Query 001943
Match_columns 993
No_of_seqs 175 out of 1489
Neff 6.9
Searched_HMMs 46136
Date Thu Mar 28 12:56:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001943.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001943hhsearch_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-222 5E-227 2070.7 83.7 930 31-988 1-941 (1103)
2 KOG0215 RNA polymerase III, se 100.0 6E-212 1E-216 1778.9 47.6 974 2-989 16-997 (1153)
3 KOG0214 RNA polymerase II, sec 100.0 6E-212 1E-216 1802.1 47.8 944 28-988 2-981 (1141)
4 KOG0216 RNA polymerase I, seco 100.0 2E-200 4E-205 1692.6 56.1 896 30-988 4-945 (1111)
5 COG0085 RpoB DNA-directed RNA 100.0 4E-194 8E-199 1735.6 61.2 872 27-989 10-915 (1060)
6 TIGR02013 rpoB DNA-directed RN 100.0 2E-176 3E-181 1633.2 66.1 778 29-988 5-925 (1065)
7 cd00653 RNA_pol_B_RPB2 RNA pol 100.0 5E-174 1E-178 1604.9 65.6 706 44-989 1-716 (866)
8 PRK00405 rpoB DNA-directed RNA 100.0 2E-172 4E-177 1604.5 67.5 780 28-988 11-965 (1112)
9 CHL00001 rpoB RNA polymerase b 100.0 1E-170 2E-175 1572.2 66.4 789 39-985 10-896 (1070)
10 CHL00207 rpoB RNA polymerase b 100.0 7E-155 2E-159 1422.8 65.8 788 38-988 4-895 (1077)
11 PRK09603 bifunctional DNA-dire 100.0 4E-145 8E-150 1376.9 63.7 790 27-965 10-1155(2890)
12 PRK14844 bifunctional DNA-dire 100.0 5E-142 1E-146 1343.1 63.3 790 24-964 11-1147(2836)
13 PRK07225 DNA-directed RNA poly 100.0 1E-124 3E-129 1108.2 38.2 438 544-989 4-444 (605)
14 TIGR03670 rpoB_arch DNA-direct 100.0 3E-124 7E-129 1103.7 36.8 435 547-989 1-438 (599)
15 PRK09606 DNA-directed RNA poly 100.0 2E-107 4E-112 959.1 45.6 486 28-531 2-492 (494)
16 PF00562 RNA_pol_Rpb2_6: RNA p 100.0 3.7E-86 7.9E-91 755.1 12.7 303 674-989 1-322 (386)
17 PF04563 RNA_pol_Rpb2_1: RNA p 100.0 6.5E-45 1.4E-49 382.9 18.4 147 43-192 1-149 (203)
18 PF04565 RNA_pol_Rpb2_3: RNA p 99.9 1.7E-26 3.6E-31 199.0 1.4 66 446-511 1-68 (68)
19 PF04561 RNA_pol_Rpb2_2: RNA p 99.9 2.1E-21 4.5E-26 202.1 11.7 175 193-370 1-190 (190)
20 PF04566 RNA_pol_Rpb2_4: RNA p 99.7 2.4E-17 5.1E-22 139.5 8.6 63 547-609 1-63 (63)
21 KOG0215 RNA polymerase III, se 98.9 1.9E-11 4.1E-16 142.7 -10.7 441 26-514 95-550 (1153)
22 PF04567 RNA_pol_Rpb2_5: RNA p 98.8 2.2E-09 4.9E-14 86.2 2.8 41 629-669 1-48 (48)
23 COG0085 RpoB DNA-directed RNA 97.9 3.6E-05 7.9E-10 96.4 10.2 74 661-754 525-598 (1060)
24 PF06883 RNA_pol_Rpa2_4: RNA p 97.5 0.00011 2.4E-09 61.4 4.3 49 554-602 1-58 (58)
25 KOG0214 RNA polymerase II, sec 95.4 0.0044 9.6E-08 75.4 0.4 212 740-973 734-954 (1141)
26 PHA03394 lef-8 DNA-directed RN 94.6 0.052 1.1E-06 66.1 6.1 79 884-968 694-774 (865)
27 PF04941 LEF-8: Late expressio 53.9 19 0.00042 44.3 5.4 34 358-391 210-243 (748)
28 PF14251 DUF4346: Domain of un 45.4 11 0.00023 36.3 1.2 13 168-180 11-23 (119)
29 PF13533 Biotin_lipoyl_2: Biot 29.8 38 0.00082 27.4 2.0 16 819-834 17-32 (50)
No 1
>PRK08565 DNA-directed RNA polymerase subunit B; Provisional
Probab=100.00 E-value=2.5e-222 Score=2070.74 Aligned_cols=930 Identities=39% Similarity=0.654 Sum_probs=844.2
Q ss_pred ccccccccccccchHHHHHHHHHHHHHhCHHHHHHhcCcccccCCCcEEEEEeeEEEcCCeeccCC-CCCCCChHHHHhc
Q 001943 31 KFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDG-VSEKLNPHMCRLS 109 (993)
Q Consensus 31 ~~~~i~~~~~~~~Lv~~hi~SFn~Fi~~gl~~ii~~~~~I~~~~~~~~~l~f~~v~i~~P~~~~~~-~~~~l~P~EcR~r 109 (993)
.|.++++||+.++|++|||||||+|+++||++++++++||+.. ++++.|+|++++|++|++.+++ ...+|+|+|||+|
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 6789999999999999997655 6678999999999
Q ss_pred CCccCceEEEEEEEEECCcccceeeEEeEEEEeeccceeccccccCCCCCHHHHHhcCCCCCCCCcEEEEcCceeEEEEe
Q 001943 110 DMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQ 189 (993)
Q Consensus 110 ~lTYs~~l~v~v~~~~~~~~~~~~i~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~gE~~~d~GGYFIInG~ERVI~~q 189 (993)
++||+|+|+|+|++..++ ..+.++++++|+|||||+|++|||++++|+||++.||||+|+||||||||+|||||+|
T Consensus 80 ~lTYsa~l~v~i~~~~~~----~~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~p~D~GGYFIING~ERVI~~q 155 (1103)
T PRK08565 80 NLTYAAPLYLTMIPVENG----IEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQ 155 (1103)
T ss_pred CCCcceEEEEEEEEEECC----eeeEEEEEEeccCCeEeCCCcccCCCCCHHHHHhcCCCccCCCCeEEECCcEEEEEEE
Confidence 999999999999997654 4455668999999999999999999999999999999999999999999999999999
Q ss_pred ecccCCEEEEEeCCCC---ceEEEEEecCCCc-ccEEEEEeeCCEEEEEEccccccccHHHHHHHhCCCCHHHHHHHhCC
Q 001943 190 EQLSKNRVIIDTDKKG---NINASVTSSTETV-KSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGR 265 (993)
Q Consensus 190 ~~~~~N~i~~~~~~~g---~~~~~v~s~~~~~-~~~~~~~~~~g~i~~~~~~~~~~IPl~ilLrALg~~sD~eI~~~i~~ 265 (993)
|++++|+++++.+.++ .+.|.++|..... .+..+++..+|.++++++++.++||+++||||||.+||+||++.++.
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 9999999998765433 3678888877644 34445555679999999987678999999999999999999999977
Q ss_pred chhhHhhhhhhHHHHHhcCC-cCHHHHHHHHhhhcccCCCCCCCCChHHHHHHHHhhhhcCCCCCCCCCCCcchhhHHHH
Q 001943 266 DPRYSALLLPSIEECANLDI-YTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLANVPVHNNNFRPKCFYVAVM 344 (993)
Q Consensus 266 ~~~~~~~l~~~l~~~~~~~i-~t~~~al~yIg~~~~~~~~~~~~~~~~e~~~~~L~~~ll~Hl~~~~~~~~~K~~~L~~M 344 (993)
+..+.+.+..++++.. .+ .|+++|+.|||++|+++ .++.. +.+.|+++|++++|||++.+..++.+|+++|++|
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 6666666777776653 25 79999999999999875 33445 7789999999999999998765567899999999
Q ss_pred HHHHHHhhcCCCCCCCcccccceEEcchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCCCcccccccccccchhhhh
Q 001943 345 LRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLE 424 (993)
Q Consensus 345 i~kLl~~~~g~~~~DD~D~l~nkRv~~~G~Ll~~lfr~~l~~~~~~ik~~l~~~~~~~~~~~~~~~~~~i~~~~It~~i~ 424 (993)
++||+++..|.+.+||+|||+||||+++|+||+.+||++|+++++.+|+++.+.+.+. ..+++..+++++.||++|+
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 2456777788889999999
Q ss_pred hhhccCCCcccccccccccceEEecccccccccccccccCccccccccccCCCcCCCCCcccccccCCCCCCcchhhhhh
Q 001943 425 RTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNL 504 (993)
Q Consensus 425 ~~~aTGnw~~~~~~~q~sG~sq~l~r~N~ls~lshlRri~~~f~~~~k~~~~R~Lhps~wG~iCPveTPEG~~cGLv~~L 504 (993)
+|||||||.. |++|+||+|+|+||+|+||||||+++++.+++|.++||+||||||||+||+|||||++||||+||
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 ccccccccCCCChhHHHHHHhcCCeeccccCccccCCCCceEEEECCeEeeeccChhhHHHHHHHHhhcCCcCceeEEEe
Q 001943 505 ALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFV 584 (993)
Q Consensus 505 A~~a~V~~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~~~V~~nG~~iG~~~~~~~~~~~lR~~rr~g~i~~~v~i~~ 584 (993)
|++|+|+.+.+.+++.++|.++|+.++..+.+... +..++|||||+|+|++++|..|++.||.+||.|.++.+++|++
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 99999999888899999999999988765544332 3578999999999999999999999999999999999999999
Q ss_pred cc--cCceEEEecCCCeeeeeEEEeecCcccchhhhHHhhhccCcchhhhhccCceeeeccccccceEEEeecCCCCCCc
Q 001943 585 NE--KQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDT 662 (993)
Q Consensus 585 ~~--~~~~i~I~td~gR~~RPl~~v~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~iE~id~~Eq~~~~Ia~~~~~~~~~~ 662 (993)
+. ..++|+|+||+||++|||++|++|++.+++++++.++.+..+|++|+++|.|||||++||++++||+.++++...+
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 8899999999999999999999999999999999988888899999999999999999999999999999987778
Q ss_pred ceeeecCceeecccccccCCCCCCCCCcccccccccCCCccceeeeeccccccceeeecCCCcceeechhhhhhCCCCCC
Q 001943 663 THIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDKLG 742 (993)
Q Consensus 663 th~Ei~p~~ilsv~AslIPF~~hNqspRn~yq~~M~KQa~G~~~~n~~~r~D~~~y~l~ypQ~PlV~t~~~~~~~~~~~p 742 (993)
||+||+|.+|||++||+|||+||||||||||||||+|||||++++|+..|+|++.|+|.|||+|||+|+.++.++++++|
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 CCceeEEEEEecCCCCCCCcEEEecccccccceeEEEEEEEEEEeecccCCccceecCCCCCC---CcchhcccCCCCcc
Q 001943 743 AGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILRPDRTG---PGAERMQILDDDGL 819 (993)
Q Consensus 743 ~G~N~~VAv~~~~Gyn~EDaiiink~~~~rg~~~s~~~~~~~~~~~~~~~~~~e~~~~p~~~~---~~~~~~~~ld~~Gi 819 (993)
+|+||+||||||+||||||||||||+|+|||+|||+||++|+++++++..+..|.++.|..+. +....|++||+|||
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 999999999999999999999999999999999999999999998876656667777653321 12246899999999
Q ss_pred ccCCceeCCCCEEEEEecCCCCCCCCCCCCCCCCcccccceEEeeCCCCCceEEEEEEEeeCCCCCeEEEEEEeeccCCC
Q 001943 820 AAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLIRHTRRPE 899 (993)
Q Consensus 820 ~~~g~~v~~gdili~k~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~e~~~~~v~~v~~~~~~~~~~~vkv~ir~~R~p~ 899 (993)
|++|++|++|||||||++|..+...... .+......+|+|++++.+| +|+||+|.++.++++.+.|||++|+.|+|+
T Consensus 781 ~~~G~~v~~gdili~k~~p~~~~~~~~~-~~~~~~~~~~~s~~~~~~e--~g~V~~V~~~~~~~~~~~vkv~ir~~R~p~ 857 (1103)
T PRK08565 781 VSPEVEVKGGDVLIGKTSPPRFLEELEE-LSLGLQERRDTSVTVRHGE--KGIVDTVLITESPEGNKLVKVRVRDLRIPE 857 (1103)
T ss_pred cCCCcEEcCCCEEEEEecCCCCCcchhh-ccccCCccccceEEecCCC--ceEEEEEEEEecCCCcEEEEEEEEEEecCc
Confidence 9999999999999999999753321111 0111234689999999999 999999999988888999999999999999
Q ss_pred ccccccccCCCcceeeeeecCCCCCCCCCCCcCeEEeCCCCCCCCCchhhhHHhhcccccccCCCceeeecCCCCCCCCC
Q 001943 900 LGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHAD 979 (993)
Q Consensus 900 iGDKfasRHGqKGvvs~i~~~~DMPf~~~G~~pDiIiNPhg~PSRMtiGql~E~~~gk~~~~~G~~~d~TpF~~~~~~~~ 979 (993)
||||||||||||||||+|||+||||||+||++|||||||||||||||||||+|+++||||+++|.+.|+|||++ .
T Consensus 858 iGDKfssRhGqKGv~s~i~~~edmPf~~~G~~pDiI~NPh~~PSRMtiG~l~E~~~gk~~~~~g~~~d~t~F~~-----~ 932 (1103)
T PRK08565 858 LGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYG-----E 932 (1103)
T ss_pred hhhhhhhhccCcceeeeecccccCCcCCCCCCccEEECCCCCcccccHHHHHHHHHHHHHHhcCceeeecCcCC-----c
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999 8
Q ss_pred CHhhHhhhC
Q 001943 980 TVESIRCFF 988 (993)
Q Consensus 980 ~~~~i~~~~ 988 (993)
.++++...|
T Consensus 933 ~~~~~~~~L 941 (1103)
T PRK08565 933 PEEELRKEL 941 (1103)
T ss_pred hHHHHHHHH
Confidence 899998776
No 2
>KOG0215 consensus RNA polymerase III, second largest subunit [Transcription]
Probab=100.00 E-value=6e-212 Score=1778.91 Aligned_cols=974 Identities=64% Similarity=1.072 Sum_probs=912.7
Q ss_pred CcccccCCCC-CCCCcccccccCCCcccccccccccccccccchHHHHHHHHHHHHHhCHHHHHHhcCcccccCCCcEEE
Q 001943 2 GLMQVEGSPK-DEQLPDKQKLAAPVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFL 80 (993)
Q Consensus 2 ~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~Lv~~hi~SFn~Fi~~gl~~ii~~~~~I~~~~~~~~~l 80 (993)
|+-+-++.+. |.+--++++.+++..+.+++|.++|+|++.+|||++|++|||+|++++|+.+++++..|.++.++.+.+
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 444456677888999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeeEEEcCCeeccCC--CCCCCChHHHHhcCCccCceEEEEEEEEECCcccceeeEEeEEEEeeccceeccccccCCCC
Q 001943 81 RFKDVRIGQPSMTVDG--VSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGK 158 (993)
Q Consensus 81 ~f~~v~i~~P~~~~~~--~~~~l~P~EcR~r~lTYs~~l~v~v~~~~~~~~~~~~i~~~~v~iG~iPIMv~S~~C~L~~~ 158 (993)
+|.++++++|.+.++. ....++|+|||+|++||+||++|+++++.++ ..+.+++|.||++|+|+||++|.|++.
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 9999999999998765 5568999999999999999999999999887 566778999999999999999999999
Q ss_pred CHHHHHhcCCCCCCCCcEEEEcCceeEEEEeecccCCEEEEEeCCCCceEEEEEecCCCcccEEEEEeeCCEEEEEEccc
Q 001943 159 DEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVIIDTDKKGNINASVTSSTETVKSKTVIQMEKGKMYLLLNQF 238 (993)
Q Consensus 159 s~~el~~~gE~~~d~GGYFIInG~ERVI~~q~~~~~N~i~~~~~~~g~~~~~v~s~~~~~~~~~~~~~~~g~i~~~~~~~ 238 (993)
+++|+++..|||.|||||||++|.||||..||+.+.|++++..+++|.+-|++.|+.++.+++++++.++++.+++++.+
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 99999999999999999999999999999999999999999877778888999999998899999999999999999999
Q ss_pred cccccHHHHHHHhCCCCHHHHHHHhCCchhhHhhhhhhHHHHHhcCCcCHHHHHHHHhhhcccCCCCCCCCChHHHHHHH
Q 001943 239 VKKIPIMVVMKAMGMESDQEVVQMVGRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSI 318 (993)
Q Consensus 239 ~~~IPl~ilLrALg~~sD~eI~~~i~~~~~~~~~l~~~l~~~~~~~i~t~~~al~yIg~~~~~~~~~~~~~~~~e~~~~~ 318 (993)
.++||++++|||+|..+|+||.+.++.+++|.+.+..+++++...+++||.+|++|++.+++... .++.+ ..+.|.++
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 99999999999999999999999998899999999999999999999999999999999987752 22334 67889999
Q ss_pred HhhhhcCCCCCCCCCCCcchhhHHHHHHHHHHhhcCCCCCCCcccccceEEcchHHHHHHHHHHHHHHHHHHHHHHHHhH
Q 001943 319 LRDVFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDII 398 (993)
Q Consensus 319 L~~~ll~Hl~~~~~~~~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~nkRv~~~G~Ll~~lfr~~l~~~~~~ik~~l~~~ 398 (993)
|...+++|+.....+++.|+.+++.|+|+++.+..+.-..||+|.++|||+.++|+|++.+|++.|+++...++..+.+.
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--ccccchhhhhhhhccCCCcccccccccccceEEecccccccccccccccCccccccccccCC
Q 001943 399 LSKPSRSSRFDLSQFI--VRDSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGP 476 (993)
Q Consensus 399 ~~~~~~~~~~~~~~~i--~~~~It~~i~~~~aTGnw~~~~~~~q~sG~sq~l~r~N~ls~lshlRri~~~f~~~~k~~~~ 476 (993)
+.+..+...+|+.+.+ ....||++|.+++|||||..++|.|.|.|++|+|.|++|+++|+.+.|++++|++++|.++|
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 8886655567777666 57899999999999999999999999999999999999999999999999999999999999
Q ss_pred CcCCCCCcccccccCCCCCCcchhhhhhccccccccCCCChhHHHHHHhcCCeeccccCccccCCCCceEEEECCeEeee
Q 001943 477 RALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGK 556 (993)
Q Consensus 477 R~Lhps~wG~iCPveTPEG~~cGLv~~LA~~a~V~~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~~~V~~nG~~iG~ 556 (993)
|.|+|||||.+||++||||+.|||++|||++++|+++.++.|+...+..+|+.++...+..+.+.++.+.|++||.++|.
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 ccChhhHHHHHHHHhhcCCcCceeEEEecccCceEEEecCCCeeeeeEEEeecCcccchhhhHHhhhccCcchhhhhccC
Q 001943 557 HRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREG 636 (993)
Q Consensus 557 ~~~~~~~~~~lR~~rr~g~i~~~v~i~~~~~~~~i~I~td~gR~~RPl~~v~~~~~~~~~~~~~~~~~~~~~~~~~l~~g 636 (993)
+..|+.|+..+|.+||+|++..+|+++.+.....++|.+|.||++||+++|+||.+.+.+.|++.++.+..+|+|+++.|
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 ceeeeccccccceEEEeecCCCCCCcceeeecCceeecccccccCCCCCCCCCcccccccccCCCccceeeeeccccccc
Q 001943 637 LIEYLDVNEENNALIALYEGDATPDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSL 716 (993)
Q Consensus 637 ~iE~id~~Eq~~~~Ia~~~~~~~~~~th~Ei~p~~ilsv~AslIPF~~hNqspRn~yq~~M~KQa~G~~~~n~~~r~D~~ 716 (993)
.|||+|++|++.++||+.++++.+.+||+||.|..+||++|+|||||||||||||+|||+|+|||||.+++|+..|+|+.
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 eeeecCCCcceeechhhhhhCCCCCCCCceeEEEEEecCCCCCCCcEEEecccccccceeEEEEEEEEEEeecccCCccc
Q 001943 717 LYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSD 796 (993)
Q Consensus 717 ~y~l~ypQ~PlV~t~~~~~~~~~~~p~G~N~~VAv~~~~Gyn~EDaiiink~~~~rg~~~s~~~~~~~~~~~~~~~~~~e 796 (993)
+|+|+|||+|+|+|++.++++++++|+||||.||||||+|||+|||+|+||+|+||||+|+.+||+.+..++++.++..|
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 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eecCCCCC---CCcchhcccCCCCccccCCceeCCCCEEEEEecCCCCCCCCCCCCCCCCcccccceEEeeCCCCCceEE
Q 001943 797 RILRPDRT---GPGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVV 873 (993)
Q Consensus 797 ~~~~p~~~---~~~~~~~~~ld~~Gi~~~g~~v~~gdili~k~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~e~~~~~v 873 (993)
++..|-.. .++-+.-..||+|||..+|..|++|+|+|.|-.|.....+..+.. ..+..|++.++.||.+| +++|
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 RIMGPQLDPNTRKPIWKHQVLDDDGLATPGERVQPGQIYINKQMPTVTGTSLPGLS-ASQVQYKAVPITYKGPE--PSYI 886 (1153)
T ss_pred hhcccccCCCcCCcchhhcccCcccCCCCccEeccCcEEEeccCCCcccccCCCCC-ccccccccccceecCCC--cchh
Confidence 99877542 223356678999999999999999999999988876554322211 11225899999999999 9999
Q ss_pred EEEEEeeCCCCCeEEEEEEeeccCCCccccccccCCCcceeeeeecCCCCCCCCCCCcCeEEeCCCCCCCCCchhhhHHh
Q 001943 874 DRVALCSDKNGDLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIEL 953 (993)
Q Consensus 874 ~~v~~~~~~~~~~~vkv~ir~~R~p~iGDKfasRHGqKGvvs~i~~~~DMPf~~~G~~pDiIiNPhg~PSRMtiGql~E~ 953 (993)
|+|+++.++++.-.+|+.+|+.|+|++|||||||||||||||.|++||||||...||+|||||||||||||||+|.++|.
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 99999999888899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcccccccCCCceeeecCCCCCCCCCCHhhHhhhCC
Q 001943 954 LGGKAGVSCGRFHYGSAFGEPSGHADTVESIRCFFP 989 (993)
Q Consensus 954 ~~gk~~~~~G~~~d~TpF~~~~~~~~~~~~i~~~~~ 989 (993)
+.||||.+.|+|+++|+|.+ .+++|+.+.|.
T Consensus 967 lsGKAGVl~G~~hYGTaFGg-----skVed~~~~Lv 997 (1153)
T KOG0215|consen 967 LSGKAGVLEGTFHYGTAFGG-----SKVEDISEELV 997 (1153)
T ss_pred hccccceeeeeEeeccccCC-----chHHHHHHHHH
Confidence 99999999999999999999 99999998763
No 3
>KOG0214 consensus RNA polymerase II, second largest subunit [Transcription]
Probab=100.00 E-value=5.7e-212 Score=1802.10 Aligned_cols=944 Identities=36% Similarity=0.606 Sum_probs=856.2
Q ss_pred cccccccccccccccchHHHHHHHHHHHHHhCHHHHHHhcCcccccC--------CCcEEEEEeeEEEcCCeeccCC-CC
Q 001943 28 VVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGI--------DPSIFLRFKDVRIGQPSMTVDG-VS 98 (993)
Q Consensus 28 ~~~~~~~i~~~~~~~~Lv~~hi~SFn~Fi~~gl~~ii~~~~~I~~~~--------~~~~~l~f~~v~i~~P~~~~~~-~~ 98 (993)
.+++|.+|++||+.+||+++|++||+.|++.++++++.+.++|+... -.++.|.|+.+++.+|++.|.| ..
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 57899999999999999999999999999999999999999987432 1358999999999999999988 88
Q ss_pred CCCChHHHHhcCCccCceEEEEEEEEECCcc-cceeeEEeEEEEeeccceeccccccCCCCCHHHHHhcCCCCCCCCcEE
Q 001943 99 EKLNPHMCRLSDMTYAAPILVNIEYVQGSHT-EKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYF 177 (993)
Q Consensus 99 ~~l~P~EcR~r~lTYs~~l~v~v~~~~~~~~-~~~~i~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~gE~~~d~GGYF 177 (993)
..++|+|||+|++|||+||||+++....... +.+..+++.|++|+||||+||..|.|+++++.+|.+.||||+|+||||
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 8999999999999999999999988743321 123455678999999999999999999999999999999999999999
Q ss_pred EEcCceeEEEEeecccCCEEEEEeCCC-Cc--eEEEEEecCCC----cccEEEEEe-eCC---EEEEEEccccccccHHH
Q 001943 178 IIKGTEKVLLIQEQLSKNRVIIDTDKK-GN--INASVTSSTET----VKSKTVIQM-EKG---KMYLLLNQFVKKIPIMV 246 (993)
Q Consensus 178 IInG~ERVI~~q~~~~~N~i~~~~~~~-g~--~~~~v~s~~~~----~~~~~~~~~-~~g---~i~~~~~~~~~~IPl~i 246 (993)
||||+|||+++||+.++|.+++++.+. |. |.+.++|+... ..++...++ +++ .+.+.+++.+.+||+++
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 999999999999999999999998765 44 56788764321 122333333 333 67788888888999999
Q ss_pred HHHHhCCCCHHHHHHHhC---CchhhHhhhhhhHHHHHhcCCcCHHHHHHHHhhhcccCCCCCCCCChHHHHHHHHhhhh
Q 001943 247 VMKAMGMESDQEVVQMVG---RDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVF 323 (993)
Q Consensus 247 lLrALg~~sD~eI~~~i~---~~~~~~~~l~~~l~~~~~~~i~t~~~al~yIg~~~~~~~~~~~~~~~~e~~~~~L~~~l 323 (993)
||||||+.+|+||++.|+ +|.++.+.++++++++.. +..++-||+|||+|-... ..+++. +++.|+++|.+.+
T Consensus 242 lfrALG~v~dreILehIcYd~~D~em~e~lkpsieeafv--iq~qn~ALdfig~rga~~-Gvtkek-ri~yakdiLqKe~ 317 (1141)
T KOG0214|consen 242 LFRALGFVSDREILEHICYDFDDAEMFESLKPSIEEAFV--IQEQNVALDFIGQRGACI-GVTKEK-RIKYAKEILQKEL 317 (1141)
T ss_pred EehhhcCCccHHHHHhhcCCCCcHHHHHHhhhhhhhhhh--hhhhHHHHHHHHhcCCCC-CCCcch-hhHHHHHHHHHHh
Confidence 999999999999999993 688999999999998764 446889999999986432 123556 8999999999999
Q ss_pred cCCCCCCCCCCCcchhhHHHHHHHHHHhhcCCCCCCCcccccceEEcchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCC
Q 001943 324 LANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPS 403 (993)
Q Consensus 324 l~Hl~~~~~~~~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~nkRv~~~G~Ll~~lfr~~l~~~~~~ik~~l~~~~~~~~ 403 (993)
|||++..+.-..+|+.||+||+++|+.++.|++.+||+|||+|||++++|.||..+||..|+++.+++...+++.+.+..
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 99999877656789999999999999999999999999999999999999999999999999999999999999887643
Q ss_pred CCCCcccccccccccchhhhhhhhccCCCc-ccccccccccceEEecccccccccccccccCccccccccccCCCcCCCC
Q 001943 404 RSSRFDLSQFIVRDSITVGLERTLSTGNFD-VKRFKMHRKGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPS 482 (993)
Q Consensus 404 ~~~~~~~~~~i~~~~It~~i~~~~aTGnw~-~~~~~~q~sG~sq~l~r~N~ls~lshlRri~~~f~~~~k~~~~R~Lhps 482 (993)
++++.-.|+++.||++++|+||||||+ .++.+..++||||+|+|+||+++||||||.++|...++|..+||+||||
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 577888889999999999999999998 5556667899999999999999999999999999999999999999999
Q ss_pred CcccccccCCCCCCcchhhhhhccccccccCCCChhHHHHHHhcCCeeccccCccccCCCCceEEEECCeEeeeccChhh
Q 001943 483 QWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKC 562 (993)
Q Consensus 483 ~wG~iCPveTPEG~~cGLv~~LA~~a~V~~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~~~V~~nG~~iG~~~~~~~ 562 (993)
|||++||+|||||++||||+|||++|.|+.+..+.||.++|.++|++.++..++... ++.++||+||.|+|.+.+|+.
T Consensus 475 hwGmvCPaeTPEGqacGLVKNLSLmayIsvGS~~sPi~EfLeewgmE~le~~~ps~~--~datkvfvNG~wvGlhrdp~~ 552 (1141)
T KOG0214|consen 475 HWGMVCPAETPEGQACGLVKNLSLMAYISVGSLESPIVEFLEEWGMENLEEISPSPS--PDATKVFVNGVWVGLHRDPEE 552 (1141)
T ss_pred cceeeccccCCCcceeeccccceEEEEEecCCCccHHHHHHHHhchhhHhhcCCCcC--CCceEEEEcccEEEecCCHHH
Confidence 999999999999999999999999999999999999999999999999998777653 478999999999999999999
Q ss_pred HHHHHHHHhhcCCcCceeEEEecccCceEEEecCCCeeeeeEEEeecCcccchhhhHHhhhcc---CcchhhhhccCcee
Q 001943 563 FADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDG---VRSFDDFLREGLIE 639 (993)
Q Consensus 563 ~~~~lR~~rr~g~i~~~v~i~~~~~~~~i~I~td~gR~~RPl~~v~~~~~~~~~~~~~~~~~~---~~~~~~~l~~g~iE 639 (993)
++..||++||...++.++++..|...++++|+||+||++|||++|+|+++.+.++|++.|+.. ..+|..|+..|.+|
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 999999999999988899999999999999999999999999999999999999999999986 57999999999999
Q ss_pred eeccccccceEEEeecCCCC-----CCcceeeecCceeecccccccCCCCCCCCCcccccccccCCCccceeeeeccccc
Q 001943 640 YLDVNEENNALIALYEGDAT-----PDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMD 714 (993)
Q Consensus 640 ~id~~Eq~~~~Ia~~~~~~~-----~~~th~Ei~p~~ilsv~AslIPF~~hNqspRn~yq~~M~KQa~G~~~~n~~~r~D 714 (993)
|||++|++.++||+.++++. ..||||||||+.|||++||.||||||||||||+||++|+|||||++.+|+..|+|
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 cceeeecCCCcceeechhhhhhCCCCCCCCceeEEEEEecCCCCCCCcEEEecccccccceeEEEEEEEEEEeecccCCc
Q 001943 715 SLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANST 794 (993)
Q Consensus 715 ~~~y~l~ypQ~PlV~t~~~~~~~~~~~p~G~N~~VAv~~~~Gyn~EDaiiink~~~~rg~~~s~~~~~~~~~~~~~~~~~ 794 (993)
+..|.|+|||+|+|+|+.+++..+.++|+|+|++||++||+|||||||+|+|+++++||+|+|.+|++|+.+..+...+.
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 99999999999999999999999999999999999999999999999999999999999999999999999988776677
Q ss_pred cceecCCCCC-CC--cchhcccCCCCccccCCceeCCCCEEEEEecCCCCCCCCCCCCCCCCcccccceEEeeCCCCCce
Q 001943 795 SDRILRPDRT-GP--GAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETC 871 (993)
Q Consensus 795 ~e~~~~p~~~-~~--~~~~~~~ld~~Gi~~~g~~v~~gdili~k~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~e~~~~ 871 (993)
++.|..|... .. ....|++||+||++.+|++|..|||+|||.+|....++.... ..+....+|+|+.++.+| .|
T Consensus 793 ee~~~~~~~~~~~~mr~~~~dkLdddG~i~~G~~vs~~Dv~iGk~t~~~~~~~~~~~-~~~~~t~~d~s~~Lr~~e--~G 869 (1141)
T KOG0214|consen 793 EEIFEEPPRGEGRGMRNGKYDKLDDDGIIMPGSRVSGGDVLIGKTTPQPAKEDESGP-EDRLYTKRDHSTKLRHTE--RG 869 (1141)
T ss_pred ccccccccccccccccccccccccccCCccccceeecCCEEeccccCCcccchhccc-cccccccccceeecccCC--cc
Confidence 7788776542 22 224799999999999999999999999999987655443221 112334689999999999 99
Q ss_pred EEEEEEEeeCCCCCeEEEEEEeeccCCCccccccccCCCcceeeeeecCCCCCCCCCCCcCeEEeCCCCCCCCCchhhhH
Q 001943 872 VVDRVALCSDKNGDLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMI 951 (993)
Q Consensus 872 ~v~~v~~~~~~~~~~~vkv~ir~~R~p~iGDKfasRHGqKGvvs~i~~~~DMPf~~~G~~pDiIiNPhg~PSRMtiGql~ 951 (993)
+||+|+++++.+|.+.+||++|+.|.|++|||||||||||||||.++++||||||.+|++|||||||||||||||||||+
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 HhhcccccccCCCceeeecCCCCCCCCCCHhhHhhhC
Q 001943 952 ELLGGKAGVSCGRFHYGSAFGEPSGHADTVESIRCFF 988 (993)
Q Consensus 952 E~~~gk~~~~~G~~~d~TpF~~~~~~~~~~~~i~~~~ 988 (993)
||++||.++..|...|||||.. .++..|+..+
T Consensus 950 Ec~lgk~~a~~~e~~~atpFs~-----v~v~~is~~l 981 (1141)
T KOG0214|consen 950 ECLLGKVAAYEGEEGDATPFSD-----VTVSKISANL 981 (1141)
T ss_pred HHhhhhhhhcccccccCCCCCc-----cchhcccchH
Confidence 9999999999999999999999 8888887765
No 4
>KOG0216 consensus RNA polymerase I, second largest subunit [Transcription]
Probab=100.00 E-value=2e-200 Score=1692.64 Aligned_cols=896 Identities=29% Similarity=0.463 Sum_probs=776.6
Q ss_pred cccccccccccccchHHHHHHHHHHHHHhCHHHHHHhcCc--ccccCCCcEEEEEeeEEEcCCeeccCC---CCCCCChH
Q 001943 30 DKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDR--IVSGIDPSIFLRFKDVRIGQPSMTVDG---VSEKLNPH 104 (993)
Q Consensus 30 ~~~~~i~~~~~~~~Lv~~hi~SFn~Fi~~gl~~ii~~~~~--I~~~~~~~~~l~f~~v~i~~P~~~~~~---~~~~l~P~ 104 (993)
..|+..|+|-+.++++++|++|||...+.||.+.--+..- ......+++.++++++.+.+|.+.... ..+++||.
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 4688889999999999999999999999887765433211 112234678999999999999997643 78899999
Q ss_pred HHHhcCCccCceEEEEEEEEECCcccceeeEEeEEEEeeccceeccccccCCCCCHHHHHhcCCCCCCCCcEEEEcCcee
Q 001943 105 MCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEK 184 (993)
Q Consensus 105 EcR~r~lTYs~~l~v~v~~~~~~~~~~~~i~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~gE~~~d~GGYFIInG~ER 184 (993)
|||+|++||+|.+.|+|.|..++ ..+...+..+|.+||||+|++|||.|++++||++++|++.|+||||||||+||
T Consensus 84 EcRqR~~TY~Gkl~v~v~wsVNg----~~~~~e~~dlG~vPIMlrSklChL~g~sp~eLV~hkEe~~EmGGYFIvNGIEK 159 (1111)
T KOG0216|consen 84 ECRQRGLTYKGKLVVRVSWSVNG----GHVVIEKRDLGHVPIMLRSKLCHLNGASPKELVKHKEESSEMGGYFIVNGIEK 159 (1111)
T ss_pred hHhhccceecceEEEEEEEEECC----eeeeeeeeecCccceEEeccccccCCCChHHHhhccCchhhcCcEEEEcChHH
Confidence 99999999999999999999988 44445678999999999999999999999999999999999999999999999
Q ss_pred EEEEeecccCCEEEEEeCCC----Cc----eEEEEEecCCCcccEEEE--EeeCCEEEEEEc--cccccccHHHHHHHhC
Q 001943 185 VLLIQEQLSKNRVIIDTDKK----GN----INASVTSSTETVKSKTVI--QMEKGKMYLLLN--QFVKKIPIMVVMKAMG 252 (993)
Q Consensus 185 VI~~q~~~~~N~i~~~~~~~----g~----~~~~v~s~~~~~~~~~~~--~~~~g~i~~~~~--~~~~~IPl~ilLrALg 252 (993)
|||++|.+++|++++..++. |. +-.+++|.+.+.++.+.. ++.||.+.+++. +....+|++++||||.
T Consensus 160 vIRmLIm~RRNHPiAiIR~Sfk~RG~~yS~yGVsmRcVReDqSsvtn~LHYLnnGtv~~~F~~rK~eylvPv~lILKAL~ 239 (1111)
T KOG0216|consen 160 VIRMLIMPRRNHPIAIIRPSFKDRGSSYSDYGVSMRCVREDQSSVTNVLHYLNNGTVMFRFSHRKREYLVPVVLILKALT 239 (1111)
T ss_pred hhhhheeccCCCceEEechhhhhcCCCccccceEEEEeccccccceeEEEEecCCcEEEEEEEeeeeehhhHHHHHHHHh
Confidence 99999999999999876532 32 345778878887766554 568996544432 2233699999999999
Q ss_pred CCCHHHHHHHh--C--CchhhHhhhhhhHHHHHhcCCcCHHHHHHHHhhhcccCCC-CCCCCChHHHHHHHHhhhhcCCC
Q 001943 253 MESDQEVVQMV--G--RDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTF-GSPPNDREGRAFSILRDVFLANV 327 (993)
Q Consensus 253 ~~sD~eI~~~i--~--~~~~~~~~l~~~l~~~~~~~i~t~~~al~yIg~~~~~~~~-~~~~~~~~e~~~~~L~~~ll~Hl 327 (993)
.+||+||++.+ + .|+++.++++.+|+++.+++++||++|++|||++|+.... .+..+ +.|+|+++|++++|+||
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 5788999999999999999999999999999999997543 34456 89999999999999999
Q ss_pred CCCCCCCCcchhhHHHHHHHHHHhhcCCCCCCCcccccceEEcchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCCC
Q 001943 328 PVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSR 407 (993)
Q Consensus 328 ~~~~~~~~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~nkRv~~~G~Ll~~lfr~~l~~~~~~ik~~l~~~~~~~~~~~~ 407 (993)
++ ..+||.+|++|++||++++.|+|.+||+|+.+||+++++|+|++..+|+.++.+++.++.++.+.+.+.....+
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 45899999999999999999999999999999999999999999999999999999887777776665332222
Q ss_pred c-c---ccccc--ccccchhhhhhhhccCCCcc-ccc-ccccccceEEecccccccccccccccC-ccccccccccCCCc
Q 001943 408 F-D---LSQFI--VRDSITVGLERTLSTGNFDV-KRF-KMHRKGMTQVLARLSFIGTLGHMTRVS-PQFEKSRKVSGPRA 478 (993)
Q Consensus 408 ~-~---~~~~i--~~~~It~~i~~~~aTGnw~~-~~~-~~q~sG~sq~l~r~N~ls~lshlRri~-~~f~~~~k~~~~R~ 478 (993)
+ + +..++ .+..|+++|++||||||+.+ +++ .+|++|+|+++||+|++++|||||.|| +.|+.+++||++||
T Consensus 395 ~~~~~~i~~~~~r~~~~Ig~~me~fLsTGnl~s~sgldLqQ~sG~tv~AEriNf~RflShFRavhRGa~f~~mrTTtvRK 474 (1111)
T KOG0216|consen 395 FLDISAIRKVFMRTNGNIGRKMEYFLSTGNLVSRSGLDLQQTSGYTVVAERINFYRFLSHFRAVHRGAFFAEMRTTTVRK 474 (1111)
T ss_pred hHhHHHHHHHHhhccccHHHHHHHHHhcCCeeeccchhhHhhcCcEEehhhhhHHHHHHHHHHHhcccchhheeehhhHh
Confidence 2 1 22222 45899999999999999974 344 367899999999999999999999999 68899999999999
Q ss_pred CCCCCcccccccCCCCCCcchhhhhhccccccccCC-CChhHHHHHHhcCCeeccccCccccCCCCceEEEECCeEeeec
Q 001943 479 LQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDE-EEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKH 557 (993)
Q Consensus 479 Lhps~wG~iCPveTPEG~~cGLv~~LA~~a~V~~~~-~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~~~V~~nG~~iG~~ 557 (993)
|.|++|||+||||||||+||||+||||..|+|++.. +...+.++|.++||.|....... .+.-++|++||+++||+
T Consensus 475 LlPEsWGFlCPVHTPDG~PCGlLnH~t~~c~I~t~~dd~s~ip~~L~~~Gm~p~~~~~~~---G~~l~~VlldGk~vG~~ 551 (1111)
T KOG0216|consen 475 LLPESWGFLCPVHTPDGAPCGLLNHMTRTCRIVTRPDDVSFIPSILFELGMVPSSHLVEA---GEPLYPVLLDGKVVGWV 551 (1111)
T ss_pred hCchhhcccccccCCCCCchhHHHhhhhheeEeecCcchhhhhHHHHhcCCCchhccccC---CCceeEEEECCEEEEee
Confidence 999999999999999999999999999999999874 45689999999999886643321 12478999999999999
Q ss_pred cCh--hhHHHHHHHHhhc--CCcCceeEEEec-----ccCceEEEecCCCeeeeeEEEeecCcccchhhhHHhhhccCcc
Q 001943 558 RRP--KCFADVMRKLRRA--GKIGEFVSVFVN-----EKQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRS 628 (993)
Q Consensus 558 ~~~--~~~~~~lR~~rr~--g~i~~~v~i~~~-----~~~~~i~I~td~gR~~RPl~~v~~~~~~~~~~~~~~~~~~~~~ 628 (993)
..+ ..+++.||.+|.. +.+|.+.+|.+. ...|++||+|++||++|||.+
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 855 8899999999965 668887777543 246999999999999999875
Q ss_pred hhhhhccCceeeeccccccceEEEeecCCCCCC-cceeeecCceeecccccccCCCCCCCCCcccccccccCCCccceee
Q 001943 629 FDDFLREGLIEYLDVNEENNALIALYEGDATPD-TTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAF 707 (993)
Q Consensus 629 ~~~~l~~g~iE~id~~Eq~~~~Ia~~~~~~~~~-~th~Ei~p~~ilsv~AslIPF~~hNqspRn~yq~~M~KQa~G~~~~ 707 (993)
++.+.+|||++.||.++.||+.++++.+. +||.|++|+.+||++|+||||+||||||||||||||+||+||++++
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 33366899999999999999999998765 8999999999999999999999999999999999999999999999
Q ss_pred eeccccccceeeecCCCcceeechhhhhhCCCCCCCCceeEEEEEecCCCCCCCcEEEecccccccceeEEEEEEEEEEe
Q 001943 708 NQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAIN 787 (993)
Q Consensus 708 n~~~r~D~~~y~l~ypQ~PlV~t~~~~~~~~~~~p~G~N~~VAv~~~~Gyn~EDaiiink~~~~rg~~~s~~~~~~~~~~ 787 (993)
+++.|.|+|+|+|++||.|+|++..++.++++++|.|+||+|||+|||||||||||||||+|+||||+++.+||+..+++
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-CCCCCCCcchhcccCCCCccccCCceeCCCCEEEEEecCCCCCCCCCCCCCCCCcccccceEEeeCC
Q 001943 788 QKYANSTSDRIL-RPDRTGPGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGP 866 (993)
Q Consensus 788 ~~~~~~~~e~~~-~p~~~~~~~~~~~~ld~~Gi~~~g~~v~~gdili~k~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~ 866 (993)
.+... ....|. .|+.. ..++||+||+|.+|+++..||+++..+.-.. .+....+|+..
T Consensus 766 ~~~~~-r~~~F~~~p~~~-----~~~~ld~dgLP~~G~kl~~~dp~~~y~d~~t---------------~~~~~~~~~~~ 824 (1111)
T KOG0216|consen 766 SKKRS-RSKHFGRSPGEP-----ELKKLDADGLPSIGQKLEYGDPYYAYFDEET---------------GKTRIKKYHGT 824 (1111)
T ss_pred hhccc-ceeeeeeCCCCc-----cccccCCCCCCCCcccccCCCcEEEEEcccC---------------CceEEEEecCC
Confidence 64322 123343 35442 4789999999999999999999998765432 24456788888
Q ss_pred CCCceEEEEEEEeeCCCCC--eEEEEEEeeccCCCccccccccCCCcceeeeeecCCCCCCCCCCCcCeEEeCCCCCCCC
Q 001943 867 DGETCVVDRVALCSDKNGD--LCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSR 944 (993)
Q Consensus 867 e~~~~~v~~v~~~~~~~~~--~~vkv~ir~~R~p~iGDKfasRHGqKGvvs~i~~~~DMPf~~~G~~pDiIiNPhg~PSR 944 (993)
| +|+||.|.+..++.+. +++.|++|.+|+|.||||||||||||||||+.||.+||||||+|++|||||||||||||
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 9 9999999999877665 78999999999999999999999999999999999999999999999999999999999
Q ss_pred CchhhhHHhhcccccccCCCceeeecCCCCCCCCCC-HhhHhhhC
Q 001943 945 MTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADT-VESIRCFF 988 (993)
Q Consensus 945 MtiGql~E~~~gk~~~~~G~~~d~TpF~~~~~~~~~-~~~i~~~~ 988 (993)
|||||++|++|||+||++|..+|||||.. .++++ +|.+.+.|
T Consensus 903 MTIgM~iEs~AgK~~alhG~~~Datpf~~--~E~~t~~dyfg~~L 945 (1111)
T KOG0216|consen 903 MTIGMLIESMAGKAGALHGNAQDATPFIF--SEENTAIDYFGEML 945 (1111)
T ss_pred ccHHHHHHHHhchhhccccccccCCceee--cCcccHHHHHHHHH
Confidence 99999999999999999999999999975 22233 34555444
No 5
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]
Probab=100.00 E-value=3.7e-194 Score=1735.56 Aligned_cols=872 Identities=31% Similarity=0.475 Sum_probs=782.5
Q ss_pred ccccccccccccccccchHHHHHHHHHHHHHhCHHHHHHhcCcccccCCCcEEEEEeeEEEcCCeeccCCCCCCCChHHH
Q 001943 27 SVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDGVSEKLNPHMC 106 (993)
Q Consensus 27 ~~~~~~~~i~~~~~~~~Lv~~hi~SFn~Fi~~gl~~ii~~~~~I~~~~~~~~~l~f~~v~i~~P~~~~~~~~~~l~P~Ec 106 (993)
+.++.|++++++|+.++|+++|++|||+|+.+||++++++++||+.. +++++|+|.++++++| ++++|.||
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 77889999999999999999999999999999999999999999754 7789999999999998 35699999
Q ss_pred HhcCCccCceEEEEEEEEECCccccee-eEEeEEEEeeccceeccccccCCCCCHHHHHhcCCCCCCCCcEEEEcCceeE
Q 001943 107 RLSDMTYAAPILVNIEYVQGSHTEKTT-MEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKV 185 (993)
Q Consensus 107 R~r~lTYs~~l~v~v~~~~~~~~~~~~-i~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~gE~~~d~GGYFIInG~ERV 185 (993)
|+|++||+|||+|+++++.++. .+ +++++|++|+||+||+ ||||||||+|||
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 9999999999999999998764 33 6778999999999994 999999999999
Q ss_pred EEEeecccCCEEEEEeC-CCC---ceEEEEEecCCCcccEEEEEeeCCEEEEEEccccccccHHHHHHHhCCCCHHHHHH
Q 001943 186 LLIQEQLSKNRVIIDTD-KKG---NINASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQ 261 (993)
Q Consensus 186 I~~q~~~~~N~i~~~~~-~~g---~~~~~v~s~~~~~~~~~~~~~~~g~i~~~~~~~~~~IPl~ilLrALg~~sD~eI~~ 261 (993)
|++||++|||.++..+. +++ .+.|.+.+++ ..|..+....++.+++++++. ++||+++||||||++||+||++
T Consensus 134 IVsQ~~rSPgvif~~~~~k~~~~~~~~a~vIp~r--G~wl~~e~d~~d~~~~rId~~-rkiPvtilLRALG~~tDeeI~~ 210 (1060)
T COG0085 134 IVSQEHRSPGVIFVEKKDKTGSKVLYVARVIPYR--GSWLEFEFDPKDNLYVRIDRK-RKIPVTILLRALGLETDEEIIE 210 (1060)
T ss_pred EEEEeecCCCeEEecccccCCcceEEEEEEecCC--cceEEEEEccCccEEEEeeeE-EEeeHHHHHHHhCCCcHHHHHH
Confidence 99999999997776653 334 2568888763 256666666788999999985 3899999999999999999999
Q ss_pred HhCCc-------hhhHhhhhhhHHHHHhcCCcCHHHHHHHHhhhcccCCCC-CCCCChHHHHHHHHhhhhcCCCCCC--C
Q 001943 262 MVGRD-------PRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFG-SPPNDREGRAFSILRDVFLANVPVH--N 331 (993)
Q Consensus 262 ~i~~~-------~~~~~~l~~~l~~~~~~~i~t~~~al~yIg~~~~~~~~~-~~~~~~~e~~~~~L~~~ll~Hl~~~--~ 331 (993)
.++.+ ....+.+...+++.....+.++. |++||++++...... .... +.+.++.++.+.+|||++.. .
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 12222333333333223344444 999999999876332 2445 78999999999999999963 2
Q ss_pred C--CCCcchhhHHHHHHHHHHhhcCCCCCCCcccccceEEcchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCCCcc
Q 001943 332 N--NFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFD 409 (993)
Q Consensus 332 ~--~~~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~nkRv~~~G~Ll~~lfr~~l~~~~~~ik~~l~~~~~~~~~~~~~~ 409 (993)
+ ....|+.+|+.|+++|+++..|++.+||+|||+||||+++|+||+++||.+|.+|++.+|++|.+...+
T Consensus 289 ~~l~~~~k~~di~~mi~~l~~L~~G~~~~DDiDHlGNKRlrlvGeLl~n~fR~gl~rmer~ikerm~~~~~r-------- 360 (1060)
T COG0085 289 YDLSRVGKAKDIIAMIKYLIELRLGKGEEDDIDHLGNRRLRLVGELLENLFRVGLSRMERDVKERLEKADKR-------- 360 (1060)
T ss_pred cchhhhHHHHHHHHHHHHHHHHhcCCCCCCCCccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh--------
Confidence 2 245588899999999999999999999999999999999999999999999999999999999886432
Q ss_pred cccccccccchhhhhhhhccCCCcccccccccccceEEecccccccccccccccCc-cccccccccCCCcCCCCCccccc
Q 001943 410 LSQFIVRDSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSP-QFEKSRKVSGPRALQPSQWGMLC 488 (993)
Q Consensus 410 ~~~~i~~~~It~~i~~~~aTGnw~~~~~~~q~sG~sq~l~r~N~ls~lshlRri~~-~f~~~~k~~~~R~Lhps~wG~iC 488 (993)
..++.++.||.++.+|++||||+ ++|+||+|||+||||+|||+||++| +++++++.++|||||||||||||
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 22335678999999999999996 6899999999999999999999999 99999999999999999999999
Q ss_pred ccCCCCCCcchhhhhhccccccc-cCCCChhHHHHHH-hcCCeeccccCccccCCCCceEEEECCeEeeeccChhhHHHH
Q 001943 489 PCDTPEGEACGLVKNLALMTHVT-TDEEEGPLISLCY-CLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADV 566 (993)
Q Consensus 489 PveTPEG~~cGLv~~LA~~a~V~-~~~~~~~i~~~l~-~~g~~~~~~~~~~~~~~~~~~~V~~nG~~iG~~~~~~~~~~~ 566 (993)
|+|||||+|||||||||++|+|+ .+++++|+++++. .+|+.++.++++.+ ..|++||.++|.++++..|++.
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 7799999999998 59999999888754 4599999999999999999999
Q ss_pred HHHHhhcCCcCceeEEEecccCc----eEEEecCCCeeeeeEEEeecCcccchhhhHHhhhcc-CcchhhhhccCceeee
Q 001943 567 MRKLRRAGKIGEFVSVFVNEKQR----CVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDG-VRSFDDFLREGLIEYL 641 (993)
Q Consensus 567 lR~~rr~g~i~~~v~i~~~~~~~----~i~I~td~gR~~RPl~~v~~~~~~~~~~~~~~~~~~-~~~~~~~l~~g~iE~i 641 (993)
+|.+|+ | +..+++++...... ++++.+|.||.+||++.++++..+++.++++++..+ ..+|.+++.+| +||+
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 77778887665544 899999999999999999999999999999988887 67999999999 9999
Q ss_pred ccccccceEEEeecCCCCCCcceeeecCceeecccccccCCCCCCCCCcccccccccCCCccceeeeeccccccceeeec
Q 001943 642 DVNEENNALIALYEGDATPDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLV 721 (993)
Q Consensus 642 d~~Eq~~~~Ia~~~~~~~~~~th~Ei~p~~ilsv~AslIPF~~hNqspRn~yq~~M~KQa~G~~~~n~~~r~D~~~y~l~ 721 (993)
++.|+.++.||..+++ +||+|++|..|+|.+|++|||++|||||||||||+|+||++|++..|+..|.|+..|.++
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 9999999999999987 799999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCcceeechhhhhhCCCCCCCCceeEEEEEecCCCCCCCcEEEecccccccceeEEEEEEEEEEeecccCCccceecCC
Q 001943 722 YPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILRP 801 (993)
Q Consensus 722 ypQ~PlV~t~~~~~~~~~~~p~G~N~~VAv~~~~Gyn~EDaiiink~~~~rg~~~s~~~~~~~~~~~~~~~~~~e~~~~p 801 (993)
|||.|+|+| +|+|+|||++||||||+||||||||||||++++||+|||+||++|++++++++.|.+|.+..|
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 999999998 899999999999999999999999999999999999999999999999999999998987779
Q ss_pred CCCCCcchhcccCCCCccccCCceeCCCCEEEEEecCCCCCCCCCC-----CCCCCCcccccceEEeeCCCCCceEEEEE
Q 001943 802 DRTGPGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMS-----PTGQTDSRYRSARQTYKGPDGETCVVDRV 876 (993)
Q Consensus 802 ~~~~~~~~~~~~ld~~Gi~~~g~~v~~gdili~k~~~~~~~~~~~~-----~~~~~~~~~~~~s~~~~~~e~~~~~v~~v 876 (993)
+.+ ...|++||+|||+++|++|++|||||||++|+++.+.... -++++ .+|+|++++++| +|+|+.|
T Consensus 732 ~~~---e~~~~~Lde~Gii~ig~~V~~gdilvgk~tP~~~~~~~~ee~ll~i~~ek---~rdtsl~~~~g~--~G~V~~V 803 (1060)
T COG0085 732 NVS---EEALRNLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRIFGEK---VRDTSLRVPHGE--EGIVDDV 803 (1060)
T ss_pred CcC---HHHHhcCCccCccccccEEcCCCEEEEeeCCCCCCCCCchhhhhccccce---eeccceeecCCC--CeEEEEE
Confidence 875 3689999999999999999999999999999998765321 12333 799999999999 9999999
Q ss_pred EEeeCCC----CCeEEEEEEeeccCCCccccccccCCCcceeeeeecCCCCCCCCCCCcCeEEeCCCCCCCCCchhhhHH
Q 001943 877 ALCSDKN----GDLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIE 952 (993)
Q Consensus 877 ~~~~~~~----~~~~vkv~ir~~R~p~iGDKfasRHGqKGvvs~i~~~~DMPf~~~G~~pDiIiNPhg~PSRMtiGql~E 952 (993)
.++++++ +.+.|||++|+.|+|++|||||||||||||||+|||+||||||+||++||||+|||||||||||||++|
T Consensus 804 ~~~~~~~~~~g~~~~vkV~v~~~R~~~~GDK~a~RHG~KGVis~i~p~eDMPf~~~G~~~DiilNP~gvPSRM~iGqilE 883 (1060)
T COG0085 804 QVFTREDGDPGVNKLVKVYVAQKRKPQIGDKMAGRHGNKGVVSKIVPQEDMPFLEDGTPPDIILNPLGVPSRMNIGQILE 883 (1060)
T ss_pred EEEeccCCCcCceEEEEEEEEEeccCCccccccccCCCCceeeeecCcccCCcCCCCCcccEEECCCCCCccccHHHHHH
Confidence 9998876 789999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcccccccCCCceeeecCCCCCCCCCCHhhHhhhCC
Q 001943 953 LLGGKAGVSCGRFHYGSAFGEPSGHADTVESIRCFFP 989 (993)
Q Consensus 953 ~~~gk~~~~~G~~~d~TpF~~~~~~~~~~~~i~~~~~ 989 (993)
+++||||+++|...|+|||++ ++.++|+..|.
T Consensus 884 ~~lG~a~~~~G~~~~~~~F~g-----~~~~~~~~~l~ 915 (1060)
T COG0085 884 THLGKAAALLGIPVDTPVFDG-----APEEDIRELLK 915 (1060)
T ss_pred HHHHHHHHhcCceeccCCcCC-----CCHHHHHHHHH
Confidence 999999999999999999999 99999998764
No 6
>TIGR02013 rpoB DNA-directed RNA polymerase, beta subunit. This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit.
Probab=100.00 E-value=1.5e-176 Score=1633.21 Aligned_cols=778 Identities=25% Similarity=0.416 Sum_probs=674.1
Q ss_pred ccccccccccccccchHHHHHHHHHHHHH----------hCHHHHHHhcCcccccCCCcEEEEEeeEEEcCCeeccCCCC
Q 001943 29 VDKFQLLPEFLKVRGLVKQHLDSFNYFVN----------TGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDGVS 98 (993)
Q Consensus 29 ~~~~~~i~~~~~~~~Lv~~hi~SFn~Fi~----------~gl~~ii~~~~~I~~~~~~~~~l~f~~v~i~~P~~~~~~~~ 98 (993)
+..|..++.+|+.++|++||++||||||+ +||++++++.+||+.. ++++.|+|.++++++|.+
T Consensus 5 r~~~~~~~~~~~~p~Lv~~Qi~SFn~FL~~~~~~~~~~~~gL~eii~~~~pI~~~-~~~~~l~f~~~~l~~P~~------ 77 (1065)
T TIGR02013 5 RIDFGKIPEVLEVPNLLEIQLDSYDWFLQQDTPPEKRKEEGLEEVFKSIFPIEDY-TGNIELEYLSYRLGEPKY------ 77 (1065)
T ss_pred eeecccCcccccCCCHHHHHHHHHHHHHcCCCcccccccccHHHHHhccCcEEec-CCcEEEEEEEEEeCCCCC------
Confidence 45699999999999999999999999999 8999999999999765 678999999999999987
Q ss_pred CCCChHHHHhcCCccCceEEEEEEEEECCcccceeeEEeEEEEeeccceeccccccCCCCCHHHHHhcCCCCCCCCcEEE
Q 001943 99 EKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFI 178 (993)
Q Consensus 99 ~~l~P~EcR~r~lTYs~~l~v~v~~~~~~~~~~~~i~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~gE~~~d~GGYFI 178 (993)
+|+|||+|++||+|||+|+++++..+....+++++++|++|+||+|+ .|||||
T Consensus 78 ---~p~Ear~r~lTYsa~l~v~v~l~~~~~~~~~~i~~~~V~iG~iPiMt------------------------~gGyFI 130 (1065)
T TIGR02013 78 ---SVEECKERGLTYSAPLKVKLRLINKEEDGTKEIKEQDVYMGDIPLMT------------------------DRGTFI 130 (1065)
T ss_pred ---CHHHHHHhCCCcceeEEEEEEEEEeccCCccceeeeeEEEeCCCccC------------------------CCceEE
Confidence 69999999999999999999997432101145666799999999997 599999
Q ss_pred EcCceeEEEEeecccCCEEEEEeC---CCC--ceEEEEEecCCCcccEEEEEeeCCEEEEEEccccccccHHHHHHHhCC
Q 001943 179 IKGTEKVLLIQEQLSKNRVIIDTD---KKG--NINASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGM 253 (993)
Q Consensus 179 InG~ERVI~~q~~~~~N~i~~~~~---~~g--~~~~~v~s~~~~~~~~~~~~~~~g~i~~~~~~~~~~IPl~ilLrALg~ 253 (993)
|||+||||++||++|||.++.+.. ++| .+.|.++|.++ +|..+.+.+++.+|++++++. +||+++||||||+
T Consensus 131 INGsERVIV~Qe~rspg~~~~~~~~~~~~~~~~~~a~iis~rg--swl~~e~~~~~~i~v~i~~~~-kIPi~illrALG~ 207 (1065)
T TIGR02013 131 INGAERVVVSQLHRSPGVFFSSEKDTHKSGKVLFSARIIPYRG--SWLEFETDKKDVLYVRIDRKR-KLPATVLLRALGY 207 (1065)
T ss_pred ECCcEEEEEEEeecCCCEEEEEccccCCCCceEEEEEEEeCCC--CceEEEEecCCeEEEEecCCC-ceeHHHHHHHcCC
Confidence 999999999999999998887653 345 47899998863 566666778899999999975 9999999999999
Q ss_pred CCHHHHHHHhCCchhhHhhhhhhHHHHHhcCCcCHHHHHHHHhhhcccCCCCCCCCChHHHHHHHHhhhhcC-------C
Q 001943 254 ESDQEVVQMVGRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLA-------N 326 (993)
Q Consensus 254 ~sD~eI~~~i~~~~~~~~~l~~~l~~~~~~~i~t~~~al~yIg~~~~~~~~~~~~~~~~e~~~~~L~~~ll~-------H 326 (993)
++|+||++.++.+..+.+ .|++. ...++++|+.|||++++++ ... ..+.|+++|++.||+ |
T Consensus 208 ~sd~eI~~~i~~~~~i~~----~l~~~---~~~~~e~Al~~i~~~~~~g----~~~-~~~~a~~~l~~~f~~~~rY~Lgh 275 (1065)
T TIGR02013 208 TIDTLILNRLGSGEYIRN----TLRKD---PTNSEEEALVEIYRKLRPG----EPP-TVEAARSLLENLFFDPKRYDLGR 275 (1065)
T ss_pred CcchhhhhhcCchHHHHH----HHHhc---cccCHHHHHHHHHhhcCCC----Ccc-hHHHHHHHHHHHhcCcccccccc
Confidence 999999999976544433 33322 3679999999999999876 234 678899999999987 9
Q ss_pred CCCCC------------CCCCcchhhHHHHHHHHHHhhcCCCCCCCcccccceEEcchHHHHHHHHHHHHHHHHHHHHHH
Q 001943 327 VPVHN------------NNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKT 394 (993)
Q Consensus 327 l~~~~------------~~~~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~nkRv~~~G~Ll~~lfr~~l~~~~~~ik~~ 394 (993)
+|..+ .....|++||+ |+++|+++..|.+.+||+|||+||||+++|+||+.|||.+|+++++.++++
T Consensus 276 iGr~kln~Kl~~~~~~~~~~l~k~d~l~-mi~~Ll~~~~g~~~~DD~Dhl~NKRvr~aGeLL~~~fr~~l~rl~k~ik~~ 354 (1065)
T TIGR02013 276 VGRYKLNKKLGLDVPEDIGVLTKEDIIA-TIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRER 354 (1065)
T ss_pred cchhhhhhhcCcCcCcccceehHHHHHH-HHHHHHHhhcCCCCCcchhhhhccchhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99421 11124889997 999999999999999999999999999999999999999999999999999
Q ss_pred HHhHhcCCCCCCCcccccccccccchhhhhhhhccCCCcccccccccccceEEecccccccccccccccCc----ccccc
Q 001943 395 VDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSP----QFEKS 470 (993)
Q Consensus 395 l~~~~~~~~~~~~~~~~~~i~~~~It~~i~~~~aTGnw~~~~~~~q~sG~sq~l~r~N~ls~lshlRri~~----~f~~~ 470 (993)
+.+. + ...+++..+++++.||+++++||+|| |+||+|+|+||||+|||+||+++ +++++
T Consensus 355 l~~~--~---~~~~~~~~~i~~~~it~~i~~ff~tg------------glSQ~Ldr~NpLs~lsh~RRlsslgpggl~r~ 417 (1065)
T TIGR02013 355 MSTQ--D---TDTLTPQDLINAKPISAAIKEFFGSS------------QLSQFMDQTNPLAELTHKRRLSALGPGGLTRE 417 (1065)
T ss_pred hhhc--c---cccCCHHHhcCccchHHHHHHHhccC------------CcccccccCCHHHhhhhhceecccCCCCcCcc
Confidence 8753 1 12466788889999999999999987 89999999999999999999997 69999
Q ss_pred ccccCCCcCCCCCcccccccCCCCCCcchhhhhhccccccccCCCChhHHHHHHhcCCeeccccCccccCCCCceEEEEC
Q 001943 471 RKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFN 550 (993)
Q Consensus 471 ~k~~~~R~Lhps~wG~iCPveTPEG~~cGLv~~LA~~a~V~~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~~~V~~n 550 (993)
++.++||+|||||||||||+|||||+|||||+|||++|+|+.
T Consensus 418 ~~~~~~RdlHpShyGrICPiETPEG~n~GLVknLA~~a~i~~-------------------------------------- 459 (1065)
T TIGR02013 418 RAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNE-------------------------------------- 459 (1065)
T ss_pred ccCCccCccCccccccccCCCCCCCCccccccchhhhcccCc--------------------------------------
Confidence 999999999999999999999999999999999999999851
Q ss_pred CeEeeeccChhhHHHHHHHHhhcCCcCceeEEEecccCceEEEecCCCeeeeeEEEeecCcccchhhhHHhhhccCcchh
Q 001943 551 GLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFD 630 (993)
Q Consensus 551 G~~iG~~~~~~~~~~~lR~~rr~g~i~~~v~i~~~~~~~~i~I~td~gR~~RPl~~v~~~~~~~~~~~~~~~~~~~~~~~ 630 (993)
.|.+.||++.|+||++.
T Consensus 460 ----------------------------------------------~G~i~~P~~~V~ng~~~----------------- 476 (1065)
T TIGR02013 460 ----------------------------------------------YGFIETPYRKVKDGKVV----------------- 476 (1065)
T ss_pred ----------------------------------------------ceEEeCCeEEEECCeEe-----------------
Confidence 14466999999988653
Q ss_pred hhhccCceeeeccccccceEEEeecCCCC-----------------------CCcceeeecCceeecccccccCCCCCCC
Q 001943 631 DFLREGLIEYLDVNEENNALIALYEGDAT-----------------------PDTTHIEIEPFTILGVIAGLIPYPHHNQ 687 (993)
Q Consensus 631 ~~l~~g~iE~id~~Eq~~~~Ia~~~~~~~-----------------------~~~th~Ei~p~~ilsv~AslIPF~~hNq 687 (993)
.++.+||+|++|++++.||..+.++. ..+||+||+|.+|||++||||||+||||
T Consensus 477 ---~~~~i~yl~a~eE~~~~Ia~~~~~l~~~~~~~~~~i~~r~~~~f~~~~~~~vt~~ei~p~~ilsv~aslIPFleHNd 553 (1065)
T TIGR02013 477 ---VTDEVDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDD 553 (1065)
T ss_pred ---ccceeEECChHHhCCcEEEecCcCcCccCccccceeeEEEcCceeecChhHeeEEeeChhhhhhhHhhcCCCccccC
Confidence 23579999999999999999776543 2469999999999999999999999999
Q ss_pred CCcccccccccCCCccce-----------------------------------eeeecccccc---------ceee----
Q 001943 688 SPRNTYQCAMGKQAMGNI-----------------------------------AFNQLCRMDS---------LLYL---- 719 (993)
Q Consensus 688 spRn~yq~~M~KQa~G~~-----------------------------------~~n~~~r~D~---------~~y~---- 719 (993)
||||||||||||||||++ ++++..|.|+ +.|.
T Consensus 554 s~R~lmgsnM~kQavpl~~~e~p~VgTg~E~~v~~ds~~~i~a~~~G~v~~v~~~~~~~r~d~~~~~~~~~~~~y~L~~~ 633 (1065)
T TIGR02013 554 ANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRYDEDEDEPDGGIDIYRLLKY 633 (1065)
T ss_pred CcchhhhhhhhhhhhcccccCCCEEEcCcchhhhccccceeEeccCCEEEEEccceEEEEecCCcccccccceEEEeecc
Confidence 999999999999999988 8899999995 3455
Q ss_pred ------ecCCCcceeechh----hhhh------CCCCCCCCceeEEEEEecCCCCCCCcEEEecccccccceeEEEEEEE
Q 001943 720 ------LVYPQRPLLTTRT----IELV------GYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKY 783 (993)
Q Consensus 720 ------l~ypQ~PlV~t~~----~~~~------~~~~~p~G~N~~VAv~~~~Gyn~EDaiiink~~~~rg~~~s~~~~~~ 783 (993)
++|||+|||+|+. .+++ .++|+|+|+|++||||||+||||||||||||+|+|||+|+|+||++|
T Consensus 634 ~~snq~~~~~q~Plv~~~~~v~~~~~l~d~~~~~~~e~~~G~N~~VAvm~y~GYn~EDAiiink~~i~rg~~~s~~~~~~ 713 (1065)
T TIGR02013 634 QRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEY 713 (1065)
T ss_pred cccccCceEEeeeeeccCCeEeeeeEecccccccCCcCcCccceEEEEEeeecccccceEEeehhhhcCCceEEEEEEEE
Confidence 5699999999964 4443 39999999999999999999999999999999999999999999999
Q ss_pred EEEeecccCCccceecC--CCCCCCcchhcccCCCCccccCCceeCCCCEEEEEecCCCCCCCCCC------CCCCCCcc
Q 001943 784 TAINQKYANSTSDRILR--PDRTGPGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMS------PTGQTDSR 855 (993)
Q Consensus 784 ~~~~~~~~~~~~e~~~~--p~~~~~~~~~~~~ld~~Gi~~~g~~v~~gdili~k~~~~~~~~~~~~------~~~~~~~~ 855 (993)
++++++++.|. |.+.. |+.. ...|++||+||||++|++|++|||||||++|....+.... -++.+...
T Consensus 714 ~~~~~~~~~g~-e~~~~~~p~~~---~~~~~~Ld~dGi~~~G~~v~~gdilvgk~~p~~~~~~~~~~~l~~~~~~~~~~~ 789 (1065)
T TIGR02013 714 EVEARDTKLGP-EEITRDIPNVS---EEALRNLDENGIVRIGAEVKAGDILVGKVTPKGETELTPEEKLLRAIFGEKARD 789 (1065)
T ss_pred EEEeeccCCCc-eEeeccCCCCc---hhhhhccCCCCCccCccEeCCCCEEEEEecCCcccccChhhhhhhhhcccCCcc
Confidence 99998776665 54443 6542 2479999999999999999999999999998653321110 12333344
Q ss_pred cccceEEeeCCCCCceEEEEEEEeeCCCC-------CeEEEEEEeeccCCCccccccccCCCcceeeeeecCCCCCCCCC
Q 001943 856 YRSARQTYKGPDGETCVVDRVALCSDKNG-------DLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSER 928 (993)
Q Consensus 856 ~~~~s~~~~~~e~~~~~v~~v~~~~~~~~-------~~~vkv~ir~~R~p~iGDKfasRHGqKGvvs~i~~~~DMPf~~~ 928 (993)
.+|+|++++.++ +|+||+|.++.++++ .+.|+|++|+.|+|+||||||||||||||||+|||+||||||+|
T Consensus 790 ~~d~s~~~~~~~--~g~V~~V~~~~~~~~~~~~~~~~~~vkv~ir~~R~p~iGDKfasRHGqKGvis~i~~~eDMPf~~~ 867 (1065)
T TIGR02013 790 VRDTSLRVPPGV--EGTVIDVKVFSRKQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLED 867 (1065)
T ss_pred ccccceEccCCC--CEEEEEEEEEeccCCCccCcCccEEEEEEEeecccccccchhhhcccCceeEEeEecCCCCCccCC
Confidence 789999999999 999999999876665 57899999999999999999999999999999999999999999
Q ss_pred CCcCeEEeCCCCCCCCCchhhhHHhhcccccccC--CCceeeec-CCCCCCCCCCHhhHhhhC
Q 001943 929 GICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSC--GRFHYGSA-FGEPSGHADTVESIRCFF 988 (993)
Q Consensus 929 G~~pDiIiNPhg~PSRMtiGql~E~~~gk~~~~~--G~~~d~Tp-F~~~~~~~~~~~~i~~~~ 988 (993)
|++|||||||||||||||||||+|+++||||++. |.+.++|| |++ .+.+++...+
T Consensus 868 G~~pDiIiNPhg~PSRMtiGqllE~~~gka~~~~~~~~~~~~tp~f~~-----~~~~~~~~~l 925 (1065)
T TIGR02013 868 GTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRKGVPIATPVFDG-----ASEEEIKEYL 925 (1065)
T ss_pred CCCccEEECCCCCcccccHHHHHHHHHHHHHHhccCCCeEEeccCcCC-----ccHHHHHHHH
Confidence 9999999999999999999999999999999997 67889999 888 8888887765
No 7
>cd00653 RNA_pol_B_RPB2 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.
Probab=100.00 E-value=5.2e-174 Score=1604.88 Aligned_cols=706 Identities=45% Similarity=0.735 Sum_probs=624.8
Q ss_pred hHHHHHHHHHHHHHhCHHHHHHhcCcccccC-CCcEEEEEeeEEEcCCeeccCCCCCCCChHHHHhcCCccCceEEEEEE
Q 001943 44 LVKQHLDSFNYFVNTGIRKIVRANDRIVSGI-DPSIFLRFKDVRIGQPSMTVDGVSEKLNPHMCRLSDMTYAAPILVNIE 122 (993)
Q Consensus 44 Lv~~hi~SFn~Fi~~gl~~ii~~~~~I~~~~-~~~~~l~f~~v~i~~P~~~~~~~~~~l~P~EcR~r~lTYs~~l~v~v~ 122 (993)
|++||++|||+|+++||++++++.++|.... +..+.++|+++++++|.+.++....+++|+|||+|++||+|+++|+++
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 6789999999999999999999999997653 467899999999999998765556789999999999999999999999
Q ss_pred EEECCcccceeeEEeEEEEeeccceeccccccCCCCCHHHHHhcCCCCCCCCcEEEEcCceeEEEEeecccCCEEEEEeC
Q 001943 123 YVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVIIDTD 202 (993)
Q Consensus 123 ~~~~~~~~~~~i~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~gE~~~d~GGYFIInG~ERVI~~q~~~~~N~i~~~~~ 202 (993)
++.++. ..+.++++++|+|||||+|++|||++++++|+++.||||.|+||||||||+|||||+||++++|+++++ +
T Consensus 81 ~~~~~~---~~~~~~~v~iG~iPIMv~S~~C~L~~~~~~el~~~~E~p~d~GGYFIInG~EkVIi~qi~~~~N~~~~~-~ 156 (866)
T cd00653 81 LTVNDK---GKIKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVE-D 156 (866)
T ss_pred EEEecc---eeEEEEEEEEeeCCcccCcccccccCCCHHHHHhcCCCcccCCCEEEECCceeEEEEEEeccCCeEEEe-c
Confidence 986552 233567899999999999999999999999999999999999999999999999999999999999887 4
Q ss_pred CCCceEEEEEecCCC---c-ccEEEEEee-CCEEEEEEccccccccHHHHHHHhCCCCHHHHHHHhCCchhhHhhhhhhH
Q 001943 203 KKGNINASVTSSTET---V-KSKTVIQME-KGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGRDPRYSALLLPSI 277 (993)
Q Consensus 203 ~~g~~~~~v~s~~~~---~-~~~~~~~~~-~g~i~~~~~~~~~~IPl~ilLrALg~~sD~eI~~~i~~~~~~~~~l~~~l 277 (993)
+.+.+.+.+++.... . .+..+.... ++.++.+++...
T Consensus 157 ~~~~~~~~~~s~~~~~~~~~s~~~~~~~~~~~~i~~~i~~~~-------------------------------------- 198 (866)
T cd00653 157 SKGKRIYTKTSIPSYSPYRGSWLEVKSDKKKDRIYVRIDLKR-------------------------------------- 198 (866)
T ss_pred CCCcEEEEEEEccCCCcCccEEEEEEEccCCCeEEEEecccC--------------------------------------
Confidence 445566666665432 1 222222222 345666666531
Q ss_pred HHHHhcCCcCHHHHHHHHhhhcccCCCCCCCCChHHHHHHHHhhhhcCCCCCCCCCCCcchhhHHHHHHHHHHhhcCCCC
Q 001943 278 EECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDA 357 (993)
Q Consensus 278 ~~~~~~~i~t~~~al~yIg~~~~~~~~~~~~~~~~e~~~~~L~~~ll~Hl~~~~~~~~~K~~~L~~Mi~kLl~~~~g~~~ 357 (993)
+++|++|||++| .+|++|++||+++..|.+.
T Consensus 199 ----------~~~al~~ig~~~---------------------------------------~~L~~Mi~kLl~~~~g~~~ 229 (866)
T cd00653 199 ----------QEEALKYIGKRF---------------------------------------EDLIYMIRKLILLVLGKGK 229 (866)
T ss_pred ----------HHHHHHHHHHHH---------------------------------------HHHHHHHHHHHHHhcCCCC
Confidence 678999999864 6799999999999999999
Q ss_pred CCCcccccceEEcchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCCCcccccccccccchhhhhhhhccCCCccccc
Q 001943 358 MDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFDVKRF 437 (993)
Q Consensus 358 ~DD~D~l~nkRv~~~G~Ll~~lfr~~l~~~~~~ik~~l~~~~~~~~~~~~~~~~~~i~~~~It~~i~~~~aTGnw~~~~~ 437 (993)
+||+|||+||||+++|+||+.+|++.|+++++.++..+.+...+.+ .+++..+++++.||++|++|||||||...+.
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 3456666788899999999999999997766
Q ss_pred ccccccceEEecccccccccccccccCc-cccccccccCCCcCCCCCcccccccCCCCCCcchhhhhhccccccccCCCC
Q 001943 438 KMHRKGMTQVLARLSFIGTLGHMTRVSP-QFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEE 516 (993)
Q Consensus 438 ~~q~sG~sq~l~r~N~ls~lshlRri~~-~f~~~~k~~~~R~Lhps~wG~iCPveTPEG~~cGLv~~LA~~a~V~~~~~~ 516 (993)
.+|++|+||+|+|+||+|+|||+||+|+ ++++++|++++|+||||||||+||+|||||++||||+|||++|+|+
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 9999999999999999999999999999999999999999999873
Q ss_pred hhHHHHHHhcCCeeccccCccccCCCCceEEEECCeEeeeccChhhHHHHHHHHhhcCCcCceeEEEecccCceEEEecC
Q 001943 517 GPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASD 596 (993)
Q Consensus 517 ~~i~~~l~~~g~~~~~~~~~~~~~~~~~~~V~~nG~~iG~~~~~~~~~~~lR~~rr~g~i~~~v~i~~~~~~~~i~I~td 596 (993)
T Consensus 382 -------------------------------------------------------------------------------- 381 (866)
T cd00653 382 -------------------------------------------------------------------------------- 381 (866)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred CCeeeeeEEEeecCcccchhhhHHhhhccCcchhhhhccCceeeeccccccceEEEeecCCCCCCcceeeecCceeeccc
Q 001943 597 GGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTTHIEIEPFTILGVI 676 (993)
Q Consensus 597 ~gR~~RPl~~v~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~iE~id~~Eq~~~~Ia~~~~~~~~~~th~Ei~p~~ilsv~ 676 (993)
||++||+++|+ ..+||+||+|.++||++
T Consensus 382 -Gr~~rP~~~v~---------------------------------------------------~~~th~ei~~~~~ls~~ 409 (866)
T cd00653 382 -GRIERPYRIVE---------------------------------------------------KEVTHIEISPSQILSVA 409 (866)
T ss_pred -eEeeeeEEEec---------------------------------------------------cceEEEEeCccceeeee
Confidence 89999999753 13699999999999999
Q ss_pred ccccCCCCCCCCCcccccccccCCCccceeeeeccccccceeeecCCCcceeechhhhhhCCCCCCCCceeEEEEEecCC
Q 001943 677 AGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSG 756 (993)
Q Consensus 677 AslIPF~~hNqspRn~yq~~M~KQa~G~~~~n~~~r~D~~~y~l~ypQ~PlV~t~~~~~~~~~~~p~G~N~~VAv~~~~G 756 (993)
||+|||+||||||||||||||+|||||++++|++.|+|++.|+|.|||+|||+|+..+.++++++|+|+|++||||||+|
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 CCCCCcEEEecccccccceeEEEEEEEEEEeecccCCccceecCCCCCCCcchhcccCCCCccccCCceeCCCCEEEEEe
Q 001943 757 YDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILRPDRTGPGAERMQILDDDGLAAPGEIIKPNDVYINKE 836 (993)
Q Consensus 757 yn~EDaiiink~~~~rg~~~s~~~~~~~~~~~~~~~~~~e~~~~p~~~~~~~~~~~~ld~~Gi~~~g~~v~~gdili~k~ 836 (993)
|||||||||||+|+|||+|+|+||++|++++++...+..+.+. ++........|++||+||||++|++|++||+||||+
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 9999999999999999999999999999999876655555544 111111235799999999999999999999999999
Q ss_pred cCCCCCCCCCCCCCCCCcccccceEEeeCCCCCceEEEEEEEee---CCCCCeEEEEEEeeccCCCccccccccCCCcce
Q 001943 837 SPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCS---DKNGDLCIKFLIRHTRRPELGDKFSSRHGQKGV 913 (993)
Q Consensus 837 ~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~e~~~~~v~~v~~~~---~~~~~~~vkv~ir~~R~p~iGDKfasRHGqKGv 913 (993)
+|....+... .++.+....+|.+++++.+| .|+||+|.++. +.++...|+|++|+.|+|+||||||||||||||
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 11222334689999999999 99999999987 567789999999999999999999999999999
Q ss_pred eeeeecCCCCCCCCCCCcCeEEeCCCCCCCCCchhhhHHhhcccccccCCCceeeecCCCCCCCCCCHhhHhhhCC
Q 001943 914 CGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADTVESIRCFFP 989 (993)
Q Consensus 914 vs~i~~~~DMPf~~~G~~pDiIiNPhg~PSRMtiGql~E~~~gk~~~~~G~~~d~TpF~~~~~~~~~~~~i~~~~~ 989 (993)
||++||+||||||+||++|||||||||||||||||||+|+++||||+++|.+.|+|||++ ++.+++...|.
T Consensus 646 ~s~i~~~~dmPf~~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~t~f~~-----~~~~~~~~~l~ 716 (866)
T cd00653 646 ISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDG-----AEEEDISELLG 716 (866)
T ss_pred EEEEeccccCCcccCCCCCcEEecCCcCcccccHHHHHHHHHHHHHHhcCCcccccccCc-----chHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999998 88888887653
No 8
>PRK00405 rpoB DNA-directed RNA polymerase subunit beta; Reviewed
Probab=100.00 E-value=2.1e-172 Score=1604.52 Aligned_cols=780 Identities=24% Similarity=0.405 Sum_probs=663.6
Q ss_pred cccccccccccccccchHHHHHHHHHHHH-------HhCHHHHHHhcCcccccCCCcEEEEEeeEEEcCCeeccCCCCCC
Q 001943 28 VVDKFQLLPEFLKVRGLVKQHLDSFNYFV-------NTGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDGVSEK 100 (993)
Q Consensus 28 ~~~~~~~i~~~~~~~~Lv~~hi~SFn~Fi-------~~gl~~ii~~~~~I~~~~~~~~~l~f~~v~i~~P~~~~~~~~~~ 100 (993)
.+..+..++.++..++|++||++|||||| ++||++++++.+||+.. ++++.|+|.++++++|.+
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 34567888899999999999999999999 99999999999999764 678999999999999975
Q ss_pred CChHHHHhcCCccCceEEEEEEEEECCcccceeeEEeEEEEeeccceeccccccCCCCCHHHHHhcCCCCCCCCcEEEEc
Q 001943 101 LNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIK 180 (993)
Q Consensus 101 l~P~EcR~r~lTYs~~l~v~v~~~~~~~~~~~~i~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~gE~~~d~GGYFIIn 180 (993)
+|+|||+|++||+|||+|+++++..+. +++++++|++|+||||+ +|||||||
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 799999999999999999999986432 45667799999999997 89999999
Q ss_pred CceeEEEEeecccCCEEEEEeCC-----CCceEEEEEecCCCcccEEEEEeeCCEEEEEEccccccccHHHHHHHhCCCC
Q 001943 181 GTEKVLLIQEQLSKNRVIIDTDK-----KGNINASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMES 255 (993)
Q Consensus 181 G~ERVI~~q~~~~~N~i~~~~~~-----~g~~~~~v~s~~~~~~~~~~~~~~~g~i~~~~~~~~~~IPl~ilLrALg~~s 255 (993)
|+||||++||++|||.++.++.. +..|.|+++|.++ +|..+.+.+++.+|+++++. ++||+++||||||+ |
T Consensus 134 G~ERVIVsQe~rSPg~~~~~~~~k~~~~k~~y~a~Iis~rG--swl~~e~d~k~~I~vri~~~-~kIPi~iLLrALGl-s 209 (1112)
T PRK00405 134 GTERVIVSQLHRSPGVYFDHDKDKTSSGKLLYSARIIPYRG--SWLEFEFDPKDILYVRIDRR-RKLPVTVLLRALGY-S 209 (1112)
T ss_pred CeEEEEEEEeecCCCEEEEEeccccCCCceeEEEEEEECCC--CcEEEEEecCCeEEEEecCC-CcccHHHHHHHcCC-C
Confidence 99999999999999987765432 2237899999863 57777777889999999986 69999999999999 8
Q ss_pred HHHHHHHhCCchhhH-------------------------h------------hhhhhHHHHH-hcCCcCHHHHHHHHhh
Q 001943 256 DQEVVQMVGRDPRYS-------------------------A------------LLLPSIEECA-NLDIYTQEKALEYLEG 297 (993)
Q Consensus 256 D~eI~~~i~~~~~~~-------------------------~------------~l~~~l~~~~-~~~i~t~~~al~yIg~ 297 (993)
|+||++.++.+..+. + .+...+.+.. .+...++++|+.||++
T Consensus 210 d~eIl~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ei~~~~~~~~~~~~~~~~i~~~l~~~~~~t~e~Al~~I~k 289 (1112)
T PRK00405 210 DEEILDLFYEKEEFGKEIEVPVEYLLGKVLAEDIVDEETGEVLAEANDEITEELDGPYIRNTLEKDPTSSREEALVEIYR 289 (1112)
T ss_pred HHHHHHHhcccccccceeccchHHhcccchhhhhcccccceeeeccCCccchhhhhHHHHHHHhhccccCHHHHHHHHHh
Confidence 999999996332221 0 0112232222 2346799999999999
Q ss_pred hcccCCCCCCCCChHHHHHHHHhhhhc-------CCCCCCCCC--------CC----cchhhHHHHHHHHHHhhcCCCCC
Q 001943 298 KVKRSTFGSPPNDREGRAFSILRDVFL-------ANVPVHNNN--------FR----PKCFYVAVMLRRMVEAMLNKDAM 358 (993)
Q Consensus 298 ~~~~~~~~~~~~~~~e~~~~~L~~~ll-------~Hl~~~~~~--------~~----~K~~~L~~Mi~kLl~~~~g~~~~ 358 (993)
+++++ ... ..+.|+++|++.|| ||+|..+.+ .. .|+++ ++|+++|+++..|.+.+
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-TVEAARSLLENLFFDPKRYDLSKVGRYKLNKKLGLDEDEDVRVLTKEDI-IATIKYLINLRNGKGEV 363 (1112)
T ss_pred hcCCC----Ccc-hHHHHHHHHHHHhcCccccccccCCceecchhcccCcccccccccHHHH-HHHHHHHHhhhcccCCC
Confidence 99876 234 66889999999886 999965322 11 34555 88999999999999999
Q ss_pred CCcccccceEEcchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCCCcccccccccccchhhhhhhhccCCCcccccc
Q 001943 359 DDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFDVKRFK 438 (993)
Q Consensus 359 DD~D~l~nkRv~~~G~Ll~~lfr~~l~~~~~~ik~~l~~~~~~~~~~~~~~~~~~i~~~~It~~i~~~~aTGnw~~~~~~ 438 (993)
||+|||+||||+++|+||+.|||.+|+++++.+++++.+.. ...+++..+++++.||++|++||+||
T Consensus 364 DDiDhl~NKRvr~aGeLL~~~fr~~~~rl~k~ik~~l~~~~-----~~~~~~~~lin~~~it~~i~~ff~tg-------- 430 (1112)
T PRK00405 364 DDIDHLGNRRVRSVGELLQNQFRIGLSRMERAVRERMSLQD-----LDTLTPQDLINAKPVVAAIKEFFGSS-------- 430 (1112)
T ss_pred cchhHHhcchhhhHHHHHHHHHHHHHHHHHHHHHHHhhhcc-----cccCCHHHhhCchhHHHHHHHhhccC--------
Confidence 99999999999999999999999999999999999987541 13467888899999999999999987
Q ss_pred cccccceEEecccccccccccccccCc----cccccccccCCCcCCCCCcccccccCCCCCCcchhhhhhccccccccCC
Q 001943 439 MHRKGMTQVLARLSFIGTLGHMTRVSP----QFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDE 514 (993)
Q Consensus 439 ~q~sG~sq~l~r~N~ls~lshlRri~~----~f~~~~k~~~~R~Lhps~wG~iCPveTPEG~~cGLv~~LA~~a~V~~~~ 514 (993)
|+||+|+|+||||+|||+||+++ ++.++++.+.||+|||||||||||+|||||++||||+|||++|+|+.
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 89999999999999999999997 69999999999999999999999999999999999999999999983
Q ss_pred CChhHHHHHHhcCCeeccccCccccCCCCceEEEECCeEeeeccChhhHHHHHHHHhhcCCcCceeEEEecccCceEEEe
Q 001943 515 EEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIA 594 (993)
Q Consensus 515 ~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~~~V~~nG~~iG~~~~~~~~~~~lR~~rr~g~i~~~v~i~~~~~~~~i~I~ 594 (993)
+|+.. ..|.+++||.|- .
T Consensus 505 -----------~G~~~------------tp~~~~~nG~~~---~------------------------------------ 522 (1112)
T PRK00405 505 -----------YGFIE------------TPYRKVVDGKVT---D------------------------------------ 522 (1112)
T ss_pred -----------CCccc------------cceEEEECCeEc---c------------------------------------
Confidence 44421 236677888751 0
Q ss_pred cCCCeeeeeEEEeecCcccchhhhHHhhhccCcchhhhhccCceeeeccccccceEEEeecCCCC---------------
Q 001943 595 SDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDAT--------------- 659 (993)
Q Consensus 595 td~gR~~RPl~~v~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~iE~id~~Eq~~~~Ia~~~~~~~--------------- 659 (993)
.+||+|++||+++.||..+.++.
T Consensus 523 ------------------------------------------~i~yl~a~eE~~~~Ia~~~~~l~~~~~~~~~~i~~r~~ 560 (1112)
T PRK00405 523 ------------------------------------------EIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYK 560 (1112)
T ss_pred ------------------------------------------ceEECCHHHhcCcEEEecCcccCCCCcccCceEEEEec
Confidence 15778888888888887654432
Q ss_pred --------CCcceeeecCceeecccccccCCCCCCCCCcccccccccCCCccceee------------------------
Q 001943 660 --------PDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAF------------------------ 707 (993)
Q Consensus 660 --------~~~th~Ei~p~~ilsv~AslIPF~~hNqspRn~yq~~M~KQa~G~~~~------------------------ 707 (993)
..+||+||+|.+++|++||||||+||||||||+|||||||||||++..
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 236999999999999999999999999999999999999999999888
Q ss_pred -----------eecccc-----------------ccceee-ecCCCcceeechh----hhhh------CCCCCCCCceeE
Q 001943 708 -----------NQLCRM-----------------DSLLYL-LVYPQRPLLTTRT----IELV------GYDKLGAGQNAT 748 (993)
Q Consensus 708 -----------n~~~r~-----------------D~~~y~-l~ypQ~PlV~t~~----~~~~------~~~~~p~G~N~~ 748 (993)
++..|. |+..+. ++|||+|||+|+. .+++ +++|+|+|+|++
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 787888 555566 7999999999994 4554 799999999999
Q ss_pred EEEEecCCCCCCCcEEEecccccccceeEEEEEEEEEEeecccCCccceec-CCCCCCCcchhcccCCCCccccCCceeC
Q 001943 749 VAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRIL-RPDRTGPGAERMQILDDDGLAAPGEIIK 827 (993)
Q Consensus 749 VAv~~~~Gyn~EDaiiink~~~~rg~~~s~~~~~~~~~~~~~~~~~~e~~~-~p~~~~~~~~~~~~ld~~Gi~~~g~~v~ 827 (993)
||||||+||||||||||||+|+|||+|+|+||++|++++++++.|..+.+. .|+.+ ...|++||+||||++|++|+
T Consensus 721 VA~~~y~GYn~EDaiiink~si~rg~~~s~~~~~~~~~~~~~~~~~~~~~~~~p~~~---~~~~~~Ld~dGi~~~G~~v~ 797 (1112)
T PRK00405 721 VAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVS---EEALRNLDESGIVRIGAEVK 797 (1112)
T ss_pred EEEEeecccCccceEEEEhhhhccCceEEEEEeeeeeEeeccCCCceeecccCCCCC---hHHhhccCCCCCccCccEec
Confidence 999999999999999999999999999999999999999877766543332 25432 24799999999999999999
Q ss_pred CCCEEEEEecCCCCCCCCCC------CCCCCCcccccceEEeeCCCCCceEEEEEEEeeC-CCC-------CeEEEEEEe
Q 001943 828 PNDVYINKESPLETRGSIMS------PTGQTDSRYRSARQTYKGPDGETCVVDRVALCSD-KNG-------DLCIKFLIR 893 (993)
Q Consensus 828 ~gdili~k~~~~~~~~~~~~------~~~~~~~~~~~~s~~~~~~e~~~~~v~~v~~~~~-~~~-------~~~vkv~ir 893 (993)
+|||||||++|....+.... -++.+....+|+|++++.+| .|+||+|.++.+ .++ .+.|+|++|
T Consensus 798 ~gDiligk~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~s~~~~~~~--~g~V~~v~~~~~~~~~~~~~~~~~~~vkv~ir 875 (1112)
T PRK00405 798 PGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGE--EGTVIDVKVFTRIEQGDELPPGVNKLVKVYIA 875 (1112)
T ss_pred CCCEEEEEecCCCccccChhhhhhhhhhcccccccccceEEcCCCC--CEEEEEEEEeeccccCCccCcCcceEEEEEEe
Confidence 99999999998653321110 02223344789999999999 999999999876 554 468999999
Q ss_pred eccCCCccccccccCCCcceeeeeecCCCCCCCCCCCcCeEEeCCCCCCCCCchhhhHHhhcccccccCCCceeeec-CC
Q 001943 894 HTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSA-FG 972 (993)
Q Consensus 894 ~~R~p~iGDKfasRHGqKGvvs~i~~~~DMPf~~~G~~pDiIiNPhg~PSRMtiGql~E~~~gk~~~~~G~~~d~Tp-F~ 972 (993)
+.|+|+||||||||||||||||+|||+||||||+||++|||||||||||||||||||+|+++||||++.|.+ |+|| |+
T Consensus 876 ~~R~p~iGDKfasRHGqKGvis~i~~~eDMPf~~~G~~pDiIiNPhg~PSRMtiGql~E~~~gk~~~~~g~~-~~tp~f~ 954 (1112)
T PRK00405 876 QKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIK-FATPVFD 954 (1112)
T ss_pred eecccCcccchhhccCCceeEEeEeccCCCCcCCCCCCCcEEECCCCCcccccHHHHHHHHhhHHHHhcCCe-EecCccC
Confidence 999999999999999999999999999999999999999999999999999999999999999999999975 8999 88
Q ss_pred CCCCCCCCHhhHhhhC
Q 001943 973 EPSGHADTVESIRCFF 988 (993)
Q Consensus 973 ~~~~~~~~~~~i~~~~ 988 (993)
+ .+.+++...|
T Consensus 955 ~-----~~~~~~~~~l 965 (1112)
T PRK00405 955 G-----AKEEEIKELL 965 (1112)
T ss_pred C-----ccHHHHHHHH
Confidence 8 8888887765
No 9
>CHL00001 rpoB RNA polymerase beta subunit
Probab=100.00 E-value=1.1e-170 Score=1572.15 Aligned_cols=789 Identities=22% Similarity=0.315 Sum_probs=664.2
Q ss_pred ccccchHHHHHHHHHHHHHhCHHHHHHhcCcccccCCCcEEE--EEeeEEEcCCeeccCCCCCCCChHHHHhcCCccCce
Q 001943 39 LKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFL--RFKDVRIGQPSMTVDGVSEKLNPHMCRLSDMTYAAP 116 (993)
Q Consensus 39 ~~~~~Lv~~hi~SFn~Fi~~gl~~ii~~~~~I~~~~~~~~~l--~f~~v~i~~P~~~~~~~~~~l~P~EcR~r~lTYs~~ 116 (993)
++.++|+++|++||||||++||++++++++||+ +.++++.+ .++++++++|.+ +|+|||+|++||+|+
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 667999999999999999999999999999997 55666544 456999999987 699999999999999
Q ss_pred EEEEEEEEECCcccceeeEEeEEEEeeccceeccccccCCCCCHHHHHhcCCCCCCCCcEEEEcCceeEEEEeecccCCE
Q 001943 117 ILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNR 196 (993)
Q Consensus 117 l~v~v~~~~~~~~~~~~i~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~gE~~~d~GGYFIInG~ERVI~~q~~~~~N~ 196 (993)
|+|+++++..+. +.+++++|++|+||+|. +||||||||+||||++|++++||.
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 55667799999999994 999999999999999999999997
Q ss_pred EEEEeC-CC--CceEEEEEecCCCcccEEEEEeeCCEEEEEEccccccccHHHHHHHhCCCCHHHHHHHhCCchhhHhhh
Q 001943 197 VIIDTD-KK--GNINASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGRDPRYSALL 273 (993)
Q Consensus 197 i~~~~~-~~--g~~~~~v~s~~~~~~~~~~~~~~~g~i~~~~~~~~~~IPl~ilLrALg~~sD~eI~~~i~~~~~~~~~l 273 (993)
++.+.. +. ..|.|.++|.++ +|..+.+.+++.+|+++++. ++||+++||||||++ |+||++.++.+ +.+
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 776543 22 348899999876 46666667789999999996 699999999999995 99999999643 233
Q ss_pred hhhHHHHHhcCCcCHHHHHHHHhhhcccCCCCCCCCChHHHHHHHHhhhhcCC------CCCCCCCCC------cchhhH
Q 001943 274 LPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLAN------VPVHNNNFR------PKCFYV 341 (993)
Q Consensus 274 ~~~l~~~~~~~i~t~~~al~yIg~~~~~~~~~~~~~~~~e~~~~~L~~~ll~H------l~~~~~~~~------~K~~~L 341 (993)
..+|.+.....+.++++|+.||++++... ..... ..+.|+.+|.+.+|+| +|..+.+.. .|..+|
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 34444443345789999999999998431 11344 6788999999999998 886543322 566666
Q ss_pred -----HHHHHHHHHhhcCCCCCCCcccccceEEcchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCCCccccccccc
Q 001943 342 -----AVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVR 416 (993)
Q Consensus 342 -----~~Mi~kLl~~~~g~~~~DD~D~l~nkRv~~~G~Ll~~lfr~~l~~~~~~ik~~l~~~~~~~~~~~~~~~~~~i~~ 416 (993)
++|+++|+++..|.+.+||+|||+||||+++|+||+.|||.+|+++++.++++|.+.+++. ..+++..++++
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 8999999999999999999999999999999999999999999999999999998765332 24678889999
Q ss_pred ccchhhhhhhhccCCCcccccccccccceEEecccccccccccccccCc--ccccccccc--CCCcCCCCCcccccccCC
Q 001943 417 DSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSP--QFEKSRKVS--GPRALQPSQWGMLCPCDT 492 (993)
Q Consensus 417 ~~It~~i~~~~aTGnw~~~~~~~q~sG~sq~l~r~N~ls~lshlRri~~--~f~~~~k~~--~~R~Lhps~wG~iCPveT 492 (993)
+.||++|++||+| +|+||+|||+|+||+|||+||+++ |...+++.. .||+|||||||||||+||
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 9999999999986 589999999999999999999997 777776665 899999999999999999
Q ss_pred CCCCcchhhhhhccccccc-cCCCChhHHHHHHhcCCeeccccCccccCCCCceEEEECCeEeeeccChhhHHHHHHHHh
Q 001943 493 PEGEACGLVKNLALMTHVT-TDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLR 571 (993)
Q Consensus 493 PEG~~cGLv~~LA~~a~V~-~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~~~V~~nG~~iG~~~~~~~~~~~lR~~r 571 (993)
|||+|||||++||++|+|+ .+..++|+++++...+++.+.++++.+. +.+.|+ +|.|+|...+
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 5688999999998888888888887652 568888 9999973211
Q ss_pred hcCCcCceeEEEecccCceEEEecCCCeeeeeEEEeecCcccchhhhHHhhhccCcchhhhhccCceeeeccccccceEE
Q 001943 572 RAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALI 651 (993)
Q Consensus 572 r~g~i~~~v~i~~~~~~~~i~I~td~gR~~RPl~~v~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~iE~id~~Eq~~~~I 651 (993)
.+ ...++.+. + + ++++.|
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 EeecCCCCCCcceeeecCceeecccccccCCCCCCCCCcccccccccCCCccceeee---------ecccc---------
Q 001943 652 ALYEGDATPDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFN---------QLCRM--------- 713 (993)
Q Consensus 652 a~~~~~~~~~~th~Ei~p~~ilsv~AslIPF~~hNqspRn~yq~~M~KQa~G~~~~n---------~~~r~--------- 713 (993)
++. ..||+||+|.||+||+||||||+||||||||+|||||||||||++..+ +..|.
T Consensus 509 ~~~------~i~~~dIsP~qi~svaasLIPFleHndanRalmgsnMqrQAvpll~~~~p~VgTG~E~~~~~ds~~~i~a~ 582 (1070)
T CHL00001 509 AWE------QIHLRSIFPFQYFSIGASLIPFLEHNDANRALMGSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVVAIAE 582 (1070)
T ss_pred chH------HCcEEeeChhhhhhhhhhcCCCccccCcchhhhhhccchhccccccCCCCEeecCcchhhhhcccceeEEc
Confidence 433 249999999999999999999999999999999999999999999888 66666
Q ss_pred --------c-----------c-ceeeecC---------CCcceeechhhhh----------hCCCCCCCCceeEEEEEec
Q 001943 714 --------D-----------S-LLYLLVY---------PQRPLLTTRTIEL----------VGYDKLGAGQNATVAVMSY 754 (993)
Q Consensus 714 --------D-----------~-~~y~l~y---------pQ~PlV~t~~~~~----------~~~~~~p~G~N~~VAv~~~ 754 (993)
| + ..|++.| ||||||+++.+.- +..+|+|+|+|++||||||
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 9999999995432 3389999999999999999
Q ss_pred CCCCCCCcEEEecccccccceeEEEEEEEEEEeecccCCccceecC--CCCCCCcchhcccCCCCccccCCceeCCCCEE
Q 001943 755 SGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILR--PDRTGPGAERMQILDDDGLAAPGEIIKPNDVY 832 (993)
Q Consensus 755 ~Gyn~EDaiiink~~~~rg~~~s~~~~~~~~~~~~~~~~~~e~~~~--p~~~~~~~~~~~~ld~~Gi~~~g~~v~~gdil 832 (993)
+||||||||||||++++||+|+|+||++|++++++++.|. |.++. |+.+. ..|++||+||||++|++|++||||
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 479999999999999999999999
Q ss_pred EEEecCCCCCCCCC--------CCCCCCCcccccceEEeeCCCCCceEEEEEEEeeC----CCCCeEEEEEEeeccCCCc
Q 001943 833 INKESPLETRGSIM--------SPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSD----KNGDLCIKFLIRHTRRPEL 900 (993)
Q Consensus 833 i~k~~~~~~~~~~~--------~~~~~~~~~~~~~s~~~~~~e~~~~~v~~v~~~~~----~~~~~~vkv~ir~~R~p~i 900 (993)
|||++|....+... .-++.+....+|+|++++.++ .|+|++|.++.. .++...|||++|+.|+|++
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 99999973222211 113444556789999999999 999999998873 4567899999999999999
Q ss_pred cccccccCCCcceeeeeecCCCCCCCCCCCcCeEEeCCCCCCCCCchhhhHHhhcccccccCCCceeeecCCCCCCCCCC
Q 001943 901 GDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADT 980 (993)
Q Consensus 901 GDKfasRHGqKGvvs~i~~~~DMPf~~~G~~pDiIiNPhg~PSRMtiGql~E~~~gk~~~~~G~~~d~TpF~~~~~~~~~ 980 (993)
|||||||||||||||+|||+|||||++||++|||||||||||||||||||+|+++||||+++|.+.|+|||++ ..
T Consensus 817 GDK~asRHGqKGvvs~i~~~eDMPf~~dG~~pDiIlNP~gvPSRMtiGqllE~~~G~a~~~~g~~~~~~pf~~-----~~ 891 (1070)
T CHL00001 817 GDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLLNRHYRIAPFDE-----RY 891 (1070)
T ss_pred CcccccccCCcceEeeeecccCCCcccCCCCCceeeccccccccccHHHHHHHHhHHHHhhcCceeeeccCCC-----cc
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999998 66
Q ss_pred HhhHh
Q 001943 981 VESIR 985 (993)
Q Consensus 981 ~~~i~ 985 (993)
.++++
T Consensus 892 ~~~~~ 896 (1070)
T CHL00001 892 EQEAS 896 (1070)
T ss_pred hhhhh
Confidence 66665
No 10
>CHL00207 rpoB RNA polymerase beta subunit; Provisional
Probab=100.00 E-value=7.3e-155 Score=1422.79 Aligned_cols=788 Identities=22% Similarity=0.358 Sum_probs=622.6
Q ss_pred cccccchHHHHHHHHHHHHHhCHHHHHHhcCcccccCCCcEEEEEe--eEEEcCCeeccCCCCCCCChHHHHhcCCccCc
Q 001943 38 FLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLRFK--DVRIGQPSMTVDGVSEKLNPHMCRLSDMTYAA 115 (993)
Q Consensus 38 ~~~~~~Lv~~hi~SFn~Fi~~gl~~ii~~~~~I~~~~~~~~~l~f~--~v~i~~P~~~~~~~~~~l~P~EcR~r~lTYs~ 115 (993)
-|+.++|+..|++||+|||++||++++++.+||+. .++++.++|. ++++++|.+ +|.|||+|++||++
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 35678999999999999999999999999999964 5667777776 799999986 69999999999999
Q ss_pred eEEEEEEEEECCcccceeeEEeEEEEeeccceeccccccCCCCCHHHHHhcCCCCCCCCcEEEEcCceeEEEEeecccCC
Q 001943 116 PILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKN 195 (993)
Q Consensus 116 ~l~v~v~~~~~~~~~~~~i~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~gE~~~d~GGYFIInG~ERVI~~q~~~~~N 195 (993)
||+|+++++.+++ +++++++|++|+||+|+ ++|||||||+||||++|+.++|+
T Consensus 74 ~l~v~~~l~~~~~---~~i~~~~V~lG~iPlMT------------------------~~GtFIING~ERViVsQl~RSPG 126 (1077)
T CHL00207 74 QIYLPLKFINLKT---NKIKFINYLIGNLPKMT------------------------QRGTFIINGLERVIVSQIIRSPG 126 (1077)
T ss_pred eEEEEEEEEEcCC---ceEEEEEEEEeccCccC------------------------CCCEEEEcCceeEEEEEeccCCe
Confidence 9999999986552 56678899999999997 89999999999999999988885
Q ss_pred EEEEEeC--CCCc--eEEEEEecCCCcccEEEEEeeCCEEEEEEccccccccHHHHHHHhCCCCHHHHHHHhCC--chhh
Q 001943 196 RVIIDTD--KKGN--INASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGR--DPRY 269 (993)
Q Consensus 196 ~i~~~~~--~~g~--~~~~v~s~~~~~~~~~~~~~~~g~i~~~~~~~~~~IPl~ilLrALg~~sD~eI~~~i~~--~~~~ 269 (993)
+|+... +.+. +.|.+++.++ .|..+.+++++.+|+++++. ++||+++||||||+ |++||++.++. +..+
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 888654 3343 7799998765 68888888899999999995 59999999999999 79999999953 2222
Q ss_pred HhhhhhhHHHHHhcCCcCHHHHHHHHhhhcccCCCCCCCCChHHHHHHHH-------hhhhcCCCCCCCC----------
Q 001943 270 SALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSIL-------RDVFLANVPVHNN---------- 332 (993)
Q Consensus 270 ~~~l~~~l~~~~~~~i~t~~~al~yIg~~~~~~~~~~~~~~~~e~~~~~L-------~~~ll~Hl~~~~~---------- 332 (993)
+...+. ..+..++++|+.+|+++++++ ... ..+.++.+| +++.|+|+|.-+.
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 224568999999999999887 223 456677766 4555788886221
Q ss_pred -CCCcchhhHHHHHHHHHHhhcCCCCCCCcccccceEEcchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCCCcccc
Q 001943 333 -NFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLS 411 (993)
Q Consensus 333 -~~~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~nkRv~~~G~Ll~~lfr~~l~~~~~~ik~~l~~~~~~~~~~~~~~~~ 411 (993)
...-+...+..|+++|+.+..|....||+|||+||||+++|+||++|||.+|.++++.++++|.+.. ...+.+.
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 1122334466799999999999999999999999999999999999999999999999999997532 1246778
Q ss_pred cccccccchhhhhhhhccCCCcccccccccccceEEecccccccccccccccCc----cccccccccCCCcCCCCCcccc
Q 001943 412 QFIVRDSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSP----QFEKSRKVSGPRALQPSQWGML 487 (993)
Q Consensus 412 ~~i~~~~It~~i~~~~aTGnw~~~~~~~q~sG~sq~l~r~N~ls~lshlRri~~----~f~~~~k~~~~R~Lhps~wG~i 487 (993)
++++++.|+..|++||++ +++||.+|++|+||.|+|.||+++ ++.+++..+.+|++||||||||
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 889999999999999964 588999999999999999999996 7899999999999999999999
Q ss_pred cccCCCCCCcchhhhhhccccccccCCCChhHHHHHHhcCCeeccccCccccCCCCceEEEECCeEeeeccChhhHHHHH
Q 001943 488 CPCDTPEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVM 567 (993)
Q Consensus 488 CPveTPEG~~cGLv~~LA~~a~V~~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~~~V~~nG~~iG~~~~~~~~~~~l 567 (993)
||+|||||+|||||++||.+|+|+.. |+.. ..|....||.+.- .++
T Consensus 414 CPIETPEG~n~Gli~~la~~~~in~~-------------Gfie------------tPy~~v~~g~v~~-~~~-------- 459 (1077)
T CHL00207 414 CPIETPEGPNCGLIGSLATNARINKF-------------GFIE------------TPFYKVINGKVKK-FGN-------- 459 (1077)
T ss_pred cCCCCCCCcccccccchhhhccccCC-------------Ccee------------CceEEEEcCcccc-cCc--------
Confidence 99999999999999999999999863 3221 1222334554320 000
Q ss_pred HHHhhcCCcCceeEEEeccc-CceEEEecCCCeeeeeEEEeecCcccchhhhHHhhhccCcchhhhhccCceeeeccccc
Q 001943 568 RKLRRAGKIGEFVSVFVNEK-QRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEE 646 (993)
Q Consensus 568 R~~rr~g~i~~~v~i~~~~~-~~~i~I~td~gR~~RPl~~v~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~iE~id~~Eq 646 (993)
.+++... .....|+...-- .-+++. +....|.-.- -+
T Consensus 460 -------------i~ylsa~~e~~~~Ia~~~~~------~~~~~~---------------------~~~~~v~~r~--~~ 497 (1077)
T CHL00207 460 -------------PIYLTADSEDLYRIAPNDIN------LNKNNY---------------------FKKNIIPVRY--KQ 497 (1077)
T ss_pred -------------eeecChHHhcCcEEEecCcc------CCCCCc---------------------ccCCEEEEEE--CC
Confidence 0111111 122222221100 001110 0000011000 01
Q ss_pred cceEEEeecCCCCCCcceeeecCceeecccccccCCCCCCCCCcccccccccCCCccceee-------e-----------
Q 001943 647 NNALIALYEGDATPDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAF-------N----------- 708 (993)
Q Consensus 647 ~~~~Ia~~~~~~~~~~th~Ei~p~~ilsv~AslIPF~~hNqspRn~yq~~M~KQa~G~~~~-------n----------- 708 (993)
++.. +.+ ...++++++|.|++|++||||||++||||+|++||||||||||++... .
T Consensus 498 ef~~--~~~----~~v~~~~vsp~Q~~SvaasLIPFLehdDanRaLMGsnMqrQaVPll~~e~p~VgTg~e~~~a~ds~~ 571 (1077)
T CHL00207 498 EFKT--VNP----SKVDFIAISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIVGTGYEKQIALDSGM 571 (1077)
T ss_pred cEEE--ECh----HHceEEEeCcchhcchhhhcCCcccccccchhhhhhccccccccccccCCCeEECCcchHhhhhcch
Confidence 1111 111 235899999999999999999999999999999999999999975311 1
Q ss_pred -------------eccc----cc---cceeee----------cCCCcceeechhhh----------hhCCCCCCCCceeE
Q 001943 709 -------------QLCR----MD---SLLYLL----------VYPQRPLLTTRTIE----------LVGYDKLGAGQNAT 748 (993)
Q Consensus 709 -------------~~~r----~D---~~~y~l----------~ypQ~PlV~t~~~~----------~~~~~~~p~G~N~~ 748 (993)
...| .+ ...|.| |.+|||+|+.+... .+.++|+|+|+|++
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 1111 11 123544 67999999998753 35699999999999
Q ss_pred EEEEecCCCCCCCcEEEecccccccceeEEEEEEEEEEeecccCCccceec--CCCCCCCcchhcccCCCCccccCCcee
Q 001943 749 VAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRIL--RPDRTGPGAERMQILDDDGLAAPGEII 826 (993)
Q Consensus 749 VAv~~~~Gyn~EDaiiink~~~~rg~~~s~~~~~~~~~~~~~~~~~~e~~~--~p~~~~~~~~~~~~ld~~Gi~~~g~~v 826 (993)
||||||+||||||||||||++++||+|+|+|+++|++++++++.|. |.++ .|+.+ ...|++||+||||++|++|
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 4454 36543 2579999999999999999
Q ss_pred CCCCEEEEEecCCCCCCCCCC------CCCCCCcccccceEEeeCCCCCceEEEEEEEeeCCC--CC-----eEEEEEEe
Q 001943 827 KPNDVYINKESPLETRGSIMS------PTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKN--GD-----LCIKFLIR 893 (993)
Q Consensus 827 ~~gdili~k~~~~~~~~~~~~------~~~~~~~~~~~~s~~~~~~e~~~~~v~~v~~~~~~~--~~-----~~vkv~ir 893 (993)
++|||||||++|+...+.... -++.+....+|+|++++.++ .|+|++|.++.+++ +. ..|||++|
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 999999999999653332110 13444455799999999999 99999999987532 22 45999999
Q ss_pred eccCCCccccccccCCCcceeeeeecCCCCCCCCCCCcCeEEeCCCCCCCCCchhhhHHhhcccccccCCCceeeecCCC
Q 001943 894 HTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGE 973 (993)
Q Consensus 894 ~~R~p~iGDKfasRHGqKGvvs~i~~~~DMPf~~~G~~pDiIiNPhg~PSRMtiGql~E~~~gk~~~~~G~~~d~TpF~~ 973 (993)
+.|+|+||||||||||||||||+|||+|||||++||++|||||||||||||||||||+|+++||||+++|...++|||++
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 99999999999999999999999999999999999999999999999999999999999999999999888889999998
Q ss_pred CCCCCCCHhhHhhhC
Q 001943 974 PSGHADTVESIRCFF 988 (993)
Q Consensus 974 ~~~~~~~~~~i~~~~ 988 (993)
...++++..+
T Consensus 886 -----~~~~~~~~~l 895 (1077)
T CHL00207 886 -----MYGSEYSRIL 895 (1077)
T ss_pred -----CcHHHHHHHH
Confidence 7777665443
No 11
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=100.00 E-value=3.5e-145 Score=1376.92 Aligned_cols=790 Identities=21% Similarity=0.346 Sum_probs=619.6
Q ss_pred ccccccccccccccccchHHHHHHHHHHHHH------hCHHHHHHhcCcccccCCCcEEEEEeeEEEcCCeeccCCCCCC
Q 001943 27 SVVDKFQLLPEFLKVRGLVKQHLDSFNYFVN------TGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDGVSEK 100 (993)
Q Consensus 27 ~~~~~~~~i~~~~~~~~Lv~~hi~SFn~Fi~------~gl~~ii~~~~~I~~~~~~~~~l~f~~v~i~~P~~~~~~~~~~ 100 (993)
+.+.+|+.++..++.++|++.|.+||+||++ +||++++++++||+ +.++++.|+|.+|++++|.+
T Consensus 10 ~~R~~f~k~~~~~~iPdLleIQ~~SF~~FLq~~~~~~~GL~e~f~~~fPI~-d~~g~~~Lefv~Y~l~~Pk~-------- 80 (2890)
T PRK09603 10 RLRADFTKTPTDLEVPNLLLLQRDSYDSFLYSKDGKESGIEKVFKSIFPIQ-DEHNRITLEYAGCEFGKSKY-------- 80 (2890)
T ss_pred eEEeecccCCccCCCCCHHHHHHHHHHHHHhCCCcccccHHHHHHhcCCeE-CCCCcEEEEEEEEEeCCCCC--------
Confidence 3566789999999999999999999999998 79999999999995 45788999999999999998
Q ss_pred CChHHHHhcCCccCceEEEEEEEEE---CCcc----cceeeEEeEEEEeeccceeccccccCCCCCHHHHHhcCCCCCCC
Q 001943 101 LNPHMCRLSDMTYAAPILVNIEYVQ---GSHT----EKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDP 173 (993)
Q Consensus 101 l~P~EcR~r~lTYs~~l~v~v~~~~---~~~~----~~~~i~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~gE~~~d~ 173 (993)
+|.||++|++||++||+|+++++. +.++ ..+++++++|++|+||+|+ +
T Consensus 81 -~~~Ec~~rg~TYsapL~v~~rL~~~~~~~~t~~~~~ikeikeq~VylGdiPLMT------------------------~ 135 (2890)
T PRK09603 81 -TVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQSIFIREIPLMT------------------------E 135 (2890)
T ss_pred -CHHHHHhhCCcccccEEEEEEEEEeeccccccccccccceEEeeEEEecCCccC------------------------C
Confidence 589999999999999999999984 2211 1135778899999999999 7
Q ss_pred CcEEEEcCceeEEEEeecccCCEEEEEeCCC----Cc--eEEEEEecCCCcccEEEEEeeCCEEEEEEccccccccHHHH
Q 001943 174 GGYFIIKGTEKVLLIQEQLSKNRVIIDTDKK----GN--INASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVV 247 (993)
Q Consensus 174 GGYFIInG~ERVI~~q~~~~~N~i~~~~~~~----g~--~~~~v~s~~~~~~~~~~~~~~~g~i~~~~~~~~~~IPl~il 247 (993)
.|+|||||+||||++|++|||+ +|+..+.+ |. |.|+++|.++ +|..+..++++.+|+++++ +++||+++|
T Consensus 136 ~GTFIING~ERVIVsQL~RSPG-VyF~~~~~k~~s~k~lysa~IIP~RG--sWLefE~D~kd~l~vrIDr-krKipit~l 211 (2890)
T PRK09603 136 RTSFIINGVERVVVNQLHRSPG-VIFKEEESSTSLNKLIYTGQIIPDRG--SWLYFEYDSKDVLYARINK-RRKVPVTIL 211 (2890)
T ss_pred CceEEEcCceeEEEeeeccCCe-eEEeeccCcCCCCceeEEEEEecCCc--ceEEEEEcCCCeEEEEEcC-cceecHHHH
Confidence 9999999999999999999997 88765421 32 6799998765 6888888999999999999 469999999
Q ss_pred HHHhCCCCHHHHHHHhCC-------ch---------hh-----------------------------------------H
Q 001943 248 MKAMGMESDQEVVQMVGR-------DP---------RY-----------------------------------------S 270 (993)
Q Consensus 248 LrALg~~sD~eI~~~i~~-------~~---------~~-----------------------------------------~ 270 (993)
|||||+ |++||++.++. +. .+ .
T Consensus 212 LrAlG~-s~edIl~~f~~~~~~~i~~~~~~~~~~~~~l~~~~~~di~d~~g~vlv~~g~rit~~~~~~l~~~g~k~l~~~ 290 (2890)
T PRK09603 212 FRAMDY-QKQDIIKMFYPLVKVRYENDKYLIPFASLDANQRMEFDLKDPQGKIILLAGKKLTSRKIKELKENHLEWVEYP 290 (2890)
T ss_pred HHHhCC-CHHHHHHHhcccceEEEcccceeecccHHHhcCccceeecccCCCEEEecCccccHHHHHHHHhcCCceeccc
Confidence 999999 68999998741 00 00 0
Q ss_pred -----------------hhhh--------hhHHHHHhcC--------------------------------------CcC
Q 001943 271 -----------------ALLL--------PSIEECANLD--------------------------------------IYT 287 (993)
Q Consensus 271 -----------------~~l~--------~~l~~~~~~~--------------------------------------i~t 287 (993)
+.+. ..++.....+ ..+
T Consensus 291 ~~~l~g~~laedivd~~Evl~~~~~~Itee~le~i~~~gi~~i~vl~~~~~~~~~~i~~t~~~d~~~~~~~~~t~~~~~~ 370 (2890)
T PRK09603 291 MDILLNRHLAEPVMVGKEVLLDMLTQLDKNKLEKIHDLGVQEFVIINDLALGHDASIIHSFSADSESLKLLKQTEKIDDE 370 (2890)
T ss_pred hhhhcceeeeeeccCccceeeccCChhcHHHHHHHHHcCCceEEEEeecccccccccccccccccccchhhhhccccccc
Confidence 0000 0000000000 014
Q ss_pred HHHHHHHHhhhcccCCCCCCCCChHHHHHHHHhhhhcC-------CCCCCCC------------CCCcchhhHHHHHHHH
Q 001943 288 QEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLA-------NVPVHNN------------NFRPKCFYVAVMLRRM 348 (993)
Q Consensus 288 ~~~al~yIg~~~~~~~~~~~~~~~~e~~~~~L~~~ll~-------Hl~~~~~------------~~~~K~~~L~~Mi~kL 348 (993)
+++|+..|+++++++ ... ..+.|+.++.+.||. .+|.-+. ....+.++++ .+++|
T Consensus 371 ~eeAl~~iyr~lrpg----ep~-~~e~A~~l~~~lFFn~~rYdLg~vGR~klN~kL~l~~~~~~~~Lt~~Dil~-~i~~l 444 (2890)
T PRK09603 371 NALAAIRIHKVMKPG----DPV-TTEVAKQFVKKLFFDPERYDLTMVGRMKMNHKLGLHVPDYITTLTHEDIIT-TVKYL 444 (2890)
T ss_pred hHHHHHHHHhccCCC----CCC-cHHHHHHHHHHHhcCcccccccccchhhhHhhhCCCCCCcccEecchhHHH-HHHHH
Confidence 588999999999987 344 667788888887754 2221110 0112345564 79999
Q ss_pred HHhhcCCCCCCCcccccceEEcchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCCCcccccccccccchhhhhhhhc
Q 001943 349 VEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLS 428 (993)
Q Consensus 349 l~~~~g~~~~DD~D~l~nkRv~~~G~Ll~~lfr~~l~~~~~~ik~~l~~~~~~~~~~~~~~~~~~i~~~~It~~i~~~~a 428 (993)
+.+..|....||+|||+||||+++|+||++|||.+|.++++.+|++|...... ...+.+.+++|++.+++.+++||+
T Consensus 445 i~l~~g~~~~DDiDhL~NRRvr~vGELl~~qfr~gl~rler~irerm~~~~~~---~~~~~p~~lin~k~i~~~ikeFFg 521 (2890)
T PRK09603 445 MKIKNNQGKIDDRDHLGNRRIRAVGELLANELHSGLVKMQKTIKDKLTTMSGA---FDSLMPHDLVNSKMITSTIMEFFM 521 (2890)
T ss_pred HHHHhCCCCCCcchhhhcchhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc---ccccChhhhhccHHHHHHHHHHhc
Confidence 99999999999999999999999999999999999999999999999753211 234667888999999999999997
Q ss_pred cCCCcccccccccccceEEecccccccccccccccCc----cccccccccCCCcCCCCCcccccccCCCCCCcchhhhhh
Q 001943 429 TGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSP----QFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNL 504 (993)
Q Consensus 429 TGnw~~~~~~~q~sG~sq~l~r~N~ls~lshlRri~~----~f~~~~k~~~~R~Lhps~wG~iCPveTPEG~~cGLv~~L 504 (993)
|+ .+||.+|++|+||.|+|.||+++ .+.+.+..+.+|++||||||||||+|||||+|||||++|
T Consensus 522 ss------------qLSQfmDQtNpLseltHKRRlSaLGPGGlsr~ra~fevRdVH~shYGRiCPIETPEG~NiGLI~SL 589 (2890)
T PRK09603 522 GG------------QLSQFMDQTNPLSEVTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTL 589 (2890)
T ss_pred cC------------chhhhhcccChhhhhhhcccccccCCCCccccccCCcccccCcccccccCCCCCCCCCcccchhhh
Confidence 65 36899999999999999999983 477889999999999999999999999999999999999
Q ss_pred ccccccccCCCChhHHHHHHhcCCeeccccCccccCCCCceEEEECCeEeeeccChhhHHHHHHHHhhcCCcCceeEEEe
Q 001943 505 ALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFV 584 (993)
Q Consensus 505 A~~a~V~~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~~~V~~nG~~iG~~~~~~~~~~~lR~~rr~g~i~~~v~i~~ 584 (993)
|.+|+|+.. |+.. ..|....||.+- +++ +|+
T Consensus 590 a~~a~in~~-------------Gfie------------tPy~kV~~g~v~---~~i---------------------~yl 620 (2890)
T PRK09603 590 STFTRVNDL-------------GFIE------------APYKKVVDGKVV---GET---------------------IYL 620 (2890)
T ss_pred hhheecccC-------------ccee------------cceEEEecCccc---cce---------------------eee
Confidence 999999863 3321 122222455521 100 112
Q ss_pred ccc-CceEEEecCCCeeeeeEEEeecCcccchhhhHHhhhccCcchhhhhccCceeeeccccccceEEEeecCCCCCCcc
Q 001943 585 NEK-QRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTT 663 (993)
Q Consensus 585 ~~~-~~~i~I~td~gR~~RPl~~v~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~iE~id~~Eq~~~~Ia~~~~~~~~~~t 663 (993)
... .....|+...-.+ -++|.. . ...|.--- .+++..+. + ...+
T Consensus 621 sa~eE~~~~IA~a~~~~------~~~~~~--------------------~-~~~v~~R~--~~e~~~~~--~----~~v~ 665 (2890)
T PRK09603 621 TAIQEDSHIIAPASTPI------DEEGNI--------------------L-GDLIETRV--EGEIVLNE--K----SKVT 665 (2890)
T ss_pred CHHHhcCceEeccCCcc------CCCCcc--------------------c-CCeEeEEE--CCceEEEC--h----HHce
Confidence 111 1222222211000 011100 0 00000000 01111111 1 2358
Q ss_pred eeeecCceeecccccccCCCCCCCCCcccccccccCCCcccee-------------------------------eeec--
Q 001943 664 HIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIA-------------------------------FNQL-- 710 (993)
Q Consensus 664 h~Ei~p~~ilsv~AslIPF~~hNqspRn~yq~~M~KQa~G~~~-------------------------------~n~~-- 710 (993)
+++++|.|++|++||||||++||||+|++||||||||||++.. +...
T Consensus 666 ~~dvsp~Q~vSvaasLIPFLEhdDAnRALMGSNMQRQAVPLl~~e~piVgTG~E~~va~dSg~~i~a~~~G~V~yvd~~~ 745 (2890)
T PRK09603 666 LMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTGIEKIIARDSWGAIKANRAGVVEKIDSKN 745 (2890)
T ss_pred EEEeCccceeeehhhcCCccccCccccccccccchhhhhhhccccCCeEecCcchhhhccccceeEecCCeEEEEecCcE
Confidence 9999999999999999999999999999999999999997421 1111
Q ss_pred --ccccc------ceeee----------cCCCcceeechhhh----------hhCCCCCCCCceeEEEEEecCCCCCCCc
Q 001943 711 --CRMDS------LLYLL----------VYPQRPLLTTRTIE----------LVGYDKLGAGQNATVAVMSYSGYDIEDA 762 (993)
Q Consensus 711 --~r~D~------~~y~l----------~ypQ~PlV~t~~~~----------~~~~~~~p~G~N~~VAv~~~~Gyn~EDa 762 (993)
.|.+. ..|.| |++|||+|+.+... .+..+|+++|+|++||||||.|||||||
T Consensus 746 I~i~~~~~~~~~~~~Y~L~Ky~RSNQ~TcinqrPiV~~Gd~V~kGdilADG~st~~GELALG~NvlVAfmpW~GYNfEDA 825 (2890)
T PRK09603 746 IYILGEGKEEAYIDAYSLQKNLRTNQNTSFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDA 825 (2890)
T ss_pred EEEEecCCCCceeeEEeeccccccCCCceeeeccEecCCCEeccCCEEecCcccccCeeccCcccEEEEeeeccccCccc
Confidence 11111 23665 77999999988753 3569999999999999999999999999
Q ss_pred EEEecccccccceeEEEEEEEEEEeecccCCccceecC-CCCCCCcchhcccCCCCccccCCceeCCCCEEEEEecCCCC
Q 001943 763 IVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILR-PDRTGPGAERMQILDDDGLAAPGEIIKPNDVYINKESPLET 841 (993)
Q Consensus 763 iiink~~~~rg~~~s~~~~~~~~~~~~~~~~~~e~~~~-p~~~~~~~~~~~~ld~~Gi~~~g~~v~~gdili~k~~~~~~ 841 (993)
|+||++.+.+++|||+|+++|++++++++.|.+|.+.. |+.+. +..++||++|||++|++|++|||||||++|+.+
T Consensus 826 IlISERlV~eD~fTSIHIee~ei~~r~Tk~G~EeITrdIPnvse---~~l~~LDe~GII~iGa~V~~GDILVGKvTPkge 902 (2890)
T PRK09603 826 IVVSERITKDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKE---EALAHLDESGIVKVGTYVSAGMILVGKTSPKGE 902 (2890)
T ss_pred cccchhhhcCccceEEEEeeeEEEEEecCCCCcEEeccCCCCCH---HHHhcCCCCCCEeeCCEECCCCEEEEeeccCCC
Confidence 99999999999999999999999999999887666654 88753 689999999999999999999999999999976
Q ss_pred CCCCCC------CCCCCCcccccceEEeeCCCCCceEEEEEEEeeCC---------------------------------
Q 001943 842 RGSIMS------PTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDK--------------------------------- 882 (993)
Q Consensus 842 ~~~~~~------~~~~~~~~~~~~s~~~~~~e~~~~~v~~v~~~~~~--------------------------------- 882 (993)
.+..+. -|+++....+|+|++++.+. .|+|-.|.+++..
T Consensus 903 ~~~tPEekLLraIFGeka~~vkDtSLrvp~G~--~G~Vidv~~f~r~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 980 (2890)
T PRK09603 903 IKSTPEERLLRAIFGDKAGHVVNKSLYCPPSL--EGTVIDVKVFTKKGYEKDARVLSAYEEEKAKLDMEHFDRLTMLNRE 980 (2890)
T ss_pred CCCChHHHHHHHHhcccccccccCceecCCCC--cEEEEEEEEecccccchhHHHHHHHHHHHHHHhHhhHHHHHHHHHH
Confidence 655432 16788888999999998888 9999988876521
Q ss_pred --------------------------------------------------------------------------------
Q 001943 883 -------------------------------------------------------------------------------- 882 (993)
Q Consensus 883 -------------------------------------------------------------------------------- 882 (993)
T Consensus 981 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k 1060 (2890)
T PRK09603 981 ELLRVSSLLSQAILEEPFSHNGKDYKEGDQIPKEEIASINRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEK 1060 (2890)
T ss_pred HHHhhhhhccccccccccccccccccccccccHHHHhhCCHHHhhhhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence
Q ss_pred -----CC-------CeEEEEEEeeccCCCccccccccCCCcceeeeeecCCCCCCCCCCCcCeEEeCCCCCCCCCchhhh
Q 001943 883 -----NG-------DLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKM 950 (993)
Q Consensus 883 -----~~-------~~~vkv~ir~~R~p~iGDKfasRHGqKGvvs~i~~~~DMPf~~~G~~pDiIiNPhg~PSRMtiGql 950 (993)
.| .+.|||++|+.|+|++|||||||||||||||+|||+|||||++||++||||+||||||||||||||
T Consensus 1061 ~~~~~~gdeL~~Gv~~~VkV~ia~kR~~qvGDK~AgRHGnKGViS~I~p~EDMPfl~dG~~pDIIlNPlGvPSRMnIGQi 1140 (2890)
T PRK09603 1061 LSILEKDDILPNGVIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQI 1140 (2890)
T ss_pred HHHhhcCCcCCCCcceEEEEEEEEeecccccchhhhccCCCeeEEEEEchhcCCCCCCCCCCcEEECCCCCCccccHHHH
Confidence 01 357999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcccccccCCCc
Q 001943 951 IELLGGKAGVSCGRF 965 (993)
Q Consensus 951 ~E~~~gk~~~~~G~~ 965 (993)
+|+++||||+.+|.+
T Consensus 1141 lE~~LG~aa~~lg~~ 1155 (2890)
T PRK09603 1141 LEMHLGLVGKEFGKQ 1155 (2890)
T ss_pred HHHHHHHHHHhcCcC
Confidence 999999999998754
No 12
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=100.00 E-value=5.3e-142 Score=1343.07 Aligned_cols=790 Identities=22% Similarity=0.344 Sum_probs=621.3
Q ss_pred CCccccccccc-ccccccccchHHHHHHHHHHHHH-----hCHHHHHHhcCcccccCCCcEEEEEeeEEEcCCeeccCCC
Q 001943 24 PVKSVVDKFQL-LPEFLKVRGLVKQHLDSFNYFVN-----TGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDGV 97 (993)
Q Consensus 24 ~~~~~~~~~~~-i~~~~~~~~Lv~~hi~SFn~Fi~-----~gl~~ii~~~~~I~~~~~~~~~l~f~~v~i~~P~~~~~~~ 97 (993)
+-...+.+|+. .+..++.++|++.|.+||+||++ +||++++++++||+ +.++++.|+|.++++++|.+
T Consensus 11 ~~~~~R~~f~~~~~~~~~~PdL~~iQ~~Sf~~Fl~~~~~~~GL~~~f~~ifPI~-d~~g~~~lefv~y~l~~Pk~----- 84 (2836)
T PRK14844 11 GAFVPRVSYSRSIDLKDSLLDLVKVQKESYDSFTPKNKGNERLEVIFHTIFPIN-DPLHRATIEFISCRVDDPKY----- 84 (2836)
T ss_pred CCceeeeecccCCcccCCCCCHHHHHHHHHHHHhcCCCccccHHHHHHhcCCeE-CCCCCEEEEEEEEEeCCCCC-----
Confidence 44556667886 55568999999999999999997 69999999999995 55788999999999999998
Q ss_pred CCCCChHHHHhcCCccCceEEEEEEEEE-C-----------Ccc--------cceeeEEeEEEEeeccceeccccccCCC
Q 001943 98 SEKLNPHMCRLSDMTYAAPILVNIEYVQ-G-----------SHT--------EKTTMEKNDVVIGRIPIMLRSCRCVLYG 157 (993)
Q Consensus 98 ~~~l~P~EcR~r~lTYs~~l~v~v~~~~-~-----------~~~--------~~~~i~~~~v~iG~iPIMv~S~~C~L~~ 157 (993)
++.||++|++||++||+|+++++. + .++ .++++++++|++|+||+|+
T Consensus 85 ----~~~Ec~~r~~TYsapl~v~~rL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ikeq~VylGdiPLMT--------- 151 (2836)
T PRK14844 85 ----DESECIKRGITFSAQVIASIRLVIMQDGISLDEYKSIKESGDHSKLATVIKSIEEQEVHFCELPMMT--------- 151 (2836)
T ss_pred ----CHHHHHhcCCcceeeEEEEEEEEEeccccccccccccccccccccccccccceeeeeEEEecCCccC---------
Confidence 589999999999999999999975 1 110 1246678889999999999
Q ss_pred CCHHHHHhcCCCCCCCCcEEEEcCceeEEEEeecccCCEEEEEeCC-----CCc--eEEEEEecCCCcccEEEEEeeCCE
Q 001943 158 KDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVIIDTDK-----KGN--INASVTSSTETVKSKTVIQMEKGK 230 (993)
Q Consensus 158 ~s~~el~~~gE~~~d~GGYFIInG~ERVI~~q~~~~~N~i~~~~~~-----~g~--~~~~v~s~~~~~~~~~~~~~~~g~ 230 (993)
..|+|||||+||||++|++|||+ +|+..+. .|. |.|+++|.++ +|..+..+.++.
T Consensus 152 ---------------~~GTFIING~ERVIVSQL~RSPG-VyF~~~~~kt~~sgk~lysa~IIP~RG--sWLefE~D~kd~ 213 (2836)
T PRK14844 152 ---------------DKGTFIINGVEKVIVSQMHRSPG-VFFDSDKGKTYNSGKLIYSARVIPYRG--SWLDIEFDVKDH 213 (2836)
T ss_pred ---------------CCeEEEEcCcceEEEEcceeCCe-EEEEcccCcccCCCceeEEEEEecCCc--ceEEEEEcCCCe
Confidence 79999999999999999999997 8876432 233 7799998765 688888889999
Q ss_pred EEEEEccccccccHHHHHHHhCCCCHHHHHHHhCCc-------h---------hhH------------------------
Q 001943 231 MYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGRD-------P---------RYS------------------------ 270 (993)
Q Consensus 231 i~~~~~~~~~~IPl~ilLrALg~~sD~eI~~~i~~~-------~---------~~~------------------------ 270 (993)
+|+++++ ++++|+++||||||+ |++||++.++.. . .+.
T Consensus 214 lyvRIDR-kRKiPiT~LLrALGl-s~edIL~~F~~~~~~~~~d~~~~~~~~~e~l~g~~~~~Di~d~~g~vlvdkgrrit 291 (2836)
T PRK14844 214 LYFRIDR-KRKLPISVLLKALGL-SNNDILDRFYEKIKYIKHKDGWKVPFVPDKFKGVRLPFDLMDVEGNVLLKANVRIT 291 (2836)
T ss_pred EEEEecC-CeeeeHHHHHHHhCC-ChHHHHHhhcCceEEEEccCceeeccCHHHHhCCccceeeeccCCCEEEecCcccc
Confidence 9999999 469999999999999 689999977321 0 000
Q ss_pred ----hhhh--------------------h---------------------hHH---H-----------------------
Q 001943 271 ----ALLL--------------------P---------------------SIE---E----------------------- 279 (993)
Q Consensus 271 ----~~l~--------------------~---------------------~l~---~----------------------- 279 (993)
..+. . .+. .
T Consensus 292 ~~~~krlk~~gvkkl~i~~~~l~g~~LaeDIVD~eTGEiL~eagteIT~e~ik~l~~~gi~~i~~l~~d~~~~~~~i~~t 371 (2836)
T PRK14844 292 SRLAKKLYDNELKEYLVPFDSICGLFLAEDLIDSASSTKILSAGESIKLEDIKKLELLSIDEISVLNIDNLSVGPYILNT 371 (2836)
T ss_pred HHHHHHHHHcccCcccCchHhhcCceehhhhcCCCCCeEEEcCCCccCHHHHHHHHHcCCCceeeEeecccccchHHHHH
Confidence 0000 0 000 0
Q ss_pred HHhcCCcCHHHHHHHHhhhcccCCCCCCCCChHHHHHHHHhhhhcC-------CCCCCCC------------CCCcchhh
Q 001943 280 CANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLA-------NVPVHNN------------NFRPKCFY 340 (993)
Q Consensus 280 ~~~~~i~t~~~al~yIg~~~~~~~~~~~~~~~~e~~~~~L~~~ll~-------Hl~~~~~------------~~~~K~~~ 340 (993)
...+...++++|+..|++++|++ ... ..+.|+.++.+.||. .+|.-+. ....+.++
T Consensus 372 L~~D~~~~~e~Al~eIy~~lRpg----e~~-~~e~a~~l~~~~ff~~~~YdLg~vGR~k~N~kl~~~~~~~~~~l~~~Di 446 (2836)
T PRK14844 372 LFLDENMSYQDALYEIYKVLRPG----EVP-VLEIVEEFFRNLFFSPEYYDLSNIGRLKLNSYLGLNYDEDLTVLTHEDI 446 (2836)
T ss_pred HhhcccccHHHHHHHHHHhcCCC----CCC-cHHHHHHHHHHHhcCccccccccchhhhhhhhhccCCCCCCcEecHHHH
Confidence 00123357899999999999987 334 667788888887754 2221110 01112355
Q ss_pred HHHHHHHHHHhhcCCCCCCCcccccceEEcchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCCCcccccccccccch
Q 001943 341 VAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSIT 420 (993)
Q Consensus 341 L~~Mi~kLl~~~~g~~~~DD~D~l~nkRv~~~G~Ll~~lfr~~l~~~~~~ik~~l~~~~~~~~~~~~~~~~~~i~~~~It 420 (993)
+ .++++|+.+..|....||+|||+||||+++|+||+.+||.+|.++.+.++++|... ....+++..+++++.++
T Consensus 447 i-~~i~~Li~l~~g~~~~DDiDhL~NRRvr~vGeLl~~qfr~gl~r~~~~i~e~~~~~-----~~~~~~p~~lin~~~l~ 520 (2836)
T PRK14844 447 I-EIVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSMSTS-----SLDKVSPSDFINPKVLT 520 (2836)
T ss_pred H-HHHHHHHHHhcCCCcccchhhhhccccchHHHHHHHHHHHHHHHHHHHHHHHHhhc-----cccccchhhcccchhHH
Confidence 5 58999999999999999999999999999999999999999999999999998632 12346788889999999
Q ss_pred hhhhhhhccCCCcccccccccccceEEecccccccccccccccCc----cccccccccCCCcCCCCCcccccccCCCCCC
Q 001943 421 VGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSP----QFEKSRKVSGPRALQPSQWGMLCPCDTPEGE 496 (993)
Q Consensus 421 ~~i~~~~aTGnw~~~~~~~q~sG~sq~l~r~N~ls~lshlRri~~----~f~~~~k~~~~R~Lhps~wG~iCPveTPEG~ 496 (993)
+.+++||+| +++||+||++|+||.|+|.||+++ ++.++++.+.+|++||||||||||+|||||+
T Consensus 521 ~~i~~ff~s------------s~LSQfmDQtNpLseltHkRRlsaLGPGGL~r~~a~fevRdvH~shyGRiCPIETPEG~ 588 (2836)
T PRK14844 521 NVLRDFFNS------------SQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQ 588 (2836)
T ss_pred HHHHHHhcc------------cchhhhccCcChhhhhhhcceecccCCCCcccccCCCcccccCccccccccCCCCCCCC
Confidence 999999976 478999999999999999999996 6889999999999999999999999999999
Q ss_pred cchhhhhhccccccccCCCChhHHHHHHhcCCeeccccCccccCCCCceEEEECCeEeeeccChhhHHHHHHHHhhcCCc
Q 001943 497 ACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKI 576 (993)
Q Consensus 497 ~cGLv~~LA~~a~V~~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~~~V~~nG~~iG~~~~~~~~~~~lR~~rr~g~i 576 (993)
|||||++||.+|+|+.. |+.. ..|....||.+- +.+
T Consensus 589 NiGLI~SLA~yarIn~~-------------Gfie------------tPy~kV~~g~v~---~~i---------------- 624 (2836)
T PRK14844 589 NIGLINSLAIYARINKY-------------GFIE------------SPYRKVVNRVVT---DQI---------------- 624 (2836)
T ss_pred cccchhhhhhheeccCC-------------ceEe------------CCcEEEEcCcCc---ccc----------------
Confidence 99999999999999863 3321 122222455421 110
Q ss_pred CceeEEEeccc-CceEEEecCCCeeeeeEEEeecCcccchhhhHHhhhccCcchhhhhccCceeeeccccccceEEEeec
Q 001943 577 GEFVSVFVNEK-QRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYE 655 (993)
Q Consensus 577 ~~~v~i~~~~~-~~~i~I~td~gR~~RPl~~v~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~iE~id~~Eq~~~~Ia~~~ 655 (993)
.|+... .....|.... -|+ -++|.. .. ..+.-- ..+++..+ .+
T Consensus 625 -----~ylsa~~E~~~~Ia~a~----~~~--~~~~~~-~~--------------------~~v~~R--~~~ef~~~--~~ 668 (2836)
T PRK14844 625 -----EYLSAIDEGLYYIADTS----AKL--DENNCF-VD--------------------DMLYCR--YAGSFVMV--SS 668 (2836)
T ss_pred -----cccChHHhcCcEEEeCC----ccC--CCCCcc-cC--------------------CeEEEe--cCCceEEe--cH
Confidence 011111 1222232221 000 011110 00 000000 00111111 11
Q ss_pred CCCCCCcceeeecCceeecccccccCCCCCCCCCcccccccccCCCcccee-----------------------------
Q 001943 656 GDATPDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIA----------------------------- 706 (993)
Q Consensus 656 ~~~~~~~th~Ei~p~~ilsv~AslIPF~~hNqspRn~yq~~M~KQa~G~~~----------------------------- 706 (993)
...++++++|.|++|++||||||.+||||+|++||||||||||++..
T Consensus 669 ----~~v~~~dvsp~Q~~SvaasLIPFLEhdDAnRALMGSNMQRQAVPLl~~e~PiVGTG~E~~vA~DSg~~v~A~~~G~ 744 (2836)
T PRK14844 669 ----DQVSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESFVASGSGAVVLAKRDGI 744 (2836)
T ss_pred ----HHceEEEeCcchhhhhHhhcCCccccCccccccccccccccccccccCCCCeEecCcchhhhhcccceEEeccCce
Confidence 23589999999999999999999999999999999999999997531
Q ss_pred --eeec----ccccc---------ceeee----------cCCCcceeechhhh----------hhCCCCCCCCceeEEEE
Q 001943 707 --FNQL----CRMDS---------LLYLL----------VYPQRPLLTTRTIE----------LVGYDKLGAGQNATVAV 751 (993)
Q Consensus 707 --~n~~----~r~D~---------~~y~l----------~ypQ~PlV~t~~~~----------~~~~~~~p~G~N~~VAv 751 (993)
+... .|.+. ..|.| |++|||+|+.+... .+..+|+++|+|++|||
T Consensus 745 V~yVda~kIvI~~~~~~~~~~~~~~~Y~L~ky~RSNQ~TcinQrPiV~~Gd~V~kGdilADG~st~~GELALG~NvlVAf 824 (2836)
T PRK14844 745 VDSSDSNSIVIRAFDKERVNYLDVDIYHLRKFQRSNHNTCINQKPLVCVGDYVKEGDVIADGPAINSGELALGQNLLVAF 824 (2836)
T ss_pred EEEEcCCEEEEEeCCCccccccccceEEeccccccccceeeeecceecCCCEeccCCEeccChhhcccccccccceEEEE
Confidence 1111 11111 23655 77999999988753 35699999999999999
Q ss_pred EecCCCCCCCcEEEecccccccceeEEEEEEEEEEeecccCCccceecC-CCCCCCcchhcccCCCCccccCCceeCCCC
Q 001943 752 MSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILR-PDRTGPGAERMQILDDDGLAAPGEIIKPND 830 (993)
Q Consensus 752 ~~~~Gyn~EDaiiink~~~~rg~~~s~~~~~~~~~~~~~~~~~~e~~~~-p~~~~~~~~~~~~ld~~Gi~~~g~~v~~gd 830 (993)
|||.||||||||+||++++++++|||+|+++|++++++++.|.+|.+.. |+.+. +..++||++|||++|++|++||
T Consensus 825 mpW~GYNfEDAIliSErlv~eD~fTSiHIee~ei~~r~Tk~G~EeITrdIPnv~e---~~lr~LDe~GIV~iGa~V~~GD 901 (2836)
T PRK14844 825 MSWQGYNFEDSIIISSEVVKKDLFTSIHIEEFECVVHDTPLGSEKITRAIPGVNE---ENLYHLDDSGIVKIGTRVGPGY 901 (2836)
T ss_pred eccCCcccccccccchhhccCceeEEEeecceEEEEEeccCCCceecccCCCCCh---HHHhcCCCCCCeecCCEECCCC
Confidence 9999999999999999999999999999999999999998887666554 88753 6899999999999999999999
Q ss_pred EEEEEecCCCCCCCCCC------CCCCCCcccccceEEeeCCCCCceEEEEEEEeeCC----------------------
Q 001943 831 VYINKESPLETRGSIMS------PTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDK---------------------- 882 (993)
Q Consensus 831 ili~k~~~~~~~~~~~~------~~~~~~~~~~~~s~~~~~~e~~~~~v~~v~~~~~~---------------------- 882 (993)
|||||++|+.+.+.++. -|+++....+|+|++++.+. .|+|-.|.+++..
T Consensus 902 ILVGKvtPk~e~~~tPEekLL~aIFGek~~~vkdtSLrvp~G~--~G~Vidv~~f~~~~~~~~~~~~~~~~~~~~~~~~~ 979 (2836)
T PRK14844 902 ILVGKVTPKPSLSLPPETKLLMTIFGEKSFDCADSSLYTSPDV--EGTVIDVQVFTRRGVEENERALLIKQKEINDFEKE 979 (2836)
T ss_pred EEEEeecCCCCCCCCHHHHHHHHHhCCcccccccCceecCCCC--CEEEEEEEEEcccccccchhhhhhhhhhhhhhhhh
Confidence 99999999987655432 16788888999999999888 9999988876532
Q ss_pred -------------------------------------------------------------------------------C
Q 001943 883 -------------------------------------------------------------------------------N 883 (993)
Q Consensus 883 -------------------------------------------------------------------------------~ 883 (993)
.
T Consensus 980 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~ 1059 (2836)
T PRK14844 980 RDYIINVTSEYFYDELKKLLINSGSQDREKFDSIEREQWWGIGLKNQSISEQVKSLKKDFDEKVSHAIAQFKRKVEKLHE 1059 (2836)
T ss_pred hhhhhhhhhhhhhhhhhhhhcccccccHHHHhhccHHhhhhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 0
Q ss_pred C-------CeEEEEEEeeccCCCccccccccCCCcceeeeeecCCCCCCCCCCCcCeEEeCCCCCCCCCchhhhHHhhcc
Q 001943 884 G-------DLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGG 956 (993)
Q Consensus 884 ~-------~~~vkv~ir~~R~p~iGDKfasRHGqKGvvs~i~~~~DMPf~~~G~~pDiIiNPhg~PSRMtiGql~E~~~g 956 (993)
| .+.|||+|+++|++++|||||||||||||||+|+|.|||||++||+++|||+||+|+||||||||++|+|+|
T Consensus 1060 gdeL~~gv~~~VkVyia~KRkiqvGDKmAGRHGNKGVIS~IlP~eDMPyL~DGtpvDIvLNPLGVPSRMNvGQilE~hLG 1139 (2836)
T PRK14844 1060 GYDLPQGVSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVG 1139 (2836)
T ss_pred CCcCCCCCceEEEEEEEEeecCCccccccccCCCCceEeEEcccCCCCcCCCCCCceEEeCCCCCCccccHHHHHHHHHH
Confidence 1 257999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccCCC
Q 001943 957 KAGVSCGR 964 (993)
Q Consensus 957 k~~~~~G~ 964 (993)
|||..+|.
T Consensus 1140 ~A~~~L~~ 1147 (2836)
T PRK14844 1140 WACKKLGE 1147 (2836)
T ss_pred HHHhhhhh
Confidence 99999983
No 13
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated
Probab=100.00 E-value=1.3e-124 Score=1108.20 Aligned_cols=438 Identities=44% Similarity=0.718 Sum_probs=408.2
Q ss_pred ceEEEECCeEeeeccChhhHHHHHHHHhhcCCcCceeEEEecccCceEEEecCCCeeeeeEEEeecCcccchhhhHHhhh
Q 001943 544 SFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELL 623 (993)
Q Consensus 544 ~~~V~~nG~~iG~~~~~~~~~~~lR~~rr~g~i~~~v~i~~~~~~~~i~I~td~gR~~RPl~~v~~~~~~~~~~~~~~~~ 623 (993)
.++|||||+|+|++++|.+|++.||.+||.|.++.+++|+++...++|+|+||+||++|||++|++|++.++++|+++++
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 46899999999999999999999999999999999999999988899999999999999999999999999999999998
Q ss_pred ccCcchhhhhccCceeeeccccccceEEEeecCCCCCCcceeeecCceeecccccccCCCCCCCCCcccccccccCCCcc
Q 001943 624 DGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMG 703 (993)
Q Consensus 624 ~~~~~~~~~l~~g~iE~id~~Eq~~~~Ia~~~~~~~~~~th~Ei~p~~ilsv~AslIPF~~hNqspRn~yq~~M~KQa~G 703 (993)
.++.+|+||+++|.|||||++||++++||+.++++...+||+||+|+++||++||+|||+||||||||||||||+|||||
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 88889999999999999999999999999999998777899999999999999999999999999999999999999999
Q ss_pred ceeeeeccccccceeeecCCCcceeechhhhhhCCCCCCCCceeEEEEEecCCCCCCCcEEEecccccccceeEEEEEEE
Q 001943 704 NIAFNQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKY 783 (993)
Q Consensus 704 ~~~~n~~~r~D~~~y~l~ypQ~PlV~t~~~~~~~~~~~p~G~N~~VAv~~~~Gyn~EDaiiink~~~~rg~~~s~~~~~~ 783 (993)
++++|+..|+|++.|+|+|||+|||+|+.++.++++++|+|+|++||||||+||||||||||||+|+|||||||+||++|
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---CcchhcccCCCCccccCCceeCCCCEEEEEecCCCCCCCCCCCCCCCCcccccce
Q 001943 784 TAINQKYANSTSDRILRPDRTG---PGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSAR 860 (993)
Q Consensus 784 ~~~~~~~~~~~~e~~~~p~~~~---~~~~~~~~ld~~Gi~~~g~~v~~gdili~k~~~~~~~~~~~~~~~~~~~~~~~~s 860 (993)
+++++++..+..+.+..|+... .....|++||+||||++|++|++|||||||++|..+.++. ..++......+|+|
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 9999887767677887776421 1224699999999999999999999999999997543221 11112223468999
Q ss_pred EEeeCCCCCceEEEEEEEeeCCCCCeEEEEEEeeccCCCccccccccCCCcceeeeeecCCCCCCCCCCCcCeEEeCCCC
Q 001943 861 QTYKGPDGETCVVDRVALCSDKNGDLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHG 940 (993)
Q Consensus 861 ~~~~~~e~~~~~v~~v~~~~~~~~~~~vkv~ir~~R~p~iGDKfasRHGqKGvvs~i~~~~DMPf~~~G~~pDiIiNPhg 940 (993)
++++.+| .|+||+|.++.+.++.+.|||++|+.|+|+||||||||||||||||+|||+||||||+||++|||||||||
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 99999999998888889999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCchhhhHHhhcccccccCCCceeeecCCCCCCCCCCHhhHhhhCC
Q 001943 941 FPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADTVESIRCFFP 989 (993)
Q Consensus 941 ~PSRMtiGql~E~~~gk~~~~~G~~~d~TpF~~~~~~~~~~~~i~~~~~ 989 (993)
||||||||||+|+++||||++.|.+.|+|||++ .++++|+..|.
T Consensus 401 ~PSRMTiGql~E~~~gk~~~~~g~~~d~t~F~~-----~~~~~~~~~L~ 444 (605)
T PRK07225 401 IPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSG-----EDEEDLREALE 444 (605)
T ss_pred ccccCcHHHHHHHHHHHHHHhcCceEeecCCCC-----chHHHHHHHHH
Confidence 999999999999999999999999999999999 88999987763
No 14
>TIGR03670 rpoB_arch DNA-directed RNA polymerase subunit B. This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.
Probab=100.00 E-value=3.3e-124 Score=1103.68 Aligned_cols=435 Identities=45% Similarity=0.743 Sum_probs=405.4
Q ss_pred EEECCeEeeeccChhhHHHHHHHHhhcCCcCceeEEEecccCceEEEecCCCeeeeeEEEeecCcccchhhhHHhhhccC
Q 001943 547 VIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGV 626 (993)
Q Consensus 547 V~~nG~~iG~~~~~~~~~~~lR~~rr~g~i~~~v~i~~~~~~~~i~I~td~gR~~RPl~~v~~~~~~~~~~~~~~~~~~~ 626 (993)
|||||+|+|++++|.+|++.||.+||.|.++.+++|+++...++|+|+||+||++|||++|++|++.++++|++.++.+.
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 79999999999999999999999999999999999999988899999999999999999999999999999999998777
Q ss_pred cchhhhhccCceeeeccccccceEEEeecCCCCCCcceeeecCceeecccccccCCCCCCCCCcccccccccCCCcccee
Q 001943 627 RSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIA 706 (993)
Q Consensus 627 ~~~~~~l~~g~iE~id~~Eq~~~~Ia~~~~~~~~~~th~Ei~p~~ilsv~AslIPF~~hNqspRn~yq~~M~KQa~G~~~ 706 (993)
.+|++|+++|+|||||++||+++.||+.++++...+||+||+|+++||++||+|||+||||||||||||||+|||||+++
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 89999999999999999999999999999998778999999999999999999999999999999999999999999999
Q ss_pred eeeccccccceeeecCCCcceeechhhhhhCCCCCCCCceeEEEEEecCCCCCCCcEEEecccccccceeEEEEEEEEEE
Q 001943 707 FNQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAI 786 (993)
Q Consensus 707 ~n~~~r~D~~~y~l~ypQ~PlV~t~~~~~~~~~~~p~G~N~~VAv~~~~Gyn~EDaiiink~~~~rg~~~s~~~~~~~~~ 786 (993)
+|+..|+|+++|+|+|||+|||+|+.++.++++++|+|+||+||||||+||||||||||||+|+|||+|||+||++|+++
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 eecccCCccceecCCCCC---CCcchhcccCCCCccccCCceeCCCCEEEEEecCCCCCCCCCCCCCCCCcccccceEEe
Q 001943 787 NQKYANSTSDRILRPDRT---GPGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTY 863 (993)
Q Consensus 787 ~~~~~~~~~e~~~~p~~~---~~~~~~~~~ld~~Gi~~~g~~v~~gdili~k~~~~~~~~~~~~~~~~~~~~~~~~s~~~ 863 (993)
++++..+..|.+..|+.. ......|++||+||||++|++|++|||||||++|..+.+. ...++.+....+|.|+++
T Consensus 241 ~~~~~~~~~e~~~~p~~~~~~~~~~~~~~~LD~dGi~~~G~~v~~gdiligk~~p~~~~~~-~~~~~~~~~~~~d~s~~~ 319 (599)
T TIGR03670 241 ERRYPGGQEDRFEIPEPDVRGYRGEEAYKHLDEDGIVYPEVEVKGGDVLIGKTSPPRFLEE-LRELGLVTERRRDTSVTV 319 (599)
T ss_pred eeccCCCCceEEecCCchhccccchhhhccCCCCCCcCCCcEeCCCCEEEEEecCCCCccc-hhhhccccccCceEEEEe
Confidence 987776666777767532 1122468999999999999999999999999999754322 111112233468999999
Q ss_pred eCCCCCceEEEEEEEeeCCCCCeEEEEEEeeccCCCccccccccCCCcceeeeeecCCCCCCCCCCCcCeEEeCCCCCCC
Q 001943 864 KGPDGETCVVDRVALCSDKNGDLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPS 943 (993)
Q Consensus 864 ~~~e~~~~~v~~v~~~~~~~~~~~vkv~ir~~R~p~iGDKfasRHGqKGvvs~i~~~~DMPf~~~G~~pDiIiNPhg~PS 943 (993)
+.+| .|+||+|.++.++++.+.|||++|+.|+|+||||||||||||||||+|||+||||||+||++||||||||||||
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 CCchhhhHHhhcccccccCCCceeeecCCCCCCCCCCHhhHhhhCC
Q 001943 944 RMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADTVESIRCFFP 989 (993)
Q Consensus 944 RMtiGql~E~~~gk~~~~~G~~~d~TpF~~~~~~~~~~~~i~~~~~ 989 (993)
|||||||+|+++||||+++|.+.|+|||++ .++++++..|.
T Consensus 398 RMTiGqllE~~~gk~~~~~g~~~d~t~F~~-----~~~~~~~~~L~ 438 (599)
T TIGR03670 398 RMTVGQLLEMIAGKVAALEGRRVDGTPFEG-----EPEEELRKELL 438 (599)
T ss_pred cccHHHHHHHHHHHHHHhcCCEEEeCCCCC-----ccHHHHHHHHH
Confidence 999999999999999999999999999999 88999887764
No 15
>PRK09606 DNA-directed RNA polymerase subunit B''; Validated
Probab=100.00 E-value=2e-107 Score=959.12 Aligned_cols=486 Identities=33% Similarity=0.591 Sum_probs=430.9
Q ss_pred cccccccccccccccchHHHHHHHHHHHHHhCHHHHHHhcCcccccCCCcEEEEEeeEEEcCCeeccCC-CCCCCChHHH
Q 001943 28 VVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDG-VSEKLNPHMC 106 (993)
Q Consensus 28 ~~~~~~~i~~~~~~~~Lv~~hi~SFn~Fi~~gl~~ii~~~~~I~~~~~~~~~l~f~~v~i~~P~~~~~~-~~~~l~P~Ec 106 (993)
+++.|.++++||+.++|++|||+|||+|+++||++++++.+||+...++.+.|+|+++++++|++.+++ ...+++|+||
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 357899999999999999999999999999999999999999987666778999999999999987655 5678999999
Q ss_pred HhcCCccCceEEEEEEEEECCcccceeeEEeEEEEeeccceeccccccCCCCCHHHHHhcCCCCCCCCcEEEEcCceeEE
Q 001943 107 RLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVL 186 (993)
Q Consensus 107 R~r~lTYs~~l~v~v~~~~~~~~~~~~i~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~gE~~~d~GGYFIInG~ERVI 186 (993)
|+|++||+|+++|+|.++.++ .....+++++|+|||||+|++|||++++++||++.||||+|+||||||||+||||
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---CceEEEEEecCCCcc-cEEEEEeeCCEEEEEEccccccccHHHHHHHhCCCCHHHHHHH
Q 001943 187 LIQEQLSKNRVIIDTDKK---GNINASVTSSTETVK-SKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQM 262 (993)
Q Consensus 187 ~~q~~~~~N~i~~~~~~~---g~~~~~v~s~~~~~~-~~~~~~~~~g~i~~~~~~~~~~IPl~ilLrALg~~sD~eI~~~ 262 (993)
|+|++++||++++++++. ..+.+.++|.....+ +..+++..+|.+++++++...+||++++|||||.+||+||++.
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 237788888776332 2334455679999999986668999999999999999999999
Q ss_pred hCCchhhHhhhhhhHHHHHhcCCcCHHHHHHHHhhhcccCCCCCCCCChHHHHHHHHhhhhcCCCCCCCCCCCcchhhHH
Q 001943 263 VGRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLANVPVHNNNFRPKCFYVA 342 (993)
Q Consensus 263 i~~~~~~~~~l~~~l~~~~~~~i~t~~~al~yIg~~~~~~~~~~~~~~~~e~~~~~L~~~ll~Hl~~~~~~~~~K~~~L~ 342 (993)
++.+..+.+.+..++++ .++.|+++|+.|||++++++. ++.. ..+.|+++|++++|||+|.+..+..+|+++|+
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 97665555555555544 357899999999999998752 3444 67899999999999999976655678999999
Q ss_pred HHHHHHHHhhcCCCCCCCcccccceEEcchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCCCcccccccccccchhh
Q 001943 343 VMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVG 422 (993)
Q Consensus 343 ~Mi~kLl~~~~g~~~~DD~D~l~nkRv~~~G~Ll~~lfr~~l~~~~~~ik~~l~~~~~~~~~~~~~~~~~~i~~~~It~~ 422 (993)
+|++||++++.|.+.+||+|||+||||+++|+||+.+||++|+++++.++..+.+...+. ..+++..+++++.||++
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 24567778888999999
Q ss_pred hhhhhccCCCcccccccccccceEEecccccccccccccccCccccccccccCCCcCCCCCcccccccCCCCCCcchhhh
Q 001943 423 LERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVK 502 (993)
Q Consensus 423 i~~~~aTGnw~~~~~~~q~sG~sq~l~r~N~ls~lshlRri~~~f~~~~k~~~~R~Lhps~wG~iCPveTPEG~~cGLv~ 502 (993)
|++|||||||.. +++|+||+|+|+||+|+|||+||+|+++.+.++.++||+||||||||+||||||||+|||||+
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 hhccccccccCCCChhHHHHHHhcCCeec
Q 001943 503 NLALMTHVTTDEEEGPLISLCYCLGVEDL 531 (993)
Q Consensus 503 ~LA~~a~V~~~~~~~~i~~~l~~~g~~~~ 531 (993)
|||++|+|+.+.+.+++.++|.++|+.++
T Consensus 464 ~La~~a~V~~~~~~~~i~~~l~~lg~~~~ 492 (494)
T PRK09606 464 NFAQMVEISTGEDEEEVKEILKELGVEPE 492 (494)
T ss_pred hhhceEEEeCCCChHHHHHHHHHCcCeeC
Confidence 99999999999888899999999999865
No 16
>PF00562 RNA_pol_Rpb2_6: RNA polymerase Rpb2, domain 6; InterPro: IPR007120 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerases (2.7.7.6 from EC) catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain represents the hybrid-binding domain and the wall domain []. The hybrid-binding domain binds the nascent RNA strand/template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion []. This domain is also involved in binding to Rpb1 and Rpb3 []. Many of the bacterial members contain large insertions within this domain, which are known as dispensable region 2 (DRII).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2Y0S_R 3HKZ_B 2PMZ_R 3H0G_B 3S17_B 1I6H_B 4A3B_B 3K1F_B 4A3I_B 1TWA_B ....
Probab=100.00 E-value=3.7e-86 Score=755.13 Aligned_cols=303 Identities=44% Similarity=0.707 Sum_probs=252.9
Q ss_pred cccccccCCCCCCCCCcccccccccCCCccceeeeeccccccceeeecCCCcceeech-hhhhhC---------CCCCCC
Q 001943 674 GVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTR-TIELVG---------YDKLGA 743 (993)
Q Consensus 674 sv~AslIPF~~hNqspRn~yq~~M~KQa~G~~~~n~~~r~D~~~y~l~ypQ~PlV~t~-~~~~~~---------~~~~p~ 743 (993)
||+|++|||++|||||||+|||||+|||||++.+|+..|+|+.. +|||+|||+|+ .++..+ ++|+|+
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 99999999999 677777 999999
Q ss_pred CceeEEEEEecCCCCCCCcEEEecccccccceeEEEEEEEEEEeecccCCccceec-CCCCCCCcchhcccCCCCccccC
Q 001943 744 GQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRIL-RPDRTGPGAERMQILDDDGLAAP 822 (993)
Q Consensus 744 G~N~~VAv~~~~Gyn~EDaiiink~~~~rg~~~s~~~~~~~~~~~~~~~~~~e~~~-~p~~~~~~~~~~~~ld~~Gi~~~ 822 (993)
|+|++||||||+||||||||||||++++||+|+|+||++ +++++.++.+..+.+. .|... ....|++||+||||++
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 8888877766645444 33221 2368999999999999
Q ss_pred CceeCCCCEEEEEec-CCCCCCCCCCCCCCCCcccccceEEeeCCCCCceEEEEEEE-------eeCCCCCeEEEEEEee
Q 001943 823 GEIIKPNDVYINKES-PLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVAL-------CSDKNGDLCIKFLIRH 894 (993)
Q Consensus 823 g~~v~~gdili~k~~-~~~~~~~~~~~~~~~~~~~~~~s~~~~~~e~~~~~v~~v~~-------~~~~~~~~~vkv~ir~ 894 (993)
|++|++||+||||++ +..........++++....+|+|++++.+| .|+||+|.+ ..+.++...|+|++|+
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 221110000001223334789999999999 999999999 5667789999999999
Q ss_pred ccCCCccccccccCCCcceeeeeecCCCCCCCCCCCcCeEEeCCCCCCCCCchhhhHHhhcccccccCCCceeeecCCCC
Q 001943 895 TRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEP 974 (993)
Q Consensus 895 ~R~p~iGDKfasRHGqKGvvs~i~~~~DMPf~~~G~~pDiIiNPhg~PSRMtiGql~E~~~gk~~~~~G~~~d~TpF~~~ 974 (993)
.|+|+||||||||||||||||+|||+||||||++|++|||||||||||||||||||+|+++||+|++.|.+.|+|||++
T Consensus 233 ~R~p~iGDKfssRHGqKGVvs~i~~~eDMPft~~G~~pDiIiNPhgiPSRMtiGqllE~~~g~~~~~~g~~~~~t~F~~- 311 (386)
T PF00562_consen 233 TRRPQIGDKFSSRHGQKGVVSKILPQEDMPFTEDGIVPDIIINPHGIPSRMTIGQLLESLLGKAGALNGRFVDATPFDE- 311 (386)
T ss_dssp EEE--TTEEEEETTSEEEEEEEEE-TTTSEEETTSEB-SEEE-GGGSTTTTBTHHHHHHHHHHHHHHSTCEEB-TTTSS-
T ss_pred cccchhHHHHhhhhcCceEEeeeeccccCccccCCCcceeeecccccccccchHHHHhhhhhhhhhccccceecCCCCC-
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCHhhHhhhCC
Q 001943 975 SGHADTVESIRCFFP 989 (993)
Q Consensus 975 ~~~~~~~~~i~~~~~ 989 (993)
.+.++|...|.
T Consensus 312 ----~~~~~i~~~l~ 322 (386)
T PF00562_consen 312 ----SSEEDISELLK 322 (386)
T ss_dssp ----S-HHHHHHHHH
T ss_pred ----cchhhhHhhhh
Confidence 88888887663
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=6.5e-45 Score=382.93 Aligned_cols=147 Identities=45% Similarity=0.837 Sum_probs=125.8
Q ss_pred chHHHHHHHHHHHHHhCHHHHHHhcCcccccC-CCcEEEEEeeEEEcCCeeccCC-CCCCCChHHHHhcCCccCceEEEE
Q 001943 43 GLVKQHLDSFNYFVNTGIRKIVRANDRIVSGI-DPSIFLRFKDVRIGQPSMTVDG-VSEKLNPHMCRLSDMTYAAPILVN 120 (993)
Q Consensus 43 ~Lv~~hi~SFn~Fi~~gl~~ii~~~~~I~~~~-~~~~~l~f~~v~i~~P~~~~~~-~~~~l~P~EcR~r~lTYs~~l~v~ 120 (993)
||++|||+|||||+++||++++++.+||..+. +..+.++|++++|++|++.+.+ ...++||+|||+|++||+|+++|+
T Consensus 1 ~Lv~~qi~SFn~Fl~~gl~~i~~~~~~i~~~~~~~~~~l~~~~~~i~~P~~~~~~~~~~~l~P~ecR~r~~TYs~~l~v~ 80 (203)
T PF04563_consen 1 GLVKHQIDSFNYFLNNGLKEILKEFPPIEFESSNNRISLKFENIRIGKPTYSESDGRERPLYPRECRLRGLTYSAPLYVD 80 (203)
T ss_dssp TTTHHHHHHHHHHHCTSSHHHHSCSSSCEECCCSTTEEEEEEEEEEESESSEHTTSCEEE--HHHHHHTT-B-EEEEEEE
T ss_pred CchHHHHHHHHHHHHCCCHHHhccCCceEecCCcceEEEEeeEEEEeeeeeccccccccCCCHHHHHhcCCCCCCccceE
Confidence 68999999999999999999999999998764 5689999999999999998744 888999999999999999999999
Q ss_pred EEEEECCcccceeeEEeEEEEeeccceeccccccCCCCCHHHHHhcCCCCCCCCcEEEEcCceeEEEEeecc
Q 001943 121 IEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQL 192 (993)
Q Consensus 121 v~~~~~~~~~~~~i~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~gE~~~d~GGYFIInG~ERVI~~q~~~ 192 (993)
|+++.++. ..+...++.+|+|||||+|++|||++++++|+++.||||+|+||||||||+|||||+|+++
T Consensus 81 i~~~~~~~---~~~~~~~v~iG~iPiMv~S~~C~L~~~~~~~l~~~~E~~~d~GGYFIInG~EkVi~~q~~~ 149 (203)
T PF04563_consen 81 IELTVNNK---KEIKEQEVFIGKIPIMVRSKRCNLNGLSPKELVQLGECPNDPGGYFIINGSEKVIRMQIMR 149 (203)
T ss_dssp EEEEESST---TEEEESEEEEEEEE-BTTTTTSGGGT--HHHHHHTTS-TT---SSEEETTEEEEE-EEEEE
T ss_pred EEEEeecc---ceEEeeEEEEeeCCeEeecceeeCCCCCHHHHHHcCCCCcCCCCEEEECCChhheehhhhh
Confidence 99998872 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=1.7e-26 Score=198.96 Aligned_cols=66 Identities=50% Similarity=0.899 Sum_probs=59.6
Q ss_pred EEecccccccccccccccC--ccccccccccCCCcCCCCCcccccccCCCCCCcchhhhhhccccccc
Q 001943 446 QVLARLSFIGTLGHMTRVS--PQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVT 511 (993)
Q Consensus 446 q~l~r~N~ls~lshlRri~--~~f~~~~k~~~~R~Lhps~wG~iCPveTPEG~~cGLv~~LA~~a~V~ 511 (993)
|+|+|+|++++|||+||++ +++.++.|++.+|+|||||||||||+|||||++|||++|||++|+|+
T Consensus 1 Q~l~r~N~l~~ls~~Rri~~~~~~~~~~~~~~~R~lh~s~~G~iCPveTPEG~~~GLv~~La~~a~I~ 68 (68)
T PF04565_consen 1 QYLDRTNPLSELSHLRRINRLGPLSKESKSTEPRQLHPSQYGRICPVETPEGENCGLVKNLALMARIT 68 (68)
T ss_dssp EE--TSSHHHHHHHHTEEESCSSTSSSSSSSTTTSTTGGGTTTBSSSSS-SSTSTTTEEEBBTT-EE-
T ss_pred CCcccccHHHHHHHHHhcccccccchhhcccccccccccceeEEeecccCCCccEeehheeeeeEEeC
Confidence 8899999999999999999 68999999999999999999999999999999999999999999985
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=2.1e-21 Score=202.05 Aligned_cols=175 Identities=26% Similarity=0.374 Sum_probs=119.3
Q ss_pred cCCEEEEEeCCCCceE-EEEEecCCCcccEEEEE-eeCCEEEEEEccccccccHHHHHHHhCCCCHHHHHHHhCC-chhh
Q 001943 193 SKNRVIIDTDKKGNIN-ASVTSSTETVKSKTVIQ-MEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGR-DPRY 269 (993)
Q Consensus 193 ~~N~i~~~~~~~g~~~-~~v~s~~~~~~~~~~~~-~~~g~i~~~~~~~~~~IPl~ilLrALg~~sD~eI~~~i~~-~~~~ 269 (993)
+.|+|+++++++++.. +++++.....++....+ .++..+.+.......+||+++||||||++||+||++.|+. +...
T Consensus 1 Rsn~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IPi~ilLrALG~~sd~eI~~~i~~~~~~~ 80 (190)
T PF04561_consen 1 RSNGIYVEKDKDGNKIIRSVRSDIISSRGSWHYLEKDKKIIIFSRPKKKFKIPIVILLRALGIESDKEIIELICYSEEDF 80 (190)
T ss_dssp ESSSEEEEE-SSSSSCSSCEEEEECCSSSEEEEEECETTTEEEEETTSSSEEEHHHHHHHTT--STCHHHHHHCCCSTCH
T ss_pred CCCEEEEEEccCCCCeeEEEEeecCCCcceEEEEecCCcEEEEEEcCcccccceEEeehhhcCcCcccccceeecccccc
Confidence 3578999987665533 33333333223333222 3444454555555678999999999999999999999963 3333
Q ss_pred HhhhhhhHHHHHhcCCcCHHHHHHHHhhhcccCCCCCCCCChHHHHHHHH---------hhhhcC-CCCCCCCCCC--cc
Q 001943 270 SALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSIL---------RDVFLA-NVPVHNNNFR--PK 337 (993)
Q Consensus 270 ~~~l~~~l~~~~~~~i~t~~~al~yIg~~~~~~~~~~~~~~~~e~~~~~L---------~~~ll~-Hl~~~~~~~~--~K 337 (993)
......+++.....++.|+++|+.|||++++.. ..+.. ..+.++.+| .+++|+ |++....... .|
T Consensus 81 ~~~~~~~~~~~~~~~~~t~~~al~~i~~~~~~~--~~~~~-~~~~~~~~l~~~y~l~~i~r~~l~~hl~~~~~~~~~~~k 157 (190)
T PF04561_consen 81 EDIEELMLSELEEEEIYTQEQALEYIGKKFRFR--QGKPP-KVEEARNFLQKRYDLGFIGRYKLNKHLGSDEPNENDRLK 157 (190)
T ss_dssp SCSTTTHHHHCCCTSSCSCHHHHHHHHHCCHSS--SSCHC-CHCHHHHHHTTCSSTCCCHHHCCHTTTTSSSSSSSSSCH
T ss_pred cccccccccccccccccccccceeEeccceeee--ccccc-chhhhhcccccccccccccccceeeeeeeeecccccccc
Confidence 333334455555678999999999999944433 12334 667778776 466777 9997764333 49
Q ss_pred hhhHHHHHHHHHHhhcCCCCCCCcccccceEEc
Q 001943 338 CFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLE 370 (993)
Q Consensus 338 ~~~L~~Mi~kLl~~~~g~~~~DD~D~l~nkRv~ 370 (993)
+.+|++|++||+.++.|.+.+||+|||+||||+
T Consensus 158 ~~~l~~m~~~ll~~~~g~~~~Dd~D~l~NkRv~ 190 (190)
T PF04561_consen 158 AEDLGLMIRKLLKLANGECEPDDRDHLGNKRVR 190 (190)
T ss_dssp HHHHHHHHHHHHHHHTTSS-S-STTSCCCEEEE
T ss_pred hhhHHHHHHHHHHHhcCCCCCCCccccCCcCCc
Confidence 999999999999999999999999999999996
No 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=99.71 E-value=2.4e-17 Score=139.54 Aligned_cols=63 Identities=37% Similarity=0.757 Sum_probs=59.5
Q ss_pred EEECCeEeeeccChhhHHHHHHHHhhcCCcCceeEEEecccCceEEEecCCCeeeeeEEEeec
Q 001943 547 VIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADK 609 (993)
Q Consensus 547 V~~nG~~iG~~~~~~~~~~~lR~~rr~g~i~~~v~i~~~~~~~~i~I~td~gR~~RPl~~v~~ 609 (993)
|||||.|+|++++|..|+..||.+||+|.++.++||+++...++|+|+||+||++|||++|+|
T Consensus 1 VFlNG~~iG~~~~p~~l~~~lr~~RR~g~i~~~vsi~~~~~~~ei~I~tD~GR~~RPL~vV~n 63 (63)
T PF04566_consen 1 VFLNGVWIGIHSDPEELVKTLRNLRRSGKISKEVSIVYDIREKEIRINTDAGRLCRPLFVVEN 63 (63)
T ss_dssp EEETTEEEEEESSHHHHHHHHHHHHHTTSS-TTSEEEEETTTTEEEEE-SSCEEEEEEEEESS
T ss_pred CEECCEEEEEEcCHHHHHHHHHHHhhccCCcceeEEEEeccCCEEEEEccCCcccceeEEecC
Confidence 799999999999999999999999999999999999999999999999999999999999985
No 21
>KOG0215 consensus RNA polymerase III, second largest subunit [Transcription]
Probab=98.86 E-value=1.9e-11 Score=142.73 Aligned_cols=441 Identities=8% Similarity=-0.077 Sum_probs=242.3
Q ss_pred cccccccccccccccccchHHHHHHHHHHHHHhCHHHHHHhcCcccccC---CCcEEEEEeeEEEcCCeeccCC-CCCCC
Q 001943 26 KSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGI---DPSIFLRFKDVRIGQPSMTVDG-VSEKL 101 (993)
Q Consensus 26 ~~~~~~~~~i~~~~~~~~Lv~~hi~SFn~Fi~~gl~~ii~~~~~I~~~~---~~~~~l~f~~v~i~~P~~~~~~-~~~~l 101 (993)
....+.|-..|++.+..++++.||.+|+.++..-... .||..+. .++-.+.=.++-|++ ....- ..+-+
T Consensus 95 lky~dirvg~Ps~~~~~~~~~~~i~p~ecrlrd~tys-----a~i~vdieytrg~~~~~~~~v~igr--mpimlrs~rcv 167 (1153)
T KOG0215|consen 95 LKYLDIRVGKPSIEEGNNVTNDNITPHECRLRDMTYS-----APIYVDIEYTRGRQIIAKRDVIIGR--MPIMLRSSKCV 167 (1153)
T ss_pred heeeeeeccCcchhhccccccccCCchheeehhhhcc-----cceeEEEEEecCcceEEeccccccc--chhhhhccccc
Confidence 3445678889999999999999999999998643222 2332221 111111112333322 21111 34455
Q ss_pred ChHHHHhcCCccC-ceEEEEEEEEECCcccceeeEEeEEEEeeccceeccccccCCCCCHHHHHhcCCCCCCCCcEEEEc
Q 001943 102 NPHMCRLSDMTYA-APILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIK 180 (993)
Q Consensus 102 ~P~EcR~r~lTYs-~~l~v~v~~~~~~~~~~~~i~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~gE~~~d~GGYFIIn 180 (993)
.|.+|+.+..-|. +| ..+--.-+..|.-|||+.+.-|.+++...+ -...|||+.+.++||+.+
T Consensus 168 l~~~~e~~~a~~~ecp---------------ldpggyfiv~G~ekViLiqeqlsknrii~~-~~k~~~~~~svtsst~e~ 231 (1153)
T KOG0215|consen 168 LRGKDEEELARLNECP---------------LDPGGYFIVKGTEKVILIQEQLSKNRIIVE-EDKKGNLQASVTSSTHER 231 (1153)
T ss_pred cCCccHHHHHHhccCC---------------CCCCceeEeccceeEEEehhhhhccCeeec-cccCCccccccccceeee
Confidence 6666663322221 11 111122467899999999999999999887 677899999999999999
Q ss_pred CceeEEEEeecccCCEEEEEeCCCCceEEEEEecCC-CcccEEEEEeeCCEEEEEEccccccccHHHHHHHhCCCCHHHH
Q 001943 181 GTEKVLLIQEQLSKNRVIIDTDKKGNINASVTSSTE-TVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEV 259 (993)
Q Consensus 181 G~ERVI~~q~~~~~N~i~~~~~~~g~~~~~v~s~~~-~~~~~~~~~~~~g~i~~~~~~~~~~IPl~ilLrALg~~sD~eI 259 (993)
+++.+|..+....+++...+.+..+..++...+... +...... ...+..|..+--..-..|+.+-+. +-++-
T Consensus 232 kskt~v~~k~~k~ylk~~~~~d~ipiviv~ka~g~~sd~ei~~~--vg~~~~y~~~~~~s~ee~~~~~v~-----tqqqa 304 (1153)
T KOG0215|consen 232 KSKTYVTTKKGKYYLKHNSFTDDIPIVIVLKAMGLESDQEIVQL--VGGDSKYQDIFAPSLEECVSLGVY-----TQQQA 304 (1153)
T ss_pred cceEEEEeccceeeeehhhhhccCCEEEEEeeccccchHHHHHH--hhcchHHHHhhccchhhhhhhhhH-----HHHHH
Confidence 999999999888887766665544432221111111 0000000 011222222111111233333222 22333
Q ss_pred HHHhCCchhhHhhhhhhHHHHHhcCCcCHHHHHHHHhhhcccCCCCCCC---CC-hHH--HHHHHHhhhhcCCCCCCCCC
Q 001943 260 VQMVGRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPP---ND-REG--RAFSILRDVFLANVPVHNNN 333 (993)
Q Consensus 260 ~~~i~~~~~~~~~l~~~l~~~~~~~i~t~~~al~yIg~~~~~~~~~~~~---~~-~~e--~~~~~L~~~ll~Hl~~~~~~ 333 (993)
+++++..-... + .....-.++|++.+...+..-..-++- .+ ... ..+.++.-. -|.....+.
T Consensus 305 l~y~~~kvk~~-------~---~t~~~~~~e~~~~l~~~~lahv~v~~~~~r~K~~yi~~m~rr~~~a~--l~~~~~ddr 372 (1153)
T KOG0215|consen 305 LEYIGSKVKVK-------R---GTTPTKDEEALEVLSTTVLAHVPVPDLNFRMKAIYIGLMVRRVIQAM--LNKLAMDDR 372 (1153)
T ss_pred HHHhhheEEec-------c---CCCCCchHHHHHHHHhhheeceeccCCCCcceeehHHHHHHHHHHHH--hCcccccch
Confidence 33331000000 0 001112356666666555432211111 00 111 111222111 122211111
Q ss_pred CCcchhhHHHHHHHHHHhhcCCCCCCCcccccceEEcchHHHHHHHHHHHHHHHH--H-HHHHHHHhHhcCCCCCCCccc
Q 001943 334 FRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMI--S-EVQKTVDIILSKPSRSSRFDL 410 (993)
Q Consensus 334 ~~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~nkRv~~~G~Ll~~lfr~~l~~~~--~-~ik~~l~~~~~~~~~~~~~~~ 410 (993)
..-+-..|.+|. .|+.+..+.---++.+.|++.+-...+.++..++-++++.+. + .+-..+.++++..+. ++
T Consensus 373 d~~gnkrlelag-qllsllfeD~fk~~n~e~k~~~dk~l~k~~ra~~fD~~~~~n~~~~~it~~l~ra~stgnw----~i 447 (1153)
T KOG0215|consen 373 DYVGNKRLELAG-QLLSLLFEDLFKRFNSELKKNIDKILKKPIRAQEFDALKHLNVRANMITSGLERAISTGNW----SI 447 (1153)
T ss_pred hhhccchHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHhcchhhhhhhHHHHHHHHHHHHHHHHHHHHhhcCch----HH
Confidence 122223355444 445555666666788888888888888888888888888874 1 222233444433322 22
Q ss_pred ccccccccchhhhhhhhccCCCcccccccccccceEEecccccccccccccccCccccccccccCCCcCCCCCccccccc
Q 001943 411 SQFIVRDSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPC 490 (993)
Q Consensus 411 ~~~i~~~~It~~i~~~~aTGnw~~~~~~~q~sG~sq~l~r~N~ls~lshlRri~~~f~~~~k~~~~R~Lhps~wG~iCPv 490 (993)
.. ++..-++...--+-.|++|....+-...+++.++..+..+-|....--++..++.+..+..-.+-.+++.|+-|||-
T Consensus 448 Kr-frmer~gvt~VlsrlSyisaLgmmtri~s~fektrkvsgprSlq~sqwgmlcp~dtpegeacglvknlalmthittd 526 (1153)
T KOG0215|consen 448 KR-FRMERAGVTQVLSRLSYISALGMMTRINSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITTD 526 (1153)
T ss_pred HH-hhhhhccceeeehhhhhhhhhhhheehhhhheeehhccCccccChhhcccccCCCCCCccccccccchHHHhcccCC
Confidence 21 11111111111223456665433333457888887776666666666666677888777888899999999999999
Q ss_pred CCCCCCcchhhhhhccccccccCC
Q 001943 491 DTPEGEACGLVKNLALMTHVTTDE 514 (993)
Q Consensus 491 eTPEG~~cGLv~~LA~~a~V~~~~ 514 (993)
++|++..|++.+..+...++..+.
T Consensus 527 ~ee~pi~~~~~k~gv~di~~v~~~ 550 (1153)
T KOG0215|consen 527 SEEKPILKLCYKLGVEDIHVVSGR 550 (1153)
T ss_pred CCcchhHHHHHHhcceeeeeeccc
Confidence 999999999999999999887653
No 22
>PF04567 RNA_pol_Rpb2_5: RNA polymerase Rpb2, domain 5; InterPro: IPR007647 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Domain 5, is also known as the external 2 domain [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3S17_B 1I6H_B 4A3B_B 3K1F_B 4A3I_B 1TWA_B 3S14_B 3S15_B 2NVX_B 3M3Y_B ....
Probab=98.81 E-value=2.2e-09 Score=86.24 Aligned_cols=41 Identities=46% Similarity=0.818 Sum_probs=33.3
Q ss_pred hhhhhccCceeeeccccccceEEEeecCCC-------CCCcceeeecC
Q 001943 629 FDDFLREGLIEYLDVNEENNALIALYEGDA-------TPDTTHIEIEP 669 (993)
Q Consensus 629 ~~~~l~~g~iE~id~~Eq~~~~Ia~~~~~~-------~~~~th~Ei~p 669 (993)
|++|+++|+|||||++||++++||++++++ ...||||||||
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 789999999999999999999999998665 34699999998
No 23
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]
Probab=97.90 E-value=3.6e-05 Score=96.39 Aligned_cols=74 Identities=23% Similarity=0.374 Sum_probs=60.3
Q ss_pred CcceeeecCceeecccccccCCCCCCCCCcccccccccCCCccceeeeeccccccceeeecCCCcceeechhhhhhCCCC
Q 001943 661 DTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDK 740 (993)
Q Consensus 661 ~~th~Ei~p~~ilsv~AslIPF~~hNqspRn~yq~~M~KQa~G~~~~n~~~r~D~~~y~l~ypQ~PlV~t~~~~~~~~~~ 740 (993)
..+|++++|.++.|+.+++|||.+|.++.|++|+++|+|||+| |..+..|||.|+ ++..+-.
T Consensus 525 ~~~~~dv~~~~~~~~~~~~~P~l~~dd~~~~l~~~~mqr~~~~----------------l~~~~~~lv~tG-~E~~~a~- 586 (1060)
T COG0085 525 GVDYMDVSPKQVVSVGRSLIPFLEHDDANRALMGSNMQRQAVP----------------LLRTEAPLVGTG-MEYLDAE- 586 (1060)
T ss_pred cccceeccceEEeccccccCceeEEcCchHhhhhhhhhhhccc----------------ccccccccccCC-ceeeccc-
Confidence 3678999999999999999999999999999999999999999 457889999999 6654311
Q ss_pred CCCCceeEEEEEec
Q 001943 741 LGAGQNATVAVMSY 754 (993)
Q Consensus 741 ~p~G~N~~VAv~~~ 754 (993)
---|++||.-++
T Consensus 587 --e~~~~~ia~~~~ 598 (1060)
T COG0085 587 --DSGAAVIAKRPG 598 (1060)
T ss_pred --cccceeEeccCC
Confidence 123556665443
No 24
>PF06883 RNA_pol_Rpa2_4: RNA polymerase I, Rpa2 specific domain ; InterPro: IPR009674 This domain is found between domain 3 and domain 5, but shows no homology to domain 4 of Rpb2. The external domains in multisubunit RNA polymerase (those most distant from the active site) are known to demonstrate more sequence variability [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=97.52 E-value=0.00011 Score=61.41 Aligned_cols=49 Identities=18% Similarity=0.268 Sum_probs=41.5
Q ss_pred eeecc--ChhhHHHHHHHHhhcC--CcCceeEEEecc-----cCceEEEecCCCeeee
Q 001943 554 LGKHR--RPKCFADVMRKLRRAG--KIGEFVSVFVNE-----KQRCVYIASDGGRVCR 602 (993)
Q Consensus 554 iG~~~--~~~~~~~~lR~~rr~g--~i~~~v~i~~~~-----~~~~i~I~td~gR~~R 602 (993)
|||++ ....+++.||.+|..| .+|.+.+|.+.+ ..|++||||+++|++|
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 47765 5688999999999887 689999997743 3599999999999998
No 25
>KOG0214 consensus RNA polymerase II, second largest subunit [Transcription]
Probab=95.43 E-value=0.0044 Score=75.38 Aligned_cols=212 Identities=8% Similarity=-0.117 Sum_probs=127.1
Q ss_pred CCCCCceeEEEEEecCCCCCCCcEEEecccccccceeEEEEEEEEEEeecccCCccceecC--CCCCC-CcchhcccCCC
Q 001943 740 KLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILR--PDRTG-PGAERMQILDD 816 (993)
Q Consensus 740 ~~p~G~N~~VAv~~~~Gyn~EDaiiink~~~~rg~~~s~~~~~~~~~~~~~~~~~~e~~~~--p~~~~-~~~~~~~~ld~ 816 (993)
..+.+.++-++.+.+.++..++...-|--..+.+++++++...|. +.++. .+.... |+... ++...-...-.
T Consensus 734 l~~~eL~aG~NaiVAi~~~~GYNqEDsvimn~s~v~rg~FrS~~~---RsYk~--q~~~~~~~~ee~~~~~~~~~~~~mr 808 (1141)
T KOG0214|consen 734 LRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSVDRGLFRSFFI---RSYKD--QEHKKDQGPEEIFEEPPRGEGRGMR 808 (1141)
T ss_pred hhhhhcccccceEEEEecccCccHHHHHHHHhhhhhcchhhhhhh---hHHHh--hhhhccccccccccccccccccccc
Confidence 456799999999999999999999999999999999999875443 33321 222222 22211 00000000111
Q ss_pred CccccCCceeCCCCEEEEEecCCCCCCCCCCCCCCCCcccccceEEeeCCC------CCceEEEEEEEeeCCCCCeEEEE
Q 001943 817 DGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPD------GETCVVDRVALCSDKNGDLCIKF 890 (993)
Q Consensus 817 ~Gi~~~g~~v~~gdili~k~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~e------~~~~~v~~v~~~~~~~~~~~vkv 890 (993)
+|...-.. ..|=+-.| +.....+ ....+..++.-...+ .-.++..++.+..++.| ...+|
T Consensus 809 ~~~~dkLd--ddG~i~~G--~~vs~~D---------v~iGk~t~~~~~~~~~~~~~~~~t~~d~s~~Lr~~e~G-ivd~V 874 (1141)
T KOG0214|consen 809 NGKYDKLD--DDGIIMPG--SRVSGGD---------VLIGKTTPQPAKEDESGPEDRLYTKRDHSTKLRHTERG-IVDQV 874 (1141)
T ss_pred cccccccc--ccCCcccc--ceeecCC---------EEeccccCCcccchhccccccccccccceeecccCCcc-eEEEE
Confidence 11110000 01101111 0000000 000011111111111 01346667777777666 55555
Q ss_pred EEeeccCCCccccccccCCCcceeeeeecCCCCCCCCCCCcCeEEeCCCCCCCCCchhhhHHhhcccccccCCCceeeec
Q 001943 891 LIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSA 970 (993)
Q Consensus 891 ~ir~~R~p~iGDKfasRHGqKGvvs~i~~~~DMPf~~~G~~pDiIiNPhg~PSRMtiGql~E~~~gk~~~~~G~~~d~Tp 970 (993)
.+.. .+.|+||+.+|++++-+..+-...++++-.-|+.++++.+++.-+++|+|-..++.-.-..-+..+-=+...|
T Consensus 875 ~vt~---n~~G~kF~kv~vr~~ripqiGDKfasrHgqKG~ig~~~~qedmpft~eGi~pDiiiNPhaiPSRmtig~liEc 951 (1141)
T KOG0214|consen 875 WVTK---NSEGPKFVKVRVRQVRIPQIGDKFASRHGQKGTIGITYRQEDMPFTIEGIVPDIIINPHAIPSRMTIGQLIEC 951 (1141)
T ss_pred EEec---CCCCCceeEEEEeecccccccchhccccccCccccceeecCCCCccccCCCcceEECcccCccccchhhhHHH
Confidence 5555 8999999999999999999999999999999999999999999999999988877655544444433344555
Q ss_pred CCC
Q 001943 971 FGE 973 (993)
Q Consensus 971 F~~ 973 (993)
+.+
T Consensus 952 ~lg 954 (1141)
T KOG0214|consen 952 LLG 954 (1141)
T ss_pred hhh
Confidence 543
No 26
>PHA03394 lef-8 DNA-directed RNA polymerase subunit beta-like protein; Provisional
Probab=94.59 E-value=0.052 Score=66.10 Aligned_cols=79 Identities=25% Similarity=0.302 Sum_probs=57.7
Q ss_pred CCeEEEEEEeeccCCCccccccccCCCcceeeeeecCCCCCC--CCCCCcCeEEeCCCCCCCCCchhhhHHhhccccccc
Q 001943 884 GDLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPF--SERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVS 961 (993)
Q Consensus 884 ~~~~vkv~ir~~R~p~iGDKfasRHGqKGvvs~i~~~~DMPf--~~~G~~pDiIiNPhg~PSRMtiGql~E~~~gk~~~~ 961 (993)
+...+|+++-..=.=-.|=|.||=||||||+.. .||+-= .|||+.|-|.+.|.++-||.|. ++-+--|-...
T Consensus 694 d~v~lKl~~Vtst~dLeGlKICgIHGQKGVln~---seDLtew~aeDg~~aQIclSPiSyLsRQtn---f~~~~~Ky~v~ 767 (865)
T PHA03394 694 DTVYLKIRLVTSTSDLEGLKICGIHGQKGVLNG---SEDLTEWMAEDGTHAQICLSPISYLSRQTN---FDDIERKYVVR 767 (865)
T ss_pred CEEEEEEEEEEEecCcceeEEeeecccccccCC---cchhhhhhccCCCcceEEechHHhhccccc---cccCceEEEEE
Confidence 355677766555555569999999999999864 566542 3799999999999999999986 34444555566
Q ss_pred CCCceee
Q 001943 962 CGRFHYG 968 (993)
Q Consensus 962 ~G~~~d~ 968 (993)
-|.+.|.
T Consensus 768 gg~~~~~ 774 (865)
T PHA03394 768 GGDHSDP 774 (865)
T ss_pred CCCcCCC
Confidence 5655443
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=53.90 E-value=19 Score=44.30 Aligned_cols=34 Identities=18% Similarity=0.200 Sum_probs=28.2
Q ss_pred CCCcccccceEEcchHHHHHHHHHHHHHHHHHHH
Q 001943 358 MDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEV 391 (993)
Q Consensus 358 ~DD~D~l~nkRv~~~G~Ll~~lfr~~l~~~~~~i 391 (993)
.=.+|+|+||=+.-...||...++..++.+...+
T Consensus 210 ~Y~IDsLsNKiIYkh~yLl~l~y~~~L~~~~~~~ 243 (748)
T PF04941_consen 210 NYSIDSLSNKIIYKHSYLLELTYKPILKKYENLI 243 (748)
T ss_pred CceecccccceeeCHHHHHHHHHHHHHHHHHHHH
Confidence 3489999999999999999999988777665544
No 28
>PF14251 DUF4346: Domain of unknown function (DUF4346)
Probab=45.38 E-value=11 Score=36.29 Aligned_cols=13 Identities=62% Similarity=0.984 Sum_probs=10.4
Q ss_pred CCCCCCCcEEEEc
Q 001943 168 ECPLDPGGYFIIK 180 (993)
Q Consensus 168 E~~~d~GGYFIIn 180 (993)
--..||+|||||.
T Consensus 11 ~i~LDp~GYfiI~ 23 (119)
T PF14251_consen 11 FIDLDPAGYFIIY 23 (119)
T ss_pred ccccCCCccEEEE
Confidence 3457899999986
No 29
>PF13533 Biotin_lipoyl_2: Biotin-lipoyl like
Probab=29.81 E-value=38 Score=27.45 Aligned_cols=16 Identities=25% Similarity=0.426 Sum_probs=14.3
Q ss_pred cccCCceeCCCCEEEE
Q 001943 819 LAAPGEIIKPNDVYIN 834 (993)
Q Consensus 819 i~~~g~~v~~gdili~ 834 (993)
.++.|+.|++||+|+-
T Consensus 17 ~V~~G~~VkkGd~L~~ 32 (50)
T PF13533_consen 17 YVKEGQQVKKGDVLLV 32 (50)
T ss_pred EecCCCEEcCCCEEEE
Confidence 5789999999999985
Done!