Query 003180
Match_columns 842
No_of_seqs 177 out of 1717
Neff 6.5
Searched_HMMs 46136
Date Thu Mar 28 18:34:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003180.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003180hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK08565 DNA-directed RNA poly 100.0 1E-229 2E-234 2096.0 68.5 809 1-830 289-1102(1103)
2 KOG0214 RNA polymerase II, sec 100.0 1E-229 3E-234 1924.4 39.8 821 1-828 317-1140(1141)
3 KOG0215 RNA polymerase III, se 100.0 1E-216 2E-221 1797.1 38.6 810 1-831 334-1152(1153)
4 KOG0216 RNA polymerase I, seco 100.0 2E-211 5E-216 1761.8 47.1 761 1-828 314-1111(1111)
5 COG0085 RpoB DNA-directed RNA 100.0 3E-205 7E-210 1803.7 48.4 762 1-830 278-1059(1060)
6 cd00653 RNA_pol_B_RPB2 RNA pol 100.0 1E-192 2E-197 1736.6 53.1 652 15-826 209-866 (866)
7 PRK07225 DNA-directed RNA poly 100.0 1E-190 3E-195 1640.8 53.0 597 217-829 4-603 (605)
8 TIGR03670 rpoB_arch DNA-direct 100.0 2E-189 4E-194 1629.4 50.7 594 220-829 1-597 (599)
9 TIGR02013 rpoB DNA-directed RN 100.0 1E-184 2E-189 1675.2 48.6 668 14-825 297-1065(1065)
10 PRK00405 rpoB DNA-directed RNA 100.0 1E-181 3E-186 1656.4 51.7 678 2-826 318-1106(1112)
11 CHL00001 rpoB RNA polymerase b 100.0 9E-177 2E-181 1597.6 44.2 696 2-831 258-1061(1070)
12 CHL00207 rpoB RNA polymerase b 100.0 8E-165 2E-169 1485.4 50.0 675 11-829 272-1054(1077)
13 PRK09603 bifunctional DNA-dire 100.0 9E-152 2E-156 1414.7 47.7 667 20-830 438-1376(2890)
14 PRK14844 bifunctional DNA-dire 100.0 2E-146 3E-151 1363.0 46.1 666 19-830 446-1434(2836)
15 PF00562 RNA_pol_Rpb2_6: RNA p 100.0 3E-113 7E-118 959.2 22.5 364 362-734 1-386 (386)
16 PRK09606 DNA-directed RNA poly 100.0 1.5E-50 3.3E-55 467.4 16.8 202 1-207 292-493 (494)
17 PF04560 RNA_pol_Rpb2_7: RNA p 100.0 3.6E-32 7.9E-37 238.5 6.5 81 736-827 1-81 (81)
18 PF04565 RNA_pol_Rpb2_3: RNA p 99.9 2.8E-27 6E-32 201.4 3.7 66 121-186 1-68 (68)
19 PF04566 RNA_pol_Rpb2_4: RNA p 99.8 1E-19 2.2E-24 152.3 9.5 63 220-282 1-63 (63)
20 KOG0214 RNA polymerase II, sec 99.3 2.8E-13 6E-18 157.8 -3.1 420 374-822 681-1101(1141)
21 PF04567 RNA_pol_Rpb2_5: RNA p 99.2 5.8E-12 1.3E-16 100.1 2.7 48 306-357 1-48 (48)
22 PF06883 RNA_pol_Rpa2_4: RNA p 97.6 6.2E-05 1.4E-09 62.3 4.3 49 227-275 1-58 (58)
23 KOG0215 RNA polymerase III, se 97.5 2E-06 4.4E-11 100.5 -9.0 263 11-278 372-639 (1153)
24 COG0085 RpoB DNA-directed RNA 97.4 0.00015 3.3E-09 89.5 5.5 109 314-442 476-598 (1060)
25 PHA03394 lef-8 DNA-directed RN 96.6 0.0049 1.1E-07 73.6 8.3 141 551-699 674-828 (865)
26 PF04563 RNA_pol_Rpb2_1: RNA p 96.6 0.0028 6.1E-08 65.9 5.4 54 52-105 150-203 (203)
27 PF09082 DUF1922: Domain of un 71.6 2 4.3E-05 36.8 1.1 48 768-817 1-54 (68)
28 PRK00398 rpoP DNA-directed RNA 65.1 6 0.00013 31.1 2.6 28 770-797 3-30 (46)
29 PF04941 LEF-8: Late expressio 62.1 12 0.00027 45.2 5.6 35 35-69 209-243 (748)
30 COG1997 RPL43A Ribosomal prote 61.8 4.6 0.0001 36.2 1.5 29 768-796 33-61 (89)
31 cd00729 rubredoxin_SM Rubredox 60.3 6.9 0.00015 29.0 2.0 26 770-797 2-27 (34)
32 PRK06266 transcription initiat 59.1 6.6 0.00014 40.2 2.4 46 750-796 98-144 (178)
33 COG1592 Rubrerythrin [Energy p 55.2 8.8 0.00019 38.8 2.4 24 770-796 134-157 (166)
34 COG1096 Predicted RNA-binding 54.2 8 0.00017 39.6 2.0 35 771-808 150-184 (188)
35 cd00350 rubredoxin_like Rubred 51.8 9.6 0.00021 27.9 1.6 26 770-797 1-26 (33)
36 TIGR00373 conserved hypothetic 50.4 10 0.00023 38.0 2.1 46 750-796 90-136 (158)
37 PF08792 A2L_zn_ribbon: A2L zi 49.4 14 0.00031 27.3 2.1 28 770-797 3-30 (33)
38 COG1645 Uncharacterized Zn-fin 49.3 9.7 0.00021 36.9 1.6 25 771-797 29-53 (131)
39 PF12760 Zn_Tnp_IS1595: Transp 48.2 13 0.00027 29.3 1.8 26 771-796 19-45 (46)
40 COG1996 RPC10 DNA-directed RNA 47.6 13 0.00029 29.9 1.9 30 768-797 4-33 (49)
41 KOG0703 Predicted GTPase-activ 47.1 20 0.00044 39.3 3.8 64 756-824 15-88 (287)
42 smart00531 TFIIE Transcription 46.5 12 0.00026 36.9 1.9 43 753-796 83-131 (147)
43 PF08271 TF_Zn_Ribbon: TFIIB z 46.2 17 0.00038 28.1 2.3 26 771-796 1-27 (43)
44 smart00661 RPOL9 RNA polymeras 44.0 14 0.0003 29.4 1.6 25 772-796 2-28 (52)
45 PF09538 FYDLN_acid: Protein o 43.9 12 0.00026 35.2 1.3 31 769-800 8-38 (108)
46 PF07754 DUF1610: Domain of un 43.6 15 0.00034 25.2 1.4 23 773-795 1-23 (24)
47 PRK14890 putative Zn-ribbon RN 42.1 11 0.00025 31.4 0.7 30 767-796 4-33 (59)
48 PRK00420 hypothetical protein; 41.6 17 0.00037 34.4 1.9 26 771-797 24-49 (112)
49 PF07295 DUF1451: Protein of u 38.8 21 0.00046 35.4 2.2 28 770-797 112-139 (146)
50 COG1545 Predicted nucleic-acid 38.7 19 0.00041 35.4 1.8 36 767-806 26-61 (140)
51 PF11781 RRN7: RNA polymerase 37.0 20 0.00044 26.9 1.4 24 772-796 10-33 (36)
52 TIGR02300 FYDLN_acid conserved 36.9 19 0.0004 34.8 1.4 29 768-797 7-35 (129)
53 smart00659 RPOLCX RNA polymera 35.6 31 0.00068 27.1 2.3 27 770-797 2-28 (44)
54 PF01780 Ribosomal_L37ae: Ribo 35.2 27 0.00059 31.8 2.1 29 768-796 33-61 (90)
55 PF13248 zf-ribbon_3: zinc-rib 33.1 20 0.00043 24.8 0.7 22 771-796 3-24 (26)
56 PF02150 RNA_POL_M_15KD: RNA p 32.1 38 0.00082 25.3 2.1 26 771-796 2-28 (35)
57 PF03604 DNA_RNApol_7kD: DNA d 31.7 37 0.0008 25.0 1.9 25 771-796 1-25 (32)
58 PF10385 RNA_pol_Rpb2_45: RNA 31.3 58 0.0013 27.8 3.4 27 313-339 11-37 (66)
59 PF07282 OrfB_Zn_ribbon: Putat 31.3 26 0.00057 29.6 1.3 29 768-796 26-54 (69)
60 KOG3507 DNA-directed RNA polym 30.1 34 0.00073 28.6 1.6 28 768-796 18-45 (62)
61 PRK11032 hypothetical protein; 30.0 37 0.0008 34.3 2.3 28 770-797 124-151 (160)
62 PF06677 Auto_anti-p27: Sjogre 27.8 46 0.00099 25.9 2.0 23 772-795 19-41 (41)
63 PF14803 Nudix_N_2: Nudix N-te 27.1 35 0.00076 25.4 1.2 24 772-795 2-29 (34)
64 PF05191 ADK_lid: Adenylate ki 26.0 31 0.00068 25.9 0.8 26 771-796 2-29 (36)
65 COG0266 Nei Formamidopyrimidin 25.8 41 0.00089 36.8 1.9 24 772-795 247-272 (273)
66 COG2888 Predicted Zn-ribbon RN 25.0 27 0.00059 29.2 0.3 27 770-796 9-35 (61)
67 COG2401 ABC-type ATPase fused 23.8 47 0.001 38.5 1.9 54 759-817 117-174 (593)
68 TIGR00280 L37a ribosomal prote 23.8 40 0.00087 30.8 1.2 29 768-796 33-61 (91)
69 COG2956 Predicted N-acetylgluc 22.3 70 0.0015 35.9 2.9 42 755-804 343-384 (389)
70 PHA00626 hypothetical protein 21.2 69 0.0015 26.6 1.9 25 772-796 2-31 (59)
71 PF11202 PRTase_1: Phosphoribo 21.1 1.6E+02 0.0035 31.9 5.1 45 217-273 145-191 (257)
72 PF13533 Biotin_lipoyl_2: Biot 20.7 71 0.0015 25.5 1.9 17 510-526 17-33 (50)
73 PF13240 zinc_ribbon_2: zinc-r 20.6 46 0.001 22.5 0.7 20 773-796 2-21 (23)
74 PRK10556 hypothetical protein; 20.4 66 0.0014 29.6 1.8 35 608-642 77-111 (111)
75 PF04810 zf-Sec23_Sec24: Sec23 20.1 46 0.00099 25.5 0.7 26 772-797 4-33 (40)
No 1
>PRK08565 DNA-directed RNA polymerase subunit B; Provisional
Probab=100.00 E-value=1.1e-229 Score=2095.95 Aligned_cols=809 Identities=49% Similarity=0.821 Sum_probs=757.4
Q ss_pred CccccCCCCCCcchHHHHHHHHHHHHHhhcCCCCCCCCCCccCCcEECchhHHHHHHHHHHHHHHHHHHHHHHHHhhhcC
Q 003180 1 MLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNG 80 (842)
Q Consensus 1 llpHl~~~~~~~~~K~~~L~~Mi~kLl~~~~g~~~~Dd~D~~~nkRv~~~G~Ll~~lf~~~~~~~~~~~~~~~~~~~~~~ 80 (842)
||||++.+..++.+|+.||++|++||+++..|.+.+||+|||+||||+++|+||+.+||+.|+++++.+++.+.+.+.+.
T Consensus 289 ll~Hig~~~~~~~~K~~~L~~Mi~kLl~l~~g~~~~DD~D~l~NKRv~l~G~Ll~~~fr~~l~~~~~~ik~~l~~~~~~~ 368 (1103)
T PRK08565 289 LLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARG 368 (1103)
T ss_pred CcccCCCcccchhHHHHHHHHHHHHHHhhhcCCCCCCCccccCCcEEccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 68999987766778999999999999999999999999999999999999999999999999999999999998876666
Q ss_pred CCCchhccccccchhhhhhhhhccCccccccccccccceeEeccccChhhhhcccccccCCcccCCCcCCcccccCCCcc
Q 003180 81 KDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWG 160 (842)
Q Consensus 81 ~~~~~~~~~~~~~it~~i~~~~sTGnw~~~~~~~~~~G~sq~l~r~N~l~~lShlRrv~~~~~~~~K~t~~R~LhpS~wG 160 (842)
+.+++..+++++.||++|++|||||||.+ |++||||+|+|+||+++|||||||++++.+++|.++||+|||||||
T Consensus 369 ~~~~~~~~i~~~~It~~i~~~~sTGnw~~-----~~sGvSq~ldr~N~l~~lSh~Rrv~s~~~r~~~~~~vR~Lhps~wG 443 (1103)
T PRK08565 369 RKLDLRAIVRPDIITERIRHALATGNWVG-----GRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWG 443 (1103)
T ss_pred ccCCHHHhcccchhhHHHHHHHhcCcccc-----CCcceEEecccCCHHHHHHHHhhccCCcccCCCCccccccChhhcc
Confidence 67788888888899999999999999995 6899999999999999999999999999999999999999999999
Q ss_pred ccccCCCCCCCcchhhhhcccceEEecCCCchhHHHHHHHhCCccccccCCCCCCCcEEEEECCEEEEEEcChHHHHHHH
Q 003180 161 MMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKTL 240 (842)
Q Consensus 161 fiCPveTPEG~~cGLvknLA~~a~Is~~~~~~~i~~~L~~~g~~~~~~~~~~~~~~~~~VflnG~~iG~~~~~~~lv~~l 240 (842)
|+||+|||||++||||||||++|+|+++.+.++|.++|.++||.++.++.+...+..++|||||+|||++++|..|++.|
T Consensus 444 ~iCPveTPEG~~cGLv~~LA~~a~It~~~~~~~i~~~l~~~G~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~l~~~l 523 (1103)
T PRK08565 444 RICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKI 523 (1103)
T ss_pred ccCCCCCCCccccchhhhhhcccccccCCChHHHHHHHHHcCCCchhhcCcccCCCceEEEECCEEEEEECCHHHHHHHH
Confidence 99999999999999999999999999998999999999999999987666555667799999999999999999999999
Q ss_pred HHhhhcCCCCCcEEEEEec--cCCeEEEecCCCeeeeeEEEeecccccccHHHHHHHhcCCCCCCCCchhccccCcEEEe
Q 003180 241 RRLRRRVDVNTEVGVVRDI--RLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRESPEDGGWHDLVAKGFIEYI 318 (842)
Q Consensus 241 R~lRr~~~i~~~vsi~~~~--~~~~i~I~td~GRl~RPl~vv~n~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~g~IE~I 318 (842)
|.+||+|.|+.++||++++ ..++|+|+||+||++|||++|+++++.+++++++.++.+. .+|++|+++|.||||
T Consensus 524 R~~Rr~g~i~~~v~I~~~~~~~~~~i~I~sd~GRl~RP~~~v~~g~~~~~~~~~~~l~~~~----~~~~~l~~~g~iEyi 599 (1103)
T PRK08565 524 RELRRSGKISDEVNVAYIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGE----LTFDDLVKMGVIEYL 599 (1103)
T ss_pred HHHhhcCCCCCeEEEEEccccccceEEEecCCceeeeeEEEEecCceeccHHHHHHhhccc----cchhhHhhcCcEEee
Confidence 9999999999999999998 8899999999999999999999999999999999886543 489999999999999
Q ss_pred ccccccceeEeecccccccccCCCCcCCCCceeeeeccCCccccccccccCCCCCCCCccchhhhcccccccccccceeE
Q 003180 319 DTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQ 398 (842)
Q Consensus 319 d~~Eq~~~~Ia~~~~~l~~~~~~~k~~~~~~~TH~EI~Ps~ilgv~AslIPF~~HNqSpRn~yq~~M~KQaig~~~~n~~ 398 (842)
|++||++++||++++++.. .+||+||+|++|||++||+|||+||||||||||||||+|||||++.+|+.
T Consensus 600 d~~Ee~~~~Ia~~~~~l~~-----------~~th~Ei~p~~ilsv~asliPF~~hNqspRn~yq~~M~KQa~g~~~~n~~ 668 (1103)
T PRK08565 600 DAEEEENAYVALDPEDLTP-----------EHTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFR 668 (1103)
T ss_pred CHHHhcCcEEeccccccCc-----------ceeccccCCccccceeeeccCCcccCcccchhhhhhhhhcccccccccce
Confidence 9999999999999998843 47999999999999999999999999999999999999999999999999
Q ss_pred EecccCcceeccCCcceeeccccccccCCCCCCCceeeEEeeeccCCCCCCceeeeccccccCceeEEEEEEEEeeehhc
Q 003180 399 FRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKM 478 (842)
Q Consensus 399 ~R~Dt~~~~L~ypQ~PlV~t~~~~~~~~~e~p~G~N~iVAvmsy~GYn~EDAiIiNk~si~rG~f~s~~~~~~~~~~~~~ 478 (842)
+|+|++.|+|+|||+|||+|++++.++++++|+|+||+||||||+||||||||||||+|+|||||||+||++|++++++.
T Consensus 669 ~r~d~~~~~l~~pQ~Plv~t~~~~~~~~~~~p~G~N~iVAv~sy~GYn~EDaiIink~s~~rG~~~s~~~~~~~~~~~~~ 748 (1103)
T PRK08565 669 IRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKY 748 (1103)
T ss_pred EeecCCcceeecCceeEEEeccccccccccCCCCeeEEEEEEcccCcchHHhhhhhhhhhhcCCceEEEEEEEEEEeeec
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999988765
Q ss_pred CCccccccccCCCCCCCCCCC-CCccCCCCCCCcCCCcEEcCCCEEEEeeCCCCc--cccccccCCCccceeeEEeeccc
Q 003180 479 GTLVKEDFGRPDRSNTMGMRH-GSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQ--DEAQGQASRYTRRDHSISLRHSE 555 (842)
Q Consensus 479 ~~~~~e~~~~p~~~~~~~~k~-~~~~~Ld~dGl~~~G~~v~~gdvli~k~~~~~~--~~~~~~~~~~~~~d~s~~~~~~e 555 (842)
..+..+.|+.|.. +..+.+. ..|++||+||||++|++|++|||||||++|... +...........+|+|++++.+|
T Consensus 749 ~~~~~~~~~~~~~-~~~~~~~~~~~~~Ld~dGi~~~G~~v~~gdili~k~~p~~~~~~~~~~~~~~~~~~~~s~~~~~~e 827 (1103)
T PRK08565 749 PGGQEDKIEIPEP-NVRGYRGEEYYRKLDEDGIVSPEVEVKGGDVLIGKTSPPRFLEELEELSLGLQERRDTSVTVRHGE 827 (1103)
T ss_pred CCCCceEEecCCC-cccccCchhhhhcCCCCCCcCCCcEEcCCCEEEEEecCCCCCcchhhccccCCccccceEEecCCC
Confidence 4444467877743 2223333 358999999999999999999999999998541 11011111124789999999999
Q ss_pred cceEEeEEEeecCCCceEEEEEEeeecCCcccccccccCCCcceeeeeecccCCCCCCCCCCceEEeCCCCCCCCCcHHH
Q 003180 556 TGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQ 635 (842)
Q Consensus 556 ~g~Vd~V~~~~~~~~~~~v~v~~r~~R~p~iGDKfssRhGqKGvvs~i~~~~dmPft~~G~~pDiIiNPh~~PSRMtiGq 635 (842)
+|+||+|.++.+.++.+.|||++|+.|+|+||||||||||||||||+|||+||||||+||++||||||||||||||||||
T Consensus 828 ~g~V~~V~~~~~~~~~~~vkv~ir~~R~p~iGDKfssRhGqKGv~s~i~~~edmPf~~~G~~pDiI~NPh~~PSRMtiG~ 907 (1103)
T PRK08565 828 KGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQ 907 (1103)
T ss_pred ceEEEEEEEEecCCCcEEEEEEEEEEecCchhhhhhhhccCcceeeeecccccCCcCCCCCCccEEECCCCCcccccHHH
Confidence 99999999999888899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhhhhccCCcceecCCCCCCHHHHHHHHHHcCCCCCCeEEEeeCCCCcEEeeeEeEeeehhhhccCccCcceEE
Q 003180 636 LIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHS 715 (842)
Q Consensus 636 l~E~~~gk~~~~~g~~~d~tpF~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~ 715 (842)
|+|+++|||+++.|.+.|+|||++...+++++.|+++||+++|+|.||||+||++|+++||+|++|||||+|||.||+||
T Consensus 908 l~E~~~gk~~~~~g~~~d~t~F~~~~~~~~~~~L~~~g~~~~G~e~l~~G~tG~~~~~~if~G~~yy~rL~HmV~DK~~~ 987 (1103)
T PRK08565 908 LLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHA 987 (1103)
T ss_pred HHHHHHHHHHHhcCceeeecCcCCchHHHHHHHHHHcCCCCCCcEEEEcCCCCCCcccceEEeehhheechhhhchhhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eccCCccccccCCCCcccCCCcceeeehhhHHHHhhccHHHHHHhhhcCCCceeeeeccccCcceeecccCCceeeccCC
Q 003180 716 RGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCK 795 (842)
Q Consensus 716 R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~cG~~~~~~~~~~~~~C~~C~ 795 (842)
|++||++.|||||++||+|+|||||||||||||+|||||++|+|||+++||.+.++||.+||++++.+.+++.++|+.|+
T Consensus 988 R~~Gp~~~lt~QP~~Gr~~~GG~R~GEME~d~l~a~Gas~~L~erL~~~SD~~~~~vC~~Cg~~~~~~~~~~~~~C~~c~ 1067 (1103)
T PRK08565 988 RARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHIAWYDRRKNKYVCPIHG 1067 (1103)
T ss_pred ccCCCcchhhhCCccccccCCCeeeecchHHHHHhcccHHHHHHHhhccccceeeeeecccccccccccccCceeccccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999877667788999999
Q ss_pred CCCCceeecchHhHHHHHHHHHhCCCceEEEEccC
Q 003180 796 NKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKED 830 (842)
Q Consensus 796 ~~~~i~~v~iPy~~kll~~EL~sm~I~~~l~~~~~ 830 (842)
++..+.++.||||||||+|||+||||+++|.+++.
T Consensus 1068 ~~~~~~~v~iPy~~k~l~~EL~sm~i~~~l~~~~~ 1102 (1103)
T PRK08565 1068 DKGNISPVEVSYAFKLLLQELMSMGISPRLKLGDK 1102 (1103)
T ss_pred CCCcceeccCChhHHHHHHHHHhCCCceEEEeeec
Confidence 98899999999999999999999999999999753
No 2
>KOG0214 consensus RNA polymerase II, second largest subunit [Transcription]
Probab=100.00 E-value=1.3e-229 Score=1924.43 Aligned_cols=821 Identities=73% Similarity=1.174 Sum_probs=790.9
Q ss_pred CccccCCCCCCcchHHHHHHHHHHHHHhhcCCCCCCCCCCccCCcEECchhHHHHHHHHHHHHHHHHHHHHHHHHhhhcC
Q 003180 1 MLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNG 80 (842)
Q Consensus 1 llpHl~~~~~~~~~K~~~L~~Mi~kLl~~~~g~~~~Dd~D~~~nkRv~~~G~Ll~~lf~~~~~~~~~~~~~~~~~~~~~~ 80 (842)
+|||++..+.-.+.||+||+|||++|+.++.|++.+||||||+|||++++|.|++.+||..|+++.+++..++++.+++.
T Consensus 317 ~lPhi~~~e~~etkKA~fLGYmi~rlll~aLgRr~~ddRDHfG~KRLDlaGpLLa~lfR~lf~~l~rd~~~~mQk~le~~ 396 (1141)
T KOG0214|consen 317 LLPHVGLGEICETKKAYFLGYMVHRLLLAALGRRELDDRDHFGNKRLDLAGPLLAKLFRSLFAKLLRDVTRYMQKCLENG 396 (1141)
T ss_pred hccccccchhhhhhHHHHHHhhHHHHHHHHcCCCCccchhhccccchhhchhHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 69999988766789999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCchhccccccchhhhhhhhhccCcccccc-ccccccceeEeccccChhhhhcccccccCCcccCCCcCCcccccCCCc
Q 003180 81 KDVNLQFAIKAKTITSGLKYSLATGNWGQAN-AAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQW 159 (842)
Q Consensus 81 ~~~~~~~~~~~~~it~~i~~~~sTGnw~~~~-~~~~~~G~sq~l~r~N~l~~lShlRrv~~~~~~~~K~t~~R~LhpS~w 159 (842)
+++++.-++++++||++++|+||||||+.++ ....++||||+|+|+||+++|||+||+++|+++++|.+.||+||||||
T Consensus 397 ~dfni~~aika~iIt~gl~yslaTgnwgdq~ka~~~ragVsQVLnR~t~~sTLsHlRR~n~Pigr~GKlAkpRqlHnthw 476 (1141)
T KOG0214|consen 397 VDFNIELAIKAKIITNGLNYALATGNWGDQKKAMQGRAGVSQVLNRLNPLSTLSHLRRTNSPIGRTGKLAKPRQLHNSHW 476 (1141)
T ss_pred ccceEEEEEEeeeecccceeeeccCCccchhHHhhccccHHHHhccccHHHHHHHHhhcCCccccccccCCccccCcccc
Confidence 9999999999999999999999999999665 777899999999999999999999999999999999999999999999
Q ss_pred cccccCCCCCCCcchhhhhcccceEEecCCCchhHHHHHHHhCCccccccCCCCCCCcEEEEECCEEEEEEcChHHHHHH
Q 003180 160 GMMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKT 239 (842)
Q Consensus 160 GfiCPveTPEG~~cGLvknLA~~a~Is~~~~~~~i~~~L~~~g~~~~~~~~~~~~~~~~~VflnG~~iG~~~~~~~lv~~ 239 (842)
|++||+|||||++||||||||+|++|++|+.+.||.++|.++||+.+++++|..+++.++|||||+|+|+|++|++++++
T Consensus 477 GmvCPaeTPEGqacGLVKNLSLmayIsvGS~~sPi~EfLeewgmE~le~~~ps~~~datkvfvNG~wvGlhrdp~~l~~t 556 (1141)
T KOG0214|consen 477 GMVCPAETPEGQACGLVKNLSLMAYISVGSLESPIVEFLEEWGMENLEEISPSPSPDATKVFVNGVWVGLHRDPEELVAT 556 (1141)
T ss_pred eeeccccCCCcceeeccccceEEEEEecCCCccHHHHHHHHhchhhHhhcCCCcCCCceEEEEcccEEEecCCHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhhcCCCCCcEEEEEeccCCeEEEecCCCeeeeeEEEeecccccccHHHHHHHhcCCCCCCCCchhccccCcEEEec
Q 003180 240 LRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRESPEDGGWHDLVAKGFIEYID 319 (842)
Q Consensus 240 lR~lRr~~~i~~~vsi~~~~~~~~i~I~td~GRl~RPl~vv~n~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~g~IE~Id 319 (842)
||.+||+..++.++|+++|.+++|++||||+||.|||||+|+|+++.++|+|+++|++.+. +..+|..|+.+|++||||
T Consensus 557 lr~lRR~~di~~Evs~vRDIr~kE~ri~tDaGR~~rPLliven~~l~~~k~hi~~L~~~~~-~~~~w~~lv~~G~ie~id 635 (1141)
T KOG0214|consen 557 LKRLRRQFDIIAEVSMVRDIRDKEIRIFTDAGRSLRPLLIVENAKLLIKKRHIRALKQSKP-NEYRWAHLLSSGEVEYID 635 (1141)
T ss_pred HHHHHHhhccchhhhhhccccccceeeeeccCccccceEEEechhhhhhhHHHHHHhhCch-hhcchhhhccccceeeec
Confidence 9999999999999999999999999999999999999999999999999999999987632 356999999999999999
Q ss_pred cccccceeEeecccccccccCCCCcCCCCceeeeeccCCccccccccccCCCCCCCCccchhhhcccccccccccceeEE
Q 003180 320 TEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQF 399 (842)
Q Consensus 320 ~~Eq~~~~Ia~~~~~l~~~~~~~k~~~~~~~TH~EI~Ps~ilgv~AslIPF~~HNqSpRn~yq~~M~KQaig~~~~n~~~ 399 (842)
++||+..+|||.++||.+. .++..||||||||++||||+||+||||||||||||+||++|+|||||++.+|+..
T Consensus 636 teeEEtvmiam~~~dL~~~------~~~~~~THCEiHpsmILgv~asiIpFpdh~qspr~tYQsa~~kqamg~y~tn~~v 709 (1141)
T KOG0214|consen 636 TEEEETVMIAMGPKDLAES------AYPKTYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYHTNPQV 709 (1141)
T ss_pred cchhhhHHHhcCHHHHhhc------cCCcccccccccHHHhhhhceeeeecCCCCCchHHHHHHHHhhhcceeeeecchh
Confidence 9999999999999999762 2367899999999999999999999999999999999999999999999999999
Q ss_pred ecccCcceeccCCcceeeccccccccCCCCCCCceeeEEeeeccCCCCCCceeeeccccccCceeEEEEEEEEeeehhcC
Q 003180 400 RMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMG 479 (842)
Q Consensus 400 R~Dt~~~~L~ypQ~PlV~t~~~~~~~~~e~p~G~N~iVAvmsy~GYn~EDAiIiNk~si~rG~f~s~~~~~~~~~~~~~~ 479 (842)
|+||..|+|+|||+|+|+|++++++.+.++|+|+|+|||+++|+|||||||||+|++++|||+|||++||+|++++.+..
T Consensus 710 R~dtl~~~l~ypqkpl~tt~~~e~l~~~eL~aG~NaiVAi~~~~GYNqEDsvimn~s~v~rg~FrS~~~RsYk~q~~~~~ 789 (1141)
T KOG0214|consen 710 RMDTLAKVLYYPQKPLVTTRAMEYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSVDRGLFRSFFIRSYKDQEHKKD 789 (1141)
T ss_pred hhhhhhhcccccccchhhHHHHhhhhhhhcccccceEEEEecccCccHHHHHHHHhhhhhcchhhhhhhhHHHhhhhhcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999998776
Q ss_pred CccccccccCCCCCCCCCCCCCccCCCCCCCcCCCcEEcCCCEEEEeeCCCCc--cccccccCCCccceeeEEeeccccc
Q 003180 480 TLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQ--DEAQGQASRYTRRDHSISLRHSETG 557 (842)
Q Consensus 480 ~~~~e~~~~p~~~~~~~~k~~~~~~Ld~dGl~~~G~~v~~gdvli~k~~~~~~--~~~~~~~~~~~~~d~s~~~~~~e~g 557 (842)
.+..+.|+.|....+.++|++.|++||+||++.||++|+.|||+|||+.|... ++.+...+....+|+|+.++++|.|
T Consensus 790 ~~~ee~~~~~~~~~~~~mr~~~~dkLdddG~i~~G~~vs~~Dv~iGk~t~~~~~~~~~~~~~~~~t~~d~s~~Lr~~e~G 869 (1141)
T KOG0214|consen 790 QGPEEIFEEPPRGEGRGMRNGKYDKLDDDGIIMPGSRVSGGDVLIGKTTPQPAKEDESGPEDRLYTKRDHSTKLRHTERG 869 (1141)
T ss_pred cccccccccccccccccccccccccccccCCccccceeecCCEEeccccCCcccchhccccccccccccceeecccCCcc
Confidence 77788899998888889999999999999999999999999999999998653 3344445556789999999999999
Q ss_pred eEEeEEEeecCCCceEEEEEEeeecCCcccccccccCCCcceeeeeecccCCCCCCCCCCceEEeCCCCCCCCCcHHHHH
Q 003180 558 MVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLI 637 (842)
Q Consensus 558 ~Vd~V~~~~~~~~~~~v~v~~r~~R~p~iGDKfssRhGqKGvvs~i~~~~dmPft~~G~~pDiIiNPh~~PSRMtiGql~ 637 (842)
+||+|++++|.+|.+.++|++|+.|.|++|||||||||||||||.++++||||||.+|++|||||||||||||||||||+
T Consensus 870 ivd~V~vt~n~~G~kF~kv~vr~~ripqiGDKfasrHgqKG~ig~~~~qedmpft~eGi~pDiiiNPhaiPSRmtig~li 949 (1141)
T KOG0214|consen 870 IVDQVWVTKNSEGPKFVKVRVRQVRIPQIGDKFASRHGQKGTIGITYRQEDMPFTIEGIVPDIIINPHAIPSRMTIGQLI 949 (1141)
T ss_pred eEEEEEEecCCCCCceeEEEEeecccccccchhccccccCccccceeecCCCCccccCCCcceEECcccCccccchhhhH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhhhhhccCCcceecCCCCCCHHHHHHHHHHcCCCCCCeEEEeeCCCCcEEeeeEeEeeehhhhccCccCcceEEec
Q 003180 638 ECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRG 717 (842)
Q Consensus 638 E~~~gk~~~~~g~~~d~tpF~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~ 717 (842)
|+++||.++..|.-.|+|||+...+..++..|+++||+++|+|.||||+||++|.+.||+||.|||||+|||+||+|+|+
T Consensus 950 Ec~lgk~~a~~~e~~~atpFs~v~v~~is~~l~~~g~~~~G~e~~ynGrtG~~~~~~if~GptyyqrL~Hmvd~kih~R~ 1029 (1141)
T KOG0214|consen 950 ECLLGKVAAYEGEEGDATPFSDVTVSKISANLHVYGYQYRGNERMYNGRTGRKLRAQIFIGPTYYQRLKHMVDDKIHSRA 1029 (1141)
T ss_pred HHhhhhhhhcccccccCCCCCccchhcccchHHHhccccCCCEEEecCCCCceeeeeeecCchHHHHHHHhhhheeeecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCccccccCCCCcccCCCcceeeehhhHHHHhhccHHHHHHhhhcCCCceeeeeccccCcceeecccCCceeeccCCCC
Q 003180 718 RGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNK 797 (842)
Q Consensus 718 ~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~cG~~~~~~~~~~~~~C~~C~~~ 797 (842)
+||++.+||||++||||+||||||||||||+|||||+++|+|||+..||.|.+++|..||.++.++...+.+.|+.|.+.
T Consensus 1030 ~Gp~q~ltRQP~~gRsr~GGlRfGEMErdc~iahGaa~~L~ERL~~~SD~~~~~~c~~c~l~~i~~~~~n~~~ck~c~n~ 1109 (1141)
T KOG0214|consen 1030 RGPVQILTRQPVEGRSRDGGLRFGEMERDCLIAHGAAAFLKERLFEKSDAYRVHICVLCGLTAIAGLIPNSFECRGCENK 1109 (1141)
T ss_pred cCCceeeeccccccccccCCeeeehhHHHHHHHhhHHHHHHHHhhccCccceEEEeccchhhhhhccCCCccccccccCc
Confidence 99999999999999999999999999999999999999999999999999999999999977777878888899999999
Q ss_pred CCceeecchHhHHHHHHHHHhCCCceEEEEc
Q 003180 798 TDIVQVHIPYACKLLFQELMAMAIAPRMLTK 828 (842)
Q Consensus 798 ~~i~~v~iPy~~kll~~EL~sm~I~~~l~~~ 828 (842)
+.|+.|.+|||||||+|||+||||.+|+.+.
T Consensus 1110 ~~v~~v~ipya~kLl~qelmsmni~pr~~~~ 1140 (1141)
T KOG0214|consen 1110 TLVVRVYIPYAAKLLFQELMSMNIAPRRKTK 1140 (1141)
T ss_pred cceEEEechhHHHHHHHHHHhccCccccccC
Confidence 9999999999999999999999999998764
No 3
>KOG0215 consensus RNA polymerase III, second largest subunit [Transcription]
Probab=100.00 E-value=1e-216 Score=1797.14 Aligned_cols=810 Identities=44% Similarity=0.738 Sum_probs=763.4
Q ss_pred CccccCCCCCCcchHHHHHHHHHHHHHhhcCCCCCCCCCCccCCcEECchhHHHHHHHHHHHHHHHHHHHHHHHHhhhcC
Q 003180 1 MLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNG 80 (842)
Q Consensus 1 llpHl~~~~~~~~~K~~~L~~Mi~kLl~~~~g~~~~Dd~D~~~nkRv~~~G~Ll~~lf~~~~~~~~~~~~~~~~~~~~~~ 80 (842)
+++|+.....+++.|+.|++.|+|+++.+..+.-..||+|.++|||++++|+|+..+|++.|+++...+++...+.+.+.
T Consensus 334 ~lahv~v~~~~~r~K~~yi~~m~rr~~~a~l~~~~~ddrd~~gnkrlelagqllsllfeD~fk~~n~e~k~~~dk~l~k~ 413 (1153)
T KOG0215|consen 334 VLAHVPVPDLNFRMKAIYIGLMVRRVIQAMLNKLAMDDRDYVGNKRLELAGQLLSLLFEDLFKRFNSELKKNIDKILKKP 413 (1153)
T ss_pred heeceeccCCCCcceeehHHHHHHHHHHHHhCcccccchhhhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcch
Confidence 47899988888999999999999999999999999999999999999999999999999999999999999988887663
Q ss_pred ---CCCchhccc--cccchhhhhhhhhccCccccccccccccceeEeccccChhhhhcccccccCCcccCCCcCCccccc
Q 003180 81 ---KDVNLQFAI--KAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLH 155 (842)
Q Consensus 81 ---~~~~~~~~~--~~~~it~~i~~~~sTGnw~~~~~~~~~~G~sq~l~r~N~l~~lShlRrv~~~~~~~~K~t~~R~Lh 155 (842)
..+++...+ .++.||++|.+|+|||||..+++.|.+.|++|+|.|++|.+.|.++.|++++|.+++|..+||.|+
T Consensus 414 ~ra~~fD~~~~~n~~~~~it~~l~ra~stgnw~iKrfrmer~gvt~VlsrlSyisaLgmmtri~s~fektrkvsgprSlq 493 (1153)
T KOG0215|consen 414 IRAQEFDALKHLNVRANMITSGLERAISTGNWSIKRFRMERAGVTQVLSRLSYISALGMMTRINSQFEKTRKVSGPRSLQ 493 (1153)
T ss_pred hhhhhhHHHHHHHHHHHHHHHHHHHHhhcCchHHHHhhhhhccceeeehhhhhhhhhhhheehhhhheeehhccCccccC
Confidence 245665555 468999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCccccccCCCCCCCcchhhhhcccceEEecCCCchhHHHHHHHhCCccccccCCCCC--CCcEEEEECCEEEEEEcCh
Q 003180 156 NSQWGMMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVI--PQATKIFVNGCWVGIHRDP 233 (842)
Q Consensus 156 pS~wGfiCPveTPEG~~cGLvknLA~~a~Is~~~~~~~i~~~L~~~g~~~~~~~~~~~~--~~~~~VflnG~~iG~~~~~ 233 (842)
|||||++||+|||||++||||||||++++||++..++|+...+..+|++.+..++..+. +..+-|||||.++|.+..|
T Consensus 494 ~sqwgmlcp~dtpegeacglvknlalmthittd~ee~pi~~~~~k~gv~di~~v~~~e~~~~~~~~v~Lng~iig~~~~~ 573 (1153)
T KOG0215|consen 494 PSQWGMLCPSDTPEGEACGLVKNLALMTHITTDSEEKPILKLCYKLGVEDIHVVSGRELHTPDSFLVFLNGLIIGITRRP 573 (1153)
T ss_pred hhhcccccCCCCCCccccccccchHHHhcccCCCCcchhHHHHHHhcceeeeeecccccCCCceEEEEecceeeccccch
Confidence 99999999999999999999999999999999999999999999999998876655544 5668899999999999999
Q ss_pred HHHHHHHHHhhhcCCCCCcEEEEEeccCCeEEEecCCCeeeeeEEEeecccccccHHHHHHHhcCCCCCCCCchhccccC
Q 003180 234 EMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRESPEDGGWHDLVAKG 313 (842)
Q Consensus 234 ~~lv~~lR~lRr~~~i~~~vsi~~~~~~~~i~I~td~GRl~RPl~vv~n~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~g 313 (842)
+.++..+|.+||.|.|..+||++....+..++|.||+||+|||+++++++...+...|++++.++.. .|+||++.|
T Consensus 574 ~~~v~~~r~lrr~G~i~~fvsv~~~~~q~~v~i~sdggr~crp~Iiv~~~~~~v~~~h~~el~~g~r----~F~DFl~~g 649 (1153)
T KOG0215|consen 574 QYFVNSFRRLRRKGKIGEFVSVFTNTTQRCVYIASDGGRVCRPLIIVDNGRPRVKQHHMDELLDGKR----TFDDFLKDG 649 (1153)
T ss_pred HHHHHHHHHHHHcCcccceeeeeeeeeeEEEEEecCCCeEeeeEEEEeCCcchhhhhhHHHHHHhhh----hHHHHHHhc
Confidence 9999999999999999999999999999999999999999999999999999999999999988876 899999999
Q ss_pred cEEEeccccccceeEeecccccccccCCCCcCCCCceeeeeccCCccccccccccCCCCCCCCccchhhhcccccccccc
Q 003180 314 FIEYIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIY 393 (842)
Q Consensus 314 ~IE~Id~~Eq~~~~Ia~~~~~l~~~~~~~k~~~~~~~TH~EI~Ps~ilgv~AslIPF~~HNqSpRn~yq~~M~KQaig~~ 393 (842)
.|||+|.+||++++||+.++++.+ .+||+||.|..+||+||+|||||+|||||||+|||+|+|||||..
T Consensus 650 lvEYLDVNEEND~~Ialye~~I~~-----------~TTHLEIEPFTiLGv~AGLIPYPHHNQSPRNTYQCAMGKQAmG~I 718 (1153)
T KOG0215|consen 650 LIEYLDVNEENDSLIALYEEDIGP-----------ETTHLEIEPFTILGVVAGLIPYPHHNQSPRNTYQCAMGKQAMGAI 718 (1153)
T ss_pred hhheeecccccCceEEechhhcCC-----------CcceeeecchhhhhhhccccCCCCCCCCCcchhhhhhhhhhhhhh
Confidence 999999999999999999999965 689999999999999999999999999999999999999999999
Q ss_pred cceeEEecccCcceeccCCcceeeccccccccCCCCCCCceeeEEeeeccCCCCCCceeeeccccccCceeEEEEEEEEe
Q 003180 394 VTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRD 473 (842)
Q Consensus 394 ~~n~~~R~Dt~~~~L~ypQ~PlV~t~~~~~~~~~e~p~G~N~iVAvmsy~GYn~EDAiIiNk~si~rG~f~s~~~~~~~~ 473 (842)
++|+..|.|+.+|+|.|||+|+|+|++.|+++++++|+||||.||||||+|||+|||+|+||+|+||||+|+.+|++-+.
T Consensus 719 aYNQ~~RiDtlmYll~YPq~PmVkTKTIELi~ydKLPAGQNAtVAVMSYSGYDIEDALVLNKsSlDRGfGRC~Vyk~~~~ 798 (1153)
T KOG0215|consen 719 AYNQKKRIDSLLYLLVYPQRPMVKTKTIELINYDKLPAGQNATVAVMSYSGYDIEDALVLNKSSIDRGFGRCEVYKKTTT 798 (1153)
T ss_pred hhhhhhhHHHHHHHHhcCCCccccceeEEeeccccCCCCCccEEEEEeccCCchhhhhhcccchhccCcceEEEEeeeee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eehhcCCccccccccCCCCCCCCCCCCCccCCCCCCCcCCCcEEcCCCEEEEeeCCCCcccc--ccccCCCccceeeEEe
Q 003180 474 EEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEA--QGQASRYTRRDHSISL 551 (842)
Q Consensus 474 ~~~~~~~~~~e~~~~p~~~~~~~~k~~~~~~Ld~dGl~~~G~~v~~gdvli~k~~~~~~~~~--~~~~~~~~~~d~s~~~ 551 (842)
..+++.++..+++..|..+...+....+.+.||+|||..||..|++|+|+|+|-.|.....+ +.......+++.++.|
T Consensus 799 ~~kkY~N~T~Drimgp~~d~~t~kpi~kh~vLd~DGl~~pG~~V~~~qi~iNK~mP~vt~~~~~~~~~~~~~Yk~~pity 878 (1153)
T KOG0215|consen 799 TLKKYANGTFDRIMGPQLDPNTRKPIWKHQVLDDDGLATPGERVQPGQIYINKQMPTVTGTSLPGLSASQVQYKAVPITY 878 (1153)
T ss_pred eeeecCCCchhhhcccccCCCcCCcchhhcccCcccCCCCccEeccCcEEEeccCCCcccccCCCCCcccccccccccee
Confidence 99999888888888776543322222356779999999999999999999999777543222 2223333589999999
Q ss_pred eccccceEEeEEEeecCCCceEEEEEEeeecCCcccccccccCCCcceeeeeecccCCCCCCCCCCceEEeCCCCCCCCC
Q 003180 552 RHSETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRM 631 (842)
Q Consensus 552 ~~~e~g~Vd~V~~~~~~~~~~~v~v~~r~~R~p~iGDKfssRhGqKGvvs~i~~~~dmPft~~G~~pDiIiNPh~~PSRM 631 (842)
+..|+++||+|+++.++++.-++|+.+|+.|+|++|||||||||||||||.|++||||||+..||+||||+|||||||||
T Consensus 879 kgpepsyidkVmls~n~~dq~LIK~llRQTRrPElGDKFSSRHGQKGVcGlIv~QEDMPFnD~GIcPDiIMNPHGFPSRM 958 (1153)
T KOG0215|consen 879 KGPEPSYIDRVMLTSNDEDQFLIKVLLRQTRRPELGDKFSSRHGQKGVCGLIVQQEDMPFNDQGICPDIIMNPHGFPSRM 958 (1153)
T ss_pred cCCCcchhheeEeecCccccHHHHHHHhhccCcccccccccccCCCceeeEEeeccCCCCcccCCCcccccCCCCCcccc
Confidence 99999999999999998888899999999999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHHhhhhhhccCCcceecCCCCCCHHHHHHHHHHcCCCCCCeEEEeeCCCCcEEeeeEeEeeehhhhccCccCc
Q 003180 632 TIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDD 711 (842)
Q Consensus 632 tiGql~E~~~gk~~~~~g~~~d~tpF~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if~G~~yy~rL~Hmv~D 711 (842)
|||.++|.+.||||.+.|.|.++|+|.+..++++++.|.++||||.||+.+|||+||++++|+||+||+|||||+|||.|
T Consensus 959 TVGK~iELlsGKAGVl~G~~hYGTaFGgskVed~~~~Lv~hGfnY~GKD~ltSGITGepLeAYIffGPiYYQKLKHMVlD 1038 (1153)
T KOG0215|consen 959 TVGKMIELLSGKAGVLEGTFHYGTAFGGSKVEDISEELVEHGFNYSGKDMLTSGITGEPLEAYIFFGPIYYQKLKHMVLD 1038 (1153)
T ss_pred hHHHHHHHhccccceeeeeEeeccccCCchHHHHHHHHHHhccCccCccccccCCCCCcceeeEEechHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceEEeccCCccccccCCCCcccCCCcceeeehhhHHHHhhccHHHHHHhhhcCCCceeeeeccccCcceeecccCCceee
Q 003180 712 KIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFEC 791 (842)
Q Consensus 712 K~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~cG~~~~~~~~~~~~~C 791 (842)
|+|||++||+..|||||++||||+||+|+||||||||||||||.+|-|||+.+||.++++||..||.+++.. ||
T Consensus 1039 KMHARARGPRAvLTRQPTEGRSrdGGLRLGEMERDCLIaYGASmLl~ERLMiSSDaFeVdVC~~CGllgykg------wC 1112 (1153)
T KOG0215|consen 1039 KMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIAYGASMLLLERLMISSDAFEVDVCRQCGLLGYKG------WC 1112 (1153)
T ss_pred HHhhhccCCceeeecCCCCCcCCCCCcccchhhhhhhhhccHHHHHHHHHhhcCcceeeeeccccccceech------hh
Confidence 999999999999999999999999999999999999999999999999999999999999999999999743 89
Q ss_pred ccCCCCCCceeecchHhHHHHHHHHHhCCCceEEEEccCC
Q 003180 792 RGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKEDT 831 (842)
Q Consensus 792 ~~C~~~~~i~~v~iPy~~kll~~EL~sm~I~~~l~~~~~~ 831 (842)
..|+++.++.++.||||||||||||+||||-|||.+++..
T Consensus 1113 ~~Ckss~~v~~~~iPYAcKLLFQEL~SMNi~PrL~L~~~~ 1152 (1153)
T KOG0215|consen 1113 TTCKSSKNVAKMKIPYACKLLFQELQSMNIVPRLKLEDYF 1152 (1153)
T ss_pred hhccCCCceeeeeccHHHHHHHHHHHhcCccceeeecccc
Confidence 9999999999999999999999999999999999998753
No 4
>KOG0216 consensus RNA polymerase I, second largest subunit [Transcription]
Probab=100.00 E-value=2.2e-211 Score=1761.78 Aligned_cols=761 Identities=35% Similarity=0.566 Sum_probs=688.3
Q ss_pred CccccCCCCCCcchHHHHHHHHHHHHHhhcCCCCCCCCCCccCCcEECchhHHHHHHHHHHHHHHHHHHHHHHHHhhhcC
Q 003180 1 MLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNG 80 (842)
Q Consensus 1 llpHl~~~~~~~~~K~~~L~~Mi~kLl~~~~g~~~~Dd~D~~~nkRv~~~G~Ll~~lf~~~~~~~~~~~~~~~~~~~~~~ 80 (842)
+|.|++++. +||.+|.+|+|||++++.|++.+||+|+.+||+++++|+|+...+|+.++.|++.++.++.+.+++.
T Consensus 314 VlvHLd~~~----DKF~lLifmiqKL~slv~ge~~~dnpDs~q~qEil~~ghl~~~~LkEriEe~l~~~~~~vr~~l~~~ 389 (1111)
T KOG0216|consen 314 VLVHLDSDE----DKFNLLIFMIQKLYSLVDGECTPDNPDSPQNQEILLPGHLYGSILKERIEEWLRFISAQVRRDLYKL 389 (1111)
T ss_pred eEEEecccH----HHHHHHHHHHHHHHHHhcCCcCCCCCCChhhhhcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 578998866 9999999999999999999999999999999999999999999999999999998888887777652
Q ss_pred -CCC---c---hhcccc--ccchhhhhhhhhccCcccccc--ccccccceeEeccccChhhhhcccccccC-CcccCCCc
Q 003180 81 -KDV---N---LQFAIK--AKTITSGLKYSLATGNWGQAN--AAGTRAGVSQVLNRLTYASTLSHLRRLNS-PIGREGKL 148 (842)
Q Consensus 81 -~~~---~---~~~~~~--~~~it~~i~~~~sTGnw~~~~--~~~~~~G~sq~l~r~N~l~~lShlRrv~~-~~~~~~K~ 148 (842)
... + +..++. +..|+++|++||||||+.+.. +++|++|+|.++||+|++++|||||.||+ ++|+++||
T Consensus 390 ~~~~~~~~~~~i~~~~~r~~~~Ig~~me~fLsTGnl~s~sgldLqQ~sG~tv~AEriNf~RflShFRavhRGa~f~~mrT 469 (1111)
T KOG0216|consen 390 GFKEDFLDISAIRKVFMRTNGNIGRKMEYFLSTGNLVSRSGLDLQQTSGYTVVAERINFYRFLSHFRAVHRGAFFAEMRT 469 (1111)
T ss_pred cCCchhHhHHHHHHHHhhccccHHHHHHHHHhcCCeeeccchhhHhhcCcEEehhhhhHHHHHHHHHHHhcccchhheee
Confidence 222 2 333332 478999999999999999988 78999999999999999999999999997 89999999
Q ss_pred CCcccccCCCccccccCCCCCCCcchhhhhcccceEEecC-CCchhHHHHHHHhCCccccccCCCCCCCcEEEEECCEEE
Q 003180 149 AKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITVG-SAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWV 227 (842)
Q Consensus 149 t~~R~LhpS~wGfiCPveTPEG~~cGLvknLA~~a~Is~~-~~~~~i~~~L~~~g~~~~~~~~~~~~~~~~~VflnG~~i 227 (842)
|++|||.|++|||+||||||||+||||+||||..|+|++. .+...|.++|.++||.|........ +..++|++||+++
T Consensus 470 TtvRKLlPEsWGFlCPVHTPDG~PCGlLnH~t~~c~I~t~~dd~s~ip~~L~~~Gm~p~~~~~~~G-~~l~~VlldGk~v 548 (1111)
T KOG0216|consen 470 TTVRKLLPESWGFLCPVHTPDGAPCGLLNHMTRTCRIVTRPDDVSFIPSILFELGMVPSSHLVEAG-EPLYPVLLDGKVV 548 (1111)
T ss_pred hhhHhhCchhhcccccccCCCCCchhHHHhhhhheeEeecCcchhhhhHHHHhcCCCchhccccCC-CceeEEEECCEEE
Confidence 9999999999999999999999999999999999999995 4567899999999999865322221 2368999999999
Q ss_pred EEEcC--hHHHHHHHHHhhhc--CCCCCcEEEEEecc-----CCeEEEecCCCeeeeeEEEeecccccccHHHHHHHhcC
Q 003180 228 GIHRD--PEMLVKTLRRLRRR--VDVNTEVGVVRDIR-----LKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQR 298 (842)
Q Consensus 228 G~~~~--~~~lv~~lR~lRr~--~~i~~~vsi~~~~~-----~~~i~I~td~GRl~RPl~vv~n~~~~~~~~~~~~l~~~ 298 (842)
|++.. ++.+++.||.+|.. ..||.+.+|.+.+. -|++||+|++||++|||.++.
T Consensus 549 G~~s~~~a~~i~~~lR~~Kv~~p~~iP~~leIg~Vp~s~~gqyPglyi~s~~aR~~RpV~nl~----------------- 611 (1111)
T KOG0216|consen 549 GWVSSPLAKKIVDYLRYYKVEAPAVIPNDLEIGYVPTSTNGQYPGLYIFSGPARMIRPVKNLS----------------- 611 (1111)
T ss_pred EeeccHHHHHHHHHHHHHhhcCcccCCCcceEeeeecCCCCCCceeEEecCchhhhhehhccc-----------------
Confidence 99865 48999999999976 46999988877653 389999999999999998764
Q ss_pred CCCCCCCchhccccCcEEEeccccccceeEeecccccccccCCCCcCCCCceeeeeccCCccccccccccCCCCCCCCcc
Q 003180 299 ESPEDGGWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPR 378 (842)
Q Consensus 299 ~~~~~~~~~~l~~~g~IE~Id~~Eq~~~~Ia~~~~~l~~~~~~~k~~~~~~~TH~EI~Ps~ilgv~AslIPF~~HNqSpR 378 (842)
| +.+|||++.||.++.||+.++++.. .-+||.|++|+.+||++|+||||+|||||||
T Consensus 612 -------~------~~~e~iG~fEQvym~i~~~~~e~~~----------~v~th~E~~pt~~ls~~anliP~sD~NQSPR 668 (1111)
T KOG0216|consen 612 -------L------DSVEWIGPFEQVYMNIAIDPKEIFP----------DVTTHVELHPTGILSIVANLIPFSDHNQSPR 668 (1111)
T ss_pred -------c------CchhhcccHHHhhhhhccchhhcCC----------CcceeEEecccchHhHhhcCccccccCCCch
Confidence 3 5689999999999999999988864 4589999999999999999999999999999
Q ss_pred chhhhcccccccccccceeEEecccCcceeccCCcceeeccccccccCCCCCCCceeeEEeeeccCCCCCCceeeecccc
Q 003180 379 NTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSI 458 (842)
Q Consensus 379 n~yq~~M~KQaig~~~~n~~~R~Dt~~~~L~ypQ~PlV~t~~~~~~~~~e~p~G~N~iVAvmsy~GYn~EDAiIiNk~si 458 (842)
|||||||+||+||+|.++++.|+|+++|+|++||.|+|++..+|.+++|++|.|+||+|||+|||||||||||||||+|+
T Consensus 669 NmYQCQMgKQtmg~p~~a~~~radnklYrlqt~qsP~vr~~~y~~y~~d~yp~GtNaiVAVisyTgyDMeDAmiiNK~s~ 748 (1111)
T KOG0216|consen 669 NMYQCQMGKQTMGTPGHALRTRADNKLYRLQTPQSPIVRPELYDTYGMDDYPNGTNAIVAVISYTGYDMEDAMIINKSSY 748 (1111)
T ss_pred hHHHhhhhhhhcCCccccchhcccCceEEecCCCCceeecccccccccccCCCCcceEEEEEeecccChhhhhhhchhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCceeEEEEEEEEeeehhcCCcccccccc-CCCCCCCCCCCCCccCCCCCCCcCCCcEEcCCCEEEEeeCCCCcccccc
Q 003180 459 DRGFFRSLFFRSYRDEEKKMGTLVKEDFGR-PDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQG 537 (842)
Q Consensus 459 ~rG~f~s~~~~~~~~~~~~~~~~~~e~~~~-p~~~~~~~~k~~~~~~Ld~dGl~~~G~~v~~gdvli~k~~~~~~~~~~~ 537 (842)
||||+++++|++..+++.+... ....|.. |.. ....+||+||||.+|++++.||+++....- +
T Consensus 749 eRGf~~G~vykte~i~L~~~~~-r~~~F~~~p~~--------~~~~~ld~dgLP~~G~kl~~~dp~~~y~d~----~--- 812 (1111)
T KOG0216|consen 749 ERGFAYGTVYKTEKIDLSKKRS-RSKHFGRSPGE--------PELKKLDADGLPSIGQKLEYGDPYYAYFDE----E--- 812 (1111)
T ss_pred hccccceeEEeeeeechhhccc-ceeeeeeCCCC--------ccccccCCCCCCCCcccccCCCcEEEEEcc----c---
Confidence 9999999999999988743211 1233432 332 126789999999999999999999998763 1
Q ss_pred ccCCCccceeeEEeeccccceEEeEEEeecCCCc--eEEEEEEeeecCCcccccccccCCCcceeeeeecccCCCCCCCC
Q 003180 538 QASRYTRRDHSISLRHSETGMVDQVLLTTNADGL--RFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEG 615 (842)
Q Consensus 538 ~~~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~--~~v~v~~r~~R~p~iGDKfssRhGqKGvvs~i~~~~dmPft~~G 615 (842)
..+....++...|+|+||.|.+..++.|. +.+.|++|..|+|.||||||||||||||||+.||.+|||||++|
T Consensus 813 -----t~~~~~~~~~~~ep~~vd~vr~~~~~~~~~~k~~~i~~Ri~R~p~IGDKFsSRhGQKGicS~~wP~~dmPFtesG 887 (1111)
T KOG0216|consen 813 -----TGKTRIKKYHGTEPGIVDEVRVLGNDMGDQEKCATITLRIPRNPIIGDKFSSRHGQKGICSQKWPTIDMPFTESG 887 (1111)
T ss_pred -----CCceEEEEecCCCCeeeEEEEEccccCCCccceEEEEEEecCCCcccchhhhhccccccccccCCCCCCCccccC
Confidence 13344568888999999999999887666 78999999999999999999999999999999999999999999
Q ss_pred CCceEEeCCCCCCCCCcHHHHHHHHhhhhhhccCCcceecCCC----CCCHHHHHHHHHHcCCCCCCeEEEeeCCCCcEE
Q 003180 616 ITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT----DVTVDNISKALHKCGYQMRGFETMYNGHTGRRL 691 (842)
Q Consensus 616 ~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tpF~----~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~ 691 (842)
++|||||||||||||||||||||++|||+||++|..+|+|||. +..+++|+++|+++||||||+|+||+|.+|++|
T Consensus 888 m~PDii~NPH~FPSRMTIgM~iEs~AgK~~alhG~~~Datpf~~~E~~t~~dyfg~~L~~~GyNyyGnE~~YSGv~G~e~ 967 (1111)
T KOG0216|consen 888 MVPDIIINPHAFPSRMTIGMLIESMAGKAGALHGNAQDATPFIFSEENTAIDYFGEMLKKAGYNYYGNEPMYSGVDGREM 967 (1111)
T ss_pred cCcceeeCCCCCcccccHHHHHHHHhchhhccccccccCCceeecCcccHHHHHHHHHHHcCcCccCCccccccccccee
Confidence 9999999999999999999999999999999999999999997 346899999999999999999999999999999
Q ss_pred eeeEeEeeehhhhccCccCcceEEeccCCccccccCCCCcccCCCcceeeehhhHHHHhhccHHHHHHhhhcCCCceeee
Q 003180 692 TAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVH 771 (842)
Q Consensus 692 ~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~ 771 (842)
+|+||+|+||||||+|||.||+|+|+|||++.+|+||++||+|+||+||||||||||||||||++|||||+.|||.+.++
T Consensus 968 ~adIf~GvVyYQRLrHMv~DKfQVRstG~v~~~T~QPvkGRkr~GGiRfGEMERDali~HGtsfllqDRL~~~SD~~~a~ 1047 (1111)
T KOG0216|consen 968 RADIFFGVVYYQRLRHMVSDKFQVRSTGPVDSLTHQPVKGRKRGGGIRFGEMERDALIAHGTSFLLQDRLLNSSDYTVAE 1047 (1111)
T ss_pred eeeEEEeehhHHHHHHHhcceeeeeeccCccccccCCccCcccCCCccccchhhhhHhhcchHhhhhhhhccCcchhHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eccccCcceee--------cccCCceeeccCCCCCCceeecchHhHHHHHHHHHhCCCceEEEEc
Q 003180 772 VCEHCGLIAIA--------NLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTK 828 (842)
Q Consensus 772 vC~~cG~~~~~--------~~~~~~~~C~~C~~~~~i~~v~iPy~~kll~~EL~sm~I~~~l~~~ 828 (842)
||..||+++.. ........|+.|+. ..+..|.|||+||||..||+||||++++.++
T Consensus 1048 vC~~cgsil~~~~~l~~~~~~~~~~~~C~~c~~-~~~~~v~~P~vfkYL~aEL~amnIk~~l~l~ 1111 (1111)
T KOG0216|consen 1048 VCRTCGSILSTQQKLIKEPGGSTSTVTCRSCDG-KGVTTVAMPYVFKYLTAELAAMNIKMRLDLE 1111 (1111)
T ss_pred HHHHhhhhhhhhhhhhcccCCCCCceeEEecCC-CceEEEEccHHHHHHHHHHhhCceeEEeccC
Confidence 99999999853 11234568999965 5889999999999999999999999999864
No 5
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]
Probab=100.00 E-value=3e-205 Score=1803.75 Aligned_cols=762 Identities=37% Similarity=0.559 Sum_probs=710.2
Q ss_pred CccccCCC---CC-CcchHHHHHHHHHHHHHhhcCCCCCCCCCCccCCcEECchhHHHHHHHHHHHHHHHHHHHHHHHHh
Q 003180 1 MLPHVGTG---DF-CETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKC 76 (842)
Q Consensus 1 llpHl~~~---~~-~~~~K~~~L~~Mi~kLl~~~~g~~~~Dd~D~~~nkRv~~~G~Ll~~lf~~~~~~~~~~~~~~~~~~ 76 (842)
+|||++.. .+ ++..|+.+|+.|+++|+.+..|.+.+||+|||+||||+++|+|++.+||..|+++++.++++|++.
T Consensus 278 ~L~hL~~~~~~~~l~~~~k~~di~~mi~~l~~L~~G~~~~DDiDHlGNKRlrlvGeLl~n~fR~gl~rmer~ikerm~~~ 357 (1060)
T COG0085 278 LLPHLGEAGERYDLSRVGKAKDIIAMIKYLIELRLGKGEEDDIDHLGNRRLRLVGELLENLFRVGLSRMERDVKERLEKA 357 (1060)
T ss_pred HHhhhcccccccchhhhHHHHHHHHHHHHHHHHhcCCCCCCCCccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 48999973 22 355699999999999999999999999999999999999999999999999999999999999887
Q ss_pred hhcCCCCchhccccccchhhhhhhhhccCccccccccccccceeEeccccChhhhhcccccccC-CcccCCCcCCccccc
Q 003180 77 VDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS-PIGREGKLAKPRQLH 155 (842)
Q Consensus 77 ~~~~~~~~~~~~~~~~~it~~i~~~~sTGnw~~~~~~~~~~G~sq~l~r~N~l~~lShlRrv~~-~~~~~~K~t~~R~Lh 155 (842)
..+ ..++.++.||.++.+|++||||+ ++|+||+|||+||+|+|||+|||++ +++++++.++||+||
T Consensus 358 ~~r------~~i~p~dlIn~k~~~Alitgffg-------~sqlSQfmDqtNpLSeLSHkRRIsAlgLsRera~fEvRDvH 424 (1060)
T COG0085 358 DKR------DTLVPQDLINAKPIHALITGFFG-------RSQLSQFMDQTNPLSELSHKRRLSALGLSRERAGFEVRDVH 424 (1060)
T ss_pred hhh------hccCchhhcchhHHHHHHhcccc-------ccceeeeeecCChHHhhhhhhceeccCcCccCCCCcccccC
Confidence 543 33445678999999999999998 8999999999999999999999999 999999999999999
Q ss_pred CCCccccccCCCCCCCcchhhhhcccceEEe-cCCCchhHHHHHHH-hCCccccccCCCCCCCcEEEEECCEEEEEEcCh
Q 003180 156 NSQWGMMCPAETPEGQACGLVKNLALMVYIT-VGSAAYPILEFLEE-WGTENFEEISPAVIPQATKIFVNGCWVGIHRDP 233 (842)
Q Consensus 156 pS~wGfiCPveTPEG~~cGLvknLA~~a~Is-~~~~~~~i~~~L~~-~g~~~~~~~~~~~~~~~~~VflnG~~iG~~~~~ 233 (842)
||||||+||+|||||+|||||||||++|+|+ .|++++|+++++.. +++.+++..+.. ...|++||.++|.++++
T Consensus 425 pTHyGRiCPiETPEGpNiGLI~sLA~~A~Vn~~Gf~etPy~kv~~g~~~v~~i~~l~~~----~~~~~~~~~~~~~~~~~ 500 (1060)
T COG0085 425 PTHYGRICPIETPEGPNIGLIKSLALYARINEYGFLETPYRKVLDGSLVVDEIEYLSAD----EEDVYVIGQANGTLDEP 500 (1060)
T ss_pred cccccccCCCCCCCCcchhHHHHHHHHeEecccCCCCCceEEEEeccccccceeeeccc----ccceEEEeEeeeeecCC
Confidence 9999999999999999999999999999999 79999999998884 888877655433 36899999999999999
Q ss_pred HHHHHHHHHhhhcCCCCCcEEEEEeccCC----eEEEecCCCeeeeeEEEeecccccccHHHHHHHhcCCCCCCCCchhc
Q 003180 234 EMLVKTLRRLRRRVDVNTEVGVVRDIRLK----ELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRESPEDGGWHDL 309 (842)
Q Consensus 234 ~~lv~~lR~lRr~~~i~~~vsi~~~~~~~----~i~I~td~GRl~RPl~vv~n~~~~~~~~~~~~l~~~~~~~~~~~~~l 309 (842)
..|++.+|.+|| + +..+++++.....+ ++++.+|.||.|||++.++++..++..++++++..+.. .+|.+|
T Consensus 501 ~~~~~~~~~~R~-~-~~~~~~~~~~~~~~~~dv~~~~~~~~~~~~~P~l~~dd~~~~l~~~~mqr~~~~l~---~~~~~l 575 (1060)
T COG0085 501 GELVEELVECRR-G-GSGEVSVADPEGVDYMDVSPKQVVSVGRSLIPFLEHDDANRALMGSNMQRQAVPLL---RTEAPL 575 (1060)
T ss_pred CceeeeEEEEee-c-ccccceeecCccccceeccceEEeccccccCceeEEcCchHhhhhhhhhhhccccc---cccccc
Confidence 999999999999 5 88889988777665 89999999999999999999999999999999876532 489999
Q ss_pred cccCcEEEeccccccceeEeecccccccccCCCCcCCCCceeeeeccCCccccccccccCCCCCCCCccchhhhcccccc
Q 003180 310 VAKGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQA 389 (842)
Q Consensus 310 ~~~g~IE~Id~~Eq~~~~Ia~~~~~l~~~~~~~k~~~~~~~TH~EI~Ps~ilgv~AslIPF~~HNqSpRn~yq~~M~KQa 389 (842)
+..| +||++|+|+++++||..+. .+||+|++|..|+|++|++|||++|||||||||||+|+||+
T Consensus 576 v~tG-~E~~~a~e~~~~~ia~~~~---------------~~~~ve~~~~~I~~~~~~~~~~~~~n~~~~n~~~~~~~~Q~ 639 (1060)
T COG0085 576 VGTG-MEYLDAEDSGAAVIAKRPG---------------VVTHVEISPIVILGIEASLIPYPEHNQSPYNLYKFARSNQA 639 (1060)
T ss_pred ccCC-ceeeccccccceeEeccCC---------------cEEEEeeeeeEEEeeccccCCccccCcChHHHHHHhhhhcc
Confidence 9999 9999999999999998764 47999999999999999999999999999999999999999
Q ss_pred cccccceeEEecccCcceeccCCcceeeccccccccCCCCCCCceeeEEeeeccCCCCCCceeeeccccccCceeEEEEE
Q 003180 390 MGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFR 469 (842)
Q Consensus 390 ig~~~~n~~~R~Dt~~~~L~ypQ~PlV~t~~~~~~~~~e~p~G~N~iVAvmsy~GYn~EDAiIiNk~si~rG~f~s~~~~ 469 (842)
+|++..|+..|.|+..|.++|||.|+|+| +|+|+|||++||||||+||||||||||||++++||+|||+||+
T Consensus 640 ~~~~~~~~~~~~d~~~~~~~~~~~P~~~~--------~e~~~GqN~~VA~m~~~GYn~EDAiiin~~~v~~~~~ts~~~~ 711 (1060)
T COG0085 640 TGINQRPLVKRGDTVEKGLVYADGPSVDT--------GELALGQNALVAFMPWNGYNYEDAIIISERSVERDLFTSIHIE 711 (1060)
T ss_pred cCCCcccceeccccccccceecCCCcccc--------CcccCCceeEEEEecccCcChhHheecccchhhcCCceEEEEE
Confidence 99999999999999999999999999998 8899999999999999999999999999999999999999999
Q ss_pred EEEeeehhcCCccccccccCCCCCCCCCCCCCccCCCCCCCcCCCcEEcCCCEEEEeeCCCCccccccc-----cCCCcc
Q 003180 470 SYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQGQ-----ASRYTR 544 (842)
Q Consensus 470 ~~~~~~~~~~~~~~e~~~~p~~~~~~~~k~~~~~~Ld~dGl~~~G~~v~~gdvli~k~~~~~~~~~~~~-----~~~~~~ 544 (842)
+|++++++++.+..|.+++|+.. ...|.+||+|||++||++|++|||||||++|+...+.... ....+.
T Consensus 712 ~~~~~~r~~~~g~e~~~~iP~~~------e~~~~~Lde~Gii~ig~~V~~gdilvgk~tP~~~~~~~~ee~ll~i~~ek~ 785 (1060)
T COG0085 712 EYETEARDTKLGPEEIRDIPNVS------EEALRNLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRIFGEKV 785 (1060)
T ss_pred EEeeeeeccCCCccccccCCCcC------HHHHhcCCccCccccccEEcCCCEEEEeeCCCCCCCCCchhhhhcccccee
Confidence 99999999988888888999864 2458999999999999999999999999999874331111 112347
Q ss_pred ceeeEEeeccccceEEeEEEeecCC----CceEEEEEEeeecCCcccccccccCCCcceeeeeecccCCCCCCCCCCceE
Q 003180 545 RDHSISLRHSETGMVDQVLLTTNAD----GLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDI 620 (842)
Q Consensus 545 ~d~s~~~~~~e~g~Vd~V~~~~~~~----~~~~v~v~~r~~R~p~iGDKfssRhGqKGvvs~i~~~~dmPft~~G~~pDi 620 (842)
||+|++++++++|+||.|.++++++ +.+.|||++|+.|.|++|||||||||||||||+|||+||||||+||++|||
T Consensus 786 rdtsl~~~~g~~G~V~~V~~~~~~~~~~g~~~~vkV~v~~~R~~~~GDK~a~RHG~KGVis~i~p~eDMPf~~~G~~~Di 865 (1060)
T COG0085 786 RDTSLRVPHGEEGIVDDVQVFTREDGDPGVNKLVKVYVAQKRKPQIGDKMAGRHGNKGVVSKIVPQEDMPFLEDGTPPDI 865 (1060)
T ss_pred eccceeecCCCCeEEEEEEEEeccCCCcCceEEEEEEEEEeccCCccccccccCCCCceeeeecCcccCCcCCCCCcccE
Confidence 8999999999999999999999877 789999999999999999999999999999999999999999999999999
Q ss_pred EeCCCCCCCCCcHHHHHHHHhhhhhhccCCcceecCCCCCCHHHHHHHHHHcCCCCCCeEEEeeCCCCcEEeeeEeEeee
Q 003180 621 IVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPT 700 (842)
Q Consensus 621 IiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tpF~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if~G~~ 700 (842)
|+|||||||||||||++|+++||||++.|...|+|||++.+.+++.+.|.++||++.|++.||||+||++|+++||+|++
T Consensus 866 ilNP~gvPSRM~iGqilE~~lG~a~~~~G~~~~~~~F~g~~~~~~~~~l~~~g~~~~Gk~~lydG~TGe~~~~~i~vG~~ 945 (1060)
T COG0085 866 ILNPLGVPSRMNIGQILETHLGKAAALLGIPVDTPVFDGAPEEDIRELLKEAGFPYSGKEVLYDGRTGEPFDAPIFVGVM 945 (1060)
T ss_pred EECCCCCCccccHHHHHHHHHHHHHHhcCceeccCCcCCCCHHHHHHHHHHcCCCCCCCEEeecCCCCCcccccEEEEeh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhccCccCcceEEeccCCccccccCCCCcccCCCcceeeehhhHHHHhhccHHHHHHhhhcCCCceeeeeccccCcce
Q 003180 701 YYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIA 780 (842)
Q Consensus 701 yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~cG~~~ 780 (842)
|||||+|||+|||||||||||+.|||||++||+|.|||||||||||||+|||||++|||||+.+||.+ ||+++
T Consensus 946 Y~~kL~HmV~dK~HaRs~GP~s~lT~QP~~Gka~~GG~RfGEME~~aL~ayGAa~~LqE~L~~~SD~~-------~G~~~ 1018 (1060)
T COG0085 946 YYQKLHHMVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTVKSDDV-------CGRIK 1018 (1060)
T ss_pred HHHhHHhhhcccceeeccCCceeeecCCCCcccccCCccccchHHHHHHHHhHHHHHHHHhhccchhc-------ccchh
Confidence 99999999999999999999999999999999999999999999999999999999999999999954 99998
Q ss_pred eecccCCceeeccCCCCCCceeecchHhHHHHHHHHHhCCCceEEEEccC
Q 003180 781 IANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKED 830 (842)
Q Consensus 781 ~~~~~~~~~~C~~C~~~~~i~~v~iPy~~kll~~EL~sm~I~~~l~~~~~ 830 (842)
+. .|..|+ .++.++.||||||+|++||+||||++++.+++.
T Consensus 1019 ~y-------~~~v~g--~~~~~~~ip~sFk~L~~El~sl~i~~~l~~~~~ 1059 (1060)
T COG0085 1019 IY-------ECIVKG--ENIPEVGIPESFKVLLKELRSLGIDVRLELEDG 1059 (1060)
T ss_pred hh-------cCcccC--CCCCCCCCCHHHHHHHHHHHHCCCceEEeecCC
Confidence 54 399998 578999999999999999999999999998764
No 6
>cd00653 RNA_pol_B_RPB2 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.
Probab=100.00 E-value=1.1e-192 Score=1736.60 Aligned_cols=652 Identities=53% Similarity=0.828 Sum_probs=608.9
Q ss_pred HHHHHHHHHHHHHhhcCCCCCCCCCCccCCcEECchhHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCchhccccccch
Q 003180 15 KAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTI 94 (842)
Q Consensus 15 K~~~L~~Mi~kLl~~~~g~~~~Dd~D~~~nkRv~~~G~Ll~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i 94 (842)
++.+|++|++||+++..|.+.+||+|||+||||+++|+||+.+|++.|+++++.+++.+.+...+.+.+++..++++..|
T Consensus 209 ~~~~L~~Mi~kLl~~~~g~~~~Dd~D~~~NkRv~~~G~Ll~~lfr~~l~~~~~~~k~~l~~~~~~~~~~~~~~~~~~~~I 288 (866)
T cd00653 209 RFEDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPI 288 (866)
T ss_pred HHHHHHHHHHHHHHHhcCCCCCCCchhhhCeEEeeHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcccccCHHHhccchHH
Confidence 44799999999999999999999999999999999999999999999999999999999888766556777778888899
Q ss_pred hhhhhhhhccCccccccccccccceeEeccccChhhhhcccccccC-CcccCCCcCCcccccCCCccccccCCCCCCCcc
Q 003180 95 TSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS-PIGREGKLAKPRQLHNSQWGMMCPAETPEGQAC 173 (842)
Q Consensus 95 t~~i~~~~sTGnw~~~~~~~~~~G~sq~l~r~N~l~~lShlRrv~~-~~~~~~K~t~~R~LhpS~wGfiCPveTPEG~~c 173 (842)
|++|++||+||||.+++..++++|+||+|||+||+++|||+||||+ ++++++|+++||+||||||||+||+|||||++|
T Consensus 289 t~~i~~~~~TGnw~~~~~~~~~~Gvsq~ldr~N~ls~lsh~Rrv~~~~~~~~~k~~~~R~lhps~~G~iCPveTPEG~~c 368 (866)
T cd00653 289 TSGIKEFLATGNWGSKRFLMQRSGLSQVLDRLNPLSELSHKRRISSLGLFRERKGFEVRDLHPSHWGRICPIETPEGENC 368 (866)
T ss_pred HHHHHHHhhcCCccccccccccceEEEEcccCCHHHHHHhhhhcccccccccccCCcccccCcccCCccCCCCCCCCccc
Confidence 9999999999999998888899999999999999999999999999 999999999999999999999999999999999
Q ss_pred hhhhhcccceEEecCCCchhHHHHHHHhCCccccccCCCCCCCcEEEEECCEEEEEEcChHHHHHHHHHhhhcCCCCCcE
Q 003180 174 GLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKTLRRLRRRVDVNTEV 253 (842)
Q Consensus 174 GLvknLA~~a~Is~~~~~~~i~~~L~~~g~~~~~~~~~~~~~~~~~VflnG~~iG~~~~~~~lv~~lR~lRr~~~i~~~v 253 (842)
|||||||++|+|+
T Consensus 369 GLv~~LA~~a~Is------------------------------------------------------------------- 381 (866)
T cd00653 369 GLVKNLALMARIS------------------------------------------------------------------- 381 (866)
T ss_pred cchhhhhceEeee-------------------------------------------------------------------
Confidence 9999999999987
Q ss_pred EEEEeccCCeEEEecCCCeeeeeEEEeecccccccHHHHHHHhcCCCCCCCCchhccccCcEEEeccccccceeEeeccc
Q 003180 254 GVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRESPEDGGWHDLVAKGFIEYIDTEEEETTMISMTIN 333 (842)
Q Consensus 254 si~~~~~~~~i~I~td~GRl~RPl~vv~n~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~g~IE~Id~~Eq~~~~Ia~~~~ 333 (842)
||++||+++|++
T Consensus 382 -----------------Gr~~rP~~~v~~--------------------------------------------------- 393 (866)
T cd00653 382 -----------------GRIERPYRIVEK--------------------------------------------------- 393 (866)
T ss_pred -----------------eEeeeeEEEecc---------------------------------------------------
Confidence 999999998741
Q ss_pred ccccccCCCCcCCCCceeeeeccCCccccccccccCCCCCCCCccchhhhcccccccccccceeEEecccCcceeccCCc
Q 003180 334 DLVQARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQK 413 (842)
Q Consensus 334 ~l~~~~~~~k~~~~~~~TH~EI~Ps~ilgv~AslIPF~~HNqSpRn~yq~~M~KQaig~~~~n~~~R~Dt~~~~L~ypQ~ 413 (842)
.+||+||+|+++||++||+|||+||||||||||||||+|||||++.+|++.|+|++.|+|+|||+
T Consensus 394 ---------------~~th~ei~~~~~ls~~asliPf~~hNqspRn~~~~~M~kQa~g~~~~n~~~r~d~~~~~l~~pq~ 458 (866)
T cd00653 394 ---------------EVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQK 458 (866)
T ss_pred ---------------ceEEEEeCccceeeeeeeccCCCCcccccchhhhhcccCCccCchhccccccccchheeeccCCC
Confidence 38999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceeeccccccccCCCCCCCceeeEEeeeccCCCCCCceeeeccccccCceeEEEEEEEEeeehhcCCccccccccCCCCC
Q 003180 414 PLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSN 493 (842)
Q Consensus 414 PlV~t~~~~~~~~~e~p~G~N~iVAvmsy~GYn~EDAiIiNk~si~rG~f~s~~~~~~~~~~~~~~~~~~e~~~~p~~~~ 493 (842)
|||+|+..+.++++++|+|+|++||||||+||||||||||||+|+|||||||+||++|++++++...+..+.+. +.
T Consensus 459 plv~T~~~~~~~~~~~~~G~N~~VAv~~y~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~~~~~-~~--- 534 (866)
T cd00653 459 PLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITR-GD--- 534 (866)
T ss_pred CccccchHHHhCCCccCCCceEEEEEeccccccccceeeeehhhhhcCceeEEEEEEEEEEEEecCCCcceEec-CC---
Confidence 99999999999999999999999999999999999999999999999999999999999998775444333332 11
Q ss_pred CCCCCCCCccCCCCCCCcCCCcEEcCCCEEEEeeCCCCccccc--cccCCCccceeeEEeeccccceEEeEEEee---cC
Q 003180 494 TMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ--GQASRYTRRDHSISLRHSETGMVDQVLLTT---NA 568 (842)
Q Consensus 494 ~~~~k~~~~~~Ld~dGl~~~G~~v~~gdvli~k~~~~~~~~~~--~~~~~~~~~d~s~~~~~~e~g~Vd~V~~~~---~~ 568 (842)
....+...|++||+||+|++|++|++||+||||++|...++.. ........+|+|++++.+|+|+||+|.++. +.
T Consensus 535 ~~~~~~~~~~~ld~dGi~~~g~~v~~gd~li~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~v~~v~~~~~~~~~ 614 (866)
T cd00653 535 IPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRELND 614 (866)
T ss_pred CCCCChHHhhccCCCCCcCCCCEecCCCEEEEEecCcccccccccccccCCcceEEEEEecCCCceEEEEEEEeccccCC
Confidence 1112335699999999999999999999999999986533210 011123478999999999999999999987 56
Q ss_pred CCceEEEEEEeeecCCcccccccccCCCcceeeeeecccCCCCCCCCCCceEEeCCCCCCCCCcHHHHHHHHhhhhhhcc
Q 003180 569 DGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHM 648 (842)
Q Consensus 569 ~~~~~v~v~~r~~R~p~iGDKfssRhGqKGvvs~i~~~~dmPft~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~ 648 (842)
++...|+|++|+.|+|+||||||||||||||||+|||+||||||+||++|||||||||||||||||||+|+++||++++.
T Consensus 615 ~~~~~v~v~~r~~R~p~iGDKfssRhGqKGv~s~i~~~~dmPf~~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~ 694 (866)
T cd00653 615 GGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALL 694 (866)
T ss_pred CCcEEEEEEEeEEecCCcccccccccCCCcEEEEEeccccCCcccCCCCCcEEecCCcCcccccHHHHHHHHHHHHHHhc
Confidence 77889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcceecCCCCCCHHHHHHHHHHcCCCCCCeEEEeeCCCCcEEeeeEeEeeehhhhccCccCcceEEeccCCccccccCC
Q 003180 649 GKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQP 728 (842)
Q Consensus 649 g~~~d~tpF~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP 728 (842)
|.+.|+|||++...+++.+.|.++||+++|+|.||||+||++++++||+|++|||||+|||.||+|||++||++.|||||
T Consensus 695 g~~~d~t~f~~~~~~~~~~~l~~~g~~~~G~e~~y~g~tG~~~~~~if~G~~yyqrL~Hmv~DK~~~R~~Gp~~~lT~QP 774 (866)
T cd00653 695 GKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQP 774 (866)
T ss_pred CCcccccccCcchHHHHHHHHHHcCCCCCCcEEEEcCCCCCCcccceEEeehhhhhhhhhhchhhhhcccCCcchhccCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcccCCCcceeeehhhHHHHhhccHHHHHHhhhcCCCceeeeeccccCcceeecccCCceeeccCCCCCCceeecchHh
Q 003180 729 AEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYA 808 (842)
Q Consensus 729 ~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~cG~~~~~~~~~~~~~C~~C~~~~~i~~v~iPy~ 808 (842)
++||+|+|||||||||||||+|||||++|+|||+++||.+.++||.+||.+++.+ +|+.|+++.++.++.+|||
T Consensus 775 ~~Gr~~~GG~R~GEMErd~lia~Gas~~l~erl~~~SD~~~~~vc~~cg~i~~~~------~c~~c~~~~~~~~~~ipy~ 848 (866)
T cd00653 775 LKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSAN------LCRLCKKGTNISKVGIPYA 848 (866)
T ss_pred CccccccCCeEEEEEehhhhhhhhhHHHHHHHHhcCCccceEEEeccCccccccc------ccccccCCCceeecCCCHH
Confidence 9999999999999999999999999999999999999999999999999999532 3999999999999999999
Q ss_pred HHHHHHHHHhCCCceEEE
Q 003180 809 CKLLFQELMAMAIAPRML 826 (842)
Q Consensus 809 ~kll~~EL~sm~I~~~l~ 826 (842)
||||+|||+||||++++.
T Consensus 849 ~kll~~EL~sm~i~~~~~ 866 (866)
T cd00653 849 FKLLFQELQSMNIDPRLK 866 (866)
T ss_pred HHHHHHHHHHCCcceEeC
Confidence 999999999999999973
No 7
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated
Probab=100.00 E-value=1.2e-190 Score=1640.82 Aligned_cols=597 Identities=48% Similarity=0.809 Sum_probs=561.7
Q ss_pred cEEEEECCEEEEEEcChHHHHHHHHHhhhcCCCCCcEEEEEeccCCeEEEecCCCeeeeeEEEeecccccccHHHHHHHh
Q 003180 217 ATKIFVNGCWVGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQ 296 (842)
Q Consensus 217 ~~~VflnG~~iG~~~~~~~lv~~lR~lRr~~~i~~~vsi~~~~~~~~i~I~td~GRl~RPl~vv~n~~~~~~~~~~~~l~ 296 (842)
.++|||||+|+|+|++|++|++.||.+||+|.|+.+|||+++++.++|+||||+||++|||++|++|++.++++|+++|+
T Consensus 4 ~~~VflNG~~vG~~~~~~~lv~~lR~lRr~g~i~~~vsI~~~~~~~ei~I~tD~GR~~RPl~iv~~g~~~l~~~~~~~l~ 83 (605)
T PRK07225 4 KAKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEPLLTEEHIEKLK 83 (605)
T ss_pred ccEEEECCEEEEEECCHHHHHHHHHHHHccCCCCCcEEEEEECCCCEEEEEccCCccceeEEEEeCCcccCCHHHHHHHH
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999997
Q ss_pred cCCCCCCCCchhccccCcEEEeccccccceeEeecccccccccCCCCcCCCCceeeeeccCCccccccccccCCCCCCCC
Q 003180 297 QRESPEDGGWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQS 376 (842)
Q Consensus 297 ~~~~~~~~~~~~l~~~g~IE~Id~~Eq~~~~Ia~~~~~l~~~~~~~k~~~~~~~TH~EI~Ps~ilgv~AslIPF~~HNqS 376 (842)
+++ .+|++|+++|+|||||++||++++||++++++.+ .+||+||+|+++|||+||+|||+|||||
T Consensus 84 ~~~----~~~~dl~~~G~IEyida~EE~~~~IA~~~~~l~~-----------~~th~Ei~p~~ilgv~AslIPF~~hNQS 148 (605)
T PRK07225 84 NGE----LTFDDLVKQGVIEYLDAEEEENAYIAVYEEDLTE-----------EHTHLEIDPSLILGIGAGMIPYPEHNAS 148 (605)
T ss_pred cCC----CChHHHHhCCCeeecChhhhcCeEeccchhhhcc-----------cccccccCCcceeEEEeeccCCCCCCcc
Confidence 554 4899999999999999999999999999998843 4799999999999999999999999999
Q ss_pred ccchhhhcccccccccccceeEEecccCcceeccCCcceeeccccccccCCCCCCCceeeEEeeeccCCCCCCceeeecc
Q 003180 377 PRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQS 456 (842)
Q Consensus 377 pRn~yq~~M~KQaig~~~~n~~~R~Dt~~~~L~ypQ~PlV~t~~~~~~~~~e~p~G~N~iVAvmsy~GYn~EDAiIiNk~ 456 (842)
|||||||||+|||||++++|+..|+|++.|+|+|||+|||+|+.++.++++++|+|+||+||||||+||||||||||||+
T Consensus 149 PRn~yq~~M~KQa~g~~~~n~~~r~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~p~G~N~iVAvmsy~GYn~EDAiIiNks 228 (605)
T PRK07225 149 PRITMGAGMIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKA 228 (605)
T ss_pred chhhhhhhhhhcccCccccceeeecCCcccEEeeCCcceEEccchHhhCCCccCCCeeEEEEEECcCCCChhHeeeeehh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCceeEEEEEEEEeeehhcCCccccccccCCCCCCCCCCC-CCccCCCCCCCcCCCcEEcCCCEEEEeeCCCCcc-c
Q 003180 457 SIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRH-GSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQD-E 534 (842)
Q Consensus 457 si~rG~f~s~~~~~~~~~~~~~~~~~~e~~~~p~~~~~~~~k~-~~~~~Ld~dGl~~~G~~v~~gdvli~k~~~~~~~-~ 534 (842)
|+|||||||+||++|+.+++++..+..+.|+.|... ..+.+. ..|++||+||||++|++|++|||||||++|.... +
T Consensus 229 sidRGlf~s~~~k~~~~~~~~~~~~~~~~~~~p~~~-~~~~~~~~~~~~LD~dGi~~~G~~v~~gdiligk~sp~~~~~~ 307 (605)
T PRK07225 229 SIERGLGRSHFFRTYEGEERRYPGGQEDRFEIPDKD-VRGYRGEEAYRHLDEDGLVNPETEVKEGDVLIGKTSPPRFLEE 307 (605)
T ss_pred hhhcCceEEEEEEEEEEEeeecCCCcceEEecCCch-hccccChHHhhcCCCCCCccCCCEECCCCEEEEEecCCCCccc
Confidence 999999999999999999887666666788888642 122222 3599999999999999999999999999986421 1
Q ss_pred c-ccccCCCccceeeEEeeccccceEEeEEEeecCCCceEEEEEEeeecCCcccccccccCCCcceeeeeecccCCCCCC
Q 003180 535 A-QGQASRYTRRDHSISLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTV 613 (842)
Q Consensus 535 ~-~~~~~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~v~v~~r~~R~p~iGDKfssRhGqKGvvs~i~~~~dmPft~ 613 (842)
. .........+|+|++++.+|+|+||+|.++.+.++.+.|||++|+.|+|+||||||||||||||||+|||+||||||+
T Consensus 308 ~~~~~~~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~vkv~ir~~R~p~iGDKfssRHGQKGvvs~i~~~eDMPft~ 387 (605)
T PRK07225 308 PDDFGISPEKRRETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTE 387 (605)
T ss_pred hhhhcccccCcceeeEEecCCCcEEEEEEEEEecCCCCEEEEEEEEEEEeccccchhhhcccCceeEEeEeccccCCcCC
Confidence 0 001112347899999999999999999999888889999999999999999999999999999999999999999999
Q ss_pred CCCCceEEeCCCCCCCCCcHHHHHHHHhhhhhhccCCcceecCCCCCCHHHHHHHHHHcCCCCCCeEEEeeCCCCcEEee
Q 003180 614 EGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTA 693 (842)
Q Consensus 614 ~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tpF~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~ 693 (842)
||++|||||||||||||||||||+|+++|||+++.|.+.|+|||.+..++++++.|+++||+++|+|+||||+||++|++
T Consensus 388 ~G~~PDiIiNPhg~PSRMTiGql~E~~~gk~~~~~g~~~d~t~F~~~~~~~~~~~L~~~g~~~~G~e~my~G~TG~~~~~ 467 (605)
T PRK07225 388 SGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEA 467 (605)
T ss_pred CCCcccEEECcccccccCcHHHHHHHHHHHHHHhcCceEeecCCCCchHHHHHHHHHHhCcCCCCeEEEEcCCCCCEecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEeEeeehhhhccCccCcceEEeccCCccccccCCCCcccCCCcceeeehhhHHHHhhccHHHHHHhhhcCCCceeeeec
Q 003180 694 MIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVC 773 (842)
Q Consensus 694 ~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC 773 (842)
+||+|++|||||+|||.||+|||++||++.|||||++||+|+|||||||||||||+|||||++|+|||+++||.++++||
T Consensus 468 ~if~G~~yYqrL~HmV~DK~haR~~Gp~~~lTrQP~~GR~r~GG~RfGEMErd~lia~Gas~~L~Erl~~~SD~~~~~vC 547 (605)
T PRK07225 468 EIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKVEIYVC 547 (605)
T ss_pred cEEEeehheeechhhhcchhhhccCCCCcccccCCccccccCCCeeeeeeehhhhhhhhhHHHHHHHHhccCcceeEEee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCcceeecccCCceeeccCCCCCCceeecchHhHHHHHHHHHhCCCceEEEEcc
Q 003180 774 EHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKE 829 (842)
Q Consensus 774 ~~cG~~~~~~~~~~~~~C~~C~~~~~i~~v~iPy~~kll~~EL~sm~I~~~l~~~~ 829 (842)
.+||++++.+.+.+.++|+.|+++..|.++.||||||||+|||+||||+++|.+++
T Consensus 548 ~~CG~~~~~~~~~~~~~C~~C~~~~~i~~v~iPya~kll~~EL~sm~i~~~l~~~~ 603 (605)
T PRK07225 548 AKCGMIAIYDKKRNRKYCPICGEETDIYPVEMSYAFKLLLDELKSLGIAPRLELED 603 (605)
T ss_pred cCcCcceehhcccCceeecccCCCCceeeccCChhHHHHHHHHHHCCceeEEEecc
Confidence 99999998776667788999999889999999999999999999999999999874
No 8
>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=1.8e-189 Score=1629.44 Aligned_cols=594 Identities=50% Similarity=0.841 Sum_probs=558.8
Q ss_pred EEECCEEEEEEcChHHHHHHHHHhhhcCCCCCcEEEEEeccCCeEEEecCCCeeeeeEEEeecccccccHHHHHHHhcCC
Q 003180 220 IFVNGCWVGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRE 299 (842)
Q Consensus 220 VflnG~~iG~~~~~~~lv~~lR~lRr~~~i~~~vsi~~~~~~~~i~I~td~GRl~RPl~vv~n~~~~~~~~~~~~l~~~~ 299 (842)
|||||+|||+|++|++|+++||.+||+|.|+.++||+++++.++|+||||+||+||||++|+++++.++++|+++++.+.
T Consensus 1 VflNG~~vG~~~~~~~lv~~LR~lRr~g~i~~~vsI~~~~~~~ei~I~tD~GR~~RPl~iv~~g~l~l~~~~l~~l~~~~ 80 (599)
T TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEGE 80 (599)
T ss_pred CEECCEEEEEECCHHHHHHHHHHHhCcCCCCCcEEEEEeCCCCEEEEEcCCCccceeEEEeeCCCccccHHHHHHHhccC
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999997544
Q ss_pred CCCCCCchhccccCcEEEeccccccceeEeecccccccccCCCCcCCCCceeeeeccCCccccccccccCCCCCCCCccc
Q 003180 300 SPEDGGWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRN 379 (842)
Q Consensus 300 ~~~~~~~~~l~~~g~IE~Id~~Eq~~~~Ia~~~~~l~~~~~~~k~~~~~~~TH~EI~Ps~ilgv~AslIPF~~HNqSpRn 379 (842)
.+|++|+++|+|||||++||++++||+.++++.+ .+||+||+|+++|||+||+|||+||||||||
T Consensus 81 ----~~~~~ll~~G~IEyida~Ee~~~~IA~~~~~l~~-----------~~th~Ei~p~~ilgv~AslIPF~~hNqSpRn 145 (599)
T TIGR03670 81 ----LTWDDLVKQGVIEYLDAEEEENAYIALDPEELTP-----------EHTHLEIDPSAILGIIASTIPYPEHNQSPRN 145 (599)
T ss_pred ----CCHHHHHhcCCeEecCchhhcCeEEecchHHhcc-----------CcCccccCCcceeeEEeeccCCCCcCcchhh
Confidence 4899999999999999999999999999998843 4799999999999999999999999999999
Q ss_pred hhhhcccccccccccceeEEecccCcceeccCCcceeeccccccccCCCCCCCceeeEEeeeccCCCCCCceeeeccccc
Q 003180 380 TYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSID 459 (842)
Q Consensus 380 ~yq~~M~KQaig~~~~n~~~R~Dt~~~~L~ypQ~PlV~t~~~~~~~~~e~p~G~N~iVAvmsy~GYn~EDAiIiNk~si~ 459 (842)
||||||+|||||++.+|++.|+||++|+|+|||+|||+|++++.++++++|+|+||+||||||+||||||||||||+|+|
T Consensus 146 ~YQc~M~KQamG~~~~n~~~R~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~p~G~N~iVAvmsy~GYn~EDAiIink~si~ 225 (599)
T TIGR03670 146 TMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIE 225 (599)
T ss_pred HHHHhhhhccccccccChhhcccccceEEcCCCCceeeeeeHHHhCccccCCCeeEEEEEEcccCcChhHeeeechhhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCceeEEEEEEEEeeehhcCCccccccccCCCCCCCCCCC-CCccCCCCCCCcCCCcEEcCCCEEEEeeCCCCccccc--
Q 003180 460 RGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRH-GSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ-- 536 (842)
Q Consensus 460 rG~f~s~~~~~~~~~~~~~~~~~~e~~~~p~~~~~~~~k~-~~~~~Ld~dGl~~~G~~v~~gdvli~k~~~~~~~~~~-- 536 (842)
||||||+||++|+.+++++..+..|.++.|+.. ..+.+. ..|++||+||||++|++|++|||||||++|....+..
T Consensus 226 rG~f~s~~~~~~~~~~~~~~~~~~e~~~~p~~~-~~~~~~~~~~~~LD~dGi~~~G~~v~~gdiligk~~p~~~~~~~~~ 304 (599)
T TIGR03670 226 RGLARSTFFRTYEAEERRYPGGQEDRFEIPEPD-VRGYRGEEAYKHLDEDGIVYPEVEVKGGDVLIGKTSPPRFLEELRE 304 (599)
T ss_pred cCCeEEEEEEEEEEEeeccCCCCceEEecCCch-hccccchhhhccCCCCCCcCCCcEeCCCCEEEEEecCCCCccchhh
Confidence 999999999999999887655556778888643 222232 3599999999999999999999999999986421100
Q ss_pred cccCCCccceeeEEeeccccceEEeEEEeecCCCceEEEEEEeeecCCcccccccccCCCcceeeeeecccCCCCCCCCC
Q 003180 537 GQASRYTRRDHSISLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGI 616 (842)
Q Consensus 537 ~~~~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~v~v~~r~~R~p~iGDKfssRhGqKGvvs~i~~~~dmPft~~G~ 616 (842)
........+|+|++++++|+|+||+|.++.++++.+.|||++|+.|+|+||||||||||||||||+|||+||||||+||+
T Consensus 305 ~~~~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~vkv~~r~~R~p~iGDKfssRHGQKGvvs~i~~~eDMPft~~G~ 384 (599)
T TIGR03670 305 LGLVTERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGI 384 (599)
T ss_pred hccccccCceEEEEecCCCcEEEEEEEEEecCCCcEEEEEEEeeeecCcchhhhhhhccCcceEEeEeccCCCCcCCCCC
Confidence 00112347899999999999999999999988888999999999999999999999999999999999999999999999
Q ss_pred CceEEeCCCCCCCCCcHHHHHHHHhhhhhhccCCcceecCCCCCCHHHHHHHHHHcCCCCCCeEEEeeCCCCcEEeeeEe
Q 003180 617 TPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIF 696 (842)
Q Consensus 617 ~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tpF~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if 696 (842)
+|||||||||||||||||||+|+++|||+++.|.+.|+|||++..++++++.|+++||+++|+|.||||+||++|+++||
T Consensus 385 ~pDiIiNPhg~PSRMTiGqllE~~~gk~~~~~g~~~d~t~F~~~~~~~~~~~L~~~g~~~~G~e~ly~G~TG~~~~~~if 464 (599)
T TIGR03670 385 VPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIF 464 (599)
T ss_pred CCCEEECcccccccccHHHHHHHHHHHHHHhcCCEEEeCCCCCccHHHHHHHHHHcCCCCCCCEEEEcCCCCCCccccEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EeeehhhhccCccCcceEEeccCCccccccCCCCcccCCCcceeeehhhHHHHhhccHHHHHHhhhcCCCceeeeecccc
Q 003180 697 LGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHC 776 (842)
Q Consensus 697 ~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~c 776 (842)
+|++|||||+|||.||+|||++||++.|||||++||||+|||||||||||||+|||||++|+|||+++||.+.++||.+|
T Consensus 465 ~G~~yyqrL~HmV~DK~h~Rs~Gp~~~lTrQP~~Gr~r~GG~RfGEMErd~lia~Gas~~L~ErL~~~SD~~~~~vC~~C 544 (599)
T TIGR03670 465 IGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENC 544 (599)
T ss_pred EEehhheechhhhcchhhhcccCCCcccccCCccccccCCCeeeeeeehhhHhhcchHHHHHHHHhccCcceeEEeeccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcceeecccCCceeeccCCCCCCceeecchHhHHHHHHHHHhCCCceEEEEcc
Q 003180 777 GLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKE 829 (842)
Q Consensus 777 G~~~~~~~~~~~~~C~~C~~~~~i~~v~iPy~~kll~~EL~sm~I~~~l~~~~ 829 (842)
|++++.+.+++.++|+.|+++.+|.++.+|||||||+|||+||||++++.+++
T Consensus 545 G~~~~~~~~~~~~~C~~c~~~~~i~~v~iPy~~k~l~~EL~am~i~~~l~~~~ 597 (599)
T TIGR03670 545 GHIAWEDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLELGD 597 (599)
T ss_pred CceeehhcccCceeccccCCCCceeeecCChhHHHHHHHHHhCCcceEEEecc
Confidence 99998776667789999999889999999999999999999999999999874
No 9
>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=1.1e-184 Score=1675.23 Aligned_cols=668 Identities=30% Similarity=0.478 Sum_probs=593.6
Q ss_pred hHHHHHHHHHHHHHhhcCCCCCCCCCCccCCcEECchhHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCchhccccccc
Q 003180 14 KKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKT 93 (842)
Q Consensus 14 ~K~~~L~~Mi~kLl~~~~g~~~~Dd~D~~~nkRv~~~G~Ll~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 93 (842)
.|++||+ |+++||++..|...+||+|||+||||+++|+||+.+|+..|+++++.+++++.+. +.+.+++..+++++.
T Consensus 297 ~k~d~l~-mi~~Ll~~~~g~~~~DD~Dhl~NKRvr~aGeLL~~~fr~~l~rl~k~ik~~l~~~--~~~~~~~~~~i~~~~ 373 (1065)
T TIGR02013 297 TKEDIIA-TIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERMSTQ--DTDTLTPQDLINAKP 373 (1065)
T ss_pred hHHHHHH-HHHHHHHhhcCCCCCcchhhhhccchhhHHHHHHHHHHHHHHHHHHHHHHHhhhc--ccccCCHHHhcCccc
Confidence 4999997 9999999999999999999999999999999999999999999999999988754 224667888999999
Q ss_pred hhhhhhhhhccCccccccccccccceeEeccccChhhhhcccccccC----CcccCCCcCCcccccCCCccccccCCCCC
Q 003180 94 ITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS----PIGREGKLAKPRQLHNSQWGMMCPAETPE 169 (842)
Q Consensus 94 it~~i~~~~sTGnw~~~~~~~~~~G~sq~l~r~N~l~~lShlRrv~~----~~~~~~K~t~~R~LhpS~wGfiCPveTPE 169 (842)
||.+|++||+|| ||||+|||+||+++|||+||+++ ++.++++.++||+|||||||+|||+||||
T Consensus 374 it~~i~~ff~tg------------glSQ~Ldr~NpLs~lsh~RRlsslgpggl~r~~~~~~~RdlHpShyGrICPiETPE 441 (1065)
T TIGR02013 374 ISAAIKEFFGSS------------QLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPE 441 (1065)
T ss_pred hHHHHHHHhccC------------CcccccccCCHHHhhhhhceecccCCCCcCccccCCccCccCccccccccCCCCCC
Confidence 999999999876 99999999999999999999998 58999999999999999999999999999
Q ss_pred CCcchhhhhcccceEEecCCCchhHHHHHHHhCCccccccCCCCCCCcEEEEECCEEEEEEcChHHHHHHHHHhhhcCCC
Q 003180 170 GQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKTLRRLRRRVDV 249 (842)
Q Consensus 170 G~~cGLvknLA~~a~Is~~~~~~~i~~~L~~~g~~~~~~~~~~~~~~~~~VflnG~~iG~~~~~~~lv~~lR~lRr~~~i 249 (842)
|++||||||||++|+|+ |
T Consensus 442 G~n~GLVknLA~~a~i~---------------------------------------~----------------------- 459 (1065)
T TIGR02013 442 GPNIGLINSLSTYARVN---------------------------------------E----------------------- 459 (1065)
T ss_pred CCccccccchhhhcccC---------------------------------------c-----------------------
Confidence 99999999999999985 1
Q ss_pred CCcEEEEEeccCCeEEEecCCCeeeeeEEEeecccccccHHHHHHHhcCCCCCCCCchhccccCcEEEeccccccceeEe
Q 003180 250 NTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRESPEDGGWHDLVAKGFIEYIDTEEEETTMIS 329 (842)
Q Consensus 250 ~~~vsi~~~~~~~~i~I~td~GRl~RPl~vv~n~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~g~IE~Id~~Eq~~~~Ia 329 (842)
.|.+.||++.|.|+++. .++.|||+|++||+++.||
T Consensus 460 --------------------~G~i~~P~~~V~ng~~~------------------------~~~~i~yl~a~eE~~~~Ia 495 (1065)
T TIGR02013 460 --------------------YGFIETPYRKVKDGKVV------------------------VTDEVDYLTADEEDNYVIA 495 (1065)
T ss_pred --------------------ceEEeCCeEEEECCeEe------------------------ccceeEECChHHhCCcEEE
Confidence 23455899999887532 1367999999999999999
Q ss_pred ecccccccccCCCC---------c---CCCCceeeeeccCCccccccccccCCCCCCCCccchhhhcccccccccc----
Q 003180 330 MTINDLVQARLHPE---------E---AYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIY---- 393 (842)
Q Consensus 330 ~~~~~l~~~~~~~k---------~---~~~~~~TH~EI~Ps~ilgv~AslIPF~~HNqSpRn~yq~~M~KQaig~~---- 393 (842)
+.+.++.......+ + ..+.++||+||+|.+|||++||||||+||||||||+|||||+|||||++
T Consensus 496 ~~~~~l~~~~~~~~~~i~~r~~~~f~~~~~~~vt~~ei~p~~ilsv~aslIPFleHNds~R~lmgsnM~kQavpl~~~e~ 575 (1065)
T TIGR02013 496 QANAPLDENGRFVEDLVVARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEA 575 (1065)
T ss_pred ecCcCcCccCccccceeeEEEcCceeecChhHeeEEeeChhhhhhhHhhcCCCccccCCcchhhhhhhhhhhhcccccCC
Confidence 99888754321100 0 0134689999999999999999999999999999999999999999999
Q ss_pred -------------------------------cceeEEeccc---------Ccc----------eeccCCcceeec----c
Q 003180 394 -------------------------------VTNYQFRMDT---------LAY----------VLYYPQKPLVTT----R 419 (842)
Q Consensus 394 -------------------------------~~n~~~R~Dt---------~~~----------~L~ypQ~PlV~t----~ 419 (842)
+.|+..|.|+ ..| .++|||+|||+| +
T Consensus 576 p~VgTg~E~~v~~ds~~~i~a~~~G~v~~v~~~~~~~r~d~~~~~~~~~~~~y~L~~~~~snq~~~~~q~Plv~~~~~v~ 655 (1065)
T TIGR02013 576 PLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRYDEDEDEPDGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVE 655 (1065)
T ss_pred CEEEcCcchhhhccccceeEeccCCEEEEEccceEEEEecCCcccccccceEEEeecccccccCceEEeeeeeccCCeEe
Confidence 8999999996 233 356999999999 5
Q ss_pred cccccc------CCCCCCCceeeEEeeeccCCCCCCceeeeccccccCceeEEEEEEEEeeehhcCCcccccccc--CCC
Q 003180 420 AMEHLH------FRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGR--PDR 491 (842)
Q Consensus 420 ~~~~~~------~~e~p~G~N~iVAvmsy~GYn~EDAiIiNk~si~rG~f~s~~~~~~~~~~~~~~~~~~e~~~~--p~~ 491 (842)
..+++. ++|+|+|+|++||||||+||||||||||||+|+|||+|||+||++|++++++...+ .|.|.. |+.
T Consensus 656 ~~~~l~d~~~~~~~e~~~G~N~~VAvm~y~GYn~EDAiiink~~i~rg~~~s~~~~~~~~~~~~~~~g-~e~~~~~~p~~ 734 (1065)
T TIGR02013 656 AGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLG-PEEITRDIPNV 734 (1065)
T ss_pred eeeEecccccccCCcCcCccceEEEEEeeecccccceEEeehhhhcCCceEEEEEEEEEEEeeccCCC-ceEeeccCCCC
Confidence 667654 99999999999999999999999999999999999999999999999998765443 355543 542
Q ss_pred CCCCCCCCCCccCCCCCCCcCCCcEEcCCCEEEEeeCCCCccccc---------cccCCCccceeeEEeeccccceEEeE
Q 003180 492 SNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ---------GQASRYTRRDHSISLRHSETGMVDQV 562 (842)
Q Consensus 492 ~~~~~~k~~~~~~Ld~dGl~~~G~~v~~gdvli~k~~~~~~~~~~---------~~~~~~~~~d~s~~~~~~e~g~Vd~V 562 (842)
+...|++||+||+|++|++|++|||||||++|....+.. ...+....+|+|++++.+++|+||+|
T Consensus 735 ------~~~~~~~Ld~dGi~~~G~~v~~gdilvgk~~p~~~~~~~~~~~l~~~~~~~~~~~~~d~s~~~~~~~~g~V~~V 808 (1065)
T TIGR02013 735 ------SEEALRNLDENGIVRIGAEVKAGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDV 808 (1065)
T ss_pred ------chhhhhccCCCCCccCccEeCCCCEEEEEecCCcccccChhhhhhhhhcccCCccccccceEccCCCCEEEEEE
Confidence 224699999999999999999999999999986421100 01112236899999999999999999
Q ss_pred EEeecCCC-------ceEEEEEEeeecCCcccccccccCCCcceeeeeecccCCCCCCCCCCceEEeCCCCCCCCCcHHH
Q 003180 563 LLTTNADG-------LRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQ 635 (842)
Q Consensus 563 ~~~~~~~~-------~~~v~v~~r~~R~p~iGDKfssRhGqKGvvs~i~~~~dmPft~~G~~pDiIiNPh~~PSRMtiGq 635 (842)
.++.++++ .+.|+|++|+.|+|+||||||||||||||||+|||+||||||+||++||||||||||||||||||
T Consensus 809 ~~~~~~~~~~~~~~~~~~vkv~ir~~R~p~iGDKfasRHGqKGvis~i~~~eDMPf~~~G~~pDiIiNPhg~PSRMtiGq 888 (1065)
T TIGR02013 809 KVFSRKQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQ 888 (1065)
T ss_pred EEEeccCCCccCcCccEEEEEEEeecccccccchhhhcccCceeEEeEecCCCCCccCCCCCccEEECCCCCcccccHHH
Confidence 99887666 46899999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhhhhcc--CCcceecC-CCCCCHHHHHHHHHHcCCCCCCeEEEeeCCCCcEEeeeEeEeeehhhhccCccCcc
Q 003180 636 LIECIMGKVAAHM--GKEGDATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDK 712 (842)
Q Consensus 636 l~E~~~gk~~~~~--g~~~d~tp-F~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if~G~~yy~rL~Hmv~DK 712 (842)
|+|+++||||++. |.+.++|| |++.+.+++.+.|+++||+++|+|.||||+||++|+++||+|++|||||+|||+||
T Consensus 889 llE~~~gka~~~~~~~~~~~~tp~f~~~~~~~~~~~l~~~g~~~~G~e~l~~G~TG~~~~~~ifvG~~yy~rL~HmV~DK 968 (1065)
T TIGR02013 889 ILETHLGWAGKRLGRKGVPIATPVFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDK 968 (1065)
T ss_pred HHHHHHHHHHHhccCCCeEEeccCcCCccHHHHHHHHHHcCCCCCCCEEEEcCCCCCCccccEEEeehheeechhhhcch
Confidence 9999999999987 67788999 99999999999999999999999999999999999999999999999999999999
Q ss_pred eEEeccCCccccccCCCCcccCCCcceeeehhhHHHHhhccHHHHHHhhhcCCCceeeeeccccCcceeecccCCceeec
Q 003180 713 IHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECR 792 (842)
Q Consensus 713 ~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~cG~~~~~~~~~~~~~C~ 792 (842)
+|||++||++.|||||++||+|+|||||||||||||+|||||++|+|||+.+||.+ ||+.. .++.
T Consensus 969 ~haRs~Gp~~~lT~QP~~Grsr~GG~R~GEME~d~l~a~Gas~~L~E~l~~~SD~~-------~g~~~--------~~~~ 1033 (1065)
T TIGR02013 969 MHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV-------VGRTK--------AYEA 1033 (1065)
T ss_pred hhhcccCCccceeeCCCcccccCCCeeeeeeeHHHHHhhhhHHHHHHHHhccChhh-------hhhhh--------hhhh
Confidence 99999999999999999999999999999999999999999999999999999965 45431 1234
Q ss_pred cCCCCCCceeecchHhHHHHHHHHHhCCCceEE
Q 003180 793 GCKNKTDIVQVHIPYACKLLFQELMAMAIAPRM 825 (842)
Q Consensus 793 ~C~~~~~i~~v~iPy~~kll~~EL~sm~I~~~l 825 (842)
.| ++..+.++.+|||||||+|||+||||++++
T Consensus 1034 ~~-~~~~i~~~~~p~sfklL~~EL~sm~i~~~~ 1065 (1065)
T TIGR02013 1034 IV-KGENVPEPGIPESFNVLIKELQSLGLDIEL 1065 (1065)
T ss_pred hc-CCCccccccCCccHHHHHHHHHhCCccccC
Confidence 45 567899999999999999999999999874
No 10
>PRK00405 rpoB DNA-directed RNA polymerase subunit beta; Reviewed
Probab=100.00 E-value=1.3e-181 Score=1656.36 Aligned_cols=678 Identities=31% Similarity=0.473 Sum_probs=598.2
Q ss_pred ccccCCCCCC--------cc----hHHHHHHHHHHHHHhhcCCCCCCCCCCccCCcEECchhHHHHHHHHHHHHHHHHHH
Q 003180 2 LPHVGTGDFC--------ET----KKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDV 69 (842)
Q Consensus 2 lpHl~~~~~~--------~~----~K~~~L~~Mi~kLl~~~~g~~~~Dd~D~~~nkRv~~~G~Ll~~lf~~~~~~~~~~~ 69 (842)
|||+|....+ .. .|++ +++|+++||.+..|...+||+|||+||||+++|+||+.+|+..|+++++.+
T Consensus 318 L~hiGr~k~nkKl~l~~~~~~~~L~~~d-~~~mi~~Ll~l~~g~~~~DDiDhl~NKRvr~aGeLL~~~fr~~~~rl~k~i 396 (1112)
T PRK00405 318 LSKVGRYKLNKKLGLDEDEDVRVLTKED-IIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERAV 396 (1112)
T ss_pred cccCCceecchhcccCcccccccccHHH-HHHHHHHHHhhhcccCCCcchhHHhcchhhhHHHHHHHHHHHHHHHHHHHH
Confidence 6999964322 11 3454 499999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhcCCCCchhccccccchhhhhhhhhccCccccccccccccceeEeccccChhhhhcccccccC----CcccC
Q 003180 70 RAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS----PIGRE 145 (842)
Q Consensus 70 ~~~~~~~~~~~~~~~~~~~~~~~~it~~i~~~~sTGnw~~~~~~~~~~G~sq~l~r~N~l~~lShlRrv~~----~~~~~ 145 (842)
++++.+. ..+.+++..+++++.||.+|++||+|| ||||+|||+||+++|||+||+++ ++.++
T Consensus 397 k~~l~~~--~~~~~~~~~lin~~~it~~i~~ff~tg------------glSQ~Ldq~NpLselshkRRlss~gpggl~r~ 462 (1112)
T PRK00405 397 RERMSLQ--DLDTLTPQDLINAKPVVAAIKEFFGSS------------QLSQFMDQTNPLSELTHKRRLSALGPGGLTRE 462 (1112)
T ss_pred HHHhhhc--ccccCCHHHhhCchhHHHHHHHhhccC------------CcceeeccCCHHHhhhhhceecccCCCCcCcc
Confidence 9988754 235678889999999999999999876 99999999999999999999998 68999
Q ss_pred CCcCCcccccCCCccccccCCCCCCCcchhhhhcccceEEecCCCchhHHHHHHHhCCccccccCCCCCCCcEEEEECCE
Q 003180 146 GKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGC 225 (842)
Q Consensus 146 ~K~t~~R~LhpS~wGfiCPveTPEG~~cGLvknLA~~a~Is~~~~~~~i~~~L~~~g~~~~~~~~~~~~~~~~~VflnG~ 225 (842)
++.++||+|||||||+|||+|||||++||||+|||++|+|+. +|.. + ..+.+++||.
T Consensus 463 ~a~~~~R~lH~ShyGriCPiETPEG~n~GLV~nLA~~a~i~~-------------~G~~--~--------tp~~~~~nG~ 519 (1112)
T PRK00405 463 RAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNE-------------YGFI--E--------TPYRKVVDGK 519 (1112)
T ss_pred ccCCcccccCccccccccCcCCCCCCccccccchhhcccccc-------------CCcc--c--------cceEEEECCe
Confidence 999999999999999999999999999999999999999984 2322 0 1267788987
Q ss_pred EEEEEcChHHHHHHHHHhhhcCCCCCcEEEEEeccCCeEEEecCCCeeeeeEEEeecccccccHHHHHHHhcCCCCCCCC
Q 003180 226 WVGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRESPEDGG 305 (842)
Q Consensus 226 ~iG~~~~~~~lv~~lR~lRr~~~i~~~vsi~~~~~~~~i~I~td~GRl~RPl~vv~n~~~~~~~~~~~~l~~~~~~~~~~ 305 (842)
| +
T Consensus 520 ~---~--------------------------------------------------------------------------- 521 (1112)
T PRK00405 520 V---T--------------------------------------------------------------------------- 521 (1112)
T ss_pred E---c---------------------------------------------------------------------------
Confidence 5 1
Q ss_pred chhccccCcEEEeccccccceeEeecccccccccCCCC---------c---CCCCceeeeeccCCccccccccccCCCCC
Q 003180 306 WHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPE---------E---AYADTYTHCEIHPSLILGVCASIIPFPDH 373 (842)
Q Consensus 306 ~~~l~~~g~IE~Id~~Eq~~~~Ia~~~~~l~~~~~~~k---------~---~~~~~~TH~EI~Ps~ilgv~AslIPF~~H 373 (842)
..|||+|++||+++.||....++.+.....+ + ..+..+||+||+|.+|+|++||||||+||
T Consensus 522 -------~~i~yl~a~eE~~~~Ia~~~~~l~~~~~~~~~~i~~r~~~e~~~~~~~~~~~~~i~p~qi~sv~aslIPFleH 594 (1112)
T PRK00405 522 -------DEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEH 594 (1112)
T ss_pred -------cceEECCHHHhcCcEEEecCcccCCCCcccCceEEEEecCcceeechhhceEEeechhhhceehhhccCcccc
Confidence 1278999999999999998877754221100 0 01346899999999999999999999999
Q ss_pred CCCccchhhhcccccccccccc-----------------------------------eeEEec-----------------
Q 003180 374 NQSPRNTYQSAMGKQAMGIYVT-----------------------------------NYQFRM----------------- 401 (842)
Q Consensus 374 NqSpRn~yq~~M~KQaig~~~~-----------------------------------n~~~R~----------------- 401 (842)
||||||+|||+|+|||||++.. |+..|.
T Consensus 595 nda~R~lmgSnMqrQAvpl~~~~~p~vgTg~e~~~~~ds~~~i~a~~~G~v~~v~~~~i~ir~~~~~~~~~~~~~y~L~~ 674 (1112)
T PRK00405 595 DDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIVVRVEELDPGEDGVDIYNLIK 674 (1112)
T ss_pred cCCcchhhhhhhhhhhhhhccccCCeeecCcchhhhhhcchheEeccCCEEEEEeCCEEEEeecccccCCCCeeEEEecc
Confidence 9999999999999999999988 898988
Q ss_pred ccCcce-eccCCcceeecc----ccccc------cCCCCCCCceeeEEeeeccCCCCCCceeeeccccccCceeEEEEEE
Q 003180 402 DTLAYV-LYYPQKPLVTTR----AMEHL------HFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRS 470 (842)
Q Consensus 402 Dt~~~~-L~ypQ~PlV~t~----~~~~~------~~~e~p~G~N~iVAvmsy~GYn~EDAiIiNk~si~rG~f~s~~~~~ 470 (842)
|+..++ ++|||+|||+|+ ..+++ +++|+|+|+|++||||||+||||||||||||+|+|||||+|+||++
T Consensus 675 ~~~sn~~~~~~q~Plv~~~~~v~~g~~lad~~~~~~~e~~~G~N~~VA~~~y~GYn~EDaiiink~si~rg~~~s~~~~~ 754 (1112)
T PRK00405 675 FQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEE 754 (1112)
T ss_pred cccccccceeecceeeecCCeEeeccEeecccccCcccccCCcceEEEEEeecccCccceEEEEhhhhccCceEEEEEee
Confidence 667777 899999999998 56765 7999999999999999999999999999999999999999999999
Q ss_pred EEeeehhcCCccccccc--cCCCCCCCCCCCCCccCCCCCCCcCCCcEEcCCCEEEEeeCCCCccccc---------ccc
Q 003180 471 YRDEEKKMGTLVKEDFG--RPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ---------GQA 539 (842)
Q Consensus 471 ~~~~~~~~~~~~~e~~~--~p~~~~~~~~k~~~~~~Ld~dGl~~~G~~v~~gdvli~k~~~~~~~~~~---------~~~ 539 (842)
|+.+++++..+. +.+. .|... ...|++||+||||++|++|++|||||||++|....+.. ...
T Consensus 755 ~~~~~~~~~~~~-~~~~~~~p~~~------~~~~~~Ld~dGi~~~G~~v~~gDiligk~~~~~~~~~~~~~~~~~~~~~~ 827 (1112)
T PRK00405 755 YEIEARDTKLGP-EEITRDIPNVS------EEALRNLDESGIVRIGAEVKPGDILVGKVTPKGETELTPEEKLLRAIFGE 827 (1112)
T ss_pred eeeEeeccCCCc-eeecccCCCCC------hHHhhccCCCCCccCccEecCCCEEEEEecCCCccccChhhhhhhhhhcc
Confidence 999987764443 3443 44321 23589999999999999999999999999986422110 011
Q ss_pred CCCccceeeEEeeccccceEEeEEEeec-CCC-------ceEEEEEEeeecCCcccccccccCCCcceeeeeecccCCCC
Q 003180 540 SRYTRRDHSISLRHSETGMVDQVLLTTN-ADG-------LRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPW 611 (842)
Q Consensus 540 ~~~~~~d~s~~~~~~e~g~Vd~V~~~~~-~~~-------~~~v~v~~r~~R~p~iGDKfssRhGqKGvvs~i~~~~dmPf 611 (842)
+....+|+|++++++++|+||+|.++.+ .++ .+.|+|++|+.|+|+||||||||||||||||+|||+|||||
T Consensus 828 ~~~~~~d~s~~~~~~~~g~V~~v~~~~~~~~~~~~~~~~~~~vkv~ir~~R~p~iGDKfasRHGqKGvis~i~~~eDMPf 907 (1112)
T PRK00405 828 KARDVKDTSLRVPHGEEGTVIDVKVFTRIEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPY 907 (1112)
T ss_pred cccccccceEEcCCCCCEEEEEEEEeeccccCCccCcCcceEEEEEEeeecccCcccchhhccCCceeEEeEeccCCCCc
Confidence 1223789999999999999999999877 555 46899999999999999999999999999999999999999
Q ss_pred CCCCCCceEEeCCCCCCCCCcHHHHHHHHhhhhhhccCCcceecC-CCCCCHHHHHHHHHHcCCCCCCeEEEeeCCCCcE
Q 003180 612 TVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRR 690 (842)
Q Consensus 612 t~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tp-F~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~ 690 (842)
|+||++|||||||||||||||||||+|+++||||++.|.+ |+|| |.+.+.+++++.|+++||+++|+|.||||+||++
T Consensus 908 ~~~G~~pDiIiNPhg~PSRMtiGql~E~~~gk~~~~~g~~-~~tp~f~~~~~~~~~~~l~~~g~~~~G~e~l~~G~tG~~ 986 (1112)
T PRK00405 908 LEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIK-FATPVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEP 986 (1112)
T ss_pred CCCCCCCcEEECCCCCcccccHHHHHHHHhhHHHHhcCCe-EecCccCCccHHHHHHHHHHcCcCCCCCEEEECCCCCCC
Confidence 9999999999999999999999999999999999999987 7888 9999999999999999999999999999999999
Q ss_pred EeeeEeEeeehhhhccCccCcceEEeccCCccccccCCCCcccCCCcceeeehhhHHHHhhccHHHHHHhhhcCCCceee
Q 003180 691 LTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRV 770 (842)
Q Consensus 691 ~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~ 770 (842)
|+++||+|++|||||+|||+||+|||++||++.|||||++||+|+|||||||||||||+|||||++|+|||+.+||.+.
T Consensus 987 ~~~~if~G~~yy~rL~HmV~DK~haRs~Gp~~~lT~QP~~Grsr~GG~R~GEME~d~l~a~Gas~~L~Erl~~~SD~~~- 1065 (1112)
T PRK00405 987 FDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVV- 1065 (1112)
T ss_pred CcccEEEEehhheechhhhcchhhhcccCCccceeeCCCcccccCCCeeeeeeehhhHhhhhhHHHHHHHhhccCcccc-
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999999754
Q ss_pred eeccccCcceeecccCCceeeccCCCCCCceeecchHhHHHHHHHHHhCCCceEEE
Q 003180 771 HVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRML 826 (842)
Q Consensus 771 ~vC~~cG~~~~~~~~~~~~~C~~C~~~~~i~~v~iPy~~kll~~EL~sm~I~~~l~ 826 (842)
|+.. .+.| .| ++..+.++.+|||||||+|||+||||++++.
T Consensus 1066 ------g~~~-------~~~~-~~-~~~~i~~~~~p~~fklL~~EL~sm~i~~~~~ 1106 (1112)
T PRK00405 1066 ------GRTK-------VYEA-IV-KGENIPEPGIPESFNVLVKELQSLGLDVELL 1106 (1112)
T ss_pred ------ccee-------EEEE-ee-cCCcccccCCChHHHHHHHHHHHCccceEEe
Confidence 5433 2346 56 5678999999999999999999999999998
No 11
>CHL00001 rpoB RNA polymerase beta subunit
Probab=100.00 E-value=9.2e-177 Score=1597.59 Aligned_cols=696 Identities=27% Similarity=0.419 Sum_probs=596.3
Q ss_pred ccccCCCCCCcc------hHHHHH-----HHHHHHHHhhcCCCCCCCCCCccCCcEECchhHHHHHHHHHHHHHHHHHHH
Q 003180 2 LPHVGTGDFCET------KKAYYF-----GYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVR 70 (842)
Q Consensus 2 lpHl~~~~~~~~------~K~~~L-----~~Mi~kLl~~~~g~~~~Dd~D~~~nkRv~~~G~Ll~~lf~~~~~~~~~~~~ 70 (842)
|+|+|....|.. .|+.+| ++|+++|+.+..|...+||+|||+||||+++|+||+.+||..|+++++.++
T Consensus 258 Lg~vGr~~~n~kl~~~~~~~~~~L~~~Di~~~i~~Ll~l~~G~~~~DDiDhLgNKRvr~vGeLL~~qfr~~l~r~~r~ik 337 (1070)
T CHL00001 258 LGRIGRRNMNRKLNLDIPENNTFLLPQDVLAAADYLIGMKFGMGTLDDIDHLKNKRIRSVADLLQDQFGLALNRLENAVR 337 (1070)
T ss_pred ccccCchhhhhhhcccccccceEecHHHHHHHHHHHHHhhcCCCCccchhHHhccccchHHHHHHHHHHHHHHHHHHHHH
Confidence 344886554433 577878 999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhcCCCCchhccccccchhhhhhhhhccCccccccccccccceeEeccccChhhhhcccccccC--CcccCCCc
Q 003180 71 AYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS--PIGREGKL 148 (842)
Q Consensus 71 ~~~~~~~~~~~~~~~~~~~~~~~it~~i~~~~sTGnw~~~~~~~~~~G~sq~l~r~N~l~~lShlRrv~~--~~~~~~K~ 148 (842)
+++.+.+.+.+.+++..+++++.||.+|++||+| +|+||+|||+||+++|||+||+++ |.+.+++.
T Consensus 338 ~~m~~~~~~~~~~~~~~lin~~~It~~ik~ff~t------------s~LSQflDqtNpLseltHkRRlsslGpgglsr~~ 405 (1070)
T CHL00001 338 GTICGAIRRKLIPTPQNLVTSTPLTTTYESFFGS------------HPLSQFLDQTNPLTEIVHGRKLSSLGPGGLTGRT 405 (1070)
T ss_pred HHHHHHhcccccCCHHHhhCcchHHHHHHhhhcC------------CcceeeeccCCHHHhhhhhhcccccCCCCccccc
Confidence 9998766555677899999999999999999984 799999999999999999999998 88888887
Q ss_pred C--CcccccCCCccccccCCCCCCCcchhhhhcccceEEe-cCCCchhHHHHHHHhCCccccccCCCCCCCcEEEEECCE
Q 003180 149 A--KPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYIT-VGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGC 225 (842)
Q Consensus 149 t--~~R~LhpS~wGfiCPveTPEG~~cGLvknLA~~a~Is-~~~~~~~i~~~L~~~g~~~~~~~~~~~~~~~~~VflnG~ 225 (842)
+ +||++||||||+|||+|||||++||||+|||++|+|+ .|..++|+.+++...+...+..+++.. ...++|+ ||.
T Consensus 406 a~fevRdvHpShyGRICPIETPEG~NiGLI~sLA~~A~In~~GfietP~~~v~~~~~~~~i~ylsa~e-e~~~~Ia-~g~ 483 (1070)
T CHL00001 406 ASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIGHWGSLESPFYEISERSKEERMVYLSPSE-DEYYMIA-AGN 483 (1070)
T ss_pred cCCcccccCccccccccCCCCCCcccccchhhhhhhcccccCCCcccceeeeccccccceeEEccccc-cCceEEE-eCc
Confidence 7 9999999999999999999999999999999999999 589999999998776666665554443 4567888 999
Q ss_pred EEEEEcChHHHHHHHHHhhhcCCCCCcEEEEEeccCCeEEEecCCCeeeeeEEEeecccccccHHHHHHHhcCCCCCCCC
Q 003180 226 WVGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRESPEDGG 305 (842)
Q Consensus 226 ~iG~~~~~~~lv~~lR~lRr~~~i~~~vsi~~~~~~~~i~I~td~GRl~RPl~vv~n~~~~~~~~~~~~l~~~~~~~~~~ 305 (842)
|+|...+. +. +-++..
T Consensus 484 ~~~~~~~~---------------~~-------------------------~~~~~~------------------------ 499 (1070)
T CHL00001 484 SLALNQGI---------------QE-------------------------EQVVPA------------------------ 499 (1070)
T ss_pred eeeccCCc---------------cc-------------------------cceeEE------------------------
Confidence 98842210 00 000000
Q ss_pred chhccccCcEEEeccccccceeEeecccccccccCCCCcCCCCceeeeeccCCccccccccccCCCCCCCCccchhhhcc
Q 003180 306 WHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAM 385 (842)
Q Consensus 306 ~~~l~~~g~IE~Id~~Eq~~~~Ia~~~~~l~~~~~~~k~~~~~~~TH~EI~Ps~ilgv~AslIPF~~HNqSpRn~yq~~M 385 (842)
.+ -+++.+|+.. +.|||||+|.+|+||+||||||+||||||||+|||||
T Consensus 500 ----------r~----~~e~~~i~~~-----------------~i~~~dIsP~qi~svaasLIPFleHndanRalmgsnM 548 (1070)
T CHL00001 500 ----------RY----RQEFLTIAWE-----------------QIHLRSIFPFQYFSIGASLIPFLEHNDANRALMGSNM 548 (1070)
T ss_pred ----------Ee----cCeEEEEchH-----------------HCcEEeeChhhhhhhhhhcCCCccccCcchhhhhhcc
Confidence 00 0123444332 3689999999999999999999999999999999999
Q ss_pred cccccccccce---------eEEec-----------------c-----------c-Ccceecc---------CCcceeec
Q 003180 386 GKQAMGIYVTN---------YQFRM-----------------D-----------T-LAYVLYY---------PQKPLVTT 418 (842)
Q Consensus 386 ~KQaig~~~~n---------~~~R~-----------------D-----------t-~~~~L~y---------pQ~PlV~t 418 (842)
+|||||++..| +..|. | + ..|++.| ||+|||++
T Consensus 549 qrQAvpll~~~~p~VgTG~E~~~~~ds~~~i~a~~~G~V~~vd~~~I~i~~~~~~~~y~l~~y~rsnq~t~~~QkPlV~~ 628 (1070)
T CHL00001 549 QRQAVPLSRSEKCIVGTGLERQVALDSGVVAIAEHEGKIIYTDTDKIILSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRR 628 (1070)
T ss_pred chhccccccCCCCEeecCcchhhhhcccceeEEccCCEEEEEeCCEEEEEcCCCeEEEEeeceeccCCCcccccCCEEec
Confidence 99999999988 77777 6 4 4566778 99999999
Q ss_pred ccccccc------------CCCCCCCceeeEEeeeccCCCCCCceeeeccccccCceeEEEEEEEEeeehhcCCcccccc
Q 003180 419 RAMEHLH------------FRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDF 486 (842)
Q Consensus 419 ~~~~~~~------------~~e~p~G~N~iVAvmsy~GYn~EDAiIiNk~si~rG~f~s~~~~~~~~~~~~~~~~~~e~~ 486 (842)
+ +.++ .+|+|+|+|++||||||+||||||||||||+|++||+|||+||++|+++++++..+ .|.+
T Consensus 629 g--~~v~~g~~ladg~~~~~gel~~G~N~~VA~m~~~GYn~EDAiiin~~~v~~g~~~s~~~~~~~~~~~~~~~g-~e~i 705 (1070)
T CHL00001 629 G--KCVKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQG-PERI 705 (1070)
T ss_pred C--CEEccCCEeccChhhccccccCCccceeeeeeccccccchhhhhhhhhhcCCceEEEEEeeeeEEEeccCCC-cceE
Confidence 7 6665 89999999999999999999999999999999999999999999999999876544 3666
Q ss_pred cc--CCCCCCCCCCCCCccCCCCCCCcCCCcEEcCCCEEEEeeCCCCcccc--cc---------ccCCCccceeeEEeec
Q 003180 487 GR--PDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEA--QG---------QASRYTRRDHSISLRH 553 (842)
Q Consensus 487 ~~--p~~~~~~~~k~~~~~~Ld~dGl~~~G~~v~~gdvli~k~~~~~~~~~--~~---------~~~~~~~~d~s~~~~~ 553 (842)
.. |+.. ...|++||+||++++|++|++|||||||++|....+. .. ..+....+|+|+++++
T Consensus 706 ~~~~p~~~------~~~~~~Ld~dGi~~~G~~v~~gDilvgK~~p~~~~~~~~~~~~~~~~~if~~~~~~~~d~sl~~~~ 779 (1070)
T CHL00001 706 TKEIPHLE------AHLLRNLDKNGIVMLGSWVETGDILVGKLTPQEAEESSYAPEGRLLRAIFGIQVSTSKETCLKLPI 779 (1070)
T ss_pred eccCCCCc------hhhhhccCCCCCccCCcEecCCCEEEEEecCCcccccccCcchhhhhhhhccccCcceeCeEECCC
Confidence 53 5432 2358999999999999999999999999999631111 00 1122347899999999
Q ss_pred cccceEEeEEEeec----CCCceEEEEEEeeecCCcccccccccCCCcceeeeeecccCCCCCCCCCCceEEeCCCCCCC
Q 003180 554 SETGMVDQVLLTTN----ADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPS 629 (842)
Q Consensus 554 ~e~g~Vd~V~~~~~----~~~~~~v~v~~r~~R~p~iGDKfssRhGqKGvvs~i~~~~dmPft~~G~~pDiIiNPh~~PS 629 (842)
+++|+|++|.+++. .++.+.|||++|+.|+|++|||||||||||||||+|||+||||||+||++||||||||||||
T Consensus 780 ~~~g~V~~v~~~~~~~~~~~~~~~vkv~i~~~R~~~vGDK~asRHGqKGvvs~i~~~eDMPf~~dG~~pDiIlNP~gvPS 859 (1070)
T CHL00001 780 GGRGRVIDVRWIQKKGGSSYNPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPS 859 (1070)
T ss_pred CCceEEEEEEEEecccCCCCCcEEEEEEEEEEecCCCCcccccccCCcceEeeeecccCCCcccCCCCCceeeccccccc
Confidence 99999999998873 45678999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcHHHHHHHHhhhhhhccCCcceecCCCCCCHHHHH-----HHHHHcCC----------CCCCeEEEeeCCCCcEEeee
Q 003180 630 RMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNIS-----KALHKCGY----------QMRGFETMYNGHTGRRLTAM 694 (842)
Q Consensus 630 RMtiGql~E~~~gk~~~~~g~~~d~tpF~~~~~~~~~-----~~l~~~g~----------~~~G~e~ly~g~tG~~~~~~ 694 (842)
|||||||+|+++||||++.|.+.|++||++...+++. ..|.++|+ +++|+|.||||+||++|+++
T Consensus 860 RMtiGqllE~~~G~a~~~~g~~~~~~pf~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~Gk~~l~dG~TG~~~~~~ 939 (1070)
T CHL00001 860 RMNVGQIFECLLGLAGDLLNRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRLFDGRTGDPFEQP 939 (1070)
T ss_pred cccHHHHHHHHhHHHHhhcCceeeeccCCCcchhhhhhhhhhHHHHHHHHhcCCceeccCCCCCeEEEEcCCCCCCccce
Confidence 9999999999999999999999999999987776666 56777776 44599999999999999999
Q ss_pred EeEeeehhhhccCccCcceEEeccCCccccccCCCCcccCCCcceeeehhhHHHHhhccHHHHHHhhhcCCCceeeeecc
Q 003180 695 IFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCE 774 (842)
Q Consensus 695 if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~ 774 (842)
||+|++|||||+|||+||+|||++|||+.|||||++||+|+|||||||||||||+|||||++|+|||+.+||.....
T Consensus 940 i~vG~~Yy~kL~HmV~DKihaRs~Gp~~~lT~QP~~Grsr~GG~RfGEME~~al~a~GAs~~L~E~L~~~SD~~~~r--- 1016 (1070)
T CHL00001 940 VTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRAR--- 1016 (1070)
T ss_pred EEEEecceeEchhhccccceeeccCCCcccccCCCCcccCCCCeeeecchHHHHHhhhHHHHHHHHHhccCccHHHH---
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999975532
Q ss_pred ccCcceeecccCCceeeccCCCCCCcee-ecchHhHHHHHHHHHhCCCceEEEEccCC
Q 003180 775 HCGLIAIANLKKNSFECRGCKNKTDIVQ-VHIPYACKLLFQELMAMAIAPRMLTKEDT 831 (842)
Q Consensus 775 ~cG~~~~~~~~~~~~~C~~C~~~~~i~~-v~iPy~~kll~~EL~sm~I~~~l~~~~~~ 831 (842)
|+. +.|..+ +..+.+ +.+||+||+|++||+|||+++++..-+.-
T Consensus 1017 -~~~----------~~~i~~--g~~~~~~~~~pesfk~l~~El~~l~l~i~~~~~~~~ 1061 (1070)
T CHL00001 1017 -QEV----------LGAIIT--GGTIPKPEDAPESFRLLVRELRSLALELNHFLVSEK 1061 (1070)
T ss_pred -HHH----------HHhhhc--CCcccCCCCCCchhhHHHHHHHhCccceEEEEEecc
Confidence 211 112222 335666 79999999999999999999999875443
No 12
>CHL00207 rpoB RNA polymerase beta subunit; Provisional
Probab=100.00 E-value=8e-165 Score=1485.41 Aligned_cols=675 Identities=28% Similarity=0.440 Sum_probs=570.3
Q ss_pred CcchHHHHHHHHHHHHHhhcCCCCCCCCCCccCCcEECchhHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCchhcccc
Q 003180 11 CETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIK 90 (842)
Q Consensus 11 ~~~~K~~~L~~Mi~kLl~~~~g~~~~Dd~D~~~nkRv~~~G~Ll~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 90 (842)
.+.-++.-++.|+++|+.+..|....||+|||+||||+++|+|++.+|+..|.++.+.+++++.... .+.+++..+++
T Consensus 272 ~~~l~~~Dil~~i~~Li~l~~g~~~~DDiDHL~NRRvrsvGELlq~qfr~gl~rler~ike~m~~~~--~~~~tp~~lin 349 (1077)
T CHL00207 272 VRNLTYEDILSIIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTICD--IDSLSKFNLIN 349 (1077)
T ss_pred CceecHHHHHHHHHHHHHhhcCCCcccchhhhhcccccchhHHHHHHHHHHHHHHHHHHHHHhhhcc--cccCChhhccc
Confidence 3455667788999999999998889999999999999999999999999999999999999987542 24567888999
Q ss_pred ccchhhhhhhhhccCccccccccccccceeEeccccChhhhhcccccccC----CcccCCCcCCcccccCCCccccccCC
Q 003180 91 AKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS----PIGREGKLAKPRQLHNSQWGMMCPAE 166 (842)
Q Consensus 91 ~~~it~~i~~~~sTGnw~~~~~~~~~~G~sq~l~r~N~l~~lShlRrv~~----~~~~~~K~t~~R~LhpS~wGfiCPve 166 (842)
++.+|..|+.||+ ++++||++||+|||++|+|+||+++ .+.+++..+++|++||||||+|||+|
T Consensus 350 ~k~lt~~ikeFFg------------ss~LSQfmDQtNpLselTHKRRlsaLGpGGLsR~ra~fevRdvH~thyGRiCPIE 417 (1077)
T CHL00207 350 PKPLIALIREFFG------------SSQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISFAVRDIHPSHYGRICPIE 417 (1077)
T ss_pred chhHHHHHHHhhc------------cCCccceecccChHHhhhccceeeccCCCcccccccCCcccccCccccccccCCC
Confidence 9999999999996 7899999999999999999999997 56788889999999999999999999
Q ss_pred CCCCCcchhhhhcccceEEec-CCCchhHHHHHHHhCCccccccCCCCCCCcEEEEECCEEEEEEcChHHHHHHHHHhhh
Q 003180 167 TPEGQACGLVKNLALMVYITV-GSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKTLRRLRR 245 (842)
Q Consensus 167 TPEG~~cGLvknLA~~a~Is~-~~~~~~i~~~L~~~g~~~~~~~~~~~~~~~~~VflnG~~iG~~~~~~~lv~~lR~lRr 245 (842)
||||++||||++||.+|.|+. |..+.| ..+| .||.+.
T Consensus 418 TPEG~n~Gli~~la~~~~in~~GfietP-----------------------y~~v-~~g~v~------------------ 455 (1077)
T CHL00207 418 TPEGPNCGLIGSLATNARINKFGFIETP-----------------------FYKV-INGKVK------------------ 455 (1077)
T ss_pred CCCCcccccccchhhhccccCCCceeCc-----------------------eEEE-EcCccc------------------
Confidence 999999999999999999976 443333 1223 344320
Q ss_pred cCCCCCcEEEEEeccCCeEEEecCCCeeeeeEEEeecccccccHHHHHHHhcCCCCCCCCchhccccCcEEEeccccccc
Q 003180 246 RVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRESPEDGGWHDLVAKGFIEYIDTEEEET 325 (842)
Q Consensus 246 ~~~i~~~vsi~~~~~~~~i~I~td~GRl~RPl~vv~n~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~g~IE~Id~~Eq~~ 325 (842)
....++|++|.||+.
T Consensus 456 -----------------------------------------------------------------~~~~i~ylsa~~e~~ 470 (1077)
T CHL00207 456 -----------------------------------------------------------------KFGNPIYLTADSEDL 470 (1077)
T ss_pred -----------------------------------------------------------------ccCceeecChHHhcC
Confidence 002356777777777
Q ss_pred eeEeecccccccccCCC---------C---cCCCCceeeeeccCCccccccccccCCCCCCCCccchhhhcccccccccc
Q 003180 326 TMISMTINDLVQARLHP---------E---EAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIY 393 (842)
Q Consensus 326 ~~Ia~~~~~l~~~~~~~---------k---~~~~~~~TH~EI~Ps~ilgv~AslIPF~~HNqSpRn~yq~~M~KQaig~~ 393 (842)
..||.....+.+..... . ...+.+.++++++|.+++|++||||||.+||+++|++|++||++||+|+.
T Consensus 471 ~~Ia~~~~~~~~~~~~~~~~v~~r~~~ef~~~~~~~v~~~~vsp~Q~~SvaasLIPFLehdDanRaLMGsnMqrQaVPll 550 (1077)
T CHL00207 471 YRIAPNDINLNKNNYFKKNIIPVRYKQEFKTVNPSKVDFIAISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLL 550 (1077)
T ss_pred cEEEecCccCCCCCcccCCEEEEEECCcEEEEChHHceEEEeCcchhcchhhhcCCcccccccchhhhhhcccccccccc
Confidence 77775543333211100 0 00134578999999999999999999999999999999999999999985
Q ss_pred cce-----------------------------------eEEeccc---Cccee----------ccCCcceeeccc----c
Q 003180 394 VTN-----------------------------------YQFRMDT---LAYVL----------YYPQKPLVTTRA----M 421 (842)
Q Consensus 394 ~~n-----------------------------------~~~R~Dt---~~~~L----------~ypQ~PlV~t~~----~ 421 (842)
..+ +..+.|. ..|.| ++.|||+|+.+. .
T Consensus 551 ~~e~p~VgTg~e~~~a~ds~~~i~a~~~G~v~~v~~~~I~i~~~~~~~~~y~l~~~~rsNq~t~i~qrp~V~~G~~v~~G 630 (1077)
T CHL00207 551 YPEKPIVGTGYEKQIALDSGMTIISLTEGIVVSVSAYKIIIQDDNNRYIHYYLQKYQRSNQNTCINYRPIVWVGEKINIG 630 (1077)
T ss_pred ccCCCeEECCcchHhhhhcchheEeccCcEEEEecCcEEEEEeCCCceeEEEeccccccccCceeecccccCCCCEEecC
Confidence 321 1122211 12333 579999998742 2
Q ss_pred c------cccCCCCCCCceeeEEeeeccCCCCCCceeeeccccccCceeEEEEEEEEeeehhcCCccccccc--cCCCCC
Q 003180 422 E------HLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFG--RPDRSN 493 (842)
Q Consensus 422 ~------~~~~~e~p~G~N~iVAvmsy~GYn~EDAiIiNk~si~rG~f~s~~~~~~~~~~~~~~~~~~e~~~--~p~~~~ 493 (842)
+ .+.++|+|+|+|++||||||+||||||||||||++++||+|||+|+++|+.+++.+..+ .|.|. .|...
T Consensus 631 ~iladg~~~~~~el~lG~N~lVA~m~y~GYN~EDAiiink~~v~rg~f~Si~~~~~~~e~~~~~~g-~e~i~~~~p~~~- 708 (1077)
T CHL00207 631 QILADGSDIDNSELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEKYEIELRQTKLG-SEEITRNIPNVS- 708 (1077)
T ss_pred CEEecchhccCCcccCCcccEEEEEeeeccccchhhhhhhhhhcCCceEEEEEEEeeeEEeecCCC-ceEEeccCCCCC-
Confidence 2 24799999999999999999999999999999999999999999999999998765443 35565 45421
Q ss_pred CCCCCCCCccCCCCCCCcCCCcEEcCCCEEEEeeCCCCccccc---------cccCCCccceeeEEeeccccceEEeEEE
Q 003180 494 TMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ---------GQASRYTRRDHSISLRHSETGMVDQVLL 564 (842)
Q Consensus 494 ~~~~k~~~~~~Ld~dGl~~~G~~v~~gdvli~k~~~~~~~~~~---------~~~~~~~~~d~s~~~~~~e~g~Vd~V~~ 564 (842)
...|++||+||||++|++|++|||||||++|....+.. ...+....+|+|++++++++|+|++|.+
T Consensus 709 -----~~~~~~LD~dGiv~iG~~V~~gDilvgK~tp~~~~~~~~~~~ll~~i~~~~~~~~kd~sl~~~~~~~g~V~~V~~ 783 (1077)
T CHL00207 709 -----EYSLKNLDENGIISIGSKVLAGDILVGKITPKGESDQLPEGKLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEI 783 (1077)
T ss_pred -----hHHhhccCccCCCcCCcEeCCCCEEEEEecCccccccChhhhhhhhhhccCCCcceEeEEEcCCCCcEEEEEEEE
Confidence 23589999999999999999999999999985421110 0112234799999999999999999999
Q ss_pred eecCC--Cc-----eEEEEEEeeecCCcccccccccCCCcceeeeeecccCCCCCCCCCCceEEeCCCCCCCCCcHHHHH
Q 003180 565 TTNAD--GL-----RFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLI 637 (842)
Q Consensus 565 ~~~~~--~~-----~~v~v~~r~~R~p~iGDKfssRhGqKGvvs~i~~~~dmPft~~G~~pDiIiNPh~~PSRMtiGql~ 637 (842)
+.+++ +. ..|+|.+|+.|+|+||||||||||||||||+|||+|||||++||++|||||||||||||||||||+
T Consensus 784 ~~~~~~~~~~~~~~~~vkv~i~~~R~p~vGDKfasRHGqKGVvs~i~p~eDMPf~~dG~~pDiIlNPhg~PSRMtiGqll 863 (1077)
T CHL00207 784 FSRSKGDELKFGYYLKIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLF 863 (1077)
T ss_pred EecCCCCcccccccEEEEEEEEEEecCCcccccccccCCceeEEeeeccCCCCccCCCCCccEEECCccccccccHHHHH
Confidence 87533 22 358889999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhhhhhccCCcceecCCCCCCHHHHHHHHHHc---------------CCCCCCeEEEeeCCCCcEEeeeEeEeeehh
Q 003180 638 ECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKC---------------GYQMRGFETMYNGHTGRRLTAMIFLGPTYY 702 (842)
Q Consensus 638 E~~~gk~~~~~g~~~d~tpF~~~~~~~~~~~l~~~---------------g~~~~G~e~ly~g~tG~~~~~~if~G~~yy 702 (842)
|+++||||++.|...+++||++.+.+++.+.|.+. +|+++|++.||||+||++|+++||+|++||
T Consensus 864 E~~lGka~~~l~~~~~~tpF~~~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~Gk~~lydG~TGe~~~~~i~vG~~Yy 943 (1077)
T CHL00207 864 ECLLGLAGDNLNKRFKILPFDEMYGSEYSRILINNKLNQASIKNNEYWLFNSYHPGKMVLRDGRTGYKFKNPVTVGIAYM 943 (1077)
T ss_pred HHHHHHHHHhcCCcEeeccCCCCcHHHHHHHHHhhhhhhccchhccccccCCCCCCCEEEECCCCCCCccCceEEEecce
Confidence 99999999998888899999998888888777654 377899999999999999999999999999
Q ss_pred hhccCccCcceEEeccCCccccccCCCCcccCCCcceeeehhhHHHHhhccHHHHHHhhhcCCCceeeeeccccCcceee
Q 003180 703 QRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIA 782 (842)
Q Consensus 703 ~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~cG~~~~~ 782 (842)
|||+|||+||+|||++|||+.|||||++||+|+|||||||||||||+|||||++|+|||+.+||.+..
T Consensus 944 ~kL~HmV~DKihaRs~Gp~s~lTqQP~~Grsr~GG~RfGEME~~aL~a~GAa~~L~E~L~~kSD~~~~------------ 1011 (1077)
T CHL00207 944 LKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSDDMQG------------ 1011 (1077)
T ss_pred eEchhhccccceeeccCCCcccccCCCCccccCCCeeeecccHHHHHhhhhHHHHHHHhhcCCcccee------------
Confidence 99999999999999999999999999999999999999999999999999999999999999997762
Q ss_pred cccCCceeeccCCCCCCceeecchHhHHHHHHHHHhCCCceEEEEcc
Q 003180 783 NLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKE 829 (842)
Q Consensus 783 ~~~~~~~~C~~C~~~~~i~~v~iPy~~kll~~EL~sm~I~~~l~~~~ 829 (842)
...+|..|.++.++.++.+|||||+|+|||+||||.+++.-..
T Consensus 1012 ----r~~~~~~~~~~~~i~~~~~P~sfklL~~EL~sl~i~~~~~~~~ 1054 (1077)
T CHL00207 1012 ----RNETLNAIVKGQPIPKPGTPESFKVLMRELQSLGLDIEAYKIE 1054 (1077)
T ss_pred ----hHHHHHhhhCCCeecCCCCCchHHHHHHHHHHCCcCcEecccc
Confidence 1235999988889999999999999999999999999998644
No 13
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=100.00 E-value=8.8e-152 Score=1414.67 Aligned_cols=667 Identities=28% Similarity=0.434 Sum_probs=564.4
Q ss_pred HHHHHHHHhhcCCCCCCCCCCccCCcEECchhHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCchhccccccchhhhhh
Q 003180 20 GYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLK 99 (842)
Q Consensus 20 ~~Mi~kLl~~~~g~~~~Dd~D~~~nkRv~~~G~Ll~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~it~~i~ 99 (842)
...++.|+.+..|....||+|||+||||+++|+||+.+|+..|.++.+.+++++.........+++..+++++.++..++
T Consensus 438 l~~i~~li~l~~g~~~~DDiDhL~NRRvr~vGELl~~qfr~gl~rler~irerm~~~~~~~~~~~p~~lin~k~i~~~ik 517 (2890)
T PRK09603 438 ITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELHSGLVKMQKTIKDKLTTMSGAFDSLMPHDLVNSKMITSTIM 517 (2890)
T ss_pred HHHHHHHHHHHhCCCCCCcchhhhcchhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccChhhhhccHHHHHHHH
Confidence 37789999999999999999999999999999999999999999999999999875433345667888999999999999
Q ss_pred hhhccCccccccccccccceeEeccccChhhhhcccccccC--C--cccCCCcCCcccccCCCccccccCCCCCCCcchh
Q 003180 100 YSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS--P--IGREGKLAKPRQLHNSQWGMMCPAETPEGQACGL 175 (842)
Q Consensus 100 ~~~sTGnw~~~~~~~~~~G~sq~l~r~N~l~~lShlRrv~~--~--~~~~~K~t~~R~LhpS~wGfiCPveTPEG~~cGL 175 (842)
.||. ++.+||++|++|+++.|+|.||+++ | +.+++..+++|++||||||+|||+|||||++|||
T Consensus 518 eFFg------------ssqLSQfmDQtNpLseltHKRRlSaLGPGGlsr~ra~fevRdVH~shYGRiCPIETPEG~NiGL 585 (2890)
T PRK09603 518 EFFM------------GGQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGL 585 (2890)
T ss_pred HHhc------------cCchhhhhcccChhhhhhhcccccccCCCCccccccCCcccccCcccccccCCCCCCCCCcccc
Confidence 9996 4569999999999999999999985 4 4577788899999999999999999999999999
Q ss_pred hhhcccceEEec-CCCchhHHHHHHHhCCccccccCCCCCCCcEEEEECCEEEEEEcChHHHHHHHHHhhhcCCCCCcEE
Q 003180 176 VKNLALMVYITV-GSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKTLRRLRRRVDVNTEVG 254 (842)
Q Consensus 176 vknLA~~a~Is~-~~~~~~i~~~L~~~g~~~~~~~~~~~~~~~~~VflnG~~iG~~~~~~~lv~~lR~lRr~~~i~~~vs 254 (842)
|++||.+|+|+. |+.++| +.+| .||.+ +
T Consensus 586 I~SLa~~a~in~~GfietP-----------------------y~kV-~~g~v---~------------------------ 614 (2890)
T PRK09603 586 INTLSTFTRVNDLGFIEAP-----------------------YKKV-VDGKV---V------------------------ 614 (2890)
T ss_pred hhhhhhheecccCcceecc-----------------------eEEE-ecCcc---c------------------------
Confidence 999999999987 444333 2333 34432 0
Q ss_pred EEEeccCCeEEEecCCCeeeeeEEEeecccccccHHHHHHHhcCCCCCCCCchhccccCcEEEeccccccceeEeecccc
Q 003180 255 VVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRESPEDGGWHDLVAKGFIEYIDTEEEETTMISMTIND 334 (842)
Q Consensus 255 i~~~~~~~~i~I~td~GRl~RPl~vv~n~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~g~IE~Id~~Eq~~~~Ia~~~~~ 334 (842)
..++|++|.||+...||.....
T Consensus 615 ----------------------------------------------------------~~i~ylsa~eE~~~~IA~a~~~ 636 (2890)
T PRK09603 615 ----------------------------------------------------------GETIYLTAIQEDSHIIAPASTP 636 (2890)
T ss_pred ----------------------------------------------------------cceeeeCHHHhcCceEeccCCc
Confidence 1245666666666666654433
Q ss_pred cccccCCCC---------c---CCCCceeeeeccCCccccccccccCCCCCCCCccchhhhcccccccccccc-------
Q 003180 335 LVQARLHPE---------E---AYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVT------- 395 (842)
Q Consensus 335 l~~~~~~~k---------~---~~~~~~TH~EI~Ps~ilgv~AslIPF~~HNqSpRn~yq~~M~KQaig~~~~------- 395 (842)
+.+.+...+ + ..+...++++++|.+++||+||||||.+||+++|++|+|||++||+|+...
T Consensus 637 ~~~~~~~~~~~v~~R~~~e~~~~~~~~v~~~dvsp~Q~vSvaasLIPFLEhdDAnRALMGSNMQRQAVPLl~~e~piVgT 716 (2890)
T PRK09603 637 IDEEGNILGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGT 716 (2890)
T ss_pred cCCCCcccCCeEeEEECCceEEEChHHceEEEeCccceeeehhhcCCccccCccccccccccchhhhhhhccccCCeEec
Confidence 322111100 0 013457899999999999999999999999999999999999999998521
Q ss_pred ----------------------------eeEEeccc------Cccee----------ccCCcceeeccc----cc-----
Q 003180 396 ----------------------------NYQFRMDT------LAYVL----------YYPQKPLVTTRA----ME----- 422 (842)
Q Consensus 396 ----------------------------n~~~R~Dt------~~~~L----------~ypQ~PlV~t~~----~~----- 422 (842)
.+..|.+. ..|.| ++.|+|+|+.+. .+
T Consensus 717 G~E~~va~dSg~~i~a~~~G~V~yvd~~~I~i~~~~~~~~~~~~Y~L~Ky~RSNQ~TcinqrPiV~~Gd~V~kGdilADG 796 (2890)
T PRK09603 717 GIEKIIARDSWGAIKANRAGVVEKIDSKNIYILGEGKEEAYIDAYSLQKNLRTNQNTSFNQVPIVKVGDKVEAGQIIADG 796 (2890)
T ss_pred CcchhhhccccceeEecCCeEEEEecCcEEEEEecCCCCceeeEEeeccccccCCCceeeeccEecCCCEeccCCEEecC
Confidence 12222221 12544 579999998642 22
Q ss_pred -cccCCCCCCCceeeEEeeeccCCCCCCceeeeccccccCceeEEEEEEEEeeehhcCCcccccc--ccCCCCCCCCCCC
Q 003180 423 -HLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDF--GRPDRSNTMGMRH 499 (842)
Q Consensus 423 -~~~~~e~p~G~N~iVAvmsy~GYn~EDAiIiNk~si~rG~f~s~~~~~~~~~~~~~~~~~~e~~--~~p~~~~~~~~k~ 499 (842)
.+..+|+++|+|++||||+|.|||+|||||||++.+..++|||+|+.+|+++.+.+..+ .|.| ++|+.+ .
T Consensus 797 ~st~~GELALG~NvlVAfmpW~GYNfEDAIlISERlV~eD~fTSIHIee~ei~~r~Tk~G-~EeITrdIPnvs------e 869 (2890)
T PRK09603 797 PSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVDARELKHG-VEEFTADIPDVK------E 869 (2890)
T ss_pred cccccCeeccCcccEEEEeeeccccCccccccchhhhcCccceEEEEeeeEEEEEecCCC-CcEEeccCCCCC------H
Confidence 24789999999999999999999999999999999999999999999999999887654 3555 467643 2
Q ss_pred CCccCCCCCCCcCCCcEEcCCCEEEEeeCCCCccccc---------cccCCCccceeeEEeeccccceEEeEEEeecC--
Q 003180 500 GSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ---------GQASRYTRRDHSISLRHSETGMVDQVLLTTNA-- 568 (842)
Q Consensus 500 ~~~~~Ld~dGl~~~G~~v~~gdvli~k~~~~~~~~~~---------~~~~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~-- 568 (842)
...++||++||+++|++|++|||||||++|+...+.. ...+....+|+|++++++..|+|..|.+++..
T Consensus 870 ~~l~~LDe~GII~iGa~V~~GDILVGKvTPkge~~~tPEekLLraIFGeka~~vkDtSLrvp~G~~G~Vidv~~f~r~~~ 949 (2890)
T PRK09603 870 EALAHLDESGIVKVGTYVSAGMILVGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGY 949 (2890)
T ss_pred HHHhcCCCCCCEeeCCEECCCCEEEEeeccCCCCCCChHHHHHHHHhcccccccccCceecCCCCcEEEEEEEEeccccc
Confidence 3578999999999999999999999999998632211 12344568999999999999999999877532
Q ss_pred --------------------------------------------------------------------------------
Q 003180 569 -------------------------------------------------------------------------------- 568 (842)
Q Consensus 569 -------------------------------------------------------------------------------- 568 (842)
T Consensus 950 ~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1029 (2890)
T PRK09603 950 EKDARVLSAYEEEKAKLDMEHFDRLTMLNREELLRVSSLLSQAILEEPFSHNGKDYKEGDQIPKEEIASINRFTLASLVK 1029 (2890)
T ss_pred chhHHHHHHHHHHHHHHhHhhHHHHHHHHHHHHHhhhhhccccccccccccccccccccccccHHHHhhCCHHHhhhhhc
Confidence
Q ss_pred ------------------------------------CC-------ceEEEEEEeeecCCcccccccccCCCcceeeeeec
Q 003180 569 ------------------------------------DG-------LRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYT 605 (842)
Q Consensus 569 ------------------------------------~~-------~~~v~v~~r~~R~p~iGDKfssRhGqKGvvs~i~~ 605 (842)
.| .+.|||++|+.|+|++|||||||||||||||+|||
T Consensus 1030 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~gdeL~~Gv~~~VkV~ia~kR~~qvGDK~AgRHGnKGViS~I~p 1109 (2890)
T PRK09603 1030 KYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNGVIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVP 1109 (2890)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCcCCCCcceEEEEEEEEeecccccchhhhccCCCeeEEEEEc
Confidence 01 35799999999999999999999999999999999
Q ss_pred ccCCCCCCCCCCceEEeCCCCCCCCCcHHHHHHHHhhhhhhccCCc----------------------------------
Q 003180 606 QEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKE---------------------------------- 651 (842)
Q Consensus 606 ~~dmPft~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~---------------------------------- 651 (842)
+|||||++||++||||+||||||||||||||+|+++|+||+..|.+
T Consensus 1110 ~EDMPfl~dG~~pDIIlNPlGvPSRMnIGQilE~~LG~aa~~lg~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1189 (2890)
T PRK09603 1110 VADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGKQIASMLEDKTKDFAKELRAKMLEIANAINEKDPLT 1189 (2890)
T ss_pred hhcCCCCCCCCCCcEEECCCCCCccccHHHHHHHHHHHHHHhcCcChhhhhhhcchhhhHHHHHHHHhhhcccccccccc
Confidence 9999999999999999999999999999999999999999988754
Q ss_pred -----------------------ceecC-CCCCCHHHHHHHHHHcCCCCCCeEEEeeCCCCcEEeeeEeEeeehhhhccC
Q 003180 652 -----------------------GDATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKH 707 (842)
Q Consensus 652 -----------------------~d~tp-F~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if~G~~yy~rL~H 707 (842)
.++|| |++.+.+++.+.|+++||+++|++.||||+||++|+++||+|++|||||+|
T Consensus 1190 ~~~~~~~~~~~~~~~~~~~~~g~~~~tpvF~g~~~~~i~~~l~~aG~~~~Gk~~LyDGrTGe~f~~~V~vG~~YylKL~H 1269 (2890)
T PRK09603 1190 IHALENCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHH 1269 (2890)
T ss_pred cccccccchHHHHhhhhhhccCCcccCCCCCCCCHHHHHHHHHHcCCCCCCCEEEEcCCCCCCccceEEEEeeceeechh
Confidence 24678 999999999999999999999999999999999999999999999999999
Q ss_pred ccCcceEEeccCCccccccCCCCcccCCCcceeeehhhHHHHhhccHHHHHHhhhcCCCceeeeeccccCcceeecccCC
Q 003180 708 MVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKN 787 (842)
Q Consensus 708 mv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~cG~~~~~~~~~~ 787 (842)
||+||+||||+|||+.+||||++||+++|||||||||+|||+|||||++|||||+.+||... |+..
T Consensus 1270 mVdDKiHaRstGPyslvTqQPl~GKs~~GGqRfGEMEvwALeAyGAa~~LqE~Lt~kSDdv~-------gR~~------- 1335 (2890)
T PRK09603 1270 LVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDIR-------GREN------- 1335 (2890)
T ss_pred hccchhhhccCCCcchhhhCCCcccccCCCceeeeeeHHHHHHhhHHHHHHHHHhcCCcchh-------hhhh-------
Confidence 99999999999999999999999999999999999999999999999999999999999655 3322
Q ss_pred ceeeccCCCCCCceeecchHhHHHHHHHHHhCCCceEEEEccC
Q 003180 788 SFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKED 830 (842)
Q Consensus 788 ~~~C~~C~~~~~i~~v~iPy~~kll~~EL~sm~I~~~l~~~~~ 830 (842)
.|..|.++.++..+.+||+||+|++||+||||++++...+.
T Consensus 1336 --~y~~i~~g~~i~~~~iPeSFkvL~~EL~sL~l~i~~~~~~~ 1376 (2890)
T PRK09603 1336 --AYRAIAKGEQVGESEIPETFYVLTKELQSLALDINIFGDDV 1376 (2890)
T ss_pred --hhhhhcCCCcccccCCCHHHHHHHHHHHhCCcceEEEeecc
Confidence 35667777889999999999999999999999999987644
No 14
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=100.00 E-value=1.5e-146 Score=1363.01 Aligned_cols=666 Identities=30% Similarity=0.448 Sum_probs=559.1
Q ss_pred HHHHHHHHHhhcCCCCCCCCCCccCCcEECchhHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCchhccccccchhhhh
Q 003180 19 FGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGL 98 (842)
Q Consensus 19 L~~Mi~kLl~~~~g~~~~Dd~D~~~nkRv~~~G~Ll~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~it~~i 98 (842)
+..++++|+.+..|....||+|||+||||+++|+||+.+|+..|.++.+.++.++.. .+.+.+++..++++..++..+
T Consensus 446 ii~~i~~Li~l~~g~~~~DDiDhL~NRRvr~vGeLl~~qfr~gl~r~~~~i~e~~~~--~~~~~~~p~~lin~~~l~~~i 523 (2836)
T PRK14844 446 IIEIVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSMST--SSLDKVSPSDFINPKVLTNVL 523 (2836)
T ss_pred HHHHHHHHHHHhcCCCcccchhhhhccccchHHHHHHHHHHHHHHHHHHHHHHHHhh--ccccccchhhcccchhHHHHH
Confidence 448999999999999999999999999999999999999999999999999998853 233567888999999999999
Q ss_pred hhhhccCccccccccccccceeEeccccChhhhhcccccccC--C--cccCCCcCCcccccCCCccccccCCCCCCCcch
Q 003180 99 KYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS--P--IGREGKLAKPRQLHNSQWGMMCPAETPEGQACG 174 (842)
Q Consensus 99 ~~~~sTGnw~~~~~~~~~~G~sq~l~r~N~l~~lShlRrv~~--~--~~~~~K~t~~R~LhpS~wGfiCPveTPEG~~cG 174 (842)
++||+ ++++||+|||+||+++|+|+||+++ | +.+++..+++|++||||||+|||+|||||++||
T Consensus 524 ~~ff~------------ss~LSQfmDQtNpLseltHkRRlsaLGPGGL~r~~a~fevRdvH~shyGRiCPIETPEG~NiG 591 (2836)
T PRK14844 524 RDFFN------------SSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIG 591 (2836)
T ss_pred HHHhc------------ccchhhhccCcChhhhhhhcceecccCCCCcccccCCCcccccCccccccccCCCCCCCCccc
Confidence 99996 4799999999999999999999997 4 678889999999999999999999999999999
Q ss_pred hhhhcccceEEec-CCCchhHHHHHHHhCCccccccCCCCCCCcEEEEECCEEEEEEcChHHHHHHHHHhhhcCCCCCcE
Q 003180 175 LVKNLALMVYITV-GSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKTLRRLRRRVDVNTEV 253 (842)
Q Consensus 175 LvknLA~~a~Is~-~~~~~~i~~~L~~~g~~~~~~~~~~~~~~~~~VflnG~~iG~~~~~~~lv~~lR~lRr~~~i~~~v 253 (842)
||++||.+|.|+. |+.+.| +.+| .||.+ +
T Consensus 592 LI~SLA~yarIn~~GfietP-----------------------y~kV-~~g~v---~----------------------- 621 (2836)
T PRK14844 592 LINSLAIYARINKYGFIESP-----------------------YRKV-VNRVV---T----------------------- 621 (2836)
T ss_pred chhhhhhheeccCCceEeCC-----------------------cEEE-EcCcC---c-----------------------
Confidence 9999999999987 443333 1233 34431 0
Q ss_pred EEEEeccCCeEEEecCCCeeeeeEEEeecccccccHHHHHHHhcCCCCCCCCchhccccCcEEEeccccccceeEeeccc
Q 003180 254 GVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRESPEDGGWHDLVAKGFIEYIDTEEEETTMISMTIN 333 (842)
Q Consensus 254 si~~~~~~~~i~I~td~GRl~RPl~vv~n~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~g~IE~Id~~Eq~~~~Ia~~~~ 333 (842)
..++|+.|.||+...||....
T Consensus 622 -----------------------------------------------------------~~i~ylsa~~E~~~~Ia~a~~ 642 (2836)
T PRK14844 622 -----------------------------------------------------------DQIEYLSAIDEGLYYIADTSA 642 (2836)
T ss_pred -----------------------------------------------------------ccccccChHHhcCcEEEeCCc
Confidence 124566666666666665543
Q ss_pred ccccccCCCC---------c---CCCCceeeeeccCCccccccccccCCCCCCCCccchhhhcccccccccccc------
Q 003180 334 DLVQARLHPE---------E---AYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVT------ 395 (842)
Q Consensus 334 ~l~~~~~~~k---------~---~~~~~~TH~EI~Ps~ilgv~AslIPF~~HNqSpRn~yq~~M~KQaig~~~~------ 395 (842)
.+.+.....+ + ..+.+.++++++|.+++||+||||||.+||+++|++|+|||++||+|+...
T Consensus 643 ~~~~~~~~~~~~v~~R~~~ef~~~~~~~v~~~dvsp~Q~~SvaasLIPFLEhdDAnRALMGSNMQRQAVPLl~~e~PiVG 722 (2836)
T PRK14844 643 KLDENNCFVDDMLYCRYAGSFVMVSSDQVSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVA 722 (2836)
T ss_pred cCCCCCcccCCeEEEecCCceEEecHHHceEEEeCcchhhhhHhhcCCccccCccccccccccccccccccccCCCCeEe
Confidence 3332111100 0 013457899999999999999999999999999999999999999998521
Q ss_pred -----------------------------eeEEecccC---------ccee----------ccCCcceeeccc----cc-
Q 003180 396 -----------------------------NYQFRMDTL---------AYVL----------YYPQKPLVTTRA----ME- 422 (842)
Q Consensus 396 -----------------------------n~~~R~Dt~---------~~~L----------~ypQ~PlV~t~~----~~- 422 (842)
.+..|.+.. .|.| ++.|+|+|+.+. .+
T Consensus 723 TG~E~~vA~DSg~~v~A~~~G~V~yVda~kIvI~~~~~~~~~~~~~~~Y~L~ky~RSNQ~TcinQrPiV~~Gd~V~kGdi 802 (2836)
T PRK14844 723 TGMESFVASGSGAVVLAKRDGIVDSSDSNSIVIRAFDKERVNYLDVDIYHLRKFQRSNHNTCINQKPLVCVGDYVKEGDV 802 (2836)
T ss_pred cCcchhhhhcccceEEeccCceEEEEcCCEEEEEeCCCccccccccceEEeccccccccceeeeecceecCCCEeccCCE
Confidence 123333221 2444 579999998643 22
Q ss_pred -----cccCCCCCCCceeeEEeeeccCCCCCCceeeeccccccCceeEEEEEEEEeeehhcCCcccccc--ccCCCCCCC
Q 003180 423 -----HLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDF--GRPDRSNTM 495 (842)
Q Consensus 423 -----~~~~~e~p~G~N~iVAvmsy~GYn~EDAiIiNk~si~rG~f~s~~~~~~~~~~~~~~~~~~e~~--~~p~~~~~~ 495 (842)
.+..+|+++|+|++||||+|.|||+|||||||++.+++++|||+|++.|+++.+.+..+ .|.+ .+|+.+
T Consensus 803 lADG~st~~GELALG~NvlVAfmpW~GYNfEDAIliSErlv~eD~fTSiHIee~ei~~r~Tk~G-~EeITrdIPnv~--- 878 (2836)
T PRK14844 803 IADGPAINSGELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTSIHIEEFECVVHDTPLG-SEKITRAIPGVN--- 878 (2836)
T ss_pred eccChhhcccccccccceEEEEeccCCcccccccccchhhccCceeEEEeecceEEEEEeccCC-CceecccCCCCC---
Confidence 24789999999999999999999999999999999999999999999999999887654 3555 467642
Q ss_pred CCCCCCccCCCCCCCcCCCcEEcCCCEEEEeeCCCCccccc---------cccCCCccceeeEEeeccccceEEeEEEee
Q 003180 496 GMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ---------GQASRYTRRDHSISLRHSETGMVDQVLLTT 566 (842)
Q Consensus 496 ~~k~~~~~~Ld~dGl~~~G~~v~~gdvli~k~~~~~~~~~~---------~~~~~~~~~d~s~~~~~~e~g~Vd~V~~~~ 566 (842)
....++||++||+++|++|++|||||||++|+...+.. ...+....+|+|++++++..|+|..|.+++
T Consensus 879 ---e~~lr~LDe~GIV~iGa~V~~GDILVGKvtPk~e~~~tPEekLL~aIFGek~~~vkdtSLrvp~G~~G~Vidv~~f~ 955 (2836)
T PRK14844 879 ---EENLYHLDDSGIVKIGTRVGPGYILVGKVTPKPSLSLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFT 955 (2836)
T ss_pred ---hHHHhcCCCCCCeecCCEECCCCEEEEeecCCCCCCCCHHHHHHHHHhCCcccccccCceecCCCCCEEEEEEEEEc
Confidence 33578999999999999999999999999998642211 123445689999999999999999998776
Q ss_pred cC------------------------------------------------------------------------------
Q 003180 567 NA------------------------------------------------------------------------------ 568 (842)
Q Consensus 567 ~~------------------------------------------------------------------------------ 568 (842)
..
T Consensus 956 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1035 (2836)
T PRK14844 956 RRGVEENERALLIKQKEINDFEKERDYIINVTSEYFYDELKKLLINSGSQDREKFDSIEREQWWGIGLKNQSISEQVKSL 1035 (2836)
T ss_pred ccccccchhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhcccccccHHHHhhccHHhhhhcccCCHHHHHHHHHH
Confidence 42
Q ss_pred -----------------------CC-------ceEEEEEEeeecCCcccccccccCCCcceeeeeecccCCCCCCCCCCc
Q 003180 569 -----------------------DG-------LRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITP 618 (842)
Q Consensus 569 -----------------------~~-------~~~v~v~~r~~R~p~iGDKfssRhGqKGvvs~i~~~~dmPft~~G~~p 618 (842)
.| .+.|||.+.+.|.+++|||+|||||||||||+|+|.|||||++||+++
T Consensus 1036 ~~~~~~~~~~~~~~~~~k~~~~~~gdeL~~gv~~~VkVyia~KRkiqvGDKmAGRHGNKGVIS~IlP~eDMPyL~DGtpv 1115 (2836)
T PRK14844 1036 KKDFDEKVSHAIAQFKRKVEKLHEGYDLPQGVSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPV 1115 (2836)
T ss_pred HHHHHHHHHHHHHHHHHHHHhccCCCcCCCCCceEEEEEEEEeecCCccccccccCCCCceEeEEcccCCCCcCCCCCCc
Confidence 11 257999999999999999999999999999999999999999999999
Q ss_pred eEEeCCCCCCCCCcHHHHHHHHhhhhhhccCCcc----------------------------------------------
Q 003180 619 DIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEG---------------------------------------------- 652 (842)
Q Consensus 619 DiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~---------------------------------------------- 652 (842)
|||+||+|+||||||||++|+++|.||...|...
T Consensus 1116 DIvLNPLGVPSRMNvGQilE~hLG~A~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~ 1195 (2836)
T PRK14844 1116 DIILNPLGVPSRMNVGQILETHVGWACKKLGEKVGNILDEINKIKSAFCKGIRSLNDDNFTKFAAAYLDNKKIENIDDDE 1195 (2836)
T ss_pred eEEeCCCCCCccccHHHHHHHHHHHHHhhhhhhhHhhhhhhhcccccccccccccccccccccccccccccccccccccc
Confidence 9999999999999999999999999998875210
Q ss_pred ----------------------------------------------------------------------------eecC
Q 003180 653 ----------------------------------------------------------------------------DATP 656 (842)
Q Consensus 653 ----------------------------------------------------------------------------d~tp 656 (842)
-+||
T Consensus 1196 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~tp 1275 (2836)
T PRK14844 1196 ITASVLNTPNKNALNDELNELVENYLNSCKSAYSNLRNFLIEVYSCGSNVSICNNIRDISDNNLIEFARKLRDGIPVAAP 1275 (2836)
T ss_pred ccccccccccccccccccccchhccccccchhhHHHHHHHHHhhhcccccccccccccccHHHHHHHHhhhccCCeecCC
Confidence 0233
Q ss_pred -CCCCCHHHHHHHHHHcCCCCCCeEEEeeCCCCcEEeeeEeEeeehhhhccCccCcceEEeccCCccccccCCCCcccCC
Q 003180 657 -FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRD 735 (842)
Q Consensus 657 -F~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~ 735 (842)
|++.+.+++.+.|+++||+++|++.||||+||++|+++||+|++|||||+|||.||+|||++|||+.|||||++||+++
T Consensus 1276 vf~g~~~~~i~~~L~~~g~~~~Gk~~l~dG~TGe~f~~~v~vG~~yy~kL~HmV~DKihaRs~Gp~s~lT~QPl~Gr~~~ 1355 (2836)
T PRK14844 1276 VFEGPKDEQIAKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHF 1355 (2836)
T ss_pred CcCCCCHHHHHHHHHHhCcCCCCCEEEEcCCCCCccchhheeCcchhhhhhhhhcchhhhcccCCCcccccCCCcccccC
Confidence 7777889999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcceeeehhhHHHHhhccHHHHHHhhhcCCCceeeeeccccCcceeecccCCceeeccCCCCCCceeecchHhHHHHHHH
Q 003180 736 GGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQE 815 (842)
Q Consensus 736 GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~cG~~~~~~~~~~~~~C~~C~~~~~i~~v~iPy~~kll~~E 815 (842)
|||||||||+|||+|||||++|||||+.+||.+. |+.+. +|..|+.. ...+..+||+||+|+||
T Consensus 1356 GG~RfGEME~~al~a~Gaa~~L~E~Lt~kSD~~~-------gr~~~--------~~~ivkG~-~~~~~~~PesfkvL~~E 1419 (2836)
T PRK14844 1356 GGQRFGEMECWALQAYGAAYTLQEMLTVKSDDIN-------GRVKI--------YESIIKGD-SNFECGIPESFNVMIKE 1419 (2836)
T ss_pred CCceeecchHHHHHHHhHHHHHHHHhcccccchh-------hhhHh--------hhhhccCC-CCCcCCCCchHHHHHHH
Confidence 9999999999999999999999999999999776 44442 23333322 23345899999999999
Q ss_pred HHhCCCceEEEEccC
Q 003180 816 LMAMAIAPRMLTKED 830 (842)
Q Consensus 816 L~sm~I~~~l~~~~~ 830 (842)
|+||||.+++.+++.
T Consensus 1420 L~sl~i~~~~~~~~~ 1434 (2836)
T PRK14844 1420 LRSLCLNVDLKQNDV 1434 (2836)
T ss_pred HHhCccceEEeccch
Confidence 999999999988654
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=3.3e-113 Score=959.17 Aligned_cols=364 Identities=52% Similarity=0.842 Sum_probs=313.5
Q ss_pred cccccccCCCCCCCCccchhhhcccccccccccceeEEecccCcceeccCCcceeecc-cccccc---------CCCCCC
Q 003180 362 GVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTR-AMEHLH---------FRQLPA 431 (842)
Q Consensus 362 gv~AslIPF~~HNqSpRn~yq~~M~KQaig~~~~n~~~R~Dt~~~~L~ypQ~PlV~t~-~~~~~~---------~~e~p~ 431 (842)
||+|++|||++|||||||+|||+|+|||||+|.+|+..|+|+.. +|||+|||+|+ ..+..+ ++|+|+
T Consensus 1 si~As~ipf~~hn~s~R~~~~~~m~kQa~~~y~~~~~~R~d~~~---~~~q~Plv~~~~~~~~~~ilad~~~~~~~e~~~ 77 (386)
T PF00562_consen 1 SIVASLIPFPEHNQSPRNLYQCNMQKQAIGTYSLNKFNRSDQNT---CYPQKPLVKTGDRVEKGQILADGPSTKFGELPL 77 (386)
T ss_dssp -THGGTSSSGGGC-HHHHHHHHHHGCGBCSEEETTTTTS-TSSE---SS-BEESSBSSSTBTTTTECEE-TTECTTTS-S
T ss_pred CEEeCCCCEEEEEcCCcEEEEeCcCCCcccceeeeeeeccCcce---eccccceEEeeccccccCccccccccccccCcc
Confidence 68999999999999999999999999999999999999999988 89999999999 777777 999999
Q ss_pred CceeeEEeeeccCCCCCCceeeeccccccCceeEEEEEEEEeeehhcCCcccccc-ccCCCCCCCCCCCCCccCCCCCCC
Q 003180 432 GINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDF-GRPDRSNTMGMRHGSYDKLDDDGL 510 (842)
Q Consensus 432 G~N~iVAvmsy~GYn~EDAiIiNk~si~rG~f~s~~~~~~~~~~~~~~~~~~e~~-~~p~~~~~~~~k~~~~~~Ld~dGl 510 (842)
|+|++||||||+||||||||||||+|++||||||+||++ +.+++....+..+.+ ..|... +...|++||+|||
T Consensus 78 G~N~iVAvmsy~GYN~EDAiIiNkssv~rG~f~s~~~k~-~~~~~~~~~g~~e~~~~~~~~~-----~~~~~~~LD~dGi 151 (386)
T PF00562_consen 78 GQNAIVAVMSYTGYNQEDAIIINKSSVDRGLFTSIHYKT-EIEIRDNKGGPSEEIFRPIPNV-----KEYNYSKLDEDGI 151 (386)
T ss_dssp SEEEEEEESBSSSTTTSSEEEEECHHHHTTTTEEEEEEE-EEEEEEETTSEEBBESS--TSS-----TSTTGGGBCTTSB
T ss_pred eeeeeEEeeehhcccchhhhhhhhhhhhcCeeeEEEEEE-EeeeecccCCcccccccccccc-----hhhhhhhcccccc
Confidence 999999999999999999999999999999999999999 777665545554444 333321 4457999999999
Q ss_pred cCCCcEEcCCCEEEEeeC-CCCcc---ccccccCCCccceeeEEeeccccceEEeEEE-------eecCCCceEEEEEEe
Q 003180 511 APPGTRVSGEDVIIGKTT-PISQD---EAQGQASRYTRRDHSISLRHSETGMVDQVLL-------TTNADGLRFVKVRVR 579 (842)
Q Consensus 511 ~~~G~~v~~gdvli~k~~-~~~~~---~~~~~~~~~~~~d~s~~~~~~e~g~Vd~V~~-------~~~~~~~~~v~v~~r 579 (842)
|++|++|++||+||||+. |.... ......+....+|+|++++.+|.|+||+|.+ ..+.++...|+|++|
T Consensus 152 i~~G~~v~~gDiligk~~~~~~~~~~~~~~~~~~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~~~~~~~~iki~ir 231 (386)
T PF00562_consen 152 IKIGSRVEKGDILIGKITSPPRFSPLLKKIFGEKNRNYRDTSIKYKSGESGRVDKVIIFSNEKKDTSNNEGYKKIKIRIR 231 (386)
T ss_dssp B-TTCEEETTSEEEEEEESTSC--HHHHHHHHSSSCSEEEEEEES-TT-EEEEEEEEEECCCSSBEEETTCEEEEEEEEE
T ss_pred cccCcEEecceeEEEEEecccccccchhhccccccccccceeecccccEEeEeccccccccccccccccCcceEEEEEec
Confidence 999999999999999995 22110 0001122223789999999999999999999 567788899999999
Q ss_pred eecCCcccccccccCCCcceeeeeecccCCCCCCCCCCceEEeCCCCCCCCCcHHHHHHHHhhhhhhccCCcceecCCCC
Q 003180 580 SVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTD 659 (842)
Q Consensus 580 ~~R~p~iGDKfssRhGqKGvvs~i~~~~dmPft~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tpF~~ 659 (842)
+.|+|+||||||||||||||||+|||+||||||+||++|||||||||||||||||||+|+++||++++.|.+.|+|||++
T Consensus 232 ~~R~p~iGDKfssRHGqKGVvs~i~~~eDMPft~~G~~pDiIiNPhgiPSRMtiGqllE~~~g~~~~~~g~~~~~t~F~~ 311 (386)
T PF00562_consen 232 STRRPQIGDKFSSRHGQKGVVSKILPQEDMPFTEDGIVPDIIINPHGIPSRMTIGQLLESLLGKAGALNGRFVDATPFDE 311 (386)
T ss_dssp EEEE--TTEEEEETTSEEEEEEEEE-TTTSEEETTSEB-SEEE-GGGSTTTTBTHHHHHHHHHHHHHHSTCEEB-TTTSS
T ss_pred ccccchhHHHHhhhhcCceEEeeeeccccCccccCCCcceeeecccccccccchHHHHhhhhhhhhhccccceecCCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCHHHHHHHHHHcCCCCCCeEEEeeCCCCcEEeeeEeEeeehhhhccCccCcceEEeccCCccccccCCCCcccC
Q 003180 660 VTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSR 734 (842)
Q Consensus 660 ~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~ 734 (842)
.+.+++++.|.++||+++|+|.||||+||++++++||+|++|||||+|||+||+|||++||++.|||||++||+|
T Consensus 312 ~~~~~i~~~l~~~g~~~~g~~~l~~g~tG~~~~~~i~~G~~yy~rL~Hmv~DK~h~Rs~Gp~~~lT~QP~~Gr~r 386 (386)
T PF00562_consen 312 SSEEDISELLKKAGYNYPGKEVLYDGRTGEKFEAPIFIGPVYYQRLKHMVDDKIHARSRGPYSLLTRQPVEGRSR 386 (386)
T ss_dssp S-HHHHHHHHHHTTSHTTSEEEEBESSSSSBESSEEEEEEEEEEEBSTCGGGSTEEESS--BBSSSSSB-SSSSS
T ss_pred cchhhhHhhhhcccccccceEEEEcCccCceEEeEEEeeeEEeccceEeCCcEEEEEecCCCccccCCCCCCCCC
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999997
No 16
>PRK09606 DNA-directed RNA polymerase subunit B''; Validated
Probab=100.00 E-value=1.5e-50 Score=467.40 Aligned_cols=202 Identities=45% Similarity=0.766 Sum_probs=190.2
Q ss_pred CccccCCCCCCcchHHHHHHHHHHHHHhhcCCCCCCCCCCccCCcEECchhHHHHHHHHHHHHHHHHHHHHHHHHhhhcC
Q 003180 1 MLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNG 80 (842)
Q Consensus 1 llpHl~~~~~~~~~K~~~L~~Mi~kLl~~~~g~~~~Dd~D~~~nkRv~~~G~Ll~~lf~~~~~~~~~~~~~~~~~~~~~~ 80 (842)
+|||+|.+..++.+|++||++|++||++++.|.+.+||+|||+||||+++|+||+.+||+.|+++++.++..+++...+.
T Consensus 292 ~l~hig~~~~~~~~K~~~L~~m~~kLl~~~~g~~~~Dd~D~l~nkRv~~~G~Ll~~~fr~~l~~~~~~~k~~l~~~~~~~ 371 (494)
T PRK09606 292 LLPHLGVEPEVRRAKAHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERANMRN 371 (494)
T ss_pred hhcccCCCcchhhHHHHHHHHHHHHHHHHhcCCCCCCCcccccCceeeccchhHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 68999987766778999999999999999999999999999999999999999999999999999999998888776555
Q ss_pred CCCchhccccccchhhhhhhhhccCccccccccccccceeEeccccChhhhhcccccccCCcccCCCcCCcccccCCCcc
Q 003180 81 KDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWG 160 (842)
Q Consensus 81 ~~~~~~~~~~~~~it~~i~~~~sTGnw~~~~~~~~~~G~sq~l~r~N~l~~lShlRrv~~~~~~~~K~t~~R~LhpS~wG 160 (842)
+.+++..+++++.||++|++|||||||.+ +++|+||+|||+||+++|||+||||+++.++++.++||+|||||||
T Consensus 372 ~~~~~~~~~~~~~It~~l~~~~~TGnw~~-----~~~glSq~ldr~N~la~lSh~Rrv~s~~~r~~~~~~vR~lhps~~G 446 (494)
T PRK09606 372 RELSIKTAVRSDVLTERLEHAMATGNWVG-----GRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQWG 446 (494)
T ss_pred CCCCHHHhcCchhhhHHHHHHhhcccccC-----CCceEEEEccCCCHHHHhhHHHhccCCccccCccccccccCcccce
Confidence 66788888998999999999999999996 3789999999999999999999999999999999999999999999
Q ss_pred ccccCCCCCCCcchhhhhcccceEEecCCCchhHHHHHHHhCCcccc
Q 003180 161 MMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFE 207 (842)
Q Consensus 161 fiCPveTPEG~~cGLvknLA~~a~Is~~~~~~~i~~~L~~~g~~~~~ 207 (842)
|+||||||||++||||||||++|+|+++.+.+++.++|.++||+++.
T Consensus 447 ~iCPveTPEG~~cGLv~~La~~a~V~~~~~~~~i~~~l~~lg~~~~~ 493 (494)
T PRK09606 447 RICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKELGVEPER 493 (494)
T ss_pred ecccCcCCCCCcccHHHhhhceEEEeCCCChHHHHHHHHHCcCeeCC
Confidence 99999999999999999999999999998889999999999998753
No 17
>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=99.97 E-value=3.6e-32 Score=238.48 Aligned_cols=81 Identities=60% Similarity=1.029 Sum_probs=76.8
Q ss_pred CcceeeehhhHHHHhhccHHHHHHhhhcCCCceeeeeccccCcceeecccCCceeeccCCCCCCceeecchHhHHHHHHH
Q 003180 736 GGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQE 815 (842)
Q Consensus 736 GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~cG~~~~~~~~~~~~~C~~C~~~~~i~~v~iPy~~kll~~E 815 (842)
|||||||||||||+|||||++|+|||+++||.++++||.+||.+++ .|+.+.++.++.+|||||||+||
T Consensus 1 GG~R~GEMErd~LiahGas~~L~erl~~~SD~~~~~vc~~cg~~~~-----------~~~~~~~~~~~~ipy~~klL~~E 69 (81)
T PF04560_consen 1 GGLRFGEMERDALIAHGASFLLKERLFDKSDKYEIDVCSRCGSIAS-----------ICKGKPEVKKIEIPYSFKLLIQE 69 (81)
T ss_dssp CBEEEEHHHHHHHHHTTBHHHHHHHHTTTTTEEEEEEECCCHHHHH-----------TTTTSSSEEEEEEEHHHHHHHHH
T ss_pred CCcchhHHHHHHHHHhhHHHHHHHHhcCCCcCcchhhhccCCCcee-----------EECCCCeEEeeeCCHHHHHHHHH
Confidence 8999999999999999999999999999999999999999999984 56667789999999999999999
Q ss_pred HHhCCCceEEEE
Q 003180 816 LMAMAIAPRMLT 827 (842)
Q Consensus 816 L~sm~I~~~l~~ 827 (842)
|+||||++++.+
T Consensus 70 L~sm~I~~~~~~ 81 (81)
T PF04560_consen 70 LRSMGIKIRIKT 81 (81)
T ss_dssp HHCTTEEEEEEE
T ss_pred HHHCcCceEEeC
Confidence 999999999974
No 18
>PF04565 RNA_pol_Rpb2_3: RNA polymerase Rpb2, domain 3; InterPro: IPR007645 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Domain 3, is also known as the fork domain and is proximal to catalytic site [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_B 1SMY_M 3DXJ_M 3AOI_C 2A68_M 1ZYR_C 3AOH_H 1IW7_M 2O5J_C 2CW0_M ....
Probab=99.93 E-value=2.8e-27 Score=201.41 Aligned_cols=66 Identities=62% Similarity=1.007 Sum_probs=59.8
Q ss_pred EeccccChhhhhccccccc--CCcccCCCcCCcccccCCCccccccCCCCCCCcchhhhhcccceEEe
Q 003180 121 QVLNRLTYASTLSHLRRLN--SPIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYIT 186 (842)
Q Consensus 121 q~l~r~N~l~~lShlRrv~--~~~~~~~K~t~~R~LhpS~wGfiCPveTPEG~~cGLvknLA~~a~Is 186 (842)
|+|||+|++++|||+|||+ ++++++.|++++|+|||||||||||+|||||++|||+||||++|.||
T Consensus 1 Q~l~r~N~l~~ls~~Rri~~~~~~~~~~~~~~~R~lh~s~~G~iCPveTPEG~~~GLv~~La~~a~I~ 68 (68)
T PF04565_consen 1 QYLDRTNPLSELSHLRRINRLGPLSKESKSTEPRQLHPSQYGRICPVETPEGENCGLVKNLALMARIT 68 (68)
T ss_dssp EE--TSSHHHHHHHHTEEESCSSTSSSSSSSTTTSTTGGGTTTBSSSSS-SSTSTTTEEEBBTT-EE-
T ss_pred CCcccccHHHHHHHHHhcccccccchhhcccccccccccceeEEeecccCCCccEeehheeeeeEEeC
Confidence 8999999999999999999 58999999999999999999999999999999999999999999986
No 19
>PF04566 RNA_pol_Rpb2_4: RNA polymerase Rpb2, domain 4; InterPro: IPR007646 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Domain 4, is also known as the external 2 domain [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3S17_B 1I6H_B 4A3B_B 3K1F_B 4A3I_B 1TWA_B 3S14_B 3S15_B 2NVX_B 3M3Y_B ....
Probab=99.81 E-value=1e-19 Score=152.32 Aligned_cols=63 Identities=62% Similarity=1.032 Sum_probs=59.8
Q ss_pred EEECCEEEEEEcChHHHHHHHHHhhhcCCCCCcEEEEEeccCCeEEEecCCCeeeeeEEEeec
Q 003180 220 IFVNGCWVGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEK 282 (842)
Q Consensus 220 VflnG~~iG~~~~~~~lv~~lR~lRr~~~i~~~vsi~~~~~~~~i~I~td~GRl~RPl~vv~n 282 (842)
|||||.|+|+|++|+.|++.||.+||+|.|+.++||++|...++|+|+||+||+||||++|+|
T Consensus 1 VFlNG~~iG~~~~p~~l~~~lr~~RR~g~i~~~vsi~~~~~~~ei~I~tD~GR~~RPL~vV~n 63 (63)
T PF04566_consen 1 VFLNGVWIGIHSDPEELVKTLRNLRRSGKISKEVSIVYDIREKEIRINTDAGRLCRPLFVVEN 63 (63)
T ss_dssp EEETTEEEEEESSHHHHHHHHHHHHHTTSS-TTSEEEEETTTTEEEEE-SSCEEEEEEEEESS
T ss_pred CEECCEEEEEEcCHHHHHHHHHHHhhccCCcceeEEEEeccCCEEEEEccCCcccceeEEecC
Confidence 899999999999999999999999999999999999999999999999999999999999985
No 20
>KOG0214 consensus RNA polymerase II, second largest subunit [Transcription]
Probab=99.27 E-value=2.8e-13 Score=157.78 Aligned_cols=420 Identities=10% Similarity=-0.101 Sum_probs=258.4
Q ss_pred CCCccchhhhcccccccccccceeEEecccCcceeccCCcceeeccccccccCCCCCCCceeeEEeeeccCCCCCCceee
Q 003180 374 NQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIM 453 (842)
Q Consensus 374 NqSpRn~yq~~M~KQaig~~~~n~~~R~Dt~~~~L~ypQ~PlV~t~~~~~~~~~e~p~G~N~iVAvmsy~GYn~EDAiIi 453 (842)
-|.+++.++.-|. |..+-....+..+.+...-.|.+++.++-.+......-.-..+.+.++-++.+.+.+++.++...-
T Consensus 681 pdh~qspr~tYQs-a~~kqamg~y~tn~~vR~dtl~~~l~ypqkpl~tt~~~e~l~~~eL~aG~NaiVAi~~~~GYNqED 759 (1141)
T KOG0214|consen 681 PDHNQSPRNTYQS-AMGKQAMGVYHTNPQVRMDTLAKVLYYPQKPLVTTRAMEYLRFRELPAGQNAIVAIACYSGYNQED 759 (1141)
T ss_pred CCCCCchHHHHHH-HHhhhcceeeeecchhhhhhhhhcccccccchhhHHHHhhhhhhhcccccceEEEEecccCccHHH
Confidence 3444444444444 222233333444444444444455555544444333333345679999999999999999999999
Q ss_pred eccccccCceeEEEEEEEEeeehhcCCccccccccCCCCCCCCCCCCCccCCCCCCCcCCCcEEcCCCEEEE-eeCCCCc
Q 003180 454 NQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIG-KTTPISQ 532 (842)
Q Consensus 454 Nk~si~rG~f~s~~~~~~~~~~~~~~~~~~e~~~~p~~~~~~~~k~~~~~~Ld~dGl~~~G~~v~~gdvli~-k~~~~~~ 532 (842)
|--..+.+++|++++..|--..+.+.......++.+-..-....+..-+ +.-.|-+-.-|-.-....|..+ ++.++..
T Consensus 760 svimn~s~v~rg~FrS~~~RsYk~q~~~~~~~~ee~~~~~~~~~~~~mr-~~~~dkLdddG~i~~G~~vs~~Dv~iGk~t 838 (1141)
T KOG0214|consen 760 SVIMNQSSVDRGLFRSFFIRSYKDQEHKKDQGPEEIFEEPPRGEGRGMR-NGKYDKLDDDGIIMPGSRVSGGDVLIGKTT 838 (1141)
T ss_pred HHHHHhhhhhcchhhhhhhhHHHhhhhhccccccccccccccccccccc-ccccccccccCCccccceeecCCEEecccc
Confidence 9999999999999986664433332221111222221111111111111 1111111111111111111110 1111000
Q ss_pred cccccccCCCccceeeEEeeccccceEEeEEEeecCCCceEEEEEEeeecCCcccccccccCCCcceeeeeecccCCCCC
Q 003180 533 DEAQGQASRYTRRDHSISLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWT 612 (842)
Q Consensus 533 ~~~~~~~~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~v~v~~r~~R~p~iGDKfssRhGqKGvvs~i~~~~dmPft 612 (842)
. ..+ ..+.+-.-..-..++..++.+..++.| ...+|.++. .+.|+||+..|++++-+.++-...++++-
T Consensus 839 ~---~~~----~~~~~~~~~~~~t~~d~s~~Lr~~e~G-ivd~V~vt~---n~~G~kF~kv~vr~~ripqiGDKfasrHg 907 (1141)
T KOG0214|consen 839 P---QPA----KEDESGPEDRLYTKRDHSTKLRHTERG-IVDQVWVTK---NSEGPKFVKVRVRQVRIPQIGDKFASRHG 907 (1141)
T ss_pred C---Ccc----cchhccccccccccccceeecccCCcc-eEEEEEEec---CCCCCceeEEEEeecccccccchhccccc
Confidence 0 000 000000000011346677777777776 444555554 89999999999999999999999999999
Q ss_pred CCCCCceEEeCCCCCCCCCcHHHHHHHHhhhhhhccCCcceecCCCCCCHHHHHHHHHHcCCCCCCeEEEeeCCCCcEEe
Q 003180 613 VEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLT 692 (842)
Q Consensus 613 ~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tpF~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~ 692 (842)
.-|++++++.+++.-+++|+|--.++.-.-. .|-. ..+..+.+-|. |-..-++..++++.++.. -
T Consensus 908 qKG~ig~~~~qedmpft~eGi~pDiiiNPha-----------iPSR-mtig~liEc~l--gk~~a~~~e~~~atpFs~-v 972 (1141)
T KOG0214|consen 908 QKGTIGITYRQEDMPFTIEGIVPDIIINPHA-----------IPSR-MTIGQLIECLL--GKVAAYEGEEGDATPFSD-V 972 (1141)
T ss_pred cCccccceeecCCCCccccCCCcceEECccc-----------Cccc-cchhhhHHHhh--hhhhhcccccccCCCCCc-c
Confidence 9999999999999999999887655432221 1111 11222211111 112222334455555555 4
Q ss_pred eeEeEeeehhhhccCccCcceEEeccCCccccccCCCCcccCCCcceeeehhhHHHHhhccHHHHHHhhhcCCCceeeee
Q 003180 693 AMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHV 772 (842)
Q Consensus 693 ~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~v 772 (842)
+-.+++..+++...|+..++.+++.+++....+++++.+.-.+++.+++||+++|=.+++.+-+.++.+...|+..-..+
T Consensus 973 ~v~~is~~l~~~g~~~~G~e~~ynGrtG~~~~~~if~GptyyqrL~Hmvd~kih~R~~Gp~q~ltRQP~~gRsr~GGlRf 1052 (1141)
T KOG0214|consen 973 TVSKISANLHVYGYQYRGNERMYNGRTGRKLRAQIFIGPTYYQRLKHMVDDKIHSRARGPVQILTRQPVEGRSRDGGLRF 1052 (1141)
T ss_pred chhcccchHHHhccccCCCEEEecCCCCceeeeeeecCchHHHHHHHhhhheeeecccCCceeeeccccccccccCCeee
Confidence 46688999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCcceeecccCCceeeccCCCCCCceeecchHhHHHHHHHHHhCCCc
Q 003180 773 CEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIA 822 (842)
Q Consensus 773 C~~cG~~~~~~~~~~~~~C~~C~~~~~i~~v~iPy~~kll~~EL~sm~I~ 822 (842)
|+.|+..+.+.-......|+.|..++.+.....++ |.|++.+...+|+-
T Consensus 1053 GEMErdc~iahGaa~~L~ERL~~~SD~~~~~~c~~-c~l~~i~~~~~n~~ 1101 (1141)
T KOG0214|consen 1053 GEMERDCLIAHGAAAFLKERLFEKSDAYRVHICVL-CGLTAIAGLIPNSF 1101 (1141)
T ss_pred ehhHHHHHHHhhHHHHHHHHhhccCccceEEEecc-chhhhhhccCCCcc
Confidence 99998654221111223466666665555555555 44777777777654
No 21
>PF04567 RNA_pol_Rpb2_5: RNA polymerase Rpb2, domain 5; InterPro: IPR007647 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Domain 5, is also known as the external 2 domain [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3S17_B 1I6H_B 4A3B_B 3K1F_B 4A3I_B 1TWA_B 3S14_B 3S15_B 2NVX_B 3M3Y_B ....
Probab=99.21 E-value=5.8e-12 Score=100.07 Aligned_cols=48 Identities=58% Similarity=1.041 Sum_probs=37.0
Q ss_pred chhccccCcEEEeccccccceeEeecccccccccCCCCcCCCCceeeeeccC
Q 003180 306 WHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHP 357 (842)
Q Consensus 306 ~~~l~~~g~IE~Id~~Eq~~~~Ia~~~~~l~~~~~~~k~~~~~~~TH~EI~P 357 (842)
|++|+++|+|||||++||++++|||++++|. .. ...+...||||||||
T Consensus 1 w~~ll~~G~vE~id~eEEe~~~Iam~~~dl~-~~---~~~~~~~~TH~EI~P 48 (48)
T PF04567_consen 1 WDDLLKEGVVEYIDAEEEETCMIAMSPEDLE-ST---NEDITHTYTHCEIHP 48 (48)
T ss_dssp HHHHHHTTSEEEEETTTCTT--EESSCCCCC-HS---GGCCSST-SEEES-G
T ss_pred ChhHhhCCCEEEecchhccccEEEEeccccc-cc---CCCCCCccEEEeEeC
Confidence 8999999999999999999999999999997 21 112246899999998
No 22
>PF06883 RNA_pol_Rpa2_4: RNA polymerase I, Rpa2 specific domain ; InterPro: IPR009674 This domain is found between domain 3 and domain 5, but shows no homology to domain 4 of Rpb2. The external domains in multisubunit RNA polymerase (those most distant from the active site) are known to demonstrate more sequence variability [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=97.63 E-value=6.2e-05 Score=62.29 Aligned_cols=49 Identities=20% Similarity=0.232 Sum_probs=42.1
Q ss_pred EEEE--cChHHHHHHHHHhhhcC--CCCCcEEEEEeccC-----CeEEEecCCCeeee
Q 003180 227 VGIH--RDPEMLVKTLRRLRRRV--DVNTEVGVVRDIRL-----KELRIYTDYGRCSR 275 (842)
Q Consensus 227 iG~~--~~~~~lv~~lR~lRr~~--~i~~~vsi~~~~~~-----~~i~I~td~GRl~R 275 (842)
||++ +.++.++++||.+|..+ .+|.++||++.+.. |+++|||+++|++|
T Consensus 1 iG~~~~~~a~~~~~~LR~~Kv~~~~~vP~~lEI~~VP~~~~g~yPGLyLft~~aRm~R 58 (58)
T PF06883_consen 1 IGYVSPEEAEQIADQLRYLKVEGEHGVPPTLEIGYVPPSKGGQYPGLYLFTTPARMMR 58 (58)
T ss_pred CceecHHHHHHHHHHHHHHHHcCCCCCCCceEEEEEECCCCCCCCeEEEeCCcccccC
Confidence 4665 45789999999999887 69999999987754 79999999999998
No 23
>KOG0215 consensus RNA polymerase III, second largest subunit [Transcription]
Probab=97.47 E-value=2e-06 Score=100.48 Aligned_cols=263 Identities=6% Similarity=-0.175 Sum_probs=161.0
Q ss_pred CcchHHHHHHHHHHHHHhhcCCCCCCCCCCccCCcEECchhHHHHHHHHHHHHHHHHHHHHHHHHhhhcC---CCCchhc
Q 003180 11 CETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNG---KDVNLQF 87 (842)
Q Consensus 11 ~~~~K~~~L~~Mi~kLl~~~~g~~~~Dd~D~~~nkRv~~~G~Ll~~lf~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~ 87 (842)
.+..+-..|-+|.+.|..+. +.-.-++.+.+++++-...+.+...++-++++++. ..++.+..-+.+. ...+++.
T Consensus 372 rd~~gnkrlelagqllsllf-eD~fk~~n~e~k~~~dk~l~k~~ra~~fD~~~~~n-~~~~~it~~l~ra~stgnw~iKr 449 (1153)
T KOG0215|consen 372 RDYVGNKRLELAGQLLSLLF-EDLFKRFNSELKKNIDKILKKPIRAQEFDALKHLN-VRANMITSGLERAISTGNWSIKR 449 (1153)
T ss_pred hhhhccchHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHhcchhhhhhhHHHHHHH-HHHHHHHHHHHHHhhcCchHHHH
Confidence 34456667777877655544 44455788899999999999988888888888875 3333232222221 1222332
Q ss_pred cccccchhhhhhhhhccCccccccccccccceeEeccccChhhhhcccccccCCcccCCCcCCcccccCCCccccccCCC
Q 003180 88 AIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWGMMCPAET 167 (842)
Q Consensus 88 ~~~~~~it~~i~~~~sTGnw~~~~~~~~~~G~sq~l~r~N~l~~lShlRrv~~~~~~~~K~t~~R~LhpS~wGfiCPveT 167 (842)
+ +-.-++.+.--+-.|++|.....-..++++.++..+..|-+-...--.+..|+.+..+.+-.+-..++.|+.|||-++
T Consensus 450 f-rmer~gvt~VlsrlSyisaLgmmtri~s~fektrkvsgprSlq~sqwgmlcp~dtpegeacglvknlalmthittd~e 528 (1153)
T KOG0215|consen 450 F-RMERAGVTQVLSRLSYISALGMMTRINSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITTDSE 528 (1153)
T ss_pred h-hhhhccceeeehhhhhhhhhhhheehhhhheeehhccCccccChhhcccccCCCCCCccccccccchHHHhcccCCCC
Confidence 2 111222222234567777766655678999999988888777766666777888888899999999999999999999
Q ss_pred CCCCcchhhhhcccceEEecCCCchhHHHHHHHhCCccccc-cCCCCC-CCcEEEEECCEEEEEEcChHHHHHHHHHhhh
Q 003180 168 PEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEE-ISPAVI-PQATKIFVNGCWVGIHRDPEMLVKTLRRLRR 245 (842)
Q Consensus 168 PEG~~cGLvknLA~~a~Is~~~~~~~i~~~L~~~g~~~~~~-~~~~~~-~~~~~VflnG~~iG~~~~~~~lv~~lR~lRr 245 (842)
|++..|++.|+.+...+++.+...-+...++..++...+.- ..++.. .+...++.+|.+-+++......++..+-.++
T Consensus 529 e~pi~~~~~k~gv~di~~v~~~e~~~~~~~~v~Lng~iig~~~~~~~~v~~~r~lrr~G~i~~fvsv~~~~~q~~v~i~s 608 (1153)
T KOG0215|consen 529 EKPILKLCYKLGVEDIHVVSGRELHTPDSFLVFLNGLIIGITRRPQYFVNSFRRLRRKGKIGEFVSVFTNTTQRCVYIAS 608 (1153)
T ss_pred cchhHHHHHHhcceeeeeecccccCCCceEEEEecceeeccccchHHHHHHHHHHHHcCcccceeeeeeeeeeEEEEEec
Confidence 99999999999999999988654433333443333332221 111111 1122345556555554433333333333333
Q ss_pred cCCCCCcEEEEEeccCCeEEEecCCCeeeeeEE
Q 003180 246 RVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLF 278 (842)
Q Consensus 246 ~~~i~~~vsi~~~~~~~~i~I~td~GRl~RPl~ 278 (842)
.|-.--...|+.+...+ +|-++.+|.|+|-.
T Consensus 609 dggr~crp~Iiv~~~~~--~v~~~h~~el~~g~ 639 (1153)
T KOG0215|consen 609 DGGRVCRPLIIVDNGRP--RVKQHHMDELLDGK 639 (1153)
T ss_pred CCCeEeeeEEEEeCCcc--hhhhhhHHHHHHhh
Confidence 33322333444333322 66666677666643
No 24
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]
Probab=97.41 E-value=0.00015 Score=89.55 Aligned_cols=109 Identities=27% Similarity=0.342 Sum_probs=80.1
Q ss_pred cEEEeccccccceeEeecccccccccCCC------C----c----CCCCceeeeeccCCccccccccccCCCCCCCCccc
Q 003180 314 FIEYIDTEEEETTMISMTINDLVQARLHP------E----E----AYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRN 379 (842)
Q Consensus 314 ~IE~Id~~Eq~~~~Ia~~~~~l~~~~~~~------k----~----~~~~~~TH~EI~Ps~ilgv~AslIPF~~HNqSpRn 379 (842)
-|||+.+.|+....++.....+.+..... . . ..+...++++..|.++.++.+++|||.+|.++.|.
T Consensus 476 ~i~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~~~~~~~~~~~~~~~~~~dv~~~~~~~~~~~~~P~l~~dd~~~~ 555 (1060)
T COG0085 476 EIEYLSADEEDVYVIGQANGTLDEPGELVEELVECRRGGSGEVSVADPEGVDYMDVSPKQVVSVGRSLIPFLEHDDANRA 555 (1060)
T ss_pred ceeeecccccceEEEeEeeeeecCCCceeeeEEEEeecccccceeecCccccceeccceEEeccccccCceeEEcCchHh
Confidence 47899999988888886544433321110 0 0 01345678899999999999999999999999999
Q ss_pred hhhhcccccccccccceeEEecccCcceeccCCcceeeccccccccCCCCCCCceeeEEeeec
Q 003180 380 TYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACY 442 (842)
Q Consensus 380 ~yq~~M~KQaig~~~~n~~~R~Dt~~~~L~ypQ~PlV~t~~~~~~~~~e~p~G~N~iVAvmsy 442 (842)
+++++|+|||+|+ ..+..|||.|. .|++.-.| -.|++||.-+.
T Consensus 556 l~~~~mqr~~~~l----------------~~~~~~lv~tG-~E~~~a~e---~~~~~ia~~~~ 598 (1060)
T COG0085 556 LMGSNMQRQAVPL----------------LRTEAPLVGTG-MEYLDAED---SGAAVIAKRPG 598 (1060)
T ss_pred hhhhhhhhhcccc----------------cccccccccCC-ceeecccc---ccceeEeccCC
Confidence 9999999999993 46888999999 77653332 23566666443
No 25
>PHA03394 lef-8 DNA-directed RNA polymerase subunit beta-like protein; Provisional
Probab=96.64 E-value=0.0049 Score=73.56 Aligned_cols=141 Identities=23% Similarity=0.343 Sum_probs=84.7
Q ss_pred eeccccceEEeEEEeec-CCCceEEEEEEeeecCCcccccccccCCCcceeeeeecccCCC-C-CCCCCCceEEeCCCCC
Q 003180 551 LRHSETGMVDQVLLTTN-ADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMP-W-TVEGITPDIIVNPHAI 627 (842)
Q Consensus 551 ~~~~e~g~Vd~V~~~~~-~~~~~~v~v~~r~~R~p~iGDKfssRhGqKGvvs~i~~~~dmP-f-t~~G~~pDiIiNPh~~ 627 (842)
++....-+|++|.-.-. .++.-.+|+++-..=.=-.|=|.||=||||||+. ..||+- | .|||+.|-|.++|.+|
T Consensus 674 fR~~~~Q~ie~l~s~m~~~nd~v~lKl~~Vtst~dLeGlKICgIHGQKGVln---~seDLtew~aeDg~~aQIclSPiSy 750 (865)
T PHA03394 674 FRQIKNQRIERLDSEMTVINDTVYLKIRLVTSTSDLEGLKICGIHGQKGVLN---GSEDLTEWMAEDGTHAQICLSPISY 750 (865)
T ss_pred EEecCCeEEEEEeeEEEEcCCEEEEEEEEEEEecCcceeEEeeecccccccC---CcchhhhhhccCCCcceEEechHHh
Confidence 44455556666632221 1223456666544334456999999999999964 467776 4 5699999999999999
Q ss_pred CCCCcHHHHHHHHhhhhhhccCCccee---------cCCC--CCCHHHHHHHHHHcCCCCCCeEEEeeCCCCcEEeeeEe
Q 003180 628 PSRMTIGQLIECIMGKVAAHMGKEGDA---------TPFT--DVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIF 696 (842)
Q Consensus 628 PSRMtiGql~E~~~gk~~~~~g~~~d~---------tpF~--~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if 696 (842)
-||.|.= +-+--|-....|.+.|. .|+. ....+++.++.. +-++.|-|.+=--++-+.--...|
T Consensus 751 LsRQtnf---~~~~~Ky~v~gg~~~~~~~~rypi~~IPYm~FnnTPDnI~kEf~--~~n~TG~EKvEGTRlDqwTINqsF 825 (865)
T PHA03394 751 LSRQTNF---DDIERKYVVRGGDHSDPNAKRYPIFNIPYMLFNNTPDNIYKEFI--KKNYTGHEKVEGTRLDQWTINQSF 825 (865)
T ss_pred hcccccc---ccCceEEEEECCCcCCCCCcccceEecceehhcCCchHHHHHHh--ccCCcceeecceeeccceeEccee
Confidence 9999852 33333444444555543 3422 345566666553 345666665532233333334566
Q ss_pred Eee
Q 003180 697 LGP 699 (842)
Q Consensus 697 ~G~ 699 (842)
+|-
T Consensus 826 ~gN 828 (865)
T PHA03394 826 VGN 828 (865)
T ss_pred ccc
Confidence 664
No 26
>PF04563 RNA_pol_Rpb2_1: RNA polymerase beta subunit; InterPro: IPR007644 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the protrusion domain []. The other lobe, RNA polymerase Rpb2, domain 2, is nested within this domain.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_B 3LTI_A 3IYD_C 3LU0_C 1SMY_M 3DXJ_M 3AOI_C 2A68_M 1ZYR_C 3AOH_H ....
Probab=96.59 E-value=0.0028 Score=65.88 Aligned_cols=54 Identities=31% Similarity=0.547 Sum_probs=50.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCchhccccccchhhhhhhhhccC
Q 003180 52 PLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATG 105 (842)
Q Consensus 52 ~Ll~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~it~~i~~~~sTG 105 (842)
+||+.+|++.|+++.+.+++.+.+...+.+.+++..+++++.||++|++|||||
T Consensus 150 ~Ll~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~It~~~~~f~~TG 203 (203)
T PF04563_consen 150 ELLQELFREGLKRLEKNIKKKMNKKISKKKKFNPKSLINSKIITNGIRYFFSTG 203 (203)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHTTTSTTCSSCTTSSHSHHHHHHHHHHHHTS
T ss_pred hhHHHHHHHHHHHhHHHHHHHHHHhhccCCccCHHHccCchHHHHHHHHHHcCC
Confidence 999999999999999999999988876666788899999999999999999998
No 27
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=71.63 E-value=2 Score=36.81 Aligned_cols=48 Identities=19% Similarity=0.398 Sum_probs=28.9
Q ss_pred eeeeeccccCcceeecccCCceeeccCCCCCCceeecchH------hHHHHHHHHH
Q 003180 768 YRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPY------ACKLLFQELM 817 (842)
Q Consensus 768 ~~~~vC~~cG~~~~~~~~~~~~~C~~C~~~~~i~~v~iPy------~~kll~~EL~ 817 (842)
|.++-| .||+.+++.....+..| .|+..-+|.+..|=. -..-+.++||
T Consensus 1 ylifrC-~Cgr~lya~e~~kTkkC-~CG~~l~vk~~rIl~~~~~~~eA~eiVrklQ 54 (68)
T PF09082_consen 1 YLIFRC-DCGRYLYAKEGAKTKKC-VCGKTLKVKERRILARAENAEEASEIVRKLQ 54 (68)
T ss_dssp EEEEEE-TTS--EEEETT-SEEEE-TTTEEEE--SSS-BS--SSHHHHHHHHHHHS
T ss_pred CEEEEe-cCCCEEEecCCcceeEe-cCCCeeeeeeEEEEEecCCHHHHHHHHHHHH
Confidence 456779 79999998877777899 999876666655432 2334555554
No 28
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=65.10 E-value=6 Score=31.08 Aligned_cols=28 Identities=18% Similarity=0.377 Sum_probs=20.7
Q ss_pred eeeccccCcceeecccCCceeeccCCCC
Q 003180 770 VHVCEHCGLIAIANLKKNSFECRGCKNK 797 (842)
Q Consensus 770 ~~vC~~cG~~~~~~~~~~~~~C~~C~~~ 797 (842)
.+.|.+||.....+.......|+.|++.
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~ 30 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYR 30 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCe
Confidence 5789999997755444336789999873
No 29
>PF04941 LEF-8: Late expression factor 8 (LEF-8); InterPro: IPR007025 Late expression factor 8 (LEF-8) is one of the primary components of RNA polymerase produced by polyhedrosis viruses. LEF-8 shows homology to the second largest subunit of prokaryotic DNA-directed RNA polymerase[].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=62.12 E-value=12 Score=45.21 Aligned_cols=35 Identities=17% Similarity=0.156 Sum_probs=28.4
Q ss_pred CCCCCCccCCcEECchhHHHHHHHHHHHHHHHHHH
Q 003180 35 AEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDV 69 (842)
Q Consensus 35 ~~Dd~D~~~nkRv~~~G~Ll~~lf~~~~~~~~~~~ 69 (842)
..=.+|+++||=|.-...|++.+++..++.+...+
T Consensus 209 i~Y~IDsLsNKiIYkh~yLl~l~y~~~L~~~~~~~ 243 (748)
T PF04941_consen 209 INYSIDSLSNKIIYKHSYLLELTYKPILKKYENLI 243 (748)
T ss_pred CCceecccccceeeCHHHHHHHHHHHHHHHHHHHH
Confidence 34579999999999999999999987776665443
No 30
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=61.85 E-value=4.6 Score=36.24 Aligned_cols=29 Identities=28% Similarity=0.761 Sum_probs=24.4
Q ss_pred eeeeeccccCcceeecccCCceeeccCCC
Q 003180 768 YRVHVCEHCGLIAIANLKKNSFECRGCKN 796 (842)
Q Consensus 768 ~~~~vC~~cG~~~~~~~~~~~~~C~~C~~ 796 (842)
+..|+|+.||+..+.-.....|.|+.|+.
T Consensus 33 ~~~~~Cp~C~~~~VkR~a~GIW~C~kCg~ 61 (89)
T COG1997 33 RAKHVCPFCGRTTVKRIATGIWKCRKCGA 61 (89)
T ss_pred hcCCcCCCCCCcceeeeccCeEEcCCCCC
Confidence 34678999999987777778899999986
No 31
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=60.27 E-value=6.9 Score=28.96 Aligned_cols=26 Identities=31% Similarity=0.580 Sum_probs=18.7
Q ss_pred eeeccccCcceeecccCCceeeccCCCC
Q 003180 770 VHVCEHCGLIAIANLKKNSFECRGCKNK 797 (842)
Q Consensus 770 ~~vC~~cG~~~~~~~~~~~~~C~~C~~~ 797 (842)
.|+|..||.+..... .-..|+.|+..
T Consensus 2 ~~~C~~CG~i~~g~~--~p~~CP~Cg~~ 27 (34)
T cd00729 2 VWVCPVCGYIHEGEE--APEKCPICGAP 27 (34)
T ss_pred eEECCCCCCEeECCc--CCCcCcCCCCc
Confidence 689999998864321 22479999874
No 32
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=59.06 E-value=6.6 Score=40.20 Aligned_cols=46 Identities=20% Similarity=0.395 Sum_probs=33.7
Q ss_pred hhccHHHHHHhhhcCCCceeeeeccccCcceee-cccCCceeeccCCC
Q 003180 750 AHGASHFLKERLFDQSDAYRVHVCEHCGLIAIA-NLKKNSFECRGCKN 796 (842)
Q Consensus 750 a~Gas~~l~erl~~~SD~~~~~vC~~cG~~~~~-~~~~~~~~C~~C~~ 796 (842)
.|-...-|+++|-..++. ..++|++||..... ......|.|+.|+.
T Consensus 98 ~~~~~~klk~~l~~e~~~-~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~ 144 (178)
T PRK06266 98 KMEELKKLKEQLEEEENN-MFFFCPNCHIRFTFDEAMEYGFRCPQCGE 144 (178)
T ss_pred HHHHHHHHHHHhhhccCC-CEEECCCCCcEEeHHHHhhcCCcCCCCCC
Confidence 356677889999877775 78999999975531 11234689999987
No 33
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=55.17 E-value=8.8 Score=38.82 Aligned_cols=24 Identities=29% Similarity=0.573 Sum_probs=18.6
Q ss_pred eeeccccCcceeecccCCceeeccCCC
Q 003180 770 VHVCEHCGLIAIANLKKNSFECRGCKN 796 (842)
Q Consensus 770 ~~vC~~cG~~~~~~~~~~~~~C~~C~~ 796 (842)
+|||..||-+... .....|+.|+.
T Consensus 134 ~~vC~vCGy~~~g---e~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYTHEG---EAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCCcccC---CCCCcCCCCCC
Confidence 9999999988743 22347999985
No 34
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=54.17 E-value=8 Score=39.64 Aligned_cols=35 Identities=26% Similarity=0.582 Sum_probs=27.6
Q ss_pred eeccccCcceeecccCCceeeccCCCCCCceeecchHh
Q 003180 771 HVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYA 808 (842)
Q Consensus 771 ~vC~~cG~~~~~~~~~~~~~C~~C~~~~~i~~v~iPy~ 808 (842)
-.|.+||..+.. ..+..+|+.|++ +...++..||-
T Consensus 150 A~CsrC~~~L~~--~~~~l~Cp~Cg~-tEkRKia~~y~ 184 (188)
T COG1096 150 ARCSRCRAPLVK--KGNMLKCPNCGN-TEKRKIAKDYG 184 (188)
T ss_pred EEccCCCcceEE--cCcEEECCCCCC-EEeeeeccccc
Confidence 469999998855 345679999987 57888888873
No 35
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=51.83 E-value=9.6 Score=27.89 Aligned_cols=26 Identities=27% Similarity=0.592 Sum_probs=19.1
Q ss_pred eeeccccCcceeecccCCceeeccCCCC
Q 003180 770 VHVCEHCGLIAIANLKKNSFECRGCKNK 797 (842)
Q Consensus 770 ~~vC~~cG~~~~~~~~~~~~~C~~C~~~ 797 (842)
.|+|..||-+... ....+.|+.|+..
T Consensus 1 ~~~C~~CGy~y~~--~~~~~~CP~Cg~~ 26 (33)
T cd00350 1 KYVCPVCGYIYDG--EEAPWVCPVCGAP 26 (33)
T ss_pred CEECCCCCCEECC--CcCCCcCcCCCCc
Confidence 4789999987633 2245789999874
No 36
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=50.44 E-value=10 Score=37.98 Aligned_cols=46 Identities=15% Similarity=0.283 Sum_probs=32.4
Q ss_pred hhccHHHHHHhhhcCCCceeeeeccccCcceee-cccCCceeeccCCC
Q 003180 750 AHGASHFLKERLFDQSDAYRVHVCEHCGLIAIA-NLKKNSFECRGCKN 796 (842)
Q Consensus 750 a~Gas~~l~erl~~~SD~~~~~vC~~cG~~~~~-~~~~~~~~C~~C~~ 796 (842)
.|.....|+++|-..++ ...++|++||..... ......|.|+.|+.
T Consensus 90 ~~~~~~~lk~~l~~e~~-~~~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~ 136 (158)
T TIGR00373 90 LEETAKKLREKLEFETN-NMFFICPNMCVRFTFNEAMELNFTCPRCGA 136 (158)
T ss_pred HHHHHHHHHHHHhhccC-CCeEECCCCCcEeeHHHHHHcCCcCCCCCC
Confidence 45677788898876665 467899999965421 11234689999987
No 37
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=49.43 E-value=14 Score=27.25 Aligned_cols=28 Identities=25% Similarity=0.497 Sum_probs=21.8
Q ss_pred eeeccccCcceeecccCCceeeccCCCC
Q 003180 770 VHVCEHCGLIAIANLKKNSFECRGCKNK 797 (842)
Q Consensus 770 ~~vC~~cG~~~~~~~~~~~~~C~~C~~~ 797 (842)
.+.|..||.....+..++..+|..|+..
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~~ 30 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIFCGSS 30 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcccCCcE
Confidence 3679999988766556677899999863
No 38
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=49.32 E-value=9.7 Score=36.94 Aligned_cols=25 Identities=24% Similarity=0.575 Sum_probs=20.0
Q ss_pred eeccccCcceeecccCCceeeccCCCC
Q 003180 771 HVCEHCGLIAIANLKKNSFECRGCKNK 797 (842)
Q Consensus 771 ~vC~~cG~~~~~~~~~~~~~C~~C~~~ 797 (842)
.-|+.||..+.. +.+..+|++|+..
T Consensus 29 ~hCp~Cg~PLF~--KdG~v~CPvC~~~ 53 (131)
T COG1645 29 KHCPKCGTPLFR--KDGEVFCPVCGYR 53 (131)
T ss_pred hhCcccCCccee--eCCeEECCCCCce
Confidence 349999999865 6677899999853
No 39
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=48.18 E-value=13 Score=29.34 Aligned_cols=26 Identities=35% Similarity=0.947 Sum_probs=19.6
Q ss_pred eeccccCcceeecccC-CceeeccCCC
Q 003180 771 HVCEHCGLIAIANLKK-NSFECRGCKN 796 (842)
Q Consensus 771 ~vC~~cG~~~~~~~~~-~~~~C~~C~~ 796 (842)
.+|..||...+..++. ..|.|..|+.
T Consensus 19 ~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 6799999976544444 6789999964
No 40
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=47.55 E-value=13 Score=29.90 Aligned_cols=30 Identities=17% Similarity=0.428 Sum_probs=22.3
Q ss_pred eeeeeccccCcceeecccCCceeeccCCCC
Q 003180 768 YRVHVCEHCGLIAIANLKKNSFECRGCKNK 797 (842)
Q Consensus 768 ~~~~vC~~cG~~~~~~~~~~~~~C~~C~~~ 797 (842)
...++|..||.............|+.|+..
T Consensus 4 ~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 4 MMEYKCARCGREVELDQETRGIRCPYCGSR 33 (49)
T ss_pred eEEEEhhhcCCeeehhhccCceeCCCCCcE
Confidence 457899999998743444556789999863
No 41
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=47.12 E-value=20 Score=39.27 Aligned_cols=64 Identities=22% Similarity=0.411 Sum_probs=42.8
Q ss_pred HHHHhhhcCCCceeeeeccccCcce--eecccCCceeeccCCCC--------CCceeecchHhHHHHHHHHHhCCCceE
Q 003180 756 FLKERLFDQSDAYRVHVCEHCGLIA--IANLKKNSFECRGCKNK--------TDIVQVHIPYACKLLFQELMAMAIAPR 824 (842)
Q Consensus 756 ~l~erl~~~SD~~~~~vC~~cG~~~--~~~~~~~~~~C~~C~~~--------~~i~~v~iPy~~kll~~EL~sm~I~~~ 824 (842)
.|.| |+..+| ..+|..||... |+..+-+.|.|..|..- .+|..|.+=.=.-==+++|.+|| +.+
T Consensus 15 ~l~~-Ll~~~~---N~~CADC~a~~P~WaSwnlGvFiC~~C~giHR~lg~hiSkVkSv~LD~W~~eqv~~m~~~G-N~~ 88 (287)
T KOG0703|consen 15 RLRE-LLREPD---NKVCADCGAKGPRWASWNLGVFICLRCAGIHRSLGVHISKVKSVTLDEWTDEQVDFMISMG-NAK 88 (287)
T ss_pred HHHH-HHcCcc---cCcccccCCCCCCeEEeecCeEEEeecccccccccchhheeeeeeccccCHHHHHHHHHHc-chh
Confidence 4556 445566 67899999875 56677789999999762 23444555444444567788877 443
No 42
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=46.48 E-value=12 Score=36.93 Aligned_cols=43 Identities=19% Similarity=0.354 Sum_probs=28.7
Q ss_pred cHHHHHHhhhcCCCceeeeeccccCcceeec------ccCCceeeccCCC
Q 003180 753 ASHFLKERLFDQSDAYRVHVCEHCGLIAIAN------LKKNSFECRGCKN 796 (842)
Q Consensus 753 as~~l~erl~~~SD~~~~~vC~~cG~~~~~~------~~~~~~~C~~C~~ 796 (842)
+..-|++++-..++ ...++|++||...... -..+.+.|+.|+.
T Consensus 83 ~~~~L~~~l~~e~~-~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~ 131 (147)
T smart00531 83 MRKRLEDKLEDETN-NAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGE 131 (147)
T ss_pred HHHHHHHHHhcccC-CcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCC
Confidence 34456788866665 4589999999754211 1233489999986
No 43
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=46.18 E-value=17 Score=28.06 Aligned_cols=26 Identities=19% Similarity=0.600 Sum_probs=17.6
Q ss_pred eeccccCcce-eecccCCceeeccCCC
Q 003180 771 HVCEHCGLIA-IANLKKNSFECRGCKN 796 (842)
Q Consensus 771 ~vC~~cG~~~-~~~~~~~~~~C~~C~~ 796 (842)
++|+.||.-. ..+...+.++|+.|+.
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~ 27 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCGL 27 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-B
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCCC
Confidence 4688998854 3455566678999964
No 44
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=44.01 E-value=14 Score=29.39 Aligned_cols=25 Identities=40% Similarity=0.860 Sum_probs=16.9
Q ss_pred eccccCcceeec-cc-CCceeeccCCC
Q 003180 772 VCEHCGLIAIAN-LK-KNSFECRGCKN 796 (842)
Q Consensus 772 vC~~cG~~~~~~-~~-~~~~~C~~C~~ 796 (842)
.|+.||.++... .. .+.++|+.|+-
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~ 28 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGY 28 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCC
Confidence 488999887532 22 23678999974
No 45
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=43.95 E-value=12 Score=35.25 Aligned_cols=31 Identities=23% Similarity=0.531 Sum_probs=22.3
Q ss_pred eeeeccccCcceeecccCCceeeccCCCCCCc
Q 003180 769 RVHVCEHCGLIAIANLKKNSFECRGCKNKTDI 800 (842)
Q Consensus 769 ~~~vC~~cG~~~~~~~~~~~~~C~~C~~~~~i 800 (842)
+-++|..||...| .+++.--+|+.|+..-.+
T Consensus 8 tKR~Cp~CG~kFY-DLnk~PivCP~CG~~~~~ 38 (108)
T PF09538_consen 8 TKRTCPSCGAKFY-DLNKDPIVCPKCGTEFPP 38 (108)
T ss_pred CcccCCCCcchhc-cCCCCCccCCCCCCccCc
Confidence 4578999998775 345556679999985333
No 46
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=43.56 E-value=15 Score=25.17 Aligned_cols=23 Identities=26% Similarity=0.694 Sum_probs=14.0
Q ss_pred ccccCcceeecccCCceeeccCC
Q 003180 773 CEHCGLIAIANLKKNSFECRGCK 795 (842)
Q Consensus 773 C~~cG~~~~~~~~~~~~~C~~C~ 795 (842)
|..||.....-.....|.|+.|+
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCG 23 (24)
T ss_pred CccCCCcccCcccCceEeCCCCC
Confidence 67787765322223457888886
No 47
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=42.11 E-value=11 Score=31.42 Aligned_cols=30 Identities=23% Similarity=0.531 Sum_probs=16.4
Q ss_pred ceeeeeccccCcceeecccCCceeeccCCC
Q 003180 767 AYRVHVCEHCGLIAIANLKKNSFECRGCKN 796 (842)
Q Consensus 767 ~~~~~vC~~cG~~~~~~~~~~~~~C~~C~~ 796 (842)
.....+|..||......-+.-.|.|+.|+.
T Consensus 4 ~~~~~~CtSCg~~i~~~~~~~~F~CPnCG~ 33 (59)
T PRK14890 4 MMEPPKCTSCGIEIAPREKAVKFLCPNCGE 33 (59)
T ss_pred cccCccccCCCCcccCCCccCEeeCCCCCC
Confidence 344556777776553222223566777765
No 48
>PRK00420 hypothetical protein; Validated
Probab=41.58 E-value=17 Score=34.45 Aligned_cols=26 Identities=23% Similarity=0.391 Sum_probs=19.8
Q ss_pred eeccccCcceeecccCCceeeccCCCC
Q 003180 771 HVCEHCGLIAIANLKKNSFECRGCKNK 797 (842)
Q Consensus 771 ~vC~~cG~~~~~~~~~~~~~C~~C~~~ 797 (842)
..|+.||...... +.+..+|+.|+..
T Consensus 24 ~~CP~Cg~pLf~l-k~g~~~Cp~Cg~~ 49 (112)
T PRK00420 24 KHCPVCGLPLFEL-KDGEVVCPVHGKV 49 (112)
T ss_pred CCCCCCCCcceec-CCCceECCCCCCe
Confidence 3599999888543 4567899999873
No 49
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=38.75 E-value=21 Score=35.43 Aligned_cols=28 Identities=25% Similarity=0.498 Sum_probs=20.7
Q ss_pred eeeccccCcceeecccCCceeeccCCCC
Q 003180 770 VHVCEHCGLIAIANLKKNSFECRGCKNK 797 (842)
Q Consensus 770 ~~vC~~cG~~~~~~~~~~~~~C~~C~~~ 797 (842)
.+||.+||...........+-|+.|+..
T Consensus 112 ~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~ 139 (146)
T PF07295_consen 112 TLVCENCGHEVELTHPERLPPCPKCGHT 139 (146)
T ss_pred eEecccCCCEEEecCCCcCCCCCCCCCC
Confidence 6799999987654434446789999874
No 50
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=38.65 E-value=19 Score=35.43 Aligned_cols=36 Identities=19% Similarity=0.462 Sum_probs=25.0
Q ss_pred ceeeeeccccCcceeecccCCceeeccCCCCCCceeecch
Q 003180 767 AYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIP 806 (842)
Q Consensus 767 ~~~~~vC~~cG~~~~~~~~~~~~~C~~C~~~~~i~~v~iP 806 (842)
+-..--|.+||+...- -..+|..|++.+++..+.+|
T Consensus 26 kl~g~kC~~CG~v~~P----Pr~~Cp~C~~~~~~E~vels 61 (140)
T COG1545 26 KLLGTKCKKCGRVYFP----PRAYCPKCGSETELEWVELS 61 (140)
T ss_pred cEEEEEcCCCCeEEcC----CcccCCCCCCCCceEEEEeC
Confidence 3455679999998742 13479999987665556555
No 51
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=37.03 E-value=20 Score=26.93 Aligned_cols=24 Identities=21% Similarity=0.476 Sum_probs=18.3
Q ss_pred eccccCcceeecccCCceeeccCCC
Q 003180 772 VCEHCGLIAIANLKKNSFECRGCKN 796 (842)
Q Consensus 772 vC~~cG~~~~~~~~~~~~~C~~C~~ 796 (842)
.|..||... .....+.++|..|+.
T Consensus 10 ~C~~C~~~~-~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 10 PCPVCGSRW-FYSDDGFYYCDRCGH 33 (36)
T ss_pred cCCCCCCeE-eEccCCEEEhhhCce
Confidence 399999984 444556789999986
No 52
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=36.91 E-value=19 Score=34.79 Aligned_cols=29 Identities=10% Similarity=0.130 Sum_probs=22.1
Q ss_pred eeeeeccccCcceeecccCCceeeccCCCC
Q 003180 768 YRVHVCEHCGLIAIANLKKNSFECRGCKNK 797 (842)
Q Consensus 768 ~~~~vC~~cG~~~~~~~~~~~~~C~~C~~~ 797 (842)
-.-++|.+||...| .+++.-.+|+.|+..
T Consensus 7 GtKr~Cp~cg~kFY-DLnk~p~vcP~cg~~ 35 (129)
T TIGR02300 7 GTKRICPNTGSKFY-DLNRRPAVSPYTGEQ 35 (129)
T ss_pred CccccCCCcCcccc-ccCCCCccCCCcCCc
Confidence 34578999998775 455566789999875
No 53
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=35.62 E-value=31 Score=27.11 Aligned_cols=27 Identities=26% Similarity=0.709 Sum_probs=19.6
Q ss_pred eeeccccCcceeecccCCceeeccCCCC
Q 003180 770 VHVCEHCGLIAIANLKKNSFECRGCKNK 797 (842)
Q Consensus 770 ~~vC~~cG~~~~~~~~~~~~~C~~C~~~ 797 (842)
.++|..||...... ..+...|+.|+..
T Consensus 2 ~Y~C~~Cg~~~~~~-~~~~irC~~CG~r 28 (44)
T smart00659 2 IYICGECGRENEIK-SKDVVRCRECGYR 28 (44)
T ss_pred EEECCCCCCEeecC-CCCceECCCCCce
Confidence 58999999865332 3456789999874
No 54
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=35.23 E-value=27 Score=31.79 Aligned_cols=29 Identities=17% Similarity=0.608 Sum_probs=23.0
Q ss_pred eeeeeccccCcceeecccCCceeeccCCC
Q 003180 768 YRVHVCEHCGLIAIANLKKNSFECRGCKN 796 (842)
Q Consensus 768 ~~~~vC~~cG~~~~~~~~~~~~~C~~C~~ 796 (842)
+.-+.|+.||.....-...+.|.|..|+.
T Consensus 33 ~~ky~Cp~Cgk~~vkR~a~GIW~C~~C~~ 61 (90)
T PF01780_consen 33 HAKYTCPFCGKTSVKRVATGIWKCKKCGK 61 (90)
T ss_dssp HS-BEESSSSSSEEEEEETTEEEETTTTE
T ss_pred hCCCcCCCCCCceeEEeeeEEeecCCCCC
Confidence 45688999999886655667899999985
No 55
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=33.11 E-value=20 Score=24.80 Aligned_cols=22 Identities=23% Similarity=0.578 Sum_probs=15.4
Q ss_pred eeccccCcceeecccCCceeeccCCC
Q 003180 771 HVCEHCGLIAIANLKKNSFECRGCKN 796 (842)
Q Consensus 771 ~vC~~cG~~~~~~~~~~~~~C~~C~~ 796 (842)
..|.+||..... +..+|+.|+.
T Consensus 3 ~~Cp~Cg~~~~~----~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDP----DAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCc----ccccChhhCC
Confidence 469999985422 3447999986
No 56
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=32.07 E-value=38 Score=25.27 Aligned_cols=26 Identities=27% Similarity=0.713 Sum_probs=15.6
Q ss_pred eeccccCcceeecc-cCCceeeccCCC
Q 003180 771 HVCEHCGLIAIANL-KKNSFECRGCKN 796 (842)
Q Consensus 771 ~vC~~cG~~~~~~~-~~~~~~C~~C~~ 796 (842)
.-|..||.+++... +.....|+.|+-
T Consensus 2 ~FCp~C~nlL~p~~~~~~~~~C~~C~Y 28 (35)
T PF02150_consen 2 RFCPECGNLLYPKEDKEKRVACRTCGY 28 (35)
T ss_dssp -BETTTTSBEEEEEETTTTEEESSSS-
T ss_pred eeCCCCCccceEcCCCccCcCCCCCCC
Confidence 35999999985321 122227999964
No 57
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=31.66 E-value=37 Score=24.96 Aligned_cols=25 Identities=20% Similarity=0.563 Sum_probs=16.4
Q ss_pred eeccccCcceeecccCCceeeccCCC
Q 003180 771 HVCEHCGLIAIANLKKNSFECRGCKN 796 (842)
Q Consensus 771 ~vC~~cG~~~~~~~~~~~~~C~~C~~ 796 (842)
++|..||.... ....+...|+.|+-
T Consensus 1 Y~C~~Cg~~~~-~~~~~~irC~~CG~ 25 (32)
T PF03604_consen 1 YICGECGAEVE-LKPGDPIRCPECGH 25 (32)
T ss_dssp EBESSSSSSE--BSTSSTSSBSSSS-
T ss_pred CCCCcCCCeeE-cCCCCcEECCcCCC
Confidence 57999998764 22334558999975
No 58
>PF10385 RNA_pol_Rpb2_45: RNA polymerase beta subunit external 1 domain; InterPro: IPR019462 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 catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This entry represents a domain in prokaryotic polymerases that spans the gap between domains 4 and 5 of the protein. It is also known as the external 1 region of the polymerase and is bound in association with the external 2 region []. ; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2GHO_C 1YNN_C 1I6V_C 1YNJ_C 1HQM_C 1SMY_M 3DXJ_M 3AOI_C 2A68_M 1ZYR_C ....
Probab=31.31 E-value=58 Score=27.83 Aligned_cols=27 Identities=30% Similarity=0.380 Sum_probs=21.2
Q ss_pred CcEEEeccccccceeEeeccccccccc
Q 003180 313 GFIEYIDTEEEETTMISMTINDLVQAR 339 (842)
Q Consensus 313 g~IE~Id~~Eq~~~~Ia~~~~~l~~~~ 339 (842)
..|+||.|.||+...||.....+.+.+
T Consensus 11 ~~i~YLtA~eEe~~~IAqA~~~ld~~g 37 (66)
T PF10385_consen 11 DEIEYLTADEEEKYVIAQANAPLDEDG 37 (66)
T ss_dssp CEEEEEECTTCCCSEEE-TTS-BSSTT
T ss_pred CeeEEEchhhcCCcEecccCeeeecCC
Confidence 458999999999999999887776643
No 59
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=31.30 E-value=26 Score=29.64 Aligned_cols=29 Identities=24% Similarity=0.598 Sum_probs=22.3
Q ss_pred eeeeeccccCcceeecccCCceeeccCCC
Q 003180 768 YRVHVCEHCGLIAIANLKKNSFECRGCKN 796 (842)
Q Consensus 768 ~~~~vC~~cG~~~~~~~~~~~~~C~~C~~ 796 (842)
++...|..||...........+.|+.|+-
T Consensus 26 ~TSq~C~~CG~~~~~~~~~r~~~C~~Cg~ 54 (69)
T PF07282_consen 26 YTSQTCPRCGHRNKKRRSGRVFTCPNCGF 54 (69)
T ss_pred CCccCccCcccccccccccceEEcCCCCC
Confidence 35567999998875545566789999975
No 60
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=30.12 E-value=34 Score=28.59 Aligned_cols=28 Identities=21% Similarity=0.571 Sum_probs=19.7
Q ss_pred eeeeeccccCcceeecccCCceeeccCCC
Q 003180 768 YRVHVCEHCGLIAIANLKKNSFECRGCKN 796 (842)
Q Consensus 768 ~~~~vC~~cG~~~~~~~~~~~~~C~~C~~ 796 (842)
..++||..||.-.. -..++...|+-|+-
T Consensus 18 ~miYiCgdC~~en~-lk~~D~irCReCG~ 45 (62)
T KOG3507|consen 18 TMIYICGDCGQENT-LKRGDVIRCRECGY 45 (62)
T ss_pred cEEEEecccccccc-ccCCCcEehhhcch
Confidence 35799999997552 12345678999974
No 61
>PRK11032 hypothetical protein; Provisional
Probab=29.95 E-value=37 Score=34.26 Aligned_cols=28 Identities=21% Similarity=0.303 Sum_probs=20.7
Q ss_pred eeeccccCcceeecccCCceeeccCCCC
Q 003180 770 VHVCEHCGLIAIANLKKNSFECRGCKNK 797 (842)
Q Consensus 770 ~~vC~~cG~~~~~~~~~~~~~C~~C~~~ 797 (842)
+.||.+||...........+-|+.|+..
T Consensus 124 ~LvC~~Cg~~~~~~~p~~i~pCp~C~~~ 151 (160)
T PRK11032 124 NLVCEKCHHHLAFYTPEVLPLCPKCGHD 151 (160)
T ss_pred eEEecCCCCEEEecCCCcCCCCCCCCCC
Confidence 5689999987754444445679999874
No 62
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=27.85 E-value=46 Score=25.88 Aligned_cols=23 Identities=26% Similarity=0.715 Sum_probs=17.2
Q ss_pred eccccCcceeecccCCceeeccCC
Q 003180 772 VCEHCGLIAIANLKKNSFECRGCK 795 (842)
Q Consensus 772 vC~~cG~~~~~~~~~~~~~C~~C~ 795 (842)
.|+.||.+...+ +++..+|..|+
T Consensus 19 ~Cp~C~~PL~~~-k~g~~~Cv~C~ 41 (41)
T PF06677_consen 19 HCPDCGTPLMRD-KDGKIYCVSCG 41 (41)
T ss_pred ccCCCCCeeEEe-cCCCEECCCCC
Confidence 589999988653 34567899985
No 63
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=27.11 E-value=35 Score=25.40 Aligned_cols=24 Identities=21% Similarity=0.567 Sum_probs=11.1
Q ss_pred eccccCcceee----cccCCceeeccCC
Q 003180 772 VCEHCGLIAIA----NLKKNSFECRGCK 795 (842)
Q Consensus 772 vC~~cG~~~~~----~~~~~~~~C~~C~ 795 (842)
-|..||..+.. .....+.+|..|+
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg 29 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPACG 29 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTTT
T ss_pred ccccccChhhhhcCCCCCccceECCCCC
Confidence 37888876532 1234467788885
No 64
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=26.00 E-value=31 Score=25.94 Aligned_cols=26 Identities=31% Similarity=0.589 Sum_probs=17.1
Q ss_pred eeccccCccee--ecccCCceeeccCCC
Q 003180 771 HVCEHCGLIAI--ANLKKNSFECRGCKN 796 (842)
Q Consensus 771 ~vC~~cG~~~~--~~~~~~~~~C~~C~~ 796 (842)
++|..||.+.. .+..+....|-.|+.
T Consensus 2 r~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~ 29 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNPPKVEGVCDNCGG 29 (36)
T ss_dssp EEETTTTEEEETTTB--SSTTBCTTTTE
T ss_pred cCcCCCCCccccccCCCCCCCccCCCCC
Confidence 58999998763 233333457998876
No 65
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=25.77 E-value=41 Score=36.82 Aligned_cols=24 Identities=25% Similarity=0.589 Sum_probs=17.1
Q ss_pred eccccCcceeec--ccCCceeeccCC
Q 003180 772 VCEHCGLIAIAN--LKKNSFECRGCK 795 (842)
Q Consensus 772 vC~~cG~~~~~~--~~~~~~~C~~C~ 795 (842)
-|..||...... -..+.|||+.|.
T Consensus 247 pC~~CGt~I~k~~~~gR~t~~CP~CQ 272 (273)
T COG0266 247 PCRRCGTPIEKIKLGGRSTFYCPVCQ 272 (273)
T ss_pred CCCccCCEeEEEEEcCCcCEeCCCCC
Confidence 499999876322 134578999996
No 66
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=24.98 E-value=27 Score=29.23 Aligned_cols=27 Identities=26% Similarity=0.588 Sum_probs=14.9
Q ss_pred eeeccccCcceeecccCCceeeccCCC
Q 003180 770 VHVCEHCGLIAIANLKKNSFECRGCKN 796 (842)
Q Consensus 770 ~~vC~~cG~~~~~~~~~~~~~C~~C~~ 796 (842)
..+|..||........--.|.|+.|++
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe 35 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGE 35 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCc
Confidence 456777776552222222466777764
No 67
>COG2401 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]
Probab=23.84 E-value=47 Score=38.53 Aligned_cols=54 Identities=35% Similarity=0.651 Sum_probs=37.5
Q ss_pred HhhhcCCCcee--eeeccccCcceeecccCCceeeccCCCCCCceeec--chHhHHHHHHHHH
Q 003180 759 ERLFDQSDAYR--VHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVH--IPYACKLLFQELM 817 (842)
Q Consensus 759 erl~~~SD~~~--~~vC~~cG~~~~~~~~~~~~~C~~C~~~~~i~~v~--iPy~~kll~~EL~ 817 (842)
|-....||+-. .|-|..||.+..+|.+ +.| .|++..++..|. +| |.++|+-||-
T Consensus 117 eqyhyas~k~~va~w~c~~cg~~iean~k---p~c-~cg~~~~~~ei~gs~p-asrf~i~el~ 174 (593)
T COG2401 117 EQYHYASQKEKVALWRCEKCGTIIEANTK---PEC-KCGSHVHILEIKGSTP-ASRFLIVELV 174 (593)
T ss_pred HHhhhccccceEEEEecchhchhhhhcCC---ccc-CCCCceEEEEeecCCc-chheeeeehh
Confidence 55677887765 5779999999877653 579 898855554442 34 5677777764
No 68
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=23.77 E-value=40 Score=30.77 Aligned_cols=29 Identities=24% Similarity=0.556 Sum_probs=22.5
Q ss_pred eeeeeccccCcceeecccCCceeeccCCC
Q 003180 768 YRVHVCEHCGLIAIANLKKNSFECRGCKN 796 (842)
Q Consensus 768 ~~~~vC~~cG~~~~~~~~~~~~~C~~C~~ 796 (842)
+..+.|+-||.....-...+.|.|..|+.
T Consensus 33 ~a~y~CpfCgk~~vkR~a~GIW~C~~C~~ 61 (91)
T TIGR00280 33 KAKYVCPFCGKKTVKRGSTGIWTCRKCGA 61 (91)
T ss_pred hcCccCCCCCCCceEEEeeEEEEcCCCCC
Confidence 45678999998776555556789999986
No 69
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=22.32 E-value=70 Score=35.90 Aligned_cols=42 Identities=21% Similarity=0.529 Sum_probs=28.8
Q ss_pred HHHHHhhhcCCCceeeeeccccCcceeecccCCceeeccCCCCCCceeec
Q 003180 755 HFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVH 804 (842)
Q Consensus 755 ~~l~erl~~~SD~~~~~vC~~cG~~~~~~~~~~~~~C~~C~~~~~i~~v~ 804 (842)
.++.|++-.+++ +-|.+||.-+..- .|.|+.|+.=..|+.+.
T Consensus 343 ~mvge~l~~~~~----YRC~~CGF~a~~l----~W~CPsC~~W~TikPir 384 (389)
T COG2956 343 DMVGEQLRRKPR----YRCQNCGFTAHTL----YWHCPSCRAWETIKPIR 384 (389)
T ss_pred HHHHHHHhhcCC----ceecccCCcceee----eeeCCCcccccccCCcc
Confidence 455677766665 5699999777432 56799998866665543
No 70
>PHA00626 hypothetical protein
Probab=21.19 E-value=69 Score=26.61 Aligned_cols=25 Identities=20% Similarity=0.508 Sum_probs=15.8
Q ss_pred eccccCcce-eec----ccCCceeeccCCC
Q 003180 772 VCEHCGLIA-IAN----LKKNSFECRGCKN 796 (842)
Q Consensus 772 vC~~cG~~~-~~~----~~~~~~~C~~C~~ 796 (842)
.|++||+-- +.. .-.+.|.|+.|+=
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY 31 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGY 31 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCC
Confidence 599999832 111 1135789999973
No 71
>PF11202 PRTase_1: Phosphoribosyl transferase (PRTase); InterPro: IPR011215 This is a family of uncharacterised bacterial proteins.
Probab=21.08 E-value=1.6e+02 Score=31.85 Aligned_cols=45 Identities=27% Similarity=0.533 Sum_probs=29.7
Q ss_pred cEEEEECCEEEEEEcChHHHHHHHHHhhhcCC--CCCcEEEEEeccCCeEEEecCCCee
Q 003180 217 ATKIFVNGCWVGIHRDPEMLVKTLRRLRRRVD--VNTEVGVVRDIRLKELRIYTDYGRC 273 (842)
Q Consensus 217 ~~~VflnG~~iG~~~~~~~lv~~lR~lRr~~~--i~~~vsi~~~~~~~~i~I~td~GRl 273 (842)
...||||| |-|.-.=..+|.+.++.+..+.- ++ +.+.+.+|+|..
T Consensus 145 ~~ivFVDG-WTGKGaI~~eL~~al~~~~~~~~~~~~-----------~~LaVLaDp~g~ 191 (257)
T PF11202_consen 145 ESIVFVDG-WTGKGAITRELKKALAAFNARYGTRLS-----------PDLAVLADPAGC 191 (257)
T ss_pred cceEEEec-CccccHHHHHHHHHHHHHHhhcCCCCC-----------CCeEEEecCccc
Confidence 34699998 88865545678888877765432 33 456666777653
No 72
>PF13533 Biotin_lipoyl_2: Biotin-lipoyl like
Probab=20.71 E-value=71 Score=25.46 Aligned_cols=17 Identities=24% Similarity=0.335 Sum_probs=14.5
Q ss_pred CcCCCcEEcCCCEEEEe
Q 003180 510 LAPPGTRVSGEDVIIGK 526 (842)
Q Consensus 510 l~~~G~~v~~gdvli~k 526 (842)
.++.|+.|++||+|+--
T Consensus 17 ~V~~G~~VkkGd~L~~l 33 (50)
T PF13533_consen 17 YVKEGQQVKKGDVLLVL 33 (50)
T ss_pred EecCCCEEcCCCEEEEE
Confidence 46789999999999764
No 73
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=20.56 E-value=46 Score=22.47 Aligned_cols=20 Identities=25% Similarity=0.677 Sum_probs=13.8
Q ss_pred ccccCcceeecccCCceeeccCCC
Q 003180 773 CEHCGLIAIANLKKNSFECRGCKN 796 (842)
Q Consensus 773 C~~cG~~~~~~~~~~~~~C~~C~~ 796 (842)
|.+||.-... +..+|..|+.
T Consensus 2 Cp~CG~~~~~----~~~fC~~CG~ 21 (23)
T PF13240_consen 2 CPNCGAEIED----DAKFCPNCGT 21 (23)
T ss_pred CcccCCCCCC----cCcchhhhCC
Confidence 8899976632 2346999975
No 74
>PRK10556 hypothetical protein; Provisional
Probab=20.38 E-value=66 Score=29.63 Aligned_cols=35 Identities=20% Similarity=0.406 Sum_probs=29.4
Q ss_pred CCCCCCCCCCceEEeCCCCCCCCCcHHHHHHHHhh
Q 003180 608 DMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMG 642 (842)
Q Consensus 608 dmPft~~G~~pDiIiNPh~~PSRMtiGql~E~~~g 642 (842)
..|---.|-.++-.=-||||-|||-+-..+.++.|
T Consensus 77 ~FPlyl~g~~~~~yGIpHGFsSR~~L~ryl~~mF~ 111 (111)
T PRK10556 77 QFPLYLAGERHEHYGIPHGFSSREALERYLNGMFG 111 (111)
T ss_pred ccccccccCccccccCCcCcchHHHHHHHHHHhcC
Confidence 57777788889988899999999998888877654
No 75
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=20.11 E-value=46 Score=25.46 Aligned_cols=26 Identities=19% Similarity=0.432 Sum_probs=13.9
Q ss_pred eccccCcce----eecccCCceeeccCCCC
Q 003180 772 VCEHCGLIA----IANLKKNSFECRGCKNK 797 (842)
Q Consensus 772 vC~~cG~~~----~~~~~~~~~~C~~C~~~ 797 (842)
-|..|+.+. .-+...+.++|.+|+..
T Consensus 4 rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 4 RCRRCRAYLNPFCQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp B-TTT--BS-TTSEEETTTTEEEETTT--E
T ss_pred ccCCCCCEECCcceEcCCCCEEECcCCCCc
Confidence 588998765 12223457899999864
Done!