Query 001179
Match_columns 1131
No_of_seqs 209 out of 1894
Neff 6.6
Searched_HMMs 46136
Date Thu Mar 28 17:59:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001179.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001179hhsearch_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 4E-285 9E-290 2421.9 74.1 1062 2-1126 5-1111(1111)
2 PRK08565 DNA-directed RNA poly 100.0 6E-259 1E-263 2436.5 91.7 1012 8-1129 7-1103(1103)
3 KOG0215 RNA polymerase III, se 100.0 2E-245 4E-250 2082.5 47.5 1013 8-1128 52-1151(1153)
4 KOG0214 RNA polymerase II, sec 100.0 5E-245 1E-249 2105.4 51.5 1025 8-1126 11-1140(1141)
5 COG0085 RpoB DNA-directed RNA 100.0 6E-227 1E-231 2049.3 67.2 959 5-1128 17-1059(1060)
6 cd00653 RNA_pol_B_RPB2 RNA pol 100.0 4E-218 8E-223 2027.5 69.4 808 15-1124 1-866 (866)
7 TIGR02013 rpoB DNA-directed RN 100.0 4E-209 9E-214 1952.5 71.3 873 8-1123 13-1065(1065)
8 PRK00405 rpoB DNA-directed RNA 100.0 2E-207 3E-212 1947.7 75.1 887 10-1125 22-1107(1112)
9 CHL00001 rpoB RNA polymerase b 100.0 9E-202 2E-206 1875.5 71.0 903 7-1127 7-1059(1070)
10 CHL00207 rpoB RNA polymerase b 100.0 1E-190 2E-195 1764.8 73.4 894 8-1126 3-1053(1077)
11 PRK09603 bifunctional DNA-dire 100.0 1E-176 2E-181 1686.2 69.3 936 10-1127 22-1375(2890)
12 PRK14844 bifunctional DNA-dire 100.0 5E-171 1E-175 1627.5 68.9 936 10-1129 27-1435(2836)
13 PRK07225 DNA-directed RNA poly 100.0 2E-172 4E-177 1537.8 49.7 561 516-1129 4-605 (605)
14 TIGR03670 rpoB_arch DNA-direct 100.0 3E-172 7E-177 1533.9 46.0 558 519-1129 1-599 (599)
15 PF00562 RNA_pol_Rpb2_6: RNA p 100.0 3E-107 6E-112 942.8 23.2 354 639-1014 1-386 (386)
16 PRK09606 DNA-directed RNA poly 100.0 6.8E-96 1E-100 874.0 45.5 438 8-504 11-492 (494)
17 PF04563 RNA_pol_Rpb2_1: RNA p 100.0 1E-35 2.2E-40 318.3 12.9 107 14-122 1-149 (203)
18 PF04560 RNA_pol_Rpb2_7: RNA p 100.0 2.2E-30 4.8E-35 234.5 6.6 81 1016-1125 1-81 (81)
19 PF04565 RNA_pol_Rpb2_3: RNA p 99.9 5.2E-27 1.1E-31 206.2 4.6 67 407-473 1-68 (68)
20 PF04561 RNA_pol_Rpb2_2: RNA p 99.8 8E-22 1.7E-26 208.1 6.7 174 123-322 1-190 (190)
21 PF04566 RNA_pol_Rpb2_4: RNA p 99.4 6.2E-13 1.3E-17 115.1 9.2 63 519-590 1-63 (63)
22 PF06883 RNA_pol_Rpa2_4: RNA p 99.0 3.3E-10 7.2E-15 96.2 5.9 58 526-583 1-58 (58)
23 KOG0214 RNA polymerase II, sec 98.8 1.6E-10 3.4E-15 139.1 -4.5 365 651-1060 681-1060(1141)
24 PF04567 RNA_pol_Rpb2_5: RNA p 98.4 1E-07 2.3E-12 78.3 2.4 40 595-634 7-48 (48)
25 KOG0215 RNA polymerase III, se 97.8 1.4E-05 3E-10 96.4 3.8 353 67-478 189-552 (1153)
26 COG0085 RpoB DNA-directed RNA 97.7 5.3E-05 1.2E-09 96.5 7.3 73 627-719 526-598 (1060)
27 PHA03394 lef-8 DNA-directed RN 94.2 0.052 1.1E-06 67.2 5.1 77 837-919 697-774 (865)
28 PF14251 DUF4346: Domain of un 48.8 8.5 0.00018 37.8 1.1 13 98-110 11-23 (119)
29 COG1545 Predicted nucleic-acid 48.7 9.5 0.00021 38.9 1.6 37 1046-1104 25-61 (140)
30 PF04941 LEF-8: Late expressio 36.1 43 0.00094 42.2 4.7 32 309-340 209-240 (748)
31 smart00661 RPOL9 RNA polymeras 31.2 31 0.00068 28.5 1.8 11 1052-1062 2-12 (52)
32 PF09082 DUF1922: Domain of un 28.0 20 0.00044 32.0 0.1 35 1049-1103 2-36 (68)
33 PRK00420 hypothetical protein; 27.9 35 0.00077 33.5 1.7 26 1050-1094 23-48 (112)
34 PRK06266 transcription initiat 27.8 36 0.00078 36.2 1.9 30 1031-1061 99-128 (178)
35 COG1645 Uncharacterized Zn-fin 27.8 28 0.0006 35.1 1.0 31 1048-1098 26-56 (131)
36 PRK14890 putative Zn-ribbon RN 26.6 26 0.00057 30.4 0.5 18 1045-1062 2-19 (59)
37 PF13248 zf-ribbon_3: zinc-rib 26.2 31 0.00067 24.8 0.8 11 1051-1061 3-13 (26)
38 PRK00398 rpoP DNA-directed RNA 26.0 50 0.0011 26.9 2.0 27 1050-1094 3-29 (46)
39 PF14803 Nudix_N_2: Nudix N-te 24.8 45 0.00097 25.8 1.4 28 1052-1093 2-29 (34)
40 COG1997 RPL43A Ribosomal prote 24.0 43 0.00093 31.3 1.4 30 1047-1094 32-61 (89)
41 COG2956 Predicted N-acetylgluc 23.7 54 0.0012 38.0 2.4 10 247-256 71-80 (389)
42 PF02150 RNA_POL_M_15KD: RNA p 23.0 41 0.00089 26.1 0.9 13 1051-1063 2-14 (35)
43 COG1592 Rubrerythrin [Energy p 23.0 54 0.0012 34.5 2.1 12 1050-1061 134-145 (166)
44 PF06677 Auto_anti-p27: Sjogre 22.7 54 0.0012 26.5 1.6 25 1050-1093 17-41 (41)
45 CHL00207 rpoB RNA polymerase b 22.3 2.6E+02 0.0056 38.0 8.5 37 579-615 440-477 (1077)
46 PRK00432 30S ribosomal protein 22.1 51 0.0011 27.7 1.4 24 1050-1093 20-44 (50)
47 cd00729 rubredoxin_SM Rubredox 22.0 57 0.0012 25.1 1.5 12 1050-1061 2-13 (34)
48 PF12760 Zn_Tnp_IS1595: Transp 21.6 61 0.0013 26.5 1.7 28 1050-1094 18-45 (46)
49 COG1096 Predicted RNA-binding 21.1 47 0.001 35.4 1.2 36 1050-1106 149-184 (188)
50 cd00350 rubredoxin_like Rubred 20.2 63 0.0014 24.5 1.4 26 1050-1095 1-26 (33)
No 1
>KOG0216 consensus RNA polymerase I, second largest subunit [Transcription]
Probab=100.00 E-value=4.2e-285 Score=2421.88 Aligned_cols=1062 Identities=54% Similarity=0.924 Sum_probs=998.7
Q ss_pred CCCCcCccccchhhHHHHHHHHHHHHHHhHHHHH--------------------------------------------HH
Q 001179 2 ARKKSADFEPLRELVRHHIESFDYMLDEGLSEMF--------------------------------------------DH 37 (1131)
Q Consensus 2 ~~~~~~~~~~~~~Lv~~hi~SFn~Fi~~gl~~ii--------------------------------------------~e 37 (1131)
|+++..+++.++.++++|++|||...+.||...- .|
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 4566677889999999999999999998876654 99
Q ss_pred HHHcCCeeeEEEEEEEEEEEecCCCceEEEEEeecccceeeccCcccCCCCChHHHHhhccccccCCcEEEEcCceeEEE
Q 001179 38 CRQAKISYTGKLMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFR 117 (1131)
Q Consensus 38 cR~r~~TYsa~l~v~v~~~~~~~~~~~~~~~v~iG~iPIMvkS~~C~L~~ls~~el~~~gE~~~D~GGYFIING~EKVIr 117 (1131)
||+|.+||++.+.|+|.|.+| ++.+......+|.+||||+|++|||.+++++||++++|++.|+||||||||+|||||
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 999999999999999999998 777778889999999999999999999999999999999999999999999999999
Q ss_pred EEEeccCCceEEEEeccccCCCcceeeEEEEEeeeecCCCceEEEEEEEeCCeEEEEEEEecccccccHhhHHHhccCCC
Q 001179 118 SVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTN 197 (1131)
Q Consensus 118 ~qi~~~~N~~~~~~r~s~~~r~~~~t~~~i~iRs~~~~~~s~~~~l~~~~~g~~~l~~~~~k~~~~IPi~ilLkALg~~s 197 (1131)
++|+++||+|++++|++|++|+++|++|+++||||++|+++.+++|||+.||.+.++|.++|.++.+|++++||||-..|
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 HHHHHHhhccccchhhhcccCCCCChhHHHHHHHHHHHHHhccccCHHHHHHHHhhcccccccCCCCccHHHHHHHHHHh
Q 001179 198 DLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRD 277 (1131)
Q Consensus 198 D~eI~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~lL~~~~~~~i~t~~~AL~yIG~~~r~~~~~~~~~~~~e~g~~~L~~ 277 (1131)
|+|||+.|+ +++..++|+.++++.||+++.+.+++||++||.|||++||+++..-+++++.|+|+++|++
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 5777899999999999999999999999999999999999776655559999999999999
Q ss_pred hhcccCCCchhhHHHHHHHHHHHHhhcCCCCCCCCcccccccEeccchhhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCc
Q 001179 278 YIFVHLNDNNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKK 357 (1131)
Q Consensus 278 ~ll~Hl~~~~~K~~~L~~MvrkLl~l~~G~~~~DD~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~~~~l~~~~~~~~~~ 357 (1131)
++++||+++.+||.+|++|++||++++.|++.+||+|+..|||++++|+|++..|+|+++++++.++.++++.+.+.+.+
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 99999999999999999999999999999999999999999999999999999999999999999999999999876667
Q ss_pred cccchhHHHHHHHhcCCCcchHHHHHHHhcccCcccccccccccccceEEEccccchHHHhhhccccccCCccccccccc
Q 001179 358 FDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTS 437 (1131)
Q Consensus 358 ~~~~~~~~~~~~i~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~~GvsqvleRln~~~~lSh~Rrv~rg~~~~~~K~t~ 437 (1131)
.++.+..++.+++.+++ ..|+++|++||||||++++++++++|++|++++|||+||+|||||||.||||++|++|++|+
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 77777888888998877 49999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccCCcccccccCCCCCCccccccccccceEEEeeccCCCCcccccchhhhHHHHHHHhcCceecCcccccCCCCCce
Q 001179 438 VRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVL 517 (1131)
Q Consensus 438 ~R~Lhps~wGfICPveTPEG~~CGLvk~LA~~a~It~~~~~~~~~~~~~~~~~~i~~~L~~lG~~~~~~~~~~~~~~~~~ 517 (1131)
+|||.|++||||||||||||+||||+||||..|+|++..++.+ .|.++|.++||.|... .... ....|
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 9999999999999999999999999999999999999888763 5889999999998642 2222 23479
Q ss_pred EEEECCEEEeeecCchHHHHHHHHHHHHhhcCCCCCCCceEEEEeCCCCCCCCeEEEEcCCCcceeeEEEecCCCCCCcc
Q 001179 518 SVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSEESQN 597 (1131)
Q Consensus 518 ~V~lnG~~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~~~~~~~~~~i~i~td~GRl~RPv~~~~~~~~~~g~ 597 (1131)
+|++||+++||++.+.+..+++.||++|......||.++||.||+.+.+++||++||+|++||++|||.++..+ .
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 eeeecccceeeeeeecCCCCCCCCCCCCceeEEeecCCCcccceeccccCCCCCCCccccccccccccccccccceEEEe
Q 001179 598 IELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFR 677 (1131)
Q Consensus 598 iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~P~~ilsv~AslIPF~~HNqspRn~yqc~M~KQAiG~~~~n~~~R 677 (1131)
+||||++||+++.||+.++++.+.. +||.|++|+.+||++|+||||+|||||||||||||||||+||+|.++++.|
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 9999999999999999999998876 899999999999999999999999999999999999999999999999999
Q ss_pred cccceeeecCCCcceeecCcccccCcccCCCCcceEEEEEeccCCCCCceEEeeccccccCceeeeEEEEEEEEecccCC
Q 001179 678 ADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGN 757 (1131)
Q Consensus 678 ~D~~~y~L~ypQ~PLV~t~~~~~~~~~~~~~G~N~iVAv~~y~Gyn~EDaiiink~s~~rG~~~~~~y~~~~~~~~~~~~ 757 (1131)
.|+|+|+|++||.|+|++..|+.+++|++|.|+||+|||+|||||||||||||||+|+||||+++++||++.+++.+...
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 99999999999999999999999999999999999999999999999999999999999999999999999999876553
Q ss_pred Ccccccccccc-CCCChhhhcccCCCCCcccCcEEcCCCCeeEEeecCCCcEEeeecCCCcceEEEEEEEeccCCCCCCe
Q 001179 758 KVDRGQKLFRR-NKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTTNSWRTNSRKGSESVFVDYVAVDMKNSKNLPQ 836 (1131)
Q Consensus 758 ~~~~~~~~f~~-~~~~~~~~~~Ld~dGi~~~G~~v~~gdil~~~~~~~~~~~~~~~~~~~e~g~Vd~v~~~~~~~~~~~~ 836 (1131)
+ +..|.. |...+ ..+||+||||.+|+++..||++++.++..+++.+..+|++.|+|+||.|++..++.++..+
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 334553 33333 6899999999999999999999999999999999999999999999999999998876558
Q ss_pred EEEEEEeeecCCCCCcccccccCCcceeeeeecCCCCCccCCCCCcccEEeCCCCCCCccchhHhHHHHHhhhccccCce
Q 001179 837 KANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKGGSLHGKF 916 (1131)
Q Consensus 837 ~~~i~~r~~R~p~iGDKf~sRHGqKGvvs~i~~~~dmPf~~~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~ 916 (1131)
.+.|++|.+|+|.||||||||||||||||+.||.+||||| ++|++|||||||||||||||||||+|+||||+||++|..
T Consensus 845 ~~~i~~Ri~R~p~IGDKFsSRhGQKGicS~~wP~~dmPFt-esGm~PDii~NPH~FPSRMTIgM~iEs~AgK~~alhG~~ 923 (1111)
T KOG0216|consen 845 CATITLRIPRNPIIGDKFSSRHGQKGICSQKWPTIDMPFT-ESGMVPDIIINPHAFPSRMTIGMLIESMAGKAGALHGNA 923 (1111)
T ss_pred eEEEEEEecCCCcccchhhhhccccccccccCCCCCCCcc-ccCcCcceeeCCCCCcccccHHHHHHHHhchhhcccccc
Confidence 8999999999999999999999999999999999999999 999999999999999999999999999999999999999
Q ss_pred eccccccccccccCCCCCCCCchhhHHHHHHHHHHCCCCCCCcEEEeeCCCCcEeeeeeeeeceeEEeeccccccceeee
Q 001179 917 MDATPFANSVKKTNGDTGTDESKSLVDELGEMLRTCGFNYHGVEVLYSGVYGTELTCEIFIGPVYYQRLRHMVSDKFQVR 996 (1131)
Q Consensus 917 ~d~tpf~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~~~G~e~~y~g~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R 996 (1131)
+|+|||..+ ++++++|+||++|+++||||||+|+||||.+|++|+|+||+|+||||||+|||.||+|||
T Consensus 924 ~Datpf~~~-----------E~~t~~dyfg~~L~~~GyNyyGnE~~YSGv~G~e~~adIf~GvVyYQRLrHMv~DKfQVR 992 (1111)
T KOG0216|consen 924 QDATPFIFS-----------EENTAIDYFGEMLKKAGYNYYGNEPMYSGVDGREMRADIFFGVVYYQRLRHMVSDKFQVR 992 (1111)
T ss_pred ccCCceeec-----------CcccHHHHHHHHHHHcCcCccCCcccccccccceeeeeEEEeehhHHHHHHHhcceeeee
Confidence 999999877 777899999999999999999999999999999999999999999999999999999999
Q ss_pred ecccccceeecccCcccccCceeeeehhhhHHhhhchHHHHHHhhccCCCccceeccccccccccccccccccccccccC
Q 001179 997 STGTMDQITRQPIKGRKRGGGIRFGEMERDSLLAHGAAYLLHDRLHTCSDYHVADVCSLCGSVLTATFIHPQKRAIREIG 1076 (1131)
Q Consensus 997 ~~Gp~~~lTrQP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~Cg~~~~~~~~~~~~~~~~~~~ 1076 (1131)
+|||++.+|+||++||||+||+||||||||||||||||++|||||++|||.+.++||..||++++..- .....
T Consensus 993 stG~v~~~T~QPvkGRkr~GGiRfGEMERDali~HGtsfllqDRL~~~SD~~~a~vC~~cgsil~~~~-----~l~~~-- 1065 (1111)
T KOG0216|consen 993 STGPVDSLTHQPVKGRKRGGGIRFGEMERDALIAHGTSFLLQDRLLNSSDYTVAEVCRTCGSILSTQQ-----KLIKE-- 1065 (1111)
T ss_pred eccCccccccCCccCcccCCCccccchhhhhHhhcchHhhhhhhhccCcchhHHHHHHHhhhhhhhhh-----hhhcc--
Confidence 99999999999999999999999999999999999999999999999999999999999999998630 00000
Q ss_pred CCCCCCCCCCeeeccCcCCCCcceecchHhHHHHHHHHHhCCceeEEEec
Q 001179 1077 GLPPARAPKKVTCHACQTSKGMETVAMPYVFRYLAAELAAMNIKITLQLG 1126 (1131)
Q Consensus 1077 ~~~~~~~~~~~~C~~c~~~~~~~~v~iPy~~klL~~EL~sm~I~~~l~~~ 1126 (1131)
.....+.-.|+.|+ +..+..|+|||+||||..||+||||+++++++
T Consensus 1066 ---~~~~~~~~~C~~c~-~~~~~~v~~P~vfkYL~aEL~amnIk~~l~l~ 1111 (1111)
T KOG0216|consen 1066 ---PGGSTSTVTCRSCD-GKGVTTVAMPYVFKYLTAELAAMNIKMRLDLE 1111 (1111)
T ss_pred ---cCCCCCceeEEecC-CCceEEEEccHHHHHHHHHHhhCceeEEeccC
Confidence 11233456899995 77899999999999999999999999999875
No 2
>PRK08565 DNA-directed RNA polymerase subunit B; Provisional
Probab=100.00 E-value=6.4e-259 Score=2436.46 Aligned_cols=1012 Identities=31% Similarity=0.505 Sum_probs=899.4
Q ss_pred ccccchhhHHHHHHHHHHHHHHhHHHHH---------------------------------------HHHHHcCCeeeEE
Q 001179 8 DFEPLRELVRHHIESFDYMLDEGLSEMF---------------------------------------DHCRQAKISYTGK 48 (1131)
Q Consensus 8 ~~~~~~~Lv~~hi~SFn~Fi~~gl~~ii---------------------------------------~ecR~r~~TYsa~ 48 (1131)
++...++|++|||||||+||++||++|+ +|||+|++||+||
T Consensus 7 ~~~~~~~Lv~~qidSFn~Fi~~gL~~iv~~~~pI~~~~~~~~L~f~~i~l~~P~~~~~~~~~~~l~P~ecR~r~lTYsa~ 86 (1103)
T PRK08565 7 AYFKEKGLVRQHLDSYNDFIERGLQEIVDEFGEIKTEIPGLKIVLGKIRVGEPEIKEADGSERPITPMEARLRNLTYAAP 86 (1103)
T ss_pred HHhcccChHHHHHHHHHHHHHHhHHHHHHhcCCEEecCCCEEEEEEEEEECCCcccccccccCCCCHHHHHhcCCCcceE
Confidence 4667899999999999999999999998 8999999999999
Q ss_pred EEEEEEEEEecCCCceEEEEEeecccceeeccCcccCCCCChHHHHhhccccccCCcEEEEcCceeEEEEEEeccCCceE
Q 001179 49 LMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPM 128 (1131)
Q Consensus 49 l~v~v~~~~~~~~~~~~~~~v~iG~iPIMvkS~~C~L~~ls~~el~~~gE~~~D~GGYFIING~EKVIr~qi~~~~N~~~ 128 (1131)
|+|+|+++.+ +.++.+++|++|+|||||+|++|||++++++|+++.||||+|+||||||||+|||||+|+++++|+|+
T Consensus 87 l~v~i~~~~~--~~~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~p~D~GGYFIING~ERVI~~q~~~s~n~~~ 164 (1103)
T PRK08565 87 LYLTMIPVEN--GIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQEDLAPNRVL 164 (1103)
T ss_pred EEEEEEEEEC--CeeeEEEEEEeccCCeEeCCCcccCCCCCHHHHHhcCCCccCCCCeEEECCcEEEEEEEEecCCCEEE
Confidence 9999999765 55555678999999999999999999999999999999999999999999999999999999999998
Q ss_pred EEEeccccCCCcceeeEEEEEeeeecCCCceEEEEEEEeCCeEEEEEEEecccccccHhhHHHhccCCCHHHHHHhhccc
Q 001179 129 SMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCC 208 (1131)
Q Consensus 129 ~~~r~s~~~r~~~~t~~~i~iRs~~~~~~s~~~~l~~~~~g~~~l~~~~~k~~~~IPi~ilLkALg~~sD~eI~~~I~~~ 208 (1131)
++.+. ++..++.++..+++ +. ..+.|+.++|+.+|.++++|... +++||+++||||||..||+||++.|+.
T Consensus 165 ~~~~~----~~~~~~~~a~i~s~-~~-~~~~~~~l~~~~~g~i~~~~~~~--~~~IPi~illkALG~~sD~eI~~~i~~- 235 (1103)
T PRK08565 165 VDKGE----AGSSITHTAKVISS-RA-GYRAQVTVERRKDGTIYVSFPAV--PGKIPFVILMRALGLETDRDIVYAVSL- 235 (1103)
T ss_pred EEEec----CCCcceEEEEEEec-cC-CCcceEEEEEecCCeEEEEEcCc--ccEeeHHHHHHHcCCCCHHHHHHHhcc-
Confidence 87543 34445544444433 33 33468899999999999999854 458999999999999999999999962
Q ss_pred cchhhhcccCCCCChhHHHHHHHHHHHHHhccc-cCHHHHHHHHhhcccccccCCCCccHHHHHHHHHHhhhcccCCC--
Q 001179 209 YDEKYKKEKGAVGSPLVSERVKIILAEVQDLSL-TTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHLND-- 285 (1131)
Q Consensus 209 ~~~~~~~~~~~~~~~~~~~~~~~lL~~~~~~~i-~t~~~AL~yIG~~~r~~~~~~~~~~~~e~g~~~L~~~ll~Hl~~-- 285 (1131)
+..+.+.+...+++. ..+ .|+++||.|||++|+.. .++.++.++|+++|++++|||++.
T Consensus 236 -------------~~~~~~~l~~~l~~~--~~~~~t~~~al~~ig~~~~~~---~~~~~~~e~~~~~L~~~ll~Hig~~~ 297 (1103)
T PRK08565 236 -------------DPEIQQELLPSLEQA--SSIAATVEDALDYIGKRVAIG---QPREYRIERAEQILDKYLLPHLGTSP 297 (1103)
T ss_pred -------------cHHHHHHHHHHHHHh--hccccCHHHHHHHHHHhccCC---CCCccHHHHHHHHHHhhCcccCCCcc
Confidence 111223333344433 235 79999999999999853 345677899999999999999995
Q ss_pred --chhhHHHHHHHHHHHHhhcCCCCCCCCcccccccEeccchhhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccccchh
Q 001179 286 --NNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNL 363 (1131)
Q Consensus 286 --~~~K~~~L~~MvrkLl~l~~G~~~~DD~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~ 363 (1131)
+.+|+++|++|++||+.++.|.+.+||+|||+||||+++|+||+.+|++.|+++++.++..+++.+.+ ++.++
T Consensus 298 ~~~~~K~~~L~~Mi~kLl~l~~g~~~~DD~D~l~NKRv~l~G~Ll~~~fr~~l~~~~~~ik~~l~~~~~~-~~~~~---- 372 (1103)
T PRK08565 298 EDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYAR-GRKLD---- 372 (1103)
T ss_pred cchhHHHHHHHHHHHHHHhhhcCCCCCCCccccCCcEEccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-cccCC----
Confidence 35799999999999999999999999999999999999999999999999999999999999877654 33332
Q ss_pred HHHHHHHhcCCCcchHHHHHHHhcccCcccccccccccccceEEEccccchHHHhhhccccccCCccccccccccccccC
Q 001179 364 ANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTSVRKLLP 443 (1131)
Q Consensus 364 ~~~~~~i~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~~GvsqvleRln~~~~lSh~Rrv~rg~~~~~~K~t~~R~Lhp 443 (1131)
+..+++ ++.||++|++||+||||.+ |++||||+|+|+||+|+|||||||+. ++.+++|.++||+|||
T Consensus 373 --~~~~i~---~~~It~~i~~~~sTGnw~~-------~~sGvSq~ldr~N~l~~lSh~Rrv~s-~~~r~~~~~~vR~Lhp 439 (1103)
T PRK08565 373 --LRAIVR---PDIITERIRHALATGNWVG-------GRTGVSQLLDRTNYLSTLSHLRRVVS-PLSRGQPHFEARDLHG 439 (1103)
T ss_pred --HHHhcc---cchhhHHHHHHHhcCcccc-------CCcceEEecccCCHHHHHHHHhhccC-CcccCCCCccccccCh
Confidence 334443 3489999999999999974 67999999999999999999999986 4678999999999999
Q ss_pred CcccccccCCCCCCccccccccccceEEEeeccCCCCcccccchhhhHHHHHHHhcCceecCcccccCCCCCceEEEECC
Q 001179 444 ESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDG 523 (1131)
Q Consensus 444 s~wGfICPveTPEG~~CGLvk~LA~~a~It~~~~~~~~~~~~~~~~~~i~~~L~~lG~~~~~~~~~~~~~~~~~~V~lnG 523 (1131)
|||||+||+|||||++||||||||++|+|++..+.+ .|.++|.++|+.++. .+........++|||||
T Consensus 440 s~wG~iCPveTPEG~~cGLv~~LA~~a~It~~~~~~-----------~i~~~l~~~G~~~~~-~~~~~~~~~~~~V~lnG 507 (1103)
T PRK08565 440 TQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEE-----------EVEEILYELGVVPVE-EAREEEYISWSRVYLNG 507 (1103)
T ss_pred hhccccCCCCCCCccccchhhhhhcccccccCCChH-----------HHHHHHHHcCCCchh-hcCcccCCCceEEEECC
Confidence 999999999999999999999999999999876554 688999999998762 22222234568999999
Q ss_pred EEEeeecCchHHHHHHHHHHHHhhcCCCCCCCceEEEEeCCCCCCCCeEEEEcCCCcceeeEEEecCCCC----------
Q 001179 524 RVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSE---------- 593 (1131)
Q Consensus 524 ~~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~~~~~~~~~~i~i~td~GRl~RPv~~~~~~~~---------- 593 (1131)
+|+|+++ ++..+++.||.+||.+ .++.++||++++. +.+++|+||||+||++|||+++++++.
T Consensus 508 ~~iG~~~--~~~~l~~~lR~~Rr~g--~i~~~v~I~~~~~---~~~~~i~I~sd~GRl~RP~~~v~~g~~~~~~~~~~~l 580 (1103)
T PRK08565 508 RLIGYHP--DGEELAEKIRELRRSG--KISDEVNVAYIET---GEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKL 580 (1103)
T ss_pred EEEEEEC--CHHHHHHHHHHHhhcC--CCCCeEEEEEccc---cccceEEEecCCceeeeeEEEEecCceeccHHHHHHh
Confidence 9999995 5799999999999998 7999999998763 468999999999999999999987631
Q ss_pred -----------CCcceeeecccceeeeeeecCCCCCCCCCCCCceeEEeecCCCcccceeccccCCCCCCCccccccccc
Q 001179 594 -----------ESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQM 662 (1131)
Q Consensus 594 -----------~~g~iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~P~~ilsv~AslIPF~~HNqspRn~yqc~M 662 (1131)
.+|.|||||++||++++||+.++++... +||+||+|++|||++||+|||+||||||||||||||
T Consensus 581 ~~~~~~~~~l~~~g~iEyid~~Ee~~~~Ia~~~~~l~~~-----~th~Ei~p~~ilsv~asliPF~~hNqspRn~yq~~M 655 (1103)
T PRK08565 581 KKGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTPE-----HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAM 655 (1103)
T ss_pred hccccchhhHhhcCcEEeeCHHHhcCcEEeccccccCcc-----eeccccCCccccceeeeccCCcccCcccchhhhhhh
Confidence 2589999999999999999999988544 799999999999999999999999999999999999
Q ss_pred cccccccccceEEEecccceeeecCCCcceeecCcccccCcccCCCCcceEEEEEeccCCCCCceEEeeccccccCceee
Q 001179 663 AKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHG 742 (1131)
Q Consensus 663 ~KQAiG~~~~n~~~R~D~~~y~L~ypQ~PLV~t~~~~~~~~~~~~~G~N~iVAv~~y~Gyn~EDaiiink~s~~rG~~~~ 742 (1131)
+|||||++++|+..|.|++.|+|.|||+|||+|+.++.++++++|+|+||+||||||+||||||||||||+|+||||||+
T Consensus 656 ~KQa~g~~~~n~~~r~d~~~~~l~~pQ~Plv~t~~~~~~~~~~~p~G~N~iVAv~sy~GYn~EDaiIink~s~~rG~~~s 735 (1103)
T PRK08565 656 AKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARS 735 (1103)
T ss_pred hhcccccccccceEeecCCcceeecCceeEEEeccccccccccCCCCeeEEEEEEcccCcchHHhhhhhhhhhhcCCceE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEEEEEEEecccCCCccccccccccCC--C----ChhhhcccCCCCCcccCcEEcCCCCeeEEeec-------------
Q 001179 743 QIYQTETIDLSDDGNKVDRGQKLFRRNK--D----AKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDK------------- 803 (1131)
Q Consensus 743 ~~y~~~~~~~~~~~~~~~~~~~~f~~~~--~----~~~~~~~Ld~dGi~~~G~~v~~gdil~~~~~~------------- 803 (1131)
++|++|+++...... +..+.|+.|. . ....+++||+||+|++|+.|++||||+||+++
T Consensus 736 ~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~Ld~dGi~~~G~~v~~gdili~k~~p~~~~~~~~~~~~~ 812 (1103)
T PRK08565 736 TFFRTYETEERKYPG---GQEDKIEIPEPNVRGYRGEEYYRKLDEDGIVSPEVEVKGGDVLIGKTSPPRFLEELEELSLG 812 (1103)
T ss_pred EEEEEEEEEeeecCC---CCceEEecCCCcccccCchhhhhcCCCCCCcCCCcEEcCCCEEEEEecCCCCCcchhhcccc
Confidence 999999886543211 1123344441 1 23457999999999999999999999999876
Q ss_pred -CCCcEEeeecCCCcceEEEEEEEeccCCCCCCeEEEEEEeeecCCCCCcccccccCCcceeeeeecCCCCCccCCCCCc
Q 001179 804 -TTNSWRTNSRKGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMR 882 (1131)
Q Consensus 804 -~~~~~~~~~~~~~e~g~Vd~v~~~~~~~~~~~~~~~i~~r~~R~p~iGDKf~sRHGqKGvvs~i~~~~dmPf~~~~G~~ 882 (1131)
...++.+++++.+|+|+||+|.++.+++ +.+.|+|++|+.|+|+||||||||||||||||+|||+|||||| +||++
T Consensus 813 ~~~~~~~s~~~~~~e~g~V~~V~~~~~~~--~~~~vkv~ir~~R~p~iGDKfssRhGqKGv~s~i~~~edmPf~-~~G~~ 889 (1103)
T PRK08565 813 LQERRDTSVTVRHGEKGIVDTVLITESPE--GNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFT-EDGIV 889 (1103)
T ss_pred CCccccceEEecCCCceEEEEEEEEecCC--CcEEEEEEEEEEecCchhhhhhhhccCcceeeeecccccCCcC-CCCCC
Confidence 2245678899999999999999998765 3578999999999999999999999999999999999999999 99999
Q ss_pred ccEEeCCCCCCCccchhHhHHHHHhhhccccCceeccccccccccccCCCCCCCCchhhHHHHHHHHHHCCCCCCCcEEE
Q 001179 883 PDLIINPHAFPSRMTIAMLLESVAAKGGSLHGKFMDATPFANSVKKTNGDTGTDESKSLVDELGEMLRTCGFNYHGVEVL 962 (1131)
Q Consensus 883 pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tpf~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~~~G~e~~ 962 (1131)
|||||||||||||||||||+|+++||||++.|.+.|+|||... .+++++++|+++||+++|+|.|
T Consensus 890 pDiI~NPh~~PSRMtiG~l~E~~~gk~~~~~g~~~d~t~F~~~---------------~~~~~~~~L~~~g~~~~G~e~l 954 (1103)
T PRK08565 890 PDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGE---------------PEEELRKELLKLGYKPDGTEVM 954 (1103)
T ss_pred ccEEECCCCCcccccHHHHHHHHHHHHHHhcCceeeecCcCCc---------------hHHHHHHHHHHcCCCCCCcEEE
Confidence 9999999999999999999999999999999999999999876 5899999999999999999999
Q ss_pred eeCCCCcEeeeeeeeeceeEEeeccccccceeeeecccccceeecccCcccccCceeeeehhhhHHhhhchHHHHHHhhc
Q 001179 963 YSGVYGTELTCEIFIGPVYYQRLRHMVSDKFQVRSTGTMDQITRQPIKGRKRGGGIRFGEMERDSLLAHGAAYLLHDRLH 1042 (1131)
Q Consensus 963 y~g~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lTrQP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~ 1042 (1131)
|||+||++|+++||+|++|||||+|||+||+|||++||+++|||||++||||+|||||||||||||+|||||++|+|||+
T Consensus 955 ~~G~tG~~~~~~if~G~~yy~rL~HmV~DK~~~R~~Gp~~~lt~QP~~Gr~~~GG~R~GEME~d~l~a~Gas~~L~erL~ 1034 (1103)
T PRK08565 955 YDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLL 1034 (1103)
T ss_pred EcCCCCCCcccceEEeehhheechhhhchhhhhccCCCcchhhhCCccccccCCCeeeecchHHHHHhcccHHHHHHHhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCccceeccccccccccccccccccccccccCCCCCCCCCCCeeeccCcCCCCcceecchHhHHHHHHHHHhCCceeE
Q 001179 1043 TCSDYHVADVCSLCGSVLTATFIHPQKRAIREIGGLPPARAPKKVTCHACQTSKGMETVAMPYVFRYLAAELAAMNIKIT 1122 (1131)
Q Consensus 1043 ~~SD~~~~~vC~~Cg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~v~iPy~~klL~~EL~sm~I~~~ 1122 (1131)
++||+++++||.+||+++..+ .+++.++|+.|+++.++.++.||||||||+|||+||||+++
T Consensus 1035 ~~SD~~~~~vC~~Cg~~~~~~------------------~~~~~~~C~~c~~~~~~~~v~iPy~~k~l~~EL~sm~i~~~ 1096 (1103)
T PRK08565 1035 DSSDKTTIYVCELCGHIAWYD------------------RRKNKYVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPR 1096 (1103)
T ss_pred ccccceeeeeecccccccccc------------------cccCceeccccCCCCcceeccCChhHHHHHHHHHhCCCceE
Confidence 999999999999999998653 12346789999988899999999999999999999999999
Q ss_pred EEeccCC
Q 001179 1123 LQLGDGA 1129 (1131)
Q Consensus 1123 l~~~~~~ 1129 (1131)
|++++.+
T Consensus 1097 l~~~~~~ 1103 (1103)
T PRK08565 1097 LKLGDKV 1103 (1103)
T ss_pred EEeeecC
Confidence 9998653
No 3
>KOG0215 consensus RNA polymerase III, second largest subunit [Transcription]
Probab=100.00 E-value=1.7e-245 Score=2082.52 Aligned_cols=1013 Identities=31% Similarity=0.510 Sum_probs=899.8
Q ss_pred ccccchhhHHHHHHHHHHHHHHhHHHHH-----------------------------------------HHHHHcCCeee
Q 001179 8 DFEPLRELVRHHIESFDYMLDEGLSEMF-----------------------------------------DHCRQAKISYT 46 (1131)
Q Consensus 8 ~~~~~~~Lv~~hi~SFn~Fi~~gl~~ii-----------------------------------------~ecR~r~~TYs 46 (1131)
+|++.+|||+||+||||||++++|+.|+ +|||+|++||+
T Consensus 52 ~flkvkglvkqhldsfnyfv~~~ik~iv~an~~itsd~dp~fylky~dirvg~Ps~~~~~~~~~~~i~p~ecrlrd~tys 131 (1153)
T KOG0215|consen 52 AFLKVKGLVKQHLDSFNYFVDVDIKKIVKANQLITSDVDPSFYLKYLDIRVGKPSIEEGNNVTNDNITPHECRLRDMTYS 131 (1153)
T ss_pred HHHhhhhHHHHHHhhhhhhhhhhHHHHHHhhcccCcCcCchhhheeeeeeccCcchhhccccccccCCchheeehhhhcc
Confidence 4678999999999999999999999998 99999999999
Q ss_pred EEEEEEEEEEEecCCCceEEEEEeecccceeeccCcccCCCCChHHHHhhccccccCCcEEEEcCceeEEEEEEeccCCc
Q 001179 47 GKLMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNY 126 (1131)
Q Consensus 47 a~l~v~v~~~~~~~~~~~~~~~v~iG~iPIMvkS~~C~L~~ls~~el~~~gE~~~D~GGYFIING~EKVIr~qi~~~~N~ 126 (1131)
||++|+++++.. ...+....|.||++|||++|++|+|++.+++++++.+|||+|||||||++|.||||..|.+.+.|+
T Consensus 132 a~i~vdieytrg--~~~~~~~~v~igrmpimlrs~rcvl~~~~e~~~a~~~ecpldpggyfiv~G~ekViLiqeqlsknr 209 (1153)
T KOG0215|consen 132 APIYVDIEYTRG--RQIIAKRDVIIGRMPIMLRSSKCVLRGKDEEELARLNECPLDPGGYFIVKGTEKVILIQEQLSKNR 209 (1153)
T ss_pred cceeEEEEEecC--cceEEecccccccchhhhhccccccCCccHHHHHHhccCCCCCCceeEeccceeEEEehhhhhccC
Confidence 999999999987 566778899999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEEEeccccCCCcceeeEEEEEeeeecCCCceEEEEEEEeCCeEEEEEEEecccccccHhhHHHhccCCCHHHHHHhhc
Q 001179 127 PMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLT 206 (1131)
Q Consensus 127 ~~~~~r~s~~~r~~~~t~~~i~iRs~~~~~~s~~~~l~~~~~g~~~l~~~~~k~~~~IPi~ilLkALg~~sD~eI~~~I~ 206 (1131)
++.. ..+++. ..++.-|......++++.+ .++|..+++.... ..+||++++|||||..||+||.+.++
T Consensus 210 ii~~----~~k~~~----~~~svtsst~e~kskt~v~--~k~~k~ylk~~~~--~d~ipiviv~ka~g~~sd~ei~~~vg 277 (1153)
T KOG0215|consen 210 IIVE----EDKKGN----LQASVTSSTHERKSKTYVT--TKKGKYYLKHNSF--TDDIPIVIVLKAMGLESDQEIVQLVG 277 (1153)
T ss_pred eeec----cccCCc----cccccccceeeecceEEEE--eccceeeeehhhh--hccCCEEEEEeeccccchHHHHHHhh
Confidence 8774 112232 2334444444555556555 6677666655432 24799999999999999999999998
Q ss_pred cccchhhhcccCCCCChhHHHHHHHHHHHHHhccccCHHHHHHHHhhcccccccCCCCccHHHHHHHHHHhhhcccCC--
Q 001179 207 CCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHLN-- 284 (1131)
Q Consensus 207 ~~~~~~~~~~~~~~~~~~~~~~~~~lL~~~~~~~i~t~~~AL~yIG~~~r~~~~~~~~~~~~e~g~~~L~~~ll~Hl~-- 284 (1131)
. ++++.+.....++++...+++||++||+|++.+.+... +...+..+.|.++|...+++|++
T Consensus 278 ~--------------~~~y~~~~~~s~ee~~~~~v~tqqqal~y~~~kvk~~~--~t~~~~~~e~~~~l~~~~lahv~v~ 341 (1153)
T KOG0215|consen 278 G--------------DSKYQDIFAPSLEECVSLGVYTQQQALEYIGSKVKVKR--GTTPTKDEEALEVLSTTVLAHVPVP 341 (1153)
T ss_pred c--------------chHHHHhhccchhhhhhhhhHHHHHHHHHhhheEEecc--CCCCCchHHHHHHHHhhheeceecc
Confidence 2 45666788888899888999999999999999887432 34556778899999999999997
Q ss_pred --CchhhHHHHHHHHHHHHhhcCCCCCCCCcccccccEeccchhhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccccch
Q 001179 285 --DNNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFN 362 (1131)
Q Consensus 285 --~~~~K~~~L~~MvrkLl~l~~G~~~~DD~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~ 362 (1131)
++..|+.+++.|+|+++.+..+.-..||+|+++|||++++|+||+++|++.|++++.++++.+++.+.+..+...++
T Consensus 342 ~~~~r~K~~yi~~m~rr~~~a~l~~~~~ddrd~~gnkrlelagqllsllfeD~fk~~n~e~k~~~dk~l~k~~ra~~fD- 420 (1153)
T KOG0215|consen 342 DLNFRMKAIYIGLMVRRVIQAMLNKLAMDDRDYVGNKRLELAGQLLSLLFEDLFKRFNSELKKNIDKILKKPIRAQEFD- 420 (1153)
T ss_pred CCCCcceeehHHHHHHHHHHHHhCcccccchhhhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhhhhhhH-
Confidence 56899999999999999999999999999999999999999999999999999999999999998887744433332
Q ss_pred hHHHHHHHhcCCCcchHHHHHHHhcccCcccccccccccccceEEEccccchHHHhhhccccccCCcccccccccccccc
Q 001179 363 LANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTSVRKLL 442 (1131)
Q Consensus 363 ~~~~~~~i~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~~GvsqvleRln~~~~lSh~Rrv~rg~~~~~~K~t~~R~Lh 442 (1131)
.++.+-. ..+.||++|.+++|||||+.++ |.|.+.|++|||+|++|++.|..+.|++. +|.+++|.++||.||
T Consensus 421 --~~~~~n~--~~~~it~~l~ra~stgnw~iKr--frmer~gvt~VlsrlSyisaLgmmtri~s-~fektrkvsgprSlq 493 (1153)
T KOG0215|consen 421 --ALKHLNV--RANMITSGLERAISTGNWSIKR--FRMERAGVTQVLSRLSYISALGMMTRINS-QFEKTRKVSGPRSLQ 493 (1153)
T ss_pred --HHHHHHH--HHHHHHHHHHHHhhcCchHHHH--hhhhhccceeeehhhhhhhhhhhheehhh-hheeehhccCccccC
Confidence 1221111 1247999999999999999875 57899999999999999999999999995 799999999999999
Q ss_pred CCcccccccCCCCCCccccccccccceEEEeeccCCCCcccccchhhhHHHHHHHhcCceecCc-ccccCCCCCceEEEE
Q 001179 443 PESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLP-KLVKSGPPAVLSVLL 521 (1131)
Q Consensus 443 ps~wGfICPveTPEG~~CGLvk~LA~~a~It~~~~~~~~~~~~~~~~~~i~~~L~~lG~~~~~~-~~~~~~~~~~~~V~l 521 (1131)
|||||++||+|||||++|||+||||++++|+++.+++ ++...+..+|+..+.. .......++.+.|||
T Consensus 494 ~sqwgmlcp~dtpegeacglvknlalmthittd~ee~-----------pi~~~~~k~gv~di~~v~~~e~~~~~~~~v~L 562 (1153)
T KOG0215|consen 494 PSQWGMLCPSDTPEGEACGLVKNLALMTHITTDSEEK-----------PILKLCYKLGVEDIHVVSGRELHTPDSFLVFL 562 (1153)
T ss_pred hhhcccccCCCCCCccccccccchHHHhcccCCCCcc-----------hhHHHHHHhcceeeeeecccccCCCceEEEEe
Confidence 9999999999999999999999999999999876666 6889999999987631 112334567799999
Q ss_pred CCEEEeeecCchHHHHHHHHHHHHhhcCCCCCCCceEEEEeCCCCCCCCeEEEEcCCCcceeeEEEecCCCC--------
Q 001179 522 DGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSE-------- 593 (1131)
Q Consensus 522 nG~~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~~~~~~~~~~i~i~td~GRl~RPv~~~~~~~~-------- 593 (1131)
||.++|.+. .++.++..+|.+||+| ++.. |++.+.+.....++|.||.||++||++.+.++.+
T Consensus 563 ng~iig~~~--~~~~~v~~~r~lrr~G--~i~~-----fvsv~~~~~q~~v~i~sdggr~crp~Iiv~~~~~~v~~~h~~ 633 (1153)
T KOG0215|consen 563 NGLIIGITR--RPQYFVNSFRRLRRKG--KIGE-----FVSVFTNTTQRCVYIASDGGRVCRPLIIVDNGRPRVKQHHMD 633 (1153)
T ss_pred cceeecccc--chHHHHHHHHHHHHcC--cccc-----eeeeeeeeeeEEEEEecCCCeEeeeEEEEeCCcchhhhhhHH
Confidence 999999985 5689999999999999 6665 4444444455799999999999999999987743
Q ss_pred -------------CCcceeeecccceeeeeeecCCCCCCCCCCCCceeEEeecCCCcccceeccccCCCCCCCccccccc
Q 001179 594 -------------ESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQC 660 (1131)
Q Consensus 594 -------------~~g~iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~P~~ilsv~AslIPF~~HNqspRn~yqc 660 (1131)
..|.|||+|++|++.++||+.++++.++ +||+||.|..+||+||+|||||||||||||+|||
T Consensus 634 el~~g~r~F~DFl~~glvEYLDVNEEND~~Ialye~~I~~~-----TTHLEIEPFTiLGv~AGLIPYPHHNQSPRNTYQC 708 (1153)
T KOG0215|consen 634 ELLDGKRTFDDFLKDGLIEYLDVNEENDSLIALYEEDIGPE-----TTHLEIEPFTILGVVAGLIPYPHHNQSPRNTYQC 708 (1153)
T ss_pred HHHHhhhhHHHHHHhchhheeecccccCceEEechhhcCCC-----cceeeecchhhhhhhccccCCCCCCCCCcchhhh
Confidence 3689999999999999999999999887 8999999999999999999999999999999999
Q ss_pred cccccccccccceEEEecccceeeecCCCcceeecCcccccCcccCCCCcceEEEEEeccCCCCCceEEeeccccccCce
Q 001179 661 QMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMC 740 (1131)
Q Consensus 661 ~M~KQAiG~~~~n~~~R~D~~~y~L~ypQ~PLV~t~~~~~~~~~~~~~G~N~iVAv~~y~Gyn~EDaiiink~s~~rG~~ 740 (1131)
+|||||||+.++|+..|.|+.+|.|.|||+|+|+|++++..+++.+|+||||+||||||+|||+|||+|+||+|+||||+
T Consensus 709 AMGKQAmG~IaYNQ~~RiDtlmYll~YPq~PmVkTKTIELi~ydKLPAGQNAtVAVMSYSGYDIEDALVLNKsSlDRGfG 788 (1153)
T KOG0215|consen 709 AMGKQAMGAIAYNQKKRIDSLLYLLVYPQRPMVKTKTIELINYDKLPAGQNATVAVMSYSGYDIEDALVLNKSSIDRGFG 788 (1153)
T ss_pred hhhhhhhhhhhhhhhhhHHHHHHHHhcCCCccccceeEEeeccccCCCCCccEEEEEeccCCchhhhhhcccchhccCcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeEEEEEEEEecccCCCccccccccccC----CC--ChhhhcccCCCCCcccCcEEcCCCCeeEEeecCC---------
Q 001179 741 HGQIYQTETIDLSDDGNKVDRGQKLFRRN----KD--AKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTT--------- 805 (1131)
Q Consensus 741 ~~~~y~~~~~~~~~~~~~~~~~~~~f~~~----~~--~~~~~~~Ld~dGi~~~G~~v~~gdil~~~~~~~~--------- 805 (1131)
|+.+||+.+..+....+. -.+.+..| +. +--..+.||+|||..||..|++|+|++.|-.|..
T Consensus 789 RC~Vyk~~~~~~kkY~N~---T~Drimgp~~d~~t~kpi~kh~vLd~DGl~~pG~~V~~~qi~iNK~mP~vt~~~~~~~~ 865 (1153)
T KOG0215|consen 789 RCEVYKKTTTTLKKYANG---TFDRIMGPQLDPNTRKPIWKHQVLDDDGLATPGERVQPGQIYINKQMPTVTGTSLPGLS 865 (1153)
T ss_pred eEEEEeeeeeeeeecCCC---chhhhcccccCCCcCCcchhhcccCcccCCCCccEeccCcEEEeccCCCcccccCCCCC
Confidence 999999988776443321 11122222 11 1123478999999999999999999999932211
Q ss_pred -----CcEEeeecCCCcceEEEEEEEeccCCCCCCeEEEEEEeeecCCCCCcccccccCCcceeeeeecCCCCCccCCCC
Q 001179 806 -----NSWRTNSRKGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTG 880 (1131)
Q Consensus 806 -----~~~~~~~~~~~e~g~Vd~v~~~~~~~~~~~~~~~i~~r~~R~p~iGDKf~sRHGqKGvvs~i~~~~dmPf~~~~G 880 (1131)
.+.....|++.|+++||+|.++.+++ +...+|+-+|++|+|++|||||||||||||||.|++||||||. ..|
T Consensus 866 ~~~~~Yk~~pitykgpepsyidkVmls~n~~--dq~LIK~llRQTRrPElGDKFSSRHGQKGVcGlIv~QEDMPFn-D~G 942 (1153)
T KOG0215|consen 866 ASQVQYKAVPITYKGPEPSYIDRVMLTSNDE--DQFLIKVLLRQTRRPELGDKFSSRHGQKGVCGLIVQQEDMPFN-DQG 942 (1153)
T ss_pred ccccccccccceecCCCcchhheeEeecCcc--ccHHHHHHHhhccCcccccccccccCCCceeeEEeeccCCCCc-ccC
Confidence 24557889988999999999998864 3578899999999999999999999999999999999999999 999
Q ss_pred CcccEEeCCCCCCCccchhHhHHHHHhhhccccCceeccccccccccccCCCCCCCCchhhHHHHHHHHHHCCCCCCCcE
Q 001179 881 MRPDLIINPHAFPSRMTIAMLLESVAAKGGSLHGKFMDATPFANSVKKTNGDTGTDESKSLVDELGEMLRTCGFNYHGVE 960 (1131)
Q Consensus 881 ~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tpf~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~~~G~e 960 (1131)
|+|||||||||||||||+|+++|.+.||||++.|.+.++|+|.++ .++++++.|.++||||.||+
T Consensus 943 IcPDiIMNPHGFPSRMTVGK~iELlsGKAGVl~G~~hYGTaFGgs---------------kVed~~~~Lv~hGfnY~GKD 1007 (1153)
T KOG0215|consen 943 ICPDIIMNPHGFPSRMTVGKMIELLSGKAGVLEGTFHYGTAFGGS---------------KVEDISEELVEHGFNYSGKD 1007 (1153)
T ss_pred CCcccccCCCCCcccchHHHHHHHhccccceeeeeEeeccccCCc---------------hHHHHHHHHHHhccCccCcc
Confidence 999999999999999999999999999999999999999999988 69999999999999999999
Q ss_pred EEeeCCCCcEeeeeeeeeceeEEeeccccccceeeeecccccceeecccCcccccCceeeeehhhhHHhhhchHHHHHHh
Q 001179 961 VLYSGVYGTELTCEIFIGPVYYQRLRHMVSDKFQVRSTGTMDQITRQPIKGRKRGGGIRFGEMERDSLLAHGAAYLLHDR 1040 (1131)
Q Consensus 961 ~~y~g~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lTrQP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~er 1040 (1131)
.+|||+||++++|+||+||+|||||+|||.||||||++||+..|||||++||||+||+|+||||||||||||||.+|-||
T Consensus 1008 ~ltSGITGepLeAYIffGPiYYQKLKHMVlDKMHARARGPRAvLTRQPTEGRSrdGGLRLGEMERDCLIaYGASmLl~ER 1087 (1153)
T KOG0215|consen 1008 MLTSGITGEPLEAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIAYGASMLLLER 1087 (1153)
T ss_pred ccccCCCCCcceeeEEechHHHHHHHHHHHHHHhhhccCCceeeecCCCCCcCCCCCcccchhhhhhhhhccHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hccCCCccceeccccccccccccccccccccccccCCCCCCCCCCCeeeccCcCCCCcceecchHhHHHHHHHHHhCCce
Q 001179 1041 LHTCSDYHVADVCSLCGSVLTATFIHPQKRAIREIGGLPPARAPKKVTCHACQTSKGMETVAMPYVFRYLAAELAAMNIK 1120 (1131)
Q Consensus 1041 l~~~SD~~~~~vC~~Cg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~v~iPy~~klL~~EL~sm~I~ 1120 (1131)
|+.+||.+++.||..||.+++. .||..|+++.++.++.||||||||||||+||||-
T Consensus 1088 LMiSSDaFeVdVC~~CGllgyk------------------------gwC~~Ckss~~v~~~~iPYAcKLLFQEL~SMNi~ 1143 (1153)
T KOG0215|consen 1088 LMISSDAFEVDVCRQCGLLGYK------------------------GWCTTCKSSKNVAKMKIPYACKLLFQELQSMNIV 1143 (1153)
T ss_pred HhhcCcceeeeeccccccceec------------------------hhhhhccCCCceeeeeccHHHHHHHHHHHhcCcc
Confidence 9999999999999999999875 5999999999999999999999999999999999
Q ss_pred eEEEeccC
Q 001179 1121 ITLQLGDG 1128 (1131)
Q Consensus 1121 ~~l~~~~~ 1128 (1131)
+||.+++-
T Consensus 1144 PrL~L~~~ 1151 (1153)
T KOG0215|consen 1144 PRLKLEDY 1151 (1153)
T ss_pred ceeeeccc
Confidence 99999764
No 4
>KOG0214 consensus RNA polymerase II, second largest subunit [Transcription]
Probab=100.00 E-value=5.3e-245 Score=2105.44 Aligned_cols=1025 Identities=31% Similarity=0.480 Sum_probs=904.4
Q ss_pred ccccchhhHHHHHHHHHHHHHHhHHHHH------------------------------------------------HHHH
Q 001179 8 DFEPLRELVRHHIESFDYMLDEGLSEMF------------------------------------------------DHCR 39 (1131)
Q Consensus 8 ~~~~~~~Lv~~hi~SFn~Fi~~gl~~ii------------------------------------------------~ecR 39 (1131)
++...+||++||+|||+.||+.++++|+ +|||
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 5678999999999999999999999999 9999
Q ss_pred HcCCeeeEEEEEEEEEEEecCC---CceEEEEEeecccceeeccCcccCCCCChHHHHhhccccccCCcEEEEcCceeEE
Q 001179 40 QAKISYTGKLMADVEFQYLDAG---SPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVF 116 (1131)
Q Consensus 40 ~r~~TYsa~l~v~v~~~~~~~~---~~~~~~~v~iG~iPIMvkS~~C~L~~ls~~el~~~gE~~~D~GGYFIING~EKVI 116 (1131)
+|++|||||||||++..+..+. ...+.++|+||+||||+||..|.|++++..+|.++||||+|+||||||||+|||+
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 9999999999999998765322 2344679999999999999999999999999999999999999999999999999
Q ss_pred EEEEeccCCceEEEEeccccCCCcceeeEEEEEeeeecCCCce--EEEEEEEeCC----eEEEEEEEecccccccHhhHH
Q 001179 117 RSVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSV--TLKLYYLLNG----SVRLGFWLQGKEYLLPVGIVL 190 (1131)
Q Consensus 117 r~qi~~~~N~~~~~~r~s~~~r~~~~t~~~i~iRs~~~~~~s~--~~~l~~~~~g----~~~l~~~~~k~~~~IPi~ilL 190 (1131)
+.|+.++.|.+++++. ..+.-..|..++||+.+..++. ++.+..+..+ .+.+.+++.|+ +|||+|||
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 9999999998877643 3334456788999976654433 3333334333 35567777776 59999999
Q ss_pred HhccCCCHHHHHHhhccccchhhhcccCCCCChhHHHHHHHHHHHHHhccccCHHHHHHHHhhcccccccCCCCccHHHH
Q 001179 191 KALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAV 270 (1131)
Q Consensus 191 kALg~~sD~eI~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~lL~~~~~~~i~t~~~AL~yIG~~~r~~~~~~~~~~~~e~ 270 (1131)
||||+.+|+||+++|+ || .+|..+-+.+.+.+++. .-+..++.||+|||++-... .-..+.++++
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--FVIQEQNVALDFIGQRGACI--GVTKEKRIKY 308 (1141)
T ss_pred hhhcCCccHHHHHhhc--CC---------CCcHHHHHHhhhhhhhh--hhhhhhHHHHHHHHhcCCCC--CCCcchhhHH
Confidence 9999999999999998 54 23454444555555544 35677888999999985321 1345678999
Q ss_pred HHHHHHhhhcccCCCc----hhhHHHHHHHHHHHHhhcCCCCCCCCcccccccEeccchhhHHHHHHHHHHHHHHHHHHH
Q 001179 271 AETVIRDYIFVHLNDN----NDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKL 346 (1131)
Q Consensus 271 g~~~L~~~ll~Hl~~~----~~K~~~L~~MvrkLl~l~~G~~~~DD~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~~~~ 346 (1131)
|+++|++++|||++.- ..|++||+|||++|+.++.|++.+||+|||+|||++++|+||+.+||..|+++++++.+.
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 9999999999999853 599999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhcCCccccchhHHHHHHHhcCCCcchHHHHHHHhcccCcccccccccccccceEEEccccchHHHhhhcccccc
Q 001179 347 IQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHR 426 (1131)
Q Consensus 347 l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~~GvsqvleRln~~~~lSh~Rrv~r 426 (1131)
+++.++. ++.+++. -+++ .+.||++++|+||||||+.+.. .|..++||||||+|+||.++|||+||++.
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 5444432 2332 3589999999999999986643 46789999999999999999999999994
Q ss_pred CCccccccccccccccCCcccccccCCCCCCccccccccccceEEEeeccCCCCcccccchhhhHHHHHHHhcCceecCc
Q 001179 427 GASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLP 506 (1131)
Q Consensus 427 g~~~~~~K~t~~R~Lhps~wGfICPveTPEG~~CGLvk~LA~~a~It~~~~~~~~~~~~~~~~~~i~~~L~~lG~~~~~~ 506 (1131)
+ ..+++|...||+|||||||++||+|||||++||||||||+||.|+++..+. +|.++|.++||..+ .
T Consensus 458 P-igr~GKlAkpRqlHnthwGmvCPaeTPEGqacGLVKNLSLmayIsvGS~~s-----------Pi~EfLeewgmE~l-e 524 (1141)
T KOG0214|consen 458 P-IGRTGKLAKPRQLHNSHWGMVCPAETPEGQACGLVKNLSLMAYISVGSLES-----------PIVEFLEEWGMENL-E 524 (1141)
T ss_pred c-cccccccCCccccCcccceeeccccCCCcceeeccccceEEEEEecCCCcc-----------HHHHHHHHhchhhH-h
Confidence 3 468999999999999999999999999999999999999999998876665 79999999999987 3
Q ss_pred ccccCCCCCceEEEECCEEEeeecCchHHHHHHHHHHHHhhcCCCCCCCceEEEEeCCCCCCCCeEEEEcCCCcceeeEE
Q 001179 507 KLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVR 586 (1131)
Q Consensus 507 ~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~~~~~~~~~~i~i~td~GRl~RPv~ 586 (1131)
++......+.++||+||.|+|.+. +++++++.||++||.. .++ .|++.+.+ ...++++||||+||.+||++
T Consensus 525 ~~~ps~~~datkvfvNG~wvGlhr--dp~~l~~tlr~lRR~~--di~--~Evs~vRD---Ir~kE~ri~tDaGR~~rPLl 595 (1141)
T KOG0214|consen 525 EISPSPSPDATKVFVNGVWVGLHR--DPEELVATLKRLRRQF--DII--AEVSMVRD---IRDKEIRIFTDAGRSLRPLL 595 (1141)
T ss_pred hcCCCcCCCceEEEEcccEEEecC--CHHHHHHHHHHHHHhh--ccc--hhhhhhcc---ccccceeeeeccCccccceE
Confidence 566666778899999999999985 6799999999999976 343 37777764 34579999999999999999
Q ss_pred EecCCCC------------------------CCcceeeecccceeeeeeecCCCCCCCCCCCCceeEEeecCCCccccee
Q 001179 587 NISLPSE------------------------ESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVA 642 (1131)
Q Consensus 587 ~~~~~~~------------------------~~g~iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~P~~ilsv~A 642 (1131)
++++++- ..|.+||||++||+.++||+.++++........||||||||+.|||++|
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 9988731 3699999999999999999999999775445669999999999999999
Q ss_pred ccccCCCCCCCccccccccccccccccccceEEEecccceeeecCCCcceeecCcccccCcccCCCCcceEEEEEeccCC
Q 001179 643 NLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGY 722 (1131)
Q Consensus 643 slIPF~~HNqspRn~yqc~M~KQAiG~~~~n~~~R~D~~~y~L~ypQ~PLV~t~~~~~~~~~~~~~G~N~iVAv~~y~Gy 722 (1131)
|.||||||||||||+||++|+|||||.+.+|+..|+|+..|.|+|||+|||+|+.+++..+.++|+|+|++||++||+||
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 CCCceEEeeccccccCceeeeEEEEEEEEecccCCCccccccccccCCC------ChhhhcccCCCCCcccCcEEcCCCC
Q 001179 723 DMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFRRNKD------AKSLHSVIDSDGLPYVGQMIHPGEP 796 (1131)
Q Consensus 723 n~EDaiiink~s~~rG~~~~~~y~~~~~~~~~~~~~~~~~~~~f~~~~~------~~~~~~~Ld~dGi~~~G~~v~~gdi 796 (1131)
|||||+|+|++++|||+||+.+|++|+.+. .+...+..+.|+.|.. ....+++||+||++.+|++|..|||
T Consensus 756 NqEDsvimn~s~v~rg~FrS~~~RsYk~q~---~~~~~~~ee~~~~~~~~~~~~mr~~~~dkLdddG~i~~G~~vs~~Dv 832 (1141)
T KOG0214|consen 756 NQEDSVIMNQSSVDRGLFRSFFIRSYKDQE---HKKDQGPEEIFEEPPRGEGRGMRNGKYDKLDDDGIIMPGSRVSGGDV 832 (1141)
T ss_pred cHHHHHHHHhhhhhcchhhhhhhhHHHhhh---hhcccccccccccccccccccccccccccccccCCccccceeecCCE
Confidence 999999999999999999999999997532 1122234456666532 2335689999999999999999999
Q ss_pred eeEEeecC--------------CCcEEeeecCCCcceEEEEEEEeccCCCCCCeEEEEEEeeecCCCCCcccccccCCcc
Q 001179 797 YCSIYDKT--------------TNSWRTNSRKGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKG 862 (1131)
Q Consensus 797 l~~~~~~~--------------~~~~~~~~~~~~e~g~Vd~v~~~~~~~~~~~~~~~i~~r~~R~p~iGDKf~sRHGqKG 862 (1131)
++||..+. +.++.++.++.+|.|+||+|.++.+.+ +.+.++|++|+.|.|++||||||||||||
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 LIGKTTPQPAKEDESGPEDRLYTKRDHSTKLRHTERGIVDQVWVTKNSE--GPKFVKVRVRQVRIPQIGDKFASRHGQKG 910 (1141)
T ss_pred EeccccCCcccchhccccccccccccceeecccCCcceEEEEEEecCCC--CCceeEEEEeecccccccchhccccccCc
Confidence 99997642 124668899999999999999998765 46899999999999999999999999999
Q ss_pred eeeeeecCCCCCccCCCCCcccEEeCCCCCCCccchhHhHHHHHhhhccccCceeccccccccccccCCCCCCCCchhhH
Q 001179 863 VCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKGGSLHGKFMDATPFANSVKKTNGDTGTDESKSLV 942 (1131)
Q Consensus 863 vvs~i~~~~dmPf~~~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tpf~~~~~~~~~~~~~~~~~~~~ 942 (1131)
|||.++++|||||| .+|++|||||||||||||||+|||+||++||.++..|+..|+|||++. .+
T Consensus 911 ~ig~~~~qedmpft-~eGi~pDiiiNPhaiPSRmtig~liEc~lgk~~a~~~e~~~atpFs~v---------------~v 974 (1141)
T KOG0214|consen 911 TIGITYRQEDMPFT-IEGIVPDIIINPHAIPSRMTIGQLIECLLGKVAAYEGEEGDATPFSDV---------------TV 974 (1141)
T ss_pred cccceeecCCCCcc-ccCCCcceEECcccCccccchhhhHHHhhhhhhhcccccccCCCCCcc---------------ch
Confidence 99999999999999 999999999999999999999999999999999999999999999986 57
Q ss_pred HHHHHHHHHCCCCCCCcEEEeeCCCCcEeeeeeeeeceeEEeeccccccceeeeecccccceeecccCcccccCceeeee
Q 001179 943 DELGEMLRTCGFNYHGVEVLYSGVYGTELTCEIFIGPVYYQRLRHMVSDKFQVRSTGTMDQITRQPIKGRKRGGGIRFGE 1022 (1131)
Q Consensus 943 ~~~~~~l~~~g~~~~G~e~~y~g~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lTrQP~~Gr~~~GG~R~GE 1022 (1131)
+.++..|.++||++.|+|.||||+||++|.+.||+||.|||||+|||+||+|+|++||++.+||||++||||+|||||||
T Consensus 975 ~~is~~l~~~g~~~~G~e~~ynGrtG~~~~~~if~GptyyqrL~Hmvd~kih~R~~Gp~q~ltRQP~~gRsr~GGlRfGE 1054 (1141)
T KOG0214|consen 975 SKISANLHVYGYQYRGNERMYNGRTGRKLRAQIFIGPTYYQRLKHMVDDKIHSRARGPVQILTRQPVEGRSRDGGLRFGE 1054 (1141)
T ss_pred hcccchHHHhccccCCCEEEecCCCCceeeeeeecCchHHHHHHHhhhheeeecccCCceeeeccccccccccCCeeeeh
Confidence 88999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhHHhhhchHHHHHHhhccCCCccceeccccccccccccccccccccccccCCCCCCCCCCCeeeccCcCCCCcceec
Q 001179 1023 MERDSLLAHGAAYLLHDRLHTCSDYHVADVCSLCGSVLTATFIHPQKRAIREIGGLPPARAPKKVTCHACQTSKGMETVA 1102 (1131)
Q Consensus 1023 MErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~Cg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~v~ 1102 (1131)
|||||+|||||+++|+|||+..||.+.+++|..||.++... .+.+.+.|+.|.+.+.++.|.
T Consensus 1055 MErdc~iahGaa~~L~ERL~~~SD~~~~~~c~~c~l~~i~~------------------~~~n~~~ck~c~n~~~v~~v~ 1116 (1141)
T KOG0214|consen 1055 MERDCLIAHGAAAFLKERLFEKSDAYRVHICVLCGLTAIAG------------------LIPNSFECRGCENKTLVVRVY 1116 (1141)
T ss_pred hHHHHHHHhhHHHHHHHHhhccCccceEEEeccchhhhhhc------------------cCCCccccccccCccceEEEe
Confidence 99999999999999999999999999999999999554443 233346899999999999999
Q ss_pred chHhHHHHHHHHHhCCceeEEEec
Q 001179 1103 MPYVFRYLAAELAAMNIKITLQLG 1126 (1131)
Q Consensus 1103 iPy~~klL~~EL~sm~I~~~l~~~ 1126 (1131)
+|||||||+|||+||||.+++.++
T Consensus 1117 ipya~kLl~qelmsmni~pr~~~~ 1140 (1141)
T KOG0214|consen 1117 IPYAAKLLFQELMSMNIAPRRKTK 1140 (1141)
T ss_pred chhHHHHHHHHHHhccCccccccC
Confidence 999999999999999999999764
No 5
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]
Probab=100.00 E-value=6.1e-227 Score=2049.33 Aligned_cols=959 Identities=28% Similarity=0.403 Sum_probs=833.1
Q ss_pred CcCccccchhhHHHHHHHHHHHHHHhHHHHH------------------------------HHHHHcCCeeeEEEEEEEE
Q 001179 5 KSADFEPLRELVRHHIESFDYMLDEGLSEMF------------------------------DHCRQAKISYTGKLMADVE 54 (1131)
Q Consensus 5 ~~~~~~~~~~Lv~~hi~SFn~Fi~~gl~~ii------------------------------~ecR~r~~TYsa~l~v~v~ 54 (1131)
.-.++..+++|+++|++|||+|+.+||++++ .|||+|++||||||+|+++
T Consensus 17 ~i~~~~~~p~Lv~~QldSyn~ff~~gLq~i~~~i~PI~~~~~~~~Lef~~~~l~~p~k~~p~EcR~R~lTYsapLyv~lr 96 (1060)
T COG0085 17 KIPEFLDLPNLVEIQLDSYNAFFLEGLQEVFREIFPIESYNGNTELEYGSYRLGEPPKFYPEECRLRGLTYSAPLYVKLR 96 (1060)
T ss_pred hcccccCCccHHHHHHHHHHHHHHHHHHHHHHhcCceecCCCCEEEEEEEEEecCCCCCCHHHHHhcCCccccceEEEEE
Confidence 3456788999999999999999999999999 8999999999999999999
Q ss_pred EEEecCCCceEEEEEeecccceeeccCcccCCCCChHHHHhhccccccCCcEEEEcCceeEEEEEEeccCCceEEEEecc
Q 001179 55 FQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRSS 134 (1131)
Q Consensus 55 ~~~~~~~~~~~~~~v~iG~iPIMvkS~~C~L~~ls~~el~~~gE~~~D~GGYFIING~EKVIr~qi~~~~N~~~~~~r~s 134 (1131)
++++..+..+++++|++|+||+|++ ||||||||+||||++|++++||.+|.....+
T Consensus 97 lv~~~~~e~~k~~eV~iG~iPlMt~------------------------gGyFIINGsERVIVsQ~~rSPgvif~~~~~k 152 (1060)
T COG0085 97 LVVNETGEEIKEQEVYMGDIPLMTR------------------------GGYFIINGTERVIVSQEHRSPGVIFVEKKDK 152 (1060)
T ss_pred EEECCcccccccceEEeccCcEecC------------------------CcEEEECCeEEEEEEEeecCCCeEEeccccc
Confidence 9887322226789999999999998 9999999999999999999999877654332
Q ss_pred ccCCCcceeeEEEEEeeeecCCCceEEEEEEEeCCeEEEEEEEecccccccHhhHHHhccCCCHHHHHHhhccccchhhh
Q 001179 135 FRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYK 214 (1131)
Q Consensus 135 ~~~r~~~~t~~~i~iRs~~~~~~s~~~~l~~~~~g~~~l~~~~~k~~~~IPi~ilLkALg~~sD~eI~~~I~~~~~~~~~ 214 (1131)
... ...|+...++.|+ .|+.++++.++.+++++..++ +||+++||||||+.||+||++.+.. ++
T Consensus 153 ~~~-~~~~~a~vIp~rG-------~wl~~e~d~~d~~~~rId~~r---kiPvtilLRALG~~tDeeI~~~~~~--~~--- 216 (1060)
T COG0085 153 TGS-KVLYVARVIPYRG-------SWLEFEFDPKDNLYVRIDRKR---KIPVTILLRALGLETDEEIIEAFGG--DE--- 216 (1060)
T ss_pred CCc-ceEEEEEEecCCc-------ceEEEEEccCccEEEEeeeEE---EeeHHHHHHHhCCCcHHHHHHHhcc--cc---
Confidence 211 2245555555443 488888888899999999876 7999999999999999999999973 10
Q ss_pred cccCCCCChhHHHHHHHHHHHHHhc---cccCHHHHHHHHhhcccccccCCCCccHHHHHHHHHHhhhcccCCC------
Q 001179 215 KEKGAVGSPLVSERVKIILAEVQDL---SLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHLND------ 285 (1131)
Q Consensus 215 ~~~~~~~~~~~~~~~~~lL~~~~~~---~i~t~~~AL~yIG~~~r~~~~~~~~~~~~e~g~~~L~~~ll~Hl~~------ 285 (1131)
..+.+.....+++++.+.+. .+.++ .|++|||+++...........+.+.++.++.+++||||..
T Consensus 217 -----~~~~~~~~~~~~ll~~~~~~~~~~i~~~-~a~~~i~~r~~~~~~~~~~~gR~k~~~~vl~~~~L~hL~~~~~~~~ 290 (1060)
T COG0085 217 -----LTDLVPPEGEEALLEIYEEAKGEKITAR-NALELIGSRVFVVKRYDAKEGRYKRAKYVLDKELLPHLGEAGERYD 290 (1060)
T ss_pred -----cccccchHHHHHhHHHHhhccCCCcchH-HHHHHHhcccccccccccchhhhhhhhhhhhhhHHhhhcccccccc
Confidence 01111135667777776643 34444 4999999998754321135668899999999999999995
Q ss_pred --chhhHHHHHHHHHHHHhhcCCCCCCCCcccccccEeccchhhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccccchh
Q 001179 286 --NNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNL 363 (1131)
Q Consensus 286 --~~~K~~~L~~MvrkLl~l~~G~~~~DD~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~ 363 (1131)
...|+.+|+.|+++|+++..|.+.+||+|||+||||+++|+||+++||..|.++.+.++.++.+...+
T Consensus 291 l~~~~k~~di~~mi~~l~~L~~G~~~~DDiDHlGNKRlrlvGeLl~n~fR~gl~rmer~ikerm~~~~~r---------- 360 (1060)
T COG0085 291 LSRVGKAKDIIAMIKYLIELRLGKGEEDDIDHLGNRRLRLVGELLENLFRVGLSRMERDVKERLEKADKR---------- 360 (1060)
T ss_pred hhhhHHHHHHHHHHHHHHHHhcCCCCCCCCccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh----------
Confidence 23588899999999999999999999999999999999999999999998888888887777655432
Q ss_pred HHHHHHHhcCCCcchHHHHHHHhcccCcccccccccccccceEEEccccchHHHhhhccccccCCccccccccccccccC
Q 001179 364 ANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTSVRKLLP 443 (1131)
Q Consensus 364 ~~~~~~i~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~~GvsqvleRln~~~~lSh~Rrv~rg~~~~~~K~t~~R~Lhp 443 (1131)
..+. .++.||+++.+|++||||+ ++||||+++|.||+|.|||+|||++.+++++++.++||+|||
T Consensus 361 ----~~i~--p~dlIn~k~~~Alitgffg---------~sqlSQfmDqtNpLSeLSHkRRIsAlgLsRera~fEvRDvHp 425 (1060)
T COG0085 361 ----DTLV--PQDLINAKPIHALITGFFG---------RSQLSQFMDQTNPLSELSHKRRLSALGLSRERAGFEVRDVHP 425 (1060)
T ss_pred ----hccC--chhhcchhHHHHHHhcccc---------ccceeeeeecCChHHhhhhhhceeccCcCccCCCCcccccCc
Confidence 0111 2348999999999999997 589999999999999999999999966889999999999999
Q ss_pred CcccccccCCCCCCccccccccccceEEEeeccCCCCcccccchhhhHHHHHHH-hcCceecCcccccCCCCCceEEEEC
Q 001179 444 ESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLI-GVGMIPSLPKLVKSGPPAVLSVLLD 522 (1131)
Q Consensus 444 s~wGfICPveTPEG~~CGLvk~LA~~a~It~~~~~~~~~~~~~~~~~~i~~~L~-~lG~~~~~~~~~~~~~~~~~~V~ln 522 (1131)
||||||||+|||||+|||||||||++|+|+.....+++ ..+++. .+|+.++. .++ .....|++|
T Consensus 426 THyGRiCPiETPEGpNiGLI~sLA~~A~Vn~~Gf~etP----------y~kv~~g~~~v~~i~-~l~----~~~~~~~~~ 490 (1060)
T COG0085 426 THYGRICPIETPEGPNIGLIKSLALYARINEYGFLETP----------YRKVLDGSLVVDEIE-YLS----ADEEDVYVI 490 (1060)
T ss_pred ccccccCCCCCCCCcchhHHHHHHHHeEecccCCCCCc----------eEEEEecccccccee-eec----ccccceEEE
Confidence 99999999999999999999999999999955454433 223333 36666542 111 122689999
Q ss_pred CEEEeeecCchHHHHHHHHHHHHhhcCCCCCCCceEEEEeCC-CCCCCCeEEEEcCCCcceeeEEEecCCCC--------
Q 001179 523 GRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLS-LGGAYPGLYLFTSPPKFVRPVRNISLPSE-------- 593 (1131)
Q Consensus 523 G~~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~~~-~~~~~~~i~i~td~GRl~RPv~~~~~~~~-------- 593 (1131)
|.++|.++ ++..|++.+|.+|+. +.. |+..+... .+...-++++.+|.||.+||++.+.++..
T Consensus 491 ~~~~~~~~--~~~~~~~~~~~~R~~----~~~--~~~~~~~~~~~~~dv~~~~~~~~~~~~~P~l~~dd~~~~l~~~~mq 562 (1060)
T COG0085 491 GQANGTLD--EPGELVEELVECRRG----GSG--EVSVADPEGVDYMDVSPKQVVSVGRSLIPFLEHDDANRALMGSNMQ 562 (1060)
T ss_pred eEeeeeec--CCCceeeeEEEEeec----ccc--cceeecCccccceeccceEEeccccccCceeEEcCchHhhhhhhhh
Confidence 99999886 458899999999983 122 22222211 11122378999999999999998876631
Q ss_pred --------------CCcceeeecccceeeeeeecCCCCCCCCCCCCceeEEeecCCCcccceeccccCCCCCCCcccccc
Q 001179 594 --------------ESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQ 659 (1131)
Q Consensus 594 --------------~~g~iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~P~~ilsv~AslIPF~~HNqspRn~yq 659 (1131)
+.| +||+++.|+.++.||..+.+ +||+|++|..|+|++|++|||+|||||||||||
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 468 99999999999999999876 799999999999999999999999999999999
Q ss_pred ccccccccccccceEEEecccceeeecCCCcceeecCcccccCcccCCCCcceEEEEEeccCCCCCceEEeeccccccCc
Q 001179 660 CQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGM 739 (1131)
Q Consensus 660 c~M~KQAiG~~~~n~~~R~D~~~y~L~ypQ~PLV~t~~~~~~~~~~~~~G~N~iVAv~~y~Gyn~EDaiiink~s~~rG~ 739 (1131)
|+|+||++|++..|+..|.|+..|.++|||.|+|+| +|+|+|+|++||||||+||||||||||||+++|||+
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 999999999999999999999999999999999998 899999999999999999999999999999999999
Q ss_pred eeeeEEEEEEEEecccCCCccccccccccCCCChhhhcccCCCCCcccCcEEcCCCCeeEEeecCCC-------------
Q 001179 740 CHGQIYQTETIDLSDDGNKVDRGQKLFRRNKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTTN------------- 806 (1131)
Q Consensus 740 ~~~~~y~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~Ld~dGi~~~G~~v~~gdil~~~~~~~~~------------- 806 (1131)
|+|++|++|.+++.+.+.. ..+.+.+|+.++.++++||+|||+++|++|++||||+||++|+..
T Consensus 705 ~ts~~~~~~~~~~r~~~~g---~e~~~~iP~~~e~~~~~Lde~Gii~ig~~V~~gdilvgk~tP~~~~~~~~ee~ll~i~ 781 (1060)
T COG0085 705 FTSIHIEEYETEARDTKLG---PEEIRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRIF 781 (1060)
T ss_pred ceEEEEEEEeeeeeccCCC---ccccccCCCcCHHHHhcCCccCccccccEEcCCCEEEEeeCCCCCCCCCchhhhhccc
Confidence 9999999999988766643 334578899999999999999999999999999999999888642
Q ss_pred ----cEEeeecCCCcceEEEEEEEeccCCCC--CCeEEEEEEeeecCCCCCcccccccCCcceeeeeecCCCCCccCCCC
Q 001179 807 ----SWRTNSRKGSESVFVDYVAVDMKNSKN--LPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTG 880 (1131)
Q Consensus 807 ----~~~~~~~~~~e~g~Vd~v~~~~~~~~~--~~~~~~i~~r~~R~p~iGDKf~sRHGqKGvvs~i~~~~dmPf~~~~G 880 (1131)
+++|++++++|+|+||+|.++++++++ ..+.|||++|+.|.|++|||||||||||||||+|||+|||||+ +||
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 246899999999999999999987643 5789999999999999999999999999999999999999999 999
Q ss_pred CcccEEeCCCCCCCccchhHhHHHHHhhhccccCceeccccccccccccCCCCCCCCchhhHHHHHHHHHHCCCCCCCcE
Q 001179 881 MRPDLIINPHAFPSRMTIAMLLESVAAKGGSLHGKFMDATPFANSVKKTNGDTGTDESKSLVDELGEMLRTCGFNYHGVE 960 (1131)
Q Consensus 881 ~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tpf~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~~~G~e 960 (1131)
++||||+|||||||||||||++|+++||||++.|..+|+|||... ..+++.++|.++||++.|++
T Consensus 861 ~~~DiilNP~gvPSRM~iGqilE~~lG~a~~~~G~~~~~~~F~g~---------------~~~~~~~~l~~~g~~~~Gk~ 925 (1060)
T COG0085 861 TPPDIILNPLGVPSRMNIGQILETHLGKAAALLGIPVDTPVFDGA---------------PEEDIRELLKEAGFPYSGKE 925 (1060)
T ss_pred CcccEEECCCCCCccccHHHHHHHHHHHHHHhcCceeccCCcCCC---------------CHHHHHHHHHHcCCCCCCCE
Confidence 999999999999999999999999999999999999999999987 58899999999999999999
Q ss_pred EEeeCCCCcEeeeeeeeeceeEEeeccccccceeeeecccccceeecccCcccccCceeeeehhhhHHhhhchHHHHHHh
Q 001179 961 VLYSGVYGTELTCEIFIGPVYYQRLRHMVSDKFQVRSTGTMDQITRQPIKGRKRGGGIRFGEMERDSLLAHGAAYLLHDR 1040 (1131)
Q Consensus 961 ~~y~g~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lTrQP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~er 1040 (1131)
.||||+||++|+++||||++|||||+|||+||+||||||||+.+||||++||+|+|||||||||||||+|||||++||||
T Consensus 926 ~lydG~TGe~~~~~i~vG~~Y~~kL~HmV~dK~HaRs~GP~s~lT~QP~~Gka~~GG~RfGEME~~aL~ayGAa~~LqE~ 1005 (1060)
T COG0085 926 VLYDGRTGEPFDAPIFVGVMYYQKLHHMVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQER 1005 (1060)
T ss_pred EeecCCCCCcccccEEEEehHHHhHHhhhcccceeeccCCceeeecCCCCcccccCCccccchHHHHHHHHhHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hccCCCccceeccccccccccccccccccccccccCCCCCCCCCCCeeeccCcCCCCcceecchHhHHHHHHHHHhCCce
Q 001179 1041 LHTCSDYHVADVCSLCGSVLTATFIHPQKRAIREIGGLPPARAPKKVTCHACQTSKGMETVAMPYVFRYLAAELAAMNIK 1120 (1131)
Q Consensus 1041 l~~~SD~~~~~vC~~Cg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~v~iPy~~klL~~EL~sm~I~ 1120 (1131)
|+.+||++ ||+++.+ -|..|+ .++.++.||||||||++||+||||+
T Consensus 1006 L~~~SD~~-------~G~~~~y-------------------------~~~v~g--~~~~~~~ip~sFk~L~~El~sl~i~ 1051 (1060)
T COG0085 1006 LTVKSDDV-------CGRIKIY-------------------------ECIVKG--ENIPEVGIPESFKVLLKELRSLGID 1051 (1060)
T ss_pred hhccchhc-------ccchhhh-------------------------cCcccC--CCCCCCCCCHHHHHHHHHHHHCCCc
Confidence 99999999 9988664 388896 7899999999999999999999999
Q ss_pred eEEEeccC
Q 001179 1121 ITLQLGDG 1128 (1131)
Q Consensus 1121 ~~l~~~~~ 1128 (1131)
++|.+++.
T Consensus 1052 ~~l~~~~~ 1059 (1060)
T COG0085 1052 VRLELEDG 1059 (1060)
T ss_pred eEEeecCC
Confidence 99998875
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=3.5e-218 Score=2027.46 Aligned_cols=808 Identities=38% Similarity=0.638 Sum_probs=714.8
Q ss_pred hHHHHHHHHHHHHHHhHHHHH----------------------------------------HHHHHcCCeeeEEEEEEEE
Q 001179 15 LVRHHIESFDYMLDEGLSEMF----------------------------------------DHCRQAKISYTGKLMADVE 54 (1131)
Q Consensus 15 Lv~~hi~SFn~Fi~~gl~~ii----------------------------------------~ecR~r~~TYsa~l~v~v~ 54 (1131)
|++|||+|||+|+++||++++ +|||+|++||+|||+|++.
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 689999999999999999997 8999999999999999999
Q ss_pred EEEecCCCceEEEEEeecccceeeccCcccCCCCChHHHHhhccccccCCcEEEEcCceeEEEEEEeccCCceEEEEecc
Q 001179 55 FQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRSS 134 (1131)
Q Consensus 55 ~~~~~~~~~~~~~~v~iG~iPIMvkS~~C~L~~ls~~el~~~gE~~~D~GGYFIING~EKVIr~qi~~~~N~~~~~~r~s 134 (1131)
++.+. +..+..++|.+|+|||||+|++|||++++++|+++.||||.|+||||||||+|||||+|+++++|+|+++.
T Consensus 81 ~~~~~-~~~~~~~~v~iG~iPIMv~S~~C~L~~~~~~el~~~~E~p~d~GGYFIInG~EkVIi~qi~~~~N~~~~~~--- 156 (866)
T cd00653 81 LTVND-KGKIKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVED--- 156 (866)
T ss_pred EEEec-ceeEEEEEEEEeeCCcccCcccccccCCCHHHHHhcCCCcccCCCEEEECCceeEEEEEEeccCCeEEEec---
Confidence 98761 22235679999999999999999999999999999999999999999999999999999999999998651
Q ss_pred ccCCCcceeeEEEEEeeeecC--CCceEEEEEEEe-CCeEEEEEEEecccccccHhhHHHhccCCCHHHHHHhhccccch
Q 001179 135 FRDRREGYTDKAVVIRCVRKD--QSSVTLKLYYLL-NGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDE 211 (1131)
Q Consensus 135 ~~~r~~~~t~~~i~iRs~~~~--~~s~~~~l~~~~-~g~~~l~~~~~k~~~~IPi~ilLkALg~~sD~eI~~~I~~~~~~ 211 (1131)
+.. . +....++.... ....+..+..+. .+.+++++..
T Consensus 157 --~~~-~---~~~~~~s~~~~~~~~~s~~~~~~~~~~~~i~~~i~~---------------------------------- 196 (866)
T cd00653 157 --SKG-K---RIYTKTSIPSYSPYRGSWLEVKSDKKKDRIYVRIDL---------------------------------- 196 (866)
T ss_pred --CCC-c---EEEEEEEccCCCcCccEEEEEEEccCCCeEEEEecc----------------------------------
Confidence 111 0 12222222111 011122222221 1112211111
Q ss_pred hhhcccCCCCChhHHHHHHHHHHHHHhccccCHHHHHHHHhhcccccccCCCCccHHHHHHHHHHhhhcccCCCchhhHH
Q 001179 212 KYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHLNDNNDKFN 291 (1131)
Q Consensus 212 ~~~~~~~~~~~~~~~~~~~~lL~~~~~~~i~t~~~AL~yIG~~~r~~~~~~~~~~~~e~g~~~L~~~ll~Hl~~~~~K~~ 291 (1131)
..+++||+|||++| .
T Consensus 197 ------------------------------~~~~~al~~ig~~~-----------------------------------~ 211 (866)
T cd00653 197 ------------------------------KRQEEALKYIGKRF-----------------------------------E 211 (866)
T ss_pred ------------------------------cCHHHHHHHHHHHH-----------------------------------H
Confidence 01678999999875 6
Q ss_pred HHHHHHHHHHhhcCCCCCCCCcccccccEeccchhhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccccchhHHHHHHHh
Q 001179 292 LLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVME 371 (1131)
Q Consensus 292 ~L~~MvrkLl~l~~G~~~~DD~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~i~ 371 (1131)
+|++|++||++++.|.+.+||+|||+||||+++|+||+.+|++.|+++++.+++.+++...+ .+.++ +..+++
T Consensus 212 ~L~~Mi~kLl~~~~g~~~~Dd~D~~~NkRv~~~G~Ll~~lfr~~l~~~~~~~k~~l~~~~~~-~~~~~------~~~~~~ 284 (866)
T cd00653 212 DLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSK-KKDLT------PQLLIN 284 (866)
T ss_pred HHHHHHHHHHHHhcCCCCCCCchhhhCeEEeeHHHHHHHHHHHHHHHHHHHHHHHHHhhhhc-ccccC------HHHhcc
Confidence 89999999999999999999999999999999999999999999999999999999887654 22111 222332
Q ss_pred cCCCcchHHHHHHHhcccCcccccccccccccceEEEccccchHHHhhhccccccCCccccccccccccccCCccccccc
Q 001179 372 KNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTSVRKLLPESWGFLCP 451 (1131)
Q Consensus 372 ~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~~GvsqvleRln~~~~lSh~Rrv~rg~~~~~~K~t~~R~Lhps~wGfICP 451 (1131)
++.||++|++||+||||.++.+ ++|++||+|+|+|+||+|++||+||||+|++++++|+++||+|||||||||||
T Consensus 285 ---~~~It~~i~~~~~TGnw~~~~~--~~~~~Gvsq~ldr~N~ls~lsh~Rrv~~~~~~~~~k~~~~R~lhps~~G~iCP 359 (866)
T cd00653 285 ---SKPITSGIKEFLATGNWGSKRF--LMQRSGLSQVLDRLNPLSELSHKRRISSLGLFRERKGFEVRDLHPSHWGRICP 359 (866)
T ss_pred ---chHHHHHHHHHhhcCCcccccc--ccccceEEEEcccCCHHHHHHhhhhcccccccccccCCcccccCcccCCccCC
Confidence 3489999999999999998765 78999999999999999999999999998899999999999999999999999
Q ss_pred CCCCCCccccccccccceEEEeeccCCCCcccccchhhhHHHHHHHhcCceecCcccccCCCCCceEEEECCEEEeeecC
Q 001179 452 VHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIPS 531 (1131)
Q Consensus 452 veTPEG~~CGLvk~LA~~a~It~~~~~~~~~~~~~~~~~~i~~~L~~lG~~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~ 531 (1131)
||||||++||||||||++|+|+
T Consensus 360 veTPEG~~cGLv~~LA~~a~Is---------------------------------------------------------- 381 (866)
T cd00653 360 IETPEGENCGLVKNLALMARIS---------------------------------------------------------- 381 (866)
T ss_pred CCCCCCccccchhhhhceEeee----------------------------------------------------------
Confidence 9999999999999999999873
Q ss_pred chHHHHHHHHHHHHhhcCCCCCCCceEEEEeCCCCCCCCeEEEEcCCCcceeeEEEecCCCCCCcceeeecccceeeeee
Q 001179 532 SEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSEESQNIELIGPFEQVFMEI 611 (1131)
Q Consensus 532 ~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~~~~~~~~~~i~i~td~GRl~RPv~~~~~~~~~~g~iE~i~~~Eq~~~~I 611 (1131)
||++||+++++.
T Consensus 382 -----------------------------------------------Gr~~rP~~~v~~--------------------- 393 (866)
T cd00653 382 -----------------------------------------------GRIERPYRIVEK--------------------- 393 (866)
T ss_pred -----------------------------------------------eEeeeeEEEecc---------------------
Confidence 899999997631
Q ss_pred ecCCCCCCCCCCCCceeEEeecCCCcccceeccccCCCCCCCccccccccccccccccccceEEEecccceeeecCCCcc
Q 001179 612 RCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTP 691 (1131)
Q Consensus 612 a~~~~~~~~~~~~~~~th~EI~P~~ilsv~AslIPF~~HNqspRn~yqc~M~KQAiG~~~~n~~~R~D~~~y~L~ypQ~P 691 (1131)
. +||+||+|.++||++||+|||+||||||||||||||+|||||++++|+..|.|++.|+|.|||+|
T Consensus 394 ---------~-----~th~ei~~~~~ls~~asliPf~~hNqspRn~~~~~M~kQa~g~~~~n~~~r~d~~~~~l~~pq~p 459 (866)
T cd00653 394 ---------E-----VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKP 459 (866)
T ss_pred ---------c-----eEEEEeCccceeeeeeeccCCCCcccccchhhhhcccCCccCchhccccccccchheeeccCCCC
Confidence 1 89999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeecCcccccCcccCCCCcceEEEEEeccCCCCCceEEeeccccccCceeeeEEEEEEEEecccCCCccccccccccCCC
Q 001179 692 IVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFRRNKD 771 (1131)
Q Consensus 692 LV~t~~~~~~~~~~~~~G~N~iVAv~~y~Gyn~EDaiiink~s~~rG~~~~~~y~~~~~~~~~~~~~~~~~~~~f~~~~~ 771 (1131)
||.|+.++.++++++|+|+|++||||||+||||||||||||+|+|||||++.+|++|++++............ ...|..
T Consensus 460 lv~T~~~~~~~~~~~~~G~N~~VAv~~y~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~~~~~-~~~~~~ 538 (866)
T cd00653 460 LVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITR-GDIPNV 538 (866)
T ss_pred ccccchHHHhCCCccCCCceEEEEEeccccccccceeeeehhhhhcCceeEEEEEEEEEEEEecCCCcceEec-CCCCCC
Confidence 9999999999999999999999999999999999999999999999999999999999987543321111111 123444
Q ss_pred ChhhhcccCCCCCcccCcEEcCCCCeeEEeecCC--------------CcEEeeecCCCcceEEEEEEEeccCC-CCCCe
Q 001179 772 AKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTT--------------NSWRTNSRKGSESVFVDYVAVDMKNS-KNLPQ 836 (1131)
Q Consensus 772 ~~~~~~~Ld~dGi~~~G~~v~~gdil~~~~~~~~--------------~~~~~~~~~~~e~g~Vd~v~~~~~~~-~~~~~ 836 (1131)
....+++||+||+|++|+.|++||+|+||+++.. .++.+.+++.+|+|+||+|.++..+. .++..
T Consensus 539 ~~~~~~~ld~dGi~~~g~~v~~gd~li~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~v~~v~~~~~~~~~~~~~ 618 (866)
T cd00653 539 SEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRELNDGGNK 618 (866)
T ss_pred ChHHhhccCCCCCcCCCCEecCCCEEEEEecCcccccccccccccCCcceEEEEEecCCCceEEEEEEEeccccCCCCcE
Confidence 5566899999999999999999999999987642 45679999999999999999997321 13468
Q ss_pred EEEEEEeeecCCCCCcccccccCCcceeeeeecCCCCCccCCCCCcccEEeCCCCCCCccchhHhHHHHHhhhccccCce
Q 001179 837 KANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKGGSLHGKF 916 (1131)
Q Consensus 837 ~~~i~~r~~R~p~iGDKf~sRHGqKGvvs~i~~~~dmPf~~~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~ 916 (1131)
.|+|++|+.|+|+||||||||||||||||+|||+|||||| +||++|||||||||||||||||||+|+++||||++.|.+
T Consensus 619 ~v~v~~r~~R~p~iGDKfssRhGqKGv~s~i~~~~dmPf~-~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~ 697 (866)
T cd00653 619 LVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFT-EDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKF 697 (866)
T ss_pred EEEEEEeEEecCCcccccccccCCCcEEEEEeccccCCcc-cCCCCCcEEecCCcCcccccHHHHHHHHHHHHHHhcCCc
Confidence 9999999999999999999999999999999999999999 999999999999999999999999999999999999999
Q ss_pred eccccccccccccCCCCCCCCchhhHHHHHHHHHHCCCCCCCcEEEeeCCCCcEeeeeeeeeceeEEeeccccccceeee
Q 001179 917 MDATPFANSVKKTNGDTGTDESKSLVDELGEMLRTCGFNYHGVEVLYSGVYGTELTCEIFIGPVYYQRLRHMVSDKFQVR 996 (1131)
Q Consensus 917 ~d~tpf~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~~~G~e~~y~g~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R 996 (1131)
.|+|||... ..+++.+.|.++||+++|+|.||||+||++++++||+|++|||||+|||+||+|||
T Consensus 698 ~d~t~f~~~---------------~~~~~~~~l~~~g~~~~G~e~~y~g~tG~~~~~~if~G~~yyqrL~Hmv~DK~~~R 762 (866)
T cd00653 698 GDATPFDGA---------------EEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHAR 762 (866)
T ss_pred ccccccCcc---------------hHHHHHHHHHHcCCCCCCcEEEEcCCCCCCcccceEEeehhhhhhhhhhchhhhhc
Confidence 999999876 47788999999999999999999999999999999999999999999999999999
Q ss_pred ecccccceeecccCcccccCceeeeehhhhHHhhhchHHHHHHhhccCCCccceeccccccccccccccccccccccccC
Q 001179 997 STGTMDQITRQPIKGRKRGGGIRFGEMERDSLLAHGAAYLLHDRLHTCSDYHVADVCSLCGSVLTATFIHPQKRAIREIG 1076 (1131)
Q Consensus 997 ~~Gp~~~lTrQP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~Cg~~~~~~~~~~~~~~~~~~~ 1076 (1131)
++||++.|||||++||+|+|||||||||||||+|||||++|+|||+.+||+++++||.+||++++..
T Consensus 763 ~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~lia~Gas~~l~erl~~~SD~~~~~vc~~cg~i~~~~------------- 829 (866)
T cd00653 763 STGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSAN------------- 829 (866)
T ss_pred ccCCcchhccCcCccccccCCeEEEEEehhhhhhhhhHHHHHHHHhcCCccceEEEeccCccccccc-------------
Confidence 9999999999999999999999999999999999999999999999999999999999999998653
Q ss_pred CCCCCCCCCCeeeccCcCCCCcceecchHhHHHHHHHHHhCCceeEEE
Q 001179 1077 GLPPARAPKKVTCHACQTSKGMETVAMPYVFRYLAAELAAMNIKITLQ 1124 (1131)
Q Consensus 1077 ~~~~~~~~~~~~C~~c~~~~~~~~v~iPy~~klL~~EL~sm~I~~~l~ 1124 (1131)
+|+.|+++.++.++.+|||||||+|||+||||++++.
T Consensus 830 -----------~c~~c~~~~~~~~~~ipy~~kll~~EL~sm~i~~~~~ 866 (866)
T cd00653 830 -----------LCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866 (866)
T ss_pred -----------ccccccCCCceeecCCCHHHHHHHHHHHHCCcceEeC
Confidence 4999999999999999999999999999999999973
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=3.9e-209 Score=1952.50 Aligned_cols=873 Identities=24% Similarity=0.365 Sum_probs=736.3
Q ss_pred ccccchhhHHHHHHHHHHHHH----------HhHHHHH-----------------------------HHHHHcCCeeeEE
Q 001179 8 DFEPLRELVRHHIESFDYMLD----------EGLSEMF-----------------------------DHCRQAKISYTGK 48 (1131)
Q Consensus 8 ~~~~~~~Lv~~hi~SFn~Fi~----------~gl~~ii-----------------------------~ecR~r~~TYsa~ 48 (1131)
.+...++|++||++|||+||+ +||++++ +|||+|++|||||
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 456799999999999999999 8999999 9999999999999
Q ss_pred EEEEEEEEEecC--CCceEEEEEeecccceeeccCcccCCCCChHHHHhhccccccCCcEEEEcCceeEEEEEEeccCCc
Q 001179 49 LMADVEFQYLDA--GSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNY 126 (1131)
Q Consensus 49 l~v~v~~~~~~~--~~~~~~~~v~iG~iPIMvkS~~C~L~~ls~~el~~~gE~~~D~GGYFIING~EKVIr~qi~~~~N~ 126 (1131)
|+|+++++.... ++.+.+++|+||+||||++ ||||||||+||||++|+++++|.
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 999999975421 2356678999999999986 99999999999999999999998
Q ss_pred eEEEEeccccCCCcceeeEEEEEeeeecCCCceEEEEEEEeCCeEEEEEEEecccccccHhhHHHhccCCCHHHHHHhhc
Q 001179 127 PMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLT 206 (1131)
Q Consensus 127 ~~~~~r~s~~~r~~~~t~~~i~iRs~~~~~~s~~~~l~~~~~g~~~l~~~~~k~~~~IPi~ilLkALg~~sD~eI~~~I~ 206 (1131)
++..... ..+++ ...|.+.++|.+ ..|+.+.+++++.+|++++..+ +||+++||||||+++|+||++.++
T Consensus 149 ~~~~~~~-~~~~~--~~~~~a~iis~r----gswl~~e~~~~~~i~v~i~~~~---kIPi~illrALG~~sd~eI~~~i~ 218 (1065)
T TIGR02013 149 FFSSEKD-THKSG--KVLFSARIIPYR----GSWLEFETDKKDVLYVRIDRKR---KLPATVLLRALGYTIDTLILNRLG 218 (1065)
T ss_pred EEEEccc-cCCCC--ceEEEEEEEeCC----CCceEEEEecCCeEEEEecCCC---ceeHHHHHHHcCCCcchhhhhhcC
Confidence 8776432 11112 112445555543 3488888888999999998764 799999999999999999999886
Q ss_pred cccchhhhcccCCCCChhHHHHHHHHHHHHHhccccCHHHHHHHHhhcccccccCCCCccHHHHHHHHHHhhhcc-----
Q 001179 207 CCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFV----- 281 (1131)
Q Consensus 207 ~~~~~~~~~~~~~~~~~~~~~~~~~lL~~~~~~~i~t~~~AL~yIG~~~r~~~~~~~~~~~~e~g~~~L~~~ll~----- 281 (1131)
. +.+ +...| .+..+.|+++||.||+++++. ......+.|+++|++.||+
T Consensus 219 ~--------------~~~----i~~~l---~~~~~~~~e~Al~~i~~~~~~-----g~~~~~~~a~~~l~~~f~~~~rY~ 272 (1065)
T TIGR02013 219 S--------------GEY----IRNTL---RKDPTNSEEEALVEIYRKLRP-----GEPPTVEAARSLLENLFFDPKRYD 272 (1065)
T ss_pred c--------------hHH----HHHHH---HhccccCHHHHHHHHHhhcCC-----CCcchHHHHHHHHHHHhcCccccc
Confidence 1 121 22222 233478999999999999863 2344568899999999987
Q ss_pred --cCCCc----------------hhhHHHHHHHHHHHHhhcCCCCCCCCcccccccEeccchhhHHHHHHHHHHHHHHHH
Q 001179 282 --HLNDN----------------NDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKG 343 (1131)
Q Consensus 282 --Hl~~~----------------~~K~~~L~~MvrkLl~l~~G~~~~DD~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~ 343 (1131)
|+|.. ..|+++|+ |+++|+++..|...+||+|||+||||+++|+||+.||+..|+++.+.+
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 99931 24888885 999999999999999999999999999999999999999888888877
Q ss_pred HHHHHHHHHhcCCccccchhHHHHHHHhcCCCcchHHHHHHHhcccCcccccccccccccceEEEccccchHHHhhhccc
Q 001179 344 KKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRA 423 (1131)
Q Consensus 344 ~~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~~GvsqvleRln~~~~lSh~Rr 423 (1131)
+..+.+. . .+ .+ .++.+++ ++.||+++++||+|| ||||+|+|+||++.|||+||
T Consensus 352 k~~l~~~--~-~~--~~----~~~~~i~---~~~it~~i~~ff~tg--------------glSQ~Ldr~NpLs~lsh~RR 405 (1065)
T TIGR02013 352 RERMSTQ--D-TD--TL----TPQDLIN---AKPISAAIKEFFGSS--------------QLSQFMDQTNPLAELTHKRR 405 (1065)
T ss_pred HHHhhhc--c-cc--cC----CHHHhcC---ccchHHHHHHHhccC--------------CcccccccCCHHHhhhhhce
Confidence 7666532 1 11 11 2445553 468999999999997 89999999999999999999
Q ss_pred ccc---CCccccccccccccccCCcccccccCCCCCCccccccccccceEEEeeccCCCCcccccchhhhHHHHHHHhcC
Q 001179 424 VHR---GASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVG 500 (1131)
Q Consensus 424 v~r---g~~~~~~K~t~~R~Lhps~wGfICPveTPEG~~CGLvk~LA~~a~It~~~~~~~~~~~~~~~~~~i~~~L~~lG 500 (1131)
++. |++.+++++++||+|||||||||||+|||||++||||+|||++|+|+ .+|
T Consensus 406 lsslgpggl~r~~~~~~~RdlHpShyGrICPiETPEG~n~GLVknLA~~a~i~------------------------~~G 461 (1065)
T TIGR02013 406 LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVN------------------------EYG 461 (1065)
T ss_pred ecccCCCCcCccccCCccCccCccccccccCCCCCCCCccccccchhhhcccC------------------------cce
Confidence 994 57889999999999999999999999999999999999999999997 234
Q ss_pred ceecCcccccCCCCCceEEEECCEEEeeecCchHHHHHHHHHHHHhhcCCCCCCCceEEEEeCCCCCCCCeEEEEcCCCc
Q 001179 501 MIPSLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPK 580 (1131)
Q Consensus 501 ~~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~~~~~~~~~~i~i~td~GR 580 (1131)
+... | +.++.||++.
T Consensus 462 ~i~~-P----------~~~V~ng~~~------------------------------------------------------ 476 (1065)
T TIGR02013 462 FIET-P----------YRKVKDGKVV------------------------------------------------------ 476 (1065)
T ss_pred EEeC-C----------eEEEECCeEe------------------------------------------------------
Confidence 4322 1 2233444321
Q ss_pred ceeeEEEecCCCCCCcceeeecccceeeeeeecCCCCCCCCC------------------CCCceeEEeecCCCccccee
Q 001179 581 FVRPVRNISLPSEESQNIELIGPFEQVFMEIRCPDGGDGGRR------------------NAFPATHEEIHPTGMLSVVA 642 (1131)
Q Consensus 581 l~RPv~~~~~~~~~~g~iE~i~~~Eq~~~~Ia~~~~~~~~~~------------------~~~~~th~EI~P~~ilsv~A 642 (1131)
..+.+||++++||+++.||..+.++.... ....+||+||+|.+|||++|
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 01367788888888888887766553210 01237999999999999999
Q ss_pred ccccCCCCCCCccccccccccccccccc-----------------------------------cceEEEeccc-------
Q 001179 643 NLTPYSDHNQSPRNMYQCQMAKQTMGFS-----------------------------------VQALKFRADQ------- 680 (1131)
Q Consensus 643 slIPF~~HNqspRn~yqc~M~KQAiG~~-----------------------------------~~n~~~R~D~------- 680 (1131)
|||||+||||||||+|||||||||||+. ++|+..|.|+
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 9999999999999999999999999777 8999999995
Q ss_pred --ceeeec----------CCCcceeecCc----ccccC------cccCCCCcceEEEEEeccCCCCCceEEeeccccccC
Q 001179 681 --KLYHLQ----------TPQTPIVRTNT----YTKYG------IDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRG 738 (1131)
Q Consensus 681 --~~y~L~----------ypQ~PLV~t~~----~~~~~------~~~~~~G~N~iVAv~~y~Gyn~EDaiiink~s~~rG 738 (1131)
+.|.|. |||+|||+|+. .+.+. ++|+|+|+|++||||||+||||||||||||+|+|||
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 99999999954 44444 899999999999999999999999999999999999
Q ss_pred ceeeeEEEEEEEEecccCCCccccccccc--cCCCChhhhcccCCCCCcccCcEEcCCCCeeEEeecCC-----------
Q 001179 739 MCHGQIYQTETIDLSDDGNKVDRGQKLFR--RNKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTT----------- 805 (1131)
Q Consensus 739 ~~~~~~y~~~~~~~~~~~~~~~~~~~~f~--~~~~~~~~~~~Ld~dGi~~~G~~v~~gdil~~~~~~~~----------- 805 (1131)
+|++.+|++|++++...+.. .+.|. .|+.....+++||+||+|++|+.|++||||+||+++..
T Consensus 704 ~~~s~~~~~~~~~~~~~~~g----~e~~~~~~p~~~~~~~~~Ld~dGi~~~G~~v~~gdilvgk~~p~~~~~~~~~~~l~ 779 (1065)
T TIGR02013 704 VFTSIHIEEYEVEARDTKLG----PEEITRDIPNVSEEALRNLDENGIVRIGAEVKAGDILVGKVTPKGETELTPEEKLL 779 (1065)
T ss_pred ceEEEEEEEEEEEeeccCCC----ceEeeccCCCCchhhhhccCCCCCccCccEeCCCCEEEEEecCCcccccChhhhhh
Confidence 99999999999987553321 13333 35555567899999999999999999999999987632
Q ss_pred ----------CcEEeeecCCCcceEEEEEEEeccCCCCC-----CeEEEEEEeeecCCCCCcccccccCCcceeeeeecC
Q 001179 806 ----------NSWRTNSRKGSESVFVDYVAVDMKNSKNL-----PQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPD 870 (1131)
Q Consensus 806 ----------~~~~~~~~~~~e~g~Vd~v~~~~~~~~~~-----~~~~~i~~r~~R~p~iGDKf~sRHGqKGvvs~i~~~ 870 (1131)
.++++++++.+|+|+||+|.++.++++.. ...|+|++|+.|+|+||||||||||||||||+|||+
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 13558899999999999999997765421 468999999999999999999999999999999999
Q ss_pred CCCCccCCCCCcccEEeCCCCCCCccchhHhHHHHHhhhcccc--Cceecccc-ccccccccCCCCCCCCchhhHHHHHH
Q 001179 871 IDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKGGSLH--GKFMDATP-FANSVKKTNGDTGTDESKSLVDELGE 947 (1131)
Q Consensus 871 ~dmPf~~~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~--g~~~d~tp-f~~~~~~~~~~~~~~~~~~~~~~~~~ 947 (1131)
|||||| +||++|||||||||||||||||||+|+++||||++. |.+.++|| |... ..+++++
T Consensus 860 eDMPf~-~~G~~pDiIiNPhg~PSRMtiGqllE~~~gka~~~~~~~~~~~~tp~f~~~---------------~~~~~~~ 923 (1065)
T TIGR02013 860 EDMPFL-EDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRKGVPIATPVFDGA---------------SEEEIKE 923 (1065)
T ss_pred CCCCcc-CCCCCccEEECCCCCcccccHHHHHHHHHHHHHHhccCCCeEEeccCcCCc---------------cHHHHHH
Confidence 999999 999999999999999999999999999999999987 67788999 5543 5789999
Q ss_pred HHHHCCCCCCCcEEEeeCCCCcEeeeeeeeeceeEEeeccccccceeeeecccccceeecccCcccccCceeeeehhhhH
Q 001179 948 MLRTCGFNYHGVEVLYSGVYGTELTCEIFIGPVYYQRLRHMVSDKFQVRSTGTMDQITRQPIKGRKRGGGIRFGEMERDS 1027 (1131)
Q Consensus 948 ~l~~~g~~~~G~e~~y~g~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lTrQP~~Gr~~~GG~R~GEMErd~ 1027 (1131)
.|.++||+++|+|.||||+||++|+++||+|++|||||+|||+||+|||++||++.|||||++||+|+||||||||||||
T Consensus 924 ~l~~~g~~~~G~e~l~~G~TG~~~~~~ifvG~~yy~rL~HmV~DK~haRs~Gp~~~lT~QP~~Grsr~GG~R~GEME~d~ 1003 (1065)
T TIGR02013 924 YLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWA 1003 (1065)
T ss_pred HHHHcCCCCCCCEEEEcCCCCCCccccEEEeehheeechhhhcchhhhcccCCccceeeCCCcccccCCCeeeeeeeHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhhchHHHHHHhhccCCCccceeccccccccccccccccccccccccCCCCCCCCCCCeeeccCcCCCCcceecchHhH
Q 001179 1028 LLAHGAAYLLHDRLHTCSDYHVADVCSLCGSVLTATFIHPQKRAIREIGGLPPARAPKKVTCHACQTSKGMETVAMPYVF 1107 (1131)
Q Consensus 1028 l~a~Gas~~l~erl~~~SD~~~~~vC~~Cg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~v~iPy~~ 1107 (1131)
|+|||||++|+|||+.+||++..+. ..++..| ++.++.++.+||||
T Consensus 1004 l~a~Gas~~L~E~l~~~SD~~~g~~---------------------------------~~~~~~~-~~~~i~~~~~p~sf 1049 (1065)
T TIGR02013 1004 LEAYGAAYTLQEMLTVKSDDVVGRT---------------------------------KAYEAIV-KGENVPEPGIPESF 1049 (1065)
T ss_pred HHhhhhHHHHHHHHhccChhhhhhh---------------------------------hhhhhhc-CCCccccccCCccH
Confidence 9999999999999999999995321 0123345 57889999999999
Q ss_pred HHHHHHHHhCCceeEE
Q 001179 1108 RYLAAELAAMNIKITL 1123 (1131)
Q Consensus 1108 klL~~EL~sm~I~~~l 1123 (1131)
|||+|||+||||++++
T Consensus 1050 klL~~EL~sm~i~~~~ 1065 (1065)
T TIGR02013 1050 NVLIKELQSLGLDIEL 1065 (1065)
T ss_pred HHHHHHHHhCCccccC
Confidence 9999999999999875
No 8
>PRK00405 rpoB DNA-directed RNA polymerase subunit beta; Reviewed
Probab=100.00 E-value=1.6e-207 Score=1947.71 Aligned_cols=887 Identities=23% Similarity=0.351 Sum_probs=734.1
Q ss_pred ccchhhHHHHHHHHHHHH-------HHhHHHHH-----------------------------HHHHHcCCeeeEEEEEEE
Q 001179 10 EPLRELVRHHIESFDYML-------DEGLSEMF-----------------------------DHCRQAKISYTGKLMADV 53 (1131)
Q Consensus 10 ~~~~~Lv~~hi~SFn~Fi-------~~gl~~ii-----------------------------~ecR~r~~TYsa~l~v~v 53 (1131)
...++|++||++|||+|| ++||++++ +|||+|++||||||+|++
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 468999999999999999 99999999 999999999999999999
Q ss_pred EEEEecCCCceEEEEEeecccceeeccCcccCCCCChHHHHhhccccccCCcEEEEcCceeEEEEEEeccCCceEEEEec
Q 001179 54 EFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRS 133 (1131)
Q Consensus 54 ~~~~~~~~~~~~~~~v~iG~iPIMvkS~~C~L~~ls~~el~~~gE~~~D~GGYFIING~EKVIr~qi~~~~N~~~~~~r~ 133 (1131)
+++.. .++++.+++|+||+||||+ +||||||||+||||++|+++++|.++.....
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 4999999999999999999999987766543
Q ss_pred cccCCCcceeeEEEEEeeeecCCCceEEEEEEEeCCeEEEEEEEecccccccHhhHHHhccCCCHHHHHHhhccccchhh
Q 001179 134 SFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKY 213 (1131)
Q Consensus 134 s~~~r~~~~t~~~i~iRs~~~~~~s~~~~l~~~~~g~~~l~~~~~k~~~~IPi~ilLkALg~~sD~eI~~~I~~~~~~~~ 213 (1131)
+....+.. |.+.+.|.+ ..|+.+.++.++.+|+++...+ +||+++||||||+ ||+||++.|+. ++..
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 KTSSGKLL---YSARIIPYR----GSWLEFEFDPKDILYVRIDRRR---KLPVTVLLRALGY-SDEEILDLFYE--KEEF 223 (1112)
T ss_pred ccCCCcee---EEEEEEECC----CCcEEEEEecCCeEEEEecCCC---cccHHHHHHHcCC-CHHHHHHHhcc--cccc
Confidence 11111222 445555543 3488888999999999999543 7999999999999 99999999962 1100
Q ss_pred h---c----------ccCCCCC----hhH-------HH-HH-HHHHHHHHhccccCHHHHHHHHhhcccccccCCCCccH
Q 001179 214 K---K----------EKGAVGS----PLV-------SE-RV-KIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESY 267 (1131)
Q Consensus 214 ~---~----------~~~~~~~----~~~-------~~-~~-~~lL~~~~~~~i~t~~~AL~yIG~~~r~~~~~~~~~~~ 267 (1131)
. . +..+..+ ..+ .+ .+ ..+.+.+.+.++.|+++|+.||+++++. .....
T Consensus 224 ~~~~~~~~~~~~~~~~~~~~~~~~~~ei~~~~~~~~~~~~~~~~i~~~l~~~~~~t~e~Al~~I~k~l~~-----g~~~~ 298 (1112)
T PRK00405 224 GKEIEVPVEYLLGKVLAEDIVDEETGEVLAEANDEITEELDGPYIRNTLEKDPTSSREEALVEIYRRLRP-----GEPPT 298 (1112)
T ss_pred cceeccchHHhcccchhhhhcccccceeeeccCCccchhhhhHHHHHHHhhccccCHHHHHHHHHhhcCC-----CCcch
Confidence 0 0 0000000 000 00 01 1222233334678999999999999863 33445
Q ss_pred HHHHHHHHHhhhc-------ccCCCc-----------h-----hhHHHHHHHHHHHHhhcCCCCCCCCcccccccEeccc
Q 001179 268 YAVAETVIRDYIF-------VHLNDN-----------N-----DKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLP 324 (1131)
Q Consensus 268 ~e~g~~~L~~~ll-------~Hl~~~-----------~-----~K~~~L~~MvrkLl~l~~G~~~~DD~D~l~NkRv~l~ 324 (1131)
.+.|+.+|++.|| ||+|.. . .|+ ++++|+++||.+..|.+.+||+|||+||||+++
T Consensus 299 ~e~a~~~l~~~ff~~~rYdL~hiGr~k~nkKl~l~~~~~~~~L~~~-d~~~mi~~Ll~l~~g~~~~DDiDhl~NKRvr~a 377 (1112)
T PRK00405 299 VEAARSLLENLFFDPKRYDLSKVGRYKLNKKLGLDEDEDVRVLTKE-DIIATIKYLINLRNGKGEVDDIDHLGNRRVRSV 377 (1112)
T ss_pred HHHHHHHHHHHhcCccccccccCCceecchhcccCcccccccccHH-HHHHHHHHHHhhhcccCCCcchhHHhcchhhhH
Confidence 6789999999886 999942 1 344 569999999999999999999999999999999
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccccchhHHHHHHHhcCCCcchHHHHHHHhcccCcccccccccccccc
Q 001179 325 GHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAG 404 (1131)
Q Consensus 325 G~Ll~~lf~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~~G 404 (1131)
|+||+.+|+..|+++.+.++..+... . .+ ++ .++.+++ ++.||++|++||+|| |
T Consensus 378 GeLL~~~fr~~~~rl~k~ik~~l~~~--~-~~--~~----~~~~lin---~~~it~~i~~ff~tg--------------g 431 (1112)
T PRK00405 378 GELLQNQFRIGLSRMERAVRERMSLQ--D-LD--TL----TPQDLIN---AKPVVAAIKEFFGSS--------------Q 431 (1112)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhc--c-cc--cC----CHHHhhC---chhHHHHHHHhhccC--------------C
Confidence 99999999998888887777666533 1 11 11 2455663 468999999999987 8
Q ss_pred eEEEccccchHHHhhhccccc---cCCccccccccccccccCCcccccccCCCCCCccccccccccceEEEeeccCCCCc
Q 001179 405 YTVQAERLNFLRFISFFRAVH---RGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGN 481 (1131)
Q Consensus 405 vsqvleRln~~~~lSh~Rrv~---rg~~~~~~K~t~~R~Lhps~wGfICPveTPEG~~CGLvk~LA~~a~It~~~~~~~~ 481 (1131)
|||+++|+|+++.|||+||++ +|++.+++++++||+|||||||||||+|||||++||||+|||++|+|+
T Consensus 432 lSQ~Ldq~NpLselshkRRlss~gpggl~r~~a~~~~R~lH~ShyGriCPiETPEG~n~GLV~nLA~~a~i~-------- 503 (1112)
T PRK00405 432 LSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVN-------- 503 (1112)
T ss_pred cceeeccCCHHHhhhhhceecccCCCCcCccccCCcccccCccccccccCcCCCCCCccccccchhhccccc--------
Confidence 999999999999999999999 467889999999999999999999999999999999999999999998
Q ss_pred ccccchhhhHHHHHHHhcCceecCcccccCCCCCceEEEECCEEEeeecCchHHHHHHHHHHHHhhcCCCCCCCceEEEE
Q 001179 482 IRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYV 561 (1131)
Q Consensus 482 ~~~~~~~~~~i~~~L~~lG~~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v 561 (1131)
++|++.. + |.+++||.|-.
T Consensus 504 ----------------~~G~~~t-p----------~~~~~nG~~~~---------------------------------- 522 (1112)
T PRK00405 504 ----------------EYGFIET-P----------YRKVVDGKVTD---------------------------------- 522 (1112)
T ss_pred ----------------cCCcccc-c----------eEEEECCeEcc----------------------------------
Confidence 3566532 2 78889998611
Q ss_pred eCCCCCCCCeEEEEcCCCcceeeEEEecCCCCCCcceeeecccceeeeeeecCCCCCCCC------------------CC
Q 001179 562 PLSLGGAYPGLYLFTSPPKFVRPVRNISLPSEESQNIELIGPFEQVFMEIRCPDGGDGGR------------------RN 623 (1131)
Q Consensus 562 ~~~~~~~~~~i~i~td~GRl~RPv~~~~~~~~~~g~iE~i~~~Eq~~~~Ia~~~~~~~~~------------------~~ 623 (1131)
.+||+|++||++..||....++... ..
T Consensus 523 -----------------------------------~i~yl~a~eE~~~~Ia~~~~~l~~~~~~~~~~i~~r~~~e~~~~~ 567 (1112)
T PRK00405 523 -----------------------------------EIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYKGEFVLVP 567 (1112)
T ss_pred -----------------------------------ceEECCHHHhcCcEEEecCcccCCCCcccCceEEEEecCcceeec
Confidence 1234444444444444433332210 00
Q ss_pred CCceeEEeecCCCcccceeccccCCCCCCCccccccccccccccccccc-------------------------------
Q 001179 624 AFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQ------------------------------- 672 (1131)
Q Consensus 624 ~~~~th~EI~P~~ilsv~AslIPF~~HNqspRn~yqc~M~KQAiG~~~~------------------------------- 672 (1131)
...+||+||+|.+++|++||||||+||||||||+|||||||||||+...
T Consensus 568 ~~~~~~~~i~p~qi~sv~aslIPFleHnda~R~lmgSnMqrQAvpl~~~~~p~vgTg~e~~~~~ds~~~i~a~~~G~v~~ 647 (1112)
T PRK00405 568 PEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAKRDGVVEY 647 (1112)
T ss_pred hhhceEEeechhhhceehhhccCcccccCCcchhhhhhhhhhhhhhccccCCeeecCcchhhhhhcchheEeccCCEEEE
Confidence 1127999999999999999999999999999999999999999998777
Q ss_pred ----eEEEec-----------------ccceee-ecCCCcceeecCc----cccc------CcccCCCCcceEEEEEecc
Q 001179 673 ----ALKFRA-----------------DQKLYH-LQTPQTPIVRTNT----YTKY------GIDEYPTGTNAIVAVLAYT 720 (1131)
Q Consensus 673 ----n~~~R~-----------------D~~~y~-L~ypQ~PLV~t~~----~~~~------~~~~~~~G~N~iVAv~~y~ 720 (1131)
|+..|. |+..+. +.|||+|||+|+. .+.+ +++++|+|+|++||||||+
T Consensus 648 v~~~~i~ir~~~~~~~~~~~~~y~L~~~~~sn~~~~~~q~Plv~~~~~v~~g~~lad~~~~~~~e~~~G~N~~VA~~~y~ 727 (1112)
T PRK00405 648 VDASRIVVRVEELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQNVLVAFMPWN 727 (1112)
T ss_pred EeCCEEEEeecccccCCCCeeEEEecccccccccceeecceeeecCCeEeeccEeecccccCcccccCCcceEEEEEeec
Confidence 888888 555555 7899999999995 3444 6899999999999999999
Q ss_pred CCCCCceEEeeccccccCceeeeEEEEEEEEecccCCCccccccccc--cCCCChhhhcccCCCCCcccCcEEcCCCCee
Q 001179 721 GYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFR--RNKDAKSLHSVIDSDGLPYVGQMIHPGEPYC 798 (1131)
Q Consensus 721 Gyn~EDaiiink~s~~rG~~~~~~y~~~~~~~~~~~~~~~~~~~~f~--~~~~~~~~~~~Ld~dGi~~~G~~v~~gdil~ 798 (1131)
||||||||||||+|+|||+|++.+|++|+.++...+... +.+. .|+.+...+++||+||||++|+.|++||||+
T Consensus 728 GYn~EDaiiink~si~rg~~~s~~~~~~~~~~~~~~~~~----~~~~~~~p~~~~~~~~~Ld~dGi~~~G~~v~~gDili 803 (1112)
T PRK00405 728 GYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGP----EEITRDIPNVSEEALRNLDESGIVRIGAEVKPGDILV 803 (1112)
T ss_pred ccCccceEEEEhhhhccCceEEEEEeeeeeEeeccCCCc----eeecccCCCCChHHhhccCCCCCccCccEecCCCEEE
Confidence 999999999999999999999999999998765433221 1222 4555555689999999999999999999999
Q ss_pred EEeecCC---------------------CcEEeeecCCCcceEEEEEEEecc-CCCC-----CCeEEEEEEeeecCCCCC
Q 001179 799 SIYDKTT---------------------NSWRTNSRKGSESVFVDYVAVDMK-NSKN-----LPQKANIRFRHTRNPIIG 851 (1131)
Q Consensus 799 ~~~~~~~---------------------~~~~~~~~~~~e~g~Vd~v~~~~~-~~~~-----~~~~~~i~~r~~R~p~iG 851 (1131)
||+++.. .++++++++.+|+|+||+|.++.+ ++++ ....|+|++|+.|+|+||
T Consensus 804 gk~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~s~~~~~~~~g~V~~v~~~~~~~~~~~~~~~~~~~vkv~ir~~R~p~iG 883 (1112)
T PRK00405 804 GKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTRIEQGDELPPGVNKLVKVYIAQKRKIQVG 883 (1112)
T ss_pred EEecCCCccccChhhhhhhhhhcccccccccceEEcCCCCCEEEEEEEEeeccccCCccCcCcceEEEEEEeeecccCcc
Confidence 9987632 235688999999999999999877 4432 146899999999999999
Q ss_pred cccccccCCcceeeeeecCCCCCccCCCCCcccEEeCCCCCCCccchhHhHHHHHhhhccccCceecccc-ccccccccC
Q 001179 852 DKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKGGSLHGKFMDATP-FANSVKKTN 930 (1131)
Q Consensus 852 DKf~sRHGqKGvvs~i~~~~dmPf~~~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tp-f~~~~~~~~ 930 (1131)
||||||||||||||+|||+|||||+ +||++|||||||||||||||||||+|+++||||++.|.+ |+|| |...
T Consensus 884 DKfasRHGqKGvis~i~~~eDMPf~-~~G~~pDiIiNPhg~PSRMtiGql~E~~~gk~~~~~g~~-~~tp~f~~~----- 956 (1112)
T PRK00405 884 DKMAGRHGNKGVVSRILPVEDMPYL-EDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIK-FATPVFDGA----- 956 (1112)
T ss_pred cchhhccCCceeEEeEeccCCCCcC-CCCCCCcEEECCCCCcccccHHHHHHHHhhHHHHhcCCe-EecCccCCc-----
Confidence 9999999999999999999999999 999999999999999999999999999999999999987 7888 5543
Q ss_pred CCCCCCCchhhHHHHHHHHHHCCCCCCCcEEEeeCCCCcEeeeeeeeeceeEEeeccccccceeeeecccccceeecccC
Q 001179 931 GDTGTDESKSLVDELGEMLRTCGFNYHGVEVLYSGVYGTELTCEIFIGPVYYQRLRHMVSDKFQVRSTGTMDQITRQPIK 1010 (1131)
Q Consensus 931 ~~~~~~~~~~~~~~~~~~l~~~g~~~~G~e~~y~g~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lTrQP~~ 1010 (1131)
.++++++.|.++||+++|+|.||||+||++|+++||+|++|||||+|||+||+|||++||++.|||||++
T Consensus 957 ----------~~~~~~~~l~~~g~~~~G~e~l~~G~tG~~~~~~if~G~~yy~rL~HmV~DK~haRs~Gp~~~lT~QP~~ 1026 (1112)
T PRK00405 957 ----------KEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLG 1026 (1112)
T ss_pred ----------cHHHHHHHHHHcCcCCCCCEEEECCCCCCCCcccEEEEehhheechhhhcchhhhcccCCccceeeCCCc
Confidence 5789999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccCceeeeehhhhHHhhhchHHHHHHhhccCCCccceeccccccccccccccccccccccccCCCCCCCCCCCeeec
Q 001179 1011 GRKRGGGIRFGEMERDSLLAHGAAYLLHDRLHTCSDYHVADVCSLCGSVLTATFIHPQKRAIREIGGLPPARAPKKVTCH 1090 (1131)
Q Consensus 1011 Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~Cg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~ 1090 (1131)
||+|+|||||||||||||+|||||++|+|||+.+||++..+.+ .+.|
T Consensus 1027 Grsr~GG~R~GEME~d~l~a~Gas~~L~Erl~~~SD~~~g~~~--------------------------------~~~~- 1073 (1112)
T PRK00405 1027 GKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTK--------------------------------VYEA- 1073 (1112)
T ss_pred ccccCCCeeeeeeehhhHhhhhhHHHHHHHhhccCccccccee--------------------------------EEEE-
Confidence 9999999999999999999999999999999999999874321 1345
Q ss_pred cCcCCCCcceecchHhHHHHHHHHHhCCceeEEEe
Q 001179 1091 ACQTSKGMETVAMPYVFRYLAAELAAMNIKITLQL 1125 (1131)
Q Consensus 1091 ~c~~~~~~~~v~iPy~~klL~~EL~sm~I~~~l~~ 1125 (1131)
.| ++.++.++.+|||||||+|||+||||++++.-
T Consensus 1074 ~~-~~~~i~~~~~p~~fklL~~EL~sm~i~~~~~~ 1107 (1112)
T PRK00405 1074 IV-KGENIPEPGIPESFNVLVKELQSLGLDVELLD 1107 (1112)
T ss_pred ee-cCCcccccCCChHHHHHHHHHHHCccceEEec
Confidence 56 57899999999999999999999999999984
No 9
>CHL00001 rpoB RNA polymerase beta subunit
Probab=100.00 E-value=8.6e-202 Score=1875.51 Aligned_cols=903 Identities=21% Similarity=0.289 Sum_probs=734.8
Q ss_pred CccccchhhHHHHHHHHHHHHHHhHHHHH-------------------------------HHHHHcCCeeeEEEEEEEEE
Q 001179 7 ADFEPLRELVRHHIESFDYMLDEGLSEMF-------------------------------DHCRQAKISYTGKLMADVEF 55 (1131)
Q Consensus 7 ~~~~~~~~Lv~~hi~SFn~Fi~~gl~~ii-------------------------------~ecR~r~~TYsa~l~v~v~~ 55 (1131)
.....+++|+++|++|||+||++||++++ +|||+|++||+|||+|++++
T Consensus 7 ~~~~~~P~Lv~~Q~~SF~~Fl~~gL~~i~~~~~pI~~~~~~~~~~~~~~~~~l~~P~~~p~ear~r~lTYsa~l~v~v~l 86 (1070)
T CHL00001 7 EGMSTIPGFNQIQFEGFCRFIDQGLTEELSKFPKIEDTDQEIEFQLFVETYQLVEPLIKERDAVYESLTYSSELYVPAGL 86 (1070)
T ss_pred CCccCCCCHHHHHHHHHHHHHHHhHHHHHHhcCCeECCCCCEEEEEEeCeEEECCCCCCHHHHHHhCCCCCceeEEEEEE
Confidence 34457999999999999999999999999 99999999999999999999
Q ss_pred EEecCCCceEEEEEeecccceeeccCcccCCCCChHHHHhhccccccCCcEEEEcCceeEEEEEEeccCCceEEEEeccc
Q 001179 56 QYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRSSF 135 (1131)
Q Consensus 56 ~~~~~~~~~~~~~v~iG~iPIMvkS~~C~L~~ls~~el~~~gE~~~D~GGYFIING~EKVIr~qi~~~~N~~~~~~r~s~ 135 (1131)
+.. .++.+.+++|++|+||+| |+||||||||+||||++|+++++|.++.....
T Consensus 87 ~~~-~~~~i~~~~V~iG~iPlM------------------------t~gG~FIING~ERVIVsQ~~rSpg~~~~~~~~-- 139 (1070)
T CHL00001 87 IWK-KSRDMQEQTVFIGNIPLM------------------------NSLGTFIINGIYRVVINQILRSPGIYYRSELD-- 139 (1070)
T ss_pred EEc-CceeEEEeEEEEecCCcc------------------------CCCcEEEEcCcEEEEEEEEeccCCEEEEEecC--
Confidence 743 234566789999999999 46999999999999999999999988776432
Q ss_pred cCCCcceeeEEEEEeeeecCCCceEEEEEEEeCCeEEEEEEEecccccccHhhHHHhccCCCHHHHHHhhccccchhhhc
Q 001179 136 RDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKK 215 (1131)
Q Consensus 136 ~~r~~~~t~~~i~iRs~~~~~~s~~~~l~~~~~g~~~l~~~~~k~~~~IPi~ilLkALg~~sD~eI~~~I~~~~~~~~~~ 215 (1131)
.+.+..|+ +.+++.+. .|+.+.++.++.+|+++...+ +||+++||||||+ +|+||++.++ ++
T Consensus 140 ~~~~~~y~---a~iis~rg----swl~~e~d~~~~i~vri~~~~---kiPi~ilLrALG~-sd~eIl~~~~--~~----- 201 (1070)
T CHL00001 140 HNGISVYT---GTIISDWG----GRLELEIDRKARIWARVSRKQ---KISILVLLSAMGL-NLREILDNVC--YP----- 201 (1070)
T ss_pred CCCceeEE---EEEEecCC----CceEEEEecCCeEEEEecCCC---cccHHHHHHHcCC-CHHHHHHHhC--cH-----
Confidence 12223344 44444332 378888898999999988764 7999999999999 6999999986 11
Q ss_pred ccCCCCChhHHHHHHHHHHHHHhccccCHHHHHHHHhhcccccccCCCCccHHHHHHHHHHhhhccc------CCCc--h
Q 001179 216 EKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVH------LNDN--N 287 (1131)
Q Consensus 216 ~~~~~~~~~~~~~~~~lL~~~~~~~i~t~~~AL~yIG~~~r~~~~~~~~~~~~e~g~~~L~~~ll~H------l~~~--~ 287 (1131)
+.+..+|.+..+.++.|+++||.||++++... +......+.|+.+|.+.+|+| +|.. +
T Consensus 202 -----------~~l~~~l~~~~~~~~~t~e~Al~~i~~~l~~r---~~~~~~~~~a~~~l~~~ff~~rY~Lg~vGr~~~n 267 (1070)
T CHL00001 202 -----------EIFLSFLNDKEKKKIGSKENAILEFYQQFACV---GGDPVFSESLCKELQKKFFQQRCELGRIGRRNMN 267 (1070)
T ss_pred -----------HHHHHHHHHHhhccccCHHHHHHHHHHhhccC---CCCcchHHHHHHHHHHHhccccccccccCchhhh
Confidence 22333343333456889999999999987321 244556788999999999999 8742 2
Q ss_pred --------hhHHHH-----HHHHHHHHhhcCCCCCCCCcccccccEeccchhhHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 001179 288 --------DKFNLL-----IFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENN 354 (1131)
Q Consensus 288 --------~K~~~L-----~~MvrkLl~l~~G~~~~DD~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~~~~l~~~~~~~ 354 (1131)
.|+.+| ++|+++|+.+..|....||+|||+||||+++|+||+.+|+..|+++.+.++..+.+.+.+
T Consensus 268 ~kl~~~~~~~~~~L~~~Di~~~i~~Ll~l~~G~~~~DDiDhLgNKRvr~vGeLL~~qfr~~l~r~~r~ik~~m~~~~~~- 346 (1070)
T CHL00001 268 RKLNLDIPENNTFLLPQDVLAAADYLIGMKFGMGTLDDIDHLKNKRIRSVADLLQDQFGLALNRLENAVRGTICGAIRR- 346 (1070)
T ss_pred hhhcccccccceEecHHHHHHHHHHHHHhhcCCCCccchhHHhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-
Confidence 344545 999999999999999999999999999999999999999999888888887777654433
Q ss_pred CCccccchhHHHHHHHhcCCCcchHHHHHHHhcccCcccccccccccccceEEEccccchHHHhhhccccc---cCCccc
Q 001179 355 GKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVH---RGASFA 431 (1131)
Q Consensus 355 ~~~~~~~~~~~~~~~i~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~~GvsqvleRln~~~~lSh~Rrv~---rg~~~~ 431 (1131)
.+.+ .++.+++ ++.||++|++||+| +||||.++|+|+++.|||+||++ +|+..+
T Consensus 347 ~~~~------~~~~lin---~~~It~~ik~ff~t--------------s~LSQflDqtNpLseltHkRRlsslGpgglsr 403 (1070)
T CHL00001 347 KLIP------TPQNLVT---STPLTTTYESFFGS--------------HPLSQFLDQTNPLTEIVHGRKLSSLGPGGLTG 403 (1070)
T ss_pred cccC------CHHHhhC---cchHHHHHHhhhcC--------------CcceeeeccCCHHHhhhhhhcccccCCCCccc
Confidence 2211 2455663 46899999999997 69999999999999999999999 455667
Q ss_pred cccccccccccCCcccccccCCCCCCccccccccccceEEEeeccCCCCcccccchhhhHHHHHHHhcCceecCcccccC
Q 001179 432 GLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKS 511 (1131)
Q Consensus 432 ~~K~t~~R~Lhps~wGfICPveTPEG~~CGLvk~LA~~a~It~~~~~~~~~~~~~~~~~~i~~~L~~lG~~~~~~~~~~~ 511 (1131)
+++.++||+|||||||||||+|||||++||||+|||++|+|+.....++ ||+.+ +...+...+ ..++..
T Consensus 404 ~~a~fevRdvHpShyGRICPIETPEG~NiGLI~sLA~~A~In~~Gfiet---P~~~v-------~~~~~~~~i-~ylsa~ 472 (1070)
T CHL00001 404 RTASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIGHWGSLES---PFYEI-------SERSKEERM-VYLSPS 472 (1070)
T ss_pred cccCCcccccCccccccccCCCCCCcccccchhhhhhhcccccCCCccc---ceeee-------cccccccee-EEcccc
Confidence 7777899999999999999999999999999999999999996555553 23333 323333322 111111
Q ss_pred CCCCceEEEECCEEEeeecCchHHHHHHHHHHHHhhcCCCCCCCceEEEEeCCCCCCCCeEEEEcCCCcceeeEEEecCC
Q 001179 512 GPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLP 591 (1131)
Q Consensus 512 ~~~~~~~V~lnG~~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~~~~~~~~~~i~i~td~GRl~RPv~~~~~~ 591 (1131)
..+.+.|+ ||.|+|..... +. .+ .+ |+. .
T Consensus 473 -ee~~~~Ia-~g~~~~~~~~~-------------------~~--~~--~~----------------------~~r---~- 501 (1070)
T CHL00001 473 -EDEYYMIA-AGNSLALNQGI-------------------QE--EQ--VV----------------------PAR---Y- 501 (1070)
T ss_pred -ccCceEEE-eCceeeccCCc-------------------cc--cc--ee----------------------EEE---e-
Confidence 24457777 89888732100 00 00 00 010 0
Q ss_pred CCCCcceeeecccceeeeeeecCCCCCCCCCCCCceeEEeecCCCcccceeccccCCCCCCCcccccccccccccccccc
Q 001179 592 SEESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSV 671 (1131)
Q Consensus 592 ~~~~g~iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~P~~ilsv~AslIPF~~HNqspRn~yqc~M~KQAiG~~~ 671 (1131)
-++++.||+. + .||+||+|.+|+|++||||||+||||||||+|||||||||||+..
T Consensus 502 -------------~~e~~~i~~~--~---------i~~~dIsP~qi~svaasLIPFleHndanRalmgsnMqrQAvpll~ 557 (1070)
T CHL00001 502 -------------RQEFLTIAWE--Q---------IHLRSIFPFQYFSIGASLIPFLEHNDANRALMGSNMQRQAVPLSR 557 (1070)
T ss_pred -------------cCeEEEEchH--H---------CcEEeeChhhhhhhhhhcCCCccccCcchhhhhhccchhcccccc
Confidence 0224566665 2 589999999999999999999999999999999999999999987
Q ss_pred ce---------EEEec-----------------c-----------c-ceeeecC---------CCcceeecCcccccC--
Q 001179 672 QA---------LKFRA-----------------D-----------Q-KLYHLQT---------PQTPIVRTNTYTKYG-- 702 (1131)
Q Consensus 672 ~n---------~~~R~-----------------D-----------~-~~y~L~y---------pQ~PLV~t~~~~~~~-- 702 (1131)
.+ ...|. | + ..|.+.| ||||||+++.+...|
T Consensus 558 ~~~p~VgTG~E~~~~~ds~~~i~a~~~G~V~~vd~~~I~i~~~~~~~~y~l~~y~rsnq~t~~~QkPlV~~g~~v~~g~~ 637 (1070)
T CHL00001 558 SEKCIVGTGLERQVALDSGVVAIAEHEGKIIYTDTDKIILSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCVKKGQI 637 (1070)
T ss_pred CCCCEeecCcchhhhhcccceeEEccCCEEEEEeCCEEEEEcCCCeEEEEeeceeccCCCcccccCCEEecCCEEccCCE
Confidence 77 55565 5 4 3456678 999999999655543
Q ss_pred --------cccCCCCcceEEEEEeccCCCCCceEEeeccccccCceeeeEEEEEEEEecccCCCccccccccc--cCCCC
Q 001179 703 --------IDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFR--RNKDA 772 (1131)
Q Consensus 703 --------~~~~~~G~N~iVAv~~y~Gyn~EDaiiink~s~~rG~~~~~~y~~~~~~~~~~~~~~~~~~~~f~--~~~~~ 772 (1131)
.+++|+|+|++||||||+||||||||||||++++||+|++.+|++|++++...+... +.+. .|+.+
T Consensus 638 ladg~~~~~gel~~G~N~~VA~m~~~GYn~EDAiiin~~~v~~g~~~s~~~~~~~~~~~~~~~g~----e~i~~~~p~~~ 713 (1070)
T CHL00001 638 LADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQGP----ERITKEIPHLE 713 (1070)
T ss_pred eccChhhccccccCCccceeeeeeccccccchhhhhhhhhhcCCceEEEEEeeeeEEEeccCCCc----ceEeccCCCCc
Confidence 799999999999999999999999999999999999999999999998876544222 3333 36666
Q ss_pred hhhhcccCCCCCcccCcEEcCCCCeeEEeecCC-----------------------CcEEeeecCCCcceEEEEEEEecc
Q 001179 773 KSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTT-----------------------NSWRTNSRKGSESVFVDYVAVDMK 829 (1131)
Q Consensus 773 ~~~~~~Ld~dGi~~~G~~v~~gdil~~~~~~~~-----------------------~~~~~~~~~~~e~g~Vd~v~~~~~ 829 (1131)
+..+++||+||+|++|+.|++||||+||++|+. .++.+++++.+++|+|++|.++..
T Consensus 714 ~~~~~~Ld~dGi~~~G~~v~~gDilvgK~~p~~~~~~~~~~~~~~~~~if~~~~~~~~d~sl~~~~~~~g~V~~v~~~~~ 793 (1070)
T CHL00001 714 AHLLRNLDKNGIVMLGSWVETGDILVGKLTPQEAEESSYAPEGRLLRAIFGIQVSTSKETCLKLPIGGRGRVIDVRWIQK 793 (1070)
T ss_pred hhhhhccCCCCCccCCcEecCCCEEEEEecCCcccccccCcchhhhhhhhccccCcceeCeEECCCCCceEEEEEEEEec
Confidence 667899999999999999999999999987741 235688999999999999999975
Q ss_pred CCC--CCCeEEEEEEeeecCCCCCcccccccCCcceeeeeecCCCCCccCCCCCcccEEeCCCCCCCccchhHhHHHHHh
Q 001179 830 NSK--NLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAA 907 (1131)
Q Consensus 830 ~~~--~~~~~~~i~~r~~R~p~iGDKf~sRHGqKGvvs~i~~~~dmPf~~~~G~~pDiIiNPh~~PSRMtiGql~E~~~g 907 (1131)
++. +....|+|++|+.|+|+||||||||||||||||+|||+|||||+ +||++|||||||||||||||||||+|+++|
T Consensus 794 ~~~~~~~~~~vkv~i~~~R~~~vGDK~asRHGqKGvvs~i~~~eDMPf~-~dG~~pDiIlNP~gvPSRMtiGqllE~~~G 872 (1070)
T CHL00001 794 KGGSSYNPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYL-QDGTPVDMVLNPLGVPSRMNVGQIFECLLG 872 (1070)
T ss_pred ccCCCCCcEEEEEEEEEEecCCCCcccccccCCcceEeeeecccCCCcc-cCCCCCceeeccccccccccHHHHHHHHhH
Confidence 321 24679999999999999999999999999999999999999999 999999999999999999999999999999
Q ss_pred hhccccCceeccccccccccccCCCCCCCCchhhHHHHHHHHHHCCC----------CCCCcEEEeeCCCCcEeeeeeee
Q 001179 908 KGGSLHGKFMDATPFANSVKKTNGDTGTDESKSLVDELGEMLRTCGF----------NYHGVEVLYSGVYGTELTCEIFI 977 (1131)
Q Consensus 908 k~~~~~g~~~d~tpf~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~----------~~~G~e~~y~g~tG~~~~~~if~ 977 (1131)
|||++.|.++|+|||+..+..+ ..-......|.++|| +++|+|.||||+||++|+++||+
T Consensus 873 ~a~~~~g~~~~~~pf~~~~~~~----------~~~~~~~~~l~~~~~~~~~~~~~~~~~~Gk~~l~dG~TG~~~~~~i~v 942 (1070)
T CHL00001 873 LAGDLLNRHYRIAPFDERYEQE----------ASRKLVFSELYEASKQTANPWVFEPEYPGKSRLFDGRTGDPFEQPVTI 942 (1070)
T ss_pred HHHhhcCceeeeccCCCcchhh----------hhhhhhhHHHHHHHHhcCCceeccCCCCCeEEEEcCCCCCCccceEEE
Confidence 9999999999999998752110 000112245566555 45599999999999999999999
Q ss_pred eceeEEeeccccccceeeeecccccceeecccCcccccCceeeeehhhhHHhhhchHHHHHHhhccCCCccceecccccc
Q 001179 978 GPVYYQRLRHMVSDKFQVRSTGTMDQITRQPIKGRKRGGGIRFGEMERDSLLAHGAAYLLHDRLHTCSDYHVADVCSLCG 1057 (1131)
Q Consensus 978 G~~yy~rL~Hmv~DK~~~R~~Gp~~~lTrQP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~Cg 1057 (1131)
|++|||||+|||+||+||||+|||++|||||++||+|+|||||||||||||+|||||++|+|||+.+||++.++. ..
T Consensus 943 G~~Yy~kL~HmV~DKihaRs~Gp~~~lT~QP~~Grsr~GG~RfGEME~~al~a~GAs~~L~E~L~~~SD~~~~r~-~~-- 1019 (1070)
T CHL00001 943 GKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQ-EV-- 1019 (1070)
T ss_pred EecceeEchhhccccceeeccCCCcccccCCCCcccCCCCeeeecchHHHHHhhhHHHHHHHHHhccCccHHHHH-HH--
Confidence 999999999999999999999999999999999999999999999999999999999999999999999998872 11
Q ss_pred ccccccccccccccccccCCCCCCCCCCCeeeccCcCCCCcce-ecchHhHHHHHHHHHhCCceeEEEecc
Q 001179 1058 SVLTATFIHPQKRAIREIGGLPPARAPKKVTCHACQTSKGMET-VAMPYVFRYLAAELAAMNIKITLQLGD 1127 (1131)
Q Consensus 1058 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~-v~iPy~~klL~~EL~sm~I~~~l~~~~ 1127 (1131)
+..|.++.++.+ +.+||+||+|++||+|||+++.+..-+
T Consensus 1020 -------------------------------~~~i~~g~~~~~~~~~pesfk~l~~El~~l~l~i~~~~~~ 1059 (1070)
T CHL00001 1020 -------------------------------LGAIITGGTIPKPEDAPESFRLLVRELRSLALELNHFLVS 1059 (1070)
T ss_pred -------------------------------HHhhhcCCcccCCCCCCchhhHHHHHHHhCccceEEEEEe
Confidence 223445667777 799999999999999999999986543
No 10
>CHL00207 rpoB RNA polymerase beta subunit; Provisional
Probab=100.00 E-value=1.1e-190 Score=1764.81 Aligned_cols=894 Identities=23% Similarity=0.334 Sum_probs=716.9
Q ss_pred ccccchhhHHHHHHHHHHHHHHhHHHHH-------------------------------HHHHHcCCeeeEEEEEEEEEE
Q 001179 8 DFEPLRELVRHHIESFDYMLDEGLSEMF-------------------------------DHCRQAKISYTGKLMADVEFQ 56 (1131)
Q Consensus 8 ~~~~~~~Lv~~hi~SFn~Fi~~gl~~ii-------------------------------~ecR~r~~TYsa~l~v~v~~~ 56 (1131)
+...+++|++.|++||+||+++||++++ .|||+|++||++||+|+++++
T Consensus 3 ~~~~~Pdll~iQ~~SF~~FL~~GL~~~~~~~~pI~~~~~~~~l~~~~~~y~l~~P~~~~~Ea~~r~~TYsa~l~v~~~l~ 82 (1077)
T CHL00207 3 MNFALPDFLEIQRTSFCWFLNEGLNEELNIFSKIFDYTGNLELLLFGKNYKLKYPKYNLLSAKSYDSNYSIQIYLPLKFI 82 (1077)
T ss_pred cccCCCCHHHHHHHHHHHHHHHHHHHHHHhcCCeECCCCCEEEEEecceEEEcCCCCCHHHHHHhCCccceeEEEEEEEE
Confidence 3456899999999999999999999998 999999999999999999997
Q ss_pred EecCCCceEEEEEeecccceeeccCcccCCCCChHHHHhhccccccCCcEEEEcCceeEEEEEEeccCCceEEEEecccc
Q 001179 57 YLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRSSFR 136 (1131)
Q Consensus 57 ~~~~~~~~~~~~v~iG~iPIMvkS~~C~L~~ls~~el~~~gE~~~D~GGYFIING~EKVIr~qi~~~~N~~~~~~r~s~~ 136 (1131)
.. +++++++++|++|+||+|+. +|||||||+||||++|+.++++..+..... +
T Consensus 83 ~~-~~~~i~~~~V~lG~iPlMT~------------------------~GtFIING~ERViVsQl~RSPGiyf~~~~~--k 135 (1077)
T CHL00207 83 NL-KTNKIKFINYLIGNLPKMTQ------------------------RGTFIINGLERVIVSQIIRSPGIYFKKEIK--K 135 (1077)
T ss_pred Ec-CCceEEEEEEEEeccCccCC------------------------CCEEEEcCceeEEEEEeccCCeEEEEEecC--c
Confidence 54 34567789999999999976 999999999999999999888854433221 2
Q ss_pred CCCcceeeEEEEEeeeecCCCceEEEEEEEeCCeEEEEEEEecccccccHhhHHHhccCCCHHHHHHhhccccchhhhcc
Q 001179 137 DRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKKE 216 (1131)
Q Consensus 137 ~r~~~~t~~~i~iRs~~~~~~s~~~~l~~~~~g~~~l~~~~~k~~~~IPi~ilLkALg~~sD~eI~~~I~~~~~~~~~~~ 216 (1131)
+.+..|+...++.|+. |+.+++++++.+|+++..++ +||+++||||||+ ||+||++.+.. .
T Consensus 136 ~~~~~y~a~IIp~rGs-------wl~~e~d~k~~i~vridr~r---Kipit~lLrALGl-s~~eIl~~~~~--~------ 196 (1077)
T CHL00207 136 NSNKIYSATLIPNRGS-------WIKFELDKNKEIWIRIDKNR---KKPLIIFLKALGL-TDQDIYSRLTK--S------ 196 (1077)
T ss_pred CCceEEEEEEEcCCCc-------eEEEEEcCCCeEEEEecCCc---eeeHHHHHHHhCC-CHHHHHHHHhc--c------
Confidence 2334688888887764 99999999999999998655 7999999999999 99999998862 0
Q ss_pred cCCCCChhHHHHHHHHHHHHHhccccCHHHHHHHHhhcccccccCCCCccHHHHHHHHH-------HhhhcccCCC----
Q 001179 217 KGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVI-------RDYIFVHLND---- 285 (1131)
Q Consensus 217 ~~~~~~~~~~~~~~~lL~~~~~~~i~t~~~AL~yIG~~~r~~~~~~~~~~~~e~g~~~L-------~~~ll~Hl~~---- 285 (1131)
.+. +.+..++ ...+..++++|+.+|+++++.. .....+.++.+| ++|.|+|+|.
T Consensus 197 ----~~~---~~~~~~l---~~~~~~~~e~Al~~Iy~~lrp~-----~~~~~~~a~~~l~~~ff~~~rYdLg~vGR~klN 261 (1077)
T CHL00207 197 ----EFL---KKLKPIL---LNSNSYTNEEILLEIYKNLSPI-----EPATVNDANQNLFSRFFDPKNYDLGKVGRYKIN 261 (1077)
T ss_pred ----chH---HHHHHHH---hccCcccHHHHHHHHHHhcCCC-----CCccHHHHHHHHHHHhcChhcccccccchhhhh
Confidence 011 1122222 2345678999999999998742 223344455555 3455667764
Q ss_pred -----------chhhHHHHHHHHHHHHhhcCCCCCCCCcccccccEeccchhhHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 001179 286 -----------NNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENN 354 (1131)
Q Consensus 286 -----------~~~K~~~L~~MvrkLl~l~~G~~~~DD~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~~~~l~~~~~~~ 354 (1131)
...++.+++.|+++|+.+..|....||+|||+||||+++|+||+++|+..|.++ .+.+++++...
T Consensus 262 ~kl~~~~~~~~~~l~~~Dil~~i~~Li~l~~g~~~~DDiDHL~NRRvrsvGELlq~qfr~gl~rl----er~ike~m~~~ 337 (1077)
T CHL00207 262 NKLNLNIPERVRNLTYEDILSIIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIGLKRL----ERILRNRMTIC 337 (1077)
T ss_pred hhccCCcCccCceecHHHHHHHHHHHHHhhcCCCcccchhhhhcccccchhHHHHHHHHHHHHHH----HHHHHHHhhhc
Confidence 234566799999999999999999999999999999999999999999855554 45555554431
Q ss_pred CCccccchhHHHHHHHhcCCCcchHHHHHHHhcccCcccccccccccccceEEEccccchHHHhhhccccc---cCCccc
Q 001179 355 GKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVH---RGASFA 431 (1131)
Q Consensus 355 ~~~~~~~~~~~~~~~i~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~~GvsqvleRln~~~~lSh~Rrv~---rg~~~~ 431 (1131)
. . + ...++.++ ++++||+.|++||+++ ++||.++++|+++.|+|+||++ +|++.+
T Consensus 338 ~-~---~-~~tp~~li---n~k~lt~~ikeFFgss--------------~LSQfmDQtNpLselTHKRRlsaLGpGGLsR 395 (1077)
T CHL00207 338 D-I---D-SLSKFNLI---NPKPLIALIREFFGSS--------------QLSQYMDQTNPLSELTHKRRISILGPGGLDK 395 (1077)
T ss_pred c-c---c-cCChhhcc---cchhHHHHHHHhhccC--------------CccceecccChHHhhhccceeeccCCCcccc
Confidence 1 0 0 11244555 4569999999999864 4555556666666699999999 688999
Q ss_pred cccccccccccCCcccccccCCCCCCccccccccccceEEEeeccCCCCcccccchhhhHHHHHHHhcCceecCcccccC
Q 001179 432 GLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKS 511 (1131)
Q Consensus 432 ~~K~t~~R~Lhps~wGfICPveTPEG~~CGLvk~LA~~a~It~~~~~~~~~~~~~~~~~~i~~~L~~lG~~~~~~~~~~~ 511 (1131)
+++++++|++||||||+|||+|||||++||||++||++|+|+ ++|++.+ |
T Consensus 396 ~ra~fevRdvH~thyGRiCPIETPEG~n~Gli~~la~~~~in------------------------~~Gfiet-P----- 445 (1077)
T CHL00207 396 DRISFAVRDIHPSHYGRICPIETPEGPNCGLIGSLATNARIN------------------------KFGFIET-P----- 445 (1077)
T ss_pred cccCCcccccCccccccccCCCCCCCcccccccchhhhcccc------------------------CCCceeC-c-----
Confidence 999999999999999999999999999999999999999998 4677755 3
Q ss_pred CCCCceEEEECCEEEeeecCchHHHHHHHHHHHHhhcCCCCCCCceEEEEeCCCCCCCCeEEEEcCCCcceeeEEEecCC
Q 001179 512 GPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLP 591 (1131)
Q Consensus 512 ~~~~~~~V~lnG~~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~~~~~~~~~~i~i~td~GRl~RPv~~~~~~ 591 (1131)
|....||++.- .+ .+-++- .+.|-.|+-+..+ +. ..+.|.+.-+.+.++..
T Consensus 446 -----y~~v~~g~v~~-~~---------~i~yls--------a~~e~~~~Ia~~~-----~~-~~~~~~~~~~~v~~r~~ 496 (1077)
T CHL00207 446 -----FYKVINGKVKK-FG---------NPIYLT--------ADSEDLYRIAPND-----IN-LNKNNYFKKNIIPVRYK 496 (1077)
T ss_pred -----eEEEEcCcccc-cC---------ceeecC--------hHHhcCcEEEecC-----cc-CCCCCcccCCEEEEEEC
Confidence 55556776421 00 001111 1112222211111 11 23345555555544432
Q ss_pred CCCCcceeeecccceeeeeeecCCCCCCCCCCCCceeEEeecCCCcccceeccccCCCCCCCccccccccccccccccc-
Q 001179 592 SEESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFS- 670 (1131)
Q Consensus 592 ~~~~g~iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~P~~ilsv~AslIPF~~HNqspRn~yqc~M~KQAiG~~- 670 (1131)
++|..++. ++ .++++++|.|++|++||||||.+||||+|++|||||++|||.+.
T Consensus 497 --------------~ef~~~~~--~~---------v~~~~vsp~Q~~SvaasLIPFLehdDanRaLMGsnMqrQaVPll~ 551 (1077)
T CHL00207 497 --------------QEFKTVNP--SK---------VDFIAISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLY 551 (1077)
T ss_pred --------------CcEEEECh--HH---------ceEEEeCcchhcchhhhcCCcccccccchhhhhhccccccccccc
Confidence 22222222 11 68999999999999999999999999999999999999998531
Q ss_pred ----------------------------------cceEEEecc---cceeeec----------CCCcceeecCcccccC-
Q 001179 671 ----------------------------------VQALKFRAD---QKLYHLQ----------TPQTPIVRTNTYTKYG- 702 (1131)
Q Consensus 671 ----------------------------------~~n~~~R~D---~~~y~L~----------ypQ~PLV~t~~~~~~~- 702 (1131)
+..+..|.+ ...|.|. ..|||+|+.+.....|
T Consensus 552 ~e~p~VgTg~e~~~a~ds~~~i~a~~~G~v~~v~~~~I~i~~~~~~~~~y~l~~~~rsNq~t~i~qrp~V~~G~~v~~G~ 631 (1077)
T CHL00207 552 PEKPIVGTGYEKQIALDSGMTIISLTEGIVVSVSAYKIIIQDDNNRYIHYYLQKYQRSNQNTCINYRPIVWVGEKINIGQ 631 (1077)
T ss_pred cCCCeEECCcchHhhhhcchheEeccCcEEEEecCcEEEEEeCCCceeEEEeccccccccCceeecccccCCCCEEecCC
Confidence 122233332 2346665 4899999999886655
Q ss_pred ---------cccCCCCcceEEEEEeccCCCCCceEEeeccccccCceeeeEEEEEEEEecccCCCccccccccc--cCCC
Q 001179 703 ---------IDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFR--RNKD 771 (1131)
Q Consensus 703 ---------~~~~~~G~N~iVAv~~y~Gyn~EDaiiink~s~~rG~~~~~~y~~~~~~~~~~~~~~~~~~~~f~--~~~~ 771 (1131)
.+|+|+|+|++||||||+||||||||||||++++||+|++.+|++|++++...+... +.|. .|+.
T Consensus 632 iladg~~~~~~el~lG~N~lVA~m~y~GYN~EDAiiink~~v~rg~f~Si~~~~~~~e~~~~~~g~----e~i~~~~p~~ 707 (1077)
T CHL00207 632 ILADGSDIDNSELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEKYEIELRQTKLGS----EEITRNIPNV 707 (1077)
T ss_pred EEecchhccCCcccCCcccEEEEEeeeccccchhhhhhhhhhcCCceEEEEEEEeeeEEeecCCCc----eEEeccCCCC
Confidence 699999999999999999999999999999999999999999999998876544322 2333 5666
Q ss_pred ChhhhcccCCCCCcccCcEEcCCCCeeEEeecCC---------------------CcEEeeecCCCcceEEEEEEEeccC
Q 001179 772 AKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTT---------------------NSWRTNSRKGSESVFVDYVAVDMKN 830 (1131)
Q Consensus 772 ~~~~~~~Ld~dGi~~~G~~v~~gdil~~~~~~~~---------------------~~~~~~~~~~~e~g~Vd~v~~~~~~ 830 (1131)
+...+++||+||||++|+.|++||||+||++|+. .++.+++++.+++|+|++|.++.++
T Consensus 708 ~~~~~~~LD~dGiv~iG~~V~~gDilvgK~tp~~~~~~~~~~~ll~~i~~~~~~~~kd~sl~~~~~~~g~V~~V~~~~~~ 787 (1077)
T CHL00207 708 SEYSLKNLDENGIISIGSKVLAGDILVGKITPKGESDQLPEGKLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRS 787 (1077)
T ss_pred ChHHhhccCccCCCcCCcEeCCCCEEEEEecCccccccChhhhhhhhhhccCCCcceEeEEEcCCCCcEEEEEEEEEecC
Confidence 6667899999999999999999999999987631 2567899999999999999999864
Q ss_pred CCCCC-----eEEEEEEeeecCCCCCcccccccCCcceeeeeecCCCCCccCCCCCcccEEeCCCCCCCccchhHhHHHH
Q 001179 831 SKNLP-----QKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESV 905 (1131)
Q Consensus 831 ~~~~~-----~~~~i~~r~~R~p~iGDKf~sRHGqKGvvs~i~~~~dmPf~~~~G~~pDiIiNPh~~PSRMtiGql~E~~ 905 (1131)
++++. ..|+|++|+.|+|+||||||||||||||||+|||+|||||+ +||++|||||||||||||||||||+|++
T Consensus 788 ~~~~~~~~~~~~vkv~i~~~R~p~vGDKfasRHGqKGVvs~i~p~eDMPf~-~dG~~pDiIlNPhg~PSRMtiGqllE~~ 866 (1077)
T CHL00207 788 KGDELKFGYYLKIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYL-PDGTPPDIILNPLGVPSRMNVGQLFECL 866 (1077)
T ss_pred CCCcccccccEEEEEEEEEEecCCcccccccccCCceeEEeeeccCCCCcc-CCCCCccEEECCccccccccHHHHHHHH
Confidence 43322 46999999999999999999999999999999999999999 9999999999999999999999999999
Q ss_pred HhhhccccCceeccccccccccccCCCCCCCCchhhHHHHHHHHH-----HC----------CCCCCCcEEEeeCCCCcE
Q 001179 906 AAKGGSLHGKFMDATPFANSVKKTNGDTGTDESKSLVDELGEMLR-----TC----------GFNYHGVEVLYSGVYGTE 970 (1131)
Q Consensus 906 ~gk~~~~~g~~~d~tpf~~~~~~~~~~~~~~~~~~~~~~~~~~l~-----~~----------g~~~~G~e~~y~g~tG~~ 970 (1131)
+||||++.|..+++|||++. ..+++.+.|. ++ +|+++|++.||||+||++
T Consensus 867 lGka~~~l~~~~~~tpF~~~---------------~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~Gk~~lydG~TGe~ 931 (1077)
T CHL00207 867 LGLAGDNLNKRFKILPFDEM---------------YGSEYSRILINNKLNQASIKNNEYWLFNSYHPGKMVLRDGRTGYK 931 (1077)
T ss_pred HHHHHHhcCCcEeeccCCCC---------------cHHHHHHHHHhhhhhhccchhccccccCCCCCCCEEEECCCCCCC
Confidence 99999988888899999875 1333334433 33 377889999999999999
Q ss_pred eeeeeeeeceeEEeeccccccceeeeecccccceeecccCcccccCceeeeehhhhHHhhhchHHHHHHhhccCCCccce
Q 001179 971 LTCEIFIGPVYYQRLRHMVSDKFQVRSTGTMDQITRQPIKGRKRGGGIRFGEMERDSLLAHGAAYLLHDRLHTCSDYHVA 1050 (1131)
Q Consensus 971 ~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lTrQP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~ 1050 (1131)
|+++||+|++|||||+|||+||+||||+|||+.|||||++||||+|||||||||||||+|||||++|+|||+.+||++.+
T Consensus 932 ~~~~i~vG~~Yy~kL~HmV~DKihaRs~Gp~s~lTqQP~~Grsr~GG~RfGEME~~aL~a~GAa~~L~E~L~~kSD~~~~ 1011 (1077)
T CHL00207 932 FKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSDDMQG 1011 (1077)
T ss_pred ccCceEEEecceeEchhhccccceeeccCCCcccccCCCCccccCCCeeeecccHHHHHhhhhHHHHHHHhhcCCcccee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999996
Q ss_pred eccccccccccccccccccccccccCCCCCCCCCCCeeeccCcCCCCcceecchHhHHHHHHHHHhCCceeEEEec
Q 001179 1051 DVCSLCGSVLTATFIHPQKRAIREIGGLPPARAPKKVTCHACQTSKGMETVAMPYVFRYLAAELAAMNIKITLQLG 1126 (1131)
Q Consensus 1051 ~vC~~Cg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~v~iPy~~klL~~EL~sm~I~~~l~~~ 1126 (1131)
+. .+|..|.++.++.++.+|||||+|+|||+||||.+.+.-.
T Consensus 1012 r~----------------------------------~~~~~~~~~~~i~~~~~P~sfklL~~EL~sl~i~~~~~~~ 1053 (1077)
T CHL00207 1012 RN----------------------------------ETLNAIVKGQPIPKPGTPESFKVLMRELQSLGLDIEAYKI 1053 (1077)
T ss_pred hH----------------------------------HHHHhhhCCCeecCCCCCchHHHHHHHHHHCCcCcEeccc
Confidence 42 3699999999999999999999999999999999998643
No 11
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=100.00 E-value=1e-176 Score=1686.19 Aligned_cols=936 Identities=22% Similarity=0.300 Sum_probs=728.3
Q ss_pred ccchhhHHHHHHHHHHHHH------HhHHHHH-----------------------------HHHHHcCCeeeEEEEEEEE
Q 001179 10 EPLRELVRHHIESFDYMLD------EGLSEMF-----------------------------DHCRQAKISYTGKLMADVE 54 (1131)
Q Consensus 10 ~~~~~Lv~~hi~SFn~Fi~------~gl~~ii-----------------------------~ecR~r~~TYsa~l~v~v~ 54 (1131)
..+|+|++.|.+||++|++ +||++++ .||++|++||++||+|+++
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 3699999999999999998 7999998 9999999999999999999
Q ss_pred EEE---ecCCC------ceEEEEEeecccceeeccCcccCCCCChHHHHhhccccccCCcEEEEcCceeEEEEEEeccCC
Q 001179 55 FQY---LDAGS------PVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQN 125 (1131)
Q Consensus 55 ~~~---~~~~~------~~~~~~v~iG~iPIMvkS~~C~L~~ls~~el~~~gE~~~D~GGYFIING~EKVIr~qi~~~~N 125 (1131)
+++ +.+++ ++++++|++|+||+|+. .|+|||||+||||++|++++|+
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 46789999999999997 8999999999999999999999
Q ss_pred ceEEEEeccccCCCcceeeEEEEEeeeecCCCceEEEEEEEeCCeEEEEEEEecccccccHhhHHHhccCCCHHHHHHhh
Q 001179 126 YPMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHL 205 (1131)
Q Consensus 126 ~~~~~~r~s~~~r~~~~t~~~i~iRs~~~~~~s~~~~l~~~~~g~~~l~~~~~k~~~~IPi~ilLkALg~~sD~eI~~~I 205 (1131)
..|.....+..+.+..|+...|+.|+. |+.++++.++.+|+++..+| +||+++||||||+ |++||++.+
T Consensus 158 VyF~~~~~k~~s~k~lysa~IIP~RGs-------WLefE~D~kd~l~vrIDrkr---Kipit~lLrAlG~-s~edIl~~f 226 (2890)
T PRK09603 158 VIFKEEESSTSLNKLIYTGQIIPDRGS-------WLYFEYDSKDVLYARINKRR---KVPVTILFRAMDY-QKQDIIKMF 226 (2890)
T ss_pred eEEeeccCcCCCCceeEEEEEecCCcc-------eEEEEEcCCCeEEEEEcCcc---eecHHHHHHHhCC-CHHHHHHHh
Confidence 655443322223345599999998886 99999999999999999876 7999999999999 899999987
Q ss_pred cccc-------------ch-hhh-------------------------------c-----ccCC------------CCC-
Q 001179 206 TCCY-------------DE-KYK-------------------------------K-----EKGA------------VGS- 222 (1131)
Q Consensus 206 ~~~~-------------~~-~~~-------------------------------~-----~~~~------------~~~- 222 (1131)
.... .+ ... . +... ..+
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 5100 00 000 0 0000 000
Q ss_pred -hhHH----HHHHHHHHHHHhcc--------------------------------------ccCHHHHHHHHhhccccc-
Q 001179 223 -PLVS----ERVKIILAEVQDLS--------------------------------------LTTRLQCLQHIGEHFQPV- 258 (1131)
Q Consensus 223 -~~~~----~~~~~lL~~~~~~~--------------------------------------i~t~~~AL~yIG~~~r~~- 258 (1131)
..+. ..-+..++.+.+.+ ..++++|+..|.+++|+.
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 0000 00011122211110 114588999999988742
Q ss_pred --------------ccCCCCccHHHHHHHHHHhhhcccCCC--chhhHHHHHHHHHHHHhhcCCCCCCCCcccccccEec
Q 001179 259 --------------IDGLQSESYYAVAETVIRDYIFVHLND--NNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEIL 322 (1131)
Q Consensus 259 --------------~~~~~~~~~~e~g~~~L~~~ll~Hl~~--~~~K~~~L~~MvrkLl~l~~G~~~~DD~D~l~NkRv~ 322 (1131)
++.|.+++..++||..||+.|-.++.. .......++..+++|+.+..|....||+|||+||||+
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 122444555556666666665443221 1111235789999999999999999999999999999
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccccchhHHHHHHHhcCCCcchHHHHHHHhcccCcccccccccccc
Q 001179 323 LPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQR 402 (1131)
Q Consensus 323 l~G~Ll~~lf~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~ 402 (1131)
++|+||+.+|+.. +.+|.+.++++++......+ ...++.++ +++++++.+++||+|++++ |+|+|+
T Consensus 467 ~vGELl~~qfr~g----l~rler~irerm~~~~~~~~---~~~p~~li---n~k~i~~~ikeFFgssqLS----QfmDQt 532 (2890)
T PRK09603 467 AVGELLANELHSG----LVKMQKTIKDKLTTMSGAFD---SLMPHDLV---NSKMITSTIMEFFMGGQLS----QFMDQT 532 (2890)
T ss_pred hHHHHHHHHHHHH----HHHHHHHHHHHHHhhhcccc---ccChhhhh---ccHHHHHHHHHHhccCchh----hhhccc
Confidence 9999999999885 55555566665543111111 12245566 3568999999999998764 678888
Q ss_pred cceEEEccccchHHHhhhccccc---cCCccccccccccccccCCcccccccCCCCCCccccccccccceEEEeeccCCC
Q 001179 403 AGYTVQAERLNFLRFISFFRAVH---RGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSR 479 (1131)
Q Consensus 403 ~GvsqvleRln~~~~lSh~Rrv~---rg~~~~~~K~t~~R~Lhps~wGfICPveTPEG~~CGLvk~LA~~a~It~~~~~~ 479 (1131)
|++|+ |+|.||++ +|++.++++++++|++||||||+|||+|||||+|||||++||.+|+|+
T Consensus 533 NpLse----------ltHKRRlSaLGPGGlsr~ra~fevRdVH~shYGRiCPIETPEG~NiGLI~SLa~~a~in------ 596 (2890)
T PRK09603 533 NPLSE----------VTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVN------ 596 (2890)
T ss_pred Chhhh----------hhhcccccccCCCCccccccCCcccccCcccccccCCCCCCCCCcccchhhhhhheecc------
Confidence 88775 99999999 888999999999999999999999999999999999999999999998
Q ss_pred CcccccchhhhHHHHHHHhcCceecCcccccCCCCCceEEEECCEEEeeecCchHHHHHHHHHHHHhhcCCCCCCCceEE
Q 001179 480 GNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVG 559 (1131)
Q Consensus 480 ~~~~~~~~~~~~i~~~L~~lG~~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~ 559 (1131)
++|++.+ | |....||++-.. +.++.+ +.|-.
T Consensus 597 ------------------~~Gfiet-P----------y~kV~~g~v~~~------------i~ylsa--------~eE~~ 627 (2890)
T PRK09603 597 ------------------DLGFIEA-P----------YKKVVDGKVVGE------------TIYLTA--------IQEDS 627 (2890)
T ss_pred ------------------cCcceec-c----------eEEEecCccccc------------eeeeCH--------HHhcC
Confidence 5677765 3 444467764211 112221 11222
Q ss_pred EEeCCCCCCCCeEEEEcCCCcceeeEEEecCCCCCCcceeeecccceeeeeeecCCCCCCCCCCCCceeEEeecCCCccc
Q 001179 560 YVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSEESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLS 639 (1131)
Q Consensus 560 ~v~~~~~~~~~~i~i~td~GRl~RPv~~~~~~~~~~g~iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~P~~ils 639 (1131)
|+-+..+ + ...+.|++....+.++.. +++..++.. + .++++++|.|++|
T Consensus 628 ~~IA~a~-----~-~~~~~~~~~~~~v~~R~~--------------~e~~~~~~~--~---------v~~~dvsp~Q~vS 676 (2890)
T PRK09603 628 HIIAPAS-----T-PIDEEGNILGDLIETRVE--------------GEIVLNEKS--K---------VTLMDLSSSMLVG 676 (2890)
T ss_pred ceEeccC-----C-ccCCCCcccCCeEeEEEC--------------CceEEEChH--H---------ceEEEeCccceee
Confidence 2221111 1 124457776666655433 222222211 1 6899999999999
Q ss_pred ceeccccCCCCCCCccccccccccccccccc-----------------------------------cceEEEeccc----
Q 001179 640 VVANLTPYSDHNQSPRNMYQCQMAKQTMGFS-----------------------------------VQALKFRADQ---- 680 (1131)
Q Consensus 640 v~AslIPF~~HNqspRn~yqc~M~KQAiG~~-----------------------------------~~n~~~R~D~---- 680 (1131)
++||||||.+||||+|++||||||+|||++- +..+..|.+.
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 9999999999999999999999999998431 1233333321
Q ss_pred --ceeeec----------CCCcceeecCcccccC----------cccCCCCcceEEEEEeccCCCCCceEEeeccccccC
Q 001179 681 --KLYHLQ----------TPQTPIVRTNTYTKYG----------IDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRG 738 (1131)
Q Consensus 681 --~~y~L~----------ypQ~PLV~t~~~~~~~----------~~~~~~G~N~iVAv~~y~Gyn~EDaiiink~s~~rG 738 (1131)
..|.|. +.|||+|+.+.....| .+|+++|+|++||+|||.|||+|||||||++.+..+
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 237774 4899999999887665 599999999999999999999999999999999999
Q ss_pred ceeeeEEEEEEEEecccCCCccccccccccCCCChhhhcccCCCCCcccCcEEcCCCCeeEEeecCC-------------
Q 001179 739 MCHGQIYQTETIDLSDDGNKVDRGQKLFRRNKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTT------------- 805 (1131)
Q Consensus 739 ~~~~~~y~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~Ld~dGi~~~G~~v~~gdil~~~~~~~~------------- 805 (1131)
.|+|.|...|.+++.+.+...+.++. .+|+.++...++||++||+++|++|++||||+||++|+.
T Consensus 837 ~fTSIHIee~ei~~r~Tk~G~EeITr--dIPnvse~~l~~LDe~GII~iGa~V~~GDILVGKvTPkge~~~tPEekLLra 914 (2890)
T PRK09603 837 IFTSTHIYEKEVDARELKHGVEEFTA--DIPDVKEEALAHLDESGIVKVGTYVSAGMILVGKTSPKGEIKSTPEERLLRA 914 (2890)
T ss_pred cceEEEEeeeEEEEEecCCCCcEEec--cCCCCCHHHHhcCCCCCCEeeCCEECCCCEEEEeeccCCCCCCChHHHHHHH
Confidence 99999999999998887755444433 368888888999999999999999999999999988763
Q ss_pred --------CcEEeeecCCCcceEEEEEEEeccCC----------------------------------------------
Q 001179 806 --------NSWRTNSRKGSESVFVDYVAVDMKNS---------------------------------------------- 831 (1131)
Q Consensus 806 --------~~~~~~~~~~~e~g~Vd~v~~~~~~~---------------------------------------------- 831 (1131)
-++.|++++.+..|+|.+|.++..+.
T Consensus 915 IFGeka~~vkDtSLrvp~G~~G~Vidv~~f~r~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 994 (2890)
T PRK09603 915 IFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDARVLSAYEEEKAKLDMEHFDRLTMLNREELLRVSSLLSQAIL 994 (2890)
T ss_pred HhcccccccccCceecCCCCcEEEEEEEEecccccchhHHHHHHHHHHHHHHhHhhHHHHHHHHHHHHHhhhhhcccccc
Confidence 24669999999999999999987420
Q ss_pred ------------------------------------------------------------------------CC-----C
Q 001179 832 ------------------------------------------------------------------------KN-----L 834 (1131)
Q Consensus 832 ------------------------------------------------------------------------~~-----~ 834 (1131)
|+ -
T Consensus 995 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~gdeL~~Gv 1074 (2890)
T PRK09603 995 EEPFSHNGKDYKEGDQIPKEEIASINRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNGV 1074 (2890)
T ss_pred ccccccccccccccccccHHHHhhCCHHHhhhhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCcCCCCc
Confidence 00 1
Q ss_pred CeEEEEEEeeecCCCCCcccccccCCcceeeeeecCCCCCccCCCCCcccEEeCCCCCCCccchhHhHHHHHhhhccccC
Q 001179 835 PQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKGGSLHG 914 (1131)
Q Consensus 835 ~~~~~i~~r~~R~p~iGDKf~sRHGqKGvvs~i~~~~dmPf~~~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g 914 (1131)
...|+|++|+.|+|+||||||||||||||||+|||+|||||+ +||++||||+||||||||||||||+|+++||||+..|
T Consensus 1075 ~~~VkV~ia~kR~~qvGDK~AgRHGnKGViS~I~p~EDMPfl-~dG~~pDIIlNPlGvPSRMnIGQilE~~LG~aa~~lg 1153 (2890)
T PRK09603 1075 IKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYT-ADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFG 1153 (2890)
T ss_pred ceEEEEEEEEeecccccchhhhccCCCeeEEEEEchhcCCCC-CCCCCCcEEECCCCCCccccHHHHHHHHHHHHHHhcC
Confidence 357999999999999999999999999999999999999999 9999999999999999999999999999999999988
Q ss_pred ceecc-----c-cccccc--------c----c-----------------cCCCCCCC--------CchhhHHHHHHHHHH
Q 001179 915 KFMDA-----T-PFANSV--------K----K-----------------TNGDTGTD--------ESKSLVDELGEMLRT 951 (1131)
Q Consensus 915 ~~~d~-----t-pf~~~~--------~----~-----------------~~~~~~~~--------~~~~~~~~~~~~l~~ 951 (1131)
.+++. + ||.... . . +....|.. -+....+++.+.|.+
T Consensus 1154 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~tpvF~g~~~~~i~~~l~~ 1233 (2890)
T PRK09603 1154 KQIASMLEDKTKDFAKELRAKMLEIANAINEKDPLTIHALENCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFEL 1233 (2890)
T ss_pred cChhhhhhhcchhhhHHHHHHHHhhhcccccccccccccccccchHHHHhhhhhhccCCcccCCCCCCCCHHHHHHHHHH
Confidence 76431 1 221100 0 0 00001110 011247899999999
Q ss_pred CCCCCCCcEEEeeCCCCcEeeeeeeeeceeEEeeccccccceeeeecccccceeecccCcccccCceeeeehhhhHHhhh
Q 001179 952 CGFNYHGVEVLYSGVYGTELTCEIFIGPVYYQRLRHMVSDKFQVRSTGTMDQITRQPIKGRKRGGGIRFGEMERDSLLAH 1031 (1131)
Q Consensus 952 ~g~~~~G~e~~y~g~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lTrQP~~Gr~~~GG~R~GEMErd~l~a~ 1031 (1131)
+||+++|++.||||+||++|+++||+|++|||||+|||+||+||||+|||+++||||++||+++|||||||||||||+||
T Consensus 1234 aG~~~~Gk~~LyDGrTGe~f~~~V~vG~~YylKL~HmVdDKiHaRstGPyslvTqQPl~GKs~~GGqRfGEMEvwALeAy 1313 (2890)
T PRK09603 1234 AKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAY 1313 (2890)
T ss_pred cCCCCCCCEEEEcCCCCCCccceEEEEeeceeechhhccchhhhccCCCcchhhhCCCcccccCCCceeeeeeHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chHHHHHHhhccCCCccceeccccccccccccccccccccccccCCCCCCCCCCCeeeccCcCCCCcceecchHhHHHHH
Q 001179 1032 GAAYLLHDRLHTCSDYHVADVCSLCGSVLTATFIHPQKRAIREIGGLPPARAPKKVTCHACQTSKGMETVAMPYVFRYLA 1111 (1131)
Q Consensus 1032 Gas~~l~erl~~~SD~~~~~vC~~Cg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~v~iPy~~klL~ 1111 (1131)
|||++|||||+.+||++.++. ..|..|.++.++..+.+||+||+|+
T Consensus 1314 GAa~~LqE~Lt~kSDdv~gR~----------------------------------~~y~~i~~g~~i~~~~iPeSFkvL~ 1359 (2890)
T PRK09603 1314 GAAHTLKEMLTIKSDDIRGRE----------------------------------NAYRAIAKGEQVGESEIPETFYVLT 1359 (2890)
T ss_pred hHHHHHHHHHhcCCcchhhhh----------------------------------hhhhhhcCCCcccccCCCHHHHHHH
Confidence 999999999999999998664 2457788899999999999999999
Q ss_pred HHHHhCCceeEEEecc
Q 001179 1112 AELAAMNIKITLQLGD 1127 (1131)
Q Consensus 1112 ~EL~sm~I~~~l~~~~ 1127 (1131)
+||+||||++++...+
T Consensus 1360 ~EL~sL~l~i~~~~~~ 1375 (2890)
T PRK09603 1360 KELQSLALDINIFGDD 1375 (2890)
T ss_pred HHHHhCCcceEEEeec
Confidence 9999999999997643
No 12
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=100.00 E-value=5.5e-171 Score=1627.46 Aligned_cols=936 Identities=21% Similarity=0.325 Sum_probs=725.1
Q ss_pred ccchhhHHHHHHHHHHHHH-----HhHHHHH-----------------------------HHHHHcCCeeeEEEEEEEEE
Q 001179 10 EPLRELVRHHIESFDYMLD-----EGLSEMF-----------------------------DHCRQAKISYTGKLMADVEF 55 (1131)
Q Consensus 10 ~~~~~Lv~~hi~SFn~Fi~-----~gl~~ii-----------------------------~ecR~r~~TYsa~l~v~v~~ 55 (1131)
..+|+|++.|.+||++|++ +||++++ .||++|++||++||+|++++
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 4689999999999999997 6999998 99999999999999999999
Q ss_pred EEec------------CC----------CceEEEEEeecccceeeccCcccCCCCChHHHHhhccccccCCcEEEEcCce
Q 001179 56 QYLD------------AG----------SPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLE 113 (1131)
Q Consensus 56 ~~~~------------~~----------~~~~~~~v~iG~iPIMvkS~~C~L~~ls~~el~~~gE~~~D~GGYFIING~E 113 (1131)
+..+ ++ +.+++++|++|+||+|+. .|+|||||+|
T Consensus 107 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ikeq~VylGdiPLMT~------------------------~GTFIING~E 162 (2836)
T PRK14844 107 VIMQDGISLDEYKSIKESGDHSKLATVIKSIEEQEVHFCELPMMTD------------------------KGTFIINGVE 162 (2836)
T ss_pred EEeccccccccccccccccccccccccccceeeeeEEEecCCccCC------------------------CeEEEEcCcc
Confidence 7611 11 245678999999999997 8999999999
Q ss_pred eEEEEEEeccCCceEEEEeccccC-CCcceeeEEEEEeeeecCCCceEEEEEEEeCCeEEEEEEEecccccccHhhHHHh
Q 001179 114 RVFRSVILPKQNYPMSMVRSSFRD-RREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKA 192 (1131)
Q Consensus 114 KVIr~qi~~~~N~~~~~~r~s~~~-r~~~~t~~~i~iRs~~~~~~s~~~~l~~~~~g~~~l~~~~~k~~~~IPi~ilLkA 192 (1131)
|||++|++++|+..|.....+.++ .+..|+...|+.||. |+.++++.++.+|+++..+| ++|+++||||
T Consensus 163 RVIVSQL~RSPGVyF~~~~~kt~~sgk~lysa~IIP~RGs-------WLefE~D~kd~lyvRIDRkR---KiPiT~LLrA 232 (2836)
T PRK14844 163 KVIVSQMHRSPGVFFDSDKGKTYNSGKLIYSARVIPYRGS-------WLDIEFDVKDHLYFRIDRKR---KLPISVLLKA 232 (2836)
T ss_pred eEEEEcceeCCeEEEEcccCcccCCCceeEEEEEecCCcc-------eEEEEEcCCCeEEEEecCCe---eeeHHHHHHH
Confidence 999999999999655443332222 334799999998876 99999999999999999876 7999999999
Q ss_pred ccCCCHHHHHHhhcccc-----chhh-----h-cccCC--------C-CC------------------------------
Q 001179 193 LVDTNDLEIFNHLTCCY-----DEKY-----K-KEKGA--------V-GS------------------------------ 222 (1131)
Q Consensus 193 Lg~~sD~eI~~~I~~~~-----~~~~-----~-~~~~~--------~-~~------------------------------ 222 (1131)
||+ |++||++.+.... ++.. . ++.+. . .+
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 8999999774210 0000 0 00000 0 00
Q ss_pred ----hhHH---------------------HHH----------------------HHHHHHHHhccccCHHHHHHHHhhcc
Q 001179 223 ----PLVS---------------------ERV----------------------KIILAEVQDLSLTTRLQCLQHIGEHF 255 (1131)
Q Consensus 223 ----~~~~---------------------~~~----------------------~~lL~~~~~~~i~t~~~AL~yIG~~~ 255 (1131)
.+++ +.+ ..+...+..+...++++|+..|++++
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 0000 000 01112223345668899999999998
Q ss_pred ccc---------------ccCCCCccHHHHHHHHHHhhhcccCC-C-chhhHHHHHHHHHHHHhhcCCCCCCCCcccccc
Q 001179 256 QPV---------------IDGLQSESYYAVAETVIRDYIFVHLN-D-NNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQN 318 (1131)
Q Consensus 256 r~~---------------~~~~~~~~~~e~g~~~L~~~ll~Hl~-~-~~~K~~~L~~MvrkLl~l~~G~~~~DD~D~l~N 318 (1131)
|+. ++.|.+++..++||..|++.|-.+.. . ..-....++.++++|+.+..|....||+|||+|
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 753 12244555556666666666644321 1 112223588999999999999999999999999
Q ss_pred cEeccchhhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccccchhHHHHHHHhcCCCcchHHHHHHHhcccCcccccccc
Q 001179 319 QEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLD 398 (1131)
Q Consensus 319 kRv~l~G~Ll~~lf~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~It~~i~~~~sTGnw~~~~~~~ 398 (1131)
|||+++|+||+.+|+..|.++. +.+++++.. .... ...++.++ +++.||+.+++||+|+
T Consensus 472 RRvr~vGeLl~~qfr~gl~r~~----~~i~e~~~~-~~~~----~~~p~~li---n~~~l~~~i~~ff~ss--------- 530 (2836)
T PRK14844 472 RRVRSVGEFIENQFRTGLLKLE----RAVVDSMST-SSLD----KVSPSDFI---NPKVLTNVLRDFFNSS--------- 530 (2836)
T ss_pred cccchHHHHHHHHHHHHHHHHH----HHHHHHHhh-cccc----ccchhhcc---cchhHHHHHHHHhccc---------
Confidence 9999999999999998655554 444544432 1111 11244556 3568999999999884
Q ss_pred cccccceEEEccccchHHHhhhccccc---cCCccccccccccccccCCcccccccCCCCCCccccccccccceEEEeec
Q 001179 399 LQQRAGYTVQAERLNFLRFISFFRAVH---RGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASY 475 (1131)
Q Consensus 399 ~~q~~GvsqvleRln~~~~lSh~Rrv~---rg~~~~~~K~t~~R~Lhps~wGfICPveTPEG~~CGLvk~LA~~a~It~~ 475 (1131)
++||.+++.|+++.|+|+||++ +|++.++++.+++|++||||||+|||+|||||+|||||++||.+|+|+
T Consensus 531 -----~LSQfmDQtNpLseltHkRRlsaLGPGGL~r~~a~fevRdvH~shyGRiCPIETPEG~NiGLI~SLA~yarIn-- 603 (2836)
T PRK14844 531 -----QLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARIN-- 603 (2836)
T ss_pred -----chhhhccCcChhhhhhhcceecccCCCCcccccCCCcccccCccccccccCCCCCCCCcccchhhhhhheecc--
Confidence 4555566666666799999999 688899999999999999999999999999999999999999999998
Q ss_pred cCCCCcccccchhhhHHHHHHHhcCceecCcccccCCCCCceEEEECCEEEeeecCchHHHHHHHHHHHHhhcCCCCCCC
Q 001179 476 YDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDD 555 (1131)
Q Consensus 476 ~~~~~~~~~~~~~~~~i~~~L~~lG~~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~ 555 (1131)
++|++.+ | |....||++-. .+.++.+ +
T Consensus 604 ----------------------~~Gfiet-P----------y~kV~~g~v~~------------~i~ylsa--------~ 630 (2836)
T PRK14844 604 ----------------------KYGFIES-P----------YRKVVNRVVTD------------QIEYLSA--------I 630 (2836)
T ss_pred ----------------------CCceEeC-C----------cEEEEcCcCcc------------cccccCh--------H
Confidence 5677765 3 44557886321 1122221 1
Q ss_pred ceEEEEeCCCCCCCCeEEEEcCCCcceeeEEEecCCCCCCcceeeecccceeeeeeecCCCCCCCCCCCCceeEEeecCC
Q 001179 556 LEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSEESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPT 635 (1131)
Q Consensus 556 ~ei~~v~~~~~~~~~~i~i~td~GRl~RPv~~~~~~~~~~g~iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~P~ 635 (1131)
.|-.|.-+..+ + ...+.|++..+.+.++.. |. |..+.. ++ .++++++|.
T Consensus 631 ~E~~~~Ia~a~-----~-~~~~~~~~~~~~v~~R~~----~e----------f~~~~~--~~---------v~~~dvsp~ 679 (2836)
T PRK14844 631 DEGLYYIADTS-----A-KLDENNCFVDDMLYCRYA----GS----------FVMVSS--DQ---------VSYIDVSPK 679 (2836)
T ss_pred HhcCcEEEeCC-----c-cCCCCCcccCCeEEEecC----Cc----------eEEecH--HH---------ceEEEeCcc
Confidence 22223222111 1 124457777777766543 12 222211 11 689999999
Q ss_pred CcccceeccccCCCCCCCcccccccccccccccc-----------------------------------ccceEEEeccc
Q 001179 636 GMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGF-----------------------------------SVQALKFRADQ 680 (1131)
Q Consensus 636 ~ilsv~AslIPF~~HNqspRn~yqc~M~KQAiG~-----------------------------------~~~n~~~R~D~ 680 (1131)
|++|++||||||.+||||+|++||||||||||++ .+..+..|.+.
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 9999999999999999999999999999999953 11233344322
Q ss_pred ---------ceeeec----------CCCcceeecCcccccC----------cccCCCCcceEEEEEeccCCCCCceEEee
Q 001179 681 ---------KLYHLQ----------TPQTPIVRTNTYTKYG----------IDEYPTGTNAIVAVLAYTGYDMEDAMILN 731 (1131)
Q Consensus 681 ---------~~y~L~----------ypQ~PLV~t~~~~~~~----------~~~~~~G~N~iVAv~~y~Gyn~EDaiiin 731 (1131)
..|.|. +.|+|+|+.+.....| .+|+++|+|++||+|||.|||+||||+||
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 247775 4999999999987765 59999999999999999999999999999
Q ss_pred ccccccCceeeeEEEEEEEEecccCCCccccccccccCCCChhhhcccCCCCCcccCcEEcCCCCeeEEeecCC------
Q 001179 732 KSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFRRNKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTT------ 805 (1131)
Q Consensus 732 k~s~~rG~~~~~~y~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~Ld~dGi~~~G~~v~~gdil~~~~~~~~------ 805 (1131)
++.+.+++|+|.|...|+++..+.+...+.++. ..|+.++...++||++||+++|++|++||||+||++|+.
T Consensus 840 Erlv~eD~fTSiHIee~ei~~r~Tk~G~EeITr--dIPnv~e~~lr~LDe~GIV~iGa~V~~GDILVGKvtPk~e~~~tP 917 (2836)
T PRK14844 840 SEVVKKDLFTSIHIEEFECVVHDTPLGSEKITR--AIPGVNEENLYHLDDSGIVKIGTRVGPGYILVGKVTPKPSLSLPP 917 (2836)
T ss_pred hhhccCceeEEEeecceEEEEEeccCCCceecc--cCCCCChHHHhcCCCCCCeecCCEECCCCEEEEeecCCCCCCCCH
Confidence 999999999999999999998887755444443 368888888999999999999999999999999988763
Q ss_pred ---------------CcEEeeecCCCcceEEEEEEEeccCC---------------------------------------
Q 001179 806 ---------------NSWRTNSRKGSESVFVDYVAVDMKNS--------------------------------------- 831 (1131)
Q Consensus 806 ---------------~~~~~~~~~~~e~g~Vd~v~~~~~~~--------------------------------------- 831 (1131)
-+++|++++.+..|+|.+|.++..+.
T Consensus 918 EekLL~aIFGek~~~vkdtSLrvp~G~~G~Vidv~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 997 (2836)
T PRK14844 918 ETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFTRRGVEENERALLIKQKEINDFEKERDYIINVTSEYFYDELKK 997 (2836)
T ss_pred HHHHHHHHhCCcccccccCceecCCCCCEEEEEEEEEcccccccchhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
Confidence 24669999999999999999997530
Q ss_pred --------------------------------------------------------------CC-----CCeEEEEEEee
Q 001179 832 --------------------------------------------------------------KN-----LPQKANIRFRH 844 (1131)
Q Consensus 832 --------------------------------------------------------------~~-----~~~~~~i~~r~ 844 (1131)
|+ -...|+|++.+
T Consensus 998 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~gdeL~~gv~~~VkVyia~ 1077 (2836)
T PRK14844 998 LLINSGSQDREKFDSIEREQWWGIGLKNQSISEQVKSLKKDFDEKVSHAIAQFKRKVEKLHEGYDLPQGVSMSVKVFIAV 1077 (2836)
T ss_pred hhcccccccHHHHhhccHHhhhhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCCCCceEEEEEEEE
Confidence 11 02579999999
Q ss_pred ecCCCCCcccccccCCcceeeeeecCCCCCccCCCCCcccEEeCCCCCCCccchhHhHHHHHhhhccccCceec------
Q 001179 845 TRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKGGSLHGKFMD------ 918 (1131)
Q Consensus 845 ~R~p~iGDKf~sRHGqKGvvs~i~~~~dmPf~~~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~d------ 918 (1131)
.|.++||||+|||||||||||.|+|.|||||+ +||+++|||+||+|+||||||||++|+++|+||...|..+-
T Consensus 1078 KRkiqvGDKmAGRHGNKGVIS~IlP~eDMPyL-~DGtpvDIvLNPLGVPSRMNvGQilE~hLG~A~~~L~~~~~~~~~~~ 1156 (2836)
T PRK14844 1078 KHSLQPGDKMAGRHGNKGVISRVVPVEDMPYL-EDGTPVDIILNPLGVPSRMNVGQILETHVGWACKKLGEKVGNILDEI 1156 (2836)
T ss_pred eecCCccccccccCCCCceEeEEcccCCCCcC-CCCCCceEEeCCCCCCccccHHHHHHHHHHHHHhhhhhhhHhhhhhh
Confidence 99999999999999999999999999999999 99999999999999999999999999999999987763220
Q ss_pred ---------------------------------cccccccccc----c--------------------------------
Q 001179 919 ---------------------------------ATPFANSVKK----T-------------------------------- 929 (1131)
Q Consensus 919 ---------------------------------~tpf~~~~~~----~-------------------------------- 929 (1131)
..||....-+ .
T Consensus 1157 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1236 (2836)
T PRK14844 1157 NKIKSAFCKGIRSLNDDNFTKFAAAYLDNKKIENIDDDEITASVLNTPNKNALNDELNELVENYLNSCKSAYSNLRNFLI 1236 (2836)
T ss_pred hccccccccccccccccccccccccccccccccccccccccccccccccccccccccccchhccccccchhhHHHHHHHH
Confidence 0112110000 0
Q ss_pred -------------------------------CCCCCCC--CchhhHHHHHHHHHHCCCCCCCcEEEeeCCCCcEeeeeee
Q 001179 930 -------------------------------NGDTGTD--ESKSLVDELGEMLRTCGFNYHGVEVLYSGVYGTELTCEIF 976 (1131)
Q Consensus 930 -------------------------------~~~~~~~--~~~~~~~~~~~~l~~~g~~~~G~e~~y~g~tG~~~~~~if 976 (1131)
.|..+.. -+....+++.+.|+++||+++|++.||||+||++|+++||
T Consensus 1237 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~tpvf~g~~~~~i~~~L~~~g~~~~Gk~~l~dG~TGe~f~~~v~ 1316 (2836)
T PRK14844 1237 EVYSCGSNVSICNNIRDISDNNLIEFARKLRDGIPVAAPVFEGPKDEQIAKLFELAGLDNSGQAVLYDGCSGEKFDRKVT 1316 (2836)
T ss_pred HhhhcccccccccccccccHHHHHHHHhhhccCCeecCCCcCCCCHHHHHHHHHHhCcCCCCCEEEEcCCCCCccchhhe
Confidence 0000000 0112467889999999999999999999999999999999
Q ss_pred eeceeEEeeccccccceeeeecccccceeecccCcccccCceeeeehhhhHHhhhchHHHHHHhhccCCCccceeccccc
Q 001179 977 IGPVYYQRLRHMVSDKFQVRSTGTMDQITRQPIKGRKRGGGIRFGEMERDSLLAHGAAYLLHDRLHTCSDYHVADVCSLC 1056 (1131)
Q Consensus 977 ~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lTrQP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~C 1056 (1131)
+|++|||||+|||+||+|+|++|||+.+||||++||+|+|||||||||||||+|||||++|||||+.+||++..++|.
T Consensus 1317 vG~~yy~kL~HmV~DKihaRs~Gp~s~lT~QPl~Gr~~~GG~RfGEME~~al~a~Gaa~~L~E~Lt~kSD~~~gr~~~-- 1394 (2836)
T PRK14844 1317 VGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDINGRVKI-- 1394 (2836)
T ss_pred eCcchhhhhhhhhcchhhhcccCCCcccccCCCcccccCCCceeecchHHHHHHHhHHHHHHHHhcccccchhhhhHh--
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999977642
Q ss_pred cccccccccccccccccccCCCCCCCCCCCeeeccCcCCCCcceecchHhHHHHHHHHHhCCceeEEEeccCC
Q 001179 1057 GSVLTATFIHPQKRAIREIGGLPPARAPKKVTCHACQTSKGMETVAMPYVFRYLAAELAAMNIKITLQLGDGA 1129 (1131)
Q Consensus 1057 g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~v~iPy~~klL~~EL~sm~I~~~l~~~~~~ 1129 (1131)
+|..|+ +.+..+..+||+||+|+|||+||||.+++.+++.+
T Consensus 1395 -------------------------------~~~ivk-G~~~~~~~~PesfkvL~~EL~sl~i~~~~~~~~~~ 1435 (2836)
T PRK14844 1395 -------------------------------YESIIK-GDSNFECGIPESFNVMIKELRSLCLNVDLKQNDVV 1435 (2836)
T ss_pred -------------------------------hhhhcc-CCCCCcCCCCchHHHHHHHHHhCccceEEeccchh
Confidence 223332 44455568999999999999999999999987654
No 13
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated
Probab=100.00 E-value=1.8e-172 Score=1537.82 Aligned_cols=561 Identities=35% Similarity=0.571 Sum_probs=517.3
Q ss_pred ceEEEECCEEEeeecCchHHHHHHHHHHHHhhcCCCCCCCceEEEEeCCCCCCCCeEEEEcCCCcceeeEEEecCCCC--
Q 001179 516 VLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSE-- 593 (1131)
Q Consensus 516 ~~~V~lnG~~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~~~~~~~~~~i~i~td~GRl~RPv~~~~~~~~-- 593 (1131)
..+|||||+|+|+++ ++.+|++.||.+||.| .++.++||++.+. .++|+||||+||++|||+++++++.
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--EISEEVNVSYKEE-----TNEVIINTDAGRARRPLIVVENGEPLL 74 (605)
T ss_pred ccEEEECCEEEEEEC--CHHHHHHHHHHHHccC--CCCCcEEEEEECC-----CCEEEEEccCCccceeEEEEeCCcccC
Confidence 368999999999985 5899999999999998 6899999988652 4699999999999999999988542
Q ss_pred -------------------CCcceeeecccceeeeeeecCCCCCCCCCCCCceeEEeecCCCcccceeccccCCCCCCCc
Q 001179 594 -------------------ESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSP 654 (1131)
Q Consensus 594 -------------------~~g~iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~P~~ilsv~AslIPF~~HNqsp 654 (1131)
++|.|||||++||++++||+.++++... +||+||+|+++||++||+|||+||||||
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 2499999999999999999999887654 7999999999999999999999999999
Q ss_pred cccccccccccccccccceEEEecccceeeecCCCcceeecCcccccCcccCCCCcceEEEEEeccCCCCCceEEeeccc
Q 001179 655 RNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSS 734 (1131)
Q Consensus 655 Rn~yqc~M~KQAiG~~~~n~~~R~D~~~y~L~ypQ~PLV~t~~~~~~~~~~~~~G~N~iVAv~~y~Gyn~EDaiiink~s 734 (1131)
||||||||+|||||++++|+..|.|++.|+|+|||+|||+|+.++.++++++|+|+||+||||||+||||||||||||+|
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 cccCceeeeEEEEEEEEecccCCCccccccccccCCC------ChhhhcccCCCCCcccCcEEcCCCCeeEEeecC----
Q 001179 735 VDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFRRNKD------AKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKT---- 804 (1131)
Q Consensus 735 ~~rG~~~~~~y~~~~~~~~~~~~~~~~~~~~f~~~~~------~~~~~~~Ld~dGi~~~G~~v~~gdil~~~~~~~---- 804 (1131)
+||||||+.+|++|+++...... +..+.|..|+. ....+++||+||||++|+.|++||||+||..|.
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 99999999999999876543221 12345666642 123578999999999999999999999997652
Q ss_pred ----------CCcEEeeecCCCcceEEEEEEEeccCCCCCCeEEEEEEeeecCCCCCcccccccCCcceeeeeecCCCCC
Q 001179 805 ----------TNSWRTNSRKGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMP 874 (1131)
Q Consensus 805 ----------~~~~~~~~~~~~e~g~Vd~v~~~~~~~~~~~~~~~i~~r~~R~p~iGDKf~sRHGqKGvvs~i~~~~dmP 874 (1131)
..++.+++++.+|+|+||+|.++.++++ .+.|+|++|+.|+|+||||||||||||||||+|||+||||
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 1356788999999999999999977653 5789999999999999999999999999999999999999
Q ss_pred ccCCCCCcccEEeCCCCCCCccchhHhHHHHHhhhccccCceeccccccccccccCCCCCCCCchhhHHHHHHHHHHCCC
Q 001179 875 FSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKGGSLHGKFMDATPFANSVKKTNGDTGTDESKSLVDELGEMLRTCGF 954 (1131)
Q Consensus 875 f~~~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tpf~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~ 954 (1131)
|| +||++|||||||||||||||||||+|+++||||++.|.+.|+|||... .++++++.|.++||
T Consensus 385 ft-~~G~~PDiIiNPhg~PSRMTiGql~E~~~gk~~~~~g~~~d~t~F~~~---------------~~~~~~~~L~~~g~ 448 (605)
T PRK07225 385 FT-ESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGE---------------DEEDLREALEKLGF 448 (605)
T ss_pred cC-CCCCcccEEECcccccccCcHHHHHHHHHHHHHHhcCceEeecCCCCc---------------hHHHHHHHHHHhCc
Confidence 99 999999999999999999999999999999999999999999999876 58899999999999
Q ss_pred CCCCcEEEeeCCCCcEeeeeeeeeceeEEeeccccccceeeeecccccceeecccCcccccCceeeeehhhhHHhhhchH
Q 001179 955 NYHGVEVLYSGVYGTELTCEIFIGPVYYQRLRHMVSDKFQVRSTGTMDQITRQPIKGRKRGGGIRFGEMERDSLLAHGAA 1034 (1131)
Q Consensus 955 ~~~G~e~~y~g~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lTrQP~~Gr~~~GG~R~GEMErd~l~a~Gas 1034 (1131)
+++|+|+||||+||++|+++||+||+|||||+|||+||+|||++||++.|||||++||||+|||||||||||||+|||||
T Consensus 449 ~~~G~e~my~G~TG~~~~~~if~G~~yYqrL~HmV~DK~haR~~Gp~~~lTrQP~~GR~r~GG~RfGEMErd~lia~Gas 528 (605)
T PRK07225 449 EHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAA 528 (605)
T ss_pred CCCCeEEEEcCCCCCEecccEEEeehheeechhhhcchhhhccCCCCcccccCCccccccCCCeeeeeeehhhhhhhhhH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhccCCCccceeccccccccccccccccccccccccCCCCCCCCCCCeeeccCcCCCCcceecchHhHHHHHHHH
Q 001179 1035 YLLHDRLHTCSDYHVADVCSLCGSVLTATFIHPQKRAIREIGGLPPARAPKKVTCHACQTSKGMETVAMPYVFRYLAAEL 1114 (1131)
Q Consensus 1035 ~~l~erl~~~SD~~~~~vC~~Cg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~v~iPy~~klL~~EL 1114 (1131)
++|+|||+.+||.++++||.+||++++.+ .+.+.++|+.|+++.++.++.||||||||+|||
T Consensus 529 ~~L~Erl~~~SD~~~~~vC~~CG~~~~~~------------------~~~~~~~C~~C~~~~~i~~v~iPya~kll~~EL 590 (605)
T PRK07225 529 MLLKERLLDESDKVEIYVCAKCGMIAIYD------------------KKRNRKYCPICGEETDIYPVEMSYAFKLLLDEL 590 (605)
T ss_pred HHHHHHHhccCcceeEEeecCcCcceehh------------------cccCceeecccCCCCceeeccCChhHHHHHHHH
Confidence 99999999999999999999999998754 123457899999889999999999999999999
Q ss_pred HhCCceeEEEeccCC
Q 001179 1115 AAMNIKITLQLGDGA 1129 (1131)
Q Consensus 1115 ~sm~I~~~l~~~~~~ 1129 (1131)
+||||+++|.+++.+
T Consensus 591 ~sm~i~~~l~~~~~~ 605 (605)
T PRK07225 591 KSLGIAPRLELEDKV 605 (605)
T ss_pred HHCCceeEEEecccC
Confidence 999999999998653
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=3.4e-172 Score=1533.88 Aligned_cols=558 Identities=36% Similarity=0.604 Sum_probs=515.1
Q ss_pred EEECCEEEeeecCchHHHHHHHHHHHHhhcCCCCCCCceEEEEeCCCCCCCCeEEEEcCCCcceeeEEEecCCCC-----
Q 001179 519 VLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSE----- 593 (1131)
Q Consensus 519 V~lnG~~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~~~~~~~~~~i~i~td~GRl~RPv~~~~~~~~----- 593 (1131)
|||||+|+|+++ ++.+|++.||.+||.+ .++.++||++++. .++|+||||+||++|||+++++++.
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 799999999985 5899999999999998 6899999988753 4899999999999999999988651
Q ss_pred ----------------CCcceeeecccceeeeeeecCCCCCCCCCCCCceeEEeecCCCcccceeccccCCCCCCCcccc
Q 001179 594 ----------------ESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNM 657 (1131)
Q Consensus 594 ----------------~~g~iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~P~~ilsv~AslIPF~~HNqspRn~ 657 (1131)
.+|.|||||++||++++||+.++++... +||+||+|+++||++||+|||+|||||||||
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 3588999999999999999999887544 7999999999999999999999999999999
Q ss_pred ccccccccccccccceEEEecccceeeecCCCcceeecCcccccCcccCCCCcceEEEEEeccCCCCCceEEeecccccc
Q 001179 658 YQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDR 737 (1131)
Q Consensus 658 yqc~M~KQAiG~~~~n~~~R~D~~~y~L~ypQ~PLV~t~~~~~~~~~~~~~G~N~iVAv~~y~Gyn~EDaiiink~s~~r 737 (1131)
|||||+|||||++++|+..|.|+++|+|+|||+|||+|+.++.++++++|+|+||+||||||+||||||||||||+|+||
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 CceeeeEEEEEEEEecccCCCccccccccccCCC------ChhhhcccCCCCCcccCcEEcCCCCeeEEeecC-------
Q 001179 738 GMCHGQIYQTETIDLSDDGNKVDRGQKLFRRNKD------AKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKT------- 804 (1131)
Q Consensus 738 G~~~~~~y~~~~~~~~~~~~~~~~~~~~f~~~~~------~~~~~~~Ld~dGi~~~G~~v~~gdil~~~~~~~------- 804 (1131)
||||+++|++|+++...... +..+.|..|+. ....+++||+||||++|+.|++||||+||++|.
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 99999999999876543221 11234555532 223578999999999999999999999998752
Q ss_pred -------CCcEEeeecCCCcceEEEEEEEeccCCCCCCeEEEEEEeeecCCCCCcccccccCCcceeeeeecCCCCCccC
Q 001179 805 -------TNSWRTNSRKGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSG 877 (1131)
Q Consensus 805 -------~~~~~~~~~~~~e~g~Vd~v~~~~~~~~~~~~~~~i~~r~~R~p~iGDKf~sRHGqKGvvs~i~~~~dmPf~~ 877 (1131)
..++.+++++.+|+|+||+|.++.++++ .+.|+|++|+.|+|+||||||||||||||||+|||+||||||
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 1356788999999999999999987653 578999999999999999999999999999999999999999
Q ss_pred CCCCcccEEeCCCCCCCccchhHhHHHHHhhhccccCceeccccccccccccCCCCCCCCchhhHHHHHHHHHHCCCCCC
Q 001179 878 VTGMRPDLIINPHAFPSRMTIAMLLESVAAKGGSLHGKFMDATPFANSVKKTNGDTGTDESKSLVDELGEMLRTCGFNYH 957 (1131)
Q Consensus 878 ~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tpf~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~~~ 957 (1131)
+||++|||||||||||||||||||+|+++||||++.|.++|+|||... .++++++.|.++||+++
T Consensus 381 ~~G~~pDiIiNPhg~PSRMTiGqllE~~~gk~~~~~g~~~d~t~F~~~---------------~~~~~~~~L~~~g~~~~ 445 (599)
T TIGR03670 381 EDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGE---------------PEEELRKELLKLGFKPD 445 (599)
T ss_pred CCCCCCCEEECcccccccccHHHHHHHHHHHHHHhcCCEEEeCCCCCc---------------cHHHHHHHHHHcCCCCC
Confidence 999999999999999999999999999999999999999999999976 47999999999999999
Q ss_pred CcEEEeeCCCCcEeeeeeeeeceeEEeeccccccceeeeecccccceeecccCcccccCceeeeehhhhHHhhhchHHHH
Q 001179 958 GVEVLYSGVYGTELTCEIFIGPVYYQRLRHMVSDKFQVRSTGTMDQITRQPIKGRKRGGGIRFGEMERDSLLAHGAAYLL 1037 (1131)
Q Consensus 958 G~e~~y~g~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lTrQP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l 1037 (1131)
|+|.||||+||++|+++||+||+|||||+|||+||+|||++||++.|||||++||||+|||||||||||||+|||||++|
T Consensus 446 G~e~ly~G~TG~~~~~~if~G~~yyqrL~HmV~DK~h~Rs~Gp~~~lTrQP~~Gr~r~GG~RfGEMErd~lia~Gas~~L 525 (599)
T TIGR03670 446 GKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLL 525 (599)
T ss_pred CCEEEEcCCCCCCccccEEEEehhheechhhhcchhhhcccCCCcccccCCccccccCCCeeeeeeehhhHhhcchHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhccCCCccceeccccccccccccccccccccccccCCCCCCCCCCCeeeccCcCCCCcceecchHhHHHHHHHHHhC
Q 001179 1038 HDRLHTCSDYHVADVCSLCGSVLTATFIHPQKRAIREIGGLPPARAPKKVTCHACQTSKGMETVAMPYVFRYLAAELAAM 1117 (1131)
Q Consensus 1038 ~erl~~~SD~~~~~vC~~Cg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~v~iPy~~klL~~EL~sm 1117 (1131)
+|||+++||.++++||.+||+++..+ .+.+.++|+.|+++.++.++.+|||||||+|||+||
T Consensus 526 ~ErL~~~SD~~~~~vC~~CG~~~~~~------------------~~~~~~~C~~c~~~~~i~~v~iPy~~k~l~~EL~am 587 (599)
T TIGR03670 526 KERLLDESDKYVVYVCENCGHIAWED------------------KRKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSL 587 (599)
T ss_pred HHHHhccCcceeEEeecccCceeehh------------------cccCceeccccCCCCceeeecCChhHHHHHHHHHhC
Confidence 99999999999999999999998754 123467899999888999999999999999999999
Q ss_pred CceeEEEeccCC
Q 001179 1118 NIKITLQLGDGA 1129 (1131)
Q Consensus 1118 ~I~~~l~~~~~~ 1129 (1131)
||+++|.+++.+
T Consensus 588 ~i~~~l~~~~~~ 599 (599)
T TIGR03670 588 GISPRLELGDKV 599 (599)
T ss_pred CcceEEEecccC
Confidence 999999998653
No 15
>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=2.9e-107 Score=942.80 Aligned_cols=354 Identities=47% Similarity=0.753 Sum_probs=305.9
Q ss_pred cceeccccCCCCCCCccccccccccccccccccceEEEecccceeeecCCCcceeecC-cccccC---------cccCCC
Q 001179 639 SVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTN-TYTKYG---------IDEYPT 708 (1131)
Q Consensus 639 sv~AslIPF~~HNqspRn~yqc~M~KQAiG~~~~n~~~R~D~~~y~L~ypQ~PLV~t~-~~~~~~---------~~~~~~ 708 (1131)
||+|++|||++|||||||+|||||+|||||++.+|+..|.|+.. .|||+|||+|+ .++..+ ++++|+
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 68999999999999999999999999999999999999999998 99999999999 777788 899999
Q ss_pred CcceEEEEEeccCCCCCceEEeeccccccCceeeeEEEEEEEEecccCCCccccccccccC-CCChhhhcccCCCCCccc
Q 001179 709 GTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFRRN-KDAKSLHSVIDSDGLPYV 787 (1131)
Q Consensus 709 G~N~iVAv~~y~Gyn~EDaiiink~s~~rG~~~~~~y~~~~~~~~~~~~~~~~~~~~f~~~-~~~~~~~~~Ld~dGi~~~ 787 (1131)
|+|++||||||+||||||||||||+|+|||+|++++|++ .++++..+.. ...+.|..+ +.....+++||+||||++
T Consensus 78 G~N~iVAvmsy~GYN~EDAiIiNkssv~rG~f~s~~~k~-~~~~~~~~~g--~~e~~~~~~~~~~~~~~~~LD~dGii~~ 154 (386)
T PF00562_consen 78 GQNAIVAVMSYTGYNQEDAIIINKSSVDRGLFTSIHYKT-EIEIRDNKGG--PSEEIFRPIPNVKEYNYSKLDEDGIIKI 154 (386)
T ss_dssp SEEEEEEESBSSSTTTSSEEEEECHHHHTTTTEEEEEEE-EEEEEEETTS--EEBBESS--TSSTSTTGGGBCTTSBB-T
T ss_pred eeeeeEEeeehhcccchhhhhhhhhhhhcCeeeEEEEEE-EeeeecccCC--cccccccccccchhhhhhhccccccccc
Confidence 999999999999999999999999999999999999999 7776544321 112334433 445677899999999999
Q ss_pred CcEEcCCCCeeEEee--------------cC--CCcEEeeecCCCcceEEEEEEEeccC-----CCCCCeEEEEEEeeec
Q 001179 788 GQMIHPGEPYCSIYD--------------KT--TNSWRTNSRKGSESVFVDYVAVDMKN-----SKNLPQKANIRFRHTR 846 (1131)
Q Consensus 788 G~~v~~gdil~~~~~--------------~~--~~~~~~~~~~~~e~g~Vd~v~~~~~~-----~~~~~~~~~i~~r~~R 846 (1131)
|+.|++||+|+||+. .. ..++.+++++.+|.|+||+|.++.+. ...+...|+|++|+.|
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 11 13577999999999999999995421 1135789999999999
Q ss_pred CCCCCcccccccCCcceeeeeecCCCCCccCCCCCcccEEeCCCCCCCccchhHhHHHHHhhhccccCceeccccccccc
Q 001179 847 NPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKGGSLHGKFMDATPFANSV 926 (1131)
Q Consensus 847 ~p~iGDKf~sRHGqKGvvs~i~~~~dmPf~~~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tpf~~~~ 926 (1131)
+|+||||||||||||||||+|||+|||||| ++|++|||||||||||||||||||+|+++||++++.|.++|+|||...
T Consensus 235 ~p~iGDKfssRHGqKGVvs~i~~~eDMPft-~~G~~pDiIiNPhgiPSRMtiGqllE~~~g~~~~~~g~~~~~t~F~~~- 312 (386)
T PF00562_consen 235 RPQIGDKFSSRHGQKGVVSKILPQEDMPFT-EDGIVPDIIINPHGIPSRMTIGQLLESLLGKAGALNGRFVDATPFDES- 312 (386)
T ss_dssp E--TTEEEEETTSEEEEEEEEE-TTTSEEE-TTSEB-SEEE-GGGSTTTTBTHHHHHHHHHHHHHHSTCEEB-TTTSSS-
T ss_pred cchhHHHHhhhhcCceEEeeeeccccCccc-cCCCcceeeecccccccccchHHHHhhhhhhhhhccccceecCCCCCc-
Confidence 999999999999999999999999999999 999999999999999999999999999999999999999999999987
Q ss_pred cccCCCCCCCCchhhHHHHHHHHHHCCCCCCCcEEEeeCCCCcEeeeeeeeeceeEEeeccccccceeeeecccccceee
Q 001179 927 KKTNGDTGTDESKSLVDELGEMLRTCGFNYHGVEVLYSGVYGTELTCEIFIGPVYYQRLRHMVSDKFQVRSTGTMDQITR 1006 (1131)
Q Consensus 927 ~~~~~~~~~~~~~~~~~~~~~~l~~~g~~~~G~e~~y~g~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lTr 1006 (1131)
..+++++.|.++||+++|+|.||||+||++++++||+|++|||||+|||+||+|||++||++.|||
T Consensus 313 --------------~~~~i~~~l~~~g~~~~g~~~l~~g~tG~~~~~~i~~G~~yy~rL~Hmv~DK~h~Rs~Gp~~~lT~ 378 (386)
T PF00562_consen 313 --------------SEEDISELLKKAGYNYPGKEVLYDGRTGEKFEAPIFIGPVYYQRLKHMVDDKIHARSRGPYSLLTR 378 (386)
T ss_dssp ---------------HHHHHHHHHHTTSHTTSEEEEBESSSSSBESSEEEEEEEEEEEBSTCGGGSTEEESS--BBSSSS
T ss_pred --------------chhhhHhhhhcccccccceEEEEcCccCceEEeEEEeeeEEeccceEeCCcEEEEEecCCCccccC
Confidence 458999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCcccc
Q 001179 1007 QPIKGRKR 1014 (1131)
Q Consensus 1007 QP~~Gr~~ 1014 (1131)
||++||+|
T Consensus 379 QP~~Gr~r 386 (386)
T PF00562_consen 379 QPVEGRSR 386 (386)
T ss_dssp SB-SSSSS
T ss_pred CCCCCCCC
Confidence 99999997
No 16
>PRK09606 DNA-directed RNA polymerase subunit B''; Validated
Probab=100.00 E-value=6.8e-96 Score=873.96 Aligned_cols=438 Identities=24% Similarity=0.396 Sum_probs=378.2
Q ss_pred ccccchhhHHHHHHHHHHHHHHhHHHHH----------------------------------------HHHHHcCCeeeE
Q 001179 8 DFEPLRELVRHHIESFDYMLDEGLSEMF----------------------------------------DHCRQAKISYTG 47 (1131)
Q Consensus 8 ~~~~~~~Lv~~hi~SFn~Fi~~gl~~ii----------------------------------------~ecR~r~~TYsa 47 (1131)
++...++|++|||+|||+||++||++++ +|||+|++||+|
T Consensus 11 ~~~~~~~lv~~qi~SFn~Fi~~gl~~ii~~~~~i~~~~~~~~~l~~~~~~l~~P~~~~~~~~~~~l~P~eaR~r~~TYs~ 90 (494)
T PRK09606 11 AYFKEHRLVRHHIDSYNDFVDNGLQKIIDEQGPIETEIEDGVYVELGKIRVGKPVVKEADGSEREIYPMEARLRNLTYSA 90 (494)
T ss_pred HHHCCCChHHHHHHHHHHHHHHhHHHHHHhcCCEEEecCCcEEEEEEEEEECCCcccccCCccccCCHHHHHhcCCCccc
Confidence 3556889999999999999999999998 799999999999
Q ss_pred EEEEEEEEEEecCCCceEEEEEeecccceeeccCcccCCCCChHHHHhhccccccCCcEEEEcCceeEEEEEEeccCCce
Q 001179 48 KLMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYP 127 (1131)
Q Consensus 48 ~l~v~v~~~~~~~~~~~~~~~v~iG~iPIMvkS~~C~L~~ls~~el~~~gE~~~D~GGYFIING~EKVIr~qi~~~~N~~ 127 (1131)
|++|+|.++.+ +.+...++|++|+|||||+|++|||++++++|+++.||||+|+||||||||+|||||+|+++++|++
T Consensus 91 ~l~v~i~~~~~--~~~~~~~~v~iG~iPiMv~S~~C~L~~~~~~~l~~~~E~~~d~GGyFIING~ErVi~~q~~~~~n~~ 168 (494)
T PRK09606 91 PLYLEMSPVEG--GEEEEPEEVYIGELPVMVGSKICNLYGLSEEELIEVGEDPLDPGGYFIVNGSERVLMTLEDLAPNKI 168 (494)
T ss_pred eEEEEEEEEEC--CCceEEeeEEeccCCeEeccCcccCCCCCHHHHHhcCCCcCCCCCeEEECCCeEEEEEEEeccCCee
Confidence 99999999754 4344567999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEeccccCCCcceeeEEEEEeeeecCCCceEEEEEEEeCCeEEEEEEEecccccccHhhHHHhccCCCHHHHHHhhcc
Q 001179 128 MSMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTC 207 (1131)
Q Consensus 128 ~~~~r~s~~~r~~~~t~~~i~iRs~~~~~~s~~~~l~~~~~g~~~l~~~~~k~~~~IPi~ilLkALg~~sD~eI~~~I~~ 207 (1131)
+++.++.+.++ .| ...+++... ..+.+..++|+.+|.+|++|.. .+++||+++||||||..||+||++.|..
T Consensus 169 ~~~~~~~~~~~--~~---~~~i~s~~~-~~~~~~~l~~~~~g~i~~~~~~--~~~~iPi~~llkALg~~sd~eI~~~i~~ 240 (494)
T PRK09606 169 LVEKDERYGDR--IE---VAKVFSQRR-GYRALVTVERNRDGLLEVSFPS--VPGSIPFVILMRALGLETDEEIVEAVSD 240 (494)
T ss_pred EEEeccCCCcc--ce---EEEEEcccc-cceeeEEEEEecCCeEEEEEcC--ccccccHHHHHHHcCCCCHHHHHHHhCC
Confidence 99887644322 13 344444322 2345678999999999999865 3457999999999999999999999952
Q ss_pred ccchhhhcccCCCCChhHHHHHHHHHHHHHhccccCHHHHHHHHhhcccccccCCCCccHHHHHHHHHHhhhcccCCC--
Q 001179 208 CYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHLND-- 285 (1131)
Q Consensus 208 ~~~~~~~~~~~~~~~~~~~~~~~~lL~~~~~~~i~t~~~AL~yIG~~~r~~~~~~~~~~~~e~g~~~L~~~ll~Hl~~-- 285 (1131)
++ ++++.++..+.+..+.|+++||.|||++++... ++.+..+.|+++|++++|||+|.
T Consensus 241 --------------~~---~~~~~l~~~~~~~~~~t~~~al~~ig~~~~~~~---~~~~~~~~~~~~l~~~~l~hig~~~ 300 (494)
T PRK09606 241 --------------DP---EIVKFMLENLEEAEVDTQEEALEYIGKRVAPGQ---TKEYRIKRAEYVIDRYLLPHLGVEP 300 (494)
T ss_pred --------------cH---HHHHHHHHHHHhcccCCHHHHHHHHHHhcCCCC---CcchHHHHHHHHHHHhhhcccCCCc
Confidence 11 356677777777789999999999999997531 35567789999999999999995
Q ss_pred --chhhHHHHHHHHHHHHhhcCCCCCCCCcccccccEeccchhhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccccchh
Q 001179 286 --NNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNL 363 (1131)
Q Consensus 286 --~~~K~~~L~~MvrkLl~l~~G~~~~DD~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~ 363 (1131)
..+|++||++|++||++++.|.+.+||+|||+||||+++|+||+.+|++.|+++++.++..+++...+ ++..+
T Consensus 301 ~~~~~K~~~L~~m~~kLl~~~~g~~~~Dd~D~l~nkRv~~~G~Ll~~~fr~~l~~~~~~~k~~l~~~~~~-~~~~~---- 375 (494)
T PRK09606 301 EVRRAKAHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERANMR-NRELS---- 375 (494)
T ss_pred chhhHHHHHHHHHHHHHHHHhcCCCCCCCcccccCceeeccchhHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCCC----
Confidence 45799999999999999999999999999999999999999999999999999999999888876643 33222
Q ss_pred HHHHHHHhcCCCcchHHHHHHHhcccCcccccccccccccceEEEccccchHHHhhhccccccCCccccccccccccccC
Q 001179 364 ANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTSVRKLLP 443 (1131)
Q Consensus 364 ~~~~~~i~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~~GvsqvleRln~~~~lSh~Rrv~rg~~~~~~K~t~~R~Lhp 443 (1131)
+..+++ ++.||++|++|||||||.+ +++||||+|+|+||+|+||||||||. ++.+++|.++||+|||
T Consensus 376 --~~~~~~---~~~It~~l~~~~~TGnw~~-------~~~glSq~ldr~N~la~lSh~Rrv~s-~~~r~~~~~~vR~lhp 442 (494)
T PRK09606 376 --IKTAVR---SDVLTERLEHAMATGNWVG-------GRTGVSQLLDRTDYMATLSHLRRVVS-PLSRSQPHFEARDLHP 442 (494)
T ss_pred --HHHhcC---chhhhHHHHHHhhcccccC-------CCceEEEEccCCCHHHHhhHHHhccC-CccccCccccccccCc
Confidence 344554 3489999999999999985 36899999999999999999999997 4678889999999999
Q ss_pred CcccccccCCCCCCccccccccccceEEEeeccCCCCcccccchhhhHHHHHHHhcCceec
Q 001179 444 ESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPS 504 (1131)
Q Consensus 444 s~wGfICPveTPEG~~CGLvk~LA~~a~It~~~~~~~~~~~~~~~~~~i~~~L~~lG~~~~ 504 (1131)
|||||+||||||||+|||||||||++|+|+++.+.+ .|.++|.++|+.++
T Consensus 443 s~~G~iCPveTPEG~~cGLv~~La~~a~V~~~~~~~-----------~i~~~l~~lg~~~~ 492 (494)
T PRK09606 443 TQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEE-----------EVKEILKELGVEPE 492 (494)
T ss_pred ccceecccCcCCCCCcccHHHhhhceEEEeCCCChH-----------HHHHHHHHCcCeeC
Confidence 999999999999999999999999999999885444 68899999999875
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=1e-35 Score=318.25 Aligned_cols=107 Identities=36% Similarity=0.773 Sum_probs=92.1
Q ss_pred hhHHHHHHHHHHHHHHhHHHHH-----------------------------------------HHHHHcCCeeeEEEEEE
Q 001179 14 ELVRHHIESFDYMLDEGLSEMF-----------------------------------------DHCRQAKISYTGKLMAD 52 (1131)
Q Consensus 14 ~Lv~~hi~SFn~Fi~~gl~~ii-----------------------------------------~ecR~r~~TYsa~l~v~ 52 (1131)
||++|||+|||+|+++||++++ +|||+|++||+||++|+
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-ceEEEEEeecccceeeccCcccCCCCChHHHHhhccccccCCcEEEEcCceeEEEEEEec
Q 001179 53 VEFQYLDAGS-PVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILP 122 (1131)
Q Consensus 53 v~~~~~~~~~-~~~~~~v~iG~iPIMvkS~~C~L~~ls~~el~~~gE~~~D~GGYFIING~EKVIr~qi~~ 122 (1131)
|+++++ +. .....+|.+|+|||||+|++|||++++++|+++.||||+|+||||||||+|||||+|+++
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 567789999999999999999999999999999999999999999999999999999876
No 18
>PF04560 RNA_pol_Rpb2_7: RNA polymerase Rpb2, domain 7; InterPro: IPR007641 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 comprised of the structural domains anchor and clamp. The clamp region (C-terminal) contains a zinc-binding motif. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed switch 4. The switches within the polymerase are thought to signal different stages of transcription [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1SMY_M 3DXJ_M 3AOI_C 2A68_M 1ZYR_C 3AOH_H 1IW7_M 2O5J_C 2CW0_M 2O5I_M ....
Probab=99.96 E-value=2.2e-30 Score=234.45 Aligned_cols=81 Identities=48% Similarity=0.901 Sum_probs=75.7
Q ss_pred CceeeeehhhhHHhhhchHHHHHHhhccCCCccceeccccccccccccccccccccccccCCCCCCCCCCCeeeccCcCC
Q 001179 1016 GGIRFGEMERDSLLAHGAAYLLHDRLHTCSDYHVADVCSLCGSVLTATFIHPQKRAIREIGGLPPARAPKKVTCHACQTS 1095 (1131)
Q Consensus 1016 GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~Cg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~ 1095 (1131)
|||||||||||||+|||||++|+|||+++||.++++||.+||++++ .|+.+
T Consensus 1 GG~R~GEMErd~LiahGas~~L~erl~~~SD~~~~~vc~~cg~~~~-----------------------------~~~~~ 51 (81)
T PF04560_consen 1 GGLRFGEMERDALIAHGASFLLKERLFDKSDKYEIDVCSRCGSIAS-----------------------------ICKGK 51 (81)
T ss_dssp CBEEEEHHHHHHHHHTTBHHHHHHHHTTTTTEEEEEEECCCHHHHH-----------------------------TTTTS
T ss_pred CCcchhHHHHHHHHHhhHHHHHHHHhcCCCcCcchhhhccCCCcee-----------------------------EECCC
Confidence 8999999999999999999999999999999999999999998765 35566
Q ss_pred CCcceecchHhHHHHHHHHHhCCceeEEEe
Q 001179 1096 KGMETVAMPYVFRYLAAELAAMNIKITLQL 1125 (1131)
Q Consensus 1096 ~~~~~v~iPy~~klL~~EL~sm~I~~~l~~ 1125 (1131)
.++.++.+|||||||+|||+||||++++.+
T Consensus 52 ~~~~~~~ipy~~klL~~EL~sm~I~~~~~~ 81 (81)
T PF04560_consen 52 PEVKKIEIPYSFKLLIQELRSMGIKIRIKT 81 (81)
T ss_dssp SSEEEEEEEHHHHHHHHHHHCTTEEEEEEE
T ss_pred CeEEeeeCCHHHHHHHHHHHHCcCceEEeC
Confidence 789999999999999999999999999974
No 19
>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=99.93 E-value=5.2e-27 Score=206.16 Aligned_cols=67 Identities=34% Similarity=0.659 Sum_probs=60.7
Q ss_pred EEccccchHHHhhhcccccc-CCccccccccccccccCCcccccccCCCCCCccccccccccceEEEe
Q 001179 407 VQAERLNFLRFISFFRAVHR-GASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVA 473 (1131)
Q Consensus 407 qvleRln~~~~lSh~Rrv~r-g~~~~~~K~t~~R~Lhps~wGfICPveTPEG~~CGLvk~LA~~a~It 473 (1131)
|+|+|+|++++|||+|||++ |.+++++|.+++|+|||||||||||||||||++|||+||||++|+||
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 88899999999999999999999999999999999999999999996
No 20
>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=8e-22 Score=208.12 Aligned_cols=174 Identities=20% Similarity=0.198 Sum_probs=115.3
Q ss_pred cCCceEEEEeccccCCCcceeeEEEEEeeeecCCCceEEEEEEEeCCeEEEEEEEecccccccHhhHHHhccCCCHHHHH
Q 001179 123 KQNYPMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIF 202 (1131)
Q Consensus 123 ~~N~~~~~~r~s~~~r~~~~t~~~i~iRs~~~~~~s~~~~l~~~~~g~~~l~~~~~k~~~~IPi~ilLkALg~~sD~eI~ 202 (1131)
|+|+|++..+.++......+++ .....+..|..+....+ .+.+...+..++||+++||||||++||+||+
T Consensus 1 Rsn~i~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~IPi~ilLrALG~~sd~eI~ 70 (190)
T PF04561_consen 1 RSNGIYVEKDKDGNKIIRSVRS-------DIISSRGSWHYLEKDKK---IIIFSRPKKKFKIPIVILLRALGIESDKEII 70 (190)
T ss_dssp ESSSEEEEE-SSSSSCSSCEEE-------EECCSSSEEEEEECETT---TEEEEETTSSSEEEHHHHHHHTT--STCHHH
T ss_pred CCCEEEEEEccCCCCeeEEEEe-------ecCCCcceEEEEecCCc---EEEEEEcCcccccceEEeehhhcCcCccccc
Confidence 4688888776554432111221 11122333444433333 3344555556789999999999999999999
Q ss_pred HhhccccchhhhcccCCCCChhHHHHHHHHHHHHHhccccCHHHHHHHHhhcccccccCCCCccHHHHHHHHH-------
Q 001179 203 NHLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVI------- 275 (1131)
Q Consensus 203 ~~I~~~~~~~~~~~~~~~~~~~~~~~~~~lL~~~~~~~i~t~~~AL~yIG~~~r~~~~~~~~~~~~e~g~~~L------- 275 (1131)
+.|+. ++ .........+++.....++.|+++||.|||++++. .+.+....+.++.+|
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 11111223345556667899999999999994332 144555666788877
Q ss_pred --Hhhhcc-cCCCchh------hHHHHHHHHHHHHhhcCCCCCCCCcccccccEec
Q 001179 276 --RDYIFV-HLNDNND------KFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEIL 322 (1131)
Q Consensus 276 --~~~ll~-Hl~~~~~------K~~~L~~MvrkLl~l~~G~~~~DD~D~l~NkRv~ 322 (1131)
.+++|+ ||+.... |+.+|++|++||+.++.|.+.+||+|||+||||+
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 467777 9985433 9999999999999999999999999999999996
No 21
>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=99.42 E-value=6.2e-13 Score=115.14 Aligned_cols=63 Identities=24% Similarity=0.381 Sum_probs=54.0
Q ss_pred EEECCEEEeeecCchHHHHHHHHHHHHhhcCCCCCCCceEEEEeCCCCCCCCeEEEEcCCCcceeeEEEecC
Q 001179 519 VLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISL 590 (1131)
Q Consensus 519 V~lnG~~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~~~~~~~~~~i~i~td~GRl~RPv~~~~~ 590 (1131)
|||||.|+|.++ ++.+|+..||.+||+| .++.+++|++.. ..++|+|+||+||++|||+++++
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 VFLNGVWIGIHS--DPEELVKTLRNLRRSG--KISKEVSIVYDI-----REKEIRINTDAGRLCRPLFVVEN 63 (63)
T ss_dssp EEETTEEEEEES--SHHHHHHHHHHHHHTT--SS-TTSEEEEET-----TTTEEEEE-SSCEEEEEEEEESS
T ss_pred CEECCEEEEEEc--CHHHHHHHHHHHhhcc--CCcceeEEEEec-----cCCEEEEEccCCcccceeEEecC
Confidence 799999999986 6799999999999999 788888887643 46899999999999999998864
No 22
>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=99.04 E-value=3.3e-10 Score=96.24 Aligned_cols=58 Identities=48% Similarity=0.940 Sum_probs=55.4
Q ss_pred EeeecCchHHHHHHHHHHHHhhcCCCCCCCceEEEEeCCCCCCCCeEEEEcCCCccee
Q 001179 526 VGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVR 583 (1131)
Q Consensus 526 iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~~~~~~~~~~i~i~td~GRl~R 583 (1131)
|||++++++.++++.||++|..+...+|.++||+|++.+..++||+|||||+++|++|
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 6899999999999999999999988999999999999988899999999999999998
No 23
>KOG0214 consensus RNA polymerase II, second largest subunit [Transcription]
Probab=98.84 E-value=1.6e-10 Score=139.13 Aligned_cols=365 Identities=8% Similarity=-0.148 Sum_probs=235.9
Q ss_pred CCCccccccccccccccccccceEEEecccceeeecCCCcceeecCcccccCcccCCCCcceEEEEEeccCCCCCceEEe
Q 001179 651 NQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMIL 730 (1131)
Q Consensus 651 NqspRn~yqc~M~KQAiG~~~~n~~~R~D~~~y~L~ypQ~PLV~t~~~~~~~~~~~~~G~N~iVAv~~y~Gyn~EDaiii 730 (1131)
-|.+++.++.-|+ |..+-....+..+.+...-.|.+++.++-++......-.-..+.+.++-++.+.+.++..++...-
T Consensus 681 pdh~qspr~tYQs-a~~kqamg~y~tn~~vR~dtl~~~l~ypqkpl~tt~~~e~l~~~eL~aG~NaiVAi~~~~GYNqED 759 (1141)
T KOG0214|consen 681 PDHNQSPRNTYQS-AMGKQAMGVYHTNPQVRMDTLAKVLYYPQKPLVTTRAMEYLRFRELPAGQNAIVAIACYSGYNQED 759 (1141)
T ss_pred CCCCCchHHHHHH-HHhhhcceeeeecchhhhhhhhhcccccccchhhHHHHhhhhhhhcccccceEEEEecccCccHHH
Confidence 4555666655555 222333344555555555566666666665555554433445779999999999999999999999
Q ss_pred eccccccCceeeeEEEEEEEEecccCCCccccccccccCCCChhhhcccCCCCCcccCc---EEcCCCCeeEEeecC---
Q 001179 731 NKSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFRRNKDAKSLHSVIDSDGLPYVGQ---MIHPGEPYCSIYDKT--- 804 (1131)
Q Consensus 731 nk~s~~rG~~~~~~y~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~Ld~dGi~~~G~---~v~~gdil~~~~~~~--- 804 (1131)
|--..++++.|+.++..+ +. ..+......... ++..-........-|. +-|. .-..|=+..|.-...
T Consensus 760 svimn~s~v~rg~FrS~~-~R--sYk~q~~~~~~~---~ee~~~~~~~~~~~~m-r~~~~dkLdddG~i~~G~~vs~~Dv 832 (1141)
T KOG0214|consen 760 SVIMNQSSVDRGLFRSFF-IR--SYKDQEHKKDQG---PEEIFEEPPRGEGRGM-RNGKYDKLDDDGIIMPGSRVSGGDV 832 (1141)
T ss_pred HHHHHhhhhhcchhhhhh-hh--HHHhhhhhcccc---cccccccccccccccc-cccccccccccCCccccceeecCCE
Confidence 999999999998855433 21 111100000000 1100000000100011 0000 001111112211100
Q ss_pred -CCcEEeeecCCCcc--------eEEEEEEEeccCCCCCCeEEEEEEeeecCCCCCcccccccCCcceeeeeecCCCCCc
Q 001179 805 -TNSWRTNSRKGSES--------VFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPF 875 (1131)
Q Consensus 805 -~~~~~~~~~~~~e~--------g~Vd~v~~~~~~~~~~~~~~~i~~r~~R~p~iGDKf~sRHGqKGvvs~i~~~~dmPf 875 (1131)
-++.....-+..+. ++..++.+-.++.| ...+|.++. ++.|+||+..|++++-+.++-...++++
T Consensus 833 ~iGk~t~~~~~~~~~~~~~~~~t~~d~s~~Lr~~e~G---ivd~V~vt~---n~~G~kF~kv~vr~~ripqiGDKfasrH 906 (1141)
T KOG0214|consen 833 LIGKTTPQPAKEDESGPEDRLYTKRDHSTKLRHTERG---IVDQVWVTK---NSEGPKFVKVRVRQVRIPQIGDKFASRH 906 (1141)
T ss_pred EeccccCCcccchhccccccccccccceeecccCCcc---eEEEEEEec---CCCCCceeEEEEeecccccccchhcccc
Confidence 01211111222222 35566666555433 233444443 7999999999999999999999999999
Q ss_pred cCCCCCcccEEeCCCCCCCccchhHhHHHHHhhhccccCceeccccccccccccCCCCCCCCchhhHHHHHHHHHHCCCC
Q 001179 876 SGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKGGSLHGKFMDATPFANSVKKTNGDTGTDESKSLVDELGEMLRTCGFN 955 (1131)
Q Consensus 876 ~~~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tpf~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~ 955 (1131)
- ..|++++++.+++.-++++++-..+++-.-+. |-.. .+..+.+-+. |-.
T Consensus 907 g-qKG~ig~~~~qedmpft~eGi~pDiiiNPhai-----------PSRm----------------tig~liEc~l--gk~ 956 (1141)
T KOG0214|consen 907 G-QKGTIGITYRQEDMPFTIEGIVPDIIINPHAI-----------PSRM----------------TIGQLIECLL--GKV 956 (1141)
T ss_pred c-cCccccceeecCCCCccccCCCcceEECcccC-----------cccc----------------chhhhHHHhh--hhh
Confidence 9 99999999999999999999887776532221 1111 1222222221 112
Q ss_pred CCCcEEEeeCCCCcEeeeeeeeeceeEEeeccccccceeeeecccccceeecccCcccccCceeeeehhhhHHhhhchHH
Q 001179 956 YHGVEVLYSGVYGTELTCEIFIGPVYYQRLRHMVSDKFQVRSTGTMDQITRQPIKGRKRGGGIRFGEMERDSLLAHGAAY 1035 (1131)
Q Consensus 956 ~~G~e~~y~g~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lTrQP~~Gr~~~GG~R~GEMErd~l~a~Gas~ 1035 (1131)
.-++..++++.++.. -+-.+++..+++...|+..++.+++.+++....+++++++.-..++.+++||+++|=..++.+-
T Consensus 957 ~a~~~e~~~atpFs~-v~v~~is~~l~~~g~~~~G~e~~ynGrtG~~~~~~if~GptyyqrL~Hmvd~kih~R~~Gp~q~ 1035 (1141)
T KOG0214|consen 957 AAYEGEEGDATPFSD-VTVSKISANLHVYGYQYRGNERMYNGRTGRKLRAQIFIGPTYYQRLKHMVDDKIHSRARGPVQI 1035 (1141)
T ss_pred hhcccccccCCCCCc-cchhcccchHHHhccccCCCEEEecCCCCceeeeeeecCchHHHHHHHhhhheeeecccCCcee
Confidence 223445556555555 4567899999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhccCCCccceeccccccccc
Q 001179 1036 LLHDRLHTCSDYHVADVCSLCGSVL 1060 (1131)
Q Consensus 1036 ~l~erl~~~SD~~~~~vC~~Cg~~~ 1060 (1131)
+.++.+...|++...++|+-|+..+
T Consensus 1036 ltRQP~~gRsr~GGlRfGEMErdc~ 1060 (1141)
T KOG0214|consen 1036 LTRQPVEGRSRDGGLRFGEMERDCL 1060 (1141)
T ss_pred eeccccccccccCCeeeehhHHHHH
Confidence 9999999999999999999999644
No 24
>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=98.43 E-value=1e-07 Score=78.35 Aligned_cols=40 Identities=25% Similarity=0.185 Sum_probs=30.1
Q ss_pred CcceeeecccceeeeeeecCCCCCC--CCCCCCceeEEeecC
Q 001179 595 SQNIELIGPFEQVFMEIRCPDGGDG--GRRNAFPATHEEIHP 634 (1131)
Q Consensus 595 ~g~iE~i~~~Eq~~~~Ia~~~~~~~--~~~~~~~~th~EI~P 634 (1131)
.|.|||||++||++++||++++++. +......||||||||
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 4799999999999999999998886 322345699999998
No 25
>KOG0215 consensus RNA polymerase III, second largest subunit [Transcription]
Probab=97.79 E-value=1.4e-05 Score=96.43 Aligned_cols=353 Identities=11% Similarity=-0.054 Sum_probs=188.9
Q ss_pred EEEeecccceeeccCcccCCCCChHHHHhhccccccCCcEEEEcCceeEEEEEEeccCCceEEEEeccccCCCcceeeEE
Q 001179 67 ERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRSSFRDRREGYTDKA 146 (1131)
Q Consensus 67 ~~v~iG~iPIMvkS~~C~L~~ls~~el~~~gE~~~D~GGYFIING~EKVIr~qi~~~~N~~~~~~r~s~~~r~~~~t~~~ 146 (1131)
..+..|.-|||+.+.-|.+++...+ ....|||+.++++||+.++++.+|.++..-..+ +-.++.++.+ -.
T Consensus 189 yfiv~G~ekViLiqeqlsknrii~~-~~k~~~~~~svtsst~e~kskt~v~~k~~k~yl-----k~~~~~d~ip----iv 258 (1153)
T KOG0215|consen 189 YFIVKGTEKVILIQEQLSKNRIIVE-EDKKGNLQASVTSSTHERKSKTYVTTKKGKYYL-----KHNSFTDDIP----IV 258 (1153)
T ss_pred eeEeccceeEEEehhhhhccCeeec-cccCCccccccccceeeecceEEEEeccceeee-----ehhhhhccCC----EE
Confidence 4578999999999999999998887 677899999999999999999999555332222 2223333332 11
Q ss_pred EEEeee--ecCCCceEEEEEEEeCCeEEEEEEEecccccccHhhHHHhccCCCHHHHHHhhccccchhhhcccCCCCChh
Q 001179 147 VVIRCV--RKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSPL 224 (1131)
Q Consensus 147 i~iRs~--~~~~~s~~~~l~~~~~g~~~l~~~~~k~~~~IPi~ilLkALg~~sD~eI~~~I~~~~~~~~~~~~~~~~~~~ 224 (1131)
+.++-+ ..|+....+.- .+.-+.+.... ....|+.+-+.+. +.-++.+.. ++....
T Consensus 259 iv~ka~g~~sd~ei~~~vg----~~~~y~~~~~~--s~ee~~~~~v~tq-----qqal~y~~~-------kvk~~~---- 316 (1153)
T KOG0215|consen 259 IVLKAMGLESDQEIVQLVG----GDSKYQDIFAP--SLEECVSLGVYTQ-----QQALEYIGS-------KVKVKR---- 316 (1153)
T ss_pred EEEeeccccchHHHHHHhh----cchHHHHhhcc--chhhhhhhhhHHH-----HHHHHHhhh-------eEEecc----
Confidence 221111 01111100000 00000000000 0012222222222 111222110 000000
Q ss_pred HHHHHHHHHHHHHhccccCHHHHHHHHhhcccccccC-----CCCccHH-HHHHHHHHhhhcccCCCc--hhhHHHHHHH
Q 001179 225 VSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDG-----LQSESYY-AVAETVIRDYIFVHLNDN--NDKFNLLIFM 296 (1131)
Q Consensus 225 ~~~~~~~lL~~~~~~~i~t~~~AL~yIG~~~r~~~~~-----~~~~~~~-e~g~~~L~~~ll~Hl~~~--~~K~~~L~~M 296 (1131)
.....-.++|++.+...+...... +.+.-.+ -..+.++.-.+-+-.-++ .-+-..|-.|
T Consensus 317 -------------~t~~~~~~e~~~~l~~~~lahv~v~~~~~r~K~~yi~~m~rr~~~a~l~~~~~ddrd~~gnkrlela 383 (1153)
T KOG0215|consen 317 -------------GTTPTKDEEALEVLSTTVLAHVPVPDLNFRMKAIYIGLMVRRVIQAMLNKLAMDDRDYVGNKRLELA 383 (1153)
T ss_pred -------------CCCCCchHHHHHHHHhhheeceeccCCCCcceeehHHHHHHHHHHHHhCcccccchhhhccchHHHH
Confidence 001122455666666554433221 1111111 122222222222211121 1122235555
Q ss_pred HHHHHhhcCCCCCCCCcccccccEeccchhhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccccchhHHHHHHHhcCCCc
Q 001179 297 LQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSK 376 (1131)
Q Consensus 297 vrkLl~l~~G~~~~DD~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~ 376 (1131)
.+ |+.+..+.-..++.+.|++.+-...+.++..++-+.++.+. ..+..+..-+.+. .+.- ...++. ++ ..
T Consensus 384 gq-llsllfeD~fk~~n~e~k~~~dk~l~k~~ra~~fD~~~~~n-~~~~~it~~l~ra-~stg---nw~iKr-fr---me 453 (1153)
T KOG0215|consen 384 GQ-LLSLLFEDLFKRFNSELKKNIDKILKKPIRAQEFDALKHLN-VRANMITSGLERA-ISTG---NWSIKR-FR---ME 453 (1153)
T ss_pred HH-HHHHHHHHHHHHHHHHHHHHHHHHhcchhhhhhhHHHHHHH-HHHHHHHHHHHHH-hhcC---chHHHH-hh---hh
Confidence 44 56666777777899999999999999999888888888775 4455554444331 1100 011211 11 11
Q ss_pred chHHHHHHHhcccCcccccccccccccceEEEccccchHHHh-hhccccccCCccccccccccccccCCcccccccCCCC
Q 001179 377 QIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFI-SFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTP 455 (1131)
Q Consensus 377 ~It~~i~~~~sTGnw~~~~~~~~~q~~GvsqvleRln~~~~l-Sh~Rrv~rg~~~~~~K~t~~R~Lhps~wGfICPveTP 455 (1131)
-++...--+..|++|... ..-.-++++.++..+..+.|.. |.++++-+ +.+....+-++-.++..|+.|||-++|
T Consensus 454 r~gvt~VlsrlSyisaLg--mmtri~s~fektrkvsgprSlq~sqwgmlcp--~dtpegeacglvknlalmthittd~ee 529 (1153)
T KOG0215|consen 454 RAGVTQVLSRLSYISALG--MMTRINSQFEKTRKVSGPRSLQPSQWGMLCP--SDTPEGEACGLVKNLALMTHITTDSEE 529 (1153)
T ss_pred hccceeeehhhhhhhhhh--hheehhhhheeehhccCccccChhhcccccC--CCCCCccccccccchHHHhcccCCCCc
Confidence 222223334556777643 1224678888887765554433 34444442 345666778899999999999999999
Q ss_pred CCccccccccccceEEEeeccCC
Q 001179 456 DGEPCGLLNHMTSTCRVASYYDS 478 (1131)
Q Consensus 456 EG~~CGLvk~LA~~a~It~~~~~ 478 (1131)
++..|++.|+.+...+++.+...
T Consensus 530 ~pi~~~~~k~gv~di~~v~~~e~ 552 (1153)
T KOG0215|consen 530 KPILKLCYKLGVEDIHVVSGREL 552 (1153)
T ss_pred chhHHHHHHhcceeeeeeccccc
Confidence 99999999999999999876443
No 26
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]
Probab=97.70 E-value=5.3e-05 Score=96.48 Aligned_cols=73 Identities=21% Similarity=0.376 Sum_probs=60.7
Q ss_pred eeEEeecCCCcccceeccccCCCCCCCccccccccccccccccccceEEEecccceeeecCCCcceeecCcccccCcccC
Q 001179 627 ATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEY 706 (1131)
Q Consensus 627 ~th~EI~P~~ilsv~AslIPF~~HNqspRn~yqc~M~KQAiG~~~~n~~~R~D~~~y~L~ypQ~PLV~t~~~~~~~~~~~ 706 (1131)
.+||+++|.++.++.+++|||.+|+++.|.+|+++|+|||+| |..+..|||.|+ ++...-.|
T Consensus 526 ~~~~dv~~~~~~~~~~~~~P~l~~dd~~~~l~~~~mqr~~~~----------------l~~~~~~lv~tG-~E~~~a~e- 587 (1060)
T COG0085 526 VDYMDVSPKQVVSVGRSLIPFLEHDDANRALMGSNMQRQAVP----------------LLRTEAPLVGTG-MEYLDAED- 587 (1060)
T ss_pred ccceeccceEEeccccccCceeEEcCchHhhhhhhhhhhccc----------------ccccccccccCC-ceeecccc-
Confidence 689999999999999999999999999999999999999998 556899999999 77653221
Q ss_pred CCCcceEEEEEec
Q 001179 707 PTGTNAIVAVLAY 719 (1131)
Q Consensus 707 ~~G~N~iVAv~~y 719 (1131)
-.|++||.-+.
T Consensus 588 --~~~~~ia~~~~ 598 (1060)
T COG0085 588 --SGAAVIAKRPG 598 (1060)
T ss_pred --ccceeEeccCC
Confidence 23556665443
No 27
>PHA03394 lef-8 DNA-directed RNA polymerase subunit beta-like protein; Provisional
Probab=94.23 E-value=0.052 Score=67.22 Aligned_cols=77 Identities=26% Similarity=0.313 Sum_probs=52.5
Q ss_pred EEEEEEeeecCCCCCcccccccCCcceeeeeecCCCCC-ccCCCCCcccEEeCCCCCCCccchhHhHHHHHhhhccccCc
Q 001179 837 KANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMP-FSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKGGSLHGK 915 (1131)
Q Consensus 837 ~~~i~~r~~R~p~iGDKf~sRHGqKGvvs~i~~~~dmP-f~~~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~ 915 (1131)
.+++++-..=.=-.|=|.||=||||||+.. .||+- |..|||+.|-|.++|.++-||.|.=-=+| -|-....|.
T Consensus 697 ~lKl~~Vtst~dLeGlKICgIHGQKGVln~---seDLtew~aeDg~~aQIclSPiSyLsRQtnf~~~~---~Ky~v~gg~ 770 (865)
T PHA03394 697 YLKIRLVTSTSDLEGLKICGIHGQKGVLNG---SEDLTEWMAEDGTHAQICLSPISYLSRQTNFDDIE---RKYVVRGGD 770 (865)
T ss_pred EEEEEEEEEecCcceeEEeeecccccccCC---cchhhhhhccCCCcceEEechHHhhccccccccCc---eEEEEECCC
Confidence 344444222223459999999999999864 55653 44489999999999999999998633333 354555555
Q ss_pred eecc
Q 001179 916 FMDA 919 (1131)
Q Consensus 916 ~~d~ 919 (1131)
+.|.
T Consensus 771 ~~~~ 774 (865)
T PHA03394 771 HSDP 774 (865)
T ss_pred cCCC
Confidence 5543
No 28
>PF14251 DUF4346: Domain of unknown function (DUF4346)
Probab=48.75 E-value=8.5 Score=37.78 Aligned_cols=13 Identities=31% Similarity=0.501 Sum_probs=10.7
Q ss_pred cccccCCcEEEEc
Q 001179 98 EEAAEMGGYFILN 110 (1131)
Q Consensus 98 E~~~D~GGYFIIN 110 (1131)
--.+||+|||||.
T Consensus 11 ~i~LDp~GYfiI~ 23 (119)
T PF14251_consen 11 FIDLDPAGYFIIY 23 (119)
T ss_pred ccccCCCccEEEE
Confidence 3457999999996
No 29
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=48.68 E-value=9.5 Score=38.93 Aligned_cols=37 Identities=22% Similarity=0.520 Sum_probs=27.6
Q ss_pred CccceeccccccccccccccccccccccccCCCCCCCCCCCeeeccCcCCCCcceecch
Q 001179 1046 DYHVADVCSLCGSVLTATFIHPQKRAIREIGGLPPARAPKKVTCHACQTSKGMETVAMP 1104 (1131)
Q Consensus 1046 D~~~~~vC~~Cg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~v~iP 1104 (1131)
-...+-.|.+||.+.++- +.+|..|.+..++..+++|
T Consensus 25 ~kl~g~kC~~CG~v~~PP----------------------r~~Cp~C~~~~~~E~vels 61 (140)
T COG1545 25 GKLLGTKCKKCGRVYFPP----------------------RAYCPKCGSETELEWVELS 61 (140)
T ss_pred CcEEEEEcCCCCeEEcCC----------------------cccCCCCCCCCceEEEEeC
Confidence 456678899999987763 3689999877666666654
No 30
>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=36.14 E-value=43 Score=42.20 Aligned_cols=32 Identities=25% Similarity=0.287 Sum_probs=25.3
Q ss_pred CCCCcccccccEeccchhhHHHHHHHHHHHHH
Q 001179 309 VSDNPDSLQNQEILLPGHLITIYLKEKLEDWL 340 (1131)
Q Consensus 309 ~~DD~D~l~NkRv~l~G~Ll~~lf~~~~~~~l 340 (1131)
..=.+|+|+||=+--...||..++...++.+.
T Consensus 209 i~Y~IDsLsNKiIYkh~yLl~l~y~~~L~~~~ 240 (748)
T PF04941_consen 209 INYSIDSLSNKIIYKHSYLLELTYKPILKKYE 240 (748)
T ss_pred CCceecccccceeeCHHHHHHHHHHHHHHHHH
Confidence 33578999999999999999998876555444
No 31
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=31.23 E-value=31 Score=28.49 Aligned_cols=11 Identities=36% Similarity=1.035 Sum_probs=8.8
Q ss_pred ccccccccccc
Q 001179 1052 VCSLCGSVLTA 1062 (1131)
Q Consensus 1052 vC~~Cg~~~~~ 1062 (1131)
.|+.||.++..
T Consensus 2 FCp~Cg~~l~~ 12 (52)
T smart00661 2 FCPKCGNMLIP 12 (52)
T ss_pred CCCCCCCcccc
Confidence 58999988765
No 32
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=28.02 E-value=20 Score=31.95 Aligned_cols=35 Identities=23% Similarity=0.471 Sum_probs=20.5
Q ss_pred ceeccccccccccccccccccccccccCCCCCCCCCCCeeeccCcCCCCcceecc
Q 001179 1049 VADVCSLCGSVLTATFIHPQKRAIREIGGLPPARAPKKVTCHACQTSKGMETVAM 1103 (1131)
Q Consensus 1049 ~~~vC~~Cg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~v~i 1103 (1131)
.++-| .||..+++. ...+...| .|+..-+|.++.|
T Consensus 2 lifrC-~Cgr~lya~------------------e~~kTkkC-~CG~~l~vk~~rI 36 (68)
T PF09082_consen 2 LIFRC-DCGRYLYAK------------------EGAKTKKC-VCGKTLKVKERRI 36 (68)
T ss_dssp EEEEE-TTS--EEEE------------------TT-SEEEE-TTTEEEE--SSS-
T ss_pred EEEEe-cCCCEEEec------------------CCcceeEe-cCCCeeeeeeEEE
Confidence 35679 799988875 22345689 9998777766665
No 33
>PRK00420 hypothetical protein; Validated
Probab=27.93 E-value=35 Score=33.55 Aligned_cols=26 Identities=23% Similarity=0.497 Sum_probs=19.3
Q ss_pred eeccccccccccccccccccccccccCCCCCCCCCCCeeeccCcC
Q 001179 1050 ADVCSLCGSVLTATFIHPQKRAIREIGGLPPARAPKKVTCHACQT 1094 (1131)
Q Consensus 1050 ~~vC~~Cg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~ 1094 (1131)
...|+.||..++.. +.+..+|+.|+.
T Consensus 23 ~~~CP~Cg~pLf~l-------------------k~g~~~Cp~Cg~ 48 (112)
T PRK00420 23 SKHCPVCGLPLFEL-------------------KDGEVVCPVHGK 48 (112)
T ss_pred cCCCCCCCCcceec-------------------CCCceECCCCCC
Confidence 36799999887752 234579999985
No 34
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=27.79 E-value=36 Score=36.21 Aligned_cols=30 Identities=17% Similarity=0.204 Sum_probs=22.4
Q ss_pred hchHHHHHHhhccCCCccceecccccccccc
Q 001179 1031 HGAAYLLHDRLHTCSDYHVADVCSLCGSVLT 1061 (1131)
Q Consensus 1031 ~Gas~~l~erl~~~SD~~~~~vC~~Cg~~~~ 1061 (1131)
|-...-|+++|-..++. ..++|++||.-.+
T Consensus 99 ~~~~~klk~~l~~e~~~-~~Y~Cp~C~~ryt 128 (178)
T PRK06266 99 MEELKKLKEQLEEEENN-MFFFCPNCHIRFT 128 (178)
T ss_pred HHHHHHHHHHhhhccCC-CEEECCCCCcEEe
Confidence 44566788988776665 7899999996544
No 35
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=27.77 E-value=28 Score=35.10 Aligned_cols=31 Identities=26% Similarity=0.525 Sum_probs=22.2
Q ss_pred cceeccccccccccccccccccccccccCCCCCCCCCCCeeeccCcCCCCc
Q 001179 1048 HVADVCSLCGSVLTATFIHPQKRAIREIGGLPPARAPKKVTCHACQTSKGM 1098 (1131)
Q Consensus 1048 ~~~~vC~~Cg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~ 1098 (1131)
....-|+.||..++. +.+.-+|+.|+....+
T Consensus 26 ML~~hCp~Cg~PLF~--------------------KdG~v~CPvC~~~~~~ 56 (131)
T COG1645 26 MLAKHCPKCGTPLFR--------------------KDGEVFCPVCGYREVV 56 (131)
T ss_pred HHHhhCcccCCccee--------------------eCCeEECCCCCceEEE
Confidence 346679999998875 3456799999854333
No 36
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=26.63 E-value=26 Score=30.37 Aligned_cols=18 Identities=22% Similarity=0.527 Sum_probs=11.7
Q ss_pred CCccceeccccccccccc
Q 001179 1045 SDYHVADVCSLCGSVLTA 1062 (1131)
Q Consensus 1045 SD~~~~~vC~~Cg~~~~~ 1062 (1131)
++.....+|..||..+..
T Consensus 2 ~~~~~~~~CtSCg~~i~~ 19 (59)
T PRK14890 2 SEMMEPPKCTSCGIEIAP 19 (59)
T ss_pred cccccCccccCCCCcccC
Confidence 345566778888866553
No 37
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=26.23 E-value=31 Score=24.76 Aligned_cols=11 Identities=27% Similarity=0.791 Sum_probs=7.9
Q ss_pred ecccccccccc
Q 001179 1051 DVCSLCGSVLT 1061 (1131)
Q Consensus 1051 ~vC~~Cg~~~~ 1061 (1131)
..|++||....
T Consensus 3 ~~Cp~Cg~~~~ 13 (26)
T PF13248_consen 3 MFCPNCGAEID 13 (26)
T ss_pred CCCcccCCcCC
Confidence 46999997433
No 38
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=25.98 E-value=50 Score=26.89 Aligned_cols=27 Identities=22% Similarity=0.470 Sum_probs=17.9
Q ss_pred eeccccccccccccccccccccccccCCCCCCCCCCCeeeccCcC
Q 001179 1050 ADVCSLCGSVLTATFIHPQKRAIREIGGLPPARAPKKVTCHACQT 1094 (1131)
Q Consensus 1050 ~~vC~~Cg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~ 1094 (1131)
.+.|++||...... .......|+.|+.
T Consensus 3 ~y~C~~CG~~~~~~------------------~~~~~~~Cp~CG~ 29 (46)
T PRK00398 3 EYKCARCGREVELD------------------EYGTGVRCPYCGY 29 (46)
T ss_pred EEECCCCCCEEEEC------------------CCCCceECCCCCC
Confidence 57899999765542 0111478999974
No 39
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=24.85 E-value=45 Score=25.80 Aligned_cols=28 Identities=29% Similarity=0.789 Sum_probs=13.1
Q ss_pred ccccccccccccccccccccccccCCCCCCCCCCCeeeccCc
Q 001179 1052 VCSLCGSVLTATFIHPQKRAIREIGGLPPARAPKKVTCHACQ 1093 (1131)
Q Consensus 1052 vC~~Cg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~ 1093 (1131)
.|+.||..+...+ ..+....+.+|..|+
T Consensus 2 fC~~CG~~l~~~i--------------p~gd~r~R~vC~~Cg 29 (34)
T PF14803_consen 2 FCPQCGGPLERRI--------------PEGDDRERLVCPACG 29 (34)
T ss_dssp B-TTT--B-EEE----------------TT-SS-EEEETTTT
T ss_pred ccccccChhhhhc--------------CCCCCccceECCCCC
Confidence 4899997765431 111234568899986
No 40
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=24.02 E-value=43 Score=31.34 Aligned_cols=30 Identities=23% Similarity=0.551 Sum_probs=21.2
Q ss_pred ccceeccccccccccccccccccccccccCCCCCCCCCCCeeeccCcC
Q 001179 1047 YHVADVCSLCGSVLTATFIHPQKRAIREIGGLPPARAPKKVTCHACQT 1094 (1131)
Q Consensus 1047 ~~~~~vC~~Cg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~ 1094 (1131)
....++|+.||+-...- .....|.|+.|+.
T Consensus 32 ~~~~~~Cp~C~~~~VkR------------------~a~GIW~C~kCg~ 61 (89)
T COG1997 32 QRAKHVCPFCGRTTVKR------------------IATGIWKCRKCGA 61 (89)
T ss_pred HhcCCcCCCCCCcceee------------------eccCeEEcCCCCC
Confidence 34578999999875432 1335689999975
No 41
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=23.71 E-value=54 Score=38.00 Aligned_cols=10 Identities=20% Similarity=0.454 Sum_probs=5.7
Q ss_pred HHHHHhhccc
Q 001179 247 CLQHIGEHFQ 256 (1131)
Q Consensus 247 AL~yIG~~~r 256 (1131)
+=--||+.||
T Consensus 71 ~~ltLGnLfR 80 (389)
T COG2956 71 AHLTLGNLFR 80 (389)
T ss_pred HHHHHHHHHH
Confidence 4445666666
No 42
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 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. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=22.99 E-value=41 Score=26.05 Aligned_cols=13 Identities=31% Similarity=0.825 Sum_probs=10.2
Q ss_pred ecccccccccccc
Q 001179 1051 DVCSLCGSVLTAT 1063 (1131)
Q Consensus 1051 ~vC~~Cg~~~~~~ 1063 (1131)
.-|+.||.++...
T Consensus 2 ~FCp~C~nlL~p~ 14 (35)
T PF02150_consen 2 RFCPECGNLLYPK 14 (35)
T ss_dssp -BETTTTSBEEEE
T ss_pred eeCCCCCccceEc
Confidence 4699999999864
No 43
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=22.99 E-value=54 Score=34.50 Aligned_cols=12 Identities=33% Similarity=0.728 Sum_probs=9.8
Q ss_pred eecccccccccc
Q 001179 1050 ADVCSLCGSVLT 1061 (1131)
Q Consensus 1050 ~~vC~~Cg~~~~ 1061 (1131)
+|||..||-+.-
T Consensus 134 ~~vC~vCGy~~~ 145 (166)
T COG1592 134 VWVCPVCGYTHE 145 (166)
T ss_pred EEEcCCCCCccc
Confidence 999999996543
No 44
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=22.68 E-value=54 Score=26.46 Aligned_cols=25 Identities=28% Similarity=0.696 Sum_probs=17.7
Q ss_pred eeccccccccccccccccccccccccCCCCCCCCCCCeeeccCc
Q 001179 1050 ADVCSLCGSVLTATFIHPQKRAIREIGGLPPARAPKKVTCHACQ 1093 (1131)
Q Consensus 1050 ~~vC~~Cg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~ 1093 (1131)
...|+.||..+..+ +.+..+|..|+
T Consensus 17 ~~~Cp~C~~PL~~~-------------------k~g~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCPDCGTPLMRD-------------------KDGKIYCVSCG 41 (41)
T ss_pred cCccCCCCCeeEEe-------------------cCCCEECCCCC
Confidence 35699999887653 23457899884
No 45
>CHL00207 rpoB RNA polymerase beta subunit; Provisional
Probab=22.33 E-value=2.6e+02 Score=37.96 Aligned_cols=37 Identities=11% Similarity=-0.049 Sum_probs=24.1
Q ss_pred CcceeeEEEecCCCC-CCcceeeecccceeeeeeecCC
Q 001179 579 PKFVRPVRNISLPSE-ESQNIELIGPFEQVFMEIRCPD 615 (1131)
Q Consensus 579 GRl~RPv~~~~~~~~-~~g~iE~i~~~Eq~~~~Ia~~~ 615 (1131)
|=+--|.+.+.+++. ....++|+.+.|+....||-..
T Consensus 440 GfietPy~~v~~g~v~~~~~i~ylsa~~e~~~~Ia~~~ 477 (1077)
T CHL00207 440 GFIETPFYKVINGKVKKFGNPIYLTADSEDLYRIAPND 477 (1077)
T ss_pred CceeCceEEEEcCcccccCceeecChHHhcCcEEEecC
Confidence 444445665555432 1236889999999999998543
No 46
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=22.13 E-value=51 Score=27.71 Aligned_cols=24 Identities=25% Similarity=0.718 Sum_probs=17.4
Q ss_pred eeccccccc-cccccccccccccccccCCCCCCCCCCCeeeccCc
Q 001179 1050 ADVCSLCGS-VLTATFIHPQKRAIREIGGLPPARAPKKVTCHACQ 1093 (1131)
Q Consensus 1050 ~~vC~~Cg~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~ 1093 (1131)
...|++||+ ++... ...+.|..|+
T Consensus 20 ~~fCP~Cg~~~m~~~--------------------~~r~~C~~Cg 44 (50)
T PRK00432 20 NKFCPRCGSGFMAEH--------------------LDRWHCGKCG 44 (50)
T ss_pred cCcCcCCCcchhecc--------------------CCcEECCCcC
Confidence 458999998 65542 2368999996
No 47
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=21.97 E-value=57 Score=25.07 Aligned_cols=12 Identities=33% Similarity=0.814 Sum_probs=9.6
Q ss_pred eecccccccccc
Q 001179 1050 ADVCSLCGSVLT 1061 (1131)
Q Consensus 1050 ~~vC~~Cg~~~~ 1061 (1131)
.|+|..||-+..
T Consensus 2 ~~~C~~CG~i~~ 13 (34)
T cd00729 2 VWVCPVCGYIHE 13 (34)
T ss_pred eEECCCCCCEeE
Confidence 589999997644
No 48
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=21.57 E-value=61 Score=26.48 Aligned_cols=28 Identities=29% Similarity=0.681 Sum_probs=18.5
Q ss_pred eeccccccccccccccccccccccccCCCCCCCCCCCeeeccCcC
Q 001179 1050 ADVCSLCGSVLTATFIHPQKRAIREIGGLPPARAPKKVTCHACQT 1094 (1131)
Q Consensus 1050 ~~vC~~Cg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~ 1094 (1131)
..+|+.||+.....+ .....+.|..|..
T Consensus 18 g~~CP~Cg~~~~~~~-----------------~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 18 GFVCPHCGSTKHYRL-----------------KTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCCeeeEEe-----------------CCCCeEECCCCCC
Confidence 377999998744321 1235688999963
No 49
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=21.10 E-value=47 Score=35.44 Aligned_cols=36 Identities=22% Similarity=0.445 Sum_probs=26.2
Q ss_pred eeccccccccccccccccccccccccCCCCCCCCCCCeeeccCcCCCCcceecchHh
Q 001179 1050 ADVCSLCGSVLTATFIHPQKRAIREIGGLPPARAPKKVTCHACQTSKGMETVAMPYV 1106 (1131)
Q Consensus 1050 ~~vC~~Cg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~v~iPy~ 1106 (1131)
--.|++||..+... -...+|+.|+ .+...++..||-
T Consensus 149 ~A~CsrC~~~L~~~--------------------~~~l~Cp~Cg-~tEkRKia~~y~ 184 (188)
T COG1096 149 YARCSRCRAPLVKK--------------------GNMLKCPNCG-NTEKRKIAKDYG 184 (188)
T ss_pred EEEccCCCcceEEc--------------------CcEEECCCCC-CEEeeeeccccc
Confidence 34799999876642 1247999998 467788888874
No 50
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=20.19 E-value=63 Score=24.53 Aligned_cols=26 Identities=23% Similarity=0.660 Sum_probs=17.7
Q ss_pred eeccccccccccccccccccccccccCCCCCCCCCCCeeeccCcCC
Q 001179 1050 ADVCSLCGSVLTATFIHPQKRAIREIGGLPPARAPKKVTCHACQTS 1095 (1131)
Q Consensus 1050 ~~vC~~Cg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~ 1095 (1131)
.++|..||-+.... ...+.|+.|+.+
T Consensus 1 ~~~C~~CGy~y~~~--------------------~~~~~CP~Cg~~ 26 (33)
T cd00350 1 KYVCPVCGYIYDGE--------------------EAPWVCPVCGAP 26 (33)
T ss_pred CEECCCCCCEECCC--------------------cCCCcCcCCCCc
Confidence 37899999664432 124689999754
Done!