Query 001125
Match_columns 1149
No_of_seqs 237 out of 1611
Neff 6.8
Searched_HMMs 46136
Date Thu Mar 28 16:30:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001125.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001125hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK08565 DNA-directed RNA poly 100.0 5E-278 1E-282 2618.6 93.9 1090 31-1148 1-1101(1103)
2 KOG0215 RNA polymerase III, se 100.0 2E-275 4E-280 2329.8 54.4 1112 17-1148 32-1150(1153)
3 KOG0214 RNA polymerase II, sec 100.0 1E-265 2E-270 2278.4 56.0 1103 28-1147 2-1140(1141)
4 KOG0216 RNA polymerase I, seco 100.0 2E-258 3E-263 2200.0 67.9 1055 30-1147 4-1111(1111)
5 COG0085 RpoB DNA-directed RNA 100.0 9E-250 2E-254 2252.2 69.9 1015 27-1148 10-1058(1060)
6 cd00653 RNA_pol_B_RPB2 RNA pol 100.0 7E-227 1E-231 2111.5 74.2 856 44-1145 1-866 (866)
7 TIGR02013 rpoB DNA-directed RN 100.0 2E-226 5E-231 2113.3 72.7 920 28-1144 4-1065(1065)
8 PRK00405 rpoB DNA-directed RNA 100.0 1E-222 3E-227 2090.0 75.9 922 28-1146 11-1107(1112)
9 CHL00001 rpoB RNA polymerase b 100.0 4E-219 9E-224 2035.1 72.9 940 38-1146 9-1057(1070)
10 CHL00207 rpoB RNA polymerase b 100.0 4E-205 1E-209 1896.8 74.2 931 38-1146 4-1052(1077)
11 PRK09603 bifunctional DNA-dire 100.0 2E-194 5E-199 1851.0 73.0 951 28-1147 11-1374(2890)
12 PRK14844 bifunctional DNA-dire 100.0 5E-190 1E-194 1804.8 72.3 958 24-1148 11-1433(2836)
13 PRK07225 DNA-directed RNA poly 100.0 4E-184 1E-188 1640.0 52.0 597 544-1148 4-603 (605)
14 TIGR03670 rpoB_arch DNA-direct 100.0 3E-183 7E-188 1630.9 49.9 594 547-1148 1-597 (599)
15 PF00562 RNA_pol_Rpb2_6: RNA p 100.0 1E-111 2E-116 981.7 19.7 367 674-1053 1-386 (386)
16 PRK09606 DNA-directed RNA poly 100.0 2E-106 4E-111 966.9 43.3 486 28-531 2-492 (494)
17 PF04563 RNA_pol_Rpb2_1: RNA p 100.0 1.7E-44 3.8E-49 386.4 15.4 147 43-192 1-149 (203)
18 PF04560 RNA_pol_Rpb2_7: RNA p 100.0 6E-31 1.3E-35 237.7 6.0 81 1055-1146 1-81 (81)
19 PF04565 RNA_pol_Rpb2_3: RNA p 99.9 3.3E-26 7.2E-31 200.7 1.9 66 446-511 1-68 (68)
20 PF04561 RNA_pol_Rpb2_2: RNA p 99.8 2.2E-21 4.8E-26 205.5 10.4 175 193-370 1-190 (190)
21 PF04566 RNA_pol_Rpb2_4: RNA p 99.7 4.9E-17 1.1E-21 140.1 8.9 63 547-609 1-63 (63)
22 KOG0215 RNA polymerase III, se 99.1 6.9E-13 1.5E-17 156.8 -12.3 537 22-604 91-638 (1153)
23 KOG0214 RNA polymerase II, sec 99.0 2.2E-11 4.7E-16 146.3 -4.7 317 740-1098 734-1059(1141)
24 PF04567 RNA_pol_Rpb2_5: RNA p 98.8 1.6E-09 3.6E-14 88.7 2.7 41 629-669 1-48 (48)
25 COG0085 RpoB DNA-directed RNA 98.1 9.2E-06 2E-10 103.2 10.2 75 661-755 525-599 (1060)
26 PF06883 RNA_pol_Rpa2_4: RNA p 97.5 0.0001 2.2E-09 62.9 4.4 49 554-602 1-58 (58)
27 PHA03394 lef-8 DNA-directed RN 95.8 0.025 5.5E-07 69.8 8.5 124 884-1018 694-828 (865)
28 COG1645 Uncharacterized Zn-fin 53.0 8.7 0.00019 38.5 2.0 28 1089-1118 28-55 (131)
29 PF04941 LEF-8: Late expressio 51.1 23 0.00049 44.5 5.4 35 357-391 209-243 (748)
30 PF09082 DUF1922: Domain of un 43.9 15 0.00032 32.6 1.8 48 1088-1137 2-55 (68)
31 PF14251 DUF4346: Domain of un 41.6 13 0.00029 36.4 1.2 14 167-180 10-23 (119)
32 PRK00398 rpoP DNA-directed RNA 38.2 28 0.00061 28.3 2.5 27 1089-1115 3-29 (46)
33 COG1545 Predicted nucleic-acid 36.1 23 0.0005 36.1 2.1 37 1085-1125 25-61 (140)
34 PF09538 FYDLN_acid: Protein o 34.3 20 0.00043 35.0 1.2 31 1088-1119 8-38 (108)
35 PRK06266 transcription initiat 33.8 24 0.00053 37.5 1.9 45 1070-1115 99-144 (178)
36 PRK14890 putative Zn-ribbon RN 33.8 19 0.00041 31.1 0.8 32 1084-1115 2-33 (59)
37 PF02150 RNA_POL_M_15KD: RNA p 33.3 27 0.00058 27.0 1.5 26 1090-1115 2-28 (35)
38 smart00661 RPOL9 RNA polymeras 33.0 25 0.00055 29.0 1.5 25 1091-1115 2-28 (52)
39 COG1096 Predicted RNA-binding 31.5 28 0.00061 37.0 1.8 35 1090-1127 150-184 (188)
40 PRK00420 hypothetical protein; 30.9 30 0.00065 33.9 1.8 25 1090-1115 24-48 (112)
41 PF07754 DUF1610: Domain of un 30.6 31 0.00068 24.4 1.3 23 1092-1114 1-23 (24)
42 PF06677 Auto_anti-p27: Sjogre 30.3 37 0.0008 27.3 1.9 24 1090-1114 18-41 (41)
43 cd00729 rubredoxin_SM Rubredox 25.7 48 0.001 25.4 1.7 26 1089-1116 2-27 (34)
44 TIGR02300 FYDLN_acid conserved 24.9 41 0.00089 33.6 1.6 28 1088-1116 8-35 (129)
45 PRK13130 H/ACA RNA-protein com 24.6 56 0.0012 28.1 2.1 24 1088-1117 4-27 (56)
46 PF13248 zf-ribbon_3: zinc-rib 24.2 33 0.00072 24.5 0.6 22 1090-1115 3-24 (26)
47 PF13533 Biotin_lipoyl_2: Biot 24.1 55 0.0012 27.1 2.0 16 819-834 17-32 (50)
48 PF08271 TF_Zn_Ribbon: TFIIB z 23.2 64 0.0014 25.8 2.1 24 1091-1114 2-26 (43)
49 PF07295 DUF1451: Protein of u 22.9 60 0.0013 33.5 2.4 26 1090-1115 113-138 (146)
50 COG0266 Nei Formamidopyrimidin 22.7 51 0.0011 37.4 2.0 12 173-184 77-88 (273)
51 COG2956 Predicted N-acetylgluc 20.9 77 0.0017 36.7 2.9 16 287-302 67-82 (389)
52 TIGR00373 conserved hypothetic 20.8 55 0.0012 34.1 1.6 45 1070-1115 91-136 (158)
53 COG1592 Rubrerythrin [Energy p 20.7 70 0.0015 33.6 2.4 24 1089-1115 134-157 (166)
54 COG1996 RPC10 DNA-directed RNA 20.3 66 0.0014 26.9 1.7 28 1088-1115 5-32 (49)
No 1
>PRK08565 DNA-directed RNA polymerase subunit B; Provisional
Probab=100.00 E-value=5e-278 Score=2618.64 Aligned_cols=1090 Identities=41% Similarity=0.696 Sum_probs=999.0
Q ss_pred ccccccccccccchHHHHHHHHHHHHHhCHHHHHHhcccceecCCCcEEEEEeEEEEcCCccccCC-cCCCCChhhHhhc
Q 001125 31 KFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDG-VSEKLNPHMCRLS 109 (1149)
Q Consensus 31 ~~~~i~~~~~~~~Lv~~qi~SFn~Fi~~gL~~ii~~~~~I~~~~~~~~~l~~~~i~i~~P~~~e~~-~~~~l~P~EcR~r 109 (1149)
.|.++++||+.++|++||++|||+|+++||++++++++||+.. ++++.|+|++++|++|++.+++ ...+|+|+|||+|
T Consensus 1 ~~~li~~~~~~~~Lv~~qidSFn~Fi~~gL~~iv~~~~pI~~~-~~~~~L~f~~i~l~~P~~~~~~~~~~~l~P~ecR~r 79 (1103)
T PRK08565 1 RWTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDEFGEIKTE-IPGLKIVLGKIRVGEPEIKEADGSERPITPMEARLR 79 (1103)
T ss_pred CchHHHHHhcccChHHHHHHHHHHHHHHhHHHHHHhcCCEEec-CCCEEEEEEEEEECCCcccccccccCCCCHHHHHhc
Confidence 4999999999999999999999999999999999999999764 6789999999999999997665 5678999999999
Q ss_pred CCccCccEEEEEEEEECCcccceeeEEeeEEeeccceeeccccccCCCCCHHHHHhcCCCCCCCCcEEEEcCchhhhHHh
Q 001125 110 DMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQ 189 (1149)
Q Consensus 110 ~lTYsa~l~v~i~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~elv~~~E~~~d~GGYFIING~ERVI~~q 189 (1149)
++||+|||+|+|+++.++ ...++++|++|+|||||+|++|||++++|+||++.||||+|+||||||||+|||||+|
T Consensus 80 ~lTYsa~l~v~i~~~~~~----~~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~p~D~GGYFIING~ERVI~~q 155 (1103)
T PRK08565 80 NLTYAAPLYLTMIPVENG----IEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQ 155 (1103)
T ss_pred CCCcceEEEEEEEEEECC----eeeEEEEEEeccCCeEeCCCcccCCCCCHHHHHhcCCCccCCCCeEEECCcEEEEEEE
Confidence 999999999999997654 4455668999999999999999999999999999999999999999999999999999
Q ss_pred hhccCCeEEEEeCCCC---cEEEEEEecCCCcc-eEEEEEeeCCEEEEEEceeeccccHHHHHHHhCCCCHHHHHHHhCC
Q 001125 190 EQLSKNRVIIDTDKKG---NINASVTSSTETVK-SKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGR 265 (1149)
Q Consensus 190 ~~~s~N~i~~~~~~~g---~~~a~v~s~~~~~~-s~~~~~~k~g~i~~r~~~~~~~IPi~ilLrALG~~sD~eI~~~i~~ 265 (1149)
|++++|+++++.+.++ .+.|.++|.++..+ +..+++..+|.++++++++.++||+++||||||++||+||++.|+.
T Consensus 156 ~~~s~n~~~~~~~~~~~~~~~~a~i~s~~~~~~~~~~l~~~~~g~i~~~~~~~~~~IPi~illkALG~~sD~eI~~~i~~ 235 (1103)
T PRK08565 156 EDLAPNRVLVDKGEAGSSITHTAKVISSRAGYRAQVTVERRKDGTIYVSFPAVPGKIPFVILMRALGLETDRDIVYAVSL 235 (1103)
T ss_pred EecCCCEEEEEEecCCCcceEEEEEEeccCCCcceEEEEEecCCeEEEEEcCcccEeeHHHHHHHcCCCCHHHHHHHhcc
Confidence 9999999998765432 36788988876543 3444445678999999987678999999999999999999999976
Q ss_pred chhHHhhhHHhHHHHHhcCC-cCHHHHHHHHhhhcccCCCCCCCCChHHHHHHHHHhhhccCCCCCCCCCCCccchHHHH
Q 001125 266 DPRYSALLLPSIEECANLDI-YTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLANVPVHNNNFRPKCFYVAVM 344 (1149)
Q Consensus 266 ~~~~~~~l~~~l~~~~~~~i-~t~~~al~yIg~~~r~~~~~~~~~~~~e~~~~~L~~~ll~Hl~~~~~~~~~K~~~L~~M 344 (1149)
+..+.+.+..+++++. .+ .|+++||.|||++|++. .++.+ ..+.|+++|++++|||++.+..++.+|+++|++|
T Consensus 236 ~~~~~~~l~~~l~~~~--~~~~t~~~al~~ig~~~~~~--~~~~~-~~e~~~~~L~~~ll~Hig~~~~~~~~K~~~L~~M 310 (1103)
T PRK08565 236 DPEIQQELLPSLEQAS--SIAATVEDALDYIGKRVAIG--QPREY-RIERAEQILDKYLLPHLGTSPEDRIKKAYFLGQM 310 (1103)
T ss_pred cHHHHHHHHHHHHHhh--ccccCHHHHHHHHHHhccCC--CCCcc-HHHHHHHHHHhhCcccCCCcccchhHHHHHHHHH
Confidence 6666677777777653 25 79999999999999875 33445 6789999999999999997665567899999999
Q ss_pred HHHHHHhhcCCCCCCCcccccccEEccccHhHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccccccchHHHHH
Q 001125 345 LRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLE 424 (1149)
Q Consensus 345 i~kLl~~~~g~~~~DD~D~l~NkRv~l~G~Ll~~lfr~~l~~~~~~ik~~i~k~~~~~~~~~~~~~~~~i~~~~It~~i~ 424 (1149)
++||+++..|.+.+||+|||+||||+++|+||+.+||++|+++++.+|+++.+.+.+. ..+++..+++++.||++|+
T Consensus 311 i~kLl~l~~g~~~~DD~D~l~NKRv~l~G~Ll~~~fr~~l~~~~~~ik~~l~~~~~~~---~~~~~~~~i~~~~It~~i~ 387 (1103)
T PRK08565 311 ASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARG---RKLDLRAIVRPDIITERIR 387 (1103)
T ss_pred HHHHHhhhcCCCCCCCccccCCcEEccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc---ccCCHHHhcccchhhHHHH
Confidence 9999999999999999999999999999999999999999999999999998765432 2456777778889999999
Q ss_pred HHhccCCCcccccccccccceEEccccccccccccccccccccccccccCCCCccCCCCCcccccCCCCCCCcchhhhhc
Q 001125 425 RTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNL 504 (1149)
Q Consensus 425 ~~~sTGnw~~~~~~~q~sGvsq~l~rln~ls~LshlRrv~~~f~~~~k~t~~R~Lhps~wG~iCPveTPEG~~cGLi~~L 504 (1149)
+|||||||.. |++|+||+|+|+||+|+||||||+++++.+++|.++||+||||||||+||||||||++||||+||
T Consensus 388 ~~~sTGnw~~-----~~sGvSq~ldr~N~l~~lSh~Rrv~s~~~r~~~~~~vR~Lhps~wG~iCPveTPEG~~cGLv~~L 462 (1103)
T PRK08565 388 HALATGNWVG-----GRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNL 462 (1103)
T ss_pred HHHhcCcccc-----CCcceEEecccCCHHHHHHHHhhccCCcccCCCCccccccChhhccccCCCCCCCccccchhhhh
Confidence 9999999984 67999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cceeeeccCCCchhHHHHHhhcCceeccccCccccCCCCceEEEECCeEEEeecChhhHHHHHHHHhhcCCcCceeEEEe
Q 001125 505 ALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFV 584 (1149)
Q Consensus 505 A~~a~Vt~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~lr~~rr~g~i~~~v~i~~ 584 (1149)
|++|+|+++.+..++.++|.++|+.++..+++... ...++|||||+|||++++|..|++.||.+||+|.++.+++|++
T Consensus 463 A~~a~It~~~~~~~i~~~l~~~G~~~~~~~~~~~~--~~~~~V~lnG~~iG~~~~~~~l~~~lR~~Rr~g~i~~~v~I~~ 540 (1103)
T PRK08565 463 ALMAQISVGVDEEEVEEILYELGVVPVEEAREEEY--ISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVAY 540 (1103)
T ss_pred hcccccccCCChHHHHHHHHHcCCCchhhcCcccC--CCceEEEECCEEEEEECCHHHHHHHHHHHhhcCCCCCeEEEEE
Confidence 99999999888899999999999998765544332 3568999999999999999999999999999999999999999
Q ss_pred cc--cCceEEEecCCCeeeeeEEEeecCcccchhhhHHhhhcCCcchhhhhccCceeEeccccccceEEEeecCCCCCCc
Q 001125 585 NE--KQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDT 662 (1149)
Q Consensus 585 ~~--~~~~i~I~td~GRl~RPl~~v~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~iE~id~~Eq~~~~Ia~~~~~~~~~~ 662 (1149)
+. ..++|+|+||+||++|||++|++|++.+++++++.++.+..+|++|+++|.|||||++||++++||+.++++...+
T Consensus 541 ~~~~~~~~i~I~sd~GRl~RP~~~v~~g~~~~~~~~~~~l~~~~~~~~~l~~~g~iEyid~~Ee~~~~Ia~~~~~l~~~~ 620 (1103)
T PRK08565 541 IETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTPEH 620 (1103)
T ss_pred ccccccceEEEecCCceeeeeEEEEecCceeccHHHHHHhhccccchhhHhhcCcEEeeCHHHhcCcEEeccccccCcce
Confidence 98 8899999999999999999999999999999999888778899999999999999999999999999999998778
Q ss_pred eeeeecCceeccccccccCCCCCCCCCccccccccccCCcccceeeeccccccceeeecCCCcceeechhhhhccCCCCC
Q 001125 663 THIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDKLG 742 (1149)
Q Consensus 663 th~Ei~P~~ilsv~AslIPF~~hNqSpRn~yq~~M~KQa~G~~~~n~~~R~D~~~y~L~ypQ~PlV~t~~~~~~~~~~~p 742 (1149)
||+||+|.+|||++||+|||+||||||||||||||||||||++++|+..|+|++.|+|+|||+|||+|+.++.++++++|
T Consensus 621 th~Ei~p~~ilsv~asliPF~~hNqspRn~yq~~M~KQa~g~~~~n~~~r~d~~~~~l~~pQ~Plv~t~~~~~~~~~~~p 700 (1103)
T PRK08565 621 THLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRP 700 (1103)
T ss_pred eccccCCccccceeeeccCCcccCcccchhhhhhhhhcccccccccceEeecCCcceeecCceeEEEeccccccccccCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcceEEEEEecCCCCCCCcEEeecccccccceeEEEEEEEEEEeecccCCccceecCCCCCC---CchhhhccCCCCcc
Q 001125 743 AGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILRPDRTG---PGAERMQILDDDGL 819 (1149)
Q Consensus 743 ~G~N~iVAv~~~~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~~~~~~p~~~~---~~~~~~~~Ld~dGi 819 (1149)
+|+||+||||||+||||||||||||+|+|||||||+||++|+++++++..+..+.+..|.... .+...|++||+|||
T Consensus 701 ~G~N~iVAv~sy~GYn~EDaiIink~s~~rG~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ld~dGi 780 (1103)
T PRK08565 701 AGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIPEPNVRGYRGEEYYRKLDEDGI 780 (1103)
T ss_pred CCeeEEEEEEcccCcchHHhhhhhhhhhhcCCceEEEEEEEEEEeeecCCCCceEEecCCCcccccCchhhhhcCCCCCC
Confidence 999999999999999999999999999999999999999999998876666666676653211 12246899999999
Q ss_pred cCCCceeCCCCEEEEEecCCCCCCCCCCCCCCCCcccccceeeecCCCCCceEEEEEEEeeCCCCcEEEEEEEeeecCCC
Q 001125 820 AAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLIRHTRRPE 899 (1149)
Q Consensus 820 ~~~G~~v~~gd~l~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~v~~~~~~~~~~~vkv~~~~~R~p~ 899 (1149)
|++|++|++|||||||++|..+...... .+......+++|++++.+| .|+||+|.++.++++.+.|||++|+.|+|+
T Consensus 781 ~~~G~~v~~gdili~k~~p~~~~~~~~~-~~~~~~~~~~~s~~~~~~e--~g~V~~V~~~~~~~~~~~vkv~ir~~R~p~ 857 (1103)
T PRK08565 781 VSPEVEVKGGDVLIGKTSPPRFLEELEE-LSLGLQERRDTSVTVRHGE--KGIVDTVLITESPEGNKLVKVRVRDLRIPE 857 (1103)
T ss_pred cCCCcEEcCCCEEEEEecCCCCCcchhh-ccccCCccccceEEecCCC--ceEEEEEEEEecCCCcEEEEEEEEEEecCc
Confidence 9999999999999999999753321100 0111234789999999998 999999999988888999999999999999
Q ss_pred ccccccccCCCccEEEeeeccCCCCCCCCCCCCcEEeCCCCCCCCchHHHHHHHhccccccccCceeeeeeccCCCCCCC
Q 001125 900 LGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHAD 979 (1149)
Q Consensus 900 iGDKf~sRhGqKGvvs~i~~~eDmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tpF~~~~~~~~ 979 (1149)
||||||||||||||||+|||+||||||+||++|||||||||||||||||||+|+++||||++.|.+.|+|||. +.
T Consensus 858 iGDKfssRhGqKGv~s~i~~~edmPf~~~G~~pDiI~NPh~~PSRMtiG~l~E~~~gk~~~~~g~~~d~t~F~-----~~ 932 (1103)
T PRK08565 858 LGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFY-----GE 932 (1103)
T ss_pred hhhhhhhhccCcceeeeecccccCCcCCCCCCccEEECCCCCcccccHHHHHHHHHHHHHHhcCceeeecCcC-----Cc
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999 57
Q ss_pred CHHHHHHHHHHcCCCCCCceEEEeCCCCcEEeeeEeEeeeeecccccccCcccEEecccCcccccccCcccccCCCceee
Q 001125 980 TVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGLRV 1059 (1149)
Q Consensus 980 ~~~~~~~~l~~~g~~~~G~e~ly~G~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~ 1059 (1149)
.++++++.|+++||+++|+|+||||+||++|+++||+|++|||||+|||+||+|||++||++.|||||++||||+|||||
T Consensus 933 ~~~~~~~~L~~~g~~~~G~e~l~~G~tG~~~~~~if~G~~yy~rL~HmV~DK~~~R~~Gp~~~lt~QP~~Gr~~~GG~R~ 1012 (1103)
T PRK08565 933 PEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRF 1012 (1103)
T ss_pred hHHHHHHHHHHcCCCCCCcEEEEcCCCCCCcccceEEeehhheechhhhchhhhhccCCCcchhhhCCccccccCCCeee
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred echhhhHHHHcccHHHHHHhhccCCCceeeeecccCCcceeecccccceecccccCCCccccccccHhHHHHHHHHHhCC
Q 001125 1060 GEMERDCLIAYGASMLIFERLMVSSDPFEVQVCRVCGLLGYYNHKLKAGICSTCKNGDNISSMKLPYACKLLIQELQSMN 1139 (1149)
Q Consensus 1060 GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~cg~~~~~~~~~~~~~C~~c~~~~~~~~v~iPy~~k~l~~EL~sm~ 1139 (1149)
||||||||+|||||++|+|||+++||++.++||.+||++++.+.+.+..+|+.|+++.++.++.+|||||||+|||+|||
T Consensus 1013 GEME~d~l~a~Gas~~L~erL~~~SD~~~~~vC~~Cg~~~~~~~~~~~~~C~~c~~~~~~~~v~iPy~~k~l~~EL~sm~ 1092 (1103)
T PRK08565 1013 GEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHIAWYDRRKNKYVCPIHGDKGNISPVEVSYAFKLLLQELMSMG 1092 (1103)
T ss_pred ecchHHHHHhcccHHHHHHHhhccccceeeeeecccccccccccccCceeccccCCCCcceeccCChhHHHHHHHHHhCC
Confidence 99999999999999999999999999999999999999997655555677999999888999999999999999999999
Q ss_pred cccEEEecc
Q 001125 1140 IVPRLKLAE 1148 (1149)
Q Consensus 1140 i~~~l~~~~ 1148 (1149)
|+++|.+++
T Consensus 1093 i~~~l~~~~ 1101 (1103)
T PRK08565 1093 ISPRLKLGD 1101 (1103)
T ss_pred CceEEEeee
Confidence 999999975
No 2
>KOG0215 consensus RNA polymerase III, second largest subunit [Transcription]
Probab=100.00 E-value=1.7e-275 Score=2329.85 Aligned_cols=1112 Identities=67% Similarity=1.128 Sum_probs=1062.1
Q ss_pred ccccccCCCcccccccccccccccccchHHHHHHHHHHHHHhCHHHHHHhcccceecCCCcEEEEEeEEEEcCCccccCC
Q 001125 17 DKQKLAAPVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDG 96 (1149)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~i~~~~~~~~Lv~~qi~SFn~Fi~~gL~~ii~~~~~I~~~~~~~~~l~~~~i~i~~P~~~e~~ 96 (1149)
+++..+++..+.+|+|.++|+||+.+|||++|++|||+|++++|+.|++++..|.++.++.+.|+|.++++++|.+.++.
T Consensus 32 ~~~~~~~~i~~~~dk~~lvp~flkvkglvkqhldsfnyfv~~~ik~iv~an~~itsd~dp~fylky~dirvg~Ps~~~~~ 111 (1153)
T KOG0215|consen 32 DGKKLSDPIKPLEDKWQLVPAFLKVKGLVKQHLDSFNYFVDVDIKKIVKANQLITSDVDPSFYLKYLDIRVGKPSIEEGN 111 (1153)
T ss_pred ccccccCCCCChHHhHHhHHHHHhhhhHHHHHHhhhhhhhhhhHHHHHHhhcccCcCcCchhhheeeeeeccCcchhhcc
Confidence 56678889999999999999999999999999999999999999999999999999999999999999999999998765
Q ss_pred --cCCCCChhhHhhcCCccCccEEEEEEEEECCcccceeeEEeeEEeeccceeeccccccCCCCCHHHHHhcCCCCCCCC
Q 001125 97 --VSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPG 174 (1149)
Q Consensus 97 --~~~~l~P~EcR~r~lTYsa~l~v~i~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~elv~~~E~~~d~G 174 (1149)
....++|+|||+|++||+||++|+++++.+. ..+.+++|.||++|||+||++|+|++.++.|+++.+|||+|||
T Consensus 112 ~~~~~~i~p~ecrlrd~tysa~i~vdieytrg~----~~~~~~~v~igrmpimlrs~rcvl~~~~e~~~a~~~ecpldpg 187 (1153)
T KOG0215|consen 112 NVTNDNITPHECRLRDMTYSAPIYVDIEYTRGR----QIIAKRDVIIGRMPIMLRSSKCVLRGKDEEELARLNECPLDPG 187 (1153)
T ss_pred ccccccCCchheeehhhhcccceeEEEEEecCc----ceEEecccccccchhhhhccccccCCccHHHHHHhccCCCCCC
Confidence 5568999999999999999999999999887 5677889999999999999999999999999999999999999
Q ss_pred cEEEEcCchhhhHHhhhccCCeEEEEeCCCCcEEEEEEecCCCcceEEEEEeeCCEEEEEEceeeccccHHHHHHHhCCC
Q 001125 175 GYFIIKGTEKVLLIQEQLSKNRVIIDTDKKGNINASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGME 254 (1149)
Q Consensus 175 GYFIING~ERVI~~q~~~s~N~i~~~~~~~g~~~a~v~s~~~~~~s~~~~~~k~g~i~~r~~~~~~~IPi~ilLrALG~~ 254 (1149)
|||||+|.||||+.||+.+.|++++..+++|++-|++.|++.+.+++++++.+++++|++++.+.++||++++|||+|..
T Consensus 188 gyfiv~G~ekViLiqeqlsknrii~~~~k~~~~~~svtsst~e~kskt~v~~k~~k~ylk~~~~~d~ipiviv~ka~g~~ 267 (1153)
T KOG0215|consen 188 GYFIVKGTEKVILIQEQLSKNRIIVEEDKKGNLQASVTSSTHERKSKTYVTTKKGKYYLKHNSFTDDIPIVIVLKAMGLE 267 (1153)
T ss_pred ceeEeccceeEEEehhhhhccCeeeccccCCccccccccceeeecceEEEEeccceeeeehhhhhccCCEEEEEeecccc
Confidence 99999999999999999999999997777888999999999999999999999999999999999999999999999999
Q ss_pred CHHHHHHHhCCchhHHhhhHHhHHHHHhcCCcCHHHHHHHHhhhcccCCCCCCCCChHHHHHHHHHhhhccCCCCCCCCC
Q 001125 255 SDQEVVQMVGRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLANVPVHNNNF 334 (1149)
Q Consensus 255 sD~eI~~~i~~~~~~~~~l~~~l~~~~~~~i~t~~~al~yIg~~~r~~~~~~~~~~~~e~~~~~L~~~ll~Hl~~~~~~~ 334 (1149)
+|+||.+.++.+++|.+.+.++++++...+++|+++||+|++.++.... .+..+ ..+.|.++|...+++|++....++
T Consensus 268 sd~ei~~~vg~~~~y~~~~~~s~ee~~~~~v~tqqqal~y~~~kvk~~~-~t~~~-~~~e~~~~l~~~~lahv~v~~~~~ 345 (1153)
T KOG0215|consen 268 SDQEIVQLVGGDSKYQDIFAPSLEECVSLGVYTQQQALEYIGSKVKVKR-GTTPT-KDEEALEVLSTTVLAHVPVPDLNF 345 (1153)
T ss_pred chHHHHHHhhcchHHHHhhccchhhhhhhhhHHHHHHHHHhhheEEecc-CCCCC-chHHHHHHHHhhheeceeccCCCC
Confidence 9999999998899999999999999999999999999999999887653 22334 678899999999999999988899
Q ss_pred CCccchHHHHHHHHHHhhcCCCCCCCcccccccEEccccHhHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccc
Q 001125 335 RPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFI 414 (1149)
Q Consensus 335 ~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~NkRv~l~G~Ll~~lfr~~l~~~~~~ik~~i~k~~~~~~~~~~~~~~~~i 414 (1149)
+.|+.+++.|+|+++....+.-..||+|.++|||+.++|+|+..+|++.|+++...++..+.+.+.+......+|+.+.+
T Consensus 346 r~K~~yi~~m~rr~~~a~l~~~~~ddrd~~gnkrlelagqllsllfeD~fk~~n~e~k~~~dk~l~k~~ra~~fD~~~~~ 425 (1153)
T KOG0215|consen 346 RMKAIYIGLMVRRVIQAMLNKLAMDDRDYVGNKRLELAGQLLSLLFEDLFKRFNSELKKNIDKILKKPIRAQEFDALKHL 425 (1153)
T ss_pred cceeehHHHHHHHHHHHHhCcccccchhhhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhhhhhhHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999998886666678887777
Q ss_pred --cccchHHHHHHHhccCCCcccccccccccceEEccccccccccccccccccccccccccCCCCccCCCCCcccccCCC
Q 001125 415 --VRDSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDT 492 (1149)
Q Consensus 415 --~~~~It~~i~~~~sTGnw~~~~~~~q~sGvsq~l~rln~ls~LshlRrv~~~f~~~~k~t~~R~Lhps~wG~iCPveT 492 (1149)
.++.||++|..++|||||..++|.|.|+|+||+|+|++|+++|+++.|++++|++++|.++||.|||||||.+||++|
T Consensus 426 n~~~~~it~~l~ra~stgnw~iKrfrmer~gvt~VlsrlSyisaLgmmtri~s~fektrkvsgprSlq~sqwgmlcp~dt 505 (1153)
T KOG0215|consen 426 NVRANMITSGLERAISTGNWSIKRFRMERAGVTQVLSRLSYISALGMMTRINSQFEKTRKVSGPRSLQPSQWGMLCPSDT 505 (1153)
T ss_pred HHHHHHHHHHHHHHhhcCchHHHHhhhhhccceeeehhhhhhhhhhhheehhhhheeehhccCccccChhhcccccCCCC
Confidence 578999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCcchhhhhccceeeeccCCCchhHHHHHhhcCceeccccCccccCCCCceEEEECCeEEEeecChhhHHHHHHHHhh
Q 001125 493 PEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRR 572 (1149)
Q Consensus 493 PEG~~cGLi~~LA~~a~Vt~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~lr~~rr 572 (1149)
|||+.|||++|||++++|+++..+.|+..++..+|+.++..++..+++.+..+.|||||.++|.+..|+.|+..+|.+||
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 99999999999999999999999999999999999999998888888888899999999999999999999999999999
Q ss_pred cCCcCceeEEEecccCceEEEecCCCeeeeeEEEeecCcccchhhhHHhhhcCCcchhhhhccCceeEeccccccceEEE
Q 001125 573 AGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIA 652 (1149)
Q Consensus 573 ~g~i~~~v~i~~~~~~~~i~I~td~GRl~RPl~~v~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~iE~id~~Eq~~~~Ia 652 (1149)
+|.+..+|+++.+..+..++|.||+||+|||+++|++|.+.+++.|+++++.+..+|+||++.|.|||+|++||+.++||
T Consensus 586 ~G~i~~fvsv~~~~~q~~v~i~sdggr~crp~Iiv~~~~~~v~~~h~~el~~g~r~F~DFl~~glvEYLDVNEEND~~Ia 665 (1153)
T KOG0215|consen 586 KGKIGEFVSVFTNTTQRCVYIASDGGRVCRPLIIVDNGRPRVKQHHMDELLDGKRTFDDFLKDGLIEYLDVNEENDSLIA 665 (1153)
T ss_pred cCcccceeeeeeeeeeEEEEEecCCCeEeeeEEEEeCCcchhhhhhHHHHHHhhhhHHHHHHhchhheeecccccCceEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eecCCCCCCceeeeecCceeccccccccCCCCCCCCCccccccccccCCcccceeeeccccccceeeecCCCcceeechh
Q 001125 653 LYEGDATPDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRT 732 (1149)
Q Consensus 653 ~~~~~~~~~~th~Ei~P~~ilsv~AslIPF~~hNqSpRn~yq~~M~KQa~G~~~~n~~~R~D~~~y~L~ypQ~PlV~t~~ 732 (1149)
+.++++.+++||+||.|..+||+||+|||||||||||||+|||+|+|||||.++||+..|+|+.+|.|.|||+|+|+|++
T Consensus 666 lye~~I~~~TTHLEIEPFTiLGv~AGLIPYPHHNQSPRNTYQCAMGKQAmG~IaYNQ~~RiDtlmYll~YPq~PmVkTKT 745 (1153)
T KOG0215|consen 666 LYEEDIGPETTHLEIEPFTILGVVAGLIPYPHHNQSPRNTYQCAMGKQAMGAIAYNQKKRIDSLLYLLVYPQRPMVKTKT 745 (1153)
T ss_pred echhhcCCCcceeeecchhhhhhhccccCCCCCCCCCcchhhhhhhhhhhhhhhhhhhhhHHHHHHHHhcCCCcccccee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhccCCCCCCCcceEEEEEecCCCCCCCcEEeecccccccceeEEEEEEEEEEeecccCCccceecCCCCC---CCchh
Q 001125 733 IELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILRPDRT---GPGAE 809 (1149)
Q Consensus 733 ~~~~~~~~~p~G~N~iVAv~~~~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~~~~~~p~~~---~~~~~ 809 (1149)
+++++++++|+||||.||||||+|||+|||+|+||+|+||||+|+.+||+.++.++++.++..|++..|-.+ .++..
T Consensus 746 IELi~ydKLPAGQNAtVAVMSYSGYDIEDALVLNKsSlDRGfGRC~Vyk~~~~~~kkY~N~T~Drimgp~~d~~t~kpi~ 825 (1153)
T KOG0215|consen 746 IELINYDKLPAGQNATVAVMSYSGYDIEDALVLNKSSIDRGFGRCEVYKKTTTTLKKYANGTFDRIMGPQLDPNTRKPIW 825 (1153)
T ss_pred EEeeccccCCCCCccEEEEEeccCCchhhhhhcccchhccCcceEEEEeeeeeeeeecCCCchhhhcccccCCCcCCcch
Confidence 999999999999999999999999999999999999999999999999999999999999988988877643 33445
Q ss_pred hhccCCCCcccCCCceeCCCCEEEEEecCCCCCCCCCCCCCCCCcccccceeeecCCCCCceEEEEEEEeeCCCCcEEEE
Q 001125 810 RMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGDLCIK 889 (1149)
Q Consensus 810 ~~~~Ld~dGi~~~G~~v~~gd~l~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~v~~~~~~~~~~~vk 889 (1149)
....||+|||..||..|++|+|+|.|-.|.....+..+. ...+..|++.++.||.+| +++||+|.++.++++..++|
T Consensus 826 kh~vLd~DGl~~pG~~V~~~qi~iNK~mP~vt~~~~~~~-~~~~~~Yk~~pitykgpe--psyidkVmls~n~~dq~LIK 902 (1153)
T KOG0215|consen 826 KHQVLDDDGLATPGERVQPGQIYINKQMPTVTGTSLPGL-SASQVQYKAVPITYKGPE--PSYIDRVMLTSNDEDQFLIK 902 (1153)
T ss_pred hhcccCcccCCCCccEeccCcEEEeccCCCcccccCCCC-CccccccccccceecCCC--cchhheeEeecCccccHHHH
Confidence 667899999999999999999999998887665432221 112235899999999999 99999999999989999999
Q ss_pred EEEeeecCCCccccccccCCCccEEEeeeccCCCCCCCCCCCCcEEeCCCCCCCCchHHHHHHHhccccccccCceeeee
Q 001125 890 FLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGS 969 (1149)
Q Consensus 890 v~~~~~R~p~iGDKf~sRhGqKGvvs~i~~~eDmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~t 969 (1149)
+.+|+.|+|++|||||||||||||||.|++||||||...||+|||||||||||||||||.++|.+.||||.+.|.|++||
T Consensus 903 ~llRQTRrPElGDKFSSRHGQKGVcGlIv~QEDMPFnD~GIcPDiIMNPHGFPSRMTVGK~iELlsGKAGVl~G~~hYGT 982 (1153)
T KOG0215|consen 903 VLLRQTRRPELGDKFSSRHGQKGVCGLIVQQEDMPFNDQGICPDIIMNPHGFPSRMTVGKMIELLSGKAGVLEGTFHYGT 982 (1153)
T ss_pred HHHhhccCcccccccccccCCCceeeEEeeccCCCCcccCCCcccccCCCCCcccchHHHHHHHhccccceeeeeEeecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eccCCCCCCCCHHHHHHHHHHcCCCCCCceEEEeCCCCcEEeeeEeEeeeeecccccccCcccEEecccCcccccccCcc
Q 001125 970 AFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTE 1049 (1149)
Q Consensus 970 pF~~~~~~~~~~~~~~~~l~~~g~~~~G~e~ly~G~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~ 1049 (1149)
+|. +++++++++.|.++||||.||+.+|||+||+|++|+||+||+|||||+|||.||+|||++||+..|||||++
T Consensus 983 aFG-----gskVed~~~~Lv~hGfnY~GKD~ltSGITGepLeAYIffGPiYYQKLKHMVlDKMHARARGPRAvLTRQPTE 1057 (1153)
T KOG0215|consen 983 AFG-----GSKVEDISEELVEHGFNYSGKDMLTSGITGEPLEAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTE 1057 (1153)
T ss_pred ccC-----CchHHHHHHHHHHhccCccCccccccCCCCCcceeeEEechHHHHHHHHHHHHHHhhhccCCceeeecCCCC
Confidence 999 899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCCceeeechhhhHHHHcccHHHHHHhhccCCCceeeeecccCCcceeecccccceecccccCCCccccccccHhHH
Q 001125 1050 GRARNGGLRVGEMERDCLIAYGASMLIFERLMVSSDPFEVQVCRVCGLLGYYNHKLKAGICSTCKNGDNISSMKLPYACK 1129 (1149)
Q Consensus 1050 Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~cg~~~~~~~~~~~~~C~~c~~~~~~~~v~iPy~~k 1129 (1149)
||||+||+|+||||||||||||||.+|-|||+++||.+++.||..||.++|. .||..|+++.++.++.||||||
T Consensus 1058 GRSrdGGLRLGEMERDCLIaYGASmLl~ERLMiSSDaFeVdVC~~CGllgyk------gwC~~Ckss~~v~~~~iPYAcK 1131 (1153)
T KOG0215|consen 1058 GRSRDGGLRLGEMERDCLIAYGASMLLLERLMISSDAFEVDVCRQCGLLGYK------GWCTTCKSSKNVAKMKIPYACK 1131 (1153)
T ss_pred CcCCCCCcccchhhhhhhhhccHHHHHHHHHhhcCcceeeeeccccccceec------hhhhhccCCCceeeeeccHHHH
Confidence 9999999999999999999999999999999999999999999999999998 9999999999999999999999
Q ss_pred HHHHHHHhCCcccEEEecc
Q 001125 1130 LLIQELQSMNIVPRLKLAE 1148 (1149)
Q Consensus 1130 ~l~~EL~sm~i~~~l~~~~ 1148 (1149)
||||||+||||-|||.+++
T Consensus 1132 LLFQEL~SMNi~PrL~L~~ 1150 (1153)
T KOG0215|consen 1132 LLFQELQSMNIVPRLKLED 1150 (1153)
T ss_pred HHHHHHHhcCccceeeecc
Confidence 9999999999999999875
No 3
>KOG0214 consensus RNA polymerase II, second largest subunit [Transcription]
Probab=100.00 E-value=1.1e-265 Score=2278.35 Aligned_cols=1103 Identities=38% Similarity=0.645 Sum_probs=1011.1
Q ss_pred cccccccccccccccchHHHHHHHHHHHHHhCHHHHHHhcccceecC--------CCcEEEEEeEEEEcCCccccCC-cC
Q 001125 28 VVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGI--------DPSIFLRFKDVRIGQPSMTVDG-VS 98 (1149)
Q Consensus 28 ~~~~~~~i~~~~~~~~Lv~~qi~SFn~Fi~~gL~~ii~~~~~I~~~~--------~~~~~l~~~~i~i~~P~~~e~~-~~ 98 (1149)
+++.|.+|++||+.+||+++|++|||.||+.++++|+.+.++|+... -.++.|.|+.+++.+|+..|.| ..
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 68899999999999999999999999999999999999999987431 2358999999999999999988 88
Q ss_pred CCCChhhHhhcCCccCccEEEEEEEEECCcc-cceeeEEeeEEeeccceeeccccccCCCCCHHHHHhcCCCCCCCCcEE
Q 001125 99 EKLNPHMCRLSDMTYAAPILVNIEYVQGSHT-EKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYF 177 (1149)
Q Consensus 99 ~~l~P~EcR~r~lTYsa~l~v~i~~~~~~~~-~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~elv~~~E~~~d~GGYF 177 (1149)
..++|+|||+|++|||+||||++........ ++...+++.|+||+||||+||..|.|+++++.+|.+.+|||+|+||||
T Consensus 82 ~~m~p~eARlrnLTYSspLyVd~~k~~~~~~~~~~~~~~qkvfIGkIPiMlrS~~C~l~~~~d~dl~~l~eCp~DqgGyf 161 (1141)
T KOG0214|consen 82 STMFPNEARLRNLTYSSPLYVDATKIVKTSRDEVEDMQEQKVFIGKIPIMLRSSYCLLSGLTDKDLTELGECPYDQGGYF 161 (1141)
T ss_pred cccCchhhHhhhcccccceEEEeEEEEeeccccccccccceeeEeccceeeehhhhhhcccchhhhhhccCCCcCCCceE
Confidence 8999999999999999999999987743311 123445678999999999999999999999999999999999999999
Q ss_pred EEcCchhhhHHhhhccCCeEEEEeCCC-Cc--EEEEEEecCC----CcceEEEEEe-eCC---EEEEEEceeeccccHHH
Q 001125 178 IIKGTEKVLLIQEQLSKNRVIIDTDKK-GN--INASVTSSTE----TVKSKTVIQM-EKG---KMYLLLNQFVKKIPIMV 246 (1149)
Q Consensus 178 IING~ERVI~~q~~~s~N~i~~~~~~~-g~--~~a~v~s~~~----~~~s~~~~~~-k~g---~i~~r~~~~~~~IPi~i 246 (1149)
||||+|||+++||++++|.+|+++.+. |. |.+.++|+.. ...+....++ +++ .+.+..++.+.+||+++
T Consensus 162 IINGseKVlIAQe~matn~vyvf~k~~p~~~ay~~EirS~le~~sR~~stl~v~~~ar~~~gq~i~~tlpyikqeIPI~i 241 (1141)
T KOG0214|consen 162 IINGSEKVLIAQEKMATNIVYVFKKAHPGTYAYTGEIRSCLERSSRFISTLSVNMDARAGKGQEIIATLPYIKQEIPILI 241 (1141)
T ss_pred EEcCceeeeeehhhccCceEEEEecCCCCceeEeeeeehhhhccCCCcceeeeeeccccCCCceEEEEeeeecccCcEEE
Confidence 999999999999999999999998654 44 5678887422 1122223333 333 67778888888999999
Q ss_pred HHHHhCCCCHHHHHHHhC---CchhHHhhhHHhHHHHHhcCCcCHHHHHHHHhhhcccCCCCCCCCChHHHHHHHHHhhh
Q 001125 247 VMKAMGMESDQEVVQMVG---RDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVF 323 (1149)
Q Consensus 247 lLrALG~~sD~eI~~~i~---~~~~~~~~l~~~l~~~~~~~i~t~~~al~yIg~~~r~~~~~~~~~~~~e~~~~~L~~~l 323 (1149)
||||||+.+|+||++.|. +|.++.+.+.++++++.- +..+.-||+|||+|-... ..+++. +++.|+++|.+++
T Consensus 242 lfrALG~v~dreILehIcYd~~D~em~e~lkpsieeafv--iq~qn~ALdfig~rga~~-Gvtkek-ri~yakdiLqKe~ 317 (1141)
T KOG0214|consen 242 LFRALGFVSDREILEHICYDFDDAEMFESLKPSIEEAFV--IQEQNVALDFIGQRGACI-GVTKEK-RIKYAKEILQKEL 317 (1141)
T ss_pred EehhhcCCccHHHHHhhcCCCCcHHHHHHhhhhhhhhhh--hhhhHHHHHHHHhcCCCC-CCCcch-hhHHHHHHHHHHh
Confidence 999999999999999993 688899999999998753 557889999999986432 123455 8899999999999
Q ss_pred ccCCCCCCCCCCCccchHHHHHHHHHHhhcCCCCCCCcccccccEEccccHhHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 001125 324 LANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPS 403 (1149)
Q Consensus 324 l~Hl~~~~~~~~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~NkRv~l~G~Ll~~lfr~~l~~~~~~ik~~i~k~~~~~~ 403 (1149)
|||++..+.....|++||+|||++|+.++.|++.+||+|||+|||++++|+||+.+||..|+++++++...++|.+++..
T Consensus 318 lPhi~~~e~~etkKA~fLGYmi~rlll~aLgRr~~ddRDHfG~KRLDlaGpLLa~lfR~lf~~l~rd~~~~mQk~le~~~ 397 (1141)
T KOG0214|consen 318 LPHVGLGEICETKKAYFLGYMVHRLLLAALGRRELDDRDHFGNKRLDLAGPLLAKLFRSLFAKLLRDVTRYMQKCLENGV 397 (1141)
T ss_pred ccccccchhhhhhHHHHHHhhHHHHHHHHcCCCCccchhhccccchhhchhHHHHHHHHHHHHHHHHHHHHHHHHHhcCc
Confidence 99999887777899999999999999999999999999999999999999999999999999999999999999988743
Q ss_pred CCCCCcccccccccchHHHHHHHhccCCCc-ccccccccccceEEccccccccccccccccccccccccccCCCCccCCC
Q 001125 404 RSSRFDLSQFIVRDSITVGLERTLSTGNFD-VKRFKMHRKGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPS 482 (1149)
Q Consensus 404 ~~~~~~~~~~i~~~~It~~i~~~~sTGnw~-~~~~~~q~sGvsq~l~rln~ls~LshlRrv~~~f~~~~k~t~~R~Lhps 482 (1149)
++++.-.|+++.||++++|+||||||+ .++.+..++||||+|+|+||+++||||||+++|+..++|...||+||||
T Consensus 398 ---dfni~~aika~iIt~gl~yslaTgnwgdq~ka~~~ragVsQVLnR~t~~sTLsHlRR~n~Pigr~GKlAkpRqlHnt 474 (1141)
T KOG0214|consen 398 ---DFNIELAIKAKIITNGLNYALATGNWGDQKKAMQGRAGVSQVLNRLNPLSTLSHLRRTNSPIGRTGKLAKPRQLHNS 474 (1141)
T ss_pred ---cceEEEEEEeeeecccceeeeccCCccchhHHhhccccHHHHhccccHHHHHHHHhhcCCccccccccCCccccCcc
Confidence 577877889999999999999999998 4555667899999999999999999999999999999999999999999
Q ss_pred CCcccccCCCCCCCcchhhhhccceeeeccCCCchhHHHHHhhcCceeccccCccccCCCCceEEEECCeEEEeecChhh
Q 001125 483 QWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKC 562 (1149)
Q Consensus 483 ~wG~iCPveTPEG~~cGLi~~LA~~a~Vt~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~ 562 (1149)
|||++||+|||||++||||||||+||.|+.+..+.|+.++|.++|++.++.+++... ++.++||+||.|+|.+.+|+.
T Consensus 475 hwGmvCPaeTPEGqacGLVKNLSLmayIsvGS~~sPi~EfLeewgmE~le~~~ps~~--~datkvfvNG~wvGlhrdp~~ 552 (1141)
T KOG0214|consen 475 HWGMVCPAETPEGQACGLVKNLSLMAYISVGSLESPIVEFLEEWGMENLEEISPSPS--PDATKVFVNGVWVGLHRDPEE 552 (1141)
T ss_pred cceeeccccCCCcceeeccccceEEEEEecCCCccHHHHHHHHhchhhHhhcCCCcC--CCceEEEEcccEEEecCCHHH
Confidence 999999999999999999999999999999999999999999999999998887654 368899999999999999999
Q ss_pred HHHHHHHHhhcCCcCceeEEEecccCceEEEecCCCeeeeeEEEeecCcccchhhhHHhhhcC---CcchhhhhccCcee
Q 001125 563 FADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDG---VRSFDDFLREGLIE 639 (1149)
Q Consensus 563 ~~~~lr~~rr~g~i~~~v~i~~~~~~~~i~I~td~GRl~RPl~~v~~~~~~~~~~~~~~~~~~---~~~~~~l~~~g~iE 639 (1149)
+++.||++||...++.++++..+...++++||||+||+|||+++|+|+++.+.++|++.|+.. ..+|..|+..|.+|
T Consensus 553 l~~tlr~lRR~~di~~Evs~vRDIr~kE~ri~tDaGR~~rPLliven~~l~~~k~hi~~L~~~~~~~~~w~~lv~~G~ie 632 (1141)
T KOG0214|consen 553 LVATLKRLRRQFDIIAEVSMVRDIRDKEIRIFTDAGRSLRPLLIVENAKLLIKKRHIRALKQSKPNEYRWAHLLSSGEVE 632 (1141)
T ss_pred HHHHHHHHHHhhccchhhhhhccccccceeeeeccCccccceEEEechhhhhhhHHHHHHhhCchhhcchhhhcccccee
Confidence 999999999999999999999999999999999999999999999999999999999999876 57999999999999
Q ss_pred EeccccccceEEEeecCCCCC-----CceeeeecCceeccccccccCCCCCCCCCccccccccccCCcccceeeeccccc
Q 001125 640 YLDVNEENNALIALYEGDATP-----DTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMD 714 (1149)
Q Consensus 640 ~id~~Eq~~~~Ia~~~~~~~~-----~~th~Ei~P~~ilsv~AslIPF~~hNqSpRn~yq~~M~KQa~G~~~~n~~~R~D 714 (1149)
|||++||+.++||+.++|+.. .||||||||+.|||++||.||||||||||||+||++|+|||||++.+|+..|+|
T Consensus 633 ~idteeEEtvmiam~~~dL~~~~~~~~~THCEiHpsmILgv~asiIpFpdh~qspr~tYQsa~~kqamg~y~tn~~vR~d 712 (1141)
T KOG0214|consen 633 YIDTEEEETVMIAMGPKDLAESAYPKTYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYHTNPQVRMD 712 (1141)
T ss_pred eeccchhhhHHHhcCHHHHhhccCCcccccccccHHHhhhhceeeeecCCCCCchHHHHHHHHhhhcceeeeecchhhhh
Confidence 999999999999999998853 599999999999999999999999999999999999999999999999999999
Q ss_pred cceeeecCCCcceeechhhhhccCCCCCCCcceEEEEEecCCCCCCCcEEeecccccccceeEEEEEEEEEEeecccCCc
Q 001125 715 SLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANST 794 (1149)
Q Consensus 715 ~~~y~L~ypQ~PlV~t~~~~~~~~~~~p~G~N~iVAv~~~~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~ 794 (1149)
+..|.|+|||+|+|+|+.+++..+.++|+|+|||||++||+|||||||||+|+++++||+|+|++|++|+.+..+...+.
T Consensus 713 tl~~~l~ypqkpl~tt~~~e~l~~~eL~aG~NaiVAi~~~~GYNqEDsvimn~s~v~rg~FrS~~~RsYk~q~~~~~~~~ 792 (1141)
T KOG0214|consen 713 TLAKVLYYPQKPLVTTRAMEYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSVDRGLFRSFFIRSYKDQEHKKDQGP 792 (1141)
T ss_pred hhhhcccccccchhhHHHHhhhhhhhcccccceEEEEecccCccHHHHHHHHhhhhhcchhhhhhhhHHHhhhhhccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999988777777
Q ss_pred cceecCCCCC-C--CchhhhccCCCCcccCCCceeCCCCEEEEEecCCCCCCCCCCCCCCCCcccccceeeecCCCCCce
Q 001125 795 SDRILRPDRT-G--PGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETC 871 (1149)
Q Consensus 795 ~~~~~~p~~~-~--~~~~~~~~Ld~dGi~~~G~~v~~gd~l~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 871 (1149)
++.|..|... . .....|++||+||++.+|++|..|||+|||.+|....++..... .+....+|+|+.++++| .|
T Consensus 793 ee~~~~~~~~~~~~mr~~~~dkLdddG~i~~G~~vs~~Dv~iGk~t~~~~~~~~~~~~-~~~~t~~d~s~~Lr~~e--~G 869 (1141)
T KOG0214|consen 793 EEIFEEPPRGEGRGMRNGKYDKLDDDGIIMPGSRVSGGDVLIGKTTPQPAKEDESGPE-DRLYTKRDHSTKLRHTE--RG 869 (1141)
T ss_pred ccccccccccccccccccccccccccCCccccceeecCCEEeccccCCcccchhcccc-ccccccccceeecccCC--cc
Confidence 7888877652 2 23357999999999999999999999999999876654322211 12234689999999999 99
Q ss_pred EEEEEEEeeCCCCcEEEEEEEeeecCCCccccccccCCCccEEEeeeccCCCCCCCCCCCCcEEeCCCCCCCCchHHHHH
Q 001125 872 VVDRVALCSDKNGDLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMI 951 (1149)
Q Consensus 872 ~v~~v~~~~~~~~~~~vkv~~~~~R~p~iGDKf~sRhGqKGvvs~i~~~eDmPf~~~G~~pDiI~NPh~~PSRMtiGql~ 951 (1149)
+||+|+++.+.+|.+.+||++|+.|.|++|||||||||||||||.++++||||||.+|++|||||||||||||||||||+
T Consensus 870 ivd~V~vt~n~~G~kF~kv~vr~~ripqiGDKfasrHgqKG~ig~~~~qedmpft~eGi~pDiiiNPhaiPSRmtig~li 949 (1141)
T KOG0214|consen 870 IVDQVWVTKNSEGPKFVKVRVRQVRIPQIGDKFASRHGQKGTIGITYRQEDMPFTIEGIVPDIIINPHAIPSRMTIGQLI 949 (1141)
T ss_pred eEEEEEEecCCCCCceeEEEEeecccccccchhccccccCccccceeecCCCCccccCCCcceEECcccCccccchhhhH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhccccccccCceeeeeeccCCCCCCCCHHHHHHHHHHcCCCCCCceEEEeCCCCcEEeeeEeEeeeeecccccccCcc
Q 001125 952 ELLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDK 1031 (1149)
Q Consensus 952 E~~~gk~~~~~g~~~d~tpF~~~~~~~~~~~~~~~~l~~~g~~~~G~e~ly~G~tG~~~~~~if~G~~yy~rL~Hmv~DK 1031 (1149)
||++||.++..|...|+|||+ ...+..+...|.++||+++|+|+||||+||++|.+.||+||.|||||+|||+||
T Consensus 950 Ec~lgk~~a~~~e~~~atpFs-----~v~v~~is~~l~~~g~~~~G~e~~ynGrtG~~~~~~if~GptyyqrL~Hmvd~k 1024 (1141)
T KOG0214|consen 950 ECLLGKVAAYEGEEGDATPFS-----DVTVSKISANLHVYGYQYRGNERMYNGRTGRKLRAQIFIGPTYYQRLKHMVDDK 1024 (1141)
T ss_pred HHhhhhhhhcccccccCCCCC-----ccchhcccchHHHhccccCCCEEEecCCCCceeeeeeecCchHHHHHHHhhhhe
Confidence 999999999999999999999 578899999999999999999999999999999999999999999999999999
Q ss_pred cEEecccCcccccccCcccccCCCceeeechhhhHHHHcccHHHHHHhhccCCCceeeeecccCCcceeecccccceecc
Q 001125 1032 MHARGSGPRVMLTRQPTEGRARNGGLRVGEMERDCLIAYGASMLIFERLMVSSDPFEVQVCRVCGLLGYYNHKLKAGICS 1111 (1149)
Q Consensus 1032 ~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~cg~~~~~~~~~~~~~C~ 1111 (1149)
+|+|++||++.+||||++||||+||||||||||||+||||||++|+|||+..||.+.+++|..||..+..+.+.+...|+
T Consensus 1025 ih~R~~Gp~q~ltRQP~~gRsr~GGlRfGEMErdc~iahGaa~~L~ERL~~~SD~~~~~~c~~c~l~~i~~~~~n~~~ck 1104 (1141)
T KOG0214|consen 1025 IHSRARGPVQILTRQPVEGRSRDGGLRFGEMERDCLIAHGAAAFLKERLFEKSDAYRVHICVLCGLTAIAGLIPNSFECR 1104 (1141)
T ss_pred eeecccCCceeeeccccccccccCCeeeehhHHHHHHHhhHHHHHHHHhhccCccceEEEeccchhhhhhccCCCccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999665555555667899
Q ss_pred cccCCCccccccccHhHHHHHHHHHhCCcccEEEec
Q 001125 1112 TCKNGDNISSMKLPYACKLLIQELQSMNIVPRLKLA 1147 (1149)
Q Consensus 1112 ~c~~~~~~~~v~iPy~~k~l~~EL~sm~i~~~l~~~ 1147 (1149)
.|.+...++.+.+|||||||+|||+||||.+|+.++
T Consensus 1105 ~c~n~~~v~~v~ipya~kLl~qelmsmni~pr~~~~ 1140 (1141)
T KOG0214|consen 1105 GCENKTLVVRVYIPYAAKLLFQELMSMNIAPRRKTK 1140 (1141)
T ss_pred cccCccceEEEechhHHHHHHHHHHhccCccccccC
Confidence 999999999999999999999999999999999764
No 4
>KOG0216 consensus RNA polymerase I, second largest subunit [Transcription]
Probab=100.00 E-value=1.6e-258 Score=2199.97 Aligned_cols=1055 Identities=31% Similarity=0.518 Sum_probs=932.9
Q ss_pred cccccccccccccchHHHHHHHHHHHHHhCHHHHHHhcc--cceecCCCcEEEEEeEEEEcCCccccCC---cCCCCChh
Q 001125 30 DKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRAND--RIVSGIDPSIFLRFKDVRIGQPSMTVDG---VSEKLNPH 104 (1149)
Q Consensus 30 ~~~~~i~~~~~~~~Lv~~qi~SFn~Fi~~gL~~ii~~~~--~I~~~~~~~~~l~~~~i~i~~P~~~e~~---~~~~l~P~ 104 (1149)
..|+..|+|-+++.++++|++|||...+.||....-+.. .......+.+.++++++.+.+|.++... ..++++|.
T Consensus 4 ~~~k~~p~fp~l~~a~~pHi~sfnal~~~gll~~~v~~~~ek~~~~~g~kis~~ve~i~iakP~l~~~~~ss~~r~lyPa 83 (1111)
T KOG0216|consen 4 NPPKDYPSFPELQDAASPHIDSFNALTNGGLLNAGVAGIAEKVPLKAGDKISMKVESIQIAKPMLSDKVHSSDTRKLYPA 83 (1111)
T ss_pred CCcccCccchhhhhhhhhhhccccchhhhhHHHHHhhchhhhcccccCCceeEEEEEEEecCCCCCccccccccccccch
Confidence 468888999999999999999999999988877644321 1112235678999999999999998643 78899999
Q ss_pred hHhhcCCccCccEEEEEEEEECCcccceeeEEeeEEeeccceeeccccccCCCCCHHHHHhcCCCCCCCCcEEEEcCchh
Q 001125 105 MCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEK 184 (1149)
Q Consensus 105 EcR~r~lTYsa~l~v~i~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~elv~~~E~~~d~GGYFIING~ER 184 (1149)
|||+|++||+|.+.|+|.|..|+ ......+..+|.+||||||++|||.|++|+||++++|++.|+||||||||+||
T Consensus 84 EcRqR~~TY~Gkl~v~v~wsVNg----~~~~~e~~dlG~vPIMlrSklChL~g~sp~eLV~hkEe~~EmGGYFIvNGIEK 159 (1111)
T KOG0216|consen 84 ECRQRGLTYKGKLVVRVSWSVNG----GHVVIEKRDLGHVPIMLRSKLCHLNGASPKELVKHKEESSEMGGYFIVNGIEK 159 (1111)
T ss_pred hHhhccceecceEEEEEEEEECC----eeeeeeeeecCccceEEeccccccCCCChHHHhhccCchhhcCcEEEEcChHH
Confidence 99999999999999999999988 45555678999999999999999999999999999999999999999999999
Q ss_pred hhHHhhhccCCeEEEEeCCC----Cc----EEEEEEecCCCcceEEEEE--eeCCEEEEEEce--eeccccHHHHHHHhC
Q 001125 185 VLLIQEQLSKNRVIIDTDKK----GN----INASVTSSTETVKSKTVIQ--MEKGKMYLLLNQ--FVKKIPIMVVMKAMG 252 (1149)
Q Consensus 185 VI~~q~~~s~N~i~~~~~~~----g~----~~a~v~s~~~~~~s~~~~~--~k~g~i~~r~~~--~~~~IPi~ilLrALG 252 (1149)
|||++|.+++|+|++..++. |. +...+++.+++.++.+..+ +.||...+++.. ....+|++++||||-
T Consensus 160 vIRmLIm~RRNHPiAiIR~Sfk~RG~~yS~yGVsmRcVReDqSsvtn~LHYLnnGtv~~~F~~rK~eylvPv~lILKAL~ 239 (1111)
T KOG0216|consen 160 VIRMLIMPRRNHPIAIIRPSFKDRGSSYSDYGVSMRCVREDQSSVTNVLHYLNNGTVMFRFSHRKREYLVPVVLILKALT 239 (1111)
T ss_pred hhhhheeccCCCceEEechhhhhcCCCccccceEEEEeccccccceeEEEEecCCcEEEEEEEeeeeehhhHHHHHHHHh
Confidence 99999999999999876532 32 3456777778887776654 588865554432 234699999999999
Q ss_pred CCCHHHHHHHh--C--CchhHHhhhHHhHHHHHhcCCcCHHHHHHHHhhhcccCCC-CCCCCChHHHHHHHHHhhhccCC
Q 001125 253 MESDQEVVQMV--G--RDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTF-GSPPNDREGRAFSILRDVFLANV 327 (1149)
Q Consensus 253 ~~sD~eI~~~i--~--~~~~~~~~l~~~l~~~~~~~i~t~~~al~yIg~~~r~~~~-~~~~~~~~e~~~~~L~~~ll~Hl 327 (1149)
.+||+||++.+ + .+.++.++++.+|++..+.+++||++|+.|||++||+.+. .++.+ +.|+|+++|++++|.|+
T Consensus 240 ~tsDeEIf~~lv~g~~gdqfl~~rv~~mLr~v~ee~l~trtqcl~yLGs~FRaVl~~v~~~~-D~evg~fILr~~VlvHL 318 (1111)
T KOG0216|consen 240 NTTDEEIFEGLVGGDEGDQFLTSRVELMLREVQEENLFTRTQCLQYLGSRFRAVLDFVPEQP-DLEVGRFILREYVLVHL 318 (1111)
T ss_pred ccCHHHHHHHHhCCccCceeHHHHHHHHHHHHhhcccccHHHHHHHHhhhhhhhhcCCCCCc-hHHHHHHHHHhheEEEe
Confidence 99999999998 2 4788999999999999999999999999999999997654 44456 89999999999999999
Q ss_pred CCCCCCCCCccchHHHHHHHHHHhhcCCCCCCCcccccccEEccccHhHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCC
Q 001125 328 PVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSR 407 (1149)
Q Consensus 328 ~~~~~~~~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~NkRv~l~G~Ll~~lfr~~l~~~~~~ik~~i~k~~~~~~~~~~ 407 (1149)
+. ..+|+.+|++|++||++++.|+|.+||+|+.+|||++++|+|++..+|+.+++|++.++.++.+.+.+.....+
T Consensus 319 d~----~~DKF~lLifmiqKL~slv~ge~~~dnpDs~q~qEil~~ghl~~~~LkEriEe~l~~~~~~vr~~l~~~~~~~~ 394 (1111)
T KOG0216|consen 319 DS----DEDKFNLLIFMIQKLYSLVDGECTPDNPDSPQNQEILLPGHLYGSILKERIEEWLRFISAQVRRDLYKLGFKED 394 (1111)
T ss_pred cc----cHHHHHHHHHHHHHHHHHhcCCcCCCCCCChhhhhcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCch
Confidence 94 46899999999999999999999999999999999999999999999999999999888888887776432222
Q ss_pred C-c---ccccc--cccchHHHHHHHhccCCCcc-cccc-cccccceEEccccccccccccccccc-cccccccccCCCCc
Q 001125 408 F-D---LSQFI--VRDSITVGLERTLSTGNFDV-KRFK-MHRKGMTQVLARLSFIGTLGHMTRVS-PQFEKSRKVSGPRA 478 (1149)
Q Consensus 408 ~-~---~~~~i--~~~~It~~i~~~~sTGnw~~-~~~~-~q~sGvsq~l~rln~ls~LshlRrv~-~~f~~~~k~t~~R~ 478 (1149)
+ + +.+.+ .+..|+++|++||||||+.+ ++++ +|++|+|++++|+||+++|||||.|| +.|+.+++||++||
T Consensus 395 ~~~~~~i~~~~~r~~~~Ig~~me~fLsTGnl~s~sgldLqQ~sG~tv~AEriNf~RflShFRavhRGa~f~~mrTTtvRK 474 (1111)
T KOG0216|consen 395 FLDISAIRKVFMRTNGNIGRKMEYFLSTGNLVSRSGLDLQQTSGYTVVAERINFYRFLSHFRAVHRGAFFAEMRTTTVRK 474 (1111)
T ss_pred hHhHHHHHHHHhhccccHHHHHHHHHhcCCeeeccchhhHhhcCcEEehhhhhHHHHHHHHHHHhcccchhheeehhhHh
Confidence 2 2 22222 45899999999999999985 3444 57799999999999999999999999 68999999999999
Q ss_pred cCCCCCcccccCCCCCCCcchhhhhccceeeeccCC-CchhHHHHHhhcCceeccccCccccCCCCceEEEECCeEEEee
Q 001125 479 LQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDE-EEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKH 557 (1149)
Q Consensus 479 Lhps~wG~iCPveTPEG~~cGLi~~LA~~a~Vt~~~-~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~~~V~lnG~~iG~~ 557 (1149)
|.|++|||+||||||||+||||+||||..|+|++.. +.+.+.++|.++||.|....... -+.-++|++||+++|++
T Consensus 475 LlPEsWGFlCPVHTPDG~PCGlLnH~t~~c~I~t~~dd~s~ip~~L~~~Gm~p~~~~~~~---G~~l~~VlldGk~vG~~ 551 (1111)
T KOG0216|consen 475 LLPESWGFLCPVHTPDGAPCGLLNHMTRTCRIVTRPDDVSFIPSILFELGMVPSSHLVEA---GEPLYPVLLDGKVVGWV 551 (1111)
T ss_pred hCchhhcccccccCCCCCchhHHHhhhhheeEeecCcchhhhhHHHHhcCCCchhccccC---CCceeEEEECCEEEEee
Confidence 999999999999999999999999999999999874 46789999999999885422211 11368999999999999
Q ss_pred cC--hhhHHHHHHHHhhc--CCcCceeEEEe-----cccCceEEEecCCCeeeeeEEEeecCcccchhhhHHhhhcCCcc
Q 001125 558 RR--PKCFADVMRKLRRA--GKIGEFVSVFV-----NEKQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRS 628 (1149)
Q Consensus 558 ~~--~~~~~~~lr~~rr~--g~i~~~v~i~~-----~~~~~~i~I~td~GRl~RPl~~v~~~~~~~~~~~~~~~~~~~~~ 628 (1149)
.. ++.+++.||.+|.. +.+|...+|-+ +.++|++||+|++||++|||.++
T Consensus 552 s~~~a~~i~~~lR~~Kv~~p~~iP~~leIg~Vp~s~~gqyPglyi~s~~aR~~RpV~nl--------------------- 610 (1111)
T KOG0216|consen 552 SSPLAKKIVDYLRYYKVEAPAVIPNDLEIGYVPTSTNGQYPGLYIFSGPARMIRPVKNL--------------------- 610 (1111)
T ss_pred ccHHHHHHHHHHHHHhhcCcccCCCcceEeeeecCCCCCCceeEEecCchhhhhehhcc---------------------
Confidence 84 49999999999965 55787766643 34679999999999999999752
Q ss_pred hhhhhccCceeEeccccccceEEEeecCCCCCC-ceeeeecCceeccccccccCCCCCCCCCccccccccccCCccccee
Q 001125 629 FDDFLREGLIEYLDVNEENNALIALYEGDATPD-TTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAF 707 (1149)
Q Consensus 629 ~~~l~~~g~iE~id~~Eq~~~~Ia~~~~~~~~~-~th~Ei~P~~ilsv~AslIPF~~hNqSpRn~yq~~M~KQa~G~~~~ 707 (1149)
+.+.+|||++.||.++.||+.+.++.+. +||.|++|+.+||++|+||||+||||||||||||||+|||||++.+
T Consensus 611 -----~~~~~e~iG~fEQvym~i~~~~~e~~~~v~th~E~~pt~~ls~~anliP~sD~NQSPRNmYQCQMgKQtmg~p~~ 685 (1111)
T KOG0216|consen 611 -----SLDSVEWIGPFEQVYMNIAIDPKEIFPDVTTHVELHPTGILSIVANLIPFSDHNQSPRNMYQCQMGKQTMGTPGH 685 (1111)
T ss_pred -----ccCchhhcccHHHhhhhhccchhhcCCCcceeEEecccchHhHhhcCccccccCCCchhHHHhhhhhhhcCCccc
Confidence 3356899999999999999999999876 8999999999999999999999999999999999999999999999
Q ss_pred eeccccccceeeecCCCcceeechhhhhccCCCCCCCcceEEEEEecCCCCCCCcEEeecccccccceeEEEEEEEEEEe
Q 001125 708 NQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAIN 787 (1149)
Q Consensus 708 n~~~R~D~~~y~L~ypQ~PlV~t~~~~~~~~~~~p~G~N~iVAv~~~~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~ 787 (1149)
+++.|.|+|+|+|++||.|+|++..++.+++|++|.|+||+|||+|||||||||||||||+|+||||+++.+||+..+++
T Consensus 686 a~~~radnklYrlqt~qsP~vr~~~y~~y~~d~yp~GtNaiVAVisyTgyDMeDAmiiNK~s~eRGf~~G~vykte~i~L 765 (1111)
T KOG0216|consen 686 ALRTRADNKLYRLQTPQSPIVRPELYDTYGMDDYPNGTNAIVAVISYTGYDMEDAMIINKSSYERGFAYGTVYKTEKIDL 765 (1111)
T ss_pred cchhcccCceEEecCCCCceeecccccccccccCCCCcceEEEEEeecccChhhhhhhchhhhhccccceeEEeeeeech
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecccCCccceecC-CCCCCCchhhhccCCCCcccCCCceeCCCCEEEEEecCCCCCCCCCCCCCCCCcccccceeeecCC
Q 001125 788 QKYANSTSDRILR-PDRTGPGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGP 866 (1149)
Q Consensus 788 ~~~~~~~~~~~~~-p~~~~~~~~~~~~Ld~dGi~~~G~~v~~gd~l~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 866 (1149)
.+... ....|.. |+.. .+++||+||||.+|++++.||+++....-.. .+....+|+..
T Consensus 766 ~~~~~-r~~~F~~~p~~~-----~~~~ld~dgLP~~G~kl~~~dp~~~y~d~~t---------------~~~~~~~~~~~ 824 (1111)
T KOG0216|consen 766 SKKRS-RSKHFGRSPGEP-----ELKKLDADGLPSIGQKLEYGDPYYAYFDEET---------------GKTRIKKYHGT 824 (1111)
T ss_pred hhccc-ceeeeeeCCCCc-----cccccCCCCCCCCcccccCCCcEEEEEcccC---------------CceEEEEecCC
Confidence 75322 1233433 5532 3789999999999999999999998755332 24455678888
Q ss_pred CCCceEEEEEEEeeCCCCc--EEEEEEEeeecCCCccccccccCCCccEEEeeeccCCCCCCCCCCCCcEEeCCCCCCCC
Q 001125 867 DGETCVVDRVALCSDKNGD--LCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSR 944 (1149)
Q Consensus 867 ~~~~~~v~~v~~~~~~~~~--~~vkv~~~~~R~p~iGDKf~sRhGqKGvvs~i~~~eDmPf~~~G~~pDiI~NPh~~PSR 944 (1149)
| +++||.|.+..++.+. +++.|++|..|+|.||||||||||||||||+.||.+|||||++|++|||||||||||||
T Consensus 825 e--p~~vd~vr~~~~~~~~~~k~~~i~~Ri~R~p~IGDKFsSRhGQKGicS~~wP~~dmPFtesGm~PDii~NPH~FPSR 902 (1111)
T KOG0216|consen 825 E--PGIVDEVRVLGNDMGDQEKCATITLRIPRNPIIGDKFSSRHGQKGICSQKWPTIDMPFTESGMVPDIIINPHAFPSR 902 (1111)
T ss_pred C--CeeeEEEEEccccCCCccceEEEEEEecCCCcccchhhhhccccccccccCCCCCCCccccCcCcceeeCCCCCccc
Confidence 8 9999999999877665 78999999999999999999999999999999999999999999999999999999999
Q ss_pred chHHHHHHHhccccccccCceeeeeeccCCCCCCCCHHHHHHHHHHcCCCCCCceEEEeCCCCcEEeeeEeEeeeeeccc
Q 001125 945 MTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKL 1024 (1149)
Q Consensus 945 MtiGql~E~~~gk~~~~~g~~~d~tpF~~~~~~~~~~~~~~~~l~~~g~~~~G~e~ly~G~tG~~~~~~if~G~~yy~rL 1024 (1149)
||||||||++|||+||++|..+|+|||.+++ ++..+++|+++|+++||||||+|+||||.+|++|+|+||+|+||||||
T Consensus 903 MTIgM~iEs~AgK~~alhG~~~Datpf~~~E-~~t~~dyfg~~L~~~GyNyyGnE~~YSGv~G~e~~adIf~GvVyYQRL 981 (1111)
T KOG0216|consen 903 MTIGMLIESMAGKAGALHGNAQDATPFIFSE-ENTAIDYFGEMLKKAGYNYYGNEPMYSGVDGREMRADIFFGVVYYQRL 981 (1111)
T ss_pred ccHHHHHHHHhchhhccccccccCCceeecC-cccHHHHHHHHHHHcCcCccCCcccccccccceeeeeEEEeehhHHHH
Confidence 9999999999999999999999999998754 456899999999999999999999999999999999999999999999
Q ss_pred ccccCcccEEecccCcccccccCcccccCCCceeeechhhhHHHHcccHHHHHHhhccCCCceeeeecccCCcceeecc-
Q 001125 1025 KHMVLDKMHARGSGPRVMLTRQPTEGRARNGGLRVGEMERDCLIAYGASMLIFERLMVSSDPFEVQVCRVCGLLGYYNH- 1103 (1149)
Q Consensus 1025 ~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~cg~~~~~~~- 1103 (1149)
+|||.||+|+|+|||++.+|+||++||+|+||+|||||||||||||||||+|||||+.|||.+.++||..||++++...
T Consensus 982 rHMv~DKfQVRstG~v~~~T~QPvkGRkr~GGiRfGEMERDali~HGtsfllqDRL~~~SD~~~a~vC~~cgsil~~~~~ 1061 (1111)
T KOG0216|consen 982 RHMVSDKFQVRSTGPVDSLTHQPVKGRKRGGGIRFGEMERDALIAHGTSFLLQDRLLNSSDYTVAEVCRTCGSILSTQQK 1061 (1111)
T ss_pred HHHhcceeeeeeccCccccccCCccCcccCCCccccchhhhhHhhcchHhhhhhhhccCcchhHHHHHHHhhhhhhhhhh
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999987511
Q ss_pred -------cccceecccccCCCccccccccHhHHHHHHHHHhCCcccEEEec
Q 001125 1104 -------KLKAGICSTCKNGDNISSMKLPYACKLLIQELQSMNIVPRLKLA 1147 (1149)
Q Consensus 1104 -------~~~~~~C~~c~~~~~~~~v~iPy~~k~l~~EL~sm~i~~~l~~~ 1147 (1149)
......|+.|. +..+..|.|||+||||..||+||||+++|.++
T Consensus 1062 l~~~~~~~~~~~~C~~c~-~~~~~~v~~P~vfkYL~aEL~amnIk~~l~l~ 1111 (1111)
T KOG0216|consen 1062 LIKEPGGSTSTVTCRSCD-GKGVTTVAMPYVFKYLTAELAAMNIKMRLDLE 1111 (1111)
T ss_pred hhcccCCCCCceeEEecC-CCceEEEEccHHHHHHHHHHhhCceeEEeccC
Confidence 22334699995 57788999999999999999999999999874
No 5
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]
Probab=100.00 E-value=8.6e-250 Score=2252.25 Aligned_cols=1015 Identities=33% Similarity=0.522 Sum_probs=921.8
Q ss_pred ccccccccccccccccchHHHHHHHHHHHHHhCHHHHHHhcccceecCCCcEEEEEeEEEEcCCccccCCcCCCCChhhH
Q 001125 27 SVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDGVSEKLNPHMC 106 (1149)
Q Consensus 27 ~~~~~~~~i~~~~~~~~Lv~~qi~SFn~Fi~~gL~~ii~~~~~I~~~~~~~~~l~~~~i~i~~P~~~e~~~~~~l~P~Ec 106 (1149)
+.+++|+++++||+.++|+++|++|||+|+.+||++++++.+||+.. ++++.|+|.++++++| ++++|.||
T Consensus 10 r~r~~~~~i~~~~~~p~Lv~~QldSyn~ff~~gLq~i~~~i~PI~~~-~~~~~Lef~~~~l~~p--------~k~~p~Ec 80 (1060)
T COG0085 10 RIRDSFGKIPEFLDLPNLVEIQLDSYNAFFLEGLQEVFREIFPIESY-NGNTELEYGSYRLGEP--------PKFYPEEC 80 (1060)
T ss_pred ccccchhhcccccCCccHHHHHHHHHHHHHHHHHHHHHHhcCceecC-CCCEEEEEEEEEecCC--------CCCCHHHH
Confidence 78899999999999999999999999999999999999999999754 7789999999999998 35799999
Q ss_pred hhcCCccCccEEEEEEEEECCccccee-eEEeeEEeeccceeeccccccCCCCCHHHHHhcCCCCCCCCcEEEEcCchhh
Q 001125 107 RLSDMTYAAPILVNIEYVQGSHTEKTT-MEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKV 185 (1149)
Q Consensus 107 R~r~lTYsa~l~v~i~~~~~~~~~~~~-~~~~~v~lG~IPIMvkS~~C~L~~~s~~elv~~~E~~~d~GGYFIING~ERV 185 (1149)
|+|++||+|||+|+++++.++. .+ +++++|++|+||+|| .||||||||+|||
T Consensus 81 R~R~lTYsapLyv~lrlv~~~~---~e~~k~~eV~iG~iPlMt------------------------~gGyFIINGsERV 133 (1060)
T COG0085 81 RLRGLTYSAPLYVKLRLVVNET---GEEIKEQEVYMGDIPLMT------------------------RGGYFIINGTERV 133 (1060)
T ss_pred HhcCCccccceEEEEEEEECCc---ccccccceEEeccCcEec------------------------CCcEEEECCeEEE
Confidence 9999999999999999998774 33 678899999999999 4999999999999
Q ss_pred hHHhhhccCCeEEEEeC-CCC---cEEEEEEecCCCcceEEEEEeeCCEEEEEEceeeccccHHHHHHHhCCCCHHHHHH
Q 001125 186 LLIQEQLSKNRVIIDTD-KKG---NINASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQ 261 (1149)
Q Consensus 186 I~~q~~~s~N~i~~~~~-~~g---~~~a~v~s~~~~~~s~~~~~~k~g~i~~r~~~~~~~IPi~ilLrALG~~sD~eI~~ 261 (1149)
|++||++|||.++..+. +++ .+.|.+++.++ .|..+....++.+++++++. ++||+++||||||++||+||++
T Consensus 134 IVsQ~~rSPgvif~~~~~k~~~~~~~~a~vIp~rG--~wl~~e~d~~d~~~~rId~~-rkiPvtilLRALG~~tDeeI~~ 210 (1060)
T COG0085 134 IVSQEHRSPGVIFVEKKDKTGSKVLYVARVIPYRG--SWLEFEFDPKDNLYVRIDRK-RKIPVTILLRALGLETDEEIIE 210 (1060)
T ss_pred EEEEeecCCCeEEecccccCCcceEEEEEEecCCc--ceEEEEEccCccEEEEeeeE-EEeeHHHHHHHhCCCcHHHHHH
Confidence 99999999997776653 334 35788888732 44555555678999999985 4899999999999999999999
Q ss_pred HhCCc-------hhHHhhhHHhHHHHHhcCCcCHHHHHHHHhhhcccCCCC-CCCCChHHHHHHHHHhhhccCCCCC--C
Q 001125 262 MVGRD-------PRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFG-SPPNDREGRAFSILRDVFLANVPVH--N 331 (1149)
Q Consensus 262 ~i~~~-------~~~~~~l~~~l~~~~~~~i~t~~~al~yIg~~~r~~~~~-~~~~~~~e~~~~~L~~~ll~Hl~~~--~ 331 (1149)
.|+.+ ....+.+...+++.....+.++. |++||++++...... .... +.+.++.++.+.+|||+... .
T Consensus 211 ~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~i~~~~-a~~~i~~r~~~~~~~~~~~g-R~k~~~~vl~~~~L~hL~~~~~~ 288 (1060)
T COG0085 211 AFGGDELTDLVPPEGEEALLEIYEEAKGEKITARN-ALELIGSRVFVVKRYDAKEG-RYKRAKYVLDKELLPHLGEAGER 288 (1060)
T ss_pred HhcccccccccchHHHHHhHHHHhhccCCCcchHH-HHHHHhcccccccccccchh-hhhhhhhhhhhhHHhhhcccccc
Confidence 99642 11222222333333223344444 999999999876332 2344 78999999999999999963 2
Q ss_pred C--CCCCccchHHHHHHHHHHhhcCCCCCCCcccccccEEccccHhHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCc
Q 001125 332 N--NFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFD 409 (1149)
Q Consensus 332 ~--~~~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~NkRv~l~G~Ll~~lfr~~l~~~~~~ik~~i~k~~~~~~~~~~~~ 409 (1149)
. ....|+.+|+.|+++|+++..|.+.+||+|||+||||+++|+||+++||.+|.+|++.+|++|.+...+
T Consensus 289 ~~l~~~~k~~di~~mi~~l~~L~~G~~~~DDiDHlGNKRlrlvGeLl~n~fR~gl~rmer~ikerm~~~~~r-------- 360 (1060)
T COG0085 289 YDLSRVGKAKDIIAMIKYLIELRLGKGEEDDIDHLGNRRLRLVGELLENLFRVGLSRMERDVKERLEKADKR-------- 360 (1060)
T ss_pred cchhhhHHHHHHHHHHHHHHHHhcCCCCCCCCccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh--------
Confidence 2 244588899999999999999999999999999999999999999999999999999999999886442
Q ss_pred ccccccccchHHHHHHHhccCCCcccccccccccceEEcccccccccccccccccc-ccccccccCCCCccCCCCCcccc
Q 001125 410 LSQFIVRDSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSP-QFEKSRKVSGPRALQPSQWGMLC 488 (1149)
Q Consensus 410 ~~~~i~~~~It~~i~~~~sTGnw~~~~~~~q~sGvsq~l~rln~ls~LshlRrv~~-~f~~~~k~t~~R~Lhps~wG~iC 488 (1149)
..+..++.|++++.+|++||||+ ++|+||+|||+||+|+|||+||++| ++.++++.++|||||||||||||
T Consensus 361 -~~i~p~dlIn~k~~~Alitgffg-------~sqlSQfmDqtNpLSeLSHkRRIsAlgLsRera~fEvRDvHpTHyGRiC 432 (1060)
T COG0085 361 -DTLVPQDLINAKPIHALITGFFG-------RSQLSQFMDQTNPLSELSHKRRLSALGLSRERAGFEVRDVHPTHYGRIC 432 (1060)
T ss_pred -hccCchhhcchhHHHHHHhcccc-------ccceeeeeecCChHHhhhhhhceeccCcCccCCCCcccccCcccccccC
Confidence 12235678999999999999997 5799999999999999999999999 99999999999999999999999
Q ss_pred cCCCCCCCcchhhhhccceeeec-cCCCchhHHHHHh-hcCceeccccCccccCCCCceEEEECCeEEEeecChhhHHHH
Q 001125 489 PCDTPEGEACGLVKNLALMTHVT-TDEEEGPLISLCY-CLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADV 566 (1149)
Q Consensus 489 PveTPEG~~cGLi~~LA~~a~Vt-~~~~~~~i~~~l~-~~g~~~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~ 566 (1149)
|+|||||+|||||||||++|+|+ .++++.|+++++. .+|+++++++++.+ ..|++||.++|.++++..|++.
T Consensus 433 PiETPEGpNiGLI~sLA~~A~Vn~~Gf~etPy~kv~~g~~~v~~i~~l~~~~------~~~~~~~~~~~~~~~~~~~~~~ 506 (1060)
T COG0085 433 PIETPEGPNIGLIKSLALYARINEYGFLETPYRKVLDGSLVVDEIEYLSADE------EDVYVIGQANGTLDEPGELVEE 506 (1060)
T ss_pred CCCCCCCcchhHHHHHHHHeEecccCCCCCceEEEEeccccccceeeecccc------cceEEEeEeeeeecCCCceeee
Confidence 99999999999999999999999 7899999999999 49999999888653 4599999999999999999999
Q ss_pred HHHHhhcCCcCceeEEEecccCc----eEEEecCCCeeeeeEEEeecCcccchhhhHHhhhcC-CcchhhhhccCceeEe
Q 001125 567 MRKLRRAGKIGEFVSVFVNEKQR----CVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDG-VRSFDDFLREGLIEYL 641 (1149)
Q Consensus 567 lr~~rr~g~i~~~v~i~~~~~~~----~i~I~td~GRl~RPl~~v~~~~~~~~~~~~~~~~~~-~~~~~~l~~~g~iE~i 641 (1149)
+|.+|+ | +..+++++...... ++++.+|.||.+||++.+++++++++.+|++++..+ ..+|.+|+.+| +||+
T Consensus 507 ~~~~R~-~-~~~~~~~~~~~~~~~~dv~~~~~~~~~~~~~P~l~~dd~~~~l~~~~mqr~~~~l~~~~~~lv~tG-~E~~ 583 (1060)
T COG0085 507 LVECRR-G-GSGEVSVADPEGVDYMDVSPKQVVSVGRSLIPFLEHDDANRALMGSNMQRQAVPLLRTEAPLVGTG-MEYL 583 (1060)
T ss_pred EEEEee-c-ccccceeecCccccceeccceEEeccccccCceeEEcCchHhhhhhhhhhhcccccccccccccCC-ceee
Confidence 999999 6 77778887766555 899999999999999999999999999999999887 67999999999 9999
Q ss_pred ccccccceEEEeecCCCCCCceeeeecCceeccccccccCCCCCCCCCccccccccccCCcccceeeeccccccceeeec
Q 001125 642 DVNEENNALIALYEGDATPDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLV 721 (1149)
Q Consensus 642 d~~Eq~~~~Ia~~~~~~~~~~th~Ei~P~~ilsv~AslIPF~~hNqSpRn~yq~~M~KQa~G~~~~n~~~R~D~~~y~L~ 721 (1149)
++.|+.+++||..+.+ +||+|++|..|+|++|++|||+||||||||||||+|+||++|++.+|+..|.|+..|.++
T Consensus 584 ~a~e~~~~~ia~~~~~----~~~ve~~~~~I~~~~~~~~~~~~~n~~~~n~~~~~~~~Q~~~~~~~~~~~~~d~~~~~~~ 659 (1060)
T COG0085 584 DAEDSGAAVIAKRPGV----VTHVEISPIVILGIEASLIPYPEHNQSPYNLYKFARSNQATGINQRPLVKRGDTVEKGLV 659 (1060)
T ss_pred ccccccceeEeccCCc----EEEEeeeeeEEEeeccccCCccccCcChHHHHHHhhhhcccCCCcccceeccccccccce
Confidence 9999999999999876 899999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCcceeechhhhhccCCCCCCCcceEEEEEecCCCCCCCcEEeecccccccceeEEEEEEEEEEeecccCCccceecCC
Q 001125 722 YPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILRP 801 (1149)
Q Consensus 722 ypQ~PlV~t~~~~~~~~~~~p~G~N~iVAv~~~~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~~~~~~p 801 (1149)
|||.|+|+| +|+|+|||++||||||+||||||||||||++++||+|||+||++|++++++++.|.+|++..|
T Consensus 660 ~~~~P~~~~--------~e~~~GqN~~VA~m~~~GYn~EDAiiin~~~v~~~~~ts~~~~~~~~~~r~~~~g~e~~~~iP 731 (1060)
T COG0085 660 YADGPSVDT--------GELALGQNALVAFMPWNGYNYEDAIIISERSVERDLFTSIHIEEYETEARDTKLGPEEIRDIP 731 (1060)
T ss_pred ecCCCcccc--------CcccCCceeEEEEecccCcChhHheecccchhhcCCceEEEEEEEeeeeeccCCCccccccCC
Confidence 999999999 899999999999999999999999999999999999999999999999999999999997779
Q ss_pred CCCCCchhhhccCCCCcccCCCceeCCCCEEEEEecCCCCCCCCCC-----CCCCCCcccccceeeecCCCCCceEEEEE
Q 001125 802 DRTGPGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMS-----PTGQTDSRYRSARQTYKGPDGETCVVDRV 876 (1149)
Q Consensus 802 ~~~~~~~~~~~~Ld~dGi~~~G~~v~~gd~l~~k~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~v~~v 876 (1149)
+.+. ..|++||+|||++||++|++|||||||++|+++.+.... .++++ .||+|+++++++ +|+||.|
T Consensus 732 ~~~e---~~~~~Lde~Gii~ig~~V~~gdilvgk~tP~~~~~~~~ee~ll~i~~ek---~rdtsl~~~~g~--~G~V~~V 803 (1060)
T COG0085 732 NVSE---EALRNLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRIFGEK---VRDTSLRVPHGE--EGIVDDV 803 (1060)
T ss_pred CcCH---HHHhcCCccCccccccEEcCCCEEEEeeCCCCCCCCCchhhhhccccce---eeccceeecCCC--CeEEEEE
Confidence 8753 589999999999999999999999999999998764321 12222 799999999999 9999999
Q ss_pred EEeeCCC----CcEEEEEEEeeecCCCccccccccCCCccEEEeeeccCCCCCCCCCCCCcEEeCCCCCCCCchHHHHHH
Q 001125 877 ALCSDKN----GDLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIE 952 (1149)
Q Consensus 877 ~~~~~~~----~~~~vkv~~~~~R~p~iGDKf~sRhGqKGvvs~i~~~eDmPf~~~G~~pDiI~NPh~~PSRMtiGql~E 952 (1149)
.++++++ +.+.|||++|+.|.|++|||||||||||||||+|||+||||||+||++||||+|||||||||||||++|
T Consensus 804 ~~~~~~~~~~g~~~~vkV~v~~~R~~~~GDK~a~RHG~KGVis~i~p~eDMPf~~~G~~~DiilNP~gvPSRM~iGqilE 883 (1060)
T COG0085 804 QVFTREDGDPGVNKLVKVYVAQKRKPQIGDKMAGRHGNKGVVSKIVPQEDMPFLEDGTPPDIILNPLGVPSRMNIGQILE 883 (1060)
T ss_pred EEEeccCCCcCceEEEEEEEEEeccCCccccccccCCCCceeeeecCcccCCcCCCCCcccEEECCCCCCccccHHHHHH
Confidence 9998877 789999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhccccccccCceeeeeeccCCCCCCCCHHHHHHHHHHcCCCCCCceEEEeCCCCcEEeeeEeEeeeeecccccccCccc
Q 001125 953 LLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKM 1032 (1149)
Q Consensus 953 ~~~gk~~~~~g~~~d~tpF~~~~~~~~~~~~~~~~l~~~g~~~~G~e~ly~G~tG~~~~~~if~G~~yy~rL~Hmv~DK~ 1032 (1149)
+++||||++.|...|+|||+ +++.+++.+.|+++||++.||++||||+||++|+++||+|++|||||+|||+|||
T Consensus 884 ~~lG~a~~~~G~~~~~~~F~-----g~~~~~~~~~l~~~g~~~~Gk~~lydG~TGe~~~~~i~vG~~Y~~kL~HmV~dK~ 958 (1060)
T COG0085 884 THLGKAAALLGIPVDTPVFD-----GAPEEDIRELLKEAGFPYSGKEVLYDGRTGEPFDAPIFVGVMYYQKLHHMVDDKI 958 (1060)
T ss_pred HHHHHHHHhcCceeccCCcC-----CCCHHHHHHHHHHcCCCCCCCEEeecCCCCCcccccEEEEehHHHhHHhhhcccc
Confidence 99999999999999999999 8999999999999999999999999999999999999999999999999999999
Q ss_pred EEecccCcccccccCcccccCCCceeeechhhhHHHHcccHHHHHHhhccCCCceeeeecccCCcceeecccccceeccc
Q 001125 1033 HARGSGPRVMLTRQPTEGRARNGGLRVGEMERDCLIAYGASMLIFERLMVSSDPFEVQVCRVCGLLGYYNHKLKAGICST 1112 (1149)
Q Consensus 1033 ~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~cg~~~~~~~~~~~~~C~~ 1112 (1149)
||||||||+.|||||++||||+|||||||||||||+|||||++|||||+++||++ ||.+++. -|..
T Consensus 959 HaRs~GP~s~lT~QP~~Gka~~GG~RfGEME~~aL~ayGAa~~LqE~L~~~SD~~-------~G~~~~y-------~~~v 1024 (1060)
T COG0085 959 HARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTVKSDDV-------CGRIKIY-------ECIV 1024 (1060)
T ss_pred eeeccCCceeeecCCCCcccccCCccccchHHHHHHHHhHHHHHHHHhhccchhc-------ccchhhh-------cCcc
Confidence 9999999999999999999999999999999999999999999999999999998 8887665 2999
Q ss_pred ccCCCccccccccHhHHHHHHHHHhCCcccEEEecc
Q 001125 1113 CKNGDNISSMKLPYACKLLIQELQSMNIVPRLKLAE 1148 (1149)
Q Consensus 1113 c~~~~~~~~v~iPy~~k~l~~EL~sm~i~~~l~~~~ 1148 (1149)
|+ .++.++.||||||||++||+||||+++|.+++
T Consensus 1025 ~g--~~~~~~~ip~sFk~L~~El~sl~i~~~l~~~~ 1058 (1060)
T COG0085 1025 KG--ENIPEVGIPESFKVLLKELRSLGIDVRLELED 1058 (1060)
T ss_pred cC--CCCCCCCCCHHHHHHHHHHHHCCCceEEeecC
Confidence 97 78899999999999999999999999999876
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=6.9e-227 Score=2111.45 Aligned_cols=856 Identities=47% Similarity=0.785 Sum_probs=773.3
Q ss_pred hHHHHHHHHHHHHHhCHHHHHHhcccceecC-CCcEEEEEeEEEEcCCccccCCcCCCCChhhHhhcCCccCccEEEEEE
Q 001125 44 LVKQHLDSFNYFVNTGIRKIVRANDRIVSGI-DPSIFLRFKDVRIGQPSMTVDGVSEKLNPHMCRLSDMTYAAPILVNIE 122 (1149)
Q Consensus 44 Lv~~qi~SFn~Fi~~gL~~ii~~~~~I~~~~-~~~~~l~~~~i~i~~P~~~e~~~~~~l~P~EcR~r~lTYsa~l~v~i~ 122 (1149)
|++||++|||+|+++||+++++++++|+... +..+.++|.++++++|.+.++....+++|+|||+|++||+|+++|+++
T Consensus 1 Lv~~qi~SFn~Fl~~gl~~ii~~~~~i~~~~~~~~~~l~f~~i~i~~P~~~~~~~~~~l~P~ecRlr~lTYs~~l~v~i~ 80 (866)
T cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDDDGRLKLKFGDIYLGKPKVEEGGVTRKLTPNECRLRDLTYSAPLYVDIR 80 (866)
T ss_pred CchhHHHHHHHHHHHHHHHHHHhcCCeeeccCCCeEEEEEEEEEECCccccccCccccCCHHHHHhhCCccceeEEEEEE
Confidence 6889999999999999999999999997653 467899999999999998765555789999999999999999999999
Q ss_pred EEECCcccceeeEEeeEEeeccceeeccccccCCCCCHHHHHhcCCCCCCCCcEEEEcCchhhhHHhhhccCCeEEEEeC
Q 001125 123 YVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVIIDTD 202 (1149)
Q Consensus 123 ~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~elv~~~E~~~d~GGYFIING~ERVI~~q~~~s~N~i~~~~~ 202 (1149)
++.++. ....+++|++|+|||||+|++|||++++++||++.||||.|+||||||||+|||||+||++++|+++++ +
T Consensus 81 ~~~~~~---~~~~~~~v~iG~iPIMv~S~~C~L~~~~~~el~~~~E~p~d~GGYFIInG~EkVIi~qi~~~~N~~~~~-~ 156 (866)
T cd00653 81 LTVNDK---GKIKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVE-D 156 (866)
T ss_pred EEEecc---eeEEEEEEEEeeCCcccCcccccccCCCHHHHHhcCCCcccCCCEEEECCceeEEEEEEeccCCeEEEe-c
Confidence 986552 233567899999999999999999999999999999999999999999999999999999999999888 4
Q ss_pred CCCcEEEEEEecCCC---cce-EEEEEee-CCEEEEEEceeeccccHHHHHHHhCCCCHHHHHHHhCCchhHHhhhHHhH
Q 001125 203 KKGNINASVTSSTET---VKS-KTVIQME-KGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGRDPRYSALLLPSI 277 (1149)
Q Consensus 203 ~~g~~~a~v~s~~~~---~~s-~~~~~~k-~g~i~~r~~~~~~~IPi~ilLrALG~~sD~eI~~~i~~~~~~~~~l~~~l 277 (1149)
+.+.+.+.+++.... ..+ ....... ++.++.+++...
T Consensus 157 ~~~~~~~~~~s~~~~~~~~~s~~~~~~~~~~~~i~~~i~~~~-------------------------------------- 198 (866)
T cd00653 157 SKGKRIYTKTSIPSYSPYRGSWLEVKSDKKKDRIYVRIDLKR-------------------------------------- 198 (866)
T ss_pred CCCcEEEEEEEccCCCcCccEEEEEEEccCCCeEEEEecccC--------------------------------------
Confidence 445566666665432 122 2222222 345666666531
Q ss_pred HHHHhcCCcCHHHHHHHHhhhcccCCCCCCCCChHHHHHHHHHhhhccCCCCCCCCCCCccchHHHHHHHHHHhhcCCCC
Q 001125 278 EECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDA 357 (1149)
Q Consensus 278 ~~~~~~~i~t~~~al~yIg~~~r~~~~~~~~~~~~e~~~~~L~~~ll~Hl~~~~~~~~~K~~~L~~Mi~kLl~~~~g~~~ 357 (1149)
+++|+.|||++| .+|++|++||+++..|.+.
T Consensus 199 ----------~~~al~~ig~~~---------------------------------------~~L~~Mi~kLl~~~~g~~~ 229 (866)
T cd00653 199 ----------QEEALKYIGKRF---------------------------------------EDLIYMIRKLILLVLGKGK 229 (866)
T ss_pred ----------HHHHHHHHHHHH---------------------------------------HHHHHHHHHHHHHhcCCCC
Confidence 678999999864 6799999999999999999
Q ss_pred CCCcccccccEEccccHhHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccccccchHHHHHHHhccCCCccccc
Q 001125 358 MDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFDVKRF 437 (1149)
Q Consensus 358 ~DD~D~l~NkRv~l~G~Ll~~lfr~~l~~~~~~ik~~i~k~~~~~~~~~~~~~~~~i~~~~It~~i~~~~sTGnw~~~~~ 437 (1149)
+||+|||+||||+++|+||+.+||+.|+++++.++..+.+...+.+ .+++...++++.||++|++||+||||..+++
T Consensus 230 ~Dd~D~~~NkRv~~~G~Ll~~lfr~~l~~~~~~~k~~l~~~~~~~~---~~~~~~~~~~~~It~~i~~~~~TGnw~~~~~ 306 (866)
T cd00653 230 LDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKK---DLTPQLLINSKPITSGIKEFLATGNWGSKRF 306 (866)
T ss_pred CCCchhhhCeEEeeHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccc---ccCHHHhccchHHHHHHHHHhhcCCcccccc
Confidence 9999999999999999999999999999999999999988765422 3455566678899999999999999997766
Q ss_pred ccccccceEEcccccccccccccccccc-ccccccccCCCCccCCCCCcccccCCCCCCCcchhhhhccceeeeccCCCc
Q 001125 438 KMHRKGMTQVLARLSFIGTLGHMTRVSP-QFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEE 516 (1149)
Q Consensus 438 ~~q~sGvsq~l~rln~ls~LshlRrv~~-~f~~~~k~t~~R~Lhps~wG~iCPveTPEG~~cGLi~~LA~~a~Vt~~~~~ 516 (1149)
.+|++|+||+|+|+||+|+|||+||||+ ++++++|+++||+||||||||+||||||||++||||||||++|+|+
T Consensus 307 ~~~~~Gvsq~ldr~N~ls~lsh~Rrv~~~~~~~~~k~~~~R~lhps~~G~iCPveTPEG~~cGLv~~LA~~a~Is----- 381 (866)
T cd00653 307 LMQRSGLSQVLDRLNPLSELSHKRRISSLGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS----- 381 (866)
T ss_pred ccccceEEEEcccCCHHHHHHhhhhcccccccccccCCcccccCcccCCccCCCCCCCCccccchhhhhceEeee-----
Confidence 7899999999999999999999999998 9999999999999999999999999999999999999999999874
Q ss_pred hhHHHHHhhcCceeccccCccccCCCCceEEEECCeEEEeecChhhHHHHHHHHhhcCCcCceeEEEecccCceEEEecC
Q 001125 517 GPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASD 596 (1149)
Q Consensus 517 ~~i~~~l~~~g~~~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~lr~~rr~g~i~~~v~i~~~~~~~~i~I~td 596 (1149)
T Consensus 382 -------------------------------------------------------------------------------- 381 (866)
T cd00653 382 -------------------------------------------------------------------------------- 381 (866)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred CCeeeeeEEEeecCcccchhhhHHhhhcCCcchhhhhccCceeEeccccccceEEEeecCCCCCCceeeeecCceecccc
Q 001125 597 GGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTTHIEIEPFTILGVI 676 (1149)
Q Consensus 597 ~GRl~RPl~~v~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~iE~id~~Eq~~~~Ia~~~~~~~~~~th~Ei~P~~ilsv~ 676 (1149)
||++||+++|+ ..+||+||+|.++||++
T Consensus 382 -Gr~~rP~~~v~---------------------------------------------------~~~th~ei~~~~~ls~~ 409 (866)
T cd00653 382 -GRIERPYRIVE---------------------------------------------------KEVTHIEISPSQILSVA 409 (866)
T ss_pred -eEeeeeEEEec---------------------------------------------------cceEEEEeCccceeeee
Confidence 99999998742 13799999999999999
Q ss_pred ccccCCCCCCCCCccccccccccCCcccceeeeccccccceeeecCCCcceeechhhhhccCCCCCCCcceEEEEEecCC
Q 001125 677 AGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSG 756 (1149)
Q Consensus 677 AslIPF~~hNqSpRn~yq~~M~KQa~G~~~~n~~~R~D~~~y~L~ypQ~PlV~t~~~~~~~~~~~p~G~N~iVAv~~~~G 756 (1149)
||+|||+||||||||||||||+|||||++++|+..|+|++.|+|.|||+|||+|+..+.++++|+|+|+||+||||||+|
T Consensus 410 asliPf~~hNqspRn~~~~~M~kQa~g~~~~n~~~r~d~~~~~l~~pq~plv~T~~~~~~~~~~~~~G~N~~VAv~~y~G 489 (866)
T cd00653 410 ASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSG 489 (866)
T ss_pred eeccCCCCcccccchhhhhcccCCccCchhccccccccchheeeccCCCCccccchHHHhCCCccCCCceEEEEEecccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCcEEeecccccccceeEEEEEEEEEEeecccCCccceecCCCCCCCchhhhccCCCCcccCCCceeCCCCEEEEEe
Q 001125 757 YDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILRPDRTGPGAERMQILDDDGLAAPGEIIKPNDVYINKE 836 (1149)
Q Consensus 757 yn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~Ld~dGi~~~G~~v~~gd~l~~k~ 836 (1149)
|||||||||||+|+|||+|||+||++|++++++...+..+.+.. +........|++||+||||++|++|++||+||||+
T Consensus 490 yn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~ld~dGi~~~g~~v~~gd~li~k~ 568 (866)
T cd00653 490 YNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRG-DIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKI 568 (866)
T ss_pred ccccceeeeehhhhhcCceeEEEEEEEEEEEEecCCCcceEecC-CCCCCChHHhhccCCCCCcCCCCEecCCCEEEEEe
Confidence 99999999999999999999999999999998876665555541 11111234799999999999999999999999999
Q ss_pred cCCCCCCCCCCCCCCCCcccccceeeecCCCCCceEEEEEEEee---CCCCcEEEEEEEeeecCCCccccccccCCCccE
Q 001125 837 SPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCS---DKNGDLCIKFLIRHTRRPELGDKFSSRHGQKGV 913 (1149)
Q Consensus 837 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~v~~~~---~~~~~~~vkv~~~~~R~p~iGDKf~sRhGqKGv 913 (1149)
+|....+... .++......++++++++.++ .|+||+|.++. +.++...|+|++|+.|+|+||||||||||||||
T Consensus 569 ~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~--~g~v~~v~~~~~~~~~~~~~~v~v~~r~~R~p~iGDKfssRhGqKGv 645 (866)
T cd00653 569 TPKGETESTP-IFGEKARDVRDTSLKYPGGE--KGIVDDVKIFSRELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGV 645 (866)
T ss_pred cCcccccccc-cccccCCcceEEEEEecCCC--ceEEEEEEEeccccCCCCcEEEEEEEeEEecCCcccccccccCCCcE
Confidence 9875433211 01222334689999999999 99999999987 567789999999999999999999999999999
Q ss_pred EEeeeccCCCCCCCCCCCCcEEeCCCCCCCCchHHHHHHHhccccccccCceeeeeeccCCCCCCCCHHHHHHHHHHcCC
Q 001125 914 CGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGF 993 (1149)
Q Consensus 914 vs~i~~~eDmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tpF~~~~~~~~~~~~~~~~l~~~g~ 993 (1149)
||+|||+||||||+||++|||||||||||||||||||+|+++||+|++.|.+.|+|||+ ....+++.+.|.++||
T Consensus 646 ~s~i~~~~dmPf~~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~t~f~-----~~~~~~~~~~l~~~g~ 720 (866)
T cd00653 646 ISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFD-----GAEEEDISELLGEAGL 720 (866)
T ss_pred EEEEeccccCCcccCCCCCcEEecCCcCcccccHHHHHHHHHHHHHHhcCCcccccccC-----cchHHHHHHHHHHcCC
Confidence 99999999999999999999999999999999999999999999999999999999998 5778899999999999
Q ss_pred CCCCceEEEeCCCCcEEeeeEeEeeeeecccccccCcccEEecccCcccccccCcccccCCCceeeechhhhHHHHcccH
Q 001125 994 SYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGLRVGEMERDCLIAYGAS 1073 (1149)
Q Consensus 994 ~~~G~e~ly~G~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas 1073 (1149)
+++|+|.||||+||++|+++||+|++|||||+|||+||+|||++||++.|||||++||+|+|||||||||||||+|||||
T Consensus 721 ~~~G~e~~y~g~tG~~~~~~if~G~~yyqrL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~lia~Gas 800 (866)
T cd00653 721 NYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAA 800 (866)
T ss_pred CCCCcEEEEcCCCCCCcccceEEeehhhhhhhhhhchhhhhcccCCcchhccCcCccccccCCeEEEEEehhhhhhhhhH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhccCCCceeeeecccCCcceeecccccceecccccCCCccccccccHhHHHHHHHHHhCCcccEEE
Q 001125 1074 MLIFERLMVSSDPFEVQVCRVCGLLGYYNHKLKAGICSTCKNGDNISSMKLPYACKLLIQELQSMNIVPRLK 1145 (1149)
Q Consensus 1074 ~~l~erl~~~SD~~~~~vC~~cg~~~~~~~~~~~~~C~~c~~~~~~~~v~iPy~~k~l~~EL~sm~i~~~l~ 1145 (1149)
++|+|||+++||++.++||..||.+++. .+|+.|+++.++.++.+|||||||+|||+||||+++|.
T Consensus 801 ~~l~erl~~~SD~~~~~vc~~cg~i~~~------~~c~~c~~~~~~~~~~ipy~~kll~~EL~sm~i~~~~~ 866 (866)
T cd00653 801 YLLQERLTIKSDDVVARVCVKCGIILSA------NLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866 (866)
T ss_pred HHHHHHHhcCCccceEEEeccCcccccc------cccccccCCCceeecCCCHHHHHHHHHHHHCCcceEeC
Confidence 9999999999999999999999999876 45999999999999999999999999999999999973
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=2.1e-226 Score=2113.27 Aligned_cols=920 Identities=27% Similarity=0.433 Sum_probs=804.4
Q ss_pred cccccccccccccccchHHHHHHHHHHHHH----------hCHHHHHHhcccceecCCCcEEEEEeEEEEcCCccccCCc
Q 001125 28 VVDKFQLLPEFLKVRGLVKQHLDSFNYFVN----------TGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDGV 97 (1149)
Q Consensus 28 ~~~~~~~i~~~~~~~~Lv~~qi~SFn~Fi~----------~gL~~ii~~~~~I~~~~~~~~~l~~~~i~i~~P~~~e~~~ 97 (1149)
.+..|..++.+|+.++|++||++||||||+ +||++++++.+||+.. ++++.|+|.++++++|++
T Consensus 4 ~r~~~~~~~~~~~~p~Lv~~Qi~SFn~FL~~~~~~~~~~~~gL~eii~~~~pI~~~-~~~~~l~f~~~~l~~P~~----- 77 (1065)
T TIGR02013 4 IRIDFGKIPEVLEVPNLLEIQLDSYDWFLQQDTPPEKRKEEGLEEVFKSIFPIEDY-TGNIELEYLSYRLGEPKY----- 77 (1065)
T ss_pred eeeecccCcccccCCCHHHHHHHHHHHHHcCCCcccccccccHHHHHhccCcEEec-CCcEEEEEEEEEeCCCCC-----
Confidence 345699999999999999999999999999 8999999999999754 678999999999999987
Q ss_pred CCCCChhhHhhcCCccCccEEEEEEEEECCcccceeeEEeeEEeeccceeeccccccCCCCCHHHHHhcCCCCCCCCcEE
Q 001125 98 SEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYF 177 (1149)
Q Consensus 98 ~~~l~P~EcR~r~lTYsa~l~v~i~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~elv~~~E~~~d~GGYF 177 (1149)
+|+|||+|++||+|||+|+++++..+.+..+++++++|++|+||||+ .||||
T Consensus 78 ----~p~Ear~r~lTYsa~l~v~v~l~~~~~~~~~~i~~~~V~iG~iPiMt------------------------~gGyF 129 (1065)
T TIGR02013 78 ----SVEECKERGLTYSAPLKVKLRLINKEEDGTKEIKEQDVYMGDIPLMT------------------------DRGTF 129 (1065)
T ss_pred ----CHHHHHHhCCCcceeEEEEEEEEEeccCCccceeeeeEEEeCCCccC------------------------CCceE
Confidence 69999999999999999999997432100135566799999999997 59999
Q ss_pred EEcCchhhhHHhhhccCCeEEEEeC---CCC--cEEEEEEecCCCcceEEEEEeeCCEEEEEEceeeccccHHHHHHHhC
Q 001125 178 IIKGTEKVLLIQEQLSKNRVIIDTD---KKG--NINASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMG 252 (1149)
Q Consensus 178 IING~ERVI~~q~~~s~N~i~~~~~---~~g--~~~a~v~s~~~~~~s~~~~~~k~g~i~~r~~~~~~~IPi~ilLrALG 252 (1149)
||||+||||++||++|||.++.+.. ++| .++|.++|.++ +|..+.+.+++.+|++++++. +||+++||||||
T Consensus 130 IINGsERVIV~Qe~rspg~~~~~~~~~~~~~~~~~~a~iis~rg--swl~~e~~~~~~i~v~i~~~~-kIPi~illrALG 206 (1065)
T TIGR02013 130 IINGAERVVVSQLHRSPGVFFSSEKDTHKSGKVLFSARIIPYRG--SWLEFETDKKDVLYVRIDRKR-KLPATVLLRALG 206 (1065)
T ss_pred EECCcEEEEEEEeecCCCEEEEEccccCCCCceEEEEEEEeCCC--CceEEEEecCCeEEEEecCCC-ceeHHHHHHHcC
Confidence 9999999999999999998887653 345 57899999763 456666667889999999974 999999999999
Q ss_pred CCCHHHHHHHhCCchhHHhhhHHhHHHHHhcCCcCHHHHHHHHhhhcccCCCCCCCCChHHHHHHHHHhhhcc-------
Q 001125 253 MESDQEVVQMVGRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLA------- 325 (1149)
Q Consensus 253 ~~sD~eI~~~i~~~~~~~~~l~~~l~~~~~~~i~t~~~al~yIg~~~r~~~~~~~~~~~~e~~~~~L~~~ll~------- 325 (1149)
+++|+||++.++.+..+.+.+ ++ ....++++|+.|||++++++ ... ..+.|+++|++.|||
T Consensus 207 ~~sd~eI~~~i~~~~~i~~~l----~~---~~~~~~e~Al~~i~~~~~~g----~~~-~~~~a~~~l~~~f~~~~rY~Lg 274 (1065)
T TIGR02013 207 YTIDTLILNRLGSGEYIRNTL----RK---DPTNSEEEALVEIYRKLRPG----EPP-TVEAARSLLENLFFDPKRYDLG 274 (1065)
T ss_pred CCcchhhhhhcCchHHHHHHH----Hh---ccccCHHHHHHHHHhhcCCC----Ccc-hHHHHHHHHHHHhcCccccccc
Confidence 999999999997654444333 22 23679999999999999875 234 678899999999987
Q ss_pred CCCCCC------------CCCCCccchHHHHHHHHHHhhcCCCCCCCcccccccEEccccHhHHHHHHHHHHHHHHHHHH
Q 001125 326 NVPVHN------------NNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQK 393 (1149)
Q Consensus 326 Hl~~~~------------~~~~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~NkRv~l~G~Ll~~lfr~~l~~~~~~ik~ 393 (1149)
|+|... .....|++||+ |+++|+++..|...+||+|||+||||+++|+||+.|||.+|+++.+.+++
T Consensus 275 hiGr~kln~Kl~~~~~~~~~~l~k~d~l~-mi~~Ll~~~~g~~~~DD~Dhl~NKRvr~aGeLL~~~fr~~l~rl~k~ik~ 353 (1065)
T TIGR02013 275 RVGRYKLNKKLGLDVPEDIGVLTKEDIIA-TIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRE 353 (1065)
T ss_pred ccchhhhhhhcCcCcCcccceehHHHHHH-HHHHHHHhhcCCCCCcchhhhhccchhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 999421 11123889997 99999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcCCCCCCCCcccccccccchHHHHHHHhccCCCcccccccccccceEEcccccccccccccccccc----cccc
Q 001125 394 TVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSP----QFEK 469 (1149)
Q Consensus 394 ~i~k~~~~~~~~~~~~~~~~i~~~~It~~i~~~~sTGnw~~~~~~~q~sGvsq~l~rln~ls~LshlRrv~~----~f~~ 469 (1149)
++.+. + ...+++..+++++.||+++++||+|| ||||+|+|+||+|+|||+||+++ ++.+
T Consensus 354 ~l~~~--~---~~~~~~~~~i~~~~it~~i~~ff~tg------------glSQ~Ldr~NpLs~lsh~RRlsslgpggl~r 416 (1065)
T TIGR02013 354 RMSTQ--D---TDTLTPQDLINAKPISAAIKEFFGSS------------QLSQFMDQTNPLAELTHKRRLSALGPGGLTR 416 (1065)
T ss_pred Hhhhc--c---cccCCHHHhcCccchHHHHHHHhccC------------CcccccccCCHHHhhhhhceecccCCCCcCc
Confidence 98753 1 12456778889999999999999987 89999999999999999999998 6999
Q ss_pred ccccCCCCccCCCCCcccccCCCCCCCcchhhhhccceeeeccCCCchhHHHHHhhcCceeccccCccccCCCCceEEEE
Q 001125 470 SRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIF 549 (1149)
Q Consensus 470 ~~k~t~~R~Lhps~wG~iCPveTPEG~~cGLi~~LA~~a~Vt~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~~~V~l 549 (1149)
+++.++||+|||||||||||+|||||+|||||+|||++|+|+.
T Consensus 417 ~~~~~~~RdlHpShyGrICPiETPEG~n~GLVknLA~~a~i~~------------------------------------- 459 (1065)
T TIGR02013 417 ERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNE------------------------------------- 459 (1065)
T ss_pred cccCCccCccCccccccccCCCCCCCCccccccchhhhcccCc-------------------------------------
Confidence 9999999999999999999999999999999999999999851
Q ss_pred CCeEEEeecChhhHHHHHHHHhhcCCcCceeEEEecccCceEEEecCCCeeeeeEEEeecCcccchhhhHHhhhcCCcch
Q 001125 550 NGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSF 629 (1149)
Q Consensus 550 nG~~iG~~~~~~~~~~~lr~~rr~g~i~~~v~i~~~~~~~~i~I~td~GRl~RPl~~v~~~~~~~~~~~~~~~~~~~~~~ 629 (1149)
.|.+.||++.|+||++.
T Consensus 460 -----------------------------------------------~G~i~~P~~~V~ng~~~---------------- 476 (1065)
T TIGR02013 460 -----------------------------------------------YGFIETPYRKVKDGKVV---------------- 476 (1065)
T ss_pred -----------------------------------------------ceEEeCCeEEEECCeEe----------------
Confidence 13456899999887643
Q ss_pred hhhhccCceeEeccccccceEEEeecCCCC-----------------------CCceeeeecCceeccccccccCCCCCC
Q 001125 630 DDFLREGLIEYLDVNEENNALIALYEGDAT-----------------------PDTTHIEIEPFTILGVIAGLIPYPHHN 686 (1149)
Q Consensus 630 ~~l~~~g~iE~id~~Eq~~~~Ia~~~~~~~-----------------------~~~th~Ei~P~~ilsv~AslIPF~~hN 686 (1149)
.++.+||+|++||+++.||..+.++. ..+||+||+|.+|||++||||||+|||
T Consensus 477 ----~~~~i~yl~a~eE~~~~Ia~~~~~l~~~~~~~~~~i~~r~~~~f~~~~~~~vt~~ei~p~~ilsv~aslIPFleHN 552 (1065)
T TIGR02013 477 ----VTDEVDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHD 552 (1065)
T ss_pred ----ccceeEECChHHhCCcEEEecCcCcCccCccccceeeEEEcCceeecChhHeeEEeeChhhhhhhHhhcCCCcccc
Confidence 23569999999999999999876553 246999999999999999999999999
Q ss_pred CCCccccccccccCCcccc-----------------------------------eeeecccccc---------ceee---
Q 001125 687 QSPRNTYQCAMGKQAMGNI-----------------------------------AFNQLCRMDS---------LLYL--- 719 (1149)
Q Consensus 687 qSpRn~yq~~M~KQa~G~~-----------------------------------~~n~~~R~D~---------~~y~--- 719 (1149)
|||||||||||||||||++ ++++..|.|+ +.|.
T Consensus 553 ds~R~lmgsnM~kQavpl~~~e~p~VgTg~E~~v~~ds~~~i~a~~~G~v~~v~~~~~~~r~d~~~~~~~~~~~~y~L~~ 632 (1065)
T TIGR02013 553 DANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRYDEDEDEPDGGIDIYRLLK 632 (1065)
T ss_pred CCcchhhhhhhhhhhhcccccCCCEEEcCcchhhhccccceeEeccCCEEEEEccceEEEEecCCcccccccceEEEeec
Confidence 9999999999999999988 8899999995 3455
Q ss_pred -------ecCCCcceeechh----hhhc------cCCCCCCCcceEEEEEecCCCCCCCcEEeecccccccceeEEEEEE
Q 001125 720 -------LVYPQRPLLTTRT----IELV------GYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKK 782 (1149)
Q Consensus 720 -------L~ypQ~PlV~t~~----~~~~------~~~~~p~G~N~iVAv~~~~Gyn~EDaiiink~s~~rg~~~s~~~~~ 782 (1149)
++|||+|||+|+. .+.+ .++|+|+|+||+||||||+||||||||||||+|++||+|||+||++
T Consensus 633 ~~~snq~~~~~q~Plv~~~~~v~~~~~l~d~~~~~~~e~~~G~N~~VAvm~y~GYn~EDAiiink~~i~rg~~~s~~~~~ 712 (1065)
T TIGR02013 633 YQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEE 712 (1065)
T ss_pred ccccccCceEEeeeeeccCCeEeeeeEecccccccCCcCcCccceEEEEEeeecccccceEEeehhhhcCCceEEEEEEE
Confidence 5699999999964 4443 3899999999999999999999999999999999999999999999
Q ss_pred EEEEeecccCCccceecC-CCCCCCchhhhccCCCCcccCCCceeCCCCEEEEEecCCCCCCCCCC------CCCCCCcc
Q 001125 783 YTAINQKYANSTSDRILR-PDRTGPGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMS------PTGQTDSR 855 (1149)
Q Consensus 783 ~~~~~~~~~~~~~~~~~~-p~~~~~~~~~~~~Ld~dGi~~~G~~v~~gd~l~~k~~~~~~~~~~~~------~~~~~~~~ 855 (1149)
|++++++++.|.++.+.. |+.. ...|++||+||||++|++|++|||||||++|....+.... .++++...
T Consensus 713 ~~~~~~~~~~g~e~~~~~~p~~~---~~~~~~Ld~dGi~~~G~~v~~gdilvgk~~p~~~~~~~~~~~l~~~~~~~~~~~ 789 (1065)
T TIGR02013 713 YEVEARDTKLGPEEITRDIPNVS---EEALRNLDENGIVRIGAEVKAGDILVGKVTPKGETELTPEEKLLRAIFGEKARD 789 (1065)
T ss_pred EEEEeeccCCCceEeeccCCCCc---hhhhhccCCCCCccCccEeCCCCEEEEEecCCcccccChhhhhhhhhcccCCcc
Confidence 999998877665333333 6542 2479999999999999999999999999998654321110 12333345
Q ss_pred cccceeeecCCCCCceEEEEEEEeeCCCC-------cEEEEEEEeeecCCCccccccccCCCccEEEeeeccCCCCCCCC
Q 001125 856 YRSARQTYKGPDGETCVVDRVALCSDKNG-------DLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSER 928 (1149)
Q Consensus 856 ~~~~~~~~~~~~~~~~~v~~v~~~~~~~~-------~~~vkv~~~~~R~p~iGDKf~sRhGqKGvvs~i~~~eDmPf~~~ 928 (1149)
.+|+|++++.++ .|+||+|.++.++++ ...|+|++|+.|+|+||||||||||||||||+|||+||||||+|
T Consensus 790 ~~d~s~~~~~~~--~g~V~~V~~~~~~~~~~~~~~~~~~vkv~ir~~R~p~iGDKfasRHGqKGvis~i~~~eDMPf~~~ 867 (1065)
T TIGR02013 790 VRDTSLRVPPGV--EGTVIDVKVFSRKQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLED 867 (1065)
T ss_pred ccccceEccCCC--CEEEEEEEEEeccCCCccCcCccEEEEEEEeecccccccchhhhcccCceeEEeEecCCCCCccCC
Confidence 789999999998 999999999876665 57899999999999999999999999999999999999999999
Q ss_pred CCCCcEEeCCCCCCCCchHHHHHHHhcccccccc--Cceeeeee-ccCCCCCCCCHHHHHHHHHHcCCCCCCceEEEeCC
Q 001125 929 GICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSC--GRFHYGSA-FGEPSGHADTVESISETLVKHGFSYNGKDMIYSGI 1005 (1149)
Q Consensus 929 G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~--g~~~d~tp-F~~~~~~~~~~~~~~~~l~~~g~~~~G~e~ly~G~ 1005 (1149)
|++|||||||||||||||||||+||++||||++. |.+.++|| |. +.+.+++.+.|+++||+++|+|.||||+
T Consensus 868 G~~pDiIiNPhg~PSRMtiGqllE~~~gka~~~~~~~~~~~~tp~f~-----~~~~~~~~~~l~~~g~~~~G~e~l~~G~ 942 (1065)
T TIGR02013 868 GTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRKGVPIATPVFD-----GASEEEIKEYLEKAGLPRDGKVRLYDGR 942 (1065)
T ss_pred CCCccEEECCCCCcccccHHHHHHHHHHHHHHhccCCCeEEeccCcC-----CccHHHHHHHHHHcCCCCCCCEEEEcCC
Confidence 9999999999999999999999999999999987 66788999 66 6789999999999999999999999999
Q ss_pred CCcEEeeeEeEeeeeecccccccCcccEEecccCcccccccCcccccCCCceeeechhhhHHHHcccHHHHHHhhccCCC
Q 001125 1006 TGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGLRVGEMERDCLIAYGASMLIFERLMVSSD 1085 (1149)
Q Consensus 1006 tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD 1085 (1149)
||++|+++||+|++|||||+|||+||+|||++|||+.|||||++||||+|||||||||||||+|||||++|+|||+.+||
T Consensus 943 TG~~~~~~ifvG~~yy~rL~HmV~DK~haRs~Gp~~~lT~QP~~Grsr~GG~R~GEME~d~l~a~Gas~~L~E~l~~~SD 1022 (1065)
T TIGR02013 943 TGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1022 (1065)
T ss_pred CCCCccccEEEeehheeechhhhcchhhhcccCCccceeeCCCcccccCCCeeeeeeeHHHHHhhhhHHHHHHHHhccCh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceeeeecccCCcceeecccccceecccccCCCccccccccHhHHHHHHHHHhCCcccEE
Q 001125 1086 PFEVQVCRVCGLLGYYNHKLKAGICSTCKNGDNISSMKLPYACKLLIQELQSMNIVPRL 1144 (1149)
Q Consensus 1086 ~~~~~vC~~cg~~~~~~~~~~~~~C~~c~~~~~~~~v~iPy~~k~l~~EL~sm~i~~~l 1144 (1149)
++..+ . ..++..| ++.++.++.+|||||||+|||+||||++++
T Consensus 1023 ~~~g~-------~--------~~~~~~~-~~~~i~~~~~p~sfklL~~EL~sm~i~~~~ 1065 (1065)
T TIGR02013 1023 DVVGR-------T--------KAYEAIV-KGENVPEPGIPESFNVLIKELQSLGLDIEL 1065 (1065)
T ss_pred hhhhh-------h--------hhhhhhc-CCCccccccCCccHHHHHHHHHhCCccccC
Confidence 99643 1 1223445 568899999999999999999999999875
No 8
>PRK00405 rpoB DNA-directed RNA polymerase subunit beta; Reviewed
Probab=100.00 E-value=1.2e-222 Score=2090.02 Aligned_cols=922 Identities=26% Similarity=0.433 Sum_probs=797.6
Q ss_pred cccccccccccccccchHHHHHHHHHHHH-------HhCHHHHHHhcccceecCCCcEEEEEeEEEEcCCccccCCcCCC
Q 001125 28 VVDKFQLLPEFLKVRGLVKQHLDSFNYFV-------NTGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDGVSEK 100 (1149)
Q Consensus 28 ~~~~~~~i~~~~~~~~Lv~~qi~SFn~Fi-------~~gL~~ii~~~~~I~~~~~~~~~l~~~~i~i~~P~~~e~~~~~~ 100 (1149)
.+..+..++.+++.++|++||++|||||| ++||++++++.+||+. .++++.|+|.++++++|.+
T Consensus 11 ~r~~~~~~~~~~~~p~Lv~~Qi~SFn~Fl~~~~~~~~~gL~~ii~~~~pI~~-~~~~~~l~f~~~~l~~P~~-------- 81 (1112)
T PRK00405 11 IRKSFGKIKEVLELPNLLEIQLDSFDWFLQLDVPPEDEGLEEVFRSIFPIED-FNGNLSLEFVSYELGEPKY-------- 81 (1112)
T ss_pred eEeecccccccCCCCCHHHHHHHHHHHHHhcCCcccchhHHHHHHhcCCEEe-cCCcEEEEEeeeEcCCCCC--------
Confidence 34568888899999999999999999999 9999999999999986 4678999999999999964
Q ss_pred CChhhHhhcCCccCccEEEEEEEEECCcccceeeEEeeEEeeccceeeccccccCCCCCHHHHHhcCCCCCCCCcEEEEc
Q 001125 101 LNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIK 180 (1149)
Q Consensus 101 l~P~EcR~r~lTYsa~l~v~i~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~elv~~~E~~~d~GGYFIIN 180 (1149)
+|+|||+|++||+|||+|+++++..+. +++++++|++|+||||+ +|||||||
T Consensus 82 -tp~Ear~r~lTYSaplyv~v~l~~~~~---~~i~~~~V~iG~iPiMt------------------------~gGyFIIN 133 (1112)
T PRK00405 82 -DVEECKERGLTYSAPLRVKLRLINKET---GEIKEQEVYMGDIPLMT------------------------ENGTFIIN 133 (1112)
T ss_pred -CHHHHHHhCCCCCeeEEEEEEEEEecc---CceeeeeEEEecccccc------------------------CCceEEEC
Confidence 899999999999999999999975432 35566799999999997 89999999
Q ss_pred CchhhhHHhhhccCCeEEEEeCC-----CCcEEEEEEecCCCcceEEEEEeeCCEEEEEEceeeccccHHHHHHHhCCCC
Q 001125 181 GTEKVLLIQEQLSKNRVIIDTDK-----KGNINASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMES 255 (1149)
Q Consensus 181 G~ERVI~~q~~~s~N~i~~~~~~-----~g~~~a~v~s~~~~~~s~~~~~~k~g~i~~r~~~~~~~IPi~ilLrALG~~s 255 (1149)
|+||||++||++|||.++.+... +..|+|+++|.++ +|..+.+.+++.+|+++++. ++||+++||||||+ |
T Consensus 134 G~ERVIVsQe~rSPg~~~~~~~~k~~~~k~~y~a~Iis~rG--swl~~e~d~k~~I~vri~~~-~kIPi~iLLrALGl-s 209 (1112)
T PRK00405 134 GTERVIVSQLHRSPGVYFDHDKDKTSSGKLLYSARIIPYRG--SWLEFEFDPKDILYVRIDRR-RKLPVTVLLRALGY-S 209 (1112)
T ss_pred CeEEEEEEEeecCCCEEEEEeccccCCCceeEEEEEEECCC--CcEEEEEecCCeEEEEecCC-CcccHHHHHHHcCC-C
Confidence 99999999999999987765432 2347899999863 56666667789999999986 69999999999999 8
Q ss_pred HHHHHHHhCCchhHH-------------------------h------------hhHHhHHHHH-hcCCcCHHHHHHHHhh
Q 001125 256 DQEVVQMVGRDPRYS-------------------------A------------LLLPSIEECA-NLDIYTQEKALEYLEG 297 (1149)
Q Consensus 256 D~eI~~~i~~~~~~~-------------------------~------------~l~~~l~~~~-~~~i~t~~~al~yIg~ 297 (1149)
|+||++.|+.+..+. + .+...+.+.. ..++.++++|+.|||+
T Consensus 210 d~eIl~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ei~~~~~~~~~~~~~~~~i~~~l~~~~~~t~e~Al~~I~k 289 (1112)
T PRK00405 210 DEEILDLFYEKEEFGKEIEVPVEYLLGKVLAEDIVDEETGEVLAEANDEITEELDGPYIRNTLEKDPTSSREEALVEIYR 289 (1112)
T ss_pred HHHHHHHhcccccccceeccchHHhcccchhhhhcccccceeeeccCCccchhhhhHHHHHHHhhccccCHHHHHHHHHh
Confidence 999999996332221 0 0112232222 2356799999999999
Q ss_pred hcccCCCCCCCCChHHHHHHHHHhhhc-------cCCCCCCCC--------CC----CccchHHHHHHHHHHhhcCCCCC
Q 001125 298 KVKRSTFGSPPNDREGRAFSILRDVFL-------ANVPVHNNN--------FR----PKCFYVAVMLRRMVEAMLNKDAM 358 (1149)
Q Consensus 298 ~~r~~~~~~~~~~~~e~~~~~L~~~ll-------~Hl~~~~~~--------~~----~K~~~L~~Mi~kLl~~~~g~~~~ 358 (1149)
+++++ ... ..+.|+++|++.|| ||+|..+.+ .. .|+ .+++|+++|+++..|.+.+
T Consensus 290 ~l~~g----~~~-~~e~a~~~l~~~ff~~~rYdL~hiGr~k~nkKl~l~~~~~~~~L~~~-d~~~mi~~Ll~l~~g~~~~ 363 (1112)
T PRK00405 290 RLRPG----EPP-TVEAARSLLENLFFDPKRYDLSKVGRYKLNKKLGLDEDEDVRVLTKE-DIIATIKYLINLRNGKGEV 363 (1112)
T ss_pred hcCCC----Ccc-hHHHHHHHHHHHhcCccccccccCCceecchhcccCcccccccccHH-HHHHHHHHHHhhhcccCCC
Confidence 99876 234 66889999999886 999965332 11 234 4589999999999999999
Q ss_pred CCcccccccEEccccHhHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccccccchHHHHHHHhccCCCcccccc
Q 001125 359 DDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFDVKRFK 438 (1149)
Q Consensus 359 DD~D~l~NkRv~l~G~Ll~~lfr~~l~~~~~~ik~~i~k~~~~~~~~~~~~~~~~i~~~~It~~i~~~~sTGnw~~~~~~ 438 (1149)
||+|||+||||+++|+||+.|||.+|+++++.+++++.+.. ...+++..+++++.||++|++||+||
T Consensus 364 DDiDhl~NKRvr~aGeLL~~~fr~~~~rl~k~ik~~l~~~~-----~~~~~~~~lin~~~it~~i~~ff~tg-------- 430 (1112)
T PRK00405 364 DDIDHLGNRRVRSVGELLQNQFRIGLSRMERAVRERMSLQD-----LDTLTPQDLINAKPVVAAIKEFFGSS-------- 430 (1112)
T ss_pred cchhHHhcchhhhHHHHHHHHHHHHHHHHHHHHHHHhhhcc-----cccCCHHHhhCchhHHHHHHHhhccC--------
Confidence 99999999999999999999999999999999999987541 13467888899999999999999987
Q ss_pred cccccceEEcccccccccccccccccc----ccccccccCCCCccCCCCCcccccCCCCCCCcchhhhhccceeeeccCC
Q 001125 439 MHRKGMTQVLARLSFIGTLGHMTRVSP----QFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDE 514 (1149)
Q Consensus 439 ~q~sGvsq~l~rln~ls~LshlRrv~~----~f~~~~k~t~~R~Lhps~wG~iCPveTPEG~~cGLi~~LA~~a~Vt~~~ 514 (1149)
||||+|+|+||+|+|||+||+++ ++.++++.+.||+|||||||||||+|||||+|||||+|||++|+|+
T Consensus 431 ----glSQ~Ldq~NpLselshkRRlss~gpggl~r~~a~~~~R~lH~ShyGriCPiETPEG~n~GLV~nLA~~a~i~--- 503 (1112)
T PRK00405 431 ----QLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVN--- 503 (1112)
T ss_pred ----CcceeeccCCHHHhhhhhceecccCCCCcCccccCCcccccCccccccccCcCCCCCCccccccchhhccccc---
Confidence 88999999999999999999998 6999999999999999999999999999999999999999999998
Q ss_pred CchhHHHHHhhcCceeccccCccccCCCCceEEEECCeEEEeecChhhHHHHHHHHhhcCCcCceeEEEecccCceEEEe
Q 001125 515 EEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIA 594 (1149)
Q Consensus 515 ~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~lr~~rr~g~i~~~v~i~~~~~~~~i~I~ 594 (1149)
.+|+.. .+|.+++||.|- +
T Consensus 504 ----------~~G~~~------------tp~~~~~nG~~~---~------------------------------------ 522 (1112)
T PRK00405 504 ----------EYGFIE------------TPYRKVVDGKVT---D------------------------------------ 522 (1112)
T ss_pred ----------cCCccc------------cceEEEECCeEc---c------------------------------------
Confidence 355431 247788898761 0
Q ss_pred cCCCeeeeeEEEeecCcccchhhhHHhhhcCCcchhhhhccCceeEeccccccceEEEeecCCCC---------------
Q 001125 595 SDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDAT--------------- 659 (1149)
Q Consensus 595 td~GRl~RPl~~v~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~iE~id~~Eq~~~~Ia~~~~~~~--------------- 659 (1149)
.+||+|++||++..||....++.
T Consensus 523 ------------------------------------------~i~yl~a~eE~~~~Ia~~~~~l~~~~~~~~~~i~~r~~ 560 (1112)
T PRK00405 523 ------------------------------------------EIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYK 560 (1112)
T ss_pred ------------------------------------------ceEECCHHHhcCcEEEecCcccCCCCcccCceEEEEec
Confidence 15777777777777777654432
Q ss_pred --------CCceeeeecCceeccccccccCCCCCCCCCccccccccccCCccccee------------------------
Q 001125 660 --------PDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAF------------------------ 707 (1149)
Q Consensus 660 --------~~~th~Ei~P~~ilsv~AslIPF~~hNqSpRn~yq~~M~KQa~G~~~~------------------------ 707 (1149)
..+||+||+|.+++|++||||||+||||||||+|||||||||||++..
T Consensus 561 ~e~~~~~~~~~~~~~i~p~qi~sv~aslIPFleHnda~R~lmgSnMqrQAvpl~~~~~p~vgTg~e~~~~~ds~~~i~a~ 640 (1112)
T PRK00405 561 GEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAK 640 (1112)
T ss_pred CcceeechhhceEEeechhhhceehhhccCcccccCCcchhhhhhhhhhhhhhccccCCeeecCcchhhhhhcchheEec
Confidence 246999999999999999999999999999999999999999999877
Q ss_pred -----------eecccc-----------------ccceee-ecCCCcceeechh----hhhc------cCCCCCCCcceE
Q 001125 708 -----------NQLCRM-----------------DSLLYL-LVYPQRPLLTTRT----IELV------GYDKLGAGQNAT 748 (1149)
Q Consensus 708 -----------n~~~R~-----------------D~~~y~-L~ypQ~PlV~t~~----~~~~------~~~~~p~G~N~i 748 (1149)
++..|. |+..+. ++|||||||+|+. .+.+ +++|+|+|+|++
T Consensus 641 ~~G~v~~v~~~~i~ir~~~~~~~~~~~~~y~L~~~~~sn~~~~~~q~Plv~~~~~v~~g~~lad~~~~~~~e~~~G~N~~ 720 (1112)
T PRK00405 641 RDGVVEYVDASRIVVRVEELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQNVL 720 (1112)
T ss_pred cCCEEEEEeCCEEEEeecccccCCCCeeEEEecccccccccceeecceeeecCCeEeeccEeecccccCcccccCCcceE
Confidence 777777 555666 7999999999995 4554 799999999999
Q ss_pred EEEEecCCCCCCCcEEeecccccccceeEEEEEEEEEEeecccCCccceecC-CCCCCCchhhhccCCCCcccCCCceeC
Q 001125 749 VAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILR-PDRTGPGAERMQILDDDGLAAPGEIIK 827 (1149)
Q Consensus 749 VAv~~~~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~~~~~~-p~~~~~~~~~~~~Ld~dGi~~~G~~v~ 827 (1149)
||||||+||||||||||||+|++||+|+|+||++|++++++++.|..+.+.. |+.+ ...|++||+||||++|++|+
T Consensus 721 VA~~~y~GYn~EDaiiink~si~rg~~~s~~~~~~~~~~~~~~~~~~~~~~~~p~~~---~~~~~~Ld~dGi~~~G~~v~ 797 (1112)
T PRK00405 721 VAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVS---EEALRNLDESGIVRIGAEVK 797 (1112)
T ss_pred EEEEeecccCccceEEEEhhhhccCceEEEEEeeeeeEeeccCCCceeecccCCCCC---hHHhhccCCCCCccCccEec
Confidence 9999999999999999999999999999999999999999877775443332 5432 24799999999999999999
Q ss_pred CCCEEEEEecCCCCCCCCCC------CCCCCCcccccceeeecCCCCCceEEEEEEEeeC-CCC-------cEEEEEEEe
Q 001125 828 PNDVYINKESPLETRGSIMS------PTGQTDSRYRSARQTYKGPDGETCVVDRVALCSD-KNG-------DLCIKFLIR 893 (1149)
Q Consensus 828 ~gd~l~~k~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~v~~v~~~~~-~~~-------~~~vkv~~~ 893 (1149)
+|||||||++|....+.... .++++....+|+|+++++++ .|+||+|.++.+ .++ ...|||++|
T Consensus 798 ~gDiligk~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~s~~~~~~~--~g~V~~v~~~~~~~~~~~~~~~~~~~vkv~ir 875 (1112)
T PRK00405 798 PGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGE--EGTVIDVKVFTRIEQGDELPPGVNKLVKVYIA 875 (1112)
T ss_pred CCCEEEEEecCCCccccChhhhhhhhhhcccccccccceEEcCCCC--CEEEEEEEEeeccccCCccCcCcceEEEEEEe
Confidence 99999999998754321110 12223344789999999998 999999999876 554 478999999
Q ss_pred eecCCCccccccccCCCccEEEeeeccCCCCCCCCCCCCcEEeCCCCCCCCchHHHHHHHhccccccccCceeeeee-cc
Q 001125 894 HTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSA-FG 972 (1149)
Q Consensus 894 ~~R~p~iGDKf~sRhGqKGvvs~i~~~eDmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tp-F~ 972 (1149)
+.|+|+||||||||||||||||+|||+||||||+||++|||||||||||||||||||+|+++||||++.|.+ |+|| |.
T Consensus 876 ~~R~p~iGDKfasRHGqKGvis~i~~~eDMPf~~~G~~pDiIiNPhg~PSRMtiGql~E~~~gk~~~~~g~~-~~tp~f~ 954 (1112)
T PRK00405 876 QKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIK-FATPVFD 954 (1112)
T ss_pred eecccCcccchhhccCCceeEEeEeccCCCCcCCCCCCCcEEECCCCCcccccHHHHHHHHhhHHHHhcCCe-EecCccC
Confidence 999999999999999999999999999999999999999999999999999999999999999999999985 8999 76
Q ss_pred CCCCCCCCHHHHHHHHHHcCCCCCCceEEEeCCCCcEEeeeEeEeeeeecccccccCcccEEecccCcccccccCccccc
Q 001125 973 EPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRA 1052 (1149)
Q Consensus 973 ~~~~~~~~~~~~~~~l~~~g~~~~G~e~ly~G~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~ 1052 (1149)
+.+.+++++.|.++||+++|+|+||||+||++|+++||+|++|||||+|||+||+|||++|||+.|||||++||+
T Consensus 955 -----~~~~~~~~~~l~~~g~~~~G~e~l~~G~tG~~~~~~if~G~~yy~rL~HmV~DK~haRs~Gp~~~lT~QP~~Grs 1029 (1112)
T PRK00405 955 -----GAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKA 1029 (1112)
T ss_pred -----CccHHHHHHHHHHcCcCCCCCEEEECCCCCCCCcccEEEEehhheechhhhcchhhhcccCCccceeeCCCcccc
Confidence 678999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCceeeechhhhHHHHcccHHHHHHhhccCCCceeeeecccCCcceeecccccceecccccCCCccccccccHhHHHHH
Q 001125 1053 RNGGLRVGEMERDCLIAYGASMLIFERLMVSSDPFEVQVCRVCGLLGYYNHKLKAGICSTCKNGDNISSMKLPYACKLLI 1132 (1149)
Q Consensus 1053 ~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~cg~~~~~~~~~~~~~C~~c~~~~~~~~v~iPy~~k~l~ 1132 (1149)
|+|||||||||||||+|||||++|+|||+.+||++.++.+ ...| .| ++.++.++.+|||||||+
T Consensus 1030 r~GG~R~GEME~d~l~a~Gas~~L~Erl~~~SD~~~g~~~--------------~~~~-~~-~~~~i~~~~~p~~fklL~ 1093 (1112)
T PRK00405 1030 QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTK--------------VYEA-IV-KGENIPEPGIPESFNVLV 1093 (1112)
T ss_pred cCCCeeeeeeehhhHhhhhhHHHHHHHhhccCccccccee--------------EEEE-ee-cCCcccccCCChHHHHHH
Confidence 9999999999999999999999999999999999975432 1235 45 668899999999999999
Q ss_pred HHHHhCCcccEEEe
Q 001125 1133 QELQSMNIVPRLKL 1146 (1149)
Q Consensus 1133 ~EL~sm~i~~~l~~ 1146 (1149)
|||+||||++++.-
T Consensus 1094 ~EL~sm~i~~~~~~ 1107 (1112)
T PRK00405 1094 KELQSLGLDVELLD 1107 (1112)
T ss_pred HHHHHCccceEEec
Confidence 99999999999974
No 9
>CHL00001 rpoB RNA polymerase beta subunit
Probab=100.00 E-value=4.2e-219 Score=2035.15 Aligned_cols=940 Identities=23% Similarity=0.350 Sum_probs=795.9
Q ss_pred cccccchHHHHHHHHHHHHHhCHHHHHHhcccceecCCCcEEEE--EeEEEEcCCccccCCcCCCCChhhHhhcCCccCc
Q 001125 38 FLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLR--FKDVRIGQPSMTVDGVSEKLNPHMCRLSDMTYAA 115 (1149)
Q Consensus 38 ~~~~~~Lv~~qi~SFn~Fi~~gL~~ii~~~~~I~~~~~~~~~l~--~~~i~i~~P~~~e~~~~~~l~P~EcR~r~lTYsa 115 (1149)
-++.++|+++|++||||||++||++++++++||+ +.++.+.++ ++++++++|++ +|.|||+|++||+|
T Consensus 9 ~~~~P~Lv~~Q~~SF~~Fl~~gL~~i~~~~~pI~-~~~~~~~~~~~~~~~~l~~P~~---------~p~ear~r~lTYsa 78 (1070)
T CHL00001 9 MSTIPGFNQIQFEGFCRFIDQGLTEELSKFPKIE-DTDQEIEFQLFVETYQLVEPLI---------KERDAVYESLTYSS 78 (1070)
T ss_pred ccCCCCHHHHHHHHHHHHHHHhHHHHHHhcCCeE-CCCCCEEEEEEeCeEEECCCCC---------CHHHHHHhCCCCCc
Confidence 3678999999999999999999999999999998 566665554 55999999987 79999999999999
Q ss_pred cEEEEEEEEECCcccceeeEEeeEEeeccceeeccccccCCCCCHHHHHhcCCCCCCCCcEEEEcCchhhhHHhhhccCC
Q 001125 116 PILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKN 195 (1149)
Q Consensus 116 ~l~v~i~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~elv~~~E~~~d~GGYFIING~ERVI~~q~~~s~N 195 (1149)
||+|+++++..+. +.+++++|++|+||+|+ +||||||||+||||++|+++|||
T Consensus 79 ~l~v~v~l~~~~~---~~i~~~~V~iG~iPlMt------------------------~gG~FIING~ERVIVsQ~~rSpg 131 (1070)
T CHL00001 79 ELYVPAGLIWKKS---RDMQEQTVFIGNIPLMN------------------------SLGTFIINGIYRVVINQILRSPG 131 (1070)
T ss_pred eeEEEEEEEEcCc---eeEEEeEEEEecCCccC------------------------CCcEEEEcCcEEEEEEEEeccCC
Confidence 9999999975442 45667799999999995 99999999999999999999999
Q ss_pred eEEEEeC-CC--CcEEEEEEecCCCcceEEEEEeeCCEEEEEEceeeccccHHHHHHHhCCCCHHHHHHHhCCchhHHhh
Q 001125 196 RVIIDTD-KK--GNINASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGRDPRYSAL 272 (1149)
Q Consensus 196 ~i~~~~~-~~--g~~~a~v~s~~~~~~s~~~~~~k~g~i~~r~~~~~~~IPi~ilLrALG~~sD~eI~~~i~~~~~~~~~ 272 (1149)
.++.+.. +. ..|.|.++|.++ +|..+.+.+++.+|+++++. ++||+++||||||++ |+||++.++.+ +.
T Consensus 132 ~~~~~~~~~~~~~~y~a~iis~rg--swl~~e~d~~~~i~vri~~~-~kiPi~ilLrALG~s-d~eIl~~~~~~----~~ 203 (1070)
T CHL00001 132 IYYRSELDHNGISVYTGTIISDWG--GRLELEIDRKARIWARVSRK-QKISILVLLSAMGLN-LREILDNVCYP----EI 203 (1070)
T ss_pred EEEEEecCCCCceeEEEEEEecCC--CceEEEEecCCeEEEEecCC-CcccHHHHHHHcCCC-HHHHHHHhCcH----HH
Confidence 7776542 22 348899999876 45666666778999999997 699999999999995 99999999643 23
Q ss_pred hHHhHHHHHhcCCcCHHHHHHHHhhhcccCCCCCCCCChHHHHHHHHHhhhccC------CCCCCCCCC------Cccch
Q 001125 273 LLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLAN------VPVHNNNFR------PKCFY 340 (1149)
Q Consensus 273 l~~~l~~~~~~~i~t~~~al~yIg~~~r~~~~~~~~~~~~e~~~~~L~~~ll~H------l~~~~~~~~------~K~~~ 340 (1149)
+..++.+..+.++.++++||.||++++.+. ..+.. ..+.|+.+|.+.||+| +|..+.+.+ .|+.+
T Consensus 204 l~~~l~~~~~~~~~t~e~Al~~i~~~l~~r--~~~~~-~~~~a~~~l~~~ff~~rY~Lg~vGr~~~n~kl~~~~~~~~~~ 280 (1070)
T CHL00001 204 FLSFLNDKEKKKIGSKENAILEFYQQFACV--GGDPV-FSESLCKELQKKFFQQRCELGRIGRRNMNRKLNLDIPENNTF 280 (1070)
T ss_pred HHHHHHHHhhccccCHHHHHHHHHHhhccC--CCCcc-hHHHHHHHHHHHhccccccccccCchhhhhhhcccccccceE
Confidence 444444443456789999999999998432 11334 6788999999999999 776544333 56777
Q ss_pred H-----HHHHHHHHHhhcCCCCCCCcccccccEEccccHhHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCccccccc
Q 001125 341 V-----AVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIV 415 (1149)
Q Consensus 341 L-----~~Mi~kLl~~~~g~~~~DD~D~l~NkRv~l~G~Ll~~lfr~~l~~~~~~ik~~i~k~~~~~~~~~~~~~~~~i~ 415 (1149)
| ++|+++|+++..|...+||+|||+||||+++|+||++|||.+|+++++.++++|.+.+.+. ..+++..+++
T Consensus 281 L~~~Di~~~i~~Ll~l~~G~~~~DDiDhLgNKRvr~vGeLL~~qfr~~l~r~~r~ik~~m~~~~~~~---~~~~~~~lin 357 (1070)
T CHL00001 281 LLPQDVLAAADYLIGMKFGMGTLDDIDHLKNKRIRSVADLLQDQFGLALNRLENAVRGTICGAIRRK---LIPTPQNLVT 357 (1070)
T ss_pred ecHHHHHHHHHHHHHhhcCCCCccchhHHhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc---ccCCHHHhhC
Confidence 7 9999999999999999999999999999999999999999999999999999998765432 2467888899
Q ss_pred ccchHHHHHHHhccCCCcccccccccccceEEcccccccccccccccccc--ccccccccC--CCCccCCCCCcccccCC
Q 001125 416 RDSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSP--QFEKSRKVS--GPRALQPSQWGMLCPCD 491 (1149)
Q Consensus 416 ~~~It~~i~~~~sTGnw~~~~~~~q~sGvsq~l~rln~ls~LshlRrv~~--~f~~~~k~t--~~R~Lhps~wG~iCPve 491 (1149)
+++||++|++||+| +|+||+|||+|++|+|+|+||+++ |...+++.+ .||+|||||||||||+|
T Consensus 358 ~~~It~~ik~ff~t------------s~LSQflDqtNpLseltHkRRlsslGpgglsr~~a~fevRdvHpShyGRICPIE 425 (1070)
T CHL00001 358 STPLTTTYESFFGS------------HPLSQFLDQTNPLTEIVHGRKLSSLGPGGLTGRTASFRVRDIHPSHYGRICPID 425 (1070)
T ss_pred cchHHHHHHhhhcC------------CcceeeeccCCHHHhhhhhhcccccCCCCccccccCCcccccCccccccccCCC
Confidence 99999999999987 589999999999999999999997 888888776 89999999999999999
Q ss_pred CCCCCcchhhhhccceeeec-cCCCchhHHHHHhhcCceeccccCccccCCCCceEEEECCeEEEeecChhhHHHHHHHH
Q 001125 492 TPEGEACGLVKNLALMTHVT-TDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKL 570 (1149)
Q Consensus 492 TPEG~~cGLi~~LA~~a~Vt-~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~lr~~ 570 (1149)
||||+|||||+|||++|+|+ .+..++|+.+++...+++.+.++++.+. ..+.|+ ||.|+|...+.
T Consensus 426 TPEG~NiGLI~sLA~~A~In~~GfietP~~~v~~~~~~~~i~ylsa~ee---~~~~Ia-~g~~~~~~~~~---------- 491 (1070)
T CHL00001 426 TSEGINAGLIGSLAIHARIGHWGSLESPFYEISERSKEERMVYLSPSED---EYYMIA-AGNSLALNQGI---------- 491 (1070)
T ss_pred CCCcccccchhhhhhhcccccCCCcccceeeeccccccceeEEcccccc---CceEEE-eCceeeccCCc----------
Confidence 99999999999999999999 5788999999998888888888887652 468888 99998732110
Q ss_pred hhcCCcCceeEEEecccCceEEEecCCCeeeeeEEEeecCcccchhhhHHhhhcCCcchhhhhccCceeEeccccccceE
Q 001125 571 RRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNAL 650 (1149)
Q Consensus 571 rr~g~i~~~v~i~~~~~~~~i~I~td~GRl~RPl~~v~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~iE~id~~Eq~~~~ 650 (1149)
+...++.++ + + ++++.
T Consensus 492 -----------------------------~~~~~~~~r--------------------~----~-----------~e~~~ 507 (1070)
T CHL00001 492 -----------------------------QEEQVVPAR--------------------Y----R-----------QEFLT 507 (1070)
T ss_pred -----------------------------cccceeEEE--------------------e----c-----------CeEEE
Confidence 000011100 0 0 11234
Q ss_pred EEeecCCCCCCceeeeecCceeccccccccCCCCCCCCCccccccccccCCcccceee---------ecccc--------
Q 001125 651 IALYEGDATPDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFN---------QLCRM-------- 713 (1149)
Q Consensus 651 Ia~~~~~~~~~~th~Ei~P~~ilsv~AslIPF~~hNqSpRn~yq~~M~KQa~G~~~~n---------~~~R~-------- 713 (1149)
||.. +.||+||+|.||+||+||||||+||||||||+|||||||||||++..+ +..|.
T Consensus 508 i~~~------~i~~~dIsP~qi~svaasLIPFleHndanRalmgsnMqrQAvpll~~~~p~VgTG~E~~~~~ds~~~i~a 581 (1070)
T CHL00001 508 IAWE------QIHLRSIFPFQYFSIGASLIPFLEHNDANRALMGSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVVAIA 581 (1070)
T ss_pred EchH------HCcEEeeChhhhhhhhhhcCCCccccCcchhhhhhccchhccccccCCCCEeecCcchhhhhcccceeEE
Confidence 4433 248999999999999999999999999999999999999999998887 66666
Q ss_pred ---------c-----------c-ceeeecC---------CCcceeechhhhh----------ccCCCCCCCcceEEEEEe
Q 001125 714 ---------D-----------S-LLYLLVY---------PQRPLLTTRTIEL----------VGYDKLGAGQNATVAVMS 753 (1149)
Q Consensus 714 ---------D-----------~-~~y~L~y---------pQ~PlV~t~~~~~----------~~~~~~p~G~N~iVAv~~ 753 (1149)
| + ..|++.| ||||||+++.+.. +..+|+|+|+|++|||||
T Consensus 582 ~~~G~V~~vd~~~I~i~~~~~~~~y~l~~y~rsnq~t~~~QkPlV~~g~~v~~g~~ladg~~~~~gel~~G~N~~VA~m~ 661 (1070)
T CHL00001 582 EHEGKIIYTDTDKIILSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCVKKGQILADGAATVGGELALGKNVLVAYMP 661 (1070)
T ss_pred ccCCEEEEEeCCEEEEEcCCCeEEEEeeceeccCCCcccccCCEEecCCEEccCCEeccChhhccccccCCccceeeeee
Confidence 5 4 3455568 9999999995432 238999999999999999
Q ss_pred cCCCCCCCcEEeecccccccceeEEEEEEEEEEeecccCCccceecC--CCCCCCchhhhccCCCCcccCCCceeCCCCE
Q 001125 754 YSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILR--PDRTGPGAERMQILDDDGLAAPGEIIKPNDV 831 (1149)
Q Consensus 754 ~~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~~~~~~--p~~~~~~~~~~~~Ld~dGi~~~G~~v~~gd~ 831 (1149)
|+||||||||||||+|++||+|||+||++|++++++++.|. |.++. |+.+. ..|++||+||||++|++|++|||
T Consensus 662 ~~GYn~EDAiiin~~~v~~g~~~s~~~~~~~~~~~~~~~g~-e~i~~~~p~~~~---~~~~~Ld~dGi~~~G~~v~~gDi 737 (1070)
T CHL00001 662 WEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQGP-ERITKEIPHLEA---HLLRNLDKNGIVMLGSWVETGDI 737 (1070)
T ss_pred ccccccchhhhhhhhhhcCCceEEEEEeeeeEEEeccCCCc-ceEeccCCCCch---hhhhccCCCCCccCCcEecCCCE
Confidence 99999999999999999999999999999999999887775 55543 66532 47999999999999999999999
Q ss_pred EEEEecCCCCCCCCC--------CCCCCCCcccccceeeecCCCCCceEEEEEEEeeC----CCCcEEEEEEEeeecCCC
Q 001125 832 YINKESPLETRGSIM--------SPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSD----KNGDLCIKFLIRHTRRPE 899 (1149)
Q Consensus 832 l~~k~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~~~v~~v~~~~~----~~~~~~vkv~~~~~R~p~ 899 (1149)
||||++|....+... ..++++...++|+|+++++++ .|+|++|.++.. .++...|||++|+.|+|+
T Consensus 738 lvgK~~p~~~~~~~~~~~~~~~~~if~~~~~~~~d~sl~~~~~~--~g~V~~v~~~~~~~~~~~~~~~vkv~i~~~R~~~ 815 (1070)
T CHL00001 738 LVGKLTPQEAEESSYAPEGRLLRAIFGIQVSTSKETCLKLPIGG--RGRVIDVRWIQKKGGSSYNPETIHVYILQKREIQ 815 (1070)
T ss_pred EEEEecCCcccccccCcchhhhhhhhccccCcceeCeEECCCCC--ceEEEEEEEEecccCCCCCcEEEEEEEEEEecCC
Confidence 999999973222111 113444556799999999988 999999998773 456789999999999999
Q ss_pred ccccccccCCCccEEEeeeccCCCCCCCCCCCCcEEeCCCCCCCCchHHHHHHHhccccccccCceeeeeeccCCCCCCC
Q 001125 900 LGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHAD 979 (1149)
Q Consensus 900 iGDKf~sRhGqKGvvs~i~~~eDmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tpF~~~~~~~~ 979 (1149)
||||||||||||||||+|||+||||||+||++|||||||||||||||||||+|+++||||++.|.+.|+|||+..+.+..
T Consensus 816 vGDK~asRHGqKGvvs~i~~~eDMPf~~dG~~pDiIlNP~gvPSRMtiGqllE~~~G~a~~~~g~~~~~~pf~~~~~~~~ 895 (1070)
T CHL00001 816 VGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLLNRHYRIAPFDERYEQEA 895 (1070)
T ss_pred CCcccccccCCcceEeeeecccCCCcccCCCCCceeeccccccccccHHHHHHHHhHHHHhhcCceeeeccCCCcchhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999994322222
Q ss_pred CHHHHHHHHHHcCC----------CCCCceEEEeCCCCcEEeeeEeEeeeeecccccccCcccEEecccCcccccccCcc
Q 001125 980 TVESISETLVKHGF----------SYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTE 1049 (1149)
Q Consensus 980 ~~~~~~~~l~~~g~----------~~~G~e~ly~G~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~ 1049 (1149)
....+...|.++|+ +++|+|.||||+||++|+++||+|++|||||+|||+||+||||+|||++|||||++
T Consensus 896 ~~~~~~~~l~~~~~~~~~~~~~~~~~~Gk~~l~dG~TG~~~~~~i~vG~~Yy~kL~HmV~DKihaRs~Gp~~~lT~QP~~ 975 (1070)
T CHL00001 896 SRKLVFSELYEASKQTANPWVFEPEYPGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLR 975 (1070)
T ss_pred hhhhhhHHHHHHHHhcCCceeccCCCCCeEEEEcCCCCCCccceEEEEecceeEchhhccccceeeccCCCcccccCCCC
Confidence 22233466777776 45599999999999999999999999999999999999999999999999999999
Q ss_pred cccCCCceeeechhhhHHHHcccHHHHHHhhccCCCceeeeecccCCcceeecccccceecccccCCCcccc-ccccHhH
Q 001125 1050 GRARNGGLRVGEMERDCLIAYGASMLIFERLMVSSDPFEVQVCRVCGLLGYYNHKLKAGICSTCKNGDNISS-MKLPYAC 1128 (1149)
Q Consensus 1050 Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~cg~~~~~~~~~~~~~C~~c~~~~~~~~-v~iPy~~ 1128 (1149)
||||+|||||||||||||+|||||++|||||+.+||++.++ |+. +..|.++.++.+ +.+||||
T Consensus 976 Grsr~GG~RfGEME~~al~a~GAs~~L~E~L~~~SD~~~~r----~~~------------~~~i~~g~~~~~~~~~pesf 1039 (1070)
T CHL00001 976 GRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRAR----QEV------------LGAIITGGTIPKPEDAPESF 1039 (1070)
T ss_pred cccCCCCeeeecchHHHHHhhhHHHHHHHHHhccCccHHHH----HHH------------HHhhhcCCcccCCCCCCchh
Confidence 99999999999999999999999999999999999999886 221 123455667777 8999999
Q ss_pred HHHHHHHHhCCcccEEEe
Q 001125 1129 KLLIQELQSMNIVPRLKL 1146 (1149)
Q Consensus 1129 k~l~~EL~sm~i~~~l~~ 1146 (1149)
|+|++||+|||+++++..
T Consensus 1040 k~l~~El~~l~l~i~~~~ 1057 (1070)
T CHL00001 1040 RLLVRELRSLALELNHFL 1057 (1070)
T ss_pred hHHHHHHHhCccceEEEE
Confidence 999999999999999865
No 10
>CHL00207 rpoB RNA polymerase beta subunit; Provisional
Probab=100.00 E-value=4.4e-205 Score=1896.84 Aligned_cols=931 Identities=24% Similarity=0.375 Sum_probs=759.3
Q ss_pred cccccchHHHHHHHHHHHHHhCHHHHHHhcccceecCCCcEEEEEe--EEEEcCCccccCCcCCCCChhhHhhcCCccCc
Q 001125 38 FLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLRFK--DVRIGQPSMTVDGVSEKLNPHMCRLSDMTYAA 115 (1149)
Q Consensus 38 ~~~~~~Lv~~qi~SFn~Fi~~gL~~ii~~~~~I~~~~~~~~~l~~~--~i~i~~P~~~e~~~~~~l~P~EcR~r~lTYsa 115 (1149)
-|+.++|++.|++||+||+++||++++++.+||+. .++.+.++|. ++++++|.+ +|.|||+|++||++
T Consensus 4 ~~~~Pdll~iQ~~SF~~FL~~GL~~~~~~~~pI~~-~~~~~~l~~~~~~y~l~~P~~---------~~~Ea~~r~~TYsa 73 (1077)
T CHL00207 4 NFALPDFLEIQRTSFCWFLNEGLNEELNIFSKIFD-YTGNLELLLFGKNYKLKYPKY---------NLLSAKSYDSNYSI 73 (1077)
T ss_pred ccCCCCHHHHHHHHHHHHHHHHHHHHHHhcCCeEC-CCCCEEEEEecceEEEcCCCC---------CHHHHHHhCCccce
Confidence 46789999999999999999999999999999974 5667777776 799999976 78999999999999
Q ss_pred cEEEEEEEEECCcccceeeEEeeEEeeccceeeccccccCCCCCHHHHHhcCCCCCCCCcEEEEcCchhhhHHhhhccCC
Q 001125 116 PILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKN 195 (1149)
Q Consensus 116 ~l~v~i~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~elv~~~E~~~d~GGYFIING~ERVI~~q~~~s~N 195 (1149)
||+|+++++.++. +++++++|++|+||+|+ ++|||||||+||||++|++++|+
T Consensus 74 ~l~v~~~l~~~~~---~~i~~~~V~lG~iPlMT------------------------~~GtFIING~ERViVsQl~RSPG 126 (1077)
T CHL00207 74 QIYLPLKFINLKT---NKIKFINYLIGNLPKMT------------------------QRGTFIINGLERVIVSQIIRSPG 126 (1077)
T ss_pred eEEEEEEEEEcCC---ceEEEEEEEEeccCccC------------------------CCCEEEEcCceeEEEEEeccCCe
Confidence 9999999986552 56677899999999997 89999999999999999998885
Q ss_pred eEEEEeC--CCCc--EEEEEEecCCCcceEEEEEeeCCEEEEEEceeeccccHHHHHHHhCCCCHHHHHHHhCC--chhH
Q 001125 196 RVIIDTD--KKGN--INASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGR--DPRY 269 (1149)
Q Consensus 196 ~i~~~~~--~~g~--~~a~v~s~~~~~~s~~~~~~k~g~i~~r~~~~~~~IPi~ilLrALG~~sD~eI~~~i~~--~~~~ 269 (1149)
+|+... +.+. +.|.++|.++ .|..+.+.+++.+|+++++. ++||+++||||||+ ||+||++.++. +..+
T Consensus 127 -iyf~~~~~k~~~~~y~a~IIp~rG--swl~~e~d~k~~i~vridr~-rKipit~lLrALGl-s~~eIl~~~~~~~~~~~ 201 (1077)
T CHL00207 127 -IYFKKEIKKNSNKIYSATLIPNRG--SWIKFELDKNKEIWIRIDKN-RKKPLIIFLKALGL-TDQDIYSRLTKSEFLKK 201 (1077)
T ss_pred -EEEEEecCcCCceEEEEEEEcCCC--ceEEEEEcCCCeEEEEecCC-ceeeHHHHHHHhCC-CHHHHHHHHhccchHHH
Confidence 887643 3343 7899998765 67777778889999999985 59999999999999 79999999953 2222
Q ss_pred HhhhHHhHHHHHhcCCcCHHHHHHHHhhhcccCCCCCCCCChHHHHHHHHH-------hhhccCCCCCCC----------
Q 001125 270 SALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILR-------DVFLANVPVHNN---------- 332 (1149)
Q Consensus 270 ~~~l~~~l~~~~~~~i~t~~~al~yIg~~~r~~~~~~~~~~~~e~~~~~L~-------~~ll~Hl~~~~~---------- 332 (1149)
+...+. ..+..++++|+.+|+++++++ ... ..+.++.+|. +|.|+|+|.-+.
T Consensus 202 ---~~~~l~---~~~~~~~e~Al~~Iy~~lrp~----~~~-~~~~a~~~l~~~ff~~~rYdLg~vGR~klN~kl~~~~~~ 270 (1077)
T CHL00207 202 ---LKPILL---NSNSYTNEEILLEIYKNLSPI----EPA-TVNDANQNLFSRFFDPKNYDLGKVGRYKINNKLNLNIPE 270 (1077)
T ss_pred ---HHHHHh---ccCcccHHHHHHHHHHhcCCC----CCc-cHHHHHHHHHHHhcChhcccccccchhhhhhhccCCcCc
Confidence 222222 234568999999999999886 333 4566777764 555778885221
Q ss_pred -CCCCccchHHHHHHHHHHhhcCCCCCCCcccccccEEccccHhHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCccc
Q 001125 333 -NFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLS 411 (1149)
Q Consensus 333 -~~~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~NkRv~l~G~Ll~~lfr~~l~~~~~~ik~~i~k~~~~~~~~~~~~~~ 411 (1149)
...-++..+..|+++|+++..|....||+|||+||||+++|+||++|||.+|.++.+.++++|.+.. ...+.+.
T Consensus 271 ~~~~l~~~Dil~~i~~Li~l~~g~~~~DDiDHL~NRRvrsvGELlq~qfr~gl~rler~ike~m~~~~-----~~~~tp~ 345 (1077)
T CHL00207 271 RVRNLTYEDILSIIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTICD-----IDSLSKF 345 (1077)
T ss_pred cCceecHHHHHHHHHHHHHhhcCCCcccchhhhhcccccchhHHHHHHHHHHHHHHHHHHHHHhhhcc-----cccCChh
Confidence 1112334466799999999999999999999999999999999999999999999999999997542 1245677
Q ss_pred ccccccchHHHHHHHhccCCCcccccccccccceEEcccccccccccccccccc----ccccccccCCCCccCCCCCccc
Q 001125 412 QFIVRDSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSP----QFEKSRKVSGPRALQPSQWGML 487 (1149)
Q Consensus 412 ~~i~~~~It~~i~~~~sTGnw~~~~~~~q~sGvsq~l~rln~ls~LshlRrv~~----~f~~~~k~t~~R~Lhps~wG~i 487 (1149)
+++++++|++.|++||++ +++||++|++|+||.|+|.||+++ ++.+.+..+.+|++||||||||
T Consensus 346 ~lin~k~lt~~ikeFFgs------------s~LSQfmDQtNpLselTHKRRlsaLGpGGLsR~ra~fevRdvH~thyGRi 413 (1077)
T CHL00207 346 NLINPKPLIALIREFFGS------------SQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISFAVRDIHPSHYGRI 413 (1077)
T ss_pred hcccchhHHHHHHHhhcc------------CCccceecccChHHhhhccceeeccCCCcccccccCCcccccCccccccc
Confidence 888999999999999965 478999999999999999999996 6888899999999999999999
Q ss_pred ccCCCCCCCcchhhhhccceeeeccCCCchhHHHHHhhcCceeccccCccccCCCCceEEEECCeEEEeecChhhHHHHH
Q 001125 488 CPCDTPEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVM 567 (1149)
Q Consensus 488 CPveTPEG~~cGLi~~LA~~a~Vt~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~l 567 (1149)
||+|||||+|||||++||.+|+|+. +|+.. .+|....||.+. ..++
T Consensus 414 CPIETPEG~n~Gli~~la~~~~in~-------------~Gfie------------tPy~~v~~g~v~-~~~~-------- 459 (1077)
T CHL00207 414 CPIETPEGPNCGLIGSLATNARINK-------------FGFIE------------TPFYKVINGKVK-KFGN-------- 459 (1077)
T ss_pred cCCCCCCCcccccccchhhhccccC-------------CCcee------------CceEEEEcCccc-ccCc--------
Confidence 9999999999999999999999984 45432 244444677552 0000
Q ss_pred HHHhhcCCcCceeEEEecc-cCceEEEecCCCeeeeeEEEeecCcccchhhhHHhhhcCCcchhhhhccCceeEeccccc
Q 001125 568 RKLRRAGKIGEFVSVFVNE-KQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEE 646 (1149)
Q Consensus 568 r~~rr~g~i~~~v~i~~~~-~~~~i~I~td~GRl~RPl~~v~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~iE~id~~Eq 646 (1149)
.+|+.. .+....|+...-- .-+++.. . ...|.--- -+
T Consensus 460 -------------i~ylsa~~e~~~~Ia~~~~~------~~~~~~~--~-------------------~~~v~~r~--~~ 497 (1077)
T CHL00207 460 -------------PIYLTADSEDLYRIAPNDIN------LNKNNYF--K-------------------KNIIPVRY--KQ 497 (1077)
T ss_pred -------------eeecChHHhcCcEEEecCcc------CCCCCcc--c-------------------CCEEEEEE--CC
Confidence 112222 1233444332200 0011100 0 00000000 01
Q ss_pred cceEEEeecCCCCCCceeeeecCceeccccccccCCCCCCCCCccccccccccCCcccce--------------------
Q 001125 647 NNALIALYEGDATPDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIA-------------------- 706 (1149)
Q Consensus 647 ~~~~Ia~~~~~~~~~~th~Ei~P~~ilsv~AslIPF~~hNqSpRn~yq~~M~KQa~G~~~-------------------- 706 (1149)
++..+ .+ .+.++++++|.|++|++||||||++||||+|++||||||||||++..
T Consensus 498 ef~~~--~~----~~v~~~~vsp~Q~~SvaasLIPFLehdDanRaLMGsnMqrQaVPll~~e~p~VgTg~e~~~a~ds~~ 571 (1077)
T CHL00207 498 EFKTV--NP----SKVDFIAISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIVGTGYEKQIALDSGM 571 (1077)
T ss_pred cEEEE--Ch----HHceEEEeCcchhcchhhhcCCcccccccchhhhhhccccccccccccCCCeEECCcchHhhhhcch
Confidence 11111 11 23589999999999999999999999999999999999999997521
Q ss_pred -----------eeecccc----c---cceeee----------cCCCcceeechhhh----------hccCCCCCCCcceE
Q 001125 707 -----------FNQLCRM----D---SLLYLL----------VYPQRPLLTTRTIE----------LVGYDKLGAGQNAT 748 (1149)
Q Consensus 707 -----------~n~~~R~----D---~~~y~L----------~ypQ~PlV~t~~~~----------~~~~~~~p~G~N~i 748 (1149)
+....|+ + ...|.| |++|||+|+.+.+. .+.++|+|+|+|++
T Consensus 572 ~i~a~~~G~v~~v~~~~I~i~~~~~~~~~y~l~~~~rsNq~t~i~qrp~V~~G~~v~~G~iladg~~~~~~el~lG~N~l 651 (1077)
T CHL00207 572 TIISLTEGIVVSVSAYKIIIQDDNNRYIHYYLQKYQRSNQNTCINYRPIVWVGEKINIGQILADGSDIDNSELALGQNVL 651 (1077)
T ss_pred heEeccCcEEEEecCcEEEEEeCCCceeEEEeccccccccCceeecccccCCCCEEecCCEEecchhccCCcccCCcccE
Confidence 1111111 1 123554 67999999998764 34599999999999
Q ss_pred EEEEecCCCCCCCcEEeecccccccceeEEEEEEEEEEeecccCCccceec-CCCCCCCchhhhccCCCCcccCCCceeC
Q 001125 749 VAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRIL-RPDRTGPGAERMQILDDDGLAAPGEIIK 827 (1149)
Q Consensus 749 VAv~~~~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~~~~~-~p~~~~~~~~~~~~Ld~dGi~~~G~~v~ 827 (1149)
||||||+||||||||||||++++||+|||+||++|++++++++.|.+++.. .|+.+ ...+++||+||||++|++|+
T Consensus 652 VA~m~y~GYN~EDAiiink~~v~rg~f~Si~~~~~~~e~~~~~~g~e~i~~~~p~~~---~~~~~~LD~dGiv~iG~~V~ 728 (1077)
T CHL00207 652 VAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEKYEIELRQTKLGSEEITRNIPNVS---EYSLKNLDENGIISIGSKVL 728 (1077)
T ss_pred EEEEeeeccccchhhhhhhhhhcCCceEEEEEEEeeeEEeecCCCceEEeccCCCCC---hHHhhccCccCCCcCCcEeC
Confidence 999999999999999999999999999999999999999988777644432 36543 24799999999999999999
Q ss_pred CCCEEEEEecCCCCCCCCCC------CCCCCCcccccceeeecCCCCCceEEEEEEEeeCCC--Cc-----EEEEEEEee
Q 001125 828 PNDVYINKESPLETRGSIMS------PTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKN--GD-----LCIKFLIRH 894 (1149)
Q Consensus 828 ~gd~l~~k~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~v~~v~~~~~~~--~~-----~~vkv~~~~ 894 (1149)
+|||||||++|....+.... -++++.+..+|+|+++++++ .|+|++|.++.+++ +. ..|||++|+
T Consensus 729 ~gDilvgK~tp~~~~~~~~~~~ll~~i~~~~~~~~kd~sl~~~~~~--~g~V~~V~~~~~~~~~~~~~~~~~~vkv~i~~ 806 (1077)
T CHL00207 729 AGDILVGKITPKGESDQLPEGKLLRAIFGEKAKDVKDTSLRMPNGG--YGRVIKVEIFSRSKGDELKFGYYLKIRVFIAQ 806 (1077)
T ss_pred CCCEEEEEecCccccccChhhhhhhhhhccCCCcceEeEEEcCCCC--cEEEEEEEEEecCCCCcccccccEEEEEEEEE
Confidence 99999999999653332110 12344455799999999998 99999999987532 22 459999999
Q ss_pred ecCCCccccccccCCCccEEEeeeccCCCCCCCCCCCCcEEeCCCCCCCCchHHHHHHHhccccccccCceeeeeeccCC
Q 001125 895 TRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEP 974 (1149)
Q Consensus 895 ~R~p~iGDKf~sRhGqKGvvs~i~~~eDmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tpF~~~ 974 (1149)
.|+|+||||||||||||||||+|||+||||||+||++|||||||||||||||||||+|+++||||++.|...++|||+
T Consensus 807 ~R~p~vGDKfasRHGqKGVvs~i~p~eDMPf~~dG~~pDiIlNPhg~PSRMtiGqllE~~lGka~~~l~~~~~~tpF~-- 884 (1077)
T CHL00207 807 IRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGDNLNKRFKILPFD-- 884 (1077)
T ss_pred EecCCcccccccccCCceeEEeeeccCCCCccCCCCCccEEECCccccccccHHHHHHHHHHHHHHhcCCcEeeccCC--
Confidence 999999999999999999999999999999999999999999999999999999999999999999888778899999
Q ss_pred CCCCCCHHHHHHHHHHc---------------CCCCCCceEEEeCCCCcEEeeeEeEeeeeecccccccCcccEEecccC
Q 001125 975 SGHADTVESISETLVKH---------------GFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGP 1039 (1149)
Q Consensus 975 ~~~~~~~~~~~~~l~~~---------------g~~~~G~e~ly~G~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp 1039 (1149)
+...+++.+.|... +|+++|+++||||+||++|+++||+|++|||||+|||+||+||||+||
T Consensus 885 ---~~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~Gk~~lydG~TGe~~~~~i~vG~~Yy~kL~HmV~DKihaRs~Gp 961 (1077)
T CHL00207 885 ---EMYGSEYSRILINNKLNQASIKNNEYWLFNSYHPGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGP 961 (1077)
T ss_pred ---CCcHHHHHHHHHhhhhhhccchhccccccCCCCCCCEEEECCCCCCCccCceEEEecceeEchhhccccceeeccCC
Confidence 44555666665543 377889999999999999999999999999999999999999999999
Q ss_pred cccccccCcccccCCCceeeechhhhHHHHcccHHHHHHhhccCCCceeeeecccCCcceeecccccceecccccCCCcc
Q 001125 1040 RVMLTRQPTEGRARNGGLRVGEMERDCLIAYGASMLIFERLMVSSDPFEVQVCRVCGLLGYYNHKLKAGICSTCKNGDNI 1119 (1149)
Q Consensus 1040 ~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~cg~~~~~~~~~~~~~C~~c~~~~~~ 1119 (1149)
|++|||||++||||+|||||||||||||+|||||++|||||+.+||++.++ ..+|..|.++.++
T Consensus 962 ~s~lTqQP~~Grsr~GG~RfGEME~~aL~a~GAa~~L~E~L~~kSD~~~~r----------------~~~~~~~~~~~~i 1025 (1077)
T CHL00207 962 YSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSDDMQGR----------------NETLNAIVKGQPI 1025 (1077)
T ss_pred CcccccCCCCccccCCCeeeecccHHHHHhhhhHHHHHHHhhcCCccceeh----------------HHHHHhhhCCCee
Confidence 999999999999999999999999999999999999999999999999963 1469999999999
Q ss_pred ccccccHhHHHHHHHHHhCCcccEEEe
Q 001125 1120 SSMKLPYACKLLIQELQSMNIVPRLKL 1146 (1149)
Q Consensus 1120 ~~v~iPy~~k~l~~EL~sm~i~~~l~~ 1146 (1149)
.++.+|||||+|+|||+||||++++..
T Consensus 1026 ~~~~~P~sfklL~~EL~sl~i~~~~~~ 1052 (1077)
T CHL00207 1026 PKPGTPESFKVLMRELQSLGLDIEAYK 1052 (1077)
T ss_pred cCCCCCchHHHHHHHHHHCCcCcEecc
Confidence 999999999999999999999999864
No 11
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=100.00 E-value=2.5e-194 Score=1851.00 Aligned_cols=951 Identities=23% Similarity=0.363 Sum_probs=770.4
Q ss_pred cccccccccccccccchHHHHHHHHHHHHH------hCHHHHHHhcccceecCCCcEEEEEeEEEEcCCccccCCcCCCC
Q 001125 28 VVDKFQLLPEFLKVRGLVKQHLDSFNYFVN------TGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDGVSEKL 101 (1149)
Q Consensus 28 ~~~~~~~i~~~~~~~~Lv~~qi~SFn~Fi~------~gL~~ii~~~~~I~~~~~~~~~l~~~~i~i~~P~~~e~~~~~~l 101 (1149)
.+.+|+.++..++.|+|++.|.+||+||++ +||++++++++||+ +.++++.|+|.++++++|.+
T Consensus 11 ~R~~f~k~~~~~~iPdLleIQ~~SF~~FLq~~~~~~~GL~e~f~~~fPI~-d~~g~~~Lefv~Y~l~~Pk~--------- 80 (2890)
T PRK09603 11 LRADFTKTPTDLEVPNLLLLQRDSYDSFLYSKDGKESGIEKVFKSIFPIQ-DEHNRITLEYAGCEFGKSKY--------- 80 (2890)
T ss_pred EEeecccCCccCCCCCHHHHHHHHHHHHHhCCCcccccHHHHHHhcCCeE-CCCCcEEEEEEEEEeCCCCC---------
Confidence 456799999999999999999999999998 79999999999996 56788999999999999987
Q ss_pred ChhhHhhcCCccCccEEEEEEEEE---CCcc----cceeeEEeeEEeeccceeeccccccCCCCCHHHHHhcCCCCCCCC
Q 001125 102 NPHMCRLSDMTYAAPILVNIEYVQ---GSHT----EKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPG 174 (1149)
Q Consensus 102 ~P~EcR~r~lTYsa~l~v~i~~~~---~~~~----~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~elv~~~E~~~d~G 174 (1149)
+|.||++|++||++||+|+++++. +.++ ..+++++++|++|+||+|+ ..
T Consensus 81 ~~~Ec~~rg~TYsapL~v~~rL~~~~~~~~t~~~~~ikeikeq~VylGdiPLMT------------------------~~ 136 (2890)
T PRK09603 81 TVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQSIFIREIPLMT------------------------ER 136 (2890)
T ss_pred CHHHHHhhCCcccccEEEEEEEEEeeccccccccccccceEEeeEEEecCCccC------------------------CC
Confidence 579999999999999999999984 2211 1125778899999999999 79
Q ss_pred cEEEEcCchhhhHHhhhccCCeEEEEeCC--C--Cc--EEEEEEecCCCcceEEEEEeeCCEEEEEEceeeccccHHHHH
Q 001125 175 GYFIIKGTEKVLLIQEQLSKNRVIIDTDK--K--GN--INASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVM 248 (1149)
Q Consensus 175 GYFIING~ERVI~~q~~~s~N~i~~~~~~--~--g~--~~a~v~s~~~~~~s~~~~~~k~g~i~~r~~~~~~~IPi~ilL 248 (1149)
|+|||||+|||||+|++|||+ +|+..+. . |. |.|.++|.++ +|..+..++++.+|+|+++. ++||+++||
T Consensus 137 GTFIING~ERVIVsQL~RSPG-VyF~~~~~k~~s~k~lysa~IIP~RG--sWLefE~D~kd~l~vrIDrk-rKipit~lL 212 (2890)
T PRK09603 137 TSFIINGVERVVVNQLHRSPG-VIFKEEESSTSLNKLIYTGQIIPDRG--SWLYFEYDSKDVLYARINKR-RKVPVTILF 212 (2890)
T ss_pred ceEEEcCceeEEEeeeccCCe-eEEeeccCcCCCCceeEEEEEecCCc--ceEEEEEcCCCeEEEEEcCc-ceecHHHHH
Confidence 999999999999999999997 8876432 1 32 6799998765 58888888899999999994 799999999
Q ss_pred HHhCCCCHHHHHHHhCC-------ch---------hH-----------------------------------------H-
Q 001125 249 KAMGMESDQEVVQMVGR-------DP---------RY-----------------------------------------S- 270 (1149)
Q Consensus 249 rALG~~sD~eI~~~i~~-------~~---------~~-----------------------------------------~- 270 (1149)
||||+ +++||++.++. +. .+ .
T Consensus 213 rAlG~-s~edIl~~f~~~~~~~i~~~~~~~~~~~~~l~~~~~~di~d~~g~vlv~~g~rit~~~~~~l~~~g~k~l~~~~ 291 (2890)
T PRK09603 213 RAMDY-QKQDIIKMFYPLVKVRYENDKYLIPFASLDANQRMEFDLKDPQGKIILLAGKKLTSRKIKELKENHLEWVEYPM 291 (2890)
T ss_pred HHhCC-CHHHHHHHhcccceEEEcccceeecccHHHhcCccceeecccCCCEEEecCccccHHHHHHHHhcCCceeccch
Confidence 99999 68999998741 00 00 0
Q ss_pred ----------------hhhH--------HhHHHHHhcC--------------------------------------CcCH
Q 001125 271 ----------------ALLL--------PSIEECANLD--------------------------------------IYTQ 288 (1149)
Q Consensus 271 ----------------~~l~--------~~l~~~~~~~--------------------------------------i~t~ 288 (1149)
+.+. ..++...+.+ ..++
T Consensus 292 ~~l~g~~laedivd~~Evl~~~~~~Itee~le~i~~~gi~~i~vl~~~~~~~~~~i~~t~~~d~~~~~~~~~t~~~~~~~ 371 (2890)
T PRK09603 292 DILLNRHLAEPVMVGKEVLLDMLTQLDKNKLEKIHDLGVQEFVIINDLALGHDASIIHSFSADSESLKLLKQTEKIDDEN 371 (2890)
T ss_pred hhhcceeeeeeccCccceeeccCChhcHHHHHHHHHcCCceEEEEeecccccccccccccccccccchhhhhccccccch
Confidence 0000 0000000000 1245
Q ss_pred HHHHHHHhhhcccCCCCCCCCChHHHHHHHHHhhhcc----CCCC-CCCCC--------------CCccchHHHHHHHHH
Q 001125 289 EKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLA----NVPV-HNNNF--------------RPKCFYVAVMLRRMV 349 (1149)
Q Consensus 289 ~~al~yIg~~~r~~~~~~~~~~~~e~~~~~L~~~ll~----Hl~~-~~~~~--------------~~K~~~L~~Mi~kLl 349 (1149)
++|+..|++++|++ +.. ..+.|+.++++.||. .++. +...+ ..+.+++ ..+++|+
T Consensus 372 eeAl~~iyr~lrpg----ep~-~~e~A~~l~~~lFFn~~rYdLg~vGR~klN~kL~l~~~~~~~~Lt~~Dil-~~i~~li 445 (2890)
T PRK09603 372 ALAAIRIHKVMKPG----DPV-TTEVAKQFVKKLFFDPERYDLTMVGRMKMNHKLGLHVPDYITTLTHEDII-TTVKYLM 445 (2890)
T ss_pred HHHHHHHHhccCCC----CCC-cHHHHHHHHHHHhcCcccccccccchhhhHhhhCCCCCCcccEecchhHH-HHHHHHH
Confidence 89999999999987 444 667788888887764 1211 01111 1123444 4799999
Q ss_pred HhhcCCCCCCCcccccccEEccccHhHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccccccchHHHHHHHhcc
Q 001125 350 EAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLST 429 (1149)
Q Consensus 350 ~~~~g~~~~DD~D~l~NkRv~l~G~Ll~~lfr~~l~~~~~~ik~~i~k~~~~~~~~~~~~~~~~i~~~~It~~i~~~~sT 429 (1149)
.+..|....||+|||+||||+++|+||+++||.+|.++.+.+|++|...... ...+.+..++|++++++.+++||+|
T Consensus 446 ~l~~g~~~~DDiDhL~NRRvr~vGELl~~qfr~gl~rler~irerm~~~~~~---~~~~~p~~lin~k~i~~~ikeFFgs 522 (2890)
T PRK09603 446 KIKNNQGKIDDRDHLGNRRIRAVGELLANELHSGLVKMQKTIKDKLTTMSGA---FDSLMPHDLVNSKMITSTIMEFFMG 522 (2890)
T ss_pred HHHhCCCCCCcchhhhcchhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc---ccccChhhhhccHHHHHHHHHHhcc
Confidence 9999999999999999999999999999999999999999999999753221 2245677888999999999999977
Q ss_pred CCCcccccccccccceEEcccccccccccccccccc----ccccccccCCCCccCCCCCcccccCCCCCCCcchhhhhcc
Q 001125 430 GNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSP----QFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLA 505 (1149)
Q Consensus 430 Gnw~~~~~~~q~sGvsq~l~rln~ls~LshlRrv~~----~f~~~~k~t~~R~Lhps~wG~iCPveTPEG~~cGLi~~LA 505 (1149)
+. +||++|++|+||.|+|.||+++ .+.+.+..+.+|++||||||||||+|||||+|||||++||
T Consensus 523 sq------------LSQfmDQtNpLseltHKRRlSaLGPGGlsr~ra~fevRdVH~shYGRiCPIETPEG~NiGLI~SLa 590 (2890)
T PRK09603 523 GQ------------LSQFMDQTNPLSEVTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLS 590 (2890)
T ss_pred Cc------------hhhhhcccChhhhhhhcccccccCCCCccccccCCcccccCcccccccCCCCCCCCCcccchhhhh
Confidence 53 5999999999999999999984 3567788889999999999999999999999999999999
Q ss_pred ceeeeccCCCchhHHHHHhhcCceeccccCccccCCCCceEEEECCeEEEeecChhhHHHHHHHHhhcCCcCceeEEEec
Q 001125 506 LMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVN 585 (1149)
Q Consensus 506 ~~a~Vt~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~lr~~rr~g~i~~~v~i~~~ 585 (1149)
.+|+|+. +|+.. .+|....||++- ++ .+|+.
T Consensus 591 ~~a~in~-------------~Gfie------------tPy~kV~~g~v~---~~---------------------i~yls 621 (2890)
T PRK09603 591 TFTRVND-------------LGFIE------------APYKKVVDGKVV---GE---------------------TIYLT 621 (2890)
T ss_pred hheeccc-------------Cccee------------cceEEEecCccc---cc---------------------eeeeC
Confidence 9999984 55532 234334677641 11 01222
Q ss_pred c-cCceEEEecCCCeeeeeEEEeecCcccchhhhHHhhhcCCcchhhhhccCceeEeccccccceEEEeecCCCCCCcee
Q 001125 586 E-KQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTTH 664 (1149)
Q Consensus 586 ~-~~~~i~I~td~GRl~RPl~~v~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~iE~id~~Eq~~~~Ia~~~~~~~~~~th 664 (1149)
. .+....|+...-. + -++|.. .++ .|.-- ..+++..++ ....++
T Consensus 622 a~eE~~~~IA~a~~~----~--~~~~~~--~~~-------------------~v~~R--~~~e~~~~~------~~~v~~ 666 (2890)
T PRK09603 622 AIQEDSHIIAPASTP----I--DEEGNI--LGD-------------------LIETR--VEGEIVLNE------KSKVTL 666 (2890)
T ss_pred HHHhcCceEeccCCc----c--CCCCcc--cCC-------------------eEeEE--ECCceEEEC------hHHceE
Confidence 2 1233444432200 0 011110 000 00000 001111111 123689
Q ss_pred eeecCceeccccccccCCCCCCCCCccccccccccCCcccc-------------------------------eeeeccc-
Q 001125 665 IEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNI-------------------------------AFNQLCR- 712 (1149)
Q Consensus 665 ~Ei~P~~ilsv~AslIPF~~hNqSpRn~yq~~M~KQa~G~~-------------------------------~~n~~~R- 712 (1149)
++++|.|++|++||||||+|||||+|++||||||||||++. .+....+
T Consensus 667 ~dvsp~Q~vSvaasLIPFLEhdDAnRALMGSNMQRQAVPLl~~e~piVgTG~E~~va~dSg~~i~a~~~G~V~yvd~~~I 746 (2890)
T PRK09603 667 MDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTGIEKIIARDSWGAIKANRAGVVEKIDSKNI 746 (2890)
T ss_pred EEeCccceeeehhhcCCccccCccccccccccchhhhhhhccccCCeEecCcchhhhccccceeEecCCeEEEEecCcEE
Confidence 99999999999999999999999999999999999999752 1111111
Q ss_pred ---ccc------ceeee----------cCCCcceeechhhh----------hccCCCCCCCcceEEEEEecCCCCCCCcE
Q 001125 713 ---MDS------LLYLL----------VYPQRPLLTTRTIE----------LVGYDKLGAGQNATVAVMSYSGYDIEDAI 763 (1149)
Q Consensus 713 ---~D~------~~y~L----------~ypQ~PlV~t~~~~----------~~~~~~~p~G~N~iVAv~~~~Gyn~EDai 763 (1149)
.+. ..|.| |++|||+|+.+... .+..+|+++|+|++||||||.||||||||
T Consensus 747 ~i~~~~~~~~~~~~Y~L~Ky~RSNQ~TcinqrPiV~~Gd~V~kGdilADG~st~~GELALG~NvlVAfmpW~GYNfEDAI 826 (2890)
T PRK09603 747 YILGEGKEEAYIDAYSLQKNLRTNQNTSFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAI 826 (2890)
T ss_pred EEEecCCCCceeeEEeeccccccCCCceeeeccEecCCCEeccCCEEecCcccccCeeccCcccEEEEeeeccccCcccc
Confidence 111 23665 77999999998764 34589999999999999999999999999
Q ss_pred EeecccccccceeEEEEEEEEEEeecccCCccceecC-CCCCCCchhhhccCCCCcccCCCceeCCCCEEEEEecCCCCC
Q 001125 764 VMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILR-PDRTGPGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETR 842 (1149)
Q Consensus 764 iink~s~~rg~~~s~~~~~~~~~~~~~~~~~~~~~~~-p~~~~~~~~~~~~Ld~dGi~~~G~~v~~gd~l~~k~~~~~~~ 842 (1149)
|||++.+.+++|||+|+++|++++++++.|.+|++.+ |+.+. +.+++||++|||++|++|++|||||||++|+++.
T Consensus 827 lISERlV~eD~fTSIHIee~ei~~r~Tk~G~EeITrdIPnvse---~~l~~LDe~GII~iGa~V~~GDILVGKvTPkge~ 903 (2890)
T PRK09603 827 VVSERITKDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKE---EALAHLDESGIVKVGTYVSAGMILVGKTSPKGEI 903 (2890)
T ss_pred ccchhhhcCccceEEEEeeeEEEEEecCCCCcEEeccCCCCCH---HHHhcCCCCCCEeeCCEECCCCEEEEeeccCCCC
Confidence 9999999999999999999999999999998777665 88753 5899999999999999999999999999999776
Q ss_pred CCCCC------CCCCCCcccccceeeecCCCCCceEEEEEEEeeCC----------------------------------
Q 001125 843 GSIMS------PTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDK---------------------------------- 882 (1149)
Q Consensus 843 ~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~v~~v~~~~~~---------------------------------- 882 (1149)
+..+. -++++....+|+|+++.++. .|+|-.|.+++..
T Consensus 904 ~~tPEekLLraIFGeka~~vkDtSLrvp~G~--~G~Vidv~~f~r~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 981 (2890)
T PRK09603 904 KSTPEERLLRAIFGDKAGHVVNKSLYCPPSL--EGTVIDVKVFTKKGYEKDARVLSAYEEEKAKLDMEHFDRLTMLNREE 981 (2890)
T ss_pred CCChHHHHHHHHhcccccccccCceecCCCC--cEEEEEEEEecccccchhHHHHHHHHHHHHHHhHhhHHHHHHHHHHH
Confidence 54432 26778888999999988877 8988888765421
Q ss_pred --------------------------------------------------------------------------------
Q 001125 883 -------------------------------------------------------------------------------- 882 (1149)
Q Consensus 883 -------------------------------------------------------------------------------- 882 (1149)
T Consensus 982 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~ 1061 (2890)
T PRK09603 982 LLRVSSLLSQAILEEPFSHNGKDYKEGDQIPKEEIASINRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKL 1061 (2890)
T ss_pred HHhhhhhccccccccccccccccccccccccHHHHhhCCHHHhhhhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence
Q ss_pred ----C-------CcEEEEEEEeeecCCCccccccccCCCccEEEeeeccCCCCCCCCCCCCcEEeCCCCCCCCchHHHHH
Q 001125 883 ----N-------GDLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMI 951 (1149)
Q Consensus 883 ----~-------~~~~vkv~~~~~R~p~iGDKf~sRhGqKGvvs~i~~~eDmPf~~~G~~pDiI~NPh~~PSRMtiGql~ 951 (1149)
. ..+.|||++|+.|+|+||||||||||||||||+|||+|||||++||++||||+||||||||||||||+
T Consensus 1062 ~~~~~gdeL~~Gv~~~VkV~ia~kR~~qvGDK~AgRHGnKGViS~I~p~EDMPfl~dG~~pDIIlNPlGvPSRMnIGQil 1141 (2890)
T PRK09603 1062 SILEKDDILPNGVIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQIL 1141 (2890)
T ss_pred HHhhcCCcCCCCcceEEEEEEEEeecccccchhhhccCCCeeEEEEEchhcCCCCCCCCCCcEEECCCCCCccccHHHHH
Confidence 0 13579999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhccccccccCce---------------------------------------------------------eeeeeccCC
Q 001125 952 ELLGGKAGVSCGRF---------------------------------------------------------HYGSAFGEP 974 (1149)
Q Consensus 952 E~~~gk~~~~~g~~---------------------------------------------------------~d~tpF~~~ 974 (1149)
|+++||||+..|.+ .++||
T Consensus 1142 E~~LG~aa~~lg~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~tp---- 1217 (2890)
T PRK09603 1142 EMHLGLVGKEFGKQIASMLEDKTKDFAKELRAKMLEIANAINEKDPLTIHALENCSDEELLEYAKDWSKGVKMAIP---- 1217 (2890)
T ss_pred HHHHHHHHHhcCcChhhhhhhcchhhhHHHHHHHHhhhcccccccccccccccccchHHHHhhhhhhccCCcccCC----
Confidence 99999999988754 12334
Q ss_pred CCCCCCHHHHHHHHHHcCCCCCCceEEEeCCCCcEEeeeEeEeeeeecccccccCcccEEecccCcccccccCcccccCC
Q 001125 975 SGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARN 1054 (1149)
Q Consensus 975 ~~~~~~~~~~~~~l~~~g~~~~G~e~ly~G~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~ 1054 (1149)
.+++.+.+++.+.|+++||+++|++.||||+||++|+++||+|++|||||+|||+||+||||+|||+++||||++||+++
T Consensus 1218 vF~g~~~~~i~~~l~~aG~~~~Gk~~LyDGrTGe~f~~~V~vG~~YylKL~HmVdDKiHaRstGPyslvTqQPl~GKs~~ 1297 (2890)
T PRK09603 1218 VFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALF 1297 (2890)
T ss_pred CCCCCCHHHHHHHHHHcCCCCCCCEEEEcCCCCCCccceEEEEeeceeechhhccchhhhccCCCcchhhhCCCcccccC
Confidence 23378899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CceeeechhhhHHHHcccHHHHHHhhccCCCceeeeecccCCcceeecccccceecccccCCCccccccccHhHHHHHHH
Q 001125 1055 GGLRVGEMERDCLIAYGASMLIFERLMVSSDPFEVQVCRVCGLLGYYNHKLKAGICSTCKNGDNISSMKLPYACKLLIQE 1134 (1149)
Q Consensus 1055 GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~cg~~~~~~~~~~~~~C~~c~~~~~~~~v~iPy~~k~l~~E 1134 (1149)
|||||||||||||+|||||++|||||+.+||++.++. ..|..|.++.++..+.+|||||+|++|
T Consensus 1298 GGqRfGEMEvwALeAyGAa~~LqE~Lt~kSDdv~gR~----------------~~y~~i~~g~~i~~~~iPeSFkvL~~E 1361 (2890)
T PRK09603 1298 GGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDIRGRE----------------NAYRAIAKGEQVGESEIPETFYVLTKE 1361 (2890)
T ss_pred CCceeeeeeHHHHHHhhHHHHHHHHHhcCCcchhhhh----------------hhhhhhcCCCcccccCCCHHHHHHHHH
Confidence 9999999999999999999999999999999998652 245677888999999999999999999
Q ss_pred HHhCCcccEEEec
Q 001125 1135 LQSMNIVPRLKLA 1147 (1149)
Q Consensus 1135 L~sm~i~~~l~~~ 1147 (1149)
|+||||++++...
T Consensus 1362 L~sL~l~i~~~~~ 1374 (2890)
T PRK09603 1362 LQSLALDINIFGD 1374 (2890)
T ss_pred HHhCCcceEEEee
Confidence 9999999999764
No 12
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=100.00 E-value=4.7e-190 Score=1804.76 Aligned_cols=958 Identities=23% Similarity=0.371 Sum_probs=771.9
Q ss_pred CCccccccccc-ccccccccchHHHHHHHHHHHHH-----hCHHHHHHhcccceecCCCcEEEEEeEEEEcCCccccCCc
Q 001125 24 PVKSVVDKFQL-LPEFLKVRGLVKQHLDSFNYFVN-----TGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDGV 97 (1149)
Q Consensus 24 ~~~~~~~~~~~-i~~~~~~~~Lv~~qi~SFn~Fi~-----~gL~~ii~~~~~I~~~~~~~~~l~~~~i~i~~P~~~e~~~ 97 (1149)
.....+.+|+. .+..++.|+|++.|.+||+||++ +||++++++++||+ +.++++.|+|.++++++|.+
T Consensus 11 ~~~~~R~~f~~~~~~~~~~PdL~~iQ~~Sf~~Fl~~~~~~~GL~~~f~~ifPI~-d~~g~~~lefv~y~l~~Pk~----- 84 (2836)
T PRK14844 11 GAFVPRVSYSRSIDLKDSLLDLVKVQKESYDSFTPKNKGNERLEVIFHTIFPIN-DPLHRATIEFISCRVDDPKY----- 84 (2836)
T ss_pred CCceeeeecccCCcccCCCCCHHHHHHHHHHHHhcCCCccccHHHHHHhcCCeE-CCCCCEEEEEEEEEeCCCCC-----
Confidence 44556677887 55568999999999999999998 69999999999996 56788999999999999987
Q ss_pred CCCCChhhHhhcCCccCccEEEEEEEEE-C-----------Ccc--------cceeeEEeeEEeeccceeeccccccCCC
Q 001125 98 SEKLNPHMCRLSDMTYAAPILVNIEYVQ-G-----------SHT--------EKTTMEKNDVVIGRIPIMLRSCRCVLYG 157 (1149)
Q Consensus 98 ~~~l~P~EcR~r~lTYsa~l~v~i~~~~-~-----------~~~--------~~~~~~~~~v~lG~IPIMvkS~~C~L~~ 157 (1149)
++.||++|++||+|||+|+++++. + .++ ..+++++++|++|+||+|+
T Consensus 85 ----~~~Ec~~r~~TYsapl~v~~rL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ikeq~VylGdiPLMT--------- 151 (2836)
T PRK14844 85 ----DESECIKRGITFSAQVIASIRLVIMQDGISLDEYKSIKESGDHSKLATVIKSIEEQEVHFCELPMMT--------- 151 (2836)
T ss_pred ----CHHHHHhcCCcceeeEEEEEEEEEeccccccccccccccccccccccccccceeeeeEEEecCCccC---------
Confidence 579999999999999999999975 1 110 1135678899999999999
Q ss_pred CCHHHHHhcCCCCCCCCcEEEEcCchhhhHHhhhccCCeEEEEeCC-----CCc--EEEEEEecCCCcceEEEEEeeCCE
Q 001125 158 KDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVIIDTDK-----KGN--INASVTSSTETVKSKTVIQMEKGK 230 (1149)
Q Consensus 158 ~s~~elv~~~E~~~d~GGYFIING~ERVI~~q~~~s~N~i~~~~~~-----~g~--~~a~v~s~~~~~~s~~~~~~k~g~ 230 (1149)
..|+|||||+|||||+|++|||+ +|+..+. .|. |.|+++|.++ +|..+....++.
T Consensus 152 ---------------~~GTFIING~ERVIVSQL~RSPG-VyF~~~~~kt~~sgk~lysa~IIP~RG--sWLefE~D~kd~ 213 (2836)
T PRK14844 152 ---------------DKGTFIINGVEKVIVSQMHRSPG-VFFDSDKGKTYNSGKLIYSARVIPYRG--SWLDIEFDVKDH 213 (2836)
T ss_pred ---------------CCeEEEEcCcceEEEEcceeCCe-EEEEcccCcccCCCceeEEEEEecCCc--ceEEEEEcCCCe
Confidence 89999999999999999999997 8776432 243 7899998765 588888888899
Q ss_pred EEEEEceeeccccHHHHHHHhCCCCHHHHHHHhCCc-------h---------hHH------------------------
Q 001125 231 MYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGRD-------P---------RYS------------------------ 270 (1149)
Q Consensus 231 i~~r~~~~~~~IPi~ilLrALG~~sD~eI~~~i~~~-------~---------~~~------------------------ 270 (1149)
+|+|+++. +++|+++||||||+ |++||++.++.. . .+.
T Consensus 214 lyvRIDRk-RKiPiT~LLrALGl-s~edIL~~F~~~~~~~~~d~~~~~~~~~e~l~g~~~~~Di~d~~g~vlvdkgrrit 291 (2836)
T PRK14844 214 LYFRIDRK-RKLPISVLLKALGL-SNNDILDRFYEKIKYIKHKDGWKVPFVPDKFKGVRLPFDLMDVEGNVLLKANVRIT 291 (2836)
T ss_pred EEEEecCC-eeeeHHHHHHHhCC-ChHHHHHhhcCceEEEEccCceeeccCHHHHhCCccceeeeccCCCEEEecCcccc
Confidence 99999984 69999999999999 689999977421 0 000
Q ss_pred ----hhh--------------------HH---------------------hHH--------------------------H
Q 001125 271 ----ALL--------------------LP---------------------SIE--------------------------E 279 (1149)
Q Consensus 271 ----~~l--------------------~~---------------------~l~--------------------------~ 279 (1149)
..+ .. .+. .
T Consensus 292 ~~~~krlk~~gvkkl~i~~~~l~g~~LaeDIVD~eTGEiL~eagteIT~e~ik~l~~~gi~~i~~l~~d~~~~~~~i~~t 371 (2836)
T PRK14844 292 SRLAKKLYDNELKEYLVPFDSICGLFLAEDLIDSASSTKILSAGESIKLEDIKKLELLSIDEISVLNIDNLSVGPYILNT 371 (2836)
T ss_pred HHHHHHHHHcccCcccCchHhhcCceehhhhcCCCCCeEEEcCCCccCHHHHHHHHHcCCCceeeEeecccccchHHHHH
Confidence 000 00 000 0
Q ss_pred HHhcCCcCHHHHHHHHhhhcccCCCCCCCCChHHHHHHHHHhhhccC----CCC-CCCCCC--------------Cccch
Q 001125 280 CANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLAN----VPV-HNNNFR--------------PKCFY 340 (1149)
Q Consensus 280 ~~~~~i~t~~~al~yIg~~~r~~~~~~~~~~~~e~~~~~L~~~ll~H----l~~-~~~~~~--------------~K~~~ 340 (1149)
...+...++++|+..|++++|++ +.. ..+.|+.++++.||.. ++. +...++ .+.++
T Consensus 372 L~~D~~~~~e~Al~eIy~~lRpg----e~~-~~e~a~~l~~~~ff~~~~YdLg~vGR~k~N~kl~~~~~~~~~~l~~~Di 446 (2836)
T PRK14844 372 LFLDENMSYQDALYEIYKVLRPG----EVP-VLEIVEEFFRNLFFSPEYYDLSNIGRLKLNSYLGLNYDEDLTVLTHEDI 446 (2836)
T ss_pred HhhcccccHHHHHHHHHHhcCCC----CCC-cHHHHHHHHHHHhcCccccccccchhhhhhhhhccCCCCCCcEecHHHH
Confidence 01123457899999999999987 444 6677888888877642 111 011111 12244
Q ss_pred HHHHHHHHHHhhcCCCCCCCcccccccEEccccHhHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccccccchH
Q 001125 341 VAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSIT 420 (1149)
Q Consensus 341 L~~Mi~kLl~~~~g~~~~DD~D~l~NkRv~l~G~Ll~~lfr~~l~~~~~~ik~~i~k~~~~~~~~~~~~~~~~i~~~~It 420 (1149)
+ .++++|+.+..|....||+|||+||||+++|+||+++||.+|.++.+.+++++... ....+++..++++++|+
T Consensus 447 i-~~i~~Li~l~~g~~~~DDiDhL~NRRvr~vGeLl~~qfr~gl~r~~~~i~e~~~~~-----~~~~~~p~~lin~~~l~ 520 (2836)
T PRK14844 447 I-EIVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSMSTS-----SLDKVSPSDFINPKVLT 520 (2836)
T ss_pred H-HHHHHHHHHhcCCCcccchhhhhccccchHHHHHHHHHHHHHHHHHHHHHHHHhhc-----cccccchhhcccchhHH
Confidence 4 58999999999999999999999999999999999999999999999999998642 12346778889999999
Q ss_pred HHHHHHhccCCCcccccccccccceEEcccccccccccccccccc----ccccccccCCCCccCCCCCcccccCCCCCCC
Q 001125 421 VGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSP----QFEKSRKVSGPRALQPSQWGMLCPCDTPEGE 496 (1149)
Q Consensus 421 ~~i~~~~sTGnw~~~~~~~q~sGvsq~l~rln~ls~LshlRrv~~----~f~~~~k~t~~R~Lhps~wG~iCPveTPEG~ 496 (1149)
+.+++||+| +++||+||++|++|.|+|.||+++ ++.+.+..+.+|++||||||||||+|||||+
T Consensus 521 ~~i~~ff~s------------s~LSQfmDQtNpLseltHkRRlsaLGPGGL~r~~a~fevRdvH~shyGRiCPIETPEG~ 588 (2836)
T PRK14844 521 NVLRDFFNS------------SQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQ 588 (2836)
T ss_pred HHHHHHhcc------------cchhhhccCcChhhhhhhcceecccCCCCcccccCCCcccccCccccccccCCCCCCCC
Confidence 999999977 378999999999999999999996 5788899999999999999999999999999
Q ss_pred cchhhhhccceeeeccCCCchhHHHHHhhcCceeccccCccccCCCCceEEEECCeEEEeecChhhHHHHHHHHhhcCCc
Q 001125 497 ACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKI 576 (1149)
Q Consensus 497 ~cGLi~~LA~~a~Vt~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~lr~~rr~g~i 576 (1149)
|||||+|||.+|+|+. +|+.. .+|....||++- +++
T Consensus 589 NiGLI~SLA~yarIn~-------------~Gfie------------tPy~kV~~g~v~---~~i---------------- 624 (2836)
T PRK14844 589 NIGLINSLAIYARINK-------------YGFIE------------SPYRKVVNRVVT---DQI---------------- 624 (2836)
T ss_pred cccchhhhhhheeccC-------------CceEe------------CCcEEEEcCcCc---ccc----------------
Confidence 9999999999999984 45432 234444677532 111
Q ss_pred CceeEEEecc-cCceEEEecCCCeeeeeEEEeecCcccchhhhHHhhhcCCcchhhhhccCceeEeccccccceEEEeec
Q 001125 577 GEFVSVFVNE-KQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYE 655 (1149)
Q Consensus 577 ~~~v~i~~~~-~~~~i~I~td~GRl~RPl~~v~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~iE~id~~Eq~~~~Ia~~~ 655 (1149)
.|+.. .+....|.... -|+ -++|.. .++. +.. ...| ||+ .+ .
T Consensus 625 -----~ylsa~~E~~~~Ia~a~----~~~--~~~~~~--~~~~---v~~--------R~~~--ef~--------~~--~- 667 (2836)
T PRK14844 625 -----EYLSAIDEGLYYIADTS----AKL--DENNCF--VDDM---LYC--------RYAG--SFV--------MV--S- 667 (2836)
T ss_pred -----cccChHHhcCcEEEeCC----ccC--CCCCcc--cCCe---EEE--------ecCC--ceE--------Ee--c-
Confidence 12222 22334444322 011 111110 0000 000 0001 111 11 0
Q ss_pred CCCCCCceeeeecCceeccccccccCCCCCCCCCccccccccccCCcccce-----------------------------
Q 001125 656 GDATPDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIA----------------------------- 706 (1149)
Q Consensus 656 ~~~~~~~th~Ei~P~~ilsv~AslIPF~~hNqSpRn~yq~~M~KQa~G~~~----------------------------- 706 (1149)
..+.++++++|.|++|++||||||+|||||+|++||||||||||++.-
T Consensus 668 ---~~~v~~~dvsp~Q~~SvaasLIPFLEhdDAnRALMGSNMQRQAVPLl~~e~PiVGTG~E~~vA~DSg~~v~A~~~G~ 744 (2836)
T PRK14844 668 ---SDQVSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESFVASGSGAVVLAKRDGI 744 (2836)
T ss_pred ---HHHceEEEeCcchhhhhHhhcCCccccCccccccccccccccccccccCCCCeEecCcchhhhhcccceEEeccCce
Confidence 123589999999999999999999999999999999999999997521
Q ss_pred --eeec----ccccc---------ceeee----------cCCCcceeechhhh----------hccCCCCCCCcceEEEE
Q 001125 707 --FNQL----CRMDS---------LLYLL----------VYPQRPLLTTRTIE----------LVGYDKLGAGQNATVAV 751 (1149)
Q Consensus 707 --~n~~----~R~D~---------~~y~L----------~ypQ~PlV~t~~~~----------~~~~~~~p~G~N~iVAv 751 (1149)
+... .|.+. ..|.| |++|||+|+.+.+. .+..+|+++|+|++|||
T Consensus 745 V~yVda~kIvI~~~~~~~~~~~~~~~Y~L~ky~RSNQ~TcinQrPiV~~Gd~V~kGdilADG~st~~GELALG~NvlVAf 824 (2836)
T PRK14844 745 VDSSDSNSIVIRAFDKERVNYLDVDIYHLRKFQRSNHNTCINQKPLVCVGDYVKEGDVIADGPAINSGELALGQNLLVAF 824 (2836)
T ss_pred EEEEcCCEEEEEeCCCccccccccceEEeccccccccceeeeecceecCCCEeccCCEeccChhhcccccccccceEEEE
Confidence 1111 11111 23655 77999999998764 34589999999999999
Q ss_pred EecCCCCCCCcEEeecccccccceeEEEEEEEEEEeecccCCccceecC-CCCCCCchhhhccCCCCcccCCCceeCCCC
Q 001125 752 MSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILR-PDRTGPGAERMQILDDDGLAAPGEIIKPND 830 (1149)
Q Consensus 752 ~~~~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~~~~~~-p~~~~~~~~~~~~Ld~dGi~~~G~~v~~gd 830 (1149)
|||.||||||||+||++++++++|||+|+++|++++++++.|.++++.+ |+.+. +.+++||++|||++|++|++||
T Consensus 825 mpW~GYNfEDAIliSErlv~eD~fTSiHIee~ei~~r~Tk~G~EeITrdIPnv~e---~~lr~LDe~GIV~iGa~V~~GD 901 (2836)
T PRK14844 825 MSWQGYNFEDSIIISSEVVKKDLFTSIHIEEFECVVHDTPLGSEKITRAIPGVNE---ENLYHLDDSGIVKIGTRVGPGY 901 (2836)
T ss_pred eccCCcccccccccchhhccCceeEEEeecceEEEEEeccCCCceecccCCCCCh---HHHhcCCCCCCeecCCEECCCC
Confidence 9999999999999999999999999999999999999999998776665 88753 5899999999999999999999
Q ss_pred EEEEEecCCCCCCCCCC------CCCCCCcccccceeeecCCCCCceEEEEEEEeeCC----------------------
Q 001125 831 VYINKESPLETRGSIMS------PTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDK---------------------- 882 (1149)
Q Consensus 831 ~l~~k~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~v~~v~~~~~~---------------------- 882 (1149)
|||||++|+++.+..+. -++++....+|+|+++.++. .|+|-.|.++...
T Consensus 902 ILVGKvtPk~e~~~tPEekLL~aIFGek~~~vkdtSLrvp~G~--~G~Vidv~~f~~~~~~~~~~~~~~~~~~~~~~~~~ 979 (2836)
T PRK14844 902 ILVGKVTPKPSLSLPPETKLLMTIFGEKSFDCADSSLYTSPDV--EGTVIDVQVFTRRGVEENERALLIKQKEINDFEKE 979 (2836)
T ss_pred EEEEeecCCCCCCCCHHHHHHHHHhCCcccccccCceecCCCC--CEEEEEEEEEcccccccchhhhhhhhhhhhhhhhh
Confidence 99999999987654332 26778888999999998877 8988888766531
Q ss_pred -------------------------------------------------------------------------------C
Q 001125 883 -------------------------------------------------------------------------------N 883 (1149)
Q Consensus 883 -------------------------------------------------------------------------------~ 883 (1149)
.
T Consensus 980 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~ 1059 (2836)
T PRK14844 980 RDYIINVTSEYFYDELKKLLINSGSQDREKFDSIEREQWWGIGLKNQSISEQVKSLKKDFDEKVSHAIAQFKRKVEKLHE 1059 (2836)
T ss_pred hhhhhhhhhhhhhhhhhhhhcccccccHHHHhhccHHhhhhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 0
Q ss_pred C-------cEEEEEEEeeecCCCccccccccCCCccEEEeeeccCCCCCCCCCCCCcEEeCCCCCCCCchHHHHHHHhcc
Q 001125 884 G-------DLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGG 956 (1149)
Q Consensus 884 ~-------~~~vkv~~~~~R~p~iGDKf~sRhGqKGvvs~i~~~eDmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~~~g 956 (1149)
| ...|||+|+++|++|||||+|||||||||||+|+|.|||||++||+++|||+||+|+||||||||++|+++|
T Consensus 1060 gdeL~~gv~~~VkVyia~KRkiqvGDKmAGRHGNKGVIS~IlP~eDMPyL~DGtpvDIvLNPLGVPSRMNvGQilE~hLG 1139 (2836)
T PRK14844 1060 GYDLPQGVSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVG 1139 (2836)
T ss_pred CCcCCCCCceEEEEEEEEeecCCccccccccCCCCceEeEEcccCCCCcCCCCCCceEEeCCCCCCccccHHHHHHHHHH
Confidence 1 257999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccCcee----------------------------------------------------------------------
Q 001125 957 KAGVSCGRFH---------------------------------------------------------------------- 966 (1149)
Q Consensus 957 k~~~~~g~~~---------------------------------------------------------------------- 966 (1149)
+||...|...
T Consensus 1140 ~A~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1219 (2836)
T PRK14844 1140 WACKKLGEKVGNILDEINKIKSAFCKGIRSLNDDNFTKFAAAYLDNKKIENIDDDEITASVLNTPNKNALNDELNELVEN 1219 (2836)
T ss_pred HHHhhhhhhhHhhhhhhhccccccccccccccccccccccccccccccccccccccccccccccccccccccccccchhc
Confidence 9998875210
Q ss_pred ------------------------------------------------eeeeccCCCCCCCCHHHHHHHHHHcCCCCCCc
Q 001125 967 ------------------------------------------------YGSAFGEPSGHADTVESISETLVKHGFSYNGK 998 (1149)
Q Consensus 967 ------------------------------------------------d~tpF~~~~~~~~~~~~~~~~l~~~g~~~~G~ 998 (1149)
.|.||..+.+++.+.+++.+.|+++||+++|+
T Consensus 1220 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~tpvf~g~~~~~i~~~L~~~g~~~~Gk 1299 (2836)
T PRK14844 1220 YLNSCKSAYSNLRNFLIEVYSCGSNVSICNNIRDISDNNLIEFARKLRDGIPVAAPVFEGPKDEQIAKLFELAGLDNSGQ 1299 (2836)
T ss_pred cccccchhhHHHHHHHHHhhhcccccccccccccccHHHHHHHHhhhccCCeecCCCcCCCCHHHHHHHHHHhCcCCCCC
Confidence 02233444566888999999999999999999
Q ss_pred eEEEeCCCCcEEeeeEeEeeeeecccccccCcccEEecccCcccccccCcccccCCCceeeechhhhHHHHcccHHHHHH
Q 001125 999 DMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGLRVGEMERDCLIAYGASMLIFE 1078 (1149)
Q Consensus 999 e~ly~G~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~e 1078 (1149)
+.||||+||++|+++||+|++|||||+|||+||+|||++|||++|||||++||+|+|||||||||||||+|||||++|||
T Consensus 1300 ~~l~dG~TGe~f~~~v~vG~~yy~kL~HmV~DKihaRs~Gp~s~lT~QPl~Gr~~~GG~RfGEME~~al~a~Gaa~~L~E 1379 (2836)
T PRK14844 1300 AVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQE 1379 (2836)
T ss_pred EEEEcCCCCCccchhheeCcchhhhhhhhhcchhhhcccCCCcccccCCCcccccCCCceeecchHHHHHHHhHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhccCCCceeeeecccCCcceeecccccceecccccCCCccccccccHhHHHHHHHHHhCCcccEEEecc
Q 001125 1079 RLMVSSDPFEVQVCRVCGLLGYYNHKLKAGICSTCKNGDNISSMKLPYACKLLIQELQSMNIVPRLKLAE 1148 (1149)
Q Consensus 1079 rl~~~SD~~~~~vC~~cg~~~~~~~~~~~~~C~~c~~~~~~~~v~iPy~~k~l~~EL~sm~i~~~l~~~~ 1148 (1149)
||+.+||++.+++|. +|..|+ +.+..+..+|||||+|+|||+||||++++.+++
T Consensus 1380 ~Lt~kSD~~~gr~~~---------------~~~ivk-G~~~~~~~~PesfkvL~~EL~sl~i~~~~~~~~ 1433 (2836)
T PRK14844 1380 MLTVKSDDINGRVKI---------------YESIIK-GDSNFECGIPESFNVMIKELRSLCLNVDLKQND 1433 (2836)
T ss_pred HhcccccchhhhhHh---------------hhhhcc-CCCCCcCCCCchHHHHHHHHHhCccceEEeccc
Confidence 999999999987651 233343 344556799999999999999999999998864
No 13
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated
Probab=100.00 E-value=4.4e-184 Score=1639.99 Aligned_cols=597 Identities=47% Similarity=0.777 Sum_probs=563.2
Q ss_pred ceEEEECCeEEEeecChhhHHHHHHHHhhcCCcCceeEEEecccCceEEEecCCCeeeeeEEEeecCcccchhhhHHhhh
Q 001125 544 SFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELL 623 (1149)
Q Consensus 544 ~~~V~lnG~~iG~~~~~~~~~~~lr~~rr~g~i~~~v~i~~~~~~~~i~I~td~GRl~RPl~~v~~~~~~~~~~~~~~~~ 623 (1149)
.++|||||+|+|++++|..|++.||.+||.|.++.+++|+++...++|+|+||+||++|||++|++|++.++++|+++++
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 46899999999999999999999999999999999999999988889999999999999999999999999999999998
Q ss_pred cCCcchhhhhccCceeEeccccccceEEEeecCCCCCCceeeeecCceeccccccccCCCCCCCCCccccccccccCCcc
Q 001125 624 DGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMG 703 (1149)
Q Consensus 624 ~~~~~~~~l~~~g~iE~id~~Eq~~~~Ia~~~~~~~~~~th~Ei~P~~ilsv~AslIPF~~hNqSpRn~yq~~M~KQa~G 703 (1149)
.++.+|++|+++|.|||||++||++++||+.++++...+||+||+|+++||++||+|||+||||||||||||||+|||||
T Consensus 84 ~~~~~~~dl~~~G~IEyida~EE~~~~IA~~~~~l~~~~th~Ei~p~~ilgv~AslIPF~~hNQSPRn~yq~~M~KQa~g 163 (605)
T PRK07225 84 NGELTFDDLVKQGVIEYLDAEEEENAYIAVYEEDLTEEHTHLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLG 163 (605)
T ss_pred cCCCChHHHHhCCCeeecChhhhcCeEeccchhhhcccccccccCCcceeEEEeeccCCCCCCccchhhhhhhhhhcccC
Confidence 77889999999999999999999999999999998877999999999999999999999999999999999999999999
Q ss_pred cceeeeccccccceeeecCCCcceeechhhhhccCCCCCCCcceEEEEEecCCCCCCCcEEeecccccccceeEEEEEEE
Q 001125 704 NIAFNQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKY 783 (1149)
Q Consensus 704 ~~~~n~~~R~D~~~y~L~ypQ~PlV~t~~~~~~~~~~~p~G~N~iVAv~~~~Gyn~EDaiiink~s~~rg~~~s~~~~~~ 783 (1149)
++++|+..|+|++.|+|+|||+|||+|+.++.++++++|+|+||+||||||+||||||||||||+|+|||||||+||++|
T Consensus 164 ~~~~n~~~r~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~p~G~N~iVAvmsy~GYn~EDAiIiNkssidRGlf~s~~~k~~ 243 (605)
T PRK07225 164 LPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTY 243 (605)
T ss_pred ccccceeeecCCcccEEeeCCcceEEccchHhhCCCccCCCeeEEEEEECcCCCChhHeeeeehhhhhcCceEEEEEEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEeecccCCccceecCCCCCC---CchhhhccCCCCcccCCCceeCCCCEEEEEecCCCCCCCCCCCCCCCCcccccce
Q 001125 784 TAINQKYANSTSDRILRPDRTG---PGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSAR 860 (1149)
Q Consensus 784 ~~~~~~~~~~~~~~~~~p~~~~---~~~~~~~~Ld~dGi~~~G~~v~~gd~l~~k~~~~~~~~~~~~~~~~~~~~~~~~~ 860 (1149)
+++++++..+..+.+..|+.+. .....|++||+||||++|++|++|||||||++|..+.+.. ..++......+++|
T Consensus 244 ~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~LD~dGi~~~G~~v~~gdiligk~sp~~~~~~~-~~~~~~~~~~~d~s 322 (605)
T PRK07225 244 EGEERRYPGGQEDRFEIPDKDVRGYRGEEAYRHLDEDGLVNPETEVKEGDVLIGKTSPPRFLEEP-DDFGISPEKRRETS 322 (605)
T ss_pred EEEeeecCCCcceEEecCCchhccccChHHhhcCCCCCCccCCCEECCCCEEEEEecCCCCccch-hhhcccccCcceee
Confidence 9999887777677777776421 1224689999999999999999999999999997533211 11112223478999
Q ss_pred eeecCCCCCceEEEEEEEeeCCCCcEEEEEEEeeecCCCccccccccCCCccEEEeeeccCCCCCCCCCCCCcEEeCCCC
Q 001125 861 QTYKGPDGETCVVDRVALCSDKNGDLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHG 940 (1149)
Q Consensus 861 ~~~~~~~~~~~~v~~v~~~~~~~~~~~vkv~~~~~R~p~iGDKf~sRhGqKGvvs~i~~~eDmPf~~~G~~pDiI~NPh~ 940 (1149)
++++.+| .|+||+|.++.+.++.+.|||++|+.|+|+||||||||||||||||+|||+||||||++|++|||||||||
T Consensus 323 ~~~~~~e--~g~Vd~V~~~~~~~~~~~vkv~ir~~R~p~iGDKfssRHGQKGvvs~i~~~eDMPft~~G~~PDiIiNPhg 400 (605)
T PRK07225 323 VTMRSGE--EGIVDTVILTETEEGSRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHA 400 (605)
T ss_pred EEecCCC--cEEEEEEEEEecCCCCEEEEEEEEEEEeccccchhhhcccCceeEEeEeccccCCcCCCCCcccEEECccc
Confidence 9999998 99999999998888889999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCchHHHHHHHhccccccccCceeeeeeccCCCCCCCCHHHHHHHHHHcCCCCCCceEEEeCCCCcEEeeeEeEeeee
Q 001125 941 FPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIY 1020 (1149)
Q Consensus 941 ~PSRMtiGql~E~~~gk~~~~~g~~~d~tpF~~~~~~~~~~~~~~~~l~~~g~~~~G~e~ly~G~tG~~~~~~if~G~~y 1020 (1149)
||||||||||+|+++||||++.|.+.|+|||. +..++++++.|.++||+++|+|+||||+||++|+++||+|++|
T Consensus 401 ~PSRMTiGql~E~~~gk~~~~~g~~~d~t~F~-----~~~~~~~~~~L~~~g~~~~G~e~my~G~TG~~~~~~if~G~~y 475 (605)
T PRK07225 401 IPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFS-----GEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIY 475 (605)
T ss_pred ccccCcHHHHHHHHHHHHHHhcCceEeecCCC-----CchHHHHHHHHHHhCcCCCCeEEEEcCCCCCEecccEEEeehh
Confidence 99999999999999999999999999999999 5679999999999999999999999999999999999999999
Q ss_pred ecccccccCcccEEecccCcccccccCcccccCCCceeeechhhhHHHHcccHHHHHHhhccCCCceeeeecccCCccee
Q 001125 1021 YQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGLRVGEMERDCLIAYGASMLIFERLMVSSDPFEVQVCRVCGLLGY 1100 (1149)
Q Consensus 1021 y~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~cg~~~~ 1100 (1149)
||||+|||.||+|||++||++.|||||++||||+|||||||||||||+|||||++|+|||+++||+++++||.+||++++
T Consensus 476 YqrL~HmV~DK~haR~~Gp~~~lTrQP~~GR~r~GG~RfGEMErd~lia~Gas~~L~Erl~~~SD~~~~~vC~~CG~~~~ 555 (605)
T PRK07225 476 YQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKVEIYVCAKCGMIAI 555 (605)
T ss_pred eeechhhhcchhhhccCCCCcccccCCccccccCCCeeeeeeehhhhhhhhhHHHHHHHHhccCcceeEEeecCcCccee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred ecccccceecccccCCCccccccccHhHHHHHHHHHhCCcccEEEecc
Q 001125 1101 YNHKLKAGICSTCKNGDNISSMKLPYACKLLIQELQSMNIVPRLKLAE 1148 (1149)
Q Consensus 1101 ~~~~~~~~~C~~c~~~~~~~~v~iPy~~k~l~~EL~sm~i~~~l~~~~ 1148 (1149)
.+.+.+..+|+.|+++.++.++.||||||||+|||+||||++||.+++
T Consensus 556 ~~~~~~~~~C~~C~~~~~i~~v~iPya~kll~~EL~sm~i~~~l~~~~ 603 (605)
T PRK07225 556 YDKKRNRKYCPICGEETDIYPVEMSYAFKLLLDELKSLGIAPRLELED 603 (605)
T ss_pred hhcccCceeecccCCCCceeeccCChhHHHHHHHHHHCCceeEEEecc
Confidence 765566678999999899999999999999999999999999999875
No 14
>TIGR03670 rpoB_arch DNA-directed RNA polymerase subunit B. This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.
Probab=100.00 E-value=3.3e-183 Score=1630.88 Aligned_cols=594 Identities=47% Similarity=0.798 Sum_probs=559.7
Q ss_pred EEECCeEEEeecChhhHHHHHHHHhhcCCcCceeEEEecccCceEEEecCCCeeeeeEEEeecCcccchhhhHHhhhcCC
Q 001125 547 VIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGV 626 (1149)
Q Consensus 547 V~lnG~~iG~~~~~~~~~~~lr~~rr~g~i~~~v~i~~~~~~~~i~I~td~GRl~RPl~~v~~~~~~~~~~~~~~~~~~~ 626 (1149)
|||||+|+|++++|..|++.||.+||.|.++.+++|+++...++|+|+||+||++|||++|++|++.++++|++.++.+.
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 79999999999999999999999999999999999999998899999999999999999999999999999999998777
Q ss_pred cchhhhhccCceeEeccccccceEEEeecCCCCCCceeeeecCceeccccccccCCCCCCCCCccccccccccCCcccce
Q 001125 627 RSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIA 706 (1149)
Q Consensus 627 ~~~~~l~~~g~iE~id~~Eq~~~~Ia~~~~~~~~~~th~Ei~P~~ilsv~AslIPF~~hNqSpRn~yq~~M~KQa~G~~~ 706 (1149)
.+|++|+++|+|||||++||+++.||+.++++...+||+||+|+++||++||+|||+||||||||||||||+|||||+++
T Consensus 81 ~~~~~ll~~G~IEyida~Ee~~~~IA~~~~~l~~~~th~Ei~p~~ilgv~AslIPF~~hNqSpRn~YQc~M~KQamG~~~ 160 (599)
T TIGR03670 81 LTWDDLVKQGVIEYLDAEEEENAYIALDPEELTPEHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYA 160 (599)
T ss_pred CCHHHHHhcCCeEecCchhhcCeEEecchHHhccCcCccccCCcceeeEEeeccCCCCcCcchhhHHHHhhhhccccccc
Confidence 89999999999999999999999999999998878999999999999999999999999999999999999999999999
Q ss_pred eeeccccccceeeecCCCcceeechhhhhccCCCCCCCcceEEEEEecCCCCCCCcEEeecccccccceeEEEEEEEEEE
Q 001125 707 FNQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAI 786 (1149)
Q Consensus 707 ~n~~~R~D~~~y~L~ypQ~PlV~t~~~~~~~~~~~p~G~N~iVAv~~~~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~ 786 (1149)
+|+..|+||++|+|+|||+|||+|+.++.++++++|+|+||+||||||+||||||||||||+|+|||||||+||++|+++
T Consensus 161 ~n~~~R~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~p~G~N~iVAvmsy~GYn~EDAiIink~si~rG~f~s~~~~~~~~~ 240 (599)
T TIGR03670 161 ANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAE 240 (599)
T ss_pred cChhhcccccceEEcCCCCceeeeeeHHHhCccccCCCeeEEEEEEcccCcChhHeeeechhhhhcCCeEEEEEEEEEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eecccCCccceecCCCCCC---CchhhhccCCCCcccCCCceeCCCCEEEEEecCCCCCCCCCCCCCCCCcccccceeee
Q 001125 787 NQKYANSTSDRILRPDRTG---PGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTY 863 (1149)
Q Consensus 787 ~~~~~~~~~~~~~~p~~~~---~~~~~~~~Ld~dGi~~~G~~v~~gd~l~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 863 (1149)
++++..+..|.+..|+... .....|++||+||||++|++|++|||||||++|..+.+. ...++.+....+|+|+++
T Consensus 241 ~~~~~~~~~e~~~~p~~~~~~~~~~~~~~~LD~dGi~~~G~~v~~gdiligk~~p~~~~~~-~~~~~~~~~~~~d~s~~~ 319 (599)
T TIGR03670 241 ERRYPGGQEDRFEIPEPDVRGYRGEEAYKHLDEDGIVYPEVEVKGGDVLIGKTSPPRFLEE-LRELGLVTERRRDTSVTV 319 (599)
T ss_pred eeccCCCCceEEecCCchhccccchhhhccCCCCCCcCCCcEeCCCCEEEEEecCCCCccc-hhhhccccccCceEEEEe
Confidence 9887767667777675321 122468999999999999999999999999998754321 001112223478999999
Q ss_pred cCCCCCceEEEEEEEeeCCCCcEEEEEEEeeecCCCccccccccCCCccEEEeeeccCCCCCCCCCCCCcEEeCCCCCCC
Q 001125 864 KGPDGETCVVDRVALCSDKNGDLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPS 943 (1149)
Q Consensus 864 ~~~~~~~~~v~~v~~~~~~~~~~~vkv~~~~~R~p~iGDKf~sRhGqKGvvs~i~~~eDmPf~~~G~~pDiI~NPh~~PS 943 (1149)
+++| .|+||+|.++.++++.+.|||++|+.|+|+||||||||||||||||+|||+||||||+||++||||||||||||
T Consensus 320 ~~~e--~g~Vd~V~~~~~~~~~~~vkv~~r~~R~p~iGDKfssRHGQKGvvs~i~~~eDMPft~~G~~pDiIiNPhg~PS 397 (599)
T TIGR03670 320 RHGE--KGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPS 397 (599)
T ss_pred cCCC--cEEEEEEEEEecCCCcEEEEEEEeeeecCcchhhhhhhccCcceEEeEeccCCCCcCCCCCCCCEEECcccccc
Confidence 9999 99999999998888889999999999999999999999999999999999999999999999999999999999
Q ss_pred CchHHHHHHHhccccccccCceeeeeeccCCCCCCCCHHHHHHHHHHcCCCCCCceEEEeCCCCcEEeeeEeEeeeeecc
Q 001125 944 RMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQK 1023 (1149)
Q Consensus 944 RMtiGql~E~~~gk~~~~~g~~~d~tpF~~~~~~~~~~~~~~~~l~~~g~~~~G~e~ly~G~tG~~~~~~if~G~~yy~r 1023 (1149)
|||||||+|+++||||++.|.+.|+|||+ +..++++++.|+++||+++|+|+||||+||++|+++||+|++||||
T Consensus 398 RMTiGqllE~~~gk~~~~~g~~~d~t~F~-----~~~~~~~~~~L~~~g~~~~G~e~ly~G~TG~~~~~~if~G~~yyqr 472 (599)
T TIGR03670 398 RMTVGQLLEMIAGKVAALEGRRVDGTPFE-----GEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQK 472 (599)
T ss_pred cccHHHHHHHHHHHHHHhcCCEEEeCCCC-----CccHHHHHHHHHHcCCCCCCCEEEEcCCCCCCccccEEEEehhhee
Confidence 99999999999999999999999999999 5678999999999999999999999999999999999999999999
Q ss_pred cccccCcccEEecccCcccccccCcccccCCCceeeechhhhHHHHcccHHHHHHhhccCCCceeeeecccCCcceeecc
Q 001125 1024 LKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGLRVGEMERDCLIAYGASMLIFERLMVSSDPFEVQVCRVCGLLGYYNH 1103 (1149)
Q Consensus 1024 L~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~cg~~~~~~~ 1103 (1149)
|+|||+||+|||++||++.|||||++||||+|||||||||||||+|||||++|+|||+++||++.++||.+||++++.+.
T Consensus 473 L~HmV~DK~h~Rs~Gp~~~lTrQP~~Gr~r~GG~RfGEMErd~lia~Gas~~L~ErL~~~SD~~~~~vC~~CG~~~~~~~ 552 (599)
T TIGR03670 473 LHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIAWEDK 552 (599)
T ss_pred chhhhcchhhhcccCCCcccccCCccccccCCCeeeeeeehhhHhhcchHHHHHHHHhccCcceeEEeecccCceeehhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999997655
Q ss_pred cccceecccccCCCccccccccHhHHHHHHHHHhCCcccEEEecc
Q 001125 1104 KLKAGICSTCKNGDNISSMKLPYACKLLIQELQSMNIVPRLKLAE 1148 (1149)
Q Consensus 1104 ~~~~~~C~~c~~~~~~~~v~iPy~~k~l~~EL~sm~i~~~l~~~~ 1148 (1149)
+.+..+|+.|+++.++.++.+|||||||+|||+||||++||.+++
T Consensus 553 ~~~~~~C~~c~~~~~i~~v~iPy~~k~l~~EL~am~i~~~l~~~~ 597 (599)
T TIGR03670 553 RKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLELGD 597 (599)
T ss_pred ccCceeccccCCCCceeeecCChhHHHHHHHHHhCCcceEEEecc
Confidence 555677999999889999999999999999999999999999875
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=1e-111 Score=981.70 Aligned_cols=367 Identities=47% Similarity=0.770 Sum_probs=314.8
Q ss_pred cccccccCCCCCCCCCccccccccccCCcccceeeeccccccceeeecCCCcceeech-hhhhcc---------CCCCCC
Q 001125 674 GVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTR-TIELVG---------YDKLGA 743 (1149)
Q Consensus 674 sv~AslIPF~~hNqSpRn~yq~~M~KQa~G~~~~n~~~R~D~~~y~L~ypQ~PlV~t~-~~~~~~---------~~~~p~ 743 (1149)
||+|++|||++|||||||+|||||+|||||++.+|+..|+|+.. +|||+|||+|+ .++..+ ++|+|+
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 68999999999999999999999999999999999999999888 99999999999 677777 999999
Q ss_pred CcceEEEEEecCCCCCCCcEEeecccccccceeEEEEEEEEEEeecccCCccce-ecCCCCCCCchhhhccCCCCcccCC
Q 001125 744 GQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDR-ILRPDRTGPGAERMQILDDDGLAAP 822 (1149)
Q Consensus 744 G~N~iVAv~~~~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~~~-~~~p~~~~~~~~~~~~Ld~dGi~~~ 822 (1149)
|+|++||||||+||||||||||||+|++||+|||+||++ +++++.++.+..+. +..|... +...|++||+||||++
T Consensus 78 G~N~iVAvmsy~GYN~EDAiIiNkssv~rG~f~s~~~k~-~~~~~~~~~g~~e~~~~~~~~~--~~~~~~~LD~dGii~~ 154 (386)
T PF00562_consen 78 GQNAIVAVMSYTGYNQEDAIIINKSSVDRGLFTSIHYKT-EIEIRDNKGGPSEEIFRPIPNV--KEYNYSKLDEDGIIKI 154 (386)
T ss_dssp SEEEEEEESBSSSTTTSSEEEEECHHHHTTTTEEEEEEE-EEEEEEETTSEEBBESS--TSS--TSTTGGGBCTTSBB-T
T ss_pred eeeeeEEeeehhcccchhhhhhhhhhhhcCeeeEEEEEE-EeeeecccCCcccccccccccc--hhhhhhhccccccccc
Confidence 999999999999999999999999999999999999999 88888777776444 4443322 2358999999999999
Q ss_pred CceeCCCCEEEEEec-CCCCCCCCCCCCCCCCcccccceeeecCCCCCceEEEEEEE-------eeCCCCcEEEEEEEee
Q 001125 823 GEIIKPNDVYINKES-PLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVAL-------CSDKNGDLCIKFLIRH 894 (1149)
Q Consensus 823 G~~v~~gd~l~~k~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~v~~-------~~~~~~~~~vkv~~~~ 894 (1149)
|++|++|||||||++ |..........++++....+|+|++++.++ .|+||+|.+ ..+.++...|+|++|+
T Consensus 155 G~~v~~gDiligk~~~~~~~~~~~~~~~~~~~~~~~d~s~~~~~~e--~g~Vd~V~~~~~~~~~~~~~~~~~~iki~ir~ 232 (386)
T PF00562_consen 155 GSRVEKGDILIGKITSPPRFSPLLKKIFGEKNRNYRDTSIKYKSGE--SGRVDKVIIFSNEKKDTSNNEGYKKIKIRIRS 232 (386)
T ss_dssp TCEEETTSEEEEEEESTSC--HHHHHHHHSSSCSEEEEEEES-TT---EEEEEEEEEECCCSSBEEETTCEEEEEEEEEE
T ss_pred CcEEecceeEEEEEecccccccchhhccccccccccceeecccccE--EeEeccccccccccccccccCcceEEEEEecc
Confidence 999999999999996 222110000001122333789999999998 999999999 5567789999999999
Q ss_pred ecCCCccccccccCCCccEEEeeeccCCCCCCCCCCCCcEEeCCCCCCCCchHHHHHHHhccccccccCceeeeeeccCC
Q 001125 895 TRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEP 974 (1149)
Q Consensus 895 ~R~p~iGDKf~sRhGqKGvvs~i~~~eDmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tpF~~~ 974 (1149)
.|+|+||||||||||||||||+|||+||||||++|++|||||||||||||||||||+|+++||++++.|.+.|+|||.
T Consensus 233 ~R~p~iGDKfssRHGqKGVvs~i~~~eDMPft~~G~~pDiIiNPhgiPSRMtiGqllE~~~g~~~~~~g~~~~~t~F~-- 310 (386)
T PF00562_consen 233 TRRPQIGDKFSSRHGQKGVVSKILPQEDMPFTEDGIVPDIIINPHGIPSRMTIGQLLESLLGKAGALNGRFVDATPFD-- 310 (386)
T ss_dssp EEE--TTEEEEETTSEEEEEEEEE-TTTSEEETTSEB-SEEE-GGGSTTTTBTHHHHHHHHHHHHHHSTCEEB-TTTS--
T ss_pred cccchhHHHHhhhhcCceEEeeeeccccCccccCCCcceeeecccccccccchHHHHhhhhhhhhhccccceecCCCC--
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCHHHHHHHHHHcCCCCCCceEEEeCCCCcEEeeeEeEeeeeecccccccCcccEEecccCcccccccCcccccC
Q 001125 975 SGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRAR 1053 (1149)
Q Consensus 975 ~~~~~~~~~~~~~l~~~g~~~~G~e~ly~G~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~ 1053 (1149)
+.+.+++++.|.++||+++|+|.||||+||++++++||+|++|||||+|||+||+|||++||++.|||||++||+|
T Consensus 311 ---~~~~~~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 311 ---ESSEEDISELLKKAGYNYPGKEVLYDGRTGEKFEAPIFIGPVYYQRLKHMVDDKIHARSRGPYSLLTRQPVEGRSR 386 (386)
T ss_dssp ---SS-HHHHHHHHHHTTSHTTSEEEEBESSSSSBESSEEEEEEEEEEEBSTCGGGSTEEESS--BBSSSSSB-SSSSS
T ss_pred ---CcchhhhHhhhhcccccccceEEEEcCccCceEEeEEEeeeEEeccceEeCCcEEEEEecCCCccccCCCCCCCCC
Confidence 5677999999999999999999999999999999999999999999999999999999999999999999999997
No 16
>PRK09606 DNA-directed RNA polymerase subunit B''; Validated
Probab=100.00 E-value=1.9e-106 Score=966.88 Aligned_cols=486 Identities=33% Similarity=0.592 Sum_probs=430.7
Q ss_pred cccccccccccccccchHHHHHHHHHHHHHhCHHHHHHhcccceecCCCcEEEEEeEEEEcCCccccCC-cCCCCChhhH
Q 001125 28 VVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDG-VSEKLNPHMC 106 (1149)
Q Consensus 28 ~~~~~~~i~~~~~~~~Lv~~qi~SFn~Fi~~gL~~ii~~~~~I~~~~~~~~~l~~~~i~i~~P~~~e~~-~~~~l~P~Ec 106 (1149)
.+|.|.++++||+.++|++|||+|||+|+++||++++++.+||+....+.+.|+|+++++++|++.+++ ...+++|+||
T Consensus 2 ~~~~~~~i~~~~~~~~lv~~qi~SFn~Fi~~gl~~ii~~~~~i~~~~~~~~~l~~~~~~l~~P~~~~~~~~~~~l~P~ea 81 (494)
T PRK09606 2 MEDRRVLSDAYFKEHRLVRHHIDSYNDFVDNGLQKIIDEQGPIETEIEDGVYVELGKIRVGKPVVKEADGSEREIYPMEA 81 (494)
T ss_pred chHHHHHHHHHHCCCChHHHHHHHHHHHHHHhHHHHHHhcCCEEEecCCcEEEEEEEEEECCCcccccCCccccCCHHHH
Confidence 367899999999999999999999999999999999999999987666778999999999999987655 5678999999
Q ss_pred hhcCCccCccEEEEEEEEECCcccceeeEEeeEEeeccceeeccccccCCCCCHHHHHhcCCCCCCCCcEEEEcCchhhh
Q 001125 107 RLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVL 186 (1149)
Q Consensus 107 R~r~lTYsa~l~v~i~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~elv~~~E~~~d~GGYFIING~ERVI 186 (1149)
|+|++||+|+++|+|.++.++ .....+++++|+|||||||++|||++++|+||++.||||+|+||||||||+||||
T Consensus 82 R~r~~TYs~~l~v~i~~~~~~----~~~~~~~v~iG~iPiMv~S~~C~L~~~~~~~l~~~~E~~~d~GGyFIING~ErVi 157 (494)
T PRK09606 82 RLRNLTYSAPLYLEMSPVEGG----EEEEPEEVYIGELPVMVGSKICNLYGLSEEELIEVGEDPLDPGGYFIVNGSERVL 157 (494)
T ss_pred HhcCCCccceEEEEEEEEECC----CceEEeeEEeccCCeEeccCcccCCCCCHHHHHhcCCCcCCCCCeEEECCCeEEE
Confidence 999999999999999998654 2234568999999999999999999999999999999999999999999999999
Q ss_pred HHhhhccCCeEEEEeCCC---CcEEEEEEecCCCcce-EEEEEeeCCEEEEEEceeeccccHHHHHHHhCCCCHHHHHHH
Q 001125 187 LIQEQLSKNRVIIDTDKK---GNINASVTSSTETVKS-KTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQM 262 (1149)
Q Consensus 187 ~~q~~~s~N~i~~~~~~~---g~~~a~v~s~~~~~~s-~~~~~~k~g~i~~r~~~~~~~IPi~ilLrALG~~sD~eI~~~ 262 (1149)
|+||+++||++++++++. ..+.+.++|..+..+. ..+.+..+|.+++++++..++||++++|||||.+||+||++.
T Consensus 158 ~~q~~~~~n~~~~~~~~~~~~~~~~~~i~s~~~~~~~~~~l~~~~~g~i~~~~~~~~~~iPi~~llkALg~~sd~eI~~~ 237 (494)
T PRK09606 158 MTLEDLAPNKILVEKDERYGDRIEVAKVFSQRRGYRALVTVERNRDGLLEVSFPSVPGSIPFVILMRALGLETDEEIVEA 237 (494)
T ss_pred EEEEeccCCeeEEEeccCCCccceEEEEEcccccceeeEEEEEecCCeEEEEEcCccccccHHHHHHHcCCCCHHHHHHH
Confidence 999999999999887543 2378889887764332 334445678999999987678999999999999999999999
Q ss_pred hCCchhHHhhhHHhHHHHHhcCCcCHHHHHHHHhhhcccCCCCCCCCChHHHHHHHHHhhhccCCCCCCCCCCCccchHH
Q 001125 263 VGRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLANVPVHNNNFRPKCFYVA 342 (1149)
Q Consensus 263 i~~~~~~~~~l~~~l~~~~~~~i~t~~~al~yIg~~~r~~~~~~~~~~~~e~~~~~L~~~ll~Hl~~~~~~~~~K~~~L~ 342 (1149)
++.+..+.+.+..++++ .++.|+++||.|||+++++. .++.. ..+.|+.+|++++|||+|.+..+..+|+++|+
T Consensus 238 i~~~~~~~~~l~~~~~~---~~~~t~~~al~~ig~~~~~~--~~~~~-~~~~~~~~l~~~~l~hig~~~~~~~~K~~~L~ 311 (494)
T PRK09606 238 VSDDPEIVKFMLENLEE---AEVDTQEEALEYIGKRVAPG--QTKEY-RIKRAEYVIDRYLLPHLGVEPEVRRAKAHYLG 311 (494)
T ss_pred hCCcHHHHHHHHHHHHh---cccCCHHHHHHHHHHhcCCC--CCcch-HHHHHHHHHHHhhhcccCCCcchhhHHHHHHH
Confidence 97655555555555543 35789999999999999875 23344 67899999999999999976656678999999
Q ss_pred HHHHHHHHhhcCCCCCCCcccccccEEccccHhHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccccccchHHH
Q 001125 343 VMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVG 422 (1149)
Q Consensus 343 ~Mi~kLl~~~~g~~~~DD~D~l~NkRv~l~G~Ll~~lfr~~l~~~~~~ik~~i~k~~~~~~~~~~~~~~~~i~~~~It~~ 422 (1149)
+|++||++++.|.+.+||+|||+||||+++|+||+.+||++|+++++.++..+.+...+.+ .+++..+++++.||++
T Consensus 312 ~m~~kLl~~~~g~~~~Dd~D~l~nkRv~~~G~Ll~~~fr~~l~~~~~~~k~~l~~~~~~~~---~~~~~~~~~~~~It~~ 388 (494)
T PRK09606 312 RMAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERANMRNR---ELSIKTAVRSDVLTER 388 (494)
T ss_pred HHHHHHHHHhcCCCCCCCcccccCceeeccchhHHHHHHHHHHHHHHHHHHHHHHHHhcCC---CCCHHHhcCchhhhHH
Confidence 9999999999999999999999999999999999999999999999999988887653322 4567777888899999
Q ss_pred HHHHhccCCCcccccccccccceEEccccccccccccccccccccccccccCCCCccCCCCCcccccCCCCCCCcchhhh
Q 001125 423 LERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVK 502 (1149)
Q Consensus 423 i~~~~sTGnw~~~~~~~q~sGvsq~l~rln~ls~LshlRrv~~~f~~~~k~t~~R~Lhps~wG~iCPveTPEG~~cGLi~ 502 (1149)
|++|||||||.. +++|+||+|+|+||+|+|||+||+|+++.+.++.++||+||||||||+||||||||+||||||
T Consensus 389 l~~~~~TGnw~~-----~~~glSq~ldr~N~la~lSh~Rrv~s~~~r~~~~~~vR~lhps~~G~iCPveTPEG~~cGLv~ 463 (494)
T PRK09606 389 LEHAMATGNWVG-----GRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVK 463 (494)
T ss_pred HHHHhhcccccC-----CCceEEEEccCCCHHHHhhHHHhccCCccccCccccccccCcccceecccCcCCCCCcccHHH
Confidence 999999999985 468999999999999999999999999999999999999999999999999999999999999
Q ss_pred hccceeeeccCCCchhHHHHHhhcCceec
Q 001125 503 NLALMTHVTTDEEEGPLISLCYCLGVEDL 531 (1149)
Q Consensus 503 ~LA~~a~Vt~~~~~~~i~~~l~~~g~~~~ 531 (1149)
|||++|+|+++.+..++.++|.++|+.++
T Consensus 464 ~La~~a~V~~~~~~~~i~~~l~~lg~~~~ 492 (494)
T PRK09606 464 NFAQMVEISTGEDEEEVKEILKELGVEPE 492 (494)
T ss_pred hhhceEEEeCCCChHHHHHHHHHCcCeeC
Confidence 99999999999888899999999999874
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=1.7e-44 Score=386.43 Aligned_cols=147 Identities=45% Similarity=0.837 Sum_probs=125.8
Q ss_pred chHHHHHHHHHHHHHhCHHHHHHhcccceecC-CCcEEEEEeEEEEcCCccccCC-cCCCCChhhHhhcCCccCccEEEE
Q 001125 43 GLVKQHLDSFNYFVNTGIRKIVRANDRIVSGI-DPSIFLRFKDVRIGQPSMTVDG-VSEKLNPHMCRLSDMTYAAPILVN 120 (1149)
Q Consensus 43 ~Lv~~qi~SFn~Fi~~gL~~ii~~~~~I~~~~-~~~~~l~~~~i~i~~P~~~e~~-~~~~l~P~EcR~r~lTYsa~l~v~ 120 (1149)
||++|||+|||+|+++||++++++.+||..+. +..+.++|++++|++|++.+.+ ...+++|+|||+|++||+|+++|+
T Consensus 1 ~Lv~~qi~SFn~Fl~~gl~~i~~~~~~i~~~~~~~~~~l~~~~~~i~~P~~~~~~~~~~~l~P~ecR~r~~TYs~~l~v~ 80 (203)
T PF04563_consen 1 GLVKHQIDSFNYFLNNGLKEILKEFPPIEFESSNNRISLKFENIRIGKPTYSESDGRERPLYPRECRLRGLTYSAPLYVD 80 (203)
T ss_dssp TTTHHHHHHHHHHHCTSSHHHHSCSSSCEECCCSTTEEEEEEEEEEESESSEHTTSCEEE--HHHHHHTT-B-EEEEEEE
T ss_pred CchHHHHHHHHHHHHCCCHHHhccCCceEecCCcceEEEEeeEEEEeeeeeccccccccCCCHHHHHhcCCCCCCccceE
Confidence 68999999999999999999999999998764 5689999999999999998855 788999999999999999999999
Q ss_pred EEEEECCcccceeeEEeeEEeeccceeeccccccCCCCCHHHHHhcCCCCCCCCcEEEEcCchhhhHHhhhc
Q 001125 121 IEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQL 192 (1149)
Q Consensus 121 i~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~elv~~~E~~~d~GGYFIING~ERVI~~q~~~ 192 (1149)
|+++.++. ......+|.+|+|||||+|++|||++++++|+++.||||+|+||||||||+|||||+|+++
T Consensus 81 i~~~~~~~---~~~~~~~v~iG~iPiMv~S~~C~L~~~~~~~l~~~~E~~~d~GGYFIInG~EkVi~~q~~~ 149 (203)
T PF04563_consen 81 IELTVNNK---KEIKEQEVFIGKIPIMVRSKRCNLNGLSPKELVQLGECPNDPGGYFIINGSEKVIRMQIMR 149 (203)
T ss_dssp EEEEESST---TEEEESEEEEEEEE-BTTTTTSGGGT--HHHHHHTTS-TT---SSEEETTEEEEE-EEEEE
T ss_pred EEEEeecc---ceEEeeEEEEeeCCeEeecceeeCCCCCHHHHHHcCCCCcCCCCEEEECCChhheehhhhh
Confidence 99998872 3567778999999999999999999999999999999999999999999999999999988
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=6e-31 Score=237.68 Aligned_cols=81 Identities=53% Similarity=0.892 Sum_probs=76.3
Q ss_pred CceeeechhhhHHHHcccHHHHHHhhccCCCceeeeecccCCcceeecccccceecccccCCCccccccccHhHHHHHHH
Q 001125 1055 GGLRVGEMERDCLIAYGASMLIFERLMVSSDPFEVQVCRVCGLLGYYNHKLKAGICSTCKNGDNISSMKLPYACKLLIQE 1134 (1149)
Q Consensus 1055 GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~cg~~~~~~~~~~~~~C~~c~~~~~~~~v~iPy~~k~l~~E 1134 (1149)
|||||||||||||+|||||++|||||+++||.+.++||.+||.+++ .|+.+.++.++.+|||||||+||
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 8999999999999999999999999999999999999999998766 46777789999999999999999
Q ss_pred HHhCCcccEEEe
Q 001125 1135 LQSMNIVPRLKL 1146 (1149)
Q Consensus 1135 L~sm~i~~~l~~ 1146 (1149)
|+||||++++.+
T Consensus 70 L~sm~I~~~~~~ 81 (81)
T PF04560_consen 70 LRSMGIKIRIKT 81 (81)
T ss_dssp HHCTTEEEEEEE
T ss_pred HHHCcCceEEeC
Confidence 999999999974
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=3.3e-26 Score=200.69 Aligned_cols=66 Identities=50% Similarity=0.899 Sum_probs=59.7
Q ss_pred EEccccccccccccccccc--cccccccccCCCCccCCCCCcccccCCCCCCCcchhhhhccceeeec
Q 001125 446 QVLARLSFIGTLGHMTRVS--PQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVT 511 (1149)
Q Consensus 446 q~l~rln~ls~LshlRrv~--~~f~~~~k~t~~R~Lhps~wG~iCPveTPEG~~cGLi~~LA~~a~Vt 511 (1149)
|+|+|+|++++|||+|||+ +++.++.|++.+|+|||||||||||||||||++|||++|||++|+||
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 8899999999999999999 68999999999999999999999999999999999999999999986
No 20
>PF04561 RNA_pol_Rpb2_2: RNA polymerase Rpb2, domain 2; InterPro: IPR007642 RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain []. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble. Many of the bacterial members contain large insertions within this domain, a region known as dispensable region 1 (DRI).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_B 3LTI_A 3IYD_C 3LU0_C 2Y0S_R 1SMY_M 3DXJ_M 3AOI_C 2A68_M 1ZYR_C ....
Probab=99.85 E-value=2.2e-21 Score=205.51 Aligned_cols=175 Identities=26% Similarity=0.374 Sum_probs=119.1
Q ss_pred cCCeEEEEeCCCCcEE-EEEEecCCCcceEEEEE-eeCCEEEEEEceeeccccHHHHHHHhCCCCHHHHHHHhCC-chhH
Q 001125 193 SKNRVIIDTDKKGNIN-ASVTSSTETVKSKTVIQ-MEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGR-DPRY 269 (1149)
Q Consensus 193 s~N~i~~~~~~~g~~~-a~v~s~~~~~~s~~~~~-~k~g~i~~r~~~~~~~IPi~ilLrALG~~sD~eI~~~i~~-~~~~ 269 (1149)
+.|+|+++.+++++.. +++.+.....++....+ .++..+.+....+..+||+++||||||++||+||++.|+. +...
T Consensus 1 Rsn~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IPi~ilLrALG~~sd~eI~~~i~~~~~~~ 80 (190)
T PF04561_consen 1 RSNGIYVEKDKDGNKIIRSVRSDIISSRGSWHYLEKDKKIIIFSRPKKKFKIPIVILLRALGIESDKEIIELICYSEEDF 80 (190)
T ss_dssp ESSSEEEEE-SSSSSCSSCEEEEECCSSSEEEEEECETTTEEEEETTSSSEEEHHHHHHHTT--STCHHHHHHCCCSTCH
T ss_pred CCCEEEEEEccCCCCeeEEEEeecCCCcceEEEEecCCcEEEEEEcCcccccceEEeehhhcCcCcccccceeecccccc
Confidence 3578999987665432 33333322223332222 3444455555555678999999999999999999999963 3333
Q ss_pred HhhhHHhHHHHHhcCCcCHHHHHHHHhhhcccCCCCCCCCChHHHHHHHH---------Hhhhcc-CCCCCCCCCC--Cc
Q 001125 270 SALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSIL---------RDVFLA-NVPVHNNNFR--PK 337 (1149)
Q Consensus 270 ~~~l~~~l~~~~~~~i~t~~~al~yIg~~~r~~~~~~~~~~~~e~~~~~L---------~~~ll~-Hl~~~~~~~~--~K 337 (1149)
......++......++.|+++|+.|||++++.. ..+.. ..+.++.+| .+++|+ |++....+.. .|
T Consensus 81 ~~~~~~~~~~~~~~~~~t~~~al~~i~~~~~~~--~~~~~-~~~~~~~~l~~~y~l~~i~r~~l~~hl~~~~~~~~~~~k 157 (190)
T PF04561_consen 81 EDIEELMLSELEEEEIYTQEQALEYIGKKFRFR--QGKPP-KVEEARNFLQKRYDLGFIGRYKLNKHLGSDEPNENDRLK 157 (190)
T ss_dssp SCSTTTHHHHCCCTSSCSCHHHHHHHHHCCHSS--SSCHC-CHCHHHHHHTTCSSTCCCHHHCCHTTTTSSSSSSSSSCH
T ss_pred cccccccccccccccccccccceeEeccceeee--ccccc-chhhhhcccccccccccccccceeeeeeeeecccccccc
Confidence 333334455555678999999999999944433 12334 566777776 467777 9997755334 49
Q ss_pred cchHHHHHHHHHHhhcCCCCCCCcccccccEEc
Q 001125 338 CFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLE 370 (1149)
Q Consensus 338 ~~~L~~Mi~kLl~~~~g~~~~DD~D~l~NkRv~ 370 (1149)
+.+|++|++||+.++.|.+.+||+|||+||||+
T Consensus 158 ~~~l~~m~~~ll~~~~g~~~~Dd~D~l~NkRv~ 190 (190)
T PF04561_consen 158 AEDLGLMIRKLLKLANGECEPDDRDHLGNKRVR 190 (190)
T ss_dssp HHHHHHHHHHHHHHHTTSS-S-STTSCCCEEEE
T ss_pred hhhHHHHHHHHHHHhcCCCCCCCccccCCcCCc
Confidence 999999999999999999999999999999996
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=99.70 E-value=4.9e-17 Score=140.13 Aligned_cols=63 Identities=37% Similarity=0.757 Sum_probs=59.5
Q ss_pred EEECCeEEEeecChhhHHHHHHHHhhcCCcCceeEEEecccCceEEEecCCCeeeeeEEEeec
Q 001125 547 VIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADK 609 (1149)
Q Consensus 547 V~lnG~~iG~~~~~~~~~~~lr~~rr~g~i~~~v~i~~~~~~~~i~I~td~GRl~RPl~~v~~ 609 (1149)
|||||.|+|++++|..|+..||.+||+|.++.++||+++...++|+|+||+||++|||++|+|
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 799999999999999999999999999999999999999999999999999999999999875
No 22
>KOG0215 consensus RNA polymerase III, second largest subunit [Transcription]
Probab=99.07 E-value=6.9e-13 Score=156.76 Aligned_cols=537 Identities=8% Similarity=-0.100 Sum_probs=287.1
Q ss_pred cCCCcccccccccccccccccchHHHHHHHHHHHHHhCHHHHHHhcccceecC---CCcEEEEEeEEEEcCCccccCC-c
Q 001125 22 AAPVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGI---DPSIFLRFKDVRIGQPSMTVDG-V 97 (1149)
Q Consensus 22 ~~~~~~~~~~~~~i~~~~~~~~Lv~~qi~SFn~Fi~~gL~~ii~~~~~I~~~~---~~~~~l~~~~i~i~~P~~~e~~-~ 97 (1149)
++.-+.-.|.|-..|++.+..++++.||.+++.++..-...+ ||..+. .++-.+.=.++-|+ ..+.-- .
T Consensus 91 p~fylky~dirvg~Ps~~~~~~~~~~~i~p~ecrlrd~tysa-----~i~vdieytrg~~~~~~~~v~ig--rmpimlrs 163 (1153)
T KOG0215|consen 91 PSFYLKYLDIRVGKPSIEEGNNVTNDNITPHECRLRDMTYSA-----PIYVDIEYTRGRQIIAKRDVIIG--RMPIMLRS 163 (1153)
T ss_pred chhhheeeeeeccCcchhhccccccccCCchheeehhhhccc-----ceeEEEEEecCcceEEecccccc--cchhhhhc
Confidence 345556678888899999999999999999999986543322 332221 11111112233333 222111 3
Q ss_pred CCCCChhhHhhcCCccC-ccEEEEEEEEECCcccceeeEEeeEEeeccceeeccccccCCCCCHHHHHhcCCCCCCCCcE
Q 001125 98 SEKLNPHMCRLSDMTYA-APILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGY 176 (1149)
Q Consensus 98 ~~~l~P~EcR~r~lTYs-a~l~v~i~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~elv~~~E~~~d~GGY 176 (1149)
.+-+.|.+|+.+..-|. +| -.+--.-+..|.-|||+.+.-|.+++..++ -...|||+.+.++|
T Consensus 164 ~rcvl~~~~e~~~a~~~ecp---------------ldpggyfiv~G~ekViLiqeqlsknrii~~-~~k~~~~~~svtss 227 (1153)
T KOG0215|consen 164 SKCVLRGKDEEELARLNECP---------------LDPGGYFIVKGTEKVILIQEQLSKNRIIVE-EDKKGNLQASVTSS 227 (1153)
T ss_pred cccccCCccHHHHHHhccCC---------------CCCCceeEeccceeEEEehhhhhccCeeec-cccCCccccccccc
Confidence 45566777774433322 11 111122477899999999999999999887 67889999999999
Q ss_pred EEEcCchhhhHHhhhccCCeEEEEeCCCCcEEEEEEecCCCcceEEEEEeeCCEEEEEEceeeccccHHHHHHHhCCCCH
Q 001125 177 FIIKGTEKVLLIQEQLSKNRVIIDTDKKGNINASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESD 256 (1149)
Q Consensus 177 FIING~ERVI~~q~~~s~N~i~~~~~~~g~~~a~v~s~~~~~~s~~~~~~k~g~i~~r~~~~~~~IPi~ilLrALG~~sD 256 (1149)
|+..+++.+|.++....+++...+.+..+..++...+........+.. ...+..|.++.......|+.+-+.+.
T Consensus 228 t~e~kskt~v~~k~~k~ylk~~~~~d~ipiviv~ka~g~~sd~ei~~~-vg~~~~y~~~~~~s~ee~~~~~v~tq----- 301 (1153)
T KOG0215|consen 228 THERKSKTYVTTKKGKYYLKHNSFTDDIPIVIVLKAMGLESDQEIVQL-VGGDSKYQDIFAPSLEECVSLGVYTQ----- 301 (1153)
T ss_pred eeeecceEEEEeccceeeeehhhhhccCCEEEEEeeccccchHHHHHH-hhcchHHHHhhccchhhhhhhhhHHH-----
Confidence 999999999999987777665555444333222111111100000000 01122333322222234443333332
Q ss_pred HHHHHHhCCchhHHhhhHHhHHHHHhcCCcCHHHHHHHHhhhcccCCCCCCC----CChHHH--HHHHHHhhhccCCCCC
Q 001125 257 QEVVQMVGRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPP----NDREGR--AFSILRDVFLANVPVH 330 (1149)
Q Consensus 257 ~eI~~~i~~~~~~~~~l~~~l~~~~~~~i~t~~~al~yIg~~~r~~~~~~~~----~~~~e~--~~~~L~~~ll~Hl~~~ 330 (1149)
+.-+++++.. +.. .+ .....--++|++.+...+.+...-++- ...... .+.++.- +-|....
T Consensus 302 qqal~y~~~k------vk~-~~---~t~~~~~~e~~~~l~~~~lahv~v~~~~~r~K~~yi~~m~rr~~~a--~l~~~~~ 369 (1153)
T KOG0215|consen 302 QQALEYIGSK------VKV-KR---GTTPTKDEEALEVLSTTVLAHVPVPDLNFRMKAIYIGLMVRRVIQA--MLNKLAM 369 (1153)
T ss_pred HHHHHHhhhe------EEe-cc---CCCCCchHHHHHHHHhhheeceeccCCCCcceeehHHHHHHHHHHH--HhCcccc
Confidence 2223333100 000 00 001122356666666555443221111 101111 1222221 2233222
Q ss_pred CCCCCCccchHHHHHHHHHHhhcCCCCCCCcccccccEEccccHhHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcc
Q 001125 331 NNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDL 410 (1149)
Q Consensus 331 ~~~~~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~NkRv~l~G~Ll~~lfr~~l~~~~~~ik~~i~k~~~~~~~~~~~~~ 410 (1149)
++...-+-..|.+|.+. +.+..+.--.++.+.|++.+-...+.++..++-++++.+. ..++.+...+.+.....+.++
T Consensus 370 ddrd~~gnkrlelagql-lsllfeD~fk~~n~e~k~~~dk~l~k~~ra~~fD~~~~~n-~~~~~it~~l~ra~stgnw~i 447 (1153)
T KOG0215|consen 370 DDRDYVGNKRLELAGQL-LSLLFEDLFKRFNSELKKNIDKILKKPIRAQEFDALKHLN-VRANMITSGLERAISTGNWSI 447 (1153)
T ss_pred cchhhhccchHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHhcchhhhhhhHHHHHHH-HHHHHHHHHHHHHhhcCchHH
Confidence 22222333445555554 4455555566788889999988899888888888888875 333333322222111112222
Q ss_pred cccccccchHHHHHHHhccCCCcccccccccccceEEccccccccccccccccccccccccccCCCCccCCCCCcccccC
Q 001125 411 SQFIVRDSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPC 490 (1149)
Q Consensus 411 ~~~i~~~~It~~i~~~~sTGnw~~~~~~~q~sGvsq~l~rln~ls~LshlRrv~~~f~~~~k~t~~R~Lhps~wG~iCPv 490 (1149)
..+ +-.-++...--+-.|++|....+-+..++|.++..+..+-|.....-.+..++.+..+.+-.+-..+..|+-|||-
T Consensus 448 Krf-rmer~gvt~VlsrlSyisaLgmmtri~s~fektrkvsgprSlq~sqwgmlcp~dtpegeacglvknlalmthittd 526 (1153)
T KOG0215|consen 448 KRF-RMERAGVTQVLSRLSYISALGMMTRINSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITTD 526 (1153)
T ss_pred HHh-hhhhccceeeehhhhhhhhhhhheehhhhheeehhccCccccChhhcccccCCCCCCccccccccchHHHhcccCC
Confidence 221 1111122222233456665433334568899998877777777777777778888888888999999999999999
Q ss_pred CCCCCCcchhhhhccceeeeccCCCchhHHHHHhhcCceeccccCccccCCCCceEEEECCeEEEeecChhhHHHHHHHH
Q 001125 491 DTPEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKL 570 (1149)
Q Consensus 491 eTPEG~~cGLi~~LA~~a~Vt~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~lr~~ 570 (1149)
++|++.-|++.+..+...++..+....+.-.++.-++...+......+....+-..++.+|.+-++++.....++..+.+
T Consensus 527 ~ee~pi~~~~~k~gv~di~~v~~~e~~~~~~~~v~Lng~iig~~~~~~~~v~~~r~lrr~G~i~~fvsv~~~~~q~~v~i 606 (1153)
T KOG0215|consen 527 SEEKPILKLCYKLGVEDIHVVSGRELHTPDSFLVFLNGLIIGITRRPQYFVNSFRRLRRKGKIGEFVSVFTNTTQRCVYI 606 (1153)
T ss_pred CCcchhHHHHHHhcceeeeeecccccCCCceEEEEecceeeccccchHHHHHHHHHHHHcCcccceeeeeeeeeeEEEEE
Confidence 99999999999999999998775433333233333443333222211111112223566777766665433333333333
Q ss_pred hhcCCcCceeEEEecccCceEEEecCCCeeeeeE
Q 001125 571 RRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPL 604 (1149)
Q Consensus 571 rr~g~i~~~v~i~~~~~~~~i~I~td~GRl~RPl 604 (1149)
++.|-......|..+...+ +|-++.+|.++|-
T Consensus 607 ~sdggr~crp~Iiv~~~~~--~v~~~h~~el~~g 638 (1153)
T KOG0215|consen 607 ASDGGRVCRPLIIVDNGRP--RVKQHHMDELLDG 638 (1153)
T ss_pred ecCCCeEeeeEEEEeCCcc--hhhhhhHHHHHHh
Confidence 3333322222222222112 4555555655554
No 23
>KOG0214 consensus RNA polymerase II, second largest subunit [Transcription]
Probab=98.98 E-value=2.2e-11 Score=146.26 Aligned_cols=317 Identities=8% Similarity=-0.118 Sum_probs=211.2
Q ss_pred CCCCCcceEEEEEecCCCCCCCcEEeecccccccceeEEEEEEEEEEeecccCCccceecC--CCCCC-CchhhhccCCC
Q 001125 740 KLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILR--PDRTG-PGAERMQILDD 816 (1149)
Q Consensus 740 ~~p~G~N~iVAv~~~~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~~~~~~--p~~~~-~~~~~~~~Ld~ 816 (1149)
..+.+.+|-++.+.+.+++.++...-|--..+.+++++++...|. +.++. .+.... |.... ++...-...-.
T Consensus 734 l~~~eL~aG~NaiVAi~~~~GYNqEDsvimn~s~v~rg~FrS~~~---RsYk~--q~~~~~~~~ee~~~~~~~~~~~~mr 808 (1141)
T KOG0214|consen 734 LRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSVDRGLFRSFFI---RSYKD--QEHKKDQGPEEIFEEPPRGEGRGMR 808 (1141)
T ss_pred hhhhhcccccceEEEEecccCccHHHHHHHHhhhhhcchhhhhhh---hHHHh--hhhhccccccccccccccccccccc
Confidence 456799999999999999999999999999999999999865544 33321 111211 22211 11000000001
Q ss_pred CcccCCCceeCCCCEEEEEecCCCCCCCCCCCCCCCCcccccceeeecCCC-C-----CceEEEEEEEeeCCCCcEEEEE
Q 001125 817 DGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPD-G-----ETCVVDRVALCSDKNGDLCIKF 890 (1149)
Q Consensus 817 dGi~~~G~~v~~gd~l~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~-----~~~~v~~v~~~~~~~~~~~vkv 890 (1149)
+|...... ..|=+-.| +..... ..-..+.+++.-+..+ + -.+...++.+..++.| ...+|
T Consensus 809 ~~~~dkLd--ddG~i~~G--~~vs~~---------Dv~iGk~t~~~~~~~~~~~~~~~~t~~d~s~~Lr~~e~G-ivd~V 874 (1141)
T KOG0214|consen 809 NGKYDKLD--DDGIIMPG--SRVSGG---------DVLIGKTTPQPAKEDESGPEDRLYTKRDHSTKLRHTERG-IVDQV 874 (1141)
T ss_pred cccccccc--ccCCcccc--ceeecC---------CEEeccccCCcccchhccccccccccccceeecccCCcc-eEEEE
Confidence 11100000 00101011 000000 0000111111111111 0 0335566777766666 55555
Q ss_pred EEeeecCCCccccccccCCCccEEEeeeccCCCCCCCCCCCCcEEeCCCCCCCCchHHHHHHHhccccccccCceeeeee
Q 001125 891 LIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSA 970 (1149)
Q Consensus 891 ~~~~~R~p~iGDKf~sRhGqKGvvs~i~~~eDmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tp 970 (1149)
.++. .+.|+||+.+|++++-+.++-...++++-+-|+.++++.+++.-+++|+|--.+++-.-. .|
T Consensus 875 ~vt~---n~~G~kF~kv~vr~~ripqiGDKfasrHgqKG~ig~~~~qedmpft~eGi~pDiiiNPha-----------iP 940 (1141)
T KOG0214|consen 875 WVTK---NSEGPKFVKVRVRQVRIPQIGDKFASRHGQKGTIGITYRQEDMPFTIEGIVPDIIINPHA-----------IP 940 (1141)
T ss_pred EEec---CCCCCceeEEEEeecccccccchhccccccCccccceeecCCCCccccCCCcceEECccc-----------Cc
Confidence 5554 999999999999999999999999999999999999999999999999886444332211 11
Q ss_pred ccCCCCCCCCHHHHHHHHHHcCCCCCCceEEEeCCCCcEEeeeEeEeeeeecccccccCcccEEecccCcccccccCccc
Q 001125 971 FGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEG 1050 (1149)
Q Consensus 971 F~~~~~~~~~~~~~~~~l~~~g~~~~G~e~ly~G~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~G 1050 (1149)
= .-.+..+.+-|. |-..-++..++++.++.. -+-.+++..+++...|+..++.+++.+++....+++++++
T Consensus 941 S------Rmtig~liEc~l--gk~~a~~~e~~~atpFs~-v~v~~is~~l~~~g~~~~G~e~~ynGrtG~~~~~~if~Gp 1011 (1141)
T KOG0214|consen 941 S------RMTIGQLIECLL--GKVAAYEGEEGDATPFSD-VTVSKISANLHVYGYQYRGNERMYNGRTGRKLRAQIFIGP 1011 (1141)
T ss_pred c------ccchhhhHHHhh--hhhhhcccccccCCCCCc-cchhcccchHHHhccccCCCEEEecCCCCceeeeeeecCc
Confidence 1 122333333221 112223344566666655 4667889999999999999999999999999999999999
Q ss_pred ccCCCceeeechhhhHHHHcccHHHHHHhhccCCCceeeeecccCCcc
Q 001125 1051 RARNGGLRVGEMERDCLIAYGASMLIFERLMVSSDPFEVQVCRVCGLL 1098 (1149)
Q Consensus 1051 r~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~cg~~ 1098 (1149)
.-..++.+++||+++|=..++.+-+.++.+...|++...++|..|+..
T Consensus 1012 tyyqrL~Hmvd~kih~R~~Gp~q~ltRQP~~gRsr~GGlRfGEMErdc 1059 (1141)
T KOG0214|consen 1012 TYYQRLKHMVDDKIHSRARGPVQILTRQPVEGRSRDGGLRFGEMERDC 1059 (1141)
T ss_pred hHHHHHHHhhhheeeecccCCceeeeccccccccccCCeeeehhHHHH
Confidence 999999999999999999999999999999999999999999888754
No 24
>PF04567 RNA_pol_Rpb2_5: RNA polymerase Rpb2, domain 5; InterPro: IPR007647 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Domain 5, is also known as the external 2 domain [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3S17_B 1I6H_B 4A3B_B 3K1F_B 4A3I_B 1TWA_B 3S14_B 3S15_B 2NVX_B 3M3Y_B ....
Probab=98.83 E-value=1.6e-09 Score=88.68 Aligned_cols=41 Identities=46% Similarity=0.818 Sum_probs=33.3
Q ss_pred hhhhhccCceeEeccccccceEEEeecCCC-------CCCceeeeecC
Q 001125 629 FDDFLREGLIEYLDVNEENNALIALYEGDA-------TPDTTHIEIEP 669 (1149)
Q Consensus 629 ~~~l~~~g~iE~id~~Eq~~~~Ia~~~~~~-------~~~~th~Ei~P 669 (1149)
|++|+++|.|||||++||++++||++++++ ...||||||||
T Consensus 1 w~~ll~~G~vE~id~eEEe~~~Iam~~~dl~~~~~~~~~~~TH~EI~P 48 (48)
T PF04567_consen 1 WDDLLKEGVVEYIDAEEEETCMIAMSPEDLESTNEDITHTYTHCEIHP 48 (48)
T ss_dssp HHHHHHTTSEEEEETTTCTT--EESSCCCCCHSGGCCSST-SEEES-G
T ss_pred ChhHhhCCCEEEecchhccccEEEEecccccccCCCCCCccEEEeEeC
Confidence 788999999999999999999999998665 34699999998
No 25
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]
Probab=98.10 E-value=9.2e-06 Score=103.24 Aligned_cols=75 Identities=23% Similarity=0.368 Sum_probs=62.1
Q ss_pred CceeeeecCceeccccccccCCCCCCCCCccccccccccCCcccceeeeccccccceeeecCCCcceeechhhhhccCCC
Q 001125 661 DTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDK 740 (1149)
Q Consensus 661 ~~th~Ei~P~~ilsv~AslIPF~~hNqSpRn~yq~~M~KQa~G~~~~n~~~R~D~~~y~L~ypQ~PlV~t~~~~~~~~~~ 740 (1149)
..++|+++|.++.|+.+++|||.+|++++|++|+++|+|||+| |..+..|||.|+ ++...-.|
T Consensus 525 ~~~~~dv~~~~~~~~~~~~~P~l~~dd~~~~l~~~~mqr~~~~----------------l~~~~~~lv~tG-~E~~~a~e 587 (1060)
T COG0085 525 GVDYMDVSPKQVVSVGRSLIPFLEHDDANRALMGSNMQRQAVP----------------LLRTEAPLVGTG-MEYLDAED 587 (1060)
T ss_pred cccceeccceEEeccccccCceeEEcCchHhhhhhhhhhhccc----------------ccccccccccCC-ceeecccc
Confidence 4689999999999999999999999999999999999999999 567899999999 77654211
Q ss_pred CCCCcceEEEEEecC
Q 001125 741 LGAGQNATVAVMSYS 755 (1149)
Q Consensus 741 ~p~G~N~iVAv~~~~ 755 (1149)
--|++||.-++.
T Consensus 588 ---~~~~~ia~~~~~ 599 (1060)
T COG0085 588 ---SGAAVIAKRPGV 599 (1060)
T ss_pred ---ccceeEeccCCc
Confidence 235666665543
No 26
>PF06883 RNA_pol_Rpa2_4: RNA polymerase I, Rpa2 specific domain ; InterPro: IPR009674 This domain is found between domain 3 and domain 5, but shows no homology to domain 4 of Rpb2. The external domains in multisubunit RNA polymerase (those most distant from the active site) are known to demonstrate more sequence variability [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=97.54 E-value=0.0001 Score=62.88 Aligned_cols=49 Identities=18% Similarity=0.266 Sum_probs=41.4
Q ss_pred EEeec--ChhhHHHHHHHHhhcC--CcCceeEEEec-----ccCceEEEecCCCeeee
Q 001125 554 LGKHR--RPKCFADVMRKLRRAG--KIGEFVSVFVN-----EKQRCVYIASDGGRVCR 602 (1149)
Q Consensus 554 iG~~~--~~~~~~~~lr~~rr~g--~i~~~v~i~~~-----~~~~~i~I~td~GRl~R 602 (1149)
||+++ .++.+++.||.+|..| .+|.+++|.+. ..+|++||||+++|++|
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 46665 6799999999999888 68888898663 35799999999999998
No 27
>PHA03394 lef-8 DNA-directed RNA polymerase subunit beta-like protein; Provisional
Probab=95.78 E-value=0.025 Score=69.85 Aligned_cols=124 Identities=21% Similarity=0.260 Sum_probs=81.7
Q ss_pred CcEEEEEEEeeecCCCccccccccCCCccEEEeeeccCCCC-C-CCCCCCCcEEeCCCCCCCCchHHHHHHHhccccccc
Q 001125 884 GDLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFP-F-SERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVS 961 (1149)
Q Consensus 884 ~~~~vkv~~~~~R~p~iGDKf~sRhGqKGvvs~i~~~eDmP-f-~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~ 961 (1149)
+...+|+++-..=.=-.|=|.||=||||||+. ..||+- | .|||+.|-|.++|.+|-||.|. ++-+--|-...
T Consensus 694 d~v~lKl~~Vtst~dLeGlKICgIHGQKGVln---~seDLtew~aeDg~~aQIclSPiSyLsRQtn---f~~~~~Ky~v~ 767 (865)
T PHA03394 694 DTVYLKIRLVTSTSDLEGLKICGIHGQKGVLN---GSEDLTEWMAEDGTHAQICLSPISYLSRQTN---FDDIERKYVVR 767 (865)
T ss_pred CEEEEEEEEEEEecCcceeEEeeecccccccC---CcchhhhhhccCCCcceEEechHHhhccccc---cccCceEEEEE
Confidence 34566666555555567999999999999986 456664 2 4789999999999999999986 34444455555
Q ss_pred cCceeee---------eeccCCCCCCCCHHHHHHHHHHcCCCCCCceEEEeCCCCcEEeeeEeEee
Q 001125 962 CGRFHYG---------SAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGP 1018 (1149)
Q Consensus 962 ~g~~~d~---------tpF~~~~~~~~~~~~~~~~l~~~g~~~~G~e~ly~G~tG~~~~~~if~G~ 1018 (1149)
.|.+.|. +|+.+- ..+.+++.++.. |-++.|-|.+=--|.-++--...|+|.
T Consensus 768 gg~~~~~~~~rypi~~IPYm~F---nnTPDnI~kEf~--~~n~TG~EKvEGTRlDqwTINqsF~gN 828 (865)
T PHA03394 768 GGDHSDPNAKRYPIFNIPYMLF---NNTPDNIYKEFI--KKNYTGHEKVEGTRLDQWTINQSFVGN 828 (865)
T ss_pred CCCcCCCCCcccceEecceehh---cCCchHHHHHHh--ccCCcceeecceeeccceeEcceeccc
Confidence 4544432 455532 355666766653 346678776544444444445666664
No 28
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=52.96 E-value=8.7 Score=38.47 Aligned_cols=28 Identities=21% Similarity=0.455 Sum_probs=22.2
Q ss_pred eeecccCCcceeecccccceecccccCCCc
Q 001125 1089 VQVCRVCGLLGYYNHKLKAGICSTCKNGDN 1118 (1149)
Q Consensus 1089 ~~vC~~cg~~~~~~~~~~~~~C~~c~~~~~ 1118 (1149)
+.-|+.||..++. +.+..+|+.|.....
T Consensus 28 ~~hCp~Cg~PLF~--KdG~v~CPvC~~~~~ 55 (131)
T COG1645 28 AKHCPKCGTPLFR--KDGEVFCPVCGYREV 55 (131)
T ss_pred HhhCcccCCccee--eCCeEECCCCCceEE
Confidence 4459999999998 677788999985333
No 29
>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=51.06 E-value=23 Score=44.53 Aligned_cols=35 Identities=17% Similarity=0.187 Sum_probs=28.6
Q ss_pred CCCCcccccccEEccccHhHHHHHHHHHHHHHHHH
Q 001125 357 AMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEV 391 (1149)
Q Consensus 357 ~~DD~D~l~NkRv~l~G~Ll~~lfr~~l~~~~~~i 391 (1149)
..=.+|+|+||=+--...|+...++..++.+...+
T Consensus 209 i~Y~IDsLsNKiIYkh~yLl~l~y~~~L~~~~~~~ 243 (748)
T PF04941_consen 209 INYSIDSLSNKIIYKHSYLLELTYKPILKKYENLI 243 (748)
T ss_pred CCceecccccceeeCHHHHHHHHHHHHHHHHHHHH
Confidence 34479999999999999999999988777666544
No 30
>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=43.90 E-value=15 Score=32.61 Aligned_cols=48 Identities=19% Similarity=0.382 Sum_probs=27.8
Q ss_pred eeeecccCCcceeecccccceecccccCCCcccccccc------HhHHHHHHHHHh
Q 001125 1088 EVQVCRVCGLLGYYNHKLKAGICSTCKNGDNISSMKLP------YACKLLIQELQS 1137 (1149)
Q Consensus 1088 ~~~vC~~cg~~~~~~~~~~~~~C~~c~~~~~~~~v~iP------y~~k~l~~EL~s 1137 (1149)
.+.-| .||..+|.+....+.-| .|+..-+|.+..|= .-..-++++||.
T Consensus 2 lifrC-~Cgr~lya~e~~kTkkC-~CG~~l~vk~~rIl~~~~~~~eA~eiVrklQ~ 55 (68)
T PF09082_consen 2 LIFRC-DCGRYLYAKEGAKTKKC-VCGKTLKVKERRILARAENAEEASEIVRKLQE 55 (68)
T ss_dssp EEEEE-TTS--EEEETT-SEEEE-TTTEEEE--SSS-BS--SSHHHHHHHHHHHSS
T ss_pred EEEEe-cCCCEEEecCCcceeEe-cCCCeeeeeeEEEEEecCCHHHHHHHHHHHHH
Confidence 35569 79999998776667779 99987666665542 223445555553
No 31
>PF14251 DUF4346: Domain of unknown function (DUF4346)
Probab=41.56 E-value=13 Score=36.36 Aligned_cols=14 Identities=57% Similarity=0.890 Sum_probs=11.0
Q ss_pred CCCCCCCCcEEEEc
Q 001125 167 GECPLDPGGYFIIK 180 (1149)
Q Consensus 167 ~E~~~d~GGYFIIN 180 (1149)
.--..||+|||||.
T Consensus 10 R~i~LDp~GYfiI~ 23 (119)
T PF14251_consen 10 RFIDLDPAGYFIIY 23 (119)
T ss_pred CccccCCCccEEEE
Confidence 34467999999996
No 32
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=38.22 E-value=28 Score=28.30 Aligned_cols=27 Identities=19% Similarity=0.257 Sum_probs=19.0
Q ss_pred eeecccCCcceeecccccceecccccC
Q 001125 1089 VQVCRVCGLLGYYNHKLKAGICSTCKN 1115 (1149)
Q Consensus 1089 ~~vC~~cg~~~~~~~~~~~~~C~~c~~ 1115 (1149)
.+.|.+||.............|+.|+.
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~ 29 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGY 29 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCC
Confidence 468999998765543333456999975
No 33
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=36.10 E-value=23 Score=36.11 Aligned_cols=37 Identities=16% Similarity=0.456 Sum_probs=26.1
Q ss_pred CceeeeecccCCcceeecccccceecccccCCCcccccccc
Q 001125 1085 DPFEVQVCRVCGLLGYYNHKLKAGICSTCKNGDNISSMKLP 1125 (1149)
Q Consensus 1085 D~~~~~vC~~cg~~~~~~~~~~~~~C~~c~~~~~~~~v~iP 1125 (1149)
-+..+..|.+||...+.. ..+|+.|.+..++..+.+|
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 455677899999987762 3679999987554444443
No 34
>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=34.33 E-value=20 Score=35.00 Aligned_cols=31 Identities=19% Similarity=0.357 Sum_probs=21.5
Q ss_pred eeeecccCCcceeecccccceecccccCCCcc
Q 001125 1088 EVQVCRVCGLLGYYNHKLKAGICSTCKNGDNI 1119 (1149)
Q Consensus 1088 ~~~vC~~cg~~~~~~~~~~~~~C~~c~~~~~~ 1119 (1149)
.-|+|..||...|-= ++.-.+|+.|+..-.+
T Consensus 8 tKR~Cp~CG~kFYDL-nk~PivCP~CG~~~~~ 38 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDL-NKDPIVCPKCGTEFPP 38 (108)
T ss_pred CcccCCCCcchhccC-CCCCccCCCCCCccCc
Confidence 457999999988852 2233559999875443
No 35
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=33.80 E-value=24 Score=37.45 Aligned_cols=45 Identities=13% Similarity=0.168 Sum_probs=31.4
Q ss_pred cccHHHHHHhhccCCCceeeeecccCCcceee-cccccceecccccC
Q 001125 1070 YGASMLIFERLMVSSDPFEVQVCRVCGLLGYY-NHKLKAGICSTCKN 1115 (1149)
Q Consensus 1070 ~Gas~~l~erl~~~SD~~~~~vC~~cg~~~~~-~~~~~~~~C~~c~~ 1115 (1149)
|-...-|+++|-..++. ..++|++||..... .+....+.|+.|+.
T Consensus 99 ~~~~~klk~~l~~e~~~-~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~ 144 (178)
T PRK06266 99 MEELKKLKEQLEEEENN-MFFFCPNCHIRFTFDEAMEYGFRCPQCGE 144 (178)
T ss_pred HHHHHHHHHHhhhccCC-CEEECCCCCcEEeHHHHhhcCCcCCCCCC
Confidence 45567788988777765 67899999976442 22233466999975
No 36
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=33.78 E-value=19 Score=31.07 Aligned_cols=32 Identities=25% Similarity=0.464 Sum_probs=19.4
Q ss_pred CCceeeeecccCCcceeecccccceecccccC
Q 001125 1084 SDPFEVQVCRVCGLLGYYNHKLKAGICSTCKN 1115 (1149)
Q Consensus 1084 SD~~~~~vC~~cg~~~~~~~~~~~~~C~~c~~ 1115 (1149)
++.....+|..||..+....+...+.|+.|+.
T Consensus 2 ~~~~~~~~CtSCg~~i~~~~~~~~F~CPnCG~ 33 (59)
T PRK14890 2 SEMMEPPKCTSCGIEIAPREKAVKFLCPNCGE 33 (59)
T ss_pred cccccCccccCCCCcccCCCccCEeeCCCCCC
Confidence 34455667888887766533333455777754
No 37
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=33.29 E-value=27 Score=26.96 Aligned_cols=26 Identities=31% Similarity=0.626 Sum_probs=16.9
Q ss_pred eecccCCcceeecccccc-eecccccC
Q 001125 1090 QVCRVCGLLGYYNHKLKA-GICSTCKN 1115 (1149)
Q Consensus 1090 ~vC~~cg~~~~~~~~~~~-~~C~~c~~ 1115 (1149)
.-|..||.+++....... ..|+.|.-
T Consensus 2 ~FCp~C~nlL~p~~~~~~~~~C~~C~Y 28 (35)
T PF02150_consen 2 RFCPECGNLLYPKEDKEKRVACRTCGY 28 (35)
T ss_dssp -BETTTTSBEEEEEETTTTEEESSSS-
T ss_pred eeCCCCCccceEcCCCccCcCCCCCCC
Confidence 359999999986333222 26999964
No 38
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=33.04 E-value=25 Score=28.99 Aligned_cols=25 Identities=20% Similarity=0.495 Sum_probs=16.3
Q ss_pred ecccCCcceeecccc--cceecccccC
Q 001125 1091 VCRVCGLLGYYNHKL--KAGICSTCKN 1115 (1149)
Q Consensus 1091 vC~~cg~~~~~~~~~--~~~~C~~c~~ 1115 (1149)
.|+.||.+++..... ...+|+.|+-
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~ 28 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGY 28 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCC
Confidence 488888888763322 2455888874
No 39
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=31.54 E-value=28 Score=36.99 Aligned_cols=35 Identities=20% Similarity=0.304 Sum_probs=26.2
Q ss_pred eecccCCcceeecccccceecccccCCCccccccccHh
Q 001125 1090 QVCRVCGLLGYYNHKLKAGICSTCKNGDNISSMKLPYA 1127 (1149)
Q Consensus 1090 ~vC~~cg~~~~~~~~~~~~~C~~c~~~~~~~~v~iPy~ 1127 (1149)
-.|++||..+.. ......|+.|++ ....|+..||-
T Consensus 150 A~CsrC~~~L~~--~~~~l~Cp~Cg~-tEkRKia~~y~ 184 (188)
T COG1096 150 ARCSRCRAPLVK--KGNMLKCPNCGN-TEKRKIAKDYG 184 (188)
T ss_pred EEccCCCcceEE--cCcEEECCCCCC-EEeeeeccccc
Confidence 369999988765 334467999987 66778888873
No 40
>PRK00420 hypothetical protein; Validated
Probab=30.90 E-value=30 Score=33.95 Aligned_cols=25 Identities=28% Similarity=0.488 Sum_probs=19.4
Q ss_pred eecccCCcceeecccccceecccccC
Q 001125 1090 QVCRVCGLLGYYNHKLKAGICSTCKN 1115 (1149)
Q Consensus 1090 ~vC~~cg~~~~~~~~~~~~~C~~c~~ 1115 (1149)
..|+.||..++.. +.+..+|+.|+.
T Consensus 24 ~~CP~Cg~pLf~l-k~g~~~Cp~Cg~ 48 (112)
T PRK00420 24 KHCPVCGLPLFEL-KDGEVVCPVHGK 48 (112)
T ss_pred CCCCCCCCcceec-CCCceECCCCCC
Confidence 5699999988762 455678999986
No 41
>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=30.57 E-value=31 Score=24.43 Aligned_cols=23 Identities=22% Similarity=0.417 Sum_probs=14.3
Q ss_pred cccCCcceeecccccceeccccc
Q 001125 1092 CRVCGLLGYYNHKLKAGICSTCK 1114 (1149)
Q Consensus 1092 C~~cg~~~~~~~~~~~~~C~~c~ 1114 (1149)
|..||..+........+.|+.|+
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCG 23 (24)
T ss_pred CccCCCcccCcccCceEeCCCCC
Confidence 67787766653333345588885
No 42
>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=30.33 E-value=37 Score=27.27 Aligned_cols=24 Identities=25% Similarity=0.429 Sum_probs=18.3
Q ss_pred eecccCCcceeecccccceeccccc
Q 001125 1090 QVCRVCGLLGYYNHKLKAGICSTCK 1114 (1149)
Q Consensus 1090 ~vC~~cg~~~~~~~~~~~~~C~~c~ 1114 (1149)
..|..||.++.. .+.+..+|..|.
T Consensus 18 ~~Cp~C~~PL~~-~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 18 EHCPDCGTPLMR-DKDGKIYCVSCG 41 (41)
T ss_pred CccCCCCCeeEE-ecCCCEECCCCC
Confidence 359999999887 345567899984
No 43
>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=25.71 E-value=48 Score=25.36 Aligned_cols=26 Identities=31% Similarity=0.588 Sum_probs=17.4
Q ss_pred eeecccCCcceeecccccceecccccCC
Q 001125 1089 VQVCRVCGLLGYYNHKLKAGICSTCKNG 1116 (1149)
Q Consensus 1089 ~~vC~~cg~~~~~~~~~~~~~C~~c~~~ 1116 (1149)
.++|..||-+.... ..-..|+.|+..
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 58999999764431 112369999864
No 44
>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=24.88 E-value=41 Score=33.56 Aligned_cols=28 Identities=11% Similarity=0.158 Sum_probs=20.5
Q ss_pred eeeecccCCcceeecccccceecccccCC
Q 001125 1088 EVQVCRVCGLLGYYNHKLKAGICSTCKNG 1116 (1149)
Q Consensus 1088 ~~~vC~~cg~~~~~~~~~~~~~C~~c~~~ 1116 (1149)
.-|+|.+||...|- ..+.-.+|+.|+..
T Consensus 8 tKr~Cp~cg~kFYD-Lnk~p~vcP~cg~~ 35 (129)
T TIGR02300 8 TKRICPNTGSKFYD-LNRRPAVSPYTGEQ 35 (129)
T ss_pred ccccCCCcCccccc-cCCCCccCCCcCCc
Confidence 45799999998885 22234569999864
No 45
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=24.65 E-value=56 Score=28.07 Aligned_cols=24 Identities=25% Similarity=0.757 Sum_probs=18.0
Q ss_pred eeeecccCCcceeecccccceecccccCCC
Q 001125 1088 EVQVCRVCGLLGYYNHKLKAGICSTCKNGD 1117 (1149)
Q Consensus 1088 ~~~vC~~cg~~~~~~~~~~~~~C~~c~~~~ 1117 (1149)
..++|.+||..... ..|+.|+...
T Consensus 4 ~mr~C~~CgvYTLk------~~CP~CG~~t 27 (56)
T PRK13130 4 KIRKCPKCGVYTLK------EICPVCGGKT 27 (56)
T ss_pred cceECCCCCCEEcc------ccCcCCCCCC
Confidence 46789999976543 6799998753
No 46
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=24.21 E-value=33 Score=24.50 Aligned_cols=22 Identities=27% Similarity=0.554 Sum_probs=15.3
Q ss_pred eecccCCcceeecccccceecccccC
Q 001125 1090 QVCRVCGLLGYYNHKLKAGICSTCKN 1115 (1149)
Q Consensus 1090 ~vC~~cg~~~~~~~~~~~~~C~~c~~ 1115 (1149)
..|.+||..... ...+|+.|+.
T Consensus 3 ~~Cp~Cg~~~~~----~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDP----DAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCc----ccccChhhCC
Confidence 469999985333 2467999975
No 47
>PF13533 Biotin_lipoyl_2: Biotin-lipoyl like
Probab=24.13 E-value=55 Score=27.10 Aligned_cols=16 Identities=25% Similarity=0.426 Sum_probs=14.2
Q ss_pred ccCCCceeCCCCEEEE
Q 001125 819 LAAPGEIIKPNDVYIN 834 (1149)
Q Consensus 819 i~~~G~~v~~gd~l~~ 834 (1149)
.++.|+.|++||+|+-
T Consensus 17 ~V~~G~~VkkGd~L~~ 32 (50)
T PF13533_consen 17 YVKEGQQVKKGDVLLV 32 (50)
T ss_pred EecCCCEEcCCCEEEE
Confidence 5788999999999975
No 48
>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=23.19 E-value=64 Score=25.81 Aligned_cols=24 Identities=21% Similarity=0.616 Sum_probs=14.8
Q ss_pred ecccCCcce-eecccccceeccccc
Q 001125 1091 VCRVCGLLG-YYNHKLKAGICSTCK 1114 (1149)
Q Consensus 1091 vC~~cg~~~-~~~~~~~~~~C~~c~ 1114 (1149)
+|+.||+-. ..+..+...+|+.|+
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG 26 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCG 26 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-
T ss_pred CCcCCcCCceEEcCCCCeEECCCCC
Confidence 588888754 333445556788885
No 49
>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=22.85 E-value=60 Score=33.45 Aligned_cols=26 Identities=27% Similarity=0.551 Sum_probs=16.4
Q ss_pred eecccCCcceeecccccceecccccC
Q 001125 1090 QVCRVCGLLGYYNHKLKAGICSTCKN 1115 (1149)
Q Consensus 1090 ~vC~~cg~~~~~~~~~~~~~C~~c~~ 1115 (1149)
.||.+||............-|+.|+.
T Consensus 113 l~C~~Cg~~~~~~~~~~l~~Cp~C~~ 138 (146)
T PF07295_consen 113 LVCENCGHEVELTHPERLPPCPKCGH 138 (146)
T ss_pred EecccCCCEEEecCCCcCCCCCCCCC
Confidence 47888887665433334455888865
No 50
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=22.71 E-value=51 Score=37.41 Aligned_cols=12 Identities=17% Similarity=0.135 Sum_probs=8.7
Q ss_pred CCcEEEEcCchh
Q 001125 173 PGGYFIIKGTEK 184 (1149)
Q Consensus 173 ~GGYFIING~ER 184 (1149)
.|.|+|....++
T Consensus 77 ~G~~~~~~~~~~ 88 (273)
T COG0266 77 SGSLRLEARGEP 88 (273)
T ss_pred ceEEEEecCCCC
Confidence 488888885555
No 51
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=20.93 E-value=77 Score=36.74 Aligned_cols=16 Identities=13% Similarity=-0.062 Sum_probs=9.9
Q ss_pred CHHHHHHHHhhhcccC
Q 001125 287 TQEKALEYLEGKVKRS 302 (1149)
Q Consensus 287 t~~~al~yIg~~~r~~ 302 (1149)
++-|+---||+.||.+
T Consensus 67 ~t~e~~ltLGnLfRsR 82 (389)
T COG2956 67 ETFEAHLTLGNLFRSR 82 (389)
T ss_pred hhhHHHHHHHHHHHhc
Confidence 3445555677777765
No 52
>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=20.82 E-value=55 Score=34.13 Aligned_cols=45 Identities=11% Similarity=0.127 Sum_probs=29.8
Q ss_pred cccHHHHHHhhccCCCceeeeecccCCcceee-cccccceecccccC
Q 001125 1070 YGASMLIFERLMVSSDPFEVQVCRVCGLLGYY-NHKLKAGICSTCKN 1115 (1149)
Q Consensus 1070 ~Gas~~l~erl~~~SD~~~~~vC~~cg~~~~~-~~~~~~~~C~~c~~ 1115 (1149)
|....-|+++|-.-++. ..++|++|+..... .+....+.|+.|+.
T Consensus 91 ~~~~~~lk~~l~~e~~~-~~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~ 136 (158)
T TIGR00373 91 EETAKKLREKLEFETNN-MFFICPNMCVRFTFNEAMELNFTCPRCGA 136 (158)
T ss_pred HHHHHHHHHHHhhccCC-CeEECCCCCcEeeHHHHHHcCCcCCCCCC
Confidence 45666788888665553 57899999965442 22223466999975
No 53
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=20.66 E-value=70 Score=33.62 Aligned_cols=24 Identities=33% Similarity=0.661 Sum_probs=16.9
Q ss_pred eeecccCCcceeecccccceecccccC
Q 001125 1089 VQVCRVCGLLGYYNHKLKAGICSTCKN 1115 (1149)
Q Consensus 1089 ~~vC~~cg~~~~~~~~~~~~~C~~c~~ 1115 (1149)
+|||..||-+... ..-..|+.|+.
T Consensus 134 ~~vC~vCGy~~~g---e~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYTHEG---EAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCCcccC---CCCCcCCCCCC
Confidence 8999999976543 11235999974
No 54
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=20.34 E-value=66 Score=26.89 Aligned_cols=28 Identities=18% Similarity=0.354 Sum_probs=19.2
Q ss_pred eeeecccCCcceeecccccceecccccC
Q 001125 1088 EVQVCRVCGLLGYYNHKLKAGICSTCKN 1115 (1149)
Q Consensus 1088 ~~~vC~~cg~~~~~~~~~~~~~C~~c~~ 1115 (1149)
..++|..||.............|+.|+.
T Consensus 5 ~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 5 MEYKCARCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred EEEEhhhcCCeeehhhccCceeCCCCCc
Confidence 4689999998874322333445999975
Done!