Query 014847
Match_columns 417
No_of_seqs 187 out of 1395
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 09:05:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014847.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014847hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK07225 DNA-directed RNA poly 100.0 4E-121 8E-126 973.0 30.5 377 1-409 129-603 (605)
2 TIGR03670 rpoB_arch DNA-direct 100.0 1E-120 3E-125 968.1 29.5 377 1-409 123-597 (599)
3 PRK08565 DNA-directed RNA poly 100.0 2E-114 4E-119 976.3 26.9 377 1-409 627-1101(1103)
4 cd00653 RNA_pol_B_RPB2 RNA pol 100.0 2E-110 4E-115 926.1 28.8 370 1-406 402-866 (866)
5 KOG0216 RNA polymerase I, seco 100.0 3E-110 7E-115 880.7 22.5 375 1-408 647-1111(1111)
6 KOG0215 RNA polymerase III, se 100.0 4E-111 8E-116 884.9 11.4 374 1-410 682-1151(1153)
7 COG0085 RpoB DNA-directed RNA 100.0 4E-107 9E-112 891.8 26.2 374 1-410 607-1059(1060)
8 TIGR02013 rpoB DNA-directed RN 100.0 5E-106 1E-110 900.3 24.9 369 1-405 535-1065(1065)
9 PRK00405 rpoB DNA-directed RNA 100.0 4E-104 1E-108 888.5 28.0 370 1-407 578-1107(1112)
10 CHL00001 rpoB RNA polymerase b 100.0 5E-102 1E-106 865.4 25.4 379 1-407 520-1057(1070)
11 CHL00207 rpoB RNA polymerase b 100.0 1.7E-99 4E-104 842.7 26.1 383 1-410 514-1055(1077)
12 KOG0214 RNA polymerase II, sec 100.0 9E-101 2E-105 814.6 11.0 376 1-408 667-1140(1141)
13 PRK09603 bifunctional DNA-dire 100.0 6.8E-92 1.5E-96 811.8 26.9 375 1-411 671-1377(2890)
14 PRK14844 bifunctional DNA-dire 100.0 4.1E-88 9E-93 778.2 25.8 373 1-409 678-1433(2836)
15 PF00562 RNA_pol_Rpb2_6: RNA p 100.0 5.2E-82 1.1E-86 645.6 19.9 286 6-325 1-386 (386)
16 PF04560 RNA_pol_Rpb2_7: RNA p 99.9 1.9E-26 4.2E-31 187.8 4.3 78 327-407 1-81 (81)
17 COG0085 RpoB DNA-directed RNA 96.2 0.0017 3.6E-08 74.3 1.3 60 1-80 533-594 (1060)
18 KOG0214 RNA polymerase II, sec 96.2 0.001 2.3E-08 74.0 -0.4 184 136-352 835-1041(1141)
19 PHA03394 lef-8 DNA-directed RN 69.0 7.2 0.00016 44.1 5.0 21 180-200 708-728 (865)
20 PF04941 LEF-8: Late expressio 68.2 8 0.00017 43.2 5.1 53 142-198 683-736 (748)
21 PF04564 U-box: U-box domain; 24.8 42 0.00091 26.4 1.4 46 269-323 5-52 (73)
22 PF08259 Periviscerokin: Periv 23.7 33 0.00073 18.0 0.4 8 9-16 3-10 (11)
23 PRK00420 hypothetical protein; 20.1 77 0.0017 27.7 2.1 24 353-376 25-49 (112)
No 1
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated
Probab=100.00 E-value=3.7e-121 Score=973.01 Aligned_cols=377 Identities=31% Similarity=0.489 Sum_probs=347.7
Q ss_pred CcccccccccccCCCCCcCCCcccccccccccCCccccccccccchhhcccccccccCccceEeeccccccCCC------
Q 014847 1 MSFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRPLFWILISDCLGRP------ 74 (417)
Q Consensus 1 p~~ilsi~AslIPF~~h~~NqSpRn~yq~~~M~KQamG~~~~n~~~R~D~~~~~l~ypQ~PLV~t~~~d~lg~n------ 74 (417)
|+++||++||+|||+|| ||||||||||| |+|||||++++|+..|+|++.|.|+|||+|||+|+.++.++++
T Consensus 129 p~~ilgv~AslIPF~~h--NQSPRn~yq~~-M~KQa~g~~~~n~~~r~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~p~G~ 205 (605)
T PRK07225 129 PSLILGIGAGMIPYPEH--NASPRITMGAG-MIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQ 205 (605)
T ss_pred CcceeEEEeeccCCCCC--Cccchhhhhhh-hhhcccCccccceeeecCCcccEEeeCCcceEEccchHhhCCCccCCCe
Confidence 78999999999999999 99999999999 8999999999999999999999999999999999998865443
Q ss_pred --------------CCeEEEecceecccceeeEEEEEEEec--------ccccC---------------CCCCCCccccc
Q 014847 75 --------------EDSLVMNQASLECGVFRSESYKAEVDN--------KDIQV---------------KSRPSDDMLNF 117 (417)
Q Consensus 75 --------------EDAiIiNKssidRG~f~s~~Yk~e~~~--------~~~~~---------------~~~~~~g~~~~ 117 (417)
||||||||+|+|||||||++|+++... .+.++ +.+|.||++.+
T Consensus 206 N~iVAvmsy~GYn~EDAiIiNkssidRGlf~s~~~k~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~LD~dGi~~~ 285 (605)
T PRK07225 206 NFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGEERRYPGGQEDRFEIPDKDVRGYRGEEAYRHLDEDGLVNP 285 (605)
T ss_pred eEEEEEECcCCCChhHeeeeehhhhhcCceEEEEEEEEEEEeeecCCCcceEEecCCchhccccChHHhhcCCCCCCccC
Confidence 999999999999999999988765421 11111 23678999999
Q ss_pred cccccccCCeEEEEeccC---------------CceeEEEecCCCceeEEEEEEEeCCCCCeEEEEEEeecccccccccc
Q 014847 118 GKIQSKSGDIVIGKYAEI---------------GADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACL 182 (417)
Q Consensus 118 g~~~v~~GDiligk~~~~---------------~~d~s~~~k~~e~g~Vd~V~i~~~~~g~~~vkv~ir~~~~~~R~p~i 182 (417)
|. .|++|||||||++|. .+|+|++++++|+|+||+|.++.++++.+.|||++|+ .|+|+|
T Consensus 286 G~-~v~~gdiligk~sp~~~~~~~~~~~~~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~vkv~ir~----~R~p~i 360 (605)
T PRK07225 286 ET-EVKEGDVLIGKTSPPRFLEEPDDFGISPEKRRETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRD----LRIPEL 360 (605)
T ss_pred CC-EECCCCEEEEEecCCCCccchhhhcccccCcceeeEEecCCCcEEEEEEEEEecCCCCEEEEEEEEE----EEeccc
Confidence 96 899999999998862 3789999999999999999999988888999999999 999999
Q ss_pred ccccccccCCceeEeeec--------------------------cchhHHHHHhhhhh-hhcCCceeecCCCCCCHHHHH
Q 014847 183 GDKFSSMHGQKGVLGFLE--------------------------QTPAQLLEAALGKG-ACDGLMSYATPFATSTGGVIT 235 (417)
Q Consensus 183 GDKfssRHGqKGvvs~i~--------------------------MtiGql~E~~~g~~-~~~g~~~~~tpF~~~~~~~i~ 235 (417)
|||||||||||||||+|| ||||||+|+++||+ ++.|.+.|+|||...+.+++.
T Consensus 361 GDKfssRHGQKGvvs~i~~~eDMPft~~G~~PDiIiNPhg~PSRMTiGql~E~~~gk~~~~~g~~~d~t~F~~~~~~~~~ 440 (605)
T PRK07225 361 GDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDEEDLR 440 (605)
T ss_pred cchhhhcccCceeEEeEeccccCCcCCCCCcccEEECcccccccCcHHHHHHHHHHHHHHhcCceEeecCCCCchHHHHH
Confidence 999999999999999999 99999999999999 789999999999999999999
Q ss_pred HHHHH-hcccccccccCCCCCeeEeeccccceeeccCCCCccccceeeeeeEEEeeehhhhccccccccccccccCCCCC
Q 014847 236 EQHQS-FVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQP 314 (417)
Q Consensus 236 ~~l~~-~~~~~g~~~~~~~~gk~~l~~g~~~~~~~~~~~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~ 314 (417)
+.|.+ ||+++|+ |.|||| +||++|+++||+|++|||||+|||+||+|+|++||++.
T Consensus 441 ~~L~~~g~~~~G~---------e~my~G--------------~TG~~~~~~if~G~~yYqrL~HmV~DK~haR~~Gp~~~ 497 (605)
T PRK07225 441 EALEKLGFEHTGK---------EVMYDG--------------ITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQV 497 (605)
T ss_pred HHHHHhCcCCCCe---------EEEEcC--------------CCCCEecccEEEeehheeechhhhcchhhhccCCCCcc
Confidence 99999 9999888 999999 99999999999999999999999999999999999999
Q ss_pred cccCCcccccCCCceeeeeccchhhhhcchhhhhhhhh----------ccccccccccc--ccCCeeecccCCCCccccc
Q 014847 315 LTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERL----------KCKNVANVIQR--VVGGPYCRICNSADDIIKA 382 (417)
Q Consensus 315 lT~QP~~Gr~~~GG~RfGEME~d~LiahGas~~L~ErL----------~c~~~~~~~~~--~~~~~~c~~c~~~~~~~~~ 382 (417)
|||||++||+|+|||||||||||||+|||||++|+||| .|..|+.+... .....+|+.|.++..+.++
T Consensus 498 lTrQP~~GR~r~GG~RfGEMErd~lia~Gas~~L~Erl~~~SD~~~~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~i~~v 577 (605)
T PRK07225 498 LTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKVEIYVCAKCGMIAIYDKKRNRKYCPICGEETDIYPV 577 (605)
T ss_pred cccCCccccccCCCeeeeeeehhhhhhhhhHHHHHHHHhccCcceeEEeecCcCcceehhcccCceeecccCCCCceeec
Confidence 99999999999999999999999999999999999999 77777766532 2235679999998899999
Q ss_pred cChHhHHHHHHHHHhhcCCeEEEEecc
Q 014847 383 NVPYGAKLLSQELSFSMGITLKFDTQL 409 (417)
Q Consensus 383 ~ipy~~k~l~~EL~~sm~i~~~l~~~~ 409 (417)
.+|||||||+||| +||||+++|.+++
T Consensus 578 ~iPya~kll~~EL-~sm~i~~~l~~~~ 603 (605)
T PRK07225 578 EMSYAFKLLLDEL-KSLGIAPRLELED 603 (605)
T ss_pred cCChhHHHHHHHH-HHCCceeEEEecc
Confidence 9999999999999 9999999999874
No 2
>TIGR03670 rpoB_arch DNA-directed RNA polymerase subunit B. This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.
Probab=100.00 E-value=1.2e-120 Score=968.14 Aligned_cols=377 Identities=33% Similarity=0.501 Sum_probs=347.7
Q ss_pred CcccccccccccCCCCCcCCCcccccccccccCCccccccccccchhhcccccccccCccceEeeccccccCCC------
Q 014847 1 MSFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRPLFWILISDCLGRP------ 74 (417)
Q Consensus 1 p~~ilsi~AslIPF~~h~~NqSpRn~yq~~~M~KQamG~~~~n~~~R~D~~~~~l~ypQ~PLV~t~~~d~lg~n------ 74 (417)
|+++||++||+|||+|| ||||||||||| |+|||||++.+|+..|+|++.|.|+|||+|||+|+.++.++++
T Consensus 123 p~~ilgv~AslIPF~~h--NqSpRn~YQc~-M~KQamG~~~~n~~~R~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~p~G~ 199 (599)
T TIGR03670 123 PSAILGIIASTIPYPEH--NQSPRNTMGAA-MAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQ 199 (599)
T ss_pred CcceeeEEeeccCCCCc--CcchhhHHHHh-hhhccccccccChhhcccccceEEcCCCCceeeeeeHHHhCccccCCCe
Confidence 78999999999999999 99999999999 8999999999999999999999999999999999998866544
Q ss_pred --------------CCeEEEecceecccceeeEEEEEEEec--------cccc---------------CCCCCCCccccc
Q 014847 75 --------------EDSLVMNQASLECGVFRSESYKAEVDN--------KDIQ---------------VKSRPSDDMLNF 117 (417)
Q Consensus 75 --------------EDAiIiNKssidRG~f~s~~Yk~e~~~--------~~~~---------------~~~~~~~g~~~~ 117 (417)
||||||||+|+|||||||++|+++... .+.+ -+.+|.||++.+
T Consensus 200 N~iVAvmsy~GYn~EDAiIink~si~rG~f~s~~~~~~~~~~~~~~~~~~e~~~~p~~~~~~~~~~~~~~~LD~dGi~~~ 279 (599)
T TIGR03670 200 NFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEDRFEIPEPDVRGYRGEEAYKHLDEDGIVYP 279 (599)
T ss_pred eEEEEEEcccCcChhHeeeechhhhhcCCeEEEEEEEEEEEeeccCCCCceEEecCCchhccccchhhhccCCCCCCcCC
Confidence 999999999999999999988765421 0111 123678999999
Q ss_pred cccccccCCeEEEEeccC---------------CceeEEEecCCCceeEEEEEEEeCCCCCeEEEEEEeecccccccccc
Q 014847 118 GKIQSKSGDIVIGKYAEI---------------GADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACL 182 (417)
Q Consensus 118 g~~~v~~GDiligk~~~~---------------~~d~s~~~k~~e~g~Vd~V~i~~~~~g~~~vkv~ir~~~~~~R~p~i 182 (417)
|. .|++||||+||++|. .+|+|++++++|+|+||+|.++.++++.+.++|++|+ .|+|+|
T Consensus 280 G~-~v~~gdiligk~~p~~~~~~~~~~~~~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~vkv~~r~----~R~p~i 354 (599)
T TIGR03670 280 EV-EVKGGDVLIGKTSPPRFLEELRELGLVTERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRD----LRIPEL 354 (599)
T ss_pred Cc-EeCCCCEEEEEecCCCCccchhhhccccccCceEEEEecCCCcEEEEEEEEEecCCCcEEEEEEEee----eecCcc
Confidence 96 799999999998862 3789999999999999999999998888999999999 999999
Q ss_pred ccccccccCCceeEeeec--------------------------cchhHHHHHhhhhh-hhcCCceeecCCCCCCHHHHH
Q 014847 183 GDKFSSMHGQKGVLGFLE--------------------------QTPAQLLEAALGKG-ACDGLMSYATPFATSTGGVIT 235 (417)
Q Consensus 183 GDKfssRHGqKGvvs~i~--------------------------MtiGql~E~~~g~~-~~~g~~~~~tpF~~~~~~~i~ 235 (417)
|||||||||||||||+|| ||||||+|+++||+ ++.|.+.|+|||++.+.+++.
T Consensus 355 GDKfssRHGQKGvvs~i~~~eDMPft~~G~~pDiIiNPhg~PSRMTiGqllE~~~gk~~~~~g~~~d~t~F~~~~~~~~~ 434 (599)
T TIGR03670 355 GDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELR 434 (599)
T ss_pred hhhhhhhccCcceEEeEeccCCCCcCCCCCCCCEEECcccccccccHHHHHHHHHHHHHHhcCCEEEeCCCCCccHHHHH
Confidence 999999999999999999 99999999999999 789999999999999999999
Q ss_pred HHHHH-hcccccccccCCCCCeeEeeccccceeeccCCCCccccceeeeeeEEEeeehhhhccccccccccccccCCCCC
Q 014847 236 EQHQS-FVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQP 314 (417)
Q Consensus 236 ~~l~~-~~~~~g~~~~~~~~gk~~l~~g~~~~~~~~~~~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~ 314 (417)
+.|++ ||+++|+ |.|||| +||++|+++||+|++|||||+|||+||+|+|++||++.
T Consensus 435 ~~L~~~g~~~~G~---------e~ly~G--------------~TG~~~~~~if~G~~yyqrL~HmV~DK~h~Rs~Gp~~~ 491 (599)
T TIGR03670 435 KELLKLGFKPDGK---------EVMYDG--------------ITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQV 491 (599)
T ss_pred HHHHHcCCCCCCC---------EEEEcC--------------CCCCCccccEEEEehhheechhhhcchhhhcccCCCcc
Confidence 99999 9999888 999999 99999999999999999999999999999999999999
Q ss_pred cccCCcccccCCCceeeeeccchhhhhcchhhhhhhhh----------ccccccccccc--ccCCeeecccCCCCccccc
Q 014847 315 LTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERL----------KCKNVANVIQR--VVGGPYCRICNSADDIIKA 382 (417)
Q Consensus 315 lT~QP~~Gr~~~GG~RfGEME~d~LiahGas~~L~ErL----------~c~~~~~~~~~--~~~~~~c~~c~~~~~~~~~ 382 (417)
|||||++||+|+|||||||||||||+|||||++|+||| .|..|+.+... .....+|+.|.++.++.++
T Consensus 492 lTrQP~~Gr~r~GG~RfGEMErd~lia~Gas~~L~ErL~~~SD~~~~~vC~~CG~~~~~~~~~~~~~C~~c~~~~~i~~v 571 (599)
T TIGR03670 492 LTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIAWEDKRKGTAYCPVCGETGDISPV 571 (599)
T ss_pred cccCCccccccCCCeeeeeeehhhHhhcchHHHHHHHHhccCcceeEEeecccCceeehhcccCceeccccCCCCceeee
Confidence 99999999999999999999999999999999999999 67777766532 2235679999998899999
Q ss_pred cChHhHHHHHHHHHhhcCCeEEEEecc
Q 014847 383 NVPYGAKLLSQELSFSMGITLKFDTQL 409 (417)
Q Consensus 383 ~ipy~~k~l~~EL~~sm~i~~~l~~~~ 409 (417)
.+|||||||+||| +||||+++|.+++
T Consensus 572 ~iPy~~k~l~~EL-~am~i~~~l~~~~ 597 (599)
T TIGR03670 572 EMSYAFKLLLDEL-KSLGISPRLELGD 597 (599)
T ss_pred cCChhHHHHHHHH-HhCCcceEEEecc
Confidence 9999999999999 9999999999873
No 3
>PRK08565 DNA-directed RNA polymerase subunit B; Provisional
Probab=100.00 E-value=1.7e-114 Score=976.29 Aligned_cols=377 Identities=34% Similarity=0.497 Sum_probs=347.7
Q ss_pred CcccccccccccCCCCCcCCCcccccccccccCCccccccccccchhhcccccccccCccceEeeccccccCCC------
Q 014847 1 MSFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRPLFWILISDCLGRP------ 74 (417)
Q Consensus 1 p~~ilsi~AslIPF~~h~~NqSpRn~yq~~~M~KQamG~~~~n~~~R~D~~~~~l~ypQ~PLV~t~~~d~lg~n------ 74 (417)
|++|||++||+|||+|| ||||||||||| |+|||||++.+|+..|+|++.|.|+|||+|||+|++++.+|++
T Consensus 627 p~~ilsv~asliPF~~h--NqspRn~yq~~-M~KQa~g~~~~n~~~r~d~~~~~l~~pQ~Plv~t~~~~~~~~~~~p~G~ 703 (1103)
T PRK08565 627 PPAILGITASIIPYPEH--NQSPRNTYQAA-MAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQ 703 (1103)
T ss_pred CccccceeeeccCCccc--Ccccchhhhhh-hhhcccccccccceEeecCCcceeecCceeEEEeccccccccccCCCCe
Confidence 78999999999999999 99999999999 8999999999999999999999999999999999998866444
Q ss_pred --------------CCeEEEecceecccceeeEEEEEEEec--------cccc---------------CCCCCCCccccc
Q 014847 75 --------------EDSLVMNQASLECGVFRSESYKAEVDN--------KDIQ---------------VKSRPSDDMLNF 117 (417)
Q Consensus 75 --------------EDAiIiNKssidRG~f~s~~Yk~e~~~--------~~~~---------------~~~~~~~g~~~~ 117 (417)
||||||||+|+|||||||++|+++... .+.+ -+.+|.||++.+
T Consensus 704 N~iVAv~sy~GYn~EDaiIink~s~~rG~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ld~dGi~~~ 783 (1103)
T PRK08565 704 NAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIPEPNVRGYRGEEYYRKLDEDGIVSP 783 (1103)
T ss_pred eEEEEEEcccCcchHHhhhhhhhhhhcCCceEEEEEEEEEEeeecCCCCceEEecCCCcccccCchhhhhcCCCCCCcCC
Confidence 999999999999999999988775421 0111 123578999999
Q ss_pred cccccccCCeEEEEecc---------------CCceeEEEecCCCceeEEEEEEEeCCCCCeEEEEEEeecccccccccc
Q 014847 118 GKIQSKSGDIVIGKYAE---------------IGADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACL 182 (417)
Q Consensus 118 g~~~v~~GDiligk~~~---------------~~~d~s~~~k~~e~g~Vd~V~i~~~~~g~~~vkv~ir~~~~~~R~p~i 182 (417)
|. .|++|||||||++| ..+|+|++++++|+|+||+|.+++++++.+.|+|++|+ .|+|+|
T Consensus 784 G~-~v~~gdili~k~~p~~~~~~~~~~~~~~~~~~~~s~~~~~~e~g~V~~V~~~~~~~~~~~vkv~ir~----~R~p~i 858 (1103)
T PRK08565 784 EV-EVKGGDVLIGKTSPPRFLEELEELSLGLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRD----LRIPEL 858 (1103)
T ss_pred Cc-EEcCCCEEEEEecCCCCCcchhhccccCCccccceEEecCCCceEEEEEEEEecCCCcEEEEEEEEE----EecCch
Confidence 97 79999999999986 14789999999999999999999998888999999999 999999
Q ss_pred ccccccccCCceeEeeec--------------------------cchhHHHHHhhhhh-hhcCCceeecCCCCCCHHHHH
Q 014847 183 GDKFSSMHGQKGVLGFLE--------------------------QTPAQLLEAALGKG-ACDGLMSYATPFATSTGGVIT 235 (417)
Q Consensus 183 GDKfssRHGqKGvvs~i~--------------------------MtiGql~E~~~g~~-~~~g~~~~~tpF~~~~~~~i~ 235 (417)
|||||||||||||||+|| ||||||+|+++||+ ++.|.+.|+|||.+...+++.
T Consensus 859 GDKfssRhGqKGv~s~i~~~edmPf~~~G~~pDiI~NPh~~PSRMtiG~l~E~~~gk~~~~~g~~~d~t~F~~~~~~~~~ 938 (1103)
T PRK08565 859 GDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELR 938 (1103)
T ss_pred hhhhhhhccCcceeeeecccccCCcCCCCCCccEEECCCCCcccccHHHHHHHHHHHHHHhcCceeeecCcCCchHHHHH
Confidence 999999999999999999 99999999999999 788999999999999999999
Q ss_pred HHHHH-hcccccccccCCCCCeeEeeccccceeeccCCCCccccceeeeeeEEEeeehhhhccccccccccccccCCCCC
Q 014847 236 EQHQS-FVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQP 314 (417)
Q Consensus 236 ~~l~~-~~~~~g~~~~~~~~gk~~l~~g~~~~~~~~~~~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~ 314 (417)
+.|++ ||+++|+ |.|||| +||++|+++||+|++|||||+|||+||+|||++||++.
T Consensus 939 ~~L~~~g~~~~G~---------e~l~~G--------------~tG~~~~~~if~G~~yy~rL~HmV~DK~~~R~~Gp~~~ 995 (1103)
T PRK08565 939 KELLKLGYKPDGT---------EVMYDG--------------RTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQI 995 (1103)
T ss_pred HHHHHcCCCCCCc---------EEEEcC--------------CCCCCcccceEEeehhheechhhhchhhhhccCCCcch
Confidence 99999 9999888 999999 99999999999999999999999999999999999999
Q ss_pred cccCCcccccCCCceeeeeccchhhhhcchhhhhhhhh----------ccccccccccc--ccCCeeecccCCCCccccc
Q 014847 315 LTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERL----------KCKNVANVIQR--VVGGPYCRICNSADDIIKA 382 (417)
Q Consensus 315 lT~QP~~Gr~~~GG~RfGEME~d~LiahGas~~L~ErL----------~c~~~~~~~~~--~~~~~~c~~c~~~~~~~~~ 382 (417)
|||||++||+|+|||||||||||||+|||||++|+||| .|..|+.+... .....+|+.|.++..+.++
T Consensus 996 lt~QP~~Gr~~~GG~R~GEME~d~l~a~Gas~~L~erL~~~SD~~~~~vC~~Cg~~~~~~~~~~~~~C~~c~~~~~~~~v 1075 (1103)
T PRK08565 996 LTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHIAWYDRRKNKYVCPIHGDKGNISPV 1075 (1103)
T ss_pred hhhCCccccccCCCeeeecchHHHHHhcccHHHHHHHhhccccceeeeeecccccccccccccCceeccccCCCCcceec
Confidence 99999999999999999999999999999999999999 77777776532 1335679999998889999
Q ss_pred cChHhHHHHHHHHHhhcCCeEEEEecc
Q 014847 383 NVPYGAKLLSQELSFSMGITLKFDTQL 409 (417)
Q Consensus 383 ~ipy~~k~l~~EL~~sm~i~~~l~~~~ 409 (417)
.+|||||||+||| +||||+++|.+++
T Consensus 1076 ~iPy~~k~l~~EL-~sm~i~~~l~~~~ 1101 (1103)
T PRK08565 1076 EVSYAFKLLLQEL-MSMGISPRLKLGD 1101 (1103)
T ss_pred cCChhHHHHHHHH-HhCCCceEEEeee
Confidence 9999999999999 9999999999884
No 4
>cd00653 RNA_pol_B_RPB2 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.
Probab=100.00 E-value=2.1e-110 Score=926.14 Aligned_cols=370 Identities=36% Similarity=0.536 Sum_probs=339.2
Q ss_pred CcccccccccccCCCCCcCCCcccccccccccCCccccccccccchhhcccccccccCccceEeeccccccC--------
Q 014847 1 MSFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRPLFWILISDCLG-------- 72 (417)
Q Consensus 1 p~~ilsi~AslIPF~~h~~NqSpRn~yq~~~M~KQamG~~~~n~~~R~D~~~~~l~ypQ~PLV~t~~~d~lg-------- 72 (417)
|+++||++||+|||+|| ||||||||||| |+|||||++++|++.|+|++.|.|+|||+|||+|.+++.++
T Consensus 402 ~~~~ls~~asliPf~~h--NqspRn~~~~~-M~kQa~g~~~~n~~~r~d~~~~~l~~pq~plv~T~~~~~~~~~~~~~G~ 478 (866)
T cd00653 402 PSQILSVAASLIPFPEH--NQSPRNLYQSN-MQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQ 478 (866)
T ss_pred ccceeeeeeeccCCCCc--ccccchhhhhc-ccCCccCchhccccccccchheeeccCCCCccccchHHHhCCCccCCCc
Confidence 78999999999999999 99999999999 89999999999999999999999999999999999877443
Q ss_pred -----------CC-CCeEEEecceecccceeeEEEEEEEecc--------ccc-----------CCCCCCCccccccccc
Q 014847 73 -----------RP-EDSLVMNQASLECGVFRSESYKAEVDNK--------DIQ-----------VKSRPSDDMLNFGKIQ 121 (417)
Q Consensus 73 -----------~n-EDAiIiNKssidRG~f~s~~Yk~e~~~~--------~~~-----------~~~~~~~g~~~~g~~~ 121 (417)
+| ||||||||+|+|||+|||++|+++..+. +.. -+.++.||++.+|. .
T Consensus 479 N~~VAv~~y~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ld~dGi~~~g~-~ 557 (866)
T cd00653 479 NAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRGDIPNVSEEKLKNLDEDGIIRPGA-R 557 (866)
T ss_pred eEEEEEeccccccccceeeeehhhhhcCceeEEEEEEEEEEEEecCCCcceEecCCCCCCChHHhhccCCCCCcCCCC-E
Confidence 33 9999999999999999999887755321 111 02367899999997 7
Q ss_pred cccCCeEEEEeccC---------------CceeEEEecCCCceeEEEEEEEe---CCCCCeEEEEEEeeccccccccccc
Q 014847 122 SKSGDIVIGKYAEI---------------GADHSIKLKHTERGLVLKVLLSS---NDDGKNFAVVSIRQSVNMVHSACLG 183 (417)
Q Consensus 122 v~~GDiligk~~~~---------------~~d~s~~~k~~e~g~Vd~V~i~~---~~~g~~~vkv~ir~~~~~~R~p~iG 183 (417)
|++||+|+||++|. .+|+|++++.+|+|+||+|.++. +.++...++|++|+ .|+|+||
T Consensus 558 v~~gd~li~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~v~~v~~~~~~~~~~~~~~v~v~~r~----~R~p~iG 633 (866)
T cd00653 558 VEPGDILVGKITPKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRELNDGGNKLVKVYIRQ----KRKPQIG 633 (866)
T ss_pred ecCCCEEEEEecCcccccccccccccCCcceEEEEEecCCCceEEEEEEEeccccCCCCcEEEEEEEeE----EecCCcc
Confidence 89999999999874 47899999999999999999998 45677899999999 9999999
Q ss_pred cccccccCCceeEeeec--------------------------cchhHHHHHhhhhh-hhcCCceeecCCCCCCHHHHHH
Q 014847 184 DKFSSMHGQKGVLGFLE--------------------------QTPAQLLEAALGKG-ACDGLMSYATPFATSTGGVITE 236 (417)
Q Consensus 184 DKfssRHGqKGvvs~i~--------------------------MtiGql~E~~~g~~-~~~g~~~~~tpF~~~~~~~i~~ 236 (417)
||||||||||||||+|| ||||||+|+++||+ ++.|.+.|+|||+....+++.+
T Consensus 634 DKfssRhGqKGv~s~i~~~~dmPf~~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~t~f~~~~~~~~~~ 713 (866)
T cd00653 634 DKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISE 713 (866)
T ss_pred cccccccCCCcEEEEEeccccCCcccCCCCCcEEecCCcCcccccHHHHHHHHHHHHHHhcCCcccccccCcchHHHHHH
Confidence 99999999999999999 99999999999999 7889999999999989999999
Q ss_pred HHHH-hcccccccccCCCCCeeEeeccccceeeccCCCCccccceeeeeeEEEeeehhhhccccccccccccccCCCCCc
Q 014847 237 QHQS-FVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPL 315 (417)
Q Consensus 237 ~l~~-~~~~~g~~~~~~~~gk~~l~~g~~~~~~~~~~~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~l 315 (417)
.|.+ ||+++|+ |.|||| +||++++++||+|++|||||+|||+||+|||++||++.|
T Consensus 714 ~l~~~g~~~~G~---------e~~y~g--------------~tG~~~~~~if~G~~yyqrL~Hmv~DK~~~R~~Gp~~~l 770 (866)
T cd00653 714 LLGEAGLNYYGK---------EVLYDG--------------RTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLL 770 (866)
T ss_pred HHHHcCCCCCCc---------EEEEcC--------------CCCCCcccceEEeehhhhhhhhhhchhhhhcccCCcchh
Confidence 9999 9988888 999999 999999999999999999999999999999999999999
Q ss_pred ccCCcccccCCCceeeeeccchhhhhcchhhhhhhhh----------cccccccccccccCCeeecccCCCCccccccCh
Q 014847 316 TGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERL----------KCKNVANVIQRVVGGPYCRICNSADDIIKANVP 385 (417)
Q Consensus 316 T~QP~~Gr~~~GG~RfGEME~d~LiahGas~~L~ErL----------~c~~~~~~~~~~~~~~~c~~c~~~~~~~~~~ip 385 (417)
||||++||+|+|||||||||||||+|||||++|+||| .|..|+.+.. ..+|+.|.++.++.++.+|
T Consensus 771 T~QP~~Gr~~~GG~R~GEMErd~lia~Gas~~l~erl~~~SD~~~~~vc~~cg~i~~----~~~c~~c~~~~~~~~~~ip 846 (866)
T cd00653 771 TRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILS----ANLCRLCKKGTNISKVGIP 846 (866)
T ss_pred ccCcCccccccCCeEEEEEehhhhhhhhhHHHHHHHHhcCCccceEEEeccCccccc----ccccccccCCCceeecCCC
Confidence 9999999999999999999999999999999999999 5666655432 2459999999999999999
Q ss_pred HhHHHHHHHHHhhcCCeEEEE
Q 014847 386 YGAKLLSQELSFSMGITLKFD 406 (417)
Q Consensus 386 y~~k~l~~EL~~sm~i~~~l~ 406 (417)
||||||++|| +||||++++.
T Consensus 847 y~~kll~~EL-~sm~i~~~~~ 866 (866)
T cd00653 847 YAFKLLFQEL-QSMNIDPRLK 866 (866)
T ss_pred HHHHHHHHHH-HHCCcceEeC
Confidence 9999999999 9999999973
No 5
>KOG0216 consensus RNA polymerase I, second largest subunit [Transcription]
Probab=100.00 E-value=3.1e-110 Score=880.68 Aligned_cols=375 Identities=32% Similarity=0.443 Sum_probs=345.3
Q ss_pred CcccccccccccCCCCCcCCCcccccccccccCCccccccccccchhhcccccccccCccceEeeccccccCCC------
Q 014847 1 MSFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRPLFWILISDCLGRP------ 74 (417)
Q Consensus 1 p~~ilsi~AslIPF~~h~~NqSpRn~yq~~~M~KQamG~~~~n~~~R~D~~~~~l~ypQ~PLV~t~~~d~lg~n------ 74 (417)
|+.+||++|+||||+|| ||||||||||| |+||+||+|.++++.|.|+++|+|++||.|+|++..+|.+++|
T Consensus 647 pt~~ls~~anliP~sD~--NQSPRNmYQCQ-MgKQtmg~p~~a~~~radnklYrlqt~qsP~vr~~~y~~y~~d~yp~Gt 723 (1111)
T KOG0216|consen 647 PTGILSIVANLIPFSDH--NQSPRNMYQCQ-MGKQTMGTPGHALRTRADNKLYRLQTPQSPIVRPELYDTYGMDDYPNGT 723 (1111)
T ss_pred ccchHhHhhcCcccccc--CCCchhHHHhh-hhhhhcCCccccchhcccCceEEecCCCCceeecccccccccccCCCCc
Confidence 78899999999999999 99999999999 8999999999999999999999999999999999999966655
Q ss_pred --------------CCeEEEecceecccceeeEEEEEEEeccc-------ccC--------CCCCCCccccccccccccC
Q 014847 75 --------------EDSLVMNQASLECGVFRSESYKAEVDNKD-------IQV--------KSRPSDDMLNFGKIQSKSG 125 (417)
Q Consensus 75 --------------EDAiIiNKssidRG~f~s~~Yk~e~~~~~-------~~~--------~~~~~~g~~~~g~~~v~~G 125 (417)
||||||||+|+||||+++++||+|..+.. .|. +.++.||++.+|. .++.|
T Consensus 724 NaiVAVisyTgyDMeDAmiiNK~s~eRGf~~G~vykte~i~L~~~~~r~~~F~~~p~~~~~~~ld~dgLP~~G~-kl~~~ 802 (1111)
T KOG0216|consen 724 NAIVAVISYTGYDMEDAMIINKSSYERGFAYGTVYKTEKIDLSKKRSRSKHFGRSPGEPELKKLDADGLPSIGQ-KLEYG 802 (1111)
T ss_pred ceEEEEEeecccChhhhhhhchhhhhccccceeEEeeeeechhhcccceeeeeeCCCCccccccCCCCCCCCcc-cccCC
Confidence 99999999999999999999999986421 121 3468899999996 78899
Q ss_pred CeEEEEecc-CCceeEEEecCCCceeEEEEEEEeCCCCC--eEEEEEEeeccccccccccccccccccCCceeEeeec--
Q 014847 126 DIVIGKYAE-IGADHSIKLKHTERGLVLKVLLSSNDDGK--NFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLE-- 200 (417)
Q Consensus 126 Diligk~~~-~~~d~s~~~k~~e~g~Vd~V~i~~~~~g~--~~vkv~ir~~~~~~R~p~iGDKfssRHGqKGvvs~i~-- 200 (417)
|+++..+.. .++....+|+..|+++||.|++..+++|. +.+.|++|. .|+|.||||||||||||||+|+.|
T Consensus 803 dp~~~y~d~~t~~~~~~~~~~~ep~~vd~vr~~~~~~~~~~k~~~i~~Ri----~R~p~IGDKFsSRhGQKGicS~~wP~ 878 (1111)
T KOG0216|consen 803 DPYYAYFDEETGKTRIKKYHGTEPGIVDEVRVLGNDMGDQEKCATITLRI----PRNPIIGDKFSSRHGQKGICSQKWPT 878 (1111)
T ss_pred CcEEEEEcccCCceEEEEecCCCCeeeEEEEEccccCCCccceEEEEEEe----cCCCcccchhhhhccccccccccCCC
Confidence 999999886 47889999999999999999999998876 679999999 999999999999999999999999
Q ss_pred ------------------------cchhHHHHHhhhhh-hhcCCceeecCCCCC----CHHHHHHHHHH-hccccccccc
Q 014847 201 ------------------------QTPAQLLEAALGKG-ACDGLMSYATPFATS----TGGVITEQHQS-FVSQLLNCIG 250 (417)
Q Consensus 201 ------------------------MtiGql~E~~~g~~-~~~g~~~~~tpF~~~----~~~~i~~~l~~-~~~~~g~~~~ 250 (417)
|||||++|+++||+ |+.|+..|+|||... ..++++++|++ |||++|+
T Consensus 879 ~dmPFtesGm~PDii~NPH~FPSRMTIgM~iEs~AgK~~alhG~~~Datpf~~~E~~t~~dyfg~~L~~~GyNyyGn--- 955 (1111)
T KOG0216|consen 879 IDMPFTESGMVPDIIINPHAFPSRMTIGMLIESMAGKAGALHGNAQDATPFIFSEENTAIDYFGEMLKKAGYNYYGN--- 955 (1111)
T ss_pred CCCCccccCcCcceeeCCCCCcccccHHHHHHHHhchhhccccccccCCceeecCcccHHHHHHHHHHHcCcCccCC---
Confidence 99999999999999 999999999998543 37889999999 9999999
Q ss_pred CCCCCeeEeeccccceeeccCCCCccccceeeeeeEEEeeehhhhccccccccccccccCCCCCcccCCcccccCCCcee
Q 014847 251 ARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIE 330 (417)
Q Consensus 251 ~~~~gk~~l~~g~~~~~~~~~~~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R 330 (417)
|.||+| .+|++++++||+|++|||||+|||.||+|+|+|||++.+|+||++||+|+||||
T Consensus 956 ------E~~YSG--------------v~G~e~~adIf~GvVyYQRLrHMv~DKfQVRstG~v~~~T~QPvkGRkr~GGiR 1015 (1111)
T KOG0216|consen 956 ------EPMYSG--------------VDGREMRADIFFGVVYYQRLRHMVSDKFQVRSTGPVDSLTHQPVKGRKRGGGIR 1015 (1111)
T ss_pred ------cccccc--------------cccceeeeeEEEeehhHHHHHHHhcceeeeeeccCccccccCCccCcccCCCcc
Confidence 999999 999999999999999999999999999999999999999999999999999999
Q ss_pred eeeccchhhhhcchhhhhhhhh----------ccccccccccc----------ccCCeeecccCCCCccccccChHhHHH
Q 014847 331 FGEMKCDCLIAHGASGNLHERL----------KCKNVANVIQR----------VVGGPYCRICNSADDIIKANVPYGAKL 390 (417)
Q Consensus 331 fGEME~d~LiahGas~~L~ErL----------~c~~~~~~~~~----------~~~~~~c~~c~~~~~~~~~~ipy~~k~ 390 (417)
|||||||||||||||++|+||| .|..|++++.- ......|+.|.+ ..+..+.+||+|||
T Consensus 1016 fGEMERDali~HGtsfllqDRL~~~SD~~~a~vC~~cgsil~~~~~l~~~~~~~~~~~~C~~c~~-~~~~~v~~P~vfkY 1094 (1111)
T KOG0216|consen 1016 FGEMERDALIAHGTSFLLQDRLLNSSDYTVAEVCRTCGSILSTQQKLIKEPGGSTSTVTCRSCDG-KGVTTVAMPYVFKY 1094 (1111)
T ss_pred ccchhhhhHhhcchHhhhhhhhccCcchhHHHHHHHhhhhhhhhhhhhcccCCCCCceeEEecCC-CceEEEEccHHHHH
Confidence 9999999999999999999999 67777766542 334568999954 57889999999999
Q ss_pred HHHHHHhhcCCeEEEEec
Q 014847 391 LSQELSFSMGITLKFDTQ 408 (417)
Q Consensus 391 l~~EL~~sm~i~~~l~~~ 408 (417)
|..|| .||||+++|.++
T Consensus 1095 L~aEL-~amnIk~~l~l~ 1111 (1111)
T KOG0216|consen 1095 LTAEL-AAMNIKMRLDLE 1111 (1111)
T ss_pred HHHHH-hhCceeEEeccC
Confidence 99999 999999999874
No 6
>KOG0215 consensus RNA polymerase III, second largest subunit [Transcription]
Probab=100.00 E-value=3.6e-111 Score=884.90 Aligned_cols=374 Identities=33% Similarity=0.459 Sum_probs=345.0
Q ss_pred CcccccccccccCCCCCcCCCcccccccccccCCccccccccccchhhcccccccccCccceEeeccccccCCC------
Q 014847 1 MSFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRPLFWILISDCLGRP------ 74 (417)
Q Consensus 1 p~~ilsi~AslIPF~~h~~NqSpRn~yq~~~M~KQamG~~~~n~~~R~D~~~~~l~ypQ~PLV~t~~~d~lg~n------ 74 (417)
|..|||++|+||||||| ||||||+|||+ |+|||||..++|+..|+|+.+|.|.|||+|+|+|++.|.++||
T Consensus 682 PFTiLGv~AGLIPYPHH--NQSPRNTYQCA-MGKQAmG~IaYNQ~~RiDtlmYll~YPq~PmVkTKTIELi~ydKLPAGQ 758 (1153)
T KOG0215|consen 682 PFTILGVVAGLIPYPHH--NQSPRNTYQCA-MGKQAMGAIAYNQKKRIDSLLYLLVYPQRPMVKTKTIELINYDKLPAGQ 758 (1153)
T ss_pred chhhhhhhccccCCCCC--CCCCcchhhhh-hhhhhhhhhhhhhhhhHHHHHHHHhcCCCccccceeEEeeccccCCCCC
Confidence 77899999999999999 99999999999 8999999999999999999999999999999999998877666
Q ss_pred --------------CCeEEEecceecccceeeEEEEEEEe------c--cccc---------CC------CCCCCccccc
Q 014847 75 --------------EDSLVMNQASLECGVFRSESYKAEVD------N--KDIQ---------VK------SRPSDDMLNF 117 (417)
Q Consensus 75 --------------EDAiIiNKssidRG~f~s~~Yk~e~~------~--~~~~---------~~------~~~~~g~~~~ 117 (417)
|||+|+||+|+||||+|+.+||...- | .|.+ .+ -++.||+...
T Consensus 759 NAtVAVMSYSGYDIEDALVLNKsSlDRGfGRC~Vyk~~~~~~kkY~N~T~Drimgp~~d~~t~kpi~kh~vLd~DGl~~p 838 (1153)
T KOG0215|consen 759 NATVAVMSYSGYDIEDALVLNKSSIDRGFGRCEVYKKTTTTLKKYANGTFDRIMGPQLDPNTRKPIWKHQVLDDDGLATP 838 (1153)
T ss_pred ccEEEEEeccCCchhhhhhcccchhccCcceEEEEeeeeeeeeecCCCchhhhcccccCCCcCCcchhhcccCcccCCCC
Confidence 99999999999999999999976431 1 0111 11 2578899888
Q ss_pred cccccccCCeEEEEeccC---------------CceeEEEecCCCceeEEEEEEEeCCCCCeEEEEEEeecccccccccc
Q 014847 118 GKIQSKSGDIVIGKYAEI---------------GADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACL 182 (417)
Q Consensus 118 g~~~v~~GDiligk~~~~---------------~~d~s~~~k~~e~g~Vd~V~i~~~~~g~~~vkv~ir~~~~~~R~p~i 182 (417)
|+ .|++|+++|+|-.|. .++.++.||+.|+++||+|.+++++++..++|+.+|+ +|+|++
T Consensus 839 G~-~V~~~qi~iNK~mP~vt~~~~~~~~~~~~~Yk~~pitykgpepsyidkVmls~n~~dq~LIK~llRQ----TRrPEl 913 (1153)
T KOG0215|consen 839 GE-RVQPGQIYINKQMPTVTGTSLPGLSASQVQYKAVPITYKGPEPSYIDRVMLTSNDEDQFLIKVLLRQ----TRRPEL 913 (1153)
T ss_pred cc-EeccCcEEEeccCCCcccccCCCCCccccccccccceecCCCcchhheeEeecCccccHHHHHHHhh----ccCccc
Confidence 97 789999999995442 4789999999999999999999998888899999999 999999
Q ss_pred ccccccccCCceeEeeec--------------------------cchhHHHHHhhhhh-hhcCCceeecCCCCCCHHHHH
Q 014847 183 GDKFSSMHGQKGVLGFLE--------------------------QTPAQLLEAALGKG-ACDGLMSYATPFATSTGGVIT 235 (417)
Q Consensus 183 GDKfssRHGqKGvvs~i~--------------------------MtiGql~E~~~g~~-~~~g~~~~~tpF~~~~~~~i~ 235 (417)
|||||||||||||||.|+ ||+|.++|.+.||| .+.|.+.++|.|.+..++++.
T Consensus 914 GDKFSSRHGQKGVcGlIv~QEDMPFnD~GIcPDiIMNPHGFPSRMTVGK~iELlsGKAGVl~G~~hYGTaFGgskVed~~ 993 (1153)
T KOG0215|consen 914 GDKFSSRHGQKGVCGLIVQQEDMPFNDQGICPDIIMNPHGFPSRMTVGKMIELLSGKAGVLEGTFHYGTAFGGSKVEDIS 993 (1153)
T ss_pred ccccccccCCCceeeEEeeccCCCCcccCCCcccccCCCCCcccchHHHHHHHhccccceeeeeEeeccccCCchHHHHH
Confidence 999999999999999998 99999999999999 789999999999999999999
Q ss_pred HHHHH-hcccccccccCCCCCeeEeeccccceeeccCCCCccccceeeeeeEEEeeehhhhccccccccccccccCCCCC
Q 014847 236 EQHQS-FVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQP 314 (417)
Q Consensus 236 ~~l~~-~~~~~g~~~~~~~~gk~~l~~g~~~~~~~~~~~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~ 314 (417)
+.|.+ |||+.|+ ..+|+| +||+++++.||+||+|||||+|||.||+|+|++||+..
T Consensus 994 ~~Lv~hGfnY~GK---------D~ltSG--------------ITGepLeAYIffGPiYYQKLKHMVlDKMHARARGPRAv 1050 (1153)
T KOG0215|consen 994 EELVEHGFNYSGK---------DMLTSG--------------ITGEPLEAYIFFGPIYYQKLKHMVLDKMHARARGPRAV 1050 (1153)
T ss_pred HHHHHhccCccCc---------cccccC--------------CCCCcceeeEEechHHHHHHHHHHHHHHhhhccCCcee
Confidence 99999 9998887 999999 99999999999999999999999999999999999999
Q ss_pred cccCCcccccCCCceeeeeccchhhhhcchhhhhhhhh----------cccccccccccccCCeeecccCCCCccccccC
Q 014847 315 LTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERL----------KCKNVANVIQRVVGGPYCRICNSADDIIKANV 384 (417)
Q Consensus 315 lT~QP~~Gr~~~GG~RfGEME~d~LiahGas~~L~ErL----------~c~~~~~~~~~~~~~~~c~~c~~~~~~~~~~i 384 (417)
|||||++||+|+||+|+||||||||||||||.+|.||| +|..|+-. +. ..||..|.++.++.++.|
T Consensus 1051 LTRQPTEGRSrdGGLRLGEMERDCLIaYGASmLl~ERLMiSSDaFeVdVC~~CGll-gy---kgwC~~Ckss~~v~~~~i 1126 (1153)
T KOG0215|consen 1051 LTRQPTEGRSRDGGLRLGEMERDCLIAYGASMLLLERLMISSDAFEVDVCRQCGLL-GY---KGWCTTCKSSKNVAKMKI 1126 (1153)
T ss_pred eecCCCCCcCCCCCcccchhhhhhhhhccHHHHHHHHHhhcCcceeeeeccccccc-ee---chhhhhccCCCceeeeec
Confidence 99999999999999999999999999999999999999 66666532 21 368999999999999999
Q ss_pred hHhHHHHHHHHHhhcCCeEEEEeccC
Q 014847 385 PYGAKLLSQELSFSMGITLKFDTQLS 410 (417)
Q Consensus 385 py~~k~l~~EL~~sm~i~~~l~~~~~ 410 (417)
|||||||+||| +||||-+||.+++.
T Consensus 1127 PYAcKLLFQEL-~SMNi~PrL~L~~~ 1151 (1153)
T KOG0215|consen 1127 PYACKLLFQEL-QSMNIVPRLKLEDY 1151 (1153)
T ss_pred cHHHHHHHHHH-HhcCccceeeeccc
Confidence 99999999999 99999999999864
No 7
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]
Probab=100.00 E-value=4.2e-107 Score=891.76 Aligned_cols=374 Identities=28% Similarity=0.405 Sum_probs=343.4
Q ss_pred CcccccccccccCCCCCcCCCcccccccccccCCccccccccccchhhcccccccccCccceEeec-----------ccc
Q 014847 1 MSFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRPLFWIL-----------ISD 69 (417)
Q Consensus 1 p~~ilsi~AslIPF~~h~~NqSpRn~yq~~~M~KQamG~~~~n~~~R~D~~~~~l~ypQ~PLV~t~-----------~~d 69 (417)
|..|+|+.|++|||++| ||||||||||+ |+||++|++..|+..|.|+..+.++|||.|+|+|. .+-
T Consensus 607 ~~~I~~~~~~~~~~~~~--n~~~~n~~~~~-~~~Q~~~~~~~~~~~~~d~~~~~~~~~~~P~~~~~e~~~GqN~~VA~m~ 683 (1060)
T COG0085 607 PIVILGIEASLIPYPEH--NQSPYNLYKFA-RSNQATGINQRPLVKRGDTVEKGLVYADGPSVDTGELALGQNALVAFMP 683 (1060)
T ss_pred eeEEEeeccccCCcccc--CcChHHHHHHh-hhhcccCCCcccceeccccccccceecCCCccccCcccCCceeEEEEec
Confidence 57899999999999999 99999999999 89999999999999999999999999999999972 233
Q ss_pred ccCCC-CCeEEEecceecccceeeEEEEEEEe---c-----ccccC---------CCCCCCccccccccccccCCeEEEE
Q 014847 70 CLGRP-EDSLVMNQASLECGVFRSESYKAEVD---N-----KDIQV---------KSRPSDDMLNFGKIQSKSGDIVIGK 131 (417)
Q Consensus 70 ~lg~n-EDAiIiNKssidRG~f~s~~Yk~e~~---~-----~~~~~---------~~~~~~g~~~~g~~~v~~GDiligk 131 (417)
+-|+| ||||||||++++||+|||++|+++.. + .+++. +.+|++|++.+|. .|++|||||||
T Consensus 684 ~~GYn~EDAiiin~~~v~~~~~ts~~~~~~~~~~r~~~~g~e~~~~iP~~~e~~~~~Lde~Gii~ig~-~V~~gdilvgk 762 (1060)
T COG0085 684 WNGYNYEDAIIISERSVERDLFTSIHIEEYETEARDTKLGPEEIRDIPNVSEEALRNLDEDGIIRIGA-EVKGGDILVGK 762 (1060)
T ss_pred ccCcChhHheecccchhhcCCceEEEEEEEeeeeeccCCCccccccCCCcCHHHHhcCCccCcccccc-EEcCCCEEEEe
Confidence 56777 99999999999999999997766442 1 12221 3478999999996 89999999999
Q ss_pred eccCC------------------ceeEEEecCCCceeEEEEEEEeCCC----CCeEEEEEEeeccccccccccccccccc
Q 014847 132 YAEIG------------------ADHSIKLKHTERGLVLKVLLSSNDD----GKNFAVVSIRQSVNMVHSACLGDKFSSM 189 (417)
Q Consensus 132 ~~~~~------------------~d~s~~~k~~e~g~Vd~V~i~~~~~----g~~~vkv~ir~~~~~~R~p~iGDKfssR 189 (417)
++|++ +|+|++++++|+|+||+|.++++++ +.++|||++|+ .|.|++|||||||
T Consensus 763 ~tP~~~~~~~~ee~ll~i~~ek~rdtsl~~~~g~~G~V~~V~~~~~~~~~~g~~~~vkV~v~~----~R~~~~GDK~a~R 838 (1060)
T COG0085 763 VTPKGETELTPEERLLRIFGEKVRDTSLRVPHGEEGIVDDVQVFTREDGDPGVNKLVKVYVAQ----KRKPQIGDKMAGR 838 (1060)
T ss_pred eCCCCCCCCCchhhhhccccceeeccceeecCCCCeEEEEEEEEeccCCCcCceEEEEEEEEE----eccCCcccccccc
Confidence 99864 5899999999999999999999987 67899999999 9999999999999
Q ss_pred cCCceeEeeec--------------------------cchhHHHHHhhhhh-hhcCCceeecCCCCCCHHHHHHHHHH-h
Q 014847 190 HGQKGVLGFLE--------------------------QTPAQLLEAALGKG-ACDGLMSYATPFATSTGGVITEQHQS-F 241 (417)
Q Consensus 190 HGqKGvvs~i~--------------------------MtiGql~E~~~g~~-~~~g~~~~~tpF~~~~~~~i~~~l~~-~ 241 (417)
||||||||+|| |||||++|+++||+ ++.|...+++||++.+.+++.+.|.+ |
T Consensus 839 HG~KGVis~i~p~eDMPf~~~G~~~DiilNP~gvPSRM~iGqilE~~lG~a~~~~G~~~~~~~F~g~~~~~~~~~l~~~g 918 (1060)
T COG0085 839 HGNKGVVSKIVPQEDMPFLEDGTPPDIILNPLGVPSRMNIGQILETHLGKAAALLGIPVDTPVFDGAPEEDIRELLKEAG 918 (1060)
T ss_pred CCCCceeeeecCcccCCcCCCCCcccEEECCCCCCccccHHHHHHHHHHHHHHhcCceeccCCcCCCCHHHHHHHHHHcC
Confidence 99999999999 99999999999999 78999999999999999999999999 9
Q ss_pred cccccccccCCCCCeeEeeccccceeeccCCCCccccceeeeeeEEEeeehhhhccccccccccccccCCCCCcccCCcc
Q 014847 242 VSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVA 321 (417)
Q Consensus 242 ~~~~g~~~~~~~~gk~~l~~g~~~~~~~~~~~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~ 321 (417)
|+..|+ +.|||| +||++|+++||||++|||||+|||+||+||||||||+.+||||++
T Consensus 919 ~~~~Gk---------~~lydG--------------~TGe~~~~~i~vG~~Y~~kL~HmV~dK~HaRs~GP~s~lT~QP~~ 975 (1060)
T COG0085 919 FPYSGK---------EVLYDG--------------RTGEPFDAPIFVGVMYYQKLHHMVDDKIHARSTGPYSLVTQQPLG 975 (1060)
T ss_pred CCCCCC---------EEeecC--------------CCCCcccccEEEEehHHHhHHhhhcccceeeccCCceeeecCCCC
Confidence 988777 999999 999999999999999999999999999999999999999999999
Q ss_pred cccCCCceeeeeccchhhhhcchhhhhhhhhcccccccccccccCCeeecccCCCCccccccChHhHHHHHHHHHhhcCC
Q 014847 322 DRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGI 401 (417)
Q Consensus 322 Gr~~~GG~RfGEME~d~LiahGas~~L~ErL~c~~~~~~~~~~~~~~~c~~c~~~~~~~~~~ipy~~k~l~~EL~~sm~i 401 (417)
||+|+|||||||||||||+|||||++|+|||+.+|| +++.|.. ..-|..|. .++..+.||||||+|++|| +||||
T Consensus 976 Gka~~GG~RfGEME~~aL~ayGAa~~LqE~L~~~SD-~~~G~~~-~y~~~v~g--~~~~~~~ip~sFk~L~~El-~sl~i 1050 (1060)
T COG0085 976 GKAQFGGQRFGEMEVWALEAYGAAYTLQERLTVKSD-DVCGRIK-IYECIVKG--ENIPEVGIPESFKVLLKEL-RSLGI 1050 (1060)
T ss_pred cccccCCccccchHHHHHHHHhHHHHHHHHhhccch-hcccchh-hhcCcccC--CCCCCCCCCHHHHHHHHHH-HHCCC
Confidence 999999999999999999999999999999999998 5666643 34499997 4889999999999999999 99999
Q ss_pred eEEEEeccC
Q 014847 402 TLKFDTQLS 410 (417)
Q Consensus 402 ~~~l~~~~~ 410 (417)
++++.+++.
T Consensus 1051 ~~~l~~~~~ 1059 (1060)
T COG0085 1051 DVRLELEDG 1059 (1060)
T ss_pred ceEEeecCC
Confidence 999998764
No 8
>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=5.3e-106 Score=900.27 Aligned_cols=369 Identities=24% Similarity=0.338 Sum_probs=327.0
Q ss_pred CcccccccccccCCCCCcCCCcccccccccccCCcccccc-----------------------------------ccccc
Q 014847 1 MSFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFP-----------------------------------TTNPN 45 (417)
Q Consensus 1 p~~ilsi~AslIPF~~h~~NqSpRn~yq~~~M~KQamG~~-----------------------------------~~n~~ 45 (417)
|.+|||++||||||+|| ||||||+|||| |+|||||++ ++|+.
T Consensus 535 p~~ilsv~aslIPFleH--Nds~R~lmgsn-M~kQavpl~~~e~p~VgTg~E~~v~~ds~~~i~a~~~G~v~~v~~~~~~ 611 (1065)
T TIGR02013 535 PKQVVSVAASLIPFLEH--DDANRALMGSN-MQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIV 611 (1065)
T ss_pred hhhhhhhHhhcCCCccc--cCCcchhhhhh-hhhhhhcccccCCCEEEcCcchhhhccccceeEeccCCEEEEEccceEE
Confidence 78999999999999999 99999999999 899999998 88999
Q ss_pred hhhcc-------------------cccccccCccceEeec----ccc-------------------------ccCCC-CC
Q 014847 46 IRVDT-------------------LLQQLFYPQRPLFWIL----ISD-------------------------CLGRP-ED 76 (417)
Q Consensus 46 ~R~D~-------------------~~~~l~ypQ~PLV~t~----~~d-------------------------~lg~n-ED 76 (417)
.|.|+ ++|.++|||+|||+|. ..| +.|+| ||
T Consensus 612 ~r~d~~~~~~~~~~~~y~L~~~~~snq~~~~~q~Plv~~~~~v~~~~~l~d~~~~~~~e~~~G~N~~VAvm~y~GYn~ED 691 (1065)
T TIGR02013 612 IRYDEDEDEPDGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYED 691 (1065)
T ss_pred EEecCCcccccccceEEEeecccccccCceEEeeeeeccCCeEeeeeEecccccccCCcCcCccceEEEEEeeecccccc
Confidence 99984 4567899999999982 222 23444 99
Q ss_pred eEEEecceecccceeeEEEEEEEe---c-c---ccc-----------CCCCCCCccccccccccccCCeEEEEeccC---
Q 014847 77 SLVMNQASLECGVFRSESYKAEVD---N-K---DIQ-----------VKSRPSDDMLNFGKIQSKSGDIVIGKYAEI--- 135 (417)
Q Consensus 77 AiIiNKssidRG~f~s~~Yk~e~~---~-~---~~~-----------~~~~~~~g~~~~g~~~v~~GDiligk~~~~--- 135 (417)
||||||+|+|||+|||++|+++.. . + +.+ -+.+|.||++.+|. .|++|||||||++|.
T Consensus 692 Aiiink~~i~rg~~~s~~~~~~~~~~~~~~~g~e~~~~~~p~~~~~~~~~Ld~dGi~~~G~-~v~~gdilvgk~~p~~~~ 770 (1065)
T TIGR02013 692 AILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGA-EVKAGDILVGKVTPKGET 770 (1065)
T ss_pred eEEeehhhhcCCceEEEEEEEEEEEeeccCCCceEeeccCCCCchhhhhccCCCCCccCcc-EeCCCCEEEEEecCCccc
Confidence 999999999999999997765431 1 0 111 12367899999997 899999999999872
Q ss_pred -------------------CceeEEEecCCCceeEEEEEEEeCCCC-------CeEEEEEEeeccccccccccccccccc
Q 014847 136 -------------------GADHSIKLKHTERGLVLKVLLSSNDDG-------KNFAVVSIRQSVNMVHSACLGDKFSSM 189 (417)
Q Consensus 136 -------------------~~d~s~~~k~~e~g~Vd~V~i~~~~~g-------~~~vkv~ir~~~~~~R~p~iGDKfssR 189 (417)
.+|+|++++++|+|+||+|.+++++++ ...++|++|+ .|+|+||||||||
T Consensus 771 ~~~~~~~l~~~~~~~~~~~~~d~s~~~~~~~~g~V~~V~~~~~~~~~~~~~~~~~~vkv~ir~----~R~p~iGDKfasR 846 (1065)
T TIGR02013 771 ELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSRKQGDELPPGVNKLVKVYIAQ----KRKIQVGDKMAGR 846 (1065)
T ss_pred ccChhhhhhhhhcccCCccccccceEccCCCCEEEEEEEEEeccCCCccCcCccEEEEEEEee----cccccccchhhhc
Confidence 258899999999999999999987766 4679999999 9999999999999
Q ss_pred cCCceeEeeec--------------------------cchhHHHHHhhhhh-hhc--CCceeecC-CCCCCHHHHHHHHH
Q 014847 190 HGQKGVLGFLE--------------------------QTPAQLLEAALGKG-ACD--GLMSYATP-FATSTGGVITEQHQ 239 (417)
Q Consensus 190 HGqKGvvs~i~--------------------------MtiGql~E~~~g~~-~~~--g~~~~~tp-F~~~~~~~i~~~l~ 239 (417)
||||||||+|| ||||||+|+++||+ ++. |...++|| |++.+.+++.+.|+
T Consensus 847 HGqKGvis~i~~~eDMPf~~~G~~pDiIiNPhg~PSRMtiGqllE~~~gka~~~~~~~~~~~~tp~f~~~~~~~~~~~l~ 926 (1065)
T TIGR02013 847 HGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRKGVPIATPVFDGASEEEIKEYLE 926 (1065)
T ss_pred ccCceeEEeEecCCCCCccCCCCCccEEECCCCCcccccHHHHHHHHHHHHHHhccCCCeEEeccCcCCccHHHHHHHHH
Confidence 99999999999 99999999999999 544 66788999 99889999999999
Q ss_pred H-hcccccccccCCCCCeeEeeccccceeeccCCCCccccceeeeeeEEEeeehhhhccccccccccccccCCCCCcccC
Q 014847 240 S-FVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGR 318 (417)
Q Consensus 240 ~-~~~~~g~~~~~~~~gk~~l~~g~~~~~~~~~~~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~Q 318 (417)
+ ||+++|+ |.|||| +||++|+++||+|++|||||+|||+||+|||++||++.||||
T Consensus 927 ~~g~~~~G~---------e~l~~G--------------~TG~~~~~~ifvG~~yy~rL~HmV~DK~haRs~Gp~~~lT~Q 983 (1065)
T TIGR02013 927 KAGLPRDGK---------VRLYDG--------------RTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQ 983 (1065)
T ss_pred HcCCCCCCC---------EEEEcC--------------CCCCCccccEEEeehheeechhhhcchhhhcccCCccceeeC
Confidence 8 9988877 999999 999999999999999999999999999999999999999999
Q ss_pred CcccccCCCceeeeeccchhhhhcchhhhhhhhhcccccccccccccCCeeecccCCCCccccccChHhHHHHHHHHHhh
Q 014847 319 PVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFS 398 (417)
Q Consensus 319 P~~Gr~~~GG~RfGEME~d~LiahGas~~L~ErL~c~~~~~~~~~~~~~~~c~~c~~~~~~~~~~ipy~~k~l~~EL~~s 398 (417)
|++||+|+|||||||||||||+|||||++|+|||+.+|| ++.+|.. .++..| ++..+.++.+|||||||++|| +|
T Consensus 984 P~~Grsr~GG~R~GEME~d~l~a~Gas~~L~E~l~~~SD-~~~g~~~--~~~~~~-~~~~i~~~~~p~sfklL~~EL-~s 1058 (1065)
T TIGR02013 984 PLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD-DVVGRTK--AYEAIV-KGENVPEPGIPESFNVLIKEL-QS 1058 (1065)
T ss_pred CCcccccCCCeeeeeeeHHHHHhhhhHHHHHHHHhccCh-hhhhhhh--hhhhhc-CCCccccccCCccHHHHHHHH-Hh
Confidence 999999999999999999999999999999999999998 5555542 455666 567899999999999999999 99
Q ss_pred cCCeEEE
Q 014847 399 MGITLKF 405 (417)
Q Consensus 399 m~i~~~l 405 (417)
|||++++
T Consensus 1059 m~i~~~~ 1065 (1065)
T TIGR02013 1059 LGLDIEL 1065 (1065)
T ss_pred CCccccC
Confidence 9999875
No 9
>PRK00405 rpoB DNA-directed RNA polymerase subunit beta; Reviewed
Probab=100.00 E-value=4.4e-104 Score=888.50 Aligned_cols=370 Identities=25% Similarity=0.357 Sum_probs=325.5
Q ss_pred CcccccccccccCCCCCcCCCcccccccccccCCcccccccc-----------------------------------ccc
Q 014847 1 MSFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTT-----------------------------------NPN 45 (417)
Q Consensus 1 p~~ilsi~AslIPF~~h~~NqSpRn~yq~~~M~KQamG~~~~-----------------------------------n~~ 45 (417)
|.++||++||||||++| ||||||+|||+ |+|||||+... |+.
T Consensus 578 p~qi~sv~aslIPFleH--nda~R~lmgSn-MqrQAvpl~~~~~p~vgTg~e~~~~~ds~~~i~a~~~G~v~~v~~~~i~ 654 (1112)
T PRK00405 578 PKQVVSVAASLIPFLEH--DDANRALMGSN-MQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIV 654 (1112)
T ss_pred hhhhceehhhccCcccc--cCCcchhhhhh-hhhhhhhhccccCCeeecCcchhhhhhcchheEeccCCEEEEEeCCEEE
Confidence 78999999999999999 99999999999 89999999988 777
Q ss_pred hhh-----------------cccccc-cccCccceEeecc----cc-------------------------ccCCC-CCe
Q 014847 46 IRV-----------------DTLLQQ-LFYPQRPLFWILI----SD-------------------------CLGRP-EDS 77 (417)
Q Consensus 46 ~R~-----------------D~~~~~-l~ypQ~PLV~t~~----~d-------------------------~lg~n-EDA 77 (417)
.|. |+..+. ++|||+|||+|.. .| +.|+| |||
T Consensus 655 ir~~~~~~~~~~~~~y~L~~~~~sn~~~~~~q~Plv~~~~~v~~g~~lad~~~~~~~e~~~G~N~~VA~~~y~GYn~EDa 734 (1112)
T PRK00405 655 VRVEELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQNVLVAFMPWNGYNFEDA 734 (1112)
T ss_pred EeecccccCCCCeeEEEecccccccccceeecceeeecCCeEeeccEeecccccCcccccCCcceEEEEEeecccCccce
Confidence 777 544444 9999999999872 22 22444 999
Q ss_pred EEEecceecccceeeEEEEEEE---ec-c---ccc-----------CCCCCCCccccccccccccCCeEEEEeccC----
Q 014847 78 LVMNQASLECGVFRSESYKAEV---DN-K---DIQ-----------VKSRPSDDMLNFGKIQSKSGDIVIGKYAEI---- 135 (417)
Q Consensus 78 iIiNKssidRG~f~s~~Yk~e~---~~-~---~~~-----------~~~~~~~g~~~~g~~~v~~GDiligk~~~~---- 135 (417)
|||||+|+|||+|+|++|+... .. + +.+ -+.+|.||++.+|. .|++|||||||++|+
T Consensus 735 iiink~si~rg~~~s~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~Ld~dGi~~~G~-~v~~gDiligk~~~~~~~~ 813 (1112)
T PRK00405 735 ILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGA-EVKPGDILVGKVTPKGETE 813 (1112)
T ss_pred EEEEhhhhccCceEEEEEeeeeeEeeccCCCceeecccCCCCChHHhhccCCCCCccCcc-EecCCCEEEEEecCCCccc
Confidence 9999999999999999765433 11 0 111 12367899999997 899999999999863
Q ss_pred ------------------CceeEEEecCCCceeEEEEEEEeC-CCC-------CeEEEEEEeeccccccccccccccccc
Q 014847 136 ------------------GADHSIKLKHTERGLVLKVLLSSN-DDG-------KNFAVVSIRQSVNMVHSACLGDKFSSM 189 (417)
Q Consensus 136 ------------------~~d~s~~~k~~e~g~Vd~V~i~~~-~~g-------~~~vkv~ir~~~~~~R~p~iGDKfssR 189 (417)
.+|+|++++++|+|+||+|.++++ +++ ...++|++|+ .|+|+||||||||
T Consensus 814 ~~~~~~~~~~~~~~~~~~~~d~s~~~~~~~~g~V~~v~~~~~~~~~~~~~~~~~~~vkv~ir~----~R~p~iGDKfasR 889 (1112)
T PRK00405 814 LTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTRIEQGDELPPGVNKLVKVYIAQ----KRKIQVGDKMAGR 889 (1112)
T ss_pred cChhhhhhhhhhcccccccccceEEcCCCCCEEEEEEEEeeccccCCccCcCcceEEEEEEee----ecccCcccchhhc
Confidence 257999999999999999999987 555 3689999999 9999999999999
Q ss_pred cCCceeEeeec--------------------------cchhHHHHHhhhhh-hhcCCceeecC-CCCCCHHHHHHHHHH-
Q 014847 190 HGQKGVLGFLE--------------------------QTPAQLLEAALGKG-ACDGLMSYATP-FATSTGGVITEQHQS- 240 (417)
Q Consensus 190 HGqKGvvs~i~--------------------------MtiGql~E~~~g~~-~~~g~~~~~tp-F~~~~~~~i~~~l~~- 240 (417)
||||||||+|| ||||||+|+++||+ ++.|.+ ++|| |++.+.+++.+.|.+
T Consensus 890 HGqKGvis~i~~~eDMPf~~~G~~pDiIiNPhg~PSRMtiGql~E~~~gk~~~~~g~~-~~tp~f~~~~~~~~~~~l~~~ 968 (1112)
T PRK00405 890 HGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIK-FATPVFDGAKEEEIKELLEEA 968 (1112)
T ss_pred cCCceeEEeEeccCCCCcCCCCCCCcEEECCCCCcccccHHHHHHHHhhHHHHhcCCe-EecCccCCccHHHHHHHHHHc
Confidence 99999999999 99999999999999 667765 8998 998899999999999
Q ss_pred hcccccccccCCCCCeeEeeccccceeeccCCCCccccceeeeeeEEEeeehhhhccccccccccccccCCCCCcccCCc
Q 014847 241 FVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPV 320 (417)
Q Consensus 241 ~~~~~g~~~~~~~~gk~~l~~g~~~~~~~~~~~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~ 320 (417)
||+++|+ |.|||| +||++|+++||+|++|||||+|||+||+|||++||++.|||||+
T Consensus 969 g~~~~G~---------e~l~~G--------------~tG~~~~~~if~G~~yy~rL~HmV~DK~haRs~Gp~~~lT~QP~ 1025 (1112)
T PRK00405 969 GLPEDGK---------TTLYDG--------------RTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPL 1025 (1112)
T ss_pred CcCCCCC---------EEEECC--------------CCCCCCcccEEEEehhheechhhhcchhhhcccCCccceeeCCC
Confidence 9998888 999999 99999999999999999999999999999999999999999999
Q ss_pred ccccCCCceeeeeccchhhhhcchhhhhhhhhcccccccccccccCCeeecccCCCCccccccChHhHHHHHHHHHhhcC
Q 014847 321 ADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMG 400 (417)
Q Consensus 321 ~Gr~~~GG~RfGEME~d~LiahGas~~L~ErL~c~~~~~~~~~~~~~~~c~~c~~~~~~~~~~ipy~~k~l~~EL~~sm~ 400 (417)
+||+|+|||||||||||||+|||||++|+|||+-+|| ++.+|.. .++..| ++..+.++.+|||||+|+||| +|||
T Consensus 1026 ~Grsr~GG~R~GEME~d~l~a~Gas~~L~Erl~~~SD-~~~g~~~--~~~~~~-~~~~i~~~~~p~~fklL~~EL-~sm~ 1100 (1112)
T PRK00405 1026 GGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD-DVVGRTK--VYEAIV-KGENIPEPGIPESFNVLVKEL-QSLG 1100 (1112)
T ss_pred cccccCCCeeeeeeehhhHhhhhhHHHHHHHhhccCc-cccccee--EEEEee-cCCcccccCCChHHHHHHHHH-HHCc
Confidence 9999999999999999999999999999999988888 4445543 343366 567899999999999999999 9999
Q ss_pred CeEEEEe
Q 014847 401 ITLKFDT 407 (417)
Q Consensus 401 i~~~l~~ 407 (417)
|++++..
T Consensus 1101 i~~~~~~ 1107 (1112)
T PRK00405 1101 LDVELLD 1107 (1112)
T ss_pred cceEEec
Confidence 9999984
No 10
>CHL00001 rpoB RNA polymerase beta subunit
Probab=100.00 E-value=5.4e-102 Score=865.44 Aligned_cols=379 Identities=20% Similarity=0.254 Sum_probs=322.2
Q ss_pred CcccccccccccCCCCCcCCCcccccccccccCCccccccccc---------cchhh-----------------c-----
Q 014847 1 MSFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTN---------PNIRV-----------------D----- 49 (417)
Q Consensus 1 p~~ilsi~AslIPF~~h~~NqSpRn~yq~~~M~KQamG~~~~n---------~~~R~-----------------D----- 49 (417)
|.+++|++||||||+|| ||||||+|||| |+|||||+...| +..|. |
T Consensus 520 P~qi~svaasLIPFleH--ndanRalmgsn-MqrQAvpll~~~~p~VgTG~E~~~~~ds~~~i~a~~~G~V~~vd~~~I~ 596 (1070)
T CHL00001 520 PFQYFSIGASLIPFLEH--NDANRALMGSN-MQRQAVPLSRSEKCIVGTGLERQVALDSGVVAIAEHEGKIIYTDTDKII 596 (1070)
T ss_pred hhhhhhhhhhcCCCccc--cCcchhhhhhc-cchhccccccCCCCEeecCcchhhhhcccceeEEccCCEEEEEeCCEEE
Confidence 78999999999999999 99999999999 899999999988 66666 5
Q ss_pred ------c-ccccccc---------CccceEeec--------ccc---------------------ccCCC-CCeEEEecc
Q 014847 50 ------T-LLQQLFY---------PQRPLFWIL--------ISD---------------------CLGRP-EDSLVMNQA 83 (417)
Q Consensus 50 ------~-~~~~l~y---------pQ~PLV~t~--------~~d---------------------~lg~n-EDAiIiNKs 83 (417)
+ ..+.+.| ||+|||++. ++| +.|+| ||||||||+
T Consensus 597 i~~~~~~~~y~l~~y~rsnq~t~~~QkPlV~~g~~v~~g~~ladg~~~~~gel~~G~N~~VA~m~~~GYn~EDAiiin~~ 676 (1070)
T CHL00001 597 LSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCVKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISER 676 (1070)
T ss_pred EEcCCCeEEEEeeceeccCCCcccccCCEEecCCEEccCCEeccChhhccccccCCccceeeeeeccccccchhhhhhhh
Confidence 3 2344445 999999964 222 23445 999999999
Q ss_pred eecccceeeEEEEEEE---ec-c---cccC-----------CCCCCCccccccccccccCCeEEEEeccC----------
Q 014847 84 SLECGVFRSESYKAEV---DN-K---DIQV-----------KSRPSDDMLNFGKIQSKSGDIVIGKYAEI---------- 135 (417)
Q Consensus 84 sidRG~f~s~~Yk~e~---~~-~---~~~~-----------~~~~~~g~~~~g~~~v~~GDiligk~~~~---------- 135 (417)
|++||+|+|++|+.+. .. + +.+. +.+|+||++.+|. +|++|||||||++|+
T Consensus 677 ~v~~g~~~s~~~~~~~~~~~~~~~g~e~i~~~~p~~~~~~~~~Ld~dGi~~~G~-~v~~gDilvgK~~p~~~~~~~~~~~ 755 (1070)
T CHL00001 677 LVYEDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEAHLLRNLDKNGIVMLGS-WVETGDILVGKLTPQEAEESSYAPE 755 (1070)
T ss_pred hhcCCceEEEEEeeeeEEEeccCCCcceEeccCCCCchhhhhccCCCCCccCCc-EecCCCEEEEEecCCcccccccCcc
Confidence 9999999999765433 21 1 1111 2367899999996 899999999999874
Q ss_pred --------------CceeEEEecCCCceeEEEEEEEeC----CCCCeEEEEEEeeccccccccccccccccccCCceeEe
Q 014847 136 --------------GADHSIKLKHTERGLVLKVLLSSN----DDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLG 197 (417)
Q Consensus 136 --------------~~d~s~~~k~~e~g~Vd~V~i~~~----~~g~~~vkv~ir~~~~~~R~p~iGDKfssRHGqKGvvs 197 (417)
.+|+|++++++++|+|++|.+++. .++...|+|++|+ .|+|++|||||||||||||||
T Consensus 756 ~~~~~~if~~~~~~~~d~sl~~~~~~~g~V~~v~~~~~~~~~~~~~~~vkv~i~~----~R~~~vGDK~asRHGqKGvvs 831 (1070)
T CHL00001 756 GRLLRAIFGIQVSTSKETCLKLPIGGRGRVIDVRWIQKKGGSSYNPETIHVYILQ----KREIQVGDKVAGRHGNKGIIS 831 (1070)
T ss_pred hhhhhhhhccccCcceeCeEECCCCCceEEEEEEEEecccCCCCCcEEEEEEEEE----EecCCCCcccccccCCcceEe
Confidence 258999999999999999999984 3456789999999 999999999999999999999
Q ss_pred eec--------------------------cchhHHHHHhhhhh-hhcCCceeecCCCCCCHHHHH-----HHHHH-hccc
Q 014847 198 FLE--------------------------QTPAQLLEAALGKG-ACDGLMSYATPFATSTGGVIT-----EQHQS-FVSQ 244 (417)
Q Consensus 198 ~i~--------------------------MtiGql~E~~~g~~-~~~g~~~~~tpF~~~~~~~i~-----~~l~~-~~~~ 244 (417)
+|+ ||||||+|+++||+ ++.|.+.+++||++...+++. ..|.+ ++.
T Consensus 832 ~i~~~eDMPf~~dG~~pDiIlNP~gvPSRMtiGqllE~~~G~a~~~~g~~~~~~pf~~~~~~~~~~~~~~~~l~~~~~~- 910 (1070)
T CHL00001 832 KILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLLNRHYRIAPFDERYEQEASRKLVFSELYEASKQ- 910 (1070)
T ss_pred eeecccCCCcccCCCCCceeeccccccccccHHHHHHHHhHHHHhhcCceeeeccCCCcchhhhhhhhhhHHHHHHHHh-
Confidence 999 99999999999999 678999999999987666655 34555 552
Q ss_pred ccccc--cCCCCCeeEeeccccceeeccCCCCccccceeeeeeEEEeeehhhhccccccccccccccCCCCCcccCCccc
Q 014847 245 LLNCI--GARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVAD 322 (417)
Q Consensus 245 ~g~~~--~~~~~gk~~l~~g~~~~~~~~~~~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~G 322 (417)
.++.| +++.+||+.|||| +||++|+++||+|++|||||+|||+||+|||++|||+.|||||++|
T Consensus 911 ~~~~~~~~~~~~Gk~~l~dG--------------~TG~~~~~~i~vG~~Yy~kL~HmV~DKihaRs~Gp~~~lT~QP~~G 976 (1070)
T CHL00001 911 TANPWVFEPEYPGKSRLFDG--------------RTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRG 976 (1070)
T ss_pred cCCceeccCCCCCeEEEEcC--------------CCCCCccceEEEEecceeEchhhccccceeeccCCCcccccCCCCc
Confidence 12223 4677899999999 9999999999999999999999999999999999999999999999
Q ss_pred ccCCCceeeeeccchhhhhcchhhhhhhhhcccccccccccccCCeeecccCCCCcccc-ccChHhHHHHHHHHHhhcCC
Q 014847 323 RKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVIQRVVGGPYCRICNSADDIIK-ANVPYGAKLLSQELSFSMGI 401 (417)
Q Consensus 323 r~~~GG~RfGEME~d~LiahGas~~L~ErL~c~~~~~~~~~~~~~~~c~~c~~~~~~~~-~~ipy~~k~l~~EL~~sm~i 401 (417)
|+|+|||||||||||||+|||||++|+|||+.+|| ++.+|.. .+..|..+..+.+ +.+|||||+|++|| +|||+
T Consensus 977 rsr~GG~RfGEME~~al~a~GAs~~L~E~L~~~SD-~~~~r~~---~~~~i~~g~~~~~~~~~pesfk~l~~El-~~l~l 1051 (1070)
T CHL00001 977 RSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSD-HIRARQE---VLGAIITGGTIPKPEDAPESFRLLVREL-RSLAL 1051 (1070)
T ss_pred ccCCCCeeeecchHHHHHhhhHHHHHHHHHhccCc-cHHHHHH---HHHhhhcCCcccCCCCCCchhhHHHHHH-HhCcc
Confidence 99999999999999999999999999999999998 5655532 2223455667777 79999999999999 99999
Q ss_pred eEEEEe
Q 014847 402 TLKFDT 407 (417)
Q Consensus 402 ~~~l~~ 407 (417)
++++..
T Consensus 1052 ~i~~~~ 1057 (1070)
T CHL00001 1052 ELNHFL 1057 (1070)
T ss_pred ceEEEE
Confidence 998864
No 11
>CHL00207 rpoB RNA polymerase beta subunit; Provisional
Probab=100.00 E-value=1.7e-99 Score=842.67 Aligned_cols=383 Identities=23% Similarity=0.296 Sum_probs=329.4
Q ss_pred CcccccccccccCCCCCcCCCcccccccccccCCcccccccc--------------------------------------
Q 014847 1 MSFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTT-------------------------------------- 42 (417)
Q Consensus 1 p~~ilsi~AslIPF~~h~~NqSpRn~yq~~~M~KQamG~~~~-------------------------------------- 42 (417)
|.+++|++||||||.+| |+++|++|||| |++||+++...
T Consensus 514 p~Q~~SvaasLIPFLeh--dDanRaLMGsn-MqrQaVPll~~e~p~VgTg~e~~~a~ds~~~i~a~~~G~v~~v~~~~I~ 590 (1077)
T CHL00207 514 PIQVFSIAESLIPFLEH--NDANRALMGSN-MQRQAVPLLYPEKPIVGTGYEKQIALDSGMTIISLTEGIVVSVSAYKII 590 (1077)
T ss_pred cchhcchhhhcCCcccc--cccchhhhhhc-cccccccccccCCCeEECCcchHhhhhcchheEeccCcEEEEecCcEEE
Confidence 78899999999999999 99999999999 89999988531
Q ss_pred ----------ccchhhcccccccccCccceEe--------ecccc---------------------ccCCC-CCeEEEec
Q 014847 43 ----------NPNIRVDTLLQQLFYPQRPLFW--------ILISD---------------------CLGRP-EDSLVMNQ 82 (417)
Q Consensus 43 ----------n~~~R~D~~~~~l~ypQ~PLV~--------t~~~d---------------------~lg~n-EDAiIiNK 82 (417)
....+|.++||.+++.|+|+|+ +.++| +.|+| ||||||||
T Consensus 591 i~~~~~~~~~y~l~~~~rsNq~t~i~qrp~V~~G~~v~~G~iladg~~~~~~el~lG~N~lVA~m~y~GYN~EDAiiink 670 (1077)
T CHL00207 591 IQDDNNRYIHYYLQKYQRSNQNTCINYRPIVWVGEKINIGQILADGSDIDNSELALGQNVLVAYMPWEGYNFEDAILINK 670 (1077)
T ss_pred EEeCCCceeEEEeccccccccCceeecccccCCCCEEecCCEEecchhccCCcccCCcccEEEEEeeeccccchhhhhhh
Confidence 1234567889999999999998 23444 33555 99999999
Q ss_pred ceecccceeeEEEEE---EEec-c---ccc-----------CCCCCCCccccccccccccCCeEEEEeccC---------
Q 014847 83 ASLECGVFRSESYKA---EVDN-K---DIQ-----------VKSRPSDDMLNFGKIQSKSGDIVIGKYAEI--------- 135 (417)
Q Consensus 83 ssidRG~f~s~~Yk~---e~~~-~---~~~-----------~~~~~~~g~~~~g~~~v~~GDiligk~~~~--------- 135 (417)
++++||+|+|++|+. +... + +.+ -+.+|+||++.+|. .|++|||||||++|+
T Consensus 671 ~~v~rg~f~Si~~~~~~~e~~~~~~g~e~i~~~~p~~~~~~~~~LD~dGiv~iG~-~V~~gDilvgK~tp~~~~~~~~~~ 749 (1077)
T CHL00207 671 RLVYEDLFTSIHIEKYEIELRQTKLGSEEITRNIPNVSEYSLKNLDENGIISIGS-KVLAGDILVGKITPKGESDQLPEG 749 (1077)
T ss_pred hhhcCCceEEEEEEEeeeEEeecCCCceEEeccCCCCChHHhhccCccCCCcCCc-EeCCCCEEEEEecCccccccChhh
Confidence 999999999996544 3321 0 111 13467899999996 899999999999873
Q ss_pred -------------CceeEEEecCCCceeEEEEEEEeCCCCC-------eEEEEEEeeccccccccccccccccccCCcee
Q 014847 136 -------------GADHSIKLKHTERGLVLKVLLSSNDDGK-------NFAVVSIRQSVNMVHSACLGDKFSSMHGQKGV 195 (417)
Q Consensus 136 -------------~~d~s~~~k~~e~g~Vd~V~i~~~~~g~-------~~vkv~ir~~~~~~R~p~iGDKfssRHGqKGv 195 (417)
.+|+|++++++++|+|++|.+++++++. ..++|.+|+ .|+|+||||||||||||||
T Consensus 750 ~ll~~i~~~~~~~~kd~sl~~~~~~~g~V~~V~~~~~~~~~~~~~~~~~~vkv~i~~----~R~p~vGDKfasRHGqKGV 825 (1077)
T CHL00207 750 KLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRSKGDELKFGYYLKIRVFIAQ----IRKIQVGDKLAGRHGNKGI 825 (1077)
T ss_pred hhhhhhhccCCCcceEeEEEcCCCCcEEEEEEEEEecCCCCcccccccEEEEEEEEE----EecCCcccccccccCCcee
Confidence 2789999999999999999999864332 248888999 9999999999999999999
Q ss_pred Eeeec--------------------------cchhHHHHHhhhhh-hhcCCceeecCCCCCCHHHHHHHHHH-hcc----
Q 014847 196 LGFLE--------------------------QTPAQLLEAALGKG-ACDGLMSYATPFATSTGGVITEQHQS-FVS---- 243 (417)
Q Consensus 196 vs~i~--------------------------MtiGql~E~~~g~~-~~~g~~~~~tpF~~~~~~~i~~~l~~-~~~---- 243 (417)
||+|| ||||||+|+++||+ ++.|...+++||++...+++.+.|.. +..
T Consensus 826 vs~i~p~eDMPf~~dG~~pDiIlNPhg~PSRMtiGqllE~~lGka~~~l~~~~~~tpF~~~~~~~~~~~l~~~~l~~~~~ 905 (1077)
T CHL00207 826 ISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGDNLNKRFKILPFDEMYGSEYSRILINNKLNQASI 905 (1077)
T ss_pred EEeeeccCCCCccCCCCCccEEECCccccccccHHHHHHHHHHHHHHhcCCcEeeccCCCCcHHHHHHHHHhhhhhhccc
Confidence 99999 99999999999999 55577777999999888888777765 322
Q ss_pred cccccc--cCCCCCeeEeeccccceeeccCCCCccccceeeeeeEEEeeehhhhccccccccccccccCCCCCcccCCcc
Q 014847 244 QLLNCI--GARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVA 321 (417)
Q Consensus 244 ~~g~~~--~~~~~gk~~l~~g~~~~~~~~~~~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~ 321 (417)
..|+.| +++.+||+.|||| +||++|+++||+|++|||||+|||+||+|||++|||+.|||||++
T Consensus 906 ~~~~~~~~~~~~~Gk~~lydG--------------~TGe~~~~~i~vG~~Yy~kL~HmV~DKihaRs~Gp~s~lTqQP~~ 971 (1077)
T CHL00207 906 KNNEYWLFNSYHPGKMVLRDG--------------RTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLG 971 (1077)
T ss_pred hhccccccCCCCCCCEEEECC--------------CCCCCccCceEEEecceeEchhhccccceeeccCCCcccccCCCC
Confidence 225555 4556799999999 999999999999999999999999999999999999999999999
Q ss_pred cccCCCceeeeeccchhhhhcchhhhhhhhhcccccccccccccCCeeecccCCCCccccccChHhHHHHHHHHHhhcCC
Q 014847 322 DRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGI 401 (417)
Q Consensus 322 Gr~~~GG~RfGEME~d~LiahGas~~L~ErL~c~~~~~~~~~~~~~~~c~~c~~~~~~~~~~ipy~~k~l~~EL~~sm~i 401 (417)
||+|+|||||||||||||+|||||++|+|||+.+|| ++.+|. .+|..|.++.++.++.+|||||+|+||| +||||
T Consensus 972 Grsr~GG~RfGEME~~aL~a~GAa~~L~E~L~~kSD-~~~~r~---~~~~~~~~~~~i~~~~~P~sfklL~~EL-~sl~i 1046 (1077)
T CHL00207 972 GKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSD-DMQGRN---ETLNAIVKGQPIPKPGTPESFKVLMREL-QSLGL 1046 (1077)
T ss_pred ccccCCCeeeecccHHHHHhhhhHHHHHHHhhcCCc-cceehH---HHHHhhhCCCeecCCCCCchHHHHHHHH-HHCCc
Confidence 999999999999999999999999999999999999 555554 5799999999999999999999999999 99999
Q ss_pred eEEEEeccC
Q 014847 402 TLKFDTQLS 410 (417)
Q Consensus 402 ~~~l~~~~~ 410 (417)
++++.....
T Consensus 1047 ~~~~~~~~~ 1055 (1077)
T CHL00207 1047 DIEAYKIEN 1055 (1077)
T ss_pred CcEeccccc
Confidence 999876553
No 12
>KOG0214 consensus RNA polymerase II, second largest subunit [Transcription]
Probab=100.00 E-value=8.5e-101 Score=814.57 Aligned_cols=376 Identities=39% Similarity=0.567 Sum_probs=342.8
Q ss_pred CcccccccccccCCCCCcCCCcccccccccccCCccccccccccchhhcccccccccCccceEeecccccc---------
Q 014847 1 MSFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRPLFWILISDCL--------- 71 (417)
Q Consensus 1 p~~ilsi~AslIPF~~h~~NqSpRn~yq~~~M~KQamG~~~~n~~~R~D~~~~~l~ypQ~PLV~t~~~d~l--------- 71 (417)
|++|||++||.|||||| ||||||+||++ |+|||||.+.+|++.|+|+..|.|+|||+|+|+|+.++++
T Consensus 667 psmILgv~asiIpFpdh--~qspr~tYQsa-~~kqamg~y~tn~~vR~dtl~~~l~ypqkpl~tt~~~e~l~~~eL~aG~ 743 (1141)
T KOG0214|consen 667 PSMILGVCASIIPFPDH--NQSPRNTYQSA-MGKQAMGVYHTNPQVRMDTLAKVLYYPQKPLVTTRAMEYLRFRELPAGQ 743 (1141)
T ss_pred HHHhhhhceeeeecCCC--CCchHHHHHHH-HhhhcceeeeecchhhhhhhhhcccccccchhhHHHHhhhhhhhccccc
Confidence 78999999999999999 99999999999 8999999999999999999999999999999999988855
Q ss_pred ----------CCC-CCeEEEecceecccceeeEEEEEEEe---c-----ccccC---------------CCCCCCccccc
Q 014847 72 ----------GRP-EDSLVMNQASLECGVFRSESYKAEVD---N-----KDIQV---------------KSRPSDDMLNF 117 (417)
Q Consensus 72 ----------g~n-EDAiIiNKssidRG~f~s~~Yk~e~~---~-----~~~~~---------------~~~~~~g~~~~ 117 (417)
|+| |||+|+|++++|||+|||..|+.+.+ . .+.++ ..++.||++.+
T Consensus 744 NaiVAi~~~~GYNqEDsvimn~s~v~rg~FrS~~~RsYk~q~~~~~~~~ee~~~~~~~~~~~~mr~~~~dkLdddG~i~~ 823 (1141)
T KOG0214|consen 744 NAIVAIACYSGYNQEDSVIMNQSSVDRGLFRSFFIRSYKDQEHKKDQGPEEIFEEPPRGEGRGMRNGKYDKLDDDGIIMP 823 (1141)
T ss_pred ceEEEEecccCccHHHHHHHHhhhhhcchhhhhhhhHHHhhhhhcccccccccccccccccccccccccccccccCCccc
Confidence 334 99999999999999999996544331 1 11111 13577899998
Q ss_pred cccccccCCeEEEEeccC---------------CceeEEEecCCCceeEEEEEEEeCCCCCeEEEEEEeecccccccccc
Q 014847 118 GKIQSKSGDIVIGKYAEI---------------GADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACL 182 (417)
Q Consensus 118 g~~~v~~GDiligk~~~~---------------~~d~s~~~k~~e~g~Vd~V~i~~~~~g~~~vkv~ir~~~~~~R~p~i 182 (417)
|. +|..|||+|||.+|. ++|+|++++++|.|+||+|.+++|.+|.++++|++|+ .|.|++
T Consensus 824 G~-~vs~~Dv~iGk~t~~~~~~~~~~~~~~~~t~~d~s~~Lr~~e~Givd~V~vt~n~~G~kF~kv~vr~----~ripqi 898 (1141)
T KOG0214|consen 824 GS-RVSGGDVLIGKTTPQPAKEDESGPEDRLYTKRDHSTKLRHTERGIVDQVWVTKNSEGPKFVKVRVRQ----VRIPQI 898 (1141)
T ss_pred cc-eeecCCEEeccccCCcccchhccccccccccccceeecccCCcceEEEEEEecCCCCCceeEEEEee----cccccc
Confidence 86 889999999998851 3799999999999999999999999999999999999 999999
Q ss_pred ccccccccCCceeEeeec--------------------------cchhHHHHHhhhhh-hhcCCceeecCCCCCCHHHHH
Q 014847 183 GDKFSSMHGQKGVLGFLE--------------------------QTPAQLLEAALGKG-ACDGLMSYATPFATSTGGVIT 235 (417)
Q Consensus 183 GDKfssRHGqKGvvs~i~--------------------------MtiGql~E~~~g~~-~~~g~~~~~tpF~~~~~~~i~ 235 (417)
|||||||||||||||.++ ||+|||+||++||. |..|...++|||+..++..|+
T Consensus 899 GDKfasrHgqKG~ig~~~~qedmpft~eGi~pDiiiNPhaiPSRmtig~liEc~lgk~~a~~~e~~~atpFs~v~v~~is 978 (1141)
T KOG0214|consen 899 GDKFASRHGQKGTIGITYRQEDMPFTIEGIVPDIIINPHAIPSRMTIGQLIECLLGKVAAYEGEEGDATPFSDVTVSKIS 978 (1141)
T ss_pred cchhccccccCccccceeecCCCCccccCCCcceEECcccCccccchhhhHHHhhhhhhhcccccccCCCCCccchhccc
Confidence 999999999999999988 99999999999999 889999999999999999999
Q ss_pred HHHHH-hcccccccccCCCCCeeEeeccccceeeccCCCCccccceeeeeeEEEeeehhhhccccccccccccccCCCCC
Q 014847 236 EQHQS-FVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQP 314 (417)
Q Consensus 236 ~~l~~-~~~~~g~~~~~~~~gk~~l~~g~~~~~~~~~~~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~ 314 (417)
..|.+ ||..+|+ |.|||| +||+++.++||+|+.|||||+|||+||+|+|++||++.
T Consensus 979 ~~l~~~g~~~~G~---------e~~ynG--------------rtG~~~~~~if~GptyyqrL~Hmvd~kih~R~~Gp~q~ 1035 (1141)
T KOG0214|consen 979 ANLHVYGYQYRGN---------ERMYNG--------------RTGRKLRAQIFIGPTYYQRLKHMVDDKIHSRARGPVQI 1035 (1141)
T ss_pred chHHHhccccCCC---------EEEecC--------------CCCceeeeeeecCchHHHHHHHhhhheeeecccCCcee
Confidence 99999 9999999 999999 99999999999999999999999999999999999999
Q ss_pred cccCCcccccCCCceeeeeccchhhhhcchhhhhhhhh----------cccccccc--cccccCCeeecccCCCCccccc
Q 014847 315 LTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERL----------KCKNVANV--IQRVVGGPYCRICNSADDIIKA 382 (417)
Q Consensus 315 lT~QP~~Gr~~~GG~RfGEME~d~LiahGas~~L~ErL----------~c~~~~~~--~~~~~~~~~c~~c~~~~~~~~~ 382 (417)
+||||++||+|+||+|||||||||+|||||+++|+||| .|..|+.. .........|+.|.+.+.++.+
T Consensus 1036 ltRQP~~gRsr~GGlRfGEMErdc~iahGaa~~L~ERL~~~SD~~~~~~c~~c~l~~i~~~~~n~~~ck~c~n~~~v~~v 1115 (1141)
T KOG0214|consen 1036 LTRQPVEGRSRDGGLRFGEMERDCLIAHGAAAFLKERLFEKSDAYRVHICVLCGLTAIAGLIPNSFECRGCENKTLVVRV 1115 (1141)
T ss_pred eeccccccccccCCeeeehhHHHHHHHhhHHHHHHHHhhccCccceEEEeccchhhhhhccCCCccccccccCccceEEE
Confidence 99999999999999999999999999999999999999 45555411 1223344689999999999999
Q ss_pred cChHhHHHHHHHHHhhcCCeEEEEec
Q 014847 383 NVPYGAKLLSQELSFSMGITLKFDTQ 408 (417)
Q Consensus 383 ~ipy~~k~l~~EL~~sm~i~~~l~~~ 408 (417)
.+||++|||+||| .+|||.+++.+.
T Consensus 1116 ~ipya~kLl~qel-msmni~pr~~~~ 1140 (1141)
T KOG0214|consen 1116 YIPYAAKLLFQEL-MSMNIAPRRKTK 1140 (1141)
T ss_pred echhHHHHHHHHH-HhccCccccccC
Confidence 9999999999999 999999998764
No 13
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=100.00 E-value=6.8e-92 Score=811.84 Aligned_cols=375 Identities=22% Similarity=0.290 Sum_probs=328.8
Q ss_pred CcccccccccccCCCCCcCCCcccccccccccCCcccccccc--------------------------------------
Q 014847 1 MSFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTT-------------------------------------- 42 (417)
Q Consensus 1 p~~ilsi~AslIPF~~h~~NqSpRn~yq~~~M~KQamG~~~~-------------------------------------- 42 (417)
|.+++|++||||||++| |+++|++|||| |++||+++...
T Consensus 671 p~Q~vSvaasLIPFLEh--dDAnRALMGSN-MQRQAVPLl~~e~piVgTG~E~~va~dSg~~i~a~~~G~V~yvd~~~I~ 747 (2890)
T PRK09603 671 SSMLVGVAASLIPFLEH--DDANRALMGTN-MQRQAVPLLRSDAPIVGTGIEKIIARDSWGAIKANRAGVVEKIDSKNIY 747 (2890)
T ss_pred ccceeeehhhcCCcccc--Ccccccccccc-chhhhhhhccccCCeEecCcchhhhccccceeEecCCeEEEEecCcEEE
Confidence 78999999999999999 99999999999 89999988521
Q ss_pred ----c--------c-chhhcccccccccCccceEe--------ecccc---------ccCCC-------------CCeEE
Q 014847 43 ----N--------P-NIRVDTLLQQLFYPQRPLFW--------ILISD---------CLGRP-------------EDSLV 79 (417)
Q Consensus 43 ----n--------~-~~R~D~~~~~l~ypQ~PLV~--------t~~~d---------~lg~n-------------EDAiI 79 (417)
+ | ..+|.++||.+++.|+|+|+ +.++| +||.| |||||
T Consensus 748 i~~~~~~~~~~~~Y~L~Ky~RSNQ~TcinqrPiV~~Gd~V~kGdilADG~st~~GELALG~NvlVAfmpW~GYNfEDAIl 827 (2890)
T PRK09603 748 ILGEGKEEAYIDAYSLQKNLRTNQNTSFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIV 827 (2890)
T ss_pred EEecCCCCceeeEEeeccccccCCCceeeeccEecCCCEeccCCEEecCcccccCeeccCcccEEEEeeeccccCccccc
Confidence 0 1 24667889999999999998 34555 56665 99999
Q ss_pred EecceecccceeeE---EEEEEEec-c--------ccc------CCCCCCCccccccccccccCCeEEEEeccCC-----
Q 014847 80 MNQASLECGVFRSE---SYKAEVDN-K--------DIQ------VKSRPSDDMLNFGKIQSKSGDIVIGKYAEIG----- 136 (417)
Q Consensus 80 iNKssidRG~f~s~---~Yk~e~~~-~--------~~~------~~~~~~~g~~~~g~~~v~~GDiligk~~~~~----- 136 (417)
||++.+..++|+|+ .|+++..+ + +++ -+.+|++|++.+|. +|++|||||||++|++
T Consensus 828 ISERlV~eD~fTSIHIee~ei~~r~Tk~G~EeITrdIPnvse~~l~~LDe~GII~iGa-~V~~GDILVGKvTPkge~~~t 906 (2890)
T PRK09603 828 VSERITKDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGT-YVSAGMILVGKTSPKGEIKST 906 (2890)
T ss_pred cchhhhcCccceEEEEeeeEEEEEecCCCCcEEeccCCCCCHHHHhcCCCCCCEeeCC-EECCCCEEEEeeccCCCCCCC
Confidence 99999999999999 45665532 1 111 13578999999996 8999999999999874
Q ss_pred -----------------ceeEEEecCCCceeEEEEEEEeCC---------------------------------------
Q 014847 137 -----------------ADHSIKLKHTERGLVLKVLLSSND--------------------------------------- 160 (417)
Q Consensus 137 -----------------~d~s~~~k~~e~g~Vd~V~i~~~~--------------------------------------- 160 (417)
+|+|++++++..|+|.+|.+++.+
T Consensus 907 PEekLLraIFGeka~~vkDtSLrvp~G~~G~Vidv~~f~r~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 986 (2890)
T PRK09603 907 PEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDARVLSAYEEEKAKLDMEHFDRLTMLNREELLRVS 986 (2890)
T ss_pred hHHHHHHHHhcccccccccCceecCCCCcEEEEEEEEecccccchhHHHHHHHHHHHHHHhHhhHHHHHHHHHHHHHhhh
Confidence 799999999999999999998742
Q ss_pred -------------------------------------------------------------------------------C
Q 014847 161 -------------------------------------------------------------------------------D 161 (417)
Q Consensus 161 -------------------------------------------------------------------------------~ 161 (417)
+
T Consensus 987 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~ 1066 (2890)
T PRK09603 987 SLLSQAILEEPFSHNGKDYKEGDQIPKEEIASINRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEK 1066 (2890)
T ss_pred hhccccccccccccccccccccccccHHHHhhCCHHHhhhhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 0
Q ss_pred C-------CeEEEEEEeeccccccccccccccccccCCceeEeeec--------------------------cchhHHHH
Q 014847 162 G-------KNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLE--------------------------QTPAQLLE 208 (417)
Q Consensus 162 g-------~~~vkv~ir~~~~~~R~p~iGDKfssRHGqKGvvs~i~--------------------------MtiGql~E 208 (417)
| .+.|+|++|+ .|+|++|||||||||||||||+|+ |||||++|
T Consensus 1067 gdeL~~Gv~~~VkV~ia~----kR~~qvGDK~AgRHGnKGViS~I~p~EDMPfl~dG~~pDIIlNPlGvPSRMnIGQilE 1142 (2890)
T PRK09603 1067 DDILPNGVIKKVKLYIAT----KRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILE 1142 (2890)
T ss_pred CCcCCCCcceEEEEEEEE----eecccccchhhhccCCCeeEEEEEchhcCCCCCCCCCCcEEECCCCCCccccHHHHHH
Confidence 1 1369999999 999999999999999999999999 99999999
Q ss_pred Hhhhhh-hhcCCc---------------------------------------------------------eeecC-CCCC
Q 014847 209 AALGKG-ACDGLM---------------------------------------------------------SYATP-FATS 229 (417)
Q Consensus 209 ~~~g~~-~~~g~~---------------------------------------------------------~~~tp-F~~~ 229 (417)
+++||+ +..|.. .++|| |++.
T Consensus 1143 ~~LG~aa~~lg~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~tpvF~g~ 1222 (2890)
T PRK09603 1143 MHLGLVGKEFGKQIASMLEDKTKDFAKELRAKMLEIANAINEKDPLTIHALENCSDEELLEYAKDWSKGVKMAIPVFEGI 1222 (2890)
T ss_pred HHHHHHHHhcCcChhhhhhhcchhhhHHHHHHHHhhhcccccccccccccccccchHHHHhhhhhhccCCcccCCCCCCC
Confidence 999998 433322 35788 9999
Q ss_pred CHHHHHHHHHH-hcccccccccCCCCCeeEeeccccceeeccCCCCccccceeeeeeEEEeeehhhhccccccccccccc
Q 014847 230 TGGVITEQHQS-FVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRN 308 (417)
Q Consensus 230 ~~~~i~~~l~~-~~~~~g~~~~~~~~gk~~l~~g~~~~~~~~~~~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~ 308 (417)
+.++|.+.|.+ ||+++|+ +.|||| +||++|+++||||++|||||+|||+||+|||+
T Consensus 1223 ~~~~i~~~l~~aG~~~~Gk---------~~LyDG--------------rTGe~f~~~V~vG~~YylKL~HmVdDKiHaRs 1279 (2890)
T PRK09603 1223 SQEKFYKLFELAKIAMDGK---------MDLYDG--------------RTGEKMRERVNVGYMYMIKLHHLVDEKVHARS 1279 (2890)
T ss_pred CHHHHHHHHHHcCCCCCCC---------EEEEcC--------------CCCCCccceEEEEeeceeechhhccchhhhcc
Confidence 99999999988 8888777 999999 99999999999999999999999999999999
Q ss_pred cCCCCCcccCCcccccCCCceeeeeccchhhhhcchhhhhhhhhcccccccccccccCCeeecccCCCCccccccChHhH
Q 014847 309 TGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGA 388 (417)
Q Consensus 309 ~Gp~~~lT~QP~~Gr~~~GG~RfGEME~d~LiahGas~~L~ErL~c~~~~~~~~~~~~~~~c~~c~~~~~~~~~~ipy~~ 388 (417)
+|||+++||||++||+++|||||||||+|||+|||||++|+|||+.+|| ++.+|.. .|..|.++.++..+.+||||
T Consensus 1280 tGPyslvTqQPl~GKs~~GGqRfGEMEvwALeAyGAa~~LqE~Lt~kSD-dv~gR~~---~y~~i~~g~~i~~~~iPeSF 1355 (2890)
T PRK09603 1280 TGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSD-DIRGREN---AYRAIAKGEQVGESEIPETF 1355 (2890)
T ss_pred CCCcchhhhCCCcccccCCCceeeeeeHHHHHHhhHHHHHHHHHhcCCc-chhhhhh---hhhhhcCCCcccccCCCHHH
Confidence 9999999999999999999999999999999999999999999999999 6666653 45778888899999999999
Q ss_pred HHHHHHHHhhcCCeEEEEeccCC
Q 014847 389 KLLSQELSFSMGITLKFDTQLSG 411 (417)
Q Consensus 389 k~l~~EL~~sm~i~~~l~~~~~~ 411 (417)
|+|++|| +||||++++.....+
T Consensus 1356 kvL~~EL-~sL~l~i~~~~~~~~ 1377 (2890)
T PRK09603 1356 YVLTKEL-QSLALDINIFGDDVD 1377 (2890)
T ss_pred HHHHHHH-HhCCcceEEEeeccc
Confidence 9999999 999999999876543
No 14
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=100.00 E-value=4.1e-88 Score=778.22 Aligned_cols=373 Identities=22% Similarity=0.322 Sum_probs=321.1
Q ss_pred CcccccccccccCCCCCcCCCcccccccccccCCcccccccc--------------------------------------
Q 014847 1 MSFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTT-------------------------------------- 42 (417)
Q Consensus 1 p~~ilsi~AslIPF~~h~~NqSpRn~yq~~~M~KQamG~~~~-------------------------------------- 42 (417)
|.+++|++||||||.+| |+++|++|||| |++||+++...
T Consensus 678 p~Q~~SvaasLIPFLEh--dDAnRALMGSN-MQRQAVPLl~~e~PiVGTG~E~~vA~DSg~~v~A~~~G~V~yVda~kIv 754 (2836)
T PRK14844 678 PKQVISVAASLIPFLEN--DDANRALMGSN-MQRQAVPLLKPTAPLVATGMESFVASGSGAVVLAKRDGIVDSSDSNSIV 754 (2836)
T ss_pred cchhhhhHhhcCCcccc--Ccccccccccc-ccccccccccCCCCeEecCcchhhhhcccceEEeccCceEEEEcCCEEE
Confidence 78999999999999999 99999999999 89999988521
Q ss_pred ----------------ccchhhcccccccccCccceEe--------ecccc---------ccCCC-------------CC
Q 014847 43 ----------------NPNIRVDTLLQQLFYPQRPLFW--------ILISD---------CLGRP-------------ED 76 (417)
Q Consensus 43 ----------------n~~~R~D~~~~~l~ypQ~PLV~--------t~~~d---------~lg~n-------------ED 76 (417)
....+|.++|+.+++.|+|+|+ +.++| +||.| ||
T Consensus 755 I~~~~~~~~~~~~~~~Y~L~ky~RSNQ~TcinQrPiV~~Gd~V~kGdilADG~st~~GELALG~NvlVAfmpW~GYNfED 834 (2836)
T PRK14844 755 IRAFDKERVNYLDVDIYHLRKFQRSNHNTCINQKPLVCVGDYVKEGDVIADGPAINSGELALGQNLLVAFMSWQGYNFED 834 (2836)
T ss_pred EEeCCCccccccccceEEeccccccccceeeeecceecCCCEeccCCEeccChhhcccccccccceEEEEeccCCccccc
Confidence 0134566789999999999998 34555 45555 99
Q ss_pred eEEEecceecccceeeE---EEEEEEec-c--------ccc------CCCCCCCccccccccccccCCeEEEEeccCC--
Q 014847 77 SLVMNQASLECGVFRSE---SYKAEVDN-K--------DIQ------VKSRPSDDMLNFGKIQSKSGDIVIGKYAEIG-- 136 (417)
Q Consensus 77 AiIiNKssidRG~f~s~---~Yk~e~~~-~--------~~~------~~~~~~~g~~~~g~~~v~~GDiligk~~~~~-- 136 (417)
|||||++.+.+++|+|+ .|+++..+ + +++ -+.+|++|++.+|. +|++|||||||++|++
T Consensus 835 AIliSErlv~eD~fTSiHIee~ei~~r~Tk~G~EeITrdIPnv~e~~lr~LDe~GIV~iGa-~V~~GDILVGKvtPk~e~ 913 (2836)
T PRK14844 835 SIIISSEVVKKDLFTSIHIEEFECVVHDTPLGSEKITRAIPGVNEENLYHLDDSGIVKIGT-RVGPGYILVGKVTPKPSL 913 (2836)
T ss_pred ccccchhhccCceeEEEeecceEEEEEeccCCCceecccCCCCChHHHhcCCCCCCeecCC-EECCCCEEEEeecCCCCC
Confidence 99999999999999999 46666543 1 121 14578999999996 8999999999999864
Q ss_pred --------------------ceeEEEecCCCceeEEEEEEEeCC------------------------------------
Q 014847 137 --------------------ADHSIKLKHTERGLVLKVLLSSND------------------------------------ 160 (417)
Q Consensus 137 --------------------~d~s~~~k~~e~g~Vd~V~i~~~~------------------------------------ 160 (417)
+|+|++++++..|+|.+|.+++.+
T Consensus 914 ~~tPEekLL~aIFGek~~~vkdtSLrvp~G~~G~Vidv~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 993 (2836)
T PRK14844 914 SLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFTRRGVEENERALLIKQKEINDFEKERDYIINVTSEYFYD 993 (2836)
T ss_pred CCCHHHHHHHHHhCCcccccccCceecCCCCCEEEEEEEEEcccccccchhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
Confidence 799999999999999999999753
Q ss_pred -----------------------------------------------------------------CCC-------eEEEE
Q 014847 161 -----------------------------------------------------------------DGK-------NFAVV 168 (417)
Q Consensus 161 -----------------------------------------------------------------~g~-------~~vkv 168 (417)
+|+ ..|||
T Consensus 994 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~gdeL~~gv~~~VkV 1073 (2836)
T PRK14844 994 ELKKLLINSGSQDREKFDSIEREQWWGIGLKNQSISEQVKSLKKDFDEKVSHAIAQFKRKVEKLHEGYDLPQGVSMSVKV 1073 (2836)
T ss_pred hhhhhhcccccccHHHHhhccHHhhhhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCCCCceEEEE
Confidence 111 35888
Q ss_pred EEeeccccccccccccccccccCCceeEeeec--------------------------cchhHHHHHhhhhhhhc-CC--
Q 014847 169 SIRQSVNMVHSACLGDKFSSMHGQKGVLGFLE--------------------------QTPAQLLEAALGKGACD-GL-- 219 (417)
Q Consensus 169 ~ir~~~~~~R~p~iGDKfssRHGqKGvvs~i~--------------------------MtiGql~E~~~g~~~~~-g~-- 219 (417)
.|++ .|.+++|||+|||||||||||+|+ |||||++|+++|+||.. |.
T Consensus 1074 yia~----KRkiqvGDKmAGRHGNKGVIS~IlP~eDMPyL~DGtpvDIvLNPLGVPSRMNvGQilE~hLG~A~~~L~~~~ 1149 (2836)
T PRK14844 1074 FIAV----KHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGWACKKLGEKV 1149 (2836)
T ss_pred EEEE----eecCCccccccccCCCCceEeEEcccCCCCcCCCCCCceEEeCCCCCCccccHHHHHHHHHHHHHhhhhhhh
Confidence 8888 999999999999999999999999 99999999999999432 10
Q ss_pred --------------------------------------------------------------------------------
Q 014847 220 -------------------------------------------------------------------------------- 219 (417)
Q Consensus 220 -------------------------------------------------------------------------------- 219 (417)
T Consensus 1150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1229 (2836)
T PRK14844 1150 GNILDEINKIKSAFCKGIRSLNDDNFTKFAAAYLDNKKIENIDDDEITASVLNTPNKNALNDELNELVENYLNSCKSAYS 1229 (2836)
T ss_pred HhhhhhhhccccccccccccccccccccccccccccccccccccccccccccccccccccccccccchhccccccchhhH
Confidence
Q ss_pred ----------------------------------------ceeecC-CCCCCHHHHHHHHHH-hcccccccccCCCCCee
Q 014847 220 ----------------------------------------MSYATP-FATSTGGVITEQHQS-FVSQLLNCIGARNSGIT 257 (417)
Q Consensus 220 ----------------------------------------~~~~tp-F~~~~~~~i~~~l~~-~~~~~g~~~~~~~~gk~ 257 (417)
+..+|| |++.+.++|.+.|++ ||+++|+ +
T Consensus 1230 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~tpvf~g~~~~~i~~~L~~~g~~~~Gk---------~ 1300 (2836)
T PRK14844 1230 NLRNFLIEVYSCGSNVSICNNIRDISDNNLIEFARKLRDGIPVAAPVFEGPKDEQIAKLFELAGLDNSGQ---------A 1300 (2836)
T ss_pred HHHHHHHHhhhcccccccccccccccHHHHHHHHhhhccCCeecCCCcCCCCHHHHHHHHHHhCcCCCCC---------E
Confidence 012556 788888888888888 8887777 9
Q ss_pred EeeccccceeeccCCCCccccceeeeeeEEEeeehhhhccccccccccccccCCCCCcccCCcccccCCCceeeeeccch
Q 014847 258 FIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCD 337 (417)
Q Consensus 258 ~l~~g~~~~~~~~~~~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~RfGEME~d 337 (417)
.|||| +||++|+++||+|++|||||+|||+||+|+|++|||+.|||||++||+++|||||||||+|
T Consensus 1301 ~l~dG--------------~TGe~f~~~v~vG~~yy~kL~HmV~DKihaRs~Gp~s~lT~QPl~Gr~~~GG~RfGEME~~ 1366 (2836)
T PRK14844 1301 VLYDG--------------CSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECW 1366 (2836)
T ss_pred EEEcC--------------CCCCccchhheeCcchhhhhhhhhcchhhhcccCCCcccccCCCcccccCCCceeecchHH
Confidence 99999 9999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhcchhhhhhhhhcccccccccccccCCeeecccCCCCccccccChHhHHHHHHHHHhhcCCeEEEEecc
Q 014847 338 CLIAHGASGNLHERLKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLKFDTQL 409 (417)
Q Consensus 338 ~LiahGas~~L~ErL~c~~~~~~~~~~~~~~~c~~c~~~~~~~~~~ipy~~k~l~~EL~~sm~i~~~l~~~~ 409 (417)
||+|||||++|+|||+.+|| ++.+|.. .||.+|... ......+|||||+|+||| +||||++++.+++
T Consensus 1367 al~a~Gaa~~L~E~Lt~kSD-~~~gr~~--~~~~ivkG~-~~~~~~~PesfkvL~~EL-~sl~i~~~~~~~~ 1433 (2836)
T PRK14844 1367 ALQAYGAAYTLQEMLTVKSD-DINGRVK--IYESIIKGD-SNFECGIPESFNVMIKEL-RSLCLNVDLKQND 1433 (2836)
T ss_pred HHHHHhHHHHHHHHhccccc-chhhhhH--hhhhhccCC-CCCcCCCCchHHHHHHHH-HhCccceEEeccc
Confidence 99999999999999999999 6667654 678887543 455679999999999999 9999999988654
No 15
>PF00562 RNA_pol_Rpb2_6: RNA polymerase Rpb2, domain 6; InterPro: IPR007120 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerases (2.7.7.6 from EC) catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain represents the hybrid-binding domain and the wall domain []. The hybrid-binding domain binds the nascent RNA strand/template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion []. This domain is also involved in binding to Rpb1 and Rpb3 []. Many of the bacterial members contain large insertions within this domain, which are known as dispensable region 2 (DRII).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2Y0S_R 3HKZ_B 2PMZ_R 3H0G_B 3S17_B 1I6H_B 4A3B_B 3K1F_B 4A3I_B 1TWA_B ....
Probab=100.00 E-value=5.2e-82 Score=645.55 Aligned_cols=286 Identities=34% Similarity=0.474 Sum_probs=245.7
Q ss_pred cccccccCCCCCcCCCcccccccccccCCccccccccccchhhcccccccccCccceEeec-cccc--------------
Q 014847 6 GLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRPLFWIL-ISDC-------------- 70 (417)
Q Consensus 6 si~AslIPF~~h~~NqSpRn~yq~~~M~KQamG~~~~n~~~R~D~~~~~l~ypQ~PLV~t~-~~d~-------------- 70 (417)
||+|++|||++| |||||++|||+ |+|||||+|.+|+..|+|+.. +|||+|||+|. .++.
T Consensus 1 si~As~ipf~~h--n~s~R~~~~~~-m~kQa~~~y~~~~~~R~d~~~---~~~q~Plv~~~~~~~~~~ilad~~~~~~~e 74 (386)
T PF00562_consen 1 SIVASLIPFPEH--NQSPRNLYQCN-MQKQAIGTYSLNKFNRSDQNT---CYPQKPLVKTGDRVEKGQILADGPSTKFGE 74 (386)
T ss_dssp -THGGTSSSGGG--C-HHHHHHHHH-HGCGBCSEEETTTTTS-TSSE---SS-BEESSBSSSTBTTTTECEE-TTECTTT
T ss_pred CEEeCCCCEEEE--EcCCcEEEEeC-cCCCcccceeeeeeeccCcce---eccccceEEeeccccccCcccccccccccc
Confidence 689999999999 99999999999 899999999999999999877 89999999987 5442
Q ss_pred --------------cCCC-CCeEEEecceecccceeeEEEEEEEe--c------ccccC----------CCCCCCccccc
Q 014847 71 --------------LGRP-EDSLVMNQASLECGVFRSESYKAEVD--N------KDIQV----------KSRPSDDMLNF 117 (417)
Q Consensus 71 --------------lg~n-EDAiIiNKssidRG~f~s~~Yk~e~~--~------~~~~~----------~~~~~~g~~~~ 117 (417)
.|+| ||||||||+|+|||+|||++|+++.+ + .+.+. ..+++||++.+
T Consensus 75 ~~~G~N~iVAvmsy~GYN~EDAiIiNkssv~rG~f~s~~~k~~~~~~~~~~g~~e~~~~~~~~~~~~~~~~LD~dGii~~ 154 (386)
T PF00562_consen 75 LPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGLFTSIHYKTEIEIRDNKGGPSEEIFRPIPNVKEYNYSKLDEDGIIKI 154 (386)
T ss_dssp S-SSEEEEEEESBSSSTTTSSEEEEECHHHHTTTTEEEEEEEEEEEEEETTSEEBBESS--TSSTSTTGGGBCTTSBB-T
T ss_pred CcceeeeeEEeeehhcccchhhhhhhhhhhhcCeeeEEEEEEEeeeecccCCcccccccccccchhhhhhhccccccccc
Confidence 3444 99999999999999999999988221 1 11111 23578999999
Q ss_pred cccccccCCeEEEEec--------------cC---CceeEEEecCCCceeEEEEEE-------EeCCCCCeEEEEEEeec
Q 014847 118 GKIQSKSGDIVIGKYA--------------EI---GADHSIKLKHTERGLVLKVLL-------SSNDDGKNFAVVSIRQS 173 (417)
Q Consensus 118 g~~~v~~GDiligk~~--------------~~---~~d~s~~~k~~e~g~Vd~V~i-------~~~~~g~~~vkv~ir~~ 173 (417)
|. .+++||+||||++ ++ .+|+|++++.+|.|+||+|.+ ..+.++...++|++|+
T Consensus 155 G~-~v~~gDiligk~~~~~~~~~~~~~~~~~~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~~~~~~~~iki~ir~- 232 (386)
T PF00562_consen 155 GS-RVEKGDILIGKITSPPRFSPLLKKIFGEKNRNYRDTSIKYKSGESGRVDKVIIFSNEKKDTSNNEGYKKIKIRIRS- 232 (386)
T ss_dssp TC-EEETTSEEEEEEESTSC--HHHHHHHHSSSCSEEEEEEES-TT-EEEEEEEEEECCCSSBEEETTCEEEEEEEEEE-
T ss_pred Cc-EEecceeEEEEEecccccccchhhccccccccccceeecccccEEeEeccccccccccccccccCcceEEEEEecc-
Confidence 97 7999999999994 11 278999999999999999999 5566678899999999
Q ss_pred cccccccccccccccccCCceeEeeec--------------------------cchhHHHHHhhhhh-hhcCCceeecCC
Q 014847 174 VNMVHSACLGDKFSSMHGQKGVLGFLE--------------------------QTPAQLLEAALGKG-ACDGLMSYATPF 226 (417)
Q Consensus 174 ~~~~R~p~iGDKfssRHGqKGvvs~i~--------------------------MtiGql~E~~~g~~-~~~g~~~~~tpF 226 (417)
.|+|+||||||||||||||||+|+ ||||||+|+++||+ ++.|.+.++|||
T Consensus 233 ---~R~p~iGDKfssRHGqKGVvs~i~~~eDMPft~~G~~pDiIiNPhgiPSRMtiGqllE~~~g~~~~~~g~~~~~t~F 309 (386)
T PF00562_consen 233 ---TRRPQIGDKFSSRHGQKGVVSKILPQEDMPFTEDGIVPDIIINPHGIPSRMTIGQLLESLLGKAGALNGRFVDATPF 309 (386)
T ss_dssp ---EEE--TTEEEEETTSEEEEEEEEE-TTTSEEETTSEB-SEEE-GGGSTTTTBTHHHHHHHHHHHHHHSTCEEB-TTT
T ss_pred ---cccchhHHHHhhhhcCceEEeeeeccccCccccCCCcceeeecccccccccchHHHHhhhhhhhhhccccceecCCC
Confidence 999999999999999999999999 99999999999999 789999999999
Q ss_pred CCCCHHHHHHHHHH-hcccccccccCCCCCeeEeeccccceeeccCCCCccccceeeeeeEEEeeehhhhcccccccccc
Q 014847 227 ATSTGGVITEQHQS-FVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVK 305 (417)
Q Consensus 227 ~~~~~~~i~~~l~~-~~~~~g~~~~~~~~gk~~l~~g~~~~~~~~~~~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~ 305 (417)
++.+.++|.++|.+ +|+++|+ |.|||| +||++++++||+|++|||||+|||+||+|
T Consensus 310 ~~~~~~~i~~~l~~~g~~~~g~---------~~l~~g--------------~tG~~~~~~i~~G~~yy~rL~Hmv~DK~h 366 (386)
T PF00562_consen 310 DESSEEDISELLKKAGYNYPGK---------EVLYDG--------------RTGEKFEAPIFIGPVYYQRLKHMVDDKIH 366 (386)
T ss_dssp SSS-HHHHHHHHHHTTSHTTSE---------EEEBES--------------SSSSBESSEEEEEEEEEEEBSTCGGGSTE
T ss_pred CCcchhhhHhhhhcccccccce---------EEEEcC--------------ccCceEEeEEEeeeEEeccceEeCCcEEE
Confidence 99999999999999 9999888 999999 99999999999999999999999999999
Q ss_pred ccccCCCCCcccCCcccccC
Q 014847 306 FRNTGSFQPLTGRPVADRKR 325 (417)
Q Consensus 306 ~R~~Gp~~~lT~QP~~Gr~~ 325 (417)
+|++||++.|||||++||+|
T Consensus 367 ~Rs~Gp~~~lT~QP~~Gr~r 386 (386)
T PF00562_consen 367 ARSRGPYSLLTRQPVEGRSR 386 (386)
T ss_dssp EESS--BBSSSSSB-SSSSS
T ss_pred EEecCCCccccCCCCCCCCC
Confidence 99999999999999999987
No 16
>PF04560 RNA_pol_Rpb2_7: RNA polymerase Rpb2, domain 7; InterPro: IPR007641 RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp. The clamp region (C-terminal) contains a zinc-binding motif. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed switch 4. The switches within the polymerase are thought to signal different stages of transcription [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1SMY_M 3DXJ_M 3AOI_C 2A68_M 1ZYR_C 3AOH_H 1IW7_M 2O5J_C 2CW0_M 2O5I_M ....
Probab=99.92 E-value=1.9e-26 Score=187.79 Aligned_cols=78 Identities=49% Similarity=0.707 Sum_probs=63.6
Q ss_pred Cceeeeeccchhhhhcchhhhhhhhhccccccccc---ccccCCeeecccCCCCccccccChHhHHHHHHHHHhhcCCeE
Q 014847 327 GGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVI---QRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITL 403 (417)
Q Consensus 327 GG~RfGEME~d~LiahGas~~L~ErL~c~~~~~~~---~~~~~~~~c~~c~~~~~~~~~~ipy~~k~l~~EL~~sm~i~~ 403 (417)
|||||||||||||+|||||++|+|||..+||.... .+ -..+..+|..+.++.++.+||+||+|++|| +||||++
T Consensus 1 GG~R~GEMErd~LiahGas~~L~erl~~~SD~~~~~vc~~--cg~~~~~~~~~~~~~~~~ipy~~klL~~EL-~sm~I~~ 77 (81)
T PF04560_consen 1 GGLRFGEMERDALIAHGASFLLKERLFDKSDKYEIDVCSR--CGSIASICKGKPEVKKIEIPYSFKLLIQEL-RSMGIKI 77 (81)
T ss_dssp CBEEEEHHHHHHHHHTTBHHHHHHHHTTTTTEEEEEEECC--CHHHHHTTTTSSSEEEEEEEHHHHHHHHHH-HCTTEEE
T ss_pred CCcchhHHHHHHHHHhhHHHHHHHHhcCCCcCcchhhhcc--CCCceeEECCCCeEEeeeCCHHHHHHHHHH-HHCcCce
Confidence 89999999999999999999999999777774321 11 012223456677889999999999999999 9999999
Q ss_pred EEEe
Q 014847 404 KFDT 407 (417)
Q Consensus 404 ~l~~ 407 (417)
++.+
T Consensus 78 ~~~~ 81 (81)
T PF04560_consen 78 RIKT 81 (81)
T ss_dssp EEEE
T ss_pred EEeC
Confidence 9975
No 17
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]
Probab=96.24 E-value=0.0017 Score=74.33 Aligned_cols=60 Identities=17% Similarity=0.167 Sum_probs=50.9
Q ss_pred CcccccccccccCCCCCcCCCcccccccccccCCccccccccccchhhcccccccccCccceEeeccccccCCC--CCeE
Q 014847 1 MSFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRPLFWILISDCLGRP--EDSL 78 (417)
Q Consensus 1 p~~ilsi~AslIPF~~h~~NqSpRn~yq~~~M~KQamG~~~~n~~~R~D~~~~~l~ypQ~PLV~t~~~d~lg~n--EDAi 78 (417)
|.++.++.+++|||.+| .++.|.+++++ |+|||.| |..+..|||.|- ++++.-. |+|+
T Consensus 533 ~~~~~~~~~~~~P~l~~--dd~~~~l~~~~-mqr~~~~----------------l~~~~~~lv~tG-~E~~~a~e~~~~~ 592 (1060)
T COG0085 533 PKQVVSVGRSLIPFLEH--DDANRALMGSN-MQRQAVP----------------LLRTEAPLVGTG-MEYLDAEDSGAAV 592 (1060)
T ss_pred ceEEeccccccCceeEE--cCchHhhhhhh-hhhhccc----------------ccccccccccCC-ceeecccccccee
Confidence 56788999999999999 99999999999 8999999 447889999999 7776655 5555
Q ss_pred EE
Q 014847 79 VM 80 (417)
Q Consensus 79 Ii 80 (417)
|-
T Consensus 593 ia 594 (1060)
T COG0085 593 IA 594 (1060)
T ss_pred Ee
Confidence 53
No 18
>KOG0214 consensus RNA polymerase II, second largest subunit [Transcription]
Probab=96.23 E-value=0.001 Score=74.04 Aligned_cols=184 Identities=10% Similarity=-0.075 Sum_probs=119.4
Q ss_pred CceeEEEecCCCce--------eEEEEEEEeCCCCCeEEEEEEeeccccccccccccccccccCCceeEeeec-------
Q 014847 136 GADHSIKLKHTERG--------LVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLE------- 200 (417)
Q Consensus 136 ~~d~s~~~k~~e~g--------~Vd~V~i~~~~~g~~~vkv~ir~~~~~~R~p~iGDKfssRHGqKGvvs~i~------- 200 (417)
++.+++.-+..+.+ ...++.+..++.| ...+|.+ +..+.|+||+.+|++++.+.++-
T Consensus 835 Gk~t~~~~~~~~~~~~~~~~t~~d~s~~Lr~~e~G-ivd~V~v-------t~n~~G~kF~kv~vr~~ripqiGDKfasrH 906 (1141)
T KOG0214|consen 835 GKTTPQPAKEDESGPEDRLYTKRDHSTKLRHTERG-IVDQVWV-------TKNSEGPKFVKVRVRQVRIPQIGDKFASRH 906 (1141)
T ss_pred ccccCCcccchhccccccccccccceeecccCCcc-eEEEEEE-------ecCCCCCceeEEEEeecccccccchhcccc
Confidence 35555445555555 6666766666655 3334443 33799999999999999988875
Q ss_pred ---cchhHHHHHhhhhhhhcCCcee--ecCCCCC---CHHHHHHHHHHhcccccccccCCCCCeeEeeccccceeeccCC
Q 014847 201 ---QTPAQLLEAALGKGACDGLMSY--ATPFATS---TGGVITEQHQSFVSQLLNCIGARNSGITFIFKHYFLFCLFECP 272 (417)
Q Consensus 201 ---MtiGql~E~~~g~~~~~g~~~~--~tpF~~~---~~~~i~~~l~~~~~~~g~~~~~~~~gk~~l~~g~~~~~~~~~~ 272 (417)
-|+|.+++---=--...|...| ..|..-+ +++.+.+-+... ....+...+++
T Consensus 907 gqKG~ig~~~~qedmpft~eGi~pDiiiNPhaiPSRmtig~liEc~lgk----------~~a~~~e~~~a---------- 966 (1141)
T KOG0214|consen 907 GQKGTIGITYRQEDMPFTIEGIVPDIIINPHAIPSRMTIGQLIECLLGK----------VAAYEGEEGDA---------- 966 (1141)
T ss_pred ccCccccceeecCCCCccccCCCcceEECcccCccccchhhhHHHhhhh----------hhhcccccccC----------
Confidence 3333332210000001121111 1232222 244444433221 11111344554
Q ss_pred CCccccceeeeeeEEEeeehhhhccccccccccccccCCCCCcccCCcccccCCCceeeeeccchhhhhcchhhhhhhhh
Q 014847 273 MDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERL 352 (417)
Q Consensus 273 ~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~RfGEME~d~LiahGas~~L~ErL 352 (417)
.+... -.-.+++..+++...|+..++.+++.+++....+++++.+.-..++.+++||++++=..++.+-+.++.+
T Consensus 967 ----tpFs~-v~v~~is~~l~~~g~~~~G~e~~ynGrtG~~~~~~if~GptyyqrL~Hmvd~kih~R~~Gp~q~ltRQP~ 1041 (1141)
T KOG0214|consen 967 ----TPFSD-VTVSKISANLHVYGYQYRGNERMYNGRTGRKLRAQIFIGPTYYQRLKHMVDDKIHSRARGPVQILTRQPV 1041 (1141)
T ss_pred ----CCCCc-cchhcccchHHHhccccCCCEEEecCCCCceeeeeeecCchHHHHHHHhhhheeeecccCCceeeecccc
Confidence 22222 3445688999999999999999999999999999999999999999999999999999999999999999
No 19
>PHA03394 lef-8 DNA-directed RNA polymerase subunit beta-like protein; Provisional
Probab=69.02 E-value=7.2 Score=44.15 Aligned_cols=21 Identities=48% Similarity=0.547 Sum_probs=17.4
Q ss_pred cccccccccccCCceeEeeec
Q 014847 180 ACLGDKFSSMHGQKGVLGFLE 200 (417)
Q Consensus 180 p~iGDKfssRHGqKGvvs~i~ 200 (417)
=-.|=|.||=||||||+..-.
T Consensus 708 dLeGlKICgIHGQKGVln~se 728 (865)
T PHA03394 708 DLEGLKICGIHGQKGVLNGSE 728 (865)
T ss_pred CcceeEEeeecccccccCCcc
Confidence 346999999999999987643
No 20
>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=68.22 E-value=8 Score=43.24 Aligned_cols=53 Identities=23% Similarity=0.237 Sum_probs=29.8
Q ss_pred EecCCCceeEEEEEEEeCC-CCCeEEEEEEeeccccccccccccccccccCCceeEee
Q 014847 142 KLKHTERGLVLKVLLSSND-DGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGF 198 (417)
Q Consensus 142 ~~k~~e~g~Vd~V~i~~~~-~g~~~vkv~ir~~~~~~R~p~iGDKfssRHGqKGvvs~ 198 (417)
.++....-.|++|.-.-.- ++.-.+|+++-. .-.=-.|=|.||=||||||+-.
T Consensus 683 YfR~~~~Q~ve~l~sem~~~nd~v~vKl~~V~----st~dLeGlKICgIHGQKGVln~ 736 (748)
T PF04941_consen 683 YFRKVKGQRVEKLDSEMTCINDTVYVKLTLVT----STSDLEGLKICGIHGQKGVLNG 736 (748)
T ss_pred EEEecCCEEEEEEeeEEEEeCCEEEEEEEEEE----EecCccceEEeeeecccccccC
Confidence 3444444455555433211 122344544444 3344569999999999999753
No 21
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=24.79 E-value=42 Score=26.43 Aligned_cols=46 Identities=24% Similarity=0.410 Sum_probs=26.4
Q ss_pred ccCCCCccccceeeeeeEEE--eeehhhhccccccccccccccCCCCCcccCCcccc
Q 014847 269 FECPMDWIAFICLVRSLIFT--WITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADR 323 (417)
Q Consensus 269 ~~~~~~~~~tG~~~~~~if~--G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr 323 (417)
|-|| +||+.|..++.. |.+|=..-..-- .+..++.+++|+||+.-+
T Consensus 5 f~Cp----It~~lM~dPVi~~~G~tyer~~I~~~-----l~~~~~~~P~t~~~l~~~ 52 (73)
T PF04564_consen 5 FLCP----ITGELMRDPVILPSGHTYERSAIERW-----LEQNGGTDPFTRQPLSES 52 (73)
T ss_dssp GB-T----TTSSB-SSEEEETTSEEEEHHHHHHH-----HCTTSSB-TTT-SB-SGG
T ss_pred cCCc----CcCcHhhCceeCCcCCEEcHHHHHHH-----HHcCCCCCCCCCCcCCcc
Confidence 4577 999999999986 545433322211 112688999999998754
No 22
>PF08259 Periviscerokin: Periviscerokinin family; InterPro: IPR013231 Perviscerokinin neuropeptides are found in the abdominal perisympathetic organs of insects. They mediate visceral muscle contractile activity (myotropic activity). CAPA, which are in the periviscerokinin and pyrokinin peptide families, has potential medical importance. This is due to its myotropic effects on, for example, heart muscles and due to its occurrence in the Ixodoidea (ticks), which are important vectors in the transmission of many animal diseases []. These peptides also have a strong diuretic or anti-diuretic effect, suggesting they have significant medical implications [].
Probab=23.66 E-value=33 Score=18.01 Aligned_cols=8 Identities=38% Similarity=0.625 Sum_probs=6.2
Q ss_pred ccccCCCC
Q 014847 9 CGIIPSHL 16 (417)
Q Consensus 9 AslIPF~~ 16 (417)
.+|||||.
T Consensus 3 sGlI~fpR 10 (11)
T PF08259_consen 3 SGLIPFPR 10 (11)
T ss_pred ccccccCC
Confidence 57899974
No 23
>PRK00420 hypothetical protein; Validated
Probab=20.14 E-value=77 Score=27.70 Aligned_cols=24 Identities=13% Similarity=0.236 Sum_probs=19.0
Q ss_pred ccccccccccc-ccCCeeecccCCC
Q 014847 353 KCKNVANVIQR-VVGGPYCRICNSA 376 (417)
Q Consensus 353 ~c~~~~~~~~~-~~~~~~c~~c~~~ 376 (417)
.|..|+....+ ..+..+|+.|+..
T Consensus 25 ~CP~Cg~pLf~lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 25 HCPVCGLPLFELKDGEVVCPVHGKV 49 (112)
T ss_pred CCCCCCCcceecCCCceECCCCCCe
Confidence 78888877666 6678999999873
Done!