~~~Gm~p~~~-~~~~-G~~l~ 539 (1111)
T KOG0216|consen 472 VRKLLPESWGFLCPVHTPDGAPCGLLNHMTRTCRIVTRPDDVS----------FIPSILFELGMVPSSH-LVEA-GEPLY 539 (1111)
T ss_pred hHhhCchhhcccccccCCCCCchhHHHhhhhheeEeecCcchh----------hhhHHHHhcCCCchhc-cccC-CCcee
Confidence 9999999999999999999999999999999999999887753 3899999999998732 2222 23479
Q ss_pred EEEECCEEEeeecCccHHHHHHHHHHHHHhcCCCCCCCceEEEEEcCCCCCCCceEeecCCCceeceEEeecCCCCCCCc
Q 002545 518 SVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSEESQN 597 (910)
Q Consensus 518 ~V~lnG~~iG~~~~~~~~~~~~~lr~~k~~~~~~i~~~~eI~~v~~~~~~~~~~i~i~td~gR~~RPv~~~~~~~~~~g~ 597 (910)
+|++||+++|+++...+..+++.||++|......||.++||+||+.+.+++||++||++++||++|||.+++.+ .
T Consensus 540 ~VlldGk~vG~~s~~~a~~i~~~lR~~Kv~~p~~iP~~leIg~Vp~s~~gqyPglyi~s~~aR~~RpV~nl~~~-----~ 614 (1111)
T KOG0216|consen 540 PVLLDGKVVGWVSSPLAKKIVDYLRYYKVEAPAVIPNDLEIGYVPTSTNGQYPGLYIFSGPARMIRPVKNLSLD-----S 614 (1111)
T ss_pred EEEECCEEEEeeccHHHHHHHHHHHHHhhcCcccCCCcceEeeeecCCCCCCceeEEecCchhhhhehhccccC-----c
Confidence 99999999999999999999999999999877789999999999999999999999999999999999999887 8
Q ss_pred eeeeCccceeeeeeecCCCCCCCCCCCCCceecccCCCccccceeecccCCCCCCcchhhhhhhccccccccceeEEEEe
Q 002545 598 IELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFR 677 (910)
Q Consensus 598 iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~p~~~ls~~asliPF~~hNqspRn~yq~~M~KQaig~~~~n~~~R 677 (910)
+||||++||+++.||+.++++.+.. +||.|++|+.+||++|+||||+|||||||||||||||||+||+|.++|..|
T Consensus 615 ~e~iG~fEQvym~i~~~~~e~~~~v----~th~E~~pt~~ls~~anliP~sD~NQSPRNmYQCQMgKQtmg~p~~a~~~r 690 (1111)
T KOG0216|consen 615 VEWIGPFEQVYMNIAIDPKEIFPDV----TTHVELHPTGILSIVANLIPFSDHNQSPRNMYQCQMGKQTMGTPGHALRTR 690 (1111)
T ss_pred hhhcccHHHhhhhhccchhhcCCCc----ceeEEecccchHhHhhcCccccccCCCchhHHHhhhhhhhcCCccccchhc
Confidence 9999999999999999999998875 899999999999999999999999999999999999999999999999999
Q ss_pred ccCceeecCCCCeeeEecccccccCccccCCCceeeEEEEeccCCCcccceeeeccccccCcceeeEEEEEEEEeeccCC
Q 002545 678 ADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGN 757 (910)
Q Consensus 678 ~D~~~y~L~~pQ~Plv~t~~~~~~~~~~~~~G~N~iVav~~y~Gyn~EDaiiink~s~~rG~~~~~~~~~~~~~~~~~~~ 757 (910)
+|+|+|+|++||.|+|++..++.+++|++|.|+||+|||+|||||||||||||||+|+||||+++++||++.++|.++..
T Consensus 691 adnklYrlqt~qsP~vr~~~y~~y~~d~yp~GtNaiVAVisyTgyDMeDAmiiNK~s~eRGf~~G~vykte~i~L~~~~~ 770 (1111)
T KOG0216|consen 691 ADNKLYRLQTPQSPIVRPELYDTYGMDDYPNGTNAIVAVISYTGYDMEDAMIINKSSYERGFAYGTVYKTEKIDLSKKRS 770 (1111)
T ss_pred ccCceEEecCCCCceeecccccccccccCCCCcceEEEEEeecccChhhhhhhchhhhhccccceeEEeeeeechhhccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999866553
Q ss_pred CcCccceeecc-CCCChhhhcccCCCCCcccCceecCCCcEEEeeccCCCceeeeeecCCCceEEEEEEEEecCCCCCCe
Q 002545 758 KVDRGQKLFRR-NKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTTNSWRTNSRKGSESVFVDYVAVDMKNSKNLPQ 836 (910)
Q Consensus 758 ~~~~~~~~f~~-~~~~~~~~~~ld~dG~~~~g~~v~~gd~l~~~~~~~~~~~~~~~~~~~e~g~v~~v~~~~~~~~~~~~ 836 (910)
+ ...|.. |...+ .++||+||||.+|+++..||++++.|+...++++..+|++.|+|+||.|++..++.|+..+
T Consensus 771 r----~~~F~~~p~~~~--~~~ld~dgLP~~G~kl~~~dp~~~y~d~~t~~~~~~~~~~~ep~~vd~vr~~~~~~~~~~k 844 (1111)
T KOG0216|consen 771 R----SKHFGRSPGEPE--LKKLDADGLPSIGQKLEYGDPYYAYFDEETGKTRIKKYHGTEPGIVDEVRVLGNDMGDQEK 844 (1111)
T ss_pred c----eeeeeeCCCCcc--ccccCCCCCCCCcccccCCCcEEEEEcccCCceEEEEecCCCCeeeEEEEEccccCCCccc
Confidence 2 445654 33333 6889999999999999999999999999999999999999999999999999998876558
Q ss_pred EEEEEEeeeeCCCcccceeccCCCccEEeeeecCcCcCccCCCCCcCcEEeCCCCccccccHHHHHHHhhccc
Q 002545 837 KANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKE 909 (910)
Q Consensus 837 ~v~i~~r~~R~p~iGDKf~sRHGqKGv~s~i~~~~dMPf~~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gK~ 909 (910)
.+.|++|.+|+|.||||||||||||||||..||.+||||| ++|++|||||||||||||||||||+|+||||+
T Consensus 845 ~~~i~~Ri~R~p~IGDKFsSRhGQKGicS~~wP~~dmPFt-esGm~PDii~NPH~FPSRMTIgM~iEs~AgK~ 916 (1111)
T KOG0216|consen 845 CATITLRIPRNPIIGDKFSSRHGQKGICSQKWPTIDMPFT-ESGMVPDIIINPHAFPSRMTIGMLIESMAGKA 916 (1111)
T ss_pred eEEEEEEecCCCcccchhhhhccccccccccCCCCCCCcc-ccCcCcceeeCCCCCcccccHHHHHHHHhchh
Confidence 8999999999999999999999999999999999999999 99999999999999999999999999999996
No 2
>PRK08565 DNA-directed RNA polymerase subunit B; Provisional
Probab=100.00 E-value=1.8e-200 Score=1853.45 Aligned_cols=824 Identities=28% Similarity=0.447 Sum_probs=718.7
Q ss_pred ccCchhhHHHHHHHHHHHHHHhHHHHH---------------------------------------HHHHHcCCeeeeEE
Q 002545 9 FEPLRELVRHHIESFDYMLDEGLSEMF---------------------------------------DHCRQAKISYTGKL 49 (910)
Q Consensus 9 ~~~~~~Lv~~hi~SFn~Fi~~gl~~i~---------------------------------------~ecR~r~~TY~~~l 49 (910)
+...++|++||+||||||+++||++++ +|||+|++||+|+|
T Consensus 8 ~~~~~~Lv~~qidSFn~Fi~~gL~~iv~~~~pI~~~~~~~~L~f~~i~l~~P~~~~~~~~~~~l~P~ecR~r~lTYsa~l 87 (1103)
T PRK08565 8 YFKEKGLVRQHLDSYNDFIERGLQEIVDEFGEIKTEIPGLKIVLGKIRVGEPEIKEADGSERPITPMEARLRNLTYAAPL 87 (1103)
T ss_pred HhcccChHHHHHHHHHHHHHHhHHHHHHhcCCEEecCCCEEEEEEEEEECCCcccccccccCCCCHHHHHhcCCCcceEE
Confidence 456789999999999999999999998 89999999999999
Q ss_pred EEEEEEEEecCCCceeeeEeeecccceeecCCCccCCCCChHHHHhcccccccCCcEEEEcCceeEEEEEEeecCCccEE
Q 002545 50 MADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMS 129 (910)
Q Consensus 50 ~v~i~~~~~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~~~~~el~~~~E~~~D~GGYFIInG~EKVIr~qi~~~~N~~~~ 129 (910)
+|+++++.+ +.+.+.+++++|+|||||+|++|||++++++||++.||||+|+||||||||+|||||+||++++|+|++
T Consensus 88 ~v~i~~~~~--~~~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~p~D~GGYFIING~ERVI~~q~~~s~n~~~~ 165 (1103)
T PRK08565 88 YLTMIPVEN--GIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQEDLAPNRVLV 165 (1103)
T ss_pred EEEEEEEEC--CeeeEEEEEEeccCCeEeCCCcccCCCCCHHHHHhcCCCccCCCCeEEECCcEEEEEEEEecCCCEEEE
Confidence 999999765 555666789999999999999999999999999999999999999999999999999999999999988
Q ss_pred EEeccccCCCCcceeeEEEEEeeecCCCceEEEEEEEeCCeEEEEEEeecccccccHHHHHHhccCCCHHHHHHHhcccc
Q 002545 130 MVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCY 209 (910)
Q Consensus 130 ~~r~~~~~~~~~~t~~~v~~r~~~~~~~~~~~~l~y~~~g~~~l~~~~~~~~~~IPi~ilLkALg~~sD~EI~~~i~~~~ 209 (910)
+.+. ++..++.++..+++ +. ..+.|+.++|+.+|.++++|... +++||+++||||||..||+||++.|+.
T Consensus 166 ~~~~----~~~~~~~~a~i~s~-~~-~~~~~~~l~~~~~g~i~~~~~~~--~~~IPi~illkALG~~sD~eI~~~i~~-- 235 (1103)
T PRK08565 166 DKGE----AGSSITHTAKVISS-RA-GYRAQVTVERRKDGTIYVSFPAV--PGKIPFVILMRALGLETDRDIVYAVSL-- 235 (1103)
T ss_pred EEec----CCCcceEEEEEEec-cC-CCcceEEEEEecCCeEEEEEcCc--ccEeeHHHHHHHcCCCCHHHHHHHhcc--
Confidence 7543 34455544444444 33 23368999999999999999854 457999999999999999999999962
Q ss_pred cchhhcccCCCCChhhHHHHHHHHHHHHhccc-ccHHHHHHHHhhcccccccCCCCccHHHHHHHHHHhHhccCCCC---
Q 002545 210 DEKYKKEKGAVGSPLVSERVKIILAEVQDLSL-TTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHLND--- 285 (910)
Q Consensus 210 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i-~t~~~al~yLg~~fr~~~~~~~~~~~~~~g~~~L~~~ll~Hl~~--- 285 (910)
+..+.+.+...+++. ..+ .|+++|+.|||++|++. .++.++.++|+++|++++|||++.
T Consensus 236 ------------~~~~~~~l~~~l~~~--~~~~~t~~~al~~ig~~~~~~---~~~~~~~e~~~~~L~~~ll~Hig~~~~ 298 (1103)
T PRK08565 236 ------------DPEIQQELLPSLEQA--SSIAATVEDALDYIGKRVAIG---QPREYRIERAEQILDKYLLPHLGTSPE 298 (1103)
T ss_pred ------------cHHHHHHHHHHHHHh--hccccCHHHHHHHHHHhccCC---CCCccHHHHHHHHHHhhCcccCCCccc
Confidence 111222333333332 235 79999999999999853 345677899999999999999995
Q ss_pred -CcchHHHHHHHHHHHHhhcCCCCCCCCcccccccEEcccchhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCcccccchH
Q 002545 286 -NNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLA 364 (910)
Q Consensus 286 -~~~K~~~L~~Mi~kLl~~~~g~~~~Dd~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~ 364 (910)
+..|+++|++|++||+.++.|.+.+||+|||+||||+++|+||+.+||+.|+++++.++..+.+.+.+ ++..+
T Consensus 299 ~~~~K~~~L~~Mi~kLl~l~~g~~~~DD~D~l~NKRv~l~G~Ll~~~fr~~l~~~~~~ik~~l~~~~~~-~~~~~----- 372 (1103)
T PRK08565 299 DRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYAR-GRKLD----- 372 (1103)
T ss_pred chhHHHHHHHHHHHHHHhhhcCCCCCCCccccCCcEEccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-cccCC-----
Confidence 34799999999999999999999999999999999999999999999999999999999998876654 33222
Q ss_pred HHHHHHhcCCCcchHHHHHhHhcccCcccccccccccccceEEEccccchhhHhhhhcccccCCcccccccccccccCCC
Q 002545 365 NIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTSVRKLLPE 444 (910)
Q Consensus 365 ~~~~~~~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~sGvsqvleRln~~~~lSH~Rrv~rg~~~~~~k~t~vR~Lhps 444 (910)
++.+++ ++.||++|++|||||||.+ |++||||+|+|+||+|+|||||||+. ++.+++|.++||+||||
T Consensus 373 -~~~~i~---~~~It~~i~~~~sTGnw~~-------~~sGvSq~ldr~N~l~~lSh~Rrv~s-~~~r~~~~~~vR~Lhps 440 (1103)
T PRK08565 373 -LRAIVR---PDIITERIRHALATGNWVG-------GRTGVSQLLDRTNYLSTLSHLRRVVS-PLSRGQPHFEARDLHGT 440 (1103)
T ss_pred -HHHhcc---cchhhHHHHHHHhcCcccc-------CCcceEEecccCCHHHHHHHHhhccC-CcccCCCCccccccChh
Confidence 333443 3489999999999999964 67999999999999999999999986 45689999999999999
Q ss_pred CccccccCCCCCCccccccccccceeEEeeecCCCCcccccchhhHHHHHHHHhcCCeecCCccccCCCCceeEEEECCE
Q 002545 445 SWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGR 524 (910)
Q Consensus 445 ~wG~iCPveTPEG~~cGLv~~LA~~~~Is~~~~~~~~~~~~~~~~~~i~~~L~~lG~~~~~~~~~~~~~~~~~~V~lnG~ 524 (910)
||||+||+|||||++||||||||++|+|++..+.+ .|.++|.++|+.++. .+........++|||||+
T Consensus 441 ~wG~iCPveTPEG~~cGLv~~LA~~a~It~~~~~~-----------~i~~~l~~~G~~~~~-~~~~~~~~~~~~V~lnG~ 508 (1103)
T PRK08565 441 QWGRICPFETPEGPNCGLVKNLALMAQISVGVDEE-----------EVEEILYELGVVPVE-EAREEEYISWSRVYLNGR 508 (1103)
T ss_pred hccccCCCCCCCccccchhhhhhcccccccCCChH-----------HHHHHHHHcCCCchh-hcCcccCCCceEEEECCE
Confidence 99999999999999999999999999999875443 588999999998762 222222345589999999
Q ss_pred EEeeecCccHHHHHHHHHHHHHhcCCCCCCCceEEEEEcCCCCCCCceEeecCCCceeceEEeecCCCC-----------
Q 002545 525 VVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSE----------- 593 (910)
Q Consensus 525 ~iG~~~~~~~~~~~~~lr~~k~~~~~~i~~~~eI~~v~~~~~~~~~~i~i~td~gR~~RPv~~~~~~~~----------- 593 (910)
|+|+++ ++..|++.||.+||+| .|+.++||.+++. +.+++|+||||+||++|||+++++++.
T Consensus 509 ~iG~~~--~~~~l~~~lR~~Rr~g--~i~~~v~I~~~~~---~~~~~i~I~sd~GRl~RP~~~v~~g~~~~~~~~~~~l~ 581 (1103)
T PRK08565 509 LIGYHP--DGEELAEKIRELRRSG--KISDEVNVAYIET---GEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLK 581 (1103)
T ss_pred EEEEEC--CHHHHHHHHHHHhhcC--CCCCeEEEEEccc---cccceEEEecCCceeeeeEEEEecCceeccHHHHHHhh
Confidence 999984 5899999999999998 5899999988753 568999999999999999999987642
Q ss_pred ----------CCCceeeeCccceeeeeeecCCCCCCCCCCCCCceecccCCCccccceeecccCCCCCCcchhhhhhhcc
Q 002545 594 ----------ESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMA 663 (910)
Q Consensus 594 ----------~~g~iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~p~~~ls~~asliPF~~hNqspRn~yq~~M~ 663 (910)
..|.+||||++||++++||++++++... +||+||+|++|||++||+|||+||||||||||||||+
T Consensus 582 ~~~~~~~~l~~~g~iEyid~~Ee~~~~Ia~~~~~l~~~-----~th~Ei~p~~ilsv~asliPF~~hNqspRn~yq~~M~ 656 (1103)
T PRK08565 582 KGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTPE-----HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMA 656 (1103)
T ss_pred ccccchhhHhhcCcEEeeCHHHhcCcEEeccccccCcc-----eeccccCCccccceeeeccCCcccCcccchhhhhhhh
Confidence 2479999999999999999999988543 6999999999999999999999999999999999999
Q ss_pred ccccccceeEEEEeccCceeecCCCCeeeEecccccccCccccCCCceeeEEEEeccCCCcccceeeeccccccCcceee
Q 002545 664 KQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQ 743 (910)
Q Consensus 664 KQaig~~~~n~~~R~D~~~y~L~~pQ~Plv~t~~~~~~~~~~~~~G~N~iVav~~y~Gyn~EDaiiink~s~~rG~~~~~ 743 (910)
|||||++.+|+.+|.|++.|+|+|||+|||+|+.++..+++++|+|+||+||||||+|||||||||+||+|+||||||++
T Consensus 657 KQa~g~~~~n~~~r~d~~~~~l~~pQ~Plv~t~~~~~~~~~~~p~G~N~iVAv~sy~GYn~EDaiIink~s~~rG~~~s~ 736 (1103)
T PRK08565 657 KQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARST 736 (1103)
T ss_pred hcccccccccceEeecCCcceeecCceeEEEeccccccccccCCCCeeEEEEEEcccCcchHHhhhhhhhhhhcCCceEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEEEEeeccCCCcCccceeeccCC--C----ChhhhcccCCCCCcccCceecCCCcEEEeeccC-------------
Q 002545 744 IYQTETIDLSDDGNKVDRGQKLFRRNK--D----AKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKT------------- 804 (910)
Q Consensus 744 ~~~~~~~~~~~~~~~~~~~~~~f~~~~--~----~~~~~~~ld~dG~~~~g~~v~~gd~l~~~~~~~------------- 804 (910)
+|++|+++..... . ...+.|+.|. . ....+++||+||+|++|+.|++||||+||++|.
T Consensus 737 ~~~~~~~~~~~~~--~-~~~~~~~~~~~~~~~~~~~~~~~~Ld~dGi~~~G~~v~~gdili~k~~p~~~~~~~~~~~~~~ 813 (1103)
T PRK08565 737 FFRTYETEERKYP--G-GQEDKIEIPEPNVRGYRGEEYYRKLDEDGIVSPEVEVKGGDVLIGKTSPPRFLEELEELSLGL 813 (1103)
T ss_pred EEEEEEEEeeecC--C-CCceEEecCCCcccccCchhhhhcCCCCCCcCCCcEEcCCCEEEEEecCCCCCcchhhccccC
Confidence 9999988653221 1 1223455442 1 234579999999999999999999999998762
Q ss_pred -CCceeeeeecCCCceEEEEEEEEecCCCCCCeEEEEEEeeeeCCCcccceeccCCCccEEeeeecCcCcCccCCCCCcC
Q 002545 805 -TNSWRTNSRKGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRP 883 (910)
Q Consensus 805 -~~~~~~~~~~~~e~g~v~~v~~~~~~~~~~~~~v~i~~r~~R~p~iGDKf~sRHGqKGv~s~i~~~~dMPf~~~~G~~p 883 (910)
..++.+++++.+|+|+||+|.++.++++ .+.|+|++|+.|+|+||||||||||||||||++||+|||||| +||++|
T Consensus 814 ~~~~~~s~~~~~~e~g~V~~V~~~~~~~~--~~~vkv~ir~~R~p~iGDKfssRhGqKGv~s~i~~~edmPf~-~~G~~p 890 (1103)
T PRK08565 814 QERRDTSVTVRHGEKGIVDTVLITESPEG--NKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFT-EDGIVP 890 (1103)
T ss_pred CccccceEEecCCCceEEEEEEEEecCCC--cEEEEEEEEEEecCchhhhhhhhccCcceeeeecccccCCcC-CCCCCc
Confidence 2456688999999999999999987654 478999999999999999999999999999999999999999 999999
Q ss_pred cEEeCCCCccccccHHHHHHHhhccc
Q 002545 884 DLIINPHAFPSRMTIAMLLESVAAKE 909 (910)
Q Consensus 884 DiI~NPh~~PSRMtiGql~E~~~gK~ 909 (910)
||||||||||||||||||+|+++||+
T Consensus 891 DiI~NPh~~PSRMtiG~l~E~~~gk~ 916 (1103)
T PRK08565 891 DLIINPHAIPSRMTVGQLLESIAGKV 916 (1103)
T ss_pred cEEECCCCCcccccHHHHHHHHHHHH
Confidence 99999999999999999999999996
No 3
>KOG0214 consensus RNA polymerase II, second largest subunit [Transcription]
Probab=100.00 E-value=1.1e-192 Score=1630.63 Aligned_cols=841 Identities=28% Similarity=0.419 Sum_probs=730.5
Q ss_pred CccCchhhHHHHHHHHHHHHHHhHHHHH------------------------------------------------HHHH
Q 002545 8 DFEPLRELVRHHIESFDYMLDEGLSEMF------------------------------------------------DHCR 39 (910)
Q Consensus 8 ~~~~~~~Lv~~hi~SFn~Fi~~gl~~i~------------------------------------------------~ecR 39 (910)
++...++|+++|++|||.||+.++++|+ +|||
T Consensus 11 ~~f~ekglvrqQldsFdeFiq~~~qeiv~~~p~i~l~~~~qh~~~~~~r~~l~f~qiylskP~~~e~dg~~~~m~p~eAR 90 (1141)
T KOG0214|consen 11 AYFEEKGLVRQQLDSFDEFIQQTLQEIVADSPKIELQDEAQHTQENPARYQLFFEQIYLSKPTHTESDGSTSTMFPNEAR 90 (1141)
T ss_pred hhhcccchHHHHHHHHHHHHHHHHHHHHhcCCCceehhhhhhhccCccceEEEeeeEEEecccccccCCCccccCchhhH
Confidence 4567899999999999999999999999 9999
Q ss_pred HcCCeeeeEEEEEEEEEEecCC---CceeeeEeeecccceeecCCCccCCCCChHHHHhcccccccCCcEEEEcCceeEE
Q 002545 40 QAKISYTGKLMADVEFQYLDAG---SPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVF 116 (910)
Q Consensus 40 ~r~~TY~~~l~v~i~~~~~~~~---~~~~~~~v~iG~iPIMv~S~~C~L~~~~~~el~~~~E~~~D~GGYFIInG~EKVI 116 (910)
+|++|||+||||++...+.... ...+.+.|+||+||||+||..|.|+++++++|.++||||+|+||||||||+|||+
T Consensus 91 lrnLTYSspLyVd~~k~~~~~~~~~~~~~~qkvfIGkIPiMlrS~~C~l~~~~d~dl~~l~eCp~DqgGyfIINGseKVl 170 (1141)
T KOG0214|consen 91 LRNLTYSSPLYVDATKIVKTSRDEVEDMQEQKVFIGKIPIMLRSSYCLLSGLTDKDLTELGECPYDQGGYFIINGSEKVL 170 (1141)
T ss_pred hhhcccccceEEEeEEEEeeccccccccccceeeEeccceeeehhhhhhcccchhhhhhccCCCcCCCceEEEcCceeee
Confidence 9999999999999998775332 2345778999999999999999999999999999999999999999999999999
Q ss_pred EEEEeecCCccEEEEeccccCCCCcceeeEEEEEeeecCCCceEEE--EEEEe-CC---eEEEEEEeecccccccHHHHH
Q 002545 117 RSVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLK--LYYLL-NG---SVRLGFWLQGKEYLLPVGIVL 190 (910)
Q Consensus 117 r~qi~~~~N~~~~~~r~~~~~~~~~~t~~~v~~r~~~~~~~~~~~~--l~y~~-~g---~~~l~~~~~~~~~~IPi~ilL 190 (910)
+.|+.++.|.+.+++. ..+.-..|..++||+.+..++...+ +..+. ++ .+.+.+++.|+ +||+++|+
T Consensus 171 IAQe~matn~vyvf~k-----~~p~~~ay~~EirS~le~~sR~~stl~v~~~ar~~~gq~i~~tlpyikq--eIPI~ilf 243 (1141)
T KOG0214|consen 171 IAQEKMATNIVYVFKK-----AHPGTYAYTGEIRSCLERSSRFISTLSVNMDARAGKGQEIIATLPYIKQ--EIPILILF 243 (1141)
T ss_pred eehhhccCceEEEEec-----CCCCceeEeeeeehhhhccCCCcceeeeeeccccCCCceEEEEeeeecc--cCcEEEEe
Confidence 9999999998887754 2222345778899876654443333 33333 33 35566777776 59999999
Q ss_pred HhccCCCHHHHHHHhcccccchhhcccCCCCChhhHHHHHHHHHHHHhcccccHHHHHHHHhhcccccccCCCCccHHHH
Q 002545 191 KALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAV 270 (910)
Q Consensus 191 kALg~~sD~EI~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i~t~~~al~yLg~~fr~~~~~~~~~~~~~~ 270 (910)
||||+.+|+||+++|+ || .+|..+.+.+...+++. +-+..++.||+|+|++-.. .+..++...++
T Consensus 244 rALG~v~dreILehIc--Yd---------~~D~em~e~lkpsieea--fviq~qn~ALdfig~rga~--~Gvtkekri~y 308 (1141)
T KOG0214|consen 244 RALGFVSDREILEHIC--YD---------FDDAEMFESLKPSIEEA--FVIQEQNVALDFIGQRGAC--IGVTKEKRIKY 308 (1141)
T ss_pred hhhcCCccHHHHHhhc--CC---------CCcHHHHHHhhhhhhhh--hhhhhhHHHHHHHHhcCCC--CCCCcchhhHH
Confidence 9999999999999998 54 23444444444444442 3577888999999998432 13556778999
Q ss_pred HHHHHHhHhccCCCCC----cchHHHHHHHHHHHHhhcCCCCCCCCcccccccEEcccchhhHHHHHHHHHHHHHHHHHH
Q 002545 271 AETVIRDYIFVHLNDN----NDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKL 346 (910)
Q Consensus 271 g~~~L~~~ll~Hl~~~----~~K~~~L~~Mi~kLl~~~~g~~~~Dd~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~~~~ 346 (910)
|+++|.+.+|||++.- ..|++||+||+++|+.++.|++.+||+||++|||++++|+||..+||..|+++++++.+.
T Consensus 309 akdiLqKe~lPhi~~~e~~etkKA~fLGYmi~rlll~aLgRr~~ddRDHfG~KRLDlaGpLLa~lfR~lf~~l~rd~~~~ 388 (1141)
T KOG0214|consen 309 AKEILQKELLPHVGLGEICETKKAYFLGYMVHRLLLAALGRRELDDRDHFGNKRLDLAGPLLAKLFRSLFAKLLRDVTRY 388 (1141)
T ss_pred HHHHHHHHhccccccchhhhhhHHHHHHhhHHHHHHHHcCCCCccchhhccccchhhchhHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999953 499999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhcCCcccccchHHHHHHHhcCCCcchHHHHHhHhcccCcccccccccccccceEEEccccchhhHhhhhccccc
Q 002545 347 IQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHR 426 (910)
Q Consensus 347 i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~sGvsqvleRln~~~~lSH~Rrv~r 426 (910)
.++.++. ++.+++. -+++ .+.||++++|+||||||+.+.. .|..++||||||+|+||+++|||+||++.
T Consensus 389 mQk~le~-~~dfni~------~aik---a~iIt~gl~yslaTgnwgdq~k-a~~~ragVsQVLnR~t~~sTLsHlRR~n~ 457 (1141)
T KOG0214|consen 389 MQKCLEN-GVDFNIE------LAIK---AKIITNGLNYALATGNWGDQKK-AMQGRAGVSQVLNRLNPLSTLSHLRRTNS 457 (1141)
T ss_pred HHHHHhc-CccceEE------EEEE---eeeecccceeeeccCCccchhH-HhhccccHHHHhccccHHHHHHHHhhcCC
Confidence 9999987 5544432 1232 4589999999999999986543 46799999999999999999999999994
Q ss_pred CCcccccccccccccCCCCccccccCCCCCCccccccccccceeEEeeecCCCCcccccchhhHHHHHHHHhcCCeecCC
Q 002545 427 GASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLP 506 (910)
Q Consensus 427 g~~~~~~k~t~vR~Lhps~wG~iCPveTPEG~~cGLv~~LA~~~~Is~~~~~~~~~~~~~~~~~~i~~~L~~lG~~~~~~ 506 (910)
...+++|...||+|||||||++||+|||||++||||||||+|+.|+++..+. +|.++|.++|++.+ .
T Consensus 458 -Pigr~GKlAkpRqlHnthwGmvCPaeTPEGqacGLVKNLSLmayIsvGS~~s-----------Pi~EfLeewgmE~l-e 524 (1141)
T KOG0214|consen 458 -PIGRTGKLAKPRQLHNSHWGMVCPAETPEGQACGLVKNLSLMAYISVGSLES-----------PIVEFLEEWGMENL-E 524 (1141)
T ss_pred -ccccccccCCccccCcccceeeccccCCCcceeeccccceEEEEEecCCCcc-----------HHHHHHHHhchhhH-h
Confidence 4468999999999999999999999999999999999999999998876654 49999999999988 4
Q ss_pred ccccCCCCceeEEEECCEEEeeecCccHHHHHHHHHHHHHhcCCCCCCCceEEEEEcCCCCCCCceEeecCCCceeceEE
Q 002545 507 KLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVR 586 (910)
Q Consensus 507 ~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~~~lr~~k~~~~~~i~~~~eI~~v~~~~~~~~~~i~i~td~gR~~RPv~ 586 (910)
++......+.++||+||+|+|.+ .+|+.+++.||.+||..+ ++ .|++.+ ++...++++||||+||.+||++
T Consensus 525 ~~~ps~~~datkvfvNG~wvGlh--rdp~~l~~tlr~lRR~~d--i~--~Evs~v---RDIr~kE~ri~tDaGR~~rPLl 595 (1141)
T KOG0214|consen 525 EISPSPSPDATKVFVNGVWVGLH--RDPEELVATLKRLRRQFD--II--AEVSMV---RDIRDKEIRIFTDAGRSLRPLL 595 (1141)
T ss_pred hcCCCcCCCceEEEEcccEEEec--CCHHHHHHHHHHHHHhhc--cc--hhhhhh---ccccccceeeeeccCccccceE
Confidence 56666677889999999999995 678999999999999873 33 366555 4456789999999999999999
Q ss_pred eecCCCC------------------------CCCceeeeCccceeeeeeecCCCCCCCCCCCCCceecccCCCcccccee
Q 002545 587 NISLPSE------------------------ESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVA 642 (910)
Q Consensus 587 ~~~~~~~------------------------~~g~iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~p~~~ls~~a 642 (910)
.+++.+. ..|.+||||++|++.++||+.++++......+.||||||||+.|||++|
T Consensus 596 iven~~l~~~k~hi~~L~~~~~~~~~w~~lv~~G~ie~idteeEEtvmiam~~~dL~~~~~~~~~THCEiHpsmILgv~a 675 (1141)
T KOG0214|consen 596 IVENAKLLIKKRHIRALKQSKPNEYRWAHLLSSGEVEYIDTEEEETVMIAMGPKDLAESAYPKTYTHCEIHPSMILGVCA 675 (1141)
T ss_pred EEechhhhhhhHHHHHHhhCchhhcchhhhccccceeeeccchhhhHHHhcCHHHHhhccCCcccccccccHHHhhhhce
Confidence 9988732 2589999999999999999999999875556779999999999999999
Q ss_pred ecccCCCCCCcchhhhhhhccccccccceeEEEEeccCceeecCCCCeeeEecccccccCccccCCCceeeEEEEeccCC
Q 002545 643 NLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGY 722 (910)
Q Consensus 643 sliPF~~hNqspRn~yq~~M~KQaig~~~~n~~~R~D~~~y~L~~pQ~Plv~t~~~~~~~~~~~~~G~N~iVav~~y~Gy 722 (910)
|+|||||||||||||||++|+|||||++.+|+..|+|+..|.|+|||+|+++|+.+++..+.++|+|+|+|||++||+||
T Consensus 676 siIpFpdh~qspr~tYQsa~~kqamg~y~tn~~vR~dtl~~~l~ypqkpl~tt~~~e~l~~~eL~aG~NaiVAi~~~~GY 755 (1141)
T KOG0214|consen 676 SIIPFPDHNQSPRNTYQSAMGKQAMGVYHTNPQVRMDTLAKVLYYPQKPLVTTRAMEYLRFRELPAGQNAIVAIACYSGY 755 (1141)
T ss_pred eeeecCCCCCchHHHHHHHHhhhcceeeeecchhhhhhhhhcccccccchhhHHHHhhhhhhhcccccceEEEEecccCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcccceeeeccccccCcceeeEEEEEEEEeeccCCCcCccceeeccCCC------ChhhhcccCCCCCcccCceecCCCc
Q 002545 723 DMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFRRNKD------AKSLHSVIDSDGLPYVGQMIHPGEP 796 (910)
Q Consensus 723 n~EDaiiink~s~~rG~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~------~~~~~~~ld~dG~~~~g~~v~~gd~ 796 (910)
|+|||||+|+++++||||++.+|++|+... .. ......+.|+.|.. ....+++||+||++.+|++|..|||
T Consensus 756 NqEDsvimn~s~v~rg~FrS~~~RsYk~q~--~~-~~~~~ee~~~~~~~~~~~~mr~~~~dkLdddG~i~~G~~vs~~Dv 832 (1141)
T KOG0214|consen 756 NQEDSVIMNQSSVDRGLFRSFFIRSYKDQE--HK-KDQGPEEIFEEPPRGEGRGMRNGKYDKLDDDGIIMPGSRVSGGDV 832 (1141)
T ss_pred cHHHHHHHHhhhhhcchhhhhhhhHHHhhh--hh-cccccccccccccccccccccccccccccccCCccccceeecCCE
Confidence 999999999999999999999999998642 11 12245666776643 2445789999999999999999999
Q ss_pred EEEeeccCC--------------CceeeeeecCCCceEEEEEEEEecCCCCCCeEEEEEEeeeeCCCcccceeccCCCcc
Q 002545 797 YCSIYDKTT--------------NSWRTNSRKGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKG 862 (910)
Q Consensus 797 l~~~~~~~~--------------~~~~~~~~~~~e~g~v~~v~~~~~~~~~~~~~v~i~~r~~R~p~iGDKf~sRHGqKG 862 (910)
++||..+.. .++.++.++.+|.|+||+|.++.+.+| .+.++|++|+.|.|++||||||||||||
T Consensus 833 ~iGk~t~~~~~~~~~~~~~~~~t~~d~s~~Lr~~e~Givd~V~vt~n~~G--~kF~kv~vr~~ripqiGDKfasrHgqKG 910 (1141)
T KOG0214|consen 833 LIGKTTPQPAKEDESGPEDRLYTKRDHSTKLRHTERGIVDQVWVTKNSEG--PKFVKVRVRQVRIPQIGDKFASRHGQKG 910 (1141)
T ss_pred EeccccCCcccchhccccccccccccceeecccCCcceEEEEEEecCCCC--CceeEEEEeecccccccchhccccccCc
Confidence 999976421 235588899999999999999988764 5889999999999999999999999999
Q ss_pred EEeeeecCcCcCccCCCCCcCcEEeCCCCccccccHHHHHHHhhccc
Q 002545 863 VCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKE 909 (910)
Q Consensus 863 v~s~i~~~~dMPf~~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gK~ 909 (910)
|||.+++++||||| .+|++|||||||||||||||||||+||++||+
T Consensus 911 ~ig~~~~qedmpft-~eGi~pDiiiNPhaiPSRmtig~liEc~lgk~ 956 (1141)
T KOG0214|consen 911 TIGITYRQEDMPFT-IEGIVPDIIINPHAIPSRMTIGQLIECLLGKV 956 (1141)
T ss_pred cccceeecCCCCcc-ccCCCcceEECcccCccccchhhhHHHhhhhh
Confidence 99999999999999 99999999999999999999999999999995
No 4
>KOG0215 consensus RNA polymerase III, second largest subunit [Transcription]
Probab=100.00 E-value=2.9e-178 Score=1493.39 Aligned_cols=832 Identities=28% Similarity=0.458 Sum_probs=716.5
Q ss_pred ccCchhhHHHHHHHHHHHHHHhHHHHH-----------------------------------------HHHHHcCCeeee
Q 002545 9 FEPLRELVRHHIESFDYMLDEGLSEMF-----------------------------------------DHCRQAKISYTG 47 (910)
Q Consensus 9 ~~~~~~Lv~~hi~SFn~Fi~~gl~~i~-----------------------------------------~ecR~r~~TY~~ 47 (910)
+...+|||+||++|||||++++++.|+ +|||+|++||+|
T Consensus 53 flkvkglvkqhldsfnyfv~~~ik~iv~an~~itsd~dp~fylky~dirvg~Ps~~~~~~~~~~~i~p~ecrlrd~tysa 132 (1153)
T KOG0215|consen 53 FLKVKGLVKQHLDSFNYFVDVDIKKIVKANQLITSDVDPSFYLKYLDIRVGKPSIEEGNNVTNDNITPHECRLRDMTYSA 132 (1153)
T ss_pred HHhhhhHHHHHHhhhhhhhhhhHHHHHHhhcccCcCcCchhhheeeeeeccCcchhhccccccccCCchheeehhhhccc
Confidence 346799999999999999999999998 899999999999
Q ss_pred EEEEEEEEEEecCCCceeeeEeeecccceeecCCCccCCCCChHHHHhcccccccCCcEEEEcCceeEEEEEEeecCCcc
Q 002545 48 KLMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYP 127 (910)
Q Consensus 48 ~l~v~i~~~~~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~~~~~el~~~~E~~~D~GGYFIInG~EKVIr~qi~~~~N~~ 127 (910)
|++|+++++.. ...+.+.+|.||++|||++|++|+|++.++.++++.+|||.|||||||++|+||||..|++.+.|++
T Consensus 133 ~i~vdieytrg--~~~~~~~~v~igrmpimlrs~rcvl~~~~e~~~a~~~ecpldpggyfiv~G~ekViLiqeqlsknri 210 (1153)
T KOG0215|consen 133 PIYVDIEYTRG--RQIIAKRDVIIGRMPIMLRSSKCVLRGKDEEELARLNECPLDPGGYFIVKGTEKVILIQEQLSKNRI 210 (1153)
T ss_pred ceeEEEEEecC--cceEEecccccccchhhhhccccccCCccHHHHHHhccCCCCCCceeEeccceeEEEehhhhhccCe
Confidence 99999999876 5566788999999999999999999999999999999999999999999999999999999999998
Q ss_pred EEEEeccccCCCCcceeeEEEEEeeecCCCceEEEEEEEeCCeEEEEEEeecccccccHHHHHHhccCCCHHHHHHHhcc
Q 002545 128 MSMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTC 207 (910)
Q Consensus 128 ~~~~r~~~~~~~~~~t~~~v~~r~~~~~~~~~~~~l~y~~~g~~~l~~~~~~~~~~IPi~ilLkALg~~sD~EI~~~i~~ 207 (910)
++- . .+++.. -+...|......+.+..+ .++|..+++....- ..||+++++||||..||+||.+.++.
T Consensus 211 i~~-~---~k~~~~----~~svtsst~e~kskt~v~--~k~~k~ylk~~~~~--d~ipiviv~ka~g~~sd~ei~~~vg~ 278 (1153)
T KOG0215|consen 211 IVE-E---DKKGNL----QASVTSSTHERKSKTYVT--TKKGKYYLKHNSFT--DDIPIVIVLKAMGLESDQEIVQLVGG 278 (1153)
T ss_pred eec-c---ccCCcc----ccccccceeeecceEEEE--eccceeeeehhhhh--ccCCEEEEEeeccccchHHHHHHhhc
Confidence 764 1 123322 122233333344455544 66777777665432 37999999999999999999999972
Q ss_pred cccchhhcccCCCCChhhHHHHHHHHHHHHhcccccHHHHHHHHhhcccccccCCCCccHHHHHHHHHHhHhccCCC---
Q 002545 208 CYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHLN--- 284 (910)
Q Consensus 208 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i~t~~~al~yLg~~fr~~~~~~~~~~~~~~g~~~L~~~ll~Hl~--- 284 (910)
+.++.+....+++++...+++|+.+|++|++.+.+... +...+..+.+..+|...+++|++
T Consensus 279 --------------~~~y~~~~~~s~ee~~~~~v~tqqqal~y~~~kvk~~~--~t~~~~~~e~~~~l~~~~lahv~v~~ 342 (1153)
T KOG0215|consen 279 --------------DSKYQDIFAPSLEECVSLGVYTQQQALEYIGSKVKVKR--GTTPTKDEEALEVLSTTVLAHVPVPD 342 (1153)
T ss_pred --------------chHHHHhhccchhhhhhhhhHHHHHHHHHhhheEEecc--CCCCCchHHHHHHHHhhheeceeccC
Confidence 35666778888999999999999999999999886532 33456678899999999999998
Q ss_pred -CCcchHHHHHHHHHHHHhhcCCCCCCCCcccccccEEcccchhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCcccccch
Q 002545 285 -DNNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNL 363 (910)
Q Consensus 285 -~~~~K~~~L~~Mi~kLl~~~~g~~~~Dd~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~ 363 (910)
+...|+.+++.|+|+++.+..+.-..||+|+++|||++++|+|++.+|++.|+.+...+++.+.+.+.+..+...++
T Consensus 343 ~~~r~K~~yi~~m~rr~~~a~l~~~~~ddrd~~gnkrlelagqllsllfeD~fk~~n~e~k~~~dk~l~k~~ra~~fD-- 420 (1153)
T KOG0215|consen 343 LNFRMKAIYIGLMVRRVIQAMLNKLAMDDRDYVGNKRLELAGQLLSLLFEDLFKRFNSELKKNIDKILKKPIRAQEFD-- 420 (1153)
T ss_pred CCCcceeehHHHHHHHHHHHHhCcccccchhhhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhhhhhhH--
Confidence 46799999999999999999999999999999999999999999999999999999999999998887754433332
Q ss_pred HHHHHHHhcCCCcchHHHHHhHhcccCcccccccccccccceEEEccccchhhHhhhhcccccCCcccccccccccccCC
Q 002545 364 ANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTSVRKLLP 443 (910)
Q Consensus 364 ~~~~~~~~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~sGvsqvleRln~~~~lSH~Rrv~rg~~~~~~k~t~vR~Lhp 443 (910)
.++.+-. ..+.||++|.+++|||||..+. |.|.+.|++||+.|++|++.|..+.|+++ +|.+++|..+||.|+|
T Consensus 421 -~~~~~n~--~~~~it~~l~ra~stgnw~iKr--frmer~gvt~VlsrlSyisaLgmmtri~s-~fektrkvsgprSlq~ 494 (1153)
T KOG0215|consen 421 -ALKHLNV--RANMITSGLERAISTGNWSIKR--FRMERAGVTQVLSRLSYISALGMMTRINS-QFEKTRKVSGPRSLQP 494 (1153)
T ss_pred -HHHHHHH--HHHHHHHHHHHHhhcCchHHHH--hhhhhccceeeehhhhhhhhhhhheehhh-hheeehhccCccccCh
Confidence 2221111 1347999999999999998864 67899999999999999999999999996 7889999999999999
Q ss_pred CCccccccCCCCCCccccccccccceeEEeeecCCCCcccccchhhHHHHHHHHhcCCeecCC-ccccCCCCceeEEEEC
Q 002545 444 ESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLP-KLVKSGPPAVLSVLLD 522 (910)
Q Consensus 444 s~wG~iCPveTPEG~~cGLv~~LA~~~~Is~~~~~~~~~~~~~~~~~~i~~~L~~lG~~~~~~-~~~~~~~~~~~~V~ln 522 (910)
||||++||+|||||+.||||+|||++++|+++.+.+ .+...+..+|++.+.. ........+.+-||||
T Consensus 495 sqwgmlcp~dtpegeacglvknlalmthittd~ee~-----------pi~~~~~k~gv~di~~v~~~e~~~~~~~~v~Ln 563 (1153)
T KOG0215|consen 495 SQWGMLCPSDTPEGEACGLVKNLALMTHITTDSEEK-----------PILKLCYKLGVEDIHVVSGRELHTPDSFLVFLN 563 (1153)
T ss_pred hhcccccCCCCCCccccccccchHHHhcccCCCCcc-----------hhHHHHHHhcceeeeeecccccCCCceEEEEec
Confidence 999999999999999999999999999999876665 4888999999987621 1122234567999999
Q ss_pred CEEEeeecCccHHHHHHHHHHHHHhcCCCCCCCceEEEEEcCCCCCCCceEeecCCCceeceEEeecCCCC---------
Q 002545 523 GRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSE--------- 593 (910)
Q Consensus 523 G~~iG~~~~~~~~~~~~~lr~~k~~~~~~i~~~~eI~~v~~~~~~~~~~i~i~td~gR~~RPv~~~~~~~~--------- 593 (910)
|.++|.+ ..++.|+..+|.+||+| .|.. ||+.+.+.....++|-||.||.+||++++.++..
T Consensus 564 g~iig~~--~~~~~~v~~~r~lrr~G--~i~~-----fvsv~~~~~q~~v~i~sdggr~crp~Iiv~~~~~~v~~~h~~e 634 (1153)
T KOG0215|consen 564 GLIIGIT--RRPQYFVNSFRRLRRKG--KIGE-----FVSVFTNTTQRCVYIASDGGRVCRPLIIVDNGRPRVKQHHMDE 634 (1153)
T ss_pred ceeeccc--cchHHHHHHHHHHHHcC--cccc-----eeeeeeeeeeEEEEEecCCCeEeeeEEEEeCCcchhhhhhHHH
Confidence 9999996 56789999999999999 4444 4554444556689999999999999999987743
Q ss_pred ------------CCCceeeeCccceeeeeeecCCCCCCCCCCCCCceecccCCCccccceeecccCCCCCCcchhhhhhh
Q 002545 594 ------------ESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQ 661 (910)
Q Consensus 594 ------------~~g~iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~p~~~ls~~asliPF~~hNqspRn~yq~~ 661 (910)
..|.|||+|++|++.++||+.++++.+. +||+||.|..+||++|+|||||+|||||||||||+
T Consensus 635 l~~g~r~F~DFl~~glvEYLDVNEEND~~Ialye~~I~~~-----TTHLEIEPFTiLGv~AGLIPYPHHNQSPRNTYQCA 709 (1153)
T KOG0215|consen 635 LLDGKRTFDDFLKDGLIEYLDVNEENDSLIALYEEDIGPE-----TTHLEIEPFTILGVVAGLIPYPHHNQSPRNTYQCA 709 (1153)
T ss_pred HHHhhhhHHHHHHhchhheeecccccCceEEechhhcCCC-----cceeeecchhhhhhhccccCCCCCCCCCcchhhhh
Confidence 3689999999999999999999999887 89999999999999999999999999999999999
Q ss_pred ccccccccceeEEEEeccCceeecCCCCeeeEecccccccCccccCCCceeeEEEEeccCCCcccceeeeccccccCcce
Q 002545 662 MAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCH 741 (910)
Q Consensus 662 M~KQaig~~~~n~~~R~D~~~y~L~~pQ~Plv~t~~~~~~~~~~~~~G~N~iVav~~y~Gyn~EDaiiink~s~~rG~~~ 741 (910)
|||||||..++|+..|.|+.+|+|.|||+|+|+|++.+..+++++|+|+||.||||||+|||+|||+|+||+|+||||+|
T Consensus 710 MGKQAmG~IaYNQ~~RiDtlmYll~YPq~PmVkTKTIELi~ydKLPAGQNAtVAVMSYSGYDIEDALVLNKsSlDRGfGR 789 (1153)
T KOG0215|consen 710 MGKQAMGAIAYNQKKRIDSLLYLLVYPQRPMVKTKTIELINYDKLPAGQNATVAVMSYSGYDIEDALVLNKSSIDRGFGR 789 (1153)
T ss_pred hhhhhhhhhhhhhhhhHHHHHHHHhcCCCccccceeEEeeccccCCCCCccEEEEEeccCCchhhhhhcccchhccCcce
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeEEEEEEEEeeccCCCcCccceeeccC----CC-Chh-hhcccCCCCCcccCceecCCCcEEEeeccC-----------
Q 002545 742 GQIYQTETIDLSDDGNKVDRGQKLFRRN----KD-AKS-LHSVIDSDGLPYVGQMIHPGEPYCSIYDKT----------- 804 (910)
Q Consensus 742 ~~~~~~~~~~~~~~~~~~~~~~~~f~~~----~~-~~~-~~~~ld~dG~~~~g~~v~~gd~l~~~~~~~----------- 804 (910)
+.+|+..+.-++...+. ... .+.-| +. +.. ..+.||+|||..||.+|++|+|+++|--|-
T Consensus 790 C~Vyk~~~~~~kkY~N~--T~D-rimgp~~d~~t~kpi~kh~vLd~DGl~~pG~~V~~~qi~iNK~mP~vt~~~~~~~~~ 866 (1153)
T KOG0215|consen 790 CEVYKKTTTTLKKYANG--TFD-RIMGPQLDPNTRKPIWKHQVLDDDGLATPGERVQPGQIYINKQMPTVTGTSLPGLSA 866 (1153)
T ss_pred EEEEeeeeeeeeecCCC--chh-hhcccccCCCcCCcchhhcccCcccCCCCccEeccCcEEEeccCCCcccccCCCCCc
Confidence 99999988765433221 111 11112 11 111 246799999999999999999999992221
Q ss_pred ---CCceeeeeecCCCceEEEEEEEEecCCCCCCeEEEEEEeeeeCCCcccceeccCCCccEEeeeecCcCcCccCCCCC
Q 002545 805 ---TNSWRTNSRKGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGM 881 (910)
Q Consensus 805 ---~~~~~~~~~~~~e~g~v~~v~~~~~~~~~~~~~v~i~~r~~R~p~iGDKf~sRHGqKGv~s~i~~~~dMPf~~~~G~ 881 (910)
..+..+..|++.|+++||+|.++.+++. .-.+|+.+|++|+|++|||||||||||||||.|++||||||. ..||
T Consensus 867 ~~~~Yk~~pitykgpepsyidkVmls~n~~d--q~LIK~llRQTRrPElGDKFSSRHGQKGVcGlIv~QEDMPFn-D~GI 943 (1153)
T KOG0215|consen 867 SQVQYKAVPITYKGPEPSYIDRVMLTSNDED--QFLIKVLLRQTRRPELGDKFSSRHGQKGVCGLIVQQEDMPFN-DQGI 943 (1153)
T ss_pred cccccccccceecCCCcchhheeEeecCccc--cHHHHHHHhhccCcccccccccccCCCceeeEEeeccCCCCc-ccCC
Confidence 1344578899999999999999998653 356999999999999999999999999999999999999999 9999
Q ss_pred cCcEEeCCCCccccccHHHHHHHhhccc
Q 002545 882 RPDLIINPHAFPSRMTIAMLLESVAAKE 909 (910)
Q Consensus 882 ~pDiI~NPh~~PSRMtiGql~E~~~gK~ 909 (910)
+|||||||||||||||||.++|.++|||
T Consensus 944 cPDiIMNPHGFPSRMTVGK~iELlsGKA 971 (1153)
T KOG0215|consen 944 CPDIIMNPHGFPSRMTVGKMIELLSGKA 971 (1153)
T ss_pred CcccccCCCCCcccchHHHHHHHhcccc
Confidence 9999999999999999999999999997
No 5
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]
Probab=100.00 E-value=6e-170 Score=1512.48 Aligned_cols=785 Identities=24% Similarity=0.340 Sum_probs=665.1
Q ss_pred CCccCchhhHHHHHHHHHHHHHHhHHHHH------------------------------HHHHHcCCeeeeEEEEEEEEE
Q 002545 7 ADFEPLRELVRHHIESFDYMLDEGLSEMF------------------------------DHCRQAKISYTGKLMADVEFQ 56 (910)
Q Consensus 7 ~~~~~~~~Lv~~hi~SFn~Fi~~gl~~i~------------------------------~ecR~r~~TY~~~l~v~i~~~ 56 (910)
.++..+++|+++|++|||+|+.+||++++ .|||+|++||+|||+|++++.
T Consensus 19 ~~~~~~p~Lv~~QldSyn~ff~~gLq~i~~~i~PI~~~~~~~~Lef~~~~l~~p~k~~p~EcR~R~lTYsapLyv~lrlv 98 (1060)
T COG0085 19 PEFLDLPNLVEIQLDSYNAFFLEGLQEVFREIFPIESYNGNTELEYGSYRLGEPPKFYPEECRLRGLTYSAPLYVKLRLV 98 (1060)
T ss_pred ccccCCccHHHHHHHHHHHHHHHHHHHHHHhcCceecCCCCEEEEEEEEEecCCCCCCHHHHHhcCCccccceEEEEEEE
Confidence 45667999999999999999999999999 899999999999999999998
Q ss_pred EecCCCc-eeeeEeeecccceeecCCCccCCCCChHHHHhcccccccCCcEEEEcCceeEEEEEEeecCCccEEEEeccc
Q 002545 57 YLDAGSP-VVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRSSF 135 (910)
Q Consensus 57 ~~~~~~~-~~~~~v~iG~iPIMv~S~~C~L~~~~~~el~~~~E~~~D~GGYFIInG~EKVIr~qi~~~~N~~~~~~r~~~ 135 (910)
++. +++ ++.++|++|+||+||+ ||||||||+||||++|++++||.+|.....
T Consensus 99 ~~~-~~e~~k~~eV~iG~iPlMt~------------------------gGyFIINGsERVIVsQ~~rSPgvif~~~~~-- 151 (1060)
T COG0085 99 VNE-TGEEIKEQEVYMGDIPLMTR------------------------GGYFIINGTERVIVSQEHRSPGVIFVEKKD-- 151 (1060)
T ss_pred ECC-cccccccceEEeccCcEecC------------------------CcEEEECCeEEEEEEEeecCCCeEEecccc--
Confidence 873 334 6788999999999998 999999999999999999999977664332
Q ss_pred cCCCC--cceeeEEEEEeeecCCCceEEEEEEEeCCeEEEEEEeecccccccHHHHHHhccCCCHHHHHHHhcccccchh
Q 002545 136 RDRRE--GYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKY 213 (910)
Q Consensus 136 ~~~~~--~~t~~~v~~r~~~~~~~~~~~~l~y~~~g~~~l~~~~~~~~~~IPi~ilLkALg~~sD~EI~~~i~~~~~~~~ 213 (910)
+++. .|+...++ . .+.|+.++++.++.+++++..++ +||+++||||||+.||+||++.+.. +
T Consensus 152 -k~~~~~~~~a~vIp------~-rG~wl~~e~d~~d~~~~rId~~r---kiPvtilLRALG~~tDeeI~~~~~~--~--- 215 (1060)
T COG0085 152 -KTGSKVLYVARVIP------Y-RGSWLEFEFDPKDNLYVRIDRKR---KIPVTILLRALGLETDEEIIEAFGG--D--- 215 (1060)
T ss_pred -cCCcceEEEEEEec------C-CcceEEEEEccCccEEEEeeeEE---EeeHHHHHHHhCCCcHHHHHHHhcc--c---
Confidence 2332 33333332 2 34699998888899999998765 6999999999999999999999973 1
Q ss_pred hcccCCCCChhhHHHHHHHHHHHHhc---ccccHHHHHHHHhhcccccccCCCCccHHHHHHHHHHhHhccCCCC-----
Q 002545 214 KKEKGAVGSPLVSERVKIILAEVQDL---SLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHLND----- 285 (910)
Q Consensus 214 ~~~~~~~~~~~~~~~~~~~l~~~~~~---~i~t~~~al~yLg~~fr~~~~~~~~~~~~~~g~~~L~~~ll~Hl~~----- 285 (910)
+..+.+.....+++++.+.+. .+.++ .|++||+++|...........+.++++.++.+.+||||..
T Consensus 216 -----~~~~~~~~~~~~~ll~~~~~~~~~~i~~~-~a~~~i~~r~~~~~~~~~~~gR~k~~~~vl~~~~L~hL~~~~~~~ 289 (1060)
T COG0085 216 -----ELTDLVPPEGEEALLEIYEEAKGEKITAR-NALELIGSRVFVVKRYDAKEGRYKRAKYVLDKELLPHLGEAGERY 289 (1060)
T ss_pred -----ccccccchHHHHHhHHHHhhccCCCcchH-HHHHHHhcccccccccccchhhhhhhhhhhhhhHHhhhccccccc
Confidence 011112245677777777643 24444 4999999999753221135567889999999999999995
Q ss_pred ---CcchHHHHHHHHHHHHhhcCCCCCCCCcccccccEEcccchhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCcccccc
Q 002545 286 ---NNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFN 362 (910)
Q Consensus 286 ---~~~K~~~L~~Mi~kLl~~~~g~~~~Dd~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~ 362 (910)
...|+.+|+.|+++|+.+..|++.+||+|||+||||+++|+||+++||..|.++.+.++.++.+...+
T Consensus 290 ~l~~~~k~~di~~mi~~l~~L~~G~~~~DDiDHlGNKRlrlvGeLl~n~fR~gl~rmer~ikerm~~~~~r--------- 360 (1060)
T COG0085 290 DLSRVGKAKDIIAMIKYLIELRLGKGEEDDIDHLGNRRLRLVGELLENLFRVGLSRMERDVKERLEKADKR--------- 360 (1060)
T ss_pred chhhhHHHHHHHHHHHHHHHHhcCCCCCCCCccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh---------
Confidence 23588899999999999999999999999999999999999999999998888888877776654331
Q ss_pred hHHHHHHHhcCCCcchHHHHHhHhcccCcccccccccccccceEEEccccchhhHhhhhcccccCCcccccccccccccC
Q 002545 363 LANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTSVRKLL 442 (910)
Q Consensus 363 ~~~~~~~~~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~sGvsqvleRln~~~~lSH~Rrv~rg~~~~~~k~t~vR~Lh 442 (910)
..+. ..+.||.++.+|++||||+ ++||||+++|+||+|.|||+|||++.+++++++.++||+||
T Consensus 361 ----~~i~---p~dlIn~k~~~Alitgffg---------~sqlSQfmDqtNpLSeLSHkRRIsAlgLsRera~fEvRDvH 424 (1060)
T COG0085 361 ----DTLV---PQDLINAKPIHALITGFFG---------RSQLSQFMDQTNPLSELSHKRRLSALGLSRERAGFEVRDVH 424 (1060)
T ss_pred ----hccC---chhhcchhHHHHHHhcccc---------ccceeeeeecCChHHhhhhhhceeccCcCccCCCCcccccC
Confidence 0011 2347999999999999995 69999999999999999999999997778999999999999
Q ss_pred CCCccccccCCCCCCccccccccccceeEEeeecCCCCcccccchhhHHHHHHHH-hcCCeecCCccccCCCCceeEEEE
Q 002545 443 PESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLI-GVGMIPSLPKLVKSGPPAVLSVLL 521 (910)
Q Consensus 443 ps~wG~iCPveTPEG~~cGLv~~LA~~~~Is~~~~~~~~~~~~~~~~~~i~~~L~-~lG~~~~~~~~~~~~~~~~~~V~l 521 (910)
||||||+||+|||||+|||||||||++|+|+.....++++ .+.+. .+|+.++. .++ .....|++
T Consensus 425 pTHyGRiCPiETPEGpNiGLI~sLA~~A~Vn~~Gf~etPy----------~kv~~g~~~v~~i~-~l~----~~~~~~~~ 489 (1060)
T COG0085 425 PTHYGRICPIETPEGPNIGLIKSLALYARINEYGFLETPY----------RKVLDGSLVVDEIE-YLS----ADEEDVYV 489 (1060)
T ss_pred cccccccCCCCCCCCcchhHHHHHHHHeEecccCCCCCce----------EEEEecccccccee-eec----ccccceEE
Confidence 9999999999999999999999999999999555555442 22322 35666542 111 11267999
Q ss_pred CCEEEeeecCccHHHHHHHHHHHHHhcCCCCCCCceEEEEEcCCCCCCCceEeecCCCceeceEEeecCCCC--------
Q 002545 522 DGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSE-------- 593 (910)
Q Consensus 522 nG~~iG~~~~~~~~~~~~~lr~~k~~~~~~i~~~~eI~~v~~~~~~~~~~i~i~td~gR~~RPv~~~~~~~~-------- 593 (910)
||.++|.+ +++..|++.+|.+|+ + +..++.+. .+...+...-++++.+|.||.+||++.+.++..
T Consensus 490 ~~~~~~~~--~~~~~~~~~~~~~R~-~---~~~~~~~~-~~~~~~~~dv~~~~~~~~~~~~~P~l~~dd~~~~l~~~~mq 562 (1060)
T COG0085 490 IGQANGTL--DEPGELVEELVECRR-G---GSGEVSVA-DPEGVDYMDVSPKQVVSVGRSLIPFLEHDDANRALMGSNMQ 562 (1060)
T ss_pred EeEeeeee--cCCCceeeeEEEEee-c---ccccceee-cCccccceeccceEEeccccccCceeEEcCchHhhhhhhhh
Confidence 99999987 456889999999997 3 23333332 111122233478999999999999998877631
Q ss_pred --------------CCCceeeeCccceeeeeeecCCCCCCCCCCCCCceecccCCCccccceeecccCCCCCCcchhhhh
Q 002545 594 --------------ESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQ 659 (910)
Q Consensus 594 --------------~~g~iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~p~~~ls~~asliPF~~hNqspRn~yq 659 (910)
+.| +||+++.|+.++.||..+.+ +||+|++|..|++.+|++|||++||||||||||
T Consensus 563 r~~~~l~~~~~~lv~tG-~E~~~a~e~~~~~ia~~~~~---------~~~ve~~~~~I~~~~~~~~~~~~~n~~~~n~~~ 632 (1060)
T COG0085 563 RQAVPLLRTEAPLVGTG-MEYLDAEDSGAAVIAKRPGV---------VTHVEISPIVILGIEASLIPYPEHNQSPYNLYK 632 (1060)
T ss_pred hhcccccccccccccCC-ceeeccccccceeEeccCCc---------EEEEeeeeeEEEeeccccCCccccCcChHHHHH
Confidence 367 99999999999999999876 799999999999999999999999999999999
Q ss_pred hhccccccccceeEEEEeccCceeecCCCCeeeEecccccccCccccCCCceeeEEEEeccCCCcccceeeeccccccCc
Q 002545 660 CQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGM 739 (910)
Q Consensus 660 ~~M~KQaig~~~~n~~~R~D~~~y~L~~pQ~Plv~t~~~~~~~~~~~~~G~N~iVav~~y~Gyn~EDaiiink~s~~rG~ 739 (910)
|+|+||++|++..|+..|.|+..|.++|||.|+|++ +|+|+|+|++||||||+||||||||||||++++||+
T Consensus 633 ~~~~~Q~~~~~~~~~~~~~d~~~~~~~~~~~P~~~~--------~e~~~GqN~~VA~m~~~GYn~EDAiiin~~~v~~~~ 704 (1060)
T COG0085 633 FARSNQATGINQRPLVKRGDTVEKGLVYADGPSVDT--------GELALGQNALVAFMPWNGYNYEDAIIISERSVERDL 704 (1060)
T ss_pred HhhhhcccCCCcccceeccccccccceecCCCcccc--------CcccCCceeEEEEecccCcChhHheecccchhhcCC
Confidence 999999999999999999999999999999999997 899999999999999999999999999999999999
Q ss_pred ceeeEEEEEEEEeeccCCCcCccceeeccCCCChhhhcccCCCCCcccCceecCCCcEEEeeccCCC-------------
Q 002545 740 CHGQIYQTETIDLSDDGNKVDRGQKLFRRNKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTTN------------- 806 (910)
Q Consensus 740 ~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~ld~dG~~~~g~~v~~gd~l~~~~~~~~~------------- 806 (910)
|++++|++|.++..+.+. +..+.+.+|+..+..+++||+|||++||++|+.||||+||++|+..
T Consensus 705 ~ts~~~~~~~~~~r~~~~---g~e~~~~iP~~~e~~~~~Lde~Gii~ig~~V~~gdilvgk~tP~~~~~~~~ee~ll~i~ 781 (1060)
T COG0085 705 FTSIHIEEYETEARDTKL---GPEEIRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRIF 781 (1060)
T ss_pred ceEEEEEEEeeeeeccCC---CccccccCCCcCHHHHhcCCccCccccccEEcCCCEEEEeeCCCCCCCCCchhhhhccc
Confidence 999999999997655443 3445578999999999999999999999999999999999988742
Q ss_pred ----ceeeeeecCCCceEEEEEEEEecCCCC--CCeEEEEEEeeeeCCCcccceeccCCCccEEeeeecCcCcCccCCCC
Q 002545 807 ----SWRTNSRKGSESVFVDYVAVDMKNSKN--LPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTG 880 (910)
Q Consensus 807 ----~~~~~~~~~~e~g~v~~v~~~~~~~~~--~~~~v~i~~r~~R~p~iGDKf~sRHGqKGv~s~i~~~~dMPf~~~~G 880 (910)
++.|++++++|+|+||+|.++++++|+ ..+.|||++|+.|.|++|||||||||||||||+|||+|||||+ +||
T Consensus 782 ~ek~rdtsl~~~~g~~G~V~~V~~~~~~~~~~g~~~~vkV~v~~~R~~~~GDK~a~RHG~KGVis~i~p~eDMPf~-~~G 860 (1060)
T COG0085 782 GEKVRDTSLRVPHGEEGIVDDVQVFTREDGDPGVNKLVKVYVAQKRKPQIGDKMAGRHGNKGVVSKIVPQEDMPFL-EDG 860 (1060)
T ss_pred cceeeccceeecCCCCeEEEEEEEEeccCCCcCceEEEEEEEEEeccCCccccccccCCCCceeeeecCcccCCcC-CCC
Confidence 236889999999999999999987654 5789999999999999999999999999999999999999999 999
Q ss_pred CcCcEEeCCCCccccccHHHHHHHhhccc
Q 002545 881 MRPDLIINPHAFPSRMTIAMLLESVAAKE 909 (910)
Q Consensus 881 ~~pDiI~NPh~~PSRMtiGql~E~~~gK~ 909 (910)
++||||+|||||||||||||++|+++|||
T Consensus 861 ~~~DiilNP~gvPSRM~iGqilE~~lG~a 889 (1060)
T COG0085 861 TPPDIILNPLGVPSRMNIGQILETHLGKA 889 (1060)
T ss_pred CcccEEECCCCCCccccHHHHHHHHHHHH
Confidence 99999999999999999999999999996
No 6
>cd00653 RNA_pol_B_RPB2 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.
Probab=100.00 E-value=1.4e-162 Score=1487.54 Aligned_cols=629 Identities=34% Similarity=0.558 Sum_probs=544.5
Q ss_pred hHHHHHHHHHHHHHHhHHHHH----------------------------------------HHHHHcCCeeeeEEEEEEE
Q 002545 15 LVRHHIESFDYMLDEGLSEMF----------------------------------------DHCRQAKISYTGKLMADVE 54 (910)
Q Consensus 15 Lv~~hi~SFn~Fi~~gl~~i~----------------------------------------~ecR~r~~TY~~~l~v~i~ 54 (910)
|++||++|||+|+++||++++ +|||+|++||+|+++|+++
T Consensus 1 Lv~~qi~SFn~Fl~~gl~~ii~~~~~i~~~~~~~~~~l~f~~i~i~~P~~~~~~~~~~l~P~ecRlr~lTYs~~l~v~i~ 80 (866)
T cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDDDGRLKLKFGDIYLGKPKVEEGGVTRKLTPNECRLRDLTYSAPLYVDIR 80 (866)
T ss_pred CchhHHHHHHHHHHHHHHHHHHhcCCeeeccCCCeEEEEEEEEEECCccccccCccccCCHHHHHhhCCccceeEEEEEE
Confidence 689999999999999999998 8999999999999999999
Q ss_pred EEEecCCCce-eeeEeeecccceeecCCCccCCCCChHHHHhcccccccCCcEEEEcCceeEEEEEEeecCCccEEEEec
Q 002545 55 FQYLDAGSPV-VRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRS 133 (910)
Q Consensus 55 ~~~~~~~~~~-~~~~v~iG~iPIMv~S~~C~L~~~~~~el~~~~E~~~D~GGYFIInG~EKVIr~qi~~~~N~~~~~~r~ 133 (910)
++.+ ++.. ..+++.+|+|||||+|++|||++++++|+++.||||.|+||||||||+|||||+|+++++|+++++ .
T Consensus 81 ~~~~--~~~~~~~~~v~iG~iPIMv~S~~C~L~~~~~~el~~~~E~p~d~GGYFIInG~EkVIi~qi~~~~N~~~~~-~- 156 (866)
T cd00653 81 LTVN--DKGKIKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVE-D- 156 (866)
T ss_pred EEEe--cceeEEEEEEEEeeCCcccCcccccccCCCHHHHHhcCCCcccCCCEEEECCceeEEEEEEeccCCeEEEe-c-
Confidence 9876 3333 567999999999999999999999999999999999999999999999999999999999999865 1
Q ss_pred cccCCCCcceeeEEEEEeeecC--CCceEEEEEEEe-CCeEEEEEEeecccccccHHHHHHhccCCCHHHHHHHhccccc
Q 002545 134 SFRDRREGYTDKAVVIRCVRKD--QSSVTLKLYYLL-NGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYD 210 (910)
Q Consensus 134 ~~~~~~~~~t~~~v~~r~~~~~--~~~~~~~l~y~~-~g~~~l~~~~~~~~~~IPi~ilLkALg~~sD~EI~~~i~~~~~ 210 (910)
++.. +....++.... ....|..+..+. ...++++++..
T Consensus 157 ---~~~~----~~~~~~s~~~~~~~~~s~~~~~~~~~~~~i~~~i~~~-------------------------------- 197 (866)
T cd00653 157 ---SKGK----RIYTKTSIPSYSPYRGSWLEVKSDKKKDRIYVRIDLK-------------------------------- 197 (866)
T ss_pred ---CCCc----EEEEEEEccCCCcCccEEEEEEEccCCCeEEEEeccc--------------------------------
Confidence 1110 11122222110 011222232222 12222222110
Q ss_pred chhhcccCCCCChhhHHHHHHHHHHHHhcccccHHHHHHHHhhcccccccCCCCccHHHHHHHHHHhHhccCCCCCcchH
Q 002545 211 EKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHLNDNNDKF 290 (910)
Q Consensus 211 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i~t~~~al~yLg~~fr~~~~~~~~~~~~~~g~~~L~~~ll~Hl~~~~~K~ 290 (910)
.+++|++|||++|
T Consensus 198 --------------------------------~~~~al~~ig~~~----------------------------------- 210 (866)
T cd00653 198 --------------------------------RQEEALKYIGKRF----------------------------------- 210 (866)
T ss_pred --------------------------------CHHHHHHHHHHHH-----------------------------------
Confidence 0568999999986
Q ss_pred HHHHHHHHHHHhhcCCCCCCCCcccccccEEcccchhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCcccccchHHHHHHH
Q 002545 291 NLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVM 370 (910)
Q Consensus 291 ~~L~~Mi~kLl~~~~g~~~~Dd~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~ 370 (910)
.+|++|++||+.++.|.+.+||+|||+||||+++|+||+.+|++.|+++++.++..+++..++ .+... ...++
T Consensus 211 ~~L~~Mi~kLl~~~~g~~~~Dd~D~~~NkRv~~~G~Ll~~lfr~~l~~~~~~~k~~l~~~~~~-~~~~~------~~~~~ 283 (866)
T cd00653 211 EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSK-KKDLT------PQLLI 283 (866)
T ss_pred HHHHHHHHHHHHHhcCCCCCCCchhhhCeEEeeHHHHHHHHHHHHHHHHHHHHHHHHHhhhhc-ccccC------HHHhc
Confidence 689999999999999999999999999999999999999999999999999999998877654 22111 12233
Q ss_pred hcCCCcchHHHHHhHhcccCcccccccccccccceEEEccccchhhHhhhhcccccCCcccccccccccccCCCCccccc
Q 002545 371 EKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTSVRKLLPESWGFLC 450 (910)
Q Consensus 371 ~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~sGvsqvleRln~~~~lSH~Rrv~rg~~~~~~k~t~vR~Lhps~wG~iC 450 (910)
+++.||++|++||+||||.++.+ ++|++|+||+|+|+||+++|||+||||+|++++++|+++||+||||||||+|
T Consensus 284 ---~~~~It~~i~~~~~TGnw~~~~~--~~~~~Gvsq~ldr~N~ls~lsh~Rrv~~~~~~~~~k~~~~R~lhps~~G~iC 358 (866)
T cd00653 284 ---NSKPITSGIKEFLATGNWGSKRF--LMQRSGLSQVLDRLNPLSELSHKRRISSLGLFRERKGFEVRDLHPSHWGRIC 358 (866)
T ss_pred ---cchHHHHHHHHHhhcCCcccccc--ccccceEEEEcccCCHHHHHHhhhhcccccccccccCCcccccCcccCCccC
Confidence 23489999999999999988765 7899999999999999999999999999989999999999999999999999
Q ss_pred cCCCCCCccccccccccceeEEeeecCCCCcccccchhhHHHHHHHHhcCCeecCCccccCCCCceeEEEECCEEEeeec
Q 002545 451 PVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIP 530 (910)
Q Consensus 451 PveTPEG~~cGLv~~LA~~~~Is~~~~~~~~~~~~~~~~~~i~~~L~~lG~~~~~~~~~~~~~~~~~~V~lnG~~iG~~~ 530 (910)
|+|||||++||||||||++|+|+
T Consensus 359 PveTPEG~~cGLv~~LA~~a~Is--------------------------------------------------------- 381 (866)
T cd00653 359 PIETPEGENCGLVKNLALMARIS--------------------------------------------------------- 381 (866)
T ss_pred CCCCCCCccccchhhhhceEeee---------------------------------------------------------
Confidence 99999999999999999999872
Q ss_pred CccHHHHHHHHHHHHHhcCCCCCCCceEEEEEcCCCCCCCceEeecCCCceeceEEeecCCCCCCCceeeeCccceeeee
Q 002545 531 SSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSEESQNIELIGPFEQVFME 610 (910)
Q Consensus 531 ~~~~~~~~~~lr~~k~~~~~~i~~~~eI~~v~~~~~~~~~~i~i~td~gR~~RPv~~~~~~~~~~g~iE~i~~~Eq~~~~ 610 (910)
||++||+++++.
T Consensus 382 ------------------------------------------------Gr~~rP~~~v~~-------------------- 393 (866)
T cd00653 382 ------------------------------------------------GRIERPYRIVEK-------------------- 393 (866)
T ss_pred ------------------------------------------------eEeeeeEEEecc--------------------
Confidence 888999997631
Q ss_pred eecCCCCCCCCCCCCCceecccCCCccccceeecccCCCCCCcchhhhhhhccccccccceeEEEEeccCceeecCCCCe
Q 002545 611 IRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQT 690 (910)
Q Consensus 611 Ia~~~~~~~~~~~~~~~th~EI~p~~~ls~~asliPF~~hNqspRn~yq~~M~KQaig~~~~n~~~R~D~~~y~L~~pQ~ 690 (910)
.+||+||+|.++||++||+|||+||||||||||||||+|||||++++|+..|.|++.|+|.|||+
T Consensus 394 ---------------~~th~ei~~~~~ls~~asliPf~~hNqspRn~~~~~M~kQa~g~~~~n~~~r~d~~~~~l~~pq~ 458 (866)
T cd00653 394 ---------------EVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQK 458 (866)
T ss_pred ---------------ceEEEEeCccceeeeeeeccCCCCcccccchhhhhcccCCccCchhccccccccchheeeccCCC
Confidence 17999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeEecccccccCccccCCCceeeEEEEeccCCCcccceeeeccccccCcceeeEEEEEEEEeeccCCCcCccceee--cc
Q 002545 691 PIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLF--RR 768 (910)
Q Consensus 691 Plv~t~~~~~~~~~~~~~G~N~iVav~~y~Gyn~EDaiiink~s~~rG~~~~~~~~~~~~~~~~~~~~~~~~~~~f--~~ 768 (910)
|||.|+.++..+++++|+|+|++||||||+||||||||||||+|+|||||++.+|++|.+++...... ..+.+ ..
T Consensus 459 plv~T~~~~~~~~~~~~~G~N~~VAv~~y~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~---~~~~~~~~~ 535 (866)
T cd00653 459 PLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNG---PEEITRGDI 535 (866)
T ss_pred CccccchHHHhCCCccCCCceEEEEEeccccccccceeeeehhhhhcCceeEEEEEEEEEEEEecCCC---cceEecCCC
Confidence 99999999999999999999999999999999999999999999999999999999999987543321 11222 23
Q ss_pred CCCChhhhcccCCCCCcccCceecCCCcEEEeeccCC--------------CceeeeeecCCCceEEEEEEEEecC-CCC
Q 002545 769 NKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTT--------------NSWRTNSRKGSESVFVDYVAVDMKN-SKN 833 (910)
Q Consensus 769 ~~~~~~~~~~ld~dG~~~~g~~v~~gd~l~~~~~~~~--------------~~~~~~~~~~~e~g~v~~v~~~~~~-~~~ 833 (910)
|......+++||+||+|++|+.|++||+|+||+++.. .++.+.+++.+|+|+|++|.++.+. +.+
T Consensus 536 ~~~~~~~~~~ld~dGi~~~g~~v~~gd~li~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~v~~v~~~~~~~~~~ 615 (866)
T cd00653 536 PNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRELNDG 615 (866)
T ss_pred CCCChHHhhccCCCCCcCCCCEecCCCEEEEEecCcccccccccccccCCcceEEEEEecCCCceEEEEEEEeccccCCC
Confidence 4555567899999999999999999999999988752 3566899999999999999998832 113
Q ss_pred CCeEEEEEEeeeeCCCcccceeccCCCccEEeeeecCcCcCccCCCCCcCcEEeCCCCccccccHHHHHHHhhccc
Q 002545 834 LPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKE 909 (910)
Q Consensus 834 ~~~~v~i~~r~~R~p~iGDKf~sRHGqKGv~s~i~~~~dMPf~~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gK~ 909 (910)
+...|+|++|+.|+|+||||||||||||||||++||+|||||| +||++|||||||||||||||||||+|+++||+
T Consensus 616 ~~~~v~v~~r~~R~p~iGDKfssRhGqKGv~s~i~~~~dmPf~-~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~ 690 (866)
T cd00653 616 GNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFT-EDGIPPDIILNPHGFPSRMTIGQLLESLLGKA 690 (866)
T ss_pred CcEEEEEEEeEEecCCcccccccccCCCcEEEEEeccccCCcc-cCCCCCcEEecCCcCcccccHHHHHHHHHHHH
Confidence 4689999999999999999999999999999999999999999 99999999999999999999999999999996
No 7
>TIGR02013 rpoB DNA-directed RNA polymerase, beta subunit. This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit.
Probab=100.00 E-value=8.2e-158 Score=1451.35 Aligned_cols=708 Identities=21% Similarity=0.337 Sum_probs=583.7
Q ss_pred CccCchhhHHHHHHHHHHHHH----------HhHHHHH-----------------------------HHHHHcCCeeeeE
Q 002545 8 DFEPLRELVRHHIESFDYMLD----------EGLSEMF-----------------------------DHCRQAKISYTGK 48 (910)
Q Consensus 8 ~~~~~~~Lv~~hi~SFn~Fi~----------~gl~~i~-----------------------------~ecR~r~~TY~~~ 48 (910)
.+...++|++||++||||||+ +||++++ +|||+|++||+|+
T Consensus 13 ~~~~~p~Lv~~Qi~SFn~FL~~~~~~~~~~~~gL~eii~~~~pI~~~~~~~~l~f~~~~l~~P~~~p~Ear~r~lTYsa~ 92 (1065)
T TIGR02013 13 EVLEVPNLLEIQLDSYDWFLQQDTPPEKRKEEGLEEVFKSIFPIEDYTGNIELEYLSYRLGEPKYSVEECKERGLTYSAP 92 (1065)
T ss_pred ccccCCCHHHHHHHHHHHHHcCCCcccccccccHHHHHhccCcEEecCCcEEEEEEEEEeCCCCCCHHHHHHhCCCccee
Confidence 345689999999999999999 8999999 9999999999999
Q ss_pred EEEEEEEEEecC--CCceeeeEeeecccceeecCCCccCCCCChHHHHhcccccccCCcEEEEcCceeEEEEEEeecCCc
Q 002545 49 LMADVEFQYLDA--GSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNY 126 (910)
Q Consensus 49 l~v~i~~~~~~~--~~~~~~~~v~iG~iPIMv~S~~C~L~~~~~~el~~~~E~~~D~GGYFIInG~EKVIr~qi~~~~N~ 126 (910)
|+|+++++.... +++++.++|+||+||||++ ||||||||+||||++|+++++|.
T Consensus 93 l~v~v~l~~~~~~~~~~i~~~~V~iG~iPiMt~------------------------gGyFIINGsERVIV~Qe~rspg~ 148 (1065)
T TIGR02013 93 LKVKLRLINKEEDGTKEIKEQDVYMGDIPLMTD------------------------RGTFIINGAERVVVSQLHRSPGV 148 (1065)
T ss_pred EEEEEEEEEeccCCccceeeeeEEEeCCCccCC------------------------CceEEECCcEEEEEEEeecCCCE
Confidence 999999975411 2355677999999999986 99999999999999999999999
Q ss_pred cEEEEeccccCCCCcceeeEEEEEeeecCCCceEEEEEEEeCCeEEEEEEeecccccccHHHHHHhccCCCHHHHHHHhc
Q 002545 127 PMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLT 206 (910)
Q Consensus 127 ~~~~~r~~~~~~~~~~t~~~v~~r~~~~~~~~~~~~l~y~~~g~~~l~~~~~~~~~~IPi~ilLkALg~~sD~EI~~~i~ 206 (910)
++..... ..++++ ..|.+.++|.+ ..|+.++++.++.+|++++..+ +||+++||||||+.+|+||++.++
T Consensus 149 ~~~~~~~-~~~~~~--~~~~a~iis~r----gswl~~e~~~~~~i~v~i~~~~---kIPi~illrALG~~sd~eI~~~i~ 218 (1065)
T TIGR02013 149 FFSSEKD-THKSGK--VLFSARIIPYR----GSWLEFETDKKDVLYVRIDRKR---KLPATVLLRALGYTIDTLILNRLG 218 (1065)
T ss_pred EEEEccc-cCCCCc--eEEEEEEEeCC----CCceEEEEecCCeEEEEecCCC---ceeHHHHHHHcCCCcchhhhhhcC
Confidence 8776432 111221 12445566543 4588998888999999998754 699999999999999999999885
Q ss_pred ccccchhhcccCCCCChhhHHHHHHHHHHHHhcccccHHHHHHHHhhcccccccCCCCccHHHHHHHHHHhHhcc-----
Q 002545 207 CCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFV----- 281 (910)
Q Consensus 207 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i~t~~~al~yLg~~fr~~~~~~~~~~~~~~g~~~L~~~ll~----- 281 (910)
. +.++ ...| .+....|+++|+.||++++++. .....+.|+.+|++.+|+
T Consensus 219 ~--------------~~~i----~~~l---~~~~~~~~e~Al~~i~~~~~~g-----~~~~~~~a~~~l~~~f~~~~rY~ 272 (1065)
T TIGR02013 219 S--------------GEYI----RNTL---RKDPTNSEEEALVEIYRKLRPG-----EPPTVEAARSLLENLFFDPKRYD 272 (1065)
T ss_pred c--------------hHHH----HHHH---HhccccCHHHHHHHHHhhcCCC-----CcchHHHHHHHHHHHhcCccccc
Confidence 1 1222 1222 2334789999999999998642 233467899999999987
Q ss_pred --CCCC----------------CcchHHHHHHHHHHHHhhcCCCCCCCCcccccccEEcccchhhHHHHHHHHHHHHHHH
Q 002545 282 --HLND----------------NNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKG 343 (910)
Q Consensus 282 --Hl~~----------------~~~K~~~L~~Mi~kLl~~~~g~~~~Dd~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~ 343 (910)
|+|. ...|+++|+ |+++|+.+..|...+||+|||+||||+++|+||+.+|+..|+++.+.+
T Consensus 273 LghiGr~kln~Kl~~~~~~~~~~l~k~d~l~-mi~~Ll~~~~g~~~~DD~Dhl~NKRvr~aGeLL~~~fr~~l~rl~k~i 351 (1065)
T TIGR02013 273 LGRVGRYKLNKKLGLDVPEDIGVLTKEDIIA-TIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIV 351 (1065)
T ss_pred ccccchhhhhhhcCcCcCcccceehHHHHHH-HHHHHHHhhcCCCCCcchhhhhccchhhHHHHHHHHHHHHHHHHHHHH
Confidence 9992 124788775 999999999999999999999999999999999999999888887777
Q ss_pred HHHHHHHHhhcCCcccccchHHHHHHHhcCCCcchHHHHHhHhcccCcccccccccccccceEEEccccchhhHhhhhcc
Q 002545 344 KKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRA 423 (910)
Q Consensus 344 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~sGvsqvleRln~~~~lSH~Rr 423 (910)
+..+.+. . .+ .+ .++.++ +++.||+++++||+|| ||||+++|+||++.|||+||
T Consensus 352 k~~l~~~-~--~~--~~----~~~~~i---~~~~it~~i~~ff~tg--------------glSQ~Ldr~NpLs~lsh~RR 405 (1065)
T TIGR02013 352 RERMSTQ-D--TD--TL----TPQDLI---NAKPISAAIKEFFGSS--------------QLSQFMDQTNPLAELTHKRR 405 (1065)
T ss_pred HHHhhhc-c--cc--cC----CHHHhc---CccchHHHHHHHhccC--------------CcccccccCCHHHhhhhhce
Confidence 6665422 1 11 11 134455 3568999999999985 99999999999999999999
Q ss_pred cc---cCCcccccccccccccCCCCccccccCCCCCCccccccccccceeEEeeecCCCCcccccchhhHHHHHHHHhcC
Q 002545 424 VH---RGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVG 500 (910)
Q Consensus 424 v~---rg~~~~~~k~t~vR~Lhps~wG~iCPveTPEG~~cGLv~~LA~~~~Is~~~~~~~~~~~~~~~~~~i~~~L~~lG 500 (910)
++ +|++.+++|+++||+|||||||||||+|||||++||||+|||++|+|+. +|
T Consensus 406 lsslgpggl~r~~~~~~~RdlHpShyGrICPiETPEG~n~GLVknLA~~a~i~~------------------------~G 461 (1065)
T TIGR02013 406 LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNE------------------------YG 461 (1065)
T ss_pred ecccCCCCcCccccCCccCccCccccccccCCCCCCCCccccccchhhhcccCc------------------------ce
Confidence 99 4678899999999999999999999999999999999999999999962 34
Q ss_pred CeecCCccccCCCCceeEEEECCEEEeeecCccHHHHHHHHHHHHHhcCCCCCCCceEEEEEcCCCCCCCceEeecCCCc
Q 002545 501 MIPSLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPK 580 (910)
Q Consensus 501 ~~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~~~lr~~k~~~~~~i~~~~eI~~v~~~~~~~~~~i~i~td~gR 580 (910)
++.. | |.++.||++.
T Consensus 462 ~i~~-P----------~~~V~ng~~~------------------------------------------------------ 476 (1065)
T TIGR02013 462 FIET-P----------YRKVKDGKVV------------------------------------------------------ 476 (1065)
T ss_pred EEeC-C----------eEEEECCeEe------------------------------------------------------
Confidence 4321 2 3333444321
Q ss_pred eeceEEeecCCCCCCCceeeeCccceeeeeeecCCCCCCCCC------------------CCCCceecccCCCcccccee
Q 002545 581 FVRPVRNISLPSEESQNIELIGPFEQVFMEIRCPDGGDGGRR------------------NAFPATHEEIHPTGMLSVVA 642 (910)
Q Consensus 581 ~~RPv~~~~~~~~~~g~iE~i~~~Eq~~~~Ia~~~~~~~~~~------------------~~~~~th~EI~p~~~ls~~a 642 (910)
..+.+||++++|++++.||..+.++.... ....+||+||+|.+|||++|
T Consensus 477 -------------~~~~i~yl~a~eE~~~~Ia~~~~~l~~~~~~~~~~i~~r~~~~f~~~~~~~vt~~ei~p~~ilsv~a 543 (1065)
T TIGR02013 477 -------------VTDEVDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYRGEITLVSPDQVDYMDVSPKQVVSVAA 543 (1065)
T ss_pred -------------ccceeEECChHHhCCcEEEecCcCcCccCccccceeeEEEcCceeecChhHeeEEeeChhhhhhhHh
Confidence 01267888888888888887766553210 01347999999999999999
Q ss_pred ecccCCCCCCcchhhhhhhccccccccc-----------------------------------eeEEEEeccC-------
Q 002545 643 NLTPYSDHNQSPRNMYQCQMAKQTMGFS-----------------------------------VQALKFRADQ------- 680 (910)
Q Consensus 643 sliPF~~hNqspRn~yq~~M~KQaig~~-----------------------------------~~n~~~R~D~------- 680 (910)
|||||+||||||||||||||||||||+. ++|+..|.|+
T Consensus 544 slIPFleHNds~R~lmgsnM~kQavpl~~~e~p~VgTg~E~~v~~ds~~~i~a~~~G~v~~v~~~~~~~r~d~~~~~~~~ 623 (1065)
T TIGR02013 544 SLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRYDEDEDEPDG 623 (1065)
T ss_pred hcCCCccccCCcchhhhhhhhhhhhcccccCCCEEEcCcchhhhccccceeEeccCCEEEEEccceEEEEecCCcccccc
Confidence 9999999999999999999999999877 8999999995
Q ss_pred --ceeecC----------CCCeeeEeccc----ccccC------ccccCCCceeeEEEEeccCCCcccceeeeccccccC
Q 002545 681 --KLYHLQ----------TPQTPIVRTNT----YTKYG------IDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRG 738 (910)
Q Consensus 681 --~~y~L~----------~pQ~Plv~t~~----~~~~~------~~~~~~G~N~iVav~~y~Gyn~EDaiiink~s~~rG 738 (910)
+.|.|. |||+|||+|+. .+.+. ++|+|+|+|++||||||+||||||||||||+|++||
T Consensus 624 ~~~~y~L~~~~~snq~~~~~q~Plv~~~~~v~~~~~l~d~~~~~~~e~~~G~N~~VAvm~y~GYn~EDAiiink~~i~rg 703 (1065)
T TIGR02013 624 GIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERLVKDD 703 (1065)
T ss_pred cceEEEeecccccccCceEEeeeeeccCCeEeeeeEecccccccCCcCcCccceEEEEEeeecccccceEEeehhhhcCC
Confidence 456644 99999999964 33333 899999999999999999999999999999999999
Q ss_pred cceeeEEEEEEEEeeccCCCcCccceeec--cCCCChhhhcccCCCCCcccCceecCCCcEEEeeccCC-----------
Q 002545 739 MCHGQIYQTETIDLSDDGNKVDRGQKLFR--RNKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTT----------- 805 (910)
Q Consensus 739 ~~~~~~~~~~~~~~~~~~~~~~~~~~~f~--~~~~~~~~~~~ld~dG~~~~g~~v~~gd~l~~~~~~~~----------- 805 (910)
+|++.+|++|++++...+. ..+.|. .|+.....+++||+||+|++|+.|++||||+||++|..
T Consensus 704 ~~~s~~~~~~~~~~~~~~~----g~e~~~~~~p~~~~~~~~~Ld~dGi~~~G~~v~~gdilvgk~~p~~~~~~~~~~~l~ 779 (1065)
T TIGR02013 704 VFTSIHIEEYEVEARDTKL----GPEEITRDIPNVSEEALRNLDENGIVRIGAEVKAGDILVGKVTPKGETELTPEEKLL 779 (1065)
T ss_pred ceEEEEEEEEEEEeeccCC----CceEeeccCCCCchhhhhccCCCCCccCccEeCCCCEEEEEecCCcccccChhhhhh
Confidence 9999999999998644321 123333 36555567899999999999999999999999987632
Q ss_pred ----------CceeeeeecCCCceEEEEEEEEecCCCCC-----CeEEEEEEeeeeCCCcccceeccCCCccEEeeeecC
Q 002545 806 ----------NSWRTNSRKGSESVFVDYVAVDMKNSKNL-----PQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPD 870 (910)
Q Consensus 806 ----------~~~~~~~~~~~e~g~v~~v~~~~~~~~~~-----~~~v~i~~r~~R~p~iGDKf~sRHGqKGv~s~i~~~ 870 (910)
.++.+++++.+|+|+||+|.++.+++++. .+.|+|++|+.|+|++|||||||||||||||+|||+
T Consensus 780 ~~~~~~~~~~~~d~s~~~~~~~~g~V~~V~~~~~~~~~~~~~~~~~~vkv~ir~~R~p~iGDKfasRHGqKGvis~i~~~ 859 (1065)
T TIGR02013 780 RAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSRKQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPI 859 (1065)
T ss_pred hhhcccCCccccccceEccCCCCEEEEEEEEEeccCCCccCcCccEEEEEEEeecccccccchhhhcccCceeEEeEecC
Confidence 13458899999999999999998765532 468999999999999999999999999999999999
Q ss_pred cCcCccCCCCCcCcEEeCCCCccccccHHHHHHHhhccc
Q 002545 871 IDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKE 909 (910)
Q Consensus 871 ~dMPf~~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gK~ 909 (910)
|||||| +||++|||||||||||||||||||+|+++|||
T Consensus 860 eDMPf~-~~G~~pDiIiNPhg~PSRMtiGqllE~~~gka 897 (1065)
T TIGR02013 860 EDMPFL-EDGTPVDIVLNPLGVPSRMNIGQILETHLGWA 897 (1065)
T ss_pred CCCCcc-CCCCCccEEECCCCCcccccHHHHHHHHHHHH
Confidence 999999 99999999999999999999999999999996
No 8
>PRK00405 rpoB DNA-directed RNA polymerase subunit beta; Reviewed
Probab=100.00 E-value=5.4e-156 Score=1442.50 Aligned_cols=722 Identities=21% Similarity=0.317 Sum_probs=579.5
Q ss_pred cCchhhHHHHHHHHHHHH-------HHhHHHHH-----------------------------HHHHHcCCeeeeEEEEEE
Q 002545 10 EPLRELVRHHIESFDYML-------DEGLSEMF-----------------------------DHCRQAKISYTGKLMADV 53 (910)
Q Consensus 10 ~~~~~Lv~~hi~SFn~Fi-------~~gl~~i~-----------------------------~ecR~r~~TY~~~l~v~i 53 (910)
...++|++||++|||||| ++||++++ +|||+|++||+|||+|++
T Consensus 22 ~~~p~Lv~~Qi~SFn~Fl~~~~~~~~~gL~~ii~~~~pI~~~~~~~~l~f~~~~l~~P~~tp~Ear~r~lTYSaplyv~v 101 (1112)
T PRK00405 22 LELPNLLEIQLDSFDWFLQLDVPPEDEGLEEVFRSIFPIEDFNGNLSLEFVSYELGEPKYDVEECKERGLTYSAPLRVKL 101 (1112)
T ss_pred CCCCCHHHHHHHHHHHHHhcCCcccchhHHHHHHhcCCEEecCCcEEEEEeeeEcCCCCCCHHHHHHhCCCCCeeEEEEE
Confidence 358999999999999999 99999999 999999999999999999
Q ss_pred EEEEecCCCceeeeEeeecccceeecCCCccCCCCChHHHHhcccccccCCcEEEEcCceeEEEEEEeecCCccEEEEec
Q 002545 54 EFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRS 133 (910)
Q Consensus 54 ~~~~~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~~~~~el~~~~E~~~D~GGYFIInG~EKVIr~qi~~~~N~~~~~~r~ 133 (910)
+++.. .+++++.++|+||+||||+ +||||||||+||||++|+++++|.++.....
T Consensus 102 ~l~~~-~~~~i~~~~V~iG~iPiMt------------------------~gGyFIING~ERVIVsQe~rSPg~~~~~~~~ 156 (1112)
T PRK00405 102 RLINK-ETGEIKEQEVYMGDIPLMT------------------------ENGTFIINGTERVIVSQLHRSPGVYFDHDKD 156 (1112)
T ss_pred EEEEe-ccCceeeeeEEEecccccc------------------------CCceEEECCeEEEEEEEeecCCCEEEEEecc
Confidence 99754 1346677899999999997 4999999999999999999999987766542
Q ss_pred cccCCCCcceeeEEEEEeeecCCCceEEEEEEEeCCeEEEEEEeecccccccHHHHHHhccCCCHHHHHHHhcccccchh
Q 002545 134 SFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKY 213 (910)
Q Consensus 134 ~~~~~~~~~t~~~v~~r~~~~~~~~~~~~l~y~~~g~~~l~~~~~~~~~~IPi~ilLkALg~~sD~EI~~~i~~~~~~~~ 213 (910)
+. ..++ ..|.+.+.+.+ ..|+.++++.++.+|++++..+ +||+++||||||+ ||+||++.++. +..+
T Consensus 157 k~-~~~k--~~y~a~Iis~r----Gswl~~e~d~k~~I~vri~~~~---kIPi~iLLrALGl-sd~eIl~~i~~--~~~~ 223 (1112)
T PRK00405 157 KT-SSGK--LLYSARIIPYR----GSWLEFEFDPKDILYVRIDRRR---KLPVTVLLRALGY-SDEEILDLFYE--KEEF 223 (1112)
T ss_pred cc-CCCc--eeEEEEEEECC----CCcEEEEEecCCeEEEEecCCC---cccHHHHHHHcCC-CHHHHHHHhcc--cccc
Confidence 11 1111 12455666543 4599999999999999998543 6999999999999 99999999962 1110
Q ss_pred h--------ccc-----C---CCC-Chhh-------HH-HH-HHHHHHHHhcccccHHHHHHHHhhcccccccCCCCccH
Q 002545 214 K--------KEK-----G---AVG-SPLV-------SE-RV-KIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESY 267 (910)
Q Consensus 214 ~--------~~~-----~---~~~-~~~~-------~~-~~-~~~l~~~~~~~i~t~~~al~yLg~~fr~~~~~~~~~~~ 267 (910)
. ... . +.+ ...+ .+ .. ..+.+.+.+.+..|+++|+.||++++++. ....
T Consensus 224 ~~~~~~~~~~~~~~~~~~~~~~~~~~ei~~~~~~~~~~~~~~~~i~~~l~~~~~~t~e~Al~~I~k~l~~g-----~~~~ 298 (1112)
T PRK00405 224 GKEIEVPVEYLLGKVLAEDIVDEETGEVLAEANDEITEELDGPYIRNTLEKDPTSSREEALVEIYRRLRPG-----EPPT 298 (1112)
T ss_pred cceeccchHHhcccchhhhhcccccceeeeccCCccchhhhhHHHHHHHhhccccCHHHHHHHHHhhcCCC-----Ccch
Confidence 0 000 0 000 0000 00 01 11222233345789999999999998642 2334
Q ss_pred HHHHHHHHHhHhc-------cCCCCC-----------c----chHHHHHHHHHHHHhhcCCCCCCCCcccccccEEcccc
Q 002545 268 YAVAETVIRDYIF-------VHLNDN-----------N----DKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPG 325 (910)
Q Consensus 268 ~~~g~~~L~~~ll-------~Hl~~~-----------~----~K~~~L~~Mi~kLl~~~~g~~~~Dd~D~l~NkRv~l~G 325 (910)
.+.|+.+|++.+| ||+|.. . .+..++++|+++|+.+..|...+||+|||+||||+++|
T Consensus 299 ~e~a~~~l~~~ff~~~rYdL~hiGr~k~nkKl~l~~~~~~~~L~~~d~~~mi~~Ll~l~~g~~~~DDiDhl~NKRvr~aG 378 (1112)
T PRK00405 299 VEAARSLLENLFFDPKRYDLSKVGRYKLNKKLGLDEDEDVRVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVG 378 (1112)
T ss_pred HHHHHHHHHHHhcCccccccccCCceecchhcccCcccccccccHHHHHHHHHHHHhhhcccCCCcchhHHhcchhhhHH
Confidence 5779999999886 999931 1 13445699999999999999999999999999999999
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCcccccchHHHHHHHhcCCCcchHHHHHhHhcccCcccccccccccccce
Q 002545 326 HLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGY 405 (910)
Q Consensus 326 ~Ll~~lf~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~sGv 405 (910)
+||+.+|+..|+++.+.++..+... . .+ .+ .++.++ +++.||++|++||+|| ||
T Consensus 379 eLL~~~fr~~~~rl~k~ik~~l~~~--~-~~--~~----~~~~li---n~~~it~~i~~ff~tg--------------gl 432 (1112)
T PRK00405 379 ELLQNQFRIGLSRMERAVRERMSLQ--D-LD--TL----TPQDLI---NAKPVVAAIKEFFGSS--------------QL 432 (1112)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhc--c-cc--cC----CHHHhh---CchhHHHHHHHhhccC--------------Cc
Confidence 9999999988888777776665432 1 11 11 144455 4568999999999985 89
Q ss_pred EEEccccchhhHhhhhcccc---cCCcccccccccccccCCCCccccccCCCCCCccccccccccceeEEeeecCCCCcc
Q 002545 406 TVQAERLNFLRFISFFRAVH---RGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNI 482 (910)
Q Consensus 406 sqvleRln~~~~lSH~Rrv~---rg~~~~~~k~t~vR~Lhps~wG~iCPveTPEG~~cGLv~~LA~~~~Is~~~~~~~~~ 482 (910)
||+++|+|+++.|||+||++ +|++.+++++++||+|||||||||||+|||||++||||+|||++|+|+
T Consensus 433 SQ~Ldq~NpLselshkRRlss~gpggl~r~~a~~~~R~lH~ShyGriCPiETPEG~n~GLV~nLA~~a~i~--------- 503 (1112)
T PRK00405 433 SQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVN--------- 503 (1112)
T ss_pred ceeeccCCHHHhhhhhceecccCCCCcCccccCCcccccCccccccccCcCCCCCCccccccchhhccccc---------
Confidence 99999999999999999999 567889999999999999999999999999999999999999999997
Q ss_pred cccchhhHHHHHHHHhcCCeecCCccccCCCCceeEEEECCEEEeeecCccHHHHHHHHHHHHHhcCCCCCCCceEEEEE
Q 002545 483 RDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVP 562 (910)
Q Consensus 483 ~~~~~~~~~i~~~L~~lG~~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~~~lr~~k~~~~~~i~~~~eI~~v~ 562 (910)
++|++.. + |.+++||.|.-
T Consensus 504 ---------------~~G~~~t-p----------~~~~~nG~~~~----------------------------------- 522 (1112)
T PRK00405 504 ---------------EYGFIET-P----------YRKVVDGKVTD----------------------------------- 522 (1112)
T ss_pred ---------------cCCcccc-c----------eEEEECCeEcc-----------------------------------
Confidence 2565532 2 77889998621
Q ss_pred cCCCCCCCceEeecCCCceeceEEeecCCCCCCCceeeeCccceeeeeeecCCCCCCCC------------------CCC
Q 002545 563 LSLGGAYPGLYLFTSPPKFVRPVRNISLPSEESQNIELIGPFEQVFMEIRCPDGGDGGR------------------RNA 624 (910)
Q Consensus 563 ~~~~~~~~~i~i~td~gR~~RPv~~~~~~~~~~g~iE~i~~~Eq~~~~Ia~~~~~~~~~------------------~~~ 624 (910)
.+||+|++||+...||..+.++... ...
T Consensus 523 ----------------------------------~i~yl~a~eE~~~~Ia~~~~~l~~~~~~~~~~i~~r~~~e~~~~~~ 568 (1112)
T PRK00405 523 ----------------------------------EIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYKGEFVLVPP 568 (1112)
T ss_pred ----------------------------------ceEECCHHHhcCcEEEecCcccCCCCcccCceEEEEecCcceeech
Confidence 1344444444444444433333210 001
Q ss_pred CCceecccCCCccccceeecccCCCCCCcchhhhhhhcccccccccee--------------------------------
Q 002545 625 FPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQ-------------------------------- 672 (910)
Q Consensus 625 ~~~th~EI~p~~~ls~~asliPF~~hNqspRn~yq~~M~KQaig~~~~-------------------------------- 672 (910)
..+||+||+|.+++|++||||||++|||||||+|||||||||||+...
T Consensus 569 ~~~~~~~i~p~qi~sv~aslIPFleHnda~R~lmgSnMqrQAvpl~~~~~p~vgTg~e~~~~~ds~~~i~a~~~G~v~~v 648 (1112)
T PRK00405 569 EEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAKRDGVVEYV 648 (1112)
T ss_pred hhceEEeechhhhceehhhccCcccccCCcchhhhhhhhhhhhhhccccCCeeecCcchhhhhhcchheEeccCCEEEEE
Confidence 237999999999999999999999999999999999999999999877
Q ss_pred ---EEEEec-----------------cCceee-cCCCCeeeEecccc----ccc------CccccCCCceeeEEEEeccC
Q 002545 673 ---ALKFRA-----------------DQKLYH-LQTPQTPIVRTNTY----TKY------GIDEYPTGTNAIVAVLAYTG 721 (910)
Q Consensus 673 ---n~~~R~-----------------D~~~y~-L~~pQ~Plv~t~~~----~~~------~~~~~~~G~N~iVav~~y~G 721 (910)
|+..|. |+..++ +.|||+|||+|+.+ +.+ +++++|+|+|++||||||+|
T Consensus 649 ~~~~i~ir~~~~~~~~~~~~~y~L~~~~~sn~~~~~~q~Plv~~~~~v~~g~~lad~~~~~~~e~~~G~N~~VA~~~y~G 728 (1112)
T PRK00405 649 DASRIVVRVEELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQNVLVAFMPWNG 728 (1112)
T ss_pred eCCEEEEeecccccCCCCeeEEEecccccccccceeecceeeecCCeEeeccEeecccccCcccccCCcceEEEEEeecc
Confidence 888888 445555 68999999999954 443 68999999999999999999
Q ss_pred CCcccceeeeccccccCcceeeEEEEEEEEeeccCCCcCccceeec--cCCCChhhhcccCCCCCcccCceecCCCcEEE
Q 002545 722 YDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFR--RNKDAKSLHSVIDSDGLPYVGQMIHPGEPYCS 799 (910)
Q Consensus 722 yn~EDaiiink~s~~rG~~~~~~~~~~~~~~~~~~~~~~~~~~~f~--~~~~~~~~~~~ld~dG~~~~g~~v~~gd~l~~ 799 (910)
|||||||||||+|++||||++.+|++|..++..... ..+.+. .|+.....+++||+||||++|+.|++||||+|
T Consensus 729 Yn~EDaiiink~si~rg~~~s~~~~~~~~~~~~~~~----~~~~~~~~~p~~~~~~~~~Ld~dGi~~~G~~v~~gDilig 804 (1112)
T PRK00405 729 YNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKL----GPEEITRDIPNVSEEALRNLDESGIVRIGAEVKPGDILVG 804 (1112)
T ss_pred cCccceEEEEhhhhccCceEEEEEeeeeeEeeccCC----CceeecccCCCCChHHhhccCCCCCccCccEecCCCEEEE
Confidence 999999999999999999999999999987643321 122333 55555556899999999999999999999999
Q ss_pred eeccCC---------------------CceeeeeecCCCceEEEEEEEEec-CCCCC-----CeEEEEEEeeeeCCCccc
Q 002545 800 IYDKTT---------------------NSWRTNSRKGSESVFVDYVAVDMK-NSKNL-----PQKANIRFRHTRNPIIGD 852 (910)
Q Consensus 800 ~~~~~~---------------------~~~~~~~~~~~e~g~v~~v~~~~~-~~~~~-----~~~v~i~~r~~R~p~iGD 852 (910)
|++++. .++.+++++.+|+|+||+|.++.+ ++++. .+.|+|++|+.|+|+|||
T Consensus 805 k~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~s~~~~~~~~g~V~~v~~~~~~~~~~~~~~~~~~~vkv~ir~~R~p~iGD 884 (1112)
T PRK00405 805 KVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTRIEQGDELPPGVNKLVKVYIAQKRKIQVGD 884 (1112)
T ss_pred EecCCCccccChhhhhhhhhhcccccccccceEEcCCCCCEEEEEEEEeeccccCCccCcCcceEEEEEEeeecccCccc
Confidence 987632 234688899999999999999987 55421 468999999999999999
Q ss_pred ceeccCCCccEEeeeecCcCcCccCCCCCcCcEEeCCCCccccccHHHHHHHhhccc
Q 002545 853 KFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKE 909 (910)
Q Consensus 853 Kf~sRHGqKGv~s~i~~~~dMPf~~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gK~ 909 (910)
|||||||||||||+|||+|||||+ +||++|||||||||||||||||||+|+++||+
T Consensus 885 KfasRHGqKGvis~i~~~eDMPf~-~~G~~pDiIiNPhg~PSRMtiGql~E~~~gk~ 940 (1112)
T PRK00405 885 KMAGRHGNKGVVSRILPVEDMPYL-EDGTPVDIVLNPLGVPSRMNIGQILETHLGWA 940 (1112)
T ss_pred chhhccCCceeEEeEeccCCCCcC-CCCCCCcEEECCCCCcccccHHHHHHHHhhHH
Confidence 999999999999999999999999 99999999999999999999999999999996
No 9
>CHL00001 rpoB RNA polymerase beta subunit
Probab=100.00 E-value=7.7e-153 Score=1399.79 Aligned_cols=728 Identities=19% Similarity=0.253 Sum_probs=584.3
Q ss_pred CccCchhhHHHHHHHHHHHHHHhHHHHH-------------------------------HHHHHcCCeeeeEEEEEEEEE
Q 002545 8 DFEPLRELVRHHIESFDYMLDEGLSEMF-------------------------------DHCRQAKISYTGKLMADVEFQ 56 (910)
Q Consensus 8 ~~~~~~~Lv~~hi~SFn~Fi~~gl~~i~-------------------------------~ecR~r~~TY~~~l~v~i~~~ 56 (910)
....+++|+++|++||||||++||++++ +|||+|++||+|+|+|+++++
T Consensus 8 ~~~~~P~Lv~~Q~~SF~~Fl~~gL~~i~~~~~pI~~~~~~~~~~~~~~~~~l~~P~~~p~ear~r~lTYsa~l~v~v~l~ 87 (1070)
T CHL00001 8 GMSTIPGFNQIQFEGFCRFIDQGLTEELSKFPKIEDTDQEIEFQLFVETYQLVEPLIKERDAVYESLTYSSELYVPAGLI 87 (1070)
T ss_pred CccCCCCHHHHHHHHHHHHHHHhHHHHHHhcCCeECCCCCEEEEEEeCeEEECCCCCCHHHHHHhCCCCCceeEEEEEEE
Confidence 3457899999999999999999999999 999999999999999999997
Q ss_pred EecCCCceeeeEeeecccceeecCCCccCCCCChHHHHhcccccccCCcEEEEcCceeEEEEEEeecCCccEEEEecccc
Q 002545 57 YLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRSSFR 136 (910)
Q Consensus 57 ~~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~~~~~el~~~~E~~~D~GGYFIInG~EKVIr~qi~~~~N~~~~~~r~~~~ 136 (910)
.. .++.++.++|++|+||+| |+||||||||+||||++|+.+++|.++.....+
T Consensus 88 ~~-~~~~i~~~~V~iG~iPlM------------------------t~gG~FIING~ERVIVsQ~~rSpg~~~~~~~~~-- 140 (1070)
T CHL00001 88 WK-KSRDMQEQTVFIGNIPLM------------------------NSLGTFIINGIYRVVINQILRSPGIYYRSELDH-- 140 (1070)
T ss_pred Ec-CceeEEEeEEEEecCCcc------------------------CCCcEEEEcCcEEEEEEEEeccCCEEEEEecCC--
Confidence 43 234566789999999999 459999999999999999999999887764321
Q ss_pred CCCCcceeeEEEEEeeecCCCceEEEEEEEeCCeEEEEEEeecccccccHHHHHHhccCCCHHHHHHHhcccccchhhcc
Q 002545 137 DRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKKE 216 (910)
Q Consensus 137 ~~~~~~t~~~v~~r~~~~~~~~~~~~l~y~~~g~~~l~~~~~~~~~~IPi~ilLkALg~~sD~EI~~~i~~~~~~~~~~~ 216 (910)
+.... |.+.+++.+. .|+.++++.++.+|+++...+ +||+++||||||+ +|+||++.++ ++
T Consensus 141 ~~~~~---y~a~iis~rg----swl~~e~d~~~~i~vri~~~~---kiPi~ilLrALG~-sd~eIl~~~~--~~------ 201 (1070)
T CHL00001 141 NGISV---YTGTIISDWG----GRLELEIDRKARIWARVSRKQ---KISILVLLSAMGL-NLREILDNVC--YP------ 201 (1070)
T ss_pred CCcee---EEEEEEecCC----CceEEEEecCCeEEEEecCCC---cccHHHHHHHcCC-CHHHHHHHhC--cH------
Confidence 11223 4455555432 488898898899999998753 7999999999999 6999999885 11
Q ss_pred cCCCCChhhHHHHHHHHHHHHhcccccHHHHHHHHhhcccccccCCCCccHHHHHHHHHHhHhccC------CCCC----
Q 002545 217 KGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVH------LNDN---- 286 (910)
Q Consensus 217 ~~~~~~~~~~~~~~~~l~~~~~~~i~t~~~al~yLg~~fr~~~~~~~~~~~~~~g~~~L~~~ll~H------l~~~---- 286 (910)
+.+..++.+..+.++.|+++|+.||++++... +......+.++.+|.+.+|+| +|..
T Consensus 202 ----------~~l~~~l~~~~~~~~~t~e~Al~~i~~~l~~r---~~~~~~~~~a~~~l~~~ff~~rY~Lg~vGr~~~n~ 268 (1070)
T CHL00001 202 ----------EIFLSFLNDKEKKKIGSKENAILEFYQQFACV---GGDPVFSESLCKELQKKFFQQRCELGRIGRRNMNR 268 (1070)
T ss_pred ----------HHHHHHHHHHhhccccCHHHHHHHHHHhhccC---CCCcchHHHHHHHHHHHhccccccccccCchhhhh
Confidence 12233333333346889999999999997321 233445678999999999999 7731
Q ss_pred c------chHHHH-----HHHHHHHHhhcCCCCCCCCcccccccEEcccchhhHHHHHHHHHHHHHHHHHHHHHHHhhcC
Q 002545 287 N------DKFNLL-----IFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNG 355 (910)
Q Consensus 287 ~------~K~~~L-----~~Mi~kLl~~~~g~~~~Dd~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~~~~i~~~~~~~~ 355 (910)
. .|+.+| ++|+++|+.+..|....||+|||+||||+++|+||+++||..|+++.+.++..+.+.+.+ .
T Consensus 269 kl~~~~~~~~~~L~~~Di~~~i~~Ll~l~~G~~~~DDiDhLgNKRvr~vGeLL~~qfr~~l~r~~r~ik~~m~~~~~~-~ 347 (1070)
T CHL00001 269 KLNLDIPENNTFLLPQDVLAAADYLIGMKFGMGTLDDIDHLKNKRIRSVADLLQDQFGLALNRLENAVRGTICGAIRR-K 347 (1070)
T ss_pred hhcccccccceEecHHHHHHHHHHHHHhhcCCCCccchhHHhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-c
Confidence 1 345555 999999999999999999999999999999999999999988888877777777654332 2
Q ss_pred CcccccchHHHHHHHhcCCCcchHHHHHhHhcccCcccccccccccccceEEEccccchhhHhhhhcccc---cCCcccc
Q 002545 356 KKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVH---RGASFAG 432 (910)
Q Consensus 356 ~~~~~~~~~~~~~~~~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~sGvsqvleRln~~~~lSH~Rrv~---rg~~~~~ 432 (910)
+. + .++.++ ++++||++|++||+| +||||+++|+|+++.|||+||++ +|+..++
T Consensus 348 ~~--~----~~~~li---n~~~It~~ik~ff~t--------------s~LSQflDqtNpLseltHkRRlsslGpgglsr~ 404 (1070)
T CHL00001 348 LI--P----TPQNLV---TSTPLTTTYESFFGS--------------HPLSQFLDQTNPLTEIVHGRKLSSLGPGGLTGR 404 (1070)
T ss_pred cc--C----CHHHhh---CcchHHHHHHhhhcC--------------CcceeeeccCCHHHhhhhhhcccccCCCCcccc
Confidence 21 1 144455 456899999999997 79999999999999999999999 5566678
Q ss_pred cccccccccCCCCccccccCCCCCCccccccccccceeEEeeecCCCCcccccchhhHHHHHHHHhcCCeecCCccccCC
Q 002545 433 LRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSG 512 (910)
Q Consensus 433 ~k~t~vR~Lhps~wG~iCPveTPEG~~cGLv~~LA~~~~Is~~~~~~~~~~~~~~~~~~i~~~L~~lG~~~~~~~~~~~~ 512 (910)
++.++||+|||||||||||+|||||++||||++||++|+|+.....+++ |+. ++...+..++ ..++..
T Consensus 405 ~a~fevRdvHpShyGRICPIETPEG~NiGLI~sLA~~A~In~~GfietP---~~~-------v~~~~~~~~i-~ylsa~- 472 (1070)
T CHL00001 405 TASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIGHWGSLESP---FYE-------ISERSKEERM-VYLSPS- 472 (1070)
T ss_pred ccCCcccccCccccccccCCCCCCcccccchhhhhhhcccccCCCcccc---eee-------ecccccccee-EEcccc-
Confidence 8888999999999999999999999999999999999999976655544 222 2223333322 111111
Q ss_pred CCceeEEEECCEEEeeecCccHHHHHHHHHHHHHhcCCCCCCCceEEEEEcCCCCCCCceEeecCCCceeceEEeecCCC
Q 002545 513 PPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPS 592 (910)
Q Consensus 513 ~~~~~~V~lnG~~iG~~~~~~~~~~~~~lr~~k~~~~~~i~~~~eI~~v~~~~~~~~~~i~i~td~gR~~RPv~~~~~~~ 592 (910)
.++.+.|+ ||.|+|..... ..+. .+ |+..
T Consensus 473 ee~~~~Ia-~g~~~~~~~~~------------------~~~~-----~~----------------------~~r~----- 501 (1070)
T CHL00001 473 EDEYYMIA-AGNSLALNQGI------------------QEEQ-----VV----------------------PARY----- 501 (1070)
T ss_pred ccCceEEE-eCceeeccCCc------------------cccc-----ee----------------------EEEe-----
Confidence 24557777 99998742100 0000 01 1110
Q ss_pred CCCCceeeeCccceeeeeeecCCCCCCCCCCCCCceecccCCCccccceeecccCCCCCCcchhhhhhhcccccccccee
Q 002545 593 EESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQ 672 (910)
Q Consensus 593 ~~~g~iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~p~~~ls~~asliPF~~hNqspRn~yq~~M~KQaig~~~~ 672 (910)
-++|+.+|+. + .|||||+|.+|+|++||||||+||||||||+|||||||||||+...
T Consensus 502 ------------~~e~~~i~~~--~---------i~~~dIsP~qi~svaasLIPFleHndanRalmgsnMqrQAvpll~~ 558 (1070)
T CHL00001 502 ------------RQEFLTIAWE--Q---------IHLRSIFPFQYFSIGASLIPFLEHNDANRALMGSNMQRQAVPLSRS 558 (1070)
T ss_pred ------------cCeEEEEchH--H---------CcEEeeChhhhhhhhhhcCCCccccCcchhhhhhccchhccccccC
Confidence 0224556654 2 5999999999999999999999999999999999999999999877
Q ss_pred E---------EEEec-----------------c-----------C-ceeecCC---------CCeeeEecccccccC---
Q 002545 673 A---------LKFRA-----------------D-----------Q-KLYHLQT---------PQTPIVRTNTYTKYG--- 702 (910)
Q Consensus 673 n---------~~~R~-----------------D-----------~-~~y~L~~---------pQ~Plv~t~~~~~~~--- 702 (910)
+ +..|. | + ..|++.| ||||||+++.+...|
T Consensus 559 ~~p~VgTG~E~~~~~ds~~~i~a~~~G~V~~vd~~~I~i~~~~~~~~y~l~~y~rsnq~t~~~QkPlV~~g~~v~~g~~l 638 (1070)
T CHL00001 559 EKCIVGTGLERQVALDSGVVAIAEHEGKIIYTDTDKIILSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCVKKGQIL 638 (1070)
T ss_pred CCCEeecCcchhhhhcccceeEEccCCEEEEEeCCEEEEEcCCCeEEEEeeceeccCCCcccccCCEEecCCEEccCCEe
Confidence 7 55555 5 3 3466778 999999999766654
Q ss_pred -------ccccCCCceeeEEEEeccCCCcccceeeeccccccCcceeeEEEEEEEEeeccCCCcCccceeec--cCCCCh
Q 002545 703 -------IDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFR--RNKDAK 773 (910)
Q Consensus 703 -------~~~~~~G~N~iVav~~y~Gyn~EDaiiink~s~~rG~~~~~~~~~~~~~~~~~~~~~~~~~~~f~--~~~~~~ 773 (910)
.+|+|+|+|++||||||+||||||||||||++++||+|++.+|++|.+++...+. ..+.++ .|+..+
T Consensus 639 adg~~~~~gel~~G~N~~VA~m~~~GYn~EDAiiin~~~v~~g~~~s~~~~~~~~~~~~~~~----g~e~i~~~~p~~~~ 714 (1070)
T CHL00001 639 ADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQ----GPERITKEIPHLEA 714 (1070)
T ss_pred ccChhhccccccCCccceeeeeeccccccchhhhhhhhhhcCCceEEEEEeeeeEEEeccCC----CcceEeccCCCCch
Confidence 7999999999999999999999999999999999999999999999987644322 123343 466666
Q ss_pred hhhcccCCCCCcccCceecCCCcEEEeeccCC-----------------------CceeeeeecCCCceEEEEEEEEecC
Q 002545 774 SLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTT-----------------------NSWRTNSRKGSESVFVDYVAVDMKN 830 (910)
Q Consensus 774 ~~~~~ld~dG~~~~g~~v~~gd~l~~~~~~~~-----------------------~~~~~~~~~~~e~g~v~~v~~~~~~ 830 (910)
..+++||+||++++|++|++||||+||++|+. .++.+++++.+++|+|++|.++...
T Consensus 715 ~~~~~Ld~dGi~~~G~~v~~gDilvgK~~p~~~~~~~~~~~~~~~~~if~~~~~~~~d~sl~~~~~~~g~V~~v~~~~~~ 794 (1070)
T CHL00001 715 HLLRNLDKNGIVMLGSWVETGDILVGKLTPQEAEESSYAPEGRLLRAIFGIQVSTSKETCLKLPIGGRGRVIDVRWIQKK 794 (1070)
T ss_pred hhhhccCCCCCccCCcEecCCCEEEEEecCCcccccccCcchhhhhhhhccccCcceeCeEECCCCCceEEEEEEEEecc
Confidence 67899999999999999999999999988751 2345788889999999999999853
Q ss_pred CC--CCCeEEEEEEeeeeCCCcccceeccCCCccEEeeeecCcCcCccCCCCCcCcEEeCCCCccccccHHHHHHHhhcc
Q 002545 831 SK--NLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAK 908 (910)
Q Consensus 831 ~~--~~~~~v~i~~r~~R~p~iGDKf~sRHGqKGv~s~i~~~~dMPf~~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gK 908 (910)
++ +..+.|+|++|+.|+|++|||||||||||||||+|||+|||||+ +||++|||||||||||||||||||+|+++||
T Consensus 795 ~~~~~~~~~vkv~i~~~R~~~vGDK~asRHGqKGvvs~i~~~eDMPf~-~dG~~pDiIlNP~gvPSRMtiGqllE~~~G~ 873 (1070)
T CHL00001 795 GGSSYNPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYL-QDGTPVDMVLNPLGVPSRMNVGQIFECLLGL 873 (1070)
T ss_pred cCCCCCcEEEEEEEEEEecCCCCcccccccCCcceEeeeecccCCCcc-cCCCCCceeeccccccccccHHHHHHHHhHH
Confidence 22 24678999999999999999999999999999999999999999 9999999999999999999999999999999
Q ss_pred c
Q 002545 909 E 909 (910)
Q Consensus 909 ~ 909 (910)
|
T Consensus 874 a 874 (1070)
T CHL00001 874 A 874 (1070)
T ss_pred H
Confidence 6
No 10
>CHL00207 rpoB RNA polymerase beta subunit; Provisional
Probab=100.00 E-value=5.7e-141 Score=1287.89 Aligned_cols=730 Identities=22% Similarity=0.316 Sum_probs=567.9
Q ss_pred ccCchhhHHHHHHHHHHHHHHhHHHHH-------------------------------HHHHHcCCeeeeEEEEEEEEEE
Q 002545 9 FEPLRELVRHHIESFDYMLDEGLSEMF-------------------------------DHCRQAKISYTGKLMADVEFQY 57 (910)
Q Consensus 9 ~~~~~~Lv~~hi~SFn~Fi~~gl~~i~-------------------------------~ecR~r~~TY~~~l~v~i~~~~ 57 (910)
...+++|++.|++||+||+++||++++ .|||+|++||+++|+|+++++.
T Consensus 4 ~~~~Pdll~iQ~~SF~~FL~~GL~~~~~~~~pI~~~~~~~~l~~~~~~y~l~~P~~~~~Ea~~r~~TYsa~l~v~~~l~~ 83 (1077)
T CHL00207 4 NFALPDFLEIQRTSFCWFLNEGLNEELNIFSKIFDYTGNLELLLFGKNYKLKYPKYNLLSAKSYDSNYSIQIYLPLKFIN 83 (1077)
T ss_pred ccCCCCHHHHHHHHHHHHHHHHHHHHHHhcCCeECCCCCEEEEEecceEEEcCCCCCHHHHHHhCCccceeEEEEEEEEE
Confidence 456899999999999999999999998 8999999999999999999875
Q ss_pred ecCCCceeeeEeeecccceeecCCCccCCCCChHHHHhcccccccCCcEEEEcCceeEEEEEEeecCCccEEEEeccccC
Q 002545 58 LDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRSSFRD 137 (910)
Q Consensus 58 ~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~~~~~el~~~~E~~~D~GGYFIInG~EKVIr~qi~~~~N~~~~~~r~~~~~ 137 (910)
. .+++++.++|++|+||+|+. +|||||||+||||++|+.++|+..+..... ++
T Consensus 84 ~-~~~~i~~~~V~lG~iPlMT~------------------------~GtFIING~ERViVsQl~RSPGiyf~~~~~--k~ 136 (1077)
T CHL00207 84 L-KTNKIKFINYLIGNLPKMTQ------------------------RGTFIINGLERVIVSQIIRSPGIYFKKEIK--KN 136 (1077)
T ss_pred c-CCceEEEEEEEEeccCccCC------------------------CCEEEEcCceeEEEEEeccCCeEEEEEecC--cC
Confidence 4 34567788999999999975 999999999999999998888854432221 12
Q ss_pred CCCcceeeEEEEEeeecCCCceEEEEEEEeCCeEEEEEEeecccccccHHHHHHhccCCCHHHHHHHhcccccchhhccc
Q 002545 138 RREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEK 217 (910)
Q Consensus 138 ~~~~~t~~~v~~r~~~~~~~~~~~~l~y~~~g~~~l~~~~~~~~~~IPi~ilLkALg~~sD~EI~~~i~~~~~~~~~~~~ 217 (910)
....|+...++.|+ .|+.++++.++.+|+++...+ +||+++||||||+ ||+||++.+..
T Consensus 137 ~~~~y~a~IIp~rG-------swl~~e~d~k~~i~vridr~r---Kipit~lLrALGl-s~~eIl~~~~~---------- 195 (1077)
T CHL00207 137 SNKIYSATLIPNRG-------SWIKFELDKNKEIWIRIDKNR---KKPLIIFLKALGL-TDQDIYSRLTK---------- 195 (1077)
T ss_pred CceEEEEEEEcCCC-------ceEEEEEcCCCeEEEEecCCc---eeeHHHHHHHhCC-CHHHHHHHHhc----------
Confidence 23356666665554 499999999999999998654 6999999999999 99999998851
Q ss_pred CCCCChhhHHHHHHHHHHHHhcccccHHHHHHHHhhccccc---------------ccCCCCccHHHHHHHHHHhHhccC
Q 002545 218 GAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPV---------------IDGLQSESYYAVAETVIRDYIFVH 282 (910)
Q Consensus 218 ~~~~~~~~~~~~~~~l~~~~~~~i~t~~~al~yLg~~fr~~---------------~~~~~~~~~~~~g~~~L~~~ll~H 282 (910)
. .+. +.+..++ .+.+..++++|+.+|++++++. ++.+.+|++..+||..||++|-.+
T Consensus 196 ~--~~~---~~~~~~l---~~~~~~~~e~Al~~Iy~~lrp~~~~~~~~a~~~l~~~ff~~~rYdLg~vGR~klN~kl~~~ 267 (1077)
T CHL00207 196 S--EFL---KKLKPIL---LNSNSYTNEEILLEIYKNLSPIEPATVNDANQNLFSRFFDPKNYDLGKVGRYKINNKLNLN 267 (1077)
T ss_pred c--chH---HHHHHHH---hccCcccHHHHHHHHHHhcCCCCCccHHHHHHHHHHHhcChhcccccccchhhhhhhccCC
Confidence 0 001 1111122 1234567788888888777542 233566677777777777777666
Q ss_pred CC--CCcchHHHHHHHHHHHHhhcCCCCCCCCcccccccEEcccchhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCcccc
Q 002545 283 LN--DNNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDF 360 (910)
Q Consensus 283 l~--~~~~K~~~L~~Mi~kLl~~~~g~~~~Dd~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~~~~i~~~~~~~~~~~~~ 360 (910)
+. ....++.+++.|+++|+.+..|....||+|||+||||+++|+||+++||-. |.++.+.++++++.... ..
T Consensus 268 ~~~~~~~l~~~Dil~~i~~Li~l~~g~~~~DDiDHL~NRRvrsvGELlq~qfr~g----l~rler~ike~m~~~~~-~~- 341 (1077)
T CHL00207 268 IPERVRNLTYEDILSIIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIG----LKRLERILRNRMTICDI-DS- 341 (1077)
T ss_pred cCccCceecHHHHHHHHHHHHHhhcCCCcccchhhhhcccccchhHHHHHHHHHH----HHHHHHHHHHHhhhccc-cc-
Confidence 43 245778889999999999999999999999999999999999999999954 55555566666553111 01
Q ss_pred cchHHHHHHHhcCCCcchHHHHHhHhcccCcccccccccccccceEEEccccchhhHhhhhcccc---cCCccccccccc
Q 002545 361 FNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVH---RGASFAGLRTTS 437 (910)
Q Consensus 361 ~~~~~~~~~~~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~sGvsqvleRln~~~~lSH~Rrv~---rg~~~~~~k~t~ 437 (910)
..+++++ ++++||..|++||++ ++|||.++++|+++.|||+||++ +|++.+++++++
T Consensus 342 ---~tp~~li---n~k~lt~~ikeFFgs--------------s~LSQfmDQtNpLselTHKRRlsaLGpGGLsR~ra~fe 401 (1077)
T CHL00207 342 ---LSKFNLI---NPKPLIALIREFFGS--------------SQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISFA 401 (1077)
T ss_pred ---CChhhcc---cchhHHHHHHHhhcc--------------CCccceecccChHHhhhccceeeccCCCcccccccCCc
Confidence 1134444 467999999999985 56777788888888899999999 788999999999
Q ss_pred ccccCCCCccccccCCCCCCccccccccccceeEEeeecCCCCcccccchhhHHHHHHHHhcCCeecCCccccCCCCcee
Q 002545 438 VRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVL 517 (910)
Q Consensus 438 vR~Lhps~wG~iCPveTPEG~~cGLv~~LA~~~~Is~~~~~~~~~~~~~~~~~~i~~~L~~lG~~~~~~~~~~~~~~~~~ 517 (910)
+|++||||||||||+|||||++||||++||.+|+|+ ++|+++. | |
T Consensus 402 vRdvH~thyGRiCPIETPEG~n~Gli~~la~~~~in------------------------~~Gfiet-P----------y 446 (1077)
T CHL00207 402 VRDIHPSHYGRICPIETPEGPNCGLIGSLATNARIN------------------------KFGFIET-P----------F 446 (1077)
T ss_pred ccccCccccccccCCCCCCCcccccccchhhhcccc------------------------CCCceeC-c----------e
Confidence 999999999999999999999999999999999997 4677655 3 5
Q ss_pred EEEECCEEEeeecCccHHHHHHHHHHHHHhcCCCCCCCceEEEEEcCCCCCCCceEeecCCCceeceEEeecCCCCCCCc
Q 002545 518 SVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSEESQN 597 (910)
Q Consensus 518 ~V~lnG~~iG~~~~~~~~~~~~~lr~~k~~~~~~i~~~~eI~~v~~~~~~~~~~i~i~td~gR~~RPv~~~~~~~~~~g~ 597 (910)
..+.||++.- .+ + .-+| ..+.|-.|+-...+. . ..+.|.+.-..+.+...
T Consensus 447 ~~v~~g~v~~-~~--~-------i~yl--------sa~~e~~~~Ia~~~~-----~-~~~~~~~~~~~v~~r~~------ 496 (1077)
T CHL00207 447 YKVINGKVKK-FG--N-------PIYL--------TADSEDLYRIAPNDI-----N-LNKNNYFKKNIIPVRYK------ 496 (1077)
T ss_pred EEEEcCcccc-cC--c-------eeec--------ChHHhcCcEEEecCc-----c-CCCCCcccCCEEEEEEC------
Confidence 5557887521 00 0 0011 111111122111110 0 12234444333333221
Q ss_pred eeeeCccceeeeeeecCCCCCCCCCCCCCceecccCCCccccceeecccCCCCCCcchhhhhhhccccccccc-------
Q 002545 598 IELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFS------- 670 (910)
Q Consensus 598 iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~p~~~ls~~asliPF~~hNqspRn~yq~~M~KQaig~~------- 670 (910)
++|..++. ++ .++++++|.+++|++||||||++||||+|++|||||++|||++.
T Consensus 497 --------~ef~~~~~--~~---------v~~~~vsp~Q~~SvaasLIPFLehdDanRaLMGsnMqrQaVPll~~e~p~V 557 (1077)
T CHL00207 497 --------QEFKTVNP--SK---------VDFIAISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIV 557 (1077)
T ss_pred --------CcEEEECh--HH---------ceEEEeCcchhcchhhhcCCcccccccchhhhhhccccccccccccCCCeE
Confidence 22222222 11 68999999999999999999999999999999999999999652
Q ss_pred ----------------------------eeEEEEeccC---ceeecC----------CCCeeeEecccccccC-------
Q 002545 671 ----------------------------VQALKFRADQ---KLYHLQ----------TPQTPIVRTNTYTKYG------- 702 (910)
Q Consensus 671 ----------------------------~~n~~~R~D~---~~y~L~----------~pQ~Plv~t~~~~~~~------- 702 (910)
+..+..|.+. ..|.|. ..|||+|+.+.+...|
T Consensus 558 gTg~e~~~a~ds~~~i~a~~~G~v~~v~~~~I~i~~~~~~~~~y~l~~~~rsNq~t~i~qrp~V~~G~~v~~G~iladg~ 637 (1077)
T CHL00207 558 GTGYEKQIALDSGMTIISLTEGIVVSVSAYKIIIQDDNNRYIHYYLQKYQRSNQNTCINYRPIVWVGEKINIGQILADGS 637 (1077)
T ss_pred ECCcchHhhhhcchheEeccCcEEEEecCcEEEEEeCCCceeEEEeccccccccCceeecccccCCCCEEecCCEEecch
Confidence 1122233321 346655 4899999999987776
Q ss_pred ---ccccCCCceeeEEEEeccCCCcccceeeeccccccCcceeeEEEEEEEEeeccCCCcCccceeec--cCCCChhhhc
Q 002545 703 ---IDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFR--RNKDAKSLHS 777 (910)
Q Consensus 703 ---~~~~~~G~N~iVav~~y~Gyn~EDaiiink~s~~rG~~~~~~~~~~~~~~~~~~~~~~~~~~~f~--~~~~~~~~~~ 777 (910)
++|+|+|+|++||||||+||||||||||||++++||+|++.+|++|.+++...+. ..+.++ .|+..+..++
T Consensus 638 ~~~~~el~lG~N~lVA~m~y~GYN~EDAiiink~~v~rg~f~Si~~~~~~~e~~~~~~----g~e~i~~~~p~~~~~~~~ 713 (1077)
T CHL00207 638 DIDNSELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEKYEIELRQTKL----GSEEITRNIPNVSEYSLK 713 (1077)
T ss_pred hccCCcccCCcccEEEEEeeeccccchhhhhhhhhhcCCceEEEEEEEeeeEEeecCC----CceEEeccCCCCChHHhh
Confidence 7999999999999999999999999999999999999999999999987644322 123344 5666666789
Q ss_pred ccCCCCCcccCceecCCCcEEEeeccCC---------------------CceeeeeecCCCceEEEEEEEEecCCCCCC-
Q 002545 778 VIDSDGLPYVGQMIHPGEPYCSIYDKTT---------------------NSWRTNSRKGSESVFVDYVAVDMKNSKNLP- 835 (910)
Q Consensus 778 ~ld~dG~~~~g~~v~~gd~l~~~~~~~~---------------------~~~~~~~~~~~e~g~v~~v~~~~~~~~~~~- 835 (910)
+||+||+|++|++|++||||+||++|+. .++.+++++++++|+|++|.++.++++++.
T Consensus 714 ~LD~dGiv~iG~~V~~gDilvgK~tp~~~~~~~~~~~ll~~i~~~~~~~~kd~sl~~~~~~~g~V~~V~~~~~~~~~~~~ 793 (1077)
T CHL00207 714 NLDENGIISIGSKVLAGDILVGKITPKGESDQLPEGKLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRSKGDELK 793 (1077)
T ss_pred ccCccCCCcCCcEeCCCCEEEEEecCccccccChhhhhhhhhhccCCCcceEeEEEcCCCCcEEEEEEEEEecCCCCccc
Confidence 9999999999999999999999987732 245688999999999999999986544332
Q ss_pred ----eEEEEEEeeeeCCCcccceeccCCCccEEeeeecCcCcCccCCCCCcCcEEeCCCCccccccHHHHHHHhhccc
Q 002545 836 ----QKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKE 909 (910)
Q Consensus 836 ----~~v~i~~r~~R~p~iGDKf~sRHGqKGv~s~i~~~~dMPf~~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gK~ 909 (910)
..|+|++|+.|+|++|||||||||||||||+|||+|||||+ +||++|||||||||||||||||||+|+++|||
T Consensus 794 ~~~~~~vkv~i~~~R~p~vGDKfasRHGqKGVvs~i~p~eDMPf~-~dG~~pDiIlNPhg~PSRMtiGqllE~~lGka 870 (1077)
T CHL00207 794 FGYYLKIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYL-PDGTPPDIILNPLGVPSRMNVGQLFECLLGLA 870 (1077)
T ss_pred ccccEEEEEEEEEEecCCcccccccccCCceeEEeeeccCCCCcc-CCCCCccEEECCccccccccHHHHHHHHHHHH
Confidence 46999999999999999999999999999999999999999 99999999999999999999999999999996
No 11
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=100.00 E-value=3.3e-129 Score=1221.10 Aligned_cols=750 Identities=21% Similarity=0.288 Sum_probs=568.7
Q ss_pred cCchhhHHHHHHHHHHHHH------HhHHHHH-----------------------------HHHHHcCCeeeeEEEEEEE
Q 002545 10 EPLRELVRHHIESFDYMLD------EGLSEMF-----------------------------DHCRQAKISYTGKLMADVE 54 (910)
Q Consensus 10 ~~~~~Lv~~hi~SFn~Fi~------~gl~~i~-----------------------------~ecR~r~~TY~~~l~v~i~ 54 (910)
..+|+|++.|.+||+||++ +||++++ .||++|++||++||+|+++
T Consensus 22 ~~iPdLleIQ~~SF~~FLq~~~~~~~GL~e~f~~~fPI~d~~g~~~Lefv~Y~l~~Pk~~~~Ec~~rg~TYsapL~v~~r 101 (2890)
T PRK09603 22 LEVPNLLLLQRDSYDSFLYSKDGKESGIEKVFKSIFPIQDEHNRITLEYAGCEFGKSKYTVREAMERGITYSIPLKIKVR 101 (2890)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccccHHHHHHhcCCeECCCCcEEEEEEEEEeCCCCCCHHHHHhhCCcccccEEEEEE
Confidence 3689999999999999997 7999998 9999999999999999999
Q ss_pred EEE---ecCCC------ceeeeEeeecccceeecCCCccCCCCChHHHHhcccccccCCcEEEEcCceeEEEEEEeecCC
Q 002545 55 FQY---LDAGS------PVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQN 125 (910)
Q Consensus 55 ~~~---~~~~~------~~~~~~v~iG~iPIMv~S~~C~L~~~~~~el~~~~E~~~D~GGYFIInG~EKVIr~qi~~~~N 125 (910)
+++ +..++ ++++++|++|+||+|+. .|+|||||+||||++|++++|+
T Consensus 102 L~~~~~~~~t~~~~~ikeikeq~VylGdiPLMT~------------------------~GTFIING~ERVIVsQL~RSPG 157 (2890)
T PRK09603 102 LILWEKDTKSGEKNGIKDIKEQSIFIREIPLMTE------------------------RTSFIINGVERVVVNQLHRSPG 157 (2890)
T ss_pred EEEeeccccccccccccceEEeeEEEecCCccCC------------------------CceEEEcCceeEEEeeeccCCe
Confidence 985 21122 46788999999999997 8999999999999999999999
Q ss_pred ccEEEEeccccCCCCcceeeEEEEEeeecCCCceEEEEEEEeCCeEEEEEEeecccccccHHHHHHhccCCCHHHHHHHh
Q 002545 126 YPMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHL 205 (910)
Q Consensus 126 ~~~~~~r~~~~~~~~~~t~~~v~~r~~~~~~~~~~~~l~y~~~g~~~l~~~~~~~~~~IPi~ilLkALg~~sD~EI~~~i 205 (910)
..|.....+..+.+..|+...++.|| .|+.++++.++.+|+++..++ +||+.+||||||+ |++||++.+
T Consensus 158 VyF~~~~~k~~s~k~lysa~IIP~RG-------sWLefE~D~kd~l~vrIDrkr---Kipit~lLrAlG~-s~edIl~~f 226 (2890)
T PRK09603 158 VIFKEEESSTSLNKLIYTGQIIPDRG-------SWLYFEYDSKDVLYARINKRR---KVPVTILFRAMDY-QKQDIIKMF 226 (2890)
T ss_pred eEEeeccCcCCCCceeEEEEEecCCc-------ceEEEEEcCCCeEEEEEcCcc---eecHHHHHHHhCC-CHHHHHHHh
Confidence 65543332111223448877777776 399999999999999999766 6999999999999 899999977
Q ss_pred ccc-------------ccchhhccc-----CCCC----------------------------------------------
Q 002545 206 TCC-------------YDEKYKKEK-----GAVG---------------------------------------------- 221 (910)
Q Consensus 206 ~~~-------------~~~~~~~~~-----~~~~---------------------------------------------- 221 (910)
... +........ .+.+
T Consensus 227 ~~~~~~~i~~~~~~~~~~~~~l~~~~~~di~d~~g~vlv~~g~rit~~~~~~l~~~g~k~l~~~~~~l~g~~laedivd~ 306 (2890)
T PRK09603 227 YPLVKVRYENDKYLIPFASLDANQRMEFDLKDPQGKIILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHLAEPVMVG 306 (2890)
T ss_pred cccceEEEcccceeecccHHHhcCccceeecccCCCEEEecCccccHHHHHHHHhcCCceeccchhhhcceeeeeeccCc
Confidence 410 000000000 0000
Q ss_pred ChhhHH----HHHHHHHHHHhcc--------------------------------------cccHHHHHHHHhhccccc-
Q 002545 222 SPLVSE----RVKIILAEVQDLS--------------------------------------LTTRLQCLQHIGEHFQPV- 258 (910)
Q Consensus 222 ~~~~~~----~~~~~l~~~~~~~--------------------------------------i~t~~~al~yLg~~fr~~- 258 (910)
+..+.+ .-+..++.+.+.+ ..++++|+..|.+++|+.
T Consensus 307 ~Evl~~~~~~Itee~le~i~~~gi~~i~vl~~~~~~~~~~i~~t~~~d~~~~~~~~~t~~~~~~~eeAl~~iyr~lrpge 386 (2890)
T PRK09603 307 KEVLLDMLTQLDKNKLEKIHDLGVQEFVIINDLALGHDASIIHSFSADSESLKLLKQTEKIDDENALAAIRIHKVMKPGD 386 (2890)
T ss_pred cceeeccCChhcHHHHHHHHHcCCceEEEEeecccccccccccccccccccchhhhhccccccchHHHHHHHHhccCCCC
Confidence 000000 0011122111110 014477888887777641
Q ss_pred --------------ccCCCCccHHHHHHHHHHhHhccCCCC--CcchHHHHHHHHHHHHhhcCCCCCCCCcccccccEEc
Q 002545 259 --------------IDGLQSESYYAVAETVIRDYIFVHLND--NNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEIL 322 (910)
Q Consensus 259 --------------~~~~~~~~~~~~g~~~L~~~ll~Hl~~--~~~K~~~L~~Mi~kLl~~~~g~~~~Dd~D~l~NkRv~ 322 (910)
++.+++|++.++||..||++|-.+... .......++..++.|+.+..|....||+|||+||||+
T Consensus 387 p~~~e~A~~l~~~lFFn~~rYdLg~vGR~klN~kL~l~~~~~~~~Lt~~Dil~~i~~li~l~~g~~~~DDiDhL~NRRvr 466 (2890)
T PRK09603 387 PVTTEVAKQFVKKLFFDPERYDLTMVGRMKMNHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIR 466 (2890)
T ss_pred CCcHHHHHHHHHHHhcCcccccccccchhhhHhhhCCCCCCcccEecchhHHHHHHHHHHHHhCCCCCCcchhhhcchhh
Confidence 346788999999999999999776432 2334446889999999999999999999999999999
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCcccccchHHHHHHHhcCCCcchHHHHHhHhcccCcccccccccccc
Q 002545 323 LPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQR 402 (910)
Q Consensus 323 l~G~Ll~~lf~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~ 402 (910)
++|+||+++|+- .|.+|++.++++++......+ ...++.++ ++++++..+++||+|+++ +|+|+|+
T Consensus 467 ~vGELl~~qfr~----gl~rler~irerm~~~~~~~~---~~~p~~li---n~k~i~~~ikeFFgssqL----SQfmDQt 532 (2890)
T PRK09603 467 AVGELLANELHS----GLVKMQKTIKDKLTTMSGAFD---SLMPHDLV---NSKMITSTIMEFFMGGQL----SQFMDQT 532 (2890)
T ss_pred hHHHHHHHHHHH----HHHHHHHHHHHHHHhhhcccc---ccChhhhh---ccHHHHHHHHHHhccCch----hhhhccc
Confidence 999999999995 566666667666653111111 11234455 467999999999998765 4666666
Q ss_pred cceEEEccccchhhHhhhhcccc---cCCcccccccccccccCCCCccccccCCCCCCccccccccccceeEEeeecCCC
Q 002545 403 AGYTVQAERLNFLRFISFFRAVH---RGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSR 479 (910)
Q Consensus 403 sGvsqvleRln~~~~lSH~Rrv~---rg~~~~~~k~t~vR~Lhps~wG~iCPveTPEG~~cGLv~~LA~~~~Is~~~~~~ 479 (910)
|++| .|+|+||++ +|++.++++++++|++||||||||||+|||||+|||||++||.+|+|+
T Consensus 533 NpLs----------eltHKRRlSaLGPGGlsr~ra~fevRdVH~shYGRiCPIETPEG~NiGLI~SLa~~a~in------ 596 (2890)
T PRK09603 533 NPLS----------EVTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVN------ 596 (2890)
T ss_pred Chhh----------hhhhcccccccCCCCccccccCCcccccCcccccccCCCCCCCCCcccchhhhhhheecc------
Confidence 6665 499999999 899999999999999999999999999999999999999999999997
Q ss_pred CcccccchhhHHHHHHHHhcCCeecCCccccCCCCceeEEEECCEEEeeecCccHHHHHHHHHHHHHhcCCCCCCCceEE
Q 002545 480 GNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVG 559 (910)
Q Consensus 480 ~~~~~~~~~~~~i~~~L~~lG~~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~~~lr~~k~~~~~~i~~~~eI~ 559 (910)
++|+++. | |..+.||++.-.+ -|| ..+.|-.
T Consensus 597 ------------------~~Gfiet-P----------y~kV~~g~v~~~i------------~yl--------sa~eE~~ 627 (2890)
T PRK09603 597 ------------------DLGFIEA-P----------YKKVVDGKVVGET------------IYL--------TAIQEDS 627 (2890)
T ss_pred ------------------cCcceec-c----------eEEEecCccccce------------eee--------CHHHhcC
Confidence 4677655 3 4445788742111 111 1111111
Q ss_pred EEEcCCCCCCCceEeecCCCceeceEEeecCCCCCCCceeeeCccceeeeeeecCCCCCCCCCCCCCceecccCCCcccc
Q 002545 560 YVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSEESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLS 639 (910)
Q Consensus 560 ~v~~~~~~~~~~i~i~td~gR~~RPv~~~~~~~~~~g~iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~p~~~ls 639 (910)
|+....+ + ...+.|++....+.++.. +++..++. + ..++++++|.+++|
T Consensus 628 ~~IA~a~-----~-~~~~~~~~~~~~v~~R~~--------------~e~~~~~~--~---------~v~~~dvsp~Q~vS 676 (2890)
T PRK09603 628 HIIAPAS-----T-PIDEEGNILGDLIETRVE--------------GEIVLNEK--S---------KVTLMDLSSSMLVG 676 (2890)
T ss_pred ceEeccC-----C-ccCCCCcccCCeEeEEEC--------------CceEEECh--H---------HceEEEeCccceee
Confidence 2221111 0 113345555554444322 22222221 1 16899999999999
Q ss_pred ceeecccCCCCCCcchhhhhhhccccccccc-----------------------------------eeEEEEeccC----
Q 002545 640 VVANLTPYSDHNQSPRNMYQCQMAKQTMGFS-----------------------------------VQALKFRADQ---- 680 (910)
Q Consensus 640 ~~asliPF~~hNqspRn~yq~~M~KQaig~~-----------------------------------~~n~~~R~D~---- 680 (910)
++||||||++||||+|++||||||+|||++. +..+.+|.+.
T Consensus 677 vaasLIPFLEhdDAnRALMGSNMQRQAVPLl~~e~piVgTG~E~~va~dSg~~i~a~~~G~V~yvd~~~I~i~~~~~~~~ 756 (2890)
T PRK09603 677 VAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTGIEKIIARDSWGAIKANRAGVVEKIDSKNIYILGEGKEEA 756 (2890)
T ss_pred ehhhcCCccccCccccccccccchhhhhhhccccCCeEecCcchhhhccccceeEecCCeEEEEecCcEEEEEecCCCCc
Confidence 9999999999999999999999999999652 1223333321
Q ss_pred --ceeecC----------CCCeeeEecccccccC----------ccccCCCceeeEEEEeccCCCcccceeeeccccccC
Q 002545 681 --KLYHLQ----------TPQTPIVRTNTYTKYG----------IDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRG 738 (910)
Q Consensus 681 --~~y~L~----------~pQ~Plv~t~~~~~~~----------~~~~~~G~N~iVav~~y~Gyn~EDaiiink~s~~rG 738 (910)
..|.|. +.|||+|+.+.....| .+|+++|+|++||||||.|||+||||+||++.+..+
T Consensus 757 ~~~~Y~L~Ky~RSNQ~TcinqrPiV~~Gd~V~kGdilADG~st~~GELALG~NvlVAfmpW~GYNfEDAIlISERlV~eD 836 (2890)
T PRK09603 757 YIDAYSLQKNLRTNQNTSFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDD 836 (2890)
T ss_pred eeeEEeeccccccCCCceeeeccEecCCCEeccCCEEecCcccccCeeccCcccEEEEeeeccccCccccccchhhhcCc
Confidence 237764 4999999999988776 699999999999999999999999999999999988
Q ss_pred cceeeEEEEEEEEeeccCCCcCccceee--ccCCCChhhhcccCCCCCcccCceecCCCcEEEeeccCC-----------
Q 002545 739 MCHGQIYQTETIDLSDDGNKVDRGQKLF--RRNKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTT----------- 805 (910)
Q Consensus 739 ~~~~~~~~~~~~~~~~~~~~~~~~~~~f--~~~~~~~~~~~~ld~dG~~~~g~~v~~gd~l~~~~~~~~----------- 805 (910)
.|.|.+...|.++..+.+. ..|.+ .+|+.++...++||++|||++|++|++|||||||++|+.
T Consensus 837 ~fTSIHIee~ei~~r~Tk~----G~EeITrdIPnvse~~l~~LDe~GII~iGa~V~~GDILVGKvTPkge~~~tPEekLL 912 (2890)
T PRK09603 837 IFTSTHIYEKEVDARELKH----GVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMILVGKTSPKGEIKSTPEERLL 912 (2890)
T ss_pred cceEEEEeeeEEEEEecCC----CCcEEeccCCCCCHHHHhcCCCCCCEeeCCEECCCCEEEEeeccCCCCCCChHHHHH
Confidence 8777766666665544332 22333 378888888999999999999999999999999998873
Q ss_pred ----------CceeeeeecCCCceEEEEEEEEecC---------------------------------------------
Q 002545 806 ----------NSWRTNSRKGSESVFVDYVAVDMKN--------------------------------------------- 830 (910)
Q Consensus 806 ----------~~~~~~~~~~~e~g~v~~v~~~~~~--------------------------------------------- 830 (910)
.++.|++.+.+..|+|.+|.+++.+
T Consensus 913 raIFGeka~~vkDtSLrvp~G~~G~Vidv~~f~r~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 992 (2890)
T PRK09603 913 RAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDARVLSAYEEEKAKLDMEHFDRLTMLNREELLRVSSLLSQA 992 (2890)
T ss_pred HHHhcccccccccCceecCCCCcEEEEEEEEecccccchhHHHHHHHHHHHHHHhHhhHHHHHHHHHHHHHhhhhhcccc
Confidence 2355889999999999999999742
Q ss_pred -------------------------------------------------------------------------CCC----
Q 002545 831 -------------------------------------------------------------------------SKN---- 833 (910)
Q Consensus 831 -------------------------------------------------------------------------~~~---- 833 (910)
.|+
T Consensus 993 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~gdeL~~ 1072 (2890)
T PRK09603 993 ILEEPFSHNGKDYKEGDQIPKEEIASINRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPN 1072 (2890)
T ss_pred ccccccccccccccccccccHHHHhhCCHHHhhhhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCcCCC
Confidence 011
Q ss_pred -CCeEEEEEEeeeeCCCcccceeccCCCccEEeeeecCcCcCccCCCCCcCcEEeCCCCccccccHHHHHHHhhccc
Q 002545 834 -LPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKE 909 (910)
Q Consensus 834 -~~~~v~i~~r~~R~p~iGDKf~sRHGqKGv~s~i~~~~dMPf~~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gK~ 909 (910)
-.+.|+|++|+.|+|++|||||||||||||||+|||+|||||+ +||++||||+|||||||||||||++|+++|||
T Consensus 1073 Gv~~~VkV~ia~kR~~qvGDK~AgRHGnKGViS~I~p~EDMPfl-~dG~~pDIIlNPlGvPSRMnIGQilE~~LG~a 1148 (2890)
T PRK09603 1073 GVIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYT-ADGEPVDIVLNPLGVPSRMNIGQILEMHLGLV 1148 (2890)
T ss_pred CcceEEEEEEEEeecccccchhhhccCCCeeEEEEEchhcCCCC-CCCCCCcEEECCCCCCccccHHHHHHHHHHHH
Confidence 1357999999999999999999999999999999999999999 99999999999999999999999999999985
No 12
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=100.00 E-value=3.5e-127 Score=1198.42 Aligned_cols=748 Identities=20% Similarity=0.302 Sum_probs=575.1
Q ss_pred cCchhhHHHHHHHHHHHHH-----HhHHHHH-----------------------------HHHHHcCCeeeeEEEEEEEE
Q 002545 10 EPLRELVRHHIESFDYMLD-----EGLSEMF-----------------------------DHCRQAKISYTGKLMADVEF 55 (910)
Q Consensus 10 ~~~~~Lv~~hi~SFn~Fi~-----~gl~~i~-----------------------------~ecR~r~~TY~~~l~v~i~~ 55 (910)
..+|+|++.|.+||+||++ +||++++ .||++|++||++||+|++++
T Consensus 27 ~~~PdL~~iQ~~Sf~~Fl~~~~~~~GL~~~f~~ifPI~d~~g~~~lefv~y~l~~Pk~~~~Ec~~r~~TYsapl~v~~rL 106 (2836)
T PRK14844 27 DSLLDLVKVQKESYDSFTPKNKGNERLEVIFHTIFPINDPLHRATIEFISCRVDDPKYDESECIKRGITFSAQVIASIRL 106 (2836)
T ss_pred CCCCCHHHHHHHHHHHHhcCCCccccHHHHHHhcCCeECCCCCEEEEEEEEEeCCCCCCHHHHHhcCCcceeeEEEEEEE
Confidence 3589999999999999997 6999998 99999999999999999999
Q ss_pred EEec------------CC----------CceeeeEeeecccceeecCCCccCCCCChHHHHhcccccccCCcEEEEcCce
Q 002545 56 QYLD------------AG----------SPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLE 113 (910)
Q Consensus 56 ~~~~------------~~----------~~~~~~~v~iG~iPIMv~S~~C~L~~~~~~el~~~~E~~~D~GGYFIInG~E 113 (910)
+..+ .+ +++++++|++|+||+|+. .|+|||||+|
T Consensus 107 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ikeq~VylGdiPLMT~------------------------~GTFIING~E 162 (2836)
T PRK14844 107 VIMQDGISLDEYKSIKESGDHSKLATVIKSIEEQEVHFCELPMMTD------------------------KGTFIINGVE 162 (2836)
T ss_pred EEeccccccccccccccccccccccccccceeeeeEEEecCCccCC------------------------CeEEEEcCcc
Confidence 7611 11 355678999999999997 8999999999
Q ss_pred eEEEEEEeecCCccEEEEeccccCCC-CcceeeEEEEEeeecCCCceEEEEEEEeCCeEEEEEEeecccccccHHHHHHh
Q 002545 114 RVFRSVILPKQNYPMSMVRSSFRDRR-EGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKA 192 (910)
Q Consensus 114 KVIr~qi~~~~N~~~~~~r~~~~~~~-~~~t~~~v~~r~~~~~~~~~~~~l~y~~~g~~~l~~~~~~~~~~IPi~ilLkA 192 (910)
|||++|++++|+..|.....+.++.+ ..|+...++.|| .|+.++++.++.+|+++..++ ++|+.+||||
T Consensus 163 RVIVSQL~RSPGVyF~~~~~kt~~sgk~lysa~IIP~RG-------sWLefE~D~kd~lyvRIDRkR---KiPiT~LLrA 232 (2836)
T PRK14844 163 KVIVSQMHRSPGVFFDSDKGKTYNSGKLIYSARVIPYRG-------SWLDIEFDVKDHLYFRIDRKR---KLPISVLLKA 232 (2836)
T ss_pred eEEEEcceeCCeEEEEcccCcccCCCceeEEEEEecCCc-------ceEEEEEcCCCeEEEEecCCe---eeeHHHHHHH
Confidence 99999999999965543332222233 368887777776 399999999999999999776 6999999999
Q ss_pred ccCCCHHHHHHHhcccc--c---chh------hcccC--------CCC--------------------------------
Q 002545 193 LVDTNDLEIFNHLTCCY--D---EKY------KKEKG--------AVG-------------------------------- 221 (910)
Q Consensus 193 Lg~~sD~EI~~~i~~~~--~---~~~------~~~~~--------~~~-------------------------------- 221 (910)
||+ |++||++.+.... . ... ..+.+ +.+
T Consensus 233 LGl-s~edIL~~F~~~~~~~~~d~~~~~~~~~e~l~g~~~~~Di~d~~g~vlvdkgrrit~~~~krlk~~gvkkl~i~~~ 311 (2836)
T PRK14844 233 LGL-SNNDILDRFYEKIKYIKHKDGWKVPFVPDKFKGVRLPFDLMDVEGNVLLKANVRITSRLAKKLYDNELKEYLVPFD 311 (2836)
T ss_pred hCC-ChHHHHHhhcCceEEEEccCceeeccCHHHHhCCccceeeeccCCCEEEecCccccHHHHHHHHHcccCcccCchH
Confidence 999 8999999774200 0 000 00000 000
Q ss_pred ---ChhhH---------------------HHHH----------------------HHHHHHHhcccccHHHHHHHHhhcc
Q 002545 222 ---SPLVS---------------------ERVK----------------------IILAEVQDLSLTTRLQCLQHIGEHF 255 (910)
Q Consensus 222 ---~~~~~---------------------~~~~----------------------~~l~~~~~~~i~t~~~al~yLg~~f 255 (910)
..++. +.++ .+...+......++++|+..|.+++
T Consensus 312 ~l~g~~LaeDIVD~eTGEiL~eagteIT~e~ik~l~~~gi~~i~~l~~d~~~~~~~i~~tL~~D~~~~~e~Al~eIy~~l 391 (2836)
T PRK14844 312 SICGLFLAEDLIDSASSTKILSAGESIKLEDIKKLELLSIDEISVLNIDNLSVGPYILNTLFLDENMSYQDALYEIYKVL 391 (2836)
T ss_pred hhcCceehhhhcCCCCCeEEEcCCCccCHHHHHHHHHcCCCceeeEeecccccchHHHHHHhhcccccHHHHHHHHHHhc
Confidence 00000 0000 0111122234557788998888888
Q ss_pred ccc---------------ccCCCCccHHHHHHHHHHhHhccCCC--CCcchHHHHHHHHHHHHhhcCCCCCCCCcccccc
Q 002545 256 QPV---------------IDGLQSESYYAVAETVIRDYIFVHLN--DNNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQN 318 (910)
Q Consensus 256 r~~---------------~~~~~~~~~~~~g~~~L~~~ll~Hl~--~~~~K~~~L~~Mi~kLl~~~~g~~~~Dd~D~l~N 318 (910)
|+. ++.+.+|++.++||..||++|-.+.. ........++.++++|+.+..|....||+|||+|
T Consensus 392 Rpge~~~~e~a~~l~~~~ff~~~~YdLg~vGR~k~N~kl~~~~~~~~~~l~~~Dii~~i~~Li~l~~g~~~~DDiDhL~N 471 (2836)
T PRK14844 392 RPGEVPVLEIVEEFFRNLFFSPEYYDLSNIGRLKLNSYLGLNYDEDLTVLTHEDIIEIVRKIVLLRDGQGSVDDIDHLGN 471 (2836)
T ss_pred CCCCCCcHHHHHHHHHHHhcCccccccccchhhhhhhhhccCCCCCCcEecHHHHHHHHHHHHHHhcCCCcccchhhhhc
Confidence 652 34578889999999999999976632 2334445788999999999999999999999999
Q ss_pred cEEcccchhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCcccccchHHHHHHHhcCCCcchHHHHHhHhcccCcccccccc
Q 002545 319 QEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLD 398 (910)
Q Consensus 319 kRv~l~G~Ll~~lf~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~It~~i~~~~sTGnw~~~~~~~ 398 (910)
|||+++|+||+++|+-. +.++.+.++.+++.... .. -.++.++ ++++|++++++||+|
T Consensus 472 RRvr~vGeLl~~qfr~g----l~r~~~~i~e~~~~~~~-~~----~~p~~li---n~~~l~~~i~~ff~s---------- 529 (2836)
T PRK14844 472 RRVRSVGEFIENQFRTG----LLKLERAVVDSMSTSSL-DK----VSPSDFI---NPKVLTNVLRDFFNS---------- 529 (2836)
T ss_pred cccchHHHHHHHHHHHH----HHHHHHHHHHHHhhccc-cc----cchhhcc---cchhHHHHHHHHhcc----------
Confidence 99999999999999965 45555555555543111 01 1234455 467899999999987
Q ss_pred cccccceEEEccccchhhHhhhhcccc---cCCcccccccccccccCCCCccccccCCCCCCccccccccccceeEEeee
Q 002545 399 LQQRAGYTVQAERLNFLRFISFFRAVH---RGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASY 475 (910)
Q Consensus 399 ~~q~sGvsqvleRln~~~~lSH~Rrv~---rg~~~~~~k~t~vR~Lhps~wG~iCPveTPEG~~cGLv~~LA~~~~Is~~ 475 (910)
+++||.++++|+++.|||+||++ +|++.++++.+++|++||||||+|||+|||||+|||||++||.+|+|+
T Consensus 530 ----s~LSQfmDQtNpLseltHkRRlsaLGPGGL~r~~a~fevRdvH~shyGRiCPIETPEG~NiGLI~SLA~yarIn-- 603 (2836)
T PRK14844 530 ----SQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARIN-- 603 (2836)
T ss_pred ----cchhhhccCcChhhhhhhcceecccCCCCcccccCCCcccccCccccccccCCCCCCCCcccchhhhhhheecc--
Confidence 56777778888888899999999 788899999999999999999999999999999999999999999997
Q ss_pred cCCCCcccccchhhHHHHHHHHhcCCeecCCccccCCCCceeEEEECCEEEeeecCccHHHHHHHHHHHHHhcCCCCCCC
Q 002545 476 YDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDD 555 (910)
Q Consensus 476 ~~~~~~~~~~~~~~~~i~~~L~~lG~~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~~~lr~~k~~~~~~i~~~ 555 (910)
++|++.. | |..+.||++... +.+| ..+
T Consensus 604 ----------------------~~Gfiet-P----------y~kV~~g~v~~~------------i~yl--------sa~ 630 (2836)
T PRK14844 604 ----------------------KYGFIES-P----------YRKVVNRVVTDQ------------IEYL--------SAI 630 (2836)
T ss_pred ----------------------CCceEeC-C----------cEEEEcCcCccc------------cccc--------ChH
Confidence 4677665 3 555578874311 1122 111
Q ss_pred ceEEEEEcCCCCCCCceEeecCCCceeceEEeecCCCCCCCceeeeCccceeeeeeecCCCCCCCCCCCCCceecccCCC
Q 002545 556 LEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSEESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPT 635 (910)
Q Consensus 556 ~eI~~v~~~~~~~~~~i~i~td~gR~~RPv~~~~~~~~~~g~iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~p~ 635 (910)
.|-.|.....+ + ...+.|++..+.+.++.. ++|.++.. + ..++++++|.
T Consensus 631 ~E~~~~Ia~a~-----~-~~~~~~~~~~~~v~~R~~--------------~ef~~~~~--~---------~v~~~dvsp~ 679 (2836)
T PRK14844 631 DEGLYYIADTS-----A-KLDENNCFVDDMLYCRYA--------------GSFVMVSS--D---------QVSYIDVSPK 679 (2836)
T ss_pred HhcCcEEEeCC-----c-cCCCCCcccCCeEEEecC--------------CceEEecH--H---------HceEEEeCcc
Confidence 22222222111 1 113456666666555432 12222211 1 1689999999
Q ss_pred ccccceeecccCCCCCCcchhhhhhhccccccccc-----------------------------------eeEEEEeccC
Q 002545 636 GMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFS-----------------------------------VQALKFRADQ 680 (910)
Q Consensus 636 ~~ls~~asliPF~~hNqspRn~yq~~M~KQaig~~-----------------------------------~~n~~~R~D~ 680 (910)
+++|++||||||.+||||+|++||||||||||++. +..+.+|.+.
T Consensus 680 Q~~SvaasLIPFLEhdDAnRALMGSNMQRQAVPLl~~e~PiVGTG~E~~vA~DSg~~v~A~~~G~V~yVda~kIvI~~~~ 759 (2836)
T PRK14844 680 QVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESFVASGSGAVVLAKRDGIVDSSDSNSIVIRAFD 759 (2836)
T ss_pred hhhhhHhhcCCccccCccccccccccccccccccccCCCCeEecCcchhhhhcccceEEeccCceEEEEcCCEEEEEeCC
Confidence 99999999999999999999999999999999652 1223344432
Q ss_pred ---------ceeecC----------CCCeeeEecccccccC----------ccccCCCceeeEEEEeccCCCcccceeee
Q 002545 681 ---------KLYHLQ----------TPQTPIVRTNTYTKYG----------IDEYPTGTNAIVAVLAYTGYDMEDAMILN 731 (910)
Q Consensus 681 ---------~~y~L~----------~pQ~Plv~t~~~~~~~----------~~~~~~G~N~iVav~~y~Gyn~EDaiiin 731 (910)
..|.|. +.|||+|+.+.....| .+|+++|+|++||||||.|||+||||+||
T Consensus 760 ~~~~~~~~~~~Y~L~ky~RSNQ~TcinQrPiV~~Gd~V~kGdilADG~st~~GELALG~NvlVAfmpW~GYNfEDAIliS 839 (2836)
T PRK14844 760 KERVNYLDVDIYHLRKFQRSNHNTCINQKPLVCVGDYVKEGDVIADGPAINSGELALGQNLLVAFMSWQGYNFEDSIIIS 839 (2836)
T ss_pred CccccccccceEEeccccccccceeeeecceecCCCEeccCCEeccChhhcccccccccceEEEEeccCCcccccccccc
Confidence 236666 4999999999988876 59999999999999999999999999999
Q ss_pred ccccccCcceeeEEEEEEEEeeccCCCcCccceee--ccCCCChhhhcccCCCCCcccCceecCCCcEEEeeccCC----
Q 002545 732 KSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLF--RRNKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTT---- 805 (910)
Q Consensus 732 k~s~~rG~~~~~~~~~~~~~~~~~~~~~~~~~~~f--~~~~~~~~~~~~ld~dG~~~~g~~v~~gd~l~~~~~~~~---- 805 (910)
++.+..++|+|.+...|.++..+.+.. .|.+ .+|+.++...++||++||+++|++|++|||||||++|+.
T Consensus 840 Erlv~eD~fTSiHIee~ei~~r~Tk~G----~EeITrdIPnv~e~~lr~LDe~GIV~iGa~V~~GDILVGKvtPk~e~~~ 915 (2836)
T PRK14844 840 SEVVKKDLFTSIHIEEFECVVHDTPLG----SEKITRAIPGVNEENLYHLDDSGIVKIGTRVGPGYILVGKVTPKPSLSL 915 (2836)
T ss_pred hhhccCceeEEEeecceEEEEEeccCC----CceecccCCCCChHHHhcCCCCCCeecCCEECCCCEEEEeecCCCCCCC
Confidence 999999987777777777665444322 2333 368888888999999999999999999999999998873
Q ss_pred -----------------CceeeeeecCCCceEEEEEEEEecC--------------------------------------
Q 002545 806 -----------------NSWRTNSRKGSESVFVDYVAVDMKN-------------------------------------- 830 (910)
Q Consensus 806 -----------------~~~~~~~~~~~e~g~v~~v~~~~~~-------------------------------------- 830 (910)
.++.|++.+.+..|+|.+|.+++.+
T Consensus 916 tPEekLL~aIFGek~~~vkdtSLrvp~G~~G~Vidv~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 995 (2836)
T PRK14844 916 PPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFTRRGVEENERALLIKQKEINDFEKERDYIINVTSEYFYDEL 995 (2836)
T ss_pred CHHHHHHHHHhCCcccccccCceecCCCCCEEEEEEEEEcccccccchhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
Confidence 2355899999999999999999753
Q ss_pred ---------------------------------------------------------------CCCC-----CeEEEEEE
Q 002545 831 ---------------------------------------------------------------SKNL-----PQKANIRF 842 (910)
Q Consensus 831 ---------------------------------------------------------------~~~~-----~~~v~i~~ 842 (910)
.|++ .+.|+|++
T Consensus 996 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~gdeL~~gv~~~VkVyi 1075 (2836)
T PRK14844 996 KKLLINSGSQDREKFDSIEREQWWGIGLKNQSISEQVKSLKKDFDEKVSHAIAQFKRKVEKLHEGYDLPQGVSMSVKVFI 1075 (2836)
T ss_pred hhhhcccccccHHHHhhccHHhhhhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCCCCceEEEEEE
Confidence 1111 25799999
Q ss_pred eeeeCCCcccceeccCCCccEEeeeecCcCcCccCCCCCcCcEEeCCCCccccccHHHHHHHhhccc
Q 002545 843 RHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKE 909 (910)
Q Consensus 843 r~~R~p~iGDKf~sRHGqKGv~s~i~~~~dMPf~~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gK~ 909 (910)
++.|.+++|||+|||||||||||+|+|.|||||+ +||+++|||+||+|+||||||||++|+++|.|
T Consensus 1076 a~KRkiqvGDKmAGRHGNKGVIS~IlP~eDMPyL-~DGtpvDIvLNPLGVPSRMNvGQilE~hLG~A 1141 (2836)
T PRK14844 1076 AVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYL-EDGTPVDIILNPLGVPSRMNVGQILETHVGWA 1141 (2836)
T ss_pred EEeecCCccccccccCCCCceEeEEcccCCCCcC-CCCCCceEEeCCCCCCccccHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999 99999999999999999999999999999975
No 13
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated
Probab=100.00 E-value=1.5e-109 Score=970.89 Aligned_cols=374 Identities=31% Similarity=0.486 Sum_probs=338.5
Q ss_pred eeEEEECCEEEeeecCccHHHHHHHHHHHHHhcCCCCCCCceEEEEEcCCCCCCCceEeecCCCceeceEEeecCCCC--
Q 002545 516 VLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSE-- 593 (910)
Q Consensus 516 ~~~V~lnG~~iG~~~~~~~~~~~~~lr~~k~~~~~~i~~~~eI~~v~~~~~~~~~~i~i~td~gR~~RPv~~~~~~~~-- 593 (910)
.++|||||+|+|+++ +|.+|++.||.+||.| .|+.++||.+++ ..++|+||||+||++|||+++++++.
T Consensus 4 ~~~VflNG~~vG~~~--~~~~lv~~lR~lRr~g--~i~~~vsI~~~~-----~~~ei~I~tD~GR~~RPl~iv~~g~~~l 74 (605)
T PRK07225 4 KAKVYVNGKLIGTHD--DPEELVEEIREARRSG--EISEEVNVSYKE-----ETNEVIINTDAGRARRPLIVVENGEPLL 74 (605)
T ss_pred ccEEEECCEEEEEEC--CHHHHHHHHHHHHccC--CCCCcEEEEEEC-----CCCEEEEEccCCccceeEEEEeCCcccC
Confidence 378999999999984 5999999999999998 588899998763 24699999999999999999988542
Q ss_pred -------------------CCCceeeeCccceeeeeeecCCCCCCCCCCCCCceecccCCCccccceeecccCCCCCCcc
Q 002545 594 -------------------ESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSP 654 (910)
Q Consensus 594 -------------------~~g~iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~p~~~ls~~asliPF~~hNqsp 654 (910)
..|.|||||++||++++||+.++++.+. +||+||+|+++||++||+|||+||||||
T Consensus 75 ~~~~~~~l~~~~~~~~dl~~~G~IEyida~EE~~~~IA~~~~~l~~~-----~th~Ei~p~~ilgv~AslIPF~~hNQSP 149 (605)
T PRK07225 75 TEEHIEKLKNGELTFDDLVKQGVIEYLDAEEEENAYIAVYEEDLTEE-----HTHLEIDPSLILGIGAGMIPYPEHNASP 149 (605)
T ss_pred CHHHHHHHHcCCCChHHHHhCCCeeecChhhhcCeEeccchhhhccc-----ccccccCCcceeEEEeeccCCCCCCccc
Confidence 2389999999999999999999888554 6999999999999999999999999999
Q ss_pred hhhhhhhccccccccceeEEEEeccCceeecCCCCeeeEecccccccCccccCCCceeeEEEEeccCCCcccceeeeccc
Q 002545 655 RNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSS 734 (910)
Q Consensus 655 Rn~yq~~M~KQaig~~~~n~~~R~D~~~y~L~~pQ~Plv~t~~~~~~~~~~~~~G~N~iVav~~y~Gyn~EDaiiink~s 734 (910)
||||||||+|||||++++|+..|.|++.|+|+|||+|||+|+.++.++++++|+|+||+||||||+|||||||||+||+|
T Consensus 150 Rn~yq~~M~KQa~g~~~~n~~~r~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~p~G~N~iVAvmsy~GYn~EDAiIiNkss 229 (605)
T PRK07225 150 RITMGAGMIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKAS 229 (605)
T ss_pred hhhhhhhhhhcccCccccceeeecCCcccEEeeCCcceEEccchHhhCCCccCCCeeEEEEEECcCCCChhHeeeeehhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCcceeeEEEEEEEEeeccCCCcCccceeeccCCC------ChhhhcccCCCCCcccCceecCCCcEEEeeccC----
Q 002545 735 VDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFRRNKD------AKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKT---- 804 (910)
Q Consensus 735 ~~rG~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~------~~~~~~~ld~dG~~~~g~~v~~gd~l~~~~~~~---- 804 (910)
+||||||+.+|++|+++...... ...+.|..|+. ....+++||+||||++|++|++||||+||..|.
T Consensus 230 idRGlf~s~~~k~~~~~~~~~~~---~~~~~~~~p~~~~~~~~~~~~~~~LD~dGi~~~G~~v~~gdiligk~sp~~~~~ 306 (605)
T PRK07225 230 IERGLGRSHFFRTYEGEERRYPG---GQEDRFEIPDKDVRGYRGEEAYRHLDEDGLVNPETEVKEGDVLIGKTSPPRFLE 306 (605)
T ss_pred hhcCceEEEEEEEEEEEeeecCC---CcceEEecCCchhccccChHHhhcCCCCCCccCCCEECCCCEEEEEecCCCCcc
Confidence 99999999999999976533211 22346666642 124579999999999999999999999997763
Q ss_pred ----------CCceeeeeecCCCceEEEEEEEEecCCCCCCeEEEEEEeeeeCCCcccceeccCCCccEEeeeecCcCcC
Q 002545 805 ----------TNSWRTNSRKGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMP 874 (910)
Q Consensus 805 ----------~~~~~~~~~~~~e~g~v~~v~~~~~~~~~~~~~v~i~~r~~R~p~iGDKf~sRHGqKGv~s~i~~~~dMP 874 (910)
..++.+++++.+|+|+||+|.++.+++| .+.|+|++|+.|+|+||||||||||||||||++||+||||
T Consensus 307 ~~~~~~~~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~--~~~vkv~ir~~R~p~iGDKfssRHGQKGvvs~i~~~eDMP 384 (605)
T PRK07225 307 EPDDFGISPEKRRETSVTMRSGEEGIVDTVILTETEEG--SRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMP 384 (605)
T ss_pred chhhhcccccCcceeeEEecCCCcEEEEEEEEEecCCC--CEEEEEEEEEEEeccccchhhhcccCceeEEeEeccccCC
Confidence 1345688999999999999999987654 4789999999999999999999999999999999999999
Q ss_pred ccCCCCCcCcEEeCCCCccccccHHHHHHHhhccc
Q 002545 875 FSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKE 909 (910)
Q Consensus 875 f~~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gK~ 909 (910)
|| ++|++|||||||||||||||||||+|+++||+
T Consensus 385 ft-~~G~~PDiIiNPhg~PSRMTiGql~E~~~gk~ 418 (605)
T PRK07225 385 FT-ESGVVPDLIINPHAIPSRMTVGHVLEMIGGKV 418 (605)
T ss_pred cC-CCCCcccEEECcccccccCcHHHHHHHHHHHH
Confidence 99 99999999999999999999999999999996
No 14
>TIGR03670 rpoB_arch DNA-directed RNA polymerase subunit B. This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.
Probab=100.00 E-value=1.3e-109 Score=970.60 Aligned_cols=371 Identities=32% Similarity=0.522 Sum_probs=336.4
Q ss_pred EEECCEEEeeecCccHHHHHHHHHHHHHhcCCCCCCCceEEEEEcCCCCCCCceEeecCCCceeceEEeecCCCC-----
Q 002545 519 VLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSE----- 593 (910)
Q Consensus 519 V~lnG~~iG~~~~~~~~~~~~~lr~~k~~~~~~i~~~~eI~~v~~~~~~~~~~i~i~td~gR~~RPv~~~~~~~~----- 593 (910)
|||||+|+|+++ ++.+|++.||.+||.| .++.++||.+++. .++|+||||+||++|||+++++++.
T Consensus 1 VflNG~~vG~~~--~~~~lv~~LR~lRr~g--~i~~~vsI~~~~~-----~~ei~I~tD~GR~~RPl~iv~~g~l~l~~~ 71 (599)
T TIGR03670 1 VYLNGRLIGYHD--DPEELVEEVRKLRRSG--KLSQEVNVAYYEE-----TNEVYINCDAGRIRRPLIVVENGKPKLTRE 71 (599)
T ss_pred CEECCEEEEEEC--CHHHHHHHHHHHhCcC--CCCCcEEEEEeCC-----CCEEEEEcCCCccceeEEEeeCCCccccHH
Confidence 799999999984 5999999999999998 5899999987742 4899999999999999999988761
Q ss_pred ----------------CCCceeeeCccceeeeeeecCCCCCCCCCCCCCceecccCCCccccceeecccCCCCCCcchhh
Q 002545 594 ----------------ESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNM 657 (910)
Q Consensus 594 ----------------~~g~iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~p~~~ls~~asliPF~~hNqspRn~ 657 (910)
..|.+||||++||++++||+.++++... +||+||+|+++||++||+|||+|||||||||
T Consensus 72 ~l~~l~~~~~~~~~ll~~G~IEyida~Ee~~~~IA~~~~~l~~~-----~th~Ei~p~~ilgv~AslIPF~~hNqSpRn~ 146 (599)
T TIGR03670 72 HVEKLKEGELTWDDLVKQGVIEYLDAEEEENAYIALDPEELTPE-----HTHLEIDPSAILGIIASTIPYPEHNQSPRNT 146 (599)
T ss_pred HHHHHhccCCCHHHHHhcCCeEecCchhhcCeEEecchHHhccC-----cCccccCCcceeeEEeeccCCCCcCcchhhH
Confidence 3578999999999999999999988544 7999999999999999999999999999999
Q ss_pred hhhhccccccccceeEEEEeccCceeecCCCCeeeEecccccccCccccCCCceeeEEEEeccCCCcccceeeecccccc
Q 002545 658 YQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDR 737 (910)
Q Consensus 658 yq~~M~KQaig~~~~n~~~R~D~~~y~L~~pQ~Plv~t~~~~~~~~~~~~~G~N~iVav~~y~Gyn~EDaiiink~s~~r 737 (910)
|||||+|||||++++|+..|.|+++|+|+|||+|||+|+.++.++++++|+|+||+||||||+|||||||||+||+|+||
T Consensus 147 YQc~M~KQamG~~~~n~~~R~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~p~G~N~iVAvmsy~GYn~EDAiIink~si~r 226 (599)
T TIGR03670 147 MGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIER 226 (599)
T ss_pred HHHhhhhccccccccChhhcccccceEEcCCCCceeeeeeHHHhCccccCCCeeEEEEEEcccCcChhHeeeechhhhhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcceeeEEEEEEEEeeccCCCcCccceeeccCCC------ChhhhcccCCCCCcccCceecCCCcEEEeeccC-------
Q 002545 738 GMCHGQIYQTETIDLSDDGNKVDRGQKLFRRNKD------AKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKT------- 804 (910)
Q Consensus 738 G~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~------~~~~~~~ld~dG~~~~g~~v~~gd~l~~~~~~~------- 804 (910)
||||+.+|++|+++...... ...+.|..|+. .+..+++||+||||++|++|++||||+||++|.
T Consensus 227 G~f~s~~~~~~~~~~~~~~~---~~~e~~~~p~~~~~~~~~~~~~~~LD~dGi~~~G~~v~~gdiligk~~p~~~~~~~~ 303 (599)
T TIGR03670 227 GLARSTFFRTYEAEERRYPG---GQEDRFEIPEPDVRGYRGEEAYKHLDEDGIVYPEVEVKGGDVLIGKTSPPRFLEELR 303 (599)
T ss_pred CCeEEEEEEEEEEEeeccCC---CCceEEecCCchhccccchhhhccCCCCCCcCCCcEeCCCCEEEEEecCCCCccchh
Confidence 99999999999986533211 12234555542 234579999999999999999999999998752
Q ss_pred -------CCceeeeeecCCCceEEEEEEEEecCCCCCCeEEEEEEeeeeCCCcccceeccCCCccEEeeeecCcCcCccC
Q 002545 805 -------TNSWRTNSRKGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSG 877 (910)
Q Consensus 805 -------~~~~~~~~~~~~e~g~v~~v~~~~~~~~~~~~~v~i~~r~~R~p~iGDKf~sRHGqKGv~s~i~~~~dMPf~~ 877 (910)
..++.+++++.+|+|+||+|.++.++++ .+.|+|++|+.|+|+||||||||||||||||++||+||||||
T Consensus 304 ~~~~~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~--~~~vkv~~r~~R~p~iGDKfssRHGQKGvvs~i~~~eDMPft- 380 (599)
T TIGR03670 304 ELGLVTERRRDTSVTVRHGEKGIVDKVIITETEEG--NKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFT- 380 (599)
T ss_pred hhccccccCceEEEEecCCCcEEEEEEEEEecCCC--cEEEEEEEeeeecCcchhhhhhhccCcceEEeEeccCCCCcC-
Confidence 1346688999999999999999987654 478999999999999999999999999999999999999999
Q ss_pred CCCCcCcEEeCCCCccccccHHHHHHHhhccc
Q 002545 878 VTGMRPDLIINPHAFPSRMTIAMLLESVAAKE 909 (910)
Q Consensus 878 ~~G~~pDiI~NPh~~PSRMtiGql~E~~~gK~ 909 (910)
+||++|||||||||||||||||||+|+++||+
T Consensus 381 ~~G~~pDiIiNPhg~PSRMTiGqllE~~~gk~ 412 (599)
T TIGR03670 381 EDGIVPDLIINPHAIPSRMTVGQLLEMIAGKV 412 (599)
T ss_pred CCCCCCCEEECcccccccccHHHHHHHHHHHH
Confidence 99999999999999999999999999999996
No 15
>PRK09606 DNA-directed RNA polymerase subunit B''; Validated
Probab=100.00 E-value=4.5e-97 Score=862.25 Aligned_cols=437 Identities=24% Similarity=0.400 Sum_probs=375.8
Q ss_pred ccCchhhHHHHHHHHHHHHHHhHHHHH----------------------------------------HHHHHcCCeeeeE
Q 002545 9 FEPLRELVRHHIESFDYMLDEGLSEMF----------------------------------------DHCRQAKISYTGK 48 (910)
Q Consensus 9 ~~~~~~Lv~~hi~SFn~Fi~~gl~~i~----------------------------------------~ecR~r~~TY~~~ 48 (910)
+...++|++||++|||+|+++||++++ +|||+|++||+|+
T Consensus 12 ~~~~~~lv~~qi~SFn~Fi~~gl~~ii~~~~~i~~~~~~~~~l~~~~~~l~~P~~~~~~~~~~~l~P~eaR~r~~TYs~~ 91 (494)
T PRK09606 12 YFKEHRLVRHHIDSYNDFVDNGLQKIIDEQGPIETEIEDGVYVELGKIRVGKPVVKEADGSEREIYPMEARLRNLTYSAP 91 (494)
T ss_pred HHCCCChHHHHHHHHHHHHHHhHHHHHHhcCCEEEecCCcEEEEEEEEEECCCcccccCCccccCCHHHHHhcCCCccce
Confidence 345789999999999999999999998 7999999999999
Q ss_pred EEEEEEEEEecCCCceeeeEeeecccceeecCCCccCCCCChHHHHhcccccccCCcEEEEcCceeEEEEEEeecCCccE
Q 002545 49 LMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPM 128 (910)
Q Consensus 49 l~v~i~~~~~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~~~~~el~~~~E~~~D~GGYFIInG~EKVIr~qi~~~~N~~~ 128 (910)
++|++.++.+ +.+...+++++|+|||||+|++|||++++++|+++.||||+|+||||||||+|||||+|+++++|+++
T Consensus 92 l~v~i~~~~~--~~~~~~~~v~iG~iPiMv~S~~C~L~~~~~~~l~~~~E~~~d~GGyFIING~ErVi~~q~~~~~n~~~ 169 (494)
T PRK09606 92 LYLEMSPVEG--GEEEEPEEVYIGELPVMVGSKICNLYGLSEEELIEVGEDPLDPGGYFIVNGSERVLMTLEDLAPNKIL 169 (494)
T ss_pred EEEEEEEEEC--CCceEEeeEEeccCCeEeccCcccCCCCCHHHHHhcCCCcCCCCCeEEECCCeEEEEEEEeccCCeeE
Confidence 9999999765 43446678999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEeccccCCCCcceeeEEEEEeeecCCCceEEEEEEEeCCeEEEEEEeecccccccHHHHHHhccCCCHHHHHHHhccc
Q 002545 129 SMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCC 208 (910)
Q Consensus 129 ~~~r~~~~~~~~~~t~~~v~~r~~~~~~~~~~~~l~y~~~g~~~l~~~~~~~~~~IPi~ilLkALg~~sD~EI~~~i~~~ 208 (910)
++.++.+.++ . +...+++... ..+.+..++|+.+|.+|+++.. .+++||+++||||||..||+||++.|..
T Consensus 170 ~~~~~~~~~~--~---~~~~i~s~~~-~~~~~~~l~~~~~g~i~~~~~~--~~~~iPi~~llkALg~~sd~eI~~~i~~- 240 (494)
T PRK09606 170 VEKDERYGDR--I---EVAKVFSQRR-GYRALVTVERNRDGLLEVSFPS--VPGSIPFVILMRALGLETDEEIVEAVSD- 240 (494)
T ss_pred EEeccCCCcc--c---eEEEEEcccc-cceeeEEEEEecCCeEEEEEcC--ccccccHHHHHHHcCCCCHHHHHHHhCC-
Confidence 9887644321 1 2234444322 1234688999999999998865 3457999999999999999999999951
Q ss_pred ccchhhcccCCCCChhhHHHHHHHHHHHHhcccccHHHHHHHHhhcccccccCCCCccHHHHHHHHHHhHhccCCCC---
Q 002545 209 YDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHLND--- 285 (910)
Q Consensus 209 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i~t~~~al~yLg~~fr~~~~~~~~~~~~~~g~~~L~~~ll~Hl~~--- 285 (910)
+ . ++++.++..+.+.++.|+++|+.|||++|+.. ..+.+..+.|+.+|++++|||+|.
T Consensus 241 ----------~---~---~~~~~l~~~~~~~~~~t~~~al~~ig~~~~~~---~~~~~~~~~~~~~l~~~~l~hig~~~~ 301 (494)
T PRK09606 241 ----------D---P---EIVKFMLENLEEAEVDTQEEALEYIGKRVAPG---QTKEYRIKRAEYVIDRYLLPHLGVEPE 301 (494)
T ss_pred ----------c---H---HHHHHHHHHHHhcccCCHHHHHHHHHHhcCCC---CCcchHHHHHHHHHHHhhhcccCCCcc
Confidence 1 1 35667777777778999999999999999753 235566789999999999999995
Q ss_pred -CcchHHHHHHHHHHHHhhcCCCCCCCCcccccccEEcccchhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCcccccchH
Q 002545 286 -NNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLA 364 (910)
Q Consensus 286 -~~~K~~~L~~Mi~kLl~~~~g~~~~Dd~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~ 364 (910)
...|++||++|++||+.++.|.+.+||+|||+||||+++|+||+.+||+.|+++++.++..+++...+ ++..+
T Consensus 302 ~~~~K~~~L~~m~~kLl~~~~g~~~~Dd~D~l~nkRv~~~G~Ll~~~fr~~l~~~~~~~k~~l~~~~~~-~~~~~----- 375 (494)
T PRK09606 302 VRRAKAHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERANMR-NRELS----- 375 (494)
T ss_pred hhhHHHHHHHHHHHHHHHHhcCCCCCCCcccccCceeeccchhHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCCC-----
Confidence 34799999999999999999999999999999999999999999999999999999999888776543 33222
Q ss_pred HHHHHHhcCCCcchHHHHHhHhcccCcccccccccccccceEEEccccchhhHhhhhcccccCCcccccccccccccCCC
Q 002545 365 NIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTSVRKLLPE 444 (910)
Q Consensus 365 ~~~~~~~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~sGvsqvleRln~~~~lSH~Rrv~rg~~~~~~k~t~vR~Lhps 444 (910)
++.+++ ++.||++|++|||||||.+ +++||||+|+|+||+|+||||||||. ++.+++|.++||+||||
T Consensus 376 -~~~~~~---~~~It~~l~~~~~TGnw~~-------~~~glSq~ldr~N~la~lSh~Rrv~s-~~~r~~~~~~vR~lhps 443 (494)
T PRK09606 376 -IKTAVR---SDVLTERLEHAMATGNWVG-------GRTGVSQLLDRTDYMATLSHLRRVVS-PLSRSQPHFEARDLHPT 443 (494)
T ss_pred -HHHhcC---chhhhHHHHHHhhcccccC-------CCceEEEEccCCCHHHHhhHHHhccC-CccccCccccccccCcc
Confidence 344553 3589999999999999975 46899999999999999999999997 45688899999999999
Q ss_pred CccccccCCCCCCccccccccccceeEEeeecCCCCcccccchhhHHHHHHHHhcCCeec
Q 002545 445 SWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPS 504 (910)
Q Consensus 445 ~wG~iCPveTPEG~~cGLv~~LA~~~~Is~~~~~~~~~~~~~~~~~~i~~~L~~lG~~~~ 504 (910)
||||+||||||||++||||||||++|+|+++.+.+ .+.++|.++|+.+.
T Consensus 444 ~~G~iCPveTPEG~~cGLv~~La~~a~V~~~~~~~-----------~i~~~l~~lg~~~~ 492 (494)
T PRK09606 444 QWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEE-----------EVKEILKELGVEPE 492 (494)
T ss_pred cceecccCcCCCCCcccHHHhhhceEEEeCCCChH-----------HHHHHHHHCcCeeC
Confidence 99999999999999999999999999999874433 58899999999865
No 16
>PF00562 RNA_pol_Rpb2_6: RNA polymerase Rpb2, domain 6; InterPro: IPR007120 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerases (2.7.7.6 from EC) catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain represents the hybrid-binding domain and the wall domain []. The hybrid-binding domain binds the nascent RNA strand/template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion []. This domain is also involved in binding to Rpb1 and Rpb3 []. Many of the bacterial members contain large insertions within this domain, which are known as dispensable region 2 (DRII).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2Y0S_R 3HKZ_B 2PMZ_R 3H0G_B 3S17_B 1I6H_B 4A3B_B 3K1F_B 4A3I_B 1TWA_B ....
Probab=100.00 E-value=3e-78 Score=683.14 Aligned_cols=264 Identities=44% Similarity=0.667 Sum_probs=221.8
Q ss_pred cceeecccCCCCCCcchhhhhhhccccccccceeEEEEeccCceeecCCCCeeeEecc-cccccC---------ccccCC
Q 002545 639 SVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTN-TYTKYG---------IDEYPT 708 (910)
Q Consensus 639 s~~asliPF~~hNqspRn~yq~~M~KQaig~~~~n~~~R~D~~~y~L~~pQ~Plv~t~-~~~~~~---------~~~~~~ 708 (910)
|++|++|||++||||||++|||||+|||||++.+|+..|+|+.. .|||+|||+|+ .++..+ ++++|+
T Consensus 1 si~As~ipf~~hn~s~R~~~~~~m~kQa~~~y~~~~~~R~d~~~---~~~q~Plv~~~~~~~~~~ilad~~~~~~~e~~~ 77 (386)
T PF00562_consen 1 SIVASLIPFPEHNQSPRNLYQCNMQKQAIGTYSLNKFNRSDQNT---CYPQKPLVKTGDRVEKGQILADGPSTKFGELPL 77 (386)
T ss_dssp -THGGTSSSGGGC-HHHHHHHHHHGCGBCSEEETTTTTS-TSSE---SS-BEESSBSSSTBTTTTECEE-TTECTTTS-S
T ss_pred CEEeCCCCEEEEEcCCcEEEEeCcCCCcccceeeeeeeccCcce---eccccceEEeeccccccCccccccccccccCcc
Confidence 68999999999999999999999999999999999999999988 79999999999 677777 899999
Q ss_pred CceeeEEEEeccCCCcccceeeeccccccCcceeeEEEEEEEEeeccCCCcCccceeecc-CCCChhhhcccCCCCCccc
Q 002545 709 GTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFRR-NKDAKSLHSVIDSDGLPYV 787 (910)
Q Consensus 709 G~N~iVav~~y~Gyn~EDaiiink~s~~rG~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~-~~~~~~~~~~ld~dG~~~~ 787 (910)
|+|++||||||+||||||||||||++++||||++++|++ .++++.... ....+.|.. |+..+..+++||+||||++
T Consensus 78 G~N~iVAvmsy~GYN~EDAiIiNkssv~rG~f~s~~~k~-~~~~~~~~~--g~~e~~~~~~~~~~~~~~~~LD~dGii~~ 154 (386)
T PF00562_consen 78 GQNAIVAVMSYTGYNQEDAIIINKSSVDRGLFTSIHYKT-EIEIRDNKG--GPSEEIFRPIPNVKEYNYSKLDEDGIIKI 154 (386)
T ss_dssp SEEEEEEESBSSSTTTSSEEEEECHHHHTTTTEEEEEEE-EEEEEEETT--SEEBBESS--TSSTSTTGGGBCTTSBB-T
T ss_pred eeeeeEEeeehhcccchhhhhhhhhhhhcCeeeEEEEEE-EeeeecccC--Ccccccccccccchhhhhhhccccccccc
Confidence 999999999999999999999999999999999999999 766643331 112333443 3446677899999999999
Q ss_pred CceecCCCcEEEeec--------------cCC--CceeeeeecCCCceEEEEEEEEecC-----CCCCCeEEEEEEeeee
Q 002545 788 GQMIHPGEPYCSIYD--------------KTT--NSWRTNSRKGSESVFVDYVAVDMKN-----SKNLPQKANIRFRHTR 846 (910)
Q Consensus 788 g~~v~~gd~l~~~~~--------------~~~--~~~~~~~~~~~e~g~v~~v~~~~~~-----~~~~~~~v~i~~r~~R 846 (910)
|+.|++||+|+||+. .+. .++.+++++.+|.|+||+|.++.+. ...+...|+|++|+.|
T Consensus 155 G~~v~~gDiligk~~~~~~~~~~~~~~~~~~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~~~~~~~~iki~ir~~R 234 (386)
T PF00562_consen 155 GSRVEKGDILIGKITSPPRFSPLLKKIFGEKNRNYRDTSIKYKSGESGRVDKVIIFSNEKKDTSNNEGYKKIKIRIRSTR 234 (386)
T ss_dssp TCEEETTSEEEEEEESTSC--HHHHHHHHSSSCSEEEEEEES-TT-EEEEEEEEEECCCSSBEEETTCEEEEEEEEEEEE
T ss_pred CcEEecceeEEEEEecccccccchhhccccccccccceeecccccEEeEeccccccccccccccccCcceEEEEEecccc
Confidence 999999999999984 111 2567899999999999999995421 1235689999999999
Q ss_pred CCCcccceeccCCCccEEeeeecCcCcCccCCCCCcCcEEeCCCCccccccHHHHHHHhhccc
Q 002545 847 NPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKE 909 (910)
Q Consensus 847 ~p~iGDKf~sRHGqKGv~s~i~~~~dMPf~~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gK~ 909 (910)
+|++|||||||||||||||+|||+|||||| ++|++|||||||||||||||||||+|+++||+
T Consensus 235 ~p~iGDKfssRHGqKGVvs~i~~~eDMPft-~~G~~pDiIiNPhgiPSRMtiGqllE~~~g~~ 296 (386)
T PF00562_consen 235 RPQIGDKFSSRHGQKGVVSKILPQEDMPFT-EDGIVPDIIINPHGIPSRMTIGQLLESLLGKA 296 (386)
T ss_dssp E--TTEEEEETTSEEEEEEEEE-TTTSEEE-TTSEB-SEEE-GGGSTTTTBTHHHHHHHHHHH
T ss_pred cchhHHHHhhhhcCceEEeeeeccccCccc-cCCCcceeeecccccccccchHHHHhhhhhhh
Confidence 999999999999999999999999999999 99999999999999999999999999999996
No 17
>PF04563 RNA_pol_Rpb2_1: RNA polymerase beta subunit; InterPro: IPR007644 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the protrusion domain []. The other lobe, RNA polymerase Rpb2, domain 2, is nested within this domain.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_B 3LTI_A 3IYD_C 3LU0_C 1SMY_M 3DXJ_M 3AOI_C 2A68_M 1ZYR_C 3AOH_H ....
Probab=100.00 E-value=2.3e-36 Score=314.81 Aligned_cols=107 Identities=36% Similarity=0.773 Sum_probs=92.3
Q ss_pred hhHHHHHHHHHHHHHHhHHHHH-----------------------------------------HHHHHcCCeeeeEEEEE
Q 002545 14 ELVRHHIESFDYMLDEGLSEMF-----------------------------------------DHCRQAKISYTGKLMAD 52 (910)
Q Consensus 14 ~Lv~~hi~SFn~Fi~~gl~~i~-----------------------------------------~ecR~r~~TY~~~l~v~ 52 (910)
||++||++|||||+++||++++ +|||+|++||+|+++|+
T Consensus 1 ~Lv~~qi~SFn~Fl~~gl~~i~~~~~~i~~~~~~~~~~l~~~~~~i~~P~~~~~~~~~~~l~P~ecR~r~~TYs~~l~v~ 80 (203)
T PF04563_consen 1 GLVKHQIDSFNYFLNNGLKEILKEFPPIEFESSNNRISLKFENIRIGKPTYSESDGRERPLYPRECRLRGLTYSAPLYVD 80 (203)
T ss_dssp TTTHHHHHHHHHHHCTSSHHHHSCSSSCEECCCSTTEEEEEEEEEEESESSEHTTSCEEE--HHHHHHTT-B-EEEEEEE
T ss_pred CchHHHHHHHHHHHHCCCHHHhccCCceEecCCcceEEEEeeEEEEeeeeeccccccccCCCHHHHHhcCCCCCCccceE
Confidence 6899999999999999999998 89999999999999999
Q ss_pred EEEEEecCCC-ceeeeEeeecccceeecCCCccCCCCChHHHHhcccccccCCcEEEEcCceeEEEEEEee
Q 002545 53 VEFQYLDAGS-PVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILP 122 (910)
Q Consensus 53 i~~~~~~~~~-~~~~~~v~iG~iPIMv~S~~C~L~~~~~~el~~~~E~~~D~GGYFIInG~EKVIr~qi~~ 122 (910)
++++++ +. +....++.+|+|||||+|++|||++++++|+++.||||+|+||||||||+|||||+|+++
T Consensus 81 i~~~~~--~~~~~~~~~v~iG~iPiMv~S~~C~L~~~~~~~l~~~~E~~~d~GGYFIInG~EkVi~~q~~~ 149 (203)
T PF04563_consen 81 IELTVN--NKKEIKEQEVFIGKIPIMVRSKRCNLNGLSPKELVQLGECPNDPGGYFIINGSEKVIRMQIMR 149 (203)
T ss_dssp EEEEES--STTEEEESEEEEEEEE-BTTTTTSGGGT--HHHHHHTTS-TT---SSEEETTEEEEE-EEEEE
T ss_pred EEEEee--ccceEEeeEEEEeeCCeEeecceeeCCCCCHHHHHHcCCCCcCCCCEEEECCChhheehhhhh
Confidence 999987 44 677889999999999999999999999999999999999999999999999999999875
No 18
>PF04565 RNA_pol_Rpb2_3: RNA polymerase Rpb2, domain 3; InterPro: IPR007645 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Domain 3, is also known as the fork domain and is proximal to catalytic site [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_B 1SMY_M 3DXJ_M 3AOI_C 2A68_M 1ZYR_C 3AOH_H 1IW7_M 2O5J_C 2CW0_M ....
Probab=99.94 E-value=1.1e-27 Score=204.60 Aligned_cols=67 Identities=34% Similarity=0.659 Sum_probs=60.7
Q ss_pred EEccccchhhHhhhhccccc-CCcccccccccccccCCCCccccccCCCCCCccccccccccceeEEe
Q 002545 407 VQAERLNFLRFISFFRAVHR-GASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVA 473 (910)
Q Consensus 407 qvleRln~~~~lSH~Rrv~r-g~~~~~~k~t~vR~Lhps~wG~iCPveTPEG~~cGLv~~LA~~~~Is 473 (910)
|+|+|+|++++|||+|||++ |.+++++|.+++|+|||||||||||+|||||++|||++|||++|+|+
T Consensus 1 Q~l~r~N~l~~ls~~Rri~~~~~~~~~~~~~~~R~lh~s~~G~iCPveTPEG~~~GLv~~La~~a~I~ 68 (68)
T PF04565_consen 1 QYLDRTNPLSELSHLRRINRLGPLSKESKSTEPRQLHPSQYGRICPVETPEGENCGLVKNLALMARIT 68 (68)
T ss_dssp EE--TSSHHHHHHHHTEEESCSSTSSSSSSSTTTSTTGGGTTTBSSSSS-SSTSTTTEEEBBTT-EE-
T ss_pred CCcccccHHHHHHHHHhcccccccchhhcccccccccccceeEEeecccCCCccEeehheeeeeEEeC
Confidence 78999999999999999998 88889999999999999999999999999999999999999999996
No 19
>PF04561 RNA_pol_Rpb2_2: RNA polymerase Rpb2, domain 2; InterPro: IPR007642 RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain []. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble. Many of the bacterial members contain large insertions within this domain, a region known as dispensable region 1 (DRI).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_B 3LTI_A 3IYD_C 3LU0_C 2Y0S_R 1SMY_M 3DXJ_M 3AOI_C 2A68_M 1ZYR_C ....
Probab=99.85 E-value=3.7e-22 Score=205.23 Aligned_cols=174 Identities=20% Similarity=0.197 Sum_probs=113.6
Q ss_pred cCCccEEEEeccccCCCCcceeeEEEEEeeecCCCceEEEEEEEeCCeEEEEEEeecccccccHHHHHHhccCCCHHHHH
Q 002545 123 KQNYPMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIF 202 (910)
Q Consensus 123 ~~N~~~~~~r~~~~~~~~~~t~~~v~~r~~~~~~~~~~~~l~y~~~g~~~l~~~~~~~~~~IPi~ilLkALg~~sD~EI~ 202 (910)
|.|+|++..+..+......++ +.....+..|..+....+ .+.+...+..++||+++||||||++||+||+
T Consensus 1 Rsn~i~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~IPi~ilLrALG~~sd~eI~ 70 (190)
T PF04561_consen 1 RSNGIYVEKDKDGNKIIRSVR-------SDIISSRGSWHYLEKDKK---IIIFSRPKKKFKIPIVILLRALGIESDKEII 70 (190)
T ss_dssp ESSSEEEEE-SSSSSCSSCEE-------EEECCSSSEEEEEECETT---TEEEEETTSSSEEEHHHHHHHTT--STCHHH
T ss_pred CCCEEEEEEccCCCCeeEEEE-------eecCCCcceEEEEecCCc---EEEEEEcCcccccceEEeehhhcCcCccccc
Confidence 468888876654433211111 111223334555543332 3344454556689999999999999999999
Q ss_pred HHhcccccchhhcccCCCCChhhHHHHHHHHHHHHhcccccHHHHHHHHhhcccccccCCCCccHHHHHHHHH-------
Q 002545 203 NHLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVI------- 275 (910)
Q Consensus 203 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i~t~~~al~yLg~~fr~~~~~~~~~~~~~~g~~~L------- 275 (910)
+.|+. .+ .........+++.....++.|+++|+.|||++++. .+.+....+.++.+|
T Consensus 71 ~~i~~--~~-----------~~~~~~~~~~~~~~~~~~~~t~~~al~~i~~~~~~---~~~~~~~~~~~~~~l~~~y~l~ 134 (190)
T PF04561_consen 71 ELICY--SE-----------EDFEDIEELMLSELEEEEIYTQEQALEYIGKKFRF---RQGKPPKVEEARNFLQKRYDLG 134 (190)
T ss_dssp HHHCC--CS-----------TCHSCSTTTHHHHCCCTSSCSCHHHHHHHHHCCHS---SSSCHCCHCHHHHHHTTCSSTC
T ss_pred ceeec--cc-----------ccccccccccccccccccccccccceeEeccceee---ecccccchhhhhcccccccccc
Confidence 99982 11 11112223345555667899999999999994332 233444556677776
Q ss_pred --HhHhcc-CCCCCcc------hHHHHHHHHHHHHhhcCCCCCCCCcccccccEEc
Q 002545 276 --RDYIFV-HLNDNND------KFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEIL 322 (910)
Q Consensus 276 --~~~ll~-Hl~~~~~------K~~~L~~Mi~kLl~~~~g~~~~Dd~D~l~NkRv~ 322 (910)
.+++|+ ||+.... |+.+|++|+++|+.++.|.+.+||+|||+||||+
T Consensus 135 ~i~r~~l~~hl~~~~~~~~~~~k~~~l~~m~~~ll~~~~g~~~~Dd~D~l~NkRv~ 190 (190)
T PF04561_consen 135 FIGRYKLNKHLGSDEPNENDRLKAEDLGLMIRKLLKLANGECEPDDRDHLGNKRVR 190 (190)
T ss_dssp CCHHHCCHTTTTSSSSSSSSSCHHHHHHHHHHHHHHHHTTSS-S-STTSCCCEEEE
T ss_pred cccccceeeeeeeeecccccccchhhHHHHHHHHHHHhcCCCCCCCccccCCcCCc
Confidence 466777 9985433 9999999999999999999999999999999995
No 20
>PF04566 RNA_pol_Rpb2_4: RNA polymerase Rpb2, domain 4; InterPro: IPR007646 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Domain 4, is also known as the external 2 domain [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3S17_B 1I6H_B 4A3B_B 3K1F_B 4A3I_B 1TWA_B 3S14_B 3S15_B 2NVX_B 3M3Y_B ....
Probab=99.48 E-value=1.8e-13 Score=115.07 Aligned_cols=63 Identities=25% Similarity=0.381 Sum_probs=53.7
Q ss_pred EEECCEEEeeecCccHHHHHHHHHHHHHhcCCCCCCCceEEEEEcCCCCCCCceEeecCCCceeceEEeecC
Q 002545 519 VLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISL 590 (910)
Q Consensus 519 V~lnG~~iG~~~~~~~~~~~~~lr~~k~~~~~~i~~~~eI~~v~~~~~~~~~~i~i~td~gR~~RPv~~~~~ 590 (910)
|||||.|+|++ .+|.+|+..||.+||+| .++.+++|.+. ...++|+||||+||++|||+.+++
T Consensus 1 VFlNG~~iG~~--~~p~~l~~~lr~~RR~g--~i~~~vsi~~~-----~~~~ei~I~tD~GR~~RPL~vV~n 63 (63)
T PF04566_consen 1 VFLNGVWIGIH--SDPEELVKTLRNLRRSG--KISKEVSIVYD-----IREKEIRINTDAGRLCRPLFVVEN 63 (63)
T ss_dssp EEETTEEEEEE--SSHHHHHHHHHHHHHTT--SS-TTSEEEEE-----TTTTEEEEE-SSCEEEEEEEEESS
T ss_pred CEECCEEEEEE--cCHHHHHHHHHHHhhcc--CCcceeEEEEe-----ccCCEEEEEccCCcccceeEEecC
Confidence 79999999997 47899999999999999 67888887654 456899999999999999998864
No 21
>PF06883 RNA_pol_Rpa2_4: RNA polymerase I, Rpa2 specific domain ; InterPro: IPR009674 This domain is found between domain 3 and domain 5, but shows no homology to domain 4 of Rpb2. The external domains in multisubunit RNA polymerase (those most distant from the active site) are known to demonstrate more sequence variability [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=99.12 E-value=7.8e-11 Score=97.18 Aligned_cols=58 Identities=48% Similarity=0.940 Sum_probs=55.3
Q ss_pred EeeecCccHHHHHHHHHHHHHhcCCCCCCCceEEEEEcCCCCCCCceEeecCCCceec
Q 002545 526 VGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVR 583 (910)
Q Consensus 526 iG~~~~~~~~~~~~~lr~~k~~~~~~i~~~~eI~~v~~~~~~~~~~i~i~td~gR~~R 583 (910)
||++++++++++++.||++|..+...||.++||+||+.+.+++||+|||||+++|++|
T Consensus 1 iG~~~~~~a~~~~~~LR~~Kv~~~~~vP~~lEI~~VP~~~~g~yPGLyLft~~aRm~R 58 (58)
T PF06883_consen 1 IGYVSPEEAEQIADQLRYLKVEGEHGVPPTLEIGYVPPSKGGQYPGLYLFTTPARMMR 58 (58)
T ss_pred CceecHHHHHHHHHHHHHHHHcCCCCCCCceEEEEEECCCCCCCCeEEEeCCcccccC
Confidence 5889889999999999999999988999999999999988899999999999999998
No 22
>PF04567 RNA_pol_Rpb2_5: RNA polymerase Rpb2, domain 5; InterPro: IPR007647 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Domain 5, is also known as the external 2 domain [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3S17_B 1I6H_B 4A3B_B 3K1F_B 4A3I_B 1TWA_B 3S14_B 3S15_B 2NVX_B 3M3Y_B ....
Probab=98.53 E-value=4.3e-08 Score=78.24 Aligned_cols=40 Identities=25% Similarity=0.185 Sum_probs=30.0
Q ss_pred CCceeeeCccceeeeeeecCCCCCC--CCCCCCCceecccCC
Q 002545 595 SQNIELIGPFEQVFMEIRCPDGGDG--GRRNAFPATHEEIHP 634 (910)
Q Consensus 595 ~g~iE~i~~~Eq~~~~Ia~~~~~~~--~~~~~~~~th~EI~p 634 (910)
.|.|||||++||++++||++++++. +......||||||||
T Consensus 7 ~G~vE~id~eEEe~~~Iam~~~dl~~~~~~~~~~~TH~EI~P 48 (48)
T PF04567_consen 7 EGVVEYIDAEEEETCMIAMSPEDLESTNEDITHTYTHCEIHP 48 (48)
T ss_dssp TTSEEEEETTTCTT--EESSCCCCCHSGGCCSST-SEEES-G
T ss_pred CCCEEEecchhccccEEEEecccccccCCCCCCccEEEeEeC
Confidence 3699999999999999999999887 322355699999998
No 23
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]
Probab=97.65 E-value=6e-05 Score=93.65 Aligned_cols=73 Identities=19% Similarity=0.367 Sum_probs=59.5
Q ss_pred ceecccCCCccccceeecccCCCCCCcchhhhhhhccccccccceeEEEEeccCceeecCCCCeeeEecccccccCcccc
Q 002545 627 ATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEY 706 (910)
Q Consensus 627 ~th~EI~p~~~ls~~asliPF~~hNqspRn~yq~~M~KQaig~~~~n~~~R~D~~~y~L~~pQ~Plv~t~~~~~~~~~~~ 706 (910)
.+|++++|.++.|+.+++|||.+|+++.|.+|+++|+|||+|. ..+..|||.|+ ++...-.+
T Consensus 526 ~~~~dv~~~~~~~~~~~~~P~l~~dd~~~~l~~~~mqr~~~~l----------------~~~~~~lv~tG-~E~~~a~e- 587 (1060)
T COG0085 526 VDYMDVSPKQVVSVGRSLIPFLEHDDANRALMGSNMQRQAVPL----------------LRTEAPLVGTG-MEYLDAED- 587 (1060)
T ss_pred ccceeccceEEeccccccCceeEEcCchHhhhhhhhhhhcccc----------------cccccccccCC-ceeecccc-
Confidence 5899999999999999999999999999999999999999993 46899999999 77643211
Q ss_pred CCCceeeEEEEec
Q 002545 707 PTGTNAIVAVLAY 719 (910)
Q Consensus 707 ~~G~N~iVav~~y 719 (910)
-.|++||.-+.
T Consensus 588 --~~~~~ia~~~~ 598 (1060)
T COG0085 588 --SGAAVIAKRPG 598 (1060)
T ss_pred --ccceeEeccCC
Confidence 13455555443
No 24
>KOG0215 consensus RNA polymerase III, second largest subunit [Transcription]
Probab=97.17 E-value=0.00017 Score=85.30 Aligned_cols=350 Identities=11% Similarity=-0.025 Sum_probs=178.4
Q ss_pred EeeecccceeecCCCccCCCCChHHHHhcccccccCCcEEEEcCceeEEEEEEeecCCccEEEEeccccCCCCcceeeEE
Q 002545 68 RFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRSSFRDRREGYTDKAV 147 (910)
Q Consensus 68 ~v~iG~iPIMv~S~~C~L~~~~~~el~~~~E~~~D~GGYFIInG~EKVIr~qi~~~~N~~~~~~r~~~~~~~~~~t~~~v 147 (910)
.+..|.-|||+.+.-|.+.+...+ -...|||+.++++||+.++++.+|.++.....++. .++.++.+ -.+
T Consensus 190 fiv~G~ekViLiqeqlsknrii~~-~~k~~~~~~svtsst~e~kskt~v~~k~~k~ylk~-----~~~~d~ip----ivi 259 (1153)
T KOG0215|consen 190 FIVKGTEKVILIQEQLSKNRIIVE-EDKKGNLQASVTSSTHERKSKTYVTTKKGKYYLKH-----NSFTDDIP----IVI 259 (1153)
T ss_pred eEeccceeEEEehhhhhccCeeec-cccCCccccccccceeeecceEEEEeccceeeeeh-----hhhhccCC----EEE
Confidence 477899999999999999998887 66789999999999999999999976644332221 12222211 111
Q ss_pred EEEee--ecCCCceEEEEEEEeCCeEEEEEEeecccccccHHHHHHhccCCCHHHHHHHhcccccchhhcccCCCCChhh
Q 002545 148 VIRCV--RKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSPLV 225 (910)
Q Consensus 148 ~~r~~--~~~~~~~~~~l~y~~~g~~~l~~~~~~~~~~IPi~ilLkALg~~sD~EI~~~i~~~~~~~~~~~~~~~~~~~~ 225 (910)
.+.-+ .+|+....+... +..+.+.... ....|+.+-+.+.+ .-++.+.. +.+...+
T Consensus 260 v~ka~g~~sd~ei~~~vg~----~~~y~~~~~~--s~ee~~~~~v~tqq-----qal~y~~~----kvk~~~~------- 317 (1153)
T KOG0215|consen 260 VLKAMGLESDQEIVQLVGG----DSKYQDIFAP--SLEECVSLGVYTQQ-----QALEYIGS----KVKVKRG------- 317 (1153)
T ss_pred EEeeccccchHHHHHHhhc----chHHHHhhcc--chhhhhhhhhHHHH-----HHHHHhhh----eEEeccC-------
Confidence 11111 111111000000 0000000000 01223332222222 22222210 0000000
Q ss_pred HHHHHHHHHHHHhcccccHHHHHHHHhhcccccccC-----CCCccH-HHHHHHHHHhHhccCCCCCc--chHHHHHHHH
Q 002545 226 SERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDG-----LQSESY-YAVAETVIRDYIFVHLNDNN--DKFNLLIFML 297 (910)
Q Consensus 226 ~~~~~~~l~~~~~~~i~t~~~al~yLg~~fr~~~~~-----~~~~~~-~~~g~~~L~~~ll~Hl~~~~--~K~~~L~~Mi 297 (910)
....-.++|++.|...+.+.... +.+.-. .-..|.++.-.+-+..-+++ -+...|-+|.
T Consensus 318 -------------t~~~~~~e~~~~l~~~~lahv~v~~~~~r~K~~yi~~m~rr~~~a~l~~~~~ddrd~~gnkrlelag 384 (1153)
T KOG0215|consen 318 -------------TTPTKDEEALEVLSTTVLAHVPVPDLNFRMKAIYIGLMVRRVIQAMLNKLAMDDRDYVGNKRLELAG 384 (1153)
T ss_pred -------------CCCCchHHHHHHHHhhheeceeccCCCCcceeehHHHHHHHHHHHHhCcccccchhhhccchHHHHH
Confidence 01122334666555544332221 111111 11233333333333222221 1222344444
Q ss_pred HHHHhhcCCCCCCCCcccccccEEcccchhhHHHHHHHHHHHHHHHHHHHHHHHhhc--CCcccccchHHHHHHHhcCCC
Q 002545 298 QKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENN--GKKFDFFNLANIKKVMEKNPS 375 (910)
Q Consensus 298 ~kLl~~~~g~~~~Dd~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~~~~i~~~~~~~--~~~~~~~~~~~~~~~~~~~~~ 375 (910)
+|+.+.++.-..++.+.|++.+-...+.++..++-+.++.+. ..+..+..-+.+. ..++++ +.++ +.+.
T Consensus 385 -qllsllfeD~fk~~n~e~k~~~dk~l~k~~ra~~fD~~~~~n-~~~~~it~~l~ra~stgnw~i---Krfr--mer~-- 455 (1153)
T KOG0215|consen 385 -QLLSLLFEDLFKRFNSELKKNIDKILKKPIRAQEFDALKHLN-VRANMITSGLERAISTGNWSI---KRFR--MERA-- 455 (1153)
T ss_pred -HHHHHHHHHHHHHHHHHHHHHHHHHhcchhhhhhhHHHHHHH-HHHHHHHHHHHHHhhcCchHH---HHhh--hhhc--
Confidence 455555666666788899999999999988888888877764 4444444444331 111111 1111 1111
Q ss_pred cchHHHHHhHhcccCcccccccccccccceEEEccccchhhHh-hhhcccccCCcccccccccccccCCCCccccccCCC
Q 002545 376 KQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFI-SFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHT 454 (910)
Q Consensus 376 ~~It~~i~~~~sTGnw~~~~~~~~~q~sGvsqvleRln~~~~l-SH~Rrv~rg~~~~~~k~t~vR~Lhps~wG~iCPveT 454 (910)
.+|.-+ +-.|++|.- +..-.-++++.++..+..+-+.. |.++.+.+ +-+.....-.+-..+..|+.|||-++
T Consensus 456 -gvt~Vl--srlSyisaL--gmmtri~s~fektrkvsgprSlq~sqwgmlcp--~dtpegeacglvknlalmthittd~e 528 (1153)
T KOG0215|consen 456 -GVTQVL--SRLSYISAL--GMMTRINSQFEKTRKVSGPRSLQPSQWGMLCP--SDTPEGEACGLVKNLALMTHITTDSE 528 (1153)
T ss_pred -cceeee--hhhhhhhhh--hhheehhhhheeehhccCccccChhhcccccC--CCCCCccccccccchHHHhcccCCCC
Confidence 122211 223455522 11113667787776644433322 22222222 22455566689999999999999999
Q ss_pred CCCccccccccccceeEEeeecCC
Q 002545 455 PDGEPCGLLNHMTSTCRVASYYDS 478 (910)
Q Consensus 455 PEG~~cGLv~~LA~~~~Is~~~~~ 478 (910)
|++.-|++.|..+...+++.....
T Consensus 529 e~pi~~~~~k~gv~di~~v~~~e~ 552 (1153)
T KOG0215|consen 529 EKPILKLCYKLGVEDIHVVSGREL 552 (1153)
T ss_pred cchhHHHHHHhcceeeeeeccccc
Confidence 999999999999999999877443
No 25
>KOG0214 consensus RNA polymerase II, second largest subunit [Transcription]
Probab=95.63 E-value=0.0062 Score=73.57 Aligned_cols=233 Identities=7% Similarity=-0.118 Sum_probs=143.5
Q ss_pred CCCcchhhhhhhccccccccceeEEEEeccCceeecCCCCeeeEecccccccCccccCCCceeeEEEEeccCCCccccee
Q 002545 650 HNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMI 729 (910)
Q Consensus 650 hNqspRn~yq~~M~KQaig~~~~n~~~R~D~~~y~L~~pQ~Plv~t~~~~~~~~~~~~~G~N~iVav~~y~Gyn~EDaii 729 (910)
.-|.+++.++.-|+ |..+.....+..+.+...-.|.+++.++-++......-.-..+.+.++-++.+.+.++..++...
T Consensus 680 Fpdh~qspr~tYQs-a~~kqamg~y~tn~~vR~dtl~~~l~ypqkpl~tt~~~e~l~~~eL~aG~NaiVAi~~~~GYNqE 758 (1141)
T KOG0214|consen 680 FPDHNQSPRNTYQS-AMGKQAMGVYHTNPQVRMDTLAKVLYYPQKPLVTTRAMEYLRFRELPAGQNAIVAIACYSGYNQE 758 (1141)
T ss_pred cCCCCCchHHHHHH-HHhhhcceeeeecchhhhhhhhhcccccccchhhHHHHhhhhhhhcccccceEEEEecccCccHH
Confidence 34666777777666 33334445555666666666667777766666655554556678999999999999999999999
Q ss_pred eeccccccCcceeeEEEEEEEEeeccCCCcCccceeeccCCCChhhhcccC-------CCCCcccCceecCCCcEE--Ee
Q 002545 730 LNKSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFRRNKDAKSLHSVID-------SDGLPYVGQMIHPGEPYC--SI 800 (910)
Q Consensus 730 ink~s~~rG~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~ld-------~dG~~~~g~~v~~gd~l~--~~ 800 (910)
-|--..++++.|+. |++..+.-++. ++..-. ...+...++.. .+|..- .+ ..|-++ |.
T Consensus 759 Dsvimn~s~v~rg~-FrS~~~RsYk~------q~~~~~--~~~ee~~~~~~~~~~~~mr~~~~d---kL-dddG~i~~G~ 825 (1141)
T KOG0214|consen 759 DSVIMNQSSVDRGL-FRSFFIRSYKD------QEHKKD--QGPEEIFEEPPRGEGRGMRNGKYD---KL-DDDGIIMPGS 825 (1141)
T ss_pred HHHHHHhhhhhcch-hhhhhhhHHHh------hhhhcc--cccccccccccccccccccccccc---cc-cccCCccccc
Confidence 99999999998887 45555432111 111100 01111111110 011100 00 011111 11
Q ss_pred ----eccCCCceeeeeecCCCce--------EEEEEEEEecCCCCCCeEEEEEEeeeeCCCcccceeccCCCccEEeeee
Q 002545 801 ----YDKTTNSWRTNSRKGSESV--------FVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLW 868 (910)
Q Consensus 801 ----~~~~~~~~~~~~~~~~e~g--------~v~~v~~~~~~~~~~~~~v~i~~r~~R~p~iGDKf~sRHGqKGv~s~i~ 868 (910)
-+..-++......+..+.+ +..++.+-.++.| ...+|.++. ++.|+||+.+|++++-+.++-
T Consensus 826 ~vs~~Dv~iGk~t~~~~~~~~~~~~~~~~t~~d~s~~Lr~~e~G---ivd~V~vt~---n~~G~kF~kv~vr~~ripqiG 899 (1141)
T KOG0214|consen 826 RVSGGDVLIGKTTPQPAKEDESGPEDRLYTKRDHSTKLRHTERG---IVDQVWVTK---NSEGPKFVKVRVRQVRIPQIG 899 (1141)
T ss_pred eeecCCEEeccccCCcccchhccccccccccccceeecccCCcc---eEEEEEEec---CCCCCceeEEEEeeccccccc
Confidence 0001122222222222333 5566666555432 334444443 899999999999999999999
Q ss_pred cCcCcCccCCCCCcCcEEeCCCCccccccHHHHHH
Q 002545 869 PDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLE 903 (910)
Q Consensus 869 ~~~dMPf~~~~G~~pDiI~NPh~~PSRMtiGql~E 903 (910)
...++++- ..|++++++.+++.-+++|++-..++
T Consensus 900 DKfasrHg-qKG~ig~~~~qedmpft~eGi~pDii 933 (1141)
T KOG0214|consen 900 DKFASRHG-QKGTIGITYRQEDMPFTIEGIVPDII 933 (1141)
T ss_pred chhccccc-cCccccceeecCCCCccccCCCcceE
Confidence 99999999 99999999999999999998865443
No 26
>PHA03394 lef-8 DNA-directed RNA polymerase subunit beta-like protein; Provisional
Probab=93.79 E-value=0.096 Score=63.37 Aligned_cols=60 Identities=27% Similarity=0.402 Sum_probs=46.2
Q ss_pred eEEEEEEeeeeCCCcccceeccCCCccEEeeeecCcCcC-ccCCCCCcCcEEeCCCCccccccH
Q 002545 836 QKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMP-FSGVTGMRPDLIINPHAFPSRMTI 898 (910)
Q Consensus 836 ~~v~i~~r~~R~p~iGDKf~sRHGqKGv~s~i~~~~dMP-f~~~~G~~pDiI~NPh~~PSRMti 898 (910)
-.+|+++-..=.=-.|=|.||=||||||+.. .||+- |..|||+.|-|.++|.+|-||.|.
T Consensus 696 v~lKl~~Vtst~dLeGlKICgIHGQKGVln~---seDLtew~aeDg~~aQIclSPiSyLsRQtn 756 (865)
T PHA03394 696 VYLKIRLVTSTSDLEGLKICGIHGQKGVLNG---SEDLTEWMAEDGTHAQICLSPISYLSRQTN 756 (865)
T ss_pred EEEEEEEEEEecCcceeEEeeecccccccCC---cchhhhhhccCCCcceEEechHHhhccccc
Confidence 3455554444445579999999999999864 56653 444899999999999999999874
No 27
>PF14251 DUF4346: Domain of unknown function (DUF4346)
Probab=52.79 E-value=6.7 Score=37.28 Aligned_cols=14 Identities=29% Similarity=0.529 Sum_probs=11.2
Q ss_pred ccccccCCcEEEEc
Q 002545 97 KEEAAEMGGYFILN 110 (910)
Q Consensus 97 ~E~~~D~GGYFIIn 110 (910)
.--..||+|||||.
T Consensus 10 R~i~LDp~GYfiI~ 23 (119)
T PF14251_consen 10 RFIDLDPAGYFIIY 23 (119)
T ss_pred CccccCCCccEEEE
Confidence 34457999999997
No 28
>PF04941 LEF-8: Late expression factor 8 (LEF-8); InterPro: IPR007025 Late expression factor 8 (LEF-8) is one of the primary components of RNA polymerase produced by polyhedrosis viruses. LEF-8 shows homology to the second largest subunit of prokaryotic DNA-directed RNA polymerase[].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=49.23 E-value=21 Score=43.59 Aligned_cols=31 Identities=26% Similarity=0.256 Sum_probs=24.7
Q ss_pred CCcccccccEEcccchhhHHHHHHHHHHHHH
Q 002545 311 DNPDSLQNQEILLPGHLITIYLKEKLEDWLR 341 (910)
Q Consensus 311 Dd~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~ 341 (910)
=.+|+|+||=+--...||..+++..++.+..
T Consensus 211 Y~IDsLsNKiIYkh~yLl~l~y~~~L~~~~~ 241 (748)
T PF04941_consen 211 YSIDSLSNKIIYKHSYLLELTYKPILKKYEN 241 (748)
T ss_pred ceecccccceeeCHHHHHHHHHHHHHHHHHH
Confidence 4689999999999999999888765554443
No 29
>PF13375 RnfC_N: RnfC Barrel sandwich hybrid domain
Probab=28.44 E-value=1.8e+02 Score=27.22 Aligned_cols=52 Identities=13% Similarity=0.058 Sum_probs=35.0
Q ss_pred CcccCceecCCCcEEEeeccCCCceeeeeecCCCceEEEEEEEEecCCCCCCeEEEE
Q 002545 784 LPYVGQMIHPGEPYCSIYDKTTNSWRTNSRKGSESVFVDYVAVDMKNSKNLPQKANI 840 (910)
Q Consensus 784 ~~~~g~~v~~gd~l~~~~~~~~~~~~~~~~~~~e~g~v~~v~~~~~~~~~~~~~v~i 840 (910)
++++|+.|+.|+.|.-. ....+...+..-+|+|..|.-.....|.....|.|
T Consensus 45 ~V~~Gd~V~~GQ~Ia~~-----~~~~sa~iHAsvSG~V~~I~~~~~~~g~~~~~ivI 96 (101)
T PF13375_consen 45 VVKVGDKVKKGQLIAEA-----EGFLSAPIHASVSGTVTAIEKRPIPHGSKVPAIVI 96 (101)
T ss_pred EEcCCCEEcCCCEEEec-----CCCcEeeEEcCCCeEEEEEeeeEcCCCCCCCEEEE
Confidence 68899999999998532 11224455667899999988776655544444443
No 30
>PF13533 Biotin_lipoyl_2: Biotin-lipoyl like
Probab=21.86 E-value=55 Score=26.21 Aligned_cols=16 Identities=19% Similarity=0.223 Sum_probs=14.0
Q ss_pred CcccCceecCCCcEEE
Q 002545 784 LPYVGQMIHPGEPYCS 799 (910)
Q Consensus 784 ~~~~g~~v~~gd~l~~ 799 (910)
.++.|+.|++||+|+-
T Consensus 17 ~V~~G~~VkkGd~L~~ 32 (50)
T PF13533_consen 17 YVKEGQQVKKGDVLLV 32 (50)
T ss_pred EecCCCEEcCCCEEEE
Confidence 4779999999999975
Done!