Query 001050
Match_columns 1173
No_of_seqs 208 out of 1924
Neff 6.7
Searched_HMMs 46136
Date Thu Mar 28 14:26:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001050.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001050hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0214 RNA polymerase II, sec 100.0 4E-274 9E-279 2355.3 57.6 1091 23-1171 2-1140(1141)
2 PRK08565 DNA-directed RNA poly 100.0 7E-270 1E-274 2548.4 91.4 1058 26-1171 1-1100(1103)
3 KOG0216 RNA polymerase I, seco 100.0 1E-250 3E-255 2139.7 60.2 1049 26-1171 5-1111(1111)
4 KOG0215 RNA polymerase III, se 100.0 1E-249 3E-254 2121.8 46.3 1066 19-1171 39-1149(1153)
5 COG0085 RpoB DNA-directed RNA 100.0 6E-244 1E-248 2206.0 70.2 987 22-1171 10-1057(1060)
6 TIGR02013 rpoB DNA-directed RN 100.0 2E-223 3E-228 2091.6 71.8 911 26-1168 7-1065(1065)
7 cd00653 RNA_pol_B_RPB2 RNA pol 100.0 5E-221 1E-225 2062.0 73.7 837 39-1169 1-866 (866)
8 PRK00405 rpoB DNA-directed RNA 100.0 3E-220 7E-225 2071.8 75.2 912 27-1170 15-1107(1112)
9 CHL00001 rpoB RNA polymerase b 100.0 4E-217 9E-222 2021.6 72.6 920 34-1170 10-1057(1070)
10 CHL00207 rpoB RNA polymerase b 100.0 2E-203 5E-208 1885.5 71.6 904 33-1170 4-1052(1077)
11 PRK09603 bifunctional DNA-dire 100.0 2E-192 4E-197 1837.7 70.9 936 26-1171 14-1374(2890)
12 PRK14844 bifunctional DNA-dire 100.0 7E-189 1E-193 1798.0 70.7 943 26-1171 18-1432(2836)
13 PRK07225 DNA-directed RNA poly 100.0 1E-177 3E-182 1587.8 51.4 578 560-1171 4-602 (605)
14 TIGR03670 rpoB_arch DNA-direct 100.0 7E-177 2E-181 1580.1 49.8 575 563-1171 1-596 (599)
15 PF00562 RNA_pol_Rpb2_6: RNA p 100.0 3E-109 7E-114 963.0 26.1 360 692-1070 1-386 (386)
16 PRK09606 DNA-directed RNA poly 100.0 2E-104 4E-109 951.6 42.9 472 24-549 3-492 (494)
17 PF04563 RNA_pol_Rpb2_1: RNA p 100.0 9.3E-42 2E-46 366.3 14.2 143 38-211 1-149 (203)
18 PF04560 RNA_pol_Rpb2_7: RNA p 100.0 1.1E-30 2.3E-35 237.1 5.9 81 1072-1170 1-81 (81)
19 PF04565 RNA_pol_Rpb2_3: RNA p 99.9 7.3E-27 1.6E-31 205.8 3.3 66 465-530 1-68 (68)
20 PF04561 RNA_pol_Rpb2_2: RNA p 99.8 2.6E-20 5.7E-25 197.6 9.9 149 231-390 24-190 (190)
21 PF04566 RNA_pol_Rpb2_4: RNA p 99.7 9.3E-17 2E-21 139.1 8.8 63 563-625 1-63 (63)
22 PF04567 RNA_pol_Rpb2_5: RNA p 99.0 3.2E-10 7E-15 93.3 2.8 48 639-687 1-48 (48)
23 KOG0214 RNA polymerase II, sec 98.9 2.2E-11 4.9E-16 146.6 -7.9 354 770-1163 734-1099(1141)
24 KOG0215 RNA polymerase III, se 98.8 2E-10 4.3E-15 136.9 -7.0 438 12-533 86-550 (1153)
25 PF06883 RNA_pol_Rpa2_4: RNA p 97.7 4.1E-05 8.8E-10 65.6 4.5 49 570-618 1-58 (58)
26 COG0085 RpoB DNA-directed RNA 97.1 0.00053 1.1E-08 88.0 5.7 91 647-755 476-583 (1060)
27 PHA03394 lef-8 DNA-directed RN 94.6 0.047 1E-06 67.8 5.9 121 901-1035 695-828 (865)
28 PF04941 LEF-8: Late expressio 50.9 21 0.00046 44.9 5.2 34 378-411 210-243 (748)
29 PF14251 DUF4346: Domain of un 45.1 11 0.00024 37.1 1.3 11 189-199 13-23 (119)
30 PF10385 RNA_pol_Rpb2_45: RNA 33.6 31 0.00067 30.7 2.2 26 646-671 11-36 (66)
31 PRK06266 transcription initiat 31.4 28 0.00061 37.1 1.9 47 1086-1139 98-144 (178)
32 COG1592 Rubrerythrin [Energy p 28.1 33 0.00071 36.2 1.6 24 1106-1139 134-157 (166)
33 cd00729 rubredoxin_SM Rubredox 27.9 40 0.00086 26.0 1.6 26 1106-1140 2-27 (34)
34 cd00350 rubredoxin_like Rubred 26.1 44 0.00096 25.4 1.6 26 1106-1140 1-26 (33)
35 PRK00398 rpoP DNA-directed RNA 24.8 46 0.00099 27.2 1.6 28 1106-1140 3-30 (46)
36 COG1545 Predicted nucleic-acid 23.6 41 0.00088 34.5 1.3 35 1104-1149 27-61 (140)
37 TIGR00373 conserved hypothetic 23.1 48 0.001 34.7 1.8 47 1086-1139 90-136 (158)
38 PF13533 Biotin_lipoyl_2: Biot 21.6 56 0.0012 27.2 1.5 17 853-869 17-33 (50)
No 1
>KOG0214 consensus RNA polymerase II, second largest subunit [Transcription]
Probab=100.00 E-value=4.4e-274 Score=2355.32 Aligned_cols=1091 Identities=42% Similarity=0.675 Sum_probs=1020.1
Q ss_pred hhhhhhhcccccCcCCchHHHHHHHHHHHHhHHHHHhcccCceEeCCCCCCCCCCCCcceeEEEEEceEEEccCccccCC
Q 001050 23 KTFCRKAAVSFFNEYGLVSHQINSYNEFIKNGLQKAFDSFGETIVEPGYDPSKKGEGEWRYASMRFGQVTLDKPSFFAGN 102 (1173)
Q Consensus 23 ~~~~~~~i~~~f~~~~Lv~~qi~SFN~Fi~~gL~~ii~~~~pI~~~~~~~~~~~~~~~~~~~~l~f~~i~i~~P~~~e~~ 102 (1173)
+|++|.+|++||..+||+++|++||+.|++.++++|+++.++|+.....++. .....++.|.|+++++.+|+..|.|
T Consensus 2 qe~~w~vis~~f~ekglvrqQldsFdeFiq~~~qeiv~~~p~i~l~~~~qh~---~~~~~r~~l~f~qiylskP~~~e~d 78 (1141)
T KOG0214|consen 2 QEDCWDVISAYFEEKGLVRQQLDSFDEFIQQTLQEIVADSPKIELQDEAQHT---QENPARYQLFFEQIYLSKPTHTESD 78 (1141)
T ss_pred hhHHHHHHHhhhcccchHHHHHHHHHHHHHHHHHHHHhcCCCceehhhhhhh---ccCccceEEEeeeEEEecccccccC
Confidence 7899999999999999999999999999999999999999999876544443 1234568999999999999999999
Q ss_pred CCCcCCCChhhHHhcCCcccceEEEEEEEEEeeccccccccccccccceeeccccccceeEEEecccceEecCCccccCC
Q 001050 103 GGDEHDMFPRHARLQNMTYSSRMKVKVQFQVYTQKRVTSDKFKTGREQYIQKEVLSDETTNIIIGRIPVMVKSDLCWMKG 182 (1173)
Q Consensus 103 ~~~~~~l~P~ecR~r~~TYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~ 182 (1173)
|....++|+|||+|++|||+||||+++..+... ..+ ..+.+.++|+||+||||+||.+|.|++
T Consensus 79 -g~~~~m~p~eARlrnLTYSspLyVd~~k~~~~~------~~~----------~~~~~~qkvfIGkIPiMlrS~~C~l~~ 141 (1141)
T KOG0214|consen 79 -GSTSTMFPNEARLRNLTYSSPLYVDATKIVKTS------RDE----------VEDMQEQKVFIGKIPIMLRSSYCLLSG 141 (1141)
T ss_pred -CCccccCchhhHhhhcccccceEEEeEEEEeec------ccc----------ccccccceeeEeccceeeehhhhhhcc
Confidence 999999999999999999999999999877431 000 122346789999999999999999999
Q ss_pred ------CcCCCCcCCCCcEEEEeCcEEEeEeeeeeccceEEE-ecCC----ceEEEEEeecCC-----ceEEEEEEecCc
Q 001050 183 ------VEKGDCDFDHGGYFIIKGAEKVFVAQEQICLKRLWV-SNSM----GWTVAYKSENKR-----NRLIVRLVDMSK 246 (1173)
Q Consensus 183 ------~~~gE~~~D~GGYFIING~ERVIi~Qe~~spnr~~i-~~~~----~~~a~irS~~~~-----~~~~i~~~~~~~ 246 (1173)
.+.||||+|+||||||||+|||+|+||++|+|++|+ .+.. .|++++||..++ ++.|+++.....
T Consensus 142 ~~d~dl~~l~eCp~DqgGyfIINGseKVlIAQe~matn~vyvf~k~~p~~~ay~~EirS~le~~sR~~stl~v~~~ar~~ 221 (1141)
T KOG0214|consen 142 LTDKDLTELGECPYDQGGYFIINGSEKVLIAQEKMATNIVYVFKKAHPGTYAYTGEIRSCLERSSRFISTLSVNMDARAG 221 (1141)
T ss_pred cchhhhhhccCCCcCCCceEEEcCceeeeeehhhccCceEEEEecCCCCceeEeeeeehhhhccCCCcceeeeeeccccC
Confidence 789999999999999999999999999999999999 4322 679999987665 777888764321
Q ss_pred cccccCCEEEEEEeeccccccHhhHHHHhcCCChHHHHHHhcCCCCchHHHHHHHHhhHhhhccCCcCCCHHHHHHHHHh
Q 001050 247 FEDIKGGEKVLSVYFLSTEIPIWILFFALGVSSDKEIVNLIDFTCEDCSILNILFASIHDADNKCDEFRKGRNALKYVDK 326 (1173)
Q Consensus 247 ~~~~~~~~i~v~i~~~k~~IPl~illrALG~~sD~eI~~~i~~~~~d~~~~~~l~~~l~~~~~~~~~i~t~e~al~yig~ 326 (1173)
+.-.|.++++|++++||+++||||||+.+|+||+++|+|+.+|.+|.+++.++++++ +-+..+..||+|||+
T Consensus 222 ----~gq~i~~tlpyikqeIPI~ilfrALG~v~dreILehIcYd~~D~em~e~lkpsieea----fviq~qn~ALdfig~ 293 (1141)
T KOG0214|consen 222 ----KGQEIIATLPYIKQEIPILILFRALGFVSDREILEHICYDFDDAEMFESLKPSIEEA----FVIQEQNVALDFIGQ 293 (1141)
T ss_pred ----CCceEEEEeeeecccCcEEEEehhhcCCccHHHHHhhcCCCCcHHHHHHhhhhhhhh----hhhhhhHHHHHHHHh
Confidence 123788999999999999999999999999999999999999999999999999998 558889999999998
Q ss_pred h---ccCCCCCChhhHHHHHhhcccCcCCCcc----cccchHHHHHHHHHhhccCCCCCCCcccccCcEEeehhhhHHHH
Q 001050 327 L---IKGTTFPPGESTEECMNTYLFPSLHGTK----QKARFLGYMVKCLLQAYSGRRKCDNRDDFRNKRLELAGELLERE 399 (1173)
Q Consensus 327 ~---~~~~~~~~~e~~~~~L~~~llpHl~~~~----~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~nkRv~l~G~Ll~~l 399 (1173)
+ .+..++.++++|+++|.+++|||++..+ +|++||+|||++|+.++.|++.+||+|||+|||++++|+||..+
T Consensus 294 rga~~Gvtkekri~yakdiLqKe~lPhi~~~e~~etkKA~fLGYmi~rlll~aLgRr~~ddRDHfG~KRLDlaGpLLa~l 373 (1141)
T KOG0214|consen 294 RGACIGVTKEKRIKYAKEILQKELLPHVGLGEICETKKAYFLGYMVHRLLLAALGRRELDDRDHFGNKRLDLAGPLLAKL 373 (1141)
T ss_pred cCCCCCCCcchhhHHHHHHHHHHhccccccchhhhhhHHHHHHhhHHHHHHHHcCCCCccchhhccccchhhchhHHHHH
Confidence 7 5667888999999999999999999887 89999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhhcccCCcccccccccccccchhhccccccccccccccCccccccccceeecCCCChhhhhccc
Q 001050 400 LKVHIAHARKRMAKALQRDLYGDRTVRPIEYYLDASILTNGLSRAFSTGAWSHPFKRTERISGIVANLGRANPLQTLVDL 479 (1173)
Q Consensus 400 fr~~l~~~~~~i~~~l~~~~~~~~~~~~~~~~i~~~~It~~i~~~~sTGnw~~~~~~~~q~sGvSQvldRlN~ls~lSh~ 479 (1173)
||..|+++++++...+++++++..++ ++..+++++.||++++|+||||||+.++..|+.++||||||+|+||+++|||+
T Consensus 374 fR~lf~~l~rd~~~~mQk~le~~~df-ni~~aika~iIt~gl~yslaTgnwgdq~ka~~~ragVsQVLnR~t~~sTLsHl 452 (1141)
T KOG0214|consen 374 FRSLFAKLLRDVTRYMQKCLENGVDF-NIELAIKAKIITNGLNYALATGNWGDQKKAMQGRAGVSQVLNRLNPLSTLSHL 452 (1141)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCccc-eEEEEEEeeeecccceeeeccCCccchhHHhhccccHHHHhccccHHHHHHHH
Confidence 99999999999999999999998889 89999999999999999999999999988899999999999999999999999
Q ss_pred cccccccccCCcccccCCCCCCCcceeeecCCCCCcccccccccceeeeeecCc-chhHHHHHHhcCceecccccCccCC
Q 001050 480 RRTRQQVQYTGKVGDARYPHPSHWGKICFLSTPDGENCGLVKNLGVTGLVSTSI-LEPIFEQLFNSGMEKLADDASYSLG 558 (1173)
Q Consensus 480 Rrv~s~~~~~~k~t~vR~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~It~~~-~~~i~~~l~~~g~~~~~~~~~~~~~ 558 (1173)
||+|+|.++++|.+.||+|||||||++||+|||||++||||||||+||.|+.|. ++|++++|+++||+.++++++....
T Consensus 453 RR~n~Pigr~GKlAkpRqlHnthwGmvCPaeTPEGqacGLVKNLSLmayIsvGS~~sPi~EfLeewgmE~le~~~ps~~~ 532 (1141)
T KOG0214|consen 453 RRTNSPIGRTGKLAKPRQLHNSHWGMVCPAETPEGQACGLVKNLSLMAYISVGSLESPIVEFLEEWGMENLEEISPSPSP 532 (1141)
T ss_pred hhcCCccccccccCCccccCcccceeeccccCCCcceeeccccceEEEEEecCCCccHHHHHHHHhchhhHhhcCCCcCC
Confidence 999999999999999999999999999999999999999999999999999998 9999999999999999999999888
Q ss_pred CcceeeeccEEEEEecChhHHHHHHHHHHhcCCCCceEEEEEeccCCeEEEeecCCeeeeeEEEeeccc------c---c
Q 001050 559 GKFKVFVDGDWIGVCKDSLSFVSELRRKRRRKELPTQVEIKRDELQSEVRIFMDAGRILRPLLVVENMG------K---I 629 (1173)
Q Consensus 559 ~~~~VflnG~~iG~~~~~~~~~~~lR~~rr~~~i~~~~~i~~~~~~~~i~I~sd~GRl~RP~l~v~~~~------~---~ 629 (1173)
+.++||+||.|+|++++|+.++..||.+||+..++.++++++|...++++||||+||++||||+|+|++ + +
T Consensus 533 datkvfvNG~wvGlhrdp~~l~~tlr~lRR~~di~~Evs~vRDIr~kE~ri~tDaGR~~rPLliven~~l~~~k~hi~~L 612 (1141)
T KOG0214|consen 533 DATKVFVNGVWVGLHRDPEELVATLKRLRRQFDIIAEVSMVRDIRDKEIRIFTDAGRSLRPLLIVENAKLLIKKRHIRAL 612 (1141)
T ss_pred CceEEEEcccEEEecCCHHHHHHHHHHHHHhhccchhhhhhccccccceeeeeccCccccceEEEechhhhhhhHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999999999995 2 3
Q ss_pred ccccCCcchhHhhhhcCceeeecccccceeEEeecccccccccCCCCCceeeeecccccccccceeecccccCCCccchh
Q 001050 630 KSLEGKNYTFQALLDHGIIELVGTEEEEDCCTAWGIKYLLKDIEDKKPIKFTHCELDMSFLLGLSCGIIPFANHDHARRV 709 (1173)
Q Consensus 630 ~~~~~~~~~~~~l~~~g~iE~id~~Eq~~~~Ia~~~~~~~~~~~~~~~~~~th~Ei~p~~ilgv~aslIPF~~hNqspRn 709 (1173)
+.......+|..|+.+|.+||||++||+..+||+.++++.+. ..+..||||||||+.|||++||.||||||||||||
T Consensus 613 ~~~~~~~~~w~~lv~~G~ie~idteeEEtvmiam~~~dL~~~---~~~~~~THCEiHpsmILgv~asiIpFpdh~qspr~ 689 (1141)
T KOG0214|consen 613 KQSKPNEYRWAHLLSSGEVEYIDTEEEETVMIAMGPKDLAES---AYPKTYTHCEIHPSMILGVCASIIPFPDHNQSPRN 689 (1141)
T ss_pred hhCchhhcchhhhccccceeeeccchhhhHHHhcCHHHHhhc---cCCcccccccccHHHhhhhceeeeecCCCCCchHH
Confidence 333345789999999999999999999999999999999742 23678999999999999999999999999999999
Q ss_pred hhhhcccccccccccccCCeeeeeccccccccCCcceEeccccccccCCcccCCCCCCCCCccCCcccEEEEEecCCCCC
Q 001050 710 LYQSQKHSSQAIGFPTTNPSIRVDTLSHQLFYPQRPLFRTMISDCLGKPGYGHNHILPRPELYNGQNAIVAVNVHLGYNQ 789 (1173)
Q Consensus 710 ~yqc~~M~KQaig~~~~n~~~r~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~~~~~~~~~~~~~~G~N~~VAv~~~~Gyn~ 789 (1173)
+||++ |+|||||++.+|+..|+||..|.|+|||+|+|+|+++++. .+.++|+|+|++||++||+||||
T Consensus 690 tYQsa-~~kqamg~y~tn~~vR~dtl~~~l~ypqkpl~tt~~~e~l-----------~~~eL~aG~NaiVAi~~~~GYNq 757 (1141)
T KOG0214|consen 690 TYQSA-MGKQAMGVYHTNPQVRMDTLAKVLYYPQKPLVTTRAMEYL-----------RFRELPAGQNAIVAIACYSGYNQ 757 (1141)
T ss_pred HHHHH-HhhhcceeeeecchhhhhhhhhcccccccchhhHHHHhhh-----------hhhhcccccceEEEEecccCccH
Confidence 99999 9999999999999999999999999999999999999999 89999999999999999999999
Q ss_pred CCeEEEecceeecCceEEEEEEEEEEEeeeccccccccccccccccccccccccccCCCCCCCCcccCcEEccCCeEEEE
Q 001050 790 EDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVKRRSSDDMVNFGKIQSKIGRVDSLDDDGFPFIGANLQSGDIVIGK 869 (1173)
Q Consensus 790 EDaiiin~~~~~rg~f~s~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~Ld~dGi~~~g~~v~~gdili~k 869 (1173)
|||||+|+++++||+|+|++|++|+.+...... +..+.|+.|........+.+.|++||+||++.+|++|..|||+|||
T Consensus 758 EDsvimn~s~v~rg~FrS~~~RsYk~q~~~~~~-~~ee~~~~~~~~~~~~mr~~~~dkLdddG~i~~G~~vs~~Dv~iGk 836 (1141)
T KOG0214|consen 758 EDSVIMNQSSVDRGLFRSFFIRSYKDQEHKKDQ-GPEEIFEEPPRGEGRGMRNGKYDKLDDDGIIMPGSRVSGGDVLIGK 836 (1141)
T ss_pred HHHHHHHhhhhhcchhhhhhhhHHHhhhhhccc-ccccccccccccccccccccccccccccCCccccceeecCCEEecc
Confidence 999999999999999999999999988765432 3445678888777777888889999999999999999999999999
Q ss_pred ecCC---------------CceeeEEccCCCceEEEEEEEEeCCCCCeEEEEEEeeccCCCccccccccCCCceEEeeee
Q 001050 870 YADS---------------GADHSIKLKHTERGMVQKVVLSSNDDGKNFSVVSLRQVRSPCLGDKFSSMHGQKGVLGFLE 934 (1173)
Q Consensus 870 ~~~~---------------~~~~s~~~~~~~~g~v~~v~~~~~~~~~~~~~v~~r~~R~~~iGDK~ssRhGqKGvvs~i~ 934 (1173)
.+|. .+|.|++++++|.|+||+|.++++.+|.++++|++|+.|.|++|||||||||||||||.++
T Consensus 837 ~t~~~~~~~~~~~~~~~~t~~d~s~~Lr~~e~Givd~V~vt~n~~G~kF~kv~vr~~ripqiGDKfasrHgqKG~ig~~~ 916 (1141)
T KOG0214|consen 837 TTPQPAKEDESGPEDRLYTKRDHSTKLRHTERGIVDQVWVTKNSEGPKFVKVRVRQVRIPQIGDKFASRHGQKGTIGITY 916 (1141)
T ss_pred ccCCcccchhccccccccccccceeecccCCcceEEEEEEecCCCCCceeEEEEeecccccccchhccccccCcccccee
Confidence 9974 5899999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCcCCCCCCCcCcEEeCCCCCCCCCChHHHHHHHHHHHHHhcCccccCCCEEEecCCCCCCHHHHHHHHHHcCCCCCC
Q 001050 935 SQENFPFTIQGIVPDIVINPHAFPSRQTPGQLLEAALGKGIAALGKGICSGLKRYATPFATPSVDAITEQLHRAGFSKWG 1014 (1173)
Q Consensus 935 ~~~dmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~~~~~~~g~~~~~tpF~~~~~~~~~~~l~~~g~~~~G 1014 (1173)
++||||||.+|++|||||||||||||||||||+||++||.++ +.|...|+|||++..+..+...|.++||..+|
T Consensus 917 ~qedmpft~eGi~pDiiiNPhaiPSRmtig~liEc~lgk~~a------~~~e~~~atpFs~v~v~~is~~l~~~g~~~~G 990 (1141)
T KOG0214|consen 917 RQEDMPFTIEGIVPDIIINPHAIPSRMTIGQLIECLLGKVAA------YEGEEGDATPFSDVTVSKISANLHVYGYQYRG 990 (1141)
T ss_pred ecCCCCccccCCCcceEECcccCccccchhhhHHHhhhhhhh------cccccccCCCCCccchhcccchHHHhccccCC
Confidence 999999999999999999999999999999999999999999 99999999999999999999999999999999
Q ss_pred ceEeeeCCCCcEEEeeEeEeeeehhccccccCccceeeecCCCCccccCCcccccccCceeeeehhhhHHHHhhhHHHHH
Q 001050 1015 TERLYDGRTGEMVRSLIFIGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGAAANLH 1094 (1173)
Q Consensus 1015 ~e~ly~g~tG~~~~~~i~~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEME~d~l~a~Ga~~~l~ 1094 (1173)
+|.||+|+||++|.++||+||.|||||+|||+||+|+|++||++.+||||++||||+||||||||||||+||||||++|+
T Consensus 991 ~e~~ynGrtG~~~~~~if~GptyyqrL~Hmvd~kih~R~~Gp~q~ltRQP~~gRsr~GGlRfGEMErdc~iahGaa~~L~ 1070 (1141)
T KOG0214|consen 991 NERMYNGRTGRKLRAQIFIGPTYYQRLKHMVDDKIHSRARGPVQILTRQPVEGRSRDGGLRFGEMERDCLIAHGAAAFLK 1070 (1141)
T ss_pred CEEEecCCCCceeeeeeecCchHHHHHHHhhhheeeecccCCceeeeccccccccccCCeeeehhHHHHHHHhhHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhhcCCCccceecccccCCccchheeeecCCcccCCccccccCCCCCcccccchHhHHHHHHHHHhcCCcEEEEEe
Q 001050 1095 ERLFTLSDSYQMHICRKCKNVANVIQRVVGGGRKVRGPYCRICDSGDDIVKANVPYGAKLLCQELFSMGITLKFDTE 1171 (1173)
Q Consensus 1095 erl~~~SD~~~~~vc~~cg~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~iPy~~k~L~~EL~sm~i~~~l~~~ 1171 (1173)
|||+..||.|.+|+|..||..+ ..+.+.+.+.|+.|.+.+.+..+.+|||||||+|||+||||.+++.++
T Consensus 1071 ERL~~~SD~~~~~~c~~c~l~~-------i~~~~~n~~~ck~c~n~~~v~~v~ipya~kLl~qelmsmni~pr~~~~ 1140 (1141)
T KOG0214|consen 1071 ERLFEKSDAYRVHICVLCGLTA-------IAGLIPNSFECRGCENKTLVVRVYIPYAAKLLFQELMSMNIAPRRKTK 1140 (1141)
T ss_pred HHhhccCccceEEEeccchhhh-------hhccCCCccccccccCccceEEEechhHHHHHHHHHHhccCccccccC
Confidence 9999999999999999999544 556666678999999999999999999999999999999999998764
No 2
>PRK08565 DNA-directed RNA polymerase subunit B; Provisional
Probab=100.00 E-value=6.7e-270 Score=2548.44 Aligned_cols=1058 Identities=36% Similarity=0.574 Sum_probs=961.6
Q ss_pred hhhhcccccCcCCchHHHHHHHHHHHHhHHHHHhcccCceEeCCCCCCCCCCCCcceeEEEEEceEEEccCccccCCCCC
Q 001050 26 CRKAAVSFFNEYGLVSHQINSYNEFIKNGLQKAFDSFGETIVEPGYDPSKKGEGEWRYASMRFGQVTLDKPSFFAGNGGD 105 (1173)
Q Consensus 26 ~~~~i~~~f~~~~Lv~~qi~SFN~Fi~~gL~~ii~~~~pI~~~~~~~~~~~~~~~~~~~~l~f~~i~i~~P~~~e~~~~~ 105 (1173)
+|+++++||+.++|++||+||||||+++||++++++++||++.. ..+.|+|.+++|++|++.+.+ +.
T Consensus 1 ~~~li~~~~~~~~Lv~~qidSFn~Fi~~gL~~iv~~~~pI~~~~------------~~~~L~f~~i~l~~P~~~~~~-~~ 67 (1103)
T PRK08565 1 RWTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDEFGEIKTEI------------PGLKIVLGKIRVGEPEIKEAD-GS 67 (1103)
T ss_pred CchHHHHHhcccChHHHHHHHHHHHHHHhHHHHHHhcCCEEecC------------CCEEEEEEEEEECCCcccccc-cc
Confidence 59999999999999999999999999999999999999998631 248899999999999997766 56
Q ss_pred cCCCChhhHHhcCCcccceEEEEEEEEEeeccccccccccccccceeeccccccceeEEEecccceEecCCccccCC---
Q 001050 106 EHDMFPRHARLQNMTYSSRMKVKVQFQVYTQKRVTSDKFKTGREQYIQKEVLSDETTNIIIGRIPVMVKSDLCWMKG--- 182 (1173)
Q Consensus 106 ~~~l~P~ecR~r~~TYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~--- 182 (1173)
.++|||+|||+|++||+|||+|+|++...+ . ..+.+++++|+|||||+|++|||++
T Consensus 68 ~~~l~P~ecR~r~lTYsa~l~v~i~~~~~~-----------~----------~~~~~~v~iG~iPIMv~S~~C~L~~~s~ 126 (1103)
T PRK08565 68 ERPITPMEARLRNLTYAAPLYLTMIPVENG-----------I----------EYEPEEVKIGDLPIMVKSKICPLSGLSP 126 (1103)
T ss_pred cCCCCHHHHHhcCCCcceEEEEEEEEEECC-----------e----------eeEEEEEEeccCCeEeCCCcccCCCCCH
Confidence 788999999999999999999999996521 0 1124589999999999999999999
Q ss_pred ---CcCCCCcCCCCcEEEEeCcEEEeEeeeeeccceEEE-ec-C---CceEEEEEeecCCceEEEEEEecCccccccCCE
Q 001050 183 ---VEKGDCDFDHGGYFIIKGAEKVFVAQEQICLKRLWV-SN-S---MGWTVAYKSENKRNRLIVRLVDMSKFEDIKGGE 254 (1173)
Q Consensus 183 ---~~~gE~~~D~GGYFIING~ERVIi~Qe~~spnr~~i-~~-~---~~~~a~irS~~~~~~~~i~~~~~~~~~~~~~~~ 254 (1173)
++.||||+|+||||||||+||||++||++|||++++ .+ + ..|.|.++|..+....|+.+. +..+|.
T Consensus 127 ~el~~~~E~p~D~GGYFIING~ERVI~~q~~~s~n~~~~~~~~~~~~~~~~a~i~s~~~~~~~~~~l~------~~~~g~ 200 (1103)
T PRK08565 127 DELIEIGEDPKDPGGYFIINGSERVIVSQEDLAPNRVLVDKGEAGSSITHTAKVISSRAGYRAQVTVE------RRKDGT 200 (1103)
T ss_pred HHHHhcCCCccCCCCeEEECCcEEEEEEEEecCCCEEEEEEecCCCcceEEEEEEeccCCCcceEEEE------EecCCe
Confidence 789999999999999999999999999999999888 32 2 257899998776544455443 334689
Q ss_pred EEEEEeeccccccHhhHHHHhcCCChHHHHHHhcCCCCchHHHHHHHHhhHhhhccCCcC-CCHHHHHHHHHhhccCC--
Q 001050 255 KVLSVYFLSTEIPIWILFFALGVSSDKEIVNLIDFTCEDCSILNILFASIHDADNKCDEF-RKGRNALKYVDKLIKGT-- 331 (1173)
Q Consensus 255 i~v~i~~~k~~IPl~illrALG~~sD~eI~~~i~~~~~d~~~~~~l~~~l~~~~~~~~~i-~t~e~al~yig~~~~~~-- 331 (1173)
++++++++..+||+++||||||+.||+||++.++. +..+.+.+..+++++ ..+ .|+++||.|||++|++.
T Consensus 201 i~~~~~~~~~~IPi~illkALG~~sD~eI~~~i~~---~~~~~~~l~~~l~~~----~~~~~t~~~al~~ig~~~~~~~~ 273 (1103)
T PRK08565 201 IYVSFPAVPGKIPFVILMRALGLETDRDIVYAVSL---DPEIQQELLPSLEQA----SSIAATVEDALDYIGKRVAIGQP 273 (1103)
T ss_pred EEEEEcCcccEeeHHHHHHHcCCCCHHHHHHHhcc---cHHHHHHHHHHHHHh----hccccCHHHHHHHHHHhccCCCC
Confidence 99999997678999999999999999999999964 556677777888775 235 89999999999999764
Q ss_pred CCCChhhHHHHHhhcccCcCCCcc----cccchHHHHHHHHHhhccCCCCCCCcccccCcEEeehhhhHHHHHHHHHHHH
Q 001050 332 TFPPGESTEECMNTYLFPSLHGTK----QKARFLGYMVKCLLQAYSGRRKCDNRDDFRNKRLELAGELLERELKVHIAHA 407 (1173)
Q Consensus 332 ~~~~~e~~~~~L~~~llpHl~~~~----~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~nkRv~l~G~Ll~~lfr~~l~~~ 407 (1173)
.....+.|+++|++++|||++.+. +|+++|++|++||+++..|.+.+||+|||+||||+++|+||+.+||+.|+++
T Consensus 274 ~~~~~e~~~~~L~~~ll~Hig~~~~~~~~K~~~L~~Mi~kLl~l~~g~~~~DD~D~l~NKRv~l~G~Ll~~~fr~~l~~~ 353 (1103)
T PRK08565 274 REYRIERAEQILDKYLLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQL 353 (1103)
T ss_pred CccHHHHHHHHHHhhCcccCCCcccchhHHHHHHHHHHHHHHhhhcCCCCCCCccccCCcEEccHHHHHHHHHHHHHHHH
Confidence 334568899999999999999753 7999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhhcccCCcccccccccccccchhhccccccccccccccCccccccccceeecCCCChhhhhccccccccccc
Q 001050 408 RKRMAKALQRDLYGDRTVRPIEYYLDASILTNGLSRAFSTGAWSHPFKRTERISGIVANLGRANPLQTLVDLRRTRQQVQ 487 (1173)
Q Consensus 408 ~~~i~~~l~~~~~~~~~~~~~~~~i~~~~It~~i~~~~sTGnw~~~~~~~~q~sGvSQvldRlN~ls~lSh~Rrv~s~~~ 487 (1173)
++.+++++.+.+.+.+.+ ++..+++++.||++|++|||||||.+ |++||||+|||+||+|+|||||||++++.
T Consensus 354 ~~~ik~~l~~~~~~~~~~-~~~~~i~~~~It~~i~~~~sTGnw~~------~~sGvSq~ldr~N~l~~lSh~Rrv~s~~~ 426 (1103)
T PRK08565 354 VKDLKYQLEKSYARGRKL-DLRAIVRPDIITERIRHALATGNWVG------GRTGVSQLLDRTNYLSTLSHLRRVVSPLS 426 (1103)
T ss_pred HHHHHHHHHHHHhccccC-CHHHhcccchhhHHHHHHHhcCcccc------CCcceEEecccCCHHHHHHHHhhccCCcc
Confidence 999999998765554555 67778888899999999999999997 57999999999999999999999999999
Q ss_pred cCCcccccCCCCCCCcceeeecCCCCCcccccccccceeeeeecCc-chhHHHHHHhcCceecccccCccCCCcceeeec
Q 001050 488 YTGKVGDARYPHPSHWGKICFLSTPDGENCGLVKNLGVTGLVSTSI-LEPIFEQLFNSGMEKLADDASYSLGGKFKVFVD 566 (1173)
Q Consensus 488 ~~~k~t~vR~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~It~~~-~~~i~~~l~~~g~~~~~~~~~~~~~~~~~Vfln 566 (1173)
++++.++||+||||||||+||+|||||++||||+|||++|+|+++. ..++.++|.++|+.++..+.+......++||||
T Consensus 427 r~~~~~~vR~Lhps~wG~iCPveTPEG~~cGLv~~LA~~a~It~~~~~~~i~~~l~~~G~~~~~~~~~~~~~~~~~V~ln 506 (1103)
T PRK08565 427 RGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLN 506 (1103)
T ss_pred cCCCCccccccChhhccccCCCCCCCccccchhhhhhcccccccCCChHHHHHHHHHcCCCchhhcCcccCCCceEEEEC
Confidence 9999999999999999999999999999999999999999999977 888999999999998865554445567899999
Q ss_pred cEEEEEecChhHHHHHHHHHHhcCCCCceEEEEEec--cCCeEEEeecCCeeeeeEEEeeccc------ccccccCCcch
Q 001050 567 GDWIGVCKDSLSFVSELRRKRRRKELPTQVEIKRDE--LQSEVRIFMDAGRILRPLLVVENMG------KIKSLEGKNYT 638 (1173)
Q Consensus 567 G~~iG~~~~~~~~~~~lR~~rr~~~i~~~~~i~~~~--~~~~i~I~sd~GRl~RP~l~v~~~~------~~~~~~~~~~~ 638 (1173)
|+|+|++++|..|++.||.+||+|.|+.++||++++ ..++|+||||+||++|||++|++++ ++..++.+..+
T Consensus 507 G~~iG~~~~~~~l~~~lR~~Rr~g~i~~~v~I~~~~~~~~~~i~I~sd~GRl~RP~~~v~~g~~~~~~~~~~~l~~~~~~ 586 (1103)
T PRK08565 507 GRLIGYHPDGEELAEKIRELRRSGKISDEVNVAYIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGELT 586 (1103)
T ss_pred CEEEEEECCHHHHHHHHHHHhhcCCCCCeEEEEEccccccceEEEecCCceeeeeEEEEecCceeccHHHHHHhhccccc
Confidence 999999999999999999999999999999999998 7899999999999999999999875 22222334679
Q ss_pred hHhhhhcCceeeecccccceeEEeecccccccccCCCCCceeeeecccccccccceeecccccCCCccchhhhhhccccc
Q 001050 639 FQALLDHGIIELVGTEEEEDCCTAWGIKYLLKDIEDKKPIKFTHCELDMSFLLGLSCGIIPFANHDHARRVLYQSQKHSS 718 (1173)
Q Consensus 639 ~~~l~~~g~iE~id~~Eq~~~~Ia~~~~~~~~~~~~~~~~~~th~Ei~p~~ilgv~aslIPF~~hNqspRn~yqc~~M~K 718 (1173)
|++|++.|.|||||++||+++.||+.++++. ..+||+||+|++|||++||+|||+||||||||||||| |+|
T Consensus 587 ~~~l~~~g~iEyid~~Ee~~~~Ia~~~~~l~--------~~~th~Ei~p~~ilsv~asliPF~~hNqspRn~yq~~-M~K 657 (1103)
T PRK08565 587 FDDLVKMGVIEYLDAEEEENAYVALDPEDLT--------PEHTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAA-MAK 657 (1103)
T ss_pred hhhHhhcCcEEeeCHHHhcCcEEeccccccC--------cceeccccCCccccceeeeccCCcccCcccchhhhhh-hhh
Confidence 9999999999999999999999999998873 3479999999999999999999999999999999999 999
Q ss_pred ccccccccCCeeeeeccccccccCCcceEeccccccccCCcccCCCCCCCCCccCCcccEEEEEecCCCCCCCeEEEecc
Q 001050 719 QAIGFPTTNPSIRVDTLSHQLFYPQRPLFRTMISDCLGKPGYGHNHILPRPELYNGQNAIVAVNVHLGYNQEDSLVMNRA 798 (1173)
Q Consensus 719 Qaig~~~~n~~~r~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~~~~~~~~~~~~~~G~N~~VAv~~~~Gyn~EDaiiin~~ 798 (1173)
||||++.+|+..|.|+++|+|+|||+|||+|+.++.+ +++++|+|+||+||||||+||||||||||||+
T Consensus 658 Qa~g~~~~n~~~r~d~~~~~l~~pQ~Plv~t~~~~~~-----------~~~~~p~G~N~iVAv~sy~GYn~EDaiIink~ 726 (1103)
T PRK08565 658 QSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEII-----------GYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKA 726 (1103)
T ss_pred cccccccccceEeecCCcceeecCceeEEEecccccc-----------ccccCCCCeeEEEEEEcccCcchHHhhhhhhh
Confidence 9999999999999999999999999999999999999 89999999999999999999999999999999
Q ss_pred eeecCceEEEEEEEEEEEeeeccccccccccccccccccccccccccCCCCCCCCcccCcEEccCCeEEEEecCC-----
Q 001050 799 SLERGMFRSEHIRSYKAEVDNKEMQVKRRSSDDMVNFGKIQSKIGRVDSLDDDGFPFIGANLQSGDIVIGKYADS----- 873 (1173)
Q Consensus 799 ~~~rg~f~s~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~Ld~dGi~~~g~~v~~gdili~k~~~~----- 873 (1173)
|+|||+|||+||++|+++.++... +..+.++.|............|++||+||+|++|++|++|||||||++|.
T Consensus 727 s~~rG~~~s~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~Ld~dGi~~~G~~v~~gdili~k~~p~~~~~~ 805 (1103)
T PRK08565 727 SIERGLARSTFFRTYETEERKYPG-GQEDKIEIPEPNVRGYRGEEYYRKLDEDGIVSPEVEVKGGDVLIGKTSPPRFLEE 805 (1103)
T ss_pred hhhcCCceEEEEEEEEEEeeecCC-CCceEEecCCCcccccCchhhhhcCCCCCCcCCCcEEcCCCEEEEEecCCCCCcc
Confidence 999999999999999998876432 22355665533111101123489999999999999999999999999871
Q ss_pred ----------CceeeEEccCCCceEEEEEEEEeCCCCCeEEEEEEeeccCCCccccccccCCCceEEeeeecCCCcCCCC
Q 001050 874 ----------GADHSIKLKHTERGMVQKVVLSSNDDGKNFSVVSLRQVRSPCLGDKFSSMHGQKGVLGFLESQENFPFTI 943 (1173)
Q Consensus 874 ----------~~~~s~~~~~~~~g~v~~v~~~~~~~~~~~~~v~~r~~R~~~iGDK~ssRhGqKGvvs~i~~~~dmPf~~ 943 (1173)
.+|+|++++.+|+|+||+|.++.+.++.+.|+|++|+.|+|+||||||||||||||||+|||+||||||+
T Consensus 806 ~~~~~~~~~~~~~~s~~~~~~e~g~V~~V~~~~~~~~~~~vkv~ir~~R~p~iGDKfssRhGqKGv~s~i~~~edmPf~~ 885 (1103)
T PRK08565 806 LEELSLGLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTE 885 (1103)
T ss_pred hhhccccCCccccceEEecCCCceEEEEEEEEecCCCcEEEEEEEEEEecCchhhhhhhhccCcceeeeecccccCCcCC
Confidence 5789999999999999999999988899999999999999999999999999999999999999999999
Q ss_pred CCCcCcEEeCCCCCCCCCChHHHHHHHHHHHHHhcCccccCCCEEEecCCCCCCHHHHHHHHHHcCCCCCCceEeeeCCC
Q 001050 944 QGIVPDIVINPHAFPSRQTPGQLLEAALGKGIAALGKGICSGLKRYATPFATPSVDAITEQLHRAGFSKWGTERLYDGRT 1023 (1173)
Q Consensus 944 ~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~~~~~~~g~~~~~tpF~~~~~~~~~~~l~~~g~~~~G~e~ly~g~t 1023 (1173)
||++|||||||||||||||||||+|+++||||+ +.|.+.|+|||++...+++++.|+++||+++|+|.||||+|
T Consensus 886 ~G~~pDiI~NPh~~PSRMtiG~l~E~~~gk~~~------~~g~~~d~t~F~~~~~~~~~~~L~~~g~~~~G~e~l~~G~t 959 (1103)
T PRK08565 886 DGIVPDLIINPHAIPSRMTVGQLLESIAGKVAA------LEGRFVDATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRT 959 (1103)
T ss_pred CCCCccEEECCCCCcccccHHHHHHHHHHHHHH------hcCceeeecCcCCchHHHHHHHHHHcCCCCCCcEEEEcCCC
Confidence 999999999999999999999999999999999 99999999999999999999999999999999999999999
Q ss_pred CcEEEeeEeEeeeehhccccccCccceeeecCCCCccccCCcccccccCceeeeehhhhHHHHhhhHHHHHHhhhcCCCc
Q 001050 1024 GEMVRSLIFIGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGAAANLHERLFTLSDS 1103 (1173)
Q Consensus 1024 G~~~~~~i~~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEME~d~l~a~Ga~~~l~erl~~~SD~ 1103 (1173)
|++|+++||+|++|||||+|||+||+|||++||+++|||||++||||+|||||||||||||+|||||++|+|||+++||.
T Consensus 960 G~~~~~~if~G~~yy~rL~HmV~DK~~~R~~Gp~~~lt~QP~~Gr~~~GG~R~GEME~d~l~a~Gas~~L~erL~~~SD~ 1039 (1103)
T PRK08565 960 GEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDK 1039 (1103)
T ss_pred CCCcccceEEeehhheechhhhchhhhhccCCCcchhhhCCccccccCCCeeeecchHHHHHhcccHHHHHHHhhccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cceecccccCCccchheeeecCCcccCCccccccCCCCCcccccchHhHHHHHHHHHhcCCcEEEEEe
Q 001050 1104 YQMHICRKCKNVANVIQRVVGGGRKVRGPYCRICDSGDDIVKANVPYGAKLLCQELFSMGITLKFDTE 1171 (1173)
Q Consensus 1104 ~~~~vc~~cg~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~iPy~~k~L~~EL~sm~i~~~l~~~ 1171 (1173)
++++||.+||+++ ..+.+...++|+.|+++.++.++.+|||||||+|||+||||+++|.++
T Consensus 1040 ~~~~vC~~Cg~~~-------~~~~~~~~~~C~~c~~~~~~~~v~iPy~~k~l~~EL~sm~i~~~l~~~ 1100 (1103)
T PRK08565 1040 TTIYVCELCGHIA-------WYDRRKNKYVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLKLG 1100 (1103)
T ss_pred eeeeeeccccccc-------ccccccCceeccccCCCCcceeccCChhHHHHHHHHHhCCCceEEEee
Confidence 9999999999998 333445578899999988999999999999999999999999999886
No 3
>KOG0216 consensus RNA polymerase I, second largest subunit [Transcription]
Probab=100.00 E-value=1.5e-250 Score=2139.73 Aligned_cols=1049 Identities=30% Similarity=0.452 Sum_probs=932.5
Q ss_pred hhhhcccccCcCCchHHHHHHHHHHHHhHHHHHhcccCceEeCCCCCCCCCCCCcceeEEEEEceEEEccCccccCCC-C
Q 001050 26 CRKAAVSFFNEYGLVSHQINSYNEFIKNGLQKAFDSFGETIVEPGYDPSKKGEGEWRYASMRFGQVTLDKPSFFAGNG-G 104 (1173)
Q Consensus 26 ~~~~i~~~f~~~~Lv~~qi~SFN~Fi~~gL~~ii~~~~pI~~~~~~~~~~~~~~~~~~~~l~f~~i~i~~P~~~e~~~-~ 104 (1173)
.|+-.++|-..+.++++|++|||...+.||....-+...-.. . ....++++++++++++.+|+++.... .
T Consensus 5 ~~k~~p~fp~l~~a~~pHi~sfnal~~~gll~~~v~~~~ek~-----~----~~~g~kis~~ve~i~iakP~l~~~~~ss 75 (1111)
T KOG0216|consen 5 PPKDYPSFPELQDAASPHIDSFNALTNGGLLNAGVAGIAEKV-----P----LKAGDKISMKVESIQIAKPMLSDKVHSS 75 (1111)
T ss_pred CcccCccchhhhhhhhhhhccccchhhhhHHHHHhhchhhhc-----c----cccCCceeEEEEEEEecCCCCCcccccc
Confidence 577788898999999999999999998887655433211110 0 01124688999999999999986442 5
Q ss_pred CcCCCChhhHHhcCCcccceEEEEEEEEEeeccccccccccccccceeeccccccceeEEEecccceEecCCccccCC--
Q 001050 105 DEHDMFPRHARLQNMTYSSRMKVKVQFQVYTQKRVTSDKFKTGREQYIQKEVLSDETTNIIIGRIPVMVKSDLCWMKG-- 182 (1173)
Q Consensus 105 ~~~~l~P~ecR~r~~TYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~-- 182 (1173)
..++|||.|||+|++||++.+.|+|.|.+++. + ....+..+|.+||||+|++|||.|
T Consensus 76 ~~r~lyPaEcRqR~~TY~Gkl~v~v~wsVNg~-----------~----------~~~e~~dlG~vPIMlrSklChL~g~s 134 (1111)
T KOG0216|consen 76 DTRKLYPAECRQRGLTYKGKLVVRVSWSVNGG-----------H----------VVIEKRDLGHVPIMLRSKLCHLNGAS 134 (1111)
T ss_pred ccccccchhHhhccceecceEEEEEEEEECCe-----------e----------eeeeeeecCccceEEeccccccCCCC
Confidence 78899999999999999999999999999651 1 123678999999999999999999
Q ss_pred ----CcCCCCcCCCCcEEEEeCcEEEeEeeeeeccceEEE-ecCCceEEEEE-eecCC------ceEEEEEEecCc----
Q 001050 183 ----VEKGDCDFDHGGYFIIKGAEKVFVAQEQICLKRLWV-SNSMGWTVAYK-SENKR------NRLIVRLVDMSK---- 246 (1173)
Q Consensus 183 ----~~~gE~~~D~GGYFIING~ERVIi~Qe~~spnr~~i-~~~~~~~a~ir-S~~~~------~~~~i~~~~~~~---- 246 (1173)
++++|++.|+||||||||+|||| |++| +++|+++|.+| ||.++ +++.+||+++|+
T Consensus 135 p~eLV~hkEe~~EmGGYFIvNGIEKvI---------RmLIm~RRNHPiAiIR~Sfk~RG~~yS~yGVsmRcVReDqSsvt 205 (1111)
T KOG0216|consen 135 PKELVKHKEESSEMGGYFIVNGIEKVI---------RMLIMPRRNHPIAIIRPSFKDRGSSYSDYGVSMRCVREDQSSVT 205 (1111)
T ss_pred hHHHhhccCchhhcCcEEEEcChHHhh---------hhheeccCCCceEEechhhhhcCCCccccceEEEEeccccccce
Confidence 89999999999999999999999 9999 89999999999 67665 999999999876
Q ss_pred --cccccCCEEEEEEeecccc--ccHhhHHHHhcCCChHHHHHHhcCCC-CchHHHHHHHHhhHhhhccCCcCCCHHHHH
Q 001050 247 --FEDIKGGEKVLSVYFLSTE--IPIWILFFALGVSSDKEIVNLIDFTC-EDCSILNILFASIHDADNKCDEFRKGRNAL 321 (1173)
Q Consensus 247 --~~~~~~~~i~v~i~~~k~~--IPl~illrALG~~sD~eI~~~i~~~~-~d~~~~~~l~~~l~~~~~~~~~i~t~e~al 321 (1173)
.||++||+..+++.+.+++ +|++++||||...||+||++.++.+. .|..+.+++..+|.+..+ .+++||++|+
T Consensus 206 n~LHYLnnGtv~~~F~~rK~eylvPv~lILKAL~~tsDeEIf~~lv~g~~gdqfl~~rv~~mLr~v~e--e~l~trtqcl 283 (1111)
T KOG0216|consen 206 NVLHYLNNGTVMFRFSHRKREYLVPVVLILKALTNTTDEEIFEGLVGGDEGDQFLTSRVELMLREVQE--ENLFTRTQCL 283 (1111)
T ss_pred eEEEEecCCcEEEEEEEeeeeehhhHHHHHHHHhccCHHHHHHHHhCCccCceeHHHHHHHHHHHHhh--cccccHHHHH
Confidence 5899999999999998775 99999999999999999999998663 356677777777777654 3499999999
Q ss_pred HHHHhhcc-----CCCCCChhhHHHHHhhcccCcCCCcccccchHHHHHHHHHhhccCCCCCCCcccccCcEEeehhhhH
Q 001050 322 KYVDKLIK-----GTTFPPGESTEECMNTYLFPSLHGTKQKARFLGYMVKCLLQAYSGRRKCDNRDDFRNKRLELAGELL 396 (1173)
Q Consensus 322 ~yig~~~~-----~~~~~~~e~~~~~L~~~llpHl~~~~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~nkRv~l~G~Ll 396 (1173)
+|||++|+ .+.+++.|+|+++|+++++.||+++.+|+.+|.+|++||++++.|+|.+||+|+.+||+++++|+|+
T Consensus 284 ~yLGs~FRaVl~~v~~~~D~evg~fILr~~VlvHLd~~~DKF~lLifmiqKL~slv~ge~~~dnpDs~q~qEil~~ghl~ 363 (1111)
T KOG0216|consen 284 QYLGSRFRAVLDFVPEQPDLEVGRFILREYVLVHLDSDEDKFNLLIFMIQKLYSLVDGECTPDNPDSPQNQEILLPGHLY 363 (1111)
T ss_pred HHHhhhhhhhhcCCCCCchHHHHHHHHHhheEEEecccHHHHHHHHHHHHHHHHHhcCCcCCCCCCChhhhhcccccchH
Confidence 99999997 2457889999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcccCC-ccc--c---ccccccc--ccchhhccccccccccccccCc-cccccccceeec
Q 001050 397 ERELKVHIAHARKRMAKALQRDLYGD-RTV--R---PIEYYLD--ASILTNGLSRAFSTGAWSHPFK-RTERISGIVANL 467 (1173)
Q Consensus 397 ~~lfr~~l~~~~~~i~~~l~~~~~~~-~~~--~---~~~~~i~--~~~It~~i~~~~sTGnw~~~~~-~~~q~sGvSQvl 467 (1173)
+..+|+.++.|++.++.++.+.+.+. ... . .+.++++ +..|+++|++||||||+.++++ +++|.+|+|.++
T Consensus 364 ~~~LkEriEe~l~~~~~~vr~~l~~~~~~~~~~~~~~i~~~~~r~~~~Ig~~me~fLsTGnl~s~sgldLqQ~sG~tv~A 443 (1111)
T KOG0216|consen 364 GSILKERIEEWLRFISAQVRRDLYKLGFKEDFLDISAIRKVFMRTNGNIGRKMEYFLSTGNLVSRSGLDLQQTSGYTVVA 443 (1111)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhcCCchhHhHHHHHHHHhhccccHHHHHHHHHhcCCeeeccchhhHhhcCcEEeh
Confidence 99999999999997777776665442 111 0 1233333 2479999999999999999999 599999999999
Q ss_pred CCCChhhhhcccccccc-ccccCCcccccCCCCCCCcceeeecCCCCCcccccccccceeeeeecCc--chhHHHHHHhc
Q 001050 468 GRANPLQTLVDLRRTRQ-QVQYTGKVGDARYPHPSHWGKICFLSTPDGENCGLVKNLGVTGLVSTSI--LEPIFEQLFNS 544 (1173)
Q Consensus 468 dRlN~ls~lSh~Rrv~s-~~~~~~k~t~vR~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~It~~~--~~~i~~~l~~~ 544 (1173)
+|+|++++|||||.||+ ++++++|||++|+|.|++|||+||||||||+||||+||||..|+|++.. .+.+.++|.++
T Consensus 444 EriNf~RflShFRavhRGa~f~~mrTTtvRKLlPEsWGFlCPVHTPDG~PCGlLnH~t~~c~I~t~~dd~s~ip~~L~~~ 523 (1111)
T KOG0216|consen 444 ERINFYRFLSHFRAVHRGAFFAEMRTTTVRKLLPESWGFLCPVHTPDGAPCGLLNHMTRTCRIVTRPDDVSFIPSILFEL 523 (1111)
T ss_pred hhhhHHHHHHHHHHHhcccchhheeehhhHhhCchhhcccccccCCCCCchhHHHhhhhheeEeecCcchhhhhHHHHhc
Confidence 99999999999999987 8999999999999999999999999999999999999999999999976 67899999999
Q ss_pred CceecccccCccCCCcceeeeccEEEEEecCh--hHHHHHHHHHHhc--CCCCceEEEEEecc-----CCeEEEeecCCe
Q 001050 545 GMEKLADDASYSLGGKFKVFVDGDWIGVCKDS--LSFVSELRRKRRR--KELPTQVEIKRDEL-----QSEVRIFMDAGR 615 (1173)
Q Consensus 545 g~~~~~~~~~~~~~~~~~VflnG~~iG~~~~~--~~~~~~lR~~rr~--~~i~~~~~i~~~~~-----~~~i~I~sd~GR 615 (1173)
||.|......... .-++|++||+++||+..+ ..+++.||.+|.. +.||.+.||.+.+. .|++||+|++||
T Consensus 524 Gm~p~~~~~~~G~-~l~~VlldGk~vG~~s~~~a~~i~~~lR~~Kv~~p~~iP~~leIg~Vp~s~~gqyPglyi~s~~aR 602 (1111)
T KOG0216|consen 524 GMVPSSHLVEAGE-PLYPVLLDGKVVGWVSSPLAKKIVDYLRYYKVEAPAVIPNDLEIGYVPTSTNGQYPGLYIFSGPAR 602 (1111)
T ss_pred CCCchhccccCCC-ceeEEEECCEEEEeeccHHHHHHHHHHHHHhhcCcccCCCcceEeeeecCCCCCCceeEEecCchh
Confidence 9998763332222 368999999999998755 7899999999976 66999999998774 379999999999
Q ss_pred eeeeEEEeecccccccccCCcchhHhhhhcCceeeecccccceeEEeecccccccccCCCCCceeeeeccccccccccee
Q 001050 616 ILRPLLVVENMGKIKSLEGKNYTFQALLDHGIIELVGTEEEEDCCTAWGIKYLLKDIEDKKPIKFTHCELDMSFLLGLSC 695 (1173)
Q Consensus 616 l~RP~l~v~~~~~~~~~~~~~~~~~~l~~~g~iE~id~~Eq~~~~Ia~~~~~~~~~~~~~~~~~~th~Ei~p~~ilgv~a 695 (1173)
++|||.+. ..+.+|||++.||.++.||+.+.+.. +..+||.|++|+.++|++|
T Consensus 603 ~~RpV~nl--------------------~~~~~e~iG~fEQvym~i~~~~~e~~-------~~v~th~E~~pt~~ls~~a 655 (1111)
T KOG0216|consen 603 MIRPVKNL--------------------SLDSVEWIGPFEQVYMNIAIDPKEIF-------PDVTTHVELHPTGILSIVA 655 (1111)
T ss_pred hhhehhcc--------------------ccCchhhcccHHHhhhhhccchhhcC-------CCcceeEEecccchHhHhh
Confidence 99999753 33679999999999999999999876 7789999999999999999
Q ss_pred ecccccCCCccchhhhhhcccccccccccccCCeeeeeccccccccCCcceEeccccccccCCcccCCCCCCCCCccCCc
Q 001050 696 GIIPFANHDHARRVLYQSQKHSSQAIGFPTTNPSIRVDTLSHQLFYPQRPLFRTMISDCLGKPGYGHNHILPRPELYNGQ 775 (1173)
Q Consensus 696 slIPF~~hNqspRn~yqc~~M~KQaig~~~~n~~~r~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~~~~~~~~~~~~~~G~ 775 (1173)
++|||+||||||||||||| ||||+||+|.++++.|.|+++|+|++||.|+|++..++.+ .++++|.|+
T Consensus 656 nliP~sD~NQSPRNmYQCQ-MgKQtmg~p~~a~~~radnklYrlqt~qsP~vr~~~y~~y-----------~~d~yp~Gt 723 (1111)
T KOG0216|consen 656 NLIPFSDHNQSPRNMYQCQ-MGKQTMGTPGHALRTRADNKLYRLQTPQSPIVRPELYDTY-----------GMDDYPNGT 723 (1111)
T ss_pred cCccccccCCCchhHHHhh-hhhhhcCCccccchhcccCceEEecCCCCceeeccccccc-----------ccccCCCCc
Confidence 9999999999999999999 9999999999999999999999999999999999999999 899999999
Q ss_pred ccEEEEEecCCCCCCCeEEEecceeecCceEEEEEEEEEEEeeeccccccccccccccccccccccccccCCCCCCCCcc
Q 001050 776 NAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVKRRSSDDMVNFGKIQSKIGRVDSLDDDGFPF 855 (1173)
Q Consensus 776 N~~VAv~~~~Gyn~EDaiiin~~~~~rg~f~s~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~Ld~dGi~~ 855 (1173)
||+|||+|||||||||||||||+|+||||+++++||+..+.+.+... ....|...+. .....+||+||+|.
T Consensus 724 NaiVAVisyTgyDMeDAmiiNK~s~eRGf~~G~vykte~i~L~~~~~--r~~~F~~~p~-------~~~~~~ld~dgLP~ 794 (1111)
T KOG0216|consen 724 NAIVAVISYTGYDMEDAMIINKSSYERGFAYGTVYKTEKIDLSKKRS--RSKHFGRSPG-------EPELKKLDADGLPS 794 (1111)
T ss_pred ceEEEEEeecccChhhhhhhchhhhhccccceeEEeeeeechhhccc--ceeeeeeCCC-------CccccccCCCCCCC
Confidence 99999999999999999999999999999999999998887754221 1223432111 12278999999999
Q ss_pred cCcEEccCCeEEEEecCC-CceeeEEccCCCceEEEEEEEEeCCCCC--eEEEEEEeeccCCCccccccccCCCceEEee
Q 001050 856 IGANLQSGDIVIGKYADS-GADHSIKLKHTERGMVQKVVLSSNDDGK--NFSVVSLRQVRSPCLGDKFSSMHGQKGVLGF 932 (1173)
Q Consensus 856 ~g~~v~~gdili~k~~~~-~~~~s~~~~~~~~g~v~~v~~~~~~~~~--~~~~v~~r~~R~~~iGDK~ssRhGqKGvvs~ 932 (1173)
+|+++..||+++..+... .+....++...|+|+||.|++..++.|. +.+.|++|..|+|.||||||||||||||||+
T Consensus 795 ~G~kl~~~dp~~~y~d~~t~~~~~~~~~~~ep~~vd~vr~~~~~~~~~~k~~~i~~Ri~R~p~IGDKFsSRhGQKGicS~ 874 (1111)
T KOG0216|consen 795 IGQKLEYGDPYYAYFDEETGKTRIKKYHGTEPGIVDEVRVLGNDMGDQEKCATITLRIPRNPIIGDKFSSRHGQKGICSQ 874 (1111)
T ss_pred CcccccCCCcEEEEEcccCCceEEEEecCCCCeeeEEEEEccccCCCccceEEEEEEecCCCcccchhhhhccccccccc
Confidence 999999999999998877 6677789999999999999999887666 7799999999999999999999999999999
Q ss_pred eecCCCcCCCCCCCcCcEEeCCCCCCCCCChHHHHHHHHHHHHHhcCccccCCCEEEecCCC----CCCHHHHHHHHHHc
Q 001050 933 LESQENFPFTIQGIVPDIVINPHAFPSRQTPGQLLEAALGKGIAALGKGICSGLKRYATPFA----TPSVDAITEQLHRA 1008 (1173)
Q Consensus 933 i~~~~dmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~~~~~~~g~~~~~tpF~----~~~~~~~~~~l~~~ 1008 (1173)
.||.+|||||++|++|||||||||||||||||||+|+++||+|| ++|..+|+|||. +..+++++++|+++
T Consensus 875 ~wP~~dmPFtesGm~PDii~NPH~FPSRMTIgM~iEs~AgK~~a------lhG~~~Datpf~~~E~~t~~dyfg~~L~~~ 948 (1111)
T KOG0216|consen 875 KWPTIDMPFTESGMVPDIIINPHAFPSRMTIGMLIESMAGKAGA------LHGNAQDATPFIFSEENTAIDYFGEMLKKA 948 (1111)
T ss_pred cCCCCCCCccccCcCcceeeCCCCCcccccHHHHHHHHhchhhc------cccccccCCceeecCcccHHHHHHHHHHHc
Confidence 99999999999999999999999999999999999999999999 999999999984 45799999999999
Q ss_pred CCCCCCceEeeeCCCCcEEEeeEeEeeeehhccccccCccceeeecCCCCccccCCcccccccCceeeeehhhhHHHHhh
Q 001050 1009 GFSKWGTERLYDGRTGEMVRSLIFIGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHG 1088 (1173)
Q Consensus 1009 g~~~~G~e~ly~g~tG~~~~~~i~~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEME~d~l~a~G 1088 (1173)
|||+||+|+||+|.+|++++++||+|+||||||+|||.||+|+|+|||++.+|+||++||+|+||+||||||||||||||
T Consensus 949 GyNyyGnE~~YSGv~G~e~~adIf~GvVyYQRLrHMv~DKfQVRstG~v~~~T~QPvkGRkr~GGiRfGEMERDali~HG 1028 (1111)
T KOG0216|consen 949 GYNYYGNEPMYSGVDGREMRADIFFGVVYYQRLRHMVSDKFQVRSTGPVDSLTHQPVKGRKRGGGIRFGEMERDALIAHG 1028 (1111)
T ss_pred CcCccCCcccccccccceeeeeEEEeehhHHHHHHHhcceeeeeeccCccccccCCccCcccCCCccccchhhhhHhhcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHhhhcCCCccceecccccCCccchheeeec-CCcccCCccccccCCCCCcccccchHhHHHHHHHHHhcCCcEE
Q 001050 1089 AAANLHERLFTLSDSYQMHICRKCKNVANVIQRVVG-GGRKVRGPYCRICDSGDDIVKANVPYGAKLLCQELFSMGITLK 1167 (1173)
Q Consensus 1089 a~~~l~erl~~~SD~~~~~vc~~cg~~~~~~~~~~~-~~~~~~~~~c~~c~~~~~~~~~~iPy~~k~L~~EL~sm~i~~~ 1167 (1173)
||++|||||+.|||.+.++||..||++.+..+.... -....+.-.|+.|+ +..+..+.|||+||||..||+||||+++
T Consensus 1029 tsfllqDRL~~~SD~~~a~vC~~cgsil~~~~~l~~~~~~~~~~~~C~~c~-~~~~~~v~~P~vfkYL~aEL~amnIk~~ 1107 (1111)
T KOG0216|consen 1029 TSFLLQDRLLNSSDYTVAEVCRTCGSILSTQQKLIKEPGGSTSTVTCRSCD-GKGVTTVAMPYVFKYLTAELAAMNIKMR 1107 (1111)
T ss_pred hHhhhhhhhccCcchhHHHHHHHhhhhhhhhhhhhcccCCCCCceeEEecC-CCceEEEEccHHHHHHHHHHhhCceeEE
Confidence 999999999999999999999999999864222211 12233456899995 5589999999999999999999999999
Q ss_pred EEEe
Q 001050 1168 FDTE 1171 (1173)
Q Consensus 1168 l~~~ 1171 (1173)
+.++
T Consensus 1108 l~l~ 1111 (1111)
T KOG0216|consen 1108 LDLE 1111 (1111)
T ss_pred eccC
Confidence 9874
No 4
>KOG0215 consensus RNA polymerase III, second largest subunit [Transcription]
Probab=100.00 E-value=1.3e-249 Score=2121.85 Aligned_cols=1066 Identities=34% Similarity=0.536 Sum_probs=976.1
Q ss_pred cccchhhhhhhcccccCcCCchHHHHHHHHHHHHhHHHHHhcccCceEeCCCCCCCCCCCCcceeEEEEEceEEEccCcc
Q 001050 19 EEFLKTFCRKAAVSFFNEYGLVSHQINSYNEFIKNGLQKAFDSFGETIVEPGYDPSKKGEGEWRYASMRFGQVTLDKPSF 98 (1173)
Q Consensus 19 ~~~~~~~~~~~i~~~f~~~~Lv~~qi~SFN~Fi~~gL~~ii~~~~pI~~~~~~~~~~~~~~~~~~~~l~f~~i~i~~P~~ 98 (1173)
.....+|.|.++++|++.+|||+||++|||||++.+|+.|++++..|..+ .++ .+.++|.++++++|++
T Consensus 39 ~i~~~~dk~~lvp~flkvkglvkqhldsfnyfv~~~ik~iv~an~~itsd--~dp---------~fylky~dirvg~Ps~ 107 (1153)
T KOG0215|consen 39 PIKPLEDKWQLVPAFLKVKGLVKQHLDSFNYFVDVDIKKIVKANQLITSD--VDP---------SFYLKYLDIRVGKPSI 107 (1153)
T ss_pred CCCChHHhHHhHHHHHhhhhHHHHHHhhhhhhhhhhHHHHHHhhcccCcC--cCc---------hhhheeeeeeccCcch
Confidence 35677889999999999999999999999999999999999999888642 222 4679999999999998
Q ss_pred ccCCCCCcCCCChhhHHhcCCcccceEEEEEEEEEeeccccccccccccccceeeccccccceeEEEecccceEecCCcc
Q 001050 99 FAGNGGDEHDMFPRHARLQNMTYSSRMKVKVQFQVYTQKRVTSDKFKTGREQYIQKEVLSDETTNIIIGRIPVMVKSDLC 178 (1173)
Q Consensus 99 ~e~~~~~~~~l~P~ecR~r~~TYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C 178 (1173)
.+...-....++|+|||+|++||+||++|+++++... + . ....+|.||++|||++|++|
T Consensus 108 ~~~~~~~~~~i~p~ecrlrd~tysa~i~vdieytrg~------------~-~--------~~~~~v~igrmpimlrs~rc 166 (1153)
T KOG0215|consen 108 EEGNNVTNDNITPHECRLRDMTYSAPIYVDIEYTRGR------------Q-I--------IAKRDVIIGRMPIMLRSSKC 166 (1153)
T ss_pred hhccccccccCCchheeehhhhcccceeEEEEEecCc------------c-e--------EEecccccccchhhhhcccc
Confidence 8765224457999999999999999999999997632 1 1 22468999999999999999
Q ss_pred ccCC------CcCCCCcCCCCcEEEEeCcEEEeEeeeeeccceEEE--ecCCceEEEEE-eecCC-ceEEEEEEecCccc
Q 001050 179 WMKG------VEKGDCDFDHGGYFIIKGAEKVFVAQEQICLKRLWV--SNSMGWTVAYK-SENKR-NRLIVRLVDMSKFE 248 (1173)
Q Consensus 179 ~L~~------~~~gE~~~D~GGYFIING~ERVIi~Qe~~spnr~~i--~~~~~~~a~ir-S~~~~-~~~~i~~~~~~~~~ 248 (1173)
.|++ ++.+|||.|||||||++|.||||+.||++|.||+.+ .+.+.+-|.+- |+.++ +...+..
T Consensus 167 vl~~~~e~~~a~~~ecpldpggyfiv~G~ekViLiqeqlsknrii~~~~k~~~~~~svtsst~e~kskt~v~~------- 239 (1153)
T KOG0215|consen 167 VLRGKDEEELARLNECPLDPGGYFIVKGTEKVILIQEQLSKNRIIVEEDKKGNLQASVTSSTHERKSKTYVTT------- 239 (1153)
T ss_pred ccCCccHHHHHHhccCCCCCCceeEeccceeEEEehhhhhccCeeeccccCCccccccccceeeecceEEEEe-------
Confidence 9999 789999999999999999999999999999999999 34567777777 45554 5555544
Q ss_pred cccCCEEEEEEeeccccccHhhHHHHhcCCChHHHHHHhcCCCCchHHHHHHHHhhHhhhccCCcCCCHHHHHHHHHhhc
Q 001050 249 DIKGGEKVLSVYFLSTEIPIWILFFALGVSSDKEIVNLIDFTCEDCSILNILFASIHDADNKCDEFRKGRNALKYVDKLI 328 (1173)
Q Consensus 249 ~~~~~~i~v~i~~~k~~IPl~illrALG~~sD~eI~~~i~~~~~d~~~~~~l~~~l~~~~~~~~~i~t~e~al~yig~~~ 328 (1173)
+++.++++++.+..+||++++|||+|..||+||.+.++. ++.+++.+.++++++.... ++||.+||+|++.++
T Consensus 240 --k~~k~ylk~~~~~d~ipiviv~ka~g~~sd~ei~~~vg~---~~~y~~~~~~s~ee~~~~~--v~tqqqal~y~~~kv 312 (1153)
T KOG0215|consen 240 --KKGKYYLKHNSFTDDIPIVIVLKAMGLESDQEIVQLVGG---DSKYQDIFAPSLEECVSLG--VYTQQQALEYIGSKV 312 (1153)
T ss_pred --ccceeeeehhhhhccCCEEEEEeeccccchHHHHHHhhc---chHHHHhhccchhhhhhhh--hHHHHHHHHHhhheE
Confidence 368999999999999999999999999999999999985 6788889999999886643 899999999999888
Q ss_pred cC---CCCCChhhHHHHHhhcccCcCCCcc----cccchHHHHHHHHHhhccCCCCCCCcccccCcEEeehhhhHHHHHH
Q 001050 329 KG---TTFPPGESTEECMNTYLFPSLHGTK----QKARFLGYMVKCLLQAYSGRRKCDNRDDFRNKRLELAGELLERELK 401 (1173)
Q Consensus 329 ~~---~~~~~~e~~~~~L~~~llpHl~~~~----~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~nkRv~l~G~Ll~~lfr 401 (1173)
+. .+....+.|.++|...+++|+.... .|+.+++.|+|+++.+..+.-..||+|.++|||++++|+|++.+|+
T Consensus 313 k~~~~t~~~~~~e~~~~l~~~~lahv~v~~~~~r~K~~yi~~m~rr~~~a~l~~~~~ddrd~~gnkrlelagqllsllfe 392 (1153)
T KOG0215|consen 313 KVKRGTTPTKDEEALEVLSTTVLAHVPVPDLNFRMKAIYIGLMVRRVIQAMLNKLAMDDRDYVGNKRLELAGQLLSLLFE 392 (1153)
T ss_pred EeccCCCCCchHHHHHHHHhhheeceeccCCCCcceeehHHHHHHHHHHHHhCcccccchhhhccchHHHHHHHHHHHHH
Confidence 53 3345678899999999999998665 8999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhhcccCCcccc--cccccc--cccchhhccccccccccccccCccccccccceeecCCCChhhhhc
Q 001050 402 VHIAHARKRMAKALQRDLYGDRTVR--PIEYYL--DASILTNGLSRAFSTGAWSHPFKRTERISGIVANLGRANPLQTLV 477 (1173)
Q Consensus 402 ~~l~~~~~~i~~~l~~~~~~~~~~~--~~~~~i--~~~~It~~i~~~~sTGnw~~~~~~~~q~sGvSQvldRlN~ls~lS 477 (1173)
+.|+++....++.+.+.+.+..... ++.+.+ .++.||++|.+++|||||..+++.|. +.|++||+.|++|++.|.
T Consensus 393 D~fk~~n~e~k~~~dk~l~k~~ra~~fD~~~~~n~~~~~it~~l~ra~stgnw~iKrfrme-r~gvt~VlsrlSyisaLg 471 (1153)
T KOG0215|consen 393 DLFKRFNSELKKNIDKILKKPIRAQEFDALKHLNVRANMITSGLERAISTGNWSIKRFRME-RAGVTQVLSRLSYISALG 471 (1153)
T ss_pred HHHHHHHHHHHHHHHHHhcchhhhhhhHHHHHHHHHHHHHHHHHHHHhhcCchHHHHhhhh-hccceeeehhhhhhhhhh
Confidence 9999999999998887765522110 222333 45689999999999999999999876 899999999999999999
Q ss_pred cccccccccccCCcccccCCCCCCCcceeeecCCCCCcccccccccceeeeeecCc-chhHHHHHHhcCceecccccCcc
Q 001050 478 DLRRTRQQVQYTGKVGDARYPHPSHWGKICFLSTPDGENCGLVKNLGVTGLVSTSI-LEPIFEQLFNSGMEKLADDASYS 556 (1173)
Q Consensus 478 h~Rrv~s~~~~~~k~t~vR~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~It~~~-~~~i~~~l~~~g~~~~~~~~~~~ 556 (1173)
++.|++++|.+++|..+||.|||||||.+||+|||||+.|||++|||++++|++.. +.|+...+..+|++.+...+..+
T Consensus 472 mmtri~s~fektrkvsgprSlq~sqwgmlcp~dtpegeacglvknlalmthittd~ee~pi~~~~~k~gv~di~~v~~~e 551 (1153)
T KOG0215|consen 472 MMTRINSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITTDSEEKPILKLCYKLGVEDIHVVSGRE 551 (1153)
T ss_pred hheehhhhheeehhccCccccChhhcccccCCCCCCccccccccchHHHhcccCCCCcchhHHHHHHhcceeeeeecccc
Confidence 99999999999999999999999999999999999999999999999999999987 99999999999999987666555
Q ss_pred CC--CcceeeeccEEEEEecChhHHHHHHHHHHhcCCCCceEEEEEeccCCeEEEeecCCeeeeeEEEeeccc------c
Q 001050 557 LG--GKFKVFVDGDWIGVCKDSLSFVSELRRKRRRKELPTQVEIKRDELQSEVRIFMDAGRILRPLLVVENMG------K 628 (1173)
Q Consensus 557 ~~--~~~~VflnG~~iG~~~~~~~~~~~lR~~rr~~~i~~~~~i~~~~~~~~i~I~sd~GRl~RP~l~v~~~~------~ 628 (1173)
.+ ..+-||+||.++|.+..|+.|+..+|.+||.|.|..+++++.+.....++|.||+||+|||+++++++. +
T Consensus 552 ~~~~~~~~v~Lng~iig~~~~~~~~v~~~r~lrr~G~i~~fvsv~~~~~q~~v~i~sdggr~crp~Iiv~~~~~~v~~~h 631 (1153)
T KOG0215|consen 552 LHTPDSFLVFLNGLIIGITRRPQYFVNSFRRLRRKGKIGEFVSVFTNTTQRCVYIASDGGRVCRPLIIVDNGRPRVKQHH 631 (1153)
T ss_pred cCCCceEEEEecceeeccccchHHHHHHHHHHHHcCcccceeeeeeeeeeEEEEEecCCCeEeeeEEEEeCCcchhhhhh
Confidence 53 458899999999999999999999999999999999999999888889999999999999999999986 4
Q ss_pred cccccCCcchhHhhhhcCceeeecccccceeEEeecccccccccCCCCCceeeeecccccccccceeecccccCCCccch
Q 001050 629 IKSLEGKNYTFQALLDHGIIELVGTEEEEDCCTAWGIKYLLKDIEDKKPIKFTHCELDMSFLLGLSCGIIPFANHDHARR 708 (1173)
Q Consensus 629 ~~~~~~~~~~~~~l~~~g~iE~id~~Eq~~~~Ia~~~~~~~~~~~~~~~~~~th~Ei~p~~ilgv~aslIPF~~hNqspR 708 (1173)
+...+.+..+|+||++.|.|||+|.+||++++||+.++++ ..++||+||.|..+||++|+|||||+||||||
T Consensus 632 ~~el~~g~r~F~DFl~~glvEYLDVNEEND~~Ialye~~I--------~~~TTHLEIEPFTiLGv~AGLIPYPHHNQSPR 703 (1153)
T KOG0215|consen 632 MDELLDGKRTFDDFLKDGLIEYLDVNEENDSLIALYEEDI--------GPETTHLEIEPFTILGVVAGLIPYPHHNQSPR 703 (1153)
T ss_pred HHHHHHhhhhHHHHHHhchhheeecccccCceEEechhhc--------CCCcceeeecchhhhhhhccccCCCCCCCCCc
Confidence 4566777889999999999999999999999999999988 46799999999999999999999999999999
Q ss_pred hhhhhcccccccccccccCCeeeeeccccccccCCcceEeccccccccCCcccCCCCCCCCCccCCcccEEEEEecCCCC
Q 001050 709 VLYQSQKHSSQAIGFPTTNPSIRVDTLSHQLFYPQRPLFRTMISDCLGKPGYGHNHILPRPELYNGQNAIVAVNVHLGYN 788 (1173)
Q Consensus 709 n~yqc~~M~KQaig~~~~n~~~r~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~~~~~~~~~~~~~~G~N~~VAv~~~~Gyn 788 (1173)
|+|||+ |||||||..+.|+..|+|+.+|+|.|||+|+|+|++.+.+ +++++|+||||.||||||+|||
T Consensus 704 NTYQCA-MGKQAmG~IaYNQ~~RiDtlmYll~YPq~PmVkTKTIELi-----------~ydKLPAGQNAtVAVMSYSGYD 771 (1153)
T KOG0215|consen 704 NTYQCA-MGKQAMGAIAYNQKKRIDSLLYLLVYPQRPMVKTKTIELI-----------NYDKLPAGQNATVAVMSYSGYD 771 (1153)
T ss_pred chhhhh-hhhhhhhhhhhhhhhhHHHHHHHHhcCCCccccceeEEee-----------ccccCCCCCccEEEEEeccCCc
Confidence 999999 9999999999999999999999999999999999999999 9999999999999999999999
Q ss_pred CCCeEEEecceeecCceEEEEEEEEEEEeeeccccccccccccccccccccccccccCCCCCCCCcccCcEEccCCeEEE
Q 001050 789 QEDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVKRRSSDDMVNFGKIQSKIGRVDSLDDDGFPFIGANLQSGDIVIG 868 (1173)
Q Consensus 789 ~EDaiiin~~~~~rg~f~s~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~Ld~dGi~~~g~~v~~gdili~ 868 (1173)
+|||+|+||+|+||||+|+.+||+.+..++++.. +-.+++..|..+...+...+....||+|||..||..|++|+|+|.
T Consensus 772 IEDALVLNKsSlDRGfGRC~Vyk~~~~~~kkY~N-~T~Drimgp~~d~~t~kpi~kh~vLd~DGl~~pG~~V~~~qi~iN 850 (1153)
T KOG0215|consen 772 IEDALVLNKSSIDRGFGRCEVYKKTTTTLKKYAN-GTFDRIMGPQLDPNTRKPIWKHQVLDDDGLATPGERVQPGQIYIN 850 (1153)
T ss_pred hhhhhhcccchhccCcceEEEEeeeeeeeeecCC-CchhhhcccccCCCcCCcchhhcccCcccCCCCccEeccCcEEEe
Confidence 9999999999999999999999999999998765 455667666655444444455778999999999999999999999
Q ss_pred EecCC---------------CceeeEEccCCCceEEEEEEEEeCCCCCeEEEEEEeeccCCCccccccccCCCceEEeee
Q 001050 869 KYADS---------------GADHSIKLKHTERGMVQKVVLSSNDDGKNFSVVSLRQVRSPCLGDKFSSMHGQKGVLGFL 933 (1173)
Q Consensus 869 k~~~~---------------~~~~s~~~~~~~~g~v~~v~~~~~~~~~~~~~v~~r~~R~~~iGDK~ssRhGqKGvvs~i 933 (1173)
|-.|. +++.++.|++.++++||+|++++++++.-.+|+-+||+|+|++|||||||||||||||.|
T Consensus 851 K~mP~vt~~~~~~~~~~~~~Yk~~pitykgpepsyidkVmls~n~~dq~LIK~llRQTRrPElGDKFSSRHGQKGVcGlI 930 (1153)
T KOG0215|consen 851 KQMPTVTGTSLPGLSASQVQYKAVPITYKGPEPSYIDRVMLTSNDEDQFLIKVLLRQTRRPELGDKFSSRHGQKGVCGLI 930 (1153)
T ss_pred ccCCCcccccCCCCCccccccccccceecCCCcchhheeEeecCccccHHHHHHHhhccCcccccccccccCCCceeeEE
Confidence 96554 578889999999999999999999888888999999999999999999999999999999
Q ss_pred ecCCCcCCCCCCCcCcEEeCCCCCCCCCChHHHHHHHHHHHHHhcCccccCCCEEEecCCCCCCHHHHHHHHHHcCCCCC
Q 001050 934 ESQENFPFTIQGIVPDIVINPHAFPSRQTPGQLLEAALGKGIAALGKGICSGLKRYATPFATPSVDAITEQLHRAGFSKW 1013 (1173)
Q Consensus 934 ~~~~dmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~~~~~~~g~~~~~tpF~~~~~~~~~~~l~~~g~~~~ 1013 (1173)
++||||||...||+|||||||||||||||+|.|+|.+.||||. +.|.++++|+|.+..++++++.|.++||+|.
T Consensus 931 v~QEDMPFnD~GIcPDiIMNPHGFPSRMTVGK~iELlsGKAGV------l~G~~hYGTaFGgskVed~~~~Lv~hGfnY~ 1004 (1153)
T KOG0215|consen 931 VQQEDMPFNDQGICPDIIMNPHGFPSRMTVGKMIELLSGKAGV------LEGTFHYGTAFGGSKVEDISEELVEHGFNYS 1004 (1153)
T ss_pred eeccCCCCcccCCCcccccCCCCCcccchHHHHHHHhccccce------eeeeEeeccccCCchHHHHHHHHHHhccCcc
Confidence 9999999999999999999999999999999999999999999 9999999999999999999999999999999
Q ss_pred CceEeeeCCCCcEEEeeEeEeeeehhccccccCccceeeecCCCCccccCCcccccccCceeeeehhhhHHHHhhhHHHH
Q 001050 1014 GTERLYDGRTGEMVRSLIFIGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGAAANL 1093 (1173)
Q Consensus 1014 G~e~ly~g~tG~~~~~~i~~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEME~d~l~a~Ga~~~l 1093 (1173)
||+.+|+|+||++++|+||+||+|||||+|||.||+|||++||+..|||||++||||+||+|+||||||||||||||.+|
T Consensus 1005 GKD~ltSGITGepLeAYIffGPiYYQKLKHMVlDKMHARARGPRAvLTRQPTEGRSrdGGLRLGEMERDCLIaYGASmLl 1084 (1153)
T KOG0215|consen 1005 GKDMLTSGITGEPLEAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIAYGASMLL 1084 (1153)
T ss_pred CccccccCCCCCcceeeEEechHHHHHHHHHHHHHHhhhccCCceeeecCCCCCcCCCCCcccchhhhhhhhhccHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhhcCCCccceecccccCCccchheeeecCCcccCCccccccCCCCCcccccchHhHHHHHHHHHhcCCcEEEEEe
Q 001050 1094 HERLFTLSDSYQMHICRKCKNVANVIQRVVGGGRKVRGPYCRICDSGDDIVKANVPYGAKLLCQELFSMGITLKFDTE 1171 (1173)
Q Consensus 1094 ~erl~~~SD~~~~~vc~~cg~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~iPy~~k~L~~EL~sm~i~~~l~~~ 1171 (1173)
-|||+++||.|+++||..||.++ + ..||..|++..++.++.||||||||||||+||||-+||.++
T Consensus 1085 ~ERLMiSSDaFeVdVC~~CGllg-------y------kgwC~~Ckss~~v~~~~iPYAcKLLFQEL~SMNi~PrL~L~ 1149 (1153)
T KOG0215|consen 1085 LERLMISSDAFEVDVCRQCGLLG-------Y------KGWCTTCKSSKNVAKMKIPYACKLLFQELQSMNIVPRLKLE 1149 (1153)
T ss_pred HHHHhhcCcceeeeeccccccce-------e------chhhhhccCCCceeeeeccHHHHHHHHHHHhcCccceeeec
Confidence 99999999999999999999987 3 45999999999999999999999999999999999999886
No 5
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]
Probab=100.00 E-value=6.3e-244 Score=2206.04 Aligned_cols=987 Identities=30% Similarity=0.442 Sum_probs=882.6
Q ss_pred chhhhhhhcccccCcCCchHHHHHHHHHHHHhHHHHHhcccCceEeCCCCCCCCCCCCcceeEEEEEceEEEccCccccC
Q 001050 22 LKTFCRKAAVSFFNEYGLVSHQINSYNEFIKNGLQKAFDSFGETIVEPGYDPSKKGEGEWRYASMRFGQVTLDKPSFFAG 101 (1173)
Q Consensus 22 ~~~~~~~~i~~~f~~~~Lv~~qi~SFN~Fi~~gL~~ii~~~~pI~~~~~~~~~~~~~~~~~~~~l~f~~i~i~~P~~~e~ 101 (1173)
...+.|.++++||+.++|+++|++|||+|+.+||++++++++||+.. ..++.|+|.++++++|
T Consensus 10 r~r~~~~~i~~~~~~p~Lv~~QldSyn~ff~~gLq~i~~~i~PI~~~------------~~~~~Lef~~~~l~~p----- 72 (1060)
T COG0085 10 RIRDSFGKIPEFLDLPNLVEIQLDSYNAFFLEGLQEVFREIFPIESY------------NGNTELEYGSYRLGEP----- 72 (1060)
T ss_pred ccccchhhcccccCCccHHHHHHHHHHHHHHHHHHHHHHhcCceecC------------CCCEEEEEEEEEecCC-----
Confidence 66788999999999999999999999999999999999999999742 1468999999999999
Q ss_pred CCCCcCCCChhhHHhcCCcccceEEEEEEEEEeeccccccccccccccceeeccccccceeEEEecccceEecCCccccC
Q 001050 102 NGGDEHDMFPRHARLQNMTYSSRMKVKVQFQVYTQKRVTSDKFKTGREQYIQKEVLSDETTNIIIGRIPVMVKSDLCWMK 181 (1173)
Q Consensus 102 ~~~~~~~l~P~ecR~r~~TYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~ 181 (1173)
.+++|.|||+|++||+|||+|++++..++ +++ ..++++|++|+||+|++
T Consensus 73 -----~k~~p~EcR~R~lTYsapLyv~lrlv~~~----------~~e---------~~k~~eV~iG~iPlMt~------- 121 (1060)
T COG0085 73 -----PKFYPEECRLRGLTYSAPLYVKLRLVVNE----------TGE---------EIKEQEVYMGDIPLMTR------- 121 (1060)
T ss_pred -----CCCCHHHHHhcCCccccceEEEEEEEECC----------ccc---------ccccceEEeccCcEecC-------
Confidence 35789999999999999999999998754 111 13468999999999998
Q ss_pred CCcCCCCcCCCCcEEEEeCcEEEeEeeeeeccceEEEecC---C---ceEEEEEeecCCceEEEEEEecCccccccCCEE
Q 001050 182 GVEKGDCDFDHGGYFIIKGAEKVFVAQEQICLKRLWVSNS---M---GWTVAYKSENKRNRLIVRLVDMSKFEDIKGGEK 255 (1173)
Q Consensus 182 ~~~~gE~~~D~GGYFIING~ERVIi~Qe~~spnr~~i~~~---~---~~~a~irS~~~~~~~~i~~~~~~~~~~~~~~~i 255 (1173)
||||||||+|||||+||++|||+++..+. . .|.|.+.+. ++.|+.+.. +.++.+
T Consensus 122 -----------gGyFIINGsERVIVsQ~~rSPgvif~~~~~k~~~~~~~~a~vIp~---rG~wl~~e~------d~~d~~ 181 (1060)
T COG0085 122 -----------GGYFIINGTERVIVSQEHRSPGVIFVEKKDKTGSKVLYVARVIPY---RGSWLEFEF------DPKDNL 181 (1060)
T ss_pred -----------CcEEEECCeEEEEEEEeecCCCeEEecccccCCcceEEEEEEecC---CcceEEEEE------ccCccE
Confidence 99999999999999999999999888321 2 345666544 455555532 235789
Q ss_pred EEEEeeccccccHhhHHHHhcCCChHHHHHHhcCC----CCchHHHHHHHHhhHhhhccCCcCCCHHHHHHHHHhhccCC
Q 001050 256 VLSVYFLSTEIPIWILFFALGVSSDKEIVNLIDFT----CEDCSILNILFASIHDADNKCDEFRKGRNALKYVDKLIKGT 331 (1173)
Q Consensus 256 ~v~i~~~k~~IPl~illrALG~~sD~eI~~~i~~~----~~d~~~~~~l~~~l~~~~~~~~~i~t~e~al~yig~~~~~~ 331 (1173)
+++++..+ +||+++||||||++||+||++.+..+ ....+..+.+...+++... ..+ +.++|++||+++|...
T Consensus 182 ~~rId~~r-kiPvtilLRALG~~tDeeI~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~--~~i-~~~~a~~~i~~r~~~~ 257 (1060)
T COG0085 182 YVRIDRKR-KIPVTILLRALGLETDEEIIEAFGGDELTDLVPPEGEEALLEIYEEAKG--EKI-TARNALELIGSRVFVV 257 (1060)
T ss_pred EEEeeeEE-EeeHHHHHHHhCCCcHHHHHHHhcccccccccchHHHHHhHHHHhhccC--CCc-chHHHHHHHhcccccc
Confidence 99999854 89999999999999999999999863 1223444555555554321 123 3445999999998533
Q ss_pred -----CCCChhhHHHHHhhcccCcCCCc----c----cccchHHHHHHHHHhhccCCCCCCCcccccCcEEeehhhhHHH
Q 001050 332 -----TFPPGESTEECMNTYLFPSLHGT----K----QKARFLGYMVKCLLQAYSGRRKCDNRDDFRNKRLELAGELLER 398 (1173)
Q Consensus 332 -----~~~~~e~~~~~L~~~llpHl~~~----~----~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~nkRv~l~G~Ll~~ 398 (1173)
...+.+.++.++.++++|||+.. . .|+.+|+.|+++|+.+..|.+.+||+|||+||||+++|+||++
T Consensus 258 ~~~~~~~gR~k~~~~vl~~~~L~hL~~~~~~~~l~~~~k~~di~~mi~~l~~L~~G~~~~DDiDHlGNKRlrlvGeLl~n 337 (1060)
T COG0085 258 KRYDAKEGRYKRAKYVLDKELLPHLGEAGERYDLSRVGKAKDIIAMIKYLIELRLGKGEEDDIDHLGNRRLRLVGELLEN 337 (1060)
T ss_pred cccccchhhhhhhhhhhhhhHHhhhcccccccchhhhHHHHHHHHHHHHHHHHhcCCCCCCCCccccccchhhHHHHHHH
Confidence 34568899999999999999963 1 4888999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhhhcccCCcccccccccccccchhhccccccccccccccCccccccccceeecCCCChhhhhcc
Q 001050 399 ELKVHIAHARKRMAKALQRDLYGDRTVRPIEYYLDASILTNGLSRAFSTGAWSHPFKRTERISGIVANLGRANPLQTLVD 478 (1173)
Q Consensus 399 lfr~~l~~~~~~i~~~l~~~~~~~~~~~~~~~~i~~~~It~~i~~~~sTGnw~~~~~~~~q~sGvSQvldRlN~ls~lSh 478 (1173)
+||.+|.+|++.++++|++...+ ..+..++.||.++.+|++||||+ ++||||+|||+||||+|||
T Consensus 338 ~fR~gl~rmer~ikerm~~~~~r-------~~i~p~dlIn~k~~~Alitgffg--------~sqlSQfmDqtNpLSeLSH 402 (1060)
T COG0085 338 LFRVGLSRMERDVKERLEKADKR-------DTLVPQDLINAKPIHALITGFFG--------RSQLSQFMDQTNPLSELSH 402 (1060)
T ss_pred HHHHHHHHHHHHHHHHHhhhhhh-------hccCchhhcchhHHHHHHhcccc--------ccceeeeeecCChHHhhhh
Confidence 99999999999999999886432 23445568999999999999999 5899999999999999999
Q ss_pred cccccc-ccccCCcccccCCCCCCCcceeeecCCCCCcccccccccceeeeee-cCc-chhHHHHHH-hcCceecccccC
Q 001050 479 LRRTRQ-QVQYTGKVGDARYPHPSHWGKICFLSTPDGENCGLVKNLGVTGLVS-TSI-LEPIFEQLF-NSGMEKLADDAS 554 (1173)
Q Consensus 479 ~Rrv~s-~~~~~~k~t~vR~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~It-~~~-~~~i~~~l~-~~g~~~~~~~~~ 554 (1173)
||||++ +++++++.++||+|||||||||||+|||||+|||||||||++|+|+ .|+ ++|+.+++. .+++.++..++.
T Consensus 403 kRRIsAlgLsRera~fEvRDvHpTHyGRiCPiETPEGpNiGLI~sLA~~A~Vn~~Gf~etPy~kv~~g~~~v~~i~~l~~ 482 (1060)
T COG0085 403 KRRLSALGLSRERAGFEVRDVHPTHYGRICPIETPEGPNIGLIKSLALYARINEYGFLETPYRKVLDGSLVVDEIEYLSA 482 (1060)
T ss_pred hhceeccCcCccCCCCcccccCcccccccCCCCCCCCcchhHHHHHHHHeEecccCCCCCceEEEEeccccccceeeecc
Confidence 999999 9999999999999999999999999999999999999999999999 688 999999988 488888765544
Q ss_pred ccCCCcceeeeccEEEEEecChhHHHHHHHHHHhcCCCCceEEEEEeccCC----eEEEeecCCeeeeeEEEeeccc-cc
Q 001050 555 YSLGGKFKVFVDGDWIGVCKDSLSFVSELRRKRRRKELPTQVEIKRDELQS----EVRIFMDAGRILRPLLVVENMG-KI 629 (1173)
Q Consensus 555 ~~~~~~~~VflnG~~iG~~~~~~~~~~~lR~~rr~~~i~~~~~i~~~~~~~----~i~I~sd~GRl~RP~l~v~~~~-~~ 629 (1173)
.. ..|++||.++|.++++..|++.+|.+|+ + +..+++++..+... ++++.+|.||.+|||++++|++ ++
T Consensus 483 ~~----~~~~~~~~~~~~~~~~~~~~~~~~~~R~-~-~~~~~~~~~~~~~~~~dv~~~~~~~~~~~~~P~l~~dd~~~~l 556 (1060)
T COG0085 483 DE----EDVYVIGQANGTLDEPGELVEELVECRR-G-GSGEVSVADPEGVDYMDVSPKQVVSVGRSLIPFLEHDDANRAL 556 (1060)
T ss_pred cc----cceEEEeEeeeeecCCCceeeeEEEEee-c-ccccceeecCccccceeccceEEeccccccCceeEEcCchHhh
Confidence 33 5689999999999999999999999999 5 77778887766544 7899999999999999999998 55
Q ss_pred ccc-----cCC-cchhHhhhhcCceeeecccccceeEEeecccccccccCCCCCceeeeecccccccccceeecccccCC
Q 001050 630 KSL-----EGK-NYTFQALLDHGIIELVGTEEEEDCCTAWGIKYLLKDIEDKKPIKFTHCELDMSFLLGLSCGIIPFANH 703 (1173)
Q Consensus 630 ~~~-----~~~-~~~~~~l~~~g~iE~id~~Eq~~~~Ia~~~~~~~~~~~~~~~~~~th~Ei~p~~ilgv~aslIPF~~h 703 (1173)
|+. ... ..+|.+|+..| +||++++|++++.||..+ ..+||+|++|..|+|++|++|||++|
T Consensus 557 ~~~~mqr~~~~l~~~~~~lv~tG-~E~~~a~e~~~~~ia~~~------------~~~~~ve~~~~~I~~~~~~~~~~~~~ 623 (1060)
T COG0085 557 MGSNMQRQAVPLLRTEAPLVGTG-MEYLDAEDSGAAVIAKRP------------GVVTHVEISPIVILGIEASLIPYPEH 623 (1060)
T ss_pred hhhhhhhhcccccccccccccCC-ceeeccccccceeEeccC------------CcEEEEeeeeeEEEeeccccCCcccc
Confidence 433 222 56999999999 999999999999999765 44799999999999999999999999
Q ss_pred CccchhhhhhcccccccccccccCCeeeeeccccccccCCcceEeccccccccCCcccCCCCCCCCCccCCcccEEEEEe
Q 001050 704 DHARRVLYQSQKHSSQAIGFPTTNPSIRVDTLSHQLFYPQRPLFRTMISDCLGKPGYGHNHILPRPELYNGQNAIVAVNV 783 (1173)
Q Consensus 704 NqspRn~yqc~~M~KQaig~~~~n~~~r~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~~~~~~~~~~~~~~G~N~~VAv~~ 783 (1173)
||||||||||+ |+||++|++..|+..|.|+..|.++|||.|+|+| +|+|+|||++|||||
T Consensus 624 n~~~~n~~~~~-~~~Q~~~~~~~~~~~~~d~~~~~~~~~~~P~~~~-------------------~e~~~GqN~~VA~m~ 683 (1060)
T COG0085 624 NQSPYNLYKFA-RSNQATGINQRPLVKRGDTVEKGLVYADGPSVDT-------------------GELALGQNALVAFMP 683 (1060)
T ss_pred CcChHHHHHHh-hhhcccCCCcccceeccccccccceecCCCcccc-------------------CcccCCceeEEEEec
Confidence 99999999999 9999999999999999999999999999999975 689999999999999
Q ss_pred cCCCCCCCeEEEecceeecCceEEEEEEEEEEEeeeccccccccc-cccccccccccccccccCCCCCCCCcccCcEEcc
Q 001050 784 HLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVKRRS-SDDMVNFGKIQSKIGRVDSLDDDGFPFIGANLQS 862 (1173)
Q Consensus 784 ~~Gyn~EDaiiin~~~~~rg~f~s~~~~~~~~~~~~~~~~~~~e~-~~~~~~~~~~~~~~~~~~~Ld~dGi~~~g~~v~~ 862 (1173)
|+||||||||||||++++||+|||+||++|+.++++++. +.|. +.+|... ...|++||+|||++||++|++
T Consensus 684 ~~GYn~EDAiiin~~~v~~~~~ts~~~~~~~~~~r~~~~--g~e~~~~iP~~~------e~~~~~Lde~Gii~ig~~V~~ 755 (1060)
T COG0085 684 WNGYNYEDAIIISERSVERDLFTSIHIEEYETEARDTKL--GPEEIRDIPNVS------EEALRNLDEDGIIRIGAEVKG 755 (1060)
T ss_pred ccCcChhHheecccchhhcCCceEEEEEEEeeeeeccCC--CccccccCCCcC------HHHHhcCCccCccccccEEcC
Confidence 999999999999999999999999999999999999774 5544 4555543 234899999999999999999
Q ss_pred CCeEEEEecCC------------------CceeeEEccCCCceEEEEEEEEeCCC----CCeEEEEEEeeccCCCccccc
Q 001050 863 GDIVIGKYADS------------------GADHSIKLKHTERGMVQKVVLSSNDD----GKNFSVVSLRQVRSPCLGDKF 920 (1173)
Q Consensus 863 gdili~k~~~~------------------~~~~s~~~~~~~~g~v~~v~~~~~~~----~~~~~~v~~r~~R~~~iGDK~ 920 (1173)
|||||||++|+ .+|+|++++++++|+|++|+++++++ +.+.|||++|+.|+|++||||
T Consensus 756 gdilvgk~tP~~~~~~~~ee~ll~i~~ek~rdtsl~~~~g~~G~V~~V~~~~~~~~~~g~~~~vkV~v~~~R~~~~GDK~ 835 (1060)
T COG0085 756 GDILVGKVTPKGETELTPEERLLRIFGEKVRDTSLRVPHGEEGIVDDVQVFTREDGDPGVNKLVKVYVAQKRKPQIGDKM 835 (1060)
T ss_pred CCEEEEeeCCCCCCCCCchhhhhccccceeeccceeecCCCCeEEEEEEEEeccCCCcCceEEEEEEEEEeccCCccccc
Confidence 99999999998 36899999999999999999999877 789999999999999999999
Q ss_pred cccCCCceEEeeeecCCCcCCCCCCCcCcEEeCCCCCCCCCChHHHHHHHHHHHHHhcCccccCCCEEEecCCCCCCHHH
Q 001050 921 SSMHGQKGVLGFLESQENFPFTIQGIVPDIVINPHAFPSRQTPGQLLEAALGKGIAALGKGICSGLKRYATPFATPSVDA 1000 (1173)
Q Consensus 921 ssRhGqKGvvs~i~~~~dmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~~~~~~~g~~~~~tpF~~~~~~~ 1000 (1173)
|||||||||||+|||+||||||+||++||||+|||||||||||||++|+++||||+ +.|...++|||++.+.++
T Consensus 836 a~RHG~KGVis~i~p~eDMPf~~~G~~~DiilNP~gvPSRM~iGqilE~~lG~a~~------~~G~~~~~~~F~g~~~~~ 909 (1060)
T COG0085 836 AGRHGNKGVVSKIVPQEDMPFLEDGTPPDIILNPLGVPSRMNIGQILETHLGKAAA------LLGIPVDTPVFDGAPEED 909 (1060)
T ss_pred cccCCCCceeeeecCcccCCcCCCCCcccEEECCCCCCccccHHHHHHHHHHHHHH------hcCceeccCCcCCCCHHH
Confidence 99999999999999999999999999999999999999999999999999999999 999999999999999999
Q ss_pred HHHHHHHcCCCCCCceEeeeCCCCcEEEeeEeEeeeehhccccccCccceeeecCCCCccccCCcccccccCceeeeehh
Q 001050 1001 ITEQLHRAGFSKWGTERLYDGRTGEMVRSLIFIGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEME 1080 (1173)
Q Consensus 1001 ~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~i~~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEME 1080 (1173)
+.++|.++||++.||+.||||+||++|+++||||++|||||+|||+|||||||||||+.|||||++||+|+|||||||||
T Consensus 910 ~~~~l~~~g~~~~Gk~~lydG~TGe~~~~~i~vG~~Y~~kL~HmV~dK~HaRs~GP~s~lT~QP~~Gka~~GG~RfGEME 989 (1060)
T COG0085 910 IRELLKEAGFPYSGKEVLYDGRTGEPFDAPIFVGVMYYQKLHHMVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEME 989 (1060)
T ss_pred HHHHHHHcCCCCCCCEEeecCCCCCcccccEEEEehHHHhHHhhhcccceeeccCCceeeecCCCCcccccCCccccchH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHhhhHHHHHHhhhcCCCccceecccccCCccchheeeecCCcccCCccccccCCCCCcccccchHhHHHHHHHHH
Q 001050 1081 RDCLIAHGAAANLHERLFTLSDSYQMHICRKCKNVANVIQRVVGGGRKVRGPYCRICDSGDDIVKANVPYGAKLLCQELF 1160 (1173)
Q Consensus 1081 ~d~l~a~Ga~~~l~erl~~~SD~~~~~vc~~cg~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~iPy~~k~L~~EL~ 1160 (1173)
||||+|||||++|||||+++||. .||+++ .+.|.+|+ .++.++.||||||||++||+
T Consensus 990 ~~aL~ayGAa~~LqE~L~~~SD~-------~~G~~~--------------~y~~~v~g--~~~~~~~ip~sFk~L~~El~ 1046 (1060)
T COG0085 990 VWALEAYGAAYTLQERLTVKSDD-------VCGRIK--------------IYECIVKG--ENIPEVGIPESFKVLLKELR 1046 (1060)
T ss_pred HHHHHHHhHHHHHHHHhhccchh-------cccchh--------------hhcCcccC--CCCCCCCCCHHHHHHHHHHH
Confidence 99999999999999999999994 399887 34599997 68999999999999999999
Q ss_pred hcCCcEEEEEe
Q 001050 1161 SMGITLKFDTE 1171 (1173)
Q Consensus 1161 sm~i~~~l~~~ 1171 (1173)
||||+++|.++
T Consensus 1047 sl~i~~~l~~~ 1057 (1060)
T COG0085 1047 SLGIDVRLELE 1057 (1060)
T ss_pred HCCCceEEeec
Confidence 99999999875
No 6
>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=1.5e-223 Score=2091.59 Aligned_cols=911 Identities=26% Similarity=0.384 Sum_probs=801.5
Q ss_pred hhhhcccccCcCCchHHHHHHHHHHHH----------hHHHHHhcccCceEeCCCCCCCCCCCCcceeEEEEEceEEEcc
Q 001050 26 CRKAAVSFFNEYGLVSHQINSYNEFIK----------NGLQKAFDSFGETIVEPGYDPSKKGEGEWRYASMRFGQVTLDK 95 (1173)
Q Consensus 26 ~~~~i~~~f~~~~Lv~~qi~SFN~Fi~----------~gL~~ii~~~~pI~~~~~~~~~~~~~~~~~~~~l~f~~i~i~~ 95 (1173)
.|..+++||..++|++||++||||||+ +||++++++++||+.. ...+.|+|.++++++
T Consensus 7 ~~~~~~~~~~~p~Lv~~Qi~SFn~FL~~~~~~~~~~~~gL~eii~~~~pI~~~------------~~~~~l~f~~~~l~~ 74 (1065)
T TIGR02013 7 DFGKIPEVLEVPNLLEIQLDSYDWFLQQDTPPEKRKEEGLEEVFKSIFPIEDY------------TGNIELEYLSYRLGE 74 (1065)
T ss_pred ecccCcccccCCCHHHHHHHHHHHHHcCCCcccccccccHHHHHhccCcEEec------------CCcEEEEEEEEEeCC
Confidence 489999999999999999999999999 8999999999999753 135889999999999
Q ss_pred CccccCCCCCcCCCChhhHHhcCCcccceEEEEEEEEEeeccccccccccccccceeeccccccceeEEEecccceEecC
Q 001050 96 PSFFAGNGGDEHDMFPRHARLQNMTYSSRMKVKVQFQVYTQKRVTSDKFKTGREQYIQKEVLSDETTNIIIGRIPVMVKS 175 (1173)
Q Consensus 96 P~~~e~~~~~~~~l~P~ecR~r~~TYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS 175 (1173)
|.+ +|+|||+|++||+|||+|+++++..+ .++.+ ..+.++|+||+||||++
T Consensus 75 P~~-----------~p~Ear~r~lTYsa~l~v~v~l~~~~---------~~~~~--------~i~~~~V~iG~iPiMt~- 125 (1065)
T TIGR02013 75 PKY-----------SVEECKERGLTYSAPLKVKLRLINKE---------EDGTK--------EIKEQDVYMGDIPLMTD- 125 (1065)
T ss_pred CCC-----------CHHHHHHhCCCcceeEEEEEEEEEec---------cCCcc--------ceeeeeEEEeCCCccCC-
Confidence 976 58999999999999999999997522 00100 12246899999999987
Q ss_pred CccccCCCcCCCCcCCCCcEEEEeCcEEEeEeeeeeccceEEE-ec---C-C--ceEEEEEeecCCceEEEEEEecCccc
Q 001050 176 DLCWMKGVEKGDCDFDHGGYFIIKGAEKVFVAQEQICLKRLWV-SN---S-M--GWTVAYKSENKRNRLIVRLVDMSKFE 248 (1173)
Q Consensus 176 ~~C~L~~~~~gE~~~D~GGYFIING~ERVIi~Qe~~spnr~~i-~~---~-~--~~~a~irS~~~~~~~~i~~~~~~~~~ 248 (1173)
||||||||+|||||+||++|||++|+ .. + + .|+|+++|.+ +.|++++.
T Consensus 126 -----------------gGyFIINGsERVIV~Qe~rspg~~~~~~~~~~~~~~~~~~a~iis~r---gswl~~e~----- 180 (1065)
T TIGR02013 126 -----------------RGTFIINGAERVVVSQLHRSPGVFFSSEKDTHKSGKVLFSARIIPYR---GSWLEFET----- 180 (1065)
T ss_pred -----------------CceEEECCcEEEEEEEeecCCCEEEEEccccCCCCceEEEEEEEeCC---CCceEEEE-----
Confidence 99999999999999999999999998 32 1 2 5899999875 34566542
Q ss_pred cccCCEEEEEEeeccccccHhhHHHHhcCCChHHHHHHhcCCCCchHHHHHHHHhhHhhhccCCcCCCHHHHHHHHHhhc
Q 001050 249 DIKGGEKVLSVYFLSTEIPIWILFFALGVSSDKEIVNLIDFTCEDCSILNILFASIHDADNKCDEFRKGRNALKYVDKLI 328 (1173)
Q Consensus 249 ~~~~~~i~v~i~~~k~~IPl~illrALG~~sD~eI~~~i~~~~~d~~~~~~l~~~l~~~~~~~~~i~t~e~al~yig~~~ 328 (1173)
++++.+|+++++.+ +||+++||||||+++|+||++.+++ +..+.+.| ++. ...|+++|+.||++++
T Consensus 181 -~~~~~i~v~i~~~~-kIPi~illrALG~~sd~eI~~~i~~---~~~i~~~l----~~~-----~~~~~e~Al~~i~~~~ 246 (1065)
T TIGR02013 181 -DKKDVLYVRIDRKR-KLPATVLLRALGYTIDTLILNRLGS---GEYIRNTL----RKD-----PTNSEEEALVEIYRKL 246 (1065)
T ss_pred -ecCCeEEEEecCCC-ceeHHHHHHHcCCCcchhhhhhcCc---hHHHHHHH----Hhc-----cccCHHHHHHHHHhhc
Confidence 23678999999975 9999999999999999999999874 33444433 332 2679999999999999
Q ss_pred cCCCCCChhhHHHHHhhcccC-------cCCCc----------------ccccchHHHHHHHHHhhccCCCCCCCccccc
Q 001050 329 KGTTFPPGESTEECMNTYLFP-------SLHGT----------------KQKARFLGYMVKCLLQAYSGRRKCDNRDDFR 385 (1173)
Q Consensus 329 ~~~~~~~~e~~~~~L~~~llp-------Hl~~~----------------~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~ 385 (1173)
++......+.|+++|++.||| |+|+. ..|++||+ |+++|+++..|...+||+|||+
T Consensus 247 ~~g~~~~~~~a~~~l~~~f~~~~rY~LghiGr~kln~Kl~~~~~~~~~~l~k~d~l~-mi~~Ll~~~~g~~~~DD~Dhl~ 325 (1065)
T TIGR02013 247 RPGEPPTVEAARSLLENLFFDPKRYDLGRVGRYKLNKKLGLDVPEDIGVLTKEDIIA-TIKYLIKLRNGKGEIDDIDHLG 325 (1065)
T ss_pred CCCCcchHHHHHHHHHHHhcCcccccccccchhhhhhhcCcCcCcccceehHHHHHH-HHHHHHHhhcCCCCCcchhhhh
Confidence 776666678899999999987 99942 14889997 9999999999999999999999
Q ss_pred CcEEeehhhhHHHHHHHHHHHHHHHHHHHhhhcccCCcccccccccccccchhhccccccccccccccCcccccccccee
Q 001050 386 NKRLELAGELLERELKVHIAHARKRMAKALQRDLYGDRTVRPIEYYLDASILTNGLSRAFSTGAWSHPFKRTERISGIVA 465 (1173)
Q Consensus 386 nkRv~l~G~Ll~~lfr~~l~~~~~~i~~~l~~~~~~~~~~~~~~~~i~~~~It~~i~~~~sTGnw~~~~~~~~q~sGvSQ 465 (1173)
||||+++|+||+.|||.+|+++.+.+++++.+.. .+.+ ++..+++++.||+++++||+|| ||||
T Consensus 326 NKRvr~aGeLL~~~fr~~l~rl~k~ik~~l~~~~--~~~~-~~~~~i~~~~it~~i~~ff~tg-------------glSQ 389 (1065)
T TIGR02013 326 NRRIRSVGELLQNQFRVGLARMERIVRERMSTQD--TDTL-TPQDLINAKPISAAIKEFFGSS-------------QLSQ 389 (1065)
T ss_pred ccchhhHHHHHHHHHHHHHHHHHHHHHHHhhhcc--cccC-CHHHhcCccchHHHHHHHhccC-------------Cccc
Confidence 9999999999999999999999999999988642 2345 5778999999999999999875 8999
Q ss_pred ecCCCChhhhhcccccccc----ccccCCcccccCCCCCCCcceeeecCCCCCcccccccccceeeeeecCcchhHHHHH
Q 001050 466 NLGRANPLQTLVDLRRTRQ----QVQYTGKVGDARYPHPSHWGKICFLSTPDGENCGLVKNLGVTGLVSTSILEPIFEQL 541 (1173)
Q Consensus 466 vldRlN~ls~lSh~Rrv~s----~~~~~~k~t~vR~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~It~~~~~~i~~~l 541 (1173)
+|||+||||+|||+||+++ ++.+++++++||+|||||||||||+|||||+|||||+|||++|+|+.
T Consensus 390 ~Ldr~NpLs~lsh~RRlsslgpggl~r~~~~~~~RdlHpShyGrICPiETPEG~n~GLVknLA~~a~i~~---------- 459 (1065)
T TIGR02013 390 FMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNE---------- 459 (1065)
T ss_pred ccccCCHHHhhhhhceecccCCCCcCccccCCccCccCccccccccCCCCCCCCccccccchhhhcccCc----------
Confidence 9999999999999999998 58999999999999999999999999999999999999999998741
Q ss_pred HhcCceecccccCccCCCcceeeeccEEEEEecChhHHHHHHHHHHhcCCCCceEEEEEeccCCeEEEeecCCeeeeeEE
Q 001050 542 FNSGMEKLADDASYSLGGKFKVFVDGDWIGVCKDSLSFVSELRRKRRRKELPTQVEIKRDELQSEVRIFMDAGRILRPLL 621 (1173)
Q Consensus 542 ~~~g~~~~~~~~~~~~~~~~~VflnG~~iG~~~~~~~~~~~lR~~rr~~~i~~~~~i~~~~~~~~i~I~sd~GRl~RP~l 621 (1173)
.|.+.||++
T Consensus 460 -----------------------------------------------------------------------~G~i~~P~~ 468 (1065)
T TIGR02013 460 -----------------------------------------------------------------------YGFIETPYR 468 (1065)
T ss_pred -----------------------------------------------------------------------ceEEeCCeE
Confidence 233458888
Q ss_pred EeecccccccccCCcchhHhhhhcCceeeecccccceeEEeecccccccccCC---------------CCCceeeeeccc
Q 001050 622 VVENMGKIKSLEGKNYTFQALLDHGIIELVGTEEEEDCCTAWGIKYLLKDIED---------------KKPIKFTHCELD 686 (1173)
Q Consensus 622 ~v~~~~~~~~~~~~~~~~~~l~~~g~iE~id~~Eq~~~~Ia~~~~~~~~~~~~---------------~~~~~~th~Ei~ 686 (1173)
.|+|++.. .+|.+||+|++||+++.||..+.++.+.... ..+..+||+||+
T Consensus 469 ~V~ng~~~--------------~~~~i~yl~a~eE~~~~Ia~~~~~l~~~~~~~~~~i~~r~~~~f~~~~~~~vt~~ei~ 534 (1065)
T TIGR02013 469 KVKDGKVV--------------VTDEVDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYRGEITLVSPDQVDYMDVS 534 (1065)
T ss_pred EEECCeEe--------------ccceeEECChHHhCCcEEEecCcCcCccCccccceeeEEEcCceeecChhHeeEEeeC
Confidence 88776411 3478999999999999999998877532110 113467999999
Q ss_pred ccccccceeecccccCCCccchhhhhhccccccccccc-----------------------------------ccCCeee
Q 001050 687 MSFLLGLSCGIIPFANHDHARRVLYQSQKHSSQAIGFP-----------------------------------TTNPSIR 731 (1173)
Q Consensus 687 p~~ilgv~aslIPF~~hNqspRn~yqc~~M~KQaig~~-----------------------------------~~n~~~r 731 (1173)
|.+|+|++||+|||+||||||||+|||+ |+|||||++ +.|+..|
T Consensus 535 p~~ilsv~aslIPFleHNds~R~lmgsn-M~kQavpl~~~e~p~VgTg~E~~v~~ds~~~i~a~~~G~v~~v~~~~~~~r 613 (1065)
T TIGR02013 535 PKQVVSVAASLIPFLEHDDANRALMGSN-MQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIR 613 (1065)
T ss_pred hhhhhhhHhhcCCCccccCCcchhhhhh-hhhhhhcccccCCCEEEcCcchhhhccccceeEeccCCEEEEEccceEEEE
Confidence 9999999999999999999999999999 999999998 8999999
Q ss_pred eec---------ccc----------ccccCCcceEeccccccccCCcc-cCCCCCCCCCccCCcccEEEEEecCCCCCCC
Q 001050 732 VDT---------LSH----------QLFYPQRPLFRTMISDCLGKPGY-GHNHILPRPELYNGQNAIVAVNVHLGYNQED 791 (1173)
Q Consensus 732 ~D~---------~~~----------~l~ypQ~Plv~t~~~~~~~~~~~-~~~~~~~~~~~~~G~N~~VAv~~~~Gyn~ED 791 (1173)
.|+ ..| .++|||+|||+| ++++.+|++ +|+.++.++|+|+|+|++||||||+||||||
T Consensus 614 ~d~~~~~~~~~~~~y~L~~~~~snq~~~~~q~Plv~~--~~~v~~~~~l~d~~~~~~~e~~~G~N~~VAvm~y~GYn~ED 691 (1065)
T TIGR02013 614 YDEDEDEPDGGIDIYRLLKYQRSNQDTCINQRPIVSV--GDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYED 691 (1065)
T ss_pred ecCCcccccccceEEEeecccccccCceEEeeeeecc--CCeEeeeeEecccccccCCcCcCccceEEEEEeeecccccc
Confidence 996 222 467999999997 578889999 9999999999999999999999999999999
Q ss_pred eEEEecceeecCceEEEEEEEEEEEeeecccccccccccc--ccccccccccccccCCCCCCCCcccCcEEccCCeEEEE
Q 001050 792 SLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVKRRSSDD--MVNFGKIQSKIGRVDSLDDDGFPFIGANLQSGDIVIGK 869 (1173)
Q Consensus 792 aiiin~~~~~rg~f~s~~~~~~~~~~~~~~~~~~~e~~~~--~~~~~~~~~~~~~~~~Ld~dGi~~~g~~v~~gdili~k 869 (1173)
||||||+|++||+|||+||++|++++++++ .+.|.|.. |.. +...|++||+||+|++|++|++|||||||
T Consensus 692 Aiiink~~i~rg~~~s~~~~~~~~~~~~~~--~g~e~~~~~~p~~------~~~~~~~Ld~dGi~~~G~~v~~gdilvgk 763 (1065)
T TIGR02013 692 AILISERLVKDDVFTSIHIEEYEVEARDTK--LGPEEITRDIPNV------SEEALRNLDENGIVRIGAEVKAGDILVGK 763 (1065)
T ss_pred eEEeehhhhcCCceEEEEEEEEEEEeeccC--CCceEeeccCCCC------chhhhhccCCCCCccCccEeCCCCEEEEE
Confidence 999999999999999999999999998754 34465543 331 12348999999999999999999999999
Q ss_pred ecCC----------------------CceeeEEccCCCceEEEEEEEEeCCCC-------CeEEEEEEeeccCCCccccc
Q 001050 870 YADS----------------------GADHSIKLKHTERGMVQKVVLSSNDDG-------KNFSVVSLRQVRSPCLGDKF 920 (1173)
Q Consensus 870 ~~~~----------------------~~~~s~~~~~~~~g~v~~v~~~~~~~~-------~~~~~v~~r~~R~~~iGDK~ 920 (1173)
++|. .+|+|++++++++|+|++|.++.+.++ .+.|+|++|+.|+|+|||||
T Consensus 764 ~~p~~~~~~~~~~~l~~~~~~~~~~~~~d~s~~~~~~~~g~V~~V~~~~~~~~~~~~~~~~~~vkv~ir~~R~p~iGDKf 843 (1065)
T TIGR02013 764 VTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSRKQGDELPPGVNKLVKVYIAQKRKIQVGDKM 843 (1065)
T ss_pred ecCCcccccChhhhhhhhhcccCCccccccceEccCCCCEEEEEEEEEeccCCCccCcCccEEEEEEEeecccccccchh
Confidence 9873 368899999999999999999987666 46899999999999999999
Q ss_pred cccCCCceEEeeeecCCCcCCCCCCCcCcEEeCCCCCCCCCChHHHHHHHHHHHHHhcCccccC--CCEEEecC-CCCCC
Q 001050 921 SSMHGQKGVLGFLESQENFPFTIQGIVPDIVINPHAFPSRQTPGQLLEAALGKGIAALGKGICS--GLKRYATP-FATPS 997 (1173)
Q Consensus 921 ssRhGqKGvvs~i~~~~dmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~~~~~~~--g~~~~~tp-F~~~~ 997 (1173)
|||||||||||+|||+||||||+||++|||||||||||||||||||+||++||||+ +. |.+.++|| |++.+
T Consensus 844 asRHGqKGvis~i~~~eDMPf~~~G~~pDiIiNPhg~PSRMtiGqllE~~~gka~~------~~~~~~~~~~tp~f~~~~ 917 (1065)
T TIGR02013 844 AGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGK------RLGRKGVPIATPVFDGAS 917 (1065)
T ss_pred hhcccCceeEEeEecCCCCCccCCCCCccEEECCCCCcccccHHHHHHHHHHHHHH------hccCCCeEEeccCcCCcc
Confidence 99999999999999999999999999999999999999999999999999999999 65 66788999 99999
Q ss_pred HHHHHHHHHHcCCCCCCceEeeeCCCCcEEEeeEeEeeeehhccccccCccceeeecCCCCccccCCcccccccCceeee
Q 001050 998 VDAITEQLHRAGFSKWGTERLYDGRTGEMVRSLIFIGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFG 1077 (1173)
Q Consensus 998 ~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~i~~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~G 1077 (1173)
.+++.+.|+++||+++|+|.||||+||++|+++||+|++|||||+|||+||+|||++|||+.|||||++||||+||||||
T Consensus 918 ~~~~~~~l~~~g~~~~G~e~l~~G~TG~~~~~~ifvG~~yy~rL~HmV~DK~haRs~Gp~~~lT~QP~~Grsr~GG~R~G 997 (1065)
T TIGR02013 918 EEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFG 997 (1065)
T ss_pred HHHHHHHHHHcCCCCCCCEEEEcCCCCCCccccEEEeehheeechhhhcchhhhcccCCccceeeCCCcccccCCCeeee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ehhhhHHHHhhhHHHHHHhhhcCCCccceecccccCCccchheeeecCCcccCCccccccCCCCCcccccchHhHHHHHH
Q 001050 1078 EMERDCLIAHGAAANLHERLFTLSDSYQMHICRKCKNVANVIQRVVGGGRKVRGPYCRICDSGDDIVKANVPYGAKLLCQ 1157 (1173)
Q Consensus 1078 EME~d~l~a~Ga~~~l~erl~~~SD~~~~~vc~~cg~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~iPy~~k~L~~ 1157 (1173)
|||||||+|||||++|+|||+.+||.+ ||+.. .++.+| ++.++.++.+|||||||+|
T Consensus 998 EME~d~l~a~Gas~~L~E~l~~~SD~~-------~g~~~---------------~~~~~~-~~~~i~~~~~p~sfklL~~ 1054 (1065)
T TIGR02013 998 EMEVWALEAYGAAYTLQEMLTVKSDDV-------VGRTK---------------AYEAIV-KGENVPEPGIPESFNVLIK 1054 (1065)
T ss_pred eeeHHHHHhhhhHHHHHHHHhccChhh-------hhhhh---------------hhhhhc-CCCccccccCCccHHHHHH
Confidence 999999999999999999999999943 34421 234556 5679999999999999999
Q ss_pred HHHhcCCcEEE
Q 001050 1158 ELFSMGITLKF 1168 (1173)
Q Consensus 1158 EL~sm~i~~~l 1168 (1173)
||+||||++++
T Consensus 1055 EL~sm~i~~~~ 1065 (1065)
T TIGR02013 1055 ELQSLGLDIEL 1065 (1065)
T ss_pred HHHhCCccccC
Confidence 99999999874
No 7
>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=5.2e-221 Score=2061.98 Aligned_cols=837 Identities=39% Similarity=0.630 Sum_probs=758.3
Q ss_pred chHHHHHHHHHHHHhHHHHHhcccCceEeCCCCCCCCCCCCcceeEEEEEceEEEccCccccCCCCCcCCCChhhHHhcC
Q 001050 39 LVSHQINSYNEFIKNGLQKAFDSFGETIVEPGYDPSKKGEGEWRYASMRFGQVTLDKPSFFAGNGGDEHDMFPRHARLQN 118 (1173)
Q Consensus 39 Lv~~qi~SFN~Fi~~gL~~ii~~~~pI~~~~~~~~~~~~~~~~~~~~l~f~~i~i~~P~~~e~~~~~~~~l~P~ecR~r~ 118 (1173)
|++||++|||+|+++||++++++++||++..+ ...+.++|+++++++|.+.+. +..++++|+|||+|+
T Consensus 1 Lv~~qi~SFn~Fl~~gl~~ii~~~~~i~~~~~----------~~~~~l~f~~i~i~~P~~~~~--~~~~~l~P~ecRlr~ 68 (866)
T cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDD----------DGRLKLKFGDIYLGKPKVEEG--GVTRKLTPNECRLRD 68 (866)
T ss_pred CchhHHHHHHHHHHHHHHHHHHhcCCeeeccC----------CCeEEEEEEEEEECCcccccc--CccccCCHHHHHhhC
Confidence 68999999999999999999999999986421 135789999999999998765 466899999999999
Q ss_pred CcccceEEEEEEEEEeeccccccccccccccceeeccccccceeEEEecccceEecCCccccCC------CcCCCCcCCC
Q 001050 119 MTYSSRMKVKVQFQVYTQKRVTSDKFKTGREQYIQKEVLSDETTNIIIGRIPVMVKSDLCWMKG------VEKGDCDFDH 192 (1173)
Q Consensus 119 ~TYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~------~~~gE~~~D~ 192 (1173)
+||+|+++|++.++..+ .. ....+++.+|+|||||+|++|||++ ++.||||.||
T Consensus 69 lTYs~~l~v~i~~~~~~-----------~~---------~~~~~~v~iG~iPIMv~S~~C~L~~~~~~el~~~~E~p~d~ 128 (866)
T cd00653 69 LTYSAPLYVDIRLTVND-----------KG---------KIKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDP 128 (866)
T ss_pred CccceeEEEEEEEEEec-----------ce---------eEEEEEEEEeeCCcccCcccccccCCCHHHHHhcCCCcccC
Confidence 99999999999997643 00 0124689999999999999999999 7899999999
Q ss_pred CcEEEEeCcEEEeEeeeeeccceEEEe-cCCceEEEEEeecCC---ceEEEEEEecCccccccCCEEEEEEeeccccccH
Q 001050 193 GGYFIIKGAEKVFVAQEQICLKRLWVS-NSMGWTVAYKSENKR---NRLIVRLVDMSKFEDIKGGEKVLSVYFLSTEIPI 268 (1173)
Q Consensus 193 GGYFIING~ERVIi~Qe~~spnr~~i~-~~~~~~a~irS~~~~---~~~~i~~~~~~~~~~~~~~~i~v~i~~~k~~IPl 268 (1173)
||||||||+||||++||++++|++++. +...+.+..+|.... ...++.+. .+. ..+.+++++++.+
T Consensus 129 GGYFIInG~EkVIi~qi~~~~N~~~~~~~~~~~~~~~~s~~~~~~~~~s~~~~~-~~~----~~~~i~~~i~~~~----- 198 (866)
T cd00653 129 GGYFIINGTEKVIINQEQRSPNVIIVEDSKGKRIYTKTSIPSYSPYRGSWLEVK-SDK----KKDRIYVRIDLKR----- 198 (866)
T ss_pred CCEEEECCceeEEEEEEeccCCeEEEecCCCcEEEEEEEccCCCcCccEEEEEE-Ecc----CCCeEEEEecccC-----
Confidence 999999999999999999999999984 333567777766553 33333332 211 0345666666632
Q ss_pred hhHHHHhcCCChHHHHHHhcCCCCchHHHHHHHHhhHhhhccCCcCCCHHHHHHHHHhhccCCCCCChhhHHHHHhhccc
Q 001050 269 WILFFALGVSSDKEIVNLIDFTCEDCSILNILFASIHDADNKCDEFRKGRNALKYVDKLIKGTTFPPGESTEECMNTYLF 348 (1173)
Q Consensus 269 ~illrALG~~sD~eI~~~i~~~~~d~~~~~~l~~~l~~~~~~~~~i~t~e~al~yig~~~~~~~~~~~e~~~~~L~~~ll 348 (1173)
+++|++|||++|
T Consensus 199 ------------------------------------------------~~~al~~ig~~~-------------------- 210 (866)
T cd00653 199 ------------------------------------------------QEEALKYIGKRF-------------------- 210 (866)
T ss_pred ------------------------------------------------HHHHHHHHHHHH--------------------
Confidence 578999999987
Q ss_pred CcCCCcccccchHHHHHHHHHhhccCCCCCCCcccccCcEEeehhhhHHHHHHHHHHHHHHHHHHHhhhcccCCcccccc
Q 001050 349 PSLHGTKQKARFLGYMVKCLLQAYSGRRKCDNRDDFRNKRLELAGELLERELKVHIAHARKRMAKALQRDLYGDRTVRPI 428 (1173)
Q Consensus 349 pHl~~~~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~nkRv~l~G~Ll~~lfr~~l~~~~~~i~~~l~~~~~~~~~~~~~ 428 (1173)
.+|++|++||+++..|.+.+||+|||+||||+++|+||+.+|++.|+++++.++..+.+...+.+.+ ++
T Consensus 211 ----------~~L~~Mi~kLl~~~~g~~~~Dd~D~~~NkRv~~~G~Ll~~lfr~~l~~~~~~~k~~l~~~~~~~~~~-~~ 279 (866)
T cd00653 211 ----------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDL-TP 279 (866)
T ss_pred ----------HHHHHHHHHHHHHhcCCCCCCCchhhhCeEEeeHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccccc-CH
Confidence 7899999999999999999999999999999999999999999999999999999998876554444 56
Q ss_pred cccccccchhhccccccccccccccCccccccccceeecCCCChhhhhcccccccc-ccccCCcccccCCCCCCCcceee
Q 001050 429 EYYLDASILTNGLSRAFSTGAWSHPFKRTERISGIVANLGRANPLQTLVDLRRTRQ-QVQYTGKVGDARYPHPSHWGKIC 507 (1173)
Q Consensus 429 ~~~i~~~~It~~i~~~~sTGnw~~~~~~~~q~sGvSQvldRlN~ls~lSh~Rrv~s-~~~~~~k~t~vR~Lhps~wG~iC 507 (1173)
..+++++.||++|++||+||||..+++ ++|++|+||+|||+||+|+|||+|||++ ++++++|+++||+||||||||+|
T Consensus 280 ~~~~~~~~It~~i~~~~~TGnw~~~~~-~~~~~Gvsq~ldr~N~ls~lsh~Rrv~~~~~~~~~k~~~~R~lhps~~G~iC 358 (866)
T cd00653 280 QLLINSKPITSGIKEFLATGNWGSKRF-LMQRSGLSQVLDRLNPLSELSHKRRISSLGLFRERKGFEVRDLHPSHWGRIC 358 (866)
T ss_pred HHhccchHHHHHHHHHhhcCCcccccc-ccccceEEEEcccCCHHHHHHhhhhcccccccccccCCcccccCcccCCccC
Confidence 677788899999999999999999987 7789999999999999999999999999 99999999999999999999999
Q ss_pred ecCCCCCcccccccccceeeeeecCcchhHHHHHHhcCceecccccCccCCCcceeeeccEEEEEecChhHHHHHHHHHH
Q 001050 508 FLSTPDGENCGLVKNLGVTGLVSTSILEPIFEQLFNSGMEKLADDASYSLGGKFKVFVDGDWIGVCKDSLSFVSELRRKR 587 (1173)
Q Consensus 508 PveTPEG~~cGLvk~LA~~a~It~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~VflnG~~iG~~~~~~~~~~~lR~~r 587 (1173)
|+|||||++||||+|||++|+|+
T Consensus 359 PveTPEG~~cGLv~~LA~~a~Is--------------------------------------------------------- 381 (866)
T cd00653 359 PIETPEGENCGLVKNLALMARIS--------------------------------------------------------- 381 (866)
T ss_pred CCCCCCCccccchhhhhceEeee---------------------------------------------------------
Confidence 99999999999999999999865
Q ss_pred hcCCCCceEEEEEeccCCeEEEeecCCeeeeeEEEeecccccccccCCcchhHhhhhcCceeeecccccceeEEeecccc
Q 001050 588 RRKELPTQVEIKRDELQSEVRIFMDAGRILRPLLVVENMGKIKSLEGKNYTFQALLDHGIIELVGTEEEEDCCTAWGIKY 667 (1173)
Q Consensus 588 r~~~i~~~~~i~~~~~~~~i~I~sd~GRl~RP~l~v~~~~~~~~~~~~~~~~~~l~~~g~iE~id~~Eq~~~~Ia~~~~~ 667 (1173)
||++|||++|+
T Consensus 382 --------------------------Gr~~rP~~~v~------------------------------------------- 392 (866)
T cd00653 382 --------------------------GRIERPYRIVE------------------------------------------- 392 (866)
T ss_pred --------------------------eEeeeeEEEec-------------------------------------------
Confidence 99999999751
Q ss_pred cccccCCCCCceeeeecccccccccceeecccccCCCccchhhhhhcccccccccccccCCeeeeeccccccccCCcceE
Q 001050 668 LLKDIEDKKPIKFTHCELDMSFLLGLSCGIIPFANHDHARRVLYQSQKHSSQAIGFPTTNPSIRVDTLSHQLFYPQRPLF 747 (1173)
Q Consensus 668 ~~~~~~~~~~~~~th~Ei~p~~ilgv~aslIPF~~hNqspRn~yqc~~M~KQaig~~~~n~~~r~D~~~~~l~ypQ~Plv 747 (1173)
..+||+||+|.++||++||+|||+||||||||||||| |+|||||++.+|+..|+|+++|+|+|||+|||
T Consensus 393 ----------~~~th~ei~~~~~ls~~asliPf~~hNqspRn~~~~~-M~kQa~g~~~~n~~~r~d~~~~~l~~pq~plv 461 (866)
T cd00653 393 ----------KEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSN-MQKQAVGTPALNQQYRMDTKLYLLLYPQKPLV 461 (866)
T ss_pred ----------cceEEEEeCccceeeeeeeccCCCCcccccchhhhhc-ccCCccCchhccccccccchheeeccCCCCcc
Confidence 1279999999999999999999999999999999999 99999999999999999999999999999999
Q ss_pred eccccccccCCcccCCCCCCCCCccCCcccEEEEEecCCCCCCCeEEEecceeecCceEEEEEEEEEEEeeecccccccc
Q 001050 748 RTMISDCLGKPGYGHNHILPRPELYNGQNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVKRR 827 (1173)
Q Consensus 748 ~t~~~~~~~~~~~~~~~~~~~~~~~~G~N~~VAv~~~~Gyn~EDaiiin~~~~~rg~f~s~~~~~~~~~~~~~~~~~~~e 827 (1173)
+|+..+.+ +++++|+|+|++||||||+||||||||||||+|+|||+|||+||++|+++++..+. +.+
T Consensus 462 ~T~~~~~~-----------~~~~~~~G~N~~VAv~~y~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~--~~~ 528 (866)
T cd00653 462 GTGIEEYI-----------AFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKN--GPE 528 (866)
T ss_pred ccchHHHh-----------CCCccCCCceEEEEEeccccccccceeeeehhhhhcCceeEEEEEEEEEEEEecCC--Ccc
Confidence 99999999 89999999999999999999999999999999999999999999999999976442 222
Q ss_pred ccccccccccccccccccCCCCCCCCcccCcEEccCCeEEEEecCC---------------CceeeEEccCCCceEEEEE
Q 001050 828 SSDDMVNFGKIQSKIGRVDSLDDDGFPFIGANLQSGDIVIGKYADS---------------GADHSIKLKHTERGMVQKV 892 (1173)
Q Consensus 828 ~~~~~~~~~~~~~~~~~~~~Ld~dGi~~~g~~v~~gdili~k~~~~---------------~~~~s~~~~~~~~g~v~~v 892 (1173)
++..+.. ...+...|++||+||+|++|++|++||+||||++|. .+|+|++++.+++|+|++|
T Consensus 529 ~~~~~~~---~~~~~~~~~~ld~dGi~~~g~~v~~gd~li~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~v~~v 605 (866)
T cd00653 529 EITRGDI---PNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDV 605 (866)
T ss_pred eEecCCC---CCCChHHhhccCCCCCcCCCCEecCCCEEEEEecCcccccccccccccCCcceEEEEEecCCCceEEEEE
Confidence 2211111 111233589999999999999999999999999885 5789999999999999999
Q ss_pred EEEe---CCCCCeEEEEEEeeccCCCccccccccCCCceEEeeeecCCCcCCCCCCCcCcEEeCCCCCCCCCChHHHHHH
Q 001050 893 VLSS---NDDGKNFSVVSLRQVRSPCLGDKFSSMHGQKGVLGFLESQENFPFTIQGIVPDIVINPHAFPSRQTPGQLLEA 969 (1173)
Q Consensus 893 ~~~~---~~~~~~~~~v~~r~~R~~~iGDK~ssRhGqKGvvs~i~~~~dmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~ 969 (1173)
.++. +.++...|+|++|+.|+|+||||||||||||||||+|||+||||||+||++|||||||||||||||||||+|+
T Consensus 606 ~~~~~~~~~~~~~~v~v~~r~~R~p~iGDKfssRhGqKGv~s~i~~~~dmPf~~~G~~pDiIiNPh~~PSRMtiGql~E~ 685 (866)
T cd00653 606 KIFSRELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLES 685 (866)
T ss_pred EEeccccCCCCcEEEEEEEeEEecCCcccccccccCCCcEEEEEeccccCCcccCCCCCcEEecCCcCcccccHHHHHHH
Confidence 9998 5677889999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhcCccccCCCEEEecCCCCCCHHHHHHHHHHcCCCCCCceEeeeCCCCcEEEeeEeEeeeehhccccccCccc
Q 001050 970 ALGKGIAALGKGICSGLKRYATPFATPSVDAITEQLHRAGFSKWGTERLYDGRTGEMVRSLIFIGPTFYQRLIHMSEDKV 1049 (1173)
Q Consensus 970 ~~gk~~~~~~~~~~~g~~~~~tpF~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~i~~G~~yy~rL~Hmv~dK~ 1049 (1173)
++||+|+ +.|.+.|+|||++...+++.+.|.++||+++|+|.||||+||++|+++||+|++|||||+|||+||+
T Consensus 686 ~~gk~~~------~~g~~~d~t~f~~~~~~~~~~~l~~~g~~~~G~e~~y~g~tG~~~~~~if~G~~yyqrL~Hmv~DK~ 759 (866)
T cd00653 686 LLGKAGA------LLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKI 759 (866)
T ss_pred HHHHHHH------hcCCcccccccCcchHHHHHHHHHHcCCCCCCcEEEEcCCCCCCcccceEEeehhhhhhhhhhchhh
Confidence 9999999 9999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeecCCCCccccCCcccccccCceeeeehhhhHHHHhhhHHHHHHhhhcCCCccceecccccCCccchheeeecCCccc
Q 001050 1050 KFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGAAANLHERLFTLSDSYQMHICRKCKNVANVIQRVVGGGRKV 1129 (1173)
Q Consensus 1050 ~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEME~d~l~a~Ga~~~l~erl~~~SD~~~~~vc~~cg~~~~~~~~~~~~~~~~ 1129 (1173)
|||++||++.|||||++||+|+|||||||||||||+|||||++|+|||+++||.++++||..||.+++
T Consensus 760 ~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~lia~Gas~~l~erl~~~SD~~~~~vc~~cg~i~~------------ 827 (866)
T cd00653 760 HARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILS------------ 827 (866)
T ss_pred hhcccCCcchhccCcCccccccCCeEEEEEehhhhhhhhhHHHHHHHHhcCCccceEEEeccCccccc------------
Confidence 99999999999999999999999999999999999999999999999999999999999999999973
Q ss_pred CCccccccCCCCCcccccchHhHHHHHHHHHhcCCcEEEE
Q 001050 1130 RGPYCRICDSGDDIVKANVPYGAKLLCQELFSMGITLKFD 1169 (1173)
Q Consensus 1130 ~~~~c~~c~~~~~~~~~~iPy~~k~L~~EL~sm~i~~~l~ 1169 (1173)
..+|+.|+++.++.++.+|||||||+|||+||||++++.
T Consensus 828 -~~~c~~c~~~~~~~~~~ipy~~kll~~EL~sm~i~~~~~ 866 (866)
T cd00653 828 -ANLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866 (866)
T ss_pred -ccccccccCCCceeecCCCHHHHHHHHHHHHCCcceEeC
Confidence 234999999999999999999999999999999999974
No 8
>PRK00405 rpoB DNA-directed RNA polymerase subunit beta; Reviewed
Probab=100.00 E-value=3.4e-220 Score=2071.77 Aligned_cols=912 Identities=26% Similarity=0.389 Sum_probs=795.6
Q ss_pred hhhcccccCcCCchHHHHHHHHHHH-------HhHHHHHhcccCceEeCCCCCCCCCCCCcceeEEEEEceEEEccCccc
Q 001050 27 RKAAVSFFNEYGLVSHQINSYNEFI-------KNGLQKAFDSFGETIVEPGYDPSKKGEGEWRYASMRFGQVTLDKPSFF 99 (1173)
Q Consensus 27 ~~~i~~~f~~~~Lv~~qi~SFN~Fi-------~~gL~~ii~~~~pI~~~~~~~~~~~~~~~~~~~~l~f~~i~i~~P~~~ 99 (1173)
+..++.+|..++|++||++|||||| ++||++++++++||+.. ...+.|+|.++++++|.
T Consensus 15 ~~~~~~~~~~p~Lv~~Qi~SFn~Fl~~~~~~~~~gL~~ii~~~~pI~~~------------~~~~~l~f~~~~l~~P~-- 80 (1112)
T PRK00405 15 FGKIKEVLELPNLLEIQLDSFDWFLQLDVPPEDEGLEEVFRSIFPIEDF------------NGNLSLEFVSYELGEPK-- 80 (1112)
T ss_pred cccccccCCCCCHHHHHHHHHHHHHhcCCcccchhHHHHHHhcCCEEec------------CCcEEEEEeeeEcCCCC--
Confidence 5567788899999999999999999 99999999999999852 13588999999999995
Q ss_pred cCCCCCcCCCChhhHHhcCCcccceEEEEEEEEEeeccccccccccccccceeeccccccceeEEEecccceEecCCccc
Q 001050 100 AGNGGDEHDMFPRHARLQNMTYSSRMKVKVQFQVYTQKRVTSDKFKTGREQYIQKEVLSDETTNIIIGRIPVMVKSDLCW 179 (1173)
Q Consensus 100 e~~~~~~~~l~P~ecR~r~~TYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~ 179 (1173)
++|+|||+|++||+|||+|+++++..+ +++ .+.++|+||+||||+
T Consensus 81 ---------~tp~Ear~r~lTYSaplyv~v~l~~~~----------~~~----------i~~~~V~iG~iPiMt------ 125 (1112)
T PRK00405 81 ---------YDVEECKERGLTYSAPLRVKLRLINKE----------TGE----------IKEQEVYMGDIPLMT------ 125 (1112)
T ss_pred ---------CCHHHHHHhCCCCCeeEEEEEEEEEec----------cCc----------eeeeeEEEecccccc------
Confidence 579999999999999999999997532 111 124689999999996
Q ss_pred cCCCcCCCCcCCCCcEEEEeCcEEEeEeeeeeccceEEE-ecC------CceEEEEEeecCCceEEEEEEecCccccccC
Q 001050 180 MKGVEKGDCDFDHGGYFIIKGAEKVFVAQEQICLKRLWV-SNS------MGWTVAYKSENKRNRLIVRLVDMSKFEDIKG 252 (1173)
Q Consensus 180 L~~~~~gE~~~D~GGYFIING~ERVIi~Qe~~spnr~~i-~~~------~~~~a~irS~~~~~~~~i~~~~~~~~~~~~~ 252 (1173)
+||||||||+|||||+||++|||++|+ ... ..|+|+++|.+ +.|++++. +++
T Consensus 126 ------------~gGyFIING~ERVIVsQe~rSPg~~~~~~~~k~~~~k~~y~a~Iis~r---Gswl~~e~------d~k 184 (1112)
T PRK00405 126 ------------ENGTFIINGTERVIVSQLHRSPGVYFDHDKDKTSSGKLLYSARIIPYR---GSWLEFEF------DPK 184 (1112)
T ss_pred ------------CCceEEECCeEEEEEEEeecCCCEEEEEeccccCCCceeEEEEEEECC---CCcEEEEE------ecC
Confidence 499999999999999999999999988 321 25899999875 45666642 236
Q ss_pred CEEEEEEeeccccccHhhHHHHhcCCChHHHHHHhcCCCCch-------------------------H------------
Q 001050 253 GEKVLSVYFLSTEIPIWILFFALGVSSDKEIVNLIDFTCEDC-------------------------S------------ 295 (1173)
Q Consensus 253 ~~i~v~i~~~k~~IPl~illrALG~~sD~eI~~~i~~~~~d~-------------------------~------------ 295 (1173)
+.+|+++++. ++||+++||||||+ ||+||++.++....+. +
T Consensus 185 ~~I~vri~~~-~kIPi~iLLrALGl-sd~eIl~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ei~~~~~~~~~~~ 262 (1112)
T PRK00405 185 DILYVRIDRR-RKLPVTVLLRALGY-SDEEILDLFYEKEEFGKEIEVPVEYLLGKVLAEDIVDEETGEVLAEANDEITEE 262 (1112)
T ss_pred CeEEEEecCC-CcccHHHHHHHcCC-CHHHHHHHhcccccccceeccchHHhcccchhhhhcccccceeeeccCCccchh
Confidence 7899999986 69999999999999 9999999997532221 0
Q ss_pred -HHHHHHHhhHhhhccCCcCCCHHHHHHHHHhhccCCCCCChhhHHHHHhhccc-------CcCCCcc------------
Q 001050 296 -ILNILFASIHDADNKCDEFRKGRNALKYVDKLIKGTTFPPGESTEECMNTYLF-------PSLHGTK------------ 355 (1173)
Q Consensus 296 -~~~~l~~~l~~~~~~~~~i~t~e~al~yig~~~~~~~~~~~e~~~~~L~~~ll-------pHl~~~~------------ 355 (1173)
....+..+++. ....|+++|+.||++++++......+.|+++|++.|| ||+|+..
T Consensus 263 ~~~~~i~~~l~~-----~~~~t~e~Al~~I~k~l~~g~~~~~e~a~~~l~~~ff~~~rYdL~hiGr~k~nkKl~l~~~~~ 337 (1112)
T PRK00405 263 LDGPYIRNTLEK-----DPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPKRYDLSKVGRYKLNKKLGLDEDED 337 (1112)
T ss_pred hhhHHHHHHHhh-----ccccCHHHHHHHHHhhcCCCCcchHHHHHHHHHHHhcCccccccccCCceecchhcccCcccc
Confidence 11222222321 2367999999999999987666677889999999876 9999642
Q ss_pred ----cccchHHHHHHHHHhhccCCCCCCCcccccCcEEeehhhhHHHHHHHHHHHHHHHHHHHhhhcccCCccccccccc
Q 001050 356 ----QKARFLGYMVKCLLQAYSGRRKCDNRDDFRNKRLELAGELLERELKVHIAHARKRMAKALQRDLYGDRTVRPIEYY 431 (1173)
Q Consensus 356 ----~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~nkRv~l~G~Ll~~lfr~~l~~~~~~i~~~l~~~~~~~~~~~~~~~~ 431 (1173)
.|++ +++|+++|+++..|.+.+||+|||+||||+++|+||+.|||.+|+++.+.+++++.+.. .+.+ ++..+
T Consensus 338 ~~~L~~~d-~~~mi~~Ll~l~~g~~~~DDiDhl~NKRvr~aGeLL~~~fr~~~~rl~k~ik~~l~~~~--~~~~-~~~~l 413 (1112)
T PRK00405 338 VRVLTKED-IIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERAVRERMSLQD--LDTL-TPQDL 413 (1112)
T ss_pred cccccHHH-HHHHHHHHHhhhcccCCCcchhHHhcchhhhHHHHHHHHHHHHHHHHHHHHHHHhhhcc--cccC-CHHHh
Confidence 2344 48999999999999999999999999999999999999999999999999999998652 2345 67889
Q ss_pred ccccchhhccccccccccccccCccccccccceeecCCCChhhhhcccccccc----ccccCCcccccCCCCCCCcceee
Q 001050 432 LDASILTNGLSRAFSTGAWSHPFKRTERISGIVANLGRANPLQTLVDLRRTRQ----QVQYTGKVGDARYPHPSHWGKIC 507 (1173)
Q Consensus 432 i~~~~It~~i~~~~sTGnw~~~~~~~~q~sGvSQvldRlN~ls~lSh~Rrv~s----~~~~~~k~t~vR~Lhps~wG~iC 507 (1173)
++++.||++|++||+|| ||||+|||+||||+|||+||+++ ++.+++++++||+||||||||||
T Consensus 414 in~~~it~~i~~ff~tg-------------glSQ~Ldq~NpLselshkRRlss~gpggl~r~~a~~~~R~lH~ShyGriC 480 (1112)
T PRK00405 414 INAKPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRIC 480 (1112)
T ss_pred hCchhHHHHHHHhhccC-------------CcceeeccCCHHHhhhhhceecccCCCCcCccccCCcccccCcccccccc
Confidence 99999999999999875 89999999999999999999998 58999999999999999999999
Q ss_pred ecCCCCCcccccccccceeeeeecCcchhHHHHHHhcCceecccccCccCCCcceeeeccEEEEEecChhHHHHHHHHHH
Q 001050 508 FLSTPDGENCGLVKNLGVTGLVSTSILEPIFEQLFNSGMEKLADDASYSLGGKFKVFVDGDWIGVCKDSLSFVSELRRKR 587 (1173)
Q Consensus 508 PveTPEG~~cGLvk~LA~~a~It~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~VflnG~~iG~~~~~~~~~~~lR~~r 587 (1173)
|+|||||++||||+|||++|+|+. +|... ..+.+++||.|- +
T Consensus 481 PiETPEG~n~GLV~nLA~~a~i~~------------~G~~~----------tp~~~~~nG~~~---~------------- 522 (1112)
T PRK00405 481 PIETPEGPNIGLINSLATYARVNE------------YGFIE----------TPYRKVVDGKVT---D------------- 522 (1112)
T ss_pred CcCCCCCCccccccchhhcccccc------------CCccc----------cceEEEECCeEc---c-------------
Confidence 999999999999999999999985 22210 125567888751 0
Q ss_pred hcCCCCceEEEEEeccCCeEEEeecCCeeeeeEEEeecccccccccCCcchhHhhhhcCceeeecccccceeEEeecccc
Q 001050 588 RRKELPTQVEIKRDELQSEVRIFMDAGRILRPLLVVENMGKIKSLEGKNYTFQALLDHGIIELVGTEEEEDCCTAWGIKY 667 (1173)
Q Consensus 588 r~~~i~~~~~i~~~~~~~~i~I~sd~GRl~RP~l~v~~~~~~~~~~~~~~~~~~l~~~g~iE~id~~Eq~~~~Ia~~~~~ 667 (1173)
.+||+|++||++..||....+
T Consensus 523 -----------------------------------------------------------~i~yl~a~eE~~~~Ia~~~~~ 543 (1112)
T PRK00405 523 -----------------------------------------------------------EIVYLTADEEDNYVIAQANAP 543 (1112)
T ss_pred -----------------------------------------------------------ceEECCHHHhcCcEEEecCcc
Confidence 278999999999999998877
Q ss_pred cccccCC---------------CCCceeeeecccccccccceeecccccCCCccchhhhhhccccccccccccc------
Q 001050 668 LLKDIED---------------KKPIKFTHCELDMSFLLGLSCGIIPFANHDHARRVLYQSQKHSSQAIGFPTT------ 726 (1173)
Q Consensus 668 ~~~~~~~---------------~~~~~~th~Ei~p~~ilgv~aslIPF~~hNqspRn~yqc~~M~KQaig~~~~------ 726 (1173)
+.+.... ..+..+|||||+|.+++|++||+|||++|||||||+|||+ |+|||||+...
T Consensus 544 l~~~~~~~~~~i~~r~~~e~~~~~~~~~~~~~i~p~qi~sv~aslIPFleHnda~R~lmgSn-MqrQAvpl~~~~~p~vg 622 (1112)
T PRK00405 544 LDEDGRFVDELVTARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSN-MQRQAVPLLRPEAPLVG 622 (1112)
T ss_pred cCCCCcccCceEEEEecCcceeechhhceEEeechhhhceehhhccCcccccCCcchhhhhh-hhhhhhhhccccCCeee
Confidence 7532110 1124579999999999999999999999999999999999 99999999988
Q ss_pred -----------------------------CCeeee-----------------eccccc-cccCCcceEeccccccccCCc
Q 001050 727 -----------------------------NPSIRV-----------------DTLSHQ-LFYPQRPLFRTMISDCLGKPG 759 (1173)
Q Consensus 727 -----------------------------n~~~r~-----------------D~~~~~-l~ypQ~Plv~t~~~~~~~~~~ 759 (1173)
|+..|. |+.+|+ ++|||||||+|+ +++.+|+
T Consensus 623 Tg~e~~~~~ds~~~i~a~~~G~v~~v~~~~i~ir~~~~~~~~~~~~~y~L~~~~~sn~~~~~~q~Plv~~~--~~v~~g~ 700 (1112)
T PRK00405 623 TGMERRVARDSGAVVVAKRDGVVEYVDASRIVVRVEELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVG--DRVEKGD 700 (1112)
T ss_pred cCcchhhhhhcchheEeccCCEEEEEeCCEEEEeecccccCCCCeeEEEecccccccccceeecceeeecC--CeEeecc
Confidence 888888 778888 999999999974 7888899
Q ss_pred c-cCCCCCCCCCccCCcccEEEEEecCCCCCCCeEEEecceeecCceEEEEEEEEEEEeeeccccccccccc--cccccc
Q 001050 760 Y-GHNHILPRPELYNGQNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVKRRSSD--DMVNFG 836 (1173)
Q Consensus 760 ~-~~~~~~~~~~~~~G~N~~VAv~~~~Gyn~EDaiiin~~~~~rg~f~s~~~~~~~~~~~~~~~~~~~e~~~--~~~~~~ 836 (1173)
+ ||+.++.++|+|+|+|++||||||+||||||||||||+|++||+|+|+||++|+.+++.++. +.+++. .|...
T Consensus 701 ~lad~~~~~~~e~~~G~N~~VA~~~y~GYn~EDaiiink~si~rg~~~s~~~~~~~~~~~~~~~--~~~~~~~~~p~~~- 777 (1112)
T PRK00405 701 VLADGPSTDNGELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKL--GPEEITRDIPNVS- 777 (1112)
T ss_pred EeecccccCcccccCCcceEEEEEeecccCccceEEEEhhhhccCceEEEEEeeeeeEeeccCC--CceeecccCCCCC-
Confidence 9 99999999999999999999999999999999999999999999999999999999977542 445553 33211
Q ss_pred cccccccccCCCCCCCCcccCcEEccCCeEEEEecCC----------------------CceeeEEccCCCceEEEEEEE
Q 001050 837 KIQSKIGRVDSLDDDGFPFIGANLQSGDIVIGKYADS----------------------GADHSIKLKHTERGMVQKVVL 894 (1173)
Q Consensus 837 ~~~~~~~~~~~Ld~dGi~~~g~~v~~gdili~k~~~~----------------------~~~~s~~~~~~~~g~v~~v~~ 894 (1173)
...|++||+||+|++|++|++|||||||++|. .+|+|++++++++|+|++|.+
T Consensus 778 -----~~~~~~Ld~dGi~~~G~~v~~gDiligk~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~s~~~~~~~~g~V~~v~~ 852 (1112)
T PRK00405 778 -----EEALRNLDESGIVRIGAEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKV 852 (1112)
T ss_pred -----hHHhhccCCCCCccCccEecCCCEEEEEecCCCccccChhhhhhhhhhcccccccccceEEcCCCCCEEEEEEEE
Confidence 22489999999999999999999999999873 367999999999999999999
Q ss_pred EeC-CCC-------CeEEEEEEeeccCCCccccccccCCCceEEeeeecCCCcCCCCCCCcCcEEeCCCCCCCCCChHHH
Q 001050 895 SSN-DDG-------KNFSVVSLRQVRSPCLGDKFSSMHGQKGVLGFLESQENFPFTIQGIVPDIVINPHAFPSRQTPGQL 966 (1173)
Q Consensus 895 ~~~-~~~-------~~~~~v~~r~~R~~~iGDK~ssRhGqKGvvs~i~~~~dmPf~~~G~~pDiI~NPh~~PSRMtiGql 966 (1173)
+++ .++ .+.|+|++|+.|+|+||||||||||||||||+|||+|||||++||++|||||||||||||||||||
T Consensus 853 ~~~~~~~~~~~~~~~~~vkv~ir~~R~p~iGDKfasRHGqKGvis~i~~~eDMPf~~~G~~pDiIiNPhg~PSRMtiGql 932 (1112)
T PRK00405 853 FTRIEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQI 932 (1112)
T ss_pred eeccccCCccCcCcceEEEEEEeeecccCcccchhhccCCceeEEeEeccCCCCcCCCCCCCcEEECCCCCcccccHHHH
Confidence 987 555 468999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhcCccccCCCEEEecC-CCCCCHHHHHHHHHHcCCCCCCceEeeeCCCCcEEEeeEeEeeeehhcccccc
Q 001050 967 LEAALGKGIAALGKGICSGLKRYATP-FATPSVDAITEQLHRAGFSKWGTERLYDGRTGEMVRSLIFIGPTFYQRLIHMS 1045 (1173)
Q Consensus 967 ~E~~~gk~~~~~~~~~~~g~~~~~tp-F~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~i~~G~~yy~rL~Hmv 1045 (1173)
+|+++||||+ +.|.+ ++|| |++.+.+++++.|+++||+++|+|.||||+||++|+++||+|++|||||+|||
T Consensus 933 ~E~~~gk~~~------~~g~~-~~tp~f~~~~~~~~~~~l~~~g~~~~G~e~l~~G~tG~~~~~~if~G~~yy~rL~HmV 1005 (1112)
T PRK00405 933 LETHLGWAAK------GLGIK-FATPVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLV 1005 (1112)
T ss_pred HHHHhhHHHH------hcCCe-EecCccCCccHHHHHHHHHHcCcCCCCCEEEECCCCCCCCcccEEEEehhheechhhh
Confidence 9999999999 78866 7888 99999999999999999999999999999999999999999999999999999
Q ss_pred CccceeeecCCCCccccCCcccccccCceeeeehhhhHHHHhhhHHHHHHhhhcCCCccceecccccCCccchheeeecC
Q 001050 1046 EDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGAAANLHERLFTLSDSYQMHICRKCKNVANVIQRVVGG 1125 (1173)
Q Consensus 1046 ~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEME~d~l~a~Ga~~~l~erl~~~SD~~~~~vc~~cg~~~~~~~~~~~~ 1125 (1173)
+||+|||++|||+.|||||++||||+|||||||||||||+|||||++|+|||+.+||.+ +|+..
T Consensus 1006 ~DK~haRs~Gp~~~lT~QP~~Grsr~GG~R~GEME~d~l~a~Gas~~L~Erl~~~SD~~-------~g~~~--------- 1069 (1112)
T PRK00405 1006 DDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV-------VGRTK--------- 1069 (1112)
T ss_pred cchhhhcccCCccceeeCCCcccccCCCeeeeeeehhhHhhhhhHHHHHHHhhccCccc-------cccee---------
Confidence 99999999999999999999999999999999999999999999999999999999954 35432
Q ss_pred CcccCCccccccCCCCCcccccchHhHHHHHHHHHhcCCcEEEEE
Q 001050 1126 GRKVRGPYCRICDSGDDIVKANVPYGAKLLCQELFSMGITLKFDT 1170 (1173)
Q Consensus 1126 ~~~~~~~~c~~c~~~~~~~~~~iPy~~k~L~~EL~sm~i~~~l~~ 1170 (1173)
.+.| +| ++.++.++.+|||||||+|||+||||++++..
T Consensus 1070 -----~~~~-~~-~~~~i~~~~~p~~fklL~~EL~sm~i~~~~~~ 1107 (1112)
T PRK00405 1070 -----VYEA-IV-KGENIPEPGIPESFNVLVKELQSLGLDVELLD 1107 (1112)
T ss_pred -----EEEE-ee-cCCcccccCCChHHHHHHHHHHHCccceEEec
Confidence 2345 56 56799999999999999999999999999873
No 9
>CHL00001 rpoB RNA polymerase beta subunit
Probab=100.00 E-value=4.1e-217 Score=2021.58 Aligned_cols=920 Identities=24% Similarity=0.338 Sum_probs=786.6
Q ss_pred cCcCCchHHHHHHHHHHHHhHHHHHhcccCceEeCCCCCCCCCCCCcceeEEEEEceEEEccCccccCCCCCcCCCChhh
Q 001050 34 FNEYGLVSHQINSYNEFIKNGLQKAFDSFGETIVEPGYDPSKKGEGEWRYASMRFGQVTLDKPSFFAGNGGDEHDMFPRH 113 (1173)
Q Consensus 34 f~~~~Lv~~qi~SFN~Fi~~gL~~ii~~~~pI~~~~~~~~~~~~~~~~~~~~l~f~~i~i~~P~~~e~~~~~~~~l~P~e 113 (1173)
|..|+|+++|++||||||++||++++++++||+. .+ . ...+.+.|+++++++|++ +|+|
T Consensus 10 ~~~P~Lv~~Q~~SF~~Fl~~gL~~i~~~~~pI~~-~~--~-------~~~~~~~~~~~~l~~P~~-----------~p~e 68 (1070)
T CHL00001 10 STIPGFNQIQFEGFCRFIDQGLTEELSKFPKIED-TD--Q-------EIEFQLFVETYQLVEPLI-----------KERD 68 (1070)
T ss_pred cCCCCHHHHHHHHHHHHHHHhHHHHHHhcCCeEC-CC--C-------CEEEEEEeCeEEECCCCC-----------CHHH
Confidence 5679999999999999999999999999999972 11 1 134666778999999976 5788
Q ss_pred HHhcCCcccceEEEEEEEEEeeccccccccccccccceeeccccccceeEEEecccceEecCCccccCCCcCCCCcCCCC
Q 001050 114 ARLQNMTYSSRMKVKVQFQVYTQKRVTSDKFKTGREQYIQKEVLSDETTNIIIGRIPVMVKSDLCWMKGVEKGDCDFDHG 193 (1173)
Q Consensus 114 cR~r~~TYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~~~gE~~~D~G 193 (1173)
||+|++||+|||+|+++++..+ ++ ..++++|++|+||+| |+|
T Consensus 69 ar~r~lTYsa~l~v~v~l~~~~----------~~----------~i~~~~V~iG~iPlM------------------t~g 110 (1070)
T CHL00001 69 AVYESLTYSSELYVPAGLIWKK----------SR----------DMQEQTVFIGNIPLM------------------NSL 110 (1070)
T ss_pred HHHhCCCCCceeEEEEEEEEcC----------ce----------eEEEeEEEEecCCcc------------------CCC
Confidence 9999999999999999997422 11 112468999999999 679
Q ss_pred cEEEEeCcEEEeEeeeeeccceEEE-ec----CCceEEEEEeecCCceEEEEEEecCccccccCCEEEEEEeeccccccH
Q 001050 194 GYFIIKGAEKVFVAQEQICLKRLWV-SN----SMGWTVAYKSENKRNRLIVRLVDMSKFEDIKGGEKVLSVYFLSTEIPI 268 (1173)
Q Consensus 194 GYFIING~ERVIi~Qe~~spnr~~i-~~----~~~~~a~irS~~~~~~~~i~~~~~~~~~~~~~~~i~v~i~~~k~~IPl 268 (1173)
|||||||+|||||+||++|||++|+ .. +..|+|+++|.++ + |+.++. ++++.+|+++++. ++||+
T Consensus 111 G~FIING~ERVIVsQ~~rSpg~~~~~~~~~~~~~~y~a~iis~rg-s--wl~~e~------d~~~~i~vri~~~-~kiPi 180 (1070)
T CHL00001 111 GTFIINGIYRVVINQILRSPGIYYRSELDHNGISVYTGTIISDWG-G--RLELEI------DRKARIWARVSRK-QKISI 180 (1070)
T ss_pred cEEEEcCcEEEEEEEEeccCCEEEEEecCCCCceeEEEEEEecCC-C--ceEEEE------ecCCeEEEEecCC-CcccH
Confidence 9999999999999999999999998 32 1268999998766 3 555542 2357899999996 69999
Q ss_pred hhHHHHhcCCChHHHHHHhcCCCCchHHHHHHHHhhHhhhccCCcCCCHHHHHHHHHhhc--cCCCCCChhhHHHHHhhc
Q 001050 269 WILFFALGVSSDKEIVNLIDFTCEDCSILNILFASIHDADNKCDEFRKGRNALKYVDKLI--KGTTFPPGESTEECMNTY 346 (1173)
Q Consensus 269 ~illrALG~~sD~eI~~~i~~~~~d~~~~~~l~~~l~~~~~~~~~i~t~e~al~yig~~~--~~~~~~~~e~~~~~L~~~ 346 (1173)
++||||||+ +|+||++.++++ +.+..++.+... ..+.|+++||.||++++ ++......+.|+.+|.+.
T Consensus 181 ~ilLrALG~-sd~eIl~~~~~~-------~~l~~~l~~~~~--~~~~t~e~Al~~i~~~l~~r~~~~~~~~~a~~~l~~~ 250 (1070)
T CHL00001 181 LVLLSAMGL-NLREILDNVCYP-------EIFLSFLNDKEK--KKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKK 250 (1070)
T ss_pred HHHHHHcCC-CHHHHHHHhCcH-------HHHHHHHHHHhh--ccccCHHHHHHHHHHhhccCCCCcchHHHHHHHHHHH
Confidence 999999999 599999999752 234444433211 23789999999999998 445556678899999999
Q ss_pred ccCc------CCCcc----------cccchH-----HHHHHHHHhhccCCCCCCCcccccCcEEeehhhhHHHHHHHHHH
Q 001050 347 LFPS------LHGTK----------QKARFL-----GYMVKCLLQAYSGRRKCDNRDDFRNKRLELAGELLERELKVHIA 405 (1173)
Q Consensus 347 llpH------l~~~~----------~K~~~L-----~~Mi~kLl~~~~g~~~~DD~D~l~nkRv~l~G~Ll~~lfr~~l~ 405 (1173)
+|+| +|+.+ .|..+| ++|+++|+.+..|...+||+|||+||||+++|+||+.|||.+|+
T Consensus 251 ff~~rY~Lg~vGr~~~n~kl~~~~~~~~~~L~~~Di~~~i~~Ll~l~~G~~~~DDiDhLgNKRvr~vGeLL~~qfr~~l~ 330 (1070)
T CHL00001 251 FFQQRCELGRIGRRNMNRKLNLDIPENNTFLLPQDVLAAADYLIGMKFGMGTLDDIDHLKNKRIRSVADLLQDQFGLALN 330 (1070)
T ss_pred hccccccccccCchhhhhhhcccccccceEecHHHHHHHHHHHHHhhcCCCCccchhHHhccccchHHHHHHHHHHHHHH
Confidence 9998 88653 356667 89999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhhcccCCcccccccccccccchhhccccccccccccccCccccccccceeecCCCChhhhhcccccccc-
Q 001050 406 HARKRMAKALQRDLYGDRTVRPIEYYLDASILTNGLSRAFSTGAWSHPFKRTERISGIVANLGRANPLQTLVDLRRTRQ- 484 (1173)
Q Consensus 406 ~~~~~i~~~l~~~~~~~~~~~~~~~~i~~~~It~~i~~~~sTGnw~~~~~~~~q~sGvSQvldRlN~ls~lSh~Rrv~s- 484 (1173)
++.+.++++|++.+.+.+.+ ++..+++++.||++|++||+| +||||+|||+||||+|||+||+++
T Consensus 331 r~~r~ik~~m~~~~~~~~~~-~~~~lin~~~It~~ik~ff~t-------------s~LSQflDqtNpLseltHkRRlssl 396 (1070)
T CHL00001 331 RLENAVRGTICGAIRRKLIP-TPQNLVTSTPLTTTYESFFGS-------------HPLSQFLDQTNPLTEIVHGRKLSSL 396 (1070)
T ss_pred HHHHHHHHHHHHHhcccccC-CHHHhhCcchHHHHHHhhhcC-------------CcceeeeccCCHHHhhhhhhccccc
Confidence 99999999998765444455 688899999999999999984 799999999999999999999998
Q ss_pred -ccccCCccc--ccCCCCCCCcceeeecCCCCCcccccccccceeeeeec-Cc-chhHHHHHHhcCceecccccCccCCC
Q 001050 485 -QVQYTGKVG--DARYPHPSHWGKICFLSTPDGENCGLVKNLGVTGLVST-SI-LEPIFEQLFNSGMEKLADDASYSLGG 559 (1173)
Q Consensus 485 -~~~~~~k~t--~vR~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~It~-~~-~~~i~~~l~~~g~~~~~~~~~~~~~~ 559 (1173)
|.+.+++.+ +||+|||||||||||+|||||+|||||+|||++|+|+. |+ ++|+++++...+...+..++..+ .+
T Consensus 397 Gpgglsr~~a~fevRdvHpShyGRICPIETPEG~NiGLI~sLA~~A~In~~GfietP~~~v~~~~~~~~i~ylsa~e-e~ 475 (1070)
T CHL00001 397 GPGGLTGRTASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIGHWGSLESPFYEISERSKEERMVYLSPSE-DE 475 (1070)
T ss_pred CCCCccccccCCcccccCccccccccCCCCCCcccccchhhhhhhcccccCCCcccceeeeccccccceeEEccccc-cC
Confidence 887777766 99999999999999999999999999999999999994 88 99999998776666665554444 45
Q ss_pred cceeeeccEEEEEecChhHHHHHHHHHHhcCCCCceEEEEEeccCCeEEEeecCCeeeeeEEEeecccccccccCCcchh
Q 001050 560 KFKVFVDGDWIGVCKDSLSFVSELRRKRRRKELPTQVEIKRDELQSEVRIFMDAGRILRPLLVVENMGKIKSLEGKNYTF 639 (1173)
Q Consensus 560 ~~~VflnG~~iG~~~~~~~~~~~lR~~rr~~~i~~~~~i~~~~~~~~i~I~sd~GRl~RP~l~v~~~~~~~~~~~~~~~~ 639 (1173)
.+.|+ ||.|+|...+. +. +. ..|..
T Consensus 476 ~~~Ia-~g~~~~~~~~~---------------~~-----------~~----------~~~~r------------------ 500 (1070)
T CHL00001 476 YYMIA-AGNSLALNQGI---------------QE-----------EQ----------VVPAR------------------ 500 (1070)
T ss_pred ceEEE-eCceeeccCCc---------------cc-----------cc----------eeEEE------------------
Confidence 67887 99998743210 00 00 00000
Q ss_pred HhhhhcCceeeecccccceeEEeecccccccccCCCCCceeeeecccccccccceeecccccCCCccchhhhhhcccccc
Q 001050 640 QALLDHGIIELVGTEEEEDCCTAWGIKYLLKDIEDKKPIKFTHCELDMSFLLGLSCGIIPFANHDHARRVLYQSQKHSSQ 719 (1173)
Q Consensus 640 ~~l~~~g~iE~id~~Eq~~~~Ia~~~~~~~~~~~~~~~~~~th~Ei~p~~ilgv~aslIPF~~hNqspRn~yqc~~M~KQ 719 (1173)
+ -+++..|+.. +.|||||+|.+|+|++||+|||+||||||||+|||+ |+||
T Consensus 501 ----------~----~~e~~~i~~~--------------~i~~~dIsP~qi~svaasLIPFleHndanRalmgsn-MqrQ 551 (1070)
T CHL00001 501 ----------Y----RQEFLTIAWE--------------QIHLRSIFPFQYFSIGASLIPFLEHNDANRALMGSN-MQRQ 551 (1070)
T ss_pred ----------e----cCeEEEEchH--------------HCcEEeeChhhhhhhhhhcCCCccccCcchhhhhhc-cchh
Confidence 0 0123445432 358999999999999999999999999999999999 9999
Q ss_pred cccccccC---------Ceeee-----------------e-----------c-ccccccc---------CCcceEecccc
Q 001050 720 AIGFPTTN---------PSIRV-----------------D-----------T-LSHQLFY---------PQRPLFRTMIS 752 (1173)
Q Consensus 720 aig~~~~n---------~~~r~-----------------D-----------~-~~~~l~y---------pQ~Plv~t~~~ 752 (1173)
|||+...| +..|. | + ..|++.| ||||||+++
T Consensus 552 Avpll~~~~p~VgTG~E~~~~~ds~~~i~a~~~G~V~~vd~~~I~i~~~~~~~~y~l~~y~rsnq~t~~~QkPlV~~g-- 629 (1070)
T CHL00001 552 AVPLSRSEKCIVGTGLERQVALDSGVVAIAEHEGKIIYTDTDKIILSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRG-- 629 (1070)
T ss_pred ccccccCCCCEeecCcchhhhhcccceeEEccCCEEEEEeCCEEEEEcCCCeEEEEeeceeccCCCcccccCCEEecC--
Confidence 99999998 76777 6 4 5678888 999999986
Q ss_pred ccccCCcc-cCCCCCCCCCccCCcccEEEEEecCCCCCCCeEEEecceeecCceEEEEEEEEEEEeeecccccccccccc
Q 001050 753 DCLGKPGY-GHNHILPRPELYNGQNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVKRRSSDD 831 (1173)
Q Consensus 753 ~~~~~~~~-~~~~~~~~~~~~~G~N~~VAv~~~~Gyn~EDaiiin~~~~~rg~f~s~~~~~~~~~~~~~~~~~~~e~~~~ 831 (1173)
+++++||+ ||+.++..+|+|+|+|++||||||+||||||||||||++++||+|||+||++|++++++++ .+.|++..
T Consensus 630 ~~v~~g~~ladg~~~~~gel~~G~N~~VA~m~~~GYn~EDAiiin~~~v~~g~~~s~~~~~~~~~~~~~~--~g~e~i~~ 707 (1070)
T CHL00001 630 KCVKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTS--QGPERITK 707 (1070)
T ss_pred CEEccCCEeccChhhccccccCCccceeeeeeccccccchhhhhhhhhhcCCceEEEEEeeeeEEEeccC--CCcceEec
Confidence 99999999 9999999999999999999999999999999999999999999999999999999998755 34576643
Q ss_pred --ccccccccccccccCCCCCCCCcccCcEEccCCeEEEEecCC------------------------CceeeEEccCCC
Q 001050 832 --MVNFGKIQSKIGRVDSLDDDGFPFIGANLQSGDIVIGKYADS------------------------GADHSIKLKHTE 885 (1173)
Q Consensus 832 --~~~~~~~~~~~~~~~~Ld~dGi~~~g~~v~~gdili~k~~~~------------------------~~~~s~~~~~~~ 885 (1173)
|... ...|++||+||++++|++|++|||||||++|. .+|+|+++++++
T Consensus 708 ~~p~~~------~~~~~~Ld~dGi~~~G~~v~~gDilvgK~~p~~~~~~~~~~~~~~~~~if~~~~~~~~d~sl~~~~~~ 781 (1070)
T CHL00001 708 EIPHLE------AHLLRNLDKNGIVMLGSWVETGDILVGKLTPQEAEESSYAPEGRLLRAIFGIQVSTSKETCLKLPIGG 781 (1070)
T ss_pred cCCCCc------hhhhhccCCCCCccCCcEecCCCEEEEEecCCcccccccCcchhhhhhhhccccCcceeCeEECCCCC
Confidence 3321 13489999999999999999999999999884 468999999999
Q ss_pred ceEEEEEEEEeC----CCCCeEEEEEEeeccCCCccccccccCCCceEEeeeecCCCcCCCCCCCcCcEEeCCCCCCCCC
Q 001050 886 RGMVQKVVLSSN----DDGKNFSVVSLRQVRSPCLGDKFSSMHGQKGVLGFLESQENFPFTIQGIVPDIVINPHAFPSRQ 961 (1173)
Q Consensus 886 ~g~v~~v~~~~~----~~~~~~~~v~~r~~R~~~iGDK~ssRhGqKGvvs~i~~~~dmPf~~~G~~pDiI~NPh~~PSRM 961 (1173)
+|+|++|.++++ .++.+.|+|++|+.|+|+||||||||||||||||+|||+|||||++||++||||||||||||||
T Consensus 782 ~g~V~~v~~~~~~~~~~~~~~~vkv~i~~~R~~~vGDK~asRHGqKGvvs~i~~~eDMPf~~dG~~pDiIlNP~gvPSRM 861 (1070)
T CHL00001 782 RGRVIDVRWIQKKGGSSYNPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRM 861 (1070)
T ss_pred ceEEEEEEEEecccCCCCCcEEEEEEEEEEecCCCCcccccccCCcceEeeeecccCCCcccCCCCCceeeccccccccc
Confidence 999999999874 4556899999999999999999999999999999999999999999999999999999999999
Q ss_pred ChHHHHHHHHHHHHHhcCccccCCCEEEecCCCCCCHHHHH-----HHHHHcCC---CCC-------CceEeeeCCCCcE
Q 001050 962 TPGQLLEAALGKGIAALGKGICSGLKRYATPFATPSVDAIT-----EQLHRAGF---SKW-------GTERLYDGRTGEM 1026 (1173)
Q Consensus 962 tiGql~E~~~gk~~~~~~~~~~~g~~~~~tpF~~~~~~~~~-----~~l~~~g~---~~~-------G~e~ly~g~tG~~ 1026 (1173)
|||||+||++||||+ +.|.+.++|||++...+++. ..|.++|+ +.| |++.||||+||++
T Consensus 862 tiGqllE~~~G~a~~------~~g~~~~~~pf~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~Gk~~l~dG~TG~~ 935 (1070)
T CHL00001 862 NVGQIFECLLGLAGD------LLNRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRLFDGRTGDP 935 (1070)
T ss_pred cHHHHHHHHhHHHHh------hcCceeeeccCCCcchhhhhhhhhhHHHHHHHHhcCCceeccCCCCCeEEEEcCCCCCC
Confidence 999999999999999 89999999999977655554 67888877 444 9999999999999
Q ss_pred EEeeEeEeeeehhccccccCccceeeecCCCCccccCCcccccccCceeeeehhhhHHHHhhhHHHHHHhhhcCCCccce
Q 001050 1027 VRSLIFIGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGAAANLHERLFTLSDSYQM 1106 (1173)
Q Consensus 1027 ~~~~i~~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEME~d~l~a~Ga~~~l~erl~~~SD~~~~ 1106 (1173)
|+++||+|++|||||+|||+||+||||+|||++|||||++||||+|||||||||||||+|||||++|+|||+.+||.
T Consensus 936 ~~~~i~vG~~Yy~kL~HmV~DKihaRs~Gp~~~lT~QP~~Grsr~GG~RfGEME~~al~a~GAs~~L~E~L~~~SD~--- 1012 (1070)
T CHL00001 936 FEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSDH--- 1012 (1070)
T ss_pred ccceEEEEecceeEchhhccccceeeccCCCcccccCCCCcccCCCCeeeecchHHHHHhhhHHHHHHHHHhccCcc---
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999994
Q ss_pred ecccccCCccchheeeecCCcccCCccccccCCCCCccc-ccchHhHHHHHHHHHhcCCcEEEEE
Q 001050 1107 HICRKCKNVANVIQRVVGGGRKVRGPYCRICDSGDDIVK-ANVPYGAKLLCQELFSMGITLKFDT 1170 (1173)
Q Consensus 1107 ~vc~~cg~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~-~~iPy~~k~L~~EL~sm~i~~~l~~ 1170 (1173)
+-.+|+.+. .|.++.++.+ +.+|||||+|++||+|||+++.+..
T Consensus 1013 -~~~r~~~~~-------------------~i~~g~~~~~~~~~pesfk~l~~El~~l~l~i~~~~ 1057 (1070)
T CHL00001 1013 -IRARQEVLG-------------------AIITGGTIPKPEDAPESFRLLVRELRSLALELNHFL 1057 (1070)
T ss_pred -HHHHHHHHH-------------------hhhcCCcccCCCCCCchhhHHHHHHHhCccceEEEE
Confidence 333342221 2334556777 7999999999999999999998864
No 10
>CHL00207 rpoB RNA polymerase beta subunit; Provisional
Probab=100.00 E-value=2.4e-203 Score=1885.47 Aligned_cols=904 Identities=24% Similarity=0.324 Sum_probs=754.2
Q ss_pred ccCcCCchHHHHHHHHHHHHhHHHHHhcccCceEeCCCCCCCCCCCCcceeEEEEEc--eEEEccCccccCCCCCcCCCC
Q 001050 33 FFNEYGLVSHQINSYNEFIKNGLQKAFDSFGETIVEPGYDPSKKGEGEWRYASMRFG--QVTLDKPSFFAGNGGDEHDMF 110 (1173)
Q Consensus 33 ~f~~~~Lv~~qi~SFN~Fi~~gL~~ii~~~~pI~~~~~~~~~~~~~~~~~~~~l~f~--~i~i~~P~~~e~~~~~~~~l~ 110 (1173)
-|..|+|++.|++||+||+++||++++++++||+.. . ..+.++|. ++++++|.+ +
T Consensus 4 ~~~~Pdll~iQ~~SF~~FL~~GL~~~~~~~~pI~~~-----~-------~~~~l~~~~~~y~l~~P~~-----------~ 60 (1077)
T CHL00207 4 NFALPDFLEIQRTSFCWFLNEGLNEELNIFSKIFDY-----T-------GNLELLLFGKNYKLKYPKY-----------N 60 (1077)
T ss_pred ccCCCCHHHHHHHHHHHHHHHHHHHHHHhcCCeECC-----C-------CCEEEEEecceEEEcCCCC-----------C
Confidence 366799999999999999999999999999999731 1 12445554 799999985 4
Q ss_pred hhhHHhcCCcccceEEEEEEEEEeeccccccccccccccceeeccccccceeEEEecccceEecCCccccCCCcCCCCcC
Q 001050 111 PRHARLQNMTYSSRMKVKVQFQVYTQKRVTSDKFKTGREQYIQKEVLSDETTNIIIGRIPVMVKSDLCWMKGVEKGDCDF 190 (1173)
Q Consensus 111 P~ecR~r~~TYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~~~gE~~~ 190 (1173)
|.|||+|++||++||+|++++...+ ++ ..++++|++|+||+|+
T Consensus 61 ~~Ea~~r~~TYsa~l~v~~~l~~~~----------~~----------~i~~~~V~lG~iPlMT----------------- 103 (1077)
T CHL00207 61 LLSAKSYDSNYSIQIYLPLKFINLK----------TN----------KIKFINYLIGNLPKMT----------------- 103 (1077)
T ss_pred HHHHHHhCCccceeEEEEEEEEEcC----------Cc----------eEEEEEEEEeccCccC-----------------
Confidence 6789999999999999999986522 11 1235789999999995
Q ss_pred CCCcEEEEeCcEEEeEeeeeeccceEEEec--C---CceEEEEEeecCCceEEEEEEecCccccccCCEEEEEEeecccc
Q 001050 191 DHGGYFIIKGAEKVFVAQEQICLKRLWVSN--S---MGWTVAYKSENKRNRLIVRLVDMSKFEDIKGGEKVLSVYFLSTE 265 (1173)
Q Consensus 191 D~GGYFIING~ERVIi~Qe~~spnr~~i~~--~---~~~~a~irS~~~~~~~~i~~~~~~~~~~~~~~~i~v~i~~~k~~ 265 (1173)
++|||||||+|||||+|+.||||.+|-.. + ..|.|.+.+. ++.|++++. ++++.+|+++++. ++
T Consensus 104 -~~GtFIING~ERViVsQl~RSPGiyf~~~~~k~~~~~y~a~IIp~---rGswl~~e~------d~k~~i~vridr~-rK 172 (1077)
T CHL00207 104 -QRGTFIINGLERVIVSQIIRSPGIYFKKEIKKNSNKIYSATLIPN---RGSWIKFEL------DKNKEIWIRIDKN-RK 172 (1077)
T ss_pred -CCCEEEEcCceeEEEEEeccCCeEEEEEecCcCCceEEEEEEEcC---CCceEEEEE------cCCCeEEEEecCC-ce
Confidence 59999999999999999999999877622 1 2578898865 447888863 3468999999995 59
Q ss_pred ccHhhHHHHhcCCChHHHHHHhcCCCCchHHHHHHHHhhHhhhccCCcCCCHHHHHHHHHhhccCCCCCChhhHHHHH--
Q 001050 266 IPIWILFFALGVSSDKEIVNLIDFTCEDCSILNILFASIHDADNKCDEFRKGRNALKYVDKLIKGTTFPPGESTEECM-- 343 (1173)
Q Consensus 266 IPl~illrALG~~sD~eI~~~i~~~~~d~~~~~~l~~~l~~~~~~~~~i~t~e~al~yig~~~~~~~~~~~e~~~~~L-- 343 (1173)
||+++||||||+ ||+||++.+.+.. +..+ +...++. ....++++|+.+|++++++......+.++.+|
T Consensus 173 ipit~lLrALGl-s~~eIl~~~~~~~-~~~~---~~~~l~~-----~~~~~~e~Al~~Iy~~lrp~~~~~~~~a~~~l~~ 242 (1077)
T CHL00207 173 KPLIIFLKALGL-TDQDIYSRLTKSE-FLKK---LKPILLN-----SNSYTNEEILLEIYKNLSPIEPATVNDANQNLFS 242 (1077)
T ss_pred eeHHHHHHHhCC-CHHHHHHHHhccc-hHHH---HHHHHhc-----cCcccHHHHHHHHHHhcCCCCCccHHHHHHHHHH
Confidence 999999999999 8999999986421 1122 2223322 23568999999999999887767777788776
Q ss_pred -----hhcccCcCCCcc---------------cccchHHHHHHHHHhhccCCCCCCCcccccCcEEeehhhhHHHHHHHH
Q 001050 344 -----NTYLFPSLHGTK---------------QKARFLGYMVKCLLQAYSGRRKCDNRDDFRNKRLELAGELLERELKVH 403 (1173)
Q Consensus 344 -----~~~llpHl~~~~---------------~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~nkRv~l~G~Ll~~lfr~~ 403 (1173)
++|.|+|+|+.+ -+...++.|+++|+.+..|....||+|||+||||+++|+||++|||.+
T Consensus 243 ~ff~~~rYdLg~vGR~klN~kl~~~~~~~~~~l~~~Dil~~i~~Li~l~~g~~~~DDiDHL~NRRvrsvGELlq~qfr~g 322 (1077)
T CHL00207 243 RFFDPKNYDLGKVGRYKINNKLNLNIPERVRNLTYEDILSIIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIG 322 (1077)
T ss_pred HhcChhcccccccchhhhhhhccCCcCccCceecHHHHHHHHHHHHHhhcCCCcccchhhhhcccccchhHHHHHHHHHH
Confidence 455678888733 122335679999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhhcccCCcccccccccccccchhhccccccccccccccCccccccccceeecCCCChhhhhccccccc
Q 001050 404 IAHARKRMAKALQRDLYGDRTVRPIEYYLDASILTNGLSRAFSTGAWSHPFKRTERISGIVANLGRANPLQTLVDLRRTR 483 (1173)
Q Consensus 404 l~~~~~~i~~~l~~~~~~~~~~~~~~~~i~~~~It~~i~~~~sTGnw~~~~~~~~q~sGvSQvldRlN~ls~lSh~Rrv~ 483 (1173)
|.++.+.++++|.+... +.+ ++..++++++||..|++||+ ++||||+|||+||||+|||+||++
T Consensus 323 l~rler~ike~m~~~~~--~~~-tp~~lin~k~lt~~ikeFFg-------------ss~LSQfmDQtNpLselTHKRRls 386 (1077)
T CHL00207 323 LKRLERILRNRMTICDI--DSL-SKFNLINPKPLIALIREFFG-------------SSQLSQYMDQTNPLSELTHKRRIS 386 (1077)
T ss_pred HHHHHHHHHHHhhhccc--ccC-ChhhcccchhHHHHHHHhhc-------------cCCccceecccChHHhhhccceee
Confidence 99999999999986422 234 57889999999999999997 589999999999999999999999
Q ss_pred c----ccccCCcccccCCCCCCCcceeeecCCCCCcccccccccceeeeeec-Cc-chhHHHHHHhcCceecccccCccC
Q 001050 484 Q----QVQYTGKVGDARYPHPSHWGKICFLSTPDGENCGLVKNLGVTGLVST-SI-LEPIFEQLFNSGMEKLADDASYSL 557 (1173)
Q Consensus 484 s----~~~~~~k~t~vR~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~It~-~~-~~~i~~~l~~~g~~~~~~~~~~~~ 557 (1173)
+ .+.++++.+++|++||||||||||+|||||+|||||++||.+|+|+. |+ ++|+++
T Consensus 387 aLGpGGLsR~ra~fevRdvH~thyGRiCPIETPEG~n~Gli~~la~~~~in~~GfietPy~~------------------ 448 (1077)
T CHL00207 387 ILGPGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCGLIGSLATNARINKFGFIETPFYK------------------ 448 (1077)
T ss_pred ccCCCcccccccCCcccccCccccccccCCCCCCCcccccccchhhhccccCCCceeCceEE------------------
Confidence 8 57888999999999999999999999999999999999999999988 66 776532
Q ss_pred CCcceeeeccEEEEEecChhHHHHHHHHHHhcCCCCceEEEEEeccCCeEEEeecCCeeeeeEEEeecccccccccCCcc
Q 001050 558 GGKFKVFVDGDWIGVCKDSLSFVSELRRKRRRKELPTQVEIKRDELQSEVRIFMDAGRILRPLLVVENMGKIKSLEGKNY 637 (1173)
Q Consensus 558 ~~~~~VflnG~~iG~~~~~~~~~~~lR~~rr~~~i~~~~~i~~~~~~~~i~I~sd~GRl~RP~l~v~~~~~~~~~~~~~~ 637 (1173)
| .||.+. ..
T Consensus 449 -----v-~~g~v~-~~---------------------------------------------------------------- 457 (1077)
T CHL00207 449 -----V-INGKVK-KF---------------------------------------------------------------- 457 (1077)
T ss_pred -----E-EcCccc-cc----------------------------------------------------------------
Confidence 2 344320 00
Q ss_pred hhHhhhhcCceeeecccccceeEEeecccccccccC---------------CCCCceeeeecccccccccceeecccccC
Q 001050 638 TFQALLDHGIIELVGTEEEEDCCTAWGIKYLLKDIE---------------DKKPIKFTHCELDMSFLLGLSCGIIPFAN 702 (1173)
Q Consensus 638 ~~~~l~~~g~iE~id~~Eq~~~~Ia~~~~~~~~~~~---------------~~~~~~~th~Ei~p~~ilgv~aslIPF~~ 702 (1173)
..++|+++.||+...||.....+.+... ...+.+.++++++|.+++|++||+|||.+
T Consensus 458 --------~~i~ylsa~~e~~~~Ia~~~~~~~~~~~~~~~~v~~r~~~ef~~~~~~~v~~~~vsp~Q~~SvaasLIPFLe 529 (1077)
T CHL00207 458 --------GNPIYLTADSEDLYRIAPNDINLNKNNYFKKNIIPVRYKQEFKTVNPSKVDFIAISPIQVFSIAESLIPFLE 529 (1077)
T ss_pred --------CceeecChHHhcCcEEEecCccCCCCCcccCCEEEEEECCcEEEEChHHceEEEeCcchhcchhhhcCCccc
Confidence 0133444444444444433322211100 01134568999999999999999999999
Q ss_pred CCccchhhhhhcccccccccccccC---------------------------------Cee--eeec---ccc-------
Q 001050 703 HDHARRVLYQSQKHSSQAIGFPTTN---------------------------------PSI--RVDT---LSH------- 737 (1173)
Q Consensus 703 hNqspRn~yqc~~M~KQaig~~~~n---------------------------------~~~--r~D~---~~~------- 737 (1173)
||+++|++||++ |++|||++.... ... +.+. ..|
T Consensus 530 hdDanRaLMGsn-MqrQaVPll~~e~p~VgTg~e~~~a~ds~~~i~a~~~G~v~~v~~~~I~i~~~~~~~~~y~l~~~~r 608 (1077)
T CHL00207 530 HNDANRALMGSN-MQRQAVPLLYPEKPIVGTGYEKQIALDSGMTIISLTEGIVVSVSAYKIIIQDDNNRYIHYYLQKYQR 608 (1077)
T ss_pred ccccchhhhhhc-cccccccccccCCCeEECCcchHhhhhcchheEeccCcEEEEecCcEEEEEeCCCceeEEEeccccc
Confidence 999999999999 999999973211 111 1111 112
Q ss_pred ---ccccCCcceEeccccccccCCcc-cCCCCCCCCCccCCcccEEEEEecCCCCCCCeEEEecceeecCceEEEEEEEE
Q 001050 738 ---QLFYPQRPLFRTMISDCLGKPGY-GHNHILPRPELYNGQNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSY 813 (1173)
Q Consensus 738 ---~l~ypQ~Plv~t~~~~~~~~~~~-~~~~~~~~~~~~~G~N~~VAv~~~~Gyn~EDaiiin~~~~~rg~f~s~~~~~~ 813 (1173)
-.+..|||+|+ .++++.+||+ ||++++.++|+|+|+|++||||||+||||||||||||++++||+|+|+|+++|
T Consensus 609 sNq~t~i~qrp~V~--~G~~v~~G~iladg~~~~~~el~lG~N~lVA~m~y~GYN~EDAiiink~~v~rg~f~Si~~~~~ 686 (1077)
T CHL00207 609 SNQNTCINYRPIVW--VGEKINIGQILADGSDIDNSELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEKY 686 (1077)
T ss_pred cccCceeecccccC--CCCEEecCCEEecchhccCCcccCCcccEEEEEeeeccccchhhhhhhhhhcCCceEEEEEEEe
Confidence 13568999999 5899999999 99999999999999999999999999999999999999999999999999999
Q ss_pred EEEeeeccccccccccc--cccccccccccccccCCCCCCCCcccCcEEccCCeEEEEecCC------------------
Q 001050 814 KAEVDNKEMQVKRRSSD--DMVNFGKIQSKIGRVDSLDDDGFPFIGANLQSGDIVIGKYADS------------------ 873 (1173)
Q Consensus 814 ~~~~~~~~~~~~~e~~~--~~~~~~~~~~~~~~~~~Ld~dGi~~~g~~v~~gdili~k~~~~------------------ 873 (1173)
+.++++++ .+.|+|. .|... ...|++||+||+|++|++|++|||||||++|.
T Consensus 687 ~~e~~~~~--~g~e~i~~~~p~~~------~~~~~~LD~dGiv~iG~~V~~gDilvgK~tp~~~~~~~~~~~ll~~i~~~ 758 (1077)
T CHL00207 687 EIELRQTK--LGSEEITRNIPNVS------EYSLKNLDENGIISIGSKVLAGDILVGKITPKGESDQLPEGKLLRAIFGE 758 (1077)
T ss_pred eeEEeecC--CCceEEeccCCCCC------hHHhhccCccCCCcCCcEeCCCCEEEEEecCccccccChhhhhhhhhhcc
Confidence 99998754 3456665 33221 23489999999999999999999999999883
Q ss_pred ----CceeeEEccCCCceEEEEEEEEeCCC--CC-----eEEEEEEeeccCCCccccccccCCCceEEeeeecCCCcCCC
Q 001050 874 ----GADHSIKLKHTERGMVQKVVLSSNDD--GK-----NFSVVSLRQVRSPCLGDKFSSMHGQKGVLGFLESQENFPFT 942 (1173)
Q Consensus 874 ----~~~~s~~~~~~~~g~v~~v~~~~~~~--~~-----~~~~v~~r~~R~~~iGDK~ssRhGqKGvvs~i~~~~dmPf~ 942 (1173)
.+|+|++++++++|+|++|.++++.+ +. ..|+|++|+.|+|+||||||||||||||||+|||+|||||+
T Consensus 759 ~~~~~kd~sl~~~~~~~g~V~~V~~~~~~~~~~~~~~~~~~vkv~i~~~R~p~vGDKfasRHGqKGVvs~i~p~eDMPf~ 838 (1077)
T CHL00207 759 KAKDVKDTSLRMPNGGYGRVIKVEIFSRSKGDELKFGYYLKIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYL 838 (1077)
T ss_pred CCCcceEeEEEcCCCCcEEEEEEEEEecCCCCcccccccEEEEEEEEEEecCCcccccccccCCceeEEeeeccCCCCcc
Confidence 37999999999999999999998543 22 35899999999999999999999999999999999999999
Q ss_pred CCCCcCcEEeCCCCCCCCCChHHHHHHHHHHHHHhcCccccCCCEEEecCCCCCCHHHHHHHHHHc--------------
Q 001050 943 IQGIVPDIVINPHAFPSRQTPGQLLEAALGKGIAALGKGICSGLKRYATPFATPSVDAITEQLHRA-------------- 1008 (1173)
Q Consensus 943 ~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~~~~~~~g~~~~~tpF~~~~~~~~~~~l~~~-------------- 1008 (1173)
+||++|||||||||||||||||||+|+++||||+ +.|...++|||++...+++.+.|.+.
T Consensus 839 ~dG~~pDiIlNPhg~PSRMtiGqllE~~lGka~~------~l~~~~~~tpF~~~~~~~~~~~l~~~~l~~~~~~~~~~~~ 912 (1077)
T CHL00207 839 PDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGD------NLNKRFKILPFDEMYGSEYSRILINNKLNQASIKNNEYWL 912 (1077)
T ss_pred CCCCCccEEECCccccccccHHHHHHHHHHHHHH------hcCCcEeeccCCCCcHHHHHHHHHhhhhhhccchhccccc
Confidence 9999999999999999999999999999999999 77777889999988887777776553
Q ss_pred -CCCCCCceEeeeCCCCcEEEeeEeEeeeehhccccccCccceeeecCCCCccccCCcccccccCceeeeehhhhHHHHh
Q 001050 1009 -GFSKWGTERLYDGRTGEMVRSLIFIGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAH 1087 (1173)
Q Consensus 1009 -g~~~~G~e~ly~g~tG~~~~~~i~~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEME~d~l~a~ 1087 (1173)
+|+++|++.||||+||++|+++||+|++|||||+|||+||+||||+|||++|||||++||||+|||||||||||||+||
T Consensus 913 ~~~~~~Gk~~lydG~TGe~~~~~i~vG~~Yy~kL~HmV~DKihaRs~Gp~s~lTqQP~~Grsr~GG~RfGEME~~aL~a~ 992 (1077)
T CHL00207 913 FNSYHPGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAF 992 (1077)
T ss_pred cCCCCCCCEEEECCCCCCCccCceEEEecceeEchhhccccceeeccCCCcccccCCCCccccCCCeeeecccHHHHHhh
Confidence 3778899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHhhhcCCCccceecccccCCccchheeeecCCcccCCccccccCCCCCcccccchHhHHHHHHHHHhcCCcEE
Q 001050 1088 GAAANLHERLFTLSDSYQMHICRKCKNVANVIQRVVGGGRKVRGPYCRICDSGDDIVKANVPYGAKLLCQELFSMGITLK 1167 (1173)
Q Consensus 1088 Ga~~~l~erl~~~SD~~~~~vc~~cg~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~iPy~~k~L~~EL~sm~i~~~ 1167 (1173)
|||++|||||+.+||.+.+ + ..+|..|.++.++.++.+|||||+|+|||+||||++.
T Consensus 993 GAa~~L~E~L~~kSD~~~~-------r----------------~~~~~~~~~~~~i~~~~~P~sfklL~~EL~sl~i~~~ 1049 (1077)
T CHL00207 993 GAAYTLKELLTIKSDDMQG-------R----------------NETLNAIVKGQPIPKPGTPESFKVLMRELQSLGLDIE 1049 (1077)
T ss_pred hhHHHHHHHhhcCCcccee-------h----------------HHHHHhhhCCCeecCCCCCchHHHHHHHHHHCCcCcE
Confidence 9999999999999995442 1 2358999999999999999999999999999999998
Q ss_pred EEE
Q 001050 1168 FDT 1170 (1173)
Q Consensus 1168 l~~ 1170 (1173)
+..
T Consensus 1050 ~~~ 1052 (1077)
T CHL00207 1050 AYK 1052 (1077)
T ss_pred ecc
Confidence 864
No 11
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=100.00 E-value=1.8e-192 Score=1837.67 Aligned_cols=936 Identities=25% Similarity=0.338 Sum_probs=767.6
Q ss_pred hhhhcccccCcCCchHHHHHHHHHHHH------hHHHHHhcccCceEeCCCCCCCCCCCCcceeEEEEEceEEEccCccc
Q 001050 26 CRKAAVSFFNEYGLVSHQINSYNEFIK------NGLQKAFDSFGETIVEPGYDPSKKGEGEWRYASMRFGQVTLDKPSFF 99 (1173)
Q Consensus 26 ~~~~i~~~f~~~~Lv~~qi~SFN~Fi~------~gL~~ii~~~~pI~~~~~~~~~~~~~~~~~~~~l~f~~i~i~~P~~~ 99 (1173)
.|.-++..+..|+|++.|.+||+||++ +||++++++++||+. + ...+.|+|.++++++|.++
T Consensus 14 ~f~k~~~~~~iPdLleIQ~~SF~~FLq~~~~~~~GL~e~f~~~fPI~d-----~-------~g~~~Lefv~Y~l~~Pk~~ 81 (2890)
T PRK09603 14 DFTKTPTDLEVPNLLLLQRDSYDSFLYSKDGKESGIEKVFKSIFPIQD-----E-------HNRITLEYAGCEFGKSKYT 81 (2890)
T ss_pred ecccCCccCCCCCHHHHHHHHHHHHHhCCCcccccHHHHHHhcCCeEC-----C-------CCcEEEEEEEEEeCCCCCC
Confidence 366667778899999999999999998 799999999999973 1 1358899999999999986
Q ss_pred cCCCCCcCCCChhhHHhcCCcccceEEEEEEEEEeeccccccccccccccceeeccccccceeEEEecccceEecCCccc
Q 001050 100 AGNGGDEHDMFPRHARLQNMTYSSRMKVKVQFQVYTQKRVTSDKFKTGREQYIQKEVLSDETTNIIIGRIPVMVKSDLCW 179 (1173)
Q Consensus 100 e~~~~~~~~l~P~ecR~r~~TYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~ 179 (1173)
+ .||++|++||++||+|++++.+.++ +.++++.. .....++++|++|+||+|+.
T Consensus 82 ~-----------~Ec~~rg~TYsapL~v~~rL~~~~~------~~~t~~~~----~ikeikeq~VylGdiPLMT~----- 135 (2890)
T PRK09603 82 V-----------REAMERGITYSIPLKIKVRLILWEK------DTKSGEKN----GIKDIKEQSIFIREIPLMTE----- 135 (2890)
T ss_pred H-----------HHHHhhCCcccccEEEEEEEEEeec------cccccccc----cccceEEeeEEEecCCccCC-----
Confidence 5 5699999999999999999986431 11122100 01234568999999999987
Q ss_pred cCCCcCCCCcCCCCcEEEEeCcEEEeEeeeeeccceEEEe-cC--C----ceEEEEEeecCCceEEEEEEecCccccccC
Q 001050 180 MKGVEKGDCDFDHGGYFIIKGAEKVFVAQEQICLKRLWVS-NS--M----GWTVAYKSENKRNRLIVRLVDMSKFEDIKG 252 (1173)
Q Consensus 180 L~~~~~gE~~~D~GGYFIING~ERVIi~Qe~~spnr~~i~-~~--~----~~~a~irS~~~~~~~~i~~~~~~~~~~~~~ 252 (1173)
.|+|||||+|||||+|++||||.+|-. .. . .|+|.+++. ++.|++++. +++
T Consensus 136 -------------~GTFIING~ERVIVsQL~RSPGVyF~~~~~k~~s~k~lysa~IIP~---RGsWLefE~------D~k 193 (2890)
T PRK09603 136 -------------RTSFIINGVERVVVNQLHRSPGVIFKEEESSTSLNKLIYTGQIIPD---RGSWLYFEY------DSK 193 (2890)
T ss_pred -------------CceEEEcCceeEEEeeeccCCeeEEeeccCcCCCCceeEEEEEecC---CcceEEEEE------cCC
Confidence 999999999999999999999988873 21 1 388898854 557998863 457
Q ss_pred CEEEEEEeeccccccHhhHHHHhcCCChHHHHHHhcCCCC----------------------------------------
Q 001050 253 GEKVLSVYFLSTEIPIWILFFALGVSSDKEIVNLIDFTCE---------------------------------------- 292 (1173)
Q Consensus 253 ~~i~v~i~~~k~~IPl~illrALG~~sD~eI~~~i~~~~~---------------------------------------- 292 (1173)
+.+|+++++ ++++|+++||||||+ |++||++.+.....
T Consensus 194 d~l~vrIDr-krKipit~lLrAlG~-s~edIl~~f~~~~~~~i~~~~~~~~~~~~~l~~~~~~di~d~~g~vlv~~g~ri 271 (2890)
T PRK09603 194 DVLYARINK-RRKVPVTILFRAMDY-QKQDIIKMFYPLVKVRYENDKYLIPFASLDANQRMEFDLKDPQGKIILLAGKKL 271 (2890)
T ss_pred CeEEEEEcC-cceecHHHHHHHhCC-CHHHHHHHhcccceEEEcccceeecccHHHhcCccceeecccCCCEEEecCccc
Confidence 899999999 569999999999999 79999997751000
Q ss_pred chHHH-------------------------------HHH-----------HHhhHhhhc---------cC----------
Q 001050 293 DCSIL-------------------------------NIL-----------FASIHDADN---------KC---------- 311 (1173)
Q Consensus 293 d~~~~-------------------------------~~l-----------~~~l~~~~~---------~~---------- 311 (1173)
+.... +.+ ...+.+... ..
T Consensus 272 t~~~~~~l~~~g~k~l~~~~~~l~g~~laedivd~~Evl~~~~~~Itee~le~i~~~gi~~i~vl~~~~~~~~~~i~~t~ 351 (2890)
T PRK09603 272 TSRKIKELKENHLEWVEYPMDILLNRHLAEPVMVGKEVLLDMLTQLDKNKLEKIHDLGVQEFVIINDLALGHDASIIHSF 351 (2890)
T ss_pred cHHHHHHHHhcCCceeccchhhhcceeeeeeccCccceeeccCChhcHHHHHHHHHcCCceEEEEeeccccccccccccc
Confidence 00000 000 000000000 00
Q ss_pred --------------CcCCCHHHHHHHHHhhccCCCCCChhhHHHHHhhcccC-------cCCCcc---------------
Q 001050 312 --------------DEFRKGRNALKYVDKLIKGTTFPPGESTEECMNTYLFP-------SLHGTK--------------- 355 (1173)
Q Consensus 312 --------------~~i~t~e~al~yig~~~~~~~~~~~e~~~~~L~~~llp-------Hl~~~~--------------- 355 (1173)
....++++|+..|++++++......+.|+.++++.||- .+|+..
T Consensus 352 ~~d~~~~~~~~~t~~~~~~~eeAl~~iyr~lrpgep~~~e~A~~l~~~lFFn~~rYdLg~vGR~klN~kL~l~~~~~~~~ 431 (2890)
T PRK09603 352 SADSESLKLLKQTEKIDDENALAAIRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKMNHKLGLHVPDYITT 431 (2890)
T ss_pred ccccccchhhhhccccccchHHHHHHHHhccCCCCCCcHHHHHHHHHHHhcCcccccccccchhhhHhhhCCCCCCcccE
Confidence 00124689999999999888777788888888876653 122222
Q ss_pred -cccchHHHHHHHHHhhccCCCCCCCcccccCcEEeehhhhHHHHHHHHHHHHHHHHHHHhhhcccCCcccccccccccc
Q 001050 356 -QKARFLGYMVKCLLQAYSGRRKCDNRDDFRNKRLELAGELLERELKVHIAHARKRMAKALQRDLYGDRTVRPIEYYLDA 434 (1173)
Q Consensus 356 -~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~nkRv~l~G~Ll~~lfr~~l~~~~~~i~~~l~~~~~~~~~~~~~~~~i~~ 434 (1173)
.+.++| ..+++|+.+..|....||+|||+||||+++|+||+++||.+|.++.+.++++|.........+ .+..++|+
T Consensus 432 Lt~~Dil-~~i~~li~l~~g~~~~DDiDhL~NRRvr~vGELl~~qfr~gl~rler~irerm~~~~~~~~~~-~p~~lin~ 509 (2890)
T PRK09603 432 LTHEDII-TTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELHSGLVKMQKTIKDKLTTMSGAFDSL-MPHDLVNS 509 (2890)
T ss_pred ecchhHH-HHHHHHHHHHhCCCCCCcchhhhcchhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccccc-Chhhhhcc
Confidence 334666 599999999999999999999999999999999999999999999999999998532223344 57889999
Q ss_pred cchhhccccccccccccccCccccccccceeecCCCChhhhhcccccccc--c--cccCCcccccCCCCCCCcceeeecC
Q 001050 435 SILTNGLSRAFSTGAWSHPFKRTERISGIVANLGRANPLQTLVDLRRTRQ--Q--VQYTGKVGDARYPHPSHWGKICFLS 510 (1173)
Q Consensus 435 ~~It~~i~~~~sTGnw~~~~~~~~q~sGvSQvldRlN~ls~lSh~Rrv~s--~--~~~~~k~t~vR~Lhps~wG~iCPve 510 (1173)
++++..+++||+| +.|||+|||+||||+|+|+||+++ | +.++++.+++|++||||||||||+|
T Consensus 510 k~i~~~ikeFFgs-------------sqLSQfmDQtNpLseltHKRRlSaLGPGGlsr~ra~fevRdVH~shYGRiCPIE 576 (2890)
T PRK09603 510 KMITSTIMEFFMG-------------GQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIE 576 (2890)
T ss_pred HHHHHHHHHHhcc-------------CchhhhhcccChhhhhhhcccccccCCCCccccccCCcccccCcccccccCCCC
Confidence 9999999999974 569999999999999999999986 3 5578888999999999999999999
Q ss_pred CCCCcccccccccceeeeeec-Cc-chhHHHHHHhcCceecccccCccCCCcceeeeccEEEEEecChhHHHHHHHHHHh
Q 001050 511 TPDGENCGLVKNLGVTGLVST-SI-LEPIFEQLFNSGMEKLADDASYSLGGKFKVFVDGDWIGVCKDSLSFVSELRRKRR 588 (1173)
Q Consensus 511 TPEG~~cGLvk~LA~~a~It~-~~-~~~i~~~l~~~g~~~~~~~~~~~~~~~~~VflnG~~iG~~~~~~~~~~~lR~~rr 588 (1173)
||||+|||||++||.+|+|+. |+ ++|++ +| .||.+ ++
T Consensus 577 TPEG~NiGLI~SLa~~a~in~~GfietPy~-----------------------kV-~~g~v---~~-------------- 615 (2890)
T PRK09603 577 TPEGQNIGLINTLSTFTRVNDLGFIEAPYK-----------------------KV-VDGKV---VG-------------- 615 (2890)
T ss_pred CCCCCcccchhhhhhheecccCcceecceE-----------------------EE-ecCcc---cc--------------
Confidence 999999999999999999998 56 66653 22 34431 00
Q ss_pred cCCCCceEEEEEeccCCeEEEeecCCeeeeeEEEeecccccccccCCcchhHhhhhcCceeeecccccceeEEeeccccc
Q 001050 589 RKELPTQVEIKRDELQSEVRIFMDAGRILRPLLVVENMGKIKSLEGKNYTFQALLDHGIIELVGTEEEEDCCTAWGIKYL 668 (1173)
Q Consensus 589 ~~~i~~~~~i~~~~~~~~i~I~sd~GRl~RP~l~v~~~~~~~~~~~~~~~~~~l~~~g~iE~id~~Eq~~~~Ia~~~~~~ 668 (1173)
.++|+++.||+...||.....+
T Consensus 616 ----------------------------------------------------------~i~ylsa~eE~~~~IA~a~~~~ 637 (2890)
T PRK09603 616 ----------------------------------------------------------ETIYLTAIQEDSHIIAPASTPI 637 (2890)
T ss_pred ----------------------------------------------------------ceeeeCHHHhcCceEeccCCcc
Confidence 1345555555555555443333
Q ss_pred ccccCC---------------CCCceeeeecccccccccceeecccccCCCccchhhhhhccccccccccccc-------
Q 001050 669 LKDIED---------------KKPIKFTHCELDMSFLLGLSCGIIPFANHDHARRVLYQSQKHSSQAIGFPTT------- 726 (1173)
Q Consensus 669 ~~~~~~---------------~~~~~~th~Ei~p~~ilgv~aslIPF~~hNqspRn~yqc~~M~KQaig~~~~------- 726 (1173)
.+.... ..+...++|+++|.+++|++||+|||.+||+++|++|||+ |++||+++...
T Consensus 638 ~~~~~~~~~~v~~R~~~e~~~~~~~~v~~~dvsp~Q~vSvaasLIPFLEhdDAnRALMGSN-MQRQAVPLl~~e~piVgT 716 (2890)
T PRK09603 638 DEEGNILGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTN-MQRQAVPLLRSDAPIVGT 716 (2890)
T ss_pred CCCCcccCCeEeEEECCceEEEChHHceEEEeCccceeeehhhcCCccccCcccccccccc-chhhhhhhccccCCeEec
Confidence 221100 1245578999999999999999999999999999999999 99999997311
Q ss_pred --------------------------CCe--eeeec------cccc----------cccCCcceEeccccccccCCcc-c
Q 001050 727 --------------------------NPS--IRVDT------LSHQ----------LFYPQRPLFRTMISDCLGKPGY-G 761 (1173)
Q Consensus 727 --------------------------n~~--~r~D~------~~~~----------l~ypQ~Plv~t~~~~~~~~~~~-~ 761 (1173)
+.. .|.+. ..|. .++.|||+|+ .++++.+||+ |
T Consensus 717 G~E~~va~dSg~~i~a~~~G~V~yvd~~~I~i~~~~~~~~~~~~Y~L~Ky~RSNQ~TcinqrPiV~--~Gd~V~kGdilA 794 (2890)
T PRK09603 717 GIEKIIARDSWGAIKANRAGVVEKIDSKNIYILGEGKEEAYIDAYSLQKNLRTNQNTSFNQVPIVK--VGDKVEAGQIIA 794 (2890)
T ss_pred CcchhhhccccceeEecCCeEEEEecCcEEEEEecCCCCceeeEEeeccccccCCCceeeeccEec--CCCEeccCCEEe
Confidence 111 11111 1133 3668999999 5799999999 9
Q ss_pred CCCCCCCCCccCCcccEEEEEecCCCCCCCeEEEecceeecCceEEEEEEEEEEEeeeccccccccccc--ccccccccc
Q 001050 762 HNHILPRPELYNGQNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVKRRSSD--DMVNFGKIQ 839 (1173)
Q Consensus 762 ~~~~~~~~~~~~G~N~~VAv~~~~Gyn~EDaiiin~~~~~rg~f~s~~~~~~~~~~~~~~~~~~~e~~~--~~~~~~~~~ 839 (1173)
|++++..+||++|+|++||||||.|||||||||||++.+.+++|||+|+++|++++++++ .+.|+|. .|...
T Consensus 795 DG~st~~GELALG~NvlVAfmpW~GYNfEDAIlISERlV~eD~fTSIHIee~ei~~r~Tk--~G~EeITrdIPnvs---- 868 (2890)
T PRK09603 795 DGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVDARELK--HGVEEFTADIPDVK---- 868 (2890)
T ss_pred cCcccccCeeccCcccEEEEeeeccccCccccccchhhhcCccceEEEEeeeEEEEEecC--CCCcEEeccCCCCC----
Confidence 999999999999999999999999999999999999999999999999999999999865 5778874 44322
Q ss_pred ccccccCCCCCCCCcccCcEEccCCeEEEEecCC----------------------CceeeEEccCCCceEEEEEEEEeC
Q 001050 840 SKIGRVDSLDDDGFPFIGANLQSGDIVIGKYADS----------------------GADHSIKLKHTERGMVQKVVLSSN 897 (1173)
Q Consensus 840 ~~~~~~~~Ld~dGi~~~g~~v~~gdili~k~~~~----------------------~~~~s~~~~~~~~g~v~~v~~~~~ 897 (1173)
....++||++|||++|++|++|||||||++|+ .+|+|+++|++..|+|.+|++++.
T Consensus 869 --e~~l~~LDe~GII~iGa~V~~GDILVGKvTPkge~~~tPEekLLraIFGeka~~vkDtSLrvp~G~~G~Vidv~~f~r 946 (2890)
T PRK09603 869 --EEALAHLDESGIVKVGTYVSAGMILVGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTK 946 (2890)
T ss_pred --HHHHhcCCCCCCEeeCCEECCCCEEEEeeccCCCCCCChHHHHHHHHhcccccccccCceecCCCCcEEEEEEEEecc
Confidence 23488999999999999999999999999998 589999999999999999999874
Q ss_pred C-------------------------------------------------------------------------------
Q 001050 898 D------------------------------------------------------------------------------- 898 (1173)
Q Consensus 898 ~------------------------------------------------------------------------------- 898 (1173)
.
T Consensus 947 ~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1026 (2890)
T PRK09603 947 KGYEKDARVLSAYEEEKAKLDMEHFDRLTMLNREELLRVSSLLSQAILEEPFSHNGKDYKEGDQIPKEEIASINRFTLAS 1026 (2890)
T ss_pred cccchhHHHHHHHHHHHHHHhHhhHHHHHHHHHHHHHhhhhhccccccccccccccccccccccccHHHHhhCCHHHhhh
Confidence 2
Q ss_pred ---------------------------------------CC-------CeEEEEEEeeccCCCccccccccCCCceEEee
Q 001050 899 ---------------------------------------DG-------KNFSVVSLRQVRSPCLGDKFSSMHGQKGVLGF 932 (1173)
Q Consensus 899 ---------------------------------------~~-------~~~~~v~~r~~R~~~iGDK~ssRhGqKGvvs~ 932 (1173)
+| .+.|+|++|+.|+|++|||||||||||||||+
T Consensus 1027 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~gdeL~~Gv~~~VkV~ia~kR~~qvGDK~AgRHGnKGViS~ 1106 (2890)
T PRK09603 1027 LVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNGVIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSN 1106 (2890)
T ss_pred hhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCcCCCCcceEEEEEEEEeecccccchhhhccCCCeeEEE
Confidence 01 24699999999999999999999999999999
Q ss_pred eecCCCcCCCCCCCcCcEEeCCCCCCCCCChHHHHHHHHHHHHHhcCcccc-----------------------------
Q 001050 933 LESQENFPFTIQGIVPDIVINPHAFPSRQTPGQLLEAALGKGIAALGKGIC----------------------------- 983 (1173)
Q Consensus 933 i~~~~dmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~~~~~~----------------------------- 983 (1173)
|||+|||||++||++||||+||||||||||||||+|+++||||+.+|+.+.
T Consensus 1107 I~p~EDMPfl~dG~~pDIIlNPlGvPSRMnIGQilE~~LG~aa~~lg~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1186 (2890)
T PRK09603 1107 IVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGKQIASMLEDKTKDFAKELRAKMLEIANAINEKD 1186 (2890)
T ss_pred EEchhcCCCCCCCCCCcEEECCCCCCccccHHHHHHHHHHHHHHhcCcChhhhhhhcchhhhHHHHHHHHhhhccccccc
Confidence 999999999999999999999999999999999999999999997764420
Q ss_pred ----------------------CCCEEEecC-CCCCCHHHHHHHHHHcCCCCCCceEeeeCCCCcEEEeeEeEeeeehhc
Q 001050 984 ----------------------SGLKRYATP-FATPSVDAITEQLHRAGFSKWGTERLYDGRTGEMVRSLIFIGPTFYQR 1040 (1173)
Q Consensus 984 ----------------------~g~~~~~tp-F~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~i~~G~~yy~r 1040 (1173)
..-+.++|| |++.+.+++.+.|+++||+++|++.||||+||++|+++||+|++||||
T Consensus 1187 ~~~~~~~~~~~~~~~~~~~~~~~~g~~~~tpvF~g~~~~~i~~~l~~aG~~~~Gk~~LyDGrTGe~f~~~V~vG~~YylK 1266 (2890)
T PRK09603 1187 PLTIHALENCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIK 1266 (2890)
T ss_pred ccccccccccchHHHHhhhhhhccCCcccCCCCCCCCHHHHHHHHHHcCCCCCCCEEEEcCCCCCCccceEEEEeeceee
Confidence 001256899 999999999999999999999999999999999999999999999999
Q ss_pred cccccCccceeeecCCCCccccCCcccccccCceeeeehhhhHHHHhhhHHHHHHhhhcCCCccceecccccCCccchhe
Q 001050 1041 LIHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGAAANLHERLFTLSDSYQMHICRKCKNVANVIQ 1120 (1173)
Q Consensus 1041 L~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEME~d~l~a~Ga~~~l~erl~~~SD~~~~~vc~~cg~~~~~~~ 1120 (1173)
|+|||+||+||||+|||+++||||++||+++|||||||||||||+|||||++|||||+.+||... |+..
T Consensus 1267 L~HmVdDKiHaRstGPyslvTqQPl~GKs~~GGqRfGEMEvwALeAyGAa~~LqE~Lt~kSDdv~-------gR~~---- 1335 (2890)
T PRK09603 1267 LHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDIR-------GREN---- 1335 (2890)
T ss_pred chhhccchhhhccCCCcchhhhCCCcccccCCCceeeeeeHHHHHHhhHHHHHHHHHhcCCcchh-------hhhh----
Confidence 99999999999999999999999999999999999999999999999999999999999999433 4322
Q ss_pred eeecCCcccCCccccccCCCCCcccccchHhHHHHHHHHHhcCCcEEEEEe
Q 001050 1121 RVVGGGRKVRGPYCRICDSGDDIVKANVPYGAKLLCQELFSMGITLKFDTE 1171 (1173)
Q Consensus 1121 ~~~~~~~~~~~~~c~~c~~~~~~~~~~iPy~~k~L~~EL~sm~i~~~l~~~ 1171 (1173)
.|..|.++.++..+.+|||||+|++||+||||++++...
T Consensus 1336 ------------~y~~i~~g~~i~~~~iPeSFkvL~~EL~sL~l~i~~~~~ 1374 (2890)
T PRK09603 1336 ------------AYRAIAKGEQVGESEIPETFYVLTKELQSLALDINIFGD 1374 (2890)
T ss_pred ------------hhhhhcCCCcccccCCCHHHHHHHHHHHhCCcceEEEee
Confidence 345677788999999999999999999999999998753
No 12
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=100.00 E-value=6.7e-189 Score=1797.95 Aligned_cols=943 Identities=24% Similarity=0.343 Sum_probs=763.3
Q ss_pred hhhh-cccccCcCCchHHHHHHHHHHHH-----hHHHHHhcccCceEeCCCCCCCCCCCCcceeEEEEEceEEEccCccc
Q 001050 26 CRKA-AVSFFNEYGLVSHQINSYNEFIK-----NGLQKAFDSFGETIVEPGYDPSKKGEGEWRYASMRFGQVTLDKPSFF 99 (1173)
Q Consensus 26 ~~~~-i~~~f~~~~Lv~~qi~SFN~Fi~-----~gL~~ii~~~~pI~~~~~~~~~~~~~~~~~~~~l~f~~i~i~~P~~~ 99 (1173)
.|.- .+..+..|+|++.|.+||+||++ +||++++++++||+. + ...+.|+|.++++++|.++
T Consensus 18 ~f~~~~~~~~~~PdL~~iQ~~Sf~~Fl~~~~~~~GL~~~f~~ifPI~d-----~-------~g~~~lefv~y~l~~Pk~~ 85 (2836)
T PRK14844 18 SYSRSIDLKDSLLDLVKVQKESYDSFTPKNKGNERLEVIFHTIFPIND-----P-------LHRATIEFISCRVDDPKYD 85 (2836)
T ss_pred ecccCCcccCCCCCHHHHHHHHHHHHhcCCCccccHHHHHHhcCCeEC-----C-------CCCEEEEEEEEEeCCCCCC
Confidence 3444 44457899999999999999997 699999999999973 1 1358899999999999986
Q ss_pred cCCCCCcCCCChhhHHhcCCcccceEEEEEEEEEeeccccccccccc-ccc---ceeeccccccceeEEEecccceEecC
Q 001050 100 AGNGGDEHDMFPRHARLQNMTYSSRMKVKVQFQVYTQKRVTSDKFKT-GRE---QYIQKEVLSDETTNIIIGRIPVMVKS 175 (1173)
Q Consensus 100 e~~~~~~~~l~P~ecR~r~~TYsa~l~v~v~~~~~~~~~~~~~~~~~-~~~---~~~~~~~~~~~~~~v~lG~IPIMvkS 175 (1173)
+ .||++|++||++||+|++++...+... ..++++. .+. .-..+.....++++|++|+||+|+.
T Consensus 86 ~-----------~Ec~~r~~TYsapl~v~~rL~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~ikeq~VylGdiPLMT~- 152 (2836)
T PRK14844 86 E-----------SECIKRGITFSAQVIASIRLVIMQDGI-SLDEYKSIKESGDHSKLATVIKSIEEQEVHFCELPMMTD- 152 (2836)
T ss_pred H-----------HHHHhcCCcceeeEEEEEEEEEecccc-ccccccccccccccccccccccceeeeeEEEecCCccCC-
Confidence 5 569999999999999999997522000 0000000 000 0000001234568899999999987
Q ss_pred CccccCCCcCCCCcCCCCcEEEEeCcEEEeEeeeeeccceEEEe-c-C----C--ceEEEEEeecCCceEEEEEEecCcc
Q 001050 176 DLCWMKGVEKGDCDFDHGGYFIIKGAEKVFVAQEQICLKRLWVS-N-S----M--GWTVAYKSENKRNRLIVRLVDMSKF 247 (1173)
Q Consensus 176 ~~C~L~~~~~gE~~~D~GGYFIING~ERVIi~Qe~~spnr~~i~-~-~----~--~~~a~irS~~~~~~~~i~~~~~~~~ 247 (1173)
.|+|||||+|||||+|++||||.+|-. . + + .|+|.+++. ++.|+.++.
T Consensus 153 -----------------~GTFIING~ERVIVSQL~RSPGVyF~~~~~kt~~sgk~lysa~IIP~---RGsWLefE~---- 208 (2836)
T PRK14844 153 -----------------KGTFIINGVEKVIVSQMHRSPGVFFDSDKGKTYNSGKLIYSARVIPY---RGSWLDIEF---- 208 (2836)
T ss_pred -----------------CeEEEEcCcceEEEEcceeCCeEEEEcccCcccCCCceeEEEEEecC---CcceEEEEE----
Confidence 999999999999999999999988873 2 1 1 488998854 567998863
Q ss_pred ccccCCEEEEEEeeccccccHhhHHHHhcCCChHHHHHHhcCCC------C-------c---------------------
Q 001050 248 EDIKGGEKVLSVYFLSTEIPIWILFFALGVSSDKEIVNLIDFTC------E-------D--------------------- 293 (1173)
Q Consensus 248 ~~~~~~~i~v~i~~~k~~IPl~illrALG~~sD~eI~~~i~~~~------~-------d--------------------- 293 (1173)
+.++.+|+++++ ++++|+++||||||+ |++||++.+.... + .
T Consensus 209 --D~kd~lyvRIDR-kRKiPiT~LLrALGl-s~edIL~~F~~~~~~~~~d~~~~~~~~~e~l~g~~~~~Di~d~~g~vlv 284 (2836)
T PRK14844 209 --DVKDHLYFRIDR-KRKLPISVLLKALGL-SNNDILDRFYEKIKYIKHKDGWKVPFVPDKFKGVRLPFDLMDVEGNVLL 284 (2836)
T ss_pred --cCCCeEEEEecC-CeeeeHHHHHHHhCC-ChHHHHHhhcCceEEEEccCceeeccCHHHHhCCccceeeeccCCCEEE
Confidence 446899999999 569999999999999 8999999774310 0 0
Q ss_pred -------hHHHHHHHH--------------------------------------------hhHhhh--------------
Q 001050 294 -------CSILNILFA--------------------------------------------SIHDAD-------------- 308 (1173)
Q Consensus 294 -------~~~~~~l~~--------------------------------------------~l~~~~-------------- 308 (1173)
......+.. .+....
T Consensus 285 dkgrrit~~~~krlk~~gvkkl~i~~~~l~g~~LaeDIVD~eTGEiL~eagteIT~e~ik~l~~~gi~~i~~l~~d~~~~ 364 (2836)
T PRK14844 285 KANVRITSRLAKKLYDNELKEYLVPFDSICGLFLAEDLIDSASSTKILSAGESIKLEDIKKLELLSIDEISVLNIDNLSV 364 (2836)
T ss_pred ecCccccHHHHHHHHHcccCcccCchHhhcCceehhhhcCCCCCeEEEcCCCccCHHHHHHHHHcCCCceeeEeeccccc
Confidence 000000000 000000
Q ss_pred -c------cCCcCCCHHHHHHHHHhhccCCCCCChhhHHHHHhhcccC-------cCCCcc----------------ccc
Q 001050 309 -N------KCDEFRKGRNALKYVDKLIKGTTFPPGESTEECMNTYLFP-------SLHGTK----------------QKA 358 (1173)
Q Consensus 309 -~------~~~~i~t~e~al~yig~~~~~~~~~~~e~~~~~L~~~llp-------Hl~~~~----------------~K~ 358 (1173)
. ..+...++++|+..|++++++......+.|+.++++.||- .+|+.. .+.
T Consensus 365 ~~~i~~tL~~D~~~~~e~Al~eIy~~lRpge~~~~e~a~~l~~~~ff~~~~YdLg~vGR~k~N~kl~~~~~~~~~~l~~~ 444 (2836)
T PRK14844 365 GPYILNTLFLDENMSYQDALYEIYKVLRPGEVPVLEIVEEFFRNLFFSPEYYDLSNIGRLKLNSYLGLNYDEDLTVLTHE 444 (2836)
T ss_pred chHHHHHHhhcccccHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHhcCccccccccchhhhhhhhhccCCCCCCcEecHH
Confidence 0 0012357899999999999888777788888888876653 223222 233
Q ss_pred chHHHHHHHHHhhccCCCCCCCcccccCcEEeehhhhHHHHHHHHHHHHHHHHHHHhhhcccCCcccccccccccccchh
Q 001050 359 RFLGYMVKCLLQAYSGRRKCDNRDDFRNKRLELAGELLERELKVHIAHARKRMAKALQRDLYGDRTVRPIEYYLDASILT 438 (1173)
Q Consensus 359 ~~L~~Mi~kLl~~~~g~~~~DD~D~l~nkRv~l~G~Ll~~lfr~~l~~~~~~i~~~l~~~~~~~~~~~~~~~~i~~~~It 438 (1173)
++| .++++|+.+..|....||+|||+||||+++|+||+.+||.+|.++.+.++++|... +.+.+ ++..+++++.++
T Consensus 445 Dii-~~i~~Li~l~~g~~~~DDiDhL~NRRvr~vGeLl~~qfr~gl~r~~~~i~e~~~~~--~~~~~-~p~~lin~~~l~ 520 (2836)
T PRK14844 445 DII-EIVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSMSTS--SLDKV-SPSDFINPKVLT 520 (2836)
T ss_pred HHH-HHHHHHHHHhcCCCcccchhhhhccccchHHHHHHHHHHHHHHHHHHHHHHHHhhc--ccccc-chhhcccchhHH
Confidence 555 59999999999999999999999999999999999999999999999999999643 22345 678899999999
Q ss_pred hccccccccccccccCccccccccceeecCCCChhhhhcccccccc--c--cccCCcccccCCCCCCCcceeeecCCCCC
Q 001050 439 NGLSRAFSTGAWSHPFKRTERISGIVANLGRANPLQTLVDLRRTRQ--Q--VQYTGKVGDARYPHPSHWGKICFLSTPDG 514 (1173)
Q Consensus 439 ~~i~~~~sTGnw~~~~~~~~q~sGvSQvldRlN~ls~lSh~Rrv~s--~--~~~~~k~t~vR~Lhps~wG~iCPveTPEG 514 (1173)
+.+++||+ ++||||+|||+||||+|||+||+++ | +.++++.+++|++||||||||||+|||||
T Consensus 521 ~~i~~ff~-------------ss~LSQfmDQtNpLseltHkRRlsaLGPGGL~r~~a~fevRdvH~shyGRiCPIETPEG 587 (2836)
T PRK14844 521 NVLRDFFN-------------SSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEG 587 (2836)
T ss_pred HHHHHHhc-------------ccchhhhccCcChhhhhhhcceecccCCCCcccccCCCcccccCccccccccCCCCCCC
Confidence 99999997 4789999999999999999999998 4 67889999999999999999999999999
Q ss_pred cccccccccceeeeeec-Cc-chhHHHHHHhcCceecccccCccCCCcceeeeccEEEEEecChhHHHHHHHHHHhcCCC
Q 001050 515 ENCGLVKNLGVTGLVST-SI-LEPIFEQLFNSGMEKLADDASYSLGGKFKVFVDGDWIGVCKDSLSFVSELRRKRRRKEL 592 (1173)
Q Consensus 515 ~~cGLvk~LA~~a~It~-~~-~~~i~~~l~~~g~~~~~~~~~~~~~~~~~VflnG~~iG~~~~~~~~~~~lR~~rr~~~i 592 (1173)
+|||||+|||.+|+|+. |+ ++|+++ | .||.+ +
T Consensus 588 ~NiGLI~SLA~yarIn~~GfietPy~k-----------------------V-~~g~v---~------------------- 621 (2836)
T PRK14844 588 QNIGLINSLAIYARINKYGFIESPYRK-----------------------V-VNRVV---T------------------- 621 (2836)
T ss_pred CcccchhhhhhheeccCCceEeCCcEE-----------------------E-EcCcC---c-------------------
Confidence 99999999999999998 56 666532 2 33331 0
Q ss_pred CceEEEEEeccCCeEEEeecCCeeeeeEEEeecccccccccCCcchhHhhhhcCceeeecccccceeEEeeccccccccc
Q 001050 593 PTQVEIKRDELQSEVRIFMDAGRILRPLLVVENMGKIKSLEGKNYTFQALLDHGIIELVGTEEEEDCCTAWGIKYLLKDI 672 (1173)
Q Consensus 593 ~~~~~i~~~~~~~~i~I~sd~GRl~RP~l~v~~~~~~~~~~~~~~~~~~l~~~g~iE~id~~Eq~~~~Ia~~~~~~~~~~ 672 (1173)
..++|+.+.||+...||.....+.+..
T Consensus 622 -----------------------------------------------------~~i~ylsa~~E~~~~Ia~a~~~~~~~~ 648 (2836)
T PRK14844 622 -----------------------------------------------------DQIEYLSAIDEGLYYIADTSAKLDENN 648 (2836)
T ss_pred -----------------------------------------------------ccccccChHHhcCcEEEeCCccCCCCC
Confidence 014455555555555554443332211
Q ss_pred CC---------------CCCceeeeecccccccccceeecccccCCCccchhhhhhccccccccccccc-----------
Q 001050 673 ED---------------KKPIKFTHCELDMSFLLGLSCGIIPFANHDHARRVLYQSQKHSSQAIGFPTT----------- 726 (1173)
Q Consensus 673 ~~---------------~~~~~~th~Ei~p~~ilgv~aslIPF~~hNqspRn~yqc~~M~KQaig~~~~----------- 726 (1173)
.. ..+.+.++++++|.+++|++||+|||.+||+++|++|||+ |++||+++...
T Consensus 649 ~~~~~~v~~R~~~ef~~~~~~~v~~~dvsp~Q~~SvaasLIPFLEhdDAnRALMGSN-MQRQAVPLl~~e~PiVGTG~E~ 727 (2836)
T PRK14844 649 CFVDDMLYCRYAGSFVMVSSDQVSYIDVSPKQVISVAASLIPFLENDDANRALMGSN-MQRQAVPLLKPTAPLVATGMES 727 (2836)
T ss_pred cccCCeEEEecCCceEEecHHHceEEEeCcchhhhhHhhcCCccccCcccccccccc-ccccccccccCCCCeEecCcch
Confidence 10 1134568999999999999999999999999999999999 99999997311
Q ss_pred ------------------------CCeeeeecc---------ccc----------cccCCcceEeccccccccCCcc-cC
Q 001050 727 ------------------------NPSIRVDTL---------SHQ----------LFYPQRPLFRTMISDCLGKPGY-GH 762 (1173)
Q Consensus 727 ------------------------n~~~r~D~~---------~~~----------l~ypQ~Plv~t~~~~~~~~~~~-~~ 762 (1173)
.+..|.+.. .|. .++.|||+|+ .++++.+||+ ||
T Consensus 728 ~vA~DSg~~v~A~~~G~V~yVda~kIvI~~~~~~~~~~~~~~~Y~L~ky~RSNQ~TcinQrPiV~--~Gd~V~kGdilAD 805 (2836)
T PRK14844 728 FVASGSGAVVLAKRDGIVDSSDSNSIVIRAFDKERVNYLDVDIYHLRKFQRSNHNTCINQKPLVC--VGDYVKEGDVIAD 805 (2836)
T ss_pred hhhhcccceEEeccCceEEEEcCCEEEEEeCCCccccccccceEEeccccccccceeeeecceec--CCCEeccCCEecc
Confidence 111122111 122 4668999999 5799999999 99
Q ss_pred CCCCCCCCccCCcccEEEEEecCCCCCCCeEEEecceeecCceEEEEEEEEEEEeeeccccccccccc--cccccccccc
Q 001050 763 NHILPRPELYNGQNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVKRRSSD--DMVNFGKIQS 840 (1173)
Q Consensus 763 ~~~~~~~~~~~G~N~~VAv~~~~Gyn~EDaiiin~~~~~rg~f~s~~~~~~~~~~~~~~~~~~~e~~~--~~~~~~~~~~ 840 (1173)
++++..+||++|+|++||||||.||||||||+||++++++++|||+|+++|++++++++ .+.|+|. .|...
T Consensus 806 G~st~~GELALG~NvlVAfmpW~GYNfEDAIliSErlv~eD~fTSiHIee~ei~~r~Tk--~G~EeITrdIPnv~----- 878 (2836)
T PRK14844 806 GPAINSGELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTSIHIEEFECVVHDTP--LGSEKITRAIPGVN----- 878 (2836)
T ss_pred ChhhcccccccccceEEEEeccCCcccccccccchhhccCceeEEEeecceEEEEEecc--CCCceecccCCCCC-----
Confidence 99999999999999999999999999999999999999999999999999999999865 5778884 34322
Q ss_pred cccccCCCCCCCCcccCcEEccCCeEEEEecCC----------------------CceeeEEccCCCceEEEEEEEEeCC
Q 001050 841 KIGRVDSLDDDGFPFIGANLQSGDIVIGKYADS----------------------GADHSIKLKHTERGMVQKVVLSSND 898 (1173)
Q Consensus 841 ~~~~~~~Ld~dGi~~~g~~v~~gdili~k~~~~----------------------~~~~s~~~~~~~~g~v~~v~~~~~~ 898 (1173)
....++||++|||++|++|++|||||||++|+ .+|+|+++|++..|+|.+|+++++.
T Consensus 879 -e~~lr~LDe~GIV~iGa~V~~GDILVGKvtPk~e~~~tPEekLL~aIFGek~~~vkdtSLrvp~G~~G~Vidv~~f~~~ 957 (2836)
T PRK14844 879 -EENLYHLDDSGIVKIGTRVGPGYILVGKVTPKPSLSLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFTRR 957 (2836)
T ss_pred -hHHHhcCCCCCCeecCCEECCCCEEEEeecCCCCCCCCHHHHHHHHHhCCcccccccCceecCCCCCEEEEEEEEEccc
Confidence 23488999999999999999999999999998 5899999999999999999998742
Q ss_pred --------------------------------------------------------------------------------
Q 001050 899 -------------------------------------------------------------------------------- 898 (1173)
Q Consensus 899 -------------------------------------------------------------------------------- 898 (1173)
T Consensus 958 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1037 (2836)
T PRK14844 958 GVEENERALLIKQKEINDFEKERDYIINVTSEYFYDELKKLLINSGSQDREKFDSIEREQWWGIGLKNQSISEQVKSLKK 1037 (2836)
T ss_pred ccccchhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhcccccccHHHHhhccHHhhhhcccCCHHHHHHHHHHHH
Confidence
Q ss_pred ---------------------CC-------CeEEEEEEeeccCCCccccccccCCCceEEeeeecCCCcCCCCCCCcCcE
Q 001050 899 ---------------------DG-------KNFSVVSLRQVRSPCLGDKFSSMHGQKGVLGFLESQENFPFTIQGIVPDI 950 (1173)
Q Consensus 899 ---------------------~~-------~~~~~v~~r~~R~~~iGDK~ssRhGqKGvvs~i~~~~dmPf~~~G~~pDi 950 (1173)
.| .+.|||+++++|++++|||+|||||||||||+|+|.|||||++||+++||
T Consensus 1038 ~~~~~~~~~~~~~~~k~~~~~~gdeL~~gv~~~VkVyia~KRkiqvGDKmAGRHGNKGVIS~IlP~eDMPyL~DGtpvDI 1117 (2836)
T PRK14844 1038 DFDEKVSHAIAQFKRKVEKLHEGYDLPQGVSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDI 1117 (2836)
T ss_pred HHHHHHHHHHHHHHHHHHhccCCCcCCCCCceEEEEEEEEeecCCccccccccCCCCceEeEEcccCCCCcCCCCCCceE
Confidence 11 24699999999999999999999999999999999999999999999999
Q ss_pred EeCCCCCCCCCChHHHHHHHHHHHHHhcCcccc----------------------------C------------------
Q 001050 951 VINPHAFPSRQTPGQLLEAALGKGIAALGKGIC----------------------------S------------------ 984 (1173)
Q Consensus 951 I~NPh~~PSRMtiGql~E~~~gk~~~~~~~~~~----------------------------~------------------ 984 (1173)
|+||+|+||||||||++|+++|+||..|++++. .
T Consensus 1118 vLNPLGVPSRMNvGQilE~hLG~A~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~ 1197 (2836)
T PRK14844 1118 ILNPLGVPSRMNVGQILETHVGWACKKLGEKVGNILDEINKIKSAFCKGIRSLNDDNFTKFAAAYLDNKKIENIDDDEIT 1197 (2836)
T ss_pred EeCCCCCCccccHHHHHHHHHHHHHhhhhhhhHhhhhhhhcccccccccccccccccccccccccccccccccccccccc
Confidence 999999999999999999999999999864421 0
Q ss_pred --------------------------------------------C--------------------------CEEEecC-C
Q 001050 985 --------------------------------------------G--------------------------LKRYATP-F 993 (1173)
Q Consensus 985 --------------------------------------------g--------------------------~~~~~tp-F 993 (1173)
| -+..+|| |
T Consensus 1198 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~tpvf 1277 (2836)
T PRK14844 1198 ASVLNTPNKNALNDELNELVENYLNSCKSAYSNLRNFLIEVYSCGSNVSICNNIRDISDNNLIEFARKLRDGIPVAAPVF 1277 (2836)
T ss_pred ccccccccccccccccccchhccccccchhhHHHHHHHHHhhhcccccccccccccccHHHHHHHHhhhccCCeecCCCc
Confidence 0 0123677 9
Q ss_pred CCCCHHHHHHHHHHcCCCCCCceEeeeCCCCcEEEeeEeEeeeehhccccccCccceeeecCCCCccccCCcccccccCc
Q 001050 994 ATPSVDAITEQLHRAGFSKWGTERLYDGRTGEMVRSLIFIGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQPVADRKRFGG 1073 (1173)
Q Consensus 994 ~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~i~~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG 1073 (1173)
++.+.+++.+.|+++||+++|++.||||+||++|+++||+|++|||||+|||+||+|||++|||++|||||++||+|+||
T Consensus 1278 ~g~~~~~i~~~L~~~g~~~~Gk~~l~dG~TGe~f~~~v~vG~~yy~kL~HmV~DKihaRs~Gp~s~lT~QPl~Gr~~~GG 1357 (2836)
T PRK14844 1278 EGPKDEQIAKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGG 1357 (2836)
T ss_pred CCCCHHHHHHHHHHhCcCCCCCEEEEcCCCCCccchhheeCcchhhhhhhhhcchhhhcccCCCcccccCCCcccccCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeeehhhhHHHHhhhHHHHHHhhhcCCCccceecccccCCccchheeeecCCcccCCccccccCCCCCcccccchHhHH
Q 001050 1074 IKFGEMERDCLIAHGAAANLHERLFTLSDSYQMHICRKCKNVANVIQRVVGGGRKVRGPYCRICDSGDDIVKANVPYGAK 1153 (1173)
Q Consensus 1074 ~R~GEME~d~l~a~Ga~~~l~erl~~~SD~~~~~vc~~cg~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~iPy~~k 1153 (1173)
|||||||||||+|||||++|||||+.+||.+. |+.+ .+|..|+. .+..+..+|||||
T Consensus 1358 ~RfGEME~~al~a~Gaa~~L~E~Lt~kSD~~~-------gr~~---------------~~~~ivkG-~~~~~~~~Pesfk 1414 (2836)
T PRK14844 1358 QRFGEMECWALQAYGAAYTLQEMLTVKSDDIN-------GRVK---------------IYESIIKG-DSNFECGIPESFN 1414 (2836)
T ss_pred ceeecchHHHHHHHhHHHHHHHHhcccccchh-------hhhH---------------hhhhhccC-CCCCcCCCCchHH
Confidence 99999999999999999999999999999655 5543 24555543 3455668999999
Q ss_pred HHHHHHHhcCCcEEEEEe
Q 001050 1154 LLCQELFSMGITLKFDTE 1171 (1173)
Q Consensus 1154 ~L~~EL~sm~i~~~l~~~ 1171 (1173)
+|+|||+||||++++.++
T Consensus 1415 vL~~EL~sl~i~~~~~~~ 1432 (2836)
T PRK14844 1415 VMIKELRSLCLNVDLKQN 1432 (2836)
T ss_pred HHHHHHHhCccceEEecc
Confidence 999999999999998764
No 13
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated
Probab=100.00 E-value=1.4e-177 Score=1587.77 Aligned_cols=578 Identities=40% Similarity=0.630 Sum_probs=540.6
Q ss_pred cceeeeccEEEEEecChhHHHHHHHHHHhcCCCCceEEEEEeccCCeEEEeecCCeeeeeEEEeeccc------cccccc
Q 001050 560 KFKVFVDGDWIGVCKDSLSFVSELRRKRRRKELPTQVEIKRDELQSEVRIFMDAGRILRPLLVVENMG------KIKSLE 633 (1173)
Q Consensus 560 ~~~VflnG~~iG~~~~~~~~~~~lR~~rr~~~i~~~~~i~~~~~~~~i~I~sd~GRl~RP~l~v~~~~------~~~~~~ 633 (1173)
.++|||||+|+|++++|.+|++.||.+||.|.|+.++||++++..++|+||||+||++|||++|++++ ++..++
T Consensus 4 ~~~VflNG~~vG~~~~~~~lv~~lR~lRr~g~i~~~vsI~~~~~~~ei~I~tD~GR~~RPl~iv~~g~~~l~~~~~~~l~ 83 (605)
T PRK07225 4 KAKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEPLLTEEHIEKLK 83 (605)
T ss_pred ccEEEECCEEEEEECCHHHHHHHHHHHHccCCCCCcEEEEEECCCCEEEEEccCCccceeEEEEeCCcccCCHHHHHHHH
Confidence 46899999999999999999999999999999999999999998899999999999999999999976 233334
Q ss_pred CCcchhHhhhhcCceeeecccccceeEEeecccccccccCCCCCceeeeecccccccccceeecccccCCCccchhhhhh
Q 001050 634 GKNYTFQALLDHGIIELVGTEEEEDCCTAWGIKYLLKDIEDKKPIKFTHCELDMSFLLGLSCGIIPFANHDHARRVLYQS 713 (1173)
Q Consensus 634 ~~~~~~~~l~~~g~iE~id~~Eq~~~~Ia~~~~~~~~~~~~~~~~~~th~Ei~p~~ilgv~aslIPF~~hNqspRn~yqc 713 (1173)
.+..+|++|+++|+|||||++||+++.||+.++++. ..+||||++|+++||++||+|||+||||||||||||
T Consensus 84 ~~~~~~~dl~~~G~IEyida~EE~~~~IA~~~~~l~--------~~~th~Ei~p~~ilgv~AslIPF~~hNQSPRn~yq~ 155 (605)
T PRK07225 84 NGELTFDDLVKQGVIEYLDAEEEENAYIAVYEEDLT--------EEHTHLEIDPSLILGIGAGMIPYPEHNASPRITMGA 155 (605)
T ss_pred cCCCChHHHHhCCCeeecChhhhcCeEeccchhhhc--------ccccccccCCcceeEEEeeccCCCCCCccchhhhhh
Confidence 446799999999999999999999999999998873 347999999999999999999999999999999999
Q ss_pred cccccccccccccCCeeeeeccccccccCCcceEeccccccccCCcccCCCCCCCCCccCCcccEEEEEecCCCCCCCeE
Q 001050 714 QKHSSQAIGFPTTNPSIRVDTLSHQLFYPQRPLFRTMISDCLGKPGYGHNHILPRPELYNGQNAIVAVNVHLGYNQEDSL 793 (1173)
Q Consensus 714 ~~M~KQaig~~~~n~~~r~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~~~~~~~~~~~~~~G~N~~VAv~~~~Gyn~EDai 793 (1173)
| |+|||||++++|+..|.|+++|+|+|||+|||+|+.++.+ +++++|+|+|++||||||+||||||||
T Consensus 156 ~-M~KQa~g~~~~n~~~r~D~~~~~l~ypQ~Plv~t~~~~~~-----------~~~~~p~G~N~iVAvmsy~GYn~EDAi 223 (605)
T PRK07225 156 G-MIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEII-----------GFDERPAGQNFVVAVMSYEGYNIEDAL 223 (605)
T ss_pred h-hhhcccCccccceeeecCCcccEEeeCCcceEEccchHhh-----------CCCccCCCeeEEEEEECcCCCChhHee
Confidence 9 9999999999999999999999999999999999999999 899999999999999999999999999
Q ss_pred EEecceeecCceEEEEEEEEEEEeeeccccccccccccccccccccccccccCCCCCCCCcccCcEEccCCeEEEEecCC
Q 001050 794 VMNRASLERGMFRSEHIRSYKAEVDNKEMQVKRRSSDDMVNFGKIQSKIGRVDSLDDDGFPFIGANLQSGDIVIGKYADS 873 (1173)
Q Consensus 794 iin~~~~~rg~f~s~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~Ld~dGi~~~g~~v~~gdili~k~~~~ 873 (1173)
||||+|+|||||||+||++|+.++++... +..+.+..|............|++||+||||++|++|++|||||||++|.
T Consensus 224 IiNkssidRGlf~s~~~k~~~~~~~~~~~-~~~~~~~~p~~~~~~~~~~~~~~~LD~dGi~~~G~~v~~gdiligk~sp~ 302 (605)
T PRK07225 224 IMNKASIERGLGRSHFFRTYEGEERRYPG-GQEDRFEIPDKDVRGYRGEEAYRHLDEDGLVNPETEVKEGDVLIGKTSPP 302 (605)
T ss_pred eeehhhhhcCceEEEEEEEEEEEeeecCC-CcceEEecCCchhccccChHHhhcCCCCCCccCCCEECCCCEEEEEecCC
Confidence 99999999999999999999999877543 33456666654211111123489999999999999999999999999872
Q ss_pred ---------------CceeeEEccCCCceEEEEEEEEeCCCCCeEEEEEEeeccCCCccccccccCCCceEEeeeecCCC
Q 001050 874 ---------------GADHSIKLKHTERGMVQKVVLSSNDDGKNFSVVSLRQVRSPCLGDKFSSMHGQKGVLGFLESQEN 938 (1173)
Q Consensus 874 ---------------~~~~s~~~~~~~~g~v~~v~~~~~~~~~~~~~v~~r~~R~~~iGDK~ssRhGqKGvvs~i~~~~d 938 (1173)
.+|+|++++++|+|+||+|.++.+.+|.+.|+|++|+.|+|+||||||||||||||||+|||+||
T Consensus 303 ~~~~~~~~~~~~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~vkv~ir~~R~p~iGDKfssRHGQKGvvs~i~~~eD 382 (605)
T PRK07225 303 RFLEEPDDFGISPEKRRETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQED 382 (605)
T ss_pred CCccchhhhcccccCcceeeEEecCCCcEEEEEEEEEecCCCCEEEEEEEEEEEeccccchhhhcccCceeEEeEecccc
Confidence 57899999999999999999999888999999999999999999999999999999999999999
Q ss_pred cCCCCCCCcCcEEeCCCCCCCCCChHHHHHHHHHHHHHhcCccccCCCEEEecCCCCCCHHHHHHHHHHcCCCCCCceEe
Q 001050 939 FPFTIQGIVPDIVINPHAFPSRQTPGQLLEAALGKGIAALGKGICSGLKRYATPFATPSVDAITEQLHRAGFSKWGTERL 1018 (1173)
Q Consensus 939 mPf~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~~~~~~~g~~~~~tpF~~~~~~~~~~~l~~~g~~~~G~e~l 1018 (1173)
||||+||++|||||||||||||||||||+|+++||||+ +.|.+.|+|||.+...+++++.|.++||+++|+|.|
T Consensus 383 MPft~~G~~PDiIiNPhg~PSRMTiGql~E~~~gk~~~------~~g~~~d~t~F~~~~~~~~~~~L~~~g~~~~G~e~m 456 (605)
T PRK07225 383 MPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGS------LEGRRVDGTAFSGEDEEDLREALEKLGFEHTGKEVM 456 (605)
T ss_pred CCcCCCCCcccEEECcccccccCcHHHHHHHHHHHHHH------hcCceEeecCCCCchHHHHHHHHHHhCcCCCCeEEE
Confidence 99999999999999999999999999999999999999 999999999999999999999999999999999999
Q ss_pred eeCCCCcEEEeeEeEeeeehhccccccCccceeeecCCCCccccCCcccccccCceeeeehhhhHHHHhhhHHHHHHhhh
Q 001050 1019 YDGRTGEMVRSLIFIGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGAAANLHERLF 1098 (1173)
Q Consensus 1019 y~g~tG~~~~~~i~~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEME~d~l~a~Ga~~~l~erl~ 1098 (1173)
|||+||++|+++||+|++|||||+|||+||+|||++||++.|||||++||||+|||||||||||||+|||||++|+|||+
T Consensus 457 y~G~TG~~~~~~if~G~~yYqrL~HmV~DK~haR~~Gp~~~lTrQP~~GR~r~GG~RfGEMErd~lia~Gas~~L~Erl~ 536 (605)
T PRK07225 457 YDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLL 536 (605)
T ss_pred EcCCCCCEecccEEEeehheeechhhhcchhhhccCCCCcccccCCccccccCCCeeeeeeehhhhhhhhhHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCccceecccccCCccchheeeecCCcccCCccccccCCCCCcccccchHhHHHHHHHHHhcCCcEEEEEe
Q 001050 1099 TLSDSYQMHICRKCKNVANVIQRVVGGGRKVRGPYCRICDSGDDIVKANVPYGAKLLCQELFSMGITLKFDTE 1171 (1173)
Q Consensus 1099 ~~SD~~~~~vc~~cg~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~iPy~~k~L~~EL~sm~i~~~l~~~ 1171 (1173)
++||.++++||.+||+++ +.+.+.+.++|+.|+++.++.++.||||||||+|||+||||+++|.++
T Consensus 537 ~~SD~~~~~vC~~CG~~~-------~~~~~~~~~~C~~C~~~~~i~~v~iPya~kll~~EL~sm~i~~~l~~~ 602 (605)
T PRK07225 537 DESDKVEIYVCAKCGMIA-------IYDKKRNRKYCPICGEETDIYPVEMSYAFKLLLDELKSLGIAPRLELE 602 (605)
T ss_pred ccCcceeEEeecCcCcce-------ehhcccCceeecccCCCCceeeccCChhHHHHHHHHHHCCceeEEEec
Confidence 999999999999999998 333444577899999999999999999999999999999999999876
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=7e-177 Score=1580.10 Aligned_cols=575 Identities=40% Similarity=0.646 Sum_probs=537.5
Q ss_pred eeeccEEEEEecChhHHHHHHHHHHhcCCCCceEEEEEeccCCeEEEeecCCeeeeeEEEeeccc------ccccccCCc
Q 001050 563 VFVDGDWIGVCKDSLSFVSELRRKRRRKELPTQVEIKRDELQSEVRIFMDAGRILRPLLVVENMG------KIKSLEGKN 636 (1173)
Q Consensus 563 VflnG~~iG~~~~~~~~~~~lR~~rr~~~i~~~~~i~~~~~~~~i~I~sd~GRl~RP~l~v~~~~------~~~~~~~~~ 636 (1173)
|||||+|+|++++|.+|++.||.+||.|.|+.++||++++..++|+||||+||++|||++|++++ ++..++.+.
T Consensus 1 VflNG~~vG~~~~~~~lv~~LR~lRr~g~i~~~vsI~~~~~~~ei~I~tD~GR~~RPl~iv~~g~l~l~~~~l~~l~~~~ 80 (599)
T TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEGE 80 (599)
T ss_pred CEECCEEEEEECCHHHHHHHHHHHhCcCCCCCcEEEEEeCCCCEEEEEcCCCccceeEEEeeCCCccccHHHHHHHhccC
Confidence 79999999999999999999999999999999999999998899999999999999999999976 233333346
Q ss_pred chhHhhhhcCceeeecccccceeEEeecccccccccCCCCCceeeeecccccccccceeecccccCCCccchhhhhhccc
Q 001050 637 YTFQALLDHGIIELVGTEEEEDCCTAWGIKYLLKDIEDKKPIKFTHCELDMSFLLGLSCGIIPFANHDHARRVLYQSQKH 716 (1173)
Q Consensus 637 ~~~~~l~~~g~iE~id~~Eq~~~~Ia~~~~~~~~~~~~~~~~~~th~Ei~p~~ilgv~aslIPF~~hNqspRn~yqc~~M 716 (1173)
.+|++|+++|+|||||++||+++.||+.++++. ..+||||++|+++||++||+|||+||||||||||||| |
T Consensus 81 ~~~~~ll~~G~IEyida~Ee~~~~IA~~~~~l~--------~~~th~Ei~p~~ilgv~AslIPF~~hNqSpRn~YQc~-M 151 (599)
T TIGR03670 81 LTWDDLVKQGVIEYLDAEEEENAYIALDPEELT--------PEHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAA-M 151 (599)
T ss_pred CCHHHHHhcCCeEecCchhhcCeEEecchHHhc--------cCcCccccCCcceeeEEeeccCCCCcCcchhhHHHHh-h
Confidence 789999999999999999999999999998873 3579999999999999999999999999999999999 9
Q ss_pred ccccccccccCCeeeeeccccccccCCcceEeccccccccCCcccCCCCCCCCCccCCcccEEEEEecCCCCCCCeEEEe
Q 001050 717 SSQAIGFPTTNPSIRVDTLSHQLFYPQRPLFRTMISDCLGKPGYGHNHILPRPELYNGQNAIVAVNVHLGYNQEDSLVMN 796 (1173)
Q Consensus 717 ~KQaig~~~~n~~~r~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~~~~~~~~~~~~~~G~N~~VAv~~~~Gyn~EDaiiin 796 (1173)
+|||||++.+|+..|.||++|+|+|||+|||+|+.++.+ +++++|+|+||+||||||+|||||||||||
T Consensus 152 ~KQamG~~~~n~~~R~D~~~~~l~ypQ~Plv~t~~~~~~-----------~~~~~p~G~N~iVAvmsy~GYn~EDAiIin 220 (599)
T TIGR03670 152 AKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELI-----------GYDDRPAGQNFVVAVMSYEGYNIEDALIMN 220 (599)
T ss_pred hhccccccccChhhcccccceEEcCCCCceeeeeeHHHh-----------CccccCCCeeEEEEEEcccCcChhHeeeec
Confidence 999999999999999999999999999999999999999 899999999999999999999999999999
Q ss_pred cceeecCceEEEEEEEEEEEeeeccccccccccccccccccccccccccCCCCCCCCcccCcEEccCCeEEEEecCC---
Q 001050 797 RASLERGMFRSEHIRSYKAEVDNKEMQVKRRSSDDMVNFGKIQSKIGRVDSLDDDGFPFIGANLQSGDIVIGKYADS--- 873 (1173)
Q Consensus 797 ~~~~~rg~f~s~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~Ld~dGi~~~g~~v~~gdili~k~~~~--- 873 (1173)
|+|+|||+|||+||++|+.+++++.. +..|.+..|............|++||+||||++|++|++|||||||++|.
T Consensus 221 k~si~rG~f~s~~~~~~~~~~~~~~~-~~~e~~~~p~~~~~~~~~~~~~~~LD~dGi~~~G~~v~~gdiligk~~p~~~~ 299 (599)
T TIGR03670 221 KASIERGLARSTFFRTYEAEERRYPG-GQEDRFEIPEPDVRGYRGEEAYKHLDEDGIVYPEVEVKGGDVLIGKTSPPRFL 299 (599)
T ss_pred hhhhhcCCeEEEEEEEEEEEeeccCC-CCceEEecCCchhccccchhhhccCCCCCCcCCCcEeCCCCEEEEEecCCCCc
Confidence 99999999999999999999876542 23355666543211111123489999999999999999999999999872
Q ss_pred ------------CceeeEEccCCCceEEEEEEEEeCCCCCeEEEEEEeeccCCCccccccccCCCceEEeeeecCCCcCC
Q 001050 874 ------------GADHSIKLKHTERGMVQKVVLSSNDDGKNFSVVSLRQVRSPCLGDKFSSMHGQKGVLGFLESQENFPF 941 (1173)
Q Consensus 874 ------------~~~~s~~~~~~~~g~v~~v~~~~~~~~~~~~~v~~r~~R~~~iGDK~ssRhGqKGvvs~i~~~~dmPf 941 (1173)
.+|+|++++++|+|+||+|.++.+.++.+.|+|++|+.|+|+||||||||||||||||+|||+|||||
T Consensus 300 ~~~~~~~~~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~vkv~~r~~R~p~iGDKfssRHGQKGvvs~i~~~eDMPf 379 (599)
T TIGR03670 300 EELRELGLVTERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPF 379 (599)
T ss_pred cchhhhccccccCceEEEEecCCCcEEEEEEEEEecCCCcEEEEEEEeeeecCcchhhhhhhccCcceEEeEeccCCCCc
Confidence 47899999999999999999999888889999999999999999999999999999999999999999
Q ss_pred CCCCCcCcEEeCCCCCCCCCChHHHHHHHHHHHHHhcCccccCCCEEEecCCCCCCHHHHHHHHHHcCCCCCCceEeeeC
Q 001050 942 TIQGIVPDIVINPHAFPSRQTPGQLLEAALGKGIAALGKGICSGLKRYATPFATPSVDAITEQLHRAGFSKWGTERLYDG 1021 (1173)
Q Consensus 942 ~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~~~~~~~g~~~~~tpF~~~~~~~~~~~l~~~g~~~~G~e~ly~g 1021 (1173)
|+||++|||||||||||||||||||+|+++||||+ +.|.+.|+|||++...+++++.|+++||+++|+|.||||
T Consensus 380 t~~G~~pDiIiNPhg~PSRMTiGqllE~~~gk~~~------~~g~~~d~t~F~~~~~~~~~~~L~~~g~~~~G~e~ly~G 453 (599)
T TIGR03670 380 TEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAA------LEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDG 453 (599)
T ss_pred CCCCCCCCEEECcccccccccHHHHHHHHHHHHHH------hcCCEEEeCCCCCccHHHHHHHHHHcCCCCCCCEEEEcC
Confidence 99999999999999999999999999999999999 999999999999999999999999999999999999999
Q ss_pred CCCcEEEeeEeEeeeehhccccccCccceeeecCCCCccccCCcccccccCceeeeehhhhHHHHhhhHHHHHHhhhcCC
Q 001050 1022 RTGEMVRSLIFIGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGAAANLHERLFTLS 1101 (1173)
Q Consensus 1022 ~tG~~~~~~i~~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEME~d~l~a~Ga~~~l~erl~~~S 1101 (1173)
+||++|+++||+|++|||||+|||+||+|||++||++.|||||++||||+|||||||||||||+|||||++|+|||+++|
T Consensus 454 ~TG~~~~~~if~G~~yyqrL~HmV~DK~h~Rs~Gp~~~lTrQP~~Gr~r~GG~RfGEMErd~lia~Gas~~L~ErL~~~S 533 (599)
T TIGR03670 454 ITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDES 533 (599)
T ss_pred CCCCCccccEEEEehhheechhhhcchhhhcccCCCcccccCCccccccCCCeeeeeeehhhHhhcchHHHHHHHHhccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CccceecccccCCccchheeeecCCcccCCccccccCCCCCcccccchHhHHHHHHHHHhcCCcEEEEEe
Q 001050 1102 DSYQMHICRKCKNVANVIQRVVGGGRKVRGPYCRICDSGDDIVKANVPYGAKLLCQELFSMGITLKFDTE 1171 (1173)
Q Consensus 1102 D~~~~~vc~~cg~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~iPy~~k~L~~EL~sm~i~~~l~~~ 1171 (1173)
|.++++||.+||+++. .+.+.+.++|+.|+++.++.++.+|||||||+|||+||||++++.++
T Consensus 534 D~~~~~vC~~CG~~~~-------~~~~~~~~~C~~c~~~~~i~~v~iPy~~k~l~~EL~am~i~~~l~~~ 596 (599)
T TIGR03670 534 DKYVVYVCENCGHIAW-------EDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLELG 596 (599)
T ss_pred cceeEEeecccCceee-------hhcccCceeccccCCCCceeeecCChhHHHHHHHHHhCCcceEEEec
Confidence 9999999999999983 33344577899999999999999999999999999999999999876
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=3.2e-109 Score=963.03 Aligned_cols=360 Identities=45% Similarity=0.675 Sum_probs=316.7
Q ss_pred cceeecccccCCCccchhhhhhcccccccccccccCCeeeeeccccccccCCcceEeccccccccCCcc-cCCCCCCCCC
Q 001050 692 GLSCGIIPFANHDHARRVLYQSQKHSSQAIGFPTTNPSIRVDTLSHQLFYPQRPLFRTMISDCLGKPGY-GHNHILPRPE 770 (1173)
Q Consensus 692 gv~aslIPF~~hNqspRn~yqc~~M~KQaig~~~~n~~~r~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~-~~~~~~~~~~ 770 (1173)
||+|++|||++||||||++|||+ |+|||||++.+|+..|+|+.. +|||+|||+|+ +.+.+|++ ||+.++.++|
T Consensus 1 si~As~ipf~~hn~s~R~~~~~~-m~kQa~~~y~~~~~~R~d~~~---~~~q~Plv~~~--~~~~~~~ilad~~~~~~~e 74 (386)
T PF00562_consen 1 SIVASLIPFPEHNQSPRNLYQCN-MQKQAIGTYSLNKFNRSDQNT---CYPQKPLVKTG--DRVEKGQILADGPSTKFGE 74 (386)
T ss_dssp -THGGTSSSGGGC-HHHHHHHHH-HGCGBCSEEETTTTTS-TSSE---SS-BEESSBSS--STBTTTTECEE-TTECTTT
T ss_pred CEEeCCCCEEEEEcCCcEEEEeC-cCCCcccceeeeeeeccCcce---eccccceEEee--ccccccCcccccccccccc
Confidence 68999999999999999999999 999999999999999999988 89999999974 78888998 9999999999
Q ss_pred ccCCcccEEEEEecCCCCCCCeEEEecceeecCceEEEEEEEEEEEeeecccccccccc-ccccccccccccccccCCCC
Q 001050 771 LYNGQNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVKRRSS-DDMVNFGKIQSKIGRVDSLD 849 (1173)
Q Consensus 771 ~~~G~N~~VAv~~~~Gyn~EDaiiin~~~~~rg~f~s~~~~~~~~~~~~~~~~~~~e~~-~~~~~~~~~~~~~~~~~~Ld 849 (1173)
+|+|+|++||||||+||||||||||||++++||+|||+||++ +++++++.. +..+++ ..++.. +...|++||
T Consensus 75 ~~~G~N~iVAvmsy~GYN~EDAiIiNkssv~rG~f~s~~~k~-~~~~~~~~~-g~~e~~~~~~~~~-----~~~~~~~LD 147 (386)
T PF00562_consen 75 LPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGLFTSIHYKT-EIEIRDNKG-GPSEEIFRPIPNV-----KEYNYSKLD 147 (386)
T ss_dssp S-SSEEEEEEESBSSSTTTSSEEEEECHHHHTTTTEEEEEEE-EEEEEEETT-SEEBBESS--TSS-----TSTTGGGBC
T ss_pred CcceeeeeEEeeehhcccchhhhhhhhhhhhcCeeeEEEEEE-EeeeecccC-Ccccccccccccc-----hhhhhhhcc
Confidence 999999999999999999999999999999999999999999 777765443 333444 333322 334599999
Q ss_pred CCCCcccCcEEccCCeEEEEec-C-------------C---CceeeEEccCCCceEEEEEEE-------EeCCCCCeEEE
Q 001050 850 DDGFPFIGANLQSGDIVIGKYA-D-------------S---GADHSIKLKHTERGMVQKVVL-------SSNDDGKNFSV 905 (1173)
Q Consensus 850 ~dGi~~~g~~v~~gdili~k~~-~-------------~---~~~~s~~~~~~~~g~v~~v~~-------~~~~~~~~~~~ 905 (1173)
+||||++|++|++||+||||++ | . .+|+|++++.++.|+|++|.+ ..+.++...|+
T Consensus 148 ~dGii~~G~~v~~gDiligk~~~~~~~~~~~~~~~~~~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~~~~~~~~ik 227 (386)
T PF00562_consen 148 EDGIIKIGSRVEKGDILIGKITSPPRFSPLLKKIFGEKNRNYRDTSIKYKSGESGRVDKVIIFSNEKKDTSNNEGYKKIK 227 (386)
T ss_dssp TTSBB-TTCEEETTSEEEEEEESTSC--HHHHHHHHSSSCSEEEEEEES-TT-EEEEEEEEEECCCSSBEEETTCEEEEE
T ss_pred cccccccCcEEecceeEEEEEecccccccchhhccccccccccceeecccccEEeEeccccccccccccccccCcceEEE
Confidence 9999999999999999999994 1 1 478999999999999999999 45677889999
Q ss_pred EEEeeccCCCccccccccCCCceEEeeeecCCCcCCCCCCCcCcEEeCCCCCCCCCChHHHHHHHHHHHHHhcCccccCC
Q 001050 906 VSLRQVRSPCLGDKFSSMHGQKGVLGFLESQENFPFTIQGIVPDIVINPHAFPSRQTPGQLLEAALGKGIAALGKGICSG 985 (1173)
Q Consensus 906 v~~r~~R~~~iGDK~ssRhGqKGvvs~i~~~~dmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~~~~~~~g 985 (1173)
|++|+.|+|+||||||||||||||||+|||+||||||+||++|||||||||||||||||||+|+++||+++ +.|
T Consensus 228 i~ir~~R~p~iGDKfssRHGqKGVvs~i~~~eDMPft~~G~~pDiIiNPhgiPSRMtiGqllE~~~g~~~~------~~g 301 (386)
T PF00562_consen 228 IRIRSTRRPQIGDKFSSRHGQKGVVSKILPQEDMPFTEDGIVPDIIINPHGIPSRMTIGQLLESLLGKAGA------LNG 301 (386)
T ss_dssp EEEEEEEE--TTEEEEETTSEEEEEEEEE-TTTSEEETTSEB-SEEE-GGGSTTTTBTHHHHHHHHHHHHH------HST
T ss_pred EEecccccchhHHHHhhhhcCceEEeeeeccccCccccCCCcceeeecccccccccchHHHHhhhhhhhhh------ccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999 999
Q ss_pred CEEEecCCCCCCHHHHHHHHHHcCCCCCCceEeeeCCCCcEEEeeEeEeeeehhccccccCccceeeecCCCCccccCCc
Q 001050 986 LKRYATPFATPSVDAITEQLHRAGFSKWGTERLYDGRTGEMVRSLIFIGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQPV 1065 (1173)
Q Consensus 986 ~~~~~tpF~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~i~~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~ 1065 (1173)
.+.|+|||++.+.+++++.|.++||+++|+|.||||+||++++++||+|++|||||+|||+||+|||++||+++|||||+
T Consensus 302 ~~~~~t~F~~~~~~~i~~~l~~~g~~~~g~~~l~~g~tG~~~~~~i~~G~~yy~rL~Hmv~DK~h~Rs~Gp~~~lT~QP~ 381 (386)
T PF00562_consen 302 RFVDATPFDESSEEDISELLKKAGYNYPGKEVLYDGRTGEKFEAPIFIGPVYYQRLKHMVDDKIHARSRGPYSLLTRQPV 381 (386)
T ss_dssp CEEB-TTTSSS-HHHHHHHHHHTTSHTTSEEEEBESSSSSBESSEEEEEEEEEEEBSTCGGGSTEEESS--BBSSSSSB-
T ss_pred cceecCCCCCcchhhhHhhhhcccccccceEEEEcCccCceEEeEEEeeeEEeccceEeCCcEEEEEecCCCccccCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccc
Q 001050 1066 ADRKR 1070 (1173)
Q Consensus 1066 ~Gr~~ 1070 (1173)
+||+|
T Consensus 382 ~Gr~r 386 (386)
T PF00562_consen 382 EGRSR 386 (386)
T ss_dssp SSSSS
T ss_pred CCCCC
Confidence 99997
No 16
>PRK09606 DNA-directed RNA polymerase subunit B''; Validated
Probab=100.00 E-value=1.9e-104 Score=951.58 Aligned_cols=472 Identities=32% Similarity=0.517 Sum_probs=414.5
Q ss_pred hhhhhhcccccCcCCchHHHHHHHHHHHHhHHHHHhcccCceEeCCCCCCCCCCCCcceeEEEEEceEEEccCccccCCC
Q 001050 24 TFCRKAAVSFFNEYGLVSHQINSYNEFIKNGLQKAFDSFGETIVEPGYDPSKKGEGEWRYASMRFGQVTLDKPSFFAGNG 103 (1173)
Q Consensus 24 ~~~~~~i~~~f~~~~Lv~~qi~SFN~Fi~~gL~~ii~~~~pI~~~~~~~~~~~~~~~~~~~~l~f~~i~i~~P~~~e~~~ 103 (1173)
+|+|.++++||+.++|++|||+|||+|+++||++++++++||++..+ ..+.++|+++++++|++.+.+
T Consensus 3 ~~~~~~i~~~~~~~~lv~~qi~SFn~Fi~~gl~~ii~~~~~i~~~~~-----------~~~~l~~~~~~l~~P~~~~~~- 70 (494)
T PRK09606 3 EDRRVLSDAYFKEHRLVRHHIDSYNDFVDNGLQKIIDEQGPIETEIE-----------DGVYVELGKIRVGKPVVKEAD- 70 (494)
T ss_pred hHHHHHHHHHHCCCChHHHHHHHHHHHHHHhHHHHHHhcCCEEEecC-----------CcEEEEEEEEEECCCcccccC-
Confidence 67899999999999999999999999999999999999999986421 236899999999999987766
Q ss_pred CCcCCCChhhHHhcCCcccceEEEEEEEEEeeccccccccccccccceeeccccccceeEEEecccceEecCCccccCC-
Q 001050 104 GDEHDMFPRHARLQNMTYSSRMKVKVQFQVYTQKRVTSDKFKTGREQYIQKEVLSDETTNIIIGRIPVMVKSDLCWMKG- 182 (1173)
Q Consensus 104 ~~~~~l~P~ecR~r~~TYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~- 182 (1173)
+...+|+|+|||+|++||+|+++|+|.+...+ + ....+++++|+|||||+|++|||++
T Consensus 71 ~~~~~l~P~eaR~r~~TYs~~l~v~i~~~~~~----------~-----------~~~~~~v~iG~iPiMv~S~~C~L~~~ 129 (494)
T PRK09606 71 GSEREIYPMEARLRNLTYSAPLYLEMSPVEGG----------E-----------EEEPEEVYIGELPVMVGSKICNLYGL 129 (494)
T ss_pred CccccCCHHHHHhcCCCccceEEEEEEEEECC----------C-----------ceEEeeEEeccCCeEeccCcccCCCC
Confidence 56689999999999999999999999996422 0 0123689999999999999999999
Q ss_pred -----CcCCCCcCCCCcEEEEeCcEEEeEeeeeeccceEEE-ecCC----ceEEEEEeecCCceEEEEEEecCccccccC
Q 001050 183 -----VEKGDCDFDHGGYFIIKGAEKVFVAQEQICLKRLWV-SNSM----GWTVAYKSENKRNRLIVRLVDMSKFEDIKG 252 (1173)
Q Consensus 183 -----~~~gE~~~D~GGYFIING~ERVIi~Qe~~spnr~~i-~~~~----~~~a~irS~~~~~~~~i~~~~~~~~~~~~~ 252 (1173)
++.||||+|+||||||||+||||++||+++||++++ .++. .|.|.++|..+..+.++.+ ++..+
T Consensus 130 ~~~~l~~~~E~~~d~GGyFIING~ErVi~~q~~~~~n~~~~~~~~~~~~~~~~~~i~s~~~~~~~~~~l------~~~~~ 203 (494)
T PRK09606 130 SEEELIEVGEDPLDPGGYFIVNGSERVLMTLEDLAPNKILVEKDERYGDRIEVAKVFSQRRGYRALVTV------ERNRD 203 (494)
T ss_pred CHHHHHhcCCCcCCCCCeEEECCCeEEEEEEEeccCCeeEEEeccCCCccceEEEEEcccccceeeEEE------EEecC
Confidence 789999999999999999999999999999999998 4321 4789999776643333333 23446
Q ss_pred CEEEEEEeeccccccHhhHHHHhcCCChHHHHHHhcCCCCchHHHHHHHHhhHhhhccCCcCCCHHHHHHHHHhhccCCC
Q 001050 253 GEKVLSVYFLSTEIPIWILFFALGVSSDKEIVNLIDFTCEDCSILNILFASIHDADNKCDEFRKGRNALKYVDKLIKGTT 332 (1173)
Q Consensus 253 ~~i~v~i~~~k~~IPl~illrALG~~sD~eI~~~i~~~~~d~~~~~~l~~~l~~~~~~~~~i~t~e~al~yig~~~~~~~ 332 (1173)
|.+++++++.+.+||+++||||||.+||+||++.+. .+.++++.+..++++. .+.|+++||.|||++|++..
T Consensus 204 g~i~~~~~~~~~~iPi~~llkALg~~sd~eI~~~i~---~~~~~~~~l~~~~~~~-----~~~t~~~al~~ig~~~~~~~ 275 (494)
T PRK09606 204 GLLEVSFPSVPGSIPFVILMRALGLETDEEIVEAVS---DDPEIVKFMLENLEEA-----EVDTQEEALEYIGKRVAPGQ 275 (494)
T ss_pred CeEEEEEcCccccccHHHHHHHcCCCCHHHHHHHhC---CcHHHHHHHHHHHHhc-----ccCCHHHHHHHHHHhcCCCC
Confidence 899999999767899999999999999999999995 3455666677777664 37899999999999997532
Q ss_pred --CCChhhHHHHHhhcccCcCCCcc----cccchHHHHHHHHHhhccCCCCCCCcccccCcEEeehhhhHHHHHHHHHHH
Q 001050 333 --FPPGESTEECMNTYLFPSLHGTK----QKARFLGYMVKCLLQAYSGRRKCDNRDDFRNKRLELAGELLERELKVHIAH 406 (1173)
Q Consensus 333 --~~~~e~~~~~L~~~llpHl~~~~----~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~nkRv~l~G~Ll~~lfr~~l~~ 406 (1173)
....+.|+++|++++|||+|.+. +|++||++|++||++++.|.+.+||+|||+||||+++|+||+.+||++|++
T Consensus 276 ~~~~~~~~~~~~l~~~~l~hig~~~~~~~~K~~~L~~m~~kLl~~~~g~~~~Dd~D~l~nkRv~~~G~Ll~~~fr~~l~~ 355 (494)
T PRK09606 276 TKEYRIKRAEYVIDRYLLPHLGVEPEVRRAKAHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNR 355 (494)
T ss_pred CcchHHHHHHHHHHHhhhcccCCCcchhhHHHHHHHHHHHHHHHHhcCCCCCCCcccccCceeeccchhHHHHHHHHHHH
Confidence 33467899999999999999743 799999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhhcccCCcccccccccccccchhhccccccccccccccCccccccccceeecCCCChhhhhcccccccccc
Q 001050 407 ARKRMAKALQRDLYGDRTVRPIEYYLDASILTNGLSRAFSTGAWSHPFKRTERISGIVANLGRANPLQTLVDLRRTRQQV 486 (1173)
Q Consensus 407 ~~~~i~~~l~~~~~~~~~~~~~~~~i~~~~It~~i~~~~sTGnw~~~~~~~~q~sGvSQvldRlN~ls~lSh~Rrv~s~~ 486 (1173)
+++.++..+++...+.+.+ ++..+++++.||++|++|||||||+++ ++||||+|||+||+|+||||||||+++
T Consensus 356 ~~~~~k~~l~~~~~~~~~~-~~~~~~~~~~It~~l~~~~~TGnw~~~------~~glSq~ldr~N~la~lSh~Rrv~s~~ 428 (494)
T PRK09606 356 LARDVKYQLERANMRNREL-SIKTAVRSDVLTERLEHAMATGNWVGG------RTGVSQLLDRTDYMATLSHLRRVVSPL 428 (494)
T ss_pred HHHHHHHHHHHHHhcCCCC-CHHHhcCchhhhHHHHHHhhcccccCC------CceEEEEccCCCHHHHhhHHHhccCCc
Confidence 9999998887765444445 677889988999999999999999983 689999999999999999999999999
Q ss_pred ccCCcccccCCCCCCCcceeeecCCCCCcccccccccceeeeeecCc-chhHHHHHHhcCceec
Q 001050 487 QYTGKVGDARYPHPSHWGKICFLSTPDGENCGLVKNLGVTGLVSTSI-LEPIFEQLFNSGMEKL 549 (1173)
Q Consensus 487 ~~~~k~t~vR~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~It~~~-~~~i~~~l~~~g~~~~ 549 (1173)
.++++.++||+||||||||+||||||||+|||||+|||++|+|+.+. ..++.++|.++||.++
T Consensus 429 ~r~~~~~~vR~lhps~~G~iCPveTPEG~~cGLv~~La~~a~V~~~~~~~~i~~~l~~lg~~~~ 492 (494)
T PRK09606 429 SRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKELGVEPE 492 (494)
T ss_pred cccCccccccccCcccceecccCcCCCCCcccHHHhhhceEEEeCCCChHHHHHHHHHCcCeeC
Confidence 99999999999999999999999999999999999999999999987 7888999999999875
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=9.3e-42 Score=366.28 Aligned_cols=143 Identities=37% Similarity=0.706 Sum_probs=118.0
Q ss_pred CchHHHHHHHHHHHHhHHHHHhcccCceEeCCCCCCCCCCCCcceeEEEEEceEEEccCccccCCCCCcCCCChhhHHhc
Q 001050 38 GLVSHQINSYNEFIKNGLQKAFDSFGETIVEPGYDPSKKGEGEWRYASMRFGQVTLDKPSFFAGNGGDEHDMFPRHARLQ 117 (1173)
Q Consensus 38 ~Lv~~qi~SFN~Fi~~gL~~ii~~~~pI~~~~~~~~~~~~~~~~~~~~l~f~~i~i~~P~~~e~~~~~~~~l~P~ecR~r 117 (1173)
||++|||+|||||+++||++++++++||++... ...+.++|++++|++|++.+.+ +..++|||+|||+|
T Consensus 1 ~Lv~~qi~SFn~Fl~~gl~~i~~~~~~i~~~~~----------~~~~~l~~~~~~i~~P~~~~~~-~~~~~l~P~ecR~r 69 (203)
T PF04563_consen 1 GLVKHQIDSFNYFLNNGLKEILKEFPPIEFESS----------NNRISLKFENIRIGKPTYSESD-GRERPLYPRECRLR 69 (203)
T ss_dssp TTTHHHHHHHHHHHCTSSHHHHSCSSSCEECCC----------STTEEEEEEEEEEESESSEHTT-SCEEE--HHHHHHT
T ss_pred CchHHHHHHHHHHHHCCCHHHhccCCceEecCC----------cceEEEEeeEEEEeeeeecccc-ccccCCCHHHHHhc
Confidence 699999999999999999999999999987432 1358999999999999999865 68899999999999
Q ss_pred CCcccceEEEEEEEEEeeccccccccccccccceeeccccccceeEEEecccceEecCCccccCC------CcCCCCcCC
Q 001050 118 NMTYSSRMKVKVQFQVYTQKRVTSDKFKTGREQYIQKEVLSDETTNIIIGRIPVMVKSDLCWMKG------VEKGDCDFD 191 (1173)
Q Consensus 118 ~~TYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~------~~~gE~~~D 191 (1173)
++||+|+++|+|+++..+ . ......++.+|+|||||+|++|||++ ++.||||+|
T Consensus 70 ~~TYs~~l~v~i~~~~~~--------~------------~~~~~~~v~iG~iPiMv~S~~C~L~~~~~~~l~~~~E~~~d 129 (203)
T PF04563_consen 70 GLTYSAPLYVDIELTVNN--------K------------KEIKEQEVFIGKIPIMVRSKRCNLNGLSPKELVQLGECPND 129 (203)
T ss_dssp T-B-EEEEEEEEEEEESS--------T------------TEEEESEEEEEEEE-BTTTTTSGGGT--HHHHHHTTS-TT-
T ss_pred CCCCCCccceEEEEEeec--------c------------ceEEeeEEEEeeCCeEeecceeeCCCCCHHHHHHcCCCCcC
Confidence 999999999999998743 0 01234789999999999999999999 899999999
Q ss_pred CCcEEEEeCcEEEeEeeeee
Q 001050 192 HGGYFIIKGAEKVFVAQEQI 211 (1173)
Q Consensus 192 ~GGYFIING~ERVIi~Qe~~ 211 (1173)
+||||||||+||||++|+.+
T Consensus 130 ~GGYFIInG~EkVi~~q~~~ 149 (203)
T PF04563_consen 130 PGGYFIINGSEKVIRMQIMR 149 (203)
T ss_dssp --SSEEETTEEEEE-EEEEE
T ss_pred CCCEEEECCChhheehhhhh
Confidence 99999999999999888877
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=1.1e-30 Score=237.06 Aligned_cols=81 Identities=52% Similarity=0.960 Sum_probs=76.3
Q ss_pred CceeeeehhhhHHHHhhhHHHHHHhhhcCCCccceecccccCCccchheeeecCCcccCCccccccCCCCCcccccchHh
Q 001050 1072 GGIKFGEMERDCLIAHGAAANLHERLFTLSDSYQMHICRKCKNVANVIQRVVGGGRKVRGPYCRICDSGDDIVKANVPYG 1151 (1173)
Q Consensus 1072 GG~R~GEME~d~l~a~Ga~~~l~erl~~~SD~~~~~vc~~cg~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~iPy~ 1151 (1173)
|||||||||||||+|||||++|||||+++||+++++||.+||.+++ .|+...++.++.+|||
T Consensus 1 GG~R~GEMErd~LiahGas~~L~erl~~~SD~~~~~vc~~cg~~~~------------------~~~~~~~~~~~~ipy~ 62 (81)
T PF04560_consen 1 GGLRFGEMERDALIAHGASFLLKERLFDKSDKYEIDVCSRCGSIAS------------------ICKGKPEVKKIEIPYS 62 (81)
T ss_dssp CBEEEEHHHHHHHHHTTBHHHHHHHHTTTTTEEEEEEECCCHHHHH------------------TTTTSSSEEEEEEEHH
T ss_pred CCcchhHHHHHHHHHhhHHHHHHHHhcCCCcCcchhhhccCCCcee------------------EECCCCeEEeeeCCHH
Confidence 8999999999999999999999999999999999999999999872 4667778999999999
Q ss_pred HHHHHHHHHhcCCcEEEEE
Q 001050 1152 AKLLCQELFSMGITLKFDT 1170 (1173)
Q Consensus 1152 ~k~L~~EL~sm~i~~~l~~ 1170 (1173)
||||+|||+||||++++.+
T Consensus 63 ~klL~~EL~sm~I~~~~~~ 81 (81)
T PF04560_consen 63 FKLLIQELRSMGIKIRIKT 81 (81)
T ss_dssp HHHHHHHHHCTTEEEEEEE
T ss_pred HHHHHHHHHHCcCceEEeC
Confidence 9999999999999999975
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=7.3e-27 Score=205.77 Aligned_cols=66 Identities=44% Similarity=0.786 Sum_probs=59.7
Q ss_pred eecCCCChhhhhccccccc--cccccCCcccccCCCCCCCcceeeecCCCCCcccccccccceeeeee
Q 001050 465 ANLGRANPLQTLVDLRRTR--QQVQYTGKVGDARYPHPSHWGKICFLSTPDGENCGLVKNLGVTGLVS 530 (1173)
Q Consensus 465 QvldRlN~ls~lSh~Rrv~--s~~~~~~k~t~vR~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~It 530 (1173)
|+|||+|++++|||+|||+ ++++++.|.+++|+|||||||||||+|||||++|||++|||++|+||
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 8999999999999999999 58999999999999999999999999999999999999999999986
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=99.82 E-value=2.6e-20 Score=197.60 Aligned_cols=149 Identities=30% Similarity=0.352 Sum_probs=107.4
Q ss_pred ecCCceEEEEEEecCccccccCCEEEEEEeeccccccHhhHHHHhcCCChHHHHHHhcCCCCchHHHHHHHHhhHhhhcc
Q 001050 231 ENKRNRLIVRLVDMSKFEDIKGGEKVLSVYFLSTEIPIWILFFALGVSSDKEIVNLIDFTCEDCSILNILFASIHDADNK 310 (1173)
Q Consensus 231 ~~~~~~~~i~~~~~~~~~~~~~~~i~v~i~~~k~~IPl~illrALG~~sD~eI~~~i~~~~~d~~~~~~l~~~l~~~~~~ 310 (1173)
....++.|+.+... +..+.+.....+.+||+++||||||++||+||++.|++...+......+.......
T Consensus 24 ~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~IPi~ilLrALG~~sd~eI~~~i~~~~~~~~~~~~~~~~~~~~--- 93 (190)
T PF04561_consen 24 IISSRGSWHYLEKD-------KKIIIFSRPKKKFKIPIVILLRALGIESDKEIIELICYSEEDFEDIEELMLSELEE--- 93 (190)
T ss_dssp ECCSSSEEEEEECE-------TTTEEEEETTSSSEEEHHHHHHHTT--STCHHHHHHCCCSTCHSCSTTTHHHHCCC---
T ss_pred cCCCcceEEEEecC-------CcEEEEEEcCcccccceEEeehhhcCcCcccccceeeccccccccccccccccccc---
Confidence 33447777777521 23455555565678999999999999999999999996333222111111111111
Q ss_pred CCcCCCHHHHHHHHHh--hccCCCCCChhhHHHHH---------hhcccC-cCCCccc------ccchHHHHHHHHHhhc
Q 001050 311 CDEFRKGRNALKYVDK--LIKGTTFPPGESTEECM---------NTYLFP-SLHGTKQ------KARFLGYMVKCLLQAY 372 (1173)
Q Consensus 311 ~~~i~t~e~al~yig~--~~~~~~~~~~e~~~~~L---------~~~llp-Hl~~~~~------K~~~L~~Mi~kLl~~~ 372 (1173)
..+.|+++|+.|||+ .++.......+.++.+| .+++|+ ||+.... |+.+|++|++||+.++
T Consensus 94 -~~~~t~~~al~~i~~~~~~~~~~~~~~~~~~~~l~~~y~l~~i~r~~l~~hl~~~~~~~~~~~k~~~l~~m~~~ll~~~ 172 (190)
T PF04561_consen 94 -EEIYTQEQALEYIGKKFRFRQGKPPKVEEARNFLQKRYDLGFIGRYKLNKHLGSDEPNENDRLKAEDLGLMIRKLLKLA 172 (190)
T ss_dssp -TSSCSCHHHHHHHHHCCHSSSSCHCCHCHHHHHHTTCSSTCCCHHHCCHTTTTSSSSSSSSSCHHHHHHHHHHHHHHHH
T ss_pred -ccccccccceeEeccceeeecccccchhhhhcccccccccccccccceeeeeeeeecccccccchhhHHHHHHHHHHHh
Confidence 358999999999999 45566667778888887 356666 9997764 9999999999999999
Q ss_pred cCCCCCCCcccccCcEEe
Q 001050 373 SGRRKCDNRDDFRNKRLE 390 (1173)
Q Consensus 373 ~g~~~~DD~D~l~nkRv~ 390 (1173)
.|.+.+||+|||+||||+
T Consensus 173 ~g~~~~Dd~D~l~NkRv~ 190 (190)
T PF04561_consen 173 NGECEPDDRDHLGNKRVR 190 (190)
T ss_dssp TTSS-S-STTSCCCEEEE
T ss_pred cCCCCCCCccccCCcCCc
Confidence 999999999999999996
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=99.68 E-value=9.3e-17 Score=139.09 Aligned_cols=63 Identities=46% Similarity=0.759 Sum_probs=59.5
Q ss_pred eeeccEEEEEecChhHHHHHHHHHHhcCCCCceEEEEEeccCCeEEEeecCCeeeeeEEEeec
Q 001050 563 VFVDGDWIGVCKDSLSFVSELRRKRRRKELPTQVEIKRDELQSEVRIFMDAGRILRPLLVVEN 625 (1173)
Q Consensus 563 VflnG~~iG~~~~~~~~~~~lR~~rr~~~i~~~~~i~~~~~~~~i~I~sd~GRl~RP~l~v~~ 625 (1173)
|||||.|+|++++|..|++.||.+||+|.++.++||+++...++|+|+||+||++|||++|+|
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 VFLNGVWIGIHSDPEELVKTLRNLRRSGKISKEVSIVYDIREKEIRINTDAGRLCRPLFVVEN 63 (63)
T ss_dssp EEETTEEEEEESSHHHHHHHHHHHHHTTSS-TTSEEEEETTTTEEEEE-SSCEEEEEEEEESS
T ss_pred CEECCEEEEEEcCHHHHHHHHHHHhhccCCcceeEEEEeccCCEEEEEccCCcccceeEEecC
Confidence 799999999999999999999999999999999999999999999999999999999999976
No 22
>PF04567 RNA_pol_Rpb2_5: RNA polymerase Rpb2, domain 5; InterPro: IPR007647 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Domain 5, is also known as the external 2 domain [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3S17_B 1I6H_B 4A3B_B 3K1F_B 4A3I_B 1TWA_B 3S14_B 3S15_B 2NVX_B 3M3Y_B ....
Probab=98.96 E-value=3.2e-10 Score=93.29 Aligned_cols=48 Identities=31% Similarity=0.597 Sum_probs=37.5
Q ss_pred hHhhhhcCceeeecccccceeEEeecccccccccCCCCCceeeeecccc
Q 001050 639 FQALLDHGIIELVGTEEEEDCCTAWGIKYLLKDIEDKKPIKFTHCELDM 687 (1173)
Q Consensus 639 ~~~l~~~g~iE~id~~Eq~~~~Ia~~~~~~~~~~~~~~~~~~th~Ei~p 687 (1173)
|++|++.|+|||||++||++++||++++++. .........||||||||
T Consensus 1 w~~ll~~G~vE~id~eEEe~~~Iam~~~dl~-~~~~~~~~~~TH~EI~P 48 (48)
T PF04567_consen 1 WDDLLKEGVVEYIDAEEEETCMIAMSPEDLE-STNEDITHTYTHCEIHP 48 (48)
T ss_dssp HHHHHHTTSEEEEETTTCTT--EESSCCCCC-HSGGCCSST-SEEES-G
T ss_pred ChhHhhCCCEEEecchhccccEEEEeccccc-ccCCCCCCccEEEeEeC
Confidence 7899999999999999999999999998886 22223367899999998
No 23
>KOG0214 consensus RNA polymerase II, second largest subunit [Transcription]
Probab=98.91 E-value=2.2e-11 Score=146.59 Aligned_cols=354 Identities=9% Similarity=-0.057 Sum_probs=228.1
Q ss_pred CccCCcccEEEEEecCCCCCCCeEEEecceeecCceEEEEEEEEEEEeeeccccccccccccccccccccccccccCCCC
Q 001050 770 ELYNGQNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVKRRSSDDMVNFGKIQSKIGRVDSLD 849 (1173)
Q Consensus 770 ~~~~G~N~~VAv~~~~Gyn~EDaiiin~~~~~rg~f~s~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~Ld 849 (1173)
..+.+.++-++.+.+.+++.++...-|--..+.++++++++..|--.-++.+. .....++.+........+.+ .++.-
T Consensus 734 l~~~eL~aG~NaiVAi~~~~GYNqEDsvimn~s~v~rg~FrS~~~RsYk~q~~-~~~~~~ee~~~~~~~~~~~~-mr~~~ 811 (1141)
T KOG0214|consen 734 LRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSVDRGLFRSFFIRSYKDQEH-KKDQGPEEIFEEPPRGEGRG-MRNGK 811 (1141)
T ss_pred hhhhhcccccceEEEEecccCccHHHHHHHHhhhhhcchhhhhhhhHHHhhhh-hccccccccccccccccccc-ccccc
Confidence 44569999999999999999999999999999999999987665433332211 01111111111100000000 11111
Q ss_pred CCCCcccCcEEccCCeEE--EEecCCCceeeEEccCCCce--------EEEEEEEEeCCCCCeEEEEEEeeccCCCcccc
Q 001050 850 DDGFPFIGANLQSGDIVI--GKYADSGADHSIKLKHTERG--------MVQKVVLSSNDDGKNFSVVSLRQVRSPCLGDK 919 (1173)
Q Consensus 850 ~dGi~~~g~~v~~gdili--~k~~~~~~~~s~~~~~~~~g--------~v~~v~~~~~~~~~~~~~v~~r~~R~~~iGDK 919 (1173)
.|-+-.-|- +.+|--+. +++. .+-+.+.....+.+ +..++++..++.| ...+|.++. .+.|+|
T Consensus 812 ~dkLdddG~-i~~G~~vs~~Dv~i--Gk~t~~~~~~~~~~~~~~~~t~~d~s~~Lr~~e~G-ivd~V~vt~---n~~G~k 884 (1141)
T KOG0214|consen 812 YDKLDDDGI-IMPGSRVSGGDVLI--GKTTPQPAKEDESGPEDRLYTKRDHSTKLRHTERG-IVDQVWVTK---NSEGPK 884 (1141)
T ss_pred cccccccCC-ccccceeecCCEEe--ccccCCcccchhccccccccccccceeecccCCcc-eEEEEEEec---CCCCCc
Confidence 111111111 01111110 0111 23332222223333 6677777766666 444555544 899999
Q ss_pred ccccCCCceEEeeeecCCCcCCCCCCCcCcEEeCCCCCCCCCChHHHHHHHHHHHHHhcCccccCCCEEEecCCCCCCHH
Q 001050 920 FSSMHGQKGVLGFLESQENFPFTIQGIVPDIVINPHAFPSRQTPGQLLEAALGKGIAALGKGICSGLKRYATPFATPSVD 999 (1173)
Q Consensus 920 ~ssRhGqKGvvs~i~~~~dmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~~~~~~~g~~~~~tpF~~~~~~ 999 (1173)
|+.+|++++-+.++-...++++-.-|+.++++.+++.-+++|+|--.+++-.- +.|- -..+.
T Consensus 885 F~kv~vr~~ripqiGDKfasrHgqKG~ig~~~~qedmpft~eGi~pDiiiNPh-----------------aiPS-Rmtig 946 (1141)
T KOG0214|consen 885 FVKVRVRQVRIPQIGDKFASRHGQKGTIGITYRQEDMPFTIEGIVPDIIINPH-----------------AIPS-RMTIG 946 (1141)
T ss_pred eeEEEEeecccccccchhccccccCccccceeecCCCCccccCCCcceEECcc-----------------cCcc-ccchh
Confidence 99999999999999999999999999999999999999999988765553211 1111 11222
Q ss_pred HHHHHHHHcCCCCCCceEeeeCCCCcEEEeeEeEeeeehhccccccCccceeeecCCCCccccCCcccccccCceeeeeh
Q 001050 1000 AITEQLHRAGFSKWGTERLYDGRTGEMVRSLIFIGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEM 1079 (1173)
Q Consensus 1000 ~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~i~~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEM 1079 (1173)
.+.+-|. |...-++..++++.++.. -+-..++..+++...|+..++.+++.+++....+++++++.-..++.+++||
T Consensus 947 ~liEc~l--gk~~a~~~e~~~atpFs~-v~v~~is~~l~~~g~~~~G~e~~ynGrtG~~~~~~if~GptyyqrL~Hmvd~ 1023 (1141)
T KOG0214|consen 947 QLIECLL--GKVAAYEGEEGDATPFSD-VTVSKISANLHVYGYQYRGNERMYNGRTGRKLRAQIFIGPTYYQRLKHMVDD 1023 (1141)
T ss_pred hhHHHhh--hhhhhcccccccCCCCCc-cchhcccchHHHhccccCCCEEEecCCCCceeeeeeecCchHHHHHHHhhhh
Confidence 2222221 223333444555555555 4456899999999999999999999999999999999999999999999999
Q ss_pred hhhHHHHhhhHHHHHHhhhcCCCccceecccccCCc--cchheeeecCCcccCCccccccCCCCCcccccchHhHHHHHH
Q 001050 1080 ERDCLIAHGAAANLHERLFTLSDSYQMHICRKCKNV--ANVIQRVVGGGRKVRGPYCRICDSGDDIVKANVPYGAKLLCQ 1157 (1173)
Q Consensus 1080 E~d~l~a~Ga~~~l~erl~~~SD~~~~~vc~~cg~~--~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~iPy~~k~L~~ 1157 (1173)
+++|=..++.+-+.++.+...|+..-..+|+.|+.. ++.+ .....|+-|...+.+.....++ |.|++.
T Consensus 1024 kih~R~~Gp~q~ltRQP~~gRsr~GGlRfGEMErdc~iahGa---------a~~L~ERL~~~SD~~~~~~c~~-c~l~~i 1093 (1141)
T KOG0214|consen 1024 KIHSRARGPVQILTRQPVEGRSRDGGLRFGEMERDCLIAHGA---------AAFLKERLFEKSDAYRVHICVL-CGLTAI 1093 (1141)
T ss_pred eeeecccCCceeeeccccccccccCCeeeehhHHHHHHHhhH---------HHHHHHHhhccCccceEEEecc-chhhhh
Confidence 999999999999999999999999888888877642 2211 1122344444444444333343 335666
Q ss_pred HHHhcC
Q 001050 1158 ELFSMG 1163 (1173)
Q Consensus 1158 EL~sm~ 1163 (1173)
+...+|
T Consensus 1094 ~~~~~n 1099 (1141)
T KOG0214|consen 1094 AGLIPN 1099 (1141)
T ss_pred hccCCC
Confidence 555555
No 24
>KOG0215 consensus RNA polymerase III, second largest subunit [Transcription]
Probab=98.76 E-value=2e-10 Score=136.86 Aligned_cols=438 Identities=9% Similarity=-0.085 Sum_probs=247.4
Q ss_pred CCcccCCcccchhhhhhhcccccCcCCchHHHHHHHHHHHHhHHHHHhcccCceEeCCCCCCCCCCCCcceeEEEEEceE
Q 001050 12 TSLCDLGEEFLKTFCRKAAVSFFNEYGLVSHQINSYNEFIKNGLQKAFDSFGETIVEPGYDPSKKGEGEWRYASMRFGQV 91 (1173)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~i~~~f~~~~Lv~~qi~SFN~Fi~~gL~~ii~~~~pI~~~~~~~~~~~~~~~~~~~~l~f~~i 91 (1173)
|++-|++--+.-.|.|-..+++.+..+++..||.+|+.++..-...+ ||.++.++... .. .+.=.++
T Consensus 86 tsd~dp~fylky~dirvg~Ps~~~~~~~~~~~i~p~ecrlrd~tysa-----~i~vdieytrg-------~~-~~~~~~v 152 (1153)
T KOG0215|consen 86 TSDVDPSFYLKYLDIRVGKPSIEEGNNVTNDNITPHECRLRDMTYSA-----PIYVDIEYTRG-------RQ-IIAKRDV 152 (1153)
T ss_pred CcCcCchhhheeeeeeccCcchhhccccccccCCchheeehhhhccc-----ceeEEEEEecC-------cc-eEEeccc
Confidence 44445555566667888999999999999999999999986643222 34332222110 01 1111123
Q ss_pred EEccCccccCCCCCcCCCChhhHHhcCCcccceEEEEEEEEEeeccccccccccccccceeeccccccceeEEEecccce
Q 001050 92 TLDKPSFFAGNGGDEHDMFPRHARLQNMTYSSRMKVKVQFQVYTQKRVTSDKFKTGREQYIQKEVLSDETTNIIIGRIPV 171 (1173)
Q Consensus 92 ~i~~P~~~e~~~~~~~~l~P~ecR~r~~TYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~lG~IPI 171 (1173)
-| |.....- ...+.+.|.+|+.+..-|.- . +.+..-..+..|.-||
T Consensus 153 ~i--grmpiml-rs~rcvl~~~~e~~~a~~~e-----------------------c--------pldpggyfiv~G~ekV 198 (1153)
T KOG0215|consen 153 II--GRMPIML-RSSKCVLRGKDEEELARLNE-----------------------C--------PLDPGGYFIVKGTEKV 198 (1153)
T ss_pred cc--ccchhhh-hccccccCCccHHHHHHhcc-----------------------C--------CCCCCceeEeccceeE
Confidence 33 3222211 23466777777744332220 0 0111235688999999
Q ss_pred EecCCccccCC-----CcCCCCcCCCCcEEEEeCcEEEeEeeeeeccceEEE-ecCCceEEEEE---eecCC-ceEEEEE
Q 001050 172 MVKSDLCWMKG-----VEKGDCDFDHGGYFIIKGAEKVFVAQEQICLKRLWV-SNSMGWTVAYK---SENKR-NRLIVRL 241 (1173)
Q Consensus 172 MvkS~~C~L~~-----~~~gE~~~D~GGYFIING~ERVIi~Qe~~spnr~~i-~~~~~~~a~ir---S~~~~-~~~~i~~ 241 (1173)
|+.+.-|.+++ .+.|||+.++++||+..+++.+|+.|+...+++... .++ .+.+.+. +..++ .-+.+..
T Consensus 199 iLiqeqlsknrii~~~~k~~~~~~svtsst~e~kskt~v~~k~~k~ylk~~~~~d~-ipiviv~ka~g~~sd~ei~~~vg 277 (1153)
T KOG0215|consen 199 ILIQEQLSKNRIIVEEDKKGNLQASVTSSTHERKSKTYVTTKKGKYYLKHNSFTDD-IPIVIVLKAMGLESDQEIVQLVG 277 (1153)
T ss_pred EEehhhhhccCeeeccccCCccccccccceeeecceEEEEeccceeeeehhhhhcc-CCEEEEEeeccccchHHHHHHhh
Confidence 99999999999 578999999999999999999999998888776654 222 2222221 01110 0000000
Q ss_pred EecCccccccCCEEEEEEeeccccccHhhHHHHhcCCChHHHHHHhcCCCCchHHHHHHHHhhHhhhccCCcCCCHHHHH
Q 001050 242 VDMSKFEDIKGGEKVLSVYFLSTEIPIWILFFALGVSSDKEIVNLIDFTCEDCSILNILFASIHDADNKCDEFRKGRNAL 321 (1173)
Q Consensus 242 ~~~~~~~~~~~~~i~v~i~~~k~~IPl~illrALG~~sD~eI~~~i~~~~~d~~~~~~l~~~l~~~~~~~~~i~t~e~al 321 (1173)
.+.-|..+.-..-+.|+.+-+.+.+-..|.......... . ....-.++|+
T Consensus 278 ----------~~~~y~~~~~~s~ee~~~~~v~tqqqal~y~~~kvk~~~----------------~----t~~~~~~e~~ 327 (1153)
T KOG0215|consen 278 ----------GDSKYQDIFAPSLEECVSLGVYTQQQALEYIGSKVKVKR----------------G----TTPTKDEEAL 327 (1153)
T ss_pred ----------cchHHHHhhccchhhhhhhhhHHHHHHHHHhhheEEecc----------------C----CCCCchHHHH
Confidence 011111111111133333333333222121111111100 0 0112235566
Q ss_pred HHHHhhccCC-----------CCCChhhHHHHHhhcccCcCCCcc--cccchHHHHHHHHHhhccCCCCCCCcccccCcE
Q 001050 322 KYVDKLIKGT-----------TFPPGESTEECMNTYLFPSLHGTK--QKARFLGYMVKCLLQAYSGRRKCDNRDDFRNKR 388 (1173)
Q Consensus 322 ~yig~~~~~~-----------~~~~~e~~~~~L~~~llpHl~~~~--~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~nkR 388 (1173)
+.+...+... ...-.--.+.++.-.+-+-.-.+. -+-..|.+|. .|+.+..+.---++.+.|++.+
T Consensus 328 ~~l~~~~lahv~v~~~~~r~K~~yi~~m~rr~~~a~l~~~~~ddrd~~gnkrlelag-qllsllfeD~fk~~n~e~k~~~ 406 (1153)
T KOG0215|consen 328 EVLSTTVLAHVPVPDLNFRMKAIYIGLMVRRVIQAMLNKLAMDDRDYVGNKRLELAG-QLLSLLFEDLFKRFNSELKKNI 406 (1153)
T ss_pred HHHHhhheeceeccCCCCcceeehHHHHHHHHHHHHhCcccccchhhhccchHHHHH-HHHHHHHHHHHHHHHHHHHHHH
Confidence 6665443210 000011112222222211111111 1222344344 4566666666678889999999
Q ss_pred EeehhhhHHHHHHHHHHHHHHHHHHH----hhhcccCCcccccccccccccchhhccccccccccccccCccccccccce
Q 001050 389 LELAGELLERELKVHIAHARKRMAKA----LQRDLYGDRTVRPIEYYLDASILTNGLSRAFSTGAWSHPFKRTERISGIV 464 (1173)
Q Consensus 389 v~l~G~Ll~~lfr~~l~~~~~~i~~~----l~~~~~~~~~~~~~~~~i~~~~It~~i~~~~sTGnw~~~~~~~~q~sGvS 464 (1173)
-.+.+.++..++-+.++.+. ..++. +.+.+..++.. + +-++..-++.+.--+-.|++|.-....+ -++++.
T Consensus 407 dk~l~k~~ra~~fD~~~~~n-~~~~~it~~l~ra~stgnw~--i-Krfrmer~gvt~VlsrlSyisaLgmmtr-i~s~fe 481 (1153)
T KOG0215|consen 407 DKILKKPIRAQEFDALKHLN-VRANMITSGLERAISTGNWS--I-KRFRMERAGVTQVLSRLSYISALGMMTR-INSQFE 481 (1153)
T ss_pred HHHhcchhhhhhhHHHHHHH-HHHHHHHHHHHHHhhcCchH--H-HHhhhhhccceeeehhhhhhhhhhhhee-hhhhhe
Confidence 99999988888888888874 33333 33333222111 1 1122121222222234467776544332 368899
Q ss_pred eecCCCChhhhhccccccccccccCCcccccCCCCCCCcceeeecCCCCCcccccccccceeeeeecCc
Q 001050 465 ANLGRANPLQTLVDLRRTRQQVQYTGKVGDARYPHPSHWGKICFLSTPDGENCGLVKNLGVTGLVSTSI 533 (1173)
Q Consensus 465 QvldRlN~ls~lSh~Rrv~s~~~~~~k~t~vR~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~It~~~ 533 (1173)
++..+..|-|-....-++..|+......+-.+-..++.|+-|||-++|++.-|++.+..+...+++.+.
T Consensus 482 ktrkvsgprSlq~sqwgmlcp~dtpegeacglvknlalmthittd~ee~pi~~~~~k~gv~di~~v~~~ 550 (1153)
T KOG0215|consen 482 KTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITTDSEEKPILKLCYKLGVEDIHVVSGR 550 (1153)
T ss_pred eehhccCccccChhhcccccCCCCCCccccccccchHHHhcccCCCCcchhHHHHHHhcceeeeeeccc
Confidence 999888888888777778778888888888999999999999999999999999999999999988764
No 25
>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=97.71 E-value=4.1e-05 Score=65.61 Aligned_cols=49 Identities=20% Similarity=0.361 Sum_probs=42.6
Q ss_pred EEEec--ChhHHHHHHHHHHhcC--CCCceEEEEEeccC-----CeEEEeecCCeeee
Q 001050 570 IGVCK--DSLSFVSELRRKRRRK--ELPTQVEIKRDELQ-----SEVRIFMDAGRILR 618 (1173)
Q Consensus 570 iG~~~--~~~~~~~~lR~~rr~~--~i~~~~~i~~~~~~-----~~i~I~sd~GRl~R 618 (1173)
|||++ .+..+++.||.+|..+ .+|.++||++.+.. |+|||||++||++|
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 46654 5689999999999887 69999999998764 79999999999998
No 26
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]
Probab=97.10 E-value=0.00053 Score=88.01 Aligned_cols=91 Identities=24% Similarity=0.288 Sum_probs=72.9
Q ss_pred ceeeecccccceeEEeecccccccccC----------C-------CCCceeeeecccccccccceeecccccCCCccchh
Q 001050 647 IIELVGTEEEEDCCTAWGIKYLLKDIE----------D-------KKPIKFTHCELDMSFLLGLSCGIIPFANHDHARRV 709 (1173)
Q Consensus 647 ~iE~id~~Eq~~~~Ia~~~~~~~~~~~----------~-------~~~~~~th~Ei~p~~ilgv~aslIPF~~hNqspRn 709 (1173)
-++|+.+.|+....+|.....+.+... . ..+...++|+++|.++.++.+++|||.+|+++.|.
T Consensus 476 ~i~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~~~~~~~~~~~~~~~~~~dv~~~~~~~~~~~~~P~l~~dd~~~~ 555 (1060)
T COG0085 476 EIEYLSADEEDVYVIGQANGTLDEPGELVEELVECRRGGSGEVSVADPEGVDYMDVSPKQVVSVGRSLIPFLEHDDANRA 555 (1060)
T ss_pred ceeeecccccceEEEeEeeeeecCCCceeeeEEEEeecccccceeecCccccceeccceEEeccccccCceeEEcCchHh
Confidence 478899998888888876544332110 0 12345689999999999999999999999999999
Q ss_pred hhhhcccccccccccccCCeeeeeccccccccCCcceEeccccccc
Q 001050 710 LYQSQKHSSQAIGFPTTNPSIRVDTLSHQLFYPQRPLFRTMISDCL 755 (1173)
Q Consensus 710 ~yqc~~M~KQaig~~~~n~~~r~D~~~~~l~ypQ~Plv~t~~~~~~ 755 (1173)
+++++ |+|||+|+. .+..|||.|. .|++
T Consensus 556 l~~~~-mqr~~~~l~----------------~~~~~lv~tG-~E~~ 583 (1060)
T COG0085 556 LMGSN-MQRQAVPLL----------------RTEAPLVGTG-MEYL 583 (1060)
T ss_pred hhhhh-hhhhccccc----------------ccccccccCC-ceee
Confidence 99999 999999944 3588999998 8887
No 27
>PHA03394 lef-8 DNA-directed RNA polymerase subunit beta-like protein; Provisional
Probab=94.59 E-value=0.047 Score=67.80 Aligned_cols=121 Identities=25% Similarity=0.307 Sum_probs=72.6
Q ss_pred CeEEEEEEeeccCCCccccccccCCCceEEeeeecCCCcC-C-CCCCCcCcEEeCCCCCCCCCChHHHHHHHHHHHHHhc
Q 001050 901 KNFSVVSLRQVRSPCLGDKFSSMHGQKGVLGFLESQENFP-F-TIQGIVPDIVINPHAFPSRQTPGQLLEAALGKGIAAL 978 (1173)
Q Consensus 901 ~~~~~v~~r~~R~~~iGDK~ssRhGqKGvvs~i~~~~dmP-f-~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~ 978 (1173)
.-.+|+++-..=.=-.|=|.||=||||||+.. .||+- | .|||+.|-|.++|.++-||.|.=-=+| -|-..
T Consensus 695 ~v~lKl~~Vtst~dLeGlKICgIHGQKGVln~---seDLtew~aeDg~~aQIclSPiSyLsRQtnf~~~~---~Ky~v-- 766 (865)
T PHA03394 695 TVYLKIRLVTSTSDLEGLKICGIHGQKGVLNG---SEDLTEWMAEDGTHAQICLSPISYLSRQTNFDDIE---RKYVV-- 766 (865)
T ss_pred EEEEEEEEEEEecCcceeEEeeecccccccCC---cchhhhhhccCCCcceEEechHHhhccccccccCc---eEEEE--
Confidence 34456665444445569999999999999874 45654 2 469999999999999999998522222 11111
Q ss_pred CccccCCCEEE---------ecC--CCCCCHHHHHHHHHHcCCCCCCceEeeeCCCCcEEEeeEeEee
Q 001050 979 GKGICSGLKRY---------ATP--FATPSVDAITEQLHRAGFSKWGTERLYDGRTGEMVRSLIFIGP 1035 (1173)
Q Consensus 979 ~~~~~~g~~~~---------~tp--F~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~i~~G~ 1035 (1173)
..|.+.| -.| |=....+.+.++.. +-+..|-|.+=--|...+--...|+|-
T Consensus 767 ----~gg~~~~~~~~rypi~~IPYm~FnnTPDnI~kEf~--~~n~TG~EKvEGTRlDqwTINqsF~gN 828 (865)
T PHA03394 767 ----RGGDHSDPNAKRYPIFNIPYMLFNNTPDNIYKEFI--KKNYTGHEKVEGTRLDQWTINQSFVGN 828 (865)
T ss_pred ----ECCCcCCCCCcccceEecceehhcCCchHHHHHHh--ccCCcceeecceeeccceeEcceeccc
Confidence 2233332 244 22345566666653 334566666543344444445566664
No 28
>PF04941 LEF-8: Late expression factor 8 (LEF-8); InterPro: IPR007025 Late expression factor 8 (LEF-8) is one of the primary components of RNA polymerase produced by polyhedrosis viruses. LEF-8 shows homology to the second largest subunit of prokaryotic DNA-directed RNA polymerase[].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=50.94 E-value=21 Score=44.91 Aligned_cols=34 Identities=21% Similarity=0.112 Sum_probs=28.0
Q ss_pred CCCcccccCcEEeehhhhHHHHHHHHHHHHHHHH
Q 001050 378 CDNRDDFRNKRLELAGELLERELKVHIAHARKRM 411 (1173)
Q Consensus 378 ~DD~D~l~nkRv~l~G~Ll~~lfr~~l~~~~~~i 411 (1173)
.=.+|+|+||=+--...|+...+...++.+...+
T Consensus 210 ~Y~IDsLsNKiIYkh~yLl~l~y~~~L~~~~~~~ 243 (748)
T PF04941_consen 210 NYSIDSLSNKIIYKHSYLLELTYKPILKKYENLI 243 (748)
T ss_pred CceecccccceeeCHHHHHHHHHHHHHHHHHHHH
Confidence 3479999999999999999999988877665444
No 29
>PF14251 DUF4346: Domain of unknown function (DUF4346)
Probab=45.15 E-value=11 Score=37.05 Aligned_cols=11 Identities=64% Similarity=1.153 Sum_probs=9.6
Q ss_pred cCCCCcEEEEe
Q 001050 189 DFDHGGYFIIK 199 (1173)
Q Consensus 189 ~~D~GGYFIIN 199 (1173)
..||+|||||.
T Consensus 13 ~LDp~GYfiI~ 23 (119)
T PF14251_consen 13 DLDPAGYFIIY 23 (119)
T ss_pred ccCCCccEEEE
Confidence 46999999986
No 30
>PF10385 RNA_pol_Rpb2_45: RNA polymerase beta subunit external 1 domain; InterPro: IPR019462 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 catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This entry represents a domain in prokaryotic polymerases that spans the gap between domains 4 and 5 of the protein. It is also known as the external 1 region of the polymerase and is bound in association with the external 2 region []. ; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2GHO_C 1YNN_C 1I6V_C 1YNJ_C 1HQM_C 1SMY_M 3DXJ_M 3AOI_C 2A68_M 1ZYR_C ....
Probab=33.57 E-value=31 Score=30.73 Aligned_cols=26 Identities=31% Similarity=0.245 Sum_probs=20.6
Q ss_pred CceeeecccccceeEEeecccccccc
Q 001050 646 GIIELVGTEEEEDCCTAWGIKYLLKD 671 (1173)
Q Consensus 646 g~iE~id~~Eq~~~~Ia~~~~~~~~~ 671 (1173)
..++||.+.||+...||.....+.+.
T Consensus 11 ~~i~YLtA~eEe~~~IAqA~~~ld~~ 36 (66)
T PF10385_consen 11 DEIEYLTADEEEKYVIAQANAPLDED 36 (66)
T ss_dssp CEEEEEECTTCCCSEEE-TTS-BSST
T ss_pred CeeEEEchhhcCCcEecccCeeeecC
Confidence 35899999999999999988877654
No 31
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=31.44 E-value=28 Score=37.14 Aligned_cols=47 Identities=17% Similarity=0.289 Sum_probs=32.5
Q ss_pred HhhhHHHHHHhhhcCCCccceecccccCCccchheeeecCCcccCCccccccCC
Q 001050 1086 AHGAAANLHERLFTLSDSYQMHICRKCKNVANVIQRVVGGGRKVRGPYCRICDS 1139 (1173)
Q Consensus 1086 a~Ga~~~l~erl~~~SD~~~~~vc~~cg~~~~~~~~~~~~~~~~~~~~c~~c~~ 1139 (1173)
.|-...-|+++|-..++. ..++|.+||.--+- ...-...+.|+.|+.
T Consensus 98 ~~~~~~klk~~l~~e~~~-~~Y~Cp~C~~rytf------~eA~~~~F~Cp~Cg~ 144 (178)
T PRK06266 98 KMEELKKLKEQLEEEENN-MFFFCPNCHIRFTF------DEAMEYGFRCPQCGE 144 (178)
T ss_pred HHHHHHHHHHHhhhccCC-CEEECCCCCcEEeH------HHHhhcCCcCCCCCC
Confidence 466778889999777664 78999999964321 111123689999985
No 32
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=28.14 E-value=33 Score=36.19 Aligned_cols=24 Identities=25% Similarity=0.672 Sum_probs=17.8
Q ss_pred eecccccCCccchheeeecCCcccCCccccccCC
Q 001050 1106 MHICRKCKNVANVIQRVVGGGRKVRGPYCRICDS 1139 (1173)
Q Consensus 1106 ~~vc~~cg~~~~~~~~~~~~~~~~~~~~c~~c~~ 1139 (1173)
+|||..||-+. .+ .....|++|+.
T Consensus 134 ~~vC~vCGy~~--------~g--e~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYTH--------EG--EAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCCcc--------cC--CCCCcCCCCCC
Confidence 99999999764 22 23457999984
No 33
>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=27.87 E-value=40 Score=26.01 Aligned_cols=26 Identities=23% Similarity=0.664 Sum_probs=17.7
Q ss_pred eecccccCCccchheeeecCCcccCCccccccCCC
Q 001050 1106 MHICRKCKNVANVIQRVVGGGRKVRGPYCRICDSG 1140 (1173)
Q Consensus 1106 ~~vc~~cg~~~~~~~~~~~~~~~~~~~~c~~c~~~ 1140 (1173)
.|+|..||-+.. + ...-..|++|+..
T Consensus 2 ~~~C~~CG~i~~--------g-~~~p~~CP~Cg~~ 27 (34)
T cd00729 2 VWVCPVCGYIHE--------G-EEAPEKCPICGAP 27 (34)
T ss_pred eEECCCCCCEeE--------C-CcCCCcCcCCCCc
Confidence 589999998741 1 1123479999864
No 34
>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=26.13 E-value=44 Score=25.44 Aligned_cols=26 Identities=15% Similarity=0.453 Sum_probs=18.1
Q ss_pred eecccccCCccchheeeecCCcccCCccccccCCC
Q 001050 1106 MHICRKCKNVANVIQRVVGGGRKVRGPYCRICDSG 1140 (1173)
Q Consensus 1106 ~~vc~~cg~~~~~~~~~~~~~~~~~~~~c~~c~~~ 1140 (1173)
.|+|..||-+.. .....+.|+.|+..
T Consensus 1 ~~~C~~CGy~y~---------~~~~~~~CP~Cg~~ 26 (33)
T cd00350 1 KYVCPVCGYIYD---------GEEAPWVCPVCGAP 26 (33)
T ss_pred CEECCCCCCEEC---------CCcCCCcCcCCCCc
Confidence 378999997642 12245789999864
No 35
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=24.79 E-value=46 Score=27.20 Aligned_cols=28 Identities=18% Similarity=0.349 Sum_probs=18.1
Q ss_pred eecccccCCccchheeeecCCcccCCccccccCCC
Q 001050 1106 MHICRKCKNVANVIQRVVGGGRKVRGPYCRICDSG 1140 (1173)
Q Consensus 1106 ~~vc~~cg~~~~~~~~~~~~~~~~~~~~c~~c~~~ 1140 (1173)
.+.|.+||.... . +.......|+.|++.
T Consensus 3 ~y~C~~CG~~~~------~-~~~~~~~~Cp~CG~~ 30 (46)
T PRK00398 3 EYKCARCGREVE------L-DEYGTGVRCPYCGYR 30 (46)
T ss_pred EEECCCCCCEEE------E-CCCCCceECCCCCCe
Confidence 478999998652 1 112225789999753
No 36
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=23.64 E-value=41 Score=34.52 Aligned_cols=35 Identities=23% Similarity=0.457 Sum_probs=24.3
Q ss_pred cceecccccCCccchheeeecCCcccCCccccccCCCCCcccccch
Q 001050 1104 YQMHICRKCKNVANVIQRVVGGGRKVRGPYCRICDSGDDIVKANVP 1149 (1173)
Q Consensus 1104 ~~~~vc~~cg~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~iP 1149 (1173)
-..--|.+||++..+ +..+|..|++.+++..+.+|
T Consensus 27 l~g~kC~~CG~v~~P-----------Pr~~Cp~C~~~~~~E~vels 61 (140)
T COG1545 27 LLGTKCKKCGRVYFP-----------PRAYCPKCGSETELEWVELS 61 (140)
T ss_pred EEEEEcCCCCeEEcC-----------CcccCCCCCCCCceEEEEeC
Confidence 345679999997631 35689999987665655554
No 37
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=23.09 E-value=48 Score=34.68 Aligned_cols=47 Identities=17% Similarity=0.145 Sum_probs=31.3
Q ss_pred HhhhHHHHHHhhhcCCCccceecccccCCccchheeeecCCcccCCccccccCC
Q 001050 1086 AHGAAANLHERLFTLSDSYQMHICRKCKNVANVIQRVVGGGRKVRGPYCRICDS 1139 (1173)
Q Consensus 1086 a~Ga~~~l~erl~~~SD~~~~~vc~~cg~~~~~~~~~~~~~~~~~~~~c~~c~~ 1139 (1173)
.|.....|+++|-..++ ...++|.+||.--+ ....-...+.|+.|++
T Consensus 90 ~~~~~~~lk~~l~~e~~-~~~Y~Cp~c~~r~t------f~eA~~~~F~Cp~Cg~ 136 (158)
T TIGR00373 90 LEETAKKLREKLEFETN-NMFFICPNMCVRFT------FNEAMELNFTCPRCGA 136 (158)
T ss_pred HHHHHHHHHHHHhhccC-CCeEECCCCCcEee------HHHHHHcCCcCCCCCC
Confidence 45677888999866554 56799999995332 0001113689999975
No 38
>PF13533 Biotin_lipoyl_2: Biotin-lipoyl like
Probab=21.62 E-value=56 Score=27.22 Aligned_cols=17 Identities=18% Similarity=0.421 Sum_probs=14.6
Q ss_pred CcccCcEEccCCeEEEE
Q 001050 853 FPFIGANLQSGDIVIGK 869 (1173)
Q Consensus 853 i~~~g~~v~~gdili~k 869 (1173)
.++.|+.|++||+|+--
T Consensus 17 ~V~~G~~VkkGd~L~~l 33 (50)
T PF13533_consen 17 YVKEGQQVKKGDVLLVL 33 (50)
T ss_pred EecCCCEEcCCCEEEEE
Confidence 57899999999999753
Done!