Query 001532
Match_columns 1058
No_of_seqs 172 out of 1543
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 03:12:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001532.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001532hhsearch_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 3E-245 6E-250 2295.6 88.2 999 31-1057 1-1010(1103)
2 KOG0214 RNA polymerase II, sec 100.0 3E-236 7E-241 2014.0 50.6 1013 28-1057 2-1050(1141)
3 KOG0215 RNA polymerase III, se 100.0 9E-234 2E-238 1968.2 49.8 1042 2-1057 16-1065(1153)
4 KOG0216 RNA polymerase I, seco 100.0 3E-231 6E-236 1957.0 61.3 966 30-1057 4-1014(1111)
5 COG0085 RpoB DNA-directed RNA 100.0 2E-216 4E-221 1941.6 66.2 943 27-1057 10-983 (1060)
6 TIGR02013 rpoB DNA-directed RN 100.0 4E-198 9E-203 1839.4 72.7 848 28-1057 4-994 (1065)
7 cd00653 RNA_pol_B_RPB2 RNA pol 100.0 9E-197 2E-201 1821.2 70.8 774 44-1057 1-784 (866)
8 PRK00405 rpoB DNA-directed RNA 100.0 5E-194 1E-198 1812.1 73.8 848 28-1057 11-1034(1112)
9 CHL00001 rpoB RNA polymerase b 100.0 1E-191 3E-196 1770.7 72.1 866 39-1057 10-983 (1070)
10 CHL00207 rpoB RNA polymerase b 100.0 1E-174 3E-179 1608.6 72.8 857 38-1057 4-979 (1077)
11 PRK09603 bifunctional DNA-dire 100.0 1E-163 3E-168 1554.0 68.0 875 28-1057 11-1300(2890)
12 PRK14844 bifunctional DNA-dire 100.0 1E-160 2E-165 1522.3 64.8 881 27-1057 14-1358(2836)
13 PRK07225 DNA-directed RNA poly 100.0 1E-149 2E-154 1330.8 44.3 506 544-1057 4-512 (605)
14 TIGR03670 rpoB_arch DNA-direct 100.0 2E-149 4E-154 1327.1 42.0 503 547-1057 1-506 (599)
15 PF00562 RNA_pol_Rpb2_6: RNA p 100.0 9E-110 2E-114 956.3 19.4 367 674-1053 1-386 (386)
16 PRK09606 DNA-directed RNA poly 100.0 3E-106 7E-111 955.9 45.2 486 28-531 2-492 (494)
17 PF04563 RNA_pol_Rpb2_1: RNA p 100.0 2E-44 4.4E-49 382.1 18.9 147 43-192 1-149 (203)
18 PF04565 RNA_pol_Rpb2_3: RNA p 99.9 2.9E-26 6.3E-31 198.9 2.5 66 446-511 1-68 (68)
19 PF04561 RNA_pol_Rpb2_2: RNA p 99.8 2.8E-21 6E-26 202.7 10.6 174 194-370 2-190 (190)
20 PF04566 RNA_pol_Rpb2_4: RNA p 99.7 5E-17 1.1E-21 138.5 8.6 63 547-609 1-63 (63)
21 PF04567 RNA_pol_Rpb2_5: RNA p 98.8 3.9E-09 8.6E-14 85.4 2.6 41 629-669 1-48 (48)
22 KOG0215 RNA polymerase III, se 98.7 7.7E-11 1.7E-15 138.6 -10.6 447 24-513 93-549 (1153)
23 COG0085 RpoB DNA-directed RNA 97.6 0.00017 3.6E-09 91.3 9.4 74 661-754 525-598 (1060)
24 KOG0214 RNA polymerase II, sec 97.5 1.7E-05 3.7E-10 95.9 -1.5 299 717-1055 698-1016(1141)
25 PF06883 RNA_pol_Rpa2_4: RNA p 97.4 0.00015 3.4E-09 61.0 4.2 49 554-602 1-58 (58)
26 PHA03394 lef-8 DNA-directed RN 95.9 0.021 4.6E-07 69.8 8.3 138 870-1018 679-828 (865)
27 PF04941 LEF-8: Late expressio 59.0 15 0.00032 45.5 5.6 34 358-391 210-243 (748)
28 PF14251 DUF4346: Domain of un 42.0 13 0.00028 36.0 1.2 14 167-180 10-23 (119)
29 PF13533 Biotin_lipoyl_2: Biot 24.7 53 0.0011 26.8 1.9 16 819-834 17-32 (50)
30 PRK09603 bifunctional DNA-dire 21.5 2.7E+02 0.0059 40.7 8.6 106 596-735 597-721 (2890)
31 PRK14844 bifunctional DNA-dire 20.7 2.3E+02 0.0051 41.2 7.8 105 596-736 604-729 (2836)
No 1
>PRK08565 DNA-directed RNA polymerase subunit B; Provisional
Probab=100.00 E-value=2.8e-245 Score=2295.61 Aligned_cols=999 Identities=40% Similarity=0.680 Sum_probs=912.5
Q ss_pred ccccccccccccchHHHHHHHHHHHHHhCHHHHHHhcCcceecCCCcEEEEEeEEEEcCCccccCC-ccCCCChhhHhhc
Q 001532 31 KFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDG-VSEKLNPHMCRLS 109 (1058)
Q Consensus 31 ~~~~i~~~f~~~~Lv~~qi~SFn~Fl~~gl~~i~~~~~~i~~~~~~~~~l~~~~i~i~~P~~~~~~-~~~~l~P~EcR~r 109 (1058)
.|.++++||+.++|++||+||||+|+++||++++++++||+.. ++++.|+|++++|++|.+.+++ ...+|+|+|||+|
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 4999999999999999999999999999999999999999765 6789999999999999997654 5678999999999
Q ss_pred CCccCceEEEEEEEEECCCccceeeEEeEEEEeeeccccccccccCCCCCHHHHHhcCCCCCCCCcEEEEcCceeEEeee
Q 001532 110 DMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQ 189 (1058)
Q Consensus 110 ~lTYsa~l~v~v~~~~~~~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~ls~~elv~~gE~~~d~GGYFIING~EKVI~~q 189 (1058)
++||+|+|+|++++..++ ..+++++|++|+|||||+|++|||++++|+||++.||||.|+||||||||+|||||+|
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 999999999999998654 4455668999999999999999999999999999999999999999999999999999
Q ss_pred ecccCCEEEEEeCCCC---cEEEEEEecCCCc-ceEEEEEeeCCEEEEEEcceeccccHhhHHHHhCCCCHHHHHHHhCC
Q 001532 190 EQLSKNRVIIDTDKKG---NINASVTSSTETV-KSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGR 265 (1058)
Q Consensus 190 ~~~~~N~i~~~~~~~g---~~~~~v~s~~~~~-~s~~~~~~~~g~i~~~~~~~~~~IPl~ilLkALg~~sd~eI~~~i~~ 265 (1058)
|++++|+++++.+.++ .+.|.++|..... .+..+++..+|.++++++++.++||+++||||||..||+||++.++.
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 9999999998765443 3678888877644 34444455678999999987678999999999999999999999976
Q ss_pred chhHHhhhhhhHHHHHhcCC-cCHHHHHHHHhhcccccCCCCCCCChHHHHHHHHHhhhccCCCCCCCCCCCcchhHHHH
Q 001532 266 DPRYSALLLPSIEECANLDI-YTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLANVPVHNNNFRPKCFYVAVM 344 (1058)
Q Consensus 266 ~~~~~~~l~~~l~~~~~~~i-~t~~~al~yig~~~~~~~~~~~~~~~~e~~~~~L~~~llpHl~~~~~~~~~K~~~L~~M 344 (1058)
+..+.+.+..+++++. .+ .|+++|+.|||++|++. .++.. ..+.|+++|++++|||++.+..++.+|+.+|++|
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 6666777777777653 25 79999999999999875 33444 6789999999999999998765567899999999
Q ss_pred HHHHHHhhcCCCCCCCcccccceEEcchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCCCCccccccccccchhhhh
Q 001532 345 LRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLE 424 (1058)
Q Consensus 345 i~kLl~~~~G~~~~DD~D~l~NkRV~~~G~Ll~~lfr~~l~~~~~~ik~~i~k~~~~~~~~~~~~~~~~i~~~~It~~i~ 424 (1058)
++||++++.|.+.+||+|||+||||+++|+||+.+||++|+++++.+|+++.+.+.+. ..+++..+++++.||++|+
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 2456667778889999999
Q ss_pred hhhccCCCcccccccccccceEEcccccccccccccccccccccccccccCCCcCCCCCccccccCCCCCCCcccccccc
Q 001532 425 RTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNL 504 (1058)
Q Consensus 425 ~~~sTGn~~~~~~~~q~sG~sq~l~rln~ls~lshlRrv~~~~~~~~k~t~~R~Lhps~wG~iCPveTPEG~~cGLi~~L 504 (1058)
+|||||||.. |++|+||+|+|+||+|+||||||+++++.+++|.++||+||||||||+||||||||++|||++||
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 cceeeeecCCCChhHHHHHhhcCCeeccccCccccCCCCcEEEEECCeEEeeccChhhHHHHHHHHhhcCCcCceeEEEe
Q 001532 505 ALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFV 584 (1058)
Q Consensus 505 A~~a~Is~~~~~~~i~~~l~~~g~~~l~~~~~~~~~~~~~~~V~lnG~~vG~~~~~~~~~~~lr~~rr~~~i~~~v~i~~ 584 (1058)
|++|+|+++.+.+++.++|.++|+.++..+++... ...++|||||+|||++++|..|++.||.+||.|.++.+++|++
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 2568999999999999999999999999999999999999999
Q ss_pred cc--ccceEEEecCCCeeeeeEEEEecCcccchhhhHHHhhcCCccchhhhccCceeEeccccccceEEEeecCCCCCCc
Q 001532 585 NE--KQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDT 662 (1058)
Q Consensus 585 ~~--~~~~i~I~sd~GRl~RPll~v~~~~~~~~~~~~~~l~~~~~s~~~~~~~~~iE~id~~e~~~~~Ia~~~~~~~~~~ 662 (1058)
+. ..++|+|+||+||++|||++|++|++.+++++++.++.+..+|+||+++|.+||||++||++++||+.++++...+
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 8899999999999999999999999999999999988788899999999999999999999999999999987778
Q ss_pred eeeeecCccccccccccCCCCCCCCCCccccccccccCCccceeEeeeeccccceeeeeCCCcceeechhhhhhcCCCCC
Q 001532 663 THIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDKLG 742 (1058)
Q Consensus 663 th~Ei~p~~~ls~~asliPF~~hNqspRn~yq~~M~KQaiG~~~~n~~~R~D~~~y~l~ypQ~Plv~t~~~~~~~~~~~~ 742 (1058)
||+||+|+++||++||+|||+||||||||||||||+|||||++++|+..|+|++.|+|+|||+|||+|+.++.++++++|
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 CCcceEEEEeecCCCCCCCcEEEecceeeccceEEEEEEEEEEEeecccCCccceecCCCCCC---CcccccccCCCCcc
Q 001532 743 AGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILRPDRTG---PGAERMQILDDDGL 819 (1058)
Q Consensus 743 ~G~N~~Vav~~y~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~e~~~~p~~~~---~~~~~~~~ld~dGi 819 (1058)
+|+||+||||||+||||||||||||+|+|||+|||+||++|++++++...+..|.++.|..+. +....|++||+|||
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 999999999999999999999999999999999999999999998876556556777653321 12246899999999
Q ss_pred ccCCcEeCCCCEEEEEecCCCCCCCCCCCCCCCCcccccceEEeeCCCCCceEEEEEEEeeCCCCCEEEEEEEeecCCCc
Q 001532 820 AAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLIRHTRRPE 899 (1058)
Q Consensus 820 ~~~g~~v~~gd~li~k~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~vd~v~~~~~~~~~~~v~v~i~~~R~p~ 899 (1058)
|++|++|++|||||||++|..+..+.... +......+|.|++++.+| +|+||+|.++.++++.+.|||++|+.|+|+
T Consensus 781 ~~~G~~v~~gdili~k~~p~~~~~~~~~~-~~~~~~~~~~s~~~~~~e--~g~V~~V~~~~~~~~~~~vkv~ir~~R~p~ 857 (1103)
T PRK08565 781 VSPEVEVKGGDVLIGKTSPPRFLEELEEL-SLGLQERRDTSVTVRHGE--KGIVDTVLITESPEGNKLVKVRVRDLRIPE 857 (1103)
T ss_pred cCCCcEEcCCCEEEEEecCCCCCcchhhc-cccCCccccceEEecCCC--ceEEEEEEEEecCCCcEEEEEEEEEEecCc
Confidence 99999999999999999986533221110 111134789999999999 999999999988889999999999999999
Q ss_pred ccceecccCCCccEEEeeeccCCCCCCCCCCCCcEEeCCCCCCCcccHHHHHHHhhccchhcCCceeeeecccCCCCCCC
Q 001532 900 LGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHAD 979 (1058)
Q Consensus 900 iGDKf~sRhGqKGvvs~i~~~~DmPf~~~G~~pDiIiNP~~~PSRMtiGql~E~~~gk~~~~~g~~~~~tpf~~~~~~~~ 979 (1058)
||||||||||||||||++||+||||||+||++|||||||||||||||||||+|+++||++++.|.+.|+|||+ ..
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 56
Q ss_pred CHHHHHHHHHHcCCCCCCceEEEeCCCCcEeeeeEeeeeeeeeccccccCcceEEeccCCccccccCCcCcccCCCCC
Q 001532 980 TVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGF 1057 (1058)
Q Consensus 980 ~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~ 1057 (1058)
..+++++.|+++||+++|+|+||||+||++|+++||+|++|||||+|||.||+|||++||++.|||||++||+|+|||
T Consensus 933 ~~~~~~~~L~~~g~~~~G~e~l~~G~tG~~~~~~if~G~~yy~rL~HmV~DK~~~R~~Gp~~~lt~QP~~Gr~~~GG~ 1010 (1103)
T PRK08565 933 PEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGL 1010 (1103)
T ss_pred hHHHHHHHHHHcCCCCCCcEEEEcCCCCCCcccceEEeehhheechhhhchhhhhccCCCcchhhhCCccccccCCCe
Confidence 789999999999999999999999999999999999999999999999999999999999999999999999999997
No 2
>KOG0214 consensus RNA polymerase II, second largest subunit [Transcription]
Probab=100.00 E-value=3.4e-236 Score=2014.01 Aligned_cols=1013 Identities=37% Similarity=0.630 Sum_probs=929.8
Q ss_pred cccccccccccccccchHHHHHHHHHHHHHhCHHHHHHhcCcceecC--------CCcEEEEEeEEEEcCCccccCC-cc
Q 001532 28 VVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGI--------DPSIFLRFKDVRIGQPSMTVDG-VS 98 (1058)
Q Consensus 28 ~~~~~~~i~~~f~~~~Lv~~qi~SFn~Fl~~gl~~i~~~~~~i~~~~--------~~~~~l~~~~i~i~~P~~~~~~-~~ 98 (1058)
++++|.+|++||+.++|+++|++|||+|++.++++|+++.++|+... -.++.|.|+.|++.+|+++|.+ ..
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 68899999999999999999999999999999999999999987542 2368999999999999999986 77
Q ss_pred CCCChhhHhhcCCccCceEEEEEEEEECCCc-cceeeEEeEEEEeeeccccccccccCCCCCHHHHHhcCCCCCCCCcEE
Q 001532 99 EKLNPHMCRLSDMTYAAPILVNIEYVQGSHT-EKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYF 177 (1058)
Q Consensus 99 ~~l~P~EcR~r~lTYsa~l~v~v~~~~~~~~-~~~~~~~~~v~iG~iPIMv~S~~C~L~~ls~~elv~~gE~~~d~GGYF 177 (1058)
..++|+|||+|++|||+||||++........ +.+..+.+.|++|+||||+||..|.|+++++.+|.+++|||+|+||||
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 8999999999999999999999987754321 223455678999999999999999999999999999999999999999
Q ss_pred EEcCceeEEeeeecccCCEEEEEeCCC-Cc--EEEEEEecCC----CcceEEEEEee-CC---EEEEEEcceeccccHhh
Q 001532 178 IIKGTEKVLLIQEQLSKNRVIIDTDKK-GN--INASVTSSTE----TVKSKTVIQME-KG---KMYLLLNQFVKKIPIMV 246 (1058)
Q Consensus 178 IING~EKVI~~q~~~~~N~i~~~~~~~-g~--~~~~v~s~~~----~~~s~~~~~~~-~g---~i~~~~~~~~~~IPl~i 246 (1058)
||||+|||+++||+.++|.+++++.+. |. +.+.++|+.. ...++.+.++. ++ .+.+..++.+.+||+++
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 999999999999999999999998755 44 5677876432 22334444443 33 67788888888999999
Q ss_pred HHHHhCCCCHHHHHHHh---CCchhHHhhhhhhHHHHHhcCCcCHHHHHHHHhhcccccCCCCCCCChHHHHHHHHHhhh
Q 001532 247 VMKAMGMESDQEVVQMV---GRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVF 323 (1058)
Q Consensus 247 lLkALg~~sd~eI~~~i---~~~~~~~~~l~~~l~~~~~~~i~t~~~al~yig~~~~~~~~~~~~~~~~e~~~~~L~~~l 323 (1058)
||||||+.+|+||++.| .+|.++.+.+.++++++.. +..+..||+|||+|.... ..+++. .++.|+++|.+.+
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 99999999999999999 2789999999999998865 457889999999987442 233455 8899999999999
Q ss_pred ccCCCCCCCCCCCcchhHHHHHHHHHHhhcCCCCCCCcccccceEEcchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCC
Q 001532 324 LANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPS 403 (1058)
Q Consensus 324 lpHl~~~~~~~~~K~~~L~~Mi~kLl~~~~G~~~~DD~D~l~NkRV~~~G~Ll~~lfr~~l~~~~~~ik~~i~k~~~~~~ 403 (1058)
|||++..+...++|+.||+||+++|+.++.|++.+||+||++|||++++|+||..+||..|.++.+++...+++.+++..
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 99999887677799999999999999999999999999999999999999999999999999999999999999888743
Q ss_pred CCCCCccccccccccchhhhhhhhccCCCc-ccccccccccceEEcccccccccccccccccccccccccccCCCcCCCC
Q 001532 404 RSSRFDLSQFIVRDSITVGLERTLSTGNFD-VKRFKMHRKGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPS 482 (1058)
Q Consensus 404 ~~~~~~~~~~i~~~~It~~i~~~~sTGn~~-~~~~~~q~sG~sq~l~rln~ls~lshlRrv~~~~~~~~k~t~~R~Lhps 482 (1058)
++++.-.|+++.||++++|+||||||+ .++.+..++||||+|+|+||+++||||||.++|+..++|..+||+||||
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 577777789999999999999999998 5556678899999999999999999999999999999999999999999
Q ss_pred CccccccCCCCCCCcccccccccceeeeecCCCChhHHHHHhhcCCeeccccCccccCCCCcEEEEECCeEEeeccChhh
Q 001532 483 QWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKC 562 (1058)
Q Consensus 483 ~wG~iCPveTPEG~~cGLi~~LA~~a~Is~~~~~~~i~~~l~~~g~~~l~~~~~~~~~~~~~~~V~lnG~~vG~~~~~~~ 562 (1058)
|||++||.|||||++||||||||+||.|+.+..+.||.++|.++||++|+.+++.... +.++||+||+|+|.+.+|+.
T Consensus 475 hwGmvCPaeTPEGqacGLVKNLSLmayIsvGS~~sPi~EfLeewgmE~le~~~ps~~~--datkvfvNG~wvGlhrdp~~ 552 (1141)
T KOG0214|consen 475 HWGMVCPAETPEGQACGLVKNLSLMAYISVGSLESPIVEFLEEWGMENLEEISPSPSP--DATKVFVNGVWVGLHRDPEE 552 (1141)
T ss_pred cceeeccccCCCcceeeccccceEEEEEecCCCccHHHHHHHHhchhhHhhcCCCcCC--CceEEEEcccEEEecCCHHH
Confidence 9999999999999999999999999999999999999999999999999988876553 78999999999999999999
Q ss_pred HHHHHHHHhhcCCcCceeEEEeccccceEEEecCCCeeeeeEEEEecCcccchhhhHHHhhcC---CccchhhhccCcee
Q 001532 563 FADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDG---VRSFDDFLREGLIE 639 (1058)
Q Consensus 563 ~~~~lr~~rr~~~i~~~v~i~~~~~~~~i~I~sd~GRl~RPll~v~~~~~~~~~~~~~~l~~~---~~s~~~~~~~~~iE 639 (1058)
++.+||++||...++.++++..+...++++|+||+||++||||+|+|+++.++++|++.|+.. ..+|..|+..|.+|
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 999999999999888899999999999999999999999999999999999999999999886 56999999999999
Q ss_pred EeccccccceEEEeecCCCC-----CCceeeeecCccccccccccCCCCCCCCCCccccccccccCCccceeEeeeeccc
Q 001532 640 YLDVNEENNALIALYEGDAT-----PDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMD 714 (1058)
Q Consensus 640 ~id~~e~~~~~Ia~~~~~~~-----~~~th~Ei~p~~~ls~~asliPF~~hNqspRn~yq~~M~KQaiG~~~~n~~~R~D 714 (1058)
|||++|++.++||+.++++. ..||||||||+.+||++||.||||||||||||+||++|+|||||++.+|+..|+|
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 99999999999999998875 3699999999999999999999999999999999999999999999999999999
Q ss_pred cceeeeeCCCcceeechhhhhhcCCCCCCCcceEEEEeecCCCCCCCcEEEecceeeccceEEEEEEEEEEEeecccCCc
Q 001532 715 SLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANST 794 (1058)
Q Consensus 715 ~~~y~l~ypQ~Plv~t~~~~~~~~~~~~~G~N~~Vav~~y~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~ 794 (1058)
+..|.|+|||+|+|+|+++++..+.++|+|+|++||++||+|||||||||+|+++++||+|+|.+|++|+.+..+...+.
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--CcccccccCCCCccccCCcEeCCCCEEEEEecCCCCCCCCCCCCCCCCcccccceEEeeCCCCCce
Q 001532 795 SDRILRPDRT-G--PGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETC 871 (1058)
Q Consensus 795 ~e~~~~p~~~-~--~~~~~~~~ld~dGi~~~g~~v~~gd~li~k~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~ 871 (1058)
++.+..|... . .....|++||+||++.+|++|..|||+|||.+|....++..... .+....+|.|+.++++| .|
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 7777776642 1 23357999999999999999999999999999876655432211 12235689999999999 99
Q ss_pred EEEEEEEeeCCCCCEEEEEEEeecCCCcccceecccCCCccEEEeeeccCCCCCCCCCCCCcEEeCCCCCCCcccHHHHH
Q 001532 872 VVDRVALCSDKNGDLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMI 951 (1058)
Q Consensus 872 ~vd~v~~~~~~~~~~~v~v~i~~~R~p~iGDKf~sRhGqKGvvs~i~~~~DmPf~~~G~~pDiIiNP~~~PSRMtiGql~ 951 (1058)
+||+|+++++.+|.+.+||++|+.|.|++|||||||||||||||.++++||||||.+|++|||||||||||||||||||+
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 HHhhccchhcCCceeeeecccCCCCCCCCHHHHHHHHHHcCCCCCCceEEEeCCCCcEeeeeEeeeeeeeeccccccCcc
Q 001532 952 ELLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDK 1031 (1058)
Q Consensus 952 E~~~gk~~~~~g~~~~~tpf~~~~~~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if~G~~yy~rL~Hmv~dK 1031 (1058)
|+++||.+++.|...|+|||+ ...+..+...|.++||.++|+|+||+|+||++|.+.||+||.|||||+|||+||
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 467889999999999999999999999999999999999999999999999999
Q ss_pred eEEeccCCccccccCCcCcccCCCCC
Q 001532 1032 MHARGSGPRVMLTRQPTEGRARNGGF 1057 (1058)
Q Consensus 1032 ~~~R~~Gp~~~lT~QP~~Gr~~~GG~ 1057 (1058)
+|+|++||++.+||||++||+|+||+
T Consensus 1025 ih~R~~Gp~q~ltRQP~~gRsr~GGl 1050 (1141)
T KOG0214|consen 1025 IHSRARGPVQILTRQPVEGRSRDGGL 1050 (1141)
T ss_pred eeecccCCceeeeccccccccccCCe
Confidence 99999999999999999999999997
No 3
>KOG0215 consensus RNA polymerase III, second largest subunit [Transcription]
Probab=100.00 E-value=9.1e-234 Score=1968.15 Aligned_cols=1042 Identities=65% Similarity=1.097 Sum_probs=982.5
Q ss_pred CcccccCCCC-CCCCcccccccCCCcccccccccccccccccchHHHHHHHHHHHHHhCHHHHHHhcCcceecCCCcEEE
Q 001532 2 GLMQVEGSPK-DEQLPDKQKLAAPVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFL 80 (1058)
Q Consensus 2 ~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~i~~~f~~~~Lv~~qi~SFn~Fl~~gl~~i~~~~~~i~~~~~~~~~l 80 (1058)
|+-+-++.+. |.+--+.+..+++..+.++.|.++|+||+.++||++|++|||+|++++|+.|++++..|.++.++.+.|
T Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~i~~~~dk~~lvp~flkvkglvkqhldsfnyfv~~~ik~iv~an~~itsd~dp~fyl 95 (1153)
T KOG0215|consen 16 GLDKTELDLTLDKPVYDGKKLSDPIKPLEDKWQLVPAFLKVKGLVKQHLDSFNYFVDVDIKKIVKANQLITSDVDPSFYL 95 (1153)
T ss_pred CcccccccccccccccccccccCCCCChHHhHHhHHHHHhhhhHHHHHHhhhhhhhhhhHHHHHHhhcccCcCcCchhhh
Confidence 4444444443 344446677888999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeEEEEcCCccccCC--ccCCCChhhHhhcCCccCceEEEEEEEEECCCccceeeEEeEEEEeeeccccccccccCCCC
Q 001532 81 RFKDVRIGQPSMTVDG--VSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGK 158 (1058)
Q Consensus 81 ~~~~i~i~~P~~~~~~--~~~~l~P~EcR~r~lTYsa~l~v~v~~~~~~~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~l 158 (1058)
++.++++++|.+.++. ....++|+|||+|++||+||++|+++++.+. ..+.+.+|.+|++|+|+||++|.|++.
T Consensus 96 ky~dirvg~Ps~~~~~~~~~~~i~p~ecrlrd~tysa~i~vdieytrg~----~~~~~~~v~igrmpimlrs~rcvl~~~ 171 (1153)
T KOG0215|consen 96 KYLDIRVGKPSIEEGNNVTNDNITPHECRLRDMTYSAPIYVDIEYTRGR----QIIAKRDVIIGRMPIMLRSSKCVLRGK 171 (1153)
T ss_pred eeeeeeccCcchhhccccccccCCchheeehhhhcccceeEEEEEecCc----ceEEecccccccchhhhhccccccCCc
Confidence 9999999999998774 5568999999999999999999999999887 567778999999999999999999999
Q ss_pred CHHHHHhcCCCCCCCCcEEEEcCceeEEeeeecccCCEEEEEeCCCCcEEEEEEecCCCcceEEEEEeeCCEEEEEEcce
Q 001532 159 DEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVIIDTDKKGNINASVTSSTETVKSKTVIQMEKGKMYLLLNQF 238 (1058)
Q Consensus 159 s~~elv~~gE~~~d~GGYFIING~EKVI~~q~~~~~N~i~~~~~~~g~~~~~v~s~~~~~~s~~~~~~~~g~i~~~~~~~ 238 (1058)
++.++.+..|||.|+|||||++|.||||..||+.+.|++++..+++|.+.|.+.|++++.+++++++.++++++++++.+
T Consensus 172 ~e~~~a~~~ecpldpggyfiv~G~ekViLiqeqlsknrii~~~~k~~~~~~svtsst~e~kskt~v~~k~~k~ylk~~~~ 251 (1153)
T KOG0215|consen 172 DEEELARLNECPLDPGGYFIVKGTEKVILIQEQLSKNRIIVEEDKKGNLQASVTSSTHERKSKTYVTTKKGKYYLKHNSF 251 (1153)
T ss_pred cHHHHHHhccCCCCCCceeEeccceeEEEehhhhhccCeeeccccCCccccccccceeeecceEEEEeccceeeeehhhh
Confidence 99999999999999999999999999999999999999999877778899999999999999999999999999999999
Q ss_pred eccccHhhHHHHhCCCCHHHHHHHhCCchhHHhhhhhhHHHHHhcCCcCHHHHHHHHhhcccccCCCCCCCChHHHHHHH
Q 001532 239 VKKIPIMVVMKAMGMESDQEVVQMVGRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSI 318 (1058)
Q Consensus 239 ~~~IPl~ilLkALg~~sd~eI~~~i~~~~~~~~~l~~~l~~~~~~~i~t~~~al~yig~~~~~~~~~~~~~~~~e~~~~~ 318 (1058)
.++||++++|||+|..+|+||.+.++.+..|.+.+.++++++...+++||.+||+|++.++.... .+... ..+.|.++
T Consensus 252 ~d~ipiviv~ka~g~~sd~ei~~~vg~~~~y~~~~~~s~ee~~~~~v~tqqqal~y~~~kvk~~~-~t~~~-~~~e~~~~ 329 (1153)
T KOG0215|consen 252 TDDIPIVIVLKAMGLESDQEIVQLVGGDSKYQDIFAPSLEECVSLGVYTQQQALEYIGSKVKVKR-GTTPT-KDEEALEV 329 (1153)
T ss_pred hccCCEEEEEeeccccchHHHHHHhhcchHHHHhhccchhhhhhhhhHHHHHHHHHhhheEEecc-CCCCC-chHHHHHH
Confidence 99999999999999999999999997799999999999999999999999999999999888753 22333 67889999
Q ss_pred HHhhhccCCCCCCCCCCCcchhHHHHHHHHHHhhcCCCCCCCcccccceEEcchHHHHHHHHHHHHHHHHHHHHHHHHhH
Q 001532 319 LRDVFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDII 398 (1058)
Q Consensus 319 L~~~llpHl~~~~~~~~~K~~~L~~Mi~kLl~~~~G~~~~DD~D~l~NkRV~~~G~Ll~~lfr~~l~~~~~~ik~~i~k~ 398 (1058)
|...+++|+.....+++.|+.+++.|+|+++.+..+.-..||+|.++|||+.++|+|++.+|++.|+++...++..+.+.
T Consensus 330 l~~~~lahv~v~~~~~r~K~~yi~~m~rr~~~a~l~~~~~ddrd~~gnkrlelagqllsllfeD~fk~~n~e~k~~~dk~ 409 (1153)
T KOG0215|consen 330 LSTTVLAHVPVPDLNFRMKAIYIGLMVRRVIQAMLNKLAMDDRDYVGNKRLELAGQLLSLLFEDLFKRFNSELKKNIDKI 409 (1153)
T ss_pred HHhhheeceeccCCCCcceeehHHHHHHHHHHHHhCcccccchhhhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999888999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCCCCCCCCcccccc--ccccchhhhhhhhccCCCcccccccccccceEEcccccccccccccccccccccccccccCC
Q 001532 399 LSKPSRSSRFDLSQFI--VRDSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGP 476 (1058)
Q Consensus 399 ~~~~~~~~~~~~~~~i--~~~~It~~i~~~~sTGn~~~~~~~~q~sG~sq~l~rln~ls~lshlRrv~~~~~~~~k~t~~ 476 (1058)
+.+..+...+|+.+.+ .++.||++|..++|||||..++|.|.|+|++|||.|++|+++|+.+.|++++|++++|..+|
T Consensus 410 l~k~~ra~~fD~~~~~n~~~~~it~~l~ra~stgnw~iKrfrmer~gvt~VlsrlSyisaLgmmtri~s~fektrkvsgp 489 (1153)
T KOG0215|consen 410 LKKPIRAQEFDALKHLNVRANMITSGLERAISTGNWSIKRFRMERAGVTQVLSRLSYISALGMMTRINSQFEKTRKVSGP 489 (1153)
T ss_pred hcchhhhhhhHHHHHHHHHHHHHHHHHHHHhhcCchHHHHhhhhhccceeeehhhhhhhhhhhheehhhhheeehhccCc
Confidence 8886555567777666 67899999999999999999999999999999999999999999999999999999999999
Q ss_pred CcCCCCCccccccCCCCCCCcccccccccceeeeecCCCChhHHHHHhhcCCeeccccCccccCCCCcEEEEECCeEEee
Q 001532 477 RALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGK 556 (1058)
Q Consensus 477 R~Lhps~wG~iCPveTPEG~~cGLi~~LA~~a~Is~~~~~~~i~~~l~~~g~~~l~~~~~~~~~~~~~~~V~lnG~~vG~ 556 (1058)
|.|+|||||.+||++||||+.|||++|||++++|+++.+++|+...+..+|+.++..++..+++.++.+.||+||.++|.
T Consensus 490 rSlq~sqwgmlcp~dtpegeacglvknlalmthittd~ee~pi~~~~~k~gv~di~~v~~~e~~~~~~~~v~Lng~iig~ 569 (1153)
T KOG0215|consen 490 RSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITTDSEEKPILKLCYKLGVEDIHVVSGRELHTPDSFLVFLNGLIIGI 569 (1153)
T ss_pred cccChhhcccccCCCCCCccccccccchHHHhcccCCCCcchhHHHHHHhcceeeeeecccccCCCceEEEEecceeecc
Confidence 99999999999999999999999999999999999999999999999999999998888888888889999999999999
Q ss_pred ccChhhHHHHHHHHhhcCCcCceeEEEeccccceEEEecCCCeeeeeEEEEecCcccchhhhHHHhhcCCccchhhhccC
Q 001532 557 HRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREG 636 (1058)
Q Consensus 557 ~~~~~~~~~~lr~~rr~~~i~~~v~i~~~~~~~~i~I~sd~GRl~RPll~v~~~~~~~~~~~~~~l~~~~~s~~~~~~~~ 636 (1058)
+..|+.|+..+|.+||+|.+..+|+++-+.....++|.||.||+|||+++|++|.+.+...|+++++.+..+|+|+++.|
T Consensus 570 ~~~~~~~v~~~r~lrr~G~i~~fvsv~~~~~q~~v~i~sdggr~crp~Iiv~~~~~~v~~~h~~el~~g~r~F~DFl~~g 649 (1153)
T KOG0215|consen 570 TRRPQYFVNSFRRLRRKGKIGEFVSVFTNTTQRCVYIASDGGRVCRPLIIVDNGRPRVKQHHMDELLDGKRTFDDFLKDG 649 (1153)
T ss_pred ccchHHHHHHHHHHHHcCcccceeeeeeeeeeEEEEEecCCCeEeeeEEEEeCCcchhhhhhHHHHHHhhhhHHHHHHhc
Confidence 99999999999999999999999999999889999999999999999999999999999999999999999999999999
Q ss_pred ceeEeccccccceEEEeecCCCCCCceeeeecCccccccccccCCCCCCCCCCccccccccccCCccceeEeeeeccccc
Q 001532 637 LIEYLDVNEENNALIALYEGDATPDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSL 716 (1058)
Q Consensus 637 ~iE~id~~e~~~~~Ia~~~~~~~~~~th~Ei~p~~~ls~~asliPF~~hNqspRn~yq~~M~KQaiG~~~~n~~~R~D~~ 716 (1058)
.|||+|++|++.++||+.++++.+.+||+||.|..+||++|+|||||+|||||||+|||+|+|||||.++||+..|+|+.
T Consensus 650 lvEYLDVNEEND~~Ialye~~I~~~TTHLEIEPFTiLGv~AGLIPYPHHNQSPRNTYQCAMGKQAmG~IaYNQ~~RiDtl 729 (1153)
T KOG0215|consen 650 LIEYLDVNEENDSLIALYEEDIGPETTHLEIEPFTILGVVAGLIPYPHHNQSPRNTYQCAMGKQAMGAIAYNQKKRIDSL 729 (1153)
T ss_pred hhheeecccccCceEEechhhcCCCcceeeecchhhhhhhccccCCCCCCCCCcchhhhhhhhhhhhhhhhhhhhhHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeeeCCCcceeechhhhhhcCCCCCCCcceEEEEeecCCCCCCCcEEEecceeeccceEEEEEEEEEEEeecccCCccc
Q 001532 717 LYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSD 796 (1058)
Q Consensus 717 ~y~l~ypQ~Plv~t~~~~~~~~~~~~~G~N~~Vav~~y~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~e 796 (1058)
+|+|.|||+|+|+|++.+..+++.+|+||||.||||||+|||+|||+|+||+|+|||++++.+||+.+..++++.++..|
T Consensus 730 mYll~YPq~PmVkTKTIELi~ydKLPAGQNAtVAVMSYSGYDIEDALVLNKsSlDRGfGRC~Vyk~~~~~~kkY~N~T~D 809 (1153)
T KOG0215|consen 730 LYLLVYPQRPMVKTKTIELINYDKLPAGQNATVAVMSYSGYDIEDALVLNKSSIDRGFGRCEVYKKTTTTLKKYANGTFD 809 (1153)
T ss_pred HHHHhcCCCccccceeEEeeccccCCCCCccEEEEEeccCCchhhhhhcccchhccCcceEEEEeeeeeeeeecCCCchh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999899
Q ss_pred eecCCCCC---CCcccccccCCCCccccCCcEeCCCCEEEEEecCCCCCCCCCCCCCCCCcccccceEEeeCCCCCceEE
Q 001532 797 RILRPDRT---GPGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVV 873 (1058)
Q Consensus 797 ~~~~p~~~---~~~~~~~~~ld~dGi~~~g~~v~~gd~li~k~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~v 873 (1058)
++..|-.+ .++-+.-..||+|||..||.+|++|+|+|.|-.|.....+... ....+..|++.++.||.+| +++|
T Consensus 810 rimgp~~d~~t~kpi~kh~vLd~DGl~~pG~~V~~~qi~iNK~mP~vt~~~~~~-~~~~~~~Yk~~pitykgpe--psyi 886 (1153)
T KOG0215|consen 810 RIMGPQLDPNTRKPIWKHQVLDDDGLATPGERVQPGQIYINKQMPTVTGTSLPG-LSASQVQYKAVPITYKGPE--PSYI 886 (1153)
T ss_pred hhcccccCCCcCCcchhhcccCcccCCCCccEeccCcEEEeccCCCcccccCCC-CCccccccccccceecCCC--cchh
Confidence 99877653 2344566789999999999999999999999777665442211 1112235999999999999 9999
Q ss_pred EEEEEeeCCCCCEEEEEEEeecCCCcccceecccCCCccEEEeeeccCCCCCCCCCCCCcEEeCCCCCCCcccHHHHHHH
Q 001532 874 DRVALCSDKNGDLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIEL 953 (1058)
Q Consensus 874 d~v~~~~~~~~~~~v~v~i~~~R~p~iGDKf~sRhGqKGvvs~i~~~~DmPf~~~G~~pDiIiNP~~~PSRMtiGql~E~ 953 (1058)
|+|+++.++++.-.+|+.+|+.|+|++|||||||||||||||.|++||||||...||.||||+||||||||||+|.++|.
T Consensus 887 dkVmls~n~~dq~LIK~llRQTRrPElGDKFSSRHGQKGVcGlIv~QEDMPFnD~GIcPDiIMNPHGFPSRMTVGK~iEL 966 (1153)
T KOG0215|consen 887 DRVMLTSNDEDQFLIKVLLRQTRRPELGDKFSSRHGQKGVCGLIVQQEDMPFNDQGICPDIIMNPHGFPSRMTVGKMIEL 966 (1153)
T ss_pred heeEeecCccccHHHHHHHhhccCcccccccccccCCCceeeEEeeccCCCCcccCCCcccccCCCCCcccchHHHHHHH
Confidence 99999999888889999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhccchhcCCceeeeecccCCCCCCCCHHHHHHHHHHcCCCCCCceEEEeCCCCcEeeeeEeeeeeeeeccccccCcceE
Q 001532 954 LGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMH 1033 (1058)
Q Consensus 954 ~~gk~~~~~g~~~~~tpf~~~~~~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if~G~~yy~rL~Hmv~dK~~ 1033 (1058)
+.||||++.|+|+++|+|- +++++++++.|.++||||.||..+|||+||+|++|.||+||+|||||+|||.||+|
T Consensus 967 lsGKAGVl~G~~hYGTaFG-----gskVed~~~~Lv~hGfnY~GKD~ltSGITGepLeAYIffGPiYYQKLKHMVlDKMH 1041 (1153)
T KOG0215|consen 967 LSGKAGVLEGTFHYGTAFG-----GSKVEDISEELVEHGFNYSGKDMLTSGITGEPLEAYIFFGPIYYQKLKHMVLDKMH 1041 (1153)
T ss_pred hccccceeeeeEeeccccC-----CchHHHHHHHHHHhccCccCccccccCCCCCcceeeEEechHHHHHHHHHHHHHHh
Confidence 9999999999999999999 79999999999999999999999999999999999999999999999999999999
Q ss_pred EeccCCccccccCCcCcccCCCCC
Q 001532 1034 ARGSGPRVMLTRQPTEGRARNGGF 1057 (1058)
Q Consensus 1034 ~R~~Gp~~~lT~QP~~Gr~~~GG~ 1057 (1058)
||++||+..|||||++||+|+||+
T Consensus 1042 ARARGPRAvLTRQPTEGRSrdGGL 1065 (1153)
T KOG0215|consen 1042 ARARGPRAVLTRQPTEGRSRDGGL 1065 (1153)
T ss_pred hhccCCceeeecCCCCCcCCCCCc
Confidence 999999999999999999999997
No 4
>KOG0216 consensus RNA polymerase I, second largest subunit [Transcription]
Probab=100.00 E-value=2.7e-231 Score=1956.99 Aligned_cols=966 Identities=30% Similarity=0.499 Sum_probs=852.6
Q ss_pred cccccccccccccchHHHHHHHHHHHHHhCHHHHHHhcC--cceecCCCcEEEEEeEEEEcCCccccCC---ccCCCChh
Q 001532 30 DKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRAND--RIVSGIDPSIFLRFKDVRIGQPSMTVDG---VSEKLNPH 104 (1058)
Q Consensus 30 ~~~~~i~~~f~~~~Lv~~qi~SFn~Fl~~gl~~i~~~~~--~i~~~~~~~~~l~~~~i~i~~P~~~~~~---~~~~l~P~ 104 (1058)
..|+-.|+|-+.+.++++|++|||...+.||.+..-+.. .......+++++++++++|.+|.+.... ..+++||.
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 367888899999999999999999999988877544421 1112235689999999999999998753 78999999
Q ss_pred hHhhcCCccCceEEEEEEEEECCCccceeeEEeEEEEeeeccccccccccCCCCCHHHHHhcCCCCCCCCcEEEEcCcee
Q 001532 105 MCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEK 184 (1058)
Q Consensus 105 EcR~r~lTYsa~l~v~v~~~~~~~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~ls~~elv~~gE~~~d~GGYFIING~EK 184 (1058)
|||+|++||+|.|.|+++|.+|+ ..+...+..+|.+||||||++|||.|++|+||++++|++.|+||||||||+||
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 99999999999999999999998 44555678999999999999999999999999999999999999999999999
Q ss_pred EEeeeecccCCEEEEEeCC----CCc----EEEEEEecCCCcceEEEE--EeeCCEEEEE--EcceeccccHhhHHHHhC
Q 001532 185 VLLIQEQLSKNRVIIDTDK----KGN----INASVTSSTETVKSKTVI--QMEKGKMYLL--LNQFVKKIPIMVVMKAMG 252 (1058)
Q Consensus 185 VI~~q~~~~~N~i~~~~~~----~g~----~~~~v~s~~~~~~s~~~~--~~~~g~i~~~--~~~~~~~IPl~ilLkALg 252 (1058)
|||++|.+++|++++..++ +|. +...++|.+++.++.+.. ++.||.+.++ +.+....+|++++||||.
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 9999999999999977643 232 446677777877766554 5688854333 333334699999999999
Q ss_pred CCCHHHHHHHh--C--CchhHHhhhhhhHHHHHhcCCcCHHHHHHHHhhcccccCC-CCCCCChHHHHHHHHHhhhccCC
Q 001532 253 MESDQEVVQMV--G--RDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTF-GSPPNDREGRAFSILRDVFLANV 327 (1058)
Q Consensus 253 ~~sd~eI~~~i--~--~~~~~~~~l~~~l~~~~~~~i~t~~~al~yig~~~~~~~~-~~~~~~~~e~~~~~L~~~llpHl 327 (1058)
.+||+||++.+ + .++++.++++.+|+++.+.+++||++|++|||++|++... .++.+ +.|+|+++|+++++.||
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 99999999999 2 5788999999999999999999999999999999997644 34445 89999999999999999
Q ss_pred CCCCCCCCCcchhHHHHHHHHHHhhcCCCCCCCcccccceEEcchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCCC
Q 001532 328 PVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSR 407 (1058)
Q Consensus 328 ~~~~~~~~~K~~~L~~Mi~kLl~~~~G~~~~DD~D~l~NkRV~~~G~Ll~~lfr~~l~~~~~~ik~~i~k~~~~~~~~~~ 407 (1058)
++ ..+||.+|++|++||++++.|+|.+||+|+++|||++++|+|++..+++.++.|++.++.++.+.+.+.....+
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 95 46899999999999999999999999999999999999999999999999999999887777777665332211
Q ss_pred -Cc---ccccc--ccccchhhhhhhhccCCCccc-cc-ccccccceEEccccccccccccccccc-ccccccccccCCCc
Q 001532 408 -FD---LSQFI--VRDSITVGLERTLSTGNFDVK-RF-KMHRKGMTQVLARLSFIGTLGHMTRVS-PQFEKSRKVSGPRA 478 (1058)
Q Consensus 408 -~~---~~~~i--~~~~It~~i~~~~sTGn~~~~-~~-~~q~sG~sq~l~rln~ls~lshlRrv~-~~~~~~~k~t~~R~ 478 (1058)
++ +.+.+ .+..|+++|++||||||+.+. ++ .+|++|+|+++||+||+++|||||.|| +.|+.+++||++|+
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 12 22222 468999999999999999753 44 368899999999999999999999999 68999999999999
Q ss_pred CCCCCccccccCCCCCCCcccccccccceeeeecC-CCChhHHHHHhhcCCeeccccCccccCCCCcEEEEECCeEEeec
Q 001532 479 LQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTD-EEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKH 557 (1058)
Q Consensus 479 Lhps~wG~iCPveTPEG~~cGLi~~LA~~a~Is~~-~~~~~i~~~l~~~g~~~l~~~~~~~~~~~~~~~V~lnG~~vG~~ 557 (1058)
|.|++|||+||||||||+||||+||||..|+|++. .+.+.+.++|.++||.|.......- ..-++|++||++|||+
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 LLPESWGFLCPVHTPDGAPCGLLNHMTRTCRIVTRPDDVSFIPSILFELGMVPSSHLVEAG---EPLYPVLLDGKVVGWV 551 (1111)
T ss_pred hCchhhcccccccCCCCCchhHHHhhhhheeEeecCcchhhhhHHHHhcCCCchhccccCC---CceeEEEECCEEEEee
Confidence 99999999999999999999999999999999987 4567899999999999865333211 1368999999999999
Q ss_pred cCh--hhHHHHHHHHhhc--CCcCceeEEEe-----ccccceEEEecCCCeeeeeEEEEecCcccchhhhHHHhhcCCcc
Q 001532 558 RRP--KCFADVMRKLRRA--GKIGEFVSVFV-----NEKQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRS 628 (1058)
Q Consensus 558 ~~~--~~~~~~lr~~rr~--~~i~~~v~i~~-----~~~~~~i~I~sd~GRl~RPll~v~~~~~~~~~~~~~~l~~~~~s 628 (1058)
+.+ +.+++.||.+|.. +.+|.+.+|.+ +...|++||+|++||++|||.+
T Consensus 552 s~~~a~~i~~~lR~~Kv~~p~~iP~~leIg~Vp~s~~gqyPglyi~s~~aR~~RpV~n---------------------- 609 (1111)
T KOG0216|consen 552 SSPLAKKIVDYLRYYKVEAPAVIPNDLEIGYVPTSTNGQYPGLYIFSGPARMIRPVKN---------------------- 609 (1111)
T ss_pred ccHHHHHHHHHHHHHhhcCcccCCCcceEeeeecCCCCCCceeEEecCchhhhhehhc----------------------
Confidence 854 8999999999976 56787766644 3357999999999999999996
Q ss_pred chhhhccCceeEeccccccceEEEeecCCCCCC-ceeeeecCccccccccccCCCCCCCCCCccccccccccCCccceeE
Q 001532 629 FDDFLREGLIEYLDVNEENNALIALYEGDATPD-TTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAF 707 (1058)
Q Consensus 629 ~~~~~~~~~iE~id~~e~~~~~Ia~~~~~~~~~-~th~Ei~p~~~ls~~asliPF~~hNqspRn~yq~~M~KQaiG~~~~ 707 (1058)
++.+.+|||++.||.+++||+.++++.+. +||.|++|+.+||++|+||||+||||||||||||||+||+||++.+
T Consensus 610 ----l~~~~~e~iG~fEQvym~i~~~~~e~~~~v~th~E~~pt~~ls~~anliP~sD~NQSPRNmYQCQMgKQtmg~p~~ 685 (1111)
T KOG0216|consen 610 ----LSLDSVEWIGPFEQVYMNIAIDPKEIFPDVTTHVELHPTGILSIVANLIPFSDHNQSPRNMYQCQMGKQTMGTPGH 685 (1111)
T ss_pred ----cccCchhhcccHHHhhhhhccchhhcCCCcceeEEecccchHhHhhcCccccccCCCchhHHHhhhhhhhcCCccc
Confidence 33466899999999999999999999876 8999999999999999999999999999999999999999999999
Q ss_pred eeeeccccceeeeeCCCcceeechhhhhhcCCCCCCCcceEEEEeecCCCCCCCcEEEecceeeccceEEEEEEEEEEEe
Q 001532 708 NQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAIN 787 (1058)
Q Consensus 708 n~~~R~D~~~y~l~ypQ~Plv~t~~~~~~~~~~~~~G~N~~Vav~~y~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~ 787 (1058)
++..|.|+|+|+|++||.|+|++..++.++++++|+|+||+|||+|||||||||||||||+|+||||+++.+||+..+++
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 99999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred ecccCCccceec-CCCCCCCcccccccCCCCccccCCcEeCCCCEEEEEecCCCCCCCCCCCCCCCCcccccceEEeeCC
Q 001532 788 QKYANSTSDRIL-RPDRTGPGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGP 866 (1058)
Q Consensus 788 ~~~~~~~~e~~~-~p~~~~~~~~~~~~ld~dGi~~~g~~v~~gd~li~k~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~ 866 (1058)
.+.... ...|. .|+. ...++||+||||.+|++++.||+++..+.... .+....+|+..
T Consensus 766 ~~~~~r-~~~F~~~p~~-----~~~~~ld~dgLP~~G~kl~~~dp~~~y~d~~t---------------~~~~~~~~~~~ 824 (1111)
T KOG0216|consen 766 SKKRSR-SKHFGRSPGE-----PELKKLDADGLPSIGQKLEYGDPYYAYFDEET---------------GKTRIKKYHGT 824 (1111)
T ss_pred hhcccc-eeeeeeCCCC-----ccccccCCCCCCCCcccccCCCcEEEEEcccC---------------CceEEEEecCC
Confidence 754321 22333 2543 24789999999999999999999998765332 23445678888
Q ss_pred CCCceEEEEEEEeeCCCCC--EEEEEEEeecCCCcccceecccCCCccEEEeeeccCCCCCCCCCCCCcEEeCCCCCCCc
Q 001532 867 DGETCVVDRVALCSDKNGD--LCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSR 944 (1058)
Q Consensus 867 ~~~~~~vd~v~~~~~~~~~--~~v~v~i~~~R~p~iGDKf~sRhGqKGvvs~i~~~~DmPf~~~G~~pDiIiNP~~~PSR 944 (1058)
| +|+||.|.+..++.+. +++.|++|..|+|.||||||||||||||||..||.+|||||++|++|||||||||||||
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 9999999999876665 78999999999999999999999999999999999999999999999999999999999
Q ss_pred ccHHHHHHHhhccchhcCCceeeeecccCCCCCCCCHHHHHHHHHHcCCCCCCceEEEeCCCCcEeeeeEeeeeeeeecc
Q 001532 945 MTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKL 1024 (1058)
Q Consensus 945 MtiGql~E~~~gk~~~~~g~~~~~tpf~~~~~~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if~G~~yy~rL 1024 (1058)
||||||+|+++||+||++|..+|+|||.+. ++++.+++|+++|+++||||||+|+||||.+|++|+|+||+|+||||||
T Consensus 903 MTIgM~iEs~AgK~~alhG~~~Datpf~~~-E~~t~~dyfg~~L~~~GyNyyGnE~~YSGv~G~e~~adIf~GvVyYQRL 981 (1111)
T KOG0216|consen 903 MTIGMLIESMAGKAGALHGNAQDATPFIFS-EENTAIDYFGEMLKKAGYNYYGNEPMYSGVDGREMRADIFFGVVYYQRL 981 (1111)
T ss_pred ccHHHHHHHHhchhhccccccccCCceeec-CcccHHHHHHHHHHHcCcCccCCcccccccccceeeeeEEEeehhHHHH
Confidence 999999999999999999999999999854 4567899999999999999999999999999999999999999999999
Q ss_pred ccccCcceEEeccCCccccccCCcCcccCCCCC
Q 001532 1025 KHMVLDKMHARGSGPRVMLTRQPTEGRARNGGF 1057 (1058)
Q Consensus 1025 ~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~ 1057 (1058)
+|||.||+|||+|||++.+|+||+|||||+||+
T Consensus 982 rHMv~DKfQVRstG~v~~~T~QPvkGRkr~GGi 1014 (1111)
T KOG0216|consen 982 RHMVSDKFQVRSTGPVDSLTHQPVKGRKRGGGI 1014 (1111)
T ss_pred HHHhcceeeeeeccCccccccCCccCcccCCCc
Confidence 999999999999999999999999999999997
No 5
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]
Probab=100.00 E-value=1.8e-216 Score=1941.59 Aligned_cols=943 Identities=32% Similarity=0.504 Sum_probs=850.1
Q ss_pred ccccccccccccccccchHHHHHHHHHHHHHhCHHHHHHhcCcceecCCCcEEEEEeEEEEcCCccccCCccCCCChhhH
Q 001532 27 SVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDGVSEKLNPHMC 106 (1058)
Q Consensus 27 ~~~~~~~~i~~~f~~~~Lv~~qi~SFn~Fl~~gl~~i~~~~~~i~~~~~~~~~l~~~~i~i~~P~~~~~~~~~~l~P~Ec 106 (1058)
+.++.|++++++|+.++|+++|++|||+|+.+||++++++++||+.. .++++|+|.++++++| ++++|.||
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 78899999999999999999999999999999999999999999755 7789999999999998 45799999
Q ss_pred hhcCCccCceEEEEEEEEECCCcccee-eEEeEEEEeeeccccccccccCCCCCHHHHHhcCCCCCCCCcEEEEcCceeE
Q 001532 107 RLSDMTYAAPILVNIEYVQGSHTEKTT-MEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKV 185 (1058)
Q Consensus 107 R~r~lTYsa~l~v~v~~~~~~~~~~~~-~~~~~v~iG~iPIMv~S~~C~L~~ls~~elv~~gE~~~d~GGYFIING~EKV 185 (1058)
|+|++||+|||+|+++++.++. .+ +++++|++|+||+||+ ||||||||+|||
T Consensus 81 R~R~lTYsapLyv~lrlv~~~~---~e~~k~~eV~iG~iPlMt~------------------------gGyFIINGsERV 133 (1060)
T COG0085 81 RLRGLTYSAPLYVKLRLVVNET---GEEIKEQEVYMGDIPLMTR------------------------GGYFIINGTERV 133 (1060)
T ss_pred HhcCCccccceEEEEEEEECCc---ccccccceEEeccCcEecC------------------------CcEEEECCeEEE
Confidence 9999999999999999998774 33 6678999999999994 999999999999
Q ss_pred EeeeecccCCEEEEEeCC-CC---cEEEEEEecCCCcceEEEEEeeCCEEEEEEcceeccccHhhHHHHhCCCCHHHHHH
Q 001532 186 LLIQEQLSKNRVIIDTDK-KG---NINASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQ 261 (1058)
Q Consensus 186 I~~q~~~~~N~i~~~~~~-~g---~~~~~v~s~~~~~~s~~~~~~~~g~i~~~~~~~~~~IPl~ilLkALg~~sd~eI~~ 261 (1058)
|++||++|||.++..+.. ++ .+.|.+.+. + ..|..+....++.+++++++.. +||+++||||||++||+||++
T Consensus 134 IVsQ~~rSPgvif~~~~~k~~~~~~~~a~vIp~-r-G~wl~~e~d~~d~~~~rId~~r-kiPvtilLRALG~~tDeeI~~ 210 (1060)
T COG0085 134 IVSQEHRSPGVIFVEKKDKTGSKVLYVARVIPY-R-GSWLEFEFDPKDNLYVRIDRKR-KIPVTILLRALGLETDEEIIE 210 (1060)
T ss_pred EEEEeecCCCeEEecccccCCcceEEEEEEecC-C-cceEEEEEccCccEEEEeeeEE-EeeHHHHHHHhCCCcHHHHHH
Confidence 999999999977666543 34 246788776 3 2455555566788999999853 899999999999999999999
Q ss_pred HhCCc-------hhHHhhhhhhHHHHHhcCCcCHHHHHHHHhhcccccCCC-CCCCChHHHHHHHHHhhhccCCCCC---
Q 001532 262 MVGRD-------PRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFG-SPPNDREGRAFSILRDVFLANVPVH--- 330 (1058)
Q Consensus 262 ~i~~~-------~~~~~~l~~~l~~~~~~~i~t~~~al~yig~~~~~~~~~-~~~~~~~e~~~~~L~~~llpHl~~~--- 330 (1058)
.++.+ ....+.+...+++.....+.++. |++||++++...... .... +.+.++.++.+.+|||++..
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 22333333333333223344444 999999999876332 2334 78999999999999999963
Q ss_pred -CCCCCCcchhHHHHHHHHHHhhcCCCCCCCcccccceEEcchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCCCCc
Q 001532 331 -NNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFD 409 (1058)
Q Consensus 331 -~~~~~~K~~~L~~Mi~kLl~~~~G~~~~DD~D~l~NkRV~~~G~Ll~~lfr~~l~~~~~~ik~~i~k~~~~~~~~~~~~ 409 (1058)
......|+.+|+.|+++|+.+..|.+.+||+|||+||||+++|+||++|||.+|.+|++.+|+++.+...+
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 22345588899999999999999999999999999999999999999999999999999999999875432
Q ss_pred cccccccccchhhhhhhhccCCCcccccccccccceEEcccccccccccccccccc-cccccccccCCCcCCCCCccccc
Q 001532 410 LSQFIVRDSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSP-QFEKSRKVSGPRALQPSQWGMLC 488 (1058)
Q Consensus 410 ~~~~i~~~~It~~i~~~~sTGn~~~~~~~~q~sG~sq~l~rln~ls~lshlRrv~~-~~~~~~k~t~~R~Lhps~wG~iC 488 (1058)
..+..++.||.++.+|++||||+ ++|+||++||+||+|+|||+||++| +++++++.+.+|+||||||||+|
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 22335689999999999999997 6799999999999999999999999 99999999999999999999999
Q ss_pred cCCCCCCCcccccccccceeeee-cCCCChhHHHHHh-hcCCeeccccCccccCCCCcEEEEECCeEEeeccChhhHHHH
Q 001532 489 PCDTPEGEACGLVKNLALMTHVT-TDEEEGPLISLCY-CLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADV 566 (1058)
Q Consensus 489 PveTPEG~~cGLi~~LA~~a~Is-~~~~~~~i~~~l~-~~g~~~l~~~~~~~~~~~~~~~V~lnG~~vG~~~~~~~~~~~ 566 (1058)
|+|||||+|||||||||++|+|+ .+.++.|+++++. .+|++++++++..+ ..|++||.++|.++++..|++.
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 7899999999998 59999999888643 4599999999999999999999
Q ss_pred HHHHhhcCCcCceeEEEeccccc----eEEEecCCCeeeeeEEEEecCcccchhhhHHHhhcC-CccchhhhccCceeEe
Q 001532 567 MRKLRRAGKIGEFVSVFVNEKQR----CVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDG-VRSFDDFLREGLIEYL 641 (1058)
Q Consensus 567 lr~~rr~~~i~~~v~i~~~~~~~----~i~I~sd~GRl~RPll~v~~~~~~~~~~~~~~l~~~-~~s~~~~~~~~~iE~i 641 (1058)
+|.+|+ + +..+++++...... ++++.++.||.+||++.++|+..++..++++++..+ ..+|.+|+..| +||+
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 77778877665544 899999999999999999999999999999998877 67999999999 9999
Q ss_pred ccccccceEEEeecCCCCCCceeeeecCccccccccccCCCCCCCCCCccccccccccCCccceeEeeeeccccceeeee
Q 001532 642 DVNEENNALIALYEGDATPDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLV 721 (1058)
Q Consensus 642 d~~e~~~~~Ia~~~~~~~~~~th~Ei~p~~~ls~~asliPF~~hNqspRn~yq~~M~KQaiG~~~~n~~~R~D~~~y~l~ 721 (1058)
|+.|+.+++||..+++ +||+|++|..++|.+|++|||++|||||||||||+|+||++|++..|+..|.|+..|.++
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 9999999999999887 799999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCcceeechhhhhhcCCCCCCCcceEEEEeecCCCCCCCcEEEecceeeccceEEEEEEEEEEEeecccCCccceecCC
Q 001532 722 YPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILRP 801 (1058)
Q Consensus 722 ypQ~Plv~t~~~~~~~~~~~~~G~N~~Vav~~y~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~e~~~~p 801 (1058)
|||.|+|.+ +|+|+|||++||||||+||||||||||||++++||+|||+||++|++++++++.|.+|++..|
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 899999999999999999999999999999999999999999999999999999998887778
Q ss_pred CCCCCcccccccCCCCccccCCcEeCCCCEEEEEecCCCCCCCCCCC--CCCCCcccccceEEeeCCCCCceEEEEEEEe
Q 001532 802 DRTGPGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSP--TGQTDSRYRSARQTYKGPDGETCVVDRVALC 879 (1058)
Q Consensus 802 ~~~~~~~~~~~~ld~dGi~~~g~~v~~gd~li~k~~~~~~~~~~~~~--~~~~~~~~~~~s~~~~~~~~~~~~vd~v~~~ 879 (1058)
+.+. ..|++||+|||++||++|+.|||||||++|+++.+..... ......+.+|+|+++++++ +|+||.|.++
T Consensus 732 ~~~e---~~~~~Lde~Gii~ig~~V~~gdilvgk~tP~~~~~~~~ee~ll~i~~ek~rdtsl~~~~g~--~G~V~~V~~~ 806 (1060)
T COG0085 732 NVSE---EALRNLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRIFGEKVRDTSLRVPHGE--EGIVDDVQVF 806 (1060)
T ss_pred CcCH---HHHhcCCccCccccccEEcCCCEEEEeeCCCCCCCCCchhhhhccccceeeccceeecCCC--CeEEEEEEEE
Confidence 8753 6799999999999999999999999999999887643210 0011234799999999999 9999999999
Q ss_pred eCCC----CCEEEEEEEeecCCCcccceecccCCCccEEEeeeccCCCCCCCCCCCCcEEeCCCCCCCcccHHHHHHHhh
Q 001532 880 SDKN----GDLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLG 955 (1058)
Q Consensus 880 ~~~~----~~~~v~v~i~~~R~p~iGDKf~sRhGqKGvvs~i~~~~DmPf~~~G~~pDiIiNP~~~PSRMtiGql~E~~~ 955 (1058)
.+++ +.+.|||++|+.|.|++|||||||||||||||+|||+||||||+||++||||+|||||||||||||++|+++
T Consensus 807 ~~~~~~~g~~~~vkV~v~~~R~~~~GDK~a~RHG~KGVis~i~p~eDMPf~~~G~~~DiilNP~gvPSRM~iGqilE~~l 886 (1060)
T COG0085 807 TREDGDPGVNKLVKVYVAQKRKPQIGDKMAGRHGNKGVVSKIVPQEDMPFLEDGTPPDIILNPLGVPSRMNIGQILETHL 886 (1060)
T ss_pred eccCCCcCceEEEEEEEEEeccCCccccccccCCCCceeeeecCcccCCcCCCCCcccEEECCCCCCccccHHHHHHHHH
Confidence 8877 789999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccchhcCCceeeeecccCCCCCCCCHHHHHHHHHHcCCCCCCceEEEeCCCCcEeeeeEeeeeeeeeccccccCcceEEe
Q 001532 956 GKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHAR 1035 (1058)
Q Consensus 956 gk~~~~~g~~~~~tpf~~~~~~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if~G~~yy~rL~Hmv~dK~~~R 1035 (1058)
||||++.|...++|||+ ++..+++.++|+++||++.|+++||||+||++|+++||+|++|||||+|||+||+|||
T Consensus 887 G~a~~~~G~~~~~~~F~-----g~~~~~~~~~l~~~g~~~~Gk~~lydG~TGe~~~~~i~vG~~Y~~kL~HmV~dK~HaR 961 (1060)
T COG0085 887 GKAAALLGIPVDTPVFD-----GAPEEDIRELLKEAGFPYSGKEVLYDGRTGEPFDAPIFVGVMYYQKLHHMVDDKIHAR 961 (1060)
T ss_pred HHHHHhcCceeccCCcC-----CCCHHHHHHHHHHcCCCCCCCEEeecCCCCCcccccEEEEehHHHhHHhhhcccceee
Confidence 99999999999999999 7999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCccccccCCcCcccCCCCC
Q 001532 1036 GSGPRVMLTRQPTEGRARNGGF 1057 (1058)
Q Consensus 1036 ~~Gp~~~lT~QP~~Gr~~~GG~ 1057 (1058)
|||||+.+||||++||++.|||
T Consensus 962 s~GP~s~lT~QP~~Gka~~GG~ 983 (1060)
T COG0085 962 STGPYSLVTQQPLGGKAQFGGQ 983 (1060)
T ss_pred ccCCceeeecCCCCcccccCCc
Confidence 9999999999999999999998
No 6
>TIGR02013 rpoB DNA-directed RNA polymerase, beta subunit. This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit.
Probab=100.00 E-value=4e-198 Score=1839.39 Aligned_cols=848 Identities=26% Similarity=0.436 Sum_probs=739.8
Q ss_pred cccccccccccccccchHHHHHHHHHHHHH----------hCHHHHHHhcCcceecCCCcEEEEEeEEEEcCCccccCCc
Q 001532 28 VVDKFQLLPEFLKVRGLVKQHLDSFNYFVN----------TGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDGV 97 (1058)
Q Consensus 28 ~~~~~~~i~~~f~~~~Lv~~qi~SFn~Fl~----------~gl~~i~~~~~~i~~~~~~~~~l~~~~i~i~~P~~~~~~~ 97 (1058)
.+..|..++.+|+.++|++||++||||||+ +||++++++.++|+.. ++++.|+|.++++++|.+
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 345799999999999999999999999999 8999999999999765 578999999999999987
Q ss_pred cCCCChhhHhhcCCccCceEEEEEEEEECCCccceeeEEeEEEEeeeccccccccccCCCCCHHHHHhcCCCCCCCCcEE
Q 001532 98 SEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYF 177 (1058)
Q Consensus 98 ~~~l~P~EcR~r~lTYsa~l~v~v~~~~~~~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~ls~~elv~~gE~~~d~GGYF 177 (1058)
+|+|||+|++||+|+|+|+++++..+.+..+++++++|++|+||+|+ .||||
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 69999999999999999999997533111145566799999999997 49999
Q ss_pred EEcCceeEEeeeecccCCEEEEEeC---CCC--cEEEEEEecCCCcceEEEEEeeCCEEEEEEcceeccccHhhHHHHhC
Q 001532 178 IIKGTEKVLLIQEQLSKNRVIIDTD---KKG--NINASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMG 252 (1058)
Q Consensus 178 IING~EKVI~~q~~~~~N~i~~~~~---~~g--~~~~~v~s~~~~~~s~~~~~~~~g~i~~~~~~~~~~IPl~ilLkALg 252 (1058)
||||+||||++||++|||.++++.. ++| .+.|.++|.+ .+|..+.+.+++.+|++++++. +||+++||||||
T Consensus 130 IINGsERVIV~Qe~rspg~~~~~~~~~~~~~~~~~~a~iis~r--gswl~~e~~~~~~i~v~i~~~~-kIPi~illrALG 206 (1065)
T TIGR02013 130 IINGAERVVVSQLHRSPGVFFSSEKDTHKSGKVLFSARIIPYR--GSWLEFETDKKDVLYVRIDRKR-KLPATVLLRALG 206 (1065)
T ss_pred EECCcEEEEEEEeecCCCEEEEEccccCCCCceEEEEEEEeCC--CCceEEEEecCCeEEEEecCCC-ceeHHHHHHHcC
Confidence 9999999999999999998887654 335 4789999875 3455555677889999999975 999999999999
Q ss_pred CCCHHHHHHHhCCchhHHhhhhhhHHHHHhcCCcCHHHHHHHHhhcccccCCCCCCCChHHHHHHHHHhhhcc-------
Q 001532 253 MESDQEVVQMVGRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLA------- 325 (1058)
Q Consensus 253 ~~sd~eI~~~i~~~~~~~~~l~~~l~~~~~~~i~t~~~al~yig~~~~~~~~~~~~~~~~e~~~~~L~~~llp------- 325 (1058)
+++|+||++.++.+..+.+. |++ ..+.++++|+.||++++++. ... ..+.|+.+|++.+||
T Consensus 207 ~~sd~eI~~~i~~~~~i~~~----l~~---~~~~~~e~Al~~i~~~~~~g----~~~-~~~~a~~~l~~~f~~~~rY~Lg 274 (1065)
T TIGR02013 207 YTIDTLILNRLGSGEYIRNT----LRK---DPTNSEEEALVEIYRKLRPG----EPP-TVEAARSLLENLFFDPKRYDLG 274 (1065)
T ss_pred CCcchhhhhhcCchHHHHHH----HHh---ccccCHHHHHHHHHhhcCCC----Ccc-hHHHHHHHHHHHhcCccccccc
Confidence 99999999999655444433 322 23678999999999998775 233 678899999999987
Q ss_pred CCCCCC------------CCCCCcchhHHHHHHHHHHhhcCCCCCCCcccccceEEcchHHHHHHHHHHHHHHHHHHHHH
Q 001532 326 NVPVHN------------NNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQK 393 (1058)
Q Consensus 326 Hl~~~~------------~~~~~K~~~L~~Mi~kLl~~~~G~~~~DD~D~l~NkRV~~~G~Ll~~lfr~~l~~~~~~ik~ 393 (1058)
|+|... .....|+++|+ |+++|+++..|...+||+|||+||||+++|+||+.|||.+|+++++.+++
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 11124889997 99999999999999999999999999999999999999999999999999
Q ss_pred HHHhHhcCCCCCCCCccccccccccchhhhhhhhccCCCcccccccccccceEEcccccccccccccccccc----cccc
Q 001532 394 TVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSP----QFEK 469 (1058)
Q Consensus 394 ~i~k~~~~~~~~~~~~~~~~i~~~~It~~i~~~~sTGn~~~~~~~~q~sG~sq~l~rln~ls~lshlRrv~~----~~~~ 469 (1058)
++.+. . ...+++..+++++.||+++++||+|| |+||+|+|+||+|+|||+||+++ ++.+
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 88743 1 12466777889999999999999887 89999999999999999999997 6999
Q ss_pred cccccCCCcCCCCCccccccCCCCCCCcccccccccceeeeecCCCChhHHHHHhhcCCeeccccCccccCCCCcEEEEE
Q 001532 470 SRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIF 549 (1058)
Q Consensus 470 ~~k~t~~R~Lhps~wG~iCPveTPEG~~cGLi~~LA~~a~Is~~~~~~~i~~~l~~~g~~~l~~~~~~~~~~~~~~~V~l 549 (1058)
+++.+.||+|||||||||||+|||||+|||||+|||++|+|+.
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 CCeEEeeccChhhHHHHHHHHhhcCCcCceeEEEeccccceEEEecCCCeeeeeEEEEecCcccchhhhHHHhhcCCccc
Q 001532 550 NGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSF 629 (1058)
Q Consensus 550 nG~~vG~~~~~~~~~~~lr~~rr~~~i~~~v~i~~~~~~~~i~I~sd~GRl~RPll~v~~~~~~~~~~~~~~l~~~~~s~ 629 (1058)
.|.+.||++.|+||++.
T Consensus 460 -----------------------------------------------~G~i~~P~~~V~ng~~~---------------- 476 (1065)
T TIGR02013 460 -----------------------------------------------YGFIETPYRKVKDGKVV---------------- 476 (1065)
T ss_pred -----------------------------------------------ceEEeCCeEEEECCeEe----------------
Confidence 13355899999887543
Q ss_pred hhhhccCceeEeccccccceEEEeecCCCC-----------------------CCceeeeecCccccccccccCCCCCCC
Q 001532 630 DDFLREGLIEYLDVNEENNALIALYEGDAT-----------------------PDTTHIEIEPFTILGVIAGLIPYPHHN 686 (1058)
Q Consensus 630 ~~~~~~~~iE~id~~e~~~~~Ia~~~~~~~-----------------------~~~th~Ei~p~~~ls~~asliPF~~hN 686 (1058)
..+.+||+|++|+++..||..+.++. ..+||+||+|.+++|++||||||+|||
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 23569999999999999998765542 246999999999999999999999999
Q ss_pred CCCccccccccccCCccce-----------------------------------eEeeeecccc---------ceee---
Q 001532 687 QSPRNTYQCAMGKQAMGNI-----------------------------------AFNQLCRMDS---------LLYL--- 719 (1058)
Q Consensus 687 qspRn~yq~~M~KQaiG~~-----------------------------------~~n~~~R~D~---------~~y~--- 719 (1058)
|||||||||||||||||++ ++++..|.|+ +.|.
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 8999999995 4455
Q ss_pred -------eeCCCcceeech----hhhhhc------CCCCCCCcceEEEEeecCCCCCCCcEEEecceeeccceEEEEEEE
Q 001532 720 -------LVYPQRPLLTTR----TIELVG------YDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKK 782 (1058)
Q Consensus 720 -------l~ypQ~Plv~t~----~~~~~~------~~~~~~G~N~~Vav~~y~Gyn~EDaiiink~s~~rg~~~s~~~~~ 782 (1058)
++|||+|||+|+ ..+.+. ++|+|+|+|++||||||+||||||||||||+|++||+|+|+||++
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 469999999995 445543 899999999999999999999999999999999999999999999
Q ss_pred EEEEeecccCCccceecC--CCCCCCcccccccCCCCccccCCcEeCCCCEEEEEecCCCCCCCCCC------CCCCCCc
Q 001532 783 YTAINQKYANSTSDRILR--PDRTGPGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMS------PTGQTDS 854 (1058)
Q Consensus 783 ~~~~~~~~~~~~~e~~~~--p~~~~~~~~~~~~ld~dGi~~~g~~v~~gd~li~k~~~~~~~~~~~~------~~~~~~~ 854 (1058)
|++++++++.|. |.++. |+.. ...|++||+||||++|++|++|||||||++|....+.... -++.+..
T Consensus 713 ~~~~~~~~~~g~-e~~~~~~p~~~---~~~~~~Ld~dGi~~~G~~v~~gdilvgk~~p~~~~~~~~~~~l~~~~~~~~~~ 788 (1065)
T TIGR02013 713 YEVEARDTKLGP-EEITRDIPNVS---EEALRNLDENGIVRIGAEVKAGDILVGKVTPKGETELTPEEKLLRAIFGEKAR 788 (1065)
T ss_pred EEEEeeccCCCc-eEeeccCCCCc---hhhhhccCCCCCccCccEeCCCCEEEEEecCCcccccChhhhhhhhhcccCCc
Confidence 999998776665 54543 5542 2479999999999999999999999999998643221100 0122223
Q ss_pred ccccceEEeeCCCCCceEEEEEEEeeCCCC-------CEEEEEEEeecCCCcccceecccCCCccEEEeeeccCCCCCCC
Q 001532 855 RYRSARQTYKGPDGETCVVDRVALCSDKNG-------DLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSE 927 (1058)
Q Consensus 855 ~~~~~s~~~~~~~~~~~~vd~v~~~~~~~~-------~~~v~v~i~~~R~p~iGDKf~sRhGqKGvvs~i~~~~DmPf~~ 927 (1058)
..+|+|++++.++ +|+||+|.++.++++ .+.|+|++|+.|+|+||||||||||||||||+|||+||||||+
T Consensus 789 ~~~d~s~~~~~~~--~g~V~~V~~~~~~~~~~~~~~~~~~vkv~ir~~R~p~iGDKfasRHGqKGvis~i~~~eDMPf~~ 866 (1065)
T TIGR02013 789 DVRDTSLRVPPGV--EGTVIDVKVFSRKQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLE 866 (1065)
T ss_pred cccccceEccCCC--CEEEEEEEEEeccCCCccCcCccEEEEEEEeecccccccchhhhcccCceeEEeEecCCCCCccC
Confidence 4689999999999 999999999876665 5789999999999999999999999999999999999999999
Q ss_pred CCCCCcEEeCCCCCCCcccHHHHHHHhhccchhcC--Cceeeeec-ccCCCCCCCCHHHHHHHHHHcCCCCCCceEEEeC
Q 001532 928 RGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSC--GRFHYGSA-FGEPSGHADTVESISETLVKHGFSYNGKDMIYSG 1004 (1058)
Q Consensus 928 ~G~~pDiIiNP~~~PSRMtiGql~E~~~gk~~~~~--g~~~~~tp-f~~~~~~~~~~~~~~~~l~~~g~~~~G~e~ly~g 1004 (1058)
||++|||||||||||||||||||+|+++||+|++. |.+.++|| |. +...+++++.|.++||+++|+|.||||
T Consensus 867 ~G~~pDiIiNPhg~PSRMtiGqllE~~~gka~~~~~~~~~~~~tp~f~-----~~~~~~~~~~l~~~g~~~~G~e~l~~G 941 (1065)
T TIGR02013 867 DGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRKGVPIATPVFD-----GASEEEIKEYLEKAGLPRDGKVRLYDG 941 (1065)
T ss_pred CCCCccEEECCCCCcccccHHHHHHHHHHHHHHhccCCCeEEeccCcC-----CccHHHHHHHHHHcCCCCCCCEEEEcC
Confidence 99999999999999999999999999999999987 66788999 66 678899999999999999999999999
Q ss_pred CCCcEeeeeEeeeeeeeeccccccCcceEEeccCCccccccCCcCcccCCCCC
Q 001532 1005 ITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGF 1057 (1058)
Q Consensus 1005 ~tG~~~~~~if~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~ 1057 (1058)
+||++|+++||+|++|||||+|||+||+|||++|||+.|||||++||+|+|||
T Consensus 942 ~TG~~~~~~ifvG~~yy~rL~HmV~DK~haRs~Gp~~~lT~QP~~Grsr~GG~ 994 (1065)
T TIGR02013 942 RTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 994 (1065)
T ss_pred CCCCCccccEEEeehheeechhhhcchhhhcccCCccceeeCCCcccccCCCe
Confidence 99999999999999999999999999999999999999999999999999997
No 7
>cd00653 RNA_pol_B_RPB2 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.
Probab=100.00 E-value=9.5e-197 Score=1821.20 Aligned_cols=774 Identities=46% Similarity=0.769 Sum_probs=694.2
Q ss_pred hHHHHHHHHHHHHHhCHHHHHHhcCcceecC-CCcEEEEEeEEEEcCCccccCCccCCCChhhHhhcCCccCceEEEEEE
Q 001532 44 LVKQHLDSFNYFVNTGIRKIVRANDRIVSGI-DPSIFLRFKDVRIGQPSMTVDGVSEKLNPHMCRLSDMTYAAPILVNIE 122 (1058)
Q Consensus 44 Lv~~qi~SFn~Fl~~gl~~i~~~~~~i~~~~-~~~~~l~~~~i~i~~P~~~~~~~~~~l~P~EcR~r~lTYsa~l~v~v~ 122 (1058)
|++||++|||+|+++||+++++++++|+... +..+.++|++++|++|.+.++...++++|+|||+|++||+|+++|+++
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 6789999999999999999999999997654 467899999999999998776556889999999999999999999999
Q ss_pred EEECCCccceeeEEeEEEEeeeccccccccccCCCCCHHHHHhcCCCCCCCCcEEEEcCceeEEeeeecccCCEEEEEeC
Q 001532 123 YVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVIIDTD 202 (1058)
Q Consensus 123 ~~~~~~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~ls~~elv~~gE~~~d~GGYFIING~EKVI~~q~~~~~N~i~~~~~ 202 (1058)
++.++. ..+..++|++|+|||||+|++|||++++++|+++.||||.|+||||||||+|||||+||++++|+++++ +
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 987652 233567899999999999999999999999999999999999999999999999999999999999888 4
Q ss_pred CCCcEEEEEEecCCC---c-ceEEEEEee-CCEEEEEEcceeccccHhhHHHHhCCCCHHHHHHHhCCchhHHhhhhhhH
Q 001532 203 KKGNINASVTSSTET---V-KSKTVIQME-KGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGRDPRYSALLLPSI 277 (1058)
Q Consensus 203 ~~g~~~~~v~s~~~~---~-~s~~~~~~~-~g~i~~~~~~~~~~IPl~ilLkALg~~sd~eI~~~i~~~~~~~~~l~~~l 277 (1058)
+.+...+.+++.... . .+..+.... ++.++.+++...
T Consensus 157 ~~~~~~~~~~s~~~~~~~~~s~~~~~~~~~~~~i~~~i~~~~-------------------------------------- 198 (866)
T cd00653 157 SKGKRIYTKTSIPSYSPYRGSWLEVKSDKKKDRIYVRIDLKR-------------------------------------- 198 (866)
T ss_pred CCCcEEEEEEEccCCCcCccEEEEEEEccCCCeEEEEecccC--------------------------------------
Confidence 445566666665542 1 222222222 345666655431
Q ss_pred HHHHhcCCcCHHHHHHHHhhcccccCCCCCCCChHHHHHHHHHhhhccCCCCCCCCCCCcchhHHHHHHHHHHhhcCCCC
Q 001532 278 EECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDA 357 (1058)
Q Consensus 278 ~~~~~~~i~t~~~al~yig~~~~~~~~~~~~~~~~e~~~~~L~~~llpHl~~~~~~~~~K~~~L~~Mi~kLl~~~~G~~~ 357 (1058)
+++|++|||++| .+|++|++||+++..|.+.
T Consensus 199 ----------~~~al~~ig~~~---------------------------------------~~L~~Mi~kLl~~~~g~~~ 229 (866)
T cd00653 199 ----------QEEALKYIGKRF---------------------------------------EDLIYMIRKLILLVLGKGK 229 (866)
T ss_pred ----------HHHHHHHHHHHH---------------------------------------HHHHHHHHHHHHHhcCCCC
Confidence 678999999854 6799999999999999999
Q ss_pred CCCcccccceEEcchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCCCCccccccccccchhhhhhhhccCCCccccc
Q 001532 358 MDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFDVKRF 437 (1058)
Q Consensus 358 ~DD~D~l~NkRV~~~G~Ll~~lfr~~l~~~~~~ik~~i~k~~~~~~~~~~~~~~~~i~~~~It~~i~~~~sTGn~~~~~~ 437 (1058)
+||+|||+||||+++|+||+.+|++.|+++++.++..+.+.+.+.. .++....++++.||++|++||+||||..+..
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 3455566688899999999999999997666
Q ss_pred ccccccceEEcccccccccccccccccc-cccccccccCCCcCCCCCccccccCCCCCCCcccccccccceeeeecCCCC
Q 001532 438 KMHRKGMTQVLARLSFIGTLGHMTRVSP-QFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEE 516 (1058)
Q Consensus 438 ~~q~sG~sq~l~rln~ls~lshlRrv~~-~~~~~~k~t~~R~Lhps~wG~iCPveTPEG~~cGLi~~LA~~a~Is~~~~~ 516 (1058)
.+|++|+||+|+|+||+++|||+||||+ ++++++|++++|+||||||||+||||||||++|||++|||++|+|+
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 9999999999999999999999999999999999999999999885
Q ss_pred hhHHHHHhhcCCeeccccCccccCCCCcEEEEECCeEEeeccChhhHHHHHHHHhhcCCcCceeEEEeccccceEEEecC
Q 001532 517 GPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASD 596 (1058)
Q Consensus 517 ~~i~~~l~~~g~~~l~~~~~~~~~~~~~~~V~lnG~~vG~~~~~~~~~~~lr~~rr~~~i~~~v~i~~~~~~~~i~I~sd 596 (1058)
T Consensus 382 -------------------------------------------------------------------------------- 381 (866)
T cd00653 382 -------------------------------------------------------------------------------- 381 (866)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred CCeeeeeEEEEecCcccchhhhHHHhhcCCccchhhhccCceeEeccccccceEEEeecCCCCCCceeeeecCccccccc
Q 001532 597 GGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTTHIEIEPFTILGVI 676 (1058)
Q Consensus 597 ~GRl~RPll~v~~~~~~~~~~~~~~l~~~~~s~~~~~~~~~iE~id~~e~~~~~Ia~~~~~~~~~~th~Ei~p~~~ls~~ 676 (1058)
||++||+++|+ ..+||+||+|.++||++
T Consensus 382 -Gr~~rP~~~v~---------------------------------------------------~~~th~ei~~~~~ls~~ 409 (866)
T cd00653 382 -GRIERPYRIVE---------------------------------------------------KEVTHIEISPSQILSVA 409 (866)
T ss_pred -eEeeeeEEEec---------------------------------------------------cceEEEEeCccceeeee
Confidence 99999999753 13699999999999999
Q ss_pred cccCCCCCCCCCCccccccccccCCccceeEeeeeccccceeeeeCCCcceeechhhhhhcCCCCCCCcceEEEEeecCC
Q 001532 677 AGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSG 756 (1058)
Q Consensus 677 asliPF~~hNqspRn~yq~~M~KQaiG~~~~n~~~R~D~~~y~l~ypQ~Plv~t~~~~~~~~~~~~~G~N~~Vav~~y~G 756 (1058)
||+|||+||||||||||||||+|||||++++|+..|+|++.|+|.|||+|||+|+..+.++++++|+|+||+||||||+|
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 CCCCCcEEEecceeeccceEEEEEEEEEEEeecccCCccceecCCCCCCCcccccccCCCCccccCCcEeCCCCEEEEEe
Q 001532 757 YDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILRPDRTGPGAERMQILDDDGLAAPGEIIKPNDVYINKE 836 (1058)
Q Consensus 757 yn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~e~~~~p~~~~~~~~~~~~ld~dGi~~~g~~v~~gd~li~k~ 836 (1058)
|||||||||||+|+|||+|+|+||++|++++++...+..+.+. ++........|++||+||||++|++|++||+||||+
T Consensus 490 yn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~ld~dGi~~~g~~v~~gd~li~k~ 568 (866)
T cd00653 490 YNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITR-GDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKI 568 (866)
T ss_pred ccccceeeeehhhhhcCceeEEEEEEEEEEEEecCCCcceEec-CCCCCCChHHhhccCCCCCcCCCCEecCCCEEEEEe
Confidence 9999999999999999999999999999999876665555443 121111235799999999999999999999999999
Q ss_pred cCCCCCCCCCCCCCCCCcccccceEEeeCCCCCceEEEEEEEee---CCCCCEEEEEEEeecCCCcccceecccCCCccE
Q 001532 837 SPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCS---DKNGDLCIKFLIRHTRRPELGDKFSSRHGQKGV 913 (1058)
Q Consensus 837 ~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~vd~v~~~~---~~~~~~~v~v~i~~~R~p~iGDKf~sRhGqKGv 913 (1058)
+|....+... .+.......+|.|++++.++ .|+||+|.++. +.++...|+|++|+.|+|+||||||||||||||
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 01112234689999999999 99999999987 567889999999999999999999999999999
Q ss_pred EEeeeccCCCCCCCCCCCCcEEeCCCCCCCcccHHHHHHHhhccchhcCCceeeeecccCCCCCCCCHHHHHHHHHHcCC
Q 001532 914 CGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGF 993 (1058)
Q Consensus 914 vs~i~~~~DmPf~~~G~~pDiIiNP~~~PSRMtiGql~E~~~gk~~~~~g~~~~~tpf~~~~~~~~~~~~~~~~l~~~g~ 993 (1058)
||++||+||||||+||++|||||||||||||||||||+|+++||++++.|.+.|+|||+ ....+++.+.|.++||
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 5678899999999999
Q ss_pred CCCCceEEEeCCCCcEeeeeEeeeeeeeeccccccCcceEEeccCCccccccCCcCcccCCCCC
Q 001532 994 SYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGF 1057 (1058)
Q Consensus 994 ~~~G~e~ly~g~tG~~~~~~if~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~ 1057 (1058)
+++|+|.||||+||++|+++||+|++|||||+|||+||+|||++||++.+||||++||+|+|||
T Consensus 721 ~~~G~e~~y~g~tG~~~~~~if~G~~yyqrL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~ 784 (866)
T cd00653 721 NYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQ 784 (866)
T ss_pred CCCCcEEEEcCCCCCCcccceEEeehhhhhhhhhhchhhhhcccCCcchhccCcCccccccCCe
Confidence 9999999999999999999999999999999999999999999999999999999999999997
No 8
>PRK00405 rpoB DNA-directed RNA polymerase subunit beta; Reviewed
Probab=100.00 E-value=4.7e-194 Score=1812.06 Aligned_cols=848 Identities=25% Similarity=0.436 Sum_probs=728.4
Q ss_pred cccccccccccccccchHHHHHHHHHHHH-------HhCHHHHHHhcCcceecCCCcEEEEEeEEEEcCCccccCCccCC
Q 001532 28 VVDKFQLLPEFLKVRGLVKQHLDSFNYFV-------NTGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDGVSEK 100 (1058)
Q Consensus 28 ~~~~~~~i~~~f~~~~Lv~~qi~SFn~Fl-------~~gl~~i~~~~~~i~~~~~~~~~l~~~~i~i~~P~~~~~~~~~~ 100 (1058)
.+..+..++.++..++|++||++|||||| ++||++++++.++|+.. ++++.|+|.++++++|.+
T Consensus 11 ~r~~~~~~~~~~~~p~Lv~~Qi~SFn~Fl~~~~~~~~~gL~~ii~~~~pI~~~-~~~~~l~f~~~~l~~P~~-------- 81 (1112)
T PRK00405 11 IRKSFGKIKEVLELPNLLEIQLDSFDWFLQLDVPPEDEGLEEVFRSIFPIEDF-NGNLSLEFVSYELGEPKY-------- 81 (1112)
T ss_pred eEeecccccccCCCCCHHHHHHHHHHHHHhcCCcccchhHHHHHHhcCCEEec-CCcEEEEEeeeEcCCCCC--------
Confidence 34567778888999999999999999999 99999999999999764 678999999999999975
Q ss_pred CChhhHhhcCCccCceEEEEEEEEECCCccceeeEEeEEEEeeeccccccccccCCCCCHHHHHhcCCCCCCCCcEEEEc
Q 001532 101 LNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIK 180 (1058)
Q Consensus 101 l~P~EcR~r~lTYsa~l~v~v~~~~~~~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~ls~~elv~~gE~~~d~GGYFIIN 180 (1058)
+|+|||+|++||+|||+|+++++..+. +++++++|++|+||||+ +|||||||
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 899999999999999999999986442 35566799999999997 89999999
Q ss_pred CceeEEeeeecccCCEEEEEeCC-----CCcEEEEEEecCCCcceEEEEEeeCCEEEEEEcceeccccHhhHHHHhCCCC
Q 001532 181 GTEKVLLIQEQLSKNRVIIDTDK-----KGNINASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMES 255 (1058)
Q Consensus 181 G~EKVI~~q~~~~~N~i~~~~~~-----~g~~~~~v~s~~~~~~s~~~~~~~~g~i~~~~~~~~~~IPl~ilLkALg~~s 255 (1058)
|+||||++||+++||.++.+... +..+.|+++|.+ .+|..+.+.+++.+|+++++. ++||+++||||||+ |
T Consensus 134 G~ERVIVsQe~rSPg~~~~~~~~k~~~~k~~y~a~Iis~r--Gswl~~e~d~k~~I~vri~~~-~kIPi~iLLrALGl-s 209 (1112)
T PRK00405 134 GTERVIVSQLHRSPGVYFDHDKDKTSSGKLLYSARIIPYR--GSWLEFEFDPKDILYVRIDRR-RKLPVTVLLRALGY-S 209 (1112)
T ss_pred CeEEEEEEEeecCCCEEEEEeccccCCCceeEEEEEEECC--CCcEEEEEecCCeEEEEecCC-CcccHHHHHHHcCC-C
Confidence 99999999999999987766532 223789999875 356666667788999999986 69999999999999 8
Q ss_pred HHHHHHHhCCchhHH-------------------------h------------hhhhhHHHHH-hcCCcCHHHHHHHHhh
Q 001532 256 DQEVVQMVGRDPRYS-------------------------A------------LLLPSIEECA-NLDIYTQEKALEYLEG 297 (1058)
Q Consensus 256 d~eI~~~i~~~~~~~-------------------------~------------~l~~~l~~~~-~~~i~t~~~al~yig~ 297 (1058)
|+||++.++.+..+. + .+...+.+.. ...+.++++|+.||++
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 999999995332222 0 0112232222 2346799999999999
Q ss_pred cccccCCCCCCCChHHHHHHHHHhhhc-------cCCCCCCCC--------CC----CcchhHHHHHHHHHHhhcCCCCC
Q 001532 298 KVKRSTFGSPPNDREGRAFSILRDVFL-------ANVPVHNNN--------FR----PKCFYVAVMLRRMVEAMLNKDAM 358 (1058)
Q Consensus 298 ~~~~~~~~~~~~~~~e~~~~~L~~~ll-------pHl~~~~~~--------~~----~K~~~L~~Mi~kLl~~~~G~~~~ 358 (1058)
++++. ... ..+.|+.+|++.+| ||+|....+ .. .|++ +++|+++|+++..|.+.+
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-TVEAARSLLENLFFDPKRYDLSKVGRYKLNKKLGLDEDEDVRVLTKED-IIATIKYLINLRNGKGEV 363 (1112)
T ss_pred hcCCC----Ccc-hHHHHHHHHHHHhcCccccccccCCceecchhcccCcccccccccHHH-HHHHHHHHHhhhcccCCC
Confidence 99875 233 66789999999886 999965322 11 3444 489999999999999999
Q ss_pred CCcccccceEEcchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCCCCccccccccccchhhhhhhhccCCCcccccc
Q 001532 359 DDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFDVKRFK 438 (1058)
Q Consensus 359 DD~D~l~NkRV~~~G~Ll~~lfr~~l~~~~~~ik~~i~k~~~~~~~~~~~~~~~~i~~~~It~~i~~~~sTGn~~~~~~~ 438 (1058)
||+|||+||||+++|+||++||+.+|+++++.+++++.+.. ...+++..+++++.||++|++||+||
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 99999999999999999999999999999999999987531 13467788889999999999999887
Q ss_pred cccccceEEcccccccccccccccccc----cccccccccCCCcCCCCCccccccCCCCCCCcccccccccceeeeecCC
Q 001532 439 MHRKGMTQVLARLSFIGTLGHMTRVSP----QFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDE 514 (1058)
Q Consensus 439 ~q~sG~sq~l~rln~ls~lshlRrv~~----~~~~~~k~t~~R~Lhps~wG~iCPveTPEG~~cGLi~~LA~~a~Is~~~ 514 (1058)
|+||+|+|+|++|+|||+||+++ ++.++++.+.||+|||||||||||+|||||++||||+|||++|+|+.
T Consensus 431 ----glSQ~Ldq~NpLselshkRRlss~gpggl~r~~a~~~~R~lH~ShyGriCPiETPEG~n~GLV~nLA~~a~i~~-- 504 (1112)
T PRK00405 431 ----QLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNE-- 504 (1112)
T ss_pred ----CcceeeccCCHHHhhhhhceecccCCCCcCccccCCcccccCccccccccCcCCCCCCccccccchhhcccccc--
Confidence 88999999999999999999998 69999999999999999999999999999999999999999999983
Q ss_pred CChhHHHHHhhcCCeeccccCccccCCCCcEEEEECCeEEeeccChhhHHHHHHHHhhcCCcCceeEEEeccccceEEEe
Q 001532 515 EEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIA 594 (1058)
Q Consensus 515 ~~~~i~~~l~~~g~~~l~~~~~~~~~~~~~~~V~lnG~~vG~~~~~~~~~~~lr~~rr~~~i~~~v~i~~~~~~~~i~I~ 594 (1058)
+|+.. ..|.+++||.|- .
T Consensus 505 -----------~G~~~------------tp~~~~~nG~~~---~------------------------------------ 522 (1112)
T PRK00405 505 -----------YGFIE------------TPYRKVVDGKVT---D------------------------------------ 522 (1112)
T ss_pred -----------CCccc------------cceEEEECCeEc---c------------------------------------
Confidence 45421 246788898861 0
Q ss_pred cCCCeeeeeEEEEecCcccchhhhHHHhhcCCccchhhhccCceeEeccccccceEEEeecCCCC---------------
Q 001532 595 SDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDAT--------------- 659 (1058)
Q Consensus 595 sd~GRl~RPll~v~~~~~~~~~~~~~~l~~~~~s~~~~~~~~~iE~id~~e~~~~~Ia~~~~~~~--------------- 659 (1058)
.+||+|++|+++..||....++.
T Consensus 523 ------------------------------------------~i~yl~a~eE~~~~Ia~~~~~l~~~~~~~~~~i~~r~~ 560 (1112)
T PRK00405 523 ------------------------------------------EIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYK 560 (1112)
T ss_pred ------------------------------------------ceEECCHHHhcCcEEEecCcccCCCCcccCceEEEEec
Confidence 15677777777777776543332
Q ss_pred --------CCceeeeecCccccccccccCCCCCCCCCCccccccccccCCccceeE------------------------
Q 001532 660 --------PDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAF------------------------ 707 (1058)
Q Consensus 660 --------~~~th~Ei~p~~~ls~~asliPF~~hNqspRn~yq~~M~KQaiG~~~~------------------------ 707 (1058)
..+||+||+|.+++|++||||||+||||||||+|||||||||||++..
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 236999999999999999999999999999999999999999999887
Q ss_pred -----------eeeecc-----------------ccceee-eeCCCcceeechh----hhhh------cCCCCCCCcceE
Q 001532 708 -----------NQLCRM-----------------DSLLYL-LVYPQRPLLTTRT----IELV------GYDKLGAGQNAT 748 (1058)
Q Consensus 708 -----------n~~~R~-----------------D~~~y~-l~ypQ~Plv~t~~----~~~~------~~~~~~~G~N~~ 748 (1058)
++..|. |+.++. ++|||+|||+|+. .+++ +++|+|+|+|++
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 787887 555565 7999999999994 4554 799999999999
Q ss_pred EEEeecCCCCCCCcEEEecceeeccceEEEEEEEEEEEeecccCCccceec--CCCCCCCcccccccCCCCccccCCcEe
Q 001532 749 VAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRIL--RPDRTGPGAERMQILDDDGLAAPGEII 826 (1058)
Q Consensus 749 Vav~~y~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~e~~~--~p~~~~~~~~~~~~ld~dGi~~~g~~v 826 (1058)
||||||+||||||||||||+|++||+|+|+||++|+++++.++.|.. .++ .|+.+ ...|++||+||||++|++|
T Consensus 721 VA~~~y~GYn~EDaiiink~si~rg~~~s~~~~~~~~~~~~~~~~~~-~~~~~~p~~~---~~~~~~Ld~dGi~~~G~~v 796 (1112)
T PRK00405 721 VAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPE-EITRDIPNVS---EEALRNLDESGIVRIGAEV 796 (1112)
T ss_pred EEEEeecccCccceEEEEhhhhccCceEEEEEeeeeeEeeccCCCce-eecccCCCCC---hHHhhccCCCCCccCccEe
Confidence 99999999999999999999999999999999999999987776643 443 25432 2479999999999999999
Q ss_pred CCCCEEEEEecCCCCCCCCCC------CCCCCCcccccceEEeeCCCCCceEEEEEEEeeC-CCC-------CEEEEEEE
Q 001532 827 KPNDVYINKESPLETRGSIMS------PTGQTDSRYRSARQTYKGPDGETCVVDRVALCSD-KNG-------DLCIKFLI 892 (1058)
Q Consensus 827 ~~gd~li~k~~~~~~~~~~~~------~~~~~~~~~~~~s~~~~~~~~~~~~vd~v~~~~~-~~~-------~~~v~v~i 892 (1058)
++|||||||++|....+.... -++......+|+|++++.++ +|+||+|.++.+ .++ .+.|+|++
T Consensus 797 ~~gDiligk~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~s~~~~~~~--~g~V~~v~~~~~~~~~~~~~~~~~~~vkv~i 874 (1112)
T PRK00405 797 KPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGE--EGTVIDVKVFTRIEQGDELPPGVNKLVKVYI 874 (1112)
T ss_pred cCCCEEEEEecCCCccccChhhhhhhhhhcccccccccceEEcCCCC--CEEEEEEEEeeccccCCccCcCcceEEEEEE
Confidence 999999999998653221100 01122234789999999999 999999999876 555 47899999
Q ss_pred eecCCCcccceecccCCCccEEEeeeccCCCCCCCCCCCCcEEeCCCCCCCcccHHHHHHHhhccchhcCCceeeeec-c
Q 001532 893 RHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSA-F 971 (1058)
Q Consensus 893 ~~~R~p~iGDKf~sRhGqKGvvs~i~~~~DmPf~~~G~~pDiIiNP~~~PSRMtiGql~E~~~gk~~~~~g~~~~~tp-f 971 (1058)
|+.|+|+||||||||||||||||+|||+||||||+||++|||||||||||||||||||+|+++||++++.|.+ ++|| |
T Consensus 875 r~~R~p~iGDKfasRHGqKGvis~i~~~eDMPf~~~G~~pDiIiNPhg~PSRMtiGql~E~~~gk~~~~~g~~-~~tp~f 953 (1112)
T PRK00405 875 AQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIK-FATPVF 953 (1112)
T ss_pred eeecccCcccchhhccCCceeEEeEeccCCCCcCCCCCCCcEEECCCCCcccccHHHHHHHHhhHHHHhcCCe-EecCcc
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999986 8888 6
Q ss_pred cCCCCCCCCHHHHHHHHHHcCCCCCCceEEEeCCCCcEeeeeEeeeeeeeeccccccCcceEEeccCCccccccCCcCcc
Q 001532 972 GEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGR 1051 (1058)
Q Consensus 972 ~~~~~~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr 1051 (1058)
. +...+++++.|.++||+++|+|+||||+||++|+++||+|++|||||+|||+||+|||++|||+.|||||++||
T Consensus 954 ~-----~~~~~~~~~~l~~~g~~~~G~e~l~~G~tG~~~~~~if~G~~yy~rL~HmV~DK~haRs~Gp~~~lT~QP~~Gr 1028 (1112)
T PRK00405 954 D-----GAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGK 1028 (1112)
T ss_pred C-----CccHHHHHHHHHHcCcCCCCCEEEECCCCCCCCcccEEEEehhheechhhhcchhhhcccCCccceeeCCCccc
Confidence 6 57889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCC
Q 001532 1052 ARNGGF 1057 (1058)
Q Consensus 1052 ~~~GG~ 1057 (1058)
+|+|||
T Consensus 1029 sr~GG~ 1034 (1112)
T PRK00405 1029 AQFGGQ 1034 (1112)
T ss_pred ccCCCe
Confidence 999997
No 9
>CHL00001 rpoB RNA polymerase beta subunit
Probab=100.00 E-value=1.3e-191 Score=1770.69 Aligned_cols=866 Identities=23% Similarity=0.345 Sum_probs=727.9
Q ss_pred ccccchHHHHHHHHHHHHHhCHHHHHHhcCcceecCCCcEE--EEEeEEEEcCCccccCCccCCCChhhHhhcCCccCce
Q 001532 39 LKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIF--LRFKDVRIGQPSMTVDGVSEKLNPHMCRLSDMTYAAP 116 (1058)
Q Consensus 39 f~~~~Lv~~qi~SFn~Fl~~gl~~i~~~~~~i~~~~~~~~~--l~~~~i~i~~P~~~~~~~~~~l~P~EcR~r~lTYsa~ 116 (1058)
|..++|+++|++||||||++||++++++++||+ +.++.+. +.++++++++|.+ +|+|||+|++||+|+
T Consensus 10 ~~~P~Lv~~Q~~SF~~Fl~~gL~~i~~~~~pI~-~~~~~~~~~~~~~~~~l~~P~~---------~p~ear~r~lTYsa~ 79 (1070)
T CHL00001 10 STIPGFNQIQFEGFCRFIDQGLTEELSKFPKIE-DTDQEIEFQLFVETYQLVEPLI---------KERDAVYESLTYSSE 79 (1070)
T ss_pred cCCCCHHHHHHHHHHHHHHHhHHHHHHhcCCeE-CCCCCEEEEEEeCeEEECCCCC---------CHHHHHHhCCCCCce
Confidence 567899999999999999999999999999998 5555544 4556999999987 789999999999999
Q ss_pred EEEEEEEEECCCccceeeEEeEEEEeeeccccccccccCCCCCHHHHHhcCCCCCCCCcEEEEcCceeEEeeeecccCCE
Q 001532 117 ILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNR 196 (1058)
Q Consensus 117 l~v~v~~~~~~~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~ls~~elv~~gE~~~d~GGYFIING~EKVI~~q~~~~~N~ 196 (1058)
|+|++.++..+. +++++++|++|+||+|. +||||||||+||||++|++++||.
T Consensus 80 l~v~v~l~~~~~---~~i~~~~V~iG~iPlMt------------------------~gG~FIING~ERVIVsQ~~rSpg~ 132 (1070)
T CHL00001 80 LYVPAGLIWKKS---RDMQEQTVFIGNIPLMN------------------------SLGTFIINGIYRVVINQILRSPGI 132 (1070)
T ss_pred eEEEEEEEEcCc---eeEEEeEEEEecCCccC------------------------CCcEEEEcCcEEEEEEEEeccCCE
Confidence 999999975442 45667799999999994 899999999999999999999997
Q ss_pred EEEEeC-CC--CcEEEEEEecCCCcceEEEEEeeCCEEEEEEcceeccccHhhHHHHhCCCCHHHHHHHhCCchhHHhhh
Q 001532 197 VIIDTD-KK--GNINASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGRDPRYSALL 273 (1058)
Q Consensus 197 i~~~~~-~~--g~~~~~v~s~~~~~~s~~~~~~~~g~i~~~~~~~~~~IPl~ilLkALg~~sd~eI~~~i~~~~~~~~~l 273 (1058)
++.+.. +. ..+.|.++|.+. +|..+.+.+++.+|+++++. ++||+++||||||++ |+||++.++.+ +.+
T Consensus 133 ~~~~~~~~~~~~~y~a~iis~rg--swl~~e~d~~~~i~vri~~~-~kiPi~ilLrALG~s-d~eIl~~~~~~----~~l 204 (1070)
T CHL00001 133 YYRSELDHNGISVYTGTIISDWG--GRLELEIDRKARIWARVSRK-QKISILVLLSAMGLN-LREILDNVCYP----EIF 204 (1070)
T ss_pred EEEEecCCCCceeEEEEEEecCC--CceEEEEecCCeEEEEecCC-CcccHHHHHHHcCCC-HHHHHHHhCcH----HHH
Confidence 776653 22 347899998765 45555566778999999997 699999999999995 99999999533 334
Q ss_pred hhhHHHHHhcCCcCHHHHHHHHhhcccccCCCCCCCChHHHHHHHHHhhhccC------CCCCCCCCC------CcchhH
Q 001532 274 LPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLAN------VPVHNNNFR------PKCFYV 341 (1058)
Q Consensus 274 ~~~l~~~~~~~i~t~~~al~yig~~~~~~~~~~~~~~~~e~~~~~L~~~llpH------l~~~~~~~~------~K~~~L 341 (1058)
..++.+.....+.++++|+.||++++... ..+.. ..+.|+.+|.+.+|+| +|..+.+.+ .|..+|
T Consensus 205 ~~~l~~~~~~~~~t~e~Al~~i~~~l~~r--~~~~~-~~~~a~~~l~~~ff~~rY~Lg~vGr~~~n~kl~~~~~~~~~~L 281 (1070)
T CHL00001 205 LSFLNDKEKKKIGSKENAILEFYQQFACV--GGDPV-FSESLCKELQKKFFQQRCELGRIGRRNMNRKLNLDIPENNTFL 281 (1070)
T ss_pred HHHHHHHhhccccCHHHHHHHHHHhhccC--CCCcc-hHHHHHHHHHHHhccccccccccCchhhhhhhcccccccceEe
Confidence 44444433346789999999999998432 11334 6788999999999998 886544333 567767
Q ss_pred -----HHHHHHHHHhhcCCCCCCCcccccceEEcchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCCCCcccccccc
Q 001532 342 -----AVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVR 416 (1058)
Q Consensus 342 -----~~Mi~kLl~~~~G~~~~DD~D~l~NkRV~~~G~Ll~~lfr~~l~~~~~~ik~~i~k~~~~~~~~~~~~~~~~i~~ 416 (1058)
++|+++|+.+..|.+.+||+|||+||||+++|+||++|||.+|+++++.+++++.+.+++. ..+++..++++
T Consensus 282 ~~~Di~~~i~~Ll~l~~G~~~~DDiDhLgNKRvr~vGeLL~~qfr~~l~r~~r~ik~~m~~~~~~~---~~~~~~~lin~ 358 (1070)
T CHL00001 282 LPQDVLAAADYLIGMKFGMGTLDDIDHLKNKRIRSVADLLQDQFGLALNRLENAVRGTICGAIRRK---LIPTPQNLVTS 358 (1070)
T ss_pred cHHHHHHHHHHHHHhhcCCCCccchhHHhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc---ccCCHHHhhCc
Confidence 8999999999999999999999999999999999999999999999999999998755432 24678888899
Q ss_pred ccchhhhhhhhccCCCcccccccccccceEEcccccccccccccccccc--ccccccccc--CCCcCCCCCccccccCCC
Q 001532 417 DSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSP--QFEKSRKVS--GPRALQPSQWGMLCPCDT 492 (1058)
Q Consensus 417 ~~It~~i~~~~sTGn~~~~~~~~q~sG~sq~l~rln~ls~lshlRrv~~--~~~~~~k~t--~~R~Lhps~wG~iCPveT 492 (1058)
+.||.+|++||+| +|+||+|||+|+||.|||+||+++ |...+++.+ .+|+|||||||||||+||
T Consensus 359 ~~It~~ik~ff~t------------s~LSQflDqtNpLseltHkRRlsslGpgglsr~~a~fevRdvHpShyGRICPIET 426 (1070)
T CHL00001 359 TPLTTTYESFFGS------------HPLSQFLDQTNPLTEIVHGRKLSSLGPGGLTGRTASFRVRDIHPSHYGRICPIDT 426 (1070)
T ss_pred chHHHHHHhhhcC------------CcceeeeccCCHHHhhhhhhcccccCCCCccccccCCcccccCccccccccCCCC
Confidence 9999999999976 589999999999999999999997 887777766 899999999999999999
Q ss_pred CCCCcccccccccceeeee-cCCCChhHHHHHhhcCCeeccccCccccCCCCcEEEEECCeEEeeccChhhHHHHHHHHh
Q 001532 493 PEGEACGLVKNLALMTHVT-TDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLR 571 (1058)
Q Consensus 493 PEG~~cGLi~~LA~~a~Is-~~~~~~~i~~~l~~~g~~~l~~~~~~~~~~~~~~~V~lnG~~vG~~~~~~~~~~~lr~~r 571 (1058)
|||+|||||+|||++|+|+ .+..+.|+.+++...+++.+.++++.+. +.+.|+ ||.|+|...+
T Consensus 427 PEG~NiGLI~sLA~~A~In~~GfietP~~~v~~~~~~~~i~ylsa~ee---~~~~Ia-~g~~~~~~~~------------ 490 (1070)
T CHL00001 427 SEGINAGLIGSLAIHARIGHWGSLESPFYEISERSKEERMVYLSPSED---EYYMIA-AGNSLALNQG------------ 490 (1070)
T ss_pred CCcccccchhhhhhhcccccCCCcccceeeeccccccceeEEcccccc---CceEEE-eCceeeccCC------------
Confidence 9999999999999999999 5688999999998888888888876542 468888 9999973211
Q ss_pred hcCCcCceeEEEeccccceEEEecCCCeeeeeEEEEecCcccchhhhHHHhhcCCccchhhhccCceeEeccccccceEE
Q 001532 572 RAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALI 651 (1058)
Q Consensus 572 r~~~i~~~v~i~~~~~~~~i~I~sd~GRl~RPll~v~~~~~~~~~~~~~~l~~~~~s~~~~~~~~~iE~id~~e~~~~~I 651 (1058)
.+ ...++.++ + + ++++.|
T Consensus 491 ---~~------------------------~~~~~~~r--------------------~----~-----------~e~~~i 508 (1070)
T CHL00001 491 ---IQ------------------------EEQVVPAR--------------------Y----R-----------QEFLTI 508 (1070)
T ss_pred ---cc------------------------ccceeEEE--------------------e----c-----------CeEEEE
Confidence 00 00000000 0 0 112334
Q ss_pred EeecCCCCCCceeeeecCccccccccccCCCCCCCCCCccccccccccCCccceeEe---------eeecc---------
Q 001532 652 ALYEGDATPDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFN---------QLCRM--------- 713 (1058)
Q Consensus 652 a~~~~~~~~~~th~Ei~p~~~ls~~asliPF~~hNqspRn~yq~~M~KQaiG~~~~n---------~~~R~--------- 713 (1058)
++. + .||+||+|.+++|++||||||+||||||||+|||||||||||++..+ +..|.
T Consensus 509 ~~~--~----i~~~dIsP~qi~svaasLIPFleHndanRalmgsnMqrQAvpll~~~~p~VgTG~E~~~~~ds~~~i~a~ 582 (1070)
T CHL00001 509 AWE--Q----IHLRSIFPFQYFSIGASLIPFLEHNDANRALMGSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVVAIAE 582 (1070)
T ss_pred chH--H----CcEEeeChhhhhhhhhhcCCCccccCcchhhhhhccchhccccccCCCCEeecCcchhhhhcccceeEEc
Confidence 433 2 38999999999999999999999999999999999999999998888 66666
Q ss_pred --------c-----------c-ceeeeeC---------CCcceeechhhhh----------hcCCCCCCCcceEEEEeec
Q 001532 714 --------D-----------S-LLYLLVY---------PQRPLLTTRTIEL----------VGYDKLGAGQNATVAVMSY 754 (1058)
Q Consensus 714 --------D-----------~-~~y~l~y---------pQ~Plv~t~~~~~----------~~~~~~~~G~N~~Vav~~y 754 (1058)
| + ..|++.| ||||||+++.+.. +..+|+|+|+|++||||||
T Consensus 583 ~~G~V~~vd~~~I~i~~~~~~~~y~l~~y~rsnq~t~~~QkPlV~~g~~v~~g~~ladg~~~~~gel~~G~N~~VA~m~~ 662 (1070)
T CHL00001 583 HEGKIIYTDTDKIILSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCVKKGQILADGAATVGGELALGKNVLVAYMPW 662 (1070)
T ss_pred cCCEEEEEeCCEEEEEcCCCeEEEEeeceeccCCCcccccCCEEecCCEEccCCEeccChhhccccccCCccceeeeeec
Confidence 5 4 3456678 9999999995433 2289999999999999999
Q ss_pred CCCCCCCcEEEecceeeccceEEEEEEEEEEEeecccCCccceecC--CCCCCCcccccccCCCCccccCCcEeCCCCEE
Q 001532 755 SGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILR--PDRTGPGAERMQILDDDGLAAPGEIIKPNDVY 832 (1058)
Q Consensus 755 ~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~e~~~~--p~~~~~~~~~~~~ld~dGi~~~g~~v~~gd~l 832 (1058)
+||||||||||||+|++||+|+|+||++|++++++++.|. |.++. |+.+. ..|++||+||+|++|++|++||||
T Consensus 663 ~GYn~EDAiiin~~~v~~g~~~s~~~~~~~~~~~~~~~g~-e~i~~~~p~~~~---~~~~~Ld~dGi~~~G~~v~~gDil 738 (1070)
T CHL00001 663 EGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQGP-ERITKEIPHLEA---HLLRNLDKNGIVMLGSWVETGDIL 738 (1070)
T ss_pred cccccchhhhhhhhhhcCCceEEEEEeeeeEEEeccCCCc-ceEeccCCCCch---hhhhccCCCCCccCCcEecCCCEE
Confidence 9999999999999999999999999999999999877664 66654 66532 579999999999999999999999
Q ss_pred EEEecCCCCCCCCCC--------CCCCCCcccccceEEeeCCCCCceEEEEEEEeeC----CCCCEEEEEEEeecCCCcc
Q 001532 833 INKESPLETRGSIMS--------PTGQTDSRYRSARQTYKGPDGETCVVDRVALCSD----KNGDLCIKFLIRHTRRPEL 900 (1058)
Q Consensus 833 i~k~~~~~~~~~~~~--------~~~~~~~~~~~~s~~~~~~~~~~~~vd~v~~~~~----~~~~~~v~v~i~~~R~p~i 900 (1058)
|||++|....+.... -++.+...++|+|+++++++ .|+|++|.++.. .++...|||++|+.|+|++
T Consensus 739 vgK~~p~~~~~~~~~~~~~~~~~if~~~~~~~~d~sl~~~~~~--~g~V~~v~~~~~~~~~~~~~~~vkv~i~~~R~~~v 816 (1070)
T CHL00001 739 VGKLTPQEAEESSYAPEGRLLRAIFGIQVSTSKETCLKLPIGG--RGRVIDVRWIQKKGGSSYNPETIHVYILQKREIQV 816 (1070)
T ss_pred EEEecCCcccccccCcchhhhhhhhccccCcceeCeEECCCCC--ceEEEEEEEEecccCCCCCcEEEEEEEEEEecCCC
Confidence 999999742222111 12233345789999999999 999999998873 4567899999999999999
Q ss_pred cceecccCCCccEEEeeeccCCCCCCCCCCCCcEEeCCCCCCCcccHHHHHHHhhccchhcCCceeeeecccCCCCCCCC
Q 001532 901 GDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADT 980 (1058)
Q Consensus 901 GDKf~sRhGqKGvvs~i~~~~DmPf~~~G~~pDiIiNP~~~PSRMtiGql~E~~~gk~~~~~g~~~~~tpf~~~~~~~~~ 980 (1058)
|||||||||||||||+|||+||||||+||++||||+||||||||||||||+|+++||||++.|.+.++|||+..+.....
T Consensus 817 GDK~asRHGqKGvvs~i~~~eDMPf~~dG~~pDiIlNP~gvPSRMtiGqllE~~~G~a~~~~g~~~~~~pf~~~~~~~~~ 896 (1070)
T CHL00001 817 GDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLLNRHYRIAPFDERYEQEAS 896 (1070)
T ss_pred CcccccccCCcceEeeeecccCCCcccCCCCCceeeccccccccccHHHHHHHHhHHHHhhcCceeeeccCCCcchhhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999943222222
Q ss_pred HHHHHHHHHHcCC----------CCCCceEEEeCCCCcEeeeeEeeeeeeeeccccccCcceEEeccCCccccccCCcCc
Q 001532 981 VESISETLVKHGF----------SYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEG 1050 (1058)
Q Consensus 981 ~~~~~~~l~~~g~----------~~~G~e~ly~g~tG~~~~~~if~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~G 1050 (1058)
...+...|.++|+ +++|++.||||+||++|+++||+|++|||||+|||+||+|||++|||+.+||||++|
T Consensus 897 ~~~~~~~l~~~~~~~~~~~~~~~~~~Gk~~l~dG~TG~~~~~~i~vG~~Yy~kL~HmV~DKihaRs~Gp~~~lT~QP~~G 976 (1070)
T CHL00001 897 RKLVFSELYEASKQTANPWVFEPEYPGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRG 976 (1070)
T ss_pred hhhhhHHHHHHHHhcCCceeccCCCCCeEEEEcCCCCCCccceEEEEecceeEchhhccccceeeccCCCcccccCCCCc
Confidence 2233466777765 445999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCC
Q 001532 1051 RARNGGF 1057 (1058)
Q Consensus 1051 r~~~GG~ 1057 (1058)
|+|+|||
T Consensus 977 rsr~GG~ 983 (1070)
T CHL00001 977 RSKQGGQ 983 (1070)
T ss_pred ccCCCCe
Confidence 9999997
No 10
>CHL00207 rpoB RNA polymerase beta subunit; Provisional
Probab=100.00 E-value=1.3e-174 Score=1608.65 Aligned_cols=857 Identities=23% Similarity=0.382 Sum_probs=684.9
Q ss_pred cccccchHHHHHHHHHHHHHhCHHHHHHhcCcceecCCCcEEEEEe--EEEEcCCccccCCccCCCChhhHhhcCCccCc
Q 001532 38 FLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLRFK--DVRIGQPSMTVDGVSEKLNPHMCRLSDMTYAA 115 (1058)
Q Consensus 38 ~f~~~~Lv~~qi~SFn~Fl~~gl~~i~~~~~~i~~~~~~~~~l~~~--~i~i~~P~~~~~~~~~~l~P~EcR~r~lTYsa 115 (1058)
-|+.++|+..|++||+|||++||++++++.+||+. .++.+.++|. ++++++|.+ +|.|||+|++||++
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 35678899999999999999999999999999965 5566777775 899999986 68999999999999
Q ss_pred eEEEEEEEEECCCccceeeEEeEEEEeeeccccccccccCCCCCHHHHHhcCCCCCCCCcEEEEcCceeEEeeeecccCC
Q 001532 116 PILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKN 195 (1058)
Q Consensus 116 ~l~v~v~~~~~~~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~ls~~elv~~gE~~~d~GGYFIING~EKVI~~q~~~~~N 195 (1058)
+|+|+++++.++. +++++++|++|+||+|+ ++|||||||+||||++|+.++|+
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 9999999986553 56677899999999997 89999999999999999988886
Q ss_pred EEEEEeC--CCCc--EEEEEEecCCCcceEEEEEeeCCEEEEEEcceeccccHhhHHHHhCCCCHHHHHHHhCC--chhH
Q 001532 196 RVIIDTD--KKGN--INASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGR--DPRY 269 (1058)
Q Consensus 196 ~i~~~~~--~~g~--~~~~v~s~~~~~~s~~~~~~~~g~i~~~~~~~~~~IPl~ilLkALg~~sd~eI~~~i~~--~~~~ 269 (1058)
+|+... +.+. +.|.+++.+. .|..+.+++++.+|+++++. ++||+++||||||+ |++||++.++. +..+
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 887654 3343 6789998654 67777778888999999995 58999999999999 79999999953 2222
Q ss_pred HhhhhhhHHHHHhcCCcCHHHHHHHHhhcccccCCCCCCCChHHHHHHHH-------HhhhccCCCCCCC----------
Q 001532 270 SALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSIL-------RDVFLANVPVHNN---------- 332 (1058)
Q Consensus 270 ~~~l~~~l~~~~~~~i~t~~~al~yig~~~~~~~~~~~~~~~~e~~~~~L-------~~~llpHl~~~~~---------- 332 (1058)
+...+. ..+..++++|+.+|++++++. ... ..+.++.+| +++.|+|+|.-..
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 223 556677665 4556788886221
Q ss_pred -CCCCcchhHHHHHHHHHHhhcCCCCCCCcccccceEEcchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCCCCccc
Q 001532 333 -NFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLS 411 (1058)
Q Consensus 333 -~~~~K~~~L~~Mi~kLl~~~~G~~~~DD~D~l~NkRV~~~G~Ll~~lfr~~l~~~~~~ik~~i~k~~~~~~~~~~~~~~ 411 (1058)
...-+...+..|+++|+.+..|....||+|||+||||+++|+||++|||.+|.++++.+++++.+.. ...+.+.
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 1222344566899999999999999999999999999999999999999999999999999987531 1246677
Q ss_pred cccccccchhhhhhhhccCCCcccccccccccceEEcccccccccccccccccc----cccccccccCCCcCCCCCcccc
Q 001532 412 QFIVRDSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSP----QFEKSRKVSGPRALQPSQWGML 487 (1058)
Q Consensus 412 ~~i~~~~It~~i~~~~sTGn~~~~~~~~q~sG~sq~l~rln~ls~lshlRrv~~----~~~~~~k~t~~R~Lhps~wG~i 487 (1058)
+++++++|+..|++||++ +++||.+|++|+||.|+|.||+++ .+.+++..+.+|++||||||||
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 888999999999999963 478999999999999999999996 6889999999999999999999
Q ss_pred ccCCCCCCCcccccccccceeeeecCCCChhHHHHHhhcCCeeccccCccccCCCCcEEEEECCeEEeeccChhhHHHHH
Q 001532 488 CPCDTPEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVM 567 (1058)
Q Consensus 488 CPveTPEG~~cGLi~~LA~~a~Is~~~~~~~i~~~l~~~g~~~l~~~~~~~~~~~~~~~V~lnG~~vG~~~~~~~~~~~l 567 (1058)
||+|||||+||||+++||.+|+|+. +|+.. ..|....||.+.- .++
T Consensus 414 CPIETPEG~n~Gli~~la~~~~in~-------------~Gfie------------tPy~~v~~g~v~~-~~~-------- 459 (1077)
T CHL00207 414 CPIETPEGPNCGLIGSLATNARINK-------------FGFIE------------TPFYKVINGKVKK-FGN-------- 459 (1077)
T ss_pred cCCCCCCCcccccccchhhhccccC-------------CCcee------------CceEEEEcCcccc-cCc--------
Confidence 9999999999999999999999975 44422 1343445666420 001
Q ss_pred HHHhhcCCcCceeEEEeccc-cceEEEecCCCeeeeeEEEEecCcccchhhhHHHhhcCCccchhhhccCceeEeccccc
Q 001532 568 RKLRRAGKIGEFVSVFVNEK-QRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEE 646 (1058)
Q Consensus 568 r~~rr~~~i~~~v~i~~~~~-~~~i~I~sd~GRl~RPll~v~~~~~~~~~~~~~~l~~~~~s~~~~~~~~~iE~id~~e~ 646 (1058)
.++++.. .....|....--+ -+++. +. ...|.-.-- +
T Consensus 460 -------------i~ylsa~~e~~~~Ia~~~~~~------~~~~~--------------------~~-~~~v~~r~~--~ 497 (1077)
T CHL00207 460 -------------PIYLTADSEDLYRIAPNDINL------NKNNY--------------------FK-KNIIPVRYK--Q 497 (1077)
T ss_pred -------------eeecChHHhcCcEEEecCccC------CCCCc--------------------cc-CCEEEEEEC--C
Confidence 0122221 2223333222000 01110 00 000111100 1
Q ss_pred cceEEEeecCCCCCCceeeeecCccccccccccCCCCCCCCCCccccccccccCCcccee--------------------
Q 001532 647 NNALIALYEGDATPDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIA-------------------- 706 (1058)
Q Consensus 647 ~~~~Ia~~~~~~~~~~th~Ei~p~~~ls~~asliPF~~hNqspRn~yq~~M~KQaiG~~~-------------------- 706 (1058)
++..+ .+ ...++++++|.|++|++||||||++|||++|++||||||+|||++..
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 12578999999999999999999999999999999999999997521
Q ss_pred -----------Eeeeecc----c---cceeee----------eCCCcceeechhhhh----------hcCCCCCCCcceE
Q 001532 707 -----------FNQLCRM----D---SLLYLL----------VYPQRPLLTTRTIEL----------VGYDKLGAGQNAT 748 (1058)
Q Consensus 707 -----------~n~~~R~----D---~~~y~l----------~ypQ~Plv~t~~~~~----------~~~~~~~~G~N~~ 748 (1058)
+....|+ + ...|.| +.+|||+|+.+.+.. +.++|+|+|+|++
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 569999999987643 4599999999999
Q ss_pred EEEeecCCCCCCCcEEEecceeeccceEEEEEEEEEEEeecccCCccceec--CCCCCCCcccccccCCCCccccCCcEe
Q 001532 749 VAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRIL--RPDRTGPGAERMQILDDDGLAAPGEII 826 (1058)
Q Consensus 749 Vav~~y~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~e~~~--~p~~~~~~~~~~~~ld~dGi~~~g~~v 826 (1058)
||||||+||||||||||||++++||+|+|+|+++|++++++++.|. |.++ .|+.+ ...|++||+||||++|++|
T Consensus 652 VA~m~y~GYN~EDAiiink~~v~rg~f~Si~~~~~~~e~~~~~~g~-e~i~~~~p~~~---~~~~~~LD~dGiv~iG~~V 727 (1077)
T CHL00207 652 VAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEKYEIELRQTKLGS-EEITRNIPNVS---EYSLKNLDENGIISIGSKV 727 (1077)
T ss_pred EEEEeeeccccchhhhhhhhhhcCCceEEEEEEEeeeEEeecCCCc-eEEeccCCCCC---hHHhhccCccCCCcCCcEe
Confidence 9999999999999999999999999999999999999999877665 4455 36543 2579999999999999999
Q ss_pred CCCCEEEEEecCCCCCCCCCC------CCCCCCcccccceEEeeCCCCCceEEEEEEEeeCCC--CC-----EEEEEEEe
Q 001532 827 KPNDVYINKESPLETRGSIMS------PTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKN--GD-----LCIKFLIR 893 (1058)
Q Consensus 827 ~~gd~li~k~~~~~~~~~~~~------~~~~~~~~~~~~s~~~~~~~~~~~~vd~v~~~~~~~--~~-----~~v~v~i~ 893 (1058)
++|||||||++|+...+.... -++.+....+|+|+++++++ +|+|++|.++.+++ +. ..|||++|
T Consensus 728 ~~gDilvgK~tp~~~~~~~~~~~ll~~i~~~~~~~~kd~sl~~~~~~--~g~V~~V~~~~~~~~~~~~~~~~~~vkv~i~ 805 (1077)
T CHL00207 728 LAGDILVGKITPKGESDQLPEGKLLRAIFGEKAKDVKDTSLRMPNGG--YGRVIKVEIFSRSKGDELKFGYYLKIRVFIA 805 (1077)
T ss_pred CCCCEEEEEecCccccccChhhhhhhhhhccCCCcceEeEEEcCCCC--cEEEEEEEEEecCCCCcccccccEEEEEEEE
Confidence 999999999999643322110 02223335799999999999 99999999987532 22 45999999
Q ss_pred ecCCCcccceecccCCCccEEEeeeccCCCCCCCCCCCCcEEeCCCCCCCcccHHHHHHHhhccchhcCCceeeeecccC
Q 001532 894 HTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGE 973 (1058)
Q Consensus 894 ~~R~p~iGDKf~sRhGqKGvvs~i~~~~DmPf~~~G~~pDiIiNP~~~PSRMtiGql~E~~~gk~~~~~g~~~~~tpf~~ 973 (1058)
+.|+|+||||||||||||||||+|||+||||||+||++||||+||||||||||||||+|+++||+|++.|...++|||+.
T Consensus 806 ~~R~p~vGDKfasRHGqKGVvs~i~p~eDMPf~~dG~~pDiIlNPhg~PSRMtiGqllE~~lGka~~~l~~~~~~tpF~~ 885 (1077)
T CHL00207 806 QIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGDNLNKRFKILPFDE 885 (1077)
T ss_pred EEecCCcccccccccCCceeEEeeeccCCCCccCCCCCccEEECCccccccccHHHHHHHHHHHHHHhcCCcEeeccCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999998877778999993
Q ss_pred CCCCCCCHHHHHHHHHH-----c----------CCCCCCceEEEeCCCCcEeeeeEeeeeeeeeccccccCcceEEeccC
Q 001532 974 PSGHADTVESISETLVK-----H----------GFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSG 1038 (1058)
Q Consensus 974 ~~~~~~~~~~~~~~l~~-----~----------g~~~~G~e~ly~g~tG~~~~~~if~G~~yy~rL~Hmv~dK~~~R~~G 1038 (1058)
...+++.+.|.. + +|+++|+++||||+||++|+++||+|++|||||+|||+||+|||++|
T Consensus 886 -----~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~Gk~~lydG~TGe~~~~~i~vG~~Yy~kL~HmV~DKihaRs~G 960 (1077)
T CHL00207 886 -----MYGSEYSRILINNKLNQASIKNNEYWLFNSYHPGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTG 960 (1077)
T ss_pred -----CcHHHHHHHHHhhhhhhccchhccccccCCCCCCCEEEECCCCCCCccCceEEEecceeEchhhccccceeeccC
Confidence 444555555543 3 37788999999999999999999999999999999999999999999
Q ss_pred CccccccCCcCcccCCCCC
Q 001532 1039 PRVMLTRQPTEGRARNGGF 1057 (1058)
Q Consensus 1039 p~~~lT~QP~~Gr~~~GG~ 1057 (1058)
||+.|||||++||+|+|||
T Consensus 961 p~s~lTqQP~~Grsr~GG~ 979 (1077)
T CHL00207 961 PYSLVTQQPLGGKAQHGGQ 979 (1077)
T ss_pred CCcccccCCCCccccCCCe
Confidence 9999999999999999998
No 11
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=100.00 E-value=1.5e-163 Score=1553.99 Aligned_cols=875 Identities=22% Similarity=0.361 Sum_probs=696.2
Q ss_pred cccccccccccccccchHHHHHHHHHHHHH------hCHHHHHHhcCcceecCCCcEEEEEeEEEEcCCccccCCccCCC
Q 001532 28 VVDKFQLLPEFLKVRGLVKQHLDSFNYFVN------TGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDGVSEKL 101 (1058)
Q Consensus 28 ~~~~~~~i~~~f~~~~Lv~~qi~SFn~Fl~------~gl~~i~~~~~~i~~~~~~~~~l~~~~i~i~~P~~~~~~~~~~l 101 (1058)
.+..|+.++..++.++|++.|.+||+|||+ +||++++++++||+ +.+..+.|+|.+++|++|.+
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 456788888888999999999999999998 79999999999995 45678999999999999998
Q ss_pred ChhhHhhcCCccCceEEEEEEEEE---CCCc----cceeeEEeEEEEeeeccccccccccCCCCCHHHHHhcCCCCCCCC
Q 001532 102 NPHMCRLSDMTYAAPILVNIEYVQ---GSHT----EKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPG 174 (1058)
Q Consensus 102 ~P~EcR~r~lTYsa~l~v~v~~~~---~~~~----~~~~~~~~~v~iG~iPIMv~S~~C~L~~ls~~elv~~gE~~~d~G 174 (1058)
+|.||++|++||++||+|++.++. +.++ ..+++++++|++|+||+|+ ..
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 479999999999999999999984 2211 1235778899999999999 79
Q ss_pred cEEEEcCceeEEeeeecccCCEEEEEeCCC----Cc--EEEEEEecCCCcceEEEEEeeCCEEEEEEcceeccccHhhHH
Q 001532 175 GYFIIKGTEKVLLIQEQLSKNRVIIDTDKK----GN--INASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVM 248 (1058)
Q Consensus 175 GYFIING~EKVI~~q~~~~~N~i~~~~~~~----g~--~~~~v~s~~~~~~s~~~~~~~~g~i~~~~~~~~~~IPl~ilL 248 (1058)
|+|||||+||||++|++|+|+ +|+..+.+ |. |.|++++.+. +|+.+..++++.+|+|+++. ++||+++||
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 87765421 22 6789998654 68888888899999999995 699999999
Q ss_pred HHhCCCCHHHHHHHhCC-------ch---------hH-----------------------------------------H-
Q 001532 249 KAMGMESDQEVVQMVGR-------DP---------RY-----------------------------------------S- 270 (1058)
Q Consensus 249 kALg~~sd~eI~~~i~~-------~~---------~~-----------------------------------------~- 270 (1058)
||||+ |++||++.++. +. .+ .
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 68999997741 00 00 0
Q ss_pred ----------------hhhh--------hhHHHHHhc--------------------------------------CCcCH
Q 001532 271 ----------------ALLL--------PSIEECANL--------------------------------------DIYTQ 288 (1058)
Q Consensus 271 ----------------~~l~--------~~l~~~~~~--------------------------------------~i~t~ 288 (1058)
+.+. ..++...+. ...++
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 000000000 01145
Q ss_pred HHHHHHHhhcccccCCCCCCCChHHHHHHHHHhhhcc-------CCCCCCC------------CCCCcchhHHHHHHHHH
Q 001532 289 EKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLA-------NVPVHNN------------NFRPKCFYVAVMLRRMV 349 (1058)
Q Consensus 289 ~~al~yig~~~~~~~~~~~~~~~~e~~~~~L~~~llp-------Hl~~~~~------------~~~~K~~~L~~Mi~kLl 349 (1058)
++|+..|+++++++ +.. ..+.|+.++.+.+|. .+|.... ....+.+++ ..+++|+
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 88999999999886 333 566677777776643 1221110 111234555 4699999
Q ss_pred HhhcCCCCCCCcccccceEEcchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCCCCccccccccccchhhhhhhhcc
Q 001532 350 EAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLST 429 (1058)
Q Consensus 350 ~~~~G~~~~DD~D~l~NkRV~~~G~Ll~~lfr~~l~~~~~~ik~~i~k~~~~~~~~~~~~~~~~i~~~~It~~i~~~~sT 429 (1058)
.+..|....||+|||+||||+++|+||++|||.+|.++++.+++++...... ...+.+..++++++++..+++||+|
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 9999999999999999999999999999999999999999999999753211 2245667788999999999999976
Q ss_pred CCCcccccccccccceEEcccccccccccccccccc----cccccccccCCCcCCCCCccccccCCCCCCCccccccccc
Q 001532 430 GNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSP----QFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLA 505 (1058)
Q Consensus 430 Gn~~~~~~~~q~sG~sq~l~rln~ls~lshlRrv~~----~~~~~~k~t~~R~Lhps~wG~iCPveTPEG~~cGLi~~LA 505 (1058)
+. +||.+|++|+||.|+|.||+++ .+.+++..+.+|++||||||||||+|||||+|||||++||
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 6999999999999999999983 3667888899999999999999999999999999999999
Q ss_pred ceeeeecCCCChhHHHHHhhcCCeeccccCccccCCCCcEEEEECCeEEeeccChhhHHHHHHHHhhcCCcCceeEEEec
Q 001532 506 LMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVN 585 (1058)
Q Consensus 506 ~~a~Is~~~~~~~i~~~l~~~g~~~l~~~~~~~~~~~~~~~V~lnG~~vG~~~~~~~~~~~lr~~rr~~~i~~~v~i~~~ 585 (1058)
.+|+|+. +|+.. ..|....||.+- ++. +|+.
T Consensus 591 ~~a~in~-------------~Gfie------------tPy~kV~~g~v~---~~i---------------------~yls 621 (2890)
T PRK09603 591 TFTRVND-------------LGFIE------------APYKKVVDGKVV---GET---------------------IYLT 621 (2890)
T ss_pred hheeccc-------------Cccee------------cceEEEecCccc---cce---------------------eeeC
Confidence 9999985 44321 123333566631 111 0111
Q ss_pred cc-cceEEEe------cCCCeeeeeEEEEecCcccchhhhHHHhhcCCccchhhhccCceeEeccccccceEEEeecCCC
Q 001532 586 EK-QRCVYIA------SDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDA 658 (1058)
Q Consensus 586 ~~-~~~i~I~------sd~GRl~RPll~v~~~~~~~~~~~~~~l~~~~~s~~~~~~~~~iE~id~~e~~~~~Ia~~~~~~ 658 (1058)
.. .....|. ...|++....+.++.+ + ||.-+. +
T Consensus 622 a~eE~~~~IA~a~~~~~~~~~~~~~~v~~R~~-------------------------~--e~~~~~----------~--- 661 (2890)
T PRK09603 622 AIQEDSHIIAPASTPIDEEGNILGDLIETRVE-------------------------G--EIVLNE----------K--- 661 (2890)
T ss_pred HHHhcCceEeccCCccCCCCcccCCeEeEEEC-------------------------C--ceEEEC----------h---
Confidence 10 1111121 1235555554443310 1 111110 0
Q ss_pred CCCceeeeecCccccccccccCCCCCCCCCCccccccccccCCcccee-------------------------------E
Q 001532 659 TPDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIA-------------------------------F 707 (1058)
Q Consensus 659 ~~~~th~Ei~p~~~ls~~asliPF~~hNqspRn~yq~~M~KQaiG~~~-------------------------------~ 707 (1058)
...++++++|.|++|++||||||++||||+|++||||||+|||++.. +
T Consensus 662 -~~v~~~dvsp~Q~vSvaasLIPFLEhdDAnRALMGSNMQRQAVPLl~~e~piVgTG~E~~va~dSg~~i~a~~~G~V~y 740 (2890)
T PRK09603 662 -SKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTGIEKIIARDSWGAIKANRAGVVEK 740 (2890)
T ss_pred -HHceEEEeCccceeeehhhcCCccccCccccccccccchhhhhhhccccCCeEecCcchhhhccccceeEecCCeEEEE
Confidence 12478999999999999999999999999999999999999997421 1
Q ss_pred eeee----cccc------ceeee----------eCCCcceeechhhhh----------hcCCCCCCCcceEEEEeecCCC
Q 001532 708 NQLC----RMDS------LLYLL----------VYPQRPLLTTRTIEL----------VGYDKLGAGQNATVAVMSYSGY 757 (1058)
Q Consensus 708 n~~~----R~D~------~~y~l----------~ypQ~Plv~t~~~~~----------~~~~~~~~G~N~~Vav~~y~Gy 757 (1058)
.... |.+. ..|.| |++|||+|+.+.... +..+|+++|+|++||||+|.||
T Consensus 741 vd~~~I~i~~~~~~~~~~~~Y~L~Ky~RSNQ~TcinqrPiV~~Gd~V~kGdilADG~st~~GELALG~NvlVAfmpW~GY 820 (2890)
T PRK09603 741 IDSKNIYILGEGKEEAYIDAYSLQKNLRTNQNTSFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGY 820 (2890)
T ss_pred ecCcEEEEEecCCCCceeeEEeeccccccCCCceeeeccEecCCCEeccCCEEecCcccccCeeccCcccEEEEeeeccc
Confidence 1111 1111 23665 669999999987643 4589999999999999999999
Q ss_pred CCCCcEEEecceeeccceEEEEEEEEEEEeecccCCccceecC-CCCCCCcccccccCCCCccccCCcEeCCCCEEEEEe
Q 001532 758 DIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILR-PDRTGPGAERMQILDDDGLAAPGEIIKPNDVYINKE 836 (1058)
Q Consensus 758 n~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~e~~~~-p~~~~~~~~~~~~ld~dGi~~~g~~v~~gd~li~k~ 836 (1058)
|+|||||||++.+.+++|||+|+.+|+++.++++.|.+|.+.. |+.+. ...++||++|||++|++|++|||||||+
T Consensus 821 NfEDAIlISERlV~eD~fTSIHIee~ei~~r~Tk~G~EeITrdIPnvse---~~l~~LDe~GII~iGa~V~~GDILVGKv 897 (2890)
T PRK09603 821 NFEDAIVVSERITKDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKE---EALAHLDESGIVKVGTYVSAGMILVGKT 897 (2890)
T ss_pred cCccccccchhhhcCccceEEEEeeeEEEEEecCCCCcEEeccCCCCCH---HHHhcCCCCCCEeeCCEECCCCEEEEee
Confidence 9999999999999999999999999999999998887665544 88753 6889999999999999999999999999
Q ss_pred cCCCCCCCCCC------CCCCCCcccccceEEeeCCCCCceEEEEEEEeeCC----------------------------
Q 001532 837 SPLETRGSIMS------PTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDK---------------------------- 882 (1058)
Q Consensus 837 ~~~~~~~~~~~------~~~~~~~~~~~~s~~~~~~~~~~~~vd~v~~~~~~---------------------------- 882 (1058)
+|+.+.+..+. -++.+....+|+|+++.++. .|+|-.|.+++..
T Consensus 898 TPkge~~~tPEekLLraIFGeka~~vkDtSLrvp~G~--~G~Vidv~~f~r~~~~k~~~~~~~~~~~~~~~~~~~~~~~~ 975 (2890)
T PRK09603 898 SPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSL--EGTVIDVKVFTKKGYEKDARVLSAYEEEKAKLDMEHFDRLT 975 (2890)
T ss_pred ccCCCCCCChHHHHHHHHhcccccccccCceecCCCC--cEEEEEEEEecccccchhHHHHHHHHHHHHHHhHhhHHHHH
Confidence 99976544321 14566667899999988877 9999988866521
Q ss_pred --------------------------------------------------------------------------------
Q 001532 883 -------------------------------------------------------------------------------- 882 (1058)
Q Consensus 883 -------------------------------------------------------------------------------- 882 (1058)
T Consensus 976 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1055 (2890)
T PRK09603 976 MLNREELLRVSSLLSQAILEEPFSHNGKDYKEGDQIPKEEIASINRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGE 1055 (2890)
T ss_pred HHHHHHHHhhhhhccccccccccccccccccccccccHHHHhhCCHHHhhhhhccCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence
Q ss_pred ----------CC-------CEEEEEEEeecCCCcccceecccCCCccEEEeeeccCCCCCCCCCCCCcEEeCCCCCCCcc
Q 001532 883 ----------NG-------DLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRM 945 (1058)
Q Consensus 883 ----------~~-------~~~v~v~i~~~R~p~iGDKf~sRhGqKGvvs~i~~~~DmPf~~~G~~pDiIiNP~~~PSRM 945 (1058)
.| .+.|||+||+.|+|++|||||||||||||||+|||+|||||++||++||||+|||||||||
T Consensus 1056 ~~~~k~~~~~~gdeL~~Gv~~~VkV~ia~kR~~qvGDK~AgRHGnKGViS~I~p~EDMPfl~dG~~pDIIlNPlGvPSRM 1135 (2890)
T PRK09603 1056 EHEEKLSILEKDDILPNGVIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRM 1135 (2890)
T ss_pred HHHHHHHHhhcCCcCCCCcceEEEEEEEEeecccccchhhhccCCCeeEEEEEchhcCCCCCCCCCCcEEECCCCCCccc
Confidence 01 3579999999999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHhhccchhcCCcee-----e------------------------------------------------eeccc
Q 001532 946 TVGKMIELLGGKAGVSCGRFH-----Y------------------------------------------------GSAFG 972 (1058)
Q Consensus 946 tiGql~E~~~gk~~~~~g~~~-----~------------------------------------------------~tpf~ 972 (1058)
|||||+|+++||||+..|.+. + +.++.
T Consensus 1136 nIGQilE~~LG~aa~~lg~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~ 1215 (2890)
T PRK09603 1136 NIGQILEMHLGLVGKEFGKQIASMLEDKTKDFAKELRAKMLEIANAINEKDPLTIHALENCSDEELLEYAKDWSKGVKMA 1215 (2890)
T ss_pred cHHHHHHHHHHHHHHhcCcChhhhhhhcchhhhHHHHHHHHhhhcccccccccccccccccchHHHHhhhhhhccCCccc
Confidence 999999999999999887541 1 01112
Q ss_pred CCCCCCCCHHHHHHHHHHcCCCCCCceEEEeCCCCcEeeeeEeeeeeeeeccccccCcceEEeccCCccccccCCcCccc
Q 001532 973 EPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRA 1052 (1058)
Q Consensus 973 ~~~~~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~ 1052 (1058)
.+.+++...+++.+.|.++||+++|++.||||+||++|+++||+|++|||||+|||+||+||||+|||+.+||||++||+
T Consensus 1216 tpvF~g~~~~~i~~~l~~aG~~~~Gk~~LyDGrTGe~f~~~V~vG~~YylKL~HmVdDKiHaRstGPyslvTqQPl~GKs 1295 (2890)
T PRK09603 1216 IPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKA 1295 (2890)
T ss_pred CCCCCCCCHHHHHHHHHHcCCCCCCCEEEEcCCCCCCccceEEEEeeceeechhhccchhhhccCCCcchhhhCCCcccc
Confidence 23344788999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCC
Q 001532 1053 RNGGF 1057 (1058)
Q Consensus 1053 ~~GG~ 1057 (1058)
++|||
T Consensus 1296 ~~GGq 1300 (2890)
T PRK09603 1296 LFGGQ 1300 (2890)
T ss_pred cCCCc
Confidence 99998
No 12
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=100.00 E-value=1e-160 Score=1522.30 Aligned_cols=881 Identities=22% Similarity=0.362 Sum_probs=699.0
Q ss_pred cccccccc-ccccccccchHHHHHHHHHHHHH-----hCHHHHHHhcCcceecCCCcEEEEEeEEEEcCCccccCCccCC
Q 001532 27 SVVDKFQL-LPEFLKVRGLVKQHLDSFNYFVN-----TGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDGVSEK 100 (1058)
Q Consensus 27 ~~~~~~~~-i~~~f~~~~Lv~~qi~SFn~Fl~-----~gl~~i~~~~~~i~~~~~~~~~l~~~~i~i~~P~~~~~~~~~~ 100 (1058)
..+..|+. .+..++.++|++.|.+||+||++ +||++++++++||+ +.++++.|+|.+++|++|.+
T Consensus 14 ~~R~~f~~~~~~~~~~PdL~~iQ~~Sf~~Fl~~~~~~~GL~~~f~~ifPI~-d~~g~~~lefv~y~l~~Pk~-------- 84 (2836)
T PRK14844 14 VPRVSYSRSIDLKDSLLDLVKVQKESYDSFTPKNKGNERLEVIFHTIFPIN-DPLHRATIEFISCRVDDPKY-------- 84 (2836)
T ss_pred eeeeecccCCcccCCCCCHHHHHHHHHHHHhcCCCccccHHHHHHhcCCeE-CCCCCEEEEEEEEEeCCCCC--------
Confidence 34456775 45558999999999999999997 69999999999995 55678999999999999998
Q ss_pred CChhhHhhcCCccCceEEEEEEEEE-C-----------CCc--------cceeeEEeEEEEeeeccccccccccCCCCCH
Q 001532 101 LNPHMCRLSDMTYAAPILVNIEYVQ-G-----------SHT--------EKTTMEKNDVVIGRIPIMLRSCRCVLYGKDE 160 (1058)
Q Consensus 101 l~P~EcR~r~lTYsa~l~v~v~~~~-~-----------~~~--------~~~~~~~~~v~iG~iPIMv~S~~C~L~~ls~ 160 (1058)
++.||++|++||++||+|+++++. + .++ ..+++++++|++|+||+|+
T Consensus 85 -~~~Ec~~r~~TYsapl~v~~rL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ikeq~VylGdiPLMT------------ 151 (2836)
T PRK14844 85 -DESECIKRGITFSAQVIASIRLVIMQDGISLDEYKSIKESGDHSKLATVIKSIEEQEVHFCELPMMT------------ 151 (2836)
T ss_pred -CHHHHHhcCCcceeeEEEEEEEEEeccccccccccccccccccccccccccceeeeeEEEecCCccC------------
Confidence 469999999999999999999975 1 110 1246678889999999999
Q ss_pred HHHHhcCCCCCCCCcEEEEcCceeEEeeeecccCCEEEEEeCC-----CCc--EEEEEEecCCCcceEEEEEeeCCEEEE
Q 001532 161 AELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVIIDTDK-----KGN--INASVTSSTETVKSKTVIQMEKGKMYL 233 (1058)
Q Consensus 161 ~elv~~gE~~~d~GGYFIING~EKVI~~q~~~~~N~i~~~~~~-----~g~--~~~~v~s~~~~~~s~~~~~~~~g~i~~ 233 (1058)
..|+|||||+||||++|++|+|+ +|+..+. .|. |.|++++.+. +|+.+..+.++.+|+
T Consensus 152 ------------~~GTFIING~ERVIVSQL~RSPG-VyF~~~~~kt~~sgk~lysa~IIP~RG--sWLefE~D~kd~lyv 216 (2836)
T PRK14844 152 ------------DKGTFIINGVEKVIVSQMHRSPG-VFFDSDKGKTYNSGKLIYSARVIPYRG--SWLDIEFDVKDHLYF 216 (2836)
T ss_pred ------------CCeEEEEcCcceEEEEcceeCCe-EEEEcccCcccCCCceeEEEEEecCCc--ceEEEEEcCCCeEEE
Confidence 79999999999999999999997 8776542 233 6799998654 688888888899999
Q ss_pred EEcceeccccHhhHHHHhCCCCHHHHHHHhCCc-------h---------hHH---------------------------
Q 001532 234 LLNQFVKKIPIMVVMKAMGMESDQEVVQMVGRD-------P---------RYS--------------------------- 270 (1058)
Q Consensus 234 ~~~~~~~~IPl~ilLkALg~~sd~eI~~~i~~~-------~---------~~~--------------------------- 270 (1058)
|+++. +++|+++||||||+ |++||++.++.. . .+.
T Consensus 217 RIDRk-RKiPiT~LLrALGl-s~edIL~~F~~~~~~~~~d~~~~~~~~~e~l~g~~~~~Di~d~~g~vlvdkgrrit~~~ 294 (2836)
T PRK14844 217 RIDRK-RKLPISVLLKALGL-SNNDILDRFYEKIKYIKHKDGWKVPFVPDKFKGVRLPFDLMDVEGNVLLKANVRITSRL 294 (2836)
T ss_pred EecCC-eeeeHHHHHHHhCC-ChHHHHHhhcCceEEEEccCceeeccCHHHHhCCccceeeeccCCCEEEecCccccHHH
Confidence 99995 68999999999999 689999977311 0 000
Q ss_pred -hhh--------------------hh---------------------hH-------------------------H-HHHh
Q 001532 271 -ALL--------------------LP---------------------SI-------------------------E-ECAN 282 (1058)
Q Consensus 271 -~~l--------------------~~---------------------~l-------------------------~-~~~~ 282 (1058)
..+ .. .+ . -...
T Consensus 295 ~krlk~~gvkkl~i~~~~l~g~~LaeDIVD~eTGEiL~eagteIT~e~ik~l~~~gi~~i~~l~~d~~~~~~~i~~tL~~ 374 (2836)
T PRK14844 295 AKKLYDNELKEYLVPFDSICGLFLAEDLIDSASSTKILSAGESIKLEDIKKLELLSIDEISVLNIDNLSVGPYILNTLFL 374 (2836)
T ss_pred HHHHHHcccCcccCchHhhcCceehhhhcCCCCCeEEEcCCCccCHHHHHHHHHcCCCceeeEeecccccchHHHHHHhh
Confidence 000 00 00 0 0001
Q ss_pred cCCcCHHHHHHHHhhcccccCCCCCCCChHHHHHHHHHhhhcc-------CCCCCCC------------CCCCcchhHHH
Q 001532 283 LDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLA-------NVPVHNN------------NFRPKCFYVAV 343 (1058)
Q Consensus 283 ~~i~t~~~al~yig~~~~~~~~~~~~~~~~e~~~~~L~~~llp-------Hl~~~~~------------~~~~K~~~L~~ 343 (1058)
+...++++|+..|+++++++ +.. ..+.|+.++.+.+|. .+|.... ....+.+++ .
T Consensus 375 D~~~~~e~Al~eIy~~lRpg----e~~-~~e~a~~l~~~~ff~~~~YdLg~vGR~k~N~kl~~~~~~~~~~l~~~Dii-~ 448 (2836)
T PRK14844 375 DENMSYQDALYEIYKVLRPG----EVP-VLEIVEEFFRNLFFSPEYYDLSNIGRLKLNSYLGLNYDEDLTVLTHEDII-E 448 (2836)
T ss_pred cccccHHHHHHHHHHhcCCC----CCC-cHHHHHHHHHHHhcCccccccccchhhhhhhhhccCCCCCCcEecHHHHH-H
Confidence 23347789999999999886 333 556677777766543 1221110 011223444 5
Q ss_pred HHHHHHHhhcCCCCCCCcccccceEEcchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCCCCccccccccccchhhh
Q 001532 344 MLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGL 423 (1058)
Q Consensus 344 Mi~kLl~~~~G~~~~DD~D~l~NkRV~~~G~Ll~~lfr~~l~~~~~~ik~~i~k~~~~~~~~~~~~~~~~i~~~~It~~i 423 (1058)
++++|+.+..|....||+|||+||||+++|+||+++||.+|.++.+.+++++... +...+.+..++++++++..+
T Consensus 449 ~i~~Li~l~~g~~~~DDiDhL~NRRvr~vGeLl~~qfr~gl~r~~~~i~e~~~~~-----~~~~~~p~~lin~~~l~~~i 523 (2836)
T PRK14844 449 IVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSMSTS-----SLDKVSPSDFINPKVLTNVL 523 (2836)
T ss_pred HHHHHHHHhcCCCcccchhhhhccccchHHHHHHHHHHHHHHHHHHHHHHHHhhc-----cccccchhhcccchhHHHHH
Confidence 8999999999999999999999999999999999999999999999999998532 12346777888999999999
Q ss_pred hhhhccCCCcccccccccccceEEcccccccccccccccccc----cccccccccCCCcCCCCCccccccCCCCCCCccc
Q 001532 424 ERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSP----QFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACG 499 (1058)
Q Consensus 424 ~~~~sTGn~~~~~~~~q~sG~sq~l~rln~ls~lshlRrv~~----~~~~~~k~t~~R~Lhps~wG~iCPveTPEG~~cG 499 (1058)
++||+| +++||.+|++|+||.|+|.||+++ .+.+++..+.+|++||||||||||+|||||+|||
T Consensus 524 ~~ff~s------------s~LSQfmDQtNpLseltHkRRlsaLGPGGL~r~~a~fevRdvH~shyGRiCPIETPEG~NiG 591 (2836)
T PRK14844 524 RDFFNS------------SQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIG 591 (2836)
T ss_pred HHHhcc------------cchhhhccCcChhhhhhhcceecccCCCCcccccCCCcccccCccccccccCCCCCCCCccc
Confidence 999966 378999999999999999999996 5889999999999999999999999999999999
Q ss_pred ccccccceeeeecCCCChhHHHHHhhcCCeeccccCccccCCCCcEEEEECCeEEeeccChhhHHHHHHHHhhcCCcCce
Q 001532 500 LVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEF 579 (1058)
Q Consensus 500 Li~~LA~~a~Is~~~~~~~i~~~l~~~g~~~l~~~~~~~~~~~~~~~V~lnG~~vG~~~~~~~~~~~lr~~rr~~~i~~~ 579 (1058)
||++||.+|+|+. +|+.. .+|....||++- +++..+ -.....+.
T Consensus 592 LI~SLA~yarIn~-------------~Gfie------------tPy~kV~~g~v~---~~i~yl----sa~~E~~~---- 635 (2836)
T PRK14844 592 LINSLAIYARINK-------------YGFIE------------SPYRKVVNRVVT---DQIEYL----SAIDEGLY---- 635 (2836)
T ss_pred chhhhhhheeccC-------------CceEe------------CCcEEEEcCcCc---cccccc----ChHHhcCc----
Confidence 9999999999985 44321 123333566532 111100 00000000
Q ss_pred eEEEeccccceEEEecCCCeeeeeEEEEecCcccchhhhHHHhhcCCccchhhhccCceeEeccccccceEEEeecCCCC
Q 001532 580 VSVFVNEKQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDAT 659 (1058)
Q Consensus 580 v~i~~~~~~~~i~I~sd~GRl~RPll~v~~~~~~~~~~~~~~l~~~~~s~~~~~~~~~iE~id~~e~~~~~Ia~~~~~~~ 659 (1058)
.| ....+.+ ...|++..+.+.++.. + ||+-.. +
T Consensus 636 -~I----a~a~~~~-~~~~~~~~~~v~~R~~-------------------------~--ef~~~~----------~---- 668 (2836)
T PRK14844 636 -YI----ADTSAKL-DENNCFVDDMLYCRYA-------------------------G--SFVMVS----------S---- 668 (2836)
T ss_pred -EE----EeCCccC-CCCCcccCCeEEEecC-------------------------C--ceEEec----------H----
Confidence 00 0011111 1245666665554321 1 111110 0
Q ss_pred CCceeeeecCccccccccccCCCCCCCCCCccccccccccCCcccee-------------------------------Ee
Q 001532 660 PDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIA-------------------------------FN 708 (1058)
Q Consensus 660 ~~~th~Ei~p~~~ls~~asliPF~~hNqspRn~yq~~M~KQaiG~~~-------------------------------~n 708 (1058)
...++++++|.|++|++||||||.+||||+|++||||||||||++.. +.
T Consensus 669 ~~v~~~dvsp~Q~~SvaasLIPFLEhdDAnRALMGSNMQRQAVPLl~~e~PiVGTG~E~~vA~DSg~~v~A~~~G~V~yV 748 (2836)
T PRK14844 669 DQVSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESFVASGSGAVVLAKRDGIVDSS 748 (2836)
T ss_pred HHceEEEeCcchhhhhHhhcCCccccCccccccccccccccccccccCCCCeEecCcchhhhhcccceEEeccCceEEEE
Confidence 12478999999999999999999999999999999999999997421 11
Q ss_pred e----eecccc---------ceeee----------eCCCcceeechhhhh----------hcCCCCCCCcceEEEEeecC
Q 001532 709 Q----LCRMDS---------LLYLL----------VYPQRPLLTTRTIEL----------VGYDKLGAGQNATVAVMSYS 755 (1058)
Q Consensus 709 ~----~~R~D~---------~~y~l----------~ypQ~Plv~t~~~~~----------~~~~~~~~G~N~~Vav~~y~ 755 (1058)
. -.|.+. ..|.| |++|||+|+.+.... +..+|+++|+|++||||||.
T Consensus 749 da~kIvI~~~~~~~~~~~~~~~Y~L~ky~RSNQ~TcinQrPiV~~Gd~V~kGdilADG~st~~GELALG~NvlVAfmpW~ 828 (2836)
T PRK14844 749 DSNSIVIRAFDKERVNYLDVDIYHLRKFQRSNHNTCINQKPLVCVGDYVKEGDVIADGPAINSGELALGQNLLVAFMSWQ 828 (2836)
T ss_pred cCCEEEEEeCCCccccccccceEEeccccccccceeeeecceecCCCEeccCCEeccChhhcccccccccceEEEEeccC
Confidence 1 111111 23665 669999999987643 45899999999999999999
Q ss_pred CCCCCCcEEEecceeeccceEEEEEEEEEEEeecccCCccceecC-CCCCCCcccccccCCCCccccCCcEeCCCCEEEE
Q 001532 756 GYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILR-PDRTGPGAERMQILDDDGLAAPGEIIKPNDVYIN 834 (1058)
Q Consensus 756 Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~e~~~~-p~~~~~~~~~~~~ld~dGi~~~g~~v~~gd~li~ 834 (1058)
|||+||||+||++.+.+++|||+|+++|+++.++++.|.+|.... |+.+. ...++||++|||++|++|++||||||
T Consensus 829 GYNfEDAIliSErlv~eD~fTSiHIee~ei~~r~Tk~G~EeITrdIPnv~e---~~lr~LDe~GIV~iGa~V~~GDILVG 905 (2836)
T PRK14844 829 GYNFEDSIIISSEVVKKDLFTSIHIEEFECVVHDTPLGSEKITRAIPGVNE---ENLYHLDDSGIVKIGTRVGPGYILVG 905 (2836)
T ss_pred CcccccccccchhhccCceeEEEeecceEEEEEeccCCCceecccCCCCCh---HHHhcCCCCCCeecCCEECCCCEEEE
Confidence 999999999999999999999999999999999998887555544 88753 68899999999999999999999999
Q ss_pred EecCCCCCCCCCC------CCCCCCcccccceEEeeCCCCCceEEEEEEEeeCC--------------------------
Q 001532 835 KESPLETRGSIMS------PTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDK-------------------------- 882 (1058)
Q Consensus 835 k~~~~~~~~~~~~------~~~~~~~~~~~~s~~~~~~~~~~~~vd~v~~~~~~-------------------------- 882 (1058)
|++|+.+.+.++. -++.+....+|+|+++.++. .|+|-.|.+++..
T Consensus 906 KvtPk~e~~~tPEekLL~aIFGek~~~vkdtSLrvp~G~--~G~Vidv~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 983 (2836)
T PRK14844 906 KVTPKPSLSLPPETKLLMTIFGEKSFDCADSSLYTSPDV--EGTVIDVQVFTRRGVEENERALLIKQKEINDFEKERDYI 983 (2836)
T ss_pred eecCCCCCCCCHHHHHHHHHhCCcccccccCceecCCCC--CEEEEEEEEEcccccccchhhhhhhhhhhhhhhhhhhhh
Confidence 9999976654321 14566677899999988887 9999988876532
Q ss_pred ---------------------------------------------------------------------------CC---
Q 001532 883 ---------------------------------------------------------------------------NG--- 884 (1058)
Q Consensus 883 ---------------------------------------------------------------------------~~--- 884 (1058)
.|
T Consensus 984 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~gdeL 1063 (2836)
T PRK14844 984 INVTSEYFYDELKKLLINSGSQDREKFDSIEREQWWGIGLKNQSISEQVKSLKKDFDEKVSHAIAQFKRKVEKLHEGYDL 1063 (2836)
T ss_pred hhhhhhhhhhhhhhhhcccccccHHHHhhccHHhhhhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcC
Confidence 01
Q ss_pred ----CEEEEEEEeecCCCcccceecccCCCccEEEeeeccCCCCCCCCCCCCcEEeCCCCCCCcccHHHHHHHhhccchh
Q 001532 885 ----DLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGV 960 (1058)
Q Consensus 885 ----~~~v~v~i~~~R~p~iGDKf~sRhGqKGvvs~i~~~~DmPf~~~G~~pDiIiNP~~~PSRMtiGql~E~~~gk~~~ 960 (1058)
...|||+|++.|++++|||+|||||||||||+|+|.|||||++||+++|||+||+|+||||||||++|+++|+||.
T Consensus 1064 ~~gv~~~VkVyia~KRkiqvGDKmAGRHGNKGVIS~IlP~eDMPyL~DGtpvDIvLNPLGVPSRMNvGQilE~hLG~A~~ 1143 (2836)
T PRK14844 1064 PQGVSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGWACK 1143 (2836)
T ss_pred CCCCceEEEEEEEEeecCCccccccccCCCCceEeEEcccCCCCcCCCCCCceEEeCCCCCCccccHHHHHHHHHHHHHh
Confidence 2579999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred cCCcee--------------------------------------------------------------------------
Q 001532 961 SCGRFH-------------------------------------------------------------------------- 966 (1058)
Q Consensus 961 ~~g~~~-------------------------------------------------------------------------- 966 (1058)
..|...
T Consensus 1144 ~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1223 (2836)
T PRK14844 1144 KLGEKVGNILDEINKIKSAFCKGIRSLNDDNFTKFAAAYLDNKKIENIDDDEITASVLNTPNKNALNDELNELVENYLNS 1223 (2836)
T ss_pred hhhhhhHhhhhhhhccccccccccccccccccccccccccccccccccccccccccccccccccccccccccchhccccc
Confidence 775210
Q ss_pred --------------------------------------------eeecccCCCCCCCCHHHHHHHHHHcCCCCCCceEEE
Q 001532 967 --------------------------------------------YGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIY 1002 (1058)
Q Consensus 967 --------------------------------------------~~tpf~~~~~~~~~~~~~~~~l~~~g~~~~G~e~ly 1002 (1058)
.+.||..+.+++...+++.+.|.++||+++|++.||
T Consensus 1224 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~tpvf~g~~~~~i~~~L~~~g~~~~Gk~~l~ 1303 (2836)
T PRK14844 1224 CKSAYSNLRNFLIEVYSCGSNVSICNNIRDISDNNLIEFARKLRDGIPVAAPVFEGPKDEQIAKLFELAGLDNSGQAVLY 1303 (2836)
T ss_pred cchhhHHHHHHHHHhhhcccccccccccccccHHHHHHHHhhhccCCeecCCCcCCCCHHHHHHHHHHhCcCCCCCEEEE
Confidence 022344455678888999999999999999999999
Q ss_pred eCCCCcEeeeeEeeeeeeeeccccccCcceEEeccCCccccccCCcCcccCCCCC
Q 001532 1003 SGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGF 1057 (1058)
Q Consensus 1003 ~g~tG~~~~~~if~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~ 1057 (1058)
||+||++|+++||+|++|||||+|||.||+|||++|||+.+||||++||+++|||
T Consensus 1304 dG~TGe~f~~~v~vG~~yy~kL~HmV~DKihaRs~Gp~s~lT~QPl~Gr~~~GG~ 1358 (2836)
T PRK14844 1304 DGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQ 1358 (2836)
T ss_pred cCCCCCccchhheeCcchhhhhhhhhcchhhhcccCCCcccccCCCcccccCCCc
Confidence 9999999999999999999999999999999999999999999999999999998
No 13
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated
Probab=100.00 E-value=1e-149 Score=1330.81 Aligned_cols=506 Identities=47% Similarity=0.767 Sum_probs=476.3
Q ss_pred cEEEEECCeEEeeccChhhHHHHHHHHhhcCCcCceeEEEeccccceEEEecCCCeeeeeEEEEecCcccchhhhHHHhh
Q 001532 544 SFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELL 623 (1058)
Q Consensus 544 ~~~V~lnG~~vG~~~~~~~~~~~lr~~rr~~~i~~~v~i~~~~~~~~i~I~sd~GRl~RPll~v~~~~~~~~~~~~~~l~ 623 (1058)
.++|||||+|+|++++|..|+++||.+||.|.++.+++|+++...++|+|+||+||++|||++|++|++.++++|+++++
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 56899999999999999999999999999999999999999988899999999999999999999999999999999998
Q ss_pred cCCccchhhhccCceeEeccccccceEEEeecCCCCCCceeeeecCccccccccccCCCCCCCCCCccccccccccCCcc
Q 001532 624 DGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMG 703 (1058)
Q Consensus 624 ~~~~s~~~~~~~~~iE~id~~e~~~~~Ia~~~~~~~~~~th~Ei~p~~~ls~~asliPF~~hNqspRn~yq~~M~KQaiG 703 (1058)
.++++|+||+++|+|||||++||++++||+.++++...+||+||+|+++||++||+|||+||||||||||||||+|||||
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 88899999999999999999999999999999998777899999999999999999999999999999999999999999
Q ss_pred ceeEeeeeccccceeeeeCCCcceeechhhhhhcCCCCCCCcceEEEEeecCCCCCCCcEEEecceeeccceEEEEEEEE
Q 001532 704 NIAFNQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKY 783 (1058)
Q Consensus 704 ~~~~n~~~R~D~~~y~l~ypQ~Plv~t~~~~~~~~~~~~~G~N~~Vav~~y~Gyn~EDaiiink~s~~rg~~~s~~~~~~ 783 (1058)
++++|+..|+|++.|+|+|||+|||+|+.++.++++++|+|+||+||||||+||||||||||||+|+|||||||+||++|
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---CcccccccCCCCccccCCcEeCCCCEEEEEecCCCCCCCCCCCCCCCCcccccce
Q 001532 784 TAINQKYANSTSDRILRPDRTG---PGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSAR 860 (1058)
Q Consensus 784 ~~~~~~~~~~~~e~~~~p~~~~---~~~~~~~~ld~dGi~~~g~~v~~gd~li~k~~~~~~~~~~~~~~~~~~~~~~~~s 860 (1058)
+++++++..+..+.+..|+.+. .....|++||+||||++|++|++|||||||++|..+.++. ...+......+|.|
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 9999887766667777776421 1224689999999999999999999999999997543221 00111223478999
Q ss_pred EEeeCCCCCceEEEEEEEeeCCCCCEEEEEEEeecCCCcccceecccCCCccEEEeeeccCCCCCCCCCCCCcEEeCCCC
Q 001532 861 QTYKGPDGETCVVDRVALCSDKNGDLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHG 940 (1058)
Q Consensus 861 ~~~~~~~~~~~~vd~v~~~~~~~~~~~v~v~i~~~R~p~iGDKf~sRhGqKGvvs~i~~~~DmPf~~~G~~pDiIiNP~~ 940 (1058)
++++.+| .|+||+|.++.++++.+.|||++|+.|+|+||||||||||||||||+|||+||||||+||++|||||||||
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 9999999 99999999998888899999999999999999999999999999999999999999999999999999999
Q ss_pred CCCcccHHHHHHHhhccchhcCCceeeeecccCCCCCCCCHHHHHHHHHHcCCCCCCceEEEeCCCCcEeeeeEeeeeee
Q 001532 941 FPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIY 1020 (1058)
Q Consensus 941 ~PSRMtiGql~E~~~gk~~~~~g~~~~~tpf~~~~~~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if~G~~y 1020 (1058)
||||||||||+|+++||++++.|.+.|+|||. ...++++++.|.++||+++|+|+||||+||++|+++||+||+|
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 5678999999999999999999999999999999999999999
Q ss_pred eeccccccCcceEEeccCCccccccCCcCcccCCCCC
Q 001532 1021 YQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGF 1057 (1058)
Q Consensus 1021 y~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~ 1057 (1058)
||||+|||.||+|||++||++.|||||++||||+|||
T Consensus 476 YqrL~HmV~DK~haR~~Gp~~~lTrQP~~GR~r~GG~ 512 (605)
T PRK07225 476 YQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGL 512 (605)
T ss_pred eeechhhhcchhhhccCCCCcccccCCccccccCCCe
Confidence 9999999999999999999999999999999999997
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=1.9e-149 Score=1327.12 Aligned_cols=503 Identities=47% Similarity=0.795 Sum_probs=473.1
Q ss_pred EEECCeEEeeccChhhHHHHHHHHhhcCCcCceeEEEeccccceEEEecCCCeeeeeEEEEecCcccchhhhHHHhhcCC
Q 001532 547 VIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGV 626 (1058)
Q Consensus 547 V~lnG~~vG~~~~~~~~~~~lr~~rr~~~i~~~v~i~~~~~~~~i~I~sd~GRl~RPll~v~~~~~~~~~~~~~~l~~~~ 626 (1058)
|||||+|+|++++|..|+++||.+||.|.++.+++|+++...++|+|+||+||++|||++|++|++.++++|++.++.+.
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 79999999999999999999999999999999999999988899999999999999999999999999999999998778
Q ss_pred ccchhhhccCceeEeccccccceEEEeecCCCCCCceeeeecCccccccccccCCCCCCCCCCccccccccccCCcccee
Q 001532 627 RSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIA 706 (1058)
Q Consensus 627 ~s~~~~~~~~~iE~id~~e~~~~~Ia~~~~~~~~~~th~Ei~p~~~ls~~asliPF~~hNqspRn~yq~~M~KQaiG~~~ 706 (1058)
.+|+||+++|+|||||++||++++||+.++++...+||+||+|+++||++||+|||+||||||||||||||+|||||+++
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 89999999999999999999999999999998777999999999999999999999999999999999999999999999
Q ss_pred EeeeeccccceeeeeCCCcceeechhhhhhcCCCCCCCcceEEEEeecCCCCCCCcEEEecceeeccceEEEEEEEEEEE
Q 001532 707 FNQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAI 786 (1058)
Q Consensus 707 ~n~~~R~D~~~y~l~ypQ~Plv~t~~~~~~~~~~~~~G~N~~Vav~~y~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~ 786 (1058)
+|+..|+|++.|+|+|||+|||+|+.++.++++++|+|+||+||||||+|||||||||+||+|+|||+|||+||++|+++
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---CcccccccCCCCccccCCcEeCCCCEEEEEecCCCCCCCCCCCCCCCCcccccceEEe
Q 001532 787 NQKYANSTSDRILRPDRTG---PGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTY 863 (1058)
Q Consensus 787 ~~~~~~~~~e~~~~p~~~~---~~~~~~~~ld~dGi~~~g~~v~~gd~li~k~~~~~~~~~~~~~~~~~~~~~~~~s~~~ 863 (1058)
++++..+..|.+..|+... .....|++||+||||++|++|++|||||||++|..+.++. ..++......+|.|+++
T Consensus 241 ~~~~~~~~~e~~~~p~~~~~~~~~~~~~~~LD~dGi~~~G~~v~~gdiligk~~p~~~~~~~-~~~~~~~~~~~d~s~~~ 319 (599)
T TIGR03670 241 ERRYPGGQEDRFEIPEPDVRGYRGEEAYKHLDEDGIVYPEVEVKGGDVLIGKTSPPRFLEEL-RELGLVTERRRDTSVTV 319 (599)
T ss_pred eeccCCCCceEEecCCchhccccchhhhccCCCCCCcCCCcEeCCCCEEEEEecCCCCccch-hhhccccccCceEEEEe
Confidence 9877666667777676321 1224689999999999999999999999999987543221 00111223478999999
Q ss_pred eCCCCCceEEEEEEEeeCCCCCEEEEEEEeecCCCcccceecccCCCccEEEeeeccCCCCCCCCCCCCcEEeCCCCCCC
Q 001532 864 KGPDGETCVVDRVALCSDKNGDLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPS 943 (1058)
Q Consensus 864 ~~~~~~~~~vd~v~~~~~~~~~~~v~v~i~~~R~p~iGDKf~sRhGqKGvvs~i~~~~DmPf~~~G~~pDiIiNP~~~PS 943 (1058)
+.+| +|+||+|.++.++++.+.|||++|+.|+|+||||||||||||||||+|||+||||||+||++||||||||||||
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 cccHHHHHHHhhccchhcCCceeeeecccCCCCCCCCHHHHHHHHHHcCCCCCCceEEEeCCCCcEeeeeEeeeeeeeec
Q 001532 944 RMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQK 1023 (1058)
Q Consensus 944 RMtiGql~E~~~gk~~~~~g~~~~~tpf~~~~~~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if~G~~yy~r 1023 (1058)
|||||||+|+++||++++.|.+.|+|||+ +..++++++.|.++||+++|+|.||||+||++|+++||+||+||||
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 5668999999999999999999999999999999999999999999
Q ss_pred cccccCcceEEeccCCccccccCCcCcccCCCCC
Q 001532 1024 LKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGF 1057 (1058)
Q Consensus 1024 L~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~ 1057 (1058)
|+|||.||+|||++||++.|||||++||||+|||
T Consensus 473 L~HmV~DK~h~Rs~Gp~~~lTrQP~~Gr~r~GG~ 506 (599)
T TIGR03670 473 LHHMVADKIHARSRGPVQVLTRQPTEGRAREGGL 506 (599)
T ss_pred chhhhcchhhhcccCCCcccccCCccccccCCCe
Confidence 9999999999999999999999999999999997
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=8.7e-110 Score=956.35 Aligned_cols=367 Identities=47% Similarity=0.781 Sum_probs=314.7
Q ss_pred ccccccCCCCCCCCCCccccccccccCCccceeEeeeeccccceeeeeCCCcceeech-hhhhhc---------CCCCCC
Q 001532 674 GVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTR-TIELVG---------YDKLGA 743 (1058)
Q Consensus 674 s~~asliPF~~hNqspRn~yq~~M~KQaiG~~~~n~~~R~D~~~y~l~ypQ~Plv~t~-~~~~~~---------~~~~~~ 743 (1058)
|++|++|||++|||||||+|||||+|||||++.+|+..|.|+.. +|||+|||+|+ .++..+ ++|+|+
T Consensus 1 si~As~ipf~~hn~s~R~~~~~~m~kQa~~~y~~~~~~R~d~~~---~~~q~Plv~~~~~~~~~~ilad~~~~~~~e~~~ 77 (386)
T PF00562_consen 1 SIVASLIPFPEHNQSPRNLYQCNMQKQAIGTYSLNKFNRSDQNT---CYPQKPLVKTGDRVEKGQILADGPSTKFGELPL 77 (386)
T ss_dssp -THGGTSSSGGGC-HHHHHHHHHHGCGBCSEEETTTTTS-TSSE---SS-BEESSBSSSTBTTTTECEE-TTECTTTS-S
T ss_pred CEEeCCCCEEEEEcCCcEEEEeCcCCCcccceeeeeeeccCcce---eccccceEEeeccccccCccccccccccccCcc
Confidence 68999999999999999999999999999999999999999998 89999999999 777777 999999
Q ss_pred CcceEEEEeecCCCCCCCcEEEecceeeccceEEEEEEEEEEEeecccCCccceecC-CCCCCCcccccccCCCCccccC
Q 001532 744 GQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILR-PDRTGPGAERMQILDDDGLAAP 822 (1058)
Q Consensus 744 G~N~~Vav~~y~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~e~~~~-p~~~~~~~~~~~~ld~dGi~~~ 822 (1058)
|+|++||||||+||||||||||||+|++||+|+|+||++ +++++..+.+..+.+.. |... ....|++||+||||++
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 88888777666454443 3222 2368999999999999
Q ss_pred CcEeCCCCEEEEEec-CCCCCCCCCCCCCCCCcccccceEEeeCCCCCceEEEEEEE-------eeCCCCCEEEEEEEee
Q 001532 823 GEIIKPNDVYINKES-PLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVAL-------CSDKNGDLCIKFLIRH 894 (1058)
Q Consensus 823 g~~v~~gd~li~k~~-~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~vd~v~~-------~~~~~~~~~v~v~i~~ 894 (1058)
|++|++||+||||++ +..........+..+....+|.|++++.++ .|+||+|.+ ..+.++...|+|++|+
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 211110000001122233789999999999 999999999 5567789999999999
Q ss_pred cCCCcccceecccCCCccEEEeeeccCCCCCCCCCCCCcEEeCCCCCCCcccHHHHHHHhhccchhcCCceeeeecccCC
Q 001532 895 TRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEP 974 (1058)
Q Consensus 895 ~R~p~iGDKf~sRhGqKGvvs~i~~~~DmPf~~~G~~pDiIiNP~~~PSRMtiGql~E~~~gk~~~~~g~~~~~tpf~~~ 974 (1058)
.|+|+||||||||||||||||+|||+||||||++|++|||||||||||||||||||+|+++||++++.|.+.|+|||+
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 CCCCCCHHHHHHHHHHcCCCCCCceEEEeCCCCcEeeeeEeeeeeeeeccccccCcceEEeccCCccccccCCcCcccC
Q 001532 975 SGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRAR 1053 (1058)
Q Consensus 975 ~~~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~ 1053 (1058)
+...+++++.|.++||+++|+|.||||+||++++++||+|++|||||+|||+||+|||++||++.|||||++||+|
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=3.2e-106 Score=955.94 Aligned_cols=486 Identities=33% Similarity=0.593 Sum_probs=430.8
Q ss_pred cccccccccccccccchHHHHHHHHHHHHHhCHHHHHHhcCcceecCCCcEEEEEeEEEEcCCccccCC-ccCCCChhhH
Q 001532 28 VVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDG-VSEKLNPHMC 106 (1058)
Q Consensus 28 ~~~~~~~i~~~f~~~~Lv~~qi~SFn~Fl~~gl~~i~~~~~~i~~~~~~~~~l~~~~i~i~~P~~~~~~-~~~~l~P~Ec 106 (1058)
.+++|.++++||+.++|++||++|||+|+++||++++++.++|+....+.+.|+|++++|++|++.+++ ...+++|+||
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 357999999999999999999999999999999999999999987767778999999999999987654 5578999999
Q ss_pred hhcCCccCceEEEEEEEEECCCccceeeEEeEEEEeeeccccccccccCCCCCHHHHHhcCCCCCCCCcEEEEcCceeEE
Q 001532 107 RLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVL 186 (1058)
Q Consensus 107 R~r~lTYsa~l~v~v~~~~~~~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~ls~~elv~~gE~~~d~GGYFIING~EKVI 186 (1058)
|+|++||+|+++|++.++.++ .....++|++|+|||||+|++|||++++|+|+++.||||.|+||||||||+||||
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 eeeecccCCEEEEEeCCC---CcEEEEEEecCCCcce-EEEEEeeCCEEEEEEcceeccccHhhHHHHhCCCCHHHHHHH
Q 001532 187 LIQEQLSKNRVIIDTDKK---GNINASVTSSTETVKS-KTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQM 262 (1058)
Q Consensus 187 ~~q~~~~~N~i~~~~~~~---g~~~~~v~s~~~~~~s-~~~~~~~~g~i~~~~~~~~~~IPl~ilLkALg~~sd~eI~~~ 262 (1058)
|+||+++||++++++++. ..+.+.++|.....+. ..+.+..+|.+++++++..++||++++|||||.+||+||++.
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 2377888887663322 334455678999999987678999999999999999999999
Q ss_pred hCCchhHHhhhhhhHHHHHhcCCcCHHHHHHHHhhcccccCCCCCCCChHHHHHHHHHhhhccCCCCCCCCCCCcchhHH
Q 001532 263 VGRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLANVPVHNNNFRPKCFYVA 342 (1058)
Q Consensus 263 i~~~~~~~~~l~~~l~~~~~~~i~t~~~al~yig~~~~~~~~~~~~~~~~e~~~~~L~~~llpHl~~~~~~~~~K~~~L~ 342 (1058)
++.+..+.+.+..++++ .++.|+++||.|||+++++.. ++.. ..+.|+.+|++++|||+|.+..+..+|+++|+
T Consensus 238 i~~~~~~~~~l~~~~~~---~~~~t~~~al~~ig~~~~~~~--~~~~-~~~~~~~~l~~~~l~hig~~~~~~~~K~~~L~ 311 (494)
T PRK09606 238 VSDDPEIVKFMLENLEE---AEVDTQEEALEYIGKRVAPGQ--TKEY-RIKRAEYVIDRYLLPHLGVEPEVRRAKAHYLG 311 (494)
T ss_pred hCCcHHHHHHHHHHHHh---cccCCHHHHHHHHHHhcCCCC--Ccch-HHHHHHHHHHHhhhcccCCCcchhhHHHHHHH
Confidence 96555555555555554 357899999999999998752 3334 67899999999999999976555678999999
Q ss_pred HHHHHHHHhhcCCCCCCCcccccceEEcchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCCCCccccccccccchhh
Q 001532 343 VMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVG 422 (1058)
Q Consensus 343 ~Mi~kLl~~~~G~~~~DD~D~l~NkRV~~~G~Ll~~lfr~~l~~~~~~ik~~i~k~~~~~~~~~~~~~~~~i~~~~It~~ 422 (1058)
+|++||++++.|.+.+||+|||+||||+++|+||+.+||++|+++++.++..+++...++ ..+++..+++++.||++
T Consensus 312 ~m~~kLl~~~~g~~~~Dd~D~l~nkRv~~~G~Ll~~~fr~~l~~~~~~~k~~l~~~~~~~---~~~~~~~~~~~~~It~~ 388 (494)
T PRK09606 312 RMAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERANMRN---RELSIKTAVRSDVLTER 388 (494)
T ss_pred HHHHHHHHHhcCCCCCCCcccccCceeeccchhHHHHHHHHHHHHHHHHHHHHHHHHhcC---CCCCHHHhcCchhhhHH
Confidence 999999999999999999999999999999999999999999999999998888765332 24567777888999999
Q ss_pred hhhhhccCCCcccccccccccceEEcccccccccccccccccccccccccccCCCcCCCCCccccccCCCCCCCcccccc
Q 001532 423 LERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVK 502 (1058)
Q Consensus 423 i~~~~sTGn~~~~~~~~q~sG~sq~l~rln~ls~lshlRrv~~~~~~~~k~t~~R~Lhps~wG~iCPveTPEG~~cGLi~ 502 (1058)
|++|||||||+. +++|+||+|+|+||+|+|||+||+|+++.+.++.++||+||||||||+||||||||+||||++
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 cccceeeeecCCCChhHHHHHhhcCCeec
Q 001532 503 NLALMTHVTTDEEEGPLISLCYCLGVEDL 531 (1058)
Q Consensus 503 ~LA~~a~Is~~~~~~~i~~~l~~~g~~~l 531 (1058)
|||++|+|+.+.+.+++.++|.++|+.++
T Consensus 464 ~La~~a~V~~~~~~~~i~~~l~~lg~~~~ 492 (494)
T PRK09606 464 NFAQMVEISTGEDEEEVKEILKELGVEPE 492 (494)
T ss_pred hhhceEEEeCCCChHHHHHHHHHCcCeeC
Confidence 99999999999888899999999999875
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=2e-44 Score=382.06 Aligned_cols=147 Identities=46% Similarity=0.851 Sum_probs=126.1
Q ss_pred chHHHHHHHHHHHHHhCHHHHHHhcCcceecC-CCcEEEEEeEEEEcCCccccC-CccCCCChhhHhhcCCccCceEEEE
Q 001532 43 GLVKQHLDSFNYFVNTGIRKIVRANDRIVSGI-DPSIFLRFKDVRIGQPSMTVD-GVSEKLNPHMCRLSDMTYAAPILVN 120 (1058)
Q Consensus 43 ~Lv~~qi~SFn~Fl~~gl~~i~~~~~~i~~~~-~~~~~l~~~~i~i~~P~~~~~-~~~~~l~P~EcR~r~lTYsa~l~v~ 120 (1058)
+|++||++|||+|+++||++++++.++|..+. ...+.++|++++|++|++.+. ...+++||+|||+|++||+|+++|+
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 68999999999999999999999999998765 578999999999999999884 3789999999999999999999999
Q ss_pred EEEEECCCccceeeEEeEEEEeeeccccccccccCCCCCHHHHHhcCCCCCCCCcEEEEcCceeEEeeeecc
Q 001532 121 IEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQL 192 (1058)
Q Consensus 121 v~~~~~~~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~ls~~elv~~gE~~~d~GGYFIING~EKVI~~q~~~ 192 (1058)
++++.++. ..+...+|++|+|||||+|++|||++++++|+++.||||.|+||||||||+|||||+|+++
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 99999873 3667778999999999999999999999999999999999999999999999999999988
No 18
>PF04565 RNA_pol_Rpb2_3: RNA polymerase Rpb2, domain 3; InterPro: IPR007645 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Domain 3, is also known as the fork domain and is proximal to catalytic site [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_B 1SMY_M 3DXJ_M 3AOI_C 2A68_M 1ZYR_C 3AOH_H 1IW7_M 2O5J_C 2CW0_M ....
Probab=99.92 E-value=2.9e-26 Score=198.85 Aligned_cols=66 Identities=50% Similarity=0.899 Sum_probs=59.7
Q ss_pred EEccccccccccccccccc--ccccccccccCCCcCCCCCccccccCCCCCCCcccccccccceeeee
Q 001532 446 QVLARLSFIGTLGHMTRVS--PQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVT 511 (1058)
Q Consensus 446 q~l~rln~ls~lshlRrv~--~~~~~~~k~t~~R~Lhps~wG~iCPveTPEG~~cGLi~~LA~~a~Is 511 (1058)
|+|+|+|++++|||+|||+ +++.++.|++.+|+|||||||||||||||||++|||++|||++|+|+
T Consensus 1 Q~l~r~N~l~~ls~~Rri~~~~~~~~~~~~~~~R~lh~s~~G~iCPveTPEG~~~GLv~~La~~a~I~ 68 (68)
T PF04565_consen 1 QYLDRTNPLSELSHLRRINRLGPLSKESKSTEPRQLHPSQYGRICPVETPEGENCGLVKNLALMARIT 68 (68)
T ss_dssp EE--TSSHHHHHHHHTEEESCSSTSSSSSSSTTTSTTGGGTTTBSSSSS-SSTSTTTEEEBBTT-EE-
T ss_pred CCcccccHHHHHHHHHhcccccccchhhcccccccccccceeEEeecccCCCccEeehheeeeeEEeC
Confidence 8999999999999999999 68999999999999999999999999999999999999999999986
No 19
>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=2.8e-21 Score=202.75 Aligned_cols=174 Identities=26% Similarity=0.379 Sum_probs=119.8
Q ss_pred CCEEEEEeCCCCcEE-EEEEecCCCcceEEEEE-eeCCEEEEEEcceeccccHhhHHHHhCCCCHHHHHHHhC-CchhHH
Q 001532 194 KNRVIIDTDKKGNIN-ASVTSSTETVKSKTVIQ-MEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVG-RDPRYS 270 (1058)
Q Consensus 194 ~N~i~~~~~~~g~~~-~~v~s~~~~~~s~~~~~-~~~g~i~~~~~~~~~~IPl~ilLkALg~~sd~eI~~~i~-~~~~~~ 270 (1058)
.|+|++++++++..+ +++++.....++....+ .++..+.+.......+||+++||||||++||+||++.|+ .+....
T Consensus 2 sn~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IPi~ilLrALG~~sd~eI~~~i~~~~~~~~ 81 (190)
T PF04561_consen 2 SNGIYVEKDKDGNKIIRSVRSDIISSRGSWHYLEKDKKIIIFSRPKKKFKIPIVILLRALGIESDKEIIELICYSEEDFE 81 (190)
T ss_dssp SSSEEEEE-SSSSSCSSCEEEEECCSSSEEEEEECETTTEEEEETTSSSEEEHHHHHHHTT--STCHHHHHHCCCSTCHS
T ss_pred CCEEEEEEccCCCCeeEEEEeecCCCcceEEEEecCCcEEEEEEcCcccccceEEeehhhcCcCcccccceeeccccccc
Confidence 578999987665533 33333333333333332 344455556655567899999999999999999999995 333333
Q ss_pred hhhhhhHHHHHhcCCcCHHHHHHHHhhcccccCCCCCCCChHHHHHHHH---------Hhhhcc-CCCCCCCCCC--Ccc
Q 001532 271 ALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSIL---------RDVFLA-NVPVHNNNFR--PKC 338 (1058)
Q Consensus 271 ~~l~~~l~~~~~~~i~t~~~al~yig~~~~~~~~~~~~~~~~e~~~~~L---------~~~llp-Hl~~~~~~~~--~K~ 338 (1058)
.....++......++.|+++|+.|||++++.. ..+.. ..+.++.+| .+++|+ |++....... .|+
T Consensus 82 ~~~~~~~~~~~~~~~~t~~~al~~i~~~~~~~--~~~~~-~~~~~~~~l~~~y~l~~i~r~~l~~hl~~~~~~~~~~~k~ 158 (190)
T PF04561_consen 82 DIEELMLSELEEEEIYTQEQALEYIGKKFRFR--QGKPP-KVEEARNFLQKRYDLGFIGRYKLNKHLGSDEPNENDRLKA 158 (190)
T ss_dssp CSTTTHHHHCCCTSSCSCHHHHHHHHHCCHSS--SSCHC-CHCHHHHHHTTCSSTCCCHHHCCHTTTTSSSSSSSSSCHH
T ss_pred ccccccccccccccccccccceeEeccceeee--ccccc-chhhhhcccccccccccccccceeeeeeeeecccccccch
Confidence 33334455555678999999999999944433 22334 566777776 467777 9997754333 499
Q ss_pred hhHHHHHHHHHHhhcCCCCCCCcccccceEEc
Q 001532 339 FYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLE 370 (1058)
Q Consensus 339 ~~L~~Mi~kLl~~~~G~~~~DD~D~l~NkRV~ 370 (1058)
.+|++|+++|+.++.|.+.+||+|||+||||+
T Consensus 159 ~~l~~m~~~ll~~~~g~~~~Dd~D~l~NkRv~ 190 (190)
T PF04561_consen 159 EDLGLMIRKLLKLANGECEPDDRDHLGNKRVR 190 (190)
T ss_dssp HHHHHHHHHHHHHHTTSS-S-STTSCCCEEEE
T ss_pred hhHHHHHHHHHHHhcCCCCCCCccccCCcCCc
Confidence 99999999999999999999999999999996
No 20
>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=5e-17 Score=138.51 Aligned_cols=63 Identities=37% Similarity=0.757 Sum_probs=59.5
Q ss_pred EEECCeEEeeccChhhHHHHHHHHhhcCCcCceeEEEeccccceEEEecCCCeeeeeEEEEec
Q 001532 547 VIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADK 609 (1058)
Q Consensus 547 V~lnG~~vG~~~~~~~~~~~lr~~rr~~~i~~~v~i~~~~~~~~i~I~sd~GRl~RPll~v~~ 609 (1058)
|||||.|+|++++|..|+..||.+||.|.++.++|++++...++|+|+||+||++|||++|+|
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 799999999999999999999999999999999999999999999999999999999999975
No 21
>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=98.76 E-value=3.9e-09 Score=85.44 Aligned_cols=41 Identities=46% Similarity=0.818 Sum_probs=33.2
Q ss_pred chhhhccCceeEeccccccceEEEeecCCC-------CCCceeeeecC
Q 001532 629 FDDFLREGLIEYLDVNEENNALIALYEGDA-------TPDTTHIEIEP 669 (1058)
Q Consensus 629 ~~~~~~~~~iE~id~~e~~~~~Ia~~~~~~-------~~~~th~Ei~p 669 (1058)
|++|++.|+|||||++||++++||++++++ ...||||||||
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 22
>KOG0215 consensus RNA polymerase III, second largest subunit [Transcription]
Probab=98.75 E-value=7.7e-11 Score=138.57 Aligned_cols=447 Identities=8% Similarity=-0.089 Sum_probs=244.3
Q ss_pred CCcccccccccccccccccchHHHHHHHHHHHHHhCHHHHHHhcCcceecCCCcEEEEEeEEEEcCCccccC-CccCCCC
Q 001532 24 PVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVD-GVSEKLN 102 (1058)
Q Consensus 24 ~~~~~~~~~~~i~~~f~~~~Lv~~qi~SFn~Fl~~gl~~i~~~~~~i~~~~~~~~~l~~~~i~i~~P~~~~~-~~~~~l~ 102 (1058)
.-....+.|-..|++.+..++++.||.+|+-+|..-...+.-.. .|+...... .+.=.++-|++ .+.- ...+-+.
T Consensus 93 fylky~dirvg~Ps~~~~~~~~~~~i~p~ecrlrd~tysa~i~v-dieytrg~~-~~~~~~v~igr--mpimlrs~rcvl 168 (1153)
T KOG0215|consen 93 FYLKYLDIRVGKPSIEEGNNVTNDNITPHECRLRDMTYSAPIYV-DIEYTRGRQ-IIAKRDVIIGR--MPIMLRSSKCVL 168 (1153)
T ss_pred hhheeeeeeccCcchhhccccccccCCchheeehhhhcccceeE-EEEEecCcc-eEEeccccccc--chhhhhcccccc
Confidence 44556678888999999999999999999999875433221111 112211111 22223444433 2111 1345667
Q ss_pred hhhHhhcCCccCceEEEEEEEEECCCccceeeEEeEEEEeeeccccccccccCCCCCHHHHHhcCCCCCCCCcEEEEcCc
Q 001532 103 PHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGT 182 (1058)
Q Consensus 103 P~EcR~r~lTYsa~l~v~v~~~~~~~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~ls~~elv~~gE~~~d~GGYFIING~ 182 (1058)
|.+|+.+..-|. .-- ....-.-+..|.-|||+.+.-|.+.....+ -.+.|||+.+.++||+..++
T Consensus 169 ~~~~e~~~a~~~----------ecp----ldpggyfiv~G~ekViLiqeqlsknrii~~-~~k~~~~~~svtsst~e~ks 233 (1153)
T KOG0215|consen 169 RGKDEEELARLN----------ECP----LDPGGYFIVKGTEKVILIQEQLSKNRIIVE-EDKKGNLQASVTSSTHERKS 233 (1153)
T ss_pred CCccHHHHHHhc----------cCC----CCCCceeEeccceeEEEehhhhhccCeeec-cccCCccccccccceeeecc
Confidence 777774332221 000 112223477899999999999999998887 67889999999999999999
Q ss_pred eeEEeeeecccCCEEEEEeCCCCcEEEEEEecCCCcceEEEEEeeCCEEEEEEcceeccccHhhHHHHhCCCCHHHHHHH
Q 001532 183 EKVLLIQEQLSKNRVIIDTDKKGNINASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQM 262 (1058)
Q Consensus 183 EKVI~~q~~~~~N~i~~~~~~~g~~~~~v~s~~~~~~s~~~~~~~~g~i~~~~~~~~~~IPl~ilLkALg~~sd~eI~~~ 262 (1058)
+.+|..+....+++...+.+..+...+...+.......... +...+..|.++.-..-..|+.+-+.+. ++-+++
T Consensus 234 kt~v~~k~~k~ylk~~~~~d~ipiviv~ka~g~~sd~ei~~-~vg~~~~y~~~~~~s~ee~~~~~v~tq-----qqal~y 307 (1153)
T KOG0215|consen 234 KTYVTTKKGKYYLKHNSFTDDIPIVIVLKAMGLESDQEIVQ-LVGGDSKYQDIFAPSLEECVSLGVYTQ-----QQALEY 307 (1153)
T ss_pred eEEEEeccceeeeehhhhhccCCEEEEEeeccccchHHHHH-HhhcchHHHHhhccchhhhhhhhhHHH-----HHHHHH
Confidence 99999998887777666655444332222111110000000 001122222211111123333333322 222222
Q ss_pred hCCchhHHhhhhhhHHHHHhcCCcCHHHHHHHHhhcccccCCCCCC----CChHH--HHHHHHHhhhccCCCCCCCCCCC
Q 001532 263 VGRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPP----NDREG--RAFSILRDVFLANVPVHNNNFRP 336 (1058)
Q Consensus 263 i~~~~~~~~~l~~~l~~~~~~~i~t~~~al~yig~~~~~~~~~~~~----~~~~e--~~~~~L~~~llpHl~~~~~~~~~ 336 (1058)
++. -+.........--++|++.+...+.+-...++- ..... -.+..+.- +-|.....+.+.-
T Consensus 308 ~~~----------kvk~~~~t~~~~~~e~~~~l~~~~lahv~v~~~~~r~K~~yi~~m~rr~~~a--~l~~~~~ddrd~~ 375 (1153)
T KOG0215|consen 308 IGS----------KVKVKRGTTPTKDEEALEVLSTTVLAHVPVPDLNFRMKAIYIGLMVRRVIQA--MLNKLAMDDRDYV 375 (1153)
T ss_pred hhh----------eEEeccCCCCCchHHHHHHHHhhheeceeccCCCCcceeehHHHHHHHHHHH--HhCcccccchhhh
Confidence 210 000000001112346667666555443221111 10111 11122221 1222222222222
Q ss_pred cchhHHHHHHHHHHhhcCCCCCCCcccccceEEcchHHHHHHHHHHHHHHHH---HHHHHHHHhHhcCCCCCCCCccccc
Q 001532 337 KCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMI---SEVQKTVDIILSKPSRSSRFDLSQF 413 (1058)
Q Consensus 337 K~~~L~~Mi~kLl~~~~G~~~~DD~D~l~NkRV~~~G~Ll~~lfr~~l~~~~---~~ik~~i~k~~~~~~~~~~~~~~~~ 413 (1058)
+-..|.+|.+ |+.+.++.--.++.+.|++.+-...+.++..++-++++.+. +.+-..+.+.++..+ .++..+
T Consensus 376 gnkrlelagq-llsllfeD~fk~~n~e~k~~~dk~l~k~~ra~~fD~~~~~n~~~~~it~~l~ra~stgn----w~iKrf 450 (1153)
T KOG0215|consen 376 GNKRLELAGQ-LLSLLFEDLFKRFNSELKKNIDKILKKPIRAQEFDALKHLNVRANMITSGLERAISTGN----WSIKRF 450 (1153)
T ss_pred ccchHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHhcchhhhhhhHHHHHHHHHHHHHHHHHHHHhhcCc----hHHHHh
Confidence 3344555444 45555665566778888888888888888777778777763 222223344433322 222211
Q ss_pred cccccchhhhhhhhccCCCcccccccccccceEEcccccccccccccccccccccccccccCCCcCCCCCccccccCCCC
Q 001532 414 IVRDSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTP 493 (1058)
Q Consensus 414 i~~~~It~~i~~~~sTGn~~~~~~~~q~sG~sq~l~rln~ls~lshlRrv~~~~~~~~k~t~~R~Lhps~wG~iCPveTP 493 (1058)
+-.-++.+.--+-.|++|....+-..++++.++..+..+-|-...--.+-.++.+..+..-.+-..+..|+-|||-++|
T Consensus 451 -rmer~gvt~VlsrlSyisaLgmmtri~s~fektrkvsgprSlq~sqwgmlcp~dtpegeacglvknlalmthittd~ee 529 (1153)
T KOG0215|consen 451 -RMERAGVTQVLSRLSYISALGMMTRINSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITTDSEE 529 (1153)
T ss_pred -hhhhccceeeehhhhhhhhhhhheehhhhheeehhccCccccChhhcccccCCCCCCccccccccchHHHhcccCCCCc
Confidence 1111222222223456765433334567888886666665555555555567777777778899999999999999999
Q ss_pred CCCcccccccccceeeeecC
Q 001532 494 EGEACGLVKNLALMTHVTTD 513 (1058)
Q Consensus 494 EG~~cGLi~~LA~~a~Is~~ 513 (1058)
++.-|++.+..+...++..+
T Consensus 530 ~pi~~~~~k~gv~di~~v~~ 549 (1153)
T KOG0215|consen 530 KPILKLCYKLGVEDIHVVSG 549 (1153)
T ss_pred chhHHHHHHhcceeeeeecc
Confidence 99999999999999988775
No 23
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]
Probab=97.60 E-value=0.00017 Score=91.31 Aligned_cols=74 Identities=23% Similarity=0.378 Sum_probs=60.7
Q ss_pred CceeeeecCccccccccccCCCCCCCCCCccccccccccCCccceeEeeeeccccceeeeeCCCcceeechhhhhhcCCC
Q 001532 661 DTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDK 740 (1058)
Q Consensus 661 ~~th~Ei~p~~~ls~~asliPF~~hNqspRn~yq~~M~KQaiG~~~~n~~~R~D~~~y~l~ypQ~Plv~t~~~~~~~~~~ 740 (1058)
..+|+++.|.++.|+.+++|||.+|.++.|++|+++|+|||+| |..+..|||.|+ +++.+-.|
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 3578999999999999999999999999999999999999999 456899999999 77654211
Q ss_pred CCCCcceEEEEeec
Q 001532 741 LGAGQNATVAVMSY 754 (1058)
Q Consensus 741 ~~~G~N~~Vav~~y 754 (1058)
--|++||.-++
T Consensus 588 ---~~~~~ia~~~~ 598 (1060)
T COG0085 588 ---SGAAVIAKRPG 598 (1060)
T ss_pred ---ccceeEeccCC
Confidence 23555665444
No 24
>KOG0214 consensus RNA polymerase II, second largest subunit [Transcription]
Probab=97.47 E-value=1.7e-05 Score=95.93 Aligned_cols=299 Identities=10% Similarity=-0.065 Sum_probs=176.5
Q ss_pred eeeeeCCCcceeechhhh-------------hhcCCCCCCCcceEEEEeecCCCCCCCcEEEecceeeccceEEEEEEEE
Q 001532 717 LYLLVYPQRPLLTTRTIE-------------LVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKY 783 (1058)
Q Consensus 717 ~y~l~ypQ~Plv~t~~~~-------------~~~~~~~~~G~N~~Vav~~y~Gyn~EDaiiink~s~~rg~~~s~~~~~~ 783 (1058)
.+.-+|.++|-|+-...- ..-.-..+.+.++-++.+.+.++..++...-|--..+.+++++++...|
T Consensus 698 qamg~y~tn~~vR~dtl~~~l~ypqkpl~tt~~~e~l~~~eL~aG~NaiVAi~~~~GYNqEDsvimn~s~v~rg~FrS~~ 777 (1141)
T KOG0214|consen 698 QAMGVYHTNPQVRMDTLAKVLYYPQKPLVTTRAMEYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSVDRGLFRSFF 777 (1141)
T ss_pred hcceeeeecchhhhhhhhhcccccccchhhHHHHhhhhhhhcccccceEEEEecccCccHHHHHHHHhhhhhcchhhhhh
Confidence 344466677766654432 2223345679999999999999999999999999999999999976544
Q ss_pred EEEeecccCCccceecC--CCCCC-Ccccc----cccCCCCccccCCcEeCCCCEEEEEecCCCCCCCCCCCCCCCCccc
Q 001532 784 TAINQKYANSTSDRILR--PDRTG-PGAER----MQILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRY 856 (1058)
Q Consensus 784 ~~~~~~~~~~~~e~~~~--p~~~~-~~~~~----~~~ld~dGi~~~g~~v~~gd~li~k~~~~~~~~~~~~~~~~~~~~~ 856 (1058)
. +.++. .+.... |.... ++... .++.-.|-+-.-|= +-+|--+.| .+-...+. ......
T Consensus 778 ~---RsYk~--q~~~~~~~~ee~~~~~~~~~~~~mr~~~~dkLdddG~-i~~G~~vs~-------~Dv~iGk~-t~~~~~ 843 (1141)
T KOG0214|consen 778 I---RSYKD--QEHKKDQGPEEIFEEPPRGEGRGMRNGKYDKLDDDGI-IMPGSRVSG-------GDVLIGKT-TPQPAK 843 (1141)
T ss_pred h---hHHHh--hhhhcccccccccccccccccccccccccccccccCC-ccccceeec-------CCEEeccc-cCCccc
Confidence 4 22321 122222 22211 01000 01111111100000 001100000 00000000 000000
Q ss_pred ccceEEeeCCCCCceEEEEEEEeeCCCCCEEEEEEEeecCCCcccceecccCCCccEEEeeeccCCCCCCCCCCCCcEEe
Q 001532 857 RSARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIM 936 (1058)
Q Consensus 857 ~~~s~~~~~~~~~~~~vd~v~~~~~~~~~~~v~v~i~~~R~p~iGDKf~sRhGqKGvvs~i~~~~DmPf~~~G~~pDiIi 936 (1058)
.+.+- .... .-.++..++.+..++.| ...+|.+.. .+.|+||+.+|++++.+.++-+..++++-.-|+.++++.
T Consensus 844 ~~~~~-~~~~-~~t~~d~s~~Lr~~e~G-ivd~V~vt~---n~~G~kF~kv~vr~~ripqiGDKfasrHgqKG~ig~~~~ 917 (1141)
T KOG0214|consen 844 EDESG-PEDR-LYTKRDHSTKLRHTERG-IVDQVWVTK---NSEGPKFVKVRVRQVRIPQIGDKFASRHGQKGTIGITYR 917 (1141)
T ss_pred chhcc-cccc-ccccccceeecccCCcc-eEEEEEEec---CCCCCceeEEEEeecccccccchhccccccCccccceee
Confidence 00000 0000 01345666777666666 445555554 999999999999999999999999999999999999999
Q ss_pred CCCCCCCcccHHHHHHHhhccchhcCCceeeeecccCCCCCCCCHHHHHHHHHHcCCCCCCceEEEeCCCCcEeeeeEee
Q 001532 937 NPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFM 1016 (1058)
Q Consensus 937 NP~~~PSRMtiGql~E~~~gk~~~~~g~~~~~tpf~~~~~~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if~ 1016 (1058)
+++.-+++|+|--.++.-.- +.|-. -.+..+.+-|. |-..-++...+++.++.. -+-.++
T Consensus 918 qedmpft~eGi~pDiiiNPh-----------aiPSR------mtig~liEc~l--gk~~a~~~e~~~atpFs~-v~v~~i 977 (1141)
T KOG0214|consen 918 QEDMPFTIEGIVPDIIINPH-----------AIPSR------MTIGQLIECLL--GKVAAYEGEEGDATPFSD-VTVSKI 977 (1141)
T ss_pred cCCCCccccCCCcceEECcc-----------cCccc------cchhhhHHHhh--hhhhhcccccccCCCCCc-cchhcc
Confidence 99999999988654433221 11111 12222222221 112223445555555555 456789
Q ss_pred eeeeeeccccccCcceEEeccCCccccccCCcCcccCCC
Q 001532 1017 GPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNG 1055 (1058)
Q Consensus 1017 G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~G 1055 (1058)
+..+++...|+..++.+++.+++....+++++++.-.++
T Consensus 978 s~~l~~~g~~~~G~e~~ynGrtG~~~~~~if~Gptyyqr 1016 (1141)
T KOG0214|consen 978 SANLHVYGYQYRGNERMYNGRTGRKLRAQIFIGPTYYQR 1016 (1141)
T ss_pred cchHHHhccccCCCEEEecCCCCceeeeeeecCchHHHH
Confidence 999999999999999999999999999999998765443
No 25
>PF06883 RNA_pol_Rpa2_4: RNA polymerase I, Rpa2 specific domain ; InterPro: IPR009674 This domain is found between domain 3 and domain 5, but shows no homology to domain 4 of Rpb2. The external domains in multisubunit RNA polymerase (those most distant from the active site) are known to demonstrate more sequence variability [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=97.43 E-value=0.00015 Score=61.02 Aligned_cols=49 Identities=18% Similarity=0.268 Sum_probs=41.5
Q ss_pred Eeecc--ChhhHHHHHHHHhhcC--CcCceeEEEecc-----ccceEEEecCCCeeee
Q 001532 554 LGKHR--RPKCFADVMRKLRRAG--KIGEFVSVFVNE-----KQRCVYIASDGGRVCR 602 (1058)
Q Consensus 554 vG~~~--~~~~~~~~lr~~rr~~--~i~~~v~i~~~~-----~~~~i~I~sd~GRl~R 602 (1058)
|||++ ++..+++.||.+|..| .++.+++|.+.+ .+|++||||+++|++|
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 47766 6789999999999987 688888887643 4699999999999997
No 26
>PHA03394 lef-8 DNA-directed RNA polymerase subunit beta-like protein; Provisional
Probab=95.89 E-value=0.021 Score=69.78 Aligned_cols=138 Identities=20% Similarity=0.246 Sum_probs=85.1
Q ss_pred ceEEEEEEEeeC-CCCCEEEEEEEeecCCCcccceecccCCCccEEEeeeccCCCC-C-CCCCCCCcEEeCCCCCCCccc
Q 001532 870 TCVVDRVALCSD-KNGDLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFP-F-SERGICPDLIMNPHGFPSRMT 946 (1058)
Q Consensus 870 ~~~vd~v~~~~~-~~~~~~v~v~i~~~R~p~iGDKf~sRhGqKGvvs~i~~~~DmP-f-~~~G~~pDiIiNP~~~PSRMt 946 (1058)
.-+|+++.-.-. .++...+|+++-..=.=--|=|.||=||||||... .||+- | .|||+.|-|.++|.++-||.|
T Consensus 679 ~Q~ie~l~s~m~~~nd~v~lKl~~Vtst~dLeGlKICgIHGQKGVln~---seDLtew~aeDg~~aQIclSPiSyLsRQt 755 (865)
T PHA03394 679 NQRIERLDSEMTVINDTVYLKIRLVTSTSDLEGLKICGIHGQKGVLNG---SEDLTEWMAEDGTHAQICLSPISYLSRQT 755 (865)
T ss_pred CeEEEEEeeEEEEcCCEEEEEEEEEEEecCcceeEEeeecccccccCC---cchhhhhhccCCCcceEEechHHhhcccc
Confidence 445665542211 22456677776665556679999999999999863 55654 2 379999999999999999998
Q ss_pred HHHHHHHhhccchhcCCceee---------eecccCCCCCCCCHHHHHHHHHHcCCCCCCceEEEeCCCCcEeeeeEeee
Q 001532 947 VGKMIELLGGKAGVSCGRFHY---------GSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMG 1017 (1058)
Q Consensus 947 iGql~E~~~gk~~~~~g~~~~---------~tpf~~~~~~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if~G 1017 (1058)
. ++-+--|-....|.+.| -.|+... ...-+++.++.. +-++.|-|.+=--|.-+.--...|+|
T Consensus 756 n---f~~~~~Ky~v~gg~~~~~~~~rypi~~IPYm~F---nnTPDnI~kEf~--~~n~TG~EKvEGTRlDqwTINqsF~g 827 (865)
T PHA03394 756 N---FDDIERKYVVRGGDHSDPNAKRYPIFNIPYMLF---NNTPDNIYKEFI--KKNYTGHEKVEGTRLDQWTINQSFVG 827 (865)
T ss_pred c---cccCceEEEEECCCcCCCCCcccceEecceehh---cCCchHHHHHHh--ccCCcceeecceeeccceeEcceecc
Confidence 6 34444455555454433 3555532 344466666553 24556666653223333333555666
Q ss_pred e
Q 001532 1018 P 1018 (1058)
Q Consensus 1018 ~ 1018 (1058)
-
T Consensus 828 N 828 (865)
T PHA03394 828 N 828 (865)
T ss_pred c
Confidence 4
No 27
>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=58.96 E-value=15 Score=45.55 Aligned_cols=34 Identities=18% Similarity=0.200 Sum_probs=28.0
Q ss_pred CCCcccccceEEcchHHHHHHHHHHHHHHHHHHH
Q 001532 358 MDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEV 391 (1058)
Q Consensus 358 ~DD~D~l~NkRV~~~G~Ll~~lfr~~l~~~~~~i 391 (1058)
.=.+|+|+||=+--...|+...+...++.+...+
T Consensus 210 ~Y~IDsLsNKiIYkh~yLl~l~y~~~L~~~~~~~ 243 (748)
T PF04941_consen 210 NYSIDSLSNKIIYKHSYLLELTYKPILKKYENLI 243 (748)
T ss_pred CceecccccceeeCHHHHHHHHHHHHHHHHHHHH
Confidence 3479999999999999999999987777665544
No 28
>PF14251 DUF4346: Domain of unknown function (DUF4346)
Probab=41.96 E-value=13 Score=35.95 Aligned_cols=14 Identities=57% Similarity=0.890 Sum_probs=10.9
Q ss_pred CCCCCCCCcEEEEc
Q 001532 167 GECPLDPGGYFIIK 180 (1058)
Q Consensus 167 gE~~~d~GGYFIIN 180 (1058)
.--..||+|||||.
T Consensus 10 R~i~LDp~GYfiI~ 23 (119)
T PF14251_consen 10 RFIDLDPAGYFIIY 23 (119)
T ss_pred CccccCCCccEEEE
Confidence 33467999999986
No 29
>PF13533 Biotin_lipoyl_2: Biotin-lipoyl like
Probab=24.70 E-value=53 Score=26.83 Aligned_cols=16 Identities=25% Similarity=0.426 Sum_probs=14.3
Q ss_pred cccCCcEeCCCCEEEE
Q 001532 819 LAAPGEIIKPNDVYIN 834 (1058)
Q Consensus 819 i~~~g~~v~~gd~li~ 834 (1058)
.++.|+.|++||+|+-
T Consensus 17 ~V~~G~~VkkGd~L~~ 32 (50)
T PF13533_consen 17 YVKEGQQVKKGDVLLV 32 (50)
T ss_pred EecCCCEEcCCCEEEE
Confidence 5789999999999975
No 30
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=21.45 E-value=2.7e+02 Score=40.69 Aligned_cols=106 Identities=16% Similarity=0.111 Sum_probs=56.8
Q ss_pred CCCeeeeeEEEEecCcccchhhhHHHhhcCCccchhhhccCceeEeccccccceEEEeecCCCC------CC-------c
Q 001532 596 DGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDAT------PD-------T 662 (1058)
Q Consensus 596 d~GRl~RPll~v~~~~~~~~~~~~~~l~~~~~s~~~~~~~~~iE~id~~e~~~~~Ia~~~~~~~------~~-------~ 662 (1058)
+.|-+.-|...|.||+. + ..++|+++.|++...||.....+. .. -
T Consensus 597 ~~GfietPy~kV~~g~v--~--------------------~~i~ylsa~eE~~~~IA~a~~~~~~~~~~~~~~v~~R~~~ 654 (2890)
T PRK09603 597 DLGFIEAPYKKVVDGKV--V--------------------GETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEG 654 (2890)
T ss_pred cCcceecceEEEecCcc--c--------------------cceeeeCHHHhcCceEeccCCccCCCCcccCCeEeEEECC
Confidence 35677778777776641 1 137899999999999994332211 11 0
Q ss_pred eeeeecCccccccccccCCCCCCCCCCccccccccccCCccceeEeeeeccc--c----ceeeeeCCCcceeechhhhh
Q 001532 663 THIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMD--S----LLYLLVYPQRPLLTTRTIEL 735 (1058)
Q Consensus 663 th~Ei~p~~~ls~~asliPF~~hNqspRn~yq~~M~KQaiG~~~~n~~~R~D--~----~~y~l~ypQ~Plv~t~~~~~ 735 (1058)
++..+++.+ +-|.+ =||..+.. .+-=-||+.-+|...|.= + -.--|.+|++|+|.|+....
T Consensus 655 e~~~~~~~~--------v~~~d--vsp~Q~vS--vaasLIPFLEhdDAnRALMGSNMQRQAVPLl~~e~piVgTG~E~~ 721 (2890)
T PRK09603 655 EIVLNEKSK--------VTLMD--LSSSMLVG--VAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTGIEKI 721 (2890)
T ss_pred ceEEEChHH--------ceEEE--eCccceee--ehhhcCCccccCccccccccccchhhhhhhccccCCeEecCcchh
Confidence 122222221 11111 12222221 122234566677777752 1 12347899999999987543
No 31
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=20.70 E-value=2.3e+02 Score=41.15 Aligned_cols=105 Identities=17% Similarity=0.182 Sum_probs=57.9
Q ss_pred CCCeeeeeEEEEecCcccchhhhHHHhhcCCccchhhhccCceeEeccccccceEEEeecCCCC-------------CCc
Q 001532 596 DGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDAT-------------PDT 662 (1058)
Q Consensus 596 d~GRl~RPll~v~~~~~~~~~~~~~~l~~~~~s~~~~~~~~~iE~id~~e~~~~~Ia~~~~~~~-------------~~~ 662 (1058)
..|-+.-|...|.||+. + ..++|+.+.|++...||-....+. ...
T Consensus 604 ~~GfietPy~kV~~g~v--~--------------------~~i~ylsa~~E~~~~Ia~a~~~~~~~~~~~~~~v~~R~~~ 661 (2836)
T PRK14844 604 KYGFIESPYRKVVNRVV--T--------------------DQIEYLSAIDEGLYYIADTSAKLDENNCFVDDMLYCRYAG 661 (2836)
T ss_pred CCceEeCCcEEEEcCcC--c--------------------ccccccChHHhcCcEEEeCCccCCCCCcccCCeEEEecCC
Confidence 35777778888876641 1 137899999999999995432211 011
Q ss_pred eeeeecCccc--cccccccCCCCCCCCCCccccccccccCCccceeEeeeeccc------cceeeeeCCCcceeechhhh
Q 001532 663 THIEIEPFTI--LGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMD------SLLYLLVYPQRPLLTTRTIE 734 (1058)
Q Consensus 663 th~Ei~p~~~--ls~~asliPF~~hNqspRn~yq~~M~KQaiG~~~~n~~~R~D------~~~y~l~ypQ~Plv~t~~~~ 734 (1058)
++...+|.++ +++. |.-+. ..+-=-||+.-+|...|.= .-.--|..|++|+|.|+...
T Consensus 662 ef~~~~~~~v~~~dvs------------p~Q~~--SvaasLIPFLEhdDAnRALMGSNMQRQAVPLl~~e~PiVGTG~E~ 727 (2836)
T PRK14844 662 SFVMVSSDQVSYIDVS------------PKQVI--SVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMES 727 (2836)
T ss_pred ceEEecHHHceEEEeC------------cchhh--hhHhhcCCccccCccccccccccccccccccccCCCCeEecCcch
Confidence 3333333322 2221 11111 1111223555677766642 12234789999999998755
Q ss_pred hh
Q 001532 735 LV 736 (1058)
Q Consensus 735 ~~ 736 (1058)
..
T Consensus 728 ~v 729 (2836)
T PRK14844 728 FV 729 (2836)
T ss_pred hh
Confidence 43
Done!