Query psy3015
Match_columns 1791
No_of_seqs 624 out of 2973
Neff 5.6
Searched_HMMs 46136
Date Fri Aug 16 23:20:51 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3015.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3015hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0260|consensus 100.0 2E-188 5E-193 1714.4 52.2 894 45-1412 495-1430(1605)
2 KOG0261|consensus 100.0 5E-150 1E-154 1353.9 19.1 750 45-889 519-1366(1386)
3 PRK14977 bifunctional DNA-dire 100.0 7E-135 2E-139 1338.2 59.2 757 45-1403 495-1318(1321)
4 KOG0262|consensus 100.0 7E-119 2E-123 1106.7 49.0 405 11-462 612-1032(1640)
5 KOG0260|consensus 100.0 2E-118 4E-123 1098.8 14.5 580 957-1719 706-1292(1605)
6 PRK08566 DNA-directed RNA poly 100.0 8.4E-93 1.8E-97 924.4 31.9 373 45-465 479-864 (882)
7 TIGR02390 RNA_pol_rpoA1 DNA-di 100.0 2E-92 4.4E-97 918.3 33.4 372 45-465 475-859 (868)
8 KOG0261|consensus 100.0 1.4E-72 3.1E-77 682.3 11.8 409 976-1404 758-1364(1386)
9 TIGR02386 rpoC_TIGR DNA-direct 100.0 6.9E-71 1.5E-75 712.8 20.7 292 45-454 464-786 (1140)
10 PRK00566 DNA-directed RNA poly 100.0 3.4E-69 7.3E-74 697.8 21.8 277 45-437 472-779 (1156)
11 PRK14977 bifunctional DNA-dire 100.0 1.2E-68 2.5E-73 709.4 24.5 422 988-1718 749-1182(1321)
12 PRK09603 bifunctional DNA-dire 100.0 2.5E-62 5.5E-67 654.0 37.3 294 45-453 1871-2193(2890)
13 PRK14906 DNA-directed RNA poly 100.0 6E-63 1.3E-67 637.4 21.7 280 45-441 560-883 (1460)
14 PRK14844 bifunctional DNA-dire 100.0 1E-60 2.2E-65 636.5 15.4 286 45-442 1915-2239(2836)
15 cd02584 RNAP_II_Rpb1_C Largest 100.0 4.3E-59 9.3E-64 559.9 22.6 380 988-1401 1-410 (410)
16 cd02584 RNAP_II_Rpb1_C Largest 100.0 3.4E-52 7.3E-57 500.5 16.8 264 1391-1719 3-283 (410)
17 TIGR02389 RNA_pol_rpoA2 DNA-di 100.0 8.3E-51 1.8E-55 481.9 20.2 325 985-1401 14-367 (367)
18 cd06528 RNAP_A'' A'' subunit o 100.0 1E-49 2.2E-54 473.3 20.5 328 982-1402 8-363 (363)
19 KOG0262|consensus 100.0 4.5E-50 9.7E-55 497.9 15.0 147 982-1132 886-1032(1640)
20 PRK02597 rpoC2 DNA-directed RN 100.0 1.1E-49 2.4E-54 518.8 16.2 207 153-441 6-217 (1331)
21 PRK14897 unknown domain/DNA-di 100.0 3.2E-48 7E-53 467.6 18.8 332 984-1404 152-506 (509)
22 TIGR02388 rpoC2_cyan DNA-direc 100.0 1.1E-47 2.4E-52 496.6 24.6 206 153-440 5-215 (1227)
23 PRK04309 DNA-directed RNA poly 100.0 5.1E-48 1.1E-52 461.6 19.0 325 985-1404 30-382 (383)
24 COG0086 RpoC DNA-directed RNA 100.0 6.5E-49 1.4E-53 504.2 11.0 354 45-466 426-797 (808)
25 cd02737 RNAP_IV_NRPD1_C Larges 100.0 7.6E-47 1.7E-51 450.1 15.8 313 1028-1400 31-381 (381)
26 cd02736 RNAP_III_Rpc1_C Larges 100.0 4E-44 8.7E-49 416.2 15.0 272 1005-1396 1-300 (300)
27 cd02735 RNAP_I_Rpa1_C Largest 100.0 6.2E-42 1.3E-46 400.8 15.3 279 1005-1399 1-309 (309)
28 TIGR02386 rpoC_TIGR DNA-direct 100.0 2.3E-39 5E-44 420.6 18.6 363 989-1395 676-1135(1140)
29 PRK00566 DNA-directed RNA poly 100.0 5.2E-40 1.1E-44 427.0 12.1 345 989-1397 685-1139(1156)
30 PRK14898 DNA-directed RNA poly 100.0 2.9E-39 6.2E-44 421.5 17.6 294 1020-1404 553-852 (858)
31 PF04998 RNA_pol_Rpb1_5: RNA p 100.0 1.8E-40 3.8E-45 384.6 -2.7 66 391-456 1-66 (277)
32 TIGR02389 RNA_pol_rpoA2 DNA-di 100.0 1.5E-38 3.3E-43 377.6 13.0 221 1390-1719 18-240 (367)
33 PF04990 RNA_pol_Rpb1_7: RNA p 100.0 6.9E-39 1.5E-43 333.2 5.3 124 1527-1681 1-126 (135)
34 PRK14906 DNA-directed RNA poly 100.0 6E-38 1.3E-42 406.6 10.8 354 988-1396 783-1237(1460)
35 TIGR02390 RNA_pol_rpoA1 DNA-di 100.0 5.8E-38 1.3E-42 409.7 7.1 149 988-1141 716-864 (868)
36 cd02737 RNAP_IV_NRPD1_C Larges 100.0 1.7E-36 3.7E-41 361.7 14.7 220 1416-1726 1-252 (381)
37 cd06528 RNAP_A'' A'' subunit o 100.0 1E-36 2.2E-41 362.7 11.9 217 1390-1719 15-235 (363)
38 PRK08566 DNA-directed RNA poly 100.0 1.8E-37 3.9E-42 406.2 4.6 142 988-1133 721-862 (882)
39 PRK14897 unknown domain/DNA-di 100.0 5.9E-36 1.3E-40 361.7 13.8 219 1390-1719 157-376 (509)
40 PRK14844 bifunctional DNA-dire 100.0 1.2E-35 2.5E-40 398.3 8.1 109 1284-1394 2635-2783(2836)
41 CHL00117 rpoC2 RNA polymerase 100.0 2.9E-34 6.3E-39 379.4 18.7 205 152-441 11-223 (1364)
42 PRK04309 DNA-directed RNA poly 100.0 1.8E-34 4E-39 345.5 11.8 215 1390-1719 34-252 (383)
43 PF04998 RNA_pol_Rpb1_5: RNA p 100.0 4E-35 8.7E-40 339.9 3.4 257 1057-1352 1-275 (277)
44 PRK02597 rpoC2 DNA-directed RN 100.0 1.3E-34 2.8E-39 378.6 1.5 96 988-1104 117-213 (1331)
45 cd02736 RNAP_III_Rpc1_C Larges 100.0 5.1E-35 1.1E-39 340.3 -2.1 166 694-879 129-300 (300)
46 PRK09603 bifunctional DNA-dire 100.0 7.9E-34 1.7E-38 382.2 6.7 95 989-1104 2083-2178(2890)
47 TIGR02388 rpoC2_cyan DNA-direc 100.0 6E-34 1.3E-38 369.7 3.7 96 988-1104 116-212 (1227)
48 cd02735 RNAP_I_Rpa1_C Largest 100.0 1.2E-33 2.6E-38 331.3 -3.0 166 697-882 136-309 (309)
49 CHL00117 rpoC2 RNA polymerase 100.0 5.8E-33 1.3E-37 367.1 1.9 95 988-1103 123-218 (1364)
50 PRK14898 DNA-directed RNA poly 100.0 5.2E-30 1.1E-34 335.1 1.5 174 695-888 672-853 (858)
51 cd00630 RNAP_largest_subunit_C 99.9 2.9E-26 6.2E-31 244.9 7.1 110 1286-1395 49-158 (158)
52 cd00630 RNAP_largest_subunit_C 99.9 2.1E-26 4.5E-31 246.0 4.5 102 777-878 56-158 (158)
53 PF04983 RNA_pol_Rpb1_3: RNA p 99.9 2.1E-24 4.6E-29 232.3 6.1 142 52-207 1-158 (158)
54 PF05000 RNA_pol_Rpb1_4: RNA p 99.9 3.5E-24 7.5E-29 217.1 5.1 101 284-384 8-108 (108)
55 PF04992 RNA_pol_Rpb1_6: RNA p 99.9 5.2E-25 1.1E-29 242.2 -2.9 181 630-1009 1-187 (187)
56 COG0086 RpoC DNA-directed RNA 99.9 8E-23 1.7E-27 264.3 5.1 130 993-1130 662-791 (808)
57 cd02655 RNAP_beta'_C Largest s 99.8 1E-20 2.2E-25 209.4 8.2 109 1285-1395 54-204 (204)
58 cd02655 RNAP_beta'_C Largest s 99.8 3.1E-20 6.6E-25 205.7 5.7 96 781-878 69-204 (204)
59 PF04990 RNA_pol_Rpb1_7: RNA p 99.8 6.7E-20 1.5E-24 191.5 3.7 132 1090-1224 2-135 (135)
60 PF05000 RNA_pol_Rpb1_4: RNA p 99.1 2.4E-11 5.2E-16 123.7 4.4 61 990-1050 48-108 (108)
61 PF04992 RNA_pol_Rpb1_6: RNA p 98.7 5E-10 1.1E-14 124.3 -6.1 176 1134-1410 4-187 (187)
62 PF04997 RNA_pol_Rpb1_1: RNA p 97.8 2E-06 4.4E-11 102.4 -2.5 69 13-82 198-266 (337)
63 TIGR02387 rpoC1_cyan DNA-direc 92.0 0.087 1.9E-06 67.9 2.6 45 36-80 227-271 (619)
64 PRK02625 rpoC1 DNA-directed RN 91.7 0.1 2.3E-06 67.3 2.7 45 36-80 234-278 (627)
65 CHL00018 rpoC1 RNA polymerase 89.5 0.22 4.8E-06 65.0 2.9 42 39-80 256-297 (663)
66 smart00663 RPOLA_N RNA polymer 70.6 3.1 6.7E-05 50.4 2.9 37 45-81 1-37 (295)
No 1
>KOG0260|consensus
Probab=100.00 E-value=2.2e-188 Score=1714.42 Aligned_cols=894 Identities=62% Similarity=0.965 Sum_probs=826.8
Q ss_pred ceEEeeccCCCCCCCCCeEEe-------------cCccccHhHHHHHHhcCCccCCCCC-CCceeCCCCcccHhhhhhhc
Q psy3015 45 DWMLVTVLPVPPLSVRPAVVM-------------HGSARNQEQMMNILMFLPIWDGKMP-QPCILKPKPLWTGKQVFSLI 110 (1791)
Q Consensus 45 ~~mlv~~~iVsP~~~rP~~~i-------------~Gs~~~rddlmqLlm~~~~~~~~lP-~PaIlKP~~LWTGKQIfS~i 110 (1791)
++++|++|||+||+|||+|+| +.+|++++++|||+||++.|++..| +|||+||+||||||||||++
T Consensus 495 EL~~vpkQiispQsnkpvmgivQDTLta~R~~t~Rd~Fl~r~~vmnLlm~~p~~d~~~Pa~pai~Kp~PlWTGkQifsli 574 (1605)
T KOG0260|consen 495 ELAMVPKQIISPQSNKPVMGIVQDTLTAVRKMTKRDVFLNRAQVMNLLMYVPDWDGPPPAKPAILKPKPLWTGKQIFSLI 574 (1605)
T ss_pred HHhhhhhhhcCCcCCCcceeeehhhHHHHHHHhhHhhhhcHHHHHHHHhhccccCCCCCCCcccCCCCcccchhhheeee
Confidence 689999999999999999999 2369999999999999999999999 99999999999999999999
Q ss_pred CCCCccccccCCCCCCCCCCCCCCCCCCCCCeEEEEcCeEEEEeeccccccCCCccHHHHHHHHhCHHHHHHHHHHHHHH
Q psy3015 111 IPGNVNMTRTHSTHPDDEDSGPYQWISPGDTKVVVEHGSLLMGILCKKSLGTSSGSLLHICFLELGHEVCGRFYGNIQTV 190 (1791)
Q Consensus 111 LP~~inl~~~~~~~~~~~~~~~~~~~~~~d~~ViI~nGeLl~G~ldKk~vG~s~~gLih~i~~~yG~~~a~~fL~~lqrL 190 (1791)
+|+++|+.+.+++|++++. .|++|+|++|+|.+|+++.|++||+++|++.|+|+|++|.+.||+.|+.|++.+|+|
T Consensus 575 iP~~in~~r~~s~h~d~~~----~~~~p~dt~~lie~g~l~~g~l~Kkt~G~s~g~lvh~i~~e~Gp~~~~~f~~~iQ~l 650 (1605)
T KOG0260|consen 575 IPGGINYIRDHSTHPDSED----ELISPGDTRVLIEGGELLIGVLCKKTVGSSAGGLVHVIFLEKGPKIARGFFDSIQTL 650 (1605)
T ss_pred cCCCcceecccccCcCCCc----ccccCCCceEEEeCCceEEEEeeccccccccCceEEEeehhhCHHHHHHHHHHHHHH
Confidence 9999999999999998654 388999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhcCcccccCCcccChhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccCCCCCCcchHHHHHHHHHHH
Q psy3015 191 VNNWLLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGHSIGIGDTIADPQTYLEIQMAIKKA 270 (1791)
Q Consensus 191 ~~~~L~~~GFSiGi~D~i~~~~t~~~i~~~i~~ak~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 270 (1791)
+|.||+.+|||+||+|.+++.+++++|++.|.+|+
T Consensus 651 in~wll~~gfsigIgDtiad~~t~~~iq~~I~~ak--------------------------------------------- 685 (1605)
T KOG0260|consen 651 INSWLLREGFSIGIGDTIADAATMCVIQNTIKEAK--------------------------------------------- 685 (1605)
T ss_pred HHHHHHhcCccccccccccCHHHHHHHHHHHHHHH---------------------------------------------
Confidence 99999999999999999999999999999999988
Q ss_pred HHHHHHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhhhhhhhhhccCCCChHHHHhhcCCCcchhhHHHHHhhcc
Q psy3015 271 KEDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVG 350 (1791)
Q Consensus 271 ~~~v~~~i~~~~~~~L~~~pg~~~~~~fE~~vn~iLn~~rd~~g~~~~~~l~~~N~l~~Mv~sGSKGS~iNisQi~acvG 350 (1791)
++|.+++++++++.|++.||+|+.++||++||.+||+|||++|.++++++.+.||+++|+.+|||||++||+|+++|||
T Consensus 686 -~dv~~vi~~a~~~~L~~~pg~tlretfe~~v~~vlndArd~~gssA~~sl~esNn~k~Mv~aGSKGs~inisQ~saCVG 764 (1605)
T KOG0260|consen 686 -RDVLAVIREAQNNELEPTPGRTLRETFENKVNRVLNDARDKSGSSAQKSLSESNNFKTMVVAGSKGSFINISQVSACVG 764 (1605)
T ss_pred -HHHHHHHHHHhhccccCCcchhHHHHHHHHHHHHHHHHHHhhhhHHHhhhhhcccHHHHHhhcCCCcceehhhhhhhhc
Confidence 5677788889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcccCCceeccCCccCCCCCCCCCCCCCcccceeccccccCCChhhhhhhcccCcccchhcccccCCcchhHHHHHHhhc
Q psy3015 351 QQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAME 430 (1791)
Q Consensus 351 QQ~veGkRIp~gf~~RtLPhF~~~d~~p~srGFV~nSfl~GL~P~EfFFHaMaGREGLIDTAVKTaeTGYlQRrLvK~LE 430 (1791)
||+|||+||||||.+||||||.++||+|++||||+||||+||+|+|||||||||||||||||||||+||||||||||+||
T Consensus 765 qQnVEgkrIpFGF~~Rtlphf~kDdysPesrGfVENSyL~GLtP~EfFfHamggREglidtavktaEtGyiqRRL~kame 844 (1605)
T KOG0260|consen 765 QQNVEGKRIPFGFPKRTLPHFSKDDYSPESRGFVENSYLTGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLMKAME 844 (1605)
T ss_pred cccccccccccCCCcccccccccCCCCccccceeecccccCCCHHHHHHHHhcccchhhhhhhcccccchHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceEEeecCcEEecCCceEEEEecCCCCCcccccccccccccchhhhhhccccCCCCCCCccccchhhhhhhhcCCccccc
Q psy3015 431 SVMVHYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQRIDTVALSHKKFEDKYRFDPSNERPTLRNVSSLRRVVNSKPLLIG 510 (1791)
Q Consensus 431 Dl~V~YDgTVRns~G~IVQF~YGeDGlD~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 510 (1791)
|++|+||||||||.|++|||.|||||+|++.+|.|+.+++..++..|+++|+++..+...+..
T Consensus 845 Dimv~yDgTVRNs~gqviQf~YGeDG~d~~~vE~q~~~~l~~~~a~f~~~~~~d~ld~~~~~~----------------- 907 (1605)
T KOG0260|consen 845 DIMVAYDGTVRNSLGQVIQFKYGEDGLDGHPVEFQNGETLGSLNACFESEFAYDALDEPISLS----------------- 907 (1605)
T ss_pred HHHhhcCcceecccceeEEEEeccCccccceeeccccccccchHHHHHhhhhhhhhcCcccch-----------------
Confidence 999999999999999999999999999999999999888888777776666653222110000
Q ss_pred cccchhhHHHHHHHHHHhccccchhHHHHHHHHHHhhhhhhhhhhcCCCCCccccccccchhhHHHHhhhhhhcccCCCh
Q psy3015 511 CWKLTSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPM 590 (1791)
Q Consensus 511 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~mt~~~~~~~~~~~gi~~~~~~~~~~~~~~e~~~~i~~a~~~~~~~~~ 590 (1791)
T Consensus 908 -------------------------------------------------------------------------------- 907 (1605)
T KOG0260|consen 908 -------------------------------------------------------------------------------- 907 (1605)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred hhhHHHHHHHHHHHHHhhcccccccccccceeeeecCCCcccccccccccceeecChhhhhcccccCCchhhHhhhhccH
Q psy3015 591 RGYIQRRLIKAMESVMVHYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQRIDTVALSHKKFEDKYRFDPSNERQLRRIFNE 670 (1791)
Q Consensus 591 ~~ri~~~~~k~ie~V~~~yd~~vr~~vg~~~~~~~gE~g~~~~~ie~~~ip~i~~~~~~~~~~~~~~~~~~~~l~~~~~~ 670 (1791)
.+
T Consensus 908 ------------------------------------------------------------------------------~~ 909 (1605)
T KOG0260|consen 908 ------------------------------------------------------------------------------SE 909 (1605)
T ss_pred ------------------------------------------------------------------------------hh
Confidence 00
Q ss_pred HHHHHhhcCCCchhhhHHhhhcccchHHHHHhhhhhhHhhccCChHHHHHHHHHHHHHHHHHHHHHhhccCCCcceeecc
Q psy3015 671 DVLRELMGSGDVISELEKEMVDHFSWKQLRRIFNEDVLRELMGSGDVISELEKEWEKLCEDREALREIFSSGESNVVLPC 750 (1791)
Q Consensus 671 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~~~~~e~~kL~~~~~~Lr~i~~~~~~~~~l~~ 750 (1791)
+.+++ +..+..+++.++.||++|+.|+..++.++..++.++.+|+
T Consensus 910 ~~~~e-----------------------------------~~~~~~l~~lle~e~~~l~~dr~~l~~i~~~g~~k~~lp~ 954 (1605)
T KOG0260|consen 910 EVVNE-----------------------------------ISELLKLQNLLECEYKKLVRDRRVLLYIFEYGDAKWPLPE 954 (1605)
T ss_pred hHhhh-----------------------------------hhhhHHHHHHHHHHHHhhhhhhhhhhhhcccCCcccccch
Confidence 11111 1222345567788999999999999999999999999999
Q ss_pred hhHHHHHHHhhhhccCCcccccccceEEEeccCcccHHHHHHHHhhcceeccchhhhhhhhhhcccceecceeccccccC
Q psy3015 751 NLMEVIFILQRWKLWGNENLRFLCKIIFVLSVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQ 830 (1791)
Q Consensus 751 N~~rii~~~~~~~~~~~~~~~~~~n~i~~IaAR~~Ii~Ei~~v~~~~GIsVd~RHi~LlaD~MT~~G~v~~itR~Gl~~~ 830 (1791)
|++|+|||+++ +|.+..|..+.- +
T Consensus 955 n~~r~I~Na~~---------------~f~~~~r~~t~l-------------------------~---------------- 978 (1605)
T KOG0260|consen 955 NLQRIIWNALK---------------KFSIDERKPTDL-------------------------I---------------- 978 (1605)
T ss_pred hHHHHHHHHHh---------------hccccccccccc-------------------------c----------------
Confidence 99999999998 777877765540 0
Q ss_pred CCcccccchhhhhhHHHHHHhhccCCCCCCCcccceecCCCCCCCcceeeeccccccccCCccccccccccCCCCccccC
Q psy3015 831 DTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEKCKDGIEIPLATGMMGGPAGMFFG 910 (1791)
Q Consensus 831 ~~S~L~~aSFE~T~d~L~~Aa~~g~~D~i~GVSe~II~G~~~~iGTg~~~Ll~~~~k~k~~~~~~~~~~~~~~~~~~~~~ 910 (1791)
-.+-+.||++ +. +++
T Consensus 979 ------------------------~~~v~~g~~~----------------l~---e~l---------------------- 993 (1605)
T KOG0260|consen 979 ------------------------PFKVVKGVKE----------------LA---EKL---------------------- 993 (1605)
T ss_pred ------------------------hhhhhhhhhh----------------hh---hee----------------------
Confidence 0233445555 32 555
Q ss_pred CCCCCCCCCCCCCccccCccccccccCCCCcCCCCCCCCcccccCCcchhHHHHhcHHHHHHHHhHhhhhhHHHHhhccC
Q psy3015 911 SAATPSSMSPQMTPWAQSTPAYNALMSPGAAMTPGGPGFSPSVAGEDQLSKQANENATLLFQCLVRSTLCTKLVAENYRL 990 (1791)
Q Consensus 911 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Rs~L~sk~v~~~~rl 990 (1791)
+++.|+|.+|+ ||+ ||+|++|++|++|+|+++|||
T Consensus 994 ----------------------------------------~iv~g~~~~sr-aqr----l~~~lLrs~l~~krv~~e~rl 1028 (1605)
T KOG0260|consen 994 ----------------------------------------VIVRGEDYISR-AQR----LFNILLRSTLATKRVLEEYRL 1028 (1605)
T ss_pred ----------------------------------------EEeeCchhHHH-HHH----HHHHHHHhhHHHHHHHHHhcc
Confidence 68899999999 777 999999999999999999999
Q ss_pred CHHHHHHHHHHHhhhccceeccc--cccc---cc-----------------cCCcccCCCCcCccccccccCCCCCCCCc
Q psy3015 991 SSEAFEWLVGEIENRFQQAQVIA--CVGQ---QN-----------------VEGKRIPFGFRKRTLPHFIKDDYGPESRG 1048 (1791)
Q Consensus 991 n~~a~~~i~gei~~~~~~sqv~~--mvG~---Qs-----------------V~gKrI~~GfprRTLphf~kdd~~PESrG 1048 (1791)
|++||+|++|+|+.+|++++++| |||+ || |+.|||++|+|| |+++
T Consensus 1029 s~eaf~w~~~~Ie~~f~qa~a~pgemvg~lAaqsvgePatqmTlntfh~aGVssknVt~gvpr--lkei----------- 1095 (1605)
T KOG0260|consen 1029 SSEAFEWVLGEIEARFLQAEASPGEMVGALAAQSVGEPATQMTLNTFHYAGVSSKNVTLGVPR--LKEI----------- 1095 (1605)
T ss_pred cHHHHHHHhhhhhhheeeeecCccchHhHHHHHHhCCchhhcccchhcccceeeeeeeccCcc--hhhh-----------
Confidence 99999999999999999999999 9998 77 999999999999 9999
Q ss_pred ceeeccccCCCcceEEEeecCCCCccchhhhccchhH-HHHH-----HHHHHhcceEEEECCCCCCcccccCcceeeeec
Q psy3015 1049 FVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETV-NVLV-----FLFQVTANTAIYYDPDPQNTVIPEDQEFVNVYY 1122 (1791)
Q Consensus 1049 FV~Nsf~~GLTPsEfffhAMgGREGLiDTAvKTAEtG-YIqR-----RLvk~~Edv~V~YDgtvrnTVr~~d~~iVQf~Y 1122 (1791)
+|..++.+||+..+|+ ...+.|+.|.+ .||+ +|.++.....|+|||++.+|++++|.+||+.+|
T Consensus 1096 --~Nv~k~~ktpsLtV~l--------~g~~~k~~e~ak~v~~~le~ttl~~vt~~t~i~ydpdp~~tvI~ed~e~v~a~~ 1165 (1605)
T KOG0260|consen 1096 --INVAKNAKTPSLTVYL--------TGEAAKDNEWAKLVQCCLEHTTLKDVTRATEIYYDPDPQSTVIDEDREFVVAYY 1165 (1605)
T ss_pred --hhhhccCCCceEEEEe--------cchhhcchHHHHHHhhhcccccHHhhhccCcceecCCCcceeeccchhhHHhhh
Confidence 8999999999999999 56678888888 6776 789999999999999999999999999999999
Q ss_pred cCCCCCCCCcccceeeeeccccccccccCCHHHHHHHHhhccCCCcccccCCcccccceEEEEEecCccccccchhHHHH
Q psy3015 1123 EMPDFDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVD 1202 (1791)
Q Consensus 1123 g~dg~D~~~~~~wvlr~~Ld~~~m~dk~l~~~~I~~~I~~~~~~dl~~i~~d~n~~~l~~riri~~~~~~~~~~~ee~~~ 1202 (1791)
+.++.|..+++||++|+++|+.+|.+++++|++|.++|+..|+.|++++++++|++++++|+|+.+.+
T Consensus 1166 e~pd~D~~~ispwlLrlelDr~~m~dk~ltm~~ia~~i~~~f~~d~~~i~~ddna~klv~r~ri~~~~------------ 1233 (1605)
T KOG0260|consen 1166 EMPDEDVGRISPWLLRLELDRASMTDKKLTMEQIAEKINRGFGSDLACIFSDDNAEKLVLRLRIAKEE------------ 1233 (1605)
T ss_pred cCcccchhhcChHHHHhhhhhhhcccccccHHHHHHHHHhhccCCCceeecccCCcceEEEEEecCcc------------
Confidence 99999999999999999999999999999999999999999999999999999999999999987653
Q ss_pred hhhhhhhHHHHhhcccccceeccccccceEEEeccccCCCceEEEccCCcccccceEEEeecccchhcccccCCCCcccc
Q psy3015 1203 KMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRT 1282 (1791)
Q Consensus 1203 ~~~dr~~Lr~i~~~il~~~~LkGi~~I~kv~i~lp~~~n~~RiI~na~~~f~~~~e~~L~teG~nL~~vl~~~dVDp~rt 1282 (1791)
+++.|+++++.+++.+++++|++.|.||+|. ....|.|+...||+|+|||++|..+++.+++||.||
T Consensus 1234 --e~D~~l~~Ie~~ml~~~~l~G~~~i~kV~m~-----------~~~~G~f~~~~ew~LeTdg~~l~~v~s~~~vD~~rt 1300 (1605)
T KOG0260|consen 1234 --EDDVFLKCIEANMLGDMTLRGIPDIFKVYMS-----------PTEDGEFKPVDEWDLETDGVNLRRVLSEPDVDPART 1300 (1605)
T ss_pred --chhHHHHHHHHhhhhhcccCCccccceEEEe-----------ecCCCceeecceeEEecCchhHHhhhccCCCCcccc
Confidence 4678999999999999999999999999997 345788998899999999999999999999999999
Q ss_pred cchhHHHHHHhhhHHHHHHHHHHHHHHHhhhcCeeecccchhhhhhcccccCcccccccccccccccccccccchhhhHH
Q psy3015 1283 FSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVD 1362 (1791)
Q Consensus 1283 ~sNdI~eI~~vlGIEAaR~~li~El~~V~~~~Gi~Vn~RHL~LLaD~MT~~G~l~~itR~Gi~rq~~S~L~raSFEeTv~ 1362 (1791)
+|||++||+++|||||+|.++++|+..|+.|+|.||||||++|+||+||++|++++|+|||++++..++|+|||||+|++
T Consensus 1301 ~sn~l~ei~~vlgIea~r~a~~~e~~~vi~f~gsyVnyrhlaLl~dvmT~~g~lm~itRhg~nr~~tgaLmrcSfEetv~ 1380 (1605)
T KOG0260|consen 1301 TSNDLVEIAEVLGIEAVRKALLRELLNVISFDGSYVNYRHLALLCDVMTARGHLMAITRHGINRQDTGALMRCSFEETVD 1380 (1605)
T ss_pred cccchhhhhhhhcHHHHHhhhhhhhhheEeecccchhHHHHHHHHHHHhcccceeeeeccccchhhccccccccHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhccCCCCCCccccceeccccccCCcchhhhhccccccccccccc
Q psy3015 1363 VLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEKCKDGIEIP 1412 (1791)
Q Consensus 1363 iL~~AA~~ge~D~lkgVsenIi~Gq~~~lGTGaFd~lLge~~~~~~~~~~ 1412 (1791)
+|++||++++.|.++||+||||+||+++.|||+||++++.++++..+...
T Consensus 1381 il~~aa~~~ekd~~rgvsEnImlgqlap~gTg~~d~~ld~e~l~~~~~~~ 1430 (1605)
T KOG0260|consen 1381 ILMDAAAHAEKDPCRGVSENIMLGQLAPMGTGCFDLMLDAEKLKKGIEIP 1430 (1605)
T ss_pred HHHHHHhhhccCCCccceeeeeecccccCCCcceeeeccHHhhhccCccC
Confidence 99999999999999999999999999999999999999999998877553
No 2
>KOG0261|consensus
Probab=100.00 E-value=4.6e-150 Score=1353.91 Aligned_cols=750 Identities=32% Similarity=0.478 Sum_probs=566.9
Q ss_pred ceEEeeccCCCCCCCCCeEEe-------------cCccccHhHHHHHHhcCCcc--CCCCCCCceeCCCCcccHhhhhhh
Q psy3015 45 DWMLVTVLPVPPLSVRPAVVM-------------HGSARNQEQMMNILMFLPIW--DGKMPQPCILKPKPLWTGKQVFSL 109 (1791)
Q Consensus 45 ~~mlv~~~iVsP~~~rP~~~i-------------~Gs~~~rddlmqLlm~~~~~--~~~lP~PaIlKP~~LWTGKQIfS~ 109 (1791)
.||-+.+|+|+|.++.|.|.- ..+|++|+.++||+.++.+- ...+|||||+||..||||||+||.
T Consensus 519 ~LMgvknNlvTPr~GEpiiAAtQDFiTg~YLlt~KDtF~dRa~~~ql~s~~~d~~~~i~lppPaI~KP~~LwTGKQ~fsv 598 (1386)
T KOG0261|consen 519 VLMGVKNNLVTPRNGEPIIAATQDFITGGYLLTHKDTFLDRAEFSQLCSYMSDAMTHIDLPPPAILKPVELWTGKQLFSV 598 (1386)
T ss_pred HHhccccccccCCCCCceeehhhhhhhcceeeecccccccHHHHHHHHHHHhccccccCCCChhhcCceeeeccCEEEEE
Confidence 488899999999999999986 24699999999999876432 468999999999999999999999
Q ss_pred cCCCC------ccccccCCCCCCCCCCCCCCCCCCCCCeEEEEcCeEEEEeeccccccCC-CccHHHHHHHHhCHHHHHH
Q psy3015 110 IIPGN------VNMTRTHSTHPDDEDSGPYQWISPGDTKVVVEHGSLLMGILCKKSLGTS-SGSLLHICFLELGHEVCGR 182 (1791)
Q Consensus 110 iLP~~------inl~~~~~~~~~~~~~~~~~~~~~~d~~ViI~nGeLl~G~ldKk~vG~s-~~gLih~i~~~yG~~~a~~ 182 (1791)
++.++ +|+..+...... . .+....+|++|++|+|+|+||++|++||+++|.+ +.+|++++.++||+.+|++
T Consensus 599 lirpn~~s~v~~Nl~~k~k~~~~-~-~~k~~~mc~nDg~v~irns~l~sG~ldKs~lG~g~k~~lfy~llrDyg~~aAa~ 676 (1386)
T KOG0261|consen 599 LIRPNDDSPVRVNLDAKNKNFSL-V-KGKSFEMCPNDGYVIIRNSELISGVLDKSTLGSGKKDSLFYILLRDYGSMAAAD 676 (1386)
T ss_pred EeccCCCCceEEeeccccceeec-c-cCCCcccCCCCCeEEEecchhhhcccccccccCCCccceEeeehhhcchHHHHH
Confidence 99653 233211111000 0 1112257999999999999999999999999975 6899999999999999999
Q ss_pred HHHHHHHHHHHHHHhcCcccccCCcccChhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccCCCCCCcchHHH
Q psy3015 183 FYGNIQTVVNNWLLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGHSIGIGDTIADPQTYLE 262 (1791)
Q Consensus 183 fL~~lqrL~~~~L~~~GFSiGi~D~i~~~~t~~~i~~~i~~ak~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 262 (1791)
.|+++.+++.+||..+||||||+|+.+.+...++..+.++
T Consensus 677 am~rlaklc~r~lgnrGFSIGi~DVqPg~~L~~~k~~lv~---------------------------------------- 716 (1386)
T KOG0261|consen 677 AMNRLAKLCARFLGNRGFSIGIDDVQPGEILSQEKEELVN---------------------------------------- 716 (1386)
T ss_pred HHHHHHHhhhhhccccccccccCCCCccHHHHHHHHHHHH----------------------------------------
Confidence 9999999999999999999999999999885443333333
Q ss_pred HHHHHHHHHHHHHHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhhhhhhhhhccCCCChHHHHhhcCCCcchhhH
Q psy3015 263 IQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINI 342 (1791)
Q Consensus 263 ~~~~~~~~~~~v~~~i~~~~~~~L~~~pg~~~~~~fE~~vn~iLn~~rd~~g~~~~~~l~~~N~l~~Mv~sGSKGS~iNi 342 (1791)
.+|.+|.+.|.++..|+|+.+|||+-++++|+.+..+||.+|+++|+.|.+.|.++|++++|+.||||||.+|+
T Consensus 717 ------~gY~kc~~~I~e~~kG~L~~qpg~~~eetLEa~I~~~Ls~IRe~~G~~C~~eL~~~NsPliMa~CGSKGS~INi 790 (1386)
T KOG0261|consen 717 ------RGYAKCDEKIEEYNKGKLQLQPGCNEEETLEAEILSELSTIREEAGKICIRELHPRNSPLIMALCGSKGSKINI 790 (1386)
T ss_pred ------hHHHHHHHHHHHHhccccccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccChHHHHHhcCCCCcccH
Confidence 34578889999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhccCcccCCceeccCCccCCCCCCCCCCCCCcccceeccccccCCChhhhhhhcccCcccchhcccccCCcchhH
Q psy3015 343 SQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQ 422 (1791)
Q Consensus 343 sQi~acvGQQ~veGkRIp~gf~~RtLPhF~~~d~~p~srGFV~nSfl~GL~P~EfFFHaMaGREGLIDTAVKTaeTGYlQ 422 (1791)
|||+||||||.++|+|+|.||.+|+||||.+.+..|+|+|||.|||++||||+|||||+|||||||||||||||||||||
T Consensus 791 SQMvACVGQQ~ISG~RvPdGf~dRsLPHF~r~Sk~P~aKGFV~NSFySGLTptEFfFHtm~GREGLVDTAVKTAETGYMq 870 (1386)
T KOG0261|consen 791 SQMVACVGQQIISGHRVPDGFEDRSLPHFERHSKTPAAKGFVANSFYSGLTPTEFFFHTMSGREGLVDTAVKTAETGYMQ 870 (1386)
T ss_pred HHHHHHhhhhhhcCCcCCCccccccCccccccCCCccccchhhhhcccCCCchhhheeecccccchhhhhhhhhhhhhHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhcceEEeecCcEEecCCceEEEEecCCCCCcccccccccccccchhhhhhccccCCCCCCCccccchhhhhhhh
Q psy3015 423 RRLIKAMESVMVHYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQRIDTVALSHKKFEDKYRFDPSNERPTLRNVSSLRRVV 502 (1791)
Q Consensus 423 RrLvK~LEDl~V~YDgTVRns~G~IVQF~YGeDGlD~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 (1791)
|||||+||||+++||||||||.|.||||.||+||+||+.||+.+ .++.+.+...+.+..++.....+... .++....
T Consensus 871 RRLmK~LEDL~~~YDgTVR~s~~~vvqF~YG~DglDPa~mEg~~-~pv~f~r~~~~~~~~~~~~~~~~l~~--~el~e~~ 947 (1386)
T KOG0261|consen 871 RRLMKSLEDLSVQYDGTVRNSNGDVVQFTYGGDGLDPAMMEGKD-QPVNFNRVFDHAKAIFPHRHDPPLSS--EELDETL 947 (1386)
T ss_pred HHHHHHHHHHHHhhcCceecCCCcEEEEeecCCCCChhhhcCCC-CchhHHHHHHHHHhcCCCCCCCCCCH--HHHHHHH
Confidence 99999999999999999999999999999999999999999977 78888876666665555443322211 1221111
Q ss_pred cC--Cccccccc---------cchhhHHHHHHHHHHhccccch---------------hHHH---HHH--HHHHhhh---
Q psy3015 503 NS--KPLLIGCW---------KLTSVEKEMNTVLQFYGLYVNY---------------RHLA---LLC--DVMTAKG--- 548 (1791)
Q Consensus 503 ~~--~~~~~~~~---------~~~~~~~~~~~~~~~~~~~~~~---------------~~~~---~~~--~~mt~~~--- 548 (1791)
+. .+.+..+. -+..+.+++.++.+.|+..... +.+. +.| ..|.++.
T Consensus 948 ~~~l~~~f~~~~~~F~~~~~~~i~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~t~kql~~f~~~~~~ky~~a~~EpG 1027 (1386)
T KOG0261|consen 948 EEELLRKFTEKGDPFVHELREFIASLSKKIKKLQDKYGDECGPKFCPDLLYQISRLTEKQLEKFVERCLDKYMRAKVEPG 1027 (1386)
T ss_pred HHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHhhhcccccCCccCccceeeeeeccHHHHHHHHHHHHHHHHhhhcCCc
Confidence 11 00000000 0112222222222222210000 0000 000 1122221
Q ss_pred -hhhhhhhcCCCCCcccc----------------ccccchhhHHHH-------hhhhhhccc-----CCChhhhHHHHHH
Q psy3015 549 -HLMAITRHGINRQDTGA----------------LMRCSFEETVDV-------LMDAAAHAE-----ADPMRGYIQRRLI 599 (1791)
Q Consensus 549 -~~~~~~~~gi~~~~~~~----------------~~~~~~~e~~~~-------i~~a~~~~~-----~~~~~~ri~~~~~ 599 (1791)
..-++.+|+|++|.+|| +++++++|+|++ |++|.+... +..+++||+++++
T Consensus 1028 TavGAi~aQSIGEPGTQMTLKTFHFAGVASMNiTlGVPRIkEIINAsk~ISTPIItA~L~n~~d~~~Ar~VKgRiEKt~L 1107 (1386)
T KOG0261|consen 1028 TAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKTISTPIITAELENPHDERSARVVKGRIEKTTL 1107 (1386)
T ss_pred chhhhhhcccCCCCCceeeeeeeeecceeeeeeccCcchHHHHHhhhcccCccceeeeecCchhHHHHHHHhhhhhhhhH
Confidence 11234444444444444 234445776655 455543322 2238899999777
Q ss_pred H----HHHHHHhhcccccccccc----cceeeeecCCCcccccccccccceeecChhhhhcccccCCchhhHhhhhccHH
Q psy3015 600 K----AMESVMVHYDCTVRNSVG----QLIQLRYGEDGLCGEAVEHQRIDTVALSHKKFEDKYRFDPSNERQLRRIFNED 671 (1791)
Q Consensus 600 k----~ie~V~~~yd~~vr~~vg----~~~~~~~gE~g~~~~~ie~~~ip~i~~~~~~~~~~~~~~~~~~~~l~~~~~~~ 671 (1791)
+ ++|.|...+++++...+. ..+++.+ .+.+|..++.. .++.++.+.+.. +.++.
T Consensus 1108 ~dv~~yieeV~~p~~~fl~i~vd~~~I~~l~L~i-------------~~~~I~~sI~~-s~~~k~~~~~v~----v~~~~ 1169 (1386)
T KOG0261|consen 1108 GDVCSYIEEVYGPDSCFLLIRVDLKRISLLQLEI-------------TIESIAYSILK-SPKRKVKPNDVR----VVGET 1169 (1386)
T ss_pred HHHHHHHHHHhCCcceEEEEEecHhHHhhhhccc-------------cHHHHHHHHhc-CCccccCCcceE----Eecce
Confidence 5 588899899998776543 3333322 11112111100 001111111111 11111
Q ss_pred HHHHhhcCCCchhhhHHhhhcccchHHHHHhhhhhhHhhccC-ChHHHHHHHH-HHHHHHHHHHHHHhhccCCCc--cee
Q psy3015 672 VLRELMGSGDVISELEKEMVDHFSWKQLRRIFNEDVLRELMG-SGDVISELEK-EWEKLCEDREALREIFSSGES--NVV 747 (1791)
Q Consensus 672 ~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~-~~~vi~~~~~-e~~kL~~~~~~Lr~i~~~~~~--~~~ 747 (1791)
.+. +.....++...+|++|.||+.|++++++|++. +|.+|+..++ ..++|+.+|++||.||++.++ ..+
T Consensus 1170 ~~~-------v~~~~~~~~S~~~~lq~lk~~L~~Vvv~gip~vnr~vi~~de~~~~y~L~vEG~gLr~Vm~t~GV~g~~T 1242 (1386)
T KOG0261|consen 1170 TLR-------VTPVSDTKSSVYYNLQRLKRSLPNVVVKGIPEVNRAVINIDEKRGLYKLLVEGTGLRAVMNTDGVKGRRT 1242 (1386)
T ss_pred eEE-------EeecccccchhhhhHHHHHhhCCceEEecCcchhhhheeecccCCceEEEEeccchHHHhccCCcccccc
Confidence 000 00011122346899999999999999999988 9999987664 226677779999999997653 233
Q ss_pred ecchhHHHHHHHhhhhccCCcccccccceEEEe-ccCcccHHHHHHHHhhcceeccchhhhhhhhhhcccceecceeccc
Q psy3015 748 LPCNLMEVIFILQRWKLWGNENLRFLCKIIFVL-SVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHG 826 (1791)
Q Consensus 748 l~~N~~rii~~~~~~~~~~~~~~~~~~n~i~~I-aAR~~Ii~Ei~~v~~~~GIsVd~RHi~LlaD~MT~~G~v~~itR~G 826 (1791)
.++|+.++ ++ +.|| |||.+||+||.+||.+|||+||+||+|||||+|||+|||+||||+|
T Consensus 1243 tsNnv~Ev------~~-------------vLGIEAAR~~II~EI~ytM~~HGmsiD~RHiMLLaDvMTyrGEVlGITRfG 1303 (1386)
T KOG0261|consen 1243 TSNNVLEV------EK-------------VLGIEAARTTIISEIGYTMSNHGMSIDPRHIMLLADVMTYRGEVLGITRFG 1303 (1386)
T ss_pred ccCceEEe------eh-------------hhchHHHHHHHHHHHHHHHHhcCcccCHHHHHHHHHHhhhcceeeeeeehh
Confidence 44443221 11 2233 6999999999999999999999999999999999999999999999
Q ss_pred cccCCCcccccchhhhhhHHHHHHhhccCCCCCCCcccceecCCCCCCCcceeeecccccccc
Q psy3015 827 INRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEKCK 889 (1791)
Q Consensus 827 l~~~~~S~L~~aSFE~T~d~L~~Aa~~g~~D~i~GVSe~II~G~~~~iGTg~~~Ll~~~~k~k 889 (1791)
++||+.|+||+||||+|+||||+||++|+.|.|+|||||||||+|++||||.|+|+++.+..+
T Consensus 1304 l~KM~~SVL~lASFEkT~DhLF~AA~~~k~D~I~GVSEcIIlG~pm~iGTG~fkl~~~~~~~~ 1366 (1386)
T KOG0261|consen 1304 LAKMKDSVLMLASFEKTADHLFDAAAYGKKDAIEGVSECIILGIPMCIGTGIFKLLQRTDDKK 1366 (1386)
T ss_pred hHHHHHHHHHHHhhhhhhHHHHHHHHhcCcccccchhhheecccceeccccHHHHHHhcCCcc
Confidence 999999999999999999999999999999999999999999999999999999999887753
No 3
>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Probab=100.00 E-value=7.5e-135 Score=1338.18 Aligned_cols=757 Identities=28% Similarity=0.459 Sum_probs=608.8
Q ss_pred ceEEeeccCCCCCCCCCeEEe-------------cCccccHhHHHHHHhcCCccCCCCCCCcee-CCCCcccHhhhhhhc
Q psy3015 45 DWMLVTVLPVPPLSVRPAVVM-------------HGSARNQEQMMNILMFLPIWDGKMPQPCIL-KPKPLWTGKQVFSLI 110 (1791)
Q Consensus 45 ~~mlv~~~iVsP~~~rP~~~i-------------~Gs~~~rddlmqLlm~~~~~~~~lP~PaIl-KP~~LWTGKQIfS~i 110 (1791)
++|.+++|+++|++++|++++ .+.|+++++++||+||... ...+|+|||+ ||++|||||||||++
T Consensus 495 ~Lm~v~~niisP~~G~Pi~gliQD~l~g~~lLT~~d~fl~~~e~~~l~~~~~~-~~~lp~PaI~~kp~~lwTGKQi~s~i 573 (1321)
T PRK14977 495 ELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFDKNEASNIAMLAGI-TDPLPEPAIKTKDGPAWTGKQLFSLF 573 (1321)
T ss_pred HHHhhhhcEecCCCCCeeEEeehhhhhhhhhhccCcccCCHHHHHHHHHhCCC-ccccCCCceecCCCCeeeHHHHHHHH
Confidence 589999999999999999998 3469999999999998654 3469999999 999999999999999
Q ss_pred CCCCccccccCCCCCCCCCCCCCCCCCCCCCeEEEEcCeEEEEeeccccccC---CCccHHHHHHHHhCHHHHHHHHHHH
Q psy3015 111 IPGNVNMTRTHSTHPDDEDSGPYQWISPGDTKVVVEHGSLLMGILCKKSLGT---SSGSLLHICFLELGHEVCGRFYGNI 187 (1791)
Q Consensus 111 LP~~inl~~~~~~~~~~~~~~~~~~~~~~d~~ViI~nGeLl~G~ldKk~vG~---s~~gLih~i~~~yG~~~a~~fL~~l 187 (1791)
||+++|+....+..... +.....+.|++|++|+|+||||++|++||+++|+ +.+||||.||++||+++|.+||+++
T Consensus 574 Lp~~~n~~~~~~~~~~~-~~~~~~~~~~~d~~v~I~~geLl~G~ldK~~~G~~~~~~~~Lih~i~~~yG~~~a~~fL~~l 652 (1321)
T PRK14977 574 LPKDFNFEGIAKWSAGK-AGEAKDPSCLGDGYVLIKEGELISGVIDDNIIGALVEEPESLIDRIAKDYGEAVAIEFLNKI 652 (1321)
T ss_pred cCCCCCceecccccccc-cccccccCCCCcceEEeecCeEEeeecchHhhccccCCCCcHHHHHHHHhCHHHHHHHHHHH
Confidence 99999986543321110 0011223578899999999999999999999998 7899999999999999999999999
Q ss_pred HHHHHHHHHhcCcccccCCcccChhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccCCCCCCcchHHHHHHHH
Q psy3015 188 QTVVNNWLLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGHSIGIGDTIADPQTYLEIQMAI 267 (1791)
Q Consensus 188 qrL~~~~L~~~GFSiGi~D~i~~~~t~~~i~~~i~~ak~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 267 (1791)
|+|+++||+++|||||++|+++++++.+++.+.+++++++
T Consensus 653 ~~l~~~~L~~~GFSigi~D~~~~~~~~~~i~~~i~~~~~~---------------------------------------- 692 (1321)
T PRK14977 653 LIIAKKEILHYGFSNGPGDLIIPDEAKQEIEDDIQGMKDE---------------------------------------- 692 (1321)
T ss_pred HHHHHHHHHhCCEEEeeCcEecCHHHHHHHHHHHHHHHHH----------------------------------------
Confidence 9999999999999999999999999888888877776632
Q ss_pred HHHHHHHHHHHHHHH--------cCCCCCCCCCcHHHHHHHHHHHHHHHHHhhhhhhhhhccCCCChHHHHhhcCCCcch
Q psy3015 268 KKAKEDVIEVIQKAH--------NMDLEPTPGNTLRQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSN 339 (1791)
Q Consensus 268 ~~~~~~v~~~i~~~~--------~~~L~~~pg~~~~~~fE~~vn~iLn~~rd~~g~~~~~~l~~~N~l~~Mv~sGSKGS~ 339 (1791)
|.++++.++ .+.+++.||++.++++|+++++.|+++|+.+++.+.++++++|++++|+.||||||+
T Consensus 693 ------v~~l~~~~~~~~~i~~~~~~~~~~~G~~~~~~~e~~i~~~l~~~r~~~~~~~~~~l~~~N~l~~Mv~SGAKGS~ 766 (1321)
T PRK14977 693 ------VSDLIDQRKITRKITIYKGKEELLRGMKEEEALEADIVNELDKARDKAGSSANDCIDADNAGKIMAKTGARGSM 766 (1321)
T ss_pred ------HHHHHHHHhhhccccccccchhcCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHhhcccccCH
Confidence 223333333 677899999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHhhccCcccC--------CceeccCCccCCCCCCCCCCCCCcccceeccccccCCChhhhhhhcccCcccchhc
Q psy3015 340 INISQVIACVGQQNVE--------GKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDT 411 (1791)
Q Consensus 340 iNisQi~acvGQQ~ve--------GkRIp~gf~~RtLPhF~~~d~~p~srGFV~nSfl~GL~P~EfFFHaMaGREGLIDT 411 (1791)
+|++||+||||||+++ |+|||+||++||||||.++|++|+|+|||.|||++||+|+||||||||||||||||
T Consensus 767 ~Ni~Qi~~~lGQQ~ve~~~~~~~~G~Ri~~~~~~RtLPhF~~~d~~p~a~GfV~nsFl~GL~P~EfFFHaM~GREGLiDT 846 (1321)
T PRK14977 767 ANLAQIAGALGQQKRKTRIGFVLTGGRLHEGYKDRALSHFQEGDDNPDAHGFVKNNYREGLNAAEFFFHAMGGREGLIDK 846 (1321)
T ss_pred HHHHHHHhccccccccccccccCCCCCCcCCCCCCcCCCCCCCCCCcccccchhhhhcCCCCHHHHHHHhhccccccccc
Confidence 9999999999999999 99999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCCcchhHHHHHHhhcceEEeecCcEEecCCceEEEEecCCCCCcccccccccccccchhhhhhccccCCCCCCCcc
Q psy3015 412 AVKTAETGYIQRRLIKAMESVMVHYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQRIDTVALSHKKFEDKYRFDPSNERPT 491 (1791)
Q Consensus 412 AVKTaeTGYlQRrLvK~LEDl~V~YDgTVRns~G~IVQF~YGeDGlD~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 491 (1791)
|||||+||||||||||+||||+|+|||||||++|+||||.|||||+||+.++... ++
T Consensus 847 AVKTA~SGYLQRrLvk~lEDl~v~YD~TVR~s~g~iiQF~YGeDG~d~~~~~~~~--~~--------------------- 903 (1321)
T PRK14977 847 ARRTEDSGYFQRRLANALEDIRLEYDETVRDPHGHIIQFKFGEDGIDPQKLDHGE--AF--------------------- 903 (1321)
T ss_pred ccccCcCchhHHHHHHHhcceEEecCCeEEeCCCCEEEEeecCCCcCHHHhccCC--cc---------------------
Confidence 9999999999999999999999999999999999999999999999996553200 00
Q ss_pred ccchhhhhhhhcCCccccccccchhhHHHHHHHHHHhccccchhHHHHHHHHHHhhhhhhhhhhcCCCCCccccccccch
Q psy3015 492 LRNVSSLRRVVNSKPLLIGCWKLTSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSF 571 (1791)
Q Consensus 492 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~mt~~~~~~~~~~~gi~~~~~~~~~~~~~ 571 (1791)
+ +. .+..
T Consensus 904 --n---~~-----------------------~~~~--------------------------------------------- 910 (1321)
T PRK14977 904 --N---LE-----------------------RIIE--------------------------------------------- 910 (1321)
T ss_pred --c---HH-----------------------HHHH---------------------------------------------
Confidence 0 00 0000
Q ss_pred hhHHHHhhhhhhcccCCChhhhHHHHHHHHHHHHHhhcccccccccccceeeeecCCCcccccccccccceeecChhhhh
Q psy3015 572 EETVDVLMDAAAHAEADPMRGYIQRRLIKAMESVMVHYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQRIDTVALSHKKFE 651 (1791)
Q Consensus 572 ~e~~~~i~~a~~~~~~~~~~~ri~~~~~k~ie~V~~~yd~~vr~~vg~~~~~~~gE~g~~~~~ie~~~ip~i~~~~~~~~ 651 (1791)
.+.. . . .+.
T Consensus 911 --------------------------------~~~~--------------~-~-~~~----------------------- 919 (1321)
T PRK14977 911 --------------------------------KQKI--------------E-D-RGK----------------------- 919 (1321)
T ss_pred --------------------------------Hhhh--------------h-c-ccc-----------------------
Confidence 0000 0 0 000
Q ss_pred cccccCCchhhHhhhhccHHHHHHhhcCCCchhhhHHhhhcccchHHHHHhhhhhhHhhccCChHHHHHHHHHHHHHHHH
Q psy3015 652 DKYRFDPSNERQLRRIFNEDVLRELMGSGDVISELEKEMVDHFSWKQLRRIFNEDVLRELMGSGDVISELEKEWEKLCED 731 (1791)
Q Consensus 652 ~~~~~~~~~~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~~~~~e~~kL~~~ 731 (1791)
..++ ++.+.++.
T Consensus 920 ------------------------------------------------------------~~~~-------~~~~~~~~- 931 (1321)
T PRK14977 920 ------------------------------------------------------------GASK-------DEIEELAK- 931 (1321)
T ss_pred ------------------------------------------------------------CCCH-------HHHHHHHH-
Confidence 0000 00000000
Q ss_pred HHHHHhhccCCCcceeecchhHHHHHHHhhhhccCCcccccccceEEEeccCcccHHHHHHHHhhcceeccchhhhhhhh
Q psy3015 732 REALREIFSSGESNVVLPCNLMEVIFILQRWKLWGNENLRFLCKIIFVLSVRKSVEKEMNTVLQFYGLYVNYRHLALLCD 811 (1791)
Q Consensus 732 ~~~Lr~i~~~~~~~~~l~~N~~rii~~~~~~~~~~~~~~~~~~n~i~~IaAR~~Ii~Ei~~v~~~~GIsVd~RHi~LlaD 811 (1791)
.
T Consensus 932 ----------------------------------------------------------------~--------------- 932 (1321)
T PRK14977 932 ----------------------------------------------------------------E--------------- 932 (1321)
T ss_pred ----------------------------------------------------------------H---------------
Confidence 0
Q ss_pred hhcccceecceeccccccCCCcccccchhhhhhHHHHHHhhccCCCCCCCcccceecCCCCCCCcceeeeccccccccCC
Q psy3015 812 VMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEKCKDG 891 (1791)
Q Consensus 812 ~MT~~G~v~~itR~Gl~~~~~S~L~~aSFE~T~d~L~~Aa~~g~~D~i~GVSe~II~G~~~~iGTg~~~Ll~~~~k~k~~ 891 (1791)
+
T Consensus 933 ----------------------------------------------------------------------------~--- 933 (1321)
T PRK14977 933 ----------------------------------------------------------------------------Y--- 933 (1321)
T ss_pred ----------------------------------------------------------------------------H---
Confidence 0
Q ss_pred ccccccccccCCCCccccCCCCCCCCCCCCCCccccCccccccccCCCCcCCCCCCCCcccccCCcchhHHHHhcHHHHH
Q psy3015 892 IEIPLATGMMGGPAGMFFGSAATPSSMSPQMTPWAQSTPAYNALMSPGAAMTPGGPGFSPSVAGEDQLSKQANENATLLF 971 (1791)
Q Consensus 892 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 971 (1791)
...|
T Consensus 934 ----------------------------------------------------------------------------~~~~ 937 (1321)
T PRK14977 934 ----------------------------------------------------------------------------TKTF 937 (1321)
T ss_pred ----------------------------------------------------------------------------HHhh
Confidence 0000
Q ss_pred HHHhHhhhhhHHHHhhccCCHHHHHHHHHHHhhhccceeccc--cccc---cc-----------------cCCcccCCCC
Q psy3015 972 QCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQAQVIA--CVGQ---QN-----------------VEGKRIPFGF 1029 (1791)
Q Consensus 972 ~~~~Rs~L~sk~v~~~~rln~~a~~~i~gei~~~~~~sqv~~--mvG~---Qs-----------------V~gKrI~~Gf 1029 (1791)
+..++..++ ..++++++++++|.|++.++..+|..+++.| +||. || |.+++||+|+
T Consensus 938 ~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pGe~VG~iaAQSiGEP~TQmTLnTFH~AGv~~~nvt~Gv 1015 (1321)
T PRK14977 938 NANLPKLLA--DAIHGAELKEDELEAICAEGKEGFEKAKVEPGQAIGIISAQSIAEPGTQMTLRTFHAAGIKAMDVTHGL 1015 (1321)
T ss_pred hhhhHHHHH--HHHHHcCCCHHHHHHHHHHHHHHHHhcccCCcccchhhhhhhccCceeeecccccccccccccCcccCc
Confidence 000111111 1345567889999999999999999999999 7777 88 8889999999
Q ss_pred cCccccccccCCCCCCCCcceeeccccCCCcceEEEeecCCCCccchhhhccchhH-HHHH-----HHHHHhcceEEEEC
Q psy3015 1030 RKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETV-NVLV-----FLFQVTANTAIYYD 1103 (1791)
Q Consensus 1030 prRTLphf~kdd~~PESrGFV~Nsf~~GLTPsEfffhAMgGREGLiDTAvKTAEtG-YIqR-----RLvk~~Edv~V~YD 1103 (1791)
|| |.|+ +|+.++..||++++|+ .+....+.+.+ .+++ +|.++++++.+.||
T Consensus 1016 pR--l~Ei-------------i~a~k~~~tp~m~~~l--------~~~~~~~~~~a~~v~~~ie~~~l~~~~~~~~i~~~ 1072 (1321)
T PRK14977 1016 ER--FIEL-------------VDARAKPSTPTMDIYL--------DDECKEDIEKAIEIARNLKELKVRALIADSAIDNA 1072 (1321)
T ss_pred cc--hHHh-------------hhcccCCCCCeEEEEe--------CCcccchHHHHHHHHhheeeeEHHHhhhheEeecc
Confidence 99 9999 8999999999999999 33222233333 3332 78889999999998
Q ss_pred CCCCCcccccCcceeeeeccCCCCCCCCcccceeeeeccccccccccCCHHHHHHHHhhccCCCcccccCCcccccceEE
Q psy3015 1104 PDPQNTVIPEDQEFVNVYYEMPDFDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEKLVLR 1183 (1791)
Q Consensus 1104 gtvrnTVr~~d~~iVQf~Yg~dg~D~~~~~~wvlr~~Ld~~~m~dk~l~~~~I~~~I~~~~~~dl~~i~~d~n~~~l~~r 1183 (1791)
++. ..+.+|...+..+.++++.|.+.+.+.++.....+..+++ .+.
T Consensus 1073 ~~~------------------------------~~i~~d~~~i~~~~i~~~~i~~~i~~~~~~~~~~~~~~~~----~i~ 1118 (1321)
T PRK14977 1073 NEI------------------------------KLIKPDKRALENGCIPMERFAEIEAALAKGKKFEMELEDD----LII 1118 (1321)
T ss_pred CCc------------------------------eEEecCHHHHHhcCCCHHHHHHHHHHhhcCCceEEeecCC----EEE
Confidence 731 1234566667777789888887776655432111111111 122
Q ss_pred EEEecCccccccchhHHHHhhhhhhhHHHHhhcccccceeccccccceEEEeccccCCCceEEEccCCcccccceEEEee
Q psy3015 1184 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLET 1263 (1791)
Q Consensus 1184 iri~~~~~~~~~~~ee~~~~~~dr~~Lr~i~~~il~~~~LkGi~~I~kv~i~lp~~~n~~RiI~na~~~f~~~~e~~L~t 1263 (1791)
+++.... + .-....+++.+...+ .+++|+|+++|+++++... ... ...||+|.|
T Consensus 1119 ~~~~~~~--------~---~~~~~~~l~~l~~~l-~~~~i~Gi~~I~r~~i~~~----------~~~----~~~e~~l~t 1172 (1321)
T PRK14977 1119 LDLVEAA--------D---RDKPLATLIAIRNKI-LDKPVKGVPDIERAWVELV----------EKD----GRDEWIIQT 1172 (1321)
T ss_pred EecCccc--------c---cchHHHHHHHHHHhc-CCcEEecCCCceEEEEEee----------ccC----CCeeEEEEe
Confidence 2221100 0 000123455665444 4799999999999887521 111 124899999
Q ss_pred cccchhcccccCCCCcccccchhHHHHHHhhhHHHHHHHHHHHHHHHhhhcCeeecccchhhhhhcccccCcccccc---
Q psy3015 1264 DGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAIT--- 1340 (1791)
Q Consensus 1264 eG~nL~~vl~~~dVDp~rt~sNdI~eI~~vlGIEAaR~~li~El~~V~~~~Gi~Vn~RHL~LLaD~MT~~G~l~~it--- 1340 (1791)
+|+||.+++..++||+.||+||||+||+++|||||||++|++|++.|+..+|++||+|||+||||+||++|++++|+
T Consensus 1173 eG~nl~~vl~~~~Vd~~rt~sN~i~ei~~~lGIEAaR~~ii~Ei~~v~~~~G~~V~~rHi~LlaD~MT~~G~~~~i~~~~ 1252 (1321)
T PRK14977 1173 SGSNLAAVLEMKCIDIANTITNDCFEIAGTLGIEAARNAIFNELASILEDQGLEVDNRYIMLVADIMCSRGTIEAIGLQA 1252 (1321)
T ss_pred cCcCHHHHhCCCCCcccccEECCHHHHHHhhhHHHHHHHHHHHHHHHHHHcCCccCHHHHHHHHHHHccCceEEeccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ---cccccccccccccccchhhhHHHHHHHhhccCCCCCCccccceeccccccCCcchhhhhcccc
Q psy3015 1341 ---RHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAE 1403 (1791)
Q Consensus 1341 ---R~Gi~rq~~S~L~raSFEeTv~iL~~AA~~ge~D~lkgVsenIi~Gq~~~lGTGaFd~lLge~ 1403 (1791)
|||+++.+.|||++||||+|+++|++||++|+.|+++||+||||+|+++|+|||+||++++..
T Consensus 1253 ~~~R~Gi~~~~~s~l~~asFE~t~~~L~~AA~~g~~D~l~gvsenii~G~~~~~GTG~~~Ll~~~~ 1318 (1321)
T PRK14977 1253 AGVRHGFAGEKDSPLAKAAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIPIGSGKVDLLMDFS 1318 (1321)
T ss_pred cccccccccCCCCHHHhcCHHHHHHHHHHHHHhcCcCccCChHHhhhcCCCccCccceEEEEeccc
Confidence 999999999999999999999999999999999999999999999999999999999998854
No 4
>KOG0262|consensus
Probab=100.00 E-value=7.3e-119 Score=1106.68 Aligned_cols=405 Identities=31% Similarity=0.535 Sum_probs=341.0
Q ss_pred ccccccceeeeeecccCChhhHhhhCCCCCCCCcceEEeeccCCCCCCCCCeEEecCccccHhHHHHHHhc-CCc--cCC
Q psy3015 11 ANHVSNTSVYAWYVVPYPYEESIILGMDPKFARPDWMLVTVLPVPPLSVRPAVVMHGSARNQEQMMNILMF-LPI--WDG 87 (1791)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~d~~~lg~~~~~~~p~~mlv~~~iVsP~~~rP~~~i~Gs~~~rddlmqLlm~-~~~--~~~ 87 (1791)
-++++-.++|++--+ +..+ |-|+.+.|-..+++..+|+-.- +++.++|++||++|||++. +.. ...
T Consensus 612 Qse~araEa~~ian~---dsqY----LvPt~G~PlrGLIQDHiVsgv~----LT~rd~Fftre~y~qLv~~~l~~~~~rI 680 (1640)
T KOG0262|consen 612 QSEIARAEAYNIANT---DSQY----LVPTDGTPLRGLIQDHIVSGVL----LTMRDSFFTREDYQQLVFAGLSDTFKRI 680 (1640)
T ss_pred chhhHHHHHHHHhcc---CCce----eccCCCCchhhhhhhheeeeEE----EEecccccCHHHHHHHHHHhhhhhccce
Confidence 356666677766541 1111 3467788889999999998654 7779999999999999996 333 345
Q ss_pred CCCCCceeCCCCcccHhhhhhhcC----CC---CccccccCCCCCCCCCCCCCCCCC------CCCCeEEEEcCeEEEEe
Q psy3015 88 KMPQPCILKPKPLWTGKQVFSLII----PG---NVNMTRTHSTHPDDEDSGPYQWIS------PGDTKVVVEHGSLLMGI 154 (1791)
Q Consensus 88 ~lP~PaIlKP~~LWTGKQIfS~iL----P~---~inl~~~~~~~~~~~~~~~~~~~~------~~d~~ViI~nGeLl~G~ 154 (1791)
+++||+|+||.+|||||||||++| |+ .+|+..+.+. |++ .|.+ .+++.|+||+||||||+
T Consensus 681 ~~lpPtIlkP~~LWTGKQVIsTil~Ni~P~~~p~iNl~~kaKi-p~~------~W~~~s~e~~l~Es~v~ir~GellcGV 753 (1640)
T KOG0262|consen 681 KLLPPTILKPAPLWTGKQVISTILKNIIPEGHPPINLESKAKI-PGK------AWRVHSEEPKLNESQVLIREGELLCGV 753 (1640)
T ss_pred eccCccccccccccccchHHHHHHHhcCCCCCCcccchhcccC-chh------hcCCCCCcccCCcceEEEecCceEEEe
Confidence 789999999999999999999998 43 4677543321 221 2222 24688999999999999
Q ss_pred eccccccCCCccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCcccccCCcccChhhHHHHHHHHHHHHHHHHHHHHH
Q psy3015 155 LCKKSLGTSSGSLLHICFLELGHEVCGRFYGNIQTVVNNWLLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQK 234 (1791)
Q Consensus 155 ldKk~vG~s~~gLih~i~~~yG~~~a~~fL~~lqrL~~~~L~~~GFSiGi~D~i~~~~t~~~i~~~i~~ak~~~~~~~~~ 234 (1791)
|||+++|++.+||+|++|+.||+++++++|+.++||++.||+.+|||||++|+++++++++++++++++++..+.+++++
T Consensus 754 LDKa~~Gat~yGLvH~~~ElYG~~~s~~lLs~~srlFT~ylq~~GFT~GvdDlll~~~~D~kR~~il~e~~~vG~qa~~~ 833 (1640)
T KOG0262|consen 754 LDKAQFGATAYGLVHCCHELYGGETSGKLLSVFSRLFTAYLQMHGFTLGVDDLLLDKDADKKRREILRESRNVGNQAAKE 833 (1640)
T ss_pred echhhcCchhhhhhhhhhhhhCccchhhHHHHHHHHHHHHHHHhccccccceeeechhhhHHHHHHHHhhhcccHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhcCCCCCCCCcccccCCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhhhh
Q psy3015 235 AHNMDLEPTPGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILNDARDKTG 314 (1791)
Q Consensus 235 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~i~~~~~~~L~~~pg~~~~~~fE~~vn~iLn~~rd~~g 314 (1791)
+++++.++.. .++...|+.+|. +. ...+ ..++..+.+.+|...+.+...|-
T Consensus 834 ~~~l~~da~~----------------del~~~le~~y~-------~d-~~~~-----~~LD~~~k~~~n~~ts~I~~~cv 884 (1640)
T KOG0262|consen 834 AFGLDVDAPP----------------DELRSRLEAIYL-------KD-ADKL-----AMLDRVMKSELNGYTSEIVKKCV 884 (1640)
T ss_pred HhCCCCCCCH----------------HHHHHHHHHHHh-------cc-hhHH-----HHHHHHHHHHHhhhhHHHHhhhc
Confidence 9877654332 123322322221 00 0111 25788889999999998887775
Q ss_pred hhhhhccCCCChHHHHhhcCCCcchhhHHHHHhhccCcccCCceeccCCccCCCCCCCCCCCCCcccceeccccccCCCh
Q psy3015 315 GSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTP 394 (1791)
Q Consensus 315 ~~~~~~l~~~N~l~~Mv~sGSKGS~iNisQi~acvGQQ~veGkRIp~gf~~RtLPhF~~~d~~p~srGFV~nSfl~GL~P 394 (1791)
..-.-..+|.|++..|+.||||||++|.+||+||||||++||+|+|.|.+|||||||.++|.+|+|+|||..+|++|+.|
T Consensus 885 P~GLlk~FP~N~mqlM~~SGAKGS~VN~~QISclLGQqeLEGkRvPlMvSGKtLPsF~p~e~spraGGfI~~RFlTGi~P 964 (1640)
T KOG0262|consen 885 PDGLLKKFPENNMQLMIQSGAKGSNVNTSQISCLLGQQELEGKRVPLMVSGKTLPSFAPYETSPRAGGFIDGRFLTGIKP 964 (1640)
T ss_pred cchhhhcCCcchHHHHHHhcCCcccccHHHHHHhhhhHhhcCCccceeecCCccCCcCCCCCCCCCCCcccceeecCCCc
Confidence 54333446899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhcccCcccchhcccccCCcchhHHHHHHhhcceEEeecCcEEecCCceEEEEecCCCCCcccc
Q psy3015 395 SEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVHYDCTVRNSVGQLIQLRYGEDGLCGEAV 462 (1791)
Q Consensus 395 ~EfFFHaMaGREGLIDTAVKTaeTGYlQRrLvK~LEDl~V~YDgTVRns~G~IVQF~YGeDGlD~~~~ 462 (1791)
||||||||||||||||||||||+|||||||||||||+++|+||.||||++|+||||.|||||+|.++-
T Consensus 965 qeyfFHCMAGREGLIDTAVKTSRSGYLQRCLiKhLEgl~V~YD~TVRDsDgsvVQF~YGEDglDitKs 1032 (1640)
T KOG0262|consen 965 QEYFFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLKVHYDLTVRDSDGSVVQFMYGEDGLDITKS 1032 (1640)
T ss_pred hHHhhhhhccccchhhhHHhcccchHHHHHHHHhhhhcEEeccceEEcCCCcEEEEeecCccccccHH
Confidence 99999999999999999999999999999999999999999999999999999999999999997443
No 5
>KOG0260|consensus
Probab=100.00 E-value=1.6e-118 Score=1098.81 Aligned_cols=580 Identities=36% Similarity=0.478 Sum_probs=455.5
Q ss_pred cchhHHHHhcHHHHHHHHhHhhhhhHHHHhhccCCHHHHHHHHHHHhhhccceeccccccccccCCcccCCCCcCccccc
Q psy3015 957 DQLSKQANENATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQAQVIACVGQQNVEGKRIPFGFRKRTLPH 1036 (1791)
Q Consensus 957 ~~~~~~~~~~~~~~~~~~~Rs~L~sk~v~~~~rln~~a~~~i~gei~~~~~~sqv~~mvG~QsV~gKrI~~GfprRTLph 1036 (1791)
.++.+--.+++..+++-..+-+=++... .....|....|.+.|++|+.+|++|+.+|||||+|+||||||||++|||||
T Consensus 706 ~tlretfe~~v~~vlndArd~~gssA~~-sl~esNn~k~Mv~aGSKGs~inisQ~saCVGqQnVEgkrIpFGF~~Rtlph 784 (1605)
T KOG0260|consen 706 RTLRETFENKVNRVLNDARDKSGSSAQK-SLSESNNFKTMVVAGSKGSFINISQVSACVGQQNVEGKRIPFGFPKRTLPH 784 (1605)
T ss_pred hhHHHHHHHHHHHHHHHHHHhhhhHHHh-hhhhcccHHHHHhhcCCCcceehhhhhhhhccccccccccccCCCcccccc
Confidence 4555555666666666655433222211 123468889999999999999999999999999999999999999999999
Q ss_pred cccCCCCCCCCcceeeccccCCCcceEEEeecCCCCccchhhhccchhHHHHHHHHHHhcceEEEECCCCCCcccccCcc
Q psy3015 1037 FIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYDPDPQNTVIPEDQE 1116 (1791)
Q Consensus 1037 f~kdd~~PESrGFV~Nsf~~GLTPsEfffhAMgGREGLiDTAvKTAEtGYIqRRLvk~~Edv~V~YDgtvrnTVr~~d~~ 1116 (1791)
|.||||+|||||||+|||++||||+|||||||||||||||||+||||||||||||||+|||+||.|||||||+ -|+
T Consensus 785 f~kDdysPesrGfVENSyL~GLtP~EfFfHamggREglidtavktaEtGyiqRRL~kameDimv~yDgTVRNs----~gq 860 (1605)
T KOG0260|consen 785 FSKDDYSPESRGFVENSYLTGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLMKAMEDIMVAYDGTVRNS----LGQ 860 (1605)
T ss_pred cccCCCCccccceeecccccCCCHHHHHHHHhcccchhhhhhhcccccchHHHHHHHHHHHHHhhcCcceecc----cce
Confidence 9999999999999999999999999999999999999999999999999999999999999999999965555 489
Q ss_pred eeeeeccCCCCCCCCcccceeeeeccccccccccCCHHHHHHHHhhccCCCcccc-cCCcccccceEEEEEecCcccccc
Q psy3015 1117 FVNVYYEMPDFDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNCI-FNDDNAEKLVLRIRIMNSDDSKMQ 1195 (1791)
Q Consensus 1117 iVQf~Yg~dg~D~~~~~~wvlr~~Ld~~~m~dk~l~~~~I~~~I~~~~~~dl~~i-~~d~n~~~l~~riri~~~~~~~~~ 1195 (1791)
+|||.||+||+|+ .|++.|.++..++..+-+. +.|+.+.... ++.. .++.+-. +....+.+..
T Consensus 861 viQf~YGeDG~d~----~~vE~q~~~~l~~~~a~f~---------~~~~~d~ld~~~~~~-~~~~~~e--~~~~~~l~~l 924 (1605)
T KOG0260|consen 861 VIQFKYGEDGLDG----HPVEFQNGETLGSLNACFE---------SEFAYDALDEPISLS-SEEVVNE--ISELLKLQNL 924 (1605)
T ss_pred eEEEEeccCcccc----ceeeccccccccchHHHHH---------hhhhhhhhcCcccch-hhhHhhh--hhhhHHHHHH
Confidence 9999999999999 6788889888877765442 2333221110 0000 0000000 0111122334
Q ss_pred chhHHHHhhhhhhhHHHHhhcccccceeccccccceEEEeccccCCCceEEEccCCcccccceEEEeecccchhcccccC
Q psy3015 1196 DEEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSER 1275 (1791)
Q Consensus 1196 ~~ee~~~~~~dr~~Lr~i~~~il~~~~LkGi~~I~kv~i~lp~~~n~~RiI~na~~~f~~~~e~~L~teG~nL~~vl~~~ 1275 (1791)
++.|+.+...||.+++.+.+ .++.++++|+ |.+|+|||+++.|+... ....
T Consensus 925 le~e~~~l~~dr~~l~~i~~-------------~g~~k~~lp~--n~~r~I~Na~~~f~~~~--------------r~~t 975 (1605)
T KOG0260|consen 925 LECEYKKLVRDRRVLLYIFE-------------YGDAKWPLPE--NLQRIIWNALKKFSIDE--------------RKPT 975 (1605)
T ss_pred HHHHHHhhhhhhhhhhhhcc-------------cCCcccccch--hHHHHHHHHHhhccccc--------------cccc
Confidence 57777788888888886642 3566777777 99999999999987622 2233
Q ss_pred CCCcccccchhHHHHHHhhhHHHHHHHHHHHHHHHhhhcCeeecccchhhhhhcccccCccccccccccccccccccccc
Q psy3015 1276 DVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRC 1355 (1791)
Q Consensus 1276 dVDp~rt~sNdI~eI~~vlGIEAaR~~li~El~~V~~~~Gi~Vn~RHL~LLaD~MT~~G~l~~itR~Gi~rq~~S~L~ra 1355 (1791)
++.|.++ +.+++....+- +.+.|- .|++. | |+ |+.+
T Consensus 976 ~l~~~~v-------------~~g~~~l~e~l----~iv~g~----~~~sr-a-------------------qr---l~~~ 1011 (1605)
T KOG0260|consen 976 DLIPFKV-------------VKGVKELAEKL----VIVRGE----DYISR-A-------------------QR---LFNI 1011 (1605)
T ss_pred ccchhhh-------------hhhhhhhhhee----EEeeCc----hhHHH-H-------------------HH---HHHH
Confidence 4444433 22222221111 122221 11111 0 11 3333
Q ss_pred chhhhHHHHHHHhhccCCCCCCccccceeccccccCCcchhhhhcccccccccccccCCCCcchhh-hhhccCCCCCCCC
Q psy3015 1356 SFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEKCKDGIEIPLATGMMGGP-AGMFFGSAATPSS 1434 (1791)
Q Consensus 1356 SFEeTv~iL~~AA~~ge~D~lkgVsenIi~Gq~~~lGTGaFd~lLge~~~~~~~~~~v~pGEmVG~-aAQSIGEPa~~~~ 1434 (1791)
.+.+++.. +.|. ...++.+.+|+|++|+++.+|.++. ++||||||+ ||||+||||
T Consensus 1012 lLrs~l~~-------------krv~------~e~rls~eaf~w~~~~Ie~~f~qa~-a~pgemvg~lAaqsvgePa---- 1067 (1605)
T KOG0260|consen 1012 LLRSTLAT-------------KRVL------EEYRLSSEAFEWVLGEIEARFLQAE-ASPGEMVGALAAQSVGEPA---- 1067 (1605)
T ss_pred HHHhhHHH-------------HHHH------HHhcccHHHHHHHhhhhhhheeeee-cCccchHhHHHHHHhCCch----
Confidence 44443322 2223 2359999999999999999999999 999999999 899999999
Q ss_pred CCCCCCCcceeeeeeeccccceecccchhHHHhhccCCCCCCCCCccceeEEEEeeccccCCccccCCCCCchhhHhhHh
Q psy3015 1435 IPGPPAWYPIHIAISLLSRFTTVICIYTLKTFLEMKDFKKPPQKGFGLLTLTLMVENIHVTPRQIITPQNNRPVMGIVQD 1514 (1791)
Q Consensus 1435 ~TQmT~lnTFH~aGVs~~~~t~~lGvprlkei~nv~~~~k~~~~~~~~~~~t~~~~~I~~~pk~~~~P~~~~~~~~~vq~ 1514 (1791)
|||| |||||||||+++||| +||||||||+||.|+.|+|| |||||. | ..+ .+.+.||.+|.
T Consensus 1068 -tqmT-lntfh~aGVssknVt--~gvprlkei~Nv~k~~ktps-------LtV~l~-----g-~~~---k~~e~ak~v~~ 1127 (1605)
T KOG0260|consen 1068 -TQMT-LNTFHYAGVSSKNVT--LGVPRLKEIINVAKNAKTPS-------LTVYLT-----G-EAA---KDNEWAKLVQC 1127 (1605)
T ss_pred -hhcc-cchhcccceeeeeee--ccCcchhhhhhhhccCCCce-------EEEEec-----c-hhh---cchHHHHHHhh
Confidence 9999 999999999999998 99999999999999999998 888888 3 233 25788999999
Q ss_pred HHHHHhhccccccchhhhcceeEEEEcCCCCCCcccccHHHHHHhhcCCCCCCCCCCcceEEEEeccccccccccCHHHH
Q psy3015 1515 TLTAVRKMTKRDVFLDKVTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPDFDPTRISPWLLRIELDRKRMTDKKLTMEAI 1594 (1791)
Q Consensus 1515 ~~~~~~~~~~~~~~l~~vt~~t~i~ydpd~~~tvi~eD~~~v~~~~~~pd~~~~~~spwllr~~ldr~~m~dk~l~~~~i 1594 (1791)
.|+ ||||++||.+|+|||||||++|||+||+|||++||||||+|.+++|||||||||||++|+||+|+|++|
T Consensus 1128 ~le--------~ttl~~vt~~t~i~ydpdp~~tvI~ed~e~v~a~~e~pd~D~~~ispwlLrlelDr~~m~dk~ltm~~i 1199 (1605)
T KOG0260|consen 1128 CLE--------HTTLKDVTRATEIYYDPDPQSTVIDEDREFVVAYYEMPDEDVGRISPWLLRLELDRASMTDKKLTMEQI 1199 (1605)
T ss_pred hcc--------cccHHhhhccCcceecCCCcceeeccchhhHHhhhcCcccchhhcChHHHHhhhhhhhcccccccHHHH
Confidence 998 999999999999999999999999999999999999999999999999999999999999999988888
Q ss_pred HhhhhcCCCCCCCCCCCCchhhhHHHHHHHHHhcccCCCceeeecCCcccceEEEEEEecCCCCccchhhhhhhc----c
Q psy3015 1595 SEKINAGFGDDLNTPLSPTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDK----M 1670 (1791)
Q Consensus 1595 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~f~~~l~~i~~ddna~~lv~r~r~~~~~~~~~~~~~~~~~~----~ 1670 (1791)
|+ ||+.+|++|++|||+||||+|||+|||+++++ ++|.-++. |
T Consensus 1200 a~----------------------------~i~~~f~~d~~~i~~ddna~klv~r~ri~~~~-----e~D~~l~~Ie~~m 1246 (1605)
T KOG0260|consen 1200 AE----------------------------KINRGFGSDLACIFSDDNAEKLVLRLRIAKEE-----EDDVFLKCIEANM 1246 (1605)
T ss_pred HH----------------------------HHHhhccCCCceeecccCCcceEEEEEecCcc-----chhHHHHHHHHhh
Confidence 86 99999999999999999999999999999965 22333333 4
Q ss_pred ccceeeccccccceeEeecccC-CccccccEEEEEecccccccHHHHHhh
Q psy3015 1671 EDDMFLRCIEETDRSFVKVDFV-EPKDLVEWKTLLKQMHSDFCLAQIIKC 1719 (1791)
Q Consensus 1671 ~~~~~lr~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1719 (1791)
..++-|||++.|.||||+.+.. +++-..||.+++ +|.||+++++.
T Consensus 1247 l~~~~l~G~~~i~kV~m~~~~~G~f~~~~ew~LeT----dg~~l~~v~s~ 1292 (1605)
T KOG0260|consen 1247 LGDMTLRGIPDIFKVYMSPTEDGEFKPVDEWDLET----DGVNLRRVLSE 1292 (1605)
T ss_pred hhhcccCCccccceEEEeecCCCceeecceeEEec----CchhHHhhhcc
Confidence 5788899999999999998655 667778999999 99999999864
No 6
>PRK08566 DNA-directed RNA polymerase subunit A'; Validated
Probab=100.00 E-value=8.4e-93 Score=924.42 Aligned_cols=373 Identities=40% Similarity=0.644 Sum_probs=347.8
Q ss_pred ceEEeeccCCCCCCCCCeEEe-------------cCccccHhHHHHHHhcCCccCCCCCCCceeCCCCcccHhhhhhhcC
Q psy3015 45 DWMLVTVLPVPPLSVRPAVVM-------------HGSARNQEQMMNILMFLPIWDGKMPQPCILKPKPLWTGKQVFSLII 111 (1791)
Q Consensus 45 ~~mlv~~~iVsP~~~rP~~~i-------------~Gs~~~rddlmqLlm~~~~~~~~lP~PaIlKP~~LWTGKQIfS~iL 111 (1791)
++|.+.+|+++|++++|++++ .+.|+++++++||++|...+...+|+|||+||++|||||||||++|
T Consensus 479 ~Lm~~~~~~~sp~~g~pi~~~~QD~l~g~~~lt~~d~f~~~~~~~~l~~~~~~~~~~~~~pai~~p~~lwTGKqi~s~~l 558 (882)
T PRK08566 479 ILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAAGIDELPEPEPAIENGKPYWTGKQIFSLFL 558 (882)
T ss_pred HHhcchhcEecCCCCCeeEEeehHHHHHHHHHHhccccCCHHHHHHHHHhCCccccccCCcccCCCcccccHHHHHHHHc
Confidence 589999999999999999998 3469999999999999887777899999999999999999999999
Q ss_pred CCCccccccCCCCCCCCCCCCCCCCCCCCCeEEEEcCeEEEEeeccccccCCCccHHHHHHHHhCHHHHHHHHHHHHHHH
Q psy3015 112 PGNVNMTRTHSTHPDDEDSGPYQWISPGDTKVVVEHGSLLMGILCKKSLGTSSGSLLHICFLELGHEVCGRFYGNIQTVV 191 (1791)
Q Consensus 112 P~~inl~~~~~~~~~~~~~~~~~~~~~~d~~ViI~nGeLl~G~ldKk~vG~s~~gLih~i~~~yG~~~a~~fL~~lqrL~ 191 (1791)
|+++|+....+.... ......+.+++|+.|+|+||||++|++||++||++++||||.+|++||+++|..||+++|+|+
T Consensus 559 p~~~~~~~~~~~~~~--~~~~~~~~~~~d~~v~i~~gell~g~ldK~~lg~~~~~li~~i~~~yG~~~a~~fl~~~~~l~ 636 (882)
T PRK08566 559 PKDLNLEFKAKICSG--CDECKKEDCEHDAYVVIKNGKLLEGVIDKKAIGAEQGSILDRIVKEYGPERARRFLDSVTRLA 636 (882)
T ss_pred CCCCCceeecccccc--ccccccccCCCCceEEEecCEEEeccccHHHhhcccchHHHHHHHHhCHHHHHHHHHHHHHHH
Confidence 999998654332211 111124567889999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcCcccccCCcccChhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccCCCCCCcchHHHHHHHHHHHH
Q psy3015 192 NNWLLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGHSIGIGDTIADPQTYLEIQMAIKKAK 271 (1791)
Q Consensus 192 ~~~L~~~GFSiGi~D~i~~~~t~~~i~~~i~~ak~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 271 (1791)
++||+.+|||||++|+++++++.++++++|++++
T Consensus 637 ~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~~~---------------------------------------------- 670 (882)
T PRK08566 637 IRFIMLRGFTTGIDDEDIPEEAKEEIDEIIEEAE---------------------------------------------- 670 (882)
T ss_pred HHHHHhcCEEeehhhcccCHHHHHHHHHHHHHHH----------------------------------------------
Confidence 9999999999999999999999988888888776
Q ss_pred HHHHHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhhhhhhhhhccCCCChHHHHhhcCCCcchhhHHHHHhhccC
Q psy3015 272 EDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQ 351 (1791)
Q Consensus 272 ~~v~~~i~~~~~~~L~~~pg~~~~~~fE~~vn~iLn~~rd~~g~~~~~~l~~~N~l~~Mv~sGSKGS~iNisQi~acvGQ 351 (1791)
+++.++++++..+.+++.||+++++++|.+++.+|+++|+.+++.+.+.++++|++.+|+.||||||++|++||+|||||
T Consensus 671 ~~~~~~~~~~~~g~l~~~~~~~~~~~~e~~i~~~l~~~r~~~~~~~~~~l~~~N~~~~M~~SGsKGS~~N~~Qi~~~lGq 750 (882)
T PRK08566 671 KRVEELIEAYENGELEPLPGRTLEETLEMKIMQVLGKARDEAGEIAEKYLGLDNPAVIMARTGARGSMLNLTQMAACVGQ 750 (882)
T ss_pred HHHHHHHHHHHcCCCccccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcceeeeccccccCHHHHHHHHhccCc
Confidence 34455677788899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCceeccCCccCCCCCCCCCCCCCcccceeccccccCCChhhhhhhcccCcccchhcccccCCcchhHHHHHHhhcc
Q psy3015 352 QNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAMES 431 (1791)
Q Consensus 352 Q~veGkRIp~gf~~RtLPhF~~~d~~p~srGFV~nSfl~GL~P~EfFFHaMaGREGLIDTAVKTaeTGYlQRrLvK~LED 431 (1791)
|+++|+|||+||++||||||.++|.+|+|+|||.|||++||+|+|||||||||||||||||||||+||||||||||+|||
T Consensus 751 Q~~~g~ri~~~~~~rtLP~f~~~d~~~~~~GfV~~sF~~GL~p~EfffH~m~GReGliDTAvkTa~sGYlqRrLvk~led 830 (882)
T PRK08566 751 QSVRGERIRRGYRDRTLPHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQD 830 (882)
T ss_pred eecCCCcCccCccCccCCCCCCCCCCcccCceeeccccCCCCHHHHHHHHhhhcccccccceeeccCccchHHHHHHHhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEeecCcEEecCCceEEEEecCCCCCccccccc
Q psy3015 432 VMVHYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQ 465 (1791)
Q Consensus 432 l~V~YDgTVRns~G~IVQF~YGeDGlD~~~~e~~ 465 (1791)
|+|+||+|||||+|+||||.|||||+||+++|++
T Consensus 831 l~v~yD~tVR~s~g~iiQf~YG~dg~d~~~~~~~ 864 (882)
T PRK08566 831 LKVEYDGTVRDTRGNIVQFKYGEDGVDPMKSDHG 864 (882)
T ss_pred eEEeeCCceEcCCCcEEEEeccCCCcCHHHhcCC
Confidence 9999999999999999999999999999999865
No 7
>TIGR02390 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit A'. This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Probab=100.00 E-value=2e-92 Score=918.29 Aligned_cols=372 Identities=40% Similarity=0.654 Sum_probs=345.3
Q ss_pred ceEEeeccCCCCCCCCCeEEe-------------cCccccHhHHHHHHhcCCccCCCCCCCceeCCCCcccHhhhhhhcC
Q psy3015 45 DWMLVTVLPVPPLSVRPAVVM-------------HGSARNQEQMMNILMFLPIWDGKMPQPCILKPKPLWTGKQVFSLII 111 (1791)
Q Consensus 45 ~~mlv~~~iVsP~~~rP~~~i-------------~Gs~~~rddlmqLlm~~~~~~~~lP~PaIlKP~~LWTGKQIfS~iL 111 (1791)
++|.+.+|+++|++++|++++ .+.|+++++++||+++ ..|++.+|+|||+||++|||||||||++|
T Consensus 475 ~Lm~~~~~~~sp~~g~p~~~~~QD~l~g~~~LT~~d~f~~~~~~~~l~~~-~~~~~~~~~p~i~kp~~lwTGKqi~s~~l 553 (868)
T TIGR02390 475 ELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQTILGV-AGYFGDPPEPAIEKPKEYWTGKQIFSAFL 553 (868)
T ss_pred HHhhchhceecCCCCCeeEEeehhhhhheeeeeeccccCCHHHHHHHHhc-CCccccCCCceecCCcccccHHHHHHHhc
Confidence 589999999999999999998 2469999999999986 56778899999999999999999999999
Q ss_pred CCCccccccCCCCCCCCCCCCCCCCCCCCCeEEEEcCeEEEEeeccccccCCCccHHHHHHHHhCHHHHHHHHHHHHHHH
Q psy3015 112 PGNVNMTRTHSTHPDDEDSGPYQWISPGDTKVVVEHGSLLMGILCKKSLGTSSGSLLHICFLELGHEVCGRFYGNIQTVV 191 (1791)
Q Consensus 112 P~~inl~~~~~~~~~~~~~~~~~~~~~~d~~ViI~nGeLl~G~ldKk~vG~s~~gLih~i~~~yG~~~a~~fL~~lqrL~ 191 (1791)
|.++|+....+..... .....+.+++|+.|+|+||||++|++||+++|++++||||.+|++||+++|..||+++|+|+
T Consensus 554 p~~~n~~~~~~~~~~~--~~~~~~~~~~d~~v~i~~g~ll~G~ldK~~lg~~~~~li~~i~~~yG~~~a~~fl~~~~~l~ 631 (868)
T TIGR02390 554 PEDLNFEGRAKICSGS--DACKKEECPHDAYVVIKNGKLLKGVIDKKAIGAEKGKILHRIVREYGPEAARRFLDSVTRLF 631 (868)
T ss_pred CCCCcceecccccccc--cccccccCCCcceEEEecCeEEeeeecHHHhccCcccHHHHHHHHHCHHHHHHHHHHHHHHH
Confidence 9999986543322110 01123467889999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcCcccccCCcccChhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccCCCCCCcchHHHHHHHHHHHH
Q psy3015 192 NNWLLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGHSIGIGDTIADPQTYLEIQMAIKKAK 271 (1791)
Q Consensus 192 ~~~L~~~GFSiGi~D~i~~~~t~~~i~~~i~~ak~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 271 (1791)
++||+++|||||++|+++++++.++++++|++++
T Consensus 632 ~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~~~---------------------------------------------- 665 (868)
T TIGR02390 632 IRFITLRGFTTGIDDIDIPKEAKEEIEELIEKAE---------------------------------------------- 665 (868)
T ss_pred HHHHHhccEEeehhheeeCHHHHHHHHHHHHHHH----------------------------------------------
Confidence 9999999999999999999999888888887776
Q ss_pred HHHHHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhhhhhhhhhccCCCChHHHHhhcCCCcchhhHHHHHhhccC
Q psy3015 272 EDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQ 351 (1791)
Q Consensus 272 ~~v~~~i~~~~~~~L~~~pg~~~~~~fE~~vn~iLn~~rd~~g~~~~~~l~~~N~l~~Mv~sGSKGS~iNisQi~acvGQ 351 (1791)
+++.++++++..+.+++.||+++++++|.+++++|+++|+.+++.+.+.++++|++.+|+.||||||.+|++||+|||||
T Consensus 666 ~~~~~~~~~~~~g~l~~~~~~~~~~~~e~~i~~~l~~~r~~~~~~~~~~l~~~N~~~~M~~sGsKGS~~Ni~Qi~~~lGQ 745 (868)
T TIGR02390 666 KRVDNLIERYRNGELEPLPGRTVEETLEMKIMEVLGKARDEAGEVAEKYLDPENHAVIMARTGARGSLLNITQMAAMVGQ 745 (868)
T ss_pred HHHHHHHHHHHcCCCccCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcchhhhhhccCCcccccHHHHHhccCc
Confidence 34556677788899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCceeccCCccCCCCCCCCCCCCCcccceeccccccCCChhhhhhhcccCcccchhcccccCCcchhHHHHHHhhcc
Q psy3015 352 QNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAMES 431 (1791)
Q Consensus 352 Q~veGkRIp~gf~~RtLPhF~~~d~~p~srGFV~nSfl~GL~P~EfFFHaMaGREGLIDTAVKTaeTGYlQRrLvK~LED 431 (1791)
|+++|+|||+||.+||||||.++|.+|+|+|||.|||++||+|+|||||||||||||||||||||+||||||||||+|||
T Consensus 746 Q~~~g~ri~~~~~~rtlp~f~~~d~~~~~~GfV~~sF~~GL~p~EfFfH~m~gReGLiDTAvKTa~sGYLqRrLvk~lEd 825 (868)
T TIGR02390 746 QSVRGGRIRRGYRNRTLPHFKKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGGREGLVDTAVRTSQSGYMQRRLINALQD 825 (868)
T ss_pred cccCCCcCccccccCCCCCCCCCCCCcccCceecccccCCCCHHHHHHHHhhhccccccccccccccchhHHHHHHHHhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEeecCcEEecCCceEEEEecCCCCCccccccc
Q psy3015 432 VMVHYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQ 465 (1791)
Q Consensus 432 l~V~YDgTVRns~G~IVQF~YGeDGlD~~~~e~~ 465 (1791)
|+|+|||||||++|+||||.|||||+||+++|++
T Consensus 826 l~v~yD~tVR~~~g~iiQf~YG~dg~d~~~~~~~ 859 (868)
T TIGR02390 826 LYVEYDGTVRDTRGNLIQFKYGEDGVDPMKSDHG 859 (868)
T ss_pred eEEecCCeEEeCCCcEEEEeccCCCcCHHHhccC
Confidence 9999999999999999999999999999999865
No 8
>KOG0261|consensus
Probab=100.00 E-value=1.4e-72 Score=682.35 Aligned_cols=409 Identities=35% Similarity=0.544 Sum_probs=304.7
Q ss_pred HhhhhhHHHHhhccCCHHHHHHHHHHHhhhccceeccccccccccCCcccCCCCcCccccccccCCCCCCCCcceeeccc
Q psy3015 976 RSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQAQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYL 1055 (1791)
Q Consensus 976 Rs~L~sk~v~~~~rln~~a~~~i~gei~~~~~~sqv~~mvG~QsV~gKrI~~GfprRTLphf~kdd~~PESrGFV~Nsf~ 1055 (1791)
|..-..-.+.+.+.-|+...|+.+|++|+.+|+|||.+|||||-|+|+|||-||..|+||||.+++..|+|+|||.|||+
T Consensus 758 Re~~G~~C~~eL~~~NsPliMa~CGSKGS~INiSQMvACVGQQ~ISG~RvPdGf~dRsLPHF~r~Sk~P~aKGFV~NSFy 837 (1386)
T KOG0261|consen 758 REEAGKICIRELHPRNSPLIMALCGSKGSKINISQMVACVGQQIISGHRVPDGFEDRSLPHFERHSKTPAAKGFVANSFY 837 (1386)
T ss_pred HHHHHHHHHHhcCcccChHHHHHhcCCCCcccHHHHHHHhhhhhhcCCcCCCccccccCccccccCCCccccchhhhhcc
Confidence 44444444456689999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCcceEEEeecCCCCccchhhhccchhHHHHHHHHHHhcceEEEECCCCCCcccccCcceeeeeccCCCCCCCCcccc
Q psy3015 1056 AGLTPSEFFFHAMGGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPDFDPTRISPW 1135 (1791)
Q Consensus 1056 ~GLTPsEfffhAMgGREGLiDTAvKTAEtGYIqRRLvk~~Edv~V~YDgtvrnTVr~~d~~iVQf~Yg~dg~D~~~~~~w 1135 (1791)
.||||.|||||||||||||+|||||||||||+||||||++||+.++||+ |||++.+++|||.||+||+||..+|.-
T Consensus 838 SGLTptEFfFHtm~GREGLVDTAVKTAETGYMqRRLmK~LEDL~~~YDg----TVR~s~~~vvqF~YG~DglDPa~mEg~ 913 (1386)
T KOG0261|consen 838 SGLTPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKSLEDLSVQYDG----TVRNSNGDVVQFTYGGDGLDPAMMEGK 913 (1386)
T ss_pred cCCCchhhheeecccccchhhhhhhhhhhhhHHHHHHHHHHHHHHhhcC----ceecCCCcEEEEeecCCCCChhhhcCC
Confidence 9999999999999999999999999999999999999999999999998 566667999999999999999877632
Q ss_pred eeee----eccccc-----cccccCCHHHHHHHHh---------------------------------hccCCCc---cc
Q psy3015 1136 LLRI----ELDRKR-----MTDKKLTMEAISEKIN---------------------------------AGFGDDL---NC 1170 (1791)
Q Consensus 1136 vlr~----~Ld~~~-----m~dk~l~~~~I~~~I~---------------------------------~~~~~dl---~~ 1170 (1791)
-..+ .++..+ -.+..+..+++.+..+ ..++.+. .+
T Consensus 914 ~~pv~f~r~~~~~~~~~~~~~~~~l~~~el~e~~~~~l~~~f~~~~~~F~~~~~~~i~~~~~~~~~~~~~~~d~~~~~~~ 993 (1386)
T KOG0261|consen 914 DQPVNFNRVFDHAKAIFPHRHDPPLSSEELDETLEEELLRKFTEKGDPFVHELREFIASLSKKIKKLQDKYGDECGPKFC 993 (1386)
T ss_pred CCchhHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHhhhcccccCCccC
Confidence 1111 111110 0222333333322211 1111100 00
Q ss_pred c--------cCCcccccc----------------------------------eE---E--------E-----EE---ecC
Q psy3015 1171 I--------FNDDNAEKL----------------------------------VL---R--------I-----RI---MNS 1189 (1791)
Q Consensus 1171 i--------~~d~n~~~l----------------------------------~~---r--------i-----ri---~~~ 1189 (1791)
. .+++..+.. .+ + | |+ .+.
T Consensus 994 ~~~~~~~~~~t~kql~~f~~~~~~ky~~a~~EpGTavGAi~aQSIGEPGTQMTLKTFHFAGVASMNiTlGVPRIkEIINA 1073 (1386)
T KOG0261|consen 994 PDLLYQISRLTEKQLEKFVERCLDKYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINA 1073 (1386)
T ss_pred ccceeeeeeccHHHHHHHHHHHHHHHHhhhcCCcchhhhhhcccCCCCCceeeeeeeeecceeeeeeccCcchHHHHHhh
Confidence 0 000000000 00 0 0 00 000
Q ss_pred ------cccccc----chhHHHHhhh---hhhhHHHHh------------------------------------------
Q psy3015 1190 ------DDSKMQ----DEEDAVDKME---DDMFLRCIE------------------------------------------ 1214 (1791)
Q Consensus 1190 ------~~~~~~----~~ee~~~~~~---dr~~Lr~i~------------------------------------------ 1214 (1791)
.....+ .++...+... ++..|..+-
T Consensus 1074 sk~ISTPIItA~L~n~~d~~~Ar~VKgRiEKt~L~dv~~yieeV~~p~~~fl~i~vd~~~I~~l~L~i~~~~I~~sI~~s 1153 (1386)
T KOG0261|consen 1074 SKTISTPIITAELENPHDERSARVVKGRIEKTTLGDVCSYIEEVYGPDSCFLLIRVDLKRISLLQLEITIESIAYSILKS 1153 (1386)
T ss_pred hcccCccceeeeecCchhHHHHHHHhhhhhhhhHHHHHHHHHHHhCCcceEEEEEecHhHHhhhhccccHHHHHHHHhcC
Confidence 000000 0111111000 011111100
Q ss_pred -------------------------------------hcccccceeccccccceEEEeccccCCCceEEEccCCcccccc
Q psy3015 1215 -------------------------------------ANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIA 1257 (1791)
Q Consensus 1215 -------------------------------------~~il~~~~LkGi~~I~kv~i~lp~~~n~~RiI~na~~~f~~~~ 1257 (1791)
...|.++.++|+|. +.|.+++.+.. ..
T Consensus 1154 ~~~k~~~~~v~v~~~~~~~v~~~~~~~~S~~~~lq~lk~~L~~Vvv~gip~-------------vnr~vi~~de~---~~ 1217 (1386)
T KOG0261|consen 1154 PKRKVKPNDVRVVGETTLRVTPVSDTKSSVYYNLQRLKRSLPNVVVKGIPE-------------VNRAVINIDEK---RG 1217 (1386)
T ss_pred CccccCCcceEEecceeEEEeecccccchhhhhHHHHHhhCCceEEecCcc-------------hhhhheeeccc---CC
Confidence 00122222223222 23333333211 11
Q ss_pred eEEEeecccchhcccccCCCCcccccchhHHHHHHhhhHHHHHHHHHHHHHHHhhhcCeeecccchhhhhhcccccCccc
Q psy3015 1258 DWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLM 1337 (1791)
Q Consensus 1258 e~~L~teG~nL~~vl~~~dVDp~rt~sNdI~eI~~vlGIEAaR~~li~El~~V~~~~Gi~Vn~RHL~LLaD~MT~~G~l~ 1337 (1791)
.|.|-+||.+|+++++.++|++++|.||+++|+.++|||||||..|+.|+..++..+|+.||.||++||||+||++|++.
T Consensus 1218 ~y~L~vEG~gLr~Vm~t~GV~g~~TtsNnv~Ev~~vLGIEAAR~~II~EI~ytM~~HGmsiD~RHiMLLaDvMTyrGEVl 1297 (1386)
T KOG0261|consen 1218 LYKLLVEGTGLRAVMNTDGVKGRRTTSNNVLEVEKVLGIEAARTTIISEIGYTMSNHGMSIDPRHIMLLADVMTYRGEVL 1297 (1386)
T ss_pred ceEEEEeccchHHHhccCCccccccccCceEEeehhhchHHHHHHHHHHHHHHHHhcCcccCHHHHHHHHHHhhhcceee
Confidence 28899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccccccccccccccchhhhHHHHHHHhhccCCCCCCccccceeccccccCCcchhhhhccccc
Q psy3015 1338 AITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEK 1404 (1791)
Q Consensus 1338 ~itR~Gi~rq~~S~L~raSFEeTv~iL~~AA~~ge~D~lkgVsenIi~Gq~~~lGTGaFd~lLge~~ 1404 (1791)
||||+|+.+++.|.|+.||||.|.++|++||.++..|.+.||||||++|.+.++|||.|+++.....
T Consensus 1298 GITRfGl~KM~~SVL~lASFEkT~DhLF~AA~~~k~D~I~GVSEcIIlG~pm~iGTG~fkl~~~~~~ 1364 (1386)
T KOG0261|consen 1298 GITRFGLAKMKDSVLMLASFEKTADHLFDAAAYGKKDAIEGVSECIILGIPMCIGTGIFKLLQRTDD 1364 (1386)
T ss_pred eeeehhhHHHHHHHHHHHhhhhhhHHHHHHHHhcCcccccchhhheecccceeccccHHHHHHhcCC
Confidence 9999999999999999999999999999999999999999999999999999999999999987665
No 9
>TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit, predominant form. Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain.
Probab=100.00 E-value=6.9e-71 Score=712.83 Aligned_cols=292 Identities=22% Similarity=0.321 Sum_probs=244.6
Q ss_pred ceEEeeccCCCCCCCCCeEEe-----cC----------------ccccHhHHHHHHhcCCccCCCCCCCceeC----CCC
Q psy3015 45 DWMLVTVLPVPPLSVRPAVVM-----HG----------------SARNQEQMMNILMFLPIWDGKMPQPCILK----PKP 99 (1791)
Q Consensus 45 ~~mlv~~~iVsP~~~rP~~~i-----~G----------------s~~~rddlmqLlm~~~~~~~~lP~PaIlK----P~~ 99 (1791)
.+|++++|+++|++++|++++ .| .|.+++++++.. +++.++.|++++ +++
T Consensus 464 ~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~~~~~~~~~F~~~~e~~~~~-----~~~~i~l~~~i~~~~~g~~ 538 (1140)
T TIGR02386 464 ALMLASNNILNPKDGKPIVTPSQDMVLGLYYLTTEKPGAKGEGKIFSNVDEAIRAY-----DNGKVHLHALIGVRTSGEI 538 (1140)
T ss_pred HHhCCcccEecCCCCCceEEeechhhheeeEeeeccccccCcCceeCCHHHHHHHH-----HcCCccCCCceEEeccccE
Confidence 589999999999999999998 11 378888887643 234556666654 457
Q ss_pred cc--cHhhhhhhcCCCCccccccCCCCCCCCCCCCCCCCCCCCCeEEEEcCeEEEEeeccccccCCCccHHHHHHHHhCH
Q psy3015 100 LW--TGKQVFSLIIPGNVNMTRTHSTHPDDEDSGPYQWISPGDTKVVVEHGSLLMGILCKKSLGTSSGSLLHICFLELGH 177 (1791)
Q Consensus 100 LW--TGKQIfS~iLP~~inl~~~~~~~~~~~~~~~~~~~~~~d~~ViI~nGeLl~G~ldKk~vG~s~~gLih~i~~~yG~ 177 (1791)
+| |||||||.+||.++++... . .++||+.+| +|||.+|++||+
T Consensus 539 ~~tt~Gr~if~~ilP~~~~~~n~------------------~-------------~~l~Kk~lg----~LI~~i~~~~G~ 583 (1140)
T TIGR02386 539 LETTVGRVIFNEILPEGFPYIND------------------N-------------EPLSKKEIS----SLIDLLYEVHGI 583 (1140)
T ss_pred EEccchHHHHHHHcCCccccccc------------------c-------------cccchHHHH----HHHHHHHHHhCh
Confidence 88 6999999999987765210 0 188999996 699999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCcccccCCcccChhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccCCCCCCc
Q psy3015 178 EVCGRFYGNIQTVVNNWLLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGHSIGIGDTIADP 257 (1791)
Q Consensus 178 ~~a~~fL~~lqrL~~~~L~~~GFSiGi~D~i~~~~t~~~i~~~i~~ak~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 257 (1791)
+.|..|||.+++|+++|++.+|||||++|++++++ ..+++++|+
T Consensus 584 ~~t~~~LD~lk~Lgf~~at~~GfSigi~Dl~ip~~----K~~ii~~a~-------------------------------- 627 (1140)
T TIGR02386 584 EETAEMLDKIKALGFKYATKSGTTISASDIVVPDE----KYEILKEAD-------------------------------- 627 (1140)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCeeeeeccCCCCHH----HHHHHHHHH--------------------------------
Confidence 99999999999999999999999999999999976 245555554
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhhhhhhhhhccCC----CChHHHHhhc
Q psy3015 258 QTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILNDARDKTGGSAKKSLTE----YNNLKAMVVA 333 (1791)
Q Consensus 258 ~~~~~~~~~~~~~~~~v~~~i~~~~~~~L~~~pg~~~~~~fE~~vn~iLn~~rd~~g~~~~~~l~~----~N~l~~Mv~s 333 (1791)
++|.++.++++.|.+ .++.++++++++|+++++.+++.+++++++ .|++++|+.|
T Consensus 628 --------------~~v~~i~~~y~~G~l-------t~~er~~kvi~iw~~~~d~v~~~~~~~l~~~~~~~N~i~mMa~S 686 (1140)
T TIGR02386 628 --------------KEVAKIQKFYNKGLI-------TDEERYRKVVSIWSETKDKVTDAMMKLLKKDTYKFNPIFMMADS 686 (1140)
T ss_pred --------------HHHHHHHHHHHcCCC-------ChHHHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCcHhhhhhc
Confidence 455566667777655 256788999999999999999999999985 4999999999
Q ss_pred CCCcchhhHHHHHhhccCcccCCceeccCCccCCCCCCCCCCCCCcccceeccccccCCChhhhhhhcccCcccchhccc
Q psy3015 334 GSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAV 413 (1791)
Q Consensus 334 GSKGS~iNisQi~acvGQQ~veGkRIp~gf~~RtLPhF~~~d~~p~srGFV~nSfl~GL~P~EfFFHaMaGREGLIDTAV 413 (1791)
|||||.+|++||+||+|||+ .|. ||++|+ +|.|||++||+|+|||||||||||||+|||+
T Consensus 687 GARGS~~ni~QL~GmrGlma-----~p~---Grii~~------------PI~ssF~eGLtp~EyF~st~GaRkGLiDTAl 746 (1140)
T TIGR02386 687 GARGNISQFRQLAGMRGLMA-----KPS---GDIIEL------------PIKSSFREGLTVLEYFISTHGARKGLADTAL 746 (1140)
T ss_pred ccccCHHHHHHHHhCCCccc-----CCC---CCcccc------------chhhccccCCCHHHHhhhccchhccccchhe
Confidence 99999999999999999997 344 478886 4999999999999999999999999999999
Q ss_pred ccCCcchhHHHHHHhhcceEEeecCcEEecCCceEEEEecC
Q psy3015 414 KTAETGYIQRRLIKAMESVMVHYDCTVRNSVGQLIQLRYGE 454 (1791)
Q Consensus 414 KTaeTGYlQRrLvK~LEDl~V~YDgTVRns~G~IVQF~YGe 454 (1791)
|||+||||||||||++||++|.||-.- ...|-.|+....+
T Consensus 747 KTAdSGYLtRRLVdv~qDviV~~dDCg-T~~gi~v~~~~~~ 786 (1140)
T TIGR02386 747 KTADSGYLTRRLVDVAQDVVVREEDCG-TEEGIEVEAIVEG 786 (1140)
T ss_pred eecccceeeeehhhhhcceEEEeCCCC-CCCCEEEEEeecC
Confidence 999999999999999999999987544 3457666666533
No 10
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=100.00 E-value=3.4e-69 Score=697.80 Aligned_cols=277 Identities=25% Similarity=0.363 Sum_probs=234.5
Q ss_pred ceEEeeccCCCCCCCCCeEEe-----cC----------------ccccHhHHHHHHhcCCccCCCCCCCceeCC-----C
Q psy3015 45 DWMLVTVLPVPPLSVRPAVVM-----HG----------------SARNQEQMMNILMFLPIWDGKMPQPCILKP-----K 98 (1791)
Q Consensus 45 ~~mlv~~~iVsP~~~rP~~~i-----~G----------------s~~~rddlmqLlm~~~~~~~~lP~PaIlKP-----~ 98 (1791)
.+|++++|+++|++++|++++ .| .|.+++++++++..- ...+++|..++| .
T Consensus 472 ~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~~~~~~~~~F~~~~e~~~~~~~~---~i~l~~~i~~~~~~~~~i 548 (1156)
T PRK00566 472 VLMLSSNNILSPANGKPIIVPSQDMVLGLYYLTREREGAKGEGMVFSSPEEALRAYENG---EVDLHARIKVRITSKKLV 548 (1156)
T ss_pred HHhCCcccEEecCCCCeeEEeehhhhhhhheeecccccccCCCceeCCHHHHHHHHHcC---CCCCCCeEEecCCCCceE
Confidence 589999999999999999998 11 378999999886532 134555555554 2
Q ss_pred CcccHhhhhhhcCCCCccccccCCCCCCCCCCCCCCCCCCCCCeEEEEcCeEEEEeeccccccCCCccHHHHHHHHhCHH
Q psy3015 99 PLWTGKQVFSLIIPGNVNMTRTHSTHPDDEDSGPYQWISPGDTKVVVEHGSLLMGILCKKSLGTSSGSLLHICFLELGHE 178 (1791)
Q Consensus 99 ~LWTGKQIfS~iLP~~inl~~~~~~~~~~~~~~~~~~~~~~d~~ViI~nGeLl~G~ldKk~vG~s~~gLih~i~~~yG~~ 178 (1791)
.+||||||||.+||+++++.. .+|++||+++| +|||.+|+.||++
T Consensus 549 ~tt~Gk~if~~ilP~~~~~~n-------------------------------~~g~ldKk~Lg----~LI~~i~~~yG~~ 593 (1156)
T PRK00566 549 ETTVGRVIFNEILPEGLPFIN-------------------------------VNKPLKKKEIS----KIINEVYRRYGLK 593 (1156)
T ss_pred EcCcHHHHHHhhccccceeec-------------------------------ccceecHHHHH----HHHHHHHHHhCHH
Confidence 479999999999998655410 05899999997 5999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhcCcccccCCcccChhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccCCCCCCcc
Q psy3015 179 VCGRFYGNIQTVVNNWLLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGHSIGIGDTIADPQ 258 (1791)
Q Consensus 179 ~a~~fL~~lqrL~~~~L~~~GFSiGi~D~i~~~~t~~~i~~~i~~ak~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 258 (1791)
.|..|||.+++|+++|++.+|||||++|++++++ ..+++++|+
T Consensus 594 ~t~~~LD~ik~Lgf~yat~~GfSigi~Dl~ip~~----K~~ii~~a~--------------------------------- 636 (1156)
T PRK00566 594 ETVIFLDKIKDLGFKYATRSGISIGIDDIVIPPE----KKEIIEEAE--------------------------------- 636 (1156)
T ss_pred HHHHHHHHHHHHHHHHHHhcCeEeehhhcCcChH----HHHHHHHHH---------------------------------
Confidence 9999999999999999999999999999999985 345555554
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhhhhhhhhhccCC----CChHHHHhhcC
Q psy3015 259 TYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILNDARDKTGGSAKKSLTE----YNNLKAMVVAG 334 (1791)
Q Consensus 259 ~~~~~~~~~~~~~~~v~~~i~~~~~~~L~~~pg~~~~~~fE~~vn~iLn~~rd~~g~~~~~~l~~----~N~l~~Mv~sG 334 (1791)
++|.++.++++.|.+. ++..++++.++|+++++.+++.+.+++.+ .|++++|+.||
T Consensus 637 -------------~~v~~i~~~y~~G~lt-------~~er~~kvi~~w~~~~d~v~~~~~~~l~~~~~~~N~i~mMa~SG 696 (1156)
T PRK00566 637 -------------KEVAEIEKQYRRGLIT-------DGERYNKVIDIWSKATDEVAKAMMKNLSKDQESFNPIYMMADSG 696 (1156)
T ss_pred -------------HHHHHHHHHHHcCCCC-------chHHHHHHHHHHHHHHHHHHHHHHHhCccccCCCCChheeeecc
Confidence 4455556666666653 34567999999999999999999999976 89999999999
Q ss_pred CCcchhhHHHHHhhccCcc-cCCceeccCCccCCCCCCCCCCCCCcccceeccccccCCChhhhhhhcccCcccchhccc
Q psy3015 335 SKGSNINISQVIACVGQQN-VEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAV 413 (1791)
Q Consensus 335 SKGS~iNisQi~acvGQQ~-veGkRIp~gf~~RtLPhF~~~d~~p~srGFV~nSfl~GL~P~EfFFHaMaGREGLIDTAV 413 (1791)
||||..|++||+||+|||. .+|+.+| .||.|||++||+|+|||||||||||||+|||+
T Consensus 697 ARGS~~ni~QL~GmrGlma~p~G~iie---------------------~pI~ssFreGLt~~EyFfst~GaRkGLiDTAL 755 (1156)
T PRK00566 697 ARGSASQIRQLAGMRGLMAKPSGEIIE---------------------TPIKSNFREGLTVLEYFISTHGARKGLADTAL 755 (1156)
T ss_pred CCcCHHHHHHHHhhcCccccCCCCEee---------------------hhhhhhhhcCCCHHHHhhcCcchhhcccchhe
Confidence 9999999999999999985 4555543 27999999999999999999999999999999
Q ss_pred ccCCcchhHHHHHHhhcceEEeec
Q psy3015 414 KTAETGYIQRRLIKAMESVMVHYD 437 (1791)
Q Consensus 414 KTaeTGYlQRrLvK~LEDl~V~YD 437 (1791)
|||+|||||||||+++||+.|.||
T Consensus 756 KTAdSGYLtRRLVdvaqDviV~~~ 779 (1156)
T PRK00566 756 KTADSGYLTRRLVDVAQDVIVRED 779 (1156)
T ss_pred eeccceeeehhHHHhhCceEEEEC
Confidence 999999999999999999999874
No 11
>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Probab=100.00 E-value=1.2e-68 Score=709.36 Aligned_cols=422 Identities=19% Similarity=0.267 Sum_probs=305.5
Q ss_pred ccCCHHHHHHHHHHHhhhccceeccccccccccC--------CcccCCCCcCccccccccCCCCCCCCcceeeccccCCC
Q psy3015 988 YRLSSEAFEWLVGEIENRFQQAQVIACVGQQNVE--------GKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLT 1059 (1791)
Q Consensus 988 ~rln~~a~~~i~gei~~~~~~sqv~~mvG~QsV~--------gKrI~~GfprRTLphf~kdd~~PESrGFV~Nsf~~GLT 1059 (1791)
.+.|+..+|..+|++|+..|++|+.+|||||+++ |+|||+||.+||||||.++|++|||||||.|||++|||
T Consensus 749 ~~~N~l~~Mv~SGAKGS~~Ni~Qi~~~lGQQ~ve~~~~~~~~G~Ri~~~~~~RtLPhF~~~d~~p~a~GfV~nsFl~GL~ 828 (1321)
T PRK14977 749 DADNAGKIMAKTGARGSMANLAQIAGALGQQKRKTRIGFVLTGGRLHEGYKDRALSHFQEGDDNPDAHGFVKNNYREGLN 828 (1321)
T ss_pred CCCCcHHHHhhcccccCHHHHHHHHhccccccccccccccCCCCCCcCCCCCCcCCCCCCCCCCcccccchhhhhcCCCC
Confidence 4789999999999999999999999999999999 99999999999999999999999999999999999999
Q ss_pred cceEEEeecCCCCccchhhhccchhHHHHHHHHHHhcceEEEECCCCCCcccccCcceeeeeccCCCCCCCCcccceeee
Q psy3015 1060 PSEFFFHAMGGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPDFDPTRISPWLLRI 1139 (1791)
Q Consensus 1060 PsEfffhAMgGREGLiDTAvKTAEtGYIqRRLvk~~Edv~V~YDgtvrnTVr~~d~~iVQf~Yg~dg~D~~~~~~wvlr~ 1139 (1791)
|+|||||||||||||+|||+|||+|||+||||||+|||+.|.||+ |||+++|.+|||.||+||+|+.+.+ +.
T Consensus 829 P~EfFFHaM~GREGLiDTAVKTA~SGYLQRrLvk~lEDl~v~YD~----TVR~s~g~iiQF~YGeDG~d~~~~~-~~--- 900 (1321)
T PRK14977 829 AAEFFFHAMGGREGLIDKARRTEDSGYFQRRLANALEDIRLEYDE----TVRDPHGHIIQFKFGEDGIDPQKLD-HG--- 900 (1321)
T ss_pred HHHHHHHhhcccccccccccccCcCchhHHHHHHHhcceEEecCC----eEEeCCCCEEEEeecCCCcCHHHhc-cC---
Confidence 999999999999999999999999999999999999999999999 7788899999999999999986542 00
Q ss_pred eccccccccccCCHHHHHHHHhhccCCCcccccCCcccccceEEEEEecCccccccchhHHHHhhhhhhhHHHHhhcccc
Q psy3015 1140 ELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLS 1219 (1791)
Q Consensus 1140 ~Ld~~~m~dk~l~~~~I~~~I~~~~~~dl~~i~~d~n~~~l~~riri~~~~~~~~~~~ee~~~~~~dr~~Lr~i~~~il~ 1219 (1791)
..+..+.+.......
T Consensus 901 ---------~~~n~~~~~~~~~~~-------------------------------------------------------- 915 (1321)
T PRK14977 901 ---------EAFNLERIIEKQKIE-------------------------------------------------------- 915 (1321)
T ss_pred ---------CcccHHHHHHHhhhh--------------------------------------------------------
Confidence 011111111100000
Q ss_pred cceeccccccceEEEeccccCCCceEEEccCCcccccceEEEeecccchhcccccCCCCcccccchhHHHHHHhhhHHHH
Q psy3015 1220 DMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAV 1299 (1791)
Q Consensus 1220 ~~~LkGi~~I~kv~i~lp~~~n~~RiI~na~~~f~~~~e~~L~teG~nL~~vl~~~dVDp~rt~sNdI~eI~~vlGIEAa 1299 (1791)
+. ...+.| .++.++++.+-
T Consensus 916 -----------~~-----------------------------------------~~~~~~-----~~~~~~~~~~~---- 934 (1321)
T PRK14977 916 -----------DR-----------------------------------------GKGASK-----DEIEELAKEYT---- 934 (1321)
T ss_pred -----------cc-----------------------------------------ccCCCH-----HHHHHHHHHHH----
Confidence 00 000011 01111111000
Q ss_pred HHHHHHHHHHHhhhcCeeecccchhhhhhcccccCcccccccccccccccccccccchhhhHHHHHHHhhccCCCCCCcc
Q psy3015 1300 RKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGV 1379 (1791)
Q Consensus 1300 R~~li~El~~V~~~~Gi~Vn~RHL~LLaD~MT~~G~l~~itR~Gi~rq~~S~L~raSFEeTv~iL~~AA~~ge~D~lkgV 1379 (1791)
... . ...+..+.. .+..
T Consensus 935 -----~~~----~--------------------------------------~~~~~~~~~---~~~~------------- 951 (1321)
T PRK14977 935 -----KTF----N--------------------------------------ANLPKLLAD---AIHG------------- 951 (1321)
T ss_pred -----Hhh----h--------------------------------------hhhHHHHHH---HHHH-------------
Confidence 000 0 000000000 0000
Q ss_pred ccceeccccccCCcchhhhhcccccccccccccCCCCcchhh-hhhccCCCCCCCCCCCCCCCcceeeeeeeccccceec
Q psy3015 1380 SENIIMGQLPRMGTGCFDLLLDAEKCKDGIEIPLATGMMGGP-AGMFFGSAATPSSIPGPPAWYPIHIAISLLSRFTTVI 1458 (1791)
Q Consensus 1380 senIi~Gq~~~lGTGaFd~lLge~~~~~~~~~~v~pGEmVG~-aAQSIGEPa~~~~~TQmT~lnTFH~aGVs~~~~t~~l 1458 (1791)
.++....|+|++++...++..+. ++|||+||+ ||||||||+ |||| |||||+|||++.|+| +
T Consensus 952 ---------~~~~~~~~~~~~~~~~~~~~~~~-~~pGe~VG~iaAQSiGEP~-----TQmT-LnTFH~AGv~~~nvt--~ 1013 (1321)
T PRK14977 952 ---------AELKEDELEAICAEGKEGFEKAK-VEPGQAIGIISAQSIAEPG-----TQMT-LRTFHAAGIKAMDVT--H 1013 (1321)
T ss_pred ---------cCCCHHHHHHHHHHHHHHHHhcc-cCCcccchhhhhhhccCce-----eeec-ccccccccccccCcc--c
Confidence 12233468899999898998888 999999999 899999999 9999 999999999999988 9
Q ss_pred ccchhHHHhhccCCCCCCCCCccceeEEEEeeccccCCccccCCCCCchhhHhhHhHHHHHhhccccccchhhhcceeEE
Q psy3015 1459 CIYTLKTFLEMKDFKKPPQKGFGLLTLTLMVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVTANTAI 1538 (1791)
Q Consensus 1459 Gvprlkei~nv~~~~k~~~~~~~~~~~t~~~~~I~~~pk~~~~P~~~~~~~~~vq~~~~~~~~~~~~~~~l~~vt~~t~i 1538 (1791)
|||||+||+|++++.+||+ +|+||.+ + ... +.+.|..++..++ +|+|++|+..++|
T Consensus 1014 GvpRl~Eii~a~k~~~tp~-------m~~~l~~----~--~~~---~~~~a~~v~~~ie--------~~~l~~~~~~~~i 1069 (1321)
T PRK14977 1014 GLERFIELVDARAKPSTPT-------MDIYLDD----E--CKE---DIEKAIEIARNLK--------ELKVRALIADSAI 1069 (1321)
T ss_pred CccchHHhhhcccCCCCCe-------EEEEeCC----c--ccc---hHHHHHHHHhhee--------eeEHHHhhhheEe
Confidence 9999999999998899997 9999984 1 111 3344445555454 6999999999999
Q ss_pred EEcCCCCCCcccccHHHHHHhhcCCCCCCCCCCcceEEEEeccccccccccCHHHHHhhhhcCCCCCCCCCCCCchhhhH
Q psy3015 1539 YYDPDPQNTVIPEDQEFVNVYYEMPDFDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNTPLSPTDKKLT 1618 (1791)
Q Consensus 1539 ~ydpd~~~tvi~eD~~~v~~~~~~pd~~~~~~spwllr~~ldr~~m~dk~l~~~~i~~~i~~~~~~~~~~~~~~~~~~~~ 1618 (1791)
+|||++ .+|..|+++ +..++|+|+.|++
T Consensus 1070 ~~~~~~--~~i~~d~~~----------------------------i~~~~i~~~~i~~---------------------- 1097 (1321)
T PRK14977 1070 DNANEI--KLIKPDKRA----------------------------LENGCIPMERFAE---------------------- 1097 (1321)
T ss_pred eccCCc--eEEecCHHH----------------------------HHhcCCCHHHHHH----------------------
Confidence 999985 244444444 4444577777775
Q ss_pred HHHHHHHHhcccCCCceeeecCCcccceEEEEEEecCCCCccchhhhhhhcccc---ceeeccccccceeEeecccCCcc
Q psy3015 1619 MEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMED---DMFLRCIEETDRSFVKVDFVEPK 1695 (1791)
Q Consensus 1619 ~~~~~~~i~~~f~~~l~~i~~ddna~~lv~r~r~~~~~~~~~~~~~~~~~~~~~---~~~lr~~~~~~~~~~~~~~~~~~ 1695 (1791)
.|.+.++++..++..+|| .+++++...++. +..-..+.++++ ++.++||++|+||+|+.+. -+
T Consensus 1098 ------~i~~~~~~~~~~~~~~~~----~i~~~~~~~~~~--~~~~~~l~~l~~~l~~~~i~Gi~~I~r~~i~~~~--~~ 1163 (1321)
T PRK14977 1098 ------IEAALAKGKKFEMELEDD----LIILDLVEAADR--DKPLATLIAIRNKILDKPVKGVPDIERAWVELVE--KD 1163 (1321)
T ss_pred ------HHHHhhcCCceEEeecCC----EEEEecCccccc--chHHHHHHHHHHhcCCcEEecCCCceEEEEEeec--cC
Confidence 445555556566777766 344554321110 001112233332 4779999999999997631 11
Q ss_pred ccccEEEEEecccccccHHHHHh
Q psy3015 1696 DLVEWKTLLKQMHSDFCLAQIIK 1718 (1791)
Q Consensus 1696 ~~~~~~~~~~~~~~~~~~~~~~~ 1718 (1791)
...||.++| ||.+|++++.
T Consensus 1164 ~~~e~~l~t----eG~nl~~vl~ 1182 (1321)
T PRK14977 1164 GRDEWIIQT----SGSNLAAVLE 1182 (1321)
T ss_pred CCeeEEEEe----cCcCHHHHhC
Confidence 236899999 9999999997
No 12
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=100.00 E-value=2.5e-62 Score=654.01 Aligned_cols=294 Identities=24% Similarity=0.323 Sum_probs=236.0
Q ss_pred ceEEeeccCCCCCCCCCeEEe-----cCc----------------cccHhHHHHHHhcCCccCCCCCCCceeCCCCccc-
Q psy3015 45 DWMLVTVLPVPPLSVRPAVVM-----HGS----------------ARNQEQMMNILMFLPIWDGKMPQPCILKPKPLWT- 102 (1791)
Q Consensus 45 ~~mlv~~~iVsP~~~rP~~~i-----~Gs----------------~~~rddlmqLlm~~~~~~~~lP~PaIlKP~~LWT- 102 (1791)
.+|++++|+++|++++|++++ .|. |.+.++++..+. ...++...|.|++++|++|||
T Consensus 1871 ~LM~s~~nilsP~~G~Pi~~p~QD~vlG~y~LT~~~~~~~~~~~~F~~~~e~~~~~~-~~~~~~~~~i~~~~~p~~l~Tt 1949 (2890)
T PRK09603 1871 VLMLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKSGVKGEHKLFSSVNEIITAID-TKELDIHAKIRVLDQGNIIATS 1949 (2890)
T ss_pred HHhcccceEEEcCCCceeEEeecceeeeeEEeeccccCCCCccceeCCHHHHHHHHH-cCCCccCCcceeecCCcEEEcC
Confidence 589999999999999999998 221 334445443222 233333456678889999999
Q ss_pred -HhhhhhhcCCCCccccccCCCCCCCCCCCCCCCCCCCCCeEEEEcCeEEEEeeccccccCCCccHHHHHHHHhCHHHHH
Q psy3015 103 -GKQVFSLIIPGNVNMTRTHSTHPDDEDSGPYQWISPGDTKVVVEHGSLLMGILCKKSLGTSSGSLLHICFLELGHEVCG 181 (1791)
Q Consensus 103 -GKQIfS~iLP~~inl~~~~~~~~~~~~~~~~~~~~~~d~~ViI~nGeLl~G~ldKk~vG~s~~gLih~i~~~yG~~~a~ 181 (1791)
||||||.+||..+++ .++.|.+||+.+| +|||.+|++||++.|.
T Consensus 1950 ~GK~ifs~ilP~~~~~-------------------------------~~~n~~ldKK~Lg----~LI~~i~~~yG~~~t~ 1994 (2890)
T PRK09603 1950 AGRMIIKSILPDFIPT-------------------------------DLWNRPMKKKDIG----VLVDYVHKVGGIGITA 1994 (2890)
T ss_pred ccceeeeccCcccccc-------------------------------ccEeeeechHHHH----HHHHHHHHHHCHHHHH
Confidence 999999999964432 1245789999997 5999999999999999
Q ss_pred HHHHHHHHHHHHHHHhcCcccccCCcccChhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccCCCCCCcchHH
Q psy3015 182 RFYGNIQTVVNNWLLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGHSIGIGDTIADPQTYL 261 (1791)
Q Consensus 182 ~fL~~lqrL~~~~L~~~GFSiGi~D~i~~~~t~~~i~~~i~~ak~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 261 (1791)
.|||.+++|+++|++.+|||||++|++++++ +.+++++|+
T Consensus 1995 ~fLD~lk~LGf~yat~~G~SIgI~Dl~ip~~----K~~iI~~A~------------------------------------ 2034 (2890)
T PRK09603 1995 TFLDNLKTLGFRYATKAGISISMEDIITPKD----KQKMVEKAK------------------------------------ 2034 (2890)
T ss_pred HHHHHHHHHHHHHHHhCCEeeeeccCcccHH----HHHHHHHHH------------------------------------
Confidence 9999999999999999999999999999975 345565555
Q ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhhhhhhhhhccC----CCChHHHHhhcCCCc
Q psy3015 262 EIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILNDARDKTGGSAKKSLT----EYNNLKAMVVAGSKG 337 (1791)
Q Consensus 262 ~~~~~~~~~~~~v~~~i~~~~~~~L~~~pg~~~~~~fE~~vn~iLn~~rd~~g~~~~~~l~----~~N~l~~Mv~sGSKG 337 (1791)
++|.++.++++.|.+.. +..++++.++|+++++.+++.+.+++. +.|++++|+.|||||
T Consensus 2035 ----------~eV~ei~~~y~~G~it~-------~Er~~kvid~w~~~~d~v~~~~~~~l~~~~~~~N~i~mMa~SGARG 2097 (2890)
T PRK09603 2035 ----------VEVKKIQQQYDQGLLTD-------QERYNKIIDTWTEVNDKMSKEMMTAIAKDKEGFNSIYMMADSGARG 2097 (2890)
T ss_pred ----------HHHHHHHHHHHcCCCCc-------cHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCcHHHHHhccccc
Confidence 45666777777777642 346889999999999999998877774 479999999999999
Q ss_pred chhhHHHHHhhccCcccCCceeccCCccCCCCCCCCCCCCCcccceeccccccCCChhhhhhhcccCcccchhcccccCC
Q psy3015 338 SNINISQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAE 417 (1791)
Q Consensus 338 S~iNisQi~acvGQQ~veGkRIp~gf~~RtLPhF~~~d~~p~srGFV~nSfl~GL~P~EfFFHaMaGREGLIDTAVKTae 417 (1791)
|.+|++||+||+|||.. |.|. .. ...|.|||++||+|+|||||||||||||+|||+|||+
T Consensus 2098 S~~NI~QLaGmrGqMak-----p~G~---------ii------e~PI~snFrEGLtp~EyFfst~GaRKGLiDTALKTAd 2157 (2890)
T PRK09603 2098 SAAQIRQLSAMRGLMTK-----PDGS---------II------ETPIISNFKEGLNVLEYFNSTHGARKGLADTALKTAN 2157 (2890)
T ss_pred cHHHHHHHHHcCCcEEC-----CCCC---------cc------cChhhcCcccCCCHHHHHHhccccccchhhhhhhccc
Confidence 99999999999999763 2211 11 1238999999999999999999999999999999999
Q ss_pred cchhHHHHHHhhcceEEe-ecCcEEecCC-ceEEEEec
Q psy3015 418 TGYIQRRLIKAMESVMVH-YDCTVRNSVG-QLIQLRYG 453 (1791)
Q Consensus 418 TGYlQRrLvK~LEDl~V~-YDgTVRns~G-~IVQF~YG 453 (1791)
||||||||||++||++|. .||...+ | .|-.+..|
T Consensus 2158 SGYLTRRLVdvaQDviI~e~DCgT~~--Gi~v~~~~~~ 2193 (2890)
T PRK09603 2158 AGYLTRKLIDVSQNVKVVSDDCGTHE--GIEITDIAVG 2193 (2890)
T ss_pred cchhhhhHHHhhcceEEEeccCCCCC--CeEEEEeecC
Confidence 999999999999999997 5665433 3 34444444
No 13
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=100.00 E-value=6e-63 Score=637.38 Aligned_cols=280 Identities=22% Similarity=0.327 Sum_probs=236.8
Q ss_pred ceEEeeccCCCCCCCCCeEEe-----cC----------------ccccHhHHHHHHhcCCccCCCCCCCce---------
Q psy3015 45 DWMLVTVLPVPPLSVRPAVVM-----HG----------------SARNQEQMMNILMFLPIWDGKMPQPCI--------- 94 (1791)
Q Consensus 45 ~~mlv~~~iVsP~~~rP~~~i-----~G----------------s~~~rddlmqLlm~~~~~~~~lP~PaI--------- 94 (1791)
.+|++++|+++|++++|++++ .| .|.+.+++++++.+...++ +++|..
T Consensus 560 ~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~~~~~~~~~F~~~~e~~~a~~~~~~~~--l~~~i~~~~~~~~~~ 637 (1460)
T PRK14906 560 VLMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLTTERDGFEGEGRTFADFDDALNAYDARADLD--LQAKIVVRLSRDMTV 637 (1460)
T ss_pred HHhcchhcEecCCCCCeeEEeeeeeeeeeEEeeeccccccccCceeCCHHHHHHHHhcCCCcc--ccccEEEecCccccc
Confidence 589999999999999999998 11 3678888888887543332 222222
Q ss_pred ------------eCCCCcccHhhhhhhcCCCCccccccCCCCCCCCCCCCCCCCCCCCCeEEEEcCeEEEEeeccccccC
Q psy3015 95 ------------LKPKPLWTGKQVFSLIIPGNVNMTRTHSTHPDDEDSGPYQWISPGDTKVVVEHGSLLMGILCKKSLGT 162 (1791)
Q Consensus 95 ------------lKP~~LWTGKQIfS~iLP~~inl~~~~~~~~~~~~~~~~~~~~~~d~~ViI~nGeLl~G~ldKk~vG~ 162 (1791)
.++...|+||+||+.+||.+++ +++++++|+.+|.
T Consensus 638 ~~~~~~~~~~~~~~~~~tt~Gr~Ifn~ilP~d~~---------------------------------fvN~~l~KK~Lg~ 684 (1460)
T PRK14906 638 RGSYGDLEETKAGERIETTVGRIIFNQVLPEDYP---------------------------------YLNYKMVKKDIGR 684 (1460)
T ss_pred ccccccccCCCCCceEECCCCEEEEecccCCCcc---------------------------------cccceeeHHHHHH
Confidence 2234589999999999996432 2456899999974
Q ss_pred CCccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCcccccCCcccChhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCC
Q psy3015 163 SSGSLLHICFLELGHEVCGRFYGNIQTVVNNWLLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEP 242 (1791)
Q Consensus 163 s~~gLih~i~~~yG~~~a~~fL~~lqrL~~~~L~~~GFSiGi~D~i~~~~t~~~i~~~i~~ak~~~~~~~~~~~~~~~~~ 242 (1791)
|||.+|+.||.+.+..|||.++++.++|++.+|||||++|+.++++ ..+++++|+
T Consensus 685 ----LI~~i~~~~G~~~t~~fLD~Ik~LGf~yaT~sG~SIgi~Di~ip~~----K~~iI~~A~----------------- 739 (1460)
T PRK14906 685 ----LVNDCCNRYSTAEVEPILDGIKKTGFHYATRAGLTVSVYDATIPDD----KPEILAEAD----------------- 739 (1460)
T ss_pred ----HHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhCCEEEeecccccChH----HHHHHHHHH-----------------
Confidence 9999999999999999999999999999999999999999988865 244555554
Q ss_pred CCCcccccCCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhhhhhhhhhccC
Q psy3015 243 TPGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILNDARDKTGGSAKKSLT 322 (1791)
Q Consensus 243 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~i~~~~~~~L~~~pg~~~~~~fE~~vn~iLn~~rd~~g~~~~~~l~ 322 (1791)
++|.++.++++.|.+. ++..+++++++|+++++.+++.+++++.
T Consensus 740 -----------------------------~~V~ei~~~y~~G~iT-------~~Er~~kVi~iw~~a~d~v~~~~~~~l~ 783 (1460)
T PRK14906 740 -----------------------------EKVAAIDEDYEDGFLS-------ERERHKQVVDIWTEATEEVGEAMLAGFD 783 (1460)
T ss_pred -----------------------------HHHHHHHHHHHcCCCc-------HHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 5666777778777662 3456899999999999999999999999
Q ss_pred CCChHHHHhhcCCCcchhhHHHHHhhccCcc-cCCceeccCCccCCCCCCCCCCCCCcccceeccccccCCChhhhhhhc
Q psy3015 323 EYNNLKAMVVAGSKGSNINISQVIACVGQQN-VEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHA 401 (1791)
Q Consensus 323 ~~N~l~~Mv~sGSKGS~iNisQi~acvGQQ~-veGkRIp~gf~~RtLPhF~~~d~~p~srGFV~nSfl~GL~P~EfFFHa 401 (1791)
+.|++++|+.||||||..||+||+||+|||. ..|++|+ .+|.|||.+||+|.||||||
T Consensus 784 ~~N~i~mMa~SGARGS~~QI~QLaGmRGlma~p~G~iIe---------------------~PI~SnFrEGLt~~EyFiSt 842 (1460)
T PRK14906 784 EDNPIYMMADSGARGNIKQIRQLAGMRGLMADMKGEIID---------------------LPIKANFREGLSVLEYFIST 842 (1460)
T ss_pred cCCCeEeeeeccCcccHHHHHHHHhcccceecCCCCccc---------------------cccccccccCCCHHHHHHHc
Confidence 9999999999999999999999999999974 6787763 25999999999999999999
Q ss_pred ccCcccchhcccccCCcchhHHHHHHhhcceEEe-ecCcEE
Q psy3015 402 MGGREGLIDTAVKTAETGYIQRRLIKAMESVMVH-YDCTVR 441 (1791)
Q Consensus 402 MaGREGLIDTAVKTaeTGYlQRrLvK~LEDl~V~-YDgTVR 441 (1791)
|||||||+|||+|||+|||||||||+++||++|. .||...
T Consensus 843 ~GaRKGL~DTALKTAdSGYLTRRLVdVaQDViV~e~DCgT~ 883 (1460)
T PRK14906 843 HGARKGLVDTALRTADSGYLTRRLVDVAQDVIVREEDCGTD 883 (1460)
T ss_pred ccccchhhhhhhhccccchHHHHHHHhhhheEEEeccCCCC
Confidence 9999999999999999999999999999999996 677654
No 14
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=100.00 E-value=1e-60 Score=636.48 Aligned_cols=286 Identities=22% Similarity=0.340 Sum_probs=238.9
Q ss_pred ceEEeeccCCCCCCCCCeEEe-----cCc------------cccHhHHHHHHhcCCccCCCCCCCceeCCCCcc------
Q psy3015 45 DWMLVTVLPVPPLSVRPAVVM-----HGS------------ARNQEQMMNILMFLPIWDGKMPQPCILKPKPLW------ 101 (1791)
Q Consensus 45 ~~mlv~~~iVsP~~~rP~~~i-----~Gs------------~~~rddlmqLlm~~~~~~~~lP~PaIlKP~~LW------ 101 (1791)
.+|++++|+++|++++|++++ .|. ++...+++++++++. ++.++.++.++|+.+|
T Consensus 1915 ~Lm~~~~nilsP~~G~Pii~~~QD~ilG~y~LT~~~~~~~~~~~f~~~~~~~~a~~--~~~~~i~~~i~~~~~~~~~~~~ 1992 (2836)
T PRK14844 1915 VLMMSTNNVLSPSNGRPIIVPSKDIVLGIYYLTLQEPKEDDLPSFGAFCEVEHSLS--DGTLHIHSSIKYRMEYINSSGE 1992 (2836)
T ss_pred HHhCCcccEEecCCCceeEeehhhhhhhhhhhcccccccccccccCCHHHHHHHHH--cCCcccCceEEeeeccccCCCC
Confidence 389999999999999999998 221 234567788776543 4667778888888777
Q ss_pred ---------cHhhhhhhcCCCCccccccCCCCCCCCCCCCCCCCCCCCCeEEEEcCeEEEEeeccccccCCCccHHHHHH
Q psy3015 102 ---------TGKQVFSLIIPGNVNMTRTHSTHPDDEDSGPYQWISPGDTKVVVEHGSLLMGILCKKSLGTSSGSLLHICF 172 (1791)
Q Consensus 102 ---------TGKQIfS~iLP~~inl~~~~~~~~~~~~~~~~~~~~~~d~~ViI~nGeLl~G~ldKk~vG~s~~gLih~i~ 172 (1791)
.|||||+.+||++.++ +++++.|+++|+.++ +||+.+|
T Consensus 1993 ~~~~~~~tt~GR~if~~ilP~~~~~-----------------------------~~~~~n~~l~KK~l~----~II~~~~ 2039 (2836)
T PRK14844 1993 THYKTICTTPGRLILWQIFPKHENL-----------------------------GFDLINQVLTVKEIT----SIVDLVY 2039 (2836)
T ss_pred cccceEecccHHHHHHHHcCCcccc-----------------------------CcceEeeeechhHHH----HHHHHHH
Confidence 3999999999963221 336788999999994 5999999
Q ss_pred HHhCHHHHHHHHHHHHHHHHHHHHhcCcccccCCcccChhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccCC
Q psy3015 173 LELGHEVCGRFYGNIQTVVNNWLLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGHSIGIGD 252 (1791)
Q Consensus 173 ~~yG~~~a~~fL~~lqrL~~~~L~~~GFSiGi~D~i~~~~t~~~i~~~i~~ak~~~~~~~~~~~~~~~~~~~~~~~~~~~ 252 (1791)
++||++.+..|||.+++|.++|++.+|||+|++|+.+|++. .+++++|+
T Consensus 2040 ~~yG~~~t~~fLD~lk~LGf~yaT~~G~SIgi~Di~iP~~K----~~iI~~a~--------------------------- 2088 (2836)
T PRK14844 2040 RNCGQSATVAFSDKLMVLGFEYATFSGVSFSRCDMVIPETK----ATHVDHAR--------------------------- 2088 (2836)
T ss_pred HHhCHHHHHHHHHHHHHHHHHHHHhccEEeeHhHcccCHHH----HHHHHHHH---------------------------
Confidence 99999999999999999999999999999999999999774 33455444
Q ss_pred CCCCcchHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhhhhhhhhhccC------CCCh
Q psy3015 253 TIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILNDARDKTGGSAKKSLT------EYNN 326 (1791)
Q Consensus 253 ~~~~~~~~~~~~~~~~~~~~~v~~~i~~~~~~~L~~~pg~~~~~~fE~~vn~iLn~~rd~~g~~~~~~l~------~~N~ 326 (1791)
++|.++.++++.|.+. .+.+++++..+|+++++.+++.+++.+. +.|+
T Consensus 2089 -------------------~~v~~i~~~y~~G~it-------~~Er~~kvi~iW~~~~d~v~~~~~~~l~~~~~~~~~N~ 2142 (2836)
T PRK14844 2089 -------------------GEIKKFSMQYQDGLIT-------RSERYNKVIDEWSKCTDMIANDMLKAISIYDGNSKYNS 2142 (2836)
T ss_pred -------------------HHHHHHHHHHHcCCCC-------HHHHHHHHHHHHHHHHHHHHHHHHHhhhhccccCCCCc
Confidence 5666677777777653 3458899999999999999999888662 4799
Q ss_pred HHHHhhcCCCcchhhHHHHHhhccCcccCCceeccCCccCCCCCCCCCCCCCcccceeccccccCCChhhhhhhcccCcc
Q psy3015 327 LKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGRE 406 (1791)
Q Consensus 327 l~~Mv~sGSKGS~iNisQi~acvGQQ~veGkRIp~gf~~RtLPhF~~~d~~p~srGFV~nSfl~GL~P~EfFFHaMaGRE 406 (1791)
+++|+.||||||..|+.|++||+||+.. |.|.. -...|.|||.+||+|.||||||||||+
T Consensus 2143 i~mMa~SGARGS~sQI~QLaGmRGLmak-----p~G~i---------------Ie~PI~SNFrEGLsv~EyFiSt~GaRK 2202 (2836)
T PRK14844 2143 VYMMVNSGARGSTSQMKQLAGMRGLMTK-----PSGEI---------------IETPIISNFREGLNVFEYFNSTHGARK 2202 (2836)
T ss_pred eeeeecccCccCHHHHHHHHhcceeeec-----CCCCe---------------eecchhhhhccCCCHHHhhhhcccccc
Confidence 9999999999999999999999999753 33321 123499999999999999999999999
Q ss_pred cchhcccccCCcchhHHHHHHhhcceEEe-ecCcEEe
Q psy3015 407 GLIDTAVKTAETGYIQRRLIKAMESVMVH-YDCTVRN 442 (1791)
Q Consensus 407 GLIDTAVKTaeTGYlQRrLvK~LEDl~V~-YDgTVRn 442 (1791)
||+|||+|||+|||||||||+++||+.|. .||...+
T Consensus 2203 GL~DTALKTAdSGYLTRRLVDVaQDviI~e~DCgT~~ 2239 (2836)
T PRK14844 2203 GLADTALKTANSGYLTRRLVDVSQNCIVTKHDCKTKN 2239 (2836)
T ss_pred chhhhhhhcccccchhhhhhhhhceEEEEecccCCCC
Confidence 99999999999999999999999999995 7886543
No 15
>cd02584 RNAP_II_Rpb1_C Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain. RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.
Probab=100.00 E-value=4.3e-59 Score=559.94 Aligned_cols=380 Identities=61% Similarity=0.956 Sum_probs=338.3
Q ss_pred ccCCHHHHHHHHHHHhhhccceeccc--cccc---cc-----------------cCCcccCCCCcCccccccccCCCCCC
Q psy3015 988 YRLSSEAFEWLVGEIENRFQQAQVIA--CVGQ---QN-----------------VEGKRIPFGFRKRTLPHFIKDDYGPE 1045 (1791)
Q Consensus 988 ~rln~~a~~~i~gei~~~~~~sqv~~--mvG~---Qs-----------------V~gKrI~~GfprRTLphf~kdd~~PE 1045 (1791)
|++++++|+|+++++..+|..+++.| |||. || |++++||+|+|| |+|+
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~ge~vg~~aaQSiGEP~TQmTLnTFH~AGVas~NVTlGVPR--LkEI-------- 70 (410)
T cd02584 1 YRLNKEAFDWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPR--LKEI-------- 70 (410)
T ss_pred CCCCHHHHHHHHHHHHHHHHHhhcCCCCCcchhhhhhcCCchhcccccccccccccccccccCccc--hHHH--------
Confidence 67899999999999999999999999 8877 88 899999999999 9999
Q ss_pred CCcceeeccccCCCcceEEEeecCCCCccchhhhccchhH-HHHH-----HHHHHhcceEEEECCCCCCcccccCcceee
Q psy3015 1046 SRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETV-NVLV-----FLFQVTANTAIYYDPDPQNTVIPEDQEFVN 1119 (1791)
Q Consensus 1046 SrGFV~Nsf~~GLTPsEfffhAMgGREGLiDTAvKTAEtG-YIqR-----RLvk~~Edv~V~YDgtvrnTVr~~d~~iVQ 1119 (1791)
+|+.++.+||+.++|+ .+...++.+.+ .++. +|.++++++.+.|||++.+|++++|.+||+
T Consensus 71 -----InasK~ikTP~~tv~L--------~~~~~~d~~~A~~v~~~IE~t~l~dv~~~~~i~ydp~~~~~~i~~d~~~i~ 137 (410)
T cd02584 71 -----INVAKNIKTPSLTVYL--------EPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVE 137 (410)
T ss_pred -----hhcccCCCCCeEEEEe--------cCcccchHHHHHHHHhheeEeEHHHhhhheEEEecCcccceeecccHHHHH
Confidence 8999999999999999 44444556666 4444 899999999999999999999999999999
Q ss_pred eeccCCCCC--CCCcccceeeeeccccccccccCCHHHHHHHHhhccCCCcccccCCcccccceEEEEEecCccccccch
Q psy3015 1120 VYYEMPDFD--PTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDE 1197 (1791)
Q Consensus 1120 f~Yg~dg~D--~~~~~~wvlr~~Ld~~~m~dk~l~~~~I~~~I~~~~~~dl~~i~~d~n~~~l~~riri~~~~~~~~~~~ 1197 (1791)
.+|+.|+.+ ...+++|+++++||+.+|.++++++++|..+|+..++.++.++.++++..++++++|+........
T Consensus 138 ~~~~~~d~~~~~~~~~~~~lrl~ld~~~~~~~~i~~~~i~~~i~~~~~~~~~v~~~~~~~~~~~iri~~~~~~~~~~--- 214 (410)
T cd02584 138 SYFEFPDEDVEQDRLSPWLLRIELDRKKMTDKKLSMEQIAKKIKEEFKDDLNVIFSDDNAEKLVIRIRIINDDEEKE--- 214 (410)
T ss_pred HhhccCcccccccccCCeeEEEEECHHHHHHcCCCHHHHHHHHHHhcCCCeEEEEcCCCcceeEEEEEecCcccccc---
Confidence 999987763 467889999999999999999999999999999999988888888888888888888764321110
Q ss_pred hHHHHhhhhhhhHHHHhhcccccceeccccccceEEEeccccCCCceEEEccCCcccccceEEEeecccchhcccccCCC
Q psy3015 1198 EDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDV 1277 (1791)
Q Consensus 1198 ee~~~~~~dr~~Lr~i~~~il~~~~LkGi~~I~kv~i~lp~~~n~~RiI~na~~~f~~~~e~~L~teG~nL~~vl~~~dV 1277 (1791)
...+++.|+++++...+.+++|+|+++|+++.+.. .....+....+.++...+|+|.|+|+||.+++..++|
T Consensus 215 ----~~~~~~~~l~~~~~~~l~~i~l~Gi~~I~r~~i~~----~~~~~~~~~~g~~~~~~~~~l~teG~nl~~v~~~~~V 286 (410)
T cd02584 215 ----EDSEDDVFLKKIESNMLSDMTLKGIEGIRKVFIRE----ENKKKVDIETGEFKKREEWVLETDGVNLREVLSHPGV 286 (410)
T ss_pred ----ccchhHHHHHHHHHhhCCCcEEeCCCCceEEEEEc----CCceEecCCCCcccCCcceEEEecCcCHHHHhCCCCC
Confidence 11234457888877889999999999999999872 1122233446667777789999999999999999999
Q ss_pred CcccccchhHHHHHHhhhHHHHHHHHHHHHHHHhhhcCeeecccchhhhhhcccccCcccccccccccccccccccccch
Q psy3015 1278 DPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSF 1357 (1791)
Q Consensus 1278 Dp~rt~sNdI~eI~~vlGIEAaR~~li~El~~V~~~~Gi~Vn~RHL~LLaD~MT~~G~l~~itR~Gi~rq~~S~L~raSF 1357 (1791)
|+.|++||||++++++|||||||++|++|+++||..+|++||+|||+||||+||++|++++|||||+++.++|||++|||
T Consensus 287 d~~rt~sNdI~ei~~~lGIEAaR~~ii~Ei~~v~~~~Gi~Vd~RHl~LiaD~MT~~G~~~~i~R~Gi~~~~~S~l~~aSF 366 (410)
T cd02584 287 DPTRTTSNDIVEIFEVLGIEAARKALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDTGPLMRCSF 366 (410)
T ss_pred ccccCEeCCHHHHHHhcCHHHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHHHhhceEEeeEeeeeeeccCCChhhhccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhHHHHHHHhhccCCCCCCccccceeccccccCCcchhhhhcc
Q psy3015 1358 EETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLD 1401 (1791)
Q Consensus 1358 EeTv~iL~~AA~~ge~D~lkgVsenIi~Gq~~~lGTGaFd~lLg 1401 (1791)
|+|+++|++||.+|+.|+++||+|||++|+++|+|||+||++++
T Consensus 367 E~t~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~f~l~~d 410 (410)
T cd02584 367 EETVDILLEAAAFGETDDLKGVSENIMLGQLAPIGTGCFDLLLD 410 (410)
T ss_pred hhHHHHHHHHHhcCCCCcCCCchHheeecCccccccceEEEEeC
Confidence 99999999999999999999999999999999999999999875
No 16
>cd02584 RNAP_II_Rpb1_C Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain. RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.
Probab=100.00 E-value=3.4e-52 Score=500.48 Aligned_cols=264 Identities=41% Similarity=0.611 Sum_probs=226.6
Q ss_pred CCcchhhhhcccccccccccccCCCCcchhh-hhhccCCCCCCCCCCCCCCCcceeeeeeeccccceecccchhHHHhhc
Q psy3015 1391 MGTGCFDLLLDAEKCKDGIEIPLATGMMGGP-AGMFFGSAATPSSIPGPPAWYPIHIAISLLSRFTTVICIYTLKTFLEM 1469 (1791)
Q Consensus 1391 lGTGaFd~lLge~~~~~~~~~~v~pGEmVG~-aAQSIGEPa~~~~~TQmT~lnTFH~aGVs~~~~t~~lGvprlkei~nv 1469 (1791)
+...+|+|++++.+.++.++. ++||||||+ ||||||||+ |||| ||||||||||++||| |||||||||+|+
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~-~~~ge~vg~~aaQSiGEP~-----TQmT-LnTFH~AGVas~NVT--lGVPRLkEIIna 73 (410)
T cd02584 3 LNKEAFDWILGEIETRFNRSL-VHPGEMVGTIAAQSIGEPA-----TQMT-LNTFHFAGVSAKNVT--LGVPRLKEIINV 73 (410)
T ss_pred CCHHHHHHHHHHHHHHHHHhh-cCCCCCcchhhhhhcCCch-----hccc-ccccccccccccccc--cCccchHHHhhc
Confidence 445689999999999999998 999999999 799999999 9999 999999999999998 999999999999
Q ss_pred cCCCCCCCCCccceeEEEEeeccccCCccccCCCCCchhhHhhHhHHHHHhhccccccchhhhcceeEEEEcCCCCCCcc
Q psy3015 1470 KDFKKPPQKGFGLLTLTLMVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVTANTAIYYDPDPQNTVI 1549 (1791)
Q Consensus 1470 ~~~~k~~~~~~~~~~~t~~~~~I~~~pk~~~~P~~~~~~~~~vq~~~~~~~~~~~~~~~l~~vt~~t~i~ydpd~~~tvi 1549 (1791)
+|+++||+ +|+||.+ ...+ +.+.|+.++..+| +|+|++|+...+|+||||+.+|+|
T Consensus 74 sK~ikTP~-------~tv~L~~------~~~~---d~~~A~~v~~~IE--------~t~l~dv~~~~~i~ydp~~~~~~i 129 (410)
T cd02584 74 AKNIKTPS-------LTVYLEP------GFAK---DEEKAKKIQSRLE--------HTTLKDVTAATEIYYDPDPQNTVI 129 (410)
T ss_pred ccCCCCCe-------EEEEecC------cccc---hHHHHHHHHhhee--------EeEHHHhhhheEEEecCcccceee
Confidence 99999997 9999983 2222 5566677777776 899999999999999999999999
Q ss_pred cccHHHHHHhhcCCCC--CCCCCCcceEEEEeccccccccccCHHHHHhhhhcCCCCCCCCCCCCchhhhHHHHHHHHHh
Q psy3015 1550 PEDQEFVNVYYEMPDF--DPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNTPLSPTDKKLTMEAISEKIN 1627 (1791)
Q Consensus 1550 ~eD~~~v~~~~~~pd~--~~~~~spwllr~~ldr~~m~dk~l~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~i~ 1627 (1791)
++|++||+.||++||+ +++++|||+|||+||+++|.+++++|++|+. +|+
T Consensus 130 ~~d~~~i~~~~~~~d~~~~~~~~~~~~lrl~ld~~~~~~~~i~~~~i~~----------------------------~i~ 181 (410)
T cd02584 130 EEDKEFVESYFEFPDEDVEQDRLSPWLLRIELDRKKMTDKKLSMEQIAK----------------------------KIK 181 (410)
T ss_pred cccHHHHHHhhccCcccccccccCCeeEEEEECHHHHHHcCCCHHHHHH----------------------------HHH
Confidence 9999999999999997 4578999999999999999999999999886 788
Q ss_pred cccCCCceeeecCCcccceEEEEEEecCCCCcc-chhhh-hhh----ccccceeeccccccceeEeecccC--------C
Q psy3015 1628 AGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKM-QDEED-AVD----KMEDDMFLRCIEETDRSFVKVDFV--------E 1693 (1791)
Q Consensus 1628 ~~f~~~l~~i~~ddna~~lv~r~r~~~~~~~~~-~~~~~-~~~----~~~~~~~lr~~~~~~~~~~~~~~~--------~ 1693 (1791)
+.|++++.|+++|+|++++++|||+....+.+. +.+++ .+. ++..++.|+|+++++||++..+.. +
T Consensus 182 ~~~~~~~~v~~~~~~~~~~~iri~~~~~~~~~~~~~~~~~~l~~~~~~~l~~i~l~Gi~~I~r~~i~~~~~~~~~~~~g~ 261 (410)
T cd02584 182 EEFKDDLNVIFSDDNAEKLVIRIRIINDDEEKEEDSEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREENKKKVDIETGE 261 (410)
T ss_pred HhcCCCeEEEEcCCCcceeEEEEEecCccccccccchhHHHHHHHHHhhCCCcEEeCCCCceEEEEEcCCceEecCCCCc
Confidence 889999999999999999999999986442211 11122 122 233678899999999999987421 3
Q ss_pred ccccccEEEEEecccccccHHHHHhh
Q psy3015 1694 PKDLVEWKTLLKQMHSDFCLAQIIKC 1719 (1791)
Q Consensus 1694 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 1719 (1791)
+++..+|.++| +|++|+++++.
T Consensus 262 ~~~~~~~~l~t----eG~nl~~v~~~ 283 (410)
T cd02584 262 FKKREEWVLET----DGVNLREVLSH 283 (410)
T ss_pred ccCCcceEEEe----cCcCHHHHhCC
Confidence 45566899999 99999999864
No 17
>TIGR02389 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit A''. This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Probab=100.00 E-value=8.3e-51 Score=481.91 Aligned_cols=325 Identities=30% Similarity=0.449 Sum_probs=279.0
Q ss_pred HhhccCCHH-HHHHHHHHHhhhccceeccc--cccc---cc-----------------cCCcccCCCCcCccccccccCC
Q psy3015 985 AENYRLSSE-AFEWLVGEIENRFQQAQVIA--CVGQ---QN-----------------VEGKRIPFGFRKRTLPHFIKDD 1041 (1791)
Q Consensus 985 ~~~~rln~~-a~~~i~gei~~~~~~sqv~~--mvG~---Qs-----------------V~gKrI~~GfprRTLphf~kdd 1041 (1791)
+++++++++ +|+|+++++..+|..+++.| |||+ || |++++||+|+|| |+|+
T Consensus 14 ~~~~~~~~~~~~~~~l~~i~~ky~~alv~PGeaVG~IAAQSIGEP~TQMTLnTFH~AGVas~nVTlGVPR--lkEI---- 87 (367)
T TIGR02389 14 VKKREISDKEELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPR--LIEI---- 87 (367)
T ss_pred HHHcCCCHHHHHHHHHHHHHHHHHHhcCCCccccchhhhhhcCCccccccccccccccccccCccccchh--HHHH----
Confidence 457889999 99999999999999999999 8887 88 899999999999 9999
Q ss_pred CCCCCCcceeeccccCCCcceEEEeecCCCCccchhhhccchhH-HHHH-----HHHHHhcceEEEECCCCCCcccccCc
Q psy3015 1042 YGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETV-NVLV-----FLFQVTANTAIYYDPDPQNTVIPEDQ 1115 (1791)
Q Consensus 1042 ~~PESrGFV~Nsf~~GLTPsEfffhAMgGREGLiDTAvKTAEtG-YIqR-----RLvk~~Edv~V~YDgtvrnTVr~~d~ 1115 (1791)
+|+.++.+||+.++|+ .+...++.+.+ .++. +|.++.+++.+.|+
T Consensus 88 ---------INa~k~i~TP~~ti~L--------~~~~~~~~~~a~~v~~~iE~t~l~dv~~~~~~~~~------------ 138 (367)
T TIGR02389 88 ---------VDARKTPSTPSMTIYL--------EDEYEKDREKAEEVAKKIEATKLEDVAKDISIDLA------------ 138 (367)
T ss_pred ---------hhcccCCCCCeEEEEe--------cCcchhhHHHHHHHHHHhhheeHHHHHhhhheecc------------
Confidence 8999999999999999 45444555555 3433 56666666654432
Q ss_pred ceeeeeccCCCCCCCCcccceeeeeccccccccccCCHHHHHHHHhhccCCCcccccCCcccccceEEEEEecCcccccc
Q psy3015 1116 EFVNVYYEMPDFDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQ 1195 (1791)
Q Consensus 1116 ~iVQf~Yg~dg~D~~~~~~wvlr~~Ld~~~m~dk~l~~~~I~~~I~~~~~~dl~~i~~d~n~~~l~~riri~~~~~~~~~ 1195 (1791)
+|.++++||...|.++++++++|.++|.+.++.....+ ..++..++++...+.
T Consensus 139 ------------------~~~l~i~ld~~~l~~~~i~~~~i~~~i~~~~~~~~~~~----~~~~~~i~i~~~~~~----- 191 (367)
T TIGR02389 139 ------------------DMTVIIELDEEQLKERGITVDDVEKAIKKAKLGKVIEI----DMDGNTITIKPPKPS----- 191 (367)
T ss_pred ------------------CcEEEEEECHHHHHhcCCCHHHHHHHHHHhccccccee----ecCCCEEEEEecCch-----
Confidence 46789999999999999999999999988765543322 234566676643210
Q ss_pred chhHHHHhhhhhhhHHHHhhcccccceeccccccceEEEeccccCCCceEEEccCCcccccceEEEeecccchhcccccC
Q psy3015 1196 DEEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSER 1275 (1791)
Q Consensus 1196 ~~ee~~~~~~dr~~Lr~i~~~il~~~~LkGi~~I~kv~i~lp~~~n~~RiI~na~~~f~~~~e~~L~teG~nL~~vl~~~ 1275 (1791)
. ..|+.+.. .+.++.|+|+|+|+++.+.. ...+|+|.|+|+||.+++..+
T Consensus 192 ----~-------~~l~~l~~-~l~~~~v~Gi~gI~r~~i~~------------------~~~~~~l~teG~nl~~v~~~~ 241 (367)
T TIGR02389 192 ----L-------KELRKLKE-KIKNLHIKGIKGIKRVVIRK------------------EGDEYVIYTEGSNLKEVLKLE 241 (367)
T ss_pred ----H-------HHHHHHHH-HhhhceEeCCCCceEEEEEC------------------CCCeEEEEEeccCHHHHHcCC
Confidence 0 12444433 45689999999999998751 123799999999999999999
Q ss_pred CCCcccccchhHHHHHHhhhHHHHHHHHHHHHHHHhhhcCeeecccchhhhhhcccccCccccccccccccccccccccc
Q psy3015 1276 DVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRC 1355 (1791)
Q Consensus 1276 dVDp~rt~sNdI~eI~~vlGIEAaR~~li~El~~V~~~~Gi~Vn~RHL~LLaD~MT~~G~l~~itR~Gi~rq~~S~L~ra 1355 (1791)
+||+.|++||||++++++|||||||++|++|++.||..+|++||+|||+||||+||++|++.+|+|||+++.++|||++|
T Consensus 242 ~VD~~rt~sNdI~ei~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~RHl~LiaD~MT~~G~~~~i~R~Gi~~~~~S~l~~a 321 (367)
T TIGR02389 242 GVDKTRTTTNDIHEIAEVLGIEAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKASVLARA 321 (367)
T ss_pred CCccccCccCCHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCeecHHHHHHHHHHhcCCceEEeccccccccCCCCHHHhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chhhhHHHHHHHhhccCCCCCCccccceeccccccCCcchhhhhcc
Q psy3015 1356 SFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLD 1401 (1791)
Q Consensus 1356 SFEeTv~iL~~AA~~ge~D~lkgVsenIi~Gq~~~lGTGaFd~lLg 1401 (1791)
|||+|+++|++||.+|+.|+++||+|||++|+++|+|||+||++++
T Consensus 322 SFE~t~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~~~l~~~ 367 (367)
T TIGR02389 322 AFEVTVKHLLDAAIRGEVDELAGVIENIIVGQPIPLGTGDVDLVMD 367 (367)
T ss_pred ChHhHHHHHHHHhhcCCCCcCCChHHHhhcCCCcCCcCCeEEEeeC
Confidence 9999999999999999999999999999999999999999999874
No 18
>cd06528 RNAP_A'' A'' subunit of Archaeal RNA Polymerase (RNAP). Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.
Probab=100.00 E-value=1e-49 Score=473.32 Aligned_cols=328 Identities=29% Similarity=0.425 Sum_probs=278.7
Q ss_pred HHHHhhccCCHHHHHHHHHHHhhhccceeccc--cccc---cc-----------------cCCcccCCCCcCcccccccc
Q psy3015 982 KLVAENYRLSSEAFEWLVGEIENRFQQAQVIA--CVGQ---QN-----------------VEGKRIPFGFRKRTLPHFIK 1039 (1791)
Q Consensus 982 k~v~~~~rln~~a~~~i~gei~~~~~~sqv~~--mvG~---Qs-----------------V~gKrI~~GfprRTLphf~k 1039 (1791)
|++++++++|+.+|+|+++++..+|..+.+.| |||. || |++++||+|+|| |+|+
T Consensus 8 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~Ge~vG~iaAQSiGEP~TQMTLnTFH~AGVas~nVTlGVPR--lkEI-- 83 (363)
T cd06528 8 EEVLKEHGLTLSEAEEIIKEVLREYLRSLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPR--LIEI-- 83 (363)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHHHHhhccCccccceeeeecCccceecccccccccccccccCcccccc--HHHH--
Confidence 67889999999999999999999999999999 8777 88 899999999999 9999
Q ss_pred CCCCCCCCcceeeccccCCCcceEEEeecCCCCccchhhhccchhH-HHHH-----HHHHHhcceEEEECCCCCCccccc
Q psy3015 1040 DDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETV-NVLV-----FLFQVTANTAIYYDPDPQNTVIPE 1113 (1791)
Q Consensus 1040 dd~~PESrGFV~Nsf~~GLTPsEfffhAMgGREGLiDTAvKTAEtG-YIqR-----RLvk~~Edv~V~YDgtvrnTVr~~ 1113 (1791)
+|+.++..||+..+|+ .+...++.+.+ .++. +|.++.+++++.|+
T Consensus 84 -----------Ina~K~i~TP~mti~L--------~~~~~~~~~~a~~v~~~iE~t~l~di~~~~~i~~~---------- 134 (363)
T cd06528 84 -----------VDARKEPSTPTMTIYL--------EEEYKYDREKAEEVARKIEETTLENLAEDISIDLF---------- 134 (363)
T ss_pred -----------hhcccCCCCceEEEEe--------cCcchhhHHHHHHHHHhhceeEHHHhhhheEEecc----------
Confidence 8999999999999999 33333344444 3433 56666666655332
Q ss_pred CcceeeeeccCCCCCCCCcccceeeeeccccccccccCCHHHHHHHHhhccCCCcccccCCcccccceEEEEEecCcccc
Q psy3015 1114 DQEFVNVYYEMPDFDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSK 1193 (1791)
Q Consensus 1114 d~~iVQf~Yg~dg~D~~~~~~wvlr~~Ld~~~m~dk~l~~~~I~~~I~~~~~~dl~~i~~d~n~~~l~~riri~~~~~~~ 1193 (1791)
.|.++++||...|.++++++++|.++|.+.++.++.. .+ +.. +++....
T Consensus 135 --------------------~~~l~i~ld~~~l~~~~l~~~~i~~~i~~~~~~~~~~--~~-~~~-----~~~~~~~--- 183 (363)
T cd06528 135 --------------------NMRITIELDEEMLEDRGITVDDVLKAIEKLKKGKVGE--EG-DVT-----LIVLKAE--- 183 (363)
T ss_pred --------------------CcEEEEEECHHHHHHcCCCHHHHHHHHHHhcCCcccc--cC-Ccc-----EEEEcCC---
Confidence 4889999999999999999999999999887655432 11 111 1111111
Q ss_pred ccchhHHHHhhhhhhhHHHHhhcccccceeccccccceEEEeccccCCCceEEEccCCcccccceEEEeecccchhcccc
Q psy3015 1194 MQDEEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLS 1273 (1791)
Q Consensus 1194 ~~~~ee~~~~~~dr~~Lr~i~~~il~~~~LkGi~~I~kv~i~lp~~~n~~RiI~na~~~f~~~~e~~L~teG~nL~~vl~ 1273 (1791)
. .+..+|+.+. +.+.++.|+|+|+|+++.++.. ..+|+|.|+|+||++++.
T Consensus 184 ---~-------~~~~~l~~l~-~~l~~~~v~Gi~gI~r~~i~~~------------------~~~~~l~teG~nl~~v~~ 234 (363)
T cd06528 184 ---E-------PSIKELRKLA-EKILNTKIKGIKGIKRVIVRKE------------------EDEYVIYTEGSNLKAVLK 234 (363)
T ss_pred ---c-------chHHHHHHHH-HhhcccEEeCCCCceEEEEecC------------------CceEEEEecCcCHHHHhc
Confidence 0 1113455554 3466799999999999987611 127999999999999999
Q ss_pred cCCCCcccccchhHHHHHHhhhHHHHHHHHHHHHHHHhhhcCeeecccchhhhhhcccccCccccccccccccccccccc
Q psy3015 1274 ERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALM 1353 (1791)
Q Consensus 1274 ~~dVDp~rt~sNdI~eI~~vlGIEAaR~~li~El~~V~~~~Gi~Vn~RHL~LLaD~MT~~G~l~~itR~Gi~rq~~S~L~ 1353 (1791)
.++||+.|++||||++++++|||||||.+|++|++.||..+|++||+|||+||||+||++|++.++||+|+++.++|||+
T Consensus 235 ~~~Vd~~rt~sNdI~ei~~~lGIEAaR~~ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~G~~~~i~R~gi~~~~~S~L~ 314 (363)
T cd06528 235 VEGVDPTRTTTNNIHEIEEVLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVRQIGRHGIAGEKPSVLA 314 (363)
T ss_pred CCCCcccccccCCHHHHHHhCCHHHHHHHHHHHHHHHHHhcCCeecHHHHHHHHHHhccCCceecccchhhcCCCCChhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccchhhhHHHHHHHhhccCCCCCCccccceeccccccCCcchhhhhccc
Q psy3015 1354 RCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDA 1402 (1791)
Q Consensus 1354 raSFEeTv~iL~~AA~~ge~D~lkgVsenIi~Gq~~~lGTGaFd~lLge 1402 (1791)
+||||+|+++|++||.+|+.|+++||++||++|+++|+|||+||++++.
T Consensus 315 ~aSFE~t~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~~~l~~d~ 363 (363)
T cd06528 315 RAAFEVTVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTGDVELTMDP 363 (363)
T ss_pred hCchhhHHHHHHHHHhcCCCCcCCCcHHHeeeCCCCCCcCCeeEEEecC
Confidence 9999999999999999999999999999999999999999999999863
No 19
>KOG0262|consensus
Probab=100.00 E-value=4.5e-50 Score=497.95 Aligned_cols=147 Identities=32% Similarity=0.538 Sum_probs=141.6
Q ss_pred HHHHhhccCCHHHHHHHHHHHhhhccceeccccccccccCCcccCCCCcCccccccccCCCCCCCCcceeeccccCCCcc
Q psy3015 982 KLVAENYRLSSEAFEWLVGEIENRFQQAQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPS 1061 (1791)
Q Consensus 982 k~v~~~~rln~~a~~~i~gei~~~~~~sqv~~mvG~QsV~gKrI~~GfprRTLphf~kdd~~PESrGFV~Nsf~~GLTPs 1061 (1791)
.-++..++-|..++|.++|++|+..|.+|+..++|||..||||+|+=+.++|||.|...|.+|.|-|||-.-|++|..|+
T Consensus 886 ~GLlk~FP~N~mqlM~~SGAKGS~VN~~QISclLGQqeLEGkRvPlMvSGKtLPsF~p~e~spraGGfI~~RFlTGi~Pq 965 (1640)
T KOG0262|consen 886 DGLLKKFPENNMQLMIQSGAKGSNVNTSQISCLLGQQELEGKRVPLMVSGKTLPSFAPYETSPRAGGFIDGRFLTGIKPQ 965 (1640)
T ss_pred chhhhcCCcchHHHHHHhcCCcccccHHHHHHhhhhHhhcCCccceeecCCccCCcCCCCCCCCCCCcccceeecCCCch
Confidence 34567899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEEeecCCCCccchhhhccchhHHHHHHHHHHhcceEEEECCCCCCcccccCcceeeeeccCCCCCCCCc
Q psy3015 1062 EFFFHAMGGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPDFDPTRI 1132 (1791)
Q Consensus 1062 EfffhAMgGREGLiDTAvKTAEtGYIqRRLvk~~Edv~V~YDgtvrnTVr~~d~~iVQf~Yg~dg~D~~~~ 1132 (1791)
|||||+|+||||||||||||+.+||+||.|+|.||.+.|+||. |||++||.+|||.|||||+|.++.
T Consensus 966 eyfFHCMAGREGLIDTAVKTSRSGYLQRCLiKhLEgl~V~YD~----TVRDsDgsvVQF~YGEDglDitKs 1032 (1640)
T KOG0262|consen 966 EYFFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLKVHYDL----TVRDSDGSVVQFMYGEDGLDITKS 1032 (1640)
T ss_pred HHhhhhhccccchhhhHHhcccchHHHHHHHHhhhhcEEeccc----eEEcCCCcEEEEeecCccccccHH
Confidence 9999999999999999999999999999999999999999996 999999999999999999997654
No 20
>PRK02597 rpoC2 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=100.00 E-value=1.1e-49 Score=518.82 Aligned_cols=207 Identities=24% Similarity=0.459 Sum_probs=171.7
Q ss_pred EeeccccccCCCccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCcccccCCcccChhhHHHHHHHHHHHHHHHHHHH
Q psy3015 153 GILCKKSLGTSSGSLLHICFLELGHEVCGRFYGNIQTVVNNWLLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVI 232 (1791)
Q Consensus 153 G~ldKk~vG~s~~gLih~i~~~yG~~~a~~fL~~lqrL~~~~L~~~GFSiGi~D~i~~~~t~~~i~~~i~~ak~~~~~~~ 232 (1791)
-++||+.+| +|||.+|+.||+..|..|||.+++|+++|++.+|||+|++|+.++++ ..+++++|+
T Consensus 6 ~~idKk~l~----~LI~~~~~~yG~~~t~~~lD~lk~LGf~~aT~~G~SigidDl~ip~~----K~~li~~Ae------- 70 (1331)
T PRK02597 6 RVVDKKALK----NLIAWAFKNYGTARTAQMADNLKDLGFRYATQAGVSISVDDLKVPPA----KRDLLEQAE------- 70 (1331)
T ss_pred ccccHHHHH----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhCcEEEeecccccCHH----HHHHHHHHH-------
Confidence 468999995 69999999999999999999999999999999999999999999875 345566555
Q ss_pred HHHhcCCCCCCCCcccccCCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhh
Q psy3015 233 QKAHNMDLEPTPGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILNDARDK 312 (1791)
Q Consensus 233 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~i~~~~~~~L~~~pg~~~~~~fE~~vn~iLn~~rd~ 312 (1791)
+++.++.++++.|.+. ..+.+ .++..+|+++++.
T Consensus 71 ---------------------------------------~~v~~~~~~y~~G~it------~~Er~-~kvi~~w~~t~e~ 104 (1331)
T PRK02597 71 ---------------------------------------EEITATEERYRRGEIT------EVERF-QKVIDTWNETNER 104 (1331)
T ss_pred ---------------------------------------HHHHHHHHHHHcCCCc------hhHHH-HHHHHHHHHHHHH
Confidence 4455556667677653 23333 7888999999998
Q ss_pred hhhhhhhcc---CCCChHHHHhhcCCCcchhhHHHHHhhccCccc-CCceeccCCccCCCCCCCCCCCCCcccceecccc
Q psy3015 313 TGGSAKKSL---TEYNNLKAMVVAGSKGSNINISQVIACVGQQNV-EGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSY 388 (1791)
Q Consensus 313 ~g~~~~~~l---~~~N~l~~Mv~sGSKGS~iNisQi~acvGQQ~v-eGkRIp~gf~~RtLPhF~~~d~~p~srGFV~nSf 388 (1791)
+...+.+++ ++.|++++|+.||||||..|+.|++|+.|++.. .|+.| .|| |.|||
T Consensus 105 l~~~~~~~~~~~dp~N~v~mMa~SGARGN~sQI~QLvGmRGLma~p~G~ii-------~lP--------------I~snF 163 (1331)
T PRK02597 105 LKDEVVKNFRQNDPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEII-------DLP--------------IKTNF 163 (1331)
T ss_pred HHHHHHHHHhhcCCCCcHHHHhhccCCccHHHHHHHhcchhhccCCCCcEE-------ecc--------------hhhhh
Confidence 887777766 458999999999999977777777777776543 34443 455 99999
Q ss_pred ccCCChhhhhhhcccCcccchhcccccCCcchhHHHHHHhhcceEEe-ecCcEE
Q psy3015 389 LAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVH-YDCTVR 441 (1791)
Q Consensus 389 l~GL~P~EfFFHaMaGREGLIDTAVKTaeTGYlQRrLvK~LEDl~V~-YDgTVR 441 (1791)
.+||+|+|||||||||||||+|||+|||+|||||||||+++||+.|. .||...
T Consensus 164 rEGLs~~EyFis~~GaRKGLvDTAlKTAdSGYLTRRLVdv~QDviVre~DCgT~ 217 (1331)
T PRK02597 164 REGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTT 217 (1331)
T ss_pred hcCCCHHHhheeccccccchhhcceecccchhHHHHHHHhhcceEEEecCCCCC
Confidence 99999999999999999999999999999999999999999999997 566443
No 21
>PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Probab=100.00 E-value=3.2e-48 Score=467.59 Aligned_cols=332 Identities=30% Similarity=0.452 Sum_probs=271.0
Q ss_pred HHhhccCCHHHHHHHHHHHhhhccceeccc--cccc---cc-----------------cCCcccCCCCcCccccccccCC
Q psy3015 984 VAENYRLSSEAFEWLVGEIENRFQQAQVIA--CVGQ---QN-----------------VEGKRIPFGFRKRTLPHFIKDD 1041 (1791)
Q Consensus 984 v~~~~rln~~a~~~i~gei~~~~~~sqv~~--mvG~---Qs-----------------V~gKrI~~GfprRTLphf~kdd 1041 (1791)
++++++++..+|.|+++++..+|..+++.| |||. || |++++||+|+|| |.|+
T Consensus 152 ~~~~~~l~~~~~~~i~~ei~~~y~~~~v~pGE~VG~IAAQSIGEP~TQMTLnTFH~AGVas~NVTlGVPR--LkEI---- 225 (509)
T PRK14897 152 AMKKKELSDDEYEEILRRIREEYERARVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEMNVTLGLPR--LIEI---- 225 (509)
T ss_pred HHHHcCCCHHHHHHHHHHHHHHHHHhccCCCCCcchhhhhhhCCccccccccccccccccccccccCcch--hHHH----
Confidence 567889999999999999999999999999 8877 88 899999999999 9999
Q ss_pred CCCCCCcceeeccccCCCcceEEEeecCCCCccchhhhccchhH-HHHHHHHHHhcceEEEECCCCCCcccccCcceeee
Q psy3015 1042 YGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETV-NVLVFLFQVTANTAIYYDPDPQNTVIPEDQEFVNV 1120 (1791)
Q Consensus 1042 ~~PESrGFV~Nsf~~GLTPsEfffhAMgGREGLiDTAvKTAEtG-YIqRRLvk~~Edv~V~YDgtvrnTVr~~d~~iVQf 1120 (1791)
+|+.++..||++++|+ .+...++.+.+ .+++++. .+. + ++++.+
T Consensus 226 ---------INa~K~isTP~mtiyL--------~~~~~~d~e~A~~V~~~IE----~tt----------L----~dv~~~ 270 (509)
T PRK14897 226 ---------VDARKKPSTPTMTIYL--------KKDYREDEEKVREVAKKIE----NTT----------L----IDVADI 270 (509)
T ss_pred ---------hhcccCCCCceEEEEe--------cCcccccHHHHHHHHhhhe----eeE----------H----HHHHHH
Confidence 8999999999999999 44444555555 3443222 111 1 111111
Q ss_pred eccCCCCCCCCcccceeeeeccccccccccCCHHHHHHHHhhccCCCcccccCCcccccceEEEEEecCccccccchhHH
Q psy3015 1121 YYEMPDFDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDA 1200 (1791)
Q Consensus 1121 ~Yg~dg~D~~~~~~wvlr~~Ld~~~m~dk~l~~~~I~~~I~~~~~~dl~~i~~d~n~~~l~~riri~~~~~~~~~~~ee~ 1200 (1791)
. ..+..|.++++||...|.++++++++|.++|.+... + ....+++ .++ +.... +.+
T Consensus 271 ~--------~d~~~~~i~i~Ld~~~l~~~~l~~~~I~~~I~~~~~--~-~~~~~~~----~I~--i~~~~-------~~~ 326 (509)
T PRK14897 271 I--------TDIAEMSVVVELDEEKMKERLIEYDDILAAISKLTF--K-TVEIDDG----IIR--LKPQQ-------PSF 326 (509)
T ss_pred H--------HHhccceEEEEECHHHHHHcCCCHHHHHHHHHhccc--e-EEecCCC----EEE--EEeCc-------hHH
Confidence 1 011246689999999999999999999999976321 1 1112221 233 32211 000
Q ss_pred HHhhhhhhhHHHHhhcccccceeccccccceEEEeccccCCCceEEEccCCcccccceEEEeecccchhcccccCCCCcc
Q psy3015 1201 VDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPV 1280 (1791)
Q Consensus 1201 ~~~~~dr~~Lr~i~~~il~~~~LkGi~~I~kv~i~lp~~~n~~RiI~na~~~f~~~~e~~L~teG~nL~~vl~~~dVDp~ 1280 (1791)
..|+.+. ..+.+++|+|+|+|+++.++-.. ...+|+|.|+|+||.+++..++||+.
T Consensus 327 -------~~L~~l~-~~l~~i~I~GipgI~r~~i~~~~----------------~~~~~~L~TeG~NL~~vl~~~~VD~~ 382 (509)
T PRK14897 327 -------KKLYLLA-EKVKSLTIKGIKGIKRAIARKEN----------------DERRWVIYTQGSNLKDVLEIDEVDPT 382 (509)
T ss_pred -------HHHHHHH-HHhhccEEeCCCCccEEEEecCC----------------CCceeEEEeeccCHHHHhcCCCcccc
Confidence 1233432 34578999999999999876211 02369999999999999999999999
Q ss_pred cccchhHHHHHHhhhHHHHHHHHHHHHHHHhhhcCeeecccchhhhhhcccccCcccccccccccccccccccccchhhh
Q psy3015 1281 RTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEET 1360 (1791)
Q Consensus 1281 rt~sNdI~eI~~vlGIEAaR~~li~El~~V~~~~Gi~Vn~RHL~LLaD~MT~~G~l~~itR~Gi~rq~~S~L~raSFEeT 1360 (1791)
|++||||++++++|||||||++|++|++.||..+|++||+|||+||||+||++|.+.+|+|||+++.++|||+|||||+|
T Consensus 383 rt~SNdI~eI~~vlGIEAAR~~Ii~Ei~~V~~~~Gi~Vd~RHL~LIAD~MT~~G~v~~i~R~Gi~~~~~SpL~rASFE~T 462 (509)
T PRK14897 383 RTYTNDIIEIATVLGIEAARNAIIHEAKRTLQEQGLNVDIRHIMLVADMMTFDGSVKAIGRHGISGEKSSVLARAAFEIT 462 (509)
T ss_pred cCccCCHHHHHHhcCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHhCcCCcccccccccccccCCCHHHhcchHhH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhccCCCCCCccccceeccccccCCcchhhhhccccc
Q psy3015 1361 VDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEK 1404 (1791)
Q Consensus 1361 v~iL~~AA~~ge~D~lkgVsenIi~Gq~~~lGTGaFd~lLge~~ 1404 (1791)
+++|++||.+|+.|+|+||++||++|+++|+|||+||++++...
T Consensus 463 ~~~L~~AA~~Ge~D~L~GvsenII~G~~ipvGTG~fdL~~~~~~ 506 (509)
T PRK14897 463 GKHLLRAGILGEVDKLAGVAENIIVGQPITLGTGAVSLVYKGRK 506 (509)
T ss_pred HHHHHHHhhcCCCCcCCChHHhhhcCCccCCcCceEEEEecCCC
Confidence 99999999999999999999999999999999999999987653
No 22
>TIGR02388 rpoC2_cyan DNA-directed RNA polymerase, beta'' subunit. The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria.
Probab=100.00 E-value=1.1e-47 Score=496.62 Aligned_cols=206 Identities=23% Similarity=0.436 Sum_probs=171.1
Q ss_pred EeeccccccCCCccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCcccccCCcccChhhHHHHHHHHHHHHHHHHHHH
Q psy3015 153 GILCKKSLGTSSGSLLHICFLELGHEVCGRFYGNIQTVVNNWLLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVI 232 (1791)
Q Consensus 153 G~ldKk~vG~s~~gLih~i~~~yG~~~a~~fL~~lqrL~~~~L~~~GFSiGi~D~i~~~~t~~~i~~~i~~ak~~~~~~~ 232 (1791)
-++||+.++ +|||.+|++||++.|..|||.+++|+++|++.+|||+|++|+.++++ ..+.+++|+
T Consensus 5 ~~idKk~l~----~LI~~~~~~yG~~~t~~~lD~lk~Lgf~~aT~~G~SigidDl~ip~~----K~~li~~a~------- 69 (1227)
T TIGR02388 5 RVVDKKALK----NLISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPPA----KQDLLEAAE------- 69 (1227)
T ss_pred cccchHHHH----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCeEEeeccCCCCHH----HHHHHHHHH-------
Confidence 468999994 69999999999999999999999999999999999999999999986 344555554
Q ss_pred HHHhcCCCCCCCCcccccCCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhh
Q psy3015 233 QKAHNMDLEPTPGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILNDARDK 312 (1791)
Q Consensus 233 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~i~~~~~~~L~~~pg~~~~~~fE~~vn~iLn~~rd~ 312 (1791)
+++.+++++++.|.+.+ .+.++ ++.++|+++++.
T Consensus 70 ---------------------------------------~~v~~~~~~y~~G~it~------~Er~~-~ii~~w~~t~e~ 103 (1227)
T TIGR02388 70 ---------------------------------------KEIRATEERYRRGEITE------VERFQ-KVIDTWNGTNEE 103 (1227)
T ss_pred ---------------------------------------HHHHHHHHHHHcCCCcc------hhhHH-HHHHHHHHHHHH
Confidence 56666777888888754 34454 788899999998
Q ss_pred hhhhhhhcc---CCCChHHHHhhcCCCcchhhHHHHHhhccCcc-cCCceeccCCccCCCCCCCCCCCCCcccceecccc
Q psy3015 313 TGGSAKKSL---TEYNNLKAMVVAGSKGSNINISQVIACVGQQN-VEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSY 388 (1791)
Q Consensus 313 ~g~~~~~~l---~~~N~l~~Mv~sGSKGS~iNisQi~acvGQQ~-veGkRIp~gf~~RtLPhF~~~d~~p~srGFV~nSf 388 (1791)
+.+.+.+++ ++.|++++|+.||||||..|+.|++|+.|+|. .+|+++ .|| |.|||
T Consensus 104 ~~~~~~~~~~~~d~~N~v~mMa~SGARGNisQi~QLvGmrGlma~p~G~ii-------~lP--------------I~snF 162 (1227)
T TIGR02388 104 LKDEVVNNFRQTDPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEII-------DLP--------------IKTNF 162 (1227)
T ss_pred HHHHHHHhhhhcCCCCcHHHHhhccCcccHHHHHHHhcchheecCCCCcEe-------ecc--------------chhhh
Confidence 887777764 57899999999999995555555444444443 456554 355 99999
Q ss_pred ccCCChhhhhhhcccCcccchhcccccCCcchhHHHHHHhhcceEEe-ecCcE
Q psy3015 389 LAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVH-YDCTV 440 (1791)
Q Consensus 389 l~GL~P~EfFFHaMaGREGLIDTAVKTaeTGYlQRrLvK~LEDl~V~-YDgTV 440 (1791)
.+||+|.|||||||||||||||||||||+|||||||||+++||++|. .||..
T Consensus 163 reGLt~~EyF~sa~GaRkGLvDTAlKTAdSGYLTRRLVdv~qDviV~~~DCgT 215 (1227)
T TIGR02388 163 REGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGT 215 (1227)
T ss_pred hcCCCHHHhheeccccccchhhcceeccccchHHHHHHHhhceEEEEEcCCCC
Confidence 99999999999999999999999999999999999999999999997 46644
No 23
>PRK04309 DNA-directed RNA polymerase subunit A''; Validated
Probab=100.00 E-value=5.1e-48 Score=461.61 Aligned_cols=325 Identities=30% Similarity=0.459 Sum_probs=275.0
Q ss_pred HhhccCCHHHHHHHHHHHhhhccceeccc--cccc---cc-----------------cCCcccCCCCcCccccccccCCC
Q psy3015 985 AENYRLSSEAFEWLVGEIENRFQQAQVIA--CVGQ---QN-----------------VEGKRIPFGFRKRTLPHFIKDDY 1042 (1791)
Q Consensus 985 ~~~~rln~~a~~~i~gei~~~~~~sqv~~--mvG~---Qs-----------------V~gKrI~~GfprRTLphf~kdd~ 1042 (1791)
+.+++++++++.|+++++..+|..+++.| +||. || |++++||+|+|| |+|+
T Consensus 30 ~~~~~l~~~~~~~~~~~i~~~y~~~~v~pGe~VG~iaAQsIGEP~TQMTL~TFH~AGva~~nVTlGvPR--lkEI----- 102 (383)
T PRK04309 30 LEERKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPR--LIEI----- 102 (383)
T ss_pred HHHcCCCHHHHHHHHHHHHHHHHHhhcCCCCccchhhhhhccchhhhcccccccccCccccCcccCchh--HHHH-----
Confidence 35678999999999999999999999999 8887 87 889999999999 9999
Q ss_pred CCCCCcceeeccccCCCcceEEEeecCCCCccchhhhccchhH-HHHH-----HHHHHhcceEEEECCCCCCcccccCcc
Q psy3015 1043 GPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETV-NVLV-----FLFQVTANTAIYYDPDPQNTVIPEDQE 1116 (1791)
Q Consensus 1043 ~PESrGFV~Nsf~~GLTPsEfffhAMgGREGLiDTAvKTAEtG-YIqR-----RLvk~~Edv~V~YDgtvrnTVr~~d~~ 1116 (1791)
+|+.++.+||+.++|+ .+...++.+.+ .+++ +|.++.+++.+.|+
T Consensus 103 --------ina~K~~~TP~~tv~L--------~~~~~~d~~~a~~v~~~iE~t~L~~v~~~i~~~~~------------- 153 (383)
T PRK04309 103 --------VDARKEPSTPMMTIYL--------KDEYAYDREKAEEVARKIEATTLENLAKDISVDLA------------- 153 (383)
T ss_pred --------HhcccCCCCCeEEEEe--------cCcccccHHHHHHHHhheeeeEHhhhhhheEeccC-------------
Confidence 8999999999999999 44333444544 3443 45555555543221
Q ss_pred eeeeeccCCCCCCCCcccceeeeeccccccccccCCHHHHHHHHhhccCCCcccccCCcccccceEEEEEecCccccccc
Q psy3015 1117 FVNVYYEMPDFDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQD 1196 (1791)
Q Consensus 1117 iVQf~Yg~dg~D~~~~~~wvlr~~Ld~~~m~dk~l~~~~I~~~I~~~~~~dl~~i~~d~n~~~l~~riri~~~~~~~~~~ 1196 (1791)
.|.++++||+..+.+++++++.|.++|.+.++.++.+. ...+.++++ ..
T Consensus 154 -----------------~~~l~i~ld~~~i~~~~l~~~~I~~~i~~~~~~~~~~~-----~~~i~i~~~--~~------- 202 (383)
T PRK04309 154 -----------------NMTIIIELDEEMLEDRGLTVDDVKEAIEKKKGGEVEIE-----GNTLIISPK--EP------- 202 (383)
T ss_pred -----------------CcEEEEEECHHHHHHcCCCHHHHHHHHHHhcCcceecc-----CCeEEEEec--Cc-------
Confidence 35689999999999999999999999988776544321 223333332 10
Q ss_pred hhHHHHhhhhhhhHHHHhhcccccceeccccccceEEEeccccCCCceEEEccCCcccccceEEEeecccchhcccccCC
Q psy3015 1197 EEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERD 1276 (1791)
Q Consensus 1197 ~ee~~~~~~dr~~Lr~i~~~il~~~~LkGi~~I~kv~i~lp~~~n~~RiI~na~~~f~~~~e~~L~teG~nL~~vl~~~d 1276 (1791)
+ ...|+.+. +.+.++.|+|+|+|+++.+... ..+|+|.|+|+||.+++..++
T Consensus 203 --~-------~~~l~~l~-~~l~~~~vkGi~gI~r~~i~~~------------------~~~~~l~teG~nl~~v~~~~~ 254 (383)
T PRK04309 203 --S-------YRELRKLA-EKIRNIKIKGIKGIKRVIIRKE------------------GDEYVIYTEGSNLKEVLKVEG 254 (383)
T ss_pred --h-------HHHHHHHH-HHhcccEEECCCCceEEEEecC------------------CCeEEEEEcccCHHHHhcCCC
Confidence 0 12344443 3456899999999999987511 247999999999999999999
Q ss_pred CCcccccchhHHHHHHhhhHHHHHHHHHHHHHHHhhhcCeeecccchhhhhhcccccCcccccccccccccccccccccc
Q psy3015 1277 VDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCS 1356 (1791)
Q Consensus 1277 VDp~rt~sNdI~eI~~vlGIEAaR~~li~El~~V~~~~Gi~Vn~RHL~LLaD~MT~~G~l~~itR~Gi~rq~~S~L~raS 1356 (1791)
||+.|++||||++++++|||||||.+|++|++.||..+|++||+|||+||||+||++|++.++||||+++.++|||++||
T Consensus 255 VD~~rt~sNdI~ei~~vlGIEAAR~~ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~G~~~~i~R~Gi~~~~~S~l~~aS 334 (383)
T PRK04309 255 VDATRTTTNNIHEIEEVLGIEAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGVSGEKASVLARAA 334 (383)
T ss_pred EeeccccCCCHHHHHHHcCHHHHHHHHHHHHHHHHHHcCCeecHHHHHHHHHHhccCceEEeeechhhcCCCCCHHHhCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhHHHHHHHhhccCCCCCCccccceeccccccCCcchhhhhccccc
Q psy3015 1357 FEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEK 1404 (1791)
Q Consensus 1357 FEeTv~iL~~AA~~ge~D~lkgVsenIi~Gq~~~lGTGaFd~lLge~~ 1404 (1791)
||+|+++|++||.+|+.|+++||++||+||+++|+|||+||+++++.+
T Consensus 335 FE~T~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~~~l~~~~~~ 382 (383)
T PRK04309 335 FEVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTGDVELTMDPPL 382 (383)
T ss_pred hhhHHHHHHHHHhcCCCCCCCCcHHHhhcCCCcCCCCceEEEEcCCCC
Confidence 999999999999999999999999999999999999999999998753
No 24
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]
Probab=100.00 E-value=6.5e-49 Score=504.23 Aligned_cols=354 Identities=27% Similarity=0.314 Sum_probs=299.8
Q ss_pred ceEEeeccCCCCCCCCCeEEe-------------cCccccHhHHHHHHhcCCccCCCCCCCceeCCCCcccHhhhhhhcC
Q psy3015 45 DWMLVTVLPVPPLSVRPAVVM-------------HGSARNQEQMMNILMFLPIWDGKMPQPCILKPKPLWTGKQVFSLII 111 (1791)
Q Consensus 45 ~~mlv~~~iVsP~~~rP~~~i-------------~Gs~~~rddlmqLlm~~~~~~~~lP~PaIlKP~~LWTGKQIfS~iL 111 (1791)
.+|+++.++++|.+++|+|++ ...++...++|+++++-...+..-++|||.+|..+|||||+++.++
T Consensus 426 ~lm~tq~nilsP~~Ggpiv~~~qD~v~g~ylLt~~d~~~~~~~~~ei~l~~~~~~~~e~~~ai~~~~~~~~~k~i~~~i~ 505 (808)
T COG0086 426 GLMGTQMNILTPHYGGPIVAPIQDTVGGPYLLTIVDAKLPSTPVGEIYLKDEYADDREKAEAIAKKIELTTGKVIVSTIS 505 (808)
T ss_pred HhhccccccccCCCCCceEeecceEEeccEEEEEecccCCCCcceEEEeccccccchhhhHHHhcccceeeeeEEEEEee
Confidence 589999999999999999998 1236778889999876211123467899999999999999999988
Q ss_pred CCC--ccccccCCCCCCCCCCCCCCCCCCC-CCeEEEEcCeEEEEeeccccccCCCccHHHHHHHHhCHHHHH-HHHHHH
Q psy3015 112 PGN--VNMTRTHSTHPDDEDSGPYQWISPG-DTKVVVEHGSLLMGILCKKSLGTSSGSLLHICFLELGHEVCG-RFYGNI 187 (1791)
Q Consensus 112 P~~--inl~~~~~~~~~~~~~~~~~~~~~~-d~~ViI~nGeLl~G~ldKk~vG~s~~gLih~i~~~yG~~~a~-~fL~~l 187 (1791)
+.. .++..+.. . ..........+ |..+.|.||+++.|++||.+. .+++.||+.++. .+++.+
T Consensus 506 ~~~~~~~i~~t~~---~--~~~~~~~~~~~~d~~~~i~~~~l~~~~i~k~~~---------~i~~~~g~~~~~~~~~~~~ 571 (808)
T COG0086 506 PDLAELSIIVTTD---G--RRIFNRGLPEDKDVLVKIVNGKLIKGVIDKKIV---------TIYREYGPEVASKALVKLL 571 (808)
T ss_pred ccCCcceEEEecc---h--hhhhhccCCcccceeeEEeccccceeeehhhHH---------HHHHHhCchhhHHHHHHHH
Confidence 864 23321110 0 00000111122 578999999999999999876 788999999888 999999
Q ss_pred HHHHHHHHHhcC-cccccCCcccChhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccCCCCCCcchHHHHHHH
Q psy3015 188 QTVVNNWLLLEG-HSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGHSIGIGDTIADPQTYLEIQMA 266 (1791)
Q Consensus 188 qrL~~~~L~~~G-FSiGi~D~i~~~~t~~~i~~~i~~ak~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 266 (1791)
.+|.+.|+...| |+++++|.. .++.+++.+.+.+|.
T Consensus 572 dkl~~~~~~~~~~~~~~i~~~d--~~~~~~~~e~v~~ae----------------------------------------- 608 (808)
T COG0086 572 DKLKNLGIKGIGGFGIGIGRKD--IEAEDEKDEIVIEAE----------------------------------------- 608 (808)
T ss_pred HHHHHhheeeeccceEEeeccc--ccchHHHHHHHHHHH-----------------------------------------
Confidence 999999999988 999999987 222234445555544
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhhhhhhhhhccCCCChHHHHhhcCCCcchhhHHHHH
Q psy3015 267 IKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVI 346 (1791)
Q Consensus 267 ~~~~~~~v~~~i~~~~~~~L~~~pg~~~~~~fE~~vn~iLn~~rd~~g~~~~~~l~~~N~l~~Mv~sGSKGS~iNisQi~ 346 (1791)
.+|.+++.+++.|.++..+++++.+.++.+++..+++++.++++.+.+++..+ +..|..+|++||..|++||.
T Consensus 609 -----~~v~~~i~~~~~g~lt~~~~~~i~e~~e~~~~e~l~~ai~~~~~~~~~~~g~~--~~~i~~m~~~Gs~~n~sq~~ 681 (808)
T COG0086 609 -----GSVLKLILQYEEGDLTRTERNNIVEIIEVLGIEALRNAIIEEIKITLEEQGLD--FVDIRHMGLSGARMNISQIV 681 (808)
T ss_pred -----HHHHHHHHHhhcCCccccCCCCeEEEeehHHHHHHHHHHHHHHhhhHHhcCCc--chhHHHHhhhhhccCHHHHH
Confidence 56677788889999999999999999999999999999999999988887665 77888888899999999999
Q ss_pred hhccCcccCCceeccCCccCCCCCCCCCCCCCcccceeccccccCCChhhhhhhcccCcccchhcccccCCcchhHHHHH
Q psy3015 347 ACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLI 426 (1791)
Q Consensus 347 acvGQQ~veGkRIp~gf~~RtLPhF~~~d~~p~srGFV~nSfl~GL~P~EfFFHaMaGREGLIDTAVKTaeTGYlQRrLv 426 (1791)
+|+|||.+.|+|++.+ |||||.+.+.++++.|||.+||++||+|.|||||+|+||+||+|||+|||+|||||||||
T Consensus 682 ~~iG~~gv~g~r~~~~----~~~~Fe~~~~~~~a~~~i~s~f~eGLt~~e~f~~~~ggR~GlvDTA~KTa~sGYl~RrLv 757 (808)
T COG0086 682 QLIGQQGVMGEKISVL----ARAAFEVTVKHLEAEGPGESSFLEGLTENEYFGHPIGGRTGLVDTALKTADSGYLTRRLV 757 (808)
T ss_pred HHhhhheeeccCCCcc----cccccccccccceeeeeeecccCCCCCcceEEeecCccccchHHHhhhhcccCcceEEee
Confidence 9999999999999988 999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhcceEEeecCcEEecCCceEEEEecCCCCCcccccccc
Q psy3015 427 KAMESVMVHYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQR 466 (1791)
Q Consensus 427 K~LEDl~V~YDgTVRns~G~IVQF~YGeDGlD~~~~e~~~ 466 (1791)
+++|||+|+||++||++.+.++||.|||||+|++.....+
T Consensus 758 ~~~qdl~v~~d~~~~~g~~~~~~~~~ged~~~~~~~~~~~ 797 (808)
T COG0086 758 DVAQDLIVQEDDCVTDGIGVVIQFEYGEDGEDLTERILGR 797 (808)
T ss_pred chhcceEEEecCeEeecCceEEEEecCccccCHHHHhcCe
Confidence 9999999999999999889999999999999987766554
No 25
>cd02737 RNAP_IV_NRPD1_C Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain. Higher plants have five multi-subunit nuclear RNA polymerases: RNAP I, RNAP II and RNAP III, which are essential for viability; plus the two isoforms of the non-essential polymerase RNAP IV (IVa and IVb), which specialize in small RNA-mediated gene silencing pathways. RNAP IVa and/or RNAP IVb might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b is the largest subunit of RNAP IVb. The full subunit compositions of RNAP IVa and RNAP IVb are not known, nor are their templates or enzymatic products. However, it has been shown that RNAP IVa and, to a lesser extent, RNAP IVb are crucial for several RNA-mediated gene silencing phenomena.
Probab=100.00 E-value=7.6e-47 Score=450.08 Aligned_cols=313 Identities=19% Similarity=0.278 Sum_probs=258.4
Q ss_pred CCcCccccccccCCCCCCCCcceeec--cccCCCcceEEEeec---CCCCccchhhhccchhH-----HHHH-HHHHHhc
Q psy3015 1028 GFRKRTLPHFIKDDYGPESRGFVENS--YLAGLTPSEFFFHAM---GGREGLIDTAVKTAETV-----NVLV-FLFQVTA 1096 (1791)
Q Consensus 1028 GfprRTLphf~kdd~~PESrGFV~Ns--f~~GLTPsEfffhAM---gGREGLiDTAvKTAEtG-----YIqR-RLvk~~E 1096 (1791)
++|| |+|+ +|. .++.+||+..+|+.- .-+++. .. .+.+ .|.+ +|.++++
T Consensus 31 ~vpr--LKEi-------------Ln~~~~~~~ktps~~v~L~~~~~~~~~~~----~~-~~~a~~Vq~~Le~~tL~~v~~ 90 (381)
T cd02737 31 PLEL--LKEV-------------LECRSKSKSKENDRRVILSLHLCKCDHGF----EY-ERAALEVKNHLERVTLEDLAT 90 (381)
T ss_pred cHHH--HHHH-------------hcccccCCCCCCCEEEEEeccccccccch----HH-HHHHHHHHHHhhhccHHHhhh
Confidence 5899 9999 899 778999999999942 111122 11 2223 3333 7999999
Q ss_pred ceEEEECCCCCCcccccCcceeee-----eccCCC--CCCCCcccceeeeeccccccccccCCHHHHHHHHhhccCCCcc
Q psy3015 1097 NTAIYYDPDPQNTVIPEDQEFVNV-----YYEMPD--FDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLN 1169 (1791)
Q Consensus 1097 dv~V~YDgtvrnTVr~~d~~iVQf-----~Yg~dg--~D~~~~~~wvlr~~Ld~~~m~dk~l~~~~I~~~I~~~~~~dl~ 1169 (1791)
.++|+|||++.+|+..+|+++++. +|..++ .+.++.+||++|+++|+. ..++.+..
T Consensus 91 ~~~I~Ydp~~~~t~i~~d~~~~~~~~~~~~~~~~~~~~~~~~~spw~~r~~l~~~-----------------~~~~~~~~ 153 (381)
T cd02737 91 TSMIKYSPQATEAIVGEIGDQLNTKKKGKKKAIFSTSLKITKFSPWVCHFHLDKE-----------------CQKLSDGP 153 (381)
T ss_pred eEEEEECCCcccccccccHHHHHhhhhhhhhcccccccccccCCcceEEEEEehh-----------------HhcCCCCc
Confidence 999999999999999999999887 676654 456788999999999976 11333444
Q ss_pred cccCCcccccceEEEEEecCccccccchhHHHHhhhhhhhHHHHhhcccccceeccccccceEEEeccccCCCceEEEcc
Q psy3015 1170 CIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITE 1249 (1791)
Q Consensus 1170 ~i~~d~n~~~l~~riri~~~~~~~~~~~ee~~~~~~dr~~Lr~i~~~il~~~~LkGi~~I~kv~i~lp~~~n~~RiI~na 1249 (1791)
|+..+.+.+ .. . . .....+.+++.+++.+|. ++|||+++|++|+|.|. +..+..|..
T Consensus 154 ci~~~~~~~-------------~~-~-~----~~~~~~~~~~~i~~~lL~-~~lkG~~~I~kv~i~~~---~~~~~~~~~ 210 (381)
T cd02737 154 CLTFSVSKE-------------VS-K-S----SEELLDVLRDRIIPFLLE-TVIKGDERIKSVNILWE---DSPSTSWVK 210 (381)
T ss_pred eEEeecCcc-------------cc-c-c----hhHHHHHHHHHHHHHHhh-eeecccCCeeEEEEEec---CCCcccccc
Confidence 543332200 00 0 0 112344578888887775 99999999999999863 234556666
Q ss_pred CCcccccceEEEeec---------ccchhccc-----ccCCCCcccccchhHHHHHHhhhHHHHHHHHHHHHHHHhhhcC
Q psy3015 1250 SGEFKAIADWLLETD---------GTSLMKVL-----SERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYG 1315 (1791)
Q Consensus 1250 ~~~f~~~~e~~L~te---------G~nL~~vl-----~~~dVDp~rt~sNdI~eI~~vlGIEAaR~~li~El~~V~~~~G 1315 (1791)
...+....||+|+|+ |++|..++ ..++||+.|++||||++|+++|||||||+.|++|++.|+.++|
T Consensus 211 ~~~~~~~~E~vLe~~~~~~~~~t~G~~~~~vl~~c~~~~~~ID~~rt~sNdI~ev~~~lGIEAAR~~ii~El~~v~~~~G 290 (381)
T cd02737 211 SVGKSSRGELVLEVTVEESCKKTRGNAWNVVMDACIPVMDLIDWERSMPYSIQQIKSVLGIDAAFEQFVQRLESAVSMTG 290 (381)
T ss_pred cccccccceEEEEEEeccccccccchhHHHHHHhhhcccccCcCCCcEECCHHHHHHHHhHHHHHHHHHHHHHHHHHhcC
Confidence 666888889999987 99999999 4899999999999999999999999999999999999999999
Q ss_pred eeecccchhhhhhcccccCccccccccccccccc-----ccccccchhhhHHHHHHHhhccCCCCCCccccceecccccc
Q psy3015 1316 LYVNYRHLALLCDVMTAKGHLMAITRHGINRQDT-----GALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPR 1390 (1791)
Q Consensus 1316 i~Vn~RHL~LLaD~MT~~G~l~~itR~Gi~rq~~-----S~L~raSFEeTv~iL~~AA~~ge~D~lkgVsenIi~Gq~~~ 1390 (1791)
++||+|||.||||+||++|+++||||||+++++. |||+|||||+|+++|++||.+|+.|+++||++||+||++++
T Consensus 291 ~~Vd~rHL~LlAD~MT~~G~~~~~nR~Gi~~~~~s~~~~spl~~asFE~t~~~l~~AA~~g~~D~l~gvs~~ii~G~~~~ 370 (381)
T cd02737 291 KSVLREHLLLVADSMTYSGEFVGLNAKGYKAQRRSLKISAPFTEACFSSPIKCFLKAAKKGASDSLSGVLDACAWGKEAP 370 (381)
T ss_pred CcccHHHHHHHHHHhccCCceEEecchhhhhcccccccCCHHHHhhHHHHHHHHHHHHhccCCCCCCChHHheeeCCcCC
Confidence 9999999999999999999999999999999875 79999999999999999999999999999999999999999
Q ss_pred CCcch-hhhhc
Q psy3015 1391 MGTGC-FDLLL 1400 (1791)
Q Consensus 1391 lGTGa-Fd~lL 1400 (1791)
+|||+ ||+++
T Consensus 371 vGTG~~fdll~ 381 (381)
T cd02737 371 VGTGSKFEILW 381 (381)
T ss_pred CcCCcceeeeC
Confidence 99997 99975
No 26
>cd02736 RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain. Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Probab=100.00 E-value=4e-44 Score=416.23 Aligned_cols=272 Identities=32% Similarity=0.449 Sum_probs=228.0
Q ss_pred hccceeccc--cccc---cc-----------------cCCcccCCCCcCccccccccCCCCCCCCcceeeccccCCCcce
Q psy3015 1005 RFQQAQVIA--CVGQ---QN-----------------VEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSE 1062 (1791)
Q Consensus 1005 ~~~~sqv~~--mvG~---Qs-----------------V~gKrI~~GfprRTLphf~kdd~~PESrGFV~Nsf~~GLTPsE 1062 (1791)
+|..+++.| |||. || |++++||+|+|| |+|+ +|..++.+||+.
T Consensus 1 ky~~~~v~pGe~vG~iaaQsiGEp~TQmTL~TFH~aGv~~~nvtlGvPR--lkEI-------------inasK~~~TP~~ 65 (300)
T cd02736 1 KYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPR--IKEI-------------INASKNISTPII 65 (300)
T ss_pred CchhhccCCCccchhhhhhhcCCccccccccccccccccccccccCchH--HHHH-------------HhcccCCCCCeE
Confidence 467888999 8877 87 889999999999 9999 899999999999
Q ss_pred EEEeecCCCCccchhhhccchhH-HHHH-----HHHHHhcceEEEECCCCCCcccccCcceeeeeccCCCCCCCCcccce
Q psy3015 1063 FFFHAMGGREGLIDTAVKTAETV-NVLV-----FLFQVTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPDFDPTRISPWL 1136 (1791)
Q Consensus 1063 fffhAMgGREGLiDTAvKTAEtG-YIqR-----RLvk~~Edv~V~YDgtvrnTVr~~d~~iVQf~Yg~dg~D~~~~~~wv 1136 (1791)
++|+. + -++.+.+ .+++ +|.++.+.+.+.|||+..++++
T Consensus 66 ti~l~--------~--~~~~~~a~~v~~~ie~t~l~di~~~~~~~~~p~~~~~~i------------------------- 110 (300)
T cd02736 66 TAKLE--------N--DRDEKSARIVKGRIEKTYLGEVASYIEEVYSPDDCYILI------------------------- 110 (300)
T ss_pred EEEec--------C--cccHHHHHHHHHHHhhccHHHhhhheEEEEcCCCceEEE-------------------------
Confidence 99993 2 1344444 3433 8899999999999996655543
Q ss_pred eeeeccccccccccCCHHHHHHHHhhccCCCcccccCCcccccceEEEEEecCccccccchhHHHHhhhhhhhHHHHhhc
Q psy3015 1137 LRIELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEAN 1216 (1791)
Q Consensus 1137 lr~~Ld~~~m~dk~l~~~~I~~~I~~~~~~dl~~i~~d~n~~~l~~riri~~~~~~~~~~~ee~~~~~~dr~~Lr~i~~~ 1216 (1791)
++|.+.+.++.+. . + +..++.....+
T Consensus 111 ---~~d~~~i~~~~l~------------------------~-------------------~--------~~~~~~~~l~~ 136 (300)
T cd02736 111 ---KLDKKIIEKLQLS------------------------K-------------------S--------NLYFLLQSLKR 136 (300)
T ss_pred ---EecHHHHHHhcCC------------------------c-------------------c--------cHHHHHHHHHH
Confidence 3333322222220 0 0 00111122234
Q ss_pred ccccceeccccccceEEEeccccCCCceEEEccCCcccccceEEEeecccchhcccccCCCCcccccchhHHHHHHhhhH
Q psy3015 1217 MLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGI 1296 (1791)
Q Consensus 1217 il~~~~LkGi~~I~kv~i~lp~~~n~~RiI~na~~~f~~~~e~~L~teG~nL~~vl~~~dVDp~rt~sNdI~eI~~vlGI 1296 (1791)
.+.++.|+|+|+|+++.++... ...+|+|.|+|+||.+++..++||+.|++||||++++++|||
T Consensus 137 ~l~~~~v~Gi~gI~r~~i~~~~----------------~~~~~~l~teG~nl~~v~~~~~Vd~~rt~sNdI~ei~~~lGI 200 (300)
T cd02736 137 KLPDVVVSGIPEVKRAVINKDK----------------KKGKYKLLVEGYGLRAVMNTPGVIGTRTTSNHIMEVEKVLGI 200 (300)
T ss_pred HhccceEeCCCCceEEEEecCC----------------CCCcEEEEEecccHHHHhcCCcEeccCCccCCHHHHHHhcCH
Confidence 6778999999999999876211 024799999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhhcCeeecccchhhhhhcccccCcccccccccccccccccccccchhhhHHHHHHHhhccCCCCC
Q psy3015 1297 EAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPM 1376 (1791)
Q Consensus 1297 EAaR~~li~El~~V~~~~Gi~Vn~RHL~LLaD~MT~~G~l~~itR~Gi~rq~~S~L~raSFEeTv~iL~~AA~~ge~D~l 1376 (1791)
||||++|++|+++||..+|++||+|||+||||+||++|.++||||||++++++|||++||||+|.++|++||.+|+.|++
T Consensus 201 EAaR~~ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~G~~~~itR~gi~~~~~S~l~~aSFE~t~~~L~~AA~~g~~D~l 280 (300)
T cd02736 201 EAARSTIINEIQYTMKSHGMSIDPRHIMLLADLMTFKGEVLGITRFGIAKMKESVLMLASFEKTTDHLFNAALHGRKDSI 280 (300)
T ss_pred HHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHHHhccCceeeeecccccccCCCHHHhcchHhHHHHHHHHhhcCCCCcC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CccccceeccccccCCcchh
Q psy3015 1377 RGVSENIIMGQLPRMGTGCF 1396 (1791)
Q Consensus 1377 kgVsenIi~Gq~~~lGTGaF 1396 (1791)
+||+|||++|+++|+|||+|
T Consensus 281 ~gvse~ii~G~~~~~GTG~f 300 (300)
T cd02736 281 EGVSECIIMGKPMPIGTGLF 300 (300)
T ss_pred CCcHHHeeeCCCcCCCCCCC
Confidence 99999999999999999987
No 27
>cd02735 RNAP_I_Rpa1_C Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain. RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Probab=100.00 E-value=6.2e-42 Score=400.80 Aligned_cols=279 Identities=25% Similarity=0.377 Sum_probs=220.4
Q ss_pred hccceeccc--cccc---cc-----------------cCCcccCCCCcCccccccccCCCCCCCCccee-eccccCCCcc
Q psy3015 1005 RFQQAQVIA--CVGQ---QN-----------------VEGKRIPFGFRKRTLPHFIKDDYGPESRGFVE-NSYLAGLTPS 1061 (1791)
Q Consensus 1005 ~~~~sqv~~--mvG~---Qs-----------------V~gKrI~~GfprRTLphf~kdd~~PESrGFV~-Nsf~~GLTPs 1061 (1791)
+|..+++.| |||. || |+++|||+|+|| |.|+ + |+.++.+||+
T Consensus 1 ky~~slv~PGE~VG~iaAQSIGEPsTQMTLnTFH~AGv~~~nVTlGvPR--L~EI-------------i~~Ask~i~TP~ 65 (309)
T cd02735 1 KYMRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPR--LREI-------------LMTASKNIKTPS 65 (309)
T ss_pred CchhccCCCCcccchhhhhccCCcccccccccccccCcccccccccccc--HHHH-------------HhhhccCCCCCe
Confidence 477889999 8887 88 889999999999 9999 6 6689999999
Q ss_pred eEEEeecCCCCccchhhhccchhH-HHHH-----HHHHHhcceEEEECCCCCCcccccCcceeeeeccCCCCCCCCcccc
Q psy3015 1062 EFFFHAMGGREGLIDTAVKTAETV-NVLV-----FLFQVTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPDFDPTRISPW 1135 (1791)
Q Consensus 1062 EfffhAMgGREGLiDTAvKTAEtG-YIqR-----RLvk~~Edv~V~YDgtvrnTVr~~d~~iVQf~Yg~dg~D~~~~~~w 1135 (1791)
+++|+. +... .+.+ .+++ +|.++++.+.|.|
T Consensus 66 m~v~l~--------~~~~--~~~a~~~~~~ie~~~l~dv~~~~~v~~--------------------------------- 102 (309)
T cd02735 66 MTLPLK--------NGKS--AERAETLKKRLSRVTLSDVVEKVEVTE--------------------------------- 102 (309)
T ss_pred EEEEec--------Cchh--HHHHHHHHhheeEeEHHHhhhhhehhH---------------------------------
Confidence 999993 2211 1222 2222 3444444443333
Q ss_pred eeeeeccccccccccCCHHHHHHHHhhccCCCcccccCCcccccceEEEEEecCccccccchhHHHHhhhhhhhHHHHhh
Q psy3015 1136 LLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEA 1215 (1791)
Q Consensus 1136 vlr~~Ld~~~m~dk~l~~~~I~~~I~~~~~~dl~~i~~d~n~~~l~~riri~~~~~~~~~~~ee~~~~~~dr~~Lr~i~~ 1215 (1791)
|..++.+.|...+ ...+.+++++..+. ...++..+..
T Consensus 103 --------------------i~~~~~~~~~~~~--------~~~~~~~i~~~~~~---------------~~~~~~~~~~ 139 (309)
T cd02735 103 --------------------ILKTIERVFKKLL--------GKWCEVTIKLPLSS---------------PKLLLLSIVE 139 (309)
T ss_pred --------------------HHHHHHHHhhhhh--------CCEEEEEEEecCCc---------------hhHHHHHHHH
Confidence 3333333332211 12233444432210 1123444445
Q ss_pred cccccceeccccccceEEEeccccCCCceEEEccCCcccccceEEEeecccchhccccc-CCCCcccccchhHHHHHHhh
Q psy3015 1216 NMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSE-RDVDPVRTFSNDICEIFQVL 1294 (1791)
Q Consensus 1216 ~il~~~~LkGi~~I~kv~i~lp~~~n~~RiI~na~~~f~~~~e~~L~teG~nL~~vl~~-~dVDp~rt~sNdI~eI~~vl 1294 (1791)
..+.++.|+|+|+|+++.+.-+.. . ...+|+|.|+|+||.+++.. +.||+.|++||||++++++|
T Consensus 140 ~~l~~~~i~gi~gI~r~~i~~~~~----------~----~~~~~~l~teG~nl~~v~~~~~~vd~~r~~sNdi~ei~~~l 205 (309)
T cd02735 140 KLARKAVIREIPGITRCFVVEEDK----------G----GKTKYLVITEGVNLAALWKFSDILDVNRIYTNDIHAMLNTY 205 (309)
T ss_pred HHhcccEEeCCCCccEEEEecCcC----------C----CceEEEEEeccccHHHHHhccCccccccceeCCHHHHHHhh
Confidence 678899999999999998762210 0 12379999999999999998 67999999999999999999
Q ss_pred hHHHHHHHHHHHHHHHhhhcCeeecccchhhhhhcccccCcccccccccccccccccccccchhhhHHHHHHHhhccCCC
Q psy3015 1295 GIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEAD 1374 (1791)
Q Consensus 1295 GIEAaR~~li~El~~V~~~~Gi~Vn~RHL~LLaD~MT~~G~l~~itR~Gi~rq~~S~L~raSFEeTv~iL~~AA~~ge~D 1374 (1791)
||||||++|++|+++||..+|++||+|||+||||+||++|++.++||+|+ +.++|||++||||+|.++|.+||.+|+.|
T Consensus 206 GIEAar~~ii~Ei~~v~~~~Gi~V~~rHl~LiaD~MT~~G~~~~~nr~gi-~~~~S~l~~asFE~t~~~L~~Aa~~g~~D 284 (309)
T cd02735 206 GIEAARRAIVKEISNVFKVYGIAVDPRHLSLIADYMTFEGGYRPFNRIGM-ESSTSPLQKMSFETTLAFLKKATLNGDID 284 (309)
T ss_pred CHHHHHHHHHHHHHHHHHhcCCeeCHHHHHHHHHHHHhCCcEeecchhhe-ccCCCHHHhhhhhhHHHHHHHHhhcCCCC
Confidence 99999999999999999999999999999999999999999999999999 77899999999999999999999999999
Q ss_pred CCCccccceeccccccCCcchhhhh
Q psy3015 1375 PMRGVSENIIMGQLPRMGTGCFDLL 1399 (1791)
Q Consensus 1375 ~lkgVsenIi~Gq~~~lGTGaFd~l 1399 (1791)
+++|+++||+||+++|+|||+||++
T Consensus 285 ~l~g~s~~ii~G~~~~~GTG~fdll 309 (309)
T cd02735 285 NLSSPSSRLVVGKPVNGGTGLFDLL 309 (309)
T ss_pred CCCChHHheeeCCccCccceeEEeC
Confidence 9999999999999999999999975
No 28
>TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit, predominant form. Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain.
Probab=100.00 E-value=2.3e-39 Score=420.64 Aligned_cols=363 Identities=26% Similarity=0.348 Sum_probs=220.5
Q ss_pred cCCHHHHHHHHHHHhhhccceeccccccccccCCcccCCCCcCccccccccCCCCCCCCcceeeccccCCCcceEEEeec
Q psy3015 989 RLSSEAFEWLVGEIENRFQQAQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAM 1068 (1791)
Q Consensus 989 rln~~a~~~i~gei~~~~~~sqv~~mvG~QsV~gKrI~~GfprRTLphf~kdd~~PESrGFV~Nsf~~GLTPsEfffhAM 1068 (1791)
.+|+..+|..+|++||..|++|+.+|+|+|+ +|.| |++|++ |.|||++||||+|||||||
T Consensus 676 ~~N~i~mMa~SGARGS~~ni~QL~GmrGlma-----~p~G---rii~~P------------I~ssF~eGLtp~EyF~st~ 735 (1140)
T TIGR02386 676 KFNPIFMMADSGARGNISQFRQLAGMRGLMA-----KPSG---DIIELP------------IKSSFREGLTVLEYFISTH 735 (1140)
T ss_pred CCCcHhhhhhcccccCHHHHHHHHhCCCccc-----CCCC---Cccccc------------hhhccccCCCHHHHhhhcc
Confidence 4799999999999999999999999999987 3555 677763 8999999999999999999
Q ss_pred CCCCccchhhhccchhHHHHHHHHHHhcceEEEECCCCCCcccccCcceeeeeccCCCCCCCCcc-cceeeee----ccc
Q psy3015 1069 GGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPDFDPTRIS-PWLLRIE----LDR 1143 (1791)
Q Consensus 1069 gGREGLiDTAvKTAEtGYIqRRLvk~~Edv~V~YDgtvrnTVr~~d~~iVQf~Yg~dg~D~~~~~-~wvlr~~----Ld~ 1143 (1791)
||||||+|||+|||++||+||||||++||+.|.||... ...|-.|+...+.++.-..... .-+.|+. +|.
T Consensus 736 GaRkGLiDTAlKTAdSGYLtRRLVdv~qDviV~~dDCg-----T~~gi~v~~~~~~~~~~i~~l~~ri~GR~~~~di~~~ 810 (1140)
T TIGR02386 736 GARKGLADTALKTADSGYLTRRLVDVAQDVVVREEDCG-----TEEGIEVEAIVEGKDEIIESLKDRIVGRYSAEDVYDP 810 (1140)
T ss_pred chhccccchheeecccceeeeehhhhhcceEEEeCCCC-----CCCCEEEEEeecCCceEEeehhheeEEEEEhhheEeC
Confidence 99999999999999999999999999999999999532 2234444444322210000000 1111211 111
Q ss_pred ---cccccc--cCCHHHHHHHHhhcc------CCCcccc---------cCCcccccceEEEEEecCccccccchhHHHHh
Q psy3015 1144 ---KRMTDK--KLTMEAISEKINAGF------GDDLNCI---------FNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDK 1203 (1791)
Q Consensus 1144 ---~~m~dk--~l~~~~I~~~I~~~~------~~dl~~i---------~~d~n~~~l~~riri~~~~~~~~~~~ee~~~~ 1203 (1791)
+.+..+ .++ +.++++|.+.- +.-+.|. |..+.+..-.+.+--.-. ....+...|--.+
T Consensus 811 ~~~~~i~~~~~~i~-~~~~~~i~~~~i~~v~iRS~ltC~s~~gvC~~CYG~~La~~~~V~~GeaVG-iiAAQSIGEPGTQ 888 (1140)
T TIGR02386 811 DTGKLIAEANTLIT-EEIAEKIENSGIEKVKVRSVLTCESEHGVCQKCYGRDLATGKLVEIGEAVG-VIAAQSIGEPGTQ 888 (1140)
T ss_pred CCCcEEEeCCCCcC-HHHHHHHHHcCCCEEEecCCeeeCCCCCCccccCCCcccCCcEecccccce-eEeeeecCCCcch
Confidence 001111 122 22333332210 0001110 111111100000000000 0000111111112
Q ss_pred hhhhhhHHHHhhcccc---cceeccccccceEE-----------------Eec-c-ccCCCceEEEccC-CcccccceEE
Q psy3015 1204 MEDDMFLRCIEANMLS---DMTLQGIEAIGKVY-----------------MHL-P-QTDSKKRIIITES-GEFKAIADWL 1260 (1791)
Q Consensus 1204 ~~dr~~Lr~i~~~il~---~~~LkGi~~I~kv~-----------------i~l-p-~~~n~~RiI~na~-~~f~~~~e~~ 1260 (1791)
+.-|+|=- ..... ++ -+|+|++.+.+ +.+ . ...+..+++...+ ++. .+|.
T Consensus 889 LTmRTFHt---GGv~~~~~DI-T~GlpRv~elfear~p~~~a~iae~~G~v~~~~~~~~~~~~i~i~~~~~~~---~~y~ 961 (1140)
T TIGR02386 889 LTMRTFHT---GGVAGASGDI-TQGLPRVKELFEARTPKDKAVIAEVDGTVEIIEDIVKNKRVVVIKDENDEE---KKYT 961 (1140)
T ss_pred hehhheee---cccccccccc-ccCchhhhhhhhcccCCCceEEEecCCEEEEeecccCCcEEEEEECCCCce---eEEe
Confidence 22222100 00000 00 12333333210 000 0 0012223333322 110 1222
Q ss_pred Ee-------ecc--cchhcccccCCCCcccccchhHHHHHHhhhHHHHHHHHHHHHHHHhhhcCeeecccchhhhhhccc
Q psy3015 1261 LE-------TDG--TSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMT 1331 (1791)
Q Consensus 1261 L~-------teG--~nL~~vl~~~dVDp~rt~sNdI~eI~~vlGIEAaR~~li~El~~V~~~~Gi~Vn~RHL~LLaD~MT 1331 (1791)
+. -+| +.-++.+....+ |++|+++++||||++++|++|++.||..||++||+||+++|+++||
T Consensus 962 ip~~~~l~v~~gd~V~~G~~l~~g~~--------~~~~il~v~G~~a~~~~lv~evq~vY~~QGv~I~dKHievIvrqM~ 1033 (1140)
T TIGR02386 962 IPFGAQLRVKDGDSVSAGDKLTEGSI--------DPHDLLRIKGIQAVQEYLVKEVQKVYRLQGVEINDKHIEVIVRQML 1033 (1140)
T ss_pred ccCCceEEecCCCEEccCCcccCCCC--------CHHHHHHhcCHHHHHHHHHHHHHHHHHhCCccccchhHhHHHHHHh
Confidence 21 111 111223333333 5679999999999999999999999999999999999999999999
Q ss_pred ccCc----------------------------------------ccccccccccccccccccccchhhhHHHHHHHhhcc
Q psy3015 1332 AKGH----------------------------------------LMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHA 1371 (1791)
Q Consensus 1332 ~~G~----------------------------------------l~~itR~Gi~rq~~S~L~raSFEeTv~iL~~AA~~g 1371 (1791)
.+++ ++||||++++ ..|+|++|||++|.++|.+||++|
T Consensus 1034 ~kv~i~~~gdt~~l~g~~v~~~~~~~~n~~~~~~g~~~~~~~~~llGitkasl~--t~SflsaASFqeTtkvLt~Aai~g 1111 (1140)
T TIGR02386 1034 RKVRITDSGDSNLLPGELIDIHEFNEENRKLLEQGKKPASAIPQLLGITKASLN--TESFLSAASFQETTKVLTDAAIKG 1111 (1140)
T ss_pred CcEEEEeCCCcCCCCCCeeeHHHHHHHHHHHHhCCCCCccceeeeeeeeehhcc--CCCcccccchhhHHHHHHHHHhcC
Confidence 9943 4567777774 568999999999999999999999
Q ss_pred CCCCCCccccceeccccccCCcch
Q psy3015 1372 EADPMRGVSENIIMGQLPRMGTGC 1395 (1791)
Q Consensus 1372 e~D~lkgVsenIi~Gq~~~lGTGa 1395 (1791)
+.|+|+|+.||+++|+++|.|||.
T Consensus 1112 k~D~L~GlkENVIiG~liPaGTG~ 1135 (1140)
T TIGR02386 1112 KVDYLLGLKENVIIGNLIPAGTGL 1135 (1140)
T ss_pred CCCCCCCcccceEecCcccCCCCc
Confidence 999999999999999999999995
No 29
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=100.00 E-value=5.2e-40 Score=427.05 Aligned_cols=345 Identities=26% Similarity=0.378 Sum_probs=217.1
Q ss_pred cCCHHHHHHHHHHHhhhccceeccccccccc-cCCcccCCCCcCccccccccCCCCCCCCcceeeccccCCCcceEEEee
Q psy3015 989 RLSSEAFEWLVGEIENRFQQAQVIACVGQQN-VEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHA 1067 (1791)
Q Consensus 989 rln~~a~~~i~gei~~~~~~sqv~~mvG~Qs-V~gKrI~~GfprRTLphf~kdd~~PESrGFV~Nsf~~GLTPsEfffhA 1067 (1791)
++|+..+|..+|++||..|++|+.+|+|+|+ ++|+.|+ . ||.|||++||||+||||||
T Consensus 685 ~~N~i~mMa~SGARGS~~ni~QL~GmrGlma~p~G~iie-------~--------------pI~ssFreGLt~~EyFfst 743 (1156)
T PRK00566 685 SFNPIYMMADSGARGSASQIRQLAGMRGLMAKPSGEIIE-------T--------------PIKSNFREGLTVLEYFIST 743 (1156)
T ss_pred CCCChheeeeccCCcCHHHHHHHHhhcCccccCCCCEee-------h--------------hhhhhhhcCCCHHHHhhcC
Confidence 3899999999999999999999999999985 6777665 1 5789999999999999999
Q ss_pred cCCCCccchhhhccchhHHHHHHHHHHhcceEEEECCCCCC---cc--cccCcceeeeec----c----CCCCCCCCccc
Q psy3015 1068 MGGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYDPDPQN---TV--IPEDQEFVNVYY----E----MPDFDPTRISP 1134 (1791)
Q Consensus 1068 MgGREGLiDTAvKTAEtGYIqRRLvk~~Edv~V~YDgtvrn---TV--r~~d~~iVQf~Y----g----~dg~D~~~~~~ 1134 (1791)
|||||||+|||+|||++||+||||||++||+.|.||..-.. ++ ..++++++.-++ | +|=.|+..-
T Consensus 744 ~GaRkGLiDTALKTAdSGYLtRRLVdvaqDviV~~~DCgT~~gi~~~~~~~~~~~i~~l~~~~~GR~~~~di~~~~t~-- 821 (1156)
T PRK00566 744 HGARKGLADTALKTADSGYLTRRLVDVAQDVIVREDDCGTDRGIEVTAIIEGGEVIEPLEERILGRVLAEDVVDPETG-- 821 (1156)
T ss_pred cchhhcccchheeeccceeeehhHHHhhCceEEEECCCCCcCCEEEEEeccCCEEEeEhhheeEeEEEhhheecCCCC--
Confidence 99999999999999999999999999999999999852211 01 112233333211 1 111111100
Q ss_pred ceeeeeccccccccccCCHHHHHHHHh-----------------------hccCCCcccccCCcccccceEEEEEecCcc
Q psy3015 1135 WLLRIELDRKRMTDKKLTMEAISEKIN-----------------------AGFGDDLNCIFNDDNAEKLVLRIRIMNSDD 1191 (1791)
Q Consensus 1135 wvlr~~Ld~~~m~dk~l~~~~I~~~I~-----------------------~~~~~dl~~i~~d~n~~~l~~riri~~~~~ 1191 (1791)
.+.+.+.. .++ +.++++|. ..|+.|+.. .-.+.+--.-. .
T Consensus 822 ---~~i~~~~~----~i~-~~~~~~i~~~~i~~v~iRS~ltC~s~~gvC~~CYG~~La~--------~~~v~iGeaVG-i 884 (1156)
T PRK00566 822 ---EVIVPAGT----LID-EEIADKIEEAGIEEVKIRSVLTCETRHGVCAKCYGRDLAT--------GKLVNIGEAVG-V 884 (1156)
T ss_pred ---cEEEcCCC----ccC-HHHHHHHHHcCCCEEEEcCCeeecCCCcccHhhhCccccC--------CCCcccCccee-E
Confidence 00011111 111 12222222 112222210 00000000000 0
Q ss_pred ccccchhHHHHhhhhhhhHHHHhhccccccee------ccccccceEEE-ecc-----------------ccCCCceEEE
Q psy3015 1192 SKMQDEEDAVDKMEDDMFLRCIEANMLSDMTL------QGIEAIGKVYM-HLP-----------------QTDSKKRIII 1247 (1791)
Q Consensus 1192 ~~~~~~ee~~~~~~dr~~Lr~i~~~il~~~~L------kGi~~I~kv~i-~lp-----------------~~~n~~RiI~ 1247 (1791)
...+...|--.++.-| ..|. +|+|++.+.+= +-| ..++..+++.
T Consensus 885 IAAQSIGEPGTQLTmR------------TFHtGGvdIT~Glprv~elfear~pk~~a~ise~~G~v~~~~~~~~~~~i~i 952 (1156)
T PRK00566 885 IAAQSIGEPGTQLTMR------------TFHTGGVDITGGLPRVAELFEARKPKGPAIIAEIDGTVSFGKETKGKRRIVI 952 (1156)
T ss_pred EeeeecCCCccceeee------------eeeecceeccCCccchhhheeeccCCCceEEEecCCEEEeccccCCceEEEE
Confidence 0000011111111111 1122 23333332110 000 0112223332
Q ss_pred ccCCcccccceEEEe-------ecc--cchhcccccCCCCcccccchhHHHHHHhhhHHHHHHHHHHHHHHHhhhcCeee
Q psy3015 1248 TESGEFKAIADWLLE-------TDG--TSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYV 1318 (1791)
Q Consensus 1248 na~~~f~~~~e~~L~-------teG--~nL~~vl~~~dVDp~rt~sNdI~eI~~vlGIEAaR~~li~El~~V~~~~Gi~V 1318 (1791)
..... ...+|.+. .+| +.-++.+....+ +++|+++++|+||++++|++|++.||..||++|
T Consensus 953 ~~~~~--~~~~y~vp~~~~~~v~~gd~v~~G~~l~~g~~--------~~~~il~v~G~~~~~~~lv~eiq~vY~~QGv~I 1022 (1156)
T PRK00566 953 TPDDG--EEREYLIPKGKHLLVQEGDHVEAGDKLTDGSI--------DPHDILRVLGVEAVQNYLVNEVQKVYRLQGVKI 1022 (1156)
T ss_pred eCCCC--ceEEEEccCCCeeeecCCCEEccCCcccCCCC--------CHHHHHHhcCHHHHHHHHHHHHHHHHHhCCccc
Confidence 22110 01122221 111 111222322333 567899999999999999999999999999999
Q ss_pred cccchhhhhhccccc----------------------------------------Ccccccccccccccccccccccchh
Q psy3015 1319 NYRHLALLCDVMTAK----------------------------------------GHLMAITRHGINRQDTGALMRCSFE 1358 (1791)
Q Consensus 1319 n~RHL~LLaD~MT~~----------------------------------------G~l~~itR~Gi~rq~~S~L~raSFE 1358 (1791)
|+||+++|+++||.+ ..++||||++++ ..|+|++|||+
T Consensus 1023 ~dKHievIvrqM~~kv~i~~~gdt~~~~g~~v~~~~~~~~n~~~~~~g~~~~~~~~~llGItka~l~--t~SflsaASFQ 1100 (1156)
T PRK00566 1023 NDKHIEVIVRQMLRKVRITDPGDTDFLPGELVDRSEFEEENRKLIAEGKEPATGRPVLLGITKASLA--TESFLSAASFQ 1100 (1156)
T ss_pred ccceeehHHHHHhCCeEEecCCCcCCCCCceeeHHHHHHHHHHHHHCCCCCCcccceeeeeeecccc--cCccccccccc
Confidence 999999999999986 236889999986 46999999999
Q ss_pred hhHHHHHHHhhccCCCCCCccccceeccccccCCcchhh
Q psy3015 1359 ETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFD 1397 (1791)
Q Consensus 1359 eTv~iL~~AA~~ge~D~lkgVsenIi~Gq~~~lGTGaFd 1397 (1791)
+|.++|.+||++|+.|+|+|+.||||+|+++|+|||...
T Consensus 1101 eTtkvLt~AAi~gk~D~L~GlkENVIiG~liPaGTG~~~ 1139 (1156)
T PRK00566 1101 ETTRVLTEAAIKGKVDPLRGLKENVIIGRLIPAGTGLAR 1139 (1156)
T ss_pred chHHHHHHHHhcCCCCcCCCcccceEecCcccCCCCcch
Confidence 999999999999999999999999999999999999764
No 30
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=100.00 E-value=2.9e-39 Score=421.48 Aligned_cols=294 Identities=32% Similarity=0.489 Sum_probs=242.5
Q ss_pred cCCcccCCCCcCccccccccCCCCCCCCcceeeccccCCCcceEEEeecCCCCccchhhhccchhH-HHHH-----HHHH
Q psy3015 1020 VEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETV-NVLV-----FLFQ 1093 (1791)
Q Consensus 1020 V~gKrI~~GfprRTLphf~kdd~~PESrGFV~Nsf~~GLTPsEfffhAMgGREGLiDTAvKTAEtG-YIqR-----RLvk 1093 (1791)
|+++|||+|+|| |.|+ +|+.++.+||++++|+ .+..-++.+.+ .+++ +|.+
T Consensus 553 v~~~nVTlGvPR--L~EI-------------inask~i~TP~m~i~l--------~~~~~~~~~~a~~v~~~ie~~~L~d 609 (858)
T PRK14898 553 VAEINVTLGLPR--MIEI-------------VDARKEPSTPIMTVHL--------KGEYATDREKAEEVAKKIESLTLGD 609 (858)
T ss_pred ccccccccCCch--HHHH-------------hcccCCCCCceEEEEE--------CCCccchHHHHHHHHhheeeEEHHH
Confidence 889999999999 9999 8999999999999999 33333333444 3333 5666
Q ss_pred HhcceEEEECCCCCCcccccCcceeeeeccCCCCCCCCcccceeeeeccccccccccCCHHHHHHHHhhccCCCcccccC
Q psy3015 1094 VTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPDFDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFN 1173 (1791)
Q Consensus 1094 ~~Edv~V~YDgtvrnTVr~~d~~iVQf~Yg~dg~D~~~~~~wvlr~~Ld~~~m~dk~l~~~~I~~~I~~~~~~dl~~i~~ 1173 (1791)
+++++.+.+. .-.+++.||.+.+.++++++++|..+|...++..+.+
T Consensus 610 v~~~~~~~~~------------------------------~~~~~i~l~~~~~~~~~l~~~~i~~~i~~~~~~~~~~--- 656 (858)
T PRK14898 610 VATSIAIDLW------------------------------TQSIKVELDEETLADRGLTIESVEEAIEKKLGVKIDR--- 656 (858)
T ss_pred HHHHhhhhcc------------------------------ccEEEEEECHHHHHHcCCCHHHHHHHHHHhccccccC---
Confidence 6665542110 0025777899999999999999999998877644322
Q ss_pred CcccccceEEEEEecCccccccchhHHHHhhhhhhhHHHHhhcccccceeccccccceEEEeccccCCCceEEEccCCcc
Q psy3015 1174 DDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEF 1253 (1791)
Q Consensus 1174 d~n~~~l~~riri~~~~~~~~~~~ee~~~~~~dr~~Lr~i~~~il~~~~LkGi~~I~kv~i~lp~~~n~~RiI~na~~~f 1253 (1791)
++.+++++..... ...+++... .+.++.|+|+|+|+++.+.... .
T Consensus 657 ----~~~~~~~~~~~~~---------------~~~~~~~~~--~l~~~~i~gi~gI~~~~i~~~~----~---------- 701 (858)
T PRK14898 657 ----KGTVLYLKPKTPS---------------YKALRKRIP--KIKNIVLKGIPGIERVLVKKEE----H---------- 701 (858)
T ss_pred ----CCCEEEEEecCch---------------HHHHHHHHH--HhcCcEEECCCCccEEEEecCC----C----------
Confidence 3455666543211 112333332 4778999999999999876221 0
Q ss_pred cccceEEEeecccchhcccccCCCCcccccchhHHHHHHhhhHHHHHHHHHHHHHHHhhhcCeeecccchhhhhhccccc
Q psy3015 1254 KAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAK 1333 (1791)
Q Consensus 1254 ~~~~e~~L~teG~nL~~vl~~~dVDp~rt~sNdI~eI~~vlGIEAaR~~li~El~~V~~~~Gi~Vn~RHL~LLaD~MT~~ 1333 (1791)
....+|+|.|+|+||.+++..++||+.+++||||++|+++|||||||++|++|++.||..+|++||+|||+||||+||++
T Consensus 702 ~~~~~~~l~teG~nl~~~~~~~~vd~~~~~sN~i~~i~~~lGIEAar~~ii~Ei~~v~~~~gi~V~~rHl~liad~MT~~ 781 (858)
T PRK14898 702 ENDEEYVLYTQGSNLREVFKIEGVDTSRTTTNNIIEIQEVLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIMTAD 781 (858)
T ss_pred CCCceEEEEecCcCHHHHhcCCCCcccccccCCHHHHHHhhCHHHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHHHccC
Confidence 01248999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcccccccccccccccccccccchhhhHHHHHHHhhccCCCCCCccccceeccccccCCcchhhhhccccc
Q psy3015 1334 GHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEK 1404 (1791)
Q Consensus 1334 G~l~~itR~Gi~rq~~S~L~raSFEeTv~iL~~AA~~ge~D~lkgVsenIi~Gq~~~lGTGaFd~lLge~~ 1404 (1791)
|.+.++||+|+++.++|||++||||+|+++|++||.+|+.|+|+||++||++|+++|+|||+||+++++..
T Consensus 782 G~~~~~~r~gi~~~~~s~l~~asFe~t~~~l~~Aa~~g~~D~l~g~s~~ii~G~~~~~GTG~~~l~~~~~~ 852 (858)
T PRK14898 782 GEVKPIGRHGVAGEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTGCVDLRIDREY 852 (858)
T ss_pred CcEEEeccCCccCCCCCHHHhcChHhHHHHHHHHhhcCCCCcCCCchHHeeeCCccCCcCceEEEEecCcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999998754
No 31
>PF04998 RNA_pol_Rpb1_5: RNA polymerase Rpb1, domain 5; InterPro: IPR007081 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, domain 5, represents the discontinuous cleft domain that is required to form the central cleft or channel where the DNA is bound [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1ZYR_D 1SMY_D 2A68_N 2O5J_D 3AOH_N 2O5I_D 2CW0_N 2A6H_N 2A69_D 3EQL_D ....
Probab=100.00 E-value=1.8e-40 Score=384.57 Aligned_cols=66 Identities=70% Similarity=1.194 Sum_probs=64.6
Q ss_pred CCChhhhhhhcccCcccchhcccccCCcchhHHHHHHhhcceEEeecCcEEecCCceEEEEecCCC
Q psy3015 391 GLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVHYDCTVRNSVGQLIQLRYGEDG 456 (1791)
Q Consensus 391 GL~P~EfFFHaMaGREGLIDTAVKTaeTGYlQRrLvK~LEDl~V~YDgTVRns~G~IVQF~YGeDG 456 (1791)
||+|+|||||||||||||||||||||+||||||||||+|||+.|+||+||||+.+.|+||.||+||
T Consensus 1 Gl~~~e~f~~~~~~R~gl~dta~kTa~sGyl~R~lv~~~~~~~v~~~~~~~~~~~~i~~~~~~~~~ 66 (277)
T PF04998_consen 1 GLTPTEYFFHCMGGREGLIDTAVKTADSGYLQRRLVKVLEDLIVRYDDCVRNSGGSIIQFIYGEDG 66 (277)
T ss_dssp C-THHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHTTHEEETTSEEESTTSEEEESSCTTTS
T ss_pred CcCHHHHHHHHhcccccccccceeeeccccchhhhhhccceEEEEEcCccccccceeeeccccccc
Confidence 899999999999999999999999999999999999999999999999999999999999999999
No 32
>TIGR02389 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit A''. This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Probab=100.00 E-value=1.5e-38 Score=377.64 Aligned_cols=221 Identities=14% Similarity=0.188 Sum_probs=179.8
Q ss_pred cCCcc-hhhhhcccccccccccccCCCCcchhh-hhhccCCCCCCCCCCCCCCCcceeeeeeeccccceecccchhHHHh
Q psy3015 1390 RMGTG-CFDLLLDAEKCKDGIEIPLATGMMGGP-AGMFFGSAATPSSIPGPPAWYPIHIAISLLSRFTTVICIYTLKTFL 1467 (1791)
Q Consensus 1390 ~lGTG-aFd~lLge~~~~~~~~~~v~pGEmVG~-aAQSIGEPa~~~~~TQmT~lnTFH~aGVs~~~~t~~lGvprlkei~ 1467 (1791)
++... +|+|++++.+.+|.+++ ++||||||+ ||||||||| |||| |||||||||+++||| |||||||||+
T Consensus 18 ~~~~~~~~~~~l~~i~~ky~~al-v~PGeaVG~IAAQSIGEP~-----TQMT-LnTFH~AGVas~nVT--lGVPRlkEII 88 (367)
T TIGR02389 18 EISDKEELDEIIKRVEEEYLRSL-IDPGEAVGIVAAQSIGEPG-----TQMT-MRTFHYAGVAELNVT--LGLPRLIEIV 88 (367)
T ss_pred CCCHHHHHHHHHHHHHHHHHHhc-CCCccccchhhhhhcCCcc-----cccc-ccccccccccccCcc--ccchhHHHHh
Confidence 45556 89999999999999999 999999999 799999999 9999 999999999999998 9999999999
Q ss_pred hccCCCCCCCCCccceeEEEEeeccccCCccccCCCCCchhhHhhHhHHHHHhhccccccchhhhcceeEEEEcCCCCCC
Q psy3015 1468 EMKDFKKPPQKGFGLLTLTLMVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVTANTAIYYDPDPQNT 1547 (1791)
Q Consensus 1468 nv~~~~k~~~~~~~~~~~t~~~~~I~~~pk~~~~P~~~~~~~~~vq~~~~~~~~~~~~~~~l~~vt~~t~i~ydpd~~~t 1547 (1791)
|++|+++||+ +|+||.+ ... .+.+.|..++..++ +|+|++|+...+++|
T Consensus 89 Na~k~i~TP~-------~ti~L~~------~~~---~~~~~a~~v~~~iE--------~t~l~dv~~~~~~~~------- 137 (367)
T TIGR02389 89 DARKTPSTPS-------MTIYLED------EYE---KDREKAEEVAKKIE--------ATKLEDVAKDISIDL------- 137 (367)
T ss_pred hcccCCCCCe-------EEEEecC------cch---hhHHHHHHHHHHhh--------heeHHHHHhhhheec-------
Confidence 9999999997 9999983 122 24567777777777 899999999888664
Q ss_pred cccccHHHHHHhhcCCCCCCCCCCcceEEEEeccccccccccCHHHHHhhhhcCCCCCCCCCCCCchhhhHHHHHHHHHh
Q psy3015 1548 VIPEDQEFVNVYYEMPDFDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNTPLSPTDKKLTMEAISEKIN 1627 (1791)
Q Consensus 1548 vi~eD~~~v~~~~~~pd~~~~~~spwllr~~ldr~~m~dk~l~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~i~ 1627 (1791)
++|.|||+||+++|.+++++|++|.. +|.
T Consensus 138 -----------------------~~~~l~i~ld~~~l~~~~i~~~~i~~----------------------------~i~ 166 (367)
T TIGR02389 138 -----------------------ADMTVIIELDEEQLKERGITVDDVEK----------------------------AIK 166 (367)
T ss_pred -----------------------cCcEEEEEECHHHHHhcCCCHHHHHH----------------------------HHH
Confidence 25899999999999999999999987 556
Q ss_pred cccCCCceeeecCCcccceEEEEEEecCCCCccchhhhhhhccccceeeccccccceeEeecccCCccccccEEEEEecc
Q psy3015 1628 AGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEETDRSFVKVDFVEPKDLVEWKTLLKQM 1707 (1791)
Q Consensus 1628 ~~f~~~l~~i~~ddna~~lv~r~r~~~~~~~~~~~~~~~~~~~~~~~~lr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1707 (1791)
+.++.++.++ +++++++|||+.++.. ..-..+.+.--++.++|+++|+|+++.. +..+|.++|
T Consensus 167 ~~~~~~~~~~----~~~~~~i~i~~~~~~~----~~l~~l~~~l~~~~v~Gi~gI~r~~i~~------~~~~~~l~t--- 229 (367)
T TIGR02389 167 KAKLGKVIEI----DMDGNTITIKPPKPSL----KELRKLKEKIKNLHIKGIKGIKRVVIRK------EGDEYVIYT--- 229 (367)
T ss_pred Hhccccccee----ecCCCEEEEEecCchH----HHHHHHHHHhhhceEeCCCCceEEEEEC------CCCeEEEEE---
Confidence 6676766665 3467899999754110 0011122222468899999999999984 345899999
Q ss_pred cccccHHHHHhh
Q psy3015 1708 HSDFCLAQIIKC 1719 (1791)
Q Consensus 1708 ~~~~~~~~~~~~ 1719 (1791)
||.+|.++++.
T Consensus 230 -eG~nl~~v~~~ 240 (367)
T TIGR02389 230 -EGSNLKEVLKL 240 (367)
T ss_pred -eccCHHHHHcC
Confidence 99999999973
No 33
>PF04990 RNA_pol_Rpb1_7: RNA polymerase Rpb1, domain 7; InterPro: IPR007073 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, domain 7, represents a mobile module of the RNA polymerase. Domain 7 interacts with the lobe domain of Rpb2 (IPR007642 from INTERPRO) [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_M 1Y77_A 3CQZ_A 3GTM_A 1TWA_A 4A3I_A 2NVY_A 2NVT_A 1I6H_A 1TWF_A ....
Probab=100.00 E-value=6.9e-39 Score=333.16 Aligned_cols=124 Identities=65% Similarity=1.071 Sum_probs=99.5
Q ss_pred cchhhhcceeEEEEcCCCCCCcccccHHHHHHhhcCCC--CCCCCCCcceEEEEeccccccccccCHHHHHhhhhcCCCC
Q psy3015 1527 VFLDKVTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPD--FDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGD 1604 (1791)
Q Consensus 1527 ~~l~~vt~~t~i~ydpd~~~tvi~eD~~~v~~~~~~pd--~~~~~~spwllr~~ldr~~m~dk~l~~~~i~~~i~~~~~~ 1604 (1791)
|||++||++|||||||||+||||+||+|||++||++|| .+++++|||||||+|||++|+||+|+|++|++
T Consensus 1 TtL~~vt~~teIyYDPdp~~Tvi~eD~e~V~~y~e~pd~~~~~~~~spWlLRieLdr~~m~dk~l~m~~I~~-------- 72 (135)
T PF04990_consen 1 TTLRDVTASTEIYYDPDPRNTVIEEDREFVESYFEIPDEDDDPSRLSPWLLRIELDRKKMIDKKLTMEDIAE-------- 72 (135)
T ss_dssp ECCHCHECEEEEEE-SSTTSSSSSTTHCHHHHCCCTT-SSTT-SSBESEEEEEEE-CCCCCCTT--HHHHCC--------
T ss_pred CcHHHhhhheeEEECCCCCCCcchhhHHHHHHHHhCCCcccCcccCCCeEEEEEEcHHHHHhcCCCHHHHHH--------
Confidence 79999999999999999999999999999999999999 58999999999999999999999999999997
Q ss_pred CCCCCCCCchhhhHHHHHHHHHhcccCCCceeeecCCcccceEEEEEEecCCCCccchhhhhhhccccceeeccccc
Q psy3015 1605 DLNTPLSPTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEE 1681 (1791)
Q Consensus 1605 ~~~~~~~~~~~~~~~~~~~~~i~~~f~~~l~~i~~ddna~~lv~r~r~~~~~~~~~~~~~~~~~~~~~~~~lr~~~~ 1681 (1791)
||++.||+|++||||||||++||||||++++++.+.+++++. .|||.|||++|.
T Consensus 73 --------------------~I~~~f~~~l~vi~sddNa~~lViRIRi~~~~~~~~~~~d~~---~~dd~~Lr~~e~ 126 (135)
T PF04990_consen 73 --------------------KIKEEFGNDLHVIYSDDNAEKLVIRIRIIKDEDKKEEDEDEQ---EEDDVFLRRLES 126 (135)
T ss_dssp --------------------CHHHCCTTSEEEEE--TTSSSEEEEEEEB--S---SSSSS-----S-CHHHHHHHHH
T ss_pred --------------------HHHHhcCCCeEEEecCCCCcccEEEEEEecCcccccccccch---hhHHHHHHHHHH
Confidence 889999999999999999999999999999875443222221 257788888875
No 34
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=100.00 E-value=6e-38 Score=406.65 Aligned_cols=354 Identities=20% Similarity=0.279 Sum_probs=217.1
Q ss_pred ccCCHHHHHHHHHHHhhhccceeccccccccc-cCCcccCCCCcCccccccccCCCCCCCCcceeeccccCCCcceEEEe
Q psy3015 988 YRLSSEAFEWLVGEIENRFQQAQVIACVGQQN-VEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFH 1066 (1791)
Q Consensus 988 ~rln~~a~~~i~gei~~~~~~sqv~~mvG~Qs-V~gKrI~~GfprRTLphf~kdd~~PESrGFV~Nsf~~GLTPsEfffh 1066 (1791)
.++|+..+|..+|++||..|++|+.+|+|||+ ++|++|+ + +|.|||++||||.|||||
T Consensus 783 ~~~N~i~mMa~SGARGS~~QI~QLaGmRGlma~p~G~iIe-------~--------------PI~SnFrEGLt~~EyFiS 841 (1460)
T PRK14906 783 DEDNPIYMMADSGARGNIKQIRQLAGMRGLMADMKGEIID-------L--------------PIKANFREGLSVLEYFIS 841 (1460)
T ss_pred ccCCCeEeeeeccCcccHHHHHHHHhcccceecCCCCccc-------c--------------ccccccccCCCHHHHHHH
Confidence 46999999999999999999999999999964 7888775 3 367999999999999999
Q ss_pred ecCCCCccchhhhccchhHHHHHHHHHHhcceEEEECCCCCCcccccCcceeeeeccCCCCCCCCcccceeeeec----c
Q psy3015 1067 AMGGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPDFDPTRISPWLLRIEL----D 1142 (1791)
Q Consensus 1067 AMgGREGLiDTAvKTAEtGYIqRRLvk~~Edv~V~YDgtvrnTVr~~d~~iVQf~Yg~dg~D~~~~~~wvlr~~L----d 1142 (1791)
||||||||+|||+|||++||+||||||++||+.|..+. +. | ..|-.+........+. +..+.|... |
T Consensus 842 t~GaRKGL~DTALKTAdSGYLTRRLVdVaQDViV~e~D-Cg-T---~~Gi~v~~~~~~~~l~----~ri~GR~~~~di~~ 912 (1460)
T PRK14906 842 THGARKGLVDTALRTADSGYLTRRLVDVAQDVIVREED-CG-T---DEGVTYPLVKPKGDVD----TNLIGRCLLEDVCD 912 (1460)
T ss_pred cccccchhhhhhhhccccchHHHHHHHhhhheEEEecc-CC-C---CCCEEEEEeecccchh----heeeeEEEHhhhcC
Confidence 99999999999999999999999999999999888763 21 1 1232222211000000 000011100 0
Q ss_pred c--ccccccc--CCHHHHHHHHhh-----------------------ccCCCcccccCCcccccceEEEEEecCcccccc
Q psy3015 1143 R--KRMTDKK--LTMEAISEKINA-----------------------GFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQ 1195 (1791)
Q Consensus 1143 ~--~~m~dk~--l~~~~I~~~I~~-----------------------~~~~dl~~i~~d~n~~~l~~riri~~~~~~~~~ 1195 (1791)
. +.+..++ ++-...+++|.+ .|+.|+. ..-.+.+--.-. ....+
T Consensus 913 ~~g~~i~~~~~~I~~~~~~~~i~~~gi~~v~iRS~ltC~s~~gvC~kCYG~dLa--------tg~~V~iGeaVG-iIAAQ 983 (1460)
T PRK14906 913 PNGEVLLSAGDYIESMDDLKRLVEAGVTKVQIRTLMTCHAEYGVCQKCYGWDLA--------TRRPVNIGTAVG-IIAAQ 983 (1460)
T ss_pred CCCCEEEeCCCeeCcHHHHHHHHHCCCCEEEEeCCeeECCCCCChhhCcCCccc--------CCcEecccccee-eeeee
Confidence 0 0111111 111111232221 2222221 110000000000 00000
Q ss_pred chhHHHHhhhhhhhHHHHhhcccccceeccccccceEE-----------------EeccccCCCceEEEccC-Ccccccc
Q psy3015 1196 DEEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVY-----------------MHLPQTDSKKRIIITES-GEFKAIA 1257 (1791)
Q Consensus 1196 ~~ee~~~~~~dr~~Lr~i~~~il~~~~LkGi~~I~kv~-----------------i~lp~~~n~~RiI~na~-~~f~~~~ 1257 (1791)
...|--.++.-|+|=- ......=..+|+|++.+.+ +......+..+++.... +.. .
T Consensus 984 SIGEPGTQLTMRTFHt---GGv~~~dit~GLpRv~eLfEar~pk~~a~i~e~~G~v~i~~~~~~~~i~i~~~~~~~---~ 1057 (1460)
T PRK14906 984 SIGEPGTQLTMRTFHS---GGVAGDDITQGLPRVAELFEARKPKGEAVLAEISGTLQITGDKTEKTLTIHDQDGNS---R 1057 (1460)
T ss_pred ecCCCcceeeeeeeec---ccccccccccCcchhhhheeeccCCCceeeeccCCEEEeccCCCceEEEEECCCCce---e
Confidence 0111111111121100 0000000012233222111 00001112333443332 210 1
Q ss_pred eEEE-----------eecccchhcccccCCCCcccccchhHHHHHHhhhHHHHHHHHHHHHHHHhhhcCeeecccchhhh
Q psy3015 1258 DWLL-----------ETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALL 1326 (1791)
Q Consensus 1258 e~~L-----------~teG~nL~~vl~~~dVDp~rt~sNdI~eI~~vlGIEAaR~~li~El~~V~~~~Gi~Vn~RHL~LL 1326 (1791)
+|.+ +.+-+.-++.+....+| .++++++.|++++..+|++|++.||..||+.||++|+++|
T Consensus 1058 ~y~v~~~~~~~~~v~~gd~v~~G~~l~~G~~~--------p~~il~~~g~~~~~~ylv~eVQ~VYr~QGV~InDKHiEvI 1129 (1460)
T PRK14906 1058 EYVVSARVQFMPGVEDGVEVRVGQQITRGSVN--------PHDLLRLTDPNTTLRYIVSQVQDVYVSQGVDINDKHIEVI 1129 (1460)
T ss_pred EEEccCCcccccccCCCCEEccCCCccCCCCC--------HHHHHHhcCHHHHHHHHHHHHHHHHHhcCceeccccHHHH
Confidence 2222 22222223334444444 4688999999999999999999999999999999999999
Q ss_pred hhccccc----------------------------------------CcccccccccccccccccccccchhhhHHHHHH
Q psy3015 1327 CDVMTAK----------------------------------------GHLMAITRHGINRQDTGALMRCSFEETVDVLMD 1366 (1791)
Q Consensus 1327 aD~MT~~----------------------------------------G~l~~itR~Gi~rq~~S~L~raSFEeTv~iL~~ 1366 (1791)
+.+|+++ -.++|||+..++ ..|.|+.|||++|.++|.+
T Consensus 1130 vRQMl~kV~I~d~Gdt~fl~Ge~vd~~~~~~~n~~~~~~g~~pa~~~p~llGITKasL~--t~SflSaASFQeTtrVLt~ 1207 (1460)
T PRK14906 1130 ARQMLRKVAVTNPGDSDYLPGRQVNRYEFEDTANNLILEGKQPPVGQPLLLGITKASLA--TDSWLSAASFQETTKVLTD 1207 (1460)
T ss_pred HHHHhceEEEecCCCcCCCCCCeeeHHHHHHHHHHHHHcCCCCceeeeEEeeeeecccc--cccccccccccchHHHHHH
Confidence 9999998 148889988885 4689999999999999999
Q ss_pred HhhccCCCCCCccccceeccccccCCcchh
Q psy3015 1367 AAAHAEADPMRGVSENIIMGQLPRMGTGCF 1396 (1791)
Q Consensus 1367 AA~~ge~D~lkgVsenIi~Gq~~~lGTGaF 1396 (1791)
||+.|+.|+|+|+.||+|+|+++|.|||..
T Consensus 1208 AAi~gk~D~L~GLKENVIiG~lIPAGTG~~ 1237 (1460)
T PRK14906 1208 AAIEGKVDHLAGLKENVIIGKPIPAGTGLS 1237 (1460)
T ss_pred HHhcCCCCcCCCCccceEecceecCCCCcc
Confidence 999999999999999999999999999953
No 35
>TIGR02390 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit A'. This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Probab=100.00 E-value=5.8e-38 Score=409.68 Aligned_cols=149 Identities=36% Similarity=0.566 Sum_probs=141.1
Q ss_pred ccCCHHHHHHHHHHHhhhccceeccccccccccCCcccCCCCcCccccccccCCCCCCCCcceeeccccCCCcceEEEee
Q psy3015 988 YRLSSEAFEWLVGEIENRFQQAQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHA 1067 (1791)
Q Consensus 988 ~rln~~a~~~i~gei~~~~~~sqv~~mvG~QsV~gKrI~~GfprRTLphf~kdd~~PESrGFV~Nsf~~GLTPsEfffhA 1067 (1791)
.+.|...+|..+|++|+..|++|+.+|||||+++|+|||+||.+||||||.++|++|+|+|||.|||++||||+||||||
T Consensus 716 ~~~N~~~~M~~sGsKGS~~Ni~Qi~~~lGQQ~~~g~ri~~~~~~rtlp~f~~~d~~~~~~GfV~~sF~~GL~p~EfFfH~ 795 (868)
T TIGR02390 716 DPENHAVIMARTGARGSLLNITQMAAMVGQQSVRGGRIRRGYRNRTLPHFKKGDIGAKARGFVRSSFKKGLDPTEYFFHA 795 (868)
T ss_pred CCCcchhhhhhccCCcccccHHHHHhccCccccCCCcCccccccCCCCCCCCCCCCcccCceecccccCCCCHHHHHHHH
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCccchhhhccchhHHHHHHHHHHhcceEEEECCCCCCcccccCcceeeeeccCCCCCCCCcccceeeeec
Q psy3015 1068 MGGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPDFDPTRISPWLLRIEL 1141 (1791)
Q Consensus 1068 MgGREGLiDTAvKTAEtGYIqRRLvk~~Edv~V~YDgtvrnTVr~~d~~iVQf~Yg~dg~D~~~~~~wvlr~~L 1141 (1791)
|||||||+|||+|||+|||+||||||+|||+.|.||+ |||+++|++|||.||+||+|+++.+ +...+.|
T Consensus 796 m~gReGLiDTAvKTa~sGYLqRrLvk~lEdl~v~yD~----tVR~~~g~iiQf~YG~dg~d~~~~~-~~~~~~~ 864 (868)
T TIGR02390 796 AGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDG----TVRDTRGNLIQFKYGEDGVDPMKSD-HGKPVDV 864 (868)
T ss_pred hhhccccccccccccccchhHHHHHHHHhheEEecCC----eEEeCCCcEEEEeccCCCcCHHHhc-cCccccc
Confidence 9999999999999999999999999999999999998 7888899999999999999998766 4333333
No 36
>cd02737 RNAP_IV_NRPD1_C Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain. Higher plants have five multi-subunit nuclear RNA polymerases: RNAP I, RNAP II and RNAP III, which are essential for viability; plus the two isoforms of the non-essential polymerase RNAP IV (IVa and IVb), which specialize in small RNA-mediated gene silencing pathways. RNAP IVa and/or RNAP IVb might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b is the largest subunit of RNAP IVb. The full subunit compositions of RNAP IVa and RNAP IVb are not known, nor are their templates or enzymatic products. However, it has been shown that RNAP IVa and, to a lesser extent, RNAP IVb are crucial for several RNA-mediated gene silencing phenomena.
Probab=100.00 E-value=1.7e-36 Score=361.73 Aligned_cols=220 Identities=17% Similarity=0.168 Sum_probs=170.8
Q ss_pred Ccchhh-hhhccCCCCCCCCCCCCCCCcceeeeeeeccccceecccchhHHHhhc--cCCCCCCCCCccceeEEEEeec-
Q psy3015 1416 GMMGGP-AGMFFGSAATPSSIPGPPAWYPIHIAISLLSRFTTVICIYTLKTFLEM--KDFKKPPQKGFGLLTLTLMVEN- 1491 (1791)
Q Consensus 1416 GEmVG~-aAQSIGEPa~~~~~TQmT~lnTFH~aGVs~~~~t~~lGvprlkei~nv--~~~~k~~~~~~~~~~~t~~~~~- 1491 (1791)
|||||+ ||||||||| |||| |||||+|||| +||||||+||+ +++.|||+ ++|||..
T Consensus 1 GE~VG~LAAqSIgEPA-----tQmt-Lntfh~agvs--------~vprLKEiLn~~~~~~~ktps-------~~v~L~~~ 59 (381)
T cd02737 1 GEPVGSLAATAISEPA-----YKAL-LDPPQSLESS--------PLELLKEVLECRSKSKSKEND-------RRVILSLH 59 (381)
T ss_pred CCcchhHHHhhhcchH-----HHhh-hccchhcCCc--------cHHHHHHHhcccccCCCCCCC-------EEEEEecc
Confidence 899999 899999999 9999 9999999995 58999999999 67788997 8888872
Q ss_pred cccCCccccCCCCCchhhHhhHhHHHHHhhccccccchhhhcceeEEEEcCCCCCCcccccHHHHHH-----hhcCCCC-
Q psy3015 1492 IHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVTANTAIYYDPDPQNTVIPEDQEFVNV-----YYEMPDF- 1565 (1791)
Q Consensus 1492 I~~~pk~~~~P~~~~~~~~~vq~~~~~~~~~~~~~~~l~~vt~~t~i~ydpd~~~tvi~eD~~~v~~-----~~~~pd~- 1565 (1791)
.+...+... ..+.|+.+|..|+ ||+|++||..++|||||||++|+|+||++||+. ||++||.
T Consensus 60 ~~~~~~~~~----~~~~a~~Vq~~Le--------~~tL~~v~~~~~I~Ydp~~~~t~i~~d~~~~~~~~~~~~~~~~~~~ 127 (381)
T cd02737 60 LCKCDHGFE----YERAALEVKNHLE--------RVTLEDLATTSMIKYSPQATEAIVGEIGDQLNTKKKGKKKAIFSTS 127 (381)
T ss_pred ccccccchH----HHHHHHHHHHHhh--------hccHHHhhheEEEEECCCcccccccccHHHHHhhhhhhhhcccccc
Confidence 221111111 1346778888887 899999999999999999999999999999999 9999975
Q ss_pred -CCCCCCcceEEEEeccccccccccCHHHHHhhhhcCCCCCCCCCCCCchhhhHHHHHHHHHhcccCCCceeeecCCccc
Q psy3015 1566 -DPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNTPLSPTDKKLTMEAISEKINAGFGDDLNCIFNDDNAE 1644 (1791)
Q Consensus 1566 -~~~~~spwllr~~ldr~~m~dk~l~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~f~~~l~~i~~ddna~ 1644 (1791)
+.+++|||+||++|||. . .|++|+.||+.++|.+
T Consensus 128 ~~~~~~spw~~r~~l~~~------------~---------------------------------~~~~~~~ci~~~~~~~ 162 (381)
T cd02737 128 LKITKFSPWVCHFHLDKE------------C---------------------------------QKLSDGPCLTFSVSKE 162 (381)
T ss_pred cccccCCcceEEEEEehh------------H---------------------------------hcCCCCceEEeecCcc
Confidence 66899999999999998 1 1677999999998811
Q ss_pred ceEEEEEEecCCCCccchhhhh-hhcc----ccceeeccccccceeEeec--ccC-------CccccccEEEEEeccc--
Q psy3015 1645 KLVLRIRIMNSDDSKMQDEEDA-VDKM----EDDMFLRCIEETDRSFVKV--DFV-------EPKDLVEWKTLLKQMH-- 1708 (1791)
Q Consensus 1645 ~lv~r~r~~~~~~~~~~~~~~~-~~~~----~~~~~lr~~~~~~~~~~~~--~~~-------~~~~~~~~~~~~~~~~-- 1708 (1791)
.+.+...+.+. .+++ .+ +.|||+++|+||+|.. +.. ..+...||.+.+ .|+
T Consensus 163 -----------~~~~~~~~~~~~~~~i~~~lL~-~~lkG~~~I~kv~i~~~~~~~~~~~~~~~~~~~~E~vLe~-~~~~~ 229 (381)
T cd02737 163 -----------VSKSSEELLDVLRDRIIPFLLE-TVIKGDERIKSVNILWEDSPSTSWVKSVGKSSRGELVLEV-TVEES 229 (381)
T ss_pred -----------cccchhHHHHHHHHHHHHHHhh-eeecccCCeeEEEEEecCCCcccccccccccccceEEEEE-Eeccc
Confidence 11111122222 3443 34 8899999999999983 211 244567999998 222
Q ss_pred ----ccccHHHHH-hhccccccc
Q psy3015 1709 ----SDFCLAQII-KCIPTLSRH 1726 (1791)
Q Consensus 1709 ----~~~~~~~~~-~~~~~~~~~ 1726 (1791)
+|.+|+.++ .|+|.+.--
T Consensus 230 ~~~t~G~~~~~vl~~c~~~~~~I 252 (381)
T cd02737 230 CKKTRGNAWNVVMDACIPVMDLI 252 (381)
T ss_pred cccccchhHHHHHHhhhcccccC
Confidence 299999999 698887533
No 37
>cd06528 RNAP_A'' A'' subunit of Archaeal RNA Polymerase (RNAP). Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.
Probab=100.00 E-value=1e-36 Score=362.66 Aligned_cols=217 Identities=13% Similarity=0.174 Sum_probs=174.4
Q ss_pred cCCcchhhhhcccccccccccccCCCCcchhh-hhhccCCCCCCCCCCCCCCCcceeeeeeeccccceecccchhHHHhh
Q psy3015 1390 RMGTGCFDLLLDAEKCKDGIEIPLATGMMGGP-AGMFFGSAATPSSIPGPPAWYPIHIAISLLSRFTTVICIYTLKTFLE 1468 (1791)
Q Consensus 1390 ~lGTGaFd~lLge~~~~~~~~~~v~pGEmVG~-aAQSIGEPa~~~~~TQmT~lnTFH~aGVs~~~~t~~lGvprlkei~n 1468 (1791)
++...+|+|++++.+.++.++. ++||||||+ ||||||||| |||| |||||||||+++||| |||||||||+|
T Consensus 15 ~l~~~~~~~~~~~~~~~~~~~~-~~~Ge~vG~iaAQSiGEP~-----TQMT-LnTFH~AGVas~nVT--lGVPRlkEIIn 85 (363)
T cd06528 15 GLTLSEAEEIIKEVLREYLRSL-IEPGEAVGIVAAQSIGEPG-----TQMT-LRTFHYAGVAEINVT--LGLPRLIEIVD 85 (363)
T ss_pred CCCHHHHHHHHHHHHHHHHHHh-hccCccccceeeeecCccc-----eecc-cccccccccccccCc--cccccHHHHhh
Confidence 5666799999999999999998 999999999 799999999 9999 999999999999998 99999999999
Q ss_pred ccCCCCCCCCCccceeEEEEeeccccCCccccCCCCCchhhHhhHhHHHHHhhccccccchhhhcceeEEEEcCCCCCCc
Q psy3015 1469 MKDFKKPPQKGFGLLTLTLMVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVTANTAIYYDPDPQNTV 1548 (1791)
Q Consensus 1469 v~~~~k~~~~~~~~~~~t~~~~~I~~~pk~~~~P~~~~~~~~~vq~~~~~~~~~~~~~~~l~~vt~~t~i~ydpd~~~tv 1548 (1791)
++|+++||+ +|+||.+ ... .+.+.|..++..+| +|+|++|+...+|+|+
T Consensus 86 a~K~i~TP~-------mti~L~~------~~~---~~~~~a~~v~~~iE--------~t~l~di~~~~~i~~~------- 134 (363)
T cd06528 86 ARKEPSTPT-------MTIYLEE------EYK---YDREKAEEVARKIE--------ETTLENLAEDISIDLF------- 134 (363)
T ss_pred cccCCCCce-------EEEEecC------cch---hhHHHHHHHHHhhc--------eeEHHHhhhheEEecc-------
Confidence 999989997 9999983 122 14566777777777 8999999999998431
Q ss_pred ccccHHHHHHhhcCCCCCCCCCCcceEEEEeccccccccccCHHHHHhhhhcCCCCCCCCCCCCchhhhHHHHHHHHHhc
Q psy3015 1549 IPEDQEFVNVYYEMPDFDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNTPLSPTDKKLTMEAISEKINA 1628 (1791)
Q Consensus 1549 i~eD~~~v~~~~~~pd~~~~~~spwllr~~ldr~~m~dk~l~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~ 1628 (1791)
.|.|||+||+++|.+++|+|++|.. +|.+
T Consensus 135 -----------------------~~~l~i~ld~~~l~~~~l~~~~i~~----------------------------~i~~ 163 (363)
T cd06528 135 -----------------------NMRITIELDEEMLEDRGITVDDVLK----------------------------AIEK 163 (363)
T ss_pred -----------------------CcEEEEEECHHHHHHcCCCHHHHHH----------------------------HHHH
Confidence 4999999999999999999999997 6666
Q ss_pred ccCCCceeeecCCcccceEEEEEEecCCCCccchhhhhhhccc---cceeeccccccceeEeecccCCccccccEEEEEe
Q psy3015 1629 GFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKME---DDMFLRCIEETDRSFVKVDFVEPKDLVEWKTLLK 1705 (1791)
Q Consensus 1629 ~f~~~l~~i~~ddna~~lv~r~r~~~~~~~~~~~~~~~~~~~~---~~~~lr~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1705 (1791)
.++.++.+ + +++. ++++..++ .+...+++++ -++.|+|+++++|++|..+ ..+|.+++
T Consensus 164 ~~~~~~~~--~-~~~~-----~~~~~~~~----~~~~~l~~l~~~l~~~~v~Gi~gI~r~~i~~~------~~~~~l~t- 224 (363)
T cd06528 164 LKKGKVGE--E-GDVT-----LIVLKAEE----PSIKELRKLAEKILNTKIKGIKGIKRVIVRKE------EDEYVIYT- 224 (363)
T ss_pred hcCCcccc--c-CCcc-----EEEEcCCc----chHHHHHHHHHhhcccEEeCCCCceEEEEecC------CceEEEEe-
Confidence 67777643 2 3322 23333221 1112333332 3478999999999999864 24899999
Q ss_pred cccccccHHHHHhh
Q psy3015 1706 QMHSDFCLAQIIKC 1719 (1791)
Q Consensus 1706 ~~~~~~~~~~~~~~ 1719 (1791)
+|.+|.++++.
T Consensus 225 ---eG~nl~~v~~~ 235 (363)
T cd06528 225 ---EGSNLKAVLKV 235 (363)
T ss_pred ---cCcCHHHHhcC
Confidence 99999999963
No 38
>PRK08566 DNA-directed RNA polymerase subunit A'; Validated
Probab=100.00 E-value=1.8e-37 Score=406.16 Aligned_cols=142 Identities=42% Similarity=0.656 Sum_probs=138.0
Q ss_pred ccCCHHHHHHHHHHHhhhccceeccccccccccCCcccCCCCcCccccccccCCCCCCCCcceeeccccCCCcceEEEee
Q psy3015 988 YRLSSEAFEWLVGEIENRFQQAQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHA 1067 (1791)
Q Consensus 988 ~rln~~a~~~i~gei~~~~~~sqv~~mvG~QsV~gKrI~~GfprRTLphf~kdd~~PESrGFV~Nsf~~GLTPsEfffhA 1067 (1791)
.+.|...+|..+|++|+..|++|+.+|||||+++|+|||+||.+||||||.++|++|||+|||.|||++||||+||||||
T Consensus 721 ~~~N~~~~M~~SGsKGS~~N~~Qi~~~lGqQ~~~g~ri~~~~~~rtLP~f~~~d~~~~~~GfV~~sF~~GL~p~EfffH~ 800 (882)
T PRK08566 721 GLDNPAVIMARTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTLPHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHA 800 (882)
T ss_pred CCCCcceeeeccccccCHHHHHHHHhccCceecCCCcCccCccCccCCCCCCCCCCcccCceeeccccCCCCHHHHHHHH
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCccchhhhccchhHHHHHHHHHHhcceEEEECCCCCCcccccCcceeeeeccCCCCCCCCcc
Q psy3015 1068 MGGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPDFDPTRIS 1133 (1791)
Q Consensus 1068 MgGREGLiDTAvKTAEtGYIqRRLvk~~Edv~V~YDgtvrnTVr~~d~~iVQf~Yg~dg~D~~~~~ 1133 (1791)
|||||||+|||+|||+|||+||||||+|||+.|.||+ |||+++|++|||.||+||+|+.+.+
T Consensus 801 m~GReGliDTAvkTa~sGYlqRrLvk~ledl~v~yD~----tVR~s~g~iiQf~YG~dg~d~~~~~ 862 (882)
T PRK08566 801 MGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDG----TVRDTRGNIVQFKYGEDGVDPMKSD 862 (882)
T ss_pred hhhcccccccceeeccCccchHHHHHHHhheEEeeCC----ceEcCCCcEEEEeccCCCcCHHHhc
Confidence 9999999999999999999999999999999999998 7777899999999999999997665
No 39
>PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Probab=100.00 E-value=5.9e-36 Score=361.70 Aligned_cols=219 Identities=13% Similarity=0.184 Sum_probs=171.4
Q ss_pred cCCcchhhhhcccccccccccccCCCCcchhh-hhhccCCCCCCCCCCCCCCCcceeeeeeeccccceecccchhHHHhh
Q psy3015 1390 RMGTGCFDLLLDAEKCKDGIEIPLATGMMGGP-AGMFFGSAATPSSIPGPPAWYPIHIAISLLSRFTTVICIYTLKTFLE 1468 (1791)
Q Consensus 1390 ~lGTGaFd~lLge~~~~~~~~~~v~pGEmVG~-aAQSIGEPa~~~~~TQmT~lnTFH~aGVs~~~~t~~lGvprlkei~n 1468 (1791)
+++..+|+|++++...++.++. ++||||||+ ||||||||| |||| |||||||||++.||| ||||||+||+|
T Consensus 157 ~l~~~~~~~i~~ei~~~y~~~~-v~pGE~VG~IAAQSIGEP~-----TQMT-LnTFH~AGVas~NVT--lGVPRLkEIIN 227 (509)
T PRK14897 157 ELSDDEYEEILRRIREEYERAR-VDPYEAVGIVAAQSIGEPG-----TQMT-MRTFHYAGVAEMNVT--LGLPRLIEIVD 227 (509)
T ss_pred CCCHHHHHHHHHHHHHHHHHhc-cCCCCCcchhhhhhhCCcc-----cccc-ccccccccccccccc--cCcchhHHHhh
Confidence 6677899999999999999998 999999999 899999999 9999 999999999999998 99999999999
Q ss_pred ccCCCCCCCCCccceeEEEEeeccccCCccccCCCCCchhhHhhHhHHHHHhhccccccchhhhcceeEEEEcCCCCCCc
Q psy3015 1469 MKDFKKPPQKGFGLLTLTLMVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVTANTAIYYDPDPQNTV 1548 (1791)
Q Consensus 1469 v~~~~k~~~~~~~~~~~t~~~~~I~~~pk~~~~P~~~~~~~~~vq~~~~~~~~~~~~~~~l~~vt~~t~i~ydpd~~~tv 1548 (1791)
++++++||+ +|+||.+ .... +.+.|..++..++ +|+|++|+.
T Consensus 228 a~K~isTP~-------mtiyL~~------~~~~---d~e~A~~V~~~IE--------~ttL~dv~~-------------- 269 (509)
T PRK14897 228 ARKKPSTPT-------MTIYLKK------DYRE---DEEKVREVAKKIE--------NTTLIDVAD-------------- 269 (509)
T ss_pred cccCCCCce-------EEEEecC------cccc---cHHHHHHHHhhhe--------eeEHHHHHH--------------
Confidence 999999997 9999983 2222 5567777777777 899999984
Q ss_pred ccccHHHHHHhhcCCCCCCCCCCcceEEEEeccccccccccCHHHHHhhhhcCCCCCCCCCCCCchhhhHHHHHHHHHhc
Q psy3015 1549 IPEDQEFVNVYYEMPDFDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNTPLSPTDKKLTMEAISEKINA 1628 (1791)
Q Consensus 1549 i~eD~~~v~~~~~~pd~~~~~~spwllr~~ldr~~m~dk~l~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~ 1628 (1791)
++.+| +.|.|||+||+++|.+++|+|++|..+ |.+
T Consensus 270 ------~~~d~-----------~~~~i~i~Ld~~~l~~~~l~~~~I~~~----------------------------I~~ 304 (509)
T PRK14897 270 ------IITDI-----------AEMSVVVELDEEKMKERLIEYDDILAA----------------------------ISK 304 (509)
T ss_pred ------HHHHh-----------ccceEEEEECHHHHHHcCCCHHHHHHH----------------------------HHh
Confidence 33333 247799999999999999999999973 333
Q ss_pred ccCCCceeeecCCcccceEEEEEEecCCCCccchhhhhhhccccceeeccccccceeEeecccCCccccccEEEEEeccc
Q psy3015 1629 GFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEETDRSFVKVDFVEPKDLVEWKTLLKQMH 1708 (1791)
Q Consensus 1629 ~f~~~l~~i~~ddna~~lv~r~r~~~~~~~~~~~~~~~~~~~~~~~~lr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1708 (1791)
.. +.++.+|+| . ||+...++. . ..-..+.+.-.++.|+|+++|+|+++..+ .+..+|.+.|
T Consensus 305 ~~---~~~~~~~~~----~--I~i~~~~~~-~-~~L~~l~~~l~~i~I~GipgI~r~~i~~~----~~~~~~~L~T---- 365 (509)
T PRK14897 305 LT---FKTVEIDDG----I--IRLKPQQPS-F-KKLYLLAEKVKSLTIKGIKGIKRAIARKE----NDERRWVIYT---- 365 (509)
T ss_pred cc---ceEEecCCC----E--EEEEeCchH-H-HHHHHHHHHhhccEEeCCCCccEEEEecC----CCCceeEEEe----
Confidence 22 245556666 2 444443211 0 00011222225688999999999999975 3445799999
Q ss_pred ccccHHHHHhh
Q psy3015 1709 SDFCLAQIIKC 1719 (1791)
Q Consensus 1709 ~~~~~~~~~~~ 1719 (1791)
+|.+|.++++.
T Consensus 366 eG~NL~~vl~~ 376 (509)
T PRK14897 366 QGSNLKDVLEI 376 (509)
T ss_pred eccCHHHHhcC
Confidence 99999999976
No 40
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=100.00 E-value=1.2e-35 Score=398.28 Aligned_cols=109 Identities=35% Similarity=0.615 Sum_probs=101.9
Q ss_pred chhHHHHHHhhhHHHHHHHHHHHHHHHhhhcCeeecccchhhhhhccccc-------------Cc---------------
Q psy3015 1284 SNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAK-------------GH--------------- 1335 (1791)
Q Consensus 1284 sNdI~eI~~vlGIEAaR~~li~El~~V~~~~Gi~Vn~RHL~LLaD~MT~~-------------G~--------------- 1335 (1791)
+-+.+++++++|+||++++|++|++.||..||++||+||+++|+++|+++ |+
T Consensus 2635 ~~~p~dil~v~G~ea~~~ylv~Evq~VYr~QGV~IndKHiEvIvrQMl~kV~I~d~Gdt~~l~Ge~v~~~~~~~~n~~~~ 2714 (2836)
T PRK14844 2635 DPDLHDILRVLGLEALAHYMISEIQQVYRLQGVRIDNKHLEVILKQMLQKVEITDPGDTMYLVGESIDKLEVDRENDAMS 2714 (2836)
T ss_pred CCCHHHHHHhhCHHHHHHHHHHHHHHHHHhcCeeecccEeeeehhhhhceeEEecCCCcccCCCceecHHHHHHHHHHHH
Confidence 34678999999999999999999999999999999999999999999977 22
Q ss_pred ------------ccccccccccccccccccccchhhhHHHHHHHhhccCCCCCCccccceeccccccCCcc
Q psy3015 1336 ------------LMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTG 1394 (1791)
Q Consensus 1336 ------------l~~itR~Gi~rq~~S~L~raSFEeTv~iL~~AA~~ge~D~lkgVsenIi~Gq~~~lGTG 1394 (1791)
++||||++++ ..|+|++|||++|.++|.+||+.|+.|+|+|+.||+|+|+++|.|||
T Consensus 2715 ~~g~~pa~~~pvllGITkasL~--t~SflSaASFQeTtkVLt~AAi~Gk~D~L~GlKENVIiG~lIPaGTG 2783 (2836)
T PRK14844 2715 NSGKRPAHYLPILQGITRASLE--TSSFISAASFQETTKVLTEAAFCGKSDPLSGLKENVIVGRLIPAGTG 2783 (2836)
T ss_pred hcCCCCceeeeeeeceeecccc--CCChhhcCCcccchHHHHHHHhcCCCCcCCCcccceEecCcccCCcC
Confidence 7899999884 47999999999999999999999999999999999999999999999
No 41
>CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed
Probab=100.00 E-value=2.9e-34 Score=379.38 Aligned_cols=205 Identities=23% Similarity=0.425 Sum_probs=165.2
Q ss_pred EEeeccccccCCCccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCcccccCCcccChhhHHHHHHHHHHHHHHHHHH
Q psy3015 152 MGILCKKSLGTSSGSLLHICFLELGHEVCGRFYGNIQTVVNNWLLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEV 231 (1791)
Q Consensus 152 ~G~ldKk~vG~s~~gLih~i~~~yG~~~a~~fL~~lqrL~~~~L~~~GFSiGi~D~i~~~~t~~~i~~~i~~ak~~~~~~ 231 (1791)
.-++||+.++ +||+.+|++||++.|..|||.+++|+.+|++.+|||+|++|+.+|++ ..+++++|+
T Consensus 11 N~~~~k~~l~----~li~~~~~~~G~~~t~~~lD~lk~lgf~~at~~G~Sigi~Dl~ip~~----K~~li~~a~------ 76 (1364)
T CHL00117 11 NKVIDKTALK----RLISWLIDHFGMAYTSHILDQLKTLGFQQATAAGISLGIDDLLTPPS----KGWLVQDAE------ 76 (1364)
T ss_pred eccccHHHHH----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcceEEecCcccCCHH----HHHHHHHHH------
Confidence 3578999995 49999999999999999999999999999999999999999999976 245555555
Q ss_pred HHHHhcCCCCCCCCcccccCCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCcHHHHHHHHHHH---HHHH
Q psy3015 232 IQKAHNMDLEPTPGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNR---ILND 308 (1791)
Q Consensus 232 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~i~~~~~~~L~~~pg~~~~~~fE~~vn~---iLn~ 308 (1791)
++|.++.++++.|.+. ..|.++..+.. ..+.
T Consensus 77 ----------------------------------------~~v~~~~~~y~~G~it------~~er~~~~i~~w~~~~~~ 110 (1364)
T CHL00117 77 ----------------------------------------QQSLILEKHYHYGNVH------AVEKLRQSIEIWYATSEY 110 (1364)
T ss_pred ----------------------------------------HHHHHHHHHHHcCCCC------HHHHHHHHHHHHHHHHHH
Confidence 4555666677777763 44556555443 4444
Q ss_pred HHhhhhhhhhhccCCCChHHHHhhcCCCcchhhHHHHHhhccCccc----CCceeccCCccCCCCCCCCCCCCCccccee
Q psy3015 309 ARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQNV----EGKRIPFGFRKRTLPHFIKDDYGPESRGFV 384 (1791)
Q Consensus 309 ~rd~~g~~~~~~l~~~N~l~~Mv~sGSKGS~iNisQi~acvGQQ~v----eGkRIp~gf~~RtLPhF~~~d~~p~srGFV 384 (1791)
+++... .+.+..++.|++++|+.||||| |++||..|+|++.+ +|++| .|| |
T Consensus 111 l~~~~~-~~~~~~d~~N~v~mMa~SGARG---n~sQi~qLvGmRGlma~p~G~iI-------~~P--------------I 165 (1364)
T CHL00117 111 LKQEMN-PNFRMTDPLNPVYMMSFSGARG---NASQVHQLVGMRGLMSDPQGQII-------DLP--------------I 165 (1364)
T ss_pred HHHHHH-HhhccCCCCCcHhhhhhccCcc---cHHHHHHHhcccceeeCCCCcEe-------ecc--------------h
Confidence 455443 3445567899999999999999 67777777777665 45554 233 9
Q ss_pred ccccccCCChhhhhhhcccCcccchhcccccCCcchhHHHHHHhhcceEEe-ecCcEE
Q psy3015 385 ENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVH-YDCTVR 441 (1791)
Q Consensus 385 ~nSfl~GL~P~EfFFHaMaGREGLIDTAVKTaeTGYlQRrLvK~LEDl~V~-YDgTVR 441 (1791)
.+||.+||+|.|||||||||||||+|||+|||+|||||||||+++||+.|. .||-..
T Consensus 166 ~snFreGLs~~EyFis~~GaRkGLvDTAlkTAdSGYLtRRLVdv~qdviV~~~dCgt~ 223 (1364)
T CHL00117 166 QSNFREGLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRLVEVVQHIVVRETDCGTT 223 (1364)
T ss_pred hhhhhcCCCHHHhheeccccccchhhcceecccccchhhHHHhhhccEEEEeccCCCC
Confidence 999999999999999999999999999999999999999999999999996 787543
No 42
>PRK04309 DNA-directed RNA polymerase subunit A''; Validated
Probab=100.00 E-value=1.8e-34 Score=345.47 Aligned_cols=215 Identities=14% Similarity=0.216 Sum_probs=175.0
Q ss_pred cCCcchhhhhcccccccccccccCCCCcchhh-hhhccCCCCCCCCCCCCCCCcceeeeeeeccccceecccchhHHHhh
Q psy3015 1390 RMGTGCFDLLLDAEKCKDGIEIPLATGMMGGP-AGMFFGSAATPSSIPGPPAWYPIHIAISLLSRFTTVICIYTLKTFLE 1468 (1791)
Q Consensus 1390 ~lGTGaFd~lLge~~~~~~~~~~v~pGEmVG~-aAQSIGEPa~~~~~TQmT~lnTFH~aGVs~~~~t~~lGvprlkei~n 1468 (1791)
++...+|+|++++...++..+. +.||||||+ ||||||||| |||| |||||||||++.|+| +||||||||+|
T Consensus 34 ~l~~~~~~~~~~~i~~~y~~~~-v~pGe~VG~iaAQsIGEP~-----TQMT-L~TFH~AGva~~nVT--lGvPRlkEIin 104 (383)
T PRK04309 34 KLTEEEVEEIIEEVVREYLRSL-VEPGEAVGVVAAQSIGEPG-----TQMT-MRTFHYAGVAEINVT--LGLPRLIEIVD 104 (383)
T ss_pred CCCHHHHHHHHHHHHHHHHHhh-cCCCCccchhhhhhccchh-----hhcc-cccccccCccccCcc--cCchhHHHHHh
Confidence 4556789999999999999988 999999999 799999999 9999 999999999999998 99999999999
Q ss_pred ccCCCCCCCCCccceeEEEEeeccccCCccccCCCCCchhhHhhHhHHHHHhhccccccchhhhcceeEEEEcCCCCCCc
Q psy3015 1469 MKDFKKPPQKGFGLLTLTLMVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVTANTAIYYDPDPQNTV 1548 (1791)
Q Consensus 1469 v~~~~k~~~~~~~~~~~t~~~~~I~~~pk~~~~P~~~~~~~~~vq~~~~~~~~~~~~~~~l~~vt~~t~i~ydpd~~~tv 1548 (1791)
++|+++||+ +|+||.+ ... .+.+.|..++..++ +|+|++|+..+++.|
T Consensus 105 a~K~~~TP~-------~tv~L~~------~~~---~d~~~a~~v~~~iE--------~t~L~~v~~~i~~~~-------- 152 (383)
T PRK04309 105 ARKEPSTPM-------MTIYLKD------EYA---YDREKAEEVARKIE--------ATTLENLAKDISVDL-------- 152 (383)
T ss_pred cccCCCCCe-------EEEEecC------ccc---ccHHHHHHHHhhee--------eeEHhhhhhheEecc--------
Confidence 999889997 9999983 122 24566677777776 899999999877632
Q ss_pred ccccHHHHHHhhcCCCCCCCCCCcceEEEEeccccccccccCHHHHHhhhhcCCCCCCCCCCCCchhhhHHHHHHHHHhc
Q psy3015 1549 IPEDQEFVNVYYEMPDFDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNTPLSPTDKKLTMEAISEKINA 1628 (1791)
Q Consensus 1549 i~eD~~~v~~~~~~pd~~~~~~spwllr~~ldr~~m~dk~l~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~ 1628 (1791)
..|.|||+||+++|.+++|+|++|.. +|..
T Consensus 153 ----------------------~~~~l~i~ld~~~i~~~~l~~~~I~~----------------------------~i~~ 182 (383)
T PRK04309 153 ----------------------ANMTIIIELDEEMLEDRGLTVDDVKE----------------------------AIEK 182 (383)
T ss_pred ----------------------CCcEEEEEECHHHHHHcCCCHHHHHH----------------------------HHHH
Confidence 13679999999999999999999887 6666
Q ss_pred ccCCCceeeecCCcccceEEEEEEecCCCCccchhhhhhhcc---ccceeeccccccceeEeecccCCccccccEEEEEe
Q psy3015 1629 GFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKM---EDDMFLRCIEETDRSFVKVDFVEPKDLVEWKTLLK 1705 (1791)
Q Consensus 1629 ~f~~~l~~i~~ddna~~lv~r~r~~~~~~~~~~~~~~~~~~~---~~~~~lr~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1705 (1791)
.++.++.+. .+++++++| .. +...+.++ --++.++|+++++|+++..+ ..+|.+.+
T Consensus 183 ~~~~~~~~~-----~~~i~i~~~--~~-------~~~~l~~l~~~l~~~~vkGi~gI~r~~i~~~------~~~~~l~t- 241 (383)
T PRK04309 183 KKGGEVEIE-----GNTLIISPK--EP-------SYRELRKLAEKIRNIKIKGIKGIKRVIIRKE------GDEYVIYT- 241 (383)
T ss_pred hcCcceecc-----CCeEEEEec--Cc-------hHHHHHHHHHHhcccEEECCCCceEEEEecC------CCeEEEEE-
Confidence 677776543 466777776 11 11223222 23678999999999999864 46999999
Q ss_pred cccccccHHHHHhh
Q psy3015 1706 QMHSDFCLAQIIKC 1719 (1791)
Q Consensus 1706 ~~~~~~~~~~~~~~ 1719 (1791)
+|.+|.+++..
T Consensus 242 ---eG~nl~~v~~~ 252 (383)
T PRK04309 242 ---EGSNLKEVLKV 252 (383)
T ss_pred ---cccCHHHHhcC
Confidence 99999999963
No 43
>PF04998 RNA_pol_Rpb1_5: RNA polymerase Rpb1, domain 5; InterPro: IPR007081 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, domain 5, represents the discontinuous cleft domain that is required to form the central cleft or channel where the DNA is bound [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1ZYR_D 1SMY_D 2A68_N 2O5J_D 3AOH_N 2O5I_D 2CW0_N 2A6H_N 2A69_D 3EQL_D ....
Probab=100.00 E-value=4e-35 Score=339.87 Aligned_cols=257 Identities=34% Similarity=0.486 Sum_probs=164.7
Q ss_pred CCCcceEEEeecCCCCccchhhhccchhHHHHHHHHHHhcceEEEECCCCCCcccccCcceeeeeccCCCC-CC-CCcc-
Q psy3015 1057 GLTPSEFFFHAMGGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPDF-DP-TRIS- 1133 (1791)
Q Consensus 1057 GLTPsEfffhAMgGREGLiDTAvKTAEtGYIqRRLvk~~Edv~V~YDgtvrnTVr~~d~~iVQf~Yg~dg~-D~-~~~~- 1133 (1791)
||||.|||||||||||||+|||+|||++|||||||+|++||+.|.||+ |+|++++.++||.||+|++ +| +.+.
T Consensus 1 Gl~~~e~f~~~~~~R~gl~dta~kTa~sGyl~R~lv~~~~~~~v~~~~----~~~~~~~~i~~~~~~~~~~v~~Ge~VGi 76 (277)
T PF04998_consen 1 GLTPTEYFFHCMGGREGLIDTAVKTADSGYLQRRLVKVLEDLIVRYDD----CVRNSGGSIIQFIYGEDGLVEPGEAVGI 76 (277)
T ss_dssp C-THHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHTTHEEETTS----EEESTTSEEEESSCTTTSB--TTSBHHH
T ss_pred CcCHHHHHHHHhcccccccccceeeeccccchhhhhhccceEEEEEcC----ccccccceeeecccccccccCccccchh
Confidence 899999999999999999999999999999999999999999999998 8888899999999999863 11 0000
Q ss_pred --------cceeeeeccccc---cccccC--CHHHHHHHHhhccCCCcccccCCcccccceEEEEEecCccccccchhHH
Q psy3015 1134 --------PWLLRIELDRKR---MTDKKL--TMEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDA 1200 (1791)
Q Consensus 1134 --------~wvlr~~Ld~~~---m~dk~l--~~~~I~~~I~~~~~~dl~~i~~d~n~~~l~~riri~~~~~~~~~~~ee~ 1200 (1791)
|- -.+.|+.-. .....+ .+-.+.+.+...... ... +........... . ...
T Consensus 77 iaAQSIGEP~-TQ~TL~TFH~aG~~~~~vt~giprl~eii~~~~~~-----------~~~-~~~~~~~~~~~~-~-~~~- 140 (277)
T PF04998_consen 77 IAAQSIGEPG-TQMTLRTFHTAGVASKNVTQGIPRLKEIINASKKI-----------KTP-IITVYGKKKIIS-E-KKK- 140 (277)
T ss_dssp HHHHHHHCHG-CCSHHSCTSSSCSSTSSCSSSHHHHHHHHTTCSSS-----------SSE-EEEECSCSSECS-S-SHH-
T ss_pred hhhchhcchh-HHhhhcccccCceeeecccccceeecccccccccc-----------ccc-eEEeecccceec-c-ccc-
Confidence 00 000111100 001111 112222222211111 011 110000000000 0 000
Q ss_pred HHhhhhhhhHHHHhhcc-cccceeccccccceEEEeccccCCCceEEEccCCcccccceEEEeecccchhcccccCC-CC
Q psy3015 1201 VDKMEDDMFLRCIEANM-LSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERD-VD 1278 (1791)
Q Consensus 1201 ~~~~~dr~~Lr~i~~~i-l~~~~LkGi~~I~kv~i~lp~~~n~~RiI~na~~~f~~~~e~~L~teG~nL~~vl~~~d-VD 1278 (1791)
...++...... .......+.. .....++..........+|++.++|.++..++...+ +|
T Consensus 141 ------~~~~~~~~~~~~~~~~~~~~~~-------------~~~~~~~~~~~~~~~~~~~~l~~~g~~l~~v~~~qgvid 201 (277)
T PF04998_consen 141 ------IKIIRKKIKIIKNGKKVKNGDK-------------IKKGSIISKDILEKKSKEYVLQTEGSNLQEVYSSQGVID 201 (277)
T ss_dssp ------HHHHHHTCSSSCSTTCEHTTCE-------------SSSSCSEHHHHCEECCCCCEEECCSHHHHHHTCSTT-EE
T ss_pred ------ceEEEEeeeeeecccceeccee-------------eecceeeeeccccchhHHHHHHHHhhhchhheecccccC
Confidence 00011100000 0000000000 000111111112233468999999999999999999 89
Q ss_pred cccccchhHHHHHHhhhHHHHHHHHHHHHHHHhhhcCeeecccchhhhhhcccccCcccccccccccccccccc
Q psy3015 1279 PVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGAL 1352 (1791)
Q Consensus 1279 p~rt~sNdI~eI~~vlGIEAaR~~li~El~~V~~~~Gi~Vn~RHL~LLaD~MT~~G~l~~itR~Gi~rq~~S~L 1352 (1791)
+.++++|+|+++++++||||||+.+++|+..|+..+|++||+|||.|+||.||++|.++||||||++.+++|.+
T Consensus 202 ~~k~~sn~I~qm~~~~GIeaar~~i~~e~~~v~~~~g~~vn~rhl~llad~mt~~g~~~gitR~gl~~~~~S~~ 275 (277)
T PF04998_consen 202 NDKHISNDIRQMLSKLGIEAARNSIIKELKNVFESYGIEVNKRHLSLLADYMTYKGVLLGITRHGLNSNKSSFL 275 (277)
T ss_dssp TCHHECSHHHHHHHHHEHHHHHHHHHHHHHCHHHHCTSCCCHHHHHHHHHHHCCCSS---CCTTTTSSSSSSHH
T ss_pred CCEEEeceeEeeeeeEEEEECCCceeecCcEeeHHHHHHHHHHHHHhCCCcCeeeeEEEEEEHHHhccCCCCcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999998877755
No 44
>PRK02597 rpoC2 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=100.00 E-value=1.3e-34 Score=378.64 Aligned_cols=96 Identities=27% Similarity=0.393 Sum_probs=86.8
Q ss_pred ccCCHHHHHHHHHHHhhhccceeccccccccc-cCCcccCCCCcCccccccccCCCCCCCCcceeeccccCCCcceEEEe
Q psy3015 988 YRLSSEAFEWLVGEIENRFQQAQVIACVGQQN-VEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFH 1066 (1791)
Q Consensus 988 ~rln~~a~~~i~gei~~~~~~sqv~~mvG~Qs-V~gKrI~~GfprRTLphf~kdd~~PESrGFV~Nsf~~GLTPsEfffh 1066 (1791)
.++|+..+|..+|++||..|+.|+.+|+|+++ ..|+.|. || |.|||++||||.|||||
T Consensus 117 dp~N~v~mMa~SGARGN~sQI~QLvGmRGLma~p~G~ii~-------lP--------------I~snFrEGLs~~EyFis 175 (1331)
T PRK02597 117 DPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEIID-------LP--------------IKTNFREGLTVTEYVIS 175 (1331)
T ss_pred CCCCcHHHHhhccCCccHHHHHHHhcchhhccCCCCcEEe-------cc--------------hhhhhhcCCCHHHhhee
Confidence 45899999999999998888888888888865 5676664 77 36999999999999999
Q ss_pred ecCCCCccchhhhccchhHHHHHHHHHHhcceEEEECC
Q psy3015 1067 AMGGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYDP 1104 (1791)
Q Consensus 1067 AMgGREGLiDTAvKTAEtGYIqRRLvk~~Edv~V~YDg 1104 (1791)
||||||||+|||+|||++||+||||||++||+.|.++.
T Consensus 176 ~~GaRKGLvDTAlKTAdSGYLTRRLVdv~QDviVre~D 213 (1331)
T PRK02597 176 SYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREED 213 (1331)
T ss_pred ccccccchhhcceecccchhHHHHHHHhhcceEEEecC
Confidence 99999999999999999999999999999999988773
No 45
>cd02736 RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain. Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Probab=100.00 E-value=5.1e-35 Score=340.34 Aligned_cols=166 Identities=33% Similarity=0.510 Sum_probs=134.9
Q ss_pred cchHHHHHhhhhhhHhhccC-ChHHHHHHH--HHHHHHHHHHHHHHhhccCCCc--ceeecchhHHHHHHHhhhhccCCc
Q psy3015 694 FSWKQLRRIFNEDVLRELMG-SGDVISELE--KEWEKLCEDREALREIFSSGES--NVVLPCNLMEVIFILQRWKLWGNE 768 (1791)
Q Consensus 694 ~~~~~l~~~l~~~~~~~~~~-~~~vi~~~~--~e~~kL~~~~~~Lr~i~~~~~~--~~~l~~N~~rii~~~~~~~~~~~~ 768 (1791)
+.++.++..+++.+++|+++ .+.++...+ ++| .|..+|..|++++...++ ..+.++|+..+..
T Consensus 129 ~~~~~l~~~l~~~~v~Gi~gI~r~~i~~~~~~~~~-~l~teG~nl~~v~~~~~Vd~~rt~sNdI~ei~~----------- 196 (300)
T cd02736 129 FLLQSLKRKLPDVVVSGIPEVKRAVINKDKKKGKY-KLLVEGYGLRAVMNTPGVIGTRTTSNHIMEVEK----------- 196 (300)
T ss_pred HHHHHHHHHhccceEeCCCCceEEEEecCCCCCcE-EEEEecccHHHHhcCCcEeccCCccCCHHHHHH-----------
Confidence 55677888888888999887 555554332 122 344456666666654332 2233444433211
Q ss_pred ccccccceEEEe-ccCcccHHHHHHHHhhcceeccchhhhhhhhhhcccceecceeccccccCCCcccccchhhhhhHHH
Q psy3015 769 NLRFLCKIIFVL-SVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVL 847 (1791)
Q Consensus 769 ~~~~~~n~i~~I-aAR~~Ii~Ei~~v~~~~GIsVd~RHi~LlaD~MT~~G~v~~itR~Gl~~~~~S~L~~aSFE~T~d~L 847 (1791)
++|| |||..|++|++.||+.||++||+|||+||||+||++|+++||||+||.++++|||++||||+|++||
T Consensus 197 --------~lGIEAaR~~ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~G~~~~itR~gi~~~~~S~l~~aSFE~t~~~L 268 (300)
T cd02736 197 --------VLGIEAARSTIINEIQYTMKSHGMSIDPRHIMLLADLMTFKGEVLGITRFGIAKMKESVLMLASFEKTTDHL 268 (300)
T ss_pred --------hcCHHHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHHHhccCceeeeecccccccCCCHHHhcchHhHHHHH
Confidence 4566 6999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhccCCCCCCCcccceecCCCCCCCccee
Q psy3015 848 MDAAAHAEADPMRGVSENIIMGQLPRMGTGCF 879 (1791)
Q Consensus 848 ~~Aa~~g~~D~i~GVSe~II~G~~~~iGTg~~ 879 (1791)
++||.+|+.|++.|||||||+|+++++|||+|
T Consensus 269 ~~AA~~g~~D~l~gvse~ii~G~~~~~GTG~f 300 (300)
T cd02736 269 FNAALHGRKDSIEGVSECIIMGKPMPIGTGLF 300 (300)
T ss_pred HHHhhcCCCCcCCCcHHHeeeCCCcCCCCCCC
Confidence 99999999999999999999999999999987
No 46
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=99.98 E-value=7.9e-34 Score=382.21 Aligned_cols=95 Identities=27% Similarity=0.278 Sum_probs=84.7
Q ss_pred cCCHHHHHHHHHHHhhhccceecccccccccc-CCcccCCCCcCccccccccCCCCCCCCcceeeccccCCCcceEEEee
Q psy3015 989 RLSSEAFEWLVGEIENRFQQAQVIACVGQQNV-EGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHA 1067 (1791)
Q Consensus 989 rln~~a~~~i~gei~~~~~~sqv~~mvG~QsV-~gKrI~~GfprRTLphf~kdd~~PESrGFV~Nsf~~GLTPsEfffhA 1067 (1791)
.+|+..+|..+|++||..|++|+.+|+|||+. +|..+. . +|.|||++||||+||||||
T Consensus 2083 ~~N~i~mMa~SGARGS~~NI~QLaGmrGqMakp~G~iie-------~--------------PI~snFrEGLtp~EyFfst 2141 (2890)
T PRK09603 2083 GFNSIYMMADSGARGSAAQIRQLSAMRGLMTKPDGSIIE-------T--------------PIISNFKEGLNVLEYFNST 2141 (2890)
T ss_pred CCCcHHHHHhccccccHHHHHHHHHcCCcEECCCCCccc-------C--------------hhhcCcccCCCHHHHHHhc
Confidence 48999999999999999999999999999762 232221 2 2579999999999999999
Q ss_pred cCCCCccchhhhccchhHHHHHHHHHHhcceEEEECC
Q psy3015 1068 MGGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYDP 1104 (1791)
Q Consensus 1068 MgGREGLiDTAvKTAEtGYIqRRLvk~~Edv~V~YDg 1104 (1791)
|||||||+|||+|||++||+||||||++||+.|..+.
T Consensus 2142 ~GaRKGLiDTALKTAdSGYLTRRLVdvaQDviI~e~D 2178 (2890)
T PRK09603 2142 HGARKGLADTALKTANAGYLTRKLIDVSQNVKVVSDD 2178 (2890)
T ss_pred cccccchhhhhhhccccchhhhhHHHhhcceEEEecc
Confidence 9999999999999999999999999999999988773
No 47
>TIGR02388 rpoC2_cyan DNA-directed RNA polymerase, beta'' subunit. The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria.
Probab=99.98 E-value=6e-34 Score=369.65 Aligned_cols=96 Identities=27% Similarity=0.393 Sum_probs=85.6
Q ss_pred ccCCHHHHHHHHHHHhhhccceeccccccccc-cCCcccCCCCcCccccccccCCCCCCCCcceeeccccCCCcceEEEe
Q psy3015 988 YRLSSEAFEWLVGEIENRFQQAQVIACVGQQN-VEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFH 1066 (1791)
Q Consensus 988 ~rln~~a~~~i~gei~~~~~~sqv~~mvG~Qs-V~gKrI~~GfprRTLphf~kdd~~PESrGFV~Nsf~~GLTPsEfffh 1066 (1791)
.++|+..+|..+|++||..++.|+.+|+|+|+ +.|++|+ || |.|||++||||.|||||
T Consensus 116 d~~N~v~mMa~SGARGNisQi~QLvGmrGlma~p~G~ii~-------lP--------------I~snFreGLt~~EyF~s 174 (1227)
T TIGR02388 116 DPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEIID-------LP--------------IKTNFREGLTVTEYVIS 174 (1227)
T ss_pred CCCCcHHHHhhccCcccHHHHHHHhcchheecCCCCcEee-------cc--------------chhhhhcCCCHHHhhee
Confidence 57899999999999997777777777777765 6677765 88 35999999999999999
Q ss_pred ecCCCCccchhhhccchhHHHHHHHHHHhcceEEEECC
Q psy3015 1067 AMGGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYDP 1104 (1791)
Q Consensus 1067 AMgGREGLiDTAvKTAEtGYIqRRLvk~~Edv~V~YDg 1104 (1791)
||||||||+|||+|||++||+||||||++||+.|.++.
T Consensus 175 a~GaRkGLvDTAlKTAdSGYLTRRLVdv~qDviV~~~D 212 (1227)
T TIGR02388 175 SYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREED 212 (1227)
T ss_pred ccccccchhhcceeccccchHHHHHHHhhceEEEEEcC
Confidence 99999999999999999999999999999999988763
No 48
>cd02735 RNAP_I_Rpa1_C Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain. RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Probab=99.97 E-value=1.2e-33 Score=331.26 Aligned_cols=166 Identities=26% Similarity=0.453 Sum_probs=130.8
Q ss_pred HHHHHhhhhhhHhhccC-ChHHHHHHHH---HHHHHHHHHHHHHhhccCC---CcceeecchhHHHHHHHhhhhccCCcc
Q psy3015 697 KQLRRIFNEDVLRELMG-SGDVISELEK---EWEKLCEDREALREIFSSG---ESNVVLPCNLMEVIFILQRWKLWGNEN 769 (1791)
Q Consensus 697 ~~l~~~l~~~~~~~~~~-~~~vi~~~~~---e~~kL~~~~~~Lr~i~~~~---~~~~~l~~N~~rii~~~~~~~~~~~~~ 769 (1791)
+.+++.+.+.+++++++ .+.++...+. +.+.|..+|.+|++++... +.....++|+..+..
T Consensus 136 ~~~~~~l~~~~i~gi~gI~r~~i~~~~~~~~~~~~l~teG~nl~~v~~~~~~vd~~r~~sNdi~ei~~------------ 203 (309)
T cd02735 136 SIVEKLARKAVIREIPGITRCFVVEEDKGGKTKYLVITEGVNLAALWKFSDILDVNRIYTNDIHAMLN------------ 203 (309)
T ss_pred HHHHHHhcccEEeCCCCccEEEEecCcCCCceEEEEEeccccHHHHHhccCccccccceeCCHHHHHH------------
Confidence 34556667777778777 5555432221 1122344566666665431 123344444433221
Q ss_pred cccccceEEEe-ccCcccHHHHHHHHhhcceeccchhhhhhhhhhcccceecceeccccccCCCcccccchhhhhhHHHH
Q psy3015 770 LRFLCKIIFVL-SVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLM 848 (1791)
Q Consensus 770 ~~~~~n~i~~I-aAR~~Ii~Ei~~v~~~~GIsVd~RHi~LlaD~MT~~G~v~~itR~Gl~~~~~S~L~~aSFE~T~d~L~ 848 (1791)
+||| |||+.|++|++.||+.||++||+|||+||||+||++|+++||||+|| ++++|||++||||+|.+||+
T Consensus 204 -------~lGIEAar~~ii~Ei~~v~~~~Gi~V~~rHl~LiaD~MT~~G~~~~~nr~gi-~~~~S~l~~asFE~t~~~L~ 275 (309)
T cd02735 204 -------TYGIEAARRAIVKEISNVFKVYGIAVDPRHLSLIADYMTFEGGYRPFNRIGM-ESSTSPLQKMSFETTLAFLK 275 (309)
T ss_pred -------hhCHHHHHHHHHHHHHHHHHhcCCeeCHHHHHHHHHHHHhCCcEeecchhhe-ccCCCHHHhhhhhhHHHHHH
Confidence 4556 69999999999999999999999999999999999999999999999 78899999999999999999
Q ss_pred HHhhccCCCCCCCcccceecCCCCCCCcceeeec
Q psy3015 849 DAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLL 882 (1791)
Q Consensus 849 ~Aa~~g~~D~i~GVSe~II~G~~~~iGTg~~~Ll 882 (1791)
+||.+|+.|++.|||||||+|+++++|||+|+|+
T Consensus 276 ~Aa~~g~~D~l~g~s~~ii~G~~~~~GTG~fdll 309 (309)
T cd02735 276 KATLNGDIDNLSSPSSRLVVGKPVNGGTGLFDLL 309 (309)
T ss_pred HHhhcCCCCCCCChHHheeeCCccCccceeEEeC
Confidence 9999999999999999999999999999999986
No 49
>CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed
Probab=99.97 E-value=5.8e-33 Score=367.11 Aligned_cols=95 Identities=25% Similarity=0.391 Sum_probs=84.0
Q ss_pred ccCCHHHHHHHHHHHhhhccceeccccccc-cccCCcccCCCCcCccccccccCCCCCCCCcceeeccccCCCcceEEEe
Q psy3015 988 YRLSSEAFEWLVGEIENRFQQAQVIACVGQ-QNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFH 1066 (1791)
Q Consensus 988 ~rln~~a~~~i~gei~~~~~~sqv~~mvG~-QsV~gKrI~~GfprRTLphf~kdd~~PESrGFV~Nsf~~GLTPsEfffh 1066 (1791)
.++|+..+|..+|++|+.-++.|+.+|+|+ ...+|++|+ || |.|||++||||.|||||
T Consensus 123 d~~N~v~mMa~SGARGn~sQi~qLvGmRGlma~p~G~iI~-------~P--------------I~snFreGLs~~EyFis 181 (1364)
T CHL00117 123 DPLNPVYMMSFSGARGNASQVHQLVGMRGLMSDPQGQIID-------LP--------------IQSNFREGLSLTEYIIS 181 (1364)
T ss_pred CCCCcHhhhhhccCcccHHHHHHHhcccceeeCCCCcEee-------cc--------------hhhhhhcCCCHHHhhee
Confidence 568999999999999987777777777777 446788876 77 46999999999999999
Q ss_pred ecCCCCccchhhhccchhHHHHHHHHHHhcceEEEEC
Q psy3015 1067 AMGGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYD 1103 (1791)
Q Consensus 1067 AMgGREGLiDTAvKTAEtGYIqRRLvk~~Edv~V~YD 1103 (1791)
||||||||+|||+|||++||+||||||++||+.|.-+
T Consensus 182 ~~GaRkGLvDTAlkTAdSGYLtRRLVdv~qdviV~~~ 218 (1364)
T CHL00117 182 CYGARKGVVDTAVRTADAGYLTRRLVEVVQHIVVRET 218 (1364)
T ss_pred ccccccchhhcceecccccchhhHHHhhhccEEEEec
Confidence 9999999999999999999999999999999986543
No 50
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=99.95 E-value=5.2e-30 Score=335.09 Aligned_cols=174 Identities=34% Similarity=0.550 Sum_probs=136.8
Q ss_pred chHHHHHhhhhhhHhhccC-ChHHHHHHH----HHHHHHHHHHHHHHhhccCCCc--ceeecchhHHHHHHHhhhhccCC
Q psy3015 695 SWKQLRRIFNEDVLRELMG-SGDVISELE----KEWEKLCEDREALREIFSSGES--NVVLPCNLMEVIFILQRWKLWGN 767 (1791)
Q Consensus 695 ~~~~l~~~l~~~~~~~~~~-~~~vi~~~~----~e~~kL~~~~~~Lr~i~~~~~~--~~~l~~N~~rii~~~~~~~~~~~ 767 (1791)
.+.+++..+.+.+++|+++ .+..+...+ .+| .|..+|..|++++...++ ..+.++|+..+..
T Consensus 672 ~~~~~~~~l~~~~i~gi~gI~~~~i~~~~~~~~~~~-~l~teG~nl~~~~~~~~vd~~~~~sN~i~~i~~---------- 740 (858)
T PRK14898 672 ALRKRIPKIKNIVLKGIPGIERVLVKKEEHENDEEY-VLYTQGSNLREVFKIEGVDTSRTTTNNIIEIQE---------- 740 (858)
T ss_pred HHHHHHHHhcCcEEECCCCccEEEEecCCCCCCceE-EEEecCcCHHHHhcCCCCcccccccCCHHHHHH----------
Confidence 4555666677777888777 555443222 111 233455666666554321 2233444333211
Q ss_pred cccccccceEEEe-ccCcccHHHHHHHHhhcceeccchhhhhhhhhhcccceecceeccccccCCCcccccchhhhhhHH
Q psy3015 768 ENLRFLCKIIFVL-SVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDV 846 (1791)
Q Consensus 768 ~~~~~~~n~i~~I-aAR~~Ii~Ei~~v~~~~GIsVd~RHi~LlaD~MT~~G~v~~itR~Gl~~~~~S~L~~aSFE~T~d~ 846 (1791)
.+|| |||.+|++||+.||+.||++||+|||+||||+||++|+++||||+||+++++|||++||||+|++|
T Consensus 741 ---------~lGIEAar~~ii~Ei~~v~~~~gi~V~~rHl~liad~MT~~G~~~~~~r~gi~~~~~s~l~~asFe~t~~~ 811 (858)
T PRK14898 741 ---------VLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIMTADGEVKPIGRHGVAGEKGSVLARAAFEETVKH 811 (858)
T ss_pred ---------hhCHHHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHHHccCCcEEEeccCCccCCCCCHHHhcChHhHHHH
Confidence 3555 699999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhccCCCCCCCcccceecCCCCCCCcceeeeccccccc
Q psy3015 847 LMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEKC 888 (1791)
Q Consensus 847 L~~Aa~~g~~D~i~GVSe~II~G~~~~iGTg~~~Ll~~~~k~ 888 (1791)
|++||.+|+.|++.|||||||+|+++++|||+|+|+++.+.-
T Consensus 812 l~~Aa~~g~~D~l~g~s~~ii~G~~~~~GTG~~~l~~~~~~~ 853 (858)
T PRK14898 812 LYDAAEHGEVDKLKGVIENVIVGKPIKLGTGCVDLRIDREYE 853 (858)
T ss_pred HHHHhhcCCCCcCCCchHHeeeCCccCCcCceEEEEecCccc
Confidence 999999999999999999999999999999999999875543
No 51
>cd00630 RNAP_largest_subunit_C Largest subunit of RNA polymerase (RNAP), C-terminal domain. RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channe
Probab=99.92 E-value=2.9e-26 Score=244.89 Aligned_cols=110 Identities=46% Similarity=0.724 Sum_probs=108.7
Q ss_pred hHHHHHHhhhHHHHHHHHHHHHHHHhhhcCeeecccchhhhhhcccccCcccccccccccccccccccccchhhhHHHHH
Q psy3015 1286 DICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLM 1365 (1791)
Q Consensus 1286 dI~eI~~vlGIEAaR~~li~El~~V~~~~Gi~Vn~RHL~LLaD~MT~~G~l~~itR~Gi~rq~~S~L~raSFEeTv~iL~ 1365 (1791)
||++|+++|||||||+.|++|+++||..+|++||+|||+||||+||++|.+.++||+|+++..+|||++||||+|.++|.
T Consensus 49 dI~~i~~~lGIEAaR~~iv~El~~v~~~~Gi~V~~rHl~LIAD~MT~~G~~~ginr~g~~~~~~Spl~~aSFE~t~~~L~ 128 (158)
T cd00630 49 SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGFRASKTSPLMRASFEKTTKHLL 128 (158)
T ss_pred cHHHHHHHhCHHHHHHHHHHHHHHHHHhcCceecHHHHHHHHHHHhcCCcccccccccccccCCCHHHHcCHHHHHHHHH
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhccCCCCCCccccceeccccccCCcch
Q psy3015 1366 DAAAHAEADPMRGVSENIIMGQLPRMGTGC 1395 (1791)
Q Consensus 1366 ~AA~~ge~D~lkgVsenIi~Gq~~~lGTGa 1395 (1791)
+||.+|+.|+|+|+++||+||+++|+|||+
T Consensus 129 ~AA~~g~~D~l~g~s~~ii~Gk~~~~GTG~ 158 (158)
T cd00630 129 DAAAAGEKDELEGVSENIILGRPAPLGTGS 158 (158)
T ss_pred HHhhcCCCCCCCCcHHhhhccCCCCCCCCC
Confidence 999999999999999999999999999995
No 52
>cd00630 RNAP_largest_subunit_C Largest subunit of RNA polymerase (RNAP), C-terminal domain. RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channe
Probab=99.92 E-value=2.1e-26 Score=245.96 Aligned_cols=102 Identities=43% Similarity=0.676 Sum_probs=98.6
Q ss_pred EEEe-ccCcccHHHHHHHHhhcceeccchhhhhhhhhhcccceecceeccccccCCCcccccchhhhhhHHHHHHhhccC
Q psy3015 777 IFVL-SVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAE 855 (1791)
Q Consensus 777 i~~I-aAR~~Ii~Ei~~v~~~~GIsVd~RHi~LlaD~MT~~G~v~~itR~Gl~~~~~S~L~~aSFE~T~d~L~~Aa~~g~ 855 (1791)
+|+| |||..|++||++||+.||++||+|||+||||+||++|.++||||+||.+.++|||++||||+|.++|++||.+|+
T Consensus 56 ~lGIEAaR~~iv~El~~v~~~~Gi~V~~rHl~LIAD~MT~~G~~~ginr~g~~~~~~Spl~~aSFE~t~~~L~~AA~~g~ 135 (158)
T cd00630 56 ALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGFRASKTSPLMRASFEKTTKHLLDAAAAGE 135 (158)
T ss_pred HhCHHHHHHHHHHHHHHHHHhcCceecHHHHHHHHHHHhcCCcccccccccccccCCCHHHHcCHHHHHHHHHHHhhcCC
Confidence 4455 699999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCcccceecCCCCCCCcce
Q psy3015 856 ADPMRGVSENIIMGQLPRMGTGC 878 (1791)
Q Consensus 856 ~D~i~GVSe~II~G~~~~iGTg~ 878 (1791)
.|++.|+|+|||+|+++++|||+
T Consensus 136 ~D~l~g~s~~ii~Gk~~~~GTG~ 158 (158)
T cd00630 136 KDELEGVSENIILGRPAPLGTGS 158 (158)
T ss_pred CCCCCCcHHhhhccCCCCCCCCC
Confidence 99999999999999999999995
No 53
>PF04983 RNA_pol_Rpb1_3: RNA polymerase Rpb1, domain 3; InterPro: IPR007066 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, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1ZYR_D 1SMY_D 2A68_N 2O5J_D 3AOH_N 2O5I_D 2CW0_N 2A6H_N 2A69_D 3EQL_D ....
Probab=99.90 E-value=2.1e-24 Score=232.29 Aligned_cols=142 Identities=37% Similarity=0.533 Sum_probs=122.2
Q ss_pred cCCCCCCCCCeEEe-------------cCccccHhHHHHHHhcCCccC--CCCCCCceeCCCCcccHhhhhhhcCCCCcc
Q psy3015 52 LPVPPLSVRPAVVM-------------HGSARNQEQMMNILMFLPIWD--GKMPQPCILKPKPLWTGKQVFSLIIPGNVN 116 (1791)
Q Consensus 52 ~iVsP~~~rP~~~i-------------~Gs~~~rddlmqLlm~~~~~~--~~lP~PaIlKP~~LWTGKQIfS~iLP~~in 116 (1791)
|++||++++|++++ ...|++++++++++++...+. ...|.|+|++|+++|||||+||++||++++
T Consensus 1 NilSP~~G~Pii~~~QD~vlG~y~LT~~~~f~~~~e~~~~~~~~~~~~~~~~~~~~~I~~~~~~~tgk~~~s~il~~~i~ 80 (158)
T PF04983_consen 1 NILSPANGKPIIGPTQDMVLGAYYLTSEDTFLSRDEAQQALMNGLIDDKKIVLLHPAILKPKELWTGKQTFSRILPNEIN 80 (158)
T ss_dssp GSEETTTTEESSS--SHHHHHHHHHSSTTTEESHHHHHHHHHCSST----CHCSSSSBSSSSSCEECHHHHHTTSHTTHH
T ss_pred CccCCCCCCceEEeccceEeEEEEEEecccccchHHHHHHHHcccccccceeccchhhhccccceeeccHHHHhcccccc
Confidence 68999999999999 235899999999999986653 568899999999999999999999999888
Q ss_pred ccccCCCCCCCCCCCCCCCCCCCCCeEEEEcCeEEEEeecccccc-CCCccHHHHHHHHhCHHHHHHHHHHHHHHHHHHH
Q psy3015 117 MTRTHSTHPDDEDSGPYQWISPGDTKVVVEHGSLLMGILCKKSLG-TSSGSLLHICFLELGHEVCGRFYGNIQTVVNNWL 195 (1791)
Q Consensus 117 l~~~~~~~~~~~~~~~~~~~~~~d~~ViI~nGeLl~G~ldKk~vG-~s~~gLih~i~~~yG~~~a~~fL~~lqrL~~~~L 195 (1791)
+.... .++.|+.++|+||++++|.+||+++| ++.++|+|.||++||+++|.+|||++|+++++|+
T Consensus 81 ~~~~~--------------~~~~~~~~~i~~g~~l~g~l~k~~lgk~~~~~li~~i~~~yG~~~~~~~ld~i~~lg~~~~ 146 (158)
T PF04983_consen 81 PEGFS--------------NDPDDGYVVINNGELLSGVLDKKTLGKKSLGSLIHQIYREYGPEATVQFLDAIKRLGFRYL 146 (158)
T ss_dssp EEEST--------------SCHSSHSEEECTSSEEEC--SHHHHSCSHTTCHHHHHHHHSHHHHHHHHHHHHHHHHHHHH
T ss_pred ccccc--------------ccccccceeecCCccchhheehheecccchhhHHHHHHHHHCHHHHHHHHHHHHHHHHHHH
Confidence 85421 01226789999999999999999999 6789999999999999999999999999999999
Q ss_pred HhcCcccccCCc
Q psy3015 196 LLEGHSIGIGDT 207 (1791)
Q Consensus 196 ~~~GFSiGi~D~ 207 (1791)
+.+|||||++|+
T Consensus 147 t~~GfSvgi~D~ 158 (158)
T PF04983_consen 147 TRSGFSVGIDDM 158 (158)
T ss_dssp HHHTBB-SGGGC
T ss_pred HHcCeeEecccC
Confidence 999999999996
No 54
>PF05000 RNA_pol_Rpb1_4: RNA polymerase Rpb1, domain 4; InterPro: IPR007083 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 entry, domain 4, represents the funnel domain. The funnel domain contains the binding site for some elongation factors [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Q 3HKZ_I 1YNJ_D 1HQM_D 1YNN_D 1I6V_D 2GHO_D 2Y0S_W 3IYD_D 3LU0_D ....
Probab=99.89 E-value=3.5e-24 Score=217.08 Aligned_cols=101 Identities=53% Similarity=0.792 Sum_probs=90.0
Q ss_pred CCCCCCCCCcHHHHHHHHHHHHHHHHHhhhhhhhhhccCCCChHHHHhhcCCCcchhhHHHHHhhccCcccCCceeccCC
Q psy3015 284 MDLEPTPGNTLRQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGF 363 (1791)
Q Consensus 284 ~~L~~~pg~~~~~~fE~~vn~iLn~~rd~~g~~~~~~l~~~N~l~~Mv~sGSKGS~iNisQi~acvGQQ~veGkRIp~gf 363 (1791)
++++..+|++.++.+|..++.+++++++.+++.+.++++.+|++++|+.||||||.+|++||++|+|||.++|+|||.+|
T Consensus 8 ~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~N~l~~M~~SGaKGs~~ni~Qi~g~lGqq~~~g~ri~~~~ 87 (108)
T PF05000_consen 8 GKLEKKWGKTYEETFEQKINKILNKVRDEIGKIIKKNLPFNNSLLIMINSGAKGSMSNISQISGCLGQQSVEGKRIPRGF 87 (108)
T ss_dssp THHHHHCTCHHHHHHHHHHHHHHHHCCHHHHHHHHHCSTTTSHHHHHHHSSSS--HHHHHHHHST-EEEEETTSES--SS
T ss_pred CchHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcHHhhhhccCCCCHHHHHHHHHHHHHhhccccccccCC
Confidence 44566789999999999999999999999999999999878999999999999999999999999999999999999999
Q ss_pred ccCCCCCCCCCCCCCccccee
Q psy3015 364 RKRTLPHFIKDDYGPESRGFV 384 (1791)
Q Consensus 364 ~~RtLPhF~~~d~~p~srGFV 384 (1791)
.+||||||.+++.+|+++|||
T Consensus 88 ~~Rtlp~f~~~~~~~~~~GFI 108 (108)
T PF05000_consen 88 SGRTLPHFKPFDESPESRGFI 108 (108)
T ss_dssp TTCSSTTS-SS-SSTTTTTEE
T ss_pred CCCcCCCcCCCCCCcccCCCC
Confidence 999999999999999999998
No 55
>PF04992 RNA_pol_Rpb1_6: RNA polymerase Rpb1, domain 6; InterPro: IPR007075 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, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module [, ]. This family appears to be specific to the largest subunit of RNA polymerase II.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_M 1Y77_A 3CQZ_A 3GTM_A 1TWA_A 4A3I_A 2NVY_A 2NVT_A 1I6H_A 1TWF_A ....
Probab=99.89 E-value=5.2e-25 Score=242.22 Aligned_cols=181 Identities=46% Similarity=0.751 Sum_probs=131.2
Q ss_pred cccccccccccceeecChhhhhcccccCCc--hhhHhhhhccHHHHHHhhcCCCchhhhHHhhhcccchHHHHHhhhhhh
Q psy3015 630 LCGEAVEHQRIDTVALSHKKFEDKYRFDPS--NERQLRRIFNEDVLRELMGSGDVISELEKEMVDHFSWKQLRRIFNEDV 707 (1791)
Q Consensus 630 ~~~~~ie~~~ip~i~~~~~~~~~~~~~~~~--~~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~ 707 (1791)
+++..+|.|+++++++++..|+++|+++.. +......++..+ +
T Consensus 1 mD~~~vE~Q~l~~l~~s~~~f~~~Y~~d~~~~~~~~~~~~l~~~-----------------------------------v 45 (187)
T PF04992_consen 1 MDGAHVENQKLDTLKMSDAKFEKKYRVDLMDDDPEFGRGWLDPE-----------------------------------V 45 (187)
T ss_dssp B-GGGEEEEE-TTSSS-HHHHCCCC---TTSTTTS-GCCTCTTH------------------------------------
T ss_pred CCcceeccCcCCCCCCCHHHHHhhccccCCCCchhhhhhhCChH-----------------------------------H
Confidence 478899999999999999999999999883 333333333222 2
Q ss_pred HhhccCChHHHHHHHHHHHHHHHHHHHHH-hhccCCCcceeecchhHHHHHHHhhhhccCCcccccccceEEEeccCccc
Q psy3015 708 LRELMGSGDVISELEKEWEKLCEDREALR-EIFSSGESNVVLPCNLMEVIFILQRWKLWGNENLRFLCKIIFVLSVRKSV 786 (1791)
Q Consensus 708 ~~~~~~~~~vi~~~~~e~~kL~~~~~~Lr-~i~~~~~~~~~l~~N~~rii~~~~~~~~~~~~~~~~~~n~i~~IaAR~~I 786 (1791)
+..+..+.+++..+++||++|.+++..|| .++.+++.++++|+|+.|+||++++ .|+|..+...
T Consensus 46 ~~~l~~d~~~q~~Ld~E~~qL~~dR~~Lr~~i~~~g~~~~~LPVNi~RiI~nAq~---------------~f~i~~~~~s 110 (187)
T PF04992_consen 46 IEELRNDPEVQKLLDEEYEQLLEDRELLRKEIFPSGDDKVPLPVNIQRIIWNAQK---------------IFHIDPRKPS 110 (187)
T ss_dssp -TTTTTSHCCCHHHHHHHHHHHHHHCCCCSCCSTTT--EEEEES-HHHHCCCCCC---------------CTT--TTS-B
T ss_pred HHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcceECCccHHHHHHHHHH---------------HcCCCCCCcc
Confidence 33345567778899999999999999999 7999999999999999999999988 6666544433
Q ss_pred HHHHHHHHhhcceeccchhhhhhhhhhcccceecceeccccccCCCcccccchhhhhhHHHHHHhhccCCCCCC---Ccc
Q psy3015 787 EKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMR---GVS 863 (1791)
Q Consensus 787 i~Ei~~v~~~~GIsVd~RHi~LlaD~MT~~G~v~~itR~Gl~~~~~S~L~~aSFE~T~d~L~~Aa~~g~~D~i~---GVS 863 (1791)
. ++|.. +|.
T Consensus 111 d--------------------------------------------------------------------L~P~~Vi~~V~ 122 (187)
T PF04992_consen 111 D--------------------------------------------------------------------LSPIYVIEKVE 122 (187)
T ss_dssp S----------------------------------------------------------------------HHHHHHHHH
T ss_pred c--------------------------------------------------------------------CCHHHHHHHHH
Confidence 3 34433 454
Q ss_pred cceecCCCCCCCcceeeeccccccccCCccccccccccCCCCccccCCCCCCCCCCCCCCccccCccccccccCCCCcCC
Q psy3015 864 ENIIMGQLPRMGTGCFDLLLDAEKCKDGIEIPLATGMMGGPAGMFFGSAATPSSMSPQMTPWAQSTPAYNALMSPGAAMT 943 (1791)
Q Consensus 864 e~II~G~~~~iGTg~~~Ll~~~~k~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 943 (1791)
+ |+ ++|
T Consensus 123 ~----------------L~---~~L------------------------------------------------------- 128 (187)
T PF04992_consen 123 E----------------LL---DRL------------------------------------------------------- 128 (187)
T ss_dssp H----------------HH---TT--------------------------------------------------------
T ss_pred H----------------HH---HHH-------------------------------------------------------
Confidence 4 55 556
Q ss_pred CCCCCCcccccCCcchhHHHHhcHHHHHHHHhHhhhhhHHHHhhccCCHHHHHHHHHHHhhhccce
Q psy3015 944 PGGPGFSPSVAGEDQLSKQANENATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQA 1009 (1791)
Q Consensus 944 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Rs~L~sk~v~~~~rln~~a~~~i~gei~~~~~~s 1009 (1791)
++++|.|+||+|||+|||+||++++||+||+|+|+++||||++||+|++|||+++|+.|
T Consensus 129 -------~vv~g~D~ls~Eaq~NAtlLf~i~lRs~LasKrvi~e~rL~~~AF~wilgEIe~rF~~a 187 (187)
T PF04992_consen 129 -------VVVRGDDPLSREAQENATLLFKILLRSTLASKRVIEEYRLNKEAFDWILGEIESRFKKA 187 (187)
T ss_dssp --------SS--SSCCCCHHHHCCCHHHHHHHCCCSSHHHHHHTSB--HHHHHHHHHHHHHHHHCC
T ss_pred -------hhccCCCcchHHHHhhHHHHHHHHHHHhhhhHHHHHHhCcCHHHHHHHHHHHHHHHHcC
Confidence 68899999999999999999999999999999999999999999999999999999875
No 56
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]
Probab=99.86 E-value=8e-23 Score=264.35 Aligned_cols=130 Identities=30% Similarity=0.340 Sum_probs=122.0
Q ss_pred HHHHHHHHHHhhhccceeccccccccccCCcccCCCCcCccccccccCCCCCCCCcceeeccccCCCcceEEEeecCCCC
Q psy3015 993 EAFEWLVGEIENRFQQAQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGRE 1072 (1791)
Q Consensus 993 ~a~~~i~gei~~~~~~sqv~~mvG~QsV~gKrI~~GfprRTLphf~kdd~~PESrGFV~Nsf~~GLTPsEfffhAMgGRE 1072 (1791)
..-++.++..+++.|++|+..++|+|.|+|++++.| |||||.+.+.++++.|||.++|++||||+|||||+|||||
T Consensus 662 ~~~i~~m~~~Gs~~n~sq~~~~iG~~gv~g~r~~~~----~~~~Fe~~~~~~~a~~~i~s~f~eGLt~~e~f~~~~ggR~ 737 (808)
T COG0086 662 FVDIRHMGLSGARMNISQIVQLIGQQGVMGEKISVL----ARAAFEVTVKHLEAEGPGESSFLEGLTENEYFGHPIGGRT 737 (808)
T ss_pred chhHHHHhhhhhccCHHHHHHHhhhheeeccCCCcc----cccccccccccceeeeeeecccCCCCCcceEEeecCcccc
Confidence 456777788888899999999999999999999988 8999999999999999999999999999999999999999
Q ss_pred ccchhhhccchhHHHHHHHHHHhcceEEEECCCCCCcccccCcceeeeeccCCCCCCC
Q psy3015 1073 GLIDTAVKTAETVNVLVFLFQVTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPDFDPT 1130 (1791)
Q Consensus 1073 GLiDTAvKTAEtGYIqRRLvk~~Edv~V~YDgtvrnTVr~~d~~iVQf~Yg~dg~D~~ 1130 (1791)
||+|||+|||++||+|||||+++||+.|.||+ |+++..+..+||.||+|++|+.
T Consensus 738 GlvDTA~KTa~sGYl~RrLv~~~qdl~v~~d~----~~~~g~~~~~~~~~ged~~~~~ 791 (808)
T COG0086 738 GLVDTALKTADSGYLTRRLVDVAQDLIVQEDD----CVTDGIGVVIQFEYGEDGEDLT 791 (808)
T ss_pred chHHHhhhhcccCcceEEeechhcceEEEecC----eEeecCceEEEEecCccccCHH
Confidence 99999999999999999999999999999998 6666678999999999999853
No 57
>cd02655 RNAP_beta'_C Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain. Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations.
Probab=99.82 E-value=1e-20 Score=209.43 Aligned_cols=109 Identities=32% Similarity=0.530 Sum_probs=102.2
Q ss_pred hhHHHHHHhh--hHHHHHHHHHHHHHHHhhhcCeeecccchhhhhhcccccCcc--------------------------
Q psy3015 1285 NDICEIFQVL--GIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHL-------------------------- 1336 (1791)
Q Consensus 1285 NdI~eI~~vl--GIEAaR~~li~El~~V~~~~Gi~Vn~RHL~LLaD~MT~~G~l-------------------------- 1336 (1791)
||++++++++ ||||+|.+|++|+++||..||++||+|||++|+|+||+++++
T Consensus 54 ~~~~~il~~~~~Giea~r~~iv~EIq~Vy~~qGV~I~dKHielIv~qMT~kv~i~~~g~s~~l~Ge~v~~~~~~~~N~~~ 133 (204)
T cd02655 54 INPHDLLRIKFLGPEAVQKYLVEEIQKVYRSQGVNINDKHIEIIVRQMTSKVKIIDPGDSGFLPGELVDLNEFEEENKRL 133 (204)
T ss_pred CCHHHHHHHHhHHHHHHHHHHHHHHHHHHHhcCeeecHHHHHHHHHHHhcCeEEecCCCcccCCCceeeHHHHHHHHHHH
Confidence 7999999999 999999999999999999999999999999999999999553
Q ss_pred --------------cccccccccccccccccccchhhhHHHHHHHhhccCCCCCCccccceeccccccCCcch
Q psy3015 1337 --------------MAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGC 1395 (1791)
Q Consensus 1337 --------------~~itR~Gi~rq~~S~L~raSFEeTv~iL~~AA~~ge~D~lkgVsenIi~Gq~~~lGTGa 1395 (1791)
.||||++++ .+|+|++||||+|.++|.+||.+|+.|+|+|++||+++|+++|.|||.
T Consensus 134 ~~~~~~~~~y~p~llGItk~~l~--~~Sfls~ASFqeT~kvL~~AAi~gk~D~L~GlkeNVI~G~liPaGTG~ 204 (204)
T cd02655 134 LLLGKKPAKYEPVLLGITKASLN--TESFISAASFQETTKVLTEAAIEGKIDWLRGLKENVILGRLIPAGTGL 204 (204)
T ss_pred HhCCCCcccccceeeeeeecccc--CCCccccCChHHHHHHHHHHHhcCCCCCCCCchhheEECCccCCCCCC
Confidence 367776665 479999999999999999999999999999999999999999999994
No 58
>cd02655 RNAP_beta'_C Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain. Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations.
Probab=99.80 E-value=3.1e-20 Score=205.66 Aligned_cols=96 Identities=33% Similarity=0.551 Sum_probs=91.0
Q ss_pred ccCcccHHHHHHHHhhcceeccchhhhhhhhhhccccee----------------------------------------c
Q psy3015 781 SVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHL----------------------------------------M 820 (1791)
Q Consensus 781 aAR~~Ii~Ei~~v~~~~GIsVd~RHi~LlaD~MT~~G~v----------------------------------------~ 820 (1791)
++|..|++|++.|++.||++||.|||+||||+||++|.| +
T Consensus 69 a~r~~iv~EIq~Vy~~qGV~I~dKHielIv~qMT~kv~i~~~g~s~~l~Ge~v~~~~~~~~N~~~~~~~~~~~~y~p~ll 148 (204)
T cd02655 69 AVQKYLVEEIQKVYRSQGVNINDKHIEIIVRQMTSKVKIIDPGDSGFLPGELVDLNEFEEENKRLLLLGKKPAKYEPVLL 148 (204)
T ss_pred HHHHHHHHHHHHHHHhcCeeecHHHHHHHHHHHhcCeEEecCCCcccCCCceeeHHHHHHHHHHHHhCCCCcccccceee
Confidence 589999999999999999999999999999999999653 5
Q ss_pred ceeccccccCCCcccccchhhhhhHHHHHHhhccCCCCCCCcccceecCCCCCCCcce
Q psy3015 821 AITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGC 878 (1791)
Q Consensus 821 ~itR~Gl~~~~~S~L~~aSFE~T~d~L~~Aa~~g~~D~i~GVSe~II~G~~~~iGTg~ 878 (1791)
||||.++.. +|+|+.||||+|+++|++||+.|+.|++.|++||||+|+++|+|||+
T Consensus 149 GItk~~l~~--~Sfls~ASFqeT~kvL~~AAi~gk~D~L~GlkeNVI~G~liPaGTG~ 204 (204)
T cd02655 149 GITKASLNT--ESFISAASFQETTKVLTEAAIEGKIDWLRGLKENVILGRLIPAGTGL 204 (204)
T ss_pred eeeeccccC--CCccccCChHHHHHHHHHHHhcCCCCCCCCchhheEECCccCCCCCC
Confidence 899988874 79999999999999999999999999999999999999999999995
No 59
>PF04990 RNA_pol_Rpb1_7: RNA polymerase Rpb1, domain 7; InterPro: IPR007073 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, domain 7, represents a mobile module of the RNA polymerase. Domain 7 interacts with the lobe domain of Rpb2 (IPR007642 from INTERPRO) [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_M 1Y77_A 3CQZ_A 3GTM_A 1TWA_A 4A3I_A 2NVY_A 2NVT_A 1I6H_A 1TWF_A ....
Probab=99.78 E-value=6.7e-20 Score=191.53 Aligned_cols=132 Identities=64% Similarity=1.074 Sum_probs=105.2
Q ss_pred HHHHHhcceEEEECCCCCCcccccCcceeeeeccCCC--CCCCCcccceeeeeccccccccccCCHHHHHHHHhhccCCC
Q psy3015 1090 FLFQVTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPD--FDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDD 1167 (1791)
Q Consensus 1090 RLvk~~Edv~V~YDgtvrnTVr~~d~~iVQf~Yg~dg--~D~~~~~~wvlr~~Ld~~~m~dk~l~~~~I~~~I~~~~~~d 1167 (1791)
+|.+++..++|+|||+++|||+++|.+||+.||+.|+ .++..++||++|++||+.+|.+|+++|++|+++|++.|+++
T Consensus 2 tL~~vt~~teIyYDPdp~~Tvi~eD~e~V~~y~e~pd~~~~~~~~spWlLRieLdr~~m~dk~l~m~~I~~~I~~~f~~~ 81 (135)
T PF04990_consen 2 TLRDVTASTEIYYDPDPRNTVIEEDREFVESYFEIPDEDDDPSRLSPWLLRIELDRKKMIDKKLTMEDIAEKIKEEFGND 81 (135)
T ss_dssp CCHCHECEEEEEE-SSTTSSSSSTTHCHHHHCCCTT-SSTT-SSBESEEEEEEE-CCCCCCTT--HHHHCCCHHHCCTTS
T ss_pred cHHHhhhheeEEECCCCCCCcchhhHHHHHHHHhCCCcccCcccCCCeEEEEEEcHHHHHhcCCCHHHHHHHHHHhcCCC
Confidence 4778999999999999999999999999999999988 68899999999999999999999999999999999999999
Q ss_pred cccccCCcccccceEEEEEecCccccccchhHHHHhhhhhhhHHHHhhcccccceec
Q psy3015 1168 LNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 1224 (1791)
Q Consensus 1168 l~~i~~d~n~~~l~~riri~~~~~~~~~~~ee~~~~~~dr~~Lr~i~~~il~~~~Lk 1224 (1791)
++|+++++|++++++|||+....+.+....++ ..+++.|||+++.++|.+++||
T Consensus 82 l~vi~sddNa~~lViRIRi~~~~~~~~~~~d~---~~~dd~~Lr~~e~~lL~~~~Lr 135 (135)
T PF04990_consen 82 LHVIYSDDNAEKLVIRIRIIKDEDKKEEDEDE---QEEDDVFLRRLESNLLDDLTLR 135 (135)
T ss_dssp EEEEE--TTSSSEEEEEEEB--S---SSSSS-----S-CHHHHHHHHHHHCCS-ECC
T ss_pred eEEEecCCCCcccEEEEEEecCcccccccccc---hhhHHHHHHHHHHHhhhcCcCC
Confidence 99999999999999999998876433221111 1257799999999999998875
No 60
>PF05000 RNA_pol_Rpb1_4: RNA polymerase Rpb1, domain 4; InterPro: IPR007083 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 entry, domain 4, represents the funnel domain. The funnel domain contains the binding site for some elongation factors [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Q 3HKZ_I 1YNJ_D 1HQM_D 1YNN_D 1I6V_D 2GHO_D 2Y0S_W 3IYD_D 3LU0_D ....
Probab=99.15 E-value=2.4e-11 Score=123.74 Aligned_cols=61 Identities=48% Similarity=0.678 Sum_probs=53.0
Q ss_pred CCHHHHHHHHHHHhhhccceeccccccccccCCcccCCCCcCccccccccCCCCCCCCcce
Q psy3015 990 LSSEAFEWLVGEIENRFQQAQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFV 1050 (1791)
Q Consensus 990 ln~~a~~~i~gei~~~~~~sqv~~mvG~QsV~gKrI~~GfprRTLphf~kdd~~PESrGFV 1050 (1791)
-|+...|..+|++|+..|++|+.+|+|||+++|+||+.+|-+||||||.+.|.+|+|||||
T Consensus 48 ~N~l~~M~~SGaKGs~~ni~Qi~g~lGqq~~~g~ri~~~~~~Rtlp~f~~~~~~~~~~GFI 108 (108)
T PF05000_consen 48 NNSLLIMINSGAKGSMSNISQISGCLGQQSVEGKRIPRGFSGRTLPHFKPFDESPESRGFI 108 (108)
T ss_dssp TSHHHHHHHSSSS--HHHHHHHHST-EEEEETTSES--SSTTCSSTTS-SS-SSTTTTTEE
T ss_pred CCcHHhhhhccCCCCHHHHHHHHHHHHHhhccccccccCCCCCcCCCcCCCCCCcccCCCC
Confidence 4999999999999999999999999999999999999999999999999999999999998
No 61
>PF04992 RNA_pol_Rpb1_6: RNA polymerase Rpb1, domain 6; InterPro: IPR007075 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, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module [, ]. This family appears to be specific to the largest subunit of RNA polymerase II.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_M 1Y77_A 3CQZ_A 3GTM_A 1TWA_A 4A3I_A 2NVY_A 2NVT_A 1I6H_A 1TWF_A ....
Probab=98.69 E-value=5e-10 Score=124.27 Aligned_cols=176 Identities=21% Similarity=0.277 Sum_probs=99.8
Q ss_pred cceeeeeccccccccccCCHHHHHHHHhhccCCCccc---ccCCcccccceEEEEEecCccccccchhHHHHhhhhhhhH
Q psy3015 1134 PWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNC---IFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFL 1210 (1791)
Q Consensus 1134 ~wvlr~~Ld~~~m~dk~l~~~~I~~~I~~~~~~dl~~---i~~d~n~~~l~~riri~~~~~~~~~~~ee~~~~~~dr~~L 1210 (1791)
.|++.|.+|..+|++++|. +.|..|+.. .+.....+.-++. .+..+...+..+++|+.++.+||.+|
T Consensus 4 ~~vE~Q~l~~l~~s~~~f~---------~~Y~~d~~~~~~~~~~~~l~~~v~~-~l~~d~~~q~~Ld~E~~qL~~dR~~L 73 (187)
T PF04992_consen 4 AHVENQKLDTLKMSDAKFE---------KKYRVDLMDDDPEFGRGWLDPEVIE-ELRNDPEVQKLLDEEYEQLLEDRELL 73 (187)
T ss_dssp GGEEEEE-TTSSS-HHHHC---------CCC---TTSTTTS-GCCTCTTH--T-TTTTSHCCCHHHHHHHHHHHHHHCCC
T ss_pred ceeccCcCCCCCCCHHHHH---------hhccccCCCCchhhhhhhCChHHHH-HhcCCHHHHHHHHHHHHHHHHHHHHH
Confidence 5788999999999998765 666655521 0111111100000 01223334456789999999999988
Q ss_pred HHHhhcccccceeccccccceEEEeccccCCCceEEEccCCcccccceEEEeecccchhcccccCCCCcccccchhHHHH
Q psy3015 1211 RCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEI 1290 (1791)
Q Consensus 1211 r~i~~~il~~~~LkGi~~I~kv~i~lp~~~n~~RiI~na~~~f~~~~e~~L~teG~nL~~vl~~~dVDp~rt~sNdI~eI 1290 (1791)
|.. ++. -++..+++|+ |+.|+||||++.|++.. ...++++|..+
T Consensus 74 r~~---i~~---------~g~~~~~LPV--Ni~RiI~nAq~~f~i~~--------------~~~sdL~P~~V-------- 117 (187)
T PF04992_consen 74 RKE---IFP---------SGDDKVPLPV--NIQRIIWNAQKIFHIDP--------------RKPSDLSPIYV-------- 117 (187)
T ss_dssp CSC---CST---------TT--EEEEES---HHHHCCCCCCCTT--T--------------TS-BS--HHHH--------
T ss_pred HHH---hcc---------CCCcceECCc--cHHHHHHHHHHHcCCCC--------------CCcccCCHHHH--------
Confidence 832 121 3456777888 99999999999998522 35688999866
Q ss_pred HHhhhHHHHHHHHHHHHHHHhhhcCeeecccchhhhhhcccccCcccccccccccccccc-----cccccchhhhHHHHH
Q psy3015 1291 FQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTG-----ALMRCSFEETVDVLM 1365 (1791)
Q Consensus 1291 ~~vlGIEAaR~~li~El~~V~~~~Gi~Vn~RHL~LLaD~MT~~G~l~~itR~Gi~rq~~S-----~L~raSFEeTv~iL~ 1365 (1791)
|+++++.+.+.+ .+.|. | ..+.++|.++ .+.|+.|.+
T Consensus 118 -----i~~V~~L~~~L~----vv~g~-----------D------------~ls~Eaq~NAtlLf~i~lRs~Las------ 159 (187)
T PF04992_consen 118 -----IEKVEELLDRLV----VVRGD-----------D------------PLSREAQENATLLFKILLRSTLAS------ 159 (187)
T ss_dssp -----HHHHHHHHTT------SS--S-----------S------------CCCCHHHHCCCHHHHHHHCCCSSH------
T ss_pred -----HHHHHHHHHHHh----hccCC-----------C------------cchHHHHhhHHHHHHHHHHHhhhh------
Confidence 777777765533 33332 1 2224555554 345555554
Q ss_pred HHhhccCCCCCCccccceeccccccCCcchhhhhccccccccccc
Q psy3015 1366 DAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEKCKDGIE 1410 (1791)
Q Consensus 1366 ~AA~~ge~D~lkgVsenIi~Gq~~~lGTGaFd~lLge~~~~~~~~ 1410 (1791)
|.|. ..++++..||||++||++.+|.+|
T Consensus 160 -----------Krvi------~e~rL~~~AF~wilgEIe~rF~~a 187 (187)
T PF04992_consen 160 -----------KRVI------EEYRLNKEAFDWILGEIESRFKKA 187 (187)
T ss_dssp -----------HHHH------HTSB--HHHHHHHHHHHHHHHHCC
T ss_pred -----------HHHH------HHhCcCHHHHHHHHHHHHHHHHcC
Confidence 3333 346999999999999999999763
No 62
>PF04997 RNA_pol_Rpb1_1: RNA polymerase Rpb1, domain 1; InterPro: IPR007080 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, domain 1, represents the clamp domain, which is a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2Y0S_W 3QQC_A 1YNJ_D 1HQM_D 1YNN_D 1I6V_D 2GHO_D 2AUJ_D 1ZYR_D 1SMY_D ....
Probab=97.82 E-value=2e-06 Score=102.35 Aligned_cols=69 Identities=29% Similarity=0.585 Sum_probs=61.1
Q ss_pred ccccceeeeeecccCChhhHhhhCCCCCCCCcceEEeeccCCCCCCCCCeEEecCccccHhHHHHHHhcC
Q psy3015 13 HVSNTSVYAWYVVPYPYEESIILGMDPKFARPDWMLVTVLPVPPLSVRPAVVMHGSARNQEQMMNILMFL 82 (1791)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~d~~~lg~~~~~~~p~~mlv~~~iVsP~~~rP~~~i~Gs~~~rddlmqLlm~~ 82 (1791)
.++|++|+++|+ +|+++|+.+|||++..+||+||+++.+||||+..||++.+.|..++++|+..++..+
T Consensus 198 ~l~~~~v~~ilk-~l~~~~~~~l~~~~~~~~P~~~~l~~lpVpP~~~RP~v~~~~~~~~eddlt~~~~~I 266 (337)
T PF04997_consen 198 ILTPEEVRQILK-KLSKEDKELLGFDPSGSRPEWFFLTVLPVPPPRFRPSVQLGGGRFSEDDLTSLYRKI 266 (337)
T ss_dssp CESHHHHHHHHH-HSHHHHHHHHHHHTTTBSGGGSEEEEEEE-TGGGS-EEEESSSEEEE-HHHHHHHHH
T ss_pred hhhhhhhhhcch-hhhhhheeeeeccccccccceeEEeeeecCCceeeeeeeeecccccCchHHHHHHHH
Confidence 578999999999 999999999999999999999999999999999999999988778899998887753
No 63
>TIGR02387 rpoC1_cyan DNA-directed RNA polymerase, gamma subunit. The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''.
Probab=92.04 E-value=0.087 Score=67.86 Aligned_cols=45 Identities=27% Similarity=0.599 Sum_probs=38.0
Q ss_pred CCCCCCCCcceEEeeccCCCCCCCCCeEEecCccccHhHHHHHHh
Q psy3015 36 GMDPKFARPDWMLVTVLPVPPLSVRPAVVMHGSARNQEQMMNILM 80 (1791)
Q Consensus 36 g~~~~~~~p~~mlv~~~iVsP~~~rP~~~i~Gs~~~rddlmqLlm 80 (1791)
.|....+||+||+++++||+|++-||.+.+.|..+..+|+..++.
T Consensus 227 ~f~~~~~~PewmiL~~lPV~Pp~lRP~v~l~~g~~~~sDln~lyr 271 (619)
T TIGR02387 227 NFIATSSRPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYR 271 (619)
T ss_pred HHHhcCCCcceEEEEecccCCcccCCceEeCCCcccCCCHHHHHH
Confidence 345667899999999999999999999999877777888876654
No 64
>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional
Probab=91.69 E-value=0.1 Score=67.26 Aligned_cols=45 Identities=27% Similarity=0.581 Sum_probs=37.8
Q ss_pred CCCCCCCCcceEEeeccCCCCCCCCCeEEecCccccHhHHHHHHh
Q psy3015 36 GMDPKFARPDWMLVTVLPVPPLSVRPAVVMHGSARNQEQMMNILM 80 (1791)
Q Consensus 36 g~~~~~~~p~~mlv~~~iVsP~~~rP~~~i~Gs~~~rddlmqLlm 80 (1791)
.|-...+||+||+++++||+|++-||.+.+.|..+..+|+..++.
T Consensus 234 ~f~~~~~~PewmiL~~lPV~Pp~lRP~v~l~~g~~~~sDLn~ly~ 278 (627)
T PRK02625 234 NFIATGSRPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYR 278 (627)
T ss_pred HHHhcCCCccEEEEEeeecCCCcccCceEeCCCcccCCCHHHHHH
Confidence 345567899999999999999999999999876677778877665
No 65
>CHL00018 rpoC1 RNA polymerase beta' subunit
Probab=89.54 E-value=0.22 Score=64.96 Aligned_cols=42 Identities=24% Similarity=0.570 Sum_probs=36.4
Q ss_pred CCCCCcceEEeeccCCCCCCCCCeEEecCccccHhHHHHHHh
Q psy3015 39 PKFARPDWMLVTVLPVPPLSVRPAVVMHGSARNQEQMMNILM 80 (1791)
Q Consensus 39 ~~~~~p~~mlv~~~iVsP~~~rP~~~i~Gs~~~rddlmqLlm 80 (1791)
...++|+||+++.+||+|++-||.+.+.|..+..+|+..++.
T Consensus 256 ~~~~~PewmiL~~lPV~Pp~lRP~v~l~~g~~~~sDln~lyr 297 (663)
T CHL00018 256 RTNIEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYR 297 (663)
T ss_pred hcCCCccEEEEEeeeeCCCcccCceEcCCCcccCCChHHHHH
Confidence 445899999999999999999999999876678888877764
No 66
>smart00663 RPOLA_N RNA polymerase I subunit A N-terminus.
Probab=70.63 E-value=3.1 Score=50.39 Aligned_cols=37 Identities=38% Similarity=0.835 Sum_probs=32.9
Q ss_pred ceEEeeccCCCCCCCCCeEEecCccccHhHHHHHHhc
Q psy3015 45 DWMLVTVLPVPPLSVRPAVVMHGSARNQEQMMNILMF 81 (1791)
Q Consensus 45 ~~mlv~~~iVsP~~~rP~~~i~Gs~~~rddlmqLlm~ 81 (1791)
+||+++++||+|++.||.+.+.|....+|++..++..
T Consensus 1 e~fil~~lpVpP~~~RP~v~~~~~~~~eddlt~~l~~ 37 (295)
T smart00663 1 EWMILTVLPVPPPCLRPSVSLDGGRFAEDDLTHLLRD 37 (295)
T ss_pred CeEEEeccccCCCCCCCcEEeCCCcccCCcHHHHHHH
Confidence 6999999999999999999988777888888887764
Done!