Query 001021
Match_columns 1186
No_of_seqs 229 out of 1855
Neff 6.7
Searched_HMMs 46136
Date Thu Mar 28 13:36:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001021.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001021hhsearch_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-282 4E-287 2427.2 65.3 1132 25-1172 2-1140(1141)
2 PRK08565 DNA-directed RNA poly 100.0 7E-279 2E-283 2635.0 100.1 1095 28-1173 1-1101(1103)
3 KOG0215 RNA polymerase III, se 100.0 1E-262 3E-267 2230.4 50.3 1103 18-1174 36-1151(1153)
4 KOG0216 RNA polymerase I, seco 100.0 7E-258 2E-262 2201.8 68.5 1057 27-1172 4-1111(1111)
5 COG0085 RpoB DNA-directed RNA 100.0 1E-246 3E-251 2231.6 73.9 1021 24-1174 10-1059(1060)
6 cd00653 RNA_pol_B_RPB2 RNA pol 100.0 2E-226 4E-231 2114.5 77.8 860 41-1170 1-866 (866)
7 TIGR02013 rpoB DNA-directed RN 100.0 2E-224 4E-229 2103.0 75.3 927 27-1169 6-1065(1065)
8 PRK00405 rpoB DNA-directed RNA 100.0 2E-220 4E-225 2076.8 80.0 929 28-1171 14-1107(1112)
9 CHL00001 rpoB RNA polymerase b 100.0 2E-215 5E-220 2007.9 72.3 934 36-1175 10-1061(1070)
10 CHL00207 rpoB RNA polymerase b 100.0 2E-201 3E-206 1871.3 77.1 926 34-1175 3-1056(1077)
11 PRK09603 bifunctional DNA-dire 100.0 3E-188 7E-193 1799.9 76.4 944 27-1174 13-1376(2890)
12 PRK14844 bifunctional DNA-dire 100.0 2E-183 5E-188 1748.3 72.2 943 26-1175 16-1435(2836)
13 PRK07225 DNA-directed RNA poly 100.0 2E-184 4E-189 1649.4 53.7 597 561-1173 4-603 (605)
14 TIGR03670 rpoB_arch DNA-direct 100.0 2E-183 5E-188 1638.0 51.5 594 564-1173 1-597 (599)
15 PF00562 RNA_pol_Rpb2_6: RNA p 100.0 6E-110 1E-114 970.1 25.1 364 706-1078 1-386 (386)
16 PRK09606 DNA-directed RNA poly 100.0 6E-107 1E-111 974.9 49.5 491 25-550 2-492 (494)
17 PF04563 RNA_pol_Rpb2_1: RNA p 100.0 5.7E-44 1.2E-48 383.9 16.6 149 40-199 1-149 (203)
18 PF04560 RNA_pol_Rpb2_7: RNA p 100.0 6.5E-31 1.4E-35 238.6 6.5 81 1080-1171 1-81 (81)
19 PF04565 RNA_pol_Rpb2_3: RNA p 99.9 2.8E-26 6.1E-31 202.1 3.4 66 465-530 1-68 (68)
20 PF04561 RNA_pol_Rpb2_2: RNA p 99.8 1.5E-20 3.3E-25 199.7 10.4 139 253-392 40-190 (190)
21 PF04566 RNA_pol_Rpb2_4: RNA p 99.8 3.4E-18 7.4E-23 148.0 9.2 63 564-626 1-63 (63)
22 KOG0214 RNA polymerase II, sec 99.2 6E-13 1.3E-17 159.9 -1.9 421 717-1166 680-1101(1141)
23 PF04567 RNA_pol_Rpb2_5: RNA p 99.0 1.4E-10 3.1E-15 95.4 2.0 48 650-701 1-48 (48)
24 KOG0215 RNA polymerase III, se 98.9 8.6E-12 1.9E-16 148.2 -10.4 531 22-622 94-639 (1153)
25 PF06883 RNA_pol_Rpa2_4: RNA p 97.6 7E-05 1.5E-09 64.2 4.3 49 571-619 1-58 (58)
26 COG0085 RpoB DNA-directed RNA 97.6 6.7E-05 1.4E-09 96.0 6.1 109 658-786 476-598 (1060)
27 PHA03394 lef-8 DNA-directed RN 94.9 0.044 9.6E-07 68.1 6.6 142 894-1043 673-828 (865)
28 PF09082 DUF1922: Domain of un 61.8 3.9 8.4E-05 36.4 1.0 49 1112-1162 1-55 (68)
29 COG1997 RPL43A Ribosomal prote 61.0 4.9 0.00011 37.4 1.6 29 1112-1140 33-61 (89)
30 COG1592 Rubrerythrin [Energy p 55.1 8.5 0.00018 40.5 2.4 24 1114-1140 134-157 (166)
31 PRK00398 rpoP DNA-directed RNA 53.7 12 0.00026 30.7 2.6 28 1114-1141 3-30 (46)
32 cd00729 rubredoxin_SM Rubredox 52.7 11 0.00023 29.1 2.0 26 1114-1141 2-27 (34)
33 PF04941 LEF-8: Late expressio 51.2 26 0.00057 44.2 6.0 35 379-413 209-243 (748)
34 COG1645 Uncharacterized Zn-fin 49.9 11 0.00024 38.0 2.1 25 1115-1141 29-53 (131)
35 cd00350 rubredoxin_like Rubred 49.2 11 0.00024 28.7 1.6 26 1114-1141 1-26 (33)
36 PF14251 DUF4346: Domain of un 47.6 9.3 0.0002 37.6 1.2 14 174-187 10-23 (119)
37 PRK06266 transcription initiat 43.5 14 0.00031 39.4 2.0 46 1094-1140 98-144 (178)
38 PF10385 RNA_pol_Rpb2_45: RNA 43.2 27 0.00059 31.1 3.4 27 657-683 11-37 (66)
39 PF07754 DUF1610: Domain of un 41.2 17 0.00036 26.0 1.3 23 1117-1139 1-23 (24)
40 PF09538 FYDLN_acid: Protein o 38.4 16 0.00035 35.8 1.3 31 1113-1144 8-38 (108)
41 PF12760 Zn_Tnp_IS1595: Transp 38.3 22 0.00047 29.2 1.9 26 1115-1140 19-45 (46)
42 PRK00420 hypothetical protein; 37.9 20 0.00044 35.3 1.9 25 1116-1141 25-49 (112)
43 COG1096 Predicted RNA-binding 37.3 21 0.00045 38.1 2.0 34 1115-1151 150-183 (188)
44 PF08271 TF_Zn_Ribbon: TFIIB z 37.1 28 0.0006 28.1 2.2 26 1115-1140 1-27 (43)
45 smart00661 RPOL9 RNA polymeras 36.1 21 0.00046 29.6 1.5 25 1116-1140 2-28 (52)
46 PRK14890 putative Zn-ribbon RN 35.6 17 0.00036 31.6 0.8 31 1110-1140 3-33 (59)
47 PF01780 Ribosomal_L37ae: Ribo 35.2 25 0.00054 33.3 1.9 29 1112-1140 33-61 (90)
48 TIGR00373 conserved hypothetic 34.8 23 0.00049 37.1 1.8 46 1094-1140 90-136 (158)
49 KOG0703 Predicted GTPase-activ 34.7 27 0.00059 39.8 2.5 64 1100-1168 15-88 (287)
50 COG1996 RPC10 DNA-directed RNA 34.1 28 0.0006 29.2 1.8 30 1112-1141 4-33 (49)
51 PF08792 A2L_zn_ribbon: A2L zi 33.5 34 0.00074 26.3 2.1 28 1114-1141 3-30 (33)
52 COG1545 Predicted nucleic-acid 32.9 27 0.00058 35.8 1.9 37 1110-1150 25-61 (140)
53 smart00531 TFIIE Transcription 31.6 29 0.00062 35.8 1.9 43 1097-1140 83-131 (147)
54 TIGR02300 FYDLN_acid conserved 30.6 26 0.00057 35.1 1.4 28 1113-1141 8-35 (129)
55 PF07295 DUF1451: Protein of u 29.8 35 0.00076 35.3 2.2 28 1114-1141 112-139 (146)
56 PF11781 RRN7: RNA polymerase 28.0 34 0.00073 26.8 1.3 24 1116-1140 10-33 (36)
57 PRK11032 hypothetical protein; 27.8 41 0.00089 35.3 2.3 7 1116-1122 126-132 (160)
58 TIGR00280 L37a ribosomal prote 26.5 34 0.00073 32.4 1.3 29 1112-1140 33-61 (91)
59 COG0266 Nei Formamidopyrimidin 25.3 42 0.00092 38.2 2.0 16 336-351 158-173 (273)
60 PF06677 Auto_anti-p27: Sjogre 24.4 55 0.0012 26.5 1.9 23 1116-1139 19-41 (41)
61 smart00659 RPOLCX RNA polymera 23.2 66 0.0014 26.4 2.2 27 1114-1141 2-28 (44)
62 PTZ00255 60S ribosomal protein 22.4 46 0.001 31.5 1.3 29 1112-1140 34-62 (90)
63 PF07282 OrfB_Zn_ribbon: Putat 22.0 49 0.0011 29.3 1.4 29 1112-1140 26-54 (69)
64 PF14803 Nudix_N_2: Nudix N-te 21.8 51 0.0011 25.5 1.2 24 1116-1139 2-29 (34)
65 PF13248 zf-ribbon_3: zinc-rib 21.7 41 0.0009 24.2 0.7 22 1115-1140 3-24 (26)
66 PRK03976 rpl37ae 50S ribosomal 21.3 49 0.0011 31.4 1.2 29 1112-1140 34-62 (90)
No 1
>KOG0214 consensus RNA polymerase II, second largest subunit [Transcription]
Probab=100.00 E-value=1.8e-282 Score=2427.18 Aligned_cols=1132 Identities=72% Similarity=1.141 Sum_probs=1075.2
Q ss_pred hhhhhhhhhcccCccchHHHHHHHHHHHHHhhHHHHHhhcCCeeeCCCCCCC----CCeEEEEeeEEEeCCcccCCCCcc
Q 001021 25 QEDAWAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHN----PGQQSDFAEIYLSKPMMTESDGET 100 (1186)
Q Consensus 25 ~~~~~~~i~~~f~~~~Lv~~hi~SFN~Fl~~gL~~ii~~~~pI~~~~~~~~~----~~~~l~f~~i~i~~P~~~~~~~~~ 100 (1186)
.+++|.+|++||+.+||+++|++|||.|++.++++|+.+.++|+......+. .++.|.|+.+++.+|+..|.||..
T Consensus 2 qe~~w~vis~~f~ekglvrqQldsFdeFiq~~~qeiv~~~p~i~l~~~~qh~~~~~~r~~l~f~qiylskP~~~e~dg~~ 81 (1141)
T KOG0214|consen 2 QEDCWDVISAYFEEKGLVRQQLDSFDEFIQQTLQEIVADSPKIELQDEAQHTQENPARYQLFFEQIYLSKPTHTESDGST 81 (1141)
T ss_pred hhHHHHHHHhhhcccchHHHHHHHHHHHHHHHHHHHHhcCCCceehhhhhhhccCccceEEEeeeEEEecccccccCCCc
Confidence 5789999999999999999999999999999999999999999976544322 257899999999999999999999
Q ss_pred CCCChHHHHhcCCCcceeEEEEEEEEEeccCCCCcccccceeeEEEEecccceeeccCCccCCCCChhhhhhcCCCCCCC
Q 001021 101 ATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQ 180 (1186)
Q Consensus 101 ~~l~P~EcR~r~lTYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~eli~~gE~~~D~ 180 (1186)
..++|+|||+|++||||||+|+++..+.....+ +...+.+.|+||+||||+||..|.|+++++.+|.+.||||+|+
T Consensus 82 ~~m~p~eARlrnLTYSspLyVd~~k~~~~~~~~----~~~~~~qkvfIGkIPiMlrS~~C~l~~~~d~dl~~l~eCp~Dq 157 (1141)
T KOG0214|consen 82 STMFPNEARLRNLTYSSPLYVDATKIVKTSRDE----VEDMQEQKVFIGKIPIMLRSSYCLLSGLTDKDLTELGECPYDQ 157 (1141)
T ss_pred cccCchhhHhhhcccccceEEEeEEEEeecccc----ccccccceeeEeccceeeehhhhhhcccchhhhhhccCCCcCC
Confidence 999999999999999999999999987643321 2234578899999999999999999999999999999999999
Q ss_pred CceEEEcCeeeEEEeeeeeccCeEEEEEecCCCcceEEEEEEEeecCCCCCCceEEEEEEecCCCCCCCCCcEEEEEecc
Q 001021 181 GGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPY 260 (1186)
Q Consensus 181 GGYFIING~ERVIi~Qe~~s~N~~~~~~~~~~~~~~~~~~irs~~~~g~~~~~~~~v~~~~~~~~~~~~~~~~i~v~i~~ 260 (1186)
||||||||+|||+|+||++|+|++|+|++..++.+.|.++|||..+++++..+++.+++..++. +.-.|.+.+++
T Consensus 158 gGyfIINGseKVlIAQe~matn~vyvf~k~~p~~~ay~~EirS~le~~sR~~stl~v~~~ar~~-----~gq~i~~tlpy 232 (1141)
T KOG0214|consen 158 GGYFIINGSEKVLIAQEKMATNIVYVFKKAHPGTYAYTGEIRSCLERSSRFISTLSVNMDARAG-----KGQEIIATLPY 232 (1141)
T ss_pred CceEEEcCceeeeeehhhccCceEEEEecCCCCceeEeeeeehhhhccCCCcceeeeeeccccC-----CCceEEEEeee
Confidence 9999999999999999999999999999888889999999999999999989999999876542 14588999999
Q ss_pred ccccchHHHHHHHhcCCCHHHHHHHhccccCchhhHhhhHhhHhhhhccccHHHHHHHHhhcCcccCCCchhhHHHHHHH
Q 001021 261 IRTEIPIIIVFRALGFVADKDILEHICYDFQDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGATVGVTRDKRIKYAKEI 340 (1186)
Q Consensus 261 ~~~~IPl~ilLkALG~~sD~eI~~~i~~~~~~~~~~~~l~~~l~e~~~i~t~~~al~yIg~r~~~~~~~~~~~~e~~~~i 340 (1186)
++++||+++|+||||+.+|+||++.|+++.+|.++++++.++++++..+..+..||+|||+|...++.+++.++++|+++
T Consensus 233 ikqeIPI~ilfrALG~v~dreILehIcYd~~D~em~e~lkpsieeafviq~qn~ALdfig~rga~~Gvtkekri~yakdi 312 (1141)
T KOG0214|consen 233 IKQEIPILILFRALGFVSDREILEHICYDFDDAEMFESLKPSIEEAFVIQEQNVALDFIGQRGACIGVTKEKRIKYAKEI 312 (1141)
T ss_pred ecccCcEEEEehhhcCCccHHHHHhhcCCCCcHHHHHHhhhhhhhhhhhhhhHHHHHHHHhcCCCCCCCcchhhHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999766788889999999999
Q ss_pred HhhcccCCCCCCCccchhHHHHHHHHHHHHHHhccCCcCCCCCcccccceeccCchhhHHHHHHHHHHHHHHHHHHHhhh
Q 001021 341 LQKEMLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKC 420 (1186)
Q Consensus 341 L~~~ll~Hl~~~~~~~~~K~~~L~~Mv~kLl~l~~g~~~~DD~D~l~NkRv~l~G~Ll~~lfr~~l~~~~k~ik~~l~k~ 420 (1186)
|.+++|||++..+...+.|++||+|||++|+.++.|++.+||+|||+|||++++|+||..+||..|+++.+++...++|.
T Consensus 313 LqKe~lPhi~~~e~~etkKA~fLGYmi~rlll~aLgRr~~ddRDHfG~KRLDlaGpLLa~lfR~lf~~l~rd~~~~mQk~ 392 (1141)
T KOG0214|consen 313 LQKELLPHVGLGEICETKKAYFLGYMVHRLLLAALGRRELDDRDHFGNKRLDLAGPLLAKLFRSLFAKLLRDVTRYMQKC 392 (1141)
T ss_pred HHHHhccccccchhhhhhHHHHHHhhHHHHHHHHcCCCCccchhhccccchhhchhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999888888999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCCCccchhhhccccchhhhhhhhcccCcccccc-ccccccceeeeccccChhhhhccccccCCCCCcCCCcCcccccC
Q 001021 421 VDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQAN-AAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLH 499 (1186)
Q Consensus 421 ~~~~~~~~~~~~i~~~~It~~i~~~~sTGNw~~~~-~~~~~sGvsq~l~r~N~l~~lSh~Rrv~~~~~~~~K~t~vR~Lh 499 (1186)
+++..++++.-+++++.||++++|+||||||+-++ ..+.++||||+|+|+||+++|||+||+++|++++.|...||+||
T Consensus 393 le~~~dfni~~aika~iIt~gl~yslaTgnwgdq~ka~~~ragVsQVLnR~t~~sTLsHlRR~n~Pigr~GKlAkpRqlH 472 (1141)
T KOG0214|consen 393 LENGVDFNIELAIKAKIITNGLNYALATGNWGDQKKAMQGRAGVSQVLNRLNPLSTLSHLRRTNSPIGRTGKLAKPRQLH 472 (1141)
T ss_pred HhcCccceEEEEEEeeeecccceeeeccCCccchhHHhhccccHHHHhccccHHHHHHHHhhcCCccccccccCCccccC
Confidence 99999999999999999999999999999999555 67789999999999999999999999999999999999999999
Q ss_pred CCCccccccCCCCCCcccccccccceeEEEccCCCchhHHHHHHHhCCccccccCCCCCCCceEEEECCEEEEEEcChHH
Q 001021 500 NSQWGMMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEM 579 (1186)
Q Consensus 500 ps~wG~iCPveTPEG~~cGLvk~LA~~a~Is~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~ 579 (1186)
|||||++||+|||||++||||||||+||.|++|+++.||+++|+++||+.++++++..+++.++||+||+|+|+|.+|+.
T Consensus 473 nthwGmvCPaeTPEGqacGLVKNLSLmayIsvGS~~sPi~EfLeewgmE~le~~~ps~~~datkvfvNG~wvGlhrdp~~ 552 (1141)
T KOG0214|consen 473 NSHWGMVCPAETPEGQACGLVKNLSLMAYISVGSLESPIVEFLEEWGMENLEEISPSPSPDATKVFVNGVWVGLHRDPEE 552 (1141)
T ss_pred cccceeeccccCCCcceeeccccceEEEEEecCCCccHHHHHHHHhchhhHhhcCCCcCCCceEEEEcccEEEecCCHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhhcCCCCCceEEEEeccCCeEEEEeCCCceeeeEEEEecccchhhHHHHHHHhcCCCCCCCCccccccCCcE
Q 001021 580 LVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRESPEDGGWHDLVAKGFI 659 (1186)
Q Consensus 580 l~~~lr~~rr~~~i~~~vsi~~~~~~~~i~I~td~gRl~RPl~~v~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~g~i 659 (1186)
++.+||.+||+..|+.+++++++.+.+|++||||+||+|||||+|+|+++.++|+|+..|++.+.. ..+|..|+..|++
T Consensus 553 l~~tlr~lRR~~di~~Evs~vRDIr~kE~ri~tDaGR~~rPLliven~~l~~~k~hi~~L~~~~~~-~~~w~~lv~~G~i 631 (1141)
T KOG0214|consen 553 LVATLKRLRRQFDIIAEVSMVRDIRDKEIRIFTDAGRSLRPLLIVENAKLLIKKRHIRALKQSKPN-EYRWAHLLSSGEV 631 (1141)
T ss_pred HHHHHHHHHHhhccchhhhhhccccccceeeeeccCccccceEEEechhhhhhhHHHHHHhhCchh-hcchhhhccccce
Confidence 999999999999999999999999999999999999999999999999999999999999876321 3489999999999
Q ss_pred EEeccccccceeeeecccccccccCCCCccccccceeeecCCCccccccccccCCCCCCCCccchhhhhccccccccccc
Q 001021 660 EYIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVT 739 (1186)
Q Consensus 660 E~i~~~Ee~~~~Ia~~~~~~~~~~~~~k~~~~~~~th~Ei~p~~ilsv~AslIPF~~HNqSpRn~yqc~M~KQaig~~~~ 739 (1186)
||||++|||.++|||.++++.+.. +...||||||||++||||+||.|||||||||||||||++|+|||||++.+
T Consensus 632 e~idteeEEtvmiam~~~dL~~~~------~~~~~THCEiHpsmILgv~asiIpFpdh~qspr~tYQsa~~kqamg~y~t 705 (1141)
T KOG0214|consen 632 EYIDTEEEETVMIAMGPKDLAESA------YPKTYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYHT 705 (1141)
T ss_pred eeeccchhhhHHHhcCHHHHhhcc------CCcccccccccHHHhhhhceeeeecCCCCCchHHHHHHHHhhhcceeeee
Confidence 999999999999999999997632 25689999999999999999999999999999999999999999999999
Q ss_pred ceEEeecccceeeccCCcceeecccccccccccCCCCceeEEEEEecCCCCCCCcEEeeccccccCceEEEEEEEEEeee
Q 001021 740 NYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEE 819 (1186)
Q Consensus 740 n~~~r~D~~~~~L~ypQ~PlV~t~~~~~~~~~~~p~G~N~~VAv~sy~GYn~EDaiiink~sv~rG~~~s~~~~~~~~~~ 819 (1186)
|+..|+|+..|+|+|||+|+|+|++++++.+.++|+|+|++||++||+|||+|||+|+|+++++||+|||++||+|+.++
T Consensus 706 n~~vR~dtl~~~l~ypqkpl~tt~~~e~l~~~eL~aG~NaiVAi~~~~GYNqEDsvimn~s~v~rg~FrS~~~RsYk~q~ 785 (1141)
T KOG0214|consen 706 NPQVRMDTLAKVLYYPQKPLVTTRAMEYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSVDRGLFRSFFIRSYKDQE 785 (1141)
T ss_pred cchhhhhhhhhcccccccchhhHHHHhhhhhhhcccccceEEEEecccCccHHHHHHHHhhhhhcchhhhhhhhHHHhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred cccCCcceeeecCCCCCCCCCCCCCCcCCCCCCCccCCCcEEcCCCEEEEEeCCCCc--cccccccCccccceeeEEeec
Q 001021 820 KKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQ--DEAQGQASRYTRRDHSISLRH 897 (1186)
Q Consensus 820 ~~~~~~~~e~~~~p~~~~~~~~~~~~~~~ld~dGi~~~g~~v~~gd~l~~k~~p~~~--~~~~~~~~~~~~~~~s~~~~~ 897 (1186)
.+...+..+.|+.|....+.++++..|++||+||++.||++|+.|||+|||.+|... ++.+...+....+|+|+.+++
T Consensus 786 ~~~~~~~ee~~~~~~~~~~~~mr~~~~dkLdddG~i~~G~~vs~~Dv~iGk~t~~~~~~~~~~~~~~~~t~~d~s~~Lr~ 865 (1141)
T KOG0214|consen 786 HKKDQGPEEIFEEPPRGEGRGMRNGKYDKLDDDGIIMPGSRVSGGDVLIGKTTPQPAKEDESGPEDRLYTKRDHSTKLRH 865 (1141)
T ss_pred hhcccccccccccccccccccccccccccccccCCccccceeecCCEEeccccCCcccchhccccccccccccceeeccc
Confidence 877777788899999888999999999999999999999999999999999998653 333434445568999999999
Q ss_pred CCCcEEEEEEEEecCCCceEEEEEEEeecCCCCcccccccCCCccEEEeeecCCCCCCCCCCCCCcEEeCCCCCCCCCch
Q 001021 898 SETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTI 977 (1186)
Q Consensus 898 ~~~g~v~~v~~~~~~~~~~~vkv~~r~~R~p~iGDKfssRhGqKGvvs~i~~~~dmPf~~~G~~pDiI~NPh~~PSRMti 977 (1186)
+|.|+||+|++++|.+|.+.+||++|+.|.|++|||||||||||||||.++++||||||.+|++||||||||||||||||
T Consensus 866 ~e~Givd~V~vt~n~~G~kF~kv~vr~~ripqiGDKfasrHgqKG~ig~~~~qedmpft~eGi~pDiiiNPhaiPSRmti 945 (1141)
T KOG0214|consen 866 TERGIVDQVWVTKNSEGPKFVKVRVRQVRIPQIGDKFASRHGQKGTIGITYRQEDMPFTIEGIVPDIIINPHAIPSRMTI 945 (1141)
T ss_pred CCcceEEEEEEecCCCCCceeEEEEeecccccccchhccccccCccccceeecCCCCccccCCCcceEECcccCccccch
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHhhhhhHhhhhcCCccccCCCCCccHHHHHHHHHHcCCCCCCeEEEeeCCCCceEEeeEeEeeeehhccccccCCce
Q 001021 978 GQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKI 1057 (1186)
Q Consensus 978 Gql~E~~~gk~~~~~g~~~d~tpF~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if~G~~yy~rL~Hmv~DK~ 1057 (1186)
|||+||++||.++..|...|+|||....+..++..|+++||++.|+|.||||+||++|.+.||+||.|||||+|||+||+
T Consensus 946 g~liEc~lgk~~a~~~e~~~atpFs~v~v~~is~~l~~~g~~~~G~e~~ynGrtG~~~~~~if~GptyyqrL~Hmvd~ki 1025 (1141)
T KOG0214|consen 946 GQLIECLLGKVAAYEGEEGDATPFSDVTVSKISANLHVYGYQYRGNERMYNGRTGRKLRAQIFIGPTYYQRLKHMVDDKI 1025 (1141)
T ss_pred hhhHHHhhhhhhhcccccccCCCCCccchhcccchHHHhccccCCCEEEecCCCCceeeeeeecCchHHHHHHHhhhhee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeccCCccccccCCCCcccCCCcceeeehhhhHHHhhccHHHHHHhhhcCCCcceeeeccccCcceeeccccCceeecc
Q 001021 1058 HSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRG 1137 (1186)
Q Consensus 1058 ~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~L~erL~~~SD~~~~~vC~~cG~~~~~~~~~~~~~C~~ 1137 (1186)
|+|++||++.+||||++||||+||||||||||||+||||||++|+|||+..||.|.+++|..||..+.++.+.+.+.|+.
T Consensus 1026 h~R~~Gp~q~ltRQP~~gRsr~GGlRfGEMErdc~iahGaa~~L~ERL~~~SD~~~~~~c~~c~l~~i~~~~~n~~~ck~ 1105 (1141)
T KOG0214|consen 1026 HSRARGPVQILTRQPVEGRSRDGGLRFGEMERDCLIAHGAAAFLKERLFEKSDAYRVHICVLCGLTAIAGLIPNSFECRG 1105 (1141)
T ss_pred eecccCCceeeeccccccccccCCeeeehhHHHHHHHhhHHHHHHHHhhccCccceEEEeccchhhhhhccCCCcccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999997777888888899999
Q ss_pred CCCCCCceeecccHhhHHHHHHHHhCCCceEEEec
Q 001021 1138 CKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTK 1172 (1186)
Q Consensus 1138 C~~~~~i~~v~iPy~~k~l~~EL~sm~i~~~l~~~ 1172 (1186)
|.+.+.|..+.+|||||||+|||+||||.+|+.+.
T Consensus 1106 c~n~~~v~~v~ipya~kLl~qelmsmni~pr~~~~ 1140 (1141)
T KOG0214|consen 1106 CENKTLVVRVYIPYAAKLLFQELMSMNIAPRRKTK 1140 (1141)
T ss_pred ccCccceEEEechhHHHHHHHHHHhccCccccccC
Confidence 99999999999999999999999999999998764
No 2
>PRK08565 DNA-directed RNA polymerase subunit B; Provisional
Probab=100.00 E-value=7e-279 Score=2634.98 Aligned_cols=1095 Identities=47% Similarity=0.771 Sum_probs=1002.4
Q ss_pred hhhhhhcccCccchHHHHHHHHHHHHHhhHHHHHhhcCCeeeCCCCCCCCCeEEEEeeEEEeCCcccCCCCccCCCChHH
Q 001021 28 AWAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPMMTESDGETATLFPKA 107 (1186)
Q Consensus 28 ~~~~i~~~f~~~~Lv~~hi~SFN~Fl~~gL~~ii~~~~pI~~~~~~~~~~~~~l~f~~i~i~~P~~~~~~~~~~~l~P~E 107 (1186)
+|.++++||+.++|++|||+|||+|+++||++++++++||++. ++.+.|+|++++|++|++.+.++...+|+|+|
T Consensus 1 ~~~li~~~~~~~~Lv~~qidSFn~Fi~~gL~~iv~~~~pI~~~-----~~~~~L~f~~i~l~~P~~~~~~~~~~~l~P~e 75 (1103)
T PRK08565 1 RWTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDEFGEIKTE-----IPGLKIVLGKIRVGEPEIKEADGSERPITPME 75 (1103)
T ss_pred CchHHHHHhcccChHHHHHHHHHHHHHHhHHHHHHhcCCEEec-----CCCEEEEEEEEEECCCcccccccccCCCCHHH
Confidence 4999999999999999999999999999999999999999874 24689999999999999977766678899999
Q ss_pred HHhcCCCcceeEEEEEEEEEeccCCCCcccccceeeEEEEecccceeeccCCccCCCCChhhhhhcCCCCCCCCceEEEc
Q 001021 108 ARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIIN 187 (1186)
Q Consensus 108 cR~r~lTYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~eli~~gE~~~D~GGYFIIN 187 (1186)
||+|++||+|+|+|++++..++. ..+.+++++|+|||||+|++|||++++|+||++.||||+|+|||||||
T Consensus 76 cR~r~lTYsa~l~v~i~~~~~~~---------~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~p~D~GGYFIIN 146 (1103)
T PRK08565 76 ARLRNLTYAAPLYLTMIPVENGI---------EYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIIN 146 (1103)
T ss_pred HHhcCCCcceEEEEEEEEEECCe---------eeEEEEEEeccCCeEeCCCcccCCCCCHHHHHhcCCCccCCCCeEEEC
Confidence 99999999999999999965331 124568999999999999999999999999999999999999999999
Q ss_pred CeeeEEEeeeeeccCeEEEEEecCCCcceEEEEEEEeecCCCCCCceEEEEEEecCCCCCCCCCcEEEEEeccccccchH
Q 001021 188 GSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPI 267 (1186)
Q Consensus 188 G~ERVIi~Qe~~s~N~~~~~~~~~~~~~~~~~~irs~~~~g~~~~~~~~v~~~~~~~~~~~~~~~~i~v~i~~~~~~IPl 267 (1186)
|+||||++|+++|+|+++++.+....+..|.|+++|... .|. +.+.+++.. ++.++++++++..+||+
T Consensus 147 G~ERVI~~q~~~s~n~~~~~~~~~~~~~~~~a~i~s~~~--~~~-~~~~l~~~~---------~g~i~~~~~~~~~~IPi 214 (1103)
T PRK08565 147 GSERVIVSQEDLAPNRVLVDKGEAGSSITHTAKVISSRA--GYR-AQVTVERRK---------DGTIYVSFPAVPGKIPF 214 (1103)
T ss_pred CcEEEEEEEEecCCCEEEEEEecCCCcceEEEEEEeccC--CCc-ceEEEEEec---------CCeEEEEEcCcccEeeH
Confidence 999999999999999999887554455567898887543 221 234444421 46899999987678999
Q ss_pred HHHHHHhcCCCHHHHHHHhccccCchhhHhhhHhhHhhhhcc-ccHHHHHHHHhhcCcccCCCchhhHHHHHHHHhhccc
Q 001021 268 IIVFRALGFVADKDILEHICYDFQDTQMMELLRPSLEEAFVI-QNQQVALDYIGKRGATVGVTRDKRIKYAKEILQKEML 346 (1186)
Q Consensus 268 ~ilLkALG~~sD~eI~~~i~~~~~~~~~~~~l~~~l~e~~~i-~t~~~al~yIg~r~~~~~~~~~~~~e~~~~iL~~~ll 346 (1186)
++||||||++||+||++.|+. ++.+.+.+..++++...+ .|+++|+.|||++|+.. .++..+.+.|+++|++++|
T Consensus 215 ~illkALG~~sD~eI~~~i~~---~~~~~~~l~~~l~~~~~~~~t~~~al~~ig~~~~~~-~~~~~~~e~~~~~L~~~ll 290 (1103)
T PRK08565 215 VILMRALGLETDRDIVYAVSL---DPEIQQELLPSLEQASSIAATVEDALDYIGKRVAIG-QPREYRIERAEQILDKYLL 290 (1103)
T ss_pred HHHHHHcCCCCHHHHHHHhcc---cHHHHHHHHHHHHHhhccccCHHHHHHHHHHhccCC-CCCccHHHHHHHHHHhhCc
Confidence 999999999999999999963 455667777788776556 79999999999998753 3455667899999999999
Q ss_pred CCCCCCCccchhHHHHHHHHHHHHHHhccCCcCCCCCcccccceeccCchhhHHHHHHHHHHHHHHHHHHHhhhhcCCCc
Q 001021 347 PHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKD 426 (1186)
Q Consensus 347 ~Hl~~~~~~~~~K~~~L~~Mv~kLl~l~~g~~~~DD~D~l~NkRv~l~G~Ll~~lfr~~l~~~~k~ik~~l~k~~~~~~~ 426 (1186)
||++.+..++.+|++||++|++||++++.|.+.+||+|||+||||+++|+||+.+||+.|+++++.+++.+.+.+.+.+.
T Consensus 291 ~Hig~~~~~~~~K~~~L~~Mi~kLl~l~~g~~~~DD~D~l~NKRv~l~G~Ll~~~fr~~l~~~~~~ik~~l~~~~~~~~~ 370 (1103)
T PRK08565 291 PHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRK 370 (1103)
T ss_pred ccCCCcccchhHHHHHHHHHHHHHHhhhcCCCCCCCccccCCcEEccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence 99998765556899999999999999999999999999999999999999999999999999999999999877655567
Q ss_pred cchhhhccccchhhhhhhhcccCccccccccccccceeeeccccChhhhhccccccCCCCCcCCCcCcccccCCCCcccc
Q 001021 427 VNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWGMM 506 (1186)
Q Consensus 427 ~~~~~~i~~~~It~~i~~~~sTGNw~~~~~~~~~sGvsq~l~r~N~l~~lSh~Rrv~~~~~~~~K~t~vR~Lhps~wG~i 506 (1186)
+++..+++++.||++|++|||||||.+ |++||||+|+|+||+|+|||||||++++.+++|.++||+||||||||+
T Consensus 371 ~~~~~~i~~~~It~~i~~~~sTGnw~~-----~~sGvSq~ldr~N~l~~lSh~Rrv~s~~~r~~~~~~vR~Lhps~wG~i 445 (1103)
T PRK08565 371 LDLRAIVRPDIITERIRHALATGNWVG-----GRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRI 445 (1103)
T ss_pred CCHHHhcccchhhHHHHHHHhcCcccc-----CCcceEEecccCCHHHHHHHHhhccCCcccCCCCccccccChhhcccc
Confidence 788888998899999999999999996 679999999999999999999999999999999999999999999999
Q ss_pred ccCCCCCCcccccccccceeEEEccCCCchhHHHHHHHhCCccccccCCCCCCCceEEEECCEEEEEEcChHHHHHHHHh
Q 001021 507 CPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKTLRR 586 (1186)
Q Consensus 507 CPveTPEG~~cGLvk~LA~~a~Is~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~l~~~lr~ 586 (1186)
||+|||||++||||||||++|+|+++.+.+++.++|.++|+.++.++++......++|||||+|+|++++|..|++.||.
T Consensus 446 CPveTPEG~~cGLv~~LA~~a~It~~~~~~~i~~~l~~~G~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~l~~~lR~ 525 (1103)
T PRK08565 446 CPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRE 525 (1103)
T ss_pred CCCCCCCccccchhhhhhcccccccCCChHHHHHHHHHcCCCchhhcCcccCCCceEEEECCEEEEEECCHHHHHHHHHH
Confidence 99999999999999999999999998889999999999999998766665666779999999999999999999999999
Q ss_pred hhhcCCCCCceEEEEec--cCCeEEEEeCCCceeeeEEEEecccchhhHHHHHHHhcCCCCCCCCccccccCCcEEEecc
Q 001021 587 LRRRVDVNTEVGVVRDI--RLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRESPEDGGWHDLVAKGFIEYIDT 664 (1186)
Q Consensus 587 ~rr~~~i~~~vsi~~~~--~~~~i~I~td~gRl~RPl~~v~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~g~iE~i~~ 664 (1186)
+||+|.|+.++||++++ ..++|+|+||+||++|||++|++|++.++++|++.++.+.+ +|++|+++|.|||||+
T Consensus 526 ~Rr~g~i~~~v~I~~~~~~~~~~i~I~sd~GRl~RP~~~v~~g~~~~~~~~~~~l~~~~~----~~~~l~~~g~iEyid~ 601 (1103)
T PRK08565 526 LRRSGKISDEVNVAYIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGEL----TFDDLVKMGVIEYLDA 601 (1103)
T ss_pred HhhcCCCCCeEEEEEccccccceEEEecCCceeeeeEEEEecCceeccHHHHHHhhcccc----chhhHhhcCcEEeeCH
Confidence 99999999999999998 78999999999999999999999999999999998876544 8999999999999999
Q ss_pred ccccceeeeecccccccccCCCCccccccceeeecCCCccccccccccCCCCCCCCccchhhhhcccccccccccceEEe
Q 001021 665 EEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFR 744 (1186)
Q Consensus 665 ~Ee~~~~Ia~~~~~~~~~~~~~k~~~~~~~th~Ei~p~~ilsv~AslIPF~~HNqSpRn~yqc~M~KQaig~~~~n~~~r 744 (1186)
+||++++||++++++.. .+||+||+|++|||++||+|||+||||||||||||||||||||++++|+.+|
T Consensus 602 ~Ee~~~~Ia~~~~~l~~-----------~~th~Ei~p~~ilsv~asliPF~~hNqspRn~yq~~M~KQa~g~~~~n~~~r 670 (1103)
T PRK08565 602 EEEENAYVALDPEDLTP-----------EHTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIR 670 (1103)
T ss_pred HHhcCcEEeccccccCc-----------ceeccccCCccccceeeeccCCcccCcccchhhhhhhhhcccccccccceEe
Confidence 99999999999998743 4799999999999999999999999999999999999999999999999999
Q ss_pred ecccceeeccCCcceeecccccccccccCCCCceeEEEEEecCCCCCCCcEEeeccccccCceEEEEEEEEEeeecccCC
Q 001021 745 MDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGT 824 (1186)
Q Consensus 745 ~D~~~~~L~ypQ~PlV~t~~~~~~~~~~~p~G~N~~VAv~sy~GYn~EDaiiink~sv~rG~~~s~~~~~~~~~~~~~~~ 824 (1186)
+|++.|+|+|||+|||+|+.++.++++++|+|+||+||||||+||||||||||||+|+|||||||+||++|++++++...
T Consensus 671 ~d~~~~~l~~pQ~Plv~t~~~~~~~~~~~p~G~N~iVAv~sy~GYn~EDaiIink~s~~rG~~~s~~~~~~~~~~~~~~~ 750 (1103)
T PRK08565 671 TDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPG 750 (1103)
T ss_pred ecCCcceeecCceeEEEeccccccccccCCCCeeEEEEEEcccCcchHHhhhhhhhhhhcCCceEEEEEEEEEEeeecCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999998876544
Q ss_pred cceeeecCCCCCCCCCCCC-CCcCCCCCCCccCCCcEEcCCCEEEEEeCCCCcc--ccccccCccccceeeEEeecCCCc
Q 001021 825 LVKEDFGRPDRSNTMGMRH-GSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQD--EAQGQASRYTRRDHSISLRHSETG 901 (1186)
Q Consensus 825 ~~~e~~~~p~~~~~~~~~~-~~~~~ld~dGi~~~g~~v~~gd~l~~k~~p~~~~--~~~~~~~~~~~~~~s~~~~~~~~g 901 (1186)
+..+.|+.|.+ +..+.+. ..|++||+||||++|++|++|||||||++|.... ......+....+|+|++++.+|+|
T Consensus 751 ~~~~~~~~~~~-~~~~~~~~~~~~~Ld~dGi~~~G~~v~~gdili~k~~p~~~~~~~~~~~~~~~~~~~~s~~~~~~e~g 829 (1103)
T PRK08565 751 GQEDKIEIPEP-NVRGYRGEEYYRKLDEDGIVSPEVEVKGGDVLIGKTSPPRFLEELEELSLGLQERRDTSVTVRHGEKG 829 (1103)
T ss_pred CCceEEecCCC-cccccCchhhhhcCCCCCCcCCCcEEcCCCEEEEEecCCCCCcchhhccccCCccccceEEecCCCce
Confidence 44467877753 2222233 3489999999999999999999999999986421 111111113478999999999999
Q ss_pred EEEEEEEEecCCCceEEEEEEEeecCCCCcccccccCCCccEEEeeecCCCCCCCCCCCCCcEEeCCCCCCCCCchhhHH
Q 001021 902 MVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLI 981 (1186)
Q Consensus 902 ~v~~v~~~~~~~~~~~vkv~~r~~R~p~iGDKfssRhGqKGvvs~i~~~~dmPf~~~G~~pDiI~NPh~~PSRMtiGql~ 981 (1186)
+||+|.++.+.++.+.|||++|+.|+|+||||||||||||||||+|||+||||||+||++|||||||||||||||||||+
T Consensus 830 ~V~~V~~~~~~~~~~~vkv~ir~~R~p~iGDKfssRhGqKGv~s~i~~~edmPf~~~G~~pDiI~NPh~~PSRMtiG~l~ 909 (1103)
T PRK08565 830 IVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLL 909 (1103)
T ss_pred EEEEEEEEecCCCcEEEEEEEEEEecCchhhhhhhhccCcceeeeecccccCCcCCCCCCccEEECCCCCcccccHHHHH
Confidence 99999999988899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhHhhhhcCCccccCCCCCccHHHHHHHHHHcCCCCCCeEEEeeCCCCceEEeeEeEeeeehhccccccCCceEEec
Q 001021 982 ECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRG 1061 (1186)
Q Consensus 982 E~~~gk~~~~~g~~~d~tpF~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~ 1061 (1186)
|+++||||++.|.+.|+|||.+...+++++.|+++||+++|+|+||||+||++|+++||+|++|||||+|||+||+|||+
T Consensus 910 E~~~gk~~~~~g~~~d~t~F~~~~~~~~~~~L~~~g~~~~G~e~l~~G~tG~~~~~~if~G~~yy~rL~HmV~DK~~~R~ 989 (1103)
T PRK08565 910 ESIAGKVAALEGRFVDATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARA 989 (1103)
T ss_pred HHHHHHHHHhcCceeeecCcCCchHHHHHHHHHHcCCCCCCcEEEEcCCCCCCcccceEEeehhheechhhhchhhhhcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCccccccCCCCcccCCCcceeeehhhhHHHhhccHHHHHHhhhcCCCcceeeeccccCcceeeccccCceeeccCCCC
Q 001021 1062 RGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNK 1141 (1186)
Q Consensus 1062 ~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~L~erL~~~SD~~~~~vC~~cG~~~~~~~~~~~~~C~~C~~~ 1141 (1186)
+||++.|||||++||||+|||||||||||||+|||||++|+|||+++||.++++||.+||++++.+.+.+.++|+.|+++
T Consensus 990 ~Gp~~~lt~QP~~Gr~~~GG~R~GEME~d~l~a~Gas~~L~erL~~~SD~~~~~vC~~Cg~~~~~~~~~~~~~C~~c~~~ 1069 (1103)
T PRK08565 990 RGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHIAWYDRRKNKYVCPIHGDK 1069 (1103)
T ss_pred CCCcchhhhCCccccccCCCeeeecchHHHHHhcccHHHHHHHhhccccceeeeeecccccccccccccCceeccccCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999977666678899999998
Q ss_pred CCceeecccHhhHHHHHHHHhCCCceEEEecc
Q 001021 1142 TDIVQVHIPYACKLLFQELMAMAIAPRMLTKE 1173 (1186)
Q Consensus 1142 ~~i~~v~iPy~~k~l~~EL~sm~i~~~l~~~~ 1173 (1186)
..+.++.+|||||||+|||+||||+++|.+++
T Consensus 1070 ~~~~~v~iPy~~k~l~~EL~sm~i~~~l~~~~ 1101 (1103)
T PRK08565 1070 GNISPVEVSYAFKLLLQELMSMGISPRLKLGD 1101 (1103)
T ss_pred CcceeccCChhHHHHHHHHHhCCCceEEEeee
Confidence 89999999999999999999999999999874
No 3
>KOG0215 consensus RNA polymerase III, second largest subunit [Transcription]
Probab=100.00 E-value=1.5e-262 Score=2230.38 Aligned_cols=1103 Identities=41% Similarity=0.694 Sum_probs=1013.4
Q ss_pred ccccccchhhhhhhhhcccCccchHHHHHHHHHHHHHhhHHHHHhhcCCeeeCCCCCCCCCeEEEEeeEEEeCCcccCCC
Q 001021 18 DEEEEITQEDAWAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPMMTESD 97 (1186)
Q Consensus 18 ~~~~~~~~~~~~~~i~~~f~~~~Lv~~hi~SFN~Fl~~gL~~ii~~~~pI~~~~~~~~~~~~~l~f~~i~i~~P~~~~~~ 97 (1186)
...+.-..+|+|.++++||+.+|||++|++|||+|++++|+.|++++..|..+.++ .+.++|.++++++|++.++.
T Consensus 36 ~~~~i~~~~dk~~lvp~flkvkglvkqhldsfnyfv~~~ik~iv~an~~itsd~dp----~fylky~dirvg~Ps~~~~~ 111 (1153)
T KOG0215|consen 36 LSDPIKPLEDKWQLVPAFLKVKGLVKQHLDSFNYFVDVDIKKIVKANQLITSDVDP----SFYLKYLDIRVGKPSIEEGN 111 (1153)
T ss_pred ccCCCCChHHhHHhHHHHHhhhhHHHHHHhhhhhhhhhhHHHHHHhhcccCcCcCc----hhhheeeeeeccCcchhhcc
Confidence 34345567899999999999999999999999999999999999999999876553 47899999999999987665
Q ss_pred Cc-cCCCChHHHHhcCCCcceeEEEEEEEEEeccCCCCcccccceeeEEEEecccceeeccCCccCCCCChhhhhhcCCC
Q 001021 98 GE-TATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELGEC 176 (1186)
Q Consensus 98 ~~-~~~l~P~EcR~r~lTYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~eli~~gE~ 176 (1186)
+. ...++|+|||+|++||+||++|+++++.... .+....|.||++|||++|++|+|++.++.++++.+||
T Consensus 112 ~~~~~~i~p~ecrlrd~tysa~i~vdieytrg~~---------~~~~~~v~igrmpimlrs~rcvl~~~~e~~~a~~~ec 182 (1153)
T KOG0215|consen 112 NVTNDNITPHECRLRDMTYSAPIYVDIEYTRGRQ---------IIAKRDVIIGRMPIMLRSSKCVLRGKDEEELARLNEC 182 (1153)
T ss_pred ccccccCCchheeehhhhcccceeEEEEEecCcc---------eEEecccccccchhhhhccccccCCccHHHHHHhccC
Confidence 43 4579999999999999999999999987542 3456789999999999999999999999999999999
Q ss_pred CCCCCceEEEcCeeeEEEeeeeeccCeEEEEEecCCCcceEEEEEEEe-ecCCCCCCceEEEEEEecCCCCCCCCCcEEE
Q 001021 177 PYDQGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSM-AESQNRPPSTMFVRMLSRTSAKGGSSGQYIR 255 (1186)
Q Consensus 177 ~~D~GGYFIING~ERVIi~Qe~~s~N~~~~~~~~~~~~~~~~~~irs~-~~~g~~~~~~~~v~~~~~~~~~~~~~~~~i~ 255 (1186)
|+||||||||+|.||||+.||+.|.|++++...+ +..+-|++.|. .+++++ ..|.+ + ++.++
T Consensus 183 pldpggyfiv~G~ekViLiqeqlsknrii~~~~k---~~~~~~svtsst~e~ksk----t~v~~------k----~~k~y 245 (1153)
T KOG0215|consen 183 PLDPGGYFIVKGTEKVILIQEQLSKNRIIVEEDK---KGNLQASVTSSTHERKSK----TYVTT------K----KGKYY 245 (1153)
T ss_pred CCCCCceeEeccceeEEEehhhhhccCeeecccc---CCccccccccceeeecce----EEEEe------c----cceee
Confidence 9999999999999999999999999999984222 22345666643 455543 12211 1 66899
Q ss_pred EEeccccccchHHHHHHHhcCCCHHHHHHHhccccCchhhHhhhHhhHhhh--hccccHHHHHHHHhhcCcccCCCchhh
Q 001021 256 ATLPYIRTEIPIIIVFRALGFVADKDILEHICYDFQDTQMMELLRPSLEEA--FVIQNQQVALDYIGKRGATVGVTRDKR 333 (1186)
Q Consensus 256 v~i~~~~~~IPl~ilLkALG~~sD~eI~~~i~~~~~~~~~~~~l~~~l~e~--~~i~t~~~al~yIg~r~~~~~~~~~~~ 333 (1186)
++++.+..+||++++|||||..||+||.+.++. +..+.+.+..+++++ ..++|+.+|++|++.+.+....++.+.
T Consensus 246 lk~~~~~d~ipiviv~ka~g~~sd~ei~~~vg~---~~~y~~~~~~s~ee~~~~~v~tqqqal~y~~~kvk~~~~t~~~~ 322 (1153)
T KOG0215|consen 246 LKHNSFTDDIPIVIVLKAMGLESDQEIVQLVGG---DSKYQDIFAPSLEECVSLGVYTQQQALEYIGSKVKVKRGTTPTK 322 (1153)
T ss_pred eehhhhhccCCEEEEEeeccccchHHHHHHhhc---chHHHHhhccchhhhhhhhhHHHHHHHHHhhheEEeccCCCCCc
Confidence 999999999999999999999999999999974 567888888888887 457899999999999976544455667
Q ss_pred HHHHHHHHhhcccCCCCCCCccchhHHHHHHHHHHHHHHhccCCcCCCCCcccccceeccCchhhHHHHHHHHHHHHHHH
Q 001021 334 IKYAKEILQKEMLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDV 413 (1186)
Q Consensus 334 ~e~~~~iL~~~ll~Hl~~~~~~~~~K~~~L~~Mv~kLl~l~~g~~~~DD~D~l~NkRv~l~G~Ll~~lfr~~l~~~~k~i 413 (1186)
.+.|.++|...+++|+.....++..|+.+++.|+|+++....+.-..||+|.++|||++++|+|++.+|++.|+++...+
T Consensus 323 ~~e~~~~l~~~~lahv~v~~~~~r~K~~yi~~m~rr~~~a~l~~~~~ddrd~~gnkrlelagqllsllfeD~fk~~n~e~ 402 (1153)
T KOG0215|consen 323 DEEALEVLSTTVLAHVPVPDLNFRMKAIYIGLMVRRVIQAMLNKLAMDDRDYVGNKRLELAGQLLSLLFEDLFKRFNSEL 402 (1153)
T ss_pred hHHHHHHHHhhheeceeccCCCCcceeehHHHHHHHHHHHHhCcccccchhhhccchHHHHHHHHHHHHHHHHHHHHHHH
Confidence 78999999999999999998889999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhhhcCC---Cccchhhhcc--ccchhhhhhhhcccCccccccccccccceeeeccccChhhhhccccccCCCCCc
Q 001021 414 RAYVQKCVDNG---KDVNLQFAIK--AKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGR 488 (1186)
Q Consensus 414 k~~l~k~~~~~---~~~~~~~~i~--~~~It~~i~~~~sTGNw~~~~~~~~~sGvsq~l~r~N~l~~lSh~Rrv~~~~~~ 488 (1186)
+..+.+.+.+. ..+++...+| ++.||+++.+++|||||..++|.|.+.|++|++.|++|.+.|.++.|++++|++
T Consensus 403 k~~~dk~l~k~~ra~~fD~~~~~n~~~~~it~~l~ra~stgnw~iKrfrmer~gvt~VlsrlSyisaLgmmtri~s~fek 482 (1153)
T KOG0215|consen 403 KKNIDKILKKPIRAQEFDALKHLNVRANMITSGLERAISTGNWSIKRFRMERAGVTQVLSRLSYISALGMMTRINSQFEK 482 (1153)
T ss_pred HHHHHHHhcchhhhhhhHHHHHHHHHHHHHHHHHHHHhhcCchHHHHhhhhhccceeeehhhhhhhhhhhheehhhhhee
Confidence 99888877653 2466666664 689999999999999999999999999999999999999999999999999999
Q ss_pred CCCcCcccccCCCCccccccCCCCCCcccccccccceeEEEccCCCchhHHHHHHHhCCccccccCCCCC--CCceEEEE
Q 001021 489 EGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVI--PQATKIFV 566 (1186)
Q Consensus 489 ~~K~t~vR~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~Is~~~~~~~i~~~l~~~g~~~~~~~~~~~~--~~~~~V~l 566 (1186)
++|..+||.|+|||||++||+|||||++||||||||++++|+++..++|+...+..+|+..+..++...+ +..+.|||
T Consensus 483 trkvsgprSlq~sqwgmlcp~dtpegeacglvknlalmthittd~ee~pi~~~~~k~gv~di~~v~~~e~~~~~~~~v~L 562 (1153)
T KOG0215|consen 483 TRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITTDSEEKPILKLCYKLGVEDIHVVSGRELHTPDSFLVFL 562 (1153)
T ss_pred ehhccCccccChhhcccccCCCCCCccccccccchHHHhcccCCCCcchhHHHHHHhcceeeeeecccccCCCceEEEEe
Confidence 9999999999999999999999999999999999999999999999999999999999998876666555 45689999
Q ss_pred CCEEEEEEcChHHHHHHHHhhhhcCCCCCceEEEEeccCCeEEEEeCCCceeeeEEEEecccchhhHHHHHHHhcCCCCC
Q 001021 567 NGCWVGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRESPE 646 (1186)
Q Consensus 567 nG~~iG~~~~~~~l~~~lr~~rr~~~i~~~vsi~~~~~~~~i~I~td~gRl~RPl~~v~~~~~~~~~~~~~~l~~~~~~~ 646 (1186)
||.++|.+..|+.++..+|.+||+|.|..+|+++.+.....++|.||+||+|||+++++++.+.++..|++++..+..
T Consensus 563 ng~iig~~~~~~~~v~~~r~lrr~G~i~~fvsv~~~~~q~~v~i~sdggr~crp~Iiv~~~~~~v~~~h~~el~~g~r-- 640 (1153)
T KOG0215|consen 563 NGLIIGITRRPQYFVNSFRRLRRKGKIGEFVSVFTNTTQRCVYIASDGGRVCRPLIIVDNGRPRVKQHHMDELLDGKR-- 640 (1153)
T ss_pred cceeeccccchHHHHHHHHHHHHcCcccceeeeeeeeeeEEEEEecCCCeEeeeEEEEeCCcchhhhhhHHHHHHhhh--
Confidence 999999999999999999999999999999999998888999999999999999999999999999999999988876
Q ss_pred CCCccccccCCcEEEeccccccceeeeecccccccccCCCCccccccceeeecCCCccccccccccCCCCCCCCccchhh
Q 001021 647 DGGWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQ 726 (1186)
Q Consensus 647 ~~~~~~l~~~g~iE~i~~~Ee~~~~Ia~~~~~~~~~~~~~k~~~~~~~th~Ei~p~~ilsv~AslIPF~~HNqSpRn~yq 726 (1186)
+|+||++.|+|||+|++||+.++||+.++++.+ .+||+||.|..+||+||+|||||||||||||+||
T Consensus 641 --~F~DFl~~glvEYLDVNEEND~~Ialye~~I~~-----------~TTHLEIEPFTiLGv~AGLIPYPHHNQSPRNTYQ 707 (1153)
T KOG0215|consen 641 --TFDDFLKDGLIEYLDVNEENDSLIALYEEDIGP-----------ETTHLEIEPFTILGVVAGLIPYPHHNQSPRNTYQ 707 (1153)
T ss_pred --hHHHHHHhchhheeecccccCceEEechhhcCC-----------CcceeeecchhhhhhhccccCCCCCCCCCcchhh
Confidence 899999999999999999999999999999965 6999999999999999999999999999999999
Q ss_pred hhcccccccccccceEEeecccceeeccCCcceeecccccccccccCCCCceeEEEEEecCCCCCCCcEEeeccccccCc
Q 001021 727 SAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGF 806 (1186)
Q Consensus 727 c~M~KQaig~~~~n~~~r~D~~~~~L~ypQ~PlV~t~~~~~~~~~~~p~G~N~~VAv~sy~GYn~EDaiiink~sv~rG~ 806 (1186)
|+|||||||..++|+..|+|+.+|+|.|||+|+|+|++.++++++++|+||||.||||||+|||+|||+|+||+|+||||
T Consensus 708 CAMGKQAmG~IaYNQ~~RiDtlmYll~YPq~PmVkTKTIELi~ydKLPAGQNAtVAVMSYSGYDIEDALVLNKsSlDRGf 787 (1153)
T KOG0215|consen 708 CAMGKQAMGAIAYNQKKRIDSLLYLLVYPQRPMVKTKTIELINYDKLPAGQNATVAVMSYSGYDIEDALVLNKSSIDRGF 787 (1153)
T ss_pred hhhhhhhhhhhhhhhhhhHHHHHHHHhcCCCccccceeEEeeccccCCCCCccEEEEEeccCCchhhhhhcccchhccCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEEEEEEEEeeecccCCcceeeecCCCCCCCCCCCCCCcCCCCCCCccCCCcEEcCCCEEEEEeCCCCcccc--ccccC
Q 001021 807 FRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEA--QGQAS 884 (1186)
Q Consensus 807 ~~s~~~~~~~~~~~~~~~~~~e~~~~p~~~~~~~~~~~~~~~ld~dGi~~~g~~v~~gd~l~~k~~p~~~~~~--~~~~~ 884 (1186)
+|+.+||+-+..++++.++..+++..|..+...+..-.+.+.||+|||..||.+|.+|+++|.|-.|...... +....
T Consensus 788 GRC~Vyk~~~~~~kkY~N~T~Drimgp~~d~~t~kpi~kh~vLd~DGl~~pG~~V~~~qi~iNK~mP~vt~~~~~~~~~~ 867 (1153)
T KOG0215|consen 788 GRCEVYKKTTTTLKKYANGTFDRIMGPQLDPNTRKPIWKHQVLDDDGLATPGERVQPGQIYINKQMPTVTGTSLPGLSAS 867 (1153)
T ss_pred ceEEEEeeeeeeeeecCCCchhhhcccccCCCcCCcchhhcccCcccCCCCccEeccCcEEEeccCCCcccccCCCCCcc
Confidence 9999999999999999888888888776543322222346789999999999999999999999777653222 22223
Q ss_pred ccccceeeEEeecCCCcEEEEEEEEecCCCceEEEEEEEeecCCCCcccccccCCCccEEEeeecCCCCCCCCCCCCCcE
Q 001021 885 RYTRRDHSISLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDI 964 (1186)
Q Consensus 885 ~~~~~~~s~~~~~~~~g~v~~v~~~~~~~~~~~vkv~~r~~R~p~iGDKfssRhGqKGvvs~i~~~~dmPf~~~G~~pDi 964 (1186)
...+++.++.|+..++++||+|.++.++++.-++|+-+|++|+|++|||||||||||||||.|++||||||...||+|||
T Consensus 868 ~~~Yk~~pitykgpepsyidkVmls~n~~dq~LIK~llRQTRrPElGDKFSSRHGQKGVcGlIv~QEDMPFnD~GIcPDi 947 (1153)
T KOG0215|consen 868 QVQYKAVPITYKGPEPSYIDRVMLTSNDEDQFLIKVLLRQTRRPELGDKFSSRHGQKGVCGLIVQQEDMPFNDQGICPDI 947 (1153)
T ss_pred ccccccccceecCCCcchhheeEeecCccccHHHHHHHhhccCcccccccccccCCCceeeEEeeccCCCCcccCCCccc
Confidence 33589999999999999999999999998888999999999999999999999999999999999999999999999999
Q ss_pred EeCCCCCCCCCchhhHHhhhhhHhhhhcCCccccCCCCCccHHHHHHHHHHcCCCCCCeEEEeeCCCCceEEeeEeEeee
Q 001021 965 IVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPT 1044 (1186)
Q Consensus 965 I~NPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tpF~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if~G~~ 1044 (1186)
||||||||||||+|.++|.+.|||+.+.|.+.++|+|.+..++++++.|.++||||.|++.+|||+||+|++|+||+||+
T Consensus 948 IMNPHGFPSRMTVGK~iELlsGKAGVl~G~~hYGTaFGgskVed~~~~Lv~hGfnY~GKD~ltSGITGepLeAYIffGPi 1027 (1153)
T KOG0215|consen 948 IMNPHGFPSRMTVGKMIELLSGKAGVLEGTFHYGTAFGGSKVEDISEELVEHGFNYSGKDMLTSGITGEPLEAYIFFGPI 1027 (1153)
T ss_pred ccCCCCCcccchHHHHHHHhccccceeeeeEeeccccCCchHHHHHHHHHHhccCccCccccccCCCCCcceeeEEechH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ehhccccccCCceEEeccCCccccccCCCCcccCCCcceeeehhhhHHHhhccHHHHHHhhhcCCCcceeeeccccCcce
Q 001021 1045 YYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIA 1124 (1186)
Q Consensus 1045 yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~L~erL~~~SD~~~~~vC~~cG~~~ 1124 (1186)
|||||+|||.||+|||++||+..|||||++||||+||+|+||||||||||||||.+|-|||+.+||.+++.||..||.++
T Consensus 1028 YYQKLKHMVlDKMHARARGPRAvLTRQPTEGRSrdGGLRLGEMERDCLIaYGASmLl~ERLMiSSDaFeVdVC~~CGllg 1107 (1153)
T KOG0215|consen 1028 YYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIAYGASMLLLERLMISSDAFEVDVCRQCGLLG 1107 (1153)
T ss_pred HHHHHHHHHHHHHhhhccCCceeeecCCCCCcCCCCCcccchhhhhhhhhccHHHHHHHHHhhcCcceeeeeccccccce
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeccccCceeeccCCCCCCceeecccHhhHHHHHHHHhCCCceEEEeccC
Q 001021 1125 IANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKED 1174 (1186)
Q Consensus 1125 ~~~~~~~~~~C~~C~~~~~i~~v~iPy~~k~l~~EL~sm~i~~~l~~~~~ 1174 (1186)
+.. ||..|+++.+|.++.||||||||||||+||||-|||.+++.
T Consensus 1108 ykg------wC~~Ckss~~v~~~~iPYAcKLLFQEL~SMNi~PrL~L~~~ 1151 (1153)
T KOG0215|consen 1108 YKG------WCTTCKSSKNVAKMKIPYACKLLFQELQSMNIVPRLKLEDY 1151 (1153)
T ss_pred ech------hhhhccCCCceeeeeccHHHHHHHHHHHhcCccceeeeccc
Confidence 753 89999999999999999999999999999999999999875
No 4
>KOG0216 consensus RNA polymerase I, second largest subunit [Transcription]
Probab=100.00 E-value=7.5e-258 Score=2201.84 Aligned_cols=1057 Identities=32% Similarity=0.499 Sum_probs=932.7
Q ss_pred hhhhhhhcccCccchHHHHHHHHHHHHHhhHHHHHhhcCCeeeCCCCCCCCCeEEEEeeEEEeCCcccCCC--CccCCCC
Q 001021 27 DAWAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPMMTESD--GETATLF 104 (1186)
Q Consensus 27 ~~~~~i~~~f~~~~Lv~~hi~SFN~Fl~~gL~~ii~~~~pI~~~~~~~~~~~~~l~f~~i~i~~P~~~~~~--~~~~~l~ 104 (1186)
..|+..+++-..++++++|++|||...+.||....-+........ ...+++.++++++++.+|.++... ...++|+
T Consensus 4 ~~~k~~p~fp~l~~a~~pHi~sfnal~~~gll~~~v~~~~ek~~~--~~g~kis~~ve~i~iakP~l~~~~~ss~~r~ly 81 (1111)
T KOG0216|consen 4 NPPKDYPSFPELQDAASPHIDSFNALTNGGLLNAGVAGIAEKVPL--KAGDKISMKVESIQIAKPMLSDKVHSSDTRKLY 81 (1111)
T ss_pred CCcccCccchhhhhhhhhhhccccchhhhhHHHHHhhchhhhccc--ccCCceeEEEEEEEecCCCCCcccccccccccc
Confidence 357777888889999999999999999888766544432222111 123468999999999999997644 3578999
Q ss_pred hHHHHhcCCCcceeEEEEEEEEEeccCCCCcccccceeeEEEEecccceeeccCCccCCCCChhhhhhcCCCCCCCCceE
Q 001021 105 PKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYF 184 (1186)
Q Consensus 105 P~EcR~r~lTYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~eli~~gE~~~D~GGYF 184 (1186)
|.|||+|++||+|.+.|+|.|.+++... ...+..+|.+||||+|++|||.|++|+||++++|++.|+||||
T Consensus 82 PaEcRqR~~TY~Gkl~v~v~wsVNg~~~---------~~e~~dlG~vPIMlrSklChL~g~sp~eLV~hkEe~~EmGGYF 152 (1111)
T KOG0216|consen 82 PAECRQRGLTYKGKLVVRVSWSVNGGHV---------VIEKRDLGHVPIMLRSKLCHLNGASPKELVKHKEESSEMGGYF 152 (1111)
T ss_pred chhHhhccceecceEEEEEEEEECCeee---------eeeeeecCccceEEeccccccCCCChHHHhhccCchhhcCcEE
Confidence 9999999999999999999999987642 4567899999999999999999999999999999999999999
Q ss_pred EEcCeeeEEEeeeeeccCeEEEEE-----ecCCCcceEEEEEEEeecCCCCCCceEEEEEEecCCCCCCCCCcEEEEEec
Q 001021 185 IINGSEKVLIAQEKMSTNHVYVFK-----KRQPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATLP 259 (1186)
Q Consensus 185 IING~ERVIi~Qe~~s~N~~~~~~-----~~~~~~~~~~~~irs~~~~g~~~~~~~~v~~~~~~~~~~~~~~~~i~v~i~ 259 (1186)
||||+||||...+-..+|+|+++. +|+.+++.|.+.+||++++.+. +++.+++.+ +|+..++|.
T Consensus 153 IvNGIEKvIRmLIm~RRNHPiAiIR~Sfk~RG~~yS~yGVsmRcVReDqSs----vtn~LHYLn-------nGtv~~~F~ 221 (1111)
T KOG0216|consen 153 IVNGIEKVIRMLIMPRRNHPIAIIRPSFKDRGSSYSDYGVSMRCVREDQSS----VTNVLHYLN-------NGTVMFRFS 221 (1111)
T ss_pred EEcChHHhhhhheeccCCCceEEechhhhhcCCCccccceEEEEecccccc----ceeEEEEec-------CCcEEEEEE
Confidence 999999999777777789999865 5788889999999999997653 333443332 678999999
Q ss_pred ccccc--chHHHHHHHhcCCCHHHHHHHhccccCchh-hHhhhHhhHhhh--hccccHHHHHHHHhhcCccc--CCCchh
Q 001021 260 YIRTE--IPIIIVFRALGFVADKDILEHICYDFQDTQ-MMELLRPSLEEA--FVIQNQQVALDYIGKRGATV--GVTRDK 332 (1186)
Q Consensus 260 ~~~~~--IPl~ilLkALG~~sD~eI~~~i~~~~~~~~-~~~~l~~~l~e~--~~i~t~~~al~yIg~r~~~~--~~~~~~ 332 (1186)
+++++ +|++++||||-.+||+||++.++.+...++ +.+.+..+|++. .+++||++|+.|||++|+++ ..++.+
T Consensus 222 ~rK~eylvPv~lILKAL~~tsDeEIf~~lv~g~~gdqfl~~rv~~mLr~v~ee~l~trtqcl~yLGs~FRaVl~~v~~~~ 301 (1111)
T KOG0216|consen 222 HRKREYLVPVVLILKALTNTTDEEIFEGLVGGDEGDQFLTSRVELMLREVQEENLFTRTQCLQYLGSRFRAVLDFVPEQP 301 (1111)
T ss_pred EeeeeehhhHHHHHHHHhccCHHHHHHHHhCCccCceeHHHHHHHHHHHHhhcccccHHHHHHHHhhhhhhhhcCCCCCc
Confidence 87765 999999999999999999999987655444 334444444332 45789999999999999975 344578
Q ss_pred hHHHHHHHHhhcccCCCCCCCccchhHHHHHHHHHHHHHHhccCCcCCCCCcccccceeccCchhhHHHHHHHHHHHHHH
Q 001021 333 RIKYAKEILQKEMLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRD 412 (1186)
Q Consensus 333 ~~e~~~~iL~~~ll~Hl~~~~~~~~~K~~~L~~Mv~kLl~l~~g~~~~DD~D~l~NkRv~l~G~Ll~~lfr~~l~~~~k~ 412 (1186)
+.|+|+++|++++++||+++. +||.+|.+|++||+.++.|+|.+||+|+.+||+++++|+|++.++|+.++.|++.
T Consensus 302 D~evg~fILr~~VlvHLd~~~----DKF~lLifmiqKL~slv~ge~~~dnpDs~q~qEil~~ghl~~~~LkEriEe~l~~ 377 (1111)
T KOG0216|consen 302 DLEVGRFILREYVLVHLDSDE----DKFNLLIFMIQKLYSLVDGECTPDNPDSPQNQEILLPGHLYGSILKERIEEWLRF 377 (1111)
T ss_pred hHHHHHHHHHhheEEEecccH----HHHHHHHHHHHHHHHHhcCCcCCCCCCChhhhhcccccchHHHHHHHHHHHHHHH
Confidence 899999999999999999876 8999999999999999999999999999999999999999999999999999998
Q ss_pred HHHHHhhhhcCC-Cc--c-c---hhhhcc--ccchhhhhhhhcccCcccccc--ccccccceeeeccccChhhhhccccc
Q 001021 413 VRAYVQKCVDNG-KD--V-N---LQFAIK--AKTITSGLKYSLATGNWGQAN--AAGTRAGVSQVLNRLTYASTLSHLRR 481 (1186)
Q Consensus 413 ik~~l~k~~~~~-~~--~-~---~~~~i~--~~~It~~i~~~~sTGNw~~~~--~~~~~sGvsq~l~r~N~l~~lSh~Rr 481 (1186)
++.++.+.+.+. .. + + +.+++. +..|+++|++||||||+.+.. +++|++|+|.+++|+|++++|||||.
T Consensus 378 ~~~~vr~~l~~~~~~~~~~~~~~i~~~~~r~~~~Ig~~me~fLsTGnl~s~sgldLqQ~sG~tv~AEriNf~RflShFRa 457 (1111)
T KOG0216|consen 378 ISAQVRRDLYKLGFKEDFLDISAIRKVFMRTNGNIGRKMEYFLSTGNLVSRSGLDLQQTSGYTVVAERINFYRFLSHFRA 457 (1111)
T ss_pred HHHHHHHHHHhhcCCchhHhHHHHHHHHhhccccHHHHHHHHHhcCCeeeccchhhHhhcCcEEehhhhhHHHHHHHHHH
Confidence 887777766552 11 1 2 333442 478999999999999999998 78999999999999999999999999
Q ss_pred cCC-CCCcCCCcCcccccCCCCccccccCCCCCCcccccccccceeEEEccC-CCchhHHHHHHHhCCccccccCCCCCC
Q 001021 482 LNS-PIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITVG-SAAYPILEFLEEWGTENFEEISPAVIP 559 (1186)
Q Consensus 482 v~~-~~~~~~K~t~vR~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~Is~~-~~~~~i~~~l~~~g~~~~~~~~~~~~~ 559 (1186)
||+ ++|+++|||++|||.|++|||+||||||||+||||+||||..|+|++. .+.+.+.++|.++||.|........ +
T Consensus 458 vhRGa~f~~mrTTtvRKLlPEsWGFlCPVHTPDG~PCGlLnH~t~~c~I~t~~dd~s~ip~~L~~~Gm~p~~~~~~~G-~ 536 (1111)
T KOG0216|consen 458 VHRGAFFAEMRTTTVRKLLPESWGFLCPVHTPDGAPCGLLNHMTRTCRIVTRPDDVSFIPSILFELGMVPSSHLVEAG-E 536 (1111)
T ss_pred HhcccchhheeehhhHhhCchhhcccccccCCCCCchhHHHhhhhheeEeecCcchhhhhHHHHhcCCCchhccccCC-C
Confidence 997 899999999999999999999999999999999999999999999995 4567899999999999865322222 3
Q ss_pred CceEEEECCEEEEEEcCh--HHHHHHHHhhhhc--CCCCCceEEEEecc-----CCeEEEEeCCCceeeeEEEEecccch
Q 001021 560 QATKIFVNGCWVGIHRDP--EMLVKTLRRLRRR--VDVNTEVGVVRDIR-----LKELRIYTDYGRCSRPLFIVEKQRLL 630 (1186)
Q Consensus 560 ~~~~V~lnG~~iG~~~~~--~~l~~~lr~~rr~--~~i~~~vsi~~~~~-----~~~i~I~td~gRl~RPl~~v~~~~~~ 630 (1186)
..++|++||+++|++..+ +.+++.||.+|.. +.||...+|.+.+. -|++||+|++||++|||.++.-
T Consensus 537 ~l~~VlldGk~vG~~s~~~a~~i~~~lR~~Kv~~p~~iP~~leIg~Vp~s~~gqyPglyi~s~~aR~~RpV~nl~~---- 612 (1111)
T KOG0216|consen 537 PLYPVLLDGKVVGWVSSPLAKKIVDYLRYYKVEAPAVIPNDLEIGYVPTSTNGQYPGLYIFSGPARMIRPVKNLSL---- 612 (1111)
T ss_pred ceeEEEECCEEEEeeccHHHHHHHHHHHHHhhcCcccCCCcceEeeeecCCCCCCceeEEecCchhhhhehhcccc----
Confidence 478999999999997654 8999999999976 56999999977654 3899999999999999987663
Q ss_pred hhHHHHHHHhcCCCCCCCCccccccCCcEEEeccccccceeeeecccccccccCCCCccccccceeeecCCCcccccccc
Q 001021 631 IKKRDIIALQQRESPEDGGWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHPSLILGVCAS 710 (1186)
Q Consensus 631 ~~~~~~~~l~~~~~~~~~~~~~l~~~g~iE~i~~~Ee~~~~Ia~~~~~~~~~~~~~k~~~~~~~th~Ei~p~~ilsv~As 710 (1186)
+.+|||++.||.++.||+.++++.+ ..+||.|++|+.+||++|+
T Consensus 613 --------------------------~~~e~iG~fEQvym~i~~~~~e~~~----------~v~th~E~~pt~~ls~~an 656 (1111)
T KOG0216|consen 613 --------------------------DSVEWIGPFEQVYMNIAIDPKEIFP----------DVTTHVELHPTGILSIVAN 656 (1111)
T ss_pred --------------------------CchhhcccHHHhhhhhccchhhcCC----------CcceeEEecccchHhHhhc
Confidence 4579999999999999999998865 3589999999999999999
Q ss_pred ccCCCCCCCCccchhhhhcccccccccccceEEeecccceeeccCCcceeecccccccccccCCCCceeEEEEEecCCCC
Q 001021 711 IIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYN 790 (1186)
Q Consensus 711 lIPF~~HNqSpRn~yqc~M~KQaig~~~~n~~~r~D~~~~~L~ypQ~PlV~t~~~~~~~~~~~p~G~N~~VAv~sy~GYn 790 (1186)
||||||||||||||||||||||+||+|.++++.|.|+++|+|++||.|+|++..++.+.+|++|.|+||+|||+||||||
T Consensus 657 liP~sD~NQSPRNmYQCQMgKQtmg~p~~a~~~radnklYrlqt~qsP~vr~~~y~~y~~d~yp~GtNaiVAVisyTgyD 736 (1111)
T KOG0216|consen 657 LIPFSDHNQSPRNMYQCQMGKQTMGTPGHALRTRADNKLYRLQTPQSPIVRPELYDTYGMDDYPNGTNAIVAVISYTGYD 736 (1111)
T ss_pred CccccccCCCchhHHHhhhhhhhcCCccccchhcccCceEEecCCCCceeecccccccccccCCCCcceEEEEEeecccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCcEEeeccccccCceEEEEEEEEEeeecccCCcceeeecC-CCCCCCCCCCCCCcCCCCCCCccCCCcEEcCCCEEEE
Q 001021 791 QEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGR-PDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIG 869 (1186)
Q Consensus 791 ~EDaiiink~sv~rG~~~s~~~~~~~~~~~~~~~~~~e~~~~-p~~~~~~~~~~~~~~~ld~dGi~~~g~~v~~gd~l~~ 869 (1186)
|||||||||+|+||||+++++||+..+++.+.. .....|.. |.. .-..+||+||||.+|+++..||+++.
T Consensus 737 MeDAmiiNK~s~eRGf~~G~vykte~i~L~~~~-~r~~~F~~~p~~--------~~~~~ld~dgLP~~G~kl~~~dp~~~ 807 (1111)
T KOG0216|consen 737 MEDAMIINKSSYERGFAYGTVYKTEKIDLSKKR-SRSKHFGRSPGE--------PELKKLDADGLPSIGQKLEYGDPYYA 807 (1111)
T ss_pred hhhhhhhchhhhhccccceeEEeeeeechhhcc-cceeeeeeCCCC--------ccccccCCCCCCCCcccccCCCcEEE
Confidence 999999999999999999999999998875431 12344542 332 12678999999999999999999999
Q ss_pred EeCCCCccccccccCccccceeeEEeecCCCcEEEEEEEEecCCCc--eEEEEEEEeecCCCCcccccccCCCccEEEee
Q 001021 870 KTTPISQDEAQGQASRYTRRDHSISLRHSETGMVDQVLLTTNADGL--RFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMT 947 (1186)
Q Consensus 870 k~~p~~~~~~~~~~~~~~~~~~s~~~~~~~~g~v~~v~~~~~~~~~--~~vkv~~r~~R~p~iGDKfssRhGqKGvvs~i 947 (1186)
...- +. .+....+|+..|+|+||.|.+..++.|. +.+.|++|..|+|.||||||||||||||||+.
T Consensus 808 y~d~----~t--------~~~~~~~~~~~ep~~vd~vr~~~~~~~~~~k~~~i~~Ri~R~p~IGDKFsSRhGQKGicS~~ 875 (1111)
T KOG0216|consen 808 YFDE----ET--------GKTRIKKYHGTEPGIVDEVRVLGNDMGDQEKCATITLRIPRNPIIGDKFSSRHGQKGICSQK 875 (1111)
T ss_pred EEcc----cC--------CceEEEEecCCCCeeeEEEEEccccCCCccceEEEEEEecCCCcccchhhhhcccccccccc
Confidence 8752 21 3445668999999999999999887665 78999999999999999999999999999999
Q ss_pred ecCCCCCCCCCCCCCcEEeCCCCCCCCCchhhHHhhhhhHhhhhcCCccccCCCC----CccHHHHHHHHHHcCCCCCCe
Q 001021 948 YTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT----DVTVDNISKALHKCGYQMRGF 1023 (1186)
Q Consensus 948 ~~~~dmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tpF~----~~~~~~~~~~l~~~g~~~~G~ 1023 (1186)
||.+||||||+|++|||||||||||||||||||+|++|||+||++|..+|+|||. +..+++|+++|+++||||||+
T Consensus 876 wP~~dmPFtesGm~PDii~NPH~FPSRMTIgM~iEs~AgK~~alhG~~~Datpf~~~E~~t~~dyfg~~L~~~GyNyyGn 955 (1111)
T KOG0216|consen 876 WPTIDMPFTESGMVPDIIINPHAFPSRMTIGMLIESMAGKAGALHGNAQDATPFIFSEENTAIDYFGEMLKKAGYNYYGN 955 (1111)
T ss_pred CCCCCCCccccCcCcceeeCCCCCcccccHHHHHHHHhchhhccccccccCCceeecCcccHHHHHHHHHHHcCcCccCC
Confidence 9999999999999999999999999999999999999999999999999999986 456899999999999999999
Q ss_pred EEEeeCCCCceEEeeEeEeeeehhccccccCCceEEeccCCccccccCCCCcccCCCcceeeehhhhHHHhhccHHHHHH
Q 001021 1024 ETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKE 1103 (1186)
Q Consensus 1024 e~ly~g~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~L~e 1103 (1186)
|+||||.+|++|+|+||+|+||||||||||.||+|||+|||++.+|+||++||+|+||+||||||||||||||||++|||
T Consensus 956 E~~YSGv~G~e~~adIf~GvVyYQRLrHMv~DKfQVRstG~v~~~T~QPvkGRkr~GGiRfGEMERDali~HGtsfllqD 1035 (1111)
T KOG0216|consen 956 EPMYSGVDGREMRADIFFGVVYYQRLRHMVSDKFQVRSTGPVDSLTHQPVKGRKRGGGIRFGEMERDALIAHGTSFLLQD 1035 (1111)
T ss_pred cccccccccceeeeeEEEeehhHHHHHHHhcceeeeeeccCccccccCCccCcccCCCccccchhhhhHhhcchHhhhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhcCCCcceeeeccccCcceee--------ccccCceeeccCCCCCCceeecccHhhHHHHHHHHhCCCceEEEec
Q 001021 1104 RLFDQSDAYRVHVCEHCGLIAIA--------NLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTK 1172 (1186)
Q Consensus 1104 rL~~~SD~~~~~vC~~cG~~~~~--------~~~~~~~~C~~C~~~~~i~~v~iPy~~k~l~~EL~sm~i~~~l~~~ 1172 (1186)
||+.|||.+.++||..||+++.. ........|+.|+. ..+..|.|||+||||..||+||||++++.++
T Consensus 1036 RL~~~SD~~~a~vC~~cgsil~~~~~l~~~~~~~~~~~~C~~c~~-~~~~~v~~P~vfkYL~aEL~amnIk~~l~l~ 1111 (1111)
T KOG0216|consen 1036 RLLNSSDYTVAEVCRTCGSILSTQQKLIKEPGGSTSTVTCRSCDG-KGVTTVAMPYVFKYLTAELAAMNIKMRLDLE 1111 (1111)
T ss_pred hhccCcchhHHHHHHHhhhhhhhhhhhhcccCCCCCceeEEecCC-CceEEEEccHHHHHHHHHHhhCceeEEeccC
Confidence 99999999999999999999853 12334568999954 5899999999999999999999999999864
No 5
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]
Probab=100.00 E-value=1.4e-246 Score=2231.62 Aligned_cols=1021 Identities=36% Similarity=0.553 Sum_probs=919.6
Q ss_pred chhhhhhhhhcccCccchHHHHHHHHHHHHHhhHHHHHhhcCCeeeCCCCCCCCCeEEEEeeEEEeCCcccCCCCccCCC
Q 001021 24 TQEDAWAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPMMTESDGETATL 103 (1186)
Q Consensus 24 ~~~~~~~~i~~~f~~~~Lv~~hi~SFN~Fl~~gL~~ii~~~~pI~~~~~~~~~~~~~l~f~~i~i~~P~~~~~~~~~~~l 103 (1186)
..+++|++++++|+.++|+++|++|||+|+.+||++++++++||+.. ++++.|+|.++++++| .++
T Consensus 10 r~r~~~~~i~~~~~~p~Lv~~QldSyn~ff~~gLq~i~~~i~PI~~~-----~~~~~Lef~~~~l~~p---------~k~ 75 (1060)
T COG0085 10 RIRDSFGKIPEFLDLPNLVEIQLDSYNAFFLEGLQEVFREIFPIESY-----NGNTELEYGSYRLGEP---------PKF 75 (1060)
T ss_pred ccccchhhcccccCCccHHHHHHHHHHHHHHHHHHHHHHhcCceecC-----CCCEEEEEEEEEecCC---------CCC
Confidence 56789999999999999999999999999999999999999999853 3578999999999998 357
Q ss_pred ChHHHHhcCCCcceeEEEEEEEEEeccCCCCcccccceeeEEEEecccceeeccCCccCCCCChhhhhhcCCCCCCCCce
Q 001021 104 FPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGY 183 (1186)
Q Consensus 104 ~P~EcR~r~lTYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~eli~~gE~~~D~GGY 183 (1186)
+|.|||+|++||+|||+|++++..++..+ .++.++|++|+||+||+ |||
T Consensus 76 ~p~EcR~R~lTYsapLyv~lrlv~~~~~e-------~~k~~eV~iG~iPlMt~------------------------gGy 124 (1060)
T COG0085 76 YPEECRLRGLTYSAPLYVKLRLVVNETGE-------EIKEQEVYMGDIPLMTR------------------------GGY 124 (1060)
T ss_pred CHHHHHhcCCccccceEEEEEEEECCccc-------ccccceEEeccCcEecC------------------------CcE
Confidence 99999999999999999999999876543 15678999999999998 999
Q ss_pred EEEcCeeeEEEeeeeeccCeEEEEEecCCC-cceEEEEEEEeecCCCCCCceEEEEEEecCCCCCCCCCcEEEEEecccc
Q 001021 184 FIINGSEKVLIAQEKMSTNHVYVFKKRQPN-KYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPYIR 262 (1186)
Q Consensus 184 FIING~ERVIi~Qe~~s~N~~~~~~~~~~~-~~~~~~~irs~~~~g~~~~~~~~v~~~~~~~~~~~~~~~~i~v~i~~~~ 262 (1186)
|||||+|||||+|+++|||++|..+..... +..|+|.+ ++.+|+|...++. .++.++++++..+
T Consensus 125 FIINGsERVIVsQ~~rSPgvif~~~~~k~~~~~~~~a~v--Ip~rG~wl~~e~d-------------~~d~~~~rId~~r 189 (1060)
T COG0085 125 FIINGTERVIVSQEHRSPGVIFVEKKDKTGSKVLYVARV--IPYRGSWLEFEFD-------------PKDNLYVRIDRKR 189 (1060)
T ss_pred EEECCeEEEEEEEeecCCCeEEecccccCCcceEEEEEE--ecCCcceEEEEEc-------------cCccEEEEeeeEE
Confidence 999999999999999999999886543222 33566655 5669999654442 1457899998743
Q ss_pred ccchHHHHHHHhcCCCHHHHHHHhccc----cCchhhHhhhHhhHhhh--hccccHHHHHHHHhhcCcccCC--CchhhH
Q 001021 263 TEIPIIIVFRALGFVADKDILEHICYD----FQDTQMMELLRPSLEEA--FVIQNQQVALDYIGKRGATVGV--TRDKRI 334 (1186)
Q Consensus 263 ~~IPl~ilLkALG~~sD~eI~~~i~~~----~~~~~~~~~l~~~l~e~--~~i~t~~~al~yIg~r~~~~~~--~~~~~~ 334 (1186)
+||+++||||||++||+||++.+..+ ....+..+.+...+++. ..+ +...|++||+++|..... ....+.
T Consensus 190 -kiPvtilLRALG~~tDeeI~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~i-~~~~a~~~i~~r~~~~~~~~~~~gR~ 267 (1060)
T COG0085 190 -KIPVTILLRALGLETDEEIIEAFGGDELTDLVPPEGEEALLEIYEEAKGEKI-TARNALELIGSRVFVVKRYDAKEGRY 267 (1060)
T ss_pred -EeeHHHHHHHhCCCcHHHHHHHhcccccccccchHHHHHhHHHHhhccCCCc-chHHHHHHHhcccccccccccchhhh
Confidence 89999999999999999999999753 11233445555555544 233 444599999999865421 366778
Q ss_pred HHHHHHHhhcccCCCCCC---C-ccchhHHHHHHHHHHHHHHhccCCcCCCCCcccccceeccCchhhHHHHHHHHHHHH
Q 001021 335 KYAKEILQKEMLPHVGTG---D-FCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLT 410 (1186)
Q Consensus 335 e~~~~iL~~~ll~Hl~~~---~-~~~~~K~~~L~~Mv~kLl~l~~g~~~~DD~D~l~NkRv~l~G~Ll~~lfr~~l~~~~ 410 (1186)
+.++.++.+++|||++.. . ..+..|+.+|+.|+++|+.+..|.+.+||+|||+||||+++|+||+++||.+|.+|+
T Consensus 268 k~~~~vl~~~~L~hL~~~~~~~~l~~~~k~~di~~mi~~l~~L~~G~~~~DDiDHlGNKRlrlvGeLl~n~fR~gl~rme 347 (1060)
T COG0085 268 KRAKYVLDKELLPHLGEAGERYDLSRVGKAKDIIAMIKYLIELRLGKGEEDDIDHLGNRRLRLVGELLENLFRVGLSRME 347 (1060)
T ss_pred hhhhhhhhhhHHhhhcccccccchhhhHHHHHHHHHHHHHHHHhcCCCCCCCCccccccchhhHHHHHHHHHHHHHHHHH
Confidence 999999999999999963 2 124468889999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhhhcCCCccchhhhccccchhhhhhhhcccCccccccccccccceeeeccccChhhhhccccccCC-CCCcC
Q 001021 411 RDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS-PIGRE 489 (1186)
Q Consensus 411 k~ik~~l~k~~~~~~~~~~~~~i~~~~It~~i~~~~sTGNw~~~~~~~~~sGvsq~l~r~N~l~~lSh~Rrv~~-~~~~~ 489 (1186)
+.+|++|++...+ ..+..++.||.++.+|++||||+ ++||||+|||+||+|+|||+|||++ +++++
T Consensus 348 r~ikerm~~~~~r------~~i~p~dlIn~k~~~Alitgffg-------~sqlSQfmDqtNpLSeLSHkRRIsAlgLsRe 414 (1060)
T COG0085 348 RDVKERLEKADKR------DTLVPQDLINAKPIHALITGFFG-------RSQLSQFMDQTNPLSELSHKRRLSALGLSRE 414 (1060)
T ss_pred HHHHHHHhhhhhh------hccCchhhcchhHHHHHHhcccc-------ccceeeeeecCChHHhhhhhhceeccCcCcc
Confidence 9999999876432 23445678899999999999999 6999999999999999999999999 99999
Q ss_pred CCcCcccccCCCCccccccCCCCCCcccccccccceeEEEc-cCCCchhHHHHHHH-hCCccccccCCCCCCCceEEEEC
Q 001021 490 GKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYIT-VGSAAYPILEFLEE-WGTENFEEISPAVIPQATKIFVN 567 (1186)
Q Consensus 490 ~K~t~vR~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~Is-~~~~~~~i~~~l~~-~g~~~~~~~~~~~~~~~~~V~ln 567 (1186)
++.++||+||||||||+||+|||||+|||||||||++|+|+ .++++.|+++++.. +|+.++...++.. ..|++|
T Consensus 415 ra~fEvRDvHpTHyGRiCPiETPEGpNiGLI~sLA~~A~Vn~~Gf~etPy~kv~~g~~~v~~i~~l~~~~----~~~~~~ 490 (1060)
T COG0085 415 RAGFEVRDVHPTHYGRICPIETPEGPNIGLIKSLALYARINEYGFLETPYRKVLDGSLVVDEIEYLSADE----EDVYVI 490 (1060)
T ss_pred CCCCcccccCcccccccCCCCCCCCcchhHHHHHHHHeEecccCCCCCceEEEEeccccccceeeecccc----cceEEE
Confidence 99999999999999999999999999999999999999999 79999999988884 8888877555433 689999
Q ss_pred CEEEEEEcChHHHHHHHHhhhhcCCCCCceEEEEeccCC----eEEEEeCCCceeeeEEEEecccchhhHHHHHHHhcCC
Q 001021 568 GCWVGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDIRLK----ELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRE 643 (1186)
Q Consensus 568 G~~iG~~~~~~~l~~~lr~~rr~~~i~~~vsi~~~~~~~----~i~I~td~gRl~RPl~~v~~~~~~~~~~~~~~l~~~~ 643 (1186)
|.++|.++++..|++.+|.+|| + +..+++++...... ++++.+|.||.+||++.+++++..+..++++++..+.
T Consensus 491 ~~~~~~~~~~~~~~~~~~~~R~-~-~~~~~~~~~~~~~~~~dv~~~~~~~~~~~~~P~l~~dd~~~~l~~~~mqr~~~~l 568 (1060)
T COG0085 491 GQANGTLDEPGELVEELVECRR-G-GSGEVSVADPEGVDYMDVSPKQVVSVGRSLIPFLEHDDANRALMGSNMQRQAVPL 568 (1060)
T ss_pred eEeeeeecCCCceeeeEEEEee-c-ccccceeecCccccceeccceEEeccccccCceeEEcCchHhhhhhhhhhhcccc
Confidence 9999999999999999999999 6 88888888766555 8999999999999999999999999999999887663
Q ss_pred CCCCCCccccccCCcEEEeccccccceeeeecccccccccCCCCccccccceeeecCCCccccccccccCCCCCCCCccc
Q 001021 644 SPEDGGWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRN 723 (1186)
Q Consensus 644 ~~~~~~~~~l~~~g~iE~i~~~Ee~~~~Ia~~~~~~~~~~~~~k~~~~~~~th~Ei~p~~ilsv~AslIPF~~HNqSpRn 723 (1186)
. .+|.+|+.+| +||++|.|+++++||..+. .+||+|++|..|+|++|++|||++|||||||
T Consensus 569 ~---~~~~~lv~tG-~E~~~a~e~~~~~ia~~~~---------------~~~~ve~~~~~I~~~~~~~~~~~~~n~~~~n 629 (1060)
T COG0085 569 L---RTEAPLVGTG-MEYLDAEDSGAAVIAKRPG---------------VVTHVEISPIVILGIEASLIPYPEHNQSPYN 629 (1060)
T ss_pred c---ccccccccCC-ceeeccccccceeEeccCC---------------cEEEEeeeeeEEEeeccccCCccccCcChHH
Confidence 3 3899999999 9999999999999998653 4799999999999999999999999999999
Q ss_pred hhhhhcccccccccccceEEeecccceeeccCCcceeecccccccccccCCCCceeEEEEEecCCCCCCCcEEeeccccc
Q 001021 724 TYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSID 803 (1186)
Q Consensus 724 ~yqc~M~KQaig~~~~n~~~r~D~~~~~L~ypQ~PlV~t~~~~~~~~~~~p~G~N~~VAv~sy~GYn~EDaiiink~sv~ 803 (1186)
||||+|+||++|++..|+..|.|+..|.++|||.|+|+| +|+|+|||++||||||+||||||||||||++++
T Consensus 630 ~~~~~~~~Q~~~~~~~~~~~~~d~~~~~~~~~~~P~~~~--------~e~~~GqN~~VA~m~~~GYn~EDAiiin~~~v~ 701 (1060)
T COG0085 630 LYKFARSNQATGINQRPLVKRGDTVEKGLVYADGPSVDT--------GELALGQNALVAFMPWNGYNYEDAIIISERSVE 701 (1060)
T ss_pred HHHHhhhhcccCCCcccceeccccccccceecCCCcccc--------CcccCCceeEEEEecccCcChhHheecccchhh
Confidence 999999999999999999999999999999999999988 899999999999999999999999999999999
Q ss_pred cCceEEEEEEEEEeeecccCCcceeeecCCCCCCCCCCCCCCcCCCCCCCccCCCcEEcCCCEEEEEeCCCCccccccc-
Q 001021 804 RGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQGQ- 882 (1186)
Q Consensus 804 rG~~~s~~~~~~~~~~~~~~~~~~e~~~~p~~~~~~~~~~~~~~~ld~dGi~~~g~~v~~gd~l~~k~~p~~~~~~~~~- 882 (1186)
||+|||+||++|++++++++.+..|.+.+|+.. ...|++||+|||++||+.|++|||||||++|+...+....
T Consensus 702 ~~~~ts~~~~~~~~~~r~~~~g~e~~~~iP~~~------e~~~~~Lde~Gii~ig~~V~~gdilvgk~tP~~~~~~~~ee 775 (1060)
T COG0085 702 RDLFTSIHIEEYETEARDTKLGPEEIRDIPNVS------EEALRNLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEE 775 (1060)
T ss_pred cCCceEEEEEEEeeeeeccCCCccccccCCCcC------HHHHhcCCccCccccccEEcCCCEEEEeeCCCCCCCCCchh
Confidence 999999999999999999988888888899864 2358999999999999999999999999999985332111
Q ss_pred ----cCccccceeeEEeecCCCcEEEEEEEEecCC----CceEEEEEEEeecCCCCcccccccCCCccEEEeeecCCCCC
Q 001021 883 ----ASRYTRRDHSISLRHSETGMVDQVLLTTNAD----GLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMP 954 (1186)
Q Consensus 883 ----~~~~~~~~~s~~~~~~~~g~v~~v~~~~~~~----~~~~vkv~~r~~R~p~iGDKfssRhGqKGvvs~i~~~~dmP 954 (1186)
.-..+.||+|++++++++|+|++|.++++++ +.++|||++|+.|.|++|||||||||||||||+|||+||||
T Consensus 776 ~ll~i~~ek~rdtsl~~~~g~~G~V~~V~~~~~~~~~~g~~~~vkV~v~~~R~~~~GDK~a~RHG~KGVis~i~p~eDMP 855 (1060)
T COG0085 776 RLLRIFGEKVRDTSLRVPHGEEGIVDDVQVFTREDGDPGVNKLVKVYVAQKRKPQIGDKMAGRHGNKGVVSKIVPQEDMP 855 (1060)
T ss_pred hhhccccceeeccceeecCCCCeEEEEEEEEeccCCCcCceEEEEEEEEEeccCCccccccccCCCCceeeeecCcccCC
Confidence 1122379999999999999999999999877 78999999999999999999999999999999999999999
Q ss_pred CCCCCCCCcEEeCCCCCCCCCchhhHHhhhhhHhhhhcCCccccCCCCCccHHHHHHHHHHcCCCCCCeEEEeeCCCCce
Q 001021 955 WTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRR 1034 (1186)
Q Consensus 955 f~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tpF~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~ 1034 (1186)
|++||++||||+|||||||||||||++|+++||||++.|...|+|||++.+.+++.+.|.++||++.|+++||||+||++
T Consensus 856 f~~~G~~~DiilNP~gvPSRM~iGqilE~~lG~a~~~~G~~~~~~~F~g~~~~~~~~~l~~~g~~~~Gk~~lydG~TGe~ 935 (1060)
T COG0085 856 FLEDGTPPDIILNPLGVPSRMNIGQILETHLGKAAALLGIPVDTPVFDGAPEEDIRELLKEAGFPYSGKEVLYDGRTGEP 935 (1060)
T ss_pred cCCCCCcccEEECCCCCCccccHHHHHHHHHHHHHHhcCceeccCCcCCCCHHHHHHHHHHcCCCCCCCEEeecCCCCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeeEeEeeeehhccccccCCceEEeccCCccccccCCCCcccCCCcceeeehhhhHHHhhccHHHHHHhhhcCCCccee
Q 001021 1035 LTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRV 1114 (1186)
Q Consensus 1035 ~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~L~erL~~~SD~~~~ 1114 (1186)
|+++||||++|||||+|||+|||||||||||+.|||||++||+|.|||||||||||||+|||||++|||||+.+||.
T Consensus 936 ~~~~i~vG~~Y~~kL~HmV~dK~HaRs~GP~s~lT~QP~~Gka~~GG~RfGEME~~aL~ayGAa~~LqE~L~~~SD~--- 1012 (1060)
T COG0085 936 FDAPIFVGVMYYQKLHHMVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTVKSDD--- 1012 (1060)
T ss_pred ccccEEEEehHHHhHHhhhcccceeeccCCceeeecCCCCcccccCCccccchHHHHHHHHhHHHHHHHHhhccchh---
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999994
Q ss_pred eeccccCcceeeccccCceeeccCCCCCCceeecccHhhHHHHHHHHhCCCceEEEeccC
Q 001021 1115 HVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKED 1174 (1186)
Q Consensus 1115 ~vC~~cG~~~~~~~~~~~~~C~~C~~~~~i~~v~iPy~~k~l~~EL~sm~i~~~l~~~~~ 1174 (1186)
.||++++. .|..|+ .++.++.||||||+|++||+||||+++|.+++.
T Consensus 1013 ----~~G~~~~y-------~~~v~g--~~~~~~~ip~sFk~L~~El~sl~i~~~l~~~~~ 1059 (1060)
T COG0085 1013 ----VCGRIKIY-------ECIVKG--ENIPEVGIPESFKVLLKELRSLGIDVRLELEDG 1059 (1060)
T ss_pred ----cccchhhh-------cCcccC--CCCCCCCCCHHHHHHHHHHHHCCCceEEeecCC
Confidence 49999854 499998 689999999999999999999999999998764
No 6
>cd00653 RNA_pol_B_RPB2 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.
Probab=100.00 E-value=1.8e-226 Score=2114.53 Aligned_cols=860 Identities=50% Similarity=0.782 Sum_probs=777.7
Q ss_pred hHHHHHHHHHHHHHhhHHHHHhhcCCeeeCCCCCCCCCeEEEEeeEEEeCCcccCCCCccCCCChHHHHhcCCCcceeEE
Q 001021 41 LVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPMMTESDGETATLFPKAARLRNLTYSAPLY 120 (1186)
Q Consensus 41 Lv~~hi~SFN~Fl~~gL~~ii~~~~pI~~~~~~~~~~~~~l~f~~i~i~~P~~~~~~~~~~~l~P~EcR~r~lTYsa~l~ 120 (1186)
|++||++|||+||++||++++++++||++... ...+.++|+++++++|.+.+. +...+++|+|||+|++||+|+|+
T Consensus 1 Lv~~qi~SFn~Fl~~gl~~ii~~~~~i~~~~~---~~~~~l~f~~i~i~~P~~~~~-~~~~~l~P~ecRlr~lTYs~~l~ 76 (866)
T cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDD---DGRLKLKFGDIYLGKPKVEEG-GVTRKLTPNECRLRDLTYSAPLY 76 (866)
T ss_pred CchhHHHHHHHHHHHHHHHHHHhcCCeeeccC---CCeEEEEEEEEEECCcccccc-CccccCCHHHHHhhCCccceeEE
Confidence 68999999999999999999999999987532 245789999999999998765 56788999999999999999999
Q ss_pred EEEEEEEeccCCCCcccccceeeEEEEecccceeeccCCccCCCCChhhhhhcCCCCCCCCceEEEcCeeeEEEeeeeec
Q 001021 121 VDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMS 200 (1186)
Q Consensus 121 v~v~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~eli~~gE~~~D~GGYFIING~ERVIi~Qe~~s 200 (1186)
|++.++..+.. ....+++.+|+|||||+|++|||++++++|+++.||||.||||||||||+||||++|++++
T Consensus 77 v~i~~~~~~~~--------~~~~~~v~iG~iPIMv~S~~C~L~~~~~~el~~~~E~p~d~GGYFIInG~EkVIi~qi~~~ 148 (866)
T cd00653 77 VDIRLTVNDKG--------KIKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRS 148 (866)
T ss_pred EEEEEEEecce--------eEEEEEEEEeeCCcccCcccccccCCCHHHHHhcCCCcccCCCEEEECCceeEEEEEEecc
Confidence 99999876532 1245789999999999999999999999999999999999999999999999999999999
Q ss_pred cCeEEEEEecCCCcceEEEEEEEeecCCCCCCceEEEEEEecCCCCCCCCCcEEEEEeccccccchHHHHHHHhcCCCHH
Q 001021 201 TNHVYVFKKRQPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFRALGFVADK 280 (1186)
Q Consensus 201 ~N~~~~~~~~~~~~~~~~~~irs~~~~g~~~~~~~~v~~~~~~~~~~~~~~~~i~v~i~~~~~~IPl~ilLkALG~~sD~ 280 (1186)
+|+++++ .....+.+.++|.+..+....+.+.++... ....++++++..+
T Consensus 149 ~N~~~~~----~~~~~~~~~~~s~~~~~~~~~s~~~~~~~~--------~~~~i~~~i~~~~------------------ 198 (866)
T cd00653 149 PNVIIVE----DSKGKRIYTKTSIPSYSPYRGSWLEVKSDK--------KKDRIYVRIDLKR------------------ 198 (866)
T ss_pred CCeEEEe----cCCCcEEEEEEEccCCCcCccEEEEEEEcc--------CCCeEEEEecccC------------------
Confidence 9999986 122335677777666322222223333210 0235666666532
Q ss_pred HHHHHhccccCchhhHhhhHhhHhhhhccccHHHHHHHHhhcCcccCCCchhhHHHHHHHHhhcccCCCCCCCccchhHH
Q 001021 281 DILEHICYDFQDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGATVGVTRDKRIKYAKEILQKEMLPHVGTGDFCETKKA 360 (1186)
Q Consensus 281 eI~~~i~~~~~~~~~~~~l~~~l~e~~~i~t~~~al~yIg~r~~~~~~~~~~~~e~~~~iL~~~ll~Hl~~~~~~~~~K~ 360 (1186)
+++|+.|||++|
T Consensus 199 -------------------------------~~~al~~ig~~~------------------------------------- 210 (866)
T cd00653 199 -------------------------------QEEALKYIGKRF------------------------------------- 210 (866)
T ss_pred -------------------------------HHHHHHHHHHHH-------------------------------------
Confidence 788999999984
Q ss_pred HHHHHHHHHHHHhccCCcCCCCCcccccceeccCchhhHHHHHHHHHHHHHHHHHHHhhhhcCCCccchhhhccccchhh
Q 001021 361 YYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITS 440 (1186)
Q Consensus 361 ~~L~~Mv~kLl~l~~g~~~~DD~D~l~NkRv~l~G~Ll~~lfr~~l~~~~k~ik~~l~k~~~~~~~~~~~~~i~~~~It~ 440 (1186)
.+|++|++||+++..|.+.+||+|||+||||+++|+||+.+|++.|+++++.++..+.+...+.+.+++..++++..||+
T Consensus 211 ~~L~~Mi~kLl~~~~g~~~~Dd~D~~~NkRv~~~G~Ll~~lfr~~l~~~~~~~k~~l~~~~~~~~~~~~~~~~~~~~It~ 290 (866)
T cd00653 211 EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITS 290 (866)
T ss_pred HHHHHHHHHHHHHhcCCCCCCCchhhhCeEEeeHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcccccCHHHhccchHHHH
Confidence 68999999999999999999999999999999999999999999999999999999988766555667778888889999
Q ss_pred hhhhhcccCccccccccccccceeeeccccChhhhhccccccCC-CCCcCCCcCcccccCCCCccccccCCCCCCccccc
Q 001021 441 GLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS-PIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGL 519 (1186)
Q Consensus 441 ~i~~~~sTGNw~~~~~~~~~sGvsq~l~r~N~l~~lSh~Rrv~~-~~~~~~K~t~vR~Lhps~wG~iCPveTPEG~~cGL 519 (1186)
+|++||+||||.++++.+|++|+||+|||+||+++|||+||||+ ++++++|+++||+||||||||+||+|||||++|||
T Consensus 291 ~i~~~~~TGnw~~~~~~~~~~Gvsq~ldr~N~ls~lsh~Rrv~~~~~~~~~k~~~~R~lhps~~G~iCPveTPEG~~cGL 370 (866)
T cd00653 291 GIKEFLATGNWGSKRFLMQRSGLSQVLDRLNPLSELSHKRRISSLGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGL 370 (866)
T ss_pred HHHHHhhcCCccccccccccceEEEEcccCCHHHHHHhhhhcccccccccccCCcccccCcccCCccCCCCCCCCccccc
Confidence 99999999999999888899999999999999999999999999 99999999999999999999999999999999999
Q ss_pred ccccceeEEEccCCCchhHHHHHHHhCCccccccCCCCCCCceEEEECCEEEEEEcChHHHHHHHHhhhhcCCCCCceEE
Q 001021 520 VKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKTLRRLRRRVDVNTEVGV 599 (1186)
Q Consensus 520 vk~LA~~a~Is~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~l~~~lr~~rr~~~i~~~vsi 599 (1186)
|||||++|+|+
T Consensus 371 v~~LA~~a~Is--------------------------------------------------------------------- 381 (866)
T cd00653 371 VKNLALMARIS--------------------------------------------------------------------- 381 (866)
T ss_pred hhhhhceEeee---------------------------------------------------------------------
Confidence 99999999986
Q ss_pred EEeccCCeEEEEeCCCceeeeEEEEecccchhhHHHHHHHhcCCCCCCCCccccccCCcEEEeccccccceeeeeccccc
Q 001021 600 VRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRESPEDGGWHDLVAKGFIEYIDTEEEETTMISMTINDL 679 (1186)
Q Consensus 600 ~~~~~~~~i~I~td~gRl~RPl~~v~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~g~iE~i~~~Ee~~~~Ia~~~~~~ 679 (1186)
||++||+++|++
T Consensus 382 ---------------Gr~~rP~~~v~~----------------------------------------------------- 393 (866)
T cd00653 382 ---------------GRIERPYRIVEK----------------------------------------------------- 393 (866)
T ss_pred ---------------eEeeeeEEEecc-----------------------------------------------------
Confidence 899999987651
Q ss_pred ccccCCCCccccccceeeecCCCccccccccccCCCCCCCCccchhhhhcccccccccccceEEeecccceeeccCCcce
Q 001021 680 VQARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPL 759 (1186)
Q Consensus 680 ~~~~~~~k~~~~~~~th~Ei~p~~ilsv~AslIPF~~HNqSpRn~yqc~M~KQaig~~~~n~~~r~D~~~~~L~ypQ~Pl 759 (1186)
.+||+||+|.+|||++||+|||+||||||||||||||+|||||++++|++.|+|++.|+|+|||+||
T Consensus 394 -------------~~th~ei~~~~~ls~~asliPf~~hNqspRn~~~~~M~kQa~g~~~~n~~~r~d~~~~~l~~pq~pl 460 (866)
T cd00653 394 -------------EVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPL 460 (866)
T ss_pred -------------ceEEEEeCccceeeeeeeccCCCCcccccchhhhhcccCCccCchhccccccccchheeeccCCCCc
Confidence 3799999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eecccccccccccCCCCceeEEEEEecCCCCCCCcEEeeccccccCceEEEEEEEEEeeecccCCcceeeecCCCCCCCC
Q 001021 760 VTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTM 839 (1186)
Q Consensus 760 V~t~~~~~~~~~~~p~G~N~~VAv~sy~GYn~EDaiiink~sv~rG~~~s~~~~~~~~~~~~~~~~~~e~~~~p~~~~~~ 839 (1186)
|+|+..+.++++++|+|+||+||||||+||||||||||||+|+|||||||+||++|++++++...+..+.+. +. ..
T Consensus 461 v~T~~~~~~~~~~~~~G~N~~VAv~~y~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~~~~~-~~---~~ 536 (866)
T cd00653 461 VGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITR-GD---IP 536 (866)
T ss_pred cccchHHHhCCCccCCCceEEEEEeccccccccceeeeehhhhhcCceeEEEEEEEEEEEEecCCCcceEec-CC---CC
Confidence 999999999999999999999999999999999999999999999999999999999998875444434333 11 11
Q ss_pred CCCCCCcCCCCCCCccCCCcEEcCCCEEEEEeCCCCccccc--cccCccccceeeEEeecCCCcEEEEEEEEe---cCCC
Q 001021 840 GMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ--GQASRYTRRDHSISLRHSETGMVDQVLLTT---NADG 914 (1186)
Q Consensus 840 ~~~~~~~~~ld~dGi~~~g~~v~~gd~l~~k~~p~~~~~~~--~~~~~~~~~~~s~~~~~~~~g~v~~v~~~~---~~~~ 914 (1186)
..+...|++||+||||++|++|++||+|+||++|....+.. ........+|+|++++.+++|+|++|.++. +.++
T Consensus 537 ~~~~~~~~~ld~dGi~~~g~~v~~gd~li~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~v~~v~~~~~~~~~~~ 616 (866)
T cd00653 537 NVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRELNDGG 616 (866)
T ss_pred CCChHHhhccCCCCCcCCCCEecCCCEEEEEecCcccccccccccccCCcceEEEEEecCCCceEEEEEEEeccccCCCC
Confidence 12334689999999999999999999999999987533210 111223479999999999999999999987 5677
Q ss_pred ceEEEEEEEeecCCCCcccccccCCCccEEEeeecCCCCCCCCCCCCCcEEeCCCCCCCCCchhhHHhhhhhHhhhhcCC
Q 001021 915 LRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGK 994 (1186)
Q Consensus 915 ~~~vkv~~r~~R~p~iGDKfssRhGqKGvvs~i~~~~dmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~g~ 994 (1186)
...|+|++|+.|+|+||||||||||||||||+|||+||||||++|++|||||||||||||||||||+|+++||||++.|.
T Consensus 617 ~~~v~v~~r~~R~p~iGDKfssRhGqKGv~s~i~~~~dmPf~~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~ 696 (866)
T cd00653 617 NKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGK 696 (866)
T ss_pred cEEEEEEEeEEecCCcccccccccCCCcEEEEEeccccCCcccCCCCCcEEecCCcCcccccHHHHHHHHHHHHHHhcCC
Confidence 88999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCCCCCccHHHHHHHHHHcCCCCCCeEEEeeCCCCceEEeeEeEeeeehhccccccCCceEEeccCCccccccCCCC
Q 001021 995 EGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAE 1074 (1186)
Q Consensus 995 ~~d~tpF~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~ 1074 (1186)
+.|+|||++...+++.+.|.++||+++|+|.||||+||++|+++||+|++|||||+|||+||+|||++||++.|||||++
T Consensus 697 ~~d~t~f~~~~~~~~~~~l~~~g~~~~G~e~~y~g~tG~~~~~~if~G~~yyqrL~Hmv~DK~~~R~~Gp~~~lT~QP~~ 776 (866)
T cd00653 697 FGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLK 776 (866)
T ss_pred cccccccCcchHHHHHHHHHHcCCCCCCcEEEEcCCCCCCcccceEEeehhhhhhhhhhchhhhhcccCCcchhccCcCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCCcceeeehhhhHHHhhccHHHHHHhhhcCCCcceeeeccccCcceeeccccCceeeccCCCCCCceeecccHhhH
Q 001021 1075 GRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACK 1154 (1186)
Q Consensus 1075 Gr~~~GG~R~GEMErd~l~a~Gas~~L~erL~~~SD~~~~~vC~~cG~~~~~~~~~~~~~C~~C~~~~~i~~v~iPy~~k 1154 (1186)
||+|+|||||||||||||+|||||++|+|||+++||.+.++||..||++++.+ .|+.|+++.++.++.+|||||
T Consensus 777 Gr~~~GG~R~GEMErd~lia~Gas~~l~erl~~~SD~~~~~vc~~cg~i~~~~------~c~~c~~~~~~~~~~ipy~~k 850 (866)
T cd00653 777 GRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSAN------LCRLCKKGTNISKVGIPYAFK 850 (866)
T ss_pred cccccCCeEEEEEehhhhhhhhhHHHHHHHHhcCCccceEEEeccCccccccc------ccccccCCCceeecCCCHHHH
Confidence 99999999999999999999999999999999999999999999999999542 399999999999999999999
Q ss_pred HHHHHHHhCCCceEEE
Q 001021 1155 LLFQELMAMAIAPRML 1170 (1186)
Q Consensus 1155 ~l~~EL~sm~i~~~l~ 1170 (1186)
||+|||+||||++++.
T Consensus 851 ll~~EL~sm~i~~~~~ 866 (866)
T cd00653 851 LLFQELQSMNIDPRLK 866 (866)
T ss_pred HHHHHHHHCCcceEeC
Confidence 9999999999999973
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=1.7e-224 Score=2102.96 Aligned_cols=927 Identities=28% Similarity=0.434 Sum_probs=802.4
Q ss_pred hhhhhhhcccCccchHHHHHHHHHHHHH----------hhHHHHHhhcCCeeeCCCCCCCCCeEEEEeeEEEeCCcccCC
Q 001021 27 DAWAVISAYFEEKGLVRQQLDSFDEFIQ----------NTMQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPMMTES 96 (1186)
Q Consensus 27 ~~~~~i~~~f~~~~Lv~~hi~SFN~Fl~----------~gL~~ii~~~~pI~~~~~~~~~~~~~l~f~~i~i~~P~~~~~ 96 (1186)
..|..++.+|+.++|++||++|||+||+ +||++++++.+||+.. ++++.|+|.++++++|.+
T Consensus 6 ~~~~~~~~~~~~p~Lv~~Qi~SFn~FL~~~~~~~~~~~~gL~eii~~~~pI~~~-----~~~~~l~f~~~~l~~P~~--- 77 (1065)
T TIGR02013 6 IDFGKIPEVLEVPNLLEIQLDSYDWFLQQDTPPEKRKEEGLEEVFKSIFPIEDY-----TGNIELEYLSYRLGEPKY--- 77 (1065)
T ss_pred eecccCcccccCCCHHHHHHHHHHHHHcCCCcccccccccHHHHHhccCcEEec-----CCcEEEEEEEEEeCCCCC---
Confidence 3599999999999999999999999999 8999999999999865 246899999999999987
Q ss_pred CCccCCCChHHHHhcCCCcceeEEEEEEEEEeccCCCCcccccceeeEEEEecccceeeccCCccCCCCChhhhhhcCCC
Q 001021 97 DGETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELGEC 176 (1186)
Q Consensus 97 ~~~~~~l~P~EcR~r~lTYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~eli~~gE~ 176 (1186)
+|+|||+|++||+|||+|+++++..+... .+.++.++|+||+||||++
T Consensus 78 -------~p~Ear~r~lTYsa~l~v~v~l~~~~~~~-----~~~i~~~~V~iG~iPiMt~-------------------- 125 (1065)
T TIGR02013 78 -------SVEECKERGLTYSAPLKVKLRLINKEEDG-----TKEIKEQDVYMGDIPLMTD-------------------- 125 (1065)
T ss_pred -------CHHHHHHhCCCcceeEEEEEEEEEeccCC-----ccceeeeeEEEeCCCccCC--------------------
Confidence 69999999999999999999997543100 1123557999999999986
Q ss_pred CCCCCceEEEcCeeeEEEeeeeeccCeEEEEEec--CCCcceEEEEEEEeecCCCCCCceEEEEEEecCCCCCCCCCcEE
Q 001021 177 PYDQGGYFIINGSEKVLIAQEKMSTNHVYVFKKR--QPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYI 254 (1186)
Q Consensus 177 ~~D~GGYFIING~ERVIi~Qe~~s~N~~~~~~~~--~~~~~~~~~~irs~~~~g~~~~~~~~v~~~~~~~~~~~~~~~~i 254 (1186)
||||||||+|||||+||++|||++|++..+ ..++..|.|+|+|. +|+|...+ +.+ ++.+
T Consensus 126 ----gGyFIINGsERVIV~Qe~rspg~~~~~~~~~~~~~~~~~~a~iis~--rgswl~~e----~~~---------~~~i 186 (1065)
T TIGR02013 126 ----RGTFIINGAERVVVSQLHRSPGVFFSSEKDTHKSGKVLFSARIIPY--RGSWLEFE----TDK---------KDVL 186 (1065)
T ss_pred ----CceEEECCcEEEEEEEeecCCCEEEEEccccCCCCceEEEEEEEeC--CCCceEEE----Eec---------CCeE
Confidence 999999999999999999999999987643 22334688999774 58885432 221 4579
Q ss_pred EEEeccccccchHHHHHHHhcCCCHHHHHHHhccccCchhhHhhhHhhHhhhhccccHHHHHHHHhhcCcccCCCchhhH
Q 001021 255 RATLPYIRTEIPIIIVFRALGFVADKDILEHICYDFQDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGATVGVTRDKRI 334 (1186)
Q Consensus 255 ~v~i~~~~~~IPl~ilLkALG~~sD~eI~~~i~~~~~~~~~~~~l~~~l~e~~~i~t~~~al~yIg~r~~~~~~~~~~~~ 334 (1186)
|+++++.+ +||+++||||||+++|+||++.++. +..+.+.| ++. ...++++|+.||+++++. ......
T Consensus 187 ~v~i~~~~-kIPi~illrALG~~sd~eI~~~i~~---~~~i~~~l----~~~-~~~~~e~Al~~i~~~~~~---g~~~~~ 254 (1065)
T TIGR02013 187 YVRIDRKR-KLPATVLLRALGYTIDTLILNRLGS---GEYIRNTL----RKD-PTNSEEEALVEIYRKLRP---GEPPTV 254 (1065)
T ss_pred EEEecCCC-ceeHHHHHHHcCCCcchhhhhhcCc---hHHHHHHH----Hhc-cccCHHHHHHHHHhhcCC---CCcchH
Confidence 99999965 9999999999999999999999854 33344433 222 256899999999999743 223446
Q ss_pred HHHHHHHhhcccC-------CCCC-------------CCccchhHHHHHHHHHHHHHHhccCCcCCCCCcccccceeccC
Q 001021 335 KYAKEILQKEMLP-------HVGT-------------GDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLA 394 (1186)
Q Consensus 335 e~~~~iL~~~ll~-------Hl~~-------------~~~~~~~K~~~L~~Mv~kLl~l~~g~~~~DD~D~l~NkRv~l~ 394 (1186)
+.|+++|++.||| |+|. ....+ .|++||+ |+++|+++..|...+||+|||+||||+++
T Consensus 255 ~~a~~~l~~~f~~~~rY~LghiGr~kln~Kl~~~~~~~~~~l-~k~d~l~-mi~~Ll~~~~g~~~~DD~Dhl~NKRvr~a 332 (1065)
T TIGR02013 255 EAARSLLENLFFDPKRYDLGRVGRYKLNKKLGLDVPEDIGVL-TKEDIIA-TIKYLIKLRNGKGEIDDIDHLGNRRIRSV 332 (1065)
T ss_pred HHHHHHHHHHhcCcccccccccchhhhhhhcCcCcCccccee-hHHHHHH-HHHHHHHhhcCCCCCcchhhhhccchhhH
Confidence 8899999999987 9994 11122 4889996 99999999999999999999999999999
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHhhhhcCCCccchhhhccccchhhhhhhhcccCccccccccccccceeeeccccChhh
Q 001021 395 GPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYAS 474 (1186)
Q Consensus 395 G~Ll~~lfr~~l~~~~k~ik~~l~k~~~~~~~~~~~~~i~~~~It~~i~~~~sTGNw~~~~~~~~~sGvsq~l~r~N~l~ 474 (1186)
|+||+.||+.+|+++++.+++++.+. +.+.+++..+++++.||+++++||+|| ||||+|||+||||
T Consensus 333 GeLL~~~fr~~l~rl~k~ik~~l~~~--~~~~~~~~~~i~~~~it~~i~~ff~tg------------glSQ~Ldr~NpLs 398 (1065)
T TIGR02013 333 GELLQNQFRVGLARMERIVRERMSTQ--DTDTLTPQDLINAKPISAAIKEFFGSS------------QLSQFMDQTNPLA 398 (1065)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhc--ccccCCHHHhcCccchHHHHHHHhccC------------CcccccccCCHHH
Confidence 99999999999999999999988754 224677889999999999999999885 9999999999999
Q ss_pred hhccccccCC----CCCcCCCcCcccccCCCCccccccCCCCCCcccccccccceeEEEccCCCchhHHHHHHHhCCccc
Q 001021 475 TLSHLRRLNS----PIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENF 550 (1186)
Q Consensus 475 ~lSh~Rrv~~----~~~~~~K~t~vR~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~Is~~~~~~~i~~~l~~~g~~~~ 550 (1186)
+|||+||+++ ++.++++.++||+|||||||||||+|||||++||||+|||++|+|+.
T Consensus 399 ~lsh~RRlsslgpggl~r~~~~~~~RdlHpShyGrICPiETPEG~n~GLVknLA~~a~i~~------------------- 459 (1065)
T TIGR02013 399 ELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNE------------------- 459 (1065)
T ss_pred hhhhhceecccCCCCcCccccCCccCccCccccccccCCCCCCCCccccccchhhhcccCc-------------------
Confidence 9999999998 57899999999999999999999999999999999999999999851
Q ss_pred cccCCCCCCCceEEEECCEEEEEEcChHHHHHHHHhhhhcCCCCCceEEEEeccCCeEEEEeCCCceeeeEEEEecccch
Q 001021 551 EEISPAVIPQATKIFVNGCWVGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLL 630 (1186)
Q Consensus 551 ~~~~~~~~~~~~~V~lnG~~iG~~~~~~~l~~~lr~~rr~~~i~~~vsi~~~~~~~~i~I~td~gRl~RPl~~v~~~~~~ 630 (1186)
.|.+.||++.|+||++.
T Consensus 460 ---------------------------------------------------------------~G~i~~P~~~V~ng~~~ 476 (1065)
T TIGR02013 460 ---------------------------------------------------------------YGFIETPYRKVKDGKVV 476 (1065)
T ss_pred ---------------------------------------------------------------ceEEeCCeEEEECCeEe
Confidence 23456899999987632
Q ss_pred hhHHHHHHHhcCCCCCCCCccccccCCcEEEeccccccceeeeecccccccccCCCC---------c---cccccceeee
Q 001021 631 IKKRDIIALQQRESPEDGGWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPE---------E---AYADTYTHCE 698 (1186)
Q Consensus 631 ~~~~~~~~l~~~~~~~~~~~~~l~~~g~iE~i~~~Ee~~~~Ia~~~~~~~~~~~~~k---------~---~~~~~~th~E 698 (1186)
.++.|||+|++||+++.||+.+.++...+.+.+ + ..+.++||+|
T Consensus 477 ------------------------~~~~i~yl~a~eE~~~~Ia~~~~~l~~~~~~~~~~i~~r~~~~f~~~~~~~vt~~e 532 (1065)
T TIGR02013 477 ------------------------VTDEVDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYRGEITLVSPDQVDYMD 532 (1065)
T ss_pred ------------------------ccceeEECChHHhCCcEEEecCcCcCccCccccceeeEEEcCceeecChhHeeEEe
Confidence 126799999999999999999888765321100 0 0124579999
Q ss_pred cCCCccccccccccCCCCCCCCccchhhhhccccccccc-----------------------------------ccceEE
Q 001021 699 IHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIY-----------------------------------VTNYQF 743 (1186)
Q Consensus 699 i~p~~ilsv~AslIPF~~HNqSpRn~yqc~M~KQaig~~-----------------------------------~~n~~~ 743 (1186)
|+|.+||||+||||||+||||||||||||||||||||++ +.|+..
T Consensus 533 i~p~~ilsv~aslIPFleHNds~R~lmgsnM~kQavpl~~~e~p~VgTg~E~~v~~ds~~~i~a~~~G~v~~v~~~~~~~ 612 (1065)
T TIGR02013 533 VSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVI 612 (1065)
T ss_pred eChhhhhhhHhhcCCCccccCCcchhhhhhhhhhhhcccccCCCEEEcCcchhhhccccceeEeccCCEEEEEccceEEE
Confidence 999999999999999999999999999999999999999 899999
Q ss_pred eecc---------ccee----------eccCCcceeec----ccccccc------cccCCCCceeEEEEEecCCCCCCCc
Q 001021 744 RMDT---------LAYV----------LYYPQKPLVTT----RAMEHLH------FRQLPAGINAIVAIACYSGYNQEDS 794 (1186)
Q Consensus 744 r~D~---------~~~~----------L~ypQ~PlV~t----~~~~~~~------~~~~p~G~N~~VAv~sy~GYn~EDa 794 (1186)
|.|+ ..|. ++|||+|||+| +.++++. ++|+|+|+||+||||||+|||||||
T Consensus 613 r~d~~~~~~~~~~~~y~L~~~~~snq~~~~~q~Plv~~~~~v~~~~~l~d~~~~~~~e~~~G~N~~VAvm~y~GYn~EDA 692 (1065)
T TIGR02013 613 RYDEDEDEPDGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDA 692 (1065)
T ss_pred EecCCcccccccceEEEeecccccccCceEEeeeeeccCCeEeeeeEecccccccCCcCcCccceEEEEEeeecccccce
Confidence 9995 3344 56999999999 5677764 9999999999999999999999999
Q ss_pred EEeeccccccCceEEEEEEEEEeeecccCCcceeeecC--CCCCCCCCCCCCCcCCCCCCCccCCCcEEcCCCEEEEEeC
Q 001021 795 VIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGR--PDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTT 872 (1186)
Q Consensus 795 iiink~sv~rG~~~s~~~~~~~~~~~~~~~~~~e~~~~--p~~~~~~~~~~~~~~~ld~dGi~~~g~~v~~gd~l~~k~~ 872 (1186)
|||||+|+|||+|||+||++|++++++...+ .|.|.. |+. +...|++||+||||++|++|++|||||||++
T Consensus 693 iiink~~i~rg~~~s~~~~~~~~~~~~~~~g-~e~~~~~~p~~------~~~~~~~Ld~dGi~~~G~~v~~gdilvgk~~ 765 (1065)
T TIGR02013 693 ILISERLVKDDVFTSIHIEEYEVEARDTKLG-PEEITRDIPNV------SEEALRNLDENGIVRIGAEVKAGDILVGKVT 765 (1065)
T ss_pred EEeehhhhcCCceEEEEEEEEEEEeeccCCC-ceEeeccCCCC------chhhhhccCCCCCccCccEeCCCCEEEEEec
Confidence 9999999999999999999999998775433 365643 542 2235899999999999999999999999999
Q ss_pred CCCccccc---------cccCccccceeeEEeecCCCcEEEEEEEEecCCC-------ceEEEEEEEeecCCCCcccccc
Q 001021 873 PISQDEAQ---------GQASRYTRRDHSISLRHSETGMVDQVLLTTNADG-------LRFVKVRVRSVRIPQIGDKFSS 936 (1186)
Q Consensus 873 p~~~~~~~---------~~~~~~~~~~~s~~~~~~~~g~v~~v~~~~~~~~-------~~~vkv~~r~~R~p~iGDKfss 936 (1186)
|....+.. ...+....+|+|++++++++|+||+|.++.+.++ .+.|+|++|+.|+|+|||||||
T Consensus 766 p~~~~~~~~~~~l~~~~~~~~~~~~~d~s~~~~~~~~g~V~~V~~~~~~~~~~~~~~~~~~vkv~ir~~R~p~iGDKfas 845 (1065)
T TIGR02013 766 PKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSRKQGDELPPGVNKLVKVYIAQKRKIQVGDKMAG 845 (1065)
T ss_pred CCcccccChhhhhhhhhcccCCccccccceEccCCCCEEEEEEEEEeccCCCccCcCccEEEEEEEeecccccccchhhh
Confidence 86422110 1122234789999999999999999999887666 5789999999999999999999
Q ss_pred cCCCccEEEeeecCCCCCCCCCCCCCcEEeCCCCCCCCCchhhHHhhhhhHhhhhc--CCccccCC-CCCccHHHHHHHH
Q 001021 937 RHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHM--GKEGDATP-FTDVTVDNISKAL 1013 (1186)
Q Consensus 937 RhGqKGvvs~i~~~~dmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~--g~~~d~tp-F~~~~~~~~~~~l 1013 (1186)
|||||||||+|||+||||||+||++|||||||||||||||||||+|+++||||++. |...++|| |++.+.+++++.|
T Consensus 846 RHGqKGvis~i~~~eDMPf~~~G~~pDiIiNPhg~PSRMtiGqllE~~~gka~~~~~~~~~~~~tp~f~~~~~~~~~~~l 925 (1065)
T TIGR02013 846 RHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRKGVPIATPVFDGASEEEIKEYL 925 (1065)
T ss_pred cccCceeEEeEecCCCCCccCCCCCccEEECCCCCcccccHHHHHHHHHHHHHHhccCCCeEEeccCcCCccHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999987 66788999 9999999999999
Q ss_pred HHcCCCCCCeEEEeeCCCCceEEeeEeEeeeehhccccccCCceEEeccCCccccccCCCCcccCCCcceeeehhhhHHH
Q 001021 1014 HKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMI 1093 (1186)
Q Consensus 1014 ~~~g~~~~G~e~ly~g~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~ 1093 (1186)
+++||+++|+|.||||+||++|+++||+|++|||||+|||+||+|||++||++.|||||++||||+|||||||||||||+
T Consensus 926 ~~~g~~~~G~e~l~~G~TG~~~~~~ifvG~~yy~rL~HmV~DK~haRs~Gp~~~lT~QP~~Grsr~GG~R~GEME~d~l~ 1005 (1065)
T TIGR02013 926 EKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1005 (1065)
T ss_pred HHcCCCCCCCEEEEcCCCCCCccccEEEeehheeechhhhcchhhhcccCCccceeeCCCcccccCCCeeeeeeeHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhccHHHHHHhhhcCCCcceeeeccccCcceeeccccCceeeccCCCCCCceeecccHhhHHHHHHHHhCCCceEE
Q 001021 1094 AHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRM 1169 (1186)
Q Consensus 1094 a~Gas~~L~erL~~~SD~~~~~vC~~cG~~~~~~~~~~~~~C~~C~~~~~i~~v~iPy~~k~l~~EL~sm~i~~~l 1169 (1186)
|||||++|+|||+.+||.+ ||+.. .++..| ++.++.++.+|||||||+|||+||||++++
T Consensus 1006 a~Gas~~L~E~l~~~SD~~-------~g~~~--------~~~~~~-~~~~i~~~~~p~sfklL~~EL~sm~i~~~~ 1065 (1065)
T TIGR02013 1006 AYGAAYTLQEMLTVKSDDV-------VGRTK--------AYEAIV-KGENVPEPGIPESFNVLIKELQSLGLDIEL 1065 (1065)
T ss_pred hhhhHHHHHHHHhccChhh-------hhhhh--------hhhhhc-CCCccccccCCccHHHHHHHHHhCCccccC
Confidence 9999999999999999965 45432 123345 567899999999999999999999999874
No 8
>PRK00405 rpoB DNA-directed RNA polymerase subunit beta; Reviewed
Probab=100.00 E-value=1.8e-220 Score=2076.78 Aligned_cols=929 Identities=29% Similarity=0.437 Sum_probs=798.1
Q ss_pred hhhhhhcccCccchHHHHHHHHHHHH-------HhhHHHHHhhcCCeeeCCCCCCCCCeEEEEeeEEEeCCcccCCCCcc
Q 001021 28 AWAVISAYFEEKGLVRQQLDSFDEFI-------QNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPMMTESDGET 100 (1186)
Q Consensus 28 ~~~~i~~~f~~~~Lv~~hi~SFN~Fl-------~~gL~~ii~~~~pI~~~~~~~~~~~~~l~f~~i~i~~P~~~~~~~~~ 100 (1186)
.+..++.++..++|++||++|||+|| ++||++++++.+||+.. ++++.|+|.++++++|.+
T Consensus 14 ~~~~~~~~~~~p~Lv~~Qi~SFn~Fl~~~~~~~~~gL~~ii~~~~pI~~~-----~~~~~l~f~~~~l~~P~~------- 81 (1112)
T PRK00405 14 SFGKIKEVLELPNLLEIQLDSFDWFLQLDVPPEDEGLEEVFRSIFPIEDF-----NGNLSLEFVSYELGEPKY------- 81 (1112)
T ss_pred ecccccccCCCCCHHHHHHHHHHHHHhcCCcccchhHHHHHHhcCCEEec-----CCcEEEEEeeeEcCCCCC-------
Confidence 46777888999999999999999999 99999999999999864 346899999999999964
Q ss_pred CCCChHHHHhcCCCcceeEEEEEEEEEeccCCCCcccccceeeEEEEecccceeeccCCccCCCCChhhhhhcCCCCCCC
Q 001021 101 ATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQ 180 (1186)
Q Consensus 101 ~~l~P~EcR~r~lTYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~eli~~gE~~~D~ 180 (1186)
+|+|||+|++||+|||+|+++++..+.. .++.++|+||+||||+ +
T Consensus 82 ---tp~Ear~r~lTYSaplyv~v~l~~~~~~--------~i~~~~V~iG~iPiMt------------------------~ 126 (1112)
T PRK00405 82 ---DVEECKERGLTYSAPLRVKLRLINKETG--------EIKEQEVYMGDIPLMT------------------------E 126 (1112)
T ss_pred ---CHHHHHHhCCCCCeeEEEEEEEEEeccC--------ceeeeeEEEecccccc------------------------C
Confidence 8999999999999999999999764321 2355799999999997 4
Q ss_pred CceEEEcCeeeEEEeeeeeccCeEEEEEec--CCCcceEEEEEEEeecCCCCCCceEEEEEEecCCCCCCCCCcEEEEEe
Q 001021 181 GGYFIINGSEKVLIAQEKMSTNHVYVFKKR--QPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATL 258 (1186)
Q Consensus 181 GGYFIING~ERVIi~Qe~~s~N~~~~~~~~--~~~~~~~~~~irs~~~~g~~~~~~~~v~~~~~~~~~~~~~~~~i~v~i 258 (1186)
||||||||+|||||+|+++|||++|+++.. ..++..|.|+|+| .+|+|...++ .. ++.||+++
T Consensus 127 gGyFIING~ERVIVsQe~rSPg~~~~~~~~k~~~~k~~y~a~Iis--~rGswl~~e~----d~---------k~~I~vri 191 (1112)
T PRK00405 127 NGTFIINGTERVIVSQLHRSPGVYFDHDKDKTSSGKLLYSARIIP--YRGSWLEFEF----DP---------KDILYVRI 191 (1112)
T ss_pred CceEEECCeEEEEEEEeecCCCEEEEEeccccCCCceeEEEEEEE--CCCCcEEEEE----ec---------CCeEEEEe
Confidence 999999999999999999999999987643 2345678999976 4688854332 11 45799999
Q ss_pred ccccccchHHHHHHHhcCCCHHHHHHHhccccCch-------------------------hh-------------HhhhH
Q 001021 259 PYIRTEIPIIIVFRALGFVADKDILEHICYDFQDT-------------------------QM-------------MELLR 300 (1186)
Q Consensus 259 ~~~~~~IPl~ilLkALG~~sD~eI~~~i~~~~~~~-------------------------~~-------------~~~l~ 300 (1186)
++. ++||+++||||||+ ||+||++.++.+.... ++ ...+.
T Consensus 192 ~~~-~kIPi~iLLrALGl-sd~eIl~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ei~~~~~~~~~~~~~~~~i~ 269 (1112)
T PRK00405 192 DRR-RKLPVTVLLRALGY-SDEEILDLFYEKEEFGKEIEVPVEYLLGKVLAEDIVDEETGEVLAEANDEITEELDGPYIR 269 (1112)
T ss_pred cCC-CcccHHHHHHHcCC-CHHHHHHHhcccccccceeccchHHhcccchhhhhcccccceeeeccCCccchhhhhHHHH
Confidence 985 69999999999999 8999999996432211 00 01122
Q ss_pred hhHhhhhccccHHHHHHHHhhcCcccCCCchhhHHHHHHHHhhccc-------CCCCCCCcc--------c----hhHHH
Q 001021 301 PSLEEAFVIQNQQVALDYIGKRGATVGVTRDKRIKYAKEILQKEML-------PHVGTGDFC--------E----TKKAY 361 (1186)
Q Consensus 301 ~~l~e~~~i~t~~~al~yIg~r~~~~~~~~~~~~e~~~~iL~~~ll-------~Hl~~~~~~--------~----~~K~~ 361 (1186)
.+++. ....|+++|+.||+++++. ......+.|+++|++.+| ||+|....+ . ..|++
T Consensus 270 ~~l~~-~~~~t~e~Al~~I~k~l~~---g~~~~~e~a~~~l~~~ff~~~rYdL~hiGr~k~nkKl~l~~~~~~~~L~~~d 345 (1112)
T PRK00405 270 NTLEK-DPTSSREEALVEIYRRLRP---GEPPTVEAARSLLENLFFDPKRYDLSKVGRYKLNKKLGLDEDEDVRVLTKED 345 (1112)
T ss_pred HHHhh-ccccCHHHHHHHHHhhcCC---CCcchHHHHHHHHHHHhcCccccccccCCceecchhcccCcccccccccHHH
Confidence 22221 1246899999999999753 223445789999998775 999964322 1 13555
Q ss_pred HHHHHHHHHHHhccCCcCCCCCcccccceeccCchhhHHHHHHHHHHHHHHHHHHHhhhhcCCCccchhhhccccchhhh
Q 001021 362 YFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSG 441 (1186)
Q Consensus 362 ~L~~Mv~kLl~l~~g~~~~DD~D~l~NkRv~l~G~Ll~~lfr~~l~~~~k~ik~~l~k~~~~~~~~~~~~~i~~~~It~~ 441 (1186)
+ ++|+++|+++..|...+||+|||+||||+++|+||+.+|+.+|+++++.+++++.+.. .+.+++..+++++.||++
T Consensus 346 ~-~~mi~~Ll~l~~g~~~~DDiDhl~NKRvr~aGeLL~~~fr~~~~rl~k~ik~~l~~~~--~~~~~~~~lin~~~it~~ 422 (1112)
T PRK00405 346 I-IATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERAVRERMSLQD--LDTLTPQDLINAKPVVAA 422 (1112)
T ss_pred H-HHHHHHHHhhhcccCCCcchhHHhcchhhhHHHHHHHHHHHHHHHHHHHHHHHhhhcc--cccCCHHHhhCchhHHHH
Confidence 4 7999999999999999999999999999999999999999999999999999987542 356789999999999999
Q ss_pred hhhhcccCccccccccccccceeeeccccChhhhhccccccCC----CCCcCCCcCcccccCCCCccccccCCCCCCccc
Q 001021 442 LKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS----PIGREGKLAKPRQLHNSQWGMMCPAETPEGQAC 517 (1186)
Q Consensus 442 i~~~~sTGNw~~~~~~~~~sGvsq~l~r~N~l~~lSh~Rrv~~----~~~~~~K~t~vR~Lhps~wG~iCPveTPEG~~c 517 (1186)
|++||+|| ||||+|||+||||+|||+||+++ ++.++++.++||+|||||||||||+|||||++|
T Consensus 423 i~~ff~tg------------glSQ~Ldq~NpLselshkRRlss~gpggl~r~~a~~~~R~lH~ShyGriCPiETPEG~n~ 490 (1112)
T PRK00405 423 IKEFFGSS------------QLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNI 490 (1112)
T ss_pred HHHhhccC------------CcceeeccCCHHHhhhhhceecccCCCCcCccccCCcccccCccccccccCcCCCCCCcc
Confidence 99999885 99999999999999999999998 578999999999999999999999999999999
Q ss_pred ccccccceeEEEccCCCchhHHHHHHHhCCccccccCCCCCCCceEEEECCEEEEEEcChHHHHHHHHhhhhcCCCCCce
Q 001021 518 GLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKTLRRLRRRVDVNTEV 597 (1186)
Q Consensus 518 GLvk~LA~~a~Is~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~l~~~lr~~rr~~~i~~~v 597 (1186)
|||+|||++|+|+. +|+.. ..+.+++||.|-
T Consensus 491 GLV~nLA~~a~i~~-------------~G~~~----------tp~~~~~nG~~~-------------------------- 521 (1112)
T PRK00405 491 GLINSLATYARVNE-------------YGFIE----------TPYRKVVDGKVT-------------------------- 521 (1112)
T ss_pred ccccchhhcccccc-------------CCccc----------cceEEEECCeEc--------------------------
Confidence 99999999999984 22210 126777888651
Q ss_pred EEEEeccCCeEEEEeCCCceeeeEEEEecccchhhHHHHHHHhcCCCCCCCCccccccCCcEEEeccccccceeeeeccc
Q 001021 598 GVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRESPEDGGWHDLVAKGFIEYIDTEEEETTMISMTIN 677 (1186)
Q Consensus 598 si~~~~~~~~i~I~td~gRl~RPl~~v~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~g~iE~i~~~Ee~~~~Ia~~~~ 677 (1186)
..|||+|++||+++.||..+.
T Consensus 522 -----------------------------------------------------------~~i~yl~a~eE~~~~Ia~~~~ 542 (1112)
T PRK00405 522 -----------------------------------------------------------DEIVYLTADEEDNYVIAQANA 542 (1112)
T ss_pred -----------------------------------------------------------cceEECCHHHhcCcEEEecCc
Confidence 136899999999999999988
Q ss_pred ccccccCCCC---------c---cccccceeeecCCCccccccccccCCCCCCCCccchhhhhccccccccccc------
Q 001021 678 DLVQARLHPE---------E---AYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVT------ 739 (1186)
Q Consensus 678 ~~~~~~~~~k---------~---~~~~~~th~Ei~p~~ilsv~AslIPF~~HNqSpRn~yqc~M~KQaig~~~~------ 739 (1186)
++...+...+ + .....+||+||+|.+|+||+||||||+||||||||+|||||||||||++..
T Consensus 543 ~l~~~~~~~~~~i~~r~~~e~~~~~~~~~~~~~i~p~qi~sv~aslIPFleHnda~R~lmgSnMqrQAvpl~~~~~p~vg 622 (1112)
T PRK00405 543 PLDEDGRFVDELVTARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVG 622 (1112)
T ss_pred ccCCCCcccCceEEEEecCcceeechhhceEEeechhhhceehhhccCcccccCCcchhhhhhhhhhhhhhccccCCeee
Confidence 7755321100 0 012457999999999999999999999999999999999999999999988
Q ss_pred -----------------------------ceEEee-----------------ccccee-eccCCcceeecc----ccccc
Q 001021 740 -----------------------------NYQFRM-----------------DTLAYV-LYYPQKPLVTTR----AMEHL 768 (1186)
Q Consensus 740 -----------------------------n~~~r~-----------------D~~~~~-L~ypQ~PlV~t~----~~~~~ 768 (1186)
|+..|. |+..++ ++|||+|||+|+ .++++
T Consensus 623 Tg~e~~~~~ds~~~i~a~~~G~v~~v~~~~i~ir~~~~~~~~~~~~~y~L~~~~~sn~~~~~~q~Plv~~~~~v~~g~~l 702 (1112)
T PRK00405 623 TGMERRVARDSGAVVVAKRDGVVEYVDASRIVVRVEELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVL 702 (1112)
T ss_pred cCcchhhhhhcchheEeccCCEEEEEeCCEEEEeecccccCCCCeeEEEecccccccccceeecceeeecCCeEeeccEe
Confidence 888888 666777 899999999999 56776
Q ss_pred ------ccccCCCCceeEEEEEecCCCCCCCcEEeeccccccCceEEEEEEEEEeeecccCCcceeeec--CCCCCCCCC
Q 001021 769 ------HFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFG--RPDRSNTMG 840 (1186)
Q Consensus 769 ------~~~~~p~G~N~~VAv~sy~GYn~EDaiiink~sv~rG~~~s~~~~~~~~~~~~~~~~~~e~~~--~p~~~~~~~ 840 (1186)
+++++|+|+|++||||||+||||||||||||+|+|||+|+|+||++|+.++++...+ .+.+. .|...
T Consensus 703 ad~~~~~~~e~~~G~N~~VA~~~y~GYn~EDaiiink~si~rg~~~s~~~~~~~~~~~~~~~~-~~~~~~~~p~~~---- 777 (1112)
T PRK00405 703 ADGPSTDNGELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLG-PEEITRDIPNVS---- 777 (1112)
T ss_pred ecccccCcccccCCcceEEEEEeecccCccceEEEEhhhhccCceEEEEEeeeeeEeeccCCC-ceeecccCCCCC----
Confidence 799999999999999999999999999999999999999999999999998776444 34443 44321
Q ss_pred CCCCCcCCCCCCCccCCCcEEcCCCEEEEEeCCCCccccc---------cccCccccceeeEEeecCCCcEEEEEEEEec
Q 001021 841 MRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ---------GQASRYTRRDHSISLRHSETGMVDQVLLTTN 911 (1186)
Q Consensus 841 ~~~~~~~~ld~dGi~~~g~~v~~gd~l~~k~~p~~~~~~~---------~~~~~~~~~~~s~~~~~~~~g~v~~v~~~~~ 911 (1186)
...|++||+||||++|++|++|||||||++|....+.. ...+....+|+|++++++++|+||+|.++.+
T Consensus 778 --~~~~~~Ld~dGi~~~G~~v~~gDiligk~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~s~~~~~~~~g~V~~v~~~~~ 855 (1112)
T PRK00405 778 --EEALRNLDESGIVRIGAEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTR 855 (1112)
T ss_pred --hHHhhccCCCCCccCccEecCCCEEEEEecCCCccccChhhhhhhhhhcccccccccceEEcCCCCCEEEEEEEEeec
Confidence 23589999999999999999999999999986532110 1122234789999999999999999999877
Q ss_pred -CCC-------ceEEEEEEEeecCCCCcccccccCCCccEEEeeecCCCCCCCCCCCCCcEEeCCCCCCCCCchhhHHhh
Q 001021 912 -ADG-------LRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIEC 983 (1186)
Q Consensus 912 -~~~-------~~~vkv~~r~~R~p~iGDKfssRhGqKGvvs~i~~~~dmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~ 983 (1186)
.++ .+.|+|++|+.|+|+||||||||||||||||+|||+||||||++|++|||||||||||||||||||+|+
T Consensus 856 ~~~~~~~~~~~~~~vkv~ir~~R~p~iGDKfasRHGqKGvis~i~~~eDMPf~~~G~~pDiIiNPhg~PSRMtiGql~E~ 935 (1112)
T PRK00405 856 IEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILET 935 (1112)
T ss_pred cccCCccCcCcceEEEEEEeeecccCcccchhhccCCceeEEeEeccCCCCcCCCCCCCcEEECCCCCcccccHHHHHHH
Confidence 555 478999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhHhhhhcCCccccCC-CCCccHHHHHHHHHHcCCCCCCeEEEeeCCCCceEEeeEeEeeeehhccccccCCceEEecc
Q 001021 984 IMGKVAAHMGKEGDATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGR 1062 (1186)
Q Consensus 984 ~~gk~~~~~g~~~d~tp-F~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~ 1062 (1186)
++||||++.|.+ |+|| |++.+.+++++.|+++||+++|+|+||||+||++|+++||+|++|||||+|||+||+|||++
T Consensus 936 ~~gk~~~~~g~~-~~tp~f~~~~~~~~~~~l~~~g~~~~G~e~l~~G~tG~~~~~~if~G~~yy~rL~HmV~DK~haRs~ 1014 (1112)
T PRK00405 936 HLGWAAKGLGIK-FATPVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARST 1014 (1112)
T ss_pred HhhHHHHhcCCe-EecCccCCccHHHHHHHHHHcCcCCCCCEEEECCCCCCCCcccEEEEehhheechhhhcchhhhccc
Confidence 999999999987 8898 99999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCccccccCCCCcccCCCcceeeehhhhHHHhhccHHHHHHhhhcCCCcceeeeccccCcceeeccccCceeeccCCCCC
Q 001021 1063 GPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKT 1142 (1186)
Q Consensus 1063 Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~L~erL~~~SD~~~~~vC~~cG~~~~~~~~~~~~~C~~C~~~~ 1142 (1186)
||++.|||||++||+|+|||||||||||||+|||||++|+|||+.+||.+. |+.. .+.| .| ++.
T Consensus 1015 Gp~~~lT~QP~~Grsr~GG~R~GEME~d~l~a~Gas~~L~Erl~~~SD~~~-------g~~~-------~~~~-~~-~~~ 1078 (1112)
T PRK00405 1015 GPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVV-------GRTK-------VYEA-IV-KGE 1078 (1112)
T ss_pred CCccceeeCCCcccccCCCeeeeeeehhhHhhhhhHHHHHHHhhccCcccc-------ccee-------EEEE-ee-cCC
Confidence 999999999999999999999999999999999999999999999999653 5443 2456 56 567
Q ss_pred CceeecccHhhHHHHHHHHhCCCceEEEe
Q 001021 1143 DIVQVHIPYACKLLFQELMAMAIAPRMLT 1171 (1186)
Q Consensus 1143 ~i~~v~iPy~~k~l~~EL~sm~i~~~l~~ 1171 (1186)
++.++.+|||||||+|||+||||++++..
T Consensus 1079 ~i~~~~~p~~fklL~~EL~sm~i~~~~~~ 1107 (1112)
T PRK00405 1079 NIPEPGIPESFNVLVKELQSLGLDVELLD 1107 (1112)
T ss_pred cccccCCChHHHHHHHHHHHCccceEEec
Confidence 89999999999999999999999999983
No 9
>CHL00001 rpoB RNA polymerase beta subunit
Probab=100.00 E-value=2.4e-215 Score=2007.90 Aligned_cols=934 Identities=26% Similarity=0.389 Sum_probs=786.8
Q ss_pred cCccchHHHHHHHHHHHHHhhHHHHHhhcCCeeeCCCCCCCCCe--EEEEeeEEEeCCcccCCCCccCCCChHHHHhcCC
Q 001021 36 FEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQ--QSDFAEIYLSKPMMTESDGETATLFPKAARLRNL 113 (1186)
Q Consensus 36 f~~~~Lv~~hi~SFN~Fl~~gL~~ii~~~~pI~~~~~~~~~~~~--~l~f~~i~i~~P~~~~~~~~~~~l~P~EcR~r~l 113 (1186)
|..++|+++|++||||||++||++++++++||+ +. ++.+ .+.|+++++++|++ +|+|||+|++
T Consensus 10 ~~~P~Lv~~Q~~SF~~Fl~~gL~~i~~~~~pI~-~~----~~~~~~~~~~~~~~l~~P~~----------~p~ear~r~l 74 (1070)
T CHL00001 10 STIPGFNQIQFEGFCRFIDQGLTEELSKFPKIE-DT----DQEIEFQLFVETYQLVEPLI----------KERDAVYESL 74 (1070)
T ss_pred cCCCCHHHHHHHHHHHHHHHhHHHHHHhcCCeE-CC----CCCEEEEEEeCeEEECCCCC----------CHHHHHHhCC
Confidence 678999999999999999999999999999998 32 2334 45556999999987 7899999999
Q ss_pred CcceeEEEEEEEEEeccCCCCcccccceeeEEEEecccceeeccCCccCCCCChhhhhhcCCCCCCCCceEEEcCeeeEE
Q 001021 114 TYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIINGSEKVL 193 (1186)
Q Consensus 114 TYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~eli~~gE~~~D~GGYFIING~ERVI 193 (1186)
||+|||+|+++++..+. +.++.++|++|+||+|. +||||||||+||||
T Consensus 75 TYsa~l~v~v~l~~~~~--------~~i~~~~V~iG~iPlMt------------------------~gG~FIING~ERVI 122 (1070)
T CHL00001 75 TYSSELYVPAGLIWKKS--------RDMQEQTVFIGNIPLMN------------------------SLGTFIINGIYRVV 122 (1070)
T ss_pred CCCceeEEEEEEEEcCc--------eeEEEeEEEEecCCccC------------------------CCcEEEEcCcEEEE
Confidence 99999999999975332 12456799999999994 59999999999999
Q ss_pred EeeeeeccCeEEEEEecCCCcceEEEEEEEeecCCCCCCceEEEEEEecCCCCCCCCCcEEEEEeccccccchHHHHHHH
Q 001021 194 IAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFRA 273 (1186)
Q Consensus 194 i~Qe~~s~N~~~~~~~~~~~~~~~~~~irs~~~~g~~~~~~~~v~~~~~~~~~~~~~~~~i~v~i~~~~~~IPl~ilLkA 273 (1186)
|+|+++|||++|++.....++..|.|+|+| .+|+|.. + .+.. ++.+|+++++. ++||+++||||
T Consensus 123 VsQ~~rSpg~~~~~~~~~~~~~~y~a~iis--~rgswl~--~--e~d~---------~~~i~vri~~~-~kiPi~ilLrA 186 (1070)
T CHL00001 123 INQILRSPGIYYRSELDHNGISVYTGTIIS--DWGGRLE--L--EIDR---------KARIWARVSRK-QKISILVLLSA 186 (1070)
T ss_pred EEEEeccCCEEEEEecCCCCceeEEEEEEe--cCCCceE--E--EEec---------CCeEEEEecCC-CcccHHHHHHH
Confidence 999999999999876544456678999965 6678832 2 2221 45799999995 69999999999
Q ss_pred hcCCCHHHHHHHhccccCchhhHhhhHhhHhhh--hccccHHHHHHHHhhcCcccCCCchhhHHHHHHHHhhcccCC---
Q 001021 274 LGFVADKDILEHICYDFQDTQMMELLRPSLEEA--FVIQNQQVALDYIGKRGATVGVTRDKRIKYAKEILQKEMLPH--- 348 (1186)
Q Consensus 274 LG~~sD~eI~~~i~~~~~~~~~~~~l~~~l~e~--~~i~t~~~al~yIg~r~~~~~~~~~~~~e~~~~iL~~~ll~H--- 348 (1186)
||++ |+||++.++++ +.+..++.+. ..+.|+++|+.||++++.. .+......+.|+.+|.+.+|+|
T Consensus 187 LG~s-d~eIl~~~~~~-------~~l~~~l~~~~~~~~~t~e~Al~~i~~~l~~-r~~~~~~~~~a~~~l~~~ff~~rY~ 257 (1070)
T CHL00001 187 MGLN-LREILDNVCYP-------EIFLSFLNDKEKKKIGSKENAILEFYQQFAC-VGGDPVFSESLCKELQKKFFQQRCE 257 (1070)
T ss_pred cCCC-HHHHHHHhCcH-------HHHHHHHHHHhhccccCHHHHHHHHHHhhcc-CCCCcchHHHHHHHHHHHhcccccc
Confidence 9995 99999998642 2233333222 2467999999999999732 1234455688999999999988
Q ss_pred ---CCCCCccch------hHHHHH-----HHHHHHHHHhccCCcCCCCCcccccceeccCchhhHHHHHHHHHHHHHHHH
Q 001021 349 ---VGTGDFCET------KKAYYF-----GYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVR 414 (1186)
Q Consensus 349 ---l~~~~~~~~------~K~~~L-----~~Mv~kLl~l~~g~~~~DD~D~l~NkRv~l~G~Ll~~lfr~~l~~~~k~ik 414 (1186)
+|....+.. .|+.+| ++|+++|+.+..|...+||+|||+||||+++|+||+.|||.+|+++++.++
T Consensus 258 Lg~vGr~~~n~kl~~~~~~~~~~L~~~Di~~~i~~Ll~l~~G~~~~DDiDhLgNKRvr~vGeLL~~qfr~~l~r~~r~ik 337 (1070)
T CHL00001 258 LGRIGRRNMNRKLNLDIPENNTFLLPQDVLAAADYLIGMKFGMGTLDDIDHLKNKRIRSVADLLQDQFGLALNRLENAVR 337 (1070)
T ss_pred ccccCchhhhhhhcccccccceEecHHHHHHHHHHHHHhhcCCCCccchhHHhccccchHHHHHHHHHHHHHHHHHHHHH
Confidence 886543322 355555 899999999999999999999999999999999999999999999999999
Q ss_pred HHHhhhhcCCCccchhhhccccchhhhhhhhcccCccccccccccccceeeeccccChhhhhccccccCC--CCCcCCCc
Q 001021 415 AYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS--PIGREGKL 492 (1186)
Q Consensus 415 ~~l~k~~~~~~~~~~~~~i~~~~It~~i~~~~sTGNw~~~~~~~~~sGvsq~l~r~N~l~~lSh~Rrv~~--~~~~~~K~ 492 (1186)
+++.+.+.+.+.+++..+++++.||.+|++||+| +||||+|||+||||+|||+||+++ |++.+++.
T Consensus 338 ~~m~~~~~~~~~~~~~~lin~~~It~~ik~ff~t------------s~LSQflDqtNpLseltHkRRlsslGpgglsr~~ 405 (1070)
T CHL00001 338 GTICGAIRRKLIPTPQNLVTSTPLTTTYESFFGS------------HPLSQFLDQTNPLTEIVHGRKLSSLGPGGLTGRT 405 (1070)
T ss_pred HHHHHHhcccccCCHHHhhCcchHHHHHHhhhcC------------CcceeeeccCCHHHhhhhhhcccccCCCCccccc
Confidence 9998765555567899999999999999999986 799999999999999999999998 88888776
Q ss_pred C--cccccCCCCccccccCCCCCCcccccccccceeEEEc-cCCCchhHHHHHHHhCCccccccCCCCCCCceEEEECCE
Q 001021 493 A--KPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYIT-VGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGC 569 (1186)
Q Consensus 493 t--~vR~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~Is-~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~V~lnG~ 569 (1186)
+ +||+|||||||||||+|||||++||||+|||++|+|+ .|+.++|+++++...+...+..+++.. ...++|+ ||.
T Consensus 406 a~fevRdvHpShyGRICPIETPEG~NiGLI~sLA~~A~In~~GfietP~~~v~~~~~~~~i~ylsa~e-e~~~~Ia-~g~ 483 (1070)
T CHL00001 406 ASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIGHWGSLESPFYEISERSKEERMVYLSPSE-DEYYMIA-AGN 483 (1070)
T ss_pred cCCcccccCccccccccCCCCCCcccccchhhhhhhcccccCCCcccceeeeccccccceeEEccccc-cCceEEE-eCc
Confidence 6 9999999999999999999999999999999999999 589999999998777766665555544 5668888 999
Q ss_pred EEEEEcChHHHHHHHHhhhhcCCCCCceEEEEeccCCeEEEEeCCCceeeeEEEEecccchhhHHHHHHHhcCCCCCCCC
Q 001021 570 WVGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRESPEDGG 649 (1186)
Q Consensus 570 ~iG~~~~~~~l~~~lr~~rr~~~i~~~vsi~~~~~~~~i~I~td~gRl~RPl~~v~~~~~~~~~~~~~~l~~~~~~~~~~ 649 (1186)
|+|...+.. .+. +..+
T Consensus 484 ~~~~~~~~~--------------~~~-------------------------~~~~------------------------- 499 (1070)
T CHL00001 484 SLALNQGIQ--------------EEQ-------------------------VVPA------------------------- 499 (1070)
T ss_pred eeeccCCcc--------------ccc-------------------------eeEE-------------------------
Confidence 987322100 000 0000
Q ss_pred ccccccCCcEEEeccccccceeeeecccccccccCCCCccccccceeeecCCCccccccccccCCCCCCCCccchhhhhc
Q 001021 650 WHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAM 729 (1186)
Q Consensus 650 ~~~l~~~g~iE~i~~~Ee~~~~Ia~~~~~~~~~~~~~k~~~~~~~th~Ei~p~~ilsv~AslIPF~~HNqSpRn~yqc~M 729 (1186)
.+ -+++.+||+. +.|||||+|.+|+||+||||||+||||||||+|||||
T Consensus 500 ----------r~----~~e~~~i~~~-----------------~i~~~dIsP~qi~svaasLIPFleHndanRalmgsnM 548 (1070)
T CHL00001 500 ----------RY----RQEFLTIAWE-----------------QIHLRSIFPFQYFSIGASLIPFLEHNDANRALMGSNM 548 (1070)
T ss_pred ----------Ee----cCeEEEEchH-----------------HCcEEeeChhhhhhhhhhcCCCccccCcchhhhhhcc
Confidence 00 0123344332 3589999999999999999999999999999999999
Q ss_pred ccccccccccc---------eEEee-----------------c-----------c-cceeecc---------CCcceeec
Q 001021 730 GKQAMGIYVTN---------YQFRM-----------------D-----------T-LAYVLYY---------PQKPLVTT 762 (1186)
Q Consensus 730 ~KQaig~~~~n---------~~~r~-----------------D-----------~-~~~~L~y---------pQ~PlV~t 762 (1186)
||||||++..+ +..|. | + ..|++.| ||||||++
T Consensus 549 qrQAvpll~~~~p~VgTG~E~~~~~ds~~~i~a~~~G~V~~vd~~~I~i~~~~~~~~y~l~~y~rsnq~t~~~QkPlV~~ 628 (1070)
T CHL00001 549 QRQAVPLSRSEKCIVGTGLERQVALDSGVVAIAEHEGKIIYTDTDKIILSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRR 628 (1070)
T ss_pred chhccccccCCCCEeecCcchhhhhcccceeEEccCCEEEEEeCCEEEEEcCCCeEEEEeeceeccCCCcccccCCEEec
Confidence 99999999998 76776 6 4 4566778 99999999
Q ss_pred ccccccc------------cccCCCCceeEEEEEecCCCCCCCcEEeeccccccCceEEEEEEEEEeeecccCCcceeee
Q 001021 763 RAMEHLH------------FRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDF 830 (1186)
Q Consensus 763 ~~~~~~~------------~~~~p~G~N~~VAv~sy~GYn~EDaiiink~sv~rG~~~s~~~~~~~~~~~~~~~~~~e~~ 830 (1186)
+ ++++ .+|+|+|+|++||||||+||||||||||||+|++||+|||+||++|+++++++..+ .|.+
T Consensus 629 g--~~v~~g~~ladg~~~~~gel~~G~N~~VA~m~~~GYn~EDAiiin~~~v~~g~~~s~~~~~~~~~~~~~~~g-~e~i 705 (1070)
T CHL00001 629 G--KCVKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQG-PERI 705 (1070)
T ss_pred C--CEEccCCEeccChhhccccccCCccceeeeeeccccccchhhhhhhhhhcCCceEEEEEeeeeEEEeccCCC-cceE
Confidence 8 6665 89999999999999999999999999999999999999999999999999876444 4766
Q ss_pred cC--CCCCCCCCCCCCCcCCCCCCCccCCCcEEcCCCEEEEEeCCCCcccc--c---------cccCccccceeeEEeec
Q 001021 831 GR--PDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEA--Q---------GQASRYTRRDHSISLRH 897 (1186)
Q Consensus 831 ~~--p~~~~~~~~~~~~~~~ld~dGi~~~g~~v~~gd~l~~k~~p~~~~~~--~---------~~~~~~~~~~~s~~~~~ 897 (1186)
.. |+.+ ...|++||+|||+++|++|++|||||||++|....+. . .+.+....+|+|+++++
T Consensus 706 ~~~~p~~~------~~~~~~Ld~dGi~~~G~~v~~gDilvgK~~p~~~~~~~~~~~~~~~~~if~~~~~~~~d~sl~~~~ 779 (1070)
T CHL00001 706 TKEIPHLE------AHLLRNLDKNGIVMLGSWVETGDILVGKLTPQEAEESSYAPEGRLLRAIFGIQVSTSKETCLKLPI 779 (1070)
T ss_pred eccCCCCc------hhhhhccCCCCCccCCcEecCCCEEEEEecCCcccccccCcchhhhhhhhccccCcceeCeEECCC
Confidence 54 5432 2358999999999999999999999999999732111 0 11223457899999999
Q ss_pred CCCcEEEEEEEEec----CCCceEEEEEEEeecCCCCcccccccCCCccEEEeeecCCCCCCCCCCCCCcEEeCCCCCCC
Q 001021 898 SETGMVDQVLLTTN----ADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPS 973 (1186)
Q Consensus 898 ~~~g~v~~v~~~~~----~~~~~~vkv~~r~~R~p~iGDKfssRhGqKGvvs~i~~~~dmPf~~~G~~pDiI~NPh~~PS 973 (1186)
+++|+|++|.+++. .++.+.|||++|+.|+|+||||||||||||||||+|||+|||||++||++||||||||||||
T Consensus 780 ~~~g~V~~v~~~~~~~~~~~~~~~vkv~i~~~R~~~vGDK~asRHGqKGvvs~i~~~eDMPf~~dG~~pDiIlNP~gvPS 859 (1070)
T CHL00001 780 GGRGRVIDVRWIQKKGGSSYNPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPS 859 (1070)
T ss_pred CCceEEEEEEEEecccCCCCCcEEEEEEEEEEecCCCCcccccccCCcceEeeeecccCCCcccCCCCCceeeccccccc
Confidence 99999999998873 45678999999999999999999999999999999999999999999999999999999999
Q ss_pred CCchhhHHhhhhhHhhhhcCCccccCCCCCccHHHHH-----HHHHHcCC----------CCCCeEEEeeCCCCceEEee
Q 001021 974 RMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNIS-----KALHKCGY----------QMRGFETMYNGHTGRRLTAM 1038 (1186)
Q Consensus 974 RMtiGql~E~~~gk~~~~~g~~~d~tpF~~~~~~~~~-----~~l~~~g~----------~~~G~e~ly~g~tG~~~~~~ 1038 (1186)
|||||||+|+++||||++.|.+.|+|||++...+++. ..|.++|+ +++|++.||||+||++|+++
T Consensus 860 RMtiGqllE~~~G~a~~~~g~~~~~~pf~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~Gk~~l~dG~TG~~~~~~ 939 (1070)
T CHL00001 860 RMNVGQIFECLLGLAGDLLNRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRLFDGRTGDPFEQP 939 (1070)
T ss_pred cccHHHHHHHHhHHHHhhcCceeeeccCCCcchhhhhhhhhhHHHHHHHHhcCCceeccCCCCCeEEEEcCCCCCCccce
Confidence 9999999999999999999999999999987777666 56777776 44599999999999999999
Q ss_pred EeEeeeehhccccccCCceEEeccCCccccccCCCCcccCCCcceeeehhhhHHHhhccHHHHHHhhhcCCCcceeeecc
Q 001021 1039 IFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCE 1118 (1186)
Q Consensus 1039 if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~L~erL~~~SD~~~~~vC~ 1118 (1186)
||+|++|||||+|||+||+||||+|||+.|||||++||||+|||||||||||||+|||||++|+|||+.+||..... |.
T Consensus 940 i~vG~~Yy~kL~HmV~DKihaRs~Gp~~~lT~QP~~Grsr~GG~RfGEME~~al~a~GAs~~L~E~L~~~SD~~~~r-~~ 1018 (1070)
T CHL00001 940 VTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRAR-QE 1018 (1070)
T ss_pred EEEEecceeEchhhccccceeeccCCCcccccCCCCcccCCCCeeeecchHHHHHhhhHHHHHHHHHhccCccHHHH-HH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999975553 22
Q ss_pred ccCcceeeccccCceeeccCCCCCCcee-ecccHhhHHHHHHHHhCCCceEEEeccCC
Q 001021 1119 HCGLIAIANLKKNSFECRGCKNKTDIVQ-VHIPYACKLLFQELMAMAIAPRMLTKEDT 1175 (1186)
Q Consensus 1119 ~cG~~~~~~~~~~~~~C~~C~~~~~i~~-v~iPy~~k~l~~EL~sm~i~~~l~~~~~~ 1175 (1186)
.++ | |-.+..+.+ +.+|||||+|++||+|||+++++..-+..
T Consensus 1019 ~~~-------------~--i~~g~~~~~~~~~pesfk~l~~El~~l~l~i~~~~~~~~ 1061 (1070)
T CHL00001 1019 VLG-------------A--IITGGTIPKPEDAPESFRLLVRELRSLALELNHFLVSEK 1061 (1070)
T ss_pred HHH-------------h--hhcCCcccCCCCCCchhhHHHHHHHhCccceEEEEEecc
Confidence 111 2 333446776 79999999999999999999999865443
No 10
>CHL00207 rpoB RNA polymerase beta subunit; Provisional
Probab=100.00 E-value=1.5e-201 Score=1871.31 Aligned_cols=926 Identities=26% Similarity=0.384 Sum_probs=766.2
Q ss_pred cccCccchHHHHHHHHHHHHHhhHHHHHhhcCCeeeCCCCCCCCCeEEEEe--eEEEeCCcccCCCCccCCCChHHHHhc
Q 001021 34 AYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQSDFA--EIYLSKPMMTESDGETATLFPKAARLR 111 (1186)
Q Consensus 34 ~~f~~~~Lv~~hi~SFN~Fl~~gL~~ii~~~~pI~~~~~~~~~~~~~l~f~--~i~i~~P~~~~~~~~~~~l~P~EcR~r 111 (1186)
.-|..++|++.|++||+|||++||++++++++||+. .++.+.++|. ++++++|.+ +|.|||+|
T Consensus 3 ~~~~~Pdll~iQ~~SF~~FL~~GL~~~~~~~~pI~~-----~~~~~~l~~~~~~y~l~~P~~----------~~~Ea~~r 67 (1077)
T CHL00207 3 MNFALPDFLEIQRTSFCWFLNEGLNEELNIFSKIFD-----YTGNLELLLFGKNYKLKYPKY----------NLLSAKSY 67 (1077)
T ss_pred cccCCCCHHHHHHHHHHHHHHHHHHHHHHhcCCeEC-----CCCCEEEEEecceEEEcCCCC----------CHHHHHHh
Confidence 347789999999999999999999999999999974 2345677776 799999986 68999999
Q ss_pred CCCcceeEEEEEEEEEeccCCCCcccccceeeEEEEecccceeeccCCccCCCCChhhhhhcCCCCCCCCceEEEcCeee
Q 001021 112 NLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIINGSEK 191 (1186)
Q Consensus 112 ~lTYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~eli~~gE~~~D~GGYFIING~ER 191 (1186)
++||++||+|+++++..+. ++++.++|++|+||+|+. +|||||||+||
T Consensus 68 ~~TYsa~l~v~~~l~~~~~--------~~i~~~~V~lG~iPlMT~------------------------~GtFIING~ER 115 (1077)
T CHL00207 68 DSNYSIQIYLPLKFINLKT--------NKIKFINYLIGNLPKMTQ------------------------RGTFIINGLER 115 (1077)
T ss_pred CCccceeEEEEEEEEEcCC--------ceEEEEEEEEeccCccCC------------------------CCEEEEcCcee
Confidence 9999999999999975432 234678999999999976 99999999999
Q ss_pred EEEeeeeeccCeEEEEEecCCCcceEEEEEEEeecCCCCCCceEEEEEEecCCCCCCCCCcEEEEEeccccccchHHHHH
Q 001021 192 VLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVF 271 (1186)
Q Consensus 192 VIi~Qe~~s~N~~~~~~~~~~~~~~~~~~irs~~~~g~~~~~~~~v~~~~~~~~~~~~~~~~i~v~i~~~~~~IPl~ilL 271 (1186)
|||+|+.|||+.+|.......++..|.|.| ++.+|+|...++ . .++.+|+++++ +++||+++||
T Consensus 116 ViVsQl~RSPGiyf~~~~~k~~~~~y~a~I--Ip~rGswl~~e~----d---------~k~~i~vridr-~rKipit~lL 179 (1077)
T CHL00207 116 VIVSQIIRSPGIYFKKEIKKNSNKIYSATL--IPNRGSWIKFEL----D---------KNKEIWIRIDK-NRKKPLIIFL 179 (1077)
T ss_pred EEEEEeccCCeEEEEEecCcCCceEEEEEE--EcCCCceEEEEE----c---------CCCeEEEEecC-CceeeHHHHH
Confidence 999999999998876443333445688877 779999965333 1 15689999998 5599999999
Q ss_pred HHhcCCCHHHHHHHhccccCchhhHhhhHhhHhhhhccccHHHHHHHHhhcCcccCCCchhhHHHHHHHH-------hhc
Q 001021 272 RALGFVADKDILEHICYDFQDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGATVGVTRDKRIKYAKEIL-------QKE 344 (1186)
Q Consensus 272 kALG~~sD~eI~~~i~~~~~~~~~~~~l~~~l~e~~~i~t~~~al~yIg~r~~~~~~~~~~~~e~~~~iL-------~~~ 344 (1186)
||||+ ||+||++.+.+. .+..+ +...+. .....++++|+.+|+++++.. .....+.++.++ ++|
T Consensus 180 rALGl-s~~eIl~~~~~~-~~~~~---~~~~l~-~~~~~~~e~Al~~Iy~~lrp~---~~~~~~~a~~~l~~~ff~~~rY 250 (1077)
T CHL00207 180 KALGL-TDQDIYSRLTKS-EFLKK---LKPILL-NSNSYTNEEILLEIYKNLSPI---EPATVNDANQNLFSRFFDPKNY 250 (1077)
T ss_pred HHhCC-CHHHHHHHHhcc-chHHH---HHHHHh-ccCcccHHHHHHHHHHhcCCC---CCccHHHHHHHHHHHhcChhcc
Confidence 99999 899999998531 11222 122222 123458999999999997542 222234455554 567
Q ss_pred ccCCCCCC-----------CccchhHHHHHHHHHHHHHHhccCCcCCCCCcccccceeccCchhhHHHHHHHHHHHHHHH
Q 001021 345 MLPHVGTG-----------DFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDV 413 (1186)
Q Consensus 345 ll~Hl~~~-----------~~~~~~K~~~L~~Mv~kLl~l~~g~~~~DD~D~l~NkRv~l~G~Ll~~lfr~~l~~~~k~i 413 (1186)
.|+|+|.- .....-++..+..|+++|+.+..|....||+|||+||||+++|+||++|||.+|.++.+.+
T Consensus 251 dLg~vGR~klN~kl~~~~~~~~~~l~~~Dil~~i~~Li~l~~g~~~~DDiDHL~NRRvrsvGELlq~qfr~gl~rler~i 330 (1077)
T CHL00207 251 DLGKVGRYKINNKLNLNIPERVRNLTYEDILSIIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIGLKRLERIL 330 (1077)
T ss_pred cccccchhhhhhhccCCcCccCceecHHHHHHHHHHHHHhhcCCCcccchhhhhcccccchhHHHHHHHHHHHHHHHHHH
Confidence 78999862 1223334445668999999999998899999999999999999999999999999999999
Q ss_pred HHHHhhhhcCCCccchhhhccccchhhhhhhhcccCccccccccccccceeeeccccChhhhhccccccCC----CCCcC
Q 001021 414 RAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS----PIGRE 489 (1186)
Q Consensus 414 k~~l~k~~~~~~~~~~~~~i~~~~It~~i~~~~sTGNw~~~~~~~~~sGvsq~l~r~N~l~~lSh~Rrv~~----~~~~~ 489 (1186)
++++.+.. .+.+++.++++++.++..|++||+ ++++||+|||+||||+|||+||+++ ++.++
T Consensus 331 ke~m~~~~--~~~~tp~~lin~k~lt~~ikeFFg------------ss~LSQfmDQtNpLselTHKRRlsaLGpGGLsR~ 396 (1077)
T CHL00207 331 RNRMTICD--IDSLSKFNLINPKPLIALIREFFG------------SSQLSQYMDQTNPLSELTHKRRISILGPGGLDKD 396 (1077)
T ss_pred HHHhhhcc--cccCChhhcccchhHHHHHHHhhc------------cCCccceecccChHHhhhccceeeccCCCccccc
Confidence 99987542 245778899999999999999996 4899999999999999999999997 45788
Q ss_pred CCcCcccccCCCCccccccCCCCCCcccccccccceeEEEcc-CCCchhHHHHHHHhCCccccccCCCCCCCceEEEECC
Q 001021 490 GKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITV-GSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNG 568 (1186)
Q Consensus 490 ~K~t~vR~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~Is~-~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~V~lnG 568 (1186)
+..+++|++||||||||||+|||||++||||++||.+|.|+. |+.+.| +.+| .||
T Consensus 397 ra~fevRdvH~thyGRiCPIETPEG~n~Gli~~la~~~~in~~GfietP-----------------------y~~v-~~g 452 (1077)
T CHL00207 397 RISFAVRDIHPSHYGRICPIETPEGPNCGLIGSLATNARINKFGFIETP-----------------------FYKV-ING 452 (1077)
T ss_pred ccCCcccccCccccccccCCCCCCCcccccccchhhhccccCCCceeCc-----------------------eEEE-EcC
Confidence 899999999999999999999999999999999999999976 333322 1122 233
Q ss_pred EEEEEEcChHHHHHHHHhhhhcCCCCCceEEEEeccCCeEEEEeCCCceeeeEEEEecccchhhHHHHHHHhcCCCCCCC
Q 001021 569 CWVGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRESPEDG 648 (1186)
Q Consensus 569 ~~iG~~~~~~~l~~~lr~~rr~~~i~~~vsi~~~~~~~~i~I~td~gRl~RPl~~v~~~~~~~~~~~~~~l~~~~~~~~~ 648 (1186)
++ .
T Consensus 453 ~v-----------------------------------------------------------~------------------ 455 (1077)
T CHL00207 453 KV-----------------------------------------------------------K------------------ 455 (1077)
T ss_pred cc-----------------------------------------------------------c------------------
Confidence 21 0
Q ss_pred CccccccCCcEEEeccccccceeeeecccccccccCCC-C-----------ccccccceeeecCCCccccccccccCCCC
Q 001021 649 GWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHP-E-----------EAYADTYTHCEIHPSLILGVCASIIPFPD 716 (1186)
Q Consensus 649 ~~~~l~~~g~iE~i~~~Ee~~~~Ia~~~~~~~~~~~~~-k-----------~~~~~~~th~Ei~p~~ilsv~AslIPF~~ 716 (1186)
....++|++|.||+...||.....+...+.+. + ...+.+.++++++|.+++||+||||||.+
T Consensus 456 ------~~~~i~ylsa~~e~~~~Ia~~~~~~~~~~~~~~~~v~~r~~~ef~~~~~~~v~~~~vsp~Q~~SvaasLIPFLe 529 (1077)
T CHL00207 456 ------KFGNPIYLTADSEDLYRIAPNDINLNKNNYFKKNIIPVRYKQEFKTVNPSKVDFIAISPIQVFSIAESLIPFLE 529 (1077)
T ss_pred ------ccCceeecChHHhcCcEEEecCccCCCCCcccCCEEEEEECCcEEEEChHHceEEEeCcchhcchhhhcCCccc
Confidence 01247899999999999998766554422110 0 00134578999999999999999999999
Q ss_pred CCCCccchhhhhcccccccccccc-----------------------------------eEEeecc---cceee------
Q 001021 717 HNQSPRNTYQSAMGKQAMGIYVTN-----------------------------------YQFRMDT---LAYVL------ 752 (1186)
Q Consensus 717 HNqSpRn~yqc~M~KQaig~~~~n-----------------------------------~~~r~D~---~~~~L------ 752 (1186)
|||++|++|||||||||||+.... +..+.+. ..|.|
T Consensus 530 hdDanRaLMGsnMqrQaVPll~~e~p~VgTg~e~~~a~ds~~~i~a~~~G~v~~v~~~~I~i~~~~~~~~~y~l~~~~rs 609 (1077)
T CHL00207 530 HNDANRALMGSNMQRQAVPLLYPEKPIVGTGYEKQIALDSGMTIISLTEGIVVSVSAYKIIIQDDNNRYIHYYLQKYQRS 609 (1077)
T ss_pred ccccchhhhhhccccccccccccCCCeEECCcchHhhhhcchheEeccCcEEEEecCcEEEEEeCCCceeEEEecccccc
Confidence 999999999999999999985321 1122211 22433
Q ss_pred ----ccCCcceeeccc----ccc------cccccCCCCceeEEEEEecCCCCCCCcEEeeccccccCceEEEEEEEEEee
Q 001021 753 ----YYPQKPLVTTRA----MEH------LHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDE 818 (1186)
Q Consensus 753 ----~ypQ~PlV~t~~----~~~------~~~~~~p~G~N~~VAv~sy~GYn~EDaiiink~sv~rG~~~s~~~~~~~~~ 818 (1186)
|+.|||+|+.+. .+. +.++|+|+|+|++||||||+||||||||||||++++||+|+|+|+++|+++
T Consensus 610 Nq~t~i~qrp~V~~G~~v~~G~iladg~~~~~~el~lG~N~lVA~m~y~GYN~EDAiiink~~v~rg~f~Si~~~~~~~e 689 (1077)
T CHL00207 610 NQNTCINYRPIVWVGEKINIGQILADGSDIDNSELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEKYEIE 689 (1077)
T ss_pred ccCceeecccccCCCCEEecCCEEecchhccCCcccCCcccEEEEEeeeccccchhhhhhhhhhcCCceEEEEEEEeeeE
Confidence 579999998742 233 379999999999999999999999999999999999999999999999999
Q ss_pred ecccCCcceeeec--CCCCCCCCCCCCCCcCCCCCCCccCCCcEEcCCCEEEEEeCCCCccccc---------cccCccc
Q 001021 819 EKKMGTLVKEDFG--RPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ---------GQASRYT 887 (1186)
Q Consensus 819 ~~~~~~~~~e~~~--~p~~~~~~~~~~~~~~~ld~dGi~~~g~~v~~gd~l~~k~~p~~~~~~~---------~~~~~~~ 887 (1186)
++++..+ .|.|. .|+.. ...|++||+||||++|++|++|||||||++|+...+.. ..++...
T Consensus 690 ~~~~~~g-~e~i~~~~p~~~------~~~~~~LD~dGiv~iG~~V~~gDilvgK~tp~~~~~~~~~~~ll~~i~~~~~~~ 762 (1077)
T CHL00207 690 LRQTKLG-SEEITRNIPNVS------EYSLKNLDENGIISIGSKVLAGDILVGKITPKGESDQLPEGKLLRAIFGEKAKD 762 (1077)
T ss_pred EeecCCC-ceEEeccCCCCC------hHHhhccCccCCCcCCcEeCCCCEEEEEecCccccccChhhhhhhhhhccCCCc
Confidence 8875443 46665 45421 23589999999999999999999999999996422210 1223345
Q ss_pred cceeeEEeecCCCcEEEEEEEEecC--CCc-----eEEEEEEEeecCCCCcccccccCCCccEEEeeecCCCCCCCCCCC
Q 001021 888 RRDHSISLRHSETGMVDQVLLTTNA--DGL-----RFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGI 960 (1186)
Q Consensus 888 ~~~~s~~~~~~~~g~v~~v~~~~~~--~~~-----~~vkv~~r~~R~p~iGDKfssRhGqKGvvs~i~~~~dmPf~~~G~ 960 (1186)
.+|+|++++++++|+|++|.++.+. ++. ..|||++|+.|+|+||||||||||||||||+|||+|||||++||+
T Consensus 763 ~kd~sl~~~~~~~g~V~~V~~~~~~~~~~~~~~~~~~vkv~i~~~R~p~vGDKfasRHGqKGVvs~i~p~eDMPf~~dG~ 842 (1077)
T CHL00207 763 VKDTSLRMPNGGYGRVIKVEIFSRSKGDELKFGYYLKIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGT 842 (1077)
T ss_pred ceEeEEEcCCCCcEEEEEEEEEecCCCCcccccccEEEEEEEEEEecCCcccccccccCCceeEEeeeccCCCCccCCCC
Confidence 7999999999999999999998753 222 358999999999999999999999999999999999999999999
Q ss_pred CCcEEeCCCCCCCCCchhhHHhhhhhHhhhhcCCccccCCCCCccHHHHHHHHHHc---------------CCCCCCeEE
Q 001021 961 TPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKC---------------GYQMRGFET 1025 (1186)
Q Consensus 961 ~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tpF~~~~~~~~~~~l~~~---------------g~~~~G~e~ 1025 (1186)
+|||||||||||||||||||+|+++||||++.|...++|||++...+++.+.|... +|+++|+++
T Consensus 843 ~pDiIlNPhg~PSRMtiGqllE~~lGka~~~l~~~~~~tpF~~~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~Gk~~ 922 (1077)
T CHL00207 843 PPDIILNPLGVPSRMNVGQLFECLLGLAGDNLNKRFKILPFDEMYGSEYSRILINNKLNQASIKNNEYWLFNSYHPGKMV 922 (1077)
T ss_pred CccEEECCccccccccHHHHHHHHHHHHHHhcCCcEeeccCCCCcHHHHHHHHHhhhhhhccchhccccccCCCCCCCEE
Confidence 99999999999999999999999999999998888889999998888888777654 377899999
Q ss_pred EeeCCCCceEEeeEeEeeeehhccccccCCceEEeccCCccccccCCCCcccCCCcceeeehhhhHHHhhccHHHHHHhh
Q 001021 1026 MYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERL 1105 (1186)
Q Consensus 1026 ly~g~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~L~erL 1105 (1186)
||||+||++|+++||+|++|||||+|||+||+||||+|||+.|||||++||||+|||||||||||||+|||||++|||||
T Consensus 923 lydG~TGe~~~~~i~vG~~Yy~kL~HmV~DKihaRs~Gp~s~lTqQP~~Grsr~GG~RfGEME~~aL~a~GAa~~L~E~L 1002 (1077)
T CHL00207 923 LRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELL 1002 (1077)
T ss_pred EECCCCCCCccCceEEEecceeEchhhccccceeeccCCCcccccCCCCccccCCCeeeecccHHHHHhhhhHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCCCcceeeeccccCcceeeccccCceeeccCCCCCCceeecccHhhHHHHHHHHhCCCceEEEeccCC
Q 001021 1106 FDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKEDT 1175 (1186)
Q Consensus 1106 ~~~SD~~~~~vC~~cG~~~~~~~~~~~~~C~~C~~~~~i~~v~iPy~~k~l~~EL~sm~i~~~l~~~~~~ 1175 (1186)
+.+||.+.+. ..+|..|.++.++.++.+|||||+|+|||+||||++++......
T Consensus 1003 ~~kSD~~~~r----------------~~~~~~~~~~~~i~~~~~P~sfklL~~EL~sl~i~~~~~~~~~~ 1056 (1077)
T CHL00207 1003 TIKSDDMQGR----------------NETLNAIVKGQPIPKPGTPESFKVLMRELQSLGLDIEAYKIENF 1056 (1077)
T ss_pred hcCCccceeh----------------HHHHHhhhCCCeecCCCCCchHHHHHHHHHHCCcCcEecccccc
Confidence 9999976631 12599999999999999999999999999999999999865533
No 11
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=100.00 E-value=3.4e-188 Score=1799.94 Aligned_cols=944 Identities=26% Similarity=0.385 Sum_probs=775.2
Q ss_pred hhhhhhhcccCccchHHHHHHHHHHHHH------hhHHHHHhhcCCeeeCCCCCCCCCeEEEEeeEEEeCCcccCCCCcc
Q 001021 27 DAWAVISAYFEEKGLVRQQLDSFDEFIQ------NTMQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPMMTESDGET 100 (1186)
Q Consensus 27 ~~~~~i~~~f~~~~Lv~~hi~SFN~Fl~------~gL~~ii~~~~pI~~~~~~~~~~~~~l~f~~i~i~~P~~~~~~~~~ 100 (1186)
..|+.++..+..|+|++.|.+||+|||+ +||++++++++||+. +++.+.|+|.++++++|.+
T Consensus 13 ~~f~k~~~~~~iPdLleIQ~~SF~~FLq~~~~~~~GL~e~f~~~fPI~d-----~~g~~~Lefv~Y~l~~Pk~------- 80 (2890)
T PRK09603 13 ADFTKTPTDLEVPNLLLLQRDSYDSFLYSKDGKESGIEKVFKSIFPIQD-----EHNRITLEYAGCEFGKSKY------- 80 (2890)
T ss_pred eecccCCccCCCCCHHHHHHHHHHHHHhCCCcccccHHHHHHhcCCeEC-----CCCcEEEEEEEEEeCCCCC-------
Confidence 3577888888999999999999999998 799999999999974 3467899999999999988
Q ss_pred CCCChHHHHhcCCCcceeEEEEEEEEEeccCCCC--cccccceeeEEEEecccceeeccCCccCCCCChhhhhhcCCCCC
Q 001021 101 ATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDG--EEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPY 178 (1186)
Q Consensus 101 ~~l~P~EcR~r~lTYsa~l~v~v~~~~~~~~~~~--~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~eli~~gE~~~ 178 (1186)
+|.||++|++||++||+|++++++.+...++ +..+++++.++|++|+||+|+.
T Consensus 81 ---~~~Ec~~rg~TYsapL~v~~rL~~~~~~~~t~~~~~ikeikeq~VylGdiPLMT~---------------------- 135 (2890)
T PRK09603 81 ---TVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQSIFIREIPLMTE---------------------- 135 (2890)
T ss_pred ---CHHHHHhhCCcccccEEEEEEEEEeeccccccccccccceEEeeEEEecCCccCC----------------------
Confidence 4689999999999999999999864322211 1224467789999999999998
Q ss_pred CCCceEEEcCeeeEEEeeeeeccCeEEEEEec--CCCcceEEEEEEEeecCCCCCCceEEEEEEecCCCCCCCCCcEEEE
Q 001021 179 DQGGYFIINGSEKVLIAQEKMSTNHVYVFKKR--QPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRA 256 (1186)
Q Consensus 179 D~GGYFIING~ERVIi~Qe~~s~N~~~~~~~~--~~~~~~~~~~irs~~~~g~~~~~~~~v~~~~~~~~~~~~~~~~i~v 256 (1186)
.|+|||||+|||||+|++|||+.+|..... ..++..|+|.| +|.+|+|...+++ .++.+|+
T Consensus 136 --~GTFIING~ERVIVsQL~RSPGVyF~~~~~k~~s~k~lysa~I--IP~RGsWLefE~D-------------~kd~l~v 198 (2890)
T PRK09603 136 --RTSFIINGVERVVVNQLHRSPGVIFKEEESSTSLNKLIYTGQI--IPDRGSWLYFEYD-------------SKDVLYA 198 (2890)
T ss_pred --CceEEEcCceeEEEeeeccCCeeEEeeccCcCCCCceeEEEEE--ecCCcceEEEEEc-------------CCCeEEE
Confidence 999999999999999999999988865432 23455688887 8899999765552 2568999
Q ss_pred EeccccccchHHHHHHHhcCCCHHHHHHHhcccc----Cc--------h----------------------------hhH
Q 001021 257 TLPYIRTEIPIIIVFRALGFVADKDILEHICYDF----QD--------T----------------------------QMM 296 (1186)
Q Consensus 257 ~i~~~~~~IPl~ilLkALG~~sD~eI~~~i~~~~----~~--------~----------------------------~~~ 296 (1186)
++++ +++||+++||||||+ +++||++.+.... .+ + ...
T Consensus 199 rIDr-krKipit~lLrAlG~-s~edIl~~f~~~~~~~i~~~~~~~~~~~~~l~~~~~~di~d~~g~vlv~~g~rit~~~~ 276 (2890)
T PRK09603 199 RINK-RRKVPVTILFRAMDY-QKQDIIKMFYPLVKVRYENDKYLIPFASLDANQRMEFDLKDPQGKIILLAGKKLTSRKI 276 (2890)
T ss_pred EEcC-cceecHHHHHHHhCC-CHHHHHHHhcccceEEEcccceeecccHHHhcCccceeecccCCCEEEecCccccHHHH
Confidence 9998 679999999999999 6899999874100 00 0 000
Q ss_pred -------------------------------hhhHhh-----------Hhhh----------------------------
Q 001021 297 -------------------------------ELLRPS-----------LEEA---------------------------- 306 (1186)
Q Consensus 297 -------------------------------~~l~~~-----------l~e~---------------------------- 306 (1186)
+.+... +.+.
T Consensus 277 ~~l~~~g~k~l~~~~~~l~g~~laedivd~~Evl~~~~~~Itee~le~i~~~gi~~i~vl~~~~~~~~~~i~~t~~~d~~ 356 (2890)
T PRK09603 277 KELKENHLEWVEYPMDILLNRHLAEPVMVGKEVLLDMLTQLDKNKLEKIHDLGVQEFVIINDLALGHDASIIHSFSADSE 356 (2890)
T ss_pred HHHHhcCCceeccchhhhcceeeeeeccCccceeeccCChhcHHHHHHHHHcCCceEEEEeecccccccccccccccccc
Confidence 000000 0000
Q ss_pred --------hc-cccHHHHHHHHhhcCcccCCCchhhHHHHHHHHhhcccC-------CCCCCC------------ccchh
Q 001021 307 --------FV-IQNQQVALDYIGKRGATVGVTRDKRIKYAKEILQKEMLP-------HVGTGD------------FCETK 358 (1186)
Q Consensus 307 --------~~-i~t~~~al~yIg~r~~~~~~~~~~~~e~~~~iL~~~ll~-------Hl~~~~------------~~~~~ 358 (1186)
.. ..++++|+..|+++++. ......+.|+.++.+.+|- .+|... .....
T Consensus 357 ~~~~~~~t~~~~~~~eeAl~~iyr~lrp---gep~~~e~A~~l~~~lFFn~~rYdLg~vGR~klN~kL~l~~~~~~~~Lt 433 (2890)
T PRK09603 357 SLKLLKQTEKIDDENALAAIRIHKVMKP---GDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKMNHKLGLHVPDYITTLT 433 (2890)
T ss_pred cchhhhhccccccchHHHHHHHHhccCC---CCCCcHHHHHHHHHHHhcCcccccccccchhhhHhhhCCCCCCcccEec
Confidence 00 01458899999988754 2334456677777765543 122110 01123
Q ss_pred HHHHHHHHHHHHHHhccCCcCCCCCcccccceeccCchhhHHHHHHHHHHHHHHHHHHHhhhhcCCCccchhhhccccch
Q 001021 359 KAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTI 438 (1186)
Q Consensus 359 K~~~L~~Mv~kLl~l~~g~~~~DD~D~l~NkRv~l~G~Ll~~lfr~~l~~~~k~ik~~l~k~~~~~~~~~~~~~i~~~~I 438 (1186)
+.+++ ..+++|+.+..|....||+|||+||||+++|+||+++|+.+|.++.+.+++++.........+.+..++|++++
T Consensus 434 ~~Dil-~~i~~li~l~~g~~~~DDiDhL~NRRvr~vGELl~~qfr~gl~rler~irerm~~~~~~~~~~~p~~lin~k~i 512 (2890)
T PRK09603 434 HEDII-TTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELHSGLVKMQKTIKDKLTTMSGAFDSLMPHDLVNSKMI 512 (2890)
T ss_pred chhHH-HHHHHHHHHHhCCCCCCcchhhhcchhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccChhhhhccHHH
Confidence 44555 69999999999999999999999999999999999999999999999999999753333346778899999999
Q ss_pred hhhhhhhcccCccccccccccccceeeeccccChhhhhccccccCC--CC--CcCCCcCcccccCCCCccccccCCCCCC
Q 001021 439 TSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS--PI--GREGKLAKPRQLHNSQWGMMCPAETPEG 514 (1186)
Q Consensus 439 t~~i~~~~sTGNw~~~~~~~~~sGvsq~l~r~N~l~~lSh~Rrv~~--~~--~~~~K~t~vR~Lhps~wG~iCPveTPEG 514 (1186)
+..++.||+| +.+||+|||+||||+|+|+||+++ |. .+++..+++|++||||||||||+|||||
T Consensus 513 ~~~ikeFFgs------------sqLSQfmDQtNpLseltHKRRlSaLGPGGlsr~ra~fevRdVH~shYGRiCPIETPEG 580 (2890)
T PRK09603 513 TSTIMEFFMG------------GQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEG 580 (2890)
T ss_pred HHHHHHHhcc------------CchhhhhcccChhhhhhhcccccccCCCCccccccCCcccccCcccccccCCCCCCCC
Confidence 9999999975 579999999999999999999986 53 4778888999999999999999999999
Q ss_pred cccccccccceeEEEcc-CCCchhHHHHHHHhCCccccccCCCCCCCceEEEECCEEEEEEcChHHHHHHHHhhhhcCCC
Q 001021 515 QACGLVKNLALMVYITV-GSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKTLRRLRRRVDV 593 (1186)
Q Consensus 515 ~~cGLvk~LA~~a~Is~-~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~l~~~lr~~rr~~~i 593 (1186)
+|||||++||.+|+|+. |+.++| +.+| .||++
T Consensus 581 ~NiGLI~SLa~~a~in~~GfietP-----------------------y~kV-~~g~v----------------------- 613 (2890)
T PRK09603 581 QNIGLINTLSTFTRVNDLGFIEAP-----------------------YKKV-VDGKV----------------------- 613 (2890)
T ss_pred CcccchhhhhhheecccCcceecc-----------------------eEEE-ecCcc-----------------------
Confidence 99999999999999987 333332 1222 23321
Q ss_pred CCceEEEEeccCCeEEEEeCCCceeeeEEEEecccchhhHHHHHHHhcCCCCCCCCccccccCCcEEEeccccccceeee
Q 001021 594 NTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRESPEDGGWHDLVAKGFIEYIDTEEEETTMIS 673 (1186)
Q Consensus 594 ~~~vsi~~~~~~~~i~I~td~gRl~RPl~~v~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~g~iE~i~~~Ee~~~~Ia 673 (1186)
+..++|++|.||+...||
T Consensus 614 --------------------------------------------------------------~~~i~ylsa~eE~~~~IA 631 (2890)
T PRK09603 614 --------------------------------------------------------------VGETIYLTAIQEDSHIIA 631 (2890)
T ss_pred --------------------------------------------------------------ccceeeeCHHHhcCceEe
Confidence 023679999999999999
Q ss_pred ecccccccccCCCCc------------cccccceeeecCCCccccccccccCCCCCCCCccchhhhhccccccccccc--
Q 001021 674 MTINDLVQARLHPEE------------AYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVT-- 739 (1186)
Q Consensus 674 ~~~~~~~~~~~~~k~------------~~~~~~th~Ei~p~~ilsv~AslIPF~~HNqSpRn~yqc~M~KQaig~~~~-- 739 (1186)
.....+...+.+.+. ..+.+.++++++|.+++||+||||||++||||+|++|||||||||||+...
T Consensus 632 ~a~~~~~~~~~~~~~~v~~R~~~e~~~~~~~~v~~~dvsp~Q~vSvaasLIPFLEhdDAnRALMGSNMQRQAVPLl~~e~ 711 (2890)
T PRK09603 632 PASTPIDEEGNILGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDA 711 (2890)
T ss_pred ccCCccCCCCcccCCeEeEEECCceEEEChHHceEEEeCccceeeehhhcCCccccCccccccccccchhhhhhhccccC
Confidence 776665543221000 013456899999999999999999999999999999999999999998522
Q ss_pred ---------------------------------ceEEeecc------cceee----------ccCCcceeeccc----cc
Q 001021 740 ---------------------------------NYQFRMDT------LAYVL----------YYPQKPLVTTRA----ME 766 (1186)
Q Consensus 740 ---------------------------------n~~~r~D~------~~~~L----------~ypQ~PlV~t~~----~~ 766 (1186)
.+.+|.+. ..|.| |+.|||+|+.+. .+
T Consensus 712 piVgTG~E~~va~dSg~~i~a~~~G~V~yvd~~~I~i~~~~~~~~~~~~Y~L~Ky~RSNQ~TcinqrPiV~~Gd~V~kGd 791 (2890)
T PRK09603 712 PIVGTGIEKIIARDSWGAIKANRAGVVEKIDSKNIYILGEGKEEAYIDAYSLQKNLRTNQNTSFNQVPIVKVGDKVEAGQ 791 (2890)
T ss_pred CeEecCcchhhhccccceeEecCCeEEEEecCcEEEEEecCCCCceeeEEeeccccccCCCceeeeccEecCCCEeccCC
Confidence 12222221 12555 679999998752 23
Q ss_pred c------cccccCCCCceeEEEEEecCCCCCCCcEEeeccccccCceEEEEEEEEEeeecccCCcceeeec--CCCCCCC
Q 001021 767 H------LHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFG--RPDRSNT 838 (1186)
Q Consensus 767 ~------~~~~~~p~G~N~~VAv~sy~GYn~EDaiiink~sv~rG~~~s~~~~~~~~~~~~~~~~~~e~~~--~p~~~~~ 838 (1186)
. +..+|+++|+|++||||||.|||||||||||++.+..++|||+|+.+|+++.+.+.. ..|++. +|+.+
T Consensus 792 ilADG~st~~GELALG~NvlVAfmpW~GYNfEDAIlISERlV~eD~fTSIHIee~ei~~r~Tk~-G~EeITrdIPnvs-- 868 (2890)
T PRK09603 792 IIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVDARELKH-GVEEFTADIPDVK-- 868 (2890)
T ss_pred EEecCcccccCeeccCcccEEEEeeeccccCccccccchhhhcCccceEEEEeeeEEEEEecCC-CCcEEeccCCCCC--
Confidence 3 378999999999999999999999999999999999999999999999999988754 346664 67642
Q ss_pred CCCCCCCcCCCCCCCccCCCcEEcCCCEEEEEeCCCCccccc---------cccCccccceeeEEeecCCCcEEEEEEEE
Q 001021 839 MGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ---------GQASRYTRRDHSISLRHSETGMVDQVLLT 909 (1186)
Q Consensus 839 ~~~~~~~~~~ld~dGi~~~g~~v~~gd~l~~k~~p~~~~~~~---------~~~~~~~~~~~s~~~~~~~~g~v~~v~~~ 909 (1186)
....++||++||+++|++|++|||||||++|+...+.. .+++....+|+|++++++..|+|.+|.++
T Consensus 869 ----e~~l~~LDe~GII~iGa~V~~GDILVGKvTPkge~~~tPEekLLraIFGeka~~vkDtSLrvp~G~~G~Vidv~~f 944 (2890)
T PRK09603 869 ----EEALAHLDESGIVKVGTYVSAGMILVGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVF 944 (2890)
T ss_pred ----HHHHhcCCCCCCEeeCCEECCCCEEEEeeccCCCCCCChHHHHHHHHhcccccccccCceecCCCCcEEEEEEEEe
Confidence 23478999999999999999999999999999643321 24566789999999999999999999877
Q ss_pred ecC-----------------------------------------------------------------------------
Q 001021 910 TNA----------------------------------------------------------------------------- 912 (1186)
Q Consensus 910 ~~~----------------------------------------------------------------------------- 912 (1186)
+..
T Consensus 945 ~r~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1024 (2890)
T PRK09603 945 TKKGYEKDARVLSAYEEEKAKLDMEHFDRLTMLNREELLRVSSLLSQAILEEPFSHNGKDYKEGDQIPKEEIASINRFTL 1024 (2890)
T ss_pred cccccchhHHHHHHHHHHHHHHhHhhHHHHHHHHHHHHHhhhhhccccccccccccccccccccccccHHHHhhCCHHHh
Confidence 632
Q ss_pred -----------------------------------------CC-------ceEEEEEEEeecCCCCcccccccCCCccEE
Q 001021 913 -----------------------------------------DG-------LRFVKVRVRSVRIPQIGDKFSSRHGQKGTV 944 (1186)
Q Consensus 913 -----------------------------------------~~-------~~~vkv~~r~~R~p~iGDKfssRhGqKGvv 944 (1186)
.| .+.|||++|+.|+|+|||||||||||||||
T Consensus 1025 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~gdeL~~Gv~~~VkV~ia~kR~~qvGDK~AgRHGnKGVi 1104 (2890)
T PRK09603 1025 ASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNGVIKKVKLYIATKRKLKVGDKMAGRHGNKGIV 1104 (2890)
T ss_pred hhhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCcCCCCcceEEEEEEEEeecccccchhhhccCCCeeE
Confidence 01 357999999999999999999999999999
Q ss_pred EeeecCCCCCCCCCCCCCcEEeCCCCCCCCCchhhHHhhhhhHhhhhcCCc-----------------------------
Q 001021 945 GMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKE----------------------------- 995 (1186)
Q Consensus 945 s~i~~~~dmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~g~~----------------------------- 995 (1186)
|+|||+|||||++||++||||+||||||||||||||+|+++||||+..|.+
T Consensus 1105 S~I~p~EDMPfl~dG~~pDIIlNPlGvPSRMnIGQilE~~LG~aa~~lg~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1184 (2890)
T PRK09603 1105 SNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGKQIASMLEDKTKDFAKELRAKMLEIANAINE 1184 (2890)
T ss_pred EEEEchhcCCCCCCCCCCcEEECCCCCCccccHHHHHHHHHHHHHHhcCcChhhhhhhcchhhhHHHHHHHHhhhccccc
Confidence 999999999999999999999999999999999999999999999988754
Q ss_pred ----------------------------cccCC-CCCccHHHHHHHHHHcCCCCCCeEEEeeCCCCceEEeeEeEeeeeh
Q 001021 996 ----------------------------GDATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYY 1046 (1186)
Q Consensus 996 ----------------------------~d~tp-F~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if~G~~yy 1046 (1186)
.++|| |++.+.+++.+.|+++||+++|++.||||+||++|+++||+|++||
T Consensus 1185 ~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~tpvF~g~~~~~i~~~l~~aG~~~~Gk~~LyDGrTGe~f~~~V~vG~~Yy 1264 (2890)
T PRK09603 1185 KDPLTIHALENCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRERVNVGYMYM 1264 (2890)
T ss_pred ccccccccccccchHHHHhhhhhhccCCcccCCCCCCCCHHHHHHHHHHcCCCCCCCEEEEcCCCCCCccceEEEEeece
Confidence 34788 9999999999999999999999999999999999999999999999
Q ss_pred hccccccCCceEEeccCCccccccCCCCcccCCCcceeeehhhhHHHhhccHHHHHHhhhcCCCcceeeeccccCcceee
Q 001021 1047 QRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIA 1126 (1186)
Q Consensus 1047 ~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~L~erL~~~SD~~~~~vC~~cG~~~~~ 1126 (1186)
|||+|||+||+||||+|||+.+||||++||+++|||||||||||||+|||||++|||||+.+||.+. |+..
T Consensus 1265 lKL~HmVdDKiHaRstGPyslvTqQPl~GKs~~GGqRfGEMEvwALeAyGAa~~LqE~Lt~kSDdv~-------gR~~-- 1335 (2890)
T PRK09603 1265 IKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDIR-------GREN-- 1335 (2890)
T ss_pred eechhhccchhhhccCCCcchhhhCCCcccccCCCceeeeeeHHHHHHhhHHHHHHHHHhcCCcchh-------hhhh--
Confidence 9999999999999999999999999999999999999999999999999999999999999999654 4332
Q ss_pred ccccCceeeccCCCCCCceeecccHhhHHHHHHHHhCCCceEEEeccC
Q 001021 1127 NLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKED 1174 (1186)
Q Consensus 1127 ~~~~~~~~C~~C~~~~~i~~v~iPy~~k~l~~EL~sm~i~~~l~~~~~ 1174 (1186)
.|..|.++.++..+.+|||||+|++||+||||++++...+.
T Consensus 1336 -------~y~~i~~g~~i~~~~iPeSFkvL~~EL~sL~l~i~~~~~~~ 1376 (2890)
T PRK09603 1336 -------AYRAIAKGEQVGESEIPETFYVLTKELQSLALDINIFGDDV 1376 (2890)
T ss_pred -------hhhhhcCCCcccccCCCHHHHHHHHHHHhCCcceEEEeecc
Confidence 35667778899999999999999999999999999987654
No 12
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=100.00 E-value=2.5e-183 Score=1748.31 Aligned_cols=943 Identities=26% Similarity=0.389 Sum_probs=767.0
Q ss_pred hhhhhh-hhcccCccchHHHHHHHHHHHHH-----hhHHHHHhhcCCeeeCCCCCCCCCeEEEEeeEEEeCCcccCCCCc
Q 001021 26 EDAWAV-ISAYFEEKGLVRQQLDSFDEFIQ-----NTMQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPMMTESDGE 99 (1186)
Q Consensus 26 ~~~~~~-i~~~f~~~~Lv~~hi~SFN~Fl~-----~gL~~ii~~~~pI~~~~~~~~~~~~~l~f~~i~i~~P~~~~~~~~ 99 (1186)
..+|+. .+..++.|+|++.|.+||+||++ +||++++++++||+. +++++.|+|.++++++|.+
T Consensus 16 R~~f~~~~~~~~~~PdL~~iQ~~Sf~~Fl~~~~~~~GL~~~f~~ifPI~d-----~~g~~~lefv~y~l~~Pk~------ 84 (2836)
T PRK14844 16 RVSYSRSIDLKDSLLDLVKVQKESYDSFTPKNKGNERLEVIFHTIFPIND-----PLHRATIEFISCRVDDPKY------ 84 (2836)
T ss_pred eeecccCCcccCCCCCHHHHHHHHHHHHhcCCCccccHHHHHHhcCCeEC-----CCCCEEEEEEEEEeCCCCC------
Confidence 345665 44558999999999999999997 699999999999974 3467999999999999988
Q ss_pred cCCCChHHHHhcCCCcceeEEEEEEEEEeccC---------CCC------cccccceeeEEEEecccceeeccCCccCCC
Q 001021 100 TATLFPKAARLRNLTYSAPLYVDVTKRVIKKG---------HDG------EEVTETQDFTKVFIGKVPIMLRSSYCTLYQ 164 (1186)
Q Consensus 100 ~~~l~P~EcR~r~lTYsa~l~v~v~~~~~~~~---------~~~------~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~ 164 (1186)
++.||++|++||+|||+|+++++..+.+ .+. ...++.+++++|++|+||+|+.
T Consensus 85 ----~~~Ec~~r~~TYsapl~v~~rL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ikeq~VylGdiPLMT~-------- 152 (2836)
T PRK14844 85 ----DESECIKRGITFSAQVIASIRLVIMQDGISLDEYKSIKESGDHSKLATVIKSIEEQEVHFCELPMMTD-------- 152 (2836)
T ss_pred ----CHHHHHhcCCcceeeEEEEEEEEEeccccccccccccccccccccccccccceeeeeEEEecCCccCC--------
Confidence 4689999999999999999999863200 000 1123456788999999999997
Q ss_pred CChhhhhhcCCCCCCCCceEEEcCeeeEEEeeeeeccCeEEEEEec---CCCcceEEEEEEEeecCCCCCCceEEEEEEe
Q 001021 165 NSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFKKR---QPNKYAYVAEVRSMAESQNRPPSTMFVRMLS 241 (1186)
Q Consensus 165 ~s~~eli~~gE~~~D~GGYFIING~ERVIi~Qe~~s~N~~~~~~~~---~~~~~~~~~~irs~~~~g~~~~~~~~v~~~~ 241 (1186)
.|+|||||+|||||+|++|||+.+|..... ..++..|+|+| +|.+|+|...+++
T Consensus 153 ----------------~GTFIING~ERVIVSQL~RSPGVyF~~~~~kt~~sgk~lysa~I--IP~RGsWLefE~D----- 209 (2836)
T PRK14844 153 ----------------KGTFIINGVEKVIVSQMHRSPGVFFDSDKGKTYNSGKLIYSARV--IPYRGSWLDIEFD----- 209 (2836)
T ss_pred ----------------CeEEEEcCcceEEEEcceeCCeEEEEcccCcccCCCceeEEEEE--ecCCcceEEEEEc-----
Confidence 999999999999999999999988865432 23455688887 8899999765542
Q ss_pred cCCCCCCCCCcEEEEEeccccccchHHHHHHHhcCCCHHHHHHHhcccc----Cch---------h--------------
Q 001021 242 RTSAKGGSSGQYIRATLPYIRTEIPIIIVFRALGFVADKDILEHICYDF----QDT---------Q-------------- 294 (1186)
Q Consensus 242 ~~~~~~~~~~~~i~v~i~~~~~~IPl~ilLkALG~~sD~eI~~~i~~~~----~~~---------~-------------- 294 (1186)
.++.+|+|+++ ++++|+++||||||+ |++||++.+.... .+. .
T Consensus 210 --------~kd~lyvRIDR-kRKiPiT~LLrALGl-s~edIL~~F~~~~~~~~~d~~~~~~~~~e~l~g~~~~~Di~d~~ 279 (2836)
T PRK14844 210 --------VKDHLYFRIDR-KRKLPISVLLKALGL-SNNDILDRFYEKIKYIKHKDGWKVPFVPDKFKGVRLPFDLMDVE 279 (2836)
T ss_pred --------CCCeEEEEecC-CeeeeHHHHHHHhCC-ChHHHHHhhcCceEEEEccCceeeccCHHHHhCCccceeeeccC
Confidence 25689999998 679999999999999 6899999773210 000 0
Q ss_pred ------------------------------------------hHh-----------------------------------
Q 001021 295 ------------------------------------------MME----------------------------------- 297 (1186)
Q Consensus 295 ------------------------------------------~~~----------------------------------- 297 (1186)
+.+
T Consensus 280 g~vlvdkgrrit~~~~krlk~~gvkkl~i~~~~l~g~~LaeDIVD~eTGEiL~eagteIT~e~ik~l~~~gi~~i~~l~~ 359 (2836)
T PRK14844 280 GNVLLKANVRITSRLAKKLYDNELKEYLVPFDSICGLFLAEDLIDSASSTKILSAGESIKLEDIKKLELLSIDEISVLNI 359 (2836)
T ss_pred CCEEEecCccccHHHHHHHHHcccCcccCchHhhcCceehhhhcCCCCCeEEEcCCCccCHHHHHHHHHcCCCceeeEee
Confidence 000
Q ss_pred -------hhHhhHhhhhccccHHHHHHHHhhcCcccCCCchhhHHHHHHHHhhcccC-------CCCCCC----------
Q 001021 298 -------LLRPSLEEAFVIQNQQVALDYIGKRGATVGVTRDKRIKYAKEILQKEMLP-------HVGTGD---------- 353 (1186)
Q Consensus 298 -------~l~~~l~e~~~i~t~~~al~yIg~r~~~~~~~~~~~~e~~~~iL~~~ll~-------Hl~~~~---------- 353 (1186)
.+...+. .....++++|+..|+++++. ......+.|+.++.+.+|- .+|...
T Consensus 360 d~~~~~~~i~~tL~-~D~~~~~e~Al~eIy~~lRp---ge~~~~e~a~~l~~~~ff~~~~YdLg~vGR~k~N~kl~~~~~ 435 (2836)
T PRK14844 360 DNLSVGPYILNTLF-LDENMSYQDALYEIYKVLRP---GEVPVLEIVEEFFRNLFFSPEYYDLSNIGRLKLNSYLGLNYD 435 (2836)
T ss_pred cccccchHHHHHHh-hcccccHHHHHHHHHHhcCC---CCCCcHHHHHHHHHHHhcCccccccccchhhhhhhhhccCCC
Confidence 0000000 00124678999999998864 2333445577777665533 122110
Q ss_pred --ccchhHHHHHHHHHHHHHHhccCCcCCCCCcccccceeccCchhhHHHHHHHHHHHHHHHHHHHhhhhcCCCccchhh
Q 001021 354 --FCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQF 431 (1186)
Q Consensus 354 --~~~~~K~~~L~~Mv~kLl~l~~g~~~~DD~D~l~NkRv~l~G~Ll~~lfr~~l~~~~k~ik~~l~k~~~~~~~~~~~~ 431 (1186)
.....+.++| .++++|+.+..|....||+|||+||||+++|+||+++|+.+|.++.+.+++++... +.+.+++..
T Consensus 436 ~~~~~l~~~Dii-~~i~~Li~l~~g~~~~DDiDhL~NRRvr~vGeLl~~qfr~gl~r~~~~i~e~~~~~--~~~~~~p~~ 512 (2836)
T PRK14844 436 EDLTVLTHEDII-EIVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSMSTS--SLDKVSPSD 512 (2836)
T ss_pred CCCcEecHHHHH-HHHHHHHHHhcCCCcccchhhhhccccchHHHHHHHHHHHHHHHHHHHHHHHHhhc--cccccchhh
Confidence 0112344555 79999999999999999999999999999999999999999999999999998632 335678999
Q ss_pred hccccchhhhhhhhcccCccccccccccccceeeeccccChhhhhccccccCC--C--CCcCCCcCcccccCCCCccccc
Q 001021 432 AIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS--P--IGREGKLAKPRQLHNSQWGMMC 507 (1186)
Q Consensus 432 ~i~~~~It~~i~~~~sTGNw~~~~~~~~~sGvsq~l~r~N~l~~lSh~Rrv~~--~--~~~~~K~t~vR~Lhps~wG~iC 507 (1186)
+++++.++..+++||+| +|+||+|||+||||+|||+||+++ | +.++++.+++|++||||||+||
T Consensus 513 lin~~~l~~~i~~ff~s------------s~LSQfmDQtNpLseltHkRRlsaLGPGGL~r~~a~fevRdvH~shyGRiC 580 (2836)
T PRK14844 513 FINPKVLTNVLRDFFNS------------SQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRIC 580 (2836)
T ss_pred cccchhHHHHHHHHhcc------------cchhhhccCcChhhhhhhcceecccCCCCcccccCCCcccccCcccccccc
Confidence 99999999999999975 799999999999999999999997 5 4588899999999999999999
Q ss_pred cCCCCCCcccccccccceeEEEcc-CCCchhHHHHHHHhCCccccccCCCCCCCceEEEECCEEEEEEcChHHHHHHHHh
Q 001021 508 PAETPEGQACGLVKNLALMVYITV-GSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKTLRR 586 (1186)
Q Consensus 508 PveTPEG~~cGLvk~LA~~a~Is~-~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~l~~~lr~ 586 (1186)
|+|||||+|||||++||.+|+|+. |+.+.
T Consensus 581 PIETPEG~NiGLI~SLA~yarIn~~Gfiet-------------------------------------------------- 610 (2836)
T PRK14844 581 PIETPEGQNIGLINSLAIYARINKYGFIES-------------------------------------------------- 610 (2836)
T ss_pred CCCCCCCCcccchhhhhhheeccCCceEeC--------------------------------------------------
Confidence 999999999999999999999987 33332
Q ss_pred hhhcCCCCCceEEEEeccCCeEEEEeCCCceeeeEEEEecccchhhHHHHHHHhcCCCCCCCCccccccCCcEEEecccc
Q 001021 587 LRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRESPEDGGWHDLVAKGFIEYIDTEE 666 (1186)
Q Consensus 587 ~rr~~~i~~~vsi~~~~~~~~i~I~td~gRl~RPl~~v~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~g~iE~i~~~E 666 (1186)
|++.|.+|+. +..++|++|.|
T Consensus 611 ---------------------------------Py~kV~~g~v--------------------------~~~i~ylsa~~ 631 (2836)
T PRK14844 611 ---------------------------------PYRKVVNRVV--------------------------TDQIEYLSAID 631 (2836)
T ss_pred ---------------------------------CcEEEEcCcC--------------------------cccccccChHH
Confidence 2233333220 02368999999
Q ss_pred ccceeeeecccccccccCCCCc------------cccccceeeecCCCccccccccccCCCCCCCCccchhhhhcccccc
Q 001021 667 EETTMISMTINDLVQARLHPEE------------AYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAM 734 (1186)
Q Consensus 667 e~~~~Ia~~~~~~~~~~~~~k~------------~~~~~~th~Ei~p~~ilsv~AslIPF~~HNqSpRn~yqc~M~KQai 734 (1186)
|+...||.....+...+.+.+. ..+.+.++++++|.+++||+||||||.+||||+|++||||||||||
T Consensus 632 E~~~~Ia~a~~~~~~~~~~~~~~v~~R~~~ef~~~~~~~v~~~dvsp~Q~~SvaasLIPFLEhdDAnRALMGSNMQRQAV 711 (2836)
T PRK14844 632 EGLYYIADTSAKLDENNCFVDDMLYCRYAGSFVMVSSDQVSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAV 711 (2836)
T ss_pred hcCcEEEeCCccCCCCCcccCCeEEEecCCceEEecHHHceEEEeCcchhhhhHhhcCCccccCcccccccccccccccc
Confidence 9999999877665543221000 0134568999999999999999999999999999999999999999
Q ss_pred ccccc-----------------------------------ceEEeeccc---------ceee----------ccCCccee
Q 001021 735 GIYVT-----------------------------------NYQFRMDTL---------AYVL----------YYPQKPLV 760 (1186)
Q Consensus 735 g~~~~-----------------------------------n~~~r~D~~---------~~~L----------~ypQ~PlV 760 (1186)
|+... .+.+|.+.. .|.| |+.|||+|
T Consensus 712 PLl~~e~PiVGTG~E~~vA~DSg~~v~A~~~G~V~yVda~kIvI~~~~~~~~~~~~~~~Y~L~ky~RSNQ~TcinQrPiV 791 (2836)
T PRK14844 712 PLLKPTAPLVATGMESFVASGSGAVVLAKRDGIVDSSDSNSIVIRAFDKERVNYLDVDIYHLRKFQRSNHNTCINQKPLV 791 (2836)
T ss_pred ccccCCCCeEecCcchhhhhcccceEEeccCceEEEEcCCEEEEEeCCCccccccccceEEeccccccccceeeeeccee
Confidence 98522 122333221 2554 67999999
Q ss_pred eccc----ccc------cccccCCCCceeEEEEEecCCCCCCCcEEeeccccccCceEEEEEEEEEeeecccCCcceeee
Q 001021 761 TTRA----MEH------LHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDF 830 (1186)
Q Consensus 761 ~t~~----~~~------~~~~~~p~G~N~~VAv~sy~GYn~EDaiiink~sv~rG~~~s~~~~~~~~~~~~~~~~~~e~~ 830 (1186)
+.+. .+. +..+|+++|+|++||||||.|||+||||+||++.+.+++|||+|+..|+++.+.+.. ..|++
T Consensus 792 ~~Gd~V~kGdilADG~st~~GELALG~NvlVAfmpW~GYNfEDAIliSErlv~eD~fTSiHIee~ei~~r~Tk~-G~EeI 870 (2836)
T PRK14844 792 CVGDYVKEGDVIADGPAINSGELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTSIHIEEFECVVHDTPL-GSEKI 870 (2836)
T ss_pred cCCCEeccCCEeccChhhcccccccccceEEEEeccCCcccccccccchhhccCceeEEEeecceEEEEEeccC-CCcee
Confidence 8752 233 378999999999999999999999999999999999999999999999999988754 35666
Q ss_pred c--CCCCCCCCCCCCCCcCCCCCCCccCCCcEEcCCCEEEEEeCCCCccccc---------cccCccccceeeEEeecCC
Q 001021 831 G--RPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ---------GQASRYTRRDHSISLRHSE 899 (1186)
Q Consensus 831 ~--~p~~~~~~~~~~~~~~~ld~dGi~~~g~~v~~gd~l~~k~~p~~~~~~~---------~~~~~~~~~~~s~~~~~~~ 899 (1186)
. +|+.+ ....++||++||+++|++|++|||||||++|+...+.. .+++....+|+|++++++.
T Consensus 871 TrdIPnv~------e~~lr~LDe~GIV~iGa~V~~GDILVGKvtPk~e~~~tPEekLL~aIFGek~~~vkdtSLrvp~G~ 944 (2836)
T PRK14844 871 TRAIPGVN------EENLYHLDDSGIVKIGTRVGPGYILVGKVTPKPSLSLPPETKLLMTIFGEKSFDCADSSLYTSPDV 944 (2836)
T ss_pred cccCCCCC------hHHHhcCCCCCCeecCCEECCCCEEEEeecCCCCCCCCHHHHHHHHHhCCcccccccCceecCCCC
Confidence 4 66542 23478999999999999999999999999998743321 2356778999999999999
Q ss_pred CcEEEEEEEEecC-------------------------------------------------------------------
Q 001021 900 TGMVDQVLLTTNA------------------------------------------------------------------- 912 (1186)
Q Consensus 900 ~g~v~~v~~~~~~------------------------------------------------------------------- 912 (1186)
.|+|.+|.+++..
T Consensus 945 ~G~Vidv~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1024 (2836)
T PRK14844 945 EGTVIDVQVFTRRGVEENERALLIKQKEINDFEKERDYIINVTSEYFYDELKKLLINSGSQDREKFDSIEREQWWGIGLK 1024 (2836)
T ss_pred CEEEEEEEEEcccccccchhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhcccccccHHHHhhccHHhhhhcccC
Confidence 9999999887642
Q ss_pred ----------------------------------CC-------ceEEEEEEEeecCCCCcccccccCCCccEEEeeecCC
Q 001021 913 ----------------------------------DG-------LRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQE 951 (1186)
Q Consensus 913 ----------------------------------~~-------~~~vkv~~r~~R~p~iGDKfssRhGqKGvvs~i~~~~ 951 (1186)
.| .+.|||.+++.|.+++|||+|||||||||||.|+|.|
T Consensus 1025 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~gdeL~~gv~~~VkVyia~KRkiqvGDKmAGRHGNKGVIS~IlP~e 1104 (2836)
T PRK14844 1025 NQSISEQVKSLKKDFDEKVSHAIAQFKRKVEKLHEGYDLPQGVSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVE 1104 (2836)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCCCCceEEEEEEEEeecCCccccccccCCCCceEeEEcccC
Confidence 11 2579999999999999999999999999999999999
Q ss_pred CCCCCCCCCCCcEEeCCCCCCCCCchhhHHhhhhhHhhhhcCCc------------------------------------
Q 001021 952 DMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKE------------------------------------ 995 (1186)
Q Consensus 952 dmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~g~~------------------------------------ 995 (1186)
||||++||+++|||+||+|+||||||||++|+++|+||..+|..
T Consensus 1105 DMPyL~DGtpvDIvLNPLGVPSRMNvGQilE~hLG~A~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1184 (2836)
T PRK14844 1105 DMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGWACKKLGEKVGNILDEINKIKSAFCKGIRSLNDDNFTKFAAAYLD 1184 (2836)
T ss_pred CCCcCCCCCCceEEeCCCCCCccccHHHHHHHHHHHHHhhhhhhhHhhhhhhhccccccccccccccccccccccccccc
Confidence 99999999999999999999999999999999999999887521
Q ss_pred --------------------------------------------------------------------------------
Q 001021 996 -------------------------------------------------------------------------------- 995 (1186)
Q Consensus 996 -------------------------------------------------------------------------------- 995 (1186)
T Consensus 1185 ~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1264 (2836)
T PRK14844 1185 NKKIENIDDDEITASVLNTPNKNALNDELNELVENYLNSCKSAYSNLRNFLIEVYSCGSNVSICNNIRDISDNNLIEFAR 1264 (2836)
T ss_pred cccccccccccccccccccccccccccccccchhccccccchhhHHHHHHHHHhhhcccccccccccccccHHHHHHHHh
Confidence
Q ss_pred ------cccCC-CCCccHHHHHHHHHHcCCCCCCeEEEeeCCCCceEEeeEeEeeeehhccccccCCceEEeccCCcccc
Q 001021 996 ------GDATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQIL 1068 (1186)
Q Consensus 996 ------~d~tp-F~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~l 1068 (1186)
.-+|| |++.+.+++.+.|+++||+++|++.||||+||++|+++||+|++|||||+|||+||+|||++|||+.|
T Consensus 1265 ~~~~g~~~~tpvf~g~~~~~i~~~L~~~g~~~~Gk~~l~dG~TGe~f~~~v~vG~~yy~kL~HmV~DKihaRs~Gp~s~l 1344 (2836)
T PRK14844 1265 KLRDGIPVAAPVFEGPKDEQIAKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLV 1344 (2836)
T ss_pred hhccCCeecCCCcCCCCHHHHHHHHHHhCcCCCCCEEEEcCCCCCccchhheeCcchhhhhhhhhcchhhhcccCCCccc
Confidence 01556 88889999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCcccCCCcceeeehhhhHHHhhccHHHHHHhhhcCCCcceeeeccccCcceeeccccCceeeccCCCCCCceeec
Q 001021 1069 TRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVH 1148 (1186)
Q Consensus 1069 T~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~L~erL~~~SD~~~~~vC~~cG~~~~~~~~~~~~~C~~C~~~~~i~~v~ 1148 (1186)
||||++||+|+|||||||||||||+|||||++|||||+.+||.+. |+.+. +|..|+. .+..+..
T Consensus 1345 T~QPl~Gr~~~GG~RfGEME~~al~a~Gaa~~L~E~Lt~kSD~~~-------gr~~~--------~~~ivkG-~~~~~~~ 1408 (2836)
T PRK14844 1345 TQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDIN-------GRVKI--------YESIIKG-DSNFECG 1408 (2836)
T ss_pred ccCCCcccccCCCceeecchHHHHHHHhHHHHHHHHhcccccchh-------hhhHh--------hhhhccC-CCCCcCC
Confidence 999999999999999999999999999999999999999999766 44442 2333332 2344558
Q ss_pred ccHhhHHHHHHHHhCCCceEEEeccCC
Q 001021 1149 IPYACKLLFQELMAMAIAPRMLTKEDT 1175 (1186)
Q Consensus 1149 iPy~~k~l~~EL~sm~i~~~l~~~~~~ 1175 (1186)
+|||||+|+|||+||||++++.+++.-
T Consensus 1409 ~PesfkvL~~EL~sl~i~~~~~~~~~~ 1435 (2836)
T PRK14844 1409 IPESFNVMIKELRSLCLNVDLKQNDVV 1435 (2836)
T ss_pred CCchHHHHHHHHHhCccceEEeccchh
Confidence 999999999999999999999886543
No 13
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated
Probab=100.00 E-value=1.7e-184 Score=1649.36 Aligned_cols=597 Identities=48% Similarity=0.810 Sum_probs=562.1
Q ss_pred ceEEEECCEEEEEEcChHHHHHHHHhhhhcCCCCCceEEEEeccCCeEEEEeCCCceeeeEEEEecccchhhHHHHHHHh
Q 001021 561 ATKIFVNGCWVGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQ 640 (1186)
Q Consensus 561 ~~~V~lnG~~iG~~~~~~~l~~~lr~~rr~~~i~~~vsi~~~~~~~~i~I~td~gRl~RPl~~v~~~~~~~~~~~~~~l~ 640 (1186)
.++|||||+|+|++++|..|++.||.+||.|.|+.++||++++..++|+||||+||++|||++|++|++.++++|+++++
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 47999999999999999999999999999999999999999998899999999999999999999999999999999997
Q ss_pred cCCCCCCCCccccccCCcEEEeccccccceeeeecccccccccCCCCccccccceeeecCCCccccccccccCCCCCCCC
Q 001021 641 QRESPEDGGWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQS 720 (1186)
Q Consensus 641 ~~~~~~~~~~~~l~~~g~iE~i~~~Ee~~~~Ia~~~~~~~~~~~~~k~~~~~~~th~Ei~p~~ilsv~AslIPF~~HNqS 720 (1186)
++.+ +|++|+++|+|||||++||++++||++++++.. .+||+||+|++||||+||+|||+|||||
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 6654 899999999999999999999999999988743 4799999999999999999999999999
Q ss_pred ccchhhhhcccccccccccceEEeecccceeeccCCcceeecccccccccccCCCCceeEEEEEecCCCCCCCcEEeecc
Q 001021 721 PRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQS 800 (1186)
Q Consensus 721 pRn~yqc~M~KQaig~~~~n~~~r~D~~~~~L~ypQ~PlV~t~~~~~~~~~~~p~G~N~~VAv~sy~GYn~EDaiiink~ 800 (1186)
|||||||||+|||||++++|+.+|.|++.|+|+|||+|||+|+.++.++++++|+|+||+||||||+||||||||||||+
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 ccccCceEEEEEEEEEeeecccCCcceeeecCCCCCCCCCCCC-CCcCCCCCCCccCCCcEEcCCCEEEEEeCCCCcc-c
Q 001021 801 SIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRH-GSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQD-E 878 (1186)
Q Consensus 801 sv~rG~~~s~~~~~~~~~~~~~~~~~~e~~~~p~~~~~~~~~~-~~~~~ld~dGi~~~g~~v~~gd~l~~k~~p~~~~-~ 878 (1186)
|+|||||||+|||+|+.+++++..+..+.|+.|+.. ..+.+. ..|++||+||||++|++|++|||||||++|.... +
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 999999999999999999887665666788888642 112222 3589999999999999999999999999996421 1
Q ss_pred c-ccccCccccceeeEEeecCCCcEEEEEEEEecCCCceEEEEEEEeecCCCCcccccccCCCccEEEeeecCCCCCCCC
Q 001021 879 A-QGQASRYTRRDHSISLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTV 957 (1186)
Q Consensus 879 ~-~~~~~~~~~~~~s~~~~~~~~g~v~~v~~~~~~~~~~~vkv~~r~~R~p~iGDKfssRhGqKGvvs~i~~~~dmPf~~ 957 (1186)
. .........+|+|++++.+|+|+||+|.++.+.+|.+.|||++|+.|+|+||||||||||||||||+|||+||||||+
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 001122347999999999999999999999888899999999999999999999999999999999999999999999
Q ss_pred CCCCCcEEeCCCCCCCCCchhhHHhhhhhHhhhhcCCccccCCCCCccHHHHHHHHHHcCCCCCCeEEEeeCCCCceEEe
Q 001021 958 EGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTA 1037 (1186)
Q Consensus 958 ~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tpF~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~ 1037 (1186)
+|++|||||||||||||||||||+|+++|||+++.|.+.|+|||.+..++++++.|+++||+++|+|+||||+||++|++
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 eEeEeeeehhccccccCCceEEeccCCccccccCCCCcccCCCcceeeehhhhHHHhhccHHHHHHhhhcCCCcceeeec
Q 001021 1038 MIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVC 1117 (1186)
Q Consensus 1038 ~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~L~erL~~~SD~~~~~vC 1117 (1186)
+||+|++|||||+|||.||+|||++||++.|||||++||||+|||||||||||||+|||||++|+|||+.+||.+.++||
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 cccCcceeeccccCceeeccCCCCCCceeecccHhhHHHHHHHHhCCCceEEEecc
Q 001021 1118 EHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKE 1173 (1186)
Q Consensus 1118 ~~cG~~~~~~~~~~~~~C~~C~~~~~i~~v~iPy~~k~l~~EL~sm~i~~~l~~~~ 1173 (1186)
.+||++++.+.+.+.++|+.|+++..|.++.||||||||+|||+||||++||.+++
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 99999998776666789999999999999999999999999999999999999874
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=2.3e-183 Score=1637.97 Aligned_cols=594 Identities=50% Similarity=0.844 Sum_probs=559.0
Q ss_pred EEECCEEEEEEcChHHHHHHHHhhhhcCCCCCceEEEEeccCCeEEEEeCCCceeeeEEEEecccchhhHHHHHHHhcCC
Q 001021 564 IFVNGCWVGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRE 643 (1186)
Q Consensus 564 V~lnG~~iG~~~~~~~l~~~lr~~rr~~~i~~~vsi~~~~~~~~i~I~td~gRl~RPl~~v~~~~~~~~~~~~~~l~~~~ 643 (1186)
|||||+|+|++++|..|++.||.+||+|.|+.++||++++..++|+||||+||++|||++|++|++.++++|+++++++.
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 79999999999999999999999999999999999999998999999999999999999999999999999999997654
Q ss_pred CCCCCCccccccCCcEEEeccccccceeeeecccccccccCCCCccccccceeeecCCCccccccccccCCCCCCCCccc
Q 001021 644 SPEDGGWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRN 723 (1186)
Q Consensus 644 ~~~~~~~~~l~~~g~iE~i~~~Ee~~~~Ia~~~~~~~~~~~~~k~~~~~~~th~Ei~p~~ilsv~AslIPF~~HNqSpRn 723 (1186)
+ +|++|+++|+|||||++||++++||+++.++.. .+||+||+|++||||+||+|||+||||||||
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 4 899999999999999999999999999998743 4799999999999999999999999999999
Q ss_pred hhhhhcccccccccccceEEeecccceeeccCCcceeecccccccccccCCCCceeEEEEEecCCCCCCCcEEeeccccc
Q 001021 724 TYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSID 803 (1186)
Q Consensus 724 ~yqc~M~KQaig~~~~n~~~r~D~~~~~L~ypQ~PlV~t~~~~~~~~~~~p~G~N~~VAv~sy~GYn~EDaiiink~sv~ 803 (1186)
||||||+|||||++++|++.|+||++|+|+|||+|||+|+.++.++++++|+|+||+||||||+||||||||||||+|+|
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 cCceEEEEEEEEEeeecccCCcceeeecCCCCCCCCCCCC-CCcCCCCCCCccCCCcEEcCCCEEEEEeCCCCcccc--c
Q 001021 804 RGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRH-GSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEA--Q 880 (1186)
Q Consensus 804 rG~~~s~~~~~~~~~~~~~~~~~~e~~~~p~~~~~~~~~~-~~~~~ld~dGi~~~g~~v~~gd~l~~k~~p~~~~~~--~ 880 (1186)
||||||+||++|+.++++...+..|.++.|+.. ..+.+. ..|++||+||||++|++|++|||||||++|....+. .
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 999999999999999887655556778887643 222222 358999999999999999999999999998652111 0
Q ss_pred cccCccccceeeEEeecCCCcEEEEEEEEecCCCceEEEEEEEeecCCCCcccccccCCCccEEEeeecCCCCCCCCCCC
Q 001021 881 GQASRYTRRDHSISLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGI 960 (1186)
Q Consensus 881 ~~~~~~~~~~~s~~~~~~~~g~v~~v~~~~~~~~~~~vkv~~r~~R~p~iGDKfssRhGqKGvvs~i~~~~dmPf~~~G~ 960 (1186)
...+....+|+|++++.+|+|+||+|.++.+.++.+.|||++|+.|+|+||||||||||||||||+|||+||||||++|+
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 01122347999999999999999999999988899999999999999999999999999999999999999999999999
Q ss_pred CCcEEeCCCCCCCCCchhhHHhhhhhHhhhhcCCccccCCCCCccHHHHHHHHHHcCCCCCCeEEEeeCCCCceEEeeEe
Q 001021 961 TPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIF 1040 (1186)
Q Consensus 961 ~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tpF~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if 1040 (1186)
+|||||||||||||||||||+|+++|||+++.|.+.|+|||++..++++++.|+++||+++|+|+||||+||++|+++||
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 EeeeehhccccccCCceEEeccCCccccccCCCCcccCCCcceeeehhhhHHHhhccHHHHHHhhhcCCCcceeeecccc
Q 001021 1041 LGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHC 1120 (1186)
Q Consensus 1041 ~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~L~erL~~~SD~~~~~vC~~c 1120 (1186)
+|++|||||+|||+||+|||++||++.|||||++||||+|||||||||||||+|||||++|+|||+++||.+.++||.+|
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 CcceeeccccCceeeccCCCCCCceeecccHhhHHHHHHHHhCCCceEEEecc
Q 001021 1121 GLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKE 1173 (1186)
Q Consensus 1121 G~~~~~~~~~~~~~C~~C~~~~~i~~v~iPy~~k~l~~EL~sm~i~~~l~~~~ 1173 (1186)
|++++.+.+.+.+.|+.|+++.+|.++.+|||||||+|||+||||++||.+++
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 99997766667789999999989999999999999999999999999999874
No 15
>PF00562 RNA_pol_Rpb2_6: RNA polymerase Rpb2, domain 6; InterPro: IPR007120 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerases (2.7.7.6 from EC) catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain represents the hybrid-binding domain and the wall domain []. The hybrid-binding domain binds the nascent RNA strand/template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion []. This domain is also involved in binding to Rpb1 and Rpb3 []. Many of the bacterial members contain large insertions within this domain, which are known as dispensable region 2 (DRII).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2Y0S_R 3HKZ_B 2PMZ_R 3H0G_B 3S17_B 1I6H_B 4A3B_B 3K1F_B 4A3I_B 1TWA_B ....
Probab=100.00 E-value=6.5e-110 Score=970.05 Aligned_cols=364 Identities=52% Similarity=0.838 Sum_probs=314.6
Q ss_pred cccccccCCCCCCCCccchhhhhcccccccccccceEEeecccceeeccCCcceeecc-cccccc---------cccCCC
Q 001021 706 GVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTR-AMEHLH---------FRQLPA 775 (1186)
Q Consensus 706 sv~AslIPF~~HNqSpRn~yqc~M~KQaig~~~~n~~~r~D~~~~~L~ypQ~PlV~t~-~~~~~~---------~~~~p~ 775 (1186)
||+|++|||++|||||||+|||||+|||||+|.+|+..|+|+.. +|||+|||+|+ ..+..+ ++|+|+
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 CceeEEEEEecCCCCCCCcEEeeccccccCceEEEEEEEEEeeecccCCcceeeec-CCCCCCCCCCCCCCcCCCCCCCc
Q 001021 776 GINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFG-RPDRSNTMGMRHGSYDKLDDDGL 854 (1186)
Q Consensus 776 G~N~~VAv~sy~GYn~EDaiiink~sv~rG~~~s~~~~~~~~~~~~~~~~~~e~~~-~p~~~~~~~~~~~~~~~ld~dGi 854 (1186)
|+|++||||||+||||||||||||+|++||+|||+||++ +++++....+..+.+. .+... +...|++||+|||
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 7777655455545543 33221 3457999999999
Q ss_pred cCCCcEEcCCCEEEEEeC-CCCcc---ccccccCccccceeeEEeecCCCcEEEEEEE-------EecCCCceEEEEEEE
Q 001021 855 APPGTRVSGEDVIIGKTT-PISQD---EAQGQASRYTRRDHSISLRHSETGMVDQVLL-------TTNADGLRFVKVRVR 923 (1186)
Q Consensus 855 ~~~g~~v~~gd~l~~k~~-p~~~~---~~~~~~~~~~~~~~s~~~~~~~~g~v~~v~~-------~~~~~~~~~vkv~~r 923 (1186)
|++|++|++||+||||++ |.... .....++....+|+|++++.++.|+||+|.+ ..+.++...|+|++|
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 22210 0011222334799999999999999999999 667788999999999
Q ss_pred eecCCCCcccccccCCCccEEEeeecCCCCCCCCCCCCCcEEeCCCCCCCCCchhhHHhhhhhHhhhhcCCccccCCCCC
Q 001021 924 SVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTD 1003 (1186)
Q Consensus 924 ~~R~p~iGDKfssRhGqKGvvs~i~~~~dmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tpF~~ 1003 (1186)
+.|+|+||||||||||||||||+|||+||||||++|++|||||||||||||||||||+|+++||++++.|.+.|+|||++
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 ccHHHHHHHHHHcCCCCCCeEEEeeCCCCceEEeeEeEeeeehhccccccCCceEEeccCCccccccCCCCcccC
Q 001021 1004 VTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSR 1078 (1186)
Q Consensus 1004 ~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~ 1078 (1186)
.+.+++++.|.++||+++|+|.||||+||++++++||+|++|||||+|||+||+|||++||++.|||||++||+|
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 16
>PRK09606 DNA-directed RNA polymerase subunit B''; Validated
Probab=100.00 E-value=5.5e-107 Score=974.90 Aligned_cols=491 Identities=40% Similarity=0.697 Sum_probs=433.2
Q ss_pred hhhhhhhhhcccCccchHHHHHHHHHHHHHhhHHHHHhhcCCeeeCCCCCCCCCeEEEEeeEEEeCCcccCCCCccCCCC
Q 001021 25 QEDAWAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPMMTESDGETATLF 104 (1186)
Q Consensus 25 ~~~~~~~i~~~f~~~~Lv~~hi~SFN~Fl~~gL~~ii~~~~pI~~~~~~~~~~~~~l~f~~i~i~~P~~~~~~~~~~~l~ 104 (1186)
.+|+|.++++||+.++|++|||+|||+|+++||++++++.+||++..+ +.+.++|+++++++|++.+.++...+|+
T Consensus 2 ~~~~~~~i~~~~~~~~lv~~qi~SFn~Fi~~gl~~ii~~~~~i~~~~~----~~~~l~~~~~~l~~P~~~~~~~~~~~l~ 77 (494)
T PRK09606 2 MEDRRVLSDAYFKEHRLVRHHIDSYNDFVDNGLQKIIDEQGPIETEIE----DGVYVELGKIRVGKPVVKEADGSEREIY 77 (494)
T ss_pred chHHHHHHHHHHCCCChHHHHHHHHHHHHHHhHHHHHHhcCCEEEecC----CcEEEEEEEEEECCCcccccCCccccCC
Confidence 367999999999999999999999999999999999999999987643 3468999999999999877666678899
Q ss_pred hHHHHhcCCCcceeEEEEEEEEEeccCCCCcccccceeeEEEEecccceeeccCCccCCCCChhhhhhcCCCCCCCCceE
Q 001021 105 PKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYF 184 (1186)
Q Consensus 105 P~EcR~r~lTYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~eli~~gE~~~D~GGYF 184 (1186)
|+|||+|++||+|+++|+|.++.++.. ...+++++|+|||||+|++|||+|++|+||++.||||+|+||||
T Consensus 78 P~eaR~r~~TYs~~l~v~i~~~~~~~~---------~~~~~v~iG~iPiMv~S~~C~L~~~~~~~l~~~~E~~~d~GGyF 148 (494)
T PRK09606 78 PMEARLRNLTYSAPLYLEMSPVEGGEE---------EEPEEVYIGELPVMVGSKICNLYGLSEEELIEVGEDPLDPGGYF 148 (494)
T ss_pred HHHHHhcCCCccceEEEEEEEEECCCc---------eEEeeEEeccCCeEeccCcccCCCCCHHHHHhcCCCcCCCCCeE
Confidence 999999999999999999999754321 14568999999999999999999999999999999999999999
Q ss_pred EEcCeeeEEEeeeeeccCeEEEEEecCCCcceEEEEEEEeecCCCCCCceEEEEEEecCCCCCCCCCcEEEEEecccccc
Q 001021 185 IINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPYIRTE 264 (1186)
Q Consensus 185 IING~ERVIi~Qe~~s~N~~~~~~~~~~~~~~~~~~irs~~~~g~~~~~~~~v~~~~~~~~~~~~~~~~i~v~i~~~~~~ 264 (1186)
||||+||||++|++++||++++++++..++..|.|.++| ..|+|. ..+.+++.. ++.+++++++.+.+
T Consensus 149 IING~ErVi~~q~~~~~n~~~~~~~~~~~~~~~~~~i~s--~~~~~~-~~~~l~~~~---------~g~i~~~~~~~~~~ 216 (494)
T PRK09606 149 IVNGSERVLMTLEDLAPNKILVEKDERYGDRIEVAKVFS--QRRGYR-ALVTVERNR---------DGLLEVSFPSVPGS 216 (494)
T ss_pred EECCCeEEEEEEEeccCCeeEEEeccCCCccceEEEEEc--ccccce-eeEEEEEec---------CCeEEEEEcCcccc
Confidence 999999999999999999999987654444458899976 444442 223344321 46899999986678
Q ss_pred chHHHHHHHhcCCCHHHHHHHhccccCchhhHhhhHhhHhhhhccccHHHHHHHHhhcCcccCCCchhhHHHHHHHHhhc
Q 001021 265 IPIIIVFRALGFVADKDILEHICYDFQDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGATVGVTRDKRIKYAKEILQKE 344 (1186)
Q Consensus 265 IPl~ilLkALG~~sD~eI~~~i~~~~~~~~~~~~l~~~l~e~~~i~t~~~al~yIg~r~~~~~~~~~~~~e~~~~iL~~~ 344 (1186)
||++++|||||.+||+||++.+. .+..+++.+..++++. .+.|+++|+.|||++++.. .++....+.|+++|+++
T Consensus 217 iPi~~llkALg~~sd~eI~~~i~---~~~~~~~~l~~~~~~~-~~~t~~~al~~ig~~~~~~-~~~~~~~~~~~~~l~~~ 291 (494)
T PRK09606 217 IPFVILMRALGLETDEEIVEAVS---DDPEIVKFMLENLEEA-EVDTQEEALEYIGKRVAPG-QTKEYRIKRAEYVIDRY 291 (494)
T ss_pred ccHHHHHHHcCCCCHHHHHHHhC---CcHHHHHHHHHHHHhc-ccCCHHHHHHHHHHhcCCC-CCcchHHHHHHHHHHHh
Confidence 99999999999999999999994 3444666677777654 3679999999999998652 23555678999999999
Q ss_pred ccCCCCCCCccchhHHHHHHHHHHHHHHhccCCcCCCCCcccccceeccCchhhHHHHHHHHHHHHHHHHHHHhhhhcCC
Q 001021 345 MLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNG 424 (1186)
Q Consensus 345 ll~Hl~~~~~~~~~K~~~L~~Mv~kLl~l~~g~~~~DD~D~l~NkRv~l~G~Ll~~lfr~~l~~~~k~ik~~l~k~~~~~ 424 (1186)
+|||+|.+..+..+|++||++|++||++++.|.+.+||+|||+||||+++|+||+.+||++|+++++.++..+++...+.
T Consensus 292 ~l~hig~~~~~~~~K~~~L~~m~~kLl~~~~g~~~~Dd~D~l~nkRv~~~G~Ll~~~fr~~l~~~~~~~k~~l~~~~~~~ 371 (494)
T PRK09606 292 LLPHLGVEPEVRRAKAHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERANMRN 371 (494)
T ss_pred hhcccCCCcchhhHHHHHHHHHHHHHHHHhcCCCCCCCcccccCceeeccchhHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 99999987656678999999999999999999999999999999999999999999999999999999998888766555
Q ss_pred CccchhhhccccchhhhhhhhcccCccccccccccccceeeeccccChhhhhccccccCCCCCcCCCcCcccccCCCCcc
Q 001021 425 KDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWG 504 (1186)
Q Consensus 425 ~~~~~~~~i~~~~It~~i~~~~sTGNw~~~~~~~~~sGvsq~l~r~N~l~~lSh~Rrv~~~~~~~~K~t~vR~Lhps~wG 504 (1186)
+.+++..+++++.||++|++|||||||.+ +++|+||+|||+||+|+||||||||+++.++++.++||+|||||||
T Consensus 372 ~~~~~~~~~~~~~It~~l~~~~~TGnw~~-----~~~glSq~ldr~N~la~lSh~Rrv~s~~~r~~~~~~vR~lhps~~G 446 (494)
T PRK09606 372 RELSIKTAVRSDVLTERLEHAMATGNWVG-----GRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQWG 446 (494)
T ss_pred CCCCHHHhcCchhhhHHHHHHhhcccccC-----CCceEEEEccCCCHHHHhhHHHhccCCccccCccccccccCcccce
Confidence 56788899999999999999999999996 3689999999999999999999999999999999999999999999
Q ss_pred ccccCCCCCCcccccccccceeEEEccCCCchhHHHHHHHhCCccc
Q 001021 505 MMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENF 550 (1186)
Q Consensus 505 ~iCPveTPEG~~cGLvk~LA~~a~Is~~~~~~~i~~~l~~~g~~~~ 550 (1186)
|+||||||||+|||||||||++|+|+++.+.+++.++|.++||.++
T Consensus 447 ~iCPveTPEG~~cGLv~~La~~a~V~~~~~~~~i~~~l~~lg~~~~ 492 (494)
T PRK09606 447 RICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKELGVEPE 492 (494)
T ss_pred ecccCcCCCCCcccHHHhhhceEEEeCCCChHHHHHHHHHCcCeeC
Confidence 9999999999999999999999999999888899999999999875
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=5.7e-44 Score=383.91 Aligned_cols=149 Identities=50% Similarity=0.806 Sum_probs=125.8
Q ss_pred chHHHHHHHHHHHHHhhHHHHHhhcCCeeeCCCCCCCCCeEEEEeeEEEeCCcccCCCCccCCCChHHHHhcCCCcceeE
Q 001021 40 GLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPMMTESDGETATLFPKAARLRNLTYSAPL 119 (1186)
Q Consensus 40 ~Lv~~hi~SFN~Fl~~gL~~ii~~~~pI~~~~~~~~~~~~~l~f~~i~i~~P~~~~~~~~~~~l~P~EcR~r~lTYsa~l 119 (1186)
||++|||+|||+|+++||++++++.+||.+... ...+.++|++++|++|++.+.++...+|||+|||+|++||+|++
T Consensus 1 ~Lv~~qi~SFn~Fl~~gl~~i~~~~~~i~~~~~---~~~~~l~~~~~~i~~P~~~~~~~~~~~l~P~ecR~r~~TYs~~l 77 (203)
T PF04563_consen 1 GLVKHQIDSFNYFLNNGLKEILKEFPPIEFESS---NNRISLKFENIRIGKPTYSESDGRERPLYPRECRLRGLTYSAPL 77 (203)
T ss_dssp TTTHHHHHHHHHHHCTSSHHHHSCSSSCEECCC---STTEEEEEEEEEEESESSEHTTSCEEE--HHHHHHTT-B-EEEE
T ss_pred CchHHHHHHHHHHHHCCCHHHhccCCceEecCC---cceEEEEeeEEEEeeeeeccccccccCCCHHHHHhcCCCCCCcc
Confidence 699999999999999999999999999998643 24689999999999999988667889999999999999999999
Q ss_pred EEEEEEEEeccCCCCcccccceeeEEEEecccceeeccCCccCCCCChhhhhhcCCCCCCCCceEEEcCeeeEEEeeeee
Q 001021 120 YVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKM 199 (1186)
Q Consensus 120 ~v~v~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~eli~~gE~~~D~GGYFIING~ERVIi~Qe~~ 199 (1186)
+|+|+++..+.. .....++.+|+|||||+|++|||++++++|+++.||||+|+||||||||+||||++|+++
T Consensus 78 ~v~i~~~~~~~~--------~~~~~~v~iG~iPiMv~S~~C~L~~~~~~~l~~~~E~~~d~GGYFIInG~EkVi~~q~~~ 149 (203)
T PF04563_consen 78 YVDIELTVNNKK--------EIKEQEVFIGKIPIMVRSKRCNLNGLSPKELVQLGECPNDPGGYFIINGSEKVIRMQIMR 149 (203)
T ss_dssp EEEEEEEESSTT--------EEEESEEEEEEEE-BTTTTTSGGGT--HHHHHHTTS-TT---SSEEETTEEEEE-EEEEE
T ss_pred ceEEEEEeeccc--------eEEeeEEEEeeCCeEeecceeeCCCCCHHHHHHcCCCCcCCCCEEEECCChhheehhhhh
Confidence 999999987651 246678999999999999999999999999999999999999999999999999999986
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=6.5e-31 Score=238.56 Aligned_cols=81 Identities=60% Similarity=1.029 Sum_probs=76.8
Q ss_pred CcceeeehhhhHHHhhccHHHHHHhhhcCCCcceeeeccccCcceeeccccCceeeccCCCCCCceeecccHhhHHHHHH
Q 001021 1080 GGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQE 1159 (1186)
Q Consensus 1080 GG~R~GEMErd~l~a~Gas~~L~erL~~~SD~~~~~vC~~cG~~~~~~~~~~~~~C~~C~~~~~i~~v~iPy~~k~l~~E 1159 (1186)
|||||||||||||+|||||++|+|||+++||++.++||.+||++++ .|+.+.++.++.+|||||||+||
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 46777889999999999999999
Q ss_pred HHhCCCceEEEe
Q 001021 1160 LMAMAIAPRMLT 1171 (1186)
Q Consensus 1160 L~sm~i~~~l~~ 1171 (1186)
|+||||++++.+
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=2.8e-26 Score=202.13 Aligned_cols=66 Identities=62% Similarity=1.007 Sum_probs=59.7
Q ss_pred eeccccChhhhhccccccC--CCCCcCCCcCcccccCCCCccccccCCCCCCcccccccccceeEEEc
Q 001021 465 QVLNRLTYASTLSHLRRLN--SPIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYIT 530 (1186)
Q Consensus 465 q~l~r~N~l~~lSh~Rrv~--~~~~~~~K~t~vR~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~Is 530 (1186)
|+|||+|++++|||+|||+ +++++++|.+++|+|||||||||||+|||||++|||+||||++|.|+
T Consensus 1 Q~l~r~N~l~~ls~~Rri~~~~~~~~~~~~~~~R~lh~s~~G~iCPveTPEG~~~GLv~~La~~a~I~ 68 (68)
T PF04565_consen 1 QYLDRTNPLSELSHLRRINRLGPLSKESKSTEPRQLHPSQYGRICPVETPEGENCGLVKNLALMARIT 68 (68)
T ss_dssp EE--TSSHHHHHHHHTEEESCSSTSSSSSSSTTTSTTGGGTTTBSSSSS-SSTSTTTEEEBBTT-EE-
T ss_pred CCcccccHHHHHHHHHhcccccccchhhcccccccccccceeEEeecccCCCccEeehheeeeeEEeC
Confidence 8999999999999999999 58999999999999999999999999999999999999999999986
No 20
>PF04561 RNA_pol_Rpb2_2: RNA polymerase Rpb2, domain 2; InterPro: IPR007642 RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain []. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble. Many of the bacterial members contain large insertions within this domain, a region known as dispensable region 1 (DRI).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_B 3LTI_A 3IYD_C 3LU0_C 2Y0S_R 1SMY_M 3DXJ_M 3AOI_C 2A68_M 1ZYR_C ....
Probab=99.82 E-value=1.5e-20 Score=199.74 Aligned_cols=139 Identities=38% Similarity=0.524 Sum_probs=100.8
Q ss_pred EEEEEeccccccchHHHHHHHhcCCCHHHHHHHhccccCchhhHhhhHhhHhhhhccccHHHHHHHHhhcCcccCCCchh
Q 001021 253 YIRATLPYIRTEIPIIIVFRALGFVADKDILEHICYDFQDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGATVGVTRDK 332 (1186)
Q Consensus 253 ~i~v~i~~~~~~IPl~ilLkALG~~sD~eI~~~i~~~~~~~~~~~~l~~~l~e~~~i~t~~~al~yIg~r~~~~~~~~~~ 332 (1186)
.+.+.....+.+||+++||||||++||+||++.|++...+......+.........+.|+++|+.|||+++.. ...+..
T Consensus 40 ~~~~~~~~~~~~IPi~ilLrALG~~sd~eI~~~i~~~~~~~~~~~~~~~~~~~~~~~~t~~~al~~i~~~~~~-~~~~~~ 118 (190)
T PF04561_consen 40 IIIFSRPKKKFKIPIVILLRALGIESDKEIIELICYSEEDFEDIEELMLSELEEEEIYTQEQALEYIGKKFRF-RQGKPP 118 (190)
T ss_dssp TEEEEETTSSSEEEHHHHHHHTT--STCHHHHHHCCCSTCHSCSTTTHHHHCCCTSSCSCHHHHHHHHHCCHS-SSSCHC
T ss_pred EEEEEEcCcccccceEEeehhhcCcCcccccceeecccccccccccccccccccccccccccceeEeccceee-eccccc
Confidence 3445555557789999999999999999999999864333333333333333345678999999999994322 334445
Q ss_pred hHHHHHHHH---------hhcccC-CCCCCCccch--hHHHHHHHHHHHHHHhccCCcCCCCCcccccceec
Q 001021 333 RIKYAKEIL---------QKEMLP-HVGTGDFCET--KKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLD 392 (1186)
Q Consensus 333 ~~e~~~~iL---------~~~ll~-Hl~~~~~~~~--~K~~~L~~Mv~kLl~l~~g~~~~DD~D~l~NkRv~ 392 (1186)
..+.++.+| .+++|+ |++....... .|+.+|++|++||+.++.|.+.+||+|||+||||+
T Consensus 119 ~~~~~~~~l~~~y~l~~i~r~~l~~hl~~~~~~~~~~~k~~~l~~m~~~ll~~~~g~~~~Dd~D~l~NkRv~ 190 (190)
T PF04561_consen 119 KVEEARNFLQKRYDLGFIGRYKLNKHLGSDEPNENDRLKAEDLGLMIRKLLKLANGECEPDDRDHLGNKRVR 190 (190)
T ss_dssp CHCHHHHHHTTCSSTCCCHHHCCHTTTTSSSSSSSSSCHHHHHHHHHHHHHHHHTTSS-S-STTSCCCEEEE
T ss_pred chhhhhcccccccccccccccceeeeeeeeecccccccchhhHHHHHHHHHHHhcCCCCCCCccccCCcCCc
Confidence 566777776 466676 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=99.75 E-value=3.4e-18 Score=148.05 Aligned_cols=63 Identities=62% Similarity=1.032 Sum_probs=59.8
Q ss_pred EEECCEEEEEEcChHHHHHHHHhhhhcCCCCCceEEEEeccCCeEEEEeCCCceeeeEEEEec
Q 001021 564 IFVNGCWVGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEK 626 (1186)
Q Consensus 564 V~lnG~~iG~~~~~~~l~~~lr~~rr~~~i~~~vsi~~~~~~~~i~I~td~gRl~RPl~~v~~ 626 (1186)
|||||.|+|++++|+.|++.||.+||+|.|+.++||+++...++|+|+||+||+||||++|+|
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 799999999999999999999999999999999999999999999999999999999999986
No 22
>KOG0214 consensus RNA polymerase II, second largest subunit [Transcription]
Probab=99.24 E-value=6e-13 Score=159.89 Aligned_cols=421 Identities=10% Similarity=-0.105 Sum_probs=270.3
Q ss_pred CCCCccchhhhhcccccccccccceEEeecccceeeccCCcceeecccccccccccCCCCceeEEEEEecCCCCCCCcEE
Q 001021 717 HNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVI 796 (1186)
Q Consensus 717 HNqSpRn~yqc~M~KQaig~~~~n~~~r~D~~~~~L~ypQ~PlV~t~~~~~~~~~~~p~G~N~~VAv~sy~GYn~EDaii 796 (1186)
+-|.+++-++.-|. |..+-....+..+.+...-.|.+++.++-++........-..+.+.++-++.+.+.++..++...
T Consensus 680 Fpdh~qspr~tYQs-a~~kqamg~y~tn~~vR~dtl~~~l~ypqkpl~tt~~~e~l~~~eL~aG~NaiVAi~~~~GYNqE 758 (1141)
T KOG0214|consen 680 FPDHNQSPRNTYQS-AMGKQAMGVYHTNPQVRMDTLAKVLYYPQKPLVTTRAMEYLRFRELPAGQNAIVAIACYSGYNQE 758 (1141)
T ss_pred cCCCCCchHHHHHH-HHhhhcceeeeecchhhhhhhhhcccccccchhhHHHHhhhhhhhcccccceEEEEecccCccHH
Confidence 35666666666666 44444555566666666666667777766665544444445677999999999999999999999
Q ss_pred eeccccccCceEEEEEEEEEeeecccCCcceeeecCCCCCCCCCCCCCCcCCCCCCCccCCCcEEcCCCEEE-EEeCCCC
Q 001021 797 MNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVII-GKTTPIS 875 (1186)
Q Consensus 797 ink~sv~rG~~~s~~~~~~~~~~~~~~~~~~e~~~~p~~~~~~~~~~~~~~~ld~dGi~~~g~~v~~gd~l~-~k~~p~~ 875 (1186)
-|--..+.+++|+++...|.-.-+++.......++.+-.....+.+...+ +.-.|-+-.-|-..-.+.+.. .++.++.
T Consensus 759 Dsvimn~s~v~rg~FrS~~~RsYk~q~~~~~~~~ee~~~~~~~~~~~~mr-~~~~dkLdddG~i~~G~~vs~~Dv~iGk~ 837 (1141)
T KOG0214|consen 759 DSVIMNQSSVDRGLFRSFFIRSYKDQEHKKDQGPEEIFEEPPRGEGRGMR-NGKYDKLDDDGIIMPGSRVSGGDVLIGKT 837 (1141)
T ss_pred HHHHHHhhhhhcchhhhhhhhHHHhhhhhccccccccccccccccccccc-ccccccccccCCccccceeecCCEEeccc
Confidence 99999999999999987765444443222222222221111111111111 111111111111111111111 1111110
Q ss_pred ccccccccCccccceeeEEeecCCCcEEEEEEEEecCCCceEEEEEEEeecCCCCcccccccCCCccEEEeeecCCCCCC
Q 001021 876 QDEAQGQASRYTRRDHSISLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPW 955 (1186)
Q Consensus 876 ~~~~~~~~~~~~~~~~s~~~~~~~~g~v~~v~~~~~~~~~~~vkv~~r~~R~p~iGDKfssRhGqKGvvs~i~~~~dmPf 955 (1186)
.. ... ..+.+-.-..-..++..++.+..+..| ...+|.++. .+.|+||+.+|++++-+.++-...++++
T Consensus 838 t~---~~~----~~~~~~~~~~~~t~~d~s~~Lr~~e~G-ivd~V~vt~---n~~G~kF~kv~vr~~ripqiGDKfasrH 906 (1141)
T KOG0214|consen 838 TP---QPA----KEDESGPEDRLYTKRDHSTKLRHTERG-IVDQVWVTK---NSEGPKFVKVRVRQVRIPQIGDKFASRH 906 (1141)
T ss_pred cC---Ccc----cchhccccccccccccceeecccCCcc-eEEEEEEec---CCCCCceeEEEEeecccccccchhcccc
Confidence 00 000 000000000011346677777777766 445555555 8999999999999999999999999999
Q ss_pred CCCCCCCcEEeCCCCCCCCCchhhHHhhhhhHhhhhcCCccccCCCCCccHHHHHHHHHHcCCCCCCeEEEeeCCCCceE
Q 001021 956 TVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRL 1035 (1186)
Q Consensus 956 ~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tpF~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~ 1035 (1186)
-..|+.++++.+++.-+++++|--.+..-.-..-+. .++..+.+-|. |-..-++..++++.++..
T Consensus 907 gqKG~ig~~~~qedmpft~eGi~pDiiiNPhaiPSR------------mtig~liEc~l--gk~~a~~~e~~~atpFs~- 971 (1141)
T KOG0214|consen 907 GQKGTIGITYRQEDMPFTIEGIVPDIIINPHAIPSR------------MTIGQLIECLL--GKVAAYEGEEGDATPFSD- 971 (1141)
T ss_pred ccCccccceeecCCCCccccCCCcceEECcccCccc------------cchhhhHHHhh--hhhhhcccccccCCCCCc-
Confidence 999999999999999999999987766532221111 12222222221 112223334455555555
Q ss_pred EeeEeEeeeehhccccccCCceEEeccCCccccccCCCCcccCCCcceeeehhhhHHHhhccHHHHHHhhhcCCCcceee
Q 001021 1036 TAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVH 1115 (1186)
Q Consensus 1036 ~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~L~erL~~~SD~~~~~ 1115 (1186)
-+-.+++..+++...|+..++.+++.+++....+++++++....++.+++||+++|=.+++.+-+.++.+...|+..-..
T Consensus 972 v~v~~is~~l~~~g~~~~G~e~~ynGrtG~~~~~~if~GptyyqrL~Hmvd~kih~R~~Gp~q~ltRQP~~gRsr~GGlR 1051 (1141)
T KOG0214|consen 972 VTVSKISANLHVYGYQYRGNERMYNGRTGRKLRAQIFIGPTYYQRLKHMVDDKIHSRARGPVQILTRQPVEGRSRDGGLR 1051 (1141)
T ss_pred cchhcccchHHHhccccCCCEEEecCCCCceeeeeeecCchHHHHHHHhhhheeeecccCCceeeeccccccccccCCee
Confidence 34567899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eccccCcceeeccccCceeeccCCCCCCceeecccHhhHHHHHHHHhCCCc
Q 001021 1116 VCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIA 1166 (1186)
Q Consensus 1116 vC~~cG~~~~~~~~~~~~~C~~C~~~~~i~~v~iPy~~k~l~~EL~sm~i~ 1166 (1186)
+|+.|+.-+.+.-...-..|+-|..++.+.....++ |.|++.+...+|.-
T Consensus 1052 fGEMErdc~iahGaa~~L~ERL~~~SD~~~~~~c~~-c~l~~i~~~~~n~~ 1101 (1141)
T KOG0214|consen 1052 FGEMERDCLIAHGAAAFLKERLFEKSDAYRVHICVL-CGLTAIAGLIPNSF 1101 (1141)
T ss_pred eehhHHHHHHHhhHHHHHHHHhhccCccceEEEecc-chhhhhhccCCCcc
Confidence 999998654221111123455566555554444455 34777777666644
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=98.99 E-value=1.4e-10 Score=95.37 Aligned_cols=48 Identities=58% Similarity=1.041 Sum_probs=36.2
Q ss_pred ccccccCCcEEEeccccccceeeeecccccccccCCCCccccccceeeecCC
Q 001021 650 WHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHP 701 (1186)
Q Consensus 650 ~~~l~~~g~iE~i~~~Ee~~~~Ia~~~~~~~~~~~~~k~~~~~~~th~Ei~p 701 (1186)
|++|+++|+|||||++||++++||++++++. .. .......||||||||
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 7899999999999999999999999999987 11 011145799999998
No 24
>KOG0215 consensus RNA polymerase III, second largest subunit [Transcription]
Probab=98.93 E-value=8.6e-12 Score=148.20 Aligned_cols=531 Identities=6% Similarity=-0.113 Sum_probs=295.2
Q ss_pred ccchhhhhhhhhcccCccchHHHHHHHHHHHHHhhHHHHHhhcCCeeeCCCCCCCCCeEEEEeeEEEeCCcccCCCCccC
Q 001021 22 EITQEDAWAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPMMTESDGETA 101 (1186)
Q Consensus 22 ~~~~~~~~~~i~~~f~~~~Lv~~hi~SFN~Fl~~gL~~ii~~~~pI~~~~~~~~~~~~~l~f~~i~i~~P~~~~~~~~~~ 101 (1186)
-+.-.|.|-..+++.+..++...||.+++.+|..-...+ ||.++.+... ++-.+.=.++-|+ ..+..-.+.+
T Consensus 94 ylky~dirvg~Ps~~~~~~~~~~~i~p~ecrlrd~tysa-----~i~vdieytr-g~~~~~~~~v~ig--rmpimlrs~r 165 (1153)
T KOG0215|consen 94 YLKYLDIRVGKPSIEEGNNVTNDNITPHECRLRDMTYSA-----PIYVDIEYTR-GRQIIAKRDVIIG--RMPIMLRSSK 165 (1153)
T ss_pred hheeeeeeccCcchhhccccccccCCchheeehhhhccc-----ceeEEEEEec-CcceEEecccccc--cchhhhhccc
Confidence 444557788888889999999999999999987654333 4443322111 1112222233333 2322222456
Q ss_pred CCChHHHHhcCCCcceeEEEEEEEEEeccCCCCcccccceeeEEEEecccceeeccCCccCCCCChhhhhhcCCCCCCCC
Q 001021 102 TLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQG 181 (1186)
Q Consensus 102 ~l~P~EcR~r~lTYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~eli~~gE~~~D~G 181 (1186)
.+.|.+|+....-|. ..+. ...-..+..|.-|||+.+.-|.+....++ -...|||+.+++
T Consensus 166 cvl~~~~e~~~a~~~------------ecpl-------dpggyfiv~G~ekViLiqeqlsknrii~~-~~k~~~~~~svt 225 (1153)
T KOG0215|consen 166 CVLRGKDEEELARLN------------ECPL-------DPGGYFIVKGTEKVILIQEQLSKNRIIVE-EDKKGNLQASVT 225 (1153)
T ss_pred cccCCccHHHHHHhc------------cCCC-------CCCceeEeccceeEEEehhhhhccCeeec-cccCCccccccc
Confidence 677777774433221 1110 11235688999999999999999999887 567899999999
Q ss_pred ceEEEcCeeeEEEeeeeeccCeEEEEEecCCCcceEEEEEEEeecCCCCCCceEEEEEEecCCCCCCCCCcEEEEEeccc
Q 001021 182 GYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPYI 261 (1186)
Q Consensus 182 GYFIING~ERVIi~Qe~~s~N~~~~~~~~~~~~~~~~~~irs~~~~g~~~~~~~~v~~~~~~~~~~~~~~~~i~v~i~~~ 261 (1186)
+||+..+++.+|+.++...+++...+.++- +.+.... --|.....++. .+.- .+.-+.++...
T Consensus 226 sst~e~kskt~v~~k~~k~ylk~~~~~d~i----piviv~k---a~g~~sd~ei~-~~vg---------~~~~y~~~~~~ 288 (1153)
T KOG0215|consen 226 SSTHERKSKTYVTTKKGKYYLKHNSFTDDI----PIVIVLK---AMGLESDQEIV-QLVG---------GDSKYQDIFAP 288 (1153)
T ss_pred cceeeecceEEEEeccceeeeehhhhhccC----CEEEEEe---eccccchHHHH-HHhh---------cchHHHHhhcc
Confidence 999999999999999987666655544332 2111111 11111111110 0000 11122222222
Q ss_pred cccchHHHHHHHhcCCCHHHHHHHhccccCchhhHhhhHhhHhhhhccccHHHHHHHHhhcCccc-C-----CCch-hhH
Q 001021 262 RTEIPIIIVFRALGFVADKDILEHICYDFQDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGATV-G-----VTRD-KRI 334 (1186)
Q Consensus 262 ~~~IPl~ilLkALG~~sD~eI~~~i~~~~~~~~~~~~l~~~l~e~~~i~t~~~al~yIg~r~~~~-~-----~~~~-~~~ 334 (1186)
.-+.|+.+-+.+.+-..|..+.+..... .....-.++|++.+...+.+- . .... ..+
T Consensus 289 s~ee~~~~~v~tqqqal~y~~~kvk~~~----------------~t~~~~~~e~~~~l~~~~lahv~v~~~~~r~K~~yi 352 (1153)
T KOG0215|consen 289 SLEECVSLGVYTQQQALEYIGSKVKVKR----------------GTTPTKDEEALEVLSTTVLAHVPVPDLNFRMKAIYI 352 (1153)
T ss_pred chhhhhhhhhHHHHHHHHHhhheEEecc----------------CCCCCchHHHHHHHHhhheeceeccCCCCcceeehH
Confidence 2245555555444433332222221110 001122345566555443221 0 0111 111
Q ss_pred H-HHHHHHhhcccCCCCCCCccchhHHHHHHHHHHHHHHhccCCcCCCCCcccccceeccCchhhHHHHHHHHHHHHHHH
Q 001021 335 K-YAKEILQKEMLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDV 413 (1186)
Q Consensus 335 e-~~~~iL~~~ll~Hl~~~~~~~~~K~~~L~~Mv~kLl~l~~g~~~~DD~D~l~NkRv~l~G~Ll~~lfr~~l~~~~k~i 413 (1186)
. ..+.++.- +-|....++....+-..|.+|.+. +.+..+.-.-++.+.|++.+-.+.+..+..++-++++.+. ..
T Consensus 353 ~~m~rr~~~a--~l~~~~~ddrd~~gnkrlelagql-lsllfeD~fk~~n~e~k~~~dk~l~k~~ra~~fD~~~~~n-~~ 428 (1153)
T KOG0215|consen 353 GLMVRRVIQA--MLNKLAMDDRDYVGNKRLELAGQL-LSLLFEDLFKRFNSELKKNIDKILKKPIRAQEFDALKHLN-VR 428 (1153)
T ss_pred HHHHHHHHHH--HhCcccccchhhhccchHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHhcchhhhhhhHHHHHHH-HH
Confidence 1 11111211 112222221112222345555554 4455555556788899999999999999999999988874 22
Q ss_pred HH----HHhhhhcCCCccchhhhc-cccchhhhhhhhcccCccccccccccccceeeeccccChhhhhccccccCCCCCc
Q 001021 414 RA----YVQKCVDNGKDVNLQFAI-KAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGR 488 (1186)
Q Consensus 414 k~----~l~k~~~~~~~~~~~~~i-~~~~It~~i~~~~sTGNw~~~~~~~~~sGvsq~l~r~N~l~~lSh~Rrv~~~~~~ 488 (1186)
+. -+.+.+.. ...++..+- ....+|. --+-.|++|........++++.++..+..|-|-....-.+..|+.+
T Consensus 429 ~~~it~~l~ra~st-gnw~iKrfrmer~gvt~--VlsrlSyisaLgmmtri~s~fektrkvsgprSlq~sqwgmlcp~dt 505 (1153)
T KOG0215|consen 429 ANMITSGLERAIST-GNWSIKRFRMERAGVTQ--VLSRLSYISALGMMTRINSQFEKTRKVSGPRSLQPSQWGMLCPSDT 505 (1153)
T ss_pred HHHHHHHHHHHhhc-CchHHHHhhhhhcccee--eehhhhhhhhhhhheehhhhheeehhccCccccChhhcccccCCCC
Confidence 22 22332221 122233221 1122222 2234567787766667789999999988888877777777778888
Q ss_pred CCCcCcccccCCCCccccccCCCCCCcccccccccceeEEEccCCCchhHHHHHHHhCCccccc-cCCCCC-CCceEEEE
Q 001021 489 EGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEE-ISPAVI-PQATKIFV 566 (1186)
Q Consensus 489 ~~K~t~vR~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~Is~~~~~~~i~~~l~~~g~~~~~~-~~~~~~-~~~~~V~l 566 (1186)
..+.+-.+-.+++.|+.|||-++|++..|++.|..+...+++.+....+.-.++..|+...+.. ..++.. .....++.
T Consensus 506 pegeacglvknlalmthittd~ee~pi~~~~~k~gv~di~~v~~~e~~~~~~~~v~Lng~iig~~~~~~~~v~~~r~lrr 585 (1153)
T KOG0215|consen 506 PEGEACGLVKNLALMTHITTDSEEKPILKLCYKLGVEDIHVVSGRELHTPDSFLVFLNGLIIGITRRPQYFVNSFRRLRR 585 (1153)
T ss_pred CCccccccccchHHHhcccCCCCcchhHHHHHHhcceeeeeecccccCCCceEEEEecceeeccccchHHHHHHHHHHHH
Confidence 8888999999999999999999999999999999999999988643322222222232222110 111111 12223566
Q ss_pred CCEEEEEEcChHHHHHHHHhhhhcCCCCCceEEEEeccCCeEEEEeCCCceeeeEE
Q 001021 567 NGCWVGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLF 622 (1186)
Q Consensus 567 nG~~iG~~~~~~~l~~~lr~~rr~~~i~~~vsi~~~~~~~~i~I~td~gRl~RPl~ 622 (1186)
+|++-++.......++..+.+++.|-..-...|..+.. ..+|-++.+|.|+|..
T Consensus 586 ~G~i~~fvsv~~~~~q~~v~i~sdggr~crp~Iiv~~~--~~~v~~~h~~el~~g~ 639 (1153)
T KOG0215|consen 586 KGKIGEFVSVFTNTTQRCVYIASDGGRVCRPLIIVDNG--RPRVKQHHMDELLDGK 639 (1153)
T ss_pred cCcccceeeeeeeeeeEEEEEecCCCeEeeeEEEEeCC--cchhhhhhHHHHHHhh
Confidence 77766665544444444455555554333344444332 2377777778777754
No 25
>PF06883 RNA_pol_Rpa2_4: RNA polymerase I, Rpa2 specific domain ; InterPro: IPR009674 This domain is found between domain 3 and domain 5, but shows no homology to domain 4 of Rpb2. The external domains in multisubunit RNA polymerase (those most distant from the active site) are known to demonstrate more sequence variability [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=97.60 E-value=7e-05 Score=64.21 Aligned_cols=49 Identities=20% Similarity=0.232 Sum_probs=42.1
Q ss_pred EEEE--cChHHHHHHHHhhhhcC--CCCCceEEEEeccC-----CeEEEEeCCCceee
Q 001021 571 VGIH--RDPEMLVKTLRRLRRRV--DVNTEVGVVRDIRL-----KELRIYTDYGRCSR 619 (1186)
Q Consensus 571 iG~~--~~~~~l~~~lr~~rr~~--~i~~~vsi~~~~~~-----~~i~I~td~gRl~R 619 (1186)
||++ +.+..+++.||.+|..| .||.++||++.+.. +++||||+++||+|
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 4564 35789999999999887 69999999988754 79999999999998
No 26
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]
Probab=97.60 E-value=6.7e-05 Score=96.02 Aligned_cols=109 Identities=27% Similarity=0.342 Sum_probs=81.1
Q ss_pred cEEEeccccccceeeeecccccccccCCC------C----c----cccccceeeecCCCccccccccccCCCCCCCCccc
Q 001021 658 FIEYIDTEEEETTMISMTINDLVQARLHP------E----E----AYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRN 723 (1186)
Q Consensus 658 ~iE~i~~~Ee~~~~Ia~~~~~~~~~~~~~------k----~----~~~~~~th~Ei~p~~ilsv~AslIPF~~HNqSpRn 723 (1186)
-|+|+.+.|+....+|.....+++...+. . . ......++++++|.++.|+.+++|||.+|++++|.
T Consensus 476 ~i~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~~~~~~~~~~~~~~~~~~dv~~~~~~~~~~~~~P~l~~dd~~~~ 555 (1060)
T COG0085 476 EIEYLSADEEDVYVIGQANGTLDEPGELVEELVECRRGGSGEVSVADPEGVDYMDVSPKQVVSVGRSLIPFLEHDDANRA 555 (1060)
T ss_pred ceeeecccccceEEEeEeeeeecCCCceeeeEEEEeecccccceeecCccccceeccceEEeccccccCceeEEcCchHh
Confidence 47899999999988887655443321110 0 0 01334678899999999999999999999999999
Q ss_pred hhhhhcccccccccccceEEeecccceeeccCCcceeecccccccccccCCCCceeEEEEEec
Q 001021 724 TYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACY 786 (1186)
Q Consensus 724 ~yqc~M~KQaig~~~~n~~~r~D~~~~~L~ypQ~PlV~t~~~~~~~~~~~p~G~N~~VAv~sy 786 (1186)
+|+++|+|||+|+ ..+..|+|.|+ ++++.-.| -.|++||.-++
T Consensus 556 l~~~~mqr~~~~l----------------~~~~~~lv~tG-~E~~~a~e---~~~~~ia~~~~ 598 (1060)
T COG0085 556 LMGSNMQRQAVPL----------------LRTEAPLVGTG-MEYLDAED---SGAAVIAKRPG 598 (1060)
T ss_pred hhhhhhhhhcccc----------------cccccccccCC-ceeecccc---ccceeEeccCC
Confidence 9999999999994 45788999999 77653222 34666666443
No 27
>PHA03394 lef-8 DNA-directed RNA polymerase subunit beta-like protein; Provisional
Probab=94.90 E-value=0.044 Score=68.08 Aligned_cols=142 Identities=23% Similarity=0.326 Sum_probs=83.5
Q ss_pred EeecCCCcEEEEEEEEec-CCCceEEEEEEEeecCCCCcccccccCCCccEEEeeecCCCCC-C-CCCCCCCcEEeCCCC
Q 001021 894 SLRHSETGMVDQVLLTTN-ADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMP-W-TVEGITPDIIVNPHA 970 (1186)
Q Consensus 894 ~~~~~~~g~v~~v~~~~~-~~~~~~vkv~~r~~R~p~iGDKfssRhGqKGvvs~i~~~~dmP-f-~~~G~~pDiI~NPh~ 970 (1186)
.++....-.|++|.-.-. .++.-.+|+++-..=.=-.|=|.||=||||||+. ..||+- | .|||+.|-|.++|.+
T Consensus 673 YfR~~~~Q~ie~l~s~m~~~nd~v~lKl~~Vtst~dLeGlKICgIHGQKGVln---~seDLtew~aeDg~~aQIclSPiS 749 (865)
T PHA03394 673 YFRQIKNQRIERLDSEMTVINDTVYLKIRLVTSTSDLEGLKICGIHGQKGVLN---GSEDLTEWMAEDGTHAQICLSPIS 749 (865)
T ss_pred EEEecCCeEEEEEeeEEEEcCCEEEEEEEEEEEecCcceeEEeeecccccccC---CcchhhhhhccCCCcceEEechHH
Confidence 344445555665532111 1224456666544334456899999999999975 466765 3 569999999999999
Q ss_pred CCCCCchhhHHhhhhhHhhhhcCCcccc---------CC--CCCccHHHHHHHHHHcCCCCCCeEEEeeCCCCceEEeeE
Q 001021 971 IPSRMTIGQLIECIMGKVAAHMGKEGDA---------TP--FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMI 1039 (1186)
Q Consensus 971 ~PSRMtiGql~E~~~gk~~~~~g~~~d~---------tp--F~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~i 1039 (1186)
+-||.|.= +-+--|-....|.+.|. .| |-..+.+++.++.. |-++.|-|.+=--|.-..--...
T Consensus 750 yLsRQtnf---~~~~~Ky~v~gg~~~~~~~~rypi~~IPYm~FnnTPDnI~kEf~--~~n~TG~EKvEGTRlDqwTINqs 824 (865)
T PHA03394 750 YLSRQTNF---DDIERKYVVRGGDHSDPNAKRYPIFNIPYMLFNNTPDNIYKEFI--KKNYTGHEKVEGTRLDQWTINQS 824 (865)
T ss_pred hhcccccc---ccCceEEEEECCCcCCCCCcccceEecceehhcCCchHHHHHHh--ccCCcceeecceeeccceeEcce
Confidence 99999862 22223444444555443 34 22455666666554 34567777654222222223355
Q ss_pred eEee
Q 001021 1040 FLGP 1043 (1186)
Q Consensus 1040 f~G~ 1043 (1186)
|+|-
T Consensus 825 F~gN 828 (865)
T PHA03394 825 FVGN 828 (865)
T ss_pred eccc
Confidence 5553
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=61.76 E-value=3.9 Score=36.38 Aligned_cols=49 Identities=18% Similarity=0.387 Sum_probs=29.4
Q ss_pred ceeeeccccCcceeeccccCceeeccCCCCCCceeeccc------HhhHHHHHHHHh
Q 001021 1112 YRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIP------YACKLLFQELMA 1162 (1186)
Q Consensus 1112 ~~~~vC~~cG~~~~~~~~~~~~~C~~C~~~~~i~~v~iP------y~~k~l~~EL~s 1162 (1186)
|.++-| .||+.+++.....+..| .|+..-+|.+..|= .-..-++++|+.
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 69999998877777899 99987666665552 223445555553
No 29
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=61.05 E-value=4.9 Score=37.36 Aligned_cols=29 Identities=28% Similarity=0.761 Sum_probs=24.5
Q ss_pred ceeeeccccCcceeeccccCceeeccCCC
Q 001021 1112 YRVHVCEHCGLIAIANLKKNSFECRGCKN 1140 (1186)
Q Consensus 1112 ~~~~vC~~cG~~~~~~~~~~~~~C~~C~~ 1140 (1186)
+..|+|+.||+..+.-...+.|.|+.|+.
T Consensus 33 ~~~~~Cp~C~~~~VkR~a~GIW~C~kCg~ 61 (89)
T COG1997 33 RAKHVCPFCGRTTVKRIATGIWKCRKCGA 61 (89)
T ss_pred hcCCcCCCCCCcceeeeccCeEEcCCCCC
Confidence 34578999999987777778999999986
No 30
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=55.10 E-value=8.5 Score=40.48 Aligned_cols=24 Identities=29% Similarity=0.573 Sum_probs=18.9
Q ss_pred eeeccccCcceeeccccCceeeccCCC
Q 001021 1114 VHVCEHCGLIAIANLKKNSFECRGCKN 1140 (1186)
Q Consensus 1114 ~~vC~~cG~~~~~~~~~~~~~C~~C~~ 1140 (1186)
+|||..||-+... .....|+.|+.
T Consensus 134 ~~vC~vCGy~~~g---e~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYTHEG---EAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCCcccC---CCCCcCCCCCC
Confidence 9999999988743 23458999985
No 31
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=53.67 E-value=12 Score=30.65 Aligned_cols=28 Identities=18% Similarity=0.377 Sum_probs=20.4
Q ss_pred eeeccccCcceeeccccCceeeccCCCC
Q 001021 1114 VHVCEHCGLIAIANLKKNSFECRGCKNK 1141 (1186)
Q Consensus 1114 ~~vC~~cG~~~~~~~~~~~~~C~~C~~~ 1141 (1186)
.+.|.+||.............|+.|++.
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~ 30 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYR 30 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCe
Confidence 5789999997754433336799999863
No 32
>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=52.72 E-value=11 Score=29.06 Aligned_cols=26 Identities=31% Similarity=0.631 Sum_probs=18.8
Q ss_pred eeeccccCcceeeccccCceeeccCCCC
Q 001021 1114 VHVCEHCGLIAIANLKKNSFECRGCKNK 1141 (1186)
Q Consensus 1114 ~~vC~~cG~~~~~~~~~~~~~C~~C~~~ 1141 (1186)
.|+|.+||-+.... .....|+.|+..
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 68999999886432 123489999874
No 33
>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=51.18 E-value=26 Score=44.17 Aligned_cols=35 Identities=17% Similarity=0.156 Sum_probs=28.1
Q ss_pred CCCCCcccccceeccCchhhHHHHHHHHHHHHHHH
Q 001021 379 AEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDV 413 (1186)
Q Consensus 379 ~~DD~D~l~NkRv~l~G~Ll~~lfr~~l~~~~k~i 413 (1186)
..=.+|+|+||=|.-...||..+++..++.+...+
T Consensus 209 i~Y~IDsLsNKiIYkh~yLl~l~y~~~L~~~~~~~ 243 (748)
T PF04941_consen 209 INYSIDSLSNKIIYKHSYLLELTYKPILKKYENLI 243 (748)
T ss_pred CCceecccccceeeCHHHHHHHHHHHHHHHHHHHH
Confidence 34478999999999999999999987777665543
No 34
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=49.95 E-value=11 Score=37.99 Aligned_cols=25 Identities=24% Similarity=0.575 Sum_probs=20.4
Q ss_pred eeccccCcceeeccccCceeeccCCCC
Q 001021 1115 HVCEHCGLIAIANLKKNSFECRGCKNK 1141 (1186)
Q Consensus 1115 ~vC~~cG~~~~~~~~~~~~~C~~C~~~ 1141 (1186)
.-|+.||..+.. +.+..+|++|+..
T Consensus 29 ~hCp~Cg~PLF~--KdG~v~CPvC~~~ 53 (131)
T COG1645 29 KHCPKCGTPLFR--KDGEVFCPVCGYR 53 (131)
T ss_pred hhCcccCCccee--eCCeEECCCCCce
Confidence 349999999976 6678899999953
No 35
>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=49.16 E-value=11 Score=28.67 Aligned_cols=26 Identities=27% Similarity=0.592 Sum_probs=19.2
Q ss_pred eeeccccCcceeeccccCceeeccCCCC
Q 001021 1114 VHVCEHCGLIAIANLKKNSFECRGCKNK 1141 (1186)
Q Consensus 1114 ~~vC~~cG~~~~~~~~~~~~~C~~C~~~ 1141 (1186)
.|+|..||-+... ....+.|+.|+..
T Consensus 1 ~~~C~~CGy~y~~--~~~~~~CP~Cg~~ 26 (33)
T cd00350 1 KYVCPVCGYIYDG--EEAPWVCPVCGAP 26 (33)
T ss_pred CEECCCCCCEECC--CcCCCcCcCCCCc
Confidence 3789999987633 2246799999874
No 36
>PF14251 DUF4346: Domain of unknown function (DUF4346)
Probab=47.56 E-value=9.3 Score=37.59 Aligned_cols=14 Identities=43% Similarity=0.627 Sum_probs=11.2
Q ss_pred CCCCCCCCceEEEc
Q 001021 174 GECPYDQGGYFIIN 187 (1186)
Q Consensus 174 gE~~~D~GGYFIIN 187 (1186)
.--..||+|||||.
T Consensus 10 R~i~LDp~GYfiI~ 23 (119)
T PF14251_consen 10 RFIDLDPAGYFIIY 23 (119)
T ss_pred CccccCCCccEEEE
Confidence 44568999999986
No 37
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=43.49 E-value=14 Score=39.39 Aligned_cols=46 Identities=20% Similarity=0.395 Sum_probs=33.4
Q ss_pred hhccHHHHHHhhhcCCCcceeeeccccCcceee-ccccCceeeccCCC
Q 001021 1094 AHGASHFLKERLFDQSDAYRVHVCEHCGLIAIA-NLKKNSFECRGCKN 1140 (1186)
Q Consensus 1094 a~Gas~~L~erL~~~SD~~~~~vC~~cG~~~~~-~~~~~~~~C~~C~~ 1140 (1186)
.|-...-|+++|-..++. ..++|++||..... ......|.|+.|+.
T Consensus 98 ~~~~~~klk~~l~~e~~~-~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~ 144 (178)
T PRK06266 98 KMEELKKLKEQLEEEENN-MFFFCPNCHIRFTFDEAMEYGFRCPQCGE 144 (178)
T ss_pred HHHHHHHHHHHhhhccCC-CEEECCCCCcEEeHHHHhhcCCcCCCCCC
Confidence 366777889999877775 78999999975421 11224689999986
No 38
>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=43.18 E-value=27 Score=31.08 Aligned_cols=27 Identities=30% Similarity=0.380 Sum_probs=21.6
Q ss_pred CcEEEeccccccceeeeeccccccccc
Q 001021 657 GFIEYIDTEEEETTMISMTINDLVQAR 683 (1186)
Q Consensus 657 g~iE~i~~~Ee~~~~Ia~~~~~~~~~~ 683 (1186)
..|+||+|.||+...||.....+...+
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 458999999999999999988887654
No 39
>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=41.16 E-value=17 Score=25.97 Aligned_cols=23 Identities=26% Similarity=0.694 Sum_probs=15.0
Q ss_pred ccccCcceeeccccCceeeccCC
Q 001021 1117 CEHCGLIAIANLKKNSFECRGCK 1139 (1186)
Q Consensus 1117 C~~cG~~~~~~~~~~~~~C~~C~ 1139 (1186)
|..||......-....|.|+.|+
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCG 23 (24)
T ss_pred CccCCCcccCcccCceEeCCCCC
Confidence 67888766433223467888886
No 40
>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=38.36 E-value=16 Score=35.81 Aligned_cols=31 Identities=23% Similarity=0.504 Sum_probs=22.8
Q ss_pred eeeeccccCcceeeccccCceeeccCCCCCCc
Q 001021 1113 RVHVCEHCGLIAIANLKKNSFECRGCKNKTDI 1144 (1186)
Q Consensus 1113 ~~~vC~~cG~~~~~~~~~~~~~C~~C~~~~~i 1144 (1186)
.-++|..||...|- +++...+|+.|+..-.+
T Consensus 8 tKR~Cp~CG~kFYD-Lnk~PivCP~CG~~~~~ 38 (108)
T PF09538_consen 8 TKRTCPSCGAKFYD-LNKDPIVCPKCGTEFPP 38 (108)
T ss_pred CcccCCCCcchhcc-CCCCCccCCCCCCccCc
Confidence 45789999988754 55567789999975333
No 41
>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=38.28 E-value=22 Score=29.17 Aligned_cols=26 Identities=35% Similarity=0.947 Sum_probs=19.6
Q ss_pred eeccccCcceeecccc-CceeeccCCC
Q 001021 1115 HVCEHCGLIAIANLKK-NSFECRGCKN 1140 (1186)
Q Consensus 1115 ~vC~~cG~~~~~~~~~-~~~~C~~C~~ 1140 (1186)
.+|..||...+..++. ..|.|..|+.
T Consensus 19 ~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 6799999976544444 6789999964
No 42
>PRK00420 hypothetical protein; Validated
Probab=37.93 E-value=20 Score=35.30 Aligned_cols=25 Identities=24% Similarity=0.399 Sum_probs=19.6
Q ss_pred eccccCcceeeccccCceeeccCCCC
Q 001021 1116 VCEHCGLIAIANLKKNSFECRGCKNK 1141 (1186)
Q Consensus 1116 vC~~cG~~~~~~~~~~~~~C~~C~~~ 1141 (1186)
.|+.||...... +.+..+|+.|+..
T Consensus 25 ~CP~Cg~pLf~l-k~g~~~Cp~Cg~~ 49 (112)
T PRK00420 25 HCPVCGLPLFEL-KDGEVVCPVHGKV 49 (112)
T ss_pred CCCCCCCcceec-CCCceECCCCCCe
Confidence 599999988653 5567899999873
No 43
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=37.26 E-value=21 Score=38.12 Aligned_cols=34 Identities=26% Similarity=0.594 Sum_probs=26.5
Q ss_pred eeccccCcceeeccccCceeeccCCCCCCceeecccH
Q 001021 1115 HVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPY 1151 (1186)
Q Consensus 1115 ~vC~~cG~~~~~~~~~~~~~C~~C~~~~~i~~v~iPy 1151 (1186)
-.|.+||..+.. .....+|+.|++ +...++..||
T Consensus 150 A~CsrC~~~L~~--~~~~l~Cp~Cg~-tEkRKia~~y 183 (188)
T COG1096 150 ARCSRCRAPLVK--KGNMLKCPNCGN-TEKRKIAKDY 183 (188)
T ss_pred EEccCCCcceEE--cCcEEECCCCCC-EEeeeecccc
Confidence 469999998865 345678999987 4777888887
No 44
>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=37.10 E-value=28 Score=28.10 Aligned_cols=26 Identities=19% Similarity=0.600 Sum_probs=17.4
Q ss_pred eeccccCcce-eeccccCceeeccCCC
Q 001021 1115 HVCEHCGLIA-IANLKKNSFECRGCKN 1140 (1186)
Q Consensus 1115 ~vC~~cG~~~-~~~~~~~~~~C~~C~~ 1140 (1186)
++|+.||.-. ..+...+.++|+.|+.
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 4688898854 3445556678998864
No 45
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=36.15 E-value=21 Score=29.60 Aligned_cols=25 Identities=40% Similarity=0.881 Sum_probs=17.0
Q ss_pred eccccCcceeecc-c-cCceeeccCCC
Q 001021 1116 VCEHCGLIAIANL-K-KNSFECRGCKN 1140 (1186)
Q Consensus 1116 vC~~cG~~~~~~~-~-~~~~~C~~C~~ 1140 (1186)
.|+.||.+++... . ...++|+.|+-
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~ 28 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGY 28 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCC
Confidence 4889998875332 2 23688999974
No 46
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=35.61 E-value=17 Score=31.58 Aligned_cols=31 Identities=23% Similarity=0.543 Sum_probs=17.4
Q ss_pred CcceeeeccccCcceeeccccCceeeccCCC
Q 001021 1110 DAYRVHVCEHCGLIAIANLKKNSFECRGCKN 1140 (1186)
Q Consensus 1110 D~~~~~vC~~cG~~~~~~~~~~~~~C~~C~~ 1140 (1186)
+.....+|..||......-+.-.|.|+.|+.
T Consensus 3 ~~~~~~~CtSCg~~i~~~~~~~~F~CPnCG~ 33 (59)
T PRK14890 3 EMMEPPKCTSCGIEIAPREKAVKFLCPNCGE 33 (59)
T ss_pred ccccCccccCCCCcccCCCccCEeeCCCCCC
Confidence 3344556777776654322233566777754
No 47
>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=35.22 E-value=25 Score=33.25 Aligned_cols=29 Identities=17% Similarity=0.608 Sum_probs=23.4
Q ss_pred ceeeeccccCcceeeccccCceeeccCCC
Q 001021 1112 YRVHVCEHCGLIAIANLKKNSFECRGCKN 1140 (1186)
Q Consensus 1112 ~~~~vC~~cG~~~~~~~~~~~~~C~~C~~ 1140 (1186)
+.-+.|+.||.....-...+.|.|..|+.
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 56688999999987666667899999985
No 48
>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=34.84 E-value=23 Score=37.12 Aligned_cols=46 Identities=15% Similarity=0.298 Sum_probs=32.1
Q ss_pred hhccHHHHHHhhhcCCCcceeeeccccCccee-eccccCceeeccCCC
Q 001021 1094 AHGASHFLKERLFDQSDAYRVHVCEHCGLIAI-ANLKKNSFECRGCKN 1140 (1186)
Q Consensus 1094 a~Gas~~L~erL~~~SD~~~~~vC~~cG~~~~-~~~~~~~~~C~~C~~ 1140 (1186)
.|....-|+++|-.-++ ...++|++||.... .......|.|+.|+.
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 45677788898876665 46789999996542 111123689999986
No 49
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=34.68 E-value=27 Score=39.81 Aligned_cols=64 Identities=22% Similarity=0.408 Sum_probs=43.7
Q ss_pred HHHHhhhcCCCcceeeeccccCcce--eeccccCceeeccCCC-----CC---CceeecccHhhHHHHHHHHhCCCceE
Q 001021 1100 FLKERLFDQSDAYRVHVCEHCGLIA--IANLKKNSFECRGCKN-----KT---DIVQVHIPYACKLLFQELMAMAIAPR 1168 (1186)
Q Consensus 1100 ~L~erL~~~SD~~~~~vC~~cG~~~--~~~~~~~~~~C~~C~~-----~~---~i~~v~iPy~~k~l~~EL~sm~i~~~ 1168 (1186)
.|.| |+..+| ..+|..||... |+.++-+.|.|..|.. +. +|..|.+=.=..==++.|.+|| ..+
T Consensus 15 ~l~~-Ll~~~~---N~~CADC~a~~P~WaSwnlGvFiC~~C~giHR~lg~hiSkVkSv~LD~W~~eqv~~m~~~G-N~~ 88 (287)
T KOG0703|consen 15 RLRE-LLREPD---NKVCADCGAKGPRWASWNLGVFICLRCAGIHRSLGVHISKVKSVTLDEWTDEQVDFMISMG-NAK 88 (287)
T ss_pred HHHH-HHcCcc---cCcccccCCCCCCeEEeecCeEEEeecccccccccchhheeeeeeccccCHHHHHHHHHHc-chh
Confidence 3555 445566 67899999875 6777889999999976 22 3344555554455577788887 543
No 50
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=34.07 E-value=28 Score=29.25 Aligned_cols=30 Identities=17% Similarity=0.428 Sum_probs=22.0
Q ss_pred ceeeeccccCcceeeccccCceeeccCCCC
Q 001021 1112 YRVHVCEHCGLIAIANLKKNSFECRGCKNK 1141 (1186)
Q Consensus 1112 ~~~~vC~~cG~~~~~~~~~~~~~C~~C~~~ 1141 (1186)
...++|..||.............|+.|+..
T Consensus 4 ~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 4 MMEYKCARCGREVELDQETRGIRCPYCGSR 33 (49)
T ss_pred eEEEEhhhcCCeeehhhccCceeCCCCCcE
Confidence 457899999998743334456789999863
No 51
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=33.48 E-value=34 Score=26.28 Aligned_cols=28 Identities=25% Similarity=0.497 Sum_probs=21.4
Q ss_pred eeeccccCcceeeccccCceeeccCCCC
Q 001021 1114 VHVCEHCGLIAIANLKKNSFECRGCKNK 1141 (1186)
Q Consensus 1114 ~~vC~~cG~~~~~~~~~~~~~C~~C~~~ 1141 (1186)
.+.|..||.....+......+|..|+..
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~~ 30 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIFCGSS 30 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcccCCcE
Confidence 3679999998766555667899999863
No 52
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=32.86 E-value=27 Score=35.85 Aligned_cols=37 Identities=19% Similarity=0.451 Sum_probs=26.2
Q ss_pred CcceeeeccccCcceeeccccCceeeccCCCCCCceeeccc
Q 001021 1110 DAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIP 1150 (1186)
Q Consensus 1110 D~~~~~vC~~cG~~~~~~~~~~~~~C~~C~~~~~i~~v~iP 1150 (1186)
-+-..--|.+||+..+.- ...|..|++.+++..+.+|
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 344566799999988542 3479999988665556554
No 53
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=31.60 E-value=29 Score=35.84 Aligned_cols=43 Identities=19% Similarity=0.354 Sum_probs=28.5
Q ss_pred cHHHHHHhhhcCCCcceeeeccccCcceee-----c-cccCceeeccCCC
Q 001021 1097 ASHFLKERLFDQSDAYRVHVCEHCGLIAIA-----N-LKKNSFECRGCKN 1140 (1186)
Q Consensus 1097 as~~L~erL~~~SD~~~~~vC~~cG~~~~~-----~-~~~~~~~C~~C~~ 1140 (1186)
+-.-|+++|-..++ ...++|++||..... . -..+.+.|+.|+.
T Consensus 83 ~~~~L~~~l~~e~~-~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~ 131 (147)
T smart00531 83 MRKRLEDKLEDETN-NAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGE 131 (147)
T ss_pred HHHHHHHHHhcccC-CcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCC
Confidence 34456788866665 458899999965421 0 1233499999986
No 54
>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=30.64 E-value=26 Score=35.06 Aligned_cols=28 Identities=11% Similarity=0.182 Sum_probs=22.0
Q ss_pred eeeeccccCcceeeccccCceeeccCCCC
Q 001021 1113 RVHVCEHCGLIAIANLKKNSFECRGCKNK 1141 (1186)
Q Consensus 1113 ~~~vC~~cG~~~~~~~~~~~~~C~~C~~~ 1141 (1186)
.-++|..||...| .+++...+|+.|+..
T Consensus 8 tKr~Cp~cg~kFY-DLnk~p~vcP~cg~~ 35 (129)
T TIGR02300 8 TKRICPNTGSKFY-DLNRRPAVSPYTGEQ 35 (129)
T ss_pred ccccCCCcCcccc-ccCCCCccCCCcCCc
Confidence 4578999998875 455577899999875
No 55
>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=29.82 E-value=35 Score=35.32 Aligned_cols=28 Identities=25% Similarity=0.498 Sum_probs=15.5
Q ss_pred eeeccccCcceeeccccCceeeccCCCC
Q 001021 1114 VHVCEHCGLIAIANLKKNSFECRGCKNK 1141 (1186)
Q Consensus 1114 ~~vC~~cG~~~~~~~~~~~~~C~~C~~~ 1141 (1186)
.+||.+||....-.......-|+.|+..
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 56
>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=27.97 E-value=34 Score=26.80 Aligned_cols=24 Identities=21% Similarity=0.476 Sum_probs=18.4
Q ss_pred eccccCcceeeccccCceeeccCCC
Q 001021 1116 VCEHCGLIAIANLKKNSFECRGCKN 1140 (1186)
Q Consensus 1116 vC~~cG~~~~~~~~~~~~~C~~C~~ 1140 (1186)
.|..||... .....+.++|..|+.
T Consensus 10 ~C~~C~~~~-~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 10 PCPVCGSRW-FYSDDGFYYCDRCGH 33 (36)
T ss_pred cCCCCCCeE-eEccCCEEEhhhCce
Confidence 399999984 444567889999975
No 57
>PRK11032 hypothetical protein; Provisional
Probab=27.79 E-value=41 Score=35.30 Aligned_cols=7 Identities=57% Similarity=1.298 Sum_probs=2.8
Q ss_pred eccccCc
Q 001021 1116 VCEHCGL 1122 (1186)
Q Consensus 1116 vC~~cG~ 1122 (1186)
||.+||.
T Consensus 126 vC~~Cg~ 132 (160)
T PRK11032 126 VCEKCHH 132 (160)
T ss_pred EecCCCC
Confidence 3444443
No 58
>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=26.55 E-value=34 Score=32.45 Aligned_cols=29 Identities=24% Similarity=0.556 Sum_probs=23.2
Q ss_pred ceeeeccccCcceeeccccCceeeccCCC
Q 001021 1112 YRVHVCEHCGLIAIANLKKNSFECRGCKN 1140 (1186)
Q Consensus 1112 ~~~~vC~~cG~~~~~~~~~~~~~C~~C~~ 1140 (1186)
+..+.|+-||.....-...+.|.|..|+.
T Consensus 33 ~a~y~CpfCgk~~vkR~a~GIW~C~~C~~ 61 (91)
T TIGR00280 33 KAKYVCPFCGKKTVKRGSTGIWTCRKCGA 61 (91)
T ss_pred hcCccCCCCCCCceEEEeeEEEEcCCCCC
Confidence 45688999998876655567899999986
No 59
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=25.28 E-value=42 Score=38.21 Aligned_cols=16 Identities=19% Similarity=0.463 Sum_probs=10.1
Q ss_pred HHHHHHhhcccCCCCC
Q 001021 336 YAKEILQKEMLPHVGT 351 (1186)
Q Consensus 336 ~~~~iL~~~ll~Hl~~ 351 (1186)
....+|++.++.-+|+
T Consensus 158 IK~~LLDQ~vvaGvGN 173 (273)
T COG0266 158 IKTALLDQKVVAGVGN 173 (273)
T ss_pred hHHHhhcCCceecccH
Confidence 3445677777766664
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=24.37 E-value=55 Score=26.46 Aligned_cols=23 Identities=26% Similarity=0.715 Sum_probs=17.4
Q ss_pred eccccCcceeeccccCceeeccCC
Q 001021 1116 VCEHCGLIAIANLKKNSFECRGCK 1139 (1186)
Q Consensus 1116 vC~~cG~~~~~~~~~~~~~C~~C~ 1139 (1186)
.|+.||.++..+ +.+..+|..|+
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 599999988663 34567899885
No 61
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=23.21 E-value=66 Score=26.36 Aligned_cols=27 Identities=26% Similarity=0.709 Sum_probs=19.4
Q ss_pred eeeccccCcceeeccccCceeeccCCCC
Q 001021 1114 VHVCEHCGLIAIANLKKNSFECRGCKNK 1141 (1186)
Q Consensus 1114 ~~vC~~cG~~~~~~~~~~~~~C~~C~~~ 1141 (1186)
.++|..||...... ......|+.|+..
T Consensus 2 ~Y~C~~Cg~~~~~~-~~~~irC~~CG~r 28 (44)
T smart00659 2 IYICGECGRENEIK-SKDVVRCRECGYR 28 (44)
T ss_pred EEECCCCCCEeecC-CCCceECCCCCce
Confidence 57899999865332 3456789999864
No 62
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=22.44 E-value=46 Score=31.53 Aligned_cols=29 Identities=28% Similarity=0.675 Sum_probs=22.9
Q ss_pred ceeeeccccCcceeeccccCceeeccCCC
Q 001021 1112 YRVHVCEHCGLIAIANLKKNSFECRGCKN 1140 (1186)
Q Consensus 1112 ~~~~vC~~cG~~~~~~~~~~~~~C~~C~~ 1140 (1186)
+..+.|+-||.....-...+.|.|..|+.
T Consensus 34 ~a~y~CpfCgk~~vkR~a~GIW~C~~C~~ 62 (90)
T PTZ00255 34 HAKYFCPFCGKHAVKRQAVGIWRCKGCKK 62 (90)
T ss_pred hCCccCCCCCCCceeeeeeEEEEcCCCCC
Confidence 45688999998776555557899999986
No 63
>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=22.02 E-value=49 Score=29.27 Aligned_cols=29 Identities=24% Similarity=0.598 Sum_probs=22.3
Q ss_pred ceeeeccccCcceeeccccCceeeccCCC
Q 001021 1112 YRVHVCEHCGLIAIANLKKNSFECRGCKN 1140 (1186)
Q Consensus 1112 ~~~~vC~~cG~~~~~~~~~~~~~C~~C~~ 1140 (1186)
+....|..||...........+.|+.|+-
T Consensus 26 ~TSq~C~~CG~~~~~~~~~r~~~C~~Cg~ 54 (69)
T PF07282_consen 26 YTSQTCPRCGHRNKKRRSGRVFTCPNCGF 54 (69)
T ss_pred CCccCccCcccccccccccceEEcCCCCC
Confidence 35567999999876555666889999975
No 64
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=21.78 E-value=51 Score=25.53 Aligned_cols=24 Identities=21% Similarity=0.567 Sum_probs=11.4
Q ss_pred eccccCcceee----ccccCceeeccCC
Q 001021 1116 VCEHCGLIAIA----NLKKNSFECRGCK 1139 (1186)
Q Consensus 1116 vC~~cG~~~~~----~~~~~~~~C~~C~ 1139 (1186)
-|..||..+.. .....+++|..|+
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg 29 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPACG 29 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTTT
T ss_pred ccccccChhhhhcCCCCCccceECCCCC
Confidence 48888877632 2234467888885
No 65
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=21.73 E-value=41 Score=24.17 Aligned_cols=22 Identities=23% Similarity=0.578 Sum_probs=15.3
Q ss_pred eeccccCcceeeccccCceeeccCCC
Q 001021 1115 HVCEHCGLIAIANLKKNSFECRGCKN 1140 (1186)
Q Consensus 1115 ~vC~~cG~~~~~~~~~~~~~C~~C~~ 1140 (1186)
..|.+||..... +..+|+.|+.
T Consensus 3 ~~Cp~Cg~~~~~----~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDP----DAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCc----ccccChhhCC
Confidence 469999985432 2347999975
No 66
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=21.31 E-value=49 Score=31.36 Aligned_cols=29 Identities=31% Similarity=0.713 Sum_probs=23.0
Q ss_pred ceeeeccccCcceeeccccCceeeccCCC
Q 001021 1112 YRVHVCEHCGLIAIANLKKNSFECRGCKN 1140 (1186)
Q Consensus 1112 ~~~~vC~~cG~~~~~~~~~~~~~C~~C~~ 1140 (1186)
+..+.|+.||.....-.-.+.|.|..|+.
T Consensus 34 ~a~y~CpfCgk~~vkR~a~GIW~C~~C~~ 62 (90)
T PRK03976 34 RAKHVCPVCGRPKVKRVGTGIWECRKCGA 62 (90)
T ss_pred hcCccCCCCCCCceEEEEEEEEEcCCCCC
Confidence 45678999998876555567899999986
Done!