Query 000996
Match_columns 1195
No_of_seqs 228 out of 1686
Neff 6.7
Searched_HMMs 46136
Date Thu Mar 28 12:52:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/000996.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/000996hhsearch_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 2E-283 5E-288 2436.4 65.4 1136 25-1181 2-1140(1141)
2 PRK08565 DNA-directed RNA poly 100.0 1E-277 3E-282 2625.1 98.3 1095 28-1182 1-1101(1103)
3 KOG0215 RNA polymerase III, se 100.0 4E-259 8E-264 2203.5 48.5 1102 19-1183 37-1151(1153)
4 KOG0216 RNA polymerase I, seco 100.0 2E-251 4E-256 2149.5 66.7 1057 27-1181 4-1111(1111)
5 COG0085 RpoB DNA-directed RNA 100.0 1E-247 2E-252 2243.2 72.7 1020 24-1183 10-1059(1060)
6 cd00653 RNA_pol_B_RPB2 RNA pol 100.0 3E-225 6E-230 2105.7 75.5 860 41-1179 1-866 (866)
7 TIGR02013 rpoB DNA-directed RN 100.0 6E-225 1E-229 2108.7 73.4 927 27-1178 6-1065(1065)
8 PRK00405 rpoB DNA-directed RNA 100.0 1E-221 3E-226 2088.6 78.5 929 28-1180 14-1107(1112)
9 CHL00001 rpoB RNA polymerase b 100.0 4E-217 8E-222 2025.6 71.0 934 36-1182 10-1059(1070)
10 CHL00207 rpoB RNA polymerase b 100.0 6E-204 1E-208 1894.2 75.7 924 34-1182 3-1054(1077)
11 PRK09603 bifunctional DNA-dire 100.0 3E-192 5E-197 1839.4 74.6 944 27-1183 13-1376(2890)
12 PRK14844 bifunctional DNA-dire 100.0 1E-187 3E-192 1789.1 72.2 941 26-1183 16-1434(2836)
13 PRK07225 DNA-directed RNA poly 100.0 3E-183 7E-188 1639.5 52.3 597 570-1182 4-603 (605)
14 TIGR03670 rpoB_arch DNA-direct 100.0 6E-182 1E-186 1627.2 49.5 594 573-1182 1-597 (599)
15 PRK09606 DNA-directed RNA poly 100.0 6E-107 1E-111 975.3 48.5 491 25-559 2-492 (494)
16 PF00562 RNA_pol_Rpb2_6: RNA p 100.0 3E-109 7E-114 964.9 21.7 364 715-1087 1-386 (386)
17 PF04563 RNA_pol_Rpb2_1: RNA p 100.0 3.7E-44 8.1E-49 385.7 16.1 149 40-208 1-149 (203)
18 PF04560 RNA_pol_Rpb2_7: RNA p 100.0 6.2E-31 1.3E-35 238.9 6.5 81 1089-1180 1-81 (81)
19 PF04565 RNA_pol_Rpb2_3: RNA p 99.9 2.1E-26 4.6E-31 203.0 3.5 66 474-539 1-68 (68)
20 PF04561 RNA_pol_Rpb2_2: RNA p 99.8 2.1E-20 4.5E-25 199.0 10.1 138 263-401 41-190 (190)
21 PF04566 RNA_pol_Rpb2_4: RNA p 99.7 5.9E-18 1.3E-22 146.7 9.1 63 573-635 1-63 (63)
22 KOG0214 RNA polymerase II, sec 99.2 1E-12 2.2E-17 158.0 -3.6 411 728-1175 682-1101(1141)
23 PF04567 RNA_pol_Rpb2_5: RNA p 99.0 1.5E-10 3.2E-15 95.4 1.8 48 659-710 1-48 (48)
24 KOG0215 RNA polymerase III, se 98.9 1.2E-11 2.6E-16 147.1 -8.7 539 15-631 87-639 (1153)
25 COG0085 RpoB DNA-directed RNA 97.8 1.4E-05 3.1E-10 102.1 4.9 108 667-794 476-597 (1060)
26 PF06883 RNA_pol_Rpa2_4: RNA p 97.5 0.0001 2.2E-09 63.2 4.2 49 580-628 1-58 (58)
27 PHA03394 lef-8 DNA-directed RN 94.6 0.054 1.2E-06 67.4 6.3 141 904-1052 674-828 (865)
28 PF09082 DUF1922: Domain of un 58.4 5.2 0.00011 35.6 1.2 49 1121-1171 1-55 (68)
29 COG1997 RPL43A Ribosomal prote 56.7 13 0.00027 34.8 3.4 28 1122-1149 34-61 (89)
30 PF10385 RNA_pol_Rpb2_45: RNA 53.7 15 0.00032 32.8 3.3 27 666-692 11-37 (66)
31 PRK00398 rpoP DNA-directed RNA 52.5 13 0.00028 30.5 2.6 28 1123-1150 3-30 (46)
32 PF04941 LEF-8: Late expressio 49.2 30 0.00065 43.7 6.1 34 389-422 210-243 (748)
33 COG1645 Uncharacterized Zn-fin 47.3 13 0.00028 37.6 2.1 29 1123-1153 28-56 (131)
34 PF14251 DUF4346: Domain of un 44.7 11 0.00024 37.1 1.2 14 183-196 10-23 (119)
35 KOG0703 Predicted GTPase-activ 44.3 16 0.00034 41.7 2.5 65 1109-1178 15-89 (287)
36 PRK06266 transcription initiat 41.5 16 0.00035 39.1 2.0 45 1104-1149 99-144 (178)
37 cd00729 rubredoxin_SM Rubredox 41.3 21 0.00045 27.6 2.0 26 1123-1150 2-27 (34)
38 PF07754 DUF1610: Domain of un 38.7 20 0.00044 25.6 1.4 23 1126-1148 1-23 (24)
39 TIGR00373 conserved hypothetic 38.6 18 0.00039 37.9 1.8 46 1103-1149 90-136 (158)
40 PRK14890 putative Zn-ribbon RN 38.3 14 0.0003 32.1 0.8 31 1119-1149 3-33 (59)
41 cd00350 rubredoxin_like Rubred 37.9 23 0.0005 27.0 1.8 26 1123-1150 1-26 (33)
42 COG1592 Rubrerythrin [Energy p 37.4 24 0.00051 37.3 2.4 24 1123-1149 134-157 (166)
43 COG1096 Predicted RNA-binding 37.2 21 0.00046 38.1 2.0 35 1124-1161 150-184 (188)
44 PF12760 Zn_Tnp_IS1595: Transp 37.0 23 0.00051 29.0 1.8 26 1124-1149 19-45 (46)
45 PF08271 TF_Zn_Ribbon: TFIIB z 36.4 29 0.00062 28.0 2.2 26 1124-1149 1-27 (43)
46 PRK00420 hypothetical protein; 35.8 23 0.0005 35.0 1.9 26 1124-1150 24-49 (112)
47 PF09538 FYDLN_acid: Protein o 35.2 19 0.00042 35.3 1.3 31 1122-1153 8-38 (108)
48 COG1996 RPC10 DNA-directed RNA 35.2 29 0.00064 29.1 2.1 30 1121-1150 4-33 (49)
49 PF08792 A2L_zn_ribbon: A2L zi 33.9 33 0.00071 26.4 2.1 28 1123-1150 3-30 (33)
50 PF01780 Ribosomal_L37ae: Ribo 33.7 28 0.00061 32.9 2.0 29 1121-1149 33-61 (90)
51 COG1545 Predicted nucleic-acid 32.7 26 0.00057 35.9 1.8 37 1119-1159 25-61 (140)
52 smart00661 RPOL9 RNA polymeras 32.5 27 0.00058 29.0 1.6 25 1125-1149 2-28 (52)
53 PRK11032 hypothetical protein; 31.5 32 0.0007 36.1 2.3 7 1125-1131 126-132 (160)
54 PF07295 DUF1451: Protein of u 31.0 32 0.0007 35.6 2.1 28 1123-1150 112-139 (146)
55 CHL00207 rpoB RNA polymerase b 30.4 48 0.001 44.8 4.1 17 863-879 620-636 (1077)
56 smart00531 TFIIE Transcription 30.4 31 0.00066 35.7 1.9 42 1107-1149 84-131 (147)
57 COG0266 Nei Formamidopyrimidin 28.4 34 0.00074 39.0 2.0 16 345-360 158-173 (273)
58 TIGR02300 FYDLN_acid conserved 28.3 31 0.00066 34.6 1.4 29 1121-1150 7-35 (129)
59 PF11781 RRN7: RNA polymerase 27.0 36 0.00079 26.6 1.3 23 1126-1149 11-33 (36)
60 PF06677 Auto_anti-p27: Sjogre 26.3 48 0.001 26.8 1.9 23 1125-1148 19-41 (41)
61 PRK14844 bifunctional DNA-dire 23.8 80 0.0017 46.1 4.5 17 863-879 790-806 (2836)
62 PF13248 zf-ribbon_3: zinc-rib 22.5 40 0.00086 24.3 0.7 22 1124-1149 3-24 (26)
63 smart00659 RPOLCX RNA polymera 22.4 71 0.0015 26.2 2.2 27 1123-1150 2-28 (44)
64 TIGR00280 L37a ribosomal prote 22.1 45 0.00097 31.7 1.2 29 1121-1149 33-61 (91)
65 PF07282 OrfB_Zn_ribbon: Putat 21.2 51 0.0011 29.2 1.3 29 1121-1149 26-54 (69)
66 PRK09603 bifunctional DNA-dire 20.5 1.1E+02 0.0024 45.0 4.7 17 863-879 780-796 (2890)
67 PRK13130 H/ACA RNA-protein com 20.2 67 0.0014 27.8 1.7 26 1122-1153 4-29 (56)
No 1
>KOG0214 consensus RNA polymerase II, second largest subunit [Transcription]
Probab=100.00 E-value=2.1e-283 Score=2436.42 Aligned_cols=1136 Identities=72% Similarity=1.139 Sum_probs=1076.4
Q ss_pred hhhhhhhhhcccCccchHHHHHHHHHHHHHhhHHHHHcccCCeeeCCCCCCCCCCCCCCCCceEEEEEeEEEEccCcccc
Q 000996 25 QEDAWAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQSDFAETIYKISFGQIYLSKPMMTE 104 (1195)
Q Consensus 25 ~~~~~~~i~~~f~~~~Lv~~qi~SFn~Fi~~gL~~ii~~~~pI~~~~~~~~~~~~~~~~~~~~~~l~f~~v~v~~P~~~e 104 (1195)
.+++|.+|++||+.+||+++|++|||.|++.++++|+.+.++|+.....++.- ....++.|.|+.+++.+|+.+|
T Consensus 2 qe~~w~vis~~f~ekglvrqQldsFdeFiq~~~qeiv~~~p~i~l~~~~qh~~-----~~~~r~~l~f~qiylskP~~~e 76 (1141)
T KOG0214|consen 2 QEDCWDVISAYFEEKGLVRQQLDSFDEFIQQTLQEIVADSPKIELQDEAQHTQ-----ENPARYQLFFEQIYLSKPTHTE 76 (1141)
T ss_pred hhHHHHHHHhhhcccchHHHHHHHHHHHHHHHHHHHHhcCCCceehhhhhhhc-----cCccceEEEeeeEEEecccccc
Confidence 57899999999999999999999999999999999999999998765443331 1234599999999999999999
Q ss_pred CCCcccCCChHHHHhcCCccceeEEEEEEEEEeccCCCCcccccceeeEEEEecccceeeccCCccCCCCChhhhhhcCC
Q 000996 105 SDGETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELGE 184 (1195)
Q Consensus 105 ~~~~~~~l~P~EcR~r~lTYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~eli~~gE 184 (1195)
.||....++|+|||+|++||||||||+++..+..... ++...+.+.|+||+||||+||..|.|+++++.+|.+.||
T Consensus 77 ~dg~~~~m~p~eARlrnLTYSspLyVd~~k~~~~~~~----~~~~~~~qkvfIGkIPiMlrS~~C~l~~~~d~dl~~l~e 152 (1141)
T KOG0214|consen 77 SDGSTSTMFPNEARLRNLTYSSPLYVDATKIVKTSRD----EVEDMQEQKVFIGKIPIMLRSSYCLLSGLTDKDLTELGE 152 (1141)
T ss_pred cCCCccccCchhhHhhhcccccceEEEeEEEEeeccc----cccccccceeeEeccceeeehhhhhhcccchhhhhhccC
Confidence 9999999999999999999999999999998764431 123445788999999999999999999999999999999
Q ss_pred CCCCCCceEEEcCeeeEEeeeeeeecceEEEEEecCCCcceEEEEEEEeecCCCCCCceEEEEEEecCCCCCCCCCcEEE
Q 000996 185 CPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIR 264 (1195)
Q Consensus 185 ~~~D~GGYFIING~ERVII~Qe~~s~N~~~~~~~~~~~~~~~~~~irs~~~~g~~~~~~~~v~~~~~~~~k~~~~~~~i~ 264 (1195)
||+|+||||||||+|||+|+||++|+|.+|+|++..++.+.|.++|||..+++++..+++.+++..++. ....|.
T Consensus 153 Cp~DqgGyfIINGseKVlIAQe~matn~vyvf~k~~p~~~ay~~EirS~le~~sR~~stl~v~~~ar~~-----~gq~i~ 227 (1141)
T KOG0214|consen 153 CPYDQGGYFIINGSEKVLIAQEKMATNIVYVFKKAHPGTYAYTGEIRSCLERSSRFISTLSVNMDARAG-----KGQEII 227 (1141)
T ss_pred CCcCCCceEEEcCceeeeeehhhccCceEEEEecCCCCceeEeeeeehhhhccCCCcceeeeeeccccC-----CCceEE
Confidence 999999999999999999999999999999999988889999999999999999988999999876541 245789
Q ss_pred EEeccccccchHHHHHHHhcCCChHHHHHHhcccccchHHHHHhHhhHhhhhccCCHHHHHHHHhhcCcccCCCchhhHH
Q 000996 265 ATLPYIRTEIPIIIVFRALGFVADKDILEHICYDFQDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGATVGVTRDKRIK 344 (1195)
Q Consensus 265 v~i~~~~~~IPl~ilLrALG~~sD~eI~~~i~~~~~~~~~~~~l~~sl~e~~~i~t~~~al~yig~r~~~~~~~~~~~~e 344 (1195)
+.+++++++||+++||||||+.+|+||++.||||.+|.++++++.+++++++.+..+..||+|||+|....+.+++.+++
T Consensus 228 ~tlpyikqeIPI~ilfrALG~v~dreILehIcYd~~D~em~e~lkpsieeafviq~qn~ALdfig~rga~~Gvtkekri~ 307 (1141)
T KOG0214|consen 228 ATLPYIKQEIPILILFRALGFVSDREILEHICYDFDDAEMFESLKPSIEEAFVIQEQNVALDFIGQRGACIGVTKEKRIK 307 (1141)
T ss_pred EEeeeecccCcEEEEehhhcCCccHHHHHhhcCCCCcHHHHHHhhhhhhhhhhhhhhHHHHHHHHhcCCCCCCCcchhhH
Confidence 99999999999999999999999999999999999999999999999999999999999999999997667778899999
Q ss_pred HHHHHHHhcccCCCCCCCCcchhHHHHHHHHHHHHHHhhcCCCCCCCCCccccceecccchhHHHHHHHHHHHHHHHHHH
Q 000996 345 YAKEILQKEMLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRA 424 (1195)
Q Consensus 345 ~~~~~L~~~llpHl~~~~~~~~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~NKRv~l~G~Ll~~lfr~~l~~~~k~ik~ 424 (1195)
+|+++|.+++|||++..+...+.|++||+|||++|+.++.|++.+||+||++|||++++|+||..+||..|+++.+++..
T Consensus 308 yakdiLqKe~lPhi~~~e~~etkKA~fLGYmi~rlll~aLgRr~~ddRDHfG~KRLDlaGpLLa~lfR~lf~~l~rd~~~ 387 (1141)
T KOG0214|consen 308 YAKEILQKELLPHVGLGEICETKKAYFLGYMVHRLLLAALGRRELDDRDHFGNKRLDLAGPLLAKLFRSLFAKLLRDVTR 387 (1141)
T ss_pred HHHHHHHHHhccccccchhhhhhHHHHHHhhHHHHHHHHcCCCCccchhhccccchhhchhHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999888889999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhhhhccCCCCchhhcccccccccccccccccccccccc-cccccccceeeccccChhhhhccccccCCCCCcCCCccc
Q 000996 425 YVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQAN-AAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAK 503 (1195)
Q Consensus 425 ~l~k~~~~~~~~~~~~~i~~~~It~~i~~~~sTGnw~~~~-~~~~~sG~sq~l~r~N~ls~lSh~Rrv~~~~~~~~k~t~ 503 (1195)
.++|.+++..++++.-+++++.||++++|+||||||+.++ .++.++||||+|+|+||+++|||+||+++|+++++|.+.
T Consensus 388 ~mQk~le~~~dfni~~aika~iIt~gl~yslaTgnwgdq~ka~~~ragVsQVLnR~t~~sTLsHlRR~n~Pigr~GKlAk 467 (1141)
T KOG0214|consen 388 YMQKCLENGVDFNIELAIKAKIITNGLNYALATGNWGDQKKAMQGRAGVSQVLNRLNPLSTLSHLRRTNSPIGRTGKLAK 467 (1141)
T ss_pred HHHHHHhcCccceEEEEEEeeeecccceeeeccCCccchhHHhhccccHHHHhccccHHHHHHHHhhcCCccccccccCC
Confidence 9999999999999999999999999999999999999555 777899999999999999999999999999999999999
Q ss_pred cccccCCCcccccccCCCCCcccchhhcccccEEEccCCCchhHHHHHHHhCCccccccCCCCCCCceEEEECCEEEEEE
Q 000996 504 PRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIH 583 (1195)
Q Consensus 504 vR~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~It~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~V~lnG~~iG~~ 583 (1195)
||+|||||||++||+|||||++||||||||+||.|++|+.+.|++++|+++||+.++++++..+...++|||||.|+|+|
T Consensus 468 pRqlHnthwGmvCPaeTPEGqacGLVKNLSLmayIsvGS~~sPi~EfLeewgmE~le~~~ps~~~datkvfvNG~wvGlh 547 (1141)
T KOG0214|consen 468 PRQLHNSHWGMVCPAETPEGQACGLVKNLSLMAYISVGSLESPIVEFLEEWGMENLEEISPSPSPDATKVFVNGVWVGLH 547 (1141)
T ss_pred ccccCcccceeeccccCCCcceeeccccceEEEEEecCCCccHHHHHHHHhchhhHhhcCCCcCCCceEEEEcccEEEec
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cChHHHHHHHHhhhccCCCCcceEEEEeccCCeEEEEeCCCceeeeEEEEecccchhhHHHHHHhhcCCCCCCCCccccc
Q 000996 584 RDPEMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRESPEDGGWHDLV 663 (1195)
Q Consensus 584 ~~~~~~~~~lr~~rr~~~i~~~~~i~~~~~~~~i~I~td~GRl~RPl~~v~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~ 663 (1195)
.+|+.++.+||.+||+..++.++++++|...++++||||+||+|||||+|+|+++.++|+|+..|+..+. ++-+|..|+
T Consensus 548 rdp~~l~~tlr~lRR~~di~~Evs~vRDIr~kE~ri~tDaGR~~rPLliven~~l~~~k~hi~~L~~~~~-~~~~w~~lv 626 (1141)
T KOG0214|consen 548 RDPEELVATLKRLRRQFDIIAEVSMVRDIRDKEIRIFTDAGRSLRPLLIVENAKLLIKKRHIRALKQSKP-NEYRWAHLL 626 (1141)
T ss_pred CCHHHHHHHHHHHHHhhccchhhhhhccccccceeeeeccCccccceEEEechhhhhhhHHHHHHhhCch-hhcchhhhc
Confidence 9999999999999999999999999999999999999999999999999999999999999999987621 112899999
Q ss_pred cCCeEEEecccccccceeecccchhhcccCCCCccCCCceeeeecCCCccccccccccCCCCCCCCCccccccccccCcc
Q 000996 664 AKGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAM 743 (1195)
Q Consensus 664 ~~g~iE~i~~~Ee~~~~Ia~~~~~~~~~~~~~~~~~~~~~th~EI~P~~ilsv~AslIPF~~hNqSpRn~yqc~M~KQa~ 743 (1195)
..|++||||++||+.++|||.+.++.+. .+...||||||||++||||+||+||||||||||||+||++|+||||
T Consensus 627 ~~G~ie~idteeEEtvmiam~~~dL~~~------~~~~~~THCEiHpsmILgv~asiIpFpdh~qspr~tYQsa~~kqam 700 (1141)
T KOG0214|consen 627 SSGEVEYIDTEEEETVMIAMGPKDLAES------AYPKTYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAM 700 (1141)
T ss_pred cccceeeeccchhhhHHHhcCHHHHhhc------cCCcccccccccHHHhhhhceeeeecCCCCCchHHHHHHHHhhhcc
Confidence 9999999999999999999999999762 2356899999999999999999999999999999999999999999
Q ss_pred cccceeeEEEeeccceeeecCCCceeecccccccccccCCCCceEEEEEEecCCccCCCcEEEecceeecCceeEEEEEE
Q 000996 744 GIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRS 823 (1195)
Q Consensus 744 g~~~~n~~~r~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~~~G~N~~VAv~s~~Gyn~EDaiiink~s~~rG~f~s~~~~~ 823 (1195)
|++.+|++.|+||..|+|+|||+|+|+|++++++.+.++|+|+|++||++||+|||||||||+|+++++||+|||++||+
T Consensus 701 g~y~tn~~vR~dtl~~~l~ypqkpl~tt~~~e~l~~~eL~aG~NaiVAi~~~~GYNqEDsvimn~s~v~rg~FrS~~~Rs 780 (1141)
T KOG0214|consen 701 GVYHTNPQVRMDTLAKVLYYPQKPLVTTRAMEYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSVDRGLFRSFFIRS 780 (1141)
T ss_pred eeeeecchhhhhhhhhcccccccchhhHHHHhhhhhhhcccccceEEEEecccCccHHHHHHHHhhhhhcchhhhhhhhH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEechhccCCcccccccCCCCCCCCCCCCCCcCCCCCCCCcCCCcEECCCCEEEEEeCCCCc--cccccccCCCccceee
Q 000996 824 YRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQ--DEAQGQASRYTRRDHS 901 (1195)
Q Consensus 824 ~~~~~~~~~~~~~e~~~~p~~~~~~~~~~~~~~~Ld~dGi~~~G~~v~~gdvli~k~~~~~~--~~~~~~~~~~~~~~~s 901 (1195)
|+.++.+...+..+.|+.|....+.++|++.|++||+||++.||++|..|||+|||.+|... ++.+...+....+|+|
T Consensus 781 Yk~q~~~~~~~~ee~~~~~~~~~~~~mr~~~~dkLdddG~i~~G~~vs~~Dv~iGk~t~~~~~~~~~~~~~~~~t~~d~s 860 (1141)
T KOG0214|consen 781 YKDQEHKKDQGPEEIFEEPPRGEGRGMRNGKYDKLDDDGIIMPGSRVSGGDVLIGKTTPQPAKEDESGPEDRLYTKRDHS 860 (1141)
T ss_pred HHhhhhhcccccccccccccccccccccccccccccccCCccccceeecCCEEeccccCCcccchhccccccccccccce
Confidence 99998877677778889999888899999999999999999999999999999999998653 3344444555689999
Q ss_pred EEeecCCCcEEEEEEEEecCCCcEEEEEEEeeecCCCCcccccccCCCceeEEeeecCCCCCCCCCCCCCcEEeCCCCCC
Q 000996 902 ISLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIP 981 (1195)
Q Consensus 902 ~~~~~~~~g~v~~v~~~~~~~~~~~v~v~~~~~R~~~iGDKf~sRHGqKGvvs~i~~~~dmPf~~~G~~pDiIiNPh~~P 981 (1195)
+.++++|.|+||+|++++|.+|.+.+||++|+.|.|++|||||||||||||||.+++++|||||.+|++|||||||||||
T Consensus 861 ~~Lr~~e~Givd~V~vt~n~~G~kF~kv~vr~~ripqiGDKfasrHgqKG~ig~~~~qedmpft~eGi~pDiiiNPhaiP 940 (1141)
T KOG0214|consen 861 TKLRHTERGIVDQVWVTKNSEGPKFVKVRVRQVRIPQIGDKFASRHGQKGTIGITYRQEDMPFTIEGIVPDIIINPHAIP 940 (1141)
T ss_pred eecccCCcceEEEEEEecCCCCCceeEEEEeecccccccchhccccccCccccceeecCCCCccccCCCcceEECcccCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCchhhHHHHhhhHHhhhcCCCcccCCCCCccHHHHHHHHHHcCCCCCCeEEEeeCCCCceeeeeEeEeeeehhccccc
Q 000996 982 SRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHM 1061 (1195)
Q Consensus 982 SRMtiGql~E~~~gk~~~~~g~~~~~tpF~~~~~~~~~~~l~~~g~~~~G~~~l~~G~tG~~~~~~if~G~~yy~rL~Hm 1061 (1195)
||||||||+||++||.++..|...|+|||....+..++..|+++||+++|+|+||||+||++|.+.||+||.|||||+||
T Consensus 941 SRmtig~liEc~lgk~~a~~~e~~~atpFs~v~v~~is~~l~~~g~~~~G~e~~ynGrtG~~~~~~if~GptyyqrL~Hm 1020 (1141)
T KOG0214|consen 941 SRMTIGQLIECLLGKVAAYEGEEGDATPFSDVTVSKISANLHVYGYQYRGNERMYNGRTGRKLRAQIFIGPTYYQRLKHM 1020 (1141)
T ss_pred cccchhhhHHHhhhhhhhcccccccCCCCCccchhcccchHHHhccccCCCEEEecCCCCceeeeeeecCchHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCcccEEeccCCccccccCCCCcccCCCccccchhhhhHHHhhccHHHHHHhhhcCCCceeeeeccccCcceeeccccCc
Q 000996 1062 VDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNS 1141 (1195)
Q Consensus 1062 v~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~Erl~~~SD~~~~~vC~~cG~~~~~~~~~~~ 1141 (1195)
|+||+|+|++||++.|||||++||||+||||||||||||+||||||++|+|||+..||.|.+++|..||..+.++...+.
T Consensus 1021 vd~kih~R~~Gp~q~ltRQP~~gRsr~GGlRfGEMErdc~iahGaa~~L~ERL~~~SD~~~~~~c~~c~l~~i~~~~~n~ 1100 (1141)
T KOG0214|consen 1021 VDDKIHSRARGPVQILTRQPVEGRSRDGGLRFGEMERDCLIAHGAAAFLKERLFEKSDAYRVHICVLCGLTAIAGLIPNS 1100 (1141)
T ss_pred hhheeeecccCCceeeeccccccccccCCeeeehhHHHHHHHhhHHHHHHHHhhccCccceEEEeccchhhhhhccCCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999977778888888
Q ss_pred eeeccCCCCCCceeecchHhhHHHHHHHHhCCCceEEEec
Q 000996 1142 FECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTK 1181 (1195)
Q Consensus 1142 ~~C~~C~~~~~~~~v~iPy~~kll~~EL~sm~i~~~l~~~ 1181 (1195)
+.|+.|.+.+.++.+.+|||||||+|||+||||.+|+.++
T Consensus 1101 ~~ck~c~n~~~v~~v~ipya~kLl~qelmsmni~pr~~~~ 1140 (1141)
T KOG0214|consen 1101 FECRGCENKTLVVRVYIPYAAKLLFQELMSMNIAPRRKTK 1140 (1141)
T ss_pred cccccccCccceEEEechhHHHHHHHHHHhccCccccccC
Confidence 8999999999999999999999999999999999998764
No 2
>PRK08565 DNA-directed RNA polymerase subunit B; Provisional
Probab=100.00 E-value=1.4e-277 Score=2625.07 Aligned_cols=1095 Identities=47% Similarity=0.772 Sum_probs=1002.1
Q ss_pred hhhhhhcccCccchHHHHHHHHHHHHHhhHHHHHcccCCeeeCCCCCCCCCCCCCCCCceEEEEEeEEEEccCccccCCC
Q 000996 28 AWAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQSDFAETIYKISFGQIYLSKPMMTESDG 107 (1195)
Q Consensus 28 ~~~~i~~~f~~~~Lv~~qi~SFn~Fi~~gL~~ii~~~~pI~~~~~~~~~~~~~~~~~~~~~~l~f~~v~v~~P~~~e~~~ 107 (1195)
+|.++++||+.++|++|||+|||+|+++||++++++++||++. ...+.|+|.+++|++|++.+.++
T Consensus 1 ~~~li~~~~~~~~Lv~~qidSFn~Fi~~gL~~iv~~~~pI~~~--------------~~~~~L~f~~i~l~~P~~~~~~~ 66 (1103)
T PRK08565 1 RWTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDEFGEIKTE--------------IPGLKIVLGKIRVGEPEIKEADG 66 (1103)
T ss_pred CchHHHHHhcccChHHHHHHHHHHHHHHhHHHHHHhcCCEEec--------------CCCEEEEEEEEEECCCccccccc
Confidence 4999999999999999999999999999999999999999853 34699999999999999987776
Q ss_pred cccCCChHHHHhcCCccceeEEEEEEEEEeccCCCCcccccceeeEEEEecccceeeccCCccCCCCChhhhhhcCCCCC
Q 000996 108 ETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPY 187 (1195)
Q Consensus 108 ~~~~l~P~EcR~r~lTYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~eli~~gE~~~ 187 (1195)
...+|+|+|||+|++||+|+|+|++++..++. ....+++.+|+|||||+|++|||++++|+||++.||||+
T Consensus 67 ~~~~l~P~ecR~r~lTYsa~l~v~i~~~~~~~---------~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~p~ 137 (1103)
T PRK08565 67 SERPITPMEARLRNLTYAAPLYLTMIPVENGI---------EYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPK 137 (1103)
T ss_pred ccCCCCHHHHHhcCCCcceEEEEEEEEEECCe---------eeEEEEEEeccCCeEeCCCcccCCCCCHHHHHhcCCCcc
Confidence 77899999999999999999999999976431 124568999999999999999999999999999999999
Q ss_pred CCCceEEEcCeeeEEeeeeeeecceEEEEEecCCCcceEEEEEEEeecCCCCCCceEEEEEEecCCCCCCCCCcEEEEEe
Q 000996 188 DQGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATL 267 (1195)
Q Consensus 188 D~GGYFIING~ERVII~Qe~~s~N~~~~~~~~~~~~~~~~~~irs~~~~g~~~~~~~~v~~~~~~~~k~~~~~~~i~v~i 267 (1195)
|+||||||||+||||++|+++|||+++++.+....+..|.|.++|.+. .|. +.+.+++.. ++.+++++
T Consensus 138 D~GGYFIING~ERVI~~q~~~s~n~~~~~~~~~~~~~~~~a~i~s~~~--~~~-~~~~l~~~~---------~g~i~~~~ 205 (1103)
T PRK08565 138 DPGGYFIINGSERVIVSQEDLAPNRVLVDKGEAGSSITHTAKVISSRA--GYR-AQVTVERRK---------DGTIYVSF 205 (1103)
T ss_pred CCCCeEEECCcEEEEEEEEecCCCEEEEEEecCCCcceEEEEEEeccC--CCc-ceEEEEEec---------CCeEEEEE
Confidence 999999999999999999999999999887654455668899987543 231 234444421 46799999
Q ss_pred ccccccchHHHHHHHhcCCChHHHHHHhcccccchHHHHHhHhhHhhhhcc-CCHHHHHHHHhhcCcccCCCchhhHHHH
Q 000996 268 PYIRTEIPIIIVFRALGFVADKDILEHICYDFQDTQMMELLRPSLEEAFVI-QNQQVALDYIGKRGATVGVTRDKRIKYA 346 (1195)
Q Consensus 268 ~~~~~~IPl~ilLrALG~~sD~eI~~~i~~~~~~~~~~~~l~~sl~e~~~i-~t~~~al~yig~r~~~~~~~~~~~~e~~ 346 (1195)
+++..+||+++||||||++||+||++.|+. ++.+.+.+..++++...+ .|+++||.|||++|+.. .++.++.+.|
T Consensus 206 ~~~~~~IPi~illkALG~~sD~eI~~~i~~---~~~~~~~l~~~l~~~~~~~~t~~~al~~ig~~~~~~-~~~~~~~e~~ 281 (1103)
T PRK08565 206 PAVPGKIPFVILMRALGLETDRDIVYAVSL---DPEIQQELLPSLEQASSIAATVEDALDYIGKRVAIG-QPREYRIERA 281 (1103)
T ss_pred cCcccEeeHHHHHHHcCCCCHHHHHHHhcc---cHHHHHHHHHHHHHhhccccCHHHHHHHHHHhccCC-CCCccHHHHH
Confidence 987678999999999999999999999964 455667777788776556 79999999999998752 3455667899
Q ss_pred HHHHHhcccCCCCCCCCcchhHHHHHHHHHHHHHHhhcCCCCCCCCCccccceecccchhHHHHHHHHHHHHHHHHHHHh
Q 000996 347 KEILQKEMLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYV 426 (1195)
Q Consensus 347 ~~~L~~~llpHl~~~~~~~~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~NKRv~l~G~Ll~~lfr~~l~~~~k~ik~~l 426 (1195)
+++|++++|||++.+..++.+|++||++|++||+.++.|.+.+||+|||+||||+++|+||+.+||+.|+++++.+++++
T Consensus 282 ~~~L~~~ll~Hig~~~~~~~~K~~~L~~Mi~kLl~l~~g~~~~DD~D~l~NKRv~l~G~Ll~~~fr~~l~~~~~~ik~~l 361 (1103)
T PRK08565 282 EQILDKYLLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQL 361 (1103)
T ss_pred HHHHHhhCcccCCCcccchhHHHHHHHHHHHHHHhhhcCCCCCCCccccCCcEEccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999998765556899999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhccCCCCchhhcccccccccccccccccccccccccccccccceeeccccChhhhhccccccCCCCCcCCCcccccc
Q 000996 427 QKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQ 506 (1195)
Q Consensus 427 ~k~~~~~~~~~~~~~i~~~~It~~i~~~~sTGnw~~~~~~~~~sG~sq~l~r~N~ls~lSh~Rrv~~~~~~~~k~t~vR~ 506 (1195)
.+.+.+.+.+++..+++++.||++|++|||||||.+ |++|+||+|+|+||+|+|||||||++++.+++|.++||+
T Consensus 362 ~~~~~~~~~~~~~~~i~~~~It~~i~~~~sTGnw~~-----~~sGvSq~ldr~N~l~~lSh~Rrv~s~~~r~~~~~~vR~ 436 (1103)
T PRK08565 362 EKSYARGRKLDLRAIVRPDIITERIRHALATGNWVG-----GRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARD 436 (1103)
T ss_pred HHHHhccccCCHHHhcccchhhHHHHHHHhcCcccc-----CCcceEEecccCCHHHHHHHHhhccCCcccCCCCccccc
Confidence 887655567788888998899999999999999995 679999999999999999999999999999999999999
Q ss_pred ccCCCcccccccCCCCCcccchhhcccccEEEccCCCchhHHHHHHHhCCccccccCCCCCCCceEEEECCEEEEEEcCh
Q 000996 507 LHNSQWGMMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDP 586 (1195)
Q Consensus 507 Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~It~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~ 586 (1195)
||||||||+||+|||||++||||||||++|+|+++.+.+++.++|.++|+.++.++.+......++|||||+|||++++|
T Consensus 437 Lhps~wG~iCPveTPEG~~cGLv~~LA~~a~It~~~~~~~i~~~l~~~G~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~ 516 (1103)
T PRK08565 437 LHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDG 516 (1103)
T ss_pred cChhhccccCCCCCCCccccchhhhhhcccccccCCChHHHHHHHHHcCCCchhhcCcccCCCceEEEECCEEEEEECCH
Confidence 99999999999999999999999999999999998889999999999999998766665666779999999999999999
Q ss_pred HHHHHHHHhhhccCCCCcceEEEEec--cCCeEEEEeCCCceeeeEEEEecccchhhHHHHHHhhcCCCCCCCCcccccc
Q 000996 587 EMLVKTLRRLRRRVDVNTEVGVVRDI--RLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRESPEDGGWHDLVA 664 (1195)
Q Consensus 587 ~~~~~~lr~~rr~~~i~~~~~i~~~~--~~~~i~I~td~GRl~RPl~~v~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~ 664 (1195)
..|++.||.+||+|.|+.++||++++ ..++|+|+||+||++|||++|++|++.+++++++.++.+.+ +|++|++
T Consensus 517 ~~l~~~lR~~Rr~g~i~~~v~I~~~~~~~~~~i~I~sd~GRl~RP~~~v~~g~~~~~~~~~~~l~~~~~----~~~~l~~ 592 (1103)
T PRK08565 517 EELAEKIRELRRSGKISDEVNVAYIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGEL----TFDDLVK 592 (1103)
T ss_pred HHHHHHHHHHhhcCCCCCeEEEEEccccccceEEEecCCceeeeeEEEEecCceeccHHHHHHhhcccc----chhhHhh
Confidence 99999999999999999999999998 78999999999999999999999999999999998876655 8999999
Q ss_pred CCeEEEecccccccceeecccchhhcccCCCCccCCCceeeeecCCCccccccccccCCCCCCCCCccccccccccCccc
Q 000996 665 KGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG 744 (1195)
Q Consensus 665 ~g~iE~i~~~Ee~~~~Ia~~~~~~~~~~~~~~~~~~~~~th~EI~P~~ilsv~AslIPF~~hNqSpRn~yqc~M~KQa~g 744 (1195)
+|.|||||++||++++||++++++.. .+||+||+|++|||++||+|||+||||||||||||||||||||
T Consensus 593 ~g~iEyid~~Ee~~~~Ia~~~~~l~~-----------~~th~Ei~p~~ilsv~asliPF~~hNqspRn~yq~~M~KQa~g 661 (1103)
T PRK08565 593 MGVIEYLDAEEEENAYVALDPEDLTP-----------EHTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLG 661 (1103)
T ss_pred cCcEEeeCHHHhcCcEEeccccccCc-----------ceeccccCCccccceeeeccCCcccCcccchhhhhhhhhcccc
Confidence 99999999999999999999988742 4799999999999999999999999999999999999999999
Q ss_pred ccceeeEEEeeccceeeecCCCceeecccccccccccCCCCceEEEEEEecCCccCCCcEEEecceeecCceeEEEEEEE
Q 000996 745 IYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSY 824 (1195)
Q Consensus 745 ~~~~n~~~r~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~~~G~N~~VAv~s~~Gyn~EDaiiink~s~~rG~f~s~~~~~~ 824 (1195)
++.+|+.+|+|++.|+|+|||+|||+|+.++.++++++|+|+||+||||||+||||||||||||+|+|||||||+||++|
T Consensus 662 ~~~~n~~~r~d~~~~~l~~pQ~Plv~t~~~~~~~~~~~p~G~N~iVAv~sy~GYn~EDaiIink~s~~rG~~~s~~~~~~ 741 (1103)
T PRK08565 662 LYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTY 741 (1103)
T ss_pred cccccceEeecCCcceeecCceeEEEeccccccccccCCCCeeEEEEEEcccCcchHHhhhhhhhhhhcCCceEEEEEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EechhccCCcccccccCCCCCCCCCCCC-CCcCCCCCCCCcCCCcEECCCCEEEEEeCCCCccc--cccccCCCccceee
Q 000996 825 RDEEKKMGTLVKEDFGRPDRSNTMGMRH-GSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDE--AQGQASRYTRRDHS 901 (1195)
Q Consensus 825 ~~~~~~~~~~~~e~~~~p~~~~~~~~~~-~~~~~Ld~dGi~~~G~~v~~gdvli~k~~~~~~~~--~~~~~~~~~~~~~s 901 (1195)
++++++...+..+.|++|.. +..+.+. ..|++||+||||++|++|++|||||||++|..... ..........+|+|
T Consensus 742 ~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~Ld~dGi~~~G~~v~~gdili~k~~p~~~~~~~~~~~~~~~~~~~~s 820 (1103)
T PRK08565 742 ETEERKYPGGQEDKIEIPEP-NVRGYRGEEYYRKLDEDGIVSPEVEVKGGDVLIGKTSPPRFLEELEELSLGLQERRDTS 820 (1103)
T ss_pred EEEeeecCCCCceEEecCCC-cccccCchhhhhcCCCCCCcCCCcEEcCCCEEEEEecCCCCCcchhhccccCCccccce
Confidence 99877643344467777743 2222233 34899999999999999999999999999864211 01111113479999
Q ss_pred EEeecCCCcEEEEEEEEecCCCcEEEEEEEeeecCCCCcccccccCCCceeEEeeecCCCCCCCCCCCCCcEEeCCCCCC
Q 000996 902 ISLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIP 981 (1195)
Q Consensus 902 ~~~~~~~~g~v~~v~~~~~~~~~~~v~v~~~~~R~~~iGDKf~sRHGqKGvvs~i~~~~dmPf~~~G~~pDiIiNPh~~P 981 (1195)
++++.+|+|+||+|.++.+.++.+.|||++|+.|+|+||||||||||||||||+|||+||||||+||++|||||||||||
T Consensus 821 ~~~~~~e~g~V~~V~~~~~~~~~~~vkv~ir~~R~p~iGDKfssRhGqKGv~s~i~~~edmPf~~~G~~pDiI~NPh~~P 900 (1103)
T PRK08565 821 VTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIP 900 (1103)
T ss_pred EEecCCCceEEEEEEEEecCCCcEEEEEEEEEEecCchhhhhhhhccCcceeeeecccccCCcCCCCCCccEEECCCCCc
Confidence 99999999999999999998899999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCchhhHHHHhhhHHhhhcCCCcccCCCCCccHHHHHHHHHHcCCCCCCeEEEeeCCCCceeeeeEeEeeeehhccccc
Q 000996 982 SRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHM 1061 (1195)
Q Consensus 982 SRMtiGql~E~~~gk~~~~~g~~~~~tpF~~~~~~~~~~~l~~~g~~~~G~~~l~~G~tG~~~~~~if~G~~yy~rL~Hm 1061 (1195)
||||||||+|+++||||++.|.+.|+|||++...+++++.|+++||+++|+|+||||+||++|+++||+|++|||||+||
T Consensus 901 SRMtiG~l~E~~~gk~~~~~g~~~d~t~F~~~~~~~~~~~L~~~g~~~~G~e~l~~G~tG~~~~~~if~G~~yy~rL~Hm 980 (1103)
T PRK08565 901 SRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHM 980 (1103)
T ss_pred ccccHHHHHHHHHHHHHHhcCceeeecCcCCchHHHHHHHHHHcCCCCCCcEEEEcCCCCCCcccceEEeehhheechhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCcccEEeccCCccccccCCCCcccCCCccccchhhhhHHHhhccHHHHHHhhhcCCCceeeeeccccCcceeeccccCc
Q 000996 1062 VDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNS 1141 (1195)
Q Consensus 1062 v~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~Erl~~~SD~~~~~vC~~cG~~~~~~~~~~~ 1141 (1195)
|+||+|||++||+++|||||++||||+|||||||||||||+|||||++|||||+++||+++++||.+||++++.+.+++.
T Consensus 981 V~DK~~~R~~Gp~~~lt~QP~~Gr~~~GG~R~GEME~d~l~a~Gas~~L~erL~~~SD~~~~~vC~~Cg~~~~~~~~~~~ 1060 (1103)
T PRK08565 981 VADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHIAWYDRRKNK 1060 (1103)
T ss_pred hchhhhhccCCCcchhhhCCccccccCCCeeeecchHHHHHhcccHHHHHHHhhccccceeeeeecccccccccccccCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999987666778
Q ss_pred eeeccCCCCCCceeecchHhhHHHHHHHHhCCCceEEEecc
Q 000996 1142 FECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKE 1182 (1195)
Q Consensus 1142 ~~C~~C~~~~~~~~v~iPy~~kll~~EL~sm~i~~~l~~~~ 1182 (1195)
++|+.|+++..+.++.||||||||+|||+||||+++|.+++
T Consensus 1061 ~~C~~c~~~~~~~~v~iPy~~k~l~~EL~sm~i~~~l~~~~ 1101 (1103)
T PRK08565 1061 YVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLKLGD 1101 (1103)
T ss_pred eeccccCCCCcceeccCChhHHHHHHHHHhCCCceEEEeee
Confidence 89999999889999999999999999999999999999874
No 3
>KOG0215 consensus RNA polymerase III, second largest subunit [Transcription]
Probab=100.00 E-value=3.6e-259 Score=2203.47 Aligned_cols=1102 Identities=41% Similarity=0.693 Sum_probs=1012.4
Q ss_pred cccccchhhhhhhhhcccCccchHHHHHHHHHHHHHhhHHHHHcccCCeeeCCCCCCCCCCCCCCCCceEEEEEeEEEEc
Q 000996 19 EEEEITQEDAWAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQSDFAETIYKISFGQIYLS 98 (1195)
Q Consensus 19 ~~~~~~~~~~~~~i~~~f~~~~Lv~~qi~SFn~Fi~~gL~~ii~~~~pI~~~~~~~~~~~~~~~~~~~~~~l~f~~v~v~ 98 (1195)
..+....++.|.++++||+.+||+++|++|||+|++++|+.|++++..|.. +.+..+.++|.+++++
T Consensus 37 ~~~i~~~~dk~~lvp~flkvkglvkqhldsfnyfv~~~ik~iv~an~~its-------------d~dp~fylky~dirvg 103 (1153)
T KOG0215|consen 37 SDPIKPLEDKWQLVPAFLKVKGLVKQHLDSFNYFVDVDIKKIVKANQLITS-------------DVDPSFYLKYLDIRVG 103 (1153)
T ss_pred cCCCCChHHhHHhHHHHHhhhhHHHHHHhhhhhhhhhhHHHHHHhhcccCc-------------CcCchhhheeeeeecc
Confidence 445667789999999999999999999999999999999999999988864 3346789999999999
Q ss_pred cCccccCCCc-ccCCChHHHHhcCCccceeEEEEEEEEEeccCCCCcccccceeeEEEEecccceeeccCCccCCCCChh
Q 000996 99 KPMMTESDGE-TATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEK 177 (1195)
Q Consensus 99 ~P~~~e~~~~-~~~l~P~EcR~r~lTYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~ 177 (1195)
+|++.+..+. ...++|+|||+|++||+||++|+++++.... .+....|.||++|||++|++|+|++.++.
T Consensus 104 ~Ps~~~~~~~~~~~i~p~ecrlrd~tysa~i~vdieytrg~~---------~~~~~~v~igrmpimlrs~rcvl~~~~e~ 174 (1153)
T KOG0215|consen 104 KPSIEEGNNVTNDNITPHECRLRDMTYSAPIYVDIEYTRGRQ---------IIAKRDVIIGRMPIMLRSSKCVLRGKDEE 174 (1153)
T ss_pred CcchhhccccccccCCchheeehhhhcccceeEEEEEecCcc---------eEEecccccccchhhhhccccccCCccHH
Confidence 9998766543 4689999999999999999999999986542 34567899999999999999999999999
Q ss_pred hhhhcCCCCCCCCceEEEcCeeeEEeeeeeeecceEEEEEecCCCcceEEEEEEEee-cCCCCCCceEEEEEEecCCCCC
Q 000996 178 DLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMA-ESQNRPPSTMFVRMLSRTSAKG 256 (1195)
Q Consensus 178 eli~~gE~~~D~GGYFIING~ERVII~Qe~~s~N~~~~~~~~~~~~~~~~~~irs~~-~~g~~~~~~~~v~~~~~~~~k~ 256 (1195)
++++.+|||.||||||||+|.||||+.||+.|.|++++... .+..+-|++.|.. +++++ ..|.+ +
T Consensus 175 ~~a~~~ecpldpggyfiv~G~ekViLiqeqlsknrii~~~~---k~~~~~~svtsst~e~ksk----t~v~~------k- 240 (1153)
T KOG0215|consen 175 ELARLNECPLDPGGYFIVKGTEKVILIQEQLSKNRIIVEED---KKGNLQASVTSSTHERKSK----TYVTT------K- 240 (1153)
T ss_pred HHHHhccCCCCCCceeEeccceeEEEehhhhhccCeeeccc---cCCccccccccceeeecce----EEEEe------c-
Confidence 99999999999999999999999999999999999998421 2234456666433 44432 22211 1
Q ss_pred CCCCcEEEEEeccccccchHHHHHHHhcCCChHHHHHHhcccccchHHHHHhHhhHhhh--hccCCHHHHHHHHhhcCcc
Q 000996 257 GSSGQYIRATLPYIRTEIPIIIVFRALGFVADKDILEHICYDFQDTQMMELLRPSLEEA--FVIQNQQVALDYIGKRGAT 334 (1195)
Q Consensus 257 ~~~~~~i~v~i~~~~~~IPl~ilLrALG~~sD~eI~~~i~~~~~~~~~~~~l~~sl~e~--~~i~t~~~al~yig~r~~~ 334 (1195)
++.++++++.+..+||++++|||||..||+||.+.++. +..+++.+..+++++ ..++||.+||+|++.+.+.
T Consensus 241 ---~~k~ylk~~~~~d~ipiviv~ka~g~~sd~ei~~~vg~---~~~y~~~~~~s~ee~~~~~v~tqqqal~y~~~kvk~ 314 (1153)
T KOG0215|consen 241 ---KGKYYLKHNSFTDDIPIVIVLKAMGLESDQEIVQLVGG---DSKYQDIFAPSLEECVSLGVYTQQQALEYIGSKVKV 314 (1153)
T ss_pred ---cceeeeehhhhhccCCEEEEEeeccccchHHHHHHhhc---chHHHHhhccchhhhhhhhhHHHHHHHHHhhheEEe
Confidence 56799999999999999999999999999999999975 567888888888887 4578999999999999765
Q ss_pred cCCCchhhHHHHHHHHHhcccCCCCCCCCcchhHHHHHHHHHHHHHHhhcCCCCCCCCCccccceecccchhHHHHHHHH
Q 000996 335 VGVTRDKRIKYAKEILQKEMLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRML 414 (1195)
Q Consensus 335 ~~~~~~~~~e~~~~~L~~~llpHl~~~~~~~~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~NKRv~l~G~Ll~~lfr~~ 414 (1195)
...++.+..+.|.++|...+++|+.....++..|+.+++.|+|+++....+.-..||+|.++|||+.++|+|++.+|++.
T Consensus 315 ~~~t~~~~~~e~~~~l~~~~lahv~v~~~~~r~K~~yi~~m~rr~~~a~l~~~~~ddrd~~gnkrlelagqllsllfeD~ 394 (1153)
T KOG0215|consen 315 KRGTTPTKDEEALEVLSTTVLAHVPVPDLNFRMKAIYIGLMVRRVIQAMLNKLAMDDRDYVGNKRLELAGQLLSLLFEDL 394 (1153)
T ss_pred ccCCCCCchHHHHHHHHhhheeceeccCCCCcceeehHHHHHHHHHHHHhCcccccchhhhccchHHHHHHHHHHHHHHH
Confidence 44455667789999999999999999988899999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhhhhccC---CCCchhhccc--ccccccccccccccccccccccccccccceeeccccChhhhhcccc
Q 000996 415 FRKLTRDVRAYVQKCVDNG---KDVNLQFAIK--AKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLR 489 (1195)
Q Consensus 415 l~~~~k~ik~~l~k~~~~~---~~~~~~~~i~--~~~It~~i~~~~sTGnw~~~~~~~~~sG~sq~l~r~N~ls~lSh~R 489 (1195)
|+++...++..+.+.+.+. ..+++.+.+| ++.||++|.+++|||||..++|.|.+.|++|++.|++|.+.|.++.
T Consensus 395 fk~~n~e~k~~~dk~l~k~~ra~~fD~~~~~n~~~~~it~~l~ra~stgnw~iKrfrmer~gvt~VlsrlSyisaLgmmt 474 (1153)
T KOG0215|consen 395 FKRFNSELKKNIDKILKKPIRAQEFDALKHLNVRANMITSGLERAISTGNWSIKRFRMERAGVTQVLSRLSYISALGMMT 474 (1153)
T ss_pred HHHHHHHHHHHHHHHhcchhhhhhhHHHHHHHHHHHHHHHHHHHHhhcCchHHHHhhhhhccceeeehhhhhhhhhhhhe
Confidence 9999999999888877652 2456666664 6899999999999999999999999999999999999999999999
Q ss_pred ccCCCCCcCCCccccccccCCCcccccccCCCCCcccchhhcccccEEEccCCCchhHHHHHHHhCCccccccCCCCCC-
Q 000996 490 RLNSPIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIP- 568 (1195)
Q Consensus 490 rv~~~~~~~~k~t~vR~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~It~~~~~~~i~~~l~~~g~~~~~~~~~~~~~- 568 (1195)
|++++|.+++|..+||.|+|||||++||+|||||++||||||||++++|++...++|+...+..+|++.+..++..+++
T Consensus 475 ri~s~fektrkvsgprSlq~sqwgmlcp~dtpegeacglvknlalmthittd~ee~pi~~~~~k~gv~di~~v~~~e~~~ 554 (1153)
T KOG0215|consen 475 RINSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITTDSEEKPILKLCYKLGVEDIHVVSGRELHT 554 (1153)
T ss_pred ehhhhheeehhccCccccChhhcccccCCCCCCccccccccchHHHhcccCCCCcchhHHHHHHhcceeeeeecccccCC
Confidence 9999999999999999999999999999999999999999999999999999999999999999999998877666654
Q ss_pred -CceEEEECCEEEEEEcChHHHHHHHHhhhccCCCCcceEEEEeccCCeEEEEeCCCceeeeEEEEecccchhhHHHHHH
Q 000996 569 -QATKIFVNGCWVGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIA 647 (1195)
Q Consensus 569 -~~~~V~lnG~~iG~~~~~~~~~~~lr~~rr~~~i~~~~~i~~~~~~~~i~I~td~GRl~RPl~~v~~~~~~~~~~~~~~ 647 (1195)
..+.|||||.++|.+..|+.++..+|.+||.|.|..+++++.+..+..++|.||+||+|||+++++++.+.+++.|+..
T Consensus 555 ~~~~~v~Lng~iig~~~~~~~~v~~~r~lrr~G~i~~fvsv~~~~~q~~v~i~sdggr~crp~Iiv~~~~~~v~~~h~~e 634 (1153)
T KOG0215|consen 555 PDSFLVFLNGLIIGITRRPQYFVNSFRRLRRKGKIGEFVSVFTNTTQRCVYIASDGGRVCRPLIIVDNGRPRVKQHHMDE 634 (1153)
T ss_pred CceEEEEecceeeccccchHHHHHHHHHHHHcCcccceeeeeeeeeeEEEEEecCCCeEeeeEEEEeCCcchhhhhhHHH
Confidence 5689999999999999999999999999999999999999998888999999999999999999999999999999999
Q ss_pred hhcCCCCCCCCccccccCCeEEEecccccccceeecccchhhcccCCCCccCCCceeeeecCCCccccccccccCCCCCC
Q 000996 648 LQQRESPEDGGWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHN 727 (1195)
Q Consensus 648 l~~~~~~~~~~~~~l~~~g~iE~i~~~Ee~~~~Ia~~~~~~~~~~~~~~~~~~~~~th~EI~P~~ilsv~AslIPF~~hN 727 (1195)
++.+.. +|+||++.|+|||+|++||+.++||..+.++.+ ++||+||.|..+||+||+||||||||
T Consensus 635 l~~g~r----~F~DFl~~glvEYLDVNEEND~~Ialye~~I~~-----------~TTHLEIEPFTiLGv~AGLIPYPHHN 699 (1153)
T KOG0215|consen 635 LLDGKR----TFDDFLKDGLIEYLDVNEENDSLIALYEEDIGP-----------ETTHLEIEPFTILGVVAGLIPYPHHN 699 (1153)
T ss_pred HHHhhh----hHHHHHHhchhheeecccccCceEEechhhcCC-----------CcceeeecchhhhhhhccccCCCCCC
Confidence 998887 899999999999999999999999999999864 69999999999999999999999999
Q ss_pred CCCccccccccccCcccccceeeEEEeeccceeeecCCCceeecccccccccccCCCCceEEEEEEecCCccCCCcEEEe
Q 000996 728 QSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMN 807 (1195)
Q Consensus 728 qSpRn~yqc~M~KQa~g~~~~n~~~r~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~~~G~N~~VAv~s~~Gyn~EDaiiin 807 (1195)
|||||+|||+|+|||||..++|+..|+|+.+|.|.|||+|+|+|++.++++++++|+||||.||||||+|||+|||+|+|
T Consensus 700 QSPRNTYQCAMGKQAmG~IaYNQ~~RiDtlmYll~YPq~PmVkTKTIELi~ydKLPAGQNAtVAVMSYSGYDIEDALVLN 779 (1153)
T KOG0215|consen 700 QSPRNTYQCAMGKQAMGAIAYNQKKRIDSLLYLLVYPQRPMVKTKTIELINYDKLPAGQNATVAVMSYSGYDIEDALVLN 779 (1153)
T ss_pred CCCcchhhhhhhhhhhhhhhhhhhhhHHHHHHHHhcCCCccccceeEEeeccccCCCCCccEEEEEeccCCchhhhhhcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cceeecCceeEEEEEEEEechhccCCcccccccCCCCCCCCCCCCCCcCCCCCCCCcCCCcEECCCCEEEEEeCCCCccc
Q 000996 808 QSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDE 887 (1195)
Q Consensus 808 k~s~~rG~f~s~~~~~~~~~~~~~~~~~~e~~~~p~~~~~~~~~~~~~~~Ld~dGi~~~G~~v~~gdvli~k~~~~~~~~ 887 (1195)
|+|+||||+|..+||+-++.++++.++..+.+..|..+...+..-.+.+.||+|||..||..|.+|+|+|+|-.|.....
T Consensus 780 KsSlDRGfGRC~Vyk~~~~~~kkY~N~T~Drimgp~~d~~t~kpi~kh~vLd~DGl~~pG~~V~~~qi~iNK~mP~vt~~ 859 (1153)
T KOG0215|consen 780 KSSIDRGFGRCEVYKKTTTTLKKYANGTFDRIMGPQLDPNTRKPIWKHQVLDDDGLATPGERVQPGQIYINKQMPTVTGT 859 (1153)
T ss_pred cchhccCcceEEEEeeeeeeeeecCCCchhhhcccccCCCcCCcchhhcccCcccCCCCccEeccCcEEEeccCCCcccc
Confidence 99999999999999999999999888888888877654333222245678999999999999999999999977765322
Q ss_pred c--ccccCCCccceeeEEeecCCCcEEEEEEEEecCCCcEEEEEEEeeecCCCCcccccccCCCceeEEeeecCCCCCCC
Q 000996 888 A--QGQASRYTRRDHSISLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWT 965 (1195)
Q Consensus 888 ~--~~~~~~~~~~~~s~~~~~~~~g~v~~v~~~~~~~~~~~v~v~~~~~R~~~iGDKf~sRHGqKGvvs~i~~~~dmPf~ 965 (1195)
+ +.+..+..+++.++.|+..++++||+|.++.++++.-++|+-+|+.|+|++|||||||||||||||.|++||||||.
T Consensus 860 ~~~~~~~~~~~Yk~~pitykgpepsyidkVmls~n~~dq~LIK~llRQTRrPElGDKFSSRHGQKGVcGlIv~QEDMPFn 939 (1153)
T KOG0215|consen 860 SLPGLSASQVQYKAVPITYKGPEPSYIDRVMLTSNDEDQFLIKVLLRQTRRPELGDKFSSRHGQKGVCGLIVQQEDMPFN 939 (1153)
T ss_pred cCCCCCccccccccccceecCCCcchhheeEeecCccccHHHHHHHhhccCcccccccccccCCCceeeEEeeccCCCCc
Confidence 2 22223335899999999999999999999999888889999999999999999999999999999999999999999
Q ss_pred CCCCCCcEEeCCCCCCCCCchhhHHHHhhhHHhhhcCCCcccCCCCCccHHHHHHHHHHcCCCCCCeEEEeeCCCCceee
Q 000996 966 VEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLT 1045 (1195)
Q Consensus 966 ~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~~~tpF~~~~~~~~~~~l~~~g~~~~G~~~l~~G~tG~~~~ 1045 (1195)
..||+|||||||||||||||||.++|.+.||||.+.|.+.++|+|.+..++++++.|.++||||.||+.+|||+||+|++
T Consensus 940 D~GIcPDiIMNPHGFPSRMTVGK~iELlsGKAGVl~G~~hYGTaFGgskVed~~~~Lv~hGfnY~GKD~ltSGITGepLe 1019 (1153)
T KOG0215|consen 940 DQGICPDIIMNPHGFPSRMTVGKMIELLSGKAGVLEGTFHYGTAFGGSKVEDISEELVEHGFNYSGKDMLTSGITGEPLE 1019 (1153)
T ss_pred ccCCCcccccCCCCCcccchHHHHHHHhccccceeeeeEeeccccCCchHHHHHHHHHHhccCccCccccccCCCCCcce
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeEeEeeeehhccccccCcccEEeccCCccccccCCCCcccCCCccccchhhhhHHHhhccHHHHHHhhhcCCCceeeee
Q 000996 1046 AMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHV 1125 (1195)
Q Consensus 1046 ~~if~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~Erl~~~SD~~~~~v 1125 (1195)
|+||+||+|||||+|||.||+|||++||+..|||||++||||+||+|+||||||||||||||.+|-|||+.+||.+++.|
T Consensus 1020 AYIffGPiYYQKLKHMVlDKMHARARGPRAvLTRQPTEGRSrdGGLRLGEMERDCLIaYGASmLl~ERLMiSSDaFeVdV 1099 (1153)
T KOG0215|consen 1020 AYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIAYGASMLLLERLMISSDAFEVDV 1099 (1153)
T ss_pred eeEEechHHHHHHHHHHHHHHhhhccCCceeeecCCCCCcCCCCCcccchhhhhhhhhccHHHHHHHHHhhcCcceeeee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCcceeeccccCceeeccCCCCCCceeecchHhhHHHHHHHHhCCCceEEEeccC
Q 000996 1126 CEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKED 1183 (1195)
Q Consensus 1126 C~~cG~~~~~~~~~~~~~C~~C~~~~~~~~v~iPy~~kll~~EL~sm~i~~~l~~~~~ 1183 (1195)
|..||.+++.. ||..|+++.++.++.||||||||||||+||||-|||.+++.
T Consensus 1100 C~~CGllgykg------wC~~Ckss~~v~~~~iPYAcKLLFQEL~SMNi~PrL~L~~~ 1151 (1153)
T KOG0215|consen 1100 CRQCGLLGYKG------WCTTCKSSKNVAKMKIPYACKLLFQELQSMNIVPRLKLEDY 1151 (1153)
T ss_pred ccccccceech------hhhhccCCCceeeeeccHHHHHHHHHHHhcCccceeeeccc
Confidence 99999999743 89999999999999999999999999999999999999865
No 4
>KOG0216 consensus RNA polymerase I, second largest subunit [Transcription]
Probab=100.00 E-value=1.9e-251 Score=2149.51 Aligned_cols=1057 Identities=32% Similarity=0.496 Sum_probs=926.5
Q ss_pred hhhhhhhcccCccchHHHHHHHHHHHHHhhHHHHHcccCCeeeCCCCCCCCCCCCCCCCceEEEEEeEEEEccCccccCC
Q 000996 27 DAWAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQSDFAETIYKISFGQIYLSKPMMTESD 106 (1195)
Q Consensus 27 ~~~~~i~~~f~~~~Lv~~qi~SFn~Fi~~gL~~ii~~~~pI~~~~~~~~~~~~~~~~~~~~~~l~f~~v~v~~P~~~e~~ 106 (1195)
..|...+++-+.+.++++|++|||...+.||...--+...-... ....++++++++++.+.+|.++...
T Consensus 4 ~~~k~~p~fp~l~~a~~pHi~sfnal~~~gll~~~v~~~~ek~~-----------~~~g~kis~~ve~i~iakP~l~~~~ 72 (1111)
T KOG0216|consen 4 NPPKDYPSFPELQDAASPHIDSFNALTNGGLLNAGVAGIAEKVP-----------LKAGDKISMKVESIQIAKPMLSDKV 72 (1111)
T ss_pred CCcccCccchhhhhhhhhhhccccchhhhhHHHHHhhchhhhcc-----------cccCCceeEEEEEEEecCCCCCccc
Confidence 35777788888999999999999998888876654332111110 0335678999999999999997643
Q ss_pred --CcccCCChHHHHhcCCccceeEEEEEEEEEeccCCCCcccccceeeEEEEecccceeeccCCccCCCCChhhhhhcCC
Q 000996 107 --GETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELGE 184 (1195)
Q Consensus 107 --~~~~~l~P~EcR~r~lTYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~eli~~gE 184 (1195)
...++|+|.|||+|++||+|.+.|+|.|.+++... ......+|.+||||+|++|||.|+||+||++++|
T Consensus 73 ~ss~~r~lyPaEcRqR~~TY~Gkl~v~v~wsVNg~~~---------~~e~~dlG~vPIMlrSklChL~g~sp~eLV~hkE 143 (1111)
T KOG0216|consen 73 HSSDTRKLYPAECRQRGLTYKGKLVVRVSWSVNGGHV---------VIEKRDLGHVPIMLRSKLCHLNGASPKELVKHKE 143 (1111)
T ss_pred cccccccccchhHhhccceecceEEEEEEEEECCeee---------eeeeeecCccceEEeccccccCCCChHHHhhccC
Confidence 45789999999999999999999999999998642 3467899999999999999999999999999999
Q ss_pred CCCCCCceEEEcCeeeEEeeeeeeecceEEEEE-----ecCCCcceEEEEEEEeecCCCCCCceEEEEEEecCCCCCCCC
Q 000996 185 CPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFK-----KRQPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSS 259 (1195)
Q Consensus 185 ~~~D~GGYFIING~ERVII~Qe~~s~N~~~~~~-----~~~~~~~~~~~~irs~~~~g~~~~~~~~v~~~~~~~~k~~~~ 259 (1195)
++.|+||||||||+||||.+-+-...|+|+++. +|+.+++.|.+.+||++++.+. +++.+++.+
T Consensus 144 e~~EmGGYFIvNGIEKvIRmLIm~RRNHPiAiIR~Sfk~RG~~yS~yGVsmRcVReDqSs----vtn~LHYLn------- 212 (1111)
T KOG0216|consen 144 ESSEMGGYFIVNGIEKVIRMLIMPRRNHPIAIIRPSFKDRGSSYSDYGVSMRCVREDQSS----VTNVLHYLN------- 212 (1111)
T ss_pred chhhcCcEEEEcChHHhhhhheeccCCCceEEechhhhhcCCCccccceEEEEecccccc----ceeEEEEec-------
Confidence 999999999999999999444444459999865 5778899999999999998654 333443332
Q ss_pred CcEEEEEecccccc--chHHHHHHHhcCCChHHHHHHhcccccchH-HHHHhHhhHhhh--hccCCHHHHHHHHhhcCcc
Q 000996 260 GQYIRATLPYIRTE--IPIIIVFRALGFVADKDILEHICYDFQDTQ-MMELLRPSLEEA--FVIQNQQVALDYIGKRGAT 334 (1195)
Q Consensus 260 ~~~i~v~i~~~~~~--IPl~ilLrALG~~sD~eI~~~i~~~~~~~~-~~~~l~~sl~e~--~~i~t~~~al~yig~r~~~ 334 (1195)
+|+..+++.+.+++ +|++++||||-.+||+||++.++.+...++ +.+.+..+|++. .++.||++|++|||++|++
T Consensus 213 nGtv~~~F~~rK~eylvPv~lILKAL~~tsDeEIf~~lv~g~~gdqfl~~rv~~mLr~v~ee~l~trtqcl~yLGs~FRa 292 (1111)
T KOG0216|consen 213 NGTVMFRFSHRKREYLVPVVLILKALTNTTDEEIFEGLVGGDEGDQFLTSRVELMLREVQEENLFTRTQCLQYLGSRFRA 292 (1111)
T ss_pred CCcEEEEEEEeeeeehhhHHHHHHHHhccCHHHHHHHHhCCccCceeHHHHHHHHHHHHhhcccccHHHHHHHHhhhhhh
Confidence 57889999987765 999999999999999999999987654333 333333333322 4578999999999999996
Q ss_pred c--CCCchhhHHHHHHHHHhcccCCCCCCCCcchhHHHHHHHHHHHHHHhhcCCCCCCCCCccccceecccchhHHHHHH
Q 000996 335 V--GVTRDKRIKYAKEILQKEMLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFR 412 (1195)
Q Consensus 335 ~--~~~~~~~~e~~~~~L~~~llpHl~~~~~~~~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~NKRv~l~G~Ll~~lfr 412 (1195)
+ ..++.++.|.|+++|+++++.||+++. +||.+|.+|+|||++++.|+|.+||+|+.+||+++++|+|++..++
T Consensus 293 Vl~~v~~~~D~evg~fILr~~VlvHLd~~~----DKF~lLifmiqKL~slv~ge~~~dnpDs~q~qEil~~ghl~~~~Lk 368 (1111)
T KOG0216|consen 293 VLDFVPEQPDLEVGRFILREYVLVHLDSDE----DKFNLLIFMIQKLYSLVDGECTPDNPDSPQNQEILLPGHLYGSILK 368 (1111)
T ss_pred hhcCCCCCchHHHHHHHHHhheEEEecccH----HHHHHHHHHHHHHHHHhcCCcCCCCCCChhhhhcccccchHHHHHH
Confidence 5 344578899999999999999999876 8999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhhhhccC-CC--C-c---hhhccc--ccccccccccccccccccccc--cccccccceeeccccCh
Q 000996 413 MLFRKLTRDVRAYVQKCVDNG-KD--V-N---LQFAIK--AKTITSGLKYSLATGNWGQAN--AAGTRAGVSQVLNRLTY 481 (1195)
Q Consensus 413 ~~l~~~~k~ik~~l~k~~~~~-~~--~-~---~~~~i~--~~~It~~i~~~~sTGnw~~~~--~~~~~sG~sq~l~r~N~ 481 (1195)
+.++.|++.++.++.+.+.+. .. + + +.+++. +..|+++|++||||||+.+.. ++||++|+|.+++|+|+
T Consensus 369 EriEe~l~~~~~~vr~~l~~~~~~~~~~~~~~i~~~~~r~~~~Ig~~me~fLsTGnl~s~sgldLqQ~sG~tv~AEriNf 448 (1111)
T KOG0216|consen 369 ERIEEWLRFISAQVRRDLYKLGFKEDFLDISAIRKVFMRTNGNIGRKMEYFLSTGNLVSRSGLDLQQTSGYTVVAERINF 448 (1111)
T ss_pred HHHHHHHHHHHHHHHHHHHhhcCCchhHhHHHHHHHHhhccccHHHHHHHHHhcCCeeeccchhhHhhcCcEEehhhhhH
Confidence 999999998888887776552 11 1 2 333442 478999999999999999988 78999999999999999
Q ss_pred hhhhccccccCC-CCCcCCCccccccccCCCcccccccCCCCCcccchhhcccccEEEccC-CCchhHHHHHHHhCCccc
Q 000996 482 ASTLSHLRRLNS-PIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITVG-SAAYPILEFLEEWGTENF 559 (1195)
Q Consensus 482 ls~lSh~Rrv~~-~~~~~~k~t~vR~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~It~~-~~~~~i~~~l~~~g~~~~ 559 (1195)
+++|||||.||+ ++|.++++|++|+|.|++|||+||||||||+||||+||||..|+|++. .+...+.++|.++||.|.
T Consensus 449 ~RflShFRavhRGa~f~~mrTTtvRKLlPEsWGFlCPVHTPDG~PCGlLnH~t~~c~I~t~~dd~s~ip~~L~~~Gm~p~ 528 (1111)
T KOG0216|consen 449 YRFLSHFRAVHRGAFFAEMRTTTVRKLLPESWGFLCPVHTPDGAPCGLLNHMTRTCRIVTRPDDVSFIPSILFELGMVPS 528 (1111)
T ss_pred HHHHHHHHHHhcccchhheeehhhHhhCchhhcccccccCCCCCchhHHHhhhhheeEeecCcchhhhhHHHHhcCCCch
Confidence 999999999997 899999999999999999999999999999999999999999999995 456789999999999986
Q ss_pred cccCCCCCCCceEEEECCEEEEEEcC--hHHHHHHHHhhhcc--CCCCcceEEEEecc-----CCeEEEEeCCCceeeeE
Q 000996 560 EEISPAVIPQATKIFVNGCWVGIHRD--PEMLVKTLRRLRRR--VDVNTEVGVVRDIR-----LKELRIYTDYGRCSRPL 630 (1195)
Q Consensus 560 ~~~~~~~~~~~~~V~lnG~~iG~~~~--~~~~~~~lr~~rr~--~~i~~~~~i~~~~~-----~~~i~I~td~GRl~RPl 630 (1195)
....... +.-++|++||+++|++.. ++.+++.||.+|.. +.||..++|.+.+. -|++||+|++||++|||
T Consensus 529 ~~~~~~G-~~l~~VlldGk~vG~~s~~~a~~i~~~lR~~Kv~~p~~iP~~leIg~Vp~s~~gqyPglyi~s~~aR~~RpV 607 (1111)
T KOG0216|consen 529 SHLVEAG-EPLYPVLLDGKVVGWVSSPLAKKIVDYLRYYKVEAPAVIPNDLEIGYVPTSTNGQYPGLYIFSGPARMIRPV 607 (1111)
T ss_pred hccccCC-CceeEEEECCEEEEeeccHHHHHHHHHHHHHhhcCcccCCCcceEeeeecCCCCCCceeEEecCchhhhheh
Confidence 5332222 236899999999999765 48999999999966 56999999976653 27999999999999999
Q ss_pred EEEecccchhhHHHHHHhhcCCCCCCCCccccccCCeEEEecccccccceeecccchhhcccCCCCccCCCceeeeecCC
Q 000996 631 FIVEKQRLLIKKRDIIALQQRESPEDGGWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHP 710 (1195)
Q Consensus 631 ~~v~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~g~iE~i~~~Ee~~~~Ia~~~~~~~~~~~~~~~~~~~~~th~EI~P 710 (1195)
.++. | +.+|||++.||.++.||+.+.++.+ .-+||.|++|
T Consensus 608 ~nl~------------------------~------~~~e~iG~fEQvym~i~~~~~e~~~----------~v~th~E~~p 647 (1111)
T KOG0216|consen 608 KNLS------------------------L------DSVEWIGPFEQVYMNIAIDPKEIFP----------DVTTHVELHP 647 (1111)
T ss_pred hccc------------------------c------CchhhcccHHHhhhhhccchhhcCC----------CcceeEEecc
Confidence 8775 2 4589999999999999999988865 4589999999
Q ss_pred CccccccccccCCCCCCCCCccccccccccCcccccceeeEEEeeccceeeecCCCceeecccccccccccCCCCceEEE
Q 000996 711 SLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIV 790 (1195)
Q Consensus 711 ~~ilsv~AslIPF~~hNqSpRn~yqc~M~KQa~g~~~~n~~~r~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~~~G~N~~V 790 (1195)
+.+||++|+||||+||||||||||||||+||+||+|.++++.|.|+++|+|++||.|+|++..++.+.++++|.|+||+|
T Consensus 648 t~~ls~~anliP~sD~NQSPRNmYQCQMgKQtmg~p~~a~~~radnklYrlqt~qsP~vr~~~y~~y~~d~yp~GtNaiV 727 (1111)
T KOG0216|consen 648 TGILSIVANLIPFSDHNQSPRNMYQCQMGKQTMGTPGHALRTRADNKLYRLQTPQSPIVRPELYDTYGMDDYPNGTNAIV 727 (1111)
T ss_pred cchHhHhhcCccccccCCCchhHHHhhhhhhhcCCccccchhcccCceEEecCCCCceeecccccccccccCCCCcceEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEecCCccCCCcEEEecceeecCceeEEEEEEEEechhccCCcccccccC-CCCCCCCCCCCCCcCCCCCCCCcCCCcE
Q 000996 791 AIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGR-PDRSNTMGMRHGSYDKLDDDGLAPPGTR 869 (1195)
Q Consensus 791 Av~s~~Gyn~EDaiiink~s~~rG~f~s~~~~~~~~~~~~~~~~~~e~~~~-p~~~~~~~~~~~~~~~Ld~dGi~~~G~~ 869 (1195)
||+|||||||||||||||+|+||||+++.+||+..+++.+.. .....|.. |... ...+||+||||.+|++
T Consensus 728 AVisyTgyDMeDAmiiNK~s~eRGf~~G~vykte~i~L~~~~-~r~~~F~~~p~~~--------~~~~ld~dgLP~~G~k 798 (1111)
T KOG0216|consen 728 AVISYTGYDMEDAMIINKSSYERGFAYGTVYKTEKIDLSKKR-SRSKHFGRSPGEP--------ELKKLDADGLPSIGQK 798 (1111)
T ss_pred EEEeecccChhhhhhhchhhhhccccceeEEeeeeechhhcc-cceeeeeeCCCCc--------cccccCCCCCCCCccc
Confidence 999999999999999999999999999999999998875421 11233432 3221 1678999999999999
Q ss_pred ECCCCEEEEEeCCCCccccccccCCCccceeeEEeecCCCcEEEEEEEEecCCCc--EEEEEEEeeecCCCCcccccccC
Q 000996 870 VSGEDVIIGKTTPISQDEAQGQASRYTRRDHSISLRHSETGMVDQVLLTTNADGL--RFVKVRVRSVRIPQIGDKFSSRH 947 (1195)
Q Consensus 870 v~~gdvli~k~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~g~v~~v~~~~~~~~~--~~v~v~~~~~R~~~iGDKf~sRH 947 (1195)
+..||+++....-- ..+..-.++...|+|+||.|.+..++.|. +.+.|++|..|+|.|||||||||
T Consensus 799 l~~~dp~~~y~d~~------------t~~~~~~~~~~~ep~~vd~vr~~~~~~~~~~k~~~i~~Ri~R~p~IGDKFsSRh 866 (1111)
T KOG0216|consen 799 LEYGDPYYAYFDEE------------TGKTRIKKYHGTEPGIVDEVRVLGNDMGDQEKCATITLRIPRNPIIGDKFSSRH 866 (1111)
T ss_pred ccCCCcEEEEEccc------------CCceEEEEecCCCCeeeEEEEEccccCCCccceEEEEEEecCCCcccchhhhhc
Confidence 99999999986521 13445568899999999999999887776 78999999999999999999999
Q ss_pred CCceeEEeeecCCCCCCCCCCCCCcEEeCCCCCCCCCchhhHHHHhhhHHhhhcCCCcccCCCC----CccHHHHHHHHH
Q 000996 948 GQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT----DVTVDNISKALH 1023 (1195)
Q Consensus 948 GqKGvvs~i~~~~dmPf~~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~~~tpF~----~~~~~~~~~~l~ 1023 (1195)
|||||||+.||.+|||||++|++||||||||||||||||||++|++|||+||++|..+|+|||. +..+++|+++|+
T Consensus 867 GQKGicS~~wP~~dmPFtesGm~PDii~NPH~FPSRMTIgM~iEs~AgK~~alhG~~~Datpf~~~E~~t~~dyfg~~L~ 946 (1111)
T KOG0216|consen 867 GQKGICSQKWPTIDMPFTESGMVPDIIINPHAFPSRMTIGMLIESMAGKAGALHGNAQDATPFIFSEENTAIDYFGEMLK 946 (1111)
T ss_pred cccccccccCCCCCCCccccCcCcceeeCCCCCcccccHHHHHHHHhchhhccccccccCCceeecCcccHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999986 356899999999
Q ss_pred HcCCCCCCeEEEeeCCCCceeeeeEeEeeeehhccccccCcccEEeccCCccccccCCCCcccCCCccccchhhhhHHHh
Q 000996 1024 KCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIA 1103 (1195)
Q Consensus 1024 ~~g~~~~G~~~l~~G~tG~~~~~~if~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a 1103 (1195)
++||||+|+|+||||.+|++|+++||+|+||||||+|||.||+|+|+|||++.+|+||++||+|+||+||||||||||||
T Consensus 947 ~~GyNyyGnE~~YSGv~G~e~~adIf~GvVyYQRLrHMv~DKfQVRstG~v~~~T~QPvkGRkr~GGiRfGEMERDali~ 1026 (1111)
T KOG0216|consen 947 KAGYNYYGNEPMYSGVDGREMRADIFFGVVYYQRLRHMVSDKFQVRSTGPVDSLTHQPVKGRKRGGGIRFGEMERDALIA 1026 (1111)
T ss_pred HcCcCccCCcccccccccceeeeeEEEeehhHHHHHHHhcceeeeeeccCccccccCCccCcccCCCccccchhhhhHhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hccHHHHHHhhhcCCCceeeeeccccCcceee--------ccccCceeeccCCCCCCceeecchHhhHHHHHHHHhCCCc
Q 000996 1104 HGASHFLKERLFDQSDAYRVHVCEHCGLIAIA--------NLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIA 1175 (1195)
Q Consensus 1104 ~Gas~~l~Erl~~~SD~~~~~vC~~cG~~~~~--------~~~~~~~~C~~C~~~~~~~~v~iPy~~kll~~EL~sm~i~ 1175 (1195)
||||++|||||+.|||...++||..||+++.. ........|+.|+. ..+..|.|||+||||..||.||||+
T Consensus 1027 HGtsfllqDRL~~~SD~~~a~vC~~cgsil~~~~~l~~~~~~~~~~~~C~~c~~-~~~~~v~~P~vfkYL~aEL~amnIk 1105 (1111)
T KOG0216|consen 1027 HGTSFLLQDRLLNSSDYTVAEVCRTCGSILSTQQKLIKEPGGSTSTVTCRSCDG-KGVTTVAMPYVFKYLTAELAAMNIK 1105 (1111)
T ss_pred cchHhhhhhhhccCcchhHHHHHHHhhhhhhhhhhhhcccCCCCCceeEEecCC-CceEEEEccHHHHHHHHHHhhCcee
Confidence 99999999999999999999999999998843 11234568999954 5889999999999999999999999
Q ss_pred eEEEec
Q 000996 1176 PRMLTK 1181 (1195)
Q Consensus 1176 ~~l~~~ 1181 (1195)
+++.++
T Consensus 1106 ~~l~l~ 1111 (1111)
T KOG0216|consen 1106 MRLDLE 1111 (1111)
T ss_pred EEeccC
Confidence 999864
No 5
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]
Probab=100.00 E-value=1e-247 Score=2243.16 Aligned_cols=1020 Identities=36% Similarity=0.553 Sum_probs=919.3
Q ss_pred chhhhhhhhhcccCccchHHHHHHHHHHHHHhhHHHHHcccCCeeeCCCCCCCCCCCCCCCCceEEEEEeEEEEccCccc
Q 000996 24 TQEDAWAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQSDFAETIYKISFGQIYLSKPMMT 103 (1195)
Q Consensus 24 ~~~~~~~~i~~~f~~~~Lv~~qi~SFn~Fi~~gL~~ii~~~~pI~~~~~~~~~~~~~~~~~~~~~~l~f~~v~v~~P~~~ 103 (1195)
..++.|++++++|+.++|+++|++|||+|+.+||++++++++||+. ...++.|+|.++++++|
T Consensus 10 r~r~~~~~i~~~~~~p~Lv~~QldSyn~ff~~gLq~i~~~i~PI~~--------------~~~~~~Lef~~~~l~~p--- 72 (1060)
T COG0085 10 RIRDSFGKIPEFLDLPNLVEIQLDSYNAFFLEGLQEVFREIFPIES--------------YNGNTELEYGSYRLGEP--- 72 (1060)
T ss_pred ccccchhhcccccCCccHHHHHHHHHHHHHHHHHHHHHHhcCceec--------------CCCCEEEEEEEEEecCC---
Confidence 5678999999999999999999999999999999999999999973 24679999999999998
Q ss_pred cCCCcccCCChHHHHhcCCccceeEEEEEEEEEeccCCCCcccccceeeEEEEecccceeeccCCccCCCCChhhhhhcC
Q 000996 104 ESDGETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELG 183 (1195)
Q Consensus 104 e~~~~~~~l~P~EcR~r~lTYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~eli~~g 183 (1195)
.+++|.|||+|++||||||+|++++.++++.+ .+++++|++|+|||||+
T Consensus 73 ------~k~~p~EcR~R~lTYsapLyv~lrlv~~~~~e-------~~k~~eV~iG~iPlMt~------------------ 121 (1060)
T COG0085 73 ------PKFYPEECRLRGLTYSAPLYVKLRLVVNETGE-------EIKEQEVYMGDIPLMTR------------------ 121 (1060)
T ss_pred ------CCCCHHHHHhcCCccccceEEEEEEEECCccc-------ccccceEEeccCcEecC------------------
Confidence 35799999999999999999999999887643 15678999999999998
Q ss_pred CCCCCCCceEEEcCeeeEEeeeeeeecceEEEEEecCCC-cceEEEEEEEeecCCCCCCceEEEEEEecCCCCCCCCCcE
Q 000996 184 ECPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPN-KYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSSGQY 262 (1195)
Q Consensus 184 E~~~D~GGYFIING~ERVII~Qe~~s~N~~~~~~~~~~~-~~~~~~~irs~~~~g~~~~~~~~v~~~~~~~~k~~~~~~~ 262 (1195)
||||||||+|||||+|+++|||++|..+..... +..|+|.+ ++.+|+|...++. .+..
T Consensus 122 ------gGyFIINGsERVIVsQ~~rSPgvif~~~~~k~~~~~~~~a~v--Ip~rG~wl~~e~d-------------~~d~ 180 (1060)
T COG0085 122 ------GGYFIINGTERVIVSQEHRSPGVIFVEKKDKTGSKVLYVARV--IPYRGSWLEFEFD-------------PKDN 180 (1060)
T ss_pred ------CcEEEECCeEEEEEEEeecCCCeEEecccccCCcceEEEEEE--ecCCcceEEEEEc-------------cCcc
Confidence 999999999999999999999998876543222 34566666 5568999654442 1356
Q ss_pred EEEEeccccccchHHHHHHHhcCCChHHHHHHhccc----ccchHHHHHhHhhHhhh--hccCCHHHHHHHHhhcCcccC
Q 000996 263 IRATLPYIRTEIPIIIVFRALGFVADKDILEHICYD----FQDTQMMELLRPSLEEA--FVIQNQQVALDYIGKRGATVG 336 (1195)
Q Consensus 263 i~v~i~~~~~~IPl~ilLrALG~~sD~eI~~~i~~~----~~~~~~~~~l~~sl~e~--~~i~t~~~al~yig~r~~~~~ 336 (1195)
++++++..+ +||+++||||||+++|+||++.+..+ ....+..+.+.+++++. ..+ +...|++||+++|....
T Consensus 181 ~~~rId~~r-kiPvtilLRALG~~tDeeI~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~i-~~~~a~~~i~~r~~~~~ 258 (1060)
T COG0085 181 LYVRIDRKR-KIPVTILLRALGLETDEEIIEAFGGDELTDLVPPEGEEALLEIYEEAKGEKI-TARNALELIGSRVFVVK 258 (1060)
T ss_pred EEEEeeeEE-EeeHHHHHHHhCCCcHHHHHHHhcccccccccchHHHHHhHHHHhhccCCCc-chHHHHHHHhccccccc
Confidence 899998743 89999999999999999999999763 11233445555555554 233 34449999999986542
Q ss_pred C--CchhhHHHHHHHHHhcccCCCCCC---CC-cchhHHHHHHHHHHHHHHhhcCCCCCCCCCccccceecccchhHHHH
Q 000996 337 V--TRDKRIKYAKEILQKEMLPHVGTG---DF-CETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGL 410 (1195)
Q Consensus 337 ~--~~~~~~e~~~~~L~~~llpHl~~~---~~-~~~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~NKRv~l~G~Ll~~l 410 (1195)
. ....+.+.++.++.+++||||+.. .. ....|+.+|+.|+++|+.+..|.+.+||+|||+||||+++|+||+++
T Consensus 259 ~~~~~~gR~k~~~~vl~~~~L~hL~~~~~~~~l~~~~k~~di~~mi~~l~~L~~G~~~~DDiDHlGNKRlrlvGeLl~n~ 338 (1060)
T COG0085 259 RYDAKEGRYKRAKYVLDKELLPHLGEAGERYDLSRVGKAKDIIAMIKYLIELRLGKGEEDDIDHLGNRRLRLVGELLENL 338 (1060)
T ss_pred ccccchhhhhhhhhhhhhhHHhhhcccccccchhhhHHHHHHHHHHHHHHHHhcCCCCCCCCccccccchhhHHHHHHHH
Confidence 2 356678999999999999999973 22 24468889999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhhhhccCCCCchhhcccccccccccccccccccccccccccccccceeeccccChhhhhccccc
Q 000996 411 FRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRR 490 (1195)
Q Consensus 411 fr~~l~~~~k~ik~~l~k~~~~~~~~~~~~~i~~~~It~~i~~~~sTGnw~~~~~~~~~sG~sq~l~r~N~ls~lSh~Rr 490 (1195)
||.+|.+|++.++++|++...+ ..+..++.||.++.+|++||||+ ++||||+|||+||+|+||||||
T Consensus 339 fR~gl~rmer~ikerm~~~~~r------~~i~p~dlIn~k~~~Alitgffg-------~sqlSQfmDqtNpLSeLSHkRR 405 (1060)
T COG0085 339 FRVGLSRMERDVKERLEKADKR------DTLVPQDLINAKPIHALITGFFG-------RSQLSQFMDQTNPLSELSHKRR 405 (1060)
T ss_pred HHHHHHHHHHHHHHHHhhhhhh------hccCchhhcchhHHHHHHhcccc-------ccceeeeeecCChHHhhhhhhc
Confidence 9999999999999999986432 23445678899999999999999 7999999999999999999999
Q ss_pred cCC-CCCcCCCccccccccCCCcccccccCCCCCcccchhhcccccEEEc-cCCCchhHHHHHHH-hCCccccccCCCCC
Q 000996 491 LNS-PIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYIT-VGSAAYPILEFLEE-WGTENFEEISPAVI 567 (1195)
Q Consensus 491 v~~-~~~~~~k~t~vR~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~It-~~~~~~~i~~~l~~-~g~~~~~~~~~~~~ 567 (1195)
|++ +++++++.++||+||||||||+||+|||||+|||||||||++|+|+ .+++++|+++++.. +|+.++..++...
T Consensus 406 IsAlgLsRera~fEvRDvHpTHyGRiCPiETPEGpNiGLI~sLA~~A~Vn~~Gf~etPy~kv~~g~~~v~~i~~l~~~~- 484 (1060)
T COG0085 406 LSALGLSRERAGFEVRDVHPTHYGRICPIETPEGPNIGLIKSLALYARINEYGFLETPYRKVLDGSLVVDEIEYLSADE- 484 (1060)
T ss_pred eeccCcCccCCCCcccccCcccccccCCCCCCCCcchhHHHHHHHHeEecccCCCCCceEEEEeccccccceeeecccc-
Confidence 999 9999999999999999999999999999999999999999999999 69999999998884 8888877554433
Q ss_pred CCceEEEECCEEEEEEcChHHHHHHHHhhhccCCCCcceEEEEeccCC----eEEEEeCCCceeeeEEEEecccchhhHH
Q 000996 568 PQATKIFVNGCWVGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDIRLK----ELRIYTDYGRCSRPLFIVEKQRLLIKKR 643 (1195)
Q Consensus 568 ~~~~~V~lnG~~iG~~~~~~~~~~~lr~~rr~~~i~~~~~i~~~~~~~----~i~I~td~GRl~RPl~~v~~~~~~~~~~ 643 (1195)
..|++||.++|.++++..|++.+|.+|| + +..+++++...... ++++.+|.||.+||++.+++++..+..+
T Consensus 485 ---~~~~~~~~~~~~~~~~~~~~~~~~~~R~-~-~~~~~~~~~~~~~~~~dv~~~~~~~~~~~~~P~l~~dd~~~~l~~~ 559 (1060)
T COG0085 485 ---EDVYVIGQANGTLDEPGELVEELVECRR-G-GSGEVSVADPEGVDYMDVSPKQVVSVGRSLIPFLEHDDANRALMGS 559 (1060)
T ss_pred ---cceEEEeEeeeeecCCCceeeeEEEEee-c-ccccceeecCccccceeccceEEeccccccCceeEEcCchHhhhhh
Confidence 6899999999999999999999999999 6 88888888776655 8999999999999999999999999999
Q ss_pred HHHHhhcC-CCCCCCCccccccCCeEEEecccccccceeecccchhhcccCCCCccCCCceeeeecCCCccccccccccC
Q 000996 644 DIIALQQR-ESPEDGGWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHPSLILGVCASIIP 722 (1195)
Q Consensus 644 ~~~~l~~~-~~~~~~~~~~l~~~g~iE~i~~~Ee~~~~Ia~~~~~~~~~~~~~~~~~~~~~th~EI~P~~ilsv~AslIP 722 (1195)
+++++..+ .. +|.+|+..| +||++|.|+++++||..+. .+||+|++|..|+|++|++||
T Consensus 560 ~mqr~~~~l~~----~~~~lv~tG-~E~~~a~e~~~~~ia~~~~---------------~~~~ve~~~~~I~~~~~~~~~ 619 (1060)
T COG0085 560 NMQRQAVPLLR----TEAPLVGTG-MEYLDAEDSGAAVIAKRPG---------------VVTHVEISPIVILGIEASLIP 619 (1060)
T ss_pred hhhhhcccccc----cccccccCC-ceeeccccccceeEeccCC---------------cEEEEeeeeeEEEeeccccCC
Confidence 99988766 34 899999999 9999999999999997653 489999999999999999999
Q ss_pred CCCCCCCCccccccccccCcccccceeeEEEeeccceeeecCCCceeecccccccccccCCCCceEEEEEEecCCccCCC
Q 000996 723 FPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQED 802 (1195)
Q Consensus 723 F~~hNqSpRn~yqc~M~KQa~g~~~~n~~~r~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~~~G~N~~VAv~s~~Gyn~ED 802 (1195)
|+||||||||||||+|+||++|++.+|+..|.|+..|.++|||.|+|+| +|+|+|||++||||||+||||||
T Consensus 620 ~~~~n~~~~n~~~~~~~~Q~~~~~~~~~~~~~d~~~~~~~~~~~P~~~~--------~e~~~GqN~~VA~m~~~GYn~ED 691 (1060)
T COG0085 620 YPEHNQSPYNLYKFARSNQATGINQRPLVKRGDTVEKGLVYADGPSVDT--------GELALGQNALVAFMPWNGYNYED 691 (1060)
T ss_pred ccccCcChHHHHHHhhhhcccCCCcccceeccccccccceecCCCcccc--------CcccCCceeEEEEecccCcChhH
Confidence 9999999999999999999999999999999999999999999999998 89999999999999999999999
Q ss_pred cEEEecceeecCceeEEEEEEEEechhccCCcccccccCCCCCCCCCCCCCCcCCCCCCCCcCCCcEECCCCEEEEEeCC
Q 000996 803 SVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP 882 (1195)
Q Consensus 803 aiiink~s~~rG~f~s~~~~~~~~~~~~~~~~~~e~~~~p~~~~~~~~~~~~~~~Ld~dGi~~~G~~v~~gdvli~k~~~ 882 (1195)
||||||++++||+|||+||++|++++++++.+..|.+++|+.. ...|++||+|||++||++|++|||||||++|
T Consensus 692 Aiiin~~~v~~~~~ts~~~~~~~~~~r~~~~g~e~~~~iP~~~------e~~~~~Lde~Gii~ig~~V~~gdilvgk~tP 765 (1060)
T COG0085 692 AIIISERSVERDLFTSIHIEEYETEARDTKLGPEEIRDIPNVS------EEALRNLDEDGIIRIGAEVKGGDILVGKVTP 765 (1060)
T ss_pred heecccchhhcCCceEEEEEEEeeeeeccCCCccccccCCCcC------HHHHhcCCccCccccccEEcCCCEEEEeeCC
Confidence 9999999999999999999999999999988877888899864 2348999999999999999999999999999
Q ss_pred CCccccccc-----cCCCccceeeEEeecCCCcEEEEEEEEecCC----CcEEEEEEEeeecCCCCcccccccCCCceeE
Q 000996 883 ISQDEAQGQ-----ASRYTRRDHSISLRHSETGMVDQVLLTTNAD----GLRFVKVRVRSVRIPQIGDKFSSRHGQKGTV 953 (1195)
Q Consensus 883 ~~~~~~~~~-----~~~~~~~~~s~~~~~~~~g~v~~v~~~~~~~----~~~~v~v~~~~~R~~~iGDKf~sRHGqKGvv 953 (1195)
+...+.... ....+.||+|++++++++|+|+.|.++++++ +.++|||++|+.|.|++||||||||||||||
T Consensus 766 ~~~~~~~~ee~ll~i~~ek~rdtsl~~~~g~~G~V~~V~~~~~~~~~~g~~~~vkV~v~~~R~~~~GDK~a~RHG~KGVi 845 (1060)
T COG0085 766 KGETELTPEERLLRIFGEKVRDTSLRVPHGEEGIVDDVQVFTREDGDPGVNKLVKVYVAQKRKPQIGDKMAGRHGNKGVV 845 (1060)
T ss_pred CCCCCCCchhhhhccccceeeccceeecCCCCeEEEEEEEEeccCCCcCceEEEEEEEEEeccCCccccccccCCCCcee
Confidence 985332111 1122379999999999999999999999877 7899999999999999999999999999999
Q ss_pred EeeecCCCCCCCCCCCCCcEEeCCCCCCCCCchhhHHHHhhhHHhhhcCCCcccCCCCCccHHHHHHHHHHcCCCCCCeE
Q 000996 954 GMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFE 1033 (1195)
Q Consensus 954 s~i~~~~dmPf~~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~~~tpF~~~~~~~~~~~l~~~g~~~~G~~ 1033 (1195)
|+|||+|||||++||++||||+|||||||||||||++|+++||||++.|...|+|||++.+.+++.+.|.++||+++|++
T Consensus 846 s~i~p~eDMPf~~~G~~~DiilNP~gvPSRM~iGqilE~~lG~a~~~~G~~~~~~~F~g~~~~~~~~~l~~~g~~~~Gk~ 925 (1060)
T COG0085 846 SKIVPQEDMPFLEDGTPPDIILNPLGVPSRMNIGQILETHLGKAAALLGIPVDTPVFDGAPEEDIRELLKEAGFPYSGKE 925 (1060)
T ss_pred eeecCcccCCcCCCCCcccEEECCCCCCccccHHHHHHHHHHHHHHhcCceeccCCcCCCCHHHHHHHHHHcCCCCCCCE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeeCCCCceeeeeEeEeeeehhccccccCcccEEeccCCccccccCCCCcccCCCccccchhhhhHHHhhccHHHHHHh
Q 000996 1034 TMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKER 1113 (1195)
Q Consensus 1034 ~l~~G~tG~~~~~~if~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~Er 1113 (1195)
+||||+||++|+++||||++|||||+|||+|||||||||||+.|||||++||+|.|||||||||||||+|||||++||||
T Consensus 926 ~lydG~TGe~~~~~i~vG~~Y~~kL~HmV~dK~HaRs~GP~s~lT~QP~~Gka~~GG~RfGEME~~aL~ayGAa~~LqE~ 1005 (1060)
T COG0085 926 VLYDGRTGEPFDAPIFVGVMYYQKLHHMVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQER 1005 (1060)
T ss_pred EeecCCCCCcccccEEEEehHHHhHHhhhcccceeeccCCceeeecCCCCcccccCCccccchHHHHHHHHhHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcCCCceeeeeccccCcceeeccccCceeeccCCCCCCceeecchHhhHHHHHHHHhCCCceEEEeccC
Q 000996 1114 LFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKED 1183 (1195)
Q Consensus 1114 l~~~SD~~~~~vC~~cG~~~~~~~~~~~~~C~~C~~~~~~~~v~iPy~~kll~~EL~sm~i~~~l~~~~~ 1183 (1195)
|+.+|| +.||++++. .|+.|+ .++.++.||||||||++||+||||++++.+++.
T Consensus 1006 L~~~SD-------~~~G~~~~y-------~~~v~g--~~~~~~~ip~sFk~L~~El~sl~i~~~l~~~~~ 1059 (1060)
T COG0085 1006 LTVKSD-------DVCGRIKIY-------ECIVKG--ENIPEVGIPESFKVLLKELRSLGIDVRLELEDG 1059 (1060)
T ss_pred hhccch-------hcccchhhh-------cCcccC--CCCCCCCCCHHHHHHHHHHHHCCCceEEeecCC
Confidence 999999 459999854 499998 589999999999999999999999999998763
No 6
>cd00653 RNA_pol_B_RPB2 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.
Probab=100.00 E-value=2.7e-225 Score=2105.69 Aligned_cols=860 Identities=51% Similarity=0.786 Sum_probs=776.9
Q ss_pred hHHHHHHHHHHHHHhhHHHHHcccCCeeeCCCCCCCCCCCCCCCCceEEEEEeEEEEccCccccCCCcccCCChHHHHhc
Q 000996 41 LVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQSDFAETIYKISFGQIYLSKPMMTESDGETATLFPKAARLR 120 (1195)
Q Consensus 41 Lv~~qi~SFn~Fi~~gL~~ii~~~~pI~~~~~~~~~~~~~~~~~~~~~~l~f~~v~v~~P~~~e~~~~~~~l~P~EcR~r 120 (1195)
|++||++|||+|+++||++++++++||++.. .+..+.++|+++++++|.+.+. +...+++|+|||+|
T Consensus 1 Lv~~qi~SFn~Fl~~gl~~ii~~~~~i~~~~------------~~~~~~l~f~~i~i~~P~~~~~-~~~~~l~P~ecRlr 67 (866)
T cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTD------------DDGRLKLKFGDIYLGKPKVEEG-GVTRKLTPNECRLR 67 (866)
T ss_pred CchhHHHHHHHHHHHHHHHHHHhcCCeeecc------------CCCeEEEEEEEEEECCcccccc-CccccCCHHHHHhh
Confidence 6899999999999999999999999998642 1357899999999999998766 56788999999999
Q ss_pred CCccceeEEEEEEEEEeccCCCCcccccceeeEEEEecccceeeccCCccCCCCChhhhhhcCCCCCCCCceEEEcCeee
Q 000996 121 NLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIINGSEK 200 (1195)
Q Consensus 121 ~lTYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~eli~~gE~~~D~GGYFIING~ER 200 (1195)
++||+|+|+|++.++..+.. ....+++.+|+|||||+|++|||++++++|+++.||||.||||||||||+||
T Consensus 68 ~lTYs~~l~v~i~~~~~~~~--------~~~~~~v~iG~iPIMv~S~~C~L~~~~~~el~~~~E~p~d~GGYFIInG~Ek 139 (866)
T cd00653 68 DLTYSAPLYVDIRLTVNDKG--------KIKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEK 139 (866)
T ss_pred CCccceeEEEEEEEEEecce--------eEEEEEEEEeeCCcccCcccccccCCCHHHHHhcCCCcccCCCEEEECCcee
Confidence 99999999999999876532 1245789999999999999999999999999999999999999999999999
Q ss_pred EEeeeeeeecceEEEEEecCCCcceEEEEEEEeecCCCCCCceEEEEEEecCCCCCCCCCcEEEEEeccccccchHHHHH
Q 000996 201 VLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVF 280 (1195)
Q Consensus 201 VII~Qe~~s~N~~~~~~~~~~~~~~~~~~irs~~~~g~~~~~~~~v~~~~~~~~k~~~~~~~i~v~i~~~~~~IPl~ilL 280 (1195)
||++|+++++|+++++ .....+.+.++|.+..+....+.+.++.... ...++++++..+
T Consensus 140 VIi~qi~~~~N~~~~~----~~~~~~~~~~~s~~~~~~~~~s~~~~~~~~~--------~~~i~~~i~~~~--------- 198 (866)
T cd00653 140 VIINQEQRSPNVIIVE----DSKGKRIYTKTSIPSYSPYRGSWLEVKSDKK--------KDRIYVRIDLKR--------- 198 (866)
T ss_pred EEEEEEeccCCeEEEe----cCCCcEEEEEEEccCCCcCccEEEEEEEccC--------CCeEEEEecccC---------
Confidence 9999999999999986 2223356777776653222222233332110 235676666532
Q ss_pred HHhcCCChHHHHHHhcccccchHHHHHhHhhHhhhhccCCHHHHHHHHhhcCcccCCCchhhHHHHHHHHHhcccCCCCC
Q 000996 281 RALGFVADKDILEHICYDFQDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGATVGVTRDKRIKYAKEILQKEMLPHVGT 360 (1195)
Q Consensus 281 rALG~~sD~eI~~~i~~~~~~~~~~~~l~~sl~e~~~i~t~~~al~yig~r~~~~~~~~~~~~e~~~~~L~~~llpHl~~ 360 (1195)
+++|+.|||++|
T Consensus 199 ----------------------------------------~~~al~~ig~~~---------------------------- 210 (866)
T cd00653 199 ----------------------------------------QEEALKYIGKRF---------------------------- 210 (866)
T ss_pred ----------------------------------------HHHHHHHHHHHH----------------------------
Confidence 778999999984
Q ss_pred CCCcchhHHHHHHHHHHHHHHhhcCCCCCCCCCccccceecccchhHHHHHHHHHHHHHHHHHHHhhhhhccCCCCchhh
Q 000996 361 GDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQF 440 (1195)
Q Consensus 361 ~~~~~~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~NKRv~l~G~Ll~~lfr~~l~~~~k~ik~~l~k~~~~~~~~~~~~ 440 (1195)
.+|++|++||+.+..|.+.+||+|||+||||+++|+||+.+|++.|+++++.++..+.+...+.+.+++..
T Consensus 211 ---------~~L~~Mi~kLl~~~~g~~~~Dd~D~~~NkRv~~~G~Ll~~lfr~~l~~~~~~~k~~l~~~~~~~~~~~~~~ 281 (866)
T cd00653 211 ---------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQL 281 (866)
T ss_pred ---------HHHHHHHHHHHHHhcCCCCCCCchhhhCeEEeeHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcccccCHHH
Confidence 68999999999999999999999999999999999999999999999999999999988766555667778
Q ss_pred cccccccccccccccccccccccccccccccceeeccccChhhhhccccccCC-CCCcCCCccccccccCCCcccccccC
Q 000996 441 AIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS-PIGREGKLAKPRQLHNSQWGMMCPAE 519 (1195)
Q Consensus 441 ~i~~~~It~~i~~~~sTGnw~~~~~~~~~sG~sq~l~r~N~ls~lSh~Rrv~~-~~~~~~k~t~vR~Lhps~wG~iCPve 519 (1195)
+++++.||++|++||+||||.++++.+|++|+||+|||+||+++|||+||||+ ++++++|+++||+||||||||+||+|
T Consensus 282 ~~~~~~It~~i~~~~~TGnw~~~~~~~~~~Gvsq~ldr~N~ls~lsh~Rrv~~~~~~~~~k~~~~R~lhps~~G~iCPve 361 (866)
T cd00653 282 LINSKPITSGIKEFLATGNWGSKRFLMQRSGLSQVLDRLNPLSELSHKRRISSLGLFRERKGFEVRDLHPSHWGRICPIE 361 (866)
T ss_pred hccchHHHHHHHHHhhcCCccccccccccceEEEEcccCCHHHHHHhhhhcccccccccccCCcccccCcccCCccCCCC
Confidence 88888999999999999999999888899999999999999999999999999 99999999999999999999999999
Q ss_pred CCCCcccchhhcccccEEEccCCCchhHHHHHHHhCCccccccCCCCCCCceEEEECCEEEEEEcChHHHHHHHHhhhcc
Q 000996 520 TPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKTLRRLRRR 599 (1195)
Q Consensus 520 TPEG~~cGLvk~LA~~a~It~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~lr~~rr~ 599 (1195)
||||++||||||||++|+|+
T Consensus 362 TPEG~~cGLv~~LA~~a~Is------------------------------------------------------------ 381 (866)
T cd00653 362 TPEGENCGLVKNLALMARIS------------------------------------------------------------ 381 (866)
T ss_pred CCCCccccchhhhhceEeee------------------------------------------------------------
Confidence 99999999999999999986
Q ss_pred CCCCcceEEEEeccCCeEEEEeCCCceeeeEEEEecccchhhHHHHHHhhcCCCCCCCCccccccCCeEEEecccccccc
Q 000996 600 VDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRESPEDGGWHDLVAKGFIEYIDTEEEETT 679 (1195)
Q Consensus 600 ~~i~~~~~i~~~~~~~~i~I~td~GRl~RPl~~v~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~g~iE~i~~~Ee~~~ 679 (1195)
||++||+++|++
T Consensus 382 ------------------------Gr~~rP~~~v~~-------------------------------------------- 393 (866)
T cd00653 382 ------------------------GRIERPYRIVEK-------------------------------------------- 393 (866)
T ss_pred ------------------------eEeeeeEEEecc--------------------------------------------
Confidence 899999997741
Q ss_pred eeecccchhhcccCCCCccCCCceeeeecCCCccccccccccCCCCCCCCCccccccccccCcccccceeeEEEeeccce
Q 000996 680 MISMTINDLVQARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAY 759 (1195)
Q Consensus 680 ~Ia~~~~~~~~~~~~~~~~~~~~~th~EI~P~~ilsv~AslIPF~~hNqSpRn~yqc~M~KQa~g~~~~n~~~r~D~~~~ 759 (1195)
.+||+||+|.+|||++||+|||+||||||||||||||+|||||++++|++.|+|++.|
T Consensus 394 ----------------------~~th~ei~~~~~ls~~asliPf~~hNqspRn~~~~~M~kQa~g~~~~n~~~r~d~~~~ 451 (866)
T cd00653 394 ----------------------EVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLY 451 (866)
T ss_pred ----------------------ceEEEEeCccceeeeeeeccCCCCcccccchhhhhcccCCccCchhccccccccchhe
Confidence 3899999999999999999999999999999999999999999999999999999999
Q ss_pred eeecCCCceeecccccccccccCCCCceEEEEEEecCCccCCCcEEEecceeecCceeEEEEEEEEechhccCCcccccc
Q 000996 760 VLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDF 839 (1195)
Q Consensus 760 ~l~ypQ~Plv~t~~~~~~~~~~~~~G~N~~VAv~s~~Gyn~EDaiiink~s~~rG~f~s~~~~~~~~~~~~~~~~~~e~~ 839 (1195)
+|+|||+|||+|+..+.++++++|+|+||+||||||+||||||||||||+|+|||+|||+||++|++++++...+..+.+
T Consensus 452 ~l~~pq~plv~T~~~~~~~~~~~~~G~N~~VAv~~y~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~~~~ 531 (866)
T cd00653 452 LLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEIT 531 (866)
T ss_pred eeccCCCCccccchHHHhCCCccCCCceEEEEEeccccccccceeeeehhhhhcCceeEEEEEEEEEEEEecCCCcceEe
Confidence 99999999999999999999999999999999999999999999999999999999999999999999876544333333
Q ss_pred cCCCCCCCCCCCCCCcCCCCCCCCcCCCcEECCCCEEEEEeCCCCccccc--cccCCCccceeeEEeecCCCcEEEEEEE
Q 000996 840 GRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ--GQASRYTRRDHSISLRHSETGMVDQVLL 917 (1195)
Q Consensus 840 ~~p~~~~~~~~~~~~~~~Ld~dGi~~~G~~v~~gdvli~k~~~~~~~~~~--~~~~~~~~~~~s~~~~~~~~g~v~~v~~ 917 (1195)
. +. ....+...|++||+||||++|++|++||+||||++|...++.. ........+|+|++++.+++|+|++|.+
T Consensus 532 ~-~~---~~~~~~~~~~~ld~dGi~~~g~~v~~gd~li~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~v~~v~~ 607 (866)
T cd00653 532 R-GD---IPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKI 607 (866)
T ss_pred c-CC---CCCCChHHhhccCCCCCcCCCCEecCCCEEEEEecCcccccccccccccCCcceEEEEEecCCCceEEEEEEE
Confidence 2 11 1112234599999999999999999999999999987533210 1112234799999999999999999999
Q ss_pred Ee---cCCCcEEEEEEEeeecCCCCcccccccCCCceeEEeeecCCCCCCCCCCCCCcEEeCCCCCCCCCchhhHHHHhh
Q 000996 918 TT---NADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIM 994 (1195)
Q Consensus 918 ~~---~~~~~~~v~v~~~~~R~~~iGDKf~sRHGqKGvvs~i~~~~dmPf~~~G~~pDiIiNPh~~PSRMtiGql~E~~~ 994 (1195)
+. +.++...|+|++|+.|+|+||||||||||||||||+|||+||||||+||++|||||||||||||||||||+|+++
T Consensus 608 ~~~~~~~~~~~~v~v~~r~~R~p~iGDKfssRhGqKGv~s~i~~~~dmPf~~~G~~pDiIiNPh~~PSRMtiGql~E~~~ 687 (866)
T cd00653 608 FSRELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLL 687 (866)
T ss_pred eccccCCCCcEEEEEEEeEEecCCcccccccccCCCcEEEEEeccccCCcccCCCCCcEEecCCcCcccccHHHHHHHHH
Confidence 87 567788999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHhhhcCCCcccCCCCCccHHHHHHHHHHcCCCCCCeEEEeeCCCCceeeeeEeEeeeehhccccccCcccEEeccCCc
Q 000996 995 GKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPV 1074 (1195)
Q Consensus 995 gk~~~~~g~~~~~tpF~~~~~~~~~~~l~~~g~~~~G~~~l~~G~tG~~~~~~if~G~~yy~rL~Hmv~dK~~~R~~Gp~ 1074 (1195)
||||++.|.+.|+|||++...+++.+.|.++||+++|+|+||||+||++|+++||+|++|||||+|||+||+|||++||+
T Consensus 688 gk~~~~~g~~~d~t~f~~~~~~~~~~~l~~~g~~~~G~e~~y~g~tG~~~~~~if~G~~yyqrL~Hmv~DK~~~R~~Gp~ 767 (866)
T cd00653 688 GKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPY 767 (866)
T ss_pred HHHHHhcCCcccccccCcchHHHHHHHHHHcCCCCCCcEEEEcCCCCCCcccceEEeehhhhhhhhhhchhhhhcccCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccCCCCcccCCCccccchhhhhHHHhhccHHHHHHhhhcCCCceeeeeccccCcceeeccccCceeeccCCCCCCce
Q 000996 1075 QILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIV 1154 (1195)
Q Consensus 1075 ~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~Erl~~~SD~~~~~vC~~cG~~~~~~~~~~~~~C~~C~~~~~~~ 1154 (1195)
+.|||||++||+|+|||||||||||||+|||||++|+|||+.+||++.++||..||.+++.+ +|+.|+++.++.
T Consensus 768 ~~lT~QP~~Gr~~~GG~R~GEMErd~lia~Gas~~l~erl~~~SD~~~~~vc~~cg~i~~~~------~c~~c~~~~~~~ 841 (866)
T cd00653 768 SLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSAN------LCRLCKKGTNIS 841 (866)
T ss_pred chhccCcCccccccCCeEEEEEehhhhhhhhhHHHHHHHHhcCCccceEEEeccCccccccc------ccccccCCCcee
Confidence 99999999999999999999999999999999999999999999999999999999999542 499999999999
Q ss_pred eecchHhhHHHHHHHHhCCCceEEE
Q 000996 1155 QVHIPYACKLLFQELMAMAIAPRML 1179 (1195)
Q Consensus 1155 ~v~iPy~~kll~~EL~sm~i~~~l~ 1179 (1195)
++.+|||||||+|||+||||++++.
T Consensus 842 ~~~ipy~~kll~~EL~sm~i~~~~~ 866 (866)
T cd00653 842 KVGIPYAFKLLFQELQSMNIDPRLK 866 (866)
T ss_pred ecCCCHHHHHHHHHHHHCCcceEeC
Confidence 9999999999999999999999973
No 7
>TIGR02013 rpoB DNA-directed RNA polymerase, beta subunit. This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit.
Probab=100.00 E-value=6e-225 Score=2108.70 Aligned_cols=927 Identities=28% Similarity=0.432 Sum_probs=802.6
Q ss_pred hhhhhhhcccCccchHHHHHHHHHHHHH----------hhHHHHHcccCCeeeCCCCCCCCCCCCCCCCceEEEEEeEEE
Q 000996 27 DAWAVISAYFEEKGLVRQQLDSFDEFIQ----------NTMQEIVDESADIEIRPESQHNPGQQSDFAETIYKISFGQIY 96 (1195)
Q Consensus 27 ~~~~~i~~~f~~~~Lv~~qi~SFn~Fi~----------~gL~~ii~~~~pI~~~~~~~~~~~~~~~~~~~~~~l~f~~v~ 96 (1195)
..|+.++.+|+.++|++||++|||+||+ +||++++++++||+.. +..+.|+|.+++
T Consensus 6 ~~~~~~~~~~~~p~Lv~~Qi~SFn~FL~~~~~~~~~~~~gL~eii~~~~pI~~~--------------~~~~~l~f~~~~ 71 (1065)
T TIGR02013 6 IDFGKIPEVLEVPNLLEIQLDSYDWFLQQDTPPEKRKEEGLEEVFKSIFPIEDY--------------TGNIELEYLSYR 71 (1065)
T ss_pred eecccCcccccCCCHHHHHHHHHHHHHcCCCcccccccccHHHHHhccCcEEec--------------CCcEEEEEEEEE
Confidence 3599999999999999999999999999 8999999999999843 357999999999
Q ss_pred EccCccccCCCcccCCChHHHHhcCCccceeEEEEEEEEEeccCCCCcccccceeeEEEEecccceeeccCCccCCCCCh
Q 000996 97 LSKPMMTESDGETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSE 176 (1195)
Q Consensus 97 v~~P~~~e~~~~~~~l~P~EcR~r~lTYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~ 176 (1195)
+++|.+ +|+|||+|++||||+|+|+++++..+... .++...++|+||+||||++
T Consensus 72 l~~P~~----------~p~Ear~r~lTYsa~l~v~v~l~~~~~~~-----~~~i~~~~V~iG~iPiMt~----------- 125 (1065)
T TIGR02013 72 LGEPKY----------SVEECKERGLTYSAPLKVKLRLINKEEDG-----TKEIKEQDVYMGDIPLMTD----------- 125 (1065)
T ss_pred eCCCCC----------CHHHHHHhCCCcceeEEEEEEEEEeccCC-----ccceeeeeEEEeCCCccCC-----------
Confidence 999987 69999999999999999999997543100 1233457999999999986
Q ss_pred hhhhhcCCCCCCCCceEEEcCeeeEEeeeeeeecceEEEEEec--CCCcceEEEEEEEeecCCCCCCceEEEEEEecCCC
Q 000996 177 KDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFKKR--QPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSA 254 (1195)
Q Consensus 177 ~eli~~gE~~~D~GGYFIING~ERVII~Qe~~s~N~~~~~~~~--~~~~~~~~~~irs~~~~g~~~~~~~~v~~~~~~~~ 254 (1195)
||||||||+|||||+|+++|||++|++... ..++..|.|+|+| .+|+|...+ +..
T Consensus 126 -------------gGyFIINGsERVIV~Qe~rspg~~~~~~~~~~~~~~~~~~a~iis--~rgswl~~e----~~~---- 182 (1065)
T TIGR02013 126 -------------RGTFIINGAERVVVSQLHRSPGVFFSSEKDTHKSGKVLFSARIIP--YRGSWLEFE----TDK---- 182 (1065)
T ss_pred -------------CceEEECCcEEEEEEEeecCCCEEEEEccccCCCCceEEEEEEEe--CCCCceEEE----Eec----
Confidence 999999999999999999999999987643 2234468999987 468885432 221
Q ss_pred CCCCCCcEEEEEeccccccchHHHHHHHhcCCChHHHHHHhcccccchHHHHHhHhhHhhhhccCCHHHHHHHHhhcCcc
Q 000996 255 KGGSSGQYIRATLPYIRTEIPIIIVFRALGFVADKDILEHICYDFQDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGAT 334 (1195)
Q Consensus 255 k~~~~~~~i~v~i~~~~~~IPl~ilLrALG~~sD~eI~~~i~~~~~~~~~~~~l~~sl~e~~~i~t~~~al~yig~r~~~ 334 (1195)
++.+|+++++++ +||+++||||||+++|+||++.+++ +..+.+.| ++. ...++++|+.||+++++.
T Consensus 183 -----~~~i~v~i~~~~-kIPi~illrALG~~sd~eI~~~i~~---~~~i~~~l----~~~-~~~~~e~Al~~i~~~~~~ 248 (1065)
T TIGR02013 183 -----KDVLYVRIDRKR-KLPATVLLRALGYTIDTLILNRLGS---GEYIRNTL----RKD-PTNSEEEALVEIYRKLRP 248 (1065)
T ss_pred -----CCeEEEEecCCC-ceeHHHHHHHcCCCcchhhhhhcCc---hHHHHHHH----Hhc-cccCHHHHHHHHHhhcCC
Confidence 357999999965 9999999999999999999999864 33344433 222 256999999999999753
Q ss_pred cCCCchhhHHHHHHHHHhcccC-------CCCC-------------CCCcchhHHHHHHHHHHHHHHhhcCCCCCCCCCc
Q 000996 335 VGVTRDKRIKYAKEILQKEMLP-------HVGT-------------GDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDH 394 (1195)
Q Consensus 335 ~~~~~~~~~e~~~~~L~~~llp-------Hl~~-------------~~~~~~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~ 394 (1195)
......+.|+++|+++||| |+|. ....+ .|++||+ |+++|+++..|...+||+||
T Consensus 249 ---g~~~~~~~a~~~l~~~f~~~~rY~LghiGr~kln~Kl~~~~~~~~~~l-~k~d~l~-mi~~Ll~~~~g~~~~DD~Dh 323 (1065)
T TIGR02013 249 ---GEPPTVEAARSLLENLFFDPKRYDLGRVGRYKLNKKLGLDVPEDIGVL-TKEDIIA-TIKYLIKLRNGKGEIDDIDH 323 (1065)
T ss_pred ---CCcchHHHHHHHHHHHhcCcccccccccchhhhhhhcCcCcCccccee-hHHHHHH-HHHHHHHhhcCCCCCcchhh
Confidence 2244568899999999987 9993 11122 4889996 99999999999999999999
Q ss_pred cccceecccchhHHHHHHHHHHHHHHHHHHHhhhhhccCCCCchhhccccccccccccccccccccccccccccccccee
Q 000996 395 YGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQ 474 (1195)
Q Consensus 395 l~NKRv~l~G~Ll~~lfr~~l~~~~k~ik~~l~k~~~~~~~~~~~~~i~~~~It~~i~~~~sTGnw~~~~~~~~~sG~sq 474 (1195)
|+||||+++|+||+.|||.+|+++.+.+++++.+. +.+.+++..+++++.||+++++||+|| ||||
T Consensus 324 l~NKRvr~aGeLL~~~fr~~l~rl~k~ik~~l~~~--~~~~~~~~~~i~~~~it~~i~~ff~tg------------glSQ 389 (1065)
T TIGR02013 324 LGNRRIRSVGELLQNQFRVGLARMERIVRERMSTQ--DTDTLTPQDLINAKPISAAIKEFFGSS------------QLSQ 389 (1065)
T ss_pred hhccchhhHHHHHHHHHHHHHHHHHHHHHHHhhhc--ccccCCHHHhcCccchHHHHHHHhccC------------Cccc
Confidence 99999999999999999999999999999998754 224577889999999999999999875 9999
Q ss_pred eccccChhhhhccccccCC----CCCcCCCccccccccCCCcccccccCCCCCcccchhhcccccEEEccCCCchhHHHH
Q 000996 475 VLNRLTYASTLSHLRRLNS----PIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEF 550 (1195)
Q Consensus 475 ~l~r~N~ls~lSh~Rrv~~----~~~~~~k~t~vR~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~It~~~~~~~i~~~ 550 (1195)
+|||+||||+|||+||+++ ++.++++.++||+|||||||||||+|||||+|||||+|||++|+|+.
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 57899999999999999999999999999999999999999999851
Q ss_pred HHHhCCccccccCCCCCCCceEEEECCEEEEEEcChHHHHHHHHhhhccCCCCcceEEEEeccCCeEEEEeCCCceeeeE
Q 000996 551 LEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPL 630 (1195)
Q Consensus 551 l~~~g~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~lr~~rr~~~i~~~~~i~~~~~~~~i~I~td~GRl~RPl 630 (1195)
.|.+.||+
T Consensus 460 ------------------------------------------------------------------------~G~i~~P~ 467 (1065)
T TIGR02013 460 ------------------------------------------------------------------------YGFIETPY 467 (1065)
T ss_pred ------------------------------------------------------------------------ceEEeCCe
Confidence 23355899
Q ss_pred EEEecccchhhHHHHHHhhcCCCCCCCCccccccCCeEEEecccccccceeecccchhhcccCCCC---------c---c
Q 000996 631 FIVEKQRLLIKKRDIIALQQRESPEDGGWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPE---------E---A 698 (1195)
Q Consensus 631 ~~v~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~g~iE~i~~~Ee~~~~Ia~~~~~~~~~~~~~~---------~---~ 698 (1195)
+.|.||++. .++.+||+||+||+++.||+.+.++...+.+.+ + .
T Consensus 468 ~~V~ng~~~------------------------~~~~i~yl~a~eE~~~~Ia~~~~~l~~~~~~~~~~i~~r~~~~f~~~ 523 (1065)
T TIGR02013 468 RKVKDGKVV------------------------VTDEVDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYRGEITLV 523 (1065)
T ss_pred EEEECCeEe------------------------ccceeEECChHHhCCcEEEecCcCcCccCccccceeeEEEcCceeec
Confidence 999987642 136799999999999999999888755321100 0 0
Q ss_pred CCCceeeeecCCCccccccccccCCCCCCCCCccccccccccCccccc--------------------------------
Q 000996 699 YADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIY-------------------------------- 746 (1195)
Q Consensus 699 ~~~~~th~EI~P~~ilsv~AslIPF~~hNqSpRn~yqc~M~KQa~g~~-------------------------------- 746 (1195)
.+.++||+||+|.+||||+||||||+||||||||||||||||||||++
T Consensus 524 ~~~~vt~~ei~p~~ilsv~aslIPFleHNds~R~lmgsnM~kQavpl~~~e~p~VgTg~E~~v~~ds~~~i~a~~~G~v~ 603 (1065)
T TIGR02013 524 SPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVE 603 (1065)
T ss_pred ChhHeeEEeeChhhhhhhHhhcCCCccccCCcchhhhhhhhhhhhcccccCCCEEEcCcchhhhccccceeEeccCCEEE
Confidence 124679999999999999999999999999999999999999999999
Q ss_pred ---ceeeEEEeec---------ccee----------eecCCCceeec----ccccccc------cccCCCCceEEEEEEe
Q 000996 747 ---VTNYQFRMDT---------LAYV----------LYYPQKPLVTT----RAMEHLH------FRQLPAGINAIVAIAC 794 (1195)
Q Consensus 747 ---~~n~~~r~D~---------~~~~----------l~ypQ~Plv~t----~~~~~~~------~~~~~~G~N~~VAv~s 794 (1195)
+.|+.+|.|+ ..|. ++|||+|||+| +.++++. ++|+|+|+|++|||||
T Consensus 604 ~v~~~~~~~r~d~~~~~~~~~~~~y~L~~~~~snq~~~~~q~Plv~~~~~v~~~~~l~d~~~~~~~e~~~G~N~~VAvm~ 683 (1065)
T TIGR02013 604 YVDAKRIVIRYDEDEDEPDGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMP 683 (1065)
T ss_pred EEccceEEEEecCCcccccccceEEEeecccccccCceEEeeeeeccCCeEeeeeEecccccccCCcCcCccceEEEEEe
Confidence 8999999995 3343 56999999999 5677764 9999999999999999
Q ss_pred cCCccCCCcEEEecceeecCceeEEEEEEEEechhccCCcccccccC--CCCCCCCCCCCCCcCCCCCCCCcCCCcEECC
Q 000996 795 YSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGR--PDRSNTMGMRHGSYDKLDDDGLAPPGTRVSG 872 (1195)
Q Consensus 795 ~~Gyn~EDaiiink~s~~rG~f~s~~~~~~~~~~~~~~~~~~e~~~~--p~~~~~~~~~~~~~~~Ld~dGi~~~G~~v~~ 872 (1195)
|+||||||||||||+|++||+|||+||++|+++++....+ .|.|.. |+. +...|++||+||||++|++|++
T Consensus 684 y~GYn~EDAiiink~~i~rg~~~s~~~~~~~~~~~~~~~g-~e~~~~~~p~~------~~~~~~~Ld~dGi~~~G~~v~~ 756 (1065)
T TIGR02013 684 WNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLG-PEEITRDIPNV------SEEALRNLDENGIVRIGAEVKA 756 (1065)
T ss_pred eecccccceEEeehhhhcCCceEEEEEEEEEEEeeccCCC-ceEeeccCCCC------chhhhhccCCCCCccCccEeCC
Confidence 9999999999999999999999999999999998765433 365543 542 2235999999999999999999
Q ss_pred CCEEEEEeCCCCccccc---------cccCCCccceeeEEeecCCCcEEEEEEEEecCCC-------cEEEEEEEeeecC
Q 000996 873 EDVIIGKTTPISQDEAQ---------GQASRYTRRDHSISLRHSETGMVDQVLLTTNADG-------LRFVKVRVRSVRI 936 (1195)
Q Consensus 873 gdvli~k~~~~~~~~~~---------~~~~~~~~~~~s~~~~~~~~g~v~~v~~~~~~~~-------~~~v~v~~~~~R~ 936 (1195)
|||||||++|....+.. ...+....+|+|++++.+++|+||+|.++.++++ .+.|+|++|+.|+
T Consensus 757 gdilvgk~~p~~~~~~~~~~~l~~~~~~~~~~~~~d~s~~~~~~~~g~V~~V~~~~~~~~~~~~~~~~~~vkv~ir~~R~ 836 (1065)
T TIGR02013 757 GDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSRKQGDELPPGVNKLVKVYIAQKRK 836 (1065)
T ss_pred CCEEEEEecCCcccccChhhhhhhhhcccCCccccccceEccCCCCEEEEEEEEEeccCCCccCcCccEEEEEEEeeccc
Confidence 99999999986422110 1112234789999999999999999999887766 5789999999999
Q ss_pred CCCcccccccCCCceeEEeeecCCCCCCCCCCCCCcEEeCCCCCCCCCchhhHHHHhhhHHhhhc--CCCcccCC-CCCc
Q 000996 937 PQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHM--GKEGDATP-FTDV 1013 (1195)
Q Consensus 937 ~~iGDKf~sRHGqKGvvs~i~~~~dmPf~~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~--g~~~~~tp-F~~~ 1013 (1195)
|+||||||||||||||||+|||+||||||+||++|||||||||||||||||||+|+++||||++. |...++|| |++.
T Consensus 837 p~iGDKfasRHGqKGvis~i~~~eDMPf~~~G~~pDiIiNPhg~PSRMtiGqllE~~~gka~~~~~~~~~~~~tp~f~~~ 916 (1065)
T TIGR02013 837 IQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRKGVPIATPVFDGA 916 (1065)
T ss_pred ccccchhhhcccCceeEEeEecCCCCCccCCCCCccEEECCCCCcccccHHHHHHHHHHHHHHhccCCCeEEeccCcCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999987 66788999 9999
Q ss_pred cHHHHHHHHHHcCCCCCCeEEEeeCCCCceeeeeEeEeeeehhccccccCcccEEeccCCccccccCCCCcccCCCcccc
Q 000996 1014 TVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRF 1093 (1195)
Q Consensus 1014 ~~~~~~~~l~~~g~~~~G~~~l~~G~tG~~~~~~if~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~ 1093 (1195)
+.+++++.|+++||+++|+|+||||+||++|+++||+|++|||||+|||+||+|||++|||+.|||||++||||+|||||
T Consensus 917 ~~~~~~~~l~~~g~~~~G~e~l~~G~TG~~~~~~ifvG~~yy~rL~HmV~DK~haRs~Gp~~~lT~QP~~Grsr~GG~R~ 996 (1065)
T TIGR02013 917 SEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRF 996 (1065)
T ss_pred cHHHHHHHHHHcCCCCCCCEEEEcCCCCCCccccEEEeehheeechhhhcchhhhcccCCccceeeCCCcccccCCCeee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chhhhhHHHhhccHHHHHHhhhcCCCceeeeeccccCcceeeccccCceeeccCCCCCCceeecchHhhHHHHHHHHhCC
Q 000996 1094 GEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMA 1173 (1195)
Q Consensus 1094 GEMErd~l~a~Gas~~l~Erl~~~SD~~~~~vC~~cG~~~~~~~~~~~~~C~~C~~~~~~~~v~iPy~~kll~~EL~sm~ 1173 (1195)
||||||||+|||||++|+|||+.+||.+ ||+.. .++..| ++..+.++.+|||||||+|||+|||
T Consensus 997 GEME~d~l~a~Gas~~L~E~l~~~SD~~-------~g~~~--------~~~~~~-~~~~i~~~~~p~sfklL~~EL~sm~ 1060 (1065)
T TIGR02013 997 GEMEVWALEAYGAAYTLQEMLTVKSDDV-------VGRTK--------AYEAIV-KGENVPEPGIPESFNVLIKELQSLG 1060 (1065)
T ss_pred eeeeHHHHHhhhhHHHHHHHHhccChhh-------hhhhh--------hhhhhc-CCCccccccCCccHHHHHHHHHhCC
Confidence 9999999999999999999999999955 45432 123445 5678999999999999999999999
Q ss_pred CceEE
Q 000996 1174 IAPRM 1178 (1195)
Q Consensus 1174 i~~~l 1178 (1195)
|++++
T Consensus 1061 i~~~~ 1065 (1065)
T TIGR02013 1061 LDIEL 1065 (1065)
T ss_pred ccccC
Confidence 99874
No 8
>PRK00405 rpoB DNA-directed RNA polymerase subunit beta; Reviewed
Probab=100.00 E-value=1.4e-221 Score=2088.58 Aligned_cols=929 Identities=29% Similarity=0.435 Sum_probs=799.0
Q ss_pred hhhhhhcccCccchHHHHHHHHHHHH-------HhhHHHHHcccCCeeeCCCCCCCCCCCCCCCCceEEEEEeEEEEccC
Q 000996 28 AWAVISAYFEEKGLVRQQLDSFDEFI-------QNTMQEIVDESADIEIRPESQHNPGQQSDFAETIYKISFGQIYLSKP 100 (1195)
Q Consensus 28 ~~~~i~~~f~~~~Lv~~qi~SFn~Fi-------~~gL~~ii~~~~pI~~~~~~~~~~~~~~~~~~~~~~l~f~~v~v~~P 100 (1195)
.++.++.++..++|++||++|||+|| ++||++++++++||+.. +.++.|+|.++++++|
T Consensus 14 ~~~~~~~~~~~p~Lv~~Qi~SFn~Fl~~~~~~~~~gL~~ii~~~~pI~~~--------------~~~~~l~f~~~~l~~P 79 (1112)
T PRK00405 14 SFGKIKEVLELPNLLEIQLDSFDWFLQLDVPPEDEGLEEVFRSIFPIEDF--------------NGNLSLEFVSYELGEP 79 (1112)
T ss_pred ecccccccCCCCCHHHHHHHHHHHHHhcCCcccchhHHHHHHhcCCEEec--------------CCcEEEEEeeeEcCCC
Confidence 46777888999999999999999999 99999999999999843 4579999999999999
Q ss_pred ccccCCCcccCCChHHHHhcCCccceeEEEEEEEEEeccCCCCcccccceeeEEEEecccceeeccCCccCCCCChhhhh
Q 000996 101 MMTESDGETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLT 180 (1195)
Q Consensus 101 ~~~e~~~~~~~l~P~EcR~r~lTYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~eli 180 (1195)
.+ +|+|||+|++||||||+|+++++..+.. ++..++|+||+||||+
T Consensus 80 ~~----------tp~Ear~r~lTYSaplyv~v~l~~~~~~--------~i~~~~V~iG~iPiMt---------------- 125 (1112)
T PRK00405 80 KY----------DVEECKERGLTYSAPLRVKLRLINKETG--------EIKEQEVYMGDIPLMT---------------- 125 (1112)
T ss_pred CC----------CHHHHHHhCCCCCeeEEEEEEEEEeccC--------ceeeeeEEEecccccc----------------
Confidence 64 8999999999999999999999764321 2356799999999997
Q ss_pred hcCCCCCCCCceEEEcCeeeEEeeeeeeecceEEEEEec--CCCcceEEEEEEEeecCCCCCCceEEEEEEecCCCCCCC
Q 000996 181 ELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFKKR--QPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGS 258 (1195)
Q Consensus 181 ~~gE~~~D~GGYFIING~ERVII~Qe~~s~N~~~~~~~~--~~~~~~~~~~irs~~~~g~~~~~~~~v~~~~~~~~k~~~ 258 (1195)
+||||||||+|||||+|+++|||++|++... ..++..|.|+|+| .+|+|...++ ..
T Consensus 126 --------~gGyFIING~ERVIVsQe~rSPg~~~~~~~~k~~~~k~~y~a~Iis--~rGswl~~e~----d~-------- 183 (1112)
T PRK00405 126 --------ENGTFIINGTERVIVSQLHRSPGVYFDHDKDKTSSGKLLYSARIIP--YRGSWLEFEF----DP-------- 183 (1112)
T ss_pred --------CCceEEECCeEEEEEEEeecCCCEEEEEeccccCCCceeEEEEEEE--CCCCcEEEEE----ec--------
Confidence 4999999999999999999999999886644 2345679999977 5688954332 11
Q ss_pred CCcEEEEEeccccccchHHHHHHHhcCCChHHHHHHhcccccch-------------------------H----------
Q 000996 259 SGQYIRATLPYIRTEIPIIIVFRALGFVADKDILEHICYDFQDT-------------------------Q---------- 303 (1195)
Q Consensus 259 ~~~~i~v~i~~~~~~IPl~ilLrALG~~sD~eI~~~i~~~~~~~-------------------------~---------- 303 (1195)
++.||+++++. ++||+++||||||+ ||+||++.++.+.... +
T Consensus 184 -k~~I~vri~~~-~kIPi~iLLrALGl-sd~eIl~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ei~~~~~~~~~ 260 (1112)
T PRK00405 184 -KDILYVRIDRR-RKLPVTVLLRALGY-SDEEILDLFYEKEEFGKEIEVPVEYLLGKVLAEDIVDEETGEVLAEANDEIT 260 (1112)
T ss_pred -CCeEEEEecCC-CcccHHHHHHHcCC-CHHHHHHHhcccccccceeccchHHhcccchhhhhcccccceeeeccCCccc
Confidence 35799999985 69999999999999 8999999997532221 0
Q ss_pred ---HHHHhHhhHhhhhccCCHHHHHHHHhhcCcccCCCchhhHHHHHHHHHhccc-------CCCCCCCCc--------c
Q 000996 304 ---MMELLRPSLEEAFVIQNQQVALDYIGKRGATVGVTRDKRIKYAKEILQKEML-------PHVGTGDFC--------E 365 (1195)
Q Consensus 304 ---~~~~l~~sl~e~~~i~t~~~al~yig~r~~~~~~~~~~~~e~~~~~L~~~ll-------pHl~~~~~~--------~ 365 (1195)
+...+..+++. ....|+++|+.||+++++. ......+.|+++|++.|| ||+|....+ .
T Consensus 261 ~~~~~~~i~~~l~~-~~~~t~e~Al~~I~k~l~~---g~~~~~e~a~~~l~~~ff~~~rYdL~hiGr~k~nkKl~l~~~~ 336 (1112)
T PRK00405 261 EELDGPYIRNTLEK-DPTSSREEALVEIYRRLRP---GEPPTVEAARSLLENLFFDPKRYDLSKVGRYKLNKKLGLDEDE 336 (1112)
T ss_pred hhhhhHHHHHHHhh-ccccCHHHHHHHHHhhcCC---CCcchHHHHHHHHHHHhcCccccccccCCceecchhcccCccc
Confidence 01222222321 1256999999999999753 234456789999998775 999964322 1
Q ss_pred ----hhHHHHHHHHHHHHHHhhcCCCCCCCCCccccceecccchhHHHHHHHHHHHHHHHHHHHhhhhhccCCCCchhhc
Q 000996 366 ----TKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFA 441 (1195)
Q Consensus 366 ----~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~NKRv~l~G~Ll~~lfr~~l~~~~k~ik~~l~k~~~~~~~~~~~~~ 441 (1195)
..|+++ ++|+++|+.+..|...+||+|||+||||+++|+||+.||+.+|+++++.+++++.+. +.+.+++..+
T Consensus 337 ~~~~L~~~d~-~~mi~~Ll~l~~g~~~~DDiDhl~NKRvr~aGeLL~~~fr~~~~rl~k~ik~~l~~~--~~~~~~~~~l 413 (1112)
T PRK00405 337 DVRVLTKEDI-IATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERAVRERMSLQ--DLDTLTPQDL 413 (1112)
T ss_pred ccccccHHHH-HHHHHHHHhhhcccCCCcchhHHhcchhhhHHHHHHHHHHHHHHHHHHHHHHHhhhc--ccccCCHHHh
Confidence 135554 799999999999999999999999999999999999999999999999999998864 2356789999
Q ss_pred ccccccccccccccccccccccccccccccceeeccccChhhhhccccccCC----CCCcCCCccccccccCCCcccccc
Q 000996 442 IKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS----PIGREGKLAKPRQLHNSQWGMMCP 517 (1195)
Q Consensus 442 i~~~~It~~i~~~~sTGnw~~~~~~~~~sG~sq~l~r~N~ls~lSh~Rrv~~----~~~~~~k~t~vR~Lhps~wG~iCP 517 (1195)
++++.||++|++||+|| ||||+|||+||||+|||+||+++ ++.++++.++||+|||||||||||
T Consensus 414 in~~~it~~i~~ff~tg------------glSQ~Ldq~NpLselshkRRlss~gpggl~r~~a~~~~R~lH~ShyGriCP 481 (1112)
T PRK00405 414 INAKPVVAAIKEFFGSS------------QLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICP 481 (1112)
T ss_pred hCchhHHHHHHHhhccC------------CcceeeccCCHHHhhhhhceecccCCCCcCccccCCcccccCccccccccC
Confidence 99999999999999875 99999999999999999999998 578999999999999999999999
Q ss_pred cCCCCCcccchhhcccccEEEccCCCchhHHHHHHHhCCccccccCCCCCCCceEEEECCEEEEEEcChHHHHHHHHhhh
Q 000996 518 AETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKTLRRLR 597 (1195)
Q Consensus 518 veTPEG~~cGLvk~LA~~a~It~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~lr~~r 597 (1195)
+|||||++||||+|||++|+|+. +|.. ...+.+++||.|-
T Consensus 482 iETPEG~n~GLV~nLA~~a~i~~-------------~G~~----------~tp~~~~~nG~~~----------------- 521 (1112)
T PRK00405 482 IETPEGPNIGLINSLATYARVNE-------------YGFI----------ETPYRKVVDGKVT----------------- 521 (1112)
T ss_pred cCCCCCCccccccchhhcccccc-------------CCcc----------ccceEEEECCeEc-----------------
Confidence 99999999999999999999985 2211 0126777888861
Q ss_pred ccCCCCcceEEEEeccCCeEEEEeCCCceeeeEEEEecccchhhHHHHHHhhcCCCCCCCCccccccCCeEEEecccccc
Q 000996 598 RRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRESPEDGGWHDLVAKGFIEYIDTEEEE 677 (1195)
Q Consensus 598 r~~~i~~~~~i~~~~~~~~i~I~td~GRl~RPl~~v~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~g~iE~i~~~Ee~ 677 (1195)
..+|||||+||+
T Consensus 522 --------------------------------------------------------------------~~i~yl~a~eE~ 533 (1112)
T PRK00405 522 --------------------------------------------------------------------DEIVYLTADEED 533 (1112)
T ss_pred --------------------------------------------------------------------cceEECCHHHhc
Confidence 127899999999
Q ss_pred cceeecccchhhcccCCCC---------c---cCCCceeeeecCCCccccccccccCCCCCCCCCccccccccccCcccc
Q 000996 678 TTMISMTINDLVQARLHPE---------E---AYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGI 745 (1195)
Q Consensus 678 ~~~Ia~~~~~~~~~~~~~~---------~---~~~~~~th~EI~P~~ilsv~AslIPF~~hNqSpRn~yqc~M~KQa~g~ 745 (1195)
++.||+.+.++...+.+.+ + .....+||+||+|.+|+||+||||||+||||||||+|||||||||||+
T Consensus 534 ~~~Ia~~~~~l~~~~~~~~~~i~~r~~~e~~~~~~~~~~~~~i~p~qi~sv~aslIPFleHnda~R~lmgSnMqrQAvpl 613 (1112)
T PRK00405 534 NYVIAQANAPLDEDGRFVDELVTARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPL 613 (1112)
T ss_pred CcEEEecCcccCCCCcccCceEEEEecCcceeechhhceEEeechhhhceehhhccCcccccCCcchhhhhhhhhhhhhh
Confidence 9999999887754321100 0 012457999999999999999999999999999999999999999999
Q ss_pred cce-----------------------------------eeEEEe-----------------ecccee-eecCCCceeecc
Q 000996 746 YVT-----------------------------------NYQFRM-----------------DTLAYV-LYYPQKPLVTTR 772 (1195)
Q Consensus 746 ~~~-----------------------------------n~~~r~-----------------D~~~~~-l~ypQ~Plv~t~ 772 (1195)
+.. |+.+|. |+..++ ++|||+|||+|+
T Consensus 614 ~~~~~p~vgTg~e~~~~~ds~~~i~a~~~G~v~~v~~~~i~ir~~~~~~~~~~~~~y~L~~~~~sn~~~~~~q~Plv~~~ 693 (1112)
T PRK00405 614 LRPEAPLVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIVVRVEELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVG 693 (1112)
T ss_pred ccccCCeeecCcchhhhhhcchheEeccCCEEEEEeCCEEEEeecccccCCCCeeEEEecccccccccceeecceeeecC
Confidence 988 888888 667777 899999999998
Q ss_pred ----ccccc------ccccCCCCceEEEEEEecCCccCCCcEEEecceeecCceeEEEEEEEEechhccCCccccccc--
Q 000996 773 ----AMEHL------HFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFG-- 840 (1195)
Q Consensus 773 ----~~~~~------~~~~~~~G~N~~VAv~s~~Gyn~EDaiiink~s~~rG~f~s~~~~~~~~~~~~~~~~~~e~~~-- 840 (1195)
.++++ +++++|+|+|++||||||+||||||||||||+|+|||+|+|+|+++|+.+++....+ .+.+.
T Consensus 694 ~~v~~g~~lad~~~~~~~e~~~G~N~~VA~~~y~GYn~EDaiiink~si~rg~~~s~~~~~~~~~~~~~~~~-~~~~~~~ 772 (1112)
T PRK00405 694 DRVEKGDVLADGPSTDNGELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLG-PEEITRD 772 (1112)
T ss_pred CeEeeccEeecccccCcccccCCcceEEEEEeecccCccceEEEEhhhhccCceEEEEEeeeeeEeeccCCC-ceeeccc
Confidence 57776 899999999999999999999999999999999999999999999999988765443 34443
Q ss_pred CCCCCCCCCCCCCCcCCCCCCCCcCCCcEECCCCEEEEEeCCCCccccc---------cccCCCccceeeEEeecCCCcE
Q 000996 841 RPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ---------GQASRYTRRDHSISLRHSETGM 911 (1195)
Q Consensus 841 ~p~~~~~~~~~~~~~~~Ld~dGi~~~G~~v~~gdvli~k~~~~~~~~~~---------~~~~~~~~~~~s~~~~~~~~g~ 911 (1195)
.|... ...|++||+||||++|++|++|||||||++|....+.. ...+....+|+|++++++++|+
T Consensus 773 ~p~~~------~~~~~~Ld~dGi~~~G~~v~~gDiligk~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~s~~~~~~~~g~ 846 (1112)
T PRK00405 773 IPNVS------EEALRNLDESGIVRIGAEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGT 846 (1112)
T ss_pred CCCCC------hHHhhccCCCCCccCccEecCCCEEEEEecCCCccccChhhhhhhhhhcccccccccceEEcCCCCCEE
Confidence 44321 23589999999999999999999999999986532110 1112234789999999999999
Q ss_pred EEEEEEEec-CCC-------cEEEEEEEeeecCCCCcccccccCCCceeEEeeecCCCCCCCCCCCCCcEEeCCCCCCCC
Q 000996 912 VDQVLLTTN-ADG-------LRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSR 983 (1195)
Q Consensus 912 v~~v~~~~~-~~~-------~~~v~v~~~~~R~~~iGDKf~sRHGqKGvvs~i~~~~dmPf~~~G~~pDiIiNPh~~PSR 983 (1195)
||+|.++.+ .+| .+.|+|++|+.|+|+||||||||||||||||+|||+|||||++||++|||||||||||||
T Consensus 847 V~~v~~~~~~~~~~~~~~~~~~~vkv~ir~~R~p~iGDKfasRHGqKGvis~i~~~eDMPf~~~G~~pDiIiNPhg~PSR 926 (1112)
T PRK00405 847 VIDVKVFTRIEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSR 926 (1112)
T ss_pred EEEEEEeeccccCCccCcCcceEEEEEEeeecccCcccchhhccCCceeEEeEeccCCCCcCCCCCCCcEEECCCCCccc
Confidence 999999887 555 478999999999999999999999999999999999999999999999999999999999
Q ss_pred CchhhHHHHhhhHHhhhcCCCcccCC-CCCccHHHHHHHHHHcCCCCCCeEEEeeCCCCceeeeeEeEeeeehhcccccc
Q 000996 984 MTIGQLIECIMGKVAAHMGKEGDATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMV 1062 (1195)
Q Consensus 984 MtiGql~E~~~gk~~~~~g~~~~~tp-F~~~~~~~~~~~l~~~g~~~~G~~~l~~G~tG~~~~~~if~G~~yy~rL~Hmv 1062 (1195)
||||||+|+++||||++.|.+ ++|| |++.+.+++++.|+++||+++|+|+||||+||++|+++||+|++|||||+|||
T Consensus 927 MtiGql~E~~~gk~~~~~g~~-~~tp~f~~~~~~~~~~~l~~~g~~~~G~e~l~~G~tG~~~~~~if~G~~yy~rL~HmV 1005 (1112)
T PRK00405 927 MNIGQILETHLGWAAKGLGIK-FATPVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLV 1005 (1112)
T ss_pred ccHHHHHHHHhhHHHHhcCCe-EecCccCCccHHHHHHHHHHcCcCCCCCEEEECCCCCCCCcccEEEEehhheechhhh
Confidence 999999999999999999986 8898 99999999999999999999999999999999999999999999999999999
Q ss_pred CcccEEeccCCccccccCCCCcccCCCccccchhhhhHHHhhccHHHHHHhhhcCCCceeeeeccccCcceeeccccCce
Q 000996 1063 DDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSF 1142 (1195)
Q Consensus 1063 ~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~Erl~~~SD~~~~~vC~~cG~~~~~~~~~~~~ 1142 (1195)
+||+|||++|||+.|||||++||||+|||||||||||||+|||||++|+|||+.+||++. |+.. .+
T Consensus 1006 ~DK~haRs~Gp~~~lT~QP~~Grsr~GG~R~GEME~d~l~a~Gas~~L~Erl~~~SD~~~-------g~~~-------~~ 1071 (1112)
T PRK00405 1006 DDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVV-------GRTK-------VY 1071 (1112)
T ss_pred cchhhhcccCCccceeeCCCcccccCCCeeeeeeehhhHhhhhhHHHHHHHhhccCcccc-------ccee-------EE
Confidence 999999999999999999999999999999999999999999999999999999999653 5443 24
Q ss_pred eeccCCCCCCceeecchHhhHHHHHHHHhCCCceEEEe
Q 000996 1143 ECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLT 1180 (1195)
Q Consensus 1143 ~C~~C~~~~~~~~v~iPy~~kll~~EL~sm~i~~~l~~ 1180 (1195)
.| .| ++..+.++.+|||||||+|||+||||++++..
T Consensus 1072 ~~-~~-~~~~i~~~~~p~~fklL~~EL~sm~i~~~~~~ 1107 (1112)
T PRK00405 1072 EA-IV-KGENIPEPGIPESFNVLVKELQSLGLDVELLD 1107 (1112)
T ss_pred EE-ee-cCCcccccCCChHHHHHHHHHHHCccceEEec
Confidence 56 56 56789999999999999999999999999983
No 9
>CHL00001 rpoB RNA polymerase beta subunit
Probab=100.00 E-value=3.9e-217 Score=2025.62 Aligned_cols=934 Identities=26% Similarity=0.389 Sum_probs=788.2
Q ss_pred cCccchHHHHHHHHHHHHHhhHHHHHcccCCeeeCCCCCCCCCCCCCCCCceEEEEEeEEEEccCccccCCCcccCCChH
Q 000996 36 FEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQSDFAETIYKISFGQIYLSKPMMTESDGETATLFPK 115 (1195)
Q Consensus 36 f~~~~Lv~~qi~SFn~Fi~~gL~~ii~~~~pI~~~~~~~~~~~~~~~~~~~~~~l~f~~v~v~~P~~~e~~~~~~~l~P~ 115 (1195)
|..++|+++|++||||||++||++++++++||+ .. +....+.+.++++++++|.+ +|+
T Consensus 10 ~~~P~Lv~~Q~~SF~~Fl~~gL~~i~~~~~pI~-~~-----------~~~~~~~~~~~~~~l~~P~~----------~p~ 67 (1070)
T CHL00001 10 STIPGFNQIQFEGFCRFIDQGLTEELSKFPKIE-DT-----------DQEIEFQLFVETYQLVEPLI----------KER 67 (1070)
T ss_pred cCCCCHHHHHHHHHHHHHHHhHHHHHHhcCCeE-CC-----------CCCEEEEEEeCeEEECCCCC----------CHH
Confidence 678999999999999999999999999999998 21 12234556677999999987 789
Q ss_pred HHHhcCCccceeEEEEEEEEEeccCCCCcccccceeeEEEEecccceeeccCCccCCCCChhhhhhcCCCCCCCCceEEE
Q 000996 116 AARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFII 195 (1195)
Q Consensus 116 EcR~r~lTYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~eli~~gE~~~D~GGYFII 195 (1195)
|||+|++||+|+|+|+++++..+. +..++++|++|+||+|+ +||||||
T Consensus 68 ear~r~lTYsa~l~v~v~l~~~~~--------~~i~~~~V~iG~iPlMt------------------------~gG~FII 115 (1070)
T CHL00001 68 DAVYESLTYSSELYVPAGLIWKKS--------RDMQEQTVFIGNIPLMN------------------------SLGTFII 115 (1070)
T ss_pred HHHHhCCCCCceeEEEEEEEEcCc--------eeEEEeEEEEecCCccC------------------------CCcEEEE
Confidence 999999999999999999975432 12456799999999994 5999999
Q ss_pred cCeeeEEeeeeeeecceEEEEEecCCCcceEEEEEEEeecCCCCCCceEEEEEEecCCCCCCCCCcEEEEEeccccccch
Q 000996 196 NGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIP 275 (1195)
Q Consensus 196 NG~ERVII~Qe~~s~N~~~~~~~~~~~~~~~~~~irs~~~~g~~~~~~~~v~~~~~~~~k~~~~~~~i~v~i~~~~~~IP 275 (1195)
||+|||||+|++||||++|++.....++..|.|+|+| .+|+|.. + .+.. ++.+|+++++. ++||
T Consensus 116 NG~ERVIVsQ~~rSpg~~~~~~~~~~~~~~y~a~iis--~rgswl~--~--e~d~---------~~~i~vri~~~-~kiP 179 (1070)
T CHL00001 116 NGIYRVVINQILRSPGIYYRSELDHNGISVYTGTIIS--DWGGRLE--L--EIDR---------KARIWARVSRK-QKIS 179 (1070)
T ss_pred cCcEEEEEEEEeccCCEEEEEecCCCCceeEEEEEEe--cCCCceE--E--EEec---------CCeEEEEecCC-Cccc
Confidence 9999999999999999999877554456679999975 7778833 2 2221 35799999995 6999
Q ss_pred HHHHHHHhcCCChHHHHHHhcccccchHHHHHhHhhHhhh--hccCCHHHHHHHHhhcCcccCCCchhhHHHHHHHHHhc
Q 000996 276 IIIVFRALGFVADKDILEHICYDFQDTQMMELLRPSLEEA--FVIQNQQVALDYIGKRGATVGVTRDKRIKYAKEILQKE 353 (1195)
Q Consensus 276 l~ilLrALG~~sD~eI~~~i~~~~~~~~~~~~l~~sl~e~--~~i~t~~~al~yig~r~~~~~~~~~~~~e~~~~~L~~~ 353 (1195)
+++||||||++ |+||++.++++ +.+..++.+. ..+.|+++|+.||++++.. ...+....+.|+.+|.+.
T Consensus 180 i~ilLrALG~s-d~eIl~~~~~~-------~~l~~~l~~~~~~~~~t~e~Al~~i~~~l~~-r~~~~~~~~~a~~~l~~~ 250 (1070)
T CHL00001 180 ILVLLSAMGLN-LREILDNVCYP-------EIFLSFLNDKEKKKIGSKENAILEFYQQFAC-VGGDPVFSESLCKELQKK 250 (1070)
T ss_pred HHHHHHHcCCC-HHHHHHHhCcH-------HHHHHHHHHHhhccccCHHHHHHHHHHhhcc-CCCCcchHHHHHHHHHHH
Confidence 99999999995 99999999642 2233333222 2467999999999999632 123455668899999999
Q ss_pred ccCC------CCCCCCcch------hHHHHH-----HHHHHHHHHhhcCCCCCCCCCccccceecccchhHHHHHHHHHH
Q 000996 354 MLPH------VGTGDFCET------KKAYYF-----GYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFR 416 (1195)
Q Consensus 354 llpH------l~~~~~~~~------~K~~~L-----~~Mi~kLl~~~~g~~~~DD~D~l~NKRv~l~G~Ll~~lfr~~l~ 416 (1195)
+|+| +|....+.. .|+.+| ++|+++|+.+..|...+||+|||+||||+++|+||+.|||.+|+
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 886543322 455556 89999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhhhhccCCCCchhhcccccccccccccccccccccccccccccccceeeccccChhhhhccccccCC--C
Q 000996 417 KLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS--P 494 (1195)
Q Consensus 417 ~~~k~ik~~l~k~~~~~~~~~~~~~i~~~~It~~i~~~~sTGnw~~~~~~~~~sG~sq~l~r~N~ls~lSh~Rrv~~--~ 494 (1195)
++.+.++++|.+.+.+.+.+++..+++++.||.+|++||+| +||||+|||+||||+|||+||+++ |
T Consensus 331 r~~r~ik~~m~~~~~~~~~~~~~~lin~~~It~~ik~ff~t------------s~LSQflDqtNpLseltHkRRlsslGp 398 (1070)
T CHL00001 331 RLENAVRGTICGAIRRKLIPTPQNLVTSTPLTTTYESFFGS------------HPLSQFLDQTNPLTEIVHGRKLSSLGP 398 (1070)
T ss_pred HHHHHHHHHHHHHhcccccCCHHHhhCcchHHHHHHhhhcC------------CcceeeeccCCHHHhhhhhhcccccCC
Confidence 99999999998765555567899999999999999999985 799999999999999999999998 8
Q ss_pred CCcCCCcc--ccccccCCCcccccccCCCCCcccchhhcccccEEEc-cCCCchhHHHHHHHhCCccccccCCCCCCCce
Q 000996 495 IGREGKLA--KPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYIT-VGSAAYPILEFLEEWGTENFEEISPAVIPQAT 571 (1195)
Q Consensus 495 ~~~~~k~t--~vR~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~It-~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~ 571 (1195)
++.+++.+ +||+|||||||||||+|||||+|||||+|||++|+|+ .|+.++|+++++...+...+..+++.+ ...+
T Consensus 399 gglsr~~a~fevRdvHpShyGRICPIETPEG~NiGLI~sLA~~A~In~~GfietP~~~v~~~~~~~~i~ylsa~e-e~~~ 477 (1070)
T CHL00001 399 GGLTGRTASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIGHWGSLESPFYEISERSKEERMVYLSPSE-DEYY 477 (1070)
T ss_pred CCccccccCCcccccCccccccccCCCCCCcccccchhhhhhhcccccCCCcccceeeeccccccceeEEccccc-cCce
Confidence 88888777 9999999999999999999999999999999999999 589999999998777766665555544 5668
Q ss_pred EEEECCEEEEEEcChHHHHHHHHhhhccCCCCcceEEEEeccCCeEEEEeCCCceeeeEEEEecccchhhHHHHHHhhcC
Q 000996 572 KIFVNGCWVGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQR 651 (1195)
Q Consensus 572 ~V~lnG~~iG~~~~~~~~~~~lr~~rr~~~i~~~~~i~~~~~~~~i~I~td~GRl~RPl~~v~~~~~~~~~~~~~~l~~~ 651 (1195)
+|+ ||.|+|...+. +.. .+..+.
T Consensus 478 ~Ia-~g~~~~~~~~~---------------~~~------------------------~~~~~r----------------- 500 (1070)
T CHL00001 478 MIA-AGNSLALNQGI---------------QEE------------------------QVVPAR----------------- 500 (1070)
T ss_pred EEE-eCceeeccCCc---------------ccc------------------------ceeEEE-----------------
Confidence 888 99998842210 000 000000
Q ss_pred CCCCCCCccccccCCeEEEecccccccceeecccchhhcccCCCCccCCCceeeeecCCCccccccccccCCCCCCCCCc
Q 000996 652 ESPEDGGWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPR 731 (1195)
Q Consensus 652 ~~~~~~~~~~l~~~g~iE~i~~~Ee~~~~Ia~~~~~~~~~~~~~~~~~~~~~th~EI~P~~ilsv~AslIPF~~hNqSpR 731 (1195)
+ -+++..|++ .+.|||||+|.+|+||+||||||+|||||||
T Consensus 501 ------------------~----~~e~~~i~~-----------------~~i~~~dIsP~qi~svaasLIPFleHndanR 541 (1070)
T CHL00001 501 ------------------Y----RQEFLTIAW-----------------EQIHLRSIFPFQYFSIGASLIPFLEHNDANR 541 (1070)
T ss_pred ------------------e----cCeEEEEch-----------------HHCcEEeeChhhhhhhhhhcCCCccccCcch
Confidence 0 011233332 2369999999999999999999999999999
Q ss_pred cccccccccCccccccee---------eEEEe-----------------e-----------c-cceeeec---------C
Q 000996 732 NTYQSAMGKQAMGIYVTN---------YQFRM-----------------D-----------T-LAYVLYY---------P 764 (1195)
Q Consensus 732 n~yqc~M~KQa~g~~~~n---------~~~r~-----------------D-----------~-~~~~l~y---------p 764 (1195)
|+|||||||||||++..+ ++.|. | + ..|++.| |
T Consensus 542 almgsnMqrQAvpll~~~~p~VgTG~E~~~~~ds~~~i~a~~~G~V~~vd~~~I~i~~~~~~~~y~l~~y~rsnq~t~~~ 621 (1070)
T CHL00001 542 ALMGSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVVAIAEHEGKIIYTDTDKIILSGNGDTLSIPLVMYQRSNKNTCMH 621 (1070)
T ss_pred hhhhhccchhccccccCCCCEeecCcchhhhhcccceeEEccCCEEEEEeCCEEEEEcCCCeEEEEeeceeccCCCcccc
Confidence 999999999999999888 66666 6 4 4566678 9
Q ss_pred CCceeecccccccc------------cccCCCCceEEEEEEecCCccCCCcEEEecceeecCceeEEEEEEEEechhccC
Q 000996 765 QKPLVTTRAMEHLH------------FRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMG 832 (1195)
Q Consensus 765 Q~Plv~t~~~~~~~------------~~~~~~G~N~~VAv~s~~Gyn~EDaiiink~s~~rG~f~s~~~~~~~~~~~~~~ 832 (1195)
|+|||+++ ++++ .+|+|+|+|++||||||+||||||||||||++++||+|||+|+++|+++++++.
T Consensus 622 QkPlV~~g--~~v~~g~~ladg~~~~~gel~~G~N~~VA~m~~~GYn~EDAiiin~~~v~~g~~~s~~~~~~~~~~~~~~ 699 (1070)
T CHL00001 622 QKPQVRRG--KCVKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTS 699 (1070)
T ss_pred cCCEEecC--CEEccCCEeccChhhccccccCCccceeeeeeccccccchhhhhhhhhhcCCceEEEEEeeeeEEEeccC
Confidence 99999997 6665 999999999999999999999999999999999999999999999999988764
Q ss_pred CcccccccC--CCCCCCCCCCCCCcCCCCCCCCcCCCcEECCCCEEEEEeCCCCcccc--c---------cccCCCccce
Q 000996 833 TLVKEDFGR--PDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEA--Q---------GQASRYTRRD 899 (1195)
Q Consensus 833 ~~~~e~~~~--p~~~~~~~~~~~~~~~Ld~dGi~~~G~~v~~gdvli~k~~~~~~~~~--~---------~~~~~~~~~~ 899 (1195)
.+ .|.+.. |+.. ...|++||+||||++|++|++|||||||++|....+. . ...+....+|
T Consensus 700 ~g-~e~i~~~~p~~~------~~~~~~Ld~dGi~~~G~~v~~gDilvgK~~p~~~~~~~~~~~~~~~~~if~~~~~~~~d 772 (1070)
T CHL00001 700 QG-PERITKEIPHLE------AHLLRNLDKNGIVMLGSWVETGDILVGKLTPQEAEESSYAPEGRLLRAIFGIQVSTSKE 772 (1070)
T ss_pred CC-cceEeccCCCCc------hhhhhccCCCCCccCCcEecCCCEEEEEecCCcccccccCcchhhhhhhhccccCccee
Confidence 43 466653 5532 1358999999999999999999999999999732111 0 0112345799
Q ss_pred eeEEeecCCCcEEEEEEEEec----CCCcEEEEEEEeeecCCCCcccccccCCCceeEEeeecCCCCCCCCCCCCCcEEe
Q 000996 900 HSISLRHSETGMVDQVLLTTN----ADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIV 975 (1195)
Q Consensus 900 ~s~~~~~~~~g~v~~v~~~~~----~~~~~~v~v~~~~~R~~~iGDKf~sRHGqKGvvs~i~~~~dmPf~~~G~~pDiIi 975 (1195)
+|++++++++|+|++|.+++. .++.+.|||++|+.|+|+||||||||||||||||+|||+|||||++||++|||||
T Consensus 773 ~sl~~~~~~~g~V~~v~~~~~~~~~~~~~~~vkv~i~~~R~~~vGDK~asRHGqKGvvs~i~~~eDMPf~~dG~~pDiIl 852 (1070)
T CHL00001 773 TCLKLPIGGRGRVIDVRWIQKKGGSSYNPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVL 852 (1070)
T ss_pred CeEECCCCCceEEEEEEEEecccCCCCCcEEEEEEEEEEecCCCCcccccccCCcceEeeeecccCCCcccCCCCCceee
Confidence 999999999999999999873 4567899999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCchhhHHHHhhhHHhhhcCCCcccCCCCCccHHHHH-----HHHHHcCC----------CCCCeEEEeeCCC
Q 000996 976 NPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNIS-----KALHKCGY----------QMRGFETMYNGHT 1040 (1195)
Q Consensus 976 NPh~~PSRMtiGql~E~~~gk~~~~~g~~~~~tpF~~~~~~~~~-----~~l~~~g~----------~~~G~~~l~~G~t 1040 (1195)
||||||||||||||+|+++||||++.|.+.|+|||++...+++. ..|.++|+ +++|+++||||+|
T Consensus 853 NP~gvPSRMtiGqllE~~~G~a~~~~g~~~~~~pf~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~Gk~~l~dG~T 932 (1070)
T CHL00001 853 NPLGVPSRMNVGQIFECLLGLAGDLLNRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRLFDGRT 932 (1070)
T ss_pred ccccccccccHHHHHHHHhHHHHhhcCceeeeccCCCcchhhhhhhhhhHHHHHHHHhcCCceeccCCCCCeEEEEcCCC
Confidence 99999999999999999999999999999999999987777766 56778776 4459999999999
Q ss_pred CceeeeeEeEeeeehhccccccCcccEEeccCCccccccCCCCcccCCCccccchhhhhHHHhhccHHHHHHhhhcCCCc
Q 000996 1041 GRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDA 1120 (1195)
Q Consensus 1041 G~~~~~~if~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~Erl~~~SD~ 1120 (1195)
|++|+++||+|++|||||+|||+||+||||+|||++|||||++||||+|||||||||||||+|||||++|||||+.+||.
T Consensus 933 G~~~~~~i~vG~~Yy~kL~HmV~DKihaRs~Gp~~~lT~QP~~Grsr~GG~RfGEME~~al~a~GAs~~L~E~L~~~SD~ 1012 (1070)
T CHL00001 933 GDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSDH 1012 (1070)
T ss_pred CCCccceEEEEecceeEchhhccccceeeccCCCcccccCCCCcccCCCCeeeecchHHHHHhhhHHHHHHHHHhccCcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999996
Q ss_pred eeeeeccccCcceeeccccCceeeccCCCCCCcee-ecchHhhHHHHHHHHhCCCceEEEecc
Q 000996 1121 YRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQ-VHIPYACKLLFQELMAMAIAPRMLTKE 1182 (1195)
Q Consensus 1121 ~~~~vC~~cG~~~~~~~~~~~~~C~~C~~~~~~~~-v~iPy~~kll~~EL~sm~i~~~l~~~~ 1182 (1195)
.... |.. +.| |.++..+.+ +.+|||||+|++||+|||+++++..-.
T Consensus 1013 ~~~r-~~~-------------~~~--i~~g~~~~~~~~~pesfk~l~~El~~l~l~i~~~~~~ 1059 (1070)
T CHL00001 1013 IRAR-QEV-------------LGA--IITGGTIPKPEDAPESFRLLVRELRSLALELNHFLVS 1059 (1070)
T ss_pred HHHH-HHH-------------HHh--hhcCCcccCCCCCCchhhHHHHHHHhCccceEEEEEe
Confidence 5543 111 112 333456777 799999999999999999999998643
No 10
>CHL00207 rpoB RNA polymerase beta subunit; Provisional
Probab=100.00 E-value=6.3e-204 Score=1894.22 Aligned_cols=924 Identities=26% Similarity=0.390 Sum_probs=765.8
Q ss_pred cccCccchHHHHHHHHHHHHHhhHHHHHcccCCeeeCCCCCCCCCCCCCCCCceEEEEEe--EEEEccCccccCCCcccC
Q 000996 34 AYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQSDFAETIYKISFG--QIYLSKPMMTESDGETAT 111 (1195)
Q Consensus 34 ~~f~~~~Lv~~qi~SFn~Fi~~gL~~ii~~~~pI~~~~~~~~~~~~~~~~~~~~~~l~f~--~v~v~~P~~~e~~~~~~~ 111 (1195)
.-|..++|++.|++||+|||++||++++++++||+. ....+.++|. ++++++|.+
T Consensus 3 ~~~~~Pdll~iQ~~SF~~FL~~GL~~~~~~~~pI~~--------------~~~~~~l~~~~~~y~l~~P~~--------- 59 (1077)
T CHL00207 3 MNFALPDFLEIQRTSFCWFLNEGLNEELNIFSKIFD--------------YTGNLELLLFGKNYKLKYPKY--------- 59 (1077)
T ss_pred cccCCCCHHHHHHHHHHHHHHHHHHHHHHhcCCeEC--------------CCCCEEEEEecceEEEcCCCC---------
Confidence 347789999999999999999999999999999973 2345666665 799999986
Q ss_pred CChHHHHhcCCccceeEEEEEEEEEeccCCCCcccccceeeEEEEecccceeeccCCccCCCCChhhhhhcCCCCCCCCc
Q 000996 112 LFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGG 191 (1195)
Q Consensus 112 l~P~EcR~r~lTYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~eli~~gE~~~D~GG 191 (1195)
+|.|||+|++||+++|+|++++...+. +++++++|++|+||+|+. +|
T Consensus 60 -~~~Ea~~r~~TYsa~l~v~~~l~~~~~--------~~i~~~~V~lG~iPlMT~------------------------~G 106 (1077)
T CHL00207 60 -NLLSAKSYDSNYSIQIYLPLKFINLKT--------NKIKFINYLIGNLPKMTQ------------------------RG 106 (1077)
T ss_pred -CHHHHHHhCCccceeEEEEEEEEEcCC--------ceEEEEEEEEeccCccCC------------------------CC
Confidence 689999999999999999999975432 234678999999999975 99
Q ss_pred eEEEcCeeeEEeeeeeeecceEEEEEecCCCcceEEEEEEEeecCCCCCCceEEEEEEecCCCCCCCCCcEEEEEecccc
Q 000996 192 YFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPYIR 271 (1195)
Q Consensus 192 YFIING~ERVII~Qe~~s~N~~~~~~~~~~~~~~~~~~irs~~~~g~~~~~~~~v~~~~~~~~k~~~~~~~i~v~i~~~~ 271 (1195)
||||||+|||||+|+.|||+.+|.......++..|.|.| ++.+|+|...++ . .++.+|+++++ +
T Consensus 107 tFIING~ERViVsQl~RSPGiyf~~~~~k~~~~~y~a~I--Ip~rGswl~~e~----d---------~k~~i~vridr-~ 170 (1077)
T CHL00207 107 TFIINGLERVIVSQIIRSPGIYFKKEIKKNSNKIYSATL--IPNRGSWIKFEL----D---------KNKEIWIRIDK-N 170 (1077)
T ss_pred EEEEcCceeEEEEEeccCCeEEEEEecCcCCceEEEEEE--EcCCCceEEEEE----c---------CCCeEEEEecC-C
Confidence 999999999999999999997775443333455688888 668999965333 1 14589999998 5
Q ss_pred ccchHHHHHHHhcCCChHHHHHHhcccccchHHHHHhHhhHhhhhccCCHHHHHHHHhhcCcccCCCchhhHHHHHHHH-
Q 000996 272 TEIPIIIVFRALGFVADKDILEHICYDFQDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGATVGVTRDKRIKYAKEIL- 350 (1195)
Q Consensus 272 ~~IPl~ilLrALG~~sD~eI~~~i~~~~~~~~~~~~l~~sl~e~~~i~t~~~al~yig~r~~~~~~~~~~~~e~~~~~L- 350 (1195)
++||+++||||||+ ||+||++.+.+. .+..+ +...+.. ....++++|+.+|+++++.. .....+.++.++
T Consensus 171 rKipit~lLrALGl-s~~eIl~~~~~~-~~~~~---~~~~l~~-~~~~~~e~Al~~Iy~~lrp~---~~~~~~~a~~~l~ 241 (1077)
T CHL00207 171 RKKPLIIFLKALGL-TDQDIYSRLTKS-EFLKK---LKPILLN-SNSYTNEEILLEIYKNLSPI---EPATVNDANQNLF 241 (1077)
T ss_pred ceeeHHHHHHHhCC-CHHHHHHHHhcc-chHHH---HHHHHhc-cCcccHHHHHHHHHHhcCCC---CCccHHHHHHHHH
Confidence 59999999999999 799999998541 12222 2222221 23458999999999997542 223334566554
Q ss_pred ------HhcccCCCCCCC-----------CcchhHHHHHHHHHHHHHHhhcCCCCCCCCCccccceecccchhHHHHHHH
Q 000996 351 ------QKEMLPHVGTGD-----------FCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRM 413 (1195)
Q Consensus 351 ------~~~llpHl~~~~-----------~~~~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~NKRv~l~G~Ll~~lfr~ 413 (1195)
++|.|+|+|... ....-++..+..|+++|+.+..|....||+|||+||||+++|+||++|||.
T Consensus 242 ~~ff~~~rYdLg~vGR~klN~kl~~~~~~~~~~l~~~Dil~~i~~Li~l~~g~~~~DDiDHL~NRRvrsvGELlq~qfr~ 321 (1077)
T CHL00207 242 SRFFDPKNYDLGKVGRYKINNKLNLNIPERVRNLTYEDILSIIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRI 321 (1077)
T ss_pred HHhcChhcccccccchhhhhhhccCCcCccCceecHHHHHHHHHHHHHhhcCCCcccchhhhhcccccchhHHHHHHHHH
Confidence 566788988621 112233334568999999999999899999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhhhhccCCCCchhhcccccccccccccccccccccccccccccccceeeccccChhhhhccccccCC
Q 000996 414 LFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS 493 (1195)
Q Consensus 414 ~l~~~~k~ik~~l~k~~~~~~~~~~~~~i~~~~It~~i~~~~sTGnw~~~~~~~~~sG~sq~l~r~N~ls~lSh~Rrv~~ 493 (1195)
+|.++.+.++++|.+. ..+.+++..+++++.+|..|++||+ ++||||+|||+||||+|||+||+++
T Consensus 322 gl~rler~ike~m~~~--~~~~~tp~~lin~k~lt~~ikeFFg------------ss~LSQfmDQtNpLselTHKRRlsa 387 (1077)
T CHL00207 322 GLKRLERILRNRMTIC--DIDSLSKFNLINPKPLIALIREFFG------------SSQLSQYMDQTNPLSELTHKRRISI 387 (1077)
T ss_pred HHHHHHHHHHHHhhhc--ccccCChhhcccchhHHHHHHHhhc------------cCCccceecccChHHhhhccceeec
Confidence 9999999999999754 2245788899999999999999997 5899999999999999999999997
Q ss_pred --C--CCcCCCccccccccCCCcccccccCCCCCcccchhhcccccEEEcc-CCCchhHHHHHHHhCCccccccCCCCCC
Q 000996 494 --P--IGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITV-GSAAYPILEFLEEWGTENFEEISPAVIP 568 (1195)
Q Consensus 494 --~--~~~~~k~t~vR~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~It~-~~~~~~i~~~l~~~g~~~~~~~~~~~~~ 568 (1195)
| +.++++.+++|++||||||||||+|||||+|||||++||++|.|+. |+.++|+
T Consensus 388 LGpGGLsR~ra~fevRdvH~thyGRiCPIETPEG~n~Gli~~la~~~~in~~GfietPy--------------------- 446 (1077)
T CHL00207 388 LGPGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCGLIGSLATNARINKFGFIETPF--------------------- 446 (1077)
T ss_pred cCCCcccccccCCcccccCccccccccCCCCCCCcccccccchhhhccccCCCceeCce---------------------
Confidence 4 5677888899999999999999999999999999999999999987 5544431
Q ss_pred CceEEEECCEEEEEEcChHHHHHHHHhhhccCCCCcceEEEEeccCCeEEEEeCCCceeeeEEEEecccchhhHHHHHHh
Q 000996 569 QATKIFVNGCWVGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIAL 648 (1195)
Q Consensus 569 ~~~~V~lnG~~iG~~~~~~~~~~~lr~~rr~~~i~~~~~i~~~~~~~~i~I~td~GRl~RPl~~v~~~~~~~~~~~~~~l 648 (1195)
.+| .||.+. .
T Consensus 447 --~~v-~~g~v~-----------------------------------------------------------~-------- 456 (1077)
T CHL00207 447 --YKV-INGKVK-----------------------------------------------------------K-------- 456 (1077)
T ss_pred --EEE-EcCccc-----------------------------------------------------------c--------
Confidence 122 333320 0
Q ss_pred hcCCCCCCCCccccccCCeEEEecccccccceeecccchhhcccCCCCc------------cCCCceeeeecCCCccccc
Q 000996 649 QQRESPEDGGWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEE------------AYADTYTHCEIHPSLILGV 716 (1195)
Q Consensus 649 ~~~~~~~~~~~~~l~~~g~iE~i~~~Ee~~~~Ia~~~~~~~~~~~~~~~------------~~~~~~th~EI~P~~ilsv 716 (1195)
...++|++|.||+...||.....+...+.+.+. ..+.+.++++++|.|++||
T Consensus 457 ----------------~~~i~ylsa~~e~~~~Ia~~~~~~~~~~~~~~~~v~~r~~~ef~~~~~~~v~~~~vsp~Q~~Sv 520 (1077)
T CHL00207 457 ----------------FGNPIYLTADSEDLYRIAPNDINLNKNNYFKKNIIPVRYKQEFKTVNPSKVDFIAISPIQVFSI 520 (1077)
T ss_pred ----------------cCceeecChHHhcCcEEEecCccCCCCCcccCCEEEEEECCcEEEEChHHceEEEeCcchhcch
Confidence 023789999999999999877665543221100 0134578999999999999
Q ss_pred cccccCCCCCCCCCccccccccccCccccccee-----------------------------------eEEEeec---cc
Q 000996 717 CASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTN-----------------------------------YQFRMDT---LA 758 (1195)
Q Consensus 717 ~AslIPF~~hNqSpRn~yqc~M~KQa~g~~~~n-----------------------------------~~~r~D~---~~ 758 (1195)
+||||||++||||+|++|||||||||||+.... +.++.+. ..
T Consensus 521 aasLIPFLehdDanRaLMGsnMqrQaVPll~~e~p~VgTg~e~~~a~ds~~~i~a~~~G~v~~v~~~~I~i~~~~~~~~~ 600 (1077)
T CHL00207 521 AESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIVGTGYEKQIALDSGMTIISLTEGIVVSVSAYKIIIQDDNNRYIH 600 (1077)
T ss_pred hhhcCCcccccccchhhhhhccccccccccccCCCeEECCcchHhhhhcchheEeccCcEEEEecCcEEEEEeCCCceeE
Confidence 999999999999999999999999999985221 1222221 22
Q ss_pred eee----------ecCCCceeecc----cccc------cccccCCCCceEEEEEEecCCccCCCcEEEecceeecCceeE
Q 000996 759 YVL----------YYPQKPLVTTR----AMEH------LHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRS 818 (1195)
Q Consensus 759 ~~l----------~ypQ~Plv~t~----~~~~------~~~~~~~~G~N~~VAv~s~~Gyn~EDaiiink~s~~rG~f~s 818 (1195)
|.| |+.|||+|+.+ .++. +.++|+|+|+|++||||||+||||||||||||++++||+|||
T Consensus 601 y~l~~~~rsNq~t~i~qrp~V~~G~~v~~G~iladg~~~~~~el~lG~N~lVA~m~y~GYN~EDAiiink~~v~rg~f~S 680 (1077)
T CHL00207 601 YYLQKYQRSNQNTCINYRPIVWVGEKINIGQILADGSDIDNSELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTS 680 (1077)
T ss_pred EEeccccccccCceeecccccCCCCEEecCCEEecchhccCCcccCCcccEEEEEeeeccccchhhhhhhhhhcCCceEE
Confidence 433 57999999974 2333 379999999999999999999999999999999999999999
Q ss_pred EEEEEEEechhccCCccccccc--CCCCCCCCCCCCCCcCCCCCCCCcCCCcEECCCCEEEEEeCCCCccccc-------
Q 000996 819 LFFRSYRDEEKKMGTLVKEDFG--RPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ------- 889 (1195)
Q Consensus 819 ~~~~~~~~~~~~~~~~~~e~~~--~p~~~~~~~~~~~~~~~Ld~dGi~~~G~~v~~gdvli~k~~~~~~~~~~------- 889 (1195)
+|+++|+++++.+..+ .|+|. +|+.. ...|++||+||||++|++|++|||||||++|+...+..
T Consensus 681 i~~~~~~~e~~~~~~g-~e~i~~~~p~~~------~~~~~~LD~dGiv~iG~~V~~gDilvgK~tp~~~~~~~~~~~ll~ 753 (1077)
T CHL00207 681 IHIEKYEIELRQTKLG-SEEITRNIPNVS------EYSLKNLDENGIISIGSKVLAGDILVGKITPKGESDQLPEGKLLR 753 (1077)
T ss_pred EEEEEeeeEEeecCCC-ceEEeccCCCCC------hHHhhccCccCCCcCCcEeCCCCEEEEEecCccccccChhhhhhh
Confidence 9999999988765433 46665 45432 23589999999999999999999999999996422210
Q ss_pred --cccCCCccceeeEEeecCCCcEEEEEEEEecCC--Cc-----EEEEEEEeeecCCCCcccccccCCCceeEEeeecCC
Q 000996 890 --GQASRYTRRDHSISLRHSETGMVDQVLLTTNAD--GL-----RFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQE 960 (1195)
Q Consensus 890 --~~~~~~~~~~~s~~~~~~~~g~v~~v~~~~~~~--~~-----~~v~v~~~~~R~~~iGDKf~sRHGqKGvvs~i~~~~ 960 (1195)
...+....+|+|++++++++|+|++|.++.+++ +. ..|||++|+.|+|+||||||||||||||||+|||+|
T Consensus 754 ~i~~~~~~~~kd~sl~~~~~~~g~V~~V~~~~~~~~~~~~~~~~~~vkv~i~~~R~p~vGDKfasRHGqKGVvs~i~p~e 833 (1077)
T CHL00207 754 AIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRSKGDELKFGYYLKIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQ 833 (1077)
T ss_pred hhhccCCCcceEeEEEcCCCCcEEEEEEEEEecCCCCcccccccEEEEEEEEEEecCCcccccccccCCceeEEeeeccC
Confidence 112234579999999999999999999987543 22 358999999999999999999999999999999999
Q ss_pred CCCCCCCCCCCcEEeCCCCCCCCCchhhHHHHhhhHHhhhcCCCcccCCCCCccHHHHHHHHHHc---------------
Q 000996 961 DMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKC--------------- 1025 (1195)
Q Consensus 961 dmPf~~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~~~tpF~~~~~~~~~~~l~~~--------------- 1025 (1195)
||||++||++|||||||||||||||||||+|+++||||++.|...++|||++...+++++.|...
T Consensus 834 DMPf~~dG~~pDiIlNPhg~PSRMtiGqllE~~lGka~~~l~~~~~~tpF~~~~~~~~~~~l~~~~l~~~~~~~~~~~~~ 913 (1077)
T CHL00207 834 DMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGDNLNKRFKILPFDEMYGSEYSRILINNKLNQASIKNNEYWLF 913 (1077)
T ss_pred CCCccCCCCCccEEECCccccccccHHHHHHHHHHHHHHhcCCcEeeccCCCCcHHHHHHHHHhhhhhhccchhcccccc
Confidence 99999999999999999999999999999999999999998888899999998888888777654
Q ss_pred CCCCCCeEEEeeCCCCceeeeeEeEeeeehhccccccCcccEEeccCCccccccCCCCcccCCCccccchhhhhHHHhhc
Q 000996 1026 GYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHG 1105 (1195)
Q Consensus 1026 g~~~~G~~~l~~G~tG~~~~~~if~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~G 1105 (1195)
+|+++|+++||||+||++|+++||+|++|||||+|||+||+||||+|||++|||||++||||+|||||||||||||+|||
T Consensus 914 ~~~~~Gk~~lydG~TGe~~~~~i~vG~~Yy~kL~HmV~DKihaRs~Gp~s~lTqQP~~Grsr~GG~RfGEME~~aL~a~G 993 (1077)
T CHL00207 914 NSYHPGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFG 993 (1077)
T ss_pred CCCCCCCEEEECCCCCCCccCceEEEecceeEchhhccccceeeccCCCcccccCCCCccccCCCeeeecccHHHHHhhh
Confidence 37789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHhhhcCCCceeeeeccccCcceeeccccCceeeccCCCCCCceeecchHhhHHHHHHHHhCCCceEEEecc
Q 000996 1106 ASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKE 1182 (1195)
Q Consensus 1106 as~~l~Erl~~~SD~~~~~vC~~cG~~~~~~~~~~~~~C~~C~~~~~~~~v~iPy~~kll~~EL~sm~i~~~l~~~~ 1182 (1195)
||++|||||+.+||.+.+. ..+|..|.++.+++++.+|||||+|+|||+||||++++....
T Consensus 994 Aa~~L~E~L~~kSD~~~~r----------------~~~~~~~~~~~~i~~~~~P~sfklL~~EL~sl~i~~~~~~~~ 1054 (1077)
T CHL00207 994 AAYTLKELLTIKSDDMQGR----------------NETLNAIVKGQPIPKPGTPESFKVLMRELQSLGLDIEAYKIE 1054 (1077)
T ss_pred hHHHHHHHhhcCCccceeh----------------HHHHHhhhCCCeecCCCCCchHHHHHHHHHHCCcCcEecccc
Confidence 9999999999999977631 125999999999999999999999999999999999998654
No 11
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=100.00 E-value=2.5e-192 Score=1839.43 Aligned_cols=944 Identities=26% Similarity=0.387 Sum_probs=777.5
Q ss_pred hhhhhhhcccCccchHHHHHHHHHHHHH------hhHHHHHcccCCeeeCCCCCCCCCCCCCCCCceEEEEEeEEEEccC
Q 000996 27 DAWAVISAYFEEKGLVRQQLDSFDEFIQ------NTMQEIVDESADIEIRPESQHNPGQQSDFAETIYKISFGQIYLSKP 100 (1195)
Q Consensus 27 ~~~~~i~~~f~~~~Lv~~qi~SFn~Fi~------~gL~~ii~~~~pI~~~~~~~~~~~~~~~~~~~~~~l~f~~v~v~~P 100 (1195)
..|+.++..+..|+|++.|.+||+||++ +||+++|++++||+ +.+..+.|+|.++++++|
T Consensus 13 ~~f~k~~~~~~iPdLleIQ~~SF~~FLq~~~~~~~GL~e~f~~~fPI~--------------d~~g~~~Lefv~Y~l~~P 78 (2890)
T PRK09603 13 ADFTKTPTDLEVPNLLLLQRDSYDSFLYSKDGKESGIEKVFKSIFPIQ--------------DEHNRITLEYAGCEFGKS 78 (2890)
T ss_pred eecccCCccCCCCCHHHHHHHHHHHHHhCCCcccccHHHHHHhcCCeE--------------CCCCcEEEEEEEEEeCCC
Confidence 4578888888999999999999999998 79999999999997 445679999999999999
Q ss_pred ccccCCCcccCCChHHHHhcCCccceeEEEEEEEEEeccCCCC--cccccceeeEEEEecccceeeccCCccCCCCChhh
Q 000996 101 MMTESDGETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDG--EEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKD 178 (1195)
Q Consensus 101 ~~~e~~~~~~~l~P~EcR~r~lTYsa~l~v~v~~~~~~~~~~~--~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~e 178 (1195)
.+ +|.||++|++||++||+|++++.+.+...++ .+.++++++++|++|+||+|+.
T Consensus 79 k~----------~~~Ec~~rg~TYsapL~v~~rL~~~~~~~~t~~~~~ikeikeq~VylGdiPLMT~------------- 135 (2890)
T PRK09603 79 KY----------TVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQSIFIREIPLMTE------------- 135 (2890)
T ss_pred CC----------CHHHHHhhCCcccccEEEEEEEEEeeccccccccccccceEEeeEEEecCCccCC-------------
Confidence 88 4689999999999999999999863322111 1234567789999999999997
Q ss_pred hhhcCCCCCCCCceEEEcCeeeEEeeeeeeecceEEEEEec--CCCcceEEEEEEEeecCCCCCCceEEEEEEecCCCCC
Q 000996 179 LTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFKKR--QPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKG 256 (1195)
Q Consensus 179 li~~gE~~~D~GGYFIING~ERVII~Qe~~s~N~~~~~~~~--~~~~~~~~~~irs~~~~g~~~~~~~~v~~~~~~~~k~ 256 (1195)
.|+|||||+|||||+|++|||+.+|..... ..++..|+|.| +|.+|+|+.++++
T Consensus 136 -----------~GTFIING~ERVIVsQL~RSPGVyF~~~~~k~~s~k~lysa~I--IP~RGsWLefE~D----------- 191 (2890)
T PRK09603 136 -----------RTSFIINGVERVVVNQLHRSPGVIFKEEESSTSLNKLIYTGQI--IPDRGSWLYFEYD----------- 191 (2890)
T ss_pred -----------CceEEEcCceeEEEeeeccCCeeEEeeccCcCCCCceeEEEEE--ecCCcceEEEEEc-----------
Confidence 999999999999999999999988764422 23455688888 7799999765552
Q ss_pred CCCCcEEEEEeccccccchHHHHHHHhcCCChHHHHHHhcccc-----------------------------c-------
Q 000996 257 GSSGQYIRATLPYIRTEIPIIIVFRALGFVADKDILEHICYDF-----------------------------Q------- 300 (1195)
Q Consensus 257 ~~~~~~i~v~i~~~~~~IPl~ilLrALG~~sD~eI~~~i~~~~-----------------------------~------- 300 (1195)
.++.+|+++++ +++||+++||||||+ +++||++.+.... .
T Consensus 192 --~kd~l~vrIDr-krKipit~lLrAlG~-s~edIl~~f~~~~~~~i~~~~~~~~~~~~~l~~~~~~di~d~~g~vlv~~ 267 (2890)
T PRK09603 192 --SKDVLYARINK-RRKVPVTILFRAMDY-QKQDIIKMFYPLVKVRYENDKYLIPFASLDANQRMEFDLKDPQGKIILLA 267 (2890)
T ss_pred --CCCeEEEEEcC-cceecHHHHHHHhCC-CHHHHHHHhcccceEEEcccceeecccHHHhcCccceeecccCCCEEEec
Confidence 14689999999 679999999999999 6899999874100 0
Q ss_pred ----chHHH-------------------------------HHhHh-----------hHhhh-------------------
Q 000996 301 ----DTQMM-------------------------------ELLRP-----------SLEEA------------------- 315 (1195)
Q Consensus 301 ----~~~~~-------------------------------~~l~~-----------sl~e~------------------- 315 (1195)
+.... +.+.. .+.+.
T Consensus 268 g~rit~~~~~~l~~~g~k~l~~~~~~l~g~~laedivd~~Evl~~~~~~Itee~le~i~~~gi~~i~vl~~~~~~~~~~i 347 (2890)
T PRK09603 268 GKKLTSRKIKELKENHLEWVEYPMDILLNRHLAEPVMVGKEVLLDMLTQLDKNKLEKIHDLGVQEFVIINDLALGHDASI 347 (2890)
T ss_pred CccccHHHHHHHHhcCCceeccchhhhcceeeeeeccCccceeeccCChhcHHHHHHHHHcCCceEEEEeeccccccccc
Confidence 00000 00000 00000
Q ss_pred ------------------hccCCHHHHHHHHhhcCcccCCCchhhHHHHHHHHHhcccC-------CCCCCC--------
Q 000996 316 ------------------FVIQNQQVALDYIGKRGATVGVTRDKRIKYAKEILQKEMLP-------HVGTGD-------- 362 (1195)
Q Consensus 316 ------------------~~i~t~~~al~yig~r~~~~~~~~~~~~e~~~~~L~~~llp-------Hl~~~~-------- 362 (1195)
....++++|+..|+++++. ......+.|+.++++.||- .+|...
T Consensus 348 ~~t~~~d~~~~~~~~~t~~~~~~~eeAl~~iyr~lrp---gep~~~e~A~~l~~~lFFn~~rYdLg~vGR~klN~kL~l~ 424 (2890)
T PRK09603 348 IHSFSADSESLKLLKQTEKIDDENALAAIRIHKVMKP---GDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKMNHKLGLH 424 (2890)
T ss_pred ccccccccccchhhhhccccccchHHHHHHHHhccCC---CCCCcHHHHHHHHHHHhcCcccccccccchhhhHhhhCCC
Confidence 0001458899999988754 3334456677777766543 122110
Q ss_pred ----CcchhHHHHHHHHHHHHHHhhcCCCCCCCCCccccceecccchhHHHHHHHHHHHHHHHHHHHhhhhhccCCCCch
Q 000996 363 ----FCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNL 438 (1195)
Q Consensus 363 ----~~~~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~NKRv~l~G~Ll~~lfr~~l~~~~k~ik~~l~k~~~~~~~~~~ 438 (1195)
.....+.+++ ..+++|+.+..|....||+|||+||||+++|+||+++|+.+|.++.+.++++|.........+++
T Consensus 425 ~~~~~~~Lt~~Dil-~~i~~li~l~~g~~~~DDiDhL~NRRvr~vGELl~~qfr~gl~rler~irerm~~~~~~~~~~~p 503 (2890)
T PRK09603 425 VPDYITTLTHEDII-TTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELHSGLVKMQKTIKDKLTTMSGAFDSLMP 503 (2890)
T ss_pred CCCcccEecchhHH-HHHHHHHHHHhCCCCCCcchhhhcchhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccCh
Confidence 0112344656 59999999999999999999999999999999999999999999999999999854333456788
Q ss_pred hhcccccccccccccccccccccccccccccccceeeccccChhhhhccccccCC--CC--CcCCCccccccccCCCccc
Q 000996 439 QFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS--PI--GREGKLAKPRQLHNSQWGM 514 (1195)
Q Consensus 439 ~~~i~~~~It~~i~~~~sTGnw~~~~~~~~~sG~sq~l~r~N~ls~lSh~Rrv~~--~~--~~~~k~t~vR~Lhps~wG~ 514 (1195)
..++|++.++..++.||+| +++||+|||+||||+|+|+||+++ |. .+++..+++|++|||||||
T Consensus 504 ~~lin~k~i~~~ikeFFgs------------sqLSQfmDQtNpLseltHKRRlSaLGPGGlsr~ra~fevRdVH~shYGR 571 (2890)
T PRK09603 504 HDLVNSKMITSTIMEFFMG------------GQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGR 571 (2890)
T ss_pred hhhhccHHHHHHHHHHhcc------------CchhhhhcccChhhhhhhcccccccCCCCccccccCCcccccCcccccc
Confidence 8999999999999999974 679999999999999999999986 54 4667888999999999999
Q ss_pred ccccCCCCCcccchhhcccccEEEcc-CCCchhHHHHHHHhCCccccccCCCCCCCceEEEECCEEEEEEcChHHHHHHH
Q 000996 515 MCPAETPEGQACGLVKNLALMVYITV-GSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKTL 593 (1195)
Q Consensus 515 iCPveTPEG~~cGLvk~LA~~a~It~-~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~l 593 (1195)
|||+|||||+|||||++||.+|+|+. |+.++| +.+| .||.+
T Consensus 572 iCPIETPEG~NiGLI~SLa~~a~in~~GfietP-----------------------y~kV-~~g~v-------------- 613 (2890)
T PRK09603 572 ICPIETPEGQNIGLINTLSTFTRVNDLGFIEAP-----------------------YKKV-VDGKV-------------- 613 (2890)
T ss_pred cCCCCCCCCCcccchhhhhhheecccCcceecc-----------------------eEEE-ecCcc--------------
Confidence 99999999999999999999999987 554444 1222 23331
Q ss_pred HhhhccCCCCcceEEEEeccCCeEEEEeCCCceeeeEEEEecccchhhHHHHHHhhcCCCCCCCCccccccCCeEEEecc
Q 000996 594 RRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRESPEDGGWHDLVAKGFIEYIDT 673 (1195)
Q Consensus 594 r~~rr~~~i~~~~~i~~~~~~~~i~I~td~GRl~RPl~~v~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~g~iE~i~~ 673 (1195)
...++|++|
T Consensus 614 -----------------------------------------------------------------------~~~i~ylsa 622 (2890)
T PRK09603 614 -----------------------------------------------------------------------VGETIYLTA 622 (2890)
T ss_pred -----------------------------------------------------------------------ccceeeeCH
Confidence 012679999
Q ss_pred cccccceeecccchhhcccCCCCc------------cCCCceeeeecCCCccccccccccCCCCCCCCCccccccccccC
Q 000996 674 EEEETTMISMTINDLVQARLHPEE------------AYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQ 741 (1195)
Q Consensus 674 ~Ee~~~~Ia~~~~~~~~~~~~~~~------------~~~~~~th~EI~P~~ilsv~AslIPF~~hNqSpRn~yqc~M~KQ 741 (1195)
.||+...||.....+.+.+.+.+. ..+.+.++++++|.|++||+||||||++||||+|++||||||||
T Consensus 623 ~eE~~~~IA~a~~~~~~~~~~~~~~v~~R~~~e~~~~~~~~v~~~dvsp~Q~vSvaasLIPFLEhdDAnRALMGSNMQRQ 702 (2890)
T PRK09603 623 IQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQ 702 (2890)
T ss_pred HHhcCceEeccCCccCCCCcccCCeEeEEECCceEEEChHHceEEEeCccceeeehhhcCCccccCccccccccccchhh
Confidence 999999999877666543321100 01445789999999999999999999999999999999999999
Q ss_pred cccccce-----------------------------------eeEEEeec------cceee----------ecCCCceee
Q 000996 742 AMGIYVT-----------------------------------NYQFRMDT------LAYVL----------YYPQKPLVT 770 (1195)
Q Consensus 742 a~g~~~~-----------------------------------n~~~r~D~------~~~~l----------~ypQ~Plv~ 770 (1195)
|||+... .+.+|.+. ..|.| |++|+|+|+
T Consensus 703 AVPLl~~e~piVgTG~E~~va~dSg~~i~a~~~G~V~yvd~~~I~i~~~~~~~~~~~~Y~L~Ky~RSNQ~TcinqrPiV~ 782 (2890)
T PRK09603 703 AVPLLRSDAPIVGTGIEKIIARDSWGAIKANRAGVVEKIDSKNIYILGEGKEEAYIDAYSLQKNLRTNQNTSFNQVPIVK 782 (2890)
T ss_pred hhhhccccCCeEecCcchhhhccccceeEecCCeEEEEecCcEEEEEecCCCCceeeEEeeccccccCCCceeeeccEec
Confidence 9998421 12222221 12554 689999998
Q ss_pred ccc----ccc------cccccCCCCceEEEEEEecCCccCCCcEEEecceeecCceeEEEEEEEEechhccCCcccccc-
Q 000996 771 TRA----MEH------LHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDF- 839 (1195)
Q Consensus 771 t~~----~~~------~~~~~~~~G~N~~VAv~s~~Gyn~EDaiiink~s~~rG~f~s~~~~~~~~~~~~~~~~~~e~~- 839 (1195)
.+. ++. +..+|+++|+|++||||+|.|||||||||||++.+..++|||+|+.+|+++.+.+.. ..|+|
T Consensus 783 ~Gd~V~kGdilADG~st~~GELALG~NvlVAfmpW~GYNfEDAIlISERlV~eD~fTSIHIee~ei~~r~Tk~-G~EeIT 861 (2890)
T PRK09603 783 VGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVDARELKH-GVEEFT 861 (2890)
T ss_pred CCCEeccCCEEecCcccccCeeccCcccEEEEeeeccccCccccccchhhhcCccceEEEEeeeEEEEEecCC-CCcEEe
Confidence 742 333 479999999999999999999999999999999999999999999999999988754 45766
Q ss_pred -cCCCCCCCCCCCCCCcCCCCCCCCcCCCcEECCCCEEEEEeCCCCccccc---------cccCCCccceeeEEeecCCC
Q 000996 840 -GRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ---------GQASRYTRRDHSISLRHSET 909 (1195)
Q Consensus 840 -~~p~~~~~~~~~~~~~~~Ld~dGi~~~G~~v~~gdvli~k~~~~~~~~~~---------~~~~~~~~~~~s~~~~~~~~ 909 (1195)
++|+.+. ...++||++|||++|++|++|||||||++|+...+.. ..++....||+|++++++..
T Consensus 862 rdIPnvse------~~l~~LDe~GII~iGa~V~~GDILVGKvTPkge~~~tPEekLLraIFGeka~~vkDtSLrvp~G~~ 935 (2890)
T PRK09603 862 ADIPDVKE------EALAHLDESGIVKVGTYVSAGMILVGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLE 935 (2890)
T ss_pred ccCCCCCH------HHHhcCCCCCCEeeCCEECCCCEEEEeeccCCCCCCChHHHHHHHHhcccccccccCceecCCCCc
Confidence 4776432 3478999999999999999999999999998643321 23466779999999999999
Q ss_pred cEEEEEEEEecC--------------------------------------------------------------------
Q 000996 910 GMVDQVLLTTNA-------------------------------------------------------------------- 921 (1195)
Q Consensus 910 g~v~~v~~~~~~-------------------------------------------------------------------- 921 (1195)
|+|..|.+++.+
T Consensus 936 G~Vidv~~f~r~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1015 (2890)
T PRK09603 936 GTVIDVKVFTKKGYEKDARVLSAYEEEKAKLDMEHFDRLTMLNREELLRVSSLLSQAILEEPFSHNGKDYKEGDQIPKEE 1015 (2890)
T ss_pred EEEEEEEEecccccchhHHHHHHHHHHHHHHhHhhHHHHHHHHHHHHHhhhhhccccccccccccccccccccccccHHH
Confidence 999999887632
Q ss_pred --------------------------------------------------CC-------cEEEEEEEeeecCCCCccccc
Q 000996 922 --------------------------------------------------DG-------LRFVKVRVRSVRIPQIGDKFS 944 (1195)
Q Consensus 922 --------------------------------------------------~~-------~~~v~v~~~~~R~~~iGDKf~ 944 (1195)
.| .+.|||++|+.|+|+||||||
T Consensus 1016 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~gdeL~~Gv~~~VkV~ia~kR~~qvGDK~A 1095 (2890)
T PRK09603 1016 IASINRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNGVIKKVKLYIATKRKLKVGDKMA 1095 (2890)
T ss_pred HhhCCHHHhhhhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCcCCCCcceEEEEEEEEeecccccchhh
Confidence 01 357999999999999999999
Q ss_pred ccCCCceeEEeeecCCCCCCCCCCCCCcEEeCCCCCCCCCchhhHHHHhhhHHhhhcCCC--------------------
Q 000996 945 SRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKE-------------------- 1004 (1195)
Q Consensus 945 sRHGqKGvvs~i~~~~dmPf~~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~-------------------- 1004 (1195)
||||||||||+|||+|||||++||++||||+||||||||||||||+|+++||||+..|.+
T Consensus 1096 gRHGnKGViS~I~p~EDMPfl~dG~~pDIIlNPlGvPSRMnIGQilE~~LG~aa~~lg~~i~~~~~~~~~~~~~~~~~~~ 1175 (2890)
T PRK09603 1096 GRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGKQIASMLEDKTKDFAKELRAKM 1175 (2890)
T ss_pred hccCCCeeEEEEEchhcCCCCCCCCCCcEEECCCCCCccccHHHHHHHHHHHHHHhcCcChhhhhhhcchhhhHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999988754
Q ss_pred -------------------------------------cccCC-CCCccHHHHHHHHHHcCCCCCCeEEEeeCCCCceeee
Q 000996 1005 -------------------------------------GDATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTA 1046 (1195)
Q Consensus 1005 -------------------------------------~~~tp-F~~~~~~~~~~~l~~~g~~~~G~~~l~~G~tG~~~~~ 1046 (1195)
.++|| |++.+.+++.+.|+++||+++|++.||||+||++|++
T Consensus 1176 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~tpvF~g~~~~~i~~~l~~aG~~~~Gk~~LyDGrTGe~f~~ 1255 (2890)
T PRK09603 1176 LEIANAINEKDPLTIHALENCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRE 1255 (2890)
T ss_pred HhhhcccccccccccccccccchHHHHhhhhhhccCCcccCCCCCCCCHHHHHHHHHHcCCCCCCCEEEEcCCCCCCccc
Confidence 34788 9999999999999999999999999999999999999
Q ss_pred eEeEeeeehhccccccCcccEEeccCCccccccCCCCcccCCCccccchhhhhHHHhhccHHHHHHhhhcCCCceeeeec
Q 000996 1047 MIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVC 1126 (1195)
Q Consensus 1047 ~if~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~Erl~~~SD~~~~~vC 1126 (1195)
+||+|++|||||+|||+||+||||+|||+++||||++||+++|||||||||||||+|||||++|||||+.+||.+.
T Consensus 1256 ~V~vG~~YylKL~HmVdDKiHaRstGPyslvTqQPl~GKs~~GGqRfGEMEvwALeAyGAa~~LqE~Lt~kSDdv~---- 1331 (2890)
T PRK09603 1256 RVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDIR---- 1331 (2890)
T ss_pred eEEEEeeceeechhhccchhhhccCCCcchhhhCCCcccccCCCceeeeeeHHHHHHhhHHHHHHHHHhcCCcchh----
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999654
Q ss_pred cccCcceeeccccCceeeccCCCCCCceeecchHhhHHHHHHHHhCCCceEEEeccC
Q 000996 1127 EHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKED 1183 (1195)
Q Consensus 1127 ~~cG~~~~~~~~~~~~~C~~C~~~~~~~~v~iPy~~kll~~EL~sm~i~~~l~~~~~ 1183 (1195)
|+.. .|..|.++.++..+.+|||||+|++||+||||++++...+.
T Consensus 1332 ---gR~~---------~y~~i~~g~~i~~~~iPeSFkvL~~EL~sL~l~i~~~~~~~ 1376 (2890)
T PRK09603 1332 ---GREN---------AYRAIAKGEQVGESEIPETFYVLTKELQSLALDINIFGDDV 1376 (2890)
T ss_pred ---hhhh---------hhhhhcCCCcccccCCCHHHHHHHHHHHhCCcceEEEeecc
Confidence 4433 35667788899999999999999999999999999987543
No 12
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=100.00 E-value=1.3e-187 Score=1789.06 Aligned_cols=941 Identities=27% Similarity=0.390 Sum_probs=768.4
Q ss_pred hhhhhh-hhcccCccchHHHHHHHHHHHHH-----hhHHHHHcccCCeeeCCCCCCCCCCCCCCCCceEEEEEeEEEEcc
Q 000996 26 EDAWAV-ISAYFEEKGLVRQQLDSFDEFIQ-----NTMQEIVDESADIEIRPESQHNPGQQSDFAETIYKISFGQIYLSK 99 (1195)
Q Consensus 26 ~~~~~~-i~~~f~~~~Lv~~qi~SFn~Fi~-----~gL~~ii~~~~pI~~~~~~~~~~~~~~~~~~~~~~l~f~~v~v~~ 99 (1195)
...|+. .+..++.|+|++.|.+||+||++ +||+++|++++||+ +.+..+.|+|.++++++
T Consensus 16 R~~f~~~~~~~~~~PdL~~iQ~~Sf~~Fl~~~~~~~GL~~~f~~ifPI~--------------d~~g~~~lefv~y~l~~ 81 (2836)
T PRK14844 16 RVSYSRSIDLKDSLLDLVKVQKESYDSFTPKNKGNERLEVIFHTIFPIN--------------DPLHRATIEFISCRVDD 81 (2836)
T ss_pred eeecccCCcccCCCCCHHHHHHHHHHHHhcCCCccccHHHHHHhcCCeE--------------CCCCCEEEEEEEEEeCC
Confidence 345665 44458999999999999999997 69999999999997 44567999999999999
Q ss_pred CccccCCCcccCCChHHHHhcCCccceeEEEEEEEEEeccC---------CCC------cccccceeeEEEEecccceee
Q 000996 100 PMMTESDGETATLFPKAARLRNLTYSAPLYVDVTKRVIKKG---------HDG------EEVTETQDFTKVFIGKVPIML 164 (1195)
Q Consensus 100 P~~~e~~~~~~~l~P~EcR~r~lTYsa~l~v~v~~~~~~~~---------~~~------~~~~~~~~~~~v~lG~IPIMv 164 (1195)
|.+ ++.||++|++||++||+|+++++..+.+ .+. .+.++++++++|++|+||+|+
T Consensus 82 Pk~----------~~~Ec~~r~~TYsapl~v~~rL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ikeq~VylGdiPLMT 151 (2836)
T PRK14844 82 PKY----------DESECIKRGITFSAQVIASIRLVIMQDGISLDEYKSIKESGDHSKLATVIKSIEEQEVHFCELPMMT 151 (2836)
T ss_pred CCC----------CHHHHHhcCCcceeeEEEEEEEEEeccccccccccccccccccccccccccceeeeeEEEecCCccC
Confidence 988 4689999999999999999999863200 000 112345678899999999999
Q ss_pred ccCCccCCCCChhhhhhcCCCCCCCCceEEEcCeeeEEeeeeeeecceEEEEEec---CCCcceEEEEEEEeecCCCCCC
Q 000996 165 RSSYCTLYQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFKKR---QPNKYAYVAEVRSMAESQNRPP 241 (1195)
Q Consensus 165 kS~~C~L~~~s~~eli~~gE~~~D~GGYFIING~ERVII~Qe~~s~N~~~~~~~~---~~~~~~~~~~irs~~~~g~~~~ 241 (1195)
. .|+|||||+|||||+|++|||+.+|..... ..++..|+|+| +|.+|+|+.
T Consensus 152 ~------------------------~GTFIING~ERVIVSQL~RSPGVyF~~~~~kt~~sgk~lysa~I--IP~RGsWLe 205 (2836)
T PRK14844 152 D------------------------KGTFIINGVEKVIVSQMHRSPGVFFDSDKGKTYNSGKLIYSARV--IPYRGSWLD 205 (2836)
T ss_pred C------------------------CeEEEEcCcceEEEEcceeCCeEEEEcccCcccCCCceeEEEEE--ecCCcceEE
Confidence 7 999999999999999999999988764321 23455788888 779999976
Q ss_pred ceEEEEEEecCCCCCCCCCcEEEEEeccccccchHHHHHHHhcCCChHHHHHHhcccc------c-------ch------
Q 000996 242 STMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFRALGFVADKDILEHICYDF------Q-------DT------ 302 (1195)
Q Consensus 242 ~~~~v~~~~~~~~k~~~~~~~i~v~i~~~~~~IPl~ilLrALG~~sD~eI~~~i~~~~------~-------~~------ 302 (1195)
++++ .++.+|+|+++ ++++|+++||||||+ |++||++.+.... . .+
T Consensus 206 fE~D-------------~kd~lyvRIDR-kRKiPiT~LLrALGl-s~edIL~~F~~~~~~~~~d~~~~~~~~~e~l~g~~ 270 (2836)
T PRK14844 206 IEFD-------------VKDHLYFRIDR-KRKLPISVLLKALGL-SNNDILDRFYEKIKYIKHKDGWKVPFVPDKFKGVR 270 (2836)
T ss_pred EEEc-------------CCCeEEEEecC-CeeeeHHHHHHHhCC-ChHHHHHhhcCceEEEEccCceeeccCHHHHhCCc
Confidence 5542 14689999999 679999999999999 7899999774210 0 00
Q ss_pred ----------------------HH------------------------------------------------H-------
Q 000996 303 ----------------------QM------------------------------------------------M------- 305 (1195)
Q Consensus 303 ----------------------~~------------------------------------------------~------- 305 (1195)
.. .
T Consensus 271 ~~~Di~d~~g~vlvdkgrrit~~~~krlk~~gvkkl~i~~~~l~g~~LaeDIVD~eTGEiL~eagteIT~e~ik~l~~~g 350 (2836)
T PRK14844 271 LPFDLMDVEGNVLLKANVRITSRLAKKLYDNELKEYLVPFDSICGLFLAEDLIDSASSTKILSAGESIKLEDIKKLELLS 350 (2836)
T ss_pred cceeeeccCCCEEEecCccccHHHHHHHHHcccCcccCchHhhcCceehhhhcCCCCCeEEEcCCCccCHHHHHHHHHcC
Confidence 00 0
Q ss_pred ---------------HHhHhhHhhhhccCCHHHHHHHHhhcCcccCCCchhhHHHHHHHHHhcccC-------CCCC---
Q 000996 306 ---------------ELLRPSLEEAFVIQNQQVALDYIGKRGATVGVTRDKRIKYAKEILQKEMLP-------HVGT--- 360 (1195)
Q Consensus 306 ---------------~~l~~sl~e~~~i~t~~~al~yig~r~~~~~~~~~~~~e~~~~~L~~~llp-------Hl~~--- 360 (1195)
..+...+. .....++++|+..|+++++. ......+.|+.++++.||- .+|.
T Consensus 351 i~~i~~l~~d~~~~~~~i~~tL~-~D~~~~~e~Al~eIy~~lRp---ge~~~~e~a~~l~~~~ff~~~~YdLg~vGR~k~ 426 (2836)
T PRK14844 351 IDEISVLNIDNLSVGPYILNTLF-LDENMSYQDALYEIYKVLRP---GEVPVLEIVEEFFRNLFFSPEYYDLSNIGRLKL 426 (2836)
T ss_pred CCceeeEeecccccchHHHHHHh-hcccccHHHHHHHHHHhcCC---CCCCcHHHHHHHHHHHhcCccccccccchhhhh
Confidence 00000000 01124678999999998764 3334455677777665543 1111
Q ss_pred ----------CCCcchhHHHHHHHHHHHHHHhhcCCCCCCCCCccccceecccchhHHHHHHHHHHHHHHHHHHHhhhhh
Q 000996 361 ----------GDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCV 430 (1195)
Q Consensus 361 ----------~~~~~~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~NKRv~l~G~Ll~~lfr~~l~~~~k~ik~~l~k~~ 430 (1195)
....+ .+.+++ .++++|+.+..|....||+|||+||||+++|+||+.+|+.+|.++.+.++++|...
T Consensus 427 N~kl~~~~~~~~~~l-~~~Dii-~~i~~Li~l~~g~~~~DDiDhL~NRRvr~vGeLl~~qfr~gl~r~~~~i~e~~~~~- 503 (2836)
T PRK14844 427 NSYLGLNYDEDLTVL-THEDII-EIVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSMSTS- 503 (2836)
T ss_pred hhhhccCCCCCCcEe-cHHHHH-HHHHHHHHHhcCCCcccchhhhhccccchHHHHHHHHHHHHHHHHHHHHHHHHhhc-
Confidence 11112 344555 69999999999999999999999999999999999999999999999999999632
Q ss_pred ccCCCCchhhcccccccccccccccccccccccccccccccceeeccccChhhhhccccccCC--C--CCcCCCcccccc
Q 000996 431 DNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS--P--IGREGKLAKPRQ 506 (1195)
Q Consensus 431 ~~~~~~~~~~~i~~~~It~~i~~~~sTGnw~~~~~~~~~sG~sq~l~r~N~ls~lSh~Rrv~~--~--~~~~~k~t~vR~ 506 (1195)
+.+.+++..+++++.++..+++||+| +|+||+|||+||||+|||+||+++ | +.++++.+++|+
T Consensus 504 -~~~~~~p~~lin~~~l~~~i~~ff~s------------s~LSQfmDQtNpLseltHkRRlsaLGPGGL~r~~a~fevRd 570 (2836)
T PRK14844 504 -SLDKVSPSDFINPKVLTNVLRDFFNS------------SQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRD 570 (2836)
T ss_pred -cccccchhhcccchhHHHHHHHHhcc------------cchhhhccCcChhhhhhhcceecccCCCCcccccCCCcccc
Confidence 33567899999999999999999975 799999999999999999999997 5 457788889999
Q ss_pred ccCCCcccccccCCCCCcccchhhcccccEEEcc-CCCchhHHHHHHHhCCccccccCCCCCCCceEEEECCEEEEEEcC
Q 000996 507 LHNSQWGMMCPAETPEGQACGLVKNLALMVYITV-GSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRD 585 (1195)
Q Consensus 507 Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~It~-~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~ 585 (1195)
+||||||||||+|||||+|||||++||++|+|+. |+.++|+ .+| .||++
T Consensus 571 vH~shyGRiCPIETPEG~NiGLI~SLA~yarIn~~GfietPy-----------------------~kV-~~g~v------ 620 (2836)
T PRK14844 571 VHPTHYGRICPIETPEGQNIGLINSLAIYARINKYGFIESPY-----------------------RKV-VNRVV------ 620 (2836)
T ss_pred cCccccccccCCCCCCCCcccchhhhhhheeccCCceEeCCc-----------------------EEE-EcCcC------
Confidence 9999999999999999999999999999999987 4544431 222 23221
Q ss_pred hHHHHHHHHhhhccCCCCcceEEEEeccCCeEEEEeCCCceeeeEEEEecccchhhHHHHHHhhcCCCCCCCCccccccC
Q 000996 586 PEMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRESPEDGGWHDLVAK 665 (1195)
Q Consensus 586 ~~~~~~~lr~~rr~~~i~~~~~i~~~~~~~~i~I~td~GRl~RPl~~v~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~ 665 (1195)
.
T Consensus 621 -------------------------------------------------------------------------------~ 621 (2836)
T PRK14844 621 -------------------------------------------------------------------------------T 621 (2836)
T ss_pred -------------------------------------------------------------------------------c
Confidence 0
Q ss_pred CeEEEecccccccceeecccchhhcccCCCCc------------cCCCceeeeecCCCccccccccccCCCCCCCCCccc
Q 000996 666 GFIEYIDTEEEETTMISMTINDLVQARLHPEE------------AYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNT 733 (1195)
Q Consensus 666 g~iE~i~~~Ee~~~~Ia~~~~~~~~~~~~~~~------------~~~~~~th~EI~P~~ilsv~AslIPF~~hNqSpRn~ 733 (1195)
..++|++|.||+...||.....+...+.+.+. ..+.+.++++++|.|++||+||||||++||||+|++
T Consensus 622 ~~i~ylsa~~E~~~~Ia~a~~~~~~~~~~~~~~v~~R~~~ef~~~~~~~v~~~dvsp~Q~~SvaasLIPFLEhdDAnRAL 701 (2836)
T PRK14844 622 DQIEYLSAIDEGLYYIADTSAKLDENNCFVDDMLYCRYAGSFVMVSSDQVSYIDVSPKQVISVAASLIPFLENDDANRAL 701 (2836)
T ss_pred ccccccChHHhcCcEEEeCCccCCCCCcccCCeEEEecCCceEEecHHHceEEEeCcchhhhhHhhcCCccccCcccccc
Confidence 12679999999999999887666543221000 013457899999999999999999999999999999
Q ss_pred cccccccCcccccce-----------------------------------eeEEEeecc---------ceee--------
Q 000996 734 YQSAMGKQAMGIYVT-----------------------------------NYQFRMDTL---------AYVL-------- 761 (1195)
Q Consensus 734 yqc~M~KQa~g~~~~-----------------------------------n~~~r~D~~---------~~~l-------- 761 (1195)
|||||||||||+... .+.+|.+.. .|.|
T Consensus 702 MGSNMQRQAVPLl~~e~PiVGTG~E~~vA~DSg~~v~A~~~G~V~yVda~kIvI~~~~~~~~~~~~~~~Y~L~ky~RSNQ 781 (2836)
T PRK14844 702 MGSNMQRQAVPLLKPTAPLVATGMESFVASGSGAVVLAKRDGIVDSSDSNSIVIRAFDKERVNYLDVDIYHLRKFQRSNH 781 (2836)
T ss_pred ccccccccccccccCCCCeEecCcchhhhhcccceEEeccCceEEEEcCCEEEEEeCCCccccccccceEEecccccccc
Confidence 999999999998421 223333221 2544
Q ss_pred --ecCCCceeeccc----ccc------cccccCCCCceEEEEEEecCCccCCCcEEEecceeecCceeEEEEEEEEechh
Q 000996 762 --YYPQKPLVTTRA----MEH------LHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEK 829 (1195)
Q Consensus 762 --~ypQ~Plv~t~~----~~~------~~~~~~~~G~N~~VAv~s~~Gyn~EDaiiink~s~~rG~f~s~~~~~~~~~~~ 829 (1195)
|++|+|+|+.+. ++. +..+|+++|+|++||||||.||||||||+||++++++++|||+|+.+|+++.+
T Consensus 782 ~TcinQrPiV~~Gd~V~kGdilADG~st~~GELALG~NvlVAfmpW~GYNfEDAIliSErlv~eD~fTSiHIee~ei~~r 861 (2836)
T PRK14844 782 NTCINQKPLVCVGDYVKEGDVIADGPAINSGELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTSIHIEEFECVVH 861 (2836)
T ss_pred ceeeeecceecCCCEeccCCEeccChhhcccccccccceEEEEeccCCcccccccccchhhccCceeEEEeecceEEEEE
Confidence 689999998742 333 37999999999999999999999999999999999999999999999999998
Q ss_pred ccCCccccccc--CCCCCCCCCCCCCCcCCCCCCCCcCCCcEECCCCEEEEEeCCCCccccc---------cccCCCccc
Q 000996 830 KMGTLVKEDFG--RPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ---------GQASRYTRR 898 (1195)
Q Consensus 830 ~~~~~~~e~~~--~p~~~~~~~~~~~~~~~Ld~dGi~~~G~~v~~gdvli~k~~~~~~~~~~---------~~~~~~~~~ 898 (1195)
.+.. ..|+++ +|+.+. ...++||++|||++|++|++|||||||++|+...+.. ..++....+
T Consensus 862 ~Tk~-G~EeITrdIPnv~e------~~lr~LDe~GIV~iGa~V~~GDILVGKvtPk~e~~~tPEekLL~aIFGek~~~vk 934 (2836)
T PRK14844 862 DTPL-GSEKITRAIPGVNE------ENLYHLDDSGIVKIGTRVGPGYILVGKVTPKPSLSLPPETKLLMTIFGEKSFDCA 934 (2836)
T ss_pred eccC-CCceecccCCCCCh------HHHhcCCCCCCeecCCEECCCCEEEEeecCCCCCCCCHHHHHHHHHhCCcccccc
Confidence 8754 457774 676432 3478999999999999999999999999998743321 234667899
Q ss_pred eeeEEeecCCCcEEEEEEEEecC---------------------------------------------------------
Q 000996 899 DHSISLRHSETGMVDQVLLTTNA--------------------------------------------------------- 921 (1195)
Q Consensus 899 ~~s~~~~~~~~g~v~~v~~~~~~--------------------------------------------------------- 921 (1195)
|+|++++++..|+|..|.+++.+
T Consensus 935 dtSLrvp~G~~G~Vidv~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1014 (2836)
T PRK14844 935 DSSLYTSPDVEGTVIDVQVFTRRGVEENERALLIKQKEINDFEKERDYIINVTSEYFYDELKKLLINSGSQDREKFDSIE 1014 (2836)
T ss_pred cCceecCCCCCEEEEEEEEEcccccccchhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhcccccccHHHHhhcc
Confidence 99999999999999999887642
Q ss_pred --------------------------------------------CC-------cEEEEEEEeeecCCCCcccccccCCCc
Q 000996 922 --------------------------------------------DG-------LRFVKVRVRSVRIPQIGDKFSSRHGQK 950 (1195)
Q Consensus 922 --------------------------------------------~~-------~~~v~v~~~~~R~~~iGDKf~sRHGqK 950 (1195)
.| .+.|||++++.|+++||||+|||||||
T Consensus 1015 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~gdeL~~gv~~~VkVyia~KRkiqvGDKmAGRHGNK 1094 (2836)
T PRK14844 1015 REQWWGIGLKNQSISEQVKSLKKDFDEKVSHAIAQFKRKVEKLHEGYDLPQGVSMSVKVFIAVKHSLQPGDKMAGRHGNK 1094 (2836)
T ss_pred HHhhhhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCCCCceEEEEEEEEeecCCccccccccCCCC
Confidence 11 257999999999999999999999999
Q ss_pred eeEEeeecCCCCCCCCCCCCCcEEeCCCCCCCCCchhhHHHHhhhHHhhhcCCC--------------------------
Q 000996 951 GTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKE-------------------------- 1004 (1195)
Q Consensus 951 Gvvs~i~~~~dmPf~~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~-------------------------- 1004 (1195)
||||+|+|.|||||++||+++|||+||+|+||||||||++|+++|+||..+|..
T Consensus 1095 GVIS~IlP~eDMPyL~DGtpvDIvLNPLGVPSRMNvGQilE~hLG~A~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1174 (2836)
T PRK14844 1095 GVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGWACKKLGEKVGNILDEINKIKSAFCKGIRSLNDDN 1174 (2836)
T ss_pred ceEeEEcccCCCCcCCCCCCceEEeCCCCCCccccHHHHHHHHHHHHHhhhhhhhHhhhhhhhccccccccccccccccc
Confidence 999999999999999999999999999999999999999999999999887521
Q ss_pred --------------------------------------------------------------------------------
Q 000996 1005 -------------------------------------------------------------------------------- 1004 (1195)
Q Consensus 1005 -------------------------------------------------------------------------------- 1004 (1195)
T Consensus 1175 ~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1254 (2836)
T PRK14844 1175 FTKFAAAYLDNKKIENIDDDEITASVLNTPNKNALNDELNELVENYLNSCKSAYSNLRNFLIEVYSCGSNVSICNNIRDI 1254 (2836)
T ss_pred cccccccccccccccccccccccccccccccccccccccccchhccccccchhhHHHHHHHHHhhhcccccccccccccc
Confidence
Q ss_pred ----------------cccCC-CCCccHHHHHHHHHHcCCCCCCeEEEeeCCCCceeeeeEeEeeeehhccccccCcccE
Q 000996 1005 ----------------GDATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIH 1067 (1195)
Q Consensus 1005 ----------------~~~tp-F~~~~~~~~~~~l~~~g~~~~G~~~l~~G~tG~~~~~~if~G~~yy~rL~Hmv~dK~~ 1067 (1195)
.-+|| |++.+.+++.+.|+++||+++|++.||||+||++|+++||+|++|||||+|||+||+|
T Consensus 1255 ~~~~~~~~~~~~~~g~~~~tpvf~g~~~~~i~~~L~~~g~~~~Gk~~l~dG~TGe~f~~~v~vG~~yy~kL~HmV~DKih 1334 (2836)
T PRK14844 1255 SDNNLIEFARKLRDGIPVAAPVFEGPKDEQIAKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIH 1334 (2836)
T ss_pred cHHHHHHHHhhhccCCeecCCCcCCCCHHHHHHHHHHhCcCCCCCEEEEcCCCCCccchhheeCcchhhhhhhhhcchhh
Confidence 01455 8888999999999999999999999999999999999999999999999999999999
Q ss_pred EeccCCccccccCCCCcccCCCccccchhhhhHHHhhccHHHHHHhhhcCCCceeeeeccccCcceeeccccCceeeccC
Q 000996 1068 SRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGC 1147 (1195)
Q Consensus 1068 ~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~Erl~~~SD~~~~~vC~~cG~~~~~~~~~~~~~C~~C 1147 (1195)
||++|||++|||||++||+++|||||||||||||+|||||++|||||+.+||.+. |+.+. +|..|
T Consensus 1335 aRs~Gp~s~lT~QPl~Gr~~~GG~RfGEME~~al~a~Gaa~~L~E~Lt~kSD~~~-------gr~~~--------~~~iv 1399 (2836)
T PRK14844 1335 ARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDIN-------GRVKI--------YESII 1399 (2836)
T ss_pred hcccCCCcccccCCCcccccCCCceeecchHHHHHHHhHHHHHHHHhcccccchh-------hhhHh--------hhhhc
Confidence 9999999999999999999999999999999999999999999999999999776 44442 23334
Q ss_pred CCCCCceeecchHhhHHHHHHHHhCCCceEEEeccC
Q 000996 1148 KNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKED 1183 (1195)
Q Consensus 1148 ~~~~~~~~v~iPy~~kll~~EL~sm~i~~~l~~~~~ 1183 (1195)
+. .+..+..+|||||+|+|||+||||++++.+++.
T Consensus 1400 kG-~~~~~~~~PesfkvL~~EL~sl~i~~~~~~~~~ 1434 (2836)
T PRK14844 1400 KG-DSNFECGIPESFNVMIKELRSLCLNVDLKQNDV 1434 (2836)
T ss_pred cC-CCCCcCCCCchHHHHHHHHHhCccceEEeccch
Confidence 32 345566899999999999999999999988643
No 13
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated
Probab=100.00 E-value=3.2e-183 Score=1639.49 Aligned_cols=597 Identities=48% Similarity=0.810 Sum_probs=561.8
Q ss_pred ceEEEECCEEEEEEcChHHHHHHHHhhhccCCCCcceEEEEeccCCeEEEEeCCCceeeeEEEEecccchhhHHHHHHhh
Q 000996 570 ATKIFVNGCWVGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQ 649 (1195)
Q Consensus 570 ~~~V~lnG~~iG~~~~~~~~~~~lr~~rr~~~i~~~~~i~~~~~~~~i~I~td~GRl~RPl~~v~~~~~~~~~~~~~~l~ 649 (1195)
.++|||||+|+|++++|..|++.||.+||.|.|+.++||++++..++|+||||+||++|||++|++|++.++++|+++|+
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 47999999999999999999999999999999999999999998899999999999999999999999999999999998
Q ss_pred cCCCCCCCCccccccCCeEEEecccccccceeecccchhhcccCCCCccCCCceeeeecCCCccccccccccCCCCCCCC
Q 000996 650 QRESPEDGGWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQS 729 (1195)
Q Consensus 650 ~~~~~~~~~~~~l~~~g~iE~i~~~Ee~~~~Ia~~~~~~~~~~~~~~~~~~~~~th~EI~P~~ilsv~AslIPF~~hNqS 729 (1195)
++++ +|++|+++|+|||||++||++++||+++.++.. .+||+||+|++||||+||+|||+|||||
T Consensus 84 ~~~~----~~~dl~~~G~IEyida~EE~~~~IA~~~~~l~~-----------~~th~Ei~p~~ilgv~AslIPF~~hNQS 148 (605)
T PRK07225 84 NGEL----TFDDLVKQGVIEYLDAEEEENAYIAVYEEDLTE-----------EHTHLEIDPSLILGIGAGMIPYPEHNAS 148 (605)
T ss_pred cCCC----ChHHHHhCCCeeecChhhhcCeEeccchhhhcc-----------cccccccCCcceeEEEeeccCCCCCCcc
Confidence 7666 899999999999999999999999999988743 4799999999999999999999999999
Q ss_pred CccccccccccCcccccceeeEEEeeccceeeecCCCceeecccccccccccCCCCceEEEEEEecCCccCCCcEEEecc
Q 000996 730 PRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQS 809 (1195)
Q Consensus 730 pRn~yqc~M~KQa~g~~~~n~~~r~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~~~G~N~~VAv~s~~Gyn~EDaiiink~ 809 (1195)
|||||||||+|||||++++|+.+|+|++.|+|+|||+|||+|+.++.++++++|+|+||+||||||+||||||||||||+
T Consensus 149 PRn~yq~~M~KQa~g~~~~n~~~r~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~p~G~N~iVAvmsy~GYn~EDAiIiNks 228 (605)
T PRK07225 149 PRITMGAGMIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKA 228 (605)
T ss_pred chhhhhhhhhhcccCccccceeeecCCcccEEeeCCcceEEccchHhhCCCccCCCeeEEEEEECcCCCChhHeeeeehh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeecCceeEEEEEEEEechhccCCcccccccCCCCCCCCCCCC-CCcCCCCCCCCcCCCcEECCCCEEEEEeCCCCccc-
Q 000996 810 SIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRH-GSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDE- 887 (1195)
Q Consensus 810 s~~rG~f~s~~~~~~~~~~~~~~~~~~e~~~~p~~~~~~~~~~-~~~~~Ld~dGi~~~G~~v~~gdvli~k~~~~~~~~- 887 (1195)
|+|||||||+||++|+.++++...+..+.|++|+.. ..+.+. ..|++||+||||++|++|++|||||||++|....+
T Consensus 229 sidRGlf~s~~~k~~~~~~~~~~~~~~~~~~~p~~~-~~~~~~~~~~~~LD~dGi~~~G~~v~~gdiligk~sp~~~~~~ 307 (605)
T PRK07225 229 SIERGLGRSHFFRTYEGEERRYPGGQEDRFEIPDKD-VRGYRGEEAYRHLDEDGLVNPETEVKEGDVLIGKTSPPRFLEE 307 (605)
T ss_pred hhhcCceEEEEEEEEEEEeeecCCCcceEEecCCch-hccccChHHhhcCCCCCCccCCCEECCCCEEEEEecCCCCccc
Confidence 999999999999999998877655556788888642 112222 34899999999999999999999999999964211
Q ss_pred c-ccccCCCccceeeEEeecCCCcEEEEEEEEecCCCcEEEEEEEeeecCCCCcccccccCCCceeEEeeecCCCCCCCC
Q 000996 888 A-QGQASRYTRRDHSISLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTV 966 (1195)
Q Consensus 888 ~-~~~~~~~~~~~~s~~~~~~~~g~v~~v~~~~~~~~~~~v~v~~~~~R~~~iGDKf~sRHGqKGvvs~i~~~~dmPf~~ 966 (1195)
. .........+|+|++++.+|.|+||+|.++.+.+|.+.|||++|+.|+|+||||||||||||||||+|||+||||||+
T Consensus 308 ~~~~~~~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~vkv~ir~~R~p~iGDKfssRHGQKGvvs~i~~~eDMPft~ 387 (605)
T PRK07225 308 PDDFGISPEKRRETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTE 387 (605)
T ss_pred hhhhcccccCcceeeEEecCCCcEEEEEEEEEecCCCCEEEEEEEEEEEeccccchhhhcccCceeEEeEeccccCCcCC
Confidence 0 001122347999999999999999999999988899999999999999999999999999999999999999999999
Q ss_pred CCCCCcEEeCCCCCCCCCchhhHHHHhhhHHhhhcCCCcccCCCCCccHHHHHHHHHHcCCCCCCeEEEeeCCCCceeee
Q 000996 967 EGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTA 1046 (1195)
Q Consensus 967 ~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~~~tpF~~~~~~~~~~~l~~~g~~~~G~~~l~~G~tG~~~~~ 1046 (1195)
+|++|||||||||||||||||||+|+++|||+++.|.+.|+|||.+...+++++.|+++||+++|+|+||||+||++|++
T Consensus 388 ~G~~PDiIiNPhg~PSRMTiGql~E~~~gk~~~~~g~~~d~t~F~~~~~~~~~~~L~~~g~~~~G~e~my~G~TG~~~~~ 467 (605)
T PRK07225 388 SGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEA 467 (605)
T ss_pred CCCcccEEECcccccccCcHHHHHHHHHHHHHHhcCceEeecCCCCchHHHHHHHHHHhCcCCCCeEEEEcCCCCCEecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEeEeeeehhccccccCcccEEeccCCccccccCCCCcccCCCccccchhhhhHHHhhccHHHHHHhhhcCCCceeeeec
Q 000996 1047 MIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVC 1126 (1195)
Q Consensus 1047 ~if~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~Erl~~~SD~~~~~vC 1126 (1195)
+||+|++|||||+|||+||+|||++||++.|||||++||||+|||||||||||||+|||||++|+|||+.+||.++++||
T Consensus 468 ~if~G~~yYqrL~HmV~DK~haR~~Gp~~~lTrQP~~GR~r~GG~RfGEMErd~lia~Gas~~L~Erl~~~SD~~~~~vC 547 (605)
T PRK07225 468 EIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKVEIYVC 547 (605)
T ss_pred cEEEeehheeechhhhcchhhhccCCCCcccccCCccccccCCCeeeeeeehhhhhhhhhHHHHHHHHhccCcceeEEee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCcceeeccccCceeeccCCCCCCceeecchHhhHHHHHHHHhCCCceEEEecc
Q 000996 1127 EHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKE 1182 (1195)
Q Consensus 1127 ~~cG~~~~~~~~~~~~~C~~C~~~~~~~~v~iPy~~kll~~EL~sm~i~~~l~~~~ 1182 (1195)
.+||++++.+.+.+.++|+.|+++..+.++.||||||||+|||+||||++||.+++
T Consensus 548 ~~CG~~~~~~~~~~~~~C~~C~~~~~i~~v~iPya~kll~~EL~sm~i~~~l~~~~ 603 (605)
T PRK07225 548 AKCGMIAIYDKKRNRKYCPICGEETDIYPVEMSYAFKLLLDELKSLGIAPRLELED 603 (605)
T ss_pred cCcCcceehhcccCceeecccCCCCceeeccCChhHHHHHHHHHHCCceeEEEecc
Confidence 99999998776667789999999999999999999999999999999999999874
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=5.6e-182 Score=1627.18 Aligned_cols=594 Identities=50% Similarity=0.842 Sum_probs=558.8
Q ss_pred EEECCEEEEEEcChHHHHHHHHhhhccCCCCcceEEEEeccCCeEEEEeCCCceeeeEEEEecccchhhHHHHHHhhcCC
Q 000996 573 IFVNGCWVGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRE 652 (1195)
Q Consensus 573 V~lnG~~iG~~~~~~~~~~~lr~~rr~~~i~~~~~i~~~~~~~~i~I~td~GRl~RPl~~v~~~~~~~~~~~~~~l~~~~ 652 (1195)
|||||+|+|++++|..|++.||.+||.|.|+.++||++++..++|+||||+||++|||++|++|++.++++|+++++.+.
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 79999999999999999999999999999999999999998999999999999999999999999999999999997665
Q ss_pred CCCCCCccccccCCeEEEecccccccceeecccchhhcccCCCCccCCCceeeeecCCCccccccccccCCCCCCCCCcc
Q 000996 653 SPEDGGWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRN 732 (1195)
Q Consensus 653 ~~~~~~~~~l~~~g~iE~i~~~Ee~~~~Ia~~~~~~~~~~~~~~~~~~~~~th~EI~P~~ilsv~AslIPF~~hNqSpRn 732 (1195)
+ +|++|+++|+|||||++||+++.||+++.++.. .+||+||+|++||||+||+|||+||||||||
T Consensus 81 ~----~~~~ll~~G~IEyida~Ee~~~~IA~~~~~l~~-----------~~th~Ei~p~~ilgv~AslIPF~~hNqSpRn 145 (599)
T TIGR03670 81 L----TWDDLVKQGVIEYLDAEEEENAYIALDPEELTP-----------EHTHLEIDPSAILGIIASTIPYPEHNQSPRN 145 (599)
T ss_pred C----CHHHHHhcCCeEecCchhhcCeEEecchHHhcc-----------CcCccccCCcceeeEEeeccCCCCcCcchhh
Confidence 5 899999999999999999999999999988743 4799999999999999999999999999999
Q ss_pred ccccccccCcccccceeeEEEeeccceeeecCCCceeecccccccccccCCCCceEEEEEEecCCccCCCcEEEecceee
Q 000996 733 TYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSID 812 (1195)
Q Consensus 733 ~yqc~M~KQa~g~~~~n~~~r~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~~~G~N~~VAv~s~~Gyn~EDaiiink~s~~ 812 (1195)
||||||+|||||++++|++.|+||+.|+|+|||+|||+|+.++.++++++|+|+||+||||||+||||||||||||+|+|
T Consensus 146 ~YQc~M~KQamG~~~~n~~~R~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~p~G~N~iVAvmsy~GYn~EDAiIink~si~ 225 (599)
T TIGR03670 146 TMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIE 225 (599)
T ss_pred HHHHhhhhccccccccChhhcccccceEEcCCCCceeeeeeHHHhCccccCCCeeEEEEEEcccCcChhHeeeechhhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCceeEEEEEEEEechhccCCcccccccCCCCCCCCCCCC-CCcCCCCCCCCcCCCcEECCCCEEEEEeCCCCccccc--
Q 000996 813 RGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRH-GSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ-- 889 (1195)
Q Consensus 813 rG~f~s~~~~~~~~~~~~~~~~~~e~~~~p~~~~~~~~~~-~~~~~Ld~dGi~~~G~~v~~gdvli~k~~~~~~~~~~-- 889 (1195)
||||||+||++|+.++++...+..|.+++|+.. ..+.+. ..|++||+||||++|++|++|||||||++|....+..
T Consensus 226 rG~f~s~~~~~~~~~~~~~~~~~~e~~~~p~~~-~~~~~~~~~~~~LD~dGi~~~G~~v~~gdiligk~~p~~~~~~~~~ 304 (599)
T TIGR03670 226 RGLARSTFFRTYEAEERRYPGGQEDRFEIPEPD-VRGYRGEEAYKHLDEDGIVYPEVEVKGGDVLIGKTSPPRFLEELRE 304 (599)
T ss_pred cCCeEEEEEEEEEEEeeccCCCCceEEecCCch-hccccchhhhccCCCCCCcCCCcEeCCCCEEEEEecCCCCccchhh
Confidence 999999999999998877655555678887643 222232 3489999999999999999999999999986521110
Q ss_pred cccCCCccceeeEEeecCCCcEEEEEEEEecCCCcEEEEEEEeeecCCCCcccccccCCCceeEEeeecCCCCCCCCCCC
Q 000996 890 GQASRYTRRDHSISLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGI 969 (1195)
Q Consensus 890 ~~~~~~~~~~~s~~~~~~~~g~v~~v~~~~~~~~~~~v~v~~~~~R~~~iGDKf~sRHGqKGvvs~i~~~~dmPf~~~G~ 969 (1195)
...+....+|+|++++.+|+|+||+|.++.++++.+.|||++|+.|+|+||||||||||||||||+|||+||||||+||+
T Consensus 305 ~~~~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~vkv~~r~~R~p~iGDKfssRHGQKGvvs~i~~~eDMPft~~G~ 384 (599)
T TIGR03670 305 LGLVTERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGI 384 (599)
T ss_pred hccccccCceEEEEecCCCcEEEEEEEEEecCCCcEEEEEEEeeeecCcchhhhhhhccCcceEEeEeccCCCCcCCCCC
Confidence 00122347999999999999999999999988899999999999999999999999999999999999999999999999
Q ss_pred CCcEEeCCCCCCCCCchhhHHHHhhhHHhhhcCCCcccCCCCCccHHHHHHHHHHcCCCCCCeEEEeeCCCCceeeeeEe
Q 000996 970 TPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIF 1049 (1195)
Q Consensus 970 ~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~~~tpF~~~~~~~~~~~l~~~g~~~~G~~~l~~G~tG~~~~~~if 1049 (1195)
+|||||||||||||||||||+|+++|||+++.|.+.|+|||++...+++++.|+++||+++|+|+||||+||++|+++||
T Consensus 385 ~pDiIiNPhg~PSRMTiGqllE~~~gk~~~~~g~~~d~t~F~~~~~~~~~~~L~~~g~~~~G~e~ly~G~TG~~~~~~if 464 (599)
T TIGR03670 385 VPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIF 464 (599)
T ss_pred CCCEEECcccccccccHHHHHHHHHHHHHHhcCCEEEeCCCCCccHHHHHHHHHHcCCCCCCCEEEEcCCCCCCccccEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EeeeehhccccccCcccEEeccCCccccccCCCCcccCCCccccchhhhhHHHhhccHHHHHHhhhcCCCceeeeecccc
Q 000996 1050 LGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHC 1129 (1195)
Q Consensus 1050 ~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~Erl~~~SD~~~~~vC~~c 1129 (1195)
+|++|||||+|||+||+|||++||++.|||||++||||+|||||||||||||+|||||++|+|||+++||.+.++||.+|
T Consensus 465 ~G~~yyqrL~HmV~DK~h~Rs~Gp~~~lTrQP~~Gr~r~GG~RfGEMErd~lia~Gas~~L~ErL~~~SD~~~~~vC~~C 544 (599)
T TIGR03670 465 IGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENC 544 (599)
T ss_pred EEehhheechhhhcchhhhcccCCCcccccCCccccccCCCeeeeeeehhhHhhcchHHHHHHHHhccCcceeEEeeccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcceeeccccCceeeccCCCCCCceeecchHhhHHHHHHHHhCCCceEEEecc
Q 000996 1130 GLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKE 1182 (1195)
Q Consensus 1130 G~~~~~~~~~~~~~C~~C~~~~~~~~v~iPy~~kll~~EL~sm~i~~~l~~~~ 1182 (1195)
|++++.+.+.+.++|+.|+++.++.++.+|||||||+|||+||||++|+.+++
T Consensus 545 G~~~~~~~~~~~~~C~~c~~~~~i~~v~iPy~~k~l~~EL~am~i~~~l~~~~ 597 (599)
T TIGR03670 545 GHIAWEDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLELGD 597 (599)
T ss_pred CceeehhcccCceeccccCCCCceeeecCChhHHHHHHHHHhCCcceEEEecc
Confidence 99998776667889999999989999999999999999999999999999874
No 15
>PRK09606 DNA-directed RNA polymerase subunit B''; Validated
Probab=100.00 E-value=6.1e-107 Score=975.35 Aligned_cols=491 Identities=40% Similarity=0.696 Sum_probs=433.5
Q ss_pred hhhhhhhhhcccCccchHHHHHHHHHHHHHhhHHHHHcccCCeeeCCCCCCCCCCCCCCCCceEEEEEeEEEEccCcccc
Q 000996 25 QEDAWAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQSDFAETIYKISFGQIYLSKPMMTE 104 (1195)
Q Consensus 25 ~~~~~~~i~~~f~~~~Lv~~qi~SFn~Fi~~gL~~ii~~~~pI~~~~~~~~~~~~~~~~~~~~~~l~f~~v~v~~P~~~e 104 (1195)
.+++|.++++||+.++|++|||+|||+|+++||++++++++||++.. ...+.|+|+++++++|++.+
T Consensus 2 ~~~~~~~i~~~~~~~~lv~~qi~SFn~Fi~~gl~~ii~~~~~i~~~~-------------~~~~~l~~~~~~l~~P~~~~ 68 (494)
T PRK09606 2 MEDRRVLSDAYFKEHRLVRHHIDSYNDFVDNGLQKIIDEQGPIETEI-------------EDGVYVELGKIRVGKPVVKE 68 (494)
T ss_pred chHHHHHHHHHHCCCChHHHHHHHHHHHHHHhHHHHHHhcCCEEEec-------------CCcEEEEEEEEEECCCcccc
Confidence 36799999999999999999999999999999999999999998642 23578999999999999877
Q ss_pred CCCcccCCChHHHHhcCCccceeEEEEEEEEEeccCCCCcccccceeeEEEEecccceeeccCCccCCCCChhhhhhcCC
Q 000996 105 SDGETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELGE 184 (1195)
Q Consensus 105 ~~~~~~~l~P~EcR~r~lTYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~eli~~gE 184 (1195)
.++...+|+|+|||+|++||+|+++|+|.+..++.. ...+++++|+|||||+|++|||+|++|+||++.||
T Consensus 69 ~~~~~~~l~P~eaR~r~~TYs~~l~v~i~~~~~~~~---------~~~~~v~iG~iPiMv~S~~C~L~~~~~~~l~~~~E 139 (494)
T PRK09606 69 ADGSEREIYPMEARLRNLTYSAPLYLEMSPVEGGEE---------EEPEEVYIGELPVMVGSKICNLYGLSEEELIEVGE 139 (494)
T ss_pred cCCccccCCHHHHHhcCCCccceEEEEEEEEECCCc---------eEEeeEEeccCCeEeccCcccCCCCCHHHHHhcCC
Confidence 766678999999999999999999999999754321 13568999999999999999999999999999999
Q ss_pred CCCCCCceEEEcCeeeEEeeeeeeecceEEEEEecCCCcceEEEEEEEeecCCCCCCceEEEEEEecCCCCCCCCCcEEE
Q 000996 185 CPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIR 264 (1195)
Q Consensus 185 ~~~D~GGYFIING~ERVII~Qe~~s~N~~~~~~~~~~~~~~~~~~irs~~~~g~~~~~~~~v~~~~~~~~k~~~~~~~i~ 264 (1195)
||+|+||||||||+||||++|++++||+++++++...++..|.|.++| ..|+|. ..+.+++.. ++.++
T Consensus 140 ~~~d~GGyFIING~ErVi~~q~~~~~n~~~~~~~~~~~~~~~~~~i~s--~~~~~~-~~~~l~~~~---------~g~i~ 207 (494)
T PRK09606 140 DPLDPGGYFIVNGSERVLMTLEDLAPNKILVEKDERYGDRIEVAKVFS--QRRGYR-ALVTVERNR---------DGLLE 207 (494)
T ss_pred CcCCCCCeEEECCCeEEEEEEEeccCCeeEEEeccCCCccceEEEEEc--ccccce-eeEEEEEec---------CCeEE
Confidence 999999999999999999999999999999987654444458899986 445442 223444321 46799
Q ss_pred EEeccccccchHHHHHHHhcCCChHHHHHHhcccccchHHHHHhHhhHhhhhccCCHHHHHHHHhhcCcccCCCchhhHH
Q 000996 265 ATLPYIRTEIPIIIVFRALGFVADKDILEHICYDFQDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGATVGVTRDKRIK 344 (1195)
Q Consensus 265 v~i~~~~~~IPl~ilLrALG~~sD~eI~~~i~~~~~~~~~~~~l~~sl~e~~~i~t~~~al~yig~r~~~~~~~~~~~~e 344 (1195)
+++++.+.+||++++|||||.+||+||++.+. .+.++++.+..++++. .+.|+++||.|||++++.. .++....+
T Consensus 208 ~~~~~~~~~iPi~~llkALg~~sd~eI~~~i~---~~~~~~~~l~~~~~~~-~~~t~~~al~~ig~~~~~~-~~~~~~~~ 282 (494)
T PRK09606 208 VSFPSVPGSIPFVILMRALGLETDEEIVEAVS---DDPEIVKFMLENLEEA-EVDTQEEALEYIGKRVAPG-QTKEYRIK 282 (494)
T ss_pred EEEcCccccccHHHHHHHcCCCCHHHHHHHhC---CcHHHHHHHHHHHHhc-ccCCHHHHHHHHHHhcCCC-CCcchHHH
Confidence 99998767899999999999999999999994 3444666677777654 4789999999999998642 23455678
Q ss_pred HHHHHHHhcccCCCCCCCCcchhHHHHHHHHHHHHHHhhcCCCCCCCCCccccceecccchhHHHHHHHHHHHHHHHHHH
Q 000996 345 YAKEILQKEMLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRA 424 (1195)
Q Consensus 345 ~~~~~L~~~llpHl~~~~~~~~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~NKRv~l~G~Ll~~lfr~~l~~~~k~ik~ 424 (1195)
.|+.+|++++|||+|.+..+..+|++||++|++||+.++.|.+.+||+|||+||||+++|+||+.+||++|+++++.++.
T Consensus 283 ~~~~~l~~~~l~hig~~~~~~~~K~~~L~~m~~kLl~~~~g~~~~Dd~D~l~nkRv~~~G~Ll~~~fr~~l~~~~~~~k~ 362 (494)
T PRK09606 283 RAEYVIDRYLLPHLGVEPEVRRAKAHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKY 362 (494)
T ss_pred HHHHHHHHhhhcccCCCcchhhHHHHHHHHHHHHHHHHhcCCCCCCCcccccCceeeccchhHHHHHHHHHHHHHHHHHH
Confidence 99999999999999987655668999999999999999999999999999999999999999999999999999999998
Q ss_pred HhhhhhccCCCCchhhcccccccccccccccccccccccccccccccceeeccccChhhhhccccccCCCCCcCCCcccc
Q 000996 425 YVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKP 504 (1195)
Q Consensus 425 ~l~k~~~~~~~~~~~~~i~~~~It~~i~~~~sTGnw~~~~~~~~~sG~sq~l~r~N~ls~lSh~Rrv~~~~~~~~k~t~v 504 (1195)
.+++...+.+.+++..+++++.||++|++|||||||++ +++|+||+|||+||+|+||||||||+++.++++.++|
T Consensus 363 ~l~~~~~~~~~~~~~~~~~~~~It~~l~~~~~TGnw~~-----~~~glSq~ldr~N~la~lSh~Rrv~s~~~r~~~~~~v 437 (494)
T PRK09606 363 QLERANMRNRELSIKTAVRSDVLTERLEHAMATGNWVG-----GRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEA 437 (494)
T ss_pred HHHHHHhcCCCCCHHHhcCchhhhHHHHHHhhcccccC-----CCceEEEEccCCCHHHHhhHHHhccCCccccCccccc
Confidence 88876655556788889999999999999999999996 3689999999999999999999999999999999999
Q ss_pred ccccCCCcccccccCCCCCcccchhhcccccEEEccCCCchhHHHHHHHhCCccc
Q 000996 505 RQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENF 559 (1195)
Q Consensus 505 R~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~It~~~~~~~i~~~l~~~g~~~~ 559 (1195)
|+||||||||+||||||||+|||||||||++|+|+.+.+.+++.++|.++||.++
T Consensus 438 R~lhps~~G~iCPveTPEG~~cGLv~~La~~a~V~~~~~~~~i~~~l~~lg~~~~ 492 (494)
T PRK09606 438 RDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKELGVEPE 492 (494)
T ss_pred cccCcccceecccCcCCCCCcccHHHhhhceEEEeCCCChHHHHHHHHHCcCeeC
Confidence 9999999999999999999999999999999999999888899999999999875
No 16
>PF00562 RNA_pol_Rpb2_6: RNA polymerase Rpb2, domain 6; InterPro: IPR007120 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerases (2.7.7.6 from EC) catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain represents the hybrid-binding domain and the wall domain []. The hybrid-binding domain binds the nascent RNA strand/template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion []. This domain is also involved in binding to Rpb1 and Rpb3 []. Many of the bacterial members contain large insertions within this domain, which are known as dispensable region 2 (DRII).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2Y0S_R 3HKZ_B 2PMZ_R 3H0G_B 3S17_B 1I6H_B 4A3B_B 3K1F_B 4A3I_B 1TWA_B ....
Probab=100.00 E-value=3.3e-109 Score=964.88 Aligned_cols=364 Identities=52% Similarity=0.837 Sum_probs=313.6
Q ss_pred cccccccCCCCCCCCCccccccccccCcccccceeeEEEeeccceeeecCCCceeecc-cccccc---------cccCCC
Q 000996 715 GVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTR-AMEHLH---------FRQLPA 784 (1195)
Q Consensus 715 sv~AslIPF~~hNqSpRn~yqc~M~KQa~g~~~~n~~~r~D~~~~~l~ypQ~Plv~t~-~~~~~~---------~~~~~~ 784 (1195)
||+|++|||++|||||||+|||||+|||||+|.+|+..|+|+.. +|||+|||+|+ ..+..+ ++|+|+
T Consensus 1 si~As~ipf~~hn~s~R~~~~~~m~kQa~~~y~~~~~~R~d~~~---~~~q~Plv~~~~~~~~~~ilad~~~~~~~e~~~ 77 (386)
T PF00562_consen 1 SIVASLIPFPEHNQSPRNLYQCNMQKQAIGTYSLNKFNRSDQNT---CYPQKPLVKTGDRVEKGQILADGPSTKFGELPL 77 (386)
T ss_dssp -THGGTSSSGGGC-HHHHHHHHHHGCGBCSEEETTTTTS-TSSE---SS-BEESSBSSSTBTTTTECEE-TTECTTTS-S
T ss_pred CEEeCCCCEEEEEcCCcEEEEeCcCCCcccceeeeeeeccCcce---eccccceEEeeccccccCccccccccccccCcc
Confidence 68999999999999999999999999999999999999999988 89999999999 777777 999999
Q ss_pred CceEEEEEEecCCccCCCcEEEecceeecCceeEEEEEEEEechhccCCccccccc-CCCCCCCCCCCCCCcCCCCCCCC
Q 000996 785 GINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFG-RPDRSNTMGMRHGSYDKLDDDGL 863 (1195)
Q Consensus 785 G~N~~VAv~s~~Gyn~EDaiiink~s~~rG~f~s~~~~~~~~~~~~~~~~~~e~~~-~p~~~~~~~~~~~~~~~Ld~dGi 863 (1195)
|+|++||||||+||||||||||||++++||+|||+||++ +.+++....+..+++. .+... +...|++||+|||
T Consensus 78 G~N~iVAvmsy~GYN~EDAiIiNkssv~rG~f~s~~~k~-~~~~~~~~~g~~e~~~~~~~~~-----~~~~~~~LD~dGi 151 (386)
T PF00562_consen 78 GQNAIVAVMSYTGYNQEDAIIINKSSVDRGLFTSIHYKT-EIEIRDNKGGPSEEIFRPIPNV-----KEYNYSKLDEDGI 151 (386)
T ss_dssp SEEEEEEESBSSSTTTSSEEEEECHHHHTTTTEEEEEEE-EEEEEEETTSEEBBESS--TSS-----TSTTGGGBCTTSB
T ss_pred eeeeeEEeeehhcccchhhhhhhhhhhhcCeeeEEEEEE-EeeeecccCCcccccccccccc-----hhhhhhhcccccc
Confidence 999999999999999999999999999999999999999 7766655444435543 33211 3456999999999
Q ss_pred cCCCcEECCCCEEEEEeC-CCCccc---cccccCCCccceeeEEeecCCCcEEEEEEE-------EecCCCcEEEEEEEe
Q 000996 864 APPGTRVSGEDVIIGKTT-PISQDE---AQGQASRYTRRDHSISLRHSETGMVDQVLL-------TTNADGLRFVKVRVR 932 (1195)
Q Consensus 864 ~~~G~~v~~gdvli~k~~-~~~~~~---~~~~~~~~~~~~~s~~~~~~~~g~v~~v~~-------~~~~~~~~~v~v~~~ 932 (1195)
|++|++|++||+||||++ |..... ....++....+|+|++++.++.|+||+|.+ ..+.++...|+|++|
T Consensus 152 i~~G~~v~~gDiligk~~~~~~~~~~~~~~~~~~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~~~~~~~~iki~ir 231 (386)
T PF00562_consen 152 IKIGSRVEKGDILIGKITSPPRFSPLLKKIFGEKNRNYRDTSIKYKSGESGRVDKVIIFSNEKKDTSNNEGYKKIKIRIR 231 (386)
T ss_dssp B-TTCEEETTSEEEEEEESTSC--HHHHHHHHSSSCSEEEEEEES-TT-EEEEEEEEEECCCSSBEEETTCEEEEEEEEE
T ss_pred cccCcEEecceeEEEEEecccccccchhhccccccccccceeecccccEEeEeccccccccccccccccCcceEEEEEec
Confidence 999999999999999995 221100 011122334799999999999999999999 567788999999999
Q ss_pred eecCCCCcccccccCCCceeEEeeecCCCCCCCCCCCCCcEEeCCCCCCCCCchhhHHHHhhhHHhhhcCCCcccCCCCC
Q 000996 933 SVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTD 1012 (1195)
Q Consensus 933 ~~R~~~iGDKf~sRHGqKGvvs~i~~~~dmPf~~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~~~tpF~~ 1012 (1195)
+.|+|+||||||||||||||||+|||+||||||++|++|||||||||||||||||||+|+++||++++.|.+.|+|||++
T Consensus 232 ~~R~p~iGDKfssRHGqKGVvs~i~~~eDMPft~~G~~pDiIiNPhgiPSRMtiGqllE~~~g~~~~~~g~~~~~t~F~~ 311 (386)
T PF00562_consen 232 STRRPQIGDKFSSRHGQKGVVSKILPQEDMPFTEDGIVPDIIINPHGIPSRMTIGQLLESLLGKAGALNGRFVDATPFDE 311 (386)
T ss_dssp EEEE--TTEEEEETTSEEEEEEEEE-TTTSEEETTSEB-SEEE-GGGSTTTTBTHHHHHHHHHHHHHHSTCEEB-TTTSS
T ss_pred ccccchhHHHHhhhhcCceEEeeeeccccCccccCCCcceeeecccccccccchHHHHhhhhhhhhhccccceecCCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccHHHHHHHHHHcCCCCCCeEEEeeCCCCceeeeeEeEeeeehhccccccCcccEEeccCCccccccCCCCcccC
Q 000996 1013 VTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSR 1087 (1195)
Q Consensus 1013 ~~~~~~~~~l~~~g~~~~G~~~l~~G~tG~~~~~~if~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~ 1087 (1195)
.+.+++++.|.++||+++|+++||||+||++++++||+|++|||||+|||+||+|||++||++.|||||++||+|
T Consensus 312 ~~~~~i~~~l~~~g~~~~g~~~l~~g~tG~~~~~~i~~G~~yy~rL~Hmv~DK~h~Rs~Gp~~~lT~QP~~Gr~r 386 (386)
T PF00562_consen 312 SSEEDISELLKKAGYNYPGKEVLYDGRTGEKFEAPIFIGPVYYQRLKHMVDDKIHARSRGPYSLLTRQPVEGRSR 386 (386)
T ss_dssp S-HHHHHHHHHHTTSHTTSEEEEBESSSSSBESSEEEEEEEEEEEBSTCGGGSTEEESS--BBSSSSSB-SSSSS
T ss_pred cchhhhHhhhhcccccccceEEEEcCccCceEEeEEEeeeEEeccceEeCCcEEEEEecCCCccccCCCCCCCCC
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999997
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=3.7e-44 Score=385.65 Aligned_cols=149 Identities=49% Similarity=0.812 Sum_probs=125.9
Q ss_pred chHHHHHHHHHHHHHhhHHHHHcccCCeeeCCCCCCCCCCCCCCCCceEEEEEeEEEEccCccccCCCcccCCChHHHHh
Q 000996 40 GLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQSDFAETIYKISFGQIYLSKPMMTESDGETATLFPKAARL 119 (1195)
Q Consensus 40 ~Lv~~qi~SFn~Fi~~gL~~ii~~~~pI~~~~~~~~~~~~~~~~~~~~~~l~f~~v~v~~P~~~e~~~~~~~l~P~EcR~ 119 (1195)
||++|||+|||+|+++||++++++++||++.. ....+.++|++++|++|.+.+.++...+|+|+|||+
T Consensus 1 ~Lv~~qi~SFn~Fl~~gl~~i~~~~~~i~~~~------------~~~~~~l~~~~~~i~~P~~~~~~~~~~~l~P~ecR~ 68 (203)
T PF04563_consen 1 GLVKHQIDSFNYFLNNGLKEILKEFPPIEFES------------SNNRISLKFENIRIGKPTYSESDGRERPLYPRECRL 68 (203)
T ss_dssp TTTHHHHHHHHHHHCTSSHHHHSCSSSCEECC------------CSTTEEEEEEEEEEESESSEHTTSCEEE--HHHHHH
T ss_pred CchHHHHHHHHHHHHCCCHHHhccCCceEecC------------CcceEEEEeeEEEEeeeeeccccccccCCCHHHHHh
Confidence 69999999999999999999999999998752 245799999999999999988777889999999999
Q ss_pred cCCccceeEEEEEEEEEeccCCCCcccccceeeEEEEecccceeeccCCccCCCCChhhhhhcCCCCCCCCceEEEcCee
Q 000996 120 RNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIINGSE 199 (1195)
Q Consensus 120 r~lTYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~eli~~gE~~~D~GGYFIING~E 199 (1195)
|++||+|+++|+|++.+++.. .....++.+|+|||||+|++|||++++++|++++||||+|+||||||||+|
T Consensus 69 r~~TYs~~l~v~i~~~~~~~~--------~~~~~~v~iG~iPiMv~S~~C~L~~~~~~~l~~~~E~~~d~GGYFIInG~E 140 (203)
T PF04563_consen 69 RGLTYSAPLYVDIELTVNNKK--------EIKEQEVFIGKIPIMVRSKRCNLNGLSPKELVQLGECPNDPGGYFIINGSE 140 (203)
T ss_dssp TT-B-EEEEEEEEEEEESSTT--------EEEESEEEEEEEE-BTTTTTSGGGT--HHHHHHTTS-TT---SSEEETTEE
T ss_pred cCCCCCCccceEEEEEeeccc--------eEEeeEEEEeeCCeEeecceeeCCCCCHHHHHHcCCCCcCCCCEEEECCCh
Confidence 999999999999999998651 245678999999999999999999999999999999999999999999999
Q ss_pred eEEeeeeee
Q 000996 200 KVLIAQEKM 208 (1195)
Q Consensus 200 RVII~Qe~~ 208 (1195)
|||++|+++
T Consensus 141 kVi~~q~~~ 149 (203)
T PF04563_consen 141 KVIRMQIMR 149 (203)
T ss_dssp EEE-EEEEE
T ss_pred hheehhhhh
Confidence 999999975
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=6.2e-31 Score=238.87 Aligned_cols=81 Identities=60% Similarity=1.029 Sum_probs=76.6
Q ss_pred CccccchhhhhHHHhhccHHHHHHhhhcCCCceeeeeccccCcceeeccccCceeeccCCCCCCceeecchHhhHHHHHH
Q 000996 1089 GGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQE 1168 (1195)
Q Consensus 1089 GG~R~GEMErd~l~a~Gas~~l~Erl~~~SD~~~~~vC~~cG~~~~~~~~~~~~~C~~C~~~~~~~~v~iPy~~kll~~E 1168 (1195)
|||||||||||||+|||||++|||||+++||.++++||.+||.+++ .|+.+.++.++.+|||||||+||
T Consensus 1 GG~R~GEMErd~LiahGas~~L~erl~~~SD~~~~~vc~~cg~~~~-----------~~~~~~~~~~~~ipy~~klL~~E 69 (81)
T PF04560_consen 1 GGLRFGEMERDALIAHGASFLLKERLFDKSDKYEIDVCSRCGSIAS-----------ICKGKPEVKKIEIPYSFKLLIQE 69 (81)
T ss_dssp CBEEEEHHHHHHHHHTTBHHHHHHHHTTTTTEEEEEEECCCHHHHH-----------TTTTSSSEEEEEEEHHHHHHHHH
T ss_pred CCcchhHHHHHHHHHhhHHHHHHHHhcCCCcCcchhhhccCCCcee-----------EECCCCeEEeeeCCHHHHHHHHH
Confidence 8999999999999999999999999999999999999999999984 46667789999999999999999
Q ss_pred HHhCCCceEEEe
Q 000996 1169 LMAMAIAPRMLT 1180 (1195)
Q Consensus 1169 L~sm~i~~~l~~ 1180 (1195)
|+||||++++.+
T Consensus 70 L~sm~I~~~~~~ 81 (81)
T PF04560_consen 70 LRSMGIKIRIKT 81 (81)
T ss_dssp HHCTTEEEEEEE
T ss_pred HHHCcCceEEeC
Confidence 999999999874
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=99.92 E-value=2.1e-26 Score=203.05 Aligned_cols=66 Identities=62% Similarity=1.007 Sum_probs=59.6
Q ss_pred eeccccChhhhhccccccC--CCCCcCCCccccccccCCCcccccccCCCCCcccchhhcccccEEEc
Q 000996 474 QVLNRLTYASTLSHLRRLN--SPIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYIT 539 (1195)
Q Consensus 474 q~l~r~N~ls~lSh~Rrv~--~~~~~~~k~t~vR~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~It 539 (1195)
|+|||+|++++|||+|||+ +++++++|.+++|+|||||||||||+|||||++|||+||||++|.|+
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 58899999999999999999999999999999999999999999986
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=2.1e-20 Score=198.97 Aligned_cols=138 Identities=38% Similarity=0.529 Sum_probs=99.9
Q ss_pred EEEEeccccccchHHHHHHHhcCCChHHHHHHhcccccchHHHHHhHhhHhhhhccCCHHHHHHHHhhcCcccCCCchhh
Q 000996 263 IRATLPYIRTEIPIIIVFRALGFVADKDILEHICYDFQDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGATVGVTRDKR 342 (1195)
Q Consensus 263 i~v~i~~~~~~IPl~ilLrALG~~sD~eI~~~i~~~~~~~~~~~~l~~sl~e~~~i~t~~~al~yig~r~~~~~~~~~~~ 342 (1195)
+.+....++.+||+++||||||++||+||++.|++...+......+.........+.|+++|+.|||+++.. ...+...
T Consensus 41 ~~~~~~~~~~~IPi~ilLrALG~~sd~eI~~~i~~~~~~~~~~~~~~~~~~~~~~~~t~~~al~~i~~~~~~-~~~~~~~ 119 (190)
T PF04561_consen 41 IIFSRPKKKFKIPIVILLRALGIESDKEIIELICYSEEDFEDIEELMLSELEEEEIYTQEQALEYIGKKFRF-RQGKPPK 119 (190)
T ss_dssp EEEEETTSSSEEEHHHHHHHTT--STCHHHHHHCCCSTCHSCSTTTHHHHCCCTSSCSCHHHHHHHHHCCHS-SSSCHCC
T ss_pred EEEEEcCcccccceEEeehhhcCcCcccccceeecccccccccccccccccccccccccccceeEeccceee-ecccccc
Confidence 444455557789999999999999999999999864333222222222233345678999999999994322 2344555
Q ss_pred HHHHHHHH---------HhcccC-CCCCCCCcch--hHHHHHHHHHHHHHHhhcCCCCCCCCCccccceec
Q 000996 343 IKYAKEIL---------QKEMLP-HVGTGDFCET--KKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLD 401 (1195)
Q Consensus 343 ~e~~~~~L---------~~~llp-Hl~~~~~~~~--~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~NKRv~ 401 (1195)
.+.++.+| .+++|+ |++....... .|+.+|++|++||+.++.|.+.+||+|||+||||+
T Consensus 120 ~~~~~~~l~~~y~l~~i~r~~l~~hl~~~~~~~~~~~k~~~l~~m~~~ll~~~~g~~~~Dd~D~l~NkRv~ 190 (190)
T PF04561_consen 120 VEEARNFLQKRYDLGFIGRYKLNKHLGSDEPNENDRLKAEDLGLMIRKLLKLANGECEPDDRDHLGNKRVR 190 (190)
T ss_dssp HCHHHHHHTTCSSTCCCHHHCCHTTTTSSSSSSSSSCHHHHHHHHHHHHHHHHTTSS-S-STTSCCCEEEE
T ss_pred hhhhhcccccccccccccccceeeeeeeeecccccccchhhHHHHHHHHHHHhcCCCCCCCccccCCcCCc
Confidence 66777776 467777 9998765333 49999999999999999999999999999999995
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=99.74 E-value=5.9e-18 Score=146.65 Aligned_cols=63 Identities=62% Similarity=1.032 Sum_probs=59.7
Q ss_pred EEECCEEEEEEcChHHHHHHHHhhhccCCCCcceEEEEeccCCeEEEEeCCCceeeeEEEEec
Q 000996 573 IFVNGCWVGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEK 635 (1195)
Q Consensus 573 V~lnG~~iG~~~~~~~~~~~lr~~rr~~~i~~~~~i~~~~~~~~i~I~td~GRl~RPl~~v~~ 635 (1195)
|||||.|+|++++|+.|+..||.+||+|.|+.++||+++...++|+|+||+||+||||++|+|
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 799999999999999999999999999999999999999999999999999999999999985
No 22
>KOG0214 consensus RNA polymerase II, second largest subunit [Transcription]
Probab=99.19 E-value=1e-12 Score=158.02 Aligned_cols=411 Identities=9% Similarity=-0.103 Sum_probs=258.4
Q ss_pred CCCccccccccccCcccccceeeEEEeeccceeeecCCCceeecccccccccccCCCCceEEEEEEecCCccCCCcEEEe
Q 000996 728 QSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMN 807 (1195)
Q Consensus 728 qSpRn~yqc~M~KQa~g~~~~n~~~r~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~~~G~N~~VAv~s~~Gyn~EDaiiin 807 (1195)
|.+++.++.-|+ |..+-.-..+..+.+...-.|.+++.++-++........-..+.+.++-++.+.+.++..++...-|
T Consensus 682 dh~qspr~tYQs-a~~kqamg~y~tn~~vR~dtl~~~l~ypqkpl~tt~~~e~l~~~eL~aG~NaiVAi~~~~GYNqEDs 760 (1141)
T KOG0214|consen 682 DHNQSPRNTYQS-AMGKQAMGVYHTNPQVRMDTLAKVLYYPQKPLVTTRAMEYLRFRELPAGQNAIVAIACYSGYNQEDS 760 (1141)
T ss_pred CCCCchHHHHHH-HHhhhcceeeeecchhhhhhhhhcccccccchhhHHHHhhhhhhhcccccceEEEEecccCccHHHH
Confidence 444444444444 2222233333344444444444455544444433333344556799999999999999999999999
Q ss_pred cceeecCceeEEEEEEEEechhccCCcccccccCCCCCCCCCCCCCCcCCCCCCCCcCCCcEECCCCEEE-EEeCCCCcc
Q 000996 808 QSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVII-GKTTPISQD 886 (1195)
Q Consensus 808 k~s~~rG~f~s~~~~~~~~~~~~~~~~~~e~~~~p~~~~~~~~~~~~~~~Ld~dGi~~~G~~v~~gdvli-~k~~~~~~~ 886 (1195)
--..+.+++++++...|.-.-+.........++.+-.....+.+.. .++.-.|-+-.-|-.--.+.+.. +++.
T Consensus 761 vimn~s~v~rg~FrS~~~RsYk~q~~~~~~~~ee~~~~~~~~~~~~-mr~~~~dkLdddG~i~~G~~vs~~Dv~i----- 834 (1141)
T KOG0214|consen 761 VIMNQSSVDRGLFRSFFIRSYKDQEHKKDQGPEEIFEEPPRGEGRG-MRNGKYDKLDDDGIIMPGSRVSGGDVLI----- 834 (1141)
T ss_pred HHHHhhhhhcchhhhhhhhHHHhhhhhccccccccccccccccccc-ccccccccccccCCccccceeecCCEEe-----
Confidence 9999999999999877644333332211112222211111110000 11111111111111111111110 0111
Q ss_pred ccccccCCCccceeeEEeecC--------CCcEEEEEEEEecCCCcEEEEEEEeeecCCCCcccccccCCCceeEEeeec
Q 000996 887 EAQGQASRYTRRDHSISLRHS--------ETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYT 958 (1195)
Q Consensus 887 ~~~~~~~~~~~~~~s~~~~~~--------~~g~v~~v~~~~~~~~~~~v~v~~~~~R~~~iGDKf~sRHGqKGvvs~i~~ 958 (1195)
.+.+++..... ..++..++.+..++.| ...+|.++. .+.|+||+.+|++++-+.++-.
T Consensus 835 ----------Gk~t~~~~~~~~~~~~~~~~t~~d~s~~Lr~~e~G-ivd~V~vt~---n~~G~kF~kv~vr~~ripqiGD 900 (1141)
T KOG0214|consen 835 ----------GKTTPQPAKEDESGPEDRLYTKRDHSTKLRHTERG-IVDQVWVTK---NSEGPKFVKVRVRQVRIPQIGD 900 (1141)
T ss_pred ----------ccccCCcccchhccccccccccccceeecccCCcc-eEEEEEEec---CCCCCceeEEEEeecccccccc
Confidence 11111111111 1346777777777777 455566555 8999999999999999999999
Q ss_pred CCCCCCCCCCCCCcEEeCCCCCCCCCchhhHHHHhhhHHhhhcCCCcccCCCCCccHHHHHHHHHHcCCCCCCeEEEeeC
Q 000996 959 QEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNG 1038 (1195)
Q Consensus 959 ~~dmPf~~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~~~tpF~~~~~~~~~~~l~~~g~~~~G~~~l~~G 1038 (1195)
..++++-.-|+.++++.+++.-+++++|--.+.+-.-. .|-. .++..+.+-|. |...-++..++++
T Consensus 901 KfasrHgqKG~ig~~~~qedmpft~eGi~pDiiiNPha-----------iPSR-mtig~liEc~l--gk~~a~~~e~~~a 966 (1141)
T KOG0214|consen 901 KFASRHGQKGTIGITYRQEDMPFTIEGIVPDIIINPHA-----------IPSR-MTIGQLIECLL--GKVAAYEGEEGDA 966 (1141)
T ss_pred hhccccccCccccceeecCCCCccccCCCcceEECccc-----------Cccc-cchhhhHHHhh--hhhhhcccccccC
Confidence 99999999999999999999999999987666543221 1211 11222222211 1122233344555
Q ss_pred CCCceeeeeEeEeeeehhccccccCcccEEeccCCccccccCCCCcccCCCccccchhhhhHHHhhccHHHHHHhhhcCC
Q 000996 1039 HTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQS 1118 (1195)
Q Consensus 1039 ~tG~~~~~~if~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~Erl~~~S 1118 (1195)
.++.. -+-.+++..+++...|+..++.+++.+++....+++++++....++.+++||+++|=.+++.+-+.++.+...|
T Consensus 967 tpFs~-v~v~~is~~l~~~g~~~~G~e~~ynGrtG~~~~~~if~GptyyqrL~Hmvd~kih~R~~Gp~q~ltRQP~~gRs 1045 (1141)
T KOG0214|consen 967 TPFSD-VTVSKISANLHVYGYQYRGNERMYNGRTGRKLRAQIFIGPTYYQRLKHMVDDKIHSRARGPVQILTRQPVEGRS 1045 (1141)
T ss_pred CCCCc-cchhcccchHHHhccccCCCEEEecCCCCceeeeeeecCchHHHHHHHhhhheeeecccCCceeeecccccccc
Confidence 55544 34567899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CceeeeeccccCcceeeccccCceeeccCCCCCCceeecchHhhHHHHHHHHhCCCc
Q 000996 1119 DAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIA 1175 (1195)
Q Consensus 1119 D~~~~~vC~~cG~~~~~~~~~~~~~C~~C~~~~~~~~v~iPy~~kll~~EL~sm~i~ 1175 (1195)
+..-..+|+.|+.-+.+.-...-..|+.|..++.+.....++ |.|++.+...+|.-
T Consensus 1046 r~GGlRfGEMErdc~iahGaa~~L~ERL~~~SD~~~~~~c~~-c~l~~i~~~~~n~~ 1101 (1141)
T KOG0214|consen 1046 RDGGLRFGEMERDCLIAHGAAAFLKERLFEKSDAYRVHICVL-CGLTAIAGLIPNSF 1101 (1141)
T ss_pred ccCCeeeehhHHHHHHHhhHHHHHHHHhhccCccceEEEecc-chhhhhhccCCCcc
Confidence 999999999998644221111123466666665555555555 44777777766654
No 23
>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=98.98 E-value=1.5e-10 Score=95.35 Aligned_cols=48 Identities=58% Similarity=1.041 Sum_probs=36.4
Q ss_pred ccccccCCeEEEecccccccceeecccchhhcccCCCCccCCCceeeeecCC
Q 000996 659 WHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHP 710 (1195)
Q Consensus 659 ~~~l~~~g~iE~i~~~Ee~~~~Ia~~~~~~~~~~~~~~~~~~~~~th~EI~P 710 (1195)
|++|+++|+|||||++||++++|||+++++. .. .......||||||||
T Consensus 1 w~~ll~~G~vE~id~eEEe~~~Iam~~~dl~-~~---~~~~~~~~TH~EI~P 48 (48)
T PF04567_consen 1 WDDLLKEGVVEYIDAEEEETCMIAMSPEDLE-ST---NEDITHTYTHCEIHP 48 (48)
T ss_dssp HHHHHHTTSEEEEETTTCTT--EESSCCCCC-HS---GGCCSST-SEEES-G
T ss_pred ChhHhhCCCEEEecchhccccEEEEeccccc-cc---CCCCCCccEEEeEeC
Confidence 8899999999999999999999999999987 11 111146799999998
No 24
>KOG0215 consensus RNA polymerase III, second largest subunit [Transcription]
Probab=98.94 E-value=1.2e-11 Score=147.07 Aligned_cols=539 Identities=7% Similarity=-0.101 Sum_probs=297.9
Q ss_pred cccccccccchhhhhhhhhcccCccchHHHHHHHHHHHHHhhHHHHHcccCCeeeCCCCCCCCCCCCCCCCceEEEEEeE
Q 000996 15 EEEDEEEEITQEDAWAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQSDFAETIYKISFGQ 94 (1195)
Q Consensus 15 ~~~~~~~~~~~~~~~~~i~~~f~~~~Lv~~qi~SFn~Fi~~gL~~ii~~~~pI~~~~~~~~~~~~~~~~~~~~~~l~f~~ 94 (1195)
.+.|+.-.+.-.+.|-..+++.+..+++..||.+++.+|..-... .||.++.++. ..+- .+.+
T Consensus 87 sd~dp~fylky~dirvg~Ps~~~~~~~~~~~i~p~ecrlrd~tys-----a~i~vdieyt----------rg~~--~~~~ 149 (1153)
T KOG0215|consen 87 SDVDPSFYLKYLDIRVGKPSIEEGNNVTNDNITPHECRLRDMTYS-----APIYVDIEYT----------RGRQ--IIAK 149 (1153)
T ss_pred cCcCchhhheeeeeeccCcchhhccccccccCCchheeehhhhcc-----cceeEEEEEe----------cCcc--eEEe
Confidence 334454566667788888899999999999999999998654332 3444332211 1111 2222
Q ss_pred EEEccCccccCCCcccCCChHHHHhcCCccceeEEEEEEEEEeccCCCCcccccceeeEEEEecccceeeccCCccCCCC
Q 000996 95 IYLSKPMMTESDGETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQN 174 (1195)
Q Consensus 95 v~v~~P~~~e~~~~~~~l~P~EcR~r~lTYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~ 174 (1195)
..+.-|..+..-...+.+.|.+|+.+-.-|. ..+. ...-..+..|.-|||+.+.-|.++..
T Consensus 150 ~~v~igrmpimlrs~rcvl~~~~e~~~a~~~------------ecpl-------dpggyfiv~G~ekViLiqeqlsknri 210 (1153)
T KOG0215|consen 150 RDVIIGRMPIMLRSSKCVLRGKDEEELARLN------------ECPL-------DPGGYFIVKGTEKVILIQEQLSKNRI 210 (1153)
T ss_pred cccccccchhhhhccccccCCccHHHHHHhc------------cCCC-------CCCceeEeccceeEEEehhhhhccCe
Confidence 2333343332222456677777774433222 1110 11234688999999999999999999
Q ss_pred ChhhhhhcCCCCCCCCceEEEcCeeeEEeeeeeeecceEEEEEecCCCcceEEEEEEEeecCCCCCCceEEEEEEecCCC
Q 000996 175 SEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSA 254 (1195)
Q Consensus 175 s~~eli~~gE~~~D~GGYFIING~ERVII~Qe~~s~N~~~~~~~~~~~~~~~~~~irs~~~~g~~~~~~~~v~~~~~~~~ 254 (1195)
.++ -...|||+.++++||+..+++.+|++++...+++...+.++-+ ...... .-|.....++. .+.-
T Consensus 211 i~~-~~k~~~~~~svtsst~e~kskt~v~~k~~k~ylk~~~~~d~ip----iviv~k---a~g~~sd~ei~-~~vg---- 277 (1153)
T KOG0215|consen 211 IVE-EDKKGNLQASVTSSTHERKSKTYVTTKKGKYYLKHNSFTDDIP----IVIVLK---AMGLESDQEIV-QLVG---- 277 (1153)
T ss_pred eec-cccCCccccccccceeeecceEEEEeccceeeeehhhhhccCC----EEEEEe---eccccchHHHH-HHhh----
Confidence 888 6788999999999999999999999999766655544433321 111111 11211111110 0000
Q ss_pred CCCCCCcEEEEEeccccccchHHHHHHHhcCCChHHHHHHhcccccchHHHHHhHhhHhhhhccCCHHHHHHHHhhcCcc
Q 000996 255 KGGSSGQYIRATLPYIRTEIPIIIVFRALGFVADKDILEHICYDFQDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGAT 334 (1195)
Q Consensus 255 k~~~~~~~i~v~i~~~~~~IPl~ilLrALG~~sD~eI~~~i~~~~~~~~~~~~l~~sl~e~~~i~t~~~al~yig~r~~~ 334 (1195)
.+.-|..+.-..-+.|+.+-+.+.+-..|..+.+..... .....--++|++.+...+.+
T Consensus 278 -----~~~~y~~~~~~s~ee~~~~~v~tqqqal~y~~~kvk~~~----------------~t~~~~~~e~~~~l~~~~la 336 (1153)
T KOG0215|consen 278 -----GDSKYQDIFAPSLEECVSLGVYTQQQALEYIGSKVKVKR----------------GTTPTKDEEALEVLSTTVLA 336 (1153)
T ss_pred -----cchHHHHhhccchhhhhhhhhHHHHHHHHHhhheEEecc----------------CCCCCchHHHHHHHHhhhee
Confidence 011222222222245555555544433332222222110 00112234455555443311
Q ss_pred c------CCC-chhhHHH-HHHHHHhcccCCCCCCCCcchhHHHHHHHHHHHHHHhhcCCCCCCCCCccccceecccchh
Q 000996 335 V------GVT-RDKRIKY-AKEILQKEMLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPL 406 (1195)
Q Consensus 335 ~------~~~-~~~~~e~-~~~~L~~~llpHl~~~~~~~~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~NKRv~l~G~L 406 (1195)
- ... +...+.. .+..+.-. + |....++....+-..|..|.+ |+.+..+.-.-++.+.|++.+-...+.+
T Consensus 337 hv~v~~~~~r~K~~yi~~m~rr~~~a~-l-~~~~~ddrd~~gnkrlelagq-llsllfeD~fk~~n~e~k~~~dk~l~k~ 413 (1153)
T KOG0215|consen 337 HVPVPDLNFRMKAIYIGLMVRRVIQAM-L-NKLAMDDRDYVGNKRLELAGQ-LLSLLFEDLFKRFNSELKKNIDKILKKP 413 (1153)
T ss_pred ceeccCCCCcceeehHHHHHHHHHHHH-h-CcccccchhhhccchHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHhcch
Confidence 0 001 1111111 11122211 1 222111111122223544554 4555566666788899999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhhccC---CCCchhhcc-cccccccccccccccccccccccccccccceeeccccChh
Q 000996 407 LGGLFRMLFRKLTRDVRAYVQKCVDNG---KDVNLQFAI-KAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYA 482 (1195)
Q Consensus 407 l~~lfr~~l~~~~k~ik~~l~k~~~~~---~~~~~~~~i-~~~~It~~i~~~~sTGnw~~~~~~~~~sG~sq~l~r~N~l 482 (1195)
+..++-+.++.+. ..++.+..-+.+. .+.++..+- ....+|..+ +-.|++|........++++.++..+..|-
T Consensus 414 ~ra~~fD~~~~~n-~~~~~it~~l~ra~stgnw~iKrfrmer~gvt~Vl--srlSyisaLgmmtri~s~fektrkvsgpr 490 (1153)
T KOG0215|consen 414 IRAQEFDALKHLN-VRANMITSGLERAISTGNWSIKRFRMERAGVTQVL--SRLSYISALGMMTRINSQFEKTRKVSGPR 490 (1153)
T ss_pred hhhhhhHHHHHHH-HHHHHHHHHHHHHhhcCchHHHHhhhhhccceeee--hhhhhhhhhhhheehhhhheeehhccCcc
Confidence 9999999988875 3333333222211 223333321 122333332 34577787766666789999999888888
Q ss_pred hhhccccccCCCCCcCCCccccccccCCCcccccccCCCCCcccchhhcccccEEEccCCCchhHHHHHHHhCCcccccc
Q 000996 483 STLSHLRRLNSPIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEI 562 (1195)
Q Consensus 483 s~lSh~Rrv~~~~~~~~k~t~vR~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~It~~~~~~~i~~~l~~~g~~~~~~~ 562 (1195)
|-....-.+..|+.+....+-.+-.+++.|+.|||-++|++..|++.|+.+...++..+...-+...++..++...+.-.
T Consensus 491 Slq~sqwgmlcp~dtpegeacglvknlalmthittd~ee~pi~~~~~k~gv~di~~v~~~e~~~~~~~~v~Lng~iig~~ 570 (1153)
T KOG0215|consen 491 SLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITTDSEEKPILKLCYKLGVEDIHVVSGRELHTPDSFLVFLNGLIIGIT 570 (1153)
T ss_pred ccChhhcccccCCCCCCccccccccchHHHhcccCCCCcchhHHHHHHhcceeeeeecccccCCCceEEEEecceeeccc
Confidence 87777777777888888888899999999999999999999999999999999999886432222222222222222110
Q ss_pred -CCCCC-CCceEEEECCEEEEEEcChHHHHHHHHhhhccCCCCcceEEEEeccCCeEEEEeCCCceeeeEE
Q 000996 563 -SPAVI-PQATKIFVNGCWVGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLF 631 (1195)
Q Consensus 563 -~~~~~-~~~~~V~lnG~~iG~~~~~~~~~~~lr~~rr~~~i~~~~~i~~~~~~~~i~I~td~GRl~RPl~ 631 (1195)
.++.. .....++.+|.+-+++......++..+.+++.|-.--...|..+.. ..+|-++.+|.|+|.+
T Consensus 571 ~~~~~~v~~~r~lrr~G~i~~fvsv~~~~~q~~v~i~sdggr~crp~Iiv~~~--~~~v~~~h~~el~~g~ 639 (1153)
T KOG0215|consen 571 RRPQYFVNSFRRLRRKGKIGEFVSVFTNTTQRCVYIASDGGRVCRPLIIVDNG--RPRVKQHHMDELLDGK 639 (1153)
T ss_pred cchHHHHHHHHHHHHcCcccceeeeeeeeeeEEEEEecCCCeEeeeEEEEeCC--cchhhhhhHHHHHHhh
Confidence 11111 1222355667666665444444444444555544333334433322 2367777777777754
No 25
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]
Probab=97.82 E-value=1.4e-05 Score=102.07 Aligned_cols=108 Identities=27% Similarity=0.354 Sum_probs=80.2
Q ss_pred eEEEecccccccceeecccchhhcccCCC--------C--c----cCCCceeeeecCCCccccccccccCCCCCCCCCcc
Q 000996 667 FIEYIDTEEEETTMISMTINDLVQARLHP--------E--E----AYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRN 732 (1195)
Q Consensus 667 ~iE~i~~~Ee~~~~Ia~~~~~~~~~~~~~--------~--~----~~~~~~th~EI~P~~ilsv~AslIPF~~hNqSpRn 732 (1195)
-++|+.+.|+....+|.....+++...+. . . ......++++++|.++.|+.+++|||.+|++++|+
T Consensus 476 ~i~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~~~~~~~~~~~~~~~~~~dv~~~~~~~~~~~~~P~l~~dd~~~~ 555 (1060)
T COG0085 476 EIEYLSADEEDVYVIGQANGTLDEPGELVEELVECRRGGSGEVSVADPEGVDYMDVSPKQVVSVGRSLIPFLEHDDANRA 555 (1060)
T ss_pred ceeeecccccceEEEeEeeeeecCCCceeeeEEEEeecccccceeecCccccceeccceEEeccccccCceeEEcCchHh
Confidence 37899999999998887655443322110 0 0 01345678999999999999999999999999999
Q ss_pred ccccccccCcccccceeeEEEeeccceeeecCCCceeecccccccccccCCCCceEEEEEEe
Q 000996 733 TYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIAC 794 (1195)
Q Consensus 733 ~yqc~M~KQa~g~~~~n~~~r~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~~~G~N~~VAv~s 794 (1195)
+|+++|+|||+|+ ..+..|||.|+ ++++.-.| -.|++||.-+
T Consensus 556 l~~~~mqr~~~~l----------------~~~~~~lv~tG-~E~~~a~e---~~~~~ia~~~ 597 (1060)
T COG0085 556 LMGSNMQRQAVPL----------------LRTEAPLVGTG-MEYLDAED---SGAAVIAKRP 597 (1060)
T ss_pred hhhhhhhhhcccc----------------cccccccccCC-ceeecccc---ccceeEeccC
Confidence 9999999999994 45788999998 66653222 3456666633
No 26
>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=97.52 E-value=0.0001 Score=63.24 Aligned_cols=49 Identities=20% Similarity=0.232 Sum_probs=42.0
Q ss_pred EEEE--cChHHHHHHHHhhhccC--CCCcceEEEEeccC-----CeEEEEeCCCceee
Q 000996 580 VGIH--RDPEMLVKTLRRLRRRV--DVNTEVGVVRDIRL-----KELRIYTDYGRCSR 628 (1195)
Q Consensus 580 iG~~--~~~~~~~~~lr~~rr~~--~i~~~~~i~~~~~~-----~~i~I~td~GRl~R 628 (1195)
||++ +.++.+++.||.+|..| .||.++||++.+.. +++||||++|||+|
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 3554 35789999999999887 69999999987754 79999999999998
No 27
>PHA03394 lef-8 DNA-directed RNA polymerase subunit beta-like protein; Provisional
Probab=94.59 E-value=0.054 Score=67.42 Aligned_cols=141 Identities=24% Similarity=0.300 Sum_probs=81.2
Q ss_pred eecCCCcEEEEEEEEec-CCCcEEEEEEEeeecCCCCcccccccCCCceeEEeeecCCCCCC--CCCCCCCcEEeCCCCC
Q 000996 904 LRHSETGMVDQVLLTTN-ADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPW--TVEGITPDIIVNPHAI 980 (1195)
Q Consensus 904 ~~~~~~g~v~~v~~~~~-~~~~~~v~v~~~~~R~~~iGDKf~sRHGqKGvvs~i~~~~dmPf--~~~G~~pDiIiNPh~~ 980 (1195)
++....-+|++|.-.-. .+..-.+|+++-..=.=-.|=|.||=||||||... .||+-= .|||+.|-|.++|.++
T Consensus 674 fR~~~~Q~ie~l~s~m~~~nd~v~lKl~~Vtst~dLeGlKICgIHGQKGVln~---seDLtew~aeDg~~aQIclSPiSy 750 (865)
T PHA03394 674 FRQIKNQRIERLDSEMTVINDTVYLKIRLVTSTSDLEGLKICGIHGQKGVLNG---SEDLTEWMAEDGTHAQICLSPISY 750 (865)
T ss_pred EEecCCeEEEEEeeEEEEcCCEEEEEEEEEEEecCcceeEEeeecccccccCC---cchhhhhhccCCCcceEEechHHh
Confidence 44444455665532211 12244566665444344568899999999999754 556542 4699999999999999
Q ss_pred CCCCchhhHHHHhhhHHhhhcCCCccc---------CC--CCCccHHHHHHHHHHcCCCCCCeEEEeeCCCCceeeeeEe
Q 000996 981 PSRMTIGQLIECIMGKVAAHMGKEGDA---------TP--FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIF 1049 (1195)
Q Consensus 981 PSRMtiGql~E~~~gk~~~~~g~~~~~---------tp--F~~~~~~~~~~~l~~~g~~~~G~~~l~~G~tG~~~~~~if 1049 (1195)
-||.|.=-=+| -|-....|.+.|. .| |=..+.++|.++..+ -++.|-|.+=--|.-..--...|
T Consensus 751 LsRQtnf~~~~---~Ky~v~gg~~~~~~~~rypi~~IPYm~FnnTPDnI~kEf~~--~n~TG~EKvEGTRlDqwTINqsF 825 (865)
T PHA03394 751 LSRQTNFDDIE---RKYVVRGGDHSDPNAKRYPIFNIPYMLFNNTPDNIYKEFIK--KNYTGHEKVEGTRLDQWTINQSF 825 (865)
T ss_pred hccccccccCc---eEEEEECCCcCCCCCcccceEecceehhcCCchHHHHHHhc--cCCcceeecceeeccceeEccee
Confidence 99998622222 2333333444443 23 223456666665543 45667666532233222234556
Q ss_pred Eee
Q 000996 1050 LGP 1052 (1195)
Q Consensus 1050 ~G~ 1052 (1195)
+|-
T Consensus 826 ~gN 828 (865)
T PHA03394 826 VGN 828 (865)
T ss_pred ccc
Confidence 654
No 28
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=58.42 E-value=5.2 Score=35.63 Aligned_cols=49 Identities=18% Similarity=0.387 Sum_probs=29.1
Q ss_pred eeeeeccccCcceeeccccCceeeccCCCCCCceeecch------HhhHHHHHHHHh
Q 000996 1121 YRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIP------YACKLLFQELMA 1171 (1195)
Q Consensus 1121 ~~~~vC~~cG~~~~~~~~~~~~~C~~C~~~~~~~~v~iP------y~~kll~~EL~s 1171 (1195)
|.++-| .||+.+++.....+..| .|+..-+|.+..|= .-..-++++||.
T Consensus 1 ylifrC-~Cgr~lya~e~~kTkkC-~CG~~l~vk~~rIl~~~~~~~eA~eiVrklQ~ 55 (68)
T PF09082_consen 1 YLIFRC-DCGRYLYAKEGAKTKKC-VCGKTLKVKERRILARAENAEEASEIVRKLQE 55 (68)
T ss_dssp EEEEEE-TTS--EEEETT-SEEEE-TTTEEEE--SSS-BS--SSHHHHHHHHHHHSS
T ss_pred CEEEEe-cCCCEEEecCCcceeEe-cCCCeeeeeeEEEEEecCCHHHHHHHHHHHHH
Confidence 456779 79999998777777789 99986666554442 234455666653
No 29
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=56.70 E-value=13 Score=34.80 Aligned_cols=28 Identities=29% Similarity=0.809 Sum_probs=24.0
Q ss_pred eeeeccccCcceeeccccCceeeccCCC
Q 000996 1122 RVHVCEHCGLIAIANLKKNSFECRGCKN 1149 (1195)
Q Consensus 1122 ~~~vC~~cG~~~~~~~~~~~~~C~~C~~ 1149 (1195)
..|+|..||+..+.-...+.|.|+.|+.
T Consensus 34 ~~~~Cp~C~~~~VkR~a~GIW~C~kCg~ 61 (89)
T COG1997 34 AKHVCPFCGRTTVKRIATGIWKCRKCGA 61 (89)
T ss_pred cCCcCCCCCCcceeeeccCeEEcCCCCC
Confidence 4578999999987777778999999986
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=53.73 E-value=15 Score=32.81 Aligned_cols=27 Identities=30% Similarity=0.380 Sum_probs=21.7
Q ss_pred CeEEEecccccccceeecccchhhccc
Q 000996 666 GFIEYIDTEEEETTMISMTINDLVQAR 692 (1195)
Q Consensus 666 g~iE~i~~~Ee~~~~Ia~~~~~~~~~~ 692 (1195)
..|+||+|.||+...||.....+.+.+
T Consensus 11 ~~i~YLtA~eEe~~~IAqA~~~ld~~g 37 (66)
T PF10385_consen 11 DEIEYLTADEEEKYVIAQANAPLDEDG 37 (66)
T ss_dssp CEEEEEECTTCCCSEEE-TTS-BSSTT
T ss_pred CeeEEEchhhcCCcEecccCeeeecCC
Confidence 458999999999999999998887654
No 31
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=52.54 E-value=13 Score=30.50 Aligned_cols=28 Identities=18% Similarity=0.377 Sum_probs=20.5
Q ss_pred eeeccccCcceeeccccCceeeccCCCC
Q 000996 1123 VHVCEHCGLIAIANLKKNSFECRGCKNK 1150 (1195)
Q Consensus 1123 ~~vC~~cG~~~~~~~~~~~~~C~~C~~~ 1150 (1195)
.+.|.+||.............|+.|+..
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~ 30 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYR 30 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCe
Confidence 5789999997754433336789999863
No 32
>PF04941 LEF-8: Late expression factor 8 (LEF-8); InterPro: IPR007025 Late expression factor 8 (LEF-8) is one of the primary components of RNA polymerase produced by polyhedrosis viruses. LEF-8 shows homology to the second largest subunit of prokaryotic DNA-directed RNA polymerase[].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=49.23 E-value=30 Score=43.73 Aligned_cols=34 Identities=18% Similarity=0.169 Sum_probs=27.4
Q ss_pred CCCCCccccceecccchhHHHHHHHHHHHHHHHH
Q 000996 389 EDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDV 422 (1195)
Q Consensus 389 ~DD~D~l~NKRv~l~G~Ll~~lfr~~l~~~~k~i 422 (1195)
.=.+|+|+||=|.-...|+...+...++.+...+
T Consensus 210 ~Y~IDsLsNKiIYkh~yLl~l~y~~~L~~~~~~~ 243 (748)
T PF04941_consen 210 NYSIDSLSNKIIYKHSYLLELTYKPILKKYENLI 243 (748)
T ss_pred CceecccccceeeCHHHHHHHHHHHHHHHHHHHH
Confidence 3478999999999999999999887776655443
No 33
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=47.30 E-value=13 Score=37.55 Aligned_cols=29 Identities=21% Similarity=0.499 Sum_probs=22.0
Q ss_pred eeeccccCcceeeccccCceeeccCCCCCCc
Q 000996 1123 VHVCEHCGLIAIANLKKNSFECRGCKNKTDI 1153 (1195)
Q Consensus 1123 ~~vC~~cG~~~~~~~~~~~~~C~~C~~~~~~ 1153 (1195)
..-|+.||..+.. +.+..+|+.|+....+
T Consensus 28 ~~hCp~Cg~PLF~--KdG~v~CPvC~~~~~~ 56 (131)
T COG1645 28 AKHCPKCGTPLFR--KDGEVFCPVCGYREVV 56 (131)
T ss_pred HhhCcccCCccee--eCCeEECCCCCceEEE
Confidence 3459999999976 6677899999954333
No 34
>PF14251 DUF4346: Domain of unknown function (DUF4346)
Probab=44.72 E-value=11 Score=37.09 Aligned_cols=14 Identities=43% Similarity=0.627 Sum_probs=11.2
Q ss_pred CCCCCCCCceEEEc
Q 000996 183 GECPYDQGGYFIIN 196 (1195)
Q Consensus 183 gE~~~D~GGYFIIN 196 (1195)
.--..||+|||||.
T Consensus 10 R~i~LDp~GYfiI~ 23 (119)
T PF14251_consen 10 RFIDLDPAGYFIIY 23 (119)
T ss_pred CccccCCCccEEEE
Confidence 34468999999996
No 35
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=44.35 E-value=16 Score=41.71 Aligned_cols=65 Identities=22% Similarity=0.398 Sum_probs=43.9
Q ss_pred HHHHhhhcCCCceeeeeccccCcce--eeccccCceeeccCCC-----CCC---ceeecchHhhHHHHHHHHhCCCceEE
Q 000996 1109 FLKERLFDQSDAYRVHVCEHCGLIA--IANLKKNSFECRGCKN-----KTD---IVQVHIPYACKLLFQELMAMAIAPRM 1178 (1195)
Q Consensus 1109 ~l~Erl~~~SD~~~~~vC~~cG~~~--~~~~~~~~~~C~~C~~-----~~~---~~~v~iPy~~kll~~EL~sm~i~~~l 1178 (1195)
.|.| |+..+| ..+|..||... |+.++-+.|.|..|.. +.+ |..|.+=.=..==++.|.+|| +.+.
T Consensus 15 ~l~~-Ll~~~~---N~~CADC~a~~P~WaSwnlGvFiC~~C~giHR~lg~hiSkVkSv~LD~W~~eqv~~m~~~G-N~~a 89 (287)
T KOG0703|consen 15 RLRE-LLREPD---NKVCADCGAKGPRWASWNLGVFICLRCAGIHRSLGVHISKVKSVTLDEWTDEQVDFMISMG-NAKA 89 (287)
T ss_pred HHHH-HHcCcc---cCcccccCCCCCCeEEeecCeEEEeecccccccccchhheeeeeeccccCHHHHHHHHHHc-chhh
Confidence 3555 555666 77899999875 6777889999999986 223 333455444445577788887 5543
No 36
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=41.53 E-value=16 Score=39.06 Aligned_cols=45 Identities=20% Similarity=0.421 Sum_probs=32.8
Q ss_pred hccHHHHHHhhhcCCCceeeeeccccCccee-eccccCceeeccCCC
Q 000996 1104 HGASHFLKERLFDQSDAYRVHVCEHCGLIAI-ANLKKNSFECRGCKN 1149 (1195)
Q Consensus 1104 ~Gas~~l~Erl~~~SD~~~~~vC~~cG~~~~-~~~~~~~~~C~~C~~ 1149 (1195)
|-...-|+++|-..++. ..++|..||.... .......|.|+.|+.
T Consensus 99 ~~~~~klk~~l~~e~~~-~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~ 144 (178)
T PRK06266 99 MEELKKLKEQLEEEENN-MFFFCPNCHIRFTFDEAMEYGFRCPQCGE 144 (178)
T ss_pred HHHHHHHHHHhhhccCC-CEEECCCCCcEEeHHHHhhcCCcCCCCCC
Confidence 56677889999777764 6789999997542 112234689999986
No 37
>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=41.30 E-value=21 Score=27.55 Aligned_cols=26 Identities=31% Similarity=0.631 Sum_probs=18.4
Q ss_pred eeeccccCcceeeccccCceeeccCCCC
Q 000996 1123 VHVCEHCGLIAIANLKKNSFECRGCKNK 1150 (1195)
Q Consensus 1123 ~~vC~~cG~~~~~~~~~~~~~C~~C~~~ 1150 (1195)
.|+|..||-+.... .....|+.|+..
T Consensus 2 ~~~C~~CG~i~~g~--~~p~~CP~Cg~~ 27 (34)
T cd00729 2 VWVCPVCGYIHEGE--EAPEKCPICGAP 27 (34)
T ss_pred eEECCCCCCEeECC--cCCCcCcCCCCc
Confidence 68999999876332 112479999875
No 38
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=38.66 E-value=20 Score=25.57 Aligned_cols=23 Identities=26% Similarity=0.694 Sum_probs=14.9
Q ss_pred ccccCcceeeccccCceeeccCC
Q 000996 1126 CEHCGLIAIANLKKNSFECRGCK 1148 (1195)
Q Consensus 1126 C~~cG~~~~~~~~~~~~~C~~C~ 1148 (1195)
|..||.....-.....|.|+.|+
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCG 23 (24)
T ss_pred CccCCCcccCcccCceEeCCCCC
Confidence 67888766432223467898886
No 39
>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=38.60 E-value=18 Score=37.92 Aligned_cols=46 Identities=15% Similarity=0.298 Sum_probs=31.7
Q ss_pred hhccHHHHHHhhhcCCCceeeeeccccCccee-eccccCceeeccCCC
Q 000996 1103 AHGASHFLKERLFDQSDAYRVHVCEHCGLIAI-ANLKKNSFECRGCKN 1149 (1195)
Q Consensus 1103 a~Gas~~l~Erl~~~SD~~~~~vC~~cG~~~~-~~~~~~~~~C~~C~~ 1149 (1195)
.|.....|+++|-..++ ...++|+.||.... .......|.|+.|+.
T Consensus 90 ~~~~~~~lk~~l~~e~~-~~~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~ 136 (158)
T TIGR00373 90 LEETAKKLREKLEFETN-NMFFICPNMCVRFTFNEAMELNFTCPRCGA 136 (158)
T ss_pred HHHHHHHHHHHHhhccC-CCeEECCCCCcEeeHHHHHHcCCcCCCCCC
Confidence 35667778888866655 46789999996442 112234689999986
No 40
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=38.32 E-value=14 Score=32.05 Aligned_cols=31 Identities=23% Similarity=0.543 Sum_probs=18.7
Q ss_pred CceeeeeccccCcceeeccccCceeeccCCC
Q 000996 1119 DAYRVHVCEHCGLIAIANLKKNSFECRGCKN 1149 (1195)
Q Consensus 1119 D~~~~~vC~~cG~~~~~~~~~~~~~C~~C~~ 1149 (1195)
+.....+|..||......-+.-.|.|+.|+.
T Consensus 3 ~~~~~~~CtSCg~~i~~~~~~~~F~CPnCG~ 33 (59)
T PRK14890 3 EMMEPPKCTSCGIEIAPREKAVKFLCPNCGE 33 (59)
T ss_pred ccccCccccCCCCcccCCCccCEeeCCCCCC
Confidence 4445567888887664322234577877765
No 41
>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=37.93 E-value=23 Score=27.01 Aligned_cols=26 Identities=27% Similarity=0.592 Sum_probs=18.8
Q ss_pred eeeccccCcceeeccccCceeeccCCCC
Q 000996 1123 VHVCEHCGLIAIANLKKNSFECRGCKNK 1150 (1195)
Q Consensus 1123 ~~vC~~cG~~~~~~~~~~~~~C~~C~~~ 1150 (1195)
.++|..||-+... ....+.|+.|+..
T Consensus 1 ~~~C~~CGy~y~~--~~~~~~CP~Cg~~ 26 (33)
T cd00350 1 KYVCPVCGYIYDG--EEAPWVCPVCGAP 26 (33)
T ss_pred CEECCCCCCEECC--CcCCCcCcCCCCc
Confidence 3789999977532 2245789999874
No 42
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=37.35 E-value=24 Score=37.27 Aligned_cols=24 Identities=29% Similarity=0.573 Sum_probs=18.3
Q ss_pred eeeccccCcceeeccccCceeeccCCC
Q 000996 1123 VHVCEHCGLIAIANLKKNSFECRGCKN 1149 (1195)
Q Consensus 1123 ~~vC~~cG~~~~~~~~~~~~~C~~C~~ 1149 (1195)
+|||..||-+... .....|+.|+.
T Consensus 134 ~~vC~vCGy~~~g---e~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYTHEG---EAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCCcccC---CCCCcCCCCCC
Confidence 9999999987633 22447999985
No 43
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=37.16 E-value=21 Score=38.12 Aligned_cols=35 Identities=26% Similarity=0.582 Sum_probs=27.2
Q ss_pred eeccccCcceeeccccCceeeccCCCCCCceeecchHh
Q 000996 1124 HVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYA 1161 (1195)
Q Consensus 1124 ~vC~~cG~~~~~~~~~~~~~C~~C~~~~~~~~v~iPy~ 1161 (1195)
-.|.+||..+.. .....+|+.|++ +...|+..||-
T Consensus 150 A~CsrC~~~L~~--~~~~l~Cp~Cg~-tEkRKia~~y~ 184 (188)
T COG1096 150 ARCSRCRAPLVK--KGNMLKCPNCGN-TEKRKIAKDYG 184 (188)
T ss_pred EEccCCCcceEE--cCcEEECCCCCC-EEeeeeccccc
Confidence 469999998865 345678999987 47788888873
No 44
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=36.97 E-value=23 Score=29.01 Aligned_cols=26 Identities=35% Similarity=0.947 Sum_probs=19.4
Q ss_pred eeccccCcceeecccc-CceeeccCCC
Q 000996 1124 HVCEHCGLIAIANLKK-NSFECRGCKN 1149 (1195)
Q Consensus 1124 ~vC~~cG~~~~~~~~~-~~~~C~~C~~ 1149 (1195)
.+|..||...+..++. ..|.|..|+.
T Consensus 19 ~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 6799999976544443 7889999974
No 45
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=36.37 E-value=29 Score=28.04 Aligned_cols=26 Identities=19% Similarity=0.600 Sum_probs=17.9
Q ss_pred eeccccCcce-eeccccCceeeccCCC
Q 000996 1124 HVCEHCGLIA-IANLKKNSFECRGCKN 1149 (1195)
Q Consensus 1124 ~vC~~cG~~~-~~~~~~~~~~C~~C~~ 1149 (1195)
++|..||.-. ..+...+.++|..|+.
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~ 27 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCGL 27 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-B
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCCC
Confidence 4688999864 4455666778999964
No 46
>PRK00420 hypothetical protein; Validated
Probab=35.80 E-value=23 Score=34.96 Aligned_cols=26 Identities=23% Similarity=0.391 Sum_probs=19.9
Q ss_pred eeccccCcceeeccccCceeeccCCCC
Q 000996 1124 HVCEHCGLIAIANLKKNSFECRGCKNK 1150 (1195)
Q Consensus 1124 ~vC~~cG~~~~~~~~~~~~~C~~C~~~ 1150 (1195)
..|+.||...... +.+..+|+.|+..
T Consensus 24 ~~CP~Cg~pLf~l-k~g~~~Cp~Cg~~ 49 (112)
T PRK00420 24 KHCPVCGLPLFEL-KDGEVVCPVHGKV 49 (112)
T ss_pred CCCCCCCCcceec-CCCceECCCCCCe
Confidence 3599999988653 5567799999863
No 47
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=35.23 E-value=19 Score=35.29 Aligned_cols=31 Identities=23% Similarity=0.531 Sum_probs=22.6
Q ss_pred eeeeccccCcceeeccccCceeeccCCCCCCc
Q 000996 1122 RVHVCEHCGLIAIANLKKNSFECRGCKNKTDI 1153 (1195)
Q Consensus 1122 ~~~vC~~cG~~~~~~~~~~~~~C~~C~~~~~~ 1153 (1195)
+-++|..||...| .+++...+|+.|+..-.+
T Consensus 8 tKR~Cp~CG~kFY-DLnk~PivCP~CG~~~~~ 38 (108)
T PF09538_consen 8 TKRTCPSCGAKFY-DLNKDPIVCPKCGTEFPP 38 (108)
T ss_pred CcccCCCCcchhc-cCCCCCccCCCCCCccCc
Confidence 4578999998775 455566689999975433
No 48
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=35.18 E-value=29 Score=29.10 Aligned_cols=30 Identities=17% Similarity=0.428 Sum_probs=22.0
Q ss_pred eeeeeccccCcceeeccccCceeeccCCCC
Q 000996 1121 YRVHVCEHCGLIAIANLKKNSFECRGCKNK 1150 (1195)
Q Consensus 1121 ~~~~vC~~cG~~~~~~~~~~~~~C~~C~~~ 1150 (1195)
...++|..||.............|+.|+..
T Consensus 4 ~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 4 MMEYKCARCGREVELDQETRGIRCPYCGSR 33 (49)
T ss_pred eEEEEhhhcCCeeehhhccCceeCCCCCcE
Confidence 457899999998743434456689999864
No 49
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=33.91 E-value=33 Score=26.37 Aligned_cols=28 Identities=25% Similarity=0.497 Sum_probs=21.4
Q ss_pred eeeccccCcceeeccccCceeeccCCCC
Q 000996 1123 VHVCEHCGLIAIANLKKNSFECRGCKNK 1150 (1195)
Q Consensus 1123 ~~vC~~cG~~~~~~~~~~~~~C~~C~~~ 1150 (1195)
.+.|..||.....+......+|..|+..
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~~ 30 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIFCGSS 30 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcccCCcE
Confidence 3579999988766556677899999863
No 50
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=33.71 E-value=28 Score=32.93 Aligned_cols=29 Identities=17% Similarity=0.608 Sum_probs=23.3
Q ss_pred eeeeeccccCcceeeccccCceeeccCCC
Q 000996 1121 YRVHVCEHCGLIAIANLKKNSFECRGCKN 1149 (1195)
Q Consensus 1121 ~~~~vC~~cG~~~~~~~~~~~~~C~~C~~ 1149 (1195)
+.-|.|+.||.....-...+.|.|..|+.
T Consensus 33 ~~ky~Cp~Cgk~~vkR~a~GIW~C~~C~~ 61 (90)
T PF01780_consen 33 HAKYTCPFCGKTSVKRVATGIWKCKKCGK 61 (90)
T ss_dssp HS-BEESSSSSSEEEEEETTEEEETTTTE
T ss_pred hCCCcCCCCCCceeEEeeeEEeecCCCCC
Confidence 45688999999987666677899999985
No 51
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=32.73 E-value=26 Score=35.95 Aligned_cols=37 Identities=19% Similarity=0.451 Sum_probs=26.6
Q ss_pred CceeeeeccccCcceeeccccCceeeccCCCCCCceeecch
Q 000996 1119 DAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIP 1159 (1195)
Q Consensus 1119 D~~~~~vC~~cG~~~~~~~~~~~~~C~~C~~~~~~~~v~iP 1159 (1195)
-+....-|.+||+..+-- ...|..|++.+++..+.+|
T Consensus 25 ~kl~g~kC~~CG~v~~PP----r~~Cp~C~~~~~~E~vels 61 (140)
T COG1545 25 GKLLGTKCKKCGRVYFPP----RAYCPKCGSETELEWVELS 61 (140)
T ss_pred CcEEEEEcCCCCeEEcCC----cccCCCCCCCCceEEEEeC
Confidence 455667899999987542 3479999988665556555
No 52
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=32.53 E-value=27 Score=29.05 Aligned_cols=25 Identities=40% Similarity=0.881 Sum_probs=16.7
Q ss_pred eccccCcceeecc-c-cCceeeccCCC
Q 000996 1125 VCEHCGLIAIANL-K-KNSFECRGCKN 1149 (1195)
Q Consensus 1125 vC~~cG~~~~~~~-~-~~~~~C~~C~~ 1149 (1195)
.|..||.+++... . ...++|+.|+-
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~ 28 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGY 28 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCC
Confidence 4888998875322 1 23678998874
No 53
>PRK11032 hypothetical protein; Provisional
Probab=31.54 E-value=32 Score=36.08 Aligned_cols=7 Identities=57% Similarity=1.298 Sum_probs=3.0
Q ss_pred eccccCc
Q 000996 1125 VCEHCGL 1131 (1195)
Q Consensus 1125 vC~~cG~ 1131 (1195)
||.+||.
T Consensus 126 vC~~Cg~ 132 (160)
T PRK11032 126 VCEKCHH 132 (160)
T ss_pred EecCCCC
Confidence 3444443
No 54
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=30.99 E-value=32 Score=35.58 Aligned_cols=28 Identities=25% Similarity=0.498 Sum_probs=15.3
Q ss_pred eeeccccCcceeeccccCceeeccCCCC
Q 000996 1123 VHVCEHCGLIAIANLKKNSFECRGCKNK 1150 (1195)
Q Consensus 1123 ~~vC~~cG~~~~~~~~~~~~~C~~C~~~ 1150 (1195)
.+||.+||...........+-|+.|+..
T Consensus 112 ~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~ 139 (146)
T PF07295_consen 112 TLVCENCGHEVELTHPERLPPCPKCGHT 139 (146)
T ss_pred eEecccCCCEEEecCCCcCCCCCCCCCC
Confidence 3567777765532222334567777653
No 55
>CHL00207 rpoB RNA polymerase beta subunit; Provisional
Probab=30.43 E-value=48 Score=44.76 Aligned_cols=17 Identities=6% Similarity=0.178 Sum_probs=15.2
Q ss_pred CcCCCcEECCCCEEEEE
Q 000996 863 LAPPGTRVSGEDVIIGK 879 (1195)
Q Consensus 863 i~~~G~~v~~gdvli~k 879 (1195)
+|.+|++|++||+|.--
T Consensus 620 ~V~~G~~v~~G~iladg 636 (1077)
T CHL00207 620 IVWVGEKINIGQILADG 636 (1077)
T ss_pred ccCCCCEEecCCEEecc
Confidence 89999999999999843
No 56
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=30.42 E-value=31 Score=35.67 Aligned_cols=42 Identities=19% Similarity=0.368 Sum_probs=27.7
Q ss_pred HHHHHHhhhcCCCceeeeeccccCcceee-----c-cccCceeeccCCC
Q 000996 1107 SHFLKERLFDQSDAYRVHVCEHCGLIAIA-----N-LKKNSFECRGCKN 1149 (1195)
Q Consensus 1107 s~~l~Erl~~~SD~~~~~vC~~cG~~~~~-----~-~~~~~~~C~~C~~ 1149 (1195)
-.-|+++|-..++ ...++|+.||..... . -..+.|.|+.|+.
T Consensus 84 ~~~L~~~l~~e~~-~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~ 131 (147)
T smart00531 84 RKRLEDKLEDETN-NAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGE 131 (147)
T ss_pred HHHHHHHHhcccC-CcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCC
Confidence 3456778766655 457899999975421 0 1233499999986
No 57
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=28.36 E-value=34 Score=38.95 Aligned_cols=16 Identities=19% Similarity=0.463 Sum_probs=9.4
Q ss_pred HHHHHHHhcccCCCCC
Q 000996 345 YAKEILQKEMLPHVGT 360 (1195)
Q Consensus 345 ~~~~~L~~~llpHl~~ 360 (1195)
....+|++.++.=||+
T Consensus 158 IK~~LLDQ~vvaGvGN 173 (273)
T COG0266 158 IKTALLDQKVVAGVGN 173 (273)
T ss_pred hHHHhhcCCceecccH
Confidence 3445666666665554
No 58
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=28.28 E-value=31 Score=34.65 Aligned_cols=29 Identities=10% Similarity=0.130 Sum_probs=22.2
Q ss_pred eeeeeccccCcceeeccccCceeeccCCCC
Q 000996 1121 YRVHVCEHCGLIAIANLKKNSFECRGCKNK 1150 (1195)
Q Consensus 1121 ~~~~vC~~cG~~~~~~~~~~~~~C~~C~~~ 1150 (1195)
-+-++|..||...| .+++...+|+.|+..
T Consensus 7 GtKr~Cp~cg~kFY-DLnk~p~vcP~cg~~ 35 (129)
T TIGR02300 7 GTKRICPNTGSKFY-DLNRRPAVSPYTGEQ 35 (129)
T ss_pred CccccCCCcCcccc-ccCCCCccCCCcCCc
Confidence 34578999998775 455567799999875
No 59
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=26.98 E-value=36 Score=26.65 Aligned_cols=23 Identities=22% Similarity=0.548 Sum_probs=18.1
Q ss_pred ccccCcceeeccccCceeeccCCC
Q 000996 1126 CEHCGLIAIANLKKNSFECRGCKN 1149 (1195)
Q Consensus 1126 C~~cG~~~~~~~~~~~~~C~~C~~ 1149 (1195)
|..||.. ......+.++|..|+.
T Consensus 11 C~~C~~~-~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 11 CPVCGSR-WFYSDDGFYYCDRCGH 33 (36)
T ss_pred CCCCCCe-EeEccCCEEEhhhCce
Confidence 9999998 4445567889999975
No 60
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=26.32 E-value=48 Score=26.82 Aligned_cols=23 Identities=26% Similarity=0.715 Sum_probs=17.4
Q ss_pred eccccCcceeeccccCceeeccCC
Q 000996 1125 VCEHCGLIAIANLKKNSFECRGCK 1148 (1195)
Q Consensus 1125 vC~~cG~~~~~~~~~~~~~C~~C~ 1148 (1195)
.|+.||.++..+ +++..+|..|+
T Consensus 19 ~Cp~C~~PL~~~-k~g~~~Cv~C~ 41 (41)
T PF06677_consen 19 HCPDCGTPLMRD-KDGKIYCVSCG 41 (41)
T ss_pred ccCCCCCeeEEe-cCCCEECCCCC
Confidence 589999988764 34567899985
No 61
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=23.85 E-value=80 Score=46.11 Aligned_cols=17 Identities=35% Similarity=0.319 Sum_probs=15.1
Q ss_pred CcCCCcEECCCCEEEEE
Q 000996 863 LAPPGTRVSGEDVIIGK 879 (1195)
Q Consensus 863 i~~~G~~v~~gdvli~k 879 (1195)
+|++|++|++||||.--
T Consensus 790 iV~~Gd~V~kGdilADG 806 (2836)
T PRK14844 790 LVCVGDYVKEGDVIADG 806 (2836)
T ss_pred eecCCCEeccCCEeccC
Confidence 89999999999999743
No 62
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=22.47 E-value=40 Score=24.29 Aligned_cols=22 Identities=23% Similarity=0.578 Sum_probs=15.1
Q ss_pred eeccccCcceeeccccCceeeccCCC
Q 000996 1124 HVCEHCGLIAIANLKKNSFECRGCKN 1149 (1195)
Q Consensus 1124 ~vC~~cG~~~~~~~~~~~~~C~~C~~ 1149 (1195)
..|.+||..... +.-+|+.|+.
T Consensus 3 ~~Cp~Cg~~~~~----~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDP----DAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCc----ccccChhhCC
Confidence 469999985422 2347999975
No 63
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=22.38 E-value=71 Score=26.23 Aligned_cols=27 Identities=26% Similarity=0.709 Sum_probs=19.3
Q ss_pred eeeccccCcceeeccccCceeeccCCCC
Q 000996 1123 VHVCEHCGLIAIANLKKNSFECRGCKNK 1150 (1195)
Q Consensus 1123 ~~vC~~cG~~~~~~~~~~~~~C~~C~~~ 1150 (1195)
.++|..||...... ......|+.|+..
T Consensus 2 ~Y~C~~Cg~~~~~~-~~~~irC~~CG~r 28 (44)
T smart00659 2 IYICGECGRENEIK-SKDVVRCRECGYR 28 (44)
T ss_pred EEECCCCCCEeecC-CCCceECCCCCce
Confidence 57899999865322 3456789999864
No 64
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=22.12 E-value=45 Score=31.68 Aligned_cols=29 Identities=24% Similarity=0.556 Sum_probs=22.9
Q ss_pred eeeeeccccCcceeeccccCceeeccCCC
Q 000996 1121 YRVHVCEHCGLIAIANLKKNSFECRGCKN 1149 (1195)
Q Consensus 1121 ~~~~vC~~cG~~~~~~~~~~~~~C~~C~~ 1149 (1195)
+..|.|.-||...+.-...+.|.|..|+.
T Consensus 33 ~a~y~CpfCgk~~vkR~a~GIW~C~~C~~ 61 (91)
T TIGR00280 33 KAKYVCPFCGKKTVKRGSTGIWTCRKCGA 61 (91)
T ss_pred hcCccCCCCCCCceEEEeeEEEEcCCCCC
Confidence 45578999998876655567899999986
No 65
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=21.18 E-value=51 Score=29.15 Aligned_cols=29 Identities=24% Similarity=0.598 Sum_probs=22.4
Q ss_pred eeeeeccccCcceeeccccCceeeccCCC
Q 000996 1121 YRVHVCEHCGLIAIANLKKNSFECRGCKN 1149 (1195)
Q Consensus 1121 ~~~~vC~~cG~~~~~~~~~~~~~C~~C~~ 1149 (1195)
++...|..||...........+.|+.|+-
T Consensus 26 ~TSq~C~~CG~~~~~~~~~r~~~C~~Cg~ 54 (69)
T PF07282_consen 26 YTSQTCPRCGHRNKKRRSGRVFTCPNCGF 54 (69)
T ss_pred CCccCccCcccccccccccceEEcCCCCC
Confidence 35667999998875555667889999975
No 66
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=20.49 E-value=1.1e+02 Score=44.99 Aligned_cols=17 Identities=18% Similarity=0.380 Sum_probs=15.3
Q ss_pred CcCCCcEECCCCEEEEE
Q 000996 863 LAPPGTRVSGEDVIIGK 879 (1195)
Q Consensus 863 i~~~G~~v~~gdvli~k 879 (1195)
+|++|++|++||||.--
T Consensus 780 iV~~Gd~V~kGdilADG 796 (2890)
T PRK09603 780 IVKVGDKVEAGQIIADG 796 (2890)
T ss_pred EecCCCEeccCCEEecC
Confidence 89999999999999844
No 67
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=20.20 E-value=67 Score=27.83 Aligned_cols=26 Identities=27% Similarity=0.691 Sum_probs=18.9
Q ss_pred eeeeccccCcceeeccccCceeeccCCCCCCc
Q 000996 1122 RVHVCEHCGLIAIANLKKNSFECRGCKNKTDI 1153 (1195)
Q Consensus 1122 ~~~vC~~cG~~~~~~~~~~~~~C~~C~~~~~~ 1153 (1195)
.+.+|..||.... ...|+.|+..+.+
T Consensus 4 ~mr~C~~CgvYTL------k~~CP~CG~~t~~ 29 (56)
T PRK13130 4 KIRKCPKCGVYTL------KEICPVCGGKTKN 29 (56)
T ss_pred cceECCCCCCEEc------cccCcCCCCCCCC
Confidence 4678999997663 2269999986544
Done!