Query 019610
Match_columns 338
No_of_seqs 162 out of 1362
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 03:08:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019610.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019610hhsearch_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 3.7E-92 7.9E-97 729.7 27.4 301 1-330 225-603 (605)
2 TIGR03670 rpoB_arch DNA-direct 100.0 2.1E-91 4.6E-96 723.3 26.8 300 1-329 219-596 (599)
3 COG0085 RpoB DNA-directed RNA 100.0 1.3E-88 2.8E-93 726.9 24.1 297 1-330 695-1058(1060)
4 PRK08565 DNA-directed RNA poly 100.0 1E-87 2.3E-92 735.7 25.3 301 1-330 723-1101(1103)
5 cd00653 RNA_pol_B_RPB2 RNA pol 100.0 2.5E-84 5.5E-89 695.9 24.7 294 1-327 498-866 (866)
6 CHL00207 rpoB RNA polymerase b 100.0 3.2E-83 6.9E-88 692.9 25.1 306 1-330 668-1054(1077)
7 TIGR02013 rpoB DNA-directed RN 100.0 1.9E-83 4.2E-88 697.8 23.2 293 1-326 695-1065(1065)
8 PRK00405 rpoB DNA-directed RNA 100.0 1.1E-82 2.4E-87 694.6 25.0 294 1-328 737-1107(1112)
9 CHL00001 rpoB RNA polymerase b 100.0 1.1E-81 2.4E-86 682.6 25.3 303 1-328 673-1057(1070)
10 KOG0216 RNA polymerase I, seco 100.0 1.1E-81 2.5E-86 650.5 20.8 299 1-329 743-1111(1111)
11 KOG0215 RNA polymerase III, se 100.0 5.9E-81 1.3E-85 643.4 11.1 298 1-331 778-1151(1153)
12 KOG0214 RNA polymerase II, sec 100.0 1.6E-77 3.4E-82 623.6 13.8 300 1-329 763-1140(1141)
13 PRK09603 bifunctional DNA-dire 100.0 3.9E-74 8.5E-79 648.0 24.4 298 1-331 828-1376(2890)
14 PRK14844 bifunctional DNA-dire 100.0 5.7E-71 1.2E-75 620.8 22.1 297 1-330 838-1433(2836)
15 PF00562 RNA_pol_Rpb2_6: RNA p 100.0 5.4E-61 1.2E-65 475.9 19.3 218 1-246 99-386 (386)
16 PF04560 RNA_pol_Rpb2_7: RNA p 99.9 8E-27 1.7E-31 185.7 4.3 78 248-328 1-81 (81)
17 KOG0214 RNA polymerase II, sec 95.5 0.0024 5.3E-08 69.7 -1.2 170 71-273 857-1041(1141)
18 PF04941 LEF-8: Late expressio 75.6 4.3 9.4E-05 44.2 5.1 53 63-119 683-736 (748)
19 PHA03394 lef-8 DNA-directed RN 72.8 5.7 0.00012 43.9 5.2 20 102-121 709-728 (865)
20 PF04564 U-box: U-box domain; 23.8 38 0.00083 26.0 0.9 46 190-244 5-52 (73)
21 PRK00420 hypothetical protein; 23.7 72 0.0016 27.2 2.6 24 274-297 25-49 (112)
No 1
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated
Probab=100.00 E-value=3.7e-92 Score=729.66 Aligned_cols=301 Identities=32% Similarity=0.486 Sum_probs=275.6
Q ss_pred CcccccccccceeeeEEEEEeec--------ccccc---------------CCCCCCcccccccccCCCCeEEEEeccC-
Q 019610 1 MNQASLECGVFRSESYKAEVDNK--------DIQVK---------------SRPSDDMLNFGKIQSKSGDIVIGKYAEI- 56 (338)
Q Consensus 1 iNKsSidRG~f~s~~Ykte~~~~--------~~~~~---------------~~~~~~~~~~g~~~v~~gDvligk~~~~- 56 (338)
|||||||||||||++|+++.... +.++. .+|+||++.+|. .|++|||||||++|.
T Consensus 225 iNkssidRGlf~s~~~k~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~LD~dGi~~~G~-~v~~gdiligk~sp~~ 303 (605)
T PRK07225 225 MNKASIERGLGRSHFFRTYEGEERRYPGGQEDRFEIPDKDVRGYRGEEAYRHLDEDGLVNPET-EVKEGDVLIGKTSPPR 303 (605)
T ss_pred eehhhhhcCceEEEEEEEEEEEeeecCCCcceEEecCCchhccccChHHhhcCCCCCCccCCC-EECCCCEEEEEecCCC
Confidence 79999999999999988865311 11221 256788999888 789999999998762
Q ss_pred --------------CceeEEEecCCCceeEEEEEEEeCCCCCeeEEEEEeeccccccccccccccccccCCcceeeeec-
Q 019610 57 --------------GADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLE- 121 (338)
Q Consensus 57 --------------~~d~s~~~~~~e~g~Vd~V~~~~~~~g~~~v~v~ir~~~~~~R~~~iGDKfssRHGqKGvvs~i~- 121 (338)
.+|+|++++++|+|+||+|.++.+++|...++|++|+ .|+|+||||||||||||||||+||
T Consensus 304 ~~~~~~~~~~~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~vkv~ir~----~R~p~iGDKfssRHGQKGvvs~i~~ 379 (605)
T PRK07225 304 FLEEPDDFGISPEKRRETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRD----LRIPELGDKFASRHGQKGVIGLIVP 379 (605)
T ss_pred CccchhhhcccccCcceeeEEecCCCcEEEEEEEEEecCCCCEEEEEEEEE----EEeccccchhhhcccCceeEEeEec
Confidence 4789999999999999999999988888999999999 999999999999999999999999
Q ss_pred -------------------------cChhHHHHHHhhhh-hccCCceeecCCCCCCHHHHHHHHHh-hccccCccccCCC
Q 019610 122 -------------------------QTPAQLLEAALGKG-ACDGLMSYATPFATSTGGVITEQHQS-FVSQLLNCIGARN 174 (338)
Q Consensus 122 -------------------------MtiGql~E~~~gk~-a~~g~~~~~tpF~~~~~~~i~~~l~~-~~~~~g~~~~~~~ 174 (338)
||||||+|+++||+ ++.|.+.|+|||...+.+++.+.|.+ ||+++|+
T Consensus 380 ~eDMPft~~G~~PDiIiNPhg~PSRMTiGql~E~~~gk~~~~~g~~~d~t~F~~~~~~~~~~~L~~~g~~~~G~------ 453 (605)
T PRK07225 380 QEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDEEDLREALEKLGFEHTGK------ 453 (605)
T ss_pred cccCCcCCCCCcccEEECcccccccCcHHHHHHHHHHHHHHhcCceEeecCCCCchHHHHHHHHHHhCcCCCCe------
Confidence 99999999999999 88999999999999999999999999 9999998
Q ss_pred CCeEEEeeCCcccccccCCCcccccceeeeeeEEEeeeeeeccccccCccceeeeecCCcccccCCccccccCCceeeee
Q 019610 175 SGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGE 254 (338)
Q Consensus 175 ~gke~l~~g~~~~~~~~~p~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~GR~r~GG~RfGE 254 (338)
|.|||| +||++|+++||+|++|||||+|||+||+|+|++||++.|||||++||+|+|||||||
T Consensus 454 ---e~my~G--------------~TG~~~~~~if~G~~yYqrL~HmV~DK~haR~~Gp~~~lTrQP~~GR~r~GG~RfGE 516 (605)
T PRK07225 454 ---EVMYDG--------------ITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGE 516 (605)
T ss_pred ---EEEEcC--------------CCCCEecccEEEeehheeechhhhcchhhhccCCCCcccccCCccccccCCCeeeee
Confidence 999999 999999999999999999999999999999999999999999999999999999999
Q ss_pred ccchhhhhhchHHhhhhhh----------ccccccccccc--ccCCeeecccCCCCccccccChHhHHHHHHHHhhhcCC
Q 019610 255 MKCDCLIAHGASGNLHERL----------KCKNVANVIQR--VVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGI 322 (338)
Q Consensus 255 ME~daLiahGAs~~L~ErL----------~c~~~~~~~~~--~~~~~~c~~c~~~~~i~~~~ipy~~k~L~~EL~~sm~i 322 (338)
||||||+|||||++|+||| .|..|+.+... .....+|+.|.++..+.++.+|||||||+||| +||||
T Consensus 517 MErd~lia~Gas~~L~Erl~~~SD~~~~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~i~~v~iPya~kll~~EL-~sm~i 595 (605)
T PRK07225 517 MERDVLIGHGAAMLLKERLLDESDKVEIYVCAKCGMIAIYDKKRNRKYCPICGEETDIYPVEMSYAFKLLLDEL-KSLGI 595 (605)
T ss_pred eehhhhhhhhhHHHHHHHHhccCcceeEEeecCcCcceehhcccCceeecccCCCCceeeccCChhHHHHHHHH-HHCCc
Confidence 9999999999999999999 77788766532 22357799999988999999999999999999 99999
Q ss_pred eEEEEeee
Q 019610 323 TLKFDTQL 330 (338)
Q Consensus 323 ~~~~~~~~ 330 (338)
+++|.++.
T Consensus 596 ~~~l~~~~ 603 (605)
T PRK07225 596 APRLELED 603 (605)
T ss_pred eeEEEecc
Confidence 99999873
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=2.1e-91 Score=723.30 Aligned_cols=300 Identities=34% Similarity=0.531 Sum_probs=274.8
Q ss_pred CcccccccccceeeeEEEEEeec--------cccc---------------cCCCCCCcccccccccCCCCeEEEEeccC-
Q 019610 1 MNQASLECGVFRSESYKAEVDNK--------DIQV---------------KSRPSDDMLNFGKIQSKSGDIVIGKYAEI- 56 (338)
Q Consensus 1 iNKsSidRG~f~s~~Ykte~~~~--------~~~~---------------~~~~~~~~~~~g~~~v~~gDvligk~~~~- 56 (338)
|||||+|||||||++|++..... +.+. +.+|+||++.+|. .|++|||||||++|.
T Consensus 219 ink~si~rG~f~s~~~~~~~~~~~~~~~~~~e~~~~p~~~~~~~~~~~~~~~LD~dGi~~~G~-~v~~gdiligk~~p~~ 297 (599)
T TIGR03670 219 MNKASIERGLARSTFFRTYEAEERRYPGGQEDRFEIPEPDVRGYRGEEAYKHLDEDGIVYPEV-EVKGGDVLIGKTSPPR 297 (599)
T ss_pred echhhhhcCCeEEEEEEEEEEEeeccCCCCceEEecCCchhccccchhhhccCCCCCCcCCCc-EeCCCCEEEEEecCCC
Confidence 79999999999999998765321 1111 1256789999998 789999999998862
Q ss_pred --------------CceeEEEecCCCceeEEEEEEEeCCCCCeeEEEEEeeccccccccccccccccccCCcceeeeec-
Q 019610 57 --------------GADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLE- 121 (338)
Q Consensus 57 --------------~~d~s~~~~~~e~g~Vd~V~~~~~~~g~~~v~v~ir~~~~~~R~~~iGDKfssRHGqKGvvs~i~- 121 (338)
.+|+|++++++|+|+||+|.++.++++...++|++|+ .|+|++|||||||||||||||+||
T Consensus 298 ~~~~~~~~~~~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~vkv~~r~----~R~p~iGDKfssRHGQKGvvs~i~~ 373 (599)
T TIGR03670 298 FLEELRELGLVTERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRD----LRIPELGDKFASRHGQKGVIGMIVP 373 (599)
T ss_pred CccchhhhccccccCceEEEEecCCCcEEEEEEEEEecCCCcEEEEEEEee----eecCcchhhhhhhccCcceEEeEec
Confidence 3789999999999999999999988888899999999 999999999999999999999999
Q ss_pred -------------------------cChhHHHHHHhhhh-hccCCceeecCCCCCCHHHHHHHHHh-hccccCccccCCC
Q 019610 122 -------------------------QTPAQLLEAALGKG-ACDGLMSYATPFATSTGGVITEQHQS-FVSQLLNCIGARN 174 (338)
Q Consensus 122 -------------------------MtiGql~E~~~gk~-a~~g~~~~~tpF~~~~~~~i~~~l~~-~~~~~g~~~~~~~ 174 (338)
||||||+|+++||+ ++.|.+.|+|||++.+.+++.+.|++ ||+++|+
T Consensus 374 ~eDMPft~~G~~pDiIiNPhg~PSRMTiGqllE~~~gk~~~~~g~~~d~t~F~~~~~~~~~~~L~~~g~~~~G~------ 447 (599)
T TIGR03670 374 QEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGK------ 447 (599)
T ss_pred cCCCCcCCCCCCCCEEECcccccccccHHHHHHHHHHHHHHhcCCEEEeCCCCCccHHHHHHHHHHcCCCCCCC------
Confidence 99999999999999 88999999999999999999999999 9999999
Q ss_pred CCeEEEeeCCcccccccCCCcccccceeeeeeEEEeeeeeeccccccCccceeeeecCCcccccCCccccccCCceeeee
Q 019610 175 SGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGE 254 (338)
Q Consensus 175 ~gke~l~~g~~~~~~~~~p~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~GR~r~GG~RfGE 254 (338)
|.|||| +||++|+++||+|++|||||+|||+||+|+|++||++.|||||++||+|+|||||||
T Consensus 448 ---e~ly~G--------------~TG~~~~~~if~G~~yyqrL~HmV~DK~h~Rs~Gp~~~lTrQP~~Gr~r~GG~RfGE 510 (599)
T TIGR03670 448 ---EVMYDG--------------ITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGE 510 (599)
T ss_pred ---EEEEcC--------------CCCCCccccEEEEehhheechhhhcchhhhcccCCCcccccCCccccccCCCeeeee
Confidence 999999 999999999999999999999999999999999999999999999999999999999
Q ss_pred ccchhhhhhchHHhhhhhh----------ccccccccccc--ccCCeeecccCCCCccccccChHhHHHHHHHHhhhcCC
Q 019610 255 MKCDCLIAHGASGNLHERL----------KCKNVANVIQR--VVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGI 322 (338)
Q Consensus 255 ME~daLiahGAs~~L~ErL----------~c~~~~~~~~~--~~~~~~c~~c~~~~~i~~~~ipy~~k~L~~EL~~sm~i 322 (338)
||||||+|||||++|+||| .|..|+.+... ....++|+.|.++.++.++.+|||||+|+||| +||||
T Consensus 511 MErd~lia~Gas~~L~ErL~~~SD~~~~~vC~~CG~~~~~~~~~~~~~C~~c~~~~~i~~v~iPy~~k~l~~EL-~am~i 589 (599)
T TIGR03670 511 MERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIAWEDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDEL-KSLGI 589 (599)
T ss_pred eehhhHhhcchHHHHHHHHhccCcceeEEeecccCceeehhcccCceeccccCCCCceeeecCChhHHHHHHHH-HhCCc
Confidence 9999999999999999999 77777766532 22356799999988999999999999999999 99999
Q ss_pred eEEEEee
Q 019610 323 TLKFDTQ 329 (338)
Q Consensus 323 ~~~~~~~ 329 (338)
++++.++
T Consensus 590 ~~~l~~~ 596 (599)
T TIGR03670 590 SPRLELG 596 (599)
T ss_pred ceEEEec
Confidence 9999987
No 3
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]
Probab=100.00 E-value=1.3e-88 Score=726.93 Aligned_cols=297 Identities=28% Similarity=0.429 Sum_probs=273.9
Q ss_pred CcccccccccceeeeEEEEEeec--------cccc---------cCCCCCCcccccccccCCCCeEEEEeccCC------
Q 019610 1 MNQASLECGVFRSESYKAEVDNK--------DIQV---------KSRPSDDMLNFGKIQSKSGDIVIGKYAEIG------ 57 (338)
Q Consensus 1 iNKsSidRG~f~s~~Ykte~~~~--------~~~~---------~~~~~~~~~~~g~~~v~~gDvligk~~~~~------ 57 (338)
|||+|||||+|+|+.|+++..+. +.+. +.+|+||++.+|. .|++|||||||++|++
T Consensus 695 in~~~v~~~~~ts~~~~~~~~~~r~~~~g~e~~~~iP~~~e~~~~~Lde~Gii~ig~-~V~~gdilvgk~tP~~~~~~~~ 773 (1060)
T COG0085 695 ISERSVERDLFTSIHIEEYETEARDTKLGPEEIRDIPNVSEEALRNLDEDGIIRIGA-EVKGGDILVGKVTPKGETELTP 773 (1060)
T ss_pred cccchhhcCCceEEEEEEEeeeeeccCCCccccccCCCcCHHHHhcCCccCcccccc-EEcCCCEEEEeeCCCCCCCCCc
Confidence 79999999999999888865321 1122 2468899999998 8999999999999864
Q ss_pred ------------ceeEEEecCCCceeEEEEEEEeCCC----CCeeEEEEEeeccccccccccccccccccCCcceeeeec
Q 019610 58 ------------ADHSIKLKHTERGLVLKVLLSSNDD----GKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLE 121 (338)
Q Consensus 58 ------------~d~s~~~~~~e~g~Vd~V~~~~~~~----g~~~v~v~ir~~~~~~R~~~iGDKfssRHGqKGvvs~i~ 121 (338)
+|+|++++++++|+|++|.++++++ +.++|||++|+ .|.|++|||||||||||||||+|+
T Consensus 774 ee~ll~i~~ek~rdtsl~~~~g~~G~V~~V~~~~~~~~~~g~~~~vkV~v~~----~R~~~~GDK~a~RHG~KGVis~i~ 849 (1060)
T COG0085 774 EERLLRIFGEKVRDTSLRVPHGEEGIVDDVQVFTREDGDPGVNKLVKVYVAQ----KRKPQIGDKMAGRHGNKGVVSKIV 849 (1060)
T ss_pred hhhhhccccceeeccceeecCCCCeEEEEEEEEeccCCCcCceEEEEEEEEE----eccCCccccccccCCCCceeeeec
Confidence 5899999999999999999999877 67899999999 999999999999999999999999
Q ss_pred --------------------------cChhHHHHHHhhhh-hccCCceeecCCCCCCHHHHHHHHHh-hccccCccccCC
Q 019610 122 --------------------------QTPAQLLEAALGKG-ACDGLMSYATPFATSTGGVITEQHQS-FVSQLLNCIGAR 173 (338)
Q Consensus 122 --------------------------MtiGql~E~~~gk~-a~~g~~~~~tpF~~~~~~~i~~~l~~-~~~~~g~~~~~~ 173 (338)
|||||++|+++||+ ++.|...++|||++.+.+++.++|.+ ||+..|+
T Consensus 850 p~eDMPf~~~G~~~DiilNP~gvPSRM~iGqilE~~lG~a~~~~G~~~~~~~F~g~~~~~~~~~l~~~g~~~~Gk----- 924 (1060)
T COG0085 850 PQEDMPFLEDGTPPDIILNPLGVPSRMNIGQILETHLGKAAALLGIPVDTPVFDGAPEEDIRELLKEAGFPYSGK----- 924 (1060)
T ss_pred CcccCCcCCCCCcccEEECCCCCCccccHHHHHHHHHHHHHHhcCceeccCCcCCCCHHHHHHHHHHcCCCCCCC-----
Confidence 99999999999999 88999999999999999999999999 9998888
Q ss_pred CCCeEEEeeCCcccccccCCCcccccceeeeeeEEEeeeeeeccccccCccceeeeecCCcccccCCccccccCCceeee
Q 019610 174 NSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFG 253 (338)
Q Consensus 174 ~~gke~l~~g~~~~~~~~~p~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~GR~r~GG~RfG 253 (338)
+.|||| +||++|+++||||++|||||+|||+||+||||+|||+.+||||++||++.||||||
T Consensus 925 ----~~lydG--------------~TGe~~~~~i~vG~~Y~~kL~HmV~dK~HaRs~GP~s~lT~QP~~Gka~~GG~RfG 986 (1060)
T COG0085 925 ----EVLYDG--------------RTGEPFDAPIFVGVMYYQKLHHMVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFG 986 (1060)
T ss_pred ----EEeecC--------------CCCCcccccEEEEehHHHhHHhhhcccceeeccCCceeeecCCCCcccccCCcccc
Confidence 999999 99999999999999999999999999999999999999999999999999999999
Q ss_pred eccchhhhhhchHHhhhhhhcccccccccccccCCeeecccCCCCccccccChHhHHHHHHHHhhhcCCeEEEEeee
Q 019610 254 EMKCDCLIAHGASGNLHERLKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLKFDTQL 330 (338)
Q Consensus 254 EME~daLiahGAs~~L~ErL~c~~~~~~~~~~~~~~~c~~c~~~~~i~~~~ipy~~k~L~~EL~~sm~i~~~~~~~~ 330 (338)
|||||||+|||||++|||||+.+|| ++..|.. .+-|..|. .++.++.||||||+|++|| +||||++++.+.+
T Consensus 987 EME~~aL~ayGAa~~LqE~L~~~SD-~~~G~~~-~y~~~v~g--~~~~~~~ip~sFk~L~~El-~sl~i~~~l~~~~ 1058 (1060)
T COG0085 987 EMEVWALEAYGAAYTLQERLTVKSD-DVCGRIK-IYECIVKG--ENIPEVGIPESFKVLLKEL-RSLGIDVRLELED 1058 (1060)
T ss_pred chHHHHHHHHhHHHHHHHHhhccch-hcccchh-hhcCcccC--CCCCCCCCCHHHHHHHHHH-HHCCCceEEeecC
Confidence 9999999999999999999999998 5665543 34599997 5899999999999999999 9999999998865
No 4
>PRK08565 DNA-directed RNA polymerase subunit B; Provisional
Probab=100.00 E-value=1e-87 Score=735.71 Aligned_cols=301 Identities=34% Similarity=0.505 Sum_probs=275.4
Q ss_pred CcccccccccceeeeEEEEEeec--------cccc---------------cCCCCCCcccccccccCCCCeEEEEecc--
Q 019610 1 MNQASLECGVFRSESYKAEVDNK--------DIQV---------------KSRPSDDMLNFGKIQSKSGDIVIGKYAE-- 55 (338)
Q Consensus 1 iNKsSidRG~f~s~~Ykte~~~~--------~~~~---------------~~~~~~~~~~~g~~~v~~gDvligk~~~-- 55 (338)
|||||+|||||||++||+...+. +.++ +.+|+||++.+|+ .|++|||||||++|
T Consensus 723 ink~s~~rG~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ld~dGi~~~G~-~v~~gdili~k~~p~~ 801 (1103)
T PRK08565 723 MNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIPEPNVRGYRGEEYYRKLDEDGIVSPEV-EVKGGDVLIGKTSPPR 801 (1103)
T ss_pred hhhhhhhcCCceEEEEEEEEEEeeecCCCCceEEecCCCcccccCchhhhhcCCCCCCcCCCc-EEcCCCEEEEEecCCC
Confidence 69999999999999998865310 1111 1256789999998 78999999999987
Q ss_pred -------------CCceeEEEecCCCceeEEEEEEEeCCCCCeeEEEEEeeccccccccccccccccccCCcceeeeec-
Q 019610 56 -------------IGADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLE- 121 (338)
Q Consensus 56 -------------~~~d~s~~~~~~e~g~Vd~V~~~~~~~g~~~v~v~ir~~~~~~R~~~iGDKfssRHGqKGvvs~i~- 121 (338)
..+|+|++++++|+|+||+|.++.++++...|+|++|+ .|+|++|||||||||||||||+||
T Consensus 802 ~~~~~~~~~~~~~~~~~~s~~~~~~e~g~V~~V~~~~~~~~~~~vkv~ir~----~R~p~iGDKfssRhGqKGv~s~i~~ 877 (1103)
T PRK08565 802 FLEELEELSLGLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRD----LRIPELGDKFASRHGQKGVIGMLVP 877 (1103)
T ss_pred CCcchhhccccCCccccceEEecCCCceEEEEEEEEecCCCcEEEEEEEEE----EecCchhhhhhhhccCcceeeeecc
Confidence 25799999999999999999999988888899999999 999999999999999999999999
Q ss_pred -------------------------cChhHHHHHHhhhh-hccCCceeecCCCCCCHHHHHHHHHh-hccccCccccCCC
Q 019610 122 -------------------------QTPAQLLEAALGKG-ACDGLMSYATPFATSTGGVITEQHQS-FVSQLLNCIGARN 174 (338)
Q Consensus 122 -------------------------MtiGql~E~~~gk~-a~~g~~~~~tpF~~~~~~~i~~~l~~-~~~~~g~~~~~~~ 174 (338)
||||||+|+++||+ ++.|.+.|+|||.+...+++.+.|++ ||+++|+
T Consensus 878 ~edmPf~~~G~~pDiI~NPh~~PSRMtiG~l~E~~~gk~~~~~g~~~d~t~F~~~~~~~~~~~L~~~g~~~~G~------ 951 (1103)
T PRK08565 878 QEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKLGYKPDGT------ 951 (1103)
T ss_pred cccCCcCCCCCCccEEECCCCCcccccHHHHHHHHHHHHHHhcCceeeecCcCCchHHHHHHHHHHcCCCCCCc------
Confidence 99999999999999 88999999999999999999999999 9999999
Q ss_pred CCeEEEeeCCcccccccCCCcccccceeeeeeEEEeeeeeeccccccCccceeeeecCCcccccCCccccccCCceeeee
Q 019610 175 SGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGE 254 (338)
Q Consensus 175 ~gke~l~~g~~~~~~~~~p~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~GR~r~GG~RfGE 254 (338)
|.|||| +||++|+++||+|++|||||+|||+||+|||++||+++|||||++||+|+|||||||
T Consensus 952 ---e~l~~G--------------~tG~~~~~~if~G~~yy~rL~HmV~DK~~~R~~Gp~~~lt~QP~~Gr~~~GG~R~GE 1014 (1103)
T PRK08565 952 ---EVMYDG--------------RTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGE 1014 (1103)
T ss_pred ---EEEEcC--------------CCCCCcccceEEeehhheechhhhchhhhhccCCCcchhhhCCccccccCCCeeeec
Confidence 999999 999999999999999999999999999999999999999999999999999999999
Q ss_pred ccchhhhhhchHHhhhhhh----------ccccccccccc--ccCCeeecccCCCCccccccChHhHHHHHHHHhhhcCC
Q 019610 255 MKCDCLIAHGASGNLHERL----------KCKNVANVIQR--VVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGI 322 (338)
Q Consensus 255 ME~daLiahGAs~~L~ErL----------~c~~~~~~~~~--~~~~~~c~~c~~~~~i~~~~ipy~~k~L~~EL~~sm~i 322 (338)
||||||+|||||++|+||| .|..|+.+... ....++|+.|.++..+.++.+|||||||+||| +||||
T Consensus 1015 ME~d~l~a~Gas~~L~erL~~~SD~~~~~vC~~Cg~~~~~~~~~~~~~C~~c~~~~~~~~v~iPy~~k~l~~EL-~sm~i 1093 (1103)
T PRK08565 1015 MERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHIAWYDRRKNKYVCPIHGDKGNISPVEVSYAFKLLLQEL-MSMGI 1093 (1103)
T ss_pred chHHHHHhcccHHHHHHHhhccccceeeeeecccccccccccccCceeccccCCCCcceeccCChhHHHHHHHH-HhCCC
Confidence 9999999999999999999 77778776532 13457799999988899999999999999999 99999
Q ss_pred eEEEEeee
Q 019610 323 TLKFDTQL 330 (338)
Q Consensus 323 ~~~~~~~~ 330 (338)
+++|.++.
T Consensus 1094 ~~~l~~~~ 1101 (1103)
T PRK08565 1094 SPRLKLGD 1101 (1103)
T ss_pred ceEEEeee
Confidence 99999874
No 5
>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=2.5e-84 Score=695.87 Aligned_cols=294 Identities=37% Similarity=0.537 Sum_probs=268.0
Q ss_pred CcccccccccceeeeEEEEEeecc--------ccc-----------cCCCCCCcccccccccCCCCeEEEEeccC-----
Q 019610 1 MNQASLECGVFRSESYKAEVDNKD--------IQV-----------KSRPSDDMLNFGKIQSKSGDIVIGKYAEI----- 56 (338)
Q Consensus 1 iNKsSidRG~f~s~~Ykte~~~~~--------~~~-----------~~~~~~~~~~~g~~~v~~gDvligk~~~~----- 56 (338)
|||||+|||||||++|+++..+.. ... +.+|+||++.+|+ .|++|||||||++|.
T Consensus 498 ink~s~~rg~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ld~dGi~~~g~-~v~~gd~li~k~~~~~~~~~ 576 (866)
T cd00653 498 INKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRGDIPNVSEEKLKNLDEDGIIRPGA-RVEPGDILVGKITPKGETES 576 (866)
T ss_pred eehhhhhcCceeEEEEEEEEEEEEecCCCcceEecCCCCCCChHHhhccCCCCCcCCCC-EecCCCEEEEEecCcccccc
Confidence 799999999999999988664321 010 1367889999998 789999999998874
Q ss_pred ----------CceeEEEecCCCceeEEEEEEEe---CCCCCeeEEEEEeeccccccccccccccccccCCcceeeeec--
Q 019610 57 ----------GADHSIKLKHTERGLVLKVLLSS---NDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLE-- 121 (338)
Q Consensus 57 ----------~~d~s~~~~~~e~g~Vd~V~~~~---~~~g~~~v~v~ir~~~~~~R~~~iGDKfssRHGqKGvvs~i~-- 121 (338)
.+|+|++++++++|+|++|.++. +.++...++|++|+ .|+|++|||||||||||||||+||
T Consensus 577 ~~~~~~~~~~~~~~~~~~~~~~~g~v~~v~~~~~~~~~~~~~~v~v~~r~----~R~p~iGDKfssRhGqKGv~s~i~~~ 652 (866)
T cd00653 577 TPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRELNDGGNKLVKVYIRQ----KRKPQIGDKFASRHGQKGVISKILPQ 652 (866)
T ss_pred cccccccCCcceEEEEEecCCCceEEEEEEEeccccCCCCcEEEEEEEeE----EecCCcccccccccCCCcEEEEEecc
Confidence 57899999999999999999998 45667899999999 999999999999999999999999
Q ss_pred ------------------------cChhHHHHHHhhhh-hccCCceeecCCCCCCHHHHHHHHHh-hccccCccccCCCC
Q 019610 122 ------------------------QTPAQLLEAALGKG-ACDGLMSYATPFATSTGGVITEQHQS-FVSQLLNCIGARNS 175 (338)
Q Consensus 122 ------------------------MtiGql~E~~~gk~-a~~g~~~~~tpF~~~~~~~i~~~l~~-~~~~~g~~~~~~~~ 175 (338)
||||||+|+++||+ ++.|.+.|+|||+....+++.+.|.+ +|+++|+
T Consensus 653 ~dmPf~~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~t~f~~~~~~~~~~~l~~~g~~~~G~------- 725 (866)
T cd00653 653 EDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGK------- 725 (866)
T ss_pred ccCCcccCCCCCcEEecCCcCcccccHHHHHHHHHHHHHHhcCCcccccccCcchHHHHHHHHHHcCCCCCCc-------
Confidence 99999999999999 88999999999999999999999999 9999898
Q ss_pred CeEEEeeCCcccccccCCCcccccceeeeeeEEEeeeeeeccccccCccceeeeecCCcccccCCccccccCCceeeeec
Q 019610 176 GITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEM 255 (338)
Q Consensus 176 gke~l~~g~~~~~~~~~p~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~GR~r~GG~RfGEM 255 (338)
|.|||| +||++++++||+|++|||||+|||+||+|||++||++.|||||++||+|+||||||||
T Consensus 726 --e~~y~g--------------~tG~~~~~~if~G~~yyqrL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEM 789 (866)
T cd00653 726 --EVLYDG--------------RTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEM 789 (866)
T ss_pred --EEEEcC--------------CCCCCcccceEEeehhhhhhhhhhchhhhhcccCCcchhccCcCccccccCCeEEEEE
Confidence 999999 9999999999999999999999999999999999999999999999999999999999
Q ss_pred cchhhhhhchHHhhhhhh----------cccccccccccccCCeeecccCCCCccccccChHhHHHHHHHHhhhcCCeEE
Q 019610 256 KCDCLIAHGASGNLHERL----------KCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLK 325 (338)
Q Consensus 256 E~daLiahGAs~~L~ErL----------~c~~~~~~~~~~~~~~~c~~c~~~~~i~~~~ipy~~k~L~~EL~~sm~i~~~ 325 (338)
|||||+|||||++|+||| .|..|+.+.. ..+|..|.++..+.++.+|||||+|++|| +||||+++
T Consensus 790 Erd~lia~Gas~~l~erl~~~SD~~~~~vc~~cg~i~~----~~~c~~c~~~~~~~~~~ipy~~kll~~EL-~sm~i~~~ 864 (866)
T cd00653 790 ERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILS----ANLCRLCKKGTNISKVGIPYAFKLLFQEL-QSMNIDPR 864 (866)
T ss_pred ehhhhhhhhhHHHHHHHHhcCCccceEEEeccCccccc----ccccccccCCCceeecCCCHHHHHHHHHH-HHCCcceE
Confidence 999999999999999999 5555655432 24599999999999999999999999999 99999999
Q ss_pred EE
Q 019610 326 FD 327 (338)
Q Consensus 326 ~~ 327 (338)
+.
T Consensus 865 ~~ 866 (866)
T cd00653 865 LK 866 (866)
T ss_pred eC
Confidence 73
No 6
>CHL00207 rpoB RNA polymerase beta subunit; Provisional
Probab=100.00 E-value=3.2e-83 Score=692.92 Aligned_cols=306 Identities=23% Similarity=0.296 Sum_probs=265.8
Q ss_pred CcccccccccceeeeEEEEEe---ec----cccc-----------cCCCCCCcccccccccCCCCeEEEEeccC------
Q 019610 1 MNQASLECGVFRSESYKAEVD---NK----DIQV-----------KSRPSDDMLNFGKIQSKSGDIVIGKYAEI------ 56 (338)
Q Consensus 1 iNKsSidRG~f~s~~Ykte~~---~~----~~~~-----------~~~~~~~~~~~g~~~v~~gDvligk~~~~------ 56 (338)
|||+|++||+|+|+.|++... +. +.+. +.+|+||++.+|+ .|++|||||||++|+
T Consensus 668 ink~~v~rg~f~Si~~~~~~~e~~~~~~g~e~i~~~~p~~~~~~~~~LD~dGiv~iG~-~V~~gDilvgK~tp~~~~~~~ 746 (1077)
T CHL00207 668 INKRLVYEDLFTSIHIEKYEIELRQTKLGSEEITRNIPNVSEYSLKNLDENGIISIGS-KVLAGDILVGKITPKGESDQL 746 (1077)
T ss_pred hhhhhhcCCceEEEEEEEeeeEEeecCCCceEEeccCCCCChHHhhccCccCCCcCCc-EeCCCCEEEEEecCccccccC
Confidence 799999999999996655432 11 1111 2367899999998 899999999999873
Q ss_pred ----------------CceeEEEecCCCceeEEEEEEEeCCCC--Ce-----eEEEEEeeccccccccccccccccccCC
Q 019610 57 ----------------GADHSIKLKHTERGLVLKVLLSSNDDG--KN-----FAVVSIRQSVNMVHSACLGDKFSSMHGQ 113 (338)
Q Consensus 57 ----------------~~d~s~~~~~~e~g~Vd~V~~~~~~~g--~~-----~v~v~ir~~~~~~R~~~iGDKfssRHGq 113 (338)
.+|+|++++++++|+|++|.+++++++ .. .++|++|+ .|+|++||||||||||
T Consensus 747 ~~~~ll~~i~~~~~~~~kd~sl~~~~~~~g~V~~V~~~~~~~~~~~~~~~~~~vkv~i~~----~R~p~vGDKfasRHGq 822 (1077)
T CHL00207 747 PEGKLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRSKGDELKFGYYLKIRVFIAQ----IRKIQVGDKLAGRHGN 822 (1077)
T ss_pred hhhhhhhhhhccCCCcceEeEEEcCCCCcEEEEEEEEEecCCCCcccccccEEEEEEEEE----EecCCcccccccccCC
Confidence 279999999999999999999986433 22 37777888 9999999999999999
Q ss_pred cceeeeec--------------------------cChhHHHHHHhhhh-hccCCceeecCCCCCCHHHHHHHHHh-hcc-
Q 019610 114 KGVLGFLE--------------------------QTPAQLLEAALGKG-ACDGLMSYATPFATSTGGVITEQHQS-FVS- 164 (338)
Q Consensus 114 KGvvs~i~--------------------------MtiGql~E~~~gk~-a~~g~~~~~tpF~~~~~~~i~~~l~~-~~~- 164 (338)
|||||+|+ ||||||+|+++||+ ++.+...+++||++...+++.+.|.. +..
T Consensus 823 KGVvs~i~p~eDMPf~~dG~~pDiIlNPhg~PSRMtiGqllE~~lGka~~~l~~~~~~tpF~~~~~~~~~~~l~~~~l~~ 902 (1077)
T CHL00207 823 KGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGDNLNKRFKILPFDEMYGSEYSRILINNKLNQ 902 (1077)
T ss_pred ceeEEeeeccCCCCccCCCCCccEEECCccccccccHHHHHHHHHHHHHHhcCCcEeeccCCCCcHHHHHHHHHhhhhhh
Confidence 99999999 99999999999999 54566677999999888888877765 422
Q ss_pred ---ccCccc--cCCCCCeEEEeeCCcccccccCCCcccccceeeeeeEEEeeeeeeccccccCccceeeeecCCcccccC
Q 019610 165 ---QLLNCI--GARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGR 239 (338)
Q Consensus 165 ---~~g~~~--~~~~~gke~l~~g~~~~~~~~~p~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~Q 239 (338)
..|+.| +++.+|++.|||| +||++|+++||+|++|||||+|||+||+|||++|||+.||||
T Consensus 903 ~~~~~~~~~~~~~~~~Gk~~lydG--------------~TGe~~~~~i~vG~~Yy~kL~HmV~DKihaRs~Gp~s~lTqQ 968 (1077)
T CHL00207 903 ASIKNNEYWLFNSYHPGKMVLRDG--------------RTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQ 968 (1077)
T ss_pred ccchhccccccCCCCCCCEEEECC--------------CCCCCccCceEEEecceeEchhhccccceeeccCCCcccccC
Confidence 234444 4566799999999 999999999999999999999999999999999999999999
Q ss_pred CccccccCCceeeeeccchhhhhhchHHhhhhhhcccccccccccccCCeeecccCCCCccccccChHhHHHHHHHHhhh
Q 019610 240 PVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFS 319 (338)
Q Consensus 240 P~~GR~r~GG~RfGEME~daLiahGAs~~L~ErL~c~~~~~~~~~~~~~~~c~~c~~~~~i~~~~ipy~~k~L~~EL~~s 319 (338)
|++||+++|||||||||||||+|||||++|+|||+.+|| ++.+|. .+|..|.++.+++++.+|||||+|+||| +|
T Consensus 969 P~~Grsr~GG~RfGEME~~aL~a~GAa~~L~E~L~~kSD-~~~~r~---~~~~~~~~~~~i~~~~~P~sfklL~~EL-~s 1043 (1077)
T CHL00207 969 PLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSD-DMQGRN---ETLNAIVKGQPIPKPGTPESFKVLMREL-QS 1043 (1077)
T ss_pred CCCccccCCCeeeecccHHHHHhhhhHHHHHHHhhcCCc-cceehH---HHHHhhhCCCeecCCCCCchHHHHHHHH-HH
Confidence 999999999999999999999999999999999999999 566654 5799999999999999999999999999 99
Q ss_pred cCCeEEEEeee
Q 019610 320 MGITLKFDTQL 330 (338)
Q Consensus 320 m~i~~~~~~~~ 330 (338)
|||++++....
T Consensus 1044 l~i~~~~~~~~ 1054 (1077)
T CHL00207 1044 LGLDIEAYKIE 1054 (1077)
T ss_pred CCcCcEecccc
Confidence 99999987544
No 7
>TIGR02013 rpoB DNA-directed RNA polymerase, beta subunit. This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit.
Probab=100.00 E-value=1.9e-83 Score=697.78 Aligned_cols=293 Identities=25% Similarity=0.360 Sum_probs=262.3
Q ss_pred CcccccccccceeeeEEEEEeec-------cccc-----------cCCCCCCcccccccccCCCCeEEEEeccC------
Q 019610 1 MNQASLECGVFRSESYKAEVDNK-------DIQV-----------KSRPSDDMLNFGKIQSKSGDIVIGKYAEI------ 56 (338)
Q Consensus 1 iNKsSidRG~f~s~~Ykte~~~~-------~~~~-----------~~~~~~~~~~~g~~~v~~gDvligk~~~~------ 56 (338)
|||+|+|||||+|+.|++...+. +.+. +.+|+||++.+|+ .|++|||||||++|.
T Consensus 695 ink~~i~rg~~~s~~~~~~~~~~~~~~~g~e~~~~~~p~~~~~~~~~Ld~dGi~~~G~-~v~~gdilvgk~~p~~~~~~~ 773 (1065)
T TIGR02013 695 ISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGA-EVKAGDILVGKVTPKGETELT 773 (1065)
T ss_pred eehhhhcCCceEEEEEEEEEEEeeccCCCceEeeccCCCCchhhhhccCCCCCccCcc-EeCCCCEEEEEecCCcccccC
Confidence 79999999999999887654321 1121 1257789999998 789999999999872
Q ss_pred ----------------CceeEEEecCCCceeEEEEEEEeCCCC-------CeeEEEEEeeccccccccccccccccccCC
Q 019610 57 ----------------GADHSIKLKHTERGLVLKVLLSSNDDG-------KNFAVVSIRQSVNMVHSACLGDKFSSMHGQ 113 (338)
Q Consensus 57 ----------------~~d~s~~~~~~e~g~Vd~V~~~~~~~g-------~~~v~v~ir~~~~~~R~~~iGDKfssRHGq 113 (338)
.+|+|++++++++|+||+|.++.++++ ...++|++|+ .|+|++||||||||||
T Consensus 774 ~~~~l~~~~~~~~~~~~~d~s~~~~~~~~g~V~~V~~~~~~~~~~~~~~~~~~vkv~ir~----~R~p~iGDKfasRHGq 849 (1065)
T TIGR02013 774 PEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSRKQGDELPPGVNKLVKVYIAQ----KRKIQVGDKMAGRHGN 849 (1065)
T ss_pred hhhhhhhhhcccCCccccccceEccCCCCEEEEEEEEEeccCCCccCcCccEEEEEEEee----cccccccchhhhcccC
Confidence 268899999999999999999987766 3579999999 9999999999999999
Q ss_pred cceeeeec--------------------------cChhHHHHHHhhhh-hcc--CCceeecC-CCCCCHHHHHHHHHh-h
Q 019610 114 KGVLGFLE--------------------------QTPAQLLEAALGKG-ACD--GLMSYATP-FATSTGGVITEQHQS-F 162 (338)
Q Consensus 114 KGvvs~i~--------------------------MtiGql~E~~~gk~-a~~--g~~~~~tp-F~~~~~~~i~~~l~~-~ 162 (338)
|||||+|+ ||||||+|+++||+ ++. +...++|| |++.+.+++.+.|++ |
T Consensus 850 KGvis~i~~~eDMPf~~~G~~pDiIiNPhg~PSRMtiGqllE~~~gka~~~~~~~~~~~~tp~f~~~~~~~~~~~l~~~g 929 (1065)
T TIGR02013 850 KGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRKGVPIATPVFDGASEEEIKEYLEKAG 929 (1065)
T ss_pred ceeEEeEecCCCCCccCCCCCccEEECCCCCcccccHHHHHHHHHHHHHHhccCCCeEEeccCcCCccHHHHHHHHHHcC
Confidence 99999999 99999999999999 544 67788999 998899999999998 9
Q ss_pred ccccCccccCCCCCeEEEeeCCcccccccCCCcccccceeeeeeEEEeeeeeeccccccCccceeeeecCCcccccCCcc
Q 019610 163 VSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVA 242 (338)
Q Consensus 163 ~~~~g~~~~~~~~gke~l~~g~~~~~~~~~p~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~ 242 (338)
|+++|+ |.|||| +||++|+++||+|++|||||+|||+||+|||++||++.|||||++
T Consensus 930 ~~~~G~---------e~l~~G--------------~TG~~~~~~ifvG~~yy~rL~HmV~DK~haRs~Gp~~~lT~QP~~ 986 (1065)
T TIGR02013 930 LPRDGK---------VRLYDG--------------RTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLG 986 (1065)
T ss_pred CCCCCC---------EEEEcC--------------CCCCCccccEEEeehheeechhhhcchhhhcccCCccceeeCCCc
Confidence 998888 999999 999999999999999999999999999999999999999999999
Q ss_pred ccccCCceeeeeccchhhhhhchHHhhhhhhcccccccccccccCCeeecccCCCCccccccChHhHHHHHHHHhhhcCC
Q 019610 243 DRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGI 322 (338)
Q Consensus 243 GR~r~GG~RfGEME~daLiahGAs~~L~ErL~c~~~~~~~~~~~~~~~c~~c~~~~~i~~~~ipy~~k~L~~EL~~sm~i 322 (338)
||+|+|||||||||||||+|||||++|+|||+.+|| ++..|.. .++..| ++.++.++.+|||||+|++|| +||||
T Consensus 987 Grsr~GG~R~GEME~d~l~a~Gas~~L~E~l~~~SD-~~~g~~~--~~~~~~-~~~~i~~~~~p~sfklL~~EL-~sm~i 1061 (1065)
T TIGR02013 987 GKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD-DVVGRTK--AYEAIV-KGENVPEPGIPESFNVLIKEL-QSLGL 1061 (1065)
T ss_pred ccccCCCeeeeeeeHHHHHhhhhHHHHHHHHhccCh-hhhhhhh--hhhhhc-CCCccccccCCccHHHHHHHH-HhCCc
Confidence 999999999999999999999999999999999999 5655542 455666 567899999999999999999 99999
Q ss_pred eEEE
Q 019610 323 TLKF 326 (338)
Q Consensus 323 ~~~~ 326 (338)
++++
T Consensus 1062 ~~~~ 1065 (1065)
T TIGR02013 1062 DIEL 1065 (1065)
T ss_pred cccC
Confidence 9875
No 8
>PRK00405 rpoB DNA-directed RNA polymerase subunit beta; Reviewed
Probab=100.00 E-value=1.1e-82 Score=694.56 Aligned_cols=294 Identities=26% Similarity=0.389 Sum_probs=261.4
Q ss_pred CcccccccccceeeeEEEEEeec-------cccc-----------cCCCCCCcccccccccCCCCeEEEEeccC------
Q 019610 1 MNQASLECGVFRSESYKAEVDNK-------DIQV-----------KSRPSDDMLNFGKIQSKSGDIVIGKYAEI------ 56 (338)
Q Consensus 1 iNKsSidRG~f~s~~Ykte~~~~-------~~~~-----------~~~~~~~~~~~g~~~v~~gDvligk~~~~------ 56 (338)
|||+|+|||||+|+.|++..... +.+. +.+|+||++.+|+ .|++|||||||++|.
T Consensus 737 ink~si~rg~~~s~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~Ld~dGi~~~G~-~v~~gDiligk~~~~~~~~~~ 815 (1112)
T PRK00405 737 ISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGA-EVKPGDILVGKVTPKGETELT 815 (1112)
T ss_pred EEhhhhccCceEEEEEeeeeeEeeccCCCceeecccCCCCChHHhhccCCCCCccCcc-EecCCCEEEEEecCCCccccC
Confidence 69999999999999766544210 1111 2267889999998 789999999999873
Q ss_pred ----------------CceeEEEecCCCceeEEEEEEEeC-CCC-------CeeEEEEEeeccccccccccccccccccC
Q 019610 57 ----------------GADHSIKLKHTERGLVLKVLLSSN-DDG-------KNFAVVSIRQSVNMVHSACLGDKFSSMHG 112 (338)
Q Consensus 57 ----------------~~d~s~~~~~~e~g~Vd~V~~~~~-~~g-------~~~v~v~ir~~~~~~R~~~iGDKfssRHG 112 (338)
.+|+|++++++++|+|++|.++++ +++ ...++|++|+ .|+|++|||||||||
T Consensus 816 ~~~~~~~~~~~~~~~~~~d~s~~~~~~~~g~V~~v~~~~~~~~~~~~~~~~~~~vkv~ir~----~R~p~iGDKfasRHG 891 (1112)
T PRK00405 816 PEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTRIEQGDELPPGVNKLVKVYIAQ----KRKIQVGDKMAGRHG 891 (1112)
T ss_pred hhhhhhhhhhcccccccccceEEcCCCCCEEEEEEEEeeccccCCccCcCcceEEEEEEee----ecccCcccchhhccC
Confidence 257999999999999999999987 555 3589999999 999999999999999
Q ss_pred Ccceeeeec--------------------------cChhHHHHHHhhhh-hccCCceeecC-CCCCCHHHHHHHHHh-hc
Q 019610 113 QKGVLGFLE--------------------------QTPAQLLEAALGKG-ACDGLMSYATP-FATSTGGVITEQHQS-FV 163 (338)
Q Consensus 113 qKGvvs~i~--------------------------MtiGql~E~~~gk~-a~~g~~~~~tp-F~~~~~~~i~~~l~~-~~ 163 (338)
||||||+|| ||||||+|+++||+ ++.|.+ ++|| |++.+.+++.+.|++ ||
T Consensus 892 qKGvis~i~~~eDMPf~~~G~~pDiIiNPhg~PSRMtiGql~E~~~gk~~~~~g~~-~~tp~f~~~~~~~~~~~l~~~g~ 970 (1112)
T PRK00405 892 NKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIK-FATPVFDGAKEEEIKELLEEAGL 970 (1112)
T ss_pred CceeEEeEeccCCCCcCCCCCCCcEEECCCCCcccccHHHHHHHHhhHHHHhcCCe-EecCccCCccHHHHHHHHHHcCc
Confidence 999999999 99999999999999 667765 8998 998899999999999 99
Q ss_pred cccCccccCCCCCeEEEeeCCcccccccCCCcccccceeeeeeEEEeeeeeeccccccCccceeeeecCCcccccCCccc
Q 019610 164 SQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVAD 243 (338)
Q Consensus 164 ~~~g~~~~~~~~gke~l~~g~~~~~~~~~p~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~G 243 (338)
+++|+ |.|||| +||++|+++||+|++|||||+|||+||+|||++||++.|||||++|
T Consensus 971 ~~~G~---------e~l~~G--------------~tG~~~~~~if~G~~yy~rL~HmV~DK~haRs~Gp~~~lT~QP~~G 1027 (1112)
T PRK00405 971 PEDGK---------TTLYDG--------------RTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGG 1027 (1112)
T ss_pred CCCCC---------EEEECC--------------CCCCCCcccEEEEehhheechhhhcchhhhcccCCccceeeCCCcc
Confidence 99888 999999 9999999999999999999999999999999999999999999999
Q ss_pred cccCCceeeeeccchhhhhhchHHhhhhhhcccccccccccccCCeeecccCCCCccccccChHhHHHHHHHHhhhcCCe
Q 019610 244 RKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGIT 323 (338)
Q Consensus 244 R~r~GG~RfGEME~daLiahGAs~~L~ErL~c~~~~~~~~~~~~~~~c~~c~~~~~i~~~~ipy~~k~L~~EL~~sm~i~ 323 (338)
|+|+|||||||||||||+|||||++|+|||+-+|| ++..+.. .++..| ++.++.++.+|||||+|+||| +||||+
T Consensus 1028 rsr~GG~R~GEME~d~l~a~Gas~~L~Erl~~~SD-~~~g~~~--~~~~~~-~~~~i~~~~~p~~fklL~~EL-~sm~i~ 1102 (1112)
T PRK00405 1028 KAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD-DVVGRTK--VYEAIV-KGENIPEPGIPESFNVLVKEL-QSLGLD 1102 (1112)
T ss_pred cccCCCeeeeeeehhhHhhhhhHHHHHHHhhccCc-cccccee--EEEEee-cCCcccccCCChHHHHHHHHH-HHCccc
Confidence 99999999999999999999999999999998888 4555543 343367 567899999999999999999 999999
Q ss_pred EEEEe
Q 019610 324 LKFDT 328 (338)
Q Consensus 324 ~~~~~ 328 (338)
+++..
T Consensus 1103 ~~~~~ 1107 (1112)
T PRK00405 1103 VELLD 1107 (1112)
T ss_pred eEEec
Confidence 99984
No 9
>CHL00001 rpoB RNA polymerase beta subunit
Probab=100.00 E-value=1.1e-81 Score=682.58 Aligned_cols=303 Identities=20% Similarity=0.250 Sum_probs=260.7
Q ss_pred CcccccccccceeeeEEEEEeec-------cccc-----------cCCCCCCcccccccccCCCCeEEEEeccC------
Q 019610 1 MNQASLECGVFRSESYKAEVDNK-------DIQV-----------KSRPSDDMLNFGKIQSKSGDIVIGKYAEI------ 56 (338)
Q Consensus 1 iNKsSidRG~f~s~~Ykte~~~~-------~~~~-----------~~~~~~~~~~~g~~~v~~gDvligk~~~~------ 56 (338)
|||+|+|||+|+|+.|++..... +.+. +.+|+||++.+|+ +|++|||||||++|+
T Consensus 673 in~~~v~~g~~~s~~~~~~~~~~~~~~~g~e~i~~~~p~~~~~~~~~Ld~dGi~~~G~-~v~~gDilvgK~~p~~~~~~~ 751 (1070)
T CHL00001 673 ISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEAHLLRNLDKNGIVMLGS-WVETGDILVGKLTPQEAEESS 751 (1070)
T ss_pred hhhhhhcCCceEEEEEeeeeEEEeccCCCcceEeccCCCCchhhhhccCCCCCccCCc-EecCCCEEEEEecCCcccccc
Confidence 79999999999999776644211 2222 2257889999998 899999999999874
Q ss_pred ------------------CceeEEEecCCCceeEEEEEEEeC----CCCCeeEEEEEeeccccccccccccccccccCCc
Q 019610 57 ------------------GADHSIKLKHTERGLVLKVLLSSN----DDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQK 114 (338)
Q Consensus 57 ------------------~~d~s~~~~~~e~g~Vd~V~~~~~----~~g~~~v~v~ir~~~~~~R~~~iGDKfssRHGqK 114 (338)
.+|+|++++++++|+|++|.+++. .++...|+|++|+ .|+|++|||||||||||
T Consensus 752 ~~~~~~~~~~if~~~~~~~~d~sl~~~~~~~g~V~~v~~~~~~~~~~~~~~~vkv~i~~----~R~~~vGDK~asRHGqK 827 (1070)
T CHL00001 752 YAPEGRLLRAIFGIQVSTSKETCLKLPIGGRGRVIDVRWIQKKGGSSYNPETIHVYILQ----KREIQVGDKVAGRHGNK 827 (1070)
T ss_pred cCcchhhhhhhhccccCcceeCeEECCCCCceEEEEEEEEecccCCCCCcEEEEEEEEE----EecCCCCcccccccCCc
Confidence 258999999999999999999984 3345789999999 99999999999999999
Q ss_pred ceeeeec--------------------------cChhHHHHHHhhhh-hccCCceeecCCCCCCHHHHH-----HHHHh-
Q 019610 115 GVLGFLE--------------------------QTPAQLLEAALGKG-ACDGLMSYATPFATSTGGVIT-----EQHQS- 161 (338)
Q Consensus 115 Gvvs~i~--------------------------MtiGql~E~~~gk~-a~~g~~~~~tpF~~~~~~~i~-----~~l~~- 161 (338)
||||+|+ ||||||+|+++||+ ++.|.+.+++||++...+++. ..|.+
T Consensus 828 Gvvs~i~~~eDMPf~~dG~~pDiIlNP~gvPSRMtiGqllE~~~G~a~~~~g~~~~~~pf~~~~~~~~~~~~~~~~l~~~ 907 (1070)
T CHL00001 828 GIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLLNRHYRIAPFDERYEQEASRKLVFSELYEA 907 (1070)
T ss_pred ceEeeeecccCCCcccCCCCCceeeccccccccccHHHHHHHHhHHHHhhcCceeeeccCCCcchhhhhhhhhhHHHHHH
Confidence 9999999 99999999999999 778999999999987666665 34444
Q ss_pred hccccCcc--ccCCCCCeEEEeeCCcccccccCCCcccccceeeeeeEEEeeeeeeccccccCccceeeeecCCcccccC
Q 019610 162 FVSQLLNC--IGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGR 239 (338)
Q Consensus 162 ~~~~~g~~--~~~~~~gke~l~~g~~~~~~~~~p~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~Q 239 (338)
++. .++. ++++.+||+.|||| +||++|+++||+|++|||||+|||+||+|||++|||++||||
T Consensus 908 ~~~-~~~~~~~~~~~~Gk~~l~dG--------------~TG~~~~~~i~vG~~Yy~kL~HmV~DKihaRs~Gp~~~lT~Q 972 (1070)
T CHL00001 908 SKQ-TANPWVFEPEYPGKSRLFDG--------------RTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQ 972 (1070)
T ss_pred HHh-cCCceeccCCCCCeEEEEcC--------------CCCCCccceEEEEecceeEchhhccccceeeccCCCcccccC
Confidence 552 1222 35778899999999 999999999999999999999999999999999999999999
Q ss_pred CccccccCCceeeeeccchhhhhhchHHhhhhhhcccccccccccccCCeeecccCCCCcccc-ccChHhHHHHHHHHhh
Q 019610 240 PVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVIQRVVGGPYCRICNSADDIIK-ANVPYGAKLLSQELSF 318 (338)
Q Consensus 240 P~~GR~r~GG~RfGEME~daLiahGAs~~L~ErL~c~~~~~~~~~~~~~~~c~~c~~~~~i~~-~~ipy~~k~L~~EL~~ 318 (338)
|++||+|+|||||||||||||+|||||++|+|||+.+|| ++..|.. ....|..+..+.+ +.+|||||+|++|| +
T Consensus 973 P~~Grsr~GG~RfGEME~~al~a~GAs~~L~E~L~~~SD-~~~~r~~---~~~~i~~g~~~~~~~~~pesfk~l~~El-~ 1047 (1070)
T CHL00001 973 PLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSD-HIRARQE---VLGAIITGGTIPKPEDAPESFRLLVREL-R 1047 (1070)
T ss_pred CCCcccCCCCeeeecchHHHHHhhhHHHHHHHHHhccCc-cHHHHHH---HHHhhhcCCcccCCCCCCchhhHHHHHH-H
Confidence 999999999999999999999999999999999999999 6666642 1223444557777 79999999999999 9
Q ss_pred hcCCeEEEEe
Q 019610 319 SMGITLKFDT 328 (338)
Q Consensus 319 sm~i~~~~~~ 328 (338)
|||+++.+..
T Consensus 1048 ~l~l~i~~~~ 1057 (1070)
T CHL00001 1048 SLALELNHFL 1057 (1070)
T ss_pred hCccceEEEE
Confidence 9999999875
No 10
>KOG0216 consensus RNA polymerase I, second largest subunit [Transcription]
Probab=100.00 E-value=1.1e-81 Score=650.47 Aligned_cols=299 Identities=33% Similarity=0.459 Sum_probs=272.0
Q ss_pred CcccccccccceeeeEEEEEeecc-------ccc--------cCCCCCCcccccccccCCCCeEEEEeccC-CceeEEEe
Q 019610 1 MNQASLECGVFRSESYKAEVDNKD-------IQV--------KSRPSDDMLNFGKIQSKSGDIVIGKYAEI-GADHSIKL 64 (338)
Q Consensus 1 iNKsSidRG~f~s~~Ykte~~~~~-------~~~--------~~~~~~~~~~~g~~~v~~gDvligk~~~~-~~d~s~~~ 64 (338)
|||||+||||+++++||+|..++. .|. +.+|.||++.+|. .+..||+++..+... ++....++
T Consensus 743 iNK~s~eRGf~~G~vykte~i~L~~~~~r~~~F~~~p~~~~~~~ld~dgLP~~G~-kl~~~dp~~~y~d~~t~~~~~~~~ 821 (1111)
T KOG0216|consen 743 INKSSYERGFAYGTVYKTEKIDLSKKRSRSKHFGRSPGEPELKKLDADGLPSIGQ-KLEYGDPYYAYFDEETGKTRIKKY 821 (1111)
T ss_pred hchhhhhccccceeEEeeeeechhhcccceeeeeeCCCCccccccCCCCCCCCcc-cccCCCcEEEEEcccCCceEEEEe
Confidence 799999999999999999987642 122 2357899999888 578999999998864 78889999
Q ss_pred cCCCceeEEEEEEEeCCCCC--eeEEEEEeeccccccccccccccccccCCcceeeeec---------------------
Q 019610 65 KHTERGLVLKVLLSSNDDGK--NFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLE--------------------- 121 (338)
Q Consensus 65 ~~~e~g~Vd~V~~~~~~~g~--~~v~v~ir~~~~~~R~~~iGDKfssRHGqKGvvs~i~--------------------- 121 (338)
...|+++||.|+++.++.|. +.+.|++|. .|+|.||||||||||||||+|+.|
T Consensus 822 ~~~ep~~vd~vr~~~~~~~~~~k~~~i~~Ri----~R~p~IGDKFsSRhGQKGicS~~wP~~dmPFtesGm~PDii~NPH 897 (1111)
T KOG0216|consen 822 HGTEPGIVDEVRVLGNDMGDQEKCATITLRI----PRNPIIGDKFSSRHGQKGICSQKWPTIDMPFTESGMVPDIIINPH 897 (1111)
T ss_pred cCCCCeeeEEEEEccccCCCccceEEEEEEe----cCCCcccchhhhhccccccccccCCCCCCCccccCcCcceeeCCC
Confidence 99999999999999998776 679999999 999999999999999999999999
Q ss_pred -----cChhHHHHHHhhhh-hccCCceeecCCCCC----CHHHHHHHHHh-hccccCccccCCCCCeEEEeeCCcccccc
Q 019610 122 -----QTPAQLLEAALGKG-ACDGLMSYATPFATS----TGGVITEQHQS-FVSQLLNCIGARNSGITFIFKHYFLFCLF 190 (338)
Q Consensus 122 -----MtiGql~E~~~gk~-a~~g~~~~~tpF~~~----~~~~i~~~l~~-~~~~~g~~~~~~~~gke~l~~g~~~~~~~ 190 (338)
|||||++|+++||+ |++|+..|+|||... ..+.++++|++ |||++|| |+||+|
T Consensus 898 ~FPSRMTIgM~iEs~AgK~~alhG~~~Datpf~~~E~~t~~dyfg~~L~~~GyNyyGn---------E~~YSG------- 961 (1111)
T KOG0216|consen 898 AFPSRMTIGMLIESMAGKAGALHGNAQDATPFIFSEENTAIDYFGEMLKKAGYNYYGN---------EPMYSG------- 961 (1111)
T ss_pred CCcccccHHHHHHHHhchhhccccccccCCceeecCcccHHHHHHHHHHHcCcCccCC---------cccccc-------
Confidence 99999999999999 999999999998543 37889999999 9999999 999999
Q ss_pred cCCCcccccceeeeeeEEEeeeeeeccccccCccceeeeecCCcccccCCccccccCCceeeeeccchhhhhhchHHhhh
Q 019610 191 ECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLH 270 (338)
Q Consensus 191 ~~p~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~GR~r~GG~RfGEME~daLiahGAs~~L~ 270 (338)
.+|.+++++||+|++|||||+|||.||+|+|++||++.+|+||++||+|+|||||||||||||||||||++||
T Consensus 962 -------v~G~e~~adIf~GvVyYQRLrHMv~DKfQVRstG~v~~~T~QPvkGRkr~GGiRfGEMERDali~HGtsfllq 1034 (1111)
T KOG0216|consen 962 -------VDGREMRADIFFGVVYYQRLRHMVSDKFQVRSTGPVDSLTHQPVKGRKRGGGIRFGEMERDALIAHGTSFLLQ 1034 (1111)
T ss_pred -------cccceeeeeEEEeehhHHHHHHHhcceeeeeeccCccccccCCccCcccCCCccccchhhhhHhhcchHhhhh
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhh----------ccccccccccc----------ccCCeeecccCCCCccccccChHhHHHHHHHHhhhcCCeEEEEee
Q 019610 271 ERL----------KCKNVANVIQR----------VVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLKFDTQ 329 (338)
Q Consensus 271 ErL----------~c~~~~~~~~~----------~~~~~~c~~c~~~~~i~~~~ipy~~k~L~~EL~~sm~i~~~~~~~ 329 (338)
||| .|..|++++.- ......|+.|. +..+..+.+||+||+|..|| .||||++++.++
T Consensus 1035 DRL~~~SD~~~a~vC~~cgsil~~~~~l~~~~~~~~~~~~C~~c~-~~~~~~v~~P~vfkYL~aEL-~amnIk~~l~l~ 1111 (1111)
T KOG0216|consen 1035 DRLLNSSDYTVAEVCRTCGSILSTQQKLIKEPGGSTSTVTCRSCD-GKGVTTVAMPYVFKYLTAEL-AAMNIKMRLDLE 1111 (1111)
T ss_pred hhhccCcchhHHHHHHHhhhhhhhhhhhhcccCCCCCceeEEecC-CCceEEEEccHHHHHHHHHH-hhCceeEEeccC
Confidence 999 67777766542 23457899995 45788999999999999999 999999999864
No 11
>KOG0215 consensus RNA polymerase III, second largest subunit [Transcription]
Probab=100.00 E-value=5.9e-81 Score=643.36 Aligned_cols=298 Identities=33% Similarity=0.457 Sum_probs=272.5
Q ss_pred CcccccccccceeeeEEEEEee-----c---ccc---------cc------CCCCCCcccccccccCCCCeEEEEeccC-
Q 019610 1 MNQASLECGVFRSESYKAEVDN-----K---DIQ---------VK------SRPSDDMLNFGKIQSKSGDIVIGKYAEI- 56 (338)
Q Consensus 1 iNKsSidRG~f~s~~Ykte~~~-----~---~~~---------~~------~~~~~~~~~~g~~~v~~gDvligk~~~~- 56 (338)
+||||+||||+|+.+||...-. + +.. .+ -+|.||+..+|. .|++|+|+|+|-.|.
T Consensus 778 LNKsSlDRGfGRC~Vyk~~~~~~kkY~N~T~Drimgp~~d~~t~kpi~kh~vLd~DGl~~pG~-~V~~~qi~iNK~mP~v 856 (1153)
T KOG0215|consen 778 LNKSSIDRGFGRCEVYKKTTTTLKKYANGTFDRIMGPQLDPNTRKPIWKHQVLDDDGLATPGE-RVQPGQIYINKQMPTV 856 (1153)
T ss_pred cccchhccCcceEEEEeeeeeeeeecCCCchhhhcccccCCCcCCcchhhcccCcccCCCCcc-EeccCcEEEeccCCCc
Confidence 6999999999999999875421 1 111 11 257789999998 789999999994432
Q ss_pred --------------CceeEEEecCCCceeEEEEEEEeCCCCCeeEEEEEeeccccccccccccccccccCCcceeeeec-
Q 019610 57 --------------GADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLE- 121 (338)
Q Consensus 57 --------------~~d~s~~~~~~e~g~Vd~V~~~~~~~g~~~v~v~ir~~~~~~R~~~iGDKfssRHGqKGvvs~i~- 121 (338)
.++.++.|+.-++++||+|.+++++++.-++|+-+|+ +|+|++|||||||||||||++.|+
T Consensus 857 t~~~~~~~~~~~~~Yk~~pitykgpepsyidkVmls~n~~dq~LIK~llRQ----TRrPElGDKFSSRHGQKGVcGlIv~ 932 (1153)
T KOG0215|consen 857 TGTSLPGLSASQVQYKAVPITYKGPEPSYIDRVMLTSNDEDQFLIKVLLRQ----TRRPELGDKFSSRHGQKGVCGLIVQ 932 (1153)
T ss_pred ccccCCCCCccccccccccceecCCCcchhheeEeecCccccHHHHHHHhh----ccCcccccccccccCCCceeeEEee
Confidence 3788999999999999999999998888899999999 999999999999999999999998
Q ss_pred -------------------------cChhHHHHHHhhhh-hccCCceeecCCCCCCHHHHHHHHHh-hccccCccccCCC
Q 019610 122 -------------------------QTPAQLLEAALGKG-ACDGLMSYATPFATSTGGVITEQHQS-FVSQLLNCIGARN 174 (338)
Q Consensus 122 -------------------------MtiGql~E~~~gk~-a~~g~~~~~tpF~~~~~~~i~~~l~~-~~~~~g~~~~~~~ 174 (338)
||+|.++|.+.||| .+.|.+.++|.|.+++++++++.|.+ |||+.|+
T Consensus 933 QEDMPFnD~GIcPDiIMNPHGFPSRMTVGK~iELlsGKAGVl~G~~hYGTaFGgskVed~~~~Lv~hGfnY~GK------ 1006 (1153)
T KOG0215|consen 933 QEDMPFNDQGICPDIIMNPHGFPSRMTVGKMIELLSGKAGVLEGTFHYGTAFGGSKVEDISEELVEHGFNYSGK------ 1006 (1153)
T ss_pred ccCCCCcccCCCcccccCCCCCcccchHHHHHHHhccccceeeeeEeeccccCCchHHHHHHHHHHhccCccCc------
Confidence 99999999999999 78999999999999999999999999 9999999
Q ss_pred CCeEEEeeCCcccccccCCCcccccceeeeeeEEEeeeeeeccccccCccceeeeecCCcccccCCccccccCCceeeee
Q 019610 175 SGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGE 254 (338)
Q Consensus 175 ~gke~l~~g~~~~~~~~~p~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~GR~r~GG~RfGE 254 (338)
..+|+| .||+++++.||+||+|||||+|||.||+|+|++||+..|||||++||+|+||+|+||
T Consensus 1007 ---D~ltSG--------------ITGepLeAYIffGPiYYQKLKHMVlDKMHARARGPRAvLTRQPTEGRSrdGGLRLGE 1069 (1153)
T KOG0215|consen 1007 ---DMLTSG--------------ITGEPLEAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGE 1069 (1153)
T ss_pred ---cccccC--------------CCCCcceeeEEechHHHHHHHHHHHHHHhhhccCCceeeecCCCCCcCCCCCcccch
Confidence 999999 999999999999999999999999999999999999999999999999999999999
Q ss_pred ccchhhhhhchHHhhhhhh----------cccccccccccccCCeeecccCCCCccccccChHhHHHHHHHHhhhcCCeE
Q 019610 255 MKCDCLIAHGASGNLHERL----------KCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITL 324 (338)
Q Consensus 255 ME~daLiahGAs~~L~ErL----------~c~~~~~~~~~~~~~~~c~~c~~~~~i~~~~ipy~~k~L~~EL~~sm~i~~ 324 (338)
||||||||||||.+|-||| +|..||.+.. +.+|..|.++.++.++.||||||||+||| +||||-+
T Consensus 1070 MERDCLIaYGASmLl~ERLMiSSDaFeVdVC~~CGllgy----kgwC~~Ckss~~v~~~~iPYAcKLLFQEL-~SMNi~P 1144 (1153)
T KOG0215|consen 1070 MERDCLIAYGASMLLLERLMISSDAFEVDVCRQCGLLGY----KGWCTTCKSSKNVAKMKIPYACKLLFQEL-QSMNIVP 1144 (1153)
T ss_pred hhhhhhhhccHHHHHHHHHhhcCcceeeeecccccccee----chhhhhccCCCceeeeeccHHHHHHHHHH-HhcCccc
Confidence 9999999999999999999 7777764322 36899999999999999999999999999 9999999
Q ss_pred EEEeeec
Q 019610 325 KFDTQLS 331 (338)
Q Consensus 325 ~~~~~~~ 331 (338)
|+.++..
T Consensus 1145 rL~L~~~ 1151 (1153)
T KOG0215|consen 1145 RLKLEDY 1151 (1153)
T ss_pred eeeeccc
Confidence 9998764
No 12
>KOG0214 consensus RNA polymerase II, second largest subunit [Transcription]
Probab=100.00 E-value=1.6e-77 Score=623.63 Aligned_cols=300 Identities=39% Similarity=0.563 Sum_probs=271.0
Q ss_pred CcccccccccceeeeEEEEEee--------cccccc---------------CCCCCCcccccccccCCCCeEEEEeccC-
Q 019610 1 MNQASLECGVFRSESYKAEVDN--------KDIQVK---------------SRPSDDMLNFGKIQSKSGDIVIGKYAEI- 56 (338)
Q Consensus 1 iNKsSidRG~f~s~~Ykte~~~--------~~~~~~---------------~~~~~~~~~~g~~~v~~gDvligk~~~~- 56 (338)
||+||||||||||..|+++.+. .+.+++ .+|.||++.+|. +|..|||+|||.+|.
T Consensus 763 mn~s~v~rg~FrS~~~RsYk~q~~~~~~~~ee~~~~~~~~~~~~mr~~~~dkLdddG~i~~G~-~vs~~Dv~iGk~t~~~ 841 (1141)
T KOG0214|consen 763 MNQSSVDRGLFRSFFIRSYKDQEHKKDQGPEEIFEEPPRGEGRGMRNGKYDKLDDDGIIMPGS-RVSGGDVLIGKTTPQP 841 (1141)
T ss_pred HHhhhhhcchhhhhhhhHHHhhhhhcccccccccccccccccccccccccccccccCCccccc-eeecCCEEeccccCCc
Confidence 6999999999999955544321 112222 256788889888 889999999998852
Q ss_pred --------------CceeEEEecCCCceeEEEEEEEeCCCCCeeEEEEEeeccccccccccccccccccCCcceeeeec-
Q 019610 57 --------------GADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLE- 121 (338)
Q Consensus 57 --------------~~d~s~~~~~~e~g~Vd~V~~~~~~~g~~~v~v~ir~~~~~~R~~~iGDKfssRHGqKGvvs~i~- 121 (338)
.+|+|+.++++|+|+||+|.+++|++|.++++|++|+ .|.|++||||+|||||||||+.++
T Consensus 842 ~~~~~~~~~~~~~t~~d~s~~Lr~~e~Givd~V~vt~n~~G~kF~kv~vr~----~ripqiGDKfasrHgqKG~ig~~~~ 917 (1141)
T KOG0214|consen 842 AKEDESGPEDRLYTKRDHSTKLRHTERGIVDQVWVTKNSEGPKFVKVRVRQ----VRIPQIGDKFASRHGQKGTIGITYR 917 (1141)
T ss_pred ccchhccccccccccccceeecccCCcceEEEEEEecCCCCCceeEEEEee----cccccccchhccccccCccccceee
Confidence 2799999999999999999999999999999999999 999999999999999999999988
Q ss_pred -------------------------cChhHHHHHHhhhh-hccCCceeecCCCCCCHHHHHHHHHh-hccccCccccCCC
Q 019610 122 -------------------------QTPAQLLEAALGKG-ACDGLMSYATPFATSTGGVITEQHQS-FVSQLLNCIGARN 174 (338)
Q Consensus 122 -------------------------MtiGql~E~~~gk~-a~~g~~~~~tpF~~~~~~~i~~~l~~-~~~~~g~~~~~~~ 174 (338)
||+|||+||++||. |..|...++|||+...+..|+..|++ +|..+|+
T Consensus 918 qedmpft~eGi~pDiiiNPhaiPSRmtig~liEc~lgk~~a~~~e~~~atpFs~v~v~~is~~l~~~g~~~~G~------ 991 (1141)
T KOG0214|consen 918 QEDMPFTIEGIVPDIIINPHAIPSRMTIGQLIECLLGKVAAYEGEEGDATPFSDVTVSKISANLHVYGYQYRGN------ 991 (1141)
T ss_pred cCCCCccccCCCcceEECcccCccccchhhhHHHhhhhhhhcccccccCCCCCccchhcccchHHHhccccCCC------
Confidence 99999999999998 88999999999999999999999999 9999999
Q ss_pred CCeEEEeeCCcccccccCCCcccccceeeeeeEEEeeeeeeccccccCccceeeeecCCcccccCCccccccCCceeeee
Q 019610 175 SGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGE 254 (338)
Q Consensus 175 ~gke~l~~g~~~~~~~~~p~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~GR~r~GG~RfGE 254 (338)
|+|||| +||+++.++||+|+.|||||+|||+||+|+|++||++.+||||++||+|+|||||||
T Consensus 992 ---e~~ynG--------------rtG~~~~~~if~GptyyqrL~Hmvd~kih~R~~Gp~q~ltRQP~~gRsr~GGlRfGE 1054 (1141)
T KOG0214|consen 992 ---ERMYNG--------------RTGRKLRAQIFIGPTYYQRLKHMVDDKIHSRARGPVQILTRQPVEGRSRDGGLRFGE 1054 (1141)
T ss_pred ---EEEecC--------------CCCceeeeeeecCchHHHHHHHhhhheeeecccCCceeeeccccccccccCCeeeeh
Confidence 999999 999999999999999999999999999999999999999999999999999999999
Q ss_pred ccchhhhhhchHHhhhhhh----------cccccccc--cccccCCeeecccCCCCccccccChHhHHHHHHHHhhhcCC
Q 019610 255 MKCDCLIAHGASGNLHERL----------KCKNVANV--IQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGI 322 (338)
Q Consensus 255 ME~daLiahGAs~~L~ErL----------~c~~~~~~--~~~~~~~~~c~~c~~~~~i~~~~ipy~~k~L~~EL~~sm~i 322 (338)
|||||+|||||+++|+||| .|..|+.. .........|+.|.+.+.++.+.+||++|||+||| .+|||
T Consensus 1055 MErdc~iahGaa~~L~ERL~~~SD~~~~~~c~~c~l~~i~~~~~n~~~ck~c~n~~~v~~v~ipya~kLl~qel-msmni 1133 (1141)
T KOG0214|consen 1055 MERDCLIAHGAAAFLKERLFEKSDAYRVHICVLCGLTAIAGLIPNSFECRGCENKTLVVRVYIPYAAKLLFQEL-MSMNI 1133 (1141)
T ss_pred hHHHHHHHhhHHHHHHHHhhccCccceEEEeccchhhhhhccCCCccccccccCccceEEEechhHHHHHHHHH-HhccC
Confidence 9999999999999999999 45555411 12233446899999999999999999999999999 99999
Q ss_pred eEEEEee
Q 019610 323 TLKFDTQ 329 (338)
Q Consensus 323 ~~~~~~~ 329 (338)
.+++.+.
T Consensus 1134 ~pr~~~~ 1140 (1141)
T KOG0214|consen 1134 APRRKTK 1140 (1141)
T ss_pred ccccccC
Confidence 9998764
No 13
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=100.00 E-value=3.9e-74 Score=648.02 Aligned_cols=298 Identities=20% Similarity=0.270 Sum_probs=261.8
Q ss_pred Ccccccccccceee---eEEEEEeec----ccc-----------ccCCCCCCcccccccccCCCCeEEEEeccCC-----
Q 019610 1 MNQASLECGVFRSE---SYKAEVDNK----DIQ-----------VKSRPSDDMLNFGKIQSKSGDIVIGKYAEIG----- 57 (338)
Q Consensus 1 iNKsSidRG~f~s~---~Ykte~~~~----~~~-----------~~~~~~~~~~~~g~~~v~~gDvligk~~~~~----- 57 (338)
||+.-+...+|.|+ .|..+..+. |.+ .+.+|++|++.+|+ +|++|||||||++|++
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 57778888999999 444444331 111 13478999999999 8999999999999874
Q ss_pred -----------------ceeEEEecCCCceeEEEEEEEeCC---------------------------------------
Q 019610 58 -----------------ADHSIKLKHTERGLVLKVLLSSND--------------------------------------- 81 (338)
Q Consensus 58 -----------------~d~s~~~~~~e~g~Vd~V~~~~~~--------------------------------------- 81 (338)
+|+|+++|++..|+|.+|++++.+
T Consensus 907 PEekLLraIFGeka~~vkDtSLrvp~G~~G~Vidv~~f~r~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 986 (2890)
T PRK09603 907 PEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDARVLSAYEEEKAKLDMEHFDRLTMLNREELLRVS 986 (2890)
T ss_pred hHHHHHHHHhcccccccccCceecCCCCcEEEEEEEEecccccchhHHHHHHHHHHHHHHhHhhHHHHHHHHHHHHHhhh
Confidence 699999999999999999999742
Q ss_pred -------------------------------------------------------------------------------C
Q 019610 82 -------------------------------------------------------------------------------D 82 (338)
Q Consensus 82 -------------------------------------------------------------------------------~ 82 (338)
+
T Consensus 987 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~ 1066 (2890)
T PRK09603 987 SLLSQAILEEPFSHNGKDYKEGDQIPKEEIASINRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEK 1066 (2890)
T ss_pred hhccccccccccccccccccccccccHHHHhhCCHHHhhhhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 0
Q ss_pred C-------CeeEEEEEeeccccccccccccccccccCCcceeeeec--------------------------cChhHHHH
Q 019610 83 G-------KNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLE--------------------------QTPAQLLE 129 (338)
Q Consensus 83 g-------~~~v~v~ir~~~~~~R~~~iGDKfssRHGqKGvvs~i~--------------------------MtiGql~E 129 (338)
| .+.|+|++|+ .|+|++|||||||||||||||+|+ ||||||+|
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 1358999999 999999999999999999999999 99999999
Q ss_pred HHhhhh-hccCCc---------------------------------------------------------eeecC-CCCC
Q 019610 130 AALGKG-ACDGLM---------------------------------------------------------SYATP-FATS 150 (338)
Q Consensus 130 ~~~gk~-a~~g~~---------------------------------------------------------~~~tp-F~~~ 150 (338)
+++||| +..|.. .++|| |++.
T Consensus 1143 ~~LG~aa~~lg~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~tpvF~g~ 1222 (2890)
T PRK09603 1143 MHLGLVGKEFGKQIASMLEDKTKDFAKELRAKMLEIANAINEKDPLTIHALENCSDEELLEYAKDWSKGVKMAIPVFEGI 1222 (2890)
T ss_pred HHHHHHHHhcCcChhhhhhhcchhhhHHHHHHHHhhhcccccccccccccccccchHHHHhhhhhhccCCcccCCCCCCC
Confidence 999998 433321 35788 9999
Q ss_pred CHHHHHHHHHh-hccccCccccCCCCCeEEEeeCCcccccccCCCcccccceeeeeeEEEeeeeeeccccccCccceeee
Q 019610 151 TGGVITEQHQS-FVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRN 229 (338)
Q Consensus 151 ~~~~i~~~l~~-~~~~~g~~~~~~~~gke~l~~g~~~~~~~~~p~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~ 229 (338)
+.+++.++|++ ||+.+|+ +.|||| +||++|+++||+|++|||||+|||+||+|+|+
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 9988888 999999 99999999999999999999999999999999
Q ss_pred ecCCcccccCCccccccCCceeeeeccchhhhhhchHHhhhhhhcccccccccccccCCeeecccCCCCccccccChHhH
Q 019610 230 TGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGA 309 (338)
Q Consensus 230 ~Gp~~~lT~QP~~GR~r~GG~RfGEME~daLiahGAs~~L~ErL~c~~~~~~~~~~~~~~~c~~c~~~~~i~~~~ipy~~ 309 (338)
+|||+++||||++||+++|||||||||+|||+|||||++|+|||+.+|| ++..|.. .|..|.++.++..+.+||||
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 6777653 45777888899999999999
Q ss_pred HHHHHHHhhhcCCeEEEEeeec
Q 019610 310 KLLSQELSFSMGITLKFDTQLS 331 (338)
Q Consensus 310 k~L~~EL~~sm~i~~~~~~~~~ 331 (338)
|+|++|| +||||++++.....
T Consensus 1356 kvL~~EL-~sL~l~i~~~~~~~ 1376 (2890)
T PRK09603 1356 YVLTKEL-QSLALDINIFGDDV 1376 (2890)
T ss_pred HHHHHHH-HhCCcceEEEeecc
Confidence 9999999 99999999986543
No 14
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=100.00 E-value=5.7e-71 Score=620.80 Aligned_cols=297 Identities=22% Similarity=0.325 Sum_probs=256.2
Q ss_pred Ccccccccccceee---eEEEEEeec----ccc-----------ccCCCCCCcccccccccCCCCeEEEEeccCC-----
Q 019610 1 MNQASLECGVFRSE---SYKAEVDNK----DIQ-----------VKSRPSDDMLNFGKIQSKSGDIVIGKYAEIG----- 57 (338)
Q Consensus 1 iNKsSidRG~f~s~---~Ykte~~~~----~~~-----------~~~~~~~~~~~~g~~~v~~gDvligk~~~~~----- 57 (338)
||+..+..++|+|+ .|+.+..+. |.+ .+.+|++|++.+|+ +|++|||||||++|++
T Consensus 838 iSErlv~eD~fTSiHIee~ei~~r~Tk~G~EeITrdIPnv~e~~lr~LDe~GIV~iGa-~V~~GDILVGKvtPk~e~~~t 916 (2836)
T PRK14844 838 ISSEVVKKDLFTSIHIEEFECVVHDTPLGSEKITRAIPGVNEENLYHLDDSGIVKIGT-RVGPGYILVGKVTPKPSLSLP 916 (2836)
T ss_pred cchhhccCceeEEEeecceEEEEEeccCCCceecccCCCCChHHHhcCCCCCCeecCC-EECCCCEEEEeecCCCCCCCC
Confidence 68889999999999 455544331 111 13478999999999 8999999999999864
Q ss_pred -----------------ceeEEEecCCCceeEEEEEEEeCC---------------------------------------
Q 019610 58 -----------------ADHSIKLKHTERGLVLKVLLSSND--------------------------------------- 81 (338)
Q Consensus 58 -----------------~d~s~~~~~~e~g~Vd~V~~~~~~--------------------------------------- 81 (338)
+|+|+++|++..|+|.+|++++.+
T Consensus 917 PEekLL~aIFGek~~~vkdtSLrvp~G~~G~Vidv~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 996 (2836)
T PRK14844 917 PETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFTRRGVEENERALLIKQKEINDFEKERDYIINVTSEYFYDELK 996 (2836)
T ss_pred HHHHHHHHHhCCcccccccCceecCCCCCEEEEEEEEEcccccccchhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
Confidence 699999999999999999999853
Q ss_pred --------------------------------------------------------------CCC-------eeEEEEEe
Q 019610 82 --------------------------------------------------------------DGK-------NFAVVSIR 92 (338)
Q Consensus 82 --------------------------------------------------------------~g~-------~~v~v~ir 92 (338)
+|. ..|+|++.
T Consensus 997 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~gdeL~~gv~~~VkVyia 1076 (2836)
T PRK14844 997 KLLINSGSQDREKFDSIEREQWWGIGLKNQSISEQVKSLKKDFDEKVSHAIAQFKRKVEKLHEGYDLPQGVSMSVKVFIA 1076 (2836)
T ss_pred hhhcccccccHHHHhhccHHhhhhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCCCCceEEEEEEE
Confidence 111 24777777
Q ss_pred eccccccccccccccccccCCcceeeeec--------------------------cChhHHHHHHhhhhhccCC------
Q 019610 93 QSVNMVHSACLGDKFSSMHGQKGVLGFLE--------------------------QTPAQLLEAALGKGACDGL------ 140 (338)
Q Consensus 93 ~~~~~~R~~~iGDKfssRHGqKGvvs~i~--------------------------MtiGql~E~~~gk~a~~g~------ 140 (338)
+ .|.+++|||+|||||||||||+|+ |||||++|+++|+||....
T Consensus 1077 ~----KRkiqvGDKmAGRHGNKGVIS~IlP~eDMPyL~DGtpvDIvLNPLGVPSRMNvGQilE~hLG~A~~~L~~~~~~~ 1152 (2836)
T PRK14844 1077 V----KHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGWACKKLGEKVGNI 1152 (2836)
T ss_pred E----eecCCccccccccCCCCceEeEEcccCCCCcCCCCCCceEEeCCCCCCccccHHHHHHHHHHHHHhhhhhhhHhh
Confidence 7 999999999999999999999999 9999999999999953310
Q ss_pred --------------------------------------------------------------------------------
Q 019610 141 -------------------------------------------------------------------------------- 140 (338)
Q Consensus 141 -------------------------------------------------------------------------------- 140 (338)
T Consensus 1153 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1232 (2836)
T PRK14844 1153 LDEINKIKSAFCKGIRSLNDDNFTKFAAAYLDNKKIENIDDDEITASVLNTPNKNALNDELNELVENYLNSCKSAYSNLR 1232 (2836)
T ss_pred hhhhhccccccccccccccccccccccccccccccccccccccccccccccccccccccccccchhccccccchhhHHHH
Confidence
Q ss_pred -------------------------------------ceeecC-CCCCCHHHHHHHHHh-hccccCccccCCCCCeEEEe
Q 019610 141 -------------------------------------MSYATP-FATSTGGVITEQHQS-FVSQLLNCIGARNSGITFIF 181 (338)
Q Consensus 141 -------------------------------------~~~~tp-F~~~~~~~i~~~l~~-~~~~~g~~~~~~~~gke~l~ 181 (338)
+..+|| |++.+.++|.++|++ ||+.+|+ +.||
T Consensus 1233 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~tpvf~g~~~~~i~~~L~~~g~~~~Gk---------~~l~ 1303 (2836)
T PRK14844 1233 NFLIEVYSCGSNVSICNNIRDISDNNLIEFARKLRDGIPVAAPVFEGPKDEQIAKLFELAGLDNSGQ---------AVLY 1303 (2836)
T ss_pred HHHHHhhhcccccccccccccccHHHHHHHHhhhccCCeecCCCcCCCCHHHHHHHHHHhCcCCCCC---------EEEE
Confidence 012556 788888888888888 8888888 9999
Q ss_pred eCCcccccccCCCcccccceeeeeeEEEeeeeeeccccccCccceeeeecCCcccccCCccccccCCceeeeeccchhhh
Q 019610 182 KHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLI 261 (338)
Q Consensus 182 ~g~~~~~~~~~p~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~GR~r~GG~RfGEME~daLi 261 (338)
|| +||++|+++||+|++|||||+|||+||+|+|++|||+.+||||++||+++|||||||||+|||+
T Consensus 1304 dG--------------~TGe~f~~~v~vG~~yy~kL~HmV~DKihaRs~Gp~s~lT~QPl~Gr~~~GG~RfGEME~~al~ 1369 (2836)
T PRK14844 1304 DG--------------CSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQ 1369 (2836)
T ss_pred cC--------------CCCCccchhheeCcchhhhhhhhhcchhhhcccCCCcccccCCCcccccCCCceeecchHHHHH
Confidence 99 9999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhchHHhhhhhhcccccccccccccCCeeecccCCCCccccccChHhHHHHHHHHhhhcCCeEEEEeee
Q 019610 262 AHGASGNLHERLKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLKFDTQL 330 (338)
Q Consensus 262 ahGAs~~L~ErL~c~~~~~~~~~~~~~~~c~~c~~~~~i~~~~ipy~~k~L~~EL~~sm~i~~~~~~~~ 330 (338)
|||||++|+|||+.+|| ++..|.. .+|.+|+. ....+..+|||||+|+||| +||||++++.+..
T Consensus 1370 a~Gaa~~L~E~Lt~kSD-~~~gr~~--~~~~ivkG-~~~~~~~~PesfkvL~~EL-~sl~i~~~~~~~~ 1433 (2836)
T PRK14844 1370 AYGAAYTLQEMLTVKSD-DINGRVK--IYESIIKG-DSNFECGIPESFNVMIKEL-RSLCLNVDLKQND 1433 (2836)
T ss_pred HHhHHHHHHHHhccccc-chhhhhH--hhhhhccC-CCCCcCCCCchHHHHHHHH-HhCccceEEeccc
Confidence 99999999999999999 6777654 67888764 3455679999999999999 9999999988754
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=5.4e-61 Score=475.92 Aligned_cols=218 Identities=35% Similarity=0.504 Sum_probs=187.5
Q ss_pred CcccccccccceeeeEEEEEe--ec-----cc-cc----------cCCCCCCcccccccccCCCCeEEEEec--------
Q 019610 1 MNQASLECGVFRSESYKAEVD--NK-----DI-QV----------KSRPSDDMLNFGKIQSKSGDIVIGKYA-------- 54 (338)
Q Consensus 1 iNKsSidRG~f~s~~Ykte~~--~~-----~~-~~----------~~~~~~~~~~~g~~~v~~gDvligk~~-------- 54 (338)
|||+|+|||||+|++|+++.+ +. +. +. ..+|+||++.+|. .+++|||||||++
T Consensus 99 iNkssv~rG~f~s~~~k~~~~~~~~~~g~~e~~~~~~~~~~~~~~~~LD~dGii~~G~-~v~~gDiligk~~~~~~~~~~ 177 (386)
T PF00562_consen 99 INKSSVDRGLFTSIHYKTEIEIRDNKGGPSEEIFRPIPNVKEYNYSKLDEDGIIKIGS-RVEKGDILIGKITSPPRFSPL 177 (386)
T ss_dssp EECHHHHTTTTEEEEEEEEEEEEEETTSEEBBESS--TSSTSTTGGGBCTTSBB-TTC-EEETTSEEEEEEESTSC--HH
T ss_pred hhhhhhhcCeeeEEEEEEEeeeecccCCcccccccccccchhhhhhhcccccccccCc-EEecceeEEEEEecccccccc
Confidence 699999999999999999221 11 11 11 1257889999998 7899999999994
Q ss_pred ------cC---CceeEEEecCCCceeEEEEEE-------EeCCCCCeeEEEEEeeccccccccccccccccccCCcceee
Q 019610 55 ------EI---GADHSIKLKHTERGLVLKVLL-------SSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLG 118 (338)
Q Consensus 55 ------~~---~~d~s~~~~~~e~g~Vd~V~~-------~~~~~g~~~v~v~ir~~~~~~R~~~iGDKfssRHGqKGvvs 118 (338)
.+ .+|+|++++.+|.|+||+|.+ ..+.++...++|++|+ .|+|++|||||||||||||||
T Consensus 178 ~~~~~~~~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~~~~~~~~iki~ir~----~R~p~iGDKfssRHGqKGVvs 253 (386)
T PF00562_consen 178 LKKIFGEKNRNYRDTSIKYKSGESGRVDKVIIFSNEKKDTSNNEGYKKIKIRIRS----TRRPQIGDKFSSRHGQKGVVS 253 (386)
T ss_dssp HHHHHHSSSCSEEEEEEES-TT-EEEEEEEEEECCCSSBEEETTCEEEEEEEEEE----EEE--TTEEEEETTSEEEEEE
T ss_pred hhhccccccccccceeecccccEEeEeccccccccccccccccCcceEEEEEecc----cccchhHHHHhhhhcCceEEe
Confidence 11 279999999999999999999 4556677899999999 999999999999999999999
Q ss_pred eec--------------------------cChhHHHHHHhhhh-hccCCceeecCCCCCCHHHHHHHHHh-hccccCccc
Q 019610 119 FLE--------------------------QTPAQLLEAALGKG-ACDGLMSYATPFATSTGGVITEQHQS-FVSQLLNCI 170 (338)
Q Consensus 119 ~i~--------------------------MtiGql~E~~~gk~-a~~g~~~~~tpF~~~~~~~i~~~l~~-~~~~~g~~~ 170 (338)
+|+ ||||||+|+++||+ ++.|.+.++|||++.+.+++.++|.+ +|+.+|+
T Consensus 254 ~i~~~eDMPft~~G~~pDiIiNPhgiPSRMtiGqllE~~~g~~~~~~g~~~~~t~F~~~~~~~i~~~l~~~g~~~~g~-- 331 (386)
T PF00562_consen 254 KILPQEDMPFTEDGIVPDIIINPHGIPSRMTIGQLLESLLGKAGALNGRFVDATPFDESSEEDISELLKKAGYNYPGK-- 331 (386)
T ss_dssp EEE-TTTSEEETTSEB-SEEE-GGGSTTTTBTHHHHHHHHHHHHHHSTCEEB-TTTSSS-HHHHHHHHHHTTSHTTSE--
T ss_pred eeeccccCccccCCCcceeeecccccccccchHHHHhhhhhhhhhccccceecCCCCCcchhhhHhhhhcccccccce--
Confidence 999 99999999999999 88999999999999999999999999 9999888
Q ss_pred cCCCCCeEEEeeCCcccccccCCCcccccceeeeeeEEEeeeeeeccccccCccceeeeecCCcccccCCcccccc
Q 019610 171 GARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKR 246 (338)
Q Consensus 171 ~~~~~gke~l~~g~~~~~~~~~p~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~GR~r 246 (338)
+.|||| +||++++++||+|++|||||+|||+||+|+|++||++.|||||++||+|
T Consensus 332 -------~~l~~g--------------~tG~~~~~~i~~G~~yy~rL~Hmv~DK~h~Rs~Gp~~~lT~QP~~Gr~r 386 (386)
T PF00562_consen 332 -------EVLYDG--------------RTGEKFEAPIFIGPVYYQRLKHMVDDKIHARSRGPYSLLTRQPVEGRSR 386 (386)
T ss_dssp -------EEEBES--------------SSSSBESSEEEEEEEEEEEBSTCGGGSTEEESS--BBSSSSSB-SSSSS
T ss_pred -------EEEEcC--------------ccCceEEeEEEeeeEEeccceEeCCcEEEEEecCCCccccCCCCCCCCC
Confidence 999999 9999999999999999999999999999999999999999999999986
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=99.93 E-value=8e-27 Score=185.72 Aligned_cols=78 Identities=49% Similarity=0.715 Sum_probs=63.9
Q ss_pred CceeeeeccchhhhhhchHHhhhhhhccccccccc---ccccCCeeecccCCCCccccccChHhHHHHHHHHhhhcCCeE
Q 019610 248 GGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVI---QRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITL 324 (338)
Q Consensus 248 GG~RfGEME~daLiahGAs~~L~ErL~c~~~~~~~---~~~~~~~~c~~c~~~~~i~~~~ipy~~k~L~~EL~~sm~i~~ 324 (338)
|||||||||||||+|||||++|+|||..+||.... .+. ..+..+|+...++.++.+|||||+|+||| +||||++
T Consensus 1 GG~R~GEMErd~LiahGas~~L~erl~~~SD~~~~~vc~~c--g~~~~~~~~~~~~~~~~ipy~~klL~~EL-~sm~I~~ 77 (81)
T PF04560_consen 1 GGLRFGEMERDALIAHGASFLLKERLFDKSDKYEIDVCSRC--GSIASICKGKPEVKKIEIPYSFKLLIQEL-RSMGIKI 77 (81)
T ss_dssp CBEEEEHHHHHHHHHTTBHHHHHHHHTTTTTEEEEEEECCC--HHHHHTTTTSSSEEEEEEEHHHHHHHHHH-HCTTEEE
T ss_pred CCcchhHHHHHHHHHhhHHHHHHHHhcCCCcCcchhhhccC--CCceeEECCCCeEEeeeCCHHHHHHHHHH-HHCcCce
Confidence 89999999999999999999999999777773221 111 12223566677899999999999999999 9999999
Q ss_pred EEEe
Q 019610 325 KFDT 328 (338)
Q Consensus 325 ~~~~ 328 (338)
++.+
T Consensus 78 ~~~~ 81 (81)
T PF04560_consen 78 RIKT 81 (81)
T ss_dssp EEEE
T ss_pred EEeC
Confidence 9975
No 17
>KOG0214 consensus RNA polymerase II, second largest subunit [Transcription]
Probab=95.53 E-value=0.0024 Score=69.70 Aligned_cols=170 Identities=8% Similarity=-0.108 Sum_probs=110.6
Q ss_pred eEEEEEEEeCCCCCeeEEEEEeeccccccccccccccccccCCcceeeeec----------cChhHHHHHHhhhhhccCC
Q 019610 71 LVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLE----------QTPAQLLEAALGKGACDGL 140 (338)
Q Consensus 71 ~Vd~V~~~~~~~g~~~v~v~ir~~~~~~R~~~iGDKfssRHGqKGvvs~i~----------MtiGql~E~~~gk~a~~g~ 140 (338)
+..++.+-.++.| ...+|.+ +..+.|+||+.+|.+++.+.+|- -|||.+++------...|.
T Consensus 857 ~d~s~~Lr~~e~G-ivd~V~v-------t~n~~G~kF~kv~vr~~ripqiGDKfasrHgqKG~ig~~~~qedmpft~eGi 928 (1141)
T KOG0214|consen 857 RDHSTKLRHTERG-IVDQVWV-------TKNSEGPKFVKVRVRQVRIPQIGDKFASRHGQKGTIGITYRQEDMPFTIEGI 928 (1141)
T ss_pred ccceeecccCCcc-eEEEEEE-------ecCCCCCceeEEEEeecccccccchhccccccCccccceeecCCCCccccCC
Confidence 6667777666666 2223332 33799999999999999988875 3444333221000001122
Q ss_pred cee--ecCCCCC---CHHHHHHHHHhhccccCccccCCCCCeEEEeeCCcccccccCCCcccccceeeeeeEEEeeeeee
Q 019610 141 MSY--ATPFATS---TGGVITEQHQSFVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQ 215 (338)
Q Consensus 141 ~~~--~tpF~~~---~~~~i~~~l~~~~~~~g~~~~~~~~gke~l~~g~~~~~~~~~p~~~~~tG~~~~~~if~G~~yy~ 215 (338)
..| ..|-.-+ ++..+.+-+.. -. ..++..++++ .++.. -....++..+++
T Consensus 929 ~pDiiiNPhaiPSRmtig~liEc~lg-k~---------~a~~~e~~~a--------------tpFs~-v~v~~is~~l~~ 983 (1141)
T KOG0214|consen 929 VPDIIINPHAIPSRMTIGQLIECLLG-KV---------AAYEGEEGDA--------------TPFSD-VTVSKISANLHV 983 (1141)
T ss_pred CcceEECcccCccccchhhhHHHhhh-hh---------hhcccccccC--------------CCCCc-cchhcccchHHH
Confidence 111 1121111 23333333221 10 0011334444 22222 344568889999
Q ss_pred ccccccCccceeeeecCCcccccCCccccccCCceeeeeccchhhhhhchHHhhhhhh
Q 019610 216 QFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERL 273 (338)
Q Consensus 216 rL~Hmv~DK~~~R~~Gp~~~lT~QP~~GR~r~GG~RfGEME~daLiahGAs~~L~ErL 273 (338)
..-|+..++.+++.+++....+++++.+.-..+..+++||++++=..++.+-+.++.+
T Consensus 984 ~g~~~~G~e~~ynGrtG~~~~~~if~GptyyqrL~Hmvd~kih~R~~Gp~q~ltRQP~ 1041 (1141)
T KOG0214|consen 984 YGYQYRGNERMYNGRTGRKLRAQIFIGPTYYQRLKHMVDDKIHSRARGPVQILTRQPV 1041 (1141)
T ss_pred hccccCCCEEEecCCCCceeeeeeecCchHHHHHHHhhhheeeecccCCceeeecccc
Confidence 9999999999999999999999999999999999999999999999999999999998
No 18
>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=75.59 E-value=4.3 Score=44.21 Aligned_cols=53 Identities=23% Similarity=0.237 Sum_probs=29.6
Q ss_pred EecCCCceeEEEEEEEeCC-CCCeeEEEEEeeccccccccccccccccccCCcceeee
Q 019610 63 KLKHTERGLVLKVLLSSND-DGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGF 119 (338)
Q Consensus 63 ~~~~~e~g~Vd~V~~~~~~-~g~~~v~v~ir~~~~~~R~~~iGDKfssRHGqKGvvs~ 119 (338)
.++.....+|++|.-.-.- ++.-.+|+++-. .-.=-.|=|.||-||||||+-.
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 3444445555555433221 122234444433 3334568899999999999753
No 19
>PHA03394 lef-8 DNA-directed RNA polymerase subunit beta-like protein; Provisional
Probab=72.78 E-value=5.7 Score=43.90 Aligned_cols=20 Identities=50% Similarity=0.579 Sum_probs=17.1
Q ss_pred ccccccccccCCcceeeeec
Q 019610 102 CLGDKFSSMHGQKGVLGFLE 121 (338)
Q Consensus 102 ~iGDKfssRHGqKGvvs~i~ 121 (338)
-.|=|.||-||||||+..-.
T Consensus 709 LeGlKICgIHGQKGVln~se 728 (865)
T PHA03394 709 LEGLKICGIHGQKGVLNGSE 728 (865)
T ss_pred cceeEEeeecccccccCCcc
Confidence 46899999999999987654
No 20
>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=23.83 E-value=38 Score=25.96 Aligned_cols=46 Identities=24% Similarity=0.376 Sum_probs=26.3
Q ss_pred ccCCCcccccceeeeeeEEE--eeeeeeccccccCccceeeeecCCcccccCCcccc
Q 019610 190 FECPMDWIAFICLVRSLIFT--WITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADR 244 (338)
Q Consensus 190 ~~~p~~~~~tG~~~~~~if~--G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~GR 244 (338)
|-|| .||+.|..++.. |.+|=..-..--. +..++.+++|+||+.-+
T Consensus 5 f~Cp----It~~lM~dPVi~~~G~tyer~~I~~~l-----~~~~~~~P~t~~~l~~~ 52 (73)
T PF04564_consen 5 FLCP----ITGELMRDPVILPSGHTYERSAIERWL-----EQNGGTDPFTRQPLSES 52 (73)
T ss_dssp GB-T----TTSSB-SSEEEETTSEEEEHHHHHHHH-----CTTSSB-TTT-SB-SGG
T ss_pred cCCc----CcCcHhhCceeCCcCCEEcHHHHHHHH-----HcCCCCCCCCCCcCCcc
Confidence 4578 999999999986 5444333222111 11688899999998754
No 21
>PRK00420 hypothetical protein; Validated
Probab=23.70 E-value=72 Score=27.24 Aligned_cols=24 Identities=13% Similarity=0.236 Sum_probs=18.9
Q ss_pred ccccccccccc-ccCCeeecccCCC
Q 019610 274 KCKNVANVIQR-VVGGPYCRICNSA 297 (338)
Q Consensus 274 ~c~~~~~~~~~-~~~~~~c~~c~~~ 297 (338)
.|..|+....+ ..+..+|..|...
T Consensus 25 ~CP~Cg~pLf~lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 25 HCPVCGLPLFELKDGEVVCPVHGKV 49 (112)
T ss_pred CCCCCCCcceecCCCceECCCCCCe
Confidence 78888876666 6678999999863
Done!